Hi,
I am having trouble while saving gameXML files that includes
SequenceEdit into my chadoDB (I've attached an example). It looks like
that Apollo is looking for a refFeature, by instance an exon, but can
find anything then crash with a null pointer exception :
Exception in thread "Thread-5" java.lang.NullPointerException
at
apollo.dataadapter.chado.jdbc.ChadoFeature.<init>(ChadoFeature.java:67)
at
apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter.addSequenceEdit(PureJDBCTransactionWriter.java:1421)
at
apollo.dataadapter.chado.jdbc.JdbcChadoWriter.addSequenceEdit(JdbcChadoWriter.java:800)
at
apollo.dataadapter.chado.jdbc.JdbcChadoWriter.addSequenceEdit(JdbcChadoWriter.java:382)
at
apollo.dataadapter.chado.jdbc.JdbcChadoWriter.processSequenceEdits(JdbcChadoWriter.java:714)
at
apollo.dataadapter.chado.jdbc.JdbcChadoWriter.write(JdbcChadoWriter.java:111)
at
apollo.dataadapter.chado.ChadoAdapter.commitChanges(ChadoAdapter.java:288)
at
apollo.dataadapter.AbstractApolloAdapter.commitChanges(AbstractApolloAdapter.java:324)
at
apollo.dataadapter.chado.ChadoAdapterGUI.doOperation(ChadoAdapterGUI.java:301)
at
org.bdgp.swing.widget.DataAdapterChooser.doCommitWithExceptions(DataAdapterChooser.java:361)
at
org.bdgp.swing.widget.DataAdapterChooser.doCommit(DataAdapterChooser.java:414)
at
apollo.main.DataLoader$SaveAdapterChooser.doCommit(DataLoader.java:776)
at
org.bdgp.swing.widget.DataAdapterChooser$CommitRunnable.run(DataAdapterChooser.java:136)
at java.lang.Thread.run(Thread.java:619)
Any help is welcome.
Thanks,
Fabrice
--
Fabrice Legeai
INRA UMR Bio3P IRISA Equipe Symbiose
IRISA-INRIA, Campus de Beaulieu, 35042 Rennes cedex, France
Tél: +33 (0) 2 99 84 71 18
<?xml version="1.0" encoding="ISO-8859-1"?>
<game version="1.1">
<!-- Curational annotations from Apollo -->
<!-- Analysis of: EQ114903:13000-15800 -->
<!-- Original input read from C:\Users\Carlos Llorens\Desktop\EQ114903.fa.xml -->
<!-- Saved on Thu Jul 16 23:10:41 GMT 2009 -->
<!-- Apollo version: Apollo Genome Annotation and Curation Tool, version 1.9.0, last updated Oct 13 2008 -->
<seq id="EQ114903:13000-15800" length="2801" focus="true">
<name>EQ114903:13000-15800</name>
<organism>Acyrtosyphon pisum</organism>
<potential_sequencing_error>
<type>substitution</type>
<position>14195</position>
<base>N</base>
</potential_sequencing_error>
<residues>
TCGGATGATAGCATATACAAAATTATAATAATATTTATGTTGTTCTTTCA
GTATTCAGTAATCAGTTGATTATTGACTTCTCAAATTTGTCAATTGTTTG
TTGTATGTTGTGTTGAATCAATCTGTCTATAATTGACCTAATATTTTTTT
GAAATGAGTAAAAGTAATAAAATATGTTGTGTGGTCAACTGTAATAATAT
GTATAAAAATACCCAAGATATTAAGTTTTACACGTTTCCTAATCGAAAAT
ATGAAAAGGACCTAAAAGAAAAATGGATACGCGCAGTTAACCGTCCGGAG
TAAGTACCTTTGGTGTTTATTAAATTAATATTCTATAGTTAAAGCACATA
TTTGAATGTTAAGTCATTTGTATCTATCTATTATTCTAGAATATTAGTAC
CTACCTAGATTCATATCAGTTACATTCATATTATATTATTTAACAAATAT
GTACACCGACAATCCTATTAAAAATATGATTTTTTTTGTTAAATAACTTA
AATTCAATCAATATTATTGACAGTTACAATATATAATAGTGATTCACTAC
CAACTAAGTGTAGATACCCAATTTCTATGTCCATAATTAATATTATGAAA
TCTAGCTATGAAAAATAGATACCTAACTACAGGTGTTATAAGATTATTTT
AGAAATATGTTTGCTTATAAAATAATAGGTTTATTTTATTTTTCAGGGCA
AATGGAAGTCCATGGAAGCCGAAAGTGCACAATGTGATTTGTAGTTCACA
CTTTATTGGTAATGGGCGGTCAAATGATTCTCGTAGCGCTTCTTATGTGC
CTTCAATTTTTCCTAGAAGTATACAAGCGAAAAATAGTTGATTCAGAGCA
GTCTTGTTCAAGATATCAACTTGTTTGGCGGTTTTTGGTTGTTCGAAATT
TGTTATGGCTATTCTGTTTCTGGCTAAGGGTTTGAGGCCTTCGCTGGATA
TTTGGTGCCCTAAAAGTTCAATTTTTGGGGCGAATATATTGTATTTGGCT
GTTTTCAATGAAAATCCAAATTGGTTTATAATTTCGAATACTTTTCTTAA
ATTATGTAGAGCTGTTTCAAAGTTGTGTCCGAAGGTGGCTAGTTCGTCAA
TGAGTATGACTACTGATTTGTATAGATAATCTGAGAAAGCTTTATTGGTT
CTCTTTGAAATATTGCACTTGAGTTTTTGAAGCCTTGTGACAATTTAGTG
AATGTCATCAAGCCATGAACTGTAGTGAAAGGTAACATGTATTGATCCTG
TTCCCTTACCGGGATTTGAAAAAAAACCGCTGTTTAAGTCCAATGACGTG
AAGAACTTTGAGCCTTCTAAGTTGCGGAATAAGTCTATTGTTCTGGGTAA
TGGGTATTGGTCTGATTCTATTATGTTGTTGAGTTCTTTGTATGAAACGA
CTAATCTGTAACAGTTGTTTTTCTCCTTTTTTCGTACTAGGAATGCATGT
GAAGCAAAGTTTGATTTTGTGTGCTTGACTATGTTTGCTGTTATTAGGTT
ATCTAATTGAGTTTTAAGTTCTTGTCTTTGGGAAGGGGAAATTCTATGTG
GTGAGTTGAATTTTAGCTCCTTGACGTTTGGTTTGATTTTTGTGTGACAG
GGTTGTACTTTCACTGGTATTATGTGTGTCGTGTCAGTAGAAAATATGTG
TATGAATTGTTTTAATAATTCTACTGTTTGGTGATGTTTTTCTGGAGTTA
TATTGTTGGATATGTTGATTTGAGTTCGTTCTTTGTCATATACTTTTTCC
CTGCCATTGGTTATAATCGAGTTTATAGTTTGGATTTCCCTGTTTTGGTT
TGTTTTATTGTTTATCATTGTTTCTAATTTCAATCTGTTTTTTATGTGTT
CTATGGAAATATAATTTTTCGTATATATTATTTTTTGTGGGATTTTGATT
TTGTTTTATTTAGATTTGTTTCTTATTAGTGTGCCGGGCCACCAGTGTGG
TCTATTGTTTAGATTATACAGTACTTTGGGGGGTCTGAATCCTGATCCAT
ATACGTATCCATCTTTGGTTTTATCTGAATATATATAAGTTTCAAATCCA
TAATGATTTGCAATGCTACTTTGTTGGTCATCATGCCACCAGTAGTTGGG
TAATTCTGACAATCCTAGTAAGTCCATTATATTGGCCAAGGTTATTATCT
TCTTGGGTTTATTATCGTTTATTGCGTTGGTTAAAGCGTATAGTCCACAA
TTCCCATCGGACAGTGCGTTTCCTCCCATTTGGTATTTGGAAAATGTTTT
AATAAATTGGGGGTATTGGATTTCAATCTCATTATTTGTATGAGTAATGC
GATTGTATGTATTCTTTATACTGGATATTATGTTTGGTTTCTTGTATTTG
GGTGTGTAACATATTAGCAAGTGTATTTCTGTGTTGTTGAATATTTCAAA
TATCATATTTTCAATTGTATCCCATGTTAGTTCATTGTTTGTTATGTTAT
TCACGCATATGGCTATGTATTCATATCCTTCTGTTATGGCAGTGTTTTTT
AGATTGTAGAAATTATCGAAAATGTCTATATAGGATGTGGGCGTGTTATG
TTCTCTTTGGATATTTGATAGTGTATAGTTCTTTATTCTGTGTCAATTGT
CGTTATTTCACCTGGTATTAGTTCTAAGCTGTCGAGTATGTTGGACATGT
TGCCATATTTCTGTGTCAATTTATTTGATAGGTCTGTGTTGTGTTGAAGG
TCGGCCGAGATTGTGTGTGCTATCGAGTATTTAGGTGTGGTATTCAGTAT
ATCTATATTGGTTTCAGTTATATTAGTTGATAACATTGTCTTGCGTTCCA
T
</residues>
</seq>
<map_position seq="EQ114903:13000-15800">
<chromosome>EQ114903</chromosome>
<organism>Acyrtosyphon pisum</organism>
<arm>EQ114903</arm>
<span>
<start>13000</start>
<end>15800</end>
</span>
</map_position>
<annotation id="ACYPIG389844-gabriel">
<name>Ty3/Gypsy-like pol polyprotein_1</name>
<type>gene</type>
<property>
<type>sp_status</type>
<value>curator examined, accepted</value>
</property>
<synonym>ACYPIG389844-gabriel</synonym>
<synonym>Ty3/Gypsy-like reverse transcriptase</synonym>
<comment id="ACYPIG389844-gabriel" internal="false">
<text>
Ty3/Gypsy-like (similar to Micropia /Mdg3 clade) related to canonical LTR retrotransposons
</text>
<person>Lucia</person>
<date timestamp="0">Thu Jan 01 00:00:00 GMT 1970</date>
</comment>
<feature_set id="ACYPIG389844-gabriel-RA" produces_seq="Ty3/Gypsy-like pol polyprotein-RA">
<name>Ty3/Gypsy-like pol polyprotein_1-RA</name>
<type>transcript</type>
<author>Carlos Llorens</author>
<date>Fri Jul 17 01:09:07 CEST 2009</date>
<synonym>ACYPIT389844-gabriel</synonym>
<synonym>Ty3/Gypsy-like reverse transcriptase-gabriel</synonym>
<synonym>Ty3/Gypsy-like reverse transcriptase-RA</synonym>
<property>
<type>status</type>
<value>all done</value>
</property>
<feature_span id="ACYPIG389844-gabriel-PA">
<type>polypeptide</type>
<name>Ty3/Gypsy-like pol polyprotein_1-PA</name>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2406</start>
<end>796</end>
</span>
</seq_relationship>
</feature_span>
<property>
<type>non_canonical_splice_site</type>
<value>unapproved</value>
</property>
<feature_span>
<type>exon</type>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2406</start>
<end>1959</end>
</span>
</seq_relationship>
</feature_span>
<feature_span>
<type>exon</type>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>1850</start>
<end>793</end>
</span>
</seq_relationship>
</feature_span>
<seq id="Ty3/Gypsy-like pol polyprotein-RA" length="1506" type="cdna">
<name>Ty3/Gypsy-like pol polyprotein_1-RA</name>
<description>
reverse transcriptase-gabriel
</description>
<residues>
ATGATATTTGAAATATTCAACAACACAGAAATACACTTGCTAATATGTTA
CACACCCAAATACAAGAAACCAAACATAATATCCAGTATAAAGAATACAT
ACAATCGCATTACTCATACAAATAATGAGATTGAAATCCAATACCCCCAA
TTTATTAAAACATTTTCCAAATACCAAATGGGAGGAAACGCACTGTCCGA
TGGGAATTGTGGACTATACGCTTTAACCAACGCAATAAACGATAATAAAC
CCAAGAAGATAATAACCTTGGCCAATATAATGGACTTACTAGGATTGTCA
GAATTACCCAACTACTGGTGGCATGATGACCAACAAAGTAGCATTGCAAA
TCATTATGGATTTGAAACTTATATATATTCAGATAAAACCAAAGATGGAT
ACGTATATGGATCAGGATTCAGACCCCCCAAAGTACTGTATAATCTAAAA
CACATAAAAAACAGATTGAAATTAGAAACAATGATAAACAATAAAACAAA
CCAAAACAGGGAAATCCAAACTATAAACTCGATTATAACCAATGGCAGGG
AAAAAGTATATGACAAAGAACGAACTCAAATCAACATATCCAACAATATA
ACTCCAGAAAAACATCACCAAACAGTAGAATTATTAAAACAATTCATACA
CATATTTTCTACTGACACGACACACATAATACCAGTGAAAGTACAACCCT
GTCACACAAAAATCAAACCAAACGTCAAGGAGCTAAAATTCAACTCACCA
CATAGAATTTCCCCTTCCCAAAGACAAGAACTTAAAACTCAATTAGATAA
CCTAATAACAGCAAACATAGTCAAGCACACAAAATCAAACTTTGCTTCAC
ATGCATTCCTAGTACGAAAAAAGGAGAAAAACAACTGTTACAGATTAGTC
GTTTCATACAAAGAACTCAACAACATAATAGAATCAGACCAATACCCATT
ACCCAGAACAATAGACTTATTCCGCAACTTAGAAGGCTCAAAGTTCTTCA
CGTCATTGGACTTAAACAGCGGTTTTTTTTCAAATCCCGGTAAGGGAACA
GGATCAATACATGTTACCTTTCACTACAGTTCATGGCTTGATGACATTCA
CTNAATTGTCACAAGGCTTCAAAAACTCAAGTGCAATATTTCAAAGAGAA
CCAATAAAGCTTTCTCAGATTATCTATACAAATCAGTAGTCATACTCATT
GACGAACTAGCCACCTTCGGACACAACTTTGAAACAGCTCTACATAATTT
AAGAAAAGTATTCGAAATTATAAACCAATTTGGATTTTCATTGAAAACAG
CCAAATACAATATATTCGCCCCAAAAATTGAACTTTTAGGGCACCAAATA
TCCAGCGAAGGCCTCAAACCCTTAGCCAGAAACAGAATAGCCATAACAAA
TTTCGAACAACCAAAAACCGCCAAACAAGTTGATATCTTGAACAAGACTG
CTCTGAATCAACTATTTTTCGCTTGTATACTTCTAGGAAAAATTGAAGGC
ACATAA
</residues>
</seq>
</feature_set>
</annotation>
<seq id="O96740_DROME_4831468" length="0">
<name>O96740_DROME_4831468</name>
<dbxref>
<xref_db>O96740</xref_db>
<db_xref_id>O96740_DROME_4831468</db_xref_id>
</dbxref>
</seq>
<seq id="Q01HX8_ORYSA_4887396" length="0">
<name>Q01HX8_ORYSA_4887396</name>
<dbxref>
<xref_db>Q01HX8</xref_db>
<db_xref_id>Q01HX8_ORYSA_4887396</db_xref_id>
</dbxref>
</seq>
<seq id="Q01M17_ORYSA_4901456" length="0">
<name>Q01M17_ORYSA_4901456</name>
<dbxref>
<xref_db>Q01M17</xref_db>
<db_xref_id>Q01M17_ORYSA_4901456</db_xref_id>
</dbxref>
</seq>
<seq id="Q0D613_ORYSJ_4961331" length="0">
<name>Q0D613_ORYSJ_4961331</name>
<dbxref>
<xref_db>Q0D613</xref_db>
<db_xref_id>Q0D613_ORYSJ_4961331</db_xref_id>
</dbxref>
</seq>
<seq id="Q24310_DROME_4829758" length="0">
<name>Q24310_DROME_4829758</name>
<dbxref>
<xref_db>Q24310</xref_db>
<db_xref_id>Q24310_DROME_4829758</db_xref_id>
</dbxref>
</seq>
<seq id="Q2QSH9_ORYSJ_5116897" length="0">
<name>Q2QSH9_ORYSJ_5116897</name>
<dbxref>
<xref_db>Q2QSH9</xref_db>
<db_xref_id>Q2QSH9_ORYSJ_5116897</db_xref_id>
</dbxref>
</seq>
<seq id="Q2QVL4_ORYSJ_4834501" length="0">
<name>Q2QVL4_ORYSJ_4834501</name>
<dbxref>
<xref_db>Q2QVL4</xref_db>
<db_xref_id>Q2QVL4_ORYSJ_4834501</db_xref_id>
</dbxref>
</seq>
<computational_analysis>
<program>genscan</program>
<type>genscan</type>
<result_set id="GENSCAN_mRNA_SCAFFOLD4132_0001">
<name>GENSCAN_mRNA_SCAFFOLD4132_0001</name>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-10393</start>
<end>4615</end>
</span>
</seq_relationship>
<result_span id="GENSCAN_mRNA_SCAFFOLD4132_0001_Exon0001">
<name>genscan:2606-2781</name>
<type>genscan</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-10393</start>
<end>-10218</end>
</span>
</seq_relationship>
</result_span>
<result_span id="GENSCAN_mRNA_SCAFFOLD4132_0001_Exon0002">
<name>genscan:3111-3383</name>
<type>genscan</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-9888</start>
<end>-9616</end>
</span>
</seq_relationship>
</result_span>
<result_span id="GENSCAN_mRNA_SCAFFOLD4132_0001_Exon0003">
<name>genscan:4495-5336</name>
<type>genscan</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-8504</start>
<end>-7663</end>
</span>
</seq_relationship>
</result_span>
<result_span id="GENSCAN_mRNA_SCAFFOLD4132_0001_Exon0004">
<name>genscan:7695-8086</name>
<type>genscan</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-5304</start>
<end>-4913</end>
</span>
</seq_relationship>
</result_span>
<result_span id="GENSCAN_mRNA_SCAFFOLD4132_0001_Exon0005">
<name>genscan:8236-8798</name>
<type>genscan</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-4763</start>
<end>-4201</end>
</span>
</seq_relationship>
</result_span>
<result_span id="GENSCAN_mRNA_SCAFFOLD4132_0001_Exon0006">
<name>genscan:8854-8988</name>
<type>genscan</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-4145</start>
<end>-4011</end>
</span>
</seq_relationship>
</result_span>
<result_span id="GENSCAN_mRNA_SCAFFOLD4132_0001_Exon0007">
<name>genscan:9209-9394</name>
<type>genscan</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-3790</start>
<end>-3605</end>
</span>
</seq_relationship>
</result_span>
<result_span id="GENSCAN_mRNA_SCAFFOLD4132_0001_Exon0008">
<name>genscan:9437-9548</name>
<type>genscan</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-3562</start>
<end>-3451</end>
</span>
</seq_relationship>
</result_span>
<result_span id="GENSCAN_mRNA_SCAFFOLD4132_0001_Exon0009">
<name>genscan:9638-9774</name>
<type>genscan</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-3361</start>
<end>-3225</end>
</span>
</seq_relationship>
</result_span>
<result_span id="GENSCAN_mRNA_SCAFFOLD4132_0001_Exon0010">
<name>genscan:17407-17614</name>
<type>genscan</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>4408</start>
<end>4615</end>
</span>
</seq_relationship>
</result_span>
</result_set>
</computational_analysis>
<computational_analysis>
<program>BCM_assembler:BCM</program>
<type>BCM_assembler:BCM</type>
<result_set id="ABLF01037772-fs">
<name>ABLF01037772</name>
<result_span id="ABLF01037772">
<name>ABLF01037772</name>
<type>BCM_assembler:BCM</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-8512</start>
<end>6682</end>
</span>
</seq_relationship>
</result_span>
</result_set>
</computational_analysis>
<computational_analysis>
<program>Gnomon</program>
<type>Gnomon</type>
<result_set id="hmm304464">
<name>hmm304464</name>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-6566</start>
<end>744</end>
</span>
</seq_relationship>
<result_span id="auto5537685">
<name>Gnomon:6433-6479</name>
<type>Gnomon</type>
<score>96.9098</score>
<output>
<type>score</type>
<value>96.9098</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-6566</start>
<end>-6520</end>
</span>
</seq_relationship>
</result_span>
<result_span id="auto5537687">
<name>Gnomon:7588-8014</name>
<type>Gnomon</type>
<score>96.9098</score>
<output>
<type>score</type>
<value>96.9098</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-5411</start>
<end>-4985</end>
</span>
</seq_relationship>
</result_span>
<result_span id="auto5537688">
<name>Gnomon:8236-8602</name>
<type>Gnomon</type>
<score>96.9098</score>
<output>
<type>score</type>
<value>96.9098</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-4763</start>
<end>-4397</end>
</span>
</seq_relationship>
</result_span>
<result_span id="auto5537689">
<name>Gnomon:8700-9401</name>
<type>Gnomon</type>
<score>96.9098</score>
<output>
<type>score</type>
<value>96.9098</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-4299</start>
<end>-3598</end>
</span>
</seq_relationship>
</result_span>
<result_span id="auto5537690">
<name>Gnomon:9465-9668</name>
<type>Gnomon</type>
<score>96.9098</score>
<output>
<type>score</type>
<value>96.9098</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-3534</start>
<end>-3331</end>
</span>
</seq_relationship>
</result_span>
<result_span id="auto5537691">
<name>Gnomon:13696-13743</name>
<type>Gnomon</type>
<score>96.9098</score>
<output>
<type>score</type>
<value>96.9098</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>697</start>
<end>744</end>
</span>
</seq_relationship>
</result_span>
</result_set>
</computational_analysis>
<computational_analysis>
<program>snap</program>
<type>snap</type>
<result_set id="SCAFFOLD4132-snap.5.6:mRNA:15">
<name>SCAFFOLD4132-snap.5.6</name>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-33</start>
<end>4107</end>
</span>
</seq_relationship>
<result_span id="SCAFFOLD4132-snap.5.6:mRNA:15:exon:69">
<name>snap:12966-12972</name>
<type>snap</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>-33</start>
<end>-27</end>
</span>
</seq_relationship>
</result_span>
<result_span id="SCAFFOLD4132-snap.5.6:mRNA:15:exon:70">
<name>snap:13051-13094</name>
<type>snap</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>52</start>
<end>95</end>
</span>
</seq_relationship>
</result_span>
<result_span id="SCAFFOLD4132-snap.5.6:mRNA:15:exon:71">
<name>snap:15681-15745</name>
<type>snap</type>
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<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
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<end>2746</end>
</span>
</seq_relationship>
</result_span>
<result_span id="SCAFFOLD4132-snap.5.6:mRNA:15:exon:72">
<name>snap:16655-16954</name>
<type>snap</type>
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<output>
<type>score</type>
<value>0.0</value>
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<span>
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</span>
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<result_span id="SCAFFOLD4132-snap.5.6:mRNA:15:exon:73">
<name>snap:16974-17106</name>
<type>snap</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
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<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
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</span>
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</result_span>
</result_set>
</computational_analysis>
<computational_analysis>
<program>geneid_rm</program>
<type>geneid_rm</type>
<result_set id="SCAFFOLD4132_geneidrm_mRNA7">
<name>SCAFFOLD4132_geneidrm_mRNA7</name>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2083</start>
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</span>
</seq_relationship>
<result_span id="SCAFFOLD4132_geneidrm_mRNA7_Exon0">
<name>geneid_rm:15082-15098</name>
<type>geneid_rm</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2083</start>
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</span>
</seq_relationship>
</result_span>
<result_span id="SCAFFOLD4132_geneidrm_mRNA7_Exon1">
<name>geneid_rm:16682-16973</name>
<type>geneid_rm</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
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<span>
<start>3683</start>
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</span>
</seq_relationship>
</result_span>
</result_set>
</computational_analysis>
<computational_analysis>
<program>Gnomon</program>
<type>Gnomon</type>
<result_set id="hmm306464">
<name>hmm306464</name>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>1820</start>
<end>793</end>
</span>
</seq_relationship>
<result_span id="auto5537696">
<name>Gnomon:14817-14259</name>
<type>Gnomon</type>
<score>46.7144</score>
<output>
<type>score</type>
<value>46.7144</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>1818</start>
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</span>
</seq_relationship>
</result_span>
<result_span id="auto5537694">
<name>Gnomon:13997-13792</name>
<type>Gnomon</type>
<score>46.7144</score>
<output>
<type>score</type>
<value>46.7144</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>998</start>
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</span>
</seq_relationship>
</result_span>
<result_span>
<type>start codon</type>
<score>0.0</score>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>1818</start>
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</span>
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</result_span>
<result_span>
<type>start codon</type>
<score>0.0</score>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
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</span>
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</result_span>
</result_set>
<result_set id="hmm308464">
<name>hmm308464</name>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2803</start>
<end>1906</end>
</span>
</seq_relationship>
<result_span id="auto5537701">
<name>Gnomon:15800-15611</name>
<type>Gnomon</type>
<score>35.5407</score>
<output>
<type>score</type>
<value>35.5407</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2801</start>
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</span>
</seq_relationship>
</result_span>
<result_span id="auto5537699">
<name>Gnomon:15479-14905</name>
<type>Gnomon</type>
<score>35.5407</score>
<output>
<type>score</type>
<value>35.5407</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2480</start>
<end>1906</end>
</span>
</seq_relationship>
</result_span>
<result_span>
<type>start codon</type>
<score>0.0</score>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2801</start>
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</span>
</seq_relationship>
</result_span>
<result_span>
<type>start codon</type>
<score>0.0</score>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
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</span>
</seq_relationship>
</result_span>
</result_set>
</computational_analysis>
<computational_analysis>
<program>RefSeq-Glean4</program>
<type>RefSeq-Glean4</type>
<result_set id="ACYPI44928-RA">
<name>GLEAN_24928</name>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2803</start>
<end>793</end>
</span>
</seq_relationship>
<result_span id="ACYPI44928-RA-E1">
<name>RefSeq-Glean4:15800-15611</name>
<type>RefSeq-Glean4</type>
<score>0.897606</score>
<output>
<type>score</type>
<value>0.897606</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2801</start>
<end>2612</end>
</span>
</seq_relationship>
</result_span>
<result_span id="ACYPI44928-RA-E2">
<name>RefSeq-Glean4:15479-14969</name>
<type>RefSeq-Glean4</type>
<score>0.897606</score>
<output>
<type>score</type>
<value>0.897606</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2480</start>
<end>1970</end>
</span>
</seq_relationship>
</result_span>
<result_span id="ACYPI44928-RA-E3">
<name>RefSeq-Glean4:14788-14259</name>
<type>RefSeq-Glean4</type>
<score>0.897606</score>
<output>
<type>score</type>
<value>0.897606</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>1789</start>
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</span>
</seq_relationship>
</result_span>
<result_span id="ACYPI44928-RA-E4">
<name>RefSeq-Glean4:13997-13792</name>
<type>RefSeq-Glean4</type>
<score>0.897606</score>
<output>
<type>score</type>
<value>0.897606</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>998</start>
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</span>
</seq_relationship>
</result_span>
<result_span>
<type>start codon</type>
<score>0.0</score>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2801</start>
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</span>
</seq_relationship>
</result_span>
<result_span>
<type>start codon</type>
<score>0.0</score>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2801</start>
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</span>
</seq_relationship>
</result_span>
</result_set>
</computational_analysis>
<computational_analysis>
<program>fgenesh_pipeline</program>
<type>fgenesh_pipeline</type>
<result_set id="FGENESH_mRNA_EQ114903_0003">
<name>FGENESH_mRNA_EQ114903_0003</name>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2801</start>
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</span>
</seq_relationship>
<result_span id="FGENESH_mRNA_EQ114903_0003_Exon0004">
<name>fgenesh_pipeline:15800-15611</name>
<type>fgenesh_pipeline</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2801</start>
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</span>
</seq_relationship>
</result_span>
<result_span id="FGENESH_mRNA_EQ114903_0003_Exon0003">
<name>fgenesh_pipeline:15479-14969</name>
<type>fgenesh_pipeline</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
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</span>
</seq_relationship>
</result_span>
<result_span id="FGENESH_mRNA_EQ114903_0003_Exon0002">
<name>fgenesh_pipeline:14788-14259</name>
<type>fgenesh_pipeline</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
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</span>
</seq_relationship>
</result_span>
<result_span id="FGENESH_mRNA_EQ114903_0003_Exon0001">
<name>fgenesh_pipeline:13958-13792</name>
<type>fgenesh_pipeline</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
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</span>
</seq_relationship>
</result_span>
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</computational_analysis>
<computational_analysis>
<program>AUGUSTUS</program>
<type>AUGUSTUS</type>
<result_set id="AUG4_SCAFFOLD4132.g3.t1">
<name>AUG4_SCAFFOLD4132.g3.t1</name>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>2006</start>
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</span>
</seq_relationship>
<result_span id="auto6248451">
<name>AUGUSTUS:15005-14259</name>
<type>AUGUSTUS</type>
<score>0.17</score>
<output>
<type>score</type>
<value>0.17</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
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</span>
</seq_relationship>
</result_span>
<result_span id="auto6248448">
<name>AUGUSTUS:14111-13737</name>
<type>AUGUSTUS</type>
<score>0.17</score>
<output>
<type>score</type>
<value>0.17</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>1112</start>
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</span>
</seq_relationship>
</result_span>
</result_set>
</computational_analysis>
<computational_analysis>
<program>blastx_trembl:BiO3P</program>
<type>blastx_trembl:BiO3P</type>
<result_set id="Uniprot-trembl_BLASTX_SCAFFOLD4132_match_set18_1-fs">
<name>A.pisum</name>
<result_span>
<name>O96740_DROME_4831468</name>
<score>6.0E-23</score>
<output>
<type>score</type>
<value>6.0E-23</value>
</output>
<output>
<type>normscore</type>
<value>0.0</value>
</output>
<output>
<type>identity</type>
<value>0.0</value>
</output>
<output>
<type>significance</type>
<value>6.000000314464115E-23</value>
</output>
<output>
<type>rawscore</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>1560</start>
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</span>
</seq_relationship>
<seq_relationship type="subject" seq="O96740_DROME_4831468">
<span>
<start>282</start>
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</span>
</seq_relationship>
</result_span>
</result_set>
<result_set id="Uniprot-trembl_BLASTX_SCAFFOLD4132_match_set20_1-fs">
<name>A.pisum</name>
<result_span>
<name>Q01HX8_ORYSA_4887396</name>
<score>8.0E-23</score>
<output>
<type>score</type>
<value>8.0E-23</value>
</output>
<output>
<type>normscore</type>
<value>0.0</value>
</output>
<output>
<type>identity</type>
<value>0.0</value>
</output>
<output>
<type>significance</type>
<value>7.99999999855967E-23</value>
</output>
<output>
<type>rawscore</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>1803</start>
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</span>
</seq_relationship>
<seq_relationship type="subject" seq="Q01HX8_ORYSA_4887396">
<span>
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</span>
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</result_span>
</result_set>
<result_set id="Uniprot-trembl_BLASTX_SCAFFOLD4132_match_set25_1-fs">
<name>A.pisum</name>
<result_span>
<name>Q01M17_ORYSA_4901456</name>
<score>3.0E-23</score>
<output>
<type>score</type>
<value>3.0E-23</value>
</output>
<output>
<type>normscore</type>
<value>0.0</value>
</output>
<output>
<type>identity</type>
<value>0.0</value>
</output>
<output>
<type>significance</type>
<value>3.000000157232057E-23</value>
</output>
<output>
<type>rawscore</type>
<value>0.0</value>
</output>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
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</seq_relationship>
<seq_relationship type="subject" seq="Q01M17_ORYSA_4901456">
<span>
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</seq_relationship>
</result_span>
</result_set>
<result_set id="Uniprot-trembl_BLASTX_SCAFFOLD4132_match_set33_1-fs">
<name>A.pisum</name>
<result_span>
<name>Q0D613_ORYSJ_4961331</name>
<score>6.0E-24</score>
<output>
<type>score</type>
<value>6.0E-24</value>
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<output>
<type>normscore</type>
<value>0.0</value>
</output>
<output>
<type>identity</type>
<value>0.0</value>
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<output>
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<value>5.999999920033662E-24</value>
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<output>
<type>rawscore</type>
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<seq_relationship type="query" seq="EQ114903:13000-15800">
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<seq_relationship type="subject" seq="Q0D613_ORYSJ_4961331">
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<result_set id="Uniprot-trembl_BLASTX_SCAFFOLD4132_match_set53_1-fs">
<name>A.pisum</name>
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<name>Q24310_DROME_4829758</name>
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<type>score</type>
<value>1.0E-24</value>
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<output>
<type>normscore</type>
<value>0.0</value>
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<output>
<type>identity</type>
<value>0.0</value>
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<output>
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<output>
<type>rawscore</type>
<value>0.0</value>
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<span>
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<seq_relationship type="subject" seq="Q24310_DROME_4829758">
<span>
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<result_set id="Uniprot-trembl_BLASTX_SCAFFOLD4132_match_set67_1-fs">
<name>A.pisum</name>
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<name>Q2QSH9_ORYSJ_5116897</name>
<score>5.0E-21</score>
<output>
<type>score</type>
<value>5.0E-21</value>
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<output>
<type>normscore</type>
<value>0.0</value>
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<output>
<type>identity</type>
<value>0.0</value>
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<output>
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<value>4.999999841327613E-21</value>
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<output>
<type>rawscore</type>
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<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
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<seq_relationship type="subject" seq="Q2QSH9_ORYSJ_5116897">
<span>
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<result_set id="Uniprot-trembl_BLASTX_SCAFFOLD4132_match_set73_1-fs">
<name>A.pisum</name>
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<name>Q2QVL4_ORYSJ_4834501</name>
<score>3.0E-22</score>
<output>
<type>score</type>
<value>3.0E-22</value>
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<output>
<type>normscore</type>
<value>0.0</value>
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<output>
<type>identity</type>
<value>0.0</value>
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<output>
<type>significance</type>
<value>2.9999999047965676E-22</value>
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<output>
<type>rawscore</type>
<value>0.0</value>
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<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
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<seq_relationship type="subject" seq="Q2QVL4_ORYSJ_4834501">
<span>
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</computational_analysis>
<computational_analysis>
<program>geneid_rm</program>
<type>geneid_rm</type>
<result_set id="SCAFFOLD4132_geneidrm_mRNA6">
<name>SCAFFOLD4132_geneidrm_mRNA6</name>
<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
<start>1818</start>
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<result_span id="SCAFFOLD4132_geneidrm_mRNA6_Exon1">
<name>geneid_rm:14817-14259</name>
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<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
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<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
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</result_span>
<result_span id="SCAFFOLD4132_geneidrm_mRNA6_Exon0">
<name>geneid_rm:14108-13792</name>
<type>geneid_rm</type>
<score>0.0</score>
<output>
<type>score</type>
<value>0.0</value>
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<seq_relationship type="query" seq="EQ114903:13000-15800">
<span>
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</result_span>
</result_set>
</computational_analysis>
</game>
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