Origin IGS: agtctttttgcttttcgtggacgcgaacgttagcccacctttaataaatgcaaaaatagtaaattttagcgatataaggaaattattttgaagttattatcatttaactttcgctttttatcggtataagagaacaataaaacagaagaatagtataatttaaacgcatatattgcatatattttatggtagccaagtgcaggtatagcgtgagttcgatataagaattacgccagtgtattattcataagatacttaaagaaaggcttgattatgatttaatatgcttataatcagaaaaagtaaagcatcttcgtccttacattcctactccgaactaacgtcgttttgtgaactaaaagaaggcaacaaatgtgtaaatatttttcataagcgtaactatcgcttaacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagttaagcgatagttacgcttatgaaaaatatttacacatttgttgccttcttttagttcacaaaacgacgttagttcggagtaggaatgtaaggacgaagatgctttactttttctgattataagcatattaaatcataatcaagcctttctttaagtatcttatgaataatacactggcgtaattcttatatcgaactcacgctatacctgcacttggctaccataaaatatatgcaatatatgcgtttaaattatactattcttctgttttattgttctcttataccgataaaaagcgaaagttaaatgataataacttcaaaataatttccttatatcgctaaaatttactatttttgcatttattaaaggtgggctaacgttcgcgtccacgaaaagcaaaaagact Mask Tandem Repeat Region ================================================ agtctttttgcttttcgtggacgcgaacgttagcccacctttaataaatgcaaaaatagtaaattttagcgatataaggaaattattttgaagttattatcatttaactttcgctttttatcggtataagagaacaataaaacagaagaatagtataatttaaacgcatatattgcatatattttatggtagccaagtgcaggtatagcgtgagttcgatataagaattacgccagtgtattattcataagatacttaaagaaaggcttgattatgatttaatatgcttataatcagaaaaagtaaagcatcttcgtccttacattcctactccgaactaacgtcgttttgtgaactaaaagaaggcaacaaatgtgtaaatatttttcataagcgtaactatcgcttaacta Find is-nt database================================================ Query_seq: PI0060:PI0061|PI0060:PI0061:long-chain-fatty-acid--CoA ligase (acyl-CoA synthetase):hypothetical protein:->->:60227..60639 413 agtctttttgcttttcgtggacgcgaacgttagcccacctttaataaatgcaaaaatagtaaattttagcgatataaggaaattattttgaagttattatcatttaactttcgctttttatcggtataagagaacaataaaacagaagaatagtataatttaaacgcatatattgcatatattttatggtagccaagtgcaggtatagcgtgagttcgatataagaattacgccagtgtattattcataagatacttaaagaaaggcttgattatgatttaatatgcttataatcagaaaaagtaaagcatcttcgtccttacattcctactccgaactaacgtcgttttgtgaactaaaagaaggcaacaaatgtgtaaatatttttcataagcgtaactatcgcttaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0060:PI0061|PI0060:PI0061:long-chain-fatty-acid--CoA ligase (acyl-CoA synthetase):hypothetical protein:->->:60227..60639 413 agtctttttgcttttcgtggacgcgaacgttagcccacctttaataaatgcaaaaatagtaaattttagcgatataaggaaattattttgaagttattatcatttaactttcgctttttatcggtataagagaacaataaaacagaagaatagtataatttaaacgcatatattgcatatattttatggtagccaagtgcaggtatagcgtgagttcgatataagaattacgccagtgtattattcataagatacttaaagaaaggcttgattatgatttaatatgcttataatcagaaaaagtaaagcatcttcgtccttacattcctactccgaactaacgtcgttttgtgaactaaaagaaggcaacaaatgtgtaaatatttttcataagcgtaactatcgcttaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0060:PI0061|PI0060:PI0061:long-chain-fatty-acid--CoA ligase (acyl-CoA synthetase):hypothetical protein:->->:60227..60639 413 agtctttttgcttttcgtggacgcgaacgttagcccacctttaataaatgcaaaaatagtaaattttagcgatataaggaaattattttgaagttattatcatttaactttcgctttttatcggtataagagaacaataaaacagaagaatagtataatttaaacgcatatattgcatatattttatggtagccaagtgcaggtatagcgtgagttcgatataagaattacgccagtgtattattcataagatacttaaagaaaggcttgattatgatttaatatgcttataatcagaaaaagtaaagcatcttcgtccttacattcctactccgaactaacgtcgttttgtgaactaaaagaaggcaacaaatgtgtaaatatttttcataagcgtaactatcgcttaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtctttttgcttttcgtggacgcgaacgttagcccacctttaataaatgcaaaaatagtaaattttagcgatataaggaaattattttgaagttattatcatttaactttcgctttttatcggtataagagaacaataaaacagaagaatagtataatttaaacgcatatattgcatatattttatggtagccaagtgcaggtatagcgtgagttcgatataagaattacgccagtgtattattcataagatacttaaagaaaggcttgattatgatttaatatgcttataatcagaaaaagtaaagcatcttcgtccttacattcctactccgaactaacgtcgttttgtgaactaaaagaaggcaacaaatgtgtaaatatttttcataagcgtaactatcgcttaacta Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 284 End: 412 ........................................................................................................................................................................................................................................................................................... M L I I R K S K A S S S L H S Y S E L T S F C E L K E G N K C V N I F H K R N Y R L T . Protein_Len: 46 Strand: - Start: 107 End: 244 .......................................................................................................... S E S K I P I L S C Y F L L I T Y N L R M Y Q M Y K I T A L H L Y L T L E I Y S N R W H I M ......................................................................................................................................................................... Protein_Len: 46 Strand: - Start: 69 End: 206 .................................................................... R Y L S I I K F N N D N L K R K K D T Y S F L L V S S Y Y L K F A Y I A Y I K H Y G L A P M ............................................................................................................................................................................................................... agtctttttgcttttcgtggacgcgaacgttagcccacctttaataaatgcaaaaatagtaaattttagcgatataaggaaattattttgaagttattatcatttaactttcgctttttatcggtataagagaacaataaaacagaagaatagtataatttaaacgcatatattgcatatattttatggtagccaagtgcaggtatagcgtgagttcgatataagaattacgccagtgtattattcataagatacttaaagaaaggcttgattatgatttaatatgcttataatcagaaaaagtaaagcatcttcgtccttacattcctactccgaactaacgtcgttttgtgaactaaaagaaggcaacaaatgtgtaaatatttttcataagcgtaactatcgcttaacta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtctttttgcttttcgtggacgcgaacgttagcccacctttaataaatgcaaaaatagtaaattttagcgatataaggaaattattttgaagttattatcatttaactttcgctttttatcggtataagagaacaataaaacagaagaatagtataatttaaacgcatatattgcatatattttatggtagccaagtgcaggtatagcgtgagttcgatataagaattacgccagtgtattattcataagatacttaaagaaaggcttgattatgatttaatatgcttataatcagaaaaagtaaagcatcttcgtccttacattcctactccgaactaacgtcgttttgtgaactaaaagaaggcaacaaatgtgtaaatatttttcataagcgtaactatcgcttaacta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 43 HP_score: -2.6 Tail_Score: -3.09784 Start: 50 End: 70 Full_Region: taatttccttatatc gctaaaat ttact atttttgc atttattaaaggtgg .................................................gctaaaatttactatttttgc....................................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI0060:PI0061|PI0060:PI0061:long-chain-fatty-acid--CoA ligase (acyl-CoA synthetase):hypothetical protein:->->:60227..60639 413 agtctttttgcttttcgtggacgcgaacgttagcccacctttaataaatgcaaaaatagtaaattttagcgatataaggaaattattttgaagttattatcatttaactttcgctttttatcggtataagagaacaataaaacagaagaatagtataatttaaacgcatatattgcatatattttatggtagccaagtgcaggtatagcgtgagttcgatataagaattacgccagtgtattattcataagatacttaaagaaaggcttgattatgatttaatatgcttataatcagaaaaagtaaagcatcttcgtccttacattcctactccgaactaacgtcgttttgtgaactaaaagaaggcaacaaatgtgtaaatatttttcataagcgtaactatcgcttaacta Intra-Species Hit: Count: 1 Min: 1 Max: 413 Len: 413 Subject: pint_PI0060_PI0061|long-chain-fatty-acid--CoA ligase (acyl-CoA synthetase):hypothetical protein|POSITIVE:POSITIVE|[60227,60639]|413 HSP 1 e-value: 0.0 bit: 819.0 Len: 413 Query Start:1 Query End:413 Subject Strand: POSITIVE Subject Start: 1 Subject End: 413 agtctttttgcttttcgtggacgcgaacgttagcccacctttaataaatgcaaaaatagtaaattttagcgatataaggaaattattttgaagttattatcatttaactttcgctttttatcggtataagagaacaataaaacagaagaatagtataatttaaacgcatatattgcatatattttatggtagccaagtgcaggtatagcgtgagttcgatataagaattacgccagtgtattattcataagatacttaaagaaaggcttgattatgatttaatatgcttataatcagaaaaagtaaagcatcttcgtccttacattcctactccgaactaacgtcgttttgtgaactaaaagaaggcaacaaatgtgtaaatatttttcataagcgtaactatcgcttaacta agtctttttgcttttcgtggacgcgaacgttagcccacctttaataaatgcaaaaatagtaaattttagcgatataaggaaattattttgaagttattatcatttaactttcgctttttatcggtataagagaacaataaaacagaagaatagtataatttaaacgcatatattgcatatattttatggtagccaagtgcaggtatagcgtgagttcgatataagaattacgccagtgtattattcataagatacttaaagaaaggcttgattatgatttaatatgcttataatcagaaaaagtaaagcatcttcgtccttacattcctactccgaactaacgtcgttttgtgaactaaaagaaggcaacaaatgtgtaaatatttttcataagcgtaactatcgcttaacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCUUUUUGCUUUUCGUGGACGCGAACGUUAGCCCACCUUUAAUAAAUGCAAAAAUAGUAAAUUUUAGCGAUAUAAGGAAAUUAUUUUGAAGUUAUUAUCAUUUAACUUUCGCUUUUUAUCGGUAUAAGAGAACAAUAAAACAGAAGAAUAGUAUAAUUUAAACGCAUAUAUUGCAUAUAUUUUAUGGUAGCCAAGUGCAGGUAUAGCGUGAGUUCGAUAUAAGAAUUACGCCAGUGUAUUAUUCAUAAGAUACUUAAAGAAAGGCUUGAUUAUGAUUUAAUAUGCUUAUAAUCAGAAAAAGUAAAGCAUCUUCGUCCUUACAUUCCUACUCCGAACUAACGUCGUUUUGUGAACUAAAAGAAGGCAACAAAUGUGUAAAUAUUUUUCAUAAGCGUAACUAUCGCUUAACUA .((((((((....((((..((.((((.((((((..(............(((.(((((.....))))).)))...((((((..........(((((((.((((.....(((((......((((.((........))............((((((((((......((((.((((((((((.((((....)))).....))))).))))))))).(((((.......))))).......))))))))))....))))......)))))...)))).)))))))...((((((................)))))).....))))))............)..))))))))))))..))))....))))))))...((((((....))))))....((((((.......)))))).... (-81.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUAAGCGAUAGUUACGCUUAUGAAAAAUAUUUACACAUUUGUUGCCUUCUUUUAGUUCACAAAACGACGUUAGUUCGGAGUAGGAAUGUAAGGACGAAGAUGCUUUACUUUUUCUGAUUAUAAGCAUAUUAAAUCAUAAUCAAGCCUUUCUUUAAGUAUCUUAUGAAUAAUACACUGGCGUAAUUCUUAUAUCGAACUCACGCUAUACCUGCACUUGGCUACCAUAAAAUAUAUGCAAUAUAUGCGUUUAAAUUAUACUAUUCUUCUGUUUUAUUGUUCUCUUAUACCGAUAAAAAGCGAAAGUUAAAUGAUAAUAACUUCAAAAUAAUUUCCUUAUAUCGCUAAAAUUUACUAUUUUUGCAUUUAUUAAAGGUGGGCUAACGUUCGCGUCCACGAAAAGCAAAAAGACU ......(((((((....(((((.............((.(((.((((((.........(((.....)))...(.((((..((.(((((..((((......(((((((((.........(((((((..............)))))))...........)))))))))........)))).((((((..(((.......)))...))))))..))))).))..)))).)...........)))))).))).))......................(((((((...........)))))))))))).((((((........))))))................)))))))...........(((((((.(((.....(.((((((....)))))).).....))).))))))).... (-73.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 455 405 361 228 184 pint:PI1456|5end_conserved_hypothetical_protein_1378864..1379094_POSITIVE 454 410 362 112 56 pint:PI0991|5end_conserved_hypothetical_protein_915309..915539_POSITIVE 442 320 271 225 175 pint:PI1500|5end_hypothetical_protein_1420626..1420856_POSITIVE 413 407 361 206 162 pint:PI1253|5end_hypothetical_protein_1175516..1175746_POSITIVE 404 243 207 228 192 pint:PI0569|5end_phosphoglycerate_kinase_513297..513527_POSITIVE 390 404 361 228 174 pint:PI2030|5end_hypothetical_protein_1985601..1985831_POSITIVE 366 410 361 76 23 pint:PI1295|5end_hypothetical_protein_1208636..1208866_POSITIVE 361 395 358 160 124 pint:PI0090|5end_amidophosphoribosyltransferase_88379..88609_POSITIVE 360 410 361 201 150 pint:PI0038|5end_transcriptional_regulator,_LysR_family_39578..39808_POSITIVE 349 240 191 67 10 pint:PI0673|5end_hypothetical_protein_612206..612436_POSITIVE 347 390 341 221 172 pint:PI0286|5end_ISPg3-related_transposase_271833..272063_POSITIVE 345 410 364 124 78 pint:PI0653|5end_hypothetical_protein_596046..596276_POSITIVE 337 410 361 110 61 pint:PI2046|5end_hypothetical_protein_1999030..1999260_POSITIVE 336 403 364 143 93 pint:PI2024|5end_hypothetical_protein_1978804..1979034_POSITIVE 330 407 364 143 93 pint:PI1333|5end_conserved_hypothetical_protein_1250777..1251007_POSITIVE 329 398 358 229 189 pint:PI1206|5end_ATP-dependent_DNA_helicase,_UvrD/PcrA/Rep_family_1124698..1124928_POSITIVE 325 406 361 175 130 pint:PI1272|5end_possible_transcriptional_regulator_1191702..1191932_POSITIVE 320 389 343 83 36 pint:PI1437|5end_hypothetical_protein_1356088..1356318_POSITIVE 319 350 305 212 165 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 317 407 361 196 156 pint:PI0660|5end_conserved_hypothetical_protein_603438..603668_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 407 361 50 6 pint:PI1252|3end_hypothetical_protein_1175440..1175590_POSITIVE 385 410 364 59 13 pint:PI0568|3end_hypothetical_protein_513131..513281_POSITIVE 376 406 361 67 22 pint:PI0866|3end_hypothetical_protein_803993..804143_POSITIVE 366 410 361 76 23 pint:PI1294|3end_hypothetical_protein_1208716..1208866_POSITIVE 361 395 358 56 20 pint:PI0089|3end_hypothetical_protein_88355..88505_POSITIVE 358 405 361 149 104 pint:PI0119|3end_hypothetical_protein_111723..111873_POSITIVE 358 405 361 66 21 pint:PI0118|3end_hypothetical_protein_111640..111790_POSITIVE 336 403 364 91 41 pint:PI2023|3end_hypothetical_protein_1978832..1978982_POSITIVE 329 398 358 86 46 pint:PI1204|3end_hypothetical_protein_1124635..1124785_POSITIVE 320 389 343 147 100 pint:PI1436|3end_hypothetical_protein_1356232..1356382_POSITIVE 318 403 364 77 37 pint:PI1072|3end_hypothetical_protein_990503..990653_POSITIVE 317 407 361 74 34 pint:PI0659|3end_hypothetical_protein_603396..603546_POSITIVE 310 405 361 63 22 pint:PI0820|3end_hypothetical_protein_759980..760130_POSITIVE 308 238 197 111 73 pint:PI0721|3end_hypothetical_protein_654982..655132_POSITIVE 307 210 165 74 22 pint:PI0053|3end_hypothetical_protein_55124..55274_POSITIVE 305 235 192 101 59 pint:PI0006|3end_hypothetical_protein_8268..8418_POSITIVE 300 404 361 103 45 pint:PI1064|3end_hypothetical_protein_983324..983474_POSITIVE 298 227 181 136 90 pint:PI1019|3end_hypothetical_protein_938412..938562_POSITIVE 298 349 308 150 112 pint:PI0935|3end_collagenase,_protease_868320..868470_POSITIVE 296 404 361 151 108 pint:PI0037|3end_hypothetical_protein_39616..39766_POSITIVE