Origin IGS: taccccaagatactccctccctctctctcttcccgttcgggctgatttccatgcccaaaaatcaccttccgatttttattttcacccatcctcataatccaagggtcgaaaattcggaaaactttacacaaaacgcaaaaacaataacacactaataataagtgttttatgaaaagttttcggaaaacttttcaacaacgaagccttttcctattgtccaattaatatatacttcataacattgcaggcacaaacagaagttatttacataaaacacc .........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 ggtgttttatgtaaataacttctgtttgtgcctgcaatgttatgaagtatatattaattggacaataggaaaaggcttcgttgttgaaaagttttccgaaaacttttcataaaacacttattattagtgtgttattgtttttgcgttttgtgtaaagttttccgaattttcgacccttggattatgaggatgggtgaaaataaaaatcggaaggtgatttttgggcatggaaatcagcccgaacgggaagagagagagggagggagtatcttggggta Mask Tandem Repeat Region ================================================ taccccaagatactccctccctctctctcttcccgttcgggctgatttccatgcccaaaaatcaccttccgatttttattttcacccatcctcataatccaagggtcgaaaattcggaaaactttacacaaaacgcaaaaacaataacacactaataataagtgttttatgaaaagttttcggaaaacttttcaacaacgaagccttttcctattgtccaattaatatatacttcataacattgcaggcacaaacagaagttatttacataaaacacc Find is-nt database================================================ Query_seq: PG1128:PG1129|PG1128:PG1129:exodeoxyribonuclease VII large subunit:ribonucleotide reductase:->->:1205260..1205537 278 taccccaagatactccctccctctctctcttcccgttcgggctgatttccatgcccaaaaatcaccttccgatttttattttcacccatcctcataatccaagggtcgaaaattcggaaaactttacacaaaacgcaaaaacaataacacactaataataagtgttttatgaaaagttttcggaaaacttttcaacaacgaagccttttcctattgtccaattaatatatacttcataacattgcaggcacaaacagaagttatttacataaaacacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1128:PG1129|PG1128:PG1129:exodeoxyribonuclease VII large subunit:ribonucleotide reductase:->->:1205260..1205537 278 taccccaagatactccctccctctctctcttcccgttcgggctgatttccatgcccaaaaatcaccttccgatttttattttcacccatcctcataatccaagggtcgaaaattcggaaaactttacacaaaacgcaaaaacaataacacactaataataagtgttttatgaaaagttttcggaaaacttttcaacaacgaagccttttcctattgtccaattaatatatacttcataacattgcaggcacaaacagaagttatttacataaaacacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1128:PG1129|PG1128:PG1129:exodeoxyribonuclease VII large subunit:ribonucleotide reductase:->->:1205260..1205537 278 taccccaagatactccctccctctctctcttcccgttcgggctgatttccatgcccaaaaatcaccttccgatttttattttcacccatcctcataatccaagggtcgaaaattcggaaaactttacacaaaacgcaaaaacaataacacactaataataagtgttttatgaaaagttttcggaaaacttttcaacaacgaagccttttcctattgtccaattaatatatacttcataacattgcaggcacaaacagaagttatttacataaaacacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taccccaagatactccctccctctctctcttcccgttcgggctgatttccatgcccaaaaatcaccttccgatttttattttcacccatcctcataatccaagggtcgaaaattcggaaaactttacacaaaacgcaaaaacaataacacactaataataagtgttttatgaaaagttttcggaaaacttttcaacaacgaagccttttcctattgtccaattaatatatacttcataacattgcaggcacaaacagaagttatttacataaaacacc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 42 End: 152 ......................................... M I S M P K N H L P I F I F T H P H N P R V E N S E N F T Q N A K T I T H .............................................................................................................................. Protein_Len: 36 Strand: - Start: 170 End: 277 ......................................................................................................................................................................... S F N E S F K E V V F G K G I T W N I Y V E Y C Q L C L C F N N V Y F M . Protein_Len: 56 Strand: - Start: 3 End: 170 .. G L I S G G E R E E R E P Q N G H G F I V K R N K N E G M R M I W P D F I R F V K C L V C F C Y C V L L L H K M ............................................................................................................ taccccaagatactccctccctctctctcttcccgttcgggctgatttccatgcccaaaaatcaccttccgatttttattttcacccatcctcataatccaagggtcgaaaattcggaaaactttacacaaaacgcaaaaacaataacacactaataataagtgttttatgaaaagttttcggaaaacttttcaacaacgaagccttttcctattgtccaattaatatatacttcataacattgcaggcacaaacagaagttatttacataaaacacc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 213 End: 242 ....................................................................................................................................................................................................................ATTGTCCAATTAATATATACTTCATAACAT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taccccaagatactccctccctctctctcttcccgttcgggctgatttccatgcccaaaaatcaccttccgatttttattttcacccatcctcataatccaagggtcgaaaattcggaaaactttacacaaaacgcaaaaacaataacacactaataataagtgttttatgaaaagttttcggaaaacttttcaacaacgaagccttttcctattgtccaattaatatatacttcataacattgcaggcacaaacagaagttatttacataaaacacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1128:PG1129|PG1128:PG1129:exodeoxyribonuclease VII large subunit:ribonucleotide reductase:->->:1205260..1205537 278 taccccaagatactccctccctctctctcttcccgttcgggctgatttccatgcccaaaaatcaccttccgatttttattttcacccatcctcataatccaagggtcgaaaattcggaaaactttacacaaaacgcaaaaacaataacacactaataataagtgttttatgaaaagttttcggaaaacttttcaacaacgaagccttttcctattgtccaattaatatatacttcataacattgcaggcacaaacagaagttatttacataaaacacc Intra-Species Hit: Count: 1 Min: 1 Max: 278 Len: 278 Subject: NC_002950_PG1128_PG1129|exodeoxyribonuclease VII large subunit:ribonucleotide reductase|POSITIVE:POSITIVE|[1205260,1205537]|278 HSP 1 e-value: 1.0E-156 bit: 551.0 Len: 278 Query Start:1 Query End:278 Subject Strand: POSITIVE Subject Start: 1 Subject End: 278 taccccaagatactccctccctctctctcttcccgttcgggctgatttccatgcccaaaaatcaccttccgatttttattttcacccatcctcataatccaagggtcgaaaattcggaaaactttacacaaaacgcaaaaacaataacacactaataataagtgttttatgaaaagttttcggaaaacttttcaacaacgaagccttttcctattgtccaattaatatatacttcataacattgcaggcacaaacagaagttatttacataaaacacc taccccaagatactccctccctctctctcttcccgttcgggctgatttccatgcccaaaaatcaccttccgatttttattttcacccatcctcataatccaagggtcgaaaattcggaaaactttacacaaaacgcaaaaacaataacacactaataataagtgttttatgaaaagttttcggaaaacttttcaacaacgaagccttttcctattgtccaattaatatatacttcataacattgcaggcacaaacagaagttatttacataaaacacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACCCCAAGAUACUCCCUCCCUCUCUCUCUUCCCGUUCGGGCUGAUUUCCAUGCCCAAAAAUCACCUUCCGAUUUUUAUUUUCACCCAUCCUCAUAAUCCAAGGGUCGAAAAUUCGGAAAACUUUACACAAAACGCAAAAACAAUAACACACUAAUAAUAAGUGUUUUAUGAAAAGUUUUCGGAAAACUUUUCAACAACGAAGCCUUUUCCUAUUGUCCAAUUAAUAUAUACUUCAUAACAUUGCAGGCACAAACAGAAGUUAUUUACAUAAAACACC .................................((((.((((((.....)).))))..........((((((.....((((((((((...............)))).))))))))))))............))))..........................((((((((((.(((..((((((((((..((((......))))..))))))..((((((...........................)).))))...))))...))).)))))))))). (-46.39) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUGUUUUAUGUAAAUAACUUCUGUUUGUGCCUGCAAUGUUAUGAAGUAUAUAUUAAUUGGACAAUAGGAAAAGGCUUCGUUGUUGAAAAGUUUUCCGAAAACUUUUCAUAAAACACUUAUUAUUAGUGUGUUAUUGUUUUUGCGUUUUGUGUAAAGUUUUCCGAAUUUUCGACCCUUGGAUUAUGAGGAUGGGUGAAAAUAAAAAUCGGAAGGUGAUUUUUGGGCAUGGAAAUCAGCCCGAACGGGAAGAGAGAGAGGGAGGGAGUAUCUUGGGGUA .......((((((.(((((...(((........)))..)))))....))))))........((..(((((....(((((.((..((((((((((.....))))))))))....(((((.......)))))....((.(((((.((((.........(..((((((((((((.((((...............)))))))))).....))))))..).......((((.((.....)))))).)))).))))).)).....)).))))).)))))..)). (-61.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 421 70 24 206 168 NC_002950:PG0987|5end_hypothetical_protein_1048002..1048232_POSITIVE 392 73 31 58 6 NC_002950:PG0526|5end_putative_inner_membrane_protein_translocase_component_YidC_570746..570976_POSITIVE 358 60 16 75 30 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 354 42 2 32 5 NC_002950:PG1525|5end_isochorismate_synthase,_putative_1603865..1604095_NEGATIVE 352 69 29 188 145 NC_002950:PG1089|5end_DNA-binding_response_regulator_RprY_1156260..1156490_NEGATIVE 340 55 18 209 163 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 335 50 13 77 35 NC_002950:PG1693|5end_HesA/MoeB/ThiF_family_protein_1777919..1778149_NEGATIVE 333 50 3 195 153 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 328 53 18 182 149 NC_002950:PG1565|5end_3-deoxy-D-manno-octulosonic-acid_transferase,_putative_1645859..1646089_NEGATIVE 327 57 16 67 6 NC_002950:PG0493|5end_hypothetical_protein_534900..535130_NEGATIVE 326 77 36 185 142 NC_002950:PG0778|5end_hypothetical_protein_831869..832099_NEGATIVE 325 46 3 231 170 NC_002950:PG1003|5end_hypothetical_protein_1059232..1059462_POSITIVE 323 54 18 219 184 NC_002950:PG0984|5end_hypothetical_protein_1046919..1047149_NEGATIVE 323 70 27 50 10 NC_002950:PG0293|5end_secretion_activator_protein,_putative_328671..328901_NEGATIVE 315 57 16 67 6 NC_002950:PG1426|5end_hypothetical_protein_1511310..1511540_NEGATIVE 313 57 16 67 6 NC_002950:PG0265|5end_hypothetical_protein_298551..298781_NEGATIVE 311 45 11 170 133 NC_002950:PG0634|5end_ThiJ/PfpI_family_protein_686143..686373_POSITIVE 311 249 202 231 177 NC_002950:PG0365|5end_3'-5'_exonuclease_domain_protein_400178..400408_NEGATIVE 310 70 26 227 178 NC_002950:PG1524|5end_2-succinyl-6-hydroxy-2,_4-cyclohexadiene-1-carboxylic_acid_synthase/2-oxoglutarate_decarboxylase_1602746..1602976_NEGATIVE 308 44 12 223 195 NC_002950:PG1475|5end_conjugative_transposon_protein_TraN_1551835..1552065_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 60 16 62 17 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 340 55 18 108 62 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 335 50 13 80 38 NC_002950:PG1694|3end_hypothetical_protein_1777916..1778066_NEGATIVE 327 42 8 64 21 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 310 247 202 147 100 NC_002950:PG0366|3end_hypothetical_protein_400255..400405_NEGATIVE 306 45 9 47 13 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 299 50 5 58 13 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 299 54 13 58 5 NC_002950:PG1125|3end_hypothetical_protein_1201071..1201221_NEGATIVE 299 42 11 150 118 NC_002950:PG0633|3end_hypothetical_protein_686208..686358_POSITIVE 292 56 21 86 50 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE 291 43 15 134 98 NC_002950:PG1205|3end_DNA-binding_protein,_histone-like_family_1284503..1284653_POSITIVE 290 56 14 48 6 NC_002950:PG1136|3end_hypothetical_protein_1216699..1216849_NEGATIVE 286 44 3 133 82 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 285 50 4 124 79 NC_002950:PG0400|3end_hypothetical_protein_436245..436395_NEGATIVE 284 41 3 147 95 NC_002950:PG1002|3end_hypothetical_protein_1059237..1059387_POSITIVE 284 117 75 144 90 NC_002950:PG0173|3end_transcriptional_regulator,_putative_194388..194538_NEGATIVE 283 71 32 151 94 NC_002950:PG0637|3end_thiamine_monophosphate_kinase_689064..689214_NEGATIVE 281 50 4 135 80 NC_002950:PG0411|3end_hemagglutinin,_putative_449358..449508_POSITIVE 279 74 35 131 96 NC_002950:PG0538|3end_outer_membrane_efflux_protein_590610..590760_POSITIVE 278 54 24 65 34 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE