Origin IGS: cctcagtttcctcttttccttcttatttgaactaatacccaaagaaaattgaagttcagatttctttgaataagagctggtttttttgttgttaatatcataccattctataggaaattgtcaatcattattaagcaaaaaataaaaaccatcatttttaaaactaaaaacgatagtttttatgatttataatcaataatgttcg .........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 cgaacattattgattataaatcataaaaactatcgtttttagttttaaaaatgatggtttttattttttgcttaataatgattgacaatttcctatagaatggtatgatattaacaacaaaaaaaccagctcttattcaaagaaatctgaacttcaattttctttgggtattagttcaaataagaaggaaaagaggaaactgagg Mask Tandem Repeat Region ================================================ cctcagtttcctcttttccttcttatttgaactaatacccaaagaaaattgaagttcagatttctttgaataagagctggtttttttgttgttaatatcataccattctataggaaattgtcaatcattattaagcaaaaaataaaaaccatcatttttaaaactaaaaacgatagtttttatgatttataatcaataatgttcg Find is-nt database================================================ Query_seq: SSA_2374:SSA_2375|SSA_2374:SSA_2375:Inosine-5'-monophosphate dehydrogenase, putative:Tryptophanyl-tRNA synthetase, putative:<-<-:2377106..2377310 205 cctcagtttcctcttttccttcttatttgaactaatacccaaagaaaattgaagttcagatttctttgaataagagctggtttttttgttgttaatatcataccattctataggaaattgtcaatcattattaagcaaaaaataaaaaccatcatttttaaaactaaaaacgatagtttttatgatttataatcaataatgttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2374:SSA_2375|SSA_2374:SSA_2375:Inosine-5'-monophosphate dehydrogenase, putative:Tryptophanyl-tRNA synthetase, putative:<-<-:2377106..2377310 205 cctcagtttcctcttttccttcttatttgaactaatacccaaagaaaattgaagttcagatttctttgaataagagctggtttttttgttgttaatatcataccattctataggaaattgtcaatcattattaagcaaaaaataaaaaccatcatttttaaaactaaaaacgatagtttttatgatttataatcaataatgttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2374:SSA_2375|SSA_2374:SSA_2375:Inosine-5'-monophosphate dehydrogenase, putative:Tryptophanyl-tRNA synthetase, putative:<-<-:2377106..2377310 205 cctcagtttcctcttttccttcttatttgaactaatacccaaagaaaattgaagttcagatttctttgaataagagctggtttttttgttgttaatatcataccattctataggaaattgtcaatcattattaagcaaaaaataaaaaccatcatttttaaaactaaaaacgatagtttttatgatttataatcaataatgttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctcagtttcctcttttccttcttatttgaactaatacccaaagaaaattgaagttcagatttctttgaataagagctggtttttttgttgttaatatcataccattctataggaaattgtcaatcattattaagcaaaaaataaaaaccatcatttttaaaactaaaaacgatagtttttatgatttataatcaataatgttcg Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 70 End: 189 ..................................................................... M R A G F F V V N I I P F Y R K L S I I I K Q K I K T I I F K T K N D S F Y D L ................ Protein_Len: 33 Strand: - Start: 6 End: 101 ..... * N G R K R R I Q V L V W L F N F N L N R Q I L A P K K T T L I M ........................................................................................................ Protein_Len: 37 Strand: - Start: 1 End: 111 R L K R K E K K N S S I G L S F Q L E S K K S Y S S T K K N N I D Y W E M .............................................................................................. cctcagtttcctcttttccttcttatttgaactaatacccaaagaaaattgaagttcagatttctttgaataagagctggtttttttgttgttaatatcataccattctataggaaattgtcaatcattattaagcaaaaaataaaaaccatcatttttaaaactaaaaacgatagtttttatgatttataatcaataatgttcg 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: 81 Start: 157 End: 186 ............................................................................................................................................................TTTAAAACTAAAAACGATAGTTTTTATGAT................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cctcagtttcctcttttccttcttatttgaactaatacccaaagaaaattgaagttcagatttctttgaataagagctggtttttttgttgttaatatcataccattctataggaaattgtcaatcattattaagcaaaaaataaaaaccatcatttttaaaactaaaaacgatagtttttatgatttataatcaataatgttcg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2374:SSA_2375|SSA_2374:SSA_2375:Inosine-5'-monophosphate dehydrogenase, putative:Tryptophanyl-tRNA synthetase, putative:<-<-:2377106..2377310 205 cctcagtttcctcttttccttcttatttgaactaatacccaaagaaaattgaagttcagatttctttgaataagagctggtttttttgttgttaatatcataccattctataggaaattgtcaatcattattaagcaaaaaataaaaaccatcatttttaaaactaaaaacgatagtttttatgatttataatcaataatgttcg Intra-Species Hit: Count: 1 Min: 1 Max: 205 Len: 205 Subject: NC_009009_SSA_2374_SSA_2375|Inosine-5'-monophosphate dehydrogenase, putative:Tryptophanyl-tRNA synthetase, putative|NEGATIVE:NEGATIVE|[2377106,2377310]|205 HSP 1 e-value: 6.0E-59 bit: 228.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 cctcagtttcctcttttccttcttatttgaactaatacccaaagaaaattgaagttcagatttctttgaataagagctggnnnnnnngttgttaatatcataccattctataggaaattgtcaatcattattaagc..................................................................... cctcagtttcctcttttccttcttatttgaactaatacccaaagaaaattgaagttcagatttctttgaataagagctggtttttttgttgttaatatcataccattctataggaaattgtcaatcattattaagc..................................................................... HSP 2 e-value: 3.0E-11 bit: 69.9 Len: 35 Query Start:171 Query End:205 Subject Strand: POSITIVE Subject Start: 171 Subject End: 205 ..........................................................................................................................................................................cgatagtttttatgatttataatcaataatgttcg ..........................................................................................................................................................................cgatagtttttatgatttataatcaataatgttcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUCAGUUUCCUCUUUUCCUUCUUAUUUGAACUAAUACCCAAAGAAAAUUGAAGUUCAGAUUUCUUUGAAUAAGAGCUGGUUUUUUUGUUGUUAAUAUCAUACCAUUCUAUAGGAAAUUGUCAAUCAUUAUUAAGCAAAAAAUAAAAACCAUCAUUUUUAAAACUAAAAACGAUAGUUUUUAUGAUUUAUAAUCAAUAAUGUUCG ...(((((((((...........................((((((((.(((.....))).))))))))....((((.((((.....(((.....)))....))))))))..))))))))).....(((((((.........((((((((.(((.((((((....)))))).))).))))))))...........))))))).... (-36.55) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAACAUUAUUGAUUAUAAAUCAUAAAAACUAUCGUUUUUAGUUUUAAAAAUGAUGGUUUUUAUUUUUUGCUUAAUAAUGAUUGACAAUUUCCUAUAGAAUGGUAUGAUAUUAACAACAAAAAAACCAGCUCUUAUUCAAAGAAAUCUGAACUUCAAUUUUCUUUGGGUAUUAGUUCAAAUAAGAAGGAAAAGAGGAAACUGAGG (((.(((((((((...((((..(((((((((((((((((((....)))))))))))))))))))..)))).))))))))).)))....((((((......((((....................))))(((..((((((((((((..((.....))..))))))))))))..)))..........))))))..((....)).... (-50.15) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 778 80 31 171 122 NC_009009:SSA_2374|5end_Inosine-5'-monophosphate_dehydrogenase,_putative_2377015..2377245_NEGATIVE 276 41 1 90 40 NC_009009:SSA_1381|5end_hypothetical_protein_1399565..1399795_NEGATIVE 272 42 4 131 93 NC_009009:SSA_1051|5end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1065658..1065888_POSITIVE 263 49 2 221 180 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 261 58 11 143 94 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 245 88 53 82 42 NC_009009:SSA_0605|5end_Methyltransferase_gidB,_putative_593707..593937_NEGATIVE 240 90 55 48 14 NC_009009:SSA_1150|5end_Tautomerase,_putative_1180076..1180306_NEGATIVE 235 87 48 127 80 NC_009009:SSA_1777|5end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1765155..1765385_NEGATIVE 232 128 83 114 70 NC_009009:SSA_1184|5end_DNA_topoisomerase_I,_putative_1213605..1213835_NEGATIVE 231 45 1 140 94 NC_009009:SSA_1844|5end_hypothetical_protein_1838183..1838413_NEGATIVE 229 46 1 130 94 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 226 80 33 114 69 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 221 92 55 40 5 NC_009009:SSA_0349|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_341110..341340_POSITIVE 219 109 64 105 63 NC_009009:SSA_2214|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2,_putative_2215835..2216065_NEGATIVE 218 47 1 145 94 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 217 83 42 76 33 NC_009009:SSA_0832|5end_SecY-like_protein,_putative_816708..816938_POSITIVE 217 117 72 207 163 NC_009009:SSA_0688|5end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_671360..671590_POSITIVE 216 33 5 228 199 NC_009009:SSA_2212|5end_Possible_polysaccharide_transport_protein,_putative_2213928..2214158_NEGATIVE 216 43 10 130 99 NC_009009:SSA_1756|5end_Conserved_uncharacterized_protein_1745291..1745521_NEGATIVE 216 29 5 116 95 NC_009009:SSA_1724|5end_CBS_domain_protein,_putative_1710553..1710783_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 42 4 134 96 NC_009009:SSA_1050|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1065741..1065891_POSITIVE 261 58 11 58 9 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 252 106 61 126 73 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE 249 111 72 94 45 NC_009009:SSA_0785|3end_Proton-translocating_ATPase,_F1_sector,_delta_subunit,_putative_768660..768810_POSITIVE 236 90 43 142 88 NC_009009:SSA_0773|3end_PTS_enzyme_I,_putative_754416..754566_POSITIVE 235 87 48 140 93 NC_009009:SSA_1778|3end_Segregation_and_condensation_protein_B,_putative_1765142..1765292_NEGATIVE 234 116 75 110 64 NC_009009:SSA_1186|3end_Acetyltransferase,_CysE/LacA/Lpx_A/NodL_family,_putative_1214656..1214806_NEGATIVE 229 46 1 118 82 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 228 86 44 61 27 NC_009009:SSA_0429|3end_Histidine_ammonia-lyase,_putative_429701..429851_NEGATIVE 226 80 33 130 85 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 219 109 64 108 66 NC_009009:SSA_2215|3end_Oligosaccharide_repeat_unit_polymerase_Wzy,_putative_2215832..2215982_NEGATIVE 219 120 76 63 18 NC_009009:SSA_0568|3end_Aspartyl-tRNA_synthetase_1,_putative_563490..563640_POSITIVE 217 94 51 86 46 NC_009009:SSA_1173|3end_Lipoate_protein_ligase_A,_putative_1200092..1200242_NEGATIVE 217 117 72 57 13 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE 216 33 5 109 80 NC_009009:SSA_2213|3end_Nucleotide_sugar_dehydratase,_putative_2214047..2214197_NEGATIVE 216 43 10 139 108 NC_009009:SSA_1757|3end_hypothetical_protein_1745282..1745432_NEGATIVE 216 92 53 149 122 NC_009009:SSA_0867|3end_hypothetical_protein_860711..860861_POSITIVE 214 43 4 110 67 NC_009009:SSA_1612|3end_Diacylglycerol_kinase,_putative_1616099..1616249_NEGATIVE 213 115 76 37 7 NC_009009:SSA_1788|3end_Integral_membrane_protein,_possible_receptor,_putative_1771656..1771806_NEGATIVE 212 112 75 86 46 NC_009009:SSA_0163|3end_hypothetical_protein_162542..162692_POSITIVE