Origin IGS: ctttttctccgtatttgttctgctatctattataacacattgggctttttctatcagaagggagccttatctcgaccactctgctcgtaagccaaaccagatagacacaaatagctgccacacctaccgcaaaattcaaaaaattaacagtggtttatctggagaatcatgagaaacaaaaaacagttcaaatttgaactgttt .........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 aaacagttcaaatttgaactgttttttgtttctcatgattctccagataaaccactgttaattttttgaattttgcggtaggtgtggcagctatttgtgtctatctggtttggcttacgagcagagtggtcgagataaggctcccttctgatagaaaaagcccaatgtgttataatagatagcagaacaaatacggagaaaaag Mask Tandem Repeat Region ================================================ ctttttctccgtatttgttctgctatctattataacacattgggctttttctatcagaagggagccttatctcgaccactctgctcgtaagccaaaccagatagacacaaatagctgccacacctaccgcaaaattcaaaaaattaacagtggtttatctggagaatcatgagaaacaaaaaacagttcaaatttgaactgttt Find is-nt database================================================ Query_seq: SSA_2257:SSA_2258|SSA_2257:SSA_2258:DNA mismatch repair protein, putative:hypothetical protein:<-<-:2253275..2253478 204 ctttttctccgtatttgttctgctatctattataacacattgggctttttctatcagaagggagccttatctcgaccactctgctcgtaagccaaaccagatagacacaaatagctgccacacctaccgcaaaattcaaaaaattaacagtggtttatctggagaatcatgagaaacaaaaaacagttcaaatttgaactgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2257:SSA_2258|SSA_2257:SSA_2258:DNA mismatch repair protein, putative:hypothetical protein:<-<-:2253275..2253478 204 ctttttctccgtatttgttctgctatctattataacacattgggctttttctatcagaagggagccttatctcgaccactctgctcgtaagccaaaccagatagacacaaatagctgccacacctaccgcaaaattcaaaaaattaacagtggtttatctggagaatcatgagaaacaaaaaacagttcaaatttgaactgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2257:SSA_2258|SSA_2257:SSA_2258:DNA mismatch repair protein, putative:hypothetical protein:<-<-:2253275..2253478 204 ctttttctccgtatttgttctgctatctattataacacattgggctttttctatcagaagggagccttatctcgaccactctgctcgtaagccaaaccagatagacacaaatagctgccacacctaccgcaaaattcaaaaaattaacagtggtttatctggagaatcatgagaaacaaaaaacagttcaaatttgaactgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttttctccgtatttgttctgctatctattataacacattgggctttttctatcagaagggagccttatctcgaccactctgctcgtaagccaaaccagatagacacaaatagctgccacacctaccgcaaaattcaaaaaattaacagtggtttatctggagaatcatgagaaacaaaaaacagttcaaatttgaactgttt Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 20 End: 169 ................... M L S I I T H W A F S I R R E P Y L D H S A R K P N Q I D T N S C H T Y R K I Q K I N S G L S G E S ................................... Protein_Len: 38 Strand: - Start: 26 End: 139 ......................... R N Y C M P S K R D S P L R I E V V R S T L W V L Y V C I A A V G V A F N M ................................................................. ctttttctccgtatttgttctgctatctattataacacattgggctttttctatcagaagggagccttatctcgaccactctgctcgtaagccaaaccagatagacacaaatagctgccacacctaccgcaaaattcaaaaaattaacagtggtttatctggagaatcatgagaaacaaaaaacagttcaaatttgaactgttt 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: 83 Start: 29 End: 58 ............................TCTGATAGAAAAAGCCCAATGTGTTATAAT.................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctttttctccgtatttgttctgctatctattataacacattgggctttttctatcagaagggagccttatctcgaccactctgctcgtaagccaaaccagatagacacaaatagctgccacacctaccgcaaaattcaaaaaattaacagtggtttatctggagaatcatgagaaacaaaaaacagttcaaatttgaactgttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2257:SSA_2258|SSA_2257:SSA_2258:DNA mismatch repair protein, putative:hypothetical protein:<-<-:2253275..2253478 204 ctttttctccgtatttgttctgctatctattataacacattgggctttttctatcagaagggagccttatctcgaccactctgctcgtaagccaaaccagatagacacaaatagctgccacacctaccgcaaaattcaaaaaattaacagtggtttatctggagaatcatgagaaacaaaaaacagttcaaatttgaactgttt Intra-Species Hit: Count: 1 Min: 1 Max: 204 Len: 204 Subject: NC_009009_SSA_2257_SSA_2258|DNA mismatch repair protein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[2253275,2253478]|204 HSP 1 e-value: 1.0E-112 bit: 404.0 Len: 204 Query Start:1 Query End:204 Subject Strand: POSITIVE Subject Start: 1 Subject End: 204 ctttttctccgtatttgttctgctatctattataacacattgggctttttctatcagaagggagccttatctcgaccactctgctcgtaagccaaaccagatagacacaaatagctgccacacctaccgcaaaattcaaaaaattaacagtggtttatctggagaatcatgagaaacaaaaaacagttcaaatttgaactgttt ctttttctccgtatttgttctgctatctattataacacattgggctttttctatcagaagggagccttatctcgaccactctgctcgtaagccaaaccagatagacacaaatagctgccacacctaccgcaaaattcaaaaaattaacagtggtttatctggagaatcatgagaaacaaaaaacagttcaaatttgaactgttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUUCUCCGUAUUUGUUCUGCUAUCUAUUAUAACACAUUGGGCUUUUUCUAUCAGAAGGGAGCCUUAUCUCGACCACUCUGCUCGUAAGCCAAACCAGAUAGACACAAAUAGCUGCCACACCUACCGCAAAAUUCAAAAAAUUAACAGUGGUUUAUCUGGAGAAUCAUGAGAAACAAAAAACAGUUCAAAUUUGAACUGUUU (((.((((((.(((((((....((((((.............((((((((((.....))).)))))))...............(((....)))......))))))..)))))))...(((((............................)))))......))))))....))).......((((((((((....)))))))))) (-44.19) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACAGUUCAAAUUUGAACUGUUUUUUGUUUCUCAUGAUUCUCCAGAUAAACCACUGUUAAUUUUUUGAAUUUUGCGGUAGGUGUGGCAGCUAUUUGUGUCUAUCUGGUUUGGCUUACGAGCAGAGUGGUCGAGAUAAGGCUCCCUUCUGAUAGAAAAAGCCCAAUGUGUUAUAAUAGAUAGCAGAACAAAUACGGAGAAAAAG ((((((((((....))))))))))..............((((((.(....((((((((.(((((...)))))..))))).)))....).(((((((((......(..(((.(((((.(...(((((.((..(((......))))))))))...)...))))).)))..).....)))))))))...........)))))).... (-51.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1016 100 51 191 142 NC_009009:SSA_2257|5end_DNA_mismatch_repair_protein,_putative_2253184..2253414_NEGATIVE 350 119 71 229 176 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 324 130 97 33 7 NC_009009:SSA_1845|5end_Serine/threonine_protein_kinase,_putative_1840181..1840411_NEGATIVE 321 120 71 63 13 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 318 100 53 216 156 NC_009009:SSA_0883|5end_Glycerate_kinase,_putative_877560..877790_POSITIVE 317 118 71 210 150 NC_009009:SSA_0650|5end_GTP-binding_protein_TypA/BipA,_putative_632548..632778_POSITIVE 312 119 71 47 8 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 310 100 51 150 98 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 308 120 75 56 8 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 307 88 41 74 19 NC_009009:SSA_1711|5end_Endonuclease_III,_putative_1699636..1699866_NEGATIVE 302 109 61 53 2 NC_009009:SSA_1984|5end_Cell_surface_SD_repeat_antigen_precursor,_putative_1979035..1979265_NEGATIVE 302 110 63 78 28 NC_009009:SSA_0175|5end_Penicillin-binding_protein_1B,_putative_172152..172382_POSITIVE 300 50 1 68 10 NC_009009:SSA_0420|5end_Hydrolase,_HAD_superfamily,_putative_418620..418850_POSITIVE 299 120 76 57 19 NC_009009:SSA_0588|5end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_579800..580030_POSITIVE 296 90 47 202 146 NC_009009:SSA_0094|5end_Cell_wall_metabolism,_LysM_type_protein,_putative_95345..95575_POSITIVE 292 57 15 156 112 NC_009009:SSA_1405|5end_Copper_homeostasis_protein_CutC,_putative_1419393..1419623_NEGATIVE 292 54 16 58 21 NC_009009:SSA_0655|5end_Cell_division_protein_FtsA,_putative_638784..639014_POSITIVE 291 100 54 129 81 NC_009009:SSA_1823|5end_hypothetical_protein_1812513..1812743_NEGATIVE 289 105 65 50 1 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 288 105 63 217 169 NC_009009:SSA_1154|5end_hypothetical_protein_1182661..1182891_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 87 42 124 80 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 324 130 97 36 10 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE 317 130 81 59 12 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 309 94 52 130 86 NC_009009:SSA_1869|3end_ATP-dependent_RNA_helicase,_putative_1864152..1864302_NEGATIVE 292 57 15 94 50 NC_009009:SSA_1406|3end_Histone_acetyltransferase_HPA2,_putative_1419455..1419605_NEGATIVE 291 100 54 126 78 NC_009009:SSA_1824|3end_hypothetical_protein_1812516..1812666_NEGATIVE 289 105 65 57 8 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 289 107 64 41 1 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 282 79 38 144 102 NC_009009:SSA_1551|3end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1552652..1552802_NEGATIVE 281 86 42 71 20 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 280 90 41 89 30 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 277 122 81 151 108 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 274 100 58 66 12 NC_009009:SSA_1268|3end_Chorismate_mutase/prephenate_dehydratase,_putative_1291347..1291497_NEGATIVE 273 84 42 111 47 NC_009009:SSA_2068|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_2070931..2071081_NEGATIVE 271 124 81 52 6 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 271 90 47 79 25 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 269 86 43 89 37 NC_009009:SSA_1257|3end_hypothetical_protein_1283106..1283256_NEGATIVE 269 130 83 126 64 NC_009009:SSA_1200|3end_Formate--tetrahydrofolate_ligase,_putative_1223921..1224071_NEGATIVE 267 130 83 150 100 NC_009009:SSA_1274|3end_hypothetical_protein_1295517..1295667_NEGATIVE 267 118 77 133 92 NC_009009:SSA_1166|3end_hypothetical_protein_1192350..1192500_POSITIVE