Origin IGS: gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc .........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 gatattcctttctctactttgaaccaaaagctaggccagcagacctagctatttttaaatttattgattttcatttcaaattggaacgaagttcaatttgaaatcatctgcttctttcgccgtggtgaaagtgatggaactgatttatcagtcccatcacaggggatttttgagactctaggctcaaaaataagcaatgaaaccatcggtttgcttgcgtccctcaccacctaagaaaggagcaaaaaatc Mask Tandem Repeat Region ================================================ gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc Find is-nt database================================================ Query_seq: SMT_363:SMT_364|SMT_363:SMT_364:K02519 translation initiation factor IF-2:ribosome-binding factor A:->->:300812..301062 251 gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_363:SMT_364|SMT_363:SMT_364:K02519 translation initiation factor IF-2:ribosome-binding factor A:->->:300812..301062 251 gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_363:SMT_364|SMT_363:SMT_364:K02519 translation initiation factor IF-2:ribosome-binding factor A:->->:300812..301062 251 gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 22 End: 156 ..................... M V R D A S K P M V S L L I F E P R V S K I P C D G T D K S V P S L S P R R K K Q M I S N ............................................................................................... Protein_Len: 33 Strand: - Start: 74 End: 172 ......................................................................... L R L F G R H H S Q Y I L E M V K V V A F S A S S K L N F K T G M ............................................................................... Protein_Len: 56 Strand: - Start: 21 End: 188 .................... T T L S A L L G I T E N S I K S G L T E F I G Q S P V S L D T G D S E G R R F F C I I E F Q V E N W N S I F I M ............................................................... gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc 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: 172 End: 201 ...........................................................................................................................................................................TTTGAAATGAAAATCAATAAATTTAAAAAT.................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.9 Tail_Score: -3.53012 Start: 92 End: 121 Full_Region: TCTCAAAAATCCCCT GTGATGGGACTGA TAAA TCAGTTCCATCAC TTTCACCACGGCGAA ...........................................................................................GTGATGGGACTGATAAATCAGTTCCATCAC.................................................................................................................................. TransTerm Strand: + Conf: 89 HP_score: -10.0 Tail_Score: -4.41494 Start: 203 End: 222 Full_Region: ATAAATTTAAAAATA GCTAGGTC TGCT GGCCTAGC TTTTGGTTCAAAGTA ..........................................................................................................................................................................................................GCTAGGTCTGCTGGCCTAGC............................. Find igs database================================================ Query_seq: SMT_363:SMT_364|SMT_363:SMT_364:K02519 translation initiation factor IF-2:ribosome-binding factor A:->->:300812..301062 251 gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc Intra-Species Hit: Count: 1 Min: 1 Max: 251 Len: 251 Subject: smit_SMT_363_SMT_364|K02519 translation initiation factor IF-2:ribosome-binding factor A|POSITIVE:POSITIVE|[300812,301062]|251 HSP 1 e-value: 1.0E-140 bit: 498.0 Len: 251 Query Start:1 Query End:251 Subject Strand: POSITIVE Subject Start: 1 Subject End: 251 gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc Inter-species Hit: Count: 3 Min: 1 Max: 251 Len: 251 Subject: NC_008533_SPD_0482_SPD_0483|initiation factor IF-2:ribosome-binding factor A|POSITIVE:POSITIVE|[492236,492485]|250 HSP 1 e-value: 1.0E-118 bit: 426.0 Len: 251 Query Start:1 Query End:251 Subject Strand: POSITIVE Subject Start: 1 Subject End: 250 gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagggtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgacttcaaattgaacttcgtttcaatttaaactgaaaatcaagaagttt-aaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc Subject: NC_003028_SP_0556_SP_0557|translation initiation factor IF-2:ribosome-binding factor A|POSITIVE:POSITIVE|[526001,526250]|250 HSP 1 e-value: 1.0E-118 bit: 426.0 Len: 251 Query Start:1 Query End:251 Subject Strand: POSITIVE Subject Start: 1 Subject End: 250 gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagggtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgacttcaaattgaacttcgtttcaatttaaactgaaaatcaagaagttt-aaaatagctaggtctgctggcctagcttttggttcaaagtagagaaaggaatatc Subject: NC_003098_spr0481_spr0482|translation initiation factor IF-2:ribosome-binding factor A|POSITIVE:POSITIVE|[484706,484928]|223 HSP 1 e-value: 1.0E-102 bit: 373.0 Len: 224 Query Start:1 Query End:224 Subject Strand: POSITIVE Subject Start: 1 Subject End: 223 gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagagtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgatttcaaattgaacttcgttccaatttgaaatgaaaatcaataaatttaaaaatagctaggtctgctggcctagctt........................... gattttttgctcctttcttaggtggtgagggacgcaagcaaaccgatggtttcattgcttatttttgagcctagggtctcaaaaatcccctgtgatgggactgataaatcagttccatcactttcaccacggcgaaagaagcagatgacttcaaattgaacttcgtttcaatttaaactgaaaatcaagaagttt-aaaatagctaggtctgctggcctagctt........................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUUUUGCUCCUUUCUUAGGUGGUGAGGGACGCAAGCAAACCGAUGGUUUCAUUGCUUAUUUUUGAGCCUAGAGUCUCAAAAAUCCCCUGUGAUGGGACUGAUAAAUCAGUUCCAUCACUUUCACCACGGCGAAAGAAGCAGAUGAUUUCAAAUUGAACUUCGUUCCAAUUUGAAAUGAAAAUCAAUAAAUUUAAAAAUAGCUAGGUCUGCUGGCCUAGCUUUUGGUUCAAAGUAGAGAAAGGAAUAUC ..........(((((((((..((((((((((..((((..(((((...)))))..))))..(((((((((.(....).))))))))).))).(((((((((((((....)))))))))))))..))))))).......(((.((((..((((((((((((((...))).)))))))))))......................(((((((((....))))))))))))).)))......)))))))))..... (-91.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAUUCCUUUCUCUACUUUGAACCAAAAGCUAGGCCAGCAGACCUAGCUAUUUUUAAAUUUAUUGAUUUUCAUUUCAAAUUGGAACGAAGUUCAAUUUGAAAUCAUCUGCUUCUUUCGCCGUGGUGAAAGUGAUGGAACUGAUUUAUCAGUCCCAUCACAGGGGAUUUUUGAGACUCUAGGCUCAAAAAUAAGCAAUGAAACCAUCGGUUUGCUUGCGUCCCUCACCACCUAAGAAAGGAGCAAAAAAUC .................((((((..((.(((((((........))))))).))))))))......((((((.(((((((((((((......)))))))))))))....((((((((((...(((((((..(((((((.(((((....))))).))))))).(((.(((((((((.(.....))))))))))..((((..(((((...)))))..))))..))))))))))....)))))))))).)))))) (-83.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 567 90 43 213 164 smit:SMT_340|5end_chaperone_protein_278663..278893_POSITIVE 417 60 11 173 123 smit:SMT_1190|5end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1148232..1148462_NEGATIVE 371 58 11 156 107 smit:SMT_158|5end_putative_Holliday_junction_resolvase_103795..104025_POSITIVE 370 54 14 142 101 smit:SMT_1173|5end_CMP-N-acetylneuraminate-beta-galactosamide-alpha_-2,3-sialyltransferase_1125620..1125850_NEGATIVE 338 70 21 182 127 smit:SMT_995|5end_K07574_putative_RNA-binding_protein_containing_KH_domain_936468..936698_NEGATIVE 321 40 9 137 97 smit:SMT_600|5end_ADP-ribose_pyrophosphatase_516307..516537_POSITIVE 311 41 1 134 93 smit:SMT_403|5end_two-component_sensor_kinase_YesM_331580..331810_POSITIVE 310 129 87 73 28 smit:SMT_1683|5end_phenylalanyl-tRNA_synthetase_beta_chain_1667171..1667401_NEGATIVE 309 135 94 180 143 smit:SMT_677|5end_DNA_topoisomerase_I_587318..587548_NEGATIVE 307 60 11 214 160 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 304 135 91 225 184 smit:SMT_366|5end_hypothetical_protein_302085..302315_POSITIVE 301 129 81 180 132 smit:SMT_1506|5end_Cl-channel,_voltage-gated_family_protein_1489986..1490216_NEGATIVE 293 245 203 173 137 smit:SMT_1680|5end_hypothetical_protein_1663494..1663724_POSITIVE 293 50 6 231 185 smit:SMT_1184|5end_phosphotransferase_system,_mannose/fructose/N-acetylgalactosamine-specific_component_IIB_1142037..1142267_NEGATIVE 288 50 1 143 84 smit:SMT_1617|5end_K02015_iron_complex_transport_system_permease_protein_1604500..1604730_NEGATIVE 287 128 86 105 59 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 286 48 2 148 90 smit:SMT_169|5end_30S_ribosomal_protein_S10_114515..114745_POSITIVE 282 129 84 108 62 smit:SMT_894|5end_hypothetical_protein_841701..841931_NEGATIVE 280 228 193 33 2 smit:SMT_1371|5end_hypothetical_protein_1350794..1351024_NEGATIVE 280 100 56 191 152 smit:SMT_959|5end_1-acyl-sn-glycerol-3-phosphate_acyltransferase_905283..905513_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 54 14 145 104 smit:SMT_1174|3end_acylneuraminate_cytidylyltransferase_1125617..1125767_NEGATIVE 337 57 11 151 103 smit:SMT_157|3end_hypothetical_protein_103871..104021_POSITIVE 334 64 21 69 17 smit:SMT_447|3end_ABC-type_cobalt_transport_system,_permease_component_CbiQ_related_transporter_386987..387137_POSITIVE 321 40 9 127 87 smit:SMT_599|3end_glucosamine-1-phosphate_N-acetyltransferase_/_UDP-N-acetylglucosamine_pyrophosphorylase_516377..516527_POSITIVE 320 135 91 50 8 smit:SMT_913|3end_putative_sucrose-specific_PTS_permease,_enzyme_II_863923..864073_NEGATIVE 311 41 1 137 96 smit:SMT_402|3end_two-component_response_regulator_YesN_331663..331813_POSITIVE 309 135 94 51 14 smit:SMT_678|3end_K04096_DNA_processing_protein_587447..587597_NEGATIVE 307 59 13 142 102 smit:SMT_1448|3end_serine_hydroxymethyltransferase_1430703..1430853_NEGATIVE 304 135 91 51 10 smit:SMT_1471|3end_hypothetical_protein_1453442..1453592_NEGATIVE 302 135 91 43 1 smit:SMT_764|3end_alanyl-tRNA_synthetase_669495..669645_NEGATIVE 287 128 86 103 57 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 283 135 91 52 12 smit:SMT_1216|3end_hypothetical_protein_1175969..1176119_POSITIVE 282 129 84 115 69 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE 280 100 56 67 28 smit:SMT_958|3end_hypothetical_protein_predicted_by_Glimmer/Critica_905239..905389_POSITIVE 279 35 7 146 111 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 277 136 96 47 12 smit:SMT_1821|3end_Mg2+_and_Co2+_transporter_1794515..1794665_POSITIVE 276 135 98 53 20 smit:SMT_1315|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1280952..1281102_POSITIVE 275 100 56 78 39 smit:SMT_2024|3end_hypothetical_protein_1940690..1940840_POSITIVE 275 100 56 67 28 smit:SMT_2002|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1924145..1924295_NEGATIVE 275 100 56 78 39 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE