Origin IGS: ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagcttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtccctatcg .........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 cgatagggactgtgaaacagtctcctatcgttacggcaatcgctatggcgaatttcctaatcgccttattaattcgtcggtaaaagctatcgtttttacctcctcatgttacaattcggtgacttggtacaagaagtgagatggagaaggatggctcactgactcctctcctctcacttttactttatttaaatcaagaaataggtgaaaaaa Mask Tandem Repeat Region ================================================ ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagcttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtccctatcg Find is-nt database================================================ Query_seq: SMT_639:SMT_640|SMT_639:SMT_640:6-phospho-beta-galactosidase:PTS system, lactose-specific IIBC component:<-<-:544976..545188 213 ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagcttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtccctatcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_639:SMT_640|SMT_639:SMT_640:6-phospho-beta-galactosidase:PTS system, lactose-specific IIBC component:<-<-:544976..545188 213 ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagcttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtccctatcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_639:SMT_640|SMT_639:SMT_640:6-phospho-beta-galactosidase:PTS system, lactose-specific IIBC component:<-<-:544976..545188 213 ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagcttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtccctatcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagcttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtccctatcg Predict ORF larger than 30AA ================================================ ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagcttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtccctatcg 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================================================ ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagcttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtccctatcg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 55 HP_score: -3.9 Tail_Score: -3.7941 Start: 37 End: 78 Full_Region: TTAAATAAAGTAAAA GTGAGAGGAGAGGAGTC AGTGA GCCATCCTTCTCCATCTCAC TTCTTGTACCAAGTC ....................................GTGAGAGGAGAGGAGTCAGTGAGCCATCCTTCTCCATCTCAC....................................................................................................................................... TransTerm Strand: - Conf: 68 HP_score: -3.9 Tail_Score: -4.72863 Start: 37 End: 78 Full_Region: gacttggtacaagaa gtgagatggagaaggatggc tcact gactcctctcctctcac ttttactttatttaa ....................................gtgagatggagaaggatggctcactgactcctctcctctcac....................................................................................................................................... TransTerm Strand: - Conf: 57 HP_score: -4.5 Tail_Score: -3.83844 Start: 149 End: 167 Full_Region: tacggcaatcgctat ggcgaat ttcct aatcgcc ttattaattcgtcgg ....................................................................................................................................................ggcgaatttcctaatcgcc.............................................. Find igs database================================================ Query_seq: SMT_639:SMT_640|SMT_639:SMT_640:6-phospho-beta-galactosidase:PTS system, lactose-specific IIBC component:<-<-:544976..545188 213 ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagcttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtccctatcg Intra-Species Hit: Count: 1 Min: 1 Max: 213 Len: 213 Subject: smit_SMT_639_SMT_640|6-phospho-beta-galactosidase:PTS system, lactose-specific IIBC component|NEGATIVE:NEGATIVE|[544976,545188]|213 HSP 1 e-value: 1.0E-117 bit: 422.0 Len: 213 Query Start:1 Query End:213 Subject Strand: POSITIVE Subject Start: 1 Subject End: 213 ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagcttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtccctatcg ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagcttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtccctatcg Inter-species Hit: Count: 3 Min: 1 Max: 206 Len: 206 Subject: NC_008533_SPD_1046_SPD_1047|6-phospho-beta-galactosidase:PTS system, lactose-specific IIBC components|NEGATIVE:NEGATIVE|[1075975,1076182]|208 HSP 1 e-value: 2.0E-83 bit: 309.0 Len: 206 Query Start:1 Query End:206 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagc-ttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtc....... ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtgacatgaggaggtaaaaacgatatctttttaccgacgaattaataa------taggaaattcgccatagcgatttccgtaacgataggagactatttcagagtc....... Subject: NC_003098_spr1069_spr1070|Phospho-beta-D-galactosidase:PTS system, lactose-specific IIBC component|NEGATIVE:NEGATIVE|[1068444,1068651]|208 HSP 1 e-value: 2.0E-83 bit: 309.0 Len: 206 Query Start:1 Query End:206 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagc-ttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtc....... ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtgacatgaggaggtaaaaacgatatctttttaccgacgaattaataa------taggaaattcgccatagcgatttccgtaacgataggagactatttcagagtc....... Subject: NC_003028_SP_1184_SP_1185|6-phospho-beta-galactosidase:PTS system, lactose-specific IIBC components|NEGATIVE:NEGATIVE|[1122576,1122783]|208 HSP 1 e-value: 5.0E-81 bit: 301.0 Len: 206 Query Start:1 Query End:206 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtaacatgaggaggtaaaaacgatagc-ttttaccgacgaattaataaggcgattaggaaattcgccatagcgattgccgtaacgataggagactgtttcacagtc....... ttttttcacctatttcttgatttaaataaagtaaaagtgagaggagaggagtcagtgagccatccttctccatctcacttcttgtaccaagtcaccgaattgtgacatgaggaggtaaaaacgatatctttttaccgacgaattaataa------taggaaattcgccatagcgatttccgtaacgatgggagactatttcagagtc....... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUUCACCUAUUUCUUGAUUUAAAUAAAGUAAAAGUGAGAGGAGAGGAGUCAGUGAGCCAUCCUUCUCCAUCUCACUUCUUGUACCAAGUCACCGAAUUGUAACAUGAGGAGGUAAAAACGAUAGCUUUUACCGACGAAUUAAUAAGGCGAUUAGGAAAUUCGCCAUAGCGAUUGCCGUAACGAUAGGAGACUGUUUCACAGUC ........((((((...((((((.....(((...((((((((((((((((............))).))))).))))))))))).....))))))...((((((.......(..(((((((.(....).)))))))..)..........(((((.........)))))...))))))........)))))).(((((.....))))) (-56.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUGUGAAACAGUCUCCUAUCGUUACGGCAAUCGCUAUGGCGAAUUUCCUAAUCGCCUUAUUAAUUCGUCGGUAAAAGCUAUCGUUUUUACCUCCUCAUGUUACAAUUCGGUGACUUGGUACAAGAAGUGAGAUGGAGAAGGAUGGCUCACUGACUCCUCUCCUCUCACUUUUACUUUAUUUAAAUCAAGAAAUAGGUGAAAAAA (((((.....))))).....((((((..((....))..)))))).........((((((......(((...(((((((((....)))))))))...(((.(((((......))))).)))....((((((((((.(((((.(((...(.....)..))))))))))))))))))................)))..))))))..... (-62.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 993 90 41 181 132 smit:SMT_639|5end_6-phospho-beta-galactosidase_544885..545115_NEGATIVE 442 90 42 91 41 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 352 87 42 214 162 smit:SMT_1784|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1760755..1760985_POSITIVE 340 96 51 98 44 smit:SMT_1860|5end_hypothetical_protein_1823609..1823839_NEGATIVE 303 179 132 191 142 smit:SMT_2002|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1924405..1924635_NEGATIVE 303 179 132 230 181 smit:SMT_1966|5end_DNA_polymerase_III_alpha_subunit_1897934..1898164_POSITIVE 303 179 132 191 142 smit:SMT_1942|5end_zinc_metalloprotease_ZmpB,_truncated_1877882..1878112_POSITIVE 303 179 132 231 182 smit:SMT_1926|5end_mevalonate_kinase_1867692..1867922_POSITIVE 303 179 132 212 163 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 303 193 156 207 166 smit:SMT_676|5end_DNA_helicase_II_585266..585496_NEGATIVE 302 97 55 59 4 smit:SMT_1047|5end_chaperonin,_10_kDa_988090..988320_NEGATIVE 300 89 41 124 60 smit:SMT_380|5end_hypothetical_protein_316376..316606_POSITIVE 300 89 41 124 60 smit:SMT_371|5end_hypothetical_protein_305248..305478_POSITIVE 297 83 42 108 72 smit:SMT_403|5end_two-component_sensor_kinase_YesM_331580..331810_POSITIVE 295 87 41 50 6 smit:SMT_725|5end_hypothetical_protein_630415..630645_NEGATIVE 293 109 62 82 21 smit:SMT_824|5end_asparaginyl-tRNA_synthetase_748393..748623_NEGATIVE 291 83 41 168 135 smit:SMT_976|5end_hypothetical_protein_925183..925413_NEGATIVE 285 97 55 181 129 smit:SMT_2015|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1932655..1932885_POSITIVE 284 75 32 68 23 smit:SMT_1745|5end_UDP-glucose_4-epimerase_1725541..1725771_NEGATIVE 283 71 39 170 125 smit:SMT_2055|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1965785..1966015_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 190 148 62 15 smit:SMT_998|3end_peptide_chain_release_factor_3_939699..939849_NEGATIVE 346 84 42 148 101 smit:SMT_1783|3end_peptide_methionine_sulfoxide_reductase_1760774..1760924_POSITIVE 346 87 46 59 10 smit:SMT_1590|3end_DNA-entry_nuclease_1578980..1579130_POSITIVE 300 89 41 124 60 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE 300 89 41 124 60 smit:SMT_370|3end_acetyltransferase,_GNAT_family_305328..305478_POSITIVE 297 83 42 111 75 smit:SMT_402|3end_two-component_response_regulator_YesN_331663..331813_POSITIVE 295 87 41 53 9 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 291 83 41 99 66 smit:SMT_977|3end_conserved_hypothetical_protein,_Rrf2_family_protein_925252..925402_NEGATIVE 284 84 42 86 48 smit:SMT_1742|3end_sodium-dependent_phosphate_transporter_1724991..1725141_POSITIVE 283 71 39 72 27 smit:SMT_2054|3end_dTDP-glucose_4,6-dehydratase_1965767..1965917_POSITIVE 275 200 168 65 40 smit:SMT_1377|3end_hypothetical_protein_1355556..1355706_NEGATIVE 275 69 30 91 45 smit:SMT_1249|3end_hypothetical_protein_1210541..1210691_NEGATIVE 274 90 42 102 54 smit:SMT_1065|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1005452..1005602_POSITIVE 272 109 70 59 7 smit:SMT_825|3end_aspartate_aminotransferase_748416..748566_NEGATIVE 272 117 72 127 81 smit:SMT_187|3end_30S_ribosomal_protein_S5_123571..123721_POSITIVE 271 75 36 69 28 smit:SMT_431|3end_UDP-N-acetylmuramoyl-L-alanyl-D-glutamate_synthetase_373631..373781_POSITIVE 270 107 72 42 7 smit:SMT_613|3end_dihydrodipicolinate_synthase_524321..524471_POSITIVE 267 92 51 66 28 smit:SMT_374|3end_hypothetical_protein_311919..312069_POSITIVE 264 87 45 101 59 smit:SMT_90|3end_DNA_polymerase_III_beta_subunit_22593..22743_POSITIVE 261 76 35 70 21 smit:SMT_943|3end_hypothetical_protein_894136..894286_NEGATIVE