Origin IGS: tttcttgaaatcatccattctgagtagatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattctatctcctttaaaaataataccgtactagtatctcacaatttgtttgatttcacaaattgttattagatagtcagatatatagtttaaaactatatccctaaaaactgagaaatcacccatctactcagaatggatgatttcaagaaa Mask Tandem Repeat Region ================================================ tttcttgaaatcatccattctgagtagatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc Find is-nt database================================================ Query_seq: SMT_150:SMT_151|SMT_150:SMT_151:K02030 polar amino acid transport system substrate-binding protein:K02073 D-methionine transport system substrate-binding protein:->->:99461..99613 153 tttcttgaaatcatccattctgagtagatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_150:SMT_151|SMT_150:SMT_151:K02030 polar amino acid transport system substrate-binding protein:K02073 D-methionine transport system substrate-binding protein:->->:99461..99613 153 tttcttgaaatcatccattctgagtagatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_150:SMT_151|SMT_150:SMT_151:K02030 polar amino acid transport system substrate-binding protein:K02073 D-methionine transport system substrate-binding protein:->->:99461..99613 153 tttcttgaaatcatccattctgagtagatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttcttgaaatcatccattctgagtagatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 28 End: 120 ........................... M G D F S V F R D I V L N Y I S D Y L I T I C E I K Q I V R Y ................................. tttcttgaaatcatccattctgagtagatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc 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================================================ tttcttgaaatcatccattctgagtagatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 53 HP_score: -4.0 Tail_Score: -3.69395 Start: 89 End: 112 Full_Region: cgtactagtatctca caatttgt ttgatttc acaaattg ttattagatagtcag ........................................................................................caatttgtttgatttcacaaattg......................................... Find igs database================================================ Query_seq: SMT_150:SMT_151|SMT_150:SMT_151:K02030 polar amino acid transport system substrate-binding protein:K02073 D-methionine transport system substrate-binding protein:->->:99461..99613 153 tttcttgaaatcatccattctgagtagatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: smit_SMT_150_SMT_151|K02030 polar amino acid transport system substrate-binding protein:K02073 D-methionine transport system substrate-binding protein|POSITIVE:POSITIVE|[99461,99613]|153 HSP 1 e-value: 9.0E-82 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 tttcttgaaatcatccattctgagtagatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc tttcttgaaatcatccattctgagtagatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc Inter-species Hit: Count: 3 Min: 1 Max: 153 Len: 153 Subject: NC_008533_SPD_0150_SPD_0151|ABC transporter, substrate-binding protein:lipoprotein|POSITIVE:POSITIVE|[155301, 155453]|153 HSP 1 e-value: 1.0E-65 bit: 250.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 tttcttgaaatcatccattctgagta-gatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc tttcttgaaatcatccattctgagtaaggtgggtggtttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattattttt-aaggagaaagaatc Subject: NC_003098_spr0146_spr0147|ABC transporter substrate-binding protein - amino acid transport:ABC transporter solute-binding protein - unknown substrate|POSITIVE:POSITIVE|[155301,155453]|153 HSP 1 e-value: 1.0E-65 bit: 250.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 tttcttgaaatcatccattctgagta-gatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc tttcttgaaatcatccattctgagtaaggtgggtggtttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattattttt-aaggagaaagaatc Subject: NC_003028_SP_0148_SP_0149|ABC transporter, substrate-binding protein:lipoprotein|POSITIVE:POSITIVE|[146344, 146496]|153 HSP 1 e-value: 1.0E-65 bit: 250.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 tttcttgaaatcatccattctgagta-gatgggtgatttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattatttttaaaggagatagaatc tttcttgaaatcatccattctgagtaaggtgggtggtttctcagtttttagggatatagttttaaactatatatctgactatctaataacaatttgtgaaatcaaacaaattgtgagatactagtacggtattattttt-aaggagaaagaatc Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUGAAAUCAUCCAUUCUGAGUAGAUGGGUGAUUUCUCAGUUUUUAGGGAUAUAGUUUUAAACUAUAUAUCUGACUAUCUAAUAACAAUUUGUGAAAUCAAACAAAUUGUGAGAUACUAGUACGGUAUUAUUUUUAAAGGAGAUAGAAUC ......(((((((((((((.......))))))))))))).......((((..(((((((.....)))))))..))))((((((....(((((((((........)))))))))..((((((.....))))))...........)))))).... (-41.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUCUAUCUCCUUUAAAAAUAAUACCGUACUAGUAUCUCACAAUUUGUUUGAUUUCACAAAUUGUUAUUAGAUAGUCAGAUAUAUAGUUUAAAACUAUAUCCCUAAAAACUGAGAAAUCACCCAUCUACUCAGAAUGGAUGAUUUCAAGAAA ..((((........................((((((....(((((((((........))))))))))))))).((((.((..(((((((.....)))))))..))....)))).(((((((.((((((....)).)))).))))))).)))). (-29.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 60 11 218 168 smit:SMT_1053|5end_ABC_transporter_permease_protein_993671..993901_NEGATIVE 283 46 2 60 8 smit:SMT_1006|5end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_946599..946829_POSITIVE 263 59 11 70 15 smit:SMT_1060|5end_K03977_GTP-binding_protein_998106..998336_POSITIVE 244 47 7 219 174 smit:SMT_400|5end_hypothetical_protein_329090..329320_POSITIVE 242 33 4 65 32 smit:SMT_1055|5end_transcriptional_regulator,_GntR_family_994752..994982_NEGATIVE 236 55 21 163 136 smit:SMT_1139|5end_rRNA_(guanine-N1-)-methyltransferase_1079755..1079985_POSITIVE 234 60 14 210 158 smit:SMT_1406|5end_chloride_channel_protein_1385513..1385743_NEGATIVE 233 48 2 218 165 smit:SMT_121|5end_hypothetical_protein_73303..73533_POSITIVE 225 48 1 197 153 smit:SMT_1571|5end_CAAX_amino_terminal_protease_family_protein_1563780..1564010_POSITIVE 225 53 16 172 134 smit:SMT_292|5end_dTDP-glucose_4,6-dehydratase_234804..235034_POSITIVE 222 59 11 139 88 smit:SMT_1637|5end_hypothetical_protein_1623091..1623321_POSITIVE 222 48 3 83 33 smit:SMT_1117|5end_competence_protein_CglA_1054703..1054933_NEGATIVE 221 55 15 175 132 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 221 55 15 175 132 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 220 44 1 231 188 smit:SMT_665|5end_NAD+_kinase_576745..576975_NEGATIVE 220 40 4 33 2 smit:SMT_113|5end_hypothetical_protein_61425..61655_POSITIVE 218 49 1 210 152 smit:SMT_2020|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1937595..1937825_POSITIVE 218 49 1 210 152 smit:SMT_1317|5end_glycosyltransferase_1281921..1282151_POSITIVE 218 62 29 58 20 smit:SMT_616|5end_hypothetical_protein_525777..526007_POSITIVE 218 62 22 114 66 smit:SMT_546|5end_DNA_topoisomerase_IV_subunit_A_461377..461607_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 46 2 60 8 smit:SMT_1005|3end_possible_aluminum_resistance_protein_946679..946829_POSITIVE 268 39 7 84 52 smit:SMT_150|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_99400..99550_POSITIVE 263 59 11 56 1 smit:SMT_1059|3end_NAD(P)H-flavin_oxidoreductase_998172..998322_POSITIVE 227 57 19 76 31 smit:SMT_1583|3end_polysaccharide_transporter,_PST_family_1574609..1574759_POSITIVE 219 52 15 142 109 smit:SMT_1432|3end_hypothetical_protein_1416752..1416902_NEGATIVE 218 62 22 81 33 smit:SMT_545|3end_hypothetical_protein_predicted_by_Glimmer/Critica_461424..461574_POSITIVE 210 50 1 141 95 smit:SMT_1213|3end_fatty_acid/phospholipid_synthesis_protein_PlsX_1171663..1171813_NEGATIVE 209 80 31 61 7 smit:SMT_239|3end_hypothetical_protein_177788..177938_POSITIVE 208 58 19 149 109 smit:SMT_1419|3end_hypothetical_protein_1404582..1404732_POSITIVE 208 58 11 64 16 smit:SMT_119|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_72021..72171_POSITIVE 207 54 15 136 97 smit:SMT_1760|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1735743..1735893_NEGATIVE 206 55 11 151 104 smit:SMT_1636|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1623187..1623337_POSITIVE 206 31 4 111 77 smit:SMT_1566|3end_K03475_PTS_system,_unknown_pentitol_phosphotransferase_enzyme_IIC_component_1559344..1559494_POSITIVE 205 34 11 135 110 smit:SMT_695|3end_heat_shock_protein_HtpX_605984..606134_NEGATIVE 204 50 4 60 14 smit:SMT_159|3end_hypothetical_protein_104615..104765_POSITIVE 202 61 23 69 13 smit:SMT_1009|3end_hypothetical_protein_predicted_by_Glimmer/Critica_948360..948510_POSITIVE 201 63 23 112 62 smit:SMT_344|3end_K02503_Hit-like_protein_involved_in_cell-cycle_regulation_283564..283714_NEGATIVE 200 41 1 58 8 smit:SMT_1679|3end_hypothetical_protein_1663590..1663740_POSITIVE 200 60 18 136 99 smit:SMT_1534|3end_signal_peptidase_I_1517912..1518062_POSITIVE 200 59 28 70 34 smit:SMT_188|3end_LSU_ribosomal_protein_L30P_123767..123917_POSITIVE