Origin IGS: gagagagcgcttaaaaaccttgtccgaaacgacaataaactatgaagaaagataagaggcaagccggaggcttgcaaggaagatatttcccaccgtggtgaaagtttcagtagcaaaagctactgaaacaggggatttttgagacaataggctcaaaaataagtgatgaaatcccgtagggagttgctcacgtccccaccacttaagggaaatataaaaaaatagaaaattaactaacaaggagaaaaacac .........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 gtgtttttctccttgttagttaattttctatttttttatatttcccttaagtggtggggacgtgagcaactccctacgggatttcatcacttatttttgagcctattgtctcaaaaatcccctgtttcagtagcttttgctactgaaactttcaccacggtgggaaatatcttccttgcaagcctccggcttgcctcttatctttcttcatagtttattgtcgtttcggacaaggtttttaagcgctctctc Mask Tandem Repeat Region ================================================ gagagagcgcttaaaaaccttgtccgaaacgacaataaactatgaagaaagataagaggcaagccggaggcttgcaaggaagatatttcccaccgtggtgaaagtttcagtagcaaaagctactgaaacaggggatttttgagacaataggctcaaaaataagtgatgaaatcccgtagggagttgctcacgtccccaccacttaagggaaatataaaaaaatagaaaattaactaacaaggagaaaaacac Find is-nt database================================================ Query_seq: SMT_339:SMT_340|SMT_339:SMT_340:K03687 molecular chaperone GrpE:chaperone protein:->->:278551..278802 252 gagagagcgcttaaaaaccttgtccgaaacgacaataaactatgaagaaagataagaggcaagccggaggcttgcaaggaagatatttcccaccgtggtgaaagtttcagtagcaaaagctactgaaacaggggatttttgagacaataggctcaaaaataagtgatgaaatcccgtagggagttgctcacgtccccaccacttaagggaaatataaaaaaatagaaaattaactaacaaggagaaaaacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_339:SMT_340|SMT_339:SMT_340:K03687 molecular chaperone GrpE:chaperone protein:->->:278551..278802 252 gagagagcgcttaaaaaccttgtccgaaacgacaataaactatgaagaaagataagaggcaagccggaggcttgcaaggaagatatttcccaccgtggtgaaagtttcagtagcaaaagctactgaaacaggggatttttgagacaataggctcaaaaataagtgatgaaatcccgtagggagttgctcacgtccccaccacttaagggaaatataaaaaaatagaaaattaactaacaaggagaaaaacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_339:SMT_340|SMT_339:SMT_340:K03687 molecular chaperone GrpE:chaperone protein:->->:278551..278802 252 gagagagcgcttaaaaaccttgtccgaaacgacaataaactatgaagaaagataagaggcaagccggaggcttgcaaggaagatatttcccaccgtggtgaaagtttcagtagcaaaagctactgaaacaggggatttttgagacaataggctcaaaaataagtgatgaaatcccgtagggagttgctcacgtccccaccacttaagggaaatataaaaaaatagaaaattaactaacaaggagaaaaacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagagagcgcttaaaaaccttgtccgaaacgacaataaactatgaagaaagataagaggcaagccggaggcttgcaaggaagatatttcccaccgtggtgaaagtttcagtagcaaaagctactgaaacaggggatttttgagacaataggctcaaaaataagtgatgaaatcccgtagggagttgctcacgtccccaccacttaagggaaatataaaaaaatagaaaattaactaacaaggagaaaaacac Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: - Start: 43 End: 252 .......................................... A L F I N G V T T F T E T A F A V S V P S K Q S L L S L F L H H F G T P L Q E R G W W K L S I Y F F L F N V L L S F F M Protein_Len: 38 Strand: - Start: 3 End: 116 .. L A S L F R T R F S L L S H L F I L P L G S A Q L S S I E W R P S L K L L M ........................................................................................................................................ gagagagcgcttaaaaaccttgtccgaaacgacaataaactatgaagaaagataagaggcaagccggaggcttgcaaggaagatatttcccaccgtggtgaaagtttcagtagcaaaagctactgaaacaggggatttttgagacaataggctcaaaaataagtgatgaaatcccgtagggagttgctcacgtccccaccacttaagggaaatataaaaaaatagaaaattaactaacaaggagaaaaacac 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================================================ gagagagcgcttaaaaaccttgtccgaaacgacaataaactatgaagaaagataagaggcaagccggaggcttgcaaggaagatatttcccaccgtggtgaaagtttcagtagcaaaagctactgaaacaggggatttttgagacaataggctcaaaaataagtgatgaaatcccgtagggagttgctcacgtccccaccacttaagggaaatataaaaaaatagaaaattaactaacaaggagaaaaacac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -8.8 Tail_Score: -3.56559 Start: 58 End: 76 Full_Region: gggaaatatcttcct tgcaagcc tcc ggcttgcc tcttatctttcttca .........................................................tgcaagcctccggcttgcc................................................................................................................................................................................ TransTerm Strand: - Conf: 88 HP_score: -12.3 Tail_Score: -2.72851 Start: 59 End: 75 Full_Region: ggaaatatcttcctt gcaagcc tcc ggcttgc ctcttatctttcttc ..........................................................gcaagcctccggcttgc................................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -14.9 Tail_Score: -3.53811 Start: 104 End: 129 Full_Region: tctcaaaaatcccct gtttcagtagc tttt gctactgaaac tttcaccacggtggg .......................................................................................................gtttcagtagcttttgctactgaaac........................................................................................................................... Find igs database================================================ Query_seq: SMT_339:SMT_340|SMT_339:SMT_340:K03687 molecular chaperone GrpE:chaperone protein:->->:278551..278802 252 gagagagcgcttaaaaaccttgtccgaaacgacaataaactatgaagaaagataagaggcaagccggaggcttgcaaggaagatatttcccaccgtggtgaaagtttcagtagcaaaagctactgaaacaggggatttttgagacaataggctcaaaaataagtgatgaaatcccgtagggagttgctcacgtccccaccacttaagggaaatataaaaaaatagaaaattaactaacaaggagaaaaacac Intra-Species Hit: Count: 1 Min: 1 Max: 252 Len: 252 Subject: smit_SMT_339_SMT_340|K03687 molecular chaperone GrpE:chaperone protein|POSITIVE:POSITIVE|[278551,278802]|252 HSP 1 e-value: 1.0E-128 bit: 458.0 Len: 252 Query Start:1 Query End:252 Subject Strand: POSITIVE Subject Start: 1 Subject End: 252 gagagagcgcttaaaaaccttgtccgaaacgacaataaactatgaagaaagataagaggcaagccggaggcttgcaaggaagatatttcccaccgtggtgaaagtttcagtagcaaaagctactgaaacaggggatttttgagacaataggctcaaaaataagtgatgaaatcccgtagggagttgctcacgtccccaccacttaagggaaatatnnnnnnntagaaaattaactaacaaggagaaaaacac gagagagcgcttaaaaaccttgtccgaaacgacaataaactatgaagaaagataagaggcaagccggaggcttgcaaggaagatatttcccaccgtggtgaaagtttcagtagcaaaagctactgaaacaggggatttttgagacaataggctcaaaaataagtgatgaaatcccgtagggagttgctcacgtccccaccacttaagggaaatataaaaaaatagaaaattaactaacaaggagaaaaacac Inter-species Hit: Count: 4 Min: 19 Max: 252 Len: 234 Subject: NC_004350_SMU.81_SMU.82|heat shock protein GrpE (HSP-70 cofactor):molecular chaperone DnaK|POSITIVE:POSITIVE|[85269,85641]|373 HSP 1 e-value: 3.0E-18 bit: 93.7 Len: 133 Query Start:82 Query End:214 Subject Strand: POSITIVE Subject Start: 89 Subject End: 222 .................................................................................gatatttcccaccgtggtgaaagtttcagtagcaaaagctactgaaaca-ggggattttt-gagacaataggctcaaaaataagtgatgaaatcccgtagggagttgctcacgtccccaccacttaagggaaata...................................... .................................................................................gatatttcccgatgtggtgaaagtttcagtagcttgcgctactgaaacaaggggattttttgggacttcagtctcaaaaataagtgatgaaatcccgaagggagttgctcatatccccactac-taagggaaata...................................... Subject: NC_008533_SPD_0459_SPD_0460|heat shock protein GrpE:chaperone protein DnaK|POSITIVE:POSITIVE|[469109,469587]|479 HSP 1 e-value: 3.0E-12 bit: 73.8 Len: 37 Query Start:19 Query End:55 Subject Strand: POSITIVE Subject Start: 245 Subject End: 281 ..................cttgtccgaaacgacaataaactatgaagaaagataa..................................................................................................................................................................................................... ..................cttgtccgaaacgacaataaactatgaagaaagataa..................................................................................................................................................................................................... HSP 2 e-value: 4.0E-8 bit: 60.0 Len: 30 Query Start:223 Query End:252 Subject Strand: POSITIVE Subject Start: 450 Subject End: 479 ..............................................................................................................................................................................................................................tagaaaattaactaacaaggagaaaaacac ..............................................................................................................................................................................................................................tagaaaattaactaacaaggagaaaaacac Subject: NC_003098_spr0454_spr0455|Heat-shock protein (activation of DnaK):molecular chaperone DnaK|POSITIVE:POSITIVE|[461579,462057]|479 HSP 1 e-value: 3.0E-12 bit: 73.8 Len: 37 Query Start:19 Query End:55 Subject Strand: POSITIVE Subject Start: 245 Subject End: 281 ..................cttgtccgaaacgacaataaactatgaagaaagataa..................................................................................................................................................................................................... ..................cttgtccgaaacgacaataaactatgaagaaagataa..................................................................................................................................................................................................... HSP 2 e-value: 4.0E-8 bit: 60.0 Len: 30 Query Start:223 Query End:252 Subject Strand: POSITIVE Subject Start: 450 Subject End: 479 ..............................................................................................................................................................................................................................tagaaaattaactaacaaggagaaaaacac ..............................................................................................................................................................................................................................tagaaaattaactaacaaggagaaaaacac Subject: NC_003028_SP_0516_SP_0517|heat shock protein GrpE:molecular chaperone DnaK|POSITIVE:POSITIVE|[496997,497484]|488 HSP 1 e-value: 3.0E-12 bit: 73.8 Len: 37 Query Start:19 Query End:55 Subject Strand: POSITIVE Subject Start: 245 Subject End: 281 ..................cttgtccgaaacgacaataaactatgaagaaagataa..................................................................................................................................................................................................... ..................cttgtccgaaacgacaataaactatgaagaaagataa..................................................................................................................................................................................................... HSP 2 e-value: 4.0E-8 bit: 60.0 Len: 30 Query Start:223 Query End:252 Subject Strand: POSITIVE Subject Start: 459 Subject End: 488 ..............................................................................................................................................................................................................................tagaaaattaactaacaaggagaaaaacac ..............................................................................................................................................................................................................................tagaaaattaactaacaaggagaaaaacac Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGUCCGAAACGACAAUAAACUAUGAAGAAAGAUAAGAGGCAAGCCGGAGGCUUGCAAGGAAGAUAUUUCCCACCGUGGUGAAAGUUUCAGUAGCAAAAGCUACUGAAACAGGGGAUUUUUGAGACAAUAGGCUCAAAAAUAAGUGAUGAAAUCCCGUAGGGAGUUGCUCACGUCCCCACCACUUAAGGGAAAUAUAAAAAAAUAGAAAAUUAACUAACAAGGAGAAAAACAC .(((((......)))))....((((...............(((((((...))))))).......(((((((((...((((((...(((((((((((....))))))))))).(((.(((((((((........)))))))))..((((.....((((...)))).....))))..)))))))))....)))))))))......))))........................... (-74.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUUUUUCUCCUUGUUAGUUAAUUUUCUAUUUUUUUAUAUUUCCCUUAAGUGGUGGGGACGUGAGCAACUCCCUACGGGAUUUCAUCACUUAUUUUUGAGCCUAUUGUCUCAAAAAUCCCCUGUUUCAGUAGCUUUUGCUACUGAAACUUUCACCACGGUGGGAAAUAUCUUCCUUGCAAGCCUCCGGCUUGCCUCUUAUCUUUCUUCAUAGUUUAUUGUCGUUUCGGACAAG ...........((((((.(.((((...((((......(((((((((....((((((((((.((((.....((((...)))).....))))...((((((((.(....).))))))))))))).(((((((((((....)))))))))))....)))))...))))))))).......(((((((...)))))))...............))))...)))).)......)))))) (-75.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 60 28 46 9 smit:SMT_1878|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836577..1836807_NEGATIVE 353 85 41 72 24 smit:SMT_1073|5end_L-asparaginase_1011209..1011439_POSITIVE 345 78 33 127 87 smit:SMT_1444|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1427979..1428209_NEGATIVE 345 78 33 179 139 smit:SMT_1443|5end_23S_rRNA_m(5)U_1939_methyltransferase_1427927..1428157_NEGATIVE 338 90 41 186 140 smit:SMT_387|5end_hypothetical_protein_predicted_by_Glimmer/Critica_320937..321167_POSITIVE 334 80 38 198 150 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 332 78 40 77 25 smit:SMT_1464|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1444721..1444951_POSITIVE 330 72 32 66 16 smit:SMT_350|5end_immunity_protein_BlpL_289864..290094_POSITIVE 315 80 38 184 132 smit:SMT_187|5end_30S_ribosomal_protein_S5_122997..123227_POSITIVE 312 72 32 66 16 smit:SMT_353|5end_immunity_protein_BlpL_290880..291110_POSITIVE 309 96 52 70 20 smit:SMT_2138|5end_cell_division_protein_FtsA_2016418..2016648_POSITIVE 309 96 52 70 20 smit:SMT_2136|5end_cell_division_protein_FtsA_2015132..2015362_POSITIVE 299 185 143 105 52 smit:SMT_894|5end_hypothetical_protein_841701..841931_NEGATIVE 297 135 94 79 34 smit:SMT_1323|5end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1292187..1292417_POSITIVE 293 76 32 99 22 smit:SMT_1322|5end_K02075_zinc/manganese_transport_system_permease_protein_1291371..1291601_POSITIVE 292 78 40 63 17 smit:SMT_225|5end_pullulanase_163529..163759_NEGATIVE 287 57 21 165 117 smit:SMT_1782|5end_hypothetical_protein_1759520..1759750_POSITIVE 287 120 72 166 120 smit:SMT_174|5end_30S_ribosomal_protein_S19_117431..117661_POSITIVE 285 108 66 121 77 smit:SMT_1981|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912261..1912491_POSITIVE 283 66 33 170 136 smit:SMT_703|5end_hypothetical_protein_612345..612575_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 555 158 113 47 1 smit:SMT_363|3end_K02519_translation_initiation_factor_IF-2_300751..300901_POSITIVE 368 60 28 56 19 smit:SMT_1879|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836567..1836717_NEGATIVE 310 192 155 69 31 smit:SMT_1115|3end_K02245_competence_protein_ComGC_1052473..1052623_NEGATIVE 299 185 143 112 59 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE 298 64 21 148 103 smit:SMT_1445|3end_hypothetical_protein_1427948..1428098_NEGATIVE 297 135 94 69 24 smit:SMT_1322|3end_K02075_zinc/manganese_transport_system_permease_protein_1292257..1292407_POSITIVE 295 93 52 151 109 smit:SMT_1707|3end_cell_division_protein_FtsA_1691846..1691996_POSITIVE 294 180 155 58 26 smit:SMT_2093|3end_hypothetical_protein_LOC618557_1989186..1989336_POSITIVE 293 76 32 106 29 smit:SMT_1321|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1291458..1291608_POSITIVE 290 174 144 126 93 smit:SMT_969|3end_30S_ribosomal_protein_S15_914653..914803_NEGATIVE 288 193 157 42 5 smit:SMT_342|3end_chaperone_protein_DnaJ_283016..283166_POSITIVE 287 120 72 62 16 smit:SMT_173|3end_50S_ribosomal_protein_L2_117407..117557_POSITIVE 285 108 66 80 36 smit:SMT_2023|3end_tryptophan_synthase,_alpha_subunit_1939997..1940147_POSITIVE 285 108 66 45 1 smit:SMT_1965|3end_hypothetical_protein_1897711..1897861_POSITIVE 285 108 66 67 23 smit:SMT_1674|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1660361..1660511_NEGATIVE 285 57 35 72 48 smit:SMT_1096|3end_glyceraldehyde-3-phosphate_dehydrogenase_1037366..1037516_NEGATIVE 281 108 66 66 22 smit:SMT_2015|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1932839..1932989_POSITIVE 278 184 145 146 116 smit:SMT_2071|3end_phosphoenolpyruvate_carboxylase_1975594..1975744_NEGATIVE 272 103 64 116 74 smit:SMT_172|3end_50S_ribosomal_protein_L23_116556..116706_POSITIVE 271 186 153 110 59 smit:SMT_366|3end_hypothetical_protein_302398..302548_POSITIVE