Origin IGS: ttctttcctaggctatcctatagtttcaaactataagaaaaagctctagtcgagcttttcattaatctatactttatatgtaaagttagctacaaatagctccacaaaactaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttagttttgtggagctatttgtagctaactttacatataaagtatagattaatgaaaagctcgactagagctttttcttatagtttgaaactataggatagcctaggaaagaa Mask Tandem Repeat Region ================================================ ttctttcctaggctatcctatagtttcaaactataagaaaaagctctagtcgagcttttcattaatctatactttatatgtaaagttagctacaaatagctccacaaaactaac Find is-nt database================================================ Query_seq: SMT_1514:SMT_1515|SMT_1514:SMT_1515:methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase:amino acid ABC transporter, ATP-binding protein:<-<-:1496731..1496844 114 ttctttcctaggctatcctatagtttcaaactataagaaaaagctctagtcgagcttttcattaatctatactttatatgtaaagttagctacaaatagctccacaaaactaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1514:SMT_1515|SMT_1514:SMT_1515:methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase:amino acid ABC transporter, ATP-binding protein:<-<-:1496731..1496844 114 ttctttcctaggctatcctatagtttcaaactataagaaaaagctctagtcgagcttttcattaatctatactttatatgtaaagttagctacaaatagctccacaaaactaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1514:SMT_1515|SMT_1514:SMT_1515:methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase:amino acid ABC transporter, ATP-binding protein:<-<-:1496731..1496844 114 ttctttcctaggctatcctatagtttcaaactataagaaaaagctctagtcgagcttttcattaatctatactttatatgtaaagttagctacaaatagctccacaaaactaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctttcctaggctatcctatagtttcaaactataagaaaaagctctagtcgagcttttcattaatctatactttatatgtaaagttagctacaaatagctccacaaaactaac Predict ORF larger than 30AA ================================================ ttctttcctaggctatcctatagtttcaaactataagaaaaagctctagtcgagcttttcattaatctatactttatatgtaaagttagctacaaatagctccacaaaactaac 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================================================ ttctttcctaggctatcctatagtttcaaactataagaaaaagctctagtcgagcttttcattaatctatactttatatgtaaagttagctacaaatagctccacaaaactaac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 59 HP_score: -6.3 Tail_Score: -2.92171 Start: 34 End: 64 Full_Region: atataaagtatagat taatgaaaagctc gacta gagctttttctta tagtttgaaactata .................................taatgaaaagctcgactagagctttttctta.................................................. TransTerm Strand: + Conf: 49 HP_score: -4.9 Tail_Score: -2.61086 Start: 38 End: 60 Full_Region: GTTTCAAACTATAAG AAAAAGCTC TAGTC GAGCTTTTC ATTAATCTATACTTT .....................................AAAAAGCTCTAGTCGAGCTTTTC...................................................... TransTerm Strand: - Conf: 77 HP_score: -4.8 Tail_Score: -5.25772 Start: 43 End: 55 Full_Region: atagattaatgaaaa gctc gacta gagc tttttcttatagttt ..........................................gctcgactagagc........................................................... Find igs database================================================ Query_seq: SMT_1514:SMT_1515|SMT_1514:SMT_1515:methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase:amino acid ABC transporter, ATP-binding protein:<-<-:1496731..1496844 114 ttctttcctaggctatcctatagtttcaaactataagaaaaagctctagtcgagcttttcattaatctatactttatatgtaaagttagctacaaatagctccacaaaactaac Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: smit_SMT_1514_SMT_1515|methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase:amino acid ABC transporter, ATP-binding protein|NEGATIVE:NEGATIVE|[1496731,1496844]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 ttctttcctaggctatcctatagtttcaaactataagaaaaagctctagtcgagcttttcattaatctatactttatatgtaaagttagctacaaatagctccacaaaactaac ttctttcctaggctatcctatagtttcaaactataagaaaaagctctagtcgagcttttcattaatctatactttatatgtaaagttagctacaaatagctccacaaaactaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUUCCUAGGCUAUCCUAUAGUUUCAAACUAUAAGAAAAAGCUCUAGUCGAGCUUUUCAUUAAUCUAUACUUUAUAUGUAAAGUUAGCUACAAAUAGCUCCACAAAACUAAC .......(((((((.((.((((((.....)))))).))...))).))))..(((((..........(((.((((((....)))))))))........)))))............ (-21.17) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUAGUUUUGUGGAGCUAUUUGUAGCUAACUUUACAUAUAAAGUAUAGAUUAAUGAAAAGCUCGACUAGAGCUUUUUCUUAUAGUUUGAAACUAUAGGAUAGCCUAGGAAAGAA ............(((((.((..(..(((((((((....)))))).)))....)..)).)))))..((((.(((...(((((((((.....))))))))).)))))))....... (-30.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 829 60 11 151 102 smit:SMT_1514|5end_methylenetetrahydrofolate_dehydrogenase_(NADP+)_/_methenyltetrahydrofolate_cyclohydrolase_1496640..1496870_NEGATIVE 252 60 22 170 128 smit:SMT_549|5end_hypothetical_cytosolic_protein_467057..467287_POSITIVE 244 100 52 141 83 smit:SMT_595|5end_phosphoglycerate_mutase_512593..512823_NEGATIVE 243 90 46 231 173 smit:SMT_583|5end_ATP_synthase_F1,_delta_subunit_499497..499727_POSITIVE 243 55 21 46 7 smit:SMT_127|5end_transcriptional_regulator,_PadR_family_78563..78793_NEGATIVE 228 45 1 202 150 smit:SMT_818|5end_cystathionine_gamma-synthase_729801..730031_NEGATIVE 222 68 27 103 53 smit:SMT_1161|5end_K05837_rod_shape_determining_protein_RodA_1106408..1106638_NEGATIVE 222 57 11 210 154 smit:SMT_608|5end_laminin-binding_surface_protein_520757..520987_POSITIVE 217 65 23 72 33 smit:SMT_1960|5end_UDP-galactopyranose_mutase_1892899..1893129_POSITIVE 217 65 23 72 33 smit:SMT_287|5end_UDP-galactopyranose_mutase_230082..230312_POSITIVE 216 64 41 216 189 smit:SMT_1129|5end_hypothetical_protein_1063926..1064156_NEGATIVE 212 50 4 125 81 smit:SMT_1646|5end_3-isopropylmalate_dehydratase_large_subunit_1632011..1632241_POSITIVE 212 64 25 163 130 smit:SMT_1114|5end_competence_protein_1052555..1052785_NEGATIVE 211 46 1 143 96 smit:SMT_1520|5end_K02004_1501184..1501414_NEGATIVE 211 44 9 151 117 smit:SMT_399|5end_cytochrome_c-type_biogenesis_protein_CcdA_328366..328596_POSITIVE 210 99 51 184 138 smit:SMT_973|5end_signal_transduction_histidine_kinase_922177..922407_NEGATIVE 207 64 23 65 18 smit:SMT_1430|5end_hypothetical_protein_1414857..1415087_POSITIVE 205 50 3 85 40 smit:SMT_1380|5end_pyrroline-5-carboxylate_reductase_1358464..1358694_NEGATIVE 201 60 19 227 180 smit:SMT_1588|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1577062..1577292_POSITIVE 201 56 11 221 177 smit:SMT_832|5end_hypothetical_protein_775104..775334_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 60 22 72 30 smit:SMT_548|3end_K02035_peptide/nickel_transport_system_substrate-binding_protein_467039..467189_POSITIVE 244 100 52 144 86 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE 231 57 11 113 60 smit:SMT_651|3end_DNA_ligase_559986..560136_NEGATIVE 230 60 11 126 63 smit:SMT_964|3end_cadmium_resistance_transporter,_putative_909891..910041_NEGATIVE 222 60 15 46 1 smit:SMT_1466|3end_endopeptidase_O_1447905..1448055_POSITIVE 222 68 27 66 16 smit:SMT_1162|3end_ATP-dependent_DNA_helicase_1106445..1106595_NEGATIVE 217 65 23 60 21 smit:SMT_1959|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1892967..1893117_POSITIVE 217 55 11 98 58 smit:SMT_433|3end_cell_division_protein_DivIB_375954..376104_POSITIVE 217 65 23 60 21 smit:SMT_286|3end_polysaccharide_transporter,_PST_family_230150..230300_POSITIVE 212 90 41 105 52 smit:SMT_2081|3end_glycosyltransferase_1981336..1981486_POSITIVE 212 50 4 121 77 smit:SMT_1645|3end_hypothetical_protein_1632087..1632237_POSITIVE 212 56 11 55 9 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 211 46 1 87 40 smit:SMT_1521|3end_K02003_1501240..1501390_NEGATIVE 207 64 23 64 17 smit:SMT_1429|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1414936..1415086_POSITIVE 205 50 3 81 36 smit:SMT_1381|3end_gamma-glutamyl_phosphate_reductase_1358468..1358618_NEGATIVE 204 59 29 78 40 smit:SMT_1277|3end_PcsB_protein_1241327..1241477_POSITIVE 201 56 11 142 98 smit:SMT_833|3end_hypothetical_protein_predicted_by_Glimmer/Critica_775183..775333_NEGATIVE 201 59 22 57 15 smit:SMT_742|3end_hypothetical_protein_645784..645934_NEGATIVE 200 81 41 49 9 smit:SMT_1995|3end_phosphoglycerate_mutase_1920535..1920685_NEGATIVE 198 44 9 86 48 smit:SMT_1978|3end_hypothetical_protein_1908766..1908916_NEGATIVE