Origin IGS: agtcggcacctctctttcacaaatagaatattttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttacatagattatgcacagggaaaagggaggagtcaatctgattcagtgc .........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 gcactgaatcagattgactcctcccttttccctgtgcataatctatgtaagaaaagggaggattttatttgaaatatcagaaactgtcacgaaattaaaatgaagttcttacataagcgaatcttaaaaaatttcattttgattttaaaactgttcaagaaaatccaaaatattctatttgtgaaagagaggtgccgact Mask Tandem Repeat Region ================================================ agtcggcacctctctttcacaaatagaatattttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttacatagattatgcacagggaaaagggaggagtcaatctgattcagtgc Find is-nt database================================================ Query_seq: SMT_1136:SMT_1137|SMT_1136:SMT_1137:K02025 multiple sugar transport system permease protein:K02027 multiple sugar transport system substrate-binding protein:<-<-:1078192..1078391 200 agtcggcacctctctttcacaaatagaatattttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttacatagattatgcacagggaaaagggaggagtcaatctgattcagtgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1136:SMT_1137|SMT_1136:SMT_1137:K02025 multiple sugar transport system permease protein:K02027 multiple sugar transport system substrate-binding protein:<-<-:1078192..1078391 200 agtcggcacctctctttcacaaatagaatattttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttacatagattatgcacagggaaaagggaggagtcaatctgattcagtgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1136:SMT_1137|SMT_1136:SMT_1137:K02025 multiple sugar transport system permease protein:K02027 multiple sugar transport system substrate-binding protein:<-<-:1078192..1078391 200 agtcggcacctctctttcacaaatagaatattttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttacatagattatgcacagggaaaagggaggagtcaatctgattcagtgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtcggcacctctctttcacaaatagaatattttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttacatagattatgcacagggaaaagggaggagtcaatctgattcagtgc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 101 End: 193 .................................................................................................... K L K T V T E S I E F L I R G K R V Y I I C L S F P P T L R M ....... Protein_Len: 41 Strand: - Start: 3 End: 125 .. R C R E K V F L I N Q I K K F L K L I L I F N K L I R K H L F K M K I E H C N R M ........................................................................... agtcggcacctctctttcacaaatagaatattttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttacatagattatgcacagggaaaagggaggagtcaatctgattcagtgc 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: 85 Start: 159 End: 188 ..............................................................................................................................................................ATTGACTCCTCCCTTTTCCCTGTGCATAAT............ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 110 End: 139 .............................................................................................................CGTGACAGTTTCTGATATTTCAAATAAAAT............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtcggcacctctctttcacaaatagaatattttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttacatagattatgcacagggaaaagggaggagtcaatctgattcagtgc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 78 HP_score: -5.7 Tail_Score: -4.89521 Start: 139 End: 182 Full_Region: ctgaatcagattgac tcctcccttttccctgtgcata atc tatgtaagaaaagggagga ttttatttgaaatat ..........................................................................................................................................tcctcccttttccctgtgcataatctatgtaagaaaagggagga.................. Find igs database================================================ Query_seq: SMT_1136:SMT_1137|SMT_1136:SMT_1137:K02025 multiple sugar transport system permease protein:K02027 multiple sugar transport system substrate-binding protein:<-<-:1078192..1078391 200 agtcggcacctctctttcacaaatagaatattttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttacatagattatgcacagggaaaagggaggagtcaatctgattcagtgc Intra-Species Hit: Count: 1 Min: 1 Max: 200 Len: 200 Subject: smit_SMT_1136_SMT_1137|K02025 multiple sugar transport system permease protein:K02027 multiple sugar transport system substrate-binding protein|NEGATIVE:NEGATIVE|[1078192,1078391]|200 HSP 1 e-value: 1.0E-109 bit: 396.0 Len: 200 Query Start:1 Query End:200 Subject Strand: POSITIVE Subject Start: 1 Subject End: 200 agtcggcacctctctttcacaaatagaatattttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttacatagattatgcacagggaaaagggaggagtcaatctgattcagtgc agtcggcacctctctttcacaaatagaatattttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttacatagattatgcacagggaaaagggaggagtcaatctgattcagtgc Inter-species Hit: Count: 3 Min: 1 Max: 155 Len: 155 Subject: NC_008533_SPD_1494_SPD_1495|sugar ABC transporter, permease protein:sugar ABC transporter, sugar-binding protein|NEGATIVE:NEGATIVE|[1510533,1510762]|230 HSP 1 e-value: 1.0E-44 bit: 180.0 Len: 155 Query Start:1 Query End:155 Subject Strand: POSITIVE Subject Start: 1 Subject End: 154 agtcggcacctctctttcacaaatagaata--ttttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttaca............................................. agtcggcacctctctttca--aatagaataattttttgactttcttgaactgttttaaaatcaaaatgaaattttttatgattcgcttatgtaagaacttcattttaatttcgtgacagtttcttacattttaaacaaaagcc-cccttttcttaca............................................. Subject: NC_003098_spr1526_spr1527|ABC transporter membrane-spanning permease - sugar transport:ABC transporter substrate-binding protein - sugar transport|NEGATIVE:NEGATIVE|[1503011,1503231]|221 HSP 1 e-value: 7.0E-40 bit: 165.0 Len: 136 Query Start:20 Query End:155 Subject Strand: POSITIVE Subject Start: 9 Subject End: 145 ...................caaatagaata--ttttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttaca............................................. ...................caaatagaataattttttgactttcttgaactgttttaaaatcaaaatgaaattttttatgattcgcttatgtaagaacttcattttaatttcgtgacagtttcttacattttaaacaaaagcc-cccttttcttaca............................................. Subject: NC_003028_SP_1682_SP_1683|sugar ABC transporter, permease protein:sugar ABC transporter, sugar-binding protein|NEGATIVE:NEGATIVE|[1581946,1582166]|221 HSP 1 e-value: 7.0E-40 bit: 165.0 Len: 136 Query Start:20 Query End:155 Subject Strand: POSITIVE Subject Start: 9 Subject End: 145 ...................caaatagaata--ttttggattttcttgaacagttttaaaatcaaaatgaaattttttaagattcgcttatgtaagaacttcattttaatttcgtgacagtttctgatatttcaaataaaatcctcccttttcttaca............................................. ...................caaatagaataattttttgactttcttgaactgttttaaaatcaaaatgaaattttttatgattcgcttatgtaagaacttcattttaatttcgtgacagtttcttacattttaaacaaaagcc-cccttttcttaca............................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCGGCACCUCUCUUUCACAAAUAGAAUAUUUUGGAUUUUCUUGAACAGUUUUAAAAUCAAAAUGAAAUUUUUUAAGAUUCGCUUAUGUAAGAACUUCAUUUUAAUUUCGUGACAGUUUCUGAUAUUUCAAAUAAAAUCCUCCCUUUUCUUACA ........................((((......(((((((...((((.(((...((((.((((((((.(((((((((.....))))...))))).)))))))).))))...))).)))).(((....)))...)))))))......)))).... (-20.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAAGAAAAGGGAGGAUUUUAUUUGAAAUAUCAGAAACUGUCACGAAAUUAAAAUGAAGUUCUUACAUAAGCGAAUCUUAAAAAAUUUCAUUUUGAUUUUAAAACUGUUCAAGAAAAUCCAAAAUAUUCUAUUUGUGAAAGAGAGGUGCCGACU ..........((..(((((((.((((((....(((...)))....(((((((((((((((((.((...((((.....)))))).))))))))))))))))).......)))))))))))))......((((.(((....)))))))...)).... (-26.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 823 50 1 141 92 smit:SMT_1136|5end_K02025_multiple_sugar_transport_system_permease_protein_1078101..1078331_NEGATIVE 239 47 2 79 42 smit:SMT_218|5end_undecaprenyl_pyrophosphate_synthetase_150155..150385_POSITIVE 237 45 1 221 176 smit:SMT_1925|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_1867262..1867492_POSITIVE 229 53 15 229 183 smit:SMT_1208|5end_choline_binding_protein_PcpA_1169690..1169920_NEGATIVE 225 120 71 196 137 smit:SMT_1064|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1003308..1003538_POSITIVE 221 150 105 145 94 smit:SMT_1260|5end_hypothetical_protein_1225517..1225747_POSITIVE 219 150 107 105 47 smit:SMT_2063|5end_hypothetical_protein_1971792..1972022_NEGATIVE 219 36 1 215 181 smit:SMT_819|5end_hypothetical_protein_predicted_by_Glimmer/Critica_730421..730651_NEGATIVE 218 116 77 198 157 smit:SMT_275|5end_transcriptional_activator-exopolysaccharide_biosynthesis_217369..217599_POSITIVE 210 150 110 109 63 smit:SMT_1058|5end_primosomal_protein_DnaI_996486..996716_POSITIVE 208 126 81 111 63 smit:SMT_1996|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1921078..1921308_NEGATIVE 207 30 1 44 17 smit:SMT_1125|5end_K08987_putative_membrane_protein_1061145..1061375_NEGATIVE 206 50 1 102 56 smit:SMT_1085|5end_sensor_histidine_kinase_(homolog_to_HK11_Spn)_1022267..1022497_NEGATIVE 206 45 1 152 108 smit:SMT_384|5end_hypothetical_protein_319406..319636_POSITIVE 205 49 5 90 37 smit:SMT_444|5end_thiamine-phosphate_pyrophosphorylase_383339..383569_POSITIVE 202 147 108 159 112 smit:SMT_1123|5end_hypothetical_protein_1059292..1059522_POSITIVE 201 149 108 108 67 smit:SMT_786|5end_hypothetical_protein_697964..698194_NEGATIVE 201 149 106 109 66 smit:SMT_362|5end_K02519_translation_initiation_factor_IF-2_296230..296460_POSITIVE 200 48 2 60 11 smit:SMT_756|5end_3-dehydroquinate_dehydratase_660584..660814_NEGATIVE 199 36 2 136 93 smit:SMT_491|5end_K01998_branched-chain_amino_acid_transport_system_permease_protein_425417..425647_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 229 53 15 140 94 smit:SMT_1209|3end_choline_binding_protein_PcpA_1169779..1169929_NEGATIVE 225 120 71 115 56 smit:SMT_1063|3end_preprotein_translocase_SecA_subunit_1003307..1003457_POSITIVE 221 150 105 126 75 smit:SMT_1259|3end_hypothetical_protein_1225578..1225728_POSITIVE 210 150 110 108 62 smit:SMT_1057|3end_replicative_DNA_helicase_996565..996715_POSITIVE 208 126 81 66 18 smit:SMT_1997|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_1921123..1921273_NEGATIVE 207 30 1 32 5 smit:SMT_1126|3end_K08987_putative_membrane_protein_1061157..1061307_NEGATIVE 206 45 1 73 29 smit:SMT_383|3end_cysteinyl-tRNA_synthetase_319407..319557_POSITIVE 205 49 5 100 47 smit:SMT_443|3end_hydroxyethylthiazole_kinase_383429..383579_POSITIVE 201 149 106 92 49 smit:SMT_361|3end_hypothetical_protein_296293..296443_POSITIVE 200 48 2 63 14 smit:SMT_757|3end_K06969_putative_SAM-dependent_methyltransferase_660581..660731_NEGATIVE 199 36 2 132 89 smit:SMT_490|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_425493..425643_POSITIVE 199 122 83 124 85 smit:SMT_143|3end_hypothetical_protein_95090..95240_NEGATIVE 195 147 109 46 1 smit:SMT_1948|3end_IS1381_transposase_protein_A_1883581..1883731_POSITIVE 195 88 43 59 12 smit:SMT_1149|3end_hypothetical_protein_1094040..1094190_NEGATIVE 193 49 1 84 36 smit:SMT_612|3end_hypothetical_protein_predicted_by_Glimmer/Critica_523674..523824_POSITIVE 189 145 105 65 17 smit:SMT_1532|3end_hypothetical_protein_1515994..1516144_NEGATIVE 189 50 6 139 86 smit:SMT_1262|3end_ribosomal_protein_L11_methyltransferase_1228182..1228332_POSITIVE 189 119 77 73 29 smit:SMT_1128|3end_surface_antigen_1061935..1062085_NEGATIVE 183 50 10 44 5 smit:SMT_2091|3end_hypothetical_protein_1987037..1987187_POSITIVE 182 42 4 64 23 smit:SMT_213|3end_leucyl-tRNA_synthetase_146167..146317_POSITIVE