Origin IGS: gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acttctagttttggctagaagttttttatatataaaaattttacacatttctcttgacagggctttcatttagatgtacaatgtatgtgtagaaaaattatatataaaaatcttacacattagaaaaggaggtttccc Mask Tandem Repeat Region ================================================ gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt Find is-nt database================================================ Query_seq: SMT_127:SMT_128|SMT_127:SMT_128:transcriptional regulator, PadR family:K03449 MFS transporter, CP family, cyanate transporter:<-<-:78654..78791 138 gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_127:SMT_128|SMT_127:SMT_128:transcriptional regulator, PadR family:K03449 MFS transporter, CP family, cyanate transporter:<-<-:78654..78791 138 gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_127:SMT_128|SMT_127:SMT_128:transcriptional regulator, PadR family:K03449 MFS transporter, CP family, cyanate transporter:<-<-:78654..78791 138 gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt Predict ORF larger than 30AA ================================================ gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt 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: 87 Start: 57 End: 86 ........................................................CTTGACAGGGCTTTCATTTAGATGTACAAT.................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_127:SMT_128|SMT_127:SMT_128:transcriptional regulator, PadR family:K03449 MFS transporter, CP family, cyanate transporter:<-<-:78654..78791 138 gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: smit_SMT_127_SMT_128|transcriptional regulator, PadR family:K03449 MFS transporter, CP family, cyanate transporter|NEGATIVE:NEGATIVE|[78654,78791]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt Inter-species Hit: Count: 3 Min: 1 Max: 138 Len: 138 Subject: NC_008533_SPD_0096_SPD_0097|transcriptional regulator, PadR family protein:transporter, putative|NEGATIVE:NEGATIVE|[96656,96793]|138 HSP 1 e-value: 4.0E-68 bit: 258.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaaagaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagctaaaactagaagt Subject: NC_003098_spr0089_spr0090|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[96656,96793]|138 HSP 1 e-value: 4.0E-68 bit: 258.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaaagaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagctaaaactagaagt Subject: NC_003028_SP_0100_SP_0101|hypothetical protein:transporter, putative|NEGATIVE:NEGATIVE|[102107,102244]|138 HSP 1 e-value: 4.0E-68 bit: 258.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaatgaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagccaaaactagaagt gggaaacctccttttctaatgtgtaagatttttatatataatttttctacacatacattgtacatctaaaagaaagccctgtcaagagaaatgtgtaaaatttttatatataaaaaacttctagctaaaactagaagt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAAACCUCCUUUUCUAAUGUGUAAGAUUUUUAUAUAUAAUUUUUCUACACAUACAUUGUACAUCUAAAUGAAAGCCCUGUCAAGAGAAAUGUGUAAAAUUUUUAUAUAUAAAAAACUUCUAGCCAAAACUAGAAGU ((....))..........((((((((((.((((((((((...((((((..(((.....)))...((.....))...........)))))))))))))))).)))))))))).....((((((((......)))))))) (-30.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUCUAGUUUUGGCUAGAAGUUUUUUAUAUAUAAAAAUUUUACACAUUUCUCUUGACAGGGCUUUCAUUUAGAUGUACAAUGUAUGUGUAGAAAAAUUAUAUAUAAAAAUCUUACACAUUAGAAAAGGAGGUUUCCC (((((((((....)))))))))(((((((((((((...((((((((((.....((((((...((.......)).))).)))...))))))))))...))))))))))))).................((......)). (-32.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 788 90 41 181 132 smit:SMT_127|5end_transcriptional_regulator,_PadR_family_78563..78793_NEGATIVE 219 37 1 139 93 smit:SMT_1369|5end_alanine_dehydrogenase_1348280..1348510_POSITIVE 213 84 44 90 52 smit:SMT_2088|5end_glucose-1-phosphate_thymidylyltransferase_1984624..1984854_POSITIVE 211 49 1 147 92 smit:SMT_1221|5end_choline_binding_protein_A_1185539..1185769_NEGATIVE 210 93 59 221 187 smit:SMT_1233|5end_cadmium_resistance_protein_1194306..1194536_POSITIVE 205 67 26 168 131 smit:SMT_1309|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1274082..1274312_POSITIVE 201 89 63 53 26 smit:SMT_1540|5end_hypothetical_protein_1525005..1525235_NEGATIVE 198 85 42 63 19 smit:SMT_1862|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1824094..1824324_POSITIVE 198 85 42 63 19 smit:SMT_1763|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1738537..1738767_POSITIVE 198 50 8 144 100 smit:SMT_972|5end_ABC-type_multidrug/protein/lipid_transport_system,_ATPase_component_920767..920997_NEGATIVE 194 127 83 182 132 smit:SMT_1118|5end_hypothetical_protein_1055150..1055380_NEGATIVE 193 84 50 227 197 smit:SMT_235|5end_hypothetical_protein_174081..174311_POSITIVE 192 85 62 147 126 smit:SMT_1647|5end_3-isopropylmalate_dehydratase_small_subunit_1633403..1633633_POSITIVE 191 87 43 200 147 smit:SMT_1351|5end_dephospho-CoA_kinase_1329817..1330047_NEGATIVE 190 130 89 218 172 smit:SMT_394|5end_K07729_putative_transcriptional_regulator_324260..324490_POSITIVE 188 26 1 40 17 smit:SMT_1418|5end_lysine_decarboxylase_1403147..1403377_NEGATIVE 188 49 2 138 93 smit:SMT_1029|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_965632..965862_NEGATIVE 188 49 7 151 96 smit:SMT_98|5end_hypothetical_protein_28924..29154_POSITIVE 187 90 42 150 106 smit:SMT_297|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_238547..238777_POSITIVE 185 82 44 155 117 smit:SMT_736|5end_hypothetical_protein_642270..642500_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 209 124 82 88 46 smit:SMT_1018|3end_hypothetical_protein_predicted_by_Glimmer/Critica_954739..954889_POSITIVE 194 89 63 133 105 smit:SMT_1968|3end_transcription-repair_coupling_factor_1899951..1900101_NEGATIVE 192 85 62 137 116 smit:SMT_1646|3end_3-isopropylmalate_dehydratase_large_subunit_1633473..1633623_POSITIVE 191 90 52 54 12 smit:SMT_1351|3end_dephospho-CoA_kinase_1329212..1329362_NEGATIVE 190 130 89 71 25 smit:SMT_393|3end_hypothetical_protein_predicted_by_Glimmer/Critica_324193..324343_POSITIVE 188 49 2 103 58 smit:SMT_1030|3end_alpha-galactosidase_965667..965817_NEGATIVE 182 90 42 118 61 smit:SMT_2031|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1945633..1945783_NEGATIVE 182 45 1 103 54 smit:SMT_441|3end_L-lactate_oxidase_381279..381429_POSITIVE 181 29 7 120 102 smit:SMT_770|3end_K02053_spermidine/putrescine_transport_system_permease_protein_680586..680736_NEGATIVE 177 128 81 64 4 smit:SMT_222|3end_beta-glucosidase_156430..156580_POSITIVE 176 69 25 94 51 smit:SMT_1245|3end_SOS_responce_UmuC_protein_1205637..1205787_POSITIVE 174 27 3 138 113 smit:SMT_760|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_665693..665843_NEGATIVE 172 90 45 138 94 smit:SMT_454|3end_hypothetical_protein_391740..391890_POSITIVE 170 88 44 61 21 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE 169 16 1 83 65 smit:SMT_1046|3end_chaperonin_GroEL_987638..987788_NEGATIVE 167 89 58 40 11 smit:SMT_775|3end_alpha-acetolactate_decarboxylase_685241..685391_NEGATIVE 165 110 72 82 44 smit:SMT_1486|3end_hypothetical_protein_1466444..1466594_POSITIVE 161 96 72 41 12 smit:SMT_1724|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1710691..1710841_POSITIVE 159 37 8 137 105 smit:SMT_746|3end_LPS_biosynthesis_protein_650377..650527_NEGATIVE 158 51 11 88 42 smit:SMT_1688|3end_putative_N-acylglucosamine-6-phosphate_2-epimerase_1671603..1671753_POSITIVE