Origin IGS: agtcacactgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa .........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 tttgattctccttcatttcttatcgttactattttaccataaaggaggtcaacttgcctagaaaaaactaagatttctcgctaattctactagcttaaaggttttttgaataaattagacaaaagatttgaattttaattcaatacatgttataatcatacagtattctattttagaaagcagtgtgact Mask Tandem Repeat Region ================================================ agtcacactgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa Find is-nt database================================================ Query_seq: SMT_1516:SMT_1517|SMT_1516:SMT_1517:K02029 polar amino acid transport system permease protein:hypothetical protein predicted by Glimmer/Critica:<-->:1498263..1498452 190 agtcacactgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1516:SMT_1517|SMT_1516:SMT_1517:K02029 polar amino acid transport system permease protein:hypothetical protein predicted by Glimmer/Critica:<-->:1498263..1498452 190 agtcacactgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1516:SMT_1517|SMT_1516:SMT_1517:K02029 polar amino acid transport system permease protein:hypothetical protein predicted by Glimmer/Critica:<-->:1498263..1498452 190 agtcacactgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtcacactgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa Predict ORF larger than 30AA ================================================ agtcacactgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa 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: 91 Start: 35 End: 64 ..................................TTTGAATTTTAATTCAATACATGTTATAAT.............................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtcacactgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1516:SMT_1517|SMT_1516:SMT_1517:K02029 polar amino acid transport system permease protein:hypothetical protein predicted by Glimmer/Critica:<-->:1498263..1498452 190 agtcacactgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: smit_SMT_1516_SMT_1517|K02029 polar amino acid transport system permease protein:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:POSITIVE|[1498263,1498452]|190 HSP 1 e-value: 1.0E-104 bit: 377.0 Len: 190 Query Start:1 Query End:190 Subject Strand: POSITIVE Subject Start: 1 Subject End: 190 agtcacactgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa agtcacactgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa Inter-species Hit: Count: 3 Min: 1 Max: 190 Len: 190 Subject: NC_008533_SPD_0718_SPD_0719|hypothetical protein:amino acid ABC transporter, permease protein|NEGATIVE:POSITIVE|[734195,734383]|189 HSP 1 e-value: 1.0E-72 bit: 274.0 Len: 190 Query Start:1 Query End:190 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 189 agtcacactgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa agtcacactgctttctaaaatagaatactgtatgattataacatgttttgaattaaaatttaaattttttatccaatttatttaaaaatc-tttaaactagcagaattagcgagaaatcttagttttttctagtcaagttggcctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa Subject: NC_003098_spr0726_spr0727|hypothetical protein:ABC transporter membrane-spanning permease - glutamine transport|NEGATIVE:POSITIVE|[726664,726846]|183 HSP 1 e-value: 4.0E-69 bit: 262.0 Len: 184 Query Start:7 Query End:190 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 183 ......actgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa ......actgctttctaaaatagaatactgtatgattataacatgttttgaattaaaatttaaattttttatccaatttatttaaaaatc-tttaaactagcagaattagcgagaaatcttagttttttctagtcaagttggcctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa Subject: NC_003028_SP_0822_SP_0823|hypothetical protein:amino acid ABC transporter, permease protein|NEGATIVE:POSITIVE|[772976,773158]|183 HSP 1 e-value: 9.0E-67 bit: 254.0 Len: 184 Query Start:7 Query End:190 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 183 ......actgctttctaaaatagaatactgtatgattataacatgtattgaattaaaattcaaatcttttgtctaatttattcaaaaaacctttaagctagtagaattagcgagaaatcttagttttttctaggcaagttgacctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa ......actgctttctaaaatagaatactgtatgattataacatgttttgaattaaaatttaaattttttatccaatttatttaaaaata-tttaaactagcagaattagcgagaaatcttagttttttctagtcaagttggcctcctttatggtaaaatagtaacgataagaaatgaaggagaatcaaa Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCACACUGCUUUCUAAAAUAGAAUACUGUAUGAUUAUAACAUGUAUUGAAUUAAAAUUCAAAUCUUUUGUCUAAUUUAUUCAAAAAACCUUUAAGCUAGUAGAAUUAGCGAGAAAUCUUAGUUUUUUCUAGGCAAGUUGACCUCCUUUAUGGUAAAAUAGUAACGAUAAGAAAUGAAGGAGAAUCAAA (((((.((.(..(((((...)))))..).)).)))))..........((((((....)))))).....(((((((........(((((((......((((((...))))))((....))...))))))).))))))).((((.(((((((((......................)))))))))..)))). (-31.15) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGAUUCUCCUUCAUUUCUUAUCGUUACUAUUUUACCAUAAAGGAGGUCAACUUGCCUAGAAAAAACUAAGAUUUCUCGCUAAUUCUACUAGCUUAAAGGUUUUUUGAAUAAAUUAGACAAAAGAUUUGAAUUUUAAUUCAAUACAUGUUAUAAUCAUACAGUAUUCUAUUUUAGAAAGCAGUGUGACU .((((......((((..((((...((..(((.((((......((((((....))).)))..((((((((.((....)).((((.......)))).....))))))))...)))).)))))..))))..)))).......))))............((((((.((.(((((...))))).)).)))))).. (-28.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 787 140 91 231 182 smit:SMT_1516|5end_K02029_polar_amino_acid_transport_system_permease_protein_1498172..1498402_NEGATIVE 312 184 143 207 161 smit:SMT_954|5end_cation-transporting_ATPase,_E1-E2_family_904025..904255_NEGATIVE 286 155 111 108 54 smit:SMT_346|5end_K01992_ABC-2_type_transport_system_permease_protein_284720..284950_POSITIVE 256 190 144 92 47 smit:SMT_1799|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1773416..1773646_POSITIVE 250 150 110 106 63 smit:SMT_362|5end_K02519_translation_initiation_factor_IF-2_296230..296460_POSITIVE 247 189 144 91 47 smit:SMT_2018|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1936760..1936990_POSITIVE 247 142 102 150 107 smit:SMT_318|5end_hypothetical_protein_258282..258512_NEGATIVE 246 150 110 106 60 smit:SMT_669|5end_ribose-phosphate_pyrophosphokinase_578160..578390_POSITIVE 242 126 90 195 159 smit:SMT_2105|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1996458..1996688_POSITIVE 242 180 132 224 165 smit:SMT_782|5end_GMP_synthase_694519..694749_NEGATIVE 239 159 116 110 71 smit:SMT_1352|5end_formamidopyrimidine-DNA_glycosylase_1330641..1330871_NEGATIVE 229 150 106 104 60 smit:SMT_1388|5end_hypothetical_protein_1365214..1365444_POSITIVE 227 183 152 154 122 smit:SMT_703|5end_hypothetical_protein_612345..612575_POSITIVE 224 110 65 124 72 smit:SMT_1103|5end_hypothetical_protein_1045744..1045974_NEGATIVE 221 156 111 95 44 smit:SMT_1949|5end_IS1381_transposase_protein_B_1883518..1883748_POSITIVE 221 159 111 193 142 smit:SMT_981|5end_hypothetical_protein_928709..928939_POSITIVE 220 140 101 162 125 smit:SMT_1744|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1725288..1725518_NEGATIVE 219 155 111 230 185 smit:SMT_1409|5end_hypothetical_protein_1388514..1388744_NEGATIVE 218 148 102 103 47 smit:SMT_482|5end_hypothetical_protein_predicted_by_Glimmer/Critica_418536..418766_NEGATIVE 218 148 102 103 47 smit:SMT_470|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_407303..407533_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 155 111 111 57 smit:SMT_345|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_284803..284953_POSITIVE 250 150 110 89 46 smit:SMT_361|3end_hypothetical_protein_296293..296443_POSITIVE 247 142 102 128 85 smit:SMT_319|3end_K02356_elongation_factor_EF-P_258304..258454_NEGATIVE 239 159 116 61 22 smit:SMT_1353|3end_GTP-binding_protein_1330690..1330840_NEGATIVE 229 150 106 47 3 smit:SMT_1387|3end_hypothetical_protein_1365237..1365387_POSITIVE 225 170 125 83 35 smit:SMT_801|3end_glycyl-tRNA_synthetase_alpha_chain_709892..710042_NEGATIVE 224 110 65 73 21 smit:SMT_1104|3end_K06346_spoIIIJ-associated_protein_1045795..1045945_NEGATIVE 221 156 111 78 27 smit:SMT_1948|3end_IS1381_transposase_protein_A_1883581..1883731_POSITIVE 220 146 103 123 73 smit:SMT_363|3end_K02519_translation_initiation_factor_IF-2_300751..300901_POSITIVE 215 154 111 110 65 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 210 144 117 105 77 smit:SMT_442|3end_transcriptional_regulator,_putative_382400..382550_POSITIVE 208 170 122 136 84 smit:SMT_770|3end_K02053_spermidine/putrescine_transport_system_permease_protein_680586..680736_NEGATIVE 205 140 97 139 89 smit:SMT_1982|3end_conserved_hypothetical_protein_1913412..1913562_POSITIVE 204 169 129 44 1 smit:SMT_1444|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1427887..1428037_NEGATIVE 204 125 88 148 116 smit:SMT_960|3end_putative_esterase_906126..906276_NEGATIVE 203 147 107 52 12 smit:SMT_1903|3end_hypothetical_protein_1853195..1853345_POSITIVE 200 143 109 82 47 smit:SMT_930|3end_ATP-dependent_RNA_helicase_883389..883539_NEGATIVE 200 147 110 136 104 smit:SMT_790|3end_hypothetical_protein_701093..701243_NEGATIVE 200 156 111 136 81 smit:SMT_727|3end_phage_transcriptional_repressor_631830..631980_NEGATIVE 199 106 68 130 94 smit:SMT_692|3end_hypothetical_protein_603008..603158_NEGATIVE