Origin IGS: aaaaaacacctccatattttcaatcattaattttttaataatttgtacaaaattttatgtagtttttaattaagtcactagtatattgttaataaactacttttgttattttattttaacataaaaagaatactattacaagagagaataattgacaaagtctgaaaaatatggtagaattctttggcgttaaataatcacatcaattatttctaagcatggtgttctagtttttaacttagatggcttagttttgagattgatggaagaataaccaaatttaaaattttaggaggaaaaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttcctcctaaaattttaaatttggttattcttccatcaatctcaaaactaagccatctaagttaaaaactagaacaccatgcttagaaataattgatgtgattatttaacgccaaagaattctaccatatttttcagactttgtcaattattctctcttgtaatagtattctttttatgttaaaataaaataacaaaagtagtttattaacaatatactagtgacttaattaaaaactacataaaattttgtacaaattattaaaaaattaatgattgaaaatatggaggtgtttttt Mask Tandem Repeat Region ================================================ aaaaaacacctccatattttcaatcattaattttttaataatttgtacaaaattttatgtagtttttaattaagtcactagtatattgttaataaactacttttgttattttattttaacataaaaagaatactattacaagagagaataattgacaaagtctgaaaaatatggtagaattctttggcgttaaataatcacatcaattatttctaagcatggtgttctagtttttaacttagatggcttagttttgagattgatggaagaataaccaaatttaaaattttaggaggaaaaa Find is-nt database================================================ Query_seq: FN1619:FN1620|FN1619:FN1620:Hypothetical cytosolic protein:30S ribosomal protein S2:<-->:127735..128035 301 aaaaaacacctccatattttcaatcattaattttttaataatttgtacaaaattttatgtagtttttaattaagtcactagtatattgttaataaactacttttgttattttattttaacataaaaagaatactattacaagagagaataattgacaaagtctgaaaaatatggtagaattctttggcgttaaataatcacatcaattatttctaagcatggtgttctagtttttaacttagatggcttagttttgagattgatggaagaataaccaaatttaaaattttaggaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1619:FN1620|FN1619:FN1620:Hypothetical cytosolic protein:30S ribosomal protein S2:<-->:127735..128035 301 aaaaaacacctccatattttcaatcattaattttttaataatttgtacaaaattttatgtagtttttaattaagtcactagtatattgttaataaactacttttgttattttattttaacataaaaagaatactattacaagagagaataattgacaaagtctgaaaaatatggtagaattctttggcgttaaataatcacatcaattatttctaagcatggtgttctagtttttaacttagatggcttagttttgagattgatggaagaataaccaaatttaaaattttaggaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1619:FN1620|FN1619:FN1620:Hypothetical cytosolic protein:30S ribosomal protein S2:<-->:127735..128035 301 aaaaaacacctccatattttcaatcattaattttttaataatttgtacaaaattttatgtagtttttaattaagtcactagtatattgttaataaactacttttgttattttattttaacataaaaagaatactattacaagagagaataattgacaaagtctgaaaaatatggtagaattctttggcgttaaataatcacatcaattatttctaagcatggtgttctagtttttaacttagatggcttagttttgagattgatggaagaataaccaaatttaaaattttaggaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaaacacctccatattttcaatcattaattttttaataatttgtacaaaattttatgtagtttttaattaagtcactagtatattgttaataaactacttttgttattttattttaacataaaaagaatactattacaagagagaataattgacaaagtctgaaaaatatggtagaattctttggcgttaaataatcacatcaattatttctaagcatggtgttctagtttttaacttagatggcttagttttgagattgatggaagaataaccaaatttaaaattttaggaggaaaaa Predict ORF larger than 30AA ================================================ aaaaaacacctccatattttcaatcattaattttttaataatttgtacaaaattttatgtagtttttaattaagtcactagtatattgttaataaactacttttgttattttattttaacataaaaagaatactattacaagagagaataattgacaaagtctgaaaaatatggtagaattctttggcgttaaataatcacatcaattatttctaagcatggtgttctagtttttaacttagatggcttagttttgagattgatggaagaataaccaaatttaaaattttaggaggaaaaa 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: 151 End: 180 ......................................................................................................................................................ATTGACAAAGTCTGAAAAATATGGTAGAAT......................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 87 Start: 113 End: 142 ................................................................................................................CTTGTAATAGTATTCTTTTTATGTTAAAAT............................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 130 End: 159 .................................................................................................................................TTTGTCAATTATTCTCTCTTGTAATAGTAT.............................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaaacacctccatattttcaatcattaattttttaataatttgtacaaaattttatgtagtttttaattaagtcactagtatattgttaataaactacttttgttattttattttaacataaaaagaatactattacaagagagaataattgacaaagtctgaaaaatatggtagaattctttggcgttaaataatcacatcaattatttctaagcatggtgttctagtttttaacttagatggcttagttttgagattgatggaagaataaccaaatttaaaattttaggaggaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1619:FN1620|FN1619:FN1620:Hypothetical cytosolic protein:30S ribosomal protein S2:<-->:127735..128035 301 aaaaaacacctccatattttcaatcattaattttttaataatttgtacaaaattttatgtagtttttaattaagtcactagtatattgttaataaactacttttgttattttattttaacataaaaagaatactattacaagagagaataattgacaaagtctgaaaaatatggtagaattctttggcgttaaataatcacatcaattatttctaagcatggtgttctagtttttaacttagatggcttagttttgagattgatggaagaataaccaaatttaaaattttaggaggaaaaa Intra-Species Hit: Count: 1 Min: 74 Max: 301 Len: 228 Subject: NC_003454_FN1619_FN1620|Hypothetical cytosolic protein:30S ribosomal protein S2|NEGATIVE:POSITIVE|[127735,128035]|301 HSP 1 e-value: 1.0E-126 bit: 452.0 Len: 228 Query Start:74 Query End:301 Subject Strand: POSITIVE Subject Start: 74 Subject End: 301 .........................................................................gtcactagtatattgttaataaactacttttgttattttattttaacataaaaagaatactattacaagagagaataattgacaaagtctgaaaaatatggtagaattctttggcgttaaataatcacatcaattatttctaagcatggtgttctagtttttaacttagatggcttagttttgagattgatggaagaataaccaaatttaaaattttaggaggaaaaa .........................................................................gtcactagtatattgttaataaactacttttgttattttattttaacataaaaagaatactattacaagagagaataattgacaaagtctgaaaaatatggtagaattctttggcgttaaataatcacatcaattatttctaagcatggtgttctagtttttaacttagatggcttagttttgagattgatggaagaataaccaaatttaaaattttaggaggaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCACUAGUAUAUUGUUAAUAAACUACUUUUGUUAUUUUAUUUUAACAUAAAAAGAAUACUAUUACAAGAGAGAAUAAUUGACAAAGUCUGAAAAAUAUGGUAGAAUUCUUUGGCGUUAAAUAAUCACAUCAAUUAUUUCUAAGCAUGGUGUUCUAGUUUUUAACUUAGAUGGCUUAGUUUUGAGAUUGAUGGAAGAAUAACCAAAUUUAAAAUUUUAGGAGGAAAAA .((.((((....((((((((...((.(((((((.((..((((((.........))))))..)).)))))))))....))))))))........((((.((((...(((((((...............((((((((....((((((.......(((((........)))))..))))))......))))))))))))))).)))).))))......))))))....... (-38.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCCUCCUAAAAUUUUAAAUUUGGUUAUUCUUCCAUCAAUCUCAAAACUAAGCCAUCUAAGUUAAAAACUAGAACACCAUGCUUAGAAAUAAUUGAUGUGAUUAUUUAACGCCAAAGAAUUCUACCAUAUUUUUCAGACUUUGUCAAUUAUUCUCUCUUGUAAUAGUAUUCUUUUUAUGUUAAAAUAAAAUAACAAAAGUAGUUUAUUAACAAUAUACUAGUGAC ..........................((((((..(((((((((.......((((((..((((.((.....)))))).......)))))).....))))))).))...(((((((..(((((((.(((............(((...)))..((((........))))))).)))))))...)))))))....))))))...(.((((.(((.....))).)))).)... (-28.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 618 50 1 214 165 NC_003454:FN1619|5end_Hypothetical_cytosolic_protein_127644..127874_NEGATIVE 230 173 136 189 146 NC_003454:FN1872|5end_hypothetical_protein_363043..363273_NEGATIVE 225 166 133 201 165 NC_003454:FN2122|5end_Phenylalanyl-tRNA_synthetase_beta_chain_632194..632424_NEGATIVE 216 180 137 206 163 NC_003454:FN1108|5end_Phosphohydrolase_(MUTT/NUDIX_family_protein)_1752310..1752540_POSITIVE 214 186 143 69 20 NC_003454:FN0497|5end_Plasmid_addiction_system_poison_protein_1141133..1141363_POSITIVE 209 122 83 165 127 NC_003454:FN1329|5end_Methyltransferase_1983890..1984120_NEGATIVE 208 176 131 197 147 NC_003454:FN0578|5end_ATP-dependent_DNA_helicase_recQ_1227941..1228171_POSITIVE 203 194 155 222 182 NC_003454:FN1606|5end_3-deoxy-D-manno-octulosonic-acid_transferase_117208..117438_NEGATIVE 200 130 81 102 52 NC_003454:FN1087|5end_hypothetical_protein_1730958..1731188_POSITIVE 198 175 134 129 79 NC_003454:FN1348|5end_ABC_transporter_ATP-binding_protein_2001141..2001371_NEGATIVE 198 180 133 56 3 NC_003454:FN0828|5end_ABC_transporter_permease_protein_1488199..1488429_POSITIVE 198 163 133 106 77 NC_003454:FN0180|5end_Tetratricopeptide_repeat_family_protein_805322..805552_NEGATIVE 192 168 129 120 83 NC_003454:FN0104|5end_Acetyltransferase_739896..740126_NEGATIVE 191 208 163 157 114 NC_003454:FN2125|5end_DNA_gyrase_subunit_A_636160..636390_NEGATIVE 189 157 111 66 18 NC_003454:FN1378|5end_Citrate_lyase_acyl_carrier_protein_2026062..2026292_POSITIVE 189 176 134 87 43 NC_003454:FN1994|5end_hypothetical_protein_497577..497807_POSITIVE 189 179 135 85 35 NC_003454:FN1742|5end_V-type_sodium_ATP_synthase_subunit_G_240790..241020_NEGATIVE 189 175 131 67 25 NC_003454:FN1614|5end_MG(2+)_chelatase_family_protein_125002..125232_NEGATIVE 188 61 22 87 50 NC_003454:FN1490|5end_4-hydroxybenzoate_octaprenyltransferase_2172283..2172513_NEGATIVE 183 199 156 118 74 NC_003454:FN1411|5end_Threonine_dehydratase_2070730..2070960_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 143 108 146 116 NC_003454:FN1074|3end_Signal_recognition_particle_receptor_FtsY_1722008..1722158_POSITIVE 230 173 136 130 87 NC_003454:FN1873|3end_Bis(5'-nucleosyl)-tetraphosphatase_363102..363252_NEGATIVE 214 186 143 67 18 NC_003454:FN0496|3end_hypothetical_protein_1141211..1141361_POSITIVE 210 162 122 116 83 NC_003454:FN0270|3end_GTP-binding_protein_era_897740..897890_POSITIVE 200 130 81 96 46 NC_003454:FN1086|3end_Transporter_1731032..1731182_POSITIVE 198 175 134 120 70 NC_003454:FN1349|3end_ABC_transporter_permease_protein_2001150..2001300_NEGATIVE 198 180 133 59 6 NC_003454:FN0827|3end_ABC_transporter_ATP-binding_protein_1488282..1488432_POSITIVE 196 121 83 151 114 NC_003454:FN1330|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_1983903..1984053_NEGATIVE 189 157 111 55 7 NC_003454:FN1377|3end_CITG_protein_2026131..2026281_POSITIVE 189 176 134 80 36 NC_003454:FN1993|3end_SUA5_protein_497650..497800_POSITIVE 188 61 22 68 31 NC_003454:FN1491|3end_PTS_system,_IIA_component_2172302..2172452_NEGATIVE 183 196 173 111 89 NC_003454:FN0140|3end_Transposase_772179..772329_NEGATIVE 182 191 155 112 80 NC_003454:FN0275|3end_Transposase_900607..900757_NEGATIVE 178 150 103 148 105 NC_003454:FN2082|3end_Formate--tetrahydrofolate_ligase_593257..593407_NEGATIVE 177 173 135 120 83 NC_003454:FN0438|3end_Branched_chain_amino_acid_transport_system_II_carrier_protein_1079635..1079785_NEGATIVE 176 182 144 59 18 NC_003454:FN1470|3end_hypothetical_protein_2153066..2153216_POSITIVE 169 187 143 86 27 NC_003454:FN1809|3end_Iron/zinc/copper-binding_protein_290180..290330_NEGATIVE 168 176 147 75 42 NC_003454:FN1111|3end_Dipeptide-binding_protein_1754565..1754715_NEGATIVE 168 105 66 70 24 NC_003454:FN1018|3end_hypothetical_protein_1672145..1672295_NEGATIVE 168 158 124 126 93 NC_003454:FN0794|3end_hypothetical_protein_1451840..1451990_NEGATIVE