Origin IGS: gaaatcccaagaagtctatccccctatccttctcttaggataggggatagttctttactgatattctagaaagcacgcaagtgtgtgtgatgccggtggtgccggcacaccctcacttacgtgcttttttgtttgatcactaattcatacttgaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgtcaagtatgaattagtgatcaaacaaaaaagcacgtaagtgagggtgtgccggcaccaccggcatcacacacacttgcgtgctttctagaatatcagtaaagaactatcccctatcctaagagaaggatagggggatagacttcttgggatttc Mask Tandem Repeat Region ================================================ gaaatcccaagaagtctatccccctatccttctcttaggataggggatagttctttactgatattctagaaagcacgcaagtgtgtgtgatgccggtggtgccggcacaccctcacttacgtgcttttttgtttgatcactaattcatacttgaca Find is-nt database================================================ Query_seq: PG0042:PG0043|PG0042:PG0043:serine hydroxymethyltransferase:beta-hexosaminidase:->->:51050..51205 156 gaaatcccaagaagtctatccccctatccttctcttaggataggggatagttctttactgatattctagaaagcacgcaagtgtgtgtgatgccggtggtgccggcacaccctcacttacgtgcttttttgtttgatcactaattcatacttgaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0042:PG0043|PG0042:PG0043:serine hydroxymethyltransferase:beta-hexosaminidase:->->:51050..51205 156 gaaatcccaagaagtctatccccctatccttctcttaggataggggatagttctttactgatattctagaaagcacgcaagtgtgtgtgatgccggtggtgccggcacaccctcacttacgtgcttttttgtttgatcactaattcatacttgaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0042:PG0043|PG0042:PG0043:serine hydroxymethyltransferase:beta-hexosaminidase:->->:51050..51205 156 gaaatcccaagaagtctatccccctatccttctcttaggataggggatagttctttactgatattctagaaagcacgcaagtgtgtgtgatgccggtggtgccggcacaccctcacttacgtgcttttttgtttgatcactaattcatacttgaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaatcccaagaagtctatccccctatccttctcttaggataggggatagttctttactgatattctagaaagcacgcaagtgtgtgtgatgccggtggtgccggcacaccctcacttacgtgcttttttgtttgatcactaattcatacttgaca Predict ORF larger than 30AA ================================================ gaaatcccaagaagtctatccccctatccttctcttaggataggggatagttctttactgatattctagaaagcacgcaagtgtgtgtgatgccggtggtgccggcacaccctcacttacgtgcttttttgtttgatcactaattcatacttgaca 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================================================ gaaatcccaagaagtctatccccctatccttctcttaggataggggatagttctttactgatattctagaaagcacgcaagtgtgtgtgatgccggtggtgccggcacaccctcacttacgtgcttttttgtttgatcactaattcatacttgaca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -18.8 Tail_Score: -5.68438 Start: 73 End: 124 Full_Region: CTGATATTCTAGAAA GCACGCAAGTGTGTGTGATGCCGGT GGT GCCGGCACACCCTCACTTACGTGC TTTTTTGTTTGATCA ........................................................................GCACGCAAGTGTGTGTGATGCCGGTGGTGCCGGCACACCCTCACTTACGTGC................................ TransTerm Strand: - Conf: 100 HP_score: -20.3 Tail_Score: -3.91144 Start: 73 End: 124 Full_Region: tgatcaaacaaaaaa gcacgtaagtgagggtgtgccgg cacca ccggcatcacacacacttgcgtgc tttctagaatatcag ........................................................................gcacgtaagtgagggtgtgccggcaccaccggcatcacacacacttgcgtgc................................ Find igs database================================================ Query_seq: PG0042:PG0043|PG0042:PG0043:serine hydroxymethyltransferase:beta-hexosaminidase:->->:51050..51205 156 gaaatcccaagaagtctatccccctatccttctcttaggataggggatagttctttactgatattctagaaagcacgcaagtgtgtgtgatgccggtggtgccggcacaccctcacttacgtgcttttttgtttgatcactaattcatacttgaca Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: NC_002950_PG0042_PG0043|serine hydroxymethyltransferase:beta- hexosaminidase|POSITIVE:POSITIVE|[51050,51205]|156 HSP 1 e-value: 1.0E-83 bit: 309.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 gaaatcccaagaagtctatccccctatccttctcttaggataggggatagttctttactgatattctagaaagcacgcaagtgtgtgtgatgccggtggtgccggcacaccctcacttacgtgcttttttgtttgatcactaattcatacttgaca gaaatcccaagaagtctatccccctatccttctcttaggataggggatagttctttactgatattctagaaagcacgcaagtgtgtgtgatgccggtggtgccggcacaccctcacttacgtgcttttttgtttgatcactaattcatacttgaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAUCCCAAGAAGUCUAUCCCCCUAUCCUUCUCUUAGGAUAGGGGAUAGUUCUUUACUGAUAUUCUAGAAAGCACGCAAGUGUGUGUGAUGCCGGUGGUGCCGGCACACCCUCACUUACGUGCUUUUUUGUUUGAUCACUAAUUCAUACUUGACA .......((((....((((((((.((((((......))))))))))))))....(((.((((...(.((((((((((.(((((.(.(((.((((((.....))))))))).).))))).)))))))))).)....)))).)))......))))... (-64.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCAAGUAUGAAUUAGUGAUCAAACAAAAAAGCACGUAAGUGAGGGUGUGCCGGCACCACCGGCAUCACACACACUUGCGUGCUUUCUAGAAUAUCAGUAAAGAACUAUCCCCUAUCCUAAGAGAAGGAUAGGGGGAUAGACUUCUUGGGAUUUC ..(((((......(((.((((........((((((((((((((.(.(((((((((.....)))))).))).).)))))))))))))).......)))).)))....((((((((((((((......)))))).))))))))....)))))...... (-65.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 425 129 81 193 137 NC_002950:PG0399|5end_lipoprotein,_putative_436237..436467_NEGATIVE 410 115 72 187 137 NC_002950:PG1691|5end_hypothetical_protein_1776484..1776714_NEGATIVE 406 115 77 57 7 NC_002950:PG0401|5end_hypothetical_protein_439306..439536_NEGATIVE 405 136 94 188 139 NC_002950:PG1116|5end_methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase_1188931..1189161_POSITIVE 388 108 69 72 33 NC_002950:PG2218|5end_potassium_uptake_protein_TrkA_2331580..2331810_POSITIVE 382 124 85 157 113 NC_002950:PG0086|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_102359..102589_NEGATIVE 377 117 71 229 177 NC_002950:PG1316|5end_hypothetical_protein_1396771..1397001_NEGATIVE 354 116 74 208 158 NC_002950:PG1927|5end_50S_ribosomal_protein_L24_2019557..2019787_NEGATIVE 352 120 72 229 176 NC_002950:PG0488|5end_Holliday_junction_DNA_helicase_RuvB_528169..528399_POSITIVE 344 126 88 105 61 NC_002950:PG1259|5end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_1335465..1335695_NEGATIVE 342 116 72 43 3 NC_002950:PG0633|5end_hypothetical_protein_685301..685531_POSITIVE 341 119 73 132 75 NC_002950:PG0337|5end_hypothetical_protein_371529..371759_NEGATIVE 334 140 94 52 1 NC_002950:PG2002|5end_dihydrodipicolinate_reductase_2091587..2091817_NEGATIVE 334 128 87 187 144 NC_002950:PG1301|5end_hypothetical_protein_1379921..1380151_NEGATIVE 334 106 72 67 21 NC_002950:PG0213|5end_precorrin-3_methylase/precorrin-8X_methylmutase_250464..250694_NEGATIVE 329 125 81 226 168 NC_002950:PG2029|5end_hypothetical_protein_2126543..2126773_POSITIVE 329 112 72 183 139 NC_002950:PG0326|5end_hypothetical_protein_360974..361204_NEGATIVE 327 109 67 123 81 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 326 123 86 65 24 NC_002950:PG2171|5end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_2278972..2279202_NEGATIVE 326 107 72 228 179 NC_002950:PG0597|5end_ribosomal_protein_L9_653662..653892_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 419 126 81 92 32 NC_002950:PG0618|3end_alkyl_hydroperoxide_reductase,_C_subunit_671018..671168_POSITIVE 409 106 62 144 92 NC_002950:PG1692|3end_ABC_transporter,_ATP-binding_protein_1776514..1776664_NEGATIVE 405 136 94 64 15 NC_002950:PG1115|3end_signal_recognition_particle_protein_1188887..1189037_POSITIVE 404 55 11 82 38 NC_002950:PG0042|3end_serine_hydroxymethyltransferase_50989..51139_POSITIVE 396 135 94 146 108 NC_002950:PG0384|3end_MutS2_family_protein_418697..418847_POSITIVE 386 111 72 65 34 NC_002950:PG2063|3end_hypothetical_protein_2160390..2160540_NEGATIVE 351 106 61 141 103 NC_002950:PG0278|3end_hypothetical_protein_310477..310627_POSITIVE 344 126 88 72 28 NC_002950:PG1260|3end_anaerobic_ribonucleoside_triphosphate_reductase_1335498..1335648_NEGATIVE 340 109 66 133 91 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 334 113 73 59 23 NC_002950:PG0231|3end_hypothetical_protein_267409..267559_POSITIVE 331 114 79 69 20 NC_002950:PG0138|3end_malonyl_CoA-acyl_carrier_protein_transacylase_161634..161784_POSITIVE 324 124 83 82 46 NC_002950:PG2050|3end_hypothetical_protein_2149159..2149309_NEGATIVE 324 107 61 76 37 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 322 127 87 151 107 NC_002950:PG1310|3end_exsB_protein_1389826..1389976_POSITIVE 321 105 64 59 15 NC_002950:PG1495|3end_DNA_topoisomerase_III_1573416..1573566_POSITIVE 319 128 84 139 84 NC_002950:PG1027|3end_hypothetical_protein_1089197..1089347_NEGATIVE 317 111 76 151 113 NC_002950:PG1690|3end_Sua5/YciO/YrdC/YwlC_family_protein_1775171..1775321_NEGATIVE 315 117 73 151 110 NC_002950:PG1566|3end_glutamyl-tRNA_synthetase_1645884..1646034_NEGATIVE 314 113 80 99 52 NC_002950:PG1743|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1827530..1827680_NEGATIVE 314 133 94 54 1 NC_002950:PG0990|3end_ribosomal_protein_L35_1051159..1051309_NEGATIVE