Origin IGS: gagactagttaaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagttttgaaacagtatcactctacttgaaatatacatagaaaaagcgcataacccttaaaataagctgaaatctagtgaaaatgtacggtaaacaattgaaaaactagcctataaagtggtacaatggtagaaaaatactatagtaagagtctatcttatttagcaaaaattacagaaatgaatggtttttc .........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 gaaaaaccattcatttctgtaatttttgctaaataagatagactcttactatagtatttttctaccattgtaccactttataggctagtttttcaattgtttaccgtacattttcactagatttcagcttattttaagggttatgcgctttttctatgtatatttcaagtagagtgatactgtttcaaaactccatttcatgagaaaatgaaggaaatcttcccataataaaacgcacgatatcaagttttttcaacacctgatactatgcgatttgctgatttttaaagactttttaactagtctc Mask Tandem Repeat Region ================================================ gagactagttaaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagttttgaaacagtatcactctacttgaaatatacatagaaaaagcgcataacccttaaaataagctgaaatctagtgaaaatgtacggtaaacaattgaaaaactagcctataaagtggtacaatggtagaaaaatactatagtaagagtctatcttatttagcaaaaattacagaaatgaatggtttttc Find is-nt database================================================ Query_seq: SMT_1308:SMT_1309|SMT_1308:SMT_1309:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:->->:1273915..1274221 307 gagactagttaaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagttttgaaacagtatcactctacttgaaatatacatagaaaaagcgcataacccttaaaataagctgaaatctagtgaaaatgtacggtaaacaattgaaaaactagcctataaagtggtacaatggtagaaaaatactatagtaagagtctatcttatttagcaaaaattacagaaatgaatggtttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1308:SMT_1309|SMT_1308:SMT_1309:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:->->:1273915..1274221 307 gagactagttaaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagttttgaaacagtatcactctacttgaaatatacatagaaaaagcgcataacccttaaaataagctgaaatctagtgaaaatgtacggtaaacaattgaaaaactagcctataaagtggtacaatggtagaaaaatactatagtaagagtctatcttatttagcaaaaattacagaaatgaatggtttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1308:SMT_1309|SMT_1308:SMT_1309:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:->->:1273915..1274221 307 gagactagttaaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagttttgaaacagtatcactctacttgaaatatacatagaaaaagcgcataacccttaaaataagctgaaatctagtgaaaatgtacggtaaacaattgaaaaactagcctataaagtggtacaatggtagaaaaatactatagtaagagtctatcttatttagcaaaaattacagaaatgaatggtttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagactagttaaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagttttgaaacagtatcactctacttgaaatatacatagaaaaagcgcataacccttaaaataagctgaaatctagtgaaaatgtacggtaaacaattgaaaaactagcctataaagtggtacaatggtagaaaaatactatagtaagagtctatcttatttagcaaaaattacagaaatgaatggtttttc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 62 End: 151 ............................................................. M I S C V L L W E D F L H F L M K W S F E T V S L Y L K Y T ............................................................................................................................................................ gagactagttaaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagttttgaaacagtatcactctacttgaaatatacatagaaaaagcgcataacccttaaaataagctgaaatctagtgaaaatgtacggtaaacaattgaaaaactagcctataaagtggtacaatggtagaaaaatactatagtaagagtctatcttatttagcaaaaattacagaaatgaatggtttttc 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================================================ gagactagttaaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagttttgaaacagtatcactctacttgaaatatacatagaaaaagcgcataacccttaaaataagctgaaatctagtgaaaatgtacggtaaacaattgaaaaactagcctataaagtggtacaatggtagaaaaatactatagtaagagtctatcttatttagcaaaaattacagaaatgaatggtttttc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 80 HP_score: -6.8 Tail_Score: -4.77165 Start: 36 End: 74 Full_Region: TAAAAATCAGCAAAT CGCATAGTATCAGGTGTT GAA AAAACTTGATATCGTGCG TTTTATTATGGGAAG ...................................CGCATAGTATCAGGTGTTGAAAAAACTTGATATCGTGCG......................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 47 HP_score: -3.4 Tail_Score: -3.27674 Start: 86 End: 98 Full_Region: TGCGTTTTATTATGG GAAG ATTTC CTTC ATTTTCTCATGAAAT .....................................................................................GAAGATTTCCTTC................................................................................................................................................................................................................. TransTerm Strand: + Conf: 48 HP_score: -2.9 Tail_Score: -3.54459 Start: 260 End: 274 Full_Region: AGAAAAATACTATAG TAAGA GTCTA TCTTA TTTAGCAAAAATTAC ...................................................................................................................................................................................................................................................................TAAGAGTCTATCTTA................................. Find igs database================================================ Query_seq: SMT_1308:SMT_1309|SMT_1308:SMT_1309:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:->->:1273915..1274221 307 gagactagttaaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagttttgaaacagtatcactctacttgaaatatacatagaaaaagcgcataacccttaaaataagctgaaatctagtgaaaatgtacggtaaacaattgaaaaactagcctataaagtggtacaatggtagaaaaatactatagtaagagtctatcttatttagcaaaaattacagaaatgaatggtttttc Intra-Species Hit: Count: 1 Min: 1 Max: 307 Len: 307 Subject: smit_SMT_1308_SMT_1309|hypothetical protein:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[1273915,1274221]|307 HSP 1 e-value: 1.0E-173 bit: 609.0 Len: 307 Query Start:1 Query End:307 Subject Strand: POSITIVE Subject Start: 1 Subject End: 307 gagactagttaaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagttttgaaacagtatcactctacttgaaatatacatagaaaaagcgcataacccttaaaataagctgaaatctagtgaaaatgtacggtaaacaattgaaaaactagcctataaagtggtacaatggtagaaaaatactatagtaagagtctatcttatttagcaaaaattacagaaatgaatggtttttc gagactagttaaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagttttgaaacagtatcactctacttgaaatatacatagaaaaagcgcataacccttaaaataagctgaaatctagtgaaaatgtacggtaaacaattgaaaaactagcctataaagtggtacaatggtagaaaaatactatagtaagagtctatcttatttagcaaaaattacagaaatgaatggtttttc Inter-species Hit: Count: 5 Min: 8 Max: 307 Len: 300 Subject: NC_008533_SPD_2006_SPD_2007|hypothetical protein:transporter, major facilitator family protein|NEGATIVE:NEGATIVE|[1981671,1981983]|313 HSP 1 e-value: 2.0E-87 bit: 323.0 Len: 300 Query Start:8 Query End:307 Subject Strand: NEGATIVE Subject Start: 4 Subject End: 306 .......gttaaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagttttgaaacagtatcactctacttg-aaatatacatagaaaaagcgcataacccttaaaataagctgaaatctagtgaaaatgtacggtaaacaattgaaaaactagcctataaagtggtacaatggtagaaaaatactatagtaagagtctatctta-tttagc-aaaaattacagaaatgaatggtttttc .......gttaaaaagtctttaaaaatcagaaaagcgcatagtatcaggtgttgaaaaaacttgatattgtgtgttttattatgggaagatttacttcattgtctcctgaaatggagttttgaagcaggatcactctatttgaaaatatacatagaaaaactgtataatccttaaaataagctgaaatctattggaaacatacggtaaacaattgaaaagatactatataaagtggtacaatggtagaaaaataagctagtaagaatcactcttattttagcgaaaaattacagaaatgaatggtttttc Subject: NC_003098_spr1982_spr1983|D-alanine--D-alanyl carrier protein ligase:hypothetical protein|NEGATIVE:NEGATIVE|[1973933,1974481]|549 HSP 1 e-value: 2.0E-87 bit: 323.0 Len: 300 Query Start:8 Query End:307 Subject Strand: NEGATIVE Subject Start: 240 Subject End: 542 .......gttaaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagttttgaaacagtatcactctacttg-aaatatacatagaaaaagcgcataacccttaaaataagctgaaatctagtgaaaatgtacggtaaacaattgaaaaactagcctataaagtggtacaatggtagaaaaatactatagtaagagtctatctta-tttagc-aaaaattacagaaatgaatggtttttc .......gttaaaaagtctttaaaaatcagaaaagcgcatagtatcaggtgttgaaaaaacttgatattgtgtgttttattatgggaagatttacttcattgtctcctgaaatggagttttgaagcaggatcactctatttgaaaatatacatagaaaaactgtataatccttaaaataagctgaaatctattggaaacatacggtaaacaattgaaaagatactatataaagtggtacaatggtagaaaaataagctagtaagaatcactcttattttagcgaaaaattacagaaatgaatggtttttc Subject: NC_003028_SP_1427_SP_1428|peptidase, U32 family:hypothetical protein|NEGATIVE:NEGATIVE|[1346713,1346960]|248 HSP 1 e-value: 1.0E-20 bit: 101.0 Len: 111 Query Start:11 Query End:121 Subject Strand: POSITIVE Subject Start: 113 Subject End: 222 ..........aaaaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagtttt.......................................................................................................................................................................................... ..........aaaaagtctttaaaa-tcttaaaaacgcatagtatcaggtattgaacaatcttgatattatgcgttttattgtgggaagatttacttcattttctcttgaaattgagtttt.......................................................................................................................................................................................... Subject: NC_008533_SPD_1996_SPD_1997|fucose operon repressor, putative:zinc ABC transporter, zinc-binding lipoprotein|POSITIVE:NEGATIVE|[1972472,1973599]|1128 HSP 1 e-value: 3.0E-12 bit: 73.8 Len: 109 Query Start:13 Query End:121 Subject Strand: NEGATIVE Subject Start: 205 Subject End: 311 ............aaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagtttt.......................................................................................................................................................................................... ............aaagtctttaaaa-tcaaaaaaacgcataatatcaggtgt-gcaaaaacttgatactatgcgttttattgtgggaaggtttactccattttctcctgaaattgagtttt.......................................................................................................................................................................................... Subject: NC_003098_spr1974_spr1975|Regulator of fucose operon:ABC transporter substrate-binding protein - Zinc (Zn2+) transport|POSITIVE:NEGATIVE|[1964970,1966097]|1128 HSP 1 e-value: 3.0E-12 bit: 73.8 Len: 109 Query Start:13 Query End:121 Subject Strand: NEGATIVE Subject Start: 205 Subject End: 311 ............aaagtctttaaaaatcagcaaatcgcatagtatcaggtgttgaaaaaacttgatatcgtgcgttttattatgggaagatttccttcattttctcatgaaatggagtttt.......................................................................................................................................................................................... ............aaagtctttaaaa-tcaaaaaaacgcataatatcaggtgt-gcaaaaacttgatactatgcgttttattgtgggaaggtttactccattttctcctgaaattgagtttt.......................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUAAAAAGUCUUUAAAAAUCAGCAAAUCGCAUAGUAUCAGGUGUUGAAAAAACUUGAUAUCGUGCGUUUUAUUAUGGGAAGAUUUCCUUCAUUUUCUCAUGAAAUGGAGUUUUGAAACAGUAUCACUCUACUUGAAAUAUACAUAGAAAAAGCGCAUAACCCUUAAAAUAAGCUGAAAUCUAGUGAAAAUGUACGGUAAACAAUUGAAAAACUAGCCUAUAAAGUGGUACAAUGGUAGAAAAAUACUAUAGUAAGAGUCUAUCUUAUUUAGCAAAAAUUACAGAAAUGAAUGGUUUUUC ((((((..((.(((((((.((...(((.((((..(((((((((.((....)))))))))))..)))).))).((((((((((((.......))))))))))))....)).))))))))).((((((((............(((.((((...(((..................)))....)))))))....((((.(((.................))))))).))))))))...((((((....(((....)))....))))))...)))))).(((((((((....))..))))))).. (-61.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAACCAUUCAUUUCUGUAAUUUUUGCUAAAUAAGAUAGACUCUUACUAUAGUAUUUUUCUACCAUUGUACCACUUUAUAGGCUAGUUUUUCAAUUGUUUACCGUACAUUUUCACUAGAUUUCAGCUUAUUUUAAGGGUUAUGCGCUUUUUCUAUGUAUAUUUCAAGUAGAGUGAUACUGUUUCAAAACUCCAUUUCAUGAGAAAAUGAAGGAAAUCUUCCCAUAAUAAAACGCACGAUAUCAAGUUUUUUCAACACCUGAUACUAUGCGAUUUGCUGAUUUUUAAAGACUUUUUAAC ...............(((..((..((.((.....(((((...........((((((((.((((((......(((.(((.((((((((((((......(((.......)))........)))))..)))))))...))))))((((((.........))))))......)))))).))))))))........(((..(((((......)))))))).)))))............((((.(.(((((.((.........)).))))).).))))....)).))..))...)))......... (-43.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 418 100 54 201 154 smit:SMT_734|5end_hypothetical_protein_639967..640197_POSITIVE 292 67 22 201 150 smit:SMT_1738|5end_peptidyl-prolyl_cis-trans_isomerase_1720497..1720727_POSITIVE 271 177 137 58 20 smit:SMT_894|5end_hypothetical_protein_841701..841931_NEGATIVE 256 90 41 102 59 smit:SMT_854|5end_hypothetical_protein_799492..799722_NEGATIVE 252 101 62 72 35 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 252 101 62 72 35 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 250 110 61 183 124 smit:SMT_556|5end_putative_aminotransferase_473544..473774_POSITIVE 245 170 124 119 66 smit:SMT_1519|5end_DNA-binding_response_regulator_VncR_1499662..1499892_NEGATIVE 244 110 61 142 88 smit:SMT_1898|5end_aminotransferase_(class_V),_putative_1849929..1850159_NEGATIVE 239 110 66 229 177 smit:SMT_919|5end_hypothetical_protein_872499..872729_NEGATIVE 239 257 213 80 23 smit:SMT_809|5end_sensor_histidine_kinase_(homolog_to_BlpH_Spn)_719745..719975_NEGATIVE 236 69 23 221 176 smit:SMT_430|5end_hypothetical_protein_371830..372060_POSITIVE 232 110 65 115 64 smit:SMT_2089|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_related_enzyme_1984987..1985217_POSITIVE 232 140 91 156 94 smit:SMT_1801|5end_heavy_metal_translocating_P-type_ATPase_1773916..1774146_POSITIVE 232 110 65 115 64 smit:SMT_291|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_234197..234427_POSITIVE 231 120 78 128 92 smit:SMT_1322|5end_K02075_zinc/manganese_transport_system_permease_protein_1291371..1291601_POSITIVE 230 69 21 170 123 smit:SMT_1871|5end_modification_methylase,_HemK_family_1830501..1830731_NEGATIVE 227 110 61 153 88 smit:SMT_1159|5end_hypothetical_protein_1104544..1104774_NEGATIVE 226 120 78 188 144 smit:SMT_848|5end_hypothetical_protein_795153..795383_NEGATIVE 226 98 56 112 59 smit:SMT_198|5end_50S_ribosomal_protein_L17_128632..128862_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 496 80 31 74 27 smit:SMT_937|3end_dipeptidase_890741..890891_POSITIVE 395 50 5 60 15 smit:SMT_735|3end_putative_transposase,_ISSmu1_641395..641545_POSITIVE 355 70 29 70 29 smit:SMT_779|3end_ribonuclease_BN,_putative_687883..688033_NEGATIVE 332 115 79 75 39 smit:SMT_1019|3end_K03295_cation_efflux_system_protein,_CDF_family_954782..954932_NEGATIVE 323 87 50 42 7 smit:SMT_618|3end_methionine_aminopeptidase_527637..527787_POSITIVE 315 127 81 146 99 smit:SMT_1994|3end_phosphoglycerate_mutase_1920058..1920208_NEGATIVE 315 127 81 146 99 smit:SMT_201|3end_phosphoglycerate_mutase_132101..132251_POSITIVE 300 70 22 77 29 smit:SMT_778|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_687834..687984_POSITIVE 297 102 75 81 56 smit:SMT_2062|3end_phosphoglycerate_mutase_1970913..1971063_NEGATIVE 271 177 137 65 27 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE 262 77 31 62 17 smit:SMT_1615|3end_K02016_iron_complex_transport_system_substrate-binding_protein_1601734..1601884_NEGATIVE 257 89 41 48 2 smit:SMT_1467|3end_hydroxyacylglutathione_hydrolase_1448004..1448154_NEGATIVE 256 90 41 102 59 smit:SMT_855|3end_dihydrofolate_reductase_799492..799642_NEGATIVE 246 70 29 58 19 smit:SMT_938|3end_hypothetical_protein_890813..890963_NEGATIVE 239 110 66 140 88 smit:SMT_920|3end_serine/threonine_protein_kinase_872588..872738_NEGATIVE 232 110 65 114 63 smit:SMT_2088|3end_glucose-1-phosphate_thymidylyltransferase_1985066..1985216_POSITIVE 232 110 65 114 63 smit:SMT_290|3end_glucose-1-phosphate_thymidylyltransferase_234276..234426_POSITIVE 231 120 78 135 99 smit:SMT_1321|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1291458..1291608_POSITIVE 230 100 54 62 12 smit:SMT_1554|3end_isoleucyl-tRNA_synthetase_1539912..1540062_POSITIVE 229 108 63 79 28 smit:SMT_899|3end_5,10-methylenetetrahydrofolate_reductase_847397..847547_NEGATIVE