Origin IGS: aataagcacctcatgtgtttatagttagatattacatttttatgaacgcaaacgtttgcgctattactagtatagcttattttcttgataaatgcaagcggttttagataactttttttattattttttaaaaaatttttcttcttactcgtatatatattctttcaggaaacaaacaaaataggaataagggtttcacttatctcattaagcaaaaataaagcgagtatcctctctggtttccatttgtaaattaggcaatcgttttctcaactttttttaaatttaaaacaaaacggatttttgggattttctactattatatgacgatgaagcgtttacttttttcacaattttttaaaaaatttttacaaaaaacacttgcaaccgctttccgattgtgctatactagtcccataaaggaaaacgtttgcgtttcctcattataaaatttgttattctttaggaggaatacact .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtgtattcctcctaaagaataacaaattttataatgaggaaacgcaaacgttttcctttatgggactagtatagcacaatcggaaagcggttgcaagtgttttttgtaaaaattttttaaaaaattgtgaaaaaagtaaacgcttcatcgtcatataatagtagaaaatcccaaaaatccgttttgttttaaatttaaaaaaagttgagaaaacgattgcctaatttacaaatggaaaccagagaggatactcgctttatttttgcttaatgagataagtgaaacccttattcctattttgtttgtttcctgaaagaatatatatacgagtaagaagaaaaattttttaaaaaataataaaaaaagttatctaaaaccgcttgcatttatcaagaaaataagctatactagtaatagcgcaaacgtttgcgttcataaaaatgtaatatctaactataaacacatgaggtgcttatt Mask Tandem Repeat Region ================================================ aataagcacctcatgtgtttatagttagatattacatttttatgaacgcaaacgtttgcgctattactagtatagcttattttcttgataaatgcaagcggttttagataactttttttattattttttaaaaaatttttcttcttactcgtatatatattctttcaggaaacaaacaaaataggaataagggtttcacttatctcattaagcaaaaataaagcgagtatcctctctggtttccatttgtaaattaggcaatcgttttctcaactttttttaaatttaaaacaaaacggatttttgggattttctactattatatgacgatgaagcgtttacttttttcacaattttttaaaaaatttttacaaaaaacacttgcaaccgctttccgattgtgctatactagtcccataaaggaaaacgtttgcgtttcctcattataaaatttgttattctttaggaggaatacact Find is-nt database================================================ Query_seq: SMT_1141:SMT_1142|SMT_1141:SMT_1142:4-alpha-glucanotransferase:K02027 multiple sugar transport system substrate-binding protein:<-->:1085208..1085685 478 aataagcacctcatgtgtttatagttagatattacatttttatgaacgcaaacgtttgcgctattactagtatagcttattttcttgataaatgcaagcggttttagataactttttttattattttttaaaaaatttttcttcttactcgtatatatattctttcaggaaacaaacaaaataggaataagggtttcacttatctcattaagcaaaaataaagcgagtatcctctctggtttccatttgtaaattaggcaatcgttttctcaactttttttaaatttaaaacaaaacggatttttgggattttctactattatatgacgatgaagcgtttacttttttcacaattttttaaaaaatttttacaaaaaacacttgcaaccgctttccgattgtgctatactagtcccataaaggaaaacgtttgcgtttcctcattataaaatttgttattctttaggaggaatacact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1141:SMT_1142|SMT_1141:SMT_1142:4-alpha-glucanotransferase:K02027 multiple sugar transport system substrate-binding protein:<-->:1085208..1085685 478 aataagcacctcatgtgtttatagttagatattacatttttatgaacgcaaacgtttgcgctattactagtatagcttattttcttgataaatgcaagcggttttagataactttttttattattttttaaaaaatttttcttcttactcgtatatatattctttcaggaaacaaacaaaataggaataagggtttcacttatctcattaagcaaaaataaagcgagtatcctctctggtttccatttgtaaattaggcaatcgttttctcaactttttttaaatttaaaacaaaacggatttttgggattttctactattatatgacgatgaagcgtttacttttttcacaattttttaaaaaatttttacaaaaaacacttgcaaccgctttccgattgtgctatactagtcccataaaggaaaacgtttgcgtttcctcattataaaatttgttattctttaggaggaatacact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1141:SMT_1142|SMT_1141:SMT_1142:4-alpha-glucanotransferase:K02027 multiple sugar transport system substrate-binding protein:<-->:1085208..1085685 478 aataagcacctcatgtgtttatagttagatattacatttttatgaacgcaaacgtttgcgctattactagtatagcttattttcttgataaatgcaagcggttttagataactttttttattattttttaaaaaatttttcttcttactcgtatatatattctttcaggaaacaaacaaaataggaataagggtttcacttatctcattaagcaaaaataaagcgagtatcctctctggtttccatttgtaaattaggcaatcgttttctcaactttttttaaatttaaaacaaaacggatttttgggattttctactattatatgacgatgaagcgtttacttttttcacaattttttaaaaaatttttacaaaaaacacttgcaaccgctttccgattgtgctatactagtcccataaaggaaaacgtttgcgtttcctcattataaaatttgttattctttaggaggaatacact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aataagcacctcatgtgtttatagttagatattacatttttatgaacgcaaacgtttgcgctattactagtatagcttattttcttgataaatgcaagcggttttagataactttttttattattttttaaaaaatttttcttcttactcgtatatatattctttcaggaaacaaacaaaataggaataagggtttcacttatctcattaagcaaaaataaagcgagtatcctctctggtttccatttgtaaattaggcaatcgttttctcaactttttttaaatttaaaacaaaacggatttttgggattttctactattatatgacgatgaagcgtttacttttttcacaattttttaaaaaatttttacaaaaaacacttgcaaccgctttccgattgtgctatactagtcccataaaggaaaacgtttgcgtttcctcattataaaatttgttattctttaggaggaatacact Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 15 End: 104 .............. M F I V R Y Y I F M N A N V C A I T S I A Y F L D K C K R F ...................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 92 End: 181 ........................................................................................... M Q A V L D N F F Y Y F L K N F S S Y S Y I Y S F R K Q T K ......................................................................................................................................................................................................................................................................................................... Protein_Len: 31 Strand: + Start: 157 End: 249 ............................................................................................................................................................ M F F Q E T N K I G I R V S L I S L S K N K A S I L S G F H L ..................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 261 End: 446 .................................................................................................................................................................................................................................................................... M V F S T F F K F K T K R I F G I F Y Y Y M T M K R L L F S Q F F K K F L Q K T L A T A F R L C Y T S P I K E N V C V S ................................ Protein_Len: 52 Strand: - Start: 3 End: 158 .. L C R M H K Y N S I V N K H V C V N A S N S T Y S I K K I F A L P K L Y S K K N N K L F N K K K S T Y M ................................................................................................................................................................................................................................................................................................................................ aataagcacctcatgtgtttatagttagatattacatttttatgaacgcaaacgtttgcgctattactagtatagcttattttcttgataaatgcaagcggttttagataactttttttattattttttaaaaaatttttcttcttactcgtatatatattctttcaggaaacaaacaaaataggaataagggtttcacttatctcattaagcaaaaataaagcgagtatcctctctggtttccatttgtaaattaggcaatcgttttctcaactttttttaaatttaaaacaaaacggatttttgggattttctactattatatgacgatgaagcgtttacttttttcacaattttttaaaaaatttttacaaaaaacacttgcaaccgctttccgattgtgctatactagtcccataaaggaaaacgtttgcgtttcctcattataaaatttgttattctttaggaggaatacact 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: 84 Start: 381 End: 410 ............................................................................................................................................................................................................................................................................................................................................................................................CTTGCAACCGCTTTCCGATTGTGCTATACT.................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aataagcacctcatgtgtttatagttagatattacatttttatgaacgcaaacgtttgcgctattactagtatagcttattttcttgataaatgcaagcggttttagataactttttttattattttttaaaaaatttttcttcttactcgtatatatattctttcaggaaacaaacaaaataggaataagggtttcacttatctcattaagcaaaaataaagcgagtatcctctctggtttccatttgtaaattaggcaatcgttttctcaactttttttaaatttaaaacaaaacggatttttgggattttctactattatatgacgatgaagcgtttacttttttcacaattttttaaaaaatttttacaaaaaacacttgcaaccgctttccgattgtgctatactagtcccataaaggaaaacgtttgcgtttcctcattataaaatttgttattctttaggaggaatacact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 39 HP_score: -2.2 Tail_Score: -2.67515 Start: 385 End: 401 Full_Region: TACAAAAAACACTTG CAACCG CTTTC CGATTG TGCTATACTAGTCCC ................................................................................................................................................................................................................................................................................................................................................................................................CAACCGCTTTCCGATTG............................................................................. Find igs database================================================ Query_seq: SMT_1141:SMT_1142|SMT_1141:SMT_1142:4-alpha-glucanotransferase:K02027 multiple sugar transport system substrate-binding protein:<-->:1085208..1085685 478 aataagcacctcatgtgtttatagttagatattacatttttatgaacgcaaacgtttgcgctattactagtatagcttattttcttgataaatgcaagcggttttagataactttttttattattttttaaaaaatttttcttcttactcgtatatatattctttcaggaaacaaacaaaataggaataagggtttcacttatctcattaagcaaaaataaagcgagtatcctctctggtttccatttgtaaattaggcaatcgttttctcaactttttttaaatttaaaacaaaacggatttttgggattttctactattatatgacgatgaagcgtttacttttttcacaattttttaaaaaatttttacaaaaaacacttgcaaccgctttccgattgtgctatactagtcccataaaggaaaacgtttgcgtttcctcattataaaatttgttattctttaggaggaatacact Intra-Species Hit: Count: 1 Min: 1 Max: 478 Len: 478 Subject: smit_SMT_1141_SMT_1142|4-alpha-glucanotransferase:K02027 multiple sugar transport system substrate-binding protein|NEGATIVE:POSITIVE|[1085208,1085685]|478 HSP 1 e-value: 6.0E-95 bit: 349.0 Len: 197 Query Start:141 Query End:337 Subject Strand: POSITIVE Subject Start: 141 Subject End: 337 ............................................................................................................................................cttcttactcgtatatatattctttcaggaaacaaacaaaataggaataagggtttcacttatctcattaagcaaaaataaagcgagtatcctctctggtttccatttgtaaattaggcaatcgttttctcaacnnnnnnnaaatttaaaacaaaacggatttttgggattttctactattatatgacgatgaagcg............................................................................................................................................. ............................................................................................................................................cttcttactcgtatatatattctttcaggaaacaaacaaaataggaataagggtttcacttatctcattaagcaaaaataaagcgagtatcctctctggtttccatttgtaaattaggcaatcgttttctcaactttttttaaatttaaaacaaaacggatttttgggattttctactattatatgacgatgaagcg............................................................................................................................................. HSP 2 e-value: 9.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 aataagcacctcatgtgtttatagttagatattacatttttatgaacgcaaacgtttgcgctattactagtatagcttattttcttgataaatgcaagcggttttagataac.............................................................................................................................................................................................................................................................................................................................................................................. aataagcacctcatgtgtttatagttagatattacatttttatgaacgcaaacgtttgcgctattactagtatagcttattttcttgataaatgcaagcggttttagataac.............................................................................................................................................................................................................................................................................................................................................................................. HSP 3 e-value: 1.0E-49 bit: 198.0 Len: 100 Query Start:379 Query End:478 Subject Strand: POSITIVE Subject Start: 379 Subject End: 478 ..........................................................................................................................................................................................................................................................................................................................................................................................cacttgcaaccgctttccgattgtgctatactagtcccataaaggaaaacgtttgcgtttcctcattataaaatttgttattctttaggaggaatacact ..........................................................................................................................................................................................................................................................................................................................................................................................cacttgcaaccgctttccgattgtgctatactagtcccataaaggaaaacgtttgcgtttcctcattataaaatttgttattctttaggaggaatacact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAGCACCUCAUGUGUUUAUAGUUAGAUAUUACAUUUUUAUGAACGCAAACGUUUGCGCUAUUACUAGUAUAGCUUAUUUUCUUGAUAAAUGCAAGCGGUUUUAGAUAACUUUUUUUAUUAUUUUUUAAAAAAUUUUUCUUCUUACUCGUAUAUAUAUUCUUUCAGGAAACAAACAAAAUAGGAAUAAGGGUUUCACUUAUCUCAUUAAGCAAAAAUAAAGCGAGUAUCCUCUCUGGUUUCCAUUUGUAAAUUAGGCAAUCGUUUUCUCAACUUUUUUUAAAUUUAAAACAAAACGGAUUUUUGGGAUUUUCUACUAUUAUAUGACGAUGAAGCGUUUACUUUUUUCACAAUUUUUUAAAAAAUUUUUACAAAAAACACUUGCAACCGCUUUCCGAUUGUGCUAUACUAGUCCCAUAAAGGAAAACGUUUGCGUUUCCUCAUUAUAAAAUUUGUUAUUCUUUAGGAGGAAUACACU .((((((((.....))))))))......................(((((((((((((........(((((((((((.((((.....)))).....((((((((.(((.....(((((.((..(((((((((((((((..............................((((((..........(..(((((.......)))))..)...............((.(((....))).)).))))))....((((((...((.((((((.((((((........((((((..........))))))))))))................))))))...)))))))).........)))))))))))))))...)).)))))....))).)))))))).........))))))))))).((.....)).)))))))))))))(((((....((((...........)))).)))))....... (-91.03) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGUAUUCCUCCUAAAGAAUAACAAAUUUUAUAAUGAGGAAACGCAAACGUUUUCCUUUAUGGGACUAGUAUAGCACAAUCGGAAAGCGGUUGCAAGUGUUUUUUGUAAAAAUUUUUUAAAAAAUUGUGAAAAAAGUAAACGCUUCAUCGUCAUAUAAUAGUAGAAAAUCCCAAAAAUCCGUUUUGUUUUAAAUUUAAAAAAAGUUGAGAAAACGAUUGCCUAAUUUACAAAUGGAAACCAGAGAGGAUACUCGCUUUAUUUUUGCUUAAUGAGAUAAGUGAAACCCUUAUUCCUAUUUUGUUUGUUUCCUGAAAGAAUAUAUAUACGAGUAAGAAGAAAAAUUUUUUAAAAAAUAAUAAAAAAAGUUAUCUAAAACCGCUUGCAUUUAUCAAGAAAAUAAGCUAUACUAGUAAUAGCGCAAACGUUUGCGUUCAUAAAAAUGUAAUAUCUAACUAUAAACACAUGAGGUGCUUAUU .((((..(((((.((.(((((.....))))).))..)))))(((((((((((((..(.((((...(((((((((((..(((((.....)))))(((((((((((..((((..(((((((((((((((..............(((((.(((.((((.....((((((((..........(((((((((((((.(((((.....)))))...)))))))..............))))))....((.(((....))).))...))))))))..)))))))))))).....(((((((.(((..(((((.(((...))).)))))...))).)))))))......)))))))))))))))...........))))..)))).))))))).................))))))))))).)))).).)))))))))))))..........................)))).............. (-100.35) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 817 100 51 191 142 smit:SMT_1141|5end_4-alpha-glucanotransferase_1085117..1085347_NEGATIVE 345 439 391 179 127 smit:SMT_683|5end_similar_to_CDP-ribitol_pyrophosphorylase_592572..592802_NEGATIVE 300 270 222 83 22 smit:SMT_885|5end_single-stranded-DNA-specific_exonuclease_RecJ_832660..832890_NEGATIVE 275 170 124 198 157 smit:SMT_706|5end_hypothetical_protein_616222..616452_NEGATIVE 268 418 379 66 31 smit:SMT_1785|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763277..1763507_NEGATIVE 268 417 371 101 61 smit:SMT_521|5end_K02005_HlyD_family_secretion_protein_445566..445796_POSITIVE 265 269 222 229 174 smit:SMT_2114|5end_x-prolyl-dipeptidyl_aminopeptidase_2001484..2001714_POSITIVE 265 245 202 55 17 smit:SMT_595|5end_phosphoglycerate_mutase_512593..512823_NEGATIVE 263 276 231 195 142 smit:SMT_1279|5end_translation_elongation_factor_Ts_1242331..1242561_POSITIVE 262 269 221 145 90 smit:SMT_1660|5end_serine_protease_1650634..1650864_NEGATIVE 262 340 292 93 44 smit:SMT_1398|5end_dihydroorotase_1373204..1373434_POSITIVE 262 102 67 175 139 smit:SMT_817|5end_aminotransferase_728699..728929_NEGATIVE 262 435 393 71 31 smit:SMT_761|5end_prephenate_dehydrogenase_667150..667380_NEGATIVE 262 435 393 71 31 smit:SMT_752|5end_prephenate_dehydrogenase_656791..657021_NEGATIVE 262 120 72 174 121 smit:SMT_349|5end_sensor_histidine_kinase_(homolog_to_BlpH_Spn)_287207..287437_POSITIVE 260 101 65 117 86 smit:SMT_1064|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1003308..1003538_POSITIVE 259 440 392 72 10 smit:SMT_816|5end_SWF/SNF_family_helicase_727440..727670_NEGATIVE 259 424 384 205 169 smit:SMT_355|5end_hypothetical_protein_291622..291852_POSITIVE 258 418 377 60 19 smit:SMT_2062|5end_phosphoglycerate_mutase_1971425..1971655_NEGATIVE 258 418 377 60 19 smit:SMT_1995|5end_phosphoglycerate_mutase_1920750..1920980_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 270 222 144 83 smit:SMT_886|3end_single-stranded-DNA-specific_exonuclease_RecJ_832599..832749_NEGATIVE 274 69 21 83 19 smit:SMT_2081|3end_glycosyltransferase_1981336..1981486_POSITIVE 268 418 379 108 73 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 265 245 202 58 20 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE 263 276 231 116 63 smit:SMT_1278|3end_30S_ribosomal_protein_S2_1242332..1242482_POSITIVE 263 237 192 151 101 smit:SMT_633|3end_hypothetical_protein_538035..538185_NEGATIVE 262 269 221 85 30 smit:SMT_1661|3end_K02986_small_subunit_ribosomal_protein_S4_1650694..1650844_NEGATIVE 262 340 292 80 31 smit:SMT_1397|3end_mutator_MutT_protein_1373271..1373421_POSITIVE 262 435 393 61 21 smit:SMT_753|3end_chorismate_synthase_656801..656951_NEGATIVE 260 101 65 36 5 smit:SMT_1063|3end_preprotein_translocase_SecA_subunit_1003307..1003457_POSITIVE 255 270 223 78 25 smit:SMT_207|3end_putative_two-component_sensor_histidine_kinase_138230..138380_NEGATIVE 246 446 402 139 92 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 245 448 401 151 96 smit:SMT_1081|3end_K06901_putative_MFS_transporter,_AGZA_family,_xanthine/uracil_permease_1018595..1018745_NEGATIVE 242 246 202 57 1 smit:SMT_1995|3end_phosphoglycerate_mutase_1920535..1920685_NEGATIVE 239 417 374 104 60 smit:SMT_1275|3end_rod_shape-determining_protein_MreC_1239492..1239642_POSITIVE 239 270 226 77 36 smit:SMT_84|3end_predicted_signal_transduction_protein_with_a_C-terminal_ATPase_domain_15292..15442_NEGATIVE 237 272 231 139 94 smit:SMT_1443|3end_23S_rRNA_m(5)U_1939_methyltransferase_1426503..1426653_NEGATIVE 233 280 233 53 7 smit:SMT_1756|3end_hypothetical_protein_1733967..1734117_NEGATIVE 233 457 411 48 8 smit:SMT_921|3end_putative_PP2C_protein_phosphatase_874498..874648_NEGATIVE 233 428 386 83 36 smit:SMT_353|3end_immunity_protein_BlpL_291364..291514_POSITIVE