Origin IGS: taaaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcatataaataaattgtcacacccatcgacttaccgctctctaataatcgcgtatattgatttttatatcgagctggccgtccgtaatcattttgatgattcagctggttttatgttgttattttaggaatatccctatgtgagccgctaaaccgatacggcacgatacagaccgggcggataccgttactgtatcgtgccgtcgataaggtcggtgccggaaagcatacagtta .........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 taactgtatgctttccggcaccgaccttatcgacggcacgatacagtaacggtatccgcccggtctgtatcgtgccgtatcggtttagcggctcacatagggatattcctaaaataacaacataaaaccagctgaatcatcaaaatgattacggacggccagctcgatataaaaatcaatatacgcgattattagagagcggtaagtcgatgggtgtgacaatttatttatatgaatgtccgtatatatgcctaaaattaattatatattgctaatctacagaaatttatttcttactccaatccatgcatccaaattattgttattaaatagtttaatggagtttttaggtacaaacacggatattcattttta Mask Tandem Repeat Region ================================================ taaaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcatataaataaattgtcacacccatcgacttaccgctctctaataatcgcgtatattgatttttatatcgagctggccgtccgtaatcattttgatgattcagctggttttatgttgttattttaggaatatccctatgtgagccgctaaaccgatacggcacgatacagaccgggcggataccgttactgtatcgtgccgtcgataaggtcggtgccggaaagcatacagtta Find is-nt database================================================ Query_seq: TF1890:TF1891|TF1890:TF1891:hypothetical protein:hypothetical protein:->->:2043154..2043528 375 taaaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcatataaataaattgtcacacccatcgacttaccgctctctaataatcgcgtatattgatttttatatcgagctggccgtccgtaatcattttgatgattcagctggttttatgttgttattttaggaatatccctatgtgagccgctaaaccgatacggcacgatacagaccgggcggataccgttactgtatcgtgccgtcgataaggtcggtgccggaaagcatacagtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1890:TF1891|TF1890:TF1891:hypothetical protein:hypothetical protein:->->:2043154..2043528 375 taaaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcatataaataaattgtcacacccatcgacttaccgctctctaataatcgcgtatattgatttttatatcgagctggccgtccgtaatcattttgatgattcagctggttttatgttgttattttaggaatatccctatgtgagccgctaaaccgatacggcacgatacagaccgggcggataccgttactgtatcgtgccgtcgataaggtcggtgccggaaagcatacagtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1890:TF1891|TF1890:TF1891:hypothetical protein:hypothetical protein:->->:2043154..2043528 375 taaaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcatataaataaattgtcacacccatcgacttaccgctctctaataatcgcgtatattgatttttatatcgagctggccgtccgtaatcattttgatgattcagctggttttatgttgttattttaggaatatccctatgtgagccgctaaaccgatacggcacgatacagaccgggcggataccgttactgtatcgtgccgtcgataaggtcggtgccggaaagcatacagtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcatataaataaattgtcacacccatcgacttaccgctctctaataatcgcgtatattgatttttatatcgagctggccgtccgtaatcattttgatgattcagctggttttatgttgttattttaggaatatccctatgtgagccgctaaaccgatacggcacgatacagaccgggcggataccgttactgtatcgtgccgtcgataaggtcggtgccggaaagcatacagtta Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 118 End: 264 ..................................................................................................................... M L G I Y T D I H I N K L S H P S T Y R S L I I A Y I D F Y I E L A V R N H F D D S A G F M L L F ............................................................................................................... Protein_Len: 38 Strand: + Start: 261 End: 374 .................................................................................................................................................................................................................................................................... M L G I S L C E P L N R Y G T I Q T G R I P L L Y R A V D K V G A G K H T V . Protein_Len: 37 Strand: - Start: 262 End: 372 ..................................................................................................................................................................................................................................................................... K L F I G I H A A L G I R C S V S R A S V T V T D H R R Y P R H R F A Y M ... Protein_Len: 47 Strand: - Start: 104 End: 244 ....................................................................................................... C Y I I L K L C I Y P C E Y L Y I T V G M S K G S E L L R T Y Q N K Y R A P R G Y D N Q H N M ................................................................................................................................... Protein_Len: 46 Strand: - Start: 3 End: 140 .. F H I D T N T G L F E M L S N L L L L K S A H I P T L F L N R Y I L L I Y N I K P M Y V S M ........................................................................................................................................................................................................................................... taaaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcatataaataaattgtcacacccatcgacttaccgctctctaataatcgcgtatattgatttttatatcgagctggccgtccgtaatcattttgatgattcagctggttttatgttgttattttaggaatatccctatgtgagccgctaaaccgatacggcacgatacagaccgggcggataccgttactgtatcgtgccgtcgataaggtcggtgccggaaagcatacagtta 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================================================ taaaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcatataaataaattgtcacacccatcgacttaccgctctctaataatcgcgtatattgatttttatatcgagctggccgtccgtaatcattttgatgattcagctggttttatgttgttattttaggaatatccctatgtgagccgctaaaccgatacggcacgatacagaccgggcggataccgttactgtatcgtgccgtcgataaggtcggtgccggaaagcatacagtta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -8.4 Tail_Score: -3.55563 Start: 293 End: 346 Full_Region: ccggcaccgacctta tcgacggcacgatacagtaacgg tatccgc ccggtctgtatcgtgccgtatcgg tttagcggctcacat ....................................................................................................................................................................................................................................................................................................tcgacggcacgatacagtaacggtatccgcccggtctgtatcgtgccgtatcgg............................. TransTerm Strand: - Conf: 74 HP_score: -9.7 Tail_Score: -2.73124 Start: 294 End: 345 Full_Region: cggcaccgaccttat cgacggcacgatacagtaacgg tatccgc ccggtctgtatcgtgccgtatcg gtttagcggctcaca .....................................................................................................................................................................................................................................................................................................cgacggcacgatacagtaacggtatccgcccggtctgtatcgtgccgtatcg.............................. TransTerm Strand: - Conf: 93 HP_score: -13.6 Tail_Score: -2.64472 Start: 297 End: 344 Full_Region: ggcaccgaccttatc gacggcacgatacagtaacgg tatccgc ccggtctgtatcgtgccgta tcggtttagcggctc ........................................................................................................................................................................................................................................................................................................gacggcacgatacagtaacggtatccgcccggtctgtatcgtgccgta............................... Find igs database================================================ Query_seq: TF1890:TF1891|TF1890:TF1891:hypothetical protein:hypothetical protein:->->:2043154..2043528 375 taaaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcatataaataaattgtcacacccatcgacttaccgctctctaataatcgcgtatattgatttttatatcgagctggccgtccgtaatcattttgatgattcagctggttttatgttgttattttaggaatatccctatgtgagccgctaaaccgatacggcacgatacagaccgggcggataccgttactgtatcgtgccgtcgataaggtcggtgccggaaagcatacagtta Intra-Species Hit: Count: 8 Min: 1 Max: 375 Len: 375 Subject: tfor_TF1890_TF1891|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2043154,2043528]|375 HSP 1 e-value: 0.0 bit: 743.0 Len: 375 Query Start:1 Query End:375 Subject Strand: POSITIVE Subject Start: 1 Subject End: 375 taaaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcatataaataaattgtcacacccatcgacttaccgctctctaataatcgcgtatattgatttttatatcgagctggccgtccgtaatcattttgatgattcagctggttttatgttgttattttaggaatatccctatgtgagccgctaaaccgatacggcacgatacagaccgggcggataccgttactgtatcgtgccgtcgataaggtcggtgccggaaagcatacagtta taaaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcatataaataaattgtcacacccatcgacttaccgctctctaataatcgcgtatattgatttttatatcgagctggccgtccgtaatcattttgatgattcagctggttttatgttgttattttaggaatatccctatgtgagccgctaaaccgatacggcacgatacagaccgggcggataccgttactgtatcgtgccgtcgataaggtcggtgccggaaagcatacagtta Subject: tfor_TF2966_TF2967|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3177733,3177904]|172 HSP 1 e-value: 8.0E-75 bit: 281.0 Len: 142 Query Start:4 Query End:145 Subject Strand: POSITIVE Subject Start: 13 Subject End: 154 ...aaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcata...................................................................................................................................................................................................................................... ...aaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcata...................................................................................................................................................................................................................................... Subject: tfor_TF1369_TF1370|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1447647,1447991]|345 HSP 1 e-value: 3.0E-74 bit: 280.0 Len: 141 Query Start:5 Query End:145 Subject Strand: NEGATIVE Subject Start: 185 Subject End: 325 ....aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcata...................................................................................................................................................................................................................................... ....aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcata...................................................................................................................................................................................................................................... Subject: tfor_TF2175_TF2176|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2348876,2349050]|175 HSP 1 e-value: 5.0E-73 bit: 276.0 Len: 139 Query Start:5 Query End:143 Subject Strand: POSITIVE Subject Start: 37 Subject End: 175 ....aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca........................................................................................................................................................................................................................................ ....aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca........................................................................................................................................................................................................................................ Subject: tfor_TF2478_TF2479|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2655674,2656131]|458 HSP 1 e-value: 1.0E-49 bit: 198.0 Len: 144 Query Start:4 Query End:147 Subject Strand: NEGATIVE Subject Start: 290 Subject End: 432 ...aaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcatata.................................................................................................................................................................................................................................... ...aaataaatatccgtgtttgtacctaaaagctccattaaactatttaataacaataatttggatgtatggattgg-ggagggaataaatttctgtatatcagcaatatataattaattttaggcatatatacggacatttatata.................................................................................................................................................................................................................................... Subject: tfor_TF2162_TF2163|thermolysin precursor:hypothetical protein|POSITIVE:POSITIVE|[2340774,2340941]|168 HSP 1 e-value: 2.0E-41 bit: 170.0 Len: 118 Query Start:27 Query End:144 Subject Strand: NEGATIVE Subject Start: 51 Subject End: 168 ..........................taaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcat....................................................................................................................................................................................................................................... ..........................taaaagctccattaaactatttaataacaataatttggatgtatggattgaagcaagagataaatttctgtatatcagtaatatataattaattttaggcatatatacggacattcat....................................................................................................................................................................................................................................... Subject: tfor_TF0899_TF0901|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[946220,946820]|601 HSP 1 e-value: 3.0E-40 bit: 167.0 Len: 140 Query Start:5 Query End:144 Subject Strand: POSITIVE Subject Start: 411 Subject End: 550 ....aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcat....................................................................................................................................................................................................................................... ....aatgaatatccgtttttgcacctaaaaactctattaaactatttaacaacaataatttagatgtataggtcggagagagaaatagatttctgtatatcagcaatatataattaattttaggcatatatacggacattcat....................................................................................................................................................................................................................................... Subject: tfor_TF1905_TF1906|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2060393,2061094]|702 HSP 1 e-value: 8.0E-38 bit: 159.0 Len: 100 Query Start:276 Query End:375 Subject Strand: NEGATIVE Subject Start: 256 Subject End: 355 ...................................................................................................................................................................................................................................................................................ctatgtgagccgctaaaccgatacggcacgatacagaccgggcggataccgttactgtatcgtgccgtcgataaggtcggtgccggaaagcatacagtta ...................................................................................................................................................................................................................................................................................ctatgtgagccgctaaaccgatacggcacgatacaggccaggcggataccgttactgtatcgtgccgtcgataaggccagtgccggaaagcatacggtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAUGAAUAUCCGUGUUUGUACCUAAAAACUCCAUUAAACUAUUUAAUAACAAUAAUUUGGAUGCAUGGAUUGGAGUAAGAAAUAAAUUUCUGUAGAUUAGCAAUAUAUAAUUAAUUUUAGGCAUAUAUACGGACAUUCAUAUAAAUAAAUUGUCACACCCAUCGACUUACCGCUCUCUAAUAAUCGCGUAUAUUGAUUUUUAUAUCGAGCUGGCCGUCCGUAAUCAUUUUGAUGAUUCAGCUGGUUUUAUGUUGUUAUUUUAGGAAUAUCCCUAUGUGAGCCGCUAAACCGAUACGGCACGAUACAGACCGGGCGGAUACCGUUACUGUAUCGUGCCGUCGAUAAGGUCGGUGCCGGAAAGCAUACAGUUA .....((((((.(((((((.(((.(((((((((((((......(((((((..........))))))).......)))))).(((((....)))))...(((((........)))))..))))))).))).))))))).)))))).......((((((....(((((((((((...((((.(.((((((.(((((..(((((......)))))...(((((.(.(.((((((....))))))).).))))).))))).)))))).((((......)))).).))))........(((..(((((((((((((....(((((...))))).))))))))))))))))...)))))))))..)).......)))))). (-101.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUGUAUGCUUUCCGGCACCGACCUUAUCGACGGCACGAUACAGUAACGGUAUCCGCCCGGUCUGUAUCGUGCCGUAUCGGUUUAGCGGCUCACAUAGGGAUAUUCCUAAAAUAACAACAUAAAACCAGCUGAAUCAUCAAAAUGAUUACGGACGGCCAGCUCGAUAUAAAAAUCAAUAUACGCGAUUAUUAGAGAGCGGUAAGUCGAUGGGUGUGACAAUUUAUUUAUAUGAAUGUCCGUAUAUAUGCCUAAAAUUAAUUAUAUAUUGCUAAUCUACAGAAAUUUAUUUCUUACUCCAAUCCAUGCAUCCAAAUUAUUGUUAUUAAAUAGUUUAAUGGAGUUUUUAGGUACAAACACGGAUAUUCAUUUUUA ....(((((((((..((((.(((.........((((((((((((((...(((.......)))..))))))))))))))...((((((((((......(((((....)))))...((......))...)).)))))))).............)))...(((.((((....(((.((((.........)))).)))..)))))))..))))..)))))).)))..........((((((((((((.....(((((((((.......................(((((....)))))........(((((......((((((((.......)))))))).)))))..))))))))).....))))))))))))..... (-101.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 775 110 61 217 168 tfor:TF1370|5end_conserved_hypothetical_protein_1447852..1448082_POSITIVE 640 60 11 174 125 tfor:TF2479|5end_conserved_hypothetical_protein_2655992..2656222_POSITIVE 640 60 11 125 76 tfor:TF2163|5end_hypothetical_protein_2340802..2341032_POSITIVE 584 60 11 187 138 tfor:TF0845|5end_hypothetical_protein_896419..896649_POSITIVE 481 360 313 51 4 tfor:TF1759|5end_membrane-bound_lytic_murein_transglycosylase_D_precursor_1895472..1895702_POSITIVE 450 360 313 67 4 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 446 360 313 72 10 tfor:TF1935|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2082002..2082232_POSITIVE 433 360 311 158 99 tfor:TF0463|5end_precorrin-6Y_C5,15-methyltransferase_479015..479245_POSITIVE 430 360 313 65 24 tfor:TF2893|5end_conserved_hypothetical_protein;_possible_phosphoesterase_3080766..3080996_POSITIVE 430 362 322 173 131 tfor:TF2594|5end_hypothetical_protein_2764176..2764406_POSITIVE 430 360 314 57 6 tfor:TF0777|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_826098..826328_POSITIVE 427 355 313 60 8 tfor:TF2167|5end_hypothetical_protein_2342586..2342816_POSITIVE 427 355 313 60 8 tfor:TF0367|5end_eukaryotic-like__metalloproteinase_384007..384237_POSITIVE 426 360 312 213 168 tfor:TF1853|5end_homoserine_O-succinyltransferase_2006470..2006700_POSITIVE 419 340 292 216 165 tfor:TF0970|5end_2-keto-3-deoxygluconate_kinase_1020396..1020626_POSITIVE 418 346 301 137 88 tfor:TF2159|5end_conserved_hypothetical_protein_2334446..2334676_POSITIVE 415 355 311 60 10 tfor:TF0351|5end_hypothetical_protein_370922..371152_POSITIVE 412 360 311 208 144 tfor:TF0234|5end_5,10-methylenetetrahydrofolate_reductase_260482..260712_POSITIVE 405 340 293 75 22 tfor:TF2281|5end_hypothetical_protein_2439574..2439804_POSITIVE 404 357 311 169 134 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 506 144 106 40 2 tfor:TF2162|3end_thermolysin_precursor_2340713..2340863_POSITIVE 430 360 314 52 1 tfor:TF0776|3end_ABC_transporter,_permease_component_826173..826323_POSITIVE 416 332 296 148 103 tfor:TF3099|3end_conserved_hypothetical_protein_3331107..3331257_POSITIVE 403 320 274 57 20 tfor:TF1298|3end_possible_membrane_protein_1381197..1381347_POSITIVE 399 357 315 133 92 tfor:TF0027|3end_conserved_hypothetical_protein_24199..24349_POSITIVE 396 360 312 62 11 tfor:TF0593|3end_membrane-associated_phospholipid_phosphatase_627051..627201_POSITIVE 393 358 311 86 24 tfor:TF2343|3end_ribosome_recycling_factor_2507502..2507652_POSITIVE 390 366 324 137 95 tfor:TF2687|3end_iron-regulated_ABC-type_transporter_membrane_component_2864962..2865112_POSITIVE 386 360 313 54 5 tfor:TF2250|3end_transfer_region-related_protein,_TraD_2424173..2424323_POSITIVE 386 357 313 51 15 tfor:TF0699|3end_pyridoxal_phosphate_biosynthetic_protein_742745..742895_POSITIVE 384 360 318 45 3 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 382 360 311 60 9 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 379 359 313 123 75 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 379 360 324 62 27 tfor:TF0804|3end_possible_phosphatidylglycerophosphate_synthase_862899..863049_POSITIVE 374 337 294 150 107 tfor:TF0022|3end_two-component_system_sensor_histidine_kinase_19522..19672_POSITIVE 370 345 301 148 109 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 370 360 314 52 8 tfor:TF0247|3end_conserved_hypothetical_protein_278348..278498_POSITIVE 368 354 313 100 52 tfor:TF2315|3end_thioesterase_2474498..2474648_POSITIVE 368 366 323 50 8 tfor:TF0328|3end_conserved_hypothetical_protein_355266..355416_POSITIVE 367 319 278 150 104 tfor:TF2673|3end_conserved_hypothetical_protein_2848272..2848422_POSITIVE