Origin IGS: gatttcattttttttgatgaatttatattttctatattgtccggctcctcaccgctctccattatactcccgtttcccatacatgatattatttatttcaccgcaaatataaatataatatccgatatatcaaatattatccatataaaatctatataaaattgcatttatgccatattaaattcaatcttttctcagattagaatatcagagacaataagcatatccggaatggatgcttaccagtcgttattatgaagatcggagatatgtttgtatcgaattaggacgaatgggttttactgttcaatcttgattgaattgaaaaacttgttcacactttcgctctcccctgaaaggggcta .........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 tagcccctttcaggggagagcgaaagtgtgaacaagtttttcaattcaatcaagattgaacagtaaaacccattcgtcctaattcgatacaaacatatctccgatcttcataataacgactggtaagcatccattccggatatgcttattgtctctgatattctaatctgagaaaagattgaatttaatatggcataaatgcaattttatatagattttatatggataatatttgatatatcggatattatatttatatttgcggtgaaataaataatatcatgtatgggaaacgggagtataatggagagcggtgaggagccggacaatatagaaaatataaattcatcaaaaaaaatgaaatc Mask Tandem Repeat Region ================================================ gatttcattttttttgatgaatttatattttctatattgtccggctcctcaccgctctccattatactcccgtttcccatacatgatattatttatttcaccgcaaatataaatataatatccgatatatcaaatattatccatataaaatctatataaaattgcatttatgccatattaaattcaatcttttctcagattagaatatcagagacaataagcatatccggaatggatgcttaccagtcgttattatgaagatcggagatatgtttgtatcgaattaggacgaatgggttttactgttcaatcttgattgaattgaaaaacttgttcacactttcgctctcccctgaaaggggcta Find is-nt database================================================ Query_seq: TF1616:TF1617|TF1616:TF1617:conserved hypothetical protein; possible transcriptional regulator:conserved hypothetical protein; possible methyltransferase:->->:1732925..1733289 365 gatttcattttttttgatgaatttatattttctatattgtccggctcctcaccgctctccattatactcccgtttcccatacatgatattatttatttcaccgcaaatataaatataatatccgatatatcaaatattatccatataaaatctatataaaattgcatttatgccatattaaattcaatcttttctcagattagaatatcagagacaataagcatatccggaatggatgcttaccagtcgttattatgaagatcggagatatgtttgtatcgaattaggacgaatgggttttactgttcaatcttgattgaattgaaaaacttgttcacactttcgctctcccctgaaaggggcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1616:TF1617|TF1616:TF1617:conserved hypothetical protein; possible transcriptional regulator:conserved hypothetical protein; possible methyltransferase:->->:1732925..1733289 365 gatttcattttttttgatgaatttatattttctatattgtccggctcctcaccgctctccattatactcccgtttcccatacatgatattatttatttcaccgcaaatataaatataatatccgatatatcaaatattatccatataaaatctatataaaattgcatttatgccatattaaattcaatcttttctcagattagaatatcagagacaataagcatatccggaatggatgcttaccagtcgttattatgaagatcggagatatgtttgtatcgaattaggacgaatgggttttactgttcaatcttgattgaattgaaaaacttgttcacactttcgctctcccctgaaaggggcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1616:TF1617|TF1616:TF1617:conserved hypothetical protein; possible transcriptional regulator:conserved hypothetical protein; possible methyltransferase:->->:1732925..1733289 365 gatttcattttttttgatgaatttatattttctatattgtccggctcctcaccgctctccattatactcccgtttcccatacatgatattatttatttcaccgcaaatataaatataatatccgatatatcaaatattatccatataaaatctatataaaattgcatttatgccatattaaattcaatcttttctcagattagaatatcagagacaataagcatatccggaatggatgcttaccagtcgttattatgaagatcggagatatgtttgtatcgaattaggacgaatgggttttactgttcaatcttgattgaattgaaaaacttgttcacactttcgctctcccctgaaaggggcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatttcattttttttgatgaatttatattttctatattgtccggctcctcaccgctctccattatactcccgtttcccatacatgatattatttatttcaccgcaaatataaatataatatccgatatatcaaatattatccatataaaatctatataaaattgcatttatgccatattaaattcaatcttttctcagattagaatatcagagacaataagcatatccggaatggatgcttaccagtcgttattatgaagatcggagatatgtttgtatcgaattaggacgaatgggttttactgttcaatcttgattgaattgaaaaacttgttcacactttcgctctcccctgaaaggggcta Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 2 End: 109 . M S F F L M N L Y F L Y C P A P H R S P L Y S R F P Y M I L F I S P Q I ................................................................................................................................................................................................................................................................ Protein_Len: 50 Strand: + Start: 7 End: 156 ...... M F F D E F I F S I L S G S S P L S I I L P F P I H D I I Y F T A N I N I I S D I S N I I H I K S I ................................................................................................................................................................................................................. Protein_Len: 30 Strand: + Start: 166 End: 255 ..................................................................................................................................................................... M Y A I L N S I F S Q I R I S E T I S I S G M D A Y Q S L L .............................................................................................................. Protein_Len: 32 Strand: + Start: 268 End: 363 ........................................................................................................................................................................................................................................................................... M C L Y R I R T N G F Y C S I L I E L K N L F T L S L S P E R G .. Protein_Len: 30 Strand: - Start: 3 End: 92 .. K M K K S S N I N E I N D P E E G S E M I S G N G M C S I M ................................................................................................................................................................................................................................................................................. gatttcattttttttgatgaatttatattttctatattgtccggctcctcaccgctctccattatactcccgtttcccatacatgatattatttatttcaccgcaaatataaatataatatccgatatatcaaatattatccatataaaatctatataaaattgcatttatgccatattaaattcaatcttttctcagattagaatatcagagacaataagcatatccggaatggatgcttaccagtcgttattatgaagatcggagatatgtttgtatcgaattaggacgaatgggttttactgttcaatcttgattgaattgaaaaacttgttcacactttcgctctcccctgaaaggggcta 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: 82 Start: 115 End: 144 ..................................................................................................................ATGGATAATATTTGATATATCGGATATTAT............................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatttcattttttttgatgaatttatattttctatattgtccggctcctcaccgctctccattatactcccgtttcccatacatgatattatttatttcaccgcaaatataaatataatatccgatatatcaaatattatccatataaaatctatataaaattgcatttatgccatattaaattcaatcttttctcagattagaatatcagagacaataagcatatccggaatggatgcttaccagtcgttattatgaagatcggagatatgtttgtatcgaattaggacgaatgggttttactgttcaatcttgattgaattgaaaaacttgttcacactttcgctctcccctgaaaggggcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1616:TF1617|TF1616:TF1617:conserved hypothetical protein; possible transcriptional regulator:conserved hypothetical protein; possible methyltransferase:->->:1732925..1733289 365 gatttcattttttttgatgaatttatattttctatattgtccggctcctcaccgctctccattatactcccgtttcccatacatgatattatttatttcaccgcaaatataaatataatatccgatatatcaaatattatccatataaaatctatataaaattgcatttatgccatattaaattcaatcttttctcagattagaatatcagagacaataagcatatccggaatggatgcttaccagtcgttattatgaagatcggagatatgtttgtatcgaattaggacgaatgggttttactgttcaatcttgattgaattgaaaaacttgttcacactttcgctctcccctgaaaggggcta Intra-Species Hit: Count: 1 Min: 16 Max: 365 Len: 350 Subject: tfor_TF1616_TF1617|conserved hypothetical protein; possible transcriptional regulator:conserved hypothetical protein; possible methyltransferase|POSITIVE:POSITIVE|[1732925, 1733289]|365 HSP 1 e-value: 1.0E-101 bit: 371.0 Len: 187 Query Start:179 Query End:365 Subject Strand: POSITIVE Subject Start: 179 Subject End: 365 ..................................................................................................................................................................................taaattcaatcttttctcagattagaatatcagagacaataagcatatccggaatggatgcttaccagtcgttattatgaagatcggagatatgtttgtatcgaattaggacgaatgggttttactgttcaatcttgattgaattgaaaaacttgttcacactttcgctctcccctgaaaggggcta ..................................................................................................................................................................................taaattcaatcttttctcagattagaatatcagagacaataagcatatccggaatggatgcttaccagtcgttattatgaagatcggagatatgtttgtatcgaattaggacgaatgggttttactgttcaatcttgattgaattgaaaaacttgttcacactttcgctctcccctgaaaggggcta HSP 2 e-value: 8.0E-32 bit: 139.0 Len: 70 Query Start:16 Query End:85 Subject Strand: POSITIVE Subject Start: 16 Subject End: 85 ...............gatgaatttatattttctatattgtccggctcctcaccgctctccattatactcccgtttcccatacatg........................................................................................................................................................................................................................................................................................ ...............gatgaatttatattttctatattgtccggctcctcaccgctctccattatactcccgtttcccatacatg........................................................................................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAAUUUAUAUUUUCUAUAUUGUCCGGCUCCUCACCGCUCUCCAUUAUACUCCCGUUUCCCAUACAUGAUAUUAUUUAUUUCACCGCAAAUAUAAAUAUAAUAUCCGAUAUAUCAAAUAUUAUCCAUAUAAAAUCUAUAUAAAAUUGCAUUUAUGCCAUAUUAAAUUCAAUCUUUUCUCAGAUUAGAAUAUCAGAGACAAUAAGCAUAUCCGGAAUGGAUGCUUACCAGUCGUUAUUAUGAAGAUCGGAGAUAUGUUUGUAUCGAAUUAGGACGAAUGGGUUUUACUGUUCAAUCUUGAUUGAAUUGAAAAACUUGUUCACACUUUCGCUCUCCCCUGAAAGGGGCUA ((((((.................((((.........(((.(((.(((...((....(((((........((((((((.(((((......))))).....)))))))).(((((.((..((((.....))))..(((((....(((((((.(((((........))))).)))).)))....))))).))))))).)))))..((((((..(((.....)))))))))......))....))).))).))).(((((....)))))......))))(((..((((((.(.(((((((....))))))).).))))))..))).....)))).))..((((....))))... (-67.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCCCCUUUCAGGGGAGAGCGAAAGUGUGAACAAGUUUUUCAAUUCAAUCAAGAUUGAACAGUAAAACCCAUUCGUCCUAAUUCGAUACAAACAUAUCUCCGAUCUUCAUAAUAACGACUGGUAAGCAUCCAUUCCGGAUAUGCUUAUUGUCUCUGAUAUUCUAAUCUGAGAAAAGAUUGAAUUUAAUAUGGCAUAAAUGCAAUUUUAUAUAGAUUUUAUAUGGAUAAUAUUUGAUAUAUCGGAUAUUAUAUUUAUAUUUGCGGUGAAAUAAAUAAUAUCAUGUAUGGGAAACGGGAGUAUAAUGGAGAGCGGUGAGGAGCCGGACAAUAUAGAAAAUAUAAAUUCAUC ...((((.....))))...((....))(((((.....(((((..((((((....))))))...............((((......((((......)))).(((.(((((((.(((.(..(((.(((((((((.....)))..))))))...((((....((((.(((((......)))))))))...((((((((....))).(((((((...(....((((...(((((((((((....)))))))))))...))))....).))))))).........)))))..))))..)))..)))).))))))).))).........))))......)))))......))))). (-75.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 56 14 93 50 tfor:TF2549|5end_30S_ribosomal_protein_S7_2731711..2731941_POSITIVE 356 349 315 189 151 tfor:TF1840|5end_transposase_1990221..1990451_POSITIVE 353 57 15 65 14 tfor:TF3116|5end_conserved_hypothetical_protein_3352136..3352366_POSITIVE 353 67 21 183 125 tfor:TF0440|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_2_463655..463885_POSITIVE 339 65 26 84 27 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 336 55 14 60 13 tfor:TF0307|5end_conserved_hypothetical_protein_332783..333013_POSITIVE 332 61 25 214 165 tfor:TF2561|5end_50S_ribosomal_protein_L16_2738693..2738923_POSITIVE 332 63 21 159 118 tfor:TF1001|5end_penicillin-binding_protein_1A_1054097..1054327_POSITIVE 328 281 245 124 92 tfor:TF0465|5end_cobalamin_biosynthesis_protein_482028..482258_POSITIVE 325 349 325 37 6 tfor:TF2745|5end_hypothetical_protein_2927562..2927792_POSITIVE 324 67 24 216 173 tfor:TF0651|5end_hypothetical_protein_693338..693568_POSITIVE 322 46 20 34 3 tfor:TF2912|5end_hypothetical_protein_3106508..3106738_POSITIVE 320 63 22 205 156 tfor:TF2810|5end_conserved_hypothetical_protein_3000583..3000813_POSITIVE 310 289 248 116 64 tfor:TF0325|5end_LysM_domain_protein_351917..352147_POSITIVE 306 257 214 46 2 tfor:TF0749|5end_protease_II_795562..795792_POSITIVE 298 250 205 146 93 tfor:TF0142|5end_subtilisin-like_serine_proteinase_149740..149970_POSITIVE 295 70 27 51 10 tfor:TF3026|5end_conserved_hypothetical_protein_3249137..3249367_POSITIVE 294 62 24 132 94 tfor:TF2951|5end_O-succinylbenzoic_acid--CoA_ligase_3158496..3158726_POSITIVE 293 70 24 60 21 tfor:TF1813|5end_peptide_methionine_sulfoxide_reductase_1954170..1954400_POSITIVE 292 69 28 73 13 tfor:TF2358|5end_possible_small-conductance_mechanosensitive_channel_2523829..2524059_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 338 299 50 5 tfor:TF1104|3end_hypothetical_protein_1172194..1172344_POSITIVE 353 67 21 137 79 tfor:TF0439|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_1_463689..463839_POSITIVE 332 63 21 151 110 tfor:TF1000|3end_sec-independent_protein_translocase_1054169..1054319_POSITIVE 328 281 245 124 92 tfor:TF0464|3end_precorrin_methylase_482108..482258_POSITIVE 322 46 20 86 55 tfor:TF2911|3end_hypothetical_protein_3106640..3106790_POSITIVE 320 63 22 53 4 tfor:TF2809|3end_conserved_hypothetical_protein;_possible_translation_factor_(SUA5)_3000511..3000661_POSITIVE 319 338 299 49 4 tfor:TF1112|3end_possible_response_regulator,_LytR/AlgR_family_1183015..1183165_POSITIVE 316 45 1 107 52 tfor:TF2893|3end_conserved_hypothetical_protein;_possible_phosphoesterase_3082039..3082189_POSITIVE 310 289 248 116 64 tfor:TF0324|3end_conserved_hypothetical_protein_351997..352147_POSITIVE 301 347 325 39 14 tfor:TF0821|3end_hypothetical_protein_880195..880345_POSITIVE 301 347 325 58 33 tfor:TF0370|3end_hypothetical_protein_386317..386467_POSITIVE 299 290 248 42 1 tfor:TF2444|3end_regulatory_protein_RecX_2621549..2621699_POSITIVE 294 62 24 105 67 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 293 343 301 51 1 tfor:TF1096|3end_conserved_hypothetical_protein_1165357..1165507_POSITIVE 292 69 28 64 4 tfor:TF2357|3end_collagenase_2523900..2524050_POSITIVE 292 63 23 129 86 tfor:TF1405|3end_conserved_hypothetical_protein_1481819..1481969_POSITIVE 287 69 23 88 39 tfor:TF0664|3end_small_protein_B_(SMPB)_709570..709720_POSITIVE 284 349 308 75 42 tfor:TF2338|3end_conserved_hypothetical_protein_2500006..2500156_POSITIVE 283 349 325 77 47 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 283 349 316 63 26 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE