Origin IGS: taaaaggtacgtacataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgttttgacacacccccctcttacgaagatttactctctttgcttttta .........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 taaaaagcaaagagagtaaatcttcgtaagaggggggtgtgtcaaaacgcaatgtttgggcacaccctctttaggtgtgtaagcatgggtgaaatgcaagacgctaaggatgagagcgagggagtatacaaacgtatatgaccgagtttacattcagcaggaaacgaagcagttctcccgttatgtacgtacctttta Mask Tandem Repeat Region ================================================ taaaaggtacgtacataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgttttgacacacccccctcttacgaagatttactctctttgcttttta Find is-nt database================================================ Query_seq: TF0475:TF0476|TF0475:TF0476:possible transcriptional regulator, AraC family:conserved hypothetical protein:->->:494886..495083 198 taaaaggtacgtacataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgttttgacacacccccctcttacgaagatttactctctttgcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0475:TF0476|TF0475:TF0476:possible transcriptional regulator, AraC family:conserved hypothetical protein:->->:494886..495083 198 taaaaggtacgtacataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgttttgacacacccccctcttacgaagatttactctctttgcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0475:TF0476|TF0475:TF0476:possible transcriptional regulator, AraC family:conserved hypothetical protein:->->:494886..495083 198 taaaaggtacgtacataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgttttgacacacccccctcttacgaagatttactctctttgcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaggtacgtacataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgttttgacacacccccctcttacgaagatttactctctttgcttttta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 62 End: 154 ............................................................. M R L Y T P S L S S L A S C I S P M L T H L K R V C P N I A F ............................................ Protein_Len: 37 Strand: + Start: 88 End: 198 ....................................................................................... M L S V L H F T H A Y T P K E G V P K H C V L T H P P L T K I Y S L C F L Protein_Len: 34 Strand: - Start: 61 End: 162 ............................................................ I R K Y V G E S E D K A D Q M E G M S V C R F L T H G F M A N Q C M .................................... Protein_Len: 36 Strand: - Start: 3 End: 110 .. F T R V Y R S F Q K T E Q Q I Y V R D Y V N T Y E R A R M R L T K C K M ........................................................................................ taaaaggtacgtacataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgttttgacacacccccctcttacgaagatttactctctttgcttttta 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================================================ taaaaggtacgtacataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgttttgacacacccccctcttacgaagatttactctctttgcttttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -5.9 Tail_Score: -3.03635 Start: 129 End: 167 Full_Region: TGCTTACACACCTAA AGAGGGTGTGCCCAAAC ATTGC GTTTTGACACACCCCCC TCTTACGAAGATTTA ................................................................................................................................AGAGGGTGTGCCCAAACATTGCGTTTTGACACACCCCCC............................... TransTerm Strand: - Conf: 100 HP_score: -14.5 Tail_Score: -3.74077 Start: 130 End: 166 Full_Region: aaatcttcgtaagag gggggtgtgtcaaaacg caa tgtttgggcacaccctc tttaggtgtgtaagc .................................................................................................................................gggggtgtgtcaaaacgcaatgtttgggcacaccctc................................ Find igs database================================================ Query_seq: TF0475:TF0476|TF0475:TF0476:possible transcriptional regulator, AraC family:conserved hypothetical protein:->->:494886..495083 198 taaaaggtacgtacataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgttttgacacacccccctcttacgaagatttactctctttgcttttta Intra-Species Hit: Count: 5 Min: 1 Max: 198 Len: 198 Subject: tfor_TF0475_TF0476|possible transcriptional regulator, AraC family:conserved hypothetical protein|POSITIVE:POSITIVE|[494886,495083]|198 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 198 Query Start:1 Query End:198 Subject Strand: POSITIVE Subject Start: 1 Subject End: 198 taaaaggtacgtacataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgttttgacacacccccctcttacgaagatttactctctttgcttttta taaaaggtacgtacataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgttttgacacacccccctcttacgaagatttactctctttgcttttta Subject: tfor_TF0983_TF0984|nitroreductase family protein, possible NADH dehydrogenase/NAD(P)H nitroreductase:possible mucin-desulfating sulfatase (MdsC protein)|POSITIVE:POSITIVE|[1040095,1040398]|304 HSP 1 e-value: 6.0E-31 bit: 135.0 Len: 151 Query Start:14 Query End:164 Subject Strand: NEGATIVE Subject Start: 114 Subject End: 265 .............cataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgca-tttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgttttgacacaccc.................................. .............cataacgagcgaactgcttcgttgtttgcggaatgcgagctcggccacatacgttagtatgctccctcgctctcatccttagcgcctcccaatttcacccattcttacatacctaaagagggtgtgtccaaacattgcgttttgacacaccc.................................. Subject: tfor_TF0145_TF0146|glutamine synthetase:glutamine-dependent NAD(+) synthetase|POSITIVE:POSITIVE|[154779,154994]|216 HSP 1 e-value: 2.0E-27 bit: 123.0 Len: 142 Query Start:14 Query End:155 Subject Strand: POSITIVE Subject Start: 21 Subject End: 162 .............cataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaacattgcgtttt........................................... .............cataacgggcgaactgcttcgttgcttgcggaatgcaagctcggtcacatacgttagtatgctccctcgttcgcatccttagcgccttgcatttcacctattctgacacacctaaaaagggtggtctcaaacattgtgtttt........................................... Subject: tfor_TF0661_TF0662|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[708318,708455]|138 HSP 1 e-value: 5.0E-16 bit: 85.7 Len: 102 Query Start:63 Query End:164 Subject Strand: NEGATIVE Subject Start: 35 Subject End: 137 ..............................................................tacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgcttacacacctaaagagggtgtgcccaaa-cattgcgttttgacacaccc.................................. ..............................................................tacgttagtatgctccctcgctctcatccttagcccccccaatttccccctttcttatacacctaaggagggtgtgcccaaaacattgcgttttgacacaccc.................................. Subject: tfor_TF0795_TF0797|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[853260,853435]|176 HSP 1 e-value: 3.0E-11 bit: 69.9 Len: 103 Query Start:14 Query End:116 Subject Strand: POSITIVE Subject Start: 25 Subject End: 127 .............cataacgggagaactgcttcgtttcctgctgaatgtaaactcggtcatatacgtttgtatactccctcgctctcatccttagcgtcttgcatttcacccatgc.................................................................................. .............cataacgggcgaactgcttcgttgcttacggaatgcgtgctcggttacataccttagtatactccctcgctctcatccttaattccttgcatttcacccatgc.................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGGUACGUACAUAACGGGAGAACUGCUUCGUUUCCUGCUGAAUGUAAACUCGGUCAUAUACGUUUGUAUACUCCCUCGCUCUCAUCCUUAGCGUCUUGCAUUUCACCCAUGCUUACACACCUAAAGAGGGUGUGCCCAAACAUUGCGUUUUGACACACCCCCCUCUUACGAAGAUUUACUCUCUUUGCUUUUUA ....((((..(((......(((((...(((..(((.....(((((........))))).....)))...)))..))))).((((.........))))....((((.......)))).)))..)))).(((((((((((.(.((((.....)))).).)))))))...)))).((((((.......))))))....... (-43.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAGCAAAGAGAGUAAAUCUUCGUAAGAGGGGGGUGUGUCAAAACGCAAUGUUUGGGCACACCCUCUUUAGGUGUGUAAGCAUGGGUGAAAUGCAAGACGCUAAGGAUGAGAGCGAGGGAGUAUACAAACGUAUAUGACCGAGUUUACAUUCAGCAGGAAACGAAGCAGUUCUCCCGUUAUGUACGUACCUUUUA ......((.((((.......)))).))..((((((((((((((.((((.....)))).)))))))))))))).((((((((...(((((.(((.(((.....(((..(((((.((((..((..((((((....))))))..))..)))).)))))))).(....)...))).))).)))))....))))))))..... (-73.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 816 100 53 217 170 tfor:TF0984|5end_possible_mucin-desulfating_sulfatase_(MdsC_protein)_1040259..1040489_POSITIVE 797 170 123 162 110 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 793 169 121 204 151 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 772 160 111 205 156 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 650 170 124 75 28 tfor:TF1046|5end_hypothetical_protein_1108178..1108408_POSITIVE 625 169 121 159 113 tfor:TF2357|5end_collagenase_2522561..2522791_POSITIVE 586 170 121 202 155 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 579 170 130 227 191 tfor:TF1999|5end_ArgK_protein_with_ATPase_and_kinase_domains_2152769..2152999_POSITIVE 574 170 126 148 107 tfor:TF2947|5end_isochorismate_synthase_3153633..3153863_POSITIVE 560 60 14 224 178 tfor:TF0663|5end_conserved_hypothetical_protein_708450..708680_POSITIVE 509 168 130 192 155 tfor:TF3007|5end_conserved_hypothetical_protein_3227256..3227486_POSITIVE 468 113 75 67 32 tfor:TF2724|5end_anti-sigma_factor_2898193..2898423_POSITIVE 457 162 130 231 199 tfor:TF2414|5end_hypothetical_protein_2590725..2590955_POSITIVE 441 151 111 231 189 tfor:TF0682|5end_outer_membrane_protein,_TonB_dependent_receptor_724450..724680_POSITIVE 422 170 129 164 124 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 371 165 124 159 122 tfor:TF1317|5end_hypothetical_protein_1391378..1391608_POSITIVE 368 170 121 202 155 tfor:TF2289|5end_secretion_protein,_possible_HlyD_family_2442725..2442955_POSITIVE 357 58 11 170 122 tfor:TF1481|5end_ABC_transporter,_ATP-binding_protein_1574783..1575013_POSITIVE 351 60 19 64 24 tfor:TF2672|5end_lipoic_acid_synthetase_2846086..2846316_POSITIVE 342 117 72 158 122 tfor:TF1277|5end_electron_transfer_flavoprotein,_alpha_subunit_1363012..1363242_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 793 169 121 65 12 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 702 164 121 47 1 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 650 170 124 62 15 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 579 170 130 64 28 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 570 170 122 47 1 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 535 170 130 111 74 tfor:TF2413|3end_hypothetical_protein_2590680..2590830_POSITIVE 441 180 131 66 19 tfor:TF1416|3end_outer_membrane_protein_1499413..1499563_POSITIVE 360 168 129 60 22 tfor:TF1354|3end_TonB_protein_1435216..1435366_POSITIVE 351 60 19 61 21 tfor:TF2671|3end_dipeptidyl_peptidase_IV_(DPP_IV)_N-terminal_region_2846163..2846313_POSITIVE 342 117 72 146 110 tfor:TF1276|3end_acyl-CoA_dehydrogenase_(short_chain_coenzyme_A_dehydrogenase)_1363080..1363230_POSITIVE 339 169 124 62 3 tfor:TF1585|3end_hypothetical_protein_1690610..1690760_POSITIVE 330 116 77 118 81 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 330 57 14 62 15 tfor:TF1160|3end_MutT/nudix_family_protein_1241008..1241158_POSITIVE 328 99 53 61 12 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 319 58 17 149 114 tfor:TF0766|3end_hypothetical_protein_812256..812406_POSITIVE 317 59 19 59 22 tfor:TF2019|3end_dipeptidyl_peptidase_VI_2176401..2176551_POSITIVE 316 67 24 109 70 tfor:TF1994|3end_acyl-CoA_synthetase_2147228..2147378_POSITIVE 316 69 21 122 80 tfor:TF0788|3end_protein-export_membrane_protein_841370..841520_POSITIVE 315 99 51 57 17 tfor:TF0889|3end_conjugative_transposon_protein,_TraO_940078..940228_POSITIVE 306 177 131 62 2 tfor:TF1584|3end_hypothetical_protein_1690603..1690753_POSITIVE