Origin IGS: taagtacgctttacttattctttgaaaaagaagacaatgtgtcaaagagggtgtaccaaaacattgcgttttgatacatcctcttttctagtgaataggtctgctttaggattaaggtatcgcagttgatgggtattgtgaccggtgggtcatgatggttcttcttctttgattggatta .........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 taatccaatcaaagaagaagaaccatcatgacccaccggtcacaatacccatcaactgcgataccttaatcctaaagcagacctattcactagaaaagaggatgtatcaaaacgcaatgttttggtacaccctctttgacacattgtcttctttttcaaagaataagtaaagcgtactta Mask Tandem Repeat Region ================================================ taagtacgctttacttattctttgaaaaagaagacaatgtgtcaaagagggtgtaccaaaacattgcgttttgatacatcctcttttctagtgaataggtctgctttaggattaaggtatcgcagttgatgggtattgtgaccggtgggtcatgatggttcttcttctttgattggatta Find is-nt database================================================ Query_seq: TF0182:TF0184|TF0182:TF0184:DNA-binding protein, HU-related:dihydroneopterin aldolase:->->:195589..195768 180 taagtacgctttacttattctttgaaaaagaagacaatgtgtcaaagagggtgtaccaaaacattgcgttttgatacatcctcttttctagtgaataggtctgctttaggattaaggtatcgcagttgatgggtattgtgaccggtgggtcatgatggttcttcttctttgattggatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0182:TF0184|TF0182:TF0184:DNA-binding protein, HU-related:dihydroneopterin aldolase:->->:195589..195768 180 taagtacgctttacttattctttgaaaaagaagacaatgtgtcaaagagggtgtaccaaaacattgcgttttgatacatcctcttttctagtgaataggtctgctttaggattaaggtatcgcagttgatgggtattgtgaccggtgggtcatgatggttcttcttctttgattggatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0182:TF0184|TF0182:TF0184:DNA-binding protein, HU-related:dihydroneopterin aldolase:->->:195589..195768 180 taagtacgctttacttattctttgaaaaagaagacaatgtgtcaaagagggtgtaccaaaacattgcgttttgatacatcctcttttctagtgaataggtctgctttaggattaaggtatcgcagttgatgggtattgtgaccggtgggtcatgatggttcttcttctttgattggatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagtacgctttacttattctttgaaaaagaagacaatgtgtcaaagagggtgtaccaaaacattgcgttttgatacatcctcttttctagtgaataggtctgctttaggattaaggtatcgcagttgatgggtattgtgaccggtgggtcatgatggttcttcttctttgattggatta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 22 End: 126 ..................... M K K K T M C Q R G C T K T L R F D T S S F L V N R S A L G L R Y R S ...................................................... Protein_Len: 55 Strand: - Start: 14 End: 178 ............. K N K S F S S L T D F L T Y W F M A N Q Y M R K E L S Y T Q K L I L T D C N I P I T V P P D H H N K K K S Q M .. taagtacgctttacttattctttgaaaaagaagacaatgtgtcaaagagggtgtaccaaaacattgcgttttgatacatcctcttttctagtgaataggtctgctttaggattaaggtatcgcagttgatgggtattgtgaccggtgggtcatgatggttcttcttctttgattggatta 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: 85 Start: 17 End: 46 ................TTTGACACATTGTCTTCTTTTTCAAAGAAT...................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagtacgctttacttattctttgaaaaagaagacaatgtgtcaaagagggtgtaccaaaacattgcgttttgatacatcctcttttctagtgaataggtctgctttaggattaaggtatcgcagttgatgggtattgtgaccggtgggtcatgatggttcttcttctttgattggatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -13.2 Tail_Score: -4.4767 Start: 47 End: 83 Full_Region: AGACAATGTGTCAAA GAGGGTGTACCAAAAC ATTGC GTTTTGATACATCCTC TTTTCTAGTGAATAG ..............................................GAGGGTGTACCAAAACATTGCGTTTTGATACATCCTC................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -13.9 Tail_Score: -3.58801 Start: 47 End: 83 Full_Region: ctattcactagaaaa gaggatgtatcaaaacg caa tgttttggtacaccctc tttgacacattgtct ..............................................gaggatgtatcaaaacgcaatgttttggtacaccctc................................................................................................. Find igs database================================================ Query_seq: TF0182:TF0184|TF0182:TF0184:DNA-binding protein, HU-related:dihydroneopterin aldolase:->->:195589..195768 180 taagtacgctttacttattctttgaaaaagaagacaatgtgtcaaagagggtgtaccaaaacattgcgttttgatacatcctcttttctagtgaataggtctgctttaggattaaggtatcgcagttgatgggtattgtgaccggtgggtcatgatggttcttcttctttgattggatta Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: tfor_TF0182_TF0184|DNA-binding protein, HU-related:dihydroneopterin aldolase|POSITIVE:POSITIVE|[195589,195768]|180 HSP 1 e-value: 8.0E-98 bit: 357.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 taagtacgctttacttattctttgaaaaagaagacaatgtgtcaaagagggtgtaccaaaacattgcgttttgatacatcctcttttctagtgaataggtctgctttaggattaaggtatcgcagttgatgggtattgtgaccggtgggtcatgatggttcttcttctttgattggatta taagtacgctttacttattctttgaaaaagaagacaatgtgtcaaagagggtgtaccaaaacattgcgttttgatacatcctcttttctagtgaataggtctgctttaggattaaggtatcgcagttgatgggtattgtgaccggtgggtcatgatggttcttcttctttgattggatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUACGCUUUACUUAUUCUUUGAAAAAGAAGACAAUGUGUCAAAGAGGGUGUACCAAAACAUUGCGUUUUGAUACAUCCUCUUUUCUAGUGAAUAGGUCUGCUUUAGGAUUAAGGUAUCGCAGUUGAUGGGUAUUGUGACCGGUGGGUCAUGAUGGUUCUUCUUCUUUGAUUGGAUUA .......((...((((((((...((((.....(((.....)))..((((((((((.((((((.....)))))).))))))))))))))....))))))))..)).....((((.....((((.((..((.(..(((..(((((....)))))..)).)..).))..)).))))..)))). (-51.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCCAAUCAAAGAAGAAGAACCAUCAUGACCCACCGGUCACAAUACCCAUCAACUGCGAUACCUUAAUCCUAAAGCAGACCUAUUCACUAGAAAAGAGGAUGUAUCAAAACGCAAUGUUUUGGUACACCCUCUUUGACACAUUGUCUUCUUUUUCAAAGAAUAAGUAAAGCGUACUUA ...........((((((((((.......(((((....))))).............((((.................))))..............(((((((.(((((((((((.....))))))))))).))))))).........)))))))))).......((((((.....)))))) (-43.33) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 652 89 47 203 160 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 575 88 45 216 173 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 558 87 44 163 116 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 527 87 44 151 108 tfor:TF2947|5end_isochorismate_synthase_3153633..3153863_POSITIVE 519 89 44 210 161 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 517 87 44 78 35 tfor:TF1046|5end_hypothetical_protein_1108178..1108408_POSITIVE 497 87 47 228 191 tfor:TF1999|5end_ArgK_protein_with_ATPase_and_kinase_domains_2152769..2152999_POSITIVE 477 88 47 195 155 tfor:TF3007|5end_conserved_hypothetical_protein_3227256..3227486_POSITIVE 419 90 44 211 162 tfor:TF2289|5end_secretion_protein,_possible_HlyD_family_2442725..2442955_POSITIVE 414 170 121 187 142 tfor:TF2450|5end_outer_membrane_protein_2626471..2626701_POSITIVE 403 88 45 159 122 tfor:TF2357|5end_collagenase_2522561..2522791_POSITIVE 401 167 121 202 154 tfor:TF1835|5end_possible_dihydroxy-acid_dehydratase_1984201..1984431_POSITIVE 392 86 41 202 151 tfor:TF2320|5end_hypothetical_protein_2476654..2476884_POSITIVE 390 160 116 61 13 tfor:TF2848|5end_cobalamin_biosynthesis_protein_3036368..3036598_POSITIVE 383 89 46 167 124 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 378 77 47 231 199 tfor:TF2414|5end_hypothetical_protein_2590725..2590955_POSITIVE 359 170 122 65 14 tfor:TF2337|5end_conserved_hypothetical_protein_2497997..2498227_POSITIVE 357 164 122 129 79 tfor:TF0274|5end_hypothetical_protein_300232..300462_POSITIVE 355 160 115 217 166 tfor:TF0352|5end_transposase_element_371223..371453_POSITIVE 354 89 44 162 115 tfor:TF0137|5end_conserved_hypothetical_protein_146585..146815_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 652 89 47 64 21 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 522 88 44 58 10 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 522 86 47 113 74 tfor:TF2413|3end_hypothetical_protein_2590680..2590830_POSITIVE 519 89 44 55 6 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 517 87 44 65 22 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 497 87 47 65 28 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 463 108 61 51 1 tfor:TF1504|3end_conserved_hypothetical_protein_1610665..1610815_POSITIVE 404 86 44 47 5 tfor:TF0182|3end_DNA-binding_protein,_HU-related_195528..195678_POSITIVE 392 86 41 56 5 tfor:TF2319|3end_acyl_carrier_protein_2476588..2476738_POSITIVE 390 160 116 82 34 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 359 170 122 147 96 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 355 160 115 140 89 tfor:TF0351|3end_hypothetical_protein_371226..371376_POSITIVE 354 89 44 51 4 tfor:TF0135|3end_hypothetical_protein_146554..146704_POSITIVE 353 108 68 37 1 tfor:TF3006|3end_response_regulator,_transcriptional_regulator_RprY_3227162..3227312_POSITIVE 322 158 121 82 35 tfor:TF2503|3end_conserved_hypothetical_protein_2680111..2680261_POSITIVE 321 148 108 131 92 tfor:TF1145|3end_anaerobic_C4-dicarboxylate_membrane_transporter_1227180..1227330_POSITIVE 320 161 124 149 113 tfor:TF1528|3end_malate_dehydrogenase_1634362..1634512_POSITIVE 317 87 44 58 15 tfor:TF1416|3end_outer_membrane_protein_1499413..1499563_POSITIVE 316 158 118 48 8 tfor:TF1205|3end_beta-glucanase/beta-glucan_synthetase;_endoglucanase_related_1288580..1288730_POSITIVE 310 177 131 71 20 tfor:TF1314|3end_conserved_hypothetical_protein_1390302..1390452_POSITIVE