Origin IGS: cccgcaagggtggggtaattgatacccataccttattcagagggctgaaagcctgacatgatcgttagcggtcagttttcaagcagtcagctatcatccaacaatcaaacaactcaaccattcaacagctcaacgcccgaagggcatcacttttcatttttcgtttttca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaaaaacgaaaaatgaaaagtgatgcccttcgggcgttgagctgttgaatggttgagttgtttgattgttggatgatagctgactgcttgaaaactgaccgctaacgatcatgtcaggctttcagccctctgaataaggtatgggtatcaattaccccacccttgcggg Mask Tandem Repeat Region ================================================ cccgcaagggtggggtaattgatacccataccttattcagagggctgaaagcctgacatgatcgttagcggtcagttttcaagcagtcagctatcatccaacaatcaaacaactcaaccattcaacagctcaacgcccgaagggcatcacttttcatttttcgtttttca Find is-nt database================================================ Query_seq: TF0340:TF0341|TF0340:TF0341:hypothetical protein:conserved hypothetical protein:->->:364318..364487 170 cccgcaagggtggggtaattgatacccataccttattcagagggctgaaagcctgacatgatcgttagcggtcagttttcaagcagtcagctatcatccaacaatcaaacaactcaaccattcaacagctcaacgcccgaagggcatcacttttcatttttcgtttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0340:TF0341|TF0340:TF0341:hypothetical protein:conserved hypothetical protein:->->:364318..364487 170 cccgcaagggtggggtaattgatacccataccttattcagagggctgaaagcctgacatgatcgttagcggtcagttttcaagcagtcagctatcatccaacaatcaaacaactcaaccattcaacagctcaacgcccgaagggcatcacttttcatttttcgtttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0340:TF0341|TF0340:TF0341:hypothetical protein:conserved hypothetical protein:->->:364318..364487 170 cccgcaagggtggggtaattgatacccataccttattcagagggctgaaagcctgacatgatcgttagcggtcagttttcaagcagtcagctatcatccaacaatcaaacaactcaaccattcaacagctcaacgcccgaagggcatcacttttcatttttcgtttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cccgcaagggtggggtaattgatacccataccttattcagagggctgaaagcctgacatgatcgttagcggtcagttttcaagcagtcagctatcatccaacaatcaaacaactcaaccattcaacagctcaacgcccgaagggcatcacttttcatttttcgtttttca Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 58 End: 168 ......................................................... M I V S G Q F S S S Q L S S N N Q T T Q P F N S S T P E G H H F S F F V F .. cccgcaagggtggggtaattgatacccataccttattcagagggctgaaagcctgacatgatcgttagcggtcagttttcaagcagtcagctatcatccaacaatcaaacaactcaaccattcaacagctcaacgcccgaagggcatcacttttcatttttcgtttttca 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================================================ cccgcaagggtggggtaattgatacccataccttattcagagggctgaaagcctgacatgatcgttagcggtcagttttcaagcagtcagctatcatccaacaatcaaacaactcaaccattcaacagctcaacgcccgaagggcatcacttttcatttttcgtttttca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0340:TF0341|TF0340:TF0341:hypothetical protein:conserved hypothetical protein:->->:364318..364487 170 cccgcaagggtggggtaattgatacccataccttattcagagggctgaaagcctgacatgatcgttagcggtcagttttcaagcagtcagctatcatccaacaatcaaacaactcaaccattcaacagctcaacgcccgaagggcatcacttttcatttttcgtttttca Intra-Species Hit: Count: 2 Min: 1 Max: 170 Len: 170 Subject: tfor_TF0340_TF0341|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[364318,364487]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 cccgcaagggtggggtaattgatacccataccttattcagagggctgaaagcctgacatgatcgttagcggtcagttttcaagcagtcagctatcatccaacaatcaaacaactcaaccattcaacagctcaacgcccgaagggcatcacttttcatttttcgtttttca cccgcaagggtggggtaattgatacccataccttattcagagggctgaaagcctgacatgatcgttagcggtcagttttcaagcagtcagctatcatccaacaatcaaacaactcaaccattcaacagctcaacgcccgaagggcatcacttttcatttttcgtttttca Subject: tfor_TF2172_TF2174|hypothetical protein:possible endopeptidase precursor|POSITIVE:POSITIVE|[2346196,2346431]|236 HSP 1 e-value: 7.0E-12 bit: 71.9 Len: 89 Query Start:30 Query End:118 Subject Strand: POSITIVE Subject Start: 72 Subject End: 166 .............................accttattcagagggctgaaagcctgacatgatcgttagcggtcagttttca------agcagtcagctatcatccaacaatcaaacaactcaac.................................................... .............................accttgttcggagggctgtaagcctgacatgatcgttagcgatcagtattcagtattcagccatcagcttccatccaacaatcaaacaactcaac.................................................... HSP 2 e-value: 2.0E-8 bit: 60.0 Len: 58 Query Start:111 Query End:168 Subject Strand: POSITIVE Subject Start: 168 Subject End: 225 ..............................................................................................................aactcaaccattcaacagctcaacgcccgaagggcatcacttttcatttttcgttttt.. ..............................................................................................................aactcaacatttcaacatccaaacgcccgaagggcatcacttttcacttttagttttt.. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCGCAAGGGUGGGGUAAUUGAUACCCAUACCUUAUUCAGAGGGCUGAAAGCCUGACAUGAUCGUUAGCGGUCAGUUUUCAAGCAGUCAGCUAUCAUCCAACAAUCAAACAACUCAACCAUUCAACAGCUCAACGCCCGAAGGGCAUCACUUUUCAUUUUUCGUUUUUCA ...((.(((((((((((.....))))).)))))).....((.((((((..((.(((..((((((....))))))....))).))..)))))).))................................)).....((((...))))......................... (-44.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAAACGAAAAAUGAAAAGUGAUGCCCUUCGGGCGUUGAGCUGUUGAAUGGUUGAGUUGUUUGAUUGUUGGAUGAUAGCUGACUGCUUGAAAACUGACCGCUAACGAUCAUGUCAGGCUUUCAGCCCUCUGAAUAAGGUAUGGGUAUCAAUUACCCCACCCUUGCGGG .....................(((((((((((((.((((.(((.((..((..(.....)..))..)).))).))))...(((((..((((((....(((.((....)).)))..))))))..)))))...)))))........))))))))....(((((....)).))) (-46.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 761 90 41 121 73 tfor:TF2840|5end_hypothetical_protein_3031060..3031290_POSITIVE 740 90 41 205 157 tfor:TF3105|5end_hypothetical_protein_3338068..3338298_POSITIVE 636 76 31 230 183 tfor:TF1655|5end_long-chain-fatty-acid-CoA_ligase_1769279..1769509_POSITIVE 569 61 25 231 195 tfor:TF2745|5end_hypothetical_protein_2927562..2927792_POSITIVE 568 44 1 231 189 tfor:TF0678|5end_hypothetical_protein_721103..721333_POSITIVE 549 49 1 87 38 tfor:TF2547|5end_hypothetical_protein_2730664..2730894_POSITIVE 465 169 122 183 136 tfor:TF1818|5end_conserved_hypothetical_protein_1957967..1958197_POSITIVE 440 67 38 75 46 tfor:TF1405|5end_conserved_hypothetical_protein_1480285..1480515_POSITIVE 417 165 121 231 185 tfor:TF1205|5end_beta-glucanase/beta-glucan_synthetase;_endoglucanase_related_1287556..1287786_POSITIVE 408 26 1 228 203 tfor:TF0822|5end_hypothetical_protein_880487..880717_POSITIVE 408 26 1 228 203 tfor:TF0821|5end_hypothetical_protein_879879..880109_POSITIVE 405 50 2 212 162 tfor:TF3082|5end_conserved_hypothetical_protein_3316431..3316661_POSITIVE 405 50 2 91 41 tfor:TF2202|5end_hypothetical_protein_2378682..2378912_POSITIVE 383 56 11 217 163 tfor:TF2191|5end_hypothetical_protein_2365934..2366164_POSITIVE 380 107 65 210 168 tfor:TF0532|5end_hypothetical_protein_557509..557739_POSITIVE 378 100 51 194 140 tfor:TF1973|5end_propionyl-CoA_carboxylase,_beta_subunit_2119360..2119590_POSITIVE 377 50 2 91 41 tfor:TF1516|5end_transposase_fragment_1626407..1626637_POSITIVE 376 60 11 227 181 tfor:TF2641|5end_riboflavin_kinase/FAD_synthase_2809681..2809911_POSITIVE 372 48 1 71 23 tfor:TF2993|5end_SAM-dependent_methyltransferase_3209636..3209866_POSITIVE 364 69 24 85 43 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 728 170 124 81 35 tfor:TF1715|3end_thermolysin;_zinc_metalloprotease_1837202..1837352_POSITIVE 598 160 111 66 2 tfor:TF1657|3end_lauroyl/myristoyl_acyltransferase_1773407..1773557_POSITIVE 487 170 121 61 10 tfor:TF1204|3end_possible_metal-dependent_membrane_protease_1287461..1287611_POSITIVE 465 169 122 110 63 tfor:TF1816|3end_hypothetical_protein_1957974..1958124_POSITIVE 465 169 122 127 80 tfor:TF1817|3end_hypothetical_protein_1957991..1958141_POSITIVE 456 76 31 78 29 tfor:TF0018|3end_hypothetical_protein_12091..12241_POSITIVE 440 76 31 105 55 tfor:TF1762|3end_hypothetical_protein_1899648..1899798_POSITIVE 425 60 11 74 28 tfor:TF2922|3end_surface_antigen_BspA_3121538..3121688_POSITIVE 423 61 24 87 55 tfor:TF1585|3end_hypothetical_protein_1690610..1690760_POSITIVE 423 61 24 80 48 tfor:TF1584|3end_hypothetical_protein_1690603..1690753_POSITIVE 422 56 14 42 1 tfor:TF0677|3end_ATP-binding_protein,_Mrp/Nbp35_family,_involved_in_chromosome_partitioning_720982..721132_POSITIVE 421 147 104 75 30 tfor:TF2839|3end_ATP-dependent_exodeoxyribonuclease_3031035..3031185_POSITIVE 380 107 65 90 48 tfor:TF0531|3end_hypothetical_protein_557469..557619_POSITIVE 377 56 11 48 5 tfor:TF2169|3end_hypothetical_protein_2345354..2345504_POSITIVE 368 67 41 27 1 tfor:TF1404|3end_conserved_hypothetical_protein_1480317..1480467_POSITIVE 359 76 40 38 7 tfor:TF2047|3end_hypothetical_protein_2210298..2210448_POSITIVE 357 170 135 90 60 tfor:TF2100|3end_hypothetical_protein_2273686..2273836_POSITIVE 350 73 40 47 2 tfor:TF1839|3end_conserved_hypothetical_protein_1989699..1989849_POSITIVE 343 87 41 119 59 tfor:TF2350|3end_hypothetical_protein_2515364..2515514_POSITIVE 343 87 41 151 100 tfor:TF0490|3end_conserved_hypothetical_protein_513904..514054_POSITIVE