Origin IGS: atcaagatgtttttgaaattacaccgacaaatctacaaaaaaacagggatttcatccatgccgagaaataaaaatcaaaacagaccggagaagacagacgatcggaagcacactctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagagtgtgcttccgatcgtctgtcttctccggtctgttttgatttttatttctcggcatggatgaaatccctgtttttttgtagatttgtcggtgtaatttcaaaaacatcttgat Mask Tandem Repeat Region ================================================ atcaagatgtttttgaaattacaccgacaaatctacaaaaaaacagggatttcatccatgccgagaaataaaaatcaaaacagaccggagaagacagacgatcggaagcacactctta Find is-nt database================================================ Query_seq: TF0576:TF0577|TF0576:TF0577:hypothetical protein:possible endo-1,4-beta-xylanase B:->->:606997..607114 118 atcaagatgtttttgaaattacaccgacaaatctacaaaaaaacagggatttcatccatgccgagaaataaaaatcaaaacagaccggagaagacagacgatcggaagcacactctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0576:TF0577|TF0576:TF0577:hypothetical protein:possible endo-1,4-beta-xylanase B:->->:606997..607114 118 atcaagatgtttttgaaattacaccgacaaatctacaaaaaaacagggatttcatccatgccgagaaataaaaatcaaaacagaccggagaagacagacgatcggaagcacactctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0576:TF0577|TF0576:TF0577:hypothetical protein:possible endo-1,4-beta-xylanase B:->->:606997..607114 118 atcaagatgtttttgaaattacaccgacaaatctacaaaaaaacagggatttcatccatgccgagaaataaaaatcaaaacagaccggagaagacagacgatcggaagcacactctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcaagatgtttttgaaattacaccgacaaatctacaaaaaaacagggatttcatccatgccgagaaataaaaatcaaaacagaccggagaagacagacgatcggaagcacactctta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 1 End: 117 M K M F L K L H R Q I Y K K T G I S S M P R N K N Q N R P E K T D D R K H T L . Protein_Len: 32 Strand: - Start: 5 End: 97 .... * S T K S I V G V F R C F F L S K M W A S F Y F D F C V P S S M ..................... atcaagatgtttttgaaattacaccgacaaatctacaaaaaaacagggatttcatccatgccgagaaataaaaatcaaaacagaccggagaagacagacgatcggaagcacactctta 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================================================ atcaagatgtttttgaaattacaccgacaaatctacaaaaaaacagggatttcatccatgccgagaaataaaaatcaaaacagaccggagaagacagacgatcggaagcacactctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 86 HP_score: -5.1 Tail_Score: -5.68039 Start: 44 End: 60 Full_Region: atttttatttctcgg catggat gaa atccctg tttttttgtagattt ...........................................catggatgaaatccctg.......................................................... Find igs database================================================ Query_seq: TF0576:TF0577|TF0576:TF0577:hypothetical protein:possible endo-1,4-beta-xylanase B:->->:606997..607114 118 atcaagatgtttttgaaattacaccgacaaatctacaaaaaaacagggatttcatccatgccgagaaataaaaatcaaaacagaccggagaagacagacgatcggaagcacactctta Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: tfor_TF0576_TF0577|hypothetical protein:possible endo-1,4-beta-xylanase B|POSITIVE:POSITIVE|[606997,607114]|118 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 atcaagatgtttttgaaattacaccgacaaatctacnnnnnnncagggatttcatccatgccgagaaataaaaatcaaaacagaccggagaagacagacgatcggaagcacactctta atcaagatgtttttgaaattacaccgacaaatctacaaaaaaacagggatttcatccatgccgagaaataaaaatcaaaacagaccggagaagacagacgatcggaagcacactctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAGAUGUUUUUGAAAUUACACCGACAAAUCUACAAAAAAACAGGGAUUUCAUCCAUGCCGAGAAAUAAAAAUCAAAACAGACCGGAGAAGACAGACGAUCGGAAGCACACUCUUA ...(((((((((((((..............................((((...))))...(((......................))).............)))))))))...)))). (-12.85) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAGUGUGCUUCCGAUCGUCUGUCUUCUCCGGUCUGUUUUGAUUUUUAUUUCUCGGCAUGGAUGAAAUCCCUGUUUUUUUGUAGAUUUGUCGGUGUAAUUUCAAAAACAUCUUGAU ...(((..(((..(((((.(((((........((((......))))..........((((.((((...)))).))))......)))))..))))).)))..))).............. (-18.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 107 63 164 127 tfor:TF2528|5end_anti-sigma_factor_2708961..2709191_POSITIVE 314 88 43 52 11 tfor:TF2810|5end_conserved_hypothetical_protein_3000583..3000813_POSITIVE 298 69 22 120 79 tfor:TF2205|5end_conserved_hypothetical_protein;_possible_transcriptional_regulator_2379055..2379285_POSITIVE 298 76 31 99 53 tfor:TF2192|5end_possible__outer_membrane_protein_2366392..2366622_POSITIVE 294 110 65 42 1 tfor:TF2410|5end_possible_endo-1,4-beta-xylanase_2584000..2584230_POSITIVE 282 108 62 169 116 tfor:TF2209|5end_conserved_hypothetical_protein_2383948..2384178_POSITIVE 282 90 43 74 38 tfor:TF0137|5end_conserved_hypothetical_protein_146585..146815_POSITIVE 272 109 79 70 38 tfor:TF3068|5end_flavodoxin_A_3292812..3293042_POSITIVE 265 106 61 123 72 tfor:TF2822|5end_arginine_repressor_3011793..3012023_POSITIVE 265 107 61 187 141 tfor:TF1743|5end_conserved_hypothetical_protein_1876708..1876938_POSITIVE 261 106 61 151 107 tfor:TF0086|5end_ABC_transporter,_ATP-binding_protein_92434..92664_POSITIVE 253 109 64 227 178 tfor:TF2121|5end_phosphoenolpyruvate_synthase_2294167..2294397_POSITIVE 252 105 61 136 86 tfor:TF2280|5end_hypothetical_protein_2439140..2439370_POSITIVE 250 103 61 75 32 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 249 107 63 103 46 tfor:TF0880|5end_conserved_hypothetical_protein_934010..934240_POSITIVE 249 76 35 161 123 tfor:TF0436|5end_conserved_hyothetical_protein_459207..459437_POSITIVE 248 108 62 194 152 tfor:TF1176|5end_outer_membrane_protein_1259555..1259785_POSITIVE 248 110 80 129 97 tfor:TF0812|5end_conserved_hypothetical_protein_872087..872317_POSITIVE 247 99 54 158 114 tfor:TF0561|5end_DNA_binding_protein;_possible__HU_protein_593548..593778_POSITIVE 246 108 63 114 69 tfor:TF2278|5end_conserved_hypothetical_protein_2438662..2438892_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 107 63 130 93 tfor:TF2526|3end_outer_membrane_protein,_TonB_dependent_receptor_2709007..2709157_POSITIVE 298 69 22 107 66 tfor:TF2204|3end_conserved_hypothetical_protein_2379122..2379272_POSITIVE 294 110 65 117 76 tfor:TF2409|3end_hypothetical_protein_2584155..2584305_POSITIVE 282 108 62 129 76 tfor:TF2208|3end_conserved_hypothetical_protein_2383988..2384138_POSITIVE 273 69 25 70 21 tfor:TF2356|3end_PAP2_superfamily_protein_2522409..2522559_POSITIVE 272 109 79 55 23 tfor:TF3067|3end_conserved_hypothetical_protein_3292877..3293027_POSITIVE 265 106 61 123 72 tfor:TF2821|3end_conserved_hypothetical_protein_3011873..3012023_POSITIVE 265 107 61 87 41 tfor:TF1742|3end_TPR_repeat-containing_protein_1876688..1876838_POSITIVE 261 106 61 151 107 tfor:TF0085|3end_ABC_transporter,_ATP-binding_protein_92514..92664_POSITIVE 253 109 64 125 76 tfor:TF2122|3end_NAD-specific_glutamate_dehydrogenase_2294145..2294295_POSITIVE 252 105 61 103 53 tfor:TF2279|3end_hypothetical_protein_2439187..2439337_POSITIVE 250 103 61 69 26 tfor:TF2275|3end_conserved_hypothetical_protein_2438300..2438450_POSITIVE 249 107 63 98 41 tfor:TF0879|3end_TraG_family_protein_934085..934235_POSITIVE 248 110 80 143 111 tfor:TF0813|3end_glycosyl_hydrolase,_secreted_872181..872331_POSITIVE 246 110 82 50 17 tfor:TF3113|3end_hypothetical_protein_3349706..3349856_POSITIVE 246 108 63 97 52 tfor:TF2276|3end_conserved_hypothetical_protein_2438725..2438875_POSITIVE 244 100 55 90 50 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 243 104 64 116 73 tfor:TF0226|3end_hypothetical_protein_253847..253997_POSITIVE 241 110 72 148 98 tfor:TF2270|3end_conserved_hypothetical_protein_2435761..2435911_POSITIVE 240 108 64 120 64 tfor:TF0093|3end_outer_membrane_protein,_TonB_dependent_receptor_103618..103768_POSITIVE