Origin IGS: taaaaatccaaaaacggagagctaccctttgcatcggatgatggagggtagctgcttcttgtgcttttatcagcattcataagcctatcgcaagtgttgaattgtttagttgtttgttaaggtgtttgattgttgaggtgttgaattgtttagttgtttgttgaggtgttcgattgttgaggtgttgagttgttgatctgtttgctgaccgttgtaaaagccctgaaagggcgcattaattcagcccaatgtggagcgaagcgagttacctgattttccgacctgcgagcgtcgcaacggcgt .........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 acgccgttgcgacgctcgcaggtcggaaaatcaggtaactcgcttcgctccacattgggctgaattaatgcgccctttcagggcttttacaacggtcagcaaacagatcaacaactcaacacctcaacaatcgaacacctcaacaaacaactaaacaattcaacacctcaacaatcaaacaccttaacaaacaactaaacaattcaacacttgcgataggcttatgaatgctgataaaagcacaagaagcagctaccctccatcatccgatgcaaagggtagctctccgtttttggattttta Mask Tandem Repeat Region ================================================ taaaaatccaaaaacggagagctaccctttgcatcggatgatggagggtagctgcttcttgtgcttttatcagcattcataagcctatcgcaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntctgtttgctgaccgttgtaaaagccctgaaagggcgcattaattcagcccaatgtggagcgaagcgagttacctgattttccgacctgcgagcgtcgcaacggcgt Find is-nt database================================================ Query_seq: TF2515:TF2517|TF2515:TF2517:outer membrane protein, TonB dependent receptor:hypothetical protein:->->:2694926..2695228 303 taaaaatccaaaaacggagagctaccctttgcatcggatgatggagggtagctgcttcttgtgcttttatcagcattcataagcctatcgcaagtgttgaattgtttagttgtttgttaaggtgtttgattgttgaggtgttgaattgtttagttgtttgttgaggtgttcgattgttgaggtgttgagttgttgatctgtttgctgaccgttgtaaaagccctgaaagggcgcattaattcagcccaatgtggagcgaagcgagttacctgattttccgacctgcgagcgtcgcaacggcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2515:TF2517|TF2515:TF2517:outer membrane protein, TonB dependent receptor:hypothetical protein:->->:2694926..2695228 303 taaaaatccaaaaacggagagctaccctttgcatcggatgatggagggtagctgcttcttgtgcttttatcagcattcataagcctatcgcaagtgttgaattgtttagttgtttgttaaggtgtttgattgttgaggtgttgaattgtttagttgtttgttgaggtgttcgattgttgaggtgttgagttgttgatctgtttgctgaccgttgtaaaagccctgaaagggcgcattaattcagcccaatgtggagcgaagcgagttacctgattttccgacctgcgagcgtcgcaacggcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2515:TF2517|TF2515:TF2517:outer membrane protein, TonB dependent receptor:hypothetical protein:->->:2694926..2695228 303 taaaaatccaaaaacggagagctaccctttgcatcggatgatggagggtagctgcttcttgtgcttttatcagcattcataagcctatcgcaagtgttgaattgtttagttgtttgttaaggtgtttgattgttgaggtgttgaattgtttagttgtttgttgaggtgttcgattgttgaggtgttgagttgttgatctgtttgctgaccgttgtaaaagccctgaaagggcgcattaattcagcccaatgtggagcgaagcgagttacctgattttccgacctgcgagcgtcgcaacggcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaatccaaaaacggagagctaccctttgcatcggatgatggagggtagctgcttcttgtgcttttatcagcattcataagcctatcgcaagtgttgaattgtttagttgtttgttaaggtgtttgattgttgaggtgttgaattgtttagttgtttgttgaggtgttcgattgttgaggtgttgagttgttgatctgtttgctgaccgttgtaaaagccctgaaagggcgcattaattcagcccaatgtggagcgaagcgagttacctgattttccgacctgcgagcgtcgcaacggcgt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 69 End: 161 .................................................................... M S I H K P I A S V E L F S C L L R C L I V E V L N C L V V C .............................................................................................................................................. Protein_Len: 44 Strand: - Start: 109 End: 240 ............................................................................................................ N N T L T N S Q Q P T S N N L Q K N L H E I T S T N L Q Q D T Q Q G N Y F G Q F P A N M ............................................................... taaaaatccaaaaacggagagctaccctttgcatcggatgatggagggtagctgcttcttgtgcttttatcagcattcataagcctatcgcaagtgttgaattgtttagttgtttgttaaggtgtttgattgttgaggtgttgaattgtttagttgtttgttgaggtgttcgattgttgaggtgttgagttgttgatctgtttgctgaccgttgtaaaagccctgaaagggcgcattaattcagcccaatgtggagcgaagcgagttacctgattttccgacctgcgagcgtcgcaacggcgt 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================================================ taaaaatccaaaaacggagagctaccctttgcatcggatgatggagggtagctgcttcttgtgcttttatcagcattcataagcctatcgcaagtgttgaattgtttagttgtttgttaaggtgtttgattgttgaggtgttgaattgtttagttgtttgttgaggtgttcgattgttgaggtgttgagttgttgatctgtttgctgaccgttgtaaaagccctgaaagggcgcattaattcagcccaatgtggagcgaagcgagttacctgattttccgacctgcgagcgtcgcaacggcgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 83 HP_score: -9.1 Tail_Score: -4.08767 Start: 220 End: 232 Full_Region: gggctgaattaatgc gccct ttc agggc ttttacaacggtcag ...........................................................................................................................................................................................................................gccctttcagggc....................................................................... Find igs database================================================ Query_seq: TF2515:TF2517|TF2515:TF2517:outer membrane protein, TonB dependent receptor:hypothetical protein:->->:2694926..2695228 303 taaaaatccaaaaacggagagctaccctttgcatcggatgatggagggtagctgcttcttgtgcttttatcagcattcataagcctatcgcaagtgttgaattgtttagttgtttgttaaggtgtttgattgttgaggtgttgaattgtttagttgtttgttgaggtgttcgattgttgaggtgttgagttgttgatctgtttgctgaccgttgtaaaagccctgaaagggcgcattaattcagcccaatgtggagcgaagcgagttacctgattttccgacctgcgagcgtcgcaacggcgt Intra-Species Hit: Count: 1 Min: 1 Max: 303 Len: 303 Subject: tfor_TF2515_TF2517|outer membrane protein, TonB dependent receptor:hypothetical protein|POSITIVE:POSITIVE|[2694926,2695228]|303 HSP 1 e-value: 3.0E-46 bit: 186.0 Len: 94 Query Start:1 Query End:94 Subject Strand: POSITIVE Subject Start: 1 Subject End: 94 taaaaatccaaaaacggagagctaccctttgcatcggatgatggagggtagctgcttcttgtgcttttatcagcattcataagcctatcgcaag................................................................................................................................................................................................................. taaaaatccaaaaacggagagctaccctttgcatcggatgatggagggtagctgcttcttgtgcttttatcagcattcataagcctatcgcaag................................................................................................................................................................................................................. HSP 2 e-value: 1.0E-42 bit: 174.0 Len: 88 Query Start:216 Query End:303 Subject Strand: POSITIVE Subject Start: 216 Subject End: 303 .......................................................................................................................................................................................................................aaaagccctgaaagggcgcattaattcagcccaatgtggagcgaagcgagttacctgattttccgacctgcgagcgtcgcaacggcgt .......................................................................................................................................................................................................................aaaagccctgaaagggcgcattaattcagcccaatgtggagcgaagcgagttacctgattttccgacctgcgagcgtcgcaacggcgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAUCCAAAAACGGAGAGCUACCCUUUGCAUCGGAUGAUGGAGGGUAGCUGCUUCUUGUGCUUUUAUCAGCAUUCAUAAGCCUAUCGCAAGUGUUGAAUUGUUUAGUUGUUUGUUAAGGUGUUUGAUUGUUGAGGUGUUGAAUUGUUUAGUUGUUUGUUGAGGUGUUCGAUUGUUGAGGUGUUGAGUUGUUGAUCUGUUUGCUGACCGUUGUAAAAGCCCUGAAAGGGCGCAUUAAUUCAGCCCAAUGUGGAGCGAAGCGAGUUACCUGAUUUUCCGACCUGCGAGCGUCGCAACGGCGU ...............((((((((((((((..((((....)))))))))))))).))))....((.....((((((.(((...((((...((((..(...((....))...)..))))..))))...))).)))))).......................((((.(..(((((...((((.((.(((((((((.((.....(((((........))))).((((.....)))).)).))))))))))).....(((((.......))).))........))))...)))))..).)))).)).. (-85.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGCCGUUGCGACGCUCGCAGGUCGGAAAAUCAGGUAACUCGCUUCGCUCCACAUUGGGCUGAAUUAAUGCGCCCUUUCAGGGCUUUUACAACGGUCAGCAAACAGAUCAACAACUCAACACCUCAACAAUCGAACACCUCAACAAACAACUAAACAAUUCAACACCUCAACAAUCAAACACCUUAACAAACAACUAAACAAUUCAACACUUGCGAUAGGCUUAUGAAUGCUGAUAAAAGCACAAGAAGCAGCUACCCUCCAUCAUCCGAUGCAAAGGGUAGCUCUCCGUUUUUGGAUUUUUA .(((....)))....((((((((..(((....((((..........((((......)))).(((((.....((((.....)))).........((((........))))...............................................)))))...))))...............(((.........)))....)))...))))))))...((((.....((((......))))....)))).((((((((.((((....))))...))))))))..((((....))))...... (-61.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 909 300 252 87 39 tfor:TF1588|5end_hypothetical_protein_1702268..1702498_POSITIVE 905 300 251 77 26 tfor:TF2996|5end_hypothetical_protein_3210802..3211032_POSITIVE 885 260 211 224 175 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 863 300 251 103 52 tfor:TF2997|5end_hypothetical_protein_3211408..3211638_POSITIVE 835 250 201 171 122 tfor:TF2641|5end_riboflavin_kinase/FAD_synthase_2809681..2809911_POSITIVE 831 258 211 226 179 tfor:TF2351|5end_acetate_kinase_2515480..2515710_POSITIVE 831 299 254 86 41 tfor:TF1168|5end_hypothetical_protein_1248755..1248985_POSITIVE 812 300 251 103 52 tfor:TF1578|5end_hypothetical_protein_1686187..1686417_POSITIVE 762 258 211 204 157 tfor:TF0346|5end_hypothetical_protein_367048..367278_POSITIVE 762 258 211 204 157 tfor:TF0340|5end_hypothetical_protein_363893..364123_POSITIVE 719 264 221 228 185 tfor:TF0468|5end_hypothetical_protein_486929..487159_POSITIVE 714 258 216 228 186 tfor:TF1175|5end_membrane-fusion_protein_1258140..1258370_POSITIVE 690 260 211 212 163 tfor:TF2172|5end_hypothetical_protein_2345822..2346052_POSITIVE 690 260 211 206 157 tfor:TF2173|5end_hypothetical_protein_2345816..2346046_POSITIVE 690 250 204 196 150 tfor:TF2171|5end_hypothetical_protein_2345485..2345715_POSITIVE 690 250 204 196 150 tfor:TF2166|5end_hypothetical_protein_2342115..2342345_POSITIVE 654 300 254 217 171 tfor:TF2670|5end_hypothetical_protein_2842779..2843009_POSITIVE 654 300 254 231 185 tfor:TF2666|5end_hypothetical_protein_2841818..2842048_POSITIVE 643 258 219 115 76 tfor:TF1274|5end_hypothetical_protein_1357621..1357851_POSITIVE 583 265 221 148 103 tfor:TF2127|5end_hypothetical_protein_2304038..2304268_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 825 300 257 44 1 tfor:TF2994|3end_hypothetical_protein_3210849..3210999_POSITIVE 812 300 251 70 19 tfor:TF1577|3end_hypothetical_protein_1686234..1686384_POSITIVE 772 264 221 47 4 tfor:TF0958|3end_conserved_hypothetical_protein_1004909..1005059_POSITIVE 739 260 211 149 100 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 714 258 211 116 69 tfor:TF1592|3end_hypothetical_protein_1708557..1708707_POSITIVE 690 260 211 102 53 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 680 257 211 115 69 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 677 258 220 39 1 tfor:TF0344|3end_hypothetical_protein_366963..367113_POSITIVE 657 270 221 57 2 tfor:TF1585|3end_hypothetical_protein_1690610..1690760_POSITIVE 654 300 254 91 45 tfor:TF2668|3end_hypothetical_protein_2842733..2842883_POSITIVE 654 300 254 63 17 tfor:TF2667|3end_hypothetical_protein_2842705..2842855_POSITIVE 654 300 254 63 17 tfor:TF2664|3end_hypothetical_protein_2841730..2841880_POSITIVE 653 258 219 109 70 tfor:TF2025|3end_hypothetical_protein_2182180..2182330_POSITIVE 610 300 251 63 13 tfor:TF2665|3end_hypothetical_protein_2842235..2842385_POSITIVE 610 300 251 91 41 tfor:TF2666|3end_hypothetical_protein_2842263..2842413_POSITIVE 548 258 219 63 24 tfor:TF2342|3end_glutathione_peroxidase_2506639..2506789_POSITIVE 510 270 227 50 1 tfor:TF1584|3end_hypothetical_protein_1690603..1690753_POSITIVE 496 270 229 51 1 tfor:TF2350|3end_hypothetical_protein_2515364..2515514_POSITIVE 452 234 191 148 89 tfor:TF1170|3end_conserved_hypothetical_protein_1252799..1252949_POSITIVE 440 264 237 28 1 tfor:TF1762|3end_hypothetical_protein_1899648..1899798_POSITIVE