Origin IGS: ttgctccgaaagaaattgttcttgtttattgattcaaagatactgtttttaccttgttccaccaagcaaagtctatactttcatgtacccatggatcgcgggatagctggaaactatttgggaatatccctaaaacaagaaaaaaatcaatcgtttaataatcaactttttagatatttgtttcgtacccagacccggtacaaagtatgtataataagagaaataaaaagaatatattatgctgacaatcagttatttataattttcttatgtttggcaattttgctcatttttacctgtttttggttgaatagtacacttttagtacactttgatattcggaactttttagtatctttgcaaaataagaaaacatctgaaaataaatgagttaatgattttactcggttctatactcattcaggtacataactatcaatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattgatagttatgtacctgaatgagtatagaaccgagtaaaatcattaactcatttattttcagatgttttcttattttgcaaagatactaaaaagttccgaatatcaaagtgtactaaaagtgtactattcaaccaaaaacaggtaaaaatgagcaaaattgccaaacataagaaaattataaataactgattgtcagcataatatattctttttatttctcttattatacatactttgtaccgggtctgggtacgaaacaaatatctaaaaagttgattattaaacgattgatttttttcttgttttagggatattcccaaatagtttccagctatcccgcgatccatgggtacatgaaagtatagactttgcttggtggaacaaggtaaaaacagtatctttgaatcaataaacaagaacaatttctttcggagcaa Mask Tandem Repeat Region ================================================ ttgctccgaaagaaattgttcttgtttattgattcaaagatactgtttttaccttgttccaccaagcaaagtctatactttcatgtacccatggatcgcgggatagctggaaactatttgggaatatccctaaaacaagaaaaaaatcaatcgtttaataatcaactttttagatatttgtttcgtacccagacccggtacaaagtatgtataataagagaaataaaaagaatatattatgctgacaatcagttatttataattttcttatgtttggcaattttgctcatttttacctgtttttggttgaatagtacacttttagtacactttgatattcggaactttttagtatctttgcaaaataagaaaacatctgaaaataaatgagttaatgattttactcggttctatactcattcaggtacataactatcaatt Find is-nt database================================================ Query_seq: TF2954:TF2955|TF2954:TF2955:outer membrane protein, TonB dependent receptor:integrase:->->:3162182..3162622 441 ttgctccgaaagaaattgttcttgtttattgattcaaagatactgtttttaccttgttccaccaagcaaagtctatactttcatgtacccatggatcgcgggatagctggaaactatttgggaatatccctaaaacaagaaaaaaatcaatcgtttaataatcaactttttagatatttgtttcgtacccagacccggtacaaagtatgtataataagagaaataaaaagaatatattatgctgacaatcagttatttataattttcttatgtttggcaattttgctcatttttacctgtttttggttgaatagtacacttttagtacactttgatattcggaactttttagtatctttgcaaaataagaaaacatctgaaaataaatgagttaatgattttactcggttctatactcattcaggtacataactatcaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2954:TF2955|TF2954:TF2955:outer membrane protein, TonB dependent receptor:integrase:->->:3162182..3162622 441 ttgctccgaaagaaattgttcttgtttattgattcaaagatactgtttttaccttgttccaccaagcaaagtctatactttcatgtacccatggatcgcgggatagctggaaactatttgggaatatccctaaaacaagaaaaaaatcaatcgtttaataatcaactttttagatatttgtttcgtacccagacccggtacaaagtatgtataataagagaaataaaaagaatatattatgctgacaatcagttatttataattttcttatgtttggcaattttgctcatttttacctgtttttggttgaatagtacacttttagtacactttgatattcggaactttttagtatctttgcaaaataagaaaacatctgaaaataaatgagttaatgattttactcggttctatactcattcaggtacataactatcaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2954:TF2955|TF2954:TF2955:outer membrane protein, TonB dependent receptor:integrase:->->:3162182..3162622 441 ttgctccgaaagaaattgttcttgtttattgattcaaagatactgtttttaccttgttccaccaagcaaagtctatactttcatgtacccatggatcgcgggatagctggaaactatttgggaatatccctaaaacaagaaaaaaatcaatcgtttaataatcaactttttagatatttgtttcgtacccagacccggtacaaagtatgtataataagagaaataaaaagaatatattatgctgacaatcagttatttataattttcttatgtttggcaattttgctcatttttacctgtttttggttgaatagtacacttttagtacactttgatattcggaactttttagtatctttgcaaaataagaaaacatctgaaaataaatgagttaatgattttactcggttctatactcattcaggtacataactatcaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgctccgaaagaaattgttcttgtttattgattcaaagatactgtttttaccttgttccaccaagcaaagtctatactttcatgtacccatggatcgcgggatagctggaaactatttgggaatatccctaaaacaagaaaaaaatcaatcgtttaataatcaactttttagatatttgtttcgtacccagacccggtacaaagtatgtataataagagaaataaaaagaatatattatgctgacaatcagttatttataattttcttatgtttggcaattttgctcatttttacctgtttttggttgaatagtacacttttagtacactttgatattcggaactttttagtatctttgcaaaataagaaaacatctgaaaataaatgagttaatgattttactcggttctatactcattcaggtacataactatcaatt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 54 End: 155 ..................................................... M F H Q A K S I L S C T H G S R D S W K L F G N I P K T R K K S I V .............................................................................................................................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 1 End: 387 M L R K K L F L F I D S K I L F L P C S T K Q S L Y F H V P M D R G I A G N Y L G I S L K Q E K N Q S F N N Q L F R Y L ...................................................... Protein_Len: 31 Strand: - Start: 296 End: 388 ....................................................................................................................................................................................................................................................................................................... R N K T S Y Y V K L V S Q Y E S S K L I K A F Y S F M Q F Y M ..................................................... Protein_Len: 40 Strand: - Start: 133 End: 252 .................................................................................................................................... F L F F I L R K I I L K K S I Q K T G L G P V F Y T Y Y S F Y F S Y I I S V I M ............................................................................................................................................................................................. Protein_Len: 41 Strand: - Start: 29 End: 151 ............................ Q N L S V T K V K N W W A F D I S E H V W P D R S L Q F S N P F I G L V L F F D M .................................................................................................................................................................................................................................................................................................. ttgctccgaaagaaattgttcttgtttattgattcaaagatactgtttttaccttgttccaccaagcaaagtctatactttcatgtacccatggatcgcgggatagctggaaactatttgggaatatccctaaaacaagaaaaaaatcaatcgtttaataatcaactttttagatatttgtttcgtacccagacccggtacaaagtatgtataataagagaaataaaaagaatatattatgctgacaatcagttatttataattttcttatgtttggcaattttgctcatttttacctgtttttggttgaatagtacacttttagtacactttgatattcggaactttttagtatctttgcaaaataagaaaacatctgaaaataaatgagttaatgattttactcggttctatactcattcaggtacataactatcaatt 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================================================ ttgctccgaaagaaattgttcttgtttattgattcaaagatactgtttttaccttgttccaccaagcaaagtctatactttcatgtacccatggatcgcgggatagctggaaactatttgggaatatccctaaaacaagaaaaaaatcaatcgtttaataatcaactttttagatatttgtttcgtacccagacccggtacaaagtatgtataataagagaaataaaaagaatatattatgctgacaatcagttatttataattttcttatgtttggcaattttgctcatttttacctgtttttggttgaatagtacacttttagtacactttgatattcggaactttttagtatctttgcaaaataagaaaacatctgaaaataaatgagttaatgattttactcggttctatactcattcaggtacataactatcaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2954:TF2955|TF2954:TF2955:outer membrane protein, TonB dependent receptor:integrase:->->:3162182..3162622 441 ttgctccgaaagaaattgttcttgtttattgattcaaagatactgtttttaccttgttccaccaagcaaagtctatactttcatgtacccatggatcgcgggatagctggaaactatttgggaatatccctaaaacaagaaaaaaatcaatcgtttaataatcaactttttagatatttgtttcgtacccagacccggtacaaagtatgtataataagagaaataaaaagaatatattatgctgacaatcagttatttataattttcttatgtttggcaattttgctcatttttacctgtttttggttgaatagtacacttttagtacactttgatattcggaactttttagtatctttgcaaaataagaaaacatctgaaaataaatgagttaatgattttactcggttctatactcattcaggtacataactatcaatt Intra-Species Hit: Count: 1 Min: 1 Max: 441 Len: 441 Subject: tfor_TF2954_TF2955|outer membrane protein, TonB dependent receptor:integrase|POSITIVE:POSITIVE|[3162182, 3162622]|441 HSP 1 e-value: 0.0 bit: 833.0 Len: 441 Query Start:1 Query End:441 Subject Strand: POSITIVE Subject Start: 1 Subject End: 441 ttgctccgaaagaaattgttcttgtttattgattcaaagatactgtttttaccttgttccaccaagcaaagtctatactttcatgtacccatggatcgcgggatagctggaaactatttgggaatatccctaaaacaagnnnnnnntcaatcgtttaataatcaactttttagatatttgtttcgtacccagacccggtacaaagtatgtataataagagaaataaaaagaatatattatgctgacaatcagttatttataattttcttatgtttggcaattttgctcatttttacctgtttttggttgaatagtacacttttagtacactttgatattcggaactttttagtatctttgcaaaataagaaaacatctgaaaataaatgagttaatgattttactcggttctatactcattcaggtacataactatcaatt ttgctccgaaagaaattgttcttgtttattgattcaaagatactgtttttaccttgttccaccaagcaaagtctatactttcatgtacccatggatcgcgggatagctggaaactatttgggaatatccctaaaacaagaaaaaaatcaatcgtttaataatcaactttttagatatttgtttcgtacccagacccggtacaaagtatgtataataagagaaataaaaagaatatattatgctgacaatcagttatttataattttcttatgtttggcaattttgctcatttttacctgtttttggttgaatagtacacttttagtacactttgatattcggaactttttagtatctttgcaaaataagaaaacatctgaaaataaatgagttaatgattttactcggttctatactcattcaggtacataactatcaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCUCCGAAAGAAAUUGUUCUUGUUUAUUGAUUCAAAGAUACUGUUUUUACCUUGUUCCACCAAGCAAAGUCUAUACUUUCAUGUACCCAUGGAUCGCGGGAUAGCUGGAAACUAUUUGGGAAUAUCCCUAAAACAAGAAAAAAAUCAAUCGUUUAAUAAUCAACUUUUUAGAUAUUUGUUUCGUACCCAGACCCGGUACAAAGUAUGUAUAAUAAGAGAAAUAAAAAGAAUAUAUUAUGCUGACAAUCAGUUAUUUAUAAUUUUCUUAUGUUUGGCAAUUUUGCUCAUUUUUACCUGUUUUUGGUUGAAUAGUACACUUUUAGUACACUUUGAUAUUCGGAACUUUUUAGUAUCUUUGCAAAAUAAGAAAACAUCUGAAAAUAAAUGAGUUAAUGAUUUUACUCGGUUCUAUACUCAUUCAGGUACAUAACUAUCAAUU ..(..((((..(((((..((((..((((((....(((((((((((..........(((((......((((((...((((....(((((.........(((((((.((..((.....((((((......))))))..(((((((......................(((((...((((.(((((.(((((.......))))).))))).))))...)))))............((((....((((.....))))....)))).)))))))...))..)).)))))))..((((..(((.......))).)))).))))).....)))).))))))......)))))....))))))))))).......(((.....)))...))))))..))..))..)))))..))))..)............((((......)))).... (-86.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUGAUAGUUAUGUACCUGAAUGAGUAUAGAACCGAGUAAAAUCAUUAACUCAUUUAUUUUCAGAUGUUUUCUUAUUUUGCAAAGAUACUAAAAAGUUCCGAAUAUCAAAGUGUACUAAAAGUGUACUAUUCAACCAAAAACAGGUAAAAAUGAGCAAAAUUGCCAAACAUAAGAAAAUUAUAAAUAACUGAUUGUCAGCAUAAUAUAUUCUUUUUAUUUCUCUUAUUAUACAUACUUUGUACCGGGUCUGGGUACGAAACAAAUAUCUAAAAAGUUGAUUAUUAAACGAUUGAUUUUUUUCUUGUUUUAGGGAUAUUCCCAAAUAGUUUCCAGCUAUCCCGCGAUCCAUGGGUACAUGAAAGUAUAGACUUUGCUUGGUGGAACAAGGUAAAAACAGUAUCUUUGAAUCAAUAAACAAGAACAAUUUCUUUCGGAGCAA ............(((.((....((((.(((((...((((..........)))).))))).))))..((((((.(((((...(((((((((......((((((.....(((((((((((....(((((((............(((((((....((.(((....)))))...(((((((...((((.....(((.....))).....))))...)))))))...............))).))))...(((((((((...(((((((......(((((((..(((.......)))..)))))))..))))))).(((.....)))..(((((.....))))))))).)))))...)))))))...)))))..)))))).....))))))...((....)).)))))))))....)))))...)))))).........)).))). (-87.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 100 54 211 166 tfor:TF1334|5end_hypothetical_protein_1415996..1416226_POSITIVE 342 128 82 67 16 tfor:TF2668|5end_hypothetical_protein_2842471..2842701_POSITIVE 326 307 265 78 38 tfor:TF3109|5end_hypothetical_protein_3341998..3342228_POSITIVE 317 120 74 181 126 tfor:TF2032|5end_outer_membrane_protein,_TonB_dependent_receptor_2188269..2188499_POSITIVE 314 123 81 48 6 tfor:TF0962|5end_possible_amidohydrolase_1011593..1011823_POSITIVE 313 197 156 125 80 tfor:TF2782|5end_conserved_hypothetical_protein_2966455..2966685_POSITIVE 309 131 95 182 140 tfor:TF0112|5end_outer_membrane_protein_121244..121474_POSITIVE 305 130 84 89 44 tfor:TF1007|5end_rod_shape-determining_protein_MreB_1062354..1062584_POSITIVE 301 110 65 158 115 tfor:TF1948|5end_conserved_hypothetical_protein_2095942..2096172_POSITIVE 297 110 65 227 182 tfor:TF2256|5end_transfer_region-related_protein,_TraI_2427908..2428138_POSITIVE 288 109 64 56 12 tfor:TF1891|5end_hypothetical_protein_2043389..2043619_POSITIVE 287 122 83 221 177 tfor:TF3082|5end_conserved_hypothetical_protein_3316431..3316661_POSITIVE 287 122 83 100 56 tfor:TF2202|5end_hypothetical_protein_2378682..2378912_POSITIVE 286 130 81 58 14 tfor:TF2526|5end_outer_membrane_protein,_TonB_dependent_receptor_2705547..2705777_POSITIVE 284 109 64 219 171 tfor:TF0666|5end_conserved_hypothetical_protein_710461..710691_POSITIVE 283 113 79 174 131 tfor:TF1398|5end_conserved_hypothetical_protein_1471474..1471704_POSITIVE 281 139 91 77 17 tfor:TF1015|5end_conserved_hypothetical_protein_1072512..1072742_POSITIVE 278 200 158 229 185 tfor:TF2729|5end_possible_outer_membrane_protein_2908216..2908446_POSITIVE 277 130 92 212 179 tfor:TF2252|5end_transfer_region-related_protein,_TraF_2424621..2424851_POSITIVE 276 123 98 135 112 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 100 54 149 104 tfor:TF1333|3end_probable_acylaminoacyl_peptidase;_alanyl_dipeptidyl_peptidase_1416014..1416164_POSITIVE 314 123 81 48 6 tfor:TF0961|3end_translation_initiation_inhibitor,_endoribonuclease_activity_1011673..1011823_POSITIVE 313 197 156 116 71 tfor:TF2780|3end_hypothetical_protein_2966526..2966676_POSITIVE 305 130 84 48 3 tfor:TF1006|3end_bifunctional_purine_biosynthesis_protein,_phosphoribosylaminoimidazolecarboxamide_formyltransferase_and_IMP_cyclohydrolase_1062393..1062543_POSITIVE 301 112 71 90 53 tfor:TF0629|3end_hypothetical_protein_666710..666860_POSITIVE 297 114 77 56 16 tfor:TF1750|3end_hypothetical_protein_1886566..1886716_POSITIVE 285 130 87 43 3 tfor:TF2525|3end_conserved_hypothetical_protein_2705612..2705762_POSITIVE 284 121 81 111 69 tfor:TF0340|3end_hypothetical_protein_364257..364407_POSITIVE 277 307 276 30 1 tfor:TF3108|3end_glutamine-hydrolyzing_carbamoyl-phosphate_synthase,_large_subunit_3342030..3342180_POSITIVE 276 123 98 123 100 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 276 106 61 103 50 tfor:TF0542|3end_hypothetical_protein_572324..572474_POSITIVE 274 122 88 36 2 tfor:TF3003|3end_hypothetical_protein_3220629..3220779_POSITIVE 273 122 88 72 33 tfor:TF2659|3end_conserved_hypothetical_protein_2833055..2833205_POSITIVE 273 110 62 115 58 tfor:TF1954|3end_long-chain-fatty-acid--CoA_ligase_2106940..2107090_POSITIVE 272 313 272 54 12 tfor:TF0894|3end_conserved_hypothetical_protein_943775..943925_POSITIVE 269 100 52 83 16 tfor:TF1297|3end_hypothetical_protein_1379523..1379673_POSITIVE 265 130 88 58 3 tfor:TF3098|3end_conserved_hypothetical_protein_3330535..3330685_POSITIVE 264 122 81 151 108 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 262 69 29 89 39 tfor:TF3019|3end_tRNA_and_rRNA_cytosine-C5-methylase_3243587..3243737_POSITIVE 261 138 92 81 19 tfor:TF3111|3end_hypothetical_protein_3346836..3346986_POSITIVE