Origin IGS: tgaccgaccgcagatgaacatccccccagccccccccttcaaagggggggggaagagcggagcgaagggggggatgtaatcctttcaaagagggaatttgcagagctgaatgctgataactgacagccctcaacaactaaacatctaaaccaatcaacatgtaaacagaaagatgatttta .........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 taaaatcatctttctgtttacatgttgattggtttagatgtttagttgttgagggctgtcagttatcagcattcagctctgcaaattccctctttgaaaggattacatcccccccttcgctccgctcttccccccccctttgaaggggggggctggggggatgttcatctgcggtcggtca Mask Tandem Repeat Region ================================================ tgaccgaccgcagatgaacatccccccagccccccccttcaaagggggggggaagagcggagcgaagggggggatgtaatcctttcaaagagggaatttgcagagctgaatgctgataactgacagccctcaacaactaaacatctaaaccaatcaacatgtaaacagaaagatgatttta Find is-nt database================================================ Query_seq: TF0828:TF0830|TF0828:TF0830:hypothetical protein:hypothetical protein:->->:887569..887749 181 tgaccgaccgcagatgaacatccccccagccccccccttcaaagggggggggaagagcggagcgaagggggggatgtaatcctttcaaagagggaatttgcagagctgaatgctgataactgacagccctcaacaactaaacatctaaaccaatcaacatgtaaacagaaagatgatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0828:TF0830|TF0828:TF0830:hypothetical protein:hypothetical protein:->->:887569..887749 181 tgaccgaccgcagatgaacatccccccagccccccccttcaaagggggggggaagagcggagcgaagggggggatgtaatcctttcaaagagggaatttgcagagctgaatgctgataactgacagccctcaacaactaaacatctaaaccaatcaacatgtaaacagaaagatgatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0828:TF0830|TF0828:TF0830:hypothetical protein:hypothetical protein:->->:887569..887749 181 tgaccgaccgcagatgaacatccccccagccccccccttcaaagggggggggaagagcggagcgaagggggggatgtaatcctttcaaagagggaatttgcagagctgaatgctgataactgacagccctcaacaactaaacatctaaaccaatcaacatgtaaacagaaagatgatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaccgaccgcagatgaacatccccccagccccccccttcaaagggggggggaagagcggagcgaagggggggatgtaatcctttcaaagagggaatttgcagagctgaatgctgataactgacagccctcaacaactaaacatctaaaccaatcaacatgtaaacagaaagatgatttta Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: - Start: 2 End: 136 . V S R L H V D G W G G G E F P P P L A S R L P P H L G K L S P I Q L A S H Q Y S V A R L M ............................................. tgaccgaccgcagatgaacatccccccagccccccccttcaaagggggggggaagagcggagcgaagggggggatgtaatcctttcaaagagggaatttgcagagctgaatgctgataactgacagccctcaacaactaaacatctaaaccaatcaacatgtaaacagaaagatgatttta 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================================================ tgaccgaccgcagatgaacatccccccagccccccccttcaaagggggggggaagagcggagcgaagggggggatgtaatcctttcaaagagggaatttgcagagctgaatgctgataactgacagccctcaacaactaaacatctaaaccaatcaacatgtaaacagaaagatgatttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 83 HP_score: -13.1 Tail_Score: -3.20078 Start: 21 End: 61 Full_Region: catcccccccttcgc tccgctcttccccccccct ttg aaggggggggctgggggga tgttcatctgcggtc ....................tccgctcttccccccccctttgaaggggggggctgggggga........................................................................................................................ Find igs database================================================ Query_seq: TF0828:TF0830|TF0828:TF0830:hypothetical protein:hypothetical protein:->->:887569..887749 181 tgaccgaccgcagatgaacatccccccagccccccccttcaaagggggggggaagagcggagcgaagggggggatgtaatcctttcaaagagggaatttgcagagctgaatgctgataactgacagccctcaacaactaaacatctaaaccaatcaacatgtaaacagaaagatgatttta Intra-Species Hit: Count: 1 Min: 74 Max: 181 Len: 108 Subject: tfor_TF0828_TF0830|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[887569,887749]|181 HSP 1 e-value: 8.0E-55 bit: 214.0 Len: 108 Query Start:74 Query End:181 Subject Strand: POSITIVE Subject Start: 74 Subject End: 181 .........................................................................atgtaatcctttcaaagagggaatttgcagagctgaatgctgataactgacagccctcaacaactaaacatctaaaccaatcaacatgtaaacagaaagatgatttta .........................................................................atgtaatcctttcaaagagggaatttgcagagctgaatgctgataactgacagccctcaacaactaaacatctaaaccaatcaacatgtaaacagaaagatgatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUAAUCCUUUCAAAGAGGGAAUUUGCAGAGCUGAAUGCUGAUAACUGACAGCCCUCAACAACUAAACAUCUAAACCAAUCAACAUGUAAACAGAAAGAUGAUUUUA ........(((((...(((((....((((((((.....))).....))).)).))))).........((((..............)))).....)))))......... (-17.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUCAUCUUUCUGUUUACAUGUUGAUUGGUUUAGAUGUUUAGUUGUUGAGGGCUGUCAGUUAUCAGCAUUCAGCUCUGCAAAUUCCCUCUUUGAAAGGAUUACAU ........((((((.....((((.((((.....))))))))...((.((((((.((((........)))).))))))...)).............))))))....... (-19.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 50 1 101 54 tfor:TF1167|5end_hypothetical_protein_1248559..1248789_POSITIVE 452 50 1 75 25 tfor:TF2350|5end_hypothetical_protein_2515063..2515293_POSITIVE 377 56 11 170 125 tfor:TF0366|5end_hypothetical_protein_383564..383794_POSITIVE 377 56 11 170 125 tfor:TF0362|5end_hypothetical_protein_379952..380182_POSITIVE 368 77 31 158 113 tfor:TF2840|5end_hypothetical_protein_3031060..3031290_POSITIVE 363 59 11 173 125 tfor:TF2171|5end_hypothetical_protein_2345485..2345715_POSITIVE 363 59 11 173 125 tfor:TF2166|5end_hypothetical_protein_2342115..2342345_POSITIVE 361 57 11 170 125 tfor:TF0346|5end_hypothetical_protein_367048..367278_POSITIVE 361 57 11 170 125 tfor:TF0340|5end_hypothetical_protein_363893..364123_POSITIVE 342 56 11 175 131 tfor:TF2172|5end_hypothetical_protein_2345822..2346052_POSITIVE 342 56 11 169 125 tfor:TF2173|5end_hypothetical_protein_2345816..2346046_POSITIVE 328 60 17 114 66 tfor:TF2218|5end_two-component_system_response_regulator_2390162..2390392_POSITIVE 325 57 20 81 34 tfor:TF1274|5end_hypothetical_protein_1357621..1357851_POSITIVE 318 59 27 151 115 tfor:TF1517|5end_hypothetical_protein_1626694..1626924_POSITIVE 294 57 17 188 137 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 291 56 21 42 7 tfor:TF0454|5end_xanthine/uracil_permease_family_protein_472087..472317_POSITIVE 286 54 14 153 115 tfor:TF3140|5end_Na+-translocating_NADH-quinone_reductase,_subunit_B_3373309..3373539_POSITIVE 286 60 19 210 156 tfor:TF0359|5end_conserved_hypothetical_protein_376943..377173_POSITIVE 284 70 25 66 13 tfor:TF1965|5end_conserved_hypothetical_protein_2114313..2114543_POSITIVE 281 57 20 54 3 tfor:TF0411|5end_methyltransferase_428917..429147_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 50 1 65 18 tfor:TF1166|3end_ABC_transporter,_permease_component_1248603..1248753_POSITIVE 387 50 3 65 18 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 379 57 11 113 60 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 375 77 32 61 25 tfor:TF2161|3end_conserved_hypothetical_protein_2338362..2338512_POSITIVE 368 77 31 53 8 tfor:TF2839|3end_ATP-dependent_exodeoxyribonuclease_3031035..3031185_POSITIVE 356 40 1 78 34 tfor:TF0685|3end_hypothetical_protein_731132..731282_POSITIVE 342 56 11 65 21 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 336 57 11 82 36 tfor:TF1592|3end_hypothetical_protein_1708557..1708707_POSITIVE 330 57 17 82 33 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 318 59 27 130 94 tfor:TF1516|3end_transposase_fragment_1626753..1626903_POSITIVE 318 40 1 39 3 tfor:TF1167|3end_hypothetical_protein_1248932..1249082_POSITIVE 301 87 52 64 28 tfor:TF1174|3end_ABC_transporter,_permease_component_1257896..1258046_POSITIVE 280 54 20 79 37 tfor:TF0597|3end_hypothetical_protein_629230..629380_POSITIVE 271 50 2 119 74 tfor:TF3104|3end_outer_membrane_protein,_TonB_dependent_receptor_3337450..3337600_POSITIVE 271 40 1 101 62 tfor:TF0470|3end_hypothetical_protein_487518..487668_POSITIVE 267 54 24 80 39 tfor:TF2601|3end_conserved_hypothetical_protein_2775139..2775289_POSITIVE 263 39 3 86 52 tfor:TF1585|3end_hypothetical_protein_1690610..1690760_POSITIVE 263 39 3 79 45 tfor:TF1584|3end_hypothetical_protein_1690603..1690753_POSITIVE 261 58 19 69 30 tfor:TF2911|3end_hypothetical_protein_3106640..3106790_POSITIVE 261 55 14 144 102 tfor:TF0244|3end_DNA_recombination_protein_275776..275926_POSITIVE