Origin IGS: taattgtcaatggttatgcctttgcgggcgttgaggtgtttagttgtttagttgtttaggtgtttagttgttggctgacagctgaatactgaccgctaacgatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatcgttagcggtcagtattcagctgtcagccaacaactaaacacctaaacaactaaacaactaaacacctcaacgcccgcaaaggcataaccattgacaatta Mask Tandem Repeat Region ================================================ taattgtcaatggttatgcctttgcgggcgttgaggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggctgacagctgaatactgaccgctaacgatt Find is-nt database================================================ Query_seq: TF2839:TF2840|TF2839:TF2840:ATP-dependent exodeoxyribonuclease:hypothetical protein:->->:3031096..3031199 104 taattgtcaatggttatgcctttgcgggcgttgaggtgtttagttgtttagttgtttaggtgtttagttgttggctgacagctgaatactgaccgctaacgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2839:TF2840|TF2839:TF2840:ATP-dependent exodeoxyribonuclease:hypothetical protein:->->:3031096..3031199 104 taattgtcaatggttatgcctttgcgggcgttgaggtgtttagttgtttagttgtttaggtgtttagttgttggctgacagctgaatactgaccgctaacgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2839:TF2840|TF2839:TF2840:ATP-dependent exodeoxyribonuclease:hypothetical protein:->->:3031096..3031199 104 taattgtcaatggttatgcctttgcgggcgttgaggtgtttagttgtttagttgtttaggtgtttagttgttggctgacagctgaatactgaccgctaacgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattgtcaatggttatgcctttgcgggcgttgaggtgtttagttgtttagttgtttaggtgtttagttgttggctgacagctgaatactgaccgctaacgatt Predict ORF larger than 30AA ================================================ taattgtcaatggttatgcctttgcgggcgttgaggtgtttagttgtttagttgtttaggtgtttagttgttggctgacagctgaatactgaccgctaacgatt 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================================================ taattgtcaatggttatgcctttgcgggcgttgaggtgtttagttgtttagttgtttaggtgtttagttgttggctgacagctgaatactgaccgctaacgatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2839:TF2840|TF2839:TF2840:ATP-dependent exodeoxyribonuclease:hypothetical protein:->->:3031096..3031199 104 taattgtcaatggttatgcctttgcgggcgttgaggtgtttagttgtttagttgtttaggtgtttagttgttggctgacagctgaatactgaccgctaacgatt Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: tfor_TF2839_TF2840|ATP-dependent exodeoxyribonuclease:hypothetical protein|POSITIVE:POSITIVE|[3031096,3031199]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 taattgtcaatggttatgcctttgcgggcgttgaggtgtttagttgtttagttgtttaggtgtttagttgttggctgacagctgaatactgaccgctaacgatt taattgtcaatggttatgcctttgcgggcgttgaggtgtttagttgtttagttgtttaggtgtttagttgttggctgacagctgaatactgaccgctaacgatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUGUCAAUGGUUAUGCCUUUGCGGGCGUUGAGGUGUUUAGUUGUUUAGUUGUUUAGGUGUUUAGUUGUUGGCUGACAGCUGAAUACUGACCGCUAACGAUU .((((((((((....(((((((.((....)).)))))))...))))..((((.(((..((((((((((((((....))))))))))))))))).)))))))))) (-31.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCGUUAGCGGUCAGUAUUCAGCUGUCAGCCAACAACUAAACACCUAAACAACUAAACAACUAAACACCUCAACGCCCGCAAAGGCAUAACCAUUGACAAUUA ....(((.((.(.((((.....)))).).)).)))........................................(((......)))................. (-13.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 463 57 16 173 133 tfor:TF1172|5end_ABC_transporter,_permease_component_1252806..1253036_POSITIVE 451 95 51 216 177 tfor:TF2162|5end_thermolysin_precursor_2338669..2338899_POSITIVE 440 56 16 172 133 tfor:TF1173|5end_ABC_transporter,_permease_component_1255444..1255674_POSITIVE 438 97 51 177 131 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 436 100 51 222 178 tfor:TF2174|5end_possible_endopeptidase_precursor_2346292..2346522_POSITIVE 435 56 16 163 124 tfor:TF0351|5end_hypothetical_protein_370922..371152_POSITIVE 431 100 51 198 149 tfor:TF0341|5end_conserved_hypothetical_protein_364348..364578_POSITIVE 429 99 51 182 137 tfor:TF0359|5end_conserved_hypothetical_protein_376943..377173_POSITIVE 423 56 16 140 101 tfor:TF0367|5end_eukaryotic-like__metalloproteinase_384007..384237_POSITIVE 423 56 16 140 101 tfor:TF0364|5end_ysyl_endopeptidase_380395..380625_POSITIVE 415 76 31 197 151 tfor:TF0959|5end_periplasmic_protease_1005218..1005448_POSITIVE 386 56 16 170 131 tfor:TF0347|5end_possible_serine_protease_367542..367772_POSITIVE 371 55 18 224 188 tfor:TF2109|5end_possible_metallo-beta-lactamase_family_protein_2277942..2278172_POSITIVE 369 67 21 166 110 tfor:TF0851|5end_helicase_SNF2_family_899486..899716_POSITIVE 367 77 33 202 157 tfor:TF2021|5end_hypothetical_protein_2177702..2177932_POSITIVE 365 97 51 63 15 tfor:TF1274|5end_hypothetical_protein_1357621..1357851_POSITIVE 364 90 43 151 109 tfor:TF2601|5end_conserved_hypothetical_protein_2774721..2774951_POSITIVE 364 95 51 214 171 tfor:TF2167|5end_hypothetical_protein_2342586..2342816_POSITIVE 360 78 31 211 164 tfor:TF0725|5end_O-acetylhomoserine_(thiol)-lyase_776556..776786_POSITIVE 346 42 4 57 10 tfor:TF2263|5end_transfer_region-related_protein,_TraN_2431901..2432131_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 463 57 16 86 46 tfor:TF1170|3end_conserved_hypothetical_protein_1252799..1252949_POSITIVE 364 90 43 59 17 tfor:TF2600|3end_ribose-phosphate_pyrophosphokinase_2774709..2774859_POSITIVE 327 70 24 71 34 tfor:TF1687|3end_conserved_hypothetical_protein;_possible_periplasmic_protein_1803459..1803609_POSITIVE 323 56 11 66 9 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 318 99 53 74 24 tfor:TF1171|3end_ABC_transporter,_ATP-binding_protein_1252601..1252751_POSITIVE 306 100 75 27 1 tfor:TF0340|3end_hypothetical_protein_364257..364407_POSITIVE 298 98 51 83 32 tfor:TF1165|3end_conserved_hypothetical_protein_1245921..1246071_POSITIVE 296 63 22 149 99 tfor:TF1157|3end_glutamate_synthase,_small_subunit_1239588..1239738_POSITIVE 294 46 4 73 28 tfor:TF1854|3end_competence-damage_protein_CinA_2008808..2008958_POSITIVE 292 58 18 148 107 tfor:TF2836|3end_methyltransferase_3028028..3028178_POSITIVE 291 49 12 41 3 tfor:TF1650|3end_integrase_1761360..1761510_POSITIVE 291 43 1 66 7 tfor:TF0469|3end_hypothetical_protein_487228..487378_POSITIVE 290 39 1 121 75 tfor:TF0820|3end_hypothetical_protein_879942..880092_POSITIVE 288 95 59 145 111 tfor:TF2149|3end_deoxyribose-phosphate_aldolase_2323110..2323260_POSITIVE 284 42 3 74 29 tfor:TF2827|3end_conserved_hypothetical_protein_3019642..3019792_POSITIVE 284 60 11 128 66 tfor:TF1187|3end_hypothetical_protein_1269872..1270022_POSITIVE 284 60 11 71 9 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 283 99 58 43 1 tfor:TF2839|3end_ATP-dependent_exodeoxyribonuclease_3031035..3031185_POSITIVE 281 95 53 45 7 tfor:TF2770|3end_conserved_hypothetical_protein_2956639..2956789_POSITIVE 281 97 55 51 1 tfor:TF1575|3end_DNA-binding_response_regulator_1685895..1686045_POSITIVE