Origin IGS: tgagaaaaactaataatgagatagaacgatgaaagtaagaacatctttaaagaaacggacgcccgactgcaagattgtacgccggaaggggcgtttatatgtgattaacaagaagaaccccaagttcaaggtacgtcaggggtagtagtaaactgcaaataaactaaacatctaaataat .........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 attatttagatgtttagtttatttgcagtttactactacccctgacgtaccttgaacttggggttcttcttgttaatcacatataaacgccccttccggcgtacaatcttgcagtcgggcgtccgtttctttaaagatgttcttactttcatcgttctatctcattattagtttttctca Mask Tandem Repeat Region ================================================ tgagaaaaactaataatgagatagaacgatgaaagtaagaacatctttaaagaaacggacgcccgactgcaagattgtacgccggaaggggcgtttatatgtgattaacaagaagaaccccaagttcaaggtacgtcaggggtagtagtaaactgcaaataaactaaacatctaaataat Find is-nt database================================================ Query_seq: TF2576:TF2577|TF2576:TF2577:translation initiation factor IF-1:30S ribosomal protein S13:->->:2746268..2746447 180 tgagaaaaactaataatgagatagaacgatgaaagtaagaacatctttaaagaaacggacgcccgactgcaagattgtacgccggaaggggcgtttatatgtgattaacaagaagaaccccaagttcaaggtacgtcaggggtagtagtaaactgcaaataaactaaacatctaaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2576:TF2577|TF2576:TF2577:translation initiation factor IF-1:30S ribosomal protein S13:->->:2746268..2746447 180 tgagaaaaactaataatgagatagaacgatgaaagtaagaacatctttaaagaaacggacgcccgactgcaagattgtacgccggaaggggcgtttatatgtgattaacaagaagaaccccaagttcaaggtacgtcaggggtagtagtaaactgcaaataaactaaacatctaaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 29 Max: 142 Len: 114 Subject: gi|89107170|ref|AP_000950.1| predicted ribosomal protein [Escherichia coli W3110] HSP 1 e-value: 8.0E-8 bit: 52.4 Len: 114 Query Start:29 Query End:142 Subject Strand: null Subject Start: 1 Subject End: 41 ............................ M K V R T S L - - - K K R T P D C K I V R R K G R L Y V I N K K N P K F K V R Q G ...................................... ............................ M K V L N S L R T A K E R H P D C Q I V K R K G R L Y V I C K S N P R F K A V Q G ...................................... Find nr database================================================ Query_seq: TF2576:TF2577|TF2576:TF2577:translation initiation factor IF-1:30S ribosomal protein S13:->->:2746268..2746447 180 tgagaaaaactaataatgagatagaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagtagtaaactgcaaataaactaaacatctaaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagaaaaactaataatgagatagaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagtagtaaactgcaaataaactaaacatctaaataat Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 29 End: 142 ............................ M K V R T S L K K R T P D C K I V R R K G R L Y V I N K K N P K F K V R Q G ...................................... Protein_Len: 39 Strand: - Start: 13 End: 129 ............ Y H S L V I F T L V D K F F R V G S Q L I T R R F P R K Y T I L L F F G L N M ................................................... Protein_Len: 32 Strand: - Start: 3 End: 98 .. S F S I I L Y F S S L L F M K L S V S A R S C S Q V G S P A N M .................................................................................. tgagaaaaactaataatgagatagaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagtagtaaactgcaaataaactaaacatctaaataat 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================================================ tgagaaaaactaataatgagatagaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagtagtaaactgcaaataaactaaacatctaaataat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2576:TF2577|TF2576:TF2577:translation initiation factor IF-1:30S ribosomal protein S13:->->:2746268..2746447 180 tgagaaaaactaataatgagatagaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagtagtaaactgcaaataaactaaacatctaaataat Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: tfor_TF2576_TF2577|translation initiation factor IF-1:30S ribosomal protein S13|POSITIVE:POSITIVE|[2746268,2746447]|180 HSP 1 e-value: 4.0E-13 bit: 75.8 Len: 38 Query Start:143 Query End:180 Subject Strand: POSITIVE Subject Start: 143 Subject End: 180 ..............................................................................................................................................tagtagtaaactgcaaataaactaaacatctaaataat ..............................................................................................................................................tagtagtaaactgcaaataaactaaacatctaaataat HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 27 Query Start:1 Query End:27 Subject Strand: POSITIVE Subject Start: 1 Subject End: 27 tgagaaaaactaataatgagatagaac......................................................................................................................................................... tgagaaaaactaataatgagatagaac......................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGAAAAACUAAUAAUGAGAUAGAACGAUGAAAGUAAGAACAUCUUUAAAGAAACGGACGCCCGACUGCAAGAUUGUACGCCGGAAGGGGCGUUUAUAUGUGAUUAACAAGAAGAACCCCAAGUUCAAGGUACGUCAGGGGUAGUAGUAAACUGCAAAUAAACUAAACAUCUAAAUAAU ...........................((((..(((.......(((((........((((((((...((((....))))...(....)))))))))...(((.....))).)))))(((((..((.......))....))))).((((....))))......)))...))))........ (-32.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUUAGAUGUUUAGUUUAUUUGCAGUUUACUACUACCCCUGACGUACCUUGAACUUGGGGUUCUUCUUGUUAAUCACAUAUAAACGCCCCUUCCGGCGUACAAUCUUGCAGUCGGGCGUCCGUUUCUUUAAAGAUGUUCUUACUUUCAUCGUUCUAUCUCAUUAUUAGUUUUUCUCA ........((((...(((....((((((.........(((((.................)))))......................(((((......)))))......))))))..(((((((..(......)..)))))))..)))..))))........................... (-30.13) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 97 51 81 25 tfor:TF1304|5end_conserved_hypothetical_protein_1385008..1385238_POSITIVE 395 96 62 212 167 tfor:TF0637|5end_TPR-repeat-containing_protein_673195..673425_POSITIVE 384 102 61 51 5 tfor:TF0089|5end_conserved_hypothetical_protein_95437..95667_POSITIVE 377 93 53 165 114 tfor:TF3064|5end_oxidoreductase,_aldo/keto_reductase_family_3289765..3289995_POSITIVE 376 96 55 57 11 tfor:TF0996|5end_ribonuclease_D_1050882..1051112_POSITIVE 371 93 55 186 140 tfor:TF2825|5end_transposase_3016390..3016620_POSITIVE 371 93 55 186 140 tfor:TF2591|5end_transposase_2757641..2757871_POSITIVE 371 93 55 186 140 tfor:TF2110|5end_transposase_2279217..2279447_POSITIVE 371 93 55 186 140 tfor:TF0942|5end_transposase_982998..983228_POSITIVE 371 93 55 186 140 tfor:TF0716|5end_transposase_766297..766527_POSITIVE 363 90 56 65 33 tfor:TF1939|5end_hypothetical_protein_2086299..2086529_POSITIVE 356 95 55 127 77 tfor:TF0833|5end_conserved_hypothetical_protein_888757..888987_POSITIVE 351 98 51 156 110 tfor:TF0842|5end_long-chain-fatty-acid--CoA_ligase_893053..893283_POSITIVE 348 94 51 201 152 tfor:TF0881|5end_conserved_hypothetical_protein_934459..934689_POSITIVE 347 95 53 129 90 tfor:TF0253|5end_conserved_hypothetical_protein_283707..283937_POSITIVE 346 93 55 186 140 tfor:TF3000|5end_hypothetical_protein_3216412..3216642_POSITIVE 346 95 56 194 140 tfor:TF2372|5end_acyl-(acyl-carrier-protein)-UDP-N-acetylglucosami_ne_acyltransferase_2537558..2537788_POSITIVE 346 92 51 72 30 tfor:TF0611|5end_lysine_decarboxylase_642750..642980_POSITIVE 342 95 60 40 6 tfor:TF3105|5end_hypothetical_protein_3338068..3338298_POSITIVE 338 93 56 157 123 tfor:TF1947|5end_conserved_hypothetical_protein_2095521..2095751_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 377 93 53 141 90 tfor:TF3063|3end_ferredoxin-type_protein_3289821..3289971_POSITIVE 376 96 55 57 11 tfor:TF0995|3end_conserved_hypothetical_protein_1050962..1051112_POSITIVE 358 93 52 65 21 tfor:TF0616|3end_conserved_hypothetical_protein_650658..650808_POSITIVE 356 95 55 78 28 tfor:TF0832|3end_conserved_hypothetical_protein_888788..888938_POSITIVE 351 98 51 71 25 tfor:TF0841|3end_NADH_dehydrogenase/NAD(P)H_nitroreductase_893048..893198_POSITIVE 350 104 66 47 7 tfor:TF1327|3end_L-fucose_permease_1407195..1407345_POSITIVE 347 95 53 101 62 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 346 92 51 55 13 tfor:TF0609|3end_conserved_hypothetical_protein_642813..642963_POSITIVE 336 93 56 65 26 tfor:TF2012|3end_conserved_hypothetical_protein_2168720..2168870_POSITIVE 329 94 55 53 11 tfor:TF2205|3end_conserved_hypothetical_protein;_possible_transcriptional_regulator_2380010..2380160_POSITIVE 324 99 53 148 90 tfor:TF2189|3end_conserved_hypothetical_protein_2364884..2365034_POSITIVE 324 83 41 62 18 tfor:TF1638|3end_conserved_hypothetical_protein_1747732..1747882_POSITIVE 322 93 55 47 6 tfor:TF2409|3end_hypothetical_protein_2584155..2584305_POSITIVE 322 93 56 111 69 tfor:TF1775|3end_oxidoreductase,_Gfo/Idh/MocA_family_1914618..1914768_POSITIVE 321 96 51 61 12 tfor:TF2803|3end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_2993467..2993617_POSITIVE 321 95 56 150 109 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 320 98 59 49 6 tfor:TF2374|3end_UDP-3-O-(R-3-hydoxymyristoyl)-glucosamine-N-acylt_ransferase_2540892..2541042_POSITIVE 319 96 57 137 95 tfor:TF2893|3end_conserved_hypothetical_protein;_possible_phosphoesterase_3082039..3082189_POSITIVE 315 93 56 149 119 tfor:TF2895|3end_hypothetical_protein_3084192..3084342_POSITIVE 315 99 52 88 29 tfor:TF2444|3end_regulatory_protein_RecX_2621549..2621699_POSITIVE