Origin IGS: tagaaataaccggaggtctttttctgtctgccgacgtaacgcatagatagggggaaaacggcagccatcaggccgaccgagtcaagtctactgaatcgatggaatgttaaaattgttgtcttttatcttttttttgtccaccaaacgaaaacagacacgtcatatccccaaaaaaagaatctaacg .........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 cgttagattctttttttggggatatgacgtgtctgttttcgtttggtggacaaaaaaaagataaaagacaacaattttaacattccatcgattcagtagacttgactcggtcggcctgatggctgccgttttccccctatctatgcgttacgtcggcagacagaaaaagacctccggttatttcta Mask Tandem Repeat Region ================================================ tagaaataaccggaggtctttttctgtctgccgacgtaacgcatagatagggggaaaacggcagccatcaggccgaccgagtcaagtctactgaatcgatggaatgttaaaattgttgtcttttatcttttttttgtccaccaaacgaaaacagacacgtcatatccccaaaaaaagaatctaacg Find is-nt database================================================ Query_seq: TF3009:TF3010|TF3009:TF3010:RNA polymerase ECF-type sigma factor:possible anti-sigma factor:->->:3229770..3229955 186 tagaaataaccggaggtctttttctgtctgccgacgtaacgcatagatagggggaaaacggcagccatcaggccgaccgagtcaagtctactgaatcgatggaatgttaaaattgttgtcttttatcttttttttgtccaccaaacgaaaacagacacgtcatatccccaaaaaaagaatctaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3009:TF3010|TF3009:TF3010:RNA polymerase ECF-type sigma factor:possible anti-sigma factor:->->:3229770..3229955 186 tagaaataaccggaggtctttttctgtctgccgacgtaacgcatagatagggggaaaacggcagccatcaggccgaccgagtcaagtctactgaatcgatggaatgttaaaattgttgtcttttatcttttttttgtccaccaaacgaaaacagacacgtcatatccccaaaaaaagaatctaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3009:TF3010|TF3009:TF3010:RNA polymerase ECF-type sigma factor:possible anti-sigma factor:->->:3229770..3229955 186 tagaaataaccggaggtctttttctgtctgccgacgtaacgcatagatagggggaaaacggcagccatcaggccgaccgagtcaagtctactgaatcgatggaatgttaaaattgttgtcttttatcttttttttgtccaccaaacgaaaacagacacgtcatatccccaaaaaaagaatctaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaaataaccggaggtctttttctgtctgccgacgtaacgcatagatagggggaaaacggcagccatcaggccgaccgagtcaagtctactgaatcgatggaatgttaaaattgttgtcttttatcttttttttgtccaccaaacgaaaacagacacgtcatatccccaaaaaaagaatctaacg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 95 End: 181 .............................................................................................. M D G M L K L L S F I F F L S T K R K Q T R H I P K K R I * ..... Protein_Len: 48 Strand: + Start: 43 End: 186 .......................................... M D R G K T A A I R P T E S S L L N R W N V K I V V F Y L F F V H Q T K T D T S Y P Q K K N L T Protein_Len: 37 Strand: - Start: 3 End: 113 .. F Y G S T K K Q R G V Y R M S L P F V A A M L G V S D L R S F R H F T L M ......................................................................... tagaaataaccggaggtctttttctgtctgccgacgtaacgcatagatagggggaaaacggcagccatcaggccgaccgagtcaagtctactgaatcgatggaatgttaaaattgttgtcttttatcttttttttgtccaccaaacgaaaacagacacgtcatatccccaaaaaaagaatctaacg 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================================================ tagaaataaccggaggtctttttctgtctgccgacgtaacgcatagatagggggaaaacggcagccatcaggccgaccgagtcaagtctactgaatcgatggaatgttaaaattgttgtcttttatcttttttttgtccaccaaacgaaaacagacacgtcatatccccaaaaaaagaatctaacg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -6.8 Tail_Score: -4.13728 Start: 59 End: 79 Full_Region: tcagtagacttgact cggtcggcc tgat ggctgccg ttttccccctatcta ..........................................................cggtcggcctgatggctgccg........................................................................................................... Find igs database================================================ Query_seq: TF3009:TF3010|TF3009:TF3010:RNA polymerase ECF-type sigma factor:possible anti-sigma factor:->->:3229770..3229955 186 tagaaataaccggaggtctttttctgtctgccgacgtaacgcatagatagggggaaaacggcagccatcaggccgaccgagtcaagtctactgaatcgatggaatgttaaaattgttgtcttttatcttttttttgtccaccaaacgaaaacagacacgtcatatccccaaaaaaagaatctaacg Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: tfor_TF3009_TF3010|RNA polymerase ECF-type sigma factor:possible anti-sigma factor|POSITIVE:POSITIVE|[3229770,3229955]|186 HSP 1 e-value: 6.0E-77 bit: 287.0 Len: 169 Query Start:1 Query End:169 Subject Strand: POSITIVE Subject Start: 1 Subject End: 169 tagaaataaccggaggtctttttctgtctgccgacgtaacgcatagatagggggaaaacggcagccatcaggccgaccgagtcaagtctactgaatcgatggaatgttaaaattgttgtcttttatcnnnnnnnngtccaccaaacgaaaacagacacgtcatatcccc................. tagaaataaccggaggtctttttctgtctgccgacgtaacgcatagatagggggaaaacggcagccatcaggccgaccgagtcaagtctactgaatcgatggaatgttaaaattgttgtcttttatcttttttttgtccaccaaacgaaaacagacacgtcatatcccc................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAUAACCGGAGGUCUUUUUCUGUCUGCCGACGUAACGCAUAGAUAGGGGGAAAACGGCAGCCAUCAGGCCGACCGAGUCAAGUCUACUGAAUCGAUGGAAUGUUAAAAUUGUUGUCUUUUAUCUUUUUUUUGUCCACCAAACGAAAACAGACACGUCAUAUCCCC ..((((..(((...)))..))))(((((((.((......))..)))))))(((((...((((.(((....))).).)))......((((........(((((((.(.(((.....))).))))))))...(((((((.......))))))).))))........))))) (-32.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGGAUAUGACGUGUCUGUUUUCGUUUGGUGGACAAAAAAAAGAUAAAAGACAACAAUUUUAACAUUCCAUCGAUUCAGUAGACUUGACUCGGUCGGCCUGAUGGCUGCCGUUUUCCCCCUAUCUAUGCGUUACGUCGGCAGACAGAAAAAGACCUCCGGUUAUUUCUA (((((........(((.((((.(..((((((((.....((((...............)))).....))))))))....).))))..))).(((.(((((....))))))))...)))))...............(((....))).((((..((((...)))).)))).. (-39.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 98 53 54 12 tfor:TF0225|5end_iron-containing_alcohol_dehydrogenase_251477..251707_POSITIVE 390 75 31 97 41 tfor:TF1663|5end_ABC_transporter,_permease_component_1777680..1777910_POSITIVE 389 69 23 55 16 tfor:TF2220|5end_CTn_integrase-recombinase_protein_2392424..2392654_POSITIVE 362 77 31 59 2 tfor:TF3087|5end_conserved_hypothetical_protein_3319878..3320108_POSITIVE 361 103 61 79 31 tfor:TF1170|5end_conserved_hypothetical_protein_1251862..1252092_POSITIVE 361 103 61 67 19 tfor:TF1171|5end_ABC_transporter,_ATP-binding_protein_1251850..1252080_POSITIVE 357 80 31 52 10 tfor:TF2322|5end_conserved_hypothetical_protein;_possible_lipoprotein_2482743..2482973_POSITIVE 357 84 42 75 25 tfor:TF2250|5end_transfer_region-related_protein,_TraD_2423380..2423610_POSITIVE 357 80 31 46 4 tfor:TF1800|5end_conserved_hypothetical_protein_1941214..1941444_POSITIVE 354 96 51 88 38 tfor:TF0621|5end_phosphate_starvation-inducible_protein,_PhoH_655679..655909_POSITIVE 351 66 21 152 103 tfor:TF0065|5end_conserved_hypothetical_protein_70274..70504_POSITIVE 342 80 31 200 137 tfor:TF3064|5end_oxidoreductase,_aldo/keto_reductase_family_3289765..3289995_POSITIVE 342 60 11 226 169 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 342 78 32 114 56 tfor:TF2225|5end_CTn_excision_protein_2394935..2395165_POSITIVE 341 79 32 121 65 tfor:TF3158|5end_inner_membrane_protein_3393729..3393959_POSITIVE 335 80 31 224 167 tfor:TF2520|5end_conserved_hypothetical_protein_2698917..2699147_POSITIVE 335 79 32 186 148 tfor:TF2437|5end_elongation_factor_P_2615104..2615334_POSITIVE 335 100 53 189 136 tfor:TF2247|5end_transfer_region-related_protein,_TraA_2421463..2421693_POSITIVE 335 69 25 84 32 tfor:TF0516|5end_conserved_hypothetical_protein;_possible_membrane_protein_539684..539914_POSITIVE 334 89 41 65 6 tfor:TF1417|5end_conserved_hypothetical_protein_1499544..1499774_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 98 53 44 2 tfor:TF0224|3end_N-acetylglucosamine-6-phosphate_deacetylase_251547..251697_POSITIVE 357 80 31 46 4 tfor:TF1799|3end_quinolinate_synthetase_1941294..1941444_POSITIVE 354 96 51 64 14 tfor:TF0620|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_655735..655885_POSITIVE 342 78 32 67 9 tfor:TF2224|3end_CTn_excision_protein_2394968..2395118_POSITIVE 341 79 32 99 43 tfor:TF3157|3end_sodium/solute_symporter_3393787..3393937_POSITIVE 341 79 31 80 19 tfor:TF0242|3end_conserved_hypothetical_protein_274069..274219_POSITIVE 335 79 32 138 100 tfor:TF2435|3end_DNA_repair_protein_radC_2615136..2615286_POSITIVE 330 80 35 109 61 tfor:TF2694|3end_hypothetical_protein_2870863..2871013_POSITIVE 325 69 26 146 94 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 324 65 29 145 104 tfor:TF1448|3end_possible_competence_protein_1533050..1533200_POSITIVE 322 73 32 60 17 tfor:TF0815|3end_conserved_hypothetical_protein_873974..874124_POSITIVE 321 45 8 97 55 tfor:TF2656|3end_valyl-tRNA_synthetase_2829822..2829972_POSITIVE 317 103 62 111 72 tfor:TF2734|3end_conserved_hypothetical_protein_2916738..2916888_POSITIVE 317 100 51 82 44 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 317 80 31 139 96 tfor:TF0468|3end_hypothetical_protein_487188..487338_POSITIVE 315 77 31 147 110 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 314 92 58 52 11 tfor:TF0547|3end_DNA_gyrase_subunit_A_(topoisomerase)_580172..580322_POSITIVE 311 78 31 113 53 tfor:TF2368|3end_uridine_phosphorylase_2534618..2534768_POSITIVE 311 74 39 90 56 tfor:TF1933|3end_methionyl-tRNA_synthetase_2081884..2082034_POSITIVE 311 79 32 36 4 tfor:TF1268|3end_conserved_hypothetical_protein_1354635..1354785_POSITIVE