Origin IGS: tagcgtatttatcccagattccgcaatagaaccaattctccatgacgcgtgcaacatgttggtcggcctatggcgtaaaagcagggtctaccttgccatcgctcatattcaagaaaccacctgtgagcaccacgcccatatagttcatcttacagaacgacaaggtggtgcgataacgcttgtcaacatcggctatcgacagcccggcttctcctgttctttatttta .........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 taaaataaagaacaggagaagccgggctgtcgatagccgatgttgacaagcgttatcgcaccaccttgtcgttctgtaagatgaactatatgggcgtggtgctcacaggtggtttcttgaatatgagcgatggcaaggtagaccctgcttttacgccataggccgaccaacatgttgcacgcgtcatggagaattggttctattgcggaatctgggataaatacgcta Mask Tandem Repeat Region ================================================ tagcgtatttatcccagattccgcaatagaaccaattctccatgacgcgtgcaacatgttggtcggcctatggcgtaaaagcagggtctaccttgccatcgctcatattcaagaaaccacctgtgagcaccacgcccatatagttcatcttacagaacgacaaggtggtgcgataacgcttgtcaacatcggctatcgacagcccggcttctcctgttctttatttta Find is-nt database================================================ Query_seq: TF2092:TF2093|TF2092:TF2093:ribonuclease III:conserved hypothetical protein:->->:2261884..2262111 228 tagcgtatttatcccagattccgcaatagaaccaattctccatgacgcgtgcaacatgttggtcggcctatggcgtaaaagcagggtctaccttgccatcgctcatattcaagaaaccacctgtgagcaccacgcccatatagttcatcttacagaacgacaaggtggtgcgataacgcttgtcaacatcggctatcgacagcccggcttctcctgttctttatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2092:TF2093|TF2092:TF2093:ribonuclease III:conserved hypothetical protein:->->:2261884..2262111 228 tagcgtatttatcccagattccgcaatagaaccaattctccatgacgcgtgcaacatgttggtcggcctatggcgtaaaagcagggtctaccttgccatcgctcatattcaagaaaccacctgtgagcaccacgcccatatagttcatcttacagaacgacaaggtggtgcgataacgcttgtcaacatcggctatcgacagcccggcttctcctgttctttatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2092:TF2093|TF2092:TF2093:ribonuclease III:conserved hypothetical protein:->->:2261884..2262111 228 tagcgtatttatcccagattccgcaatagaaccaattctccatgacgcgtgcaacatgttggtcggcctatggcgtaaaagcagggtctaccttgccatcgctcatattcaagaaaccacctgtgagcaccacgcccatatagttcatcttacagaacgacaaggtggtgcgataacgcttgtcaacatcggctatcgacagcccggcttctcctgttctttatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagcgtatttatcccagattccgcaatagaaccaattctccatgacgcgtgcaacatgttggtcggcctatggcgtaaaagcagggtctaccttgccatcgctcatattcaagaaaccacctgtgagcaccacgcccatatagttcatcttacagaacgacaaggtggtgcgataacgcttgtcaacatcggctatcgacagcccggcttctcctgttctttatttta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 42 End: 140 ......................................... M T R A T C W S A Y G V K A G S T L P S L I F K K P P V S T T P I ........................................................................................ Protein_Len: 60 Strand: + Start: 11 End: 226 .......... M P D S A I E P I L H D A C N M L V G L W R K S R V Y L A I A H I Q E T T C E H H A H I V H L T E R Q G G A I T L V N I .. Protein_Len: 44 Strand: - Start: 71 End: 202 ...................................................................... P T F A P D V K G D S M N L F G G T L V V G M Y N M K C F S L T T R Y R K D V D A I S M .......................... tagcgtatttatcccagattccgcaatagaaccaattctccatgacgcgtgcaacatgttggtcggcctatggcgtaaaagcagggtctaccttgccatcgctcatattcaagaaaccacctgtgagcaccacgcccatatagttcatcttacagaacgacaaggtggtgcgataacgcttgtcaacatcggctatcgacagcccggcttctcctgttctttatttta 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================================================ tagcgtatttatcccagattccgcaatagaaccaattctccatgacgcgtgcaacatgttggtcggcctatggcgtaaaagcagggtctaccttgccatcgctcatattcaagaaaccacctgtgagcaccacgcccatatagttcatcttacagaacgacaaggtggtgcgataacgcttgtcaacatcggctatcgacagcccggcttctcctgttctttatttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2092:TF2093|TF2092:TF2093:ribonuclease III:conserved hypothetical protein:->->:2261884..2262111 228 tagcgtatttatcccagattccgcaatagaaccaattctccatgacgcgtgcaacatgttggtcggcctatggcgtaaaagcagggtctaccttgccatcgctcatattcaagaaaccacctgtgagcaccacgcccatatagttcatcttacagaacgacaaggtggtgcgataacgcttgtcaacatcggctatcgacagcccggcttctcctgttctttatttta Intra-Species Hit: Count: 1 Min: 1 Max: 228 Len: 228 Subject: tfor_TF2092_TF2093|ribonuclease III:conserved hypothetical protein|POSITIVE:POSITIVE|[2261884,2262111]|228 HSP 1 e-value: 1.0E-126 bit: 452.0 Len: 228 Query Start:1 Query End:228 Subject Strand: POSITIVE Subject Start: 1 Subject End: 228 tagcgtatttatcccagattccgcaatagaaccaattctccatgacgcgtgcaacatgttggtcggcctatggcgtaaaagcagggtctaccttgccatcgctcatattcaagaaaccacctgtgagcaccacgcccatatagttcatcttacagaacgacaaggtggtgcgataacgcttgtcaacatcggctatcgacagcccggcttctcctgttctttatttta tagcgtatttatcccagattccgcaatagaaccaattctccatgacgcgtgcaacatgttggtcggcctatggcgtaaaagcagggtctaccttgccatcgctcatattcaagaaaccacctgtgagcaccacgcccatatagttcatcttacagaacgacaaggtggtgcgataacgcttgtcaacatcggctatcgacagcccggcttctcctgttctttatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCGUAUUUAUCCCAGAUUCCGCAAUAGAACCAAUUCUCCAUGACGCGUGCAACAUGUUGGUCGGCCUAUGGCGUAAAAGCAGGGUCUACCUUGCCAUCGCUCAUAUUCAAGAAACCACCUGUGAGCACCACGCCCAUAUAGUUCAUCUUACAGAACGACAAGGUGGUGCGAUAACGCUUGUCAACAUCGGCUAUCGACAGCCCGGCUUCUCCUGUUCUUUAUUUUA ..(((.((((.....))))..)))...(((((.......((.(((((((((((.(((.(((.......((((((((....((((((....))))))....(((((((..............)))))))...))).)))))..((((........))))..))).))).)))....))))..)))).....((((......)))).))........)))))........ (-56.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUAAAGAACAGGAGAAGCCGGGCUGUCGAUAGCCGAUGUUGACAAGCGUUAUCGCACCACCUUGUCGUUCUGUAAGAUGAACUAUAUGGGCGUGGUGCUCACAGGUGGUUUCUUGAAUAUGAGCGAUGGCAAGGUAGACCCUGCUUUUACGCCAUAGGCCGACCAACAUGUUGCACGCGUCAUGGAGAAUUGGUUCUAUUGCGGAAUCUGGGAUAAAUACGCUA ............(((((((.(((..((((((((((.....))))))).)))......(((((((((..(.((((........))))...)..)).))))))).....)))..)))))))......((((..((((.((....)).))))....(((.(((((((((....((((.((....)).)))).....)))).))))).)))................)))). (-70.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 423 208 164 200 149 tfor:TF1048|5end_permease_1109241..1109471_POSITIVE 398 104 62 200 161 tfor:TF1767|5end_3-dehydroquinate_synthase_1905492..1905722_POSITIVE 397 219 177 227 178 tfor:TF1064|5end_ampG_permease_1134004..1134234_POSITIVE 396 208 165 179 139 tfor:TF1440|5end_hypothetical_protein_1524599..1524829_POSITIVE 392 102 63 54 11 tfor:TF1292|5end_sensor_histidine_protein_kinase_1372567..1372797_POSITIVE 391 98 55 78 22 tfor:TF0011|5end_conserved_hypothetical_protein_4685..4915_POSITIVE 386 210 163 156 89 tfor:TF0431|5end_hypothetical_protein_452178..452408_POSITIVE 386 210 163 141 74 tfor:TF0430|5end_hypothetical_protein_452163..452393_POSITIVE 383 210 164 57 2 tfor:TF0464|5end_precorrin_methylase_480211..480441_POSITIVE 382 208 164 227 165 tfor:TF1959|5end_conserved_hypothetical_protein_2109377..2109607_POSITIVE 380 208 162 127 65 tfor:TF1299|5end_conserved_hypothetical_protein_1380937..1381167_POSITIVE 378 216 179 69 30 tfor:TF1531|5end_potassium_uptake_protein_1636534..1636764_POSITIVE 377 208 161 76 13 tfor:TF1945|5end_glycerate_dehydrogenase_2093229..2093459_POSITIVE 376 97 51 167 117 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 374 208 161 187 144 tfor:TF1191|5end_possible_transcriptional_regulator_1273615..1273845_POSITIVE 373 208 164 207 147 tfor:TF2918|5end_hypothetical_protein_3114084..3114314_POSITIVE 373 207 165 147 103 tfor:TF0236|5end_multidrug_resistance_protein_261779..262009_POSITIVE 372 101 61 227 191 tfor:TF2695|5end_prephenate_dehydratase_2869618..2869848_POSITIVE 371 107 62 72 21 tfor:TF0773|5end_outer_membrane_efflux_protein_821218..821448_POSITIVE 370 76 32 223 186 tfor:TF1950|5end_conserved_hypothetical_protein;_possible_transporter_2099828..2100058_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 447 207 161 76 15 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 394 50 12 87 48 tfor:TF2366|3end_conserved_hypothetical_protein_2531892..2532042_POSITIVE 392 102 63 54 11 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 391 98 55 103 47 tfor:TF0010|3end_conserved_hypothetical_protein_4790..4940_POSITIVE 386 210 163 125 58 tfor:TF0429|3end_ABC_transporter,_ATP-binding_protein_452227..452377_POSITIVE 383 210 164 57 2 tfor:TF0463|3end_precorrin-6Y_C5,15-methyltransferase_480291..480441_POSITIVE 378 216 179 69 30 tfor:TF1530|3end_1-deoxyxylulose-5-phosphate_synthase_1636614..1636764_POSITIVE 377 208 161 76 13 tfor:TF1944|3end_conserved_hypothetical_protein_2093309..2093459_POSITIVE 373 207 165 137 93 tfor:TF0235|3end_hypothetical_protein_261849..261999_POSITIVE 366 107 64 58 2 tfor:TF2204|3end_conserved_hypothetical_protein_2379122..2379272_POSITIVE 364 98 51 57 4 tfor:TF0582|3end_hemolysin-related_protein,_with_CBS_domains;_possible_gliding-motility_related_protein_613263..613413_POSITIVE 362 219 171 42 1 tfor:TF2256|3end_transfer_region-related_protein,_TraI_2428614..2428764_POSITIVE 362 95 51 144 106 tfor:TF1497|3end_GTP-binding_protein,_Era/ThdF_family_1597519..1597669_POSITIVE 361 220 177 64 12 tfor:TF2575|3end_methionine_aminopeptidase_2745985..2746135_POSITIVE 358 217 171 56 9 tfor:TF2809|3end_conserved_hypothetical_protein;_possible_translation_factor_(SUA5)_3000511..3000661_POSITIVE 355 86 41 65 8 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 351 118 74 108 67 tfor:TF1951|3end_xanthosine_triphosphate_pyrophosphatase,_Ham1-like_protein_2101447..2101597_POSITIVE 351 103 62 146 94 tfor:TF1095|3end_transposase_1165199..1165349_POSITIVE 347 138 91 57 20 tfor:TF1796|3end_ABC_transporter,_ATP-binding_protein_1937216..1937366_POSITIVE 346 208 163 147 97 tfor:TF1838|3end_tRNA/rRNA_methyltransferase_1988745..1988895_POSITIVE