Origin IGS: tgacacggattaacgttctgggcggtcagcgaccagatcaaaaagggagcggctctgaacgcggtacagattgccgaatacctgctcaaagccggaggcctcggctaagatcgaaaaaaaagaggaggggaaatcctca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaggatttcccctcctcttttttttcgatcttagccgaggcctccggctttgagcaggtattcggcaatctgtaccgcgttcagagccgctccctttttgatctggtcgctgaccgcccagaacgttaatccgtgtca Mask Tandem Repeat Region ================================================ tgacacggattaacgttctgggcggtcagcgaccagatcaaaaagggagcggctctgaacgcggtacagattgccgaatacctgctcaaagccggaggcctcggctaagatcgaaaaaaaagaggaggggaaatcctca Find is-nt database================================================ Query_seq: TF2143:TF2145|TF2143:TF2145:S-adenosylmethionine:tRNA ribosyltransferase-isomerase:conserved hypothetical protein; possible rhodanese-domain protein:->->:2319765..2319903 139 tgacacggattaacgttctgggcggtcagcgaccagatcaaaaagggagcggctctgaacgcggtacagattgccgaatacctgctcaaagccggaggcctcggctaagatcgaaaaaaaagaggaggggaaatcctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2143:TF2145|TF2143:TF2145:S-adenosylmethionine:tRNA ribosyltransferase-isomerase:conserved hypothetical protein; possible rhodanese-domain protein:->->:2319765..2319903 139 tgacacggattaacgttctgggcggtcagcgaccagatcaaaaagggagcggctctgaacgcggtacagattgccgaatacctgctcaaagccggaggcctcggctaagatcgaaaaaaaagaggaggggaaatcctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2143:TF2145|TF2143:TF2145:S-adenosylmethionine:tRNA ribosyltransferase-isomerase:conserved hypothetical protein; possible rhodanese-domain protein:->->:2319765..2319903 139 tgacacggattaacgttctgggcggtcagcgaccagatcaaaaagggagcggctctgaacgcggtacagattgccgaatacctgctcaaagccggaggcctcggctaagatcgaaaaaaaagaggaggggaaatcctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgacacggattaacgttctgggcggtcagcgaccagatcaaaaagggagcggctctgaacgcggtacagattgccgaatacctgctcaaagccggaggcctcggctaagatcgaaaaaaaagaggaggggaaatcctca Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 9 End: 137 ........ M N V L G G Q R P D Q K G S G S E R G T D C R I P A Q S R R P R L R S K K K R R G N P .. Protein_Len: 33 Strand: - Start: 13 End: 111 ............ R E P R D A V L D F L S R S Q V R Y L N G F V Q E F G S A E A L M ............................ tgacacggattaacgttctgggcggtcagcgaccagatcaaaaagggagcggctctgaacgcggtacagattgccgaatacctgctcaaagccggaggcctcggctaagatcgaaaaaaaagaggaggggaaatcctca 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================================================ tgacacggattaacgttctgggcggtcagcgaccagatcaaaaagggagcggctctgaacgcggtacagattgccgaatacctgctcaaagccggaggcctcggctaagatcgaaaaaaaagaggaggggaaatcctca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2143:TF2145|TF2143:TF2145:S-adenosylmethionine:tRNA ribosyltransferase-isomerase:conserved hypothetical protein; possible rhodanese-domain protein:->->:2319765..2319903 139 tgacacggattaacgttctgggcggtcagcgaccagatcaaaaagggagcggctctgaacgcggtacagattgccgaatacctgctcaaagccggaggcctcggctaagatcgaaaaaaaagaggaggggaaatcctca Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: tfor_TF2143_TF2145|S-adenosylmethionine:tRNA ribosyltransferase-isomerase:conserved hypothetical protein; possible rhodanese-domain protein|POSITIVE:POSITIVE|[2319765,2319903]|139 HSP 1 e-value: 4.0E-59 bit: 228.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 tgacacggattaacgttctgggcggtcagcgaccagatcaaaaagggagcggctctgaacgcggtacagattgccgaatacctgctcaaagccggaggcctcggctaagatcgnnnnnnnngaggaggggaaatcctca tgacacggattaacgttctgggcggtcagcgaccagatcaaaaagggagcggctctgaacgcggtacagattgccgaatacctgctcaaagccggaggcctcggctaagatcgaaaaaaaagaggaggggaaatcctca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACACGGAUUAACGUUCUGGGCGGUCAGCGACCAGAUCAAAAAGGGAGCGGCUCUGAACGCGGUACAGAUUGCCGAAUACCUGCUCAAAGCCGGAGGCCUCGGCUAAGAUCGAAAAAAAAGAGGAGGGGAAAUCCUCA ......(((((..(.((((....((((...)))).((((....(((...((((((((.((...)).))))..))))....)))......((((((.....))))))..))))...........)))).)..)))))... (-41.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGGAUUUCCCCUCCUCUUUUUUUUCGAUCUUAGCCGAGGCCUCCGGCUUUGAGCAGGUAUUCGGCAAUCUGUACCGCGUUCAGAGCCGCUCCCUUUUUGAUCUGGUCGCUGACCGCCCAGAACGUUAAUCCGUGUCA .(((((.......))))).........(((.(((((.((((....(((((((((((.(((((..........)))))..)))))))))))...)))).....(((((.((.....)).)))))..))))).....))). (-41.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 483 69 25 47 9 tfor:TF1742|5end_TPR_repeat-containing_protein_1873129..1873359_POSITIVE 479 112 71 155 121 tfor:TF0693|5end_sigma-54_dependent_transcriptional_regulator_736902..737132_POSITIVE 459 100 51 159 106 tfor:TF0975|5end_hypothetical_protein_1023994..1024224_POSITIVE 439 105 61 186 149 tfor:TF1785|5end_histidine_ammonia-lyase_1924494..1924724_POSITIVE 423 99 51 62 15 tfor:TF2773|5end_S-adenosylmethionine_tRNA_ribosyltransferase_2958117..2958347_POSITIVE 421 69 21 61 8 tfor:TF1665|5end_conserved_hypothetical_protein_1779148..1779378_POSITIVE 404 108 61 52 17 tfor:TF1062|5end_glycosyltransferase_1131727..1131957_POSITIVE 398 70 24 217 157 tfor:TF0810|5end_possible_outer_membrane_efflux_protein_868438..868668_POSITIVE 394 99 51 104 48 tfor:TF2997|5end_hypothetical_protein_3211408..3211638_POSITIVE 394 68 21 154 96 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 392 65 22 212 172 tfor:TF0971|5end_conserved_hypothetical_protein_1021355..1021585_POSITIVE 391 99 53 200 143 tfor:TF1599|5end_ribonuclease_P_protein_component_1713564..1713794_POSITIVE 385 99 51 149 95 tfor:TF2079|5end_permease_2245585..2245815_POSITIVE 382 100 51 212 151 tfor:TF1577|5end_hypothetical_protein_1685960..1686190_POSITIVE 382 100 51 104 43 tfor:TF1576|5end_hypothetical_protein_1685852..1686082_POSITIVE 382 60 14 145 96 tfor:TF0253|5end_conserved_hypothetical_protein_283707..283937_POSITIVE 380 130 81 191 128 tfor:TF1253|5end_hypothetical_protein_1335982..1336212_POSITIVE 378 130 81 78 15 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 378 99 51 200 156 tfor:TF0474|5end_outer_membrane_efflux_protein_492104..492334_POSITIVE 377 67 22 50 7 tfor:TF2830|5end_ABC_transporter,_ATP-binding_protein_3020581..3020811_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 404 108 61 52 17 tfor:TF1061|3end_glycosyltransferase_1131807..1131957_POSITIVE 395 70 22 69 22 tfor:TF0007|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III_3599..3749_POSITIVE 394 68 21 125 67 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 393 113 74 143 101 tfor:TF2953|3end_possible_TonB-dependent_outer_membrane_receptor_3161501..3161651_POSITIVE 382 100 51 67 6 tfor:TF1575|3end_DNA-binding_response_regulator_1685895..1686045_POSITIVE 382 60 14 117 68 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 379 99 60 44 4 tfor:TF2772|3end_tRNA_pseudouridine_synthase_B_2958179..2958329_POSITIVE 377 67 22 50 7 tfor:TF2829|3end_conserved_hypothetical_protein_3020661..3020811_POSITIVE 373 98 55 68 12 tfor:TF2827|3end_conserved_hypothetical_protein_3019642..3019792_POSITIVE 372 106 61 67 7 tfor:TF1917|3end_hypothetical_protein_2070244..2070394_POSITIVE 372 130 82 65 15 tfor:TF1476|3end_outer_membrane_protein_P49_1571203..1571353_POSITIVE 368 99 51 104 45 tfor:TF0673|3end_conserved_hypothetical_protein_717355..717505_POSITIVE 364 108 61 117 66 tfor:TF0203|3end_PhoH-like_protein_230660..230810_POSITIVE 358 57 14 84 38 tfor:TF1914|3end_conserved_hypothetical_protein_2067656..2067806_POSITIVE 354 100 51 74 13 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 354 99 51 62 19 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 351 114 72 52 16 tfor:TF0037|3end_sialic_acid-specific_9-O-acetylesterase_39991..40141_POSITIVE 348 63 21 140 87 tfor:TF2435|3end_DNA_repair_protein_radC_2615136..2615286_POSITIVE 345 101 61 72 30 tfor:TF1712|3end_conserved_hypothetical_protein_1833524..1833674_POSITIVE 344 95 52 110 56 tfor:TF1951|3end_xanthosine_triphosphate_pyrophosphatase,_Ham1-like_protein_2101447..2101597_POSITIVE