Origin IGS: taacttaccgccaagaaacccaaagtggagaagcaggtggaacagtagatagcacaaccctcactattcgagttttaaccctaaaacaacaaaagaaaatggaagcaacggatttgaacgaagcacgcatctatgtaggcacttatgccaagtacaataacaaacgattgaggtcaatctggacacgcttaaagtgatgcaaagtcgtggcgtatgcaatcaaaacacagaatatcacgaccaaatcgtgaaccttgtcaatgccaacaaacggctaatccgtcagcgaatgagacaaaacagcataaagtataaaccataaaactatcacagca .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgctgtgatagttttatggtttatactttatgctgttttgtctcattcgctgacggattagccgtttgttggcattgacaaggttcacgatttggtcgtgatattctgtgttttgattgcatacgccacgactttgcatcactttaagcgtgtccagattgacctcaatcgtttgttattgtacttggcataagtgcctacatagatgcgtgcttcgttcaaatccgttgcttccattttcttttgttgttttagggttaaaactcgaatagtgagggttgtgctatctactgttccacctgcttctccactttgggtttcttggcggtaagtta Mask Tandem Repeat Region ================================================ taacttaccgccaagaaacccaaagtggagaagcaggtggaacagtagatagcacaaccctcactattcgagttttaaccctaaaacaacaaaagaaaatggaagcaacggatttgaacgaagcacgcatctatgtaggcacttatgccaagtacaataacaaacgattgaggtcaatctggacacgcttaaagtgatgcaaagtcgtggcgtatgcaatcaaaacacagaatatcacgaccaaatcgtgaaccttgtcaatgccaacaaacggctaatccgtcagcgaatgagacaaaacagcataaagtataaaccataaaactatcacagca Find is-nt database================================================ Query_seq: TF3051:TF3052|TF3051:TF3052:conserved hypothetical protein:conserved hypothetical protein:->->:3278128..3278462 335 taacttaccgccaagaaacccaaagtggagaagcaggtggaacagtagatagcacaaccctcactattcgagttttaaccctaaaacaacaaaagaaaatggaagcaacggatttgaacgaagcacgcatctatgtaggcacttatgccaagtacaataacaaacgattgaggtcaatctggacacgcttaaagtgatgcaaagtcgtggcgtatgcaatcaaaacacagaatatcacgaccaaatcgtgaaccttgtcaatgccaacaaacggctaatccgtcagcgaatgagacaaaacagcataaagtataaaccataaaactatcacagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3051:TF3052|TF3051:TF3052:conserved hypothetical protein:conserved hypothetical protein:->->:3278128..3278462 335 taacttaccgccaagaaacccaaagtggagaagcaggtggaacagtagatagcacaaccctcactattcgagttttaaccctaaaacaacaaaagaaaatggaagcaacggatttgaacgaagcacgcatctatgtaggcacttatgccaagtacaataacaaacgattgaggtcaatctggacacgcttaaagtgatgcaaagtcgtggcgtatgcaatcaaaacacagaatatcacgaccaaatcgtgaaccttgtcaatgccaacaaacggctaatccgtcagcgaatgagacaaaacagcataaagtataaaccataaaactatcacagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3051:TF3052|TF3051:TF3052:conserved hypothetical protein:conserved hypothetical protein:->->:3278128..3278462 335 taacttaccgccaagaaacccaaagtggagaagcaggtggaacagtagatagcacaaccctcactattcgagttttaaccctaaaacaacaaaagaaaatggaagcaacggatttgaacgaagcacgcatctatgtaggcacttatgccaagtacaataacaaacgattgaggtcaatctggacacgcttaaagtgatgcaaagtcgtggcgtatgcaatcaaaacacagaatatcacgaccaaatcgtgaaccttgtcaatgccaacaaacggctaatccgtcagcgaatgagacaaaacagcataaagtataaaccataaaactatcacagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 3 Min: 161 Max: 295 Len: 135 Subject: UniRef90_Q56VH5 Cluster: Ctn003; n=1; Bacteroides fragilis|Rep: Ctn003 - Bacteroides fragilis HSP 1 e-value: 1.0E-10 bit: 67.8 Len: 132 Query Start:161 Query End:292 Subject Strand: null Subject Start: 381 Subject End: 424 ................................................................................................................................................................ Q T I E V N L D T L K V M Q S R G V C N Q N T E Y H D Q I V N L V N A N K R L I R Q R M ........................................... ................................................................................................................................................................ E T I E V S L K T L K V V Q S R G V C N S N T E Y H D R I I R L V E D N A G L I R Q R M ........................................... Subject: UniRef90_Q64TG2 Cluster: Hypothetical protein; n=1; Bacteroides fragilis|Rep: Hypothetical protein - Bacteroides fragilis HSP 1 e-value: 4.0E-10 bit: 65.9 Len: 132 Query Start:161 Query End:292 Subject Strand: null Subject Start: 382 Subject End: 425 ................................................................................................................................................................ Q T I E V N L D T L K V M Q S R G V C N Q N T E Y H D Q I V N L V N A N K R L I R Q R M ........................................... ................................................................................................................................................................ E T I E V D L K T L N V V Q S R G A C N Q N T E Y H D R I I G L V E K N T R L I K Q K L ........................................... Subject: UniRef90_Q650G8 Cluster: Hypothetical protein; n=1; Bacteroides fragilis|Rep: Hypothetical protein - Bacteroides fragilis HSP 1 e-value: 3.0E-7 bit: 56.6 Len: 135 Query Start:161 Query End:295 Subject Strand: null Subject Start: 397 Subject End: 441 ................................................................................................................................................................ Q T I E V N L D T L K V M Q S R G V C N Q N T E Y H D Q I V N L V N A N K R L I R Q R M R ........................................ ................................................................................................................................................................ E T V E V D L R T L E V V Q C H G K H N Q D T E Y H E R I I D L V N K N A N L I R E R M K ........................................ taacttaccgccaagaaacccaaagtggagaagcaggtggaacagtagatagcacaaccctcactattcgagttttaaccctaaaacaacaaaagaaaatggaagcaacggatttgaacgaagcacgcatctatgtaggcacttatgccaagtacaataannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncaaaacagcataaagtataaaccataaaactatcacagca Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 66 End: 194 ................................................................. M R V L T L K Q Q K K M E A T D L N E A R I Y V G T Y A K Y N N K R L R S I W T R L K ............................................................................................................................................. Protein_Len: 33 Strand: + Start: 214 End: 312 ..................................................................................................................................................................................................................... M Q S K H R I S R P N R E P C Q C Q Q T A N P S A N E T K Q H K V ....................... Protein_Len: 51 Strand: + Start: 167 End: 319 ...................................................................................................................................................................... M E V N L D T L K V M Q S R G V C N Q N T E Y H D Q I V N L V N A N K R L I R Q R M R Q N S I K Y K P ................ Protein_Len: 39 Strand: - Start: 146 End: 262 ................................................................................................................................................. A L Y L L L R N L D I Q V R K F H H L T T A Y A I L V C F I V V L D H V K D M ......................................................................... Protein_Len: 51 Strand: - Start: 67 End: 219 .................................................................. E L K L G L V V F S F P L L P N S R L V C R H L C K H W T C Y C V I S T L R S V S L T I C L R P T H M .................................................................................................................... Protein_Len: 41 Strand: - Start: 8 End: 130 ....... R W S V W L P S A P P V T S L V V R V I R T K V R F C C F F I S A V S K F S A R M ............................................................................................................................................................................................................. taacttaccgccaagaaacccaaagtggagaagcaggtggaacagtagatagcacaaccctcactattcgagttttaaccctaaaacaacaaaagaaaatggaagcaacggatttgaacgaagcacgcatctatgtaggcacttatgccaagtacaataannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncaaaacagcataaagtataaaccataaaactatcacagca 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================================================ taacttaccgccaagaaacccaaagtggagaagcaggtggaacagtagatagcacaaccctcactattcgagttttaaccctaaaacaacaaaagaaaatggaagcaacggatttgaacgaagcacgcatctatgtaggcacttatgccaagtacaataannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncaaaacagcataaagtataaaccataaaactatcacagca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3051:TF3052|TF3051:TF3052:conserved hypothetical protein:conserved hypothetical protein:->->:3278128..3278462 335 taacttaccgccaagaaacccaaagtggagaagcaggtggaacagtagatagcacaaccctcactattcgagttttaaccctaaaacaacaaaagaaaatggaagcaacggatttgaacgaagcacgcatctatgtaggcacttatgccaagtacaataannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncaaaacagcataaagtataaaccataaaactatcacagca Intra-Species Hit: Count: 1 Min: 1 Max: 335 Len: 335 Subject: tfor_TF3051_TF3052|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[3278128,3278462]|335 HSP 1 e-value: 1.0E-85 bit: 317.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 taacttaccgccaagaaacccaaagtggagaagcaggtggaacagtagatagcacaaccctcactattcgagttttaaccctaaaacaacaaaagaaaatggaagcaacggatttgaacgaagcacgcatctatgtaggcacttatgccaagtacaataa............................................................................................................................................................................... taacttaccgccaagaaacccaaagtggagaagcaggtggaacagtagatagcacaaccctcactattcgagttttaaccctaaaacaacaaaagaaaatggaagcaacggatttgaacgaagcacgcatctatgtaggcacttatgccaagtacaataa............................................................................................................................................................................... HSP 2 e-value: 6.0E-14 bit: 79.8 Len: 40 Query Start:296 Query End:335 Subject Strand: POSITIVE Subject Start: 296 Subject End: 335 .......................................................................................................................................................................................................................................................................................................caaaacagcataaagtataaaccataaaactatcacagca .......................................................................................................................................................................................................................................................................................................caaaacagcataaagtataaaccataaaactatcacagca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUUACCGCCAAGAAACCCAAAGUGGAGAAGCAGGUGGAACAGUAGAUAGCACAACCCUCACUAUUCGAGUUUUAACCCUAAAACAACAAAAGAAAAUGGAAGCAACGGAUUUGAACGAAGCACGCAUCUAUGUAGGCACUUAUGCCAAGUACAAUAACAAACGAUUGAGGUCAAUCUGGACACGCUUAAAGUGAUGCAAAGUCGUGGCGUAUGCAAUCAAAACACAGAAUAUCACGACCAAAUCGUGAACCUUGUCAAUGCCAACAAACGGCUAAUCCGUCAGCGAAUGAGACAAAACAGCAUAAAGUAUAAACCAUAAAACUAUCACAGCA .......(((((.......((.....)).......)))))....((.(((((...................((((((....))))))...........((((..((.(((..((((.((.((((.........((((((((....))))...)))).........(((((....))))).......))))...))....))))..))).)).(((((.................((((((.....))))))...(((((...(((.......))).....((....)).....)))))....))))).........))))....))))))).... (-68.74) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUGUGAUAGUUUUAUGGUUUAUACUUUAUGCUGUUUUGUCUCAUUCGCUGACGGAUUAGCCGUUUGUUGGCAUUGACAAGGUUCACGAUUUGGUCGUGAUAUUCUGUGUUUUGAUUGCAUACGCCACGACUUUGCAUCACUUUAAGCGUGUCCAGAUUGACCUCAAUCGUUUGUUAUUGUACUUGGCAUAAGUGCCUACAUAGAUGCGUGCUUCGUUCAAAUCCGUUGCUUCCAUUUUCUUUUGUUGUUUUAGGGUUAAAACUCGAAUAGUGAGGGUUGUGCUAUCUACUGUUCCACCUGCUUCUCCACUUUGGGUUUCUUGGCGGUAAGUUA ...((..(((((...(((((....(((((.((((((((..........((.((((((((...(((.(((...((..(((((((.(((((((...)))))))...))).)))).))...))).)))..((((...((((((......((((......(((((....)))))...))))..((((...((((....))))))))..))))))....))))...)))))))))).................((((((....))))))..)))))))))))))...)))))..)))))..)).(((((...((......))......)))))....... (-76.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 70 23 226 159 tfor:TF0763|5end_chromate_transport_protein_809675..809905_POSITIVE 348 288 241 78 25 tfor:TF2275|5end_conserved_hypothetical_protein_2436934..2437164_POSITIVE 337 220 172 166 114 tfor:TF1042|5end_possible_surface_antigen_with_leucine-rich_repeat_1102957..1103187_POSITIVE 325 147 109 70 19 tfor:TF1199|5end_dephospho-CoA_kinase_1282136..1282366_POSITIVE 322 300 262 103 54 tfor:TF0325|5end_LysM_domain_protein_351917..352147_POSITIVE 320 289 245 64 9 tfor:TF2310|5end_dehydrogenase,_possible_3-oxoacyl-[acyl-carrier-protein]_reductase_2470481..2470711_POSITIVE 317 217 183 57 14 tfor:TF0984|5end_possible_mucin-desulfating_sulfatase_(MdsC_protein)_1040259..1040489_POSITIVE 313 213 181 191 161 tfor:TF3024|5end_periplasmic_protease_3247204..3247434_POSITIVE 311 290 246 53 11 tfor:TF2661|5end_hypothetical_protein_2833509..2833739_POSITIVE 311 290 248 56 7 tfor:TF0329|5end_membrane-bound_lytic_murein_transglycosylase_D_355189..355419_POSITIVE 308 230 181 195 142 tfor:TF2902|5end_holliday_junction_DNA_helicase_3097813..3098043_POSITIVE 306 306 262 45 8 tfor:TF0832|5end_conserved_hypothetical_protein_888466..888696_POSITIVE 306 289 245 128 88 tfor:TF0321|5end_glycosyltransferase_347438..347668_POSITIVE 305 288 250 163 131 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 303 208 164 203 156 tfor:TF3156|5end_conserved_hypothetical_protein_3391364..3391594_POSITIVE 299 318 272 112 65 tfor:TF1734|5end_conserved_hypothetical_protein_1856556..1856786_POSITIVE 299 265 224 231 196 tfor:TF0697|5end_glycerol-3-phosphate_cytidyltransferase_740667..740897_POSITIVE 297 228 181 55 11 tfor:TF2879|5end_tRNA_(guanine-N-1)-methyltransferase_3068254..3068484_POSITIVE 296 213 172 87 38 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 296 299 253 47 7 tfor:TF2705|5end_conserved_hypothetical_protein;_possible_SufE_Fe/S-cluster-related_protein_2876850..2877080_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 220 172 149 97 tfor:TF1041|3end_dihydroorotate_dehydrogenase,_catalytic_subunit_1103020..1103170_POSITIVE 335 47 4 63 21 tfor:TF1298|3end_possible_membrane_protein_1381197..1381347_POSITIVE 329 288 248 50 10 tfor:TF2274|3end_conserved_hypothetical_protein_2436986..2437136_POSITIVE 322 300 262 103 54 tfor:TF0324|3end_conserved_hypothetical_protein_351997..352147_POSITIVE 311 290 248 53 4 tfor:TF0328|3end_conserved_hypothetical_protein_355266..355416_POSITIVE 309 217 172 151 106 tfor:TF1954|3end_long-chain-fatty-acid--CoA_ligase_2106940..2107090_POSITIVE 308 234 193 147 105 tfor:TF1327|3end_L-fucose_permease_1407195..1407345_POSITIVE 306 289 245 128 88 tfor:TF0320|3end_dihydroorotase_347518..347668_POSITIVE 293 266 233 64 27 tfor:TF2159|3end_conserved_hypothetical_protein_2336076..2336226_POSITIVE 292 82 52 88 54 tfor:TF3133|3end_conserved_hypothetical_protein_3369913..3370063_POSITIVE 291 50 8 97 43 tfor:TF2129|3end_possible_3-oxoacyl-(acyl-carrier-protein)_synthase_2306569..2306719_POSITIVE 290 108 61 103 52 tfor:TF2916|3end_conserved_hypothetical_protein_3112178..3112328_POSITIVE 290 289 250 129 91 tfor:TF1832|3end_3-isopropylmalate_dehydratase,_small_subunit_1981502..1981652_POSITIVE 287 49 6 59 23 tfor:TF1717|3end_DNA_mismatch_repair_protein_1840494..1840644_POSITIVE 286 309 261 59 6 tfor:TF2374|3end_UDP-3-O-(R-3-hydoxymyristoyl)-glucosamine-N-acylt_ransferase_2540892..2541042_POSITIVE 284 228 182 99 41 tfor:TF2930|3end_glutamyl-tRNA_synthetase_3134352..3134502_POSITIVE 284 313 272 134 75 tfor:TF0784|3end_possible_biopolymer_transport_protein_837881..838031_POSITIVE 283 218 172 149 109 tfor:TF3127|3end_acetyltransferase,_possible_GNAT_family_3362234..3362384_POSITIVE 281 230 194 55 9 tfor:TF0423|3end_G:T/U_mismatch-specific_DNA_glycosylase_439281..439431_POSITIVE 279 149 101 87 30 tfor:TF2907|3end_CDP-diacylglycerol-serine-O-phosphatidyltransfera_se_3103681..3103831_POSITIVE