Origin IGS: aggattgtaactgtgattttgaagttagttttttcctgttatgttttaattgggcggcaagttagtcattttttaccggaggaggttcctttttccgctaaatgcgcatagtgcggattccagtcttaagagcaacgatttgataaattcaggatgaaaagctcgaaagatctttcgaaataaagttttctcagacgttttatccggatcggcctcacatctttctaatgaccgattcggagtaaaagactg .........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 cagtcttttactccgaatcggtcattagaaagatgtgaggccgatccggataaaacgtctgagaaaactttatttcgaaagatctttcgagcttttcatcctgaatttatcaaatcgttgctcttaagactggaatccgcactatgcgcatttagcggaaaaaggaacctcctccggtaaaaaatgactaacttgccgcccaattaaaacataacaggaaaaaactaacttcaaaatcacagttacaatcct Mask Tandem Repeat Region ================================================ aggattgtaactgtgattttgaagttagttttttcctgttatgttttaattgggcggcaagttagtcattttttaccggaggaggttcctttttccgctaaatgcgcatagtgcggattccagtcttaagagcaacgatttgataaattcaggatgaaaagctcgaaagatctttcgaaataaagttttctcagacgttttatccggatcggcctcacatctttctaatgaccgattcggagtaaaagactg Find is-nt database================================================ Query_seq: PG1401:PG1402|PG1401:PG1402:beta-eliminating lyase:AP endonuclease domain protein:<-<-:1484869..1485120 252 aggattgtaactgtgattttgaagttagttttttcctgttatgttttaattgggcggcaagttagtcattttttaccggaggaggttcctttttccgctaaatgcgcatagtgcggattccagtcttaagagcaacgatttgataaattcaggatgaaaagctcgaaagatctttcgaaataaagttttctcagacgttttatccggatcggcctcacatctttctaatgaccgattcggagtaaaagactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1401:PG1402|PG1401:PG1402:beta-eliminating lyase:AP endonuclease domain protein:<-<-:1484869..1485120 252 aggattgtaactgtgattttgaagttagttttttcctgttatgttttaattgggcggcaagttagtcattttttaccggaggaggttcctttttccgctaaatgcgcatagtgcggattccagtcttaagagcaacgatttgataaattcaggatgaaaagctcgaaagatctttcgaaataaagttttctcagacgttttatccggatcggcctcacatctttctaatgaccgattcggagtaaaagactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1401:PG1402|PG1401:PG1402:beta-eliminating lyase:AP endonuclease domain protein:<-<-:1484869..1485120 252 aggattgtaactgtgattttgaagttagttttttcctgttatgttttaattgggcggcaagttagtcattttttaccggaggaggttcctttttccgctaaatgcgcatagtgcggattccagtcttaagagcaacgatttgataaattcaggatgaaaagctcgaaagatctttcgaaataaagttttctcagacgttttatccggatcggcctcacatctttctaatgaccgattcggagtaaaagactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggattgtaactgtgattttgaagttagttttttcctgttatgttttaattgggcggcaagttagtcattttttaccggaggaggttcctttttccgctaaatgcgcatagtgcggattccagtcttaagagcaacgatttgataaattcaggatgaaaagctcgaaagatctttcgaaataaagttttctcagacgttttatccggatcggcctcacatctttctaatgaccgattcggagtaaaagactg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 4 End: 108 ... M V T V I L K L V F S C Y V L I G R Q V S H F L P E E V P F S A K C A ................................................................................................................................................ Protein_Len: 35 Strand: + Start: 50 End: 154 ................................................. M G G K L V I F Y R R R F L F P L N A H S A D S S L K S N D L I N S G .................................................................................................. Protein_Len: 32 Strand: + Start: 147 End: 242 .................................................................................................................................................. M Q D E K L E R S F E I K F S Q T F Y P D R P H I F L M T D S E .......... Protein_Len: 30 Strand: - Start: 129 End: 218 ................................................................................................................................ S C R N S L N L I F L E F S R E F Y L K R L R K I R I P R M .................................. Protein_Len: 32 Strand: - Start: 76 End: 171 ........................................................................... R L L N R K G S F A C L A S E L R L L L S K I F E P H F A R F M ................................................................................. aggattgtaactgtgattttgaagttagttttttcctgttatgttttaattgggcggcaagttagtcattttttaccggaggaggttcctttttccgctaaatgcgcatagtgcggattccagtcttaagagcaacgatttgataaattcaggatgaaaagctcgaaagatctttcgaaataaagttttctcagacgttttatccggatcggcctcacatctttctaatgaccgattcggagtaaaagactg 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================================================ aggattgtaactgtgattttgaagttagttttttcctgttatgttttaattgggcggcaagttagtcattttttaccggaggaggttcctttttccgctaaatgcgcatagtgcggattccagtcttaagagcaacgatttgataaattcaggatgaaaagctcgaaagatctttcgaaataaagttttctcagacgttttatccggatcggcctcacatctttctaatgaccgattcggagtaaaagactg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1401:PG1402|PG1401:PG1402:beta-eliminating lyase:AP endonuclease domain protein:<-<-:1484869..1485120 252 aggattgtaactgtgattttgaagttagttttttcctgttatgttttaattgggcggcaagttagtcattttttaccggaggaggttcctttttccgctaaatgcgcatagtgcggattccagtcttaagagcaacgatttgataaattcaggatgaaaagctcgaaagatctttcgaaataaagttttctcagacgttttatccggatcggcctcacatctttctaatgaccgattcggagtaaaagactg Intra-Species Hit: Count: 1 Min: 1 Max: 252 Len: 252 Subject: NC_002950_PG1401_PG1402|beta-eliminating lyase:AP endonuclease domain protein|NEGATIVE:NEGATIVE|[1484869,1485120]|252 HSP 1 e-value: 1.0E-140 bit: 500.0 Len: 252 Query Start:1 Query End:252 Subject Strand: POSITIVE Subject Start: 1 Subject End: 252 aggattgtaactgtgattttgaagttagttttttcctgttatgttttaattgggcggcaagttagtcattttttaccggaggaggttcctttttccgctaaatgcgcatagtgcggattccagtcttaagagcaacgatttgataaattcaggatgaaaagctcgaaagatctttcgaaataaagttttctcagacgttttatccggatcggcctcacatctttctaatgaccgattcggagtaaaagactg aggattgtaactgtgattttgaagttagttttttcctgttatgttttaattgggcggcaagttagtcattttttaccggaggaggttcctttttccgctaaatgcgcatagtgcggattccagtcttaagagcaacgatttgataaattcaggatgaaaagctcgaaagatctttcgaaataaagttttctcagacgttttatccggatcggcctcacatctttctaatgaccgattcggagtaaaagactg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAUUGUAACUGUGAUUUUGAAGUUAGUUUUUUCCUGUUAUGUUUUAAUUGGGCGGCAAGUUAGUCAUUUUUUACCGGAGGAGGUUCCUUUUUCCGCUAAAUGCGCAUAGUGCGGAUUCCAGUCUUAAGAGCAACGAUUUGAUAAAUUCAGGAUGAAAAGCUCGAAAGAUCUUUCGAAAUAAAGUUUUCUCAGACGUUUUAUCCGGAUCGGCCUCACAUCUUUCUAAUGACCGAUUCGGAGUAAAAGACUG .(((....((((...(((((((((..((((((((((((...((((..(((((....((.....((.(....((((.(((((((((...))))))))).))))..(((.....))).......).)).....))..))))).))))....)))))..)))))))(....)...)))))))))..)))).))).....(((((.((((((((((..(((...........)))))))))))))....))))).. (-58.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUCUUUUACUCCGAAUCGGUCAUUAGAAAGAUGUGAGGCCGAUCCGGAUAAAACGUCUGAGAAAACUUUAUUUCGAAAGAUCUUUCGAGCUUUUCAUCCUGAAUUUAUCAAAUCGUUGCUCUUAAGACUGGAAUCCGCACUAUGCGCAUUUAGCGGAAAAAGGAACCUCCUCCGGUAAAAAAUGACUAACUUGCCGCCCAAUUAAAACAUAACAGGAAAAAACUAACUUCAAAAUCACAGUUACAAUCCU (((.((((((.((((.(((((((.(((.(....).)))))))))).))))))))).).)))....((((....(((((((....))))))).......(((((.............((((.((.....(((((..(((((...((....))...)))))...(((.....)))))))).......)).)))).((.....))............))))).....................))))........ (-50.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 962 100 51 191 142 NC_002950:PG1401|5end_beta-eliminating_lyase_1484778..1485008_NEGATIVE 394 115 76 113 65 NC_002950:PG2146|5end_hypothetical_protein_2253815..2254045_POSITIVE 344 127 81 85 26 NC_002950:PG1901|5end_ribosome_releasing_factor_2001352..2001582_NEGATIVE 340 120 79 162 121 NC_002950:PG0934|5end_hypothetical_protein_994318..994548_NEGATIVE 337 238 196 230 182 NC_002950:PG0585|5end_YqeY_family_protein_643272..643502_POSITIVE 336 97 51 208 168 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 334 117 75 217 170 NC_002950:PG0080|5end_hypothetical_protein_93832..94062_NEGATIVE 332 127 81 181 128 NC_002950:PG1837|5end_hemagglutinin_protein_HagA_1930337..1930567_POSITIVE 330 116 75 87 44 NC_002950:PG1096|5end_hypothetical_protein_1161839..1162069_POSITIVE 321 120 76 214 163 NC_002950:PG1752|5end_hypothetical_protein_1838394..1838624_POSITIVE 321 98 51 172 116 NC_002950:PG1248|5end_hypothetical_protein_1326532..1326762_NEGATIVE 319 118 77 46 8 NC_002950:PG1496|5end_hypothetical_protein_1573342..1573572_POSITIVE 318 140 95 207 169 NC_002950:PG0248|5end_translation_initation_factor_SUI1,_putative_281842..282072_NEGATIVE 318 100 51 125 76 NC_002950:PG0201|5end_ribonuclease_P_238770..239000_NEGATIVE 315 117 77 80 37 NC_002950:PG1655|5end_hypothetical_protein_1737095..1737325_POSITIVE 315 119 75 176 128 NC_002950:PG1072|5end_MutS_family_protein_1138976..1139206_POSITIVE 313 98 55 218 172 NC_002950:PG0347|5end_UDP-glucose_4-epimerase_381274..381504_POSITIVE 312 88 43 207 158 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 310 133 95 54 25 NC_002950:PG2126|5end_conserved_hypothetical_protein_TIGR00044_2233112..2233342_NEGATIVE 308 90 42 228 187 NC_002950:PG1841|5end_hypothetical_protein_1937310..1937540_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 383 239 191 151 91 NC_002950:PG1324|3end_Holliday_junction_resolvase_1402862..1403012_NEGATIVE 333 117 77 44 1 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 332 234 196 73 39 NC_002950:PG1055|3end_thiol_protease_1121202..1121352_NEGATIVE 319 118 77 40 2 NC_002950:PG1495|3end_DNA_topoisomerase_III_1573416..1573566_POSITIVE 319 117 76 60 14 NC_002950:PG0969|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase,_putative_1028201..1028351_NEGATIVE 318 140 95 110 72 NC_002950:PG0249|3end_oxaloacetate_decarboxylase,_putative_281939..282089_NEGATIVE 318 100 51 128 79 NC_002950:PG0202|3end_uroporphyrinogen-III_synthase_HemD,_putative_238767..238917_NEGATIVE 317 99 52 45 15 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 316 114 72 147 108 NC_002950:PG1997|3end_hypothetical_protein_2087072..2087222_POSITIVE 315 117 77 66 23 NC_002950:PG1654|3end_D-alanyl-D-alanine_dipeptidase_1737161..1737311_POSITIVE 313 137 92 143 97 NC_002950:PG0354|3end_hypothetical_protein_389131..389281_NEGATIVE 312 120 77 52 6 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 310 133 95 57 28 NC_002950:PG2127|3end_hypothetical_protein_2233109..2233259_NEGATIVE 308 90 42 133 92 NC_002950:PG1840|3end_hypothetical_protein_1937295..1937445_POSITIVE 307 97 52 111 73 NC_002950:PG1799|3end_hypothetical_protein_1894788..1894938_POSITIVE 307 98 55 119 78 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 306 118 76 45 5 NC_002950:PG1773|3end_PAP2_superfamily_protein_1861232..1861382_POSITIVE 304 250 204 72 26 NC_002950:PG2102|3end_immunoreactive_61_kDa_antigen_PG91_2211424..2211574_NEGATIVE 304 218 172 78 23 NC_002950:PG1626|3end_hypothetical_protein_1710486..1710636_POSITIVE 304 240 197 119 74 NC_002950:PG0411|3end_hemagglutinin,_putative_449358..449508_POSITIVE