Origin IGS: tttgcatctcctttattctatgaaatctctctaaatgtttgctgatattataccattttcaatggtgttttttctacgggttatcaacaatcttattttttgatataatggcagcgtaaacaaaggagatatgataaacagttcggcagaaattcagccccactgtttatctgacgagttttgtgctttgcacaaaacatcgcattattatatgtgtgtgcttttcggcacacacttgaaaaaacttttttcgcaaattgatatttgctgcaaaaagtttttataggagaattatt .........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 aataattctcctataaaaactttttgcagcaaatatcaatttgcgaaaaaagttttttcaagtgtgtgccgaaaagcacacacatataataatgcgatgttttgtgcaaagcacaaaactcgtcagataaacagtggggctgaatttctgccgaactgtttatcatatctcctttgtttacgctgccattatatcaaaaaataagattgttgataacccgtagaaaaaacaccattgaaaatggtataatatcagcaaacatttagagagatttcatagaataaaggagatgcaaa Mask Tandem Repeat Region ================================================ tttgcatctcctttattctatgaaatctctctaaatgtttgctgatattataccattttcaatggtgttttttctacgggttatcaacaatcttattttttgatataatggcagcgtaaacaaaggagatatgataaacagttcggcagaaattcagccccactgtttatctgacgagttttgtgctttgcacaaaacatcgcattattatatgtgtgtgcttttcggcacacacttgaaaaaacttttttcgcaaattgatatttgctgcaaaaagtttttataggagaattatt Find is-nt database================================================ Query_seq: TDE0521:TDE0522|TDE0521:TDE0522:carboxylesterase family protein:hypothetical protein:<-->:568343..568638 296 tttgcatctcctttattctatgaaatctctctaaatgtttgctgatattataccattttcaatggtgttttttctacgggttatcaacaatcttattttttgatataatggcagcgtaaacaaaggagatatgataaacagttcggcagaaattcagccccactgtttatctgacgagttttgtgctttgcacaaaacatcgcattattatatgtgtgtgcttttcggcacacacttgaaaaaacttttttcgcaaattgatatttgctgcaaaaagtttttataggagaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0521:TDE0522|TDE0521:TDE0522:carboxylesterase family protein:hypothetical protein:<-->:568343..568638 296 tttgcatctcctttattctatgaaatctctctaaatgtttgctgatattataccattttcaatggtgttttttctacgggttatcaacaatcttattttttgatataatggcagcgtaaacaaaggagatatgataaacagttcggcagaaattcagccccactgtttatctgacgagttttgtgctttgcacaaaacatcgcattattatatgtgtgtgcttttcggcacacacttgaaaaaacttttttcgcaaattgatatttgctgcaaaaagtttttataggagaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0521:TDE0522|TDE0521:TDE0522:carboxylesterase family protein:hypothetical protein:<-->:568343..568638 296 tttgcatctcctttattctatgaaatctctctaaatgtttgctgatattataccattttcaatggtgttttttctacgggttatcaacaatcttattttttgatataatggcagcgtaaacaaaggagatatgataaacagttcggcagaaattcagccccactgtttatctgacgagttttgtgctttgcacaaaacatcgcattattatatgtgtgtgcttttcggcacacacttgaaaaaacttttttcgcaaattgatatttgctgcaaaaagtttttataggagaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 2 Min: 131 Max: 262 Len: 132 Subject: UniRef90_Q73NM1 Cluster: Hypothetical protein; n=2; Treponema denticola|Rep: Hypothetical protein - Treponema denticola HSP 1 e-value: 2.0E-14 bit: 80.1 Len: 132 Query Start:131 Query End:262 Subject Strand: null Subject Start: 1 Subject End: 45 .................................................................................................................................. M I N S S A E I Q P H C L S D E F C A L - H K T S H Y Y M C V L F G T H L K K L F S Q I D .................................. .................................................................................................................................. M I N S S A E I Q L H C L S A E F C T Y E Y K T S H Y Y M C V L F G T H L K K L F S Q I D .................................. Subject: UniRef90_Q73PV4 Cluster: Hypothetical protein; n=1; Treponema denticola|Rep: Hypothetical protein - Treponema denticola HSP 1 e-value: 4.0E-7 bit: 55.5 Len: 84 Query Start:131 Query End:214 Subject Strand: null Subject Start: 1 Subject End: 28 .................................................................................................................................. M I N S S A E I Q P H C L S D E F C A L H K T S H Y Y M .................................................................................. .................................................................................................................................. M I N S S A E I Q P H C L S I E F C A L H K T S Y Y C M .................................................................................. HSP 2 e-value: 4.0E-7 bit: 20.4 Len: 24 Query Start:235 Query End:258 Subject Strand: null Subject Start: 35 Subject End: 42 .......................................................................................................................................................................................................................................... L E K T F F A N ...................................... .......................................................................................................................................................................................................................................... L E K T F F A N ...................................... tttgcatctcctttattctatgaaatctctctaaatgtttgctgatattataccattttcaatggtgttttttctacgggttatcaacaatcttattttttgatataatggcagcgtaaacaaaggagatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatttgctgcaaaaagtttttataggagaattatt Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 131 End: 283 .................................................................................................................................. M I N S S A E I Q P H C L S D E F C A L H K T S H Y Y M C V L F G T H L K K L F S Q I D I C C K K F L ............. Protein_Len: 31 Strand: - Start: 170 End: 262 ......................................................................................................................................................................... R V L K T S Q V F C R M I I H T H K E A C V Q F F K K R L N M .................................. Protein_Len: 60 Strand: - Start: 96 End: 284 ............................................................................................... Y H C R L C L L Y S L C N P L F E A G S N I Q R T K H K A C F M A N N Y T H A K R C V S S F V K K A F Q Y K S C F T K M ............ Protein_Len: 40 Strand: - Start: 34 End: 153 ................................. I N A S I I G N E I T N K R R T I L L R I K Q Y L P L T F L P S I I F L E A S M ............................................................................................................................................... tttgcatctcctttattctatgaaatctctctaaatgtttgctgatattataccattttcaatggtgttttttctacgggttatcaacaatcttattttttgatataatggcagcgtaaacaaaggagatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatttgctgcaaaaagtttttataggagaattatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 80 End: 109 ...............................................................................GTTATCAACAATCTTATTTTTTGATATAAT........................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgcatctcctttattctatgaaatctctctaaatgtttgctgatattataccattttcaatggtgttttttctacgggttatcaacaatcttattttttgatataatggcagcgtaaacaaaggagatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatttgctgcaaaaagtttttataggagaattatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 84 HP_score: -5.9 Tail_Score: -5.25803 Start: 51 End: 67 Full_Region: TGTTTGCTGATATTA TACCATT TTC AATGGTG TTTTTTCTACGGGTT ..................................................TACCATTTTCAATGGTG..................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 71 HP_score: -6.3 Tail_Score: -4.25873 Start: 53 End: 65 Full_Region: TTTGCTGATATTATA CCATT TTC AATGG TGTTTTTTCTACGGG ....................................................CCATTTTCAATGG....................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 85 HP_score: -9.4 Tail_Score: -3.95786 Start: 172 End: 204 Full_Region: GCCCCACTGTTTATC TGACGAGTTTTGTGC TTT GCACAAAACATCGCA TTATTATATGTGTGT ...........................................................................................................................................................................TGACGAGTTTTGTGCTTTGCACAAAACATCGCA............................................................................................ TransTerm Strand: + Conf: 77 HP_score: -5.8 Tail_Score: -4.83169 Start: 245 End: 277 Full_Region: ACACACTTGAAAAAA CTTTTTTCGCAAAT TGAT ATTTGCTGCAAAAAG TTTTTATAGGAGAAT ....................................................................................................................................................................................................................................................CTTTTTTCGCAAATTGATATTTGCTGCAAAAAG................... Find igs database================================================ Query_seq: TDE0521:TDE0522|TDE0521:TDE0522:carboxylesterase family protein:hypothetical protein:<-->:568343..568638 296 tttgcatctcctttattctatgaaatctctctaaatgtttgctgatattataccattttcaatggtgttttttctacgggttatcaacaatcttattttttgatataatggcagcgtaaacaaaggagatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatttgctgcaaaaagtttttataggagaattatt Intra-Species Hit: Count: 1 Min: 1 Max: 296 Len: 296 Subject: NC_002967_TDE0521_TDE0522|carboxylesterase family protein:hypothetical protein|NEGATIVE:POSITIVE|[568343,568638]|296 HSP 1 e-value: 1.0E-67 bit: 258.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 tttgcatctcctttattctatgaaatctctctaaatgtttgctgatattataccattttcaatggtgttttttctacgggttatcaacaatcttattttttgatataatggcagcgtaaacaaaggagat...................................................................................................................................................................... tttgcatctcctttattctatgaaatctctctaaatgtttgctgatattataccattttcaatggtgttttttctacgggttatcaacaatcttattttttgatataatggcagcgtaaacaaaggagat...................................................................................................................................................................... HSP 2 e-value: 2.0E-10 bit: 67.9 Len: 34 Query Start:263 Query End:296 Subject Strand: POSITIVE Subject Start: 263 Subject End: 296 ......................................................................................................................................................................................................................................................................atttgctgcaaaaagtttttataggagaattatt ......................................................................................................................................................................................................................................................................atttgctgcaaaaagtttttataggagaattatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGCAUCUCCUUUAUUCUAUGAAAUCUCUCUAAAUGUUUGCUGAUAUUAUACCAUUUUCAAUGGUGUUUUUUCUACGGGUUAUCAACAAUCUUAUUUUUUGAUAUAAUGGCAGCGUAAACAAAGGAGAUAUGAUAAACAGUUCGGCAGAAAUUCAGCCCCACUGUUUAUCUGACGAGUUUUGUGCUUUGCACAAAACAUCGCAUUAUUAUAUGUGUGUGCUUUUCGGCACACACUUGAAAAAACUUUUUUCGCAAAUUGAUAUUUGCUGCAAAAAGUUUUUAUAGGAGAAUUAUU ......((((((......(((((.(((((.((...(((((((.((.(..(((((((.....)))))))..).))..((...((((((.((......)).))))))...)).....))))))).)))))))..((((((((((..(((.(.....).)))..)))))))))).(.((((((((((((...))))))))).))))....))))).(((((((((....)))))))))....(((((((((((.(((((((....)))))).).)))))))))))..))))))...... (-88.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAUUCUCCUAUAAAAACUUUUUGCAGCAAAUAUCAAUUUGCGAAAAAAGUUUUUUCAAGUGUGUGCCGAAAAGCACACACAUAUAAUAAUGCGAUGUUUUGUGCAAAGCACAAAACUCGUCAGAUAAACAGUGGGGCUGAAUUUCUGCCGAACUGUUUAUCAUAUCUCCUUUGUUUACGCUGCCAUUAUAUCAAAAAAUAAGAUUGUUGAUAACCCGUAGAAAAAACACCAUUGAAAAUGGUAUAAUAUCAGCAAACAUUUAGAGAGAUUUCAUAGAAUAAAGGAGAUGCAAA ..............(((((((((((...((((((....))))))..)))))))))))....((((((((......))))))))..........((((.(((((((((...)))))))))))))..((((((((((..(((.(.....).)))..)))))))))).((((((((((((((..((((..(((((((((.....(((...((((................))))...)))....)))))))))..)))).........(((....)))...)))))))))))))).... (-90.79) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 775 90 41 181 132 NC_002967:TDE0521|5end_carboxylesterase_family_protein_568252..568482_NEGATIVE 717 180 131 230 181 NC_002967:TDE1980|5end_hypothetical_protein_1992061..1992291_NEGATIVE 619 189 141 85 38 NC_002967:TDE1583|5end_hypothetical_protein_1631808..1632038_POSITIVE 586 170 124 69 23 NC_002967:TDE1326|5end_hypothetical_protein_1361661..1361891_POSITIVE 574 170 125 98 53 NC_002967:TDE2667|5end_hypothetical_protein_2704374..2704604_POSITIVE 554 290 241 76 27 NC_002967:TDE1902|5end_hypothetical_protein_1922475..1922705_NEGATIVE 447 177 133 160 112 NC_002967:TDE2479|5end_hypothetical_protein_2503290..2503520_NEGATIVE 359 170 123 163 112 NC_002967:TDE1625|5end_glycine_cleavage_system_P_protein,_subunit_1_1674823..1675053_NEGATIVE 351 174 133 150 110 NC_002967:TDE2220|5end_prolyl-tRNA_synthetase_2260885..2261115_POSITIVE 348 202 172 48 19 NC_002967:TDE2397|5end_hypothetical_protein_2425564..2425794_NEGATIVE 348 202 172 214 185 NC_002967:TDE2396|5end_putative_inner_membrane_protein_translocase_component_YidC_2425398..2425628_NEGATIVE 348 171 133 180 142 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 340 240 195 101 50 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 340 240 195 212 161 NC_002967:TDE1324|5end_hypothetical_protein_1361610..1361840_NEGATIVE 334 171 131 151 111 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 325 174 131 148 103 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 323 179 133 181 139 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 317 187 141 225 183 NC_002967:TDE0953|5end_branched-chain_amino_acid_ABC_transporter,_permease_protein_976863..977093_POSITIVE 307 171 133 189 151 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 307 171 133 167 129 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 755 180 132 69 21 NC_002967:TDE1902|3end_hypothetical_protein_1922377..1922527_NEGATIVE 552 289 241 112 64 NC_002967:TDE2393|3end_hypothetical_protein_2422588..2422738_POSITIVE 447 177 133 84 36 NC_002967:TDE2480|3end_heat_shock_protein_90_2503366..2503516_NEGATIVE 420 149 124 149 124 NC_002967:TDE1326|3end_hypothetical_protein_1361842..1361992_POSITIVE 359 170 123 75 24 NC_002967:TDE1626|3end_glycine_cleavage_system_H_protein_1674911..1675061_NEGATIVE 345 171 133 61 23 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 327 171 133 72 34 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 326 172 133 80 41 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 323 179 133 77 35 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 310 202 178 26 3 NC_002967:TDE2398|3end_conserved_hypothetical_protein_TIGR00278_2425586..2425736_NEGATIVE 307 171 133 78 40 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 307 171 133 69 31 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 307 171 133 76 38 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 307 171 133 50 12 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 307 171 133 72 34 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 307 171 133 82 44 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 305 162 124 134 93 NC_002967:TDE1434|3end_hypothetical_protein_1478238..1478388_NEGATIVE 304 175 131 84 36 NC_002967:TDE1209|3end_site-specific_recombinase,_phage_integrase_family_1243342..1243492_POSITIVE 298 171 133 82 44 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE 293 171 131 52 11 NC_002967:TDE1333|3end_hflC_protein,_putative_1370148..1370298_POSITIVE