Origin IGS: aactactccgatgtctctaaaatattgtaaacttaatcttacaaaagagtataatatatcggaaccgatattgtcaatagtttagatattttttattaataaaggagaatattcttaacttacaaataggcggaacagatgctaggagcgcgcaaaaacatcgctgctgcttagaaccaccgacctccatgtcggtactgacacacccggcgacgtaaatagagggagtaatctactcaacttgcaaataggcggaacagatgcccgcatatttgcaag .........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 cttgcaaatatgcgggcatctgttccgcctatttgcaagttgagtagattactccctctatttacgtcgccgggtgtgtcagtaccgacatggaggtcggtggttctaagcagcagcgatgtttttgcgcgctcctagcatctgttccgcctatttgtaagttaagaatattctcctttattaataaaaaatatctaaactattgacaatatcggttccgatatattatactcttttgtaagattaagtttacaatattttagagacatcggagtagtt Mask Tandem Repeat Region ================================================ aactactccgatgtctctaaaatattgtaaacttaatcttacaaaagagtataatatatcggaaccgatattgtcaatagtttagatattttttattaataaaggagaatattcttaacttacaaataggcggaacagatgctaggagcgcgcaaaaacatcgctgctgcttagaaccaccgacctccatgtcggtactgacacacccggcgacgtaaatagagggagtaatctactcaacttgcaaataggcggaacagatgcccgcatatttgcaag Find is-nt database================================================ Query_seq: TDE0922:TDE0923|TDE0922:TDE0923:ABC transporter, ATP-binding/permease protein:ABC transporter, ATP-binding/permease protein:<-<-:943731..944009 279 aactactccgatgtctctaaaatattgtaaacttaatcttacaaaagagtataatatatcggaaccgatattgtcaatagtttagatattttttattaataaaggagaatattcttaacttacaaataggcggaacagatgctaggagcgcgcaaaaacatcgctgctgcttagaaccaccgacctccatgtcggtactgacacacccggcgacgtaaatagagggagtaatctactcaacttgcaaataggcggaacagatgcccgcatatttgcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0922:TDE0923|TDE0922:TDE0923:ABC transporter, ATP-binding/permease protein:ABC transporter, ATP-binding/permease protein:<-<-:943731..944009 279 aactactccgatgtctctaaaatattgtaaacttaatcttacaaaagagtataatatatcggaaccgatattgtcaatagtttagatattttttattaataaaggagaatattcttaacttacaaataggcggaacagatgctaggagcgcgcaaaaacatcgctgctgcttagaaccaccgacctccatgtcggtactgacacacccggcgacgtaaatagagggagtaatctactcaacttgcaaataggcggaacagatgcccgcatatttgcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0922:TDE0923|TDE0922:TDE0923:ABC transporter, ATP-binding/permease protein:ABC transporter, ATP-binding/permease protein:<-<-:943731..944009 279 aactactccgatgtctctaaaatattgtaaacttaatcttacaaaagagtataatatatcggaaccgatattgtcaatagtttagatattttttattaataaaggagaatattcttaacttacaaataggcggaacagatgctaggagcgcgcaaaaacatcgctgctgcttagaaccaccgacctccatgtcggtactgacacacccggcgacgtaaatagagggagtaatctactcaacttgcaaataggcggaacagatgcccgcatatttgcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aactactccgatgtctctaaaatattgtaaacttaatcttacaaaagagtataatatatcggaaccgatattgtcaatagtttagatattttttattaataaaggagaatattcttaacttacaaataggcggaacagatgctaggagcgcgcaaaaacatcgctgctgcttagaaccaccgacctccatgtcggtactgacacacccggcgacgtaaatagagggagtaatctactcaacttgcaaataggcggaacagatgcccgcatatttgcaag Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 99 End: 215 .................................................................................................. M K E N I L N L Q I G G T D A R S A Q K H R C C L E P P T S M S V L T H P A T ................................................................ Protein_Len: 38 Strand: + Start: 164 End: 277 ................................................................................................................................................................... M L L R T T D L H V G T D T P G D V N R G S N L L N L Q I G G T D A R I F A .. Protein_Len: 42 Strand: - Start: 145 End: 270 ................................................................................................................................................ S R A F V D S S S L V V S R W T P V S V G P S T F L P L L R S L K C I P P V S A R M ......... Protein_Len: 52 Strand: - Start: 77 End: 232 ............................................................................ Y N L Y K K N I F S F I R L K C I P P V S A L L A C F C R Q Q K S G G V E M D T S V C G A V Y I S P T M ............................................... aactactccgatgtctctaaaatattgtaaacttaatcttacaaaagagtataatatatcggaaccgatattgtcaatagtttagatattttttattaataaaggagaatattcttaacttacaaataggcggaacagatgctaggagcgcgcaaaaacatcgctgctgcttagaaccaccgacctccatgtcggtactgacacacccggcgacgtaaatagagggagtaatctactcaacttgcaaataggcggaacagatgcccgcatatttgcaag 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: 81 Start: 70 End: 99 .....................................................................ATTGTCAATAGTTTAGATATTTTTTATTAA.................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aactactccgatgtctctaaaatattgtaaacttaatcttacaaaagagtataatatatcggaaccgatattgtcaatagtttagatattttttattaataaaggagaatattcttaacttacaaataggcggaacagatgctaggagcgcgcaaaaacatcgctgctgcttagaaccaccgacctccatgtcggtactgacacacccggcgacgtaaatagagggagtaatctactcaacttgcaaataggcggaacagatgcccgcatatttgcaag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -2.2 Tail_Score: -3.28712 Start: 177 End: 198 Full_Region: tcgccgggtgtgtca gtaccgac atggag gtcggtgg ttctaagcagcagcg ................................................................................................................................................................................gtaccgacatggaggtcggtgg................................................................................. Find igs database================================================ Query_seq: TDE0922:TDE0923|TDE0922:TDE0923:ABC transporter, ATP-binding/permease protein:ABC transporter, ATP-binding/permease protein:<-<-:943731..944009 279 aactactccgatgtctctaaaatattgtaaacttaatcttacaaaagagtataatatatcggaaccgatattgtcaatagtttagatattttttattaataaaggagaatattcttaacttacaaataggcggaacagatgctaggagcgcgcaaaaacatcgctgctgcttagaaccaccgacctccatgtcggtactgacacacccggcgacgtaaatagagggagtaatctactcaacttgcaaataggcggaacagatgcccgcatatttgcaag Intra-Species Hit: Count: 1 Min: 1 Max: 279 Len: 279 Subject: NC_002967_TDE0922_TDE0923|ABC transporter, ATP-binding/permease protein:ABC transporter, ATP-binding/permease protein|NEGATIVE:NEGATIVE|[943731,944009]|279 HSP 1 e-value: 1.0E-156 bit: 553.0 Len: 279 Query Start:1 Query End:279 Subject Strand: POSITIVE Subject Start: 1 Subject End: 279 aactactccgatgtctctaaaatattgtaaacttaatcttacaaaagagtataatatatcggaaccgatattgtcaatagtttagatattttttattaataaaggagaatattcttaacttacaaataggcggaacagatgctaggagcgcgcaaaaacatcgctgctgcttagaaccaccgacctccatgtcggtactgacacacccggcgacgtaaatagagggagtaatctactcaacttgcaaataggcggaacagatgcccgcatatttgcaag aactactccgatgtctctaaaatattgtaaacttaatcttacaaaagagtataatatatcggaaccgatattgtcaatagtttagatattttttattaataaaggagaatattcttaacttacaaataggcggaacagatgctaggagcgcgcaaaaacatcgctgctgcttagaaccaccgacctccatgtcggtactgacacacccggcgacgtaaatagagggagtaatctactcaacttgcaaataggcggaacagatgcccgcatatttgcaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUACUCCGAUGUCUCUAAAAUAUUGUAAACUUAAUCUUACAAAAGAGUAUAAUAUAUCGGAACCGAUAUUGUCAAUAGUUUAGAUAUUUUUUAUUAAUAAAGGAGAAUAUUCUUAACUUACAAAUAGGCGGAACAGAUGCUAGGAGCGCGCAAAAACAUCGCUGCUGCUUAGAACCACCGACCUCCAUGUCGGUACUGACACACCCGGCGACGUAAAUAGAGGGAGUAAUCUACUCAACUUGCAAAUAGGCGGAACAGAUGCCCGCAUAUUUGCAAG ...((((((.....(((((..((((((((..(((..........)))..)))))))).((((.(((((((((((....((((.(((((((((((.........)))))))).))).)))).)))...((((((........(((((((((((.........))).))).))))).....))).)))..)))))))).))))......((....))....)))))))))))..........((((((((((.((((.........)))).)))))))))) (-72.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGCAAAUAUGCGGGCAUCUGUUCCGCCUAUUUGCAAGUUGAGUAGAUUACUCCCUCUAUUUACGUCGCCGGGUGUGUCAGUACCGACAUGGAGGUCGGUGGUUCUAAGCAGCAGCGAUGUUUUUGCGCGCUCCUAGCAUCUGUUCCGCCUAUUUGUAAGUUAAGAAUAUUCUCCUUUAUUAAUAAAAAAUAUCUAAACUAUUGACAAUAUCGGUUCCGAUAUAUUAUACUCUUUUGUAAGAUUAAGUUUACAAUAUUUUAGAGACAUCGGAGUAGUU ((((((((((.((((((....).))))).)))))))))).......(((((((((.((((((((((.....(((((...((((((((((......))))))).......((((.((((.(((....))))))).)).))..)))...)))))...)))))))..)))..........................((((((.(((((...((((((....)))))).......((((....)))).........))))).))))))......))))))))) (-79.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 746 80 31 171 122 NC_002967:TDE0922|5end_ABC_transporter,_ATP-binding/permease_protein_943640..943870_NEGATIVE 505 170 123 175 124 NC_002967:TDE2010|5end_hypothetical_protein_2031318..2031548_POSITIVE 418 200 152 219 165 NC_002967:TDE2640|5end_hypothetical_protein_2680034..2680264_POSITIVE 407 186 141 117 69 NC_002967:TDE2751|5end_hypothetical_protein_2807570..2807800_POSITIVE 387 200 155 63 7 NC_002967:TDE0818|5end_ABC_transporter,_ATP-binding/permease_protein_841647..841877_NEGATIVE 384 226 184 85 39 NC_002967:TDE0603|5end_hypothetical_protein_640888..641118_POSITIVE 383 170 124 106 49 NC_002967:TDE0827|5end_hypothetical_protein_848053..848283_NEGATIVE 369 196 151 61 18 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 356 170 130 231 198 NC_002967:TDE2056|5end_outer_membrane_hemin-binding_protein_A_2085070..2085300_NEGATIVE 354 168 123 59 9 NC_002967:TDE2495|5end_hypothetical_protein_2521053..2521283_NEGATIVE 354 168 121 151 102 NC_002967:TDE0073|5end_riboflavin_biosynthesis_protein_RibF,_putative_84082..84312_NEGATIVE 343 210 166 159 116 NC_002967:TDE1603|5end_ABC_transporter,_ATP-binding_protein_1654856..1655086_NEGATIVE 342 213 174 49 3 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 342 196 152 222 181 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 341 197 151 111 53 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 340 269 223 158 110 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 338 216 172 188 143 NC_002967:TDE1734|5end_exodeoxyribonuclease_III_1788613..1788843_POSITIVE 334 179 131 226 165 NC_002967:TDE2007|5end_ABC_transporter,_ATP-binding/permease_protein_2026819..2027049_POSITIVE 326 210 163 168 126 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 321 200 159 216 166 NC_002967:TDE0569|5end_hypothetical_protein_599636..599866_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 416 198 151 82 34 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 387 200 155 61 5 NC_002967:TDE0819|3end_ABC_transporter,_ATP-binding/permease_protein_841649..841799_NEGATIVE 356 170 130 143 110 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 354 168 121 77 28 NC_002967:TDE0074|3end_amino_acid_permease_family_protein_84156..84306_NEGATIVE 334 201 162 85 44 NC_002967:TDE2482|3end_hypothetical_protein_2505822..2505972_POSITIVE 327 186 145 109 57 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 320 210 161 134 63 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 319 195 151 58 6 NC_002967:TDE2614|3end_ApbE_family_protein_2656018..2656168_NEGATIVE 319 190 141 79 31 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 317 197 151 49 2 NC_002967:TDE1999|3end_DNA_polymerase_III_domain_protein_2017796..2017946_POSITIVE 312 238 193 50 12 NC_002967:TDE0898|3end_hypothetical_protein_916557..916707_POSITIVE 307 196 151 55 13 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 303 209 161 148 103 NC_002967:TDE1361|3end_hypothetical_protein_1401106..1401256_POSITIVE 302 230 186 71 29 NC_002967:TDE0848|3end_hypothetical_protein_871558..871708_POSITIVE 297 218 180 58 11 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE 295 196 174 38 16 NC_002967:TDE1094|3end_hypothetical_protein_1129722..1129872_POSITIVE 294 209 161 84 19 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 290 169 124 49 7 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 288 170 122 137 100 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 288 168 123 81 38 NC_002967:TDE2069|3end_endoribonuclease_L-PSP,_putative_2097089..2097239_POSITIVE