Origin IGS: agtgacacctcctttattttttgaaaatatgcgggcatctgctccacctattttcaaaaatgtttattccatttatcataagcagcctctatgacgttgctaaaatatacataatcaccgtatcagaaccgccacggatggcggtagtgccaagcagtagcaagtttttcgttagaaaaactcgtcgttgaaaagtgtacacggaggtacgcttttcaacacacctgcgggtaatttttgctcatgcatcgtatctgcaccgtctatttgcaaaaggcttattcacggaattaatcgtcggaataatagtttcattaccaactacaaa .........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 tttgtagttggtaatgaaactattattccgacgattaattccgtgaataagccttttgcaaatagacggtgcagatacgatgcatgagcaaaaattacccgcaggtgtgttgaaaagcgtacctccgtgtacacttttcaacgacgagtttttctaacgaaaaacttgctactgcttggcactaccgccatccgtggcggttctgatacggtgattatgtatattttagcaacgtcatagaggctgcttatgataaatggaataaacatttttgaaaataggtggagcagatgcccgcatattttcaaaaaataaaggaggtgtcact Mask Tandem Repeat Region ================================================ agtgacacctcctttattttttgaaaatatgcgggcatctgctccacctattttcaaaaatgtttattccatttatcataagcagcctctatgacgttgctaaaatatacataatcaccgtatcagaaccgccacggatggcggtagtgccaagcagtagcaagtttttcgttagaaaaactcgtcgttgaaaagtgtacacggaggtacgcttttcaacacacctgcgggtaatttttgctcatgcatcgtatctgcaccgtctatttgcaaaaggcttattcacggaattaatcgtcggaataatagtttcattaccaactacaaa Find is-nt database================================================ Query_seq: TDE0819:TDE0820|TDE0819:TDE0820:ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family:<-<-:843476..843803 328 agtgacacctcctttattttttgaaaatatgcgggcatctgctccacctattttcaaaaatgtttattccatttatcataagcagcctctatgacgttgctaaaatatacataatcaccgtatcagaaccgccacggatggcggtagtgccaagcagtagcaagtttttcgttagaaaaactcgtcgttgaaaagtgtacacggaggtacgcttttcaacacacctgcgggtaatttttgctcatgcatcgtatctgcaccgtctatttgcaaaaggcttattcacggaattaatcgtcggaataatagtttcattaccaactacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0819:TDE0820|TDE0819:TDE0820:ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family:<-<-:843476..843803 328 agtgacacctcctttattttttgaaaatatgcgggcatctgctccacctattttcaaaaatgtttattccatttatcataagcagcctctatgacgttgctaaaatatacataatcaccgtatcagaaccgccacggatggcggtagtgccaagcagtagcaagtttttcgttagaaaaactcgtcgttgaaaagtgtacacggaggtacgcttttcaacacacctgcgggtaatttttgctcatgcatcgtatctgcaccgtctatttgcaaaaggcttattcacggaattaatcgtcggaataatagtttcattaccaactacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0819:TDE0820|TDE0819:TDE0820:ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family:<-<-:843476..843803 328 agtgacacctcctttattttttgaaaatatgcgggcatctgctccacctattttcaaaaatgtttattccatttatcataagcagcctctatgacgttgctaaaatatacataatcaccgtatcagaaccgccacggatggcggtagtgccaagcagtagcaagtttttcgttagaaaaactcgtcgttgaaaagtgtacacggaggtacgcttttcaacacacctgcgggtaatttttgctcatgcatcgtatctgcaccgtctatttgcaaaaggcttattcacggaattaatcgtcggaataatagtttcattaccaactacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtgacacctcctttattttttgaaaatatgcgggcatctgctccacctattttcaaaaatgtttattccatttatcataagcagcctctatgacgttgctaaaatatacataatcaccgtatcagaaccgccacggatggcggtagtgccaagcagtagcaagtttttcgttagaaaaactcgtcgttgaaaagtgtacacggaggtacgcttttcaacacacctgcgggtaatttttgctcatgcatcgtatctgcaccgtctatttgcaaaaggcttattcacggaattaatcgtcggaataatagtttcattaccaactacaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 2 End: 91 . M T P P L F F E N M R A S A P P I F K N V Y S I Y H K Q P L ............................................................................................................................................................................................................................................. Protein_Len: 56 Strand: + Start: 21 End: 188 .................... M K I C G H L L H L F S K M F I P F I I S S L Y D V A K I Y I I T V S E P P R M A V V P S S S K F F V R K T R R ............................................................................................................................................ Protein_Len: 44 Strand: + Start: 195 End: 326 .................................................................................................................................................................................................. M Y T E V R F S T H L R V I F A H A S Y L H R L F A K G L F T E L I V G I I V S L P T T .. Protein_Len: 47 Strand: + Start: 188 End: 328 ........................................................................................................................................................................................... M K S V H G G T L F N T P A G N F C S C I V S A P S I C K R L I H G I N R R N N S F I T N Y K Protein_Len: 36 Strand: - Start: 175 End: 282 .............................................................................................................................................................................. F F E D N F L T C P P V S K L V G A P L K Q E H M T D A G D I Q L L S M .............................................. Protein_Len: 48 Strand: - Start: 92 End: 235 ........................................................................................... S T A L I Y M I V T D S G G R I A T T G L L L L N K T L F V R R Q F T Y V S T R K E V C R R T M ............................................................................................. agtgacacctcctttattttttgaaaatatgcgggcatctgctccacctattttcaaaaatgtttattccatttatcataagcagcctctatgacgttgctaaaatatacataatcaccgtatcagaaccgccacggatggcggtagtgccaagcagtagcaagtttttcgttagaaaaactcgtcgttgaaaagtgtacacggaggtacgcttttcaacacacctgcgggtaatttttgctcatgcatcgtatctgcaccgtctatttgcaaaaggcttattcacggaattaatcgtcggaataatagtttcattaccaactacaaa 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: 85 Start: 50 End: 79 .................................................ATTTTCAAAAATGTTTATTCCATTTATCAT......................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtgacacctcctttattttttgaaaatatgcgggcatctgctccacctattttcaaaaatgtttattccatttatcataagcagcctctatgacgttgctaaaatatacataatcaccgtatcagaaccgccacggatggcggtagtgccaagcagtagcaagtttttcgttagaaaaactcgtcgttgaaaagtgtacacggaggtacgcttttcaacacacctgcgggtaatttttgctcatgcatcgtatctgcaccgtctatttgcaaaaggcttattcacggaattaatcgtcggaataatagtttcattaccaactacaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 78 HP_score: -8.7 Tail_Score: -3.74101 Start: 18 End: 60 Full_Region: TGACACCTCCTTTAT TTTTTGAAAATATGCGGGC ATCT GCTCCACCTATTTTCAAAAA TGTTTATTCCATTTA .................TTTTTGAAAATATGCGGGCATCTGCTCCACCTATTTTCAAAAA............................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 80 HP_score: -10.4 Tail_Score: -3.4178 Start: 129 End: 144 Full_Region: tactgcttggcacta ccgcca tccg tggcgg ttctgatacggtgat ................................................................................................................................ccgccatccgtggcgg........................................................................................................................................................................................ TransTerm Strand: - Conf: 66 HP_score: -2.4 Tail_Score: -4.82901 Start: 181 End: 227 Full_Region: agcaaaaattacccg caggtgtgttgaaaagcgtac ctccgt gtacacttttcaacgacgag tttttctaacgaaaa ....................................................................................................................................................................................caggtgtgttgaaaagcgtacctccgtgtacacttttcaacgacgag..................................................................................................... TransTerm Strand: - Conf: 51 HP_score: -3.6 Tail_Score: -3.49419 Start: 182 End: 224 Full_Region: aaaaattacccgcag gtgtgttgaaaagcgtac ctccgt gtacacttttcaacgacga gtttttctaacgaaa .....................................................................................................................................................................................gtgtgttgaaaagcgtacctccgtgtacacttttcaacgacga........................................................................................................ TransTerm Strand: - Conf: 58 HP_score: -7.1 Tail_Score: -2.6933 Start: 183 End: 223 Full_Region: aaaattacccgcagg tgtgttgaaaagcgtac ctccgt gtacacttttcaacgacg agtttttctaacgaa ......................................................................................................................................................................................tgtgttgaaaagcgtacctccgtgtacacttttcaacgacg......................................................................................................... Find igs database================================================ Query_seq: TDE0819:TDE0820|TDE0819:TDE0820:ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family:<-<-:843476..843803 328 agtgacacctcctttattttttgaaaatatgcgggcatctgctccacctattttcaaaaatgtttattccatttatcataagcagcctctatgacgttgctaaaatatacataatcaccgtatcagaaccgccacggatggcggtagtgccaagcagtagcaagtttttcgttagaaaaactcgtcgttgaaaagtgtacacggaggtacgcttttcaacacacctgcgggtaatttttgctcatgcatcgtatctgcaccgtctatttgcaaaaggcttattcacggaattaatcgtcggaataatagtttcattaccaactacaaa Intra-Species Hit: Count: 1 Min: 1 Max: 328 Len: 328 Subject: NC_002967_TDE0819_TDE0820|ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family|NEGATIVE:NEGATIVE|[843476,843803]|328 HSP 1 e-value: 0.0 bit: 650.0 Len: 328 Query Start:1 Query End:328 Subject Strand: POSITIVE Subject Start: 1 Subject End: 328 agtgacacctcctttattttttgaaaatatgcgggcatctgctccacctattttcaaaaatgtttattccatttatcataagcagcctctatgacgttgctaaaatatacataatcaccgtatcagaaccgccacggatggcggtagtgccaagcagtagcaagtttttcgttagaaaaactcgtcgttgaaaagtgtacacggaggtacgcttttcaacacacctgcgggtaatttttgctcatgcatcgtatctgcaccgtctatttgcaaaaggcttattcacggaattaatcgtcggaataatagtttcattaccaactacaaa agtgacacctcctttattttttgaaaatatgcgggcatctgctccacctattttcaaaaatgtttattccatttatcataagcagcctctatgacgttgctaaaatatacataatcaccgtatcagaaccgccacggatggcggtagtgccaagcagtagcaagtttttcgttagaaaaactcgtcgttgaaaagtgtacacggaggtacgcttttcaacacacctgcgggtaatttttgctcatgcatcgtatctgcaccgtctatttgcaaaaggcttattcacggaattaatcgtcggaataatagtttcattaccaactacaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGACACCUCCUUUAUUUUUUGAAAAUAUGCGGGCAUCUGCUCCACCUAUUUUCAAAAAUGUUUAUUCCAUUUAUCAUAAGCAGCCUCUAUGACGUUGCUAAAAUAUACAUAAUCACCGUAUCAGAACCGCCACGGAUGGCGGUAGUGCCAAGCAGUAGCAAGUUUUUCGUUAGAAAAACUCGUCGUUGAAAAGUGUACACGGAGGUACGCUUUUCAACACACCUGCGGGUAAUUUUUGCUCAUGCAUCGUAUCUGCACCGUCUAUUUGCAAAAGGCUUAUUCACGGAAUUAAUCGUCGGAAUAAUAGUUUCAUUACCAACUACAAA (((((.((.........((((((((((((.(.((((....)).)).).))))))))))))...(((((((..........((((((.((...)).))))))................((((......(((((((....)))))))...(((..((((((((.((((((((....)))))))).((.((((((((((((((......))))))))))))))))...((((((((.....(((....)))...))))))))..).))).))))....)))......))))...........)))))))..)).)))))............ (-98.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUAGUUGGUAAUGAAACUAUUAUUCCGACGAUUAAUUCCGUGAAUAAGCCUUUUGCAAAUAGACGGUGCAGAUACGAUGCAUGAGCAAAAAUUACCCGCAGGUGUGUUGAAAAGCGUACCUCCGUGUACACUUUUCAACGACGAGUUUUUCUAACGAAAAACUUGCUACUGCUUGGCACUACCGCCAUCCGUGGCGGUUCUGAUACGGUGAUUAUGUAUAUUUUAGCAACGUCAUAGAGGCUGCUUAUGAUAAAUGGAAUAAACAUUUUUGAAAAUAGGUGGAGCAGAUGCCCGCAUAUUUUCAAAAAAUAAAGGAGGUGUCACU ......(((((.(((((.....)))))))))).....(((((((..((((((.....((...((((((.(((.((....((((((((.......(((((.((((....(((((((((.((((......)))).)))))))))..((((((((((....))))))))))...))))....((..(((((((....)))))))..))....)))))))))))))...)).))).)))).))...)).)))))).....))))))).....((((((((((((.((((.((....)))))).))))))))))))................. (-107.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 904 50 1 141 92 NC_002967:TDE0819|5end_ABC_transporter,_ATP-binding/permease_protein_843385..843615_NEGATIVE 567 156 111 206 159 NC_002967:TDE0976|5end_hypothetical_protein_1000026..1000256_POSITIVE 511 168 127 129 90 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 486 265 222 130 77 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 460 155 115 169 132 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 459 145 111 229 193 NC_002967:TDE0569|5end_hypothetical_protein_599636..599866_POSITIVE 419 218 177 44 3 NC_002967:TDE1934|5end_hypothetical_protein_1952614..1952844_POSITIVE 399 262 225 47 11 NC_002967:TDE2346|5end_elongation_factor_Ts_2383429..2383659_NEGATIVE 399 167 129 144 107 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 369 167 127 129 90 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 358 167 123 118 60 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 355 163 126 49 3 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 352 211 178 231 198 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 350 159 113 70 20 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 345 168 125 96 47 NC_002967:TDE0848|5end_hypothetical_protein_871269..871499_POSITIVE 340 109 70 69 25 NC_002967:TDE1989|5end_acyltransferase_family_protein_2006343..2006573_NEGATIVE 337 159 117 75 35 NC_002967:TDE0682|5end_preprotein_translocase,_YajC_subunit_721078..721308_NEGATIVE 331 280 233 175 134 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 330 167 127 141 90 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 326 155 118 52 12 NC_002967:TDE2766|5end_motility_protein_A_2820874..2821104_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 490 158 118 79 34 NC_002967:TDE2516|3end_hypothetical_protein_2542193..2542343_POSITIVE 421 210 164 146 98 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 416 167 123 53 9 NC_002967:TDE2483|3end_hypothetical_protein_2505880..2506030_NEGATIVE 413 156 119 104 61 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 375 229 181 75 21 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 349 262 222 151 107 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 345 168 125 89 40 NC_002967:TDE0847|3end_hypothetical_protein_871342..871492_POSITIVE 340 109 70 45 1 NC_002967:TDE1990|3end_ATP-dependent_helicase,_DinG_family_2006367..2006517_NEGATIVE 335 218 177 85 44 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 331 210 163 78 27 NC_002967:TDE0834|3end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854291..854441_NEGATIVE 330 289 251 56 18 NC_002967:TDE2141|3end_hypothetical_protein_2175583..2175733_NEGATIVE 328 279 235 123 84 NC_002967:TDE0912|3end_hypothetical_protein_931528..931678_POSITIVE 317 230 185 64 25 NC_002967:TDE1735|3end_hypothetical_protein_1789998..1790148_POSITIVE 317 170 122 67 5 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 317 172 131 128 94 NC_002967:TDE0607|3end_ParA_family_ATPase_644125..644275_NEGATIVE 316 265 225 44 4 NC_002967:TDE1406|3end_hypothetical_protein_1448677..1448827_NEGATIVE 313 168 127 79 38 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 311 279 233 126 78 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 310 265 224 85 44 NC_002967:TDE0975|3end_hypothetical_protein_999879..1000029_POSITIVE 306 180 131 51 7 NC_002967:TDE0449|3end_ferritin,_putative_506549..506699_NEGATIVE