Origin IGS: cctatataaaatccttccttaaaattgaacagctgaacaaaatatcaattttggaagctgttcaattcgccgtttcgtaacgtcagtgagaaacggcatacaataaagcgatgtttgccgaaaggcaaactcgacagcgtttttttgacaatgccatctgcattgtcaaaaataagcattcataacttt .........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 aaagttatgaatgcttatttttgacaatgcagatggcattgtcaaaaaaacgctgtcgagtttgcctttcggcaaacatcgctttattgtatgccgtttctcactgacgttacgaaacggcgaattgaacagcttccaaaattgatattttgttcagctgttcaattttaaggaaggattttatatagg Mask Tandem Repeat Region ================================================ cctatataaaatccttccttaaaattgaacagctgaacaaaatatcaattttggaagctgttcaattcgccgtttcgtaacgtcagtgagaaacggcatacaataaagcgatgtttgccgaaaggcaaactcgacagcgtttttttgacaatgccatctgcattgtcaaaaataagcattcataacttt Find is-nt database================================================ Query_seq: TDE2418:TDE2419|TDE2418:TDE2419:hypothetical protein:hypothetical protein:<-<-:2443924..2444112 189 cctatataaaatccttccttaaaattgaacagctgaacaaaatatcaattttggaagctgttcaattcgccgtttcgtaacgtcagtgagaaacggcatacaataaagcgatgtttgccgaaaggcaaactcgacagcgtttttttgacaatgccatctgcattgtcaaaaataagcattcataacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2418:TDE2419|TDE2418:TDE2419:hypothetical protein:hypothetical protein:<-<-:2443924..2444112 189 cctatataaaatccttccttaaaattgaacagctgaacaaaatatcaattttggaagctgttcaattcgccgtttcgtaacgtcagtgagaaacggcatacaataaagcgatgtttgccgaaaggcaaactcgacagcgtttttttgacaatgccatctgcattgtcaaaaataagcattcataacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2418:TDE2419|TDE2418:TDE2419:hypothetical protein:hypothetical protein:<-<-:2443924..2444112 189 cctatataaaatccttccttaaaattgaacagctgaacaaaatatcaattttggaagctgttcaattcgccgtttcgtaacgtcagtgagaaacggcatacaataaagcgatgtttgccgaaaggcaaactcgacagcgtttttttgacaatgccatctgcattgtcaaaaataagcattcataacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctatataaaatccttccttaaaattgaacagctgaacaaaatatcaattttggaagctgttcaattcgccgtttcgtaacgtcagtgagaaacggcatacaataaagcgatgtttgccgaaaggcaaactcgacagcgtttttttgacaatgccatctgcattgtcaaaaataagcattcataacttt Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 58 End: 189 ......................................................... M F N S P F R N V S E K R H T I K R C L P K G K L D S V F L T M P S A L S K I S I H N F Protein_Len: 44 Strand: - Start: 48 End: 179 ............................................... N Q F S N L E G N R L T L S F R C V I F R H K G F P L S S L T K K V I G D A N D F I L M .......... cctatataaaatccttccttaaaattgaacagctgaacaaaatatcaattttggaagctgttcaattcgccgtttcgtaacgtcagtgagaaacggcatacaataaagcgatgtttgccgaaaggcaaactcgacagcgtttttttgacaatgccatctgcattgtcaaaaataagcattcataacttt 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: 84 Start: 144 End: 173 ...............................................................................................................................................TTTGACAATGCCATCTGCATTGTCAAAAAT................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cctatataaaatccttccttaaaattgaacagctgaacaaaatatcaattttggaagctgttcaattcgccgtttcgtaacgtcagtgagaaacggcatacaataaagcgatgtttgccgaaaggcaaactcgacagcgtttttttgacaatgccatctgcattgtcaaaaataagcattcataacttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -6.4 Tail_Score: -4.08064 Start: 25 End: 65 Full_Region: ttacgaaacggcgaa ttgaacagcttccaaaat tgat attttgttcagctgttcaa ttttaaggaaggatt ........................ttgaacagcttccaaaattgatattttgttcagctgttcaa............................................................................................................................ TransTerm Strand: - Conf: 57 HP_score: -3.7 Tail_Score: -3.92641 Start: 94 End: 120 Full_Region: gtcgagtttgccttt cggcaaaca tcgctttat tgtatgccg tttctcactgacgtt .............................................................................................cggcaaacatcgctttattgtatgccg..................................................................... TransTerm Strand: - Conf: 72 HP_score: -5.9 Tail_Score: -4.39329 Start: 108 End: 134 Full_Region: gtcaaaaaaacgctg tcgagtttgcc tttc ggcaaacatcgc tttattgtatgccgt ...........................................................................................................tcgagtttgcctttcggcaaacatcgc....................................................... TransTerm Strand: - Conf: 75 HP_score: -9.4 Tail_Score: -3.22874 Start: 109 End: 133 Full_Region: tcaaaaaaacgctgt cgagtttgcc tttc ggcaaacatcg ctttattgtatgccg ............................................................................................................cgagtttgcctttcggcaaacatcg........................................................ TransTerm Strand: - Conf: 51 HP_score: -2.9 Tail_Score: -3.84451 Start: 130 End: 184 Full_Region: aaagt tatgaatgcttatttttgacaatgc agatg gcattgtcaaaaaaacgctgtcgag tttgcctttcggcaa .................................................................................................................................tatgaatgcttatttttgacaatgcagatggcattgtcaaaaaaacgctgtcgag..... Find igs database================================================ Query_seq: TDE2418:TDE2419|TDE2418:TDE2419:hypothetical protein:hypothetical protein:<-<-:2443924..2444112 189 cctatataaaatccttccttaaaattgaacagctgaacaaaatatcaattttggaagctgttcaattcgccgtttcgtaacgtcagtgagaaacggcatacaataaagcgatgtttgccgaaaggcaaactcgacagcgtttttttgacaatgccatctgcattgtcaaaaataagcattcataacttt Intra-Species Hit: Count: 1 Min: 1 Max: 189 Len: 189 Subject: NC_002967_TDE2418_TDE2419|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2443924,2444112]|189 HSP 1 e-value: 1.0E-90 bit: 333.0 Len: 189 Query Start:1 Query End:189 Subject Strand: POSITIVE Subject Start: 1 Subject End: 189 cctatataaaatccttccttaaaattgaacagctgaacaaaatatcaattttggaagctgttcaattcgccgtttcgtaacgtcagtgagaaacggcatacaataaagcgatgtttgccgaaaggcaaactcgacagcgnnnnnnngacaatgccatctgcattgtcaaaaataagcattcataacttt cctatataaaatccttccttaaaattgaacagctgaacaaaatatcaattttggaagctgttcaattcgccgtttcgtaacgtcagtgagaaacggcatacaataaagcgatgtttgccgaaaggcaaactcgacagcgtttttttgacaatgccatctgcattgtcaaaaataagcattcataacttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUAUAUAAAAUCCUUCCUUAAAAUUGAACAGCUGAACAAAAUAUCAAUUUUGGAAGCUGUUCAAUUCGCCGUUUCGUAACGUCAGUGAGAAACGGCAUACAAUAAAGCGAUGUUUGCCGAAAGGCAAACUCGACAGCGUUUUUUUGACAAUGCCAUCUGCAUUGUCAAAAAUAAGCAUUCAUAACUUU ......................((((((((((((...((((((....))))))..)))))))))))).((((((((...((....))..))))))))...........(((.(((((((....))))))))))...((...(((((((((((((.....)))))))))))))...))............ (-71.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUUAUGAAUGCUUAUUUUUGACAAUGCAGAUGGCAUUGUCAAAAAAACGCUGUCGAGUUUGCCUUUCGGCAAACAUCGCUUUAUUGUAUGCCGUUUCUCACUGACGUUACGAAACGGCGAAUUGAACAGCUUCCAAAAUUGAUAUUUUGUUCAGCUGUUCAAUUUUAAGGAAGGAUUUUAUAUAGG .....((((((.((...(((((((((((((.....)))))))))))))...))...((((((((((....))))))).)))(((((......((((((((..((....))...)))))))).((((((((((((..((((((....))))))...)))))))))))).)))))......)))))).... (-62.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 945 140 91 231 182 NC_002967:TDE2418|5end_hypothetical_protein_2443833..2444063_NEGATIVE 706 138 91 211 164 NC_002967:TDE1514|5end_permease_domain_protein_1560652..1560882_POSITIVE 701 119 71 86 39 NC_002967:TDE2521|5end_hypothetical_protein_2548074..2548304_NEGATIVE 685 138 96 43 1 NC_002967:TDE1513|5end_hypothetical_protein_1560484..1560714_POSITIVE 672 137 91 151 105 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 672 137 91 129 83 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 672 137 91 229 183 NC_002967:TDE2093|5end_hypothetical_protein_2121003..2121233_NEGATIVE 672 137 91 212 166 NC_002967:TDE1903|5end_hypothetical_protein_1922417..1922647_POSITIVE 672 137 91 72 26 NC_002967:TDE1694|5end_hypothetical_protein_1749366..1749596_NEGATIVE 672 137 91 212 166 NC_002967:TDE1693|5end_hypothetical_protein_1749226..1749456_NEGATIVE 625 137 91 152 105 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 625 137 91 51 4 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 599 137 91 212 166 NC_002967:TDE0641|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_678282..678512_NEGATIVE 593 118 71 202 152 NC_002967:TDE0590|5end_acetyl-CoA_carboxylase,_carboxyl_transferase,_beta_subunit_629856..630086_NEGATIVE 578 150 101 231 186 NC_002967:TDE0259|5end_transcriptional_regulator,_MarR_family_293257..293487_POSITIVE 549 130 81 213 165 NC_002967:TDE2018|5end_lipoprotein,_putative_2040550..2040780_NEGATIVE 546 137 91 51 5 NC_002967:TDE2019|5end_hypothetical_protein_2040719..2040949_NEGATIVE 474 139 91 229 173 NC_002967:TDE2395|5end_Jag_protein,_putative_2423454..2423684_NEGATIVE 473 134 91 209 165 NC_002967:TDE1915|5end_alcohol_dehydrogenase,_iron-containing_1933103..1933333_NEGATIVE 406 139 92 212 159 NC_002967:TDE0495|5end_hypothetical_protein_550841..551071_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 639 133 91 151 109 NC_002967:TDE2094|3end_hypothetical_protein_2121077..2121227_NEGATIVE 592 133 91 151 108 NC_002967:TDE2223|3end_hypothetical_protein_2264826..2264976_POSITIVE 590 137 98 40 1 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 523 137 102 36 1 NC_002967:TDE2020|3end_YD_repeat_protein_2040734..2040884_NEGATIVE 507 137 108 34 5 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 507 138 109 30 1 NC_002967:TDE1512|3end_hypothetical_protein_1560551..1560701_POSITIVE 460 137 108 31 1 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 434 137 108 34 5 NC_002967:TDE0642|3end_hypothetical_protein_678460..678610_NEGATIVE 419 150 108 47 3 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 408 131 93 57 7 NC_002967:TDE1904|3end_hypothetical_protein_1923197..1923347_NEGATIVE 406 139 92 82 29 NC_002967:TDE0496|3end_DNA-binding_protein,_putative_550971..551121_NEGATIVE 381 134 106 35 5 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 363 138 109 31 1 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 354 150 108 47 3 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 346 137 91 149 98 NC_002967:TDE1972|3end_hypothetical_protein_1987102..1987252_NEGATIVE 317 134 95 58 22 NC_002967:TDE0991|3end_ribosomal_protein_L28_1017874..1018024_NEGATIVE 315 139 115 33 1 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 307 134 99 39 1 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 303 178 132 78 40 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 301 71 33 120 79 NC_002967:TDE1001|3end_orotate_phosphoribosyltransferase_1028437..1028587_POSITIVE