Origin IGS: agctatcctttttttataattatacagtatttttcttgattttgttgataaattaatttttttatttaaaaattaaaatacatttaagaatatatagtggaaaattctaatttataaaaatttctcaaatttacttttaagatattcacttatcaacatatcaatctttttttccttaaaatacaattttgccttaattttgtctatttcaagaattccgattttaattcaaattaaaaacaaagtataacatattgacaaatagtatatatcatattatgatatatacatt .........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 aatgtatatatcataatatgatatatactatttgtcaatatgttatactttgtttttaatttgaattaaaatcggaattcttgaaatagacaaaattaaggcaaaattgtattttaaggaaaaaaagattgatatgttgataagtgaatatcttaaaagtaaatttgagaaatttttataaattagaattttccactatatattcttaaatgtattttaatttttaaataaaaaaattaatttatcaacaaaatcaagaaaaatactgtataattataaaaaaaggatagct Mask Tandem Repeat Region ================================================ agctatcctttttttataattatacagtatttttcttgattttgttgataaattaatttttttatttaaaaattaaaatacatttaagaatatatagtggaaaattctaatttataaaaatttctcaaatttacttttaagatattcacttatcaacatatcaatctttttttccttaaaatacaattttgccttaattttgtctatttcaagaattccgattttaattcaaattaaaaacaaagtataacatattgacaaatagtatatatcatattatgatatatacatt Find is-nt database================================================ Query_seq: TDE0226:TDE0227|TDE0226:TDE0227:hypothetical protein:adenine-specific DNA modification methyltransferase:<-->:256784..257075 292 agctatcctttttttataattatacagtatttttcttgattttgttgataaattaatttttttatttaaaaattaaaatacatttaagaatatatagtggaaaattctaatttataaaaatttctcaaatttacttttaagatattcacttatcaacatatcaatctttttttccttaaaatacaattttgccttaattttgtctatttcaagaattccgattttaattcaaattaaaaacaaagtataacatattgacaaatagtatatatcatattatgatatatacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0226:TDE0227|TDE0226:TDE0227:hypothetical protein:adenine-specific DNA modification methyltransferase:<-->:256784..257075 292 agctatcctttttttataattatacagtatttttcttgattttgttgataaattaatttttttatttaaaaattaaaatacatttaagaatatatagtggaaaattctaatttataaaaatttctcaaatttacttttaagatattcacttatcaacatatcaatctttttttccttaaaatacaattttgccttaattttgtctatttcaagaattccgattttaattcaaattaaaaacaaagtataacatattgacaaatagtatatatcatattatgatatatacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0226:TDE0227|TDE0226:TDE0227:hypothetical protein:adenine-specific DNA modification methyltransferase:<-->:256784..257075 292 agctatcctttttttataattatacagtatttttcttgattttgttgataaattaatttttttatttaaaaattaaaatacatttaagaatatatagtggaaaattctaatttataaaaatttctcaaatttacttttaagatattcacttatcaacatatcaatctttttttccttaaaatacaattttgccttaattttgtctatttcaagaattccgattttaattcaaattaaaaacaaagtataacatattgacaaatagtatatatcatattatgatatatacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctatcctttttttataattatacagtatttttcttgattttgttgataaattaatttttttatttaaaaattaaaatacatttaagaatatatagtggaaaattctaatttataaaaatttctcaaatttacttttaagatattcacttatcaacatatcaatctttttttccttaaaatacaattttgccttaattttgtctatttcaagaattccgattttaattcaaattaaaaacaaagtataacatattgacaaatagtatatatcatattatgatatatacatt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 142 End: 234 ............................................................................................................................................. M F T Y Q H I N L F F L K I Q F C L N F V Y F K N S D F N S N .......................................................... Protein_Len: 48 Strand: + Start: 104 End: 247 ....................................................................................................... M L I Y K N F S N L L L R Y S L I N I S I F F S L K Y N F A L I L S I S R I P I L I Q I K N K V ............................................. Protein_Len: 38 Strand: - Start: 115 End: 228 .................................................................................................................. L F K E F K S K L Y E S I L M D I K K E K F Y L K A K I K D I E L I G I K M ................................................................ agctatcctttttttataattatacagtatttttcttgattttgttgataaattaatttttttatttaaaaattaaaatacatttaagaatatatagtggaaaattctaatttataaaaatttctcaaatttacttttaagatattcacttatcaacatatcaatctttttttccttaaaatacaattttgccttaattttgtctatttcaagaattccgattttaattcaaattaaaaacaaagtataacatattgacaaatagtatatatcatattatgatatatacatt 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: 91 Start: 254 End: 283 .............................................................................................................................................................................................................................................................ATTGACAAATAGTATATATCATATTATGAT......... PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 199 End: 228 ......................................................................................................................................................................................................TTTGTCTATTTCAAGAATTCCGATTTTAAT................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 233 End: 262 ........................................................................................................................................................................................................................................TTTGTCAATATGTTATACTTTGTTTTTAAT.............................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 44 End: 73 ...........................................GTTGATAAATTAATTTTTTTATTTAAAAAT........................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agctatcctttttttataattatacagtatttttcttgattttgttgataaattaatttttttatttaaaaattaaaatacatttaagaatatatagtggaaaattctaatttataaaaatttctcaaatttacttttaagatattcacttatcaacatatcaatctttttttccttaaaatacaattttgccttaattttgtctatttcaagaattccgattttaattcaaattaaaaacaaagtataacatattgacaaatagtatatatcatattatgatatatacatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 52 HP_score: -4.1 Tail_Score: -3.86015 Start: 53 End: 76 Full_Region: attcttaaatgtatt ttaattttt aaataa aaaaattaa tttatcaacaaaatc ....................................................ttaatttttaaataaaaaaattaa........................................................................................................................................................................................................................ Find igs database================================================ Query_seq: TDE0226:TDE0227|TDE0226:TDE0227:hypothetical protein:adenine-specific DNA modification methyltransferase:<-->:256784..257075 292 agctatcctttttttataattatacagtatttttcttgattttgttgataaattaatttttttatttaaaaattaaaatacatttaagaatatatagtggaaaattctaatttataaaaatttctcaaatttacttttaagatattcacttatcaacatatcaatctttttttccttaaaatacaattttgccttaattttgtctatttcaagaattccgattttaattcaaattaaaaacaaagtataacatattgacaaatagtatatatcatattatgatatatacatt Intra-Species Hit: Count: 1 Min: 124 Max: 292 Len: 169 Subject: NC_002967_TDE0226_TDE0227|hypothetical protein:adenine-specific DNA modification methyltransferase|NEGATIVE:POSITIVE|[256784,257075]|292 HSP 1 e-value: 2.0E-78 bit: 293.0 Len: 169 Query Start:124 Query End:292 Subject Strand: POSITIVE Subject Start: 124 Subject End: 292 ...........................................................................................................................ctcaaatttacttttaagatattcacttatcaacatatcaatcnnnnnnnccttaaaatacaattttgccttaattttgtctatttcaagaattccgattttaattcaaattaaaaacaaagtataacatattgacaaatagtatatatcatattatgatatatacatt ...........................................................................................................................ctcaaatttacttttaagatattcacttatcaacatatcaatctttttttccttaaaatacaattttgccttaattttgtctatttcaagaattccgattttaattcaaattaaaaacaaagtataacatattgacaaatagtatatatcatattatgatatatacatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAAAUUUACUUUUAAGAUAUUCACUUAUCAACAUAUCAAUCUUUUUUUCCUUAAAAUACAAUUUUGCCUUAAUUUUGUCUAUUUCAAGAAUUCCGAUUUUAAUUCAAAUUAAAAACAAAGUAUAACAUAUUGACAAAUAGUAUAUAUCAUAUUAUGAUAUAUACAUU .((((............((((......))))..........................((((.............(((((.......))))).....(.(((((((....))))))).)...))))......))))......(((((((((((...)))))))))))... (-19.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGUAUAUAUCAUAAUAUGAUAUAUACUAUUUGUCAAUAUGUUAUACUUUGUUUUUAAUUUGAAUUAAAAUCGGAAUUCUUGAAAUAGACAAAAUUAAGGCAAAAUUGUAUUUUAAGGAAAAAAAGAUUGAUAUGUUGAUAAGUGAAUAUCUUAAAAGUAAAUUUGAG ...(((((((((((...))))))))))).((((((((((((((((..((((..(((((((....)))))))......((((((((((..((((.............))))))))))))))...))))..))))))))))))))))......((((((......)))))) (-35.62) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 50 1 132 92 NC_002967:TDE1342|5end_hypothetical_protein_1378442..1378672_POSITIVE 227 84 43 214 173 NC_002967:TDE1598|5end_ABC_transporter,_ATP-binding_protein_1648910..1649140_NEGATIVE 227 98 58 165 126 NC_002967:TDE0858|5end_hypothetical_protein_879518..879748_POSITIVE 224 99 64 217 181 NC_002967:TDE1504|5end_ribosomal_protein_L31_1553350..1553580_POSITIVE 224 107 65 125 78 NC_002967:TDE0984|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein,_putative_1009474..1009704_POSITIVE 210 71 33 127 88 NC_002967:TDE1032|5end_hypothetical_protein_1060154..1060384_POSITIVE 207 98 51 180 126 NC_002967:TDE0290|5end_hypothetical_protein_320794..321024_NEGATIVE 203 61 21 125 86 NC_002967:TDE0328|5end_CRISPR-associated_protein_Cas1_365065..365295_POSITIVE 197 99 51 185 137 NC_002967:TDE2358|5end_hypothetical_protein_2394136..2394366_NEGATIVE 196 86 44 138 93 NC_002967:TDE1840|5end_hypothetical_protein_1871581..1871811_NEGATIVE 196 86 44 138 93 NC_002967:TDE1800|5end_hypothetical_protein_1837684..1837914_NEGATIVE 195 89 41 161 124 NC_002967:TDE1062|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_1088430..1088660_POSITIVE 195 102 68 226 189 NC_002967:TDE0198|5end_hypothetical_protein_233155..233385_POSITIVE 192 90 41 143 90 NC_002967:TDE1017|5end_exodeoxyribonuclease_VII,_large_subunit_1047935..1048165_POSITIVE 191 110 66 198 151 NC_002967:TDE0090|5end_hypothetical_protein_109206..109436_NEGATIVE 190 79 35 165 122 NC_002967:TDE2150|5end_hypothetical_protein_2188276..2188506_NEGATIVE 189 102 64 111 74 NC_002967:TDE0982|5end_dihydroorotate_dehydrogenase/oxidoreductase,_FAD-binding_1006477..1006707_POSITIVE 187 79 38 128 88 NC_002967:TDE1631|5end_citrate_lyase,_alpha_subunit_1681556..1681786_NEGATIVE 186 84 50 130 97 NC_002967:TDE2765|5end_flagellar_motor_protein_2820093..2820323_NEGATIVE 186 86 41 66 20 NC_002967:TDE2556|5end_hypothetical_protein_2583161..2583391_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 50 1 135 95 NC_002967:TDE1341|3end_hypothetical_protein_1378525..1378675_POSITIVE 226 99 64 79 36 NC_002967:TDE0582|3end_hypothetical_protein_621431..621581_POSITIVE 210 71 33 78 39 NC_002967:TDE1031|3end_hypothetical_protein_1060185..1060335_POSITIVE 203 61 21 128 89 NC_002967:TDE0327|3end_CRISPR-associated_SAG0894_family_protein_365148..365298_POSITIVE 196 86 44 148 103 NC_002967:TDE1841|3end_hypothetical_protein_1871571..1871721_NEGATIVE 196 86 44 148 103 NC_002967:TDE1801|3end_hypothetical_protein_1837674..1837824_NEGATIVE 190 79 35 101 58 NC_002967:TDE2151|3end_hypothetical_protein_2188340..2188490_NEGATIVE 189 102 64 89 52 NC_002967:TDE0981|3end_hypothetical_protein_1006535..1006685_POSITIVE 188 98 52 132 80 NC_002967:TDE2587|3end_endonuclease/exonuclease/phosphatase_family_protein_2623290..2623440_POSITIVE 187 79 38 115 75 NC_002967:TDE1632|3end_citrate_lyase,_beta_subunit_1681569..1681719_NEGATIVE 186 84 50 128 95 NC_002967:TDE2766|3end_motility_protein_A_2820095..2820245_NEGATIVE 185 101 67 124 87 NC_002967:TDE2293|3end_hypothetical_protein_2329325..2329475_NEGATIVE 185 99 52 135 95 NC_002967:TDE0220|3end_hypothetical_protein_253865..254015_NEGATIVE 183 97 51 62 20 NC_002967:TDE0092|3end_cysteinyl-tRNA_synthetase_109777..109927_NEGATIVE 178 98 51 128 89 NC_002967:TDE1282|3end_hypothetical_protein_1317471..1317621_POSITIVE 174 89 44 129 82 NC_002967:TDE0722|3end_lipoprotein,_putative_759864..760014_POSITIVE 174 82 43 112 75 NC_002967:TDE0349|3end_phosphoenolpyruvate_synthase,_putative_393650..393800_POSITIVE 172 110 75 133 97 NC_002967:TDE0343|3end_hydrolase,_alpha/beta_fold_family_384247..384397_NEGATIVE 171 50 6 91 43 NC_002967:TDE1146|3end_hypothetical_protein_1184824..1184974_NEGATIVE 168 157 130 63 38 NC_002967:TDE2084|3end_RNA_methyltransferase,_TrmH_family_2114229..2114379_POSITIVE