Origin IGS: aagtaaaaagtccgttttaccccctcctgcagctcctccataaaaaagctcaaaggcagggcattgtaaggctagtgattgttttttagtcggtttccaaataatcatataattccttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaggaattatatgattatttggaaaccgactaaaaaacaatcactagccttacaatgccctgcctttgagcttttttatggaggagctgcaggagggggtaaaacggactttttactt Mask Tandem Repeat Region ================================================ aagtaaaaagtccgttttaccccctcctgcagctcctccataaaaaagctcaaaggcagggcattgtaaggctagtgattgttttttagtcggtttccaaataatcatataattccttt Find is-nt database================================================ Query_seq: TDE1157:TDE1158|TDE1157:TDE1158:phage terminase, large subunit, putative:phage terminase, small subunit, putative:<-<-:1193384..1193502 119 aagtaaaaagtccgttttaccccctcctgcagctcctccataaaaaagctcaaaggcagggcattgtaaggctagtgattgttttttagtcggtttccaaataatcatataattccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1157:TDE1158|TDE1157:TDE1158:phage terminase, large subunit, putative:phage terminase, small subunit, putative:<-<-:1193384..1193502 119 aagtaaaaagtccgttttaccccctcctgcagctcctccataaaaaagctcaaaggcagggcattgtaaggctagtgattgttttttagtcggtttccaaataatcatataattccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1157:TDE1158|TDE1157:TDE1158:phage terminase, large subunit, putative:phage terminase, small subunit, putative:<-<-:1193384..1193502 119 aagtaaaaagtccgttttaccccctcctgcagctcctccataaaaaagctcaaaggcagggcattgtaaggctagtgattgttttttagtcggtttccaaataatcatataattccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtaaaaagtccgttttaccccctcctgcagctcctccataaaaaagctcaaaggcagggcattgtaaggctagtgattgttttttagtcggtttccaaataatcatataattccttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 1 End: 108 L L F D T K G G G A A G G Y F L E F A P C Q L A L S Q K K T P K W I I M ........... aagtaaaaagtccgttttaccccctcctgcagctcctccataaaaaagctcaaaggcagggcattgtaaggctagtgattgttttttagtcggtttccaaataatcatataattccttt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtaaaaagtccgttttaccccctcctgcagctcctccataaaaaagctcaaaggcagggcattgtaaggctagtgattgttttttagtcggtttccaaataatcatataattccttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1157:TDE1158|TDE1157:TDE1158:phage terminase, large subunit, putative:phage terminase, small subunit, putative:<-<-:1193384..1193502 119 aagtaaaaagtccgttttaccccctcctgcagctcctccataaaaaagctcaaaggcagggcattgtaaggctagtgattgttttttagtcggtttccaaataatcatataattccttt Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_002967_TDE1157_TDE1158|phage terminase, large subunit, putative:phage terminase, small subunit, putative|NEGATIVE:NEGATIVE|[1193384,1193502]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 aagtaaaaagtccgttttaccccctcctgcagctcctccataaaaaagctcaaaggcagggcattgtaaggctagtgattgttttttagtcggtttccaaataatcatataattccttt aagtaaaaagtccgttttaccccctcctgcagctcctccataaaaaagctcaaaggcagggcattgtaaggctagtgattgttttttagtcggtttccaaataatcatataattccttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAAAAAGUCCGUUUUACCCCCUCCUGCAGCUCCUCCAUAAAAAAGCUCAAAGGCAGGGCAUUGUAAGGCUAGUGAUUGUUUUUUAGUCGGUUUCCAAAUAAUCAUAUAAUUCCUUU .............(((((((.(((((((..((((............))))...))).))))....)))))))..((((((((((..............))))))))))........... (-23.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGGAAUUAUAUGAUUAUUUGGAAACCGACUAAAAAACAAUCACUAGCCUUACAAUGCCCUGCCUUUGAGCUUUUUUAUGGAGGAGCUGCAGGAGGGGGUAAAACGGACUUUUUACUU .((((.......(((((.(((((.......)))))....)))))....))))....((((((.(((...((((((((....))))))))..)))..))))))................. (-24.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1013 70 21 161 112 NC_002967:TDE1157|5end_phage_terminase,_large_subunit,_putative_1193293..1193523_NEGATIVE 375 57 11 65 22 NC_002967:TDE2660|5end_hypothetical_protein_2697517..2697747_NEGATIVE 366 62 21 230 182 NC_002967:TDE1485|5end_hypothetical_protein_1529697..1529927_POSITIVE 339 68 24 50 2 NC_002967:TDE1731|5end_hypothetical_protein_1786935..1787165_NEGATIVE 332 62 21 229 185 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 326 93 52 70 32 NC_002967:TDE2143|5end_penicillin-binding_protein_2178107..2178337_POSITIVE 325 60 11 59 5 NC_002967:TDE1132|5end_chorismate_synthase_1163415..1163645_POSITIVE 305 59 13 173 130 NC_002967:TDE1492|5end_chemotaxis_protein_CheW_1537231..1537461_POSITIVE 305 63 26 53 9 NC_002967:TDE0979|5end_penicillin_binding_protein_1003946..1004176_NEGATIVE 294 57 11 231 166 NC_002967:TDE1044|5end_hypothetical_protein_1072075..1072305_POSITIVE 291 79 33 55 2 NC_002967:TDE2211|5end_hypothetical_protein_2251316..2251546_NEGATIVE 291 58 11 167 118 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 289 59 14 142 82 NC_002967:TDE2622|5end_ABC_transporter,_ATP-binding_protein_2663590..2663820_NEGATIVE 288 78 37 133 87 NC_002967:TDE1662|5end_replicative_DNA_helicase_1715898..1716128_POSITIVE 286 57 11 218 163 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 286 50 2 109 59 NC_002967:TDE0955|5end_LemA_family_protein_978842..979072_POSITIVE 285 57 12 169 130 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 283 59 12 198 138 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 282 44 10 59 20 NC_002967:TDE0369|5end_type_I_restriction-modification_system,_M_subunit_420971..421201_NEGATIVE 281 72 34 89 46 NC_002967:TDE2731|5end_TIM-barrel_protein,_putative,_NifR3_family_2787372..2787602_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 57 11 58 15 NC_002967:TDE2661|3end_hypothetical_protein_2697524..2697674_NEGATIVE 325 60 11 95 41 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 306 62 21 46 6 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 289 59 14 148 88 NC_002967:TDE2623|3end_hypothetical_protein_2663584..2663734_NEGATIVE 288 78 37 65 19 NC_002967:TDE1661|3end_hypothetical_protein_1715910..1716060_POSITIVE 283 59 12 87 27 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 281 72 34 76 33 NC_002967:TDE2730|3end_hydrolase,_TatD_family_2787439..2787589_POSITIVE 281 75 32 46 6 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 280 37 8 124 99 NC_002967:TDE1864|3end_crossover_junction_endodeoxyribonuclease_RuvC_1888572..1888722_NEGATIVE 279 73 31 149 101 NC_002967:TDE0654|3end_peptidase,_M20/M25/M40_family_690858..691008_POSITIVE 277 98 55 65 3 NC_002967:TDE1347|3end_hypothetical_protein_1388032..1388182_POSITIVE 274 39 6 149 120 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 272 61 22 62 22 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 272 98 55 112 68 NC_002967:TDE0135|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_156377..156527_POSITIVE 267 60 13 102 54 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 266 63 23 49 12 NC_002967:TDE1751|3end_ribosomal_protein_L21_1803831..1803981_NEGATIVE 263 68 22 58 12 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 263 88 46 36 3 NC_002967:TDE0742|3end_hypothetical_protein_778450..778600_NEGATIVE 262 36 1 41 9 NC_002967:TDE2574|3end_conserved_hypothetical_protein_TIGR00650_2601094..2601244_POSITIVE 262 57 15 128 82 NC_002967:TDE1047|3end_30S_ribosomal_protein_S12_1074551..1074701_POSITIVE