Origin IGS: ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtcaatctgtaaacaaagggctaggaaaactcctgcccttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagggcaggagttttcctagccctttgtttacagattgactagaatctatcagaatgtaaaaagctaccacacctagacattcaaagacaaggaaataaag Mask Tandem Repeat Region ================================================ ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtcaatctgtaaacaaagggctaggaaaactcctgcccttt Find is-nt database================================================ Query_seq: SMT_1530:SMT_1531|SMT_1530:SMT_1531:K07456 DNA mismatch repair protein MutS2:hypothetical protein:<-<-:1515437..1515538 102 ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtcaatctgtaaacaaagggctaggaaaactcctgcccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1530:SMT_1531|SMT_1530:SMT_1531:K07456 DNA mismatch repair protein MutS2:hypothetical protein:<-<-:1515437..1515538 102 ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtcaatctgtaaacaaagggctaggaaaactcctgcccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1530:SMT_1531|SMT_1530:SMT_1531:K07456 DNA mismatch repair protein MutS2:hypothetical protein:<-<-:1515437..1515538 102 ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtcaatctgtaaacaaagggctaggaaaactcctgcccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtcaatctgtaaacaaagggctaggaaaactcctgcccttt Predict ORF larger than 30AA ================================================ ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtcaatctgtaaacaaagggctaggaaaactcctgcccttt 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: 82 Start: 46 End: 75 .............................................GTTTACAGATTGACTAGAATCTATCAGAAT........................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtcaatctgtaaacaaagggctaggaaaactcctgcccttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1530:SMT_1531|SMT_1530:SMT_1531:K07456 DNA mismatch repair protein MutS2:hypothetical protein:<-<-:1515437..1515538 102 ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtcaatctgtaaacaaagggctaggaaaactcctgcccttt Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: smit_SMT_1530_SMT_1531|K07456 DNA mismatch repair protein MutS2:hypothetical protein|NEGATIVE:NEGATIVE|[1515437,1515538]|102 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtcaatctgtaaacaaagggctaggaaaactcctgcccttt ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtcaatctgtaaacaaagggctaggaaaactcctgcccttt Inter-species Hit: Count: 3 Min: 1 Max: 102 Len: 102 Subject: NC_008533_SPD_0370_SPD_0371|CvpA family protein:MutS2 family protein|POSITIVE:POSITIVE|[373837,373939]|103 HSP 1 e-value: 6.0E-45 bit: 180.0 Len: 102 Query Start:1 Query End:102 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 103 ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtc-aatctgtaaacaaagggctaggaaaactcctgcccttt ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattcgagtcaaatctgtaaacaaagggctaggaaaactcctgcccttt Subject: NC_003098_spr0367_spr0368|hypothetical protein:DNA mismatch repair protein|POSITIVE:POSITIVE|[366308,366410]|103 HSP 1 e-value: 6.0E-45 bit: 180.0 Len: 102 Query Start:1 Query End:102 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 103 ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtc-aatctgtaaacaaagggctaggaaaactcctgcccttt ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattcgagtcaaatctgtaaacaaagggctaggaaaactcctgcccttt Subject: NC_003028_SP_0405_SP_0406|hypothetical protein:MutS2 family protein|POSITIVE:POSITIVE|[384891,384993]|103 HSP 1 e-value: 6.0E-45 bit: 180.0 Len: 102 Query Start:1 Query End:102 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 103 ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattctagtc-aatctgtaaacaaagggctaggaaaactcctgcccttt ctttatttccttgtctttgaatgtctaggtgtggtagctttttacattctgatagattcgagtcaaatctgtaaacaaagggctaggaaaactcctgcccttt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAUUUCCUUGUCUUUGAAUGUCUAGGUGUGGUAGCUUUUUACAUUCUGAUAGAUUCUAGUCAAUCUGUAAACAAAGGGCUAGGAAAACUCCUGCCCUUU ..................((((((..((((......))))...))))))..(((((((......)))))))....(((((((.((((....))))))))))) (-26.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGGGCAGGAGUUUUCCUAGCCCUUUGUUUACAGAUUGACUAGAAUCUAUCAGAAUGUAAAAAGCUACCACACCUAGACAUUCAAAGACAAGGAAAUAAAG .(((((((((......))).))))))(((((..(((((......)))))....((((((...................))))))..)))))........... (-21.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 902 100 51 191 142 smit:SMT_1530|5end_K07456_DNA_mismatch_repair_protein_MutS2_1515346..1515576_NEGATIVE 353 46 6 77 31 smit:SMT_1263|5end_hypothetical_protein_1228104..1228334_POSITIVE 264 70 21 115 63 smit:SMT_1981|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912261..1912491_POSITIVE 258 47 14 147 117 smit:SMT_1654|5end_K03110_signal_recognition_particle_receptor_1642150..1642380_POSITIVE 250 78 33 196 146 smit:SMT_741|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_645618..645848_NEGATIVE 249 38 3 195 157 smit:SMT_2086|5end_hypothetical_protein_1983696..1983926_NEGATIVE 249 57 13 201 150 smit:SMT_1727|5end_uridine_kinase_1712483..1712713_POSITIVE 249 60 14 225 169 smit:SMT_1098|5end_hypothetical_protein_1041992..1042222_NEGATIVE 248 100 78 142 119 smit:SMT_1307|5end_glycerol_uptake_facilitator_protein_1271664..1271894_POSITIVE 246 97 68 55 31 smit:SMT_134|5end_LysM_domain_protein_85427..85657_POSITIVE 239 50 1 83 31 smit:SMT_359|5end_transcription_termination-antitermination_factor_294470..294700_POSITIVE 238 86 45 215 180 smit:SMT_832|5end_hypothetical_protein_775104..775334_NEGATIVE 236 50 13 94 49 smit:SMT_370|5end_acetyltransferase,_GNAT_family_304688..304918_POSITIVE 233 55 13 230 178 smit:SMT_1614|5end_K08998_hypothetical_protein_1601330..1601560_POSITIVE 233 80 31 208 162 smit:SMT_862|5end_hypothetical_protein_predicted_by_Glimmer/Critica_808587..808817_POSITIVE 233 98 80 62 41 smit:SMT_401|5end_peptide_methionine_sulfoxide_reductase_329663..329893_POSITIVE 232 100 79 144 128 smit:SMT_1279|5end_translation_elongation_factor_Ts_1242331..1242561_POSITIVE 232 98 57 64 23 smit:SMT_1023|5end_hypothetical_protein_958884..959114_NEGATIVE 232 98 57 228 187 smit:SMT_1022|5end_glycine_betaine_transport_ATP-binding_protein_958720..958950_NEGATIVE 231 99 68 66 30 smit:SMT_416|5end_ribonuclease_Z_359423..359653_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 46 6 75 29 smit:SMT_1262|3end_ribosomal_protein_L11_methyltransferase_1228182..1228332_POSITIVE 264 70 21 74 22 smit:SMT_2023|3end_tryptophan_synthase,_alpha_subunit_1939997..1940147_POSITIVE 264 70 21 61 9 smit:SMT_1674|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1660361..1660511_NEGATIVE 264 96 57 146 107 smit:SMT_1573|3end_MutT/NUDIX_family_protein_1566960..1567110_POSITIVE 258 47 14 143 113 smit:SMT_1653|3end_hydrolase_1642226..1642376_POSITIVE 249 57 13 91 40 smit:SMT_1726|3end_tRNA_pseudouridine_synthase_B_1712453..1712603_POSITIVE 248 100 78 71 48 smit:SMT_1306|3end_alpha-glycerophosphate_oxidase_1271673..1271823_POSITIVE 246 45 1 128 89 smit:SMT_719|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_625006..625156_NEGATIVE 242 43 1 151 105 smit:SMT_1099|3end_protein_tyrosine_phosphatase_1042044..1042194_NEGATIVE 240 69 35 112 74 smit:SMT_651|3end_DNA_ligase_559986..560136_NEGATIVE 238 97 56 51 1 smit:SMT_1717|3end_DNA-3-methyladenine_glycosylase_I_1703711..1703861_NEGATIVE 238 86 45 136 101 smit:SMT_833|3end_hypothetical_protein_predicted_by_Glimmer/Critica_775183..775333_NEGATIVE 237 97 66 74 28 smit:SMT_1801|3end_heavy_metal_translocating_P-type_ATPase_1775408..1775558_POSITIVE 234 70 23 138 74 smit:SMT_2097|3end_type_I_restriction_enzyme_M_protein_1990475..1990625_NEGATIVE 233 98 80 52 31 smit:SMT_400|3end_hypothetical_protein_329733..329883_POSITIVE 232 100 79 65 49 smit:SMT_1278|3end_30S_ribosomal_protein_S2_1242332..1242482_POSITIVE 231 99 68 51 15 smit:SMT_415|3end_hypothetical_protein_359488..359638_POSITIVE 228 56 14 73 29 smit:SMT_133|3end_L-serine_dehydratase_beta_subunit_84566..84716_NEGATIVE 225 50 9 118 76 smit:SMT_2126|3end_indole-3-glycerol_phosphate_synthase_2009366..2009516_POSITIVE 222 69 25 136 68 smit:SMT_450|3end_hydroxyethylthiazole_kinase_389022..389172_POSITIVE