Origin IGS: atcactagctggaaagataatgagttctgtctgagatctttcgataatnnnnnttaattaattaannnnntgctggaagttgaaattcttgatacttttaatatttgtctaatctcatttttattacctcaaattattattgtaccatttttatcccttttatagaagaaaaatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 catttttcttctataaaagggataaaaatggtacaataataatttgaggtaataaaaatgagattagacaaatattaaaagtatcaagaatttcaacttccagcannnnnttaattaattaannnnnattatcgaaagatctcagacagaactcattatctttccagctagtgat Mask Tandem Repeat Region ================================================ atcactagctggaaagataatgagttctgtctgagatctttcgataatnnnnnttaattaattaannnnntgctggaagttgaaattcttgatacttttaatatttgtctaatctcatttttattacctcaaattattattgtaccatttttatcccttttatagaagaaaaatg Find is-nt database================================================ Query_seq: SMT_1968:SMT_1969|SMT_1968:SMT_1969:transcription-repair coupling factor:transcription-repair coupling factor:<-<-:1900731..1900905 175 atcactagctggaaagataatgagttctgtctgagatctttcgataatnnnnnttaattaattaannnnntgctggaagttgaaattcttgatacttttaatatttgtctaatctcatttttattacctcaaattattattgtaccatttttatcccttttatagaagaaaaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1968:SMT_1969|SMT_1968:SMT_1969:transcription-repair coupling factor:transcription-repair coupling factor:<-<-:1900731..1900905 175 atcactagctggaaagataatgagttctgtctgagatctttcgataatnnnnnttaattaattaannnnntgctggaagttgaaattcttgatacttttaatatttgtctaatctcatttttattacctcaaattattattgtaccatttttatcccttttatagaagaaaaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1968:SMT_1969|SMT_1968:SMT_1969:transcription-repair coupling factor:transcription-repair coupling factor:<-<-:1900731..1900905 175 atcactagctggaaagataatgagttctgtctgagatctttcgataatnnnnnttaattaattaannnnntgctggaagttgaaattcttgatacttttaatatttgtctaatctcatttttattacctcaaattattattgtaccatttttatcccttttatagaagaaaaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcactagctggaaagataatgagttctgtctgagatctttcgataatnnnnnttaattaattaannnnntgctggaagttgaaattcttgatacttttaatatttgtctaatctcatttttattacctcaaattattattgtaccatttttatcccttttatagaagaaaaatg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 61 End: 162 ............................................................ M X X X L E V E I L D T F N I C L I S F L L P Q I I I V P F L S L L ............. atcactagctggaaagataatgagttctgtctgagatctttcgataatnnnnnttaattaattaannnnntgctggaagttgaaattcttgatacttttaatatttgtctaatctcatttttattacctcaaattattattgtaccatttttatcccttttatagaagaaaaatg 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================================================ atcactagctggaaagataatgagttctgtctgagatctttcgataatnnnnnttaattaattaannnnntgctggaagttgaaattcttgatacttttaatatttgtctaatctcatttttattacctcaaattattattgtaccatttttatcccttttatagaagaaaaatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1968:SMT_1969|SMT_1968:SMT_1969:transcription-repair coupling factor:transcription-repair coupling factor:<-<-:1900731..1900905 175 atcactagctggaaagataatgagttctgtctgagatctttcgataatnnnnnttaattaattaannnnntgctggaagttgaaattcttgatacttttaatatttgtctaatctcatttttattacctcaaattattattgtaccatttttatcccttttatagaagaaaaatg Intra-Species Hit: Count: 1 Min: 1 Max: 175 Len: 175 Subject: smit_SMT_1968_SMT_1969|transcription-repair coupling factor:transcription-repair coupling factor|NEGATIVE:NEGATIVE|[1900731,1900905]|175 HSP 1 e-value: 6.0E-77 bit: 287.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 atcactagctggaaagataatgagttctgtctgagatctttcgataatnnnnnttaattaattaannnnntgctggaagttgaaattcttgatacttttaatatttgtctaatctcatttttattacctcaaattattattgtaccatttttatcccttttatagaagaaaaatg atcactagctggaaagataatgagttctgtctgagatctttcgataatnnnnnttaattaattaannnnntgctggaagttgaaattcttgatacttttaatatttgtctaatctcatttttattacctcaaattattattgtaccatttttatcccttttatagaagaaaaatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCACUAGCUGGAAAGAUAAUGAGUUCUGUCUGAGAUCUUUCGAUAAUNNNNNUUAAUUAAUUAANNNNNUGCUGGAAGUUGAAAUUCUUGAUACUUUUAAUAUUUGUCUAAUCUCAUUUUUAUUACCUCAAAUUAUUAUUGUACCAUUUUUAUCCCUUUUAUAGAAGAAAAAUG ....(((((..(((((((...((......))....)))))))..((((........))))...........)))))....(((((....((.(((...(((((((((..((((.........))))...)))).)))))..))).)).)))))...((((....))))....... (-17.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUUUUCUUCUAUAAAAGGGAUAAAAAUGGUACAAUAAUAAUUUGAGGUAAUAAAAAUGAGAUUAGACAAAUAUUAAAAGUAUCAAGAAUUUCAACUUCCAGCANNNNNUUAAUUAAUUAANNNNNAUUAUCGAAAGAUCUCAGACAGAACUCAUUAUCUUUCCAGCUAGUGAU (((((((.((((......)))).)))))))............((((((..........(((((((......((((.....))))....)))))))...................................(((....)))))))))......((((((.((....)).)))))). (-22.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 803 48 1 139 92 smit:SMT_1968|5end_transcription-repair_coupling_factor_1900640..1900870_NEGATIVE 672 170 121 143 94 smit:SMT_1676|5end_S4_domain_protein_1661764..1661994_NEGATIVE 672 170 121 143 94 smit:SMT_95|5end_S4_domain_protein_28177..28407_POSITIVE 243 91 54 208 174 smit:SMT_1993|5end_hypothetical_protein_1919800..1920030_NEGATIVE 239 85 54 139 107 smit:SMT_2033|5end_hydrolase,_haloacid_dehalogenase-like_family_1946492..1946722_POSITIVE 239 46 4 71 22 smit:SMT_1499|5end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483091..1483321_POSITIVE 228 152 113 130 84 smit:SMT_856|5end_peroxide_resistance_protein,non-heme_iron-containing_ferritin_800648..800878_NEGATIVE 223 46 2 133 95 smit:SMT_1679|5end_hypothetical_protein_1662998..1663228_POSITIVE 223 48 1 185 135 smit:SMT_1039|5end_tRNA_(uracil-5-)_-methyltransferase_982698..982928_NEGATIVE 220 115 71 166 119 smit:SMT_296|5end_hypothetical_protein_predicted_by_Glimmer/Critica_238147..238377_POSITIVE 212 32 4 192 159 smit:SMT_1767|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_1744121..1744351_NEGATIVE 212 45 5 64 6 smit:SMT_1168|5end_potassium_uptake_protein_KtrB_1116552..1116782_NEGATIVE 210 160 118 213 170 smit:SMT_999|5end_hypothetical_protein_predicted_by_Glimmer/Critica_941642..941872_NEGATIVE 209 43 4 167 125 smit:SMT_762|5end_cation-transporting_ATPase,_E1-E2_family_protein_667691..667921_NEGATIVE 208 83 54 214 185 smit:SMT_1842|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1807858..1808088_NEGATIVE 208 118 73 101 58 smit:SMT_1610|5end_tyrosine_recombinase_1598565..1598795_POSITIVE 208 80 31 191 129 smit:SMT_1254|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1220882..1221112_NEGATIVE 207 43 9 67 31 smit:SMT_691|5end_endonuclease_III_603008..603238_NEGATIVE 206 116 71 102 36 smit:SMT_1017|5end_transcriptional_regulator,_MerR_family_954448..954678_NEGATIVE 206 48 5 79 31 smit:SMT_602|5end_5'-methylthioadenosine_nucleosidase_/_S-adenosylhomocysteine_nucleosidase_517192..517422_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 672 170 121 85 36 smit:SMT_1677|3end_transcription-repair_coupling_factor_1661822..1661972_NEGATIVE 672 170 121 85 36 smit:SMT_94|3end_transcription-repair_coupling_factor_28199..28349_POSITIVE 534 150 101 66 17 smit:SMT_2117|3end_transcription-repair_coupling_factor_2003907..2004057_NEGATIVE 249 45 1 72 28 smit:SMT_349|3end_sensor_histidine_kinase_(homolog_to_BlpH_Spn)_288636..288786_POSITIVE 239 46 1 66 12 smit:SMT_423|3end_sensory_transduction_protein_kinase_367531..367681_POSITIVE 233 47 15 121 83 smit:SMT_346|3end_K01992_ABC-2_type_transport_system_permease_protein_285849..285999_POSITIVE 223 46 2 46 8 smit:SMT_1678|3end_inorganic_pyrophosphatase_1662991..1663141_POSITIVE 220 115 71 118 71 smit:SMT_295|3end_hypothetical_protein_predicted_by_Glimmer/Critica_238179..238329_POSITIVE 208 118 73 110 67 smit:SMT_1609|3end_hypothetical_protein_1598654..1598804_POSITIVE 208 80 31 86 24 smit:SMT_1255|3end_cell_division_protein_FtsH_1220987..1221137_NEGATIVE 207 43 9 67 31 smit:SMT_692|3end_hypothetical_protein_603008..603158_NEGATIVE 206 48 5 62 14 smit:SMT_601|3end_hypothetical_protein_517255..517405_POSITIVE 203 92 54 68 28 smit:SMT_463|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_402839..402989_POSITIVE 202 157 111 50 10 smit:SMT_1084|3end_hypothetical_protein_1021326..1021476_NEGATIVE 201 45 19 144 114 smit:SMT_1968|3end_transcription-repair_coupling_factor_1899951..1900101_NEGATIVE 200 147 108 31 3 smit:SMT_954|3end_cation-transporting_ATPase,_E1-E2_family_901677..901827_NEGATIVE 199 45 1 147 106 smit:SMT_1794|3end_SOS_responce_UmuC_protein_1768442..1768592_NEGATIVE 199 44 4 119 73 smit:SMT_506|3end_K07729_putative_transcriptional_regulator_437411..437561_NEGATIVE 199 44 4 119 73 smit:SMT_503|3end_K07729_putative_transcriptional_regulator_435980..436130_NEGATIVE 197 44 8 133 90 smit:SMT_2020|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1937914..1938064_POSITIVE