Origin IGS: atccacaataagtgataaacatttttaactcttgatttagcaaagataaaaccaaattcaagttttttcaaatctttctctctatttttagggggatttttattttatactagagtcagaaattgatagtgaggtttttgaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttcaaaaacctcactatcaatttctgactctagtataaaataaaaatccccctaaaaatagagagaaagatttgaaaaaacttgaatttggttttatctttgctaaatcaagagttaaaaatgtttatcacttattgtggat Mask Tandem Repeat Region ================================================ atccacaataagtgataaacatttttaactcttgatttagcaaagataaaaccaaattcaagttttttcaaatctttctctctatttttagggggatttttattttatactagagtcagaaattgatagtgaggtttttgaa Find is-nt database================================================ Query_seq: SSA_1114:SSA_1115|SSA_1114:SSA_1115:Histidine kinase, putative:Cytochrome C-type biogenesis protein, putative:->->:1141612..1141753 142 atccacaataagtgataaacatttttaactcttgatttagcaaagataaaaccaaattcaagttttttcaaatctttctctctatttttagggggatttttattttatactagagtcagaaattgatagtgaggtttttgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1114:SSA_1115|SSA_1114:SSA_1115:Histidine kinase, putative:Cytochrome C-type biogenesis protein, putative:->->:1141612..1141753 142 atccacaataagtgataaacatttttaactcttgatttagcaaagataaaaccaaattcaagttttttcaaatctttctctctatttttagggggatttttattttatactagagtcagaaattgatagtgaggtttttgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1114:SSA_1115|SSA_1114:SSA_1115:Histidine kinase, putative:Cytochrome C-type biogenesis protein, putative:->->:1141612..1141753 142 atccacaataagtgataaacatttttaactcttgatttagcaaagataaaaccaaattcaagttttttcaaatctttctctctatttttagggggatttttattttatactagagtcagaaattgatagtgaggtttttgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atccacaataagtgataaacatttttaactcttgatttagcaaagataaaaccaaattcaagttttttcaaatctttctctctatttttagggggatttttattttatactagagtcagaaattgatagtgaggtttttgaa Predict ORF larger than 30AA ================================================ atccacaataagtgataaacatttttaactcttgatttagcaaagataaaaccaaattcaagttttttcaaatctttctctctatttttagggggatttttattttatactagagtcagaaattgatagtgaggtttttgaa 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: 43 End: 72 ..........................................TTTGAAAAAACTTGAATTTGGTTTTATCTT...................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atccacaataagtgataaacatttttaactcttgatttagcaaagataaaaccaaattcaagttttttcaaatctttctctctatttttagggggatttttattttatactagagtcagaaattgatagtgaggtttttgaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 83 HP_score: -5.0 Tail_Score: -5.56263 Start: 77 End: 96 Full_Region: GTTTTTTCAAATCTT TCTCTCTA TTTT TAGGGGGA TTTTTATTTTATACT ............................................................................TCTCTCTATTTTTAGGGGGA.............................................. Find igs database================================================ Query_seq: SSA_1114:SSA_1115|SSA_1114:SSA_1115:Histidine kinase, putative:Cytochrome C-type biogenesis protein, putative:->->:1141612..1141753 142 atccacaataagtgataaacatttttaactcttgatttagcaaagataaaaccaaattcaagttttttcaaatctttctctctatttttagggggatttttattttatactagagtcagaaattgatagtgaggtttttgaa Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_009009_SSA_1114_SSA_1115|Histidine kinase, putative:Cytochrome C-type biogenesis protein, putative|POSITIVE:POSITIVE|[1141612,1141753]|142 HSP 1 e-value: 2.0E-27 bit: 123.0 Len: 62 Query Start:1 Query End:62 Subject Strand: POSITIVE Subject Start: 1 Subject End: 62 atccacaataagtgataaacatttttaactcttgatttagcaaagataaaaccaaattcaag................................................................................ atccacaataagtgataaacatttttaactcttgatttagcaaagataaaaccaaattcaag................................................................................ HSP 2 e-value: 5.0E-12 bit: 71.9 Len: 36 Query Start:107 Query End:142 Subject Strand: POSITIVE Subject Start: 107 Subject End: 142 ..........................................................................................................atactagagtcagaaattgatagtgaggtttttgaa ..........................................................................................................atactagagtcagaaattgatagtgaggtttttgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCACAAUAAGUGAUAAACAUUUUUAACUCUUGAUUUAGCAAAGAUAAAACCAAAUUCAAGUUUUUUCAAAUCUUUCUCUCUAUUUUUAGGGGGAUUUUUAUUUUAUACUAGAGUCAGAAAUUGAUAGUGAGGUUUUUGAA ((((((.....((.....)).(((((.(((((.(..........((.(((((.........))))).)).......((((((((....)))))))).............).))))).)))))......))).)))....... (-21.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAAAAACCUCACUAUCAAUUUCUGACUCUAGUAUAAAAUAAAAAUCCCCCUAAAAAUAGAGAGAAAGAUUUGAAAAAACUUGAAUUUGGUUUUAUCUUUGCUAAAUCAAGAGUUAAAAAUGUUUAUCACUUAUUGUGGAU .....((((.......((((..(((..(((((..........................)))))....))).)))).....(((((.((((((.........)))))))))))..........)))).((((.....)))).. (-18.07) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 120 71 61 11 NC_009009:SSA_0091|5end_V-type_sodium_ATPase,_subunit_A,_putative_91037..91267_POSITIVE 250 95 51 53 14 NC_009009:SSA_1259|5end_Purine_nucleoside_phosphorylase,_putative_1285722..1285952_NEGATIVE 233 97 60 119 80 NC_009009:SSA_0308|5end_hypothetical_protein_304385..304615_POSITIVE 232 66 29 180 143 NC_009009:SSA_1199|5end_Phosphinothricin_acetyltransferase,_putative_1223958..1224188_NEGATIVE 229 100 54 70 17 NC_009009:SSA_1829|5end_RNA_methyltransferase,_putative_1820329..1820559_NEGATIVE 226 134 109 83 59 NC_009009:SSA_0157|5end_hypothetical_protein_153513..153743_POSITIVE 221 102 61 194 148 NC_009009:SSA_1629|5end_Peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type,_putative_1630338..1630568_POSITIVE 220 119 74 68 10 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 220 119 73 110 69 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 216 99 52 176 135 NC_009009:SSA_0577|5end_Ancient_RNA-binding_IF3-C_fold_(CRS1/YhbY_domain),_putative_571253..571483_POSITIVE 215 118 72 63 14 NC_009009:SSA_2125|5end_Small_primase-like_protein_(Toprim_domain),_putative_2130019..2130249_NEGATIVE 213 106 62 139 93 NC_009009:SSA_1705|5end_hypothetical_protein_1696853..1697083_NEGATIVE 211 80 31 215 168 NC_009009:SSA_2366|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368869..2369099_NEGATIVE 211 106 61 88 45 NC_009009:SSA_2226|5end_Organic_radical_activating_chaperone,_putative_2227756..2227986_NEGATIVE 211 109 62 117 58 NC_009009:SSA_1318|5end_GTP-binding_protein_lepA,_putative_1335821..1336051_NEGATIVE 211 92 53 114 68 NC_009009:SSA_1251|5end_Hydrolase,_HD_superfamily,_putative_1276790..1277020_NEGATIVE 210 125 81 142 100 NC_009009:SSA_0814|5end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_796835..797065_NEGATIVE 208 95 51 193 147 NC_009009:SSA_2321|5end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326925..2327155_NEGATIVE 208 99 60 115 79 NC_009009:SSA_0217|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213183..213413_POSITIVE 206 120 75 223 164 NC_009009:SSA_2005|5end_Chaperone_protein_dnaJ,_putative_2006384..2006614_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 120 71 102 46 NC_009009:SSA_0090|3end_Acetyltransferase,_GNAT_family,_putative_91033..91183_POSITIVE 233 97 60 67 28 NC_009009:SSA_0307|3end_Glutamine_synthetase_type_1,_putative_304413..304563_POSITIVE 232 120 72 113 59 NC_009009:SSA_1661|3end_hypothetical_protein_1657759..1657909_NEGATIVE 225 99 52 45 2 NC_009009:SSA_0852|3end_ATP-dependent_DNA_helicase,_putative_841418..841568_POSITIVE 221 102 61 139 93 NC_009009:SSA_1628|3end_MutT/nudix_family_protein,_putative_1630363..1630513_POSITIVE 220 119 73 51 10 NC_009009:SSA_0538|3end_PduH_protein,_putative_534254..534404_POSITIVE 216 99 52 68 27 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 216 106 70 97 58 NC_009009:SSA_0224|3end_hypothetical_protein_218518..218668_POSITIVE 215 118 72 97 48 NC_009009:SSA_2126|3end_hypothetical_protein_2129985..2130135_NEGATIVE 211 106 61 128 85 NC_009009:SSA_2227|3end_Acetyl_transferase,_putative_2227716..2227866_NEGATIVE 211 92 53 133 87 NC_009009:SSA_1252|3end_hypothetical_protein_1276771..1276921_NEGATIVE 208 90 42 109 68 NC_009009:SSA_2388|3end_hypothetical_protein_2031667..2031817_NEGATIVE 208 99 60 122 86 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE 202 40 9 94 66 NC_009009:SSA_1428|3end_hypothetical_protein_1435638..1435788_NEGATIVE 196 70 27 103 52 NC_009009:SSA_2279|3end_hypothetical_protein_2281671..2281821_NEGATIVE 195 53 11 87 42 NC_009009:SSA_0536|3end_B12-dependent_diol_dehydratase_small_subunit,_putative_531937..532087_POSITIVE 194 80 33 106 44 NC_009009:SSA_1565|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1568608..1568758_NEGATIVE 191 97 60 129 93 NC_009009:SSA_2378|3end_Two-component_system_transcriptional_regulator,_LytR/AlgR_family,_putative_2383129..2383279_NEGATIVE 190 120 73 63 15 NC_009009:SSA_1218|3end_DNA_repair_protein_radC,_putative_1239776..1239926_NEGATIVE 189 120 71 60 7 NC_009009:SSA_0356|3end_Dipeptidase,_putative_350757..350907_POSITIVE