Origin IGS: aacttacctctttcaaatttctattgtacacgaaaatagctgagtgcgcaagctatcttaggctagaatcacagaaaaaaactgcccaatcaaggacagtttttaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctaaaaactgtccttgattgggcagtttttttctgtgattctagcctaagatagcttgcgcactcagctattttcgtgtacaatagaaatttgaaagaggtaagtt Mask Tandem Repeat Region ================================================ aacttacctctttcaaatttctattgtacacgaaaatagctgagtgcgcaagctatcttaggctagaatcacagaaaaaaactgcccaatcaaggacagtttttaga Find is-nt database================================================ Query_seq: SSA_1224:SSA_1225|SSA_1224:SSA_1225:hypothetical protein:Branched-chain amino acid aminotransferase, putative:<-<-:1247572..1247678 107 aacttacctctttcaaatttctattgtacacgaaaatagctgagtgcgcaagctatcttaggctagaatcacagaaaaaaactgcccaatcaaggacagtttttaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1224:SSA_1225|SSA_1224:SSA_1225:hypothetical protein:Branched-chain amino acid aminotransferase, putative:<-<-:1247572..1247678 107 aacttacctctttcaaatttctattgtacacgaaaatagctgagtgcgcaagctatcttaggctagaatcacagaaaaaaactgcccaatcaaggacagtttttaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1224:SSA_1225|SSA_1224:SSA_1225:hypothetical protein:Branched-chain amino acid aminotransferase, putative:<-<-:1247572..1247678 107 aacttacctctttcaaatttctattgtacacgaaaatagctgagtgcgcaagctatcttaggctagaatcacagaaaaaaactgcccaatcaaggacagtttttaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacttacctctttcaaatttctattgtacacgaaaatagctgagtgcgcaagctatcttaggctagaatcacagaaaaaaactgcccaatcaaggacagtttttaga Predict ORF larger than 30AA ================================================ aacttacctctttcaaatttctattgtacacgaaaatagctgagtgcgcaagctatcttaggctagaatcacagaaaaaaactgcccaatcaaggacagtttttaga 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: 23 End: 52 ......................CTTGCGCACTCAGCTATTTTCGTGTACAAT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacttacctctttcaaatttctattgtacacgaaaatagctgagtgcgcaagctatcttaggctagaatcacagaaaaaaactgcccaatcaaggacagtttttaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1224:SSA_1225|SSA_1224:SSA_1225:hypothetical protein:Branched-chain amino acid aminotransferase, putative:<-<-:1247572..1247678 107 aacttacctctttcaaatttctattgtacacgaaaatagctgagtgcgcaagctatcttaggctagaatcacagaaaaaaactgcccaatcaaggacagtttttaga Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_009009_SSA_1224_SSA_1225|hypothetical protein:Branched-chain amino acid aminotransferase, putative|NEGATIVE:NEGATIVE|[1247572,1247678]|107 HSP 1 e-value: 6.0E-42 bit: 170.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 aacttacctctttcaaatttctattgtacacgaaaatagctgagtgcgcaagctatcttaggctagaatcacagnnnnnnnctgcccaatcaaggacagtttttaga aacttacctctttcaaatttctattgtacacgaaaatagctgagtgcgcaagctatcttaggctagaatcacagaaaaaaactgcccaatcaaggacagtttttaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUACCUCUUUCAAAUUUCUAUUGUACACGAAAAUAGCUGAGUGCGCAAGCUAUCUUAGGCUAGAAUCACAGAAAAAAACUGCCCAAUCAAGGACAGUUUUUAGA ...............................((...((((((((.((....))...)))).))))...))......((((((((.((......)).))))))))... (-22.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAAAAACUGUCCUUGAUUGGGCAGUUUUUUUCUGUGAUUCUAGCCUAAGAUAGCUUGCGCACUCAGCUAUUUUCGUGUACAAUAGAAAUUUGAAAGAGGUAAGUU (((.((((((((((......))))))))))(((((((.......((..(((((((((.........))))))))).)).....)))))))......)))........ (-25.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 911 90 41 181 132 NC_009009:SSA_1224|5end_hypothetical_protein_1247481..1247711_NEGATIVE 297 42 3 142 95 NC_009009:SSA_1057|5end_Aminotransferase,_class-V,_putative_1073771..1074001_POSITIVE 287 71 35 148 112 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 278 74 40 206 163 NC_009009:SSA_0517|5end_Sensor_histidine_kinase,_putative_515060..515290_POSITIVE 276 76 31 48 10 NC_009009:SSA_0792|5end_hypothetical_protein_774618..774848_POSITIVE 274 79 38 217 173 NC_009009:SSA_1378|5end_hypothetical_protein_1397998..1398228_NEGATIVE 266 76 31 81 31 NC_009009:SSA_2281|5end_hypothetical_protein_2282370..2282600_NEGATIVE 262 88 42 54 14 NC_009009:SSA_1784|5end_Glutamate_racemase,_putative_1769897..1770127_NEGATIVE 261 99 63 217 180 NC_009009:SSA_2272|5end_hypothetical_protein_2272876..2273106_NEGATIVE 260 65 24 222 173 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 260 76 31 156 113 NC_009009:SSA_0155|5end_hypothetical_protein_150961..151191_POSITIVE 259 84 42 222 178 NC_009009:SSA_2208|5end_Preprotein_translocase_secE_component,_putative_2207913..2208143_NEGATIVE 259 99 56 229 194 NC_009009:SSA_2093|5end_PTS_system,_membrane_component,_putative_2097462..2097692_NEGATIVE 259 87 42 207 146 NC_009009:SSA_0678|5end_Transcriptional_regulator,_ArgR_family,_putative_660274..660504_POSITIVE 258 74 38 226 185 NC_009009:SSA_1399|5end_hypothetical_protein_1412225..1412455_NEGATIVE 256 70 37 188 145 NC_009009:SSA_0351|5end_Signal_peptidase_I,_putative_344907..345137_NEGATIVE 255 49 7 136 88 NC_009009:SSA_2018|5end_hypothetical_protein_2018801..2019031_NEGATIVE 246 58 18 198 163 NC_009009:SSA_1561|5end_Ribonuclease_III,_putative_1565883..1566113_NEGATIVE 244 49 7 130 95 NC_009009:SSA_2352|5end_ABC-type_nitrate/sulfonate/bicarbonate_transporter,_periplasmic_component,_putative_2354508..2354738_NEGATIVE 244 69 30 227 178 NC_009009:SSA_1742|5end_Ferrichrome-binding_protein,_putative_1728872..1729102_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 99 51 119 67 NC_009009:SSA_1993|3end_Conserved_uncharacterized_protein_1990380..1990530_NEGATIVE 276 76 31 55 17 NC_009009:SSA_0791|3end_UDP-N-acetylglucosamine-like_protein,_putative_774705..774855_POSITIVE 270 97 51 52 3 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 266 76 31 74 24 NC_009009:SSA_2282|3end_Phage_infection_protein,_putative_2282377..2282527_NEGATIVE 264 99 60 63 24 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 262 95 51 60 5 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE 260 76 31 65 22 NC_009009:SSA_0154|3end_hypothetical_protein_150950..151100_POSITIVE 255 49 7 125 77 NC_009009:SSA_2019|3end_hypothetical_protein_2018812..2018962_NEGATIVE 246 58 18 76 41 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 246 88 47 45 3 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE 245 52 11 48 6 NC_009009:SSA_1056|3end_Firmicute_fructose-1,6-bisphosphatase,_putative_1073750..1073900_POSITIVE 245 75 32 82 38 NC_009009:SSA_0208|3end_Conserved_uncharacterized_protein_204968..205118_NEGATIVE 244 49 7 88 53 NC_009009:SSA_2353|3end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2354550..2354700_NEGATIVE 244 69 30 147 98 NC_009009:SSA_1741|3end_ABC-type_Fe3+-siderophores_transporter,_ATPase_component,_putative_1728872..1729022_POSITIVE 242 60 35 30 6 NC_009009:SSA_0519|3end_Ethanolamine_ammonia-lyase_large_subunit,_putative_519525..519675_POSITIVE 242 87 42 67 18 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 241 70 27 147 97 NC_009009:SSA_0143|3end_Conserved_uncharacterized_protein_137880..138030_POSITIVE 230 70 23 53 7 NC_009009:SSA_1478|3end_Transposase_ORF1,_putative_1483124..1483274_POSITIVE 229 66 26 145 111 NC_009009:SSA_0548|3end_Alanine_racemase,_putative_543529..543679_POSITIVE 228 96 51 149 112 NC_009009:SSA_1640|3end_hypothetical_protein_1642108..1642258_NEGATIVE