Origin IGS: agggattcctttctgttcatcatattttagactcgcatacttttatttataatctttactccaagcggtcgtatggtgatttacactaaaagcgaatagaagtttaatcaggtaaagtgagaaaagagctgtcatactgattggcaatttactgtaactaataagaagaatgcatcccaaccccgcaatagaagcaccagttaatgcttgctccctgcaatctttcagtagttcgctaacaaacattagatatgtctgattgagtcgcaaggccaaacttaaaatagcagaataaaactaggcaactttttggttttcggtgagtattagtcgctcagttatgcctttgacgtctcatagaatttttgaagaagattatgaaatagggaagggaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attcccttccctatttcataatcttcttcaaaaattctatgagacgtcaaaggcataactgagcgactaatactcaccgaaaaccaaaaagttgcctagttttattctgctattttaagtttggccttgcgactcaatcagacatatctaatgtttgttagcgaactactgaaagattgcagggagcaagcattaactggtgcttctattgcggggttgggatgcattcttcttattagttacagtaaattgccaatcagtatgacagctcttttctcactttacctgattaaacttctattcgcttttagtgtaaatcaccatacgaccgcttggagtaaagattataaataaaagtatgcgagtctaaaatatgatgaacagaaaggaatccct Mask Tandem Repeat Region ================================================ agggattcctttctgttcatcatattttagactcgcatacttttatttataatctttactccaagcggtcgtatggtgatttacactaaaagcgaatagaagtttaatcaggtaaagtgagaaaagagctgtcatactgattggcaatttactgtaactaataagaagaatgcatcccaaccccgcaatagaagcaccagttaatgcttgctccctgcaatctttcagtagttcgctaacaaacattagatatgtctgattgagtcgcaaggccaaacttaaaatagcagaataaaactaggcaactttttggttttcggtgagtattagtcgctcagttatgcctttgacgtctcatagaatttttgaagaagattatgaaatagggaagggaat Find is-nt database================================================ Query_seq: SSA_0396:SSA_0397|SSA_0396:SSA_0397:hypothetical protein:hypothetical protein:<-<-:393686..394081 396 agggattcctttctgttcatcatattttagactcgcatacttttatttataatctttactccaagcggtcgtatggtgatttacactaaaagcgaatagaagtttaatcaggtaaagtgagaaaagagctgtcatactgattggcaatttactgtaactaataagaagaatgcatcccaaccccgcaatagaagcaccagttaatgcttgctccctgcaatctttcagtagttcgctaacaaacattagatatgtctgattgagtcgcaaggccaaacttaaaatagcagaataaaactaggcaactttttggttttcggtgagtattagtcgctcagttatgcctttgacgtctcatagaatttttgaagaagattatgaaatagggaagggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0396:SSA_0397|SSA_0396:SSA_0397:hypothetical protein:hypothetical protein:<-<-:393686..394081 396 agggattcctttctgttcatcatattttagactcgcatacttttatttataatctttactccaagcggtcgtatggtgatttacactaaaagcgaatagaagtttaatcaggtaaagtgagaaaagagctgtcatactgattggcaatttactgtaactaataagaagaatgcatcccaaccccgcaatagaagcaccagttaatgcttgctccctgcaatctttcagtagttcgctaacaaacattagatatgtctgattgagtcgcaaggccaaacttaaaatagcagaataaaactaggcaactttttggttttcggtgagtattagtcgctcagttatgcctttgacgtctcatagaatttttgaagaagattatgaaatagggaagggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0396:SSA_0397|SSA_0396:SSA_0397:hypothetical protein:hypothetical protein:<-<-:393686..394081 396 agggattcctttctgttcatcatattttagactcgcatacttttatttataatctttactccaagcggtcgtatggtgatttacactaaaagcgaatagaagtttaatcaggtaaagtgagaaaagagctgtcatactgattggcaatttactgtaactaataagaagaatgcatcccaaccccgcaatagaagcaccagttaatgcttgctccctgcaatctttcagtagttcgctaacaaacattagatatgtctgattgagtcgcaaggccaaacttaaaatagcagaataaaactaggcaactttttggttttcggtgagtattagtcgctcagttatgcctttgacgtctcatagaatttttgaagaagattatgaaatagggaagggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agggattcctttctgttcatcatattttagactcgcatacttttatttataatctttactccaagcggtcgtatggtgatttacactaaaagcgaatagaagtttaatcaggtaaagtgagaaaagagctgtcatactgattggcaatttactgtaactaataagaagaatgcatcccaaccccgcaatagaagcaccagttaatgcttgctccctgcaatctttcagtagttcgctaacaaacattagatatgtctgattgagtcgcaaggccaaacttaaaatagcagaataaaactaggcaactttttggttttcggtgagtattagtcgctcagttatgcctttgacgtctcatagaatttttgaagaagattatgaaatagggaagggaat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 161 End: 256 ................................................................................................................................................................ M R R M H P N P A I E A P V N A C S L Q S F S S S L T N I R Y V ............................................................................................................................................ Protein_Len: 60 Strand: - Start: 46 End: 285 ............................................. I L Y L S F L A T M S I P L K S Y S I L L I C G L G A I S A G T L A Q E R C D K L L E S V F M L Y T Q N L R L A L S L M ............................................................................................................... agggattcctttctgttcatcatattttagactcgcatacttttatttataatctttactccaagcggtcgtatggtgatttacactaaaagcgaatagaagtttaatcaggtaaagtgagaaaagagctgtcatactgattggcaatttactgtaactaataagaagaatgcatcccaaccccgcaatagaagcaccagttaatgcttgctccctgcaatctttcagtagttcgctaacaaacattagatatgtctgattgagtcgcaaggccaaacttaaaatagcagaataaaactaggcaactttttggttttcggtgagtattagtcgctcagttatgcctttgacgtctcatagaatttttgaagaagattatgaaatagggaagggaat 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: 24 End: 53 .......................ATTTTAGACTCGCATACTTTTATTTATAAT....................................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agggattcctttctgttcatcatattttagactcgcatacttttatttataatctttactccaagcggtcgtatggtgatttacactaaaagcgaatagaagtttaatcaggtaaagtgagaaaagagctgtcatactgattggcaatttactgtaactaataagaagaatgcatcccaaccccgcaatagaagcaccagttaatgcttgctccctgcaatctttcagtagttcgctaacaaacattagatatgtctgattgagtcgcaaggccaaacttaaaatagcagaataaaactaggcaactttttggttttcggtgagtattagtcgctcagttatgcctttgacgtctcatagaatttttgaagaagattatgaaatagggaagggaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0396:SSA_0397|SSA_0396:SSA_0397:hypothetical protein:hypothetical protein:<-<-:393686..394081 396 agggattcctttctgttcatcatattttagactcgcatacttttatttataatctttactccaagcggtcgtatggtgatttacactaaaagcgaatagaagtttaatcaggtaaagtgagaaaagagctgtcatactgattggcaatttactgtaactaataagaagaatgcatcccaaccccgcaatagaagcaccagttaatgcttgctccctgcaatctttcagtagttcgctaacaaacattagatatgtctgattgagtcgcaaggccaaacttaaaatagcagaataaaactaggcaactttttggttttcggtgagtattagtcgctcagttatgcctttgacgtctcatagaatttttgaagaagattatgaaatagggaagggaat Intra-Species Hit: Count: 1 Min: 1 Max: 396 Len: 396 Subject: NC_009009_SSA_0396_SSA_0397|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[393686,394081]|396 HSP 1 e-value: 0.0 bit: 785.0 Len: 396 Query Start:1 Query End:396 Subject Strand: POSITIVE Subject Start: 1 Subject End: 396 agggattcctttctgttcatcatattttagactcgcatacttttatttataatctttactccaagcggtcgtatggtgatttacactaaaagcgaatagaagtttaatcaggtaaagtgagaaaagagctgtcatactgattggcaatttactgtaactaataagaagaatgcatcccaaccccgcaatagaagcaccagttaatgcttgctccctgcaatctttcagtagttcgctaacaaacattagatatgtctgattgagtcgcaaggccaaacttaaaatagcagaataaaactaggcaactttttggttttcggtgagtattagtcgctcagttatgcctttgacgtctcatagaatttttgaagaagattatgaaatagggaagggaat agggattcctttctgttcatcatattttagactcgcatacttttatttataatctttactccaagcggtcgtatggtgatttacactaaaagcgaatagaagtttaatcaggtaaagtgagaaaagagctgtcatactgattggcaatttactgtaactaataagaagaatgcatcccaaccccgcaatagaagcaccagttaatgcttgctccctgcaatctttcagtagttcgctaacaaacattagatatgtctgattgagtcgcaaggccaaacttaaaatagcagaataaaactaggcaactttttggttttcggtgagtattagtcgctcagttatgcctttgacgtctcatagaatttttgaagaagattatgaaatagggaagggaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGGAUUCCUUUCUGUUCAUCAUAUUUUAGACUCGCAUACUUUUAUUUAUAAUCUUUACUCCAAGCGGUCGUAUGGUGAUUUACACUAAAAGCGAAUAGAAGUUUAAUCAGGUAAAGUGAGAAAAGAGCUGUCAUACUGAUUGGCAAUUUACUGUAACUAAUAAGAAGAAUGCAUCCCAACCCCGCAAUAGAAGCACCAGUUAAUGCUUGCUCCCUGCAAUCUUUCAGUAGUUCGCUAACAAACAUUAGAUAUGUCUGAUUGAGUCGCAAGGCCAAACUUAAAAUAGCAGAAUAAAACUAGGCAACUUUUUGGUUUUCGGUGAGUAUUAGUCGCUCAGUUAUGCCUUUGACGUCUCAUAGAAUUUUUGAAGAAGAUUAUGAAAUAGGGAAGGGAAU ....((((((((((.(...(((((.(((...(((((..((((((((((........(((.((....))..)))(((((.....))))).....))))))))))(((......))).)))))....(((.(((((.(((((.((((.((((((((.((((((.(((.....(((...........)))......((.(.((((.....((((.....))))..........((((((((.((.((((.....)))).)).(((.(((....))))))........)))).))))..)))).)))..))).))))))..))))))))....)))).)))))........))))).)))................))).)))))...).)))))))))) (-86.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCCCUUCCCUAUUUCAUAAUCUUCUUCAAAAAUUCUAUGAGACGUCAAAGGCAUAACUGAGCGACUAAUACUCACCGAAAACCAAAAAGUUGCCUAGUUUUAUUCUGCUAUUUUAAGUUUGGCCUUGCGACUCAAUCAGACAUAUCUAAUGUUUGUUAGCGAACUACUGAAAGAUUGCAGGGAGCAAGCAUUAACUGGUGCUUCUAUUGCGGGGUUGGGAUGCAUUCUUCUUAUUAGUUACAGUAAAUUGCCAAUCAGUAUGACAGCUCUUUUCUCACUUUACCUGAUUAAACUUCUAUUCGCUUUUAGUGUAAAUCACCAUACGACCGCUUGGAGUAAAGAUUAUAAAUAAAAGUAUGCGAGUCUAAAAUAUGAUGAACAGAAAGGAAUCCCU (((((.(((......(((((...................((((.(((..(((((..(((((.((((((.....................)))))).))))).......(((......)))...)))))))).))))...((((.....(((((((((((.((((.((......)).))))....))))))))))).((..((((((....((((.((((((((................(((((.((((..((.(((.(((.((((((.................))).))).)))...))).)).)))).)))))))).))).))..))))..)))))).)).....................))))....)))))......))).))))).... (-77.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 858 100 51 191 142 NC_009009:SSA_0396|5end_hypothetical_protein_393595..393825_NEGATIVE 343 219 174 60 2 NC_009009:SSA_2271|5end_hypothetical_protein_2272450..2272680_NEGATIVE 338 288 255 46 10 NC_009009:SSA_2235|5end_Conserved_uncharacterized_protein_2235450..2235680_NEGATIVE 329 218 171 74 22 NC_009009:SSA_1413|5end_GufA-like_protein,_putative_1424919..1425149_NEGATIVE 323 237 194 168 125 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 320 238 194 147 106 NC_009009:SSA_1937|5end_Malonyl-CoA:ACP_transacylase,_putative_1924771..1925001_NEGATIVE 317 218 172 66 30 NC_009009:SSA_1417|5end_SAM-dependent_methyltransferase,_putative_1427993..1428223_NEGATIVE 316 212 177 87 51 NC_009009:SSA_0463|5end_Cobyrinic_acid_A,C-diamide_synthase,_putative_466865..467095_POSITIVE 310 346 301 209 151 NC_009009:SSA_1558|5end_Hydrolase,_HAD_superfamily_1560862..1561092_NEGATIVE 309 245 205 206 160 NC_009009:SSA_0721|5end_Mn/Fe-dependent_superoxide_dismutase,_putative_706215..706445_POSITIVE 307 358 312 222 173 NC_009009:SSA_0216|5end_Histidine_kinase,_putative_211877..212107_POSITIVE 306 280 255 68 39 NC_009009:SSA_1943|5end_Aspartate_kinase,_putative_1928697..1928927_POSITIVE 305 236 193 183 148 NC_009009:SSA_0202|5end_hypothetical_protein_200534..200764_POSITIVE 304 219 171 208 138 NC_009009:SSA_0632|5end_Anthranilate_synthase_component_I,_putative_621458..621688_POSITIVE 304 239 192 226 168 NC_009009:SSA_0165|5end_hypothetical_protein_163938..164168_POSITIVE 304 218 171 202 149 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 303 370 327 69 24 NC_009009:SSA_0950|5end_hypothetical_protein_956302..956532_POSITIVE 300 318 271 79 22 NC_009009:SSA_0942|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_949939..950169_POSITIVE 298 220 172 78 18 NC_009009:SSA_1106|5end_IgA-specific_metalloendopeptidase_1125974..1126204_POSITIVE 297 352 318 193 155 NC_009009:SSA_2265|5end_Maltodextrin_phosphorylase,_putative_2264197..2264427_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 218 174 151 93 NC_009009:SSA_2052|3end_Thioredoxin,_putative_2057193..2057343_NEGATIVE 335 219 171 146 87 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 325 222 181 55 4 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE 309 245 205 143 97 NC_009009:SSA_0720|3end_hypothetical_protein_706232..706382_POSITIVE 303 370 327 82 37 NC_009009:SSA_0949|3end_hypothetical_protein_956395..956545_POSITIVE 300 318 271 82 25 NC_009009:SSA_0941|3end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_950022..950172_POSITIVE 293 338 291 122 63 NC_009009:SSA_1563|3end_Metal-dependent_hydrolase,_beta-lactamase_superfamily_I,_putative_1566456..1566606_NEGATIVE 290 237 191 151 115 NC_009009:SSA_2020|3end_hypothetical_protein_2022471..2022621_POSITIVE 282 276 234 53 6 NC_009009:SSA_1728|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713424..1713574_NEGATIVE 281 105 65 118 79 NC_009009:SSA_2372|3end_hypothetical_protein_2374285..2374435_POSITIVE 281 352 317 124 87 NC_009009:SSA_2332|3end_D-alanyl_carrier_protein,_putative_2334957..2335107_NEGATIVE 281 335 301 150 109 NC_009009:SSA_2120|3end_GTPase,_putative_2121110..2121260_NEGATIVE 280 225 182 145 111 NC_009009:SSA_0324|3end_Conserved_uncharacterized_protein_317593..317743_POSITIVE 277 346 304 144 88 NC_009009:SSA_2320|3end_hypothetical_protein_2322302..2322452_NEGATIVE 276 215 172 68 33 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 275 231 194 149 113 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 275 237 192 142 85 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 274 356 313 126 83 NC_009009:SSA_1193|3end_Dihydrodipicolinate_synthase,_putative_1219095..1219245_NEGATIVE 267 218 172 114 57 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 266 229 187 68 22 NC_009009:SSA_0907|3end_Fibronectin-binding_protein_A,_putative_917568..917718_NEGATIVE