Origin IGS: aaaagatcagttactggcaagcaaaatcagtgactgttttttctttgaacttctttgagaaatgttgtaaaatgtatctactatctcaagccctcaatggatgagataataataactccatcattgcagcaactcaactgaagcactctgaaaaccaaatggagcagaactcacacgctcaagaaacagaaattcgaggcaatcagatggaaagtttgctacgaaaaaagctatagaatttgggaaactatagcgggaggaaaagaggaaaaaat .........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 attttttcctcttttcctcccgctatagtttcccaaattctatagcttttttcgtagcaaactttccatctgattgcctcgaatttctgtttcttgagcgtgtgagttctgctccatttggttttcagagtgcttcagttgagttgctgcaatgatggagttattattatctcatccattgagggcttgagatagtagatacattttacaacatttctcaaagaagttcaaagaaaaaacagtcactgattttgcttgccagtaactgatctttt Mask Tandem Repeat Region ================================================ aaaagatcagttactggcaagcaaaatcagtgactgttttttctttgaacttctttgagaaatgttgtaaaatgtatctactatctcaagccctcaatggatgagataataataactccatcattgcagcaactcaactgaagcactctgaaaaccaaatggagcagaactcacacgctcaagaaacagaaattcgaggcaatcagatggaaagtttgctacgaaaaaagctatagaatttgggaaactatagcgggaggaaaagaggaaaaaat Find is-nt database================================================ Query_seq: SSA_1158:SSA_1161|SSA_1158:SSA_1161:hypothetical protein:hypothetical protein:->->:1187248..1187522 275 aaaagatcagttactggcaagcaaaatcagtgactgttttttctttgaacttctttgagaaatgttgtaaaatgtatctactatctcaagccctcaatggatgagataataataactccatcattgcagcaactcaactgaagcactctgaaaaccaaatggagcagaactcacacgctcaagaaacagaaattcgaggcaatcagatggaaagtttgctacgaaaaaagctatagaatttgggaaactatagcgggaggaaaagaggaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1158:SSA_1161|SSA_1158:SSA_1161:hypothetical protein:hypothetical protein:->->:1187248..1187522 275 aaaagatcagttactggcaagcaaaatcagtgactgttttttctttgaacttctttgagaaatgttgtaaaatgtatctactatctcaagccctcaatggatgagataataataactccatcattgcagcaactcaactgaagcactctgaaaaccaaatggagcagaactcacacgctcaagaaacagaaattcgaggcaatcagatggaaagtttgctacgaaaaaagctatagaatttgggaaactatagcgggaggaaaagaggaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1158:SSA_1161|SSA_1158:SSA_1161:hypothetical protein:hypothetical protein:->->:1187248..1187522 275 aaaagatcagttactggcaagcaaaatcagtgactgttttttctttgaacttctttgagaaatgttgtaaaatgtatctactatctcaagccctcaatggatgagataataataactccatcattgcagcaactcaactgaagcactctgaaaaccaaatggagcagaactcacacgctcaagaaacagaaattcgaggcaatcagatggaaagtttgctacgaaaaaagctatagaatttgggaaactatagcgggaggaaaagaggaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaagatcagttactggcaagcaaaatcagtgactgttttttctttgaacttctttgagaaatgttgtaaaatgtatctactatctcaagccctcaatggatgagataataataactccatcattgcagcaactcaactgaagcactctgaaaaccaaatggagcagaactcacacgctcaagaaacagaaattcgaggcaatcagatggaaagtttgctacgaaaaaagctatagaatttgggaaactatagcgggaggaaaagaggaaaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 6 End: 101 ..... M S Y W Q A K S V T V F S L N F F E K C C K M Y L L S Q A L N G .............................................................................................................................................................................. Protein_Len: 38 Strand: + Start: 120 End: 233 ....................................................................................................................... M I A A T Q L K H S E N Q M E Q N S H A Q E T E I R G N Q M E S L L R K K L .......................................... Protein_Len: 42 Strand: + Start: 148 End: 273 ................................................................................................................................................... M K T K W S R T H T L K K Q K F E A I R W K V C Y E K S Y R I W E T I A G G K E E K .. Protein_Len: 37 Strand: - Start: 124 End: 234 ........................................................................................................................... Q L L E V S A S Q F G F P A S S V R E L F L F E L C D S P F N A V F F A M ......................................... aaaagatcagttactggcaagcaaaatcagtgactgttttttctttgaacttctttgagaaatgttgtaaaatgtatctactatctcaagccctcaatggatgagataataataactccatcattgcagcaactcaactgaagcactctgaaaaccaaatggagcagaactcacacgctcaagaaacagaaattcgaggcaatcagatggaaagtttgctacgaaaaaagctatagaatttgggaaactatagcgggaggaaaagaggaaaaaat 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: 83 Start: 44 End: 73 ...........................................TTTGAACTTCTTTGAGAAATGTTGTAAAAT.......................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaagatcagttactggcaagcaaaatcagtgactgttttttctttgaacttctttgagaaatgttgtaaaatgtatctactatctcaagccctcaatggatgagataataataactccatcattgcagcaactcaactgaagcactctgaaaaccaaatggagcagaactcacacgctcaagaaacagaaattcgaggcaatcagatggaaagtttgctacgaaaaaagctatagaatttgggaaactatagcgggaggaaaagaggaaaaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1158:SSA_1161|SSA_1158:SSA_1161:hypothetical protein:hypothetical protein:->->:1187248..1187522 275 aaaagatcagttactggcaagcaaaatcagtgactgttttttctttgaacttctttgagaaatgttgtaaaatgtatctactatctcaagccctcaatggatgagataataataactccatcattgcagcaactcaactgaagcactctgaaaaccaaatggagcagaactcacacgctcaagaaacagaaattcgaggcaatcagatggaaagtttgctacgaaaaaagctatagaatttgggaaactatagcgggaggaaaagaggaaaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 275 Len: 275 Subject: NC_009009_SSA_1158_SSA_1161|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1187248,1187522]|275 HSP 1 e-value: 1.0E-154 bit: 545.0 Len: 275 Query Start:1 Query End:275 Subject Strand: POSITIVE Subject Start: 1 Subject End: 275 aaaagatcagttactggcaagcaaaatcagtgactgttttttctttgaacttctttgagaaatgttgtaaaatgtatctactatctcaagccctcaatggatgagataataataactccatcattgcagcaactcaactgaagcactctgaaaaccaaatggagcagaactcacacgctcaagaaacagaaattcgaggcaatcagatggaaagtttgctacgaaaaaagctatagaatttgggaaactatagcgggaggaaaagaggaaaaaat aaaagatcagttactggcaagcaaaatcagtgactgttttttctttgaacttctttgagaaatgttgtaaaatgtatctactatctcaagccctcaatggatgagataataataactccatcattgcagcaactcaactgaagcactctgaaaaccaaatggagcagaactcacacgctcaagaaacagaaattcgaggcaatcagatggaaagtttgctacgaaaaaagctatagaatttgggaaactatagcgggaggaaaagaggaaaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGAUCAGUUACUGGCAAGCAAAAUCAGUGACUGUUUUUUCUUUGAACUUCUUUGAGAAAUGUUGUAAAAUGUAUCUACUAUCUCAAGCCCUCAAUGGAUGAGAUAAUAAUAACUCCAUCAUUGCAGCAACUCAACUGAAGCACUCUGAAAACCAAAUGGAGCAGAACUCACACGCUCAAGAAACAGAAAUUCGAGGCAAUCAGAUGGAAAGUUUGCUACGAAAAAAGCUAUAGAAUUUGGGAAACUAUAGCGGGAGGAAAAGAGGAAAAAAU .(((((.((((((((((.........)))))))))).....)))))...(((((((.(((.(((((....))))).)))..(((((((..((......)).))))))).......((((....(((.(((((((((.((((.((.(((.(((.........((((...........))))............))))))))..)))).))...)).))))).))).....(((((((...........))))))).))))..)))))))....... (-64.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUUCCUCUUUUCCUCCCGCUAUAGUUUCCCAAAUUCUAUAGCUUUUUUCGUAGCAAACUUUCCAUCUGAUUGCCUCGAAUUUCUGUUUCUUGAGCGUGUGAGUUCUGCUCCAUUUGGUUUUCAGAGUGCUUCAGUUGAGUUGCUGCAAUGAUGGAGUUAUUAUUAUCUCAUCCAUUGAGGGCUUGAGAUAGUAGAUACAUUUUACAACAUUUCUCAAAGAAGUUCAAAGAAAAAACAGUCACUGAUUUUGCUUGCCAGUAACUGAUCUUUU .(((((((........((((.(((((((...........))))))).......(((((((.(((.....((((..((((((((..((........(((((.(......)))))).....))..))).))).)).))))..))))))))))......))))...(((((((((((.((......))..)))))))))))..............(((((.....))))).....)))))))((((.((((...........)))).))))....... (-64.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 45 5 52 10 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 281 269 232 140 91 NC_009009:SSA_1914|5end_hypothetical_protein_1905195..1905425_NEGATIVE 278 190 142 43 8 NC_009009:SSA_1882|5end_Subtilisin-like_serine_proteases,_putative_1880797..1881027_NEGATIVE 276 58 11 175 130 NC_009009:SSA_0471|5end_CbiG_protein,_putative_473600..473830_POSITIVE 275 150 102 203 142 NC_009009:SSA_1987|5end_hypothetical_protein_1983368..1983598_NEGATIVE 269 211 175 231 190 NC_009009:SSA_0873|5end_ATP-dependent_DNA_helicase;_DNA_polymerase_III,_epsilon_subunit,_putative_865391..865621_POSITIVE 268 203 161 64 21 NC_009009:SSA_1408|5end_hypothetical_protein_1421005..1421235_NEGATIVE 268 43 5 61 10 NC_009009:SSA_0272|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_266023..266253_POSITIVE 267 184 141 57 7 NC_009009:SSA_0927|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936049..936279_POSITIVE 265 55 13 103 66 NC_009009:SSA_0882|5end_Phosphoserine_phosphatase,_putative_876903..877133_POSITIVE 263 58 13 63 14 NC_009009:SSA_2079|5end_Acetyltransferase,_putative_2083971..2084201_POSITIVE 262 97 51 55 14 NC_009009:SSA_1325|5end_Ketoacyl_reductase_hetN,_putative_1342343..1342573_NEGATIVE 261 159 116 140 99 NC_009009:SSA_1667|5end_hypothetical_protein_1667704..1667934_NEGATIVE 260 165 121 231 180 NC_009009:SSA_1549|5end_hypothetical_protein_1552112..1552342_NEGATIVE 259 190 141 65 22 NC_009009:SSA_1984|5end_Cell_surface_SD_repeat_antigen_precursor,_putative_1979035..1979265_NEGATIVE 259 169 124 57 14 NC_009009:SSA_1573|5end_hypothetical_protein_1576536..1576766_NEGATIVE 258 270 229 72 32 NC_009009:SSA_1536|5end_Biotin_synthase,_putative_1543609..1543839_POSITIVE 258 260 213 47 2 NC_009009:SSA_0611|5end_HtpX_protease,_putative_599539..599769_POSITIVE 257 120 76 189 141 NC_009009:SSA_2097|5end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_2102918..2103148_NEGATIVE 256 210 161 130 63 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 44 1 92 49 NC_009009:SSA_1158|3end_hypothetical_protein_1187187..1187337_POSITIVE 281 269 232 59 10 NC_009009:SSA_1915|3end_hypothetical_protein_1905276..1905426_NEGATIVE 279 164 125 109 68 NC_009009:SSA_2004|3end_Zinc_metalloprotease_zmpB_precursor,_putative_1999216..1999366_NEGATIVE 266 180 138 64 27 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 265 55 13 69 32 NC_009009:SSA_0881|3end_Lipoprotein,_putative_876949..877099_POSITIVE 261 159 116 106 65 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 260 165 121 115 64 NC_009009:SSA_1550|3end_hypothetical_protein_1552228..1552378_NEGATIVE 255 190 142 66 22 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 254 270 221 86 34 NC_009009:SSA_1048|3end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1064184..1064334_POSITIVE 253 220 174 95 46 NC_009009:SSA_2140|3end_Ribonuclease_P_protein_component,_putative_2140308..2140458_NEGATIVE 253 48 4 68 16 NC_009009:SSA_0835|3end_Accessory_secretory_protein_Asp3,_putative_821595..821745_POSITIVE 250 59 15 125 79 NC_009009:SSA_2201|3end_hypothetical_protein_2202237..2202387_POSITIVE 250 234 193 50 3 NC_009009:SSA_1845|3end_Serine/threonine_protein_kinase,_putative_1838328..1838478_NEGATIVE 244 58 11 104 42 NC_009009:SSA_1395|3end_hypothetical_protein_1409045..1409195_NEGATIVE 242 129 83 56 1 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 242 43 6 51 1 NC_009009:SSA_0271|3end_Glycosylhydrolase,_family_35,_putative_266093..266243_POSITIVE 241 216 182 82 43 NC_009009:SSA_2144|3end_Glutamyl-tRNA_synthetase,_putative_2144315..2144465_NEGATIVE 241 160 116 101 44 NC_009009:SSA_0920|3end_hypothetical_protein_931071..931221_POSITIVE 239 260 214 45 1 NC_009009:SSA_0610|3end_LemA-like_protein,_putative_599617..599767_POSITIVE 238 221 188 146 111 NC_009009:SSA_0841|3end_hypothetical_protein_827236..827386_POSITIVE