Origin IGS: atcaaaatcctttcaatttctctgggaaaggcagcgttttgaaagaaatagcgcagcagctgaatatgcgtatccacatcactaaaaagccaagtatgccctttgtcgggataataggcgcattcagacctaacatttttctgtgccaacctgcggtggcagtcatgaatggtttcggcttcttttccacctgagacaaagaaagcaggattatcaaaatttatatcaatcatagataaatatactctcc .........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 ggagagtatatttatctatgattgatataaattttgataatcctgctttctttgtctcaggtggaaaagaagccgaaaccattcatgactgccaccgcaggttggcacagaaaaatgttaggtctgaatgcgcctattatcccgacaaagggcatacttggctttttagtgatgtggatacgcatattcagctgctgcgctatttctttcaaaacgctgcctttcccagagaaattgaaaggattttgat Mask Tandem Repeat Region ================================================ atcaaaatcctttcaatttctctgggaaaggcagcgttttgaaagaaatagcgcagcagctgaatatgcgtatccacatcactaaaaagccaagtatgccctttgtcgggataataggcgcattcagacctaacatttttctgtgccaacctgcggtggcagtcatgaatggtttcggcttcttttccacctgagacaaagaaagcaggattatcaaaatttatatcaatcatagataaatatactctcc Find is-nt database================================================ Query_seq: SSA_1608:SSA_1610|SSA_1608:SSA_1610:hypothetical protein:hypothetical protein:<-<-:1613844..1614093 250 atcaaaatcctttcaatttctctgggaaaggcagcgttttgaaagaaatagcgcagcagctgaatatgcgtatccacatcactaaaaagccaagtatgccctttgtcgggataataggcgcattcagacctaacatttttctgtgccaacctgcggtggcagtcatgaatggtttcggcttcttttccacctgagacaaagaaagcaggattatcaaaatttatatcaatcatagataaatatactctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1608:SSA_1610|SSA_1608:SSA_1610:hypothetical protein:hypothetical protein:<-<-:1613844..1614093 250 atcaaaatcctttcaatttctctgggaaaggcagcgttttgaaagaaatagcgcagcagctgaatatgcgtatccacatcactaaaaagccaagtatgccctttgtcgggataataggcgcattcagacctaacatttttctgtgccaacctgcggtggcagtcatgaatggtttcggcttcttttccacctgagacaaagaaagcaggattatcaaaatttatatcaatcatagataaatatactctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1608:SSA_1610|SSA_1608:SSA_1610:hypothetical protein:hypothetical protein:<-<-:1613844..1614093 250 atcaaaatcctttcaatttctctgggaaaggcagcgttttgaaagaaatagcgcagcagctgaatatgcgtatccacatcactaaaaagccaagtatgccctttgtcgggataataggcgcattcagacctaacatttttctgtgccaacctgcggtggcagtcatgaatggtttcggcttcttttccacctgagacaaagaaagcaggattatcaaaatttatatcaatcatagataaatatactctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcaaaatcctttcaatttctctgggaaaggcagcgttttgaaagaaatagcgcagcagctgaatatgcgtatccacatcactaaaaagccaagtatgccctttgtcgggataataggcgcattcagacctaacatttttctgtgccaacctgcggtggcagtcatgaatggtttcggcttcttttccacctgagacaaagaaagcaggattatcaaaatttatatcaatcatagataaatatactctcc Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 39 End: 191 ...................................... M K E I A Q Q L N M R I H I T K K P S M P F V G I I G A F R P N I F L C Q P A V A V M N G F G F F S T ........................................................... Protein_Len: 30 Strand: + Start: 143 End: 232 .............................................................................................................................................. M P T C G G S H E W F R L L F H L R Q R K Q D Y Q N L Y Q S .................. Protein_Len: 60 Strand: - Start: 3 End: 233 .. L L Q I H T D V D S F L W T H G K D P Y Y A C E S R V N K Q A L R R H C D H I T E A E K G G S V F F A P N D F N I D I M ................. Protein_Len: 60 Strand: - Start: 5 End: 220 .... F S I A C C S F I R I W M V L F G L I G K T P I I P A N L G L M K R H W G A T A T M F P K P K K E V Q S L S L L I I L M .............................. atcaaaatcctttcaatttctctgggaaaggcagcgttttgaaagaaatagcgcagcagctgaatatgcgtatccacatcactaaaaagccaagtatgccctttgtcgggataataggcgcattcagacctaacatttttctgtgccaacctgcggtggcagtcatgaatggtttcggcttcttttccacctgagacaaagaaagcaggattatcaaaatttatatcaatcatagataaatatactctcc 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================================================ atcaaaatcctttcaatttctctgggaaaggcagcgttttgaaagaaatagcgcagcagctgaatatgcgtatccacatcactaaaaagccaagtatgccctttgtcgggataataggcgcattcagacctaacatttttctgtgccaacctgcggtggcagtcatgaatggtttcggcttcttttccacctgagacaaagaaagcaggattatcaaaatttatatcaatcatagataaatatactctcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1608:SSA_1610|SSA_1608:SSA_1610:hypothetical protein:hypothetical protein:<-<-:1613844..1614093 250 atcaaaatcctttcaatttctctgggaaaggcagcgttttgaaagaaatagcgcagcagctgaatatgcgtatccacatcactaaaaagccaagtatgccctttgtcgggataataggcgcattcagacctaacatttttctgtgccaacctgcggtggcagtcatgaatggtttcggcttcttttccacctgagacaaagaaagcaggattatcaaaatttatatcaatcatagataaatatactctcc Intra-Species Hit: Count: 1 Min: 1 Max: 250 Len: 250 Subject: NC_009009_SSA_1608_SSA_1610|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1613844,1614093]|250 HSP 1 e-value: 1.0E-139 bit: 496.0 Len: 250 Query Start:1 Query End:250 Subject Strand: POSITIVE Subject Start: 1 Subject End: 250 atcaaaatcctttcaatttctctgggaaaggcagcgttttgaaagaaatagcgcagcagctgaatatgcgtatccacatcactaaaaagccaagtatgccctttgtcgggataataggcgcattcagacctaacatttttctgtgccaacctgcggtggcagtcatgaatggtttcggcttcttttccacctgagacaaagaaagcaggattatcaaaatttatatcaatcatagataaatatactctcc atcaaaatcctttcaatttctctgggaaaggcagcgttttgaaagaaatagcgcagcagctgaatatgcgtatccacatcactaaaaagccaagtatgccctttgtcgggataataggcgcattcagacctaacatttttctgtgccaacctgcggtggcagtcatgaatggtttcggcttcttttccacctgagacaaagaaagcaggattatcaaaatttatatcaatcatagataaatatactctcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAAAUCCUUUCAAUUUCUCUGGGAAAGGCAGCGUUUUGAAAGAAAUAGCGCAGCAGCUGAAUAUGCGUAUCCACAUCACUAAAAAGCCAAGUAUGCCCUUUGUCGGGAUAAUAGGCGCAUUCAGACCUAACAUUUUUCUGUGCCAACCUGCGGUGGCAGUCAUGAAUGGUUUCGGCUUCUUUUCCACCUGAGACAAAGAAAGCAGGAUUAUCAAAAUUUAUAUCAAUCAUAGAUAAAUAUACUCUCC .....(((((((((....(((((((((((((..(((((((....)))...))))...(((((((........................(((...(((.(((......))))))...))).(((((((((...(((......)))((((.((...)))))).))).))))))..))))))))))))))))...))))....)))...))))))...........((((.......))))............ (-57.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAGAGUAUAUUUAUCUAUGAUUGAUAUAAAUUUUGAUAAUCCUGCUUUCUUUGUCUCAGGUGGAAAAGAAGCCGAAACCAUUCAUGACUGCCACCGCAGGUUGGCACAGAAAAAUGUUAGGUCUGAAUGCGCCUAUUAUCCCGACAAAGGGCAUACUUGGCUUUUUAGUGAUGUGGAUACGCAUAUUCAGCUGCUGCGCUAUUUCUUUCAAAACGCUGCCUUUCCCAGAGAAAUUGAAAGGAUUUUGAU ((((((((...(((((...((((......))))..)))))...))))))))..((..(((.((((.((((((((((...((((((.((((((((((...)).)))).((......))...)))))))))).......((((((......))).))).))))))))))....(((((....))))).)))).)))..)).....(((((((((....(((.......))).....)))))))))....... (-64.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 975 70 21 161 112 NC_009009:SSA_1608|5end_hypothetical_protein_1613753..1613983_NEGATIVE 390 180 135 146 93 NC_009009:SSA_1564|5end_Histidine_kinase,_putative_1568615..1568845_NEGATIVE 390 189 141 207 164 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 385 180 135 199 139 NC_009009:SSA_0317|5end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311259..311489_POSITIVE 379 189 141 169 123 NC_009009:SSA_1209|5end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1234030..1234260_NEGATIVE 355 183 141 178 124 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 348 62 22 206 160 NC_009009:SSA_0765|5end_hypothetical_protein_745519..745749_POSITIVE 344 185 141 106 62 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 339 175 134 143 99 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 338 194 151 105 50 NC_009009:SSA_1628|5end_MutT/nudix_family_protein,_putative_1629864..1630094_POSITIVE 334 180 136 165 101 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 334 100 51 57 4 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 332 130 87 53 9 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 329 194 152 168 123 NC_009009:SSA_1463|5end_Shikimate_kinase,_putative_1470240..1470470_NEGATIVE 326 190 141 49 1 NC_009009:SSA_0356|5end_Dipeptidase,_putative_349259..349489_POSITIVE 322 188 141 222 171 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 318 188 142 226 168 NC_009009:SSA_1383|5end_Aspartate_aminotransferase,_putative_1401718..1401948_NEGATIVE 317 208 161 51 1 NC_009009:SSA_2107|5end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2111106..2111336_NEGATIVE 312 200 151 120 58 NC_009009:SSA_1942|5end_Enoyl-CoA_hydratase/carnithine_racemase,_putative_1928496..1928726_NEGATIVE 312 100 54 56 1 NC_009009:SSA_1413|5end_GufA-like_protein,_putative_1424919..1425149_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 175 134 146 102 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 337 178 135 151 100 NC_009009:SSA_1565|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1568608..1568758_NEGATIVE 308 209 161 145 93 NC_009009:SSA_1173|3end_Lipoate_protein_ligase_A,_putative_1200092..1200242_NEGATIVE 307 63 21 47 5 NC_009009:SSA_0626|3end_hypothetical_protein_617212..617362_POSITIVE 307 199 152 70 14 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 304 70 22 66 6 NC_009009:SSA_0867|3end_hypothetical_protein_860711..860861_POSITIVE 296 186 141 91 41 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 295 182 144 120 79 NC_009009:SSA_2048|3end_Serine_acetyltransferase,_putative_2049984..2050134_NEGATIVE 290 131 97 149 118 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 289 185 142 144 96 NC_009009:SSA_0536|3end_B12-dependent_diol_dehydratase_small_subunit,_putative_531937..532087_POSITIVE 288 188 142 78 24 NC_009009:SSA_1931|3end_Acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta,_putative_1918544..1918694_NEGATIVE 288 209 161 63 21 NC_009009:SSA_0307|3end_Glutamine_synthetase_type_1,_putative_304413..304563_POSITIVE 287 59 11 113 50 NC_009009:SSA_0806|3end_hypothetical_protein_789478..789628_POSITIVE 286 144 101 90 43 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 286 70 23 148 104 NC_009009:SSA_1569|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1572630..1572780_POSITIVE 286 62 22 71 27 NC_009009:SSA_1463|3end_Shikimate_kinase,_putative_1469764..1469914_NEGATIVE 284 193 154 45 13 NC_009009:SSA_0591|3end_Conserved_uncharacterized_protein_583694..583844_POSITIVE 283 197 152 124 72 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 282 130 86 47 1 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 280 126 84 89 47 NC_009009:SSA_0849|3end_Signal_peptidase_I,_putative_836764..836914_POSITIVE