Origin IGS: tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagaaaaaaagccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagattgtgtcagttttgtgacagagacctaacaaactatttcaagtaaccgagtttgttacaaggaatagacagttctgttaaataggcccgagagggctttttttctgcattttttgtgttatcatagacaggtactcatttgaaaggaatttgaaaga Mask Tandem Repeat Region ================================================ tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagaaaaaaagccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt Find is-nt database================================================ Query_seq: SMT_1128:SMT_1129|SMT_1128:SMT_1129:surface antigen:hypothetical protein:<-<-:1063231..1063392 162 tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagaaaaaaagccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1128:SMT_1129|SMT_1128:SMT_1129:surface antigen:hypothetical protein:<-<-:1063231..1063392 162 tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagaaaaaaagccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1128:SMT_1129|SMT_1128:SMT_1129:surface antigen:hypothetical protein:<-<-:1063231..1063392 162 tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagaaaaaaagccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagaaaaaaagccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt Predict ORF larger than 30AA ================================================ tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagaaaaaaagccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt 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================================================ tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagaaaaaaagccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -7.2 Tail_Score: -5.68039 Start: 62 End: 73 Full_Region: agttctgttaaatag gccc gaga gggc tttttttctgcattt .............................................................gcccgagagggc......................................................................................... Find igs database================================================ Query_seq: SMT_1128:SMT_1129|SMT_1128:SMT_1129:surface antigen:hypothetical protein:<-<-:1063231..1063392 162 tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagaaaaaaagccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt Intra-Species Hit: Count: 1 Min: 1 Max: 162 Len: 162 Subject: smit_SMT_1128_SMT_1129|surface antigen:hypothetical protein|NEGATIVE:NEGATIVE|[1063231,1063392]|162 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 162 Query Start:1 Query End:162 Subject Strand: POSITIVE Subject Start: 1 Subject End: 162 tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagnnnnnnngccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagaaaaaaagccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt Inter-species Hit: Count: 3 Min: 1 Max: 162 Len: 162 Subject: NC_008533_SPD_1874_SPD_1875|LysM domain protein:hydrolase, haloacid dehalogenase-like family protein|NEGATIVE:NEGATIVE|[1853200,1853364]|165 HSP 1 e-value: 8.0E-70 bit: 264.0 Len: 162 Query Start:1 Query End:162 Subject Strand: POSITIVE Subject Start: 1 Subject End: 162 tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagnnnnnnngccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgtagaaaaaaagccctctcgggcctatttaacagaactgtctattccttgtaacaaactaggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt Subject: NC_003098_spr1875_spr1876|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1845668,1845832]|165 HSP 1 e-value: 8.0E-70 bit: 264.0 Len: 162 Query Start:1 Query End:162 Subject Strand: POSITIVE Subject Start: 1 Subject End: 162 tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagnnnnnnngccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgtagaaaaaaagccctctcgggcctatttaacagaactgtctattccttgtaacaaactaggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt Subject: NC_003028_SP_2063_SP_2064|LysM domain-containing protein:hydrolase, haloacid dehalogenase-like family|NEGATIVE:NEGATIVE|[1964747,1964911]|165 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 162 Query Start:1 Query End:162 Subject Strand: POSITIVE Subject Start: 1 Subject End: 162 tctttcaaattcctttcaaatgagtacctgtctatgataacacaaaaaatgcagnnnnnnngccctctcgggcctatttaacagaactgtctattccttgtaacaaactcggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt tctttcaaattcctttcaaatgagtacctgtctatcataacacaaaaaatgtagaaaaaaagccctctcgggcctatttaacagaactgtctattccttgtaacaaactaggttacttgaaatagtttgttaggtctctgtcacaaaactgacacaatcttt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUCAAAUUCCUUUCAAAUGAGUACCUGUCUAUGAUAACACAAAAAAUGCAGAAAAAAAGCCCUCUCGGGCCUAUUUAACAGAACUGUCUAUUCCUUGUAACAAACUCGGUUACUUGAAAUAGUUUGUUAGGUCUCUGUCACAAAACUGACACAAUCUUU .....................(((.(((((...............................((((....))))..........(((((((...(((...(((((.......)))))..))))))))))..)))))))).((((......))))......... (-27.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAUUGUGUCAGUUUUGUGACAGAGACCUAACAAACUAUUUCAAGUAACCGAGUUUGUUACAAGGAAUAGACAGUUCUGUUAAAUAGGCCCGAGAGGGCUUUUUUUCUGCAUUUUUUGUGUUAUCAUAGACAGGUACUCAUUUGAAAGGAAUUUGAAAGA .....((.(((((......))))).))......((((...((((((((.(((..((((((((((((((((.(.(((.......(((.((((((....)))))).))).)))))))))))))).....)))))).)))....))))))))....))))..... (-37.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 920 110 61 201 152 smit:SMT_1128|5end_surface_antigen_1063140..1063370_NEGATIVE 273 110 61 101 53 smit:SMT_611|5end_aspartate-semialdehyde_dehydrogenase_522492..522722_POSITIVE 266 106 61 160 121 smit:SMT_1897|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1848858..1849088_NEGATIVE 258 93 61 45 6 smit:SMT_514|5end_tRNA_(guanine-N(1)-)-methyltransferase_441377..441607_POSITIVE 257 138 96 87 42 smit:SMT_1788|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1765029..1765259_NEGATIVE 257 138 96 201 156 smit:SMT_1787|5end_phosphoribosylformylglycinamidine_synthase_1764915..1765145_NEGATIVE 257 138 96 87 42 smit:SMT_1197|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1158751..1158981_NEGATIVE 257 138 96 201 156 smit:SMT_1196|5end_phosphoribosylformylglycinamidine_synthase_1158637..1158867_NEGATIVE 252 100 59 92 56 smit:SMT_1160|5end_K03152_4-methyl-5(b-hydroxyethyl)-thiazole_monophosphate_biosynthesis_1105174..1105404_NEGATIVE 252 68 21 192 137 smit:SMT_633|5end_hypothetical_protein_539660..539890_NEGATIVE 243 110 61 199 145 smit:SMT_1538|5end_two-component_response_regulator_YvqC_1523301..1523531_NEGATIVE 239 119 89 37 11 smit:SMT_1619|5end_K02006_cobalt_transport_system_ATP-binding_protein_1606526..1606756_NEGATIVE 237 100 51 83 30 smit:SMT_1609|5end_hypothetical_protein_1598113..1598343_POSITIVE 234 110 61 64 10 smit:SMT_1530|5end_K07456_DNA_mismatch_repair_protein_MutS2_1515346..1515576_NEGATIVE 231 92 60 206 159 smit:SMT_1331|5end_hypothetical_protein_1306236..1306466_NEGATIVE 230 101 67 231 190 smit:SMT_154|5end_K03647_protein_involved_in_ribonucleotide_reduction_101930..102160_POSITIVE 229 121 82 63 19 smit:SMT_549|5end_hypothetical_cytosolic_protein_467057..467287_POSITIVE 227 158 114 58 1 smit:SMT_1275|5end_rod_shape-determining_protein_MreC_1238594..1238824_POSITIVE 226 120 86 63 27 smit:SMT_1510|5end_ribose_5-phosphate_isomerase_1493488..1493718_NEGATIVE 222 95 62 60 18 smit:SMT_1529|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1512880..1513110_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 106 61 141 102 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 258 93 61 55 16 smit:SMT_513|3end_16S_rRNA_processing_protein_RimM_441467..441617_POSITIVE 257 138 96 146 101 smit:SMT_1788|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1764970..1765120_NEGATIVE 257 138 96 146 101 smit:SMT_1197|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1158692..1158842_NEGATIVE 252 100 59 81 45 smit:SMT_1161|3end_K05837_rod_shape_determining_protein_RodA_1105185..1105335_NEGATIVE 245 92 52 111 64 smit:SMT_724|3end_hypothetical_protein_629770..629920_NEGATIVE 238 119 71 138 89 smit:SMT_1021|3end_K05846_osmoprotectant_transport_system_permease_protein_956479..956629_NEGATIVE 237 100 51 86 33 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 221 118 71 45 6 smit:SMT_1650|3end_ribonuclease_III_1637087..1637237_POSITIVE 220 100 52 147 99 smit:SMT_1734|3end_serine/threonine_protein_phosphatase_1719366..1719516_POSITIVE 218 144 107 140 89 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 217 139 93 150 100 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 215 97 61 50 12 smit:SMT_399|3end_cytochrome_c-type_biogenesis_protein_CcdA_329156..329306_POSITIVE 213 150 104 73 19 smit:SMT_1377|3end_hypothetical_protein_1355556..1355706_NEGATIVE 211 160 111 57 9 smit:SMT_1499|3end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483425..1483575_POSITIVE 211 65 27 52 15 smit:SMT_1486|3end_hypothetical_protein_1466444..1466594_POSITIVE 211 110 61 70 18 smit:SMT_665|3end_NAD+_kinase_575927..576077_NEGATIVE 210 120 71 102 58 smit:SMT_1500|3end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1484426..1484576_POSITIVE 209 58 22 49 8 smit:SMT_1016|3end_alcohol_dehydrogenase,_zinc-containing_953057..953207_NEGATIVE 208 153 111 58 7 smit:SMT_2125|3end_3-phosphoshikimate_1-carboxyvinyltransferase_2009098..2009248_POSITIVE