Origin IGS: ctgcctttttgacaaacactggaaagacaatactaattcattgtaccatatcgactattaaaaaactataggaatgctcagagggttttatcataaaaaggagaaagaagacgctaagccttctctctcctattgatacgcaaaacaggtcaaaagatgacctaaaaatcattgaacaaattaagctcttctattttgacaaaaag .........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 ctttttgtcaaaatagaagagcttaatttgttcaatgatttttaggtcatcttttgacctgttttgcgtatcaataggagagagaaggcttagcgtcttctttctcctttttatgataaaaccctctgagcattcctatagttttttaatagtcgatatggtacaatgaattagtattgtctttccagtgtttgtcaaaaaggcag Mask Tandem Repeat Region ================================================ ctgcctttttgacaaacactggaaagacaatactaattcattgtaccatatcgactattaaaaaactataggaatgctcagagggttttatcataaaaaggagaaagaagacgctaagccttctctctcctattgatacgcaaaacaggtcaaaagatgacctaaaaatcattgaacaaattaagctcttctattttgacaaaaag Find is-nt database================================================ Query_seq: SSA_1666:SSA_1667|SSA_1666:SSA_1667:Collagen-binding surface protein, putative:hypothetical protein:<-<-:1667403..1667608 206 ctgcctttttgacaaacactggaaagacaatactaattcattgtaccatatcgactattaaaaaactataggaatgctcagagggttttatcataaaaaggagaaagaagacgctaagccttctctctcctattgatacgcaaaacaggtcaaaagatgacctaaaaatcattgaacaaattaagctcttctattttgacaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1666:SSA_1667|SSA_1666:SSA_1667:Collagen-binding surface protein, putative:hypothetical protein:<-<-:1667403..1667608 206 ctgcctttttgacaaacactggaaagacaatactaattcattgtaccatatcgactattaaaaaactataggaatgctcagagggttttatcataaaaaggagaaagaagacgctaagccttctctctcctattgatacgcaaaacaggtcaaaagatgacctaaaaatcattgaacaaattaagctcttctattttgacaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1666:SSA_1667|SSA_1666:SSA_1667:Collagen-binding surface protein, putative:hypothetical protein:<-<-:1667403..1667608 206 ctgcctttttgacaaacactggaaagacaatactaattcattgtaccatatcgactattaaaaaactataggaatgctcagagggttttatcataaaaaggagaaagaagacgctaagccttctctctcctattgatacgcaaaacaggtcaaaagatgacctaaaaatcattgaacaaattaagctcttctattttgacaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgcctttttgacaaacactggaaagacaatactaattcattgtaccatatcgactattaaaaaactataggaatgctcagagggttttatcataaaaaggagaaagaagacgctaagccttctctctcctattgatacgcaaaacaggtcaaaagatgacctaaaaatcattgaacaaattaagctcttctattttgacaaaaag Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 90 End: 206 ......................................................................................... M I K R R K K T L S L L S P I D T Q N R S K D D L K I I E Q I K L F Y F D K K Protein_Len: 47 Strand: - Start: 41 End: 181 ........................................ Q V M D V I L F S Y S H E S P K I M F L L F F V S L R R E G I S V C F L D F S S R F I M S C M ......................... ctgcctttttgacaaacactggaaagacaatactaattcattgtaccatatcgactattaaaaaactataggaatgctcagagggttttatcataaaaaggagaaagaagacgctaagccttctctctcctattgatacgcaaaacaggtcaaaagatgacctaaaaatcattgaacaaattaagctcttctattttgacaaaaag 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================================================ ctgcctttttgacaaacactggaaagacaatactaattcattgtaccatatcgactattaaaaaactataggaatgctcagagggttttatcataaaaaggagaaagaagacgctaagccttctctctcctattgatacgcaaaacaggtcaaaagatgacctaaaaatcattgaacaaattaagctcttctattttgacaaaaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 54 HP_score: -5.7 Tail_Score: -3.14132 Start: 98 End: 132 Full_Region: GGGTTTTATCATAAA AAGGAGAAAGAAGAC GCTAA GCCTTCTCTCTCCTA TTGATACGCAAAACA .................................................................................................AAGGAGAAAGAAGACGCTAAGCCTTCTCTCTCCTA.......................................................................... TransTerm Strand: + Conf: 68 HP_score: -8.3 Tail_Score: -3.13403 Start: 100 End: 130 Full_Region: GTTTTATCATAAAAA GGAGAAAGAAGAC GCTAA GCCTTCTCTCTCC TATTGATACGCAAAA ...................................................................................................GGAGAAAGAAGACGCTAAGCCTTCTCTCTCC............................................................................ TransTerm Strand: - Conf: 100 HP_score: -12.7 Tail_Score: -4.91109 Start: 100 End: 130 Full_Region: ttttgcgtatcaata ggagagagaaggc ttagc gtcttctttctcc tttttatgataaaac ...................................................................................................ggagagagaaggcttagcgtcttctttctcc............................................................................ TransTerm Strand: - Conf: 66 HP_score: -5.3 Tail_Score: -4.24204 Start: 146 End: 164 Full_Region: ttgttcaatgatttt taggtca tcttt tgacctg ttttgcgtatcaata .................................................................................................................................................taggtcatcttttgacctg.......................................... Find igs database================================================ Query_seq: SSA_1666:SSA_1667|SSA_1666:SSA_1667:Collagen-binding surface protein, putative:hypothetical protein:<-<-:1667403..1667608 206 ctgcctttttgacaaacactggaaagacaatactaattcattgtaccatatcgactattaaaaaactataggaatgctcagagggttttatcataaaaaggagaaagaagacgctaagccttctctctcctattgatacgcaaaacaggtcaaaagatgacctaaaaatcattgaacaaattaagctcttctattttgacaaaaag Intra-Species Hit: Count: 1 Min: 1 Max: 206 Len: 206 Subject: NC_009009_SSA_1666_SSA_1667|Collagen-binding surface protein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1667403,1667608]|206 HSP 1 e-value: 1.0E-113 bit: 408.0 Len: 206 Query Start:1 Query End:206 Subject Strand: POSITIVE Subject Start: 1 Subject End: 206 ctgcctttttgacaaacactggaaagacaatactaattcattgtaccatatcgactattaaaaaactataggaatgctcagagggttttatcataaaaaggagaaagaagacgctaagccttctctctcctattgatacgcaaaacaggtcaaaagatgacctaaaaatcattgaacaaattaagctcttctattttgacaaaaag ctgcctttttgacaaacactggaaagacaatactaattcattgtaccatatcgactattaaaaaactataggaatgctcagagggttttatcataaaaaggagaaagaagacgctaagccttctctctcctattgatacgcaaaacaggtcaaaagatgacctaaaaatcattgaacaaattaagctcttctattttgacaaaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGCCUUUUUGACAAACACUGGAAAGACAAUACUAAUUCAUUGUACCAUAUCGACUAUUAAAAAACUAUAGGAAUGCUCAGAGGGUUUUAUCAUAAAAAGGAGAAAGAAGACGCUAAGCCUUCUCUCUCCUAUUGAUACGCAAAACAGGUCAAAAGAUGACCUAAAAAUCAUUGAACAAAUUAAGCUCUUCUAUUUUGACAAAAAG ....(((((((.((((...(((....(((((........))))).)))...................((((((..(((......(((((((((.....((((((.(((((.(.....).))))).))))))..)))))........((((((.....))))))..........))))......)))..)))))))))).))))))) (-43.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUUGUCAAAAUAGAAGAGCUUAAUUUGUUCAAUGAUUUUUAGGUCAUCUUUUGACCUGUUUUGCGUAUCAAUAGGAGAGAGAAGGCUUAGCGUCUUCUUUCUCCUUUUUAUGAUAAAACCCUCUGAGCAUUCCUAUAGUUUUUUAAUAGUCGAUAUGGUACAAUGAAUUAGUAUUGUCUUUCCAGUGUUUGUCAAAAAGGCAG (((((((.((((...((((((((.....((((((.........((((((.....))))))((((((((((.....((((((((((((((.....))))))))))))))...)))).))))))....)))))).......))))))))...........(((.((((((......))))))....)))...)))).))))))).... (-61.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 891 120 71 211 162 NC_009009:SSA_1666|5end_Collagen-binding_surface_protein,_putative_1667312..1667542_NEGATIVE 300 129 81 207 165 NC_009009:SSA_0302|5end_Phosphoglycerate_kinase,_putative_294890..295120_POSITIVE 290 129 81 161 114 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 284 149 101 51 11 NC_009009:SSA_0086|5end_V-type_sodium_ATPase,_subunit_K,_putative_87839..88069_POSITIVE 282 120 74 72 21 NC_009009:SSA_2103|5end_hypothetical_protein_2106700..2106930_NEGATIVE 280 139 98 196 144 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 275 120 75 65 12 NC_009009:SSA_0708|5end_hypothetical_protein_694144..694374_POSITIVE 266 160 113 81 33 NC_009009:SSA_0049|5end_Dihydroxyacetone_kinase_(Dak1),_putative_53612..53842_POSITIVE 260 136 99 94 50 NC_009009:SSA_0995|5end_Antibiotic-resistance_protein,_alpha/beta_superfamily_hydrolase,_putative_995716..995946_POSITIVE 259 138 101 53 20 NC_009009:SSA_0211|5end_hypothetical_protein_208041..208271_POSITIVE 255 131 102 39 11 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 254 159 113 138 84 NC_009009:SSA_1799|5end_Acetyltransferase,_putative_1781025..1781255_NEGATIVE 252 51 30 135 114 NC_009009:SSA_1985|5end_hypothetical_protein_1981773..1982003_NEGATIVE 252 166 129 77 33 NC_009009:SSA_0782|5end_Proton-translocating_ATPase,_F0_sector,_subunit_c,_putative_766579..766809_POSITIVE 251 160 111 72 8 NC_009009:SSA_2195|5end_ATPase/kinase,_putative_2196743..2196973_NEGATIVE 251 160 111 162 123 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 249 152 113 172 138 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 246 130 89 147 94 NC_009009:SSA_1068|5end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1087355..1087585_POSITIVE 246 170 124 141 98 NC_009009:SSA_0731|5end_Integral_membrane_protein,_putative_715065..715295_POSITIVE 244 134 101 159 127 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 116 73 93 39 NC_009009:SSA_2068|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_2070931..2071081_NEGATIVE 275 101 71 64 31 NC_009009:SSA_1530|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1537510..1537660_NEGATIVE 269 131 99 110 73 NC_009009:SSA_0966|3end_Uridine_kinase,_putative_975790..975940_POSITIVE 259 138 101 56 23 NC_009009:SSA_0210|3end_hypothetical_protein_208124..208274_POSITIVE 254 159 113 126 72 NC_009009:SSA_1800|3end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1781037..1781187_NEGATIVE 247 111 82 34 6 NC_009009:SSA_0167|3end_Hypothetical_protein_(Asparagine/proline-rich)_166335..166485_POSITIVE 246 130 89 57 4 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 244 129 82 89 44 NC_009009:SSA_0774|3end_NADP-dependent_glyceraldehyde-3-phosphate_dehydrogenase,_putative_756075..756225_POSITIVE 243 135 92 89 39 NC_009009:SSA_1207|3end_Phosphate_acetyltransferase,_putative_1231297..1231447_NEGATIVE 241 152 114 143 91 NC_009009:SSA_1314|3end_Fe-S-cluster_oxidoreductase,_putative_1330746..1330896_NEGATIVE 240 156 112 133 69 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 239 119 71 51 7 NC_009009:SSA_0496|3end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_497009..497159_POSITIVE 235 132 91 83 51 NC_009009:SSA_2156|3end_Conserved_uncharacterized_protein_2156216..2156366_NEGATIVE 234 140 101 150 111 NC_009009:SSA_1642|3end_N-acetylglucosamine-1-phosphate_uridyltransferase,_putative_1643103..1643253_NEGATIVE 229 141 107 145 109 NC_009009:SSA_1134|3end_Xanthine_phosphoribosyltransferase,_putative_1160316..1160466_POSITIVE 228 148 106 137 93 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 227 149 113 57 11 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 225 140 99 68 25 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 224 119 75 57 6 NC_009009:SSA_1788|3end_Integral_membrane_protein,_possible_receptor,_putative_1771656..1771806_NEGATIVE 223 128 90 78 37 NC_009009:SSA_1915|3end_hypothetical_protein_1905276..1905426_NEGATIVE