Origin IGS: tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaactttccagcacactgnnnnnttaattaattaannnnnaaagattgcaaaaatcaaggcatagac .........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 gtctatgccttgatttttgcaatctttnnnnnttaattaattaannnnncagtgtgctggaaagttgaactttgggtacaaaaataatgtacaaaaaacgagaatatatagagctttttgattgactaattttaaaaatatatggtagaatcgggttatgaatattgtgttgttgtttcgttaaagaaggtgttctttagcaggaaaggcagggaatatgaagaactccaaccttattctaaatcaacatatatataaaaaaggagaaaaa Mask Tandem Repeat Region ================================================ tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaactttccagcacactgnnnnnttaattaattaannnnnaaagattgcaaaaatcaaggcatagac Find is-nt database================================================ Query_seq: SMT_1962:SMT_1963|SMT_1962:SMT_1963:hypothetical protein predicted by Glimmer/Critica:ribonuclease BN, putative:<-<-:1895730..1896000 271 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaactttccagcacactgnnnnnttaattaattaannnnnaaagattgcaaaaatcaaggcatagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1962:SMT_1963|SMT_1962:SMT_1963:hypothetical protein predicted by Glimmer/Critica:ribonuclease BN, putative:<-<-:1895730..1896000 271 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaactttccagcacactgnnnnnttaattaattaannnnnaaagattgcaaaaatcaaggcatagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1962:SMT_1963|SMT_1962:SMT_1963:hypothetical protein predicted by Glimmer/Critica:ribonuclease BN, putative:<-<-:1895730..1896000 271 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaactttccagcacactgnnnnnttaattaattaannnnnaaagattgcaaaaatcaaggcatagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaactttccagcacactgnnnnnttaattaattaannnnnaaagattgcaaaaatcaaggcatagac Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 109 End: 228 ............................................................................................................ M H N P I L P Y I F K I S Q S K S S I Y S R F L Y I I F V P K V Q L S S T L X X ........................................... Protein_Len: 42 Strand: + Start: 107 End: 232 .......................................................................................................... M F I T R F Y H I F L K L V N Q K A L Y I L V F C T L F L Y P K F N F P A H X X X N ....................................... Protein_Len: 38 Strand: - Start: 17 End: 130 ................ I Y T S K S Y P Q L E E Y E R G K R S F F V K K L S V V V C Y E Y G S E V M ............................................................................................................................................. tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaactttccagcacactgnnnnnttaattaattaannnnnaaagattgcaaaaatcaaggcatagac 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================================================ tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaactttccagcacactgnnnnnttaattaattaannnnnaaagattgcaaaaatcaaggcatagac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1962:SMT_1963|SMT_1962:SMT_1963:hypothetical protein predicted by Glimmer/Critica:ribonuclease BN, putative:<-<-:1895730..1896000 271 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaactttccagcacactgnnnnnttaattaattaannnnnaaagattgcaaaaatcaaggcatagac Intra-Species Hit: Count: 2 Min: 1 Max: 271 Len: 271 Subject: smit_SMT_1962_SMT_1963|hypothetical protein predicted by Glimmer/Critica:ribonuclease BN, putative|NEGATIVE:NEGATIVE|[1895730,1896000]|271 HSP 1 e-value: 1.0E-134 bit: 478.0 Len: 271 Query Start:1 Query End:271 Subject Strand: POSITIVE Subject Start: 1 Subject End: 271 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaactttccagcacactgnnnnnttaattaattaannnnnaaagattgcaaaaatcaaggcatagac tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaactttccagcacactgnnnnnttaattaattaannnnnaaagattgcaaaaatcaaggcatagac Subject: smit_SMT_823_SMT_824|putative mucus binding protein:asparaginyl-tRNA synthetase|NEGATIVE:NEGATIVE|[746881,747139]|259 HSP 1 e-value: 1.0E-113 bit: 410.0 Len: 207 Query Start:1 Query End:207 Subject Strand: POSITIVE Subject Start: 1 Subject End: 207 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaa................................................................ tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaa................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCUCCUUUUUUAUAUAUAUGUUGAUUUAGAAUAAGGUUGGAGUUCUUCAUAUUCCCUGCCUUUCCUGCUAAAGAACACCUUCUUUAACGAAACAACAACACAAUAUUCAUAACCCGAUUCUACCAUAUAUUUUUAAAAUUAGUCAAUCAAAAAGCUCUAUAUAUUCUCGUUUUUUGUACAUUAUUUUUGUACCCAAAGUUCAACUUUCCAGCACACUGNNNNNUUAAUUAAUUAANNNNNAAAGAUUGCAAAAAUCAAGGCAUAGAC ...........(((((.(((((((......(((((((((((.(((((.......)))))..)))))...((.(((((((....))))))).))...........................)))))).)))))))...)))))...(((...((((((((.............))))))))......(((((((((...((((.....)))).(((....)))............................)))))))))...)))...... (-33.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUAUGCCUUGAUUUUUGCAAUCUUUNNNNNUUAAUUAAUUAANNNNNCAGUGUGCUGGAAAGUUGAACUUUGGGUACAAAAAUAAUGUACAAAAAACGAGAAUAUAUAGAGCUUUUUGAUUGACUAAUUUUAAAAAUAUAUGGUAGAAUCGGGUUAUGAAUAUUGUGUUGUUGUUUCGUUAAAGAAGGUGUUCUUUAGCAGGAAAGGCAGGGAAUAUGAAGAACUCCAACCUUAUUCUAAAUCAACAUAUAUAUAAAAAAGGAGAAAAA .((((((.((((.((((((..............(((....))).........((((((.(((........))).))))))...........)))))).))))....)))))).............((..((((....(((((((.((((((.(((((....(((((.(.((((..(((((((((((((....))))))))).))))..)))).))))))..........))))).))))))......)))))))....))))..))..... (-46.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 877 90 41 181 132 smit:SMT_1962|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1895639..1895869_NEGATIVE 877 90 41 181 132 smit:SMT_823|5end_putative_mucus_binding_protein_746790..747020_NEGATIVE 295 222 196 223 199 smit:SMT_1971|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1903282..1903512_POSITIVE 288 222 187 84 50 smit:SMT_1961|5end_K07485_transposase_1894206..1894436_POSITIVE 284 222 190 227 193 smit:SMT_1985|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1914571..1914801_NEGATIVE 279 74 46 113 83 smit:SMT_1658|5end_hypothetical_protein_1648201..1648431_POSITIVE 279 99 51 116 61 smit:SMT_807|5end_hypothetical_protein_predicted_by_Glimmer/Critica_716815..717045_NEGATIVE 278 222 186 128 91 smit:SMT_1954|5end_6-phospho-beta-glucosidase_1888548..1888778_POSITIVE 276 222 200 119 99 smit:SMT_1944|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1879494..1879724_NEGATIVE 275 222 189 133 104 smit:SMT_1155|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099665..1099895_NEGATIVE 274 222 201 148 125 smit:SMT_2016|5end_tyrosine_recombinase_1933425..1933655_NEGATIVE 270 78 35 171 122 smit:SMT_1260|5end_hypothetical_protein_1225517..1225747_POSITIVE 267 222 195 59 38 smit:SMT_304|5end_hypothetical_protein_246580..246810_POSITIVE 265 222 188 134 107 smit:SMT_1966|5end_DNA_polymerase_III_alpha_subunit_1897934..1898164_POSITIVE 265 76 34 53 14 smit:SMT_1850|5end_K01421_putative_membrane_protein_1815062..1815292_POSITIVE 265 73 31 115 68 smit:SMT_825|5end_aspartate_aminotransferase_749594..749824_NEGATIVE 265 79 33 224 170 smit:SMT_427|5end_hypothetical_protein_predicted_by_Glimmer/Critica_368812..369042_POSITIVE 259 77 39 45 2 smit:SMT_2039|5end_malolactic_enzyme_1950427..1950657_NEGATIVE 256 77 38 173 113 smit:SMT_2071|5end_phosphoenolpyruvate_carboxylase_1975887..1976117_NEGATIVE 256 222 187 116 84 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 524 207 170 38 1 smit:SMT_824|3end_asparaginyl-tRNA_synthetase_747050..747200_NEGATIVE 278 60 22 147 108 smit:SMT_478|3end_hypothetical_protein_predicted_by_Glimmer/Critica_415257..415407_POSITIVE 272 70 21 67 11 smit:SMT_341|3end_ThiJ/PfpI_family_protein_281681..281831_POSITIVE 265 73 31 118 71 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 265 79 33 136 82 smit:SMT_426|3end_hypothetical_protein_368804..368954_POSITIVE 262 83 41 72 11 smit:SMT_1604|3end_K05833_putative_ABC_transport_system_ATP-binding_protein_1595163..1595313_POSITIVE 256 77 38 80 20 smit:SMT_2072|3end_exonuclease_RexA_1975980..1976130_NEGATIVE 256 239 194 98 58 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 255 87 45 151 93 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 254 77 35 151 103 smit:SMT_1259|3end_hypothetical_protein_1225578..1225728_POSITIVE 252 222 195 55 31 smit:SMT_1929|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1869690..1869840_NEGATIVE 247 218 181 77 39 smit:SMT_1937|3end_glycosyl_transferase,_family_2_1875422..1875572_POSITIVE 242 79 39 150 107 smit:SMT_214|3end_leucyl-tRNA_synthetase_147066..147216_POSITIVE 241 73 49 134 100 smit:SMT_909|3end_type_I_restriction_enzyme_M_protein_857223..857373_NEGATIVE 237 70 29 106 65 smit:SMT_2164|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2038759..2038909_POSITIVE 236 222 192 46 19 smit:SMT_955|3end_acyltransferase_family_protein_904703..904853_POSITIVE 232 87 42 139 79 smit:SMT_552|3end_DNA_polymerase_III,_gamma_and_tau_subunits_471180..471330_POSITIVE 231 222 187 70 38 smit:SMT_302|3end_K07444_putative_N6-adenine-specific_DNA_methylase_245319..245469_POSITIVE 230 78 36 147 103 smit:SMT_852|3end_K03978_GTP-binding_protein_797457..797607_NEGATIVE 229 72 38 63 25 smit:SMT_1920|3end_ABC_transporter,_ATP-binding_protein_1862736..1862886_NEGATIVE