Origin IGS: tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaaaaaaagaagggatttaccttctttttattataataacttttttattttattt .........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 aaataaaataaaaaagttattataataaaaagaaggtaaatcccttctttttttgaactttgggtacaaaaataatgtacaaaaaacgagaatatatagagctttttgattgactaattttaaaaatatatggtagaatcgggttatgaatattgtgttgttgtttcgttaaagaaggtgttctttagcaggaaaggcagggaatatgaagaactccaaccttattctaaatcaacatatatataaaaaaggagaaaaa Mask Tandem Repeat Region ================================================ tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaaaaaaagaagggatttaccttctttttattataataacttttttattttattt Find is-nt database================================================ Query_seq: SMT_823:SMT_824|SMT_823:SMT_824:putative mucus binding protein:asparaginyl-tRNA synthetase:<-<-:746881..747139 259 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaaaaaaagaagggatttaccttctttttattataataacttttttattttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_823:SMT_824|SMT_823:SMT_824:putative mucus binding protein:asparaginyl-tRNA synthetase:<-<-:746881..747139 259 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaaaaaaagaagggatttaccttctttttattataataacttttttattttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_823:SMT_824|SMT_823:SMT_824:putative mucus binding protein:asparaginyl-tRNA synthetase:<-<-:746881..747139 259 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaaaaaaagaagggatttaccttctttttattataataacttttttattttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaaaaaaagaagggatttaccttctttttattataataacttttttattttattt Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 109 End: 237 ............................................................................................................ 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 K K K G F T F F L L ...................... Protein_Len: 36 Strand: + Start: 150 End: 257 ..................................................................................................................................................... M K K L Y I F S F F V H Y F C T Q S S K K E G I Y L L F I I I T F L F Y .. Protein_Len: 51 Strand: + Start: 107 End: 259 .......................................................................................................... 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 K K R R D L P S F Y Y N N F F I L F 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 ................................................................................................................................. tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaaaaaaagaagggatttaccttctttttattataataacttttttattttattt 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================================================ tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaaaaaaagaagggatttaccttctttttattataataacttttttattttattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 60 HP_score: -5.7 Tail_Score: -3.4745 Start: 207 End: 234 Full_Region: TGTACCCAAAGTTCA AAAAAAGAAGG GATTTA CCTTCTTTTTA TTATAATAACTTTTT ..............................................................................................................................................................................................................AAAAAAGAAGGGATTTACCTTCTTTTTA......................... TransTerm Strand: + Conf: 77 HP_score: -4.7 Tail_Score: -5.22006 Start: 213 End: 228 Full_Region: CAAAGTTCAAAAAAA GAAGG GATTTA CCTTC TTTTTATTATAATAA ....................................................................................................................................................................................................................GAAGGGATTTACCTTC............................... Find igs database================================================ Query_seq: SMT_823:SMT_824|SMT_823:SMT_824:putative mucus binding protein:asparaginyl-tRNA synthetase:<-<-:746881..747139 259 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaaaaaaagaagggatttaccttctttttattataataacttttttattttattt Intra-Species Hit: Count: 2 Min: 1 Max: 228 Len: 228 Subject: smit_SMT_823_SMT_824|putative mucus binding protein:asparaginyl-tRNA synthetase|NEGATIVE:NEGATIVE|[746881,747139]|259 HSP 1 e-value: 1.0E-114 bit: 410.0 Len: 228 Query Start:1 Query End:228 Subject Strand: POSITIVE Subject Start: 1 Subject End: 228 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcnnnnnnngaagggatttaccttc............................... tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttcaaaaaaagaagggatttaccttc............................... 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-112 bit: 406.0 Len: 205 Query Start:1 Query End:205 Subject Strand: POSITIVE Subject Start: 1 Subject End: 205 tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttc...................................................... tttttctccttttttatatatatgttgatttagaataaggttggagttcttcatattccctgcctttcctgctaaagaacaccttctttaacgaaacaacaacacaatattcataacccgattctaccatatatttttaaaattagtcaatcaaaaagctctatatattctcgttttttgtacattatttttgtacccaaagttc...................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCUCCUUUUUUAUAUAUAUGUUGAUUUAGAAUAAGGUUGGAGUUCUUCAUAUUCCCUGCCUUUCCUGCUAAAGAACACCUUCUUUAACGAAACAACAACACAAUAUUCAUAACCCGAUUCUACCAUAUAUUUUUAAAAUUAGUCAAUCAAAAAGCUCUAUAUAUUCUCGUUUUUUGUACAUUAUUUUUGUACCCAAAGUUCAAAAAAAGAAGGGAUUUACCUUC ......(((((((((.......(((((...(((...(((((.(((((.......)))))..)))))..))).(((((((....)))))))......)))))....................................(((((.((((....((((((((.............))))))))...)))).))))).................)))))))))......... (-33.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGGUAAAUCCCUUCUUUUUUUGAACUUUGGGUACAAAAAUAAUGUACAAAAAACGAGAAUAUAUAGAGCUUUUUGAUUGACUAAUUUUAAAAAUAUAUGGUAGAAUCGGGUUAUGAAUAUUGUGUUGUUGUUUCGUUAAAGAAGGUGUUCUUUAGCAGGAAAGGCAGGGAAUAUGAAGAACUCCAACCUUAUUCUAAAUCAACAUAUAUAUAAAAAAGGAGAAAAA (((((......)))))..((((((...(((..(((((.......)))))..))).)))))).........((((((..((((......))))..(((((((.((((((.(((((....(((((.(.((((..(((((((((((((....))))))))).))))..)))).))))))..........))))).))))))......)))))))...))))))........ (-42.84) 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 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 270 78 35 171 122 smit:SMT_1260|5end_hypothetical_protein_1225517..1225747_POSITIVE 268 218 172 195 156 smit:SMT_107|5end_ribose-phosphate_pyrophosphokinase_52402..52632_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 255 87 45 153 95 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 250 70 26 196 142 smit:SMT_1393|5end_hypothetical_protein_1369106..1369336_POSITIVE 242 79 39 209 166 smit:SMT_215|5end_leucyl-tRNA_synthetase_147045..147275_POSITIVE 242 66 25 146 109 smit:SMT_156|5end_hypothetical_protein_102869..103099_POSITIVE 241 73 49 127 93 smit:SMT_908|5end_hypothetical_protein_857230..857460_NEGATIVE 238 79 39 41 1 smit:SMT_653|5end_positive_transcriptional_regulator_MutR_family_564155..564385_NEGATIVE 237 70 29 108 67 smit:SMT_2165|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2038681..2038911_POSITIVE 236 73 43 214 183 smit:SMT_876|5end_hypothetical_protein_predicted_by_Glimmer/Critica_823502..823732_NEGATIVE 232 87 42 167 107 smit:SMT_553|5end_hypothetical_protein_471128..471358_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 207 182 26 1 smit:SMT_1963|3end_ribonuclease_BN,_putative_1895911..1896061_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 268 218 172 49 10 smit:SMT_106|3end_hypothetical_protein_52336..52486_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 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 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 232 87 42 139 79 smit:SMT_552|3end_DNA_polymerase_III,_gamma_and_tau_subunits_471180..471330_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 229 79 38 39 2 smit:SMT_654|3end_K06158_ATP-binding_cassette,_sub-family_F,_member_3_564157..564307_NEGATIVE 229 74 33 58 7 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE 228 74 37 54 10 smit:SMT_109|3end_beta-galactosidase_57523..57673_POSITIVE 225 83 42 138 79 smit:SMT_1627|3end_hypothetical_protein_1616089..1616239_NEGATIVE