Origin IGS: taatagttctgggaaccatattggttccttttttagcgaaaaaagactagcagacaaaaactgctagtcttttggtattatttcatctatctttgttaaaagaaagaatatttatactcaatgaaaatcaaagagcaaactaggaagctagccgcaggctgtacttgagtacggcaaggtgaagctgacgtggtttgaagagattttcgaagagtatta .........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 taatactcttcgaaaatctcttcaaaccacgtcagcttcaccttgccgtactcaagtacagcctgcggctagcttcctagtttgctctttgattttcattgagtataaatattctttcttttaacaaagatagatgaaataataccaaaagactagcagtttttgtctgctagtcttttttcgctaaaaaaggaaccaatatggttcccagaactatta Mask Tandem Repeat Region ================================================ taatagttctgggaaccatattggttccttttttagcgaaaaaagactagcagacaaaaactgctagtcttttggtattatttcatctatctttgttaaaagaaagaatatttatactcaatgaaaatcaaagagcaaactaggaagctagccgcaggctgtacttgagtacggcaaggtgaagctgacgtggtttgaagagattttcgaagagtatta Find is-nt database================================================ Query_seq: SMT_798:SMT_799|SMT_798:SMT_799:hypothetical protein:hypothetical protein:-><-:707167..707385 219 taatagttctgggaaccatattggttccttttttagcgaaaaaagactagcagacaaaaactgctagtcttttggtattatttcatctatctttgttaaaagaaagaatatttatactcaatgaaaatcaaagagcaaactaggaagctagccgcaggctgtacttgagtacggcaaggtgaagctgacgtggtttgaagagattttcgaagagtatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_798:SMT_799|SMT_798:SMT_799:hypothetical protein:hypothetical protein:-><-:707167..707385 219 taatagttctgggaaccatattggttccttttttagcgaaaaaagactagcagacaaaaactgctagtcttttggtattatttcatctatctttgttaaaagaaagaatatttatactcaatgaaaatcaaagagcaaactaggaagctagccgcaggctgtacttgagtacggcaaggtgaagctgacgtggtttgaagagattttcgaagagtatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_798:SMT_799|SMT_798:SMT_799:hypothetical protein:hypothetical protein:-><-:707167..707385 219 taatagttctgggaaccatattggttccttttttagcgaaaaaagactagcagacaaaaactgctagtcttttggtattatttcatctatctttgttaaaagaaagaatatttatactcaatgaaaatcaaagagcaaactaggaagctagccgcaggctgtacttgagtacggcaaggtgaagctgacgtggtttgaagagattttcgaagagtatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 103 Max: 217 Len: 115 Subject: UniRef90_Q04I61 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 9.0E-6 bit: 37.4 Len: 63 Query Start:103 Query End:165 Subject Strand: null Subject Start: 20 Subject End: 40 ...................................................................................................... K E Y L Y S M K I K E Q T R K L A A G C T ...................................................... ...................................................................................................... K I F L Y S M K I K V Q T R K L A A G C S ...................................................... HSP 2 e-value: 9.0E-6 bit: 33.9 Len: 48 Query Start:170 Query End:217 Subject Strand: null Subject Start: 58 Subject End: 73 ......................................................................................................................................................................... Y G K V K L T W F E E I F E E Y .. ......................................................................................................................................................................... Y G K A T L T W F E E I F E K Y .. taatagttctgggaaccatattggttccttttttagcgaaaaaagactagcagacaaaaactgctagtcttttggtattatttcatctatctttgttaaaagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnta Predict ORF larger than 30AA ================================================ taatagttctgggaaccatattggttccttttttagcgaaaaaagactagcagacaaaaactgctagtcttttggtattatttcatctatctttgttaaaagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnta 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================================================ taatagttctgggaaccatattggttccttttttagcgaaaaaagactagcagacaaaaactgctagtcttttggtattatttcatctatctttgttaaaagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 75 HP_score: -10.2 Tail_Score: -2.7614 Start: 40 End: 74 Full_Region: TTCCTTTTTTAGCGA AAAAAGACTAGCAG ACAAAAA CTGCTAGTCTTTTG GTATTATTTCATCTA .......................................AAAAAGACTAGCAGACAAAAACTGCTAGTCTTTTG................................................................................................................................................. TransTerm Strand: + Conf: 91 HP_score: -10.1 Tail_Score: -4.52347 Start: 45 End: 69 Full_Region: TTTTTAGCGAAAAAA GACTAGCAG ACAAAAA CTGCTAGTC TTTTGGTATTATTTC ............................................GACTAGCAGACAAAAACTGCTAGTC...................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -10.1 Tail_Score: -5.08824 Start: 45 End: 69 Full_Region: gaaataataccaaaa gactagcag tttttgt ctgctagtc ttttttcgctaaaaa ............................................gactagcagtttttgtctgctagtc...................................................................................................................................................... Find igs database================================================ Query_seq: SMT_798:SMT_799|SMT_798:SMT_799:hypothetical protein:hypothetical protein:-><-:707167..707385 219 taatagttctgggaaccatattggttccttttttagcgaaaaaagactagcagacaaaaactgctagtcttttggtattatttcatctatctttgttaaaagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnta Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: smit_SMT_798_SMT_799|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[707167,707385]|219 HSP 1 e-value: 1.0E-50 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 taatagttctgggaaccatattggttccttttttagcgaaaaaagactagcagacaaaaactgctagtcttttggtattatttcatctatctttgttaaaa...................................................................................................................... taatagttctgggaaccatattggttccttttttagcgaaaaaagactagcagacaaaaactgctagtcttttggtattatttcatctatctttgttaaaa...................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAGUUCUGGGAACCAUAUUGGUUCCUUUUUUAGCGAAAAAAGACUAGCAGACAAAAACUGCUAGUCUUUUGGUAUUAUUUCAUCUAUCUUUGUUAAAA ..........(((((((.....)))))))..((((((((.(((((((((((((.......)))))))))))))((((..........)))).)))))))). (-31.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAACAAAGAUAGAUGAAAUAAUACCAAAAGACUAGCAGUUUUUGUCUGCUAGUCUUUUUUCGCUAAAAAAGGAACCAAUAUGGUUCCCAGAACUAUUA ..........(((((.............(((((((((((((.......)))))))))))))............((((((.....)))))).....))))). (-30.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 48 1 123 79 smit:SMT_1785|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763277..1763507_NEGATIVE 291 67 23 57 13 smit:SMT_147|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_97406..97636_POSITIVE 291 67 23 57 13 smit:SMT_119|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_70457..70687_POSITIVE 266 46 4 181 145 smit:SMT_2076|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1978592..1978822_NEGATIVE 253 93 55 110 66 smit:SMT_1514|5end_methylenetetrahydrofolate_dehydrogenase_(NADP+)_/_methenyltetrahydrofolate_cyclohydrolase_1496640..1496870_NEGATIVE 251 37 6 110 80 smit:SMT_1347|5end_SsrA-binding_protein_1325185..1325415_NEGATIVE 241 49 3 95 42 smit:SMT_2104|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_1995547..1995777_POSITIVE 235 50 8 132 78 smit:SMT_1701|5end_transcriptional_regulator,_RpiR_family_1684450..1684680_NEGATIVE 234 70 21 215 166 smit:SMT_1105|5end_K03217_preprotein_translocase_YidC_subunit_1047632..1047862_NEGATIVE 232 68 27 231 186 smit:SMT_1751|5end_indole-3-glycerol_phosphate_synthase_1729012..1729242_POSITIVE 230 83 46 148 107 smit:SMT_2066|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1973105..1973335_POSITIVE 230 83 46 148 107 smit:SMT_1321|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1290674..1290904_POSITIVE 229 41 5 73 39 smit:SMT_265|5end_DNA-binding_protein_204073..204303_NEGATIVE 228 92 61 99 64 smit:SMT_167|5end_acetyltransferase,_GNAT_family_113171..113401_POSITIVE 224 76 44 152 117 smit:SMT_1689|5end_PTS_enzyme,_maltose-and_glucose-specific,_factor_II_homologue_1671542..1671772_POSITIVE 224 54 11 139 95 smit:SMT_479|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416656..416886_NEGATIVE 224 54 11 139 95 smit:SMT_462|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_401658..401888_NEGATIVE 223 56 12 131 78 smit:SMT_936|5end_cobyric_acid_synthase_888669..888899_POSITIVE 219 52 11 56 5 smit:SMT_1350|5end_multidrug_resistance_efflux_pump_1329225..1329455_NEGATIVE 218 69 21 222 171 smit:SMT_1872|5end_K03217_preprotein_translocase_YidC_subunit_1831764..1831994_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 37 6 147 117 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE 241 78 34 73 26 smit:SMT_1583|3end_polysaccharide_transporter,_PST_family_1574609..1574759_POSITIVE 236 73 36 85 53 smit:SMT_1872|3end_K03217_preprotein_translocase_YidC_subunit_1830883..1831033_NEGATIVE 230 83 46 148 107 smit:SMT_2065|3end_transcriptional_regulator,_MarR_family_1973185..1973335_POSITIVE 230 83 46 148 107 smit:SMT_1320|3end_transcriptional_regulator,_MarR_family_1290754..1290904_POSITIVE 228 92 61 55 20 smit:SMT_166|3end_hypothetical_protein_113207..113357_POSITIVE 227 35 1 149 121 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 224 34 7 143 112 smit:SMT_1977|3end_endopeptidase_O_1908454..1908604_POSITIVE 224 76 44 133 98 smit:SMT_1688|3end_putative_N-acylglucosamine-6-phosphate_2-epimerase_1671603..1671753_POSITIVE 224 34 7 143 112 smit:SMT_1466|3end_endopeptidase_O_1447905..1448055_POSITIVE 223 56 12 131 78 smit:SMT_935|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_888749..888899_POSITIVE 219 52 11 69 18 smit:SMT_1351|3end_dephospho-CoA_kinase_1329212..1329362_NEGATIVE 219 73 41 50 18 smit:SMT_798|3end_hypothetical_protein_707106..707256_POSITIVE 218 69 21 117 66 smit:SMT_2044|3end_transcriptional_activator_TipA,_putative_1955274..1955424_NEGATIVE 218 69 21 117 66 smit:SMT_2026|3end_K03466_DNA_segregation_ATPase_FtsK/SpoIIIE,_S-DNA-T_family_1941905..1942055_NEGATIVE 218 69 21 117 66 smit:SMT_2016|3end_tyrosine_recombinase_1933021..1933171_NEGATIVE 218 69 21 117 66 smit:SMT_2006|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1926803..1926953_POSITIVE 218 69 21 127 76 smit:SMT_2001|3end_membrane_protease_protein_family_1923889..1924039_POSITIVE 218 69 21 127 76 smit:SMT_1985|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1914407..1914557_NEGATIVE 218 69 21 117 66 smit:SMT_1957|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1890829..1890979_POSITIVE