Origin IGS: aagaatgcacctcctatattctatttcaatgttattatatttctttgtacttaaagatgcaagcgattacacaaaaacaaattcaaatttttaataggaaaatctcctgtttttctattttattacgaatagaagagtaggaggagtaaatgtatctaaagtatttaagatttttaaaatagtttagataaattgttgacatatttaaaactgaatgttacaattatattacaaaaagatttctttatatttctaaaatattacaaaggagtagaaaa .........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 ttttctactcctttgtaatattttagaaatataaagaaatctttttgtaatataattgtaacattcagttttaaatatgtcaacaatttatctaaactattttaaaaatcttaaatactttagatacatttactcctcctactcttctattcgtaataaaatagaaaaacaggagattttcctattaaaaatttgaatttgtttttgtgtaatcgcttgcatctttaagtacaaagaaatataataacattgaaatagaatataggaggtgcattctt Mask Tandem Repeat Region ================================================ aagaatgcacctcctatattctatttcaatgttattatatttctttgtacttaaagatgcaagcgattacacaaaaacaaattcaaatttttaataggaaaatctcctgtttttctattttattacgaatagaagagtaggaggagtaaatgtatctaaagtatttaagatttttaaaatagtttagataaattgttgacatatttaaaactgaatgttacaattatattacaaaaagatttctttatatttctaaaatattacaaaggagtagaaaa Find is-nt database================================================ Query_seq: SMT_1300:SMT_1301|SMT_1300:SMT_1301:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:<-->:1262935..1263212 278 aagaatgcacctcctatattctatttcaatgttattatatttctttgtacttaaagatgcaagcgattacacaaaaacaaattcaaatttttaataggaaaatctcctgtttttctattttattacgaatagaagagtaggaggagtaaatgtatctaaagtatttaagatttttaaaatagtttagataaattgttgacatatttaaaactgaatgttacaattatattacaaaaagatttctttatatttctaaaatattacaaaggagtagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1300:SMT_1301|SMT_1300:SMT_1301:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:<-->:1262935..1263212 278 aagaatgcacctcctatattctatttcaatgttattatatttctttgtacttaaagatgcaagcgattacacaaaaacaaattcaaatttttaataggaaaatctcctgtttttctattttattacgaatagaagagtaggaggagtaaatgtatctaaagtatttaagatttttaaaatagtttagataaattgttgacatatttaaaactgaatgttacaattatattacaaaaagatttctttatatttctaaaatattacaaaggagtagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1300:SMT_1301|SMT_1300:SMT_1301:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:<-->:1262935..1263212 278 aagaatgcacctcctatattctatttcaatgttattatatttctttgtacttaaagatgcaagcgattacacaaaaacaaattcaaatttttaataggaaaatctcctgtttttctattttattacgaatagaagagtaggaggagtaaatgtatctaaagtatttaagatttttaaaatagtttagataaattgttgacatatttaaaactgaatgttacaattatattacaaaaagatttctttatatttctaaaatattacaaaggagtagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagaatgcacctcctatattctatttcaatgttattatatttctttgtacttaaagatgcaagcgattacacaaaaacaaattcaaatttttaataggaaaatctcctgtttttctattttattacgaatagaagagtaggaggagtaaatgtatctaaagtatttaagatttttaaaatagtttagataaattgttgacatatttaaaactgaatgttacaattatattacaaaaagatttctttatatttctaaaatattacaaaggagtagaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 18 End: 137 ................. M L F Q C Y Y I S L Y L K M Q A I T Q K Q I Q I F N R K I S C F S I L L R I E E ............................................................................................................................................. Protein_Len: 39 Strand: - Start: 86 End: 202 ..................................................................................... I K L L F I E Q K E I K N R I S S Y S S Y I Y R F Y K L N K F Y N L Y I T S M ............................................................................ aagaatgcacctcctatattctatttcaatgttattatatttctttgtacttaaagatgcaagcgattacacaaaaacaaattcaaatttttaataggaaaatctcctgtttttctattttattacgaatagaagagtaggaggagtaaatgtatctaaagtatttaagatttttaaaatagtttagataaattgttgacatatttaaaactgaatgttacaattatattacaaaaagatttctttatatttctaaaatattacaaaggagtagaaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 91 Start: 195 End: 224 ..................................................................................................................................................................................................GTTGACATATTTAAAACTGAATGTTACAAT...................................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 34 End: 63 .................................CTTGCATCTTTAAGTACAAAGAAATATAAT....................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagaatgcacctcctatattctatttcaatgttattatatttctttgtacttaaagatgcaagcgattacacaaaaacaaattcaaatttttaataggaaaatctcctgtttttctattttattacgaatagaagagtaggaggagtaaatgtatctaaagtatttaagatttttaaaatagtttagataaattgttgacatatttaaaactgaatgttacaattatattacaaaaagatttctttatatttctaaaatattacaaaggagtagaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 65 HP_score: -2.1 Tail_Score: -5.34632 Start: 95 End: 109 Full_Region: AATTCAAATTTTTAA TAGGA AAATC TCCTG TTTTTCTATTTTATT ..............................................................................................TAGGAAAATCTCCTG......................................................................................................................................................................... TransTerm Strand: + Conf: 55 HP_score: -2.1 Tail_Score: -4.64676 Start: 95 End: 117 Full_Region: AATTCAAATTTTTAA TAGGAAAAT CTCCT GTTTTTCTA TTTTATTACGAATAG ..............................................................................................TAGGAAAATCTCCTGTTTTTCTA................................................................................................................................................................. Find igs database================================================ Query_seq: SMT_1300:SMT_1301|SMT_1300:SMT_1301:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:<-->:1262935..1263212 278 aagaatgcacctcctatattctatttcaatgttattatatttctttgtacttaaagatgcaagcgattacacaaaaacaaattcaaatttttaataggaaaatctcctgtttttctattttattacgaatagaagagtaggaggagtaaatgtatctaaagtatttaagatttttaaaatagtttagataaattgttgacatatttaaaactgaatgttacaattatattacaaaaagatttctttatatttctaaaatattacaaaggagtagaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 278 Len: 278 Subject: smit_SMT_1300_SMT_1301|hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:POSITIVE|[1262935,1263212]|278 HSP 1 e-value: 1.0E-156 bit: 551.0 Len: 278 Query Start:1 Query End:278 Subject Strand: POSITIVE Subject Start: 1 Subject End: 278 aagaatgcacctcctatattctatttcaatgttattatatttctttgtacttaaagatgcaagcgattacacaaaaacaaattcaaatttttaataggaaaatctcctgtttttctattttattacgaatagaagagtaggaggagtaaatgtatctaaagtatttaagatttttaaaatagtttagataaattgttgacatatttaaaactgaatgttacaattatattacaaaaagatttctttatatttctaaaatattacaaaggagtagaaaa aagaatgcacctcctatattctatttcaatgttattatatttctttgtacttaaagatgcaagcgattacacaaaaacaaattcaaatttttaataggaaaatctcctgtttttctattttattacgaatagaagagtaggaggagtaaatgtatctaaagtatttaagatttttaaaatagtttagataaattgttgacatatttaaaactgaatgttacaattatattacaaaaagatttctttatatttctaaaatattacaaaggagtagaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAUGCACCUCCUAUAUUCUAUUUCAAUGUUAUUAUAUUUCUUUGUACUUAAAGAUGCAAGCGAUUACACAAAAACAAAUUCAAAUUUUUAAUAGGAAAAUCUCCUGUUUUUCUAUUUUAUUACGAAUAGAAGAGUAGGAGGAGUAAAUGUAUCUAAAGUAUUUAAGAUUUUUAAAAUAGUUUAGAUAAAUUGUUGACAUAUUUAAAACUGAAUGUUACAAUUAUAUUACAAAAAGAUUUCUUUAUAUUUCUAAAAUAUUACAAAGGAGUAGAAAA ..................(((((((((..............((((.((((((..(((((((.....((((................((((((.....))))))(((((((((((((((((......)))))))))))))))))..)))).))))))).))))))..)))).......((((.((((((..((((((.(((((............))))))))))).........((((....)))).....)))))).)))).....))))))))).. (-53.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUACUCCUUUGUAAUAUUUUAGAAAUAUAAAGAAAUCUUUUUGUAAUAUAAUUGUAACAUUCAGUUUUAAAUAUGUCAACAAUUUAUCUAAACUAUUUUAAAAAUCUUAAAUACUUUAGAUACAUUUACUCCUCCUACUCUUCUAUUCGUAAUAAAAUAGAAAAACAGGAGAUUUUCCUAUUAAAAAUUUGAAUUUGUUUUUGUGUAAUCGCUUGCAUCUUUAAGUACAAAGAAAUAUAAUAACAUUGAAAUAGAAUAUAGGAGGUGCAUUCUU .......(((((.(((..((((((((...((((((((....)))))))).....((((((..((((((((((.((((...........((((((((.(((((..........))))).)))))))).........(((((....(((((((........)))))))....))))).......)))).)))).))))))...(((((((......(((((......))))))))))))..))))))....))))))))..))).))))).......... (-46.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 721 50 1 141 92 smit:SMT_1300|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1262844..1263074_NEGATIVE 259 146 101 165 123 smit:SMT_917|5end_hydroxymethylglutaryl-CoA_synthase_871176..871406_NEGATIVE 244 41 6 129 95 smit:SMT_1429|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1414725..1414955_POSITIVE 239 139 103 161 118 smit:SMT_2029|5end_acetyltransferase,_GNAT_family_1943749..1943979_POSITIVE 239 139 103 161 118 smit:SMT_1755|5end_acetyltransferase,_GNAT_family_1733042..1733272_POSITIVE 239 158 113 153 110 smit:SMT_976|5end_hypothetical_protein_925183..925413_NEGATIVE 230 157 112 195 150 smit:SMT_1436|5end_conserved_hypothetical_protein_TIGR00147_1421255..1421485_NEGATIVE 228 170 134 225 192 smit:SMT_1843|5end_transposase,_TnpA_1808100..1808330_POSITIVE 228 170 134 225 192 smit:SMT_1238|5end_transposase,_TnpA_1198738..1198968_POSITIVE 226 80 41 42 12 smit:SMT_144|5end_hypothetical_protein_predicted_by_Glimmer/Critica_95553..95783_POSITIVE 224 169 124 148 102 smit:SMT_1168|5end_potassium_uptake_protein_KtrB_1116552..1116782_NEGATIVE 220 140 96 173 119 smit:SMT_1556|5end_phosphoglycerate_mutase_1541194..1541424_POSITIVE 219 147 107 122 70 smit:SMT_1549|5end_hypothetical_protein_1533645..1533875_POSITIVE 216 113 75 213 175 smit:SMT_1463|5end_phosphate_transport_system_protein_PhoU_1443907..1444137_POSITIVE 216 147 104 149 111 smit:SMT_919|5end_hypothetical_protein_872499..872729_NEGATIVE 214 148 101 162 97 smit:SMT_1071|5end_hypothetical_protein_1010058..1010288_POSITIVE 212 149 107 59 16 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 211 157 111 230 183 smit:SMT_156|5end_hypothetical_protein_102869..103099_POSITIVE 210 147 111 119 84 smit:SMT_97|5end_hypothetical_protein_28809..29039_POSITIVE 208 145 103 150 102 smit:SMT_1540|5end_hypothetical_protein_1525005..1525235_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 146 101 51 9 smit:SMT_918|3end_hypothetical_protein_871290..871440_NEGATIVE 239 158 113 84 41 smit:SMT_977|3end_conserved_hypothetical_protein,_Rrf2_family_protein_925252..925402_NEGATIVE 230 157 112 85 40 smit:SMT_1437|3end_ADP-ribosylglycohydrolase_1421365..1421515_NEGATIVE 228 170 134 38 5 smit:SMT_1237|3end_transposase,_TnpA_1198631..1198781_POSITIVE 224 169 124 114 68 smit:SMT_1169|3end_phosphorylase,_Pnp/UDP_family_1116586..1116736_NEGATIVE 219 147 107 117 65 smit:SMT_1548|3end_cell_division_protein_FtsZ_1533720..1533870_POSITIVE 218 154 126 141 111 smit:SMT_481|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_417641..417791_NEGATIVE 216 147 104 60 22 smit:SMT_920|3end_serine/threonine_protein_kinase_872588..872738_NEGATIVE 210 144 106 128 84 smit:SMT_455|3end_cation_transport_ATPase_393993..394143_POSITIVE 210 147 111 114 79 smit:SMT_96|3end_hypothetical_protein_28884..29034_POSITIVE 208 145 103 72 24 smit:SMT_1541|3end_isopentenyl-diphosphate_delta-isomerase_1525083..1525233_NEGATIVE 205 146 107 54 11 smit:SMT_823|3end_putative_mucus_binding_protein_740995..741145_NEGATIVE 204 146 107 82 39 smit:SMT_1581|3end_transcriptional_regulator,_biotin_repressor_family_1573120..1573270_NEGATIVE 199 47 10 137 96 smit:SMT_1564|3end_transcriptional_antiterminator,_BglG_family_1557697..1557847_POSITIVE 196 133 95 103 71 smit:SMT_1531|3end_hypothetical_protein_1515449..1515599_NEGATIVE 196 66 29 71 37 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 196 66 29 71 37 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 196 66 29 71 37 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE 196 66 29 71 37 smit:SMT_510|3end_hypothetical_protein_439357..439507_POSITIVE 195 69 23 116 59 smit:SMT_1439|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1423262..1423412_NEGATIVE