Origin IGS: agtgatttcacctgactcaacctgttctttagttttaagaacaaaatctgtagcctgctccttgacttctgtcagtttttcacagacctgctcnnnnnttaattaattaannnnntggaaaggtaaacacttccactctattattgtat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atacaataatagagtggaagtgtttacctttccannnnnttaattaattaannnnngagcaggtctgtgaaaaactgacagaagtcaaggagcaggctacagattttgttcttaaaactaaagaacaggttgagtcaggtgaaatcact Mask Tandem Repeat Region ================================================ agtgatttcacctgactcaacctgttctttagttttaagaacaaaatctgtagcctgctccttgacttctgtcagtttttcacagacctgctcnnnnnttaattaattaannnnntggaaaggtaaacacttccactctattattgtat Find is-nt database================================================ Query_seq: SMT_777:SMT_778|SMT_777:SMT_778:hypothetical protein:S-adenosylmethionine:tRNA ribosyltransferase-isomerase:<-->:686861..687009 149 agtgatttcacctgactcaacctgttctttagttttaagaacaaaatctgtagcctgctccttgacttctgtcagtttttcacagacctgctcnnnnnttaattaattaannnnntggaaaggtaaacacttccactctattattgtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_777:SMT_778|SMT_777:SMT_778:hypothetical protein:S-adenosylmethionine:tRNA ribosyltransferase-isomerase:<-->:686861..687009 149 agtgatttcacctgactcaacctgttctttagttttaagaacaaaatctgtagcctgctccttgacttctgtcagtttttcacagacctgctcnnnnnttaattaattaannnnntggaaaggtaaacacttccactctattattgtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_777:SMT_778|SMT_777:SMT_778:hypothetical protein:S-adenosylmethionine:tRNA ribosyltransferase-isomerase:<-->:686861..687009 149 agtgatttcacctgactcaacctgttctttagttttaagaacaaaatctgtagcctgctccttgacttctgtcagtttttcacagacctgctcnnnnnttaattaattaannnnntggaaaggtaaacacttccactctattattgtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtgatttcacctgactcaacctgttctttagttttaagaacaaaatctgtagcctgctccttgacttctgtcagtttttcacagacctgctcnnnnnttaattaattaannnnntggaaaggtaaacacttccactctattattgtat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 2 End: 103 . M I S P D S T C S L V L R T K S V A C S L T S V S F S Q T C S X X N .............................................. agtgatttcacctgactcaacctgttctttagttttaagaacaaaatctgtagcctgctccttgacttctgtcagtttttcacagacctgctcnnnnnttaattaattaannnnntggaaaggtaaacacttccactctattattgtat 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================================================ agtgatttcacctgactcaacctgttctttagttttaagaacaaaatctgtagcctgctccttgacttctgtcagtttttcacagacctgctcnnnnnttaattaattaannnnntggaaaggtaaacacttccactctattattgtat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_777:SMT_778|SMT_777:SMT_778:hypothetical protein:S-adenosylmethionine:tRNA ribosyltransferase-isomerase:<-->:686861..687009 149 agtgatttcacctgactcaacctgttctttagttttaagaacaaaatctgtagcctgctccttgacttctgtcagtttttcacagacctgctcnnnnnttaattaattaannnnntggaaaggtaaacacttccactctattattgtat Intra-Species Hit: Count: 1 Min: 1 Max: 149 Len: 149 Subject: smit_SMT_777_SMT_778|hypothetical protein:S-adenosylmethionine:tRNA ribosyltransferase-isomerase|NEGATIVE:POSITIVE|[686861, 687009]|149 HSP 1 e-value: 2.0E-61 bit: 236.0 Len: 149 Query Start:1 Query End:149 Subject Strand: POSITIVE Subject Start: 1 Subject End: 149 agtgatttcacctgactcaacctgttctttagttttaagaacaaaatctgtagcctgctccttgacttctgtcagtttttcacagacctgctcnnnnnttaattaattaannnnntggaaaggtaaacacttccactctattattgtat agtgatttcacctgactcaacctgttctttagttttaagaacaaaatctgtagcctgctccttgacttctgtcagtttttcacagacctgctcnnnnnttaattaattaannnnntggaaaggtaaacacttccactctattattgtat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGAUUUCACCUGACUCAACCUGUUCUUUAGUUUUAAGAACAAAAUCUGUAGCCUGCUCCUUGACUUCUGUCAGUUUUUCACAGACCUGCUCNNNNNUUAAUUAAUUAANNNNNUGGAAAGGUAAACACUUCCACUCUAUUAUUGUAU ((((.(((.((((...(((...(((((((.......)))))))......((((.(((....(((((....))))).......)))..))))........................)))..))))))))))).................. (-21.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACAAUAAUAGAGUGGAAGUGUUUACCUUUCCANNNNNUUAAUUAAUUAANNNNNGAGCAGGUCUGUGAAAAACUGACAGAAGUCAAGGAGCAGGCUACAGAUUUUGUUCUUAAAACUAAAGAACAGGUUGAGUCAGGUGAAAUCACU ............(((((.....((((((.................................(((((((.......((((....))))....)))))))...((((((((((((.......)))))))....))))).)))))).))))) (-28.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 917 90 41 181 132 smit:SMT_777|5end_hypothetical_protein_686770..687000_NEGATIVE 342 90 49 63 8 smit:SMT_442|5end_transcriptional_regulator,_putative_381652..381882_POSITIVE 310 59 11 127 75 smit:SMT_2121|5end_putative_mucus_binding_protein_2007145..2007375_NEGATIVE 310 59 11 127 75 smit:SMT_2068|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1974482..1974712_NEGATIVE 304 82 44 222 186 smit:SMT_311|5end_3-oxoacyl-_252123..252353_POSITIVE 302 69 21 162 108 smit:SMT_825|5end_aspartate_aminotransferase_749594..749824_NEGATIVE 299 71 50 231 211 smit:SMT_988|5end_N-acetylneuraminate_lyase_932889..933119_NEGATIVE 296 81 45 203 160 smit:SMT_1116|5end_K02244_competence_protein_ComGB_1053841..1054071_NEGATIVE 284 90 47 69 27 smit:SMT_1929|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1869785..1870015_NEGATIVE 284 90 47 202 160 smit:SMT_1928|5end_O-methyltransferase_family_protein_1869652..1869882_NEGATIVE 284 75 36 217 178 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 279 92 53 53 18 smit:SMT_1822|5end_hypothetical_protein_1794452..1794682_POSITIVE 279 90 44 67 18 smit:SMT_453|5end_CopAB_ATPase_metal-fist_type_repressor_390883..391113_POSITIVE 277 82 51 60 22 smit:SMT_954|5end_cation-transporting_ATPase,_E1-E2_family_904025..904255_NEGATIVE 274 79 46 227 186 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 273 92 67 151 130 smit:SMT_1287|5end_50S_ribosomal_protein_L9_1250358..1250588_POSITIVE 272 86 45 122 83 smit:SMT_1376|5end_tetrapyrrole_(corrin/porphyrin)_methylase_family_protein_1355553..1355783_NEGATIVE 270 60 11 55 6 smit:SMT_1739|5end_hypothetical_protein_1721263..1721493_POSITIVE 269 90 43 92 32 smit:SMT_1723|5end_hypothetical_protein_1709081..1709311_POSITIVE 267 90 43 168 119 smit:SMT_794|5end_hypothetical_protein_703487..703717_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 90 47 69 27 smit:SMT_1930|3end_peptide_chain_release_factor_1_1869785..1869935_NEGATIVE 279 92 53 36 1 smit:SMT_1821|3end_Mg2+_and_Co2+_transporter_1794515..1794665_POSITIVE 272 86 45 119 80 smit:SMT_1377|3end_hypothetical_protein_1355556..1355706_NEGATIVE 270 60 11 53 4 smit:SMT_1738|3end_peptidyl-prolyl_cis-trans_isomerase_1721341..1721491_POSITIVE 258 87 46 82 48 smit:SMT_1206|3end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1165697..1165847_NEGATIVE 255 90 55 37 7 smit:SMT_1749|3end_anthranilate_synthase_component_II_1728080..1728230_POSITIVE 253 93 51 135 84 smit:SMT_909|3end_type_I_restriction_enzyme_M_protein_857223..857373_NEGATIVE 247 89 41 110 65 smit:SMT_1170|3end_acetyltransferase,_CysE/LacA/LpxA/NodL_family_1117569..1117719_NEGATIVE 240 93 53 67 24 smit:SMT_921|3end_putative_PP2C_protein_phosphatase_874498..874648_NEGATIVE 237 91 52 81 33 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 232 90 48 126 78 smit:SMT_567|3end_conserved_hypothetical_protein_485752..485902_POSITIVE 231 91 56 45 9 smit:SMT_2125|3end_3-phosphoshikimate_1-carboxyvinyltransferase_2009098..2009248_POSITIVE 231 91 56 137 101 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 231 92 52 145 85 smit:SMT_1496|3end_conserved_hypothetical_protein_TIGR00150_1481522..1481672_POSITIVE 231 90 42 138 84 smit:SMT_1153|3end_alpha-mannosidase_1097383..1097533_NEGATIVE 230 78 49 68 42 smit:SMT_1689|3end_PTS_enzyme,_maltose-and_glucose-specific,_factor_II_homologue_1673139..1673289_POSITIVE 230 74 39 52 14 smit:SMT_291|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_234870..235020_POSITIVE 228 91 57 111 71 smit:SMT_1124|3end_pyrrolidone-carboxylate_peptidase_1060225..1060375_NEGATIVE 228 90 47 76 38 smit:SMT_929|3end_hypothetical_protein_883202..883352_NEGATIVE 227 90 41 85 28 smit:SMT_2033|3end_hydrolase,_haloacid_dehalogenase-like_family_1946739..1946889_POSITIVE