Origin IGS: ttttctttgaaaatcttcccacaataaaacgcatagtatcaatctttcaacacctgatactatgcgtttttcttatttgaaatacttttgactcagcctct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaggctgagtcaaaagtatttcaaataagaaaaacgcatagtatcaggtgttgaaagattgatactatgcgttttattgtgggaagattttcaaagaaaa Mask Tandem Repeat Region ================================================ ttttctttgaaaatcttcccacaataaaacgcatagtatcaatctttcaacacctgatactatgcgtttttcttatttgaaatacttttgactcagcctct Find is-nt database================================================ Query_seq: SMT_937:SMT_938|SMT_937:SMT_938:dipeptidase:hypothetical protein:-><-:890802..890902 101 ttttctttgaaaatcttcccacaataaaacgcatagtatcaatctttcaacacctgatactatgcgtttttcttatttgaaatacttttgactcagcctct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_937:SMT_938|SMT_937:SMT_938:dipeptidase:hypothetical protein:-><-:890802..890902 101 ttttctttgaaaatcttcccacaataaaacgcatagtatcaatctttcaacacctgatactatgcgtttttcttatttgaaatacttttgactcagcctct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_937:SMT_938|SMT_937:SMT_938:dipeptidase:hypothetical protein:-><-:890802..890902 101 ttttctttgaaaatcttcccacaataaaacgcatagtatcaatctttcaacacctgatactatgcgtttttcttatttgaaatacttttgactcagcctct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttctttgaaaatcttcccacaataaaacgcatagtatcaatctttcaacacctgatactatgcgtttttcttatttgaaatacttttgactcagcctct Predict ORF larger than 30AA ================================================ ttttctttgaaaatcttcccacaataaaacgcatagtatcaatctttcaacacctgatactatgcgtttttcttatttgaaatacttttgactcagcctct 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================================================ ttttctttgaaaatcttcccacaataaaacgcatagtatcaatctttcaacacctgatactatgcgtttttcttatttgaaatacttttgactcagcctct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -8.2 Tail_Score: -3.30903 Start: 25 End: 71 Full_Region: agtatttcaaataag aaaaacgcatagtatcaggtgt tga aagattgatactatgcgtttta ttgtgggaagatttt ........................aaaaacgcatagtatcaggtgttgaaagattgatactatgcgtttta.............................. TransTerm Strand: + Conf: 89 HP_score: -6.8 Tail_Score: -5.38549 Start: 30 End: 66 Full_Region: CTTCCCACAATAAAA CGCATAGTATCA ATCTTTCAACACC TGATACTATGCG TTTTTCTTATTTGAA .............................CGCATAGTATCAATCTTTCAACACCTGATACTATGCG................................... TransTerm Strand: - Conf: 87 HP_score: -8.1 Tail_Score: -4.77165 Start: 30 End: 66 Full_Region: ttcaaataagaaaaa cgcatagtatcaggtgt tga aagattgatactatgcg ttttattgtgggaag .............................cgcatagtatcaggtgttgaaagattgatactatgcg................................... Find igs database================================================ Query_seq: SMT_937:SMT_938|SMT_937:SMT_938:dipeptidase:hypothetical protein:-><-:890802..890902 101 ttttctttgaaaatcttcccacaataaaacgcatagtatcaatctttcaacacctgatactatgcgtttttcttatttgaaatacttttgactcagcctct Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: smit_SMT_937_SMT_938|dipeptidase:hypothetical protein|POSITIVE:NEGATIVE|[890802,890902]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 ttttctttgaaaatcttcccacaataaaacgcatagtatcaatctttcaacacctgatactatgcgtttttcttatttgaaatacttttgactcagcctct ttttctttgaaaatcttcccacaataaaacgcatagtatcaatctttcaacacctgatactatgcgtttttcttatttgaaatacttttgactcagcctct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUUUGAAAAUCUUCCCACAAUAAAACGCAUAGUAUCAAUCUUUCAACACCUGAUACUAUGCGUUUUUCUUAUUUGAAAUACUUUUGACUCAGCCUCU ......(..(((...(((.......((((((((((((((((.............))))))))))))))))........)))....)))..).......... (-20.78) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGGCUGAGUCAAAAGUAUUUCAAAUAAGAAAAACGCAUAGUAUCAGGUGUUGAAAGAUUGAUACUAUGCGUUUUAUUGUGGGAAGAUUUUCAAAGAAAA ....(((........))).((((..((((..((((((((((((((((...(((....))))))))))))))))))).))))..)))).............. (-28.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 89 45 47 4 smit:SMT_1018|5end_hypothetical_protein_predicted_by_Glimmer/Critica_954564..954794_POSITIVE 253 100 51 124 76 smit:SMT_104|5end_DNA_repair_protein_49623..49853_POSITIVE 248 79 34 51 4 smit:SMT_1986|5end_mercuric_reductase_1914843..1915073_POSITIVE 248 79 34 51 4 smit:SMT_1236|5end_mercuric_reductase_1195960..1196190_POSITIVE 247 97 52 182 140 smit:SMT_1153|5end_alpha-mannosidase_1098117..1098347_NEGATIVE 242 99 51 223 171 smit:SMT_1591|5end_DNA-entry_nuclease_1578873..1579103_POSITIVE 233 80 41 227 186 smit:SMT_2024|5end_hypothetical_protein_1940359..1940589_POSITIVE 233 80 41 227 186 smit:SMT_724|5end_hypothetical_protein_630060..630290_NEGATIVE 230 100 52 104 50 smit:SMT_316|5end_acetyl-CoA_carboxylase_carboxyl_transferase_subunit_alpha_256544..256774_POSITIVE 224 90 43 72 23 smit:SMT_1549|5end_hypothetical_protein_1533645..1533875_POSITIVE 224 78 31 93 34 smit:SMT_815|5end_hypothetical_protein_724294..724524_NEGATIVE 223 49 1 90 24 smit:SMT_288|5end_hypothetical_protein_231184..231414_POSITIVE 222 67 28 54 14 smit:SMT_2098|5end_similar_to_CDP-ribitol_pyrophosphorylase_1991376..1991606_POSITIVE 220 73 40 62 22 smit:SMT_187|5end_30S_ribosomal_protein_S5_122997..123227_POSITIVE 218 66 30 171 125 smit:SMT_1380|5end_pyrroline-5-carboxylate_reductase_1358464..1358694_NEGATIVE 215 98 53 134 75 smit:SMT_1801|5end_heavy_metal_translocating_P-type_ATPase_1773916..1774146_POSITIVE 214 99 58 127 86 smit:SMT_1160|5end_K03152_4-methyl-5(b-hydroxyethyl)-thiazole_monophosphate_biosynthesis_1105174..1105404_NEGATIVE 209 51 16 35 3 smit:SMT_1832|5end_tagatose-6-phosphate_kinase_1800438..1800668_POSITIVE 209 77 32 92 35 smit:SMT_520|5end_glutathione_reductase_445285..445515_NEGATIVE 207 96 56 37 1 smit:SMT_1352|5end_formamidopyrimidine-DNA_glycosylase_1330641..1330871_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 484 66 23 55 10 smit:SMT_1308|3end_hypothetical_protein_1273854..1274004_POSITIVE 417 70 21 124 73 smit:SMT_1018|3end_hypothetical_protein_predicted_by_Glimmer/Critica_954739..954889_POSITIVE 361 70 23 73 24 smit:SMT_130|3end_capsular_polysaccharide_biosynthesis_protein_82925..83075_POSITIVE 359 70 21 59 7 smit:SMT_1614|3end_K08998_hypothetical_protein_1601652..1601802_POSITIVE 357 70 26 65 21 smit:SMT_937|3end_dipeptidase_890741..890891_POSITIVE 276 70 22 78 31 smit:SMT_778|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_687834..687984_POSITIVE 263 58 14 55 11 smit:SMT_1466|3end_endopeptidase_O_1447905..1448055_POSITIVE 254 97 59 40 1 smit:SMT_736|3end_hypothetical_protein_641500..641650_NEGATIVE 247 97 52 145 103 smit:SMT_1154|3end_tryptophanyl-tRNA_synthetase_1098154..1098304_NEGATIVE 246 74 42 80 46 smit:SMT_972|3end_ABC-type_multidrug/protein/lipid_transport_system,_ATPase_component_919256..919406_NEGATIVE 230 73 31 71 28 smit:SMT_1977|3end_endopeptidase_O_1908454..1908604_POSITIVE 230 100 52 107 53 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 224 90 43 67 18 smit:SMT_1548|3end_cell_division_protein_FtsZ_1533720..1533870_POSITIVE 223 49 1 100 34 smit:SMT_287|3end_UDP-galactopyranose_mutase_231274..231424_POSITIVE 220 99 56 118 74 smit:SMT_1027|3end_K02026_multiple_sugar_transport_system_permease_protein_962641..962791_NEGATIVE 220 73 40 44 4 smit:SMT_186|3end_50S_ribosomal_protein_L18_123059..123209_POSITIVE 214 99 58 116 75 smit:SMT_1161|3end_K05837_rod_shape_determining_protein_RodA_1105185..1105335_NEGATIVE 213 70 26 71 25 smit:SMT_779|3end_ribonuclease_BN,_putative_687883..688033_NEGATIVE 210 70 30 63 14 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 207 67 30 50 19 smit:SMT_542|3end_hypothetical_protein_458400..458550_POSITIVE