Origin IGS: ctttcagcccctttctgtatctattttcctagaaattgattagtgctattataccatatttcagaaaggacagaaaagctccaccacataggagccaaatccctccacataaacaaagtcccttgtcaggtatcgtaaaatagtgtttaataaaggtgtacaataa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttattgtacacctttattaaacactattttacgatacctgacaagggactttgtttatgtggagggatttggctcctatgtggtggagcttttctgtcctttctgaaatatggtataatagcactaatcaatttctaggaaaatagatacagaaaggggctgaaag Mask Tandem Repeat Region ================================================ ctttcagcccctttctgtatctattttcctagaaattgattagtgctattataccatatttcagaaaggacagaaaagctccaccacataggagccaaatccctccacataaacaaagtcccttgtcaggtatcgtaaaatagtgtttaataaaggtgtacaataa Find is-nt database================================================ Query_seq: SMT_1719:SMT_1720|SMT_1719:SMT_1720:DNA mismatch repair protein:hypothetical protein:<-->:1706933..1707098 166 ctttcagcccctttctgtatctattttcctagaaattgattagtgctattataccatatttcagaaaggacagaaaagctccaccacataggagccaaatccctccacataaacaaagtcccttgtcaggtatcgtaaaatagtgtttaataaaggtgtacaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1719:SMT_1720|SMT_1719:SMT_1720:DNA mismatch repair protein:hypothetical protein:<-->:1706933..1707098 166 ctttcagcccctttctgtatctattttcctagaaattgattagtgctattataccatatttcagaaaggacagaaaagctccaccacataggagccaaatccctccacataaacaaagtcccttgtcaggtatcgtaaaatagtgtttaataaaggtgtacaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1719:SMT_1720|SMT_1719:SMT_1720:DNA mismatch repair protein:hypothetical protein:<-->:1706933..1707098 166 ctttcagcccctttctgtatctattttcctagaaattgattagtgctattataccatatttcagaaaggacagaaaagctccaccacataggagccaaatccctccacataaacaaagtcccttgtcaggtatcgtaaaatagtgtttaataaaggtgtacaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttcagcccctttctgtatctattttcctagaaattgattagtgctattataccatatttcagaaaggacagaaaagctccaccacataggagccaaatccctccacataaacaaagtcccttgtcaggtatcgtaaaatagtgtttaataaaggtgtacaataa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 43 End: 135 .......................................... M L L Y H I S E R T E K L H H I G A K S L H I N K V P C Q V S ............................... Protein_Len: 35 Strand: + Start: 36 End: 140 ................................... M I S A I I P Y F R K D R K A P P H R S Q I P P H K Q S P L S G I V K .......................... Protein_Len: 44 Strand: - Start: 32 End: 163 ............................... F N I L A I I G Y K L F S L F A G G C L L W I G G C L C L G K D P I T F Y H K I F T Y M ... Protein_Len: 31 Strand: - Start: 24 End: 116 ....................... K G L F Q N T S N Y W I E S L V S F S W W M P A L D R W M F M .................................................. ctttcagcccctttctgtatctattttcctagaaattgattagtgctattataccatatttcagaaaggacagaaaagctccaccacataggagccaaatccctccacataaacaaagtcccttgtcaggtatcgtaaaatagtgtttaataaaggtgtacaataa 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: 82 Start: 122 End: 151 .........................................................................................................................CTTGTCAGGTATCGTAAAATAGTGTTTAAT............... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctttcagcccctttctgtatctattttcctagaaattgattagtgctattataccatatttcagaaaggacagaaaagctccaccacataggagccaaatccctccacataaacaaagtcccttgtcaggtatcgtaaaatagtgtttaataaaggtgtacaataa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1719:SMT_1720|SMT_1719:SMT_1720:DNA mismatch repair protein:hypothetical protein:<-->:1706933..1707098 166 ctttcagcccctttctgtatctattttcctagaaattgattagtgctattataccatatttcagaaaggacagaaaagctccaccacataggagccaaatccctccacataaacaaagtcccttgtcaggtatcgtaaaatagtgtttaataaaggtgtacaataa Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: smit_SMT_1719_SMT_1720|DNA mismatch repair protein:hypothetical protein|NEGATIVE:POSITIVE|[1706933,1707098]|166 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 ctttcagcccctttctgtatctattttcctagaaattgattagtgctattataccatatttcagaaaggacagaaaagctccaccacataggagccaaatccctccacataaacaaagtcccttgtcaggtatcgtaaaatagtgtttaataaaggtgtacaataa ctttcagcccctttctgtatctattttcctagaaattgattagtgctattataccatatttcagaaaggacagaaaagctccaccacataggagccaaatccctccacataaacaaagtcccttgtcaggtatcgtaaaatagtgtttaataaaggtgtacaataa Inter-species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: NC_003098_spr0159_spr0160|hypothetical protein:DNA mismatch repair protein|NEGATIVE:POSITIVE|[167798,168071]|274 HSP 1 e-value: 2.0E-55 bit: 216.0 Len: 125 Query Start:1 Query End:125 Subject Strand: NEGATIVE Subject Start: 150 Subject End: 274 ctttcagcccctttctgtatctattttcctagaaattgattagtgctattataccatatttcagaaaggacagaaaagctccaccacataggagccaaatccctccacataaacaaagtcccttg......................................... ctttcagcccctttctgtatctattttcctagaaattaattagtgctattataccatatttcagaaagaacagaaaagctccaccacataggagcccaatccctccacatagacaaagtcccttg......................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUCAGCCCCUUUCUGUAUCUAUUUUCCUAGAAAUUGAUUAGUGCUAUUAUACCAUAUUUCAGAAAGGACAGAAAAGCUCCACCACAUAGGAGCCAAAUCCCUCCACAUAAACAAAGUCCCUUG .((((....((((((((..((((......)))).........(((......))).......))))))))...)))).(((((........))))).............................. (-19.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGGGACUUUGUUUAUGUGGAGGGAUUUGGCUCCUAUGUGGUGGAGCUUUUCUGUCCUUUCUGAAAUAUGGUAUAAUAGCACUAAUCAAUUUCUAGGAAAAUAGAUACAGAAAGGGGCUGAAAG ......(((.(((((....((((((((..((((((........)))))).....))))))))..))))).)))....((((.((..((....((((......))))....))...)))))).... (-31.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 973 110 61 201 152 smit:SMT_1719|5end_DNA_mismatch_repair_protein_1706842..1707072_NEGATIVE 327 108 61 225 176 smit:SMT_854|5end_hypothetical_protein_799492..799722_NEGATIVE 310 85 44 198 158 smit:SMT_1341|5end_putative_cell_division_protein_1319115..1319345_NEGATIVE 280 97 51 201 153 smit:SMT_592|5end_amino_acid_ABC_transporter,_ATP-binding_protein_508759..508989_POSITIVE 277 68 21 144 98 smit:SMT_1072|5end_Cof_family_protein_1011193..1011423_NEGATIVE 273 108 77 195 155 smit:SMT_1328|5end_hypothetical_protein_1304468..1304698_NEGATIVE 269 120 72 102 52 smit:SMT_1506|5end_Cl-channel,_voltage-gated_family_protein_1489986..1490216_NEGATIVE 258 108 61 120 66 smit:SMT_229|5end_mechanosensitive_ion_channel_165623..165853_NEGATIVE 256 120 88 83 45 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 253 82 47 156 121 smit:SMT_1560|5end_DNA_polymerase_III_alpha_subunit_1548612..1548842_NEGATIVE 252 99 54 70 23 smit:SMT_259|5end_dipeptide/tripeptide_permease_197629..197859_POSITIVE 248 108 72 101 59 smit:SMT_211|5end_hypothetical_protein_predicted_by_Glimmer/Critica_144135..144365_POSITIVE 247 102 68 68 35 smit:SMT_460|5end_6-phospho-beta-glucosidase_397819..398049_POSITIVE 246 79 35 155 107 smit:SMT_1106|5end_ribonuclease_P_protein_component_1047972..1048202_NEGATIVE 245 90 42 90 42 smit:SMT_1470|5end_K06188_aquaporin_Z_1452560..1452790_POSITIVE 244 96 52 178 134 smit:SMT_1617|5end_K02015_iron_complex_transport_system_permease_protein_1604500..1604730_NEGATIVE 243 118 77 72 35 smit:SMT_452|5end_phosphomethylpyrimidine_kinase_390568..390798_NEGATIVE 242 79 44 46 8 smit:SMT_1107|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1048081..1048311_NEGATIVE 242 100 67 41 9 smit:SMT_558|5end_K09014_Fe-S_cluster_assembly_protein_SufB_475255..475485_POSITIVE 241 107 62 213 165 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 115 77 117 74 smit:SMT_805|3end_hypothetical_protein_predicted_by_Glimmer/Critica_715692..715842_NEGATIVE 258 108 61 77 23 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 246 79 35 138 90 smit:SMT_1107|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1047989..1048139_NEGATIVE 245 90 42 82 34 smit:SMT_1469|3end_GTP_pyrophosphokinase_1452632..1452782_POSITIVE 239 43 2 124 79 smit:SMT_445|3end_hypothetical_protein_384949..385099_POSITIVE 238 97 54 151 104 smit:SMT_278|3end_tyrosine-protein_kinase_221048..221198_POSITIVE 237 49 7 142 100 smit:SMT_1321|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1291458..1291608_POSITIVE 236 120 79 151 118 smit:SMT_1189|3end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1146663..1146813_NEGATIVE 233 46 2 144 111 smit:SMT_1480|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1462266..1462416_POSITIVE 232 107 67 51 15 smit:SMT_399|3end_cytochrome_c-type_biogenesis_protein_CcdA_329156..329306_POSITIVE 231 94 51 50 4 smit:SMT_1342|3end_protease_maturation_protein,_putative_1319276..1319426_NEGATIVE 228 48 8 118 83 smit:SMT_187|3end_30S_ribosomal_protein_S5_123571..123721_POSITIVE 227 110 61 107 49 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 221 40 1 79 25 smit:SMT_394|3end_K07729_putative_transcriptional_regulator_324549..324699_POSITIVE 219 108 64 72 14 smit:SMT_1997|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_1921123..1921273_NEGATIVE 216 120 82 76 27 smit:SMT_1441|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1424887..1425037_NEGATIVE 215 88 47 75 22 smit:SMT_954|3end_cation-transporting_ATPase,_E1-E2_family_901677..901827_NEGATIVE 214 70 21 77 33 smit:SMT_150|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_99400..99550_POSITIVE 213 96 51 55 8 smit:SMT_2067|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1974216..1974366_POSITIVE 213 105 63 50 3 smit:SMT_1401|3end_pyruvate_dehydrogenase_E1_component_beta_subunit_1378085..1378235_POSITIVE