Origin IGS: tgaataaaacgaagaggctcgatttgagtctcttttatgattcatatagttaccttactttaaaaatctgctaaaatcacttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagaggaaaaaaacaaaaaggagaaatactc .........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 gagtatttctcctttttgtttttttcctcttcttgacttcaactcgcaaaacgacccaaaggcaactgtttcacaattcatcaagaatgagtattatcgttcacacgacaagtttcattttaccatactttttcaatattttcaagtgattttagcagatttttaaagtaaggtaactatatgaatcataaaagagactcaaatcgagcctcttcgttttattca Mask Tandem Repeat Region ================================================ tgaataaaacgaagaggctcgatttgagtctcttttatgattcatatagttaccttactttaaaaatctgctaaaatcacttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagaggaaaaaaacaaaaaggagaaatactc Find is-nt database================================================ Query_seq: SMT_1277:SMT_1278|SMT_1277:SMT_1278:PcsB protein:30S ribosomal protein S2:->->:1241388..1241612 225 tgaataaaacgaagaggctcgatttgagtctcttttatgattcatatagttaccttactttaaaaatctgctaaaatcacttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagaggaaaaaaacaaaaaggagaaatactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1277:SMT_1278|SMT_1277:SMT_1278:PcsB protein:30S ribosomal protein S2:->->:1241388..1241612 225 tgaataaaacgaagaggctcgatttgagtctcttttatgattcatatagttaccttactttaaaaatctgctaaaatcacttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagaggaaaaaaacaaaaaggagaaatactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1277:SMT_1278|SMT_1277:SMT_1278:PcsB protein:30S ribosomal protein S2:->->:1241388..1241612 225 tgaataaaacgaagaggctcgatttgagtctcttttatgattcatatagttaccttactttaaaaatctgctaaaatcacttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagaggaaaaaaacaaaaaggagaaatactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaataaaacgaagaggctcgatttgagtctcttttatgattcatatagttaccttactttaaaaatctgctaaaatcacttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagaggaaaaaaacaaaaaggagaaatactc Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 80 End: 193 ............................................................................... K F I N F F Y P L I F S T T H V I I S M R S S N H F L Q R Q T T K R T S T M ................................ Protein_Len: 53 Strand: - Start: 63 End: 221 .............................................................. F D A L I V Q F Y Q F L I T F H F K D H S R Y Y E N K I F Q S V T A K P D N Q S N F D L L P F F C F P S M .... tgaataaaacgaagaggctcgatttgagtctcttttatgattcatatagttaccttactttaaaaatctgctaaaatcacttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagaggaaaaaaacaaaaaggagaaatactc 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: 88 Start: 80 End: 109 ...............................................................................CTTGAAAATATTGAAAAAGTATGGTAAAAT.................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgaataaaacgaagaggctcgatttgagtctcttttatgattcatatagttaccttactttaaaaatctgctaaaatcacttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagaggaaaaaaacaaaaaggagaaatactc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1277:SMT_1278|SMT_1277:SMT_1278:PcsB protein:30S ribosomal protein S2:->->:1241388..1241612 225 tgaataaaacgaagaggctcgatttgagtctcttttatgattcatatagttaccttactttaaaaatctgctaaaatcacttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagaggaaaaaaacaaaaaggagaaatactc Intra-Species Hit: Count: 1 Min: 1 Max: 200 Len: 200 Subject: smit_SMT_1277_SMT_1278|PcsB protein:30S ribosomal protein S2|POSITIVE:POSITIVE|[1241388,1241612]|225 HSP 1 e-value: 1.0E-109 bit: 396.0 Len: 200 Query Start:1 Query End:200 Subject Strand: POSITIVE Subject Start: 1 Subject End: 200 tgaataaaacgaagaggctcgatttgagtctcttttatgattcatatagttaccttactttaaaaatctgctaaaatcacttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagagg......................... tgaataaaacgaagaggctcgatttgagtctcttttatgattcatatagttaccttactttaaaaatctgctaaaatcacttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagagg......................... Inter-species Hit: Count: 3 Min: 80 Max: 200 Len: 121 Subject: NC_008533_SPD_2042_SPD_2043|ribosomal protein S2:secreted 45 kDa protein precursor|NEGATIVE:NEGATIVE|[2020120,2020342]|223 HSP 1 e-value: 6.0E-53 bit: 208.0 Len: 121 Query Start:80 Query End:200 Subject Strand: NEGATIVE Subject Start: 26 Subject End: 146 ...............................................................................cttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagagg......................... ...............................................................................cttgaaaatattggaaaagtatggtaaaatgaaaattgtcgtgtgaacgataatactcattcttgatgaattgtgaagcagttgcccttgggtcgttttgcgagttgaagtcaagaagagg......................... Subject: NC_003098_spr2020_spr2021|30S ribosomal protein S2:General stress protein GSP-781|NEGATIVE:NEGATIVE|[2012620,2012842]|223 HSP 1 e-value: 6.0E-53 bit: 208.0 Len: 121 Query Start:80 Query End:200 Subject Strand: NEGATIVE Subject Start: 26 Subject End: 146 ...............................................................................cttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagagg......................... ...............................................................................cttgaaaatattggaaaagtatggtaaaatgaaaattgtcgtgtgaacgataatactcattcttgatgaattgtgaagcagttgcccttgggtcgttttgcgagttgaagtcaagaagagg......................... Subject: NC_003028_SP_2215_SP_2216|30S ribosomal protein S2:secreted 45 kd protein|NEGATIVE:NEGATIVE|[2135044,2135266]|223 HSP 1 e-value: 1.0E-50 bit: 200.0 Len: 121 Query Start:80 Query End:200 Subject Strand: NEGATIVE Subject Start: 26 Subject End: 146 ...............................................................................cttgaaaatattgaaaaagtatggtaaaatgaaacttgtcgtgtgaacgataatactcattcttgatgaattgtgaaacagttgcctttgggtcgttttgcgagttgaagtcaagaagagg......................... ...............................................................................cttgaaaatattggaaaagtatggtagaatgaaaattgtcgtgtgaacgataatactcattcttgatgaattgtgaagcagttgcccttgggtcgttttgcgagttgaagtcaagaagagg......................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGAAAAUAUUGAAAAAGUAUGGUAAAAUGAAACUUGUCGUGUGAACGAUAAUACUCAUUCUUGAUGAAUUGUGAAACAGUUGCCUUUGGGUCGUUUUGCGAGUUGAAGUCAAGAAGAGG .(((...(((((.....)))))..)))........(((((((....)))))))..(((.((((((((...(((..((((....(((....))).))))..)))......))))))))))). (-29.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUCUUCUUGACUUCAACUCGCAAAACGACCCAAAGGCAACUGUUUCACAAUUCAUCAAGAAUGAGUAUUAUCGUUCACACGACAAGUUUCAUUUUACCAUACUUUUUCAAUAUUUUCAAG .((((((((((.......(((.....))).....((....)).............))))))).))).....((((....))))...................................... (-14.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 113 82 90 58 smit:SMT_1939|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1876278..1876508_POSITIVE 268 120 75 231 173 smit:SMT_833|5end_hypothetical_protein_predicted_by_Glimmer/Critica_775362..775592_NEGATIVE 265 104 61 176 136 smit:SMT_1590|5end_DNA-entry_nuclease_1578565..1578795_POSITIVE 265 112 71 57 10 smit:SMT_1303|5end_tRNA-dihydrouridine_synthase_1265731..1265961_NEGATIVE 255 111 77 148 109 smit:SMT_118|5end_K02026_multiple_sugar_transport_system_permease_protein_69430..69660_POSITIVE 253 91 57 149 119 smit:SMT_1723|5end_hypothetical_protein_1709081..1709311_POSITIVE 253 108 65 187 136 smit:SMT_279|5end_glycosyl_transferase_CpsE_221100..221330_POSITIVE 250 92 60 46 2 smit:SMT_1992|5end_carboxynorspermidine_decarboxylase_1919207..1919437_NEGATIVE 250 92 60 46 2 smit:SMT_1415|5end_carboxynorspermidine_decarboxylase_1399570..1399800_NEGATIVE 249 102 61 65 30 smit:SMT_1561|5end_putative_mucus_binding_protein_1553809..1554039_NEGATIVE 249 108 61 212 159 smit:SMT_1212|5end_acyl_carrier_protein,_putative_1171657..1171887_NEGATIVE 248 110 62 190 132 smit:SMT_2064|5end_amino_acid_ABC_transporter,_ATP-binding_protein_1972182..1972412_POSITIVE 247 118 71 231 186 smit:SMT_1444|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1427979..1428209_NEGATIVE 247 120 86 46 5 smit:SMT_593|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_509398..509628_POSITIVE 240 109 61 219 173 smit:SMT_1539|5end_sensor_histidine_kinase,_putative_1524310..1524540_NEGATIVE 239 114 71 87 40 smit:SMT_1973|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1905438..1905668_NEGATIVE 237 90 41 57 4 smit:SMT_647|5end_DNA_gyrase,_A_subunit_554170..554400_NEGATIVE 232 113 88 175 146 smit:SMT_993|5end_hypothetical_protein_935476..935706_NEGATIVE 229 92 55 213 176 smit:SMT_1458|5end_K02040_phosphate_transport_system_substrate-binding_protein_1440277..1440507_POSITIVE 229 101 64 70 37 smit:SMT_1149|5end_hypothetical_protein_1094270..1094500_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 120 75 76 18 smit:SMT_834|3end_hypothetical_protein_775517..775667_NEGATIVE 265 104 61 137 97 smit:SMT_1589|3end_hypothetical_protein_1578606..1578756_POSITIVE 255 111 77 134 95 smit:SMT_117|3end_K02025_multiple_sugar_transport_system_permease_protein_69496..69646_POSITIVE 253 108 65 55 4 smit:SMT_278|3end_tyrosine-protein_kinase_221048..221198_POSITIVE 250 92 60 46 2 smit:SMT_1993|3end_hypothetical_protein_1919207..1919357_NEGATIVE 250 92 60 46 2 smit:SMT_1416|3end_hypothetical_protein_1399570..1399720_NEGATIVE 229 101 64 52 19 smit:SMT_1150|3end_hypothetical_protein_1094288..1094438_NEGATIVE 229 97 51 76 22 smit:SMT_671|3end_hypothetical_protein_580676..580826_POSITIVE 229 111 73 67 28 smit:SMT_174|3end_30S_ribosomal_protein_S19_117792..117942_POSITIVE 228 103 78 68 39 smit:SMT_762|3end_cation-transporting_ATPase,_E1-E2_family_protein_667368..667518_NEGATIVE 225 99 54 134 88 smit:SMT_497|3end_hypothetical_protein_431810..431960_POSITIVE 221 120 80 76 24 smit:SMT_915|3end_sucrose_operon_repressor_868619..868769_POSITIVE 221 117 71 151 115 smit:SMT_391|3end_PTS_system,_galactose-specific_IIC_component_323671..323821_POSITIVE 221 113 85 133 101 smit:SMT_176|3end_30S_ribosomal_protein_S3_118814..118964_POSITIVE 217 94 56 69 40 smit:SMT_1948|3end_IS1381_transposase_protein_A_1883581..1883731_POSITIVE 215 108 75 61 17 smit:SMT_698|3end_uracil_permease_609769..609919_POSITIVE 213 85 41 85 35 smit:SMT_1019|3end_K03295_cation_efflux_system_protein,_CDF_family_954782..954932_NEGATIVE 213 107 62 53 14 smit:SMT_220|3end_Hypothetical_zinc_metalloprotease_153086..153236_POSITIVE 209 113 92 119 98 smit:SMT_1521|3end_K02003_1501240..1501390_NEGATIVE 208 120 82 149 100 smit:SMT_1693|3end_dimethyladenosine_transferase_1676752..1676902_POSITIVE