Origin IGS: gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttattttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaataaataaaatgggaagaaatagcgtttttaacttgacctaaaagggattttaggatatgattatatttgttaattagaaataaaattggaggaatcattaac Mask Tandem Repeat Region ================================================ gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttattttt Find is-nt database================================================ Query_seq: SMT_1882:SMT_1883|SMT_1882:SMT_1883:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:<-<-:1838017..1838123 107 gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1882:SMT_1883|SMT_1882:SMT_1883:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:<-<-:1838017..1838123 107 gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1882:SMT_1883|SMT_1882:SMT_1883:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:<-<-:1838017..1838123 107 gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttattttt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 5 End: 106 .... M I P P I L F L I N K Y N H I L K S L L G Q V K N A I S S H F I Y F . gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttattttt 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: 90 Start: 42 End: 71 .........................................CTTGACCTAAAAGGGATTTTAGGATATGAT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttattttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1882:SMT_1883|SMT_1882:SMT_1883:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:<-<-:1838017..1838123 107 gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttattttt Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: smit_SMT_1882_SMT_1883|hypothetical protein predicted by Glimmer/Critica:hypothetical protein|NEGATIVE:NEGATIVE|[1838017,1838123]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttattttt gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttattttt Inter-species Hit: Count: 3 Min: 1 Max: 106 Len: 106 Subject: NC_003028_SP_1112_SP_1113|degV family protein:DNA-binding protein HU|POSITIVE:POSITIVE|[1041994,1042098]|105 HSP 1 e-value: 2.0E-44 bit: 178.0 Len: 106 Query Start:1 Query End:106 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 105 gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttatttt. gttaatgattcctccaaata-atttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttatttt. Subject: NC_008533_SPD_0996_SPD_0997|DegV family protein:DNA-binding protein HU|POSITIVE:POSITIVE|[1006093,1006197]|105 HSP 1 e-value: 1.0E-39 bit: 163.0 Len: 106 Query Start:1 Query End:106 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 105 gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttatttt. gttaatgattcctccagata-atttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttccaattttatttatttt. Subject: NC_003098_spr1019_spr1020|hypothetical protein:Histone-like DNA-binding protein|POSITIVE:POSITIVE|[998562,998666]|105 HSP 1 e-value: 1.0E-39 bit: 163.0 Len: 106 Query Start:1 Query End:106 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 105 gttaatgattcctccaattttatttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttcccattttatttatttt. gttaatgattcctccagata-atttctaattaacaaatataatcatatcctaaaatcccttttaggtcaagttaaaaacgctatttcttccaattttatttatttt. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUAAUGAUUCCUCCAAUUUUAUUUCUAAUUAACAAAUAUAAUCAUAUCCUAAAAUCCCUUUUAGGUCAAGUUAAAAACGCUAUUUCUUCCCAUUUUAUUUAUUUU ((((((......................)))))).....((((.....(((((((....)))))))....))))................................ ( -7.55) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAAAUAAAAUGGGAAGAAAUAGCGUUUUUAACUUGACCUAAAAGGGAUUUUAGGAUAUGAUUAUAUUUGUUAAUUAGAAAUAAAAUUGGAGGAAUCAUUAAC ..((((((((....(..(((((......)))))..)....(((((((....))))))).........))))))))..(((....)))................... (-11.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 754 90 41 181 132 smit:SMT_1882|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1837926..1838156_NEGATIVE 235 89 44 219 179 smit:SMT_1727|5end_uridine_kinase_1712483..1712713_POSITIVE 222 91 59 199 165 smit:SMT_1630|5end_hypothetical_protein_1617291..1617521_POSITIVE 222 91 59 199 165 smit:SMT_1241|5end_hypothetical_protein_1201040..1201270_POSITIVE 217 67 23 122 77 smit:SMT_973|5end_signal_transduction_histidine_kinase_922177..922407_NEGATIVE 207 98 55 139 100 smit:SMT_2024|5end_hypothetical_protein_1940359..1940589_POSITIVE 207 90 44 128 81 smit:SMT_1748|5end_anthranilate_synthase_component_I_1726685..1726915_POSITIVE 207 98 55 139 100 smit:SMT_724|5end_hypothetical_protein_630060..630290_NEGATIVE 201 100 59 110 66 smit:SMT_1493|5end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1475737..1475967_POSITIVE 197 97 60 172 140 smit:SMT_1157|5end_septation_ring_formation_regulator_EzrA_1101929..1102159_NEGATIVE 195 90 54 221 181 smit:SMT_1255|5end_cell_division_protein_FtsH_1221811..1222041_NEGATIVE 190 93 58 69 40 smit:SMT_1380|5end_pyrroline-5-carboxylate_reductase_1358464..1358694_NEGATIVE 187 90 43 151 82 smit:SMT_1245|5end_SOS_responce_UmuC_protein_1205120..1205350_POSITIVE 185 100 64 170 138 smit:SMT_639|5end_6-phospho-beta-galactosidase_544885..545115_NEGATIVE 185 93 58 132 99 smit:SMT_567|5end_conserved_hypothetical_protein_484845..485075_POSITIVE 184 93 54 149 104 smit:SMT_840|5end_tRNA_nucleotidyltransferase_(CCA-adding_enzyme)_787261..787491_NEGATIVE 184 90 56 70 25 smit:SMT_142|5end_hypothetical_protein_95088..95318_NEGATIVE 182 96 56 159 101 smit:SMT_754|5end_3-dehydroquinate_synthase_659044..659274_NEGATIVE 180 71 45 70 45 smit:SMT_773|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_684365..684595_NEGATIVE 178 90 42 218 171 smit:SMT_1696|5end_hypothetical_protein_1678182..1678412_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 93 56 116 76 smit:SMT_2112|3end_transcription-repair_coupling_factor_2000373..2000523_NEGATIVE 235 89 44 109 69 smit:SMT_1726|3end_tRNA_pseudouridine_synthase_B_1712453..1712603_POSITIVE 226 96 60 68 28 smit:SMT_1013|3end_galactose-1-phosphate_uridylyltransferase_949601..949751_NEGATIVE 221 94 58 107 73 smit:SMT_278|3end_tyrosine-protein_kinase_221048..221198_POSITIVE 217 67 23 129 84 smit:SMT_974|3end_DNA-binding_response_regulator_922170..922320_NEGATIVE 210 88 48 54 15 smit:SMT_1444|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1427887..1428037_NEGATIVE 207 98 55 149 110 smit:SMT_725|3end_hypothetical_protein_630050..630200_NEGATIVE 201 100 59 71 27 smit:SMT_1492|3end_DNA-directed_RNA_polymerase_beta_chain_1475778..1475928_POSITIVE 197 97 60 90 58 smit:SMT_1158|3end_DNA_gyrase_subunit_B_1102011..1102161_NEGATIVE 194 93 55 132 97 smit:SMT_658|3end_hypothetical_protein_569403..569553_NEGATIVE 190 93 58 65 36 smit:SMT_1381|3end_gamma-glutamyl_phosphate_reductase_1358468..1358618_NEGATIVE 187 90 43 100 31 smit:SMT_1244|3end_putative_repressor_protein_1205149..1205299_POSITIVE 185 93 58 110 77 smit:SMT_566|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_484903..485053_POSITIVE 184 90 56 68 23 smit:SMT_143|3end_hypothetical_protein_95090..95240_NEGATIVE 182 96 56 140 82 smit:SMT_755|3end_shikimate_5-dehydrogenase_659063..659213_NEGATIVE 178 90 64 84 50 smit:SMT_1360|3end_lactoylglutathione_lyase_1338252..1338402_NEGATIVE 176 97 56 133 76 smit:SMT_1315|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1280952..1281102_POSITIVE 175 82 41 51 6 smit:SMT_328|3end_23S_rRNA_methyltransferase_264863..265013_POSITIVE 173 75 32 120 81 smit:SMT_345|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_284803..284953_POSITIVE 171 73 39 142 104 smit:SMT_461|3end_mannose-6-phosphate_isomerase_400403..400553_POSITIVE