Origin IGS: gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagagctcctttctttttatttatcttatcaaatttcccttaaattagctagtaggattgcctcattttgttgcctaaaaacaagctgcttcaaattcagtttcagatcttctagcattgaaaaatctgttataataatagaaaaggaggagcgc Mask Tandem Repeat Region ================================================ gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt Find is-nt database================================================ Query_seq: SMT_974:SMT_975|SMT_974:SMT_975:DNA-binding response regulator:hypothetical protein:<-->:922938..923092 155 gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_974:SMT_975|SMT_974:SMT_975:DNA-binding response regulator:hypothetical protein:<-->:922938..923092 155 gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_974:SMT_975|SMT_974:SMT_975:DNA-binding response regulator:hypothetical protein:<-->:922938..923092 155 gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 17 End: 124 ................ M I I T D F S M L E D L K L N L K Q L V F R Q Q N E A I L L A N L R E I ............................... Protein_Len: 41 Strand: - Start: 1 End: 123 R E E K E I I I V S K E I S S S R F S F K F C S T K L C C F S A I R S A L K L S M ................................ gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt 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================================================ gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_974:SMT_975|SMT_974:SMT_975:DNA-binding response regulator:hypothetical protein:<-->:922938..923092 155 gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt Intra-Species Hit: Count: 1 Min: 1 Max: 155 Len: 155 Subject: smit_SMT_974_SMT_975|DNA-binding response regulator:hypothetical protein|NEGATIVE:POSITIVE|[922938,923092]|155 HSP 1 e-value: 6.0E-83 bit: 307.0 Len: 155 Query Start:1 Query End:155 Subject Strand: POSITIVE Subject Start: 1 Subject End: 155 gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt Inter-species Hit: Count: 3 Min: 1 Max: 155 Len: 155 Subject: NC_008533_SPD_1446_SPD_1447|DNA-binding response regulator:hypothetical protein|NEGATIVE:POSITIVE|[1463047,1463201]|155 HSP 1 e-value: 5.0E-40 bit: 165.0 Len: 155 Query Start:1 Query End:155 Subject Strand: POSITIVE Subject Start: 1 Subject End: 155 gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt gcgcttctccttttccattattataacagatttttccatgctagatggtctgaaactgaatttgaaatagcctgtttttagccagtacaaacaggctatgctactagctaatttgagggaaatttgctaagataaataaaaagaaaggagctctt Subject: NC_003098_spr1474_spr1475|Response regulator:hypothetical protein|NEGATIVE:POSITIVE|[1455516,1455670]|155 HSP 1 e-value: 5.0E-40 bit: 165.0 Len: 155 Query Start:1 Query End:155 Subject Strand: POSITIVE Subject Start: 1 Subject End: 155 gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt gcgcttctccttttccattattataacagatttttccatgctagatggtctgaaactgaatttgaaatagcctgtttttagccagtacaaacaggctatgctactagctaatttgagggaaatttgctaagataaataaaaagaaaggagctctt Subject: NC_003028_SP_1633_SP_1634|DNA-binding response regulator:hypothetical protein|NEGATIVE:POSITIVE|[1534193,1534347]|155 HSP 1 e-value: 5.0E-40 bit: 165.0 Len: 155 Query Start:1 Query End:155 Subject Strand: POSITIVE Subject Start: 1 Subject End: 155 gcgctcctccttttctattattataacagatttttcaatgctagaagatctgaaactgaatttgaagcagcttgtttttaggcaacaaaatgaggcaatcctactagctaatttaagggaaatttgataagataaataaaaagaaaggagctctt gcgcttctccttttccattattataacagatttttccatgctagatggtctgaaactgaatttgaaatagcctgtttttagccagtacaaacaggctatgctactagctaatttgagggaaatttgctaagataaataaaaagaaaggagctctt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGCUCCUCCUUUUCUAUUAUUAUAACAGAUUUUUCAAUGCUAGAAGAUCUGAAACUGAAUUUGAAGCAGCUUGUUUUUAGGCAACAAAAUGAGGCAAUCCUACUAGCUAAUUUAAGGGAAAUUUGAUAAGAUAAAUAAAAAGAAAGGAGCUCUU ..((((((.(((((...(((((.((.(((((((..(...(((((.((...((...((.(.((((.....(((((....)))))..)))).).)).))...)).)))))........)..))))))).)).)))))...)))))..)))))).... (-34.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAGCUCCUUUCUUUUUAUUUAUCUUAUCAAAUUUCCCUUAAAUUAGCUAGUAGGAUUGCCUCAUUUUGUUGCCUAAAAACAAGCUGCUUCAAAUUCAGUUUCAGAUCUUCUAGCAUUGAAAAAUCUGUUAUAAUAAUAGAAAAGGAGGAGCGC ....(((((((..((((((((.((..((.((.((((...((((....(((((.((((((((..(.....)..))........((((((.........))))))..))))))))))).)))).)))).)).))..))))))))))..))))))).. (-32.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 860 110 61 201 152 smit:SMT_974|5end_DNA-binding_response_regulator_922847..923077_NEGATIVE 282 109 61 223 173 smit:SMT_717|5end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_623147..623377_NEGATIVE 262 120 71 225 174 smit:SMT_1984|5end_phosphinothricin_N-acetyltransferase_1914028..1914258_NEGATIVE 262 120 71 225 174 smit:SMT_1869|5end_phosphinothricin_N-acetyltransferase_1829215..1829445_NEGATIVE 259 119 71 169 128 smit:SMT_1622|5end_K03499_trk_system_potassium_uptake_protein_TrkA_1608243..1608473_POSITIVE 256 46 2 145 97 smit:SMT_2163|5end_cell_division_protein_FtsA_2037643..2037873_POSITIVE 256 46 2 145 97 smit:SMT_2158|5end_cell_division_protein_2031534..2031764_POSITIVE 256 46 2 145 97 smit:SMT_1707|5end_cell_division_protein_FtsA_1690945..1691175_POSITIVE 256 46 2 145 97 smit:SMT_1547|5end_cell_division_protein_FtsA_1530987..1531217_POSITIVE 250 126 81 117 68 smit:SMT_387|5end_hypothetical_protein_predicted_by_Glimmer/Critica_320937..321167_POSITIVE 242 46 2 145 97 smit:SMT_2160|5end_cell_division_protein_FtsA_2033524..2033754_POSITIVE 241 106 64 54 16 smit:SMT_1362|5end_chaperone_protein_hscC_1343078..1343308_NEGATIVE 240 106 61 126 80 smit:SMT_1852|5end_1,4-alpha-glucan_branching_enzyme_1817690..1817920_NEGATIVE 239 50 2 174 121 smit:SMT_465|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_protein_403244..403474_POSITIVE 239 50 2 174 121 smit:SMT_417|5end_short_chain_dehydrogenase_360373..360603_POSITIVE 238 49 4 150 101 smit:SMT_1170|5end_acetyltransferase,_CysE/LacA/LpxA/NodL_family_1118126..1118356_NEGATIVE 234 45 4 131 98 smit:SMT_89|5end_chromosomal_replication_initiator_protein_19857..20087_POSITIVE 231 100 57 68 30 smit:SMT_2049|5end_3-oxoacyl-_1959539..1959769_NEGATIVE 231 104 62 151 103 smit:SMT_2032|5end_hydrolase,_alpha/beta_fold_family_1946421..1946651_NEGATIVE 231 88 41 197 144 smit:SMT_603|5end_hypothetical_protein_517961..518191_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 126 81 102 53 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 240 106 61 129 83 smit:SMT_1853|3end_1,4-alpha-glucan_branching_enzyme_1817687..1817837_NEGATIVE 238 49 4 54 5 smit:SMT_1171|3end_hypothetical_protein_1118222..1118372_NEGATIVE 236 70 27 149 102 smit:SMT_1569|3end_dihydroxy-acid_dehydratase_1563068..1563218_POSITIVE 232 68 24 147 102 smit:SMT_1553|3end_K04074_cell_division_initiation_protein_1536868..1537018_POSITIVE 231 100 57 68 30 smit:SMT_2050|3end_K03712_MarR_family_transcriptional_regulator_1959539..1959689_NEGATIVE 231 88 41 120 67 smit:SMT_602|3end_5'-methylthioadenosine_nucleosidase_/_S-adenosylhomocysteine_nucleosidase_517964..518114_POSITIVE 228 76 32 68 32 smit:SMT_2102|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1993982..1994132_NEGATIVE 227 88 59 119 88 smit:SMT_1945|3end_putative_dihydrolipoamide_S-acetyltransferase_1880646..1880796_POSITIVE 227 50 1 113 67 smit:SMT_790|3end_hypothetical_protein_701093..701243_NEGATIVE 226 72 32 148 107 smit:SMT_2079|3end_single_strand_binding_protein_1980499..1980649_POSITIVE 226 47 2 149 100 smit:SMT_464|3end_ribonuclease_Z_403303..403453_POSITIVE 226 47 2 149 100 smit:SMT_416|3end_ribonuclease_Z_360432..360582_POSITIVE 225 120 73 71 27 smit:SMT_1672|3end_hypothetical_protein_1659806..1659956_NEGATIVE 223 73 31 63 24 smit:SMT_1283|3end_K02240_competence_protein_ComFA_1247045..1247195_POSITIVE 219 100 60 59 20 smit:SMT_603|3end_hypothetical_protein_518532..518682_POSITIVE 218 89 48 76 40 smit:SMT_380|3end_hypothetical_protein_316944..317094_POSITIVE 216 110 62 45 5 smit:SMT_785|3end_hypothetical_protein_696307..696457_NEGATIVE 216 110 67 149 110 smit:SMT_741|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_644314..644464_NEGATIVE 216 110 69 93 46 smit:SMT_304|3end_hypothetical_protein_247583..247733_POSITIVE