Origin IGS: tctttctaagaattctcttgcttcattataacacgatttaggctttttctctatccagattgcttttttataaaattttagtgaattttttcagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaaaggagattcctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaggaatctcctttgtgttagattttataacatgattctacaccaaaagatttgtcttgtcaaatcatatctgaaaaaattcactaaaattttataaaaaagcaatctggatagagaaaaagcctaaatcgtgttataatgaagcaagagaattcttagaaaga Mask Tandem Repeat Region ================================================ tctttctaagaattctcttgcttcattataacacgatttaggctttttctctatccagattgcttttttataaaattttagtgaattttttcagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaaaggagattcctt Find is-nt database================================================ Query_seq: SMT_886:SMT_887|SMT_886:SMT_887:single-stranded-DNA-specific exonuclease RecJ:ABC-type polar amino acid transport system, ATPase component:<-->:834666..834829 164 tctttctaagaattctcttgcttcattataacacgatttaggctttttctctatccagattgcttttttataaaattttagtgaattttttcagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaaaggagattcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_886:SMT_887|SMT_886:SMT_887:single-stranded-DNA-specific exonuclease RecJ:ABC-type polar amino acid transport system, ATPase component:<-->:834666..834829 164 tctttctaagaattctcttgcttcattataacacgatttaggctttttctctatccagattgcttttttataaaattttagtgaattttttcagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaaaggagattcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_886:SMT_887|SMT_886:SMT_887:single-stranded-DNA-specific exonuclease RecJ:ABC-type polar amino acid transport system, ATPase component:<-->:834666..834829 164 tctttctaagaattctcttgcttcattataacacgatttaggctttttctctatccagattgcttttttataaaattttagtgaattttttcagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaaaggagattcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttctaagaattctcttgcttcattataacacgatttaggctttttctctatccagattgcttttttataaaattttagtgaattttttcagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaaaggagattcctt Predict ORF larger than 30AA ================================================ tctttctaagaattctcttgcttcattataacacgatttaggctttttctctatccagattgcttttttataaaattttagtgaattttttcagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaaaggagattcctt 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: 89 Start: 101 End: 130 ....................................................................................................TTTGACAAGACAAATCTTTTGGTGTAGAAT.................................. PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 25 End: 54 ........................ATAGAGAAAAAGCCTAAATCGTGTTATAAT.............................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctttctaagaattctcttgcttcattataacacgatttaggctttttctctatccagattgcttttttataaaattttagtgaattttttcagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaaaggagattcctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_886:SMT_887|SMT_886:SMT_887:single-stranded-DNA-specific exonuclease RecJ:ABC-type polar amino acid transport system, ATPase component:<-->:834666..834829 164 tctttctaagaattctcttgcttcattataacacgatttaggctttttctctatccagattgcttttttataaaattttagtgaattttttcagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaaaggagattcctt Intra-Species Hit: Count: 1 Min: 1 Max: 164 Len: 164 Subject: smit_SMT_886_SMT_887|single-stranded-DNA-specific exonuclease RecJ:ABC-type polar amino acid transport system, ATPase component|NEGATIVE:POSITIVE|[834666,834829]|164 HSP 1 e-value: 5.0E-34 bit: 145.0 Len: 73 Query Start:92 Query End:164 Subject Strand: POSITIVE Subject Start: 92 Subject End: 164 ...........................................................................................cagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaaaggagattcctt ...........................................................................................cagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaaaggagattcctt HSP 2 e-value: 2.0E-11 bit: 69.9 Len: 35 Query Start:1 Query End:35 Subject Strand: POSITIVE Subject Start: 1 Subject End: 35 tctttctaagaattctcttgcttcattataacacg................................................................................................................................. tctttctaagaattctcttgcttcattataacacg................................................................................................................................. Inter-species Hit: Count: 3 Min: 1 Max: 159 Len: 159 Subject: NC_008533_SPD_0530_SPD_0532|amino acid ABC transporter, amino acid-binding protein:single-stranded-DNA-specific exonuclease RecJ|NEGATIVE:POSITIVE|[541786,542830]|1045 HSP 1 e-value: 2.0E-9 bit: 63.9 Len: 68 Query Start:92 Query End:159 Subject Strand: NEGATIVE Subject Start: 775 Subject End: 842 ...........................................................................................cagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaaaggagat..... ...........................................................................................cagatatggtttgacaagaacattctttcactgtagaatcgtgttataaaatctaaaacaaaggagat..... HSP 2 e-value: 9.0E-8 bit: 58.0 Len: 33 Query Start:1 Query End:33 Subject Strand: NEGATIVE Subject Start: 1001 Subject End: 1033 tctttctaagaattctcttgcttcattataaca................................................................................................................................... tctttctaagaattctattgcttcattataaca................................................................................................................................... Subject: NC_003098_spr0536_spr0537|ABC transporter ATP-binding protein - glutamine, truncation:Single-stranded DNA-specific exonuclease, 5'-3'|NEGATIVE:POSITIVE|[535025,535288]|264 HSP 1 e-value: 2.0E-9 bit: 63.9 Len: 68 Query Start:92 Query End:159 Subject Strand: NEGATIVE Subject Start: 6 Subject End: 73 ...........................................................................................cagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaaaggagat..... ...........................................................................................cagatatggtttgacaagaacattctttcactgtagaatcgtgttataaaatctaaaacaaaggagat..... HSP 2 e-value: 9.0E-8 bit: 58.0 Len: 33 Query Start:1 Query End:33 Subject Strand: NEGATIVE Subject Start: 232 Subject End: 264 tctttctaagaattctcttgcttcattataaca................................................................................................................................... tctttctaagaattctattgcttcattataaca................................................................................................................................... Subject: NC_003028_SP_0610_SP_0611|amino acid ABC transporter, ATP-binding protein:single-stranded-DNA-specific exonuclease RecJ|NEGATIVE:POSITIVE|[577176,577451]|276 HSP 1 e-value: 9.0E-8 bit: 58.0 Len: 61 Query Start:92 Query End:152 Subject Strand: NEGATIVE Subject Start: 13 Subject End: 73 ...........................................................................................cagatatgatttgacaagacaaatcttttggtgtagaatcatgttataaaatctaacacaa............ ...........................................................................................cagatatgatttgacaagaacattcttttattgtagaaccgtgttataaaatataacacaa............ HSP 2 e-value: 9.0E-8 bit: 58.0 Len: 33 Query Start:1 Query End:33 Subject Strand: NEGATIVE Subject Start: 232 Subject End: 264 tctttctaagaattctcttgcttcattataaca................................................................................................................................... tctttctaagaattctattgcttcattataaca................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUCUAAGAAUUCUCUUGCUUCAUUAUAACACGAUUUAGGCUUUUUCUCUAUCCAGAUUGCUUUUUUAUAAAAUUUUAGUGAAUUUUUUCAGAUAUGAUUUGACAAGACAAAUCUUUUGGUGUAGAAUCAUGUUAUAAAAUCUAACACAAAGGAGAU .............((((((..(((((((.......((..((((....(((......)))..))))....)).......)))))))........((((((((((.(((...(((.....))).))).))))))))))................)))))). (-25.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUCCUUUGUGUUAGAUUUUAUAACAUGAUUCUACACCAAAAGAUUUGUCUUGUCAAAUCAUAUCUGAAAAAAUUCACUAAAAUUUUAUAAAAAAGCAAUCUGGAUAGAGAAAAAGCCUAAAUCGUGUUAUAAUGAAGCAAGAGAAUUCUUAGAAAGA .((((..((((.(((....((((((((((((((((..(((...((((((......)))))).....((((....))))........................))).))))............))))))))))))))).))))))))............. (-25.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 796 60 11 151 102 smit:SMT_886|5end_single-stranded-DNA-specific_exonuclease_RecJ_834575..834805_NEGATIVE 267 51 15 39 1 smit:SMT_308|5end_trans-2-enoyl-ACP_reductase_II_249439..249669_POSITIVE 255 55 12 149 100 smit:SMT_628|5end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_532831..533061_POSITIVE 250 55 12 230 182 smit:SMT_268|5end_penicillin-binding_protein_2X_205471..205701_POSITIVE 241 50 1 108 63 smit:SMT_1345|5end_K06198_competence_protein_CoiA_1323770..1324000_NEGATIVE 234 97 51 119 57 smit:SMT_1082|5end_Cof_family_protein_1020153..1020383_POSITIVE 224 58 18 102 63 smit:SMT_1813|5end_amino_acid_transporter_1787142..1787372_POSITIVE 224 24 1 225 196 smit:SMT_1680|5end_hypothetical_protein_1663494..1663724_POSITIVE 221 55 13 155 97 smit:SMT_1971|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1903282..1903512_POSITIVE 221 55 13 128 70 smit:SMT_1219|5end_hypothetical_protein_1179392..1179622_POSITIVE 218 45 1 153 107 smit:SMT_683|5end_similar_to_CDP-ribitol_pyrophosphorylase_592572..592802_NEGATIVE 216 43 15 165 127 smit:SMT_1627|5end_hypothetical_protein_1616415..1616645_NEGATIVE 216 69 21 162 108 smit:SMT_1094|5end_membrane_carboxypeptidase_(penicillin-binding_protein)_1036336..1036566_NEGATIVE 215 48 3 163 110 smit:SMT_536|5end_oxidoreductase,_aldo/keto_reductase_family_454451..454681_POSITIVE 213 71 33 60 14 smit:SMT_902|5end_hypothetical_protein_851789..852019_NEGATIVE 211 49 2 123 84 smit:SMT_791|5end_thiamine_biosynthesis_protein_ThiI_702377..702607_NEGATIVE 211 57 11 103 57 smit:SMT_357|5end_tRNA_(guanine-N7-)-methyltransferase_293185..293415_POSITIVE 209 128 82 221 178 smit:SMT_1773|5end_hypothetical_protein_1749241..1749471_POSITIVE 209 69 22 206 157 smit:SMT_1114|5end_competence_protein_1052555..1052785_NEGATIVE 208 50 5 137 80 smit:SMT_108|5end_hypothetical_protein_53488..53718_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 61 38 101 76 smit:SMT_1428|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1414269..1414419_NEGATIVE 237 64 32 36 5 smit:SMT_1752|3end_N-(5'-phosphoribosyl)-anthranilate_isomerase_1730451..1730601_POSITIVE 224 58 18 73 34 smit:SMT_1812|3end_K07485_transposase_1787193..1787343_POSITIVE 224 57 14 131 79 smit:SMT_162|3end_hypothetical_protein_107134..107284_POSITIVE 219 50 1 151 95 smit:SMT_627|3end_glucose-1-phosphate_adenylyltransferase_532921..533071_POSITIVE 215 48 3 88 35 smit:SMT_535|3end_hypothetical_protein_454456..454606_POSITIVE 211 49 2 42 3 smit:SMT_792|3end_hypothetical_protein_predicted_by_Glimmer/Critica_702458..702608_NEGATIVE 211 57 11 106 60 smit:SMT_356|3end_hypothetical_protein_293268..293418_POSITIVE 205 64 22 138 97 smit:SMT_1309|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1274296..1274446_POSITIVE 204 59 18 60 14 smit:SMT_1431|3end_K08986_putative_membrane_protein_1416654..1416804_POSITIVE 203 68 31 69 33 smit:SMT_2072|3end_exonuclease_RexA_1975980..1976130_NEGATIVE 203 110 61 71 30 smit:SMT_1729|3end_exodeoxyribonuclease_VII_small_subunit_1714858..1715008_POSITIVE 202 52 20 117 88 smit:SMT_1975|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1906952..1907102_POSITIVE 197 55 15 105 61 smit:SMT_2080|3end_glycosyl_transferase_CpsE_1980915..1981065_POSITIVE 197 55 15 105 61 smit:SMT_279|3end_glycosyl_transferase_CpsE_222421..222571_POSITIVE 196 56 14 116 72 smit:SMT_1933|3end_K02006_cobalt_transport_system_ATP-binding_protein_1871986..1872136_NEGATIVE 196 146 103 88 41 smit:SMT_1109|3end_hypothetical_protein_1049362..1049512_NEGATIVE 195 46 2 53 23 smit:SMT_986|3end_threonyl-tRNA_synthetase_931684..931834_POSITIVE 194 53 19 106 80 smit:SMT_551|3end_K07170_GAF_domain-containing_protein_469525..469675_POSITIVE 193 43 1 77 35 smit:SMT_801|3end_glycyl-tRNA_synthetase_alpha_chain_709892..710042_NEGATIVE