Origin IGS: gggcargagaatctggtcattacgactgcgactggragtcagaaaggcatttctttaaagcacactttttnnnnnttaattaattaannnnngaatacaaaaaaattatcgtgacagtggagcaggtttatcgttctacttgtttcatatgttacaaagactttcccagatgttcac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtgaacatctgggaaagtctttgtaacatatgaaacaagtagaacgataaacctgctccactgtcacgataatttttttgtattcnnnnnttaattaattaannnnnaaaaagtgtgctttaaagaaatgcctttctgactyccagtcgcagtcgtaatgaccagattctcytgccc Mask Tandem Repeat Region ================================================ gggcargagaatctggtcattacgactgcgactggragtcagaaaggcatttctttaaagcacactttttnnnnnttaattaattaannnnngaatacaaaaaaattatcgtgacagtggagcaggtttatcgttctacttgtttcatatgttacaaagactttcccagatgttcac Find is-nt database================================================ Query_seq: SMT_2072:SMT_2073|SMT_2072:SMT_2073:exonuclease RexA:hypothetical protein predicted by Glimmer/Critica:<-->:1976880..1977056 177 gggcargagaatctggtcattacgactgcgactggragtcagaaaggcatttctttaaagcacactttttnnnnnttaattaattaannnnngaatacaaaaaaattatcgtgacagtggagcaggtttatcgttctacttgtttcatatgttacaaagactttcccagatgttcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2072:SMT_2073|SMT_2072:SMT_2073:exonuclease RexA:hypothetical protein predicted by Glimmer/Critica:<-->:1976880..1977056 177 gggcargagaatctggtcattacgactgcgactggragtcagaaaggcatttctttaaagcacactttttnnnnnttaattaattaannnnngaatacaaaaaaattatcgtgacagtggagcaggtttatcgttctacttgtttcatatgttacaaagactttcccagatgttcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2072:SMT_2073|SMT_2072:SMT_2073:exonuclease RexA:hypothetical protein predicted by Glimmer/Critica:<-->:1976880..1977056 177 gggcargagaatctggtcattacgactgcgactggragtcagaaaggcatttctttaaagcacactttttnnnnnttaattaattaannnnngaatacaaaaaaattatcgtgacagtggagcaggtttatcgttctacttgtttcatatgttacaaagactttcccagatgttcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggcargagaatctggtcattacgactgcgactggragtcagaaaggcatttctttaaagcacactttttnnnnnttaattaattaannnnngaatacaaaaaaattatcgtgacagtggagcaggtttatcgttctacttgtttcatatgttacaaagactttcccagatgttcac Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 83 End: 175 .................................................................................. M X X X I Q K N Y R D S G A G L S F Y L F H M L Q R L S Q M F .. gggcargagaatctggtcattacgactgcgactggragtcagaaaggcatttctttaaagcacactttttnnnnnttaattaattaannnnngaatacaaaaaaattatcgtgacagtggagcaggtttatcgttctacttgtttcatatgttacaaagactttcccagatgttcac 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================================================ gggcargagaatctggtcattacgactgcgactggragtcagaaaggcatttctttaaagcacactttttnnnnnttaattaattaannnnngaatacaaaaaaattatcgtgacagtggagcaggtttatcgttctacttgtttcatatgttacaaagactttcccagatgttcac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2072:SMT_2073|SMT_2072:SMT_2073:exonuclease RexA:hypothetical protein predicted by Glimmer/Critica:<-->:1976880..1977056 177 gggcargagaatctggtcattacgactgcgactggragtcagaaaggcatttctttaaagcacactttttnnnnnttaattaattaannnnngaatacaaaaaaattatcgtgacagtggagcaggtttatcgttctacttgtttcatatgttacaaagactttcccagatgttcac Intra-Species Hit: Count: 1 Min: 1 Max: 177 Len: 177 Subject: smit_SMT_2072_SMT_2073|exonuclease RexA:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:POSITIVE|[1976880,1977056]|177 HSP 1 e-value: 8.0E-64 bit: 244.0 Len: 177 Query Start:1 Query End:177 Subject Strand: POSITIVE Subject Start: 1 Subject End: 177 gggcargagaatctggtcattacgactgcgactggragtcagaaaggcatttctttaaagcacactttttnnnnnttaattaattaannnnngaatacnnnnnnnttatcgtgacagtggagcaggtttatcgttctacttgtttcatatgttacaaagactttcccagatgttcac gggcargagaatctggtcattacgactgcgactggragtcagaaaggcatttctttaaagcacactttttnnnnnttaattaattaannnnngaatacaaaaaaattatcgtgacagtggagcaggtttatcgttctacttgtttcatatgttacaaagactttcccagatgttcac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGCARGAGAAUCUGGUCAUUACGACUGCGACUGGRAGUCAGAAAGGCAUUUCUUUAAAGCACACUUUUUNNNNNUUAAUUAAUUAANNNNNGAAUACAAAAAAAUUAUCGUGACAGUGGAGCAGGUUUAUCGUUCUACUUGUUUCAUAUGUUACAAAGACUUUCCCAGAUGUUCAC ((((..........((((.....))))....((((.((((.((((....)))).........................................................(((((((((((((((((..........))))))))))).))))))...))))...))))..)))).. (-35.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGAACAUCUGGGAAAGUCUUUGUAACAUAUGAAACAAGUAGAACGAUAAACCUGCUCCACUGUCACGAUAAUUUUUUUGUAUUCNNNNNUUAAUUAAUUAANNNNNAAAAAGUGUGCUUUAAAGAAAUGCCUUUCUGACUYCCAGUCGCAGUCGUAAUGACCAGAUUCUCYUGCCC ......((((((.....((((((...(((((......(((((..........)))))........((((........))))...............................)))))...))))))..(((..((.((((.....)))).))..)))....)))))).......... (-23.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 887 50 1 141 92 smit:SMT_2072|5end_exonuclease_RexA_1976789..1977019_NEGATIVE 563 70 24 50 1 smit:SMT_2017|5end_exonuclease_RexA_1936785..1937015_NEGATIVE 563 70 24 50 1 smit:SMT_1798|5end_exonuclease_RexA_1773441..1773671_NEGATIVE 288 62 23 90 52 smit:SMT_1386|5end_phosphoenolpyruvate-protein_phosphotransferase_1362806..1363036_POSITIVE 272 40 1 104 60 smit:SMT_1928|5end_O-methyltransferase_family_protein_1869652..1869882_NEGATIVE 271 53 11 54 17 smit:SMT_1084|5end_hypothetical_protein_1021925..1022155_NEGATIVE 266 50 7 72 29 smit:SMT_147|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_97406..97636_POSITIVE 266 50 7 72 29 smit:SMT_119|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_70457..70687_POSITIVE 263 49 1 204 157 smit:SMT_343|5end_hypothetical_protein_283554..283784_NEGATIVE 260 49 1 90 43 smit:SMT_1048|5end_K06518_holin-like_protein_988142..988372_POSITIVE 259 51 12 73 33 smit:SMT_2124|5end_hypothetical_protein_2008442..2008672_POSITIVE 259 51 12 73 33 smit:SMT_751|5end_hypothetical_protein_655677..655907_NEGATIVE 250 43 3 216 171 smit:SMT_700|5end_putative_signal_recognition_particle_-inhibited_division_protein_611511..611741_NEGATIVE 250 67 26 59 28 smit:SMT_412|5end_hypothetical_protein_predicted_by_Glimmer/Critica_356606..356836_NEGATIVE 248 169 121 125 80 smit:SMT_798|5end_hypothetical_protein_705788..706018_POSITIVE 248 168 124 65 23 smit:SMT_643|5end_hypothetical_protein_548495..548725_NEGATIVE 247 47 2 219 172 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 245 69 23 74 19 smit:SMT_303|5end_hypothetical_protein_245364..245594_POSITIVE 241 52 12 208 163 smit:SMT_1786|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763540..1763770_NEGATIVE 240 55 11 103 56 smit:SMT_587|5end_ATP_synthase_epsilon_chain_503950..504180_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 46 2 75 25 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 288 62 23 75 37 smit:SMT_1385|3end_phosphocarrier_protein_HPr_1362871..1363021_POSITIVE 272 40 1 66 22 smit:SMT_1929|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1869690..1869840_NEGATIVE 272 48 1 150 96 smit:SMT_588|3end_hypothetical_protein_504464..504614_NEGATIVE 271 53 11 53 16 smit:SMT_1085|3end_sensor_histidine_kinase_(homolog_to_HK11_Spn)_1021926..1022076_NEGATIVE 259 51 12 92 52 smit:SMT_2123|3end_hypothetical_protein_2008541..2008691_POSITIVE 259 51 12 62 22 smit:SMT_752|3end_prephenate_dehydrogenase_655688..655838_NEGATIVE 248 169 121 106 61 smit:SMT_797|3end_hypothetical_protein_705849..705999_POSITIVE 241 52 12 80 35 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 240 55 11 92 45 smit:SMT_586|3end_ATP_synthase_F1,_beta_subunit_504019..504169_POSITIVE 238 147 109 64 25 smit:SMT_1962|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1894848..1894998_NEGATIVE 237 57 14 43 2 smit:SMT_1710|3end_magnesium-translocating_P-type_ATPase_1695578..1695728_NEGATIVE 237 49 2 63 25 smit:SMT_1321|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1291458..1291608_POSITIVE 236 47 2 74 22 smit:SMT_2068|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1974183..1974333_NEGATIVE 234 144 112 42 12 smit:SMT_1950|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_1885069..1885219_POSITIVE 225 170 123 80 27 smit:SMT_1264|3end_oligoendopeptidase_F_1230734..1230884_POSITIVE 220 50 1 61 5 smit:SMT_213|3end_leucyl-tRNA_synthetase_146167..146317_POSITIVE 218 41 1 148 97 smit:SMT_592|3end_amino_acid_ABC_transporter,_ATP-binding_protein_509468..509618_POSITIVE 216 136 105 147 112 smit:SMT_1973|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1904878..1905028_NEGATIVE 215 147 103 79 35 smit:SMT_489|3end_K01999_branched-chain_amino_acid_transport_system_substrate-binding_protein_424507..424657_POSITIVE