Origin IGS: tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaagagtgaatctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagattcactctttctatttataattttgagggtttcccctcactttttgataggttcttaaacatcgaaacagggagtgagtcagaggctcattccctatttcaacatttttcta Mask Tandem Repeat Region ================================================ tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaagagtgaatctt Find is-nt database================================================ Query_seq: SMT_489:SMT_490|SMT_489:SMT_490:K01999 branched-chain amino acid transport system substrate-binding protein:branched-chain amino acid ABC transporter, permease protein:->->:424568..424683 116 tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaagagtgaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_489:SMT_490|SMT_489:SMT_490:K01999 branched-chain amino acid transport system substrate-binding protein:branched-chain amino acid ABC transporter, permease protein:->->:424568..424683 116 tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaagagtgaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_489:SMT_490|SMT_489:SMT_490:K01999 branched-chain amino acid transport system substrate-binding protein:branched-chain amino acid ABC transporter, permease protein:->->:424568..424683 116 tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaagagtgaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaagagtgaatctt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 2 End: 100 . S F H Q F L S H A E S E S G T E I N L F R D F L S P F G E F N Y M ................ tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaagagtgaatctt 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================================================ tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaagagtgaatctt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 80 HP_score: -10.3 Tail_Score: -3.69455 Start: 17 End: 45 Full_Region: tcttaaacatcgaaa cagggagtgagtc aga ggctcattcccta tttcaacatttttct ................cagggagtgagtcagaggctcattcccta....................................................................... TransTerm Strand: - Conf: 93 HP_score: -12.9 Tail_Score: -3.41445 Start: 19 End: 43 Full_Region: ttaaacatcgaaaca gggagtgagtc aga ggctcattccc tatttcaacattttt ..................gggagtgagtcagaggctcattccc......................................................................... Find igs database================================================ Query_seq: SMT_489:SMT_490|SMT_489:SMT_490:K01999 branched-chain amino acid transport system substrate-binding protein:branched-chain amino acid ABC transporter, permease protein:->->:424568..424683 116 tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaagagtgaatctt Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: smit_SMT_489_SMT_490|K01999 branched-chain amino acid transport system substrate-binding protein:branched-chain amino acid ABC transporter, permease protein|POSITIVE:POSITIVE|[424568,424683]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaagagtgaatctt tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaagagtgaatctt Inter-species Hit: Count: 3 Min: 1 Max: 116 Len: 116 Subject: NC_008533_SPD_0652_SPD_0653|branched-chain amino acid ABC transporter, amino acid-binding protein:branched-chain amino acid ABC transporter, permease protein|POSITIVE:POSITIVE|[671147,671413]|267 HSP 1 e-value: 2.0E-20 bit: 99.6 Len: 58 Query Start:1 Query End:58 Subject Strand: POSITIVE Subject Start: 1 Subject End: 58 tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaa.......................................................... tagaaaaatgttgaaatagggaatgagcctttgactcactccctgtttcgatatttaa.......................................................... HSP 2 e-value: 7.0E-20 bit: 97.6 Len: 61 Query Start:56 Query End:116 Subject Strand: POSITIVE Subject Start: 207 Subject End: 267 .......................................................taagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaagagtgaatctt .......................................................taagaacctatcaaaaagtgagggaaaaccctcggaattataaatagaaagagtgaatctt Subject: NC_003098_spr0659_spr0660|ABC transporter substrate-binding protein - branched chain amino acid transport:ABC transporter membrane-spanning permease - branched chain amino acid transport|POSITIVE:POSITIVE|[663616,663873]|258 HSP 1 e-value: 2.0E-20 bit: 99.6 Len: 58 Query Start:1 Query End:58 Subject Strand: POSITIVE Subject Start: 1 Subject End: 58 tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaa.......................................................... tagaaaaatgttgaaatagggaatgagcctttgactcactccctgtttcgatatttaa.......................................................... HSP 2 e-value: 2.0E-14 bit: 79.8 Len: 52 Query Start:56 Query End:107 Subject Strand: POSITIVE Subject Start: 207 Subject End: 258 .......................................................taagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaaga......... .......................................................taagaacctatcaaaaagtgagggaaaaccctcggaattataaatagaaaga......... Subject: NC_003028_SP_0749_SP_0750|branched-chain amino acid ABC transporter, amino acid-binding protein:branched-chain amino acid ABC transporter, permease protein|POSITIVE:POSITIVE|[709061,709327]|267 HSP 1 e-value: 2.0E-20 bit: 99.6 Len: 58 Query Start:1 Query End:58 Subject Strand: POSITIVE Subject Start: 1 Subject End: 58 tagaaaaatgttgaaatagggaatgagcctctgactcactccctgtttcgatgtttaa.......................................................... tagaaaaatgttgaaatagggaatgagcctttgactcactccctgtttcgatatttaa.......................................................... HSP 2 e-value: 7.0E-20 bit: 97.6 Len: 61 Query Start:56 Query End:116 Subject Strand: POSITIVE Subject Start: 207 Subject End: 267 .......................................................taagaacctatcaaaaagtgaggggaaaccctcaaaattataaatagaaagagtgaatctt .......................................................taagaacctatcaaaaagtgagggaaaaccctcggaattataaatagaaagagtgaatctt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAAAUGUUGAAAUAGGGAAUGAGCCUCUGACUCACUCCCUGUUUCGAUGUUUAAGAACCUAUCAAAAAGUGAGGGGAAACCCUCAAAAUUAUAAAUAGAAAGAGUGAAUCUU .....(((((((((((((((((.((((.......)))).)))))))))))))))))......((((.......((((((....)))))).........)))).((((.....)))) (-40.29) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUUCACUCUUUCUAUUUAUAAUUUUGAGGGUUUCCCCUCACUUUUUGAUAGGUUCUUAAACAUCGAAACAGGGAGUGAGUCAGAGGCUCAUUCCCUAUUUCAACAUUUUUCUA .(((.........((((((...((...((((((....))))))..))..))))))............((((.(((((((((((.....))))))))))).))))........))). (-35.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 90 41 56 17 smit:SMT_1528|5end_K03310_alanine_or_glycine:cation_symporter,_AGCS_family_1512667..1512897_NEGATIVE 282 67 22 108 50 smit:SMT_414|5end_K03665_GTP-binding_protein_HflX_357554..357784_POSITIVE 264 60 13 82 20 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 262 60 11 57 8 smit:SMT_882|5end_acetyl_esterase_830441..830671_NEGATIVE 260 58 16 176 131 smit:SMT_578|5end_lipoprotein_signal_peptidase_496061..496291_POSITIVE 253 66 23 126 83 smit:SMT_1474|5end_K02003_1455170..1455400_POSITIVE 251 78 35 160 106 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 251 69 30 140 99 smit:SMT_973|5end_signal_transduction_histidine_kinase_922177..922407_NEGATIVE 251 60 11 127 83 smit:SMT_314|5end_biotin_carboxylase_254277..254507_POSITIVE 248 56 11 57 15 smit:SMT_1604|5end_K05833_putative_ABC_transport_system_ATP-binding_protein_1594280..1594510_POSITIVE 243 88 43 145 98 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 242 67 21 55 9 smit:SMT_1071|5end_hypothetical_protein_1010058..1010288_POSITIVE 238 50 17 45 17 smit:SMT_141|5end_K03495_glucose_inhibited_division_protein_A_91408..91638_POSITIVE 237 51 28 29 7 smit:SMT_1473|5end_hypothetical_protein_1454320..1454550_POSITIVE 237 56 19 169 132 smit:SMT_1340|5end_phosphoenolpyruvate_carboxylase_1317867..1318097_NEGATIVE 236 52 12 161 122 smit:SMT_2073|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1976917..1977147_POSITIVE 235 52 11 64 12 smit:SMT_850|5end_hypothetical_protein_797014..797244_NEGATIVE 235 56 19 74 25 smit:SMT_310|5end_3-oxoacyl-_251370..251600_POSITIVE 234 57 11 90 34 smit:SMT_1002|5end_aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B_943627..943857_POSITIVE 234 68 27 219 173 smit:SMT_215|5end_leucyl-tRNA_synthetase_147045..147275_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 56 11 85 40 smit:SMT_489|3end_K01999_branched-chain_amino_acid_transport_system_substrate-binding_protein_424507..424657_POSITIVE 282 67 22 115 57 smit:SMT_413|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_357641..357791_POSITIVE 271 53 17 53 17 smit:SMT_1553|3end_K04074_cell_division_initiation_protein_1536868..1537018_POSITIVE 264 60 13 95 33 smit:SMT_1190|3end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1147741..1147891_NEGATIVE 251 69 30 147 106 smit:SMT_974|3end_DNA-binding_response_regulator_922170..922320_NEGATIVE 251 60 11 115 71 smit:SMT_313|3end_3R-hydroxymyristoyl_ACP_dehydrase_254345..254495_POSITIVE 248 56 11 44 2 smit:SMT_1603|3end_K05832_putative_ABC_transport_system_permease_protein_1594347..1594497_POSITIVE 243 88 43 89 42 smit:SMT_1668|3end_K+_transport_system,_NAD-binding_component_1657623..1657773_NEGATIVE 238 50 17 55 27 smit:SMT_140|3end_NUDIX_family_hydrolase_91498..91648_POSITIVE 237 56 19 144 107 smit:SMT_1341|3end_putative_cell_division_protein_1317892..1318042_NEGATIVE 235 80 31 52 4 smit:SMT_1034|3end_K05896_segregation_and_condensation_protein_A_976768..976918_NEGATIVE 234 57 11 90 34 smit:SMT_1001|3end_aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_A_943707..943857_POSITIVE 234 44 7 63 37 smit:SMT_190|3end_preprotein_translocase,_SecY_subunit_125675..125825_POSITIVE 232 73 36 47 2 smit:SMT_1864|3end_integral_membrane_protein_1827172..1827322_POSITIVE 226 56 20 49 8 smit:SMT_1752|3end_N-(5'-phosphoribosyl)-anthranilate_isomerase_1730451..1730601_POSITIVE 226 55 11 60 12 smit:SMT_786|3end_hypothetical_protein_697239..697389_NEGATIVE 223 57 13 151 108 smit:SMT_1835|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1804072..1804222_POSITIVE 222 56 15 88 41 smit:SMT_1275|3end_rod_shape-determining_protein_MreC_1239492..1239642_POSITIVE 220 55 20 74 31 smit:SMT_2072|3end_exonuclease_RexA_1975980..1976130_NEGATIVE 219 66 31 78 35 smit:SMT_157|3end_hypothetical_protein_103871..104021_POSITIVE