Origin IGS: gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc Mask Tandem Repeat Region ================================================ gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt Find is-nt database================================================ Query_seq: SMT_871:SMT_872|SMT_871:SMT_872:K03311 branched-chain amino acid:cation transporter, LIVCS family:hypothetical protein:<-<-:820251..820420 170 gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_871:SMT_872|SMT_871:SMT_872:K03311 branched-chain amino acid:cation transporter, LIVCS family:hypothetical protein:<-<-:820251..820420 170 gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_871:SMT_872|SMT_871:SMT_872:K03311 branched-chain amino acid:cation transporter, LIVCS family:hypothetical protein:<-<-:820251..820420 170 gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 44 End: 145 ........................................... S Y S Y S F L K V F Y I N F T K L I R L F S F Q R F I F D G V W D M ......................... gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt 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================================================ gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_871:SMT_872|SMT_871:SMT_872:K03311 branched-chain amino acid:cation transporter, LIVCS family:hypothetical protein:<-<-:820251..820420 170 gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt Intra-Species Hit: Count: 2 Min: 1 Max: 170 Len: 170 Subject: smit_SMT_871_SMT_872|K03311 branched-chain amino acid:cation transporter, LIVCS family:hypothetical protein|NEGATIVE:NEGATIVE|[820251,820420]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt Subject: smit_SMT_385_SMT_386|hypothetical protein:branched-chain amino acid transport system II carrier protein|POSITIVE:POSITIVE|[320323,320492]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 170 gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt Inter-species Hit: Count: 3 Min: 2 Max: 160 Len: 159 Subject: NC_008533_SPD_0545_SPD_0546|hypothetical protein:branched-chain amino acid transport system II carrier protein|POSITIVE:POSITIVE|[558043,558212]|170 HSP 1 e-value: 1.0E-47 bit: 190.0 Len: 159 Query Start:2 Query End:160 Subject Strand: NEGATIVE Subject Start: 10 Subject End: 169 .aaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaa-tcccctacccagtccacgccaagtaggagaaa.......... .aaaatctccttcatatttataaaatactgacctagtataccacgattaggagtctgaaaaaagcatcacgatgcaaatattaaatgttttcaactttcttaaaaataagaattatctaaaaataaaactctcctacccagtccacaccaagtaggagaaa.......... Subject: NC_003098_spr0550_spr0551|hypothetical protein:Branched-chain amino acid transport system carrier protein|POSITIVE:POSITIVE|[550513,550667]|155 HSP 1 e-value: 2.0E-39 bit: 163.0 Len: 145 Query Start:16 Query End:160 Subject Strand: NEGATIVE Subject Start: 10 Subject End: 155 ...............atttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaa-tcccctacccagtccacgccaagtaggagaaa.......... ...............atttataaaatactgacctagtataccacgattaggagtctgaaaaaagcatcacgatgcaaatattaaatgttttcaactttcttaaaaataagaattatctaaaaataaaactctcctacccagtccacaccaagtaggagaaa.......... Subject: NC_003028_SP_0624_SP_0626|hypothetical protein:branched-chain amino acid transport system II carrier protein|POSITIVE:POSITIVE|[592218,592819]|602 HSP 1 e-value: 2.0E-39 bit: 163.0 Len: 145 Query Start:16 Query End:160 Subject Strand: NEGATIVE Subject Start: 457 Subject End: 602 ...............atttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaa-tcccctacccagtccacgccaagtaggagaaa.......... ...............atttataaaatactgacctagtataccacgattaggagtctgaaaaaagcatcacgaggcaaatattaaatgttttcaattttcttaaaaataagaattatctaaaaataaaactctcctacccagtccacaccaagtaggagaaa.......... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCUCCUUCAUAUUUAUAAAAUACUGACCUAGUAUAUCAUGAAUAGGAGUAUGAAAAAAGCUUCACGAAGUAAAUAUUGAAUGUUUUCAAGAUUCUUAAAAAUGAGAAUUGUCUAAAAAUAAAAUCCCCUACCCAGUCCACGCCAAGUAGGAGAAA ....((((((.(.(((((((.(.((((((...)))))).).)))))))((.(((.(......((((....))))..........((((((...((((((((....)))))))).....))))))......).)))))............).)))))).. (-25.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUCCUACUUGGCGUGGACUGGGUAGGGGAUUUUAUUUUUAGACAAUUCUCAUUUUUAAGAAUCUUGAAAACAUUCAAUAUUUACUUCGUGAAGCUUUUUUCAUACUCCUAUUCAUGAUAUACUAGGUCAGUAUUUUAUAAAUAUGAAGGAGAUUUU ..(((((((((..(......)..))))))))).................((((.((((((((...))))))))..((((.((((((..(((((((..................))))))).(((((.....)))))....)))))))))).)))).... (-33.47) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 790 70 21 162 113 smit:SMT_871|5end_K03311_branched-chain_amino_acid:cation_transporter,_LIVCS_family_820160..820390_NEGATIVE 790 70 21 162 113 smit:SMT_386|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_320353..320583_POSITIVE 298 149 106 59 19 smit:SMT_521|5end_K02005_HlyD_family_secretion_protein_445566..445796_POSITIVE 234 150 105 172 128 smit:SMT_1201|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1163920..1164150_NEGATIVE 233 147 108 134 92 smit:SMT_1188|5end_hypothetical_protein_1146653..1146883_NEGATIVE 232 134 91 201 163 smit:SMT_1192|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase_/_IMP_cyclohydrolase_1151406..1151636_NEGATIVE 232 148 105 131 78 smit:SMT_301|5end_hypothetical_protein_244086..244316_POSITIVE 228 150 104 202 145 smit:SMT_1129|5end_hypothetical_protein_1063926..1064156_NEGATIVE 210 148 112 216 168 smit:SMT_1936|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1873837..1874067_POSITIVE 210 50 4 141 90 smit:SMT_1826|5end_ATP_synthase_beta_chain_1797408..1797638_POSITIVE 210 148 112 216 168 smit:SMT_1315|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1280099..1280329_POSITIVE 210 50 4 141 90 smit:SMT_586|5end_ATP_synthase_F1,_beta_subunit_502533..502763_POSITIVE 209 59 24 122 90 smit:SMT_1449|5end_K08591_putative_membrane_protein_1431937..1432167_POSITIVE 206 70 24 180 143 smit:SMT_594|5end_lysyl-tRNA_synthetase_511838..512068_NEGATIVE 206 50 5 154 103 smit:SMT_590|5end_tetratricopeptide_repeat_family_protein_506737..506967_POSITIVE 205 70 24 127 90 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 204 72 40 156 120 smit:SMT_2042|5end_K04077_chaperonin_GroEL_(Hsp60)_1953889..1954119_NEGATIVE 202 93 51 84 47 smit:SMT_1852|5end_1,4-alpha-glucan_branching_enzyme_1817690..1817920_NEGATIVE 200 147 131 227 207 smit:SMT_868|5end_D-alanyl-D-alanine_carboxypeptidase_817225..817455_NEGATIVE 200 70 36 186 150 smit:SMT_486|5end_hypothetical_protein_422305..422535_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 842 150 101 71 22 smit:SMT_385|3end_hypothetical_protein_320262..320412_POSITIVE 234 150 105 147 103 smit:SMT_1202|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1163945..1164095_NEGATIVE 233 147 108 124 82 smit:SMT_1189|3end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1146663..1146813_NEGATIVE 232 148 105 78 25 smit:SMT_300|3end_hypothetical_protein_244113..244263_POSITIVE 210 50 4 55 4 smit:SMT_1825|3end_ATP_synthase_F1,_gamma_subunit_1797402..1797552_POSITIVE 210 50 4 55 4 smit:SMT_585|3end_ATP_synthase_gamma_chain_502527..502677_POSITIVE 206 70 24 42 5 smit:SMT_595|3end_phosphoglycerate_mutase_511976..512126_NEGATIVE 203 74 32 56 21 smit:SMT_1716|3end_hypothetical_protein_1703657..1703807_POSITIVE 202 93 51 87 50 smit:SMT_1853|3end_1,4-alpha-glucan_branching_enzyme_1817687..1817837_NEGATIVE 198 148 105 76 36 smit:SMT_777|3end_hypothetical_protein_686618..686768_NEGATIVE 197 66 26 80 40 smit:SMT_327|3end_hypothetical_protein_264704..264854_POSITIVE 195 67 25 99 53 smit:SMT_633|3end_hypothetical_protein_538035..538185_NEGATIVE 192 47 5 129 73 smit:SMT_1572|3end_excinuclease_ABC_subunit_B_1566470..1566620_POSITIVE 190 59 11 82 25 smit:SMT_1310|3end_D-alanine-activating_enzyme_1275867..1276017_POSITIVE 189 76 32 62 23 smit:SMT_2061|3end_K02011_iron(III)_transport_system_permease_protein_1970802..1970952_POSITIVE 189 143 107 65 27 smit:SMT_877|3end_hypothetical_protein_823558..823708_NEGATIVE 189 76 32 62 23 smit:SMT_202|3end_K02011_iron(III)_transport_system_permease_protein_132173..132323_NEGATIVE 188 69 23 119 65 smit:SMT_520|3end_glutathione_reductase_444881..445031_NEGATIVE 188 149 108 58 27 smit:SMT_413|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_357641..357791_POSITIVE 187 142 115 135 110 smit:SMT_211|3end_hypothetical_protein_predicted_by_Glimmer/Critica_144316..144466_POSITIVE