Origin IGS: ttttagtctccttttccgaatattttcccattatatcagaaaaaacaaaaaaatgcaaatctagggacttttatgttagaagatataacataaaagctctttatttctttcttgaactgctaccacaaagtgctataataatagtatataatagaaggaaagaggacagggat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atccctgtcctctttccttctattatatactattattatagcactttgtggtagcagttcaagaaagaaataaagagcttttatgttatatcttctaacataaaagtccctagatttgcatttttttgttttttctgatataatgggaaaatattcggaaaaggagactaaaa Mask Tandem Repeat Region ================================================ ttttagtctccttttccgaatattttcccattatatcagaaaaaacaaaaaaatgcaaatctagggacttttatgttagaagatataacataaaagctctttatttctttcttgaactgctaccacaaagtgctataataatagtatataatagaaggaaagaggacagggat Find is-nt database================================================ Query_seq: SMT_1657:SMT_1658|SMT_1657:SMT_1658:glutamine-binding protein / glutamine transport system permease protein GlnP:hypothetical protein:<-->:1648168..1648340 173 ttttagtctccttttccgaatattttcccattatatcagaaaaaacaaaaaaatgcaaatctagggacttttatgttagaagatataacataaaagctctttatttctttcttgaactgctaccacaaagtgctataataatagtatataatagaaggaaagaggacagggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1657:SMT_1658|SMT_1657:SMT_1658:glutamine-binding protein / glutamine transport system permease protein GlnP:hypothetical protein:<-->:1648168..1648340 173 ttttagtctccttttccgaatattttcccattatatcagaaaaaacaaaaaaatgcaaatctagggacttttatgttagaagatataacataaaagctctttatttctttcttgaactgctaccacaaagtgctataataatagtatataatagaaggaaagaggacagggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1657:SMT_1658|SMT_1657:SMT_1658:glutamine-binding protein / glutamine transport system permease protein GlnP:hypothetical protein:<-->:1648168..1648340 173 ttttagtctccttttccgaatattttcccattatatcagaaaaaacaaaaaaatgcaaatctagggacttttatgttagaagatataacataaaagctctttatttctttcttgaactgctaccacaaagtgctataataatagtatataatagaaggaaagaggacagggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttagtctccttttccgaatattttcccattatatcagaaaaaacaaaaaaatgcaaatctagggacttttatgttagaagatataacataaaagctctttatttctttcttgaactgctaccacaaagtgctataataatagtatataatagaaggaaagaggacagggat Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 30 End: 173 ............................. M I S E K T K K C K S R D F Y V R R Y N I K A L Y F F L E L L P Q S A I I I V Y N R R K E D R D ttttagtctccttttccgaatattttcccattatatcagaaaaaacaaaaaaatgcaaatctagggacttttatgttagaagatataacataaaagctctttatttctttcttgaactgctaccacaaagtgctataataatagtatataatagaaggaaagaggacagggat 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: 88 Start: 30 End: 59 .............................TTTGCATTTTTTTGTTTTTTCTGATATAAT.................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttagtctccttttccgaatattttcccattatatcagaaaaaacaaaaaaatgcaaatctagggacttttatgttagaagatataacataaaagctctttatttctttcttgaactgctaccacaaagtgctataataatagtatataatagaaggaaagaggacagggat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 83 HP_score: -6.6 Tail_Score: -4.86861 Start: 65 End: 99 Full_Region: AAAATGCAAATCTAG GGACTTTTATGTTAGA AGA TATAACATAAAAGCTC TTTATTTCTTTCTTG ................................................................GGACTTTTATGTTAGAAGATATAACATAAAAGCTC.......................................................................... TransTerm Strand: + Conf: 76 HP_score: -9.1 Tail_Score: -2.98189 Start: 68 End: 96 Full_Region: ATGCAAATCTAGGGA CTTTTATGTTAGA AGA TATAACATAAAAG CTCTTTATTTCTTTC ...................................................................CTTTTATGTTAGAAGATATAACATAAAAG............................................................................. Find igs database================================================ Query_seq: SMT_1657:SMT_1658|SMT_1657:SMT_1658:glutamine-binding protein / glutamine transport system permease protein GlnP:hypothetical protein:<-->:1648168..1648340 173 ttttagtctccttttccgaatattttcccattatatcagaaaaaacaaaaaaatgcaaatctagggacttttatgttagaagatataacataaaagctctttatttctttcttgaactgctaccacaaagtgctataataatagtatataatagaaggaaagaggacagggat Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: smit_SMT_1657_SMT_1658|glutamine-binding protein / glutamine transport system permease protein GlnP:hypothetical protein|NEGATIVE:POSITIVE|[1648168,1648340]|173 HSP 1 e-value: 5.0E-62 bit: 238.0 Len: 120 Query Start:54 Query End:173 Subject Strand: POSITIVE Subject Start: 54 Subject End: 173 .....................................................tgcaaatctagggacttttatgttagaagatataacataaaagctctttatttctttcttgaactgctaccacaaagtgctataataatagtatataatagaaggaaagaggacagggat .....................................................tgcaaatctagggacttttatgttagaagatataacataaaagctctttatttctttcttgaactgctaccacaaagtgctataataatagtatataatagaaggaaagaggacagggat HSP 2 e-value: 1.0E-13 bit: 77.8 Len: 39 Query Start:1 Query End:39 Subject Strand: POSITIVE Subject Start: 1 Subject End: 39 ttttagtctccttttccgaatattttcccattatatcag...................................................................................................................................... ttttagtctccttttccgaatattttcccattatatcag...................................................................................................................................... Inter-species Hit: Count: 3 Min: 1 Max: 173 Len: 173 Subject: NC_008533_SPD_1097_SPD_1098|CAAX amino terminal protease family protein:amino acid ABC transporter, amino acid-binding protein/permease protein|NEGATIVE:POSITIVE|[1127017,1127188]|172 HSP 1 e-value: 4.0E-13 bit: 75.8 Len: 70 Query Start:104 Query End:173 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 69 .......................................................................................................tttctttcttgaactgctaccacaaagtgctataataatagtatataatagaaggaaagaggacagggat .......................................................................................................tttctttcttgaattgctattaaaaagtgctataataatagtatat-atagaagaaaagaggacggggat HSP 2 e-value: 6.0E-9 bit: 61.9 Len: 39 Query Start:1 Query End:39 Subject Strand: NEGATIVE Subject Start: 134 Subject End: 172 ttttagtctccttttccgaatattttcccattatatcag...................................................................................................................................... ttttagtctccttttccgaatattctctcattatatcag...................................................................................................................................... Subject: NC_003098_spr1119_spr1120|hypothetical protein:ABC transporter membrane spanning permease - glutamine transport|NEGATIVE:POSITIVE|[1119486,1119657]|172 HSP 1 e-value: 4.0E-13 bit: 75.8 Len: 70 Query Start:104 Query End:173 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 69 .......................................................................................................tttctttcttgaactgctaccacaaagtgctataataatagtatataatagaaggaaagaggacagggat .......................................................................................................tttctttcttgaattgctattaaaaagtgctataataatagtatat-atagaagaaaagaggacggggat HSP 2 e-value: 6.0E-9 bit: 61.9 Len: 39 Query Start:1 Query End:39 Subject Strand: NEGATIVE Subject Start: 134 Subject End: 172 ttttagtctccttttccgaatattttcccattatatcag...................................................................................................................................... ttttagtctccttttccgaatattctctcattatatcag...................................................................................................................................... Subject: NC_003028_SP_1240_SP_1241|hypothetical protein:amino acid ABC transporter, amino acid-binding protein/permease protein|NEGATIVE:POSITIVE|[1171332,1171500]|169 HSP 1 e-value: 6.0E-9 bit: 61.9 Len: 47 Query Start:127 Query End:173 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 46 ..............................................................................................................................aaagtgctataataatagtatataatagaaggaaagaggacagggat ..............................................................................................................................aaagtgctataataatagtatat-atagaagaaaagaggacggggat HSP 2 e-value: 6.0E-9 bit: 61.9 Len: 39 Query Start:1 Query End:39 Subject Strand: NEGATIVE Subject Start: 131 Subject End: 169 ttttagtctccttttccgaatattttcccattatatcag...................................................................................................................................... ttttagtctccttttccgaatattctctcattatatcag...................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAGUCUCCUUUUCCGAAUAUUUUCCCAUUAUAUCAGAAAAAACAAAAAAAUGCAAAUCUAGGGACUUUUAUGUUAGAAGAUAUAACAUAAAAGCUCUUUAUUUCUUUCUUGAACUGCUACCACAAAGUGCUAUAAUAAUAGUAUAUAAUAGAAGGAAAGAGGACAGGGAU ........(((((.(((.....((((((..((((....................(((....(((((((((((((((((.......))))))))))).)))))).(((......))).))).........(((((((....)))))))...))))..)))))).))).))))). (-35.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCCUGUCCUCUUUCCUUCUAUUAUAUACUAUUAUUAUAGCACUUUGUGGUAGCAGUUCAAGAAAGAAAUAAAGAGCUUUUAUGUUAUAUCUUCUAACAUAAAAGUCCCUAGAUUUGCAUUUUUUUGUUUUUUCUGAUAUAAUGGGAAAAUAUUCGGAAAAGGAGACUAAAA ......((((..(((((((((((((((((((.(((((((((....))))))))).)))...((((((((.((((((((((((((((((.......))))))))))))...............)))))))))))))).)))))))))))........)))))..).)))..... (-36.76) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 768 140 91 231 182 smit:SMT_1657|5end_glutamine-binding_protein_/_glutamine_transport_system_permease_protein_GlnP_1648077..1648307_NEGATIVE 273 134 96 141 101 smit:SMT_1576|5end_ribose_ABC_transporter_protein_RbsD_1568950..1569180_POSITIVE 267 42 7 71 35 smit:SMT_1514|5end_methylenetetrahydrofolate_dehydrogenase_(NADP+)_/_methenyltetrahydrofolate_cyclohydrolase_1496640..1496870_NEGATIVE 264 139 94 79 40 smit:SMT_472|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_409494..409724_NEGATIVE 264 139 94 79 40 smit:SMT_469|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_405812..406042_NEGATIVE 253 167 125 206 158 smit:SMT_1521|5end_K02003_1501887..1502117_NEGATIVE 250 167 124 67 31 smit:SMT_1477|5end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1460376..1460606_NEGATIVE 250 38 6 79 40 smit:SMT_846|5end_hypothetical_protein_792769..792999_NEGATIVE 250 139 95 140 101 smit:SMT_476|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_414134..414364_NEGATIVE 247 48 10 140 99 smit:SMT_222|5end_beta-glucosidase_154971..155201_POSITIVE 232 158 112 85 37 smit:SMT_557|5end_K04488_nitrogen_fixation_protein_NifU_and_related_proteins_474757..474987_POSITIVE 231 135 96 196 155 smit:SMT_2171|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2042271..2042501_POSITIVE 231 135 96 182 141 smit:SMT_2149|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2023671..2023901_POSITIVE 230 147 104 167 127 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 226 128 89 127 89 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 224 134 95 66 19 smit:SMT_1853|5end_1,4-alpha-glucan_branching_enzyme_1818064..1818294_NEGATIVE 223 36 1 78 38 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 222 44 4 132 91 smit:SMT_111|5end_alpha-1,2-mannosidase,_putative_61304..61534_NEGATIVE 219 134 105 45 17 smit:SMT_1991|5end_K03706_transcriptional_pleiotropic_repressor_1918264..1918494_NEGATIVE 217 148 106 135 95 smit:SMT_1663|5end_DNA-binding_response_regulator_1653052..1653282_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 131 97 131 97 smit:SMT_1554|3end_isoleucyl-tRNA_synthetase_1539912..1540062_POSITIVE 250 139 95 42 3 smit:SMT_477|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_414232..414382_NEGATIVE 244 48 23 41 17 smit:SMT_221|3end_prolyl-tRNA_synthetase_154952..155102_POSITIVE 232 158 112 98 50 smit:SMT_556|3end_putative_aminotransferase_474850..475000_POSITIVE 226 128 89 125 87 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 225 139 95 135 84 smit:SMT_938|3end_hypothetical_protein_890813..890963_NEGATIVE 223 36 1 76 36 smit:SMT_1733|3end_DNA_repair_protein_RecN_1718636..1718786_POSITIVE 222 44 4 58 17 smit:SMT_112|3end_hypothetical_protein_predicted_by_Glimmer/Critica_61378..61528_NEGATIVE 210 134 96 49 10 smit:SMT_1611|3end_K05896_segregation_and_condensation_protein_A_1600113..1600263_POSITIVE 207 167 126 35 1 smit:SMT_1478|3end_manganese_transport_system_membrane_protein_1460408..1460558_NEGATIVE 203 31 3 128 98 smit:SMT_1189|3end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1146663..1146813_NEGATIVE 202 67 28 80 44 smit:SMT_568|3end_hypothetical_protein_486389..486539_POSITIVE 199 164 123 75 39 smit:SMT_1672|3end_hypothetical_protein_1659806..1659956_NEGATIVE 198 134 95 129 93 smit:SMT_894|3end_hypothetical_protein_841315..841465_NEGATIVE 196 127 96 142 114 smit:SMT_214|3end_leucyl-tRNA_synthetase_147066..147216_POSITIVE 194 127 94 112 73 smit:SMT_1493|3end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1479494..1479644_POSITIVE 192 40 7 137 105 smit:SMT_1452|3end_ABC-type_uncharacterized_transport_system,_ATPase_component_1434676..1434826_NEGATIVE 190 43 7 68 25 smit:SMT_535|3end_hypothetical_protein_454456..454606_POSITIVE 187 133 97 141 107 smit:SMT_909|3end_type_I_restriction_enzyme_M_protein_857223..857373_NEGATIVE 185 84 45 75 39 smit:SMT_1491|3end_capsular_polysaccharide_biosynthesis_protein,_putative_1471967..1472117_POSITIVE