Origin IGS: agtttatgatacaaagcccataaagaacacagtgaaaataggaaactcggtgcagacgccttcagcgtcaagacgatgattatctttttcacacagttcttagggcgtgttcacttccgcgaacaatgtatcttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaacgagtaaaagctcgtcggagaatttatgtaactgaacacggacggaaagctcggaatttagataaaccaactgggattgtcaatccttccttggtttcctaaaattcaatcgctttctattcgtcctttgtatcttatttaatgtcgccctgtgaggcgacgaatagaaaggagaagatacattgttcgcggaagtgaacacgccctaagaactgtgtgaaaaagataatcatcgtcttgacgctgaaggcgtctgcaccgagtttcctattttcactgtgttctttatgggctttgtatcataaact Mask Tandem Repeat Region ================================================ agtttatgatacaaagcccataaagaacacagtgaaaataggaaactcggtgcagacgccttcagcgtcaagacgatgattatctttttcacacagttcttagggcgtgttcacttccgcgaacaatgtatcttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc Find is-nt database================================================ Query_seq: SMT_687:SMT_688|SMT_687:SMT_688:carbamoyl-phosphate synthase, large subunit:carbamoyl-phosphate synthase small chain:<-<-:599355..599665 311 agtttatgatacaaagcccataaagaacacagtgaaaataggaaactcggtgcagacgccttcagcgtcaagacgatgattatctttttcacacagttcttagggcgtgttcacttccgcgaacaatgtatcttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_687:SMT_688|SMT_687:SMT_688:carbamoyl-phosphate synthase, large subunit:carbamoyl-phosphate synthase small chain:<-<-:599355..599665 311 agtttatgatacaaagcccataaagaacacagtgaaaataggaaactcggtgcagacgccttcagcgtcaagacgatgattatctttttcacacagttcttagggcgtgttcacttccgcgaacaatgtatcttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_687:SMT_688|SMT_687:SMT_688:carbamoyl-phosphate synthase, large subunit:carbamoyl-phosphate synthase small chain:<-<-:599355..599665 311 agtttatgatacaaagcccataaagaacacagtgaaaataggaaactcggtgcagacgccttcagcgtcaagacgatgattatctttttcacacagttcttagggcgtgttcacttccgcgaacaatgtatcttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtttatgatacaaagcccataaagaacacagtgaaaataggaaactcggtgcagacgccttcagcgtcaagacgatgattatctttttcacacagttcttagggcgtgttcacttccgcgaacaatgtatcttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 76 End: 171 ........................................................................... M I I F F T Q F L G R V H F R E Q C I F S F L F V A S Q G D I K ............................................................................................................................................ Protein_Len: 40 Strand: + Start: 107 End: 226 .......................................................................................................... M F T S A N N V S S P F Y S S P H R A T L N K I Q R T N R K R L N F R K P R K D ..................................................................................... Protein_Len: 30 Strand: - Start: 7 End: 96 ...... S V F G M F F V T F I P F E T C V G E A D L R H N D K E C M ....................................................................................................................................................................................................................... Protein_Len: 30 Strand: - Start: 3 End: 92 .. K H Y L A W L S C L S F L F S P A S A K L T L V I I I K K M ........................................................................................................................................................................................................................... agtttatgatacaaagcccataaagaacacagtgaaaataggaaactcggtgcagacgccttcagcgtcaagacgatgattatctttttcacacagttcttagggcgtgttcacttccgcgaacaatgtatcttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc 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: 85 Start: 204 End: 233 ...........................................................................................................................................................................................................ATTGTCAATCCTTCCTTGGTTTCCTAAAAT.............................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 225 End: 254 ................................................................................................................................................................................................................................ATTGACAATCCCAGTTGGTTTATCTAAATT......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtttatgatacaaagcccataaagaacacagtgaaaataggaaactcggtgcagacgccttcagcgtcaagacgatgattatctttttcacacagttcttagggcgtgttcacttccgcgaacaatgtatcttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_687:SMT_688|SMT_687:SMT_688:carbamoyl-phosphate synthase, large subunit:carbamoyl-phosphate synthase small chain:<-<-:599355..599665 311 agtttatgatacaaagcccataaagaacacagtgaaaataggaaactcggtgcagacgccttcagcgtcaagacgatgattatctttttcacacagttcttagggcgtgttcacttccgcgaacaatgtatcttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc Intra-Species Hit: Count: 1 Min: 1 Max: 311 Len: 311 Subject: smit_SMT_687_SMT_688|carbamoyl-phosphate synthase, large subunit:carbamoyl-phosphate synthase small chain|NEGATIVE:NEGATIVE|[599355,599665]|311 HSP 1 e-value: 1.0E-175 bit: 617.0 Len: 311 Query Start:1 Query End:311 Subject Strand: POSITIVE Subject Start: 1 Subject End: 311 agtttatgatacaaagcccataaagaacacagtgaaaataggaaactcggtgcagacgccttcagcgtcaagacgatgattatctttttcacacagttcttagggcgtgttcacttccgcgaacaatgtatcttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc agtttatgatacaaagcccataaagaacacagtgaaaataggaaactcggtgcagacgccttcagcgtcaagacgatgattatctttttcacacagttcttagggcgtgttcacttccgcgaacaatgtatcttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc Inter-species Hit: Count: 8 Min: 132 Max: 311 Len: 180 Subject: NC_008533_SPD_1131_SPD_1132|carbamoyl-phosphate synthase, large subunit:carbamoyl-phosphate synthase, small subunit|NEGATIVE:NEGATIVE|[1165457,1165768]|312 HSP 1 e-value: 3.0E-83 bit: 309.0 Len: 180 Query Start:132 Query End:311 Subject Strand: POSITIVE Subject Start: 133 Subject End: 312 ...................................................................................................................................cttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc ...................................................................................................................................cttctcctttctattcgtcgcctctcagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaatcaaggaaggattgacaatccaagttggtttctctacattctgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc Subject: NC_003098_spr1153_spr1154|carbamoyl-phosphate synthase large subunit:carbamoyl-phosphate synthase small subunit|NEGATIVE:NEGATIVE|[1157926,1158237]|312 HSP 1 e-value: 3.0E-83 bit: 309.0 Len: 180 Query Start:132 Query End:311 Subject Strand: POSITIVE Subject Start: 133 Subject End: 312 ...................................................................................................................................cttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc ...................................................................................................................................cttctcctttctattcgtcgcctctcagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaatcaaggaaggattgacaatccaagttggtttctctacattctgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc Subject: NC_003028_SP_1275_SP_1276|carbamoyl-phosphate synthase large subunit:carbamoyl-phosphate synthase small subunit|NEGATIVE:NEGATIVE|[1211316,1211627]|312 HSP 1 e-value: 3.0E-83 bit: 309.0 Len: 180 Query Start:132 Query End:311 Subject Strand: POSITIVE Subject Start: 133 Subject End: 312 ...................................................................................................................................cttctcctttctattcgtcgcctcacagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaaccaaggaaggattgacaatcccagttggtttatctaaattccgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc ...................................................................................................................................cttctcctttctattcgtcgcctctcagggcgacattaaataagatacaaaggacgaatagaaagcgattgaattttaggaaatcaaggaaggattgacaatccaagttggtttctctacattctgagctttccgtccgtgttcagttacataaattctccgacgagcttttactcgttc Subject: NC_008023_MGAS2096_Spy0034_MGAS2096_Spy0035|hypothetical protein:Adenylosuccinate lyase|NEGATIVE:POSITIVE|[51414,51622]|209 HSP 1 e-value: 3.0E-6 bit: 54.0 Len: 39 Query Start:241 Query End:279 Subject Strand: NEGATIVE Subject Start: 99 Subject End: 137 ................................................................................................................................................................................................................................................ggtttatctaaattccgagctttccgtccgtgttcagtt................................ ................................................................................................................................................................................................................................................ggtttatctaaattccgagctttccgctcgggttcagtt................................ HSP 2 e-value: 3.0E-6 bit: 54.0 Len: 47 Query Start:172 Query End:218 Subject Strand: NEGATIVE Subject Start: 161 Subject End: 207 ...........................................................................................................................................................................taagatacaaaggacgaatagaaagcgattgaattttaggaaaccaa............................................................................................. ...........................................................................................................................................................................taagataccaagggcgaccagaaagcgactgaattttaggaaaccaa............................................................................................. Subject: NC_008021_MGAS9429_Spy0033_MGAS9429_Spy0034|hypothetical protein:adenylosuccinate lyase|NEGATIVE:POSITIVE|[51439,51647]|209 HSP 1 e-value: 3.0E-6 bit: 54.0 Len: 39 Query Start:241 Query End:279 Subject Strand: NEGATIVE Subject Start: 99 Subject End: 137 ................................................................................................................................................................................................................................................ggtttatctaaattccgagctttccgtccgtgttcagtt................................ ................................................................................................................................................................................................................................................ggtttatctaaattccgagctttccgctcgggttcagtt................................ HSP 2 e-value: 3.0E-6 bit: 54.0 Len: 47 Query Start:172 Query End:218 Subject Strand: NEGATIVE Subject Start: 161 Subject End: 207 ...........................................................................................................................................................................taagatacaaaggacgaatagaaagcgattgaattttaggaaaccaa............................................................................................. ...........................................................................................................................................................................taagataccaagggcgaccagaaagcgactgaattttaggaaaccaa............................................................................................. Subject: NC_006086_M6_Spy0081_M6_Spy0082|Hypothetical cytosolic protein:adenylosuccinate lyase|POSITIVE:POSITIVE|[92493,92707]|215 HSP 1 e-value: 3.0E-6 bit: 54.0 Len: 39 Query Start:241 Query End:279 Subject Strand: NEGATIVE Subject Start: 105 Subject End: 143 ................................................................................................................................................................................................................................................ggtttatctaaattccgagctttccgtccgtgttcagtt................................ ................................................................................................................................................................................................................................................ggtttatctaaattccgagctttccgctcgggttcagtt................................ HSP 2 e-value: 3.0E-6 bit: 54.0 Len: 47 Query Start:172 Query End:218 Subject Strand: NEGATIVE Subject Start: 167 Subject End: 213 ...........................................................................................................................................................................taagatacaaaggacgaatagaaagcgattgaattttaggaaaccaa............................................................................................. ...........................................................................................................................................................................taagataccaagggcgaccagaaagcgactgaattttaggaaaccaa............................................................................................. Subject: NC_004606_SPs0030_SPs0031|hypothetical protein:adenylosuccinate lyase|POSITIVE:POSITIVE|[45682,46049]|368 HSP 1 e-value: 3.0E-6 bit: 54.0 Len: 39 Query Start:241 Query End:279 Subject Strand: NEGATIVE Subject Start: 258 Subject End: 296 ................................................................................................................................................................................................................................................ggtttatctaaattccgagctttccgtccgtgttcagtt................................ ................................................................................................................................................................................................................................................ggtttatctaaattccgagctttccgctcgggttcagtt................................ HSP 2 e-value: 3.0E-6 bit: 54.0 Len: 47 Query Start:172 Query End:218 Subject Strand: NEGATIVE Subject Start: 320 Subject End: 366 ...........................................................................................................................................................................taagatacaaaggacgaatagaaagcgattgaattttaggaaaccaa............................................................................................. ...........................................................................................................................................................................taagataccaagggcgaccagaaagcgactgaattttaggaaaccaa............................................................................................. Subject: NC_004070_SpyM3_0029_SpyM3_0030|hypothetical protein:adenylosuccinate lyase|POSITIVE:POSITIVE|[51683,52050]|368 HSP 1 e-value: 3.0E-6 bit: 54.0 Len: 39 Query Start:241 Query End:279 Subject Strand: NEGATIVE Subject Start: 258 Subject End: 296 ................................................................................................................................................................................................................................................ggtttatctaaattccgagctttccgtccgtgttcagtt................................ ................................................................................................................................................................................................................................................ggtttatctaaattccgagctttccgctcgggttcagtt................................ HSP 2 e-value: 3.0E-6 bit: 54.0 Len: 47 Query Start:172 Query End:218 Subject Strand: NEGATIVE Subject Start: 320 Subject End: 366 ...........................................................................................................................................................................taagatacaaaggacgaatagaaagcgattgaattttaggaaaccaa............................................................................................. ...........................................................................................................................................................................taagataccaagggcgaccagaaagcgactgaattttaggaaaccaa............................................................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUCCUUUCUAUUCGUCGCCUCACAGGGCGACAUUAAAUAAGAUACAAAGGACGAAUAGAAAGCGAUUGAAUUUUAGGAAACCAAGGAAGGAUUGACAAUCCCAGUUGGUUUAUCUAAAUUCCGAGCUUUCCGUCCGUGUUCAGUUACAUAAAUUCUCCGACGAGCUUUUACUCGUUC ................(((((((....))))))).........((.(((..(((((....((((((....((((((.((((((((((....((((.....))))...))))))).)))))))))...))))))))))).))))).................((((((......)))))). (-49.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAACGAGUAAAAGCUCGUCGGAGAAUUUAUGUAACUGAACACGGACGGAAAGCUCGGAAUUUAGAUAAACCAACUGGGAUUGUCAAUCCUUCCUUGGUUUCCUAAAAUUCAAUCGCUUUCUAUUCGUCCUUUGUAUCUUAUUUAAUGUCGCCCUGUGAGGCGACGAAUAGAAAGGAGAAG ((.(((((....)))))))......................((((..((((((...((((((((..(((((((..(((((.....)))))...))))))).)).))))))....))))))..))))((((((.(((.........(((((((......))))))).))).)))))).... (-51.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 139 101 146 103 smit:SMT_596|5end_K03976_putative_transcription_regulator_513075..513305_NEGATIVE 326 150 101 76 17 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 326 40 2 231 196 smit:SMT_698|5end_uracil_permease_608406..608636_POSITIVE 313 150 101 79 26 smit:SMT_567|5end_conserved_hypothetical_protein_484845..485075_POSITIVE 312 169 123 105 50 smit:SMT_448|5end_K03707_transcriptional_activator_TenA_386789..387019_POSITIVE 302 147 101 219 175 smit:SMT_1284|5end_predicted_amidophosphoribosyltransferase_1246962..1247192_POSITIVE 295 56 14 231 197 smit:SMT_540|5end_DNA_gyrase,_B_subunit_456358..456588_POSITIVE 294 80 32 142 102 smit:SMT_841|5end_dihydrodipicolinate_reductase_788025..788255_NEGATIVE 290 180 135 67 26 smit:SMT_414|5end_K03665_GTP-binding_protein_HflX_357554..357784_POSITIVE 290 170 121 69 12 smit:SMT_260|5end_phage_transcriptional_repressor_199470..199700_POSITIVE 286 178 137 43 6 smit:SMT_1122|5end_queuine_tRNA-ribosyltransferase_1059223..1059453_NEGATIVE 284 147 101 68 20 smit:SMT_1653|5end_hydrolase_1641328..1641558_POSITIVE 284 149 103 68 19 smit:SMT_1529|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1512880..1513110_NEGATIVE 283 166 123 210 174 smit:SMT_1840|5end_6-phosphogluconate_dehydrogenase,_decarboxylating_1806285..1806515_NEGATIVE 280 168 124 190 144 smit:SMT_187|5end_30S_ribosomal_protein_S5_122997..123227_POSITIVE 276 148 105 112 62 smit:SMT_356|5end_hypothetical_protein_292394..292624_POSITIVE 275 149 102 78 36 smit:SMT_1412|5end_hypothetical_protein_1395522..1395752_POSITIVE 271 150 104 61 9 smit:SMT_1910|5end_pyruvate-formate_lyase_activating_enzyme_1856780..1857010_POSITIVE 271 56 16 155 122 smit:SMT_898|5end_polyribonucleotide_nucleotidyltransferase_846861..847091_NEGATIVE 269 146 102 157 99 smit:SMT_851|5end_conserved_hypothetical_protein,_translation_initiation_inhibitor_protein_797446..797676_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 139 101 146 103 smit:SMT_597|3end_K08974_putative_membrane_protein_513075..513225_NEGATIVE 326 150 101 74 15 smit:SMT_1733|3end_DNA_repair_protein_RecN_1718636..1718786_POSITIVE 319 40 14 27 1 smit:SMT_697|3end_glucose-inhibited_division_protein_B_608282..608432_POSITIVE 313 150 101 57 4 smit:SMT_566|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_484903..485053_POSITIVE 290 180 135 74 33 smit:SMT_413|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_357641..357791_POSITIVE 284 147 101 68 20 smit:SMT_1652|3end_Cof_family_protein_1641408..1641558_POSITIVE 283 166 123 134 98 smit:SMT_1841|3end_hypothetical_protein_1806361..1806511_NEGATIVE 283 166 123 134 98 smit:SMT_303|3end_hypothetical_protein_245758..245908_POSITIVE 280 139 91 124 77 smit:SMT_121|3end_hypothetical_protein_74414..74564_POSITIVE 277 170 125 67 16 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 276 140 91 146 93 smit:SMT_186|3end_50S_ribosomal_protein_L18_123059..123209_POSITIVE 269 146 102 146 88 smit:SMT_852|3end_K03978_GTP-binding_protein_797457..797607_NEGATIVE 265 168 126 43 3 smit:SMT_1154|3end_tryptophanyl-tRNA_synthetase_1098154..1098304_NEGATIVE 262 43 3 147 102 smit:SMT_1189|3end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1146663..1146813_NEGATIVE 259 50 5 138 85 smit:SMT_1842|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1807784..1807934_NEGATIVE 254 169 122 137 78 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 254 171 133 120 87 smit:SMT_1388|3end_hypothetical_protein_1365833..1365983_POSITIVE 253 169 128 73 27 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 252 140 104 83 42 smit:SMT_219|3end_phosphatidate_cytidylyltransferase_151805..151955_POSITIVE 251 145 104 124 77 smit:SMT_340|3end_chaperone_protein_280566..280716_POSITIVE