Origin IGS: attcccctctttttacatttttaaattagtatgttaatttattgtaaaatatacaactctttccattatacatcaactttttaaaagattctagggatagatatacaattgaacggatgggaaaaatcaagtaactaagtaattaactgatttgaaaaagctaagacgaacttcccaccacacttactttacgatttttcagaaataaactgtcaacaaaaaatgaagagaagcactatttcttctctccatctttaaaattatagtaacaaatatagattatctaaagttatgaaagcaactctttagttt .........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 aaactaaagagttgctttcataactttagataatctatatttgttactataattttaaagatggagagaagaaatagtgcttctcttcattttttgttgacagtttatttctgaaaaatcgtaaagtaagtgtggtgggaagttcgtcttagctttttcaaatcagttaattacttagttacttgatttttcccatccgttcaattgtatatctatccctagaatcttttaaaaagttgatgtataatggaaagagttgtatattttacaataaattaacatactaatttaaaaatgtaaaaagaggggaat Mask Tandem Repeat Region ================================================ attcccctctttttacatttttaaattagtatgttaatttattgtaaaatatacaactctttccattatacatcaactttttaaaagattctagggatagatatacaattgaacggatgggaaaaatcaagtaactaagtaattaactgatttgaaaaagctaagacgaacttcccaccacacttactttacgatttttcagaaataaactgtcaacaaaaaatgaagagaagcactatttcttctctccatctttaaaattatagtaacaaatatagattatctaaagttatgaaagcaactctttagttt Find is-nt database================================================ Query_seq: SMT_1177:SMT_1178|SMT_1177:SMT_1178:immunoglobulin A1 protease:choline binding protein A:<-<-:1135220..1135531 312 attcccctctttttacatttttaaattagtatgttaatttattgtaaaatatacaactctttccattatacatcaactttttaaaagattctagggatagatatacaattgaacggatgggaaaaatcaagtaactaagtaattaactgatttgaaaaagctaagacgaacttcccaccacacttactttacgatttttcagaaataaactgtcaacaaaaaatgaagagaagcactatttcttctctccatctttaaaattatagtaacaaatatagattatctaaagttatgaaagcaactctttagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1177:SMT_1178|SMT_1177:SMT_1178:immunoglobulin A1 protease:choline binding protein A:<-<-:1135220..1135531 312 attcccctctttttacatttttaaattagtatgttaatttattgtaaaatatacaactctttccattatacatcaactttttaaaagattctagggatagatatacaattgaacggatgggaaaaatcaagtaactaagtaattaactgatttgaaaaagctaagacgaacttcccaccacacttactttacgatttttcagaaataaactgtcaacaaaaaatgaagagaagcactatttcttctctccatctttaaaattatagtaacaaatatagattatctaaagttatgaaagcaactctttagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1177:SMT_1178|SMT_1177:SMT_1178:immunoglobulin A1 protease:choline binding protein A:<-<-:1135220..1135531 312 attcccctctttttacatttttaaattagtatgttaatttattgtaaaatatacaactctttccattatacatcaactttttaaaagattctagggatagatatacaattgaacggatgggaaaaatcaagtaactaagtaattaactgatttgaaaaagctaagacgaacttcccaccacacttactttacgatttttcagaaataaactgtcaacaaaaaatgaagagaagcactatttcttctctccatctttaaaattatagtaacaaatatagattatctaaagttatgaaagcaactctttagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attcccctctttttacatttttaaattagtatgttaatttattgtaaaatatacaactctttccattatacatcaactttttaaaagattctagggatagatatacaattgaacggatgggaaaaatcaagtaactaagtaattaactgatttgaaaaagctaagacgaacttcccaccacacttactttacgatttttcagaaataaactgtcaacaaaaaatgaagagaagcactatttcttctctccatctttaaaattatagtaacaaatatagattatctaaagttatgaaagcaactctttagttt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 29 End: 130 ............................ Y T L K N Y F I C S K G N Y M L K K F S E L S L Y V I S R I P F I M ...................................................................................................................................................................................... attcccctctttttacatttttaaattagtatgttaatttattgtaaaatatacaactctttccattatacatcaactttttaaaagattctagggatagatatacaattgaacggatgggaaaaatcaagtaactaagtaattaactgatttgaaaaagctaagacgaacttcccaccacacttactttacgatttttcagaaataaactgtcaacaaaaaatgaagagaagcactatttcttctctccatctttaaaattatagtaacaaatatagattatctaaagttatgaaagcaactctttagttt 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: 260 End: 289 ...................................................................................................................................................................................................................................................................CTTTAGATAATCTATATTTGTTACTATAAT....................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 48 End: 77 ...............................................GTTGATGTATAATGGAAAGAGTTGTATATT........................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 65 End: 94 ................................................................CTAGAATCTTTTAAAAAGTTGATGTATAAT.......................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attcccctctttttacatttttaaattagtatgttaatttattgtaaaatatacaactctttccattatacatcaactttttaaaagattctagggatagatatacaattgaacggatgggaaaaatcaagtaactaagtaattaactgatttgaaaaagctaagacgaacttcccaccacacttactttacgatttttcagaaataaactgtcaacaaaaaatgaagagaagcactatttcttctctccatctttaaaattatagtaacaaatatagattatctaaagttatgaaagcaactctttagttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -7.8 Tail_Score: -5.45652 Start: 224 End: 251 Full_Region: ctataattttaaaga tggagagaagaa atag tgcttctcttca ttttttgttgacagt ...............................................................................................................................................................................................................................tggagagaagaaatagtgcttctcttca............................................................. Find igs database================================================ Query_seq: SMT_1177:SMT_1178|SMT_1177:SMT_1178:immunoglobulin A1 protease:choline binding protein A:<-<-:1135220..1135531 312 attcccctctttttacatttttaaattagtatgttaatttattgtaaaatatacaactctttccattatacatcaactttttaaaagattctagggatagatatacaattgaacggatgggaaaaatcaagtaactaagtaattaactgatttgaaaaagctaagacgaacttcccaccacacttactttacgatttttcagaaataaactgtcaacaaaaaatgaagagaagcactatttcttctctccatctttaaaattatagtaacaaatatagattatctaaagttatgaaagcaactctttagttt Intra-Species Hit: Count: 1 Min: 1 Max: 312 Len: 312 Subject: smit_SMT_1177_SMT_1178|immunoglobulin A1 protease:choline binding protein A|NEGATIVE:NEGATIVE|[1135220,1135531]|312 HSP 1 e-value: 1.0E-176 bit: 618.0 Len: 312 Query Start:1 Query End:312 Subject Strand: POSITIVE Subject Start: 1 Subject End: 312 attcccctctttttacatttttaaattagtatgttaatttattgtaaaatatacaactctttccattatacatcaactttttaaaagattctagggatagatatacaattgaacggatgggaaaaatcaagtaactaagtaattaactgatttgaaaaagctaagacgaacttcccaccacacttactttacgatttttcagaaataaactgtcaacaaaaaatgaagagaagcactatttcttctctccatctttaaaattatagtaacaaatatagattatctaaagttatgaaagcaactctttagttt attcccctctttttacatttttaaattagtatgttaatttattgtaaaatatacaactctttccattatacatcaactttttaaaagattctagggatagatatacaattgaacggatgggaaaaatcaagtaactaagtaattaactgatttgaaaaagctaagacgaacttcccaccacacttactttacgatttttcagaaataaactgtcaacaaaaaatgaagagaagcactatttcttctctccatctttaaaattatagtaacaaatatagattatctaaagttatgaaagcaactctttagttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCCCCUCUUUUUACAUUUUUAAAUUAGUAUGUUAAUUUAUUGUAAAAUAUACAACUCUUUCCAUUAUACAUCAACUUUUUAAAAGAUUCUAGGGAUAGAUAUACAAUUGAACGGAUGGGAAAAAUCAAGUAACUAAGUAAUUAACUGAUUUGAAAAAGCUAAGACGAACUUCCCACCACACUUACUUUACGAUUUUUCAGAAAUAAACUGUCAACAAAAAAUGAAGAGAAGCACUAUUUCUUCUCUCCAUCUUUAAAAUUAUAGUAACAAAUAUAGAUUAUCUAAAGUUAUGAAAGCAACUCUUUAGUUU ..........(((((((....((((((((....)))))))).))))))).....................(((.((((((.....((((((((..(((((..............((.((((((...((((((...(((....)))....))))))....(......)....)))))))).............((....)).........)))))....(((.(((.(((((((........))))))).))).)))...................))))..))))))))))))).................. (-43.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUAAAGAGUUGCUUUCAUAACUUUAGAUAAUCUAUAUUUGUUACUAUAAUUUUAAAGAUGGAGAGAAGAAAUAGUGCUUCUCUUCAUUUUUUGUUGACAGUUUAUUUCUGAAAAAUCGUAAAGUAAGUGUGGUGGGAAGUUCGUCUUAGCUUUUUCAAAUCAGUUAAUUACUUAGUUACUUGAUUUUUCCCAUCCGUUCAAUUGUAUAUCUAUCCCUAGAAUCUUUUAAAAAGUUGAUGUAUAAUGGAAAGAGUUGUAUAUUUUACAAUAAAUUAACAUACUAAUUUAAAAAUGUAAAAAGAGGGGAAU .......(((((((......)))))))(((((...((((.((((((((.((((...(((((((((((((((........))))))))))))))).)))).(((.......)))...........)))))..(.((((((((....((....))......(((((((.(((((....))))).))))))))))))))))...))).))))))))).(((((....((((((.....((.((((((((((.......))))))))))..))..(((((((......)))))))........))))))))))).. (-63.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 809 140 91 231 182 smit:SMT_1177|5end_immunoglobulin_A1_protease_1135129..1135359_NEGATIVE 287 122 83 78 32 smit:SMT_862|5end_hypothetical_protein_predicted_by_Glimmer/Critica_808587..808817_POSITIVE 265 210 164 161 110 smit:SMT_355|5end_hypothetical_protein_291622..291852_POSITIVE 257 199 151 86 34 smit:SMT_373|5end_cytosine_specific_DNA_methyltransferase_308546..308776_POSITIVE 257 194 159 63 23 smit:SMT_138|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_89262..89492_POSITIVE 256 250 223 203 171 smit:SMT_743|5end_hypothetical_protein_648280..648510_NEGATIVE 244 185 141 210 168 smit:SMT_2000|5end_hypothetical_protein_1923108..1923338_NEGATIVE 243 184 148 220 182 smit:SMT_1337|5end_K05833_putative_ABC_transport_system_ATP-binding_protein_1312812..1313042_NEGATIVE 233 202 161 60 22 smit:SMT_1627|5end_hypothetical_protein_1616415..1616645_NEGATIVE 230 164 127 216 168 smit:SMT_1953|5end_hypothetical_protein_1886897..1887127_POSITIVE 228 242 207 73 40 smit:SMT_1498|5end_transcriptional_regulator,_LytR_family_1481958..1482188_POSITIVE 227 186 147 53 9 smit:SMT_1947|5end_lysine_decarboxylase_1883113..1883343_NEGATIVE 224 240 193 92 36 smit:SMT_876|5end_hypothetical_protein_predicted_by_Glimmer/Critica_823502..823732_NEGATIVE 224 240 193 210 154 smit:SMT_875|5end_nitroreductase_family_protein_823384..823614_NEGATIVE 213 217 177 185 132 smit:SMT_236|5end_ribosomal_small_subunit_pseudouridine_synthase_A_174625..174855_POSITIVE 211 288 244 132 93 smit:SMT_879|5end_hypothetical_protein_826989..827219_NEGATIVE 211 185 147 221 185 smit:SMT_672|5end_hypothetical_protein_580604..580834_POSITIVE 211 184 148 44 5 smit:SMT_629|5end_glycogen_synthase_533967..534197_POSITIVE 210 120 72 67 23 smit:SMT_1832|5end_tagatose-6-phosphate_kinase_1800438..1800668_POSITIVE 209 129 81 90 34 smit:SMT_1551|5end_K02221_YggT_family_protein_1534859..1535089_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 253 229 131 109 smit:SMT_1133|3end_cytidine/deoxycytidylate_deaminase_family_protein,_putative_1074556..1074706_NEGATIVE 265 210 164 130 79 smit:SMT_354|3end_hypothetical_protein_291671..291821_POSITIVE 228 242 207 65 32 smit:SMT_1497|3end_acetyltransferase,_GNAT_family_1482030..1482180_POSITIVE 224 252 211 79 26 smit:SMT_496|3end_superoxide_dismutase,_manganese-dependent_431118..431268_POSITIVE 219 258 211 86 40 smit:SMT_1220|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1180509..1180659_NEGATIVE 211 288 244 53 14 smit:SMT_880|3end_beta-lactam_resistance_factor_827068..827218_NEGATIVE 211 184 148 47 8 smit:SMT_628|3end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_534050..534200_POSITIVE 210 120 72 56 12 smit:SMT_1831|3end_galactose-6-phosphate_isomerase_1800507..1800657_POSITIVE 209 129 81 90 34 smit:SMT_1550|3end_hypothetical_protein_1534939..1535089_POSITIVE 209 250 210 88 47 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 209 190 148 130 86 smit:SMT_184|3end_30S_ribosomal_protein_S8_121891..122041_POSITIVE 206 218 171 141 99 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE 206 218 171 141 99 smit:SMT_370|3end_acetyltransferase,_GNAT_family_305328..305478_POSITIVE 200 101 61 44 8 smit:SMT_1973|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1904878..1905028_NEGATIVE 198 199 163 55 22 smit:SMT_1590|3end_DNA-entry_nuclease_1578980..1579130_POSITIVE 198 100 59 65 23 smit:SMT_808|3end_hypothetical_protein_predicted_by_Glimmer/Critica_717897..718047_NEGATIVE 195 204 176 113 82 smit:SMT_2073|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1977074..1977224_POSITIVE 195 193 159 150 106 smit:SMT_180|3end_50S_ribosomal_protein_L14_120126..120276_POSITIVE 192 122 82 56 13 smit:SMT_2034|3end_hydrolase,_haloacid_dehalogenase-like_family_1947257..1947407_POSITIVE 189 199 160 48 11 smit:SMT_1395|3end_K07025_putative_hydrolase_of_the_HAD_superfamily_1372082..1372232_POSITIVE