Origin IGS: tatcagactttcaatatggaagatttccacttaaacagttgaaacaaacataaacttggtatcaacttcaatcccaatatgggcttatgataggtctacacgggagcttagacaaaagatactaagactctaaccaacatgtgtactcattaataacactcgctaccacaccacatgttggaaaatctctgtgatttgacattaatcgtaaattcacaacaagtcgtgacaaaaggctaccctaattgaatgatttactgttagtagaggacaccaatgtagataaacagatagatacccaattcatctacacccaactagtgacaagttaaaagtgtgggattttctccatttagtcctatactactgactttgaaatcatcatacgtgacaataccgcttaccacccgactgacgctttcgttcagtccacgctttctgtacctagtacaaggagtaatatttt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatattactccttgtactaggtacagaaagcgtggactgaacgaaagcgtcagtcgggtggtaagcggtattgtcacgtatgatgatttcaaagtcagtagtataggactaaatggagaaaatcccacacttttaacttgtcactagttgggtgtagatgaattgggtatctatctgtttatctacattggtgtcctctactaacagtaaatcattcaattagggtagccttttgtcacgacttgttgtgaatttacgattaatgtcaaatcacagagattttccaacatgtggtgtggtagcgagtgttattaatgagtacacatgttggttagagtcttagtatcttttgtctaagctcccgtgtagacctatcataagcccatattgggattgaagttgataccaagtttatgtttgtttcaactgtttaagtggaaatcttccatattgaaagtctgata Mask Tandem Repeat Region ================================================ tatcagactttcaatatggaagatttccacttaaacagttgaaacaaacataaacttggtatcaacttcaatcccaatatgggcttatgataggtctacacgggagcttagacaaaagatactaagactctaaccaacatgtgtactcattaataacactcgctaccacaccacatgttggaaaatctctgtgatttgacattaatcgtaaattcacaacaagtcgtgacaaaaggctaccctaattgaatgatttactgttagtagaggacaccaatgtagataaacagatagatacccaattcatctacacccaactagtgacaagttaaaagtgtgggattttctccatttagtcctatactactgactttgaaatcatcatacgtgacaataccgcttaccacccgactgacgctttcgttcagtccacgctttctgtacctagtacaaggagtaatatttt Find is-nt database================================================ Query_seq: SMT_1326:SMT_1327|SMT_1326:SMT_1327:X-prolyl dipeptidyl peptidase:K03402 transcriptional regulator of arginine metabolism:->->:1303420..1303885 466 tatcagactttcaatatggaagatttccacttaaacagttgaaacaaacataaacttggtatcaacttcaatcccaatatgggcttatgataggtctacacgggagcttagacaaaagatactaagactctaaccaacatgtgtactcattaataacactcgctaccacaccacatgttggaaaatctctgtgatttgacattaatcgtaaattcacaacaagtcgtgacaaaaggctaccctaattgaatgatttactgttagtagaggacaccaatgtagataaacagatagatacccaattcatctacacccaactagtgacaagttaaaagtgtgggattttctccatttagtcctatactactgactttgaaatcatcatacgtgacaataccgcttaccacccgactgacgctttcgttcagtccacgctttctgtacctagtacaaggagtaatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1326:SMT_1327|SMT_1326:SMT_1327:X-prolyl dipeptidyl peptidase:K03402 transcriptional regulator of arginine metabolism:->->:1303420..1303885 466 tatcagactttcaatatggaagatttccacttaaacagttgaaacaaacataaacttggtatcaacttcaatcccaatatgggcttatgataggtctacacgggagcttagacaaaagatactaagactctaaccaacatgtgtactcattaataacactcgctaccacaccacatgttggaaaatctctgtgatttgacattaatcgtaaattcacaacaagtcgtgacaaaaggctaccctaattgaatgatttactgttagtagaggacaccaatgtagataaacagatagatacccaattcatctacacccaactagtgacaagttaaaagtgtgggattttctccatttagtcctatactactgactttgaaatcatcatacgtgacaataccgcttaccacccgactgacgctttcgttcagtccacgctttctgtacctagtacaaggagtaatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1326:SMT_1327|SMT_1326:SMT_1327:X-prolyl dipeptidyl peptidase:K03402 transcriptional regulator of arginine metabolism:->->:1303420..1303885 466 tatcagactttcaatatggaagatttccacttaaacagttgaaacaaacataaacttggtatcaacttcaatcccaatatgggcttatgataggtctacacgggagcttagacaaaagatactaagactctaaccaacatgtgtactcattaataacactcgctaccacaccacatgttggaaaatctctgtgatttgacattaatcgtaaattcacaacaagtcgtgacaaaaggctaccctaattgaatgatttactgttagtagaggacaccaatgtagataaacagatagatacccaattcatctacacccaactagtgacaagttaaaagtgtgggattttctccatttagtcctatactactgactttgaaatcatcatacgtgacaataccgcttaccacccgactgacgctttcgttcagtccacgctttctgtacctagtacaaggagtaatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 169 Max: 446 Len: 278 Subject: UniRef90_Q97RC8 Cluster: Xaa-Pro dipeptidyl-peptidase; n=4; Streptococcus pneumoniae|Rep: Xaa-Pro dipeptidyl-peptidase - Streptococcus pneumoniae HSP 1 e-value: 3.0E-12 bit: 56.2 Len: 198 Query Start:249 Query End:446 Subject Strand: null Subject Start: 690 Subject End: 756 ........................................................................................................................................................................................................................................................ N D L L L V E D T N V D K Q I D T Q F I Y T Q L V T S * K C G - I F S I * S Y T T D F E I I I R D N T A Y H P T D A F V Q S T L S V P .................... ........................................................................................................................................................................................................................................................ N D L L L V E D I T A D E W M D V Q F E L Q P T I Y K L K E G D T L R L V L Y T T D F E I T I R D N T D Y H L T V D L A Q S M L T L P .................... HSP 2 e-value: 3.0E-12 bit: 37.0 Len: 78 Query Start:169 Query End:246 Subject Strand: null Subject Start: 660 Subject End: 685 ........................................................................................................................................................................ H H M L E N L C D L T L I V N S Q Q V V T K G Y P N ............................................................................................................................................................................................................................ ........................................................................................................................................................................ Y H M L E N L C E L P F R P E A Q R V V T K G Y L N ............................................................................................................................................................................................................................ tatcagactttcaatatggaagatttccacttaaacagttgaaacaaacataaacttggtatcaacttcaatcccaatatgggcttatgataggtctacacgggagcttagacaaaagatactaagactctaaccaacatgtgtactcattaataacactcgctaccannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtacaaggagtaatatttt Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 337 End: 465 ................................................................................................................................................................................................................................................................................................................................................ M G F S P F S P I L L T L K S S Y V T I P L T T R L T L S F S P R F L Y L V Q G V I F . Protein_Len: 47 Strand: - Start: 321 End: 461 ................................................................................................................................................................................................................................................................................................................................ H C T L L T P N E G N L G I S S V K F D D Y T V I G S V V R S V S E N L G R K R Y R T C P T M ..... Protein_Len: 36 Strand: - Start: 125 End: 232 ............................................................................................................................ S E L W C T Y E N I V S A V V G C T P F D R H N S M L R L N V V L R S M .......................................................................................................................................................................................................................................... tatcagactttcaatatggaagatttccacttaaacagttgaaacaaacataaacttggtatcaacttcaatcccaatatgggcttatgataggtctacacgggagcttagacaaaagatactaagactctaaccaacatgtgtactcattaataacactcgctaccannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtacaaggagtaatatttt 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: 81 Start: 87 End: 116 ......................................................................................TTTGTCTAAGCTCCCGTGTAGACCTATCAT.............................................................................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatcagactttcaatatggaagatttccacttaaacagttgaaacaaacataaacttggtatcaacttcaatcccaatatgggcttatgataggtctacacgggagcttagacaaaagatactaagactctaaccaacatgtgtactcattaataacactcgctaccannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtacaaggagtaatatttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 44 HP_score: -2.6 Tail_Score: -3.15503 Start: 24 End: 44 Full_Region: ccaagtttatgtttg tttcaact gttta agtggaaa tcttccatattgaaa .......................tttcaactgtttaagtggaaa...................................................................................................................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_1326:SMT_1327|SMT_1326:SMT_1327:X-prolyl dipeptidyl peptidase:K03402 transcriptional regulator of arginine metabolism:->->:1303420..1303885 466 tatcagactttcaatatggaagatttccacttaaacagttgaaacaaacataaacttggtatcaacttcaatcccaatatgggcttatgataggtctacacgggagcttagacaaaagatactaagactctaaccaacatgtgtactcattaataacactcgctaccannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtacaaggagtaatatttt Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: smit_SMT_1326_SMT_1327|X-prolyl dipeptidyl peptidase:K03402 transcriptional regulator of arginine metabolism|POSITIVE:POSITIVE|[1303420,1303885]|466 HSP 1 e-value: 3.0E-90 bit: 333.0 Len: 168 Query Start:1 Query End:168 Subject Strand: POSITIVE Subject Start: 1 Subject End: 168 tatcagactttcaatatggaagatttccacttaaacagttgaaacaaacataaacttggtatcaacttcaatcccaatatgggcttatgataggtctacacgggagcttagacaaaagatactaagactctaaccaacatgtgtactcattaataacactcgctacca.......................................................................................................................................................................................................................................................................................................... tatcagactttcaatatggaagatttccacttaaacagttgaaacaaacataaacttggtatcaacttcaatcccaatatgggcttatgataggtctacacgggagcttagacaaaagatactaagactctaaccaacatgtgtactcattaataacactcgctacca.......................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCAGACUUUCAAUAUGGAAGAUUUCCACUUAAACAGUUGAAACAAACAUAAACUUGGUAUCAACUUCAAUCCCAAUAUGGGCUUAUGAUAGGUCUACACGGGAGCUUAGACAAAAGAUACUAAGACUCUAACCAACAUGUGUACUCAUUAAUAACACUCGCUACCA .......(((((.....))))).((((.(((.....))).))))..........(((((((((....(((..(((.....)))....)))...(((((..(....)..)))))....)))))))))..............((((...........))))......... (-29.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGUAGCGAGUGUUAUUAAUGAGUACACAUGUUGGUUAGAGUCUUAGUAUCUUUUGUCUAAGCUCCCGUGUAGACCUAUCAUAAGCCCAUAUUGGGAUUGAAGUUGAUACCAAGUUUAUGUUUGUUUCAACUGUUUAAGUGGAAAUCUUCCAUAUUGAAAGUCUGAUA ...(((((.((((.(((....))))))).)))))....(((.(((((((.....)).)))))))).....(((((...(((....(((.....)))..)))((((((...((((......))))..)))))).((((((((((.....))))).))))).)))))... (-33.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 108 70 191 156 smit:SMT_992|5end_hypothetical_protein_934882..935112_NEGATIVE 280 109 61 169 121 smit:SMT_1012|5end_xanthine_permease_949154..949384_POSITIVE 274 106 64 182 141 smit:SMT_986|5end_threonyl-tRNA_synthetase_931092..931322_POSITIVE 274 106 64 44 3 smit:SMT_985|5end_guanylate_kinase_930954..931184_POSITIVE 274 106 64 182 141 smit:SMT_925|5end_DNA-directed_RNA_polymerase_omega_chain_880283..880513_NEGATIVE 263 140 95 91 45 smit:SMT_1677|5end_transcription-repair_coupling_factor_1662112..1662342_NEGATIVE 256 109 67 42 8 smit:SMT_1793|5end_inosine-5'-monophosphate_dehydrogenase_1767985..1768215_POSITIVE 255 100 54 50 4 smit:SMT_358|5end_hypothetical_protein_293947..294177_POSITIVE 252 107 65 209 164 smit:SMT_354|5end_hypothetical_protein_291343..291573_POSITIVE 251 109 66 111 59 smit:SMT_2019|5end_dTDP-glucose_4,6-dehydratase_1937054..1937284_POSITIVE 244 135 93 43 3 smit:SMT_1004|5end_thioredoxin_945430..945660_POSITIVE 243 122 84 36 2 smit:SMT_411|5end_thymidylate_synthase_355496..355726_POSITIVE 241 107 67 174 140 smit:SMT_2161|5end_DNA_mismatch_repair_protein_2034946..2035176_POSITIVE 241 108 74 71 34 smit:SMT_1128|5end_surface_antigen_1063140..1063370_NEGATIVE 240 108 64 132 94 smit:SMT_1257|5end_acetolactate_synthase_small_subunit_1223173..1223403_NEGATIVE 237 105 61 212 173 smit:SMT_1293|5end_K02051_sulfonate/nitrate/taurine_transport_system_substrate-binding_protein_1254976..1255206_POSITIVE 237 112 77 40 9 smit:SMT_1176|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1128993..1129223_NEGATIVE 236 39 2 217 173 smit:SMT_191|5end_adenylate_kinase_125745..125975_POSITIVE 235 108 61 225 178 smit:SMT_623|5end_50S_ribosomal_protein_L21_529412..529642_POSITIVE 234 98 56 90 36 smit:SMT_1457|5end_16S_rRNA_m(2)G_1207_methyltransferase_1440209..1440439_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 119 71 146 101 smit:SMT_1080|3end_CAAX_amino_terminal_protease_family_protein_1017783..1017933_NEGATIVE 252 107 65 150 105 smit:SMT_353|3end_immunity_protein_BlpL_291364..291514_POSITIVE 241 107 67 74 40 smit:SMT_2160|3end_cell_division_protein_FtsA_2034926..2035076_POSITIVE 240 108 64 139 101 smit:SMT_1258|3end_acetolactate_synthase_large_subunit_1223166..1223316_NEGATIVE 236 39 2 67 23 smit:SMT_190|3end_preprotein_translocase,_SecY_subunit_125675..125825_POSITIVE 234 100 52 62 16 smit:SMT_1607|3end_K03341_putative_deoxyribonucleotide_triphosphate_pyrophosphatase_1597699..1597849_POSITIVE 234 120 72 75 29 smit:SMT_1048|3end_K06518_holin-like_protein_988521..988671_POSITIVE 232 97 71 146 123 smit:SMT_580|3end_K04094_glucose_inhibited_division_protein_Gid_498034..498184_POSITIVE 229 105 74 151 117 smit:SMT_1307|3end_glycerol_uptake_facilitator_protein_1272448..1272598_POSITIVE 228 149 101 70 27 smit:SMT_198|3end_50S_ribosomal_protein_L17_129281..129431_POSITIVE 226 103 61 59 7 smit:SMT_1690|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1673370..1673520_NEGATIVE 226 119 73 76 35 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 224 109 72 97 54 smit:SMT_1066|3end_holo-(acyl_carrier_protein)_synthase_1005859..1006009_POSITIVE 221 134 93 77 26 smit:SMT_1165|3end_sensor_protein_CiaH_1110486..1110636_NEGATIVE 220 108 72 73 29 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 220 119 78 121 77 smit:SMT_1902|3end_proton-translocating_NADH-quinone_oxidoreductase,_chain_L_1852028..1852178_NEGATIVE 220 109 80 38 7 smit:SMT_397|3end_NAD(+)_synthetase_327423..327573_POSITIVE 217 116 71 89 26 smit:SMT_2094|3end_serine_protease_1989243..1989393_NEGATIVE 216 130 81 67 3 smit:SMT_1866|3end_extramembranal_protein_1827939..1828089_POSITIVE 215 102 71 48 22 smit:SMT_175|3end_50S_ribosomal_protein_L22_118148..118298_POSITIVE