Origin IGS: acgctacgactaaaataggactctcgaatatggaagagccgcctccgttgccccacttcaggggtatcaggggcggctctccttcgttatgagaaagccggaacttcgatcgaagctccggcttgcttctgtacgtttttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaaacgtacagaagcaagccggagcttcgatcgaagttccggctttctcataacgaaggagagccgcccctgatacccctgaagtggggcaacggaggcggctcttccatattcgagagtcctattttagtcgtagcgt Mask Tandem Repeat Region ================================================ acgctacgactaaaataggactctcgaatatggaagagccgcctccgttgccccacttcaggggtatcaggggcggctctccttcgttatgagaaagccggaacttcgatcgaagctccggcttgcttctgtacgtttttt Find is-nt database================================================ Query_seq: PG0166:PG0167|PG0166:PG0167:peptidyl-tRNA hydrolase:ribosomal protein L25:<-<-:188461..188601 141 acgctacgactaaaataggactctcgaatatggaagagccgcctccgttgccccacttcaggggtatcaggggcggctctccttcgttatgagaaagccggaacttcgatcgaagctccggcttgcttctgtacgtttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0166:PG0167|PG0166:PG0167:peptidyl-tRNA hydrolase:ribosomal protein L25:<-<-:188461..188601 141 acgctacgactaaaataggactctcgaatatggaagagccgcctccgttgccccacttcaggggtatcaggggcggctctccttcgttatgagaaagccggaacttcgatcgaagctccggcttgcttctgtacgtttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0166:PG0167|PG0166:PG0167:peptidyl-tRNA hydrolase:ribosomal protein L25:<-<-:188461..188601 141 acgctacgactaaaataggactctcgaatatggaagagccgcctccgttgccccacttcaggggtatcaggggcggctctccttcgttatgagaaagccggaacttcgatcgaagctccggcttgcttctgtacgtttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgctacgactaaaataggactctcgaatatggaagagccgcctccgttgccccacttcaggggtatcaggggcggctctccttcgttatgagaaagccggaacttcgatcgaagctccggcttgcttctgtacgtttttt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 28 End: 141 ........................... M W K S R L R C P T S G V S G A A L L R Y E K A G T S I E A P A C F C T F F acgctacgactaaaataggactctcgaatatggaagagccgcctccgttgccccacttcaggggtatcaggggcggctctccttcgttatgagaaagccggaacttcgatcgaagctccggcttgcttctgtacgtttttt 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================================================ acgctacgactaaaataggactctcgaatatggaagagccgcctccgttgccccacttcaggggtatcaggggcggctctccttcgttatgagaaagccggaacttcgatcgaagctccggcttgcttctgtacgtttttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -17.8 Tail_Score: -3.44146 Start: 33 End: 82 Full_Region: GGACTCTCGAATATG GAAGAGCCGCCTCCGTTGCCCC ACTTCA GGGGTATCAGGGGCGGCTCTCC TTCGTTATGAGAAAG ................................GAAGAGCCGCCTCCGTTGCCCCACTTCAGGGGTATCAGGGGCGGCTCTCC........................................................... TransTerm Strand: + Conf: 95 HP_score: -18.1 Tail_Score: -2.87274 Start: 36 End: 79 Full_Region: CTCTCGAATATGGAA GAGCCGCCTCCGTTGCCCC ACTTCA GGGGTATCAGGGGCGGCTC TCCTTCGTTATGAGA ...................................GAGCCGCCTCCGTTGCCCCACTTCAGGGGTATCAGGGGCGGCTC.............................................................. TransTerm Strand: - Conf: 100 HP_score: -15.9 Tail_Score: -3.1855 Start: 36 End: 79 Full_Region: tctcataacgaagga gagccgcccctgatacccc tgaagt ggggcaacggaggcggctc ttccatattcgagag ...................................gagccgcccctgatacccctgaagtggggcaacggaggcggctc.............................................................. TransTerm Strand: + Conf: 89 HP_score: -13.3 Tail_Score: -3.50734 Start: 97 End: 122 Full_Region: CTTCGTTATGAGAAA GCCGGAACTTC GATC GAAGCTCCGGC TTGCTTCTGTACGTT ................................................................................................GCCGGAACTTCGATCGAAGCTCCGGC................... Find igs database================================================ Query_seq: PG0166:PG0167|PG0166:PG0167:peptidyl-tRNA hydrolase:ribosomal protein L25:<-<-:188461..188601 141 acgctacgactaaaataggactctcgaatatggaagagccgcctccgttgccccacttcaggggtatcaggggcggctctccttcgttatgagaaagccggaacttcgatcgaagctccggcttgcttctgtacgtttttt Intra-Species Hit: Count: 1 Min: 1 Max: 141 Len: 141 Subject: NC_002950_PG0166_PG0167|peptidyl-tRNA hydrolase:ribosomal protein L25|NEGATIVE:NEGATIVE|[188461,188601]|141 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 141 Query Start:1 Query End:141 Subject Strand: POSITIVE Subject Start: 1 Subject End: 141 acgctacgactaaaataggactctcgaatatggaagagccgcctccgttgccccacttcaggggtatcaggggcggctctccttcgttatgagaaagccggaacttcgatcgaagctccggcttgcttctgtacgtttttt acgctacgactaaaataggactctcgaatatggaagagccgcctccgttgccccacttcaggggtatcaggggcggctctccttcgttatgagaaagccggaacttcgatcgaagctccggcttgcttctgtacgtttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGCUACGACUAAAAUAGGACUCUCGAAUAUGGAAGAGCCGCCUCCGUUGCCCCACUUCAGGGGUAUCAGGGGCGGCUCUCCUUCGUUAUGAGAAAGCCGGAACUUCGAUCGAAGCUCCGGCUUGCUUCUGUACGUUUUUU (((.((((............(((.((((...(((.((((((((((.(.((((((......)))))).).)))))))))))))))))....))).((((((((.((((....)))).)))))))).....)))))))..... (-64.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAACGUACAGAAGCAAGCCGGAGCUUCGAUCGAAGUUCCGGCUUUCUCAUAACGAAGGAGAGCCGCCCCUGAUACCCCUGAAGUGGGGCAACGGAGGCGGCUCUUCCAUAUUCGAGAGUCCUAUUUUAGUCGUAGCGU .....((((((.((.(.(((((((((((((....))))))))))))).)))....(((((((((((((((.(((...((((......))))...))).)))))))))))....)))).................)).)))) (-63.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1184 80 31 171 122 NC_002950:PG0166|5end_peptidyl-tRNA_hydrolase_188370..188600_NEGATIVE 472 77 32 59 11 NC_002950:PG1621|5end_hypothetical_protein_1701431..1701661_NEGATIVE 467 88 41 52 6 NC_002950:PG2225|5end_hypothetical_protein_2339440..2339670_POSITIVE 459 76 31 98 50 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 443 86 43 97 49 NC_002950:PG2052|5end_dihydrodipicolinate_synthase_2149636..2149866_POSITIVE 436 78 31 56 2 NC_002950:PG1491|5end_hypothetical_protein_1565741..1565971_POSITIVE 419 109 61 181 113 NC_002950:PG0794|5end_penicillin-binding_protein_1A,_putative_846411..846641_POSITIVE 418 120 71 62 8 NC_002950:PG2171|5end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_2278972..2279202_NEGATIVE 412 65 21 227 172 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 411 136 95 215 164 NC_002950:PG1253|5end_DNA_ligase,_NAD-dependent_1331606..1331836_NEGATIVE 410 90 41 212 147 NC_002950:PG1655|5end_hypothetical_protein_1737095..1737325_POSITIVE 409 79 33 154 116 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 406 65 21 82 21 NC_002950:PG2185|5end_transporter,_putative_2293249..2293479_NEGATIVE 405 77 31 231 160 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 403 120 71 57 4 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 401 74 38 224 189 NC_002950:PG0680|5end_efflux_transporter,_MFP_component,_RND_family_730968..731198_POSITIVE 401 77 33 201 136 NC_002950:PG0189|5end_hypothetical_protein_225291..225521_POSITIVE 399 77 35 178 121 NC_002950:PG1173|5end_YkgG_family_protein_1252435..1252665_POSITIVE 398 120 74 220 187 NC_002950:PG0203|5end_hypothetical_protein_240211..240441_NEGATIVE 397 47 3 207 160 NC_002950:PG1961|5end_hypothetical_protein_2051153..2051383_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 524 76 31 149 92 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 522 76 31 141 87 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 472 77 32 72 24 NC_002950:PG1622|3end_DNA_topoisomerase_IV_subunit_A_1701418..1701568_NEGATIVE 466 100 51 97 32 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 422 77 32 109 64 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 406 77 35 80 31 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 399 78 31 92 40 NC_002950:PG1359|3end_hypothetical_protein_1437644..1437794_NEGATIVE 395 140 96 89 47 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE 391 77 38 141 100 NC_002950:PG0520|3end_chaperonin_GroEL_563618..563768_NEGATIVE 388 110 68 50 2 NC_002950:PG0248|3end_translation_initation_factor_SUI1,_putative_281510..281660_NEGATIVE 385 89 41 140 71 NC_002950:PG1174|3end_thioesterase_family_protein_1253210..1253360_NEGATIVE 380 77 32 81 24 NC_002950:PG1118|3end_clpB_protein_1192083..1192233_NEGATIVE 379 76 38 143 97 NC_002950:PG1205|3end_DNA-binding_protein,_histone-like_family_1284503..1284653_POSITIVE 378 118 73 151 106 NC_002950:PG0140|3end_hypothetical_protein_163151..163301_NEGATIVE 374 77 32 103 59 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 372 80 31 68 22 NC_002950:PG0387|3end_elongation_factor_Tu_421910..422060_POSITIVE 368 86 42 142 97 NC_002950:PG1743|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1827530..1827680_NEGATIVE 364 107 61 114 72 NC_002950:PG2036|3end_ion_transporter_2137552..2137702_POSITIVE 364 120 75 52 3 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 362 100 52 151 117 NC_002950:PG2141|3end_3-oxoacyl-(acyl_carrier_protein)_synthase_2247586..2247736_POSITIVE