Origin IGS: tgctgtacttcctcttctttatgtgttacggcattgcgccgcacctcctccgtctatcgggtagcacagcaatgccgtcagttaatctttctacggcttgacggagggaatgggtcttccattgactatgatttgatgaaattaaaatccggccaaccaatcggtaatgccgaaaaaatcagctccacaaaggtaagattatcacgcaaacgaaaaagatgctttgcattcagagaccattgtttttgctctgaagctatcggcaaatgtactcatcctgcaaaaaagaagagggcgacccaagaatatttggatcgccctctgttctttatgctaacttcattcagagggctgtcggctcctcctgaaaaaagtgttgtcagatcatataact .........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 agttatatgatctgacaacacttttttcaggaggagccgacagccctctgaatgaagttagcataaagaacagagggcgatccaaatattcttgggtcgccctcttcttttttgcaggatgagtacatttgccgatagcttcagagcaaaaacaatggtctctgaatgcaaagcatctttttcgtttgcgtgataatcttacctttgtggagctgattttttcggcattaccgattggttggccggattttaatttcatcaaatcatagtcaatggaagacccattccctccgtcaagccgtagaaagattaactgacggcattgctgtgctacccgatagacggaggaggtgcggcgcaatgccgtaacacataaagaagaggaagtacagca Mask Tandem Repeat Region ================================================ tgctgtacttcctcttctttatgtgttacggcattgcgccgcacctcctccgtctatcgggtagcacagcaatgccgtcagttaatctttctacggcttgacggagggaatgggtcttccattgactatgatttgatgaaattaaaatccggccaaccaatcggtaatgccgaaaaaatcagctccacaaaggtaagattatcacgcaaacgaaaaagatgctttgcattcagagaccattgtttttgctctgaagctatcggcaaatgtactcatcctgcaaaaaagaagagggcgacccaagaatatttggatcgccctctgttctttatgctaacttcattcagagggctgtcggctcctcctgaaaaaagtgttgtcagatcatataact Find is-nt database================================================ Query_seq: PG0715:PG0717|PG0715:PG0717:transporter:lipoprotein, putative:<-<-:769687..770080 394 tgctgtacttcctcttctttatgtgttacggcattgcgccgcacctcctccgtctatcgggtagcacagcaatgccgtcagttaatctttctacggcttgacggagggaatgggtcttccattgactatgatttgatgaaattaaaatccggccaaccaatcggtaatgccgaaaaaatcagctccacaaaggtaagattatcacgcaaacgaaaaagatgctttgcattcagagaccattgtttttgctctgaagctatcggcaaatgtactcatcctgcaaaaaagaagagggcgacccaagaatatttggatcgccctctgttctttatgctaacttcattcagagggctgtcggctcctcctgaaaaaagtgttgtcagatcatataact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0715:PG0717|PG0715:PG0717:transporter:lipoprotein, putative:<-<-:769687..770080 394 tgctgtacttcctcttctttatgtgttacggcattgcgccgcacctcctccgtctatcgggtagcacagcaatgccgtcagttaatctttctacggcttgacggagggaatgggtcttccattgactatgatttgatgaaattaaaatccggccaaccaatcggtaatgccgaaaaaatcagctccacaaaggtaagattatcacgcaaacgaaaaagatgctttgcattcagagaccattgtttttgctctgaagctatcggcaaatgtactcatcctgcaaaaaagaagagggcgacccaagaatatttggatcgccctctgttctttatgctaacttcattcagagggctgtcggctcctcctgaaaaaagtgttgtcagatcatataact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0715:PG0717|PG0715:PG0717:transporter:lipoprotein, putative:<-<-:769687..770080 394 tgctgtacttcctcttctttatgtgttacggcattgcgccgcacctcctccgtctatcgggtagcacagcaatgccgtcagttaatctttctacggcttgacggagggaatgggtcttccattgactatgatttgatgaaattaaaatccggccaaccaatcggtaatgccgaaaaaatcagctccacaaaggtaagattatcacgcaaacgaaaaagatgctttgcattcagagaccattgtttttgctctgaagctatcggcaaatgtactcatcctgcaaaaaagaagagggcgacccaagaatatttggatcgccctctgttctttatgctaacttcattcagagggctgtcggctcctcctgaaaaaagtgttgtcagatcatataact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgctgtacttcctcttctttatgtgttacggcattgcgccgcacctcctccgtctatcgggtagcacagcaatgccgtcagttaatctttctacggcttgacggagggaatgggtcttccattgactatgatttgatgaaattaaaatccggccaaccaatcggtaatgccgaaaaaatcagctccacaaaggtaagattatcacgcaaacgaaaaagatgctttgcattcagagaccattgtttttgctctgaagctatcggcaaatgtactcatcctgcaaaaaagaagagggcgacccaagaatatttggatcgccctctgttctttatgctaacttcattcagagggctgtcggctcctcctgaaaaaagtgttgtcagatcatataact Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 3 End: 98 .. M Y F L F F M C Y G I A P H L L R L S G S T A M P S V N L S T A ........................................................................................................................................................................................................................................................................................................ Protein_Len: 37 Strand: + Start: 224 End: 334 ............................................................................................................................................................................................................................... M H S E T I V F A L K L S A N V L I L Q K R R G R P K N I W I A L C S L C ............................................................ Protein_Len: 33 Strand: + Start: 267 End: 365 .......................................................................................................................................................................................................................................................................... M Y S S C K K E E G D P R I F G S P S V L Y A N F I Q R A V G S S ............................. Protein_Len: 60 Strand: + Start: 34 End: 393 ................................. M R R T S S V Y R V A Q Q C R Q L I F L R L D G G N G S S I D Y D L M K L K S G Q P I G N A E K I S S T K V R L S R K R . Protein_Len: 36 Strand: - Start: 276 End: 383 ................................................................................................................................................................................................................................................................................... G A F F F L A V W S Y K S R G R N K I S V E N L P S D A G G S F L T T M ........... Protein_Len: 37 Strand: - Start: 205 End: 315 ............................................................................................................................................................................................................ A F S F S A K C E S V M T K A R F S D A F T S M R C F L L P R G L F I Q M ............................................................................... Protein_Len: 46 Strand: - Start: 129 End: 266 ................................................................................................................................ S K I F N F D P W G I P L A S F I L E V F T L N D R L R F L H K A N L S W Q K Q E S A I P M ................................................................................................................................ Protein_Len: 44 Strand: - Start: 29 End: 160 ............................ P M A G C R R R R D P L V A I G D T L R E V A Q R L S H T K W Q S H N S S I L I R G V M .......................................................................................................................................................................................................................................... tgctgtacttcctcttctttatgtgttacggcattgcgccgcacctcctccgtctatcgggtagcacagcaatgccgtcagttaatctttctacggcttgacggagggaatgggtcttccattgactatgatttgatgaaattaaaatccggccaaccaatcggtaatgccgaaaaaatcagctccacaaaggtaagattatcacgcaaacgaaaaagatgctttgcattcagagaccattgtttttgctctgaagctatcggcaaatgtactcatcctgcaaaaaagaagagggcgacccaagaatatttggatcgccctctgttctttatgctaacttcattcagagggctgtcggctcctcctgaaaaaagtgttgtcagatcatataact 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================================================ tgctgtacttcctcttctttatgtgttacggcattgcgccgcacctcctccgtctatcgggtagcacagcaatgccgtcagttaatctttctacggcttgacggagggaatgggtcttccattgactatgatttgatgaaattaaaatccggccaaccaatcggtaatgccgaaaaaatcagctccacaaaggtaagattatcacgcaaacgaaaaagatgctttgcattcagagaccattgtttttgctctgaagctatcggcaaatgtactcatcctgcaaaaaagaagagggcgacccaagaatatttggatcgccctctgttctttatgctaacttcattcagagggctgtcggctcctcctgaaaaaagtgttgtcagatcatataact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.6 Tail_Score: -5.02074 Start: 288 End: 325 Full_Region: aagttagcataaaga acagagggcgatccaa atattc ttgggtcgccctcttc ttttttgcaggatga ...............................................................................................................................................................................................................................................................................................acagagggcgatccaaatattcttgggtcgccctcttc..................................................................... TransTerm Strand: + Conf: 95 HP_score: -12.6 Tail_Score: -4.11585 Start: 289 End: 324 Full_Region: CATCCTGCAAAAAAG AAGAGGGCGACCCAAG AATA TTTGGATCGCCCTCTG TTCTTTATGCTAACT ................................................................................................................................................................................................................................................................................................AAGAGGGCGACCCAAGAATATTTGGATCGCCCTCTG...................................................................... TransTerm Strand: - Conf: 100 HP_score: -16.7 Tail_Score: -4.61482 Start: 291 End: 322 Full_Region: ttagcataaagaaca gagggcgatccaa atattc ttgggtcgccctc ttcttttttgcagga ..................................................................................................................................................................................................................................................................................................gagggcgatccaaatattcttgggtcgccctc........................................................................ Find igs database================================================ Query_seq: PG0715:PG0717|PG0715:PG0717:transporter:lipoprotein, putative:<-<-:769687..770080 394 tgctgtacttcctcttctttatgtgttacggcattgcgccgcacctcctccgtctatcgggtagcacagcaatgccgtcagttaatctttctacggcttgacggagggaatgggtcttccattgactatgatttgatgaaattaaaatccggccaaccaatcggtaatgccgaaaaaatcagctccacaaaggtaagattatcacgcaaacgaaaaagatgctttgcattcagagaccattgtttttgctctgaagctatcggcaaatgtactcatcctgcaaaaaagaagagggcgacccaagaatatttggatcgccctctgttctttatgctaacttcattcagagggctgtcggctcctcctgaaaaaagtgttgtcagatcatataact Intra-Species Hit: Count: 1 Min: 1 Max: 394 Len: 394 Subject: NC_002950_PG0715_PG0717|transporter:lipoprotein, putative|NEGATIVE:NEGATIVE|[769687,770080]|394 HSP 1 e-value: 0.0 bit: 781.0 Len: 394 Query Start:1 Query End:394 Subject Strand: POSITIVE Subject Start: 1 Subject End: 394 tgctgtacttcctcttctttatgtgttacggcattgcgccgcacctcctccgtctatcgggtagcacagcaatgccgtcagttaatctttctacggcttgacggagggaatgggtcttccattgactatgatttgatgaaattaaaatccggccaaccaatcggtaatgccgaaaaaatcagctccacaaaggtaagattatcacgcaaacgaaaaagatgctttgcattcagagaccattgtttttgctctgaagctatcggcaaatgtactcatcctgcaaaaaagaagagggcgacccaagaatatttggatcgccctctgttctttatgctaacttcattcagagggctgtcggctcctcctgaaaaaagtgttgtcagatcatataact tgctgtacttcctcttctttatgtgttacggcattgcgccgcacctcctccgtctatcgggtagcacagcaatgccgtcagttaatctttctacggcttgacggagggaatgggtcttccattgactatgatttgatgaaattaaaatccggccaaccaatcggtaatgccgaaaaaatcagctccacaaaggtaagattatcacgcaaacgaaaaagatgctttgcattcagagaccattgtttttgctctgaagctatcggcaaatgtactcatcctgcaaaaaagaagagggcgacccaagaatatttggatcgccctctgttctttatgctaacttcattcagagggctgtcggctcctcctgaaaaaagtgttgtcagatcatataact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUGUACUUCCUCUUCUUUAUGUGUUACGGCAUUGCGCCGCACCUCCUCCGUCUAUCGGGUAGCACAGCAAUGCCGUCAGUUAAUCUUUCUACGGCUUGACGGAGGGAAUGGGUCUUCCAUUGACUAUGAUUUGAUGAAAUUAAAAUCCGGCCAACCAAUCGGUAAUGCCGAAAAAAUCAGCUCCACAAAGGUAAGAUUAUCACGCAAACGAAAAAGAUGCUUUGCAUUCAGAGACCAUUGUUUUUGCUCUGAAGCUAUCGGCAAAUGUACUCAUCCUGCAAAAAAGAAGAGGGCGACCCAAGAAUAUUUGGAUCGCCCUCUGUUCUUUAUGCUAACUUCAUUCAGAGGGCUGUCGGCUCCUCCUGAAAAAAGUGUUGUCAGAUCAUAUAACU ....((((....((((.(((.(((((.((((((((((...((((((............)))).))...))))))))))....((((((((((..((((.((.((((((......))))))........((((((....))))))...)).))))......((((.....)))).................))).)))))))..)))))...))).))))((((..((.(((((((.............)))))))))....))))...)))).....((((((.((((((((((((((.(((((....))))).)))))))))..)))))......((((..((((((((((.....)).))).)))))..)))).))).)))........... (-112.42) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUAUAUGAUCUGACAACACUUUUUUCAGGAGGAGCCGACAGCCCUCUGAAUGAAGUUAGCAUAAAGAACAGAGGGCGAUCCAAAUAUUCUUGGGUCGCCCUCUUCUUUUUUGCAGGAUGAGUACAUUUGCCGAUAGCUUCAGAGCAAAAACAAUGGUCUCUGAAUGCAAAGCAUCUUUUUCGUUUGCGUGAUAAUCUUACCUUUGUGGAGCUGAUUUUUUCGGCAUUACCGAUUGGUUGGCCGGAUUUUAAUUUCAUCAAAUCAUAGUCAAUGGAAGACCCAUUCCCUCCGUCAAGCCGUAGAAAGAUUAACUGACGGCAUUGCUGUGCUACCCGAUAGACGGAGGAGGUGCGGCGCAAUGCCGUAACACAUAAAGAAGAGGAAGUACAGCA .........((((......(((((.(((((.(((.((.....)))))))))).)))))..(((.(((((..((((((((((((((......)))))))))))))))))))..))).))))..((((...........((((((((((..........).))))))).))......((((((((.((((.(((.(((((((((.(((((((((.((((((.((((((...(((....)))..)))))).............)))))).....(((((.....)))))..))))).))))..)))...))))))....((((((((((((..((.((((.....))).)..))..))..))))))))))..))).)))))))))))).)))).... (-129.24) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1137 80 31 171 122 NC_002950:PG0715|5end_transporter_769596..769826_NEGATIVE 457 79 36 73 17 NC_002950:PG0150|5end_conserved_hypothetical_protein_TIGR01125_173544..173774_NEGATIVE 427 100 51 197 143 NC_002950:PG0156|5end_modification_methylase,_HemK_family_178828..179058_POSITIVE 412 70 23 217 174 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 411 78 32 116 41 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 391 108 61 177 126 NC_002950:PG1986|5end_CRISPR-associated_TM1793_family_protein_2075784..2076014_NEGATIVE 390 77 31 68 8 NC_002950:PG1807|5end_v-type_ATPase,_subunit_K_1902069..1902299_POSITIVE 387 269 221 120 66 NC_002950:PG1605|5end_aminopeptidase_C_1685179..1685409_POSITIVE 386 79 31 73 18 NC_002950:PG0021|5end_TIM-barrel_protein,_putative,_NifR3_family_25123..25353_NEGATIVE 384 300 251 221 167 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 383 70 29 55 3 NC_002950:PG1354|5end_hydrolase,_carbon-nitrogen_family_1434765..1434995_NEGATIVE 383 61 30 196 160 NC_002950:PG1074|5end_D-lysine_5,6-aminomutase,_beta_subunit_1141963..1142193_POSITIVE 383 77 37 167 126 NC_002950:PG0032|5end_beta-mannosidase,_putative_40212..40442_NEGATIVE 382 65 27 145 109 NC_002950:PG2149|5end_hypothetical_protein_2257658..2257888_NEGATIVE 380 90 44 190 151 NC_002950:PG0253|5end_hypothetical_protein_284607..284837_POSITIVE 378 70 25 155 113 NC_002950:PG1754|5end_hypothetical_protein_1839679..1839909_POSITIVE 376 78 31 214 171 NC_002950:PG1184|5end_alginate_O-acetyltransferase,_putative_1266870..1267100_NEGATIVE 371 80 32 48 2 NC_002950:PG2222|5end_acyltransferase,_HtrB/MsbB_family_2336757..2336987_POSITIVE 371 78 36 73 29 NC_002950:PG1678|5end_hypothetical_protein_1763862..1764092_NEGATIVE 371 76 35 177 102 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 457 79 36 76 20 NC_002950:PG0151|3end_signal_recognition_particle-docking_protein_FtsY_173541..173691_NEGATIVE 442 323 285 58 16 NC_002950:PG1910|3end_ribosomal_protein_L17_2010282..2010432_NEGATIVE 423 80 34 85 42 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 386 79 31 76 21 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE 384 300 251 62 8 NC_002950:PG1020|3end_hypothetical_protein_1083458..1083608_POSITIVE 383 70 29 58 6 NC_002950:PG1355|3end_acyltransferase,_putative_1434762..1434912_NEGATIVE 383 77 37 137 96 NC_002950:PG0033|3end_RmuC_domain_protein_40242..40392_NEGATIVE 382 65 27 136 100 NC_002950:PG2150|3end_LysM_domain_protein_2257667..2257817_NEGATIVE 378 70 25 137 95 NC_002950:PG1753|3end_selenide,_water_dikinase_1839741..1839891_POSITIVE 373 70 22 149 96 NC_002950:PG1625|3end_hypothetical_protein_1708718..1708868_POSITIVE 371 80 32 51 5 NC_002950:PG2221|3end_MiaB-like_tRNA_modifying_enzyme_2336840..2336990_POSITIVE 371 78 36 69 4 NC_002950:PG1247|3end_3-dehydroquinate_synthase_1325585..1325735_POSITIVE 368 70 22 150 100 NC_002950:PG0004|3end_NAD-dependent_deacetylase_3752..3902_POSITIVE 365 62 23 133 88 NC_002950:PG0330|3end_DNA-binding_protein,_histone-like_family_364478..364628_NEGATIVE 362 70 29 85 45 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 360 80 32 151 111 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 358 60 12 140 70 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 355 79 31 46 4 NC_002950:PG2034|3end_oxidoreductase,_FAD-binding,_putative_2134910..2135060_NEGATIVE 354 80 39 58 19 NC_002950:PG1007|3end_transcriptional_regulator,_GntR_family_1066518..1066668_NEGATIVE 351 269 221 62 14 NC_002950:PG1509|3end_HAD-superfamily_hydrolase,_subfamily_IA,_variant_1_family_protein_1587439..1587589_POSITIVE