Origin IGS: tgtttgatatgttttatgatgttatgaatatgttcctgaacatatgataagatctcggggaaataataaagagggacatgggccgatctttttgcgaaatatccatggagggatttaccttcggtttttcacctccaacccgataaccgcccgtaaaattagaagaaatcatcaatatgaaatataataaacctgttttcttgctttttgagccctttgcaaaaagagaaggtcatcaagaagtatcttttcggtatcgtttttgctcacctatagagtgtatcgcacaagtcatggaggaggctttagaggtattcatatctataatgacactgaaaaatcag .........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 ctgatttttcagtgtcattatagatatgaatacctctaaagcctcctccatgacttgtgcgatacactctataggtgagcaaaaacgataccgaaaagatacttcttgatgaccttctctttttgcaaagggctcaaaaagcaagaaaacaggtttattatatttcatattgatgatttcttctaattttacgggcggttatcgggttggaggtgaaaaaccgaaggtaaatccctccatggatatttcgcaaaaagatcggcccatgtccctctttattatttccccgagatcttatcatatgttcaggaacatattcataacatcataaaacatatcaaaca Mask Tandem Repeat Region ================================================ tgtttgatatgttttatgatgttatgaatatgttcctgaacatatgataagatctcggggaaataataaagagggacatgggccgatctttttgcgaaatatccatggagggatttaccttcggtttttcacctccaacccgataaccgcccgtaaaattagaagaaatcatcaatatgaaatataataaacctgttttcttgctttttgagccctttgcaaaaagagaaggtcatcaagaagtatcttttcggtatcgtttttgctcacctatagagtgtatcgcacaagtcatggaggaggctttagaggtattcatatctataatgacactgaaaaatcag Find is-nt database================================================ Query_seq: PG1424:PG1426|PG1424:PG1426:peptidylarginine deiminase:hypothetical protein:<-<-:1510898..1511241 344 tgtttgatatgttttatgatgttatgaatatgttcctgaacatatgataagatctcggggaaataataaagagggacatgggccgatctttttgcgaaatatccatggagggatttaccttcggtttttcacctccaacccgataaccgcccgtaaaattagaagaaatcatcaatatgaaatataataaacctgttttcttgctttttgagccctttgcaaaaagagaaggtcatcaagaagtatcttttcggtatcgtttttgctcacctatagagtgtatcgcacaagtcatggaggaggctttagaggtattcatatctataatgacactgaaaaatcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1424:PG1426|PG1424:PG1426:peptidylarginine deiminase:hypothetical protein:<-<-:1510898..1511241 344 tgtttgatatgttttatgatgttatgaatatgttcctgaacatatgataagatctcggggaaataataaagagggacatgggccgatctttttgcgaaatatccatggagggatttaccttcggtttttcacctccaacccgataaccgcccgtaaaattagaagaaatcatcaatatgaaatataataaacctgttttcttgctttttgagccctttgcaaaaagagaaggtcatcaagaagtatcttttcggtatcgtttttgctcacctatagagtgtatcgcacaagtcatggaggaggctttagaggtattcatatctataatgacactgaaaaatcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1424:PG1426|PG1424:PG1426:peptidylarginine deiminase:hypothetical protein:<-<-:1510898..1511241 344 tgtttgatatgttttatgatgttatgaatatgttcctgaacatatgataagatctcggggaaataataaagagggacatgggccgatctttttgcgaaatatccatggagggatttaccttcggtttttcacctccaacccgataaccgcccgtaaaattagaagaaatcatcaatatgaaatataataaacctgttttcttgctttttgagccctttgcaaaaagagaaggtcatcaagaagtatcttttcggtatcgtttttgctcacctatagagtgtatcgcacaagtcatggaggaggctttagaggtattcatatctataatgacactgaaaaatcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtttgatatgttttatgatgttatgaatatgttcctgaacatatgataagatctcggggaaataataaagagggacatgggccgatctttttgcgaaatatccatggagggatttaccttcggtttttcacctccaacccgataaccgcccgtaaaattagaagaaatcatcaatatgaaatataataaacctgttttcttgctttttgagccctttgcaaaaagagaaggtcatcaagaagtatcttttcggtatcgtttttgctcacctatagagtgtatcgcacaagtcatggaggaggctttagaggtattcatatctataatgacactgaaaaatcag Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 44 End: 184 ........................................... M I R S R G N N K E G H G P I F L R N I H G G I Y L R F F T S N P I T A R K I R R N H Q Y E I ................................................................................................................................................................ Protein_Len: 30 Strand: + Start: 184 End: 273 ....................................................................................................................................................................................... M I N L F S C F L S P L Q K E K V I K K Y L F G I V F A H L ....................................................................... Protein_Len: 33 Strand: + Start: 245 End: 343 .................................................................................................................................................................................................................................................... M F S V S F L L T Y R V Y R T S H G G G F R G I H I Y N D T E K S . Protein_Len: 59 Strand: + Start: 168 End: 344 ....................................................................................................................................................................... M I N M K Y N K P V F L L F E P F A K R E G H Q E V S F R Y R F C S P I E C I A Q V M E E A L E V F I S I M T L K N Q Protein_Len: 30 Strand: - Start: 239 End: 328 .............................................................................................................................................................................................................................................. S T D K R Y R K Q E G I S H I A C T M S S A K S T N M D I M ................ Protein_Len: 32 Strand: - Start: 175 End: 270 .............................................................................................................................................................................. Y S I Y Y V Q K R A K Q A R Q L F L L D D L L I K E T D N K S M .......................................................................... Protein_Len: 32 Strand: - Start: 162 End: 257 ................................................................................................................................................................. F F D D I H F I I F R N E Q K K L G K C F S F T M L F Y R K P M ....................................................................................... Protein_Len: 30 Strand: - Start: 25 End: 114 ........................ S Y T G S C I I L D R P F L L S P C P G I K K R F I W P P M ...................................................................................................................................................................................................................................... Protein_Len: 54 Strand: - Start: 17 End: 178 ................ S T I F I N R F M H Y S R P S I I F L S M P R D K Q S I D M S P N V K P K E G G V R Y G G T F N S S I M L M ...................................................................................................................................................................... tgtttgatatgttttatgatgttatgaatatgttcctgaacatatgataagatctcggggaaataataaagagggacatgggccgatctttttgcgaaatatccatggagggatttaccttcggtttttcacctccaacccgataaccgcccgtaaaattagaagaaatcatcaatatgaaatataataaacctgttttcttgctttttgagccctttgcaaaaagagaaggtcatcaagaagtatcttttcggtatcgtttttgctcacctatagagtgtatcgcacaagtcatggaggaggctttagaggtattcatatctataatgacactgaaaaatcag 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: 159 End: 188 ..............................................................................................................................................................TTAGAAGAAATCATCAATATGAAATATAAT............................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgtttgatatgttttatgatgttatgaatatgttcctgaacatatgataagatctcggggaaataataaagagggacatgggccgatctttttgcgaaatatccatggagggatttaccttcggtttttcacctccaacccgataaccgcccgtaaaattagaagaaatcatcaatatgaaatataataaacctgttttcttgctttttgagccctttgcaaaaagagaaggtcatcaagaagtatcttttcggtatcgtttttgctcacctatagagtgtatcgcacaagtcatggaggaggctttagaggtattcatatctataatgacactgaaaaatcag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 43 HP_score: -3.5 Tail_Score: -2.61831 Start: 108 End: 122 Full_Region: TGCGAAATATCCATG GAGGG ATTTA CCTTC GGTTTTTCACCTCCA ...........................................................................................................GAGGGATTTACCTTC.............................................................................................................................................................................................................................. Find igs database================================================ Query_seq: PG1424:PG1426|PG1424:PG1426:peptidylarginine deiminase:hypothetical protein:<-<-:1510898..1511241 344 tgtttgatatgttttatgatgttatgaatatgttcctgaacatatgataagatctcggggaaataataaagagggacatgggccgatctttttgcgaaatatccatggagggatttaccttcggtttttcacctccaacccgataaccgcccgtaaaattagaagaaatcatcaatatgaaatataataaacctgttttcttgctttttgagccctttgcaaaaagagaaggtcatcaagaagtatcttttcggtatcgtttttgctcacctatagagtgtatcgcacaagtcatggaggaggctttagaggtattcatatctataatgacactgaaaaatcag Intra-Species Hit: Count: 3 Min: 1 Max: 344 Len: 344 Subject: NC_002950_PG1424_PG1426|peptidylarginine deiminase:hypothetical protein|NEGATIVE:NEGATIVE|[1510898,1511241]|344 HSP 1 e-value: 0.0 bit: 682.0 Len: 344 Query Start:1 Query End:344 Subject Strand: POSITIVE Subject Start: 1 Subject End: 344 tgtttgatatgttttatgatgttatgaatatgttcctgaacatatgataagatctcggggaaataataaagagggacatgggccgatctttttgcgaaatatccatggagggatttaccttcggtttttcacctccaacccgataaccgcccgtaaaattagaagaaatcatcaatatgaaatataataaacctgttttcttgctttttgagccctttgcaaaaagagaaggtcatcaagaagtatcttttcggtatcgtttttgctcacctatagagtgtatcgcacaagtcatggaggaggctttagaggtattcatatctataatgacactgaaaaatcag tgtttgatatgttttatgatgttatgaatatgttcctgaacatatgataagatctcggggaaataataaagagggacatgggccgatctttttgcgaaatatccatggagggatttaccttcggtttttcacctccaacccgataaccgcccgtaaaattagaagaaatcatcaatatgaaatataataaacctgttttcttgctttttgagccctttgcaaaaagagaaggtcatcaagaagtatcttttcggtatcgtttttgctcacctatagagtgtatcgcacaagtcatggaggaggctttagaggtattcatatctataatgacactgaaaaatcag Subject: NC_002950_PG0088_PG0090|peptidase, M16 family:Dps family protein|POSITIVE:POSITIVE|[104633,105663]|1031 HSP 1 e-value: 9.0E-47 bit: 188.0 Len: 131 Query Start:210 Query End:340 Subject Strand: POSITIVE Subject Start: 170 Subject End: 295 .................................................................................................................................................................................................................gagccctttgcaaaaagagaaggtcatcaagaagtatcttttcggtatcgtttttgctcacctatagagtgtatcgcacaagtcatggaggaggctttagaggtattcatatctataatgacactgaaaaa.... .................................................................................................................................................................................................................gagccctttgcaaaaagagaaggttatcaagaagtatcttttcggtatcgtttttgctcacctatagagcgtgtcgcacaagtcatggaggag-----agaggtattcatatctataacgacactgaaaaa.... Subject: NC_002950_PG0264_PG0265|glycosyl transferase, group 2 family protein:hypothetical protein|POSITIVE:NEGATIVE|[298183,298482]|300 HSP 1 e-value: 6.0E-11 bit: 69.9 Len: 106 Query Start:235 Query End:340 Subject Strand: POSITIVE Subject Start: 200 Subject End: 297 ..........................................................................................................................................................................................................................................atcaagaagtatcttttcggtatcgtttttgctcacctatagagtgtatcgcacaagtcatggaggaggctttagaggtattcatatctataatgacactgaaaaa.... ..........................................................................................................................................................................................................................................atcaagaagtatcttttcggtatcgtttt----cacccgtagagcgtgtcgcacaagtcatagaggag-ct---gaggtattcatacctataacgacacagaaaaa.... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUGAUAUGUUUUAUGAUGUUAUGAAUAUGUUCCUGAACAUAUGAUAAGAUCUCGGGGAAAUAAUAAAGAGGGACAUGGGCCGAUCUUUUUGCGAAAUAUCCAUGGAGGGAUUUACCUUCGGUUUUUCACCUCCAACCCGAUAACCGCCCGUAAAAUUAGAAGAAAUCAUCAAUAUGAAAUAUAAUAAACCUGUUUUCUUGCUUUUUGAGCCCUUUGCAAAAAGAGAAGGUCAUCAAGAAGUAUCUUUUCGGUAUCGUUUUUGCUCACCUAUAGAGUGUAUCGCACAAGUCAUGGAGGAGGCUUUAGAGGUAUUCAUAUCUAUAAUGACACUGAAAAAUCAG .(((((.(((((((((((((.((((..(((((((....))))))).)))).))).((((........(((((.((.......))..)))))........((((..((((((((...(((...)))...)).))))))....))))....)))).......................)))))))))).))))).........((((((((((..((((..(.....)..))))...))))))))))..((((((((.(((((....(((..((((.(((((.....)))...))))))..))).......(((((....)))))..))))).))))))))..... (-80.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAUUUUUCAGUGUCAUUAUAGAUAUGAAUACCUCUAAAGCCUCCUCCAUGACUUGUGCGAUACACUCUAUAGGUGAGCAAAAACGAUACCGAAAAGAUACUUCUUGAUGACCUUCUCUUUUUGCAAAGGGCUCAAAAAGCAAGAAAACAGGUUUAUUAUAUUUCAUAUUGAUGAUUUCUUCUAAUUUUACGGGCGGUUAUCGGGUUGGAGGUGAAAAACCGAAGGUAAAUCCCUCCAUGGAUAUUUCGCAAAAAGAUCGGCCCAUGUCCCUCUUUAUUAUUUCCCCGAGAUCUUAUCAUAUGUUCAGGAACAUAUUCAUAACAUCAUAAAACAUAUCAAACA ((((....))))..........((((((...........((((.(((....(((((((.(....((((.....)))).(((((((.((...((..((((....))))..))....))..))))))).....(((.....)))..)...))))))).........((((....))))................))).)))).(((((.((((((.((...(((...)))...)))))))).((((((...((..........))..))))))..............)))))(((.((((.(((((((....)))))))..)))).)))......))))))..... (-68.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 967 120 71 211 162 NC_002950:PG1424|5end_peptidylarginine_deiminase_1510807..1511037_NEGATIVE 944 300 251 121 72 NC_002950:PG0492|5end_hypothetical_protein_534668..534898_NEGATIVE 399 260 211 211 162 NC_002950:PG1234|5end_hypothetical_protein_1310112..1310342_POSITIVE 350 307 265 46 4 NC_002950:PG0770|5end_hypothetical_protein_824575..824805_NEGATIVE 342 150 103 46 1 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 336 150 102 148 98 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 332 120 75 217 168 NC_002950:PG2082|5end_POT_family_protein_2183384..2183614_NEGATIVE 325 120 80 220 164 NC_002950:PG0464|5end_adenylosuccinate_synthetase_508874..509104_NEGATIVE 319 300 251 48 7 NC_002950:PG2174|5end_hypothetical_protein_2282578..2282808_NEGATIVE 317 319 273 66 9 NC_002950:PG0083|5end_hypothetical_protein_96952..97182_POSITIVE 315 88 54 222 187 NC_002950:PG0945|5end_ABC_transporter,_permease_protein,_putative_1006432..1006662_NEGATIVE 309 166 122 162 108 NC_002950:PG0978|5end_shikimate_5-dehydrogenase_1040033..1040263_POSITIVE 307 108 77 225 192 NC_002950:PG0040|5end_ISPg5_transposase_Orf1_47934..48164_POSITIVE 306 113 73 188 151 NC_002950:PG1342|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_1422585..1422815_POSITIVE 305 130 83 210 168 NC_002950:PG0384|5end_MutS2_family_protein_416095..416325_POSITIVE 304 93 69 108 78 NC_002950:PG1338|5end_umuC_protein_1418246..1418476_POSITIVE 304 150 107 146 110 NC_002950:PG1042|5end_glycogen_synthase,_putative_1110638..1110868_NEGATIVE 304 86 41 212 159 NC_002950:PG0222|5end_DNA-binding_protein,_histone-like_family_256380..256610_NEGATIVE 303 130 84 53 3 NC_002950:PG0599|5end_3,4-dihydroxy-2-butanone_4-phosphate_synthase/GTP_cyclohydrolase_II_656435..656665_POSITIVE 302 150 102 220 166 NC_002950:PG1009|5end_hypothetical_protein_1068495..1068725_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 861 300 254 47 1 NC_002950:PG0493|3end_hypothetical_protein_534742..534892_NEGATIVE 660 330 283 77 34 NC_002950:PG0265|3end_hypothetical_protein_298393..298543_NEGATIVE 400 242 203 54 8 NC_002950:PG2146|3end_hypothetical_protein_2254650..2254800_POSITIVE 399 260 211 94 45 NC_002950:PG1233|3end_hypothetical_protein_1310075..1310225_POSITIVE 397 142 101 151 109 NC_002950:PG1860|3end_hypothetical_protein_1958574..1958724_NEGATIVE 351 150 103 146 98 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 348 96 51 73 29 NC_002950:PG0841|3end_mobilizable_transposon,_excision_protein,_putative_902781..902931_NEGATIVE 317 319 273 60 3 NC_002950:PG0082|3end_hypothetical_protein_97026..97176_POSITIVE 314 96 53 48 4 NC_002950:PG0933|3end_translation_elongation_factor_G,_putative_992236..992386_POSITIVE 313 320 273 71 22 NC_002950:PG1886|3end_GTP-binding_protein_HflX_1983316..1983466_NEGATIVE 309 299 252 147 96 NC_002950:PG0308|3end_electron_transport_complex,_RnfABCDGE_type,_A_subunit_343827..343977_POSITIVE 308 114 77 57 14 NC_002950:PG0039|3end_hypothetical_protein_47836..47986_POSITIVE 304 93 69 100 70 NC_002950:PG1337|3end_umuD_protein_1418318..1418468_POSITIVE 304 150 107 109 73 NC_002950:PG1043|3end_ferrous_iron_transport_protein_B_1110675..1110825_NEGATIVE 294 119 73 99 57 NC_002950:PG2114|3end_hypothetical_protein_2223982..2224132_NEGATIVE 294 165 121 151 98 NC_002950:PG1311|3end_hypothetical_protein_1390355..1390505_POSITIVE 294 149 107 142 103 NC_002950:PG1056|3end_hypothetical_protein_1123479..1123629_POSITIVE 293 238 192 77 24 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 292 97 51 101 38 NC_002950:PG0424|3end_hypothetical_protein_463213..463363_POSITIVE 290 95 57 37 6 NC_002950:PG0789|3end_hypothetical_protein_840702..840852_NEGATIVE