Origin IGS: cctgatttgcttctacgtcatcgaaaagctaaaaagtaacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgtaaaaagtagggtttcaagatgaagccggttgcctaaccgactgcaaggagcaaaaaaagagggctgtgacaaaactgaattttgtcacagccctctgtcatttggaaaattcttcagtaa .........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 ttactgaagaattttccaaatgacagagggctgtgacaaaattcagttttgtcacagccctctttttttgctccttgcagtcggttaggcaaccggcttcatcttgaaaccctactttttacgtgagctcgatataaaggaatggcacaacacattggttattagtgtgttttattttccacacagtgtttttcaggcacttatattgctttcagatggctttttatctacatctgaagcccaatgacttagaagccgccccttcttcccgatcattatgcagccggagaatcacaaaagagtatgatttacagctacttgttatttttatggtatgttcgcttagatcgaactggcgttactttttagcttttcgatgacgtagaagcaaatcagg Mask Tandem Repeat Region ================================================ cctgatttgcttctacgtcatcgaaaagctaaaaagtaacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgtaaaaagtagggtttcaagatgaagccggttgcctaaccgactgcaaggagcaaaaaaagagggctgtgacaaaactgaattttgtcacagccctctgtcatttggaaaattcttcagtaa Find is-nt database================================================ Query_seq: PG2116:PG2117|PG2116:PG2117:hypothetical protein:30S ribosomal protein S16:-><-:2224928..2225324 397 cctgatttgcttctacgtcatcgaaaagctaaaaagtaacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgtaaaaagtagggtttcaagatgaagccggttgcctaaccgactgcaaggagcaaaaaaagagggctgtgacaaaactgaattttgtcacagccctctgtcatttggaaaattcttcagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2116:PG2117|PG2116:PG2117:hypothetical protein:30S ribosomal protein S16:-><-:2224928..2225324 397 cctgatttgcttctacgtcatcgaaaagctaaaaagtaacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgtaaaaagtagggtttcaagatgaagccggttgcctaaccgactgcaaggagcaaaaaaagagggctgtgacaaaactgaattttgtcacagccctctgtcatttggaaaattcttcagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2116:PG2117|PG2116:PG2117:hypothetical protein:30S ribosomal protein S16:-><-:2224928..2225324 397 cctgatttgcttctacgtcatcgaaaagctaaaaagtaacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgtaaaaagtagggtttcaagatgaagccggttgcctaaccgactgcaaggagcaaaaaaagagggctgtgacaaaactgaattttgtcacagccctctgtcatttggaaaattcttcagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctgatttgcttctacgtcatcgaaaagctaaaaagtaacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgtaaaaagtagggtttcaagatgaagccggttgcctaaccgactgcaaggagcaaaaaaagagggctgtgacaaaactgaattttgtcacagccctctgtcatttggaaaattcttcagtaa Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 67 End: 171 .................................................................. M K I T S S C K S Y S F V I L R L H N D R E E G A A S K S L G F R C R .................................................................................................................................................................................................................................. Protein_Len: 30 Strand: + Start: 306 End: 395 ................................................................................................................................................................................................................................................................................................................. M P N R L Q G A K K E G C D K T E F C H S P L S F G K F F S .. Protein_Len: 48 Strand: - Start: 154 End: 297 ......................................................................................................................................................... Q A E S T S L F G D S L L I L A Q F V S H P F Y F V S I V L T N H W E K I D L E R L F Y P K L M .................................................................................................... Protein_Len: 60 Strand: - Start: 21 End: 233 .................... L S C V M F I V L L Q L D Y E K T I R R S C L S R S S P A A E L D N P K L H L Y F A M Q F C Y L H R F F V T H F I F C M .................................................................................................................................................................... cctgatttgcttctacgtcatcgaaaagctaaaaagtaacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgtaaaaagtagggtttcaagatgaagccggttgcctaaccgactgcaaggagcaaaaaaagagggctgtgacaaaactgaattttgtcacagccctctgtcatttggaaaattcttcagtaa 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: 358 End: 387 .....................................................................................................................................................................................................................................................................................................................................................................TTTGTCACAGCCCTCTGTCATTTGGAAAAT.......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: - Score: 83 Start: 188 End: 204 ...........................................................................................................................................................................................CAGGCACTTATATTGCT................................................................................................................................................................................................. cctgatttgcttctacgtcatcgaaaagctaaaaagtaacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgtaaaaagtagggtttcaagatgaagccggttgcctaaccgactgcaaggagcaaaaaaagagggctgtgacaaaactgaattttgtcacagccctctgtcatttggaaaattcttcagtaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -13.9 Tail_Score: -3.59247 Start: 331 End: 377 Full_Region: GACTGCAAGGAGCAA AAAAAGAGGGCTGTGACAAAA CTGAA TTTTGTCACAGCCCTCTGTCA TTTGGAAAATTCTTC ..........................................................................................................................................................................................................................................................................................................................................AAAAAGAGGGCTGTGACAAAACTGAATTTTGTCACAGCCCTCTGTCA.................... TransTerm Strand: - Conf: 100 HP_score: -23.3 Tail_Score: -5.58074 Start: 336 End: 372 Full_Region: attttccaaatgaca gagggctgtgacaaaat tca gttttgtcacagccctc tttttttgctccttg ...............................................................................................................................................................................................................................................................................................................................................gagggctgtgacaaaattcagttttgtcacagccctc......................... Find igs database================================================ Query_seq: PG2116:PG2117|PG2116:PG2117:hypothetical protein:30S ribosomal protein S16:-><-:2224928..2225324 397 cctgatttgcttctacgtcatcgaaaagctaaaaagtaacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgtaaaaagtagggtttcaagatgaagccggttgcctaaccgactgcaaggagcaaaaaaagagggctgtgacaaaactgaattttgtcacagccctctgtcatttggaaaattcttcagtaa Intra-Species Hit: Count: 4 Min: 1 Max: 397 Len: 397 Subject: NC_002950_PG2116_PG2117|hypothetical protein:30S ribosomal protein S16|POSITIVE:NEGATIVE|[2224928,2225324]|397 HSP 1 e-value: 0.0 bit: 745.0 Len: 397 Query Start:1 Query End:397 Subject Strand: POSITIVE Subject Start: 1 Subject End: 397 cctgatttgcttctacgtcatcgaaaagctaaaaagtaacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgtaaaaagtagggtttcaagatgaagccggttgcctaaccgactgcaaggagcnnnnnnngagggctgtgacaaaactgaattttgtcacagccctctgtcatttggaaaattcttcagtaa cctgatttgcttctacgtcatcgaaaagctaaaaagtaacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgtaaaaagtagggtttcaagatgaagccggttgcctaaccgactgcaaggagcaaaaaaagagggctgtgacaaaactgaattttgtcacagccctctgtcatttggaaaattcttcagtaa Subject: NC_002950_PG1398_PG1401|hypothetical protein:beta-eliminating lyase|POSITIVE:NEGATIVE|[1481008,1483488]|2481 HSP 1 e-value: 1.0E-133 bit: 476.0 Len: 240 Query Start:38 Query End:277 Subject Strand: POSITIVE Subject Start: 15 Subject End: 254 .....................................aacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgt........................................................................................................................ .....................................aacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgt........................................................................................................................ Subject: NC_002950_PG2168_PG2170|hypothetical protein:sugar transporter|NEGATIVE:NEGATIVE|[2274248,2276774]|2527 HSP 1 e-value: 1.0E-126 bit: 452.0 Len: 240 Query Start:38 Query End:277 Subject Strand: POSITIVE Subject Start: 622 Subject End: 861 .....................................aacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcacgt........................................................................................................................ .....................................aacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttccaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgtctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgaactcacgt........................................................................................................................ Subject: NC_002950_PG0030_PG0031|cytidine deaminase:hypothetical protein|POSITIVE:NEGATIVE|[36463,36994]|532 HSP 1 e-value: 1.0E-125 bit: 450.0 Len: 239 Query Start:37 Query End:275 Subject Strand: NEGATIVE Subject Start: 22 Subject End: 260 ....................................taacgccagttcgatctaagcgaacataccataaaaataacaagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcagatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgagctcac.......................................................................................................................... ....................................taacgccagttcgatctaagcgaacataccataaaaataacgagtagctgtaaatcatactcttttgtgattctccggctgcataatgatcgggaagaaggggcggcttctaagtcattgggcttcatatgtagataaaaagccatctgaaagcaatataagtgcctgaaaaacactgtgtggaaaataaaacacactaataaccaatgtgttgtgccattcctttatatcgaactcac.......................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUGAUUUGCUUCUACGUCAUCGAAAAGCUAAAAAGUAACGCCAGUUCGAUCUAAGCGAACAUACCAUAAAAAUAACAAGUAGCUGUAAAUCAUACUCUUUUGUGAUUCUCCGGCUGCAUAAUGAUCGGGAAGAAGGGGCGGCUUCUAAGUCAUUGGGCUUCAGAUGUAGAUAAAAAGCCAUCUGAAAGCAAUAUAAGUGCCUGAAAAACACUGUGUGGAAAAUAAAACACACUAAUAACCAAUGUGUUGUGCCAUUCCUUUAUAUCGAGCUCACGUAAAAAGUAGGGUUUCAAGAUGAAGCCGGUUGCCUAACCGACUGCAAGGAGCAAAAAAAGAGGGCUGUGACAAAACUGAAUUUUGUCACAGCCCUCUGUCAUUUGGAAAAUUCUUCAGUAA .(((((((((((((...(((((((((..(((.......(((..((((((((.(((........................(((((((..(((((((......)))))))...))))))).........(((((...((.(((((........((((((((((((((((............)))))).))))......((((..(....).))))(((((..........)))))......)))))).))))).)).)))))))).))))))))..)))......)))..))))..))))).(((((((....)))))...)).)))))))))...(((((((((((((((((.....))))))))))))))))).................))))... (-120.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACUGAAGAAUUUUCCAAAUGACAGAGGGCUGUGACAAAAUUCAGUUUUGUCACAGCCCUCUUUUUUUGCUCCUUGCAGUCGGUUAGGCAACCGGCUUCAUCUUGAAACCCUACUUUUUACGUGAGCUCGAUAUAAAGGAAUGGCACAACACAUUGGUUAUUAGUGUGUUUUAUUUUCCACACAGUGUUUUUCAGGCACUUAUAUUGCUUUCAGAUGGCUUUUUAUCUACAUCUGAAGCCCAAUGACUUAGAAGCCGCCCCUUCUUCCCGAUCAUUAUGCAGCCGGAGAAUCACAAAAGAGUAUGAUUUACAGCUACUUGUUAUUUUUAUGGUAUGUUCGCUUAGAUCGAACUGGCGUUACUUUUUAGCUUUUCGAUGACGUAGAAGCAAAUCAGG ...((((.................((((((((((((((((((...))))))))))))))))))...((((((..((((.(((((((....))))))).(((((..((((..(((......((((.(((((........((((......(((((((((.....))))))))).....)))).....(((.(((((.(((.........((((.((((((............))))))))))..((((((..(((((......)))))....).))))).....))).))))).)))....)))..(((((((.(((.((.((..((....))..)).))..))))))))))..)).)))).......)))..))))))))).)))).)))))))))). (-115.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 479 158 112 171 126 NC_002950:PG0800|5end_hypothetical_protein_856278..856508_NEGATIVE 430 376 338 59 22 NC_002950:PG1234|5end_hypothetical_protein_1310112..1310342_POSITIVE 393 370 328 225 181 NC_002950:PG0749|5end_hypothetical_protein_795654..795884_NEGATIVE 390 159 112 196 150 NC_002950:PG2100|5end_immunoreactive_63_kDa_antigen_PG102_2210191..2210421_NEGATIVE 374 147 103 58 13 NC_002950:PG0751|5end_porT_protein_797578..797808_NEGATIVE 370 159 112 217 169 NC_002950:PG1102|5end_hypothetical_protein_1173637..1173867_NEGATIVE 370 144 110 223 180 NC_002950:PG0450|5end_hypothetical_protein_490812..491042_POSITIVE 368 138 103 52 11 NC_002950:PG0468|5end_mannose-6-phosphate_isomerase,_class_I_511384..511614_NEGATIVE 367 158 111 119 60 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 366 159 112 127 71 NC_002950:PG0499|5end_hypothetical_protein_538709..538939_POSITIVE 358 170 128 44 3 NC_002950:PG0092|5end_transporter,_putative_108598..108828_NEGATIVE 356 373 338 193 158 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 354 140 103 190 153 NC_002950:PG2225|5end_hypothetical_protein_2339440..2339670_POSITIVE 352 169 122 49 2 NC_002950:PG0608|5end_hypothetical_protein_662945..663175_POSITIVE 349 346 301 72 24 NC_002950:PG0350|5end_internalin-related_protein_386810..387040_NEGATIVE 346 140 91 161 97 NC_002950:PG0560|5end_hypothetical_protein_617423..617653_POSITIVE 345 159 112 223 164 NC_002950:PG1547|5end_hypothetical_protein_1624262..1624492_POSITIVE 344 320 271 186 135 NC_002950:PG1620|5end_carboxyl-terminal_protease-related_protein_1700491..1700721_NEGATIVE 341 326 282 60 3 NC_002950:PG1851|5end_phosphopantothenoylcysteine_decarboxylase/phosphopantothenate--cysteine_ligase_1951168..1951398_NEGATIVE 338 330 281 200 148 NC_002950:PG0447|5end_hypothetical_protein_487278..487508_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 824 260 211 54 5 NC_002950:PG0030|3end_cytidine_deaminase_36402..36552_POSITIVE 765 370 322 60 12 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 556 370 332 40 3 NC_002950:PG1950|3end_hypothetical_protein_2040840..2040990_POSITIVE 396 157 112 70 25 NC_002950:PG1408|3end_heavy_metal_efflux_pump,_CzcD_family_1492906..1493056_POSITIVE 394 370 325 61 14 NC_002950:PG0186|3end_lipoprotein_RagB_222997..223147_POSITIVE 390 159 112 109 63 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE 380 145 108 91 40 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 376 382 341 50 2 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 374 373 334 42 3 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 362 58 12 97 57 NC_002950:PG0194|3end_ISPg3,_transposase_231910..232060_POSITIVE 357 378 333 70 21 NC_002950:PG1847|3end_endoribonuclease_L-PSP,_putative_1946227..1946377_NEGATIVE 356 371 333 68 30 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 355 169 125 88 43 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 355 159 115 52 5 NC_002950:PG1661|3end_hypothetical_protein_1744835..1744985_POSITIVE 354 371 334 50 10 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 346 369 323 52 7 NC_002950:PG2170|3end_sugar_transporter_2276685..2276835_NEGATIVE 342 159 113 66 12 NC_002950:PG1012|3end_tRNA-i(6)A37_modification_enzyme_MiaB_1070089..1070239_NEGATIVE 337 134 91 85 35 NC_002950:PG1720|3end_hypothetical_protein_1810224..1810374_POSITIVE 336 328 287 65 7 NC_002950:PG1340|3end_L-lactate_permease_1420298..1420448_NEGATIVE 335 374 332 42 1 NC_002950:PG1121|3end_asparaginyl-tRNA_synthetase_1196146..1196296_NEGATIVE