Origin IGS: tcaaattaaatcttctttagtattcccttgtttctctttcgctcatcgaccgaaaagaaatacacgctaatcagcttttcacagaaagctattaagctttccgccaaatactttgaactattcggaaaaatagttataactattcagccaaatactttaagctgttccgcgaaaagctcctaagctctcagatgaaactctcatcggtggggatgcgatataatgagagaatcttgtcaatcctatagtgtatgctccgatatggagctttgtcgattcggaattgggcagatagatccatggttagagcctgttgcctgacgtgtacagaaaagagaagaggctgcccgctctaccgggcagcctccatcgttctcaaaccgtataatataatctgata .........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 tatcagattatattatacggtttgagaacgatggaggctgcccggtagagcgggcagcctcttctcttttctgtacacgtcaggcaacaggctctaaccatggatctatctgcccaattccgaatcgacaaagctccatatcggagcatacactataggattgacaagattctctcattatatcgcatccccaccgatgagagtttcatctgagagcttaggagcttttcgcggaacagcttaaagtatttggctgaatagttataactatttttccgaatagttcaaagtatttggcggaaagcttaatagctttctgtgaaaagctgattagcgtgtatttcttttcggtcgatgagcgaaagagaaacaagggaatactaaagaagatttaatttga Mask Tandem Repeat Region ================================================ tcaaattaaatcttctttagtattcccttgtttctctttcgctcatcgaccgaaaagaaatacacgctaatcagcttttcacagaaagctattaagctttccgccaaatactttgaactattcggaaaaatagttataactattcagccaaatactttaagctgttccgcgaaaagctcctaagctctcagatgaaactctcatcggtggggatgcgatataatgagagaatcttgtcaatcctatagtgtatgctccgatatggagctttgtcgattcggaattgggcagatagatccatggttagagcctgttgcctgacgtgtacagaaaagagaagaggctgcccgctctaccgggcagcctccatcgttctcaaaccgtataatataatctgata Find is-nt database================================================ Query_seq: PG1053:PG1055|PG1053:PG1055:transcriptional regulator, putative:thiol protease:-><-:1120892..1121291 400 tcaaattaaatcttctttagtattcccttgtttctctttcgctcatcgaccgaaaagaaatacacgctaatcagcttttcacagaaagctattaagctttccgccaaatactttgaactattcggaaaaatagttataactattcagccaaatactttaagctgttccgcgaaaagctcctaagctctcagatgaaactctcatcggtggggatgcgatataatgagagaatcttgtcaatcctatagtgtatgctccgatatggagctttgtcgattcggaattgggcagatagatccatggttagagcctgttgcctgacgtgtacagaaaagagaagaggctgcccgctctaccgggcagcctccatcgttctcaaaccgtataatataatctgata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1053:PG1055|PG1053:PG1055:transcriptional regulator, putative:thiol protease:-><-:1120892..1121291 400 tcaaattaaatcttctttagtattcccttgtttctctttcgctcatcgaccgaaaagaaatacacgctaatcagcttttcacagaaagctattaagctttccgccaaatactttgaactattcggaaaaatagttataactattcagccaaatactttaagctgttccgcgaaaagctcctaagctctcagatgaaactctcatcggtggggatgcgatataatgagagaatcttgtcaatcctatagtgtatgctccgatatggagctttgtcgattcggaattgggcagatagatccatggttagagcctgttgcctgacgtgtacagaaaagagaagaggctgcccgctctaccgggcagcctccatcgttctcaaaccgtataatataatctgata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1053:PG1055|PG1053:PG1055:transcriptional regulator, putative:thiol protease:-><-:1120892..1121291 400 tcaaattaaatcttctttagtattcccttgtttctctttcgctcatcgaccgaaaagaaatacacgctaatcagcttttcacagaaagctattaagctttccgccaaatactttgaactattcggaaaaatagttataactattcagccaaatactttaagctgttccgcgaaaagctcctaagctctcagatgaaactctcatcggtggggatgcgatataatgagagaatcttgtcaatcctatagtgtatgctccgatatggagctttgtcgattcggaattgggcagatagatccatggttagagcctgttgcctgacgtgtacagaaaagagaagaggctgcccgctctaccgggcagcctccatcgttctcaaaccgtataatataatctgata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaaattaaatcttctttagtattcccttgtttctctttcgctcatcgaccgaaaagaaatacacgctaatcagcttttcacagaaagctattaagctttccgccaaatactttgaactattcggaaaaatagttataactattcagccaaatactttaagctgttccgcgaaaagctcctaagctctcagatgaaactctcatcggtggggatgcgatataatgagagaatcttgtcaatcctatagtgtatgctccgatatggagctttgtcgattcggaattgggcagatagatccatggttagagcctgttgcctgacgtgtacagaaaagagaagaggctgcccgctctaccgggcagcctccatcgttctcaaaccgtataatataatctgata Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 10 End: 180 ......... M F F S I P L F L F R S S T E K K Y T L I S F S Q K A I K L S A K Y F E L F G K I V I T I Q P N T L S C S A K S S ............................................................................................................................................................................................................................ Protein_Len: 42 Strand: + Start: 120 End: 245 ....................................................................................................................... M R K N S Y N Y S A K Y F K L F R E K L L S S Q M K L S S V G M R Y N E R I L S I L ........................................................................................................................................................... Protein_Len: 33 Strand: + Start: 220 End: 318 ........................................................................................................................................................................................................................... M M R E S C Q S Y S V C S D M E L C R F G I G Q I D P W L E P V A .................................................................................. Protein_Len: 49 Strand: + Start: 252 End: 395 ........................................................................................................................................................................................................................................................... M L R Y G A L S I R N W A D R S M V R A C C L T C T E K R R G C P L Y R A A S I V L K P Y N I I * ..... Protein_Len: 48 Strand: - Start: 246 End: 389 ..................................................................................................................................................................................................................................................... L T H E S I S S Q R N P I P C I S G H N S G T A Q R T C F L S S A A R E V P C G G D N E F R I M ........... Protein_Len: 37 Strand: - Start: 191 End: 301 .............................................................................................................................................................................................. I F S E D T P I R Y L S L I K D I R Y H I S R Y P A K D I R F Q A S L D M ................................................................................................... Protein_Len: 46 Strand: - Start: 160 End: 297 ............................................................................................................................................................... A T G R F A G L S E S S V R M P P S A I Y H S F R T L G I T Y A G I H L K T S E S N P L Y M ....................................................................................................... Protein_Len: 45 Strand: - Start: 9 End: 143 ........ I K K L I G K N R K R E D V S F F Y V S I L K E C F A I L S E A L Y K S S N P F I T I V M ................................................................................................................................................................................................................................................................. tcaaattaaatcttctttagtattcccttgtttctctttcgctcatcgaccgaaaagaaatacacgctaatcagcttttcacagaaagctattaagctttccgccaaatactttgaactattcggaaaaatagttataactattcagccaaatactttaagctgttccgcgaaaagctcctaagctctcagatgaaactctcatcggtggggatgcgatataatgagagaatcttgtcaatcctatagtgtatgctccgatatggagctttgtcgattcggaattgggcagatagatccatggttagagcctgttgcctgacgtgtacagaaaagagaagaggctgcccgctctaccgggcagcctccatcgttctcaaaccgtataatataatctgata 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================================================ tcaaattaaatcttctttagtattcccttgtttctctttcgctcatcgaccgaaaagaaatacacgctaatcagcttttcacagaaagctattaagctttccgccaaatactttgaactattcggaaaaatagttataactattcagccaaatactttaagctgttccgcgaaaagctcctaagctctcagatgaaactctcatcggtggggatgcgatataatgagagaatcttgtcaatcctatagtgtatgctccgatatggagctttgtcgattcggaattgggcagatagatccatggttagagcctgttgcctgacgtgtacagaaaagagaagaggctgcccgctctaccgggcagcctccatcgttctcaaaccgtataatataatctgata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 40 HP_score: -2.3 Tail_Score: -2.71888 Start: 66 End: 97 Full_Region: agtatttggcggaaa gcttaatagcttt ctgtga aaagctgattagc gtgtatttcttttcg .................................................................gcttaatagctttctgtgaaaagctgattagc............................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 74 HP_score: -7.8 Tail_Score: -3.97368 Start: 254 End: 268 Full_Region: AATCCTATAGTGTAT GCTCCG ATA TGGAGC TTTGTCGATTCGGAA .............................................................................................................................................................................................................................................................GCTCCGATATGGAGC.................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -10.9 Tail_Score: -4.53303 Start: 335 End: 371 Full_Region: atacggtttgagaac gatggaggctgcccg gtagag cgggcagcctcttctc ttttctgtacacgtc ..............................................................................................................................................................................................................................................................................................................................................gatggaggctgcccggtagagcgggcagcctcttctc............................. TransTerm Strand: + Conf: 71 HP_score: -8.7 Tail_Score: -3.29829 Start: 336 End: 372 Full_Region: ACGTGTACAGAAAAG AGAAGAGGCTGCCCG CTCTAC CGGGCAGCCTCCATCG TTCTCAAACCGTATA ...............................................................................................................................................................................................................................................................................................................................................AGAAGAGGCTGCCCGCTCTACCGGGCAGCCTCCATCG............................ TransTerm Strand: - Conf: 100 HP_score: -18.5 Tail_Score: -4.05861 Start: 340 End: 367 Full_Region: ggtttgagaacgatg gaggctgcccg gtagag cgggcagcctc ttctcttttctgtac ...................................................................................................................................................................................................................................................................................................................................................gaggctgcccggtagagcgggcagcctc................................. Find igs database================================================ Query_seq: PG1053:PG1055|PG1053:PG1055:transcriptional regulator, putative:thiol protease:-><-:1120892..1121291 400 tcaaattaaatcttctttagtattcccttgtttctctttcgctcatcgaccgaaaagaaatacacgctaatcagcttttcacagaaagctattaagctttccgccaaatactttgaactattcggaaaaatagttataactattcagccaaatactttaagctgttccgcgaaaagctcctaagctctcagatgaaactctcatcggtggggatgcgatataatgagagaatcttgtcaatcctatagtgtatgctccgatatggagctttgtcgattcggaattgggcagatagatccatggttagagcctgttgcctgacgtgtacagaaaagagaagaggctgcccgctctaccgggcagcctccatcgttctcaaaccgtataatataatctgata Intra-Species Hit: Count: 1 Min: 1 Max: 400 Len: 400 Subject: NC_002950_PG1053_PG1055|transcriptional regulator, putative:thiol protease|POSITIVE:NEGATIVE|[1120892,1121291]|400 HSP 1 e-value: 0.0 bit: 793.0 Len: 400 Query Start:1 Query End:400 Subject Strand: POSITIVE Subject Start: 1 Subject End: 400 tcaaattaaatcttctttagtattcccttgtttctctttcgctcatcgaccgaaaagaaatacacgctaatcagcttttcacagaaagctattaagctttccgccaaatactttgaactattcggaaaaatagttataactattcagccaaatactttaagctgttccgcgaaaagctcctaagctctcagatgaaactctcatcggtggggatgcgatataatgagagaatcttgtcaatcctatagtgtatgctccgatatggagctttgtcgattcggaattgggcagatagatccatggttagagcctgttgcctgacgtgtacagaaaagagaagaggctgcccgctctaccgggcagcctccatcgttctcaaaccgtataatataatctgata tcaaattaaatcttctttagtattcccttgtttctctttcgctcatcgaccgaaaagaaatacacgctaatcagcttttcacagaaagctattaagctttccgccaaatactttgaactattcggaaaaatagttataactattcagccaaatactttaagctgttccgcgaaaagctcctaagctctcagatgaaactctcatcggtggggatgcgatataatgagagaatcttgtcaatcctatagtgtatgctccgatatggagctttgtcgattcggaattgggcagatagatccatggttagagcctgttgcctgacgtgtacagaaaagagaagaggctgcccgctctaccgggcagcctccatcgttctcaaaccgtataatataatctgata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAAUUAAAUCUUCUUUAGUAUUCCCUUGUUUCUCUUUCGCUCAUCGACCGAAAAGAAAUACACGCUAAUCAGCUUUUCACAGAAAGCUAUUAAGCUUUCCGCCAAAUACUUUGAACUAUUCGGAAAAAUAGUUAUAACUAUUCAGCCAAAUACUUUAAGCUGUUCCGCGAAAAGCUCCUAAGCUCUCAGAUGAAACUCUCAUCGGUGGGGAUGCGAUAUAAUGAGAGAAUCUUGUCAAUCCUAUAGUGUAUGCUCCGAUAUGGAGCUUUGUCGAUUCGGAAUUGGGCAGAUAGAUCCAUGGUUAGAGCCUGUUGCCUGACGUGUACAGAAAAGAGAAGAGGCUGCCCGCUCUACCGGGCAGCCUCCAUCGUUCUCAAACCGUAUAAUAUAAUCUGAUA (((.((((....((((...((((.....((..(((.(((.(((((....(((((..((.((((((....(((.((((..(((.((.((((....((((((.(((..((((.((((((.((((.((...((((((....))))))...)).)))).)))))).))))..))).))))))....)))).)).(((((.....))))).)))..)).)))))...(..((.....))..)..........))))))(((((.....)))))....))..)))))...)))))))).)))..))..(((((.((.....)))))))..))))))))..((((((((((((((((......))))))))))).....))))).............)))).))).. (-116.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCAGAUUAUAUUAUACGGUUUGAGAACGAUGGAGGCUGCCCGGUAGAGCGGGCAGCCUCUUCUCUUUUCUGUACACGUCAGGCAACAGGCUCUAACCAUGGAUCUAUCUGCCCAAUUCCGAAUCGACAAAGCUCCAUAUCGGAGCAUACACUAUAGGAUUGACAAGAUUCUCUCAUUAUAUCGCAUCCCCACCGAUGAGAGUUUCAUCUGAGAGCUUAGGAGCUUUUCGCGGAACAGCUUAAAGUAUUUGGCUGAAUAGUUAUAACUAUUUUUCCGAAUAGUUCAAAGUAUUUGGCGGAAAGCUUAAUAGCUUUCUGUGAAAAGCUGAUUAGCGUGUAUUUCUUUUCGGUCGAUGAGCGAAAGAGAAACAAGGGAAUACUAAAGAAGAUUUAAUUUGA ..((((((((........((((.(((...((.((((((((((((......))))))))))))))......((((...(....)...)))).))).))))...(((((.(((.....(((((..((((((...(((((.....))))).........((((...(((.((..((((((((................))))))))..))........(((.(..((((((((((((((.((((..((((.(((.((..((((.((..((((((((....))))))))..)).))))..)).))).))))...))))))))))))))))))..).))).)))...))))....))))))...(....).........))))).....)))))))))))))))) (-134.79) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 419 375 334 229 170 NC_002950:PG0647|5end_iron_compound_ABC_transporter,_permease_protein_700113..700343_NEGATIVE 405 375 333 205 145 NC_002950:PG0538|5end_outer_membrane_efflux_protein_589142..589372_POSITIVE 403 315 275 62 14 NC_002950:PG0654|5end_hypothetical_protein_706685..706915_NEGATIVE 400 372 340 165 116 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 392 291 256 55 20 NC_002950:PG2086|5end_hypothetical_protein_2186571..2186801_POSITIVE 390 377 334 227 171 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 387 383 342 196 151 NC_002950:PG1285|5end_glucosamine-6-phosphate_deaminase_1362894..1363124_POSITIVE 384 368 322 74 13 NC_002950:PG1195|5end_8-amino-7-oxononanoate_synthase_1273979..1274209_POSITIVE 381 377 331 174 126 NC_002950:PG1279|5end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_1356535..1356765_POSITIVE 378 320 272 218 167 NC_002950:PG1875|5end_hemolysin_1970621..1970851_NEGATIVE 378 119 71 206 155 NC_002950:PG0030|5end_cytidine_deaminase_35846..36076_POSITIVE 372 385 342 62 20 NC_002950:PG1753|5end_selenide,_water_dikinase_1838615..1838845_POSITIVE 371 388 343 72 28 NC_002950:PG1333|5end_hypothetical_protein_1415425..1415655_NEGATIVE 371 346 302 56 11 NC_002950:PG0924|5end_5'-nucleotidase,_lipoprotein_e(P4)_family_983668..983898_NEGATIVE 370 377 340 117 68 NC_002950:PG2019|5end_hypothetical_protein_2111662..2111892_NEGATIVE 369 375 339 215 172 NC_002950:PG0221|5end_hypothetical_protein_255834..256064_NEGATIVE 368 384 342 60 11 NC_002950:PG1693|5end_HesA/MoeB/ThiF_family_protein_1777919..1778149_NEGATIVE 368 350 307 222 161 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 363 382 342 198 135 NC_002950:PG1855|5end_carboxyl-terminal_protease_1955476..1955706_NEGATIVE 358 383 342 84 41 NC_002950:PG0606|5end_hypothetical_protein_662558..662788_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 474 368 322 66 10 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 456 372 336 139 107 NC_002950:PG1570|3end_rhodanese-like_domain_protein_1648582..1648732_NEGATIVE 422 369 322 63 12 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 422 378 339 72 28 NC_002950:PG1786|3end_hypothetical_protein_1875322..1875472_POSITIVE 420 367 323 61 7 NC_002950:PG0775|3end_acyl-CoA_dehydrogenase_family_protein_827432..827582_NEGATIVE 409 369 329 59 16 NC_002950:PG2177|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_2285266..2285416_NEGATIVE 401 372 335 103 65 NC_002950:PG0210|3end_precorrin-6x_reductase/cobalamin_biosynthetic_protein_CbiD_244161..244311_NEGATIVE 390 377 334 138 82 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 381 377 331 73 25 NC_002950:PG1278|3end_phosphoserine_aminotransferase_1356514..1356664_POSITIVE 372 385 342 65 23 NC_002950:PG1752|3end_hypothetical_protein_1838698..1838848_POSITIVE 371 388 343 75 31 NC_002950:PG1334|3end_band_7/Mec-2_family_protein_1415422..1415572_NEGATIVE 371 346 302 59 14 NC_002950:PG0925|3end_thymidine_kinase_983665..983815_NEGATIVE 371 368 334 39 5 NC_002950:PG0195|3end_rubrerythrin_232704..232854_POSITIVE 369 375 339 136 93 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 368 384 342 63 14 NC_002950:PG1694|3end_hypothetical_protein_1777916..1778066_NEGATIVE 368 350 307 63 2 NC_002950:PG1020|3end_hypothetical_protein_1083458..1083608_POSITIVE 367 207 161 52 3 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 362 367 321 55 17 NC_002950:PG0933|3end_translation_elongation_factor_G,_putative_992236..992386_POSITIVE 358 366 339 32 1 NC_002950:PG2107|3end_thiamine_biosynthesis_protein_ThiH_2215546..2215696_NEGATIVE 357 377 336 132 87 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE