Origin IGS: gtgtttattttagcaggaaaaaaagcccccagcaagccctaaaagcaggaactgtccggggacagattttttgaaaaatattgtataagaaatagggataatctgcactttgacttgccattatacaacaaaacaacccatctgaatcagaccgtcagtgacgacacaaacagagcaaattcaaatgggttattgattgcatattgctaaaggtcattatctgcagttacacatgcagcaaatctgacactttttc .........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 gaaaaagtgtcagatttgctgcatgtgtaactgcagataatgacctttagcaatatgcaatcaataacccatttgaatttgctctgtttgtgtcgtcactgacggtctgattcagatgggttgttttgttgtataatggcaagtcaaagtgcagattatccctatttcttatacaatatttttcaaaaaatctgtccccggacagttcctgcttttagggcttgctgggggctttttttcctgctaaaataaacac Mask Tandem Repeat Region ================================================ gtgtttattttagcaggaaaaaaagcccccagcaagccctaaaagcaggaactgtccggggacagattttttgaaaaatattgtataagaaatagggataatctgcactttgacttgccattatacaacaaaacaacccatctgaatcagaccgtcagtgacgacacaaacagagcaaattcaaatgggttattgattgcatattgctaaaggtcattatctgcagttacacatgcagcaaatctgacactttttc Find is-nt database================================================ Query_seq: SSA_2002:SSA_2004|SSA_2002:SSA_2004:tRNA pseudouridine synthase A, putative:Zinc metalloprotease zmpB precursor, putative:<-<-:1999050..1999305 256 gtgtttattttagcaggaaaaaaagcccccagcaagccctaaaagcaggaactgtccggggacagattttttgaaaaatattgtataagaaatagggataatctgcactttgacttgccattatacaacaaaacaacccatctgaatcagaccgtcagtgacgacacaaacagagcaaattcaaatgggttattgattgcatattgctaaaggtcattatctgcagttacacatgcagcaaatctgacactttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2002:SSA_2004|SSA_2002:SSA_2004:tRNA pseudouridine synthase A, putative:Zinc metalloprotease zmpB precursor, putative:<-<-:1999050..1999305 256 gtgtttattttagcaggaaaaaaagcccccagcaagccctaaaagcaggaactgtccggggacagattttttgaaaaatattgtataagaaatagggataatctgcactttgacttgccattatacaacaaaacaacccatctgaatcagaccgtcagtgacgacacaaacagagcaaattcaaatgggttattgattgcatattgctaaaggtcattatctgcagttacacatgcagcaaatctgacactttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2002:SSA_2004|SSA_2002:SSA_2004:tRNA pseudouridine synthase A, putative:Zinc metalloprotease zmpB precursor, putative:<-<-:1999050..1999305 256 gtgtttattttagcaggaaaaaaagcccccagcaagccctaaaagcaggaactgtccggggacagattttttgaaaaatattgtataagaaatagggataatctgcactttgacttgccattatacaacaaaacaacccatctgaatcagaccgtcagtgacgacacaaacagagcaaattcaaatgggttattgattgcatattgctaaaggtcattatctgcagttacacatgcagcaaatctgacactttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgtttattttagcaggaaaaaaagcccccagcaagccctaaaagcaggaactgtccggggacagattttttgaaaaatattgtataagaaatagggataatctgcactttgacttgccattatacaacaaaacaacccatctgaatcagaccgtcagtgacgacacaaacagagcaaattcaaatgggttattgattgcatattgctaaaggtcattatctgcagttacacatgcagcaaatctgacactttttc Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 52 End: 207 ................................................... M S G D R F F E K Y C I R N R D N L H F D L P L Y N K T T H L N Q T V S D D T N R A N S N G L L I A Y C ................................................. Protein_Len: 30 Strand: - Start: 42 End: 131 ......................................... F C S S D P S L N K S F Y Q I L F L S L R C K S K G N Y L M ............................................................................................................................. Protein_Len: 32 Strand: - Start: 13 End: 108 ............ C S F F G G A L G L L L F Q G P V S K K F F I T Y S I P I I Q M .................................................................................................................................................... Protein_Len: 43 Strand: - Start: 8 End: 136 ....... K L L F F L G W C A R F A P V T R P C I K Q F I N Y L F Y P Y D A S Q S A M I C C F M ........................................................................................................................ gtgtttattttagcaggaaaaaaagcccccagcaagccctaaaagcaggaactgtccggggacagattttttgaaaaatattgtataagaaatagggataatctgcactttgacttgccattatacaacaaaacaacccatctgaatcagaccgtcagtgacgacacaaacagagcaaattcaaatgggttattgattgcatattgctaaaggtcattatctgcagttacacatgcagcaaatctgacactttttc 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: 7 End: 36 ......CTTGCTGGGGGCTTTTTTTCCTGCTAAAAT............................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgtttattttagcaggaaaaaaagcccccagcaagccctaaaagcaggaactgtccggggacagattttttgaaaaatattgtataagaaatagggataatctgcactttgacttgccattatacaacaaaacaacccatctgaatcagaccgtcagtgacgacacaaacagagcaaattcaaatgggttattgattgcatattgctaaaggtcattatctgcagttacacatgcagcaaatctgacactttttc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 84 HP_score: -4.5 Tail_Score: -5.55664 Start: 25 End: 63 Full_Region: tttttcaaaaaatct gtccccggacagttcctg cttt tagggcttgctgggggc tttttttcctgctaa ........................gtccccggacagttcctgcttttagggcttgctgggggc................................................................................................................................................................................................. TransTerm Strand: + Conf: 71 HP_score: -3.2 Tail_Score: -5.02476 Start: 51 End: 66 Full_Region: GCCCTAAAAGCAGGA ACTGTC CGGG GACAGA TTTTTTGAAAAATAT ..................................................ACTGTCCGGGGACAGA.............................................................................................................................................................................................. TransTerm Strand: - Conf: 74 HP_score: -4.7 Tail_Score: -4.85918 Start: 134 End: 192 Full_Region: gcaatatgcaatcaa taacccatttgaatttgctctgtttgtg tcgt cactgacggtctgattcagatgggttg ttttgttgtataatg .....................................................................................................................................taacccatttgaatttgctctgtttgtgtcgtcactgacggtctgattcagatgggttg................................................................ Find igs database================================================ Query_seq: SSA_2002:SSA_2004|SSA_2002:SSA_2004:tRNA pseudouridine synthase A, putative:Zinc metalloprotease zmpB precursor, putative:<-<-:1999050..1999305 256 gtgtttattttagcaggaaaaaaagcccccagcaagccctaaaagcaggaactgtccggggacagattttttgaaaaatattgtataagaaatagggataatctgcactttgacttgccattatacaacaaaacaacccatctgaatcagaccgtcagtgacgacacaaacagagcaaattcaaatgggttattgattgcatattgctaaaggtcattatctgcagttacacatgcagcaaatctgacactttttc Intra-Species Hit: Count: 1 Min: 1 Max: 256 Len: 256 Subject: NC_009009_SSA_2002_SSA_2004|tRNA pseudouridine synthase A, putative:Zinc metalloprotease zmpB precursor, putative|NEGATIVE:NEGATIVE|[1999050,1999305]|256 HSP 1 e-value: 1.0E-130 bit: 466.0 Len: 256 Query Start:1 Query End:256 Subject Strand: POSITIVE Subject Start: 1 Subject End: 256 gtgtttattttagcaggnnnnnnngcccccagcaagccctaaaagcaggaactgtccggggacagattttttgaaaaatattgtataagaaatagggataatctgcactttgacttgccattatacaacaaaacaacccatctgaatcagaccgtcagtgacgacacaaacagagcaaattcaaatgggttattgattgcatattgctaaaggtcattatctgcagttacacatgcagcaaatctgacactttttc gtgtttattttagcaggaaaaaaagcccccagcaagccctaaaagcaggaactgtccggggacagattttttgaaaaatattgtataagaaatagggataatctgcactttgacttgccattatacaacaaaacaacccatctgaatcagaccgtcagtgacgacacaaacagagcaaattcaaatgggttattgattgcatattgctaaaggtcattatctgcagttacacatgcagcaaatctgacactttttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUUUAUUUUAGCAGGAAAAAAAGCCCCCAGCAAGCCCUAAAAGCAGGAACUGUCCGGGGACAGAUUUUUUGAAAAAUAUUGUAUAAGAAAUAGGGAUAAUCUGCACUUUGACUUGCCAUUAUACAACAAAACAACCCAUCUGAAUCAGACCGUCAGUGACGACACAAACAGAGCAAAUUCAAAUGGGUUAUUGAUUGCAUAUUGCUAAAGGUCAUUAUCUGCAGUUACACAUGCAGCAAAUCUGACACUUUUUC (((((...(((.(((((.......((.....))...(((((....(((((((((((....)))))..)))))).......((......))..)))))....)))))....((((((..((.(((.((((((...(((((((.(((((..(..(((..(((....)))..)).)..)..))))).))))))).))).))).))).))....))))))....(((((........))))).)))...)))))...... (-56.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAAGUGUCAGAUUUGCUGCAUGUGUAACUGCAGAUAAUGACCUUUAGCAAUAUGCAAUCAAUAACCCAUUUGAAUUUGCUCUGUUUGUGUCGUCACUGACGGUCUGAUUCAGAUGGGUUGUUUUGUUGUAUAAUGGCAAGUCAAAGUGCAGAUUAUCCCUAUUUCUUAUACAAUAUUUUUCAAAAAAUCUGUCCCCGGACAGUUCCUGCUUUUAGGGCUUGCUGGGGGCUUUUUUUCCUGCUAAAAUAAACAC ...((((.((((......(((((........)))))....)))))))).((..((((((((.(((((((((((((((((....(((((.(((....))).)))))...)))))))))))))))))..))))))))...))..........((((........((((........))))......((((((...((((((((.(((..((((....))))..))))))))))).)))))).))))............ (-79.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1032 60 11 151 102 NC_009009:SSA_2002|5end_tRNA_pseudouridine_synthase_A,_putative_1998959..1999189_NEGATIVE 369 60 11 63 16 NC_009009:SSA_1106|5end_IgA-specific_metalloendopeptidase_1125974..1126204_POSITIVE 338 70 23 103 37 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 333 69 24 208 159 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 331 67 26 72 20 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 330 66 25 184 127 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 324 62 24 222 181 NC_009009:SSA_1739|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1725540..1725770_POSITIVE 318 67 23 152 100 NC_009009:SSA_1934|5end_Biotin_carboxyl_carrier_protein_of_acetyl-CoA_carboxylase,_putative_1921800..1922030_NEGATIVE 317 140 92 51 2 NC_009009:SSA_1607|5end_Formamidopyrimidine-DNA_glycosylase,_putative_1613255..1613485_NEGATIVE 312 248 201 171 120 NC_009009:SSA_2312|5end_hypothetical_protein_2315281..2315511_NEGATIVE 306 64 22 50 6 NC_009009:SSA_1154|5end_hypothetical_protein_1182661..1182891_POSITIVE 305 80 31 76 12 NC_009009:SSA_0874|5end_hypothetical_protein_867935..868165_POSITIVE 305 66 24 162 110 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 305 79 32 220 165 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 303 59 25 69 36 NC_009009:SSA_1117|5end_hypothetical_protein_1142743..1142973_POSITIVE 292 67 22 146 94 NC_009009:SSA_1744|5end_Iron_compound_ABC_transporter,_permease_protein,_putative_1730915..1731145_POSITIVE 291 60 26 65 11 NC_009009:SSA_1417|5end_SAM-dependent_methyltransferase,_putative_1427993..1428223_NEGATIVE 290 50 9 200 154 NC_009009:SSA_1179|5end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1207806..1208036_NEGATIVE 290 66 22 77 35 NC_009009:SSA_0647|5end_hypothetical_protein_630998..631228_POSITIVE 290 68 24 70 14 NC_009009:SSA_0378|5end_TRZ/ATZ_family_hydrolase,_putative_367276..367506_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 67 26 85 33 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 330 66 25 66 9 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 318 67 23 145 93 NC_009009:SSA_1935|3end_Beta-ketoacyl-ACP_synthase_II_(3-oxoacyl-(Acyl-carrier-protein)_synthase_II),_putative_1921807..1921957_NEGATIVE 306 60 13 106 61 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 306 64 22 57 13 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 305 66 24 87 35 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 297 90 41 62 17 NC_009009:SSA_0369|3end_NADP-specific_glutamate_dehydrogenase,_putative_359723..359873_NEGATIVE 294 60 12 150 108 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 290 66 22 75 33 NC_009009:SSA_0646|3end_hypothetical_protein_631076..631226_POSITIVE 288 60 12 79 19 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 286 62 30 151 111 NC_009009:SSA_1640|3end_hypothetical_protein_1642108..1642258_NEGATIVE 284 65 23 77 39 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 283 52 13 150 102 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 283 59 12 39 2 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 282 60 11 61 20 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 281 57 13 67 6 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 279 50 4 134 69 NC_009009:SSA_1280|3end_hypothetical_protein_1301108..1301258_NEGATIVE 273 59 11 51 11 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 273 60 12 60 10 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 272 62 26 69 45 NC_009009:SSA_1703|3end_Methionyl-tRNA_synthetase,_putative_1693640..1693790_NEGATIVE