Origin IGS: gcaagaagcctctgggcttcttttttgcatcaaaaaacgtttacatgctcaaaaattttcataaaatattgacaaaaggcgaatgttcttttagaataatagaaaattaataatcaacaccgaacgaagtttttcagaaagaggcggcgcttctgactgtgaaatggacggaactctggagagaccatgaatggcaccgaaggggcaaggcggtttagaaccgctcaaactctcaggtaaaaggacagagcgaagaggcagggatttccctactccagcacatccagagtacatgttttgcatgtgctctttctttttctcggtgtgaaaaggagcttatatc .........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 gatataagctccttttcacaccgagaaaaagaaagagcacatgcaaaacatgtactctggatgtgctggagtagggaaatccctgcctcttcgctctgtccttttacctgagagtttgagcggttctaaaccgccttgccccttcggtgccattcatggtctctccagagttccgtccatttcacagtcagaagcgccgcctctttctgaaaaacttcgttcggtgttgattattaattttctattattctaaaagaacattcgccttttgtcaatattttatgaaaatttttgagcatgtaaacgttttttgatgcaaaaaagaagcccagaggcttcttgc Mask Tandem Repeat Region ================================================ gcaagaagcctctgggcttcttttttgcatcaaaaaacgtttacatgctcaaaaattttcataaaatattgacaaaaggcgaatgttcttttagaataatagaaaattaataatcaacaccgaacgaagtttttcagaaagaggcggcgcttctgactgtgaaatggacggaactctggagagaccatgaatggcaccgaaggggcaaggcggtttagaaccgctcaaactctcaggtaaaaggacagagcgaagaggcagggatttccctactccagcacatccagagtacatgttttgcatgtgctctttctttttctcggtgtgaaaaggagcttatatc Find is-nt database================================================ Query_seq: SSA_0362:SSA_0363|SSA_0362:SSA_0363:Thioredoxin, putative:D-alanine/glycine/Na permease, putative:->->:353655..353997 343 gcaagaagcctctgggcttcttttttgcatcaaaaaacgtttacatgctcaaaaattttcataaaatattgacaaaaggcgaatgttcttttagaataatagaaaattaataatcaacaccgaacgaagtttttcagaaagaggcggcgcttctgactgtgaaatggacggaactctggagagaccatgaatggcaccgaaggggcaaggcggtttagaaccgctcaaactctcaggtaaaaggacagagcgaagaggcagggatttccctactccagcacatccagagtacatgttttgcatgtgctctttctttttctcggtgtgaaaaggagcttatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0362:SSA_0363|SSA_0362:SSA_0363:Thioredoxin, putative:D-alanine/glycine/Na permease, putative:->->:353655..353997 343 gcaagaagcctctgggcttcttttttgcatcaaaaaacgtttacatgctcaaaaattttcataaaatattgacaaaaggcgaatgttcttttagaataatagaaaattaataatcaacaccgaacgaagtttttcagaaagaggcggcgcttctgactgtgaaatggacggaactctggagagaccatgaatggcaccgaaggggcaaggcggtttagaaccgctcaaactctcaggtaaaaggacagagcgaagaggcagggatttccctactccagcacatccagagtacatgttttgcatgtgctctttctttttctcggtgtgaaaaggagcttatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0362:SSA_0363|SSA_0362:SSA_0363:Thioredoxin, putative:D-alanine/glycine/Na permease, putative:->->:353655..353997 343 gcaagaagcctctgggcttcttttttgcatcaaaaaacgtttacatgctcaaaaattttcataaaatattgacaaaaggcgaatgttcttttagaataatagaaaattaataatcaacaccgaacgaagtttttcagaaagaggcggcgcttctgactgtgaaatggacggaactctggagagaccatgaatggcaccgaaggggcaaggcggtttagaaccgctcaaactctcaggtaaaaggacagagcgaagaggcagggatttccctactccagcacatccagagtacatgttttgcatgtgctctttctttttctcggtgtgaaaaggagcttatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaagaagcctctgggcttcttttttgcatcaaaaaacgtttacatgctcaaaaattttcataaaatattgacaaaaggcgaatgttcttttagaataatagaaaattaataatcaacaccgaacgaagtttttcagaaagaggcggcgcttctgactgtgaaatggacggaactctggagagaccatgaatggcaccgaaggggcaaggcggtttagaaccgctcaaactctcaggtaaaaggacagagcgaagaggcagggatttccctactccagcacatccagagtacatgttttgcatgtgctctttctttttctcggtgtgaaaaggagcttatatc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 12 End: 107 ........... M G F F F A S K N V Y M L K N F H K I L T K G E C S F R I I E N ............................................................................................................................................................................................................................................ Protein_Len: 45 Strand: + Start: 191 End: 325 .............................................................................................................................................................................................. M A P K G Q G G L E P L K L S G K R T E R R G R D F P T P A H P E Y M F C M C S F F F S V .................. Protein_Len: 35 Strand: - Start: 236 End: 340 ........................................................................................................................................................................................................................................... T F P C L S S A P I E R S W C M W L V H K A H A R E K E R H S F S S M ... Protein_Len: 60 Strand: - Start: 94 End: 303 ............................................................................................. R L K E S L P P A E S Q S I S P V R S L G H I A G F P C P P K S G S L S E P L L V S R L P L S K G V G A C G S Y M N Q M ........................................ gcaagaagcctctgggcttcttttttgcatcaaaaaacgtttacatgctcaaaaattttcataaaatattgacaaaaggcgaatgttcttttagaataatagaaaattaataatcaacaccgaacgaagtttttcagaaagaggcggcgcttctgactgtgaaatggacggaactctggagagaccatgaatggcaccgaaggggcaaggcggtttagaaccgctcaaactctcaggtaaaaggacagagcgaagaggcagggatttccctactccagcacatccagagtacatgttttgcatgtgctctttctttttctcggtgtgaaaaggagcttatatc 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: 90 Start: 68 End: 97 ...................................................................ATTGACAAAAGGCGAATGTTCTTTTAGAAT...................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcaagaagcctctgggcttcttttttgcatcaaaaaacgtttacatgctcaaaaattttcataaaatattgacaaaaggcgaatgttcttttagaataatagaaaattaataatcaacaccgaacgaagtttttcagaaagaggcggcgcttctgactgtgaaatggacggaactctggagagaccatgaatggcaccgaaggggcaaggcggtttagaaccgctcaaactctcaggtaaaaggacagagcgaagaggcagggatttccctactccagcacatccagagtacatgttttgcatgtgctctttctttttctcggtgtgaaaaggagcttatatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.2 Tail_Score: -4.97405 Start: 287 End: 309 Full_Region: ACTCCAGCACATCCA GAGTACATGT TTT GCATGTGCTC TTTCTTTTTCTCGGT ..............................................................................................................................................................................................................................................................................................GAGTACATGTTTTGCATGTGCTC.................................. Find igs database================================================ Query_seq: SSA_0362:SSA_0363|SSA_0362:SSA_0363:Thioredoxin, putative:D-alanine/glycine/Na permease, putative:->->:353655..353997 343 gcaagaagcctctgggcttcttttttgcatcaaaaaacgtttacatgctcaaaaattttcataaaatattgacaaaaggcgaatgttcttttagaataatagaaaattaataatcaacaccgaacgaagtttttcagaaagaggcggcgcttctgactgtgaaatggacggaactctggagagaccatgaatggcaccgaaggggcaaggcggtttagaaccgctcaaactctcaggtaaaaggacagagcgaagaggcagggatttccctactccagcacatccagagtacatgttttgcatgtgctctttctttttctcggtgtgaaaaggagcttatatc Intra-Species Hit: Count: 1 Min: 1 Max: 343 Len: 343 Subject: NC_009009_SSA_0362_SSA_0363|Thioredoxin, putative:D-alanine/glycine/Na permease, putative|POSITIVE:POSITIVE|[353655,353997]|343 HSP 1 e-value: 0.0 bit: 680.0 Len: 343 Query Start:1 Query End:343 Subject Strand: POSITIVE Subject Start: 1 Subject End: 343 gcaagaagcctctgggcttcttttttgcatcaaaaaacgtttacatgctcaaaaattttcataaaatattgacaaaaggcgaatgttcttttagaataatagaaaattaataatcaacaccgaacgaagtttttcagaaagaggcggcgcttctgactgtgaaatggacggaactctggagagaccatgaatggcaccgaaggggcaaggcggtttagaaccgctcaaactctcaggtaaaaggacagagcgaagaggcagggatttccctactccagcacatccagagtacatgttttgcatgtgctctttctttttctcggtgtgaaaaggagcttatatc gcaagaagcctctgggcttcttttttgcatcaaaaaacgtttacatgctcaaaaattttcataaaatattgacaaaaggcgaatgttcttttagaataatagaaaattaataatcaacaccgaacgaagtttttcagaaagaggcggcgcttctgactgtgaaatggacggaactctggagagaccatgaatggcaccgaaggggcaaggcggtttagaaccgctcaaactctcaggtaaaaggacagagcgaagaggcagggatttccctactccagcacatccagagtacatgttttgcatgtgctctttctttttctcggtgtgaaaaggagcttatatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAGAAGCCUCUGGGCUUCUUUUUUGCAUCAAAAAACGUUUACAUGCUCAAAAAUUUUCAUAAAAUAUUGACAAAAGGCGAAUGUUCUUUUAGAAUAAUAGAAAAUUAAUAAUCAACACCGAACGAAGUUUUUCAGAAAGAGGCGGCGCUUCUGACUGUGAAAUGGACGGAACUCUGGAGAGACCAUGAAUGGCACCGAAGGGGCAAGGCGGUUUAGAACCGCUCAAACUCUCAGGUAAAAGGACAGAGCGAAGAGGCAGGGAUUUCCCUACUCCAGCACAUCCAGAGUACAUGUUUUGCAUGUGCUCUUUCUUUUUCUCGGUGUGAAAAGGAGCUUAUAUC ((((((((((....)))))))....)))..................((((.....(((((((.....(((((.((((((....((((((((((..........................(((..(...(((((.(((..((((((...))))))..))).))))))..))).......(((((..........((.((....))))..((((((.....))))))....)))))...))))))))))..((...(((..((((....)))).)))..))......((((((((((.....))))))))))..)))))).)))))))))))).))))....... (-101.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAUAAGCUCCUUUUCACACCGAGAAAAAGAAAGAGCACAUGCAAAACAUGUACUCUGGAUGUGCUGGAGUAGGGAAAUCCCUGCCUCUUCGCUCUGUCCUUUUACCUGAGAGUUUGAGCGGUUCUAAACCGCCUUGCCCCUUCGGUGCCAUUCAUGGUCUCUCCAGAGUUCCGUCCAUUUCACAGUCAGAAGCGCCGCCUCUUUCUGAAAAACUUCGUUCGGUGUUGAUUAUUAAUUUUCUAUUAUUCUAAAAGAACAUUCGCCUUUUGUCAAUAUUUUAUGAAAAUUUUUGAGCAUGUAAACGUUUUUUGAUGCAAAAAAGAAGCCCAGAGGCUUCUUGC ..((((.((((....((((((((((....((((((((.(((((.....)))))..((((..((((.((((((((((....))))))......((((((.......(((.(((.((..(.(((((.....))))))..))..))).)))((((....)))).....))))))....))))...))))..))))........))))))))(((....))).))))))).))).....(((((((((.((((.((((((.........))))))..))))...)).)))))))...)))).))))..((((....)))).....((((((((....)))))))).. (-92.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 229 182 214 174 NC_009009:SSA_2281|5end_hypothetical_protein_2282370..2282600_NEGATIVE 363 289 241 59 3 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 362 182 144 217 168 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 356 289 250 210 170 NC_009009:SSA_1928|5end_Acyl-CoA_dehydrogenase,_putative_1917010..1917240_NEGATIVE 350 211 174 183 136 NC_009009:SSA_1441|5end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1445183..1445413_NEGATIVE 349 288 242 53 9 NC_009009:SSA_0794|5end_Zn-dependent_protease,_putative_775896..776126_POSITIVE 344 240 192 85 22 NC_009009:SSA_2088|5end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2093476..2093706_NEGATIVE 342 239 193 155 94 NC_009009:SSA_0570|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_563915..564145_POSITIVE 340 238 192 60 12 NC_009009:SSA_1969|5end_Acetolactate_synthase_small_subunit,_putative_1965222..1965452_NEGATIVE 340 188 143 205 142 NC_009009:SSA_1926|5end_hypothetical_protein_1914829..1915059_POSITIVE 339 183 142 212 163 NC_009009:SSA_0522|5end_Ethanolamine_utilization_protein,_putative_521067..521297_POSITIVE 338 238 194 184 130 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 332 216 183 174 140 NC_009009:SSA_0307|5end_Glutamine_synthetase_type_1,_putative_302987..303217_POSITIVE 331 226 181 194 136 NC_009009:SSA_0421|5end_Phosphoglycerate_mutase_family_protein,_putative_419564..419794_POSITIVE 327 270 226 228 184 NC_009009:SSA_0273|5end_hypothetical_protein_267071..267301_POSITIVE 326 184 143 62 10 NC_009009:SSA_2296|5end_Transcriptional_regulator,_XRE_family,_putative_2298773..2299003_NEGATIVE 325 259 211 57 7 NC_009009:SSA_0221|5end_PTS_system,_mannose-specific_IIC_component,_putative_216370..216600_POSITIVE 324 214 177 71 31 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 323 226 188 157 112 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 321 340 305 178 138 NC_009009:SSA_0311|5end_hypothetical_protein_305877..306107_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 369 260 212 127 76 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 363 289 241 66 10 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 344 240 192 85 22 NC_009009:SSA_2089|3end_L-xylulose-5-phosphate_3-epimerase,_putative_2093476..2093626_NEGATIVE 340 238 192 67 19 NC_009009:SSA_1970|3end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1965215..1965365_NEGATIVE 332 216 183 142 108 NC_009009:SSA_0306|3end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_303035..303185_POSITIVE 328 285 249 151 117 NC_009009:SSA_0780|3end_Acid_phosphatase_(PAP2_family),_putative_765328..765478_POSITIVE 327 222 188 44 1 NC_009009:SSA_2292|3end_DNA_segregation_ATPase_FtsK/SpoIIIE-like_protein,_putative_2295353..2295503_POSITIVE 327 270 226 109 65 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 326 184 143 59 7 NC_009009:SSA_2297|3end_hypothetical_protein_2298776..2298926_NEGATIVE 324 214 177 74 34 NC_009009:SSA_1552|3end_hypothetical_protein_1555130..1555280_POSITIVE 312 266 221 81 36 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 311 287 246 150 115 NC_009009:SSA_1551|3end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1552652..1552802_NEGATIVE 311 225 181 74 16 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 309 225 193 60 30 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 308 296 251 146 99 NC_009009:SSA_1478|3end_Transposase_ORF1,_putative_1483124..1483274_POSITIVE 305 317 273 129 82 NC_009009:SSA_1187|3end_Transcriptional_antiterminator,_BglG_family,_putative_1215195..1215345_NEGATIVE 304 177 132 81 44 NC_009009:SSA_1038|3end_Lipoprotein,_putative_1053714..1053864_POSITIVE 303 224 181 82 32 NC_009009:SSA_1049|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064971..1065121_POSITIVE 302 154 111 149 107 NC_009009:SSA_1810|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1794707..1794857_NEGATIVE 301 233 191 58 25 NC_009009:SSA_2092|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095697..2095847_NEGATIVE