📄 sirna.txt
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>HSFAU_348 %GC 40.0 Score 7 H.sapiens fau mRNAaagaagaagaagaagacaggtcg>HSFAU_375 %GC 60.0 Score 7 H.sapiens fau mRNAaagcggcggatgcagtacaaccg>HSFAU_408 %GC 60.0 Score 7 H.sapiens fau mRNAaacgttgtgcccacctttggcaa>HSFAU_429 %GC 60.0 Score 7 H.sapiens fau mRNAaagaagaagggccccaatgccaa>HSFAU_432 %GC 60.0 Score 7 H.sapiens fau mRNAaagaagggccccaatgccaactc>HSFAU_435 %GC 60.0 Score 7 H.sapiens fau mRNAaagggccccaatgccaactctta>HSFAU_488 %GC 40.0 Score 7 H.sapiens fau mRNAaaaaagccacttagttcagtcaa>HSFAU_489 %GC 40.0 Score 7 H.sapiens fau mRNAaaaagccacttagttcagtcaaa>HSFAU_490 %GC 40.0 Score 7 H.sapiens fau mRNAaaagccacttagttcagtcaaaa>HSFAU_491 %GC 40.0 Score 7 H.sapiens fau mRNAaagccacttagttcagtcaaaaa>HSFAU_129 %GC 55.0 Score 6 H.sapiens fau mRNAaaggctcatgtagcctcactgga [Part of this file has been deleted for brevity]gaggccctgactaccctggaagt>HSFAU_259 %GC 60.0 Score 4 H.sapiens fau mRNAcaggccgcatgcttggaggtaaa>HSFAU_266 %GC 40.0 Score 4 H.sapiens fau mRNAcatgcttggaggtaaagttcatg>HSFAU_342 %GC 40.0 Score 4 H.sapiens fau mRNAcaggagaagaagaagaagaagac>HSFAU_347 %GC 40.0 Score 4 H.sapiens fau mRNAgaagaagaagaagaagacaggtc>HSFAU_359 %GC 60.0 Score 4 H.sapiens fau mRNAgaagacaggtcgggctaagcggc>HSFAU_111 %GC 55.0 Score 3 H.sapiens fau mRNAgaaacggtcgcccagatcaaggc>HSFAU_113 %GC 65.0 Score 3 H.sapiens fau mRNAaacggtcgcccagatcaaggctc>HSFAU_172 %GC 70.0 Score 3 H.sapiens fau mRNAaagtcgtgctcctggcaggcgcg>HSFAU_443 %GC 35.0 Score 3 H.sapiens fau mRNAcaatgccaactcttaagtctttt>HSFAU_456 %GC 35.0 Score 3 H.sapiens fau mRNAtaagtcttttgtaattctggctt>HSFAU_468 %GC 30.0 Score 3 H.sapiens fau mRNAaattctggctttctctaataaaa>HSFAU_484 %GC 30.0 Score 3 H.sapiens fau mRNAaataaaaaagccacttagttcag>HSFAU_108 %GC 60.0 Score 2 H.sapiens fau mRNAcaggaaacggtcgcccagatcaa>HSFAU_135 %GC 60.0 Score 2 H.sapiens fau mRNAcatgtagcctcactggagggcat>HSFAU_139 %GC 60.0 Score 2 H.sapiens fau mRNAtagcctcactggagggcattgcc>HSFAU_150 %GC 60.0 Score 2 H.sapiens fau mRNAgagggcattgccccggaagatca>HSFAU_171 %GC 65.0 Score 2 H.sapiens fau mRNAcaagtcgtgctcctggcaggcgc>HSFAU_201 %GC 65.0 Score 2 H.sapiens fau mRNAgaggatgaggccactctgggcca>HSFAU_204 %GC 65.0 Score 2 H.sapiens fau mRNAgatgaggccactctgggccagtg>HSFAU_245 %GC 65.0 Score 2 H.sapiens fau mRNAtaccctggaagtagcaggccgca>HSFAU_256 %GC 65.0 Score 2 H.sapiens fau mRNAtagcaggccgcatgcttggaggt>HSFAU_285 %GC 65.0 Score 2 H.sapiens fau mRNAcatggttccctggcccgtgctgg>HSFAU_338 %GC 35.0 Score 2 H.sapiens fau mRNAcaaacaggagaagaagaagaaga>HSFAU_345 %GC 35.0 Score 2 H.sapiens fau mRNAgagaagaagaagaagaagacagg>HSFAU_486 %GC 35.0 Score 2 H.sapiens fau mRNAtaaaaaagccacttagttcagtc Output files for usage example 2 File: hsfau.sirna######################################### Program: sirna# Rundate: Sat 15 Jul 2006 12:00:00# Commandline: sirna# -context# -sequence tembl:hsfau# Report_format: table# Report_file: hsfau.sirna#########################################=======================================## Sequence: HSFAU from: 1 to: 518# HitCount: 85## The forward sense sequence shows the first 2 bases of# the 23 base region in brackets, this should be ignored# when ordering siRNA probes.# CDS region found in feature table starting at 57##======================================= Start End Score GC% Sense_siRNA Antisense_siRNA 308 330 9.000 50.0 (AA)AAGUGAGAGGUCAGACUCCdTdT GGAGUCUGACCUCUCACUUdTdT 309 331 9.000 50.0 (AA)AGUGAGAGGUCAGACUCCUdTdT AGGAGUCUGACCUCUCACUdTdT 310 332 9.000 50.0 (AA)GUGAGAGGUCAGACUCCUAdTdT UAGGAGUCUGACCUCUCACdTdT 351 373 9.000 50.0 (AA)GAAGAAGAAGACAGGUCGGdTdT CCGACCUGUCUUCUUCUUCdTdT 166 188 8.000 55.0 (AA)GAUCAAGUCGUGCUCCUGGdTdT CCAGGAGCACGACUUGAUCdTdT 279 301 8.000 55.0 (AA)AGUUCAUGGUUCCCUGGCCdTdT GGCCAGGGAACCAUGAACUdTdT 330 352 8.000 55.0 (AA)GGUGGCCAAACAGGAGAAGdTdT CUUCUCCUGUUUGGCCACCdTdT 354 376 8.000 55.0 (AA)GAAGAAGACAGGUCGGGCUdTdT AGCCCGACCUGUCUUCUUCdTdT 357 379 8.000 55.0 (AA)GAAGACAGGUCGGGCUAAGdTdT CUUAGCCCGACCUGUCUUCdTdT 393 415 8.000 55.0 (AA)CCGGCGCUUUGUCAACGUUdTdT AACGUUGACAAAGCGCCGGdTdT 253 275 7.000 60.0 (AA)GUAGCAGGCCGCAUGCUUGdTdT CAAGCAUGCGGCCUGCUACdTdT 280 302 7.000 60.0 (AA)GUUCAUGGUUCCCUGGCCCdTdT GGGCCAGGGAACCAUGAACdTdT 339 361 7.000 40.0 (AA)ACAGGAGAAGAAGAAGAAGdTdT CUUCUUCUUCUUCUCCUGUdTdT 340 362 7.000 40.0 (AA)CAGGAGAAGAAGAAGAAGAdTdT UCUUCUUCUUCUUCUCCUGdTdT 348 370 7.000 40.0 (AA)GAAGAAGAAGAAGACAGGUdTdT ACCUGUCUUCUUCUUCUUCdTdT 375 397 7.000 60.0 (AA)GCGGCGGAUGCAGUACAACdTdT GUUGUACUGCAUCCGCCGCdTdT 408 430 7.000 60.0 (AA)CGUUGUGCCCACCUUUGGCdTdT GCCAAAGGUGGGCACAACGdTdT 429 451 7.000 60.0 (AA)GAAGAAGGGCCCCAAUGCCdTdT GGCAUUGGGGCCCUUCUUCdTdT 432 454 7.000 60.0 (AA)GAAGGGCCCCAAUGCCAACdTdT GUUGGCAUUGGGGCCCUUCdTdT 435 457 7.000 60.0 (AA)GGGCCCCAAUGCCAACUCUdTdT AGAGUUGGCAUUGGGGCCCdTdT 488 510 7.000 40.0 (AA)AAAGCCACUUAGUUCAGUCdTdT GACUGAACUAAGUGGCUUUdTdT 489 511 7.000 40.0 (AA)AAGCCACUUAGUUCAGUCAdTdT UGACUGAACUAAGUGGCUUdTdT 490 512 7.000 40.0 (AA)AGCCACUUAGUUCAGUCAAdTdT UUGACUGAACUAAGUGGCUdTdT 491 513 7.000 40.0 (AA)GCCACUUAGUUCAGUCAAAdTdT UUUGACUGAACUAAGUGGCdTdT 129 151 6.000 55.0 (AA)GGCUCAUGUAGCCUCACUGdTdT CAGUGAGGCUACAUGAGCCdTdT 165 187 6.000 50.0 (GA)AGAUCAAGUCGUGCUCCUGdTdT CAGGAGCACGACUUGAUCUdTdT 278 300 6.000 50.0 (UA)AAGUUCAUGGUUCCCUGGCdTdT GCCAGGGAACCAUGAACUUdTdT [Part of this file has been deleted for brevity] 353 375 5.000 55.0 (GA)AGAAGAAGACAGGUCGGGCdTdT GCCCGACCUGUCUUCUUCUdTdT 360 382 5.000 65.0 (AA)GACAGGUCGGGCUAAGCGGdTdT CCGCUUAGCCCGACCUGUCdTdT 374 396 5.000 55.0 (UA)AGCGGCGGAUGCAGUACAAdTdT UUGUACUGCAUCCGCCGCUdTdT 383 405 5.000 55.0 (GA)UGCAGUACAACCGGCGCUUdTdT AAGCGCCGGUUGUACUGCAdTdT 387 409 5.000 55.0 (CA)GUACAACCGGCGCUUUGUCdTdT GACAAAGCGCCGGUUGUACdTdT 390 412 5.000 55.0 (UA)CAACCGGCGCUUUGUCAACdTdT GUUGACAAAGCGCCGGUUGdTdT 392 414 5.000 55.0 (CA)ACCGGCGCUUUGUCAACGUdTdT ACGUUGACAAAGCGCCGGUdTdT 407 429 5.000 55.0 (CA)ACGUUGUGCCCACCUUUGGdTdT CCAAAGGUGGGCACAACGUdTdT 428 450 5.000 55.0 (CA)AGAAGAAGGGCCCCAAUGCdTdT GCAUUGGGGCCCUUCUUCUdTdT 431 453 5.000 55.0 (GA)AGAAGGGCCCCAAUGCCAAdTdT UUGGCAUUGGGGCCCUUCUdTdT 434 456 5.000 60.0 (GA)AGGGCCCCAAUGCCAACUCdTdT GAGUUGGCAUUGGGGCCCUdTdT 444 466 5.000 35.0 (AA)UGCCAACUCUUAAGUCUUUdTdT AAAGACUUAAGAGUUGGCAdTdT 487 509 5.000 35.0 (AA)AAAAGCCACUUAGUUCAGUdTdT ACUGAACUAAGUGGCUUUUdTdT 123 145 4.000 50.0 (CA)GAUCAAGGCUCAUGUAGCCdTdT GGCUACAUGAGCCUUGAUCdTdT 125 147 4.000 50.0 (GA)UCAAGGCUCAUGUAGCCUCdTdT GAGGCUACAUGAGCCUUGAdTdT 128 150 4.000 50.0 (CA)AGGCUCAUGUAGCCUCACUdTdT AGUGAGGCUACAUGAGCCUdTdT 155 177 4.000 50.0 (CA)UUGCCCCGGAAGAUCAAGUdTdT ACUUGAUCUUCCGGGGCAAdTdT 234 256 4.000 60.0 (GA)GGCCCUGACUACCCUGGAAdTdT UUCCAGGGUAGUCAGGGCCdTdT 259 281 4.000 60.0 (CA)GGCCGCAUGCUUGGAGGUAdTdT UACCUCCAAGCAUGCGGCCdTdT 266 288 4.000 40.0 (CA)UGCUUGGAGGUAAAGUUCAdTdT UGAACUUUACCUCCAAGCAdTdT 342 364 4.000 40.0 (CA)GGAGAAGAAGAAGAAGAAGdTdT CUUCUUCUUCUUCUUCUCCdTdT 347 369 4.000 40.0 (GA)AGAAGAAGAAGAAGACAGGdTdT CCUGUCUUCUUCUUCUUCUdTdT 359 381 4.000 60.0 (GA)AGACAGGUCGGGCUAAGCGdTdT CGCUUAGCCCGACCUGUCUdTdT 111 133 3.000 55.0 (GA)AACGGUCGCCCAGAUCAAGdTdT CUUGAUCUGGGCGACCGUUdTdT 113 135 3.000 65.0 (AA)CGGUCGCCCAGAUCAAGGCdTdT GCCUUGAUCUGGGCGACCGdTdT 172 194 3.000 70.0 (AA)GUCGUGCUCCUGGCAGGCGdTdT CGCCUGCCAGGAGCACGACdTdT 443 465 3.000 35.0 (CA)AUGCCAACUCUUAAGUCUUdTdT AAGACUUAAGAGUUGGCAUdTdT 456 478 3.000 35.0 (UA)AGUCUUUUGUAAUUCUGGCdTdT GCCAGAAUUACAAAAGACUdTdT 468 490 3.000 30.0 (AA)UUCUGGCUUUCUCUAAUAAdTdT UUAUUAGAGAAAGCCAGAAdTdT 484 506 3.000 30.0 (AA)UAAAAAAGCCACUUAGUUCdTdT GAACUAAGUGGCUUUUUUAdTdT 108 130 2.000 60.0 (CA)GGAAACGGUCGCCCAGAUCdTdT GAUCUGGGCGACCGUUUCCdTdT 135 157 2.000 60.0 (CA)UGUAGCCUCACUGGAGGGCdTdT GCCCUCCAGUGAGGCUACAdTdT 139 161 2.000 60.0 (UA)GCCUCACUGGAGGGCAUUGdTdT CAAUGCCCUCCAGUGAGGCdTdT 150 172 2.000 60.0 (GA)GGGCAUUGCCCCGGAAGAUdTdT AUCUUCCGGGGCAAUGCCCdTdT 171 193 2.000 65.0 (CA)AGUCGUGCUCCUGGCAGGCdTdT GCCUGCCAGGAGCACGACUdTdT 201 223 2.000 65.0 (GA)GGAUGAGGCCACUCUGGGCdTdT GCCCAGAGUGGCCUCAUCCdTdT 204 226 2.000 65.0 (GA)UGAGGCCACUCUGGGCCAGdTdT CUGGCCCAGAGUGGCCUCAdTdT 245 267 2.000 65.0 (UA)CCCUGGAAGUAGCAGGCCGdTdT CGGCCUGCUACUUCCAGGGdTdT 256 278 2.000 65.0 (UA)GCAGGCCGCAUGCUUGGAGdTdT CUCCAAGCAUGCGGCCUGCdTdT 285 307 2.000 65.0 (CA)UGGUUCCCUGGCCCGUGCUdTdT AGCACGGGCCAGGGAACCAdTdT 338 360 2.000 35.0 (CA)AACAGGAGAAGAAGAAGAAdTdT UUCUUCUUCUUCUCCUGUUdTdT 345 367 2.000 35.0 (GA)GAAGAAGAAGAAGAAGACAdTdT UGUCUUCUUCUUCUUCUUCdTdT 486 508 2.000 35.0 (UA)AAAAAGCCACUUAGUUCAGdTdT CUGAACUAAGUGGCUUUUUdTdT#---------------------------------------#---------------------------------------#---------------------------------------# Total_sequences: 1# Total_hitcount: 85#--------------------------------------- The siRNAs are reported in order of best score first. sirna reports both the sense and antisense siRNAs as 5' to 3'.Data files None.Notes None.References 1. Elbashir, S. M., et al. (2001a). Duplexes of 21-nucleotide RNAs mediate RNA interference in mammalian cell culture. Nature 411: 494-498. 2. Elbashir, S. M., W. Lendeckel and T. Tuschl (2001b). RNA interference is mediated by 21 and 22 nt RNAs. Genes & Dev. 15: 188-200.Warnings It is assumed that the input sequence is mRNA.Diagnostic Error Messages None.Exit status It always exits with status 0.Known bugs None.See also Program name Description banana Bending and curvature plot in B-DNA btwisted Calculates the twisting in a B-DNA sequence chaos Create a chaos game representation plot for a sequence compseq Count composition of dimer/trimer/etc words in a sequence dan Calculates DNA RNA/DNA melting temperature freak Residue/base frequency table or plot isochore Plots isochores in large DNA sequences wordcount Counts words of a specified size in a DNA sequenceAuthor(s) Gary Williams (gwilliam ⌨️ 快捷键说明
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