Multiple sequence alignment - TraesCS5B01G025000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G025000 chr5B 100.000 7166 0 0 1 7166 23892454 23885289 0 13234
1 TraesCS5B01G025000 chr5A 95.707 7034 236 32 1 7002 20822932 20815933 0 11256
2 TraesCS5B01G025000 chr5D 96.061 4164 124 23 3021 7166 32154052 32149911 0 6745
3 TraesCS5B01G025000 chr5D 95.895 3045 86 11 1 3027 32157340 32154317 0 4894


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G025000 chr5B 23885289 23892454 7165 True 13234.0 13234 100.000 1 7166 1 chr5B.!!$R1 7165
1 TraesCS5B01G025000 chr5A 20815933 20822932 6999 True 11256.0 11256 95.707 1 7002 1 chr5A.!!$R1 7001
2 TraesCS5B01G025000 chr5D 32149911 32157340 7429 True 5819.5 6745 95.978 1 7166 2 chr5D.!!$R1 7165

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
531 545 1.364721 CAACACCATCGCCGTGAATA 58.635 50.000 3.77 0.00 35.17 1.75 F
1033 1053 1.361271 GATCGATGGCGGGTTCGTA 59.639 57.895 0.54 0.00 38.89 3.43 F
1865 1897 0.250901 AGCACAAGCACCTTACCCTG 60.251 55.000 0.00 0.00 45.49 4.45 F
2225 2257 0.904649 AGATCCCGATGTCTTGTGCA 59.095 50.000 0.00 0.00 0.00 4.57 F
2249 2281 1.409790 GGCCATTTCATAGCATGCACA 59.590 47.619 21.98 7.55 0.00 4.57 F
3497 3801 2.488153 GTTCATTTCCCAGAAGGTTCCG 59.512 50.000 0.00 0.00 36.75 4.30 F
4388 4694 2.229543 TGTGCTGCAGAATGATTTGGAC 59.770 45.455 20.43 0.00 39.69 4.02 F
5624 5933 2.100605 ACTGCCTCGAATTGAAGTCC 57.899 50.000 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1430 1462 0.469331 ACTGTTGGTCCTCCTCGTCA 60.469 55.000 0.00 0.0 34.23 4.35 R
1887 1919 0.533755 GAATCACCGGCATCTCCCAG 60.534 60.000 0.00 0.0 0.00 4.45 R
3393 3697 1.139439 TTAGCATATGGAGGCTGGCA 58.861 50.000 4.56 0.0 43.99 4.92 R
3637 3941 3.056393 AGCAAAGCTAGCAATGCAAATCA 60.056 39.130 32.80 0.0 41.18 2.57 R
4078 4383 7.660030 AATAACAATAAAATCTGAGGTGGGG 57.340 36.000 0.00 0.0 0.00 4.96 R
5004 5310 2.375174 AGGTAAGCATTGGTCCACAAGA 59.625 45.455 0.00 0.0 43.48 3.02 R
5731 6040 0.327924 CATTGGGGGCTGTAGTGACA 59.672 55.000 0.00 0.0 0.00 3.58 R
6816 7131 0.109827 CGACGCCATGAAAACATGCA 60.110 50.000 0.00 0.0 0.00 3.96 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
251 252 3.073735 CTCAGCCGCCTGTCCTCT 61.074 66.667 0.00 0.00 40.09 3.69
335 336 2.893398 GAGACCAGCACGGGGTAG 59.107 66.667 0.00 0.00 39.19 3.18
336 337 1.982938 GAGACCAGCACGGGGTAGT 60.983 63.158 0.00 0.00 39.19 2.73
337 338 2.227089 GAGACCAGCACGGGGTAGTG 62.227 65.000 0.00 0.00 44.47 2.74
370 374 2.440065 CCTGGCCGCCATTGCTTA 60.440 61.111 13.86 0.00 30.82 3.09
371 375 2.774799 CCTGGCCGCCATTGCTTAC 61.775 63.158 13.86 0.00 30.82 2.34
372 376 2.034843 TGGCCGCCATTGCTTACA 59.965 55.556 8.43 0.00 34.43 2.41
373 377 2.270297 CTGGCCGCCATTGCTTACAC 62.270 60.000 13.86 0.00 30.82 2.90
374 378 2.100216 GCCGCCATTGCTTACACG 59.900 61.111 0.00 0.00 34.43 4.49
375 379 2.791256 CCGCCATTGCTTACACGG 59.209 61.111 0.00 0.00 34.43 4.94
376 380 2.038269 CCGCCATTGCTTACACGGT 61.038 57.895 0.00 0.00 35.99 4.83
513 527 1.664649 CGTCAAAGTCTCCGCTGCA 60.665 57.895 0.00 0.00 0.00 4.41
531 545 1.364721 CAACACCATCGCCGTGAATA 58.635 50.000 3.77 0.00 35.17 1.75
1033 1053 1.361271 GATCGATGGCGGGTTCGTA 59.639 57.895 0.54 0.00 38.89 3.43
1419 1451 3.708220 CTCGTTGGCCTCCTCGAGC 62.708 68.421 19.56 0.00 39.70 5.03
1580 1612 4.007644 CGCCAGGAGCTCACCACA 62.008 66.667 17.19 0.00 40.39 4.17
1586 1618 2.746359 GAGCTCACCACAGCAGGT 59.254 61.111 9.40 0.00 42.40 4.00
1739 1771 4.463879 CAGCTCAGCGACCTGGGG 62.464 72.222 0.00 0.00 40.07 4.96
1757 1789 0.543749 GGCTCTACCCATTGCACTCT 59.456 55.000 0.00 0.00 0.00 3.24
1758 1790 1.661341 GCTCTACCCATTGCACTCTG 58.339 55.000 0.00 0.00 0.00 3.35
1865 1897 0.250901 AGCACAAGCACCTTACCCTG 60.251 55.000 0.00 0.00 45.49 4.45
2225 2257 0.904649 AGATCCCGATGTCTTGTGCA 59.095 50.000 0.00 0.00 0.00 4.57
2249 2281 1.409790 GGCCATTTCATAGCATGCACA 59.590 47.619 21.98 7.55 0.00 4.57
2284 2316 3.266772 TGTGATTCCAAGGGCTTGAGTAT 59.733 43.478 0.00 0.00 42.93 2.12
2418 2450 5.177696 AGCACATCGAGTTTAACAGAAGAAC 59.822 40.000 0.00 0.00 0.00 3.01
2545 2577 8.744008 TTAAAGTTCTTCTGACTTGATCGTAG 57.256 34.615 0.00 0.00 0.00 3.51
2677 2710 3.891366 AGCTGACTAAACACAAGGCATTT 59.109 39.130 0.00 0.00 29.70 2.32
2691 2724 4.116747 AGGCATTTGTCGAACTAGAGAG 57.883 45.455 0.00 0.00 0.00 3.20
2839 2872 6.327934 GCAGGTCGAAAGTTTACTGACTATA 58.672 40.000 12.28 0.00 0.00 1.31
2935 2968 3.684305 TGAATGCTGTTATTGACACGAGG 59.316 43.478 0.00 0.00 33.82 4.63
3218 3522 5.512232 GGTCCAATAGATGAAGATGGTCCTC 60.512 48.000 0.00 0.00 36.71 3.71
3393 3697 3.887716 GCCATCAAGGTAATGAGCAGAAT 59.112 43.478 0.00 0.00 40.61 2.40
3427 3731 7.013559 TCCATATGCTAATTCCTTCACAATGTG 59.986 37.037 7.12 7.12 34.45 3.21
3485 3789 3.138304 GGGCTTTGGTTTGTTCATTTCC 58.862 45.455 0.00 0.00 0.00 3.13
3497 3801 2.488153 GTTCATTTCCCAGAAGGTTCCG 59.512 50.000 0.00 0.00 36.75 4.30
3589 3893 8.387190 TGATATTAAATGGATGACTTGCTCAG 57.613 34.615 0.00 0.00 30.20 3.35
3605 3909 6.013812 ACTTGCTCAGGAGAATTAGAGAACTT 60.014 38.462 0.00 0.00 0.00 2.66
4078 4383 3.589988 CCTGTCTCACAGTATTGGTGAC 58.410 50.000 3.07 0.00 44.50 3.67
4097 4402 4.399303 GTGACCCCACCTCAGATTTTATTG 59.601 45.833 0.00 0.00 37.33 1.90
4266 4571 8.074370 TCTCGGTACTTCTATCATTTATGTTCG 58.926 37.037 0.00 0.00 0.00 3.95
4301 4606 6.816140 TGTTTCCCTTTGTGTTTTGAGATTTC 59.184 34.615 0.00 0.00 0.00 2.17
4388 4694 2.229543 TGTGCTGCAGAATGATTTGGAC 59.770 45.455 20.43 0.00 39.69 4.02
4889 5195 4.097286 TGTTGGAGCCACAAAACTTAGAAC 59.903 41.667 0.00 0.00 31.17 3.01
4895 5201 6.092807 GGAGCCACAAAACTTAGAACTGATAG 59.907 42.308 0.00 0.00 0.00 2.08
4934 5240 9.577003 GTTGTTCAGAACAGTTATTAAACTACG 57.423 33.333 15.61 0.00 44.28 3.51
5001 5307 9.520204 CTGGTCGAAATGATTTGCTATTTATTT 57.480 29.630 0.00 0.00 0.00 1.40
5118 5424 7.227156 ACAGATAATATTCTGAATGGACCACC 58.773 38.462 13.01 0.00 44.88 4.61
5624 5933 2.100605 ACTGCCTCGAATTGAAGTCC 57.899 50.000 0.00 0.00 0.00 3.85
5858 6167 4.652679 AATCCCTCTTAACTTCCCGTTT 57.347 40.909 0.00 0.00 37.05 3.60
5860 6169 4.442401 TCCCTCTTAACTTCCCGTTTTT 57.558 40.909 0.00 0.00 37.05 1.94
5893 6203 9.516314 GTAATCCAAATTATTTTACAGCAGTCC 57.484 33.333 0.00 0.00 30.28 3.85
5917 6227 8.336235 TCCCCTCACATTTTCAATTTCTACTAT 58.664 33.333 0.00 0.00 0.00 2.12
5962 6272 1.207329 GGTAGCATGGAAGAGTTCGGT 59.793 52.381 0.00 0.00 0.00 4.69
6050 6363 5.279156 GCCACAATCTTTGAATCTTGTCCTT 60.279 40.000 0.00 0.00 29.74 3.36
6067 6380 5.305585 TGTCCTTGGTGAGTTAACATCTTC 58.694 41.667 8.61 0.00 0.00 2.87
6212 6525 1.003928 AGCAACATGACCAGCATCTCA 59.996 47.619 0.00 0.00 34.15 3.27
6248 6561 6.647229 ACATCATCTTACTCTTGCTTGATCA 58.353 36.000 0.00 0.00 0.00 2.92
6267 6580 8.918202 TTGATCAGGTGTACAAAAAGTAAGAT 57.082 30.769 0.00 0.00 33.72 2.40
6274 6587 6.806739 GGTGTACAAAAAGTAAGATTGCATCC 59.193 38.462 0.00 0.00 33.72 3.51
6302 6615 2.290960 ACAAACCTGATTCTACTGCCCC 60.291 50.000 0.00 0.00 0.00 5.80
6311 6624 0.251165 TCTACTGCCCCTGGTTTTGC 60.251 55.000 0.00 0.00 0.00 3.68
6320 6633 1.962807 CCCTGGTTTTGCTTGTCATGA 59.037 47.619 0.00 0.00 0.00 3.07
6358 6671 3.706373 CCACCGGTGGTAGCAGCT 61.706 66.667 40.44 0.00 45.53 4.24
6386 6699 6.695713 GTGATATGATAGCAAGTGTGTAACGA 59.304 38.462 0.00 0.00 42.39 3.85
6404 6717 1.590238 CGATCGAAGACATGAACCTGC 59.410 52.381 10.26 0.00 42.51 4.85
6507 6821 2.483188 GGCGGGTGTCAGATAAGTTAGG 60.483 54.545 0.00 0.00 0.00 2.69
6725 7039 4.022416 GGGTCAATAGTGAAACATGTTGCA 60.022 41.667 15.66 15.66 41.43 4.08
6784 7098 6.480524 TCACGTGTGAAAATTATCCTCTTG 57.519 37.500 16.51 0.00 36.53 3.02
6786 7100 6.742926 TCACGTGTGAAAATTATCCTCTTGGA 60.743 38.462 16.51 0.00 40.86 3.53
6787 7101 5.643777 ACGTGTGAAAATTATCCTCTTGGAG 59.356 40.000 0.00 0.00 46.91 3.86
6809 7124 1.453155 GTTGTCTTGGATGCACCGAT 58.547 50.000 0.00 0.00 42.61 4.18
6816 7131 2.727123 TGGATGCACCGATAATGGTT 57.273 45.000 0.00 0.00 41.38 3.67
6861 7176 1.964373 AACATTGGCGTGGTCGGTC 60.964 57.895 0.00 0.00 37.56 4.79
6898 7213 2.504274 GGGACAGGTGTGGTCGTCA 61.504 63.158 0.00 0.00 36.12 4.35
6901 7216 0.603569 GACAGGTGTGGTCGTCATCT 59.396 55.000 0.00 0.00 0.00 2.90
6904 7219 0.608640 AGGTGTGGTCGTCATCTTCC 59.391 55.000 0.00 0.00 0.00 3.46
6906 7221 1.822990 GGTGTGGTCGTCATCTTCCTA 59.177 52.381 0.00 0.00 0.00 2.94
6920 7239 3.528370 CCTACCGGAGCGACCCAG 61.528 72.222 9.46 0.00 34.64 4.45
6932 7251 3.305720 AGCGACCCAGATCCACTTATTA 58.694 45.455 0.00 0.00 0.00 0.98
6936 7255 4.217767 CGACCCAGATCCACTTATTATCGA 59.782 45.833 0.00 0.00 0.00 3.59
6947 7266 6.380274 TCCACTTATTATCGAACCTGTCTTCT 59.620 38.462 0.00 0.00 0.00 2.85
6950 7270 9.021863 CACTTATTATCGAACCTGTCTTCTTAC 57.978 37.037 0.00 0.00 0.00 2.34
6961 7281 7.745620 ACCTGTCTTCTTACTTTAATGTTGG 57.254 36.000 0.00 0.00 0.00 3.77
6986 7307 0.719465 GTGACGGTCATAGTTTGGCG 59.281 55.000 14.78 0.00 0.00 5.69
7002 7323 1.069935 GCGCCTTAGGACATCTCCC 59.930 63.158 0.69 0.00 37.25 4.30
7013 7334 3.137176 AGGACATCTCCCATGGTTGTATG 59.863 47.826 11.73 10.93 37.25 2.39
7014 7335 2.880890 GACATCTCCCATGGTTGTATGC 59.119 50.000 11.73 2.55 0.00 3.14
7015 7336 2.511218 ACATCTCCCATGGTTGTATGCT 59.489 45.455 11.73 0.00 0.00 3.79
7016 7337 3.053395 ACATCTCCCATGGTTGTATGCTT 60.053 43.478 11.73 0.00 0.00 3.91
7017 7338 3.003394 TCTCCCATGGTTGTATGCTTG 57.997 47.619 11.73 0.00 0.00 4.01
7018 7339 2.026641 CTCCCATGGTTGTATGCTTGG 58.973 52.381 11.73 0.00 0.00 3.61
7019 7340 1.357420 TCCCATGGTTGTATGCTTGGT 59.643 47.619 11.73 0.00 0.00 3.67
7020 7341 2.578480 TCCCATGGTTGTATGCTTGGTA 59.422 45.455 11.73 0.00 0.00 3.25
7021 7342 2.951642 CCCATGGTTGTATGCTTGGTAG 59.048 50.000 11.73 0.00 0.00 3.18
7022 7343 3.371487 CCCATGGTTGTATGCTTGGTAGA 60.371 47.826 11.73 0.00 0.00 2.59
7023 7344 3.627577 CCATGGTTGTATGCTTGGTAGAC 59.372 47.826 2.57 0.00 0.00 2.59
7024 7345 4.517285 CATGGTTGTATGCTTGGTAGACT 58.483 43.478 0.00 0.00 0.00 3.24
7025 7346 3.937814 TGGTTGTATGCTTGGTAGACTG 58.062 45.455 0.00 0.00 0.00 3.51
7026 7347 2.678336 GGTTGTATGCTTGGTAGACTGC 59.322 50.000 0.00 0.00 0.00 4.40
7030 7351 0.692476 ATGCTTGGTAGACTGCCACA 59.308 50.000 12.36 8.49 35.46 4.17
7115 7439 3.960102 ACACCATTGACAAACTCCAATGT 59.040 39.130 12.29 0.00 44.79 2.71
7121 7445 8.865090 ACCATTGACAAACTCCAATGTAAAATA 58.135 29.630 12.29 0.00 44.79 1.40
7129 7453 9.329913 CAAACTCCAATGTAAAATAAGAGAACG 57.670 33.333 0.00 0.00 0.00 3.95
7130 7454 8.617290 AACTCCAATGTAAAATAAGAGAACGT 57.383 30.769 0.00 0.00 0.00 3.99
7148 7472 9.968870 AGAGAACGTCTTATTTATTATCTCACC 57.031 33.333 7.87 0.00 34.64 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
251 252 4.680237 CGTCCGCCTGCCAAGACA 62.680 66.667 0.00 0.00 0.00 3.41
320 321 2.264794 CACTACCCCGTGCTGGTC 59.735 66.667 0.00 0.00 37.31 4.02
335 336 3.216292 GTGCACCACCACCACCAC 61.216 66.667 5.22 0.00 0.00 4.16
375 379 1.449070 GCTGGGGCGTAGGTGTAAC 60.449 63.158 0.00 0.00 0.00 2.50
376 380 2.662070 GGCTGGGGCGTAGGTGTAA 61.662 63.158 0.00 0.00 39.81 2.41
513 527 2.325583 ATATTCACGGCGATGGTGTT 57.674 45.000 16.62 0.00 36.76 3.32
592 606 1.096386 CCGATCTCCGTCTCTTCCGT 61.096 60.000 0.00 0.00 36.31 4.69
593 607 0.814410 TCCGATCTCCGTCTCTTCCG 60.814 60.000 0.00 0.00 36.31 4.30
594 608 0.948678 CTCCGATCTCCGTCTCTTCC 59.051 60.000 0.00 0.00 36.31 3.46
595 609 1.956297 TCTCCGATCTCCGTCTCTTC 58.044 55.000 0.00 0.00 36.31 2.87
596 610 2.226330 CATCTCCGATCTCCGTCTCTT 58.774 52.381 0.00 0.00 36.31 2.85
799 816 1.760613 AGGACACGTGTCTTTTGGAGA 59.239 47.619 39.01 0.00 44.20 3.71
960 980 2.598787 CGTGGGGTCAAAGGGCCTA 61.599 63.158 6.41 0.00 0.00 3.93
1033 1053 0.320771 GCTCACACACCGACCAATCT 60.321 55.000 0.00 0.00 0.00 2.40
1430 1462 0.469331 ACTGTTGGTCCTCCTCGTCA 60.469 55.000 0.00 0.00 34.23 4.35
1739 1771 1.661341 CAGAGTGCAATGGGTAGAGC 58.339 55.000 0.00 0.00 0.00 4.09
1829 1861 2.042404 GCTCCAGCATCCTCCTCCTG 62.042 65.000 0.00 0.00 41.59 3.86
1887 1919 0.533755 GAATCACCGGCATCTCCCAG 60.534 60.000 0.00 0.00 0.00 4.45
2249 2281 2.350522 GAATCACACCGATCAGCAAGT 58.649 47.619 0.00 0.00 31.11 3.16
2284 2316 1.234821 CCTTTGTAGCCGCTTGTCAA 58.765 50.000 0.00 0.00 0.00 3.18
2418 2450 3.869623 GATCCATGGATCCATCGGG 57.130 57.895 35.69 25.01 43.71 5.14
2677 2710 4.037565 TGCTGAAAACTCTCTAGTTCGACA 59.962 41.667 0.00 0.00 45.37 4.35
2691 2724 5.842907 AGGATTAACAAACCTGCTGAAAAC 58.157 37.500 0.00 0.00 32.39 2.43
2839 2872 1.493861 TGCTCTCAATGCCTCTAGCT 58.506 50.000 0.00 0.00 44.23 3.32
2935 2968 1.895131 ACAACAAGGGCATCCACATTC 59.105 47.619 0.00 0.00 34.83 2.67
3005 3038 5.013861 GCACAAAGATGCATTGAAAACAG 57.986 39.130 0.00 0.00 45.39 3.16
3017 3050 7.119699 TCAGAAGTATTAAGTGGCACAAAGATG 59.880 37.037 21.41 6.41 44.16 2.90
3105 3409 8.134202 TCACAATGTTAATAAGAGAGTCAGGA 57.866 34.615 0.00 0.00 0.00 3.86
3218 3522 6.214191 TCTTGAGCTTACACTATTCTCCAG 57.786 41.667 0.00 0.00 0.00 3.86
3393 3697 1.139439 TTAGCATATGGAGGCTGGCA 58.861 50.000 4.56 0.00 43.99 4.92
3427 3731 8.718102 TCAATGTTCAGTATAAAGGAGCTAAC 57.282 34.615 0.00 0.00 0.00 2.34
3618 3922 9.423061 GCAAATCATGTATGGTTCTTAACTTTT 57.577 29.630 0.00 0.00 29.24 2.27
3637 3941 3.056393 AGCAAAGCTAGCAATGCAAATCA 60.056 39.130 32.80 0.00 41.18 2.57
4078 4383 7.660030 AATAACAATAAAATCTGAGGTGGGG 57.340 36.000 0.00 0.00 0.00 4.96
4339 4645 9.303537 CATAACTTAAGACTACAAAGTAGAGCC 57.696 37.037 10.09 0.91 35.56 4.70
4350 4656 6.147164 TGCAGCACAACATAACTTAAGACTAC 59.853 38.462 10.09 0.00 0.00 2.73
4889 5195 8.935844 TGAACAACAACATTACTTAGCTATCAG 58.064 33.333 0.00 0.00 0.00 2.90
4895 5201 7.414436 TGTTCTGAACAACAACATTACTTAGC 58.586 34.615 20.14 0.00 38.72 3.09
4908 5214 9.577003 CGTAGTTTAATAACTGTTCTGAACAAC 57.423 33.333 22.25 14.96 44.22 3.32
5001 5307 3.788227 AAGCATTGGTCCACAAGAGTA 57.212 42.857 0.00 0.00 43.48 2.59
5004 5310 2.375174 AGGTAAGCATTGGTCCACAAGA 59.625 45.455 0.00 0.00 43.48 3.02
5006 5312 2.969821 AGGTAAGCATTGGTCCACAA 57.030 45.000 0.00 0.00 44.54 3.33
5065 5371 5.643379 ACCAATATTGTTGCTGATCGTTT 57.357 34.783 14.25 0.00 0.00 3.60
5118 5424 9.559958 AAAAACATTCAGAAAGATTATAGCACG 57.440 29.630 0.00 0.00 0.00 5.34
5604 5913 2.093658 GGGACTTCAATTCGAGGCAGTA 60.094 50.000 0.00 0.00 0.00 2.74
5650 5959 3.611113 CGTCTGTACAGGGAATAAACACG 59.389 47.826 22.48 16.46 0.00 4.49
5731 6040 0.327924 CATTGGGGGCTGTAGTGACA 59.672 55.000 0.00 0.00 0.00 3.58
5917 6227 8.105197 CCACATTCATCTCCCTGATAATGATTA 58.895 37.037 0.00 0.00 34.31 1.75
5926 6236 2.435805 GCTACCACATTCATCTCCCTGA 59.564 50.000 0.00 0.00 0.00 3.86
5962 6272 1.938585 ATTTCACCGACAGAGGAGGA 58.061 50.000 0.00 0.00 34.73 3.71
6050 6363 3.256704 AGGGGAAGATGTTAACTCACCA 58.743 45.455 14.42 0.00 0.00 4.17
6067 6380 2.290896 TGTTCTGGTTGCAATAGAGGGG 60.291 50.000 0.59 0.00 0.00 4.79
6212 6525 2.111384 AGATGATGTCAGCTTACCGGT 58.889 47.619 13.98 13.98 40.00 5.28
6248 6561 6.952773 TGCAATCTTACTTTTTGTACACCT 57.047 33.333 0.00 0.00 0.00 4.00
6274 6587 1.884579 AGAATCAGGTTTGTGCTGCTG 59.115 47.619 0.00 0.00 0.00 4.41
6302 6615 3.645884 CCTTCATGACAAGCAAAACCAG 58.354 45.455 0.00 0.00 0.00 4.00
6311 6624 1.522668 TCCGTTGCCTTCATGACAAG 58.477 50.000 0.00 0.00 0.00 3.16
6320 6633 0.602905 CGAGGAAGTTCCGTTGCCTT 60.603 55.000 16.31 0.00 42.75 4.35
6358 6671 6.225981 ACACACTTGCTATCATATCACTCA 57.774 37.500 0.00 0.00 0.00 3.41
6386 6699 1.645034 CGCAGGTTCATGTCTTCGAT 58.355 50.000 0.00 0.00 0.00 3.59
6404 6717 0.531200 AGTTCTAGAGGAAACCCGCG 59.469 55.000 0.00 0.00 35.51 6.46
6725 7039 0.392706 TGTGCACAGATCGAACCTGT 59.607 50.000 17.42 15.43 44.92 4.00
6759 7073 7.521423 CCAAGAGGATAATTTTCACACGTGAAA 60.521 37.037 25.01 18.86 46.20 2.69
6761 7075 5.411361 CCAAGAGGATAATTTTCACACGTGA 59.589 40.000 25.01 0.00 36.89 4.35
6762 7076 5.411361 TCCAAGAGGATAATTTTCACACGTG 59.589 40.000 15.48 15.48 39.61 4.49
6763 7077 5.556915 TCCAAGAGGATAATTTTCACACGT 58.443 37.500 0.00 0.00 39.61 4.49
6764 7078 6.111768 CTCCAAGAGGATAATTTTCACACG 57.888 41.667 0.00 0.00 44.70 4.49
6782 7096 0.400213 ATCCAAGACAACGCCTCCAA 59.600 50.000 0.00 0.00 0.00 3.53
6784 7098 1.648467 GCATCCAAGACAACGCCTCC 61.648 60.000 0.00 0.00 0.00 4.30
6786 7100 1.073025 TGCATCCAAGACAACGCCT 59.927 52.632 0.00 0.00 0.00 5.52
6787 7101 1.210155 GTGCATCCAAGACAACGCC 59.790 57.895 0.00 0.00 0.00 5.68
6789 7103 0.948623 TCGGTGCATCCAAGACAACG 60.949 55.000 0.00 0.00 45.57 4.10
6790 7104 1.453155 ATCGGTGCATCCAAGACAAC 58.547 50.000 0.00 0.00 35.57 3.32
6791 7105 3.342377 TTATCGGTGCATCCAAGACAA 57.658 42.857 0.00 0.00 35.57 3.18
6792 7106 3.205338 CATTATCGGTGCATCCAAGACA 58.795 45.455 0.00 0.00 35.57 3.41
6793 7107 2.549754 CCATTATCGGTGCATCCAAGAC 59.450 50.000 0.00 0.00 35.57 3.01
6794 7108 2.172505 ACCATTATCGGTGCATCCAAGA 59.827 45.455 0.00 0.00 38.07 3.02
6809 7124 4.252073 GCCATGAAAACATGCAACCATTA 58.748 39.130 0.00 0.00 0.00 1.90
6816 7131 0.109827 CGACGCCATGAAAACATGCA 60.110 50.000 0.00 0.00 0.00 3.96
6875 7190 3.966543 CCACACCTGTCCCACCCC 61.967 72.222 0.00 0.00 0.00 4.95
6876 7191 3.175710 ACCACACCTGTCCCACCC 61.176 66.667 0.00 0.00 0.00 4.61
6904 7219 1.797211 GATCTGGGTCGCTCCGGTAG 61.797 65.000 0.00 0.00 37.00 3.18
6906 7221 3.148279 GATCTGGGTCGCTCCGGT 61.148 66.667 0.00 0.00 37.00 5.28
6920 7239 6.750148 AGACAGGTTCGATAATAAGTGGATC 58.250 40.000 0.00 0.00 0.00 3.36
6932 7251 8.095169 ACATTAAAGTAAGAAGACAGGTTCGAT 58.905 33.333 0.00 0.00 0.00 3.59
6936 7255 7.255486 GCCAACATTAAAGTAAGAAGACAGGTT 60.255 37.037 0.00 0.00 0.00 3.50
6947 7266 3.829601 CACCCCTGCCAACATTAAAGTAA 59.170 43.478 0.00 0.00 0.00 2.24
6950 7270 2.231235 GTCACCCCTGCCAACATTAAAG 59.769 50.000 0.00 0.00 0.00 1.85
6961 7281 1.144057 CTATGACCGTCACCCCTGC 59.856 63.158 2.57 0.00 0.00 4.85
6986 7307 1.072965 CCATGGGAGATGTCCTAAGGC 59.927 57.143 9.08 0.00 43.36 4.35
7002 7323 4.333649 CAGTCTACCAAGCATACAACCATG 59.666 45.833 0.00 0.00 0.00 3.66
7013 7334 2.168521 TCTATGTGGCAGTCTACCAAGC 59.831 50.000 0.00 0.00 39.39 4.01
7014 7335 4.679373 ATCTATGTGGCAGTCTACCAAG 57.321 45.455 0.00 0.00 39.39 3.61
7015 7336 5.435686 AAATCTATGTGGCAGTCTACCAA 57.564 39.130 0.00 0.00 39.39 3.67
7016 7337 5.435686 AAAATCTATGTGGCAGTCTACCA 57.564 39.130 0.00 0.00 33.84 3.25
7056 7377 2.713708 ACCTTGCCCTCTCTCTTCTTTT 59.286 45.455 0.00 0.00 0.00 2.27
7060 7381 1.625818 TCAACCTTGCCCTCTCTCTTC 59.374 52.381 0.00 0.00 0.00 2.87
7061 7382 1.734655 TCAACCTTGCCCTCTCTCTT 58.265 50.000 0.00 0.00 0.00 2.85
7070 7394 2.029918 GGTTCATGACTTCAACCTTGCC 60.030 50.000 6.30 0.00 37.24 4.52


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.