Multiple sequence alignment - TraesCS5A01G554300

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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 TraesCS5A01G554300 chr5A 100.000 1816 0 0 1 1816 706269547 706271362 0.000000e+00 3354
1 TraesCS5A01G554300 chr5A 100.000 455 0 0 2093 2547 706271639 706272093 0.000000e+00 841
2 TraesCS5A01G554300 chrUn 89.876 1294 48 19 587 1816 29798034 29799308 0.000000e+00 1587
3 TraesCS5A01G554300 chrUn 85.859 297 39 1 1105 1401 29789280 29789573 1.900000e-81 313
4 TraesCS5A01G554300 chrUn 79.476 458 54 25 1137 1575 29818867 29819303 3.210000e-74 289
5 TraesCS5A01G554300 chrUn 82.934 334 39 12 2183 2504 29799441 29799768 4.150000e-73 285
6 TraesCS5A01G554300 chrUn 74.448 724 99 58 989 1659 29990577 29989887 1.520000e-57 233
7 TraesCS5A01G554300 chr4B 89.456 901 46 15 794 1659 667855907 667855021 0.000000e+00 1092
8 TraesCS5A01G554300 chr4B 89.674 368 34 2 2183 2546 667854258 667853891 1.380000e-127 466
9 TraesCS5A01G554300 chr4B 95.536 224 8 1 536 757 667856129 667855906 8.670000e-95 357
10 TraesCS5A01G554300 chr4B 86.833 281 19 6 2 265 667856884 667856605 5.330000e-77 298
11 TraesCS5A01G554300 chr4B 84.783 276 33 4 1129 1404 667859284 667859018 4.180000e-68 268
12 TraesCS5A01G554300 chr4B 83.969 262 38 4 1156 1415 667648848 667649107 5.440000e-62 248
13 TraesCS5A01G554300 chr4B 85.556 180 9 4 346 523 667856576 667856412 3.370000e-39 172
14 TraesCS5A01G554300 chr5B 87.250 800 43 30 857 1631 689340916 689340151 0.000000e+00 857
15 TraesCS5A01G554300 chr5B 95.781 237 8 2 554 788 689341167 689340931 5.140000e-102 381
16 TraesCS5A01G554300 chr5B 77.620 563 76 34 974 1507 689337368 689336827 1.920000e-76 296
17 TraesCS5A01G554300 chr5B 83.099 142 7 8 130 254 689341483 689341342 2.070000e-21 113


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 TraesCS5A01G554300 chr5A 706269547 706272093 2546 False 2097.500000 3354 100.000000 1 2547 2 chr5A.!!$F1 2546
1 TraesCS5A01G554300 chrUn 29798034 29799768 1734 False 936.000000 1587 86.405000 587 2504 2 chrUn.!!$F3 1917
2 TraesCS5A01G554300 chrUn 29989887 29990577 690 True 233.000000 233 74.448000 989 1659 1 chrUn.!!$R1 670
3 TraesCS5A01G554300 chr4B 667853891 667859284 5393 True 442.166667 1092 88.639667 2 2546 6 chr4B.!!$R1 2544
4 TraesCS5A01G554300 chr5B 689336827 689341483 4656 True 411.750000 857 85.937500 130 1631 4 chr5B.!!$R1 1501

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
524 3008 0.037734 TCTAGCTGTGTCCAGGTCGA 59.962 55.0 0.0 0.0 46.14 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 4616 0.373716 AACGATTGATTCTTCGCCGC 59.626 50.0 8.76 0.0 38.91 6.53 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
54 2453 6.309251 TGAAAACGGAAAAAGTGTAAAAGCTG 59.691 34.615 0.00 0.00 0.00 4.24
91 2490 0.039527 CCGAAGCTTCCAAAAACCGG 60.040 55.000 20.62 12.31 0.00 5.28
125 2524 1.153353 ACGAAAGTGCATTACGTGGG 58.847 50.000 11.97 0.00 46.97 4.61
253 2669 4.277921 TGACACACAAGCTTTGCATATTCA 59.722 37.500 0.00 0.00 0.00 2.57
254 2670 5.047872 TGACACACAAGCTTTGCATATTCAT 60.048 36.000 0.00 0.00 0.00 2.57
255 2671 5.165676 ACACACAAGCTTTGCATATTCATG 58.834 37.500 0.00 0.00 35.07 3.07
256 2672 5.047872 ACACACAAGCTTTGCATATTCATGA 60.048 36.000 0.00 0.00 33.67 3.07
257 2673 5.515270 CACACAAGCTTTGCATATTCATGAG 59.485 40.000 0.00 0.00 33.67 2.90
258 2674 5.416639 ACACAAGCTTTGCATATTCATGAGA 59.583 36.000 0.00 0.00 33.67 3.27
259 2675 5.971792 CACAAGCTTTGCATATTCATGAGAG 59.028 40.000 0.00 0.00 33.67 3.20
260 2676 5.884232 ACAAGCTTTGCATATTCATGAGAGA 59.116 36.000 0.00 0.00 33.67 3.10
261 2677 6.376299 ACAAGCTTTGCATATTCATGAGAGAA 59.624 34.615 0.00 0.00 33.67 2.87
262 2678 6.621316 AGCTTTGCATATTCATGAGAGAAG 57.379 37.500 0.00 0.00 33.67 2.85
263 2679 6.354938 AGCTTTGCATATTCATGAGAGAAGA 58.645 36.000 0.00 0.00 33.67 2.87
264 2680 6.260493 AGCTTTGCATATTCATGAGAGAAGAC 59.740 38.462 0.00 0.00 33.67 3.01
265 2681 6.513066 GCTTTGCATATTCATGAGAGAAGACC 60.513 42.308 0.00 0.00 33.67 3.85
266 2682 5.619132 TGCATATTCATGAGAGAAGACCA 57.381 39.130 0.00 0.00 33.67 4.02
268 2684 6.417258 TGCATATTCATGAGAGAAGACCAAA 58.583 36.000 0.00 0.00 33.67 3.28
270 2686 7.558807 TGCATATTCATGAGAGAAGACCAAAAT 59.441 33.333 0.00 0.00 33.67 1.82
276 2693 7.453393 TCATGAGAGAAGACCAAAATAACAGT 58.547 34.615 0.00 0.00 0.00 3.55
277 2694 8.593679 TCATGAGAGAAGACCAAAATAACAGTA 58.406 33.333 0.00 0.00 0.00 2.74
278 2695 8.660373 CATGAGAGAAGACCAAAATAACAGTAC 58.340 37.037 0.00 0.00 0.00 2.73
279 2696 6.866770 TGAGAGAAGACCAAAATAACAGTACG 59.133 38.462 0.00 0.00 0.00 3.67
282 2699 5.178809 AGAAGACCAAAATAACAGTACGTGC 59.821 40.000 0.00 0.00 0.00 5.34
283 2700 3.749609 AGACCAAAATAACAGTACGTGCC 59.250 43.478 0.00 0.00 0.00 5.01
287 2704 4.394920 CCAAAATAACAGTACGTGCCTCAT 59.605 41.667 0.00 0.00 0.00 2.90
293 2710 2.028476 ACAGTACGTGCCTCATTGCTTA 60.028 45.455 0.00 0.00 0.00 3.09
297 2714 4.700213 AGTACGTGCCTCATTGCTTATTTT 59.300 37.500 0.00 0.00 0.00 1.82
298 2715 3.836949 ACGTGCCTCATTGCTTATTTTG 58.163 40.909 0.00 0.00 0.00 2.44
302 2719 5.164061 CGTGCCTCATTGCTTATTTTGTTTC 60.164 40.000 0.00 0.00 0.00 2.78
305 2722 5.578336 GCCTCATTGCTTATTTTGTTTCCTC 59.422 40.000 0.00 0.00 0.00 3.71
307 2724 7.325694 CCTCATTGCTTATTTTGTTTCCTCAT 58.674 34.615 0.00 0.00 0.00 2.90
308 2725 8.469200 CCTCATTGCTTATTTTGTTTCCTCATA 58.531 33.333 0.00 0.00 0.00 2.15
319 2736 8.836268 TTTTGTTTCCTCATATAACAGTACGT 57.164 30.769 0.00 0.00 33.74 3.57
320 2737 7.821595 TTGTTTCCTCATATAACAGTACGTG 57.178 36.000 0.00 0.00 33.74 4.49
321 2738 5.808540 TGTTTCCTCATATAACAGTACGTGC 59.191 40.000 0.00 0.00 0.00 5.34
322 2739 5.585820 TTCCTCATATAACAGTACGTGCA 57.414 39.130 6.38 0.00 0.00 4.57
323 2740 5.183014 TCCTCATATAACAGTACGTGCAG 57.817 43.478 6.38 0.00 0.00 4.41
324 2741 4.643334 TCCTCATATAACAGTACGTGCAGT 59.357 41.667 6.38 0.05 0.00 4.40
325 2742 5.126545 TCCTCATATAACAGTACGTGCAGTT 59.873 40.000 17.56 17.56 0.00 3.16
326 2743 5.459107 CCTCATATAACAGTACGTGCAGTTC 59.541 44.000 17.01 0.00 0.00 3.01
327 2744 5.956642 TCATATAACAGTACGTGCAGTTCA 58.043 37.500 17.01 7.92 0.00 3.18
328 2745 6.391537 TCATATAACAGTACGTGCAGTTCAA 58.608 36.000 17.01 7.90 0.00 2.69
329 2746 4.985044 ATAACAGTACGTGCAGTTCAAC 57.015 40.909 17.01 0.00 0.00 3.18
330 2747 1.578583 ACAGTACGTGCAGTTCAACC 58.421 50.000 6.38 0.00 0.00 3.77
331 2748 0.865769 CAGTACGTGCAGTTCAACCC 59.134 55.000 6.38 0.00 0.00 4.11
332 2749 0.466543 AGTACGTGCAGTTCAACCCA 59.533 50.000 6.38 0.00 0.00 4.51
333 2750 0.865769 GTACGTGCAGTTCAACCCAG 59.134 55.000 0.00 0.00 0.00 4.45
334 2751 0.250124 TACGTGCAGTTCAACCCAGG 60.250 55.000 0.00 0.00 0.00 4.45
335 2752 1.525995 CGTGCAGTTCAACCCAGGT 60.526 57.895 0.00 0.00 0.00 4.00
336 2753 1.785041 CGTGCAGTTCAACCCAGGTG 61.785 60.000 0.00 0.00 0.00 4.00
337 2754 0.751643 GTGCAGTTCAACCCAGGTGT 60.752 55.000 0.00 0.00 0.00 4.16
338 2755 0.840617 TGCAGTTCAACCCAGGTGTA 59.159 50.000 0.00 0.00 0.00 2.90
339 2756 1.423541 TGCAGTTCAACCCAGGTGTAT 59.576 47.619 0.00 0.00 0.00 2.29
340 2757 2.640332 TGCAGTTCAACCCAGGTGTATA 59.360 45.455 0.00 0.00 0.00 1.47
341 2758 3.265737 TGCAGTTCAACCCAGGTGTATAT 59.734 43.478 0.00 0.00 0.00 0.86
342 2759 3.627577 GCAGTTCAACCCAGGTGTATATG 59.372 47.826 0.00 0.00 0.00 1.78
343 2760 4.843728 CAGTTCAACCCAGGTGTATATGT 58.156 43.478 0.00 0.00 0.00 2.29
344 2761 4.635765 CAGTTCAACCCAGGTGTATATGTG 59.364 45.833 0.00 0.00 0.00 3.21
365 2782 1.120530 ATCCCGCCACTTCTATCGTT 58.879 50.000 0.00 0.00 0.00 3.85
367 2784 1.679680 TCCCGCCACTTCTATCGTTAG 59.320 52.381 0.00 0.00 0.00 2.34
368 2785 1.269621 CCCGCCACTTCTATCGTTAGG 60.270 57.143 0.80 0.00 0.00 2.69
378 2860 9.064706 CCACTTCTATCGTTAGGAAAGACTATA 57.935 37.037 8.27 0.00 0.00 1.31
420 2904 5.106237 ACGTATCTCTCACGCTCTTTACTTT 60.106 40.000 0.00 0.00 43.10 2.66
465 2949 0.898320 AGAGACTAGCGCACCACAAT 59.102 50.000 11.47 0.00 0.00 2.71
467 2951 2.159226 AGAGACTAGCGCACCACAATAC 60.159 50.000 11.47 0.00 0.00 1.89
468 2952 1.825474 AGACTAGCGCACCACAATACT 59.175 47.619 11.47 0.00 0.00 2.12
469 2953 3.021695 AGACTAGCGCACCACAATACTA 58.978 45.455 11.47 0.00 0.00 1.82
470 2954 3.114065 GACTAGCGCACCACAATACTAC 58.886 50.000 11.47 0.00 0.00 2.73
471 2955 2.494471 ACTAGCGCACCACAATACTACA 59.506 45.455 11.47 0.00 0.00 2.74
472 2956 2.691409 AGCGCACCACAATACTACAT 57.309 45.000 11.47 0.00 0.00 2.29
473 2957 3.812156 AGCGCACCACAATACTACATA 57.188 42.857 11.47 0.00 0.00 2.29
474 2958 4.336889 AGCGCACCACAATACTACATAT 57.663 40.909 11.47 0.00 0.00 1.78
475 2959 5.462530 AGCGCACCACAATACTACATATA 57.537 39.130 11.47 0.00 0.00 0.86
476 2960 5.227908 AGCGCACCACAATACTACATATAC 58.772 41.667 11.47 0.00 0.00 1.47
477 2961 4.387862 GCGCACCACAATACTACATATACC 59.612 45.833 0.30 0.00 0.00 2.73
491 2975 8.379428 ACTACATATACCCATGCTGATAATCA 57.621 34.615 0.00 0.00 0.00 2.57
509 2993 8.088365 TGATAATCATACACCCGTCAATTCTAG 58.912 37.037 0.00 0.00 0.00 2.43
523 3007 0.888619 TTCTAGCTGTGTCCAGGTCG 59.111 55.000 0.00 0.00 46.14 4.79
524 3008 0.037734 TCTAGCTGTGTCCAGGTCGA 59.962 55.000 0.00 0.00 46.14 4.20
525 3009 0.888619 CTAGCTGTGTCCAGGTCGAA 59.111 55.000 0.00 0.00 46.14 3.71
526 3010 0.888619 TAGCTGTGTCCAGGTCGAAG 59.111 55.000 0.00 0.00 46.14 3.79
527 3011 1.115930 AGCTGTGTCCAGGTCGAAGT 61.116 55.000 0.00 0.00 46.14 3.01
528 3012 0.601558 GCTGTGTCCAGGTCGAAGTA 59.398 55.000 0.00 0.00 39.22 2.24
529 3013 1.000506 GCTGTGTCCAGGTCGAAGTAA 59.999 52.381 0.00 0.00 39.22 2.24
532 3016 2.035449 TGTGTCCAGGTCGAAGTAACAG 59.965 50.000 0.00 0.00 0.00 3.16
533 3017 2.295349 GTGTCCAGGTCGAAGTAACAGA 59.705 50.000 0.00 0.00 0.00 3.41
534 3018 2.295349 TGTCCAGGTCGAAGTAACAGAC 59.705 50.000 0.00 0.00 0.00 3.51
538 3292 0.883833 GGTCGAAGTAACAGACGGGA 59.116 55.000 0.00 0.00 35.87 5.14
719 3496 1.197721 GTTGAATGCAGGACGTCCAAG 59.802 52.381 35.00 26.60 38.89 3.61
789 3566 2.680312 TTCAGTGCATGCTCTAGGTC 57.320 50.000 21.05 2.49 0.00 3.85
850 3627 1.605712 CGATTCATTAGACGGCTCCCC 60.606 57.143 0.00 0.00 0.00 4.81
878 3676 1.191647 GACGTCGTCGCATTTCACTTT 59.808 47.619 10.05 0.00 41.18 2.66
964 3772 1.440060 CATGGCATGCACATGGACC 59.560 57.895 27.87 9.53 41.46 4.46
965 3773 2.122797 ATGGCATGCACATGGACCG 61.123 57.895 21.36 0.00 39.16 4.79
966 3774 2.438254 GGCATGCACATGGACCGA 60.438 61.111 21.36 0.00 39.16 4.69
967 3775 1.825191 GGCATGCACATGGACCGAT 60.825 57.895 21.36 0.00 39.16 4.18
968 3776 1.357690 GCATGCACATGGACCGATG 59.642 57.895 14.21 3.26 39.16 3.84
969 3777 2.027325 CATGCACATGGACCGATGG 58.973 57.895 2.56 0.00 35.24 3.51
1662 4558 2.143122 GATCGGCTGAGTTGTGTTCAA 58.857 47.619 0.00 0.00 0.00 2.69
1687 4583 2.557452 CCAAACCAAACTGCCCCTATCT 60.557 50.000 0.00 0.00 0.00 1.98
1703 4599 7.724061 TGCCCCTATCTTAGAATTGTTAAATCC 59.276 37.037 0.00 0.00 0.00 3.01
1720 4616 0.821517 TCCAGTGGTGCGGTATGTAG 59.178 55.000 9.54 0.00 0.00 2.74
1735 4631 2.309528 TGTAGCGGCGAAGAATCAAT 57.690 45.000 12.98 0.00 0.00 2.57
1744 4640 3.544244 GGCGAAGAATCAATCGTTAGTGC 60.544 47.826 9.52 0.00 41.01 4.40
1746 4642 4.201724 GCGAAGAATCAATCGTTAGTGCTT 60.202 41.667 9.52 0.00 41.01 3.91
1761 4666 1.134946 GTGCTTTTGGTGCAGTGACTT 59.865 47.619 0.00 0.00 41.41 3.01
1762 4667 1.824230 TGCTTTTGGTGCAGTGACTTT 59.176 42.857 0.00 0.00 35.31 2.66
1763 4668 3.020274 TGCTTTTGGTGCAGTGACTTTA 58.980 40.909 0.00 0.00 35.31 1.85
1764 4669 3.066621 TGCTTTTGGTGCAGTGACTTTAG 59.933 43.478 0.00 0.00 35.31 1.85
1769 4674 5.748670 TTGGTGCAGTGACTTTAGGTATA 57.251 39.130 0.00 0.00 0.00 1.47
1776 4681 5.450965 GCAGTGACTTTAGGTATAAGCGGTA 60.451 44.000 0.00 0.00 0.00 4.02
1791 4696 5.947228 AAGCGGTATGAATGGAATACATG 57.053 39.130 0.00 0.00 40.44 3.21
2115 5020 3.689649 ACCGCGATAAAATTTCTGCTCTT 59.310 39.130 8.23 0.00 0.00 2.85
2163 5070 7.696035 TGTTGCTATATGCTTTGTAAACAATCG 59.304 33.333 0.00 0.00 43.37 3.34
2204 5903 6.194463 GCTCAAAAGAATGTTTTTGGCTTTC 58.806 36.000 12.41 0.00 0.00 2.62
2316 6015 7.624549 TGCTATCCTATTTCAAGTCAGTTTCT 58.375 34.615 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 2442 4.911514 TTTTCTGGACCAGCTTTTACAC 57.088 40.909 17.33 0.00 0.00 2.90
46 2445 6.780522 ACCTTATTTTTCTGGACCAGCTTTTA 59.219 34.615 17.33 0.00 0.00 1.52
51 2450 3.444034 GGACCTTATTTTTCTGGACCAGC 59.556 47.826 17.33 0.00 35.17 4.85
54 2453 3.946606 TCGGACCTTATTTTTCTGGACC 58.053 45.455 0.00 0.00 0.00 4.46
96 2495 3.626924 ACTTTCGTGGGAGGCGCT 61.627 61.111 7.64 0.00 0.00 5.92
107 2506 0.179200 GCCCACGTAATGCACTTTCG 60.179 55.000 0.00 0.00 34.23 3.46
120 2519 2.670251 TAGTTTTGCCGGCCCACG 60.670 61.111 26.77 0.00 43.80 4.94
125 2524 1.374343 GCTAGGGTAGTTTTGCCGGC 61.374 60.000 22.73 22.73 0.00 6.13
253 2669 7.545965 CGTACTGTTATTTTGGTCTTCTCTCAT 59.454 37.037 0.00 0.00 0.00 2.90
254 2670 6.866770 CGTACTGTTATTTTGGTCTTCTCTCA 59.133 38.462 0.00 0.00 0.00 3.27
255 2671 6.867293 ACGTACTGTTATTTTGGTCTTCTCTC 59.133 38.462 0.00 0.00 0.00 3.20
256 2672 6.645415 CACGTACTGTTATTTTGGTCTTCTCT 59.355 38.462 0.00 0.00 0.00 3.10
257 2673 6.617953 GCACGTACTGTTATTTTGGTCTTCTC 60.618 42.308 0.00 0.00 0.00 2.87
258 2674 5.178809 GCACGTACTGTTATTTTGGTCTTCT 59.821 40.000 0.00 0.00 0.00 2.85
259 2675 5.379827 GCACGTACTGTTATTTTGGTCTTC 58.620 41.667 0.00 0.00 0.00 2.87
260 2676 4.214758 GGCACGTACTGTTATTTTGGTCTT 59.785 41.667 0.00 0.00 0.00 3.01
261 2677 3.749609 GGCACGTACTGTTATTTTGGTCT 59.250 43.478 0.00 0.00 0.00 3.85
262 2678 3.749609 AGGCACGTACTGTTATTTTGGTC 59.250 43.478 0.00 0.00 0.00 4.02
263 2679 3.746940 AGGCACGTACTGTTATTTTGGT 58.253 40.909 0.00 0.00 0.00 3.67
264 2680 3.749088 TGAGGCACGTACTGTTATTTTGG 59.251 43.478 0.00 0.00 0.00 3.28
265 2681 5.545658 ATGAGGCACGTACTGTTATTTTG 57.454 39.130 0.00 0.00 0.00 2.44
266 2682 5.619086 GCAATGAGGCACGTACTGTTATTTT 60.619 40.000 0.00 0.00 0.00 1.82
268 2684 3.374058 GCAATGAGGCACGTACTGTTATT 59.626 43.478 0.00 0.00 0.00 1.40
270 2686 2.028476 AGCAATGAGGCACGTACTGTTA 60.028 45.455 0.00 0.00 35.83 2.41
273 2690 1.442769 AAGCAATGAGGCACGTACTG 58.557 50.000 0.00 0.00 35.83 2.74
276 2693 4.457603 ACAAAATAAGCAATGAGGCACGTA 59.542 37.500 0.00 0.00 35.83 3.57
277 2694 3.255642 ACAAAATAAGCAATGAGGCACGT 59.744 39.130 0.00 0.00 35.83 4.49
278 2695 3.836949 ACAAAATAAGCAATGAGGCACG 58.163 40.909 0.00 0.00 35.83 5.34
279 2696 5.120674 GGAAACAAAATAAGCAATGAGGCAC 59.879 40.000 0.00 0.00 35.83 5.01
282 2699 6.690530 TGAGGAAACAAAATAAGCAATGAGG 58.309 36.000 0.00 0.00 0.00 3.86
293 2710 9.444600 ACGTACTGTTATATGAGGAAACAAAAT 57.555 29.630 0.00 0.00 33.05 1.82
297 2714 5.808540 GCACGTACTGTTATATGAGGAAACA 59.191 40.000 0.00 0.00 0.00 2.83
298 2715 5.808540 TGCACGTACTGTTATATGAGGAAAC 59.191 40.000 0.00 0.00 0.00 2.78
302 2719 4.933330 ACTGCACGTACTGTTATATGAGG 58.067 43.478 0.00 0.00 0.00 3.86
305 2722 6.455113 GGTTGAACTGCACGTACTGTTATATG 60.455 42.308 10.61 0.00 32.60 1.78
307 2724 4.925054 GGTTGAACTGCACGTACTGTTATA 59.075 41.667 10.61 1.89 32.60 0.98
308 2725 3.744426 GGTTGAACTGCACGTACTGTTAT 59.256 43.478 10.61 0.00 32.60 1.89
309 2726 3.125316 GGTTGAACTGCACGTACTGTTA 58.875 45.455 10.61 0.00 32.60 2.41
312 2729 0.865769 GGGTTGAACTGCACGTACTG 59.134 55.000 0.00 0.00 0.00 2.74
313 2730 0.466543 TGGGTTGAACTGCACGTACT 59.533 50.000 0.00 0.00 0.00 2.73
314 2731 0.865769 CTGGGTTGAACTGCACGTAC 59.134 55.000 0.00 0.00 0.00 3.67
315 2732 0.250124 CCTGGGTTGAACTGCACGTA 60.250 55.000 0.00 0.00 0.00 3.57
316 2733 1.525995 CCTGGGTTGAACTGCACGT 60.526 57.895 0.00 0.00 0.00 4.49
317 2734 1.525995 ACCTGGGTTGAACTGCACG 60.526 57.895 0.00 0.00 0.00 5.34
318 2735 0.751643 ACACCTGGGTTGAACTGCAC 60.752 55.000 0.00 0.00 0.00 4.57
319 2736 0.840617 TACACCTGGGTTGAACTGCA 59.159 50.000 0.00 0.00 0.00 4.41
320 2737 2.200373 ATACACCTGGGTTGAACTGC 57.800 50.000 0.00 0.00 0.00 4.40
321 2738 4.635765 CACATATACACCTGGGTTGAACTG 59.364 45.833 0.00 0.00 0.00 3.16
322 2739 4.288626 ACACATATACACCTGGGTTGAACT 59.711 41.667 0.00 0.00 0.00 3.01
323 2740 4.585879 ACACATATACACCTGGGTTGAAC 58.414 43.478 0.00 0.00 0.00 3.18
324 2741 4.919774 ACACATATACACCTGGGTTGAA 57.080 40.909 0.00 0.00 0.00 2.69
325 2742 5.071250 GGATACACATATACACCTGGGTTGA 59.929 44.000 0.00 0.00 30.16 3.18
326 2743 5.305585 GGATACACATATACACCTGGGTTG 58.694 45.833 0.00 0.00 30.16 3.77
327 2744 4.349930 GGGATACACATATACACCTGGGTT 59.650 45.833 0.00 0.00 39.74 4.11
328 2745 3.908103 GGGATACACATATACACCTGGGT 59.092 47.826 0.00 0.00 39.74 4.51
329 2746 3.056107 CGGGATACACATATACACCTGGG 60.056 52.174 0.00 0.00 39.74 4.45
330 2747 3.616560 GCGGGATACACATATACACCTGG 60.617 52.174 0.00 0.00 39.74 4.45
331 2748 3.585862 GCGGGATACACATATACACCTG 58.414 50.000 0.00 0.00 39.74 4.00
332 2749 2.565834 GGCGGGATACACATATACACCT 59.434 50.000 0.00 0.00 39.74 4.00
333 2750 2.300723 TGGCGGGATACACATATACACC 59.699 50.000 0.00 0.00 39.74 4.16
334 2751 3.006537 AGTGGCGGGATACACATATACAC 59.993 47.826 0.00 0.00 39.99 2.90
335 2752 3.236047 AGTGGCGGGATACACATATACA 58.764 45.455 0.00 0.00 39.99 2.29
336 2753 3.955650 AGTGGCGGGATACACATATAC 57.044 47.619 0.00 0.00 39.99 1.47
337 2754 4.157246 AGAAGTGGCGGGATACACATATA 58.843 43.478 0.00 0.00 39.99 0.86
338 2755 2.972713 AGAAGTGGCGGGATACACATAT 59.027 45.455 0.00 0.00 39.99 1.78
339 2756 2.394632 AGAAGTGGCGGGATACACATA 58.605 47.619 0.00 0.00 39.99 2.29
340 2757 1.204146 AGAAGTGGCGGGATACACAT 58.796 50.000 0.00 0.00 39.99 3.21
341 2758 1.855295 TAGAAGTGGCGGGATACACA 58.145 50.000 0.00 0.00 39.99 3.72
342 2759 2.607282 CGATAGAAGTGGCGGGATACAC 60.607 54.545 0.00 0.00 36.54 2.90
343 2760 1.611977 CGATAGAAGTGGCGGGATACA 59.388 52.381 0.00 0.00 39.76 2.29
344 2761 1.612463 ACGATAGAAGTGGCGGGATAC 59.388 52.381 0.00 0.00 41.38 2.24
378 2860 9.862371 GAGATACGTAGATGAATGGATGTATTT 57.138 33.333 0.08 0.00 0.00 1.40
382 2864 6.717084 TGAGAGATACGTAGATGAATGGATGT 59.283 38.462 0.08 0.00 0.00 3.06
397 2879 4.539509 AGTAAAGAGCGTGAGAGATACG 57.460 45.455 0.00 0.00 43.93 3.06
420 2904 5.590663 TGGTCGTATTATTATTGCAAGCCAA 59.409 36.000 4.94 0.00 37.94 4.52
465 2949 9.487442 TGATTATCAGCATGGGTATATGTAGTA 57.513 33.333 0.00 0.00 36.16 1.82
469 2953 8.771286 TGTATGATTATCAGCATGGGTATATGT 58.229 33.333 0.29 0.00 36.16 2.29
470 2954 9.049523 GTGTATGATTATCAGCATGGGTATATG 57.950 37.037 0.29 0.00 36.16 1.78
471 2955 8.213679 GGTGTATGATTATCAGCATGGGTATAT 58.786 37.037 0.29 0.00 36.16 0.86
472 2956 7.365563 GGGTGTATGATTATCAGCATGGGTATA 60.366 40.741 0.29 0.00 36.16 1.47
473 2957 6.418101 GGTGTATGATTATCAGCATGGGTAT 58.582 40.000 0.29 0.00 36.16 2.73
474 2958 5.280470 GGGTGTATGATTATCAGCATGGGTA 60.280 44.000 0.29 0.00 36.16 3.69
475 2959 4.507335 GGGTGTATGATTATCAGCATGGGT 60.507 45.833 0.29 0.00 36.16 4.51
476 2960 4.012374 GGGTGTATGATTATCAGCATGGG 58.988 47.826 0.29 0.00 36.16 4.00
477 2961 3.686241 CGGGTGTATGATTATCAGCATGG 59.314 47.826 0.29 0.00 36.16 3.66
491 2975 3.451178 ACAGCTAGAATTGACGGGTGTAT 59.549 43.478 0.00 0.00 36.96 2.29
509 2993 0.601558 TACTTCGACCTGGACACAGC 59.398 55.000 0.00 0.00 43.53 4.40
523 3007 3.678548 GTGATGTTCCCGTCTGTTACTTC 59.321 47.826 0.00 0.00 0.00 3.01
524 3008 3.660865 GTGATGTTCCCGTCTGTTACTT 58.339 45.455 0.00 0.00 0.00 2.24
525 3009 2.352421 CGTGATGTTCCCGTCTGTTACT 60.352 50.000 0.00 0.00 0.00 2.24
526 3010 1.990563 CGTGATGTTCCCGTCTGTTAC 59.009 52.381 0.00 0.00 0.00 2.50
527 3011 1.067425 CCGTGATGTTCCCGTCTGTTA 60.067 52.381 0.00 0.00 0.00 2.41
528 3012 0.320421 CCGTGATGTTCCCGTCTGTT 60.320 55.000 0.00 0.00 0.00 3.16
529 3013 1.292223 CCGTGATGTTCCCGTCTGT 59.708 57.895 0.00 0.00 0.00 3.41
532 3016 1.740296 CCACCGTGATGTTCCCGTC 60.740 63.158 0.00 0.00 0.00 4.79
533 3017 2.345991 CCACCGTGATGTTCCCGT 59.654 61.111 0.00 0.00 0.00 5.28
534 3018 2.032634 CACCACCGTGATGTTCCCG 61.033 63.158 0.00 0.00 43.14 5.14
547 3301 2.275318 GCTAGTCTCTTGCATCACCAC 58.725 52.381 0.00 0.00 32.87 4.16
548 3302 1.134995 CGCTAGTCTCTTGCATCACCA 60.135 52.381 0.00 0.00 32.19 4.17
615 3369 0.793478 CTAGCGGACGACACGACTTG 60.793 60.000 0.00 0.00 0.00 3.16
719 3496 1.862602 GAATGGTTGACGGGCACACC 61.863 60.000 7.89 7.89 0.00 4.16
789 3566 3.087031 TCCGTTGAACACTCTACCCTAG 58.913 50.000 0.00 0.00 0.00 3.02
878 3676 7.272978 AGCAGGTAAGCGATTAAAGAAAGATA 58.727 34.615 0.00 0.00 40.15 1.98
1662 4558 1.047801 GGGCAGTTTGGTTTGGTCAT 58.952 50.000 0.00 0.00 0.00 3.06
1687 4583 6.348950 CGCACCACTGGATTTAACAATTCTAA 60.349 38.462 0.71 0.00 0.00 2.10
1703 4599 1.145759 CGCTACATACCGCACCACTG 61.146 60.000 0.00 0.00 0.00 3.66
1720 4616 0.373716 AACGATTGATTCTTCGCCGC 59.626 50.000 8.76 0.00 38.91 6.53
1735 4631 1.601903 CTGCACCAAAAGCACTAACGA 59.398 47.619 0.00 0.00 37.02 3.85
1744 4640 3.632145 ACCTAAAGTCACTGCACCAAAAG 59.368 43.478 0.00 0.00 0.00 2.27
1746 4642 3.290948 ACCTAAAGTCACTGCACCAAA 57.709 42.857 0.00 0.00 0.00 3.28
1761 4666 6.921486 TCCATTCATACCGCTTATACCTAA 57.079 37.500 0.00 0.00 0.00 2.69
1762 4667 6.921486 TTCCATTCATACCGCTTATACCTA 57.079 37.500 0.00 0.00 0.00 3.08
1763 4668 5.818678 TTCCATTCATACCGCTTATACCT 57.181 39.130 0.00 0.00 0.00 3.08
1764 4669 7.101054 TGTATTCCATTCATACCGCTTATACC 58.899 38.462 0.00 0.00 0.00 2.73
1769 4674 4.761739 CCATGTATTCCATTCATACCGCTT 59.238 41.667 0.00 0.00 0.00 4.68
1776 4681 6.989155 AGCATTTCCATGTATTCCATTCAT 57.011 33.333 0.00 0.00 32.28 2.57
1791 4696 1.607801 GAGGGCCCACAAGCATTTCC 61.608 60.000 27.56 0.00 0.00 3.13
2122 5027 4.917906 AGCAACAGAGTAGAAATTCCCT 57.082 40.909 0.00 0.00 0.00 4.20
2123 5028 7.095017 GCATATAGCAACAGAGTAGAAATTCCC 60.095 40.741 0.00 0.00 44.79 3.97
2232 5931 4.695455 TGATTGGTCTTGTTTCGAAGATCC 59.305 41.667 0.00 0.00 32.82 3.36


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

AutoCloner maintained by Alex Coulton.