Multiple sequence alignment - TraesCS5D01G127900

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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 TraesCS5D01G127900 chr5D 100.000 6090 0 0 1 6090 199080339 199086428 0.000000e+00 11247.0
1 TraesCS5D01G127900 chr5D 89.881 168 17 0 372 539 241019848 241019681 3.700000e-52 217.0
2 TraesCS5D01G127900 chr5D 85.526 76 7 1 556 631 330709187 330709258 6.550000e-10 76.8
3 TraesCS5D01G127900 chr5A 97.162 4369 100 11 1741 6090 216689802 216694165 0.000000e+00 7360.0
4 TraesCS5D01G127900 chr5A 97.212 1112 26 1 644 1750 216688561 216689672 0.000000e+00 1877.0
5 TraesCS5D01G127900 chr5A 92.761 373 22 2 1 368 216688128 216688500 8.980000e-148 534.0
6 TraesCS5D01G127900 chr5B 97.613 3435 67 12 2658 6089 209635157 209631735 0.000000e+00 5875.0
7 TraesCS5D01G127900 chr5B 95.919 2132 60 16 539 2659 209637355 209635240 0.000000e+00 3430.0
8 TraesCS5D01G127900 chr2B 95.601 3387 124 13 2264 5647 539962180 539965544 0.000000e+00 5406.0
9 TraesCS5D01G127900 chr7D 96.766 1917 49 6 3732 5647 311618775 311620679 0.000000e+00 3184.0
10 TraesCS5D01G127900 chr7D 96.485 1451 35 8 2264 3708 311617339 311618779 0.000000e+00 2383.0
11 TraesCS5D01G127900 chr7D 89.011 182 18 2 357 537 507853581 507853761 2.210000e-54 224.0
12 TraesCS5D01G127900 chr7D 90.683 161 15 0 370 530 404245328 404245488 1.330000e-51 215.0
13 TraesCS5D01G127900 chr3B 96.186 1914 67 5 3735 5647 371039939 371038031 0.000000e+00 3125.0
14 TraesCS5D01G127900 chr3B 96.621 1450 43 5 2264 3712 371041378 371039934 0.000000e+00 2401.0
15 TraesCS5D01G127900 chr3B 97.275 367 9 1 2943 3309 363589381 363589016 6.700000e-174 621.0
16 TraesCS5D01G127900 chr3B 96.109 257 9 1 3455 3711 363589022 363588767 9.440000e-113 418.0
17 TraesCS5D01G127900 chr3B 100.000 59 0 0 3019 3077 279755754 279755812 6.450000e-20 110.0
18 TraesCS5D01G127900 chr3A 96.791 1683 47 6 3966 5647 361576865 361575189 0.000000e+00 2802.0
19 TraesCS5D01G127900 chr6A 96.259 1684 55 7 3966 5647 197861226 197859549 0.000000e+00 2754.0
20 TraesCS5D01G127900 chr4B 95.974 1689 56 9 3961 5647 175308786 175307108 0.000000e+00 2732.0
21 TraesCS5D01G127900 chr4B 95.861 1039 36 6 2264 3300 175310728 175309695 0.000000e+00 1674.0
22 TraesCS5D01G127900 chr4B 95.765 1039 35 7 2264 3300 531338155 531339186 0.000000e+00 1666.0
23 TraesCS5D01G127900 chr4D 97.107 1590 41 4 4059 5647 366045591 366047176 0.000000e+00 2676.0
24 TraesCS5D01G127900 chr4D 87.222 180 23 0 372 551 316527521 316527342 8.000000e-49 206.0
25 TraesCS5D01G127900 chr3D 82.657 271 30 12 374 636 33189549 33189288 2.210000e-54 224.0
26 TraesCS5D01G127900 chr6B 89.474 171 17 1 370 540 217931400 217931569 1.330000e-51 215.0
27 TraesCS5D01G127900 chrUn 89.759 166 17 0 371 536 108810832 108810997 4.780000e-51 213.0
28 TraesCS5D01G127900 chr2D 89.222 167 18 0 364 530 528480864 528481030 6.190000e-50 209.0
29 TraesCS5D01G127900 chr6D 80.303 264 45 4 372 632 461687597 461687856 6.230000e-45 193.0
30 TraesCS5D01G127900 chr6D 84.615 78 8 2 564 637 155842237 155842314 2.350000e-09 75.0
31 TraesCS5D01G127900 chr1D 87.671 73 7 2 559 631 230670286 230670216 3.910000e-12 84.2
32 TraesCS5D01G127900 chr1D 85.526 76 7 2 556 631 47323440 47323511 6.550000e-10 76.8
33 TraesCS5D01G127900 chr2A 86.957 69 8 1 564 631 645956895 645956827 6.550000e-10 76.8
34 TraesCS5D01G127900 chr7A 82.022 89 12 2 552 636 561620732 561620820 8.470000e-09 73.1


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 TraesCS5D01G127900 chr5D 199080339 199086428 6089 False 11247.0 11247 100.000000 1 6090 1 chr5D.!!$F1 6089
1 TraesCS5D01G127900 chr5A 216688128 216694165 6037 False 3257.0 7360 95.711667 1 6090 3 chr5A.!!$F1 6089
2 TraesCS5D01G127900 chr5B 209631735 209637355 5620 True 4652.5 5875 96.766000 539 6089 2 chr5B.!!$R1 5550
3 TraesCS5D01G127900 chr2B 539962180 539965544 3364 False 5406.0 5406 95.601000 2264 5647 1 chr2B.!!$F1 3383
4 TraesCS5D01G127900 chr7D 311617339 311620679 3340 False 2783.5 3184 96.625500 2264 5647 2 chr7D.!!$F3 3383
5 TraesCS5D01G127900 chr3B 371038031 371041378 3347 True 2763.0 3125 96.403500 2264 5647 2 chr3B.!!$R2 3383
6 TraesCS5D01G127900 chr3B 363588767 363589381 614 True 519.5 621 96.692000 2943 3711 2 chr3B.!!$R1 768
7 TraesCS5D01G127900 chr3A 361575189 361576865 1676 True 2802.0 2802 96.791000 3966 5647 1 chr3A.!!$R1 1681
8 TraesCS5D01G127900 chr6A 197859549 197861226 1677 True 2754.0 2754 96.259000 3966 5647 1 chr6A.!!$R1 1681
9 TraesCS5D01G127900 chr4B 175307108 175310728 3620 True 2203.0 2732 95.917500 2264 5647 2 chr4B.!!$R1 3383
10 TraesCS5D01G127900 chr4B 531338155 531339186 1031 False 1666.0 1666 95.765000 2264 3300 1 chr4B.!!$F1 1036
11 TraesCS5D01G127900 chr4D 366045591 366047176 1585 False 2676.0 2676 97.107000 4059 5647 1 chr4D.!!$F1 1588

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
82 83 0.460987 GTGAGGAAGGAGATGCGGTG 60.461 60.000 0.00 0.00 0.00 4.94 F
154 155 1.341383 CCCTCACCTGATTTCCAAGGG 60.341 57.143 0.00 0.00 34.00 3.95 F
1350 1365 2.035940 ACCTCCGCTTCCGTCTCT 59.964 61.111 0.00 0.00 0.00 3.10 F
2430 2590 1.270550 ACAGCAAGCAAGCAATACCAC 59.729 47.619 3.19 0.00 36.85 4.16 F
3629 4023 1.268899 TCCGTTTCGAAGAGGTCTCAC 59.731 52.381 17.03 2.32 38.43 3.51 F
4529 5218 0.761323 TTGTGACGACTCAAGGGGGA 60.761 55.000 0.00 0.00 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 1365 0.755698 GACGCCATGGAGAGGAGGTA 60.756 60.000 23.45 0.00 0.00 3.08 R
1837 1996 1.276989 CATTCACAGCCTGCCCAAAAT 59.723 47.619 0.00 0.00 0.00 1.82 R
2910 3157 2.989166 GCAGTGAGCAAACAAAATAGCC 59.011 45.455 0.00 0.00 44.79 3.93 R
3910 4533 2.286359 CGAATGCATCATTGGGTGTACG 60.286 50.000 0.00 0.00 33.90 3.67 R
4757 5446 2.603075 AAGGAATAACAAGGGCAGCA 57.397 45.000 0.00 0.00 0.00 4.41 R
5892 6624 0.108186 GTGATCATCAGCGGTGACCA 60.108 55.000 21.19 12.46 34.75 4.02 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
81 82 0.616111 AGTGAGGAAGGAGATGCGGT 60.616 55.000 0.00 0.00 0.00 5.68
82 83 0.460987 GTGAGGAAGGAGATGCGGTG 60.461 60.000 0.00 0.00 0.00 4.94
123 124 5.523916 CGTGGACCAAATTAGGATAAGTCAG 59.476 44.000 0.00 0.00 0.00 3.51
132 133 2.465813 AGGATAAGTCAGACTGCAGCT 58.534 47.619 15.27 9.34 0.00 4.24
152 153 3.350833 CTTCCCTCACCTGATTTCCAAG 58.649 50.000 0.00 0.00 0.00 3.61
154 155 1.341383 CCCTCACCTGATTTCCAAGGG 60.341 57.143 0.00 0.00 34.00 3.95
156 157 2.243221 CCTCACCTGATTTCCAAGGGAT 59.757 50.000 0.00 0.00 0.00 3.85
162 163 3.118408 CCTGATTTCCAAGGGATACGTGA 60.118 47.826 0.00 0.00 37.60 4.35
190 191 5.212532 AGATGAGCGAGCTGATTTAGAAT 57.787 39.130 0.84 0.00 0.00 2.40
221 223 7.895759 TCAATAAGAAATGGTCCAAAGAAAGG 58.104 34.615 0.00 0.00 0.00 3.11
223 225 8.802267 CAATAAGAAATGGTCCAAAGAAAGGTA 58.198 33.333 0.00 0.00 0.00 3.08
251 253 7.582719 TCTATAACTCAATAAAAGCCACCCAT 58.417 34.615 0.00 0.00 0.00 4.00
253 255 5.823861 AACTCAATAAAAGCCACCCATTT 57.176 34.783 0.00 0.00 0.00 2.32
368 374 4.883585 TGCCGCTTCTTGAATTTGATCTAT 59.116 37.500 0.00 0.00 0.00 1.98
370 376 5.684626 GCCGCTTCTTGAATTTGATCTATTG 59.315 40.000 0.00 0.00 0.00 1.90
374 380 8.607459 CGCTTCTTGAATTTGATCTATTGTACT 58.393 33.333 0.00 0.00 0.00 2.73
375 381 9.928236 GCTTCTTGAATTTGATCTATTGTACTC 57.072 33.333 0.00 0.00 0.00 2.59
377 383 8.964476 TCTTGAATTTGATCTATTGTACTCCC 57.036 34.615 0.00 0.00 0.00 4.30
378 384 8.772250 TCTTGAATTTGATCTATTGTACTCCCT 58.228 33.333 0.00 0.00 0.00 4.20
379 385 8.964476 TTGAATTTGATCTATTGTACTCCCTC 57.036 34.615 0.00 0.00 0.00 4.30
380 386 8.324191 TGAATTTGATCTATTGTACTCCCTCT 57.676 34.615 0.00 0.00 0.00 3.69
381 387 8.206867 TGAATTTGATCTATTGTACTCCCTCTG 58.793 37.037 0.00 0.00 0.00 3.35
382 388 7.682787 ATTTGATCTATTGTACTCCCTCTGT 57.317 36.000 0.00 0.00 0.00 3.41
383 389 7.496346 TTTGATCTATTGTACTCCCTCTGTT 57.504 36.000 0.00 0.00 0.00 3.16
384 390 7.496346 TTGATCTATTGTACTCCCTCTGTTT 57.504 36.000 0.00 0.00 0.00 2.83
385 391 7.113658 TGATCTATTGTACTCCCTCTGTTTC 57.886 40.000 0.00 0.00 0.00 2.78
386 392 6.667848 TGATCTATTGTACTCCCTCTGTTTCA 59.332 38.462 0.00 0.00 0.00 2.69
387 393 6.928348 TCTATTGTACTCCCTCTGTTTCAA 57.072 37.500 0.00 0.00 0.00 2.69
388 394 7.311092 TCTATTGTACTCCCTCTGTTTCAAA 57.689 36.000 0.00 0.00 0.00 2.69
389 395 7.741785 TCTATTGTACTCCCTCTGTTTCAAAA 58.258 34.615 0.00 0.00 0.00 2.44
390 396 8.383175 TCTATTGTACTCCCTCTGTTTCAAAAT 58.617 33.333 0.00 0.00 0.00 1.82
391 397 9.667107 CTATTGTACTCCCTCTGTTTCAAAATA 57.333 33.333 0.00 0.00 0.00 1.40
395 401 9.667107 TGTACTCCCTCTGTTTCAAAATATAAG 57.333 33.333 0.00 0.00 0.00 1.73
396 402 9.668497 GTACTCCCTCTGTTTCAAAATATAAGT 57.332 33.333 0.00 0.00 0.00 2.24
397 403 8.794335 ACTCCCTCTGTTTCAAAATATAAGTC 57.206 34.615 0.00 0.00 0.00 3.01
398 404 8.606830 ACTCCCTCTGTTTCAAAATATAAGTCT 58.393 33.333 0.00 0.00 0.00 3.24
399 405 9.454859 CTCCCTCTGTTTCAAAATATAAGTCTT 57.545 33.333 0.00 0.00 0.00 3.01
400 406 9.807921 TCCCTCTGTTTCAAAATATAAGTCTTT 57.192 29.630 0.00 0.00 0.00 2.52
435 441 9.647797 TTTAAATGAACTATCACATACGAGTGT 57.352 29.630 0.00 0.00 38.69 3.55
444 450 9.939802 ACTATCACATACGAGTGTATATAGACA 57.060 33.333 12.18 0.00 39.28 3.41
497 503 9.952030 TTATTTTGTATGTAGTCATCTGTTGGA 57.048 29.630 0.00 0.00 35.70 3.53
498 504 8.862325 ATTTTGTATGTAGTCATCTGTTGGAA 57.138 30.769 0.00 0.00 35.70 3.53
499 505 8.862325 TTTTGTATGTAGTCATCTGTTGGAAT 57.138 30.769 0.00 0.00 35.70 3.01
500 506 8.492673 TTTGTATGTAGTCATCTGTTGGAATC 57.507 34.615 0.00 0.00 35.70 2.52
501 507 6.582636 TGTATGTAGTCATCTGTTGGAATCC 58.417 40.000 0.00 0.00 35.70 3.01
502 508 4.487714 TGTAGTCATCTGTTGGAATCCC 57.512 45.455 0.00 0.00 0.00 3.85
503 509 4.104086 TGTAGTCATCTGTTGGAATCCCT 58.896 43.478 0.00 0.00 0.00 4.20
504 510 5.277250 TGTAGTCATCTGTTGGAATCCCTA 58.723 41.667 0.00 0.00 0.00 3.53
505 511 5.724370 TGTAGTCATCTGTTGGAATCCCTAA 59.276 40.000 0.00 0.00 0.00 2.69
506 512 5.779241 AGTCATCTGTTGGAATCCCTAAA 57.221 39.130 0.00 0.00 0.00 1.85
507 513 6.139679 AGTCATCTGTTGGAATCCCTAAAA 57.860 37.500 0.00 0.00 0.00 1.52
508 514 6.552008 AGTCATCTGTTGGAATCCCTAAAAA 58.448 36.000 0.00 0.00 0.00 1.94
537 543 8.618702 CTATATTTAGGAACGGAGTGAGTAGA 57.381 38.462 0.00 0.00 45.00 2.59
538 544 9.233649 CTATATTTAGGAACGGAGTGAGTAGAT 57.766 37.037 0.00 0.00 45.00 1.98
540 546 6.939132 TTTAGGAACGGAGTGAGTAGATAG 57.061 41.667 0.00 0.00 45.00 2.08
541 547 4.506937 AGGAACGGAGTGAGTAGATAGT 57.493 45.455 0.00 0.00 45.00 2.12
542 548 5.627182 AGGAACGGAGTGAGTAGATAGTA 57.373 43.478 0.00 0.00 45.00 1.82
554 560 8.368668 AGTGAGTAGATAGTAGTTTGCAAACTT 58.631 33.333 40.87 29.20 46.52 2.66
635 641 4.851639 TCTTTACCGAGGGAGTACTACT 57.148 45.455 4.77 1.85 0.00 2.57
636 642 4.775236 TCTTTACCGAGGGAGTACTACTC 58.225 47.826 4.77 10.61 44.32 2.59
637 643 2.898729 TACCGAGGGAGTACTACTCG 57.101 55.000 28.93 28.93 45.96 4.18
724 730 9.450807 GACATAGAATGGTGTATATTTGTTTGC 57.549 33.333 0.00 0.00 33.60 3.68
728 734 8.706492 AGAATGGTGTATATTTGTTTGCATTG 57.294 30.769 0.00 0.00 0.00 2.82
1158 1173 2.544685 CTGCTCATGTTCGTCTTAGGG 58.455 52.381 0.00 0.00 0.00 3.53
1181 1196 2.974489 GAGGTTCTGTCGACGGCGA 61.974 63.158 19.89 10.67 45.71 5.54
1350 1365 2.035940 ACCTCCGCTTCCGTCTCT 59.964 61.111 0.00 0.00 0.00 3.10
1494 1509 4.037208 ACTTCTTCAGGTTTCACAATGCAG 59.963 41.667 0.00 0.00 0.00 4.41
1837 1996 7.145985 CGATTCCGATGGAAGATTAACTAGAA 58.854 38.462 4.41 0.00 45.48 2.10
1849 2008 5.360999 AGATTAACTAGAATTTTGGGCAGGC 59.639 40.000 0.00 0.00 0.00 4.85
1932 2092 7.665559 TGCTCCAAAATACTCTGAACTTAACAT 59.334 33.333 0.00 0.00 0.00 2.71
1970 2130 8.718102 TCACTCTAGTAATATTGCTCCAAAAC 57.282 34.615 9.52 0.00 0.00 2.43
2068 2228 3.006967 TCAGTCCTAAGAACTTCCAGCAC 59.993 47.826 0.00 0.00 0.00 4.40
2312 2472 1.740025 CTGGATCGTTTTTGGGCTCTC 59.260 52.381 0.00 0.00 0.00 3.20
2430 2590 1.270550 ACAGCAAGCAAGCAATACCAC 59.729 47.619 3.19 0.00 36.85 4.16
2717 2962 3.003480 GGTCTCTACCATTTGCTGTGAC 58.997 50.000 0.00 0.00 45.98 3.67
2793 3038 7.886629 ATAATTATTGACAGTGCAGTTCCAT 57.113 32.000 0.00 0.00 0.00 3.41
3629 4023 1.268899 TCCGTTTCGAAGAGGTCTCAC 59.731 52.381 17.03 2.32 38.43 3.51
3687 4281 9.066892 AGTTCTTCTGTCATACTAAAATTTGCA 57.933 29.630 0.00 0.00 0.00 4.08
3910 4533 5.449304 GTTAAAGCACTTGTGTGGATGTAC 58.551 41.667 2.61 0.00 43.97 2.90
3977 4665 6.665992 TCACAATAGGCCTGTTATACTAGG 57.334 41.667 17.99 3.58 37.14 3.02
4065 4753 5.168569 CCATCAGTTGCGTCTCTTTAGTAA 58.831 41.667 0.00 0.00 0.00 2.24
4208 4896 1.187087 CCTTCCTCTACGTTGCCTCT 58.813 55.000 0.00 0.00 0.00 3.69
4395 5083 7.446013 TCAGATGAATATGCATGCATTGAACTA 59.554 33.333 36.23 19.02 37.82 2.24
4529 5218 0.761323 TTGTGACGACTCAAGGGGGA 60.761 55.000 0.00 0.00 0.00 4.81
4777 5466 3.730215 TGCTGCCCTTGTTATTCCTTA 57.270 42.857 0.00 0.00 0.00 2.69
5097 5788 6.949117 ACAAGATGGAATATGATCTAGGCT 57.051 37.500 0.00 0.00 0.00 4.58
5167 5858 1.514678 GCACCAAAGGCACGACATCA 61.515 55.000 0.00 0.00 0.00 3.07
5370 6071 9.802039 TGTGAGGGATTTTGTAAAGTTAGTAAT 57.198 29.630 0.00 0.00 0.00 1.89
5497 6201 5.223382 AGTGCCTCGATGTATATTCGAAAG 58.777 41.667 0.00 7.40 44.25 2.62
5502 6206 6.200286 GCCTCGATGTATATTCGAAAGACAAA 59.800 38.462 0.00 0.00 44.25 2.83
5534 6245 9.061435 ACAACAACAAAGAAAGGAATTTTTCAA 57.939 25.926 5.62 0.00 39.08 2.69
5791 6522 2.554462 TCTGACGTCTAGGCTATGATGC 59.446 50.000 17.92 0.00 0.00 3.91
5792 6523 1.266989 TGACGTCTAGGCTATGATGCG 59.733 52.381 17.92 0.00 0.00 4.73
5793 6524 0.039074 ACGTCTAGGCTATGATGCGC 60.039 55.000 0.00 0.00 0.00 6.09
5823 6554 2.282887 GACCCCCGGCATGTTTGT 60.283 61.111 0.00 0.00 0.00 2.83
5892 6624 0.678048 GGCCTCTTGTTCTTCGCCAT 60.678 55.000 0.00 0.00 36.38 4.40
5897 6629 1.071542 TCTTGTTCTTCGCCATGGTCA 59.928 47.619 14.67 0.00 0.00 4.02
6037 6769 5.331906 TGGGTCAATGGATTTCTTGATTCA 58.668 37.500 0.00 0.00 34.18 2.57
6041 6773 6.253746 GTCAATGGATTTCTTGATTCACTCG 58.746 40.000 0.00 0.00 34.18 4.18
6049 6781 1.925847 CTTGATTCACTCGAGCTCTGC 59.074 52.381 13.61 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.480422 GGATCTTCCCTCTATCTCTCCTTTC 59.520 48.000 0.00 0.00 0.00 2.62
35 36 5.402630 GGATCTTCCCTCTATCTCTCCTTT 58.597 45.833 0.00 0.00 0.00 3.11
50 51 3.181474 CCTTCCTCACTAACGGATCTTCC 60.181 52.174 0.00 0.00 0.00 3.46
81 82 0.109365 CGCATTTTTCATGCCCGACA 60.109 50.000 1.28 0.00 41.71 4.35
82 83 0.109319 ACGCATTTTTCATGCCCGAC 60.109 50.000 1.28 0.00 41.71 4.79
123 124 1.376553 GGTGAGGGAAGCTGCAGTC 60.377 63.158 16.64 5.62 0.00 3.51
132 133 2.041620 CCTTGGAAATCAGGTGAGGGAA 59.958 50.000 0.00 0.00 0.00 3.97
162 163 0.318529 CAGCTCGCTCATCTACGCAT 60.319 55.000 0.00 0.00 0.00 4.73
166 167 5.114785 TCTAAATCAGCTCGCTCATCTAC 57.885 43.478 0.00 0.00 0.00 2.59
175 176 8.679288 ATTGAAAAACATTCTAAATCAGCTCG 57.321 30.769 0.00 0.00 0.00 5.03
190 191 9.323985 CTTTGGACCATTTCTTATTGAAAAACA 57.676 29.630 0.00 0.00 46.32 2.83
203 204 7.896811 AGATTTACCTTTCTTTGGACCATTTC 58.103 34.615 0.00 0.00 0.00 2.17
223 225 8.914011 GGGTGGCTTTTATTGAGTTATAGATTT 58.086 33.333 0.00 0.00 0.00 2.17
251 253 2.259012 TCTCCCTGCTACGGGTTTAAA 58.741 47.619 6.26 0.00 44.95 1.52
253 255 1.941377 TTCTCCCTGCTACGGGTTTA 58.059 50.000 6.26 0.00 44.95 2.01
370 376 9.668497 ACTTATATTTTGAAACAGAGGGAGTAC 57.332 33.333 0.00 0.00 0.00 2.73
374 380 9.807921 AAAGACTTATATTTTGAAACAGAGGGA 57.192 29.630 0.00 0.00 0.00 4.20
409 415 9.647797 ACACTCGTATGTGATAGTTCATTTAAA 57.352 29.630 11.46 0.00 40.12 1.52
418 424 9.939802 TGTCTATATACACTCGTATGTGATAGT 57.060 33.333 11.46 0.00 38.79 2.12
471 477 9.952030 TCCAACAGATGACTACATACAAAATAA 57.048 29.630 0.00 0.00 36.82 1.40
472 478 9.952030 TTCCAACAGATGACTACATACAAAATA 57.048 29.630 0.00 0.00 36.82 1.40
473 479 8.862325 TTCCAACAGATGACTACATACAAAAT 57.138 30.769 0.00 0.00 36.82 1.82
474 480 8.862325 ATTCCAACAGATGACTACATACAAAA 57.138 30.769 0.00 0.00 36.82 2.44
475 481 7.552687 GGATTCCAACAGATGACTACATACAAA 59.447 37.037 0.00 0.00 36.82 2.83
476 482 7.047891 GGATTCCAACAGATGACTACATACAA 58.952 38.462 0.00 0.00 36.82 2.41
477 483 6.408092 GGGATTCCAACAGATGACTACATACA 60.408 42.308 4.80 0.00 36.82 2.29
478 484 5.992217 GGGATTCCAACAGATGACTACATAC 59.008 44.000 4.80 0.00 36.82 2.39
479 485 5.905331 AGGGATTCCAACAGATGACTACATA 59.095 40.000 4.80 0.00 34.37 2.29
480 486 4.723789 AGGGATTCCAACAGATGACTACAT 59.276 41.667 4.80 0.00 35.93 2.29
481 487 4.104086 AGGGATTCCAACAGATGACTACA 58.896 43.478 4.80 0.00 34.83 2.74
482 488 4.762289 AGGGATTCCAACAGATGACTAC 57.238 45.455 4.80 0.00 34.83 2.73
483 489 6.884472 TTTAGGGATTCCAACAGATGACTA 57.116 37.500 4.80 0.00 34.83 2.59
484 490 5.779241 TTTAGGGATTCCAACAGATGACT 57.221 39.130 4.80 0.00 34.83 3.41
485 491 6.834168 TTTTTAGGGATTCCAACAGATGAC 57.166 37.500 4.80 0.00 34.83 3.06
512 518 8.618702 TCTACTCACTCCGTTCCTAAATATAG 57.381 38.462 0.00 0.00 0.00 1.31
514 520 9.233649 CTATCTACTCACTCCGTTCCTAAATAT 57.766 37.037 0.00 0.00 0.00 1.28
515 521 8.216423 ACTATCTACTCACTCCGTTCCTAAATA 58.784 37.037 0.00 0.00 0.00 1.40
516 522 7.061688 ACTATCTACTCACTCCGTTCCTAAAT 58.938 38.462 0.00 0.00 0.00 1.40
517 523 6.421485 ACTATCTACTCACTCCGTTCCTAAA 58.579 40.000 0.00 0.00 0.00 1.85
518 524 5.999044 ACTATCTACTCACTCCGTTCCTAA 58.001 41.667 0.00 0.00 0.00 2.69
519 525 5.627182 ACTATCTACTCACTCCGTTCCTA 57.373 43.478 0.00 0.00 0.00 2.94
520 526 4.506937 ACTATCTACTCACTCCGTTCCT 57.493 45.455 0.00 0.00 0.00 3.36
521 527 5.367302 ACTACTATCTACTCACTCCGTTCC 58.633 45.833 0.00 0.00 0.00 3.62
522 528 6.923928 AACTACTATCTACTCACTCCGTTC 57.076 41.667 0.00 0.00 0.00 3.95
523 529 6.404513 GCAAACTACTATCTACTCACTCCGTT 60.405 42.308 0.00 0.00 0.00 4.44
524 530 5.066246 GCAAACTACTATCTACTCACTCCGT 59.934 44.000 0.00 0.00 0.00 4.69
525 531 5.066117 TGCAAACTACTATCTACTCACTCCG 59.934 44.000 0.00 0.00 0.00 4.63
526 532 6.452494 TGCAAACTACTATCTACTCACTCC 57.548 41.667 0.00 0.00 0.00 3.85
527 533 8.030106 AGTTTGCAAACTACTATCTACTCACTC 58.970 37.037 37.07 9.05 46.75 3.51
528 534 7.897864 AGTTTGCAAACTACTATCTACTCACT 58.102 34.615 37.07 12.61 46.75 3.41
602 608 6.553852 TCCCTCGGTAAAGAAATATAAGAGCT 59.446 38.462 0.00 0.00 0.00 4.09
635 641 9.575868 AAGGAAAATCTATGAGAGATAGTACGA 57.424 33.333 0.00 0.00 44.68 3.43
690 696 9.770097 ATATACACCATTCTATGTCTTGTCAAG 57.230 33.333 6.21 6.21 0.00 3.02
724 730 5.991606 TCCGGCTATTAAACAGATCTCAATG 59.008 40.000 0.00 0.00 0.00 2.82
728 734 7.497925 AAATTCCGGCTATTAAACAGATCTC 57.502 36.000 0.00 0.00 0.00 2.75
983 998 2.780094 ATCGCTCGCTCCCTCAGTG 61.780 63.158 0.00 0.00 0.00 3.66
1158 1173 3.379445 TCGACAGAACCTCCGCCC 61.379 66.667 0.00 0.00 0.00 6.13
1350 1365 0.755698 GACGCCATGGAGAGGAGGTA 60.756 60.000 23.45 0.00 0.00 3.08
1837 1996 1.276989 CATTCACAGCCTGCCCAAAAT 59.723 47.619 0.00 0.00 0.00 1.82
1849 2008 5.179929 TCATTTACACTGACTGCATTCACAG 59.820 40.000 2.07 5.49 43.59 3.66
1970 2130 6.151985 ACTGAACAATACTAGACTCTGGAGTG 59.848 42.308 8.06 0.00 42.66 3.51
2068 2228 4.216257 AGGTTCGATGGACAAAAGTGAATG 59.784 41.667 0.00 0.00 0.00 2.67
2312 2472 5.327091 CATTTGAAGTCGGCAAATCTGTAG 58.673 41.667 0.00 0.00 42.33 2.74
2717 2962 6.241207 ACTTTACAAAATGAGACATCCACG 57.759 37.500 0.00 0.00 0.00 4.94
2910 3157 2.989166 GCAGTGAGCAAACAAAATAGCC 59.011 45.455 0.00 0.00 44.79 3.93
3687 4281 5.396436 GGCTACCATATCCTAAACAGTGTGT 60.396 44.000 0.00 0.00 0.00 3.72
3910 4533 2.286359 CGAATGCATCATTGGGTGTACG 60.286 50.000 0.00 0.00 33.90 3.67
3977 4665 7.434897 TCACAAACTAAGCAACAAACATCAATC 59.565 33.333 0.00 0.00 0.00 2.67
4065 4753 9.468532 GAAAGCTTCTAAATTTGTTCTGAATGT 57.531 29.630 0.00 0.00 0.00 2.71
4757 5446 2.603075 AAGGAATAACAAGGGCAGCA 57.397 45.000 0.00 0.00 0.00 4.41
4777 5466 5.431765 CAATAGCTACAGTCTTGGATGGTT 58.568 41.667 0.00 0.00 0.00 3.67
5097 5788 5.997746 GCATCCCTCAGTTATGTATGCTAAA 59.002 40.000 0.00 0.00 36.27 1.85
5167 5858 5.198207 TCAAATCCTGATCATGCAGTCAAT 58.802 37.500 0.00 0.00 34.06 2.57
5370 6071 5.948842 TGCTATATGGTGGACTACTACAGA 58.051 41.667 0.00 0.00 0.00 3.41
5371 6072 6.650427 TTGCTATATGGTGGACTACTACAG 57.350 41.667 0.00 0.00 0.00 2.74
5372 6073 7.010771 AGATTGCTATATGGTGGACTACTACA 58.989 38.462 0.00 0.00 0.00 2.74
5373 6074 7.363094 GGAGATTGCTATATGGTGGACTACTAC 60.363 44.444 0.00 0.00 0.00 2.73
5374 6075 6.663953 GGAGATTGCTATATGGTGGACTACTA 59.336 42.308 0.00 0.00 0.00 1.82
5375 6076 5.482175 GGAGATTGCTATATGGTGGACTACT 59.518 44.000 0.00 0.00 0.00 2.57
5497 6201 5.646606 TCTTTGTTGTTGTTAGCCTTTGTC 58.353 37.500 0.00 0.00 0.00 3.18
5502 6206 4.953579 TCCTTTCTTTGTTGTTGTTAGCCT 59.046 37.500 0.00 0.00 0.00 4.58
5791 6522 1.154035 GGTCCCAGCAAAAATCGCG 60.154 57.895 0.00 0.00 0.00 5.87
5792 6523 1.215382 GGGTCCCAGCAAAAATCGC 59.785 57.895 1.78 0.00 0.00 4.58
5793 6524 1.604147 GGGGGTCCCAGCAAAAATCG 61.604 60.000 10.98 0.00 44.65 3.34
5892 6624 0.108186 GTGATCATCAGCGGTGACCA 60.108 55.000 21.19 12.46 34.75 4.02
5897 6629 3.298958 ACCGTGATCATCAGCGGT 58.701 55.556 21.56 21.56 43.80 5.68
5994 6726 2.031919 CACTGCAACGCTACCCCA 59.968 61.111 0.00 0.00 0.00 4.96
6037 6769 2.881389 CTTCCGCAGAGCTCGAGT 59.119 61.111 15.13 0.23 0.00 4.18
6049 6781 1.676014 CCAAAGTCACCCTAGCTTCCG 60.676 57.143 0.00 0.00 0.00 4.30
6061 6794 3.456280 GCAAATGTCAAAGCCAAAGTCA 58.544 40.909 0.00 0.00 0.00 3.41
6063 6796 2.100584 TCGCAAATGTCAAAGCCAAAGT 59.899 40.909 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.