Multiple sequence alignment - TraesCS2D01G291200

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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 TraesCS2D01G291200 chr2D 100.000 4468 0 0 1 4468 373228929 373224462 0.000000e+00 8251
1 TraesCS2D01G291200 chr2B 93.813 3669 146 29 132 3752 442798941 442795306 0.000000e+00 5443
2 TraesCS2D01G291200 chr2B 91.787 621 16 12 3863 4468 442795167 442794567 0.000000e+00 832
3 TraesCS2D01G291200 chr2B 81.972 355 39 12 3580 3925 735827464 735827126 1.220000e-70 278
4 TraesCS2D01G291200 chr2B 82.184 348 33 15 3580 3916 780744004 780744333 5.690000e-69 272
5 TraesCS2D01G291200 chr2A 92.887 3627 135 53 42 3613 504272113 504275671 0.000000e+00 5155
6 TraesCS2D01G291200 chr2A 89.894 851 38 26 3647 4468 504275673 504276504 0.000000e+00 1051
7 TraesCS2D01G291200 chr2A 80.347 346 43 13 3580 3916 40762046 40762375 5.780000e-59 239
8 TraesCS2D01G291200 chr3B 82.370 346 36 15 3580 3916 456361726 456362055 1.220000e-70 278
9 TraesCS2D01G291200 chr3B 81.408 355 41 14 3580 3925 807584647 807584309 2.650000e-67 267
10 TraesCS2D01G291200 chr4A 82.133 347 35 14 3580 3916 661951742 661952071 5.690000e-69 272
11 TraesCS2D01G291200 chr6B 81.792 346 38 12 3580 3916 699125978 699126307 2.650000e-67 267
12 TraesCS2D01G291200 chr1B 81.503 346 39 14 3580 3916 69432280 69432609 1.230000e-65 261
13 TraesCS2D01G291200 chr1B 81.127 355 41 14 3580 3925 665780792 665780455 1.230000e-65 261
14 TraesCS2D01G291200 chr6A 80.466 343 35 15 3580 3907 196920 196595 2.690000e-57 233


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 TraesCS2D01G291200 chr2D 373224462 373228929 4467 True 8251.0 8251 100.0000 1 4468 1 chr2D.!!$R1 4467
1 TraesCS2D01G291200 chr2B 442794567 442798941 4374 True 3137.5 5443 92.8000 132 4468 2 chr2B.!!$R2 4336
2 TraesCS2D01G291200 chr2A 504272113 504276504 4391 False 3103.0 5155 91.3905 42 4468 2 chr2A.!!$F2 4426

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
695 766 0.107945 ATCGGCTCAAGCTCCAGTTC 60.108 55.0 1.46 0.0 41.70 3.01 F
857 933 0.310854 AAAGCCGCTTCTTTTGTCCG 59.689 50.0 5.98 0.0 32.78 4.79 F
1038 1124 0.589223 CGGAGATAGTCGAGCTGGTC 59.411 60.0 0.00 0.0 0.00 4.02 F
2912 3001 0.105039 CACCTCGGCTGGTATCTTCC 59.895 60.0 0.00 0.0 38.45 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2229 2318 1.066858 ACCAACTCAGCCAGATACACG 60.067 52.381 0.00 0.00 0.00 4.49 R
2624 2713 1.202582 GCTAGGAGAACTTCAGCGACA 59.797 52.381 0.00 0.00 0.00 4.35 R
2978 3067 0.179004 TTGACCTTGCATCGGTTGGT 60.179 50.000 9.32 1.46 34.19 3.67 R
3958 4121 0.461548 GTGATGTCCCATCTGCTCGA 59.538 55.000 5.87 0.00 0.00 4.04 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
20 21 0.258774 AGAGTGAGAGAGAGAGGGGC 59.741 60.000 0.00 0.00 0.00 5.80
21 22 0.258774 GAGTGAGAGAGAGAGGGGCT 59.741 60.000 0.00 0.00 0.00 5.19
22 23 1.493022 GAGTGAGAGAGAGAGGGGCTA 59.507 57.143 0.00 0.00 0.00 3.93
23 24 1.494721 AGTGAGAGAGAGAGGGGCTAG 59.505 57.143 0.00 0.00 0.00 3.42
24 25 1.493022 GTGAGAGAGAGAGGGGCTAGA 59.507 57.143 0.00 0.00 0.00 2.43
25 26 1.774254 TGAGAGAGAGAGGGGCTAGAG 59.226 57.143 0.00 0.00 0.00 2.43
26 27 1.774856 GAGAGAGAGAGGGGCTAGAGT 59.225 57.143 0.00 0.00 0.00 3.24
27 28 1.494721 AGAGAGAGAGGGGCTAGAGTG 59.505 57.143 0.00 0.00 0.00 3.51
28 29 1.493022 GAGAGAGAGGGGCTAGAGTGA 59.507 57.143 0.00 0.00 0.00 3.41
29 30 1.494721 AGAGAGAGGGGCTAGAGTGAG 59.505 57.143 0.00 0.00 0.00 3.51
30 31 0.555769 AGAGAGGGGCTAGAGTGAGG 59.444 60.000 0.00 0.00 0.00 3.86
31 32 0.469144 GAGAGGGGCTAGAGTGAGGG 60.469 65.000 0.00 0.00 0.00 4.30
32 33 0.926720 AGAGGGGCTAGAGTGAGGGA 60.927 60.000 0.00 0.00 0.00 4.20
33 34 0.469144 GAGGGGCTAGAGTGAGGGAG 60.469 65.000 0.00 0.00 0.00 4.30
34 35 0.926720 AGGGGCTAGAGTGAGGGAGA 60.927 60.000 0.00 0.00 0.00 3.71
35 36 0.469144 GGGGCTAGAGTGAGGGAGAG 60.469 65.000 0.00 0.00 0.00 3.20
36 37 0.469144 GGGCTAGAGTGAGGGAGAGG 60.469 65.000 0.00 0.00 0.00 3.69
37 38 0.553819 GGCTAGAGTGAGGGAGAGGA 59.446 60.000 0.00 0.00 0.00 3.71
38 39 1.146982 GGCTAGAGTGAGGGAGAGGAT 59.853 57.143 0.00 0.00 0.00 3.24
39 40 2.377193 GGCTAGAGTGAGGGAGAGGATA 59.623 54.545 0.00 0.00 0.00 2.59
40 41 3.561313 GGCTAGAGTGAGGGAGAGGATAG 60.561 56.522 0.00 0.00 0.00 2.08
41 42 3.561313 GCTAGAGTGAGGGAGAGGATAGG 60.561 56.522 0.00 0.00 0.00 2.57
42 43 2.795556 AGAGTGAGGGAGAGGATAGGA 58.204 52.381 0.00 0.00 0.00 2.94
43 44 3.135279 AGAGTGAGGGAGAGGATAGGAA 58.865 50.000 0.00 0.00 0.00 3.36
76 77 1.279840 GTGCGTGAGTTTGGTGAGC 59.720 57.895 0.00 0.00 0.00 4.26
120 132 4.521146 CATCCATACTTCCATAGCCCATC 58.479 47.826 0.00 0.00 0.00 3.51
121 133 2.912956 TCCATACTTCCATAGCCCATCC 59.087 50.000 0.00 0.00 0.00 3.51
122 134 2.915604 CCATACTTCCATAGCCCATCCT 59.084 50.000 0.00 0.00 0.00 3.24
123 135 4.104086 CCATACTTCCATAGCCCATCCTA 58.896 47.826 0.00 0.00 0.00 2.94
125 137 2.625639 ACTTCCATAGCCCATCCTAGG 58.374 52.381 0.82 0.82 0.00 3.02
126 138 2.089925 ACTTCCATAGCCCATCCTAGGT 60.090 50.000 9.08 0.00 0.00 3.08
127 139 2.030027 TCCATAGCCCATCCTAGGTG 57.970 55.000 9.08 6.53 0.00 4.00
128 140 1.223077 TCCATAGCCCATCCTAGGTGT 59.777 52.381 9.08 0.00 0.00 4.16
133 150 1.204146 GCCCATCCTAGGTGTTGAGA 58.796 55.000 9.08 0.00 0.00 3.27
172 189 3.186409 TCATTTCGTCTTCCTCTTTTGCG 59.814 43.478 0.00 0.00 0.00 4.85
222 240 3.123620 GCTGACTGCCGCCTCTTG 61.124 66.667 0.00 0.00 35.15 3.02
270 312 0.686769 ACCCTAAATCTCGCCTCCGT 60.687 55.000 0.00 0.00 35.54 4.69
340 385 0.684805 TCCCCCGCTTCTCTTCTCTC 60.685 60.000 0.00 0.00 0.00 3.20
341 386 0.686112 CCCCCGCTTCTCTTCTCTCT 60.686 60.000 0.00 0.00 0.00 3.10
342 387 0.744281 CCCCGCTTCTCTTCTCTCTC 59.256 60.000 0.00 0.00 0.00 3.20
343 388 1.684869 CCCCGCTTCTCTTCTCTCTCT 60.685 57.143 0.00 0.00 0.00 3.10
344 389 1.676006 CCCGCTTCTCTTCTCTCTCTC 59.324 57.143 0.00 0.00 0.00 3.20
345 390 2.643551 CCGCTTCTCTTCTCTCTCTCT 58.356 52.381 0.00 0.00 0.00 3.10
346 391 2.614057 CCGCTTCTCTTCTCTCTCTCTC 59.386 54.545 0.00 0.00 0.00 3.20
347 392 3.535561 CGCTTCTCTTCTCTCTCTCTCT 58.464 50.000 0.00 0.00 0.00 3.10
348 393 3.557595 CGCTTCTCTTCTCTCTCTCTCTC 59.442 52.174 0.00 0.00 0.00 3.20
349 394 4.681781 CGCTTCTCTTCTCTCTCTCTCTCT 60.682 50.000 0.00 0.00 0.00 3.10
350 395 4.813697 GCTTCTCTTCTCTCTCTCTCTCTC 59.186 50.000 0.00 0.00 0.00 3.20
351 396 5.396213 GCTTCTCTTCTCTCTCTCTCTCTCT 60.396 48.000 0.00 0.00 0.00 3.10
352 397 5.860941 TCTCTTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
353 398 5.523588 TCTCTTCTCTCTCTCTCTCTCTCT 58.476 45.833 0.00 0.00 0.00 3.10
354 399 5.596361 TCTCTTCTCTCTCTCTCTCTCTCTC 59.404 48.000 0.00 0.00 0.00 3.20
355 400 5.523588 TCTTCTCTCTCTCTCTCTCTCTCT 58.476 45.833 0.00 0.00 0.00 3.10
356 401 5.596361 TCTTCTCTCTCTCTCTCTCTCTCTC 59.404 48.000 0.00 0.00 0.00 3.20
357 402 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
358 403 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
359 404 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
360 405 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
377 422 1.552792 TCTCTCTCTCTCTCTCGTGCA 59.447 52.381 0.00 0.00 0.00 4.57
392 437 2.948979 TCGTGCACAAATCTGGTTCTTT 59.051 40.909 18.64 0.00 0.00 2.52
393 438 4.130857 TCGTGCACAAATCTGGTTCTTTA 58.869 39.130 18.64 0.00 0.00 1.85
394 439 4.024387 TCGTGCACAAATCTGGTTCTTTAC 60.024 41.667 18.64 0.00 0.00 2.01
409 454 7.192148 GGTTCTTTACCTCTCTCTTGTTTTC 57.808 40.000 0.00 0.00 44.10 2.29
461 507 4.202315 GCTCAAAGTACCCCCATTTTGTTT 60.202 41.667 0.00 0.00 33.46 2.83
549 599 1.203994 CGCTACGAAAAAGGGAGAGGA 59.796 52.381 0.00 0.00 0.00 3.71
598 648 4.335315 CGCATCTATGTCCCTTTTGCTTTA 59.665 41.667 0.00 0.00 0.00 1.85
632 697 4.603094 AATTTAACTAGGGGTGGGGAAG 57.397 45.455 0.00 0.00 0.00 3.46
633 698 1.975471 TTAACTAGGGGTGGGGAAGG 58.025 55.000 0.00 0.00 0.00 3.46
695 766 0.107945 ATCGGCTCAAGCTCCAGTTC 60.108 55.000 1.46 0.00 41.70 3.01
760 831 5.712152 AATAAGGTTCTTTCTTGTGCCTG 57.288 39.130 0.00 0.00 0.00 4.85
856 932 1.335964 GGAAAGCCGCTTCTTTTGTCC 60.336 52.381 5.98 4.82 36.50 4.02
857 933 0.310854 AAAGCCGCTTCTTTTGTCCG 59.689 50.000 5.98 0.00 32.78 4.79
896 972 1.079503 GGTCCTAACTTGAAGCGCAG 58.920 55.000 11.47 0.00 0.00 5.18
1038 1124 0.589223 CGGAGATAGTCGAGCTGGTC 59.411 60.000 0.00 0.00 0.00 4.02
1164 1250 1.667154 TTGACCGGCTCCTCAGATCG 61.667 60.000 0.00 0.00 0.00 3.69
1344 1430 0.877649 CCGCCATGAAGAGGATGTCG 60.878 60.000 0.00 0.00 0.00 4.35
1353 1439 4.162690 AGGATGTCGAAGCCCGCC 62.163 66.667 0.00 0.00 38.37 6.13
1523 1609 4.864704 TGGTTGAATCAGGTAAAAAGGC 57.135 40.909 0.00 0.00 0.00 4.35
1528 1614 0.802494 ATCAGGTAAAAAGGCGCACG 59.198 50.000 10.83 0.00 0.00 5.34
1530 1616 2.126618 GGTAAAAAGGCGCACGGC 60.127 61.111 10.83 8.74 42.51 5.68
2088 2177 6.367422 GCATCAGTGAAGATAGTTATGGTAGC 59.633 42.308 0.00 0.00 0.00 3.58
2152 2241 2.439156 GGGAAGCCATGAAGCGCT 60.439 61.111 2.64 2.64 38.01 5.92
2171 2260 2.555199 CTTAGCGATCCAACAAGGGAG 58.445 52.381 0.00 0.00 41.08 4.30
2229 2318 2.158623 TGGATGTGGAGATATTGGCACC 60.159 50.000 0.00 0.00 0.00 5.01
2373 2462 0.841289 TTGACCACCCGTTTCTTCCT 59.159 50.000 0.00 0.00 0.00 3.36
2514 2603 4.382147 GCTGCTAGGTAAGTAACTTCAGCT 60.382 45.833 16.61 5.22 38.21 4.24
2541 2630 7.064134 GTGGTGTTTATGTGTTATCTCATCGAA 59.936 37.037 0.00 0.00 0.00 3.71
2542 2631 7.277760 TGGTGTTTATGTGTTATCTCATCGAAG 59.722 37.037 0.00 0.00 0.00 3.79
2543 2632 7.277981 GGTGTTTATGTGTTATCTCATCGAAGT 59.722 37.037 0.00 0.00 0.00 3.01
2550 2639 6.986231 TGTGTTATCTCATCGAAGTATTGCAT 59.014 34.615 0.00 0.00 0.00 3.96
2624 2713 8.782137 ATTATATGTCCCTTTGCAGGTTTTAT 57.218 30.769 0.00 0.00 38.79 1.40
2792 2881 0.671472 TGCTTGTGAGGTGCTCATCG 60.671 55.000 0.00 0.00 42.73 3.84
2834 2923 2.429930 CCTTCCGGACCTTGTGCA 59.570 61.111 1.83 0.00 0.00 4.57
2912 3001 0.105039 CACCTCGGCTGGTATCTTCC 59.895 60.000 0.00 0.00 38.45 3.46
2942 3031 2.283532 ACACGGAGAGCTGAGCCT 60.284 61.111 0.00 0.00 0.00 4.58
2943 3032 2.183811 CACGGAGAGCTGAGCCTG 59.816 66.667 0.00 0.00 0.00 4.85
2978 3067 2.686956 TTCCGCAGCTTGTCGTCGAA 62.687 55.000 0.00 0.00 0.00 3.71
2981 3070 1.954146 GCAGCTTGTCGTCGAACCA 60.954 57.895 0.00 0.00 0.00 3.67
2984 3073 0.878961 AGCTTGTCGTCGAACCAACC 60.879 55.000 0.00 0.00 0.00 3.77
3236 3325 2.545532 CGATCTGATCAGAGGGTTGCTC 60.546 54.545 28.26 18.14 41.33 4.26
3380 3469 2.126031 GTCGACGCCTCAACCCTC 60.126 66.667 0.00 0.00 0.00 4.30
3383 3472 2.932234 CGACGCCTCAACCCTCACT 61.932 63.158 0.00 0.00 0.00 3.41
3455 3544 4.641396 TGAATGGAGACGACATTGAGTTT 58.359 39.130 0.00 0.00 38.57 2.66
3475 3564 0.179124 GAGCTCTTCTAGTGGTGGCG 60.179 60.000 6.43 0.00 0.00 5.69
3659 3748 1.823610 AGTAACTGAGTAAGGTCGGGC 59.176 52.381 0.00 0.00 0.00 6.13
3738 3827 5.277011 GGTCTTGTGCAAGCATTTTTCTTTC 60.277 40.000 7.03 0.00 38.28 2.62
3765 3919 3.558505 CAGCCATGCAATAATAGTTCGC 58.441 45.455 0.00 0.00 0.00 4.70
3820 3974 1.217001 TGCAGTAGTCGTTGTTGCTG 58.783 50.000 0.00 0.00 35.85 4.41
3825 3979 3.859961 CAGTAGTCGTTGTTGCTGGATAG 59.140 47.826 0.00 0.00 0.00 2.08
3826 3980 3.510360 AGTAGTCGTTGTTGCTGGATAGT 59.490 43.478 0.00 0.00 0.00 2.12
3827 3981 4.703575 AGTAGTCGTTGTTGCTGGATAGTA 59.296 41.667 0.00 0.00 0.00 1.82
3828 3982 4.111375 AGTCGTTGTTGCTGGATAGTAG 57.889 45.455 0.00 0.00 0.00 2.57
3829 3983 2.603560 GTCGTTGTTGCTGGATAGTAGC 59.396 50.000 0.00 0.00 41.49 3.58
3861 4023 8.877195 TCTCAAGTAAGGTCCAGTAATAAGTTT 58.123 33.333 0.00 0.00 0.00 2.66
3916 4079 7.630242 TCATAAAGTTAGGAGCAAGGATTTG 57.370 36.000 0.00 0.00 37.36 2.32
3918 4081 2.728007 AGTTAGGAGCAAGGATTTGGC 58.272 47.619 0.00 0.00 34.79 4.52
3953 4116 5.785243 TGTCACGGACTTCACAATTATGTA 58.215 37.500 5.77 0.00 33.88 2.29
3956 4119 8.035984 TGTCACGGACTTCACAATTATGTAATA 58.964 33.333 5.77 0.00 33.88 0.98
3958 4121 8.255206 TCACGGACTTCACAATTATGTAATAGT 58.745 33.333 0.00 0.00 37.82 2.12
3959 4122 8.540492 CACGGACTTCACAATTATGTAATAGTC 58.460 37.037 0.00 0.00 37.82 2.59
3960 4123 7.434307 ACGGACTTCACAATTATGTAATAGTCG 59.566 37.037 0.00 0.00 39.18 4.18
3961 4124 7.646526 CGGACTTCACAATTATGTAATAGTCGA 59.353 37.037 0.00 0.00 39.18 4.20
3964 4127 7.979537 ACTTCACAATTATGTAATAGTCGAGCA 59.020 33.333 0.00 0.00 37.82 4.26
4148 4328 4.855715 TCCTCTAGACAAGTTCACTGTG 57.144 45.455 0.17 0.17 0.00 3.66
4149 4329 3.574396 TCCTCTAGACAAGTTCACTGTGG 59.426 47.826 8.11 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.493022 GCCCCTCTCTCTCTCACTCTA 59.507 57.143 0.00 0.00 0.00 2.43
3 4 1.494721 CTAGCCCCTCTCTCTCTCACT 59.505 57.143 0.00 0.00 0.00 3.41
5 6 1.774254 CTCTAGCCCCTCTCTCTCTCA 59.226 57.143 0.00 0.00 0.00 3.27
7 8 1.494721 CACTCTAGCCCCTCTCTCTCT 59.505 57.143 0.00 0.00 0.00 3.10
10 11 1.478654 CCTCACTCTAGCCCCTCTCTC 60.479 61.905 0.00 0.00 0.00 3.20
11 12 0.555769 CCTCACTCTAGCCCCTCTCT 59.444 60.000 0.00 0.00 0.00 3.10
12 13 0.469144 CCCTCACTCTAGCCCCTCTC 60.469 65.000 0.00 0.00 0.00 3.20
13 14 0.926720 TCCCTCACTCTAGCCCCTCT 60.927 60.000 0.00 0.00 0.00 3.69
14 15 0.469144 CTCCCTCACTCTAGCCCCTC 60.469 65.000 0.00 0.00 0.00 4.30
15 16 0.926720 TCTCCCTCACTCTAGCCCCT 60.927 60.000 0.00 0.00 0.00 4.79
16 17 0.469144 CTCTCCCTCACTCTAGCCCC 60.469 65.000 0.00 0.00 0.00 5.80
17 18 0.469144 CCTCTCCCTCACTCTAGCCC 60.469 65.000 0.00 0.00 0.00 5.19
18 19 0.553819 TCCTCTCCCTCACTCTAGCC 59.446 60.000 0.00 0.00 0.00 3.93
19 20 2.675658 ATCCTCTCCCTCACTCTAGC 57.324 55.000 0.00 0.00 0.00 3.42
20 21 3.913799 TCCTATCCTCTCCCTCACTCTAG 59.086 52.174 0.00 0.00 0.00 2.43
21 22 3.955974 TCCTATCCTCTCCCTCACTCTA 58.044 50.000 0.00 0.00 0.00 2.43
22 23 2.795556 TCCTATCCTCTCCCTCACTCT 58.204 52.381 0.00 0.00 0.00 3.24
23 24 3.603965 TTCCTATCCTCTCCCTCACTC 57.396 52.381 0.00 0.00 0.00 3.51
24 25 3.533907 TCTTTCCTATCCTCTCCCTCACT 59.466 47.826 0.00 0.00 0.00 3.41
25 26 3.895041 CTCTTTCCTATCCTCTCCCTCAC 59.105 52.174 0.00 0.00 0.00 3.51
26 27 3.794399 TCTCTTTCCTATCCTCTCCCTCA 59.206 47.826 0.00 0.00 0.00 3.86
27 28 4.407365 CTCTCTTTCCTATCCTCTCCCTC 58.593 52.174 0.00 0.00 0.00 4.30
28 29 3.142028 CCTCTCTTTCCTATCCTCTCCCT 59.858 52.174 0.00 0.00 0.00 4.20
29 30 3.506398 CCTCTCTTTCCTATCCTCTCCC 58.494 54.545 0.00 0.00 0.00 4.30
30 31 3.506398 CCCTCTCTTTCCTATCCTCTCC 58.494 54.545 0.00 0.00 0.00 3.71
31 32 3.506398 CCCCTCTCTTTCCTATCCTCTC 58.494 54.545 0.00 0.00 0.00 3.20
32 33 2.181196 CCCCCTCTCTTTCCTATCCTCT 59.819 54.545 0.00 0.00 0.00 3.69
33 34 2.615391 CCCCCTCTCTTTCCTATCCTC 58.385 57.143 0.00 0.00 0.00 3.71
34 35 1.415273 GCCCCCTCTCTTTCCTATCCT 60.415 57.143 0.00 0.00 0.00 3.24
35 36 1.060729 GCCCCCTCTCTTTCCTATCC 58.939 60.000 0.00 0.00 0.00 2.59
36 37 1.418264 GTGCCCCCTCTCTTTCCTATC 59.582 57.143 0.00 0.00 0.00 2.08
37 38 1.512735 GTGCCCCCTCTCTTTCCTAT 58.487 55.000 0.00 0.00 0.00 2.57
38 39 0.620700 GGTGCCCCCTCTCTTTCCTA 60.621 60.000 0.00 0.00 0.00 2.94
39 40 1.925972 GGTGCCCCCTCTCTTTCCT 60.926 63.158 0.00 0.00 0.00 3.36
40 41 2.677848 GGTGCCCCCTCTCTTTCC 59.322 66.667 0.00 0.00 0.00 3.13
41 42 2.269241 CGGTGCCCCCTCTCTTTC 59.731 66.667 0.00 0.00 0.00 2.62
42 43 2.529389 ACGGTGCCCCCTCTCTTT 60.529 61.111 0.00 0.00 0.00 2.52
43 44 3.322466 CACGGTGCCCCCTCTCTT 61.322 66.667 0.00 0.00 0.00 2.85
88 100 1.004440 GTATGGATGCCGCTCCTCC 60.004 63.158 9.42 5.64 36.20 4.30
120 132 1.490574 CTCCCCTCTCAACACCTAGG 58.509 60.000 7.41 7.41 0.00 3.02
121 133 1.490574 CCTCCCCTCTCAACACCTAG 58.509 60.000 0.00 0.00 0.00 3.02
122 134 0.617820 GCCTCCCCTCTCAACACCTA 60.618 60.000 0.00 0.00 0.00 3.08
123 135 1.920835 GCCTCCCCTCTCAACACCT 60.921 63.158 0.00 0.00 0.00 4.00
125 137 1.298014 CTGCCTCCCCTCTCAACAC 59.702 63.158 0.00 0.00 0.00 3.32
126 138 2.596851 GCTGCCTCCCCTCTCAACA 61.597 63.158 0.00 0.00 0.00 3.33
127 139 2.270527 GCTGCCTCCCCTCTCAAC 59.729 66.667 0.00 0.00 0.00 3.18
128 140 3.011517 GGCTGCCTCCCCTCTCAA 61.012 66.667 12.43 0.00 0.00 3.02
340 385 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
341 386 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
342 387 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
343 388 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
344 389 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
345 390 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
346 391 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
347 392 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
348 393 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
349 394 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
350 395 4.023279 CGAGAGAGAGAGAGAGAGAGAGAG 60.023 54.167 0.00 0.00 0.00 3.20
351 396 3.885901 CGAGAGAGAGAGAGAGAGAGAGA 59.114 52.174 0.00 0.00 0.00 3.10
352 397 3.634448 ACGAGAGAGAGAGAGAGAGAGAG 59.366 52.174 0.00 0.00 0.00 3.20
353 398 3.381590 CACGAGAGAGAGAGAGAGAGAGA 59.618 52.174 0.00 0.00 0.00 3.10
354 399 3.711086 CACGAGAGAGAGAGAGAGAGAG 58.289 54.545 0.00 0.00 0.00 3.20
355 400 2.159099 GCACGAGAGAGAGAGAGAGAGA 60.159 54.545 0.00 0.00 0.00 3.10
356 401 2.205074 GCACGAGAGAGAGAGAGAGAG 58.795 57.143 0.00 0.00 0.00 3.20
357 402 1.552792 TGCACGAGAGAGAGAGAGAGA 59.447 52.381 0.00 0.00 0.00 3.10
358 403 1.665679 GTGCACGAGAGAGAGAGAGAG 59.334 57.143 0.00 0.00 0.00 3.20
359 404 1.002544 TGTGCACGAGAGAGAGAGAGA 59.997 52.381 13.13 0.00 0.00 3.10
360 405 1.447945 TGTGCACGAGAGAGAGAGAG 58.552 55.000 13.13 0.00 0.00 3.20
392 437 5.048643 CAGAGTCGAAAACAAGAGAGAGGTA 60.049 44.000 0.00 0.00 0.00 3.08
393 438 3.892588 AGAGTCGAAAACAAGAGAGAGGT 59.107 43.478 0.00 0.00 0.00 3.85
394 439 4.233789 CAGAGTCGAAAACAAGAGAGAGG 58.766 47.826 0.00 0.00 0.00 3.69
401 446 0.449507 CGCGCAGAGTCGAAAACAAG 60.450 55.000 8.75 0.00 0.00 3.16
404 449 0.042448 AAACGCGCAGAGTCGAAAAC 60.042 50.000 5.73 0.00 41.76 2.43
406 451 1.149361 ACAAACGCGCAGAGTCGAAA 61.149 50.000 5.73 0.00 41.76 3.46
407 452 1.590525 ACAAACGCGCAGAGTCGAA 60.591 52.632 5.73 0.00 41.76 3.71
408 453 2.027024 ACAAACGCGCAGAGTCGA 59.973 55.556 5.73 0.00 41.76 4.20
409 454 2.168621 CACAAACGCGCAGAGTCG 59.831 61.111 5.73 0.00 41.76 4.18
461 507 2.677524 GCAAGCACCAGATGGGCA 60.678 61.111 12.80 0.00 42.05 5.36
500 550 2.093658 GCAAGATCCGTAAACCTCTGGA 60.094 50.000 0.00 0.00 34.45 3.86
542 592 0.458260 GGTTTCGCTCTCTCCTCTCC 59.542 60.000 0.00 0.00 0.00 3.71
549 599 1.536662 AGGTGGGGTTTCGCTCTCT 60.537 57.895 0.00 0.00 0.00 3.10
608 673 6.480891 TTCCCCACCCCTAGTTAAATTTAA 57.519 37.500 6.54 6.54 0.00 1.52
609 674 5.043956 CCTTCCCCACCCCTAGTTAAATTTA 60.044 44.000 0.00 0.00 0.00 1.40
612 677 2.856864 CCTTCCCCACCCCTAGTTAAAT 59.143 50.000 0.00 0.00 0.00 1.40
632 697 0.031010 ATCTCCCACTAGTCACCCCC 60.031 60.000 0.00 0.00 0.00 5.40
633 698 1.123928 CATCTCCCACTAGTCACCCC 58.876 60.000 0.00 0.00 0.00 4.95
695 766 0.749649 AGCGTAGGAATCTGAGGCAG 59.250 55.000 0.00 0.00 0.00 4.85
737 808 6.539173 TCAGGCACAAGAAAGAACCTTATTA 58.461 36.000 0.00 0.00 0.00 0.98
760 831 3.003689 CAGATGGTGCGGGTATTCATTTC 59.996 47.826 0.00 0.00 0.00 2.17
896 972 2.676471 GGGTGGGTGGTGATGTGC 60.676 66.667 0.00 0.00 0.00 4.57
900 976 2.001803 CATCTGGGTGGGTGGTGAT 58.998 57.895 0.00 0.00 0.00 3.06
901 977 2.905996 GCATCTGGGTGGGTGGTGA 61.906 63.158 0.00 0.00 0.00 4.02
902 978 2.361610 GCATCTGGGTGGGTGGTG 60.362 66.667 0.00 0.00 0.00 4.17
903 979 4.033776 CGCATCTGGGTGGGTGGT 62.034 66.667 0.00 0.00 0.00 4.16
904 980 4.802051 CCGCATCTGGGTGGGTGG 62.802 72.222 0.00 0.00 34.75 4.61
1038 1124 1.084370 GGGCGTCTTTGGTCTCATCG 61.084 60.000 0.00 0.00 0.00 3.84
1146 1232 2.121538 CGATCTGAGGAGCCGGTCA 61.122 63.158 1.90 0.00 0.00 4.02
1164 1250 1.154413 CGAGGTGCGCACATTGAAC 60.154 57.895 38.60 21.81 0.00 3.18
1197 1283 1.170290 TCTTGTCCGTGCTCGTCTGA 61.170 55.000 7.47 0.00 35.01 3.27
1242 1328 0.110419 CGATCTCCGAGCTCGACATC 60.110 60.000 36.59 27.80 43.02 3.06
1353 1439 0.179187 CAGGAGTACTCGACACAGCG 60.179 60.000 16.56 0.00 0.00 5.18
1523 1609 3.726517 CTGAACCCTTGCCGTGCG 61.727 66.667 0.00 0.00 0.00 5.34
1528 1614 1.541588 CTTGTTAGCTGAACCCTTGCC 59.458 52.381 0.00 0.00 37.22 4.52
1530 1616 2.997485 GCTTGTTAGCTGAACCCTTG 57.003 50.000 0.00 0.00 44.27 3.61
1660 1746 2.310538 ACCCTTTCTCTGTTTTGCCAG 58.689 47.619 0.00 0.00 0.00 4.85
1744 1830 5.336770 CCTTCTTTTTAGTGGAGGATTTGCC 60.337 44.000 0.00 0.00 0.00 4.52
1797 1883 1.386533 CTTCGCAATGCTTCTGGGAT 58.613 50.000 2.94 0.00 35.88 3.85
2152 2241 1.406887 GCTCCCTTGTTGGATCGCTAA 60.407 52.381 0.00 0.00 38.35 3.09
2171 2260 4.095632 GCTTGAAGTTCTTCAATCCTAGGC 59.904 45.833 22.59 18.11 39.85 3.93
2229 2318 1.066858 ACCAACTCAGCCAGATACACG 60.067 52.381 0.00 0.00 0.00 4.49
2272 2361 6.012858 AGGTACTCAATGTCCATAACCTTCAA 60.013 38.462 0.00 0.00 32.21 2.69
2373 2462 7.123098 TCTGTCGTGAAATAAGAATACAGGGTA 59.877 37.037 0.00 0.00 35.08 3.69
2514 2603 6.312672 CGATGAGATAACACATAAACACCACA 59.687 38.462 0.00 0.00 0.00 4.17
2541 2630 8.284945 TCAGCTAGAAATTCAAATGCAATACT 57.715 30.769 0.00 0.00 0.00 2.12
2542 2631 8.915871 TTCAGCTAGAAATTCAAATGCAATAC 57.084 30.769 0.00 0.00 32.05 1.89
2543 2632 9.926158 TTTTCAGCTAGAAATTCAAATGCAATA 57.074 25.926 10.72 0.00 45.15 1.90
2602 2691 5.957774 ACATAAAACCTGCAAAGGGACATAT 59.042 36.000 0.00 0.00 0.00 1.78
2624 2713 1.202582 GCTAGGAGAACTTCAGCGACA 59.797 52.381 0.00 0.00 0.00 4.35
2792 2881 3.648739 AGGAGGTTCATCTCTTCCTACC 58.351 50.000 0.00 0.00 31.69 3.18
2834 2923 1.209019 AGTGGATCGATGCAGCTTTCT 59.791 47.619 20.79 10.37 0.00 2.52
2942 3031 3.138304 CGGAAGTGATGGTTTCTTCACA 58.862 45.455 12.63 0.00 45.20 3.58
2943 3032 2.095718 GCGGAAGTGATGGTTTCTTCAC 60.096 50.000 0.00 0.00 43.96 3.18
2978 3067 0.179004 TTGACCTTGCATCGGTTGGT 60.179 50.000 9.32 1.46 34.19 3.67
2981 3070 2.890311 TGAATTTGACCTTGCATCGGTT 59.110 40.909 9.32 0.00 34.19 4.44
3422 3511 1.409064 TCTCCATTCATCCGGAACTCG 59.591 52.381 9.01 0.00 38.60 4.18
3455 3544 0.898320 GCCACCACTAGAAGAGCTCA 59.102 55.000 17.77 0.00 0.00 4.26
3475 3564 6.404513 CCACTACAACTTCTACTGCTACTACC 60.405 46.154 0.00 0.00 0.00 3.18
3639 3728 1.823610 GCCCGACCTTACTCAGTTACT 59.176 52.381 0.00 0.00 0.00 2.24
3659 3748 4.454504 AGGAATAAAGTTACAGGCACAACG 59.545 41.667 0.00 0.00 0.00 4.10
3770 3924 2.753452 AGCTCATTTTCAGATGCCACTG 59.247 45.455 0.00 0.00 39.02 3.66
3771 3925 2.753452 CAGCTCATTTTCAGATGCCACT 59.247 45.455 0.00 0.00 0.00 4.00
3820 3974 8.301002 CCTTACTTGAGAATACTGCTACTATCC 58.699 40.741 0.00 0.00 0.00 2.59
3825 3979 6.127423 TGGACCTTACTTGAGAATACTGCTAC 60.127 42.308 0.00 0.00 0.00 3.58
3826 3980 5.955959 TGGACCTTACTTGAGAATACTGCTA 59.044 40.000 0.00 0.00 0.00 3.49
3827 3981 4.777896 TGGACCTTACTTGAGAATACTGCT 59.222 41.667 0.00 0.00 0.00 4.24
3828 3982 5.086104 TGGACCTTACTTGAGAATACTGC 57.914 43.478 0.00 0.00 0.00 4.40
3829 3983 6.287589 ACTGGACCTTACTTGAGAATACTG 57.712 41.667 0.00 0.00 0.00 2.74
3830 3984 8.611051 ATTACTGGACCTTACTTGAGAATACT 57.389 34.615 0.00 0.00 0.00 2.12
3834 3988 8.431910 ACTTATTACTGGACCTTACTTGAGAA 57.568 34.615 0.00 0.00 0.00 2.87
3835 3989 8.431910 AACTTATTACTGGACCTTACTTGAGA 57.568 34.615 0.00 0.00 0.00 3.27
3916 4079 3.612517 TGACAGACACATGACTGCC 57.387 52.632 10.63 1.51 40.55 4.85
3953 4116 2.388735 TGTCCCATCTGCTCGACTATT 58.611 47.619 0.00 0.00 0.00 1.73
3956 4119 0.749649 GATGTCCCATCTGCTCGACT 59.250 55.000 0.00 0.00 0.00 4.18
3958 4121 0.461548 GTGATGTCCCATCTGCTCGA 59.538 55.000 5.87 0.00 0.00 4.04
3959 4122 0.463204 AGTGATGTCCCATCTGCTCG 59.537 55.000 5.87 0.00 0.00 5.03
3960 4123 3.827008 TTAGTGATGTCCCATCTGCTC 57.173 47.619 5.87 0.00 0.00 4.26
3961 4124 4.458397 CAATTAGTGATGTCCCATCTGCT 58.542 43.478 5.87 6.49 0.00 4.24
3964 4127 4.785346 AGCAATTAGTGATGTCCCATCT 57.215 40.909 5.87 0.00 0.00 2.90
4004 4179 2.139323 ACTCACCGGTCAGCACTATA 57.861 50.000 4.93 0.00 0.00 1.31
4005 4180 2.025155 CTACTCACCGGTCAGCACTAT 58.975 52.381 4.93 0.00 0.00 2.12
4006 4181 1.460504 CTACTCACCGGTCAGCACTA 58.539 55.000 4.93 0.00 0.00 2.74
4047 4222 1.154282 CGCAGCACAGCATTCACTG 60.154 57.895 0.00 0.00 43.59 3.66
4148 4328 4.772886 ACCTCCAGGATTTGTACATACC 57.227 45.455 0.00 0.75 38.94 2.73
4149 4329 8.594550 ACATATACCTCCAGGATTTGTACATAC 58.405 37.037 0.00 0.00 38.94 2.39
4195 4377 4.189231 GGTTCATAGATGTAGCGGTGTTT 58.811 43.478 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.