Multiple sequence alignment - TraesCS7B01G217100

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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 TraesCS7B01G217100 chr7B 100.000 2611 0 0 1 2611 400626993 400624383 0.000000e+00 4822
1 TraesCS7B01G217100 chr7B 90.928 959 61 14 1160 2100 61273701 61274651 0.000000e+00 1266
2 TraesCS7B01G217100 chr7B 86.870 853 89 10 309 1140 61272661 61273511 0.000000e+00 933
3 TraesCS7B01G217100 chr7B 93.398 515 31 3 2097 2611 110149975 110150486 0.000000e+00 760
4 TraesCS7B01G217100 chr7B 90.939 309 18 6 2 304 678536471 678536167 8.700000e-110 407
5 TraesCS7B01G217100 chr1B 94.118 1020 44 6 1093 2096 635780415 635781434 0.000000e+00 1537
6 TraesCS7B01G217100 chr1B 86.957 851 88 11 311 1140 113801289 113800441 0.000000e+00 935
7 TraesCS7B01G217100 chr1B 90.803 598 43 5 301 886 635779812 635780409 0.000000e+00 789
8 TraesCS7B01G217100 chr1B 93.398 515 31 3 2097 2611 41107280 41107791 0.000000e+00 760
9 TraesCS7B01G217100 chr1B 92.842 461 33 0 1637 2097 113799821 113799361 0.000000e+00 669
10 TraesCS7B01G217100 chr1B 82.372 607 59 28 1160 1745 113800251 113799672 3.910000e-133 484
11 TraesCS7B01G217100 chr1B 91.613 310 14 4 2 304 539539418 539539114 4.020000e-113 418
12 TraesCS7B01G217100 chr5B 95.057 971 31 4 1138 2100 395676582 395675621 0.000000e+00 1511
13 TraesCS7B01G217100 chr5B 91.463 902 37 4 330 1198 395677461 395676567 0.000000e+00 1203
14 TraesCS7B01G217100 chr5B 94.961 516 23 3 2097 2611 662265959 662265446 0.000000e+00 806
15 TraesCS7B01G217100 chr5B 93.774 514 28 4 2098 2611 582441012 582441521 0.000000e+00 769
16 TraesCS7B01G217100 chr2D 93.396 954 45 7 1153 2097 584836712 584835768 0.000000e+00 1397
17 TraesCS7B01G217100 chr2D 90.711 506 47 0 635 1140 584837400 584836895 0.000000e+00 675
18 TraesCS7B01G217100 chr3B 89.572 959 53 13 1161 2103 795282935 795282008 0.000000e+00 1173
19 TraesCS7B01G217100 chr3B 94.951 515 25 1 2097 2611 152205241 152204728 0.000000e+00 806
20 TraesCS7B01G217100 chr3B 85.734 715 82 11 444 1140 582974178 582973466 0.000000e+00 737
21 TraesCS7B01G217100 chr3B 85.323 620 70 12 314 921 795283571 795282961 2.850000e-174 621
22 TraesCS7B01G217100 chr3B 90.686 204 17 2 349 551 582974409 582974207 1.190000e-68 270
23 TraesCS7B01G217100 chr5A 90.000 880 57 9 1225 2097 355770904 355771759 0.000000e+00 1109
24 TraesCS7B01G217100 chr5A 84.342 843 85 15 327 1140 355769875 355770699 0.000000e+00 782
25 TraesCS7B01G217100 chr7A 90.898 802 48 12 1164 1949 109759588 109758796 0.000000e+00 1053
26 TraesCS7B01G217100 chr7A 87.573 853 83 9 309 1140 109760585 109759735 0.000000e+00 966
27 TraesCS7B01G217100 chr6D 85.880 864 84 16 309 1140 118741334 118742191 0.000000e+00 885
28 TraesCS7B01G217100 chr6D 93.166 439 29 1 1660 2097 118742842 118743280 0.000000e+00 643
29 TraesCS7B01G217100 chr6D 84.541 621 47 19 1151 1745 118742372 118742969 1.050000e-158 569
30 TraesCS7B01G217100 chr4B 90.966 642 54 3 1457 2096 493801786 493801147 0.000000e+00 861
31 TraesCS7B01G217100 chr4B 93.981 515 27 4 2097 2611 26451487 26450977 0.000000e+00 776
32 TraesCS7B01G217100 chr4B 93.411 516 30 4 2097 2611 71355582 71356094 0.000000e+00 761
33 TraesCS7B01G217100 chr4B 91.475 305 18 4 1 305 41760641 41760937 1.870000e-111 412
34 TraesCS7B01G217100 chr2B 94.369 515 26 3 2097 2611 556858793 556858282 0.000000e+00 787
35 TraesCS7B01G217100 chr2B 93.810 517 29 2 2097 2611 740368992 740368477 0.000000e+00 774
36 TraesCS7B01G217100 chr2B 94.578 498 27 0 1601 2098 600997184 600996687 0.000000e+00 771
37 TraesCS7B01G217100 chr2B 91.148 305 20 4 2 304 596583968 596583669 8.700000e-110 407
38 TraesCS7B01G217100 chr2B 90.909 308 19 4 1 303 624998432 624998735 3.130000e-109 405
39 TraesCS7B01G217100 chr2B 92.181 243 18 1 309 551 600997493 600997252 2.490000e-90 342
40 TraesCS7B01G217100 chr4A 92.079 303 21 2 2 303 694218596 694218296 8.640000e-115 424
41 TraesCS7B01G217100 chr6B 91.475 305 20 3 2 304 195237422 195237722 5.200000e-112 414
42 TraesCS7B01G217100 chr6B 90.764 314 15 8 1 304 106235202 106234893 8.700000e-110 407
43 TraesCS7B01G217100 chr6B 90.645 310 19 3 1 304 675331480 675331785 1.130000e-108 403


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 TraesCS7B01G217100 chr7B 400624383 400626993 2610 True 4822.0 4822 100.000000 1 2611 1 chr7B.!!$R1 2610
1 TraesCS7B01G217100 chr7B 61272661 61274651 1990 False 1099.5 1266 88.899000 309 2100 2 chr7B.!!$F2 1791
2 TraesCS7B01G217100 chr7B 110149975 110150486 511 False 760.0 760 93.398000 2097 2611 1 chr7B.!!$F1 514
3 TraesCS7B01G217100 chr1B 635779812 635781434 1622 False 1163.0 1537 92.460500 301 2096 2 chr1B.!!$F2 1795
4 TraesCS7B01G217100 chr1B 41107280 41107791 511 False 760.0 760 93.398000 2097 2611 1 chr1B.!!$F1 514
5 TraesCS7B01G217100 chr1B 113799361 113801289 1928 True 696.0 935 87.390333 311 2097 3 chr1B.!!$R2 1786
6 TraesCS7B01G217100 chr5B 395675621 395677461 1840 True 1357.0 1511 93.260000 330 2100 2 chr5B.!!$R2 1770
7 TraesCS7B01G217100 chr5B 662265446 662265959 513 True 806.0 806 94.961000 2097 2611 1 chr5B.!!$R1 514
8 TraesCS7B01G217100 chr5B 582441012 582441521 509 False 769.0 769 93.774000 2098 2611 1 chr5B.!!$F1 513
9 TraesCS7B01G217100 chr2D 584835768 584837400 1632 True 1036.0 1397 92.053500 635 2097 2 chr2D.!!$R1 1462
10 TraesCS7B01G217100 chr3B 795282008 795283571 1563 True 897.0 1173 87.447500 314 2103 2 chr3B.!!$R3 1789
11 TraesCS7B01G217100 chr3B 152204728 152205241 513 True 806.0 806 94.951000 2097 2611 1 chr3B.!!$R1 514
12 TraesCS7B01G217100 chr3B 582973466 582974409 943 True 503.5 737 88.210000 349 1140 2 chr3B.!!$R2 791
13 TraesCS7B01G217100 chr5A 355769875 355771759 1884 False 945.5 1109 87.171000 327 2097 2 chr5A.!!$F1 1770
14 TraesCS7B01G217100 chr7A 109758796 109760585 1789 True 1009.5 1053 89.235500 309 1949 2 chr7A.!!$R1 1640
15 TraesCS7B01G217100 chr6D 118741334 118743280 1946 False 699.0 885 87.862333 309 2097 3 chr6D.!!$F1 1788
16 TraesCS7B01G217100 chr4B 493801147 493801786 639 True 861.0 861 90.966000 1457 2096 1 chr4B.!!$R2 639
17 TraesCS7B01G217100 chr4B 26450977 26451487 510 True 776.0 776 93.981000 2097 2611 1 chr4B.!!$R1 514
18 TraesCS7B01G217100 chr4B 71355582 71356094 512 False 761.0 761 93.411000 2097 2611 1 chr4B.!!$F2 514
19 TraesCS7B01G217100 chr2B 556858282 556858793 511 True 787.0 787 94.369000 2097 2611 1 chr2B.!!$R1 514
20 TraesCS7B01G217100 chr2B 740368477 740368992 515 True 774.0 774 93.810000 2097 2611 1 chr2B.!!$R3 514
21 TraesCS7B01G217100 chr2B 600996687 600997493 806 True 556.5 771 93.379500 309 2098 2 chr2B.!!$R4 1789

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
569 717 0.163788 CACGATTCACAGGAACGCAC 59.836 55.0 0.0 0.0 35.46 5.34 F
1016 1227 0.605083 TCGATGACTTGCTCAGCAGT 59.395 50.0 0.0 0.0 40.61 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 1842 0.530744 GTGATGGAGTGGAGCGTGTA 59.469 55.000 0.0 0.0 0.0 2.90 R
2384 2898 1.398071 GCAAGACGGAAGCGTTACAAC 60.398 52.381 0.0 0.0 0.0 3.32 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
17 18 3.320359 AGTTCGGGGGCATACCAG 58.680 61.111 0.00 0.00 42.91 4.00
18 19 1.615424 AGTTCGGGGGCATACCAGT 60.615 57.895 0.00 0.00 42.91 4.00
19 20 0.325860 AGTTCGGGGGCATACCAGTA 60.326 55.000 0.00 0.00 42.91 2.74
20 21 0.763035 GTTCGGGGGCATACCAGTAT 59.237 55.000 0.00 0.00 42.91 2.12
21 22 1.142262 GTTCGGGGGCATACCAGTATT 59.858 52.381 0.00 0.00 42.91 1.89
22 23 0.762418 TCGGGGGCATACCAGTATTG 59.238 55.000 0.00 0.00 42.91 1.90
23 24 0.472471 CGGGGGCATACCAGTATTGT 59.528 55.000 0.00 0.00 42.91 2.71
24 25 1.695242 CGGGGGCATACCAGTATTGTA 59.305 52.381 0.00 0.00 42.91 2.41
25 26 2.549349 CGGGGGCATACCAGTATTGTAC 60.549 54.545 0.00 0.00 42.91 2.90
26 27 2.709397 GGGGGCATACCAGTATTGTACT 59.291 50.000 0.00 0.00 42.91 2.73
27 28 3.905591 GGGGGCATACCAGTATTGTACTA 59.094 47.826 0.00 0.00 42.91 1.82
28 29 4.020485 GGGGGCATACCAGTATTGTACTAG 60.020 50.000 0.00 0.00 42.91 2.57
29 30 4.020485 GGGGCATACCAGTATTGTACTAGG 60.020 50.000 0.00 0.00 42.91 3.02
30 31 4.020485 GGGCATACCAGTATTGTACTAGGG 60.020 50.000 0.00 0.00 37.23 3.53
31 32 4.836736 GGCATACCAGTATTGTACTAGGGA 59.163 45.833 0.00 0.00 37.23 4.20
32 33 5.279356 GGCATACCAGTATTGTACTAGGGAC 60.279 48.000 0.00 0.00 37.23 4.46
33 34 5.303589 GCATACCAGTATTGTACTAGGGACA 59.696 44.000 0.00 0.00 37.23 4.02
34 35 6.737899 GCATACCAGTATTGTACTAGGGACAC 60.738 46.154 0.00 0.00 37.23 3.67
35 36 4.028825 ACCAGTATTGTACTAGGGACACC 58.971 47.826 0.00 0.00 37.23 4.16
36 37 3.067742 CCAGTATTGTACTAGGGACACCG 59.932 52.174 0.00 0.00 38.34 4.94
37 38 3.067742 CAGTATTGTACTAGGGACACCGG 59.932 52.174 0.00 0.00 38.34 5.28
38 39 2.537633 ATTGTACTAGGGACACCGGA 57.462 50.000 9.46 0.00 43.47 5.14
39 40 2.307496 TTGTACTAGGGACACCGGAA 57.693 50.000 9.46 0.00 43.47 4.30
40 41 1.843368 TGTACTAGGGACACCGGAAG 58.157 55.000 9.46 1.96 43.47 3.46
53 54 3.725032 GGAAGGGTTCCGGGGGTC 61.725 72.222 0.00 0.00 40.59 4.46
54 55 3.725032 GAAGGGTTCCGGGGGTCC 61.725 72.222 0.00 0.00 0.00 4.46
55 56 4.603097 AAGGGTTCCGGGGGTCCA 62.603 66.667 0.00 0.00 0.00 4.02
59 60 4.029809 GTTCCGGGGGTCCACCAG 62.030 72.222 11.81 0.00 42.91 4.00
100 101 3.211288 CCTCGTGGGCTGTAGAGG 58.789 66.667 0.00 4.90 43.43 3.69
101 102 2.427245 CCTCGTGGGCTGTAGAGGG 61.427 68.421 9.80 0.00 44.78 4.30
102 103 1.379977 CTCGTGGGCTGTAGAGGGA 60.380 63.158 0.00 0.00 0.00 4.20
103 104 0.970937 CTCGTGGGCTGTAGAGGGAA 60.971 60.000 0.00 0.00 0.00 3.97
104 105 0.970937 TCGTGGGCTGTAGAGGGAAG 60.971 60.000 0.00 0.00 0.00 3.46
105 106 1.908483 GTGGGCTGTAGAGGGAAGG 59.092 63.158 0.00 0.00 0.00 3.46
106 107 1.306997 TGGGCTGTAGAGGGAAGGG 60.307 63.158 0.00 0.00 0.00 3.95
107 108 1.003051 GGGCTGTAGAGGGAAGGGA 59.997 63.158 0.00 0.00 0.00 4.20
108 109 0.620700 GGGCTGTAGAGGGAAGGGAA 60.621 60.000 0.00 0.00 0.00 3.97
109 110 0.542333 GGCTGTAGAGGGAAGGGAAC 59.458 60.000 0.00 0.00 0.00 3.62
131 132 4.554036 CCTTAGAGGGCTGGGCGC 62.554 72.222 0.00 0.00 41.91 6.53
155 156 4.387343 CCTTGGGCCCATGCACCT 62.387 66.667 29.23 0.00 41.56 4.00
156 157 2.682846 CTTGGGCCCATGCACCTA 59.317 61.111 29.23 7.78 41.56 3.08
157 158 1.454479 CTTGGGCCCATGCACCTAG 60.454 63.158 29.23 14.85 41.56 3.02
158 159 2.916527 CTTGGGCCCATGCACCTAGG 62.917 65.000 29.23 7.41 41.56 3.02
159 160 4.209866 GGGCCCATGCACCTAGGG 62.210 72.222 19.95 10.23 45.68 3.53
160 161 4.209866 GGCCCATGCACCTAGGGG 62.210 72.222 14.81 11.05 43.04 4.79
272 273 4.845307 CCCCCTTCCCCCTCCTCC 62.845 77.778 0.00 0.00 0.00 4.30
273 274 3.711782 CCCCTTCCCCCTCCTCCT 61.712 72.222 0.00 0.00 0.00 3.69
274 275 2.341677 CCCCTTCCCCCTCCTCCTA 61.342 68.421 0.00 0.00 0.00 2.94
275 276 1.690148 CCCCTTCCCCCTCCTCCTAT 61.690 65.000 0.00 0.00 0.00 2.57
276 277 1.177104 CCCTTCCCCCTCCTCCTATA 58.823 60.000 0.00 0.00 0.00 1.31
277 278 1.512643 CCCTTCCCCCTCCTCCTATAA 59.487 57.143 0.00 0.00 0.00 0.98
278 279 2.089581 CCCTTCCCCCTCCTCCTATAAA 60.090 54.545 0.00 0.00 0.00 1.40
279 280 3.443180 CCCTTCCCCCTCCTCCTATAAAT 60.443 52.174 0.00 0.00 0.00 1.40
280 281 4.203012 CCCTTCCCCCTCCTCCTATAAATA 60.203 50.000 0.00 0.00 0.00 1.40
281 282 5.033522 CCTTCCCCCTCCTCCTATAAATAG 58.966 50.000 0.00 0.00 0.00 1.73
282 283 5.222780 CCTTCCCCCTCCTCCTATAAATAGA 60.223 48.000 0.00 0.00 32.05 1.98
283 284 5.554034 TCCCCCTCCTCCTATAAATAGAG 57.446 47.826 0.00 0.00 32.05 2.43
284 285 4.297935 TCCCCCTCCTCCTATAAATAGAGG 59.702 50.000 0.00 0.00 36.03 3.69
285 286 4.575264 CCCCCTCCTCCTATAAATAGAGGG 60.575 54.167 14.72 14.72 45.67 4.30
286 287 4.625963 CCCTCCTCCTATAAATAGAGGGG 58.374 52.174 14.00 3.40 43.17 4.79
287 288 4.034410 CCTCCTCCTATAAATAGAGGGGC 58.966 52.174 5.50 0.00 33.79 5.80
288 289 3.702045 CTCCTCCTATAAATAGAGGGGCG 59.298 52.174 5.50 0.00 33.79 6.13
289 290 3.335786 TCCTCCTATAAATAGAGGGGCGA 59.664 47.826 5.50 0.00 33.79 5.54
290 291 3.702045 CCTCCTATAAATAGAGGGGCGAG 59.298 52.174 1.51 0.00 33.79 5.03
291 292 3.702045 CTCCTATAAATAGAGGGGCGAGG 59.298 52.174 1.51 0.00 35.43 4.63
292 293 3.077088 TCCTATAAATAGAGGGGCGAGGT 59.923 47.826 1.51 0.00 35.43 3.85
293 294 3.195825 CCTATAAATAGAGGGGCGAGGTG 59.804 52.174 0.00 0.00 31.12 4.00
294 295 2.464796 TAAATAGAGGGGCGAGGTGA 57.535 50.000 0.00 0.00 0.00 4.02
295 296 1.123928 AAATAGAGGGGCGAGGTGAG 58.876 55.000 0.00 0.00 0.00 3.51
296 297 0.760945 AATAGAGGGGCGAGGTGAGG 60.761 60.000 0.00 0.00 0.00 3.86
297 298 2.664835 ATAGAGGGGCGAGGTGAGGG 62.665 65.000 0.00 0.00 0.00 4.30
304 305 4.463879 CGAGGTGAGGGCTGCAGG 62.464 72.222 17.12 0.00 0.00 4.85
402 404 7.373493 ACTAGAAAAGACCGAAGAAAATACGA 58.627 34.615 0.00 0.00 0.00 3.43
540 677 0.529773 TGGTCTCACACAACACGAGC 60.530 55.000 0.00 0.00 0.00 5.03
569 717 0.163788 CACGATTCACAGGAACGCAC 59.836 55.000 0.00 0.00 35.46 5.34
574 722 4.619227 CACAGGAACGCACCCGGT 62.619 66.667 0.00 0.00 39.22 5.28
663 843 1.605738 GCCCCATGCCCATGAGATC 60.606 63.158 9.73 0.00 41.20 2.75
730 935 3.460672 GATGAAGATCGGCGCCCCA 62.461 63.158 23.46 8.29 0.00 4.96
816 1027 2.901840 ACTGCCTGCAACACGGTG 60.902 61.111 6.58 6.58 0.00 4.94
817 1028 2.901840 CTGCCTGCAACACGGTGT 60.902 61.111 8.21 8.21 0.00 4.16
1016 1227 0.605083 TCGATGACTTGCTCAGCAGT 59.395 50.000 0.00 0.00 40.61 4.40
1053 1264 1.697432 TCATCACCACCCGTCTTCTTT 59.303 47.619 0.00 0.00 0.00 2.52
1159 1542 6.982852 TCTATTGCTATCTACTCTTTTCGGG 58.017 40.000 0.00 0.00 0.00 5.14
1235 1691 9.778741 TCTTTTTCTCTTTTGTAGCTGAATCTA 57.221 29.630 0.00 0.00 0.00 1.98
1377 1842 1.356124 AGCACTCTGTCCTCAACCAT 58.644 50.000 0.00 0.00 0.00 3.55
1419 1885 3.323115 TCTCCTCGCATGCTAGAAATCAT 59.677 43.478 20.10 0.00 0.00 2.45
1423 1889 4.001652 CTCGCATGCTAGAAATCATCCAT 58.998 43.478 17.13 0.00 0.00 3.41
1509 1975 4.756642 TGAATACTTGACTTGTTGCAGAGG 59.243 41.667 0.00 0.00 0.00 3.69
1516 1982 0.670162 CTTGTTGCAGAGGTGGTTGG 59.330 55.000 0.00 0.00 0.00 3.77
1564 2030 0.178992 CACAAGGTCCATGGTGGTGT 60.179 55.000 12.58 9.24 39.03 4.16
1672 2140 0.393820 CCATGGGCTGTTGTTGCTTT 59.606 50.000 2.85 0.00 0.00 3.51
2049 2562 6.209986 TGAAAGACCGAACTATTAGAAGACCA 59.790 38.462 0.00 0.00 0.00 4.02
2089 2602 1.957186 CGAAAAGACCGAACGCCCA 60.957 57.895 0.00 0.00 0.00 5.36
2185 2698 1.001248 AAGCCCTGCCGGAGTACTA 59.999 57.895 5.05 0.00 0.00 1.82
2204 2717 2.347114 CGCTCCATCACCACCACA 59.653 61.111 0.00 0.00 0.00 4.17
2271 2785 3.604129 TTGCTGGATCAAGGCGCGA 62.604 57.895 12.10 0.00 0.00 5.87
2274 2788 1.068753 CTGGATCAAGGCGCGAGAT 59.931 57.895 12.10 6.92 0.00 2.75
2299 2813 2.663520 CGGGCTGCACGTGTGTTA 60.664 61.111 17.53 0.66 0.00 2.41
2334 2848 2.602878 GTTGTTCGGTGCTAAGATCGA 58.397 47.619 0.00 0.00 0.00 3.59
2384 2898 1.519455 GACTCCCTCATCCGCGTTG 60.519 63.158 4.92 2.14 0.00 4.10
2473 2991 7.015584 TGCTAGTTGCTCCATAGATTGATCTTA 59.984 37.037 0.00 0.00 43.37 2.10
2568 3087 5.779922 AGTTTCTATGCACGAGTAGAACAA 58.220 37.500 6.94 0.00 36.84 2.83
2601 3120 5.221342 TGTGGGCGTAGATTTTGTCAATTTT 60.221 36.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.325860 TACTGGTATGCCCCCGAACT 60.326 55.000 0.00 0.00 0.00 3.01
1 2 0.763035 ATACTGGTATGCCCCCGAAC 59.237 55.000 0.00 0.00 0.00 3.95
2 3 1.142060 CAATACTGGTATGCCCCCGAA 59.858 52.381 0.00 0.00 0.00 4.30
3 4 0.762418 CAATACTGGTATGCCCCCGA 59.238 55.000 0.00 0.00 0.00 5.14
4 5 0.472471 ACAATACTGGTATGCCCCCG 59.528 55.000 0.00 0.00 0.00 5.73
5 6 2.709397 AGTACAATACTGGTATGCCCCC 59.291 50.000 0.00 0.00 37.69 5.40
6 7 4.020485 CCTAGTACAATACTGGTATGCCCC 60.020 50.000 0.00 0.00 39.81 5.80
7 8 4.020485 CCCTAGTACAATACTGGTATGCCC 60.020 50.000 0.00 0.00 39.81 5.36
8 9 4.836736 TCCCTAGTACAATACTGGTATGCC 59.163 45.833 0.00 0.00 39.81 4.40
9 10 5.303589 TGTCCCTAGTACAATACTGGTATGC 59.696 44.000 0.00 0.00 39.81 3.14
10 11 6.239232 GGTGTCCCTAGTACAATACTGGTATG 60.239 46.154 0.00 0.00 39.81 2.39
11 12 5.837438 GGTGTCCCTAGTACAATACTGGTAT 59.163 44.000 0.00 0.00 39.81 2.73
12 13 5.203528 GGTGTCCCTAGTACAATACTGGTA 58.796 45.833 0.00 0.00 39.81 3.25
13 14 4.028825 GGTGTCCCTAGTACAATACTGGT 58.971 47.826 0.00 0.00 39.81 4.00
14 15 3.067742 CGGTGTCCCTAGTACAATACTGG 59.932 52.174 0.00 0.00 39.81 4.00
15 16 3.067742 CCGGTGTCCCTAGTACAATACTG 59.932 52.174 0.00 0.00 39.81 2.74
16 17 3.053395 TCCGGTGTCCCTAGTACAATACT 60.053 47.826 0.00 0.00 42.68 2.12
17 18 3.290710 TCCGGTGTCCCTAGTACAATAC 58.709 50.000 0.00 0.00 0.00 1.89
18 19 3.668141 TCCGGTGTCCCTAGTACAATA 57.332 47.619 0.00 0.00 0.00 1.90
19 20 2.537633 TCCGGTGTCCCTAGTACAAT 57.462 50.000 0.00 0.00 0.00 2.71
20 21 2.173519 CTTCCGGTGTCCCTAGTACAA 58.826 52.381 0.00 0.00 0.00 2.41
21 22 1.617804 CCTTCCGGTGTCCCTAGTACA 60.618 57.143 0.00 0.00 0.00 2.90
22 23 1.109609 CCTTCCGGTGTCCCTAGTAC 58.890 60.000 0.00 0.00 0.00 2.73
23 24 0.032813 CCCTTCCGGTGTCCCTAGTA 60.033 60.000 0.00 0.00 0.00 1.82
24 25 1.305887 CCCTTCCGGTGTCCCTAGT 60.306 63.158 0.00 0.00 0.00 2.57
25 26 1.305887 ACCCTTCCGGTGTCCCTAG 60.306 63.158 0.00 0.00 46.09 3.02
26 27 2.864049 ACCCTTCCGGTGTCCCTA 59.136 61.111 0.00 0.00 46.09 3.53
36 37 3.725032 GACCCCCGGAACCCTTCC 61.725 72.222 0.73 0.00 46.62 3.46
37 38 3.725032 GGACCCCCGGAACCCTTC 61.725 72.222 0.73 0.00 0.00 3.46
38 39 4.603097 TGGACCCCCGGAACCCTT 62.603 66.667 0.73 0.00 34.29 3.95
42 43 4.029809 CTGGTGGACCCCCGGAAC 62.030 72.222 0.73 0.00 34.29 3.62
83 84 2.427245 CCCTCTACAGCCCACGAGG 61.427 68.421 0.00 0.00 42.09 4.63
84 85 0.970937 TTCCCTCTACAGCCCACGAG 60.971 60.000 0.00 0.00 0.00 4.18
85 86 0.970937 CTTCCCTCTACAGCCCACGA 60.971 60.000 0.00 0.00 0.00 4.35
86 87 1.517832 CTTCCCTCTACAGCCCACG 59.482 63.158 0.00 0.00 0.00 4.94
87 88 1.627297 CCCTTCCCTCTACAGCCCAC 61.627 65.000 0.00 0.00 0.00 4.61
88 89 1.306997 CCCTTCCCTCTACAGCCCA 60.307 63.158 0.00 0.00 0.00 5.36
89 90 0.620700 TTCCCTTCCCTCTACAGCCC 60.621 60.000 0.00 0.00 0.00 5.19
90 91 0.542333 GTTCCCTTCCCTCTACAGCC 59.458 60.000 0.00 0.00 0.00 4.85
91 92 0.542333 GGTTCCCTTCCCTCTACAGC 59.458 60.000 0.00 0.00 0.00 4.40
92 93 1.834263 CTGGTTCCCTTCCCTCTACAG 59.166 57.143 0.00 0.00 0.00 2.74
93 94 1.952621 CTGGTTCCCTTCCCTCTACA 58.047 55.000 0.00 0.00 0.00 2.74
94 95 0.542333 GCTGGTTCCCTTCCCTCTAC 59.458 60.000 0.00 0.00 0.00 2.59
95 96 0.620700 GGCTGGTTCCCTTCCCTCTA 60.621 60.000 0.00 0.00 0.00 2.43
96 97 1.925972 GGCTGGTTCCCTTCCCTCT 60.926 63.158 0.00 0.00 0.00 3.69
97 98 2.677848 GGCTGGTTCCCTTCCCTC 59.322 66.667 0.00 0.00 0.00 4.30
98 99 2.941583 GGGCTGGTTCCCTTCCCT 60.942 66.667 0.00 0.00 43.13 4.20
104 105 1.915983 CCTCTAAGGGCTGGTTCCC 59.084 63.158 0.00 0.00 46.93 3.97
114 115 4.554036 GCGCCCAGCCCTCTAAGG 62.554 72.222 0.00 0.00 40.81 2.69
138 139 2.916527 CTAGGTGCATGGGCCCAAGG 62.917 65.000 32.58 25.11 40.13 3.61
139 140 1.454479 CTAGGTGCATGGGCCCAAG 60.454 63.158 32.58 27.47 40.13 3.61
140 141 2.682846 CTAGGTGCATGGGCCCAA 59.317 61.111 32.58 10.32 40.13 4.12
141 142 3.419580 CCTAGGTGCATGGGCCCA 61.420 66.667 30.92 30.92 40.13 5.36
142 143 4.209866 CCCTAGGTGCATGGGCCC 62.210 72.222 17.59 17.59 40.13 5.80
143 144 4.209866 CCCCTAGGTGCATGGGCC 62.210 72.222 8.29 0.00 39.61 5.80
255 256 4.845307 GGAGGAGGGGGAAGGGGG 62.845 77.778 0.00 0.00 0.00 5.40
256 257 1.690148 ATAGGAGGAGGGGGAAGGGG 61.690 65.000 0.00 0.00 0.00 4.79
257 258 1.177104 TATAGGAGGAGGGGGAAGGG 58.823 60.000 0.00 0.00 0.00 3.95
258 259 3.362372 TTTATAGGAGGAGGGGGAAGG 57.638 52.381 0.00 0.00 0.00 3.46
259 260 5.916806 TCTATTTATAGGAGGAGGGGGAAG 58.083 45.833 0.00 0.00 0.00 3.46
260 261 5.222780 CCTCTATTTATAGGAGGAGGGGGAA 60.223 48.000 2.40 0.00 37.33 3.97
261 262 4.297935 CCTCTATTTATAGGAGGAGGGGGA 59.702 50.000 2.40 0.00 37.33 4.81
262 263 4.625963 CCTCTATTTATAGGAGGAGGGGG 58.374 52.174 2.40 0.00 37.33 5.40
265 266 4.034410 GCCCCTCTATTTATAGGAGGAGG 58.966 52.174 9.49 9.61 39.77 4.30
266 267 3.702045 CGCCCCTCTATTTATAGGAGGAG 59.298 52.174 9.49 0.00 34.58 3.69
267 268 3.335786 TCGCCCCTCTATTTATAGGAGGA 59.664 47.826 9.49 0.00 34.58 3.71
268 269 3.702045 CTCGCCCCTCTATTTATAGGAGG 59.298 52.174 0.00 0.00 34.58 4.30
269 270 3.702045 CCTCGCCCCTCTATTTATAGGAG 59.298 52.174 0.00 0.00 34.58 3.69
270 271 3.077088 ACCTCGCCCCTCTATTTATAGGA 59.923 47.826 0.00 0.00 34.58 2.94
271 272 3.195825 CACCTCGCCCCTCTATTTATAGG 59.804 52.174 0.00 0.00 0.00 2.57
272 273 4.087182 TCACCTCGCCCCTCTATTTATAG 58.913 47.826 0.00 0.00 0.00 1.31
273 274 4.087182 CTCACCTCGCCCCTCTATTTATA 58.913 47.826 0.00 0.00 0.00 0.98
274 275 2.900546 CTCACCTCGCCCCTCTATTTAT 59.099 50.000 0.00 0.00 0.00 1.40
275 276 2.317040 CTCACCTCGCCCCTCTATTTA 58.683 52.381 0.00 0.00 0.00 1.40
276 277 1.123928 CTCACCTCGCCCCTCTATTT 58.876 55.000 0.00 0.00 0.00 1.40
277 278 0.760945 CCTCACCTCGCCCCTCTATT 60.761 60.000 0.00 0.00 0.00 1.73
278 279 1.152440 CCTCACCTCGCCCCTCTAT 60.152 63.158 0.00 0.00 0.00 1.98
279 280 2.279073 CCTCACCTCGCCCCTCTA 59.721 66.667 0.00 0.00 0.00 2.43
280 281 4.787280 CCCTCACCTCGCCCCTCT 62.787 72.222 0.00 0.00 0.00 3.69
287 288 4.463879 CCTGCAGCCCTCACCTCG 62.464 72.222 8.66 0.00 0.00 4.63
288 289 1.965754 CTACCTGCAGCCCTCACCTC 61.966 65.000 8.66 0.00 0.00 3.85
289 290 1.992277 CTACCTGCAGCCCTCACCT 60.992 63.158 8.66 0.00 0.00 4.00
290 291 2.586792 CTACCTGCAGCCCTCACC 59.413 66.667 8.66 0.00 0.00 4.02
291 292 2.124942 GCTACCTGCAGCCCTCAC 60.125 66.667 8.66 0.00 42.31 3.51
402 404 7.396540 AATTCGGTCTTCTATTTTTGCAGAT 57.603 32.000 0.00 0.00 0.00 2.90
540 677 2.669924 CTGTGAATCGTGAGGACATGTG 59.330 50.000 1.15 0.00 34.90 3.21
569 717 0.463833 GGAGTGAATTGGCTACCGGG 60.464 60.000 6.32 0.00 0.00 5.73
574 722 2.852449 AGGAATGGGAGTGAATTGGCTA 59.148 45.455 0.00 0.00 0.00 3.93
736 942 2.930019 CTCCACTGGTCAGGGCCA 60.930 66.667 6.18 0.00 36.97 5.36
791 1002 3.258228 TTGCAGGCAGTGGAGCGAT 62.258 57.895 0.00 0.00 34.64 4.58
997 1208 0.605083 ACTGCTGAGCAAGTCATCGA 59.395 50.000 9.07 0.00 38.41 3.59
1016 1227 0.764271 TGAGTGGTGATGGACTGCAA 59.236 50.000 0.00 0.00 0.00 4.08
1053 1264 0.167470 CGAGCCGACGAACAGAGTTA 59.833 55.000 0.00 0.00 35.09 2.24
1148 1359 6.488683 TGACAATGATAAAACCCGAAAAGAGT 59.511 34.615 0.00 0.00 0.00 3.24
1156 1539 8.925161 ATACAATTTGACAATGATAAAACCCG 57.075 30.769 2.79 0.00 0.00 5.28
1235 1691 3.695556 TGTGCATCATGATGTTCGGATTT 59.304 39.130 31.09 0.00 40.80 2.17
1377 1842 0.530744 GTGATGGAGTGGAGCGTGTA 59.469 55.000 0.00 0.00 0.00 2.90
1419 1885 7.733773 TCTACTAGTTCATGGAAAAGATGGA 57.266 36.000 0.00 0.00 0.00 3.41
1423 1889 8.423906 AGTCTTCTACTAGTTCATGGAAAAGA 57.576 34.615 0.00 0.00 36.36 2.52
1509 1975 1.893137 GTCCCCAAATTCTCCAACCAC 59.107 52.381 0.00 0.00 0.00 4.16
1516 1982 1.354368 TCACCTGGTCCCCAAATTCTC 59.646 52.381 0.00 0.00 30.80 2.87
1564 2030 9.381033 ACTTGACATCAAACAAATCAATTTCAA 57.619 25.926 0.00 0.00 35.15 2.69
2013 2526 9.838339 ATAGTTCGGTCTTTCATAATTGAAGAT 57.162 29.630 0.00 0.00 42.60 2.40
2049 2562 3.368635 GGTTTGTTTGGTCCGGTCTTTTT 60.369 43.478 0.00 0.00 0.00 1.94
2185 2698 2.927856 TGGTGGTGATGGAGCGGT 60.928 61.111 0.00 0.00 0.00 5.68
2204 2717 1.968017 CCAACAGCAGCACGATGGT 60.968 57.895 0.00 0.00 34.42 3.55
2334 2848 2.417379 CGATTCAGATCACGGTGGACTT 60.417 50.000 8.50 0.00 32.33 3.01
2384 2898 1.398071 GCAAGACGGAAGCGTTACAAC 60.398 52.381 0.00 0.00 0.00 3.32
2568 3087 4.864704 ATCTACGCCCACAACAAAATTT 57.135 36.364 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.