Multiple sequence alignment - TraesCS5D01G261600

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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 TraesCS5D01G261600 chr5D 100.000 5304 0 0 1 5304 367980245 367985548 0.000000e+00 9795.0
1 TraesCS5D01G261600 chr5D 83.851 1579 247 5 1014 2587 367991281 367992856 0.000000e+00 1496.0
2 TraesCS5D01G261600 chr5D 86.036 1375 185 4 1014 2384 367996719 367998090 0.000000e+00 1469.0
3 TraesCS5D01G261600 chr5D 85.898 1319 167 11 932 2236 367812188 367813501 0.000000e+00 1387.0
4 TraesCS5D01G261600 chr5D 85.584 874 96 11 2732 3599 376353663 376354512 0.000000e+00 889.0
5 TraesCS5D01G261600 chr5D 95.094 530 20 6 4777 5304 45131535 45131010 0.000000e+00 830.0
6 TraesCS5D01G261600 chr5D 82.627 731 101 14 3832 4555 376354704 376355415 1.620000e-174 623.0
7 TraesCS5D01G261600 chr5D 83.509 285 38 8 3847 4128 367999165 367999443 1.900000e-64 257.0
8 TraesCS5D01G261600 chr5A 95.767 3591 97 23 43 3610 470032048 470035606 0.000000e+00 5738.0
9 TraesCS5D01G261600 chr5A 83.918 1567 243 5 1014 2574 470038824 470040387 0.000000e+00 1489.0
10 TraesCS5D01G261600 chr5A 96.497 885 25 4 3669 4551 470035613 470036493 0.000000e+00 1458.0
11 TraesCS5D01G261600 chr5A 85.693 1314 173 5 932 2236 469898822 469900129 0.000000e+00 1371.0
12 TraesCS5D01G261600 chr5A 84.811 1297 171 10 950 2236 469906300 469907580 0.000000e+00 1280.0
13 TraesCS5D01G261600 chr5A 84.695 869 98 14 2743 3599 477377303 477378148 0.000000e+00 835.0
14 TraesCS5D01G261600 chr5A 82.557 751 94 20 3832 4572 477378340 477379063 1.250000e-175 627.0
15 TraesCS5D01G261600 chr5A 94.737 133 4 1 4571 4700 470036743 470036875 2.500000e-48 204.0
16 TraesCS5D01G261600 chr5A 88.272 162 14 4 4696 4853 92199184 92199344 7.010000e-44 189.0
17 TraesCS5D01G261600 chr5B 94.225 3082 126 26 61 3118 435942154 435945207 0.000000e+00 4658.0
18 TraesCS5D01G261600 chr5B 94.262 1464 49 13 3101 4551 435945266 435946707 0.000000e+00 2206.0
19 TraesCS5D01G261600 chr5B 83.364 1611 255 11 1011 2614 436078316 436079920 0.000000e+00 1478.0
20 TraesCS5D01G261600 chr5B 94.350 531 19 8 4777 5304 21190063 21190585 0.000000e+00 804.0
21 TraesCS5D01G261600 chr5B 96.591 88 2 1 4614 4700 435947953 435948040 1.540000e-30 145.0
22 TraesCS5D01G261600 chr5B 77.689 251 44 9 3879 4128 436080694 436080933 5.540000e-30 143.0
23 TraesCS5D01G261600 chr5B 100.000 48 0 0 4571 4618 435947105 435947152 7.320000e-14 89.8
24 TraesCS5D01G261600 chr7D 92.320 638 16 9 4698 5304 182824459 182825094 0.000000e+00 876.0
25 TraesCS5D01G261600 chr7D 94.727 531 19 8 4777 5304 457146578 457146054 0.000000e+00 817.0
26 TraesCS5D01G261600 chr7D 94.677 526 17 7 4777 5300 138507529 138507013 0.000000e+00 806.0
27 TraesCS5D01G261600 chr6B 91.489 611 35 11 4701 5304 717509915 717509315 0.000000e+00 824.0
28 TraesCS5D01G261600 chr6B 93.023 86 6 0 3597 3682 137385853 137385768 5.580000e-25 126.0
29 TraesCS5D01G261600 chr6B 90.123 81 8 0 3597 3677 632187381 632187301 7.260000e-19 106.0
30 TraesCS5D01G261600 chr3D 94.915 531 20 7 4777 5304 384565764 384565238 0.000000e+00 824.0
31 TraesCS5D01G261600 chr1D 91.708 603 37 8 4705 5304 130283047 130282455 0.000000e+00 824.0
32 TraesCS5D01G261600 chr1D 94.896 529 16 7 4777 5304 17252308 17252826 0.000000e+00 817.0
33 TraesCS5D01G261600 chr3B 94.528 530 21 5 4777 5304 785867488 785866965 0.000000e+00 811.0
34 TraesCS5D01G261600 chr3B 89.278 485 29 16 4699 5166 19154381 19154859 2.130000e-163 586.0
35 TraesCS5D01G261600 chr3B 90.698 86 7 1 3598 3682 428685970 428685885 4.340000e-21 113.0
36 TraesCS5D01G261600 chr2B 89.873 632 33 11 4701 5304 51799590 51798962 0.000000e+00 784.0
37 TraesCS5D01G261600 chr2B 87.037 162 13 6 4699 4853 793026042 793025882 5.460000e-40 176.0
38 TraesCS5D01G261600 chr2B 88.764 89 10 0 3596 3684 3463082 3462994 5.620000e-20 110.0
39 TraesCS5D01G261600 chr2B 90.123 81 8 0 3599 3679 133850111 133850191 7.260000e-19 106.0
40 TraesCS5D01G261600 chr2B 83.495 103 13 3 3379 3479 473339482 473339382 5.660000e-15 93.5
41 TraesCS5D01G261600 chr2A 82.456 342 39 11 3269 3598 537013399 537013067 4.040000e-71 279.0
42 TraesCS5D01G261600 chr6D 92.500 80 6 0 3598 3677 127376981 127377060 1.210000e-21 115.0
43 TraesCS5D01G261600 chr6A 89.535 86 9 0 3598 3683 507148600 507148515 5.620000e-20 110.0
44 TraesCS5D01G261600 chr2D 84.211 114 14 3 3379 3490 399350470 399350359 2.020000e-19 108.0
45 TraesCS5D01G261600 chr4B 90.123 81 8 0 3599 3679 92663231 92663311 7.260000e-19 106.0


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 TraesCS5D01G261600 chr5D 367980245 367985548 5303 False 9795.00 9795 100.000000 1 5304 1 chr5D.!!$F2 5303
1 TraesCS5D01G261600 chr5D 367812188 367813501 1313 False 1387.00 1387 85.898000 932 2236 1 chr5D.!!$F1 1304
2 TraesCS5D01G261600 chr5D 367991281 367999443 8162 False 1074.00 1496 84.465333 1014 4128 3 chr5D.!!$F3 3114
3 TraesCS5D01G261600 chr5D 45131010 45131535 525 True 830.00 830 95.094000 4777 5304 1 chr5D.!!$R1 527
4 TraesCS5D01G261600 chr5D 376353663 376355415 1752 False 756.00 889 84.105500 2732 4555 2 chr5D.!!$F4 1823
5 TraesCS5D01G261600 chr5A 470032048 470040387 8339 False 2222.25 5738 92.729750 43 4700 4 chr5A.!!$F4 4657
6 TraesCS5D01G261600 chr5A 469898822 469900129 1307 False 1371.00 1371 85.693000 932 2236 1 chr5A.!!$F2 1304
7 TraesCS5D01G261600 chr5A 469906300 469907580 1280 False 1280.00 1280 84.811000 950 2236 1 chr5A.!!$F3 1286
8 TraesCS5D01G261600 chr5A 477377303 477379063 1760 False 731.00 835 83.626000 2743 4572 2 chr5A.!!$F5 1829
9 TraesCS5D01G261600 chr5B 435942154 435948040 5886 False 1774.70 4658 96.269500 61 4700 4 chr5B.!!$F2 4639
10 TraesCS5D01G261600 chr5B 436078316 436080933 2617 False 810.50 1478 80.526500 1011 4128 2 chr5B.!!$F3 3117
11 TraesCS5D01G261600 chr5B 21190063 21190585 522 False 804.00 804 94.350000 4777 5304 1 chr5B.!!$F1 527
12 TraesCS5D01G261600 chr7D 182824459 182825094 635 False 876.00 876 92.320000 4698 5304 1 chr7D.!!$F1 606
13 TraesCS5D01G261600 chr7D 457146054 457146578 524 True 817.00 817 94.727000 4777 5304 1 chr7D.!!$R2 527
14 TraesCS5D01G261600 chr7D 138507013 138507529 516 True 806.00 806 94.677000 4777 5300 1 chr7D.!!$R1 523
15 TraesCS5D01G261600 chr6B 717509315 717509915 600 True 824.00 824 91.489000 4701 5304 1 chr6B.!!$R3 603
16 TraesCS5D01G261600 chr3D 384565238 384565764 526 True 824.00 824 94.915000 4777 5304 1 chr3D.!!$R1 527
17 TraesCS5D01G261600 chr1D 130282455 130283047 592 True 824.00 824 91.708000 4705 5304 1 chr1D.!!$R1 599
18 TraesCS5D01G261600 chr1D 17252308 17252826 518 False 817.00 817 94.896000 4777 5304 1 chr1D.!!$F1 527
19 TraesCS5D01G261600 chr3B 785866965 785867488 523 True 811.00 811 94.528000 4777 5304 1 chr3B.!!$R2 527
20 TraesCS5D01G261600 chr2B 51798962 51799590 628 True 784.00 784 89.873000 4701 5304 1 chr2B.!!$R2 603

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
21 22 0.242286 CAGCTACACAGTCTGACGCT 59.758 55.0 6.91 5.59 31.46 5.07 F
22 23 0.523966 AGCTACACAGTCTGACGCTC 59.476 55.0 6.91 0.00 0.00 5.03 F
46 47 0.527565 GCGTTACACGAAGGTCCCTA 59.472 55.0 0.00 0.00 46.05 3.53 F
593 623 0.749649 ACATGAGAGGAGATGGCGAC 59.250 55.0 0.00 0.00 0.00 5.19 F
939 981 1.378531 TGCGGGACTGCATCATTAAC 58.621 50.0 0.86 0.00 40.62 2.01 F
1407 6893 2.030540 CCTTGCAACTGGTGAATGTCTG 60.031 50.0 0.00 0.00 0.00 3.51 F
1824 7323 2.293677 CTGGATCAGAGAAATGCATGGC 59.706 50.0 0.00 0.00 32.44 4.40 F
2267 7772 3.418995 GTGAGGCAGAGGATATACGGTA 58.581 50.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 7248 0.179084 GCTCTGCCGGCAGTTGTATA 60.179 55.000 45.86 29.79 43.96 1.47 R
1837 7336 2.755650 ACGACTTGGTTGAGCAGTTAG 58.244 47.619 0.00 0.00 0.00 2.34 R
2357 7863 4.048504 GCAAGTTAGCGGTTTGTCAAAAT 58.951 39.130 0.00 0.00 0.00 1.82 R
2809 8400 3.374764 GGGGACTTTGGCTATTGGAAAT 58.625 45.455 0.00 0.00 0.00 2.17 R
3240 8923 4.256110 TCGAGAACATGCAAGTCATTCAT 58.744 39.130 0.00 0.00 31.79 2.57 R
3722 9416 2.798976 TCCAGCAAACATGAAACTGC 57.201 45.000 0.00 2.27 34.96 4.40 R
4134 10034 1.511318 CGTCAACACGGGCAATGGAA 61.511 55.000 0.00 0.00 42.73 3.53 R
4502 10415 0.109086 GAACTACAGCGCAGAGAGCA 60.109 55.000 11.47 0.00 46.13 4.26 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
19 20 0.598562 ACCAGCTACACAGTCTGACG 59.401 55.000 6.91 0.00 31.46 4.35
20 21 0.734253 CCAGCTACACAGTCTGACGC 60.734 60.000 6.91 3.35 31.46 5.19
21 22 0.242286 CAGCTACACAGTCTGACGCT 59.758 55.000 6.91 5.59 31.46 5.07
22 23 0.523966 AGCTACACAGTCTGACGCTC 59.476 55.000 6.91 0.00 0.00 5.03
23 24 0.794981 GCTACACAGTCTGACGCTCG 60.795 60.000 6.91 0.00 0.00 5.03
24 25 0.794981 CTACACAGTCTGACGCTCGC 60.795 60.000 6.91 0.00 0.00 5.03
25 26 2.508755 TACACAGTCTGACGCTCGCG 62.509 60.000 6.91 10.06 46.03 5.87
26 27 4.406173 ACAGTCTGACGCTCGCGG 62.406 66.667 16.18 0.00 44.69 6.46
37 38 4.764336 CTCGCGGGCGTTACACGA 62.764 66.667 13.21 0.00 46.05 4.35
38 39 4.340019 TCGCGGGCGTTACACGAA 62.340 61.111 13.21 0.00 46.05 3.85
39 40 3.834373 CGCGGGCGTTACACGAAG 61.834 66.667 4.64 0.00 46.05 3.79
40 41 3.484547 GCGGGCGTTACACGAAGG 61.485 66.667 0.00 0.00 46.05 3.46
41 42 2.048877 CGGGCGTTACACGAAGGT 60.049 61.111 0.00 0.00 46.05 3.50
46 47 0.527565 GCGTTACACGAAGGTCCCTA 59.472 55.000 0.00 0.00 46.05 3.53
56 57 2.620886 CGAAGGTCCCTACTCTTCCTCA 60.621 54.545 0.00 0.00 33.13 3.86
117 118 2.043953 GAACCTGGGCCCCACATC 60.044 66.667 22.27 9.28 0.00 3.06
147 148 7.762588 ACACACTACTCTACCATATATGTCC 57.237 40.000 11.73 0.00 0.00 4.02
148 149 6.720288 ACACACTACTCTACCATATATGTCCC 59.280 42.308 11.73 0.00 0.00 4.46
149 150 6.948886 CACACTACTCTACCATATATGTCCCT 59.051 42.308 11.73 0.00 0.00 4.20
150 151 7.451877 CACACTACTCTACCATATATGTCCCTT 59.548 40.741 11.73 0.00 0.00 3.95
152 153 7.891183 CACTACTCTACCATATATGTCCCTTCT 59.109 40.741 11.73 0.00 0.00 2.85
153 154 9.125255 ACTACTCTACCATATATGTCCCTTCTA 57.875 37.037 11.73 0.00 0.00 2.10
161 168 8.960064 ACCATATATGTCCCTTCTATCCTTTTT 58.040 33.333 11.73 0.00 0.00 1.94
382 407 1.404717 CCGTGATTGTGAGTCCTCCAG 60.405 57.143 0.00 0.00 0.00 3.86
430 456 2.269241 GGCTGTTTCCTCCTCCGG 59.731 66.667 0.00 0.00 0.00 5.14
583 613 1.471676 GCAGTTCGGGTACATGAGAGG 60.472 57.143 0.00 0.00 0.00 3.69
584 614 2.100197 CAGTTCGGGTACATGAGAGGA 58.900 52.381 0.00 0.00 0.00 3.71
585 615 2.099921 CAGTTCGGGTACATGAGAGGAG 59.900 54.545 0.00 0.00 0.00 3.69
589 619 1.615883 CGGGTACATGAGAGGAGATGG 59.384 57.143 0.00 0.00 0.00 3.51
593 623 0.749649 ACATGAGAGGAGATGGCGAC 59.250 55.000 0.00 0.00 0.00 5.19
607 641 3.678056 TGGCGACAACATTAGAGTTCT 57.322 42.857 0.00 0.00 37.44 3.01
608 642 4.002906 TGGCGACAACATTAGAGTTCTT 57.997 40.909 0.00 0.00 37.44 2.52
609 643 3.994392 TGGCGACAACATTAGAGTTCTTC 59.006 43.478 0.00 0.00 37.44 2.87
610 644 4.246458 GGCGACAACATTAGAGTTCTTCT 58.754 43.478 0.00 0.00 40.06 2.85
611 645 4.691216 GGCGACAACATTAGAGTTCTTCTT 59.309 41.667 0.00 0.00 37.36 2.52
612 646 5.179555 GGCGACAACATTAGAGTTCTTCTTT 59.820 40.000 0.00 0.00 37.36 2.52
652 686 8.118893 CGAAAGATTATGCTTTTGGTAATTGG 57.881 34.615 0.00 0.00 38.16 3.16
673 707 5.435820 GGTAACATTGTTTTACCGTGGAA 57.564 39.130 7.45 0.00 39.28 3.53
698 732 5.034797 CGGAAGAGGCGAATTTATTTTTCC 58.965 41.667 0.00 0.00 0.00 3.13
754 788 2.973694 TTTAGATGCCGTCAGTACCC 57.026 50.000 0.00 0.00 0.00 3.69
849 890 6.866248 TCTTCCTTTGCCGACAAAATAATTTC 59.134 34.615 0.00 0.00 44.90 2.17
939 981 1.378531 TGCGGGACTGCATCATTAAC 58.621 50.000 0.86 0.00 40.62 2.01
1086 6572 5.559035 CGACCTCATTGAGCGGATATTTTTC 60.559 44.000 8.23 0.00 0.00 2.29
1269 6755 7.980662 CCTAGTGATGCTATCCTAATTGATGAG 59.019 40.741 0.00 0.00 0.00 2.90
1380 6866 6.205464 ACACAAAGACATCAACGATCAAGATT 59.795 34.615 0.00 0.00 0.00 2.40
1407 6893 2.030540 CCTTGCAACTGGTGAATGTCTG 60.031 50.000 0.00 0.00 0.00 3.51
1731 7230 6.240894 TGCAGTTATTTCCTTTGATCTCAGT 58.759 36.000 0.00 0.00 0.00 3.41
1749 7248 3.938963 TCAGTGAAGAAAGTTTTGCGACT 59.061 39.130 0.00 0.00 0.00 4.18
1824 7323 2.293677 CTGGATCAGAGAAATGCATGGC 59.706 50.000 0.00 0.00 32.44 4.40
2267 7772 3.418995 GTGAGGCAGAGGATATACGGTA 58.581 50.000 0.00 0.00 0.00 4.02
2357 7863 9.709495 CTTGATGAATGTTCCTTATTTTGGAAA 57.291 29.630 0.00 0.00 44.14 3.13
2806 8397 3.765026 AGTGCGTTAACAAGTGTTTTGG 58.235 40.909 6.39 0.00 39.31 3.28
2809 8400 4.621886 GTGCGTTAACAAGTGTTTTGGAAA 59.378 37.500 6.39 0.00 39.31 3.13
3045 8646 8.441608 GCACATGATAACATCTTGAGTATCATC 58.558 37.037 0.00 0.00 38.91 2.92
3627 9318 7.114529 CACTCCATTCCTAAATATACGACGTTC 59.885 40.741 5.50 0.00 0.00 3.95
3679 9373 8.095169 ACGTCATATATTTAGAAATGGAGGGAC 58.905 37.037 0.00 0.00 0.00 4.46
3722 9416 5.599359 TTTCATGTTCTTGCATGCATTTG 57.401 34.783 23.37 14.73 44.20 2.32
4134 10034 1.943507 GCTGGCGCTTCTTCTTCTTCT 60.944 52.381 7.64 0.00 0.00 2.85
4147 10047 1.470098 CTTCTTCTTCCATTGCCCGTG 59.530 52.381 0.00 0.00 0.00 4.94
4239 10143 7.523293 TGTCTCTATTTCATCCTGAGAGATC 57.477 40.000 3.43 0.00 43.29 2.75
4284 10188 2.196245 GCCCCCTTCGATTGGATGC 61.196 63.158 6.55 5.15 0.00 3.91
4306 10210 0.666577 GCAGCCGTTGTTCGTAGTCT 60.667 55.000 0.00 0.00 37.94 3.24
4357 10261 6.562640 GCTTGTTGTCATTACATTGCACTTTG 60.563 38.462 0.00 0.00 34.97 2.77
4502 10415 2.283145 AAGTGTCAGGCTTCATGCTT 57.717 45.000 0.00 0.00 42.39 3.91
4551 10464 5.268118 AGTTCTCACGATATGCATCTGAA 57.732 39.130 0.19 0.00 0.00 3.02
4552 10465 5.851720 AGTTCTCACGATATGCATCTGAAT 58.148 37.500 0.19 0.00 0.00 2.57
4553 10466 6.986250 AGTTCTCACGATATGCATCTGAATA 58.014 36.000 0.19 0.00 0.00 1.75
4555 10468 7.758980 AGTTCTCACGATATGCATCTGAATATC 59.241 37.037 0.19 7.78 38.93 1.63
4558 10471 7.121759 TCTCACGATATGCATCTGAATATCTGA 59.878 37.037 0.19 13.74 39.75 3.27
4559 10472 7.779073 TCACGATATGCATCTGAATATCTGAT 58.221 34.615 0.19 0.00 39.75 2.90
4569 10482 8.392372 CATCTGAATATCTGATGTTGTGGATT 57.608 34.615 15.17 0.00 43.49 3.01
4635 11733 2.599408 AGACTCTTCCTACGGTCCAA 57.401 50.000 0.00 0.00 0.00 3.53
4651 11749 4.226761 GGTCCAACTATTGCGTCTTTTTG 58.773 43.478 0.00 0.00 0.00 2.44
4703 11801 4.012138 GCCGGTGGTTTATGGCTT 57.988 55.556 1.90 0.00 44.16 4.35
4810 11943 0.107214 GGCCGATTGGATTCCAGTCA 60.107 55.000 23.32 3.75 39.75 3.41
4899 12533 3.726607 CTGTGGGCTAATTGTTTTTGCA 58.273 40.909 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.794981 GCGAGCGTCAGACTGTGTAG 60.795 60.000 1.59 0.00 0.00 2.74
6 7 1.209383 GCGAGCGTCAGACTGTGTA 59.791 57.895 1.59 0.00 0.00 2.90
7 8 2.049985 GCGAGCGTCAGACTGTGT 60.050 61.111 1.59 0.00 0.00 3.72
8 9 3.168604 CGCGAGCGTCAGACTGTG 61.169 66.667 0.00 0.00 34.35 3.66
9 10 4.406173 CCGCGAGCGTCAGACTGT 62.406 66.667 8.23 0.00 37.81 3.55
29 30 3.087781 AGAGTAGGGACCTTCGTGTAAC 58.912 50.000 0.00 0.00 0.00 2.50
30 31 3.446442 AGAGTAGGGACCTTCGTGTAA 57.554 47.619 0.00 0.00 0.00 2.41
31 32 3.350833 GAAGAGTAGGGACCTTCGTGTA 58.649 50.000 0.00 0.00 0.00 2.90
32 33 2.169330 GAAGAGTAGGGACCTTCGTGT 58.831 52.381 0.00 0.00 0.00 4.49
33 34 1.477295 GGAAGAGTAGGGACCTTCGTG 59.523 57.143 0.00 0.00 35.42 4.35
34 35 1.358445 AGGAAGAGTAGGGACCTTCGT 59.642 52.381 0.00 0.00 35.42 3.85
35 36 2.025898 GAGGAAGAGTAGGGACCTTCG 58.974 57.143 0.00 0.00 35.42 3.79
36 37 3.103080 TGAGGAAGAGTAGGGACCTTC 57.897 52.381 0.00 0.00 34.58 3.46
37 38 3.562108 TTGAGGAAGAGTAGGGACCTT 57.438 47.619 0.00 0.00 0.00 3.50
38 39 3.174779 GTTTGAGGAAGAGTAGGGACCT 58.825 50.000 0.00 0.00 0.00 3.85
39 40 3.174779 AGTTTGAGGAAGAGTAGGGACC 58.825 50.000 0.00 0.00 0.00 4.46
40 41 4.570930 CAAGTTTGAGGAAGAGTAGGGAC 58.429 47.826 0.00 0.00 0.00 4.46
41 42 3.008049 GCAAGTTTGAGGAAGAGTAGGGA 59.992 47.826 0.00 0.00 0.00 4.20
46 47 2.213499 CGTGCAAGTTTGAGGAAGAGT 58.787 47.619 0.00 0.00 0.00 3.24
90 91 3.322466 CCAGGTTCGGCCCAGTCT 61.322 66.667 0.00 0.00 38.26 3.24
91 92 4.410400 CCCAGGTTCGGCCCAGTC 62.410 72.222 0.00 0.00 38.26 3.51
179 186 2.550180 GCAGGAAGGAACAGAACAGAAC 59.450 50.000 0.00 0.00 0.00 3.01
345 370 3.040763 GGCGCGATCAGGATCAGC 61.041 66.667 12.10 14.52 39.09 4.26
444 473 2.265467 TTACAGATGGAAGGGGCGCC 62.265 60.000 21.18 21.18 0.00 6.53
532 561 6.491062 AGTGTCAAATCCAAGAACAATCATGA 59.509 34.615 0.00 0.00 0.00 3.07
583 613 3.786635 ACTCTAATGTTGTCGCCATCTC 58.213 45.455 0.00 0.00 0.00 2.75
584 614 3.895232 ACTCTAATGTTGTCGCCATCT 57.105 42.857 0.00 0.00 0.00 2.90
585 615 4.184629 AGAACTCTAATGTTGTCGCCATC 58.815 43.478 0.00 0.00 0.00 3.51
589 619 5.847670 AAGAAGAACTCTAATGTTGTCGC 57.152 39.130 0.00 0.00 32.46 5.19
619 653 7.359181 CCAAAAGCATAATCTTTCGGTCAAAAC 60.359 37.037 0.00 0.00 35.41 2.43
652 686 5.396070 CGTTTCCACGGTAAAACAATGTTAC 59.604 40.000 0.00 0.00 43.16 2.50
673 707 5.638596 AAAATAAATTCGCCTCTTCCGTT 57.361 34.783 0.00 0.00 0.00 4.44
682 716 7.414814 TTTTGACTGGAAAAATAAATTCGCC 57.585 32.000 0.00 0.00 0.00 5.54
698 732 4.536065 TGCAGCGTCTAAAATTTTGACTG 58.464 39.130 13.76 12.88 0.00 3.51
711 745 2.423018 TGCTCTGTTGCAGCGTCT 59.577 55.556 0.00 0.00 40.01 4.18
754 788 2.753043 AGCCAATGCGCCAAGGAG 60.753 61.111 4.18 0.00 44.33 3.69
828 869 6.777526 TTGAAATTATTTTGTCGGCAAAGG 57.222 33.333 15.65 0.00 44.32 3.11
849 890 7.596749 ATTACTAGACAGAAAACGGTCATTG 57.403 36.000 0.00 0.00 36.50 2.82
939 981 2.620115 ACTCTGCAAACACACATTCCAG 59.380 45.455 0.00 0.00 0.00 3.86
1062 6548 2.732412 ATATCCGCTCAATGAGGTCG 57.268 50.000 12.66 7.77 36.93 4.79
1086 6572 0.250640 AAGTGCTCACTGGAAGCCTG 60.251 55.000 2.97 0.00 41.58 4.85
1269 6755 4.736896 GTCGACGGTGACCAGGCC 62.737 72.222 1.11 0.00 32.61 5.19
1380 6866 1.133945 TCACCAGTTGCAAGGTTAGCA 60.134 47.619 7.61 0.00 40.85 3.49
1407 6893 4.074970 TCTTGGAAGGTTTCTCAAGATGC 58.925 43.478 13.70 0.00 39.65 3.91
1731 7230 7.225931 AGTTGTATAGTCGCAAAACTTTCTTCA 59.774 33.333 0.00 0.00 0.00 3.02
1749 7248 0.179084 GCTCTGCCGGCAGTTGTATA 60.179 55.000 45.86 29.79 43.96 1.47
1824 7323 7.645340 GGTTGAGCAGTTAGTATGCATATTTTG 59.355 37.037 10.16 6.68 46.31 2.44
1837 7336 2.755650 ACGACTTGGTTGAGCAGTTAG 58.244 47.619 0.00 0.00 0.00 2.34
2357 7863 4.048504 GCAAGTTAGCGGTTTGTCAAAAT 58.951 39.130 0.00 0.00 0.00 1.82
2498 8087 6.590068 AGAGAATCACCTGACTTGGATTATG 58.410 40.000 0.00 0.00 37.82 1.90
2678 8269 5.246307 GTCAGTTGTTTGGCCTAGTCTTAT 58.754 41.667 3.32 0.00 0.00 1.73
2806 8397 5.419542 GGGACTTTGGCTATTGGAAATTTC 58.580 41.667 9.83 9.83 0.00 2.17
2809 8400 3.374764 GGGGACTTTGGCTATTGGAAAT 58.625 45.455 0.00 0.00 0.00 2.17
3045 8646 4.390909 ACCTTATCCGACTTAAAACTTGCG 59.609 41.667 0.00 0.00 0.00 4.85
3235 8918 7.699391 CGAGAACATGCAAGTCATTCATTTATT 59.301 33.333 0.00 0.00 31.79 1.40
3236 8919 7.066163 TCGAGAACATGCAAGTCATTCATTTAT 59.934 33.333 0.00 0.00 31.79 1.40
3237 8920 6.371271 TCGAGAACATGCAAGTCATTCATTTA 59.629 34.615 0.00 0.00 31.79 1.40
3238 8921 5.181811 TCGAGAACATGCAAGTCATTCATTT 59.818 36.000 0.00 0.00 31.79 2.32
3239 8922 4.696877 TCGAGAACATGCAAGTCATTCATT 59.303 37.500 0.00 0.00 31.79 2.57
3240 8923 4.256110 TCGAGAACATGCAAGTCATTCAT 58.744 39.130 0.00 0.00 31.79 2.57
3390 9074 3.067106 AGTGCACGGTGAGTTGAATAAG 58.933 45.455 13.29 0.00 0.00 1.73
3391 9075 3.120321 AGTGCACGGTGAGTTGAATAA 57.880 42.857 13.29 0.00 0.00 1.40
3620 9311 4.446385 TCAATTTGAACTACCAGAACGTCG 59.554 41.667 0.00 0.00 0.00 5.12
3654 9348 8.314751 AGTCCCTCCATTTCTAAATATATGACG 58.685 37.037 0.00 0.00 0.00 4.35
3722 9416 2.798976 TCCAGCAAACATGAAACTGC 57.201 45.000 0.00 2.27 34.96 4.40
4134 10034 1.511318 CGTCAACACGGGCAATGGAA 61.511 55.000 0.00 0.00 42.73 3.53
4147 10047 4.872664 TCTTCTTCCTTCTTCTCGTCAAC 58.127 43.478 0.00 0.00 0.00 3.18
4239 10143 0.984230 TCCTTGGCAGAGGTTACAGG 59.016 55.000 13.15 3.89 38.04 4.00
4267 10171 1.893808 CGCATCCAATCGAAGGGGG 60.894 63.158 7.35 0.00 0.00 5.40
4403 10309 2.525368 TCGTTCCTGTTGGATCTCTCA 58.475 47.619 0.00 0.00 42.81 3.27
4491 10403 3.203147 GCAGAGAGCAAGCATGAAGCC 62.203 57.143 0.00 0.00 44.15 4.35
4502 10415 0.109086 GAACTACAGCGCAGAGAGCA 60.109 55.000 11.47 0.00 46.13 4.26
4551 10464 7.000472 CCAGGTTAATCCACAACATCAGATAT 59.000 38.462 0.00 0.00 39.02 1.63
4552 10465 6.356556 CCAGGTTAATCCACAACATCAGATA 58.643 40.000 0.00 0.00 39.02 1.98
4553 10466 5.195940 CCAGGTTAATCCACAACATCAGAT 58.804 41.667 0.00 0.00 39.02 2.90
4555 10468 3.696051 CCCAGGTTAATCCACAACATCAG 59.304 47.826 0.00 0.00 39.02 2.90
4558 10471 3.333680 AGTCCCAGGTTAATCCACAACAT 59.666 43.478 0.00 0.00 39.02 2.71
4559 10472 2.714250 AGTCCCAGGTTAATCCACAACA 59.286 45.455 0.00 0.00 39.02 3.33
4561 10474 3.396276 TCAAGTCCCAGGTTAATCCACAA 59.604 43.478 0.00 0.00 39.02 3.33
4563 10476 3.263425 TCTCAAGTCCCAGGTTAATCCAC 59.737 47.826 0.00 0.00 39.02 4.02
4564 10477 3.526899 TCTCAAGTCCCAGGTTAATCCA 58.473 45.455 0.00 0.00 39.02 3.41
4565 10478 4.019231 AGTTCTCAAGTCCCAGGTTAATCC 60.019 45.833 0.00 0.00 0.00 3.01
4566 10479 5.167303 AGTTCTCAAGTCCCAGGTTAATC 57.833 43.478 0.00 0.00 0.00 1.75
4567 10480 5.584551 AAGTTCTCAAGTCCCAGGTTAAT 57.415 39.130 0.00 0.00 0.00 1.40
4569 10482 5.783360 TGATAAGTTCTCAAGTCCCAGGTTA 59.217 40.000 0.00 0.00 0.00 2.85
4635 11733 2.817844 GGGACCAAAAAGACGCAATAGT 59.182 45.455 0.00 0.00 0.00 2.12
4651 11749 0.530870 GCTAGCAATCACTCGGGACC 60.531 60.000 10.63 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.