Multiple sequence alignment - TraesCS1A01G087600

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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 TraesCS1A01G087600 chr1A 100.000 3927 0 0 1 3927 74746508 74742582 0.000000e+00 7252.0
1 TraesCS1A01G087600 chr1A 86.965 537 67 3 2 537 116535478 116534944 5.610000e-168 601.0
2 TraesCS1A01G087600 chr1A 89.535 86 8 1 542 626 436069213 436069298 1.490000e-19 108.0
3 TraesCS1A01G087600 chr1A 95.000 40 0 2 3750 3787 74742727 74742688 1.180000e-05 62.1
4 TraesCS1A01G087600 chr1A 95.000 40 0 2 3782 3821 74742759 74742722 1.180000e-05 62.1
5 TraesCS1A01G087600 chr4A 97.415 2128 43 7 719 2843 58577803 58579921 0.000000e+00 3615.0
6 TraesCS1A01G087600 chr4A 96.575 146 5 0 3782 3927 58579981 58580126 3.920000e-60 243.0
7 TraesCS1A01G087600 chr4A 92.537 134 9 1 542 675 58577664 58577796 1.440000e-44 191.0
8 TraesCS1A01G087600 chr4A 97.872 94 2 0 3689 3782 58579920 58580013 3.140000e-36 163.0
9 TraesCS1A01G087600 chr6A 92.643 1237 72 13 2555 3777 523556094 523557325 0.000000e+00 1762.0
10 TraesCS1A01G087600 chr6A 92.109 735 49 7 1833 2563 523554584 523555313 0.000000e+00 1027.0
11 TraesCS1A01G087600 chr6A 90.670 418 34 5 1428 1842 523554145 523554560 5.740000e-153 551.0
12 TraesCS1A01G087600 chr6A 87.603 484 47 9 107 585 234098287 234098762 2.060000e-152 549.0
13 TraesCS1A01G087600 chr6A 83.838 99 14 2 542 638 167189072 167189170 4.180000e-15 93.5
14 TraesCS1A01G087600 chr2B 95.263 760 26 8 3027 3782 17847687 17848440 0.000000e+00 1195.0
15 TraesCS1A01G087600 chr2B 97.872 47 1 0 3782 3828 17848408 17848454 9.040000e-12 82.4
16 TraesCS1A01G087600 chrUn 83.899 1149 128 25 2283 3410 332008071 332009183 0.000000e+00 1044.0
17 TraesCS1A01G087600 chr3D 93.678 696 41 2 692 1387 438174432 438173740 0.000000e+00 1038.0
18 TraesCS1A01G087600 chr3D 86.290 124 11 5 3322 3443 313814068 313814187 3.180000e-26 130.0
19 TraesCS1A01G087600 chr3D 90.164 61 4 2 3615 3674 20534084 20534025 1.170000e-10 78.7
20 TraesCS1A01G087600 chr6D 93.768 690 39 3 698 1387 135104116 135104801 0.000000e+00 1033.0
21 TraesCS1A01G087600 chr6D 93.260 549 32 4 692 1240 76017135 76016592 0.000000e+00 804.0
22 TraesCS1A01G087600 chr6D 93.768 353 16 3 833 1185 77674831 77674485 3.480000e-145 525.0
23 TraesCS1A01G087600 chr6D 93.627 204 13 0 1184 1387 77674401 77674198 4.930000e-79 305.0
24 TraesCS1A01G087600 chr2A 93.094 695 43 4 693 1387 46360846 46360157 0.000000e+00 1013.0
25 TraesCS1A01G087600 chr2A 84.466 103 13 3 542 641 191884092 191884194 8.980000e-17 99.0
26 TraesCS1A01G087600 chr7A 92.253 697 49 4 692 1387 65379368 65378676 0.000000e+00 983.0
27 TraesCS1A01G087600 chr7A 88.848 547 55 6 2 544 711594139 711593595 0.000000e+00 667.0
28 TraesCS1A01G087600 chr7A 87.273 110 11 2 1281 1387 315506013 315506122 5.330000e-24 122.0
29 TraesCS1A01G087600 chr7A 83.495 103 11 5 542 640 585992867 585992767 1.500000e-14 91.6
30 TraesCS1A01G087600 chr7A 92.105 38 3 0 3619 3656 810243 810206 2.000000e-03 54.7
31 TraesCS1A01G087600 chr7D 92.896 549 34 4 692 1240 37889564 37890107 0.000000e+00 793.0
32 TraesCS1A01G087600 chr7D 91.028 535 45 3 2 535 100982776 100983308 0.000000e+00 719.0
33 TraesCS1A01G087600 chr7D 86.325 117 12 3 3329 3443 607218072 607217958 1.480000e-24 124.0
34 TraesCS1A01G087600 chr4D 92.350 549 35 6 692 1240 403167291 403166750 0.000000e+00 774.0
35 TraesCS1A01G087600 chr7B 90.018 541 47 5 2 537 391062965 391063503 0.000000e+00 693.0
36 TraesCS1A01G087600 chr5A 87.479 591 56 9 2 588 595906307 595905731 0.000000e+00 665.0
37 TraesCS1A01G087600 chr5A 87.523 537 64 3 2 537 36497338 36496804 5.580000e-173 617.0
38 TraesCS1A01G087600 chr1B 88.342 549 52 8 6 550 172254607 172255147 0.000000e+00 649.0
39 TraesCS1A01G087600 chr1B 86.916 107 14 0 1281 1387 469196042 469196148 1.920000e-23 121.0
40 TraesCS1A01G087600 chr1D 89.438 445 41 3 2 446 202318356 202318794 1.230000e-154 556.0
41 TraesCS1A01G087600 chr1D 89.011 364 35 4 1026 1387 458112982 458113342 2.780000e-121 446.0
42 TraesCS1A01G087600 chr3B 81.982 555 74 13 2561 3100 206179157 206178614 7.740000e-122 448.0
43 TraesCS1A01G087600 chr3B 80.597 134 18 6 510 640 357699963 357699835 3.230000e-16 97.1
44 TraesCS1A01G087600 chr3B 82.569 109 14 5 538 643 461052233 461052127 1.500000e-14 91.6
45 TraesCS1A01G087600 chr2D 81.763 329 49 6 2643 2960 39470634 39470306 8.370000e-67 265.0
46 TraesCS1A01G087600 chr2D 83.051 118 15 3 3330 3443 585212508 585212392 6.940000e-18 102.0
47 TraesCS1A01G087600 chr4B 84.559 136 14 5 502 634 28252143 28252012 1.150000e-25 128.0
48 TraesCS1A01G087600 chr4B 83.824 136 15 5 502 634 28257265 28257134 5.330000e-24 122.0
49 TraesCS1A01G087600 chr5D 84.706 85 12 1 3610 3694 334932538 334932621 2.510000e-12 84.2
50 TraesCS1A01G087600 chr5D 97.297 37 1 0 3619 3655 497944934 497944970 3.280000e-06 63.9
51 TraesCS1A01G087600 chr5B 94.595 37 2 0 3619 3655 617235035 617235071 1.520000e-04 58.4


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 TraesCS1A01G087600 chr1A 74742582 74746508 3926 True 2458.733333 7252 96.666667 1 3927 3 chr1A.!!$R2 3926
1 TraesCS1A01G087600 chr1A 116534944 116535478 534 True 601.000000 601 86.965000 2 537 1 chr1A.!!$R1 535
2 TraesCS1A01G087600 chr4A 58577664 58580126 2462 False 1053.000000 3615 96.099750 542 3927 4 chr4A.!!$F1 3385
3 TraesCS1A01G087600 chr6A 523554145 523557325 3180 False 1113.333333 1762 91.807333 1428 3777 3 chr6A.!!$F3 2349
4 TraesCS1A01G087600 chr2B 17847687 17848454 767 False 638.700000 1195 96.567500 3027 3828 2 chr2B.!!$F1 801
5 TraesCS1A01G087600 chrUn 332008071 332009183 1112 False 1044.000000 1044 83.899000 2283 3410 1 chrUn.!!$F1 1127
6 TraesCS1A01G087600 chr3D 438173740 438174432 692 True 1038.000000 1038 93.678000 692 1387 1 chr3D.!!$R2 695
7 TraesCS1A01G087600 chr6D 135104116 135104801 685 False 1033.000000 1033 93.768000 698 1387 1 chr6D.!!$F1 689
8 TraesCS1A01G087600 chr6D 76016592 76017135 543 True 804.000000 804 93.260000 692 1240 1 chr6D.!!$R1 548
9 TraesCS1A01G087600 chr6D 77674198 77674831 633 True 415.000000 525 93.697500 833 1387 2 chr6D.!!$R2 554
10 TraesCS1A01G087600 chr2A 46360157 46360846 689 True 1013.000000 1013 93.094000 693 1387 1 chr2A.!!$R1 694
11 TraesCS1A01G087600 chr7A 65378676 65379368 692 True 983.000000 983 92.253000 692 1387 1 chr7A.!!$R2 695
12 TraesCS1A01G087600 chr7A 711593595 711594139 544 True 667.000000 667 88.848000 2 544 1 chr7A.!!$R4 542
13 TraesCS1A01G087600 chr7D 37889564 37890107 543 False 793.000000 793 92.896000 692 1240 1 chr7D.!!$F1 548
14 TraesCS1A01G087600 chr7D 100982776 100983308 532 False 719.000000 719 91.028000 2 535 1 chr7D.!!$F2 533
15 TraesCS1A01G087600 chr4D 403166750 403167291 541 True 774.000000 774 92.350000 692 1240 1 chr4D.!!$R1 548
16 TraesCS1A01G087600 chr7B 391062965 391063503 538 False 693.000000 693 90.018000 2 537 1 chr7B.!!$F1 535
17 TraesCS1A01G087600 chr5A 595905731 595906307 576 True 665.000000 665 87.479000 2 588 1 chr5A.!!$R2 586
18 TraesCS1A01G087600 chr5A 36496804 36497338 534 True 617.000000 617 87.523000 2 537 1 chr5A.!!$R1 535
19 TraesCS1A01G087600 chr1B 172254607 172255147 540 False 649.000000 649 88.342000 6 550 1 chr1B.!!$F1 544
20 TraesCS1A01G087600 chr3B 206178614 206179157 543 True 448.000000 448 81.982000 2561 3100 1 chr3B.!!$R1 539

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
219 243 0.102481 GCGAGGAGTAGATTGCGGAA 59.898 55.000 0.00 0.0 0.00 4.30 F
389 413 0.304705 GACAATGCGGCAACTATCGG 59.695 55.000 6.82 0.0 0.00 4.18 F
1300 1421 1.004862 TGGTATTTGCGGGGAACATGA 59.995 47.619 0.00 0.0 0.00 3.07 F
1657 1781 2.097629 TGTCTATTCTTCAGGCGAGACG 59.902 50.000 0.00 0.0 36.86 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 2026 0.033208 ATCCCCAAACGCACATCCAT 60.033 50.000 0.00 0.0 0.0 3.41 R
2467 2630 4.104383 TGAATTGGGCTATTGGATCCTC 57.896 45.455 14.23 0.0 0.0 3.71 R
2879 3849 0.249868 TTGCACACCAGGAGACGAAG 60.250 55.000 0.00 0.0 0.0 3.79 R
3685 4669 6.786967 AAAGTACCATCTACGTTCCATACT 57.213 37.500 0.00 0.0 0.0 2.12 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
188 212 4.282195 GTCAATCCTTATGAGGGACGATCT 59.718 45.833 3.28 0.00 43.72 2.75
219 243 0.102481 GCGAGGAGTAGATTGCGGAA 59.898 55.000 0.00 0.00 0.00 4.30
245 269 2.432444 CCCTTACGCCAACTTGATGAA 58.568 47.619 0.00 0.00 0.00 2.57
248 272 3.372206 CCTTACGCCAACTTGATGAAGAG 59.628 47.826 0.00 0.00 32.98 2.85
328 352 0.322816 ATGCAGTGGCCGAGTTGATT 60.323 50.000 0.00 0.00 40.13 2.57
349 373 3.565307 TGCCTCAGGATTGACAACTTTT 58.435 40.909 0.00 0.00 0.00 2.27
354 378 4.531854 TCAGGATTGACAACTTTTGGACA 58.468 39.130 0.00 0.00 34.12 4.02
366 390 7.596494 ACAACTTTTGGACATGTTATGATCAG 58.404 34.615 0.00 0.00 34.12 2.90
367 391 7.448161 ACAACTTTTGGACATGTTATGATCAGA 59.552 33.333 0.00 0.00 34.12 3.27
389 413 0.304705 GACAATGCGGCAACTATCGG 59.695 55.000 6.82 0.00 0.00 4.18
396 420 2.499685 GCAACTATCGGCGAGGGT 59.500 61.111 17.22 13.54 0.00 4.34
448 472 6.486320 TGTGGCGATGTGTTGAAATATATGAT 59.514 34.615 0.00 0.00 0.00 2.45
449 473 7.013178 TGTGGCGATGTGTTGAAATATATGATT 59.987 33.333 0.00 0.00 0.00 2.57
570 602 9.342308 CTCCCTAATAATAAAGCACAGATTGAA 57.658 33.333 0.00 0.00 0.00 2.69
634 666 6.350110 CCTCATGTTTATGAAATCAAACCCGT 60.350 38.462 0.00 0.00 42.48 5.28
648 680 4.998672 TCAAACCCGTAGTCCACAAATAAG 59.001 41.667 0.00 0.00 0.00 1.73
968 1001 2.956333 TCGCGATCTAGATTTGGAGGAA 59.044 45.455 3.71 0.00 0.00 3.36
1020 1053 1.776662 TGTGGAAGACGGATAGAGGG 58.223 55.000 0.00 0.00 0.00 4.30
1081 1114 1.939934 CTGCTCAGAACGGTGACAAAA 59.060 47.619 0.00 0.00 0.00 2.44
1217 1338 5.107065 GGTAATCAGTCGTCAGTCAAAAAGG 60.107 44.000 0.00 0.00 0.00 3.11
1300 1421 1.004862 TGGTATTTGCGGGGAACATGA 59.995 47.619 0.00 0.00 0.00 3.07
1421 1542 5.183969 CAAGTGTCTCATGTCATCCTCAAT 58.816 41.667 0.00 0.00 0.00 2.57
1581 1704 4.164988 CAGGTATGGATTTCTTCAGGACCT 59.835 45.833 0.00 0.00 35.07 3.85
1597 1721 3.657727 AGGACCTTCCAGATTCAGGAAAA 59.342 43.478 11.23 0.00 44.07 2.29
1600 1724 6.011628 AGGACCTTCCAGATTCAGGAAAAATA 60.012 38.462 11.23 0.00 44.07 1.40
1657 1781 2.097629 TGTCTATTCTTCAGGCGAGACG 59.902 50.000 0.00 0.00 36.86 4.18
2457 2620 8.199449 AGTATGAAAAATGGTTATGCAATCCAG 58.801 33.333 12.14 0.00 34.62 3.86
2467 2630 2.662006 TGCAATCCAGTTCTCTCTCG 57.338 50.000 0.00 0.00 0.00 4.04
2879 3849 8.362639 ACCATTTCATGCCTGTTGATATTTATC 58.637 33.333 0.00 0.00 0.00 1.75
2885 3855 6.844696 TGCCTGTTGATATTTATCTTCGTC 57.155 37.500 0.00 0.00 33.88 4.20
2950 3923 5.744171 AGTATCATGCAACAGTGACCATTA 58.256 37.500 0.00 0.00 0.00 1.90
3118 4094 7.166473 GCGAATTTATTTCAGTGACATCAATCC 59.834 37.037 0.00 0.00 33.66 3.01
3491 4472 4.857588 CACACCGACATGAGAGTAACTAAC 59.142 45.833 0.00 0.00 0.00 2.34
3520 4501 9.212641 TCTTCTTCACATGAGTAATCAGAAAAG 57.787 33.333 0.00 0.76 0.00 2.27
3772 4758 7.586349 ACATTATCCTACTGGAATGGTTCAAT 58.414 34.615 0.00 0.00 46.80 2.57
3773 4759 7.503566 ACATTATCCTACTGGAATGGTTCAATG 59.496 37.037 0.00 0.00 46.80 2.82
3774 4760 5.715439 ATCCTACTGGAATGGTTCAATGA 57.285 39.130 0.00 0.00 46.80 2.57
3775 4761 4.843728 TCCTACTGGAATGGTTCAATGAC 58.156 43.478 0.00 0.00 39.87 3.06
3776 4762 4.288366 TCCTACTGGAATGGTTCAATGACA 59.712 41.667 0.00 0.00 39.87 3.58
3777 4763 4.637534 CCTACTGGAATGGTTCAATGACAG 59.362 45.833 0.00 0.00 34.57 3.51
3778 4764 4.104383 ACTGGAATGGTTCAATGACAGT 57.896 40.909 0.00 0.00 33.51 3.55
3779 4765 4.473444 ACTGGAATGGTTCAATGACAGTT 58.527 39.130 0.00 0.00 34.59 3.16
3780 4766 4.279169 ACTGGAATGGTTCAATGACAGTTG 59.721 41.667 0.00 0.00 34.59 3.16
3781 4767 4.468713 TGGAATGGTTCAATGACAGTTGA 58.531 39.130 0.00 0.00 36.38 3.18
3782 4768 5.078949 TGGAATGGTTCAATGACAGTTGAT 58.921 37.500 0.00 0.00 37.88 2.57
3783 4769 5.539574 TGGAATGGTTCAATGACAGTTGATT 59.460 36.000 0.00 0.00 37.88 2.57
3784 4770 6.718912 TGGAATGGTTCAATGACAGTTGATTA 59.281 34.615 0.00 0.00 37.88 1.75
3785 4771 7.396907 TGGAATGGTTCAATGACAGTTGATTAT 59.603 33.333 0.00 0.00 37.88 1.28
3786 4772 7.917505 GGAATGGTTCAATGACAGTTGATTATC 59.082 37.037 0.00 0.00 37.88 1.75
3787 4773 6.757897 TGGTTCAATGACAGTTGATTATCC 57.242 37.500 0.00 0.00 37.88 2.59
3788 4774 6.484288 TGGTTCAATGACAGTTGATTATCCT 58.516 36.000 0.00 0.00 37.88 3.24
3789 4775 7.629157 TGGTTCAATGACAGTTGATTATCCTA 58.371 34.615 0.00 0.00 37.88 2.94
3790 4776 7.552687 TGGTTCAATGACAGTTGATTATCCTAC 59.447 37.037 0.00 0.00 37.88 3.18
3791 4777 7.770897 GGTTCAATGACAGTTGATTATCCTACT 59.229 37.037 0.00 0.00 37.88 2.57
3792 4778 8.607459 GTTCAATGACAGTTGATTATCCTACTG 58.393 37.037 17.33 17.33 42.75 2.74
3793 4779 7.275183 TCAATGACAGTTGATTATCCTACTGG 58.725 38.462 20.70 9.03 41.69 4.00
3794 4780 7.125659 TCAATGACAGTTGATTATCCTACTGGA 59.874 37.037 20.70 11.96 41.69 3.86
3795 4781 6.867519 TGACAGTTGATTATCCTACTGGAA 57.132 37.500 20.70 10.87 46.80 3.53
3796 4782 7.437713 TGACAGTTGATTATCCTACTGGAAT 57.562 36.000 20.70 7.34 46.80 3.01
3797 4783 7.275183 TGACAGTTGATTATCCTACTGGAATG 58.725 38.462 20.70 5.12 46.80 2.67
3798 4784 6.595682 ACAGTTGATTATCCTACTGGAATGG 58.404 40.000 20.70 3.98 46.80 3.16
3799 4785 6.158695 ACAGTTGATTATCCTACTGGAATGGT 59.841 38.462 20.70 4.47 46.80 3.55
3800 4786 7.056635 CAGTTGATTATCCTACTGGAATGGTT 58.943 38.462 13.41 0.00 46.80 3.67
3801 4787 7.227512 CAGTTGATTATCCTACTGGAATGGTTC 59.772 40.741 13.41 0.00 46.80 3.62
3802 4788 6.823286 TGATTATCCTACTGGAATGGTTCA 57.177 37.500 0.00 0.00 46.80 3.18
3803 4789 7.206789 TGATTATCCTACTGGAATGGTTCAA 57.793 36.000 0.00 0.00 46.80 2.69
3838 4824 1.199615 TCGCATTGGGACTCACCATA 58.800 50.000 0.00 0.00 40.91 2.74
3847 4833 1.539065 GGACTCACCATATGTCTGGCG 60.539 57.143 1.24 0.00 40.15 5.69
3899 4885 2.593346 AAGTGAGATTAGCTGAGGCG 57.407 50.000 0.00 0.00 44.37 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.308014 TGATGTATACTTCACATGCCATCC 58.692 41.667 15.48 0.00 36.76 3.51
20 21 8.985315 TCTGCTTCCATGTATAAATCTTTGAT 57.015 30.769 0.00 0.00 0.00 2.57
21 22 8.806429 TTCTGCTTCCATGTATAAATCTTTGA 57.194 30.769 0.00 0.00 0.00 2.69
79 81 4.527816 TGCACCTTCTATGAAGGCAATTTT 59.472 37.500 22.03 3.31 41.10 1.82
86 88 3.614092 ACACATGCACCTTCTATGAAGG 58.386 45.455 20.90 20.90 43.05 3.46
134 146 2.871453 AGCGGGAAAACACTACCAAAT 58.129 42.857 0.00 0.00 0.00 2.32
188 212 1.001120 TCCTCGCACCTGGTCCATA 59.999 57.895 0.00 0.00 0.00 2.74
223 247 0.328258 ATCAAGTTGGCGTAAGGGCT 59.672 50.000 2.34 0.00 42.84 5.19
309 333 0.322816 AATCAACTCGGCCACTGCAT 60.323 50.000 2.24 0.00 40.13 3.96
328 352 2.957402 AAGTTGTCAATCCTGAGGCA 57.043 45.000 0.00 0.00 30.14 4.75
349 373 5.130809 TGTCCATCTGATCATAACATGTCCA 59.869 40.000 0.00 0.00 0.00 4.02
354 378 5.180680 CGCATTGTCCATCTGATCATAACAT 59.819 40.000 0.00 0.00 0.00 2.71
366 390 1.378531 TAGTTGCCGCATTGTCCATC 58.621 50.000 0.00 0.00 0.00 3.51
367 391 1.949525 GATAGTTGCCGCATTGTCCAT 59.050 47.619 0.00 0.00 0.00 3.41
389 413 3.383825 TCTTATACTTCTTCCACCCTCGC 59.616 47.826 0.00 0.00 0.00 5.03
396 420 4.101114 TGCCACCTCTTATACTTCTTCCA 58.899 43.478 0.00 0.00 0.00 3.53
448 472 3.454447 TCTCAAGACTTCCACAGGTGAAA 59.546 43.478 0.00 0.00 0.00 2.69
449 473 3.038280 TCTCAAGACTTCCACAGGTGAA 58.962 45.455 0.00 0.00 0.00 3.18
538 570 9.566432 CTGTGCTTTATTATTAGGGAGAGAAAT 57.434 33.333 0.00 0.00 0.00 2.17
539 571 8.768397 TCTGTGCTTTATTATTAGGGAGAGAAA 58.232 33.333 0.00 0.00 0.00 2.52
563 595 2.092914 GGTGAACCCGGAGATTCAATCT 60.093 50.000 14.84 0.00 43.70 2.40
634 666 4.069304 AGCAAACGCTTATTTGTGGACTA 58.931 39.130 6.77 0.00 40.92 2.59
702 735 3.305064 CGATGGGATGTTGAACCGTTTTT 60.305 43.478 0.00 0.00 0.00 1.94
819 852 0.757188 ATCGAAGGATGGCTCTCCGT 60.757 55.000 0.00 0.00 40.46 4.69
968 1001 3.003763 GGAACAGGAGGCGACCCT 61.004 66.667 0.00 0.00 46.74 4.34
1081 1114 2.569404 CAGAACCAAAGTAGCCTCCTCT 59.431 50.000 0.00 0.00 0.00 3.69
1125 1159 0.621571 TAGCAGCCAACCCCATCTCT 60.622 55.000 0.00 0.00 0.00 3.10
1217 1338 7.761409 TCCTACAAAATTCACATGTTAGCATC 58.239 34.615 0.00 0.00 31.99 3.91
1300 1421 4.104102 TCACTGGAGTAAATTTGGGACTGT 59.896 41.667 0.00 0.00 0.00 3.55
1581 1704 8.765488 TGCATATATTTTTCCTGAATCTGGAA 57.235 30.769 16.20 16.20 39.18 3.53
1597 1721 6.243148 TGATGGTTCTCTGCATGCATATATT 58.757 36.000 22.97 1.47 0.00 1.28
1600 1724 4.094830 TGATGGTTCTCTGCATGCATAT 57.905 40.909 22.97 7.16 0.00 1.78
1657 1781 4.454678 TGAATCATGTTCTCATAGTGGCC 58.545 43.478 0.00 0.00 32.47 5.36
1869 2026 0.033208 ATCCCCAAACGCACATCCAT 60.033 50.000 0.00 0.00 0.00 3.41
2467 2630 4.104383 TGAATTGGGCTATTGGATCCTC 57.896 45.455 14.23 0.00 0.00 3.71
2742 3711 8.801299 TCATTGTTCAATACATTTCTTAAGGCA 58.199 29.630 1.85 0.00 36.44 4.75
2848 3818 2.165167 ACAGGCATGAAATGGTCACTG 58.835 47.619 4.84 0.00 46.86 3.66
2879 3849 0.249868 TTGCACACCAGGAGACGAAG 60.250 55.000 0.00 0.00 0.00 3.79
3292 4268 7.417612 AGATTACAAATTATGCACATCGTTCC 58.582 34.615 0.00 0.00 0.00 3.62
3344 4320 9.646522 AAATATGGCAAACCTATGTCTTTCTAT 57.353 29.630 0.00 0.00 36.63 1.98
3491 4472 8.713737 TCTGATTACTCATGTGAAGAAGATTG 57.286 34.615 0.94 0.00 0.00 2.67
3631 4615 8.877864 ACCTAAAACCATGACAAGAATTATGA 57.122 30.769 0.00 0.00 0.00 2.15
3685 4669 6.786967 AAAGTACCATCTACGTTCCATACT 57.213 37.500 0.00 0.00 0.00 2.12
3772 4758 6.867519 TTCCAGTAGGATAATCAACTGTCA 57.132 37.500 9.01 0.00 45.26 3.58
3773 4759 6.708054 CCATTCCAGTAGGATAATCAACTGTC 59.292 42.308 9.01 0.00 45.26 3.51
3774 4760 6.158695 ACCATTCCAGTAGGATAATCAACTGT 59.841 38.462 9.01 0.00 45.26 3.55
3775 4761 6.595682 ACCATTCCAGTAGGATAATCAACTG 58.404 40.000 0.00 0.00 45.26 3.16
3776 4762 6.831664 ACCATTCCAGTAGGATAATCAACT 57.168 37.500 0.00 0.00 45.26 3.16
3777 4763 7.054124 TGAACCATTCCAGTAGGATAATCAAC 58.946 38.462 0.00 0.00 45.26 3.18
3778 4764 7.206789 TGAACCATTCCAGTAGGATAATCAA 57.793 36.000 0.00 0.00 45.26 2.57
3779 4765 6.823286 TGAACCATTCCAGTAGGATAATCA 57.177 37.500 0.00 0.00 45.26 2.57
3780 4766 7.939039 TCATTGAACCATTCCAGTAGGATAATC 59.061 37.037 0.00 0.00 45.26 1.75
3781 4767 7.721399 GTCATTGAACCATTCCAGTAGGATAAT 59.279 37.037 0.00 0.00 45.26 1.28
3782 4768 7.054124 GTCATTGAACCATTCCAGTAGGATAA 58.946 38.462 0.00 0.00 45.26 1.75
3783 4769 6.157820 TGTCATTGAACCATTCCAGTAGGATA 59.842 38.462 0.00 0.00 45.26 2.59
3784 4770 5.044919 TGTCATTGAACCATTCCAGTAGGAT 60.045 40.000 0.00 0.00 45.26 3.24
3785 4771 4.288366 TGTCATTGAACCATTCCAGTAGGA 59.712 41.667 0.00 0.00 43.93 2.94
3786 4772 4.588899 TGTCATTGAACCATTCCAGTAGG 58.411 43.478 0.00 0.00 0.00 3.18
3787 4773 5.248640 ACTGTCATTGAACCATTCCAGTAG 58.751 41.667 2.92 0.00 30.66 2.57
3788 4774 5.241403 ACTGTCATTGAACCATTCCAGTA 57.759 39.130 2.92 0.00 30.66 2.74
3789 4775 4.104383 ACTGTCATTGAACCATTCCAGT 57.896 40.909 0.00 0.00 0.00 4.00
3790 4776 4.520111 TCAACTGTCATTGAACCATTCCAG 59.480 41.667 0.00 0.00 35.65 3.86
3791 4777 4.468713 TCAACTGTCATTGAACCATTCCA 58.531 39.130 0.00 0.00 35.65 3.53
3792 4778 4.520492 ACTCAACTGTCATTGAACCATTCC 59.480 41.667 0.00 0.00 38.12 3.01
3793 4779 5.695851 ACTCAACTGTCATTGAACCATTC 57.304 39.130 0.00 0.00 38.12 2.67
3794 4780 5.593909 TGAACTCAACTGTCATTGAACCATT 59.406 36.000 0.00 0.00 38.12 3.16
3795 4781 5.132502 TGAACTCAACTGTCATTGAACCAT 58.867 37.500 0.00 0.00 38.12 3.55
3796 4782 4.522114 TGAACTCAACTGTCATTGAACCA 58.478 39.130 0.00 0.00 38.12 3.67
3797 4783 5.615544 CGATGAACTCAACTGTCATTGAACC 60.616 44.000 0.00 0.00 38.12 3.62
3798 4784 5.377358 CGATGAACTCAACTGTCATTGAAC 58.623 41.667 0.00 0.00 38.12 3.18
3799 4785 4.083855 GCGATGAACTCAACTGTCATTGAA 60.084 41.667 4.63 0.00 38.12 2.69
3800 4786 3.433274 GCGATGAACTCAACTGTCATTGA 59.567 43.478 4.63 0.00 37.08 2.57
3801 4787 3.187022 TGCGATGAACTCAACTGTCATTG 59.813 43.478 0.00 0.00 0.00 2.82
3802 4788 3.402110 TGCGATGAACTCAACTGTCATT 58.598 40.909 0.00 0.00 0.00 2.57
3803 4789 3.044235 TGCGATGAACTCAACTGTCAT 57.956 42.857 0.00 0.00 0.00 3.06
3838 4824 1.896220 AATCACAACACGCCAGACAT 58.104 45.000 0.00 0.00 0.00 3.06
3899 4885 0.600255 CGTGACACCTCACCCTTGTC 60.600 60.000 0.00 0.00 43.64 3.18


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

AutoCloner maintained by Alex Coulton.