Multiple sequence alignment - TraesCS6B01G252200

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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 TraesCS6B01G252200 chr6B 100.000 4021 0 0 1 4021 452191856 452187836 0.000000e+00 7426
1 TraesCS6B01G252200 chr6D 96.851 3557 77 10 1 3534 291249350 291245806 0.000000e+00 5915
2 TraesCS6B01G252200 chr6D 91.131 327 11 2 3695 4021 291245804 291245496 1.030000e-115 427
3 TraesCS6B01G252200 chr6D 96.491 171 4 1 3527 3695 32865164 32865334 8.510000e-72 281
4 TraesCS6B01G252200 chr6D 95.954 173 5 2 3525 3695 392897147 392896975 3.060000e-71 279
5 TraesCS6B01G252200 chr6A 96.254 3550 85 10 1 3534 432241980 432245497 0.000000e+00 5775
6 TraesCS6B01G252200 chr6A 95.417 240 11 0 3782 4021 432245852 432246091 2.270000e-102 383
7 TraesCS6B01G252200 chr6A 87.156 109 3 1 3695 3792 432245499 432245607 3.280000e-21 113
8 TraesCS6B01G252200 chr2D 77.907 516 94 17 1228 1728 460207265 460206755 1.820000e-78 303
9 TraesCS6B01G252200 chr2D 95.954 173 6 1 3525 3696 196347499 196347327 3.060000e-71 279
10 TraesCS6B01G252200 chr2A 77.907 516 94 15 1228 1728 603085361 603084851 1.820000e-78 303
11 TraesCS6B01G252200 chr2A 95.977 174 6 1 3522 3695 310407926 310408098 8.510000e-72 281
12 TraesCS6B01G252200 chr2B 77.670 515 97 14 1228 1728 541203134 541202624 8.450000e-77 298
13 TraesCS6B01G252200 chr1D 95.109 184 8 1 3513 3695 423269488 423269671 5.080000e-74 289
14 TraesCS6B01G252200 chr4A 97.059 170 4 1 3530 3698 582529975 582530144 6.580000e-73 285
15 TraesCS6B01G252200 chr7D 95.028 181 5 4 3527 3704 480637699 480637878 8.510000e-72 281
16 TraesCS6B01G252200 chr7D 94.915 177 7 2 3523 3698 500255155 500255330 3.960000e-70 276
17 TraesCS6B01G252200 chr5A 97.024 168 4 1 3529 3695 382566635 382566802 8.510000e-72 281


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 TraesCS6B01G252200 chr6B 452187836 452191856 4020 True 7426.000000 7426 100.000000 1 4021 1 chr6B.!!$R1 4020
1 TraesCS6B01G252200 chr6D 291245496 291249350 3854 True 3171.000000 5915 93.991000 1 4021 2 chr6D.!!$R2 4020
2 TraesCS6B01G252200 chr6A 432241980 432246091 4111 False 2090.333333 5775 92.942333 1 4021 3 chr6A.!!$F1 4020
3 TraesCS6B01G252200 chr2D 460206755 460207265 510 True 303.000000 303 77.907000 1228 1728 1 chr2D.!!$R2 500
4 TraesCS6B01G252200 chr2A 603084851 603085361 510 True 303.000000 303 77.907000 1228 1728 1 chr2A.!!$R1 500
5 TraesCS6B01G252200 chr2B 541202624 541203134 510 True 298.000000 298 77.670000 1228 1728 1 chr2B.!!$R1 500

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
275 276 2.107552 AGAAATCGGGGGTTCAACTGAA 59.892 45.455 0.0 0.0 0.0 3.02 F
1356 1372 2.093181 AGCCATCGTACTTACCATTGCA 60.093 45.455 0.0 0.0 0.0 4.08 F
1868 1892 1.134670 AGTACTCGCTTGGCTCATTCC 60.135 52.381 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 1767 3.988379 ATGTGCACAAACAAGGTACAG 57.012 42.857 25.72 0.0 32.81 2.74 R
2888 2914 0.462937 TCCCGTACCAAATCATGCCG 60.463 55.000 0.00 0.0 0.00 5.69 R
3680 3716 0.971386 TGTTGTACTCCCTCCGTTCC 59.029 55.000 0.00 0.0 0.00 3.62 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 3.741325 CGAACCCTCTCCCCCAAT 58.259 61.111 0.00 0.00 0.00 3.16
109 110 2.842462 TCCACTGGACAGGCGTGT 60.842 61.111 12.68 12.68 40.71 4.49
201 202 2.367202 ACCCCGATCCAGCATTCGT 61.367 57.895 0.00 0.00 33.60 3.85
275 276 2.107552 AGAAATCGGGGGTTCAACTGAA 59.892 45.455 0.00 0.00 0.00 3.02
500 501 2.496899 ATCGTCTTGAATTGGCCTGT 57.503 45.000 3.32 0.00 0.00 4.00
669 670 7.123997 CCAGCTACAATATGATATGGACTCTCT 59.876 40.741 0.00 0.00 0.00 3.10
670 671 7.975058 CAGCTACAATATGATATGGACTCTCTG 59.025 40.741 0.00 0.00 0.00 3.35
680 681 7.164122 TGATATGGACTCTCTGATAAATTGCC 58.836 38.462 0.00 0.00 0.00 4.52
681 682 5.643421 ATGGACTCTCTGATAAATTGCCT 57.357 39.130 0.00 0.00 0.00 4.75
716 725 6.978080 ACTTTGTACTGTGCCTTATTTGTTTG 59.022 34.615 0.00 0.00 0.00 2.93
764 773 3.679980 CCTCACTTGTGGTCTTAACATCG 59.320 47.826 0.64 0.00 0.00 3.84
790 799 4.976224 TCATGCATCCATTCTTGAACTG 57.024 40.909 0.00 0.00 0.00 3.16
861 870 5.966636 AATCTTCGAAAACAAAAGTTGGC 57.033 34.783 0.00 0.00 34.12 4.52
1342 1358 3.941483 GGTTGGGATATATTCAGCCATCG 59.059 47.826 13.90 0.00 32.98 3.84
1356 1372 2.093181 AGCCATCGTACTTACCATTGCA 60.093 45.455 0.00 0.00 0.00 4.08
1744 1767 3.118261 TGAGTATCCTGGGTGCTTGAATC 60.118 47.826 0.00 0.00 0.00 2.52
1868 1892 1.134670 AGTACTCGCTTGGCTCATTCC 60.135 52.381 0.00 0.00 0.00 3.01
2216 2240 9.844790 CTGCAATCTGTATGATTTTCAGTTTTA 57.155 29.630 0.00 0.00 43.00 1.52
2311 2335 6.913170 TGTTTCCTCTTGATTATTGTGAAGC 58.087 36.000 0.00 0.00 0.00 3.86
2335 2359 7.446625 AGCAAACAGATCTTACAGAAACAGATT 59.553 33.333 0.00 0.00 0.00 2.40
2405 2429 5.809562 TGCCGTTTGAAATGCTAAAATATGG 59.190 36.000 4.47 0.00 0.00 2.74
2429 2453 5.121454 GCACATTATAATACAGGAGCTGCTC 59.879 44.000 21.17 21.17 34.37 4.26
2888 2914 2.738846 CGGCATGACCATAGCTGTTATC 59.261 50.000 0.00 0.00 39.03 1.75
2908 2934 1.813862 CGGCATGATTTGGTACGGGAT 60.814 52.381 0.00 0.00 0.00 3.85
3014 3040 2.931325 GCAGTCTGAGCTTGATCTGAAG 59.069 50.000 3.32 0.00 0.00 3.02
3123 3149 9.481340 TCCGATTTATTCTCTTCATTCATACAG 57.519 33.333 0.00 0.00 0.00 2.74
3151 3177 2.026915 CGTTTCCGTTTTGTAGCCAC 57.973 50.000 0.00 0.00 0.00 5.01
3233 3259 8.367911 TCACAGCCAAATATAGTGGTAAGATAG 58.632 37.037 7.10 0.00 38.50 2.08
3378 3414 7.996098 AAATCTTGTTTGGCTAGCTAACTTA 57.004 32.000 23.87 15.46 0.00 2.24
3412 3448 8.994429 ATAATATCGTGAGGATTCTGAACATC 57.006 34.615 0.00 0.00 36.55 3.06
3413 3449 6.662865 ATATCGTGAGGATTCTGAACATCT 57.337 37.500 0.00 0.00 36.55 2.90
3534 3570 6.149807 TCGGTTTCAACTTCAAAACAACTACT 59.850 34.615 0.00 0.00 37.16 2.57
3535 3571 6.468000 CGGTTTCAACTTCAAAACAACTACTC 59.532 38.462 0.00 0.00 37.16 2.59
3536 3572 6.750501 GGTTTCAACTTCAAAACAACTACTCC 59.249 38.462 0.00 0.00 37.16 3.85
3537 3573 6.445357 TTCAACTTCAAAACAACTACTCCC 57.555 37.500 0.00 0.00 0.00 4.30
3538 3574 5.751586 TCAACTTCAAAACAACTACTCCCT 58.248 37.500 0.00 0.00 0.00 4.20
3539 3575 5.820947 TCAACTTCAAAACAACTACTCCCTC 59.179 40.000 0.00 0.00 0.00 4.30
3540 3576 4.715713 ACTTCAAAACAACTACTCCCTCC 58.284 43.478 0.00 0.00 0.00 4.30
3541 3577 4.412528 ACTTCAAAACAACTACTCCCTCCT 59.587 41.667 0.00 0.00 0.00 3.69
3542 3578 5.104067 ACTTCAAAACAACTACTCCCTCCTT 60.104 40.000 0.00 0.00 0.00 3.36
3543 3579 5.382664 TCAAAACAACTACTCCCTCCTTT 57.617 39.130 0.00 0.00 0.00 3.11
3544 3580 5.374071 TCAAAACAACTACTCCCTCCTTTC 58.626 41.667 0.00 0.00 0.00 2.62
3545 3581 4.368565 AAACAACTACTCCCTCCTTTCC 57.631 45.455 0.00 0.00 0.00 3.13
3546 3582 3.277416 ACAACTACTCCCTCCTTTCCT 57.723 47.619 0.00 0.00 0.00 3.36
3547 3583 4.415224 ACAACTACTCCCTCCTTTCCTA 57.585 45.455 0.00 0.00 0.00 2.94
3548 3584 4.759953 ACAACTACTCCCTCCTTTCCTAA 58.240 43.478 0.00 0.00 0.00 2.69
3549 3585 5.160386 ACAACTACTCCCTCCTTTCCTAAA 58.840 41.667 0.00 0.00 0.00 1.85
3550 3586 5.791141 ACAACTACTCCCTCCTTTCCTAAAT 59.209 40.000 0.00 0.00 0.00 1.40
3551 3587 6.964086 ACAACTACTCCCTCCTTTCCTAAATA 59.036 38.462 0.00 0.00 0.00 1.40
3552 3588 7.628101 ACAACTACTCCCTCCTTTCCTAAATAT 59.372 37.037 0.00 0.00 0.00 1.28
3553 3589 8.495260 CAACTACTCCCTCCTTTCCTAAATATT 58.505 37.037 0.00 0.00 0.00 1.28
3554 3590 8.640033 ACTACTCCCTCCTTTCCTAAATATTT 57.360 34.615 5.89 5.89 0.00 1.40
3555 3591 8.495260 ACTACTCCCTCCTTTCCTAAATATTTG 58.505 37.037 11.05 1.40 0.00 2.32
3556 3592 7.285340 ACTCCCTCCTTTCCTAAATATTTGT 57.715 36.000 11.05 0.00 0.00 2.83
3557 3593 7.347252 ACTCCCTCCTTTCCTAAATATTTGTC 58.653 38.462 11.05 0.00 0.00 3.18
3558 3594 7.184753 ACTCCCTCCTTTCCTAAATATTTGTCT 59.815 37.037 11.05 0.00 0.00 3.41
3559 3595 7.939781 TCCCTCCTTTCCTAAATATTTGTCTT 58.060 34.615 11.05 0.00 0.00 3.01
3560 3596 8.398743 TCCCTCCTTTCCTAAATATTTGTCTTT 58.601 33.333 11.05 0.00 0.00 2.52
3561 3597 9.035890 CCCTCCTTTCCTAAATATTTGTCTTTT 57.964 33.333 11.05 0.00 0.00 2.27
3579 3615 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
3580 3616 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
3593 3629 3.575506 TGGACTACCACGTACGGAT 57.424 52.632 21.06 6.82 41.77 4.18
3594 3630 1.097232 TGGACTACCACGTACGGATG 58.903 55.000 21.06 9.60 41.77 3.51
3595 3631 1.098050 GGACTACCACGTACGGATGT 58.902 55.000 21.06 15.02 35.97 3.06
3596 3632 2.288666 GGACTACCACGTACGGATGTA 58.711 52.381 21.06 15.33 35.97 2.29
3597 3633 2.880890 GGACTACCACGTACGGATGTAT 59.119 50.000 21.06 0.21 35.97 2.29
3598 3634 4.065088 GGACTACCACGTACGGATGTATA 58.935 47.826 21.06 3.97 35.97 1.47
3599 3635 4.697352 GGACTACCACGTACGGATGTATAT 59.303 45.833 21.06 8.53 35.97 0.86
3600 3636 5.391310 GGACTACCACGTACGGATGTATATG 60.391 48.000 21.06 5.74 35.97 1.78
3601 3637 5.308014 ACTACCACGTACGGATGTATATGA 58.692 41.667 21.06 0.00 32.11 2.15
3602 3638 4.494350 ACCACGTACGGATGTATATGAC 57.506 45.455 21.06 0.00 32.11 3.06
3603 3639 3.884693 ACCACGTACGGATGTATATGACA 59.115 43.478 21.06 0.00 43.97 3.58
3625 3661 9.378551 TGACATATTTTAAAGCGTAGATTCACT 57.621 29.630 0.00 0.00 31.23 3.41
3626 3662 9.851043 GACATATTTTAAAGCGTAGATTCACTC 57.149 33.333 0.00 0.00 31.23 3.51
3627 3663 9.378551 ACATATTTTAAAGCGTAGATTCACTCA 57.621 29.630 0.00 0.00 31.23 3.41
3632 3668 8.948853 TTTAAAGCGTAGATTCACTCATTTTG 57.051 30.769 0.00 0.00 31.23 2.44
3633 3669 4.606457 AGCGTAGATTCACTCATTTTGC 57.394 40.909 0.00 0.00 0.00 3.68
3634 3670 4.256920 AGCGTAGATTCACTCATTTTGCT 58.743 39.130 0.00 0.00 0.00 3.91
3635 3671 4.331168 AGCGTAGATTCACTCATTTTGCTC 59.669 41.667 0.00 0.00 0.00 4.26
3636 3672 4.494855 GCGTAGATTCACTCATTTTGCTCC 60.495 45.833 0.00 0.00 0.00 4.70
3637 3673 4.259970 CGTAGATTCACTCATTTTGCTCCG 60.260 45.833 0.00 0.00 0.00 4.63
3638 3674 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3639 3675 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3640 3676 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3641 3677 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3642 3678 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3643 3679 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3644 3680 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3645 3681 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3646 3682 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3647 3683 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
3648 3684 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
3649 3685 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
3650 3686 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
3651 3687 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
3652 3688 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
3653 3689 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
3654 3690 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
3655 3691 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
3656 3692 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
3657 3693 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
3658 3694 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
3659 3695 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
3660 3696 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
3661 3697 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
3662 3698 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
3663 3699 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
3664 3700 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
3665 3701 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
3666 3702 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
3667 3703 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
3668 3704 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
3669 3705 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
3670 3706 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
3671 3707 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
3672 3708 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
3673 3709 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
3686 3722 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3687 3723 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3688 3724 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3689 3725 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3690 3726 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3691 3727 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3692 3728 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3693 3729 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3709 3745 2.706190 GGGAGTACAACATATCTGGGCT 59.294 50.000 0.00 0.00 0.00 5.19
3763 3810 5.105834 CAGATTCTAGCCTGCATTTAAGC 57.894 43.478 0.00 0.00 0.00 3.09
3817 4119 6.071278 ACCTTCACCTCTACTGATTACACTTC 60.071 42.308 0.00 0.00 0.00 3.01
3845 4147 4.644234 CAGTAATTATGGCATGGTGGTCAA 59.356 41.667 10.98 0.00 0.00 3.18
3850 4152 2.593925 TGGCATGGTGGTCAATTACA 57.406 45.000 0.00 0.00 0.00 2.41
3851 4153 2.445427 TGGCATGGTGGTCAATTACAG 58.555 47.619 0.00 0.00 0.00 2.74
3933 4235 6.721318 TCTAAGATTGCCAGAGTTAAATGGT 58.279 36.000 4.94 0.00 38.91 3.55
3976 4278 9.442047 AACACAATAAGAGGAAGAATAGACTTG 57.558 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.923395 TGGAAGGAGGCCGGTGATT 60.923 57.895 1.90 0.00 0.00 2.57
17 18 3.319198 GTGGAAGGAGGCCGGTGA 61.319 66.667 1.90 0.00 0.00 4.02
109 110 1.779221 TTCCGGGTAGATTTCCGCTA 58.221 50.000 0.00 0.00 44.45 4.26
275 276 1.854979 TAACACAGGGCATGGGGGT 60.855 57.895 6.28 0.00 36.22 4.95
500 501 5.010922 GCAACATATGGATTATTGCTCCCAA 59.989 40.000 16.59 0.00 41.88 4.12
635 636 2.154854 TATTGTAGCTGGATCTGCGC 57.845 50.000 0.00 0.00 33.59 6.09
669 670 6.414732 AGTAACTAGCACAGGCAATTTATCA 58.585 36.000 0.00 0.00 44.61 2.15
670 671 6.927294 AGTAACTAGCACAGGCAATTTATC 57.073 37.500 0.00 0.00 44.61 1.75
680 681 5.107453 GCACAGTACAAAGTAACTAGCACAG 60.107 44.000 0.00 0.00 0.00 3.66
681 682 4.748102 GCACAGTACAAAGTAACTAGCACA 59.252 41.667 0.00 0.00 0.00 4.57
716 725 5.537188 TGGAAAAGATACAAATTGCACACC 58.463 37.500 0.00 0.00 0.00 4.16
764 773 3.949754 TCAAGAATGGATGCATGAACTCC 59.050 43.478 2.46 0.00 0.00 3.85
790 799 5.450412 CCCTAATGTGGTGTATGTGAAATGC 60.450 44.000 0.00 0.00 0.00 3.56
861 870 5.047092 AGCATCCCACAAAAATCTTAAGGTG 60.047 40.000 1.85 1.68 0.00 4.00
1342 1358 8.767478 TTACTAGTTCTTGCAATGGTAAGTAC 57.233 34.615 0.00 0.23 37.31 2.73
1744 1767 3.988379 ATGTGCACAAACAAGGTACAG 57.012 42.857 25.72 0.00 32.81 2.74
1968 1992 6.142817 CGTACCGTAACTACCATGGTATAAC 58.857 44.000 24.78 19.57 37.50 1.89
2311 2335 8.562892 ACAATCTGTTTCTGTAAGATCTGTTTG 58.437 33.333 0.00 0.00 46.36 2.93
2335 2359 7.973048 ACTATTTAGAGGGTTGATCTGTACA 57.027 36.000 0.00 0.00 0.00 2.90
2405 2429 4.999950 AGCAGCTCCTGTATTATAATGTGC 59.000 41.667 8.28 4.24 33.43 4.57
2492 2516 1.710013 ACGTTACTCTGCCATTGACG 58.290 50.000 0.00 0.00 35.39 4.35
2556 2580 7.449395 CCCATGCTCATATCCTAGAATTTCAAA 59.551 37.037 0.00 0.00 0.00 2.69
2708 2734 5.129155 ATTGGTACCAACAGCAATTATGCAT 59.871 36.000 29.35 3.79 46.01 3.96
2829 2855 0.615850 AGGCCCTCTTTTCCGAAGAG 59.384 55.000 0.00 8.46 42.53 2.85
2888 2914 0.462937 TCCCGTACCAAATCATGCCG 60.463 55.000 0.00 0.00 0.00 5.69
2908 2934 1.890041 CCTGGTTTGGACGACGCAA 60.890 57.895 0.00 0.00 0.00 4.85
3014 3040 5.923733 TTTCTAATCTCAGTCCTCAGACC 57.076 43.478 0.00 0.00 44.72 3.85
3151 3177 3.181480 GCTCAGGTACTCTCCTTTAGCTG 60.181 52.174 0.00 2.15 42.62 4.24
3307 3339 7.986320 GTCTAAGTCACCTCTCTATGTAGTGTA 59.014 40.741 0.00 0.00 0.00 2.90
3399 3435 6.042777 TCGTATGTTCAGATGTTCAGAATCC 58.957 40.000 0.00 0.00 0.00 3.01
3406 3442 6.128902 ACGTTTTCTCGTATGTTCAGATGTTC 60.129 38.462 0.00 0.00 42.35 3.18
3407 3443 5.694910 ACGTTTTCTCGTATGTTCAGATGTT 59.305 36.000 0.00 0.00 42.35 2.71
3408 3444 5.118664 CACGTTTTCTCGTATGTTCAGATGT 59.881 40.000 0.00 0.00 42.27 3.06
3409 3445 5.344933 TCACGTTTTCTCGTATGTTCAGATG 59.655 40.000 0.00 0.00 42.27 2.90
3410 3446 5.466819 TCACGTTTTCTCGTATGTTCAGAT 58.533 37.500 0.00 0.00 42.27 2.90
3411 3447 4.862350 TCACGTTTTCTCGTATGTTCAGA 58.138 39.130 0.00 0.00 42.27 3.27
3412 3448 4.090066 CCTCACGTTTTCTCGTATGTTCAG 59.910 45.833 0.00 0.00 42.27 3.02
3413 3449 3.985279 CCTCACGTTTTCTCGTATGTTCA 59.015 43.478 0.00 0.00 42.27 3.18
3482 3518 5.249622 TGAGTTGGTGTATTAATCTGGACCA 59.750 40.000 0.00 0.00 0.00 4.02
3534 3570 7.525158 AGACAAATATTTAGGAAAGGAGGGA 57.475 36.000 0.00 0.00 0.00 4.20
3535 3571 8.595362 AAAGACAAATATTTAGGAAAGGAGGG 57.405 34.615 0.00 0.00 0.00 4.30
3553 3589 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
3554 3590 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
3558 3594 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
3559 3595 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
3560 3596 7.333423 CGTGGTAGTCCATTTGAAATCTCTAAA 59.667 37.037 0.00 0.00 46.20 1.85
3561 3597 6.816640 CGTGGTAGTCCATTTGAAATCTCTAA 59.183 38.462 0.00 0.00 46.20 2.10
3562 3598 6.070995 ACGTGGTAGTCCATTTGAAATCTCTA 60.071 38.462 0.00 0.00 46.20 2.43
3563 3599 5.178797 CGTGGTAGTCCATTTGAAATCTCT 58.821 41.667 0.00 0.00 46.20 3.10
3564 3600 4.935808 ACGTGGTAGTCCATTTGAAATCTC 59.064 41.667 0.00 0.00 46.20 2.75
3565 3601 4.906618 ACGTGGTAGTCCATTTGAAATCT 58.093 39.130 0.00 0.00 46.20 2.40
3566 3602 5.220340 CGTACGTGGTAGTCCATTTGAAATC 60.220 44.000 7.22 0.00 46.20 2.17
3567 3603 4.628333 CGTACGTGGTAGTCCATTTGAAAT 59.372 41.667 7.22 0.00 46.20 2.17
3568 3604 3.989167 CGTACGTGGTAGTCCATTTGAAA 59.011 43.478 7.22 0.00 46.20 2.69
3569 3605 3.577667 CGTACGTGGTAGTCCATTTGAA 58.422 45.455 7.22 0.00 46.20 2.69
3570 3606 2.094597 CCGTACGTGGTAGTCCATTTGA 60.095 50.000 15.21 0.00 46.20 2.69
3571 3607 2.094597 TCCGTACGTGGTAGTCCATTTG 60.095 50.000 15.21 0.00 46.20 2.32
3572 3608 2.170166 TCCGTACGTGGTAGTCCATTT 58.830 47.619 15.21 0.00 46.20 2.32
3573 3609 1.838112 TCCGTACGTGGTAGTCCATT 58.162 50.000 15.21 0.00 46.20 3.16
3574 3610 1.679680 CATCCGTACGTGGTAGTCCAT 59.320 52.381 15.21 0.00 46.20 3.41
3575 3611 1.097232 CATCCGTACGTGGTAGTCCA 58.903 55.000 15.21 0.00 42.05 4.02
3576 3612 1.098050 ACATCCGTACGTGGTAGTCC 58.902 55.000 15.21 0.00 0.00 3.85
3577 3613 5.409520 TCATATACATCCGTACGTGGTAGTC 59.590 44.000 15.21 0.00 0.00 2.59
3578 3614 5.180117 GTCATATACATCCGTACGTGGTAGT 59.820 44.000 15.21 7.78 0.00 2.73
3579 3615 5.179929 TGTCATATACATCCGTACGTGGTAG 59.820 44.000 15.21 0.00 31.43 3.18
3580 3616 5.062528 TGTCATATACATCCGTACGTGGTA 58.937 41.667 15.21 13.05 31.43 3.25
3581 3617 3.884693 TGTCATATACATCCGTACGTGGT 59.115 43.478 15.21 11.27 31.43 4.16
3582 3618 4.492791 TGTCATATACATCCGTACGTGG 57.507 45.455 15.21 5.54 31.43 4.94
3583 3619 8.683550 AAATATGTCATATACATCCGTACGTG 57.316 34.615 15.21 9.44 46.15 4.49
3589 3625 9.689075 CGCTTTAAAATATGTCATATACATCCG 57.311 33.333 5.76 1.21 46.15 4.18
3599 3635 9.378551 AGTGAATCTACGCTTTAAAATATGTCA 57.621 29.630 0.00 0.00 0.00 3.58
3600 3636 9.851043 GAGTGAATCTACGCTTTAAAATATGTC 57.149 33.333 0.00 0.00 0.00 3.06
3601 3637 9.378551 TGAGTGAATCTACGCTTTAAAATATGT 57.621 29.630 0.00 0.00 0.00 2.29
3606 3642 9.393249 CAAAATGAGTGAATCTACGCTTTAAAA 57.607 29.630 0.00 0.00 0.00 1.52
3607 3643 7.537306 GCAAAATGAGTGAATCTACGCTTTAAA 59.463 33.333 0.00 0.00 0.00 1.52
3608 3644 7.021196 GCAAAATGAGTGAATCTACGCTTTAA 58.979 34.615 0.00 0.00 0.00 1.52
3609 3645 6.371548 AGCAAAATGAGTGAATCTACGCTTTA 59.628 34.615 0.00 0.00 0.00 1.85
3610 3646 5.182001 AGCAAAATGAGTGAATCTACGCTTT 59.818 36.000 0.00 0.00 0.00 3.51
3611 3647 4.697352 AGCAAAATGAGTGAATCTACGCTT 59.303 37.500 0.00 0.00 0.00 4.68
3612 3648 4.256920 AGCAAAATGAGTGAATCTACGCT 58.743 39.130 0.00 0.00 0.00 5.07
3613 3649 4.494855 GGAGCAAAATGAGTGAATCTACGC 60.495 45.833 0.00 0.00 0.00 4.42
3614 3650 4.259970 CGGAGCAAAATGAGTGAATCTACG 60.260 45.833 0.00 0.00 0.00 3.51
3615 3651 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3616 3652 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3617 3653 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3618 3654 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3619 3655 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3620 3656 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3621 3657 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3622 3658 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3623 3659 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3624 3660 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
3625 3661 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
3626 3662 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
3627 3663 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
3628 3664 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
3629 3665 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
3630 3666 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
3631 3667 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
3632 3668 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
3633 3669 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
3634 3670 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
3635 3671 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
3636 3672 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
3637 3673 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
3639 3675 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
3640 3676 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
3641 3677 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
3642 3678 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
3643 3679 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
3644 3680 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
3645 3681 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
3646 3682 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
3647 3683 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
3660 3696 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3661 3697 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
3662 3698 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3663 3699 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3664 3700 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3665 3701 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3666 3702 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3667 3703 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3668 3704 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3669 3705 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3670 3706 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3671 3707 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3672 3708 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
3673 3709 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
3674 3710 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
3675 3711 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
3676 3712 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
3677 3713 2.827921 GTTGTACTCCCTCCGTTCCTAA 59.172 50.000 0.00 0.00 0.00 2.69
3678 3714 2.225091 TGTTGTACTCCCTCCGTTCCTA 60.225 50.000 0.00 0.00 0.00 2.94
3679 3715 1.264295 GTTGTACTCCCTCCGTTCCT 58.736 55.000 0.00 0.00 0.00 3.36
3680 3716 0.971386 TGTTGTACTCCCTCCGTTCC 59.029 55.000 0.00 0.00 0.00 3.62
3681 3717 4.341520 AGATATGTTGTACTCCCTCCGTTC 59.658 45.833 0.00 0.00 0.00 3.95
3682 3718 4.099573 CAGATATGTTGTACTCCCTCCGTT 59.900 45.833 0.00 0.00 0.00 4.44
3683 3719 3.637229 CAGATATGTTGTACTCCCTCCGT 59.363 47.826 0.00 0.00 0.00 4.69
3684 3720 3.005897 CCAGATATGTTGTACTCCCTCCG 59.994 52.174 0.00 0.00 0.00 4.63
3685 3721 3.325135 CCCAGATATGTTGTACTCCCTCC 59.675 52.174 0.00 0.00 0.00 4.30
3686 3722 3.244249 GCCCAGATATGTTGTACTCCCTC 60.244 52.174 0.00 0.00 0.00 4.30
3687 3723 2.706190 GCCCAGATATGTTGTACTCCCT 59.294 50.000 0.00 0.00 0.00 4.20
3688 3724 2.706190 AGCCCAGATATGTTGTACTCCC 59.294 50.000 0.00 0.00 0.00 4.30
3689 3725 4.130118 CAAGCCCAGATATGTTGTACTCC 58.870 47.826 0.00 0.00 0.00 3.85
3690 3726 4.572389 CACAAGCCCAGATATGTTGTACTC 59.428 45.833 0.00 0.00 30.28 2.59
3691 3727 4.019321 ACACAAGCCCAGATATGTTGTACT 60.019 41.667 0.00 0.00 30.28 2.73
3692 3728 4.261801 ACACAAGCCCAGATATGTTGTAC 58.738 43.478 0.00 0.00 30.28 2.90
3693 3729 4.513442 GACACAAGCCCAGATATGTTGTA 58.487 43.478 0.00 0.00 30.28 2.41
3709 3745 3.951775 ACAAGTTTTTGCAGGACACAA 57.048 38.095 0.00 0.00 37.85 3.33
3763 3810 1.075979 GGTTGCTTATTTTGCCGCCG 61.076 55.000 0.00 0.00 0.00 6.46
3817 4119 3.181429 ACCATGCCATAATTACTGGAGGG 60.181 47.826 14.50 10.79 35.70 4.30
3845 4147 4.973168 TGCTTCTGAACACCTTCTGTAAT 58.027 39.130 0.00 0.00 30.51 1.89
3850 4152 5.105997 GCATAATTGCTTCTGAACACCTTCT 60.106 40.000 0.00 0.00 45.77 2.85
3851 4153 5.098211 GCATAATTGCTTCTGAACACCTTC 58.902 41.667 0.00 0.00 45.77 3.46
3933 4235 3.761218 TGTGTTTCCTTTGAGCTGTTGAA 59.239 39.130 0.00 0.00 0.00 2.69
3976 4278 2.355010 ATGCTTATGTTGGAGCTCCC 57.645 50.000 29.95 15.94 39.60 4.30


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

AutoCloner maintained by Alex Coulton.