Multiple sequence alignment - TraesCS2D01G237800

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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 TraesCS2D01G237800 chr2D 100.000 3498 0 0 1 3498 245376750 245380247 0.000000e+00 6460.0
1 TraesCS2D01G237800 chr2D 94.793 653 26 7 1 649 29174347 29173699 0.000000e+00 1011.0
2 TraesCS2D01G237800 chr2D 90.826 654 49 8 1 649 583225928 583226575 0.000000e+00 865.0
3 TraesCS2D01G237800 chr2B 92.475 2764 132 34 551 3283 347079944 347077226 0.000000e+00 3882.0
4 TraesCS2D01G237800 chr2B 90.137 659 45 14 4 649 774964040 774963389 0.000000e+00 839.0
5 TraesCS2D01G237800 chr2B 89.205 176 13 3 3276 3451 347077201 347077032 7.600000e-52 215.0
6 TraesCS2D01G237800 chr2A 96.258 2138 38 9 652 2780 256125927 256128031 0.000000e+00 3467.0
7 TraesCS2D01G237800 chr2A 93.373 332 17 3 2777 3105 256128147 256128476 1.460000e-133 486.0
8 TraesCS2D01G237800 chr2A 100.000 42 0 0 3297 3338 256128481 256128522 1.040000e-10 78.7
9 TraesCS2D01G237800 chr7A 93.617 658 30 11 1 649 77705361 77706015 0.000000e+00 972.0
10 TraesCS2D01G237800 chr5D 93.607 657 30 9 1 649 10751350 10750698 0.000000e+00 970.0
11 TraesCS2D01G237800 chr5D 90.411 73 7 0 2274 2346 488344351 488344423 2.870000e-16 97.1
12 TraesCS2D01G237800 chr3D 93.157 643 22 12 1 636 593317893 593317266 0.000000e+00 924.0
13 TraesCS2D01G237800 chr3D 92.175 639 42 5 18 649 172620292 172619655 0.000000e+00 896.0
14 TraesCS2D01G237800 chr3B 90.965 653 46 11 2 649 807793835 807793191 0.000000e+00 867.0
15 TraesCS2D01G237800 chr3B 90.818 599 39 12 57 649 25928286 25927698 0.000000e+00 787.0
16 TraesCS2D01G237800 chr3B 89.796 98 9 1 1 98 473253966 473253870 1.320000e-24 124.0
17 TraesCS2D01G237800 chr1D 77.329 322 63 6 2418 2729 351918187 351917866 7.710000e-42 182.0
18 TraesCS2D01G237800 chr1B 77.160 324 63 6 2418 2731 474262694 474262372 9.980000e-41 178.0
19 TraesCS2D01G237800 chr5B 91.781 73 6 0 2274 2346 601326506 601326578 6.180000e-18 102.0
20 TraesCS2D01G237800 chr5A 90.411 73 7 0 2274 2346 609195561 609195633 2.870000e-16 97.1


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 TraesCS2D01G237800 chr2D 245376750 245380247 3497 False 6460.0 6460 100.000000 1 3498 1 chr2D.!!$F1 3497
1 TraesCS2D01G237800 chr2D 29173699 29174347 648 True 1011.0 1011 94.793000 1 649 1 chr2D.!!$R1 648
2 TraesCS2D01G237800 chr2D 583225928 583226575 647 False 865.0 865 90.826000 1 649 1 chr2D.!!$F2 648
3 TraesCS2D01G237800 chr2B 347077032 347079944 2912 True 2048.5 3882 90.840000 551 3451 2 chr2B.!!$R2 2900
4 TraesCS2D01G237800 chr2B 774963389 774964040 651 True 839.0 839 90.137000 4 649 1 chr2B.!!$R1 645
5 TraesCS2D01G237800 chr2A 256125927 256128522 2595 False 1343.9 3467 96.543667 652 3338 3 chr2A.!!$F1 2686
6 TraesCS2D01G237800 chr7A 77705361 77706015 654 False 972.0 972 93.617000 1 649 1 chr7A.!!$F1 648
7 TraesCS2D01G237800 chr5D 10750698 10751350 652 True 970.0 970 93.607000 1 649 1 chr5D.!!$R1 648
8 TraesCS2D01G237800 chr3D 593317266 593317893 627 True 924.0 924 93.157000 1 636 1 chr3D.!!$R2 635
9 TraesCS2D01G237800 chr3D 172619655 172620292 637 True 896.0 896 92.175000 18 649 1 chr3D.!!$R1 631
10 TraesCS2D01G237800 chr3B 807793191 807793835 644 True 867.0 867 90.965000 2 649 1 chr3B.!!$R3 647
11 TraesCS2D01G237800 chr3B 25927698 25928286 588 True 787.0 787 90.818000 57 649 1 chr3B.!!$R1 592

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
514 551 0.250166 AAACCGGTCAGGAACCTTCG 60.250 55.0 8.04 0.0 46.87 3.79 F
1530 1569 0.614294 TCTCGTATCCCCCGCAAAAA 59.386 50.0 0.00 0.0 0.00 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2443 2500 1.602237 GCCCTCGGATTCTTCACCA 59.398 57.895 0.00 0.0 0.00 4.17 R
3098 3284 0.246635 TTAGCGTCCAGAGGCACTTC 59.753 55.000 14.15 0.0 41.55 3.01 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
435 451 9.981114 ACAGAAAAACAAAGAAAGAAGAAAAGA 57.019 25.926 0.00 0.00 0.00 2.52
514 551 0.250166 AAACCGGTCAGGAACCTTCG 60.250 55.000 8.04 0.00 46.87 3.79
528 565 4.565028 GGAACCTTCGAGAAAGTACCCAAT 60.565 45.833 0.00 0.00 32.69 3.16
674 712 2.043752 TATCTCCCCGGTCGTGCA 60.044 61.111 0.00 0.00 0.00 4.57
721 759 5.880164 AAGATACCTTCTAGGGCTTTCTC 57.120 43.478 0.00 0.00 40.58 2.87
794 832 1.738099 CGTTCTCCCAGCCGTCAAG 60.738 63.158 0.00 0.00 0.00 3.02
842 880 4.537433 GCCGCCGCTCTCCATTCT 62.537 66.667 0.00 0.00 0.00 2.40
843 881 2.279784 CCGCCGCTCTCCATTCTC 60.280 66.667 0.00 0.00 0.00 2.87
844 882 2.279784 CGCCGCTCTCCATTCTCC 60.280 66.667 0.00 0.00 0.00 3.71
845 883 2.903357 GCCGCTCTCCATTCTCCA 59.097 61.111 0.00 0.00 0.00 3.86
1120 1159 5.753744 TGTTATCTTGTTTGTAACTTGCGG 58.246 37.500 0.00 0.00 31.37 5.69
1321 1360 5.875359 AGCAGATTGTTTAGTACTAGTTGCC 59.125 40.000 0.00 0.00 30.65 4.52
1501 1540 5.484715 GGTGCAAGATAGTTGTGGTACTTA 58.515 41.667 0.00 0.00 0.00 2.24
1530 1569 0.614294 TCTCGTATCCCCCGCAAAAA 59.386 50.000 0.00 0.00 0.00 1.94
1531 1570 1.014352 CTCGTATCCCCCGCAAAAAG 58.986 55.000 0.00 0.00 0.00 2.27
1581 1620 2.107950 TGTAACATGCTGGTACCTGC 57.892 50.000 30.92 30.92 39.73 4.85
2112 2163 7.262772 CAGCATGTATTCCACATTCATCTTTT 58.737 34.615 0.00 0.00 46.01 2.27
2117 2168 6.718912 TGTATTCCACATTCATCTTTTGGACA 59.281 34.615 0.00 0.00 36.06 4.02
2189 2240 8.607441 AAAATTCTTTTGTTTCCCTATGCTTC 57.393 30.769 0.00 0.00 0.00 3.86
2229 2286 4.330620 AGCTTTTCGTTGTTTCTTCACGTA 59.669 37.500 0.00 0.00 0.00 3.57
2250 2307 5.518847 CGTATGTCGTGGAAGTATTGATGTT 59.481 40.000 0.00 0.00 34.52 2.71
2443 2500 9.401058 CTGATTTCTTTGATTTACCAGGACTAT 57.599 33.333 0.00 0.00 0.00 2.12
2527 2584 5.926214 TGTTTCATGATGCAAACATTTGG 57.074 34.783 14.65 0.00 37.54 3.28
2540 2597 3.591695 ACATTTGGGTTGGGCATTTTT 57.408 38.095 0.00 0.00 0.00 1.94
2589 2646 2.802719 TGGGCTTCCTATTGTTCCAAC 58.197 47.619 0.00 0.00 0.00 3.77
2684 2741 5.262588 TCAGCGTAAATCATCAAGAGCTA 57.737 39.130 0.00 0.00 31.98 3.32
2853 3031 1.522668 TTGTTTGAGCTGATCCCACG 58.477 50.000 0.00 0.00 0.00 4.94
2858 3036 2.315925 TGAGCTGATCCCACGAATTC 57.684 50.000 0.00 0.00 0.00 2.17
2859 3037 1.554617 TGAGCTGATCCCACGAATTCA 59.445 47.619 6.22 0.00 0.00 2.57
2898 3076 2.543238 GCTTGCTCATTTAGATGCCTGC 60.543 50.000 0.00 0.00 33.14 4.85
2930 3108 3.513515 AGTTTGAAGGAGCTCTGTAGGAG 59.486 47.826 14.64 0.00 44.49 3.69
2934 3112 4.357325 TGAAGGAGCTCTGTAGGAGAAAT 58.643 43.478 14.64 0.00 44.45 2.17
3074 3260 2.492019 TGTACGCGAGAATCCTCATG 57.508 50.000 15.93 0.00 39.39 3.07
3098 3284 9.624697 ATGTGCTGTAAATTTGTACAAACTATG 57.375 29.630 22.78 13.87 33.66 2.23
3107 3293 6.554334 TTTGTACAAACTATGAAGTGCCTC 57.446 37.500 17.01 0.00 35.62 4.70
3109 3295 5.237815 TGTACAAACTATGAAGTGCCTCTG 58.762 41.667 0.00 0.00 35.62 3.35
3112 3298 3.618690 AACTATGAAGTGCCTCTGGAC 57.381 47.619 0.00 0.00 35.62 4.02
3116 3302 0.898326 TGAAGTGCCTCTGGACGCTA 60.898 55.000 0.00 0.00 0.00 4.26
3140 3326 5.559148 AGACATTTCTAGGCTTCCCATAG 57.441 43.478 0.00 0.00 0.00 2.23
3142 3328 5.667626 AGACATTTCTAGGCTTCCCATAGAA 59.332 40.000 0.00 0.00 33.19 2.10
3153 3339 5.683876 CTTCCCATAGAAGTTCCTTCTCA 57.316 43.478 9.63 0.00 46.42 3.27
3163 3351 7.569639 AGAAGTTCCTTCTCAAAACCTAAAC 57.430 36.000 0.00 0.00 46.42 2.01
3172 3360 5.422145 TCTCAAAACCTAAACGCCTATACC 58.578 41.667 0.00 0.00 0.00 2.73
3175 3363 5.876460 TCAAAACCTAAACGCCTATACCTTC 59.124 40.000 0.00 0.00 0.00 3.46
3181 3369 4.838904 AAACGCCTATACCTTCTCCTTT 57.161 40.909 0.00 0.00 0.00 3.11
3182 3370 4.403585 AACGCCTATACCTTCTCCTTTC 57.596 45.455 0.00 0.00 0.00 2.62
3183 3371 2.699321 ACGCCTATACCTTCTCCTTTCC 59.301 50.000 0.00 0.00 0.00 3.13
3184 3372 2.966516 CGCCTATACCTTCTCCTTTCCT 59.033 50.000 0.00 0.00 0.00 3.36
3185 3373 4.150359 CGCCTATACCTTCTCCTTTCCTA 58.850 47.826 0.00 0.00 0.00 2.94
3186 3374 4.773149 CGCCTATACCTTCTCCTTTCCTAT 59.227 45.833 0.00 0.00 0.00 2.57
3187 3375 5.246429 CGCCTATACCTTCTCCTTTCCTATT 59.754 44.000 0.00 0.00 0.00 1.73
3188 3376 6.239629 CGCCTATACCTTCTCCTTTCCTATTT 60.240 42.308 0.00 0.00 0.00 1.40
3189 3377 7.162761 GCCTATACCTTCTCCTTTCCTATTTC 58.837 42.308 0.00 0.00 0.00 2.17
3190 3378 7.016760 GCCTATACCTTCTCCTTTCCTATTTCT 59.983 40.741 0.00 0.00 0.00 2.52
3191 3379 8.939932 CCTATACCTTCTCCTTTCCTATTTCTT 58.060 37.037 0.00 0.00 0.00 2.52
3259 3447 7.244166 TGCACACATTTCAACAAAATTTAGG 57.756 32.000 0.00 0.00 35.32 2.69
3359 3579 2.957491 CCACAAGTGGCAAACAAGAA 57.043 45.000 6.27 0.00 44.73 2.52
3371 3591 4.044426 GCAAACAAGAACAATGTGAGGTC 58.956 43.478 0.00 0.00 0.00 3.85
3388 3608 0.037326 GTCTGGCTCCACGTCATTGA 60.037 55.000 0.00 0.00 0.00 2.57
3393 3613 2.433970 TGGCTCCACGTCATTGATGATA 59.566 45.455 12.78 0.00 39.30 2.15
3414 3634 2.540265 ATGTTCTCATGATCCGCTCC 57.460 50.000 0.00 0.00 32.51 4.70
3415 3635 1.194218 TGTTCTCATGATCCGCTCCA 58.806 50.000 0.00 0.00 0.00 3.86
3416 3636 1.554617 TGTTCTCATGATCCGCTCCAA 59.445 47.619 0.00 0.00 0.00 3.53
3418 3638 3.387699 TGTTCTCATGATCCGCTCCAATA 59.612 43.478 0.00 0.00 0.00 1.90
3419 3639 4.141733 TGTTCTCATGATCCGCTCCAATAA 60.142 41.667 0.00 0.00 0.00 1.40
3420 3640 3.995199 TCTCATGATCCGCTCCAATAAC 58.005 45.455 0.00 0.00 0.00 1.89
3421 3641 3.643320 TCTCATGATCCGCTCCAATAACT 59.357 43.478 0.00 0.00 0.00 2.24
3422 3642 4.101585 TCTCATGATCCGCTCCAATAACTT 59.898 41.667 0.00 0.00 0.00 2.66
3423 3643 4.129380 TCATGATCCGCTCCAATAACTTG 58.871 43.478 0.00 0.00 0.00 3.16
3443 3663 2.441750 TGGGGTCCCAATACTTCATAGC 59.558 50.000 10.98 0.00 44.12 2.97
3447 3667 1.765904 TCCCAATACTTCATAGCGCCA 59.234 47.619 2.29 0.00 0.00 5.69
3451 3671 3.565482 CCAATACTTCATAGCGCCATGTT 59.435 43.478 15.44 4.45 0.00 2.71
3452 3672 4.319766 CCAATACTTCATAGCGCCATGTTC 60.320 45.833 15.44 0.00 0.00 3.18
3453 3673 2.401583 ACTTCATAGCGCCATGTTCA 57.598 45.000 15.44 0.94 0.00 3.18
3454 3674 2.009774 ACTTCATAGCGCCATGTTCAC 58.990 47.619 15.44 0.00 0.00 3.18
3455 3675 2.009051 CTTCATAGCGCCATGTTCACA 58.991 47.619 15.44 0.00 0.00 3.58
3456 3676 2.106477 TCATAGCGCCATGTTCACAA 57.894 45.000 15.44 0.00 0.00 3.33
3457 3677 2.642427 TCATAGCGCCATGTTCACAAT 58.358 42.857 15.44 0.00 0.00 2.71
3458 3678 3.016031 TCATAGCGCCATGTTCACAATT 58.984 40.909 15.44 0.00 0.00 2.32
3459 3679 2.917701 TAGCGCCATGTTCACAATTG 57.082 45.000 2.29 3.24 0.00 2.32
3460 3680 0.388907 AGCGCCATGTTCACAATTGC 60.389 50.000 2.29 0.00 0.00 3.56
3461 3681 0.666880 GCGCCATGTTCACAATTGCA 60.667 50.000 5.05 0.00 0.00 4.08
3462 3682 1.780806 CGCCATGTTCACAATTGCAA 58.219 45.000 5.05 0.00 0.00 4.08
3463 3683 2.133553 CGCCATGTTCACAATTGCAAA 58.866 42.857 1.71 0.00 0.00 3.68
3464 3684 2.543012 CGCCATGTTCACAATTGCAAAA 59.457 40.909 1.71 0.00 0.00 2.44
3465 3685 3.604314 CGCCATGTTCACAATTGCAAAAC 60.604 43.478 1.71 3.37 0.00 2.43
3466 3686 3.604314 GCCATGTTCACAATTGCAAAACG 60.604 43.478 1.71 0.00 0.00 3.60
3467 3687 3.801050 CCATGTTCACAATTGCAAAACGA 59.199 39.130 1.71 0.00 0.00 3.85
3468 3688 4.084952 CCATGTTCACAATTGCAAAACGAG 60.085 41.667 1.71 0.00 0.00 4.18
3469 3689 2.857152 TGTTCACAATTGCAAAACGAGC 59.143 40.909 1.71 0.92 0.00 5.03
3470 3690 3.115554 GTTCACAATTGCAAAACGAGCT 58.884 40.909 1.71 0.00 0.00 4.09
3471 3691 3.435105 TCACAATTGCAAAACGAGCTT 57.565 38.095 1.71 0.00 0.00 3.74
3472 3692 3.114809 TCACAATTGCAAAACGAGCTTG 58.885 40.909 1.71 4.05 0.00 4.01
3473 3693 3.114809 CACAATTGCAAAACGAGCTTGA 58.885 40.909 8.31 0.00 0.00 3.02
3474 3694 3.551082 CACAATTGCAAAACGAGCTTGAA 59.449 39.130 8.31 0.00 0.00 2.69
3475 3695 3.798337 ACAATTGCAAAACGAGCTTGAAG 59.202 39.130 8.31 0.00 0.00 3.02
3476 3696 2.490328 TTGCAAAACGAGCTTGAAGG 57.510 45.000 8.31 0.00 0.00 3.46
3477 3697 1.674359 TGCAAAACGAGCTTGAAGGA 58.326 45.000 8.31 0.00 0.00 3.36
3478 3698 2.229792 TGCAAAACGAGCTTGAAGGAT 58.770 42.857 8.31 0.00 0.00 3.24
3479 3699 2.226437 TGCAAAACGAGCTTGAAGGATC 59.774 45.455 8.31 0.00 0.00 3.36
3480 3700 2.414691 GCAAAACGAGCTTGAAGGATCC 60.415 50.000 8.31 2.48 0.00 3.36
3481 3701 2.115343 AAACGAGCTTGAAGGATCCC 57.885 50.000 8.55 0.00 0.00 3.85
3482 3702 0.253327 AACGAGCTTGAAGGATCCCC 59.747 55.000 8.55 0.90 0.00 4.81
3483 3703 0.909610 ACGAGCTTGAAGGATCCCCA 60.910 55.000 8.55 4.01 33.88 4.96
3484 3704 0.253044 CGAGCTTGAAGGATCCCCAA 59.747 55.000 8.55 12.21 33.88 4.12
3485 3705 1.340017 CGAGCTTGAAGGATCCCCAAA 60.340 52.381 8.55 0.00 33.88 3.28
3486 3706 2.807676 GAGCTTGAAGGATCCCCAAAA 58.192 47.619 8.55 0.00 33.88 2.44
3487 3707 2.493675 GAGCTTGAAGGATCCCCAAAAC 59.506 50.000 8.55 8.29 33.88 2.43
3488 3708 1.550524 GCTTGAAGGATCCCCAAAACC 59.449 52.381 8.55 1.70 33.88 3.27
3489 3709 2.823152 GCTTGAAGGATCCCCAAAACCT 60.823 50.000 8.55 0.00 33.88 3.50
3490 3710 2.899303 TGAAGGATCCCCAAAACCTC 57.101 50.000 8.55 0.00 33.88 3.85
3491 3711 2.358258 TGAAGGATCCCCAAAACCTCT 58.642 47.619 8.55 0.00 33.88 3.69
3492 3712 2.308866 TGAAGGATCCCCAAAACCTCTC 59.691 50.000 8.55 0.00 33.88 3.20
3493 3713 2.367947 AGGATCCCCAAAACCTCTCT 57.632 50.000 8.55 0.00 33.88 3.10
3494 3714 2.200955 AGGATCCCCAAAACCTCTCTC 58.799 52.381 8.55 0.00 33.88 3.20
3495 3715 1.916181 GGATCCCCAAAACCTCTCTCA 59.084 52.381 0.00 0.00 0.00 3.27
3496 3716 2.308866 GGATCCCCAAAACCTCTCTCAA 59.691 50.000 0.00 0.00 0.00 3.02
3497 3717 3.053320 GGATCCCCAAAACCTCTCTCAAT 60.053 47.826 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 7.902087 TCGGGATTTTTCAAATTTGTTATCCT 58.098 30.769 24.95 10.34 0.00 3.24
36 37 8.718102 TTGTTCGGGATTTTTCAAATTTGTTA 57.282 26.923 17.47 5.03 0.00 2.41
514 551 4.684484 ATCCGGTATTGGGTACTTTCTC 57.316 45.455 0.00 0.00 33.64 2.87
528 565 0.815213 ACGCGCTACAGTATCCGGTA 60.815 55.000 5.73 0.00 0.00 4.02
649 687 1.205417 GACCGGGGAGATACAAAACGA 59.795 52.381 6.32 0.00 0.00 3.85
650 688 1.648504 GACCGGGGAGATACAAAACG 58.351 55.000 6.32 0.00 0.00 3.60
693 731 4.345547 AGCCCTAGAAGGTATCTTAACTGC 59.654 45.833 0.00 0.00 39.71 4.40
721 759 1.283793 CAACGCTTCTGTTGGGCTG 59.716 57.895 0.00 0.00 44.27 4.85
794 832 1.448013 GCGAGTAGGGCAGGTGTTC 60.448 63.158 0.00 0.00 0.00 3.18
839 877 0.771127 CACCTTGGGACCTTGGAGAA 59.229 55.000 7.09 0.00 0.00 2.87
840 878 1.133809 CCACCTTGGGACCTTGGAGA 61.134 60.000 7.09 0.00 32.67 3.71
841 879 1.380302 CCACCTTGGGACCTTGGAG 59.620 63.158 7.09 0.56 32.67 3.86
842 880 2.840753 GCCACCTTGGGACCTTGGA 61.841 63.158 7.09 0.00 38.19 3.53
843 881 2.283173 GCCACCTTGGGACCTTGG 60.283 66.667 0.00 0.00 38.19 3.61
844 882 2.672996 CGCCACCTTGGGACCTTG 60.673 66.667 0.00 0.00 38.19 3.61
845 883 3.966543 CCGCCACCTTGGGACCTT 61.967 66.667 0.00 0.00 38.19 3.50
1120 1159 3.352648 TCATAAGTAGCCCAAAAGCACC 58.647 45.455 0.00 0.00 34.23 5.01
1501 1540 5.061179 CGGGGGATACGAGATTAAACAATT 58.939 41.667 0.00 0.00 37.60 2.32
1581 1620 4.327680 AGCTACTCTTTAGTTTGGGCAAG 58.672 43.478 0.00 0.00 37.15 4.01
1723 1774 2.290323 GGCTTCTTCCCTGCAAAGAGTA 60.290 50.000 0.00 0.00 34.42 2.59
1798 1849 3.540314 AGAGCAGTCATCAAGTCCATC 57.460 47.619 0.00 0.00 0.00 3.51
2112 2163 3.354948 AGTGAAGCATTGCTATGTCCA 57.645 42.857 12.39 2.91 38.25 4.02
2189 2240 7.908601 ACGAAAAGCTAAAACAACTTACAAGAG 59.091 33.333 0.00 0.00 0.00 2.85
2229 2286 6.429692 TCAAAACATCAATACTTCCACGACAT 59.570 34.615 0.00 0.00 0.00 3.06
2250 2307 7.122501 TGCAGAGGAAAGCATGTTAATATCAAA 59.877 33.333 0.00 0.00 35.51 2.69
2409 2466 8.073768 GGTAAATCAAAGAAATCAGTCAAACGA 58.926 33.333 0.00 0.00 0.00 3.85
2443 2500 1.602237 GCCCTCGGATTCTTCACCA 59.398 57.895 0.00 0.00 0.00 4.17
2523 2580 2.422093 GGACAAAAATGCCCAACCCAAA 60.422 45.455 0.00 0.00 0.00 3.28
2527 2584 1.336795 CGAGGACAAAAATGCCCAACC 60.337 52.381 0.00 0.00 0.00 3.77
2540 2597 3.950397 AGCATAAATGAAACCGAGGACA 58.050 40.909 0.00 0.00 0.00 4.02
2589 2646 2.740981 CTGCTAGGCTCACACTTGAAAG 59.259 50.000 0.00 0.00 0.00 2.62
2853 3031 6.749118 GCATCTTAAATGGACACTGTGAATTC 59.251 38.462 15.86 0.00 0.00 2.17
2858 3036 5.396484 CAAGCATCTTAAATGGACACTGTG 58.604 41.667 6.19 6.19 0.00 3.66
2859 3037 4.082571 GCAAGCATCTTAAATGGACACTGT 60.083 41.667 0.00 0.00 0.00 3.55
2898 3076 3.185391 GCTCCTTCAAACTCAGAACTTCG 59.815 47.826 0.00 0.00 0.00 3.79
2930 3108 8.109705 ACAATTTGGAGCCCAATTTTTATTTC 57.890 30.769 7.39 0.00 43.55 2.17
2934 3112 7.056635 TCAAACAATTTGGAGCCCAATTTTTA 58.943 30.769 7.39 0.00 43.55 1.52
3060 3243 0.935898 CAGCACATGAGGATTCTCGC 59.064 55.000 0.00 0.00 42.79 5.03
3074 3260 9.672086 TTCATAGTTTGTACAAATTTACAGCAC 57.328 29.630 23.11 8.54 33.50 4.40
3098 3284 0.246635 TTAGCGTCCAGAGGCACTTC 59.753 55.000 14.15 0.00 41.55 3.01
3107 3293 4.806247 CCTAGAAATGTCTTTAGCGTCCAG 59.194 45.833 0.00 0.00 35.12 3.86
3109 3295 3.556365 GCCTAGAAATGTCTTTAGCGTCC 59.444 47.826 0.00 0.00 35.12 4.79
3112 3298 4.271291 GGAAGCCTAGAAATGTCTTTAGCG 59.729 45.833 0.00 0.00 35.12 4.26
3116 3302 4.657814 TGGGAAGCCTAGAAATGTCTTT 57.342 40.909 0.00 0.00 35.12 2.52
3153 3339 6.058553 AGAAGGTATAGGCGTTTAGGTTTT 57.941 37.500 0.00 0.00 0.00 2.43
3163 3351 2.966516 AGGAAAGGAGAAGGTATAGGCG 59.033 50.000 0.00 0.00 0.00 5.52
3233 3421 8.344098 CCTAAATTTTGTTGAAATGTGTGCATT 58.656 29.630 0.00 0.00 46.38 3.56
3259 3447 7.326547 TCGTTTGGACTTGAAAACACTAAAAAC 59.673 33.333 0.00 0.00 36.31 2.43
3359 3579 0.326264 GGAGCCAGACCTCACATTGT 59.674 55.000 0.00 0.00 33.47 2.71
3371 3591 1.012086 CATCAATGACGTGGAGCCAG 58.988 55.000 0.00 0.00 0.00 4.85
3422 3642 2.441750 GCTATGAAGTATTGGGACCCCA 59.558 50.000 8.45 3.10 45.63 4.96
3423 3643 2.550208 CGCTATGAAGTATTGGGACCCC 60.550 54.545 8.45 2.69 0.00 4.95
3438 3658 3.110358 CAATTGTGAACATGGCGCTATG 58.890 45.455 29.52 29.52 0.00 2.23
3441 3661 0.388907 GCAATTGTGAACATGGCGCT 60.389 50.000 7.64 0.00 0.00 5.92
3443 3663 1.780806 TTGCAATTGTGAACATGGCG 58.219 45.000 7.40 0.00 0.00 5.69
3447 3667 3.490526 GCTCGTTTTGCAATTGTGAACAT 59.509 39.130 7.40 0.00 0.00 2.71
3451 3671 3.114809 CAAGCTCGTTTTGCAATTGTGA 58.885 40.909 7.40 0.00 0.00 3.58
3452 3672 3.114809 TCAAGCTCGTTTTGCAATTGTG 58.885 40.909 7.40 0.00 0.00 3.33
3453 3673 3.435105 TCAAGCTCGTTTTGCAATTGT 57.565 38.095 7.40 0.00 0.00 2.71
3454 3674 3.182972 CCTTCAAGCTCGTTTTGCAATTG 59.817 43.478 0.00 0.00 0.00 2.32
3455 3675 3.068024 TCCTTCAAGCTCGTTTTGCAATT 59.932 39.130 0.00 0.00 0.00 2.32
3456 3676 2.622942 TCCTTCAAGCTCGTTTTGCAAT 59.377 40.909 0.00 0.00 0.00 3.56
3457 3677 2.020720 TCCTTCAAGCTCGTTTTGCAA 58.979 42.857 0.00 0.00 0.00 4.08
3458 3678 1.674359 TCCTTCAAGCTCGTTTTGCA 58.326 45.000 0.00 0.00 0.00 4.08
3459 3679 2.414691 GGATCCTTCAAGCTCGTTTTGC 60.415 50.000 3.84 0.00 0.00 3.68
3460 3680 2.162408 GGGATCCTTCAAGCTCGTTTTG 59.838 50.000 12.58 0.00 0.00 2.44
3461 3681 2.437413 GGGATCCTTCAAGCTCGTTTT 58.563 47.619 12.58 0.00 0.00 2.43
3462 3682 1.340114 GGGGATCCTTCAAGCTCGTTT 60.340 52.381 12.58 0.00 0.00 3.60
3463 3683 0.253327 GGGGATCCTTCAAGCTCGTT 59.747 55.000 12.58 0.00 0.00 3.85
3464 3684 0.909610 TGGGGATCCTTCAAGCTCGT 60.910 55.000 12.58 0.00 0.00 4.18
3465 3685 0.253044 TTGGGGATCCTTCAAGCTCG 59.747 55.000 12.58 0.00 0.00 5.03
3466 3686 2.493675 GTTTTGGGGATCCTTCAAGCTC 59.506 50.000 12.58 7.46 0.00 4.09
3467 3687 2.529632 GTTTTGGGGATCCTTCAAGCT 58.470 47.619 12.58 0.00 0.00 3.74
3468 3688 1.550524 GGTTTTGGGGATCCTTCAAGC 59.449 52.381 12.58 12.20 0.00 4.01
3469 3689 3.092301 GAGGTTTTGGGGATCCTTCAAG 58.908 50.000 12.58 0.00 0.00 3.02
3470 3690 2.721906 AGAGGTTTTGGGGATCCTTCAA 59.278 45.455 12.58 13.59 0.00 2.69
3471 3691 2.308866 GAGAGGTTTTGGGGATCCTTCA 59.691 50.000 12.58 7.96 0.00 3.02
3472 3692 2.578480 AGAGAGGTTTTGGGGATCCTTC 59.422 50.000 12.58 5.20 0.00 3.46
3473 3693 2.578480 GAGAGAGGTTTTGGGGATCCTT 59.422 50.000 12.58 0.00 0.00 3.36
3474 3694 2.200955 GAGAGAGGTTTTGGGGATCCT 58.799 52.381 12.58 0.00 0.00 3.24
3475 3695 1.916181 TGAGAGAGGTTTTGGGGATCC 59.084 52.381 1.92 1.92 0.00 3.36
3476 3696 3.721087 TTGAGAGAGGTTTTGGGGATC 57.279 47.619 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.