Multiple sequence alignment - TraesCS3D01G209900

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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 TraesCS3D01G209900 chr3D 100.000 4806 0 0 1 4806 277542086 277537281 0.000000e+00 8876.0
1 TraesCS3D01G209900 chr3D 92.727 55 4 0 4622 4676 567708588 567708642 3.990000e-11 80.5
2 TraesCS3D01G209900 chr3A 96.765 3524 64 17 1 3487 361991567 361995077 0.000000e+00 5830.0
3 TraesCS3D01G209900 chr3A 96.095 1050 34 3 3578 4622 361995074 361996121 0.000000e+00 1705.0
4 TraesCS3D01G209900 chr3A 92.857 154 9 1 4655 4806 361996115 361996268 6.260000e-54 222.0
5 TraesCS3D01G209900 chr3B 95.871 3439 80 29 1 3408 372838900 372842307 0.000000e+00 5507.0
6 TraesCS3D01G209900 chr3B 92.724 1072 28 13 3580 4622 372842306 372843356 0.000000e+00 1502.0
7 TraesCS3D01G209900 chr3B 87.662 154 15 3 4656 4806 372843351 372843503 4.940000e-40 176.0
8 TraesCS3D01G209900 chr3B 96.000 50 2 0 4618 4667 628478802 628478851 1.110000e-11 82.4
9 TraesCS3D01G209900 chr3B 92.593 54 4 0 4617 4670 26648172 26648225 1.430000e-10 78.7
10 TraesCS3D01G209900 chr4D 93.636 110 6 1 3472 3580 26253940 26254049 3.850000e-36 163.0
11 TraesCS3D01G209900 chr7B 94.286 105 4 2 3483 3586 589348318 589348421 4.980000e-35 159.0
12 TraesCS3D01G209900 chr1A 93.519 108 6 1 3484 3590 351606858 351606751 4.980000e-35 159.0
13 TraesCS3D01G209900 chr7A 94.175 103 5 1 3481 3582 511927312 511927414 6.440000e-34 156.0
14 TraesCS3D01G209900 chr7A 93.333 105 5 2 3483 3586 628008575 628008472 2.320000e-33 154.0
15 TraesCS3D01G209900 chr7A 94.231 52 3 0 4620 4671 639594990 639594939 3.990000e-11 80.5
16 TraesCS3D01G209900 chr7D 93.333 105 5 2 3483 3586 545397537 545397640 2.320000e-33 154.0
17 TraesCS3D01G209900 chr7D 91.379 58 3 2 4608 4665 199127653 199127708 1.430000e-10 78.7
18 TraesCS3D01G209900 chr1B 91.892 111 7 2 3484 3592 56752488 56752378 2.320000e-33 154.0
19 TraesCS3D01G209900 chr1B 91.228 57 3 2 4618 4673 423585133 423585078 5.160000e-10 76.8
20 TraesCS3D01G209900 chr6D 90.351 114 8 3 3477 3589 368755201 368755090 3.880000e-31 147.0
21 TraesCS3D01G209900 chr4B 89.655 116 11 1 3480 3594 595278781 595278896 3.880000e-31 147.0
22 TraesCS3D01G209900 chr6B 94.545 55 1 2 4618 4672 277158983 277159035 3.080000e-12 84.2
23 TraesCS3D01G209900 chrUn 96.000 50 2 0 4618 4667 100223781 100223830 1.110000e-11 82.4
24 TraesCS3D01G209900 chr6A 92.727 55 2 2 4617 4670 613997767 613997714 1.430000e-10 78.7


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 TraesCS3D01G209900 chr3D 277537281 277542086 4805 True 8876.000000 8876 100.000000 1 4806 1 chr3D.!!$R1 4805
1 TraesCS3D01G209900 chr3A 361991567 361996268 4701 False 2585.666667 5830 95.239000 1 4806 3 chr3A.!!$F1 4805
2 TraesCS3D01G209900 chr3B 372838900 372843503 4603 False 2395.000000 5507 92.085667 1 4806 3 chr3B.!!$F3 4805

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
391 397 0.321034 ACATGATCCCATCGCCGATG 60.321 55.000 19.87 19.87 39.52 3.84 F
868 883 1.235281 ACAGCACGCGTGTAGAGAGA 61.235 55.000 36.80 0.00 0.00 3.10 F
969 1014 2.126734 CGTAAACCGACCGCTCGT 60.127 61.111 0.00 0.00 38.32 4.18 F
2057 2105 2.279517 CAGACGAGTATGCGGGCC 60.280 66.667 0.00 0.00 35.12 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 1431 0.654160 AGCGATCGTCGTCGTTGATA 59.346 50.000 17.81 0.0 42.81 2.15 R
2333 2384 2.489329 CAAAAAGTGCATCGGGTCTGAT 59.511 45.455 0.00 0.0 0.00 2.90 R
2341 2392 3.607422 TGAGTGACAAAAAGTGCATCG 57.393 42.857 0.00 0.0 0.00 3.84 R
3836 3888 1.004918 GTGAACTGCACGGCTAGGT 60.005 57.895 0.00 0.0 37.83 3.08 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
199 205 5.638234 AGAAGGTCGGTTATTCTTTCTTTCG 59.362 40.000 0.00 0.00 28.99 3.46
253 259 0.548510 AAGATGCTAACCCTCCCTGC 59.451 55.000 0.00 0.00 0.00 4.85
391 397 0.321034 ACATGATCCCATCGCCGATG 60.321 55.000 19.87 19.87 39.52 3.84
464 470 4.571984 TCTCCGCACAATCATATGACAAAG 59.428 41.667 7.78 0.96 0.00 2.77
475 481 8.767085 CAATCATATGACAAAGTGTTGCTTTTT 58.233 29.630 7.78 0.00 44.41 1.94
500 506 8.427902 TTCCAGATAGTATATGTGCTCTCATT 57.572 34.615 4.17 0.00 0.00 2.57
862 877 1.660264 CTCACACAGCACGCGTGTA 60.660 57.895 36.80 14.84 45.63 2.90
868 883 1.235281 ACAGCACGCGTGTAGAGAGA 61.235 55.000 36.80 0.00 0.00 3.10
969 1014 2.126734 CGTAAACCGACCGCTCGT 60.127 61.111 0.00 0.00 38.32 4.18
1386 1431 2.545810 CTCAGGGAGGAAGAGGACTTT 58.454 52.381 0.00 0.00 36.39 2.66
2057 2105 2.279517 CAGACGAGTATGCGGGCC 60.280 66.667 0.00 0.00 35.12 5.80
2317 2365 4.831674 TCATGCCTCATGAATATCCGAT 57.168 40.909 7.00 0.00 46.17 4.18
2318 2366 5.937975 TCATGCCTCATGAATATCCGATA 57.062 39.130 7.00 0.00 46.17 2.92
2319 2367 6.490241 TCATGCCTCATGAATATCCGATAT 57.510 37.500 7.00 0.00 46.17 1.63
2320 2368 6.519382 TCATGCCTCATGAATATCCGATATC 58.481 40.000 7.00 0.00 46.17 1.63
2333 2384 3.893521 TCCGATATCCTGTGTGTGTCTA 58.106 45.455 0.00 0.00 0.00 2.59
2341 2392 2.093973 CCTGTGTGTGTCTATCAGACCC 60.094 54.545 3.97 0.00 44.44 4.46
2512 2563 6.984474 CACCACCTCATCGTATTACAATAGTT 59.016 38.462 0.00 0.00 0.00 2.24
2527 2578 5.805728 ACAATAGTTACCCTGTGAAGAAGG 58.194 41.667 0.00 0.00 34.31 3.46
2603 2654 7.338449 TGTTTTGCTAGGTCAAAAGACTAAAGT 59.662 33.333 8.10 0.00 43.88 2.66
2627 2678 5.876357 ACCTATTGAATGGGCATACGTATT 58.124 37.500 7.55 0.00 33.57 1.89
2630 2681 7.040686 ACCTATTGAATGGGCATACGTATTTTC 60.041 37.037 7.55 5.41 33.57 2.29
2667 2719 6.209192 TGGAATGCTGTGAATTTTGTATCACT 59.791 34.615 7.35 0.00 44.86 3.41
2910 2962 1.794116 CAATTGCAAAGGAGCGGTTTG 59.206 47.619 1.71 0.00 37.85 2.93
2947 2999 4.997395 AGATAATGACGGGTACATGATTGC 59.003 41.667 0.00 0.00 0.00 3.56
3143 3195 2.186826 GGTTTGATCCGCATCCCCG 61.187 63.158 0.00 0.00 0.00 5.73
3309 3361 8.092687 GCATAATGAAAATGATGCTAAAGGGAT 58.907 33.333 1.44 0.00 41.19 3.85
3371 3423 9.799106 ATTTATACTTATATGGTGAAGCAGCTT 57.201 29.630 7.60 7.60 32.61 3.74
3456 3508 8.704668 TCATCAATCTCATTTGGCTAGTAACTA 58.295 33.333 0.00 0.00 0.00 2.24
3492 3544 9.682465 ATTTGAACTTACTTTTATACTCCCTCC 57.318 33.333 0.00 0.00 0.00 4.30
3493 3545 6.870769 TGAACTTACTTTTATACTCCCTCCG 58.129 40.000 0.00 0.00 0.00 4.63
3494 3546 6.438425 TGAACTTACTTTTATACTCCCTCCGT 59.562 38.462 0.00 0.00 0.00 4.69
3495 3547 6.462552 ACTTACTTTTATACTCCCTCCGTC 57.537 41.667 0.00 0.00 0.00 4.79
3496 3548 5.362143 ACTTACTTTTATACTCCCTCCGTCC 59.638 44.000 0.00 0.00 0.00 4.79
3497 3549 3.036819 ACTTTTATACTCCCTCCGTCCC 58.963 50.000 0.00 0.00 0.00 4.46
3498 3550 2.852714 TTTATACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
3499 3551 2.852714 TTATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
3500 3552 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
3501 3553 2.191981 ATACTCCCTCCGTCCCAAAT 57.808 50.000 0.00 0.00 0.00 2.32
3502 3554 2.852714 TACTCCCTCCGTCCCAAATA 57.147 50.000 0.00 0.00 0.00 1.40
3503 3555 1.961133 ACTCCCTCCGTCCCAAATAA 58.039 50.000 0.00 0.00 0.00 1.40
3504 3556 1.838077 ACTCCCTCCGTCCCAAATAAG 59.162 52.381 0.00 0.00 0.00 1.73
3505 3557 1.838077 CTCCCTCCGTCCCAAATAAGT 59.162 52.381 0.00 0.00 0.00 2.24
3506 3558 2.238898 CTCCCTCCGTCCCAAATAAGTT 59.761 50.000 0.00 0.00 0.00 2.66
3507 3559 2.645797 TCCCTCCGTCCCAAATAAGTTT 59.354 45.455 0.00 0.00 0.00 2.66
3508 3560 3.014623 CCCTCCGTCCCAAATAAGTTTC 58.985 50.000 0.00 0.00 0.00 2.78
3509 3561 3.308188 CCCTCCGTCCCAAATAAGTTTCT 60.308 47.826 0.00 0.00 0.00 2.52
3510 3562 3.939592 CCTCCGTCCCAAATAAGTTTCTC 59.060 47.826 0.00 0.00 0.00 2.87
3511 3563 4.564821 CCTCCGTCCCAAATAAGTTTCTCA 60.565 45.833 0.00 0.00 0.00 3.27
3512 3564 4.975631 TCCGTCCCAAATAAGTTTCTCAA 58.024 39.130 0.00 0.00 0.00 3.02
3513 3565 4.758165 TCCGTCCCAAATAAGTTTCTCAAC 59.242 41.667 0.00 0.00 0.00 3.18
3514 3566 4.760204 CCGTCCCAAATAAGTTTCTCAACT 59.240 41.667 0.00 0.00 45.89 3.16
3529 3581 9.968870 AGTTTCTCAACTTTGTACTAACTCTAG 57.031 33.333 0.00 0.00 40.66 2.43
3530 3582 9.747293 GTTTCTCAACTTTGTACTAACTCTAGT 57.253 33.333 0.00 0.00 41.43 2.57
3554 3606 6.846325 ACAAAGTTGTACTAAGCTTGAGAC 57.154 37.500 9.86 4.39 40.16 3.36
3555 3607 6.346096 ACAAAGTTGTACTAAGCTTGAGACA 58.654 36.000 9.86 7.12 40.16 3.41
3556 3608 6.258068 ACAAAGTTGTACTAAGCTTGAGACAC 59.742 38.462 9.86 7.18 40.16 3.67
3557 3609 5.793030 AGTTGTACTAAGCTTGAGACACT 57.207 39.130 9.86 7.29 0.00 3.55
3558 3610 6.163135 AGTTGTACTAAGCTTGAGACACTT 57.837 37.500 9.86 0.00 0.00 3.16
3559 3611 7.286215 AGTTGTACTAAGCTTGAGACACTTA 57.714 36.000 9.86 0.00 0.00 2.24
3560 3612 7.897864 AGTTGTACTAAGCTTGAGACACTTAT 58.102 34.615 9.86 0.00 0.00 1.73
3561 3613 8.368668 AGTTGTACTAAGCTTGAGACACTTATT 58.631 33.333 9.86 0.00 0.00 1.40
3562 3614 8.989980 GTTGTACTAAGCTTGAGACACTTATTT 58.010 33.333 9.86 0.00 0.00 1.40
3563 3615 9.555727 TTGTACTAAGCTTGAGACACTTATTTT 57.444 29.630 9.86 0.00 0.00 1.82
3566 3618 8.779354 ACTAAGCTTGAGACACTTATTTTAGG 57.221 34.615 9.86 0.00 0.00 2.69
3567 3619 8.594550 ACTAAGCTTGAGACACTTATTTTAGGA 58.405 33.333 9.86 0.00 0.00 2.94
3568 3620 9.606631 CTAAGCTTGAGACACTTATTTTAGGAT 57.393 33.333 9.86 0.00 0.00 3.24
3569 3621 7.856145 AGCTTGAGACACTTATTTTAGGATG 57.144 36.000 0.00 0.00 0.00 3.51
3570 3622 6.825721 AGCTTGAGACACTTATTTTAGGATGG 59.174 38.462 0.00 0.00 0.00 3.51
3571 3623 6.823689 GCTTGAGACACTTATTTTAGGATGGA 59.176 38.462 0.00 0.00 0.00 3.41
3572 3624 7.500559 GCTTGAGACACTTATTTTAGGATGGAT 59.499 37.037 0.00 0.00 0.00 3.41
3573 3625 8.737168 TTGAGACACTTATTTTAGGATGGATG 57.263 34.615 0.00 0.00 0.00 3.51
3574 3626 7.282585 TGAGACACTTATTTTAGGATGGATGG 58.717 38.462 0.00 0.00 0.00 3.51
3575 3627 7.127186 TGAGACACTTATTTTAGGATGGATGGA 59.873 37.037 0.00 0.00 0.00 3.41
3576 3628 7.512992 AGACACTTATTTTAGGATGGATGGAG 58.487 38.462 0.00 0.00 0.00 3.86
3577 3629 7.127955 AGACACTTATTTTAGGATGGATGGAGT 59.872 37.037 0.00 0.00 0.00 3.85
3578 3630 8.331931 ACACTTATTTTAGGATGGATGGAGTA 57.668 34.615 0.00 0.00 0.00 2.59
3579 3631 8.211629 ACACTTATTTTAGGATGGATGGAGTAC 58.788 37.037 0.00 0.00 0.00 2.73
3580 3632 8.432805 CACTTATTTTAGGATGGATGGAGTACT 58.567 37.037 0.00 0.00 0.00 2.73
3626 3678 5.220931 GGCAATTGTACTTCAGCTTATGAGG 60.221 44.000 7.40 0.00 39.68 3.86
3901 3953 6.367695 GGCACCGCAACTAAAATTATCTTTTT 59.632 34.615 0.00 0.00 33.56 1.94
4096 4153 1.699634 AGCACACAGAGTTGGTATGGT 59.300 47.619 0.00 0.00 0.00 3.55
4109 4166 1.229241 TATGGTGTGACACGGGGGA 60.229 57.895 9.90 0.00 34.83 4.81
4131 4188 2.156917 TCAGGTGCTGCTTTGATTCTG 58.843 47.619 0.00 0.00 0.00 3.02
4309 4380 4.259810 CGCAAGTTCGATAATACACACTGG 60.260 45.833 0.00 0.00 0.00 4.00
4344 4419 3.192001 TGAAATGAGATCAGCTGTTTGCC 59.808 43.478 14.67 1.51 44.23 4.52
4479 4560 6.256819 TCTATGATATAGGACAGGTGAAGGG 58.743 44.000 0.00 0.00 0.00 3.95
4616 4697 7.278875 ACTTTTGCAAGGGAAATTTTATGTCA 58.721 30.769 0.00 0.00 33.82 3.58
4617 4698 7.772757 ACTTTTGCAAGGGAAATTTTATGTCAA 59.227 29.630 0.00 0.00 33.82 3.18
4618 4699 7.489574 TTTGCAAGGGAAATTTTATGTCAAC 57.510 32.000 0.00 0.00 0.00 3.18
4619 4700 6.418057 TGCAAGGGAAATTTTATGTCAACT 57.582 33.333 0.00 0.00 0.00 3.16
4620 4701 7.531857 TGCAAGGGAAATTTTATGTCAACTA 57.468 32.000 0.00 0.00 0.00 2.24
4621 4702 7.601856 TGCAAGGGAAATTTTATGTCAACTAG 58.398 34.615 0.00 0.00 0.00 2.57
4622 4703 7.232534 TGCAAGGGAAATTTTATGTCAACTAGT 59.767 33.333 0.00 0.00 0.00 2.57
4623 4704 7.542130 GCAAGGGAAATTTTATGTCAACTAGTG 59.458 37.037 0.00 0.00 0.00 2.74
4624 4705 8.576442 CAAGGGAAATTTTATGTCAACTAGTGT 58.424 33.333 0.00 0.00 0.00 3.55
4625 4706 8.336801 AGGGAAATTTTATGTCAACTAGTGTC 57.663 34.615 0.00 0.00 0.00 3.67
4626 4707 7.942341 AGGGAAATTTTATGTCAACTAGTGTCA 59.058 33.333 0.00 0.00 0.00 3.58
4627 4708 8.573035 GGGAAATTTTATGTCAACTAGTGTCAA 58.427 33.333 0.00 0.00 0.00 3.18
4628 4709 9.959749 GGAAATTTTATGTCAACTAGTGTCAAA 57.040 29.630 0.00 0.00 0.00 2.69
4632 4713 8.829514 TTTTATGTCAACTAGTGTCAAAAACG 57.170 30.769 0.00 0.00 0.00 3.60
4633 4714 7.542534 TTATGTCAACTAGTGTCAAAAACGT 57.457 32.000 0.00 0.00 0.00 3.99
4634 4715 5.866335 TGTCAACTAGTGTCAAAAACGTT 57.134 34.783 0.00 0.00 0.00 3.99
4635 4716 5.860641 TGTCAACTAGTGTCAAAAACGTTC 58.139 37.500 0.00 0.00 0.00 3.95
4636 4717 5.640357 TGTCAACTAGTGTCAAAAACGTTCT 59.360 36.000 0.00 0.00 0.00 3.01
4637 4718 6.148150 TGTCAACTAGTGTCAAAAACGTTCTT 59.852 34.615 0.00 0.00 0.00 2.52
4638 4719 7.331440 TGTCAACTAGTGTCAAAAACGTTCTTA 59.669 33.333 0.00 0.00 0.00 2.10
4639 4720 8.333186 GTCAACTAGTGTCAAAAACGTTCTTAT 58.667 33.333 0.00 0.00 0.00 1.73
4640 4721 9.531942 TCAACTAGTGTCAAAAACGTTCTTATA 57.468 29.630 0.00 0.00 0.00 0.98
4647 4728 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
4648 4729 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
4649 4730 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
4650 4731 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
4651 4732 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
4652 4733 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
4653 4734 6.409524 ACGTTCTTATATTATGGGACGGAA 57.590 37.500 13.18 0.00 0.00 4.30
4654 4735 6.453092 ACGTTCTTATATTATGGGACGGAAG 58.547 40.000 13.18 0.00 0.00 3.46
4657 4738 6.852420 TCTTATATTATGGGACGGAAGGAG 57.148 41.667 0.00 0.00 0.00 3.69
4734 4818 9.972106 ATTTGTCTTTAGATCATCCTCTTTTCT 57.028 29.630 0.00 0.00 0.00 2.52
4743 4827 3.587061 TCATCCTCTTTTCTACCCTTGCA 59.413 43.478 0.00 0.00 0.00 4.08
4764 4848 0.034186 ATGATGGCCGTGTTGTCCAT 60.034 50.000 0.00 0.00 42.83 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 205 9.494271 TTCAAGGATGTGATTATTGAGCTATAC 57.506 33.333 0.00 0.00 32.00 1.47
253 259 0.950836 TCCAAGTTGTTGCACATCCG 59.049 50.000 1.45 0.00 31.64 4.18
391 397 1.153549 CCGGCTCAGCTAGTTCCAC 60.154 63.158 0.00 0.00 0.00 4.02
475 481 8.427902 AATGAGAGCACATATACTATCTGGAA 57.572 34.615 0.00 0.00 0.00 3.53
500 506 3.581101 AGCCTGCCTCATCTTATACAGA 58.419 45.455 0.00 0.00 35.33 3.41
751 760 7.441458 AGCTGTAGAATCCATTAATTAACGGAC 59.559 37.037 14.89 4.23 0.00 4.79
862 877 1.736586 CCGCGCCAATAGTCTCTCT 59.263 57.895 0.00 0.00 0.00 3.10
1335 1380 1.273606 CACTCCTTCATGTGGTCGTCT 59.726 52.381 7.23 0.00 0.00 4.18
1386 1431 0.654160 AGCGATCGTCGTCGTTGATA 59.346 50.000 17.81 0.00 42.81 2.15
2045 2093 2.552231 AAACCCAGGCCCGCATACTC 62.552 60.000 0.00 0.00 0.00 2.59
2055 2103 2.963101 AGGTTCAAGTTTAAACCCAGGC 59.037 45.455 14.72 3.43 44.98 4.85
2057 2105 5.278315 GCAGTAGGTTCAAGTTTAAACCCAG 60.278 44.000 14.72 5.45 44.98 4.45
2177 2225 9.297586 TGAACGATGTAAAATCATGTACTCTAC 57.702 33.333 0.00 0.00 0.00 2.59
2270 2318 4.479156 TGGTAGAAAATTTTGGGGAGGT 57.521 40.909 8.47 0.00 0.00 3.85
2315 2363 6.442952 GTCTGATAGACACACACAGGATATC 58.557 44.000 4.20 0.00 44.45 1.63
2316 2364 5.303078 GGTCTGATAGACACACACAGGATAT 59.697 44.000 10.75 0.00 46.79 1.63
2317 2365 4.645136 GGTCTGATAGACACACACAGGATA 59.355 45.833 10.75 0.00 46.79 2.59
2318 2366 3.449018 GGTCTGATAGACACACACAGGAT 59.551 47.826 10.75 0.00 46.79 3.24
2319 2367 2.826128 GGTCTGATAGACACACACAGGA 59.174 50.000 10.75 0.00 46.79 3.86
2320 2368 3.238108 GGTCTGATAGACACACACAGG 57.762 52.381 10.75 0.00 46.79 4.00
2333 2384 2.489329 CAAAAAGTGCATCGGGTCTGAT 59.511 45.455 0.00 0.00 0.00 2.90
2341 2392 3.607422 TGAGTGACAAAAAGTGCATCG 57.393 42.857 0.00 0.00 0.00 3.84
2512 2563 4.412858 TGGTTTTACCTTCTTCACAGGGTA 59.587 41.667 0.00 0.00 39.58 3.69
2527 2578 5.587289 TGCTCAAACTTGATGTGGTTTTAC 58.413 37.500 0.00 0.00 36.46 2.01
2603 2654 4.967084 ACGTATGCCCATTCAATAGGTA 57.033 40.909 0.00 0.00 0.00 3.08
2910 2962 5.098211 GTCATTATCTTTGTCAAGCTTGGC 58.902 41.667 24.15 24.15 0.00 4.52
2947 2999 5.557891 CTGGAAGTCCTAAATCAAAGCTG 57.442 43.478 0.00 0.00 36.82 4.24
3178 3230 2.290916 TCGCGCTATTCTAAGGTCTCAG 59.709 50.000 5.56 0.00 0.00 3.35
3309 3361 8.134895 ACAAATTAGCATTTCGAAGAACTTCAA 58.865 29.630 13.72 3.32 45.90 2.69
3456 3508 6.884280 AAGTAAGTTCAAATAGCTGCAGTT 57.116 33.333 16.64 12.62 0.00 3.16
3487 3539 2.801077 AACTTATTTGGGACGGAGGG 57.199 50.000 0.00 0.00 0.00 4.30
3488 3540 3.939592 GAGAAACTTATTTGGGACGGAGG 59.060 47.826 0.00 0.00 0.00 4.30
3489 3541 4.575885 TGAGAAACTTATTTGGGACGGAG 58.424 43.478 0.00 0.00 0.00 4.63
3490 3542 4.627284 TGAGAAACTTATTTGGGACGGA 57.373 40.909 0.00 0.00 0.00 4.69
3491 3543 4.760204 AGTTGAGAAACTTATTTGGGACGG 59.240 41.667 0.00 0.00 0.00 4.79
3492 3544 5.941948 AGTTGAGAAACTTATTTGGGACG 57.058 39.130 0.00 0.00 0.00 4.79
3493 3545 7.489160 ACAAAGTTGAGAAACTTATTTGGGAC 58.511 34.615 4.40 0.00 41.76 4.46
3494 3546 7.654022 ACAAAGTTGAGAAACTTATTTGGGA 57.346 32.000 4.40 0.00 41.76 4.37
3495 3547 8.630037 AGTACAAAGTTGAGAAACTTATTTGGG 58.370 33.333 4.40 0.00 41.76 4.12
3503 3555 9.968870 CTAGAGTTAGTACAAAGTTGAGAAACT 57.031 33.333 0.00 2.60 33.76 2.66
3504 3556 9.747293 ACTAGAGTTAGTACAAAGTTGAGAAAC 57.253 33.333 0.00 0.00 38.35 2.78
3530 3582 7.437267 GTGTCTCAAGCTTAGTACAACTTTGTA 59.563 37.037 0.00 0.00 42.35 2.41
3531 3583 6.258068 GTGTCTCAAGCTTAGTACAACTTTGT 59.742 38.462 0.00 0.00 44.86 2.83
3532 3584 6.480320 AGTGTCTCAAGCTTAGTACAACTTTG 59.520 38.462 0.00 0.00 0.00 2.77
3533 3585 6.583562 AGTGTCTCAAGCTTAGTACAACTTT 58.416 36.000 0.00 0.00 0.00 2.66
3534 3586 6.163135 AGTGTCTCAAGCTTAGTACAACTT 57.837 37.500 0.00 0.00 0.00 2.66
3535 3587 5.793030 AGTGTCTCAAGCTTAGTACAACT 57.207 39.130 0.00 0.00 0.00 3.16
3536 3588 8.535690 AATAAGTGTCTCAAGCTTAGTACAAC 57.464 34.615 0.00 0.00 0.00 3.32
3537 3589 9.555727 AAAATAAGTGTCTCAAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
3540 3592 9.871238 CCTAAAATAAGTGTCTCAAGCTTAGTA 57.129 33.333 0.00 0.00 0.00 1.82
3541 3593 8.594550 TCCTAAAATAAGTGTCTCAAGCTTAGT 58.405 33.333 0.00 0.00 0.00 2.24
3542 3594 9.606631 ATCCTAAAATAAGTGTCTCAAGCTTAG 57.393 33.333 0.00 0.00 0.00 2.18
3543 3595 9.383519 CATCCTAAAATAAGTGTCTCAAGCTTA 57.616 33.333 0.00 0.00 0.00 3.09
3544 3596 7.337942 CCATCCTAAAATAAGTGTCTCAAGCTT 59.662 37.037 0.00 0.00 0.00 3.74
3545 3597 6.825721 CCATCCTAAAATAAGTGTCTCAAGCT 59.174 38.462 0.00 0.00 0.00 3.74
3546 3598 6.823689 TCCATCCTAAAATAAGTGTCTCAAGC 59.176 38.462 0.00 0.00 0.00 4.01
3547 3599 8.834465 CATCCATCCTAAAATAAGTGTCTCAAG 58.166 37.037 0.00 0.00 0.00 3.02
3548 3600 7.775093 CCATCCATCCTAAAATAAGTGTCTCAA 59.225 37.037 0.00 0.00 0.00 3.02
3549 3601 7.127186 TCCATCCATCCTAAAATAAGTGTCTCA 59.873 37.037 0.00 0.00 0.00 3.27
3550 3602 7.509546 TCCATCCATCCTAAAATAAGTGTCTC 58.490 38.462 0.00 0.00 0.00 3.36
3551 3603 7.127955 ACTCCATCCATCCTAAAATAAGTGTCT 59.872 37.037 0.00 0.00 0.00 3.41
3552 3604 7.283329 ACTCCATCCATCCTAAAATAAGTGTC 58.717 38.462 0.00 0.00 0.00 3.67
3553 3605 7.213178 ACTCCATCCATCCTAAAATAAGTGT 57.787 36.000 0.00 0.00 0.00 3.55
3554 3606 8.432805 AGTACTCCATCCATCCTAAAATAAGTG 58.567 37.037 0.00 0.00 0.00 3.16
3555 3607 8.568617 AGTACTCCATCCATCCTAAAATAAGT 57.431 34.615 0.00 0.00 0.00 2.24
3556 3608 9.277783 CAAGTACTCCATCCATCCTAAAATAAG 57.722 37.037 0.00 0.00 0.00 1.73
3557 3609 8.998814 TCAAGTACTCCATCCATCCTAAAATAA 58.001 33.333 0.00 0.00 0.00 1.40
3558 3610 8.561536 TCAAGTACTCCATCCATCCTAAAATA 57.438 34.615 0.00 0.00 0.00 1.40
3559 3611 7.451731 TCAAGTACTCCATCCATCCTAAAAT 57.548 36.000 0.00 0.00 0.00 1.82
3560 3612 6.884472 TCAAGTACTCCATCCATCCTAAAA 57.116 37.500 0.00 0.00 0.00 1.52
3561 3613 7.567250 TGTATCAAGTACTCCATCCATCCTAAA 59.433 37.037 0.00 0.00 34.27 1.85
3562 3614 7.073208 TGTATCAAGTACTCCATCCATCCTAA 58.927 38.462 0.00 0.00 34.27 2.69
3563 3615 6.620429 TGTATCAAGTACTCCATCCATCCTA 58.380 40.000 0.00 0.00 34.27 2.94
3564 3616 5.467738 TGTATCAAGTACTCCATCCATCCT 58.532 41.667 0.00 0.00 34.27 3.24
3565 3617 5.808366 TGTATCAAGTACTCCATCCATCC 57.192 43.478 0.00 0.00 34.27 3.51
3566 3618 6.169094 CCATGTATCAAGTACTCCATCCATC 58.831 44.000 0.00 0.00 34.27 3.51
3567 3619 5.608437 ACCATGTATCAAGTACTCCATCCAT 59.392 40.000 0.00 0.00 34.27 3.41
3568 3620 4.968719 ACCATGTATCAAGTACTCCATCCA 59.031 41.667 0.00 0.00 34.27 3.41
3569 3621 5.070446 TGACCATGTATCAAGTACTCCATCC 59.930 44.000 0.00 0.00 34.27 3.51
3570 3622 6.161855 TGACCATGTATCAAGTACTCCATC 57.838 41.667 0.00 0.00 34.27 3.51
3571 3623 6.560003 TTGACCATGTATCAAGTACTCCAT 57.440 37.500 0.00 0.00 34.27 3.41
3572 3624 5.977635 CTTGACCATGTATCAAGTACTCCA 58.022 41.667 20.98 0.00 45.32 3.86
3580 3632 4.220382 CCCTTTTGCTTGACCATGTATCAA 59.780 41.667 8.81 8.81 34.89 2.57
3626 3678 2.568623 AGAGACCCCACACATGTTTC 57.431 50.000 0.00 0.00 0.00 2.78
3833 3885 1.553248 TGAACTGCACGGCTAGGTAAT 59.447 47.619 0.00 0.00 0.00 1.89
3836 3888 1.004918 GTGAACTGCACGGCTAGGT 60.005 57.895 0.00 0.00 37.83 3.08
3860 3912 2.328099 GCCCAGGAAAGCAGTGACG 61.328 63.158 0.00 0.00 0.00 4.35
3902 3954 3.565482 GGATGCCTATGATCTGCGAAAAA 59.435 43.478 0.00 0.00 0.00 1.94
3938 3990 3.307339 CCTTCCTGCTAGATTGCCTATCC 60.307 52.174 0.00 0.00 33.45 2.59
3941 3993 3.046283 TCCTTCCTGCTAGATTGCCTA 57.954 47.619 0.00 0.00 0.00 3.93
4096 4153 1.676968 CTGATTCCCCCGTGTCACA 59.323 57.895 3.42 0.00 0.00 3.58
4109 4166 3.192844 CAGAATCAAAGCAGCACCTGATT 59.807 43.478 13.58 13.58 42.09 2.57
4131 4188 8.223100 GCCATTTCATTTCACTAAACAATTCAC 58.777 33.333 0.00 0.00 0.00 3.18
4309 4380 5.403897 TCTCATTTCACAGAACGAAACAC 57.596 39.130 0.00 0.00 35.31 3.32
4344 4419 1.746220 CTCAACTACGGAGACAGGAGG 59.254 57.143 0.00 0.00 34.24 4.30
4479 4560 0.868406 CTCAGGAAGTGCCGAAACAC 59.132 55.000 0.00 0.00 43.43 3.32
4579 4660 1.577328 GCAAAAGTAGAGCAGCGCCA 61.577 55.000 2.29 0.00 0.00 5.69
4621 4702 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
4622 4703 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
4623 4704 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
4624 4705 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
4625 4706 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
4626 4707 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
4627 4708 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
4628 4709 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
4629 4710 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
4630 4711 6.409524 TTCCGTCCCATAATATAAGAACGT 57.590 37.500 0.00 0.00 0.00 3.99
4631 4712 5.867716 CCTTCCGTCCCATAATATAAGAACG 59.132 44.000 0.00 0.00 0.00 3.95
4632 4713 7.001099 TCCTTCCGTCCCATAATATAAGAAC 57.999 40.000 0.00 0.00 0.00 3.01
4633 4714 6.785963 ACTCCTTCCGTCCCATAATATAAGAA 59.214 38.462 0.00 0.00 0.00 2.52
4634 4715 6.320518 ACTCCTTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
4635 4716 6.607004 ACTCCTTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
4636 4717 6.154021 GCTACTCCTTCCGTCCCATAATATAA 59.846 42.308 0.00 0.00 0.00 0.98
4637 4718 5.655532 GCTACTCCTTCCGTCCCATAATATA 59.344 44.000 0.00 0.00 0.00 0.86
4638 4719 4.466726 GCTACTCCTTCCGTCCCATAATAT 59.533 45.833 0.00 0.00 0.00 1.28
4639 4720 3.830755 GCTACTCCTTCCGTCCCATAATA 59.169 47.826 0.00 0.00 0.00 0.98
4640 4721 2.633481 GCTACTCCTTCCGTCCCATAAT 59.367 50.000 0.00 0.00 0.00 1.28
4641 4722 2.037144 GCTACTCCTTCCGTCCCATAA 58.963 52.381 0.00 0.00 0.00 1.90
4642 4723 1.063492 TGCTACTCCTTCCGTCCCATA 60.063 52.381 0.00 0.00 0.00 2.74
4643 4724 0.325296 TGCTACTCCTTCCGTCCCAT 60.325 55.000 0.00 0.00 0.00 4.00
4644 4725 0.543410 TTGCTACTCCTTCCGTCCCA 60.543 55.000 0.00 0.00 0.00 4.37
4645 4726 0.611714 TTTGCTACTCCTTCCGTCCC 59.388 55.000 0.00 0.00 0.00 4.46
4646 4727 1.001633 TGTTTGCTACTCCTTCCGTCC 59.998 52.381 0.00 0.00 0.00 4.79
4647 4728 2.450609 TGTTTGCTACTCCTTCCGTC 57.549 50.000 0.00 0.00 0.00 4.79
4648 4729 2.038557 ACATGTTTGCTACTCCTTCCGT 59.961 45.455 0.00 0.00 0.00 4.69
4649 4730 2.673368 GACATGTTTGCTACTCCTTCCG 59.327 50.000 0.00 0.00 0.00 4.30
4650 4731 3.010420 GGACATGTTTGCTACTCCTTCC 58.990 50.000 0.00 0.00 0.00 3.46
4651 4732 2.673368 CGGACATGTTTGCTACTCCTTC 59.327 50.000 0.00 0.00 0.00 3.46
4652 4733 2.038557 ACGGACATGTTTGCTACTCCTT 59.961 45.455 0.00 0.00 0.00 3.36
4653 4734 1.623811 ACGGACATGTTTGCTACTCCT 59.376 47.619 0.00 0.00 0.00 3.69
4654 4735 1.732259 CACGGACATGTTTGCTACTCC 59.268 52.381 0.00 0.00 0.00 3.85
4657 4738 0.802494 CCCACGGACATGTTTGCTAC 59.198 55.000 0.00 0.00 0.00 3.58
4732 4816 1.141657 GCCATCATCTGCAAGGGTAGA 59.858 52.381 0.00 0.00 40.16 2.59
4734 4818 0.183492 GGCCATCATCTGCAAGGGTA 59.817 55.000 0.00 0.00 0.00 3.69
4743 4827 0.392998 GGACAACACGGCCATCATCT 60.393 55.000 2.24 0.00 0.00 2.90
4764 4848 1.153449 CGGGCGCTCTACAATTGGA 60.153 57.895 5.36 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.