Multiple sequence alignment - TraesCS5B01G439600

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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 TraesCS5B01G439600 chr5B 100.000 3713 0 0 1 3713 611691564 611687852 0.000000e+00 6857
1 TraesCS5B01G439600 chr5B 84.893 2747 404 11 5 2744 619918555 619915813 0.000000e+00 2763
2 TraesCS5B01G439600 chr5B 84.694 2744 406 10 5 2740 402729720 402726983 0.000000e+00 2728
3 TraesCS5B01G439600 chr2B 98.724 2743 34 1 1 2743 78076291 78079032 0.000000e+00 4870
4 TraesCS5B01G439600 chr2B 85.104 2598 380 7 5 2598 654522260 654519666 0.000000e+00 2647
5 TraesCS5B01G439600 chr3B 98.504 2741 40 1 1 2740 191133559 191136299 0.000000e+00 4833
6 TraesCS5B01G439600 chr1B 92.852 2742 191 4 6 2742 679605583 679602842 0.000000e+00 3973
7 TraesCS5B01G439600 chr3A 88.621 2742 302 6 2 2738 696291391 696294127 0.000000e+00 3326
8 TraesCS5B01G439600 chr3A 93.878 49 3 0 344 392 698021868 698021916 1.430000e-09 75
9 TraesCS5B01G439600 chr1D 87.040 2747 345 10 5 2744 75887975 75885233 0.000000e+00 3090
10 TraesCS5B01G439600 chr2A 90.826 1853 165 3 892 2740 90583618 90581767 0.000000e+00 2475
11 TraesCS5B01G439600 chr2A 92.152 892 70 0 5 896 90586240 90585349 0.000000e+00 1260
12 TraesCS5B01G439600 chr5D 91.364 579 46 4 3101 3677 495164896 495164320 0.000000e+00 789
13 TraesCS5B01G439600 chr5D 90.980 255 22 1 2853 3107 495165468 495165215 3.550000e-90 342


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 TraesCS5B01G439600 chr5B 611687852 611691564 3712 True 6857.0 6857 100.000 1 3713 1 chr5B.!!$R2 3712
1 TraesCS5B01G439600 chr5B 619915813 619918555 2742 True 2763.0 2763 84.893 5 2744 1 chr5B.!!$R3 2739
2 TraesCS5B01G439600 chr5B 402726983 402729720 2737 True 2728.0 2728 84.694 5 2740 1 chr5B.!!$R1 2735
3 TraesCS5B01G439600 chr2B 78076291 78079032 2741 False 4870.0 4870 98.724 1 2743 1 chr2B.!!$F1 2742
4 TraesCS5B01G439600 chr2B 654519666 654522260 2594 True 2647.0 2647 85.104 5 2598 1 chr2B.!!$R1 2593
5 TraesCS5B01G439600 chr3B 191133559 191136299 2740 False 4833.0 4833 98.504 1 2740 1 chr3B.!!$F1 2739
6 TraesCS5B01G439600 chr1B 679602842 679605583 2741 True 3973.0 3973 92.852 6 2742 1 chr1B.!!$R1 2736
7 TraesCS5B01G439600 chr3A 696291391 696294127 2736 False 3326.0 3326 88.621 2 2738 1 chr3A.!!$F1 2736
8 TraesCS5B01G439600 chr1D 75885233 75887975 2742 True 3090.0 3090 87.040 5 2744 1 chr1D.!!$R1 2739
9 TraesCS5B01G439600 chr2A 90581767 90586240 4473 True 1867.5 2475 91.489 5 2740 2 chr2A.!!$R1 2735
10 TraesCS5B01G439600 chr5D 495164320 495165468 1148 True 565.5 789 91.172 2853 3677 2 chr5D.!!$R1 824

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
510 512 0.329596 ATGGAGAACTGTTGCCCTCC 59.670 55.0 16.02 16.02 44.08 4.30 F
645 648 2.053259 GAGGGATAAGGCCGGGGTTC 62.053 65.0 2.18 0.00 0.00 3.62 F
2268 4017 0.387565 TCAATACGGATGCTGCGCTA 59.612 50.0 9.73 0.00 33.30 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 3977 0.895559 CTTCAACCAACCAGCTCCCC 60.896 60.000 0.0 0.0 0.0 4.81 R
2677 4426 2.156098 ACGGTTTACATCCAATTGCGT 58.844 42.857 0.0 0.0 0.0 5.24 R
3370 5447 0.102300 CAGACACACACGACTGGTCA 59.898 55.000 0.0 0.0 0.0 4.02 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
510 512 0.329596 ATGGAGAACTGTTGCCCTCC 59.670 55.000 16.02 16.02 44.08 4.30
645 648 2.053259 GAGGGATAAGGCCGGGGTTC 62.053 65.000 2.18 0.00 0.00 3.62
677 680 4.331968 TGGATTTCGCACCTCTTATTTGT 58.668 39.130 0.00 0.00 0.00 2.83
739 742 6.114767 AGTGCACAAAGGTTGAATGAAATTT 58.885 32.000 21.04 0.00 36.07 1.82
887 890 2.100989 CCTTGCCGAGAAGTACCTAGT 58.899 52.381 0.00 0.00 0.00 2.57
1402 3147 6.216456 AGAAGTTCTCAAGAGGGGTTTGATAT 59.784 38.462 0.00 0.00 34.33 1.63
2228 3977 0.539051 AAGGAGAGATGGAAGCCACG 59.461 55.000 0.00 0.00 35.80 4.94
2268 4017 0.387565 TCAATACGGATGCTGCGCTA 59.612 50.000 9.73 0.00 33.30 4.26
2677 4426 3.025978 CCTGCTTCATTGATTGCCCTAA 58.974 45.455 8.89 0.00 0.00 2.69
2756 4506 1.875963 AAAAAGATGCAGGGACGCG 59.124 52.632 3.53 3.53 33.35 6.01
2757 4507 2.200170 AAAAAGATGCAGGGACGCGC 62.200 55.000 5.73 0.00 33.35 6.86
2758 4508 3.612247 AAAGATGCAGGGACGCGCT 62.612 57.895 5.73 0.00 32.89 5.92
2759 4509 3.612247 AAGATGCAGGGACGCGCTT 62.612 57.895 5.73 0.00 32.89 4.68
2760 4510 3.869272 GATGCAGGGACGCGCTTG 61.869 66.667 5.73 0.00 32.89 4.01
2761 4511 4.393155 ATGCAGGGACGCGCTTGA 62.393 61.111 5.73 0.00 32.89 3.02
2762 4512 3.899981 ATGCAGGGACGCGCTTGAA 62.900 57.895 5.73 0.00 32.89 2.69
2763 4513 4.090057 GCAGGGACGCGCTTGAAC 62.090 66.667 5.73 0.00 0.00 3.18
2764 4514 2.357517 CAGGGACGCGCTTGAACT 60.358 61.111 5.73 0.00 0.00 3.01
2765 4515 1.961277 CAGGGACGCGCTTGAACTT 60.961 57.895 5.73 0.00 0.00 2.66
2766 4516 1.227853 AGGGACGCGCTTGAACTTT 60.228 52.632 5.73 0.00 0.00 2.66
2767 4517 1.206831 GGGACGCGCTTGAACTTTC 59.793 57.895 5.73 0.00 0.00 2.62
2768 4518 1.228657 GGGACGCGCTTGAACTTTCT 61.229 55.000 5.73 0.00 0.00 2.52
2769 4519 0.586802 GGACGCGCTTGAACTTTCTT 59.413 50.000 5.73 0.00 0.00 2.52
2770 4520 1.002792 GGACGCGCTTGAACTTTCTTT 60.003 47.619 5.73 0.00 0.00 2.52
2771 4521 2.540973 GGACGCGCTTGAACTTTCTTTT 60.541 45.455 5.73 0.00 0.00 2.27
2772 4522 3.105937 GACGCGCTTGAACTTTCTTTTT 58.894 40.909 5.73 0.00 0.00 1.94
2810 4560 8.969260 AAGCATGTGTATCATCAATTAAGAGA 57.031 30.769 0.00 0.00 34.09 3.10
2811 4561 8.604640 AGCATGTGTATCATCAATTAAGAGAG 57.395 34.615 0.00 0.00 34.09 3.20
2812 4562 7.660617 AGCATGTGTATCATCAATTAAGAGAGG 59.339 37.037 0.00 0.00 34.09 3.69
2813 4563 7.658982 GCATGTGTATCATCAATTAAGAGAGGA 59.341 37.037 0.00 0.00 34.09 3.71
2814 4564 9.205719 CATGTGTATCATCAATTAAGAGAGGAG 57.794 37.037 1.70 0.00 34.09 3.69
2815 4565 8.539117 TGTGTATCATCAATTAAGAGAGGAGA 57.461 34.615 1.70 0.00 0.00 3.71
2816 4566 8.637099 TGTGTATCATCAATTAAGAGAGGAGAG 58.363 37.037 1.70 0.00 0.00 3.20
2817 4567 8.087750 GTGTATCATCAATTAAGAGAGGAGAGG 58.912 40.741 1.70 0.00 0.00 3.69
2818 4568 6.684897 ATCATCAATTAAGAGAGGAGAGGG 57.315 41.667 1.70 0.00 0.00 4.30
2819 4569 4.346418 TCATCAATTAAGAGAGGAGAGGGC 59.654 45.833 0.00 0.00 0.00 5.19
2820 4570 3.724478 TCAATTAAGAGAGGAGAGGGCA 58.276 45.455 0.00 0.00 0.00 5.36
2821 4571 4.104086 TCAATTAAGAGAGGAGAGGGCAA 58.896 43.478 0.00 0.00 0.00 4.52
2822 4572 4.163078 TCAATTAAGAGAGGAGAGGGCAAG 59.837 45.833 0.00 0.00 0.00 4.01
2823 4573 3.474798 TTAAGAGAGGAGAGGGCAAGA 57.525 47.619 0.00 0.00 0.00 3.02
2824 4574 1.864669 AAGAGAGGAGAGGGCAAGAG 58.135 55.000 0.00 0.00 0.00 2.85
2825 4575 0.687427 AGAGAGGAGAGGGCAAGAGC 60.687 60.000 0.00 0.00 41.10 4.09
2835 4585 2.825836 GCAAGAGCCCATCCACCG 60.826 66.667 0.00 0.00 33.58 4.94
2836 4586 2.989639 CAAGAGCCCATCCACCGA 59.010 61.111 0.00 0.00 0.00 4.69
2837 4587 1.299648 CAAGAGCCCATCCACCGAA 59.700 57.895 0.00 0.00 0.00 4.30
2838 4588 0.107017 CAAGAGCCCATCCACCGAAT 60.107 55.000 0.00 0.00 0.00 3.34
2839 4589 0.625849 AAGAGCCCATCCACCGAATT 59.374 50.000 0.00 0.00 0.00 2.17
2840 4590 1.507140 AGAGCCCATCCACCGAATTA 58.493 50.000 0.00 0.00 0.00 1.40
2841 4591 1.141053 AGAGCCCATCCACCGAATTAC 59.859 52.381 0.00 0.00 0.00 1.89
2842 4592 0.916086 AGCCCATCCACCGAATTACA 59.084 50.000 0.00 0.00 0.00 2.41
2843 4593 1.494721 AGCCCATCCACCGAATTACAT 59.505 47.619 0.00 0.00 0.00 2.29
2844 4594 1.880027 GCCCATCCACCGAATTACATC 59.120 52.381 0.00 0.00 0.00 3.06
2845 4595 2.143122 CCCATCCACCGAATTACATCG 58.857 52.381 0.00 0.00 42.37 3.84
2846 4596 2.484770 CCCATCCACCGAATTACATCGT 60.485 50.000 0.00 0.00 41.16 3.73
2847 4597 3.202906 CCATCCACCGAATTACATCGTT 58.797 45.455 0.00 0.00 41.16 3.85
2848 4598 4.373527 CCATCCACCGAATTACATCGTTA 58.626 43.478 0.00 0.00 41.16 3.18
2849 4599 4.812091 CCATCCACCGAATTACATCGTTAA 59.188 41.667 0.00 0.00 41.16 2.01
2850 4600 5.050363 CCATCCACCGAATTACATCGTTAAG 60.050 44.000 0.00 0.00 41.16 1.85
2851 4601 5.327616 TCCACCGAATTACATCGTTAAGA 57.672 39.130 0.00 0.00 41.16 2.10
2871 4621 0.111089 GACGCGCTTGAACTGACTTG 60.111 55.000 5.73 0.00 0.00 3.16
2877 4627 1.813513 CTTGAACTGACTTGCGGGAT 58.186 50.000 0.00 0.00 0.00 3.85
2883 4633 2.359850 GACTTGCGGGATGTGGCA 60.360 61.111 0.00 0.00 37.39 4.92
2887 4637 1.926511 CTTGCGGGATGTGGCACTTC 61.927 60.000 21.61 21.61 39.20 3.01
2899 4649 3.253188 TGTGGCACTTCTAAGTTGCAATC 59.747 43.478 19.83 0.00 37.08 2.67
2900 4650 2.819608 TGGCACTTCTAAGTTGCAATCC 59.180 45.455 0.59 0.00 37.08 3.01
2935 4685 6.506500 AGAAAAAGATCAATCAAGCATCGT 57.493 33.333 0.00 0.00 0.00 3.73
2944 4694 4.040829 TCAATCAAGCATCGTATCCTCCAT 59.959 41.667 0.00 0.00 0.00 3.41
2950 4700 3.580022 AGCATCGTATCCTCCATTGATGA 59.420 43.478 4.34 0.00 36.25 2.92
2953 4703 5.727434 CATCGTATCCTCCATTGATGATCA 58.273 41.667 0.00 0.00 36.25 2.92
2959 4709 7.821359 CGTATCCTCCATTGATGATCACTTAAT 59.179 37.037 0.00 0.00 29.90 1.40
2971 4721 9.112725 TGATGATCACTTAATTAACATCCACTG 57.887 33.333 16.86 1.11 33.94 3.66
3038 4788 6.665992 TCTTTCATAATATACGCACTCCCT 57.334 37.500 0.00 0.00 0.00 4.20
3047 4797 1.878953 ACGCACTCCCTTGTTTGTAG 58.121 50.000 0.00 0.00 0.00 2.74
3055 4805 3.882888 CTCCCTTGTTTGTAGTCTGCAAA 59.117 43.478 11.58 11.58 33.96 3.68
3065 4815 2.262423 AGTCTGCAAACTGAACCTCC 57.738 50.000 0.00 0.00 0.00 4.30
3071 4821 2.151202 GCAAACTGAACCTCCGATTCA 58.849 47.619 0.00 0.00 34.89 2.57
3126 5201 6.200665 CCTTTTTGAAGCAAAATTCGTCATCA 59.799 34.615 6.20 0.00 41.89 3.07
3147 5222 5.708544 TCATCTTGGGCCATTATTCTTCAT 58.291 37.500 7.26 0.00 0.00 2.57
3148 5223 5.537295 TCATCTTGGGCCATTATTCTTCATG 59.463 40.000 7.26 0.00 0.00 3.07
3168 5244 6.703319 TCATGAGCAAATCATTTCCAACATT 58.297 32.000 0.00 0.00 46.97 2.71
3170 5246 6.788684 TGAGCAAATCATTTCCAACATTTG 57.211 33.333 0.00 0.00 38.65 2.32
3252 5329 8.863049 CCATGTTTTATTAAATCAAGCTCACAC 58.137 33.333 4.49 0.00 0.00 3.82
3268 5345 7.801716 AGCTCACACTGAAAATTTACAGTAA 57.198 32.000 9.34 0.00 44.07 2.24
3322 5399 2.224305 ACCGGCAGGATTATTACTGAGC 60.224 50.000 10.86 0.00 41.02 4.26
3329 5406 5.592054 CAGGATTATTACTGAGCGAACAGA 58.408 41.667 14.39 0.00 40.63 3.41
3331 5408 4.441415 GGATTATTACTGAGCGAACAGACG 59.559 45.833 14.39 0.00 40.63 4.18
3362 5439 2.125912 GCACGGATCACTGCTCGT 60.126 61.111 6.60 0.00 36.19 4.18
3370 5447 0.321919 ATCACTGCTCGTTGCCATGT 60.322 50.000 0.00 0.00 42.00 3.21
3377 5454 0.603707 CTCGTTGCCATGTGACCAGT 60.604 55.000 0.00 0.00 0.00 4.00
3382 5459 1.301716 GCCATGTGACCAGTCGTGT 60.302 57.895 0.00 0.00 0.00 4.49
3389 5466 0.102300 TGACCAGTCGTGTGTGTCTG 59.898 55.000 0.00 0.00 0.00 3.51
3391 5468 1.956170 CCAGTCGTGTGTGTCTGCC 60.956 63.158 0.00 0.00 0.00 4.85
3411 5488 0.107017 ATGGGAGGAATTGTGCGGAG 60.107 55.000 0.00 0.00 0.00 4.63
3414 5491 1.303309 GGAGGAATTGTGCGGAGATG 58.697 55.000 0.00 0.00 0.00 2.90
3460 5537 1.507141 GGCAACGCTTATCCCCATCG 61.507 60.000 0.00 0.00 0.00 3.84
3473 5550 2.436542 TCCCCATCGGATTGTATCGTTT 59.563 45.455 0.00 0.00 34.86 3.60
3478 5555 4.262292 CCATCGGATTGTATCGTTTCCCTA 60.262 45.833 0.00 0.00 0.00 3.53
3508 5585 2.073056 TGTATGCCACGCAGTTTACAG 58.927 47.619 0.00 0.00 43.65 2.74
3515 5592 0.389426 ACGCAGTTTACAGTAGGCCG 60.389 55.000 0.00 0.00 37.78 6.13
3546 5623 2.500098 TGTACCGGGAATGGAAGAGAAG 59.500 50.000 6.32 0.00 0.00 2.85
3548 5625 1.555533 ACCGGGAATGGAAGAGAAGAC 59.444 52.381 6.32 0.00 0.00 3.01
3560 5637 4.193653 GAAGACCTCTTCCGCTGC 57.806 61.111 3.95 0.00 44.93 5.25
3564 5641 3.282745 GACCTCTTCCGCTGCGTCA 62.283 63.158 21.59 3.88 0.00 4.35
3566 5643 2.383527 CCTCTTCCGCTGCGTCAAC 61.384 63.158 21.59 0.00 0.00 3.18
3579 5656 1.603739 GTCAACCTCCCTTGGTGGC 60.604 63.158 1.21 0.00 39.73 5.01
3582 5659 3.192103 AACCTCCCTTGGTGGCGAC 62.192 63.158 1.21 0.00 39.73 5.19
3603 5680 2.732619 GGGACCCTAGAACCTGCCG 61.733 68.421 2.09 0.00 0.00 5.69
3607 5684 2.125106 CCTAGAACCTGCCGCCAC 60.125 66.667 0.00 0.00 0.00 5.01
3650 5727 2.038814 GCTCTGGCTCCTAGGAAGGC 62.039 65.000 13.77 18.15 43.31 4.35
3677 5754 1.734137 GGCAACTCGGCTATCTCGA 59.266 57.895 0.00 0.00 37.17 4.04
3678 5755 0.315568 GGCAACTCGGCTATCTCGAT 59.684 55.000 0.00 0.00 36.01 3.59
3679 5756 1.269831 GGCAACTCGGCTATCTCGATT 60.270 52.381 0.00 0.00 36.01 3.34
3680 5757 2.055100 GCAACTCGGCTATCTCGATTC 58.945 52.381 0.00 0.00 36.01 2.52
3681 5758 2.667137 CAACTCGGCTATCTCGATTCC 58.333 52.381 0.00 0.00 36.01 3.01
3682 5759 1.249407 ACTCGGCTATCTCGATTCCC 58.751 55.000 0.00 0.00 36.01 3.97
3683 5760 0.528470 CTCGGCTATCTCGATTCCCC 59.472 60.000 0.00 0.00 36.01 4.81
3684 5761 0.112606 TCGGCTATCTCGATTCCCCT 59.887 55.000 0.00 0.00 0.00 4.79
3685 5762 0.969894 CGGCTATCTCGATTCCCCTT 59.030 55.000 0.00 0.00 0.00 3.95
3686 5763 1.067495 CGGCTATCTCGATTCCCCTTC 60.067 57.143 0.00 0.00 0.00 3.46
3687 5764 1.276705 GGCTATCTCGATTCCCCTTCC 59.723 57.143 0.00 0.00 0.00 3.46
3688 5765 1.971357 GCTATCTCGATTCCCCTTCCA 59.029 52.381 0.00 0.00 0.00 3.53
3689 5766 2.569404 GCTATCTCGATTCCCCTTCCAT 59.431 50.000 0.00 0.00 0.00 3.41
3690 5767 3.618507 GCTATCTCGATTCCCCTTCCATG 60.619 52.174 0.00 0.00 0.00 3.66
3691 5768 2.174685 TCTCGATTCCCCTTCCATGA 57.825 50.000 0.00 0.00 0.00 3.07
3692 5769 1.762957 TCTCGATTCCCCTTCCATGAC 59.237 52.381 0.00 0.00 0.00 3.06
3693 5770 0.464036 TCGATTCCCCTTCCATGACG 59.536 55.000 0.00 0.00 0.00 4.35
3694 5771 1.160329 CGATTCCCCTTCCATGACGC 61.160 60.000 0.00 0.00 0.00 5.19
3695 5772 0.819666 GATTCCCCTTCCATGACGCC 60.820 60.000 0.00 0.00 0.00 5.68
3696 5773 2.284515 ATTCCCCTTCCATGACGCCC 62.285 60.000 0.00 0.00 0.00 6.13
3697 5774 4.506255 CCCCTTCCATGACGCCCC 62.506 72.222 0.00 0.00 0.00 5.80
3698 5775 4.506255 CCCTTCCATGACGCCCCC 62.506 72.222 0.00 0.00 0.00 5.40
3699 5776 4.856801 CCTTCCATGACGCCCCCG 62.857 72.222 0.00 0.00 41.14 5.73
3708 5785 3.736224 ACGCCCCCGTCTCTAGGA 61.736 66.667 0.00 0.00 46.39 2.94
3709 5786 2.203509 CGCCCCCGTCTCTAGGAT 60.204 66.667 0.00 0.00 0.00 3.24
3710 5787 2.565645 CGCCCCCGTCTCTAGGATG 61.566 68.421 0.00 0.00 0.00 3.51
3712 5789 1.233369 CCCCCGTCTCTAGGATGGT 59.767 63.158 14.69 0.00 46.89 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
510 512 4.672409 GAATACCTTTTGATGGGCGAAAG 58.328 43.478 0.00 0.00 44.36 2.62
645 648 1.379642 GCGAAATCCAAGGGGCTCTG 61.380 60.000 0.00 0.00 0.00 3.35
677 680 8.792633 CCTTCATAAAAACTAAACAGTCATCCA 58.207 33.333 0.00 0.00 0.00 3.41
739 742 5.083122 TGACCCCAAATGATAAGCTTGAAA 58.917 37.500 9.86 0.00 0.00 2.69
1402 3147 3.755112 TGTTCCGTCACCAATTCTACA 57.245 42.857 0.00 0.00 0.00 2.74
2196 3945 5.069251 CCATCTCTCCTTCGTAATACACCTT 59.931 44.000 0.00 0.00 0.00 3.50
2228 3977 0.895559 CTTCAACCAACCAGCTCCCC 60.896 60.000 0.00 0.00 0.00 4.81
2677 4426 2.156098 ACGGTTTACATCCAATTGCGT 58.844 42.857 0.00 0.00 0.00 5.24
2744 4494 3.899981 TTCAAGCGCGTCCCTGCAT 62.900 57.895 8.43 0.00 34.15 3.96
2745 4495 4.617520 TTCAAGCGCGTCCCTGCA 62.618 61.111 8.43 0.00 34.15 4.41
2746 4496 4.090057 GTTCAAGCGCGTCCCTGC 62.090 66.667 8.43 0.00 0.00 4.85
2747 4497 1.507141 AAAGTTCAAGCGCGTCCCTG 61.507 55.000 8.43 0.00 0.00 4.45
2748 4498 1.227853 AAAGTTCAAGCGCGTCCCT 60.228 52.632 8.43 0.00 0.00 4.20
2749 4499 1.206831 GAAAGTTCAAGCGCGTCCC 59.793 57.895 8.43 0.00 0.00 4.46
2750 4500 0.586802 AAGAAAGTTCAAGCGCGTCC 59.413 50.000 8.43 0.00 0.00 4.79
2751 4501 2.384899 AAAGAAAGTTCAAGCGCGTC 57.615 45.000 8.43 0.00 0.00 5.19
2752 4502 2.844122 AAAAGAAAGTTCAAGCGCGT 57.156 40.000 8.43 0.00 0.00 6.01
2785 4535 8.969260 TCTCTTAATTGATGATACACATGCTT 57.031 30.769 0.00 0.00 39.56 3.91
2786 4536 7.660617 CCTCTCTTAATTGATGATACACATGCT 59.339 37.037 0.00 0.00 39.56 3.79
2787 4537 7.658982 TCCTCTCTTAATTGATGATACACATGC 59.341 37.037 0.00 0.00 39.56 4.06
2788 4538 9.205719 CTCCTCTCTTAATTGATGATACACATG 57.794 37.037 0.00 0.00 39.56 3.21
2789 4539 9.152327 TCTCCTCTCTTAATTGATGATACACAT 57.848 33.333 0.00 0.00 42.47 3.21
2790 4540 8.539117 TCTCCTCTCTTAATTGATGATACACA 57.461 34.615 0.00 0.00 0.00 3.72
2791 4541 8.087750 CCTCTCCTCTCTTAATTGATGATACAC 58.912 40.741 0.00 0.00 0.00 2.90
2792 4542 7.234371 CCCTCTCCTCTCTTAATTGATGATACA 59.766 40.741 0.00 0.00 0.00 2.29
2793 4543 7.610865 CCCTCTCCTCTCTTAATTGATGATAC 58.389 42.308 0.00 0.00 0.00 2.24
2794 4544 6.212388 GCCCTCTCCTCTCTTAATTGATGATA 59.788 42.308 0.00 0.00 0.00 2.15
2795 4545 5.012975 GCCCTCTCCTCTCTTAATTGATGAT 59.987 44.000 0.00 0.00 0.00 2.45
2796 4546 4.346418 GCCCTCTCCTCTCTTAATTGATGA 59.654 45.833 0.00 0.00 0.00 2.92
2797 4547 4.102210 TGCCCTCTCCTCTCTTAATTGATG 59.898 45.833 0.00 0.00 0.00 3.07
2798 4548 4.302067 TGCCCTCTCCTCTCTTAATTGAT 58.698 43.478 0.00 0.00 0.00 2.57
2799 4549 3.724478 TGCCCTCTCCTCTCTTAATTGA 58.276 45.455 0.00 0.00 0.00 2.57
2800 4550 4.163078 TCTTGCCCTCTCCTCTCTTAATTG 59.837 45.833 0.00 0.00 0.00 2.32
2801 4551 4.366267 TCTTGCCCTCTCCTCTCTTAATT 58.634 43.478 0.00 0.00 0.00 1.40
2802 4552 3.966665 CTCTTGCCCTCTCCTCTCTTAAT 59.033 47.826 0.00 0.00 0.00 1.40
2803 4553 3.370104 CTCTTGCCCTCTCCTCTCTTAA 58.630 50.000 0.00 0.00 0.00 1.85
2804 4554 2.952702 GCTCTTGCCCTCTCCTCTCTTA 60.953 54.545 0.00 0.00 0.00 2.10
2805 4555 1.864669 CTCTTGCCCTCTCCTCTCTT 58.135 55.000 0.00 0.00 0.00 2.85
2806 4556 0.687427 GCTCTTGCCCTCTCCTCTCT 60.687 60.000 0.00 0.00 0.00 3.10
2807 4557 1.822615 GCTCTTGCCCTCTCCTCTC 59.177 63.158 0.00 0.00 0.00 3.20
2808 4558 4.048696 GCTCTTGCCCTCTCCTCT 57.951 61.111 0.00 0.00 0.00 3.69
2818 4568 2.819984 TTCGGTGGATGGGCTCTTGC 62.820 60.000 0.00 0.00 38.76 4.01
2819 4569 0.107017 ATTCGGTGGATGGGCTCTTG 60.107 55.000 0.00 0.00 0.00 3.02
2820 4570 0.625849 AATTCGGTGGATGGGCTCTT 59.374 50.000 0.00 0.00 0.00 2.85
2821 4571 1.141053 GTAATTCGGTGGATGGGCTCT 59.859 52.381 0.00 0.00 0.00 4.09
2822 4572 1.134220 TGTAATTCGGTGGATGGGCTC 60.134 52.381 0.00 0.00 0.00 4.70
2823 4573 0.916086 TGTAATTCGGTGGATGGGCT 59.084 50.000 0.00 0.00 0.00 5.19
2824 4574 1.880027 GATGTAATTCGGTGGATGGGC 59.120 52.381 0.00 0.00 0.00 5.36
2825 4575 2.143122 CGATGTAATTCGGTGGATGGG 58.857 52.381 0.00 0.00 35.50 4.00
2826 4576 2.833794 ACGATGTAATTCGGTGGATGG 58.166 47.619 0.00 0.00 43.33 3.51
2827 4577 5.751509 TCTTAACGATGTAATTCGGTGGATG 59.248 40.000 0.00 0.00 43.33 3.51
2828 4578 5.909477 TCTTAACGATGTAATTCGGTGGAT 58.091 37.500 0.00 0.00 43.33 3.41
2829 4579 5.125900 TCTCTTAACGATGTAATTCGGTGGA 59.874 40.000 0.00 0.00 43.33 4.02
2830 4580 5.231568 GTCTCTTAACGATGTAATTCGGTGG 59.768 44.000 0.00 0.00 43.33 4.61
2831 4581 5.052567 CGTCTCTTAACGATGTAATTCGGTG 60.053 44.000 0.00 0.00 45.37 4.94
2832 4582 5.032863 CGTCTCTTAACGATGTAATTCGGT 58.967 41.667 0.00 0.00 45.37 4.69
2833 4583 4.085721 GCGTCTCTTAACGATGTAATTCGG 60.086 45.833 0.00 0.00 45.37 4.30
2834 4584 4.372738 CGCGTCTCTTAACGATGTAATTCG 60.373 45.833 0.00 0.00 45.37 3.34
2835 4585 4.603390 GCGCGTCTCTTAACGATGTAATTC 60.603 45.833 8.43 0.00 45.37 2.17
2836 4586 3.242248 GCGCGTCTCTTAACGATGTAATT 59.758 43.478 8.43 0.00 45.37 1.40
2837 4587 2.787680 GCGCGTCTCTTAACGATGTAAT 59.212 45.455 8.43 0.00 45.37 1.89
2838 4588 2.159476 AGCGCGTCTCTTAACGATGTAA 60.159 45.455 8.43 0.00 45.37 2.41
2839 4589 1.399440 AGCGCGTCTCTTAACGATGTA 59.601 47.619 8.43 0.00 45.37 2.29
2840 4590 0.170561 AGCGCGTCTCTTAACGATGT 59.829 50.000 8.43 0.00 45.37 3.06
2841 4591 1.007011 CAAGCGCGTCTCTTAACGATG 60.007 52.381 8.43 0.00 45.37 3.84
2842 4592 1.135489 TCAAGCGCGTCTCTTAACGAT 60.135 47.619 8.43 0.00 45.37 3.73
2843 4593 0.239082 TCAAGCGCGTCTCTTAACGA 59.761 50.000 8.43 0.00 45.37 3.85
2844 4594 1.057636 TTCAAGCGCGTCTCTTAACG 58.942 50.000 8.43 0.00 45.31 3.18
2845 4595 2.059541 AGTTCAAGCGCGTCTCTTAAC 58.940 47.619 8.43 10.34 0.00 2.01
2846 4596 2.058798 CAGTTCAAGCGCGTCTCTTAA 58.941 47.619 8.43 0.00 0.00 1.85
2847 4597 1.268625 TCAGTTCAAGCGCGTCTCTTA 59.731 47.619 8.43 0.00 0.00 2.10
2848 4598 0.032130 TCAGTTCAAGCGCGTCTCTT 59.968 50.000 8.43 0.00 0.00 2.85
2849 4599 0.664767 GTCAGTTCAAGCGCGTCTCT 60.665 55.000 8.43 0.00 0.00 3.10
2850 4600 0.664767 AGTCAGTTCAAGCGCGTCTC 60.665 55.000 8.43 0.00 0.00 3.36
2851 4601 0.249489 AAGTCAGTTCAAGCGCGTCT 60.249 50.000 8.43 1.94 0.00 4.18
2871 4621 0.392461 TTAGAAGTGCCACATCCCGC 60.392 55.000 0.00 0.00 0.00 6.13
2877 4627 2.340210 TGCAACTTAGAAGTGCCACA 57.660 45.000 0.00 0.84 39.66 4.17
2883 4633 3.806949 TGGGGATTGCAACTTAGAAGT 57.193 42.857 0.00 0.00 42.04 3.01
2887 4637 4.026052 AGGATTTGGGGATTGCAACTTAG 58.974 43.478 0.00 0.00 0.00 2.18
2899 4649 7.480760 TGATCTTTTTCTTTAGGATTTGGGG 57.519 36.000 0.00 0.00 0.00 4.96
2900 4650 9.591792 GATTGATCTTTTTCTTTAGGATTTGGG 57.408 33.333 0.00 0.00 0.00 4.12
2928 4678 3.580022 TCATCAATGGAGGATACGATGCT 59.420 43.478 0.00 0.00 46.39 3.79
2944 4694 9.685276 AGTGGATGTTAATTAAGTGATCATCAA 57.315 29.630 19.39 11.09 34.01 2.57
2966 4716 6.656693 AGATTTAGGACTGATCAAAACAGTGG 59.343 38.462 0.00 0.00 46.57 4.00
3021 4771 6.354130 ACAAACAAGGGAGTGCGTATATTAT 58.646 36.000 0.00 0.00 0.00 1.28
3027 4777 2.366266 ACTACAAACAAGGGAGTGCGTA 59.634 45.455 0.00 0.00 0.00 4.42
3028 4778 1.140252 ACTACAAACAAGGGAGTGCGT 59.860 47.619 0.00 0.00 0.00 5.24
3047 4797 0.868406 CGGAGGTTCAGTTTGCAGAC 59.132 55.000 0.00 0.00 0.00 3.51
3055 4805 3.981071 TGATTGAATCGGAGGTTCAGT 57.019 42.857 0.18 0.00 36.96 3.41
3056 4806 5.049818 GCTTATGATTGAATCGGAGGTTCAG 60.050 44.000 0.18 0.00 36.96 3.02
3065 4815 5.980698 AGTGTGAGCTTATGATTGAATCG 57.019 39.130 0.18 0.00 0.00 3.34
3126 5201 5.708544 TCATGAAGAATAATGGCCCAAGAT 58.291 37.500 0.00 0.00 0.00 2.40
3147 5222 6.522946 TCAAATGTTGGAAATGATTTGCTCA 58.477 32.000 10.69 9.82 37.92 4.26
3148 5223 7.424227 TTCAAATGTTGGAAATGATTTGCTC 57.576 32.000 10.69 4.96 37.92 4.26
3206 5282 2.657143 GAGTTCTCCCTATCCTGACGT 58.343 52.381 0.00 0.00 0.00 4.34
3211 5287 3.715648 ACATGGAGTTCTCCCTATCCT 57.284 47.619 15.20 0.00 32.79 3.24
3252 5329 7.973944 GGGGCATAACTTACTGTAAATTTTCAG 59.026 37.037 19.73 19.73 37.65 3.02
3268 5345 3.515562 TGAATTGTTTGGGGGCATAACT 58.484 40.909 0.00 0.00 0.00 2.24
3318 5395 2.148916 ACATTTCGTCTGTTCGCTCA 57.851 45.000 0.00 0.00 0.00 4.26
3322 5399 2.096417 GGGACAACATTTCGTCTGTTCG 60.096 50.000 0.00 0.00 34.69 3.95
3329 5406 0.951558 GTGCTGGGACAACATTTCGT 59.048 50.000 0.00 0.00 36.57 3.85
3331 5408 0.240945 CCGTGCTGGGACAACATTTC 59.759 55.000 0.00 0.00 36.57 2.17
3362 5439 0.884259 CACGACTGGTCACATGGCAA 60.884 55.000 0.00 0.00 0.00 4.52
3370 5447 0.102300 CAGACACACACGACTGGTCA 59.898 55.000 0.00 0.00 0.00 4.02
3377 5454 1.301637 CCATGGCAGACACACACGA 60.302 57.895 0.00 0.00 0.00 4.35
3382 5459 1.133181 TTCCTCCCATGGCAGACACA 61.133 55.000 3.48 0.00 0.00 3.72
3389 5466 1.818555 GCACAATTCCTCCCATGGC 59.181 57.895 6.09 0.00 0.00 4.40
3391 5468 0.394216 TCCGCACAATTCCTCCCATG 60.394 55.000 0.00 0.00 0.00 3.66
3411 5488 4.690184 TGTGATGCATCAAAGTCACATC 57.310 40.909 30.24 15.00 44.14 3.06
3414 5491 4.801891 ACATTGTGATGCATCAAAGTCAC 58.198 39.130 30.24 18.73 38.75 3.67
3440 5517 0.179018 GATGGGGATAAGCGTTGCCT 60.179 55.000 0.00 0.00 0.00 4.75
3460 5537 8.021396 GCAATTTATAGGGAAACGATACAATCC 58.979 37.037 0.00 0.00 0.00 3.01
3468 5545 7.870826 CATACATGCAATTTATAGGGAAACGA 58.129 34.615 0.00 0.00 0.00 3.85
3498 5575 1.366854 GCCGGCCTACTGTAAACTGC 61.367 60.000 18.11 0.00 0.00 4.40
3501 5578 1.296727 GATGCCGGCCTACTGTAAAC 58.703 55.000 26.77 0.00 0.00 2.01
3522 5599 3.134081 TCTCTTCCATTCCCGGTACATTC 59.866 47.826 0.00 0.00 0.00 2.67
3546 5623 2.507324 GACGCAGCGGAAGAGGTC 60.507 66.667 21.15 1.14 0.00 3.85
3548 5625 2.048222 TTGACGCAGCGGAAGAGG 60.048 61.111 21.15 0.00 0.00 3.69
3556 5633 2.032681 AAGGGAGGTTGACGCAGC 59.967 61.111 0.00 0.00 0.00 5.25
3560 5637 1.302511 CCACCAAGGGAGGTTGACG 60.303 63.158 0.00 0.00 40.77 4.35
3564 5641 2.852075 TCGCCACCAAGGGAGGTT 60.852 61.111 0.74 0.00 40.77 3.50
3566 5643 4.760047 CGTCGCCACCAAGGGAGG 62.760 72.222 0.00 0.00 38.09 4.30
3619 5696 4.421479 CAGAGCGGGCTTCGACGT 62.421 66.667 0.00 0.00 42.43 4.34
3664 5741 0.528470 GGGGAATCGAGATAGCCGAG 59.472 60.000 0.00 0.00 39.55 4.63
3667 5744 1.276705 GGAAGGGGAATCGAGATAGCC 59.723 57.143 0.00 0.00 0.00 3.93
3672 5749 1.762957 GTCATGGAAGGGGAATCGAGA 59.237 52.381 0.00 0.00 0.00 4.04
3677 5754 1.227383 GGCGTCATGGAAGGGGAAT 59.773 57.895 0.00 0.00 0.00 3.01
3678 5755 2.674754 GGCGTCATGGAAGGGGAA 59.325 61.111 0.00 0.00 0.00 3.97
3679 5756 3.407967 GGGCGTCATGGAAGGGGA 61.408 66.667 0.00 0.00 0.00 4.81
3680 5757 4.506255 GGGGCGTCATGGAAGGGG 62.506 72.222 0.00 0.00 0.00 4.79
3681 5758 4.506255 GGGGGCGTCATGGAAGGG 62.506 72.222 0.00 0.00 0.00 3.95
3682 5759 4.856801 CGGGGGCGTCATGGAAGG 62.857 72.222 0.00 0.00 0.00 3.46
3683 5760 4.096003 ACGGGGGCGTCATGGAAG 62.096 66.667 0.00 0.00 0.00 3.46
3684 5761 4.090588 GACGGGGGCGTCATGGAA 62.091 66.667 0.00 0.00 38.62 3.53
3686 5763 4.530857 GAGACGGGGGCGTCATGG 62.531 72.222 0.00 0.00 40.96 3.66
3687 5764 2.076622 CTAGAGACGGGGGCGTCATG 62.077 65.000 0.00 0.00 40.96 3.07
3688 5765 1.828660 CTAGAGACGGGGGCGTCAT 60.829 63.158 0.00 0.00 40.96 3.06
3689 5766 2.439701 CTAGAGACGGGGGCGTCA 60.440 66.667 0.00 0.00 40.96 4.35
3690 5767 2.980105 ATCCTAGAGACGGGGGCGTC 62.980 65.000 0.00 0.00 39.01 5.19
3691 5768 3.070987 ATCCTAGAGACGGGGGCGT 62.071 63.158 0.00 0.00 0.00 5.68
3692 5769 2.203509 ATCCTAGAGACGGGGGCG 60.204 66.667 0.00 0.00 0.00 6.13
3693 5770 2.210711 CCATCCTAGAGACGGGGGC 61.211 68.421 0.00 0.00 0.00 5.80
3694 5771 1.233369 ACCATCCTAGAGACGGGGG 59.767 63.158 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.