Multiple sequence alignment - TraesCS5A01G477800

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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 TraesCS5A01G477800 chr5A 100.000 2414 0 0 1 2414 651684778 651687191 0.000000e+00 4458
1 TraesCS5A01G477800 chr5A 90.372 779 68 6 998 1774 651635545 651636318 0.000000e+00 1016
2 TraesCS5A01G477800 chr5A 94.531 640 32 3 1777 2414 29722894 29722256 0.000000e+00 985
3 TraesCS5A01G477800 chr5A 92.969 640 42 3 1777 2414 12149206 12148568 0.000000e+00 929
4 TraesCS5A01G477800 chr5A 92.523 642 44 4 1776 2414 386462809 386463449 0.000000e+00 917
5 TraesCS5A01G477800 chr5A 89.474 646 63 5 1771 2414 291269430 291270072 0.000000e+00 811
6 TraesCS5A01G477800 chr5A 98.313 415 7 0 1001 1415 651763426 651763840 0.000000e+00 728
7 TraesCS5A01G477800 chr5A 83.046 755 95 24 997 1730 651588594 651589336 0.000000e+00 654
8 TraesCS5A01G477800 chr5A 85.714 546 71 6 2 543 445550863 445551405 9.680000e-159 569
9 TraesCS5A01G477800 chr5A 84.726 419 51 9 999 1415 651744412 651744819 8.030000e-110 407
10 TraesCS5A01G477800 chr5A 83.922 255 12 11 619 864 651754668 651754902 1.450000e-52 217
11 TraesCS5A01G477800 chr3A 95.000 640 29 3 1777 2414 100863260 100862622 0.000000e+00 1002
12 TraesCS5A01G477800 chr3A 93.199 647 39 5 1771 2414 691482126 691481482 0.000000e+00 946
13 TraesCS5A01G477800 chr4B 93.789 644 39 1 1772 2414 121569552 121570195 0.000000e+00 966
14 TraesCS5A01G477800 chr1A 90.062 644 61 3 1773 2414 249442587 249441945 0.000000e+00 832
15 TraesCS5A01G477800 chr1A 86.172 593 51 11 7 574 516374051 516374637 1.590000e-171 612
16 TraesCS5A01G477800 chr4A 89.612 645 59 6 1776 2414 250435801 250436443 0.000000e+00 813
17 TraesCS5A01G477800 chr5B 85.445 797 79 18 1001 1774 659604666 659605448 0.000000e+00 795
18 TraesCS5A01G477800 chr5B 79.786 935 113 43 696 1594 659679076 659679970 5.710000e-171 610
19 TraesCS5A01G477800 chr5B 85.366 492 66 5 953 1440 659635717 659636206 2.770000e-139 505
20 TraesCS5A01G477800 chr5D 84.615 819 88 21 619 1415 525316963 525317765 0.000000e+00 780
21 TraesCS5A01G477800 chr5D 82.045 763 82 23 997 1734 525250309 525251041 1.240000e-167 599
22 TraesCS5A01G477800 chr5D 84.034 595 59 18 5 574 482290158 482289575 7.590000e-150 540
23 TraesCS5A01G477800 chr7D 85.857 601 54 14 2 574 390492093 390492690 5.710000e-171 610
24 TraesCS5A01G477800 chr7D 85.524 601 56 14 2 574 71620741 71621338 1.240000e-167 599
25 TraesCS5A01G477800 chr7A 85.249 583 73 9 2 577 33088173 33087597 2.670000e-164 588
26 TraesCS5A01G477800 chr7A 93.075 361 20 4 2 359 397000320 397000678 7.650000e-145 523
27 TraesCS5A01G477800 chrUn 85.320 579 72 9 2 573 288795912 288796484 9.620000e-164 586
28 TraesCS5A01G477800 chrUn 85.320 579 72 9 2 573 326973619 326974191 9.620000e-164 586
29 TraesCS5A01G477800 chrUn 85.320 579 72 9 2 573 326976645 326977217 9.620000e-164 586
30 TraesCS5A01G477800 chr7B 88.303 436 37 10 2 429 1263344 1263773 5.950000e-141 510
31 TraesCS5A01G477800 chr1D 86.062 452 54 6 118 561 433910668 433911118 6.040000e-131 477


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 TraesCS5A01G477800 chr5A 651684778 651687191 2413 False 4458 4458 100.000 1 2414 1 chr5A.!!$F6 2413
1 TraesCS5A01G477800 chr5A 651635545 651636318 773 False 1016 1016 90.372 998 1774 1 chr5A.!!$F5 776
2 TraesCS5A01G477800 chr5A 29722256 29722894 638 True 985 985 94.531 1777 2414 1 chr5A.!!$R2 637
3 TraesCS5A01G477800 chr5A 12148568 12149206 638 True 929 929 92.969 1777 2414 1 chr5A.!!$R1 637
4 TraesCS5A01G477800 chr5A 386462809 386463449 640 False 917 917 92.523 1776 2414 1 chr5A.!!$F2 638
5 TraesCS5A01G477800 chr5A 291269430 291270072 642 False 811 811 89.474 1771 2414 1 chr5A.!!$F1 643
6 TraesCS5A01G477800 chr5A 651588594 651589336 742 False 654 654 83.046 997 1730 1 chr5A.!!$F4 733
7 TraesCS5A01G477800 chr5A 445550863 445551405 542 False 569 569 85.714 2 543 1 chr5A.!!$F3 541
8 TraesCS5A01G477800 chr3A 100862622 100863260 638 True 1002 1002 95.000 1777 2414 1 chr3A.!!$R1 637
9 TraesCS5A01G477800 chr3A 691481482 691482126 644 True 946 946 93.199 1771 2414 1 chr3A.!!$R2 643
10 TraesCS5A01G477800 chr4B 121569552 121570195 643 False 966 966 93.789 1772 2414 1 chr4B.!!$F1 642
11 TraesCS5A01G477800 chr1A 249441945 249442587 642 True 832 832 90.062 1773 2414 1 chr1A.!!$R1 641
12 TraesCS5A01G477800 chr1A 516374051 516374637 586 False 612 612 86.172 7 574 1 chr1A.!!$F1 567
13 TraesCS5A01G477800 chr4A 250435801 250436443 642 False 813 813 89.612 1776 2414 1 chr4A.!!$F1 638
14 TraesCS5A01G477800 chr5B 659604666 659605448 782 False 795 795 85.445 1001 1774 1 chr5B.!!$F1 773
15 TraesCS5A01G477800 chr5B 659679076 659679970 894 False 610 610 79.786 696 1594 1 chr5B.!!$F3 898
16 TraesCS5A01G477800 chr5D 525316963 525317765 802 False 780 780 84.615 619 1415 1 chr5D.!!$F2 796
17 TraesCS5A01G477800 chr5D 525250309 525251041 732 False 599 599 82.045 997 1734 1 chr5D.!!$F1 737
18 TraesCS5A01G477800 chr5D 482289575 482290158 583 True 540 540 84.034 5 574 1 chr5D.!!$R1 569
19 TraesCS5A01G477800 chr7D 390492093 390492690 597 False 610 610 85.857 2 574 1 chr7D.!!$F2 572
20 TraesCS5A01G477800 chr7D 71620741 71621338 597 False 599 599 85.524 2 574 1 chr7D.!!$F1 572
21 TraesCS5A01G477800 chr7A 33087597 33088173 576 True 588 588 85.249 2 577 1 chr7A.!!$R1 575
22 TraesCS5A01G477800 chrUn 288795912 288796484 572 False 586 586 85.320 2 573 1 chrUn.!!$F1 571
23 TraesCS5A01G477800 chrUn 326973619 326977217 3598 False 586 586 85.320 2 573 2 chrUn.!!$F2 571

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
991 4111 0.108615 CCTTGTTGAGCTCGTCCGAT 60.109 55.0 9.64 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 4987 0.393402 ATTTAAAGCCGGACGTCCCC 60.393 55.0 28.52 19.15 0.0 4.81 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
157 161 3.881780 TCTCGCTAAACTAGATCTCGC 57.118 47.619 0.00 0.00 0.00 5.03
207 3237 1.625818 ACTCCGTGGAAATCTGAAGCT 59.374 47.619 0.00 0.00 0.00 3.74
212 3242 2.795329 GTGGAAATCTGAAGCTCCCAA 58.205 47.619 0.00 0.00 0.00 4.12
261 3291 1.454111 GCGAGGCTAGTGAGAGGGA 60.454 63.158 0.00 0.00 0.00 4.20
349 3392 2.663852 CGTGCGAACCTTTCCCGT 60.664 61.111 0.00 0.00 0.00 5.28
350 3393 2.664436 CGTGCGAACCTTTCCCGTC 61.664 63.158 0.00 0.00 0.00 4.79
351 3394 2.356553 TGCGAACCTTTCCCGTCG 60.357 61.111 0.00 0.00 0.00 5.12
352 3395 3.785499 GCGAACCTTTCCCGTCGC 61.785 66.667 0.80 0.80 39.33 5.19
356 3399 2.444700 GAACCTTTCCCGTCGCTGGA 62.445 60.000 0.00 0.00 0.00 3.86
366 3434 2.281484 TCGCTGGAGCCGCTTTTT 60.281 55.556 0.00 0.00 37.91 1.94
368 3436 2.616330 CGCTGGAGCCGCTTTTTCA 61.616 57.895 0.00 0.00 37.91 2.69
451 3541 0.724549 ATGATCTAAAACGCGCGCAA 59.275 45.000 32.58 11.91 0.00 4.85
497 3587 0.606401 ACACTGCCGACCCAAATCTG 60.606 55.000 0.00 0.00 0.00 2.90
504 3594 2.556622 GCCGACCCAAATCTGAAAAAGA 59.443 45.455 0.00 0.00 39.94 2.52
509 3600 4.407365 ACCCAAATCTGAAAAAGACGGAT 58.593 39.130 0.00 0.00 37.88 4.18
510 3601 5.566469 ACCCAAATCTGAAAAAGACGGATA 58.434 37.500 0.00 0.00 37.88 2.59
566 3657 1.666054 ACAAAAGCACCGTCCGTTTA 58.334 45.000 0.00 0.00 0.00 2.01
574 3665 2.259204 CGTCCGTTTAGGTCGGCA 59.741 61.111 0.00 0.00 45.53 5.69
577 3668 1.564207 GTCCGTTTAGGTCGGCATAC 58.436 55.000 0.00 0.00 46.49 2.39
578 3669 1.135721 GTCCGTTTAGGTCGGCATACT 59.864 52.381 0.00 0.00 46.49 2.12
579 3670 1.406539 TCCGTTTAGGTCGGCATACTC 59.593 52.381 0.00 0.00 46.49 2.59
580 3671 1.407979 CCGTTTAGGTCGGCATACTCT 59.592 52.381 0.00 0.00 41.48 3.24
581 3672 2.620115 CCGTTTAGGTCGGCATACTCTA 59.380 50.000 0.00 0.00 41.48 2.43
582 3673 3.067180 CCGTTTAGGTCGGCATACTCTAA 59.933 47.826 0.00 0.00 41.48 2.10
583 3674 4.261909 CCGTTTAGGTCGGCATACTCTAAT 60.262 45.833 0.00 0.00 41.48 1.73
584 3675 5.048504 CCGTTTAGGTCGGCATACTCTAATA 60.049 44.000 0.00 0.00 41.48 0.98
585 3676 6.441274 CGTTTAGGTCGGCATACTCTAATAA 58.559 40.000 0.00 0.00 0.00 1.40
586 3677 7.088905 CGTTTAGGTCGGCATACTCTAATAAT 58.911 38.462 0.00 0.00 0.00 1.28
587 3678 7.061905 CGTTTAGGTCGGCATACTCTAATAATG 59.938 40.741 0.00 0.00 0.00 1.90
588 3679 7.534723 TTAGGTCGGCATACTCTAATAATGT 57.465 36.000 0.00 0.00 0.00 2.71
589 3680 6.026947 AGGTCGGCATACTCTAATAATGTC 57.973 41.667 0.00 0.00 0.00 3.06
590 3681 5.775701 AGGTCGGCATACTCTAATAATGTCT 59.224 40.000 0.00 0.00 0.00 3.41
591 3682 6.071840 AGGTCGGCATACTCTAATAATGTCTC 60.072 42.308 0.00 0.00 0.00 3.36
592 3683 6.294564 GGTCGGCATACTCTAATAATGTCTCA 60.295 42.308 0.00 0.00 0.00 3.27
593 3684 6.583050 GTCGGCATACTCTAATAATGTCTCAC 59.417 42.308 0.00 0.00 0.00 3.51
594 3685 5.864474 CGGCATACTCTAATAATGTCTCACC 59.136 44.000 0.00 0.00 0.00 4.02
595 3686 5.864474 GGCATACTCTAATAATGTCTCACCG 59.136 44.000 0.00 0.00 0.00 4.94
596 3687 5.864474 GCATACTCTAATAATGTCTCACCGG 59.136 44.000 0.00 0.00 0.00 5.28
597 3688 6.516860 GCATACTCTAATAATGTCTCACCGGT 60.517 42.308 0.00 0.00 0.00 5.28
598 3689 5.263968 ACTCTAATAATGTCTCACCGGTG 57.736 43.478 29.26 29.26 0.00 4.94
599 3690 4.051922 CTCTAATAATGTCTCACCGGTGC 58.948 47.826 30.25 16.49 0.00 5.01
600 3691 2.779755 AATAATGTCTCACCGGTGCA 57.220 45.000 30.25 21.76 0.00 4.57
601 3692 2.779755 ATAATGTCTCACCGGTGCAA 57.220 45.000 30.25 16.87 0.00 4.08
602 3693 1.803334 TAATGTCTCACCGGTGCAAC 58.197 50.000 30.25 26.66 0.00 4.17
603 3694 0.179032 AATGTCTCACCGGTGCAACA 60.179 50.000 31.10 31.10 39.98 3.33
604 3695 0.179032 ATGTCTCACCGGTGCAACAA 60.179 50.000 32.01 21.15 39.98 2.83
605 3696 1.092921 TGTCTCACCGGTGCAACAAC 61.093 55.000 30.25 20.38 39.98 3.32
606 3697 1.092921 GTCTCACCGGTGCAACAACA 61.093 55.000 30.25 9.81 39.98 3.33
607 3698 0.393132 TCTCACCGGTGCAACAACAA 60.393 50.000 30.25 9.01 39.98 2.83
608 3699 0.453793 CTCACCGGTGCAACAACAAA 59.546 50.000 30.25 8.23 39.98 2.83
609 3700 0.171455 TCACCGGTGCAACAACAAAC 59.829 50.000 30.25 0.00 39.98 2.93
610 3701 0.109086 CACCGGTGCAACAACAAACA 60.109 50.000 24.02 0.00 39.98 2.83
611 3702 0.820871 ACCGGTGCAACAACAAACAT 59.179 45.000 6.12 0.00 39.98 2.71
612 3703 1.202359 ACCGGTGCAACAACAAACATC 60.202 47.619 6.12 0.00 39.98 3.06
613 3704 1.486439 CGGTGCAACAACAAACATCC 58.514 50.000 0.98 0.00 39.98 3.51
614 3705 1.202348 CGGTGCAACAACAAACATCCA 60.202 47.619 0.98 0.00 39.98 3.41
615 3706 2.736719 CGGTGCAACAACAAACATCCAA 60.737 45.455 0.98 0.00 39.98 3.53
616 3707 2.607180 GGTGCAACAACAAACATCCAAC 59.393 45.455 0.00 0.00 39.98 3.77
617 3708 3.520569 GTGCAACAACAAACATCCAACT 58.479 40.909 0.00 0.00 36.32 3.16
621 3712 5.982516 TGCAACAACAAACATCCAACTAATC 59.017 36.000 0.00 0.00 0.00 1.75
626 3717 5.329035 ACAAACATCCAACTAATCATGGC 57.671 39.130 0.00 0.00 36.62 4.40
627 3718 4.160252 ACAAACATCCAACTAATCATGGCC 59.840 41.667 0.00 0.00 36.62 5.36
629 3720 1.881973 CATCCAACTAATCATGGCCCG 59.118 52.381 0.00 0.00 36.62 6.13
630 3721 1.208706 TCCAACTAATCATGGCCCGA 58.791 50.000 0.00 0.00 36.62 5.14
642 3733 3.649986 GCCCGATCCCATTTCGCG 61.650 66.667 0.00 0.00 35.31 5.87
644 3735 2.972505 CCGATCCCATTTCGCGGG 60.973 66.667 6.13 0.00 46.03 6.13
647 3738 3.774599 GATCCCATTTCGCGGGCCT 62.775 63.158 6.13 0.00 44.11 5.19
651 3742 2.489751 CATTTCGCGGGCCTTTCC 59.510 61.111 6.13 0.00 0.00 3.13
663 3754 1.315257 GCCTTTCCGTCCACATGCAT 61.315 55.000 0.00 0.00 0.00 3.96
674 3765 4.668666 CATGCATGTAACCGCGTG 57.331 55.556 18.91 0.00 38.67 5.34
675 3766 2.252127 ACATGCATGTAACCGCGTGC 62.252 55.000 30.50 7.88 46.79 5.34
692 3783 3.470888 CCGGGCTACCTGGGACTG 61.471 72.222 3.32 0.00 45.99 3.51
716 3807 4.034975 GGAGCAAGCTAAGCAATTACTCTG 59.965 45.833 12.91 0.00 0.00 3.35
722 3813 4.161189 AGCTAAGCAATTACTCTGAGCTGA 59.839 41.667 4.19 0.00 37.62 4.26
723 3814 4.269844 GCTAAGCAATTACTCTGAGCTGAC 59.730 45.833 4.19 0.00 35.42 3.51
724 3815 2.886081 AGCAATTACTCTGAGCTGACG 58.114 47.619 4.19 0.00 33.67 4.35
725 3816 2.232452 AGCAATTACTCTGAGCTGACGT 59.768 45.455 4.19 0.00 33.67 4.34
868 3975 3.267812 TGTACCTGGTGGCTACTAGTACT 59.732 47.826 10.23 0.00 33.90 2.73
871 3978 3.117587 ACCTGGTGGCTACTAGTACTAGG 60.118 52.174 29.05 19.20 44.49 3.02
873 3980 2.512896 TGGTGGCTACTAGTACTAGGCT 59.487 50.000 29.05 14.85 37.60 4.58
878 3985 2.807392 GCTACTAGTACTAGGCTGTCCG 59.193 54.545 29.05 12.61 37.49 4.79
893 4000 4.838152 CCGCACCGCCAGCACTAT 62.838 66.667 0.00 0.00 0.00 2.12
894 4001 2.106131 CGCACCGCCAGCACTATA 59.894 61.111 0.00 0.00 0.00 1.31
903 4013 2.423538 CGCCAGCACTATAAAAAGGCTT 59.576 45.455 0.00 0.00 38.48 4.35
912 4022 5.594317 CACTATAAAAAGGCTTACCCTGCAT 59.406 40.000 0.00 0.00 45.62 3.96
936 4046 1.077212 GAGCCACATCCACAGCCAT 60.077 57.895 0.00 0.00 0.00 4.40
963 4083 1.742761 CCACTGAATCCGCACAGAAT 58.257 50.000 0.00 0.00 37.54 2.40
970 4090 4.188462 TGAATCCGCACAGAATTACGAAT 58.812 39.130 0.00 0.00 0.00 3.34
973 4093 2.933906 TCCGCACAGAATTACGAATTCC 59.066 45.455 13.32 2.60 46.65 3.01
985 4105 2.069273 ACGAATTCCTTGTTGAGCTCG 58.931 47.619 9.64 0.00 0.00 5.03
991 4111 0.108615 CCTTGTTGAGCTCGTCCGAT 60.109 55.000 9.64 0.00 0.00 4.18
1008 4128 1.388547 GATTAGCCGCCATGGTTTCA 58.611 50.000 14.67 0.00 41.21 2.69
1062 4188 3.024356 TCGCCCCTCTCCCTCTCT 61.024 66.667 0.00 0.00 0.00 3.10
1065 4191 1.457455 GCCCCTCTCCCTCTCTCTG 60.457 68.421 0.00 0.00 0.00 3.35
1071 4197 0.628522 TCTCCCTCTCTCTGTCCCTG 59.371 60.000 0.00 0.00 0.00 4.45
1074 4200 1.700368 CCTCTCTCTGTCCCTGGGA 59.300 63.158 12.53 12.53 0.00 4.37
1081 4207 1.304547 CTGTCCCTGGGAGTCGTCT 60.305 63.158 17.73 0.00 29.39 4.18
1170 4296 2.920912 TTCCCGTCGTTCCAGGCT 60.921 61.111 0.00 0.00 0.00 4.58
1307 4436 4.873129 CCACGTCTGCGGGATCGG 62.873 72.222 0.00 0.00 45.97 4.18
1408 4537 0.739112 CGTTCTGCTCCAGCTCTTCC 60.739 60.000 0.00 0.00 42.66 3.46
1507 4641 1.782044 ATGTGCACGATTTGGTTTGC 58.218 45.000 13.13 0.00 35.45 3.68
1691 4866 4.852104 CGTTAATCCTAATGACGATCTCCG 59.148 45.833 0.00 0.00 45.44 4.63
1875 5071 2.438411 ACAGACCAAACAAACGGAACA 58.562 42.857 0.00 0.00 0.00 3.18
1914 5110 3.153369 TCTAAGGCATGCCACAAAAGA 57.847 42.857 37.18 25.73 38.92 2.52
1972 5168 2.377310 GCCAAACTAACGAGCGCGA 61.377 57.895 19.05 0.00 41.64 5.87
2036 5233 1.675641 GGCAGCAAACGGAGGTGAT 60.676 57.895 7.27 0.00 36.64 3.06
2049 5246 2.501610 GTGATGGGGCTCGAGACC 59.498 66.667 30.53 30.53 44.61 3.85
2095 5292 3.062763 CGATAGCTTGGCGATGAAGATT 58.937 45.455 0.00 0.00 0.00 2.40
2102 5299 4.739137 GCTTGGCGATGAAGATTAGACTCT 60.739 45.833 0.00 0.00 0.00 3.24
2111 5309 5.869579 TGAAGATTAGACTCTTGTTGCCTT 58.130 37.500 0.00 0.00 35.63 4.35
2184 5382 1.134438 GGGGTGAGAGGGGAACACTT 61.134 60.000 0.00 0.00 35.28 3.16
2245 5443 4.465512 CATGGCCGAAGCACACGC 62.466 66.667 0.00 0.00 42.56 5.34
2299 5497 5.127194 TCGAAGATAGGTATGACACAAGCTT 59.873 40.000 0.00 0.00 0.00 3.74
2400 5599 2.299013 AGAACACGTGGTCAGCATCTTA 59.701 45.455 33.54 0.00 33.22 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 47 0.970937 CTGAGGCCTCGTTGGGAGTA 60.971 60.000 27.43 5.86 41.46 2.59
44 48 2.203788 TGAGGCCTCGTTGGGAGT 60.204 61.111 27.43 0.00 41.46 3.85
106 110 4.351938 CGGCACCTTCGACACCGA 62.352 66.667 5.16 0.00 46.71 4.69
143 147 4.580995 CCTTCTCCTGCGAGATCTAGTTTA 59.419 45.833 4.67 0.00 44.68 2.01
148 152 1.323412 GCCTTCTCCTGCGAGATCTA 58.677 55.000 0.00 0.00 44.68 1.98
157 161 4.521062 CTCCGGCGCCTTCTCCTG 62.521 72.222 26.68 6.56 0.00 3.86
334 3377 2.356553 CGACGGGAAAGGTTCGCA 60.357 61.111 5.97 0.00 42.19 5.10
349 3392 2.281484 AAAAAGCGGCTCCAGCGA 60.281 55.556 1.45 0.00 43.26 4.93
350 3393 2.176792 GAAAAAGCGGCTCCAGCG 59.823 61.111 1.45 0.00 43.26 5.18
351 3394 1.081175 GTGAAAAAGCGGCTCCAGC 60.081 57.895 1.45 0.00 41.14 4.85
352 3395 1.581447 GGTGAAAAAGCGGCTCCAG 59.419 57.895 1.45 0.00 0.00 3.86
401 3491 2.281208 CCGTCGCCCTGGTTTTGA 60.281 61.111 0.00 0.00 0.00 2.69
451 3541 1.883638 CGGGCCGATCCATTTCATGAT 60.884 52.381 24.41 0.00 36.21 2.45
497 3587 0.656259 GCCCGCTATCCGTCTTTTTC 59.344 55.000 0.00 0.00 34.38 2.29
520 3611 1.030488 TTGTTTGTTTCGGTCGGCCA 61.030 50.000 6.96 0.00 34.09 5.36
529 3620 6.183359 GCTTTTGTTCGCTTTTTGTTTGTTTC 60.183 34.615 0.00 0.00 0.00 2.78
566 3657 5.775701 AGACATTATTAGAGTATGCCGACCT 59.224 40.000 0.00 0.00 0.00 3.85
574 3665 6.516860 GCACCGGTGAGACATTATTAGAGTAT 60.517 42.308 38.30 0.00 0.00 2.12
577 3668 4.051922 GCACCGGTGAGACATTATTAGAG 58.948 47.826 38.30 5.87 0.00 2.43
578 3669 3.449377 TGCACCGGTGAGACATTATTAGA 59.551 43.478 38.30 0.00 0.00 2.10
579 3670 3.792401 TGCACCGGTGAGACATTATTAG 58.208 45.455 38.30 7.09 0.00 1.73
580 3671 3.897141 TGCACCGGTGAGACATTATTA 57.103 42.857 38.30 7.05 0.00 0.98
581 3672 2.747446 GTTGCACCGGTGAGACATTATT 59.253 45.455 38.30 0.00 0.00 1.40
582 3673 2.290008 TGTTGCACCGGTGAGACATTAT 60.290 45.455 38.30 0.00 0.00 1.28
583 3674 1.070914 TGTTGCACCGGTGAGACATTA 59.929 47.619 38.30 15.52 0.00 1.90
584 3675 0.179032 TGTTGCACCGGTGAGACATT 60.179 50.000 38.30 0.00 0.00 2.71
585 3676 0.179032 TTGTTGCACCGGTGAGACAT 60.179 50.000 38.30 0.00 30.83 3.06
586 3677 1.092921 GTTGTTGCACCGGTGAGACA 61.093 55.000 38.30 32.64 0.00 3.41
587 3678 1.092921 TGTTGTTGCACCGGTGAGAC 61.093 55.000 38.30 30.64 0.00 3.36
588 3679 0.393132 TTGTTGTTGCACCGGTGAGA 60.393 50.000 38.30 21.74 0.00 3.27
589 3680 0.453793 TTTGTTGTTGCACCGGTGAG 59.546 50.000 38.30 13.80 0.00 3.51
590 3681 0.171455 GTTTGTTGTTGCACCGGTGA 59.829 50.000 38.30 19.89 0.00 4.02
591 3682 0.109086 TGTTTGTTGTTGCACCGGTG 60.109 50.000 30.66 30.66 0.00 4.94
592 3683 0.820871 ATGTTTGTTGTTGCACCGGT 59.179 45.000 0.00 0.00 0.00 5.28
593 3684 1.486439 GATGTTTGTTGTTGCACCGG 58.514 50.000 0.00 0.00 0.00 5.28
594 3685 1.202348 TGGATGTTTGTTGTTGCACCG 60.202 47.619 0.00 0.00 0.00 4.94
595 3686 2.593346 TGGATGTTTGTTGTTGCACC 57.407 45.000 0.00 0.00 0.00 5.01
596 3687 3.520569 AGTTGGATGTTTGTTGTTGCAC 58.479 40.909 0.00 0.00 0.00 4.57
597 3688 3.883830 AGTTGGATGTTTGTTGTTGCA 57.116 38.095 0.00 0.00 0.00 4.08
598 3689 5.982516 TGATTAGTTGGATGTTTGTTGTTGC 59.017 36.000 0.00 0.00 0.00 4.17
599 3690 7.116662 CCATGATTAGTTGGATGTTTGTTGTTG 59.883 37.037 0.00 0.00 34.81 3.33
600 3691 7.153985 CCATGATTAGTTGGATGTTTGTTGTT 58.846 34.615 0.00 0.00 34.81 2.83
601 3692 6.690530 CCATGATTAGTTGGATGTTTGTTGT 58.309 36.000 0.00 0.00 34.81 3.32
602 3693 5.577945 GCCATGATTAGTTGGATGTTTGTTG 59.422 40.000 0.00 0.00 34.81 3.33
603 3694 5.337491 GGCCATGATTAGTTGGATGTTTGTT 60.337 40.000 0.00 0.00 34.81 2.83
604 3695 4.160252 GGCCATGATTAGTTGGATGTTTGT 59.840 41.667 0.00 0.00 34.81 2.83
605 3696 4.441913 GGGCCATGATTAGTTGGATGTTTG 60.442 45.833 4.39 0.00 34.81 2.93
606 3697 3.706086 GGGCCATGATTAGTTGGATGTTT 59.294 43.478 4.39 0.00 34.81 2.83
607 3698 3.299503 GGGCCATGATTAGTTGGATGTT 58.700 45.455 4.39 0.00 34.81 2.71
608 3699 2.749466 CGGGCCATGATTAGTTGGATGT 60.749 50.000 4.39 0.00 34.81 3.06
609 3700 1.881973 CGGGCCATGATTAGTTGGATG 59.118 52.381 4.39 0.00 34.81 3.51
610 3701 1.774254 TCGGGCCATGATTAGTTGGAT 59.226 47.619 4.39 0.00 34.81 3.41
611 3702 1.208706 TCGGGCCATGATTAGTTGGA 58.791 50.000 4.39 0.00 34.81 3.53
612 3703 2.154462 GATCGGGCCATGATTAGTTGG 58.846 52.381 4.39 0.00 36.03 3.77
613 3704 2.154462 GGATCGGGCCATGATTAGTTG 58.846 52.381 4.39 0.00 0.00 3.16
614 3705 1.073923 GGGATCGGGCCATGATTAGTT 59.926 52.381 4.39 0.00 0.00 2.24
615 3706 0.693049 GGGATCGGGCCATGATTAGT 59.307 55.000 4.39 0.00 0.00 2.24
616 3707 0.692476 TGGGATCGGGCCATGATTAG 59.308 55.000 4.39 0.00 0.00 1.73
617 3708 1.371467 ATGGGATCGGGCCATGATTA 58.629 50.000 4.39 0.00 0.00 1.75
621 3712 1.518056 CGAAATGGGATCGGGCCATG 61.518 60.000 4.39 0.00 36.68 3.66
644 3735 1.315257 ATGCATGTGGACGGAAAGGC 61.315 55.000 0.00 0.00 0.00 4.35
647 3738 2.481289 TACATGCATGTGGACGGAAA 57.519 45.000 36.72 15.73 41.89 3.13
651 3742 0.373370 CGGTTACATGCATGTGGACG 59.627 55.000 36.72 30.52 41.89 4.79
675 3766 3.470888 CAGTCCCAGGTAGCCCGG 61.471 72.222 0.00 0.00 35.12 5.73
686 3777 0.107459 CTTAGCTTGCTCCCAGTCCC 60.107 60.000 0.00 0.00 0.00 4.46
687 3778 0.746204 GCTTAGCTTGCTCCCAGTCC 60.746 60.000 0.00 0.00 0.00 3.85
688 3779 0.036010 TGCTTAGCTTGCTCCCAGTC 60.036 55.000 5.60 0.00 0.00 3.51
689 3780 0.401738 TTGCTTAGCTTGCTCCCAGT 59.598 50.000 5.60 0.00 0.00 4.00
690 3781 1.760192 ATTGCTTAGCTTGCTCCCAG 58.240 50.000 5.60 0.00 0.00 4.45
691 3782 2.220653 AATTGCTTAGCTTGCTCCCA 57.779 45.000 5.60 0.00 0.00 4.37
692 3783 3.282885 AGTAATTGCTTAGCTTGCTCCC 58.717 45.455 5.60 0.00 0.00 4.30
716 3807 2.945066 GCTCGCGTACGTCAGCTC 60.945 66.667 24.71 5.92 41.18 4.09
722 3813 2.745100 TCCTCTGCTCGCGTACGT 60.745 61.111 17.90 0.00 41.18 3.57
723 3814 1.978712 TTCTCCTCTGCTCGCGTACG 61.979 60.000 11.84 11.84 42.01 3.67
724 3815 0.248296 CTTCTCCTCTGCTCGCGTAC 60.248 60.000 5.77 0.00 0.00 3.67
725 3816 1.377366 CCTTCTCCTCTGCTCGCGTA 61.377 60.000 5.77 0.00 0.00 4.42
832 3939 6.897966 CCACCAGGTACATCCATATATAGACT 59.102 42.308 0.00 0.00 39.02 3.24
838 3945 3.869310 AGCCACCAGGTACATCCATATA 58.131 45.455 0.00 0.00 39.02 0.86
840 3947 2.190398 AGCCACCAGGTACATCCATA 57.810 50.000 0.00 0.00 39.02 2.74
841 3948 1.768870 GTAGCCACCAGGTACATCCAT 59.231 52.381 0.00 0.00 46.62 3.41
842 3949 1.200519 GTAGCCACCAGGTACATCCA 58.799 55.000 0.00 0.00 46.62 3.41
878 3985 1.091537 TTTTATAGTGCTGGCGGTGC 58.908 50.000 0.00 0.00 0.00 5.01
885 3992 5.066505 CAGGGTAAGCCTTTTTATAGTGCTG 59.933 44.000 0.00 0.00 34.45 4.41
889 3996 5.187621 TGCAGGGTAAGCCTTTTTATAGT 57.812 39.130 0.00 0.00 34.45 2.12
890 3997 5.827797 TCATGCAGGGTAAGCCTTTTTATAG 59.172 40.000 0.00 0.00 34.45 1.31
891 3998 5.761205 TCATGCAGGGTAAGCCTTTTTATA 58.239 37.500 0.00 0.00 34.45 0.98
892 3999 4.609301 TCATGCAGGGTAAGCCTTTTTAT 58.391 39.130 0.00 0.00 34.45 1.40
893 4000 4.040936 TCATGCAGGGTAAGCCTTTTTA 57.959 40.909 0.00 0.00 34.45 1.52
894 4001 2.888212 TCATGCAGGGTAAGCCTTTTT 58.112 42.857 0.00 0.00 34.45 1.94
903 4013 1.748403 GCTCGGATCATGCAGGGTA 59.252 57.895 0.00 0.00 0.00 3.69
912 4022 1.264045 TGTGGATGTGGCTCGGATCA 61.264 55.000 0.00 0.00 0.00 2.92
936 4046 0.391130 CGGATTCAGTGGCTCGGAAA 60.391 55.000 6.25 0.00 34.34 3.13
963 4083 3.678072 CGAGCTCAACAAGGAATTCGTAA 59.322 43.478 15.40 0.00 0.00 3.18
970 4090 0.319555 CGGACGAGCTCAACAAGGAA 60.320 55.000 15.40 0.00 0.00 3.36
973 4093 1.714794 AATCGGACGAGCTCAACAAG 58.285 50.000 15.40 0.00 0.00 3.16
985 4105 1.961277 CCATGGCGGCTAATCGGAC 60.961 63.158 11.43 0.00 0.00 4.79
991 4111 1.340502 TGATGAAACCATGGCGGCTAA 60.341 47.619 13.04 0.00 39.03 3.09
1008 4128 6.231258 TGATCTCTGTACTGCTTCATTGAT 57.769 37.500 0.00 0.00 0.00 2.57
1062 4188 1.304217 GACGACTCCCAGGGACAGA 60.304 63.158 3.01 0.00 0.00 3.41
1065 4191 3.605895 GAGACGACTCCCAGGGAC 58.394 66.667 3.01 0.00 37.19 4.46
1081 4207 0.610174 ATCTTCTTGCTGCTGTCGGA 59.390 50.000 0.00 0.00 0.00 4.55
1087 4213 1.303799 CGGTGCATCTTCTTGCTGCT 61.304 55.000 0.00 0.00 43.18 4.24
1122 4248 0.179121 ACGTCTTGCACACGAACTCA 60.179 50.000 21.21 0.00 39.75 3.41
1170 4296 2.283676 GTCCGGTGTCCTCCCAGA 60.284 66.667 0.00 0.00 0.00 3.86
1176 4302 4.954118 TGGCTGGTCCGGTGTCCT 62.954 66.667 0.00 0.00 37.80 3.85
1303 4432 2.808206 GCCCCATCTCGAACCCGAT 61.808 63.158 0.00 0.00 44.62 4.18
1307 4436 2.190578 CCTGCCCCATCTCGAACC 59.809 66.667 0.00 0.00 0.00 3.62
1408 4537 0.457443 TCGATGGTGCAGTGCTAGAG 59.543 55.000 17.60 3.29 0.00 2.43
1507 4641 3.676172 CCAACTATTGTGCAGCAAATGTG 59.324 43.478 0.00 1.17 40.91 3.21
1664 4835 6.223852 AGATCGTCATTAGGATTAACGCAAT 58.776 36.000 0.00 0.00 33.58 3.56
1668 4840 4.852104 CGGAGATCGTCATTAGGATTAACG 59.148 45.833 0.00 0.00 30.49 3.18
1780 4969 3.956199 TCCCCGACGTCTATGTTCTAAAT 59.044 43.478 14.70 0.00 0.00 1.40
1798 4987 0.393402 ATTTAAAGCCGGACGTCCCC 60.393 55.000 28.52 19.15 0.00 4.81
1875 5071 3.177228 AGAACATGGGTGACTAGCTTCT 58.823 45.455 0.00 0.00 0.00 2.85
1914 5110 2.096614 CACTTTATTTCGCCGTCGTTGT 60.097 45.455 0.00 0.00 36.96 3.32
1972 5168 1.848886 CTTGGTTACCCCCGAGCCTT 61.849 60.000 0.00 0.00 0.00 4.35
2095 5292 2.303022 CTGGGAAGGCAACAAGAGTCTA 59.697 50.000 0.00 0.00 41.41 2.59
2102 5299 2.597217 CCGCTGGGAAGGCAACAA 60.597 61.111 0.00 0.00 34.58 2.83
2111 5309 4.641645 CAGTTGGCACCGCTGGGA 62.642 66.667 0.00 0.00 36.97 4.37
2124 5322 3.760151 TGCATCTTATTCTTGCAGCAGTT 59.240 39.130 0.00 0.00 41.18 3.16
2177 5375 8.379457 ACAAGTTTACTATTGAGGAAGTGTTC 57.621 34.615 0.00 0.00 0.00 3.18
2245 5443 4.854924 TGCGCCGGATCATGTGGG 62.855 66.667 5.05 0.00 0.00 4.61
2299 5497 1.725557 GGATCCACGCTCACGCTCTA 61.726 60.000 6.95 0.00 45.53 2.43


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

AutoCloner maintained by Alex Coulton.