Multiple sequence alignment - TraesCS7A01G067200

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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 TraesCS7A01G067200 chr7A 100.000 4604 0 0 1 4604 33543545 33548148 0.000000e+00 8503
1 TraesCS7A01G067200 chr7A 97.354 3930 82 6 694 4604 516117382 516121308 0.000000e+00 6661
2 TraesCS7A01G067200 chr7A 93.015 587 10 13 12 570 516116808 516117391 0.000000e+00 828
3 TraesCS7A01G067200 chr7A 86.765 272 33 3 80 348 134638769 134638498 2.690000e-77 300
4 TraesCS7A01G067200 chr7A 86.397 272 33 4 80 348 725797606 725797336 1.250000e-75 294
5 TraesCS7A01G067200 chr6B 95.745 3126 105 11 693 3793 711434613 711437735 0.000000e+00 5011
6 TraesCS7A01G067200 chr6B 96.642 804 27 0 3801 4604 711438070 711438873 0.000000e+00 1336
7 TraesCS7A01G067200 chr6B 91.748 206 9 1 353 558 711434420 711434617 3.510000e-71 279
8 TraesCS7A01G067200 chr5D 95.379 3138 97 16 696 3793 259633495 259636624 0.000000e+00 4948
9 TraesCS7A01G067200 chr5D 95.647 804 35 0 3801 4604 259636953 259637756 0.000000e+00 1291
10 TraesCS7A01G067200 chr5D 93.407 546 20 8 13 544 259632944 259633487 0.000000e+00 795
11 TraesCS7A01G067200 chr3D 95.092 3138 110 14 694 3793 133675576 133678707 0.000000e+00 4902
12 TraesCS7A01G067200 chr3D 95.479 1703 55 9 2111 3793 601545753 601547453 0.000000e+00 2699
13 TraesCS7A01G067200 chr3D 95.087 1486 51 9 2328 3793 119267253 119265770 0.000000e+00 2320
14 TraesCS7A01G067200 chr3D 93.028 545 23 8 13 544 133675028 133675570 0.000000e+00 782
15 TraesCS7A01G067200 chr3A 95.091 3137 107 16 694 3793 493667581 493670707 0.000000e+00 4896
16 TraesCS7A01G067200 chr3A 89.365 583 33 19 13 570 493667012 493667590 0.000000e+00 706
17 TraesCS7A01G067200 chr3A 85.932 263 33 4 88 348 168241284 168241024 1.260000e-70 278
18 TraesCS7A01G067200 chr5A 96.048 2505 68 8 693 3171 33939605 33942104 0.000000e+00 4048
19 TraesCS7A01G067200 chr5A 91.748 206 6 4 353 558 33939415 33939609 4.540000e-70 276
20 TraesCS7A01G067200 chr5A 97.600 125 3 0 570 694 332214848 332214972 1.000000e-51 215
21 TraesCS7A01G067200 chr2D 95.661 2512 84 12 1302 3793 129924402 129921896 0.000000e+00 4012
22 TraesCS7A01G067200 chr2D 95.413 2420 87 6 694 3094 370004373 370006787 0.000000e+00 3832
23 TraesCS7A01G067200 chr2D 94.128 545 17 7 13 544 370003825 370004367 0.000000e+00 815
24 TraesCS7A01G067200 chr7D 95.541 2512 86 13 1302 3793 55627852 55625347 0.000000e+00 3995
25 TraesCS7A01G067200 chr7D 95.896 804 33 0 3801 4604 109448311 109447508 0.000000e+00 1303
26 TraesCS7A01G067200 chr7D 95.647 804 35 0 3801 4604 55625026 55624223 0.000000e+00 1291
27 TraesCS7A01G067200 chr1D 94.818 1486 56 8 2328 3793 475685950 475687434 0.000000e+00 2298
28 TraesCS7A01G067200 chr1D 95.771 804 34 0 3801 4604 475687755 475688558 0.000000e+00 1297
29 TraesCS7A01G067200 chr1D 88.199 161 16 3 535 694 476677081 476677239 6.080000e-44 189
30 TraesCS7A01G067200 chrUn 94.549 1486 60 8 2328 3793 24218871 24217387 0.000000e+00 2276
31 TraesCS7A01G067200 chrUn 95.522 804 36 0 3801 4604 134338621 134339424 0.000000e+00 1286
32 TraesCS7A01G067200 chr4D 94.415 1486 62 8 2328 3793 502615424 502613940 0.000000e+00 2265
33 TraesCS7A01G067200 chr4A 95.652 805 34 1 3801 4604 405585854 405586658 0.000000e+00 1291
34 TraesCS7A01G067200 chr3B 95.652 805 34 1 3801 4604 696726633 696725829 0.000000e+00 1291
35 TraesCS7A01G067200 chr3B 100.000 125 0 0 571 695 246163850 246163974 9.960000e-57 231
36 TraesCS7A01G067200 chr3B 99.200 125 1 0 571 695 187490197 187490321 4.630000e-55 226
37 TraesCS7A01G067200 chr6A 86.029 272 34 4 80 348 545142754 545143024 5.830000e-74 289
38 TraesCS7A01G067200 chr2B 98.413 126 2 0 570 695 121691630 121691505 6.000000e-54 222
39 TraesCS7A01G067200 chr5B 98.400 125 2 0 570 694 563355471 563355347 2.160000e-53 220
40 TraesCS7A01G067200 chr4B 98.400 125 2 0 571 695 241182084 241181960 2.160000e-53 220
41 TraesCS7A01G067200 chr7B 96.875 128 4 0 567 694 482819894 482820021 1.000000e-51 215
42 TraesCS7A01G067200 chr2A 96.875 128 3 1 571 697 753232350 753232477 3.610000e-51 213


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 TraesCS7A01G067200 chr7A 33543545 33548148 4603 False 8503.000000 8503 100.000000 1 4604 1 chr7A.!!$F1 4603
1 TraesCS7A01G067200 chr7A 516116808 516121308 4500 False 3744.500000 6661 95.184500 12 4604 2 chr7A.!!$F2 4592
2 TraesCS7A01G067200 chr6B 711434420 711438873 4453 False 2208.666667 5011 94.711667 353 4604 3 chr6B.!!$F1 4251
3 TraesCS7A01G067200 chr5D 259632944 259637756 4812 False 2344.666667 4948 94.811000 13 4604 3 chr5D.!!$F1 4591
4 TraesCS7A01G067200 chr3D 133675028 133678707 3679 False 2842.000000 4902 94.060000 13 3793 2 chr3D.!!$F2 3780
5 TraesCS7A01G067200 chr3D 601545753 601547453 1700 False 2699.000000 2699 95.479000 2111 3793 1 chr3D.!!$F1 1682
6 TraesCS7A01G067200 chr3D 119265770 119267253 1483 True 2320.000000 2320 95.087000 2328 3793 1 chr3D.!!$R1 1465
7 TraesCS7A01G067200 chr3A 493667012 493670707 3695 False 2801.000000 4896 92.228000 13 3793 2 chr3A.!!$F1 3780
8 TraesCS7A01G067200 chr5A 33939415 33942104 2689 False 2162.000000 4048 93.898000 353 3171 2 chr5A.!!$F2 2818
9 TraesCS7A01G067200 chr2D 129921896 129924402 2506 True 4012.000000 4012 95.661000 1302 3793 1 chr2D.!!$R1 2491
10 TraesCS7A01G067200 chr2D 370003825 370006787 2962 False 2323.500000 3832 94.770500 13 3094 2 chr2D.!!$F1 3081
11 TraesCS7A01G067200 chr7D 55624223 55627852 3629 True 2643.000000 3995 95.594000 1302 4604 2 chr7D.!!$R2 3302
12 TraesCS7A01G067200 chr7D 109447508 109448311 803 True 1303.000000 1303 95.896000 3801 4604 1 chr7D.!!$R1 803
13 TraesCS7A01G067200 chr1D 475685950 475688558 2608 False 1797.500000 2298 95.294500 2328 4604 2 chr1D.!!$F2 2276
14 TraesCS7A01G067200 chrUn 24217387 24218871 1484 True 2276.000000 2276 94.549000 2328 3793 1 chrUn.!!$R1 1465
15 TraesCS7A01G067200 chrUn 134338621 134339424 803 False 1286.000000 1286 95.522000 3801 4604 1 chrUn.!!$F1 803
16 TraesCS7A01G067200 chr4D 502613940 502615424 1484 True 2265.000000 2265 94.415000 2328 3793 1 chr4D.!!$R1 1465
17 TraesCS7A01G067200 chr4A 405585854 405586658 804 False 1291.000000 1291 95.652000 3801 4604 1 chr4A.!!$F1 803
18 TraesCS7A01G067200 chr3B 696725829 696726633 804 True 1291.000000 1291 95.652000 3801 4604 1 chr3B.!!$R1 803

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
648 710 0.036388 CGTCTGTTAGGCCCACATGT 60.036 55.000 0.00 0.00 0.00 3.21 F
686 748 0.105964 TGCAGTTACGGCACTGAAGT 59.894 50.000 17.81 0.00 46.29 3.01 F
688 750 1.194772 GCAGTTACGGCACTGAAGTTC 59.805 52.381 17.81 0.00 46.29 3.01 F
2725 2816 0.991146 TGCTTGGGCTCATGACCTTA 59.009 50.000 3.13 2.59 43.49 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2334 2422 2.431090 TTGAAATCGACGGCGCGA 60.431 55.556 23.64 23.64 45.22 5.87 R
2725 2816 8.695456 CACCCAAAACCAAGCTATAGATTAATT 58.305 33.333 2.30 0.00 0.00 1.40 R
2739 2830 5.897824 TGTTAAATAGGTCACCCAAAACCAA 59.102 36.000 0.00 0.00 38.06 3.67 R
4574 5016 2.271800 CCATGTGTTTCCGAGACTAGC 58.728 52.381 0.00 0.00 0.00 3.42 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
394 425 1.622173 GGGATCCAAGGCCCAAATCAA 60.622 52.381 15.23 0.00 44.07 2.57
400 431 3.099141 CCAAGGCCCAAATCAACATAGT 58.901 45.455 0.00 0.00 0.00 2.12
553 615 1.000771 TCCACTCCCTCTCCACTCG 60.001 63.158 0.00 0.00 0.00 4.18
556 618 4.200283 CTCCCTCTCCACTCGCGC 62.200 72.222 0.00 0.00 0.00 6.86
560 622 2.807045 CTCTCCACTCGCGCACAC 60.807 66.667 8.75 0.00 0.00 3.82
561 623 4.700365 TCTCCACTCGCGCACACG 62.700 66.667 8.75 0.00 44.07 4.49
571 633 4.459331 CGCACACGCAAATCCCGG 62.459 66.667 0.00 0.00 38.40 5.73
572 634 3.053291 GCACACGCAAATCCCGGA 61.053 61.111 0.73 0.00 38.36 5.14
573 635 2.867472 CACACGCAAATCCCGGAC 59.133 61.111 0.73 0.00 0.00 4.79
574 636 2.740826 ACACGCAAATCCCGGACG 60.741 61.111 0.73 0.00 0.00 4.79
575 637 4.160635 CACGCAAATCCCGGACGC 62.161 66.667 0.73 0.00 0.00 5.19
576 638 4.388499 ACGCAAATCCCGGACGCT 62.388 61.111 0.73 0.00 0.00 5.07
577 639 3.864686 CGCAAATCCCGGACGCTG 61.865 66.667 0.73 0.00 0.00 5.18
578 640 4.179579 GCAAATCCCGGACGCTGC 62.180 66.667 0.73 2.45 0.00 5.25
579 641 2.436646 CAAATCCCGGACGCTGCT 60.437 61.111 0.73 0.00 0.00 4.24
580 642 2.040544 CAAATCCCGGACGCTGCTT 61.041 57.895 0.73 0.00 0.00 3.91
581 643 2.040544 AAATCCCGGACGCTGCTTG 61.041 57.895 0.73 0.00 0.00 4.01
582 644 3.976701 AATCCCGGACGCTGCTTGG 62.977 63.158 0.73 0.00 0.00 3.61
591 653 2.671619 GCTGCTTGGGTGCCGTAA 60.672 61.111 0.00 0.00 0.00 3.18
592 654 2.978018 GCTGCTTGGGTGCCGTAAC 61.978 63.158 0.00 0.00 0.00 2.50
593 655 1.302511 CTGCTTGGGTGCCGTAACT 60.303 57.895 0.00 0.00 0.00 2.24
594 656 1.577328 CTGCTTGGGTGCCGTAACTG 61.577 60.000 0.00 0.00 0.00 3.16
595 657 2.978018 GCTTGGGTGCCGTAACTGC 61.978 63.158 0.00 0.00 0.00 4.40
596 658 1.599518 CTTGGGTGCCGTAACTGCA 60.600 57.895 0.00 0.00 36.12 4.41
601 663 2.668212 TGCCGTAACTGCACCTGC 60.668 61.111 0.00 0.00 42.50 4.85
611 673 2.203337 GCACCTGCAGTTGGGTCA 60.203 61.111 13.63 0.00 41.59 4.02
612 674 1.827789 GCACCTGCAGTTGGGTCAA 60.828 57.895 13.63 0.00 41.59 3.18
613 675 1.181098 GCACCTGCAGTTGGGTCAAT 61.181 55.000 13.63 0.00 41.59 2.57
614 676 0.599558 CACCTGCAGTTGGGTCAATG 59.400 55.000 13.81 0.00 32.95 2.82
615 677 0.540365 ACCTGCAGTTGGGTCAATGG 60.540 55.000 13.81 0.00 0.00 3.16
616 678 1.588082 CTGCAGTTGGGTCAATGGC 59.412 57.895 5.25 0.00 0.00 4.40
617 679 1.152589 TGCAGTTGGGTCAATGGCA 60.153 52.632 0.00 0.00 34.62 4.92
618 680 0.542467 TGCAGTTGGGTCAATGGCAT 60.542 50.000 0.00 0.00 33.05 4.40
619 681 0.108520 GCAGTTGGGTCAATGGCATG 60.109 55.000 0.00 0.00 0.00 4.06
620 682 1.259609 CAGTTGGGTCAATGGCATGT 58.740 50.000 0.00 0.00 0.00 3.21
621 683 1.067425 CAGTTGGGTCAATGGCATGTG 60.067 52.381 0.00 1.95 0.00 3.21
622 684 0.247185 GTTGGGTCAATGGCATGTGG 59.753 55.000 0.00 0.00 0.00 4.17
623 685 0.903924 TTGGGTCAATGGCATGTGGG 60.904 55.000 0.00 0.00 0.00 4.61
624 686 2.724273 GGGTCAATGGCATGTGGGC 61.724 63.158 0.00 0.00 43.73 5.36
633 695 4.415150 CATGTGGGCCAGCCGTCT 62.415 66.667 6.40 0.00 36.85 4.18
634 696 4.415150 ATGTGGGCCAGCCGTCTG 62.415 66.667 6.40 0.00 40.02 3.51
636 698 4.643387 GTGGGCCAGCCGTCTGTT 62.643 66.667 6.40 0.00 38.66 3.16
637 699 2.925706 TGGGCCAGCCGTCTGTTA 60.926 61.111 0.00 0.00 38.66 2.41
638 700 2.125106 GGGCCAGCCGTCTGTTAG 60.125 66.667 4.39 0.00 38.66 2.34
639 701 2.125106 GGCCAGCCGTCTGTTAGG 60.125 66.667 0.00 0.00 38.66 2.69
645 707 3.065306 CCGTCTGTTAGGCCCACA 58.935 61.111 0.00 1.28 0.00 4.17
646 708 1.602237 CCGTCTGTTAGGCCCACAT 59.398 57.895 0.00 0.00 0.00 3.21
647 709 0.744414 CCGTCTGTTAGGCCCACATG 60.744 60.000 0.00 0.00 0.00 3.21
648 710 0.036388 CGTCTGTTAGGCCCACATGT 60.036 55.000 0.00 0.00 0.00 3.21
649 711 1.739067 GTCTGTTAGGCCCACATGTC 58.261 55.000 0.00 0.00 0.00 3.06
650 712 1.003118 GTCTGTTAGGCCCACATGTCA 59.997 52.381 0.00 0.00 0.00 3.58
651 713 1.915489 TCTGTTAGGCCCACATGTCAT 59.085 47.619 0.00 0.00 0.00 3.06
652 714 2.308570 TCTGTTAGGCCCACATGTCATT 59.691 45.455 0.00 0.00 0.00 2.57
653 715 2.424601 CTGTTAGGCCCACATGTCATTG 59.575 50.000 0.00 0.00 0.00 2.82
654 716 1.750778 GTTAGGCCCACATGTCATTGG 59.249 52.381 0.00 0.00 0.00 3.16
655 717 0.395586 TAGGCCCACATGTCATTGGC 60.396 55.000 14.02 14.02 41.42 4.52
656 718 2.894919 GCCCACATGTCATTGGCC 59.105 61.111 12.14 0.00 36.07 5.36
657 719 2.724273 GCCCACATGTCATTGGCCC 61.724 63.158 0.00 0.00 36.07 5.80
658 720 1.305129 CCCACATGTCATTGGCCCA 60.305 57.895 0.00 0.00 0.00 5.36
659 721 0.903924 CCCACATGTCATTGGCCCAA 60.904 55.000 0.00 0.00 0.00 4.12
660 722 0.247185 CCACATGTCATTGGCCCAAC 59.753 55.000 0.00 0.00 0.00 3.77
661 723 1.259609 CACATGTCATTGGCCCAACT 58.740 50.000 0.00 0.00 0.00 3.16
662 724 1.067425 CACATGTCATTGGCCCAACTG 60.067 52.381 0.00 0.00 0.00 3.16
663 725 0.108520 CATGTCATTGGCCCAACTGC 60.109 55.000 0.00 0.00 0.00 4.40
664 726 0.542467 ATGTCATTGGCCCAACTGCA 60.542 50.000 0.00 0.00 0.00 4.41
665 727 1.180456 TGTCATTGGCCCAACTGCAG 61.180 55.000 13.48 13.48 0.00 4.41
666 728 1.607178 TCATTGGCCCAACTGCAGG 60.607 57.895 19.93 1.24 0.00 4.85
667 729 1.909781 CATTGGCCCAACTGCAGGT 60.910 57.895 19.93 9.19 0.00 4.00
668 730 1.909781 ATTGGCCCAACTGCAGGTG 60.910 57.895 25.38 25.38 0.00 4.00
679 741 2.668212 GCAGGTGCAGTTACGGCA 60.668 61.111 6.01 6.01 41.59 5.69
685 747 2.912986 TGCAGTTACGGCACTGAAG 58.087 52.632 17.81 0.00 46.29 3.02
686 748 0.105964 TGCAGTTACGGCACTGAAGT 59.894 50.000 17.81 0.00 46.29 3.01
687 749 1.226746 GCAGTTACGGCACTGAAGTT 58.773 50.000 17.81 0.00 46.29 2.66
688 750 1.194772 GCAGTTACGGCACTGAAGTTC 59.805 52.381 17.81 0.00 46.29 3.01
689 751 2.479837 CAGTTACGGCACTGAAGTTCA 58.520 47.619 10.01 5.25 46.29 3.18
814 885 2.619484 TCCCCTCCCCTCTACGGT 60.619 66.667 0.00 0.00 0.00 4.83
822 893 1.982395 CCCTCTACGGTGCTGACCA 60.982 63.158 0.00 0.00 43.33 4.02
868 939 3.659092 CATGCGCACACAACCGGT 61.659 61.111 14.90 0.00 0.00 5.28
1107 1187 1.341679 ACCTAGGATGCGTGGTCACTA 60.342 52.381 17.98 0.00 0.00 2.74
1410 1490 3.845775 CGTTGACTAATGGTTTGATTGCG 59.154 43.478 0.00 0.00 0.00 4.85
1470 1550 6.413783 TTGTTGTTAGATGAGGTACAGTCA 57.586 37.500 0.00 0.00 0.00 3.41
1484 1567 6.008331 AGGTACAGTCACAACTACTACATCA 58.992 40.000 0.00 0.00 33.25 3.07
1551 1634 9.190858 CTACATTTACAATTAAGTTTGCTTGCA 57.809 29.630 0.00 0.00 36.22 4.08
1642 1726 9.442047 CTTCAACTATTTTCTTATCAGACCAGT 57.558 33.333 0.00 0.00 0.00 4.00
1827 1911 3.007506 AGGTCAATCGGATGTGTGTGTTA 59.992 43.478 0.00 0.00 0.00 2.41
1854 1938 7.502226 ACACAGATCTTTGATGTGGAAGTTAAA 59.498 33.333 15.71 0.00 46.74 1.52
2193 2281 7.305993 CGAACTTTGTCTCTTTTACAATTTGCC 60.306 37.037 0.00 0.00 36.75 4.52
2350 2438 3.176578 GTCGCGCCGTCGATTTCA 61.177 61.111 0.00 0.00 40.84 2.69
2725 2816 0.991146 TGCTTGGGCTCATGACCTTA 59.009 50.000 3.13 2.59 43.49 2.69
2739 2830 9.883142 GCTCATGACCTTAATTAATCTATAGCT 57.117 33.333 0.00 0.00 0.00 3.32
2970 3062 0.179156 ATTGCGATTTTGGAGCTGCG 60.179 50.000 0.00 0.00 0.00 5.18
3539 3650 5.064707 GCAAGATACACGCAATAGGAAAAGA 59.935 40.000 0.00 0.00 0.00 2.52
3558 3669 8.470002 GGAAAAGAAACTAACAGAATATGGCAT 58.530 33.333 4.88 4.88 0.00 4.40
3849 4291 1.291877 CGCCAGCTTCTTAAGTGCGT 61.292 55.000 14.14 4.50 37.90 5.24
4120 4562 8.965819 TGAGCCTTATTAATTGTCATAGCAAAA 58.034 29.630 0.00 0.00 31.63 2.44
4271 4713 0.320508 GGCGTTCCTCTCGAAACCTT 60.321 55.000 0.00 0.00 30.39 3.50
4289 4731 2.031163 GCACCACAAGCCTCGTCT 59.969 61.111 0.00 0.00 0.00 4.18
4448 4890 1.528586 CGTCTTCTGCACTGTCAAAGG 59.471 52.381 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.701040 ACATGTTATTTGACTGGGATGCC 59.299 43.478 0.00 0.00 0.00 4.40
1 2 4.989279 ACATGTTATTTGACTGGGATGC 57.011 40.909 0.00 0.00 0.00 3.91
2 3 6.513806 TCAACATGTTATTTGACTGGGATG 57.486 37.500 11.53 0.00 0.00 3.51
3 4 6.891361 TCATCAACATGTTATTTGACTGGGAT 59.109 34.615 11.53 2.98 34.61 3.85
4 5 6.244654 TCATCAACATGTTATTTGACTGGGA 58.755 36.000 11.53 0.46 34.61 4.37
5 6 6.513806 TCATCAACATGTTATTTGACTGGG 57.486 37.500 11.53 0.00 34.61 4.45
181 183 7.447238 TCTTTCGTTGGACAATTTTCCTTATCT 59.553 33.333 11.83 0.00 36.51 1.98
199 201 5.982516 TGCTTGCATGTTTTTATCTTTCGTT 59.017 32.000 1.14 0.00 0.00 3.85
394 425 3.628769 GGGAAGGAGAGAGTGGACTATGT 60.629 52.174 0.00 0.00 0.00 2.29
400 431 0.336737 GAGGGGAAGGAGAGAGTGGA 59.663 60.000 0.00 0.00 0.00 4.02
556 618 2.867472 GTCCGGGATTTGCGTGTG 59.133 61.111 0.00 0.00 0.00 3.82
560 622 3.864686 CAGCGTCCGGGATTTGCG 61.865 66.667 0.00 0.00 0.00 4.85
561 623 4.179579 GCAGCGTCCGGGATTTGC 62.180 66.667 0.00 7.29 0.00 3.68
562 624 2.040544 AAGCAGCGTCCGGGATTTG 61.041 57.895 0.00 0.42 0.00 2.32
563 625 2.040544 CAAGCAGCGTCCGGGATTT 61.041 57.895 0.00 0.00 0.00 2.17
564 626 2.436646 CAAGCAGCGTCCGGGATT 60.437 61.111 0.00 0.00 0.00 3.01
565 627 4.473520 CCAAGCAGCGTCCGGGAT 62.474 66.667 0.00 0.00 0.00 3.85
574 636 2.671619 TTACGGCACCCAAGCAGC 60.672 61.111 0.00 0.00 35.83 5.25
575 637 1.302511 AGTTACGGCACCCAAGCAG 60.303 57.895 0.00 0.00 35.83 4.24
576 638 1.599518 CAGTTACGGCACCCAAGCA 60.600 57.895 0.00 0.00 35.83 3.91
577 639 2.978018 GCAGTTACGGCACCCAAGC 61.978 63.158 2.05 0.00 0.00 4.01
578 640 1.599518 TGCAGTTACGGCACCCAAG 60.600 57.895 6.01 0.00 36.11 3.61
579 641 2.511403 TGCAGTTACGGCACCCAA 59.489 55.556 6.01 0.00 36.11 4.12
584 646 2.668212 GCAGGTGCAGTTACGGCA 60.668 61.111 6.01 6.01 41.59 5.69
594 656 1.181098 ATTGACCCAACTGCAGGTGC 61.181 55.000 26.87 13.45 36.17 5.01
595 657 0.599558 CATTGACCCAACTGCAGGTG 59.400 55.000 25.38 25.38 36.17 4.00
596 658 0.540365 CCATTGACCCAACTGCAGGT 60.540 55.000 19.93 9.19 39.75 4.00
597 659 1.880819 GCCATTGACCCAACTGCAGG 61.881 60.000 19.93 2.94 0.00 4.85
598 660 1.180456 TGCCATTGACCCAACTGCAG 61.180 55.000 13.48 13.48 31.46 4.41
599 661 0.542467 ATGCCATTGACCCAACTGCA 60.542 50.000 7.20 7.20 37.52 4.41
600 662 0.108520 CATGCCATTGACCCAACTGC 60.109 55.000 0.00 0.00 0.00 4.40
601 663 1.067425 CACATGCCATTGACCCAACTG 60.067 52.381 0.00 0.00 0.00 3.16
602 664 1.259609 CACATGCCATTGACCCAACT 58.740 50.000 0.00 0.00 0.00 3.16
603 665 0.247185 CCACATGCCATTGACCCAAC 59.753 55.000 0.00 0.00 0.00 3.77
604 666 0.903924 CCCACATGCCATTGACCCAA 60.904 55.000 0.00 0.00 0.00 4.12
605 667 1.305129 CCCACATGCCATTGACCCA 60.305 57.895 0.00 0.00 0.00 4.51
606 668 2.724273 GCCCACATGCCATTGACCC 61.724 63.158 0.00 0.00 0.00 4.46
607 669 2.894919 GCCCACATGCCATTGACC 59.105 61.111 0.00 0.00 0.00 4.02
616 678 4.415150 AGACGGCTGGCCCACATG 62.415 66.667 0.00 0.00 0.00 3.21
617 679 4.415150 CAGACGGCTGGCCCACAT 62.415 66.667 11.57 0.00 38.51 3.21
619 681 3.248446 TAACAGACGGCTGGCCCAC 62.248 63.158 24.99 0.00 46.60 4.61
620 682 2.925706 TAACAGACGGCTGGCCCA 60.926 61.111 24.99 0.65 46.60 5.36
621 683 2.125106 CTAACAGACGGCTGGCCC 60.125 66.667 24.99 0.00 46.60 5.80
622 684 2.125106 CCTAACAGACGGCTGGCC 60.125 66.667 24.99 0.00 46.60 5.36
623 685 2.820037 GCCTAACAGACGGCTGGC 60.820 66.667 24.99 13.09 46.60 4.85
624 686 2.125106 GGCCTAACAGACGGCTGG 60.125 66.667 24.99 5.44 46.60 4.85
625 687 2.125106 GGGCCTAACAGACGGCTG 60.125 66.667 19.12 19.12 45.57 4.85
626 688 2.606519 TGGGCCTAACAGACGGCT 60.607 61.111 4.53 0.00 45.57 5.52
627 689 2.436115 GTGGGCCTAACAGACGGC 60.436 66.667 4.53 0.00 45.55 5.68
628 690 0.744414 CATGTGGGCCTAACAGACGG 60.744 60.000 15.50 4.10 0.00 4.79
629 691 0.036388 ACATGTGGGCCTAACAGACG 60.036 55.000 15.50 9.88 0.00 4.18
630 692 1.003118 TGACATGTGGGCCTAACAGAC 59.997 52.381 1.15 10.30 0.00 3.51
631 693 1.357137 TGACATGTGGGCCTAACAGA 58.643 50.000 1.15 0.00 0.00 3.41
632 694 2.424601 CAATGACATGTGGGCCTAACAG 59.575 50.000 1.15 10.70 0.00 3.16
633 695 2.445427 CAATGACATGTGGGCCTAACA 58.555 47.619 1.15 13.18 0.00 2.41
634 696 1.750778 CCAATGACATGTGGGCCTAAC 59.249 52.381 1.15 1.86 0.00 2.34
635 697 1.959508 GCCAATGACATGTGGGCCTAA 60.960 52.381 1.15 0.00 38.70 2.69
636 698 0.395586 GCCAATGACATGTGGGCCTA 60.396 55.000 1.15 0.00 38.70 3.93
637 699 1.683365 GCCAATGACATGTGGGCCT 60.683 57.895 1.15 0.00 38.70 5.19
638 700 2.894919 GCCAATGACATGTGGGCC 59.105 61.111 1.15 0.00 38.70 5.80
640 702 0.903924 TTGGGCCAATGACATGTGGG 60.904 55.000 16.66 0.06 35.28 4.61
641 703 0.247185 GTTGGGCCAATGACATGTGG 59.753 55.000 23.95 0.00 38.00 4.17
642 704 1.067425 CAGTTGGGCCAATGACATGTG 60.067 52.381 23.95 7.72 0.00 3.21
643 705 1.259609 CAGTTGGGCCAATGACATGT 58.740 50.000 23.95 0.00 0.00 3.21
644 706 0.108520 GCAGTTGGGCCAATGACATG 60.109 55.000 23.95 16.27 0.00 3.21
645 707 0.542467 TGCAGTTGGGCCAATGACAT 60.542 50.000 23.95 3.67 0.00 3.06
646 708 1.152589 TGCAGTTGGGCCAATGACA 60.153 52.632 23.95 17.12 0.00 3.58
647 709 1.588082 CTGCAGTTGGGCCAATGAC 59.412 57.895 23.95 10.82 0.00 3.06
648 710 1.607178 CCTGCAGTTGGGCCAATGA 60.607 57.895 23.95 5.80 0.00 2.57
649 711 1.909781 ACCTGCAGTTGGGCCAATG 60.910 57.895 23.95 20.59 0.00 2.82
650 712 1.909781 CACCTGCAGTTGGGCCAAT 60.910 57.895 23.95 8.80 0.00 3.16
651 713 2.521465 CACCTGCAGTTGGGCCAA 60.521 61.111 16.66 16.66 0.00 4.52
662 724 2.668212 TGCCGTAACTGCACCTGC 60.668 61.111 0.00 0.00 42.50 4.85
667 729 0.105964 ACTTCAGTGCCGTAACTGCA 59.894 50.000 9.30 0.00 45.93 4.41
668 730 1.194772 GAACTTCAGTGCCGTAACTGC 59.805 52.381 9.30 0.00 45.93 4.40
670 732 2.755650 CTGAACTTCAGTGCCGTAACT 58.244 47.619 10.27 0.00 39.58 2.24
681 743 2.151202 GGATTTGCGGACTGAACTTCA 58.849 47.619 0.00 0.00 0.00 3.02
682 744 1.468914 GGGATTTGCGGACTGAACTTC 59.531 52.381 0.00 0.00 0.00 3.01
683 745 1.073923 AGGGATTTGCGGACTGAACTT 59.926 47.619 0.00 0.00 0.00 2.66
684 746 0.693049 AGGGATTTGCGGACTGAACT 59.307 50.000 0.00 0.00 0.00 3.01
685 747 2.396590 TAGGGATTTGCGGACTGAAC 57.603 50.000 0.00 0.00 0.00 3.18
686 748 3.199946 AGATTAGGGATTTGCGGACTGAA 59.800 43.478 0.00 0.00 0.00 3.02
687 749 2.771943 AGATTAGGGATTTGCGGACTGA 59.228 45.455 0.00 0.00 0.00 3.41
688 750 3.134458 GAGATTAGGGATTTGCGGACTG 58.866 50.000 0.00 0.00 0.00 3.51
689 751 2.224066 CGAGATTAGGGATTTGCGGACT 60.224 50.000 0.00 0.00 0.00 3.85
690 752 2.135933 CGAGATTAGGGATTTGCGGAC 58.864 52.381 0.00 0.00 0.00 4.79
691 753 1.070134 CCGAGATTAGGGATTTGCGGA 59.930 52.381 0.00 0.00 39.85 5.54
814 885 0.179092 CTCGATCTGCATGGTCAGCA 60.179 55.000 0.00 0.00 40.19 4.41
822 893 1.067084 CTGGTCGCTCGATCTGCAT 59.933 57.895 4.11 0.00 0.00 3.96
868 939 0.950836 CCTTTGCGTGATGTTGGTCA 59.049 50.000 0.00 0.00 0.00 4.02
1410 1490 2.561733 TGTATGTACGAGCTCACTGC 57.438 50.000 15.40 1.94 43.29 4.40
1470 1550 6.156748 TGACAGTGTTGATGTAGTAGTTGT 57.843 37.500 0.00 0.00 0.00 3.32
1484 1567 9.817809 CAGTACCAAAGTATATATGACAGTGTT 57.182 33.333 0.00 0.00 0.00 3.32
1827 1911 5.380043 ACTTCCACATCAAAGATCTGTGTT 58.620 37.500 12.74 1.52 38.85 3.32
1854 1938 7.597850 AGAGAGGTAGGATAGGACTGATATT 57.402 40.000 0.00 0.00 0.00 1.28
2074 2162 6.493115 TGCCCATAGAAATGTTCAGAAAGAAA 59.507 34.615 0.00 0.00 38.13 2.52
2334 2422 2.431090 TTGAAATCGACGGCGCGA 60.431 55.556 23.64 23.64 45.22 5.87
2725 2816 8.695456 CACCCAAAACCAAGCTATAGATTAATT 58.305 33.333 2.30 0.00 0.00 1.40
2739 2830 5.897824 TGTTAAATAGGTCACCCAAAACCAA 59.102 36.000 0.00 0.00 38.06 3.67
2970 3062 5.011023 CCAAATGATAAAGAATAGCCCCACC 59.989 44.000 0.00 0.00 0.00 4.61
3558 3669 9.693739 TCCAGCAGTATTATTTTCCTTTCATTA 57.306 29.630 0.00 0.00 0.00 1.90
3579 3690 7.268199 TCATGATCTCACAAATATTTCCAGC 57.732 36.000 0.00 0.00 0.00 4.85
3849 4291 4.838986 AGAAAGTCCTTACAGGCTGAAGTA 59.161 41.667 23.66 4.76 34.61 2.24
3870 4312 8.138074 CCTCAATGAAGAACATCGTCTATAAGA 58.862 37.037 0.00 0.00 38.38 2.10
4271 4713 2.280797 GACGAGGCTTGTGGTGCA 60.281 61.111 13.26 0.00 0.00 4.57
4289 4731 2.416296 CGGCTAATGGTCTGTGTAACGA 60.416 50.000 0.00 0.00 42.39 3.85
4448 4890 6.294620 CGGGGAGAAGAAGTAATCTACCATAC 60.295 46.154 6.39 0.00 46.86 2.39
4574 5016 2.271800 CCATGTGTTTCCGAGACTAGC 58.728 52.381 0.00 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.