Multiple sequence alignment - TraesCS3D01G111400

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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 TraesCS3D01G111400 chr3D 100.000 2886 0 0 1 2886 64772382 64769497 0.000000e+00 5330.0
1 TraesCS3D01G111400 chr3D 93.537 588 25 5 1 577 570572305 570571720 0.000000e+00 863.0
2 TraesCS3D01G111400 chr3A 92.635 2118 95 23 772 2886 75569793 75567734 0.000000e+00 2990.0
3 TraesCS3D01G111400 chr3A 90.143 558 28 11 34 577 653955029 653955573 0.000000e+00 701.0
4 TraesCS3D01G111400 chr3B 94.769 1147 50 5 1741 2886 107968018 107966881 0.000000e+00 1777.0
5 TraesCS3D01G111400 chr3B 93.360 753 34 12 877 1622 107968761 107968018 0.000000e+00 1099.0
6 TraesCS3D01G111400 chr3B 84.722 72 6 3 1498 1569 107968081 107968015 1.860000e-07 67.6
7 TraesCS3D01G111400 chr6D 94.454 577 22 6 1 577 419880787 419881353 0.000000e+00 880.0
8 TraesCS3D01G111400 chr6D 91.697 554 33 6 34 577 97818135 97817585 0.000000e+00 756.0
9 TraesCS3D01G111400 chr6B 92.650 585 29 5 1 575 423013806 423013226 0.000000e+00 830.0
10 TraesCS3D01G111400 chr4B 91.638 586 35 8 1 577 553921246 553920666 0.000000e+00 798.0
11 TraesCS3D01G111400 chr4B 89.777 538 39 6 1 538 548199722 548199201 0.000000e+00 675.0
12 TraesCS3D01G111400 chr4A 91.039 558 31 7 34 577 578180670 578180118 0.000000e+00 736.0
13 TraesCS3D01G111400 chr5A 91.139 553 30 7 34 572 33923200 33923747 0.000000e+00 732.0
14 TraesCS3D01G111400 chr1A 90.860 558 32 9 34 577 10695625 10696177 0.000000e+00 730.0
15 TraesCS3D01G111400 chr6A 90.958 553 31 7 34 572 494439159 494439706 0.000000e+00 726.0


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 TraesCS3D01G111400 chr3D 64769497 64772382 2885 True 5330.0 5330 100.000000 1 2886 1 chr3D.!!$R1 2885
1 TraesCS3D01G111400 chr3D 570571720 570572305 585 True 863.0 863 93.537000 1 577 1 chr3D.!!$R2 576
2 TraesCS3D01G111400 chr3A 75567734 75569793 2059 True 2990.0 2990 92.635000 772 2886 1 chr3A.!!$R1 2114
3 TraesCS3D01G111400 chr3A 653955029 653955573 544 False 701.0 701 90.143000 34 577 1 chr3A.!!$F1 543
4 TraesCS3D01G111400 chr3B 107966881 107968761 1880 True 981.2 1777 90.950333 877 2886 3 chr3B.!!$R1 2009
5 TraesCS3D01G111400 chr6D 419880787 419881353 566 False 880.0 880 94.454000 1 577 1 chr6D.!!$F1 576
6 TraesCS3D01G111400 chr6D 97817585 97818135 550 True 756.0 756 91.697000 34 577 1 chr6D.!!$R1 543
7 TraesCS3D01G111400 chr6B 423013226 423013806 580 True 830.0 830 92.650000 1 575 1 chr6B.!!$R1 574
8 TraesCS3D01G111400 chr4B 553920666 553921246 580 True 798.0 798 91.638000 1 577 1 chr4B.!!$R2 576
9 TraesCS3D01G111400 chr4B 548199201 548199722 521 True 675.0 675 89.777000 1 538 1 chr4B.!!$R1 537
10 TraesCS3D01G111400 chr4A 578180118 578180670 552 True 736.0 736 91.039000 34 577 1 chr4A.!!$R1 543
11 TraesCS3D01G111400 chr5A 33923200 33923747 547 False 732.0 732 91.139000 34 572 1 chr5A.!!$F1 538
12 TraesCS3D01G111400 chr1A 10695625 10696177 552 False 730.0 730 90.860000 34 577 1 chr1A.!!$F1 543
13 TraesCS3D01G111400 chr6A 494439159 494439706 547 False 726.0 726 90.958000 34 572 1 chr6A.!!$F1 538

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
646 683 0.035739 ACAAGGCACGACCCGTTTAT 59.964 50.0 0.0 0.0 38.32 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2256 0.328258 TAACCCCAGAGAGCTTTGCC 59.672 55.0 0.0 0.0 0.0 4.52 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
59 64 6.927936 CAGATCCAATGACATAAGAGTCGAAT 59.072 38.462 0.00 0.00 41.41 3.34
110 115 0.179078 TACACCAAAACGACCGTGCT 60.179 50.000 0.00 0.00 0.00 4.40
220 225 1.272781 CGGCGATGAGACAGAGAAAC 58.727 55.000 0.00 0.00 0.00 2.78
302 309 0.539051 CCAGAGATTTGGAGAGCCGT 59.461 55.000 0.00 0.00 40.87 5.68
400 436 2.025359 GAGAATGGCTCGCGTTTCGG 62.025 60.000 5.77 0.00 39.05 4.30
448 484 0.322098 CCGCTTACATGTGGGTCCAA 60.322 55.000 9.11 0.00 34.20 3.53
463 499 2.125552 CAAGCTCGTCCGGATGCA 60.126 61.111 19.40 7.18 0.00 3.96
596 633 2.831742 CGCCCGCCTAGGACTGTA 60.832 66.667 14.75 0.00 45.00 2.74
597 634 2.813200 GCCCGCCTAGGACTGTAC 59.187 66.667 14.75 0.00 45.00 2.90
598 635 2.794028 GCCCGCCTAGGACTGTACC 61.794 68.421 14.75 0.00 45.00 3.34
599 636 1.076192 CCCGCCTAGGACTGTACCT 60.076 63.158 14.75 0.00 45.00 3.08
600 637 1.392710 CCCGCCTAGGACTGTACCTG 61.393 65.000 14.75 0.00 45.00 4.00
601 638 1.392710 CCGCCTAGGACTGTACCTGG 61.393 65.000 14.75 0.00 45.00 4.45
604 641 2.517609 CTAGGACTGTACCTGGGCC 58.482 63.158 0.00 0.00 40.81 5.80
605 642 1.380785 TAGGACTGTACCTGGGCCG 60.381 63.158 0.00 0.00 40.81 6.13
606 643 4.468689 GGACTGTACCTGGGCCGC 62.469 72.222 0.00 0.00 0.00 6.53
607 644 4.814294 GACTGTACCTGGGCCGCG 62.814 72.222 0.00 0.00 0.00 6.46
609 646 4.514577 CTGTACCTGGGCCGCGAG 62.515 72.222 8.23 0.00 0.00 5.03
642 679 4.657824 CGACAAGGCACGACCCGT 62.658 66.667 0.00 0.00 42.36 5.28
643 680 2.280592 GACAAGGCACGACCCGTT 60.281 61.111 0.00 0.00 38.32 4.44
644 681 1.890510 GACAAGGCACGACCCGTTT 60.891 57.895 0.00 0.00 38.32 3.60
645 682 0.600782 GACAAGGCACGACCCGTTTA 60.601 55.000 0.00 0.00 38.32 2.01
646 683 0.035739 ACAAGGCACGACCCGTTTAT 59.964 50.000 0.00 0.00 38.32 1.40
647 684 1.161843 CAAGGCACGACCCGTTTATT 58.838 50.000 0.00 0.00 38.32 1.40
648 685 1.538075 CAAGGCACGACCCGTTTATTT 59.462 47.619 0.00 0.00 38.32 1.40
649 686 1.900245 AGGCACGACCCGTTTATTTT 58.100 45.000 0.00 0.00 38.32 1.82
650 687 2.232399 AGGCACGACCCGTTTATTTTT 58.768 42.857 0.00 0.00 38.32 1.94
684 721 7.839680 AAATGGCCCAAAATAGTCTATAAGG 57.160 36.000 0.00 0.00 0.00 2.69
685 722 4.725490 TGGCCCAAAATAGTCTATAAGGC 58.275 43.478 0.00 11.34 37.14 4.35
687 724 4.986783 GCCCAAAATAGTCTATAAGGCCT 58.013 43.478 0.00 0.00 31.59 5.19
688 725 6.123045 GCCCAAAATAGTCTATAAGGCCTA 57.877 41.667 5.16 0.00 31.59 3.93
689 726 6.540083 GCCCAAAATAGTCTATAAGGCCTAA 58.460 40.000 5.16 0.00 31.59 2.69
690 727 7.002276 GCCCAAAATAGTCTATAAGGCCTAAA 58.998 38.462 5.16 0.00 31.59 1.85
691 728 7.504574 GCCCAAAATAGTCTATAAGGCCTAAAA 59.495 37.037 5.16 0.00 31.59 1.52
692 729 9.416284 CCCAAAATAGTCTATAAGGCCTAAAAA 57.584 33.333 5.16 0.00 0.00 1.94
694 731 9.952188 CAAAATAGTCTATAAGGCCTAAAAAGC 57.048 33.333 5.16 0.00 0.00 3.51
695 732 9.695155 AAAATAGTCTATAAGGCCTAAAAAGCA 57.305 29.630 5.16 0.00 0.00 3.91
696 733 8.678593 AATAGTCTATAAGGCCTAAAAAGCAC 57.321 34.615 5.16 0.00 0.00 4.40
697 734 5.437946 AGTCTATAAGGCCTAAAAAGCACC 58.562 41.667 5.16 0.00 0.00 5.01
698 735 4.579340 GTCTATAAGGCCTAAAAAGCACCC 59.421 45.833 5.16 0.00 0.00 4.61
699 736 3.757947 ATAAGGCCTAAAAAGCACCCT 57.242 42.857 5.16 0.00 0.00 4.34
700 737 1.632589 AAGGCCTAAAAAGCACCCTG 58.367 50.000 5.16 0.00 0.00 4.45
701 738 0.900182 AGGCCTAAAAAGCACCCTGC 60.900 55.000 1.29 0.00 45.46 4.85
702 739 1.591703 GCCTAAAAAGCACCCTGCC 59.408 57.895 0.00 0.00 46.52 4.85
703 740 1.184970 GCCTAAAAAGCACCCTGCCA 61.185 55.000 0.00 0.00 46.52 4.92
704 741 0.603065 CCTAAAAAGCACCCTGCCAC 59.397 55.000 0.00 0.00 46.52 5.01
705 742 0.240945 CTAAAAAGCACCCTGCCACG 59.759 55.000 0.00 0.00 46.52 4.94
706 743 1.801309 TAAAAAGCACCCTGCCACGC 61.801 55.000 0.00 0.00 46.52 5.34
718 755 4.418401 CCACGCGGGCCAAATGTG 62.418 66.667 12.47 7.39 0.00 3.21
725 762 4.067913 GGCCAAATGTGCCGGTGG 62.068 66.667 1.90 2.06 39.48 4.61
726 763 4.067913 GCCAAATGTGCCGGTGGG 62.068 66.667 1.90 0.00 0.00 4.61
749 786 1.207593 CACGCTTACAGTGCCTTGC 59.792 57.895 0.00 0.00 32.52 4.01
750 787 1.966451 ACGCTTACAGTGCCTTGCC 60.966 57.895 0.00 0.00 0.00 4.52
751 788 1.672356 CGCTTACAGTGCCTTGCCT 60.672 57.895 0.00 0.00 0.00 4.75
752 789 1.878775 GCTTACAGTGCCTTGCCTG 59.121 57.895 0.00 0.00 34.62 4.85
753 790 1.589716 GCTTACAGTGCCTTGCCTGG 61.590 60.000 0.00 0.00 33.43 4.45
754 791 0.962356 CTTACAGTGCCTTGCCTGGG 60.962 60.000 0.00 0.00 33.43 4.45
762 799 3.379445 CTTGCCTGGGCCTTGCAG 61.379 66.667 17.66 0.77 41.09 4.41
763 800 3.873679 CTTGCCTGGGCCTTGCAGA 62.874 63.158 17.66 10.13 41.09 4.26
764 801 3.873679 TTGCCTGGGCCTTGCAGAG 62.874 63.158 17.66 0.28 41.09 3.35
765 802 4.039092 GCCTGGGCCTTGCAGAGA 62.039 66.667 4.53 0.00 34.56 3.10
766 803 2.271497 CCTGGGCCTTGCAGAGAG 59.729 66.667 4.53 0.00 0.00 3.20
767 804 2.600729 CCTGGGCCTTGCAGAGAGT 61.601 63.158 4.53 0.00 0.00 3.24
768 805 1.377994 CTGGGCCTTGCAGAGAGTT 59.622 57.895 4.53 0.00 0.00 3.01
769 806 0.615331 CTGGGCCTTGCAGAGAGTTA 59.385 55.000 4.53 0.00 0.00 2.24
770 807 1.211457 CTGGGCCTTGCAGAGAGTTAT 59.789 52.381 4.53 0.00 0.00 1.89
784 821 7.829706 TGCAGAGAGTTATACGATCCATATACT 59.170 37.037 0.00 0.00 0.00 2.12
789 826 8.828644 AGAGTTATACGATCCATATACTAAGCG 58.171 37.037 0.00 0.00 0.00 4.68
790 827 8.503458 AGTTATACGATCCATATACTAAGCGT 57.497 34.615 0.00 0.00 34.86 5.07
791 828 8.396390 AGTTATACGATCCATATACTAAGCGTG 58.604 37.037 0.00 0.00 32.62 5.34
847 884 1.714899 CCGCCGCCTCATCGAAAAAT 61.715 55.000 0.00 0.00 0.00 1.82
857 894 6.580791 CGCCTCATCGAAAAATAAAAAGTTCA 59.419 34.615 0.00 0.00 0.00 3.18
895 933 3.605749 CTCGCTCCTTTCCGGCCAA 62.606 63.158 2.24 0.00 0.00 4.52
1209 1253 2.735100 GAATCCCGCGGATCGAGC 60.735 66.667 30.73 8.20 42.27 5.03
1283 1327 0.109226 GACCTGAAGAAGTCGGACCG 60.109 60.000 7.84 7.84 34.07 4.79
1412 1456 0.317160 CACAAGGAGGTGCGTGACTA 59.683 55.000 0.00 0.00 31.10 2.59
1429 1473 0.541863 CTATTTCCCTGCGACCCTGT 59.458 55.000 0.00 0.00 0.00 4.00
1458 1502 3.355788 TCGAAATCGATTATCGTAACGCG 59.644 43.478 26.64 3.53 44.22 6.01
1485 1529 5.695816 GCTGTTCTGATTGGATACTCAGATC 59.304 44.000 3.33 3.96 45.34 2.75
1522 1567 3.418047 AGCAAGCCCGTATTTACTTTGT 58.582 40.909 0.00 0.00 0.00 2.83
1565 1610 2.628178 GCTTGGATAATTAGCAACCCCC 59.372 50.000 2.72 0.00 35.05 5.40
1580 1625 2.849942 ACCCCCGTTGTTACTTTGTAC 58.150 47.619 0.00 0.00 0.00 2.90
1632 1677 2.028876 AGCAAGCCCGTTGTTACTTTT 58.971 42.857 0.00 0.00 38.55 2.27
1661 1706 5.997746 ACTGTTAAGAATCTACTTTGCTGCA 59.002 36.000 0.00 0.00 0.00 4.41
1672 1717 3.383761 ACTTTGCTGCAAGTAATTGTGC 58.616 40.909 15.39 13.30 38.67 4.57
1863 1908 3.511934 AGACTCTTTATGCTCGGTTCACT 59.488 43.478 0.00 0.00 0.00 3.41
1903 1948 0.384669 GATTCCTGCATTGCCTCTGC 59.615 55.000 6.12 0.00 40.10 4.26
1992 2037 0.033228 GGCTCAGATAGTGCATCGCT 59.967 55.000 0.00 0.00 38.81 4.93
2052 2097 1.069049 GAGCTCCTCTCATTCCTCAGC 59.931 57.143 0.87 0.00 41.51 4.26
2067 2112 1.878522 CAGCGCGTCTGATGTACCC 60.879 63.158 21.01 0.00 45.72 3.69
2107 2152 4.966787 TTTGGCACGCCTGGGGTC 62.967 66.667 14.14 8.83 36.94 4.46
2156 2201 2.029743 GCCTTTCGCCTGTTTGTGA 58.970 52.632 0.00 0.00 0.00 3.58
2167 2212 4.669965 CGCCTGTTTGTGATAATCAGTGTG 60.670 45.833 0.00 0.00 0.00 3.82
2253 2298 3.931578 AGTTGTACTCTCATTGCCAGAC 58.068 45.455 0.00 0.00 0.00 3.51
2362 2407 9.238368 TCTTCAAGAACAAAGGAGAAACTTTAA 57.762 29.630 0.00 0.00 38.56 1.52
2515 2561 5.003160 TCACTCATGACAAGTGGGTATTTG 58.997 41.667 12.22 0.00 43.48 2.32
2524 2570 5.393866 ACAAGTGGGTATTTGTTGGAATCT 58.606 37.500 0.00 0.00 33.54 2.40
2556 2602 6.037172 CCGTGGAGGTATTCTCAATTTTACTG 59.963 42.308 0.00 0.00 44.19 2.74
2557 2603 6.037172 CGTGGAGGTATTCTCAATTTTACTGG 59.963 42.308 0.00 0.00 44.19 4.00
2572 2618 2.191128 ACTGGGAGTGCAAGTCAATC 57.809 50.000 0.00 0.00 38.29 2.67
2633 2679 2.140717 GTTCTTCGTTGTTCCGATGGT 58.859 47.619 0.00 0.00 36.62 3.55
2794 2840 3.131400 GCTAAGGAGATCAACTCGGAACT 59.869 47.826 0.00 0.00 45.76 3.01
2807 2853 0.609131 CGGAACTGGTGGCAATCCTT 60.609 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.605319 CGGCAGCAAGGGACAGTAAA 60.605 55.000 0.00 0.00 0.00 2.01
59 64 2.159490 TGGGATGGGTGTGCTTCCA 61.159 57.895 0.00 0.00 37.46 3.53
110 115 1.699083 TCTGTGGCATCAACTTCCTCA 59.301 47.619 0.00 0.00 0.00 3.86
220 225 0.103208 GGTACCCAGTGCATCTCTCG 59.897 60.000 0.00 0.00 0.00 4.04
448 484 2.755876 TCTGCATCCGGACGAGCT 60.756 61.111 21.51 0.00 0.00 4.09
463 499 0.953960 GATCGTGGGCGGTTTTGTCT 60.954 55.000 0.00 0.00 38.89 3.41
492 528 2.259204 CGCCTGGTCGGTTTCGTA 59.741 61.111 0.00 0.00 37.69 3.43
579 616 2.831742 TACAGTCCTAGGCGGGCG 60.832 66.667 2.96 0.00 44.20 6.13
580 617 2.794028 GGTACAGTCCTAGGCGGGC 61.794 68.421 2.96 0.00 37.80 6.13
581 618 1.076192 AGGTACAGTCCTAGGCGGG 60.076 63.158 2.96 0.00 35.87 6.13
582 619 1.392710 CCAGGTACAGTCCTAGGCGG 61.393 65.000 2.96 2.80 35.87 6.13
583 620 1.392710 CCCAGGTACAGTCCTAGGCG 61.393 65.000 2.96 0.00 35.87 5.52
584 621 2.517609 CCCAGGTACAGTCCTAGGC 58.482 63.158 2.96 0.00 35.87 3.93
585 622 1.049289 GGCCCAGGTACAGTCCTAGG 61.049 65.000 0.82 0.82 38.97 3.02
586 623 1.392710 CGGCCCAGGTACAGTCCTAG 61.393 65.000 0.00 0.00 35.87 3.02
587 624 1.380785 CGGCCCAGGTACAGTCCTA 60.381 63.158 0.00 0.00 35.87 2.94
588 625 2.683933 CGGCCCAGGTACAGTCCT 60.684 66.667 0.00 0.00 38.51 3.85
589 626 4.468689 GCGGCCCAGGTACAGTCC 62.469 72.222 0.00 0.00 0.00 3.85
590 627 4.814294 CGCGGCCCAGGTACAGTC 62.814 72.222 0.00 0.00 0.00 3.51
592 629 4.514577 CTCGCGGCCCAGGTACAG 62.515 72.222 6.13 0.00 0.00 2.74
625 662 4.657824 ACGGGTCGTGCCTTGTCG 62.658 66.667 0.00 0.00 39.18 4.35
626 663 0.600782 TAAACGGGTCGTGCCTTGTC 60.601 55.000 0.00 0.00 39.99 3.18
627 664 0.035739 ATAAACGGGTCGTGCCTTGT 59.964 50.000 0.00 0.00 39.99 3.16
628 665 1.161843 AATAAACGGGTCGTGCCTTG 58.838 50.000 0.00 0.00 39.99 3.61
629 666 1.900245 AAATAAACGGGTCGTGCCTT 58.100 45.000 0.00 0.00 39.99 4.35
630 667 1.900245 AAAATAAACGGGTCGTGCCT 58.100 45.000 0.00 0.00 39.99 4.75
631 668 2.710220 AAAAATAAACGGGTCGTGCC 57.290 45.000 0.00 0.00 39.99 5.01
658 695 8.704668 CCTTATAGACTATTTTGGGCCATTTTT 58.295 33.333 7.26 0.00 0.00 1.94
659 696 7.202001 GCCTTATAGACTATTTTGGGCCATTTT 60.202 37.037 7.26 0.00 0.00 1.82
660 697 6.267699 GCCTTATAGACTATTTTGGGCCATTT 59.732 38.462 7.26 0.00 0.00 2.32
661 698 5.775195 GCCTTATAGACTATTTTGGGCCATT 59.225 40.000 7.26 0.00 0.00 3.16
662 699 5.325239 GCCTTATAGACTATTTTGGGCCAT 58.675 41.667 7.26 0.00 0.00 4.40
663 700 4.725490 GCCTTATAGACTATTTTGGGCCA 58.275 43.478 0.00 0.00 0.00 5.36
665 702 4.986783 AGGCCTTATAGACTATTTTGGGC 58.013 43.478 18.43 18.43 38.87 5.36
666 703 8.990163 TTTTAGGCCTTATAGACTATTTTGGG 57.010 34.615 12.58 0.31 0.00 4.12
668 705 9.952188 GCTTTTTAGGCCTTATAGACTATTTTG 57.048 33.333 12.58 0.00 0.00 2.44
669 706 9.695155 TGCTTTTTAGGCCTTATAGACTATTTT 57.305 29.630 12.58 0.00 0.00 1.82
670 707 9.121658 GTGCTTTTTAGGCCTTATAGACTATTT 57.878 33.333 12.58 0.00 0.00 1.40
671 708 7.720074 GGTGCTTTTTAGGCCTTATAGACTATT 59.280 37.037 12.58 0.00 0.00 1.73
672 709 7.225011 GGTGCTTTTTAGGCCTTATAGACTAT 58.775 38.462 12.58 0.00 0.00 2.12
673 710 6.408891 GGGTGCTTTTTAGGCCTTATAGACTA 60.409 42.308 12.58 0.00 0.00 2.59
674 711 5.437946 GGTGCTTTTTAGGCCTTATAGACT 58.562 41.667 12.58 0.00 0.00 3.24
675 712 4.579340 GGGTGCTTTTTAGGCCTTATAGAC 59.421 45.833 12.58 0.00 0.00 2.59
676 713 4.477213 AGGGTGCTTTTTAGGCCTTATAGA 59.523 41.667 12.58 0.00 0.00 1.98
677 714 4.580580 CAGGGTGCTTTTTAGGCCTTATAG 59.419 45.833 12.58 5.60 0.00 1.31
678 715 4.532834 CAGGGTGCTTTTTAGGCCTTATA 58.467 43.478 12.58 0.00 0.00 0.98
679 716 3.365472 CAGGGTGCTTTTTAGGCCTTAT 58.635 45.455 12.58 0.00 0.00 1.73
680 717 2.802719 CAGGGTGCTTTTTAGGCCTTA 58.197 47.619 12.58 0.00 0.00 2.69
681 718 1.632589 CAGGGTGCTTTTTAGGCCTT 58.367 50.000 12.58 0.00 0.00 4.35
682 719 0.900182 GCAGGGTGCTTTTTAGGCCT 60.900 55.000 11.78 11.78 40.96 5.19
683 720 1.591703 GCAGGGTGCTTTTTAGGCC 59.408 57.895 0.00 0.00 40.96 5.19
684 721 1.184970 TGGCAGGGTGCTTTTTAGGC 61.185 55.000 0.00 0.00 44.28 3.93
685 722 0.603065 GTGGCAGGGTGCTTTTTAGG 59.397 55.000 0.00 0.00 44.28 2.69
686 723 0.240945 CGTGGCAGGGTGCTTTTTAG 59.759 55.000 0.00 0.00 44.28 1.85
687 724 1.801309 GCGTGGCAGGGTGCTTTTTA 61.801 55.000 9.49 0.00 44.28 1.52
688 725 3.128375 CGTGGCAGGGTGCTTTTT 58.872 55.556 0.00 0.00 44.28 1.94
689 726 3.605664 GCGTGGCAGGGTGCTTTT 61.606 61.111 9.49 0.00 44.28 2.27
701 738 4.418401 CACATTTGGCCCGCGTGG 62.418 66.667 8.42 8.42 37.09 4.94
708 745 4.067913 CCACCGGCACATTTGGCC 62.068 66.667 0.00 0.00 45.66 5.36
709 746 4.067913 CCCACCGGCACATTTGGC 62.068 66.667 0.00 0.00 44.96 4.52
726 763 3.788766 CACTGTAAGCGTGCCGGC 61.789 66.667 22.73 22.73 37.60 6.13
731 768 1.207593 GCAAGGCACTGTAAGCGTG 59.792 57.895 0.00 0.00 40.86 5.34
732 769 1.966451 GGCAAGGCACTGTAAGCGT 60.966 57.895 0.00 0.00 40.86 5.07
733 770 1.672356 AGGCAAGGCACTGTAAGCG 60.672 57.895 0.00 0.00 40.86 4.68
734 771 1.589716 CCAGGCAAGGCACTGTAAGC 61.590 60.000 0.00 0.00 40.86 3.09
735 772 0.962356 CCCAGGCAAGGCACTGTAAG 60.962 60.000 0.00 0.00 40.86 2.34
736 773 1.074775 CCCAGGCAAGGCACTGTAA 59.925 57.895 0.00 0.00 40.86 2.41
737 774 2.756400 CCCAGGCAAGGCACTGTA 59.244 61.111 0.00 0.00 40.86 2.74
745 782 3.379445 CTGCAAGGCCCAGGCAAG 61.379 66.667 11.50 0.38 44.11 4.01
746 783 3.873679 CTCTGCAAGGCCCAGGCAA 62.874 63.158 11.50 5.63 44.11 4.52
747 784 4.355720 CTCTGCAAGGCCCAGGCA 62.356 66.667 11.50 12.39 44.11 4.75
748 785 3.991725 CTCTCTGCAAGGCCCAGGC 62.992 68.421 0.00 0.00 41.06 4.85
749 786 2.134630 AACTCTCTGCAAGGCCCAGG 62.135 60.000 0.00 0.00 0.00 4.45
750 787 0.615331 TAACTCTCTGCAAGGCCCAG 59.385 55.000 0.00 0.00 0.00 4.45
751 788 1.289160 ATAACTCTCTGCAAGGCCCA 58.711 50.000 0.00 0.00 0.00 5.36
752 789 2.803492 CGTATAACTCTCTGCAAGGCCC 60.803 54.545 0.00 0.00 0.00 5.80
753 790 2.100916 TCGTATAACTCTCTGCAAGGCC 59.899 50.000 0.00 0.00 0.00 5.19
754 791 3.438297 TCGTATAACTCTCTGCAAGGC 57.562 47.619 0.00 0.00 0.00 4.35
755 792 4.038042 TGGATCGTATAACTCTCTGCAAGG 59.962 45.833 0.00 0.00 0.00 3.61
756 793 5.188327 TGGATCGTATAACTCTCTGCAAG 57.812 43.478 0.00 0.00 0.00 4.01
757 794 5.791336 ATGGATCGTATAACTCTCTGCAA 57.209 39.130 0.00 0.00 0.00 4.08
758 795 7.829706 AGTATATGGATCGTATAACTCTCTGCA 59.170 37.037 0.00 0.00 0.00 4.41
759 796 8.215926 AGTATATGGATCGTATAACTCTCTGC 57.784 38.462 0.00 0.00 0.00 4.26
763 800 8.828644 CGCTTAGTATATGGATCGTATAACTCT 58.171 37.037 0.00 0.00 0.00 3.24
764 801 8.610896 ACGCTTAGTATATGGATCGTATAACTC 58.389 37.037 0.00 0.00 0.00 3.01
765 802 8.396390 CACGCTTAGTATATGGATCGTATAACT 58.604 37.037 0.00 0.00 0.00 2.24
766 803 7.165483 GCACGCTTAGTATATGGATCGTATAAC 59.835 40.741 0.00 0.00 0.00 1.89
767 804 7.066645 AGCACGCTTAGTATATGGATCGTATAA 59.933 37.037 0.00 0.00 0.00 0.98
768 805 6.541278 AGCACGCTTAGTATATGGATCGTATA 59.459 38.462 0.00 0.00 0.00 1.47
769 806 5.357314 AGCACGCTTAGTATATGGATCGTAT 59.643 40.000 0.00 0.00 0.00 3.06
770 807 4.698780 AGCACGCTTAGTATATGGATCGTA 59.301 41.667 0.00 0.00 0.00 3.43
784 821 2.048597 CCCACGACAGCACGCTTA 60.049 61.111 0.00 0.00 36.70 3.09
833 870 7.381139 TGTGAACTTTTTATTTTTCGATGAGGC 59.619 33.333 0.00 0.00 0.00 4.70
840 877 6.117542 GCGGTTGTGAACTTTTTATTTTTCG 58.882 36.000 0.00 0.00 0.00 3.46
847 884 2.288458 CGAGGCGGTTGTGAACTTTTTA 59.712 45.455 0.00 0.00 0.00 1.52
870 907 1.134965 CGGAAAGGAGCGAGATGTTCT 60.135 52.381 0.00 0.00 0.00 3.01
872 909 0.108138 CCGGAAAGGAGCGAGATGTT 60.108 55.000 0.00 0.00 45.00 2.71
873 910 1.517832 CCGGAAAGGAGCGAGATGT 59.482 57.895 0.00 0.00 45.00 3.06
874 911 1.884926 GCCGGAAAGGAGCGAGATG 60.885 63.158 5.05 0.00 45.00 2.90
875 912 2.501610 GCCGGAAAGGAGCGAGAT 59.498 61.111 5.05 0.00 45.00 2.75
895 933 3.186047 GTCTGCGCGGCGTATTGT 61.186 61.111 24.46 0.00 0.00 2.71
939 977 3.612371 GAGGCGGCGCTAGGTATCG 62.612 68.421 32.30 0.56 0.00 2.92
940 978 2.258897 GAGGCGGCGCTAGGTATC 59.741 66.667 32.30 13.09 0.00 2.24
1055 1099 1.141019 TAAGGACTCCATCGTGCGC 59.859 57.895 0.00 0.00 0.00 6.09
1062 1106 3.090219 GCGGGCGTAAGGACTCCAT 62.090 63.158 0.00 0.00 31.48 3.41
1283 1327 1.153147 GGCTTGGGATCCGTCTTCC 60.153 63.158 5.45 0.00 0.00 3.46
1308 1352 0.959553 GGATCGGCTCTGGATTCGTA 59.040 55.000 0.00 0.00 0.00 3.43
1412 1456 1.299976 GACAGGGTCGCAGGGAAAT 59.700 57.895 0.00 0.00 0.00 2.17
1458 1502 1.599542 GTATCCAATCAGAACAGCGCC 59.400 52.381 2.29 0.00 0.00 6.53
1485 1529 2.987413 TGCTAATTTGACGCACAAGG 57.013 45.000 0.00 0.00 39.77 3.61
1565 1610 8.549777 TTATTTGCAAGTACAAAGTAACAACG 57.450 30.769 0.46 0.00 42.45 4.10
1600 1645 3.214328 CGGGCTTGCTAATTATCCAAGT 58.786 45.455 19.15 0.00 38.50 3.16
1601 1646 3.214328 ACGGGCTTGCTAATTATCCAAG 58.786 45.455 16.10 16.10 39.08 3.61
1605 1650 4.632538 AACAACGGGCTTGCTAATTATC 57.367 40.909 0.00 0.00 32.41 1.75
1651 1696 3.181477 TGCACAATTACTTGCAGCAAAGT 60.181 39.130 9.65 11.62 43.79 2.66
1661 1706 3.128589 CCCGTAGCATTGCACAATTACTT 59.871 43.478 11.91 0.00 0.00 2.24
1680 1725 2.283351 CGATAAAAACCGTAAGAGCCCG 59.717 50.000 0.00 0.00 43.02 6.13
1837 1882 3.357203 ACCGAGCATAAAGAGTCTGAGA 58.643 45.455 0.00 0.00 0.00 3.27
1863 1908 1.890041 CGCAGACACGACCCCAAAA 60.890 57.895 0.00 0.00 34.06 2.44
1903 1948 1.201647 CAGGCAGCAGAAATCAACCAG 59.798 52.381 0.00 0.00 0.00 4.00
1979 2024 4.248859 ACCATCATAAGCGATGCACTATC 58.751 43.478 0.00 0.00 41.27 2.08
1992 2037 4.395854 GTCAGCACACATCAACCATCATAA 59.604 41.667 0.00 0.00 0.00 1.90
2067 2112 3.996363 TGACAACCTGATCTGAATCAACG 59.004 43.478 0.38 0.00 41.33 4.10
2140 2185 5.106555 ACTGATTATCACAAACAGGCGAAAG 60.107 40.000 0.00 0.00 33.57 2.62
2156 2201 2.170397 TGATCCGGTGCACACTGATTAT 59.830 45.455 20.43 1.54 40.06 1.28
2167 2212 1.142748 CCTGAGACTGATCCGGTGC 59.857 63.158 0.00 0.00 0.00 5.01
2211 2256 0.328258 TAACCCCAGAGAGCTTTGCC 59.672 55.000 0.00 0.00 0.00 4.52
2253 2298 3.376859 TCTTGCTATTAAACACATGGCCG 59.623 43.478 0.00 0.00 0.00 6.13
2302 2347 8.908786 TTCTTAAAGCTCATCTCTCTTTTTCA 57.091 30.769 0.00 0.00 32.85 2.69
2303 2348 9.213799 TCTTCTTAAAGCTCATCTCTCTTTTTC 57.786 33.333 0.00 0.00 32.85 2.29
2304 2349 9.218440 CTCTTCTTAAAGCTCATCTCTCTTTTT 57.782 33.333 0.00 0.00 32.85 1.94
2362 2407 7.233389 TCTCTACTACACAGCAATCTTTTCT 57.767 36.000 0.00 0.00 0.00 2.52
2451 2497 4.520179 CTCCCATCTTGATGACATCAACA 58.480 43.478 23.89 16.23 43.84 3.33
2515 2561 3.756434 TCCACGGATTTTGAGATTCCAAC 59.244 43.478 0.00 0.00 0.00 3.77
2524 2570 4.224147 TGAGAATACCTCCACGGATTTTGA 59.776 41.667 0.00 0.00 41.25 2.69
2556 2602 3.065925 GCATAAGATTGACTTGCACTCCC 59.934 47.826 0.00 0.00 39.38 4.30
2557 2603 3.944015 AGCATAAGATTGACTTGCACTCC 59.056 43.478 0.00 0.00 39.38 3.85
2633 2679 5.045942 TGTCTGTATGTTCCATGCCTAGAAA 60.046 40.000 0.00 0.00 0.00 2.52
2747 2793 0.103572 ATTTCCAAGCCATGATGCGC 59.896 50.000 0.00 0.00 36.02 6.09
2807 2853 2.970379 ATGACGGTCATGGCCAGCA 61.970 57.895 22.09 13.82 35.43 4.41


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

AutoCloner maintained by Alex Coulton.