Multiple sequence alignment - TraesCS3D01G436100

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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 TraesCS3D01G436100 chr3D 100.000 3077 0 0 1 3077 548246163 548249239 0 5683
1 TraesCS3D01G436100 chr3B 92.623 2562 121 29 536 3077 725706878 725709391 0 3622
2 TraesCS3D01G436100 chr3B 94.456 487 27 0 1 487 725706390 725706876 0 750
3 TraesCS3D01G436100 chr3A 91.966 2564 111 38 536 3077 685119361 685121851 0 3506
4 TraesCS3D01G436100 chr3A 94.262 488 27 1 1 487 685118872 685119359 0 745


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 TraesCS3D01G436100 chr3D 548246163 548249239 3076 False 5683.0 5683 100.0000 1 3077 1 chr3D.!!$F1 3076
1 TraesCS3D01G436100 chr3B 725706390 725709391 3001 False 2186.0 3622 93.5395 1 3077 2 chr3B.!!$F1 3076
2 TraesCS3D01G436100 chr3A 685118872 685121851 2979 False 2125.5 3506 93.1140 1 3077 2 chr3A.!!$F1 3076

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
781 786 0.315568 GACGACCAGAAGACTGCAGT 59.684 55.0 21.88 21.88 42.25 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 2337 0.320374 CGAGAGGGTAGTGCCAAACA 59.68 55.0 0.0 0.0 39.65 2.83 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
253 254 3.403038 TGAAAGCCAGACAAAGCTAGTC 58.597 45.455 10.41 10.41 38.74 2.59
260 261 3.993081 CCAGACAAAGCTAGTCAACTCAG 59.007 47.826 18.22 4.40 38.46 3.35
303 304 4.127171 TGTAAACTCTTGACCAGCTGTTC 58.873 43.478 13.81 8.93 0.00 3.18
362 364 6.389830 TGACATGCTGACACTAATTTGTTT 57.610 33.333 0.00 0.00 0.00 2.83
368 370 7.928908 TGCTGACACTAATTTGTTTCATTTC 57.071 32.000 8.89 3.89 0.00 2.17
416 418 1.000496 GCGGAATAGTTCTCCTACGGG 60.000 57.143 0.00 0.00 0.00 5.28
448 450 2.324330 CGCGGCTGTGATTTGGTCA 61.324 57.895 0.00 0.00 0.00 4.02
487 489 8.951787 ATTATGTAGTATTTTAAGTGCGGTGA 57.048 30.769 0.00 0.00 0.00 4.02
488 490 8.774890 TTATGTAGTATTTTAAGTGCGGTGAA 57.225 30.769 0.00 0.00 0.00 3.18
490 492 6.457355 TGTAGTATTTTAAGTGCGGTGAAGA 58.543 36.000 0.00 0.00 0.00 2.87
492 494 7.604927 TGTAGTATTTTAAGTGCGGTGAAGAAT 59.395 33.333 0.00 0.00 0.00 2.40
493 495 7.448748 AGTATTTTAAGTGCGGTGAAGAATT 57.551 32.000 0.00 0.00 0.00 2.17
494 496 8.556213 AGTATTTTAAGTGCGGTGAAGAATTA 57.444 30.769 0.00 0.00 0.00 1.40
495 497 9.174166 AGTATTTTAAGTGCGGTGAAGAATTAT 57.826 29.630 0.00 0.00 0.00 1.28
496 498 9.783256 GTATTTTAAGTGCGGTGAAGAATTATT 57.217 29.630 0.00 0.00 0.00 1.40
498 500 9.705290 ATTTTAAGTGCGGTGAAGAATTATTTT 57.295 25.926 0.00 0.00 0.00 1.82
499 501 9.535878 TTTTAAGTGCGGTGAAGAATTATTTTT 57.464 25.926 0.00 0.00 0.00 1.94
500 502 8.514136 TTAAGTGCGGTGAAGAATTATTTTTG 57.486 30.769 0.00 0.00 0.00 2.44
501 503 4.923281 AGTGCGGTGAAGAATTATTTTTGC 59.077 37.500 0.00 0.00 0.00 3.68
502 504 3.917380 TGCGGTGAAGAATTATTTTTGCG 59.083 39.130 0.00 0.00 0.00 4.85
503 505 3.917985 GCGGTGAAGAATTATTTTTGCGT 59.082 39.130 0.00 0.00 0.00 5.24
504 506 5.090083 GCGGTGAAGAATTATTTTTGCGTA 58.910 37.500 0.00 0.00 0.00 4.42
505 507 5.227184 GCGGTGAAGAATTATTTTTGCGTAG 59.773 40.000 0.00 0.00 0.00 3.51
506 508 6.539324 CGGTGAAGAATTATTTTTGCGTAGA 58.461 36.000 0.00 0.00 0.00 2.59
507 509 7.018826 CGGTGAAGAATTATTTTTGCGTAGAA 58.981 34.615 0.00 0.00 0.00 2.10
508 510 7.216317 CGGTGAAGAATTATTTTTGCGTAGAAG 59.784 37.037 0.00 0.00 0.00 2.85
509 511 8.021396 GGTGAAGAATTATTTTTGCGTAGAAGT 58.979 33.333 0.00 0.00 0.00 3.01
510 512 8.840867 GTGAAGAATTATTTTTGCGTAGAAGTG 58.159 33.333 0.00 0.00 0.00 3.16
511 513 8.564574 TGAAGAATTATTTTTGCGTAGAAGTGT 58.435 29.630 0.00 0.00 0.00 3.55
512 514 8.728088 AAGAATTATTTTTGCGTAGAAGTGTG 57.272 30.769 0.00 0.00 0.00 3.82
513 515 7.305474 AGAATTATTTTTGCGTAGAAGTGTGG 58.695 34.615 0.00 0.00 0.00 4.17
514 516 6.569179 ATTATTTTTGCGTAGAAGTGTGGT 57.431 33.333 0.00 0.00 0.00 4.16
515 517 3.684103 TTTTTGCGTAGAAGTGTGGTG 57.316 42.857 0.00 0.00 0.00 4.17
516 518 2.319136 TTTGCGTAGAAGTGTGGTGT 57.681 45.000 0.00 0.00 0.00 4.16
517 519 3.455990 TTTGCGTAGAAGTGTGGTGTA 57.544 42.857 0.00 0.00 0.00 2.90
518 520 3.455990 TTGCGTAGAAGTGTGGTGTAA 57.544 42.857 0.00 0.00 0.00 2.41
519 521 3.021269 TGCGTAGAAGTGTGGTGTAAG 57.979 47.619 0.00 0.00 0.00 2.34
520 522 2.624364 TGCGTAGAAGTGTGGTGTAAGA 59.376 45.455 0.00 0.00 0.00 2.10
521 523 3.068448 TGCGTAGAAGTGTGGTGTAAGAA 59.932 43.478 0.00 0.00 0.00 2.52
522 524 3.673809 GCGTAGAAGTGTGGTGTAAGAAG 59.326 47.826 0.00 0.00 0.00 2.85
523 525 4.795308 GCGTAGAAGTGTGGTGTAAGAAGT 60.795 45.833 0.00 0.00 0.00 3.01
524 526 5.287226 CGTAGAAGTGTGGTGTAAGAAGTT 58.713 41.667 0.00 0.00 0.00 2.66
525 527 5.751990 CGTAGAAGTGTGGTGTAAGAAGTTT 59.248 40.000 0.00 0.00 0.00 2.66
526 528 6.257193 CGTAGAAGTGTGGTGTAAGAAGTTTT 59.743 38.462 0.00 0.00 0.00 2.43
527 529 7.201582 CGTAGAAGTGTGGTGTAAGAAGTTTTT 60.202 37.037 0.00 0.00 0.00 1.94
547 549 1.745232 TCTTTTGCGTGGAAGTGTGT 58.255 45.000 0.00 0.00 0.00 3.72
558 560 5.732247 GCGTGGAAGTGTGTTGTAAGAATTT 60.732 40.000 0.00 0.00 0.00 1.82
559 561 6.262601 CGTGGAAGTGTGTTGTAAGAATTTT 58.737 36.000 0.00 0.00 0.00 1.82
561 563 7.911205 CGTGGAAGTGTGTTGTAAGAATTTTAA 59.089 33.333 0.00 0.00 0.00 1.52
568 570 9.406828 GTGTGTTGTAAGAATTTTAAATCTCCC 57.593 33.333 0.00 0.00 0.00 4.30
569 571 9.362151 TGTGTTGTAAGAATTTTAAATCTCCCT 57.638 29.630 0.00 0.00 0.00 4.20
582 584 2.496899 TCTCCCTCTGGAACAAATGC 57.503 50.000 0.00 0.00 41.17 3.56
584 586 0.322456 TCCCTCTGGAACAAATGCGG 60.322 55.000 0.00 0.00 38.70 5.69
585 587 0.322456 CCCTCTGGAACAAATGCGGA 60.322 55.000 0.00 0.00 38.70 5.54
588 590 2.559698 TCTGGAACAAATGCGGAGAA 57.440 45.000 0.00 0.00 38.70 2.87
601 603 3.420893 TGCGGAGAAATGTTCAAGGAAT 58.579 40.909 0.00 0.00 0.00 3.01
606 608 5.405797 GGAGAAATGTTCAAGGAATTGCTC 58.594 41.667 0.00 0.00 35.87 4.26
613 615 4.402155 TGTTCAAGGAATTGCTCTGTTTGT 59.598 37.500 0.00 0.00 0.00 2.83
620 622 5.047802 AGGAATTGCTCTGTTTGTACATTGG 60.048 40.000 0.00 0.00 32.86 3.16
622 624 4.829064 TTGCTCTGTTTGTACATTGGTC 57.171 40.909 0.00 0.00 32.86 4.02
650 654 8.190784 AGTTAATAATGAAAAGAATTCCCTGCG 58.809 33.333 0.65 0.00 0.00 5.18
654 658 2.288152 TGAAAAGAATTCCCTGCGTTGC 60.288 45.455 0.65 0.00 0.00 4.17
658 662 1.270550 AGAATTCCCTGCGTTGCTTTG 59.729 47.619 0.65 0.00 0.00 2.77
672 676 0.449388 GCTTTGGCTGGATCTGTTCG 59.551 55.000 0.00 0.00 35.22 3.95
682 686 1.412710 GGATCTGTTCGGCTCCACATA 59.587 52.381 0.00 0.00 0.00 2.29
683 687 2.158957 GGATCTGTTCGGCTCCACATAA 60.159 50.000 0.00 0.00 0.00 1.90
684 688 3.531538 GATCTGTTCGGCTCCACATAAA 58.468 45.455 0.00 0.00 0.00 1.40
685 689 2.972625 TCTGTTCGGCTCCACATAAAG 58.027 47.619 0.00 0.00 0.00 1.85
686 690 2.565391 TCTGTTCGGCTCCACATAAAGA 59.435 45.455 0.00 0.00 0.00 2.52
687 691 2.673368 CTGTTCGGCTCCACATAAAGAC 59.327 50.000 0.00 0.00 0.00 3.01
688 692 2.007608 GTTCGGCTCCACATAAAGACC 58.992 52.381 0.00 0.00 0.00 3.85
689 693 0.539986 TCGGCTCCACATAAAGACCC 59.460 55.000 0.00 0.00 0.00 4.46
694 698 0.981183 TCCACATAAAGACCCGCTGT 59.019 50.000 0.00 0.00 0.00 4.40
696 700 0.447801 CACATAAAGACCCGCTGTGC 59.552 55.000 0.00 0.00 31.81 4.57
718 722 4.038042 GCTATTTTCCTTCCCCTTATGTGC 59.962 45.833 0.00 0.00 0.00 4.57
728 733 5.652994 TCCCCTTATGTGCAAACATAAAC 57.347 39.130 11.31 0.00 40.67 2.01
738 743 2.231235 GCAAACATAAACCCCTGTGAGG 59.769 50.000 0.00 0.00 34.30 3.86
741 746 3.652057 ACATAAACCCCTGTGAGGATG 57.348 47.619 0.00 0.00 37.67 3.51
748 753 1.492176 CCCCTGTGAGGATGCAGTAAT 59.508 52.381 0.00 0.00 37.67 1.89
752 757 4.818546 CCCTGTGAGGATGCAGTAATTTAG 59.181 45.833 0.00 0.00 37.67 1.85
757 762 3.217626 AGGATGCAGTAATTTAGCAGGC 58.782 45.455 0.00 0.00 42.14 4.85
758 763 2.951642 GGATGCAGTAATTTAGCAGGCA 59.048 45.455 0.00 0.00 42.14 4.75
760 765 3.071874 TGCAGTAATTTAGCAGGCAGT 57.928 42.857 0.00 0.00 33.75 4.40
761 766 3.009723 TGCAGTAATTTAGCAGGCAGTC 58.990 45.455 0.00 0.00 33.75 3.51
762 767 2.030946 GCAGTAATTTAGCAGGCAGTCG 59.969 50.000 0.00 0.00 0.00 4.18
763 768 3.521560 CAGTAATTTAGCAGGCAGTCGA 58.478 45.455 0.00 0.00 0.00 4.20
764 769 3.307242 CAGTAATTTAGCAGGCAGTCGAC 59.693 47.826 7.70 7.70 0.00 4.20
765 770 1.359848 AATTTAGCAGGCAGTCGACG 58.640 50.000 10.46 6.47 0.00 5.12
766 771 0.530744 ATTTAGCAGGCAGTCGACGA 59.469 50.000 10.46 0.00 0.00 4.20
767 772 0.388134 TTTAGCAGGCAGTCGACGAC 60.388 55.000 20.25 20.25 0.00 4.34
768 773 2.209064 TTAGCAGGCAGTCGACGACC 62.209 60.000 23.76 18.86 32.18 4.79
769 774 4.357947 GCAGGCAGTCGACGACCA 62.358 66.667 23.76 0.00 32.18 4.02
770 775 2.126307 CAGGCAGTCGACGACCAG 60.126 66.667 23.76 17.47 32.18 4.00
772 777 1.901948 AGGCAGTCGACGACCAGAA 60.902 57.895 23.76 0.00 32.18 3.02
773 778 1.444553 GGCAGTCGACGACCAGAAG 60.445 63.158 23.76 10.36 32.18 2.85
775 780 0.729816 GCAGTCGACGACCAGAAGAC 60.730 60.000 23.76 2.93 32.18 3.01
776 781 0.875728 CAGTCGACGACCAGAAGACT 59.124 55.000 23.76 0.07 39.31 3.24
777 782 0.875728 AGTCGACGACCAGAAGACTG 59.124 55.000 23.76 0.00 43.12 3.51
778 783 0.729816 GTCGACGACCAGAAGACTGC 60.730 60.000 17.25 0.00 42.25 4.40
780 785 0.730834 CGACGACCAGAAGACTGCAG 60.731 60.000 13.48 13.48 42.25 4.41
781 786 0.315568 GACGACCAGAAGACTGCAGT 59.684 55.000 21.88 21.88 42.25 4.40
822 838 6.704493 GTGAGTTGATTACTGGTGAGTTTACA 59.296 38.462 0.00 0.00 37.17 2.41
823 839 7.387948 GTGAGTTGATTACTGGTGAGTTTACAT 59.612 37.037 0.00 0.00 37.17 2.29
824 840 7.936847 TGAGTTGATTACTGGTGAGTTTACATT 59.063 33.333 0.00 0.00 37.17 2.71
825 841 8.324163 AGTTGATTACTGGTGAGTTTACATTC 57.676 34.615 0.00 0.00 35.19 2.67
826 842 6.961359 TGATTACTGGTGAGTTTACATTCG 57.039 37.500 0.00 0.00 33.21 3.34
827 843 6.460781 TGATTACTGGTGAGTTTACATTCGT 58.539 36.000 0.00 0.00 33.21 3.85
828 844 6.588756 TGATTACTGGTGAGTTTACATTCGTC 59.411 38.462 0.00 0.00 33.21 4.20
829 845 4.602340 ACTGGTGAGTTTACATTCGTCT 57.398 40.909 0.00 0.00 0.00 4.18
830 846 5.717078 ACTGGTGAGTTTACATTCGTCTA 57.283 39.130 0.00 0.00 0.00 2.59
831 847 6.092955 ACTGGTGAGTTTACATTCGTCTAA 57.907 37.500 0.00 0.00 0.00 2.10
832 848 6.698380 ACTGGTGAGTTTACATTCGTCTAAT 58.302 36.000 0.00 0.00 0.00 1.73
833 849 7.159372 ACTGGTGAGTTTACATTCGTCTAATT 58.841 34.615 0.00 0.00 0.00 1.40
834 850 7.660208 ACTGGTGAGTTTACATTCGTCTAATTT 59.340 33.333 0.00 0.00 0.00 1.82
835 851 7.802738 TGGTGAGTTTACATTCGTCTAATTTG 58.197 34.615 0.00 0.00 0.00 2.32
836 852 6.741358 GGTGAGTTTACATTCGTCTAATTTGC 59.259 38.462 0.00 0.00 0.00 3.68
841 857 8.730680 AGTTTACATTCGTCTAATTTGCAGATT 58.269 29.630 7.70 7.70 0.00 2.40
863 879 8.637099 AGATTTCAAGGAAAAGGAGAAAGAAAG 58.363 33.333 0.00 0.00 35.11 2.62
864 880 7.954666 TTTCAAGGAAAAGGAGAAAGAAAGA 57.045 32.000 0.00 0.00 0.00 2.52
866 882 5.527582 TCAAGGAAAAGGAGAAAGAAAGACG 59.472 40.000 0.00 0.00 0.00 4.18
870 886 2.464157 AGGAGAAAGAAAGACGGCAG 57.536 50.000 0.00 0.00 0.00 4.85
986 1004 3.959991 GAAGAGGGGGCACAGCGTC 62.960 68.421 0.00 0.00 0.00 5.19
1003 1021 2.039418 CGTCTGGGGGTGAGATAATGA 58.961 52.381 0.00 0.00 0.00 2.57
1004 1022 2.036475 CGTCTGGGGGTGAGATAATGAG 59.964 54.545 0.00 0.00 0.00 2.90
1005 1023 2.050144 TCTGGGGGTGAGATAATGAGC 58.950 52.381 0.00 0.00 0.00 4.26
1006 1024 1.770658 CTGGGGGTGAGATAATGAGCA 59.229 52.381 0.00 0.00 0.00 4.26
1007 1025 1.770658 TGGGGGTGAGATAATGAGCAG 59.229 52.381 0.00 0.00 0.00 4.24
1008 1026 1.544314 GGGGGTGAGATAATGAGCAGC 60.544 57.143 0.00 0.00 0.00 5.25
1009 1027 1.141657 GGGGTGAGATAATGAGCAGCA 59.858 52.381 0.00 0.00 0.00 4.41
1010 1028 2.492012 GGGTGAGATAATGAGCAGCAG 58.508 52.381 0.00 0.00 0.00 4.24
1011 1029 1.872313 GGTGAGATAATGAGCAGCAGC 59.128 52.381 0.00 0.00 42.56 5.25
1148 1172 2.268280 CTGGGAGAGCAGTGGCAG 59.732 66.667 0.00 0.00 44.61 4.85
1325 1351 2.093500 TGTCTGAGGAATTGGGATGACG 60.093 50.000 0.00 0.00 0.00 4.35
1329 1355 0.749454 AGGAATTGGGATGACGCTGC 60.749 55.000 0.00 0.00 0.00 5.25
1350 1376 3.492011 GCAGTGAAATTGTTTTGCAGGAG 59.508 43.478 0.00 0.00 0.00 3.69
1483 1509 8.615878 TTTAGCTAAAAGTTGTGCTGATTCTA 57.384 30.769 16.53 0.00 37.02 2.10
1762 1790 4.629092 GGATCGAGTAGTTCCATTAACCC 58.371 47.826 0.00 0.00 39.03 4.11
1766 1794 5.461327 TCGAGTAGTTCCATTAACCCCTAT 58.539 41.667 0.00 0.00 39.03 2.57
1787 1815 7.397221 CCTATTCCTCCTATTTACATGCATCA 58.603 38.462 0.00 0.00 0.00 3.07
1788 1816 8.051535 CCTATTCCTCCTATTTACATGCATCAT 58.948 37.037 0.00 0.00 0.00 2.45
1789 1817 7.934855 ATTCCTCCTATTTACATGCATCATC 57.065 36.000 0.00 0.00 0.00 2.92
1790 1818 6.692849 TCCTCCTATTTACATGCATCATCT 57.307 37.500 0.00 0.00 0.00 2.90
1805 1833 4.746089 GCATCATCTATCTGTCTTGGGCTT 60.746 45.833 0.00 0.00 0.00 4.35
1843 1871 5.482908 GACTCATGGTCTATTTGTGTCACT 58.517 41.667 4.27 0.00 41.46 3.41
2101 2129 1.086696 ATTCAGAAATGGTGGTCGCG 58.913 50.000 0.00 0.00 0.00 5.87
2125 2153 3.145286 GGCTAGATTCAGAAATGGAGGC 58.855 50.000 0.00 0.00 0.00 4.70
2266 2294 9.502091 AATTGTCAGAAAACACTATGCTACTAA 57.498 29.630 0.00 0.00 0.00 2.24
2267 2295 8.534333 TTGTCAGAAAACACTATGCTACTAAG 57.466 34.615 0.00 0.00 0.00 2.18
2268 2296 7.097192 TGTCAGAAAACACTATGCTACTAAGG 58.903 38.462 0.00 0.00 0.00 2.69
2489 2519 1.222766 GCTGATGATGAGCTGGCTCG 61.223 60.000 16.33 3.22 45.48 5.03
2496 2526 0.033228 ATGAGCTGGCTCGCTATGAC 59.967 55.000 16.33 0.00 45.48 3.06
2606 2637 9.745018 ATAACTTTCCATTCTTCTTCATCTTGA 57.255 29.630 0.00 0.00 0.00 3.02
2970 3001 6.039047 AGGAATTGAACAATCATCAGGAATCG 59.961 38.462 0.45 0.00 34.96 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
253 254 5.765182 AGATTACCTGGTTCAAACTGAGTTG 59.235 40.000 3.84 0.00 0.00 3.16
260 261 6.635030 ACAAGAAGATTACCTGGTTCAAAC 57.365 37.500 3.84 0.00 0.00 2.93
303 304 7.251704 AGTAATCCAGAAACATTAGAATGCG 57.748 36.000 2.09 0.00 40.04 4.73
362 364 2.109128 TGTACTTGCCCCCTTGAAATGA 59.891 45.455 0.00 0.00 0.00 2.57
368 370 0.625849 AGGATGTACTTGCCCCCTTG 59.374 55.000 0.00 0.00 0.00 3.61
416 418 2.704616 CGCGTCTCTCCTCGACTC 59.295 66.667 0.00 0.00 0.00 3.36
420 422 4.544689 CAGCCGCGTCTCTCCTCG 62.545 72.222 4.92 0.00 0.00 4.63
476 478 6.584563 GCAAAAATAATTCTTCACCGCACTTA 59.415 34.615 0.00 0.00 0.00 2.24
487 489 7.807907 CCACACTTCTACGCAAAAATAATTCTT 59.192 33.333 0.00 0.00 0.00 2.52
488 490 7.040686 ACCACACTTCTACGCAAAAATAATTCT 60.041 33.333 0.00 0.00 0.00 2.40
490 492 6.861055 CACCACACTTCTACGCAAAAATAATT 59.139 34.615 0.00 0.00 0.00 1.40
492 494 5.297278 ACACCACACTTCTACGCAAAAATAA 59.703 36.000 0.00 0.00 0.00 1.40
493 495 4.817464 ACACCACACTTCTACGCAAAAATA 59.183 37.500 0.00 0.00 0.00 1.40
494 496 3.630312 ACACCACACTTCTACGCAAAAAT 59.370 39.130 0.00 0.00 0.00 1.82
495 497 3.011119 ACACCACACTTCTACGCAAAAA 58.989 40.909 0.00 0.00 0.00 1.94
496 498 2.634600 ACACCACACTTCTACGCAAAA 58.365 42.857 0.00 0.00 0.00 2.44
497 499 2.319136 ACACCACACTTCTACGCAAA 57.681 45.000 0.00 0.00 0.00 3.68
498 500 3.068448 TCTTACACCACACTTCTACGCAA 59.932 43.478 0.00 0.00 0.00 4.85
499 501 2.624364 TCTTACACCACACTTCTACGCA 59.376 45.455 0.00 0.00 0.00 5.24
500 502 3.293311 TCTTACACCACACTTCTACGC 57.707 47.619 0.00 0.00 0.00 4.42
501 503 4.868067 ACTTCTTACACCACACTTCTACG 58.132 43.478 0.00 0.00 0.00 3.51
502 504 7.549615 AAAACTTCTTACACCACACTTCTAC 57.450 36.000 0.00 0.00 0.00 2.59
524 526 3.923461 CACACTTCCACGCAAAAGAAAAA 59.077 39.130 0.00 0.00 0.00 1.94
525 527 3.057174 ACACACTTCCACGCAAAAGAAAA 60.057 39.130 0.00 0.00 0.00 2.29
526 528 2.490115 ACACACTTCCACGCAAAAGAAA 59.510 40.909 0.00 0.00 0.00 2.52
527 529 2.088423 ACACACTTCCACGCAAAAGAA 58.912 42.857 0.00 0.00 0.00 2.52
528 530 1.745232 ACACACTTCCACGCAAAAGA 58.255 45.000 0.00 0.00 0.00 2.52
529 531 2.184448 CAACACACTTCCACGCAAAAG 58.816 47.619 0.00 0.00 0.00 2.27
530 532 1.542030 ACAACACACTTCCACGCAAAA 59.458 42.857 0.00 0.00 0.00 2.44
531 533 1.169577 ACAACACACTTCCACGCAAA 58.830 45.000 0.00 0.00 0.00 3.68
532 534 2.025589 TACAACACACTTCCACGCAA 57.974 45.000 0.00 0.00 0.00 4.85
533 535 1.937223 CTTACAACACACTTCCACGCA 59.063 47.619 0.00 0.00 0.00 5.24
534 536 2.206750 TCTTACAACACACTTCCACGC 58.793 47.619 0.00 0.00 0.00 5.34
535 537 5.418310 AATTCTTACAACACACTTCCACG 57.582 39.130 0.00 0.00 0.00 4.94
536 538 9.575783 TTTAAAATTCTTACAACACACTTCCAC 57.424 29.630 0.00 0.00 0.00 4.02
547 549 9.243105 CCAGAGGGAGATTTAAAATTCTTACAA 57.757 33.333 0.00 0.00 35.59 2.41
558 560 5.418840 GCATTTGTTCCAGAGGGAGATTTAA 59.581 40.000 0.00 0.00 46.01 1.52
559 561 4.949856 GCATTTGTTCCAGAGGGAGATTTA 59.050 41.667 0.00 0.00 46.01 1.40
561 563 3.359950 GCATTTGTTCCAGAGGGAGATT 58.640 45.455 0.00 0.00 46.01 2.40
568 570 2.099141 TCTCCGCATTTGTTCCAGAG 57.901 50.000 0.00 0.00 0.00 3.35
569 571 2.559698 TTCTCCGCATTTGTTCCAGA 57.440 45.000 0.00 0.00 0.00 3.86
582 584 4.082571 AGCAATTCCTTGAACATTTCTCCG 60.083 41.667 0.00 0.00 34.04 4.63
584 586 6.091437 CAGAGCAATTCCTTGAACATTTCTC 58.909 40.000 0.00 0.00 34.04 2.87
585 587 5.537674 ACAGAGCAATTCCTTGAACATTTCT 59.462 36.000 0.00 0.00 34.04 2.52
588 590 5.796424 AACAGAGCAATTCCTTGAACATT 57.204 34.783 0.00 0.00 34.04 2.71
601 603 4.203226 TGACCAATGTACAAACAGAGCAA 58.797 39.130 0.00 0.00 39.49 3.91
633 636 2.288152 GCAACGCAGGGAATTCTTTTCA 60.288 45.455 5.23 0.00 0.00 2.69
650 654 1.251251 ACAGATCCAGCCAAAGCAAC 58.749 50.000 0.00 0.00 43.56 4.17
654 658 1.089920 CCGAACAGATCCAGCCAAAG 58.910 55.000 0.00 0.00 0.00 2.77
658 662 1.522580 GAGCCGAACAGATCCAGCC 60.523 63.158 0.00 0.00 0.00 4.85
672 676 1.095807 GCGGGTCTTTATGTGGAGCC 61.096 60.000 0.00 0.00 44.01 4.70
682 686 2.200373 AAATAGCACAGCGGGTCTTT 57.800 45.000 0.00 0.00 0.00 2.52
683 687 2.084546 GAAAATAGCACAGCGGGTCTT 58.915 47.619 0.00 0.00 0.00 3.01
684 688 1.679032 GGAAAATAGCACAGCGGGTCT 60.679 52.381 0.00 0.00 0.00 3.85
685 689 0.733150 GGAAAATAGCACAGCGGGTC 59.267 55.000 0.00 0.00 0.00 4.46
686 690 0.328258 AGGAAAATAGCACAGCGGGT 59.672 50.000 0.00 0.00 0.00 5.28
687 691 1.401905 GAAGGAAAATAGCACAGCGGG 59.598 52.381 0.00 0.00 0.00 6.13
688 692 1.401905 GGAAGGAAAATAGCACAGCGG 59.598 52.381 0.00 0.00 0.00 5.52
689 693 1.401905 GGGAAGGAAAATAGCACAGCG 59.598 52.381 0.00 0.00 0.00 5.18
694 698 5.200483 CACATAAGGGGAAGGAAAATAGCA 58.800 41.667 0.00 0.00 0.00 3.49
696 700 5.200483 TGCACATAAGGGGAAGGAAAATAG 58.800 41.667 0.00 0.00 0.00 1.73
718 722 3.761897 TCCTCACAGGGGTTTATGTTTG 58.238 45.455 0.00 0.00 35.59 2.93
728 733 0.911769 TTACTGCATCCTCACAGGGG 59.088 55.000 0.00 0.00 38.25 4.79
738 743 3.629398 ACTGCCTGCTAAATTACTGCATC 59.371 43.478 0.00 0.00 36.07 3.91
741 746 2.030946 CGACTGCCTGCTAAATTACTGC 59.969 50.000 0.00 0.00 0.00 4.40
748 753 0.388134 GTCGTCGACTGCCTGCTAAA 60.388 55.000 18.09 0.00 0.00 1.85
752 757 4.357947 TGGTCGTCGACTGCCTGC 62.358 66.667 23.69 7.63 32.47 4.85
757 762 0.875728 AGTCTTCTGGTCGTCGACTG 59.124 55.000 23.69 16.62 33.99 3.51
758 763 0.875728 CAGTCTTCTGGTCGTCGACT 59.124 55.000 23.69 0.00 37.97 4.18
760 765 1.170290 TGCAGTCTTCTGGTCGTCGA 61.170 55.000 0.00 0.00 41.57 4.20
761 766 0.730834 CTGCAGTCTTCTGGTCGTCG 60.731 60.000 5.25 0.00 41.57 5.12
762 767 0.315568 ACTGCAGTCTTCTGGTCGTC 59.684 55.000 15.25 0.00 41.57 4.20
763 768 0.315568 GACTGCAGTCTTCTGGTCGT 59.684 55.000 34.54 2.84 41.65 4.34
764 769 0.315251 TGACTGCAGTCTTCTGGTCG 59.685 55.000 38.81 4.01 44.99 4.79
765 770 2.289320 ACATGACTGCAGTCTTCTGGTC 60.289 50.000 38.81 18.02 44.99 4.02
766 771 1.696336 ACATGACTGCAGTCTTCTGGT 59.304 47.619 38.81 26.07 44.99 4.00
767 772 2.469274 ACATGACTGCAGTCTTCTGG 57.531 50.000 38.81 25.52 44.99 3.86
768 773 4.309933 TGTTACATGACTGCAGTCTTCTG 58.690 43.478 38.81 32.60 44.99 3.02
769 774 4.039730 ACTGTTACATGACTGCAGTCTTCT 59.960 41.667 38.81 26.21 44.99 2.85
770 775 4.310769 ACTGTTACATGACTGCAGTCTTC 58.689 43.478 38.81 23.94 44.99 2.87
772 777 4.342862 AACTGTTACATGACTGCAGTCT 57.657 40.909 38.81 25.65 44.99 3.24
773 778 4.752101 AGAAACTGTTACATGACTGCAGTC 59.248 41.667 35.04 35.04 44.97 3.51
775 780 4.512944 ACAGAAACTGTTACATGACTGCAG 59.487 41.667 13.48 13.48 42.59 4.41
776 781 4.273235 CACAGAAACTGTTACATGACTGCA 59.727 41.667 0.00 0.00 42.59 4.41
777 782 4.511454 TCACAGAAACTGTTACATGACTGC 59.489 41.667 0.00 0.00 42.59 4.40
778 783 5.755375 ACTCACAGAAACTGTTACATGACTG 59.245 40.000 0.00 0.00 42.59 3.51
780 785 6.257849 TCAACTCACAGAAACTGTTACATGAC 59.742 38.462 0.00 0.00 42.59 3.06
781 786 6.345298 TCAACTCACAGAAACTGTTACATGA 58.655 36.000 0.00 3.25 42.59 3.07
822 838 7.121168 TCCTTGAAATCTGCAAATTAGACGAAT 59.879 33.333 0.00 0.00 0.00 3.34
823 839 6.429692 TCCTTGAAATCTGCAAATTAGACGAA 59.570 34.615 0.00 0.00 0.00 3.85
824 840 5.937540 TCCTTGAAATCTGCAAATTAGACGA 59.062 36.000 0.00 0.00 0.00 4.20
825 841 6.182039 TCCTTGAAATCTGCAAATTAGACG 57.818 37.500 0.00 0.00 0.00 4.18
826 842 8.816640 TTTTCCTTGAAATCTGCAAATTAGAC 57.183 30.769 0.00 0.00 31.34 2.59
827 843 8.090214 CCTTTTCCTTGAAATCTGCAAATTAGA 58.910 33.333 0.00 0.00 31.34 2.10
828 844 8.090214 TCCTTTTCCTTGAAATCTGCAAATTAG 58.910 33.333 0.00 0.00 31.34 1.73
829 845 7.961351 TCCTTTTCCTTGAAATCTGCAAATTA 58.039 30.769 0.00 0.00 31.34 1.40
830 846 6.829849 TCCTTTTCCTTGAAATCTGCAAATT 58.170 32.000 0.00 0.00 31.34 1.82
831 847 6.268387 TCTCCTTTTCCTTGAAATCTGCAAAT 59.732 34.615 0.00 0.00 31.34 2.32
832 848 5.598005 TCTCCTTTTCCTTGAAATCTGCAAA 59.402 36.000 0.00 0.00 31.34 3.68
833 849 5.139727 TCTCCTTTTCCTTGAAATCTGCAA 58.860 37.500 0.00 0.00 31.34 4.08
834 850 4.728772 TCTCCTTTTCCTTGAAATCTGCA 58.271 39.130 0.00 0.00 31.34 4.41
835 851 5.712152 TTCTCCTTTTCCTTGAAATCTGC 57.288 39.130 0.00 0.00 31.34 4.26
836 852 7.516198 TCTTTCTCCTTTTCCTTGAAATCTG 57.484 36.000 0.00 0.00 31.34 2.90
841 857 6.038271 CGTCTTTCTTTCTCCTTTTCCTTGAA 59.962 38.462 0.00 0.00 0.00 2.69
870 886 5.217895 GACATGTACCGTCCAGAAAATTC 57.782 43.478 0.00 0.00 0.00 2.17
986 1004 1.770658 TGCTCATTATCTCACCCCCAG 59.229 52.381 0.00 0.00 0.00 4.45
1093 1117 4.303257 GTGTGGCTTCACCCTAGC 57.697 61.111 2.86 0.00 40.53 3.42
1325 1351 2.608546 TGCAAAACAATTTCACTGCAGC 59.391 40.909 15.27 0.00 0.00 5.25
1329 1355 4.053295 CCTCCTGCAAAACAATTTCACTG 58.947 43.478 0.00 0.00 0.00 3.66
1350 1376 5.581085 GTCATACACTCCATACACAAAGTCC 59.419 44.000 0.00 0.00 0.00 3.85
1437 1463 8.209869 GCTAAAGAAACGCATGCATATAATTTG 58.790 33.333 19.57 7.72 0.00 2.32
1441 1467 6.618287 AGCTAAAGAAACGCATGCATATAA 57.382 33.333 19.57 0.00 0.00 0.98
1508 1535 4.170468 AGCCCTTCTTTTCTTCAGTTGA 57.830 40.909 0.00 0.00 0.00 3.18
1744 1772 5.803237 ATAGGGGTTAATGGAACTACTCG 57.197 43.478 0.00 0.00 38.21 4.18
1762 1790 7.397221 TGATGCATGTAAATAGGAGGAATAGG 58.603 38.462 2.46 0.00 0.00 2.57
1766 1794 7.083062 AGATGATGCATGTAAATAGGAGGAA 57.917 36.000 2.46 0.00 0.00 3.36
1787 1815 5.211973 TCAGTAAGCCCAAGACAGATAGAT 58.788 41.667 0.00 0.00 0.00 1.98
1788 1816 4.610333 TCAGTAAGCCCAAGACAGATAGA 58.390 43.478 0.00 0.00 0.00 1.98
1789 1817 5.112686 GTTCAGTAAGCCCAAGACAGATAG 58.887 45.833 0.00 0.00 0.00 2.08
1790 1818 4.381612 CGTTCAGTAAGCCCAAGACAGATA 60.382 45.833 0.00 0.00 0.00 1.98
1805 1833 3.150458 TGAGTCTTCCTCCGTTCAGTA 57.850 47.619 0.00 0.00 39.65 2.74
1839 1867 3.337605 TGTAAAGGTACTCCCCCTAGTGA 59.662 47.826 0.00 0.00 38.49 3.41
1843 1871 4.042174 CCAATGTAAAGGTACTCCCCCTA 58.958 47.826 0.00 0.00 38.49 3.53
1983 2011 3.452627 AGATGTCCATGGAGTTGTAGTCC 59.547 47.826 16.81 0.00 38.22 3.85
2101 2129 4.578105 CCTCCATTTCTGAATCTAGCCAAC 59.422 45.833 0.00 0.00 0.00 3.77
2125 2153 7.384387 CACTATCATACATGTCATCTGAACTGG 59.616 40.741 0.00 0.00 0.00 4.00
2266 2294 6.610075 ACAATTTTAGACATTTGCCATCCT 57.390 33.333 0.00 0.00 0.00 3.24
2267 2295 7.771183 TCTACAATTTTAGACATTTGCCATCC 58.229 34.615 0.00 0.00 0.00 3.51
2268 2296 8.677300 TCTCTACAATTTTAGACATTTGCCATC 58.323 33.333 0.00 0.00 0.00 3.51
2309 2337 0.320374 CGAGAGGGTAGTGCCAAACA 59.680 55.000 0.00 0.00 39.65 2.83
2317 2345 5.245526 ACTTTTGTAACATCGAGAGGGTAGT 59.754 40.000 0.00 0.00 0.00 2.73
2415 2445 1.755200 TAGGCTTCCCTTTTCACCCT 58.245 50.000 0.00 0.00 42.87 4.34
2489 2519 4.036852 GCCCCATTAGTTTCTTGTCATAGC 59.963 45.833 0.00 0.00 0.00 2.97
2496 2526 5.412286 CCAATTTTGCCCCATTAGTTTCTTG 59.588 40.000 0.00 0.00 0.00 3.02
2606 2637 2.089980 GCAGCCAACTCTTCACATCAT 58.910 47.619 0.00 0.00 0.00 2.45
2619 2650 1.841302 CTGTGACCCTAGGCAGCCAA 61.841 60.000 15.80 0.00 0.00 4.52
2970 3001 8.088365 GGCATTATTGAATGGGTAAATTCTACC 58.912 37.037 7.79 7.79 42.44 3.18


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

AutoCloner maintained by Alex Coulton.