Multiple sequence alignment - TraesCS5D01G046100

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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 TraesCS5D01G046100 chr5D 100.000 2795 0 0 1 2795 45139984 45137190 0.000000e+00 5162.0
1 TraesCS5D01G046100 chr5A 95.337 1930 65 8 889 2795 634148466 634150393 0.000000e+00 3042.0
2 TraesCS5D01G046100 chr5A 80.603 1923 334 24 901 2794 537760427 537758515 0.000000e+00 1448.0
3 TraesCS5D01G046100 chr5A 94.839 775 27 6 1 763 35804701 35803928 0.000000e+00 1197.0
4 TraesCS5D01G046100 chr2A 94.658 1928 78 7 891 2795 33552022 33550097 0.000000e+00 2966.0
5 TraesCS5D01G046100 chr4B 92.171 1405 86 7 1414 2795 458936492 458937895 0.000000e+00 1964.0
6 TraesCS5D01G046100 chr4B 80.940 1894 329 19 888 2762 630349783 630351663 0.000000e+00 1469.0
7 TraesCS5D01G046100 chr4B 95.463 529 24 0 889 1417 458931888 458932416 0.000000e+00 845.0
8 TraesCS5D01G046100 chr1D 81.499 1935 315 26 891 2794 314000502 314002424 0.000000e+00 1550.0
9 TraesCS5D01G046100 chr1D 74.293 389 94 6 1078 1464 83816831 83816447 2.880000e-35 159.0
10 TraesCS5D01G046100 chr2D 78.689 1938 368 30 890 2795 482806643 482808567 0.000000e+00 1249.0
11 TraesCS5D01G046100 chr5B 95.159 785 20 5 1 782 45035725 45034956 0.000000e+00 1223.0
12 TraesCS5D01G046100 chr5B 100.000 28 0 0 803 830 45034965 45034938 5.000000e-03 52.8
13 TraesCS5D01G046100 chr4A 81.675 573 97 3 2224 2795 618114405 618114970 1.170000e-128 470.0
14 TraesCS5D01G046100 chr4A 87.633 283 35 0 2124 2406 54386612 54386894 2.080000e-86 329.0
15 TraesCS5D01G046100 chr3A 78.416 644 138 1 2152 2795 82976572 82975930 4.310000e-113 418.0
16 TraesCS5D01G046100 chr7A 75.547 274 64 3 1078 1350 436851676 436851947 6.280000e-27 132.0
17 TraesCS5D01G046100 chr6A 80.117 171 33 1 1078 1248 536794018 536794187 2.920000e-25 126.0
18 TraesCS5D01G046100 chr6A 80.117 171 33 1 1078 1248 536797618 536797787 2.920000e-25 126.0


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 TraesCS5D01G046100 chr5D 45137190 45139984 2794 True 5162.0 5162 100.0000 1 2795 1 chr5D.!!$R1 2794
1 TraesCS5D01G046100 chr5A 634148466 634150393 1927 False 3042.0 3042 95.3370 889 2795 1 chr5A.!!$F1 1906
2 TraesCS5D01G046100 chr5A 537758515 537760427 1912 True 1448.0 1448 80.6030 901 2794 1 chr5A.!!$R2 1893
3 TraesCS5D01G046100 chr5A 35803928 35804701 773 True 1197.0 1197 94.8390 1 763 1 chr5A.!!$R1 762
4 TraesCS5D01G046100 chr2A 33550097 33552022 1925 True 2966.0 2966 94.6580 891 2795 1 chr2A.!!$R1 1904
5 TraesCS5D01G046100 chr4B 458936492 458937895 1403 False 1964.0 1964 92.1710 1414 2795 1 chr4B.!!$F2 1381
6 TraesCS5D01G046100 chr4B 630349783 630351663 1880 False 1469.0 1469 80.9400 888 2762 1 chr4B.!!$F3 1874
7 TraesCS5D01G046100 chr4B 458931888 458932416 528 False 845.0 845 95.4630 889 1417 1 chr4B.!!$F1 528
8 TraesCS5D01G046100 chr1D 314000502 314002424 1922 False 1550.0 1550 81.4990 891 2794 1 chr1D.!!$F1 1903
9 TraesCS5D01G046100 chr2D 482806643 482808567 1924 False 1249.0 1249 78.6890 890 2795 1 chr2D.!!$F1 1905
10 TraesCS5D01G046100 chr5B 45034938 45035725 787 True 637.9 1223 97.5795 1 830 2 chr5B.!!$R1 829
11 TraesCS5D01G046100 chr4A 618114405 618114970 565 False 470.0 470 81.6750 2224 2795 1 chr4A.!!$F2 571
12 TraesCS5D01G046100 chr3A 82975930 82976572 642 True 418.0 418 78.4160 2152 2795 1 chr3A.!!$R1 643

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
679 683 0.03496 GGAAGAAGAGGGTGGAAGGC 60.035 60.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2176 1.93735 TGTCTGAAGGATCTCCCCCTA 59.063 52.381 0.0 0.0 36.42 3.53 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
22 23 3.948719 TGGCCGTGGGAGGTGTTC 61.949 66.667 0.00 0.00 0.00 3.18
163 164 4.335647 AGGAGGCGGTGCACCTTG 62.336 66.667 32.28 19.50 37.77 3.61
576 580 4.778415 CCGGACGGCGAGTGTGAG 62.778 72.222 16.62 0.00 0.00 3.51
577 581 4.778415 CGGACGGCGAGTGTGAGG 62.778 72.222 16.62 0.00 0.00 3.86
578 582 4.436998 GGACGGCGAGTGTGAGGG 62.437 72.222 16.62 0.00 0.00 4.30
579 583 4.436998 GACGGCGAGTGTGAGGGG 62.437 72.222 16.62 0.00 0.00 4.79
581 585 4.003788 CGGCGAGTGTGAGGGGTT 62.004 66.667 0.00 0.00 0.00 4.11
582 586 2.430367 GGCGAGTGTGAGGGGTTT 59.570 61.111 0.00 0.00 0.00 3.27
583 587 1.966451 GGCGAGTGTGAGGGGTTTG 60.966 63.158 0.00 0.00 0.00 2.93
584 588 1.966451 GCGAGTGTGAGGGGTTTGG 60.966 63.158 0.00 0.00 0.00 3.28
585 589 1.302511 CGAGTGTGAGGGGTTTGGG 60.303 63.158 0.00 0.00 0.00 4.12
586 590 1.764571 CGAGTGTGAGGGGTTTGGGA 61.765 60.000 0.00 0.00 0.00 4.37
587 591 0.036875 GAGTGTGAGGGGTTTGGGAG 59.963 60.000 0.00 0.00 0.00 4.30
588 592 0.697854 AGTGTGAGGGGTTTGGGAGT 60.698 55.000 0.00 0.00 0.00 3.85
589 593 0.537371 GTGTGAGGGGTTTGGGAGTG 60.537 60.000 0.00 0.00 0.00 3.51
590 594 1.074951 GTGAGGGGTTTGGGAGTGG 59.925 63.158 0.00 0.00 0.00 4.00
591 595 1.386772 TGAGGGGTTTGGGAGTGGT 60.387 57.895 0.00 0.00 0.00 4.16
592 596 1.379146 GAGGGGTTTGGGAGTGGTC 59.621 63.158 0.00 0.00 0.00 4.02
593 597 2.033602 GGGGTTTGGGAGTGGTCG 59.966 66.667 0.00 0.00 0.00 4.79
594 598 2.033602 GGGTTTGGGAGTGGTCGG 59.966 66.667 0.00 0.00 0.00 4.79
595 599 2.671963 GGTTTGGGAGTGGTCGGC 60.672 66.667 0.00 0.00 0.00 5.54
596 600 3.047877 GTTTGGGAGTGGTCGGCG 61.048 66.667 0.00 0.00 0.00 6.46
630 634 4.452733 GAGACGGCGGGGGTGAAG 62.453 72.222 13.24 0.00 0.00 3.02
637 641 3.728373 CGGGGGTGAAGGGGGAAG 61.728 72.222 0.00 0.00 0.00 3.46
638 642 2.204244 GGGGGTGAAGGGGGAAGA 60.204 66.667 0.00 0.00 0.00 2.87
639 643 2.309504 GGGGGTGAAGGGGGAAGAG 61.310 68.421 0.00 0.00 0.00 2.85
640 644 2.309504 GGGGTGAAGGGGGAAGAGG 61.310 68.421 0.00 0.00 0.00 3.69
641 645 2.309504 GGGTGAAGGGGGAAGAGGG 61.310 68.421 0.00 0.00 0.00 4.30
642 646 2.309504 GGTGAAGGGGGAAGAGGGG 61.310 68.421 0.00 0.00 0.00 4.79
643 647 2.614013 TGAAGGGGGAAGAGGGGC 60.614 66.667 0.00 0.00 0.00 5.80
644 648 2.286502 GAAGGGGGAAGAGGGGCT 60.287 66.667 0.00 0.00 0.00 5.19
645 649 2.615288 AAGGGGGAAGAGGGGCTG 60.615 66.667 0.00 0.00 0.00 4.85
666 670 4.388499 GTGCGCGGGGAGGAAGAA 62.388 66.667 8.83 0.00 0.00 2.52
667 671 4.082523 TGCGCGGGGAGGAAGAAG 62.083 66.667 8.83 0.00 0.00 2.85
668 672 3.771160 GCGCGGGGAGGAAGAAGA 61.771 66.667 8.83 0.00 0.00 2.87
669 673 2.496817 CGCGGGGAGGAAGAAGAG 59.503 66.667 0.00 0.00 0.00 2.85
670 674 2.904131 GCGGGGAGGAAGAAGAGG 59.096 66.667 0.00 0.00 0.00 3.69
671 675 2.736826 GCGGGGAGGAAGAAGAGGG 61.737 68.421 0.00 0.00 0.00 4.30
672 676 1.306226 CGGGGAGGAAGAAGAGGGT 60.306 63.158 0.00 0.00 0.00 4.34
673 677 1.617947 CGGGGAGGAAGAAGAGGGTG 61.618 65.000 0.00 0.00 0.00 4.61
674 678 1.275421 GGGGAGGAAGAAGAGGGTGG 61.275 65.000 0.00 0.00 0.00 4.61
675 679 0.252742 GGGAGGAAGAAGAGGGTGGA 60.253 60.000 0.00 0.00 0.00 4.02
676 680 1.657804 GGAGGAAGAAGAGGGTGGAA 58.342 55.000 0.00 0.00 0.00 3.53
677 681 1.557371 GGAGGAAGAAGAGGGTGGAAG 59.443 57.143 0.00 0.00 0.00 3.46
678 682 1.557371 GAGGAAGAAGAGGGTGGAAGG 59.443 57.143 0.00 0.00 0.00 3.46
679 683 0.034960 GGAAGAAGAGGGTGGAAGGC 60.035 60.000 0.00 0.00 0.00 4.35
680 684 0.391793 GAAGAAGAGGGTGGAAGGCG 60.392 60.000 0.00 0.00 0.00 5.52
681 685 2.436824 GAAGAGGGTGGAAGGCGC 60.437 66.667 0.00 0.00 0.00 6.53
682 686 3.978571 GAAGAGGGTGGAAGGCGCC 62.979 68.421 21.89 21.89 0.00 6.53
684 688 4.115199 GAGGGTGGAAGGCGCCAT 62.115 66.667 31.54 19.26 40.68 4.40
685 689 4.431131 AGGGTGGAAGGCGCCATG 62.431 66.667 31.54 0.00 40.68 3.66
697 701 2.903855 GCCATGGCGGAGTGGATG 60.904 66.667 23.48 0.00 37.72 3.51
698 702 2.910360 CCATGGCGGAGTGGATGA 59.090 61.111 0.00 0.00 37.72 2.92
699 703 1.227764 CCATGGCGGAGTGGATGAG 60.228 63.158 0.00 0.00 37.72 2.90
700 704 1.524002 CATGGCGGAGTGGATGAGT 59.476 57.895 0.00 0.00 0.00 3.41
701 705 0.812811 CATGGCGGAGTGGATGAGTG 60.813 60.000 0.00 0.00 0.00 3.51
702 706 1.976132 ATGGCGGAGTGGATGAGTGG 61.976 60.000 0.00 0.00 0.00 4.00
703 707 2.660064 GGCGGAGTGGATGAGTGGT 61.660 63.158 0.00 0.00 0.00 4.16
704 708 1.327690 GGCGGAGTGGATGAGTGGTA 61.328 60.000 0.00 0.00 0.00 3.25
705 709 0.103208 GCGGAGTGGATGAGTGGTAG 59.897 60.000 0.00 0.00 0.00 3.18
706 710 1.763968 CGGAGTGGATGAGTGGTAGA 58.236 55.000 0.00 0.00 0.00 2.59
707 711 2.100197 CGGAGTGGATGAGTGGTAGAA 58.900 52.381 0.00 0.00 0.00 2.10
708 712 2.695666 CGGAGTGGATGAGTGGTAGAAT 59.304 50.000 0.00 0.00 0.00 2.40
709 713 3.133003 CGGAGTGGATGAGTGGTAGAATT 59.867 47.826 0.00 0.00 0.00 2.17
710 714 4.383118 CGGAGTGGATGAGTGGTAGAATTT 60.383 45.833 0.00 0.00 0.00 1.82
711 715 5.501156 GGAGTGGATGAGTGGTAGAATTTT 58.499 41.667 0.00 0.00 0.00 1.82
712 716 5.946377 GGAGTGGATGAGTGGTAGAATTTTT 59.054 40.000 0.00 0.00 0.00 1.94
726 730 3.273048 TTTTTGCCGCCGAGGATG 58.727 55.556 0.91 0.00 45.00 3.51
727 731 1.302913 TTTTTGCCGCCGAGGATGA 60.303 52.632 0.91 0.00 45.00 2.92
728 732 1.582610 TTTTTGCCGCCGAGGATGAC 61.583 55.000 0.91 0.00 45.00 3.06
729 733 4.812476 TTGCCGCCGAGGATGACG 62.812 66.667 0.91 0.00 45.00 4.35
733 737 4.630785 CGCCGAGGATGACGCGAT 62.631 66.667 15.93 0.00 45.76 4.58
734 738 3.032609 GCCGAGGATGACGCGATG 61.033 66.667 15.93 0.00 45.76 3.84
735 739 2.355126 CCGAGGATGACGCGATGG 60.355 66.667 15.93 0.00 45.76 3.51
736 740 2.355126 CGAGGATGACGCGATGGG 60.355 66.667 15.93 0.00 45.76 4.00
737 741 2.845550 CGAGGATGACGCGATGGGA 61.846 63.158 15.93 0.00 45.76 4.37
738 742 1.668294 GAGGATGACGCGATGGGAT 59.332 57.895 15.93 0.00 0.00 3.85
739 743 0.668706 GAGGATGACGCGATGGGATG 60.669 60.000 15.93 0.00 0.00 3.51
740 744 2.320587 GGATGACGCGATGGGATGC 61.321 63.158 15.93 0.00 0.00 3.91
747 751 3.514777 GCGATGGGATGCGAGATAA 57.485 52.632 0.00 0.00 0.00 1.75
748 752 1.795768 GCGATGGGATGCGAGATAAA 58.204 50.000 0.00 0.00 0.00 1.40
749 753 2.143122 GCGATGGGATGCGAGATAAAA 58.857 47.619 0.00 0.00 0.00 1.52
750 754 2.548057 GCGATGGGATGCGAGATAAAAA 59.452 45.455 0.00 0.00 0.00 1.94
751 755 3.364366 GCGATGGGATGCGAGATAAAAAG 60.364 47.826 0.00 0.00 0.00 2.27
752 756 4.058124 CGATGGGATGCGAGATAAAAAGA 58.942 43.478 0.00 0.00 0.00 2.52
753 757 4.692625 CGATGGGATGCGAGATAAAAAGAT 59.307 41.667 0.00 0.00 0.00 2.40
754 758 5.869344 CGATGGGATGCGAGATAAAAAGATA 59.131 40.000 0.00 0.00 0.00 1.98
755 759 6.536582 CGATGGGATGCGAGATAAAAAGATAT 59.463 38.462 0.00 0.00 0.00 1.63
756 760 7.465111 CGATGGGATGCGAGATAAAAAGATATG 60.465 40.741 0.00 0.00 0.00 1.78
757 761 6.533730 TGGGATGCGAGATAAAAAGATATGT 58.466 36.000 0.00 0.00 0.00 2.29
758 762 6.650807 TGGGATGCGAGATAAAAAGATATGTC 59.349 38.462 0.00 0.00 0.00 3.06
759 763 6.876257 GGGATGCGAGATAAAAAGATATGTCT 59.124 38.462 0.00 0.00 35.82 3.41
760 764 8.035394 GGGATGCGAGATAAAAAGATATGTCTA 58.965 37.037 0.00 0.00 33.30 2.59
761 765 8.865001 GGATGCGAGATAAAAAGATATGTCTAC 58.135 37.037 0.00 0.00 33.30 2.59
762 766 9.632807 GATGCGAGATAAAAAGATATGTCTACT 57.367 33.333 0.00 0.00 33.30 2.57
763 767 9.988815 ATGCGAGATAAAAAGATATGTCTACTT 57.011 29.630 0.00 0.00 33.30 2.24
800 804 8.745464 ACTGTAATTCTTTTTCTCGAGAGTAC 57.255 34.615 15.94 6.93 0.00 2.73
801 805 8.358148 ACTGTAATTCTTTTTCTCGAGAGTACA 58.642 33.333 15.94 10.99 0.00 2.90
802 806 9.360093 CTGTAATTCTTTTTCTCGAGAGTACAT 57.640 33.333 15.94 2.00 30.52 2.29
809 813 9.175312 TCTTTTTCTCGAGAGTACATATACTGT 57.825 33.333 15.94 0.00 41.98 3.55
833 837 8.778358 TGTAAATTTTCACAATATTGTTTGGGC 58.222 29.630 18.50 5.41 39.91 5.36
834 838 7.814264 AAATTTTCACAATATTGTTTGGGCA 57.186 28.000 18.50 1.87 39.91 5.36
835 839 7.814264 AATTTTCACAATATTGTTTGGGCAA 57.186 28.000 18.50 6.61 39.91 4.52
836 840 6.610741 TTTTCACAATATTGTTTGGGCAAC 57.389 33.333 18.50 0.00 39.91 4.17
837 841 3.906998 TCACAATATTGTTTGGGCAACG 58.093 40.909 18.50 4.58 39.91 4.10
838 842 3.570125 TCACAATATTGTTTGGGCAACGA 59.430 39.130 18.50 6.84 39.91 3.85
839 843 4.219507 TCACAATATTGTTTGGGCAACGAT 59.780 37.500 18.50 0.00 41.71 3.73
840 844 5.416013 TCACAATATTGTTTGGGCAACGATA 59.584 36.000 18.50 1.41 43.30 2.92
841 845 5.743398 CACAATATTGTTTGGGCAACGATAG 59.257 40.000 18.50 0.00 42.68 2.08
842 846 5.163561 ACAATATTGTTTGGGCAACGATAGG 60.164 40.000 15.47 2.73 42.68 2.57
843 847 0.885196 TTGTTTGGGCAACGATAGGC 59.115 50.000 0.00 0.00 38.36 3.93
844 848 6.041372 ATATTGTTTGGGCAACGATAGGCG 62.041 45.833 0.00 0.00 42.68 5.52
845 849 2.403378 TTTGGGCAACGATAGGCGC 61.403 57.895 0.00 0.00 46.04 6.53
850 854 3.261951 CAACGATAGGCGCCGGTG 61.262 66.667 23.20 14.56 46.04 4.94
851 855 4.524318 AACGATAGGCGCCGGTGG 62.524 66.667 23.20 17.15 46.04 4.61
862 866 3.544772 CCGGTGGGGCAAGTTTTT 58.455 55.556 0.00 0.00 0.00 1.94
884 888 5.682943 TTTTATTCGTCCAACTCAACAGG 57.317 39.130 0.00 0.00 0.00 4.00
885 889 2.930826 ATTCGTCCAACTCAACAGGT 57.069 45.000 0.00 0.00 0.00 4.00
886 890 5.471556 TTATTCGTCCAACTCAACAGGTA 57.528 39.130 0.00 0.00 0.00 3.08
1035 1040 1.904990 GACAGGGCAGAGGGAAGGAC 61.905 65.000 0.00 0.00 0.00 3.85
1145 1150 0.603569 GATGATGCGGACGAGGGTAT 59.396 55.000 0.00 0.00 0.00 2.73
1277 1282 5.732331 TTCAAATCTGTGGGGGAGAATAT 57.268 39.130 0.00 0.00 0.00 1.28
1300 1305 0.040514 CGTGGCTGAATTTGCGAACA 60.041 50.000 0.00 0.00 0.00 3.18
1658 1808 2.101582 AGTATGAGAACATCCCGCACTC 59.898 50.000 0.00 0.00 37.87 3.51
1774 1924 2.124983 GGGCTTCAGATGAGCGCA 60.125 61.111 11.47 0.00 40.52 6.09
1948 2099 3.606687 ACCACCGATCAATAAACAGGTC 58.393 45.455 0.00 0.00 0.00 3.85
2025 2176 4.632153 ACAGAACAAGTCGCAAAGAGTAT 58.368 39.130 0.00 0.00 30.94 2.12
2132 2306 1.382522 TTCGGCAGAGGCAATGAATC 58.617 50.000 0.00 0.00 43.71 2.52
2142 2316 2.288666 GGCAATGAATCGCCTCAGTTA 58.711 47.619 0.00 0.00 45.29 2.24
2251 2425 3.243704 TGGAGACCAAAATTTCGGCAAAG 60.244 43.478 0.00 0.00 0.00 2.77
2510 2684 1.990799 TCTTCGTACGTTGATGGCAG 58.009 50.000 16.05 0.48 0.00 4.85
2704 2878 2.024414 GGACAGTTGGGCCATGATAAC 58.976 52.381 13.91 5.65 0.00 1.89
2721 2895 5.797051 TGATAACGTAAAAGCTAGGTTGGT 58.203 37.500 8.16 2.20 0.00 3.67
2725 2899 4.572909 ACGTAAAAGCTAGGTTGGTTAGG 58.427 43.478 8.16 11.54 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.087009 GGACGTCTTCACCTTCGCG 61.087 63.158 16.46 0.00 0.00 5.87
559 563 4.778415 CTCACACTCGCCGTCCGG 62.778 72.222 0.24 0.24 37.59 5.14
560 564 4.778415 CCTCACACTCGCCGTCCG 62.778 72.222 0.00 0.00 38.61 4.79
561 565 4.436998 CCCTCACACTCGCCGTCC 62.437 72.222 0.00 0.00 0.00 4.79
562 566 4.436998 CCCCTCACACTCGCCGTC 62.437 72.222 0.00 0.00 0.00 4.79
564 568 3.530910 AAACCCCTCACACTCGCCG 62.531 63.158 0.00 0.00 0.00 6.46
565 569 1.966451 CAAACCCCTCACACTCGCC 60.966 63.158 0.00 0.00 0.00 5.54
566 570 1.966451 CCAAACCCCTCACACTCGC 60.966 63.158 0.00 0.00 0.00 5.03
567 571 1.302511 CCCAAACCCCTCACACTCG 60.303 63.158 0.00 0.00 0.00 4.18
568 572 0.036875 CTCCCAAACCCCTCACACTC 59.963 60.000 0.00 0.00 0.00 3.51
569 573 0.697854 ACTCCCAAACCCCTCACACT 60.698 55.000 0.00 0.00 0.00 3.55
570 574 0.537371 CACTCCCAAACCCCTCACAC 60.537 60.000 0.00 0.00 0.00 3.82
571 575 1.715019 CCACTCCCAAACCCCTCACA 61.715 60.000 0.00 0.00 0.00 3.58
572 576 1.074951 CCACTCCCAAACCCCTCAC 59.925 63.158 0.00 0.00 0.00 3.51
573 577 1.386772 ACCACTCCCAAACCCCTCA 60.387 57.895 0.00 0.00 0.00 3.86
574 578 1.379146 GACCACTCCCAAACCCCTC 59.621 63.158 0.00 0.00 0.00 4.30
575 579 2.526046 CGACCACTCCCAAACCCCT 61.526 63.158 0.00 0.00 0.00 4.79
576 580 2.033602 CGACCACTCCCAAACCCC 59.966 66.667 0.00 0.00 0.00 4.95
577 581 2.033602 CCGACCACTCCCAAACCC 59.966 66.667 0.00 0.00 0.00 4.11
578 582 2.671963 GCCGACCACTCCCAAACC 60.672 66.667 0.00 0.00 0.00 3.27
579 583 3.047877 CGCCGACCACTCCCAAAC 61.048 66.667 0.00 0.00 0.00 2.93
602 606 3.043419 CCGTCTCCGCCATCTAGG 58.957 66.667 0.00 0.00 41.84 3.02
603 607 2.336809 GCCGTCTCCGCCATCTAG 59.663 66.667 0.00 0.00 0.00 2.43
604 608 3.592814 CGCCGTCTCCGCCATCTA 61.593 66.667 0.00 0.00 0.00 1.98
613 617 4.452733 CTTCACCCCCGCCGTCTC 62.453 72.222 0.00 0.00 0.00 3.36
620 624 3.728373 CTTCCCCCTTCACCCCCG 61.728 72.222 0.00 0.00 0.00 5.73
621 625 2.204244 TCTTCCCCCTTCACCCCC 60.204 66.667 0.00 0.00 0.00 5.40
622 626 2.309504 CCTCTTCCCCCTTCACCCC 61.310 68.421 0.00 0.00 0.00 4.95
623 627 2.309504 CCCTCTTCCCCCTTCACCC 61.310 68.421 0.00 0.00 0.00 4.61
624 628 2.309504 CCCCTCTTCCCCCTTCACC 61.310 68.421 0.00 0.00 0.00 4.02
625 629 2.985116 GCCCCTCTTCCCCCTTCAC 61.985 68.421 0.00 0.00 0.00 3.18
626 630 2.614013 GCCCCTCTTCCCCCTTCA 60.614 66.667 0.00 0.00 0.00 3.02
627 631 2.286502 AGCCCCTCTTCCCCCTTC 60.287 66.667 0.00 0.00 0.00 3.46
628 632 2.615288 CAGCCCCTCTTCCCCCTT 60.615 66.667 0.00 0.00 0.00 3.95
649 653 4.388499 TTCTTCCTCCCCGCGCAC 62.388 66.667 8.75 0.00 0.00 5.34
650 654 4.082523 CTTCTTCCTCCCCGCGCA 62.083 66.667 8.75 0.00 0.00 6.09
651 655 3.724914 CTCTTCTTCCTCCCCGCGC 62.725 68.421 0.00 0.00 0.00 6.86
652 656 2.496817 CTCTTCTTCCTCCCCGCG 59.503 66.667 0.00 0.00 0.00 6.46
653 657 2.736826 CCCTCTTCTTCCTCCCCGC 61.737 68.421 0.00 0.00 0.00 6.13
654 658 1.306226 ACCCTCTTCTTCCTCCCCG 60.306 63.158 0.00 0.00 0.00 5.73
655 659 1.275421 CCACCCTCTTCTTCCTCCCC 61.275 65.000 0.00 0.00 0.00 4.81
656 660 0.252742 TCCACCCTCTTCTTCCTCCC 60.253 60.000 0.00 0.00 0.00 4.30
657 661 1.557371 CTTCCACCCTCTTCTTCCTCC 59.443 57.143 0.00 0.00 0.00 4.30
658 662 1.557371 CCTTCCACCCTCTTCTTCCTC 59.443 57.143 0.00 0.00 0.00 3.71
659 663 1.662686 CCTTCCACCCTCTTCTTCCT 58.337 55.000 0.00 0.00 0.00 3.36
660 664 0.034960 GCCTTCCACCCTCTTCTTCC 60.035 60.000 0.00 0.00 0.00 3.46
661 665 0.391793 CGCCTTCCACCCTCTTCTTC 60.392 60.000 0.00 0.00 0.00 2.87
662 666 1.679898 CGCCTTCCACCCTCTTCTT 59.320 57.895 0.00 0.00 0.00 2.52
663 667 2.960688 GCGCCTTCCACCCTCTTCT 61.961 63.158 0.00 0.00 0.00 2.85
664 668 2.436824 GCGCCTTCCACCCTCTTC 60.437 66.667 0.00 0.00 0.00 2.87
665 669 4.035102 GGCGCCTTCCACCCTCTT 62.035 66.667 22.15 0.00 0.00 2.85
667 671 4.115199 ATGGCGCCTTCCACCCTC 62.115 66.667 29.70 0.00 39.25 4.30
668 672 4.431131 CATGGCGCCTTCCACCCT 62.431 66.667 29.70 0.00 39.25 4.34
680 684 2.903855 CATCCACTCCGCCATGGC 60.904 66.667 27.67 27.67 37.80 4.40
681 685 1.227764 CTCATCCACTCCGCCATGG 60.228 63.158 7.63 7.63 37.32 3.66
682 686 0.812811 CACTCATCCACTCCGCCATG 60.813 60.000 0.00 0.00 0.00 3.66
683 687 1.524002 CACTCATCCACTCCGCCAT 59.476 57.895 0.00 0.00 0.00 4.40
684 688 2.659063 CCACTCATCCACTCCGCCA 61.659 63.158 0.00 0.00 0.00 5.69
685 689 1.327690 TACCACTCATCCACTCCGCC 61.328 60.000 0.00 0.00 0.00 6.13
686 690 0.103208 CTACCACTCATCCACTCCGC 59.897 60.000 0.00 0.00 0.00 5.54
687 691 1.763968 TCTACCACTCATCCACTCCG 58.236 55.000 0.00 0.00 0.00 4.63
688 692 4.762289 AATTCTACCACTCATCCACTCC 57.238 45.455 0.00 0.00 0.00 3.85
709 713 1.302913 TCATCCTCGGCGGCAAAAA 60.303 52.632 10.53 0.00 0.00 1.94
710 714 2.038269 GTCATCCTCGGCGGCAAAA 61.038 57.895 10.53 0.00 0.00 2.44
711 715 2.435938 GTCATCCTCGGCGGCAAA 60.436 61.111 10.53 0.00 0.00 3.68
712 716 4.812476 CGTCATCCTCGGCGGCAA 62.812 66.667 10.53 0.00 0.00 4.52
716 720 4.630785 ATCGCGTCATCCTCGGCG 62.631 66.667 5.77 0.00 0.00 6.46
717 721 3.032609 CATCGCGTCATCCTCGGC 61.033 66.667 5.77 0.00 0.00 5.54
718 722 2.355126 CCATCGCGTCATCCTCGG 60.355 66.667 5.77 0.00 0.00 4.63
719 723 2.147315 ATCCCATCGCGTCATCCTCG 62.147 60.000 5.77 0.00 0.00 4.63
720 724 0.668706 CATCCCATCGCGTCATCCTC 60.669 60.000 5.77 0.00 0.00 3.71
721 725 1.368950 CATCCCATCGCGTCATCCT 59.631 57.895 5.77 0.00 0.00 3.24
722 726 2.320587 GCATCCCATCGCGTCATCC 61.321 63.158 5.77 0.00 0.00 3.51
723 727 2.661566 CGCATCCCATCGCGTCATC 61.662 63.158 5.77 0.00 46.23 2.92
724 728 2.662857 CGCATCCCATCGCGTCAT 60.663 61.111 5.77 0.00 46.23 3.06
729 733 1.795768 TTTATCTCGCATCCCATCGC 58.204 50.000 0.00 0.00 0.00 4.58
730 734 4.058124 TCTTTTTATCTCGCATCCCATCG 58.942 43.478 0.00 0.00 0.00 3.84
731 735 7.335422 ACATATCTTTTTATCTCGCATCCCATC 59.665 37.037 0.00 0.00 0.00 3.51
732 736 7.170965 ACATATCTTTTTATCTCGCATCCCAT 58.829 34.615 0.00 0.00 0.00 4.00
733 737 6.533730 ACATATCTTTTTATCTCGCATCCCA 58.466 36.000 0.00 0.00 0.00 4.37
734 738 6.876257 AGACATATCTTTTTATCTCGCATCCC 59.124 38.462 0.00 0.00 0.00 3.85
735 739 7.897575 AGACATATCTTTTTATCTCGCATCC 57.102 36.000 0.00 0.00 0.00 3.51
736 740 9.632807 AGTAGACATATCTTTTTATCTCGCATC 57.367 33.333 0.00 0.00 36.29 3.91
737 741 9.988815 AAGTAGACATATCTTTTTATCTCGCAT 57.011 29.630 0.00 0.00 36.29 4.73
774 778 9.837525 GTACTCTCGAGAAAAAGAATTACAGTA 57.162 33.333 17.36 7.34 0.00 2.74
775 779 8.358148 TGTACTCTCGAGAAAAAGAATTACAGT 58.642 33.333 17.36 8.32 0.00 3.55
776 780 8.744008 TGTACTCTCGAGAAAAAGAATTACAG 57.256 34.615 17.36 2.28 0.00 2.74
783 787 9.175312 ACAGTATATGTACTCTCGAGAAAAAGA 57.825 33.333 17.36 3.70 41.60 2.52
807 811 8.778358 GCCCAAACAATATTGTGAAAATTTACA 58.222 29.630 21.46 0.00 41.31 2.41
808 812 8.778358 TGCCCAAACAATATTGTGAAAATTTAC 58.222 29.630 21.46 6.55 41.31 2.01
809 813 8.908786 TGCCCAAACAATATTGTGAAAATTTA 57.091 26.923 21.46 2.81 41.31 1.40
810 814 7.814264 TGCCCAAACAATATTGTGAAAATTT 57.186 28.000 21.46 8.33 41.31 1.82
811 815 7.519649 CGTTGCCCAAACAATATTGTGAAAATT 60.520 33.333 21.46 9.03 41.31 1.82
812 816 6.073331 CGTTGCCCAAACAATATTGTGAAAAT 60.073 34.615 21.46 2.85 41.31 1.82
813 817 5.235186 CGTTGCCCAAACAATATTGTGAAAA 59.765 36.000 21.46 8.21 41.31 2.29
814 818 4.747108 CGTTGCCCAAACAATATTGTGAAA 59.253 37.500 21.46 7.34 41.31 2.69
815 819 4.038042 TCGTTGCCCAAACAATATTGTGAA 59.962 37.500 21.46 1.02 41.31 3.18
816 820 3.570125 TCGTTGCCCAAACAATATTGTGA 59.430 39.130 21.46 8.39 41.31 3.58
817 821 3.906998 TCGTTGCCCAAACAATATTGTG 58.093 40.909 21.46 10.12 41.31 3.33
818 822 4.799564 ATCGTTGCCCAAACAATATTGT 57.200 36.364 15.47 15.47 44.72 2.71
819 823 5.280945 CCTATCGTTGCCCAAACAATATTG 58.719 41.667 14.01 14.01 38.84 1.90
820 824 4.202111 GCCTATCGTTGCCCAAACAATATT 60.202 41.667 0.00 0.00 38.84 1.28
821 825 3.317993 GCCTATCGTTGCCCAAACAATAT 59.682 43.478 0.00 0.00 38.84 1.28
822 826 2.685897 GCCTATCGTTGCCCAAACAATA 59.314 45.455 0.00 0.00 38.84 1.90
823 827 1.476488 GCCTATCGTTGCCCAAACAAT 59.524 47.619 0.00 0.00 38.84 2.71
824 828 0.885196 GCCTATCGTTGCCCAAACAA 59.115 50.000 0.00 0.00 38.84 2.83
825 829 1.302383 CGCCTATCGTTGCCCAAACA 61.302 55.000 0.00 0.00 38.84 2.83
826 830 1.427819 CGCCTATCGTTGCCCAAAC 59.572 57.895 0.00 0.00 35.25 2.93
827 831 2.403378 GCGCCTATCGTTGCCCAAA 61.403 57.895 0.00 0.00 41.07 3.28
828 832 2.822255 GCGCCTATCGTTGCCCAA 60.822 61.111 0.00 0.00 41.07 4.12
829 833 4.849310 GGCGCCTATCGTTGCCCA 62.849 66.667 22.15 0.00 41.70 5.36
833 837 3.261951 CACCGGCGCCTATCGTTG 61.262 66.667 26.68 5.84 41.07 4.10
834 838 4.524318 CCACCGGCGCCTATCGTT 62.524 66.667 26.68 0.00 41.07 3.85
845 849 3.544772 AAAAACTTGCCCCACCGG 58.455 55.556 0.00 0.00 0.00 5.28
861 865 5.591067 ACCTGTTGAGTTGGACGAATAAAAA 59.409 36.000 0.00 0.00 0.00 1.94
862 866 5.127491 ACCTGTTGAGTTGGACGAATAAAA 58.873 37.500 0.00 0.00 0.00 1.52
863 867 4.710324 ACCTGTTGAGTTGGACGAATAAA 58.290 39.130 0.00 0.00 0.00 1.40
864 868 4.345859 ACCTGTTGAGTTGGACGAATAA 57.654 40.909 0.00 0.00 0.00 1.40
865 869 5.670792 ATACCTGTTGAGTTGGACGAATA 57.329 39.130 0.00 0.00 0.00 1.75
866 870 2.930826 ACCTGTTGAGTTGGACGAAT 57.069 45.000 0.00 0.00 0.00 3.34
867 871 4.345859 AATACCTGTTGAGTTGGACGAA 57.654 40.909 0.00 0.00 0.00 3.85
868 872 4.345859 AAATACCTGTTGAGTTGGACGA 57.654 40.909 0.00 0.00 0.00 4.20
869 873 5.432885 AAAAATACCTGTTGAGTTGGACG 57.567 39.130 0.00 0.00 0.00 4.79
920 924 1.064685 CCAAAACCCTAGATCGCCCTT 60.065 52.381 0.00 0.00 0.00 3.95
972 976 4.749310 CAAGCCTGTCGCCTCGCT 62.749 66.667 0.00 0.00 38.78 4.93
1145 1150 2.281484 GCAACCACTTCTCCGGCA 60.281 61.111 0.00 0.00 0.00 5.69
1194 1199 4.272489 CATTGGTTATGGTCTGGATGTGT 58.728 43.478 0.00 0.00 0.00 3.72
1277 1282 0.040514 CGCAAATTCAGCCACGAACA 60.041 50.000 0.00 0.00 0.00 3.18
1300 1305 4.933483 GCGATCGCGATCTCTCTT 57.067 55.556 37.76 11.76 40.82 2.85
1583 1733 2.684881 GCCGATTCAATCACAATCCAGT 59.315 45.455 0.00 0.00 0.00 4.00
1658 1808 2.110967 CGGCCACATGAGAAGCAGG 61.111 63.158 2.24 0.00 0.00 4.85
1948 2099 2.427506 GGCACTTCAACCCTTCTGTAG 58.572 52.381 0.00 0.00 0.00 2.74
2025 2176 1.937350 TGTCTGAAGGATCTCCCCCTA 59.063 52.381 0.00 0.00 36.42 3.53
2251 2425 4.867608 GTGGTCTGCAGATTTTCTACTCTC 59.132 45.833 21.47 1.60 0.00 3.20
2510 2684 2.358247 CCAGGCCGTGTGTGGTAC 60.358 66.667 0.00 0.00 0.00 3.34
2704 2878 3.937079 CCCTAACCAACCTAGCTTTTACG 59.063 47.826 0.00 0.00 0.00 3.18
2721 2895 2.652348 TCTGGATTCCCAAAAGCCCTAA 59.348 45.455 0.00 0.00 42.98 2.69
2725 2899 1.186200 GGTCTGGATTCCCAAAAGCC 58.814 55.000 0.00 0.00 42.98 4.35


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

AutoCloner maintained by Alex Coulton.