Multiple sequence alignment - TraesCS2A01G474800

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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 TraesCS2A01G474800 chr2A 100.000 2748 0 0 1 2748 715812487 715815234 0.000000e+00 5075.0
1 TraesCS2A01G474800 chr2A 95.556 45 1 1 2704 2748 744282685 744282642 1.370000e-08 71.3
2 TraesCS2A01G474800 chr2D 96.832 1231 38 1 838 2067 577602656 577601426 0.000000e+00 2056.0
3 TraesCS2A01G474800 chr2D 93.675 585 28 3 16 599 577603353 577602777 0.000000e+00 867.0
4 TraesCS2A01G474800 chr2D 91.614 632 33 12 2086 2710 577601154 577600536 0.000000e+00 856.0
5 TraesCS2A01G474800 chr2D 95.588 136 5 1 612 746 577602790 577602655 1.660000e-52 217.0
6 TraesCS2A01G474800 chr2D 75.765 425 69 24 1658 2063 582493063 582493472 1.680000e-42 183.0
7 TraesCS2A01G474800 chr2D 92.523 107 4 3 735 839 211559262 211559158 1.700000e-32 150.0
8 TraesCS2A01G474800 chr2D 92.381 105 6 1 737 839 468096838 468096942 6.130000e-32 148.0
9 TraesCS2A01G474800 chr2D 83.898 118 12 6 17 131 477064969 477064856 3.740000e-19 106.0
10 TraesCS2A01G474800 chr2B 95.857 1231 45 3 838 2066 694990986 694992212 0.000000e+00 1986.0
11 TraesCS2A01G474800 chr2B 92.895 563 18 9 39 599 694990324 694990866 0.000000e+00 798.0
12 TraesCS2A01G474800 chr2B 92.424 528 24 8 2086 2607 694992481 694992998 0.000000e+00 739.0
13 TraesCS2A01G474800 chr2B 91.852 135 11 0 612 746 694990853 694990987 3.610000e-44 189.0
14 TraesCS2A01G474800 chr2B 93.137 102 5 1 741 840 548206064 548205963 6.130000e-32 148.0
15 TraesCS2A01G474800 chr3D 81.967 488 73 13 838 1320 297677659 297678136 1.530000e-107 399.0
16 TraesCS2A01G474800 chr3D 80.863 371 40 20 1419 1783 297678179 297678524 2.100000e-66 263.0
17 TraesCS2A01G474800 chr3D 89.286 84 4 2 2662 2745 11420907 11420985 1.740000e-17 100.0
18 TraesCS2A01G474800 chr3D 87.805 82 9 1 2662 2742 49483719 49483800 8.100000e-16 95.3
19 TraesCS2A01G474800 chr3A 81.314 487 77 12 838 1320 394648727 394649203 1.540000e-102 383.0
20 TraesCS2A01G474800 chr3A 80.541 370 41 20 1419 1783 394649246 394649589 3.510000e-64 255.0
21 TraesCS2A01G474800 chr3B 81.222 442 68 13 838 1274 392797764 392798195 2.620000e-90 342.0
22 TraesCS2A01G474800 chr3B 80.863 371 39 20 1419 1783 392809526 392809870 2.100000e-66 263.0
23 TraesCS2A01G474800 chr3B 97.674 43 1 0 2703 2745 704132855 704132813 1.060000e-09 75.0
24 TraesCS2A01G474800 chr6B 94.118 102 4 1 741 840 480706992 480707093 1.320000e-33 154.0
25 TraesCS2A01G474800 chr7D 93.269 104 5 1 738 839 84893576 84893679 4.740000e-33 152.0
26 TraesCS2A01G474800 chr7D 94.898 98 3 1 745 840 617181760 617181663 4.740000e-33 152.0
27 TraesCS2A01G474800 chr7D 88.095 84 5 3 2662 2745 633232594 633232672 8.100000e-16 95.3
28 TraesCS2A01G474800 chr7A 93.269 104 5 1 738 839 200010883 200010986 4.740000e-33 152.0
29 TraesCS2A01G474800 chr6A 94.898 98 3 1 744 839 600701849 600701752 4.740000e-33 152.0
30 TraesCS2A01G474800 chr6A 93.878 98 4 1 745 840 611411292 611411195 2.210000e-31 147.0
31 TraesCS2A01G474800 chr5D 94.318 88 3 1 2660 2745 519343932 519344019 1.720000e-27 134.0
32 TraesCS2A01G474800 chr5D 98.000 50 1 0 2658 2707 484305159 484305110 1.360000e-13 87.9
33 TraesCS2A01G474800 chr5D 100.000 40 0 0 2706 2745 376659848 376659809 1.060000e-09 75.0
34 TraesCS2A01G474800 chr6D 100.000 48 0 0 2660 2707 304108217 304108170 3.770000e-14 89.8
35 TraesCS2A01G474800 chr4A 100.000 48 0 0 2660 2707 150653311 150653358 3.770000e-14 89.8
36 TraesCS2A01G474800 chr7B 88.312 77 4 3 2674 2745 39769291 39769367 1.360000e-13 87.9
37 TraesCS2A01G474800 chr7B 100.000 40 0 0 2706 2745 33277904 33277943 1.060000e-09 75.0
38 TraesCS2A01G474800 chr4B 98.000 50 1 0 2660 2709 463079471 463079520 1.360000e-13 87.9


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 TraesCS2A01G474800 chr2A 715812487 715815234 2747 False 5075 5075 100.00000 1 2748 1 chr2A.!!$F1 2747
1 TraesCS2A01G474800 chr2D 577600536 577603353 2817 True 999 2056 94.42725 16 2710 4 chr2D.!!$R3 2694
2 TraesCS2A01G474800 chr2B 694990324 694992998 2674 False 928 1986 93.25700 39 2607 4 chr2B.!!$F1 2568
3 TraesCS2A01G474800 chr3D 297677659 297678524 865 False 331 399 81.41500 838 1783 2 chr3D.!!$F3 945
4 TraesCS2A01G474800 chr3A 394648727 394649589 862 False 319 383 80.92750 838 1783 2 chr3A.!!$F1 945

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
690 693 0.625316 ATGCCAAGCCTATGTGGACA 59.375 50.0 0.0 0.0 37.03 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2471 0.247735 CAGAGTTCGGACTACTCGCG 60.248 60.0 0.0 0.0 45.22 5.87 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
36 37 3.760684 GGAAGAAACTGACATGGCATTCT 59.239 43.478 11.01 11.01 0.00 2.40
86 87 2.939460 ATGCCACCTAAAATGTTCGC 57.061 45.000 0.00 0.00 0.00 4.70
173 174 1.295423 GCGAGCCCTAACCTTCACA 59.705 57.895 0.00 0.00 0.00 3.58
303 304 1.272147 GCAGGATTCCAGGGTGAAAGT 60.272 52.381 5.29 0.00 0.00 2.66
310 311 2.054799 TCCAGGGTGAAAGTAGCAAGT 58.945 47.619 0.00 0.00 0.00 3.16
359 360 4.056125 CCACTCTGCTCGTCCGCA 62.056 66.667 0.00 0.00 38.40 5.69
466 468 1.621814 CTCTGGGTCCCGACTTTGTTA 59.378 52.381 2.65 0.00 0.00 2.41
502 504 8.750515 TGATTGTTTGCTGGATCTGATTATAA 57.249 30.769 0.00 0.00 0.00 0.98
593 595 2.279935 TGGTCGCCAGGTATTGTTTT 57.720 45.000 0.00 0.00 0.00 2.43
594 596 2.156098 TGGTCGCCAGGTATTGTTTTC 58.844 47.619 0.00 0.00 0.00 2.29
595 597 1.471287 GGTCGCCAGGTATTGTTTTCC 59.529 52.381 0.00 0.00 0.00 3.13
596 598 1.471287 GTCGCCAGGTATTGTTTTCCC 59.529 52.381 0.00 0.00 0.00 3.97
597 599 1.353022 TCGCCAGGTATTGTTTTCCCT 59.647 47.619 0.00 0.00 0.00 4.20
598 600 1.743394 CGCCAGGTATTGTTTTCCCTC 59.257 52.381 0.00 0.00 0.00 4.30
599 601 2.802719 GCCAGGTATTGTTTTCCCTCA 58.197 47.619 0.00 0.00 0.00 3.86
600 602 3.365472 GCCAGGTATTGTTTTCCCTCAT 58.635 45.455 0.00 0.00 0.00 2.90
601 603 3.769300 GCCAGGTATTGTTTTCCCTCATT 59.231 43.478 0.00 0.00 0.00 2.57
602 604 4.222810 GCCAGGTATTGTTTTCCCTCATTT 59.777 41.667 0.00 0.00 0.00 2.32
603 605 5.279960 GCCAGGTATTGTTTTCCCTCATTTT 60.280 40.000 0.00 0.00 0.00 1.82
604 606 6.744056 GCCAGGTATTGTTTTCCCTCATTTTT 60.744 38.462 0.00 0.00 0.00 1.94
605 607 6.650390 CCAGGTATTGTTTTCCCTCATTTTTG 59.350 38.462 0.00 0.00 0.00 2.44
606 608 7.441017 CAGGTATTGTTTTCCCTCATTTTTGA 58.559 34.615 0.00 0.00 0.00 2.69
607 609 7.930865 CAGGTATTGTTTTCCCTCATTTTTGAA 59.069 33.333 0.00 0.00 0.00 2.69
608 610 8.659527 AGGTATTGTTTTCCCTCATTTTTGAAT 58.340 29.630 0.00 0.00 0.00 2.57
609 611 9.283768 GGTATTGTTTTCCCTCATTTTTGAATT 57.716 29.630 0.00 0.00 0.00 2.17
634 636 1.202879 TGTTTTCCCTCGTGGATGCTT 60.203 47.619 4.76 0.00 44.66 3.91
656 658 7.042590 TGCTTAAAAATCTGAACTTGCATTGTG 60.043 33.333 0.00 0.00 0.00 3.33
674 677 6.140737 GCATTGTGCTTACTCGTTTAATATGC 59.859 38.462 0.00 0.00 40.96 3.14
690 693 0.625316 ATGCCAAGCCTATGTGGACA 59.375 50.000 0.00 0.00 37.03 4.02
746 749 4.258543 TGGCAGCTGGTTATGTTAACTAC 58.741 43.478 17.12 2.72 0.00 2.73
747 750 4.019681 TGGCAGCTGGTTATGTTAACTACT 60.020 41.667 17.12 0.00 0.00 2.57
748 751 4.571176 GGCAGCTGGTTATGTTAACTACTC 59.429 45.833 17.12 0.00 0.00 2.59
749 752 4.571176 GCAGCTGGTTATGTTAACTACTCC 59.429 45.833 17.12 5.51 0.00 3.85
750 753 5.116882 CAGCTGGTTATGTTAACTACTCCC 58.883 45.833 5.57 1.58 0.00 4.30
751 754 5.030820 AGCTGGTTATGTTAACTACTCCCT 58.969 41.667 7.22 0.00 0.00 4.20
752 755 5.128991 AGCTGGTTATGTTAACTACTCCCTC 59.871 44.000 7.22 0.73 0.00 4.30
753 756 5.684291 GCTGGTTATGTTAACTACTCCCTCC 60.684 48.000 7.22 0.34 0.00 4.30
754 757 4.403432 TGGTTATGTTAACTACTCCCTCCG 59.597 45.833 7.22 0.00 0.00 4.63
755 758 4.403752 GGTTATGTTAACTACTCCCTCCGT 59.596 45.833 7.22 0.00 0.00 4.69
756 759 5.105187 GGTTATGTTAACTACTCCCTCCGTT 60.105 44.000 7.22 0.00 0.00 4.44
757 760 4.732672 ATGTTAACTACTCCCTCCGTTC 57.267 45.455 7.22 0.00 0.00 3.95
758 761 2.827921 TGTTAACTACTCCCTCCGTTCC 59.172 50.000 7.22 0.00 0.00 3.62
759 762 2.827921 GTTAACTACTCCCTCCGTTCCA 59.172 50.000 0.00 0.00 0.00 3.53
760 763 2.249309 AACTACTCCCTCCGTTCCAT 57.751 50.000 0.00 0.00 0.00 3.41
761 764 3.393426 AACTACTCCCTCCGTTCCATA 57.607 47.619 0.00 0.00 0.00 2.74
762 765 3.393426 ACTACTCCCTCCGTTCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
763 766 3.924922 ACTACTCCCTCCGTTCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
764 767 5.070823 ACTACTCCCTCCGTTCCATAATA 57.929 43.478 0.00 0.00 0.00 0.98
765 768 5.078256 ACTACTCCCTCCGTTCCATAATAG 58.922 45.833 0.00 0.00 0.00 1.73
766 769 4.194678 ACTCCCTCCGTTCCATAATAGA 57.805 45.455 0.00 0.00 0.00 1.98
767 770 4.753186 ACTCCCTCCGTTCCATAATAGAT 58.247 43.478 0.00 0.00 0.00 1.98
768 771 4.528596 ACTCCCTCCGTTCCATAATAGATG 59.471 45.833 0.00 0.00 0.00 2.90
769 772 4.747583 TCCCTCCGTTCCATAATAGATGA 58.252 43.478 0.00 0.00 0.00 2.92
770 773 4.527038 TCCCTCCGTTCCATAATAGATGAC 59.473 45.833 0.00 0.00 0.00 3.06
771 774 4.322801 CCCTCCGTTCCATAATAGATGACC 60.323 50.000 0.00 0.00 0.00 4.02
772 775 4.322801 CCTCCGTTCCATAATAGATGACCC 60.323 50.000 0.00 0.00 0.00 4.46
773 776 4.228010 TCCGTTCCATAATAGATGACCCA 58.772 43.478 0.00 0.00 0.00 4.51
774 777 4.656575 TCCGTTCCATAATAGATGACCCAA 59.343 41.667 0.00 0.00 0.00 4.12
775 778 4.755123 CCGTTCCATAATAGATGACCCAAC 59.245 45.833 0.00 0.00 0.00 3.77
776 779 5.454755 CCGTTCCATAATAGATGACCCAACT 60.455 44.000 0.00 0.00 0.00 3.16
777 780 6.055588 CGTTCCATAATAGATGACCCAACTT 58.944 40.000 0.00 0.00 0.00 2.66
778 781 6.542370 CGTTCCATAATAGATGACCCAACTTT 59.458 38.462 0.00 0.00 0.00 2.66
779 782 7.467267 CGTTCCATAATAGATGACCCAACTTTG 60.467 40.741 0.00 0.00 0.00 2.77
780 783 6.969043 TCCATAATAGATGACCCAACTTTGT 58.031 36.000 0.00 0.00 0.00 2.83
781 784 8.096621 TCCATAATAGATGACCCAACTTTGTA 57.903 34.615 0.00 0.00 0.00 2.41
782 785 8.723365 TCCATAATAGATGACCCAACTTTGTAT 58.277 33.333 0.00 0.00 0.00 2.29
783 786 9.354673 CCATAATAGATGACCCAACTTTGTATT 57.645 33.333 0.00 0.00 0.00 1.89
787 790 9.975218 AATAGATGACCCAACTTTGTATTAACT 57.025 29.630 0.00 0.00 0.00 2.24
788 791 9.975218 ATAGATGACCCAACTTTGTATTAACTT 57.025 29.630 0.00 0.00 0.00 2.66
789 792 8.706322 AGATGACCCAACTTTGTATTAACTTT 57.294 30.769 0.00 0.00 0.00 2.66
790 793 8.576442 AGATGACCCAACTTTGTATTAACTTTG 58.424 33.333 0.00 0.00 0.00 2.77
791 794 7.648039 TGACCCAACTTTGTATTAACTTTGT 57.352 32.000 0.00 0.00 0.00 2.83
792 795 8.749026 TGACCCAACTTTGTATTAACTTTGTA 57.251 30.769 0.00 0.00 0.00 2.41
793 796 8.623030 TGACCCAACTTTGTATTAACTTTGTAC 58.377 33.333 0.00 0.00 0.00 2.90
794 797 8.756486 ACCCAACTTTGTATTAACTTTGTACT 57.244 30.769 0.00 0.00 0.00 2.73
795 798 9.850198 ACCCAACTTTGTATTAACTTTGTACTA 57.150 29.630 0.00 0.00 0.00 1.82
833 836 8.930846 AATAGTCATCTATTTTGGAATGGAGG 57.069 34.615 0.00 0.00 42.20 4.30
834 837 5.699143 AGTCATCTATTTTGGAATGGAGGG 58.301 41.667 0.00 0.00 36.39 4.30
835 838 5.433051 AGTCATCTATTTTGGAATGGAGGGA 59.567 40.000 0.00 0.00 36.39 4.20
836 839 5.767168 GTCATCTATTTTGGAATGGAGGGAG 59.233 44.000 0.00 0.00 36.39 4.30
845 848 4.890988 TGGAATGGAGGGAGTATGTAAGA 58.109 43.478 0.00 0.00 0.00 2.10
1053 1059 6.594159 TCTTAAAGATTCAGAAGTTTAGGCGG 59.406 38.462 5.58 0.00 0.00 6.13
1153 1159 4.724399 TGAATTGCCCTTCTTTACAGACA 58.276 39.130 0.00 0.00 0.00 3.41
1433 1439 3.660865 GAGTCGACTTGCTTAAGGGAAA 58.339 45.455 21.08 0.00 0.00 3.13
1598 1605 8.494016 ACCATGCTGTAAGTTTCTTAATACTC 57.506 34.615 0.00 0.00 35.30 2.59
1790 1797 3.946558 AGATTCTCTTGAGGCTTCATTGC 59.053 43.478 0.00 0.00 32.27 3.56
1853 1860 2.886523 TCTTGAATTGTTCTGGCCTGTG 59.113 45.455 3.32 0.00 0.00 3.66
1858 1865 0.396435 TTGTTCTGGCCTGTGACGAT 59.604 50.000 3.32 0.00 0.00 3.73
1909 1916 6.182039 TGAGCTGTTGCAATATCAACTTAC 57.818 37.500 0.59 0.00 44.83 2.34
1912 1919 7.278646 TGAGCTGTTGCAATATCAACTTACTAG 59.721 37.037 0.59 0.00 44.83 2.57
1928 1935 6.221659 ACTTACTAGTAGTCAAAACTGTGCC 58.778 40.000 5.96 0.00 36.92 5.01
1948 1955 4.653341 TGCCGAATTTCCCCATGAATAATT 59.347 37.500 0.00 0.00 31.67 1.40
1973 1980 2.618709 GTTGCACCTAGTTGAAGCAAGT 59.381 45.455 0.00 0.00 44.73 3.16
1980 1987 2.638480 AGTTGAAGCAAGTACTGGCA 57.362 45.000 24.16 0.36 0.00 4.92
2002 2009 5.451103 GCAATCTCTTATCCCTCCTTTTTGC 60.451 44.000 0.00 0.00 0.00 3.68
2015 2022 4.497300 TCCTTTTTGCTATTGCTGAATGC 58.503 39.130 0.00 0.00 40.48 3.56
2067 2074 6.017109 GCAGAATTAGTTTGTGTTCTCTTGGA 60.017 38.462 0.00 0.00 31.37 3.53
2069 2076 6.486993 AGAATTAGTTTGTGTTCTCTTGGACC 59.513 38.462 0.00 0.00 0.00 4.46
2070 2077 3.933861 AGTTTGTGTTCTCTTGGACCT 57.066 42.857 0.00 0.00 0.00 3.85
2072 2079 4.600062 AGTTTGTGTTCTCTTGGACCTTT 58.400 39.130 0.00 0.00 0.00 3.11
2074 2081 5.125578 AGTTTGTGTTCTCTTGGACCTTTTC 59.874 40.000 0.00 0.00 0.00 2.29
2075 2082 4.229304 TGTGTTCTCTTGGACCTTTTCA 57.771 40.909 0.00 0.00 0.00 2.69
2076 2083 4.199310 TGTGTTCTCTTGGACCTTTTCAG 58.801 43.478 0.00 0.00 0.00 3.02
2090 2350 3.181476 CCTTTTCAGGTTGGGTCAAACAG 60.181 47.826 0.00 0.00 32.84 3.16
2205 2465 2.165030 GGCAGGGTTGATGATTGTTCTG 59.835 50.000 0.00 0.00 0.00 3.02
2211 2471 4.321230 GGGTTGATGATTGTTCTGTGTTCC 60.321 45.833 0.00 0.00 0.00 3.62
2232 2492 1.202054 GCGAGTAGTCCGAACTCTGAC 60.202 57.143 2.15 0.00 41.02 3.51
2289 2550 9.692749 CAACGAAGGCTAGATATATCTGTAAAA 57.307 33.333 23.03 3.98 37.76 1.52
2443 2705 7.275341 TGAAAGCAACACATTAGACACAAAAAG 59.725 33.333 0.00 0.00 0.00 2.27
2452 2714 6.539464 ACATTAGACACAAAAAGTCAACGGTA 59.461 34.615 0.00 0.00 38.46 4.02
2538 2800 3.436470 CCCCTTTCAAAACCTCCTCAGAA 60.436 47.826 0.00 0.00 0.00 3.02
2544 2806 6.597832 TTCAAAACCTCCTCAGAACAAAAA 57.402 33.333 0.00 0.00 0.00 1.94
2648 2917 6.841755 ACTCTGCTCTTTCTGGGTTATAGTAT 59.158 38.462 0.00 0.00 0.00 2.12
2653 2922 7.769044 TGCTCTTTCTGGGTTATAGTATCAAAC 59.231 37.037 0.00 0.00 0.00 2.93
2670 2939 0.971447 AACCGCTGACTACTCCCTCC 60.971 60.000 0.00 0.00 0.00 4.30
2737 3006 8.958506 AGTGAATCTACACTCTAAAATACGTCT 58.041 33.333 0.00 0.00 46.36 4.18
2747 3016 9.557338 CACTCTAAAATACGTCTATATACAGCC 57.443 37.037 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.028420 TCTTCCGAATGCCATGTCAG 57.972 50.000 0.00 0.00 0.00 3.51
1 2 2.487762 GTTTCTTCCGAATGCCATGTCA 59.512 45.455 0.00 0.00 0.00 3.58
2 3 2.749621 AGTTTCTTCCGAATGCCATGTC 59.250 45.455 0.00 0.00 0.00 3.06
3 4 2.489329 CAGTTTCTTCCGAATGCCATGT 59.511 45.455 0.00 0.00 0.00 3.21
4 5 2.749076 TCAGTTTCTTCCGAATGCCATG 59.251 45.455 0.00 0.00 0.00 3.66
5 6 2.749621 GTCAGTTTCTTCCGAATGCCAT 59.250 45.455 0.00 0.00 0.00 4.40
6 7 2.151202 GTCAGTTTCTTCCGAATGCCA 58.849 47.619 0.00 0.00 0.00 4.92
7 8 2.151202 TGTCAGTTTCTTCCGAATGCC 58.849 47.619 0.00 0.00 0.00 4.40
8 9 3.426695 CCATGTCAGTTTCTTCCGAATGC 60.427 47.826 0.00 0.00 0.00 3.56
9 10 3.426695 GCCATGTCAGTTTCTTCCGAATG 60.427 47.826 0.00 0.00 0.00 2.67
10 11 2.749621 GCCATGTCAGTTTCTTCCGAAT 59.250 45.455 0.00 0.00 0.00 3.34
11 12 2.151202 GCCATGTCAGTTTCTTCCGAA 58.849 47.619 0.00 0.00 0.00 4.30
12 13 1.071542 TGCCATGTCAGTTTCTTCCGA 59.928 47.619 0.00 0.00 0.00 4.55
13 14 1.522668 TGCCATGTCAGTTTCTTCCG 58.477 50.000 0.00 0.00 0.00 4.30
14 15 3.760684 AGAATGCCATGTCAGTTTCTTCC 59.239 43.478 0.00 0.00 0.00 3.46
36 37 1.072331 GAGGGAGTGGCAGTTTCTTCA 59.928 52.381 0.00 0.00 0.00 3.02
86 87 0.454600 GCCAGCAAGGATGACACATG 59.545 55.000 0.00 0.00 41.22 3.21
209 210 2.419739 GGTCAGGAGGTCCGAGCTC 61.420 68.421 17.67 17.67 41.73 4.09
210 211 2.363147 GGTCAGGAGGTCCGAGCT 60.363 66.667 0.00 0.00 42.08 4.09
211 212 2.363147 AGGTCAGGAGGTCCGAGC 60.363 66.667 10.27 10.27 42.08 5.03
212 213 2.115911 CGAGGTCAGGAGGTCCGAG 61.116 68.421 0.00 0.00 42.08 4.63
281 282 2.124570 CACCCTGGAATCCTGCGG 60.125 66.667 0.00 6.50 0.00 5.69
310 311 2.660064 GCCGAAGAGGAGGGAAGCA 61.660 63.158 0.00 0.00 45.00 3.91
359 360 0.783850 AGGGGGCACACCTTGTAATT 59.216 50.000 0.00 0.00 40.03 1.40
391 392 1.070445 CCAGCGCAGATTAGGGGAG 59.930 63.158 11.47 0.00 0.00 4.30
449 451 3.175594 AGTATAACAAAGTCGGGACCCA 58.824 45.455 12.15 0.00 0.00 4.51
466 468 5.047092 CCAGCAAACAATCAGGGAAAAGTAT 60.047 40.000 0.00 0.00 0.00 2.12
600 602 9.384764 ACGAGGGAAAACAATAAAATTCAAAAA 57.615 25.926 0.00 0.00 0.00 1.94
601 603 8.821894 CACGAGGGAAAACAATAAAATTCAAAA 58.178 29.630 0.00 0.00 0.00 2.44
602 604 7.439655 CCACGAGGGAAAACAATAAAATTCAAA 59.560 33.333 0.00 0.00 40.01 2.69
603 605 6.926272 CCACGAGGGAAAACAATAAAATTCAA 59.074 34.615 0.00 0.00 40.01 2.69
604 606 6.265649 TCCACGAGGGAAAACAATAAAATTCA 59.734 34.615 0.00 0.00 44.80 2.57
605 607 6.683715 TCCACGAGGGAAAACAATAAAATTC 58.316 36.000 0.00 0.00 44.80 2.17
606 608 6.658188 TCCACGAGGGAAAACAATAAAATT 57.342 33.333 0.00 0.00 44.80 1.82
634 636 6.768029 GCACAATGCAAGTTCAGATTTTTA 57.232 33.333 0.00 0.00 44.26 1.52
656 658 5.205565 GCTTGGCATATTAAACGAGTAAGC 58.794 41.667 0.00 0.00 0.00 3.09
674 677 2.198827 TTGTGTCCACATAGGCTTGG 57.801 50.000 0.20 0.00 41.52 3.61
690 693 7.524717 ACTACAGAAGGCAAAAACATATTGT 57.475 32.000 0.00 0.00 0.00 2.71
746 749 4.772624 TCATCTATTATGGAACGGAGGGAG 59.227 45.833 0.00 0.00 0.00 4.30
747 750 4.527038 GTCATCTATTATGGAACGGAGGGA 59.473 45.833 0.00 0.00 0.00 4.20
748 751 4.322801 GGTCATCTATTATGGAACGGAGGG 60.323 50.000 0.00 0.00 0.00 4.30
749 752 4.322801 GGGTCATCTATTATGGAACGGAGG 60.323 50.000 0.00 0.00 0.00 4.30
750 753 4.283467 TGGGTCATCTATTATGGAACGGAG 59.717 45.833 0.00 0.00 0.00 4.63
751 754 4.228010 TGGGTCATCTATTATGGAACGGA 58.772 43.478 0.00 0.00 0.00 4.69
752 755 4.617253 TGGGTCATCTATTATGGAACGG 57.383 45.455 0.00 0.00 0.00 4.44
753 756 5.611374 AGTTGGGTCATCTATTATGGAACG 58.389 41.667 0.00 0.00 0.00 3.95
754 757 7.339466 ACAAAGTTGGGTCATCTATTATGGAAC 59.661 37.037 0.00 0.00 0.00 3.62
755 758 7.410174 ACAAAGTTGGGTCATCTATTATGGAA 58.590 34.615 0.00 0.00 0.00 3.53
756 759 6.969043 ACAAAGTTGGGTCATCTATTATGGA 58.031 36.000 0.00 0.00 0.00 3.41
757 760 8.924511 ATACAAAGTTGGGTCATCTATTATGG 57.075 34.615 0.00 0.00 0.00 2.74
761 764 9.975218 AGTTAATACAAAGTTGGGTCATCTATT 57.025 29.630 0.00 0.00 0.00 1.73
762 765 9.975218 AAGTTAATACAAAGTTGGGTCATCTAT 57.025 29.630 0.00 0.00 0.00 1.98
763 766 9.802039 AAAGTTAATACAAAGTTGGGTCATCTA 57.198 29.630 0.00 0.00 0.00 1.98
764 767 8.576442 CAAAGTTAATACAAAGTTGGGTCATCT 58.424 33.333 0.00 0.00 0.00 2.90
765 768 8.357402 ACAAAGTTAATACAAAGTTGGGTCATC 58.643 33.333 0.00 0.00 0.00 2.92
766 769 8.245195 ACAAAGTTAATACAAAGTTGGGTCAT 57.755 30.769 0.00 0.00 0.00 3.06
767 770 7.648039 ACAAAGTTAATACAAAGTTGGGTCA 57.352 32.000 0.00 0.00 0.00 4.02
768 771 8.843262 AGTACAAAGTTAATACAAAGTTGGGTC 58.157 33.333 0.00 0.00 0.00 4.46
769 772 8.756486 AGTACAAAGTTAATACAAAGTTGGGT 57.244 30.769 0.00 0.00 0.00 4.51
809 812 7.295672 TCCCTCCATTCCAAAATAGATGACTAT 59.704 37.037 0.00 0.00 40.58 2.12
810 813 6.619437 TCCCTCCATTCCAAAATAGATGACTA 59.381 38.462 0.00 0.00 0.00 2.59
811 814 5.433051 TCCCTCCATTCCAAAATAGATGACT 59.567 40.000 0.00 0.00 0.00 3.41
812 815 5.694995 TCCCTCCATTCCAAAATAGATGAC 58.305 41.667 0.00 0.00 0.00 3.06
813 816 5.433051 ACTCCCTCCATTCCAAAATAGATGA 59.567 40.000 0.00 0.00 0.00 2.92
814 817 5.699143 ACTCCCTCCATTCCAAAATAGATG 58.301 41.667 0.00 0.00 0.00 2.90
815 818 7.074237 ACATACTCCCTCCATTCCAAAATAGAT 59.926 37.037 0.00 0.00 0.00 1.98
816 819 6.389869 ACATACTCCCTCCATTCCAAAATAGA 59.610 38.462 0.00 0.00 0.00 1.98
817 820 6.605119 ACATACTCCCTCCATTCCAAAATAG 58.395 40.000 0.00 0.00 0.00 1.73
818 821 6.590656 ACATACTCCCTCCATTCCAAAATA 57.409 37.500 0.00 0.00 0.00 1.40
819 822 5.472301 ACATACTCCCTCCATTCCAAAAT 57.528 39.130 0.00 0.00 0.00 1.82
820 823 4.946160 ACATACTCCCTCCATTCCAAAA 57.054 40.909 0.00 0.00 0.00 2.44
821 824 5.729229 TCTTACATACTCCCTCCATTCCAAA 59.271 40.000 0.00 0.00 0.00 3.28
822 825 5.285401 TCTTACATACTCCCTCCATTCCAA 58.715 41.667 0.00 0.00 0.00 3.53
823 826 4.890988 TCTTACATACTCCCTCCATTCCA 58.109 43.478 0.00 0.00 0.00 3.53
824 827 4.284746 CCTCTTACATACTCCCTCCATTCC 59.715 50.000 0.00 0.00 0.00 3.01
825 828 4.262678 GCCTCTTACATACTCCCTCCATTC 60.263 50.000 0.00 0.00 0.00 2.67
826 829 3.648545 GCCTCTTACATACTCCCTCCATT 59.351 47.826 0.00 0.00 0.00 3.16
827 830 3.243724 GCCTCTTACATACTCCCTCCAT 58.756 50.000 0.00 0.00 0.00 3.41
828 831 2.023404 TGCCTCTTACATACTCCCTCCA 60.023 50.000 0.00 0.00 0.00 3.86
829 832 2.679082 TGCCTCTTACATACTCCCTCC 58.321 52.381 0.00 0.00 0.00 4.30
830 833 3.898123 TGATGCCTCTTACATACTCCCTC 59.102 47.826 0.00 0.00 0.00 4.30
831 834 3.900601 CTGATGCCTCTTACATACTCCCT 59.099 47.826 0.00 0.00 0.00 4.20
832 835 3.556004 GCTGATGCCTCTTACATACTCCC 60.556 52.174 0.00 0.00 0.00 4.30
833 836 3.070159 TGCTGATGCCTCTTACATACTCC 59.930 47.826 0.00 0.00 38.71 3.85
834 837 4.327982 TGCTGATGCCTCTTACATACTC 57.672 45.455 0.00 0.00 38.71 2.59
835 838 4.760530 TTGCTGATGCCTCTTACATACT 57.239 40.909 0.00 0.00 38.71 2.12
836 839 5.059161 TGATTGCTGATGCCTCTTACATAC 58.941 41.667 0.00 0.00 38.71 2.39
845 848 0.815734 GTTGCTGATTGCTGATGCCT 59.184 50.000 0.00 0.00 43.37 4.75
1053 1059 0.533755 ATCCAGCATAAGACGCCAGC 60.534 55.000 0.00 0.00 0.00 4.85
1598 1605 6.991485 ACTGTTTTCAAATTTGTATCTGCG 57.009 33.333 17.47 5.53 0.00 5.18
1790 1797 9.273016 TCTTTCTTACAAATAACTGAAGGACTG 57.727 33.333 0.00 0.00 0.00 3.51
1853 1860 0.461548 TGACTCTGCCATCCATCGTC 59.538 55.000 0.00 0.00 0.00 4.20
1858 1865 2.290260 ACGATTTTGACTCTGCCATCCA 60.290 45.455 0.00 0.00 0.00 3.41
1909 1916 3.909430 TCGGCACAGTTTTGACTACTAG 58.091 45.455 0.00 0.00 0.00 2.57
1912 1919 4.483476 AATTCGGCACAGTTTTGACTAC 57.517 40.909 0.00 0.00 0.00 2.73
1928 1935 7.895759 ACCATAATTATTCATGGGGAAATTCG 58.104 34.615 9.30 0.00 45.08 3.34
1973 1980 3.904339 GGAGGGATAAGAGATTGCCAGTA 59.096 47.826 0.00 0.00 0.00 2.74
1980 1987 6.084749 AGCAAAAAGGAGGGATAAGAGATT 57.915 37.500 0.00 0.00 0.00 2.40
2015 2022 4.685169 ACACTGACACACAAAAGAGTTG 57.315 40.909 0.00 0.00 0.00 3.16
2067 2074 2.764010 GTTTGACCCAACCTGAAAAGGT 59.236 45.455 0.00 0.00 45.55 3.50
2069 2076 3.737972 GCTGTTTGACCCAACCTGAAAAG 60.738 47.826 0.00 0.00 0.00 2.27
2070 2077 2.167487 GCTGTTTGACCCAACCTGAAAA 59.833 45.455 0.00 0.00 0.00 2.29
2072 2079 1.341482 TGCTGTTTGACCCAACCTGAA 60.341 47.619 0.00 0.00 0.00 3.02
2074 2081 0.670162 CTGCTGTTTGACCCAACCTG 59.330 55.000 0.00 0.00 0.00 4.00
2075 2082 0.258774 ACTGCTGTTTGACCCAACCT 59.741 50.000 0.00 0.00 0.00 3.50
2076 2083 0.385390 CACTGCTGTTTGACCCAACC 59.615 55.000 0.00 0.00 0.00 3.77
2080 2087 1.065551 GTTCACACTGCTGTTTGACCC 59.934 52.381 11.59 3.24 33.23 4.46
2081 2088 2.017049 AGTTCACACTGCTGTTTGACC 58.983 47.619 11.59 5.79 33.23 4.02
2082 2089 3.056952 CAGTTCACACTGCTGTTTGAC 57.943 47.619 11.59 7.83 44.16 3.18
2132 2392 1.363443 CGCAACACCCACTTGCAAT 59.637 52.632 0.00 0.00 43.61 3.56
2205 2465 1.513586 CGGACTACTCGCGGAACAC 60.514 63.158 6.13 0.00 0.00 3.32
2211 2471 0.247735 CAGAGTTCGGACTACTCGCG 60.248 60.000 0.00 0.00 45.22 5.87
2292 2553 7.379797 GCCTTTTGTTAAGAAGAAATCACACTC 59.620 37.037 0.00 0.00 0.00 3.51
2375 2637 5.276461 AGATATATGCGTTCCTTGTGACA 57.724 39.130 0.00 0.00 0.00 3.58
2443 2705 9.949174 TTTTAACCTTATCTTTTTACCGTTGAC 57.051 29.630 0.00 0.00 0.00 3.18
2487 2749 4.393062 CGACCAAGCTGTTTGATAGATGTT 59.607 41.667 5.77 0.00 39.21 2.71
2538 2800 5.941555 TGGTGTTTCTGGGTTATTTTTGT 57.058 34.783 0.00 0.00 0.00 2.83
2570 2837 8.494433 ACTTTAAGCCAAAGACCAGATATGATA 58.506 33.333 13.73 0.00 45.62 2.15
2648 2917 0.606604 GGGAGTAGTCAGCGGTTTGA 59.393 55.000 0.00 0.00 0.00 2.69
2653 2922 2.482333 CGGAGGGAGTAGTCAGCGG 61.482 68.421 0.00 0.00 0.00 5.52
2721 2990 9.557338 GGCTGTATATAGACGTATTTTAGAGTG 57.443 37.037 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.