Multiple sequence alignment - TraesCS6B01G145200

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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 TraesCS6B01G145200 chr6B 100.000 2657 0 0 1 2657 145042593 145045249 0.000000e+00 4907.0
1 TraesCS6B01G145200 chr6B 85.605 1049 104 27 833 1859 144920954 144919931 0.000000e+00 1057.0
2 TraesCS6B01G145200 chr6B 94.021 485 29 0 1 485 703688934 703689418 0.000000e+00 736.0
3 TraesCS6B01G145200 chr6B 93.159 497 34 0 1 497 68187170 68187666 0.000000e+00 730.0
4 TraesCS6B01G145200 chr6B 93.200 500 29 5 1 497 206512155 206512652 0.000000e+00 730.0
5 TraesCS6B01G145200 chr6B 89.212 584 43 14 1006 1569 237416948 237416365 0.000000e+00 712.0
6 TraesCS6B01G145200 chr6B 100.000 30 0 0 1984 2013 237415953 237415924 3.690000e-04 56.5
7 TraesCS6B01G145200 chr6D 91.848 1239 58 22 806 2017 70634076 70635298 0.000000e+00 1688.0
8 TraesCS6B01G145200 chr6D 81.050 1372 140 60 833 2151 69933015 69931711 0.000000e+00 983.0
9 TraesCS6B01G145200 chr6D 80.495 646 82 25 1925 2538 70635329 70635962 3.120000e-124 455.0
10 TraesCS6B01G145200 chr6D 95.098 102 4 1 2557 2657 21051970 21052071 2.740000e-35 159.0
11 TraesCS6B01G145200 chr6D 94.231 104 6 0 2554 2657 104342723 104342826 2.740000e-35 159.0
12 TraesCS6B01G145200 chr6D 79.654 231 23 12 548 776 70633872 70634080 7.670000e-31 145.0
13 TraesCS6B01G145200 chr6D 86.667 75 9 1 1941 2015 69931441 69931368 6.100000e-12 82.4
14 TraesCS6B01G145200 chr6D 100.000 36 0 0 1966 2001 70635295 70635330 1.710000e-07 67.6
15 TraesCS6B01G145200 chr6A 90.969 1218 69 26 823 2017 87906654 87907853 0.000000e+00 1602.0
16 TraesCS6B01G145200 chr6A 83.788 1209 135 34 833 2015 87653965 87652792 0.000000e+00 1090.0
17 TraesCS6B01G145200 chr6A 88.455 589 44 12 1002 1567 180625735 180625148 0.000000e+00 689.0
18 TraesCS6B01G145200 chr6A 85.159 283 31 3 501 781 87906373 87906646 2.010000e-71 279.0
19 TraesCS6B01G145200 chr6A 91.089 202 10 4 1925 2126 87907884 87908077 1.570000e-67 267.0
20 TraesCS6B01G145200 chr6A 79.651 172 20 6 2239 2395 87908172 87908343 2.800000e-20 110.0
21 TraesCS6B01G145200 chr6A 100.000 36 0 0 1966 2001 87907850 87907885 1.710000e-07 67.6
22 TraesCS6B01G145200 chr2B 92.495 533 36 3 1040 1568 756674448 756673916 0.000000e+00 760.0
23 TraesCS6B01G145200 chr2B 93.360 497 32 1 1 497 325169969 325170464 0.000000e+00 734.0
24 TraesCS6B01G145200 chr2B 93.028 502 34 1 1 502 752517043 752516543 0.000000e+00 732.0
25 TraesCS6B01G145200 chr2B 95.098 102 4 1 2557 2657 66994806 66994705 2.740000e-35 159.0
26 TraesCS6B01G145200 chr4B 93.763 497 31 0 1 497 445246760 445246264 0.000000e+00 747.0
27 TraesCS6B01G145200 chr4B 93.387 499 31 1 1 497 496619161 496619659 0.000000e+00 737.0
28 TraesCS6B01G145200 chr4B 92.986 499 32 3 1 497 82148349 82148846 0.000000e+00 725.0
29 TraesCS6B01G145200 chr7B 93.360 497 33 0 1 497 411920852 411920356 0.000000e+00 736.0
30 TraesCS6B01G145200 chr7B 95.098 102 4 1 2557 2657 11441305 11441204 2.740000e-35 159.0
31 TraesCS6B01G145200 chr7B 93.396 106 6 1 2553 2657 650608926 650609031 3.540000e-34 156.0
32 TraesCS6B01G145200 chr5D 92.521 468 29 3 1042 1509 358798382 358798843 0.000000e+00 665.0
33 TraesCS6B01G145200 chr2D 96.040 101 4 0 2557 2657 624881947 624881847 5.880000e-37 165.0
34 TraesCS6B01G145200 chr4D 95.050 101 4 1 2558 2657 12520140 12520240 9.850000e-35 158.0
35 TraesCS6B01G145200 chr3D 92.035 113 8 1 2546 2657 6667449 6667337 9.850000e-35 158.0
36 TraesCS6B01G145200 chr3A 92.593 108 6 2 2551 2657 648037453 648037347 1.270000e-33 154.0


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 TraesCS6B01G145200 chr6B 145042593 145045249 2656 False 4907.00 4907 100.00000 1 2657 1 chr6B.!!$F2 2656
1 TraesCS6B01G145200 chr6B 144919931 144920954 1023 True 1057.00 1057 85.60500 833 1859 1 chr6B.!!$R1 1026
2 TraesCS6B01G145200 chr6B 237415924 237416948 1024 True 384.25 712 94.60600 1006 2013 2 chr6B.!!$R2 1007
3 TraesCS6B01G145200 chr6D 70633872 70635962 2090 False 588.90 1688 87.99925 548 2538 4 chr6D.!!$F3 1990
4 TraesCS6B01G145200 chr6D 69931368 69933015 1647 True 532.70 983 83.85850 833 2151 2 chr6D.!!$R1 1318
5 TraesCS6B01G145200 chr6A 87652792 87653965 1173 True 1090.00 1090 83.78800 833 2015 1 chr6A.!!$R1 1182
6 TraesCS6B01G145200 chr6A 180625148 180625735 587 True 689.00 689 88.45500 1002 1567 1 chr6A.!!$R2 565
7 TraesCS6B01G145200 chr6A 87906373 87908343 1970 False 465.12 1602 89.37360 501 2395 5 chr6A.!!$F1 1894
8 TraesCS6B01G145200 chr2B 756673916 756674448 532 True 760.00 760 92.49500 1040 1568 1 chr2B.!!$R3 528
9 TraesCS6B01G145200 chr2B 752516543 752517043 500 True 732.00 732 93.02800 1 502 1 chr2B.!!$R2 501

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
665 669 0.104672 TGTATCCCCGGACCCATCAT 60.105 55.0 0.73 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2451 3091 0.443869 CTATATGTGCATTCGCCGGC 59.556 55.0 19.07 19.07 37.32 6.13 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 2.125773 AGGAACGTGACCGAGTAGAT 57.874 50.000 0.00 0.00 37.88 1.98
85 86 4.680237 TGTTGAGCCAGCGACGGG 62.680 66.667 0.00 0.00 0.00 5.28
107 108 3.326747 CGCCTATATAAAGTGGAGGTGC 58.673 50.000 0.00 0.00 31.49 5.01
134 135 2.289631 ACTCATGTGGTTGATCGCTTCA 60.290 45.455 0.00 0.00 0.00 3.02
183 184 1.291132 GAATAGCCACCTTCACTCGC 58.709 55.000 0.00 0.00 0.00 5.03
267 268 0.602905 GTTAGAGGCGGTGCACTTGT 60.603 55.000 17.98 0.00 0.00 3.16
303 304 0.749091 TGTACGTGGGATCGGACGAT 60.749 55.000 18.77 6.95 46.28 3.73
304 305 2.676142 TGTACGTGGGATCGGACGATC 61.676 57.143 22.63 22.63 46.28 3.69
315 316 1.586564 GGACGATCGGCTGTTCGAG 60.587 63.158 28.03 5.18 42.69 4.04
317 318 1.989966 GACGATCGGCTGTTCGAGGA 61.990 60.000 28.03 0.00 42.69 3.71
334 335 1.457009 GGAAGATCGGACGAGGAGGG 61.457 65.000 0.00 0.00 0.00 4.30
350 351 4.867599 GGGACGATCCACGCGGAC 62.868 72.222 12.47 0.00 46.79 4.79
428 429 1.412710 GTGATCCATCTCCCGTAGCAA 59.587 52.381 0.00 0.00 0.00 3.91
436 437 2.244695 TCTCCCGTAGCAAGTTCTTGA 58.755 47.619 15.52 0.00 0.00 3.02
445 446 5.050091 CGTAGCAAGTTCTTGATTGTTCTGT 60.050 40.000 15.52 0.00 0.00 3.41
455 456 3.734463 TGATTGTTCTGTGCGTAGGAAA 58.266 40.909 0.00 0.00 0.00 3.13
456 457 4.130857 TGATTGTTCTGTGCGTAGGAAAA 58.869 39.130 0.00 0.00 0.00 2.29
459 460 5.508200 TTGTTCTGTGCGTAGGAAAATTT 57.492 34.783 0.00 0.00 0.00 1.82
460 461 5.508200 TGTTCTGTGCGTAGGAAAATTTT 57.492 34.783 2.28 2.28 0.00 1.82
470 471 6.926272 TGCGTAGGAAAATTTTATTTGCAGTT 59.074 30.769 2.75 0.00 33.56 3.16
486 487 1.301165 GTTGACGCACCCTACCGTT 60.301 57.895 0.00 0.00 37.87 4.44
490 491 0.390735 GACGCACCCTACCGTTGAAT 60.391 55.000 0.00 0.00 37.87 2.57
519 520 4.102035 GGACATGGATGTGCTTCTTTTC 57.898 45.455 4.17 0.00 44.46 2.29
527 528 8.789762 CATGGATGTGCTTCTTTTCATATATGA 58.210 33.333 11.49 11.49 34.44 2.15
564 567 6.561737 TCTAAGCCATCGTGTAGATTAGAG 57.438 41.667 0.00 0.00 37.52 2.43
570 573 4.262079 CCATCGTGTAGATTAGAGGGAACC 60.262 50.000 0.00 0.00 44.40 3.62
631 635 1.518325 TGCAACCTCACATACAACCG 58.482 50.000 0.00 0.00 0.00 4.44
646 650 6.099269 ACATACAACCGGTTATCATAGAGGTT 59.901 38.462 21.79 0.00 42.03 3.50
652 656 5.245526 ACCGGTTATCATAGAGGTTGTATCC 59.754 44.000 0.00 0.00 0.00 2.59
654 658 5.337330 CGGTTATCATAGAGGTTGTATCCCC 60.337 48.000 0.00 0.00 0.00 4.81
659 663 0.690077 AGAGGTTGTATCCCCGGACC 60.690 60.000 0.73 0.00 0.00 4.46
664 668 0.326713 TTGTATCCCCGGACCCATCA 60.327 55.000 0.73 0.00 0.00 3.07
665 669 0.104672 TGTATCCCCGGACCCATCAT 60.105 55.000 0.73 0.00 0.00 2.45
666 670 0.324943 GTATCCCCGGACCCATCATG 59.675 60.000 0.73 0.00 0.00 3.07
667 671 0.104672 TATCCCCGGACCCATCATGT 60.105 55.000 0.73 0.00 0.00 3.21
668 672 0.993509 ATCCCCGGACCCATCATGTT 60.994 55.000 0.73 0.00 0.00 2.71
669 673 1.211567 TCCCCGGACCCATCATGTTT 61.212 55.000 0.73 0.00 0.00 2.83
670 674 0.324275 CCCCGGACCCATCATGTTTT 60.324 55.000 0.73 0.00 0.00 2.43
671 675 1.555967 CCCGGACCCATCATGTTTTT 58.444 50.000 0.73 0.00 0.00 1.94
714 718 1.967319 TGGCTCACTGAAAACTGTCC 58.033 50.000 0.00 0.00 0.00 4.02
715 719 0.868406 GGCTCACTGAAAACTGTCCG 59.132 55.000 0.00 0.00 0.00 4.79
731 735 4.181578 CTGTCCGTTCGGTCATTTCTATT 58.818 43.478 11.04 0.00 0.00 1.73
733 737 3.308866 GTCCGTTCGGTCATTTCTATTGG 59.691 47.826 11.04 0.00 0.00 3.16
751 755 0.609662 GGGTTTGGCTCAATGCACAT 59.390 50.000 0.00 0.00 45.15 3.21
762 766 4.749099 GCTCAATGCACATAACCAAACAAA 59.251 37.500 0.00 0.00 42.31 2.83
763 767 5.409214 GCTCAATGCACATAACCAAACAAAT 59.591 36.000 0.00 0.00 42.31 2.32
764 768 6.589523 GCTCAATGCACATAACCAAACAAATA 59.410 34.615 0.00 0.00 42.31 1.40
765 769 7.411804 GCTCAATGCACATAACCAAACAAATAC 60.412 37.037 0.00 0.00 42.31 1.89
770 774 8.668510 TGCACATAACCAAACAAATACATTTT 57.331 26.923 0.00 0.00 0.00 1.82
771 775 8.768955 TGCACATAACCAAACAAATACATTTTC 58.231 29.630 0.00 0.00 0.00 2.29
772 776 8.768955 GCACATAACCAAACAAATACATTTTCA 58.231 29.630 0.00 0.00 0.00 2.69
776 780 7.650834 AACCAAACAAATACATTTTCATCCG 57.349 32.000 0.00 0.00 0.00 4.18
777 781 6.162777 ACCAAACAAATACATTTTCATCCGG 58.837 36.000 0.00 0.00 0.00 5.14
778 782 6.162777 CCAAACAAATACATTTTCATCCGGT 58.837 36.000 0.00 0.00 0.00 5.28
779 783 6.090628 CCAAACAAATACATTTTCATCCGGTG 59.909 38.462 0.00 0.00 0.00 4.94
780 784 4.743493 ACAAATACATTTTCATCCGGTGC 58.257 39.130 0.00 0.00 0.00 5.01
781 785 3.691049 AATACATTTTCATCCGGTGCG 57.309 42.857 0.00 0.00 0.00 5.34
792 796 4.303853 CGGTGCGGAACTCTATCG 57.696 61.111 0.00 0.00 0.00 2.92
793 797 1.432251 CGGTGCGGAACTCTATCGT 59.568 57.895 0.00 0.00 0.00 3.73
794 798 0.866061 CGGTGCGGAACTCTATCGTG 60.866 60.000 0.00 0.00 0.00 4.35
795 799 0.172803 GGTGCGGAACTCTATCGTGT 59.827 55.000 0.00 0.00 0.00 4.49
796 800 1.546834 GTGCGGAACTCTATCGTGTC 58.453 55.000 0.00 0.00 0.00 3.67
797 801 0.454600 TGCGGAACTCTATCGTGTCC 59.545 55.000 0.00 0.00 0.00 4.02
798 802 0.454600 GCGGAACTCTATCGTGTCCA 59.545 55.000 0.00 0.00 0.00 4.02
799 803 1.135199 GCGGAACTCTATCGTGTCCAA 60.135 52.381 0.00 0.00 0.00 3.53
800 804 2.527100 CGGAACTCTATCGTGTCCAAC 58.473 52.381 0.00 0.00 0.00 3.77
801 805 2.734492 CGGAACTCTATCGTGTCCAACC 60.734 54.545 0.00 0.00 0.00 3.77
802 806 2.232941 GGAACTCTATCGTGTCCAACCA 59.767 50.000 0.00 0.00 0.00 3.67
803 807 3.306502 GGAACTCTATCGTGTCCAACCAA 60.307 47.826 0.00 0.00 0.00 3.67
804 808 4.312443 GAACTCTATCGTGTCCAACCAAA 58.688 43.478 0.00 0.00 0.00 3.28
808 812 4.000325 TCTATCGTGTCCAACCAAACATG 59.000 43.478 0.00 0.00 34.41 3.21
816 820 3.067461 GTCCAACCAAACATGCTGTTACA 59.933 43.478 0.00 0.00 40.14 2.41
935 944 2.453242 CCCCCTCCCCTCGAATAAG 58.547 63.158 0.00 0.00 0.00 1.73
1000 1009 0.323178 CAGCAGTCAAGCAATCCCCT 60.323 55.000 0.00 0.00 36.85 4.79
1001 1010 0.034670 AGCAGTCAAGCAATCCCCTC 60.035 55.000 0.00 0.00 36.85 4.30
1026 1035 1.550976 ACATCTCTCCACTTCCCGAAC 59.449 52.381 0.00 0.00 0.00 3.95
1028 1037 0.114560 TCTCTCCACTTCCCGAACCT 59.885 55.000 0.00 0.00 0.00 3.50
1031 1040 1.346722 TCTCCACTTCCCGAACCTTTC 59.653 52.381 0.00 0.00 0.00 2.62
1035 1045 1.063654 ACTTCCCGAACCTTTCCCCA 61.064 55.000 0.00 0.00 0.00 4.96
1036 1046 0.322546 CTTCCCGAACCTTTCCCCAG 60.323 60.000 0.00 0.00 0.00 4.45
1038 1048 2.757077 CCGAACCTTTCCCCAGCT 59.243 61.111 0.00 0.00 0.00 4.24
1056 1079 4.899239 CTCGCCATGGACGCCTCC 62.899 72.222 18.40 0.00 37.04 4.30
1128 1151 2.269241 GGCCCCAGGAAGAAGTCG 59.731 66.667 0.00 0.00 0.00 4.18
1532 1566 4.576330 AGGTTCATTGCTTAGTTAGGCT 57.424 40.909 0.00 0.00 0.00 4.58
1534 1568 4.010349 GGTTCATTGCTTAGTTAGGCTGT 58.990 43.478 0.00 0.00 0.00 4.40
1596 1633 3.437395 TCAGTTCGAAGTAGACTGCTCTC 59.563 47.826 4.91 0.00 0.00 3.20
1678 1718 4.791163 ACATTTTGTTCGTTCTGTGTTTCG 59.209 37.500 0.00 0.00 0.00 3.46
1679 1719 2.445453 TTGTTCGTTCTGTGTTTCGC 57.555 45.000 0.00 0.00 0.00 4.70
1680 1720 1.647346 TGTTCGTTCTGTGTTTCGCT 58.353 45.000 0.00 0.00 0.00 4.93
1686 1726 0.749818 TTCTGTGTTTCGCTTGCCCA 60.750 50.000 0.00 0.00 0.00 5.36
1691 1749 3.353836 TTTCGCTTGCCCACGCTC 61.354 61.111 0.00 0.00 35.36 5.03
1711 1770 4.201832 GCTCTGTTCAGAATTGCATCTCTG 60.202 45.833 16.01 16.01 40.42 3.35
1732 1791 1.066929 GGTGTGGGTTTGCCATTCATC 60.067 52.381 0.00 0.00 36.17 2.92
1734 1793 2.299867 GTGTGGGTTTGCCATTCATCTT 59.700 45.455 0.00 0.00 36.17 2.40
1750 1809 8.475639 CCATTCATCTTCTTTGAATTTCATCCT 58.524 33.333 0.00 0.00 40.84 3.24
1756 1817 5.649782 TCTTTGAATTTCATCCTTCCAGC 57.350 39.130 0.00 0.00 0.00 4.85
1850 1921 1.979693 TTTCCCGCCCCAAATTCGG 60.980 57.895 0.00 0.00 42.58 4.30
1857 1930 1.815866 CCCCAAATTCGGATGGCAC 59.184 57.895 0.00 0.00 35.28 5.01
1866 1939 2.509052 TCGGATGGCACTAATCGAAG 57.491 50.000 0.00 0.00 0.00 3.79
1870 1953 3.070018 GGATGGCACTAATCGAAGATGG 58.930 50.000 0.00 0.00 45.12 3.51
1876 1959 5.066375 TGGCACTAATCGAAGATGGAAAATG 59.934 40.000 0.00 0.00 45.12 2.32
2061 2670 0.598065 GCTTCAGTTTCGTGCCCATT 59.402 50.000 0.00 0.00 0.00 3.16
2062 2671 1.401539 GCTTCAGTTTCGTGCCCATTC 60.402 52.381 0.00 0.00 0.00 2.67
2063 2672 2.154462 CTTCAGTTTCGTGCCCATTCT 58.846 47.619 0.00 0.00 0.00 2.40
2064 2673 1.522668 TCAGTTTCGTGCCCATTCTG 58.477 50.000 0.00 0.00 0.00 3.02
2065 2674 1.071542 TCAGTTTCGTGCCCATTCTGA 59.928 47.619 0.00 0.00 0.00 3.27
2066 2675 2.086869 CAGTTTCGTGCCCATTCTGAT 58.913 47.619 0.00 0.00 0.00 2.90
2106 2715 4.626287 GCAATCTTGGAACCATCTACCAGA 60.626 45.833 0.00 0.00 35.08 3.86
2112 2721 3.051803 TGGAACCATCTACCAGATCCTCT 60.052 47.826 0.00 0.00 31.32 3.69
2142 2751 1.112315 TGGGCGCACAACCAATTTCT 61.112 50.000 11.60 0.00 32.89 2.52
2158 2767 4.826274 ATTTCTGGACGGATCTCTTCAA 57.174 40.909 0.00 0.00 0.00 2.69
2160 2769 4.617253 TTCTGGACGGATCTCTTCAAAA 57.383 40.909 0.00 0.00 0.00 2.44
2164 2773 4.905429 TGGACGGATCTCTTCAAAAATGA 58.095 39.130 0.00 0.00 0.00 2.57
2165 2774 4.695455 TGGACGGATCTCTTCAAAAATGAC 59.305 41.667 0.00 0.00 0.00 3.06
2166 2775 4.695455 GGACGGATCTCTTCAAAAATGACA 59.305 41.667 0.00 0.00 0.00 3.58
2169 2779 5.997746 ACGGATCTCTTCAAAAATGACAGAA 59.002 36.000 0.00 0.00 0.00 3.02
2199 2809 2.010145 ACGACTCGGTGAATTCCATG 57.990 50.000 2.27 0.00 0.00 3.66
2205 2815 3.007940 ACTCGGTGAATTCCATGTTCAGA 59.992 43.478 2.27 0.00 36.35 3.27
2208 2818 2.420022 GGTGAATTCCATGTTCAGACGG 59.580 50.000 2.27 0.00 36.35 4.79
2209 2819 2.083774 TGAATTCCATGTTCAGACGGC 58.916 47.619 2.27 0.00 32.23 5.68
2210 2820 1.062587 GAATTCCATGTTCAGACGGCG 59.937 52.381 4.80 4.80 0.00 6.46
2212 2822 3.499737 CCATGTTCAGACGGCGGC 61.500 66.667 13.24 8.92 0.00 6.53
2213 2823 3.853330 CATGTTCAGACGGCGGCG 61.853 66.667 31.06 31.06 0.00 6.46
2236 2846 4.421554 CCTCCCCTCCAGGCTCCA 62.422 72.222 0.00 0.00 0.00 3.86
2237 2847 2.767496 CTCCCCTCCAGGCTCCAG 60.767 72.222 0.00 0.00 0.00 3.86
2270 2885 0.468214 TAGCTGATCTGGACCCGGAG 60.468 60.000 0.73 0.00 34.49 4.63
2272 2887 2.022240 GCTGATCTGGACCCGGAGAC 62.022 65.000 0.73 0.00 34.49 3.36
2293 2915 2.830370 GGAGCGGGCCATTGAAGG 60.830 66.667 4.39 0.00 0.00 3.46
2315 2937 5.119694 GGACTATTCCTTCCTTGATCACAC 58.880 45.833 0.00 0.00 39.13 3.82
2316 2938 5.338381 GGACTATTCCTTCCTTGATCACACA 60.338 44.000 0.00 0.00 39.13 3.72
2331 2965 3.179048 TCACACATTCAGTTAGATCGCG 58.821 45.455 0.00 0.00 0.00 5.87
2339 2973 4.895224 TCAGTTAGATCGCGTTAGATGT 57.105 40.909 5.77 0.00 0.00 3.06
2340 2974 5.244785 TCAGTTAGATCGCGTTAGATGTT 57.755 39.130 5.77 0.00 0.00 2.71
2341 2975 5.647589 TCAGTTAGATCGCGTTAGATGTTT 58.352 37.500 5.77 0.00 0.00 2.83
2347 2981 2.063266 TCGCGTTAGATGTTTGTGGAC 58.937 47.619 5.77 0.00 0.00 4.02
2413 3053 1.417890 CTTGTAGGCAGGGAGGGTATG 59.582 57.143 0.00 0.00 0.00 2.39
2423 3063 1.078426 GAGGGTATGCCGTGTGCTT 60.078 57.895 0.00 0.00 42.00 3.91
2447 3087 6.983906 AATAAATCTGGGGAATGGATCAAC 57.016 37.500 0.00 0.00 0.00 3.18
2448 3088 2.645838 ATCTGGGGAATGGATCAACG 57.354 50.000 0.00 0.00 0.00 4.10
2451 3091 2.186826 GGGGAATGGATCAACGGCG 61.187 63.158 4.80 4.80 0.00 6.46
2471 3111 0.443869 CCGGCGAATGCACATATAGC 59.556 55.000 9.30 0.00 45.35 2.97
2486 3126 8.356657 TGCACATATAGCATTATTAAACCCAAC 58.643 33.333 0.00 0.00 37.02 3.77
2502 3142 2.487086 CCCAACATGACTTCAGTGGTGA 60.487 50.000 0.00 0.00 32.38 4.02
2503 3143 3.415212 CCAACATGACTTCAGTGGTGAT 58.585 45.455 0.00 0.00 32.38 3.06
2506 3146 5.122869 CCAACATGACTTCAGTGGTGATTAG 59.877 44.000 0.00 0.00 32.38 1.73
2511 3151 6.358974 TGACTTCAGTGGTGATTAGATTGA 57.641 37.500 0.00 0.00 30.85 2.57
2518 3161 8.996651 TCAGTGGTGATTAGATTGAGTAGATA 57.003 34.615 0.00 0.00 0.00 1.98
2535 3178 7.292356 TGAGTAGATAACCATATGTTCCCATGT 59.708 37.037 1.24 0.00 38.42 3.21
2536 3179 8.736097 AGTAGATAACCATATGTTCCCATGTA 57.264 34.615 1.24 0.00 38.42 2.29
2537 3180 8.594550 AGTAGATAACCATATGTTCCCATGTAC 58.405 37.037 1.24 1.76 38.42 2.90
2538 3181 7.633018 AGATAACCATATGTTCCCATGTACT 57.367 36.000 1.24 0.00 38.42 2.73
2539 3182 8.736097 AGATAACCATATGTTCCCATGTACTA 57.264 34.615 1.24 0.00 38.42 1.82
2540 3183 8.594550 AGATAACCATATGTTCCCATGTACTAC 58.405 37.037 1.24 0.00 38.42 2.73
2541 3184 6.824958 AACCATATGTTCCCATGTACTACT 57.175 37.500 1.24 0.00 28.45 2.57
2542 3185 6.824958 ACCATATGTTCCCATGTACTACTT 57.175 37.500 1.24 0.00 32.29 2.24
2543 3186 7.208064 ACCATATGTTCCCATGTACTACTTT 57.792 36.000 1.24 0.00 32.29 2.66
2544 3187 7.054124 ACCATATGTTCCCATGTACTACTTTG 58.946 38.462 1.24 0.00 32.29 2.77
2545 3188 7.054124 CCATATGTTCCCATGTACTACTTTGT 58.946 38.462 1.24 0.00 32.29 2.83
2546 3189 7.226720 CCATATGTTCCCATGTACTACTTTGTC 59.773 40.741 1.24 0.00 32.29 3.18
2547 3190 4.901868 TGTTCCCATGTACTACTTTGTCC 58.098 43.478 0.00 0.00 0.00 4.02
2548 3191 3.880047 TCCCATGTACTACTTTGTCCG 57.120 47.619 0.00 0.00 0.00 4.79
2549 3192 3.167485 TCCCATGTACTACTTTGTCCGT 58.833 45.455 0.00 0.00 0.00 4.69
2550 3193 3.579586 TCCCATGTACTACTTTGTCCGTT 59.420 43.478 0.00 0.00 0.00 4.44
2551 3194 3.930848 CCCATGTACTACTTTGTCCGTTC 59.069 47.826 0.00 0.00 0.00 3.95
2552 3195 4.561938 CCCATGTACTACTTTGTCCGTTCA 60.562 45.833 0.00 0.00 0.00 3.18
2553 3196 4.387862 CCATGTACTACTTTGTCCGTTCAC 59.612 45.833 0.00 0.00 0.00 3.18
2554 3197 4.652421 TGTACTACTTTGTCCGTTCACA 57.348 40.909 0.00 0.00 0.00 3.58
2555 3198 5.008619 TGTACTACTTTGTCCGTTCACAA 57.991 39.130 0.00 0.00 34.36 3.33
2556 3199 5.417811 TGTACTACTTTGTCCGTTCACAAA 58.582 37.500 0.00 4.94 42.68 2.83
2557 3200 6.050432 TGTACTACTTTGTCCGTTCACAAAT 58.950 36.000 5.36 1.12 43.63 2.32
2558 3201 7.208777 TGTACTACTTTGTCCGTTCACAAATA 58.791 34.615 5.36 1.93 43.63 1.40
2559 3202 6.535274 ACTACTTTGTCCGTTCACAAATAC 57.465 37.500 5.36 0.00 43.63 1.89
2560 3203 6.285990 ACTACTTTGTCCGTTCACAAATACT 58.714 36.000 5.36 0.00 43.63 2.12
2561 3204 5.668558 ACTTTGTCCGTTCACAAATACTC 57.331 39.130 5.36 0.00 43.63 2.59
2562 3205 4.514066 ACTTTGTCCGTTCACAAATACTCC 59.486 41.667 5.36 0.00 43.63 3.85
2563 3206 3.048337 TGTCCGTTCACAAATACTCCC 57.952 47.619 0.00 0.00 0.00 4.30
2564 3207 2.635915 TGTCCGTTCACAAATACTCCCT 59.364 45.455 0.00 0.00 0.00 4.20
2565 3208 3.259902 GTCCGTTCACAAATACTCCCTC 58.740 50.000 0.00 0.00 0.00 4.30
2566 3209 2.235402 TCCGTTCACAAATACTCCCTCC 59.765 50.000 0.00 0.00 0.00 4.30
2567 3210 2.268298 CGTTCACAAATACTCCCTCCG 58.732 52.381 0.00 0.00 0.00 4.63
2568 3211 2.353406 CGTTCACAAATACTCCCTCCGT 60.353 50.000 0.00 0.00 0.00 4.69
2569 3212 3.671716 GTTCACAAATACTCCCTCCGTT 58.328 45.455 0.00 0.00 0.00 4.44
2570 3213 3.604875 TCACAAATACTCCCTCCGTTC 57.395 47.619 0.00 0.00 0.00 3.95
2571 3214 2.901192 TCACAAATACTCCCTCCGTTCA 59.099 45.455 0.00 0.00 0.00 3.18
2572 3215 3.517901 TCACAAATACTCCCTCCGTTCAT 59.482 43.478 0.00 0.00 0.00 2.57
2573 3216 4.712829 TCACAAATACTCCCTCCGTTCATA 59.287 41.667 0.00 0.00 0.00 2.15
2574 3217 5.188163 TCACAAATACTCCCTCCGTTCATAA 59.812 40.000 0.00 0.00 0.00 1.90
2575 3218 5.878116 CACAAATACTCCCTCCGTTCATAAA 59.122 40.000 0.00 0.00 0.00 1.40
2576 3219 6.542370 CACAAATACTCCCTCCGTTCATAAAT 59.458 38.462 0.00 0.00 0.00 1.40
2577 3220 7.713507 CACAAATACTCCCTCCGTTCATAAATA 59.286 37.037 0.00 0.00 0.00 1.40
2578 3221 8.437575 ACAAATACTCCCTCCGTTCATAAATAT 58.562 33.333 0.00 0.00 0.00 1.28
2579 3222 9.938280 CAAATACTCCCTCCGTTCATAAATATA 57.062 33.333 0.00 0.00 0.00 0.86
2582 3225 7.613551 ACTCCCTCCGTTCATAAATATAAGT 57.386 36.000 0.00 0.00 0.00 2.24
2583 3226 7.668492 ACTCCCTCCGTTCATAAATATAAGTC 58.332 38.462 0.00 0.00 0.00 3.01
2584 3227 7.509659 ACTCCCTCCGTTCATAAATATAAGTCT 59.490 37.037 0.00 0.00 0.00 3.24
2585 3228 8.258850 TCCCTCCGTTCATAAATATAAGTCTT 57.741 34.615 0.00 0.00 0.00 3.01
2586 3229 8.711170 TCCCTCCGTTCATAAATATAAGTCTTT 58.289 33.333 0.00 0.00 0.00 2.52
2587 3230 9.338622 CCCTCCGTTCATAAATATAAGTCTTTT 57.661 33.333 0.00 0.00 0.00 2.27
2605 3248 8.380742 AGTCTTTTTAGAGATTCCACTATGGA 57.619 34.615 0.00 0.00 46.61 3.41
2616 3259 4.442401 TCCACTATGGACTACATACGGA 57.558 45.455 0.00 0.00 42.67 4.69
2617 3260 4.395625 TCCACTATGGACTACATACGGAG 58.604 47.826 0.00 0.00 42.67 4.63
2618 3261 3.057456 CCACTATGGACTACATACGGAGC 60.057 52.174 0.00 0.00 40.96 4.70
2619 3262 3.568430 CACTATGGACTACATACGGAGCA 59.432 47.826 0.00 0.00 41.03 4.26
2620 3263 4.037565 CACTATGGACTACATACGGAGCAA 59.962 45.833 0.00 0.00 41.03 3.91
2621 3264 4.647853 ACTATGGACTACATACGGAGCAAA 59.352 41.667 0.00 0.00 41.03 3.68
2622 3265 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
2623 3266 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
2624 3267 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
2625 3268 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
2626 3269 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
2627 3270 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2628 3271 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2629 3272 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2630 3273 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2631 3274 4.154195 ACATACGGAGCAAAATGAGTGAAC 59.846 41.667 0.00 0.00 0.00 3.18
2632 3275 2.851195 ACGGAGCAAAATGAGTGAACT 58.149 42.857 0.00 0.00 0.00 3.01
2633 3276 4.002906 ACGGAGCAAAATGAGTGAACTA 57.997 40.909 0.00 0.00 0.00 2.24
2634 3277 4.579869 ACGGAGCAAAATGAGTGAACTAT 58.420 39.130 0.00 0.00 0.00 2.12
2635 3278 5.730550 ACGGAGCAAAATGAGTGAACTATA 58.269 37.500 0.00 0.00 0.00 1.31
2636 3279 5.581085 ACGGAGCAAAATGAGTGAACTATAC 59.419 40.000 0.00 0.00 0.00 1.47
2637 3280 5.812642 CGGAGCAAAATGAGTGAACTATACT 59.187 40.000 0.00 0.00 0.00 2.12
2638 3281 6.019479 CGGAGCAAAATGAGTGAACTATACTC 60.019 42.308 0.00 0.00 43.73 2.59
2639 3282 7.044798 GGAGCAAAATGAGTGAACTATACTCT 58.955 38.462 0.00 0.00 43.79 3.24
2640 3283 8.198109 GGAGCAAAATGAGTGAACTATACTCTA 58.802 37.037 0.00 0.00 43.79 2.43
2641 3284 9.587772 GAGCAAAATGAGTGAACTATACTCTAA 57.412 33.333 0.00 0.00 43.79 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.063764 CTACTCGGTCACGTTCCTAGC 59.936 57.143 7.64 0.00 41.85 3.42
36 37 0.479378 ACGGACCCTAAAGCCCAAAA 59.521 50.000 0.00 0.00 0.00 2.44
85 86 3.326747 CACCTCCACTTTATATAGGCGC 58.673 50.000 0.00 0.00 0.00 6.53
87 88 3.326747 CGCACCTCCACTTTATATAGGC 58.673 50.000 0.00 0.00 0.00 3.93
134 135 1.024579 CAAACCCTAATGACGGCGCT 61.025 55.000 6.90 0.00 0.00 5.92
139 140 2.487762 ACACATGCAAACCCTAATGACG 59.512 45.455 0.00 0.00 0.00 4.35
141 142 4.517952 CAACACATGCAAACCCTAATGA 57.482 40.909 0.00 0.00 0.00 2.57
183 184 3.688136 CGATAACACAGTCGGCGG 58.312 61.111 7.21 0.00 34.39 6.13
222 223 2.434884 CGCGTGCAGGAGGAACAT 60.435 61.111 11.29 0.00 0.00 2.71
283 284 0.959867 TCGTCCGATCCCACGTACAA 60.960 55.000 10.10 0.00 37.30 2.41
303 304 0.456221 GATCTTCCTCGAACAGCCGA 59.544 55.000 0.00 0.00 37.03 5.54
304 305 0.867753 CGATCTTCCTCGAACAGCCG 60.868 60.000 0.00 0.00 41.12 5.52
305 306 0.528684 CCGATCTTCCTCGAACAGCC 60.529 60.000 0.00 0.00 41.12 4.85
315 316 1.457009 CCCTCCTCGTCCGATCTTCC 61.457 65.000 0.00 0.00 0.00 3.46
317 318 1.455959 CCCCTCCTCGTCCGATCTT 60.456 63.158 0.00 0.00 0.00 2.40
428 429 3.206150 ACGCACAGAACAATCAAGAACT 58.794 40.909 0.00 0.00 0.00 3.01
436 437 5.705609 AATTTTCCTACGCACAGAACAAT 57.294 34.783 0.00 0.00 0.00 2.71
445 446 6.451393 ACTGCAAATAAAATTTTCCTACGCA 58.549 32.000 6.72 10.06 0.00 5.24
455 456 4.447389 GGTGCGTCAACTGCAAATAAAATT 59.553 37.500 0.00 0.00 45.23 1.82
456 457 3.987220 GGTGCGTCAACTGCAAATAAAAT 59.013 39.130 0.00 0.00 45.23 1.82
459 460 1.268352 GGGTGCGTCAACTGCAAATAA 59.732 47.619 0.00 0.00 45.23 1.40
460 461 0.878416 GGGTGCGTCAACTGCAAATA 59.122 50.000 0.00 0.00 45.23 1.40
470 471 1.746322 TTCAACGGTAGGGTGCGTCA 61.746 55.000 0.00 0.00 0.00 4.35
490 491 2.725637 CACATCCATGTCCATGTTGGA 58.274 47.619 6.53 6.44 45.98 3.53
499 500 4.771590 TGAAAAGAAGCACATCCATGTC 57.228 40.909 0.00 0.00 39.39 3.06
527 528 8.211629 ACGATGGCTTAGATTTAAGATAAGGTT 58.788 33.333 7.19 0.00 38.88 3.50
564 567 3.934068 TCTCGTTCACTTATTGGTTCCC 58.066 45.455 0.00 0.00 0.00 3.97
570 573 7.596749 AACACCTAATCTCGTTCACTTATTG 57.403 36.000 0.00 0.00 0.00 1.90
579 582 8.385898 TGTTTGATTTAACACCTAATCTCGTT 57.614 30.769 0.00 0.00 33.31 3.85
631 635 5.337330 CGGGGATACAACCTCTATGATAACC 60.337 48.000 0.00 0.00 39.74 2.85
646 650 0.104672 ATGATGGGTCCGGGGATACA 60.105 55.000 0.00 0.00 39.74 2.29
648 652 0.104672 ACATGATGGGTCCGGGGATA 60.105 55.000 0.00 0.00 0.00 2.59
652 656 1.555967 AAAAACATGATGGGTCCGGG 58.444 50.000 0.00 0.00 0.00 5.73
714 718 3.267483 ACCCAATAGAAATGACCGAACG 58.733 45.455 0.00 0.00 0.00 3.95
715 719 5.399013 CAAACCCAATAGAAATGACCGAAC 58.601 41.667 0.00 0.00 0.00 3.95
731 735 0.758310 TGTGCATTGAGCCAAACCCA 60.758 50.000 0.00 0.00 44.83 4.51
733 737 3.253230 GTTATGTGCATTGAGCCAAACC 58.747 45.455 0.00 0.00 44.83 3.27
751 755 7.815068 CCGGATGAAAATGTATTTGTTTGGTTA 59.185 33.333 0.00 0.00 0.00 2.85
774 778 1.299165 CGATAGAGTTCCGCACCGG 60.299 63.158 0.00 0.00 44.74 5.28
775 779 0.866061 CACGATAGAGTTCCGCACCG 60.866 60.000 0.00 0.00 41.38 4.94
776 780 0.172803 ACACGATAGAGTTCCGCACC 59.827 55.000 0.00 0.00 36.10 5.01
777 781 1.546834 GACACGATAGAGTTCCGCAC 58.453 55.000 0.00 0.00 40.98 5.34
778 782 0.454600 GGACACGATAGAGTTCCGCA 59.545 55.000 0.00 0.00 40.98 5.69
779 783 0.454600 TGGACACGATAGAGTTCCGC 59.545 55.000 0.00 0.00 40.98 5.54
780 784 2.527100 GTTGGACACGATAGAGTTCCG 58.473 52.381 0.00 0.00 40.98 4.30
781 785 2.232941 TGGTTGGACACGATAGAGTTCC 59.767 50.000 0.00 0.00 40.98 3.62
782 786 3.587797 TGGTTGGACACGATAGAGTTC 57.412 47.619 0.00 0.00 40.98 3.01
783 787 4.062991 GTTTGGTTGGACACGATAGAGTT 58.937 43.478 0.00 0.00 40.98 3.01
784 788 3.070446 TGTTTGGTTGGACACGATAGAGT 59.930 43.478 0.00 0.00 44.55 3.24
785 789 3.659786 TGTTTGGTTGGACACGATAGAG 58.340 45.455 0.00 0.00 41.38 2.43
786 790 3.755112 TGTTTGGTTGGACACGATAGA 57.245 42.857 0.00 0.00 41.38 1.98
787 791 3.426159 GCATGTTTGGTTGGACACGATAG 60.426 47.826 0.00 0.00 46.19 2.08
788 792 2.486203 GCATGTTTGGTTGGACACGATA 59.514 45.455 0.00 0.00 0.00 2.92
789 793 1.269448 GCATGTTTGGTTGGACACGAT 59.731 47.619 0.00 0.00 0.00 3.73
790 794 0.665835 GCATGTTTGGTTGGACACGA 59.334 50.000 0.00 0.00 0.00 4.35
791 795 0.667993 AGCATGTTTGGTTGGACACG 59.332 50.000 0.00 0.00 0.00 4.49
792 796 2.138596 CAGCATGTTTGGTTGGACAC 57.861 50.000 0.00 0.00 0.00 3.67
804 808 2.274437 CAGCGATCTGTAACAGCATGT 58.726 47.619 0.00 0.00 43.26 3.21
816 820 1.680735 TGCCAACAAAAACAGCGATCT 59.319 42.857 0.00 0.00 0.00 2.75
935 944 2.452105 GAGACGAGATTTGCGGAGTAC 58.548 52.381 0.00 0.00 0.00 2.73
1000 1009 2.300152 GGAAGTGGAGAGATGTGTGTGA 59.700 50.000 0.00 0.00 0.00 3.58
1001 1010 2.613977 GGGAAGTGGAGAGATGTGTGTG 60.614 54.545 0.00 0.00 0.00 3.82
1038 1048 3.838271 GAGGCGTCCATGGCGAGA 61.838 66.667 26.00 0.00 39.82 4.04
1128 1151 4.651008 TTGACGGACCGCGACACC 62.651 66.667 15.39 6.92 0.00 4.16
1407 1433 1.037030 CCGGGTTGATGTTGGGGATG 61.037 60.000 0.00 0.00 0.00 3.51
1532 1566 4.193240 TCCATACATCCCAGCTACTACA 57.807 45.455 0.00 0.00 0.00 2.74
1534 1568 4.096681 CCATCCATACATCCCAGCTACTA 58.903 47.826 0.00 0.00 0.00 1.82
1592 1629 4.647291 AAATACAACGACAAAGCGAGAG 57.353 40.909 0.00 0.00 34.83 3.20
1596 1633 4.607235 GTCAGAAAATACAACGACAAAGCG 59.393 41.667 0.00 0.00 37.29 4.68
1655 1695 4.791163 CGAAACACAGAACGAACAAAATGT 59.209 37.500 0.00 0.00 0.00 2.71
1662 1702 2.363220 CAAGCGAAACACAGAACGAAC 58.637 47.619 0.00 0.00 0.00 3.95
1678 1718 2.970974 GAACAGAGCGTGGGCAAGC 61.971 63.158 0.00 0.00 43.41 4.01
1679 1719 1.572085 CTGAACAGAGCGTGGGCAAG 61.572 60.000 0.00 0.00 43.41 4.01
1680 1720 1.597854 CTGAACAGAGCGTGGGCAA 60.598 57.895 0.00 0.00 43.41 4.52
1686 1726 1.882912 TGCAATTCTGAACAGAGCGT 58.117 45.000 4.72 0.00 38.88 5.07
1691 1749 3.377485 CCCAGAGATGCAATTCTGAACAG 59.623 47.826 24.51 12.39 42.67 3.16
1694 1752 3.245016 ACACCCAGAGATGCAATTCTGAA 60.245 43.478 24.51 0.00 42.67 3.02
1732 1791 6.098017 GCTGGAAGGATGAAATTCAAAGAAG 58.902 40.000 0.00 0.00 0.00 2.85
1734 1793 4.156556 CGCTGGAAGGATGAAATTCAAAGA 59.843 41.667 0.00 0.00 0.00 2.52
1769 1830 2.037144 TCCCACCTACCTTCGCTATTC 58.963 52.381 0.00 0.00 0.00 1.75
1773 1834 0.831307 GATTCCCACCTACCTTCGCT 59.169 55.000 0.00 0.00 0.00 4.93
1845 1916 3.069586 TCTTCGATTAGTGCCATCCGAAT 59.930 43.478 0.00 0.00 0.00 3.34
1850 1921 3.995199 TCCATCTTCGATTAGTGCCATC 58.005 45.455 0.00 0.00 0.00 3.51
1866 1939 4.173256 ACGCGGATTTTTCATTTTCCATC 58.827 39.130 12.47 0.00 0.00 3.51
1870 1953 7.253651 GGAAATAGACGCGGATTTTTCATTTTC 60.254 37.037 21.06 15.25 0.00 2.29
1876 1959 3.242969 GGGGAAATAGACGCGGATTTTTC 60.243 47.826 12.47 14.41 0.00 2.29
2031 2640 1.726853 AACTGAAGCGGGAAATCTCG 58.273 50.000 0.00 0.00 0.00 4.04
2061 2670 3.726557 AAAGGATGTGCCAGAATCAGA 57.273 42.857 0.00 0.00 40.02 3.27
2062 2671 3.675228 GCAAAAGGATGTGCCAGAATCAG 60.675 47.826 0.00 0.00 40.02 2.90
2063 2672 2.231964 GCAAAAGGATGTGCCAGAATCA 59.768 45.455 0.00 0.00 40.02 2.57
2064 2673 2.231964 TGCAAAAGGATGTGCCAGAATC 59.768 45.455 0.00 0.00 40.14 2.52
2065 2674 2.250031 TGCAAAAGGATGTGCCAGAAT 58.750 42.857 0.00 0.00 40.14 2.40
2066 2675 1.702182 TGCAAAAGGATGTGCCAGAA 58.298 45.000 0.00 0.00 40.14 3.02
2106 2715 1.944177 CCATCCGGGACATAGAGGAT 58.056 55.000 0.00 0.00 43.66 3.24
2135 2744 4.507710 TGAAGAGATCCGTCCAGAAATTG 58.492 43.478 0.00 0.00 0.00 2.32
2142 2751 4.695455 GTCATTTTTGAAGAGATCCGTCCA 59.305 41.667 0.00 0.00 0.00 4.02
2146 2755 6.486253 TTCTGTCATTTTTGAAGAGATCCG 57.514 37.500 0.00 0.00 0.00 4.18
2169 2779 2.353579 CACCGAGTCGTTGGTTCTTTTT 59.646 45.455 12.31 0.00 38.59 1.94
2174 2784 1.792006 ATTCACCGAGTCGTTGGTTC 58.208 50.000 10.37 0.00 38.59 3.62
2177 2787 1.076332 GGAATTCACCGAGTCGTTGG 58.924 55.000 10.37 0.00 0.00 3.77
2181 2791 2.010145 ACATGGAATTCACCGAGTCG 57.990 50.000 5.29 5.29 0.00 4.18
2186 2796 2.094258 CGTCTGAACATGGAATTCACCG 59.906 50.000 7.93 0.00 32.67 4.94
2219 2829 4.421554 TGGAGCCTGGAGGGGAGG 62.422 72.222 0.00 0.00 35.18 4.30
2221 2831 4.421554 CCTGGAGCCTGGAGGGGA 62.422 72.222 6.60 0.00 37.23 4.81
2225 2835 3.333219 TTGCCCTGGAGCCTGGAG 61.333 66.667 13.43 5.52 37.23 3.86
2226 2836 3.650950 GTTGCCCTGGAGCCTGGA 61.651 66.667 13.43 0.00 37.23 3.86
2227 2837 4.748144 GGTTGCCCTGGAGCCTGG 62.748 72.222 5.52 5.52 35.20 4.45
2236 2846 3.717294 CTACCCAGCGGTTGCCCT 61.717 66.667 0.00 0.00 40.58 5.19
2247 2862 2.916355 GGTCCAGATCAGCTACCCA 58.084 57.895 0.00 0.00 0.00 4.51
2262 2877 3.507009 CTCCGACGTCTCCGGGTC 61.507 72.222 14.70 0.00 46.47 4.46
2293 2915 5.734720 TGTGTGATCAAGGAAGGAATAGTC 58.265 41.667 0.00 0.00 0.00 2.59
2304 2926 6.019237 CGATCTAACTGAATGTGTGATCAAGG 60.019 42.308 0.00 0.00 37.71 3.61
2305 2927 6.509199 GCGATCTAACTGAATGTGTGATCAAG 60.509 42.308 0.00 0.00 37.71 3.02
2306 2928 5.291858 GCGATCTAACTGAATGTGTGATCAA 59.708 40.000 0.00 0.00 37.71 2.57
2307 2929 4.805719 GCGATCTAACTGAATGTGTGATCA 59.194 41.667 0.00 0.00 37.71 2.92
2308 2930 4.085363 CGCGATCTAACTGAATGTGTGATC 60.085 45.833 0.00 0.00 36.14 2.92
2309 2931 3.798878 CGCGATCTAACTGAATGTGTGAT 59.201 43.478 0.00 0.00 0.00 3.06
2315 2937 5.687730 ACATCTAACGCGATCTAACTGAATG 59.312 40.000 15.93 4.92 0.00 2.67
2316 2938 5.833082 ACATCTAACGCGATCTAACTGAAT 58.167 37.500 15.93 0.00 0.00 2.57
2340 2974 1.208535 ACCTGAGTTTGTCGTCCACAA 59.791 47.619 0.00 0.00 43.68 3.33
2341 2975 0.828022 ACCTGAGTTTGTCGTCCACA 59.172 50.000 0.00 0.00 0.00 4.17
2347 2981 6.866770 TGTAGAGAATTTACCTGAGTTTGTCG 59.133 38.462 0.00 0.00 0.00 4.35
2413 3053 3.243068 CCCAGATTTATTAAGCACACGGC 60.243 47.826 0.00 0.00 45.30 5.68
2416 3056 6.461509 CCATTCCCCAGATTTATTAAGCACAC 60.462 42.308 0.00 0.00 0.00 3.82
2423 3063 6.714810 CGTTGATCCATTCCCCAGATTTATTA 59.285 38.462 0.00 0.00 0.00 0.98
2451 3091 0.443869 CTATATGTGCATTCGCCGGC 59.556 55.000 19.07 19.07 37.32 6.13
2461 3101 8.356657 TGTTGGGTTTAATAATGCTATATGTGC 58.643 33.333 0.00 0.00 0.00 4.57
2471 3111 8.522830 ACTGAAGTCATGTTGGGTTTAATAATG 58.477 33.333 0.00 0.00 0.00 1.90
2474 3114 6.432783 CCACTGAAGTCATGTTGGGTTTAATA 59.567 38.462 0.00 0.00 0.00 0.98
2477 3117 4.141287 CCACTGAAGTCATGTTGGGTTTA 58.859 43.478 0.00 0.00 0.00 2.01
2481 3121 1.881973 CACCACTGAAGTCATGTTGGG 59.118 52.381 0.00 0.00 0.00 4.12
2486 3126 6.820152 TCAATCTAATCACCACTGAAGTCATG 59.180 38.462 0.00 0.00 0.00 3.07
2490 3130 6.365970 ACTCAATCTAATCACCACTGAAGT 57.634 37.500 0.00 0.00 0.00 3.01
2506 3146 8.375506 TGGGAACATATGGTTATCTACTCAATC 58.624 37.037 7.80 0.00 40.63 2.67
2535 3178 7.436118 AGTATTTGTGAACGGACAAAGTAGTA 58.564 34.615 13.03 1.88 46.28 1.82
2536 3179 6.285990 AGTATTTGTGAACGGACAAAGTAGT 58.714 36.000 13.03 7.67 46.28 2.73
2537 3180 6.128634 GGAGTATTTGTGAACGGACAAAGTAG 60.129 42.308 13.03 0.00 46.28 2.57
2538 3181 5.697633 GGAGTATTTGTGAACGGACAAAGTA 59.302 40.000 13.03 5.85 46.28 2.24
2539 3182 4.514066 GGAGTATTTGTGAACGGACAAAGT 59.486 41.667 13.03 6.52 46.28 2.66
2540 3183 4.083484 GGGAGTATTTGTGAACGGACAAAG 60.083 45.833 13.03 0.00 46.28 2.77
2541 3184 3.816523 GGGAGTATTTGTGAACGGACAAA 59.183 43.478 10.78 10.78 46.93 2.83
2542 3185 3.071892 AGGGAGTATTTGTGAACGGACAA 59.928 43.478 0.00 0.00 33.96 3.18
2543 3186 2.635915 AGGGAGTATTTGTGAACGGACA 59.364 45.455 0.00 0.00 0.00 4.02
2544 3187 3.259902 GAGGGAGTATTTGTGAACGGAC 58.740 50.000 0.00 0.00 0.00 4.79
2545 3188 2.235402 GGAGGGAGTATTTGTGAACGGA 59.765 50.000 0.00 0.00 0.00 4.69
2546 3189 2.629051 GGAGGGAGTATTTGTGAACGG 58.371 52.381 0.00 0.00 0.00 4.44
2547 3190 2.268298 CGGAGGGAGTATTTGTGAACG 58.732 52.381 0.00 0.00 0.00 3.95
2548 3191 3.329929 ACGGAGGGAGTATTTGTGAAC 57.670 47.619 0.00 0.00 0.00 3.18
2549 3192 3.325425 TGAACGGAGGGAGTATTTGTGAA 59.675 43.478 0.00 0.00 0.00 3.18
2550 3193 2.901192 TGAACGGAGGGAGTATTTGTGA 59.099 45.455 0.00 0.00 0.00 3.58
2551 3194 3.328382 TGAACGGAGGGAGTATTTGTG 57.672 47.619 0.00 0.00 0.00 3.33
2552 3195 5.687166 TTATGAACGGAGGGAGTATTTGT 57.313 39.130 0.00 0.00 0.00 2.83
2553 3196 8.848474 ATATTTATGAACGGAGGGAGTATTTG 57.152 34.615 0.00 0.00 0.00 2.32
2556 3199 9.322769 ACTTATATTTATGAACGGAGGGAGTAT 57.677 33.333 0.00 0.00 0.00 2.12
2557 3200 8.716674 ACTTATATTTATGAACGGAGGGAGTA 57.283 34.615 0.00 0.00 0.00 2.59
2558 3201 7.509659 AGACTTATATTTATGAACGGAGGGAGT 59.490 37.037 0.00 0.00 0.00 3.85
2559 3202 7.897864 AGACTTATATTTATGAACGGAGGGAG 58.102 38.462 0.00 0.00 0.00 4.30
2560 3203 7.850935 AGACTTATATTTATGAACGGAGGGA 57.149 36.000 0.00 0.00 0.00 4.20
2561 3204 8.904099 AAAGACTTATATTTATGAACGGAGGG 57.096 34.615 0.00 0.00 0.00 4.30
2579 3222 8.826765 TCCATAGTGGAATCTCTAAAAAGACTT 58.173 33.333 0.00 0.00 45.00 3.01
2580 3223 8.380742 TCCATAGTGGAATCTCTAAAAAGACT 57.619 34.615 0.00 0.00 45.00 3.24
2595 3238 4.395625 CTCCGTATGTAGTCCATAGTGGA 58.604 47.826 0.00 0.00 45.98 4.02
2596 3239 3.057456 GCTCCGTATGTAGTCCATAGTGG 60.057 52.174 0.00 0.00 36.71 4.00
2597 3240 3.568430 TGCTCCGTATGTAGTCCATAGTG 59.432 47.826 0.00 0.00 36.71 2.74
2598 3241 3.828921 TGCTCCGTATGTAGTCCATAGT 58.171 45.455 0.00 0.00 36.71 2.12
2599 3242 4.848562 TTGCTCCGTATGTAGTCCATAG 57.151 45.455 0.00 0.00 36.71 2.23
2600 3243 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
2601 3244 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
2602 3245 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
2603 3246 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
2604 3247 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2605 3248 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2606 3249 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2607 3250 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2608 3251 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2609 3252 4.393062 AGTTCACTCATTTTGCTCCGTATG 59.607 41.667 0.00 0.00 0.00 2.39
2610 3253 4.579869 AGTTCACTCATTTTGCTCCGTAT 58.420 39.130 0.00 0.00 0.00 3.06
2611 3254 4.002906 AGTTCACTCATTTTGCTCCGTA 57.997 40.909 0.00 0.00 0.00 4.02
2612 3255 2.851195 AGTTCACTCATTTTGCTCCGT 58.149 42.857 0.00 0.00 0.00 4.69
2613 3256 5.812642 AGTATAGTTCACTCATTTTGCTCCG 59.187 40.000 0.00 0.00 0.00 4.63
2614 3257 7.044798 AGAGTATAGTTCACTCATTTTGCTCC 58.955 38.462 5.38 0.00 44.03 4.70
2615 3258 9.587772 TTAGAGTATAGTTCACTCATTTTGCTC 57.412 33.333 5.38 0.00 44.03 4.26


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

AutoCloner maintained by Alex Coulton.