Multiple sequence alignment - TraesCS4A01G366400

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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 TraesCS4A01G366400 chr4A 100.000 2495 0 0 1 2495 639976555 639979049 0.000000e+00 4608.0
1 TraesCS4A01G366400 chr5A 92.102 823 11 8 1 802 42640915 42641704 0.000000e+00 1110.0
2 TraesCS4A01G366400 chr5A 94.487 653 13 5 232 863 42653918 42654568 0.000000e+00 985.0
3 TraesCS4A01G366400 chr5A 94.262 244 9 2 967 1210 643312079 643311841 3.920000e-98 368.0
4 TraesCS4A01G366400 chr5A 98.851 174 2 0 1 174 42642160 42642333 6.700000e-81 311.0
5 TraesCS4A01G366400 chr5A 90.667 150 13 1 1666 1814 643310852 643310703 5.440000e-47 198.0
6 TraesCS4A01G366400 chr5A 90.667 150 13 1 1666 1814 643311419 643311270 5.440000e-47 198.0
7 TraesCS4A01G366400 chrUn 88.603 895 36 26 1 863 355035942 355036802 0.000000e+00 1027.0
8 TraesCS4A01G366400 chrUn 83.607 183 24 5 683 863 39518994 39518816 1.530000e-37 167.0
9 TraesCS4A01G366400 chr1B 91.840 674 18 11 1 672 172408742 172409380 0.000000e+00 905.0
10 TraesCS4A01G366400 chr1B 85.572 201 9 9 679 863 172409421 172409617 2.530000e-45 193.0
11 TraesCS4A01G366400 chr2D 94.896 529 27 0 967 1495 633286494 633285966 0.000000e+00 828.0
12 TraesCS4A01G366400 chr2D 94.518 529 29 0 967 1495 633237304 633236776 0.000000e+00 817.0
13 TraesCS4A01G366400 chr2D 94.329 529 30 0 967 1495 633259139 633258611 0.000000e+00 811.0
14 TraesCS4A01G366400 chr2D 91.457 597 40 6 967 1554 633297768 633298362 0.000000e+00 809.0
15 TraesCS4A01G366400 chr2D 92.698 315 20 2 359 672 370011047 370011359 3.780000e-123 451.0
16 TraesCS4A01G366400 chr2D 93.852 244 11 2 967 1210 534129373 534129612 5.070000e-97 364.0
17 TraesCS4A01G366400 chr2D 84.290 331 36 10 1664 1978 633298395 633298725 2.410000e-80 309.0
18 TraesCS4A01G366400 chr2D 91.866 209 12 2 2286 2492 534124750 534124955 1.130000e-73 287.0
19 TraesCS4A01G366400 chr2D 89.806 206 19 2 1662 1866 534130041 534130245 1.900000e-66 263.0
20 TraesCS4A01G366400 chr2D 88.732 213 10 1 264 476 370010591 370010789 5.330000e-62 248.0
21 TraesCS4A01G366400 chr2D 91.667 180 12 2 686 865 129912589 129912413 1.920000e-61 246.0
22 TraesCS4A01G366400 chr2D 85.657 251 17 7 1652 1889 534123555 534123799 1.920000e-61 246.0
23 TraesCS4A01G366400 chr2D 95.035 141 5 2 1 140 370010413 370010552 1.160000e-53 220.0
24 TraesCS4A01G366400 chr2D 92.982 57 4 0 264 320 129912942 129912886 1.590000e-12 84.2
25 TraesCS4A01G366400 chr3B 86.606 769 60 25 1001 1730 798408867 798408103 0.000000e+00 809.0
26 TraesCS4A01G366400 chr3B 82.336 351 29 14 2 340 375980808 375980479 8.790000e-70 274.0
27 TraesCS4A01G366400 chr6D 88.218 679 49 14 904 1558 20475234 20474563 0.000000e+00 782.0
28 TraesCS4A01G366400 chr6D 91.111 225 16 2 1664 1884 20474532 20474308 4.030000e-78 302.0
29 TraesCS4A01G366400 chr6D 94.074 135 6 2 4 137 364891374 364891507 1.170000e-48 204.0
30 TraesCS4A01G366400 chr6D 90.741 108 9 1 1651 1757 18985220 18985327 2.590000e-30 143.0
31 TraesCS4A01G366400 chr5D 89.375 640 42 8 232 862 259645433 259646055 0.000000e+00 782.0
32 TraesCS4A01G366400 chr5D 84.335 632 62 30 1208 1819 515094060 515093446 3.580000e-163 584.0
33 TraesCS4A01G366400 chr5D 89.809 314 15 7 904 1210 515094394 515094091 1.080000e-103 387.0
34 TraesCS4A01G366400 chr5D 89.815 216 18 2 1666 1877 515039032 515038817 8.790000e-70 274.0
35 TraesCS4A01G366400 chr5D 96.454 141 4 1 1 140 259645286 259645426 5.370000e-57 231.0
36 TraesCS4A01G366400 chr5D 90.476 105 9 1 2392 2495 515038543 515038439 1.200000e-28 137.0
37 TraesCS4A01G366400 chr5D 96.970 33 1 0 198 230 259645419 259645451 3.470000e-04 56.5
38 TraesCS4A01G366400 chr3D 84.785 815 67 34 966 1730 594958399 594957592 0.000000e+00 765.0
39 TraesCS4A01G366400 chr3D 87.850 535 42 6 232 757 601564820 601565340 7.630000e-170 606.0
40 TraesCS4A01G366400 chr3D 83.846 650 65 17 232 862 133687431 133688059 1.290000e-162 582.0
41 TraesCS4A01G366400 chr3D 88.673 309 23 6 564 863 119256342 119256037 1.410000e-97 366.0
42 TraesCS4A01G366400 chr3D 95.035 141 6 1 1 140 133687284 133687424 1.160000e-53 220.0
43 TraesCS4A01G366400 chr3D 96.970 33 1 0 198 230 601564806 601564838 3.470000e-04 56.5
44 TraesCS4A01G366400 chr5B 88.590 631 40 12 967 1571 647879467 647878843 0.000000e+00 737.0
45 TraesCS4A01G366400 chr4D 88.224 535 40 6 232 757 12939385 12938865 3.530000e-173 617.0
46 TraesCS4A01G366400 chr4D 89.083 229 9 5 635 862 12938592 12938379 1.140000e-68 270.0
47 TraesCS4A01G366400 chr4D 100.000 30 0 0 201 230 12939396 12939367 3.470000e-04 56.5
48 TraesCS4A01G366400 chr7B 85.331 559 52 23 1211 1752 113445298 113444753 3.630000e-153 551.0
49 TraesCS4A01G366400 chr7D 87.333 450 39 12 1211 1648 151542347 151541904 1.330000e-137 499.0
50 TraesCS4A01G366400 chr7A 86.667 450 43 10 1211 1648 151327856 151327412 1.340000e-132 483.0
51 TraesCS4A01G366400 chr3A 93.080 289 18 2 385 672 493693065 493693352 2.970000e-114 422.0
52 TraesCS4A01G366400 chr3A 96.377 138 4 1 1 137 493692798 493692935 2.500000e-55 226.0
53 TraesCS4A01G366400 chr2B 93.227 251 14 2 2247 2495 634626899 634627148 1.410000e-97 366.0
54 TraesCS4A01G366400 chr2A 91.720 157 12 1 1651 1806 677828435 677828591 1.500000e-52 217.0
55 TraesCS4A01G366400 chr6B 78.571 294 36 17 590 862 251815918 251815631 4.270000e-38 169.0
56 TraesCS4A01G366400 chr6B 90.741 108 9 1 1651 1757 33038608 33038715 2.590000e-30 143.0


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 TraesCS4A01G366400 chr4A 639976555 639979049 2494 False 4608.000000 4608 100.000000 1 2495 1 chr4A.!!$F1 2494
1 TraesCS4A01G366400 chr5A 42653918 42654568 650 False 985.000000 985 94.487000 232 863 1 chr5A.!!$F1 631
2 TraesCS4A01G366400 chr5A 42640915 42642333 1418 False 710.500000 1110 95.476500 1 802 2 chr5A.!!$F2 801
3 TraesCS4A01G366400 chr5A 643310703 643312079 1376 True 254.666667 368 91.865333 967 1814 3 chr5A.!!$R1 847
4 TraesCS4A01G366400 chrUn 355035942 355036802 860 False 1027.000000 1027 88.603000 1 863 1 chrUn.!!$F1 862
5 TraesCS4A01G366400 chr1B 172408742 172409617 875 False 549.000000 905 88.706000 1 863 2 chr1B.!!$F1 862
6 TraesCS4A01G366400 chr2D 633285966 633286494 528 True 828.000000 828 94.896000 967 1495 1 chr2D.!!$R3 528
7 TraesCS4A01G366400 chr2D 633236776 633237304 528 True 817.000000 817 94.518000 967 1495 1 chr2D.!!$R1 528
8 TraesCS4A01G366400 chr2D 633258611 633259139 528 True 811.000000 811 94.329000 967 1495 1 chr2D.!!$R2 528
9 TraesCS4A01G366400 chr2D 633297768 633298725 957 False 559.000000 809 87.873500 967 1978 2 chr2D.!!$F4 1011
10 TraesCS4A01G366400 chr2D 534129373 534130245 872 False 313.500000 364 91.829000 967 1866 2 chr2D.!!$F3 899
11 TraesCS4A01G366400 chr2D 370010413 370011359 946 False 306.333333 451 92.155000 1 672 3 chr2D.!!$F1 671
12 TraesCS4A01G366400 chr2D 534123555 534124955 1400 False 266.500000 287 88.761500 1652 2492 2 chr2D.!!$F2 840
13 TraesCS4A01G366400 chr3B 798408103 798408867 764 True 809.000000 809 86.606000 1001 1730 1 chr3B.!!$R2 729
14 TraesCS4A01G366400 chr6D 20474308 20475234 926 True 542.000000 782 89.664500 904 1884 2 chr6D.!!$R1 980
15 TraesCS4A01G366400 chr5D 515093446 515094394 948 True 485.500000 584 87.072000 904 1819 2 chr5D.!!$R2 915
16 TraesCS4A01G366400 chr5D 259645286 259646055 769 False 356.500000 782 94.266333 1 862 3 chr5D.!!$F1 861
17 TraesCS4A01G366400 chr5D 515038439 515039032 593 True 205.500000 274 90.145500 1666 2495 2 chr5D.!!$R1 829
18 TraesCS4A01G366400 chr3D 594957592 594958399 807 True 765.000000 765 84.785000 966 1730 1 chr3D.!!$R2 764
19 TraesCS4A01G366400 chr3D 133687284 133688059 775 False 401.000000 582 89.440500 1 862 2 chr3D.!!$F1 861
20 TraesCS4A01G366400 chr3D 601564806 601565340 534 False 331.250000 606 92.410000 198 757 2 chr3D.!!$F2 559
21 TraesCS4A01G366400 chr5B 647878843 647879467 624 True 737.000000 737 88.590000 967 1571 1 chr5B.!!$R1 604
22 TraesCS4A01G366400 chr4D 12938379 12939396 1017 True 314.500000 617 92.435667 201 862 3 chr4D.!!$R1 661
23 TraesCS4A01G366400 chr7B 113444753 113445298 545 True 551.000000 551 85.331000 1211 1752 1 chr7B.!!$R1 541
24 TraesCS4A01G366400 chr3A 493692798 493693352 554 False 324.000000 422 94.728500 1 672 2 chr3A.!!$F1 671

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
902 1719 0.179121 TATCTAGCCCAACACGCACG 60.179 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 3588 0.027716 CTGAGTACGGATGGACGTCG 59.972 60.0 9.92 0.02 45.08 5.12 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
427 433 6.511416 CATGGGTTGATTTAGTTTGAACACA 58.489 36.000 0.00 0.00 34.59 3.72
522 904 1.957186 GAAACCGTACAGCGTGCCA 60.957 57.895 0.00 0.00 39.32 4.92
672 1063 2.842462 ATCGGCAGCGGGGTATGA 60.842 61.111 0.00 0.00 0.00 2.15
863 1680 8.577296 CAATTCGTCCATTAGGAGTAGAGATAA 58.423 37.037 0.00 0.00 46.92 1.75
864 1681 8.707796 ATTCGTCCATTAGGAGTAGAGATAAA 57.292 34.615 0.00 0.00 46.92 1.40
865 1682 8.707796 TTCGTCCATTAGGAGTAGAGATAAAT 57.292 34.615 0.00 0.00 46.92 1.40
866 1683 8.338072 TCGTCCATTAGGAGTAGAGATAAATC 57.662 38.462 0.00 0.00 46.92 2.17
867 1684 7.393796 TCGTCCATTAGGAGTAGAGATAAATCC 59.606 40.741 0.00 0.00 46.92 3.01
868 1685 7.363094 CGTCCATTAGGAGTAGAGATAAATCCC 60.363 44.444 0.00 0.00 46.92 3.85
869 1686 6.960542 TCCATTAGGAGTAGAGATAAATCCCC 59.039 42.308 0.00 0.00 39.61 4.81
870 1687 6.127310 CCATTAGGAGTAGAGATAAATCCCCG 60.127 46.154 0.00 0.00 36.89 5.73
871 1688 3.780626 AGGAGTAGAGATAAATCCCCGG 58.219 50.000 0.00 0.00 0.00 5.73
872 1689 3.401683 AGGAGTAGAGATAAATCCCCGGA 59.598 47.826 0.73 0.00 0.00 5.14
873 1690 4.140758 AGGAGTAGAGATAAATCCCCGGAA 60.141 45.833 0.73 0.00 0.00 4.30
874 1691 4.021280 GGAGTAGAGATAAATCCCCGGAAC 60.021 50.000 0.73 0.00 0.00 3.62
875 1692 4.553678 AGTAGAGATAAATCCCCGGAACA 58.446 43.478 0.73 0.00 0.00 3.18
876 1693 3.840124 AGAGATAAATCCCCGGAACAC 57.160 47.619 0.73 0.00 0.00 3.32
877 1694 3.385115 AGAGATAAATCCCCGGAACACT 58.615 45.455 0.73 0.00 0.00 3.55
878 1695 3.388350 AGAGATAAATCCCCGGAACACTC 59.612 47.826 0.73 0.77 0.00 3.51
879 1696 3.385115 AGATAAATCCCCGGAACACTCT 58.615 45.455 0.73 0.00 0.00 3.24
880 1697 4.553678 AGATAAATCCCCGGAACACTCTA 58.446 43.478 0.73 0.00 0.00 2.43
881 1698 5.155905 AGATAAATCCCCGGAACACTCTAT 58.844 41.667 0.73 0.00 0.00 1.98
882 1699 3.840124 AAATCCCCGGAACACTCTATC 57.160 47.619 0.73 0.00 0.00 2.08
883 1700 2.777459 ATCCCCGGAACACTCTATCT 57.223 50.000 0.73 0.00 0.00 1.98
884 1701 3.897657 ATCCCCGGAACACTCTATCTA 57.102 47.619 0.73 0.00 0.00 1.98
885 1702 3.897657 TCCCCGGAACACTCTATCTAT 57.102 47.619 0.73 0.00 0.00 1.98
886 1703 3.764218 TCCCCGGAACACTCTATCTATC 58.236 50.000 0.73 0.00 0.00 2.08
887 1704 3.398292 TCCCCGGAACACTCTATCTATCT 59.602 47.826 0.73 0.00 0.00 1.98
888 1705 4.600547 TCCCCGGAACACTCTATCTATCTA 59.399 45.833 0.73 0.00 0.00 1.98
889 1706 4.944930 CCCCGGAACACTCTATCTATCTAG 59.055 50.000 0.73 0.00 0.00 2.43
890 1707 4.396790 CCCGGAACACTCTATCTATCTAGC 59.603 50.000 0.73 0.00 0.00 3.42
891 1708 4.396790 CCGGAACACTCTATCTATCTAGCC 59.603 50.000 0.00 0.00 0.00 3.93
892 1709 4.396790 CGGAACACTCTATCTATCTAGCCC 59.603 50.000 0.00 0.00 0.00 5.19
893 1710 5.326069 GGAACACTCTATCTATCTAGCCCA 58.674 45.833 0.00 0.00 0.00 5.36
894 1711 5.775701 GGAACACTCTATCTATCTAGCCCAA 59.224 44.000 0.00 0.00 0.00 4.12
895 1712 6.294843 GGAACACTCTATCTATCTAGCCCAAC 60.295 46.154 0.00 0.00 0.00 3.77
896 1713 5.706447 ACACTCTATCTATCTAGCCCAACA 58.294 41.667 0.00 0.00 0.00 3.33
897 1714 5.536916 ACACTCTATCTATCTAGCCCAACAC 59.463 44.000 0.00 0.00 0.00 3.32
898 1715 4.762765 ACTCTATCTATCTAGCCCAACACG 59.237 45.833 0.00 0.00 0.00 4.49
899 1716 2.821991 ATCTATCTAGCCCAACACGC 57.178 50.000 0.00 0.00 0.00 5.34
900 1717 1.480789 TCTATCTAGCCCAACACGCA 58.519 50.000 0.00 0.00 0.00 5.24
901 1718 1.136305 TCTATCTAGCCCAACACGCAC 59.864 52.381 0.00 0.00 0.00 5.34
902 1719 0.179121 TATCTAGCCCAACACGCACG 60.179 55.000 0.00 0.00 0.00 5.34
923 1740 2.563427 GCACGCAAAGAAGCTCCC 59.437 61.111 0.00 0.00 0.00 4.30
926 1743 1.668151 ACGCAAAGAAGCTCCCGTC 60.668 57.895 0.00 0.00 0.00 4.79
932 1755 0.966920 AAGAAGCTCCCGTCTTTCGA 59.033 50.000 0.00 0.00 36.58 3.71
935 1758 0.179134 AAGCTCCCGTCTTTCGATCG 60.179 55.000 9.36 9.36 42.86 3.69
936 1759 2.231618 GCTCCCGTCTTTCGATCGC 61.232 63.158 11.09 0.00 42.86 4.58
937 1760 1.433879 CTCCCGTCTTTCGATCGCT 59.566 57.895 11.09 0.00 42.86 4.93
941 1764 1.583967 CGTCTTTCGATCGCTCGCT 60.584 57.895 11.09 0.00 44.65 4.93
942 1765 1.524991 CGTCTTTCGATCGCTCGCTC 61.525 60.000 11.09 0.00 44.65 5.03
943 1766 1.297672 TCTTTCGATCGCTCGCTCG 60.298 57.895 11.09 8.92 44.65 5.03
945 1768 3.396911 TTTCGATCGCTCGCTCGCT 62.397 57.895 11.09 0.00 44.65 4.93
947 1770 4.306471 CGATCGCTCGCTCGCTCT 62.306 66.667 0.26 0.00 38.20 4.09
950 1773 3.477224 ATCGCTCGCTCGCTCTTCC 62.477 63.158 0.00 0.00 0.00 3.46
953 1776 2.581953 CTCGCTCGCTCTTCCTGC 60.582 66.667 0.00 0.00 0.00 4.85
955 1778 2.581953 CGCTCGCTCTTCCTGCTC 60.582 66.667 0.00 0.00 0.00 4.26
961 1792 1.743321 CGCTCTTCCTGCTCCTAGGG 61.743 65.000 9.46 0.44 38.42 3.53
962 1793 0.689412 GCTCTTCCTGCTCCTAGGGT 60.689 60.000 9.46 0.00 38.42 4.34
963 1794 1.872773 CTCTTCCTGCTCCTAGGGTT 58.127 55.000 9.46 0.00 38.42 4.11
964 1795 2.192263 CTCTTCCTGCTCCTAGGGTTT 58.808 52.381 9.46 0.00 38.42 3.27
971 1802 1.695242 TGCTCCTAGGGTTTCGTTTCA 59.305 47.619 9.46 0.00 0.00 2.69
991 1826 1.921869 TTTCGCCTCCCAATCCTCCC 61.922 60.000 0.00 0.00 0.00 4.30
999 1834 0.407139 CCCAATCCTCCCATCCATCC 59.593 60.000 0.00 0.00 0.00 3.51
1068 1903 0.036306 ACGGCGAGGAATTTCAGGTT 59.964 50.000 16.62 0.00 0.00 3.50
1185 2020 2.231716 TCCTCTCCAAGGTCATCGAA 57.768 50.000 0.00 0.00 46.32 3.71
1332 2248 2.484417 CCTCATCCTCGCTGCAAACTAT 60.484 50.000 0.00 0.00 0.00 2.12
1457 2373 2.283966 CACACCCGAGGAGGAGGT 60.284 66.667 0.00 0.00 45.00 3.85
1496 2980 2.644798 ACCAGTGGGCTTTTGAGTAGAT 59.355 45.455 15.21 0.00 37.90 1.98
1515 3000 3.254657 AGATAAGAGTAGCATCGAGGCAC 59.745 47.826 25.38 18.82 35.83 5.01
1518 3008 0.873743 GAGTAGCATCGAGGCACTGC 60.874 60.000 25.38 12.53 41.55 4.40
1537 3029 4.155826 ACTGCTGCGTCAAATTAATGCTTA 59.844 37.500 0.00 0.00 0.00 3.09
1583 3085 6.371548 TGAGACTTTGTATGCCTATGTTTCAC 59.628 38.462 0.00 0.00 0.00 3.18
1602 3105 1.003118 ACCGCTGCCTTTTCTATGTCA 59.997 47.619 0.00 0.00 0.00 3.58
1604 3107 3.118408 ACCGCTGCCTTTTCTATGTCATA 60.118 43.478 0.00 0.00 0.00 2.15
1605 3108 3.876914 CCGCTGCCTTTTCTATGTCATAA 59.123 43.478 0.00 0.00 0.00 1.90
1607 3110 5.334414 CCGCTGCCTTTTCTATGTCATAATC 60.334 44.000 0.00 0.00 0.00 1.75
1620 3138 9.411801 TCTATGTCATAATCGTTATTCTGAAGC 57.588 33.333 0.00 0.00 32.03 3.86
1622 3140 5.758296 TGTCATAATCGTTATTCTGAAGCCC 59.242 40.000 0.00 0.00 32.03 5.19
1640 3158 5.818678 AGCCCAAACATCGTTATATCCTA 57.181 39.130 0.00 0.00 0.00 2.94
1645 3169 8.357402 GCCCAAACATCGTTATATCCTAAAAAT 58.643 33.333 0.00 0.00 0.00 1.82
1757 3309 9.502145 TTTATGCGTGTGATTTGAGATATTTTC 57.498 29.630 0.00 0.00 0.00 2.29
1760 3312 6.149308 TGCGTGTGATTTGAGATATTTTCTGT 59.851 34.615 0.00 0.00 33.74 3.41
1800 3353 9.379791 CCTTATTGTTTCCGATTTTAGTCTACT 57.620 33.333 0.00 0.00 0.00 2.57
1889 3456 1.859383 TGTCACGAATCTCAACGCAA 58.141 45.000 0.00 0.00 0.00 4.85
1891 3458 0.790207 TCACGAATCTCAACGCAAGC 59.210 50.000 0.00 0.00 45.62 4.01
1892 3459 0.517132 CACGAATCTCAACGCAAGCG 60.517 55.000 13.50 13.50 46.03 4.68
1893 3460 1.059369 CGAATCTCAACGCAAGCGG 59.941 57.895 19.30 1.78 44.69 5.52
1908 3504 2.940561 CGGGCGCGTTTTAGTTGT 59.059 55.556 15.94 0.00 0.00 3.32
1909 3505 1.439693 CGGGCGCGTTTTAGTTGTG 60.440 57.895 15.94 0.00 0.00 3.33
1910 3506 1.650363 GGGCGCGTTTTAGTTGTGT 59.350 52.632 8.43 0.00 0.00 3.72
1913 3509 1.776897 GGCGCGTTTTAGTTGTGTTTC 59.223 47.619 8.43 0.00 0.00 2.78
1937 3533 1.264295 GGTTACGGGTCTCCACTCTT 58.736 55.000 0.00 0.00 0.00 2.85
1940 3536 1.542492 TACGGGTCTCCACTCTTCAC 58.458 55.000 0.00 0.00 0.00 3.18
1950 3546 1.283029 CCACTCTTCACCCCATGTCAT 59.717 52.381 0.00 0.00 0.00 3.06
1978 3574 3.422343 CGTTTTTGCTAGCGAGAGACAAG 60.422 47.826 10.77 0.00 0.00 3.16
1979 3575 1.714794 TTTGCTAGCGAGAGACAAGC 58.285 50.000 10.77 0.00 33.85 4.01
1980 3576 0.603065 TTGCTAGCGAGAGACAAGCA 59.397 50.000 10.77 0.00 39.01 3.91
1981 3577 0.820226 TGCTAGCGAGAGACAAGCAT 59.180 50.000 10.77 0.00 36.94 3.79
1982 3578 1.207390 GCTAGCGAGAGACAAGCATG 58.793 55.000 0.00 0.00 33.57 4.06
1983 3579 1.850377 CTAGCGAGAGACAAGCATGG 58.150 55.000 0.00 0.00 0.00 3.66
1984 3580 0.179100 TAGCGAGAGACAAGCATGGC 60.179 55.000 0.00 0.00 33.34 4.40
1985 3581 2.467826 GCGAGAGACAAGCATGGCC 61.468 63.158 0.00 0.00 33.81 5.36
1986 3582 1.220206 CGAGAGACAAGCATGGCCT 59.780 57.895 3.32 0.00 33.81 5.19
1987 3583 0.809241 CGAGAGACAAGCATGGCCTC 60.809 60.000 3.32 0.00 33.81 4.70
1988 3584 0.463474 GAGAGACAAGCATGGCCTCC 60.463 60.000 3.32 0.00 33.81 4.30
1989 3585 1.452833 GAGACAAGCATGGCCTCCC 60.453 63.158 3.32 0.00 33.81 4.30
1990 3586 1.919600 GAGACAAGCATGGCCTCCCT 61.920 60.000 3.32 0.00 33.81 4.20
1991 3587 1.452833 GACAAGCATGGCCTCCCTC 60.453 63.158 3.32 0.00 0.00 4.30
1992 3588 2.123982 CAAGCATGGCCTCCCTCC 60.124 66.667 3.32 0.00 0.00 4.30
1993 3589 3.801997 AAGCATGGCCTCCCTCCG 61.802 66.667 3.32 0.00 0.00 4.63
1994 3590 4.804420 AGCATGGCCTCCCTCCGA 62.804 66.667 3.32 0.00 0.00 4.55
1995 3591 4.554036 GCATGGCCTCCCTCCGAC 62.554 72.222 3.32 0.00 0.00 4.79
1996 3592 4.227134 CATGGCCTCCCTCCGACG 62.227 72.222 3.32 0.00 0.00 5.12
1997 3593 4.779733 ATGGCCTCCCTCCGACGT 62.780 66.667 3.32 0.00 0.00 4.34
2001 3597 2.442272 CCTCCCTCCGACGTCCAT 60.442 66.667 10.58 0.00 0.00 3.41
2002 3598 2.491022 CCTCCCTCCGACGTCCATC 61.491 68.421 10.58 0.00 0.00 3.51
2003 3599 2.441532 TCCCTCCGACGTCCATCC 60.442 66.667 10.58 0.00 0.00 3.51
2004 3600 3.900892 CCCTCCGACGTCCATCCG 61.901 72.222 10.58 0.00 0.00 4.18
2005 3601 3.138798 CCTCCGACGTCCATCCGT 61.139 66.667 10.58 0.00 45.18 4.69
2006 3602 1.820906 CCTCCGACGTCCATCCGTA 60.821 63.158 10.58 0.00 41.98 4.02
2007 3603 1.354506 CTCCGACGTCCATCCGTAC 59.645 63.158 10.58 0.00 41.98 3.67
2008 3604 1.078214 TCCGACGTCCATCCGTACT 60.078 57.895 10.58 0.00 41.98 2.73
2009 3605 1.091771 TCCGACGTCCATCCGTACTC 61.092 60.000 10.58 0.00 41.98 2.59
2010 3606 1.371337 CCGACGTCCATCCGTACTCA 61.371 60.000 10.58 0.00 41.98 3.41
2011 3607 0.027716 CGACGTCCATCCGTACTCAG 59.972 60.000 10.58 0.00 41.98 3.35
2012 3608 0.248539 GACGTCCATCCGTACTCAGC 60.249 60.000 3.51 0.00 41.98 4.26
2013 3609 1.298413 CGTCCATCCGTACTCAGCG 60.298 63.158 0.00 0.00 0.00 5.18
2014 3610 1.589196 GTCCATCCGTACTCAGCGC 60.589 63.158 0.00 0.00 0.00 5.92
2015 3611 2.279517 CCATCCGTACTCAGCGCC 60.280 66.667 2.29 0.00 0.00 6.53
2016 3612 2.655364 CATCCGTACTCAGCGCCG 60.655 66.667 2.29 0.00 0.00 6.46
2017 3613 3.138798 ATCCGTACTCAGCGCCGT 61.139 61.111 2.29 1.06 0.00 5.68
2018 3614 2.707849 ATCCGTACTCAGCGCCGTT 61.708 57.895 2.29 0.00 0.00 4.44
2019 3615 1.378882 ATCCGTACTCAGCGCCGTTA 61.379 55.000 2.29 0.00 0.00 3.18
2020 3616 1.153978 CCGTACTCAGCGCCGTTAA 60.154 57.895 2.29 0.00 0.00 2.01
2021 3617 0.526954 CCGTACTCAGCGCCGTTAAT 60.527 55.000 2.29 0.00 0.00 1.40
2022 3618 1.274596 CGTACTCAGCGCCGTTAATT 58.725 50.000 2.29 0.00 0.00 1.40
2023 3619 2.453080 CGTACTCAGCGCCGTTAATTA 58.547 47.619 2.29 0.00 0.00 1.40
2024 3620 2.214914 CGTACTCAGCGCCGTTAATTAC 59.785 50.000 2.29 0.00 0.00 1.89
2025 3621 1.648504 ACTCAGCGCCGTTAATTACC 58.351 50.000 2.29 0.00 0.00 2.85
2026 3622 0.935196 CTCAGCGCCGTTAATTACCC 59.065 55.000 2.29 0.00 0.00 3.69
2027 3623 0.538118 TCAGCGCCGTTAATTACCCT 59.462 50.000 2.29 0.00 0.00 4.34
2028 3624 0.935196 CAGCGCCGTTAATTACCCTC 59.065 55.000 2.29 0.00 0.00 4.30
2029 3625 0.179065 AGCGCCGTTAATTACCCTCC 60.179 55.000 2.29 0.00 0.00 4.30
2030 3626 0.462403 GCGCCGTTAATTACCCTCCA 60.462 55.000 0.00 0.00 0.00 3.86
2031 3627 2.013058 GCGCCGTTAATTACCCTCCAA 61.013 52.381 0.00 0.00 0.00 3.53
2032 3628 2.567985 CGCCGTTAATTACCCTCCAAT 58.432 47.619 0.00 0.00 0.00 3.16
2033 3629 2.289547 CGCCGTTAATTACCCTCCAATG 59.710 50.000 0.00 0.00 0.00 2.82
2034 3630 3.284617 GCCGTTAATTACCCTCCAATGT 58.715 45.455 0.00 0.00 0.00 2.71
2039 3988 6.025280 CGTTAATTACCCTCCAATGTTTTCG 58.975 40.000 0.00 0.00 0.00 3.46
2040 3989 4.450082 AATTACCCTCCAATGTTTTCGC 57.550 40.909 0.00 0.00 0.00 4.70
2054 4003 0.675522 TTTCGCTCCGGTGGAAATCC 60.676 55.000 0.00 0.00 0.00 3.01
2057 4006 2.115291 GCTCCGGTGGAAATCCTGC 61.115 63.158 0.00 0.00 36.82 4.85
2058 4007 1.299648 CTCCGGTGGAAATCCTGCA 59.700 57.895 0.00 0.00 36.82 4.41
2077 4216 1.198759 ACTGGAACACCTACGCCCAT 61.199 55.000 0.00 0.00 0.00 4.00
2083 4222 0.686441 ACACCTACGCCCATGAGCTA 60.686 55.000 0.00 0.00 0.00 3.32
2089 4228 1.068753 CGCCCATGAGCTAGAGTGG 59.931 63.158 0.00 0.00 0.00 4.00
2122 4261 4.613031 GCGCTTCATTTGTCTTTAGTGTTC 59.387 41.667 0.00 0.00 0.00 3.18
2130 4269 5.646467 TTGTCTTTAGTGTTCTGCGTAAC 57.354 39.130 0.00 0.00 0.00 2.50
2148 4287 5.051307 GCGTAACTTTTGGGTGTTTTTCATC 60.051 40.000 0.00 0.00 0.00 2.92
2150 4289 6.531948 CGTAACTTTTGGGTGTTTTTCATCAA 59.468 34.615 0.00 0.00 0.00 2.57
2153 4292 5.821995 ACTTTTGGGTGTTTTTCATCAATGG 59.178 36.000 0.00 0.00 0.00 3.16
2155 4294 2.288702 TGGGTGTTTTTCATCAATGGCG 60.289 45.455 0.00 0.00 0.00 5.69
2165 4318 7.851387 TTTTCATCAATGGCGTTAGTATACA 57.149 32.000 5.50 0.00 0.00 2.29
2183 4336 1.024271 CAAGTGTATGGGGGCATTCG 58.976 55.000 0.00 0.00 0.00 3.34
2185 4338 2.193536 GTGTATGGGGGCATTCGGC 61.194 63.158 0.00 0.00 43.74 5.54
2203 4358 3.058450 CGGCAGAAATGATTTTTGCACA 58.942 40.909 27.41 0.00 33.91 4.57
2204 4359 3.122278 CGGCAGAAATGATTTTTGCACAG 59.878 43.478 27.41 17.26 33.91 3.66
2205 4360 3.434299 GGCAGAAATGATTTTTGCACAGG 59.566 43.478 27.41 0.00 33.91 4.00
2212 4367 0.614812 ATTTTTGCACAGGGGGATGC 59.385 50.000 0.00 0.00 42.40 3.91
2216 4371 0.630673 TTGCACAGGGGGATGCTATT 59.369 50.000 0.00 0.00 42.55 1.73
2232 4387 5.086104 TGCTATTAGTGTTCTTCAGTCCC 57.914 43.478 0.00 0.00 0.00 4.46
2233 4388 4.530553 TGCTATTAGTGTTCTTCAGTCCCA 59.469 41.667 0.00 0.00 0.00 4.37
2259 4414 0.167908 TGCGTGAATTTTGCTAGGCG 59.832 50.000 0.00 0.00 0.00 5.52
2262 4417 2.477863 GCGTGAATTTTGCTAGGCGAAT 60.478 45.455 0.00 0.00 31.52 3.34
2263 4418 3.100817 CGTGAATTTTGCTAGGCGAATG 58.899 45.455 0.00 0.00 31.52 2.67
2265 4420 2.426738 TGAATTTTGCTAGGCGAATGGG 59.573 45.455 0.00 0.00 31.52 4.00
2266 4421 2.435372 ATTTTGCTAGGCGAATGGGA 57.565 45.000 0.00 0.00 31.52 4.37
2267 4422 1.750193 TTTTGCTAGGCGAATGGGAG 58.250 50.000 0.00 0.00 31.52 4.30
2268 4423 0.748005 TTTGCTAGGCGAATGGGAGC 60.748 55.000 0.00 0.00 0.00 4.70
2269 4424 1.626356 TTGCTAGGCGAATGGGAGCT 61.626 55.000 0.00 0.00 34.19 4.09
2270 4425 1.596477 GCTAGGCGAATGGGAGCTG 60.596 63.158 0.00 0.00 0.00 4.24
2271 4426 1.826024 CTAGGCGAATGGGAGCTGT 59.174 57.895 0.00 0.00 0.00 4.40
2272 4427 0.179000 CTAGGCGAATGGGAGCTGTT 59.821 55.000 0.00 0.00 0.00 3.16
2273 4428 0.107703 TAGGCGAATGGGAGCTGTTG 60.108 55.000 0.00 0.00 0.00 3.33
2274 4429 2.486966 GCGAATGGGAGCTGTTGC 59.513 61.111 0.00 0.00 40.05 4.17
2275 4430 2.334946 GCGAATGGGAGCTGTTGCA 61.335 57.895 0.00 0.00 42.74 4.08
2276 4431 1.503542 CGAATGGGAGCTGTTGCAC 59.496 57.895 0.00 0.00 42.74 4.57
2277 4432 0.957395 CGAATGGGAGCTGTTGCACT 60.957 55.000 0.00 0.00 42.74 4.40
2278 4433 0.524862 GAATGGGAGCTGTTGCACTG 59.475 55.000 0.00 0.00 42.74 3.66
2279 4434 1.530013 AATGGGAGCTGTTGCACTGC 61.530 55.000 0.00 9.14 42.43 4.40
2287 4442 3.461946 GCTGTTGCACTGCTAACTTAG 57.538 47.619 1.98 2.12 39.55 2.18
2288 4443 2.160417 GCTGTTGCACTGCTAACTTAGG 59.840 50.000 1.98 0.87 39.55 2.69
2292 4447 0.729690 GCACTGCTAACTTAGGCTGC 59.270 55.000 0.00 0.00 0.00 5.25
2427 4708 4.177026 CGAGAGAGTGGTTAAGGTGATTG 58.823 47.826 0.00 0.00 0.00 2.67
2464 4745 4.098807 GTGGTGGACATGTTGGTTTAGTTT 59.901 41.667 0.00 0.00 0.00 2.66
2479 4760 7.725251 TGGTTTAGTTTGATTTTCTGAATGCT 58.275 30.769 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 130 7.506938 CCTTGGGTATCATCTGAATTGGTTATT 59.493 37.037 0.00 0.00 0.00 1.40
333 339 3.655777 ACCTCACAAATCAAACCCCTCTA 59.344 43.478 0.00 0.00 0.00 2.43
672 1063 1.432852 CCATCAGGATCCCCATGCCT 61.433 60.000 8.55 0.00 36.89 4.75
840 1657 8.707796 ATTTATCTCTACTCCTAATGGACGAA 57.292 34.615 0.00 0.00 37.46 3.85
863 1680 3.047695 AGATAGAGTGTTCCGGGGATT 57.952 47.619 0.00 0.00 0.00 3.01
864 1681 2.777459 AGATAGAGTGTTCCGGGGAT 57.223 50.000 0.00 0.00 0.00 3.85
865 1682 3.398292 AGATAGATAGAGTGTTCCGGGGA 59.602 47.826 0.00 0.00 0.00 4.81
866 1683 3.768878 AGATAGATAGAGTGTTCCGGGG 58.231 50.000 0.00 0.00 0.00 5.73
867 1684 4.396790 GCTAGATAGATAGAGTGTTCCGGG 59.603 50.000 0.00 0.00 0.00 5.73
868 1685 4.396790 GGCTAGATAGATAGAGTGTTCCGG 59.603 50.000 0.00 0.00 0.00 5.14
869 1686 4.396790 GGGCTAGATAGATAGAGTGTTCCG 59.603 50.000 0.00 0.00 0.00 4.30
870 1687 5.326069 TGGGCTAGATAGATAGAGTGTTCC 58.674 45.833 0.00 0.00 0.00 3.62
871 1688 6.265649 TGTTGGGCTAGATAGATAGAGTGTTC 59.734 42.308 0.00 0.00 0.00 3.18
872 1689 6.041069 GTGTTGGGCTAGATAGATAGAGTGTT 59.959 42.308 0.00 0.00 0.00 3.32
873 1690 5.536916 GTGTTGGGCTAGATAGATAGAGTGT 59.463 44.000 0.00 0.00 0.00 3.55
874 1691 5.335269 CGTGTTGGGCTAGATAGATAGAGTG 60.335 48.000 0.00 0.00 0.00 3.51
875 1692 4.762765 CGTGTTGGGCTAGATAGATAGAGT 59.237 45.833 0.00 0.00 0.00 3.24
876 1693 4.380023 GCGTGTTGGGCTAGATAGATAGAG 60.380 50.000 0.00 0.00 0.00 2.43
877 1694 3.506455 GCGTGTTGGGCTAGATAGATAGA 59.494 47.826 0.00 0.00 0.00 1.98
878 1695 3.255888 TGCGTGTTGGGCTAGATAGATAG 59.744 47.826 0.00 0.00 0.00 2.08
879 1696 3.005472 GTGCGTGTTGGGCTAGATAGATA 59.995 47.826 0.00 0.00 0.00 1.98
880 1697 2.039418 TGCGTGTTGGGCTAGATAGAT 58.961 47.619 0.00 0.00 0.00 1.98
881 1698 1.136305 GTGCGTGTTGGGCTAGATAGA 59.864 52.381 0.00 0.00 0.00 1.98
882 1699 1.571919 GTGCGTGTTGGGCTAGATAG 58.428 55.000 0.00 0.00 0.00 2.08
883 1700 0.179121 CGTGCGTGTTGGGCTAGATA 60.179 55.000 0.00 0.00 0.00 1.98
884 1701 1.447838 CGTGCGTGTTGGGCTAGAT 60.448 57.895 0.00 0.00 0.00 1.98
885 1702 2.048597 CGTGCGTGTTGGGCTAGA 60.049 61.111 0.00 0.00 0.00 2.43
886 1703 3.788766 GCGTGCGTGTTGGGCTAG 61.789 66.667 0.00 0.00 0.00 3.42
887 1704 4.610714 TGCGTGCGTGTTGGGCTA 62.611 61.111 0.00 0.00 0.00 3.93
899 1716 3.781926 TTCTTTGCGTGCGTGCGTG 62.782 57.895 3.11 0.00 37.81 5.34
900 1717 3.506312 CTTCTTTGCGTGCGTGCGT 62.506 57.895 3.11 0.00 37.81 5.24
901 1718 2.792543 CTTCTTTGCGTGCGTGCG 60.793 61.111 0.00 0.00 37.81 5.34
902 1719 3.093449 GCTTCTTTGCGTGCGTGC 61.093 61.111 0.00 0.00 0.00 5.34
923 1740 1.524991 GAGCGAGCGATCGAAAGACG 61.525 60.000 29.29 15.82 46.97 4.18
932 1755 2.025441 GAAGAGCGAGCGAGCGAT 59.975 61.111 1.41 0.00 43.00 4.58
935 1758 2.581953 CAGGAAGAGCGAGCGAGC 60.582 66.667 0.00 0.00 37.41 5.03
936 1759 2.581953 GCAGGAAGAGCGAGCGAG 60.582 66.667 0.00 0.00 0.00 5.03
937 1760 3.057547 GAGCAGGAAGAGCGAGCGA 62.058 63.158 0.00 0.00 37.01 4.93
941 1764 0.753479 CCTAGGAGCAGGAAGAGCGA 60.753 60.000 1.05 0.00 38.00 4.93
942 1765 1.739049 CCTAGGAGCAGGAAGAGCG 59.261 63.158 1.05 0.00 38.00 5.03
943 1766 0.689412 ACCCTAGGAGCAGGAAGAGC 60.689 60.000 11.48 0.00 38.00 4.09
945 1768 2.188817 GAAACCCTAGGAGCAGGAAGA 58.811 52.381 11.48 0.00 38.00 2.87
947 1770 0.902531 CGAAACCCTAGGAGCAGGAA 59.097 55.000 11.48 0.00 38.00 3.36
950 1773 2.289444 TGAAACGAAACCCTAGGAGCAG 60.289 50.000 11.48 0.00 0.00 4.24
953 1776 4.092968 CGAAATGAAACGAAACCCTAGGAG 59.907 45.833 11.48 2.69 0.00 3.69
955 1778 3.425758 GCGAAATGAAACGAAACCCTAGG 60.426 47.826 0.06 0.06 0.00 3.02
961 1792 2.581637 GGAGGCGAAATGAAACGAAAC 58.418 47.619 0.00 0.00 0.00 2.78
962 1793 1.538075 GGGAGGCGAAATGAAACGAAA 59.462 47.619 0.00 0.00 0.00 3.46
963 1794 1.161843 GGGAGGCGAAATGAAACGAA 58.838 50.000 0.00 0.00 0.00 3.85
964 1795 0.035598 TGGGAGGCGAAATGAAACGA 59.964 50.000 0.00 0.00 0.00 3.85
971 1802 0.183731 GGAGGATTGGGAGGCGAAAT 59.816 55.000 0.00 0.00 0.00 2.17
999 1834 2.124570 CCTTCCTCGGCCACCATG 60.125 66.667 2.24 0.00 0.00 3.66
1213 2114 0.033011 GTAGAGGTGGAGGAGCTGGA 60.033 60.000 0.00 0.00 30.42 3.86
1332 2248 3.614092 GAGCAATCCCTTGATGTTGAGA 58.386 45.455 0.00 0.00 34.04 3.27
1457 2373 1.001631 TTCTCCCTGCGGATCTCCA 59.998 57.895 0.00 0.00 37.60 3.86
1496 2980 2.359214 CAGTGCCTCGATGCTACTCTTA 59.641 50.000 13.93 0.00 0.00 2.10
1515 3000 3.141002 AGCATTAATTTGACGCAGCAG 57.859 42.857 0.00 0.00 0.00 4.24
1518 3008 8.841444 AATACTTAAGCATTAATTTGACGCAG 57.159 30.769 1.29 0.00 40.24 5.18
1554 3052 8.668510 AACATAGGCATACAAAGTCTCATTAG 57.331 34.615 0.00 0.00 0.00 1.73
1557 3055 7.066284 GTGAAACATAGGCATACAAAGTCTCAT 59.934 37.037 0.00 0.00 36.32 2.90
1558 3056 6.371548 GTGAAACATAGGCATACAAAGTCTCA 59.628 38.462 0.00 0.00 36.32 3.27
1559 3057 6.183360 GGTGAAACATAGGCATACAAAGTCTC 60.183 42.308 0.00 0.00 39.98 3.36
1572 3074 0.392998 AGGCAGCGGTGAAACATAGG 60.393 55.000 20.69 0.00 39.98 2.57
1583 3085 1.737838 TGACATAGAAAAGGCAGCGG 58.262 50.000 0.00 0.00 0.00 5.52
1602 3105 6.601613 TGTTTGGGCTTCAGAATAACGATTAT 59.398 34.615 0.00 0.00 0.00 1.28
1604 3107 4.764823 TGTTTGGGCTTCAGAATAACGATT 59.235 37.500 0.00 0.00 0.00 3.34
1605 3108 4.331968 TGTTTGGGCTTCAGAATAACGAT 58.668 39.130 0.00 0.00 0.00 3.73
1607 3110 4.662145 GATGTTTGGGCTTCAGAATAACG 58.338 43.478 0.00 0.00 0.00 3.18
1640 3158 5.197451 TGACCACTGACCACAACTATTTTT 58.803 37.500 0.00 0.00 0.00 1.94
1645 3169 4.591498 AGTAATGACCACTGACCACAACTA 59.409 41.667 0.00 0.00 0.00 2.24
1649 3180 3.135712 ACAAGTAATGACCACTGACCACA 59.864 43.478 0.00 0.00 0.00 4.17
1794 3346 8.747666 CGACAGATCTTTAGCAAATAAGTAGAC 58.252 37.037 0.00 0.00 0.00 2.59
1800 3353 9.161629 TGATTTCGACAGATCTTTAGCAAATAA 57.838 29.630 0.00 0.00 0.00 1.40
1889 3456 2.667199 AACTAAAACGCGCCCGCT 60.667 55.556 5.73 0.00 39.32 5.52
1890 3457 2.501008 CAACTAAAACGCGCCCGC 60.501 61.111 5.73 1.98 38.22 6.13
1891 3458 1.439693 CACAACTAAAACGCGCCCG 60.440 57.895 5.73 0.00 41.14 6.13
1892 3459 0.029700 AACACAACTAAAACGCGCCC 59.970 50.000 5.73 0.00 0.00 6.13
1893 3460 1.776897 GAAACACAACTAAAACGCGCC 59.223 47.619 5.73 0.00 0.00 6.53
1908 3504 0.758123 ACCCGTAACCCGAAGAAACA 59.242 50.000 0.00 0.00 39.56 2.83
1909 3505 1.001293 AGACCCGTAACCCGAAGAAAC 59.999 52.381 0.00 0.00 39.56 2.78
1910 3506 1.273327 GAGACCCGTAACCCGAAGAAA 59.727 52.381 0.00 0.00 39.56 2.52
1913 3509 1.252904 TGGAGACCCGTAACCCGAAG 61.253 60.000 0.00 0.00 39.56 3.79
1937 3533 1.674519 CGACGAAATGACATGGGGTGA 60.675 52.381 0.00 0.00 0.00 4.02
1940 3536 1.448985 AACGACGAAATGACATGGGG 58.551 50.000 0.00 0.00 0.00 4.96
1950 3546 1.859703 TCGCTAGCAAAAACGACGAAA 59.140 42.857 16.45 0.00 0.00 3.46
1978 3574 4.554036 GTCGGAGGGAGGCCATGC 62.554 72.222 5.01 0.00 0.00 4.06
1979 3575 4.227134 CGTCGGAGGGAGGCCATG 62.227 72.222 5.01 0.00 0.00 3.66
1980 3576 4.779733 ACGTCGGAGGGAGGCCAT 62.780 66.667 5.01 0.00 33.84 4.40
1984 3580 2.442272 ATGGACGTCGGAGGGAGG 60.442 66.667 9.92 0.00 36.61 4.30
1985 3581 2.491022 GGATGGACGTCGGAGGGAG 61.491 68.421 9.92 0.00 0.00 4.30
1986 3582 2.441532 GGATGGACGTCGGAGGGA 60.442 66.667 9.92 0.00 0.00 4.20
1987 3583 3.900892 CGGATGGACGTCGGAGGG 61.901 72.222 9.92 0.00 0.00 4.30
1988 3584 1.820906 TACGGATGGACGTCGGAGG 60.821 63.158 9.92 0.10 45.08 4.30
1989 3585 1.094073 AGTACGGATGGACGTCGGAG 61.094 60.000 9.92 1.68 45.08 4.63
1990 3586 1.078214 AGTACGGATGGACGTCGGA 60.078 57.895 9.92 0.00 45.08 4.55
1991 3587 1.354506 GAGTACGGATGGACGTCGG 59.645 63.158 9.92 0.00 45.08 4.79
1992 3588 0.027716 CTGAGTACGGATGGACGTCG 59.972 60.000 9.92 0.02 45.08 5.12
1993 3589 0.248539 GCTGAGTACGGATGGACGTC 60.249 60.000 7.13 7.13 45.08 4.34
1995 3591 1.298413 CGCTGAGTACGGATGGACG 60.298 63.158 0.00 0.00 40.31 4.79
1996 3592 1.589196 GCGCTGAGTACGGATGGAC 60.589 63.158 0.00 0.00 0.00 4.02
1997 3593 2.782222 GGCGCTGAGTACGGATGGA 61.782 63.158 7.64 0.00 0.00 3.41
1998 3594 2.279517 GGCGCTGAGTACGGATGG 60.280 66.667 7.64 0.00 0.00 3.51
1999 3595 2.655364 CGGCGCTGAGTACGGATG 60.655 66.667 11.90 0.00 0.00 3.51
2000 3596 1.378882 TAACGGCGCTGAGTACGGAT 61.379 55.000 25.98 5.31 0.00 4.18
2001 3597 1.585267 TTAACGGCGCTGAGTACGGA 61.585 55.000 25.98 0.00 0.00 4.69
2002 3598 0.526954 ATTAACGGCGCTGAGTACGG 60.527 55.000 25.98 0.00 0.00 4.02
2003 3599 1.274596 AATTAACGGCGCTGAGTACG 58.725 50.000 25.98 11.99 0.00 3.67
2004 3600 2.537214 GGTAATTAACGGCGCTGAGTAC 59.463 50.000 25.98 14.02 0.00 2.73
2005 3601 2.481795 GGGTAATTAACGGCGCTGAGTA 60.482 50.000 25.98 11.78 0.00 2.59
2006 3602 1.648504 GGTAATTAACGGCGCTGAGT 58.351 50.000 25.98 12.89 0.00 3.41
2007 3603 0.935196 GGGTAATTAACGGCGCTGAG 59.065 55.000 25.98 10.01 0.00 3.35
2008 3604 0.538118 AGGGTAATTAACGGCGCTGA 59.462 50.000 25.98 0.00 0.00 4.26
2009 3605 0.935196 GAGGGTAATTAACGGCGCTG 59.065 55.000 16.39 16.39 0.00 5.18
2010 3606 0.179065 GGAGGGTAATTAACGGCGCT 60.179 55.000 6.90 0.00 0.00 5.92
2011 3607 0.462403 TGGAGGGTAATTAACGGCGC 60.462 55.000 6.90 0.00 0.00 6.53
2012 3608 2.027003 TTGGAGGGTAATTAACGGCG 57.973 50.000 4.80 4.80 0.00 6.46
2013 3609 3.284617 ACATTGGAGGGTAATTAACGGC 58.715 45.455 0.00 0.00 0.00 5.68
2014 3610 5.907866 AAACATTGGAGGGTAATTAACGG 57.092 39.130 0.00 0.00 0.00 4.44
2015 3611 6.025280 CGAAAACATTGGAGGGTAATTAACG 58.975 40.000 0.00 0.00 0.00 3.18
2016 3612 5.803461 GCGAAAACATTGGAGGGTAATTAAC 59.197 40.000 0.00 0.00 0.00 2.01
2017 3613 5.712917 AGCGAAAACATTGGAGGGTAATTAA 59.287 36.000 0.00 0.00 0.00 1.40
2018 3614 5.258051 AGCGAAAACATTGGAGGGTAATTA 58.742 37.500 0.00 0.00 0.00 1.40
2019 3615 4.086457 AGCGAAAACATTGGAGGGTAATT 58.914 39.130 0.00 0.00 0.00 1.40
2020 3616 3.694566 GAGCGAAAACATTGGAGGGTAAT 59.305 43.478 0.00 0.00 0.00 1.89
2021 3617 3.078837 GAGCGAAAACATTGGAGGGTAA 58.921 45.455 0.00 0.00 0.00 2.85
2022 3618 2.617021 GGAGCGAAAACATTGGAGGGTA 60.617 50.000 0.00 0.00 0.00 3.69
2023 3619 1.534729 GAGCGAAAACATTGGAGGGT 58.465 50.000 0.00 0.00 0.00 4.34
2024 3620 0.811281 GGAGCGAAAACATTGGAGGG 59.189 55.000 0.00 0.00 0.00 4.30
2025 3621 0.447801 CGGAGCGAAAACATTGGAGG 59.552 55.000 0.00 0.00 0.00 4.30
2026 3622 0.447801 CCGGAGCGAAAACATTGGAG 59.552 55.000 0.00 0.00 0.00 3.86
2027 3623 0.250553 ACCGGAGCGAAAACATTGGA 60.251 50.000 9.46 0.00 0.00 3.53
2028 3624 0.109781 CACCGGAGCGAAAACATTGG 60.110 55.000 9.46 0.00 0.00 3.16
2029 3625 0.109781 CCACCGGAGCGAAAACATTG 60.110 55.000 9.46 0.00 0.00 2.82
2030 3626 0.250553 TCCACCGGAGCGAAAACATT 60.251 50.000 9.46 0.00 0.00 2.71
2031 3627 0.250553 TTCCACCGGAGCGAAAACAT 60.251 50.000 9.46 0.00 31.21 2.71
2032 3628 0.464013 TTTCCACCGGAGCGAAAACA 60.464 50.000 9.46 0.00 31.21 2.83
2033 3629 0.879090 ATTTCCACCGGAGCGAAAAC 59.121 50.000 9.46 0.00 31.21 2.43
2034 3630 1.161843 GATTTCCACCGGAGCGAAAA 58.838 50.000 9.46 1.37 31.21 2.29
2039 3988 2.115291 GCAGGATTTCCACCGGAGC 61.115 63.158 9.46 0.00 38.89 4.70
2040 3989 1.026718 GTGCAGGATTTCCACCGGAG 61.027 60.000 9.46 0.00 38.89 4.63
2054 4003 1.291877 GCGTAGGTGTTCCAGTGCAG 61.292 60.000 0.00 0.00 35.89 4.41
2057 4006 1.375523 GGGCGTAGGTGTTCCAGTG 60.376 63.158 0.00 0.00 35.89 3.66
2058 4007 1.198759 ATGGGCGTAGGTGTTCCAGT 61.199 55.000 0.00 0.00 35.89 4.00
2077 4216 4.380531 CACAAAAACTCCACTCTAGCTCA 58.619 43.478 0.00 0.00 0.00 4.26
2083 4222 0.663153 GCGCACAAAAACTCCACTCT 59.337 50.000 0.30 0.00 0.00 3.24
2089 4228 3.551485 ACAAATGAAGCGCACAAAAACTC 59.449 39.130 11.47 0.00 0.00 3.01
2122 4261 3.430333 AAACACCCAAAAGTTACGCAG 57.570 42.857 0.00 0.00 0.00 5.18
2130 4269 5.277925 GCCATTGATGAAAAACACCCAAAAG 60.278 40.000 0.00 0.00 31.70 2.27
2148 4287 7.307160 CCATACACTTGTATACTAACGCCATTG 60.307 40.741 4.17 0.00 39.06 2.82
2150 4289 6.220930 CCATACACTTGTATACTAACGCCAT 58.779 40.000 4.17 0.00 39.06 4.40
2153 4292 4.986659 CCCCATACACTTGTATACTAACGC 59.013 45.833 4.17 0.00 39.06 4.84
2155 4294 5.163280 TGCCCCCATACACTTGTATACTAAC 60.163 44.000 4.17 0.00 39.06 2.34
2165 4318 0.106719 CCGAATGCCCCCATACACTT 60.107 55.000 0.00 0.00 0.00 3.16
2183 4336 3.434299 CCTGTGCAAAAATCATTTCTGCC 59.566 43.478 5.96 0.00 34.50 4.85
2185 4338 3.998341 CCCCTGTGCAAAAATCATTTCTG 59.002 43.478 0.00 0.00 0.00 3.02
2203 4358 3.669949 AGAACACTAATAGCATCCCCCT 58.330 45.455 0.00 0.00 0.00 4.79
2204 4359 4.141482 TGAAGAACACTAATAGCATCCCCC 60.141 45.833 0.00 0.00 0.00 5.40
2205 4360 5.036117 TGAAGAACACTAATAGCATCCCC 57.964 43.478 0.00 0.00 0.00 4.81
2212 4367 7.607991 ACAATTGGGACTGAAGAACACTAATAG 59.392 37.037 10.83 0.00 0.00 1.73
2216 4371 5.071788 AGACAATTGGGACTGAAGAACACTA 59.928 40.000 10.83 0.00 0.00 2.74
2232 4387 3.737266 AGCAAAATTCACGCAGACAATTG 59.263 39.130 3.24 3.24 0.00 2.32
2233 4388 3.981211 AGCAAAATTCACGCAGACAATT 58.019 36.364 0.00 0.00 0.00 2.32
2259 4414 0.524862 CAGTGCAACAGCTCCCATTC 59.475 55.000 0.00 0.00 41.43 2.67
2262 4417 2.595463 GCAGTGCAACAGCTCCCA 60.595 61.111 11.09 0.00 46.79 4.37
2268 4423 2.160417 GCCTAAGTTAGCAGTGCAACAG 59.840 50.000 19.20 12.60 41.43 3.16
2269 4424 2.151202 GCCTAAGTTAGCAGTGCAACA 58.849 47.619 19.20 0.00 41.43 3.33
2270 4425 2.160417 CAGCCTAAGTTAGCAGTGCAAC 59.840 50.000 19.20 18.10 0.00 4.17
2271 4426 2.426522 CAGCCTAAGTTAGCAGTGCAA 58.573 47.619 19.20 6.89 0.00 4.08
2272 4427 1.945819 GCAGCCTAAGTTAGCAGTGCA 60.946 52.381 19.20 0.00 0.00 4.57
2273 4428 0.729690 GCAGCCTAAGTTAGCAGTGC 59.270 55.000 7.13 7.13 0.00 4.40
2274 4429 1.339055 TGGCAGCCTAAGTTAGCAGTG 60.339 52.381 14.15 2.78 0.00 3.66
2275 4430 0.984230 TGGCAGCCTAAGTTAGCAGT 59.016 50.000 14.15 0.00 0.00 4.40
2276 4431 2.338577 ATGGCAGCCTAAGTTAGCAG 57.661 50.000 14.15 0.00 0.00 4.24
2277 4432 2.806945 AATGGCAGCCTAAGTTAGCA 57.193 45.000 14.15 0.00 0.00 3.49
2278 4433 3.443681 TCAAAATGGCAGCCTAAGTTAGC 59.556 43.478 14.15 0.78 0.00 3.09
2279 4434 4.439289 GCTCAAAATGGCAGCCTAAGTTAG 60.439 45.833 14.15 2.65 0.00 2.34
2280 4435 3.443681 GCTCAAAATGGCAGCCTAAGTTA 59.556 43.478 14.15 0.00 0.00 2.24
2281 4436 2.232208 GCTCAAAATGGCAGCCTAAGTT 59.768 45.455 14.15 0.00 0.00 2.66
2283 4438 1.202222 CGCTCAAAATGGCAGCCTAAG 60.202 52.381 14.15 2.23 0.00 2.18
2285 4440 0.322456 ACGCTCAAAATGGCAGCCTA 60.322 50.000 14.15 0.00 0.00 3.93
2287 4442 0.099436 CTACGCTCAAAATGGCAGCC 59.901 55.000 3.66 3.66 0.00 4.85
2288 4443 0.804989 ACTACGCTCAAAATGGCAGC 59.195 50.000 0.00 0.00 0.00 5.25
2292 4447 3.189287 AGAAGCAACTACGCTCAAAATGG 59.811 43.478 0.00 0.00 42.89 3.16
2388 4580 3.734463 TCTCGTTGCCATGAACAAACTA 58.266 40.909 0.00 0.00 0.00 2.24
2390 4663 2.548057 TCTCTCGTTGCCATGAACAAAC 59.452 45.455 0.00 0.00 0.00 2.93
2427 4708 0.035056 CACCACCAATCACTCCTCCC 60.035 60.000 0.00 0.00 0.00 4.30
2464 4745 3.575256 ACAAGCCAGCATTCAGAAAATCA 59.425 39.130 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.