Multiple sequence alignment - TraesCS6A01G327400

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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 TraesCS6A01G327400 chr6A 100.000 3726 0 0 1 3726 560566626 560570351 0.000000e+00 6881.0
1 TraesCS6A01G327400 chr6A 91.818 990 79 2 1542 2530 560104775 560103787 0.000000e+00 1378.0
2 TraesCS6A01G327400 chr6A 94.528 530 19 5 387 906 262050600 262051129 0.000000e+00 809.0
3 TraesCS6A01G327400 chr6A 94.828 522 21 4 390 909 602926589 602926072 0.000000e+00 809.0
4 TraesCS6A01G327400 chr6A 97.113 381 9 2 2 381 262049439 262049818 3.140000e-180 641.0
5 TraesCS6A01G327400 chr6A 92.424 264 13 5 3190 3448 560102675 560102414 1.630000e-98 370.0
6 TraesCS6A01G327400 chr6A 92.381 105 3 4 913 1017 440540130 440540229 1.080000e-30 145.0
7 TraesCS6A01G327400 chr6A 83.459 133 17 5 3029 3160 562143282 562143410 6.540000e-23 119.0
8 TraesCS6A01G327400 chr6A 100.000 29 0 0 3114 3142 560102756 560102728 2.000000e-03 54.7
9 TraesCS6A01G327400 chr6B 91.985 1647 105 1 1024 2670 626458131 626456512 0.000000e+00 2285.0
10 TraesCS6A01G327400 chr6B 93.133 1529 101 4 1003 2529 626882445 626883971 0.000000e+00 2239.0
11 TraesCS6A01G327400 chr6B 93.226 1491 98 3 1040 2529 626811891 626813379 0.000000e+00 2191.0
12 TraesCS6A01G327400 chr6B 92.110 1521 104 8 1004 2512 626590654 626589138 0.000000e+00 2130.0
13 TraesCS6A01G327400 chr6B 95.184 706 26 2 3023 3726 626588418 626587719 0.000000e+00 1109.0
14 TraesCS6A01G327400 chr6B 91.447 456 34 4 3272 3726 626455880 626455429 4.090000e-174 621.0
15 TraesCS6A01G327400 chr6B 92.285 337 23 2 3387 3723 626886051 626886384 3.370000e-130 475.0
16 TraesCS6A01G327400 chr6B 85.619 299 23 5 3071 3349 626885593 626885891 2.810000e-76 296.0
17 TraesCS6A01G327400 chr6B 89.412 170 14 2 3023 3189 626813692 626813860 1.050000e-50 211.0
18 TraesCS6A01G327400 chr6B 82.517 143 20 5 3019 3160 630836612 630836750 1.820000e-23 121.0
19 TraesCS6A01G327400 chr6B 82.258 124 8 4 3023 3146 626456091 626455982 1.100000e-15 95.3
20 TraesCS6A01G327400 chr6B 92.308 65 5 0 2963 3027 626588523 626588459 3.960000e-15 93.5
21 TraesCS6A01G327400 chr6B 100.000 30 0 0 3160 3189 626455982 626455953 5.200000e-04 56.5
22 TraesCS6A01G327400 chr6D 93.891 1506 92 0 1024 2529 417890729 417892234 0.000000e+00 2272.0
23 TraesCS6A01G327400 chr6D 92.781 1510 103 5 1024 2530 417695284 417693778 0.000000e+00 2180.0
24 TraesCS6A01G327400 chr6D 94.382 712 25 5 3023 3726 417893791 417894495 0.000000e+00 1079.0
25 TraesCS6A01G327400 chr6D 85.655 725 34 22 3023 3726 417693220 417692545 0.000000e+00 699.0
26 TraesCS6A01G327400 chr6D 88.462 156 15 3 2872 3024 417893592 417893747 6.350000e-43 185.0
27 TraesCS6A01G327400 chr1A 94.786 537 21 5 377 906 153335527 153336063 0.000000e+00 830.0
28 TraesCS6A01G327400 chr1A 96.907 97 2 1 913 1008 539325333 539325429 1.070000e-35 161.0
29 TraesCS6A01G327400 chr5A 94.297 526 24 4 390 909 94305082 94304557 0.000000e+00 800.0
30 TraesCS6A01G327400 chr5A 94.106 526 25 5 387 906 582622163 582622688 0.000000e+00 795.0
31 TraesCS6A01G327400 chr5A 95.918 392 14 1 2 393 588408853 588409242 5.250000e-178 634.0
32 TraesCS6A01G327400 chr3A 93.962 530 22 6 390 909 555536694 555536165 0.000000e+00 793.0
33 TraesCS6A01G327400 chr3A 95.939 394 12 2 1 393 30524580 30524970 1.460000e-178 636.0
34 TraesCS6A01G327400 chr3A 94.624 93 4 1 916 1008 87930840 87930749 3.880000e-30 143.0
35 TraesCS6A01G327400 chr3A 92.708 96 7 0 913 1008 550458063 550458158 5.020000e-29 139.0
36 TraesCS6A01G327400 chr2A 94.038 520 23 4 387 901 692946606 692947122 0.000000e+00 782.0
37 TraesCS6A01G327400 chr2A 95.674 393 15 2 2 393 729208784 729209175 6.790000e-177 630.0
38 TraesCS6A01G327400 chr2A 95.431 394 13 3 1 393 752497200 752497589 1.140000e-174 623.0
39 TraesCS6A01G327400 chr2A 95.876 97 2 2 916 1012 163856566 163856472 4.980000e-34 156.0
40 TraesCS6A01G327400 chr7A 93.573 529 25 6 387 906 95233276 95233804 0.000000e+00 780.0
41 TraesCS6A01G327400 chr7A 93.678 522 28 3 390 909 686141150 686140632 0.000000e+00 776.0
42 TraesCS6A01G327400 chr7A 95.939 394 13 2 1 393 77164850 77165241 1.460000e-178 636.0
43 TraesCS6A01G327400 chr7A 95.652 391 14 3 4 393 111216668 111216280 3.160000e-175 625.0
44 TraesCS6A01G327400 chr7A 95.178 394 14 4 1 393 24448277 24447888 5.290000e-173 617.0
45 TraesCS6A01G327400 chr4A 95.652 391 13 3 4 393 681122768 681122381 3.160000e-175 625.0
46 TraesCS6A01G327400 chr4A 93.000 100 5 2 913 1011 563571360 563571458 1.080000e-30 145.0
47 TraesCS6A01G327400 chr4A 92.857 98 6 1 916 1013 563563302 563563206 1.400000e-29 141.0
48 TraesCS6A01G327400 chr4A 91.089 101 7 2 913 1011 86983551 86983651 6.490000e-28 135.0
49 TraesCS6A01G327400 chr5B 91.089 101 3 6 916 1012 710869996 710870094 8.400000e-27 132.0


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 TraesCS6A01G327400 chr6A 560566626 560570351 3725 False 6881.000000 6881 100.000000 1 3726 1 chr6A.!!$F2 3725
1 TraesCS6A01G327400 chr6A 602926072 602926589 517 True 809.000000 809 94.828000 390 909 1 chr6A.!!$R1 519
2 TraesCS6A01G327400 chr6A 262049439 262051129 1690 False 725.000000 809 95.820500 2 906 2 chr6A.!!$F4 904
3 TraesCS6A01G327400 chr6A 560102414 560104775 2361 True 600.900000 1378 94.747333 1542 3448 3 chr6A.!!$R2 1906
4 TraesCS6A01G327400 chr6B 626811891 626813860 1969 False 1201.000000 2191 91.319000 1040 3189 2 chr6B.!!$F2 2149
5 TraesCS6A01G327400 chr6B 626587719 626590654 2935 True 1110.833333 2130 93.200667 1004 3726 3 chr6B.!!$R2 2722
6 TraesCS6A01G327400 chr6B 626882445 626886384 3939 False 1003.333333 2239 90.345667 1003 3723 3 chr6B.!!$F3 2720
7 TraesCS6A01G327400 chr6B 626455429 626458131 2702 True 764.450000 2285 91.422500 1024 3726 4 chr6B.!!$R1 2702
8 TraesCS6A01G327400 chr6D 417692545 417695284 2739 True 1439.500000 2180 89.218000 1024 3726 2 chr6D.!!$R1 2702
9 TraesCS6A01G327400 chr6D 417890729 417894495 3766 False 1178.666667 2272 92.245000 1024 3726 3 chr6D.!!$F1 2702
10 TraesCS6A01G327400 chr1A 153335527 153336063 536 False 830.000000 830 94.786000 377 906 1 chr1A.!!$F1 529
11 TraesCS6A01G327400 chr5A 94304557 94305082 525 True 800.000000 800 94.297000 390 909 1 chr5A.!!$R1 519
12 TraesCS6A01G327400 chr5A 582622163 582622688 525 False 795.000000 795 94.106000 387 906 1 chr5A.!!$F1 519
13 TraesCS6A01G327400 chr3A 555536165 555536694 529 True 793.000000 793 93.962000 390 909 1 chr3A.!!$R2 519
14 TraesCS6A01G327400 chr2A 692946606 692947122 516 False 782.000000 782 94.038000 387 901 1 chr2A.!!$F1 514
15 TraesCS6A01G327400 chr7A 95233276 95233804 528 False 780.000000 780 93.573000 387 906 1 chr7A.!!$F2 519
16 TraesCS6A01G327400 chr7A 686140632 686141150 518 True 776.000000 776 93.678000 390 909 1 chr7A.!!$R3 519

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
978 1779 0.251916 TGCTGAGTAATGGAACCGGG 59.748 55.0 6.32 0.0 0.0 5.73 F
979 1780 0.463833 GCTGAGTAATGGAACCGGGG 60.464 60.0 6.32 0.0 0.0 5.73 F
1825 2633 0.606401 CGGTCAGGTGGAGTTTGCAT 60.606 55.0 0.00 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2405 3219 0.110056 GCAGACAAACTCATGCACGG 60.110 55.000 0.0 0.0 38.54 4.94 R
2516 3330 0.805322 CAGTCGCTCCAGTGCTCATC 60.805 60.000 0.0 0.0 0.00 2.92 R
2966 5665 1.009675 AGGGATACAGGGGCAAGTAGT 59.990 52.381 0.0 0.0 39.74 2.73 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
104 106 1.453928 CCCCAGGAGCCCGATTTTC 60.454 63.158 0.00 0.00 0.00 2.29
197 199 2.729491 GGCGAACTGTTTTGGCGC 60.729 61.111 13.79 13.79 46.20 6.53
237 239 1.935327 GCGTCAGCGACTCTACCCTT 61.935 60.000 7.03 0.00 41.33 3.95
343 345 1.077501 CCATTGATGCCTCACGGGT 60.078 57.895 0.00 0.00 37.43 5.28
552 1330 2.444706 CCCTGGAGGAGATCGCCA 60.445 66.667 18.44 8.63 43.16 5.69
755 1553 0.824109 CTCCTCGGCATGTAGAACCA 59.176 55.000 0.00 0.00 0.00 3.67
902 1703 8.277018 CGCCGAATTTAAACATTTTAAAAACCT 58.723 29.630 4.44 0.00 0.00 3.50
909 1710 6.918892 AAACATTTTAAAAACCTGTGAGGC 57.081 33.333 4.44 0.00 39.63 4.70
910 1711 5.606348 ACATTTTAAAAACCTGTGAGGCA 57.394 34.783 4.44 0.00 39.63 4.75
911 1712 5.600696 ACATTTTAAAAACCTGTGAGGCAG 58.399 37.500 4.44 0.00 39.63 4.85
912 1713 3.726291 TTTAAAAACCTGTGAGGCAGC 57.274 42.857 0.00 0.00 43.71 5.25
913 1714 1.616159 TAAAAACCTGTGAGGCAGCC 58.384 50.000 1.84 1.84 43.71 4.85
914 1715 1.115326 AAAAACCTGTGAGGCAGCCC 61.115 55.000 8.22 0.00 43.71 5.19
915 1716 3.513750 AAACCTGTGAGGCAGCCCC 62.514 63.158 8.22 0.00 43.71 5.80
917 1718 2.688666 CCTGTGAGGCAGCCCCTA 60.689 66.667 8.22 0.00 46.60 3.53
918 1719 2.300967 CCTGTGAGGCAGCCCCTAA 61.301 63.158 8.22 0.00 46.60 2.69
919 1720 1.222936 CTGTGAGGCAGCCCCTAAG 59.777 63.158 8.22 0.00 46.60 2.18
920 1721 1.538876 TGTGAGGCAGCCCCTAAGT 60.539 57.895 8.22 0.00 46.60 2.24
921 1722 1.078143 GTGAGGCAGCCCCTAAGTG 60.078 63.158 8.22 0.00 46.60 3.16
922 1723 1.229496 TGAGGCAGCCCCTAAGTGA 60.229 57.895 8.22 0.00 46.60 3.41
923 1724 1.267574 TGAGGCAGCCCCTAAGTGAG 61.268 60.000 8.22 0.00 46.60 3.51
924 1725 2.124529 GGCAGCCCCTAAGTGAGC 60.125 66.667 0.00 0.00 0.00 4.26
925 1726 2.674220 GGCAGCCCCTAAGTGAGCT 61.674 63.158 0.00 0.00 35.52 4.09
926 1727 4.950479 CAGCCCCTAAGTGAGCTG 57.050 61.111 0.00 0.00 45.92 4.24
927 1728 1.451028 CAGCCCCTAAGTGAGCTGC 60.451 63.158 0.00 0.00 45.44 5.25
928 1729 1.614824 AGCCCCTAAGTGAGCTGCT 60.615 57.895 0.00 0.00 33.41 4.24
929 1730 1.451028 GCCCCTAAGTGAGCTGCTG 60.451 63.158 7.01 0.00 0.00 4.41
930 1731 1.986413 CCCCTAAGTGAGCTGCTGT 59.014 57.895 7.01 0.00 0.00 4.40
931 1732 1.195115 CCCCTAAGTGAGCTGCTGTA 58.805 55.000 7.01 0.00 0.00 2.74
932 1733 1.765314 CCCCTAAGTGAGCTGCTGTAT 59.235 52.381 7.01 0.00 0.00 2.29
933 1734 2.965831 CCCCTAAGTGAGCTGCTGTATA 59.034 50.000 7.01 0.00 0.00 1.47
934 1735 3.388024 CCCCTAAGTGAGCTGCTGTATAA 59.612 47.826 7.01 0.00 0.00 0.98
935 1736 4.372656 CCCTAAGTGAGCTGCTGTATAAC 58.627 47.826 7.01 0.00 0.00 1.89
936 1737 4.100189 CCCTAAGTGAGCTGCTGTATAACT 59.900 45.833 7.01 0.00 0.00 2.24
937 1738 5.046529 CCTAAGTGAGCTGCTGTATAACTG 58.953 45.833 7.01 0.00 0.00 3.16
938 1739 3.533606 AGTGAGCTGCTGTATAACTGG 57.466 47.619 7.01 0.00 0.00 4.00
939 1740 3.099905 AGTGAGCTGCTGTATAACTGGA 58.900 45.455 7.01 0.00 0.00 3.86
940 1741 3.131933 AGTGAGCTGCTGTATAACTGGAG 59.868 47.826 7.01 1.91 38.25 3.86
941 1742 3.131223 GTGAGCTGCTGTATAACTGGAGA 59.869 47.826 7.01 0.00 37.62 3.71
942 1743 3.963374 TGAGCTGCTGTATAACTGGAGAT 59.037 43.478 7.01 3.21 37.62 2.75
943 1744 4.038522 TGAGCTGCTGTATAACTGGAGATC 59.961 45.833 7.01 13.87 45.76 2.75
944 1745 3.005261 AGCTGCTGTATAACTGGAGATCG 59.995 47.826 0.00 0.00 37.62 3.69
945 1746 3.312828 CTGCTGTATAACTGGAGATCGC 58.687 50.000 0.18 0.00 37.62 4.58
946 1747 2.287608 TGCTGTATAACTGGAGATCGCG 60.288 50.000 0.00 0.00 0.00 5.87
947 1748 2.287668 GCTGTATAACTGGAGATCGCGT 60.288 50.000 5.77 0.00 0.00 6.01
948 1749 3.795826 GCTGTATAACTGGAGATCGCGTT 60.796 47.826 5.77 0.00 0.00 4.84
949 1750 4.360563 CTGTATAACTGGAGATCGCGTTT 58.639 43.478 5.77 0.00 0.00 3.60
950 1751 4.751060 TGTATAACTGGAGATCGCGTTTT 58.249 39.130 5.77 0.00 0.00 2.43
951 1752 5.172934 TGTATAACTGGAGATCGCGTTTTT 58.827 37.500 5.77 0.00 0.00 1.94
952 1753 2.969443 AACTGGAGATCGCGTTTTTG 57.031 45.000 5.77 0.00 0.00 2.44
953 1754 1.156736 ACTGGAGATCGCGTTTTTGG 58.843 50.000 5.77 0.00 0.00 3.28
954 1755 1.156736 CTGGAGATCGCGTTTTTGGT 58.843 50.000 5.77 0.00 0.00 3.67
955 1756 1.535462 CTGGAGATCGCGTTTTTGGTT 59.465 47.619 5.77 0.00 0.00 3.67
956 1757 1.950909 TGGAGATCGCGTTTTTGGTTT 59.049 42.857 5.77 0.00 0.00 3.27
957 1758 2.031508 TGGAGATCGCGTTTTTGGTTTC 60.032 45.455 5.77 0.00 0.00 2.78
958 1759 2.031508 GGAGATCGCGTTTTTGGTTTCA 60.032 45.455 5.77 0.00 0.00 2.69
959 1760 3.365969 GGAGATCGCGTTTTTGGTTTCAT 60.366 43.478 5.77 0.00 0.00 2.57
960 1761 3.564511 AGATCGCGTTTTTGGTTTCATG 58.435 40.909 5.77 0.00 0.00 3.07
961 1762 1.482278 TCGCGTTTTTGGTTTCATGC 58.518 45.000 5.77 0.00 0.00 4.06
962 1763 1.066303 TCGCGTTTTTGGTTTCATGCT 59.934 42.857 5.77 0.00 0.00 3.79
963 1764 1.189884 CGCGTTTTTGGTTTCATGCTG 59.810 47.619 0.00 0.00 0.00 4.41
964 1765 2.468831 GCGTTTTTGGTTTCATGCTGA 58.531 42.857 0.00 0.00 0.00 4.26
965 1766 2.472488 GCGTTTTTGGTTTCATGCTGAG 59.528 45.455 0.00 0.00 0.00 3.35
966 1767 3.705604 CGTTTTTGGTTTCATGCTGAGT 58.294 40.909 0.00 0.00 0.00 3.41
967 1768 4.791411 GCGTTTTTGGTTTCATGCTGAGTA 60.791 41.667 0.00 0.00 0.00 2.59
968 1769 5.277825 CGTTTTTGGTTTCATGCTGAGTAA 58.722 37.500 0.00 0.00 0.00 2.24
969 1770 5.920273 CGTTTTTGGTTTCATGCTGAGTAAT 59.080 36.000 0.00 0.00 0.00 1.89
970 1771 6.129115 CGTTTTTGGTTTCATGCTGAGTAATG 60.129 38.462 0.00 0.00 0.00 1.90
971 1772 5.389859 TTTGGTTTCATGCTGAGTAATGG 57.610 39.130 0.00 0.00 0.00 3.16
972 1773 4.299586 TGGTTTCATGCTGAGTAATGGA 57.700 40.909 0.00 0.00 0.00 3.41
973 1774 4.661222 TGGTTTCATGCTGAGTAATGGAA 58.339 39.130 0.00 0.00 0.00 3.53
974 1775 4.458989 TGGTTTCATGCTGAGTAATGGAAC 59.541 41.667 10.97 10.97 40.26 3.62
975 1776 4.986622 GTTTCATGCTGAGTAATGGAACC 58.013 43.478 9.13 0.00 36.62 3.62
976 1777 2.905075 TCATGCTGAGTAATGGAACCG 58.095 47.619 0.00 0.00 0.00 4.44
977 1778 1.942657 CATGCTGAGTAATGGAACCGG 59.057 52.381 0.00 0.00 0.00 5.28
978 1779 0.251916 TGCTGAGTAATGGAACCGGG 59.748 55.000 6.32 0.00 0.00 5.73
979 1780 0.463833 GCTGAGTAATGGAACCGGGG 60.464 60.000 6.32 0.00 0.00 5.73
980 1781 1.200519 CTGAGTAATGGAACCGGGGA 58.799 55.000 6.32 0.00 0.00 4.81
981 1782 1.139058 CTGAGTAATGGAACCGGGGAG 59.861 57.143 6.32 0.00 0.00 4.30
983 1784 0.986550 AGTAATGGAACCGGGGAGGG 60.987 60.000 6.32 0.00 46.96 4.30
984 1785 1.694882 TAATGGAACCGGGGAGGGG 60.695 63.158 6.32 0.00 46.96 4.79
985 1786 2.197659 TAATGGAACCGGGGAGGGGA 62.198 60.000 6.32 0.00 46.96 4.81
986 1787 3.589627 ATGGAACCGGGGAGGGGAA 62.590 63.158 6.32 0.00 46.96 3.97
987 1788 3.725032 GGAACCGGGGAGGGGAAC 61.725 72.222 6.32 0.00 46.96 3.62
1033 1834 5.753721 AAGGAGCTCTCATTCTAGTGTTT 57.246 39.130 14.64 0.00 0.00 2.83
1095 1897 1.713647 TCTCTCAGTCTTCCTCCACCT 59.286 52.381 0.00 0.00 0.00 4.00
1096 1898 2.920271 TCTCTCAGTCTTCCTCCACCTA 59.080 50.000 0.00 0.00 0.00 3.08
1272 2080 1.972223 CGACGTCACCCTCCTCACT 60.972 63.158 17.16 0.00 0.00 3.41
1309 2117 4.467107 GCTCTCCCTCCTCCCCGT 62.467 72.222 0.00 0.00 0.00 5.28
1464 2272 2.363276 ATGCCCGTCAGGTCCGTA 60.363 61.111 0.00 0.00 38.26 4.02
1825 2633 0.606401 CGGTCAGGTGGAGTTTGCAT 60.606 55.000 0.00 0.00 0.00 3.96
1839 2647 1.340088 TTGCATGGCAGGTGTTTGAT 58.660 45.000 0.00 0.00 40.61 2.57
1881 2689 2.432510 GGTCTCCTGGAACTCGATGATT 59.567 50.000 0.00 0.00 0.00 2.57
1909 2717 3.803082 CAGCCAATGGACGGTGCG 61.803 66.667 2.05 0.00 0.00 5.34
1910 2718 4.329545 AGCCAATGGACGGTGCGT 62.330 61.111 2.05 0.00 45.10 5.24
1930 2738 1.089481 GGACGCCATCGAGCATTTCA 61.089 55.000 0.00 0.00 39.41 2.69
2185 2999 2.856000 AGGTGGTGCTGGGAGCTT 60.856 61.111 0.00 0.00 42.97 3.74
2205 3019 2.589540 CTTGCTGGGTGCCGGATA 59.410 61.111 5.05 0.00 42.00 2.59
2306 3120 0.999406 CTGTCAAACATCTACGCCGG 59.001 55.000 0.00 0.00 0.00 6.13
2354 3168 1.923395 TCCGGGGCCTGATGAAAGT 60.923 57.895 15.75 0.00 0.00 2.66
2516 3330 1.586422 CATGAGGCCGTGAGTTATGG 58.414 55.000 0.00 0.00 38.58 2.74
2542 3356 1.302033 CTGGAGCGACTGCCTGTTT 60.302 57.895 0.00 0.00 44.31 2.83
2543 3357 1.572085 CTGGAGCGACTGCCTGTTTG 61.572 60.000 0.00 0.00 44.31 2.93
2544 3358 2.328099 GGAGCGACTGCCTGTTTGG 61.328 63.158 0.00 0.00 44.31 3.28
2545 3359 1.301716 GAGCGACTGCCTGTTTGGA 60.302 57.895 0.00 0.00 44.31 3.53
2546 3360 0.674895 GAGCGACTGCCTGTTTGGAT 60.675 55.000 0.00 0.00 44.31 3.41
2547 3361 0.957395 AGCGACTGCCTGTTTGGATG 60.957 55.000 0.00 0.00 44.31 3.51
2548 3362 0.955428 GCGACTGCCTGTTTGGATGA 60.955 55.000 0.00 0.00 38.35 2.92
2549 3363 1.522668 CGACTGCCTGTTTGGATGAA 58.477 50.000 0.00 0.00 38.35 2.57
2550 3364 1.197721 CGACTGCCTGTTTGGATGAAC 59.802 52.381 0.00 0.00 38.35 3.18
2551 3365 2.508526 GACTGCCTGTTTGGATGAACT 58.491 47.619 0.00 0.00 38.35 3.01
2552 3366 2.485814 GACTGCCTGTTTGGATGAACTC 59.514 50.000 0.00 0.00 38.35 3.01
2553 3367 2.158623 ACTGCCTGTTTGGATGAACTCA 60.159 45.455 0.00 0.00 38.35 3.41
2554 3368 3.087031 CTGCCTGTTTGGATGAACTCAT 58.913 45.455 0.00 0.00 39.70 2.90
2566 3380 3.049708 TGAACTCATCAGAACTGCAGG 57.950 47.619 19.93 0.00 33.04 4.85
2567 3381 2.634453 TGAACTCATCAGAACTGCAGGA 59.366 45.455 19.93 5.70 33.04 3.86
2716 3710 4.097361 GGGAAGAGGCACCCGACC 62.097 72.222 0.00 0.00 36.56 4.79
2729 3723 3.069158 GCACCCGACCTGTACAGTAATAT 59.931 47.826 21.18 1.64 0.00 1.28
2732 3735 5.048224 CACCCGACCTGTACAGTAATATAGG 60.048 48.000 21.18 13.70 38.92 2.57
2749 3752 9.026121 GTAATATAGGTACAGGTGATGAGATGT 57.974 37.037 0.00 0.00 0.00 3.06
2762 3777 9.832445 AGGTGATGAGATGTATATTTTTACGTT 57.168 29.630 0.00 0.00 0.00 3.99
2778 3793 7.633361 TTTTACGTTGACAGATGAGAAGTAC 57.367 36.000 0.00 0.00 0.00 2.73
2842 4325 4.439968 TCAGCTCAATCAAGCATAGACAG 58.560 43.478 0.00 0.00 45.00 3.51
2844 4327 4.634883 CAGCTCAATCAAGCATAGACAGTT 59.365 41.667 0.00 0.00 45.00 3.16
2846 4329 6.018913 CAGCTCAATCAAGCATAGACAGTTAG 60.019 42.308 0.00 0.00 45.00 2.34
2847 4330 6.045318 GCTCAATCAAGCATAGACAGTTAGA 58.955 40.000 0.00 0.00 42.05 2.10
2848 4331 6.019156 GCTCAATCAAGCATAGACAGTTAGAC 60.019 42.308 0.00 0.00 42.05 2.59
2849 4332 6.935167 TCAATCAAGCATAGACAGTTAGACA 58.065 36.000 0.00 0.00 0.00 3.41
2882 5278 7.506114 TCTATAAGGTGAAGAACAACACAAGT 58.494 34.615 0.00 0.00 38.92 3.16
2910 5307 8.192774 CCTGAACTGATAACGGTAATGTTACTA 58.807 37.037 3.22 0.00 37.16 1.82
2915 5312 8.867097 ACTGATAACGGTAATGTTACTATGGAT 58.133 33.333 3.22 0.00 37.16 3.41
2966 5665 8.780249 TCGATTATATCACTCGTAATGTCTCAA 58.220 33.333 0.00 0.00 34.19 3.02
2975 5674 4.491676 TCGTAATGTCTCAACTACTTGCC 58.508 43.478 0.00 0.00 0.00 4.52
2978 5677 1.729586 TGTCTCAACTACTTGCCCCT 58.270 50.000 0.00 0.00 0.00 4.79
2992 5691 0.181350 GCCCCTGTATCCCTGTCAAG 59.819 60.000 0.00 0.00 0.00 3.02
3044 7126 7.334090 TCATTTCAAAGACAAGAGGGAGATAG 58.666 38.462 0.00 0.00 0.00 2.08
3104 7188 7.255520 GCCTATATATAACTATGGTGACCTCCG 60.256 44.444 2.11 0.00 0.00 4.63
3467 7701 4.416516 TGGTCTCTCATTGTTACTCCAGA 58.583 43.478 0.00 0.00 0.00 3.86
3555 7797 3.423749 TGAATCTTTTGATGAGCAGGCA 58.576 40.909 0.00 0.00 39.48 4.75
3570 7812 0.671781 AGGCAAGAAGTAGCACTGCG 60.672 55.000 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 68 2.791927 GCGACTGGGCCGATTTTC 59.208 61.111 0.00 0.00 0.00 2.29
237 239 2.260434 CGACGAAGGGGCGAGAAA 59.740 61.111 0.00 0.00 34.83 2.52
343 345 4.680237 CCGGTCTTCACTGCGCCA 62.680 66.667 4.18 0.00 0.00 5.69
347 349 1.078759 CGTCATCCGGTCTTCACTGC 61.079 60.000 0.00 0.00 0.00 4.40
384 386 4.856607 GAGGACGAAGCGGGCGAG 62.857 72.222 0.00 0.00 0.00 5.03
388 1166 4.831307 CGACGAGGACGAAGCGGG 62.831 72.222 0.00 0.00 42.66 6.13
705 1503 2.960170 GTGTAGTCACCGCCGTCT 59.040 61.111 0.00 0.00 38.51 4.18
735 1533 1.112113 GGTTCTACATGCCGAGGAGA 58.888 55.000 0.00 0.00 0.00 3.71
869 1670 3.643763 TGTTTAAATTCGGCGCAAACAT 58.356 36.364 10.83 0.00 34.97 2.71
902 1703 1.538876 ACTTAGGGGCTGCCTCACA 60.539 57.895 22.77 4.86 0.00 3.58
906 1707 2.674220 GCTCACTTAGGGGCTGCCT 61.674 63.158 19.68 1.54 0.00 4.75
909 1710 4.950479 CAGCTCACTTAGGGGCTG 57.050 61.111 9.76 9.76 44.45 4.85
910 1711 1.614824 AGCAGCTCACTTAGGGGCT 60.615 57.895 0.00 0.00 35.23 5.19
911 1712 1.451028 CAGCAGCTCACTTAGGGGC 60.451 63.158 0.00 0.00 0.00 5.80
912 1713 1.195115 TACAGCAGCTCACTTAGGGG 58.805 55.000 0.00 0.00 0.00 4.79
913 1714 4.100189 AGTTATACAGCAGCTCACTTAGGG 59.900 45.833 0.00 0.00 0.00 3.53
914 1715 5.046529 CAGTTATACAGCAGCTCACTTAGG 58.953 45.833 0.00 0.00 0.00 2.69
915 1716 5.046529 CCAGTTATACAGCAGCTCACTTAG 58.953 45.833 0.00 0.00 0.00 2.18
916 1717 4.709886 TCCAGTTATACAGCAGCTCACTTA 59.290 41.667 0.00 0.00 0.00 2.24
917 1718 3.515502 TCCAGTTATACAGCAGCTCACTT 59.484 43.478 0.00 0.00 0.00 3.16
918 1719 3.099905 TCCAGTTATACAGCAGCTCACT 58.900 45.455 0.00 0.00 0.00 3.41
919 1720 3.131223 TCTCCAGTTATACAGCAGCTCAC 59.869 47.826 0.00 0.00 0.00 3.51
920 1721 3.365472 TCTCCAGTTATACAGCAGCTCA 58.635 45.455 0.00 0.00 0.00 4.26
921 1722 4.555262 GATCTCCAGTTATACAGCAGCTC 58.445 47.826 0.00 0.00 0.00 4.09
922 1723 3.005261 CGATCTCCAGTTATACAGCAGCT 59.995 47.826 0.00 0.00 0.00 4.24
923 1724 3.312828 CGATCTCCAGTTATACAGCAGC 58.687 50.000 0.00 0.00 0.00 5.25
924 1725 3.312828 GCGATCTCCAGTTATACAGCAG 58.687 50.000 0.00 0.00 0.00 4.24
925 1726 2.287608 CGCGATCTCCAGTTATACAGCA 60.288 50.000 0.00 0.00 0.00 4.41
926 1727 2.287668 ACGCGATCTCCAGTTATACAGC 60.288 50.000 15.93 0.00 0.00 4.40
927 1728 3.627732 ACGCGATCTCCAGTTATACAG 57.372 47.619 15.93 0.00 0.00 2.74
928 1729 4.380841 AAACGCGATCTCCAGTTATACA 57.619 40.909 15.93 0.00 0.00 2.29
929 1730 5.490213 CAAAAACGCGATCTCCAGTTATAC 58.510 41.667 15.93 0.00 0.00 1.47
930 1731 4.569162 CCAAAAACGCGATCTCCAGTTATA 59.431 41.667 15.93 0.00 0.00 0.98
931 1732 3.374058 CCAAAAACGCGATCTCCAGTTAT 59.626 43.478 15.93 0.00 0.00 1.89
932 1733 2.739913 CCAAAAACGCGATCTCCAGTTA 59.260 45.455 15.93 0.00 0.00 2.24
933 1734 1.535462 CCAAAAACGCGATCTCCAGTT 59.465 47.619 15.93 0.00 0.00 3.16
934 1735 1.156736 CCAAAAACGCGATCTCCAGT 58.843 50.000 15.93 0.00 0.00 4.00
935 1736 1.156736 ACCAAAAACGCGATCTCCAG 58.843 50.000 15.93 0.00 0.00 3.86
936 1737 1.600023 AACCAAAAACGCGATCTCCA 58.400 45.000 15.93 0.00 0.00 3.86
937 1738 2.031508 TGAAACCAAAAACGCGATCTCC 60.032 45.455 15.93 0.00 0.00 3.71
938 1739 3.262135 TGAAACCAAAAACGCGATCTC 57.738 42.857 15.93 0.00 0.00 2.75
939 1740 3.564511 CATGAAACCAAAAACGCGATCT 58.435 40.909 15.93 0.00 0.00 2.75
940 1741 2.090503 GCATGAAACCAAAAACGCGATC 59.909 45.455 15.93 0.00 0.00 3.69
941 1742 2.058057 GCATGAAACCAAAAACGCGAT 58.942 42.857 15.93 0.00 0.00 4.58
942 1743 1.066303 AGCATGAAACCAAAAACGCGA 59.934 42.857 15.93 0.00 0.00 5.87
943 1744 1.189884 CAGCATGAAACCAAAAACGCG 59.810 47.619 3.53 3.53 39.69 6.01
944 1745 2.468831 TCAGCATGAAACCAAAAACGC 58.531 42.857 0.00 0.00 45.97 4.84
957 1758 1.942657 CCGGTTCCATTACTCAGCATG 59.057 52.381 0.00 0.00 37.54 4.06
958 1759 1.134098 CCCGGTTCCATTACTCAGCAT 60.134 52.381 0.00 0.00 0.00 3.79
959 1760 0.251916 CCCGGTTCCATTACTCAGCA 59.748 55.000 0.00 0.00 0.00 4.41
960 1761 0.463833 CCCCGGTTCCATTACTCAGC 60.464 60.000 0.00 0.00 0.00 4.26
961 1762 1.139058 CTCCCCGGTTCCATTACTCAG 59.861 57.143 0.00 0.00 0.00 3.35
962 1763 1.200519 CTCCCCGGTTCCATTACTCA 58.799 55.000 0.00 0.00 0.00 3.41
963 1764 0.468648 CCTCCCCGGTTCCATTACTC 59.531 60.000 0.00 0.00 0.00 2.59
964 1765 0.986550 CCCTCCCCGGTTCCATTACT 60.987 60.000 0.00 0.00 0.00 2.24
965 1766 1.530283 CCCTCCCCGGTTCCATTAC 59.470 63.158 0.00 0.00 0.00 1.89
966 1767 1.694882 CCCCTCCCCGGTTCCATTA 60.695 63.158 0.00 0.00 0.00 1.90
967 1768 3.021263 CCCCTCCCCGGTTCCATT 61.021 66.667 0.00 0.00 0.00 3.16
968 1769 3.589627 TTCCCCTCCCCGGTTCCAT 62.590 63.158 0.00 0.00 0.00 3.41
969 1770 4.273262 TTCCCCTCCCCGGTTCCA 62.273 66.667 0.00 0.00 0.00 3.53
970 1771 3.725032 GTTCCCCTCCCCGGTTCC 61.725 72.222 0.00 0.00 0.00 3.62
971 1772 3.725032 GGTTCCCCTCCCCGGTTC 61.725 72.222 0.00 0.00 0.00 3.62
972 1773 4.281074 AGGTTCCCCTCCCCGGTT 62.281 66.667 0.00 0.00 35.62 4.44
980 1781 2.192263 GATGAACAGAGAGGTTCCCCT 58.808 52.381 3.85 0.00 45.12 4.79
981 1782 2.192263 AGATGAACAGAGAGGTTCCCC 58.808 52.381 3.85 0.00 45.12 4.81
982 1783 5.422214 TTTAGATGAACAGAGAGGTTCCC 57.578 43.478 3.85 0.00 45.12 3.97
1003 1804 6.721704 AGAATGAGAGCTCCTTTTGTTTTT 57.278 33.333 10.93 0.00 0.00 1.94
1004 1805 7.001073 ACTAGAATGAGAGCTCCTTTTGTTTT 58.999 34.615 10.93 0.00 0.00 2.43
1005 1806 6.429385 CACTAGAATGAGAGCTCCTTTTGTTT 59.571 38.462 10.93 0.00 0.00 2.83
1006 1807 5.936956 CACTAGAATGAGAGCTCCTTTTGTT 59.063 40.000 10.93 0.00 0.00 2.83
1007 1808 5.012561 ACACTAGAATGAGAGCTCCTTTTGT 59.987 40.000 10.93 2.68 0.00 2.83
1008 1809 5.486526 ACACTAGAATGAGAGCTCCTTTTG 58.513 41.667 10.93 3.46 0.00 2.44
1022 1823 3.437049 GCTTTCGGCTGAAACACTAGAAT 59.563 43.478 16.83 0.00 39.13 2.40
1294 2102 2.363361 GAACGGGGAGGAGGGAGA 59.637 66.667 0.00 0.00 0.00 3.71
1617 2425 1.317431 GCATGGCATGGAAGCAGTCA 61.317 55.000 27.48 0.00 35.83 3.41
1825 2633 2.093890 CATGCTATCAAACACCTGCCA 58.906 47.619 0.00 0.00 0.00 4.92
1839 2647 1.437573 CGTCCGCTTCCTCATGCTA 59.562 57.895 0.00 0.00 0.00 3.49
1881 2689 1.530419 ATTGGCTGCAAACCCGACA 60.530 52.632 0.50 0.00 0.00 4.35
1890 2698 2.672651 CACCGTCCATTGGCTGCA 60.673 61.111 0.50 0.00 0.00 4.41
1909 2717 1.369091 AAATGCTCGATGGCGTCCAC 61.369 55.000 0.14 0.00 35.80 4.02
1910 2718 1.078497 AAATGCTCGATGGCGTCCA 60.078 52.632 0.14 1.01 38.19 4.02
1930 2738 0.324091 CCCTTCCTCTGCATTGCCTT 60.324 55.000 6.12 0.00 0.00 4.35
1940 2748 1.842381 CGGCTTGAACCCCTTCCTCT 61.842 60.000 0.00 0.00 0.00 3.69
2055 2869 0.681887 CCATCCTTGCTGTGATGCCA 60.682 55.000 0.00 0.00 37.61 4.92
2306 3120 2.186826 CCATCCCATTTCCCGACGC 61.187 63.158 0.00 0.00 0.00 5.19
2333 3147 4.731853 TCATCAGGCCCCGGACCA 62.732 66.667 15.02 0.00 0.00 4.02
2354 3168 0.614979 CCTCTTCTTCACTCCCCGGA 60.615 60.000 0.73 0.00 0.00 5.14
2405 3219 0.110056 GCAGACAAACTCATGCACGG 60.110 55.000 0.00 0.00 38.54 4.94
2516 3330 0.805322 CAGTCGCTCCAGTGCTCATC 60.805 60.000 0.00 0.00 0.00 2.92
2545 3359 3.262660 TCCTGCAGTTCTGATGAGTTCAT 59.737 43.478 13.81 0.00 39.70 2.57
2546 3360 2.634453 TCCTGCAGTTCTGATGAGTTCA 59.366 45.455 13.81 0.00 0.00 3.18
2547 3361 3.325293 TCCTGCAGTTCTGATGAGTTC 57.675 47.619 13.81 0.00 0.00 3.01
2548 3362 3.777106 TTCCTGCAGTTCTGATGAGTT 57.223 42.857 13.81 0.00 0.00 3.01
2549 3363 3.607741 CATTCCTGCAGTTCTGATGAGT 58.392 45.455 13.81 0.00 0.00 3.41
2563 3377 3.474600 CCTCCAGTATTCTGCATTCCTG 58.525 50.000 0.00 0.00 40.09 3.86
2564 3378 2.158696 GCCTCCAGTATTCTGCATTCCT 60.159 50.000 0.00 0.00 40.09 3.36
2565 3379 2.158696 AGCCTCCAGTATTCTGCATTCC 60.159 50.000 0.00 0.00 40.09 3.01
2566 3380 3.205784 AGCCTCCAGTATTCTGCATTC 57.794 47.619 0.00 0.00 40.09 2.67
2567 3381 3.659183 AAGCCTCCAGTATTCTGCATT 57.341 42.857 0.00 0.00 40.09 3.56
2670 3664 2.218603 ACATGAAACGGGAGTCACAAC 58.781 47.619 0.00 0.00 46.69 3.32
2729 3723 9.601810 AAATATACATCTCATCACCTGTACCTA 57.398 33.333 0.00 0.00 0.00 3.08
2752 3755 7.730364 ACTTCTCATCTGTCAACGTAAAAAT 57.270 32.000 0.00 0.00 0.00 1.82
2762 3777 8.753133 ACAATGATAAGTACTTCTCATCTGTCA 58.247 33.333 27.30 12.05 36.00 3.58
2785 3826 7.867403 GTGGATTTGCTTCTCAAGATTTTACAA 59.133 33.333 0.00 0.00 35.84 2.41
2797 4243 2.097825 AGCCATGTGGATTTGCTTCTC 58.902 47.619 2.55 0.00 37.39 2.87
2842 4325 7.502895 TCACCTTATAGAGATCCAGTGTCTAAC 59.497 40.741 0.00 0.00 36.42 2.34
2844 4327 7.150447 TCACCTTATAGAGATCCAGTGTCTA 57.850 40.000 0.00 0.00 37.15 2.59
2846 4329 6.547880 TCTTCACCTTATAGAGATCCAGTGTC 59.452 42.308 0.00 0.00 0.00 3.67
2847 4330 6.436027 TCTTCACCTTATAGAGATCCAGTGT 58.564 40.000 0.00 0.00 0.00 3.55
2848 4331 6.968263 TCTTCACCTTATAGAGATCCAGTG 57.032 41.667 0.00 0.00 0.00 3.66
2849 4332 6.897966 TGTTCTTCACCTTATAGAGATCCAGT 59.102 38.462 0.00 0.00 0.00 4.00
2854 4337 7.907389 TGTGTTGTTCTTCACCTTATAGAGAT 58.093 34.615 0.00 0.00 34.14 2.75
2855 4338 7.297936 TGTGTTGTTCTTCACCTTATAGAGA 57.702 36.000 0.00 0.00 34.14 3.10
2856 4339 7.657761 ACTTGTGTTGTTCTTCACCTTATAGAG 59.342 37.037 0.00 0.00 34.14 2.43
2857 4340 7.506114 ACTTGTGTTGTTCTTCACCTTATAGA 58.494 34.615 0.00 0.00 34.14 1.98
2858 4341 7.730364 ACTTGTGTTGTTCTTCACCTTATAG 57.270 36.000 0.00 0.00 34.14 1.31
2859 4342 7.227910 GGAACTTGTGTTGTTCTTCACCTTATA 59.772 37.037 0.00 0.00 42.27 0.98
2860 4343 6.039382 GGAACTTGTGTTGTTCTTCACCTTAT 59.961 38.462 0.00 0.00 42.27 1.73
2861 4344 5.355910 GGAACTTGTGTTGTTCTTCACCTTA 59.644 40.000 0.00 0.00 42.27 2.69
2882 5278 6.045072 ACATTACCGTTATCAGTTCAGGAA 57.955 37.500 0.00 0.00 0.00 3.36
2899 5296 9.998106 AGTCCAATGTATCCATAGTAACATTAC 57.002 33.333 0.00 0.00 39.80 1.89
2901 5298 9.998106 GTAGTCCAATGTATCCATAGTAACATT 57.002 33.333 0.00 0.00 41.87 2.71
2902 5299 9.381038 AGTAGTCCAATGTATCCATAGTAACAT 57.619 33.333 0.00 0.00 34.11 2.71
2953 5355 4.491676 GGCAAGTAGTTGAGACATTACGA 58.508 43.478 14.64 0.00 35.46 3.43
2966 5665 1.009675 AGGGATACAGGGGCAAGTAGT 59.990 52.381 0.00 0.00 39.74 2.73
2975 5674 2.571653 TGTTCTTGACAGGGATACAGGG 59.428 50.000 0.00 0.00 32.50 4.45
2978 5677 6.774673 TGTTATTGTTCTTGACAGGGATACA 58.225 36.000 0.00 0.00 39.94 2.29
3044 7126 9.787532 AATGTGCACAAATAAAGACATGTATAC 57.212 29.630 25.72 0.00 0.00 1.47
3104 7188 7.283580 TGTTCTCTTCTTACCTATCTAGCAGTC 59.716 40.741 0.00 0.00 0.00 3.51
3316 7428 5.118990 TCATCTTACTCCAAATACAGCTGC 58.881 41.667 15.27 0.00 0.00 5.25
3467 7701 7.553760 TCAGTTTTCATGATACTGTACATGCAT 59.446 33.333 25.63 0.00 42.17 3.96
3555 7797 1.827969 AGATCCGCAGTGCTACTTCTT 59.172 47.619 14.33 0.00 0.00 2.52
3570 7812 6.484643 TGCATGTAGATTTGCTTAGAAGATCC 59.515 38.462 0.00 0.00 39.60 3.36
3604 7846 1.167781 TATGCCACCAGATGCGCATG 61.168 55.000 30.76 16.58 42.04 4.06
3681 7923 4.838986 ACCTGTACAGTTCAGTTCCTATGT 59.161 41.667 21.18 4.61 0.00 2.29


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

AutoCloner maintained by Alex Coulton.