Multiple sequence alignment - TraesCS6A01G287900

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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 TraesCS6A01G287900 chr6A 100.000 4841 0 0 1 4841 520427579 520432419 0.000000e+00 8940.0
1 TraesCS6A01G287900 chr6D 91.640 4390 201 65 84 4429 379003633 379007900 0.000000e+00 5921.0
2 TraesCS6A01G287900 chr6D 87.887 355 26 8 4430 4773 379008135 379008483 7.550000e-108 401.0
3 TraesCS6A01G287900 chr6B 92.580 3841 185 40 84 3888 565213643 565217419 0.000000e+00 5422.0
4 TraesCS6A01G287900 chr6B 88.275 887 53 17 3922 4791 565217419 565218271 0.000000e+00 1014.0
5 TraesCS6A01G287900 chr6B 92.157 255 15 3 89 343 565213030 565213279 5.960000e-94 355.0
6 TraesCS6A01G287900 chr7D 78.058 515 91 19 2931 3442 174799661 174799166 6.090000e-79 305.0
7 TraesCS6A01G287900 chr1A 96.923 65 2 0 2 66 512457964 512457900 5.120000e-20 110.0
8 TraesCS6A01G287900 chr1A 95.588 68 3 0 1 68 577596190 577596123 5.120000e-20 110.0
9 TraesCS6A01G287900 chr1A 92.647 68 5 0 2 69 185844049 185844116 1.110000e-16 99.0
10 TraesCS6A01G287900 chr7A 95.522 67 3 0 2 68 572328108 572328174 1.840000e-19 108.0
11 TraesCS6A01G287900 chr7A 89.333 75 6 1 2 76 354684591 354684663 5.160000e-15 93.5
12 TraesCS6A01G287900 chr3A 94.030 67 4 0 2 68 734529327 734529393 8.570000e-18 102.0
13 TraesCS6A01G287900 chr3A 92.647 68 5 0 2 69 695974810 695974877 1.110000e-16 99.0
14 TraesCS6A01G287900 chr3A 97.059 34 0 1 3766 3798 60630235 60630202 6.770000e-04 56.5
15 TraesCS6A01G287900 chr2A 94.030 67 4 0 2 68 71389831 71389897 8.570000e-18 102.0
16 TraesCS6A01G287900 chr4A 89.855 69 7 0 1 69 740008187 740008119 6.670000e-14 89.8
17 TraesCS6A01G287900 chr3D 97.059 34 0 1 3766 3798 48423837 48423804 6.770000e-04 56.5


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 TraesCS6A01G287900 chr6A 520427579 520432419 4840 False 8940.000000 8940 100.0000 1 4841 1 chr6A.!!$F1 4840
1 TraesCS6A01G287900 chr6D 379003633 379008483 4850 False 3161.000000 5921 89.7635 84 4773 2 chr6D.!!$F1 4689
2 TraesCS6A01G287900 chr6B 565213030 565218271 5241 False 2263.666667 5422 91.0040 84 4791 3 chr6B.!!$F1 4707

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
949 1503 0.464554 GCGATTCCCTCCCTTCTTGG 60.465 60.0 0.00 0.0 0.0 3.61 F
1340 1899 0.170116 GGATTGCAACAATTCGCCGA 59.830 50.0 0.00 0.0 0.0 5.54 F
1809 2381 0.026933 TTTATGCACATTACGGCGCG 59.973 50.0 6.90 0.0 0.0 6.86 F
2941 3526 0.396811 ACCGCAGATATGCTTACCCC 59.603 55.0 11.09 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 2362 0.026933 CGCGCCGTAATGTGCATAAA 59.973 50.000 0.00 0.00 41.79 1.40 R
2821 3406 1.145819 GGTGAGCTCATCTGCCTCC 59.854 63.158 21.47 10.68 0.00 4.30 R
3654 4240 0.522180 AGCCGCTCTTATACCGATCG 59.478 55.000 8.51 8.51 0.00 3.69 R
4717 5559 0.031111 TCTCCATCCCGATCCCACTT 60.031 55.000 0.00 0.00 0.00 3.16 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
17 18 4.757773 AAGATCCGACGGGTCAGA 57.242 55.556 28.20 1.81 33.83 3.27
18 19 2.971676 AAGATCCGACGGGTCAGAA 58.028 52.632 28.20 0.99 33.83 3.02
19 20 0.818296 AAGATCCGACGGGTCAGAAG 59.182 55.000 28.20 0.00 33.83 2.85
20 21 1.227002 GATCCGACGGGTCAGAAGC 60.227 63.158 22.35 0.00 33.83 3.86
21 22 1.668101 GATCCGACGGGTCAGAAGCT 61.668 60.000 22.35 0.00 33.83 3.74
22 23 1.258445 ATCCGACGGGTCAGAAGCTT 61.258 55.000 15.25 0.00 33.83 3.74
23 24 1.738099 CCGACGGGTCAGAAGCTTG 60.738 63.158 2.10 0.00 0.00 4.01
24 25 1.006102 CGACGGGTCAGAAGCTTGT 60.006 57.895 2.10 0.00 0.00 3.16
26 27 1.135083 CGACGGGTCAGAAGCTTGTAT 60.135 52.381 2.10 0.00 0.00 2.29
27 28 2.541556 GACGGGTCAGAAGCTTGTATC 58.458 52.381 2.10 0.00 0.00 2.24
28 29 1.899814 ACGGGTCAGAAGCTTGTATCA 59.100 47.619 2.10 0.00 0.00 2.15
29 30 2.501723 ACGGGTCAGAAGCTTGTATCAT 59.498 45.455 2.10 0.00 0.00 2.45
30 31 2.868583 CGGGTCAGAAGCTTGTATCATG 59.131 50.000 2.10 0.00 0.00 3.07
31 32 3.209410 GGGTCAGAAGCTTGTATCATGG 58.791 50.000 2.10 0.00 0.00 3.66
33 34 3.118261 GGTCAGAAGCTTGTATCATGGGA 60.118 47.826 2.10 0.00 0.00 4.37
34 35 4.125703 GTCAGAAGCTTGTATCATGGGAG 58.874 47.826 2.10 0.00 0.00 4.30
35 36 2.877168 CAGAAGCTTGTATCATGGGAGC 59.123 50.000 2.10 0.00 0.00 4.70
36 37 2.507058 AGAAGCTTGTATCATGGGAGCA 59.493 45.455 2.10 0.00 35.86 4.26
37 38 3.137913 AGAAGCTTGTATCATGGGAGCAT 59.862 43.478 2.10 0.00 35.86 3.79
39 40 2.709934 AGCTTGTATCATGGGAGCATCT 59.290 45.455 0.00 0.00 35.86 2.90
40 41 3.906218 AGCTTGTATCATGGGAGCATCTA 59.094 43.478 0.00 0.00 35.86 1.98
41 42 4.349048 AGCTTGTATCATGGGAGCATCTAA 59.651 41.667 0.00 0.00 35.86 2.10
43 44 4.897509 TGTATCATGGGAGCATCTAAGG 57.102 45.455 0.00 0.00 33.73 2.69
44 45 2.875094 ATCATGGGAGCATCTAAGGC 57.125 50.000 0.00 0.00 33.73 4.35
45 46 1.510492 TCATGGGAGCATCTAAGGCA 58.490 50.000 0.00 0.00 33.73 4.75
48 49 0.475475 TGGGAGCATCTAAGGCATGG 59.525 55.000 0.00 0.00 33.73 3.66
50 51 1.699634 GGGAGCATCTAAGGCATGGTA 59.300 52.381 0.00 0.00 32.09 3.25
53 54 3.008375 GGAGCATCTAAGGCATGGTATCA 59.992 47.826 0.00 0.00 32.09 2.15
55 56 3.077359 GCATCTAAGGCATGGTATCACC 58.923 50.000 0.00 0.00 39.22 4.02
56 57 3.244700 GCATCTAAGGCATGGTATCACCT 60.245 47.826 0.00 0.00 39.58 4.00
57 58 4.321718 CATCTAAGGCATGGTATCACCTG 58.678 47.826 0.00 0.00 39.58 4.00
58 59 3.653164 TCTAAGGCATGGTATCACCTGA 58.347 45.455 0.00 0.00 39.58 3.86
60 61 5.402630 TCTAAGGCATGGTATCACCTGATA 58.597 41.667 0.00 0.00 39.58 2.15
61 62 6.025539 TCTAAGGCATGGTATCACCTGATAT 58.974 40.000 0.00 0.00 39.58 1.63
62 63 5.589367 AAGGCATGGTATCACCTGATATT 57.411 39.130 0.00 0.00 39.58 1.28
64 65 5.957132 AGGCATGGTATCACCTGATATTTT 58.043 37.500 0.00 0.00 39.58 1.82
69 70 7.689299 CATGGTATCACCTGATATTTTCCCTA 58.311 38.462 0.00 0.00 39.58 3.53
70 71 7.074653 TGGTATCACCTGATATTTTCCCTAC 57.925 40.000 0.00 0.00 39.58 3.18
71 72 6.043938 TGGTATCACCTGATATTTTCCCTACC 59.956 42.308 0.00 0.00 39.58 3.18
72 73 6.272558 GGTATCACCTGATATTTTCCCTACCT 59.727 42.308 0.00 0.00 39.03 3.08
74 75 5.538877 TCACCTGATATTTTCCCTACCTCT 58.461 41.667 0.00 0.00 0.00 3.69
75 76 5.602978 TCACCTGATATTTTCCCTACCTCTC 59.397 44.000 0.00 0.00 0.00 3.20
77 78 5.158889 CCTGATATTTTCCCTACCTCTCCT 58.841 45.833 0.00 0.00 0.00 3.69
78 79 6.125561 ACCTGATATTTTCCCTACCTCTCCTA 60.126 42.308 0.00 0.00 0.00 2.94
145 676 1.000385 CTGGCGATCTGATCTCTCACC 60.000 57.143 15.16 9.10 0.00 4.02
256 788 4.143301 GGCAGTTCCCCATCCCCC 62.143 72.222 0.00 0.00 0.00 5.40
425 957 0.884704 GTCCGCCCACGCATGAATAT 60.885 55.000 0.00 0.00 38.22 1.28
471 1012 1.201987 CGAAAATAACTTCACGCCCCG 60.202 52.381 0.00 0.00 0.00 5.73
864 1414 1.488527 GCGGCGCTGTATATATAGCC 58.511 55.000 26.86 15.27 37.16 3.93
940 1490 1.360911 GAGACGAGGCGATTCCCTC 59.639 63.158 9.83 9.83 46.42 4.30
944 1494 3.648694 GAGGCGATTCCCTCCCTT 58.351 61.111 9.04 0.00 44.60 3.95
946 1500 1.003573 AGGCGATTCCCTCCCTTCT 59.996 57.895 0.00 0.00 34.51 2.85
949 1503 0.464554 GCGATTCCCTCCCTTCTTGG 60.465 60.000 0.00 0.00 0.00 3.61
950 1504 0.912486 CGATTCCCTCCCTTCTTGGT 59.088 55.000 0.00 0.00 0.00 3.67
956 1510 1.376037 CTCCCTTCTTGGTGGCGTC 60.376 63.158 0.00 0.00 0.00 5.19
957 1511 1.831652 CTCCCTTCTTGGTGGCGTCT 61.832 60.000 0.00 0.00 0.00 4.18
958 1512 1.073199 CCCTTCTTGGTGGCGTCTT 59.927 57.895 0.00 0.00 0.00 3.01
1304 1863 3.695060 TGCTACTACTACCAACTCTGCTC 59.305 47.826 0.00 0.00 0.00 4.26
1330 1889 1.606668 TGTCGTTCTTGGGATTGCAAC 59.393 47.619 0.00 0.00 0.00 4.17
1331 1890 1.606668 GTCGTTCTTGGGATTGCAACA 59.393 47.619 0.00 0.00 0.00 3.33
1332 1891 2.034053 GTCGTTCTTGGGATTGCAACAA 59.966 45.455 0.00 0.42 0.00 2.83
1333 1892 2.890311 TCGTTCTTGGGATTGCAACAAT 59.110 40.909 0.00 0.00 0.00 2.71
1334 1893 3.320541 TCGTTCTTGGGATTGCAACAATT 59.679 39.130 0.00 0.00 0.00 2.32
1335 1894 3.674753 CGTTCTTGGGATTGCAACAATTC 59.325 43.478 0.00 0.00 0.00 2.17
1336 1895 3.574284 TCTTGGGATTGCAACAATTCG 57.426 42.857 0.00 0.00 0.00 3.34
1337 1896 1.994779 CTTGGGATTGCAACAATTCGC 59.005 47.619 0.00 4.46 0.00 4.70
1338 1897 0.246086 TGGGATTGCAACAATTCGCC 59.754 50.000 0.00 0.04 0.00 5.54
1339 1898 0.801836 GGGATTGCAACAATTCGCCG 60.802 55.000 0.00 0.00 0.00 6.46
1340 1899 0.170116 GGATTGCAACAATTCGCCGA 59.830 50.000 0.00 0.00 0.00 5.54
1341 1900 1.202290 GGATTGCAACAATTCGCCGAT 60.202 47.619 0.00 0.00 0.00 4.18
1342 1901 1.847999 GATTGCAACAATTCGCCGATG 59.152 47.619 0.00 0.00 0.00 3.84
1343 1902 0.877743 TTGCAACAATTCGCCGATGA 59.122 45.000 0.00 0.00 0.00 2.92
1347 1906 2.223340 GCAACAATTCGCCGATGAGATT 60.223 45.455 0.00 0.00 0.00 2.40
1348 1907 3.731867 GCAACAATTCGCCGATGAGATTT 60.732 43.478 0.00 0.00 0.00 2.17
1459 2025 7.112452 AGTTCTAATTGGTTAATCATTGCCC 57.888 36.000 0.00 0.00 0.00 5.36
1500 2067 5.446143 TGTACCGACATTTTTGATTGCTT 57.554 34.783 0.00 0.00 0.00 3.91
1501 2068 5.218885 TGTACCGACATTTTTGATTGCTTG 58.781 37.500 0.00 0.00 0.00 4.01
1565 2135 3.627395 TGTAGTGCATTTAGGGACTGG 57.373 47.619 0.00 0.00 39.92 4.00
1605 2175 9.331282 GAGCTTGGTCTTAGTGTATCAATTAAT 57.669 33.333 0.00 0.00 0.00 1.40
1613 2183 9.555727 TCTTAGTGTATCAATTAATAGGTTGGC 57.444 33.333 0.00 0.00 0.00 4.52
1647 2217 9.614792 CTTTATAGAAAAACCATGTAGTAGCCT 57.385 33.333 0.00 0.00 0.00 4.58
1675 2245 4.686191 TGGCACAATTTGGTGATTTTCT 57.314 36.364 0.78 0.00 41.32 2.52
1676 2246 4.378774 TGGCACAATTTGGTGATTTTCTG 58.621 39.130 0.78 0.00 41.32 3.02
1678 2248 4.448732 GGCACAATTTGGTGATTTTCTGTC 59.551 41.667 0.78 0.00 41.32 3.51
1679 2249 5.291971 GCACAATTTGGTGATTTTCTGTCT 58.708 37.500 0.78 0.00 41.32 3.41
1712 2284 3.864583 CCATGCCATGGTTTATTTCAACG 59.135 43.478 15.89 0.00 45.54 4.10
1766 2338 4.481368 TCAACACTATTGGGCGTAGAAT 57.519 40.909 0.00 0.00 0.00 2.40
1806 2378 5.348164 AGGAAAATTTATGCACATTACGGC 58.652 37.500 0.00 0.00 0.00 5.68
1809 2381 0.026933 TTTATGCACATTACGGCGCG 59.973 50.000 6.90 0.00 0.00 6.86
1813 2385 1.861715 GCACATTACGGCGCGTTTC 60.862 57.895 6.90 0.00 41.54 2.78
1860 2440 6.027749 CGTATGATTTTTAGTTGTCCTTGCC 58.972 40.000 0.00 0.00 0.00 4.52
1943 2523 2.166870 TCTGATGGTTTCATGCAATGGC 59.833 45.455 0.00 0.00 46.73 4.40
1991 2571 3.151912 AGCAGCTTGAAAACTCTCCAT 57.848 42.857 0.00 0.00 0.00 3.41
2033 2613 3.301794 TGGCAGACCATCATGCTTTAT 57.698 42.857 0.00 0.00 42.67 1.40
2034 2614 2.953648 TGGCAGACCATCATGCTTTATG 59.046 45.455 0.00 0.00 42.67 1.90
2035 2615 2.295349 GGCAGACCATCATGCTTTATGG 59.705 50.000 10.47 10.47 46.76 2.74
2036 2616 3.216800 GCAGACCATCATGCTTTATGGA 58.783 45.455 17.28 0.00 44.62 3.41
2037 2617 3.252701 GCAGACCATCATGCTTTATGGAG 59.747 47.826 17.28 9.05 44.62 3.86
2052 2632 7.878127 TGCTTTATGGAGTAGCATCTAATAACC 59.122 37.037 0.00 0.00 39.79 2.85
2062 2642 5.788450 AGCATCTAATAACCCTCTCATTCG 58.212 41.667 0.00 0.00 0.00 3.34
2066 2646 6.540438 TCTAATAACCCTCTCATTCGTTGT 57.460 37.500 0.00 0.00 0.00 3.32
2214 2794 5.371115 TCTACTTTTCCCATTTGCTTTCG 57.629 39.130 0.00 0.00 0.00 3.46
2230 2810 4.864806 TGCTTTCGAGCATAGTTAGAGTTG 59.135 41.667 0.00 0.00 40.23 3.16
2253 2833 4.470602 GTTTTATGCTTACCCCTATGGCT 58.529 43.478 0.00 0.00 37.83 4.75
2258 2838 3.864328 TGCTTACCCCTATGGCTGTATA 58.136 45.455 0.00 0.00 37.83 1.47
2273 2853 6.338146 TGGCTGTATACTTATGCGAATATCC 58.662 40.000 4.17 0.00 0.00 2.59
2275 2855 6.697892 GGCTGTATACTTATGCGAATATCCTC 59.302 42.308 4.17 0.00 0.00 3.71
2287 2868 5.030936 GCGAATATCCTCTTGTTTTGCTTC 58.969 41.667 0.00 0.00 0.00 3.86
2288 2869 5.163713 GCGAATATCCTCTTGTTTTGCTTCT 60.164 40.000 0.00 0.00 0.00 2.85
2516 3097 7.391620 TGCTACTTAACCTTACAATGCTACTT 58.608 34.615 0.00 0.00 0.00 2.24
2553 3138 5.695818 TGCTTACTGTTAAATTCTTTCGGC 58.304 37.500 0.00 0.00 0.00 5.54
2620 3205 1.020437 GAACTGATGCTAGGCTTGCC 58.980 55.000 18.00 2.97 0.00 4.52
2821 3406 2.162921 CTGAAGGTTGCACGCGTGAG 62.163 60.000 41.19 22.92 0.00 3.51
2854 3439 3.686016 GCTCACCAGGATGAGGTAAAAA 58.314 45.455 16.43 0.00 45.35 1.94
2860 3445 5.010012 CACCAGGATGAGGTAAAAATATGCC 59.990 44.000 0.00 0.00 39.69 4.40
2868 3453 2.223377 GGTAAAAATATGCCGGCTCTCG 59.777 50.000 29.70 0.00 38.88 4.04
2881 3466 2.612672 CGGCTCTCGTACATCAAGTAGA 59.387 50.000 0.00 0.00 32.19 2.59
2883 3468 4.611807 CGGCTCTCGTACATCAAGTAGATC 60.612 50.000 0.00 0.00 33.72 2.75
2910 3495 8.841300 TGTGTTTTGTTACATATTAACAGCTGA 58.159 29.630 23.35 0.00 38.47 4.26
2912 3497 9.062524 TGTTTTGTTACATATTAACAGCTGAGT 57.937 29.630 23.35 10.41 38.47 3.41
2917 3502 7.064609 TGTTACATATTAACAGCTGAGTTGCTC 59.935 37.037 23.35 0.89 41.98 4.26
2941 3526 0.396811 ACCGCAGATATGCTTACCCC 59.603 55.000 11.09 0.00 0.00 4.95
3058 3643 3.265791 GGAGGTTGACAGAAGTATGCAG 58.734 50.000 0.00 0.00 0.00 4.41
3064 3649 7.437748 AGGTTGACAGAAGTATGCAGATATAC 58.562 38.462 0.00 0.00 34.48 1.47
3159 3744 5.559427 TGTATCAATTGGTGCATGTACAC 57.441 39.130 16.11 5.62 39.94 2.90
3451 4037 3.314635 CCATTTGGTCATAGCTCTGCTTC 59.685 47.826 0.00 0.00 40.44 3.86
3456 4042 3.117046 GGTCATAGCTCTGCTTCGTAAC 58.883 50.000 0.00 0.00 40.44 2.50
3457 4043 2.784380 GTCATAGCTCTGCTTCGTAACG 59.216 50.000 0.00 0.00 40.44 3.18
3498 4084 8.184192 AGAACATTTTCATACTGCTAAAATCCG 58.816 33.333 0.00 0.00 32.05 4.18
3503 4089 6.844696 TTCATACTGCTAAAATCCGACATC 57.155 37.500 0.00 0.00 0.00 3.06
3548 4134 7.318141 ACATTTCAGCATCTTTAACCTGATTG 58.682 34.615 0.00 0.00 34.62 2.67
3631 4217 9.358872 GATTCAAGAAAACAATCTTATTGGACC 57.641 33.333 4.78 0.00 37.56 4.46
3654 4240 6.183360 ACCGAAAAATTATCGTTGATCTGGTC 60.183 38.462 11.28 0.00 38.60 4.02
3707 4293 9.050601 GTGGGATGAGTTCTCTAAATTAATCAG 57.949 37.037 1.53 0.00 0.00 2.90
3801 4387 5.010213 GGACTACTTCTATGCTAACCCTCAG 59.990 48.000 0.00 0.00 0.00 3.35
3822 4408 3.115892 TGTTTGCGCGATCCCGAC 61.116 61.111 12.10 0.00 38.22 4.79
3828 4414 2.026301 CGCGATCCCGACCTTCTC 59.974 66.667 0.00 0.00 38.22 2.87
3836 4422 3.839432 CGACCTTCTCCGGGCCTC 61.839 72.222 0.84 0.00 0.00 4.70
3847 4433 1.644786 CCGGGCCTCGTGACATTTTC 61.645 60.000 0.84 0.00 37.11 2.29
3857 4443 1.976474 GACATTTTCCCTGCCGGCA 60.976 57.895 30.59 30.59 0.00 5.69
3873 4459 3.963222 CACAGAGTGCACCAGCTC 58.037 61.111 14.63 4.25 42.74 4.09
3874 4460 1.070275 CACAGAGTGCACCAGCTCA 59.930 57.895 14.63 0.00 42.74 4.26
3875 4461 0.321387 CACAGAGTGCACCAGCTCAT 60.321 55.000 14.63 0.00 42.74 2.90
3876 4462 0.321387 ACAGAGTGCACCAGCTCATG 60.321 55.000 14.63 7.34 42.74 3.07
3877 4463 1.376942 AGAGTGCACCAGCTCATGC 60.377 57.895 14.63 11.13 42.74 4.06
3878 4464 2.360852 AGTGCACCAGCTCATGCC 60.361 61.111 14.63 7.43 41.33 4.40
3879 4465 2.674033 GTGCACCAGCTCATGCCA 60.674 61.111 14.62 2.49 41.33 4.92
3880 4466 2.050350 GTGCACCAGCTCATGCCAT 61.050 57.895 14.62 0.00 41.33 4.40
3881 4467 1.304630 TGCACCAGCTCATGCCATT 60.305 52.632 14.62 0.00 41.33 3.16
3882 4468 1.317431 TGCACCAGCTCATGCCATTC 61.317 55.000 14.62 0.00 41.33 2.67
3883 4469 1.035932 GCACCAGCTCATGCCATTCT 61.036 55.000 7.38 0.00 40.80 2.40
3884 4470 1.471119 CACCAGCTCATGCCATTCTT 58.529 50.000 0.00 0.00 40.80 2.52
3885 4471 1.822990 CACCAGCTCATGCCATTCTTT 59.177 47.619 0.00 0.00 40.80 2.52
3886 4472 2.232941 CACCAGCTCATGCCATTCTTTT 59.767 45.455 0.00 0.00 40.80 2.27
3887 4473 2.232941 ACCAGCTCATGCCATTCTTTTG 59.767 45.455 0.00 0.00 40.80 2.44
3888 4474 2.232941 CCAGCTCATGCCATTCTTTTGT 59.767 45.455 0.00 0.00 40.80 2.83
3889 4475 3.250744 CAGCTCATGCCATTCTTTTGTG 58.749 45.455 0.00 0.00 40.80 3.33
3890 4476 3.057104 CAGCTCATGCCATTCTTTTGTGA 60.057 43.478 0.00 0.00 40.80 3.58
3920 4506 2.225467 GCTGAACTGGGATTATCCTGC 58.775 52.381 11.40 0.00 36.57 4.85
3949 4536 0.809241 CAAGCATCGTCCTGAGGAGC 60.809 60.000 0.00 1.04 29.39 4.70
3950 4537 1.965754 AAGCATCGTCCTGAGGAGCC 61.966 60.000 0.00 0.00 29.39 4.70
3951 4538 2.415010 CATCGTCCTGAGGAGCCG 59.585 66.667 0.00 2.76 29.39 5.52
3997 4584 2.068821 GCTGGGGGCAGAGAGATCA 61.069 63.158 0.00 0.00 41.35 2.92
4002 4589 1.747774 GGGCAGAGAGATCAGAGCC 59.252 63.158 0.00 0.69 41.29 4.70
4077 4664 7.677745 AGAGGGCTGATATTCTTGTATAGATGT 59.322 37.037 0.00 0.00 31.54 3.06
4089 4676 5.023533 TGTATAGATGTTGAGGGCAAGAC 57.976 43.478 0.00 0.00 34.01 3.01
4091 4678 0.976641 AGATGTTGAGGGCAAGACGA 59.023 50.000 0.00 0.00 34.01 4.20
4092 4679 1.556911 AGATGTTGAGGGCAAGACGAT 59.443 47.619 0.00 0.00 34.01 3.73
4096 4683 2.000447 GTTGAGGGCAAGACGATACAC 59.000 52.381 0.00 0.00 34.01 2.90
4218 4812 1.450312 GTGGAACTGGGGCTGATCG 60.450 63.158 0.00 0.00 0.00 3.69
4234 4828 4.572389 GCTGATCGAGTGTAATCCAAACAT 59.428 41.667 0.00 0.00 0.00 2.71
4243 4837 3.766591 TGTAATCCAAACATGCCCGAATT 59.233 39.130 0.00 0.00 0.00 2.17
4300 4895 4.042684 AGCAATCCTCTTCTTTTCCTCTGT 59.957 41.667 0.00 0.00 0.00 3.41
4336 4932 4.163078 AGTTGCACCTCTATACTGCTTGAT 59.837 41.667 0.00 0.00 0.00 2.57
4418 5016 2.110213 GTCAACGACCCTGGTGCA 59.890 61.111 0.00 0.00 0.00 4.57
4458 5290 1.771073 TTGCGCTCGTCCACTTGTTG 61.771 55.000 9.73 0.00 0.00 3.33
4491 5323 0.798776 GGCATCTCGTTTCCAGTGTG 59.201 55.000 0.00 0.00 0.00 3.82
4505 5337 0.042131 AGTGTGGACCGGGATAGGAA 59.958 55.000 6.32 0.00 34.73 3.36
4535 5367 7.522073 CGGATTAAGGTGGGATTAACATTGATG 60.522 40.741 0.00 0.00 0.00 3.07
4564 5396 3.091318 CGTAGGAGCTTCCGGTCTA 57.909 57.895 0.00 0.00 42.75 2.59
4600 5432 5.290493 TCGTAGGAATTCAGCAATATGGT 57.710 39.130 7.93 0.00 0.00 3.55
4602 5434 6.455647 TCGTAGGAATTCAGCAATATGGTAG 58.544 40.000 7.93 0.00 0.00 3.18
4604 5436 7.231925 TCGTAGGAATTCAGCAATATGGTAGTA 59.768 37.037 7.93 0.00 0.00 1.82
4605 5437 7.542477 CGTAGGAATTCAGCAATATGGTAGTAG 59.458 40.741 7.93 0.00 0.00 2.57
4624 5461 1.099689 GTAGCCTCGTCTTGAGCTCT 58.900 55.000 16.19 0.00 43.82 4.09
4630 5467 2.344203 CGTCTTGAGCTCTCCCGGT 61.344 63.158 16.19 0.00 0.00 5.28
4631 5468 1.216710 GTCTTGAGCTCTCCCGGTG 59.783 63.158 16.19 0.00 0.00 4.94
4632 5469 1.228894 TCTTGAGCTCTCCCGGTGT 60.229 57.895 16.19 0.00 0.00 4.16
4633 5470 0.039180 TCTTGAGCTCTCCCGGTGTA 59.961 55.000 16.19 0.00 0.00 2.90
4634 5471 0.457851 CTTGAGCTCTCCCGGTGTAG 59.542 60.000 16.19 0.00 0.00 2.74
4635 5472 0.251653 TTGAGCTCTCCCGGTGTAGT 60.252 55.000 16.19 0.00 0.00 2.73
4673 5510 0.108186 CATCGTGCAAGGAGCCAGTA 60.108 55.000 0.00 0.00 44.83 2.74
4723 5565 1.595093 CCCGCCTTGCTTTAAGTGGG 61.595 60.000 0.00 0.00 41.20 4.61
4746 5589 4.417426 TCGGGATGGAGAATTTACCTTC 57.583 45.455 8.30 8.30 0.00 3.46
4777 5620 2.739287 CAACCTCGGGCGCGTTTA 60.739 61.111 23.19 2.70 0.00 2.01
4791 5634 5.376537 GGCGCGTTTAACATTGGTATATAC 58.623 41.667 8.43 4.14 0.00 1.47
4792 5635 5.178067 GGCGCGTTTAACATTGGTATATACT 59.822 40.000 8.43 0.00 0.00 2.12
4793 5636 6.294363 GCGCGTTTAACATTGGTATATACTC 58.706 40.000 8.43 3.99 0.00 2.59
4794 5637 6.617105 GCGCGTTTAACATTGGTATATACTCC 60.617 42.308 8.43 0.00 0.00 3.85
4795 5638 6.643770 CGCGTTTAACATTGGTATATACTCCT 59.356 38.462 12.54 0.00 0.00 3.69
4796 5639 7.809331 CGCGTTTAACATTGGTATATACTCCTA 59.191 37.037 12.54 0.00 0.00 2.94
4797 5640 8.919661 GCGTTTAACATTGGTATATACTCCTAC 58.080 37.037 12.54 0.00 0.00 3.18
4798 5641 9.121517 CGTTTAACATTGGTATATACTCCTACG 57.878 37.037 12.54 6.94 0.00 3.51
4799 5642 9.971922 GTTTAACATTGGTATATACTCCTACGT 57.028 33.333 12.54 0.00 0.00 3.57
4801 5644 9.578576 TTAACATTGGTATATACTCCTACGTCT 57.421 33.333 12.54 0.00 0.00 4.18
4803 5646 8.789825 ACATTGGTATATACTCCTACGTCTAG 57.210 38.462 12.54 0.00 0.00 2.43
4804 5647 8.381636 ACATTGGTATATACTCCTACGTCTAGT 58.618 37.037 12.54 0.00 0.00 2.57
4805 5648 8.881743 CATTGGTATATACTCCTACGTCTAGTC 58.118 40.741 12.54 0.00 0.00 2.59
4806 5649 7.789202 TGGTATATACTCCTACGTCTAGTCT 57.211 40.000 12.54 0.00 0.00 3.24
4807 5650 7.609960 TGGTATATACTCCTACGTCTAGTCTG 58.390 42.308 12.54 0.00 0.00 3.51
4808 5651 7.234371 TGGTATATACTCCTACGTCTAGTCTGT 59.766 40.741 12.54 0.00 0.00 3.41
4809 5652 8.093927 GGTATATACTCCTACGTCTAGTCTGTT 58.906 40.741 12.54 0.00 0.00 3.16
4810 5653 9.139174 GTATATACTCCTACGTCTAGTCTGTTC 57.861 40.741 5.58 0.00 0.00 3.18
4811 5654 4.283363 ACTCCTACGTCTAGTCTGTTCA 57.717 45.455 0.00 0.00 0.00 3.18
4812 5655 4.846040 ACTCCTACGTCTAGTCTGTTCAT 58.154 43.478 0.00 0.00 0.00 2.57
4813 5656 5.254901 ACTCCTACGTCTAGTCTGTTCATT 58.745 41.667 0.00 0.00 0.00 2.57
4814 5657 5.124138 ACTCCTACGTCTAGTCTGTTCATTG 59.876 44.000 0.00 0.00 0.00 2.82
4815 5658 4.106197 CCTACGTCTAGTCTGTTCATTGC 58.894 47.826 0.00 0.00 0.00 3.56
4816 5659 3.660501 ACGTCTAGTCTGTTCATTGCA 57.339 42.857 0.00 0.00 0.00 4.08
4817 5660 4.193826 ACGTCTAGTCTGTTCATTGCAT 57.806 40.909 0.00 0.00 0.00 3.96
4818 5661 4.569943 ACGTCTAGTCTGTTCATTGCATT 58.430 39.130 0.00 0.00 0.00 3.56
4819 5662 4.389992 ACGTCTAGTCTGTTCATTGCATTG 59.610 41.667 2.08 2.08 0.00 2.82
4820 5663 4.656041 GTCTAGTCTGTTCATTGCATTGC 58.344 43.478 0.46 0.46 0.00 3.56
4821 5664 2.624316 AGTCTGTTCATTGCATTGCG 57.376 45.000 3.84 0.00 0.00 4.85
4822 5665 0.986992 GTCTGTTCATTGCATTGCGC 59.013 50.000 0.00 0.00 42.89 6.09
4823 5666 0.883153 TCTGTTCATTGCATTGCGCT 59.117 45.000 9.73 0.00 43.06 5.92
4824 5667 0.989164 CTGTTCATTGCATTGCGCTG 59.011 50.000 9.73 0.00 43.06 5.18
4825 5668 0.388778 TGTTCATTGCATTGCGCTGG 60.389 50.000 9.73 0.00 43.06 4.85
4826 5669 1.446445 TTCATTGCATTGCGCTGGC 60.446 52.632 9.73 10.38 43.06 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.668101 GCTTCTGACCCGTCGGATCT 61.668 60.000 14.39 0.00 43.79 2.75
3 4 1.258445 AAGCTTCTGACCCGTCGGAT 61.258 55.000 14.39 0.00 43.79 4.18
5 6 1.738099 CAAGCTTCTGACCCGTCGG 60.738 63.158 3.60 3.60 37.32 4.79
6 7 0.242825 TACAAGCTTCTGACCCGTCG 59.757 55.000 0.00 0.00 0.00 5.12
7 8 2.094182 TGATACAAGCTTCTGACCCGTC 60.094 50.000 0.00 0.00 0.00 4.79
8 9 1.899814 TGATACAAGCTTCTGACCCGT 59.100 47.619 0.00 0.00 0.00 5.28
10 11 3.209410 CCATGATACAAGCTTCTGACCC 58.791 50.000 0.00 0.00 0.00 4.46
11 12 3.118261 TCCCATGATACAAGCTTCTGACC 60.118 47.826 0.00 0.00 0.00 4.02
12 13 4.125703 CTCCCATGATACAAGCTTCTGAC 58.874 47.826 0.00 0.00 0.00 3.51
13 14 3.432749 GCTCCCATGATACAAGCTTCTGA 60.433 47.826 0.00 0.00 0.00 3.27
14 15 2.877168 GCTCCCATGATACAAGCTTCTG 59.123 50.000 0.00 0.00 0.00 3.02
15 16 2.507058 TGCTCCCATGATACAAGCTTCT 59.493 45.455 0.00 0.00 34.11 2.85
16 17 2.923121 TGCTCCCATGATACAAGCTTC 58.077 47.619 0.00 0.00 34.11 3.86
17 18 3.137913 AGATGCTCCCATGATACAAGCTT 59.862 43.478 0.00 0.00 34.11 3.74
18 19 2.709934 AGATGCTCCCATGATACAAGCT 59.290 45.455 0.00 0.00 34.11 3.74
19 20 3.137446 AGATGCTCCCATGATACAAGC 57.863 47.619 0.00 0.00 0.00 4.01
20 21 5.243981 CCTTAGATGCTCCCATGATACAAG 58.756 45.833 0.00 0.00 0.00 3.16
21 22 4.505566 GCCTTAGATGCTCCCATGATACAA 60.506 45.833 0.00 0.00 0.00 2.41
22 23 3.008375 GCCTTAGATGCTCCCATGATACA 59.992 47.826 0.00 0.00 0.00 2.29
23 24 3.008375 TGCCTTAGATGCTCCCATGATAC 59.992 47.826 0.00 0.00 0.00 2.24
24 25 3.250617 TGCCTTAGATGCTCCCATGATA 58.749 45.455 0.00 0.00 0.00 2.15
26 27 1.510492 TGCCTTAGATGCTCCCATGA 58.490 50.000 0.00 0.00 0.00 3.07
27 28 2.160205 CATGCCTTAGATGCTCCCATG 58.840 52.381 0.00 0.00 0.00 3.66
28 29 1.075050 CCATGCCTTAGATGCTCCCAT 59.925 52.381 0.00 0.00 0.00 4.00
29 30 0.475475 CCATGCCTTAGATGCTCCCA 59.525 55.000 0.00 0.00 0.00 4.37
30 31 0.475906 ACCATGCCTTAGATGCTCCC 59.524 55.000 0.00 0.00 0.00 4.30
31 32 3.008375 TGATACCATGCCTTAGATGCTCC 59.992 47.826 0.00 0.00 0.00 4.70
33 34 3.244700 GGTGATACCATGCCTTAGATGCT 60.245 47.826 0.00 0.00 38.42 3.79
34 35 3.077359 GGTGATACCATGCCTTAGATGC 58.923 50.000 0.00 0.00 38.42 3.91
35 36 4.040829 TCAGGTGATACCATGCCTTAGATG 59.959 45.833 0.28 0.00 41.95 2.90
36 37 4.234550 TCAGGTGATACCATGCCTTAGAT 58.765 43.478 0.28 0.00 41.95 1.98
37 38 3.653164 TCAGGTGATACCATGCCTTAGA 58.347 45.455 0.28 0.00 41.95 2.10
39 40 6.702449 AATATCAGGTGATACCATGCCTTA 57.298 37.500 1.72 0.00 41.95 2.69
40 41 5.589367 AATATCAGGTGATACCATGCCTT 57.411 39.130 1.72 0.00 41.95 4.35
41 42 5.589367 AAATATCAGGTGATACCATGCCT 57.411 39.130 1.72 0.00 41.95 4.75
43 44 5.183904 GGGAAAATATCAGGTGATACCATGC 59.816 44.000 1.72 0.00 41.95 4.06
44 45 6.546484 AGGGAAAATATCAGGTGATACCATG 58.454 40.000 1.72 0.00 41.95 3.66
45 46 6.786843 AGGGAAAATATCAGGTGATACCAT 57.213 37.500 1.72 0.00 41.95 3.55
48 49 7.235812 AGAGGTAGGGAAAATATCAGGTGATAC 59.764 40.741 1.72 0.00 39.57 2.24
50 51 6.153924 AGAGGTAGGGAAAATATCAGGTGAT 58.846 40.000 0.00 0.00 38.51 3.06
53 54 4.908481 GGAGAGGTAGGGAAAATATCAGGT 59.092 45.833 0.00 0.00 0.00 4.00
55 56 6.439058 CCTAGGAGAGGTAGGGAAAATATCAG 59.561 46.154 1.05 0.00 40.98 2.90
56 57 6.323737 CCTAGGAGAGGTAGGGAAAATATCA 58.676 44.000 1.05 0.00 40.98 2.15
57 58 6.860790 CCTAGGAGAGGTAGGGAAAATATC 57.139 45.833 1.05 0.00 40.98 1.63
77 78 1.895238 GTCAACCACGCCTAGCCTA 59.105 57.895 0.00 0.00 0.00 3.93
78 79 2.663196 GTCAACCACGCCTAGCCT 59.337 61.111 0.00 0.00 0.00 4.58
145 676 2.221055 GTGTTGGTTAAGAGCAGTGACG 59.779 50.000 0.00 0.00 34.28 4.35
271 803 2.045926 GCTGTGATGGACGCCCTT 60.046 61.111 0.00 0.00 0.00 3.95
277 809 2.125106 GGGACGGCTGTGATGGAC 60.125 66.667 0.80 0.00 0.00 4.02
414 946 5.393678 GGTGGTTTTGGTTATATTCATGCGT 60.394 40.000 0.00 0.00 0.00 5.24
425 957 1.497223 CGCGTCGGTGGTTTTGGTTA 61.497 55.000 0.00 0.00 0.00 2.85
553 1101 4.593864 GTGGATCTCGGCTCGCCC 62.594 72.222 1.72 0.00 0.00 6.13
555 1103 2.650813 AATGGTGGATCTCGGCTCGC 62.651 60.000 0.00 0.00 0.00 5.03
644 1194 4.662961 GGCAGCAAAACACGGCCC 62.663 66.667 0.00 0.00 38.70 5.80
645 1195 3.605664 AGGCAGCAAAACACGGCC 61.606 61.111 0.00 0.00 44.92 6.13
646 1196 2.355009 CAGGCAGCAAAACACGGC 60.355 61.111 0.00 0.00 0.00 5.68
679 1229 4.718827 TAGGAAACCCCGGCCGGA 62.719 66.667 45.44 20.70 40.87 5.14
919 1469 1.515954 GGAATCGCCTCGTCTCCAA 59.484 57.895 0.00 0.00 32.25 3.53
940 1490 1.073199 AAGACGCCACCAAGAAGGG 59.927 57.895 0.00 0.00 43.89 3.95
942 1492 1.466167 CATCAAGACGCCACCAAGAAG 59.534 52.381 0.00 0.00 0.00 2.85
944 1494 0.955428 GCATCAAGACGCCACCAAGA 60.955 55.000 0.00 0.00 0.00 3.02
946 1500 0.955428 GAGCATCAAGACGCCACCAA 60.955 55.000 0.00 0.00 33.17 3.67
949 1503 1.375908 TGGAGCATCAAGACGCCAC 60.376 57.895 0.00 0.00 36.25 5.01
950 1504 1.375908 GTGGAGCATCAAGACGCCA 60.376 57.895 0.00 0.00 36.25 5.69
1263 1817 0.321653 ACTTACTCCTTGGCGGCAAG 60.322 55.000 37.09 37.09 0.00 4.01
1304 1863 0.953471 TCCCAAGAACGACAATGCGG 60.953 55.000 0.00 0.00 35.12 5.69
1330 1889 2.378806 GCAAATCTCATCGGCGAATTG 58.621 47.619 15.93 9.24 0.00 2.32
1331 1890 1.334869 GGCAAATCTCATCGGCGAATT 59.665 47.619 15.93 6.15 0.00 2.17
1332 1891 0.947244 GGCAAATCTCATCGGCGAAT 59.053 50.000 15.93 0.00 0.00 3.34
1333 1892 0.392327 TGGCAAATCTCATCGGCGAA 60.392 50.000 15.93 0.00 0.00 4.70
1334 1893 0.179048 ATGGCAAATCTCATCGGCGA 60.179 50.000 13.87 13.87 0.00 5.54
1335 1894 0.040692 CATGGCAAATCTCATCGGCG 60.041 55.000 0.00 0.00 0.00 6.46
1336 1895 0.318445 GCATGGCAAATCTCATCGGC 60.318 55.000 0.00 0.00 0.00 5.54
1337 1896 1.315690 AGCATGGCAAATCTCATCGG 58.684 50.000 0.00 0.00 0.00 4.18
1338 1897 3.113322 CAAAGCATGGCAAATCTCATCG 58.887 45.455 0.00 0.00 0.00 3.84
1339 1898 2.864343 GCAAAGCATGGCAAATCTCATC 59.136 45.455 0.00 0.00 0.00 2.92
1340 1899 2.235155 TGCAAAGCATGGCAAATCTCAT 59.765 40.909 0.00 0.00 37.03 2.90
1341 1900 1.619332 TGCAAAGCATGGCAAATCTCA 59.381 42.857 0.00 0.00 37.03 3.27
1342 1901 2.373540 TGCAAAGCATGGCAAATCTC 57.626 45.000 0.00 0.00 37.03 2.75
1367 1926 8.142485 AGGTTGAATTCAAAATCATTGGAGAT 57.858 30.769 22.07 0.00 37.63 2.75
1438 2004 7.418827 CCATTGGGCAATGATTAACCAATTAGA 60.419 37.037 17.64 0.00 46.64 2.10
1439 2005 6.707161 CCATTGGGCAATGATTAACCAATTAG 59.293 38.462 17.64 11.38 46.64 1.73
1459 2025 4.796038 ACATGCTTCTTTTCCTCCATTG 57.204 40.909 0.00 0.00 0.00 2.82
1500 2067 4.819630 GCCAACCCATAAATATCGAGTTCA 59.180 41.667 0.00 0.00 0.00 3.18
1501 2068 4.215613 GGCCAACCCATAAATATCGAGTTC 59.784 45.833 0.00 0.00 0.00 3.01
1565 2135 1.098050 AAGCTCGGGTTCATTCATGC 58.902 50.000 0.00 0.00 0.00 4.06
1620 2190 9.609346 GGCTACTACATGGTTTTTCTATAAAGA 57.391 33.333 0.00 0.00 0.00 2.52
1647 2217 5.735285 TCACCAAATTGTGCCATTATTGA 57.265 34.783 0.00 0.00 36.17 2.57
1669 2239 5.804639 TGGCATGTACTACAGACAGAAAAT 58.195 37.500 0.00 0.00 0.00 1.82
1673 2243 3.430790 GCATGGCATGTACTACAGACAGA 60.431 47.826 26.94 0.00 0.00 3.41
1674 2244 2.868583 GCATGGCATGTACTACAGACAG 59.131 50.000 26.94 0.00 0.00 3.51
1675 2245 2.419990 GGCATGGCATGTACTACAGACA 60.420 50.000 26.94 0.00 0.00 3.41
1676 2246 2.213499 GGCATGGCATGTACTACAGAC 58.787 52.381 26.94 8.20 0.00 3.51
1678 2248 2.330440 TGGCATGGCATGTACTACAG 57.670 50.000 26.94 1.03 0.00 2.74
1679 2249 2.574450 CATGGCATGGCATGTACTACA 58.426 47.619 39.96 17.96 0.00 2.74
1790 2362 0.026933 CGCGCCGTAATGTGCATAAA 59.973 50.000 0.00 0.00 41.79 1.40
1809 2381 1.133869 GTACACCATGCGCCGAAAC 59.866 57.895 4.18 0.00 0.00 2.78
1813 2385 1.062365 CAATGTACACCATGCGCCG 59.938 57.895 4.18 0.00 32.82 6.46
1943 2523 0.098728 CTCGCATTTGGTTAAGCCCG 59.901 55.000 1.51 0.00 36.04 6.13
2033 2613 5.716979 AGAGGGTTATTAGATGCTACTCCA 58.283 41.667 0.00 0.00 0.00 3.86
2034 2614 5.775701 TGAGAGGGTTATTAGATGCTACTCC 59.224 44.000 0.00 0.00 0.00 3.85
2035 2615 6.902771 TGAGAGGGTTATTAGATGCTACTC 57.097 41.667 0.00 0.00 0.00 2.59
2036 2616 7.309499 CGAATGAGAGGGTTATTAGATGCTACT 60.309 40.741 0.00 0.00 0.00 2.57
2037 2617 6.809196 CGAATGAGAGGGTTATTAGATGCTAC 59.191 42.308 0.00 0.00 0.00 3.58
2052 2632 5.230942 AGTAAACAGACAACGAATGAGAGG 58.769 41.667 0.00 0.00 0.00 3.69
2191 2771 5.181245 TCGAAAGCAAATGGGAAAAGTAGAG 59.819 40.000 0.00 0.00 0.00 2.43
2192 2772 5.067273 TCGAAAGCAAATGGGAAAAGTAGA 58.933 37.500 0.00 0.00 0.00 2.59
2214 2794 7.281100 AGCATAAAACCAACTCTAACTATGCTC 59.719 37.037 7.29 0.00 44.47 4.26
2230 2810 3.572682 GCCATAGGGGTAAGCATAAAACC 59.427 47.826 0.00 0.00 39.65 3.27
2253 2833 8.803235 ACAAGAGGATATTCGCATAAGTATACA 58.197 33.333 5.50 0.00 0.00 2.29
2258 2838 7.679638 GCAAAACAAGAGGATATTCGCATAAGT 60.680 37.037 0.00 0.00 0.00 2.24
2273 2853 6.610741 AACTCACTAGAAGCAAAACAAGAG 57.389 37.500 0.00 0.00 0.00 2.85
2275 2855 6.785191 TGAAACTCACTAGAAGCAAAACAAG 58.215 36.000 0.00 0.00 0.00 3.16
2287 2868 7.746916 CGTCGAATATATCCTGAAACTCACTAG 59.253 40.741 0.00 0.00 0.00 2.57
2288 2869 7.228108 ACGTCGAATATATCCTGAAACTCACTA 59.772 37.037 0.00 0.00 0.00 2.74
2469 3050 8.165239 AGCAAAAGACACATCTAACAATACAA 57.835 30.769 0.00 0.00 33.57 2.41
2475 3056 8.770828 GTTAAGTAGCAAAAGACACATCTAACA 58.229 33.333 0.00 0.00 33.57 2.41
2516 3097 7.897575 AACAGTAAGCATTTTCACACAAAAA 57.102 28.000 0.00 0.00 32.99 1.94
2521 3106 9.463443 AGAATTTAACAGTAAGCATTTTCACAC 57.537 29.630 0.00 0.00 0.00 3.82
2550 3135 2.972625 TCAAAGGAAGTATCTGTGCCG 58.027 47.619 0.00 0.00 0.00 5.69
2553 3138 7.912056 TTCTGAATCAAAGGAAGTATCTGTG 57.088 36.000 0.00 0.00 0.00 3.66
2620 3205 2.465813 TCCAGGGGCAAACCATTATTG 58.534 47.619 0.00 0.00 42.91 1.90
2821 3406 1.145819 GGTGAGCTCATCTGCCTCC 59.854 63.158 21.47 10.68 0.00 4.30
2854 3439 1.202582 GATGTACGAGAGCCGGCATAT 59.797 52.381 31.54 14.22 43.93 1.78
2860 3445 2.612672 TCTACTTGATGTACGAGAGCCG 59.387 50.000 0.00 0.00 45.44 5.52
2868 3453 8.311650 ACAAAACACAGATCTACTTGATGTAC 57.688 34.615 0.00 0.00 35.14 2.90
2881 3466 9.840427 GCTGTTAATATGTAACAAAACACAGAT 57.160 29.630 0.00 0.00 37.04 2.90
2883 3468 9.117145 CAGCTGTTAATATGTAACAAAACACAG 57.883 33.333 5.25 0.00 37.04 3.66
2906 3491 2.558313 GTTGGCGAGCAACTCAGC 59.442 61.111 0.00 0.00 32.46 4.26
2925 3510 1.421646 ACCAGGGGTAAGCATATCTGC 59.578 52.381 0.00 0.00 40.90 4.26
2941 3526 5.049129 GTCAATGACTTTCTCTTTCCACCAG 60.049 44.000 6.07 0.00 0.00 4.00
3004 3589 2.235898 GACAAGAGCAATCTCCTCAGGT 59.764 50.000 0.00 0.00 40.22 4.00
3058 3643 3.319137 TCTCCAGCCGCAATGTATATC 57.681 47.619 0.00 0.00 0.00 1.63
3064 3649 4.142534 CCATATATTTCTCCAGCCGCAATG 60.143 45.833 0.00 0.00 0.00 2.82
3159 3744 3.947196 TGCTGCAAAGATGTAACCATAGG 59.053 43.478 0.00 0.00 0.00 2.57
3498 4084 4.152580 CAGATCTAGCATGCACATGATGTC 59.847 45.833 21.98 8.32 41.20 3.06
3503 4089 3.875134 TGTTCAGATCTAGCATGCACATG 59.125 43.478 21.98 9.49 41.60 3.21
3582 4168 6.184789 TCCCATGAACCTGTAGGATAAAAAC 58.815 40.000 4.64 0.00 38.94 2.43
3631 4217 5.896432 CGACCAGATCAACGATAATTTTTCG 59.104 40.000 7.56 7.56 42.20 3.46
3654 4240 0.522180 AGCCGCTCTTATACCGATCG 59.478 55.000 8.51 8.51 0.00 3.69
3707 4293 2.686816 CGGTTTGCATGGACGGACC 61.687 63.158 0.00 0.00 39.54 4.46
3801 4387 2.750888 GGGATCGCGCAAACACTCC 61.751 63.158 8.75 3.26 0.00 3.85
3822 4408 4.148825 CACGAGGCCCGGAGAAGG 62.149 72.222 16.44 0.00 43.93 3.46
3828 4414 1.644786 GAAAATGTCACGAGGCCCGG 61.645 60.000 16.44 0.00 43.93 5.73
3836 4422 1.501741 CGGCAGGGAAAATGTCACG 59.498 57.895 0.00 0.00 33.41 4.35
3857 4443 0.321387 CATGAGCTGGTGCACTCTGT 60.321 55.000 17.98 0.00 42.74 3.41
3874 4460 3.592059 GCATGTCACAAAAGAATGGCAT 58.408 40.909 0.00 0.00 41.79 4.40
3875 4461 2.288948 GGCATGTCACAAAAGAATGGCA 60.289 45.455 0.00 0.00 41.85 4.92
3876 4462 2.288948 TGGCATGTCACAAAAGAATGGC 60.289 45.455 0.00 0.00 42.39 4.40
3877 4463 3.663995 TGGCATGTCACAAAAGAATGG 57.336 42.857 0.00 0.00 0.00 3.16
3878 4464 3.930229 CCATGGCATGTCACAAAAGAATG 59.070 43.478 24.80 0.00 0.00 2.67
3879 4465 3.618019 GCCATGGCATGTCACAAAAGAAT 60.618 43.478 32.08 0.00 41.49 2.40
3880 4466 2.288948 GCCATGGCATGTCACAAAAGAA 60.289 45.455 32.08 0.00 41.49 2.52
3881 4467 1.273048 GCCATGGCATGTCACAAAAGA 59.727 47.619 32.08 0.00 41.49 2.52
3882 4468 1.274167 AGCCATGGCATGTCACAAAAG 59.726 47.619 37.18 8.97 44.88 2.27
3883 4469 1.001068 CAGCCATGGCATGTCACAAAA 59.999 47.619 37.18 0.00 44.88 2.44
3884 4470 0.604073 CAGCCATGGCATGTCACAAA 59.396 50.000 37.18 0.00 44.88 2.83
3885 4471 0.251253 TCAGCCATGGCATGTCACAA 60.251 50.000 37.18 13.58 44.88 3.33
3886 4472 0.251253 TTCAGCCATGGCATGTCACA 60.251 50.000 37.18 13.91 44.88 3.58
3887 4473 0.171903 GTTCAGCCATGGCATGTCAC 59.828 55.000 37.18 24.44 44.88 3.67
3888 4474 0.038599 AGTTCAGCCATGGCATGTCA 59.961 50.000 37.18 19.06 44.88 3.58
3889 4475 0.454600 CAGTTCAGCCATGGCATGTC 59.545 55.000 37.18 23.22 44.88 3.06
3890 4476 0.968901 CCAGTTCAGCCATGGCATGT 60.969 55.000 37.18 15.78 44.88 3.21
3920 4506 1.874915 CGATGCTTGCCATTTGCCG 60.875 57.895 0.00 0.00 40.16 5.69
3963 4550 2.270527 GCCACAGGCCTTCCTCTC 59.729 66.667 0.00 0.00 44.06 3.20
3997 4584 0.322975 ACATTCAAGTGAGCGGCTCT 59.677 50.000 28.42 8.73 0.00 4.09
4002 4589 3.928992 ACATCTACACATTCAAGTGAGCG 59.071 43.478 0.57 0.00 42.05 5.03
4077 4664 1.899814 AGTGTATCGTCTTGCCCTCAA 59.100 47.619 0.00 0.00 0.00 3.02
4089 4676 7.215719 TCCTGTAGGAATGATAAGTGTATCG 57.784 40.000 0.00 0.00 42.18 2.92
4218 4812 2.097466 CGGGCATGTTTGGATTACACTC 59.903 50.000 0.00 0.00 0.00 3.51
4234 4828 2.852449 TGTCACACTTTAATTCGGGCA 58.148 42.857 0.00 0.00 0.00 5.36
4243 4837 6.403049 TGTCTCTGTTCTTTGTCACACTTTA 58.597 36.000 0.00 0.00 0.00 1.85
4300 4895 2.501723 GGTGCAACTTCTGGAGGAGATA 59.498 50.000 0.00 0.00 36.74 1.98
4418 5016 7.236474 CGCAAATACATGTATAGCATTTCGAT 58.764 34.615 28.32 8.22 35.19 3.59
4429 5027 2.800544 GGACGAGCGCAAATACATGTAT 59.199 45.455 12.75 12.75 0.00 2.29
4491 5323 1.227468 GCGTTTCCTATCCCGGTCC 60.227 63.158 0.00 0.00 0.00 4.46
4494 5326 2.095978 ATCCGCGTTTCCTATCCCGG 62.096 60.000 4.92 0.00 37.21 5.73
4505 5337 0.544697 ATCCCACCTTAATCCGCGTT 59.455 50.000 4.92 0.00 0.00 4.84
4535 5367 1.520342 CTCCTACGGCTGCTCTTGC 60.520 63.158 0.00 0.00 40.20 4.01
4600 5432 3.118334 AGCTCAAGACGAGGCTACTACTA 60.118 47.826 0.00 0.00 42.55 1.82
4602 5434 2.018515 AGCTCAAGACGAGGCTACTAC 58.981 52.381 0.00 0.00 42.55 2.73
4604 5436 1.099689 GAGCTCAAGACGAGGCTACT 58.900 55.000 9.40 0.00 42.55 2.57
4605 5437 1.064952 GAGAGCTCAAGACGAGGCTAC 59.935 57.143 17.77 0.00 42.55 3.58
4624 5461 1.250154 CGGGTTACACTACACCGGGA 61.250 60.000 6.32 0.00 40.79 5.14
4630 5467 3.053395 ACCTAGGATCGGGTTACACTACA 60.053 47.826 17.98 0.00 30.80 2.74
4631 5468 3.317430 CACCTAGGATCGGGTTACACTAC 59.683 52.174 17.98 0.00 32.95 2.73
4632 5469 3.559069 CACCTAGGATCGGGTTACACTA 58.441 50.000 17.98 0.00 32.95 2.74
4633 5470 2.385803 CACCTAGGATCGGGTTACACT 58.614 52.381 17.98 0.00 32.95 3.55
4634 5471 1.202498 GCACCTAGGATCGGGTTACAC 60.202 57.143 17.98 0.00 32.95 2.90
4635 5472 1.117150 GCACCTAGGATCGGGTTACA 58.883 55.000 17.98 0.00 32.95 2.41
4713 5555 2.438021 TCCATCCCGATCCCACTTAAAG 59.562 50.000 0.00 0.00 0.00 1.85
4717 5559 0.031111 TCTCCATCCCGATCCCACTT 60.031 55.000 0.00 0.00 0.00 3.16
4723 5565 4.625607 AGGTAAATTCTCCATCCCGATC 57.374 45.455 0.00 0.00 0.00 3.69
4746 5589 1.008538 GGTTGGTTGCTCTTGCGTG 60.009 57.895 0.00 0.00 43.34 5.34
4777 5620 9.228949 CTAGACGTAGGAGTATATACCAATGTT 57.771 37.037 9.32 0.00 0.00 2.71
4791 5634 5.574082 CAATGAACAGACTAGACGTAGGAG 58.426 45.833 0.00 0.00 0.00 3.69
4792 5635 4.142447 GCAATGAACAGACTAGACGTAGGA 60.142 45.833 0.00 0.00 0.00 2.94
4793 5636 4.106197 GCAATGAACAGACTAGACGTAGG 58.894 47.826 0.00 0.00 0.00 3.18
4794 5637 4.733850 TGCAATGAACAGACTAGACGTAG 58.266 43.478 0.00 0.00 0.00 3.51
4795 5638 4.776795 TGCAATGAACAGACTAGACGTA 57.223 40.909 0.00 0.00 0.00 3.57
4796 5639 3.660501 TGCAATGAACAGACTAGACGT 57.339 42.857 0.00 0.00 0.00 4.34
4797 5640 4.726021 GCAATGCAATGAACAGACTAGACG 60.726 45.833 5.79 0.00 0.00 4.18
4798 5641 4.656041 GCAATGCAATGAACAGACTAGAC 58.344 43.478 5.79 0.00 0.00 2.59
4799 5642 3.371898 CGCAATGCAATGAACAGACTAGA 59.628 43.478 5.79 0.00 0.00 2.43
4800 5643 3.677601 CGCAATGCAATGAACAGACTAG 58.322 45.455 5.79 0.00 0.00 2.57
4801 5644 2.159531 GCGCAATGCAATGAACAGACTA 60.160 45.455 5.79 0.00 45.45 2.59
4802 5645 1.401931 GCGCAATGCAATGAACAGACT 60.402 47.619 5.79 0.00 45.45 3.24
4803 5646 0.986992 GCGCAATGCAATGAACAGAC 59.013 50.000 5.79 0.00 45.45 3.51
4804 5647 3.404978 GCGCAATGCAATGAACAGA 57.595 47.368 5.79 0.00 45.45 3.41


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

AutoCloner maintained by Alex Coulton.