Multiple sequence alignment - TraesCS1B01G186000

Loading Multiple Alignment...

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 TraesCS1B01G186000 chr1B 100.000 3062 0 0 1 3062 332805243 332802182 0.000000e+00 5655
1 TraesCS1B01G186000 chr1B 86.890 1373 165 7 736 2105 338883694 338882334 0.000000e+00 1524
2 TraesCS1B01G186000 chr1B 86.848 1361 164 7 736 2093 339905539 339906887 0.000000e+00 1507
3 TraesCS1B01G186000 chr1B 87.034 671 80 3 736 1405 339076847 339076183 0.000000e+00 750
4 TraesCS1B01G186000 chr1B 92.466 292 16 4 2209 2495 338882269 338881979 2.200000e-111 412
5 TraesCS1B01G186000 chr1B 92.466 292 16 4 2209 2495 339906964 339907254 2.200000e-111 412
6 TraesCS1B01G186000 chr1B 77.899 457 24 24 2616 3040 339907598 339908009 2.390000e-51 213
7 TraesCS1B01G186000 chr1B 77.462 457 26 25 2616 3040 338881635 338881224 5.180000e-48 202
8 TraesCS1B01G186000 chr1D 92.866 2411 124 33 143 2527 241242026 241244414 0.000000e+00 3456
9 TraesCS1B01G186000 chr1D 90.476 84 4 2 2100 2180 433017457 433017539 1.160000e-19 108
10 TraesCS1B01G186000 chr1A 93.494 1122 61 8 684 1795 306136687 306137806 0.000000e+00 1657
11 TraesCS1B01G186000 chr1A 89.775 577 40 8 1790 2358 306143233 306143798 0.000000e+00 721
12 TraesCS1B01G186000 chr6A 91.667 84 3 2 2100 2180 91911613 91911531 2.500000e-21 113
13 TraesCS1B01G186000 chr7D 90.476 84 4 2 2100 2180 249443706 249443788 1.160000e-19 108
14 TraesCS1B01G186000 chr7A 90.476 84 4 2 2100 2180 629047059 629046977 1.160000e-19 108
15 TraesCS1B01G186000 chr2A 89.655 87 5 2 2100 2183 117530136 117530051 1.160000e-19 108
16 TraesCS1B01G186000 chr2A 87.500 96 5 4 2100 2190 654916482 654916389 1.500000e-18 104
17 TraesCS1B01G186000 chr4D 88.636 88 8 1 2085 2170 402527919 402528006 4.180000e-19 106
18 TraesCS1B01G186000 chr4B 88.636 88 8 1 2085 2170 498374448 498374535 4.180000e-19 106


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 TraesCS1B01G186000 chr1B 332802182 332805243 3061 True 5655.000000 5655 100.000000 1 3062 1 chr1B.!!$R1 3061
1 TraesCS1B01G186000 chr1B 339076183 339076847 664 True 750.000000 750 87.034000 736 1405 1 chr1B.!!$R2 669
2 TraesCS1B01G186000 chr1B 338881224 338883694 2470 True 712.666667 1524 85.606000 736 3040 3 chr1B.!!$R3 2304
3 TraesCS1B01G186000 chr1B 339905539 339908009 2470 False 710.666667 1507 85.737667 736 3040 3 chr1B.!!$F1 2304
4 TraesCS1B01G186000 chr1D 241242026 241244414 2388 False 3456.000000 3456 92.866000 143 2527 1 chr1D.!!$F1 2384
5 TraesCS1B01G186000 chr1A 306136687 306137806 1119 False 1657.000000 1657 93.494000 684 1795 1 chr1A.!!$F1 1111
6 TraesCS1B01G186000 chr1A 306143233 306143798 565 False 721.000000 721 89.775000 1790 2358 1 chr1A.!!$F2 568

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
56 57 0.033109 ATGGGCTTTACCTTCCCTGC 60.033 55.000 0.00 0.00 40.69 4.85 F
60 61 0.322906 GCTTTACCTTCCCTGCTGCT 60.323 55.000 0.00 0.00 0.00 4.24 F
62 63 0.609131 TTTACCTTCCCTGCTGCTGC 60.609 55.000 8.89 8.89 40.20 5.25 F
1698 1714 1.077930 CATCACCTCCTGGGCACTG 60.078 63.158 0.00 0.00 39.10 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1339 1.153289 CGGATGCTTGACCTCCCAG 60.153 63.158 0.00 0.00 0.00 4.45 R
1749 1765 1.288439 CCCGATCTCGCTGGATCTG 59.712 63.158 11.93 7.04 39.73 2.90 R
1816 1832 1.561076 ACTGGGCTCATACATGCTGAA 59.439 47.619 0.00 0.00 0.00 3.02 R
2926 3293 0.465705 AGATCGTATGGCCCACAGTG 59.534 55.000 0.00 0.00 0.00 3.66 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
20 21 2.708759 TGGAACCAAAAGGAGTAGGGA 58.291 47.619 0.00 0.00 0.00 4.20
21 22 3.057586 TGGAACCAAAAGGAGTAGGGAA 58.942 45.455 0.00 0.00 0.00 3.97
22 23 3.181437 TGGAACCAAAAGGAGTAGGGAAC 60.181 47.826 0.00 0.00 0.00 3.62
30 31 3.437746 GAGTAGGGAACTCGTTGGC 57.562 57.895 0.00 0.00 45.05 4.52
31 32 0.458025 GAGTAGGGAACTCGTTGGCG 60.458 60.000 0.00 0.00 45.05 5.69
32 33 0.896940 AGTAGGGAACTCGTTGGCGA 60.897 55.000 0.00 0.00 45.79 5.54
33 34 0.735287 GTAGGGAACTCGTTGGCGAC 60.735 60.000 0.00 0.00 42.81 5.19
42 43 3.810896 GTTGGCGACGGAATGGGC 61.811 66.667 0.00 0.00 0.00 5.36
43 44 4.028490 TTGGCGACGGAATGGGCT 62.028 61.111 0.00 0.00 32.23 5.19
44 45 3.561120 TTGGCGACGGAATGGGCTT 62.561 57.895 0.00 0.00 32.23 4.35
45 46 2.750237 GGCGACGGAATGGGCTTT 60.750 61.111 0.00 0.00 0.00 3.51
46 47 1.450669 GGCGACGGAATGGGCTTTA 60.451 57.895 0.00 0.00 0.00 1.85
47 48 1.712018 GGCGACGGAATGGGCTTTAC 61.712 60.000 0.00 0.00 0.00 2.01
48 49 1.712018 GCGACGGAATGGGCTTTACC 61.712 60.000 0.00 0.00 37.93 2.85
49 50 0.107848 CGACGGAATGGGCTTTACCT 60.108 55.000 0.00 0.00 39.10 3.08
50 51 1.677820 CGACGGAATGGGCTTTACCTT 60.678 52.381 0.00 0.00 39.10 3.50
51 52 2.014857 GACGGAATGGGCTTTACCTTC 58.985 52.381 0.00 0.00 39.10 3.46
52 53 1.340697 ACGGAATGGGCTTTACCTTCC 60.341 52.381 0.00 0.00 39.10 3.46
53 54 1.776662 GGAATGGGCTTTACCTTCCC 58.223 55.000 0.00 0.00 40.47 3.97
54 55 1.288037 GGAATGGGCTTTACCTTCCCT 59.712 52.381 0.00 0.00 40.69 4.20
55 56 2.379005 GAATGGGCTTTACCTTCCCTG 58.621 52.381 0.00 0.00 40.69 4.45
56 57 0.033109 ATGGGCTTTACCTTCCCTGC 60.033 55.000 0.00 0.00 40.69 4.85
57 58 1.140134 TGGGCTTTACCTTCCCTGCT 61.140 55.000 0.00 0.00 40.69 4.24
58 59 0.681243 GGGCTTTACCTTCCCTGCTG 60.681 60.000 0.00 0.00 39.10 4.41
59 60 1.315981 GGCTTTACCTTCCCTGCTGC 61.316 60.000 0.00 0.00 34.51 5.25
60 61 0.322906 GCTTTACCTTCCCTGCTGCT 60.323 55.000 0.00 0.00 0.00 4.24
61 62 1.457346 CTTTACCTTCCCTGCTGCTG 58.543 55.000 0.00 0.00 0.00 4.41
62 63 0.609131 TTTACCTTCCCTGCTGCTGC 60.609 55.000 8.89 8.89 40.20 5.25
63 64 1.492133 TTACCTTCCCTGCTGCTGCT 61.492 55.000 17.00 0.00 40.48 4.24
64 65 2.189191 TACCTTCCCTGCTGCTGCTG 62.189 60.000 17.00 15.58 40.48 4.41
65 66 3.441290 CTTCCCTGCTGCTGCTGC 61.441 66.667 22.51 22.51 40.48 5.25
66 67 3.921936 CTTCCCTGCTGCTGCTGCT 62.922 63.158 27.67 0.00 40.48 4.24
67 68 4.717313 TCCCTGCTGCTGCTGCTG 62.717 66.667 27.67 25.97 40.48 4.41
80 81 4.728110 TGCTGCTGCCGCCTGATT 62.728 61.111 13.49 0.00 38.71 2.57
81 82 3.446570 GCTGCTGCCGCCTGATTT 61.447 61.111 4.57 0.00 34.43 2.17
82 83 2.998279 GCTGCTGCCGCCTGATTTT 61.998 57.895 4.57 0.00 34.43 1.82
83 84 1.588082 CTGCTGCCGCCTGATTTTT 59.412 52.632 0.00 0.00 34.43 1.94
108 109 9.541143 TTTTTCTTTTGTTCTTTTTCACTCAGT 57.459 25.926 0.00 0.00 0.00 3.41
109 110 9.541143 TTTTCTTTTGTTCTTTTTCACTCAGTT 57.459 25.926 0.00 0.00 0.00 3.16
110 111 9.541143 TTTCTTTTGTTCTTTTTCACTCAGTTT 57.459 25.926 0.00 0.00 0.00 2.66
111 112 9.541143 TTCTTTTGTTCTTTTTCACTCAGTTTT 57.459 25.926 0.00 0.00 0.00 2.43
112 113 9.191995 TCTTTTGTTCTTTTTCACTCAGTTTTC 57.808 29.630 0.00 0.00 0.00 2.29
113 114 9.196552 CTTTTGTTCTTTTTCACTCAGTTTTCT 57.803 29.630 0.00 0.00 0.00 2.52
114 115 9.541143 TTTTGTTCTTTTTCACTCAGTTTTCTT 57.459 25.926 0.00 0.00 0.00 2.52
115 116 9.541143 TTTGTTCTTTTTCACTCAGTTTTCTTT 57.459 25.926 0.00 0.00 0.00 2.52
116 117 8.519492 TGTTCTTTTTCACTCAGTTTTCTTTG 57.481 30.769 0.00 0.00 0.00 2.77
117 118 8.141268 TGTTCTTTTTCACTCAGTTTTCTTTGT 58.859 29.630 0.00 0.00 0.00 2.83
118 119 8.639428 GTTCTTTTTCACTCAGTTTTCTTTGTC 58.361 33.333 0.00 0.00 0.00 3.18
119 120 8.110860 TCTTTTTCACTCAGTTTTCTTTGTCT 57.889 30.769 0.00 0.00 0.00 3.41
120 121 8.023128 TCTTTTTCACTCAGTTTTCTTTGTCTG 58.977 33.333 0.00 0.00 0.00 3.51
121 122 7.447374 TTTTCACTCAGTTTTCTTTGTCTGA 57.553 32.000 0.00 0.00 35.92 3.27
122 123 7.630242 TTTCACTCAGTTTTCTTTGTCTGAT 57.370 32.000 0.00 0.00 36.55 2.90
123 124 7.630242 TTCACTCAGTTTTCTTTGTCTGATT 57.370 32.000 0.00 0.00 36.55 2.57
124 125 7.630242 TCACTCAGTTTTCTTTGTCTGATTT 57.370 32.000 0.00 0.00 36.55 2.17
125 126 8.055279 TCACTCAGTTTTCTTTGTCTGATTTT 57.945 30.769 0.00 0.00 36.55 1.82
126 127 7.970061 TCACTCAGTTTTCTTTGTCTGATTTTG 59.030 33.333 0.00 0.00 36.55 2.44
127 128 7.756722 CACTCAGTTTTCTTTGTCTGATTTTGT 59.243 33.333 0.00 0.00 36.55 2.83
128 129 7.756722 ACTCAGTTTTCTTTGTCTGATTTTGTG 59.243 33.333 0.00 0.00 36.55 3.33
129 130 7.035004 TCAGTTTTCTTTGTCTGATTTTGTGG 58.965 34.615 0.00 0.00 32.95 4.17
130 131 6.813152 CAGTTTTCTTTGTCTGATTTTGTGGT 59.187 34.615 0.00 0.00 0.00 4.16
131 132 7.331687 CAGTTTTCTTTGTCTGATTTTGTGGTT 59.668 33.333 0.00 0.00 0.00 3.67
132 133 7.877612 AGTTTTCTTTGTCTGATTTTGTGGTTT 59.122 29.630 0.00 0.00 0.00 3.27
133 134 7.826260 TTTCTTTGTCTGATTTTGTGGTTTC 57.174 32.000 0.00 0.00 0.00 2.78
134 135 5.901552 TCTTTGTCTGATTTTGTGGTTTCC 58.098 37.500 0.00 0.00 0.00 3.13
135 136 5.656416 TCTTTGTCTGATTTTGTGGTTTCCT 59.344 36.000 0.00 0.00 0.00 3.36
136 137 4.916983 TGTCTGATTTTGTGGTTTCCTG 57.083 40.909 0.00 0.00 0.00 3.86
137 138 4.531854 TGTCTGATTTTGTGGTTTCCTGA 58.468 39.130 0.00 0.00 0.00 3.86
138 139 4.338118 TGTCTGATTTTGTGGTTTCCTGAC 59.662 41.667 0.00 0.00 0.00 3.51
139 140 3.888930 TCTGATTTTGTGGTTTCCTGACC 59.111 43.478 0.00 0.00 40.23 4.02
396 400 8.902806 ACTCATGAACACTTTTCTAATTCACAA 58.097 29.630 0.00 0.00 32.42 3.33
482 486 8.599055 TTTTGAGCATGCACACATTATTTTAA 57.401 26.923 21.98 4.76 32.87 1.52
483 487 8.599055 TTTGAGCATGCACACATTATTTTAAA 57.401 26.923 21.98 4.01 32.87 1.52
535 539 5.929992 CCATAACCTTTTCTTGTAGTCGTGA 59.070 40.000 0.00 0.00 0.00 4.35
607 611 3.586100 AAACAAAAACAGACTTGCGGT 57.414 38.095 0.00 0.00 0.00 5.68
608 612 2.844122 ACAAAAACAGACTTGCGGTC 57.156 45.000 1.96 1.96 44.80 4.79
682 688 3.498777 GTGGGTGCTTTCTGTCTTCTTAC 59.501 47.826 0.00 0.00 0.00 2.34
1027 1043 2.512896 CTATCCAGGTGCCAGGCC 59.487 66.667 9.64 0.00 0.00 5.19
1323 1339 2.496817 CCGTCCACCTCTAGCAGC 59.503 66.667 0.00 0.00 0.00 5.25
1572 1588 4.478371 CGAGCATGGGCAGAGGCA 62.478 66.667 0.00 0.00 44.61 4.75
1656 1672 2.996621 GGACGAGTTCTCTGAAACCATG 59.003 50.000 0.00 0.00 0.00 3.66
1658 1674 1.734465 CGAGTTCTCTGAAACCATGGC 59.266 52.381 13.04 0.00 0.00 4.40
1659 1675 1.734465 GAGTTCTCTGAAACCATGGCG 59.266 52.381 13.04 0.00 0.00 5.69
1698 1714 1.077930 CATCACCTCCTGGGCACTG 60.078 63.158 0.00 0.00 39.10 3.66
1809 1825 3.386063 TCCTCGTACCCCATTGGAATTA 58.614 45.455 3.62 0.00 38.00 1.40
1816 1832 3.474920 ACCCCATTGGAATTACCTCTCT 58.525 45.455 3.62 0.00 39.86 3.10
1917 1933 2.697431 TTGCCGTTGACATTAGCAAC 57.303 45.000 0.00 0.00 38.45 4.17
1932 1948 1.166531 GCAACGGCAAGGTGAAGTCT 61.167 55.000 0.30 0.00 40.93 3.24
1958 1974 4.707105 TCTGCATACATCAATGGTGTAGG 58.293 43.478 13.32 13.32 37.03 3.18
1989 2005 4.586618 CTCTGTGGTGAGGAAGCG 57.413 61.111 0.00 0.00 0.00 4.68
1990 2006 1.739562 CTCTGTGGTGAGGAAGCGC 60.740 63.158 0.00 0.00 37.30 5.92
2035 2051 5.279809 CCCCAGTGTTACACTAGCTTTCTTA 60.280 44.000 18.19 0.00 43.43 2.10
2059 2075 1.961277 CGACTTCGCCAAGCACCTT 60.961 57.895 0.00 0.00 32.09 3.50
2063 2079 1.812571 ACTTCGCCAAGCACCTTAATG 59.187 47.619 0.00 0.00 32.09 1.90
2097 2113 6.156256 ACCAGGTAATTGCTTCTCATGTACTA 59.844 38.462 0.00 0.00 0.00 1.82
2134 2150 9.250624 GAAATGTAAGAGCGTTTAGATAGTGAT 57.749 33.333 0.00 0.00 0.00 3.06
2135 2151 8.804688 AATGTAAGAGCGTTTAGATAGTGATC 57.195 34.615 0.00 0.00 0.00 2.92
2136 2152 7.569639 TGTAAGAGCGTTTAGATAGTGATCT 57.430 36.000 0.00 0.00 44.90 2.75
2137 2153 8.672823 TGTAAGAGCGTTTAGATAGTGATCTA 57.327 34.615 0.00 0.00 42.66 1.98
2190 2209 5.927954 ACGTATGTATTTCGTGGTTTGTT 57.072 34.783 0.00 0.00 36.46 2.83
2191 2210 6.303021 ACGTATGTATTTCGTGGTTTGTTT 57.697 33.333 0.00 0.00 36.46 2.83
2206 2225 9.186323 CGTGGTTTGTTTACAATATTCATTTGA 57.814 29.630 0.00 0.00 35.55 2.69
2222 2280 0.031616 TTGAACTGCCCCCTTTGGTT 60.032 50.000 0.00 0.00 0.00 3.67
2225 2283 0.836606 AACTGCCCCCTTTGGTTTTG 59.163 50.000 0.00 0.00 0.00 2.44
2226 2284 0.326143 ACTGCCCCCTTTGGTTTTGT 60.326 50.000 0.00 0.00 0.00 2.83
2227 2285 0.106521 CTGCCCCCTTTGGTTTTGTG 59.893 55.000 0.00 0.00 0.00 3.33
2228 2286 0.618968 TGCCCCCTTTGGTTTTGTGT 60.619 50.000 0.00 0.00 0.00 3.72
2229 2287 0.105964 GCCCCCTTTGGTTTTGTGTC 59.894 55.000 0.00 0.00 0.00 3.67
2380 2445 7.330946 TCAGTTTTTCTCATCGTATTACCTGTG 59.669 37.037 0.00 0.00 0.00 3.66
2433 2498 4.437682 TCAACCAAATCTCTCAACCTGT 57.562 40.909 0.00 0.00 0.00 4.00
2520 2822 1.400113 CCATTTATATGGCACTGCGCG 60.400 52.381 0.00 0.00 44.64 6.86
2521 2823 0.874390 ATTTATATGGCACTGCGCGG 59.126 50.000 16.39 16.39 43.84 6.46
2562 2902 0.540365 CTGGGTGCCATGGTTTCACT 60.540 55.000 14.67 0.00 30.82 3.41
2563 2903 0.105760 TGGGTGCCATGGTTTCACTT 60.106 50.000 14.67 0.00 0.00 3.16
2564 2904 1.047801 GGGTGCCATGGTTTCACTTT 58.952 50.000 14.67 0.00 0.00 2.66
2565 2905 1.000843 GGGTGCCATGGTTTCACTTTC 59.999 52.381 14.67 0.89 0.00 2.62
2566 2906 1.686052 GGTGCCATGGTTTCACTTTCA 59.314 47.619 14.67 0.00 0.00 2.69
2567 2907 2.545742 GGTGCCATGGTTTCACTTTCAC 60.546 50.000 14.67 9.07 0.00 3.18
2568 2908 1.686052 TGCCATGGTTTCACTTTCACC 59.314 47.619 14.67 0.00 0.00 4.02
2569 2909 1.963515 GCCATGGTTTCACTTTCACCT 59.036 47.619 14.67 0.00 0.00 4.00
2570 2910 2.288395 GCCATGGTTTCACTTTCACCTG 60.288 50.000 14.67 0.00 0.00 4.00
2571 2911 2.958355 CCATGGTTTCACTTTCACCTGT 59.042 45.455 2.57 0.00 0.00 4.00
2572 2912 3.004734 CCATGGTTTCACTTTCACCTGTC 59.995 47.826 2.57 0.00 0.00 3.51
2573 2913 3.644966 TGGTTTCACTTTCACCTGTCT 57.355 42.857 0.00 0.00 0.00 3.41
2574 2914 4.764050 TGGTTTCACTTTCACCTGTCTA 57.236 40.909 0.00 0.00 0.00 2.59
2575 2915 5.105567 TGGTTTCACTTTCACCTGTCTAA 57.894 39.130 0.00 0.00 0.00 2.10
2576 2916 4.879545 TGGTTTCACTTTCACCTGTCTAAC 59.120 41.667 0.00 0.00 0.00 2.34
2577 2917 5.123936 GGTTTCACTTTCACCTGTCTAACT 58.876 41.667 0.00 0.00 0.00 2.24
2578 2918 5.236695 GGTTTCACTTTCACCTGTCTAACTC 59.763 44.000 0.00 0.00 0.00 3.01
2579 2919 4.602340 TCACTTTCACCTGTCTAACTCC 57.398 45.455 0.00 0.00 0.00 3.85
2580 2920 3.964688 TCACTTTCACCTGTCTAACTCCA 59.035 43.478 0.00 0.00 0.00 3.86
2581 2921 4.593206 TCACTTTCACCTGTCTAACTCCAT 59.407 41.667 0.00 0.00 0.00 3.41
2582 2922 4.692625 CACTTTCACCTGTCTAACTCCATG 59.307 45.833 0.00 0.00 0.00 3.66
2583 2923 3.981071 TTCACCTGTCTAACTCCATGG 57.019 47.619 4.97 4.97 0.00 3.66
2584 2924 1.555075 TCACCTGTCTAACTCCATGGC 59.445 52.381 6.96 0.00 0.00 4.40
2585 2925 1.556911 CACCTGTCTAACTCCATGGCT 59.443 52.381 6.96 0.00 0.00 4.75
2586 2926 2.026822 CACCTGTCTAACTCCATGGCTT 60.027 50.000 6.96 3.16 0.00 4.35
2587 2927 2.644798 ACCTGTCTAACTCCATGGCTTT 59.355 45.455 6.96 4.82 0.00 3.51
2588 2928 3.074538 ACCTGTCTAACTCCATGGCTTTT 59.925 43.478 6.96 2.09 0.00 2.27
2589 2929 4.082125 CCTGTCTAACTCCATGGCTTTTT 58.918 43.478 6.96 0.00 0.00 1.94
2657 2997 2.283388 ACCCTGCCTGCACCATTG 60.283 61.111 0.00 0.00 0.00 2.82
2670 3010 2.279851 CATTGCGGCCCATGCATG 60.280 61.111 20.19 20.19 42.84 4.06
2677 3017 1.757731 GGCCCATGCATGCCTTACA 60.758 57.895 21.69 0.00 44.46 2.41
2706 3049 2.736144 TTGCTACCTCACACGGTAAG 57.264 50.000 0.00 0.00 38.96 2.34
2725 3068 6.626402 CGGTAAGTGTACCTGACAATCACATA 60.626 42.308 1.68 0.00 46.84 2.29
2726 3069 7.272978 GGTAAGTGTACCTGACAATCACATAT 58.727 38.462 0.00 0.00 45.72 1.78
2744 3087 5.008019 CACATATAGGTCTGGTCATTTGCAC 59.992 44.000 0.00 0.00 0.00 4.57
2794 3161 5.230182 GCATACATGTGACTTGATATCCGA 58.770 41.667 9.11 0.00 0.00 4.55
2816 3183 6.908825 CGAAAGGTTCTAATTTCCAACATCA 58.091 36.000 0.00 0.00 32.87 3.07
2817 3184 7.023575 CGAAAGGTTCTAATTTCCAACATCAG 58.976 38.462 0.00 0.00 32.87 2.90
2818 3185 7.308589 CGAAAGGTTCTAATTTCCAACATCAGT 60.309 37.037 0.00 0.00 32.87 3.41
2819 3186 7.839680 AAGGTTCTAATTTCCAACATCAGTT 57.160 32.000 0.00 0.00 38.88 3.16
2837 3204 7.821359 ACATCAGTTGTACGTACTCTTACTCTA 59.179 37.037 25.12 13.15 36.57 2.43
2855 3222 4.163649 ACTCTAAGCGGCTAACCCTAAAAT 59.836 41.667 1.35 0.00 0.00 1.82
2856 3223 4.700700 TCTAAGCGGCTAACCCTAAAATC 58.299 43.478 1.35 0.00 0.00 2.17
2863 3230 4.275936 CGGCTAACCCTAAAATCTGGATTG 59.724 45.833 0.00 0.00 0.00 2.67
2864 3231 5.445964 GGCTAACCCTAAAATCTGGATTGA 58.554 41.667 0.00 0.00 0.00 2.57
2908 3275 8.699283 AAACATTGGTAAGTACGTATTCTCTC 57.301 34.615 0.00 0.00 0.00 3.20
2920 3287 9.447157 AGTACGTATTCTCTCTTTGTACTACTT 57.553 33.333 0.00 0.00 39.23 2.24
2921 3288 9.488124 GTACGTATTCTCTCTTTGTACTACTTG 57.512 37.037 0.00 0.00 0.00 3.16
2923 3290 9.224267 ACGTATTCTCTCTTTGTACTACTTGTA 57.776 33.333 0.00 0.00 0.00 2.41
2928 3295 9.909644 TTCTCTCTTTGTACTACTTGTATTCAC 57.090 33.333 0.00 0.00 33.23 3.18
2929 3296 9.298250 TCTCTCTTTGTACTACTTGTATTCACT 57.702 33.333 0.00 0.00 33.23 3.41
2930 3297 9.347934 CTCTCTTTGTACTACTTGTATTCACTG 57.652 37.037 0.00 0.00 33.23 3.66
2931 3298 8.857098 TCTCTTTGTACTACTTGTATTCACTGT 58.143 33.333 0.00 0.00 33.23 3.55
2932 3299 8.812147 TCTTTGTACTACTTGTATTCACTGTG 57.188 34.615 0.17 0.17 33.23 3.66
2933 3300 7.870954 TCTTTGTACTACTTGTATTCACTGTGG 59.129 37.037 8.11 0.00 33.23 4.17
2934 3301 6.032956 TGTACTACTTGTATTCACTGTGGG 57.967 41.667 8.11 0.00 33.23 4.61
2935 3302 3.939066 ACTACTTGTATTCACTGTGGGC 58.061 45.455 8.11 0.00 0.00 5.36
2936 3303 2.200373 ACTTGTATTCACTGTGGGCC 57.800 50.000 8.11 0.00 0.00 5.80
2937 3304 1.423541 ACTTGTATTCACTGTGGGCCA 59.576 47.619 0.00 0.00 0.00 5.36
2938 3305 2.041620 ACTTGTATTCACTGTGGGCCAT 59.958 45.455 10.70 0.00 0.00 4.40
2939 3306 3.265737 ACTTGTATTCACTGTGGGCCATA 59.734 43.478 10.70 6.01 0.00 2.74
2940 3307 3.275617 TGTATTCACTGTGGGCCATAC 57.724 47.619 10.70 6.89 0.00 2.39
2941 3308 2.210116 GTATTCACTGTGGGCCATACG 58.790 52.381 10.70 3.56 0.00 3.06
2990 3362 1.682854 ACCAAAACACCAGCACATGAG 59.317 47.619 0.00 0.00 0.00 2.90
2992 3364 1.067364 CAAAACACCAGCACATGAGCA 59.933 47.619 17.61 0.00 36.85 4.26
2996 3368 0.956633 CACCAGCACATGAGCAGTTT 59.043 50.000 17.61 0.00 36.85 2.66
3018 3390 9.502091 AGTTTTATGTTCTGCTTATGTAACTCA 57.498 29.630 0.00 0.00 0.00 3.41
3019 3391 9.760660 GTTTTATGTTCTGCTTATGTAACTCAG 57.239 33.333 0.00 0.00 0.00 3.35
3020 3392 7.539712 TTATGTTCTGCTTATGTAACTCAGC 57.460 36.000 0.00 0.00 0.00 4.26
3036 3408 2.080693 TCAGCGTTCTGTTTGTGTTGT 58.919 42.857 0.00 0.00 41.10 3.32
3040 3412 3.936453 AGCGTTCTGTTTGTGTTGTAAGA 59.064 39.130 0.00 0.00 0.00 2.10
3041 3413 4.393680 AGCGTTCTGTTTGTGTTGTAAGAA 59.606 37.500 0.00 0.00 0.00 2.52
3042 3414 4.728608 GCGTTCTGTTTGTGTTGTAAGAAG 59.271 41.667 0.00 0.00 0.00 2.85
3043 3415 5.672819 GCGTTCTGTTTGTGTTGTAAGAAGT 60.673 40.000 0.00 0.00 0.00 3.01
3044 3416 5.732647 CGTTCTGTTTGTGTTGTAAGAAGTG 59.267 40.000 0.00 0.00 0.00 3.16
3045 3417 5.229921 TCTGTTTGTGTTGTAAGAAGTGC 57.770 39.130 0.00 0.00 0.00 4.40
3046 3418 4.941263 TCTGTTTGTGTTGTAAGAAGTGCT 59.059 37.500 0.00 0.00 0.00 4.40
3047 3419 5.064707 TCTGTTTGTGTTGTAAGAAGTGCTC 59.935 40.000 0.00 0.00 0.00 4.26
3048 3420 4.095782 TGTTTGTGTTGTAAGAAGTGCTCC 59.904 41.667 0.00 0.00 0.00 4.70
3049 3421 2.846193 TGTGTTGTAAGAAGTGCTCCC 58.154 47.619 0.00 0.00 0.00 4.30
3050 3422 2.438021 TGTGTTGTAAGAAGTGCTCCCT 59.562 45.455 0.00 0.00 0.00 4.20
3051 3423 3.067833 GTGTTGTAAGAAGTGCTCCCTC 58.932 50.000 0.00 0.00 0.00 4.30
3052 3424 2.288825 TGTTGTAAGAAGTGCTCCCTCG 60.289 50.000 0.00 0.00 0.00 4.63
3053 3425 0.895530 TGTAAGAAGTGCTCCCTCGG 59.104 55.000 0.00 0.00 0.00 4.63
3054 3426 0.896226 GTAAGAAGTGCTCCCTCGGT 59.104 55.000 0.00 0.00 0.00 4.69
3055 3427 1.275573 GTAAGAAGTGCTCCCTCGGTT 59.724 52.381 0.00 0.00 0.00 4.44
3056 3428 0.321996 AAGAAGTGCTCCCTCGGTTC 59.678 55.000 0.00 0.00 0.00 3.62
3057 3429 1.446272 GAAGTGCTCCCTCGGTTCG 60.446 63.158 0.00 0.00 0.00 3.95
3058 3430 1.874345 GAAGTGCTCCCTCGGTTCGA 61.874 60.000 0.00 0.00 0.00 3.71
3059 3431 1.469335 AAGTGCTCCCTCGGTTCGAA 61.469 55.000 0.00 0.00 34.74 3.71
3060 3432 1.005394 GTGCTCCCTCGGTTCGAAA 60.005 57.895 0.00 0.00 34.74 3.46
3061 3433 0.601841 GTGCTCCCTCGGTTCGAAAA 60.602 55.000 0.00 0.00 34.74 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.708759 TCCCTACTCCTTTTGGTTCCA 58.291 47.619 0.00 0.00 41.38 3.53
1 2 3.074094 AGTTCCCTACTCCTTTTGGTTCC 59.926 47.826 0.00 0.00 41.38 3.62
2 3 4.325119 GAGTTCCCTACTCCTTTTGGTTC 58.675 47.826 0.00 0.00 46.30 3.62
3 4 4.368565 GAGTTCCCTACTCCTTTTGGTT 57.631 45.455 0.00 0.00 46.30 3.67
13 14 0.896940 TCGCCAACGAGTTCCCTACT 60.897 55.000 0.00 0.00 45.12 2.57
14 15 1.588082 TCGCCAACGAGTTCCCTAC 59.412 57.895 0.00 0.00 45.12 3.18
15 16 4.100479 TCGCCAACGAGTTCCCTA 57.900 55.556 0.00 0.00 45.12 3.53
25 26 3.810896 GCCCATTCCGTCGCCAAC 61.811 66.667 0.00 0.00 0.00 3.77
26 27 3.561120 AAGCCCATTCCGTCGCCAA 62.561 57.895 0.00 0.00 0.00 4.52
27 28 2.186602 TAAAGCCCATTCCGTCGCCA 62.187 55.000 0.00 0.00 0.00 5.69
28 29 1.450669 TAAAGCCCATTCCGTCGCC 60.451 57.895 0.00 0.00 0.00 5.54
29 30 1.712018 GGTAAAGCCCATTCCGTCGC 61.712 60.000 0.00 0.00 0.00 5.19
30 31 0.107848 AGGTAAAGCCCATTCCGTCG 60.108 55.000 0.00 0.00 38.26 5.12
31 32 2.014857 GAAGGTAAAGCCCATTCCGTC 58.985 52.381 0.00 0.00 38.26 4.79
32 33 1.340697 GGAAGGTAAAGCCCATTCCGT 60.341 52.381 0.00 0.00 38.26 4.69
33 34 1.389555 GGAAGGTAAAGCCCATTCCG 58.610 55.000 0.00 0.00 38.26 4.30
34 35 1.288037 AGGGAAGGTAAAGCCCATTCC 59.712 52.381 0.00 0.00 44.55 3.01
35 36 2.379005 CAGGGAAGGTAAAGCCCATTC 58.621 52.381 0.00 0.00 44.55 2.67
36 37 1.619704 GCAGGGAAGGTAAAGCCCATT 60.620 52.381 0.00 0.00 44.55 3.16
37 38 0.033109 GCAGGGAAGGTAAAGCCCAT 60.033 55.000 0.00 0.00 44.55 4.00
38 39 1.140134 AGCAGGGAAGGTAAAGCCCA 61.140 55.000 0.00 0.00 44.55 5.36
39 40 0.681243 CAGCAGGGAAGGTAAAGCCC 60.681 60.000 0.00 0.00 42.37 5.19
40 41 1.315981 GCAGCAGGGAAGGTAAAGCC 61.316 60.000 0.00 0.00 37.58 4.35
41 42 0.322906 AGCAGCAGGGAAGGTAAAGC 60.323 55.000 0.00 0.00 0.00 3.51
42 43 1.457346 CAGCAGCAGGGAAGGTAAAG 58.543 55.000 0.00 0.00 0.00 1.85
43 44 0.609131 GCAGCAGCAGGGAAGGTAAA 60.609 55.000 0.00 0.00 41.58 2.01
44 45 1.002134 GCAGCAGCAGGGAAGGTAA 60.002 57.895 0.00 0.00 41.58 2.85
45 46 1.920325 AGCAGCAGCAGGGAAGGTA 60.920 57.895 3.17 0.00 45.49 3.08
46 47 3.255397 AGCAGCAGCAGGGAAGGT 61.255 61.111 3.17 0.00 45.49 3.50
47 48 2.750637 CAGCAGCAGCAGGGAAGG 60.751 66.667 3.17 0.00 45.49 3.46
48 49 3.441290 GCAGCAGCAGCAGGGAAG 61.441 66.667 4.63 0.00 45.49 3.46
49 50 3.962694 AGCAGCAGCAGCAGGGAA 61.963 61.111 12.92 0.00 45.49 3.97
50 51 4.717313 CAGCAGCAGCAGCAGGGA 62.717 66.667 12.92 0.00 45.49 4.20
82 83 9.541143 ACTGAGTGAAAAAGAACAAAAGAAAAA 57.459 25.926 0.00 0.00 0.00 1.94
83 84 9.541143 AACTGAGTGAAAAAGAACAAAAGAAAA 57.459 25.926 0.00 0.00 0.00 2.29
84 85 9.541143 AAACTGAGTGAAAAAGAACAAAAGAAA 57.459 25.926 0.00 0.00 0.00 2.52
85 86 9.541143 AAAACTGAGTGAAAAAGAACAAAAGAA 57.459 25.926 0.00 0.00 0.00 2.52
86 87 9.191995 GAAAACTGAGTGAAAAAGAACAAAAGA 57.808 29.630 0.00 0.00 0.00 2.52
87 88 9.196552 AGAAAACTGAGTGAAAAAGAACAAAAG 57.803 29.630 0.00 0.00 0.00 2.27
88 89 9.541143 AAGAAAACTGAGTGAAAAAGAACAAAA 57.459 25.926 0.00 0.00 0.00 2.44
89 90 9.541143 AAAGAAAACTGAGTGAAAAAGAACAAA 57.459 25.926 0.00 0.00 0.00 2.83
90 91 8.977505 CAAAGAAAACTGAGTGAAAAAGAACAA 58.022 29.630 0.00 0.00 0.00 2.83
91 92 8.141268 ACAAAGAAAACTGAGTGAAAAAGAACA 58.859 29.630 0.00 0.00 0.00 3.18
92 93 8.520835 ACAAAGAAAACTGAGTGAAAAAGAAC 57.479 30.769 0.00 0.00 0.00 3.01
93 94 8.576442 AGACAAAGAAAACTGAGTGAAAAAGAA 58.424 29.630 0.00 0.00 0.00 2.52
94 95 8.023128 CAGACAAAGAAAACTGAGTGAAAAAGA 58.977 33.333 0.00 0.00 32.90 2.52
95 96 8.023128 TCAGACAAAGAAAACTGAGTGAAAAAG 58.977 33.333 0.00 0.00 35.01 2.27
96 97 7.881142 TCAGACAAAGAAAACTGAGTGAAAAA 58.119 30.769 0.00 0.00 35.01 1.94
97 98 7.447374 TCAGACAAAGAAAACTGAGTGAAAA 57.553 32.000 0.00 0.00 35.01 2.29
98 99 7.630242 ATCAGACAAAGAAAACTGAGTGAAA 57.370 32.000 0.00 0.00 41.55 2.69
99 100 7.630242 AATCAGACAAAGAAAACTGAGTGAA 57.370 32.000 0.00 0.00 41.55 3.18
100 101 7.630242 AAATCAGACAAAGAAAACTGAGTGA 57.370 32.000 0.00 0.00 41.55 3.41
101 102 7.756722 ACAAAATCAGACAAAGAAAACTGAGTG 59.243 33.333 0.00 0.00 41.55 3.51
102 103 7.756722 CACAAAATCAGACAAAGAAAACTGAGT 59.243 33.333 0.00 0.00 41.55 3.41
103 104 7.221452 CCACAAAATCAGACAAAGAAAACTGAG 59.779 37.037 0.00 0.00 41.55 3.35
104 105 7.035004 CCACAAAATCAGACAAAGAAAACTGA 58.965 34.615 0.00 0.00 42.26 3.41
105 106 6.813152 ACCACAAAATCAGACAAAGAAAACTG 59.187 34.615 0.00 0.00 0.00 3.16
106 107 6.935167 ACCACAAAATCAGACAAAGAAAACT 58.065 32.000 0.00 0.00 0.00 2.66
107 108 7.595311 AACCACAAAATCAGACAAAGAAAAC 57.405 32.000 0.00 0.00 0.00 2.43
108 109 7.333174 GGAAACCACAAAATCAGACAAAGAAAA 59.667 33.333 0.00 0.00 0.00 2.29
109 110 6.816140 GGAAACCACAAAATCAGACAAAGAAA 59.184 34.615 0.00 0.00 0.00 2.52
110 111 6.154363 AGGAAACCACAAAATCAGACAAAGAA 59.846 34.615 0.00 0.00 0.00 2.52
111 112 5.656416 AGGAAACCACAAAATCAGACAAAGA 59.344 36.000 0.00 0.00 0.00 2.52
112 113 5.750067 CAGGAAACCACAAAATCAGACAAAG 59.250 40.000 0.00 0.00 0.00 2.77
113 114 5.420421 TCAGGAAACCACAAAATCAGACAAA 59.580 36.000 0.00 0.00 0.00 2.83
114 115 4.952957 TCAGGAAACCACAAAATCAGACAA 59.047 37.500 0.00 0.00 0.00 3.18
115 116 4.338118 GTCAGGAAACCACAAAATCAGACA 59.662 41.667 0.00 0.00 0.00 3.41
116 117 4.261614 GGTCAGGAAACCACAAAATCAGAC 60.262 45.833 0.00 0.00 39.27 3.51
117 118 3.888930 GGTCAGGAAACCACAAAATCAGA 59.111 43.478 0.00 0.00 39.27 3.27
118 119 3.636300 TGGTCAGGAAACCACAAAATCAG 59.364 43.478 0.00 0.00 44.40 2.90
119 120 3.636679 TGGTCAGGAAACCACAAAATCA 58.363 40.909 0.00 0.00 44.40 2.57
249 253 6.064846 TGTGAACTTCTCTCAAATTCAAGC 57.935 37.500 0.00 0.00 31.45 4.01
333 337 3.980646 TTCCAAAATGTCCACGACTTG 57.019 42.857 0.00 0.00 33.15 3.16
371 375 9.734620 TTTGTGAATTAGAAAAGTGTTCATGAG 57.265 29.630 0.00 0.00 32.19 2.90
459 463 8.774890 ATTTAAAATAATGTGTGCATGCTCAA 57.225 26.923 22.97 13.88 35.15 3.02
460 464 8.774890 AATTTAAAATAATGTGTGCATGCTCA 57.225 26.923 20.33 19.12 35.15 4.26
544 548 5.348451 CGGCCAGTTCAATTTTAATTTGGAG 59.652 40.000 2.24 0.00 28.47 3.86
545 549 5.011125 TCGGCCAGTTCAATTTTAATTTGGA 59.989 36.000 2.24 0.00 28.47 3.53
546 550 5.233988 TCGGCCAGTTCAATTTTAATTTGG 58.766 37.500 2.24 0.00 0.00 3.28
575 579 6.894517 GTCTGTTTTTGTTTTTCTCATTTCGC 59.105 34.615 0.00 0.00 0.00 4.70
608 612 4.247380 GGCCTGGCCCATCGAGAG 62.247 72.222 27.77 0.00 44.06 3.20
627 631 2.787601 TTTATAGACCGCGCGAGATT 57.212 45.000 34.63 16.01 0.00 2.40
682 688 4.462280 GGTAACCACCTCGCGGGG 62.462 72.222 27.07 27.07 42.11 5.73
990 1006 1.337118 GGTAGCTCATCTGGAGGAGG 58.663 60.000 13.01 0.00 44.22 4.30
1027 1043 2.699576 ATCGGGATGATGGCGTCGTG 62.700 60.000 6.08 0.00 35.45 4.35
1323 1339 1.153289 CGGATGCTTGACCTCCCAG 60.153 63.158 0.00 0.00 0.00 4.45
1659 1675 3.056313 GAAAGCATCGGTGGCAGGC 62.056 63.158 0.00 0.00 0.00 4.85
1698 1714 2.029365 GCCGTCGCTTTCTGTTATTCTC 59.971 50.000 0.00 0.00 0.00 2.87
1749 1765 1.288439 CCCGATCTCGCTGGATCTG 59.712 63.158 11.93 7.04 39.73 2.90
1809 1825 3.181467 GCTCATACATGCTGAAGAGAGGT 60.181 47.826 0.00 0.00 0.00 3.85
1816 1832 1.561076 ACTGGGCTCATACATGCTGAA 59.439 47.619 0.00 0.00 0.00 3.02
1917 1933 1.734465 GATGAAGACTTCACCTTGCCG 59.266 52.381 19.96 0.00 43.48 5.69
1932 1948 5.195185 ACACCATTGATGTATGCAGATGAA 58.805 37.500 0.00 0.00 0.00 2.57
1989 2005 4.290969 GTTTTTCTCTGGCAAAGTACAGC 58.709 43.478 0.00 0.00 34.76 4.40
1990 2006 4.261614 GGGTTTTTCTCTGGCAAAGTACAG 60.262 45.833 0.00 0.00 36.07 2.74
2059 2075 2.969821 ACCTGGTTCCAAGCACATTA 57.030 45.000 0.00 0.00 32.29 1.90
2063 2079 2.352715 GCAATTACCTGGTTCCAAGCAC 60.353 50.000 3.84 0.00 32.29 4.40
2097 2113 6.929606 ACGCTCTTACATTTCTTTACAGAGTT 59.070 34.615 0.00 0.00 30.86 3.01
2137 2153 9.907229 CCTCTGTAAAGAAATATAAGAGGGTTT 57.093 33.333 7.76 0.00 37.38 3.27
2141 2157 8.929487 ACTCCCTCTGTAAAGAAATATAAGAGG 58.071 37.037 8.54 8.54 39.86 3.69
2153 2169 5.831702 ACATACGTACTCCCTCTGTAAAG 57.168 43.478 0.00 0.00 0.00 1.85
2169 2185 7.289395 TGTAAACAAACCACGAAATACATACG 58.711 34.615 0.00 0.00 0.00 3.06
2190 2209 6.127196 GGGGGCAGTTCAAATGAATATTGTAA 60.127 38.462 0.00 0.00 36.33 2.41
2191 2210 5.362430 GGGGGCAGTTCAAATGAATATTGTA 59.638 40.000 0.00 0.00 36.33 2.41
2206 2225 0.836606 CAAAACCAAAGGGGGCAGTT 59.163 50.000 0.00 0.00 42.91 3.16
2222 2280 3.456644 TCAAGACTACCCTTGGACACAAA 59.543 43.478 0.00 0.00 42.72 2.83
2225 2283 3.515901 AGATCAAGACTACCCTTGGACAC 59.484 47.826 0.00 0.00 42.72 3.67
2226 2284 3.791320 AGATCAAGACTACCCTTGGACA 58.209 45.455 0.00 0.00 42.72 4.02
2227 2285 4.828072 AAGATCAAGACTACCCTTGGAC 57.172 45.455 0.00 0.00 42.72 4.02
2228 2286 5.590818 AGTAAGATCAAGACTACCCTTGGA 58.409 41.667 0.00 0.00 42.72 3.53
2229 2287 5.941555 AGTAAGATCAAGACTACCCTTGG 57.058 43.478 0.00 0.00 42.72 3.61
2315 2377 2.171659 TCTGGTCACAGCCAACTAACAA 59.828 45.455 0.00 0.00 44.54 2.83
2554 2894 5.123936 AGTTAGACAGGTGAAAGTGAAACC 58.876 41.667 0.00 0.00 37.80 3.27
2562 2902 3.559171 GCCATGGAGTTAGACAGGTGAAA 60.559 47.826 18.40 0.00 0.00 2.69
2563 2903 2.027192 GCCATGGAGTTAGACAGGTGAA 60.027 50.000 18.40 0.00 0.00 3.18
2564 2904 1.555075 GCCATGGAGTTAGACAGGTGA 59.445 52.381 18.40 0.00 0.00 4.02
2565 2905 1.556911 AGCCATGGAGTTAGACAGGTG 59.443 52.381 18.40 0.00 0.00 4.00
2566 2906 1.958288 AGCCATGGAGTTAGACAGGT 58.042 50.000 18.40 0.00 0.00 4.00
2567 2907 3.356529 AAAGCCATGGAGTTAGACAGG 57.643 47.619 18.40 0.00 0.00 4.00
2605 2945 6.518200 GCCATGGAGTTGGACAATTCTAAAAA 60.518 38.462 18.40 0.00 39.25 1.94
2606 2946 5.047377 GCCATGGAGTTGGACAATTCTAAAA 60.047 40.000 18.40 0.00 39.25 1.52
2607 2947 4.462483 GCCATGGAGTTGGACAATTCTAAA 59.538 41.667 18.40 0.00 39.25 1.85
2608 2948 4.016444 GCCATGGAGTTGGACAATTCTAA 58.984 43.478 18.40 0.00 39.25 2.10
2609 2949 3.266772 AGCCATGGAGTTGGACAATTCTA 59.733 43.478 18.40 2.37 39.25 2.10
2610 2950 2.042162 AGCCATGGAGTTGGACAATTCT 59.958 45.455 18.40 0.00 39.25 2.40
2611 2951 2.450476 AGCCATGGAGTTGGACAATTC 58.550 47.619 18.40 0.00 39.25 2.17
2612 2952 2.610438 AGCCATGGAGTTGGACAATT 57.390 45.000 18.40 0.00 39.25 2.32
2613 2953 2.564062 CAAAGCCATGGAGTTGGACAAT 59.436 45.455 18.40 0.00 39.25 2.71
2614 2954 1.962807 CAAAGCCATGGAGTTGGACAA 59.037 47.619 18.40 0.00 39.25 3.18
2619 2959 0.680618 TTGCCAAAGCCATGGAGTTG 59.319 50.000 18.40 17.50 43.54 3.16
2670 3010 2.352503 CAAATGTGCTGGTGTAAGGC 57.647 50.000 0.00 0.00 0.00 4.35
2706 3049 6.817184 ACCTATATGTGATTGTCAGGTACAC 58.183 40.000 0.00 0.00 38.00 2.90
2725 3068 4.225042 TGTAGTGCAAATGACCAGACCTAT 59.775 41.667 0.00 0.00 0.00 2.57
2726 3069 3.580895 TGTAGTGCAAATGACCAGACCTA 59.419 43.478 0.00 0.00 0.00 3.08
2771 3138 5.230182 TCGGATATCAAGTCACATGTATGC 58.770 41.667 4.83 0.00 0.00 3.14
2794 3161 7.839680 ACTGATGTTGGAAATTAGAACCTTT 57.160 32.000 0.00 0.00 0.00 3.11
2808 3175 7.787215 AGTAAGAGTACGTACAACTGATGTTGG 60.787 40.741 26.55 0.00 44.47 3.77
2809 3176 7.082602 AGTAAGAGTACGTACAACTGATGTTG 58.917 38.462 26.55 7.28 45.00 3.33
2810 3177 7.174599 AGAGTAAGAGTACGTACAACTGATGTT 59.825 37.037 26.55 12.21 38.12 2.71
2811 3178 6.654161 AGAGTAAGAGTACGTACAACTGATGT 59.346 38.462 26.55 12.47 39.47 3.06
2815 3182 6.960431 GCTTAGAGTAAGAGTACGTACAACTG 59.040 42.308 26.55 12.53 38.02 3.16
2816 3183 6.183360 CGCTTAGAGTAAGAGTACGTACAACT 60.183 42.308 26.55 21.30 38.02 3.16
2817 3184 5.956645 CGCTTAGAGTAAGAGTACGTACAAC 59.043 44.000 26.55 18.96 38.02 3.32
2818 3185 5.063944 CCGCTTAGAGTAAGAGTACGTACAA 59.936 44.000 26.55 8.56 38.02 2.41
2819 3186 4.568359 CCGCTTAGAGTAAGAGTACGTACA 59.432 45.833 26.55 3.86 38.02 2.90
2820 3187 4.551797 GCCGCTTAGAGTAAGAGTACGTAC 60.552 50.000 18.10 18.10 38.02 3.67
2821 3188 3.557595 GCCGCTTAGAGTAAGAGTACGTA 59.442 47.826 0.00 0.00 38.02 3.57
2822 3189 2.354199 GCCGCTTAGAGTAAGAGTACGT 59.646 50.000 0.00 0.00 38.02 3.57
2823 3190 2.613133 AGCCGCTTAGAGTAAGAGTACG 59.387 50.000 0.00 0.00 38.02 3.67
2824 3191 5.505489 GGTTAGCCGCTTAGAGTAAGAGTAC 60.505 48.000 0.00 0.00 38.02 2.73
2825 3192 4.578105 GGTTAGCCGCTTAGAGTAAGAGTA 59.422 45.833 0.00 0.00 38.02 2.59
2826 3193 3.380954 GGTTAGCCGCTTAGAGTAAGAGT 59.619 47.826 0.00 0.00 38.02 3.24
2827 3194 3.243468 GGGTTAGCCGCTTAGAGTAAGAG 60.243 52.174 0.00 0.00 37.52 2.85
2828 3195 2.692041 GGGTTAGCCGCTTAGAGTAAGA 59.308 50.000 0.00 0.00 37.52 2.10
2829 3196 2.694109 AGGGTTAGCCGCTTAGAGTAAG 59.306 50.000 0.00 0.00 38.80 2.34
2830 3197 2.743553 AGGGTTAGCCGCTTAGAGTAA 58.256 47.619 0.00 0.00 31.04 2.24
2831 3198 2.449137 AGGGTTAGCCGCTTAGAGTA 57.551 50.000 0.00 0.00 31.04 2.59
2832 3199 2.449137 TAGGGTTAGCCGCTTAGAGT 57.551 50.000 0.00 0.00 37.54 3.24
2833 3200 3.814005 TTTAGGGTTAGCCGCTTAGAG 57.186 47.619 0.00 0.00 37.54 2.43
2837 3204 3.279434 CAGATTTTAGGGTTAGCCGCTT 58.721 45.455 0.00 0.00 37.54 4.68
2894 3261 9.447157 AAGTAGTACAAAGAGAGAATACGTACT 57.553 33.333 0.00 0.00 40.66 2.73
2895 3262 9.488124 CAAGTAGTACAAAGAGAGAATACGTAC 57.512 37.037 0.00 0.00 0.00 3.67
2896 3263 9.224267 ACAAGTAGTACAAAGAGAGAATACGTA 57.776 33.333 0.00 0.00 0.00 3.57
2897 3264 8.108551 ACAAGTAGTACAAAGAGAGAATACGT 57.891 34.615 2.52 0.00 0.00 3.57
2908 3275 7.117812 CCCACAGTGAATACAAGTAGTACAAAG 59.882 40.741 0.62 0.00 35.05 2.77
2920 3287 2.419436 CGTATGGCCCACAGTGAATACA 60.419 50.000 0.62 0.00 0.00 2.29
2921 3288 2.159014 TCGTATGGCCCACAGTGAATAC 60.159 50.000 0.62 0.00 0.00 1.89
2923 3290 0.908910 TCGTATGGCCCACAGTGAAT 59.091 50.000 0.62 0.00 0.00 2.57
2924 3291 0.908910 ATCGTATGGCCCACAGTGAA 59.091 50.000 0.62 0.00 0.00 3.18
2926 3293 0.465705 AGATCGTATGGCCCACAGTG 59.534 55.000 0.00 0.00 0.00 3.66
2927 3294 1.204146 AAGATCGTATGGCCCACAGT 58.796 50.000 0.00 0.00 0.00 3.55
2928 3295 3.329386 CATAAGATCGTATGGCCCACAG 58.671 50.000 17.88 0.00 0.00 3.66
2929 3296 2.549992 GCATAAGATCGTATGGCCCACA 60.550 50.000 24.21 0.00 32.93 4.17
2930 3297 2.076863 GCATAAGATCGTATGGCCCAC 58.923 52.381 24.21 8.52 32.93 4.61
2931 3298 1.977854 AGCATAAGATCGTATGGCCCA 59.022 47.619 24.21 0.00 32.93 5.36
2932 3299 2.350522 CAGCATAAGATCGTATGGCCC 58.649 52.381 24.21 11.86 32.93 5.80
2933 3300 1.734465 GCAGCATAAGATCGTATGGCC 59.266 52.381 24.21 12.43 32.93 5.36
2934 3301 1.734465 GGCAGCATAAGATCGTATGGC 59.266 52.381 24.21 19.92 32.93 4.40
2935 3302 2.998670 CAGGCAGCATAAGATCGTATGG 59.001 50.000 24.21 13.23 32.93 2.74
2936 3303 2.998670 CCAGGCAGCATAAGATCGTATG 59.001 50.000 20.44 20.44 35.03 2.39
2937 3304 2.899900 TCCAGGCAGCATAAGATCGTAT 59.100 45.455 0.00 0.00 0.00 3.06
2938 3305 2.297315 CTCCAGGCAGCATAAGATCGTA 59.703 50.000 0.00 0.00 0.00 3.43
2939 3306 1.069823 CTCCAGGCAGCATAAGATCGT 59.930 52.381 0.00 0.00 0.00 3.73
2940 3307 1.069823 ACTCCAGGCAGCATAAGATCG 59.930 52.381 0.00 0.00 0.00 3.69
2941 3308 2.368221 AGACTCCAGGCAGCATAAGATC 59.632 50.000 0.00 0.00 0.00 2.75
2992 3364 9.502091 TGAGTTACATAAGCAGAACATAAAACT 57.498 29.630 0.00 0.00 0.00 2.66
2996 3368 6.255670 CGCTGAGTTACATAAGCAGAACATAA 59.744 38.462 0.00 0.00 35.33 1.90
3007 3379 5.756347 ACAAACAGAACGCTGAGTTACATAA 59.244 36.000 0.00 0.00 45.17 1.90
3018 3390 3.936453 TCTTACAACACAAACAGAACGCT 59.064 39.130 0.00 0.00 0.00 5.07
3019 3391 4.267357 TCTTACAACACAAACAGAACGC 57.733 40.909 0.00 0.00 0.00 4.84
3020 3392 5.732647 CACTTCTTACAACACAAACAGAACG 59.267 40.000 0.00 0.00 0.00 3.95
3036 3408 1.549170 GAACCGAGGGAGCACTTCTTA 59.451 52.381 0.00 0.00 0.00 2.10
3040 3412 1.469335 TTCGAACCGAGGGAGCACTT 61.469 55.000 0.00 0.00 37.14 3.16
3041 3413 1.469335 TTTCGAACCGAGGGAGCACT 61.469 55.000 0.00 0.00 37.14 4.40
3042 3414 0.601841 TTTTCGAACCGAGGGAGCAC 60.602 55.000 0.00 0.00 37.14 4.40
3043 3415 1.749665 TTTTCGAACCGAGGGAGCA 59.250 52.632 0.00 0.00 37.14 4.26
3044 3416 4.687464 TTTTCGAACCGAGGGAGC 57.313 55.556 0.00 0.00 37.14 4.70


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

AutoCloner maintained by Alex Coulton.