Multiple sequence alignment - TraesCS3D01G135500

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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 TraesCS3D01G135500 chr3D 100.000 6550 0 0 834 7383 94508384 94514933 0.000000e+00 12096.0
1 TraesCS3D01G135500 chr3D 82.636 956 133 19 6429 7383 94746296 94745373 0.000000e+00 815.0
2 TraesCS3D01G135500 chr3D 100.000 303 0 0 1 303 94507551 94507853 1.800000e-155 560.0
3 TraesCS3D01G135500 chr3D 74.824 425 74 18 4922 5329 93024074 93024482 2.130000e-35 161.0
4 TraesCS3D01G135500 chr3A 97.482 4925 93 17 1414 6327 547934791 547939695 0.000000e+00 8379.0
5 TraesCS3D01G135500 chr3A 89.087 843 59 13 6548 7383 547977711 547978527 0.000000e+00 1016.0
6 TraesCS3D01G135500 chr3A 95.573 497 11 7 846 1337 547934302 547934792 0.000000e+00 785.0
7 TraesCS3D01G135500 chr3A 90.381 551 33 12 3882 4427 25380885 25380350 0.000000e+00 706.0
8 TraesCS3D01G135500 chr3A 90.381 551 33 10 3882 4427 25396039 25395504 0.000000e+00 706.0
9 TraesCS3D01G135500 chr3A 90.461 304 20 2 7081 7381 547981815 547982112 6.940000e-105 392.0
10 TraesCS3D01G135500 chr3A 93.382 136 6 1 7063 7195 547940007 547940142 1.620000e-46 198.0
11 TraesCS3D01G135500 chr3A 91.538 130 8 2 6429 6555 547942679 547942808 7.610000e-40 176.0
12 TraesCS3D01G135500 chr3A 84.615 182 20 6 117 291 547933489 547933669 2.740000e-39 174.0
13 TraesCS3D01G135500 chr3A 88.710 124 9 4 1 123 732663377 732663496 5.970000e-31 147.0
14 TraesCS3D01G135500 chr3A 83.735 166 12 7 6790 6947 547939848 547940006 7.720000e-30 143.0
15 TraesCS3D01G135500 chr3A 90.741 108 6 3 3 106 745172474 745172367 2.780000e-29 141.0
16 TraesCS3D01G135500 chr3B 92.637 2893 151 33 3744 6597 145314695 145317564 0.000000e+00 4106.0
17 TraesCS3D01G135500 chr3B 91.771 2868 162 35 857 3688 145311652 145314481 0.000000e+00 3921.0
18 TraesCS3D01G135500 chr3B 89.801 804 55 5 6595 7383 145317752 145318543 0.000000e+00 1005.0
19 TraesCS3D01G135500 chr3B 80.952 84 14 2 5248 5329 143282852 143282935 1.720000e-06 65.8
20 TraesCS3D01G135500 chr3B 80.952 84 14 2 5248 5329 143294356 143294273 1.720000e-06 65.8
21 TraesCS3D01G135500 chr4A 90.926 551 30 10 3882 4427 319829698 319829163 0.000000e+00 723.0
22 TraesCS3D01G135500 chr4A 90.909 550 30 10 3883 4427 488538314 488537780 0.000000e+00 721.0
23 TraesCS3D01G135500 chr4A 89.009 555 36 12 3884 4426 538889674 538889133 0.000000e+00 664.0
24 TraesCS3D01G135500 chrUn 100.000 390 0 0 3421 3810 480013373 480012984 0.000000e+00 721.0
25 TraesCS3D01G135500 chr7A 90.744 551 31 10 3882 4427 439796358 439795823 0.000000e+00 717.0
26 TraesCS3D01G135500 chr2A 90.018 551 35 10 3882 4427 733337286 733337821 0.000000e+00 695.0
27 TraesCS3D01G135500 chr5B 88.355 541 48 7 3889 4424 24681665 24682195 2.910000e-178 636.0
28 TraesCS3D01G135500 chr6B 89.305 374 24 7 4058 4427 616935179 616934818 8.730000e-124 455.0
29 TraesCS3D01G135500 chr4D 96.364 110 4 0 1 110 408395684 408395793 1.640000e-41 182.0
30 TraesCS3D01G135500 chr4D 93.878 98 4 2 1 97 342306235 342306139 5.970000e-31 147.0
31 TraesCS3D01G135500 chr2D 96.907 97 3 0 27 123 28885125 28885221 5.930000e-36 163.0
32 TraesCS3D01G135500 chr2D 91.429 105 9 0 1 105 625784775 625784671 2.150000e-30 145.0
33 TraesCS3D01G135500 chr2D 90.476 105 10 0 1 105 625768524 625768420 9.990000e-29 139.0
34 TraesCS3D01G135500 chr7D 93.204 103 7 0 1 103 306293324 306293426 1.280000e-32 152.0
35 TraesCS3D01G135500 chr5A 91.262 103 8 1 1 103 554333027 554333128 9.990000e-29 139.0


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 TraesCS3D01G135500 chr3D 94507551 94514933 7382 False 6328.000000 12096 100.000000 1 7383 2 chr3D.!!$F2 7382
1 TraesCS3D01G135500 chr3D 94745373 94746296 923 True 815.000000 815 82.636000 6429 7383 1 chr3D.!!$R1 954
2 TraesCS3D01G135500 chr3A 547933489 547942808 9319 False 1642.500000 8379 91.054167 117 7195 6 chr3A.!!$F2 7078
3 TraesCS3D01G135500 chr3A 25380350 25380885 535 True 706.000000 706 90.381000 3882 4427 1 chr3A.!!$R1 545
4 TraesCS3D01G135500 chr3A 25395504 25396039 535 True 706.000000 706 90.381000 3882 4427 1 chr3A.!!$R2 545
5 TraesCS3D01G135500 chr3A 547977711 547982112 4401 False 704.000000 1016 89.774000 6548 7383 2 chr3A.!!$F3 835
6 TraesCS3D01G135500 chr3B 145311652 145318543 6891 False 3010.666667 4106 91.403000 857 7383 3 chr3B.!!$F2 6526
7 TraesCS3D01G135500 chr4A 319829163 319829698 535 True 723.000000 723 90.926000 3882 4427 1 chr4A.!!$R1 545
8 TraesCS3D01G135500 chr4A 488537780 488538314 534 True 721.000000 721 90.909000 3883 4427 1 chr4A.!!$R2 544
9 TraesCS3D01G135500 chr4A 538889133 538889674 541 True 664.000000 664 89.009000 3884 4426 1 chr4A.!!$R3 542
10 TraesCS3D01G135500 chr7A 439795823 439796358 535 True 717.000000 717 90.744000 3882 4427 1 chr7A.!!$R1 545
11 TraesCS3D01G135500 chr2A 733337286 733337821 535 False 695.000000 695 90.018000 3882 4427 1 chr2A.!!$F1 545
12 TraesCS3D01G135500 chr5B 24681665 24682195 530 False 636.000000 636 88.355000 3889 4424 1 chr5B.!!$F1 535

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
193 194 0.248784 ATAGGCCTTTCGTACGTCGC 60.249 55.000 12.58 11.89 39.67 5.19 F
1289 1381 0.744771 CTAAGCAAGCCCGGAAGTCC 60.745 60.000 0.73 0.00 0.00 3.85 F
1371 1463 0.460109 CATCTCGCCGACATGGTTCA 60.460 55.000 0.00 0.00 41.21 3.18 F
1377 1469 1.003355 CCGACATGGTTCAGGCAGT 60.003 57.895 0.00 0.00 0.00 4.40 F
1378 1470 1.300971 CCGACATGGTTCAGGCAGTG 61.301 60.000 0.00 0.00 0.00 3.66 F
1697 1806 1.419922 CGAAGTTTCGCATGACCCG 59.580 57.895 0.00 0.00 44.26 5.28 F
2598 2712 3.263425 CCTGGCTTAGTGGTTTTCCTCTA 59.737 47.826 0.00 0.00 42.80 2.43 F
4633 4980 0.747283 CCTGCTGGCATCTGAGAACC 60.747 60.000 0.00 0.00 0.00 3.62 F
6229 6586 0.036388 GATGTGTGTGTCGATGGGGT 60.036 55.000 0.00 0.00 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1431 0.677731 CGAGATGCTTCTTGCCCCAA 60.678 55.000 3.29 0.00 42.00 4.12 R
2326 2435 2.041701 AGTGGGTTTCTTTGCATTGCT 58.958 42.857 10.49 0.00 0.00 3.91 R
2921 3036 5.026790 AGGTTATGTAGAAAGCTGGAGTCT 58.973 41.667 0.00 0.00 33.62 3.24 R
2940 3055 5.140454 AGCATAGAAGTTGTTTTCCAGGTT 58.860 37.500 0.00 0.00 0.00 3.50 R
3908 4208 2.931969 TGATGCTTCATGAACAGCTACG 59.068 45.455 17.93 3.09 36.92 3.51 R
4633 4980 0.957395 ACCGGAATGAGCAACTGCAG 60.957 55.000 13.48 13.48 45.16 4.41 R
5402 5751 2.350772 CCAGTCCACAAATTCGAAGCAC 60.351 50.000 3.35 0.00 0.00 4.40 R
6350 6802 0.028770 CGCAACGGTTTTCAGCAAGA 59.971 50.000 0.00 0.00 0.00 3.02 R
7132 7803 1.058404 GTGGTGCTCGTCGTAAACTC 58.942 55.000 0.00 0.00 0.00 3.01 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
28 29 4.622364 ACGAAGTGGACGAACGAC 57.378 55.556 0.14 0.00 42.51 4.34
29 30 1.369689 ACGAAGTGGACGAACGACG 60.370 57.895 0.14 0.00 42.51 5.12
30 31 2.722130 ACGAAGTGGACGAACGACGG 62.722 60.000 0.00 0.00 43.80 4.79
42 43 4.030821 CGACGGACGGACCAAAAA 57.969 55.556 0.00 0.00 38.90 1.94
43 44 1.566077 CGACGGACGGACCAAAAAC 59.434 57.895 0.00 0.00 38.90 2.43
44 45 1.566077 GACGGACGGACCAAAAACG 59.434 57.895 0.00 0.00 38.90 3.60
45 46 1.834458 GACGGACGGACCAAAAACGG 61.834 60.000 0.00 0.00 38.90 4.44
46 47 1.594836 CGGACGGACCAAAAACGGA 60.595 57.895 0.00 0.00 38.90 4.69
47 48 1.834458 CGGACGGACCAAAAACGGAC 61.834 60.000 0.00 0.00 38.90 4.79
48 49 1.566077 GACGGACCAAAAACGGACG 59.434 57.895 0.00 0.00 36.51 4.79
49 50 0.875474 GACGGACCAAAAACGGACGA 60.875 55.000 0.00 0.00 35.19 4.20
50 51 0.461693 ACGGACCAAAAACGGACGAA 60.462 50.000 0.00 0.00 35.19 3.85
51 52 0.656785 CGGACCAAAAACGGACGAAA 59.343 50.000 0.00 0.00 33.78 3.46
52 53 1.264826 CGGACCAAAAACGGACGAAAT 59.735 47.619 0.00 0.00 33.78 2.17
53 54 2.287129 CGGACCAAAAACGGACGAAATT 60.287 45.455 0.00 0.00 33.78 1.82
54 55 3.059051 CGGACCAAAAACGGACGAAATTA 60.059 43.478 0.00 0.00 33.78 1.40
55 56 4.221342 GGACCAAAAACGGACGAAATTAC 58.779 43.478 0.00 0.00 0.00 1.89
56 57 3.875884 ACCAAAAACGGACGAAATTACG 58.124 40.909 0.00 0.00 39.31 3.18
57 58 3.227948 CCAAAAACGGACGAAATTACGG 58.772 45.455 0.00 0.00 37.61 4.02
58 59 3.303924 CCAAAAACGGACGAAATTACGGT 60.304 43.478 0.00 0.00 37.61 4.83
59 60 3.524763 AAAACGGACGAAATTACGGTG 57.475 42.857 0.00 0.00 37.61 4.94
60 61 1.431496 AACGGACGAAATTACGGTGG 58.569 50.000 0.00 0.00 37.61 4.61
61 62 0.318120 ACGGACGAAATTACGGTGGT 59.682 50.000 0.00 0.00 37.61 4.16
62 63 1.543802 ACGGACGAAATTACGGTGGTA 59.456 47.619 0.00 0.00 37.61 3.25
63 64 2.029470 ACGGACGAAATTACGGTGGTAA 60.029 45.455 0.00 0.00 42.48 2.85
64 65 2.599973 CGGACGAAATTACGGTGGTAAG 59.400 50.000 0.00 0.00 41.64 2.34
65 66 3.673052 CGGACGAAATTACGGTGGTAAGA 60.673 47.826 0.00 0.00 41.64 2.10
66 67 4.244862 GGACGAAATTACGGTGGTAAGAA 58.755 43.478 0.00 0.00 41.64 2.52
67 68 4.328169 GGACGAAATTACGGTGGTAAGAAG 59.672 45.833 0.00 0.00 41.64 2.85
68 69 3.681417 ACGAAATTACGGTGGTAAGAAGC 59.319 43.478 0.00 0.00 41.64 3.86
69 70 3.680937 CGAAATTACGGTGGTAAGAAGCA 59.319 43.478 0.00 0.00 41.64 3.91
70 71 4.152759 CGAAATTACGGTGGTAAGAAGCAA 59.847 41.667 0.00 0.00 41.64 3.91
71 72 5.163794 CGAAATTACGGTGGTAAGAAGCAAT 60.164 40.000 0.00 0.00 41.64 3.56
72 73 6.036300 CGAAATTACGGTGGTAAGAAGCAATA 59.964 38.462 0.00 0.00 41.64 1.90
73 74 7.413219 CGAAATTACGGTGGTAAGAAGCAATAA 60.413 37.037 0.00 0.00 41.64 1.40
74 75 6.673154 ATTACGGTGGTAAGAAGCAATAAC 57.327 37.500 0.00 0.00 41.64 1.89
75 76 3.340928 ACGGTGGTAAGAAGCAATAACC 58.659 45.455 0.00 0.00 34.25 2.85
76 77 2.681344 CGGTGGTAAGAAGCAATAACCC 59.319 50.000 0.00 0.00 34.25 4.11
77 78 3.021695 GGTGGTAAGAAGCAATAACCCC 58.978 50.000 0.00 0.00 34.25 4.95
78 79 3.308904 GGTGGTAAGAAGCAATAACCCCT 60.309 47.826 0.00 0.00 34.25 4.79
79 80 4.341487 GTGGTAAGAAGCAATAACCCCTT 58.659 43.478 0.00 0.00 34.25 3.95
80 81 4.770531 GTGGTAAGAAGCAATAACCCCTTT 59.229 41.667 0.00 0.00 34.25 3.11
81 82 5.947566 GTGGTAAGAAGCAATAACCCCTTTA 59.052 40.000 0.00 0.00 34.25 1.85
82 83 6.605995 GTGGTAAGAAGCAATAACCCCTTTAT 59.394 38.462 0.00 0.00 34.25 1.40
83 84 7.123697 GTGGTAAGAAGCAATAACCCCTTTATT 59.876 37.037 0.00 0.00 40.47 1.40
84 85 8.337739 TGGTAAGAAGCAATAACCCCTTTATTA 58.662 33.333 0.00 0.00 38.17 0.98
85 86 8.847196 GGTAAGAAGCAATAACCCCTTTATTAG 58.153 37.037 0.00 0.00 38.17 1.73
86 87 9.404848 GTAAGAAGCAATAACCCCTTTATTAGT 57.595 33.333 0.00 0.00 38.17 2.24
88 89 9.628500 AAGAAGCAATAACCCCTTTATTAGTAG 57.372 33.333 0.00 0.00 38.17 2.57
89 90 8.218488 AGAAGCAATAACCCCTTTATTAGTAGG 58.782 37.037 0.00 0.00 38.17 3.18
90 91 7.461633 AGCAATAACCCCTTTATTAGTAGGT 57.538 36.000 0.00 0.00 38.17 3.08
91 92 8.571460 AGCAATAACCCCTTTATTAGTAGGTA 57.429 34.615 0.00 0.00 38.17 3.08
92 93 9.179104 AGCAATAACCCCTTTATTAGTAGGTAT 57.821 33.333 0.00 0.00 38.17 2.73
170 171 4.156556 TCTTGGCTGAAATGTGCATAACTC 59.843 41.667 0.00 0.00 0.00 3.01
182 183 4.283467 TGTGCATAACTCGATATAGGCCTT 59.717 41.667 12.58 0.81 0.00 4.35
184 185 5.348997 GTGCATAACTCGATATAGGCCTTTC 59.651 44.000 12.58 5.17 0.00 2.62
185 186 4.563184 GCATAACTCGATATAGGCCTTTCG 59.437 45.833 12.58 17.90 0.00 3.46
186 187 5.710984 CATAACTCGATATAGGCCTTTCGT 58.289 41.667 23.47 12.76 33.52 3.85
187 188 6.624423 GCATAACTCGATATAGGCCTTTCGTA 60.624 42.308 23.47 14.04 33.52 3.43
189 190 3.188048 ACTCGATATAGGCCTTTCGTACG 59.812 47.826 23.47 9.53 33.52 3.67
191 192 3.187227 TCGATATAGGCCTTTCGTACGTC 59.813 47.826 23.47 0.00 33.52 4.34
192 193 3.486584 GATATAGGCCTTTCGTACGTCG 58.513 50.000 12.58 4.79 41.41 5.12
193 194 0.248784 ATAGGCCTTTCGTACGTCGC 60.249 55.000 12.58 11.89 39.67 5.19
194 195 2.582202 TAGGCCTTTCGTACGTCGCG 62.582 60.000 12.58 0.00 39.67 5.87
195 196 4.187498 GCCTTTCGTACGTCGCGC 62.187 66.667 16.05 9.52 39.67 6.86
196 197 2.503375 CCTTTCGTACGTCGCGCT 60.503 61.111 16.05 0.00 39.67 5.92
199 200 1.984351 CTTTCGTACGTCGCGCTCAC 61.984 60.000 16.05 0.24 39.67 3.51
200 201 2.714303 TTTCGTACGTCGCGCTCACA 62.714 55.000 16.05 0.00 39.67 3.58
201 202 3.521220 CGTACGTCGCGCTCACAC 61.521 66.667 7.22 0.00 0.00 3.82
202 203 3.170585 GTACGTCGCGCTCACACC 61.171 66.667 5.56 0.00 0.00 4.16
204 205 3.884581 TACGTCGCGCTCACACCAC 62.885 63.158 5.56 0.00 0.00 4.16
235 240 4.566004 CGTTCTTTCAAGGACCTATGACA 58.434 43.478 0.00 0.00 30.37 3.58
259 264 1.801178 CGTTTTGTCAGAAGAGGAGCC 59.199 52.381 0.00 0.00 0.00 4.70
274 279 4.132999 GCCGGAAGCTTCTGATCC 57.867 61.111 32.53 17.89 38.99 3.36
278 283 1.147153 GGAAGCTTCTGATCCGGGG 59.853 63.158 25.05 0.00 0.00 5.73
283 288 1.090052 GCTTCTGATCCGGGGTTTCG 61.090 60.000 0.00 0.00 0.00 3.46
284 289 1.078708 TTCTGATCCGGGGTTTCGC 60.079 57.895 0.00 0.00 0.00 4.70
865 948 1.079127 GCGAGCTTGGAGTGGCTAA 60.079 57.895 2.37 0.00 39.05 3.09
902 985 3.866582 GCGGCCTGCCTAGTCCAT 61.867 66.667 6.60 0.00 37.76 3.41
903 986 2.507854 GCGGCCTGCCTAGTCCATA 61.508 63.158 6.60 0.00 37.76 2.74
1289 1381 0.744771 CTAAGCAAGCCCGGAAGTCC 60.745 60.000 0.73 0.00 0.00 3.85
1339 1431 1.606737 GCGAAGTGTCTCTTGCCTTCT 60.607 52.381 0.00 0.00 36.40 2.85
1341 1433 2.478134 CGAAGTGTCTCTTGCCTTCTTG 59.522 50.000 0.00 0.00 36.40 3.02
1362 1454 1.811266 GCAAGAAGCATCTCGCCGA 60.811 57.895 0.00 0.00 44.04 5.54
1370 1462 1.766143 GCATCTCGCCGACATGGTTC 61.766 60.000 4.54 0.00 41.21 3.62
1371 1463 0.460109 CATCTCGCCGACATGGTTCA 60.460 55.000 0.00 0.00 41.21 3.18
1373 1465 1.811266 CTCGCCGACATGGTTCAGG 60.811 63.158 0.00 0.00 41.21 3.86
1374 1466 3.499737 CGCCGACATGGTTCAGGC 61.500 66.667 0.00 3.44 44.00 4.85
1375 1467 2.359850 GCCGACATGGTTCAGGCA 60.360 61.111 12.20 0.00 46.48 4.75
1376 1468 2.401766 GCCGACATGGTTCAGGCAG 61.402 63.158 12.20 0.00 46.48 4.85
1377 1469 1.003355 CCGACATGGTTCAGGCAGT 60.003 57.895 0.00 0.00 0.00 4.40
1378 1470 1.300971 CCGACATGGTTCAGGCAGTG 61.301 60.000 0.00 0.00 0.00 3.66
1379 1471 1.878775 GACATGGTTCAGGCAGTGC 59.121 57.895 6.55 6.55 0.00 4.40
1395 1488 2.104530 GCTAGGTCGAGCCGGTTC 59.895 66.667 11.73 8.48 43.70 3.62
1425 1518 9.082313 AGTTTAACAGTAAGCTGGTACTAGTAA 57.918 33.333 3.61 0.00 43.91 2.24
1562 1658 8.169268 CGAAACTTAGGCAGTAACTTGAAATAG 58.831 37.037 0.00 0.00 32.94 1.73
1697 1806 1.419922 CGAAGTTTCGCATGACCCG 59.580 57.895 0.00 0.00 44.26 5.28
1757 1866 4.719369 GGCGCTCTGGACGTTCGT 62.719 66.667 7.64 0.00 0.00 3.85
1990 2099 9.911788 AATCACTCATGACAATTATAGAAGGTT 57.088 29.630 0.00 0.00 37.79 3.50
2225 2334 8.450578 TTGAAGATGGTGATATGGTTATTGAC 57.549 34.615 0.00 0.00 0.00 3.18
2598 2712 3.263425 CCTGGCTTAGTGGTTTTCCTCTA 59.737 47.826 0.00 0.00 42.80 2.43
2921 3036 5.923204 ACCATTTTGCACTGGAAAAATACA 58.077 33.333 11.90 0.00 39.72 2.29
2940 3055 7.661536 AATACAGACTCCAGCTTTCTACATA 57.338 36.000 0.00 0.00 0.00 2.29
2968 3083 7.201679 CCTGGAAAACAACTTCTATGCTATCTG 60.202 40.741 0.00 0.00 0.00 2.90
3810 4110 4.004196 TCAAAACATTTCATGGCATGCA 57.996 36.364 22.56 9.47 33.60 3.96
3814 4114 3.358707 ACATTTCATGGCATGCATACG 57.641 42.857 22.56 11.54 33.60 3.06
3908 4208 5.063944 CACTTTCAGACTGGTACATATGCAC 59.936 44.000 1.58 0.00 38.20 4.57
4087 4418 8.937634 AATGGACATCTTTCTATTTTGCATTC 57.062 30.769 0.00 0.00 0.00 2.67
4633 4980 0.747283 CCTGCTGGCATCTGAGAACC 60.747 60.000 0.00 0.00 0.00 3.62
4680 5027 9.784531 TTGTCTATTTGTTTCTCTCTCTCAATT 57.215 29.630 0.00 0.00 0.00 2.32
5423 5772 1.879380 TGCTTCGAATTTGTGGACTGG 59.121 47.619 0.00 0.00 0.00 4.00
5593 5942 2.503331 CTGGGCAATCTGTGTGTTGTA 58.497 47.619 0.00 0.00 0.00 2.41
5608 5957 2.038033 TGTTGTACCAGCAGGAAGTACC 59.962 50.000 0.35 0.00 36.38 3.34
5756 6105 0.179054 GGTGAGGGAATCTTACCGCC 60.179 60.000 0.00 0.00 41.41 6.13
5762 6112 4.019141 TGAGGGAATCTTACCGCCTTTTAA 60.019 41.667 0.00 0.00 35.82 1.52
5790 6140 5.461327 TCCTATCTCATTTACTAACCCGGT 58.539 41.667 0.00 0.00 0.00 5.28
5793 6143 5.952347 ATCTCATTTACTAACCCGGTTCT 57.048 39.130 5.94 0.00 0.00 3.01
5795 6145 6.855763 TCTCATTTACTAACCCGGTTCTTA 57.144 37.500 5.94 0.00 0.00 2.10
5796 6146 6.633856 TCTCATTTACTAACCCGGTTCTTAC 58.366 40.000 5.94 0.00 0.00 2.34
5797 6147 6.211184 TCTCATTTACTAACCCGGTTCTTACA 59.789 38.462 5.94 0.00 0.00 2.41
5798 6148 6.400568 TCATTTACTAACCCGGTTCTTACAG 58.599 40.000 5.94 0.48 0.00 2.74
5799 6149 5.806654 TTTACTAACCCGGTTCTTACAGT 57.193 39.130 5.94 6.98 0.00 3.55
5801 6151 4.790765 ACTAACCCGGTTCTTACAGTAC 57.209 45.455 5.94 0.00 0.00 2.73
5802 6152 4.411013 ACTAACCCGGTTCTTACAGTACT 58.589 43.478 5.94 0.00 0.00 2.73
5806 6156 4.635223 ACCCGGTTCTTACAGTACTTTTC 58.365 43.478 0.00 0.00 0.00 2.29
5807 6157 4.101430 ACCCGGTTCTTACAGTACTTTTCA 59.899 41.667 0.00 0.00 0.00 2.69
5810 6160 6.206048 CCCGGTTCTTACAGTACTTTTCAAAT 59.794 38.462 0.00 0.00 0.00 2.32
5831 6181 8.397906 TCAAATGTAAACTGTCTCTTCAAGTTG 58.602 33.333 0.00 0.00 0.00 3.16
5833 6183 3.951979 AAACTGTCTCTTCAAGTTGCG 57.048 42.857 0.00 0.00 0.00 4.85
5835 6185 2.205074 ACTGTCTCTTCAAGTTGCGTG 58.795 47.619 0.00 0.00 0.00 5.34
5836 6186 2.205074 CTGTCTCTTCAAGTTGCGTGT 58.795 47.619 0.00 0.00 0.00 4.49
5837 6187 1.933181 TGTCTCTTCAAGTTGCGTGTG 59.067 47.619 0.00 0.00 0.00 3.82
5838 6188 1.261619 GTCTCTTCAAGTTGCGTGTGG 59.738 52.381 0.00 0.00 0.00 4.17
5839 6189 0.588252 CTCTTCAAGTTGCGTGTGGG 59.412 55.000 0.00 0.00 0.00 4.61
5843 6193 1.821759 CAAGTTGCGTGTGGGTGGA 60.822 57.895 0.00 0.00 0.00 4.02
5852 6205 1.134936 CGTGTGGGTGGATGTATCGAA 60.135 52.381 0.00 0.00 0.00 3.71
5856 6209 3.944650 TGTGGGTGGATGTATCGAATTTG 59.055 43.478 0.00 0.00 0.00 2.32
5857 6210 3.315191 GTGGGTGGATGTATCGAATTTGG 59.685 47.826 0.00 0.00 0.00 3.28
5859 6212 4.204012 GGGTGGATGTATCGAATTTGGAA 58.796 43.478 0.00 0.00 0.00 3.53
5860 6213 4.275936 GGGTGGATGTATCGAATTTGGAAG 59.724 45.833 0.00 0.00 0.00 3.46
5861 6214 4.881850 GGTGGATGTATCGAATTTGGAAGT 59.118 41.667 0.00 0.00 0.00 3.01
5863 6216 6.540914 GGTGGATGTATCGAATTTGGAAGTTA 59.459 38.462 0.00 0.00 0.00 2.24
5864 6217 7.407337 GTGGATGTATCGAATTTGGAAGTTAC 58.593 38.462 0.00 0.00 0.00 2.50
5865 6218 7.065324 GTGGATGTATCGAATTTGGAAGTTACA 59.935 37.037 0.00 0.00 0.00 2.41
5866 6219 7.773224 TGGATGTATCGAATTTGGAAGTTACAT 59.227 33.333 6.09 6.09 34.27 2.29
5873 6226 8.036273 TCGAATTTGGAAGTTACATTTAGACC 57.964 34.615 0.00 0.00 0.00 3.85
5877 6230 6.887626 TTGGAAGTTACATTTAGACCCAAC 57.112 37.500 0.00 0.00 0.00 3.77
5878 6231 6.195600 TGGAAGTTACATTTAGACCCAACT 57.804 37.500 0.00 0.00 0.00 3.16
5895 6252 3.191371 CCAACTTACCATCTTTGCAGGTC 59.809 47.826 0.00 0.00 36.87 3.85
5904 6261 0.329261 CTTTGCAGGTCATGAGGGGA 59.671 55.000 0.00 0.00 0.00 4.81
5907 6264 1.131638 TGCAGGTCATGAGGGGATAC 58.868 55.000 0.00 0.00 0.00 2.24
6045 6402 1.033746 ACTTCGGCGAGGATTACGGA 61.034 55.000 26.26 0.00 0.00 4.69
6229 6586 0.036388 GATGTGTGTGTCGATGGGGT 60.036 55.000 0.00 0.00 0.00 4.95
6350 6802 7.217200 TGTACTAGAGAAATGCTGTTCAAACT 58.783 34.615 0.00 0.00 0.00 2.66
6393 6845 3.423539 AGCTTTGCATAGTTCCACAGA 57.576 42.857 6.03 0.00 0.00 3.41
6448 6901 8.237949 TCCTTTGCAAAATCGATATTTAACGAA 58.762 29.630 13.84 3.90 41.65 3.85
6453 6906 7.136119 GCAAAATCGATATTTAACGAATCCCA 58.864 34.615 0.00 0.00 41.65 4.37
6481 6934 4.214980 AGATGCAGAAAACAACGTTGAG 57.785 40.909 33.66 15.88 0.00 3.02
6533 6986 1.140652 TGCGGGCATCAATATCACAGA 59.859 47.619 0.00 0.00 0.00 3.41
6597 7050 0.470341 TGGTTCCACGTTCCATGTCA 59.530 50.000 0.00 0.00 0.00 3.58
6600 7053 3.244596 TGGTTCCACGTTCCATGTCATAA 60.245 43.478 0.00 0.00 0.00 1.90
6629 7272 1.671054 CCTTTTCTCCGCGCCTCAA 60.671 57.895 0.00 0.00 0.00 3.02
6657 7300 1.761174 GCAGTTCCCCTTGAGACCA 59.239 57.895 0.00 0.00 0.00 4.02
6661 7304 0.035915 GTTCCCCTTGAGACCAGCTC 60.036 60.000 0.00 0.00 44.21 4.09
6807 7453 0.320683 TGTCACACCGCTCCATCAAG 60.321 55.000 0.00 0.00 0.00 3.02
6883 7533 2.438975 AGACGCGGTACATCGGGA 60.439 61.111 12.47 0.00 44.22 5.14
6888 7538 2.649034 CGGTACATCGGGATCGGG 59.351 66.667 0.00 0.00 36.95 5.14
6995 7651 2.181021 CGCGTAGAACTTCCCGCT 59.819 61.111 16.79 0.00 43.70 5.52
7221 7892 0.677098 TCGTGAGGAACCTCTCTCGG 60.677 60.000 19.61 6.29 45.27 4.63
7243 7914 2.506472 GGGGCAGGTCGATTCTCC 59.494 66.667 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.377928 CGTTCGTCCACTTCGTCTATATTATTT 59.622 37.037 0.00 0.00 0.00 1.40
2 3 6.203530 TCGTTCGTCCACTTCGTCTATATTAT 59.796 38.462 0.00 0.00 0.00 1.28
3 4 5.523552 TCGTTCGTCCACTTCGTCTATATTA 59.476 40.000 0.00 0.00 0.00 0.98
4 5 4.333649 TCGTTCGTCCACTTCGTCTATATT 59.666 41.667 0.00 0.00 0.00 1.28
5 6 3.873361 TCGTTCGTCCACTTCGTCTATAT 59.127 43.478 0.00 0.00 0.00 0.86
6 7 3.062639 GTCGTTCGTCCACTTCGTCTATA 59.937 47.826 0.00 0.00 0.00 1.31
7 8 2.079158 TCGTTCGTCCACTTCGTCTAT 58.921 47.619 0.00 0.00 0.00 1.98
8 9 1.195448 GTCGTTCGTCCACTTCGTCTA 59.805 52.381 0.00 0.00 0.00 2.59
9 10 0.040603 GTCGTTCGTCCACTTCGTCT 60.041 55.000 0.00 0.00 0.00 4.18
10 11 1.325904 CGTCGTTCGTCCACTTCGTC 61.326 60.000 0.00 0.00 34.52 4.20
11 12 1.369689 CGTCGTTCGTCCACTTCGT 60.370 57.895 0.00 0.00 34.52 3.85
12 13 2.078914 CCGTCGTTCGTCCACTTCG 61.079 63.158 0.00 0.00 37.94 3.79
13 14 1.000736 GTCCGTCGTTCGTCCACTTC 61.001 60.000 0.00 0.00 37.94 3.01
14 15 1.008079 GTCCGTCGTTCGTCCACTT 60.008 57.895 0.00 0.00 37.94 3.16
15 16 2.641559 GTCCGTCGTTCGTCCACT 59.358 61.111 0.00 0.00 37.94 4.00
16 17 2.798262 CGTCCGTCGTTCGTCCAC 60.798 66.667 0.00 0.00 37.94 4.02
17 18 4.029186 CCGTCCGTCGTTCGTCCA 62.029 66.667 0.00 0.00 37.94 4.02
18 19 3.726517 TCCGTCCGTCGTTCGTCC 61.727 66.667 0.00 0.00 37.94 4.79
19 20 2.500582 GTCCGTCCGTCGTTCGTC 60.501 66.667 0.00 0.00 37.94 4.20
20 21 4.030452 GGTCCGTCCGTCGTTCGT 62.030 66.667 0.00 0.00 37.94 3.85
21 22 3.541093 TTGGTCCGTCCGTCGTTCG 62.541 63.158 0.00 0.00 39.52 3.95
22 23 0.875474 TTTTGGTCCGTCCGTCGTTC 60.875 55.000 0.00 0.00 39.52 3.95
23 24 0.461693 TTTTTGGTCCGTCCGTCGTT 60.462 50.000 0.00 0.00 39.52 3.85
24 25 1.143620 TTTTTGGTCCGTCCGTCGT 59.856 52.632 0.00 0.00 39.52 4.34
25 26 1.566077 GTTTTTGGTCCGTCCGTCG 59.434 57.895 0.00 0.00 39.52 5.12
26 27 1.566077 CGTTTTTGGTCCGTCCGTC 59.434 57.895 0.00 0.00 39.52 4.79
27 28 1.888638 CCGTTTTTGGTCCGTCCGT 60.889 57.895 0.00 0.00 39.52 4.69
28 29 1.594836 TCCGTTTTTGGTCCGTCCG 60.595 57.895 0.00 0.00 39.52 4.79
29 30 1.834458 CGTCCGTTTTTGGTCCGTCC 61.834 60.000 0.00 0.00 0.00 4.79
30 31 0.875474 TCGTCCGTTTTTGGTCCGTC 60.875 55.000 0.00 0.00 0.00 4.79
31 32 0.461693 TTCGTCCGTTTTTGGTCCGT 60.462 50.000 0.00 0.00 0.00 4.69
32 33 0.656785 TTTCGTCCGTTTTTGGTCCG 59.343 50.000 0.00 0.00 0.00 4.79
33 34 3.358707 AATTTCGTCCGTTTTTGGTCC 57.641 42.857 0.00 0.00 0.00 4.46
34 35 3.901877 CGTAATTTCGTCCGTTTTTGGTC 59.098 43.478 0.00 0.00 0.00 4.02
35 36 3.303924 CCGTAATTTCGTCCGTTTTTGGT 60.304 43.478 3.73 0.00 0.00 3.67
36 37 3.227948 CCGTAATTTCGTCCGTTTTTGG 58.772 45.455 3.73 0.00 0.00 3.28
37 38 3.660356 CACCGTAATTTCGTCCGTTTTTG 59.340 43.478 3.73 0.00 0.00 2.44
38 39 3.303924 CCACCGTAATTTCGTCCGTTTTT 60.304 43.478 3.73 0.00 0.00 1.94
39 40 2.223845 CCACCGTAATTTCGTCCGTTTT 59.776 45.455 3.73 0.00 0.00 2.43
40 41 1.799994 CCACCGTAATTTCGTCCGTTT 59.200 47.619 3.73 0.00 0.00 3.60
41 42 1.270252 ACCACCGTAATTTCGTCCGTT 60.270 47.619 3.73 0.00 0.00 4.44
42 43 0.318120 ACCACCGTAATTTCGTCCGT 59.682 50.000 3.73 0.00 0.00 4.69
43 44 2.276472 TACCACCGTAATTTCGTCCG 57.724 50.000 3.73 0.00 0.00 4.79
44 45 3.848726 TCTTACCACCGTAATTTCGTCC 58.151 45.455 3.73 0.00 33.98 4.79
45 46 4.201656 GCTTCTTACCACCGTAATTTCGTC 60.202 45.833 3.73 0.00 33.98 4.20
46 47 3.681417 GCTTCTTACCACCGTAATTTCGT 59.319 43.478 3.73 0.00 33.98 3.85
47 48 3.680937 TGCTTCTTACCACCGTAATTTCG 59.319 43.478 0.00 0.00 33.98 3.46
48 49 5.616488 TTGCTTCTTACCACCGTAATTTC 57.384 39.130 0.00 0.00 33.98 2.17
49 50 7.362315 GGTTATTGCTTCTTACCACCGTAATTT 60.362 37.037 0.00 0.00 33.98 1.82
50 51 6.094464 GGTTATTGCTTCTTACCACCGTAATT 59.906 38.462 0.00 0.00 33.98 1.40
51 52 5.587443 GGTTATTGCTTCTTACCACCGTAAT 59.413 40.000 0.00 0.00 33.98 1.89
52 53 4.937015 GGTTATTGCTTCTTACCACCGTAA 59.063 41.667 0.00 0.00 33.39 3.18
53 54 4.506758 GGTTATTGCTTCTTACCACCGTA 58.493 43.478 0.00 0.00 0.00 4.02
54 55 3.340928 GGTTATTGCTTCTTACCACCGT 58.659 45.455 0.00 0.00 0.00 4.83
55 56 2.681344 GGGTTATTGCTTCTTACCACCG 59.319 50.000 0.00 0.00 0.00 4.94
56 57 3.021695 GGGGTTATTGCTTCTTACCACC 58.978 50.000 0.00 0.00 0.00 4.61
57 58 3.964411 AGGGGTTATTGCTTCTTACCAC 58.036 45.455 0.00 0.00 32.36 4.16
58 59 4.668138 AAGGGGTTATTGCTTCTTACCA 57.332 40.909 0.00 0.00 0.00 3.25
59 60 7.655521 AATAAAGGGGTTATTGCTTCTTACC 57.344 36.000 0.00 0.00 40.27 2.85
60 61 9.404848 ACTAATAAAGGGGTTATTGCTTCTTAC 57.595 33.333 2.35 0.00 41.55 2.34
62 63 9.628500 CTACTAATAAAGGGGTTATTGCTTCTT 57.372 33.333 2.35 0.00 41.55 2.52
63 64 8.218488 CCTACTAATAAAGGGGTTATTGCTTCT 58.782 37.037 2.35 0.00 41.55 2.85
64 65 7.997223 ACCTACTAATAAAGGGGTTATTGCTTC 59.003 37.037 2.35 0.00 41.55 3.86
65 66 7.879558 ACCTACTAATAAAGGGGTTATTGCTT 58.120 34.615 2.35 0.00 41.55 3.91
66 67 7.461633 ACCTACTAATAAAGGGGTTATTGCT 57.538 36.000 2.35 0.00 41.55 3.91
170 171 3.486584 GACGTACGAAAGGCCTATATCG 58.513 50.000 24.41 25.41 40.90 2.92
182 183 2.500369 GTGAGCGCGACGTACGAA 60.500 61.111 24.41 0.00 45.77 3.85
184 185 3.521220 GTGTGAGCGCGACGTACG 61.521 66.667 12.10 15.01 45.66 3.67
185 186 3.170585 GGTGTGAGCGCGACGTAC 61.171 66.667 12.10 2.97 0.00 3.67
186 187 3.662153 TGGTGTGAGCGCGACGTA 61.662 61.111 12.10 0.00 0.00 3.57
192 193 4.643387 AAGGGGTGGTGTGAGCGC 62.643 66.667 0.00 0.00 0.00 5.92
193 194 2.669569 CAAGGGGTGGTGTGAGCG 60.670 66.667 0.00 0.00 0.00 5.03
194 195 1.302832 CTCAAGGGGTGGTGTGAGC 60.303 63.158 0.00 0.00 31.80 4.26
195 196 1.302832 GCTCAAGGGGTGGTGTGAG 60.303 63.158 0.00 0.00 40.40 3.51
196 197 2.836154 GCTCAAGGGGTGGTGTGA 59.164 61.111 0.00 0.00 0.00 3.58
199 200 1.966451 GAACGCTCAAGGGGTGGTG 60.966 63.158 0.00 0.00 41.04 4.17
200 201 1.705997 AAGAACGCTCAAGGGGTGGT 61.706 55.000 0.00 0.00 41.04 4.16
201 202 0.537371 AAAGAACGCTCAAGGGGTGG 60.537 55.000 0.00 0.00 41.04 4.61
202 203 0.875059 GAAAGAACGCTCAAGGGGTG 59.125 55.000 0.00 0.00 41.04 4.61
204 205 1.537202 CTTGAAAGAACGCTCAAGGGG 59.463 52.381 4.28 0.00 43.15 4.79
205 206 2.977405 CTTGAAAGAACGCTCAAGGG 57.023 50.000 4.28 0.00 43.15 3.95
235 240 4.214332 GCTCCTCTTCTGACAAAACGAAAT 59.786 41.667 0.00 0.00 0.00 2.17
833 838 0.319900 GCTCGCTCACCTGTTTCTCA 60.320 55.000 0.00 0.00 0.00 3.27
865 948 1.674817 CGGCCCATTAACTGTTCTCGT 60.675 52.381 0.00 0.00 0.00 4.18
898 981 1.564818 ACGAGAGACCTCACCTATGGA 59.435 52.381 0.00 0.00 39.39 3.41
900 983 2.644676 TCACGAGAGACCTCACCTATG 58.355 52.381 0.00 0.00 39.39 2.23
901 984 3.586470 ATCACGAGAGACCTCACCTAT 57.414 47.619 0.00 0.00 39.39 2.57
902 985 4.708576 ATATCACGAGAGACCTCACCTA 57.291 45.455 0.00 0.00 39.39 3.08
903 986 3.586470 ATATCACGAGAGACCTCACCT 57.414 47.619 0.00 0.00 39.39 4.00
1289 1381 1.142870 TCCTATCCCCGCAATCAAAGG 59.857 52.381 0.00 0.00 0.00 3.11
1339 1431 0.677731 CGAGATGCTTCTTGCCCCAA 60.678 55.000 3.29 0.00 42.00 4.12
1341 1433 3.819188 CGAGATGCTTCTTGCCCC 58.181 61.111 3.29 0.00 42.00 5.80
1362 1454 0.692476 TAGCACTGCCTGAACCATGT 59.308 50.000 0.00 0.00 0.00 3.21
1370 1462 1.140589 CTCGACCTAGCACTGCCTG 59.859 63.158 0.00 0.00 0.00 4.85
1371 1463 2.716017 GCTCGACCTAGCACTGCCT 61.716 63.158 0.00 0.00 42.30 4.75
1373 1465 2.202810 GGCTCGACCTAGCACTGC 60.203 66.667 0.00 0.00 44.64 4.40
1374 1466 2.103143 CGGCTCGACCTAGCACTG 59.897 66.667 0.00 0.00 44.64 3.66
1375 1467 3.141488 CCGGCTCGACCTAGCACT 61.141 66.667 0.00 0.00 44.64 4.40
1376 1468 2.885774 GAACCGGCTCGACCTAGCAC 62.886 65.000 0.00 0.00 44.64 4.40
1377 1469 2.678934 AACCGGCTCGACCTAGCA 60.679 61.111 0.00 0.00 44.64 3.49
1378 1470 2.104530 GAACCGGCTCGACCTAGC 59.895 66.667 0.00 0.00 41.99 3.42
1379 1471 1.651240 TTCGAACCGGCTCGACCTAG 61.651 60.000 28.41 0.00 46.95 3.02
1395 1488 5.668558 ACCAGCTTACTGTTAAACTTTCG 57.331 39.130 0.00 0.00 42.81 3.46
1399 1492 7.536159 ACTAGTACCAGCTTACTGTTAAACT 57.464 36.000 8.13 0.00 42.81 2.66
1562 1658 4.072131 TGGCCAACTATCTTGAACAAGTC 58.928 43.478 0.61 0.00 39.38 3.01
1697 1806 3.179265 CCACACGATCGGTCACGC 61.179 66.667 20.98 0.00 40.69 5.34
1700 1809 1.092348 CTACTCCACACGATCGGTCA 58.908 55.000 20.98 2.92 0.00 4.02
1757 1866 7.994425 TTGTTCAAACCTTAATCATAGAGCA 57.006 32.000 0.00 0.00 0.00 4.26
1876 1985 2.800544 TCGCAGATAAGATTTAAGCGCC 59.199 45.455 2.29 0.00 42.98 6.53
1990 2099 5.067674 GCAAGCTCCCATACAAATATGTTGA 59.932 40.000 0.00 0.00 41.05 3.18
2225 2334 4.997905 TGTTTCAAGATCTGCTTTCTCG 57.002 40.909 0.00 0.00 33.60 4.04
2326 2435 2.041701 AGTGGGTTTCTTTGCATTGCT 58.958 42.857 10.49 0.00 0.00 3.91
2708 2823 7.731054 AGCATAAAAAGGTTGGAAAATACACA 58.269 30.769 0.00 0.00 0.00 3.72
2921 3036 5.026790 AGGTTATGTAGAAAGCTGGAGTCT 58.973 41.667 0.00 0.00 33.62 3.24
2940 3055 5.140454 AGCATAGAAGTTGTTTTCCAGGTT 58.860 37.500 0.00 0.00 0.00 3.50
3908 4208 2.931969 TGATGCTTCATGAACAGCTACG 59.068 45.455 17.93 3.09 36.92 3.51
4633 4980 0.957395 ACCGGAATGAGCAACTGCAG 60.957 55.000 13.48 13.48 45.16 4.41
5167 5516 4.660303 AGGATGATTGGCTAACCTGTGATA 59.340 41.667 0.00 0.00 36.63 2.15
5402 5751 2.350772 CCAGTCCACAAATTCGAAGCAC 60.351 50.000 3.35 0.00 0.00 4.40
5423 5772 3.744660 CCCATGAAGCCTCCTACATAAC 58.255 50.000 0.00 0.00 0.00 1.89
5593 5942 1.889530 GCTCGGTACTTCCTGCTGGT 61.890 60.000 9.73 0.00 33.11 4.00
5608 5957 0.105964 TGATTATGTTCGGGGGCTCG 59.894 55.000 0.00 0.00 0.00 5.03
5762 6112 8.804204 CGGGTTAGTAAATGAGATAGGAATAGT 58.196 37.037 0.00 0.00 0.00 2.12
5780 6130 4.411013 AGTACTGTAAGAACCGGGTTAGT 58.589 43.478 13.38 14.21 37.43 2.24
5795 6145 9.174166 AGACAGTTTACATTTGAAAAGTACTGT 57.826 29.630 16.88 16.88 36.44 3.55
5796 6146 9.651718 GAGACAGTTTACATTTGAAAAGTACTG 57.348 33.333 12.16 12.16 0.00 2.74
5797 6147 9.614792 AGAGACAGTTTACATTTGAAAAGTACT 57.385 29.630 0.00 0.00 0.00 2.73
5801 6151 9.787532 TTGAAGAGACAGTTTACATTTGAAAAG 57.212 29.630 0.00 0.00 0.00 2.27
5802 6152 9.787532 CTTGAAGAGACAGTTTACATTTGAAAA 57.212 29.630 0.00 0.00 0.00 2.29
5806 6156 7.166473 GCAACTTGAAGAGACAGTTTACATTTG 59.834 37.037 0.00 0.00 0.00 2.32
5807 6157 7.196331 GCAACTTGAAGAGACAGTTTACATTT 58.804 34.615 0.00 0.00 0.00 2.32
5810 6160 4.270084 CGCAACTTGAAGAGACAGTTTACA 59.730 41.667 0.00 0.00 0.00 2.41
5831 6181 1.151777 CGATACATCCACCCACACGC 61.152 60.000 0.00 0.00 0.00 5.34
5833 6183 2.684001 TTCGATACATCCACCCACAC 57.316 50.000 0.00 0.00 0.00 3.82
5835 6185 3.315191 CCAAATTCGATACATCCACCCAC 59.685 47.826 0.00 0.00 0.00 4.61
5836 6186 3.201045 TCCAAATTCGATACATCCACCCA 59.799 43.478 0.00 0.00 0.00 4.51
5837 6187 3.815809 TCCAAATTCGATACATCCACCC 58.184 45.455 0.00 0.00 0.00 4.61
5838 6188 4.881850 ACTTCCAAATTCGATACATCCACC 59.118 41.667 0.00 0.00 0.00 4.61
5839 6189 6.436843 AACTTCCAAATTCGATACATCCAC 57.563 37.500 0.00 0.00 0.00 4.02
5852 6205 7.728532 AGTTGGGTCTAAATGTAACTTCCAAAT 59.271 33.333 0.00 0.00 34.17 2.32
5856 6209 7.120285 GGTAAGTTGGGTCTAAATGTAACTTCC 59.880 40.741 0.00 0.00 32.35 3.46
5857 6210 7.662669 TGGTAAGTTGGGTCTAAATGTAACTTC 59.337 37.037 0.00 0.00 32.35 3.01
5859 6212 7.081857 TGGTAAGTTGGGTCTAAATGTAACT 57.918 36.000 0.00 0.00 0.00 2.24
5860 6213 7.827729 AGATGGTAAGTTGGGTCTAAATGTAAC 59.172 37.037 0.00 0.00 0.00 2.50
5861 6214 7.924541 AGATGGTAAGTTGGGTCTAAATGTAA 58.075 34.615 0.00 0.00 0.00 2.41
5863 6216 6.388619 AGATGGTAAGTTGGGTCTAAATGT 57.611 37.500 0.00 0.00 0.00 2.71
5864 6217 7.538575 CAAAGATGGTAAGTTGGGTCTAAATG 58.461 38.462 0.00 0.00 0.00 2.32
5865 6218 6.152831 GCAAAGATGGTAAGTTGGGTCTAAAT 59.847 38.462 0.00 0.00 0.00 1.40
5866 6219 5.475564 GCAAAGATGGTAAGTTGGGTCTAAA 59.524 40.000 0.00 0.00 0.00 1.85
5869 6222 3.181434 TGCAAAGATGGTAAGTTGGGTCT 60.181 43.478 0.00 0.00 0.00 3.85
5870 6223 3.153919 TGCAAAGATGGTAAGTTGGGTC 58.846 45.455 0.00 0.00 0.00 4.46
5871 6224 3.157087 CTGCAAAGATGGTAAGTTGGGT 58.843 45.455 0.00 0.00 0.00 4.51
5872 6225 2.493278 CCTGCAAAGATGGTAAGTTGGG 59.507 50.000 0.00 0.00 0.00 4.12
5873 6226 3.157087 ACCTGCAAAGATGGTAAGTTGG 58.843 45.455 0.00 0.00 31.50 3.77
5877 6230 4.264253 TCATGACCTGCAAAGATGGTAAG 58.736 43.478 0.00 0.00 33.74 2.34
5878 6231 4.264253 CTCATGACCTGCAAAGATGGTAA 58.736 43.478 0.00 0.00 33.74 2.85
6045 6402 4.104417 GTCGCCGCTCACTCGAGT 62.104 66.667 13.58 13.58 41.71 4.18
6220 6577 0.981183 AGCTACAACAACCCCATCGA 59.019 50.000 0.00 0.00 0.00 3.59
6258 6615 3.273434 CACTGTACTACGGTAGCTACCA 58.727 50.000 35.98 20.68 46.80 3.25
6345 6797 3.420839 ACGGTTTTCAGCAAGAGTTTG 57.579 42.857 0.00 0.00 37.36 2.93
6350 6802 0.028770 CGCAACGGTTTTCAGCAAGA 59.971 50.000 0.00 0.00 0.00 3.02
6393 6845 6.271857 ACAAGTGCTTATCCCATCTAGATGAT 59.728 38.462 30.40 19.88 41.20 2.45
6448 6901 1.562942 TCTGCATCTTGAAGCTGGGAT 59.437 47.619 0.00 0.00 0.00 3.85
6453 6906 4.614946 GTTGTTTTCTGCATCTTGAAGCT 58.385 39.130 0.00 0.00 0.00 3.74
6533 6986 3.620419 TTGCCCGATGATGCCACGT 62.620 57.895 0.00 0.00 0.00 4.49
6597 7050 6.489022 GCGGAGAAAAGGGGTTATATGTTTAT 59.511 38.462 0.00 0.00 0.00 1.40
6600 7053 4.204799 GCGGAGAAAAGGGGTTATATGTT 58.795 43.478 0.00 0.00 0.00 2.71
6629 7272 3.994931 AGGGGAACTGCGTTTACTATT 57.005 42.857 0.00 0.00 0.00 1.73
6693 7336 1.377202 GGCCTTCTTGGTCGATGCA 60.377 57.895 0.00 0.00 38.35 3.96
6780 7426 2.631428 CGGTGTGACAAGGTTGCG 59.369 61.111 0.00 0.00 0.00 4.85
6807 7453 1.595357 CGTCTCCTTGTACCACCCC 59.405 63.158 0.00 0.00 0.00 4.95
6883 7533 2.124570 GCAGCCATGTCACCCGAT 60.125 61.111 0.00 0.00 0.00 4.18
6888 7538 3.503363 GCCGAGCAGCCATGTCAC 61.503 66.667 0.00 0.00 0.00 3.67
7132 7803 1.058404 GTGGTGCTCGTCGTAAACTC 58.942 55.000 0.00 0.00 0.00 3.01
7221 7892 2.595009 GAATCGACCTGCCCCCTGAC 62.595 65.000 0.00 0.00 0.00 3.51
7234 7905 4.847516 CACGCGCCGGAGAATCGA 62.848 66.667 10.31 0.00 34.37 3.59


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

AutoCloner maintained by Alex Coulton.