Multiple sequence alignment - TraesCS2D01G008400

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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 TraesCS2D01G008400 chr2D 100.000 2648 0 0 1 2648 4495959 4498606 0.000000e+00 4891
1 TraesCS2D01G008400 chr1A 91.457 1943 109 35 741 2648 42604165 42602245 0.000000e+00 2615
2 TraesCS2D01G008400 chr1A 84.694 98 15 0 195 292 42604584 42604487 6.030000e-17 99
3 TraesCS2D01G008400 chr1B 90.503 1927 98 39 738 2608 63091733 63089836 0.000000e+00 2466
4 TraesCS2D01G008400 chr1B 80.851 188 24 3 107 292 63092228 63092051 1.280000e-28 137
5 TraesCS2D01G008400 chrUn 100.000 394 0 0 1 394 270954341 270953948 0.000000e+00 728
6 TraesCS2D01G008400 chr4B 84.375 160 16 5 554 709 100587695 100587541 5.910000e-32 148
7 TraesCS2D01G008400 chr4B 76.923 221 45 6 1230 1447 424721915 424722132 1.290000e-23 121
8 TraesCS2D01G008400 chr4D 76.923 221 45 6 1230 1447 342699089 342699306 1.290000e-23 121
9 TraesCS2D01G008400 chr4A 78.395 162 31 4 1230 1389 123247241 123247082 4.660000e-18 102


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 TraesCS2D01G008400 chr2D 4495959 4498606 2647 False 4891.0 4891 100.0000 1 2648 1 chr2D.!!$F1 2647
1 TraesCS2D01G008400 chr1A 42602245 42604584 2339 True 1357.0 2615 88.0755 195 2648 2 chr1A.!!$R1 2453
2 TraesCS2D01G008400 chr1B 63089836 63092228 2392 True 1301.5 2466 85.6770 107 2608 2 chr1B.!!$R1 2501

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
47 48 0.039798 TCCGACTTCCGAAGACGTTG 60.04 55.0 24.45 14.36 43.35 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1865 0.179234 TTGGCCAGTTGAGTGACGAA 59.821 50.0 5.11 0.0 0.0 3.85 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 3.744559 TGTCAACCTTGAAGCGCC 58.255 55.556 2.29 0.00 39.21 6.53
18 19 2.250939 TGTCAACCTTGAAGCGCCG 61.251 57.895 2.29 0.00 39.21 6.46
19 20 3.353836 TCAACCTTGAAGCGCCGC 61.354 61.111 2.29 0.00 33.55 6.53
20 21 3.659092 CAACCTTGAAGCGCCGCA 61.659 61.111 13.36 0.00 0.00 5.69
21 22 2.904866 AACCTTGAAGCGCCGCAA 60.905 55.556 13.36 8.18 0.00 4.85
22 23 3.194272 AACCTTGAAGCGCCGCAAC 62.194 57.895 13.36 5.09 0.00 4.17
23 24 3.357079 CCTTGAAGCGCCGCAACT 61.357 61.111 13.36 0.00 0.00 3.16
24 25 2.174349 CTTGAAGCGCCGCAACTC 59.826 61.111 13.36 5.31 0.00 3.01
25 26 3.314388 CTTGAAGCGCCGCAACTCC 62.314 63.158 13.36 0.00 0.00 3.85
26 27 4.617520 TGAAGCGCCGCAACTCCA 62.618 61.111 13.36 0.00 0.00 3.86
27 28 3.353836 GAAGCGCCGCAACTCCAA 61.354 61.111 13.36 0.00 0.00 3.53
28 29 2.672996 AAGCGCCGCAACTCCAAT 60.673 55.556 13.36 0.00 0.00 3.16
29 30 2.583685 GAAGCGCCGCAACTCCAATC 62.584 60.000 13.36 0.00 0.00 2.67
30 31 4.179579 GCGCCGCAACTCCAATCC 62.180 66.667 3.15 0.00 0.00 3.01
31 32 3.864686 CGCCGCAACTCCAATCCG 61.865 66.667 0.00 0.00 0.00 4.18
32 33 2.435938 GCCGCAACTCCAATCCGA 60.436 61.111 0.00 0.00 0.00 4.55
33 34 2.750888 GCCGCAACTCCAATCCGAC 61.751 63.158 0.00 0.00 0.00 4.79
34 35 1.079127 CCGCAACTCCAATCCGACT 60.079 57.895 0.00 0.00 0.00 4.18
35 36 0.673644 CCGCAACTCCAATCCGACTT 60.674 55.000 0.00 0.00 0.00 3.01
36 37 0.721718 CGCAACTCCAATCCGACTTC 59.278 55.000 0.00 0.00 0.00 3.01
37 38 1.087501 GCAACTCCAATCCGACTTCC 58.912 55.000 0.00 0.00 0.00 3.46
38 39 1.359848 CAACTCCAATCCGACTTCCG 58.640 55.000 0.00 0.00 38.18 4.30
39 40 1.067142 CAACTCCAATCCGACTTCCGA 60.067 52.381 0.00 0.00 41.76 4.55
40 41 1.263356 ACTCCAATCCGACTTCCGAA 58.737 50.000 0.00 0.00 41.76 4.30
41 42 1.204941 ACTCCAATCCGACTTCCGAAG 59.795 52.381 6.59 6.59 41.76 3.79
42 43 1.476891 CTCCAATCCGACTTCCGAAGA 59.523 52.381 15.23 0.00 41.76 2.87
43 44 1.203994 TCCAATCCGACTTCCGAAGAC 59.796 52.381 15.23 7.80 41.76 3.01
44 45 1.269166 CAATCCGACTTCCGAAGACG 58.731 55.000 21.25 21.25 44.22 4.18
45 46 0.886563 AATCCGACTTCCGAAGACGT 59.113 50.000 24.45 10.17 43.35 4.34
46 47 0.886563 ATCCGACTTCCGAAGACGTT 59.113 50.000 24.45 13.31 43.35 3.99
47 48 0.039798 TCCGACTTCCGAAGACGTTG 60.040 55.000 24.45 14.36 43.35 4.10
48 49 0.318445 CCGACTTCCGAAGACGTTGT 60.318 55.000 24.45 0.94 43.35 3.32
49 50 0.776451 CGACTTCCGAAGACGTTGTG 59.224 55.000 20.31 0.00 40.76 3.33
50 51 1.849097 GACTTCCGAAGACGTTGTGT 58.151 50.000 15.23 0.00 37.88 3.72
51 52 1.521423 GACTTCCGAAGACGTTGTGTG 59.479 52.381 15.23 0.00 37.88 3.82
52 53 1.135527 ACTTCCGAAGACGTTGTGTGA 59.864 47.619 15.23 0.00 37.88 3.58
53 54 2.223971 ACTTCCGAAGACGTTGTGTGAT 60.224 45.455 15.23 0.00 37.88 3.06
54 55 3.005050 ACTTCCGAAGACGTTGTGTGATA 59.995 43.478 15.23 0.00 37.88 2.15
55 56 3.211803 TCCGAAGACGTTGTGTGATAG 57.788 47.619 0.00 0.00 37.88 2.08
56 57 2.555325 TCCGAAGACGTTGTGTGATAGT 59.445 45.455 0.00 0.00 37.88 2.12
57 58 3.752747 TCCGAAGACGTTGTGTGATAGTA 59.247 43.478 0.00 0.00 37.88 1.82
58 59 4.397103 TCCGAAGACGTTGTGTGATAGTAT 59.603 41.667 0.00 0.00 37.88 2.12
59 60 5.100259 CCGAAGACGTTGTGTGATAGTATT 58.900 41.667 0.00 0.00 37.88 1.89
60 61 5.575606 CCGAAGACGTTGTGTGATAGTATTT 59.424 40.000 0.00 0.00 37.88 1.40
61 62 6.748658 CCGAAGACGTTGTGTGATAGTATTTA 59.251 38.462 0.00 0.00 37.88 1.40
62 63 7.434307 CCGAAGACGTTGTGTGATAGTATTTAT 59.566 37.037 0.00 0.00 37.88 1.40
63 64 8.259872 CGAAGACGTTGTGTGATAGTATTTATG 58.740 37.037 0.00 0.00 34.56 1.90
64 65 8.997621 AAGACGTTGTGTGATAGTATTTATGT 57.002 30.769 0.00 0.00 0.00 2.29
65 66 8.407457 AGACGTTGTGTGATAGTATTTATGTG 57.593 34.615 0.00 0.00 0.00 3.21
66 67 7.491372 AGACGTTGTGTGATAGTATTTATGTGG 59.509 37.037 0.00 0.00 0.00 4.17
67 68 7.101054 ACGTTGTGTGATAGTATTTATGTGGT 58.899 34.615 0.00 0.00 0.00 4.16
68 69 7.064134 ACGTTGTGTGATAGTATTTATGTGGTG 59.936 37.037 0.00 0.00 0.00 4.17
69 70 7.064134 CGTTGTGTGATAGTATTTATGTGGTGT 59.936 37.037 0.00 0.00 0.00 4.16
70 71 7.841915 TGTGTGATAGTATTTATGTGGTGTG 57.158 36.000 0.00 0.00 0.00 3.82
71 72 6.821160 TGTGTGATAGTATTTATGTGGTGTGG 59.179 38.462 0.00 0.00 0.00 4.17
72 73 6.821665 GTGTGATAGTATTTATGTGGTGTGGT 59.178 38.462 0.00 0.00 0.00 4.16
73 74 6.821160 TGTGATAGTATTTATGTGGTGTGGTG 59.179 38.462 0.00 0.00 0.00 4.17
74 75 6.821665 GTGATAGTATTTATGTGGTGTGGTGT 59.178 38.462 0.00 0.00 0.00 4.16
75 76 6.821160 TGATAGTATTTATGTGGTGTGGTGTG 59.179 38.462 0.00 0.00 0.00 3.82
76 77 3.756434 AGTATTTATGTGGTGTGGTGTGC 59.244 43.478 0.00 0.00 0.00 4.57
77 78 0.947960 TTTATGTGGTGTGGTGTGCG 59.052 50.000 0.00 0.00 0.00 5.34
78 79 1.511318 TTATGTGGTGTGGTGTGCGC 61.511 55.000 0.00 0.00 0.00 6.09
81 82 3.551407 TGGTGTGGTGTGCGCCTA 61.551 61.111 4.18 0.00 37.40 3.93
82 83 2.046314 GGTGTGGTGTGCGCCTAT 60.046 61.111 4.18 0.00 33.96 2.57
83 84 2.398554 GGTGTGGTGTGCGCCTATG 61.399 63.158 4.18 0.00 33.96 2.23
84 85 1.671054 GTGTGGTGTGCGCCTATGT 60.671 57.895 4.18 0.00 0.00 2.29
85 86 1.072332 TGTGGTGTGCGCCTATGTT 59.928 52.632 4.18 0.00 0.00 2.71
86 87 1.233950 TGTGGTGTGCGCCTATGTTG 61.234 55.000 4.18 0.00 0.00 3.33
87 88 1.072332 TGGTGTGCGCCTATGTTGT 59.928 52.632 4.18 0.00 0.00 3.32
88 89 0.321996 TGGTGTGCGCCTATGTTGTA 59.678 50.000 4.18 0.00 0.00 2.41
89 90 1.270893 TGGTGTGCGCCTATGTTGTAA 60.271 47.619 4.18 0.00 0.00 2.41
90 91 2.014128 GGTGTGCGCCTATGTTGTAAT 58.986 47.619 4.18 0.00 0.00 1.89
91 92 2.031683 GGTGTGCGCCTATGTTGTAATC 59.968 50.000 4.18 0.00 0.00 1.75
92 93 1.930503 TGTGCGCCTATGTTGTAATCG 59.069 47.619 4.18 0.00 0.00 3.34
93 94 1.260561 GTGCGCCTATGTTGTAATCGG 59.739 52.381 4.18 0.00 0.00 4.18
94 95 1.134640 TGCGCCTATGTTGTAATCGGT 60.135 47.619 4.18 0.00 0.00 4.69
95 96 1.260561 GCGCCTATGTTGTAATCGGTG 59.739 52.381 0.00 0.00 0.00 4.94
96 97 2.546778 CGCCTATGTTGTAATCGGTGT 58.453 47.619 0.00 0.00 0.00 4.16
97 98 2.933906 CGCCTATGTTGTAATCGGTGTT 59.066 45.455 0.00 0.00 0.00 3.32
98 99 3.372822 CGCCTATGTTGTAATCGGTGTTT 59.627 43.478 0.00 0.00 0.00 2.83
99 100 4.493545 CGCCTATGTTGTAATCGGTGTTTC 60.494 45.833 0.00 0.00 0.00 2.78
100 101 4.393680 GCCTATGTTGTAATCGGTGTTTCA 59.606 41.667 0.00 0.00 0.00 2.69
101 102 5.106475 GCCTATGTTGTAATCGGTGTTTCAA 60.106 40.000 0.00 0.00 0.00 2.69
102 103 6.311723 CCTATGTTGTAATCGGTGTTTCAAC 58.688 40.000 0.00 0.00 38.82 3.18
103 104 5.759506 ATGTTGTAATCGGTGTTTCAACA 57.240 34.783 16.67 16.67 46.22 3.33
104 105 5.163302 TGTTGTAATCGGTGTTTCAACAG 57.837 39.130 13.07 0.00 41.37 3.16
105 106 4.876679 TGTTGTAATCGGTGTTTCAACAGA 59.123 37.500 13.07 0.00 41.37 3.41
106 107 5.354513 TGTTGTAATCGGTGTTTCAACAGAA 59.645 36.000 13.07 0.00 41.37 3.02
107 108 6.127980 TGTTGTAATCGGTGTTTCAACAGAAA 60.128 34.615 13.07 0.00 41.37 2.52
108 109 6.438259 TGTAATCGGTGTTTCAACAGAAAA 57.562 33.333 0.00 0.00 40.05 2.29
109 110 6.853720 TGTAATCGGTGTTTCAACAGAAAAA 58.146 32.000 0.00 0.00 40.05 1.94
149 150 8.718158 ACATCCTATTCATCTTGTATCTCTCA 57.282 34.615 0.00 0.00 0.00 3.27
163 166 9.166173 CTTGTATCTCTCATATTTTTGTGGTCA 57.834 33.333 0.00 0.00 0.00 4.02
214 217 6.132791 TCATCTTACTTGCTACGAGGTAAG 57.867 41.667 0.00 0.00 41.11 2.34
256 259 9.189156 TCTCTGAAAATATGGACCCAAAATAAG 57.811 33.333 0.00 0.00 0.00 1.73
264 267 4.344359 GGACCCAAAATAAGGTGCAAAA 57.656 40.909 0.00 0.00 43.47 2.44
272 275 7.354257 CCAAAATAAGGTGCAAAATTGTCAAG 58.646 34.615 0.00 0.00 0.00 3.02
277 280 4.441792 AGGTGCAAAATTGTCAAGTTTCC 58.558 39.130 7.99 7.20 0.00 3.13
283 286 6.183360 TGCAAAATTGTCAAGTTTCCCAAATG 60.183 34.615 7.99 0.00 0.00 2.32
285 288 7.011857 GCAAAATTGTCAAGTTTCCCAAATGTA 59.988 33.333 7.99 0.00 0.00 2.29
292 295 4.584327 AGTTTCCCAAATGTAGTGCAAC 57.416 40.909 0.00 0.00 0.00 4.17
308 392 3.305897 GTGCAACTCGTTTTCCCAAAAAG 59.694 43.478 0.00 0.00 35.10 2.27
313 397 3.004419 ACTCGTTTTCCCAAAAAGCTAGC 59.996 43.478 6.62 6.62 35.10 3.42
319 403 1.892474 TCCCAAAAAGCTAGCGCAAAT 59.108 42.857 11.47 0.00 39.10 2.32
385 520 3.974912 TCATTTGAAGATGCGCAAAACA 58.025 36.364 17.11 10.07 37.52 2.83
386 521 4.366586 TCATTTGAAGATGCGCAAAACAA 58.633 34.783 17.11 15.67 37.52 2.83
402 537 6.740002 CGCAAAACAACAAAAATGTTCAATCA 59.260 30.769 0.00 0.00 39.98 2.57
404 539 8.364482 GCAAAACAACAAAAATGTTCAATCAAC 58.636 29.630 0.00 0.00 39.98 3.18
407 542 8.776376 AACAACAAAAATGTTCAATCAACTCT 57.224 26.923 0.00 0.00 36.28 3.24
410 589 7.111247 ACAAAAATGTTCAATCAACTCTCCA 57.889 32.000 0.00 0.00 35.79 3.86
417 596 6.962182 TGTTCAATCAACTCTCCATCCTAAT 58.038 36.000 0.00 0.00 35.79 1.73
421 600 8.089625 TCAATCAACTCTCCATCCTAATAACA 57.910 34.615 0.00 0.00 0.00 2.41
424 603 7.496346 TCAACTCTCCATCCTAATAACAACT 57.504 36.000 0.00 0.00 0.00 3.16
433 612 6.921857 CCATCCTAATAACAACTACTACACCG 59.078 42.308 0.00 0.00 0.00 4.94
436 615 6.886459 TCCTAATAACAACTACTACACCGAGT 59.114 38.462 0.00 0.00 0.00 4.18
437 616 6.971184 CCTAATAACAACTACTACACCGAGTG 59.029 42.308 2.92 2.92 39.75 3.51
438 617 2.719426 ACAACTACTACACCGAGTGC 57.281 50.000 4.23 0.00 36.98 4.40
439 618 1.958579 ACAACTACTACACCGAGTGCA 59.041 47.619 4.23 0.00 36.98 4.57
440 619 2.561419 ACAACTACTACACCGAGTGCAT 59.439 45.455 0.00 0.00 36.98 3.96
441 620 3.179830 CAACTACTACACCGAGTGCATC 58.820 50.000 0.00 0.00 36.98 3.91
451 630 2.787723 CGAGTGCATCGTTTGTTAGG 57.212 50.000 9.48 0.00 46.62 2.69
452 631 2.333926 CGAGTGCATCGTTTGTTAGGA 58.666 47.619 9.48 0.00 46.62 2.94
453 632 2.092211 CGAGTGCATCGTTTGTTAGGAC 59.908 50.000 9.48 0.00 46.62 3.85
454 633 2.066262 AGTGCATCGTTTGTTAGGACG 58.934 47.619 0.00 0.00 40.43 4.79
455 634 1.127951 GTGCATCGTTTGTTAGGACGG 59.872 52.381 0.00 0.00 39.59 4.79
456 635 0.725117 GCATCGTTTGTTAGGACGGG 59.275 55.000 0.00 0.00 39.59 5.28
457 636 1.365699 CATCGTTTGTTAGGACGGGG 58.634 55.000 0.00 0.00 39.59 5.73
458 637 0.978907 ATCGTTTGTTAGGACGGGGT 59.021 50.000 0.00 0.00 39.59 4.95
459 638 0.318120 TCGTTTGTTAGGACGGGGTC 59.682 55.000 0.00 0.00 39.59 4.46
477 656 4.864704 GGTCCATTGAGCCTGTTTTAAA 57.135 40.909 0.00 0.00 32.76 1.52
478 657 5.208463 GGTCCATTGAGCCTGTTTTAAAA 57.792 39.130 0.00 0.00 32.76 1.52
479 658 5.606505 GGTCCATTGAGCCTGTTTTAAAAA 58.393 37.500 1.31 0.00 32.76 1.94
592 771 9.612066 TCAAATAGATTATTGTCATGCTACACA 57.388 29.630 0.00 0.00 0.00 3.72
614 793 3.922171 AAAACACAAAAATCTGGCCCA 57.078 38.095 0.00 0.00 0.00 5.36
615 794 3.922171 AAACACAAAAATCTGGCCCAA 57.078 38.095 0.00 0.00 0.00 4.12
616 795 3.922171 AACACAAAAATCTGGCCCAAA 57.078 38.095 0.00 0.00 0.00 3.28
617 796 4.436113 AACACAAAAATCTGGCCCAAAT 57.564 36.364 0.00 0.00 0.00 2.32
618 797 4.436113 ACACAAAAATCTGGCCCAAATT 57.564 36.364 0.00 0.00 0.00 1.82
619 798 4.388485 ACACAAAAATCTGGCCCAAATTC 58.612 39.130 0.00 0.00 0.00 2.17
620 799 4.141528 ACACAAAAATCTGGCCCAAATTCA 60.142 37.500 0.00 0.00 0.00 2.57
621 800 4.820716 CACAAAAATCTGGCCCAAATTCAA 59.179 37.500 0.00 0.00 0.00 2.69
622 801 4.821260 ACAAAAATCTGGCCCAAATTCAAC 59.179 37.500 0.00 0.00 0.00 3.18
623 802 4.703379 AAAATCTGGCCCAAATTCAACA 57.297 36.364 0.00 0.00 0.00 3.33
624 803 4.703379 AAATCTGGCCCAAATTCAACAA 57.297 36.364 0.00 0.00 0.00 2.83
625 804 3.967332 ATCTGGCCCAAATTCAACAAG 57.033 42.857 0.00 0.00 0.00 3.16
626 805 2.956132 TCTGGCCCAAATTCAACAAGA 58.044 42.857 0.00 0.00 0.00 3.02
627 806 3.303938 TCTGGCCCAAATTCAACAAGAA 58.696 40.909 0.00 0.00 41.28 2.52
628 807 3.708631 TCTGGCCCAAATTCAACAAGAAA 59.291 39.130 0.00 0.00 40.22 2.52
629 808 4.163078 TCTGGCCCAAATTCAACAAGAAAA 59.837 37.500 0.00 0.00 40.22 2.29
630 809 4.848357 TGGCCCAAATTCAACAAGAAAAA 58.152 34.783 0.00 0.00 40.22 1.94
631 810 5.444176 TGGCCCAAATTCAACAAGAAAAAT 58.556 33.333 0.00 0.00 40.22 1.82
632 811 5.530543 TGGCCCAAATTCAACAAGAAAAATC 59.469 36.000 0.00 0.00 40.22 2.17
633 812 5.764686 GGCCCAAATTCAACAAGAAAAATCT 59.235 36.000 0.00 0.00 40.22 2.40
634 813 6.073058 GGCCCAAATTCAACAAGAAAAATCTC 60.073 38.462 0.00 0.00 40.22 2.75
635 814 6.482973 GCCCAAATTCAACAAGAAAAATCTCA 59.517 34.615 0.00 0.00 40.22 3.27
636 815 7.173735 GCCCAAATTCAACAAGAAAAATCTCAT 59.826 33.333 0.00 0.00 40.22 2.90
637 816 9.059260 CCCAAATTCAACAAGAAAAATCTCATT 57.941 29.630 0.00 0.00 40.22 2.57
675 854 9.868277 ATTTGTCTTTTTCTTTTGTACATCACA 57.132 25.926 0.00 0.00 34.51 3.58
676 855 9.868277 TTTGTCTTTTTCTTTTGTACATCACAT 57.132 25.926 0.00 0.00 36.90 3.21
711 890 9.981114 ATATGTTCATGAAATCTCATACGTACA 57.019 29.630 10.35 0.00 40.49 2.90
712 891 8.893219 ATGTTCATGAAATCTCATACGTACAT 57.107 30.769 10.35 2.39 40.49 2.29
713 892 9.981114 ATGTTCATGAAATCTCATACGTACATA 57.019 29.630 10.35 0.00 40.49 2.29
714 893 9.244799 TGTTCATGAAATCTCATACGTACATAC 57.755 33.333 10.35 0.00 40.49 2.39
715 894 9.464714 GTTCATGAAATCTCATACGTACATACT 57.535 33.333 10.35 0.00 40.49 2.12
718 897 9.893305 CATGAAATCTCATACGTACATACTACA 57.107 33.333 0.00 0.00 40.49 2.74
719 898 9.894783 ATGAAATCTCATACGTACATACTACAC 57.105 33.333 0.00 0.00 40.67 2.90
720 899 8.895737 TGAAATCTCATACGTACATACTACACA 58.104 33.333 0.00 0.00 0.00 3.72
721 900 9.894783 GAAATCTCATACGTACATACTACACAT 57.105 33.333 0.00 0.00 0.00 3.21
725 904 9.498176 TCTCATACGTACATACTACACATATGT 57.502 33.333 1.41 1.41 43.87 2.29
856 1035 0.811616 AGCTCGATCGGCCATCAAAC 60.812 55.000 16.41 0.00 0.00 2.93
981 1164 1.547820 AGCTCAGCTCGAAGTGAATCA 59.452 47.619 0.00 0.00 30.62 2.57
1290 1477 4.157120 ATGGTGTACGAGGCGGCC 62.157 66.667 12.11 12.11 0.00 6.13
1489 1676 2.507102 CGCAGGACGCCTACTGTG 60.507 66.667 0.00 0.00 38.65 3.66
1491 1678 2.973899 CAGGACGCCTACTGTGCT 59.026 61.111 0.00 0.00 38.67 4.40
1493 1680 2.815647 GGACGCCTACTGTGCTGC 60.816 66.667 0.00 0.00 0.00 5.25
1701 1891 0.819259 TCACTCAACTGGCCAACTGC 60.819 55.000 7.01 0.00 40.16 4.40
1702 1892 0.820891 CACTCAACTGGCCAACTGCT 60.821 55.000 7.01 0.00 40.92 4.24
1703 1893 0.764890 ACTCAACTGGCCAACTGCTA 59.235 50.000 7.01 0.00 40.92 3.49
1730 1920 1.779157 CTACGTACGCATGATTCGTGG 59.221 52.381 16.72 0.00 40.69 4.94
1842 2045 5.949233 AGATCGAGTTTGTTTTGTTTTGC 57.051 34.783 0.00 0.00 0.00 3.68
2069 2282 7.140304 AGTATCTTTAGTTCCTTACATCCCCT 58.860 38.462 0.00 0.00 0.00 4.79
2083 2296 7.559897 CCTTACATCCCCTTGTAAATGTAACAT 59.440 37.037 3.38 0.00 40.53 2.71
2084 2297 9.621629 CTTACATCCCCTTGTAAATGTAACATA 57.378 33.333 3.38 0.00 40.53 2.29
2087 2300 8.912988 ACATCCCCTTGTAAATGTAACATATTG 58.087 33.333 0.00 0.00 30.84 1.90
2089 2302 8.514330 TCCCCTTGTAAATGTAACATATTGTC 57.486 34.615 0.00 0.00 0.00 3.18
2090 2303 7.558444 TCCCCTTGTAAATGTAACATATTGTCC 59.442 37.037 0.00 0.00 0.00 4.02
2091 2304 7.559897 CCCCTTGTAAATGTAACATATTGTCCT 59.440 37.037 0.00 0.00 0.00 3.85
2092 2305 9.621629 CCCTTGTAAATGTAACATATTGTCCTA 57.378 33.333 0.00 0.00 0.00 2.94
2095 2308 9.872721 TTGTAAATGTAACATATTGTCCTACGA 57.127 29.630 0.00 0.00 0.00 3.43
2096 2309 9.524106 TGTAAATGTAACATATTGTCCTACGAG 57.476 33.333 0.00 0.00 0.00 4.18
2101 2314 4.737855 ACATATTGTCCTACGAGCACTT 57.262 40.909 0.00 0.00 0.00 3.16
2102 2315 5.847111 ACATATTGTCCTACGAGCACTTA 57.153 39.130 0.00 0.00 0.00 2.24
2103 2316 6.216801 ACATATTGTCCTACGAGCACTTAA 57.783 37.500 0.00 0.00 0.00 1.85
2104 2317 6.040878 ACATATTGTCCTACGAGCACTTAAC 58.959 40.000 0.00 0.00 0.00 2.01
2106 2319 4.325028 TTGTCCTACGAGCACTTAACAA 57.675 40.909 0.00 0.00 0.00 2.83
2107 2320 4.325028 TGTCCTACGAGCACTTAACAAA 57.675 40.909 0.00 0.00 0.00 2.83
2108 2321 4.890088 TGTCCTACGAGCACTTAACAAAT 58.110 39.130 0.00 0.00 0.00 2.32
2110 2323 3.682858 TCCTACGAGCACTTAACAAATGC 59.317 43.478 0.00 0.00 39.74 3.56
2111 2324 3.435327 CCTACGAGCACTTAACAAATGCA 59.565 43.478 0.00 0.00 41.97 3.96
2112 2325 4.094887 CCTACGAGCACTTAACAAATGCAT 59.905 41.667 0.00 0.00 41.97 3.96
2113 2326 3.825308 ACGAGCACTTAACAAATGCATG 58.175 40.909 0.00 0.00 41.97 4.06
2114 2327 3.253188 ACGAGCACTTAACAAATGCATGT 59.747 39.130 0.00 0.00 41.97 3.21
2115 2328 3.848019 CGAGCACTTAACAAATGCATGTC 59.152 43.478 0.00 0.00 41.97 3.06
2116 2329 4.613394 CGAGCACTTAACAAATGCATGTCA 60.613 41.667 0.00 0.00 41.97 3.58
2117 2330 5.395682 AGCACTTAACAAATGCATGTCAT 57.604 34.783 0.00 0.00 41.97 3.06
2118 2331 5.786311 AGCACTTAACAAATGCATGTCATT 58.214 33.333 0.00 8.87 46.82 2.57
2131 2344 7.692460 ATGCATGTCATTTTCAAGAAGACTA 57.308 32.000 0.00 0.00 29.16 2.59
2133 2346 7.755591 TGCATGTCATTTTCAAGAAGACTATC 58.244 34.615 0.00 0.00 0.00 2.08
2134 2347 7.609146 TGCATGTCATTTTCAAGAAGACTATCT 59.391 33.333 0.00 0.00 0.00 1.98
2135 2348 8.457261 GCATGTCATTTTCAAGAAGACTATCTT 58.543 33.333 0.00 0.00 39.87 2.40
2151 2364 8.388656 AGACTATCTTTTACTTTACATCCCCA 57.611 34.615 0.00 0.00 0.00 4.96
2152 2365 9.004231 AGACTATCTTTTACTTTACATCCCCAT 57.996 33.333 0.00 0.00 0.00 4.00
2153 2366 8.980481 ACTATCTTTTACTTTACATCCCCATG 57.020 34.615 0.00 0.00 35.92 3.66
2155 2368 7.881775 ATCTTTTACTTTACATCCCCATGTC 57.118 36.000 0.00 0.00 42.66 3.06
2156 2369 6.785076 TCTTTTACTTTACATCCCCATGTCA 58.215 36.000 0.00 0.00 42.66 3.58
2157 2370 7.410174 TCTTTTACTTTACATCCCCATGTCAT 58.590 34.615 0.00 0.00 42.66 3.06
2158 2371 7.893302 TCTTTTACTTTACATCCCCATGTCATT 59.107 33.333 0.00 0.00 42.66 2.57
2159 2372 8.429237 TTTTACTTTACATCCCCATGTCATTT 57.571 30.769 0.00 0.00 42.66 2.32
2161 2374 6.933514 ACTTTACATCCCCATGTCATTTTT 57.066 33.333 0.00 0.00 42.66 1.94
2167 2380 5.957168 ACATCCCCATGTCATTTTTATGTGA 59.043 36.000 0.00 0.00 39.15 3.58
2168 2381 6.612456 ACATCCCCATGTCATTTTTATGTGAT 59.388 34.615 0.00 0.00 39.15 3.06
2169 2382 7.784073 ACATCCCCATGTCATTTTTATGTGATA 59.216 33.333 0.00 0.00 39.15 2.15
2222 2458 5.730550 TGTCCTACGAGCACTTAATGAATT 58.269 37.500 0.00 0.00 0.00 2.17
2256 2492 3.644966 TTGCTCCCGAAATAACCAGAT 57.355 42.857 0.00 0.00 0.00 2.90
2331 2572 8.484641 TTCTCAGAAGTAGCATTAGTTGATTG 57.515 34.615 0.00 0.00 0.00 2.67
2475 2717 6.712998 TCAAACCGTCTTCATTATCCTTTTCA 59.287 34.615 0.00 0.00 0.00 2.69
2514 2757 7.776107 TCTTCATTATCAATCTGTCTTCGAGT 58.224 34.615 0.00 0.00 0.00 4.18
2515 2758 7.918033 TCTTCATTATCAATCTGTCTTCGAGTC 59.082 37.037 0.00 0.00 0.00 3.36
2516 2759 6.202226 TCATTATCAATCTGTCTTCGAGTCG 58.798 40.000 6.09 6.09 0.00 4.18
2558 2801 5.007682 ACGAGCCAATGGTAATTGTTAGTT 58.992 37.500 0.00 0.00 41.46 2.24
2591 2834 5.666718 AGGATGAGAGAAAGGAAGACATGAT 59.333 40.000 0.00 0.00 0.00 2.45
2608 2851 5.437060 ACATGATTTAGGGCTTACGACATT 58.563 37.500 0.00 0.00 0.00 2.71
2639 2884 7.286775 ACAATTTGGCGGTATATAAGGTTGAAT 59.713 33.333 0.78 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.250939 CGGCGCTTCAAGGTTGACA 61.251 57.895 7.64 0.00 36.83 3.58
1 2 2.556287 CGGCGCTTCAAGGTTGAC 59.444 61.111 7.64 0.00 36.83 3.18
2 3 3.353836 GCGGCGCTTCAAGGTTGA 61.354 61.111 26.86 0.00 34.92 3.18
3 4 3.192954 TTGCGGCGCTTCAAGGTTG 62.193 57.895 33.26 0.00 0.00 3.77
4 5 2.904866 TTGCGGCGCTTCAAGGTT 60.905 55.556 33.26 0.00 0.00 3.50
6 7 3.314388 GAGTTGCGGCGCTTCAAGG 62.314 63.158 33.26 0.00 0.00 3.61
7 8 2.174349 GAGTTGCGGCGCTTCAAG 59.826 61.111 33.26 0.00 0.00 3.02
8 9 3.353836 GGAGTTGCGGCGCTTCAA 61.354 61.111 33.26 16.55 0.00 2.69
9 10 4.617520 TGGAGTTGCGGCGCTTCA 62.618 61.111 33.26 15.39 0.00 3.02
10 11 2.583685 GATTGGAGTTGCGGCGCTTC 62.584 60.000 33.26 24.70 0.00 3.86
11 12 2.672996 ATTGGAGTTGCGGCGCTT 60.673 55.556 33.26 18.27 0.00 4.68
12 13 3.127533 GATTGGAGTTGCGGCGCT 61.128 61.111 33.26 13.47 0.00 5.92
13 14 4.179579 GGATTGGAGTTGCGGCGC 62.180 66.667 27.44 27.44 0.00 6.53
14 15 3.864686 CGGATTGGAGTTGCGGCG 61.865 66.667 0.51 0.51 0.00 6.46
15 16 2.435938 TCGGATTGGAGTTGCGGC 60.436 61.111 0.00 0.00 0.00 6.53
16 17 0.673644 AAGTCGGATTGGAGTTGCGG 60.674 55.000 0.00 0.00 0.00 5.69
17 18 0.721718 GAAGTCGGATTGGAGTTGCG 59.278 55.000 0.00 0.00 29.93 4.85
18 19 1.087501 GGAAGTCGGATTGGAGTTGC 58.912 55.000 0.00 0.00 31.89 4.17
19 20 1.067142 TCGGAAGTCGGATTGGAGTTG 60.067 52.381 0.00 0.00 39.77 3.16
20 21 1.263356 TCGGAAGTCGGATTGGAGTT 58.737 50.000 0.00 0.00 39.77 3.01
21 22 1.204941 CTTCGGAAGTCGGATTGGAGT 59.795 52.381 9.61 0.00 39.77 3.85
22 23 1.476891 TCTTCGGAAGTCGGATTGGAG 59.523 52.381 16.78 0.00 39.77 3.86
23 24 1.203994 GTCTTCGGAAGTCGGATTGGA 59.796 52.381 16.78 0.00 39.77 3.53
24 25 1.641577 GTCTTCGGAAGTCGGATTGG 58.358 55.000 16.78 0.00 39.77 3.16
25 26 1.269166 CGTCTTCGGAAGTCGGATTG 58.731 55.000 23.44 2.07 36.61 2.67
26 27 0.886563 ACGTCTTCGGAAGTCGGATT 59.113 50.000 30.35 14.74 42.83 3.01
27 28 0.886563 AACGTCTTCGGAAGTCGGAT 59.113 50.000 30.35 20.48 42.83 4.18
28 29 0.039798 CAACGTCTTCGGAAGTCGGA 60.040 55.000 30.35 7.64 42.83 4.55
29 30 0.318445 ACAACGTCTTCGGAAGTCGG 60.318 55.000 30.35 20.35 42.83 4.79
30 31 0.776451 CACAACGTCTTCGGAAGTCG 59.224 55.000 27.34 27.34 43.85 4.18
31 32 1.521423 CACACAACGTCTTCGGAAGTC 59.479 52.381 16.78 10.83 41.85 3.01
32 33 1.135527 TCACACAACGTCTTCGGAAGT 59.864 47.619 16.78 0.00 41.85 3.01
33 34 1.847818 TCACACAACGTCTTCGGAAG 58.152 50.000 11.54 11.54 41.85 3.46
34 35 2.519377 ATCACACAACGTCTTCGGAA 57.481 45.000 0.00 0.00 41.85 4.30
35 36 2.555325 ACTATCACACAACGTCTTCGGA 59.445 45.455 0.00 0.00 41.85 4.55
36 37 2.942710 ACTATCACACAACGTCTTCGG 58.057 47.619 0.00 0.00 41.85 4.30
37 38 6.627690 AAATACTATCACACAACGTCTTCG 57.372 37.500 0.00 0.00 43.34 3.79
38 39 9.084164 ACATAAATACTATCACACAACGTCTTC 57.916 33.333 0.00 0.00 0.00 2.87
39 40 8.869897 CACATAAATACTATCACACAACGTCTT 58.130 33.333 0.00 0.00 0.00 3.01
40 41 7.491372 CCACATAAATACTATCACACAACGTCT 59.509 37.037 0.00 0.00 0.00 4.18
41 42 7.277098 ACCACATAAATACTATCACACAACGTC 59.723 37.037 0.00 0.00 0.00 4.34
42 43 7.064134 CACCACATAAATACTATCACACAACGT 59.936 37.037 0.00 0.00 0.00 3.99
43 44 7.064134 ACACCACATAAATACTATCACACAACG 59.936 37.037 0.00 0.00 0.00 4.10
44 45 8.175069 CACACCACATAAATACTATCACACAAC 58.825 37.037 0.00 0.00 0.00 3.32
45 46 7.335673 CCACACCACATAAATACTATCACACAA 59.664 37.037 0.00 0.00 0.00 3.33
46 47 6.821160 CCACACCACATAAATACTATCACACA 59.179 38.462 0.00 0.00 0.00 3.72
47 48 6.821665 ACCACACCACATAAATACTATCACAC 59.178 38.462 0.00 0.00 0.00 3.82
48 49 6.821160 CACCACACCACATAAATACTATCACA 59.179 38.462 0.00 0.00 0.00 3.58
49 50 6.821665 ACACCACACCACATAAATACTATCAC 59.178 38.462 0.00 0.00 0.00 3.06
50 51 6.821160 CACACCACACCACATAAATACTATCA 59.179 38.462 0.00 0.00 0.00 2.15
51 52 6.238374 GCACACCACACCACATAAATACTATC 60.238 42.308 0.00 0.00 0.00 2.08
52 53 5.588648 GCACACCACACCACATAAATACTAT 59.411 40.000 0.00 0.00 0.00 2.12
53 54 4.938832 GCACACCACACCACATAAATACTA 59.061 41.667 0.00 0.00 0.00 1.82
54 55 3.756434 GCACACCACACCACATAAATACT 59.244 43.478 0.00 0.00 0.00 2.12
55 56 3.425625 CGCACACCACACCACATAAATAC 60.426 47.826 0.00 0.00 0.00 1.89
56 57 2.744741 CGCACACCACACCACATAAATA 59.255 45.455 0.00 0.00 0.00 1.40
57 58 1.539388 CGCACACCACACCACATAAAT 59.461 47.619 0.00 0.00 0.00 1.40
58 59 0.947960 CGCACACCACACCACATAAA 59.052 50.000 0.00 0.00 0.00 1.40
59 60 1.511318 GCGCACACCACACCACATAA 61.511 55.000 0.30 0.00 0.00 1.90
60 61 1.963855 GCGCACACCACACCACATA 60.964 57.895 0.30 0.00 0.00 2.29
61 62 3.286751 GCGCACACCACACCACAT 61.287 61.111 0.30 0.00 0.00 3.21
63 64 3.818121 TAGGCGCACACCACACCAC 62.818 63.158 10.83 0.00 0.00 4.16
64 65 2.889606 ATAGGCGCACACCACACCA 61.890 57.895 10.83 0.00 0.00 4.17
65 66 2.046314 ATAGGCGCACACCACACC 60.046 61.111 10.83 0.00 0.00 4.16
66 67 1.234615 AACATAGGCGCACACCACAC 61.235 55.000 10.83 0.00 0.00 3.82
67 68 1.072332 AACATAGGCGCACACCACA 59.928 52.632 10.83 0.00 0.00 4.17
68 69 1.234615 ACAACATAGGCGCACACCAC 61.235 55.000 10.83 0.00 0.00 4.16
69 70 0.321996 TACAACATAGGCGCACACCA 59.678 50.000 10.83 0.00 0.00 4.17
70 71 1.444836 TTACAACATAGGCGCACACC 58.555 50.000 10.83 0.00 0.00 4.16
71 72 2.285602 CGATTACAACATAGGCGCACAC 60.286 50.000 10.83 0.00 0.00 3.82
72 73 1.930503 CGATTACAACATAGGCGCACA 59.069 47.619 10.83 0.00 0.00 4.57
73 74 1.260561 CCGATTACAACATAGGCGCAC 59.739 52.381 10.83 0.00 0.00 5.34
74 75 1.134640 ACCGATTACAACATAGGCGCA 60.135 47.619 10.83 0.00 0.00 6.09
75 76 1.260561 CACCGATTACAACATAGGCGC 59.739 52.381 0.00 0.00 0.00 6.53
76 77 2.546778 ACACCGATTACAACATAGGCG 58.453 47.619 0.00 0.00 0.00 5.52
77 78 4.393680 TGAAACACCGATTACAACATAGGC 59.606 41.667 0.00 0.00 0.00 3.93
78 79 6.072948 TGTTGAAACACCGATTACAACATAGG 60.073 38.462 0.00 0.00 41.20 2.57
79 80 6.893759 TGTTGAAACACCGATTACAACATAG 58.106 36.000 0.00 0.00 41.20 2.23
80 81 6.706716 TCTGTTGAAACACCGATTACAACATA 59.293 34.615 0.00 0.00 43.65 2.29
81 82 5.529430 TCTGTTGAAACACCGATTACAACAT 59.471 36.000 0.00 0.00 43.65 2.71
82 83 4.876679 TCTGTTGAAACACCGATTACAACA 59.123 37.500 0.00 0.00 42.89 3.33
83 84 5.412526 TCTGTTGAAACACCGATTACAAC 57.587 39.130 0.00 0.00 38.29 3.32
84 85 6.438259 TTTCTGTTGAAACACCGATTACAA 57.562 33.333 0.00 0.00 37.27 2.41
85 86 6.438259 TTTTCTGTTGAAACACCGATTACA 57.562 33.333 0.00 0.00 41.34 2.41
123 124 9.813826 TGAGAGATACAAGATGAATAGGATGTA 57.186 33.333 0.00 0.00 0.00 2.29
146 147 9.703892 TGGTAAATTTGACCACAAAAATATGAG 57.296 29.630 1.03 0.00 46.77 2.90
185 188 8.204836 ACCTCGTAGCAAGTAAGATGATAATTT 58.795 33.333 0.00 0.00 0.00 1.82
186 189 7.727181 ACCTCGTAGCAAGTAAGATGATAATT 58.273 34.615 0.00 0.00 0.00 1.40
187 190 7.291411 ACCTCGTAGCAAGTAAGATGATAAT 57.709 36.000 0.00 0.00 0.00 1.28
188 191 6.710597 ACCTCGTAGCAAGTAAGATGATAA 57.289 37.500 0.00 0.00 0.00 1.75
189 192 7.501559 ACTTACCTCGTAGCAAGTAAGATGATA 59.498 37.037 13.95 0.00 42.71 2.15
190 193 6.321690 ACTTACCTCGTAGCAAGTAAGATGAT 59.678 38.462 13.95 0.00 42.71 2.45
191 194 5.651139 ACTTACCTCGTAGCAAGTAAGATGA 59.349 40.000 13.95 0.00 42.71 2.92
192 195 5.892568 ACTTACCTCGTAGCAAGTAAGATG 58.107 41.667 13.95 0.00 42.71 2.90
193 196 6.262720 CCTACTTACCTCGTAGCAAGTAAGAT 59.737 42.308 13.95 3.55 42.71 2.40
206 209 9.819267 AGAATTTTAAGATTCCTACTTACCTCG 57.181 33.333 13.57 0.00 36.84 4.63
243 246 4.344359 TTTTGCACCTTATTTTGGGTCC 57.656 40.909 0.00 0.00 32.95 4.46
246 249 5.762218 TGACAATTTTGCACCTTATTTTGGG 59.238 36.000 0.00 0.00 0.00 4.12
248 251 7.918643 ACTTGACAATTTTGCACCTTATTTTG 58.081 30.769 0.00 0.00 0.00 2.44
256 259 3.559655 GGGAAACTTGACAATTTTGCACC 59.440 43.478 19.28 10.24 0.00 5.01
264 267 6.738453 GCACTACATTTGGGAAACTTGACAAT 60.738 38.462 0.00 0.00 0.00 2.71
272 275 4.546570 GAGTTGCACTACATTTGGGAAAC 58.453 43.478 0.00 0.00 0.00 2.78
277 280 3.896648 AACGAGTTGCACTACATTTGG 57.103 42.857 0.00 0.00 0.00 3.28
283 286 2.215196 TGGGAAAACGAGTTGCACTAC 58.785 47.619 0.00 0.00 0.00 2.73
285 288 1.757682 TTGGGAAAACGAGTTGCACT 58.242 45.000 0.00 0.00 0.00 4.40
292 295 3.565516 GCTAGCTTTTTGGGAAAACGAG 58.434 45.455 7.70 0.00 31.72 4.18
293 296 2.031508 CGCTAGCTTTTTGGGAAAACGA 60.032 45.455 13.93 0.00 31.72 3.85
294 297 2.315901 CGCTAGCTTTTTGGGAAAACG 58.684 47.619 13.93 0.00 31.72 3.60
295 298 2.058798 GCGCTAGCTTTTTGGGAAAAC 58.941 47.619 13.93 0.00 41.01 2.43
296 299 1.683917 TGCGCTAGCTTTTTGGGAAAA 59.316 42.857 13.93 0.00 45.42 2.29
300 383 2.262211 GATTTGCGCTAGCTTTTTGGG 58.738 47.619 13.93 0.00 45.42 4.12
301 384 1.913403 CGATTTGCGCTAGCTTTTTGG 59.087 47.619 13.93 0.00 45.42 3.28
303 387 2.484264 AGACGATTTGCGCTAGCTTTTT 59.516 40.909 13.93 0.00 46.04 1.94
308 392 1.781998 GAGTAGACGATTTGCGCTAGC 59.218 52.381 9.73 4.06 46.04 3.42
319 403 8.213518 ACAACCTATTAATAACGAGTAGACGA 57.786 34.615 0.00 0.00 37.03 4.20
365 500 4.025896 TGTTGTTTTGCGCATCTTCAAATG 60.026 37.500 12.75 0.00 32.92 2.32
370 505 4.513000 TTTTGTTGTTTTGCGCATCTTC 57.487 36.364 12.75 3.00 0.00 2.87
371 506 4.935885 TTTTTGTTGTTTTGCGCATCTT 57.064 31.818 12.75 0.00 0.00 2.40
377 512 6.740002 TGATTGAACATTTTTGTTGTTTTGCG 59.260 30.769 0.00 0.00 37.43 4.85
383 518 7.492344 GGAGAGTTGATTGAACATTTTTGTTGT 59.508 33.333 0.00 0.00 36.98 3.32
385 520 7.555087 TGGAGAGTTGATTGAACATTTTTGTT 58.445 30.769 0.00 0.00 36.98 2.83
386 521 7.111247 TGGAGAGTTGATTGAACATTTTTGT 57.889 32.000 0.00 0.00 36.98 2.83
402 537 8.611051 AGTAGTTGTTATTAGGATGGAGAGTT 57.389 34.615 0.00 0.00 0.00 3.01
404 539 9.132923 TGTAGTAGTTGTTATTAGGATGGAGAG 57.867 37.037 0.00 0.00 0.00 3.20
407 542 7.201848 CGGTGTAGTAGTTGTTATTAGGATGGA 60.202 40.741 0.00 0.00 0.00 3.41
410 589 7.559170 ACTCGGTGTAGTAGTTGTTATTAGGAT 59.441 37.037 0.00 0.00 0.00 3.24
417 596 3.569277 TGCACTCGGTGTAGTAGTTGTTA 59.431 43.478 6.02 0.00 35.75 2.41
421 600 2.159421 CGATGCACTCGGTGTAGTAGTT 60.159 50.000 9.73 0.00 43.82 2.24
433 612 2.092211 CGTCCTAACAAACGATGCACTC 59.908 50.000 0.00 0.00 41.29 3.51
436 615 1.434555 CCGTCCTAACAAACGATGCA 58.565 50.000 0.00 0.00 41.29 3.96
437 616 0.725117 CCCGTCCTAACAAACGATGC 59.275 55.000 0.00 0.00 41.29 3.91
438 617 1.338389 ACCCCGTCCTAACAAACGATG 60.338 52.381 0.00 0.00 41.29 3.84
439 618 0.978907 ACCCCGTCCTAACAAACGAT 59.021 50.000 0.00 0.00 41.29 3.73
440 619 0.318120 GACCCCGTCCTAACAAACGA 59.682 55.000 0.00 0.00 41.29 3.85
441 620 2.831597 GACCCCGTCCTAACAAACG 58.168 57.895 0.00 0.00 38.58 3.60
451 630 2.124695 GGCTCAATGGACCCCGTC 60.125 66.667 0.00 0.00 0.00 4.79
452 631 2.610859 AGGCTCAATGGACCCCGT 60.611 61.111 0.00 0.00 0.00 5.28
453 632 2.124570 CAGGCTCAATGGACCCCG 60.125 66.667 0.00 0.00 0.00 5.73
454 633 0.251787 AAACAGGCTCAATGGACCCC 60.252 55.000 0.00 0.00 0.00 4.95
455 634 1.632589 AAAACAGGCTCAATGGACCC 58.367 50.000 0.00 0.00 0.00 4.46
456 635 4.864704 TTTAAAACAGGCTCAATGGACC 57.135 40.909 0.00 0.00 0.00 4.46
566 745 9.612066 TGTGTAGCATGACAATAATCTATTTGA 57.388 29.630 0.00 0.00 0.00 2.69
593 772 4.227864 TGGGCCAGATTTTTGTGTTTTT 57.772 36.364 0.00 0.00 0.00 1.94
594 773 3.922171 TGGGCCAGATTTTTGTGTTTT 57.078 38.095 0.00 0.00 0.00 2.43
595 774 3.922171 TTGGGCCAGATTTTTGTGTTT 57.078 38.095 6.23 0.00 0.00 2.83
596 775 3.922171 TTTGGGCCAGATTTTTGTGTT 57.078 38.095 6.23 0.00 0.00 3.32
597 776 4.141528 TGAATTTGGGCCAGATTTTTGTGT 60.142 37.500 21.83 0.00 0.00 3.72
598 777 4.387598 TGAATTTGGGCCAGATTTTTGTG 58.612 39.130 21.83 0.00 0.00 3.33
599 778 4.703379 TGAATTTGGGCCAGATTTTTGT 57.297 36.364 21.83 0.72 0.00 2.83
600 779 4.820716 TGTTGAATTTGGGCCAGATTTTTG 59.179 37.500 21.83 0.00 0.00 2.44
601 780 5.046288 TGTTGAATTTGGGCCAGATTTTT 57.954 34.783 21.83 2.37 0.00 1.94
602 781 4.703379 TGTTGAATTTGGGCCAGATTTT 57.297 36.364 21.83 3.13 0.00 1.82
603 782 4.347583 TCTTGTTGAATTTGGGCCAGATTT 59.652 37.500 21.83 10.18 0.00 2.17
604 783 3.903090 TCTTGTTGAATTTGGGCCAGATT 59.097 39.130 21.17 21.17 0.00 2.40
605 784 3.509442 TCTTGTTGAATTTGGGCCAGAT 58.491 40.909 6.23 4.63 0.00 2.90
606 785 2.956132 TCTTGTTGAATTTGGGCCAGA 58.044 42.857 6.23 1.42 0.00 3.86
607 786 3.749665 TTCTTGTTGAATTTGGGCCAG 57.250 42.857 6.23 0.00 0.00 4.85
608 787 4.494091 TTTTCTTGTTGAATTTGGGCCA 57.506 36.364 0.00 0.00 34.24 5.36
609 788 5.764686 AGATTTTTCTTGTTGAATTTGGGCC 59.235 36.000 0.00 0.00 34.24 5.80
610 789 6.482973 TGAGATTTTTCTTGTTGAATTTGGGC 59.517 34.615 0.00 0.00 34.24 5.36
611 790 8.611654 ATGAGATTTTTCTTGTTGAATTTGGG 57.388 30.769 0.00 0.00 34.24 4.12
649 828 9.868277 TGTGATGTACAAAAGAAAAAGACAAAT 57.132 25.926 0.00 0.00 36.06 2.32
650 829 9.868277 ATGTGATGTACAAAAGAAAAAGACAAA 57.132 25.926 0.00 0.00 43.77 2.83
685 864 9.981114 TGTACGTATGAGATTTCATGAACATAT 57.019 29.630 7.89 0.00 43.76 1.78
686 865 9.981114 ATGTACGTATGAGATTTCATGAACATA 57.019 29.630 7.89 9.71 43.76 2.29
687 866 8.893219 ATGTACGTATGAGATTTCATGAACAT 57.107 30.769 7.89 10.70 43.76 2.71
688 867 9.244799 GTATGTACGTATGAGATTTCATGAACA 57.755 33.333 7.89 3.11 43.76 3.18
689 868 9.464714 AGTATGTACGTATGAGATTTCATGAAC 57.535 33.333 7.89 0.00 43.76 3.18
692 871 9.893305 TGTAGTATGTACGTATGAGATTTCATG 57.107 33.333 8.95 0.00 43.76 3.07
693 872 9.894783 GTGTAGTATGTACGTATGAGATTTCAT 57.105 33.333 3.95 3.95 45.77 2.57
694 873 8.895737 TGTGTAGTATGTACGTATGAGATTTCA 58.104 33.333 0.00 0.00 37.81 2.69
695 874 9.894783 ATGTGTAGTATGTACGTATGAGATTTC 57.105 33.333 0.00 0.00 0.00 2.17
699 878 9.498176 ACATATGTGTAGTATGTACGTATGAGA 57.502 33.333 7.78 0.00 42.61 3.27
700 879 9.543018 CACATATGTGTAGTATGTACGTATGAG 57.457 37.037 24.91 13.64 42.61 2.90
722 901 9.301897 TGAGATAGAGTATACACATAAGCACAT 57.698 33.333 5.50 0.00 0.00 3.21
723 902 8.691661 TGAGATAGAGTATACACATAAGCACA 57.308 34.615 5.50 0.00 0.00 4.57
724 903 9.004717 TCTGAGATAGAGTATACACATAAGCAC 57.995 37.037 5.50 0.00 0.00 4.40
725 904 9.746457 ATCTGAGATAGAGTATACACATAAGCA 57.254 33.333 5.50 0.00 39.20 3.91
856 1035 0.110823 GTGTAGTTGCGGAAAGTGCG 60.111 55.000 0.00 0.00 34.24 5.34
1527 1714 4.394712 GTGGAGCCGACACCAGGG 62.395 72.222 0.00 0.00 37.20 4.45
1676 1863 0.798776 GGCCAGTTGAGTGACGAATG 59.201 55.000 0.00 0.00 0.00 2.67
1677 1864 0.396435 TGGCCAGTTGAGTGACGAAT 59.604 50.000 0.00 0.00 0.00 3.34
1678 1865 0.179234 TTGGCCAGTTGAGTGACGAA 59.821 50.000 5.11 0.00 0.00 3.85
2069 2282 9.872721 TCGTAGGACAATATGTTACATTTACAA 57.127 29.630 2.23 0.00 0.00 2.41
2083 2296 5.648178 TGTTAAGTGCTCGTAGGACAATA 57.352 39.130 8.66 0.87 39.19 1.90
2084 2297 4.530710 TGTTAAGTGCTCGTAGGACAAT 57.469 40.909 8.66 1.60 39.19 2.71
2085 2298 4.325028 TTGTTAAGTGCTCGTAGGACAA 57.675 40.909 8.66 0.00 39.19 3.18
2086 2299 4.325028 TTTGTTAAGTGCTCGTAGGACA 57.675 40.909 8.66 0.00 39.19 4.02
2087 2300 4.435651 GCATTTGTTAAGTGCTCGTAGGAC 60.436 45.833 2.34 0.00 36.76 3.85
2089 2302 3.435327 TGCATTTGTTAAGTGCTCGTAGG 59.565 43.478 9.81 0.00 39.52 3.18
2090 2303 4.661993 TGCATTTGTTAAGTGCTCGTAG 57.338 40.909 9.81 0.00 39.52 3.51
2091 2304 4.454161 ACATGCATTTGTTAAGTGCTCGTA 59.546 37.500 0.00 0.00 39.52 3.43
2092 2305 3.253188 ACATGCATTTGTTAAGTGCTCGT 59.747 39.130 0.00 4.92 39.52 4.18
2093 2306 3.825308 ACATGCATTTGTTAAGTGCTCG 58.175 40.909 0.00 4.42 39.52 5.03
2094 2307 4.797471 TGACATGCATTTGTTAAGTGCTC 58.203 39.130 0.00 1.67 39.52 4.26
2095 2308 4.852134 TGACATGCATTTGTTAAGTGCT 57.148 36.364 0.00 0.00 39.52 4.40
2107 2320 6.585695 AGTCTTCTTGAAAATGACATGCAT 57.414 33.333 0.00 0.00 39.43 3.96
2108 2321 7.609146 AGATAGTCTTCTTGAAAATGACATGCA 59.391 33.333 0.00 0.00 0.00 3.96
2124 2337 9.327628 GGGGATGTAAAGTAAAAGATAGTCTTC 57.672 37.037 0.00 0.00 35.27 2.87
2125 2338 8.832735 TGGGGATGTAAAGTAAAAGATAGTCTT 58.167 33.333 0.00 0.00 38.59 3.01
2126 2339 8.388656 TGGGGATGTAAAGTAAAAGATAGTCT 57.611 34.615 0.00 0.00 0.00 3.24
2129 2342 8.980481 ACATGGGGATGTAAAGTAAAAGATAG 57.020 34.615 0.00 0.00 32.14 2.08
2131 2344 7.410174 TGACATGGGGATGTAAAGTAAAAGAT 58.590 34.615 0.00 0.00 34.45 2.40
2133 2346 7.645058 ATGACATGGGGATGTAAAGTAAAAG 57.355 36.000 0.00 0.00 34.45 2.27
2134 2347 8.429237 AAATGACATGGGGATGTAAAGTAAAA 57.571 30.769 0.00 0.00 34.45 1.52
2135 2348 8.429237 AAAATGACATGGGGATGTAAAGTAAA 57.571 30.769 0.00 0.00 34.45 2.01
2136 2349 8.429237 AAAAATGACATGGGGATGTAAAGTAA 57.571 30.769 0.00 0.00 34.45 2.24
2138 2351 6.933514 AAAAATGACATGGGGATGTAAAGT 57.066 33.333 0.00 0.00 34.45 2.66
2143 2356 5.957168 TCACATAAAAATGACATGGGGATGT 59.043 36.000 0.00 0.00 37.50 3.06
2144 2357 6.468333 TCACATAAAAATGACATGGGGATG 57.532 37.500 0.00 0.00 0.00 3.51
2145 2358 8.961293 ATATCACATAAAAATGACATGGGGAT 57.039 30.769 0.00 0.00 0.00 3.85
2222 2458 3.290710 GGGAGCAAATAAAGAGATGCCA 58.709 45.455 0.00 0.00 39.59 4.92
2385 2627 7.448161 TCATTTTCTGCATAGGAAGAAGTCAAA 59.552 33.333 0.00 0.00 39.86 2.69
2397 2639 6.293516 GCTTCCTCATCTCATTTTCTGCATAG 60.294 42.308 0.00 0.00 0.00 2.23
2510 2753 0.516001 TCTCTCGGTCAAACGACTCG 59.484 55.000 0.00 0.00 38.06 4.18
2514 2757 1.951602 TCAACTCTCTCGGTCAAACGA 59.048 47.619 0.00 0.00 41.13 3.85
2515 2758 2.417339 TCAACTCTCTCGGTCAAACG 57.583 50.000 0.00 0.00 0.00 3.60
2516 2759 2.471743 CGTTCAACTCTCTCGGTCAAAC 59.528 50.000 0.00 0.00 0.00 2.93
2558 2801 5.780282 TCCTTTCTCTCATCCTCACACTAAA 59.220 40.000 0.00 0.00 0.00 1.85
2591 2834 2.290387 TGCCAATGTCGTAAGCCCTAAA 60.290 45.455 0.00 0.00 37.18 1.85
2608 2851 1.261480 ATACCGCCAAATTGTTGCCA 58.739 45.000 0.00 0.00 33.01 4.92


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

AutoCloner maintained by Alex Coulton.