Multiple sequence alignment - TraesCS4A01G056600

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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 TraesCS4A01G056600 chr4A 100.000 2738 0 0 1 2738 47456805 47454068 0.000000e+00 5057.0
1 TraesCS4A01G056600 chr4A 88.119 1111 96 19 1178 2272 47709506 47710596 0.000000e+00 1288.0
2 TraesCS4A01G056600 chr4A 90.219 777 64 8 1154 1923 47650087 47650858 0.000000e+00 1003.0
3 TraesCS4A01G056600 chr4A 87.642 704 56 19 83 766 47708334 47709026 0.000000e+00 789.0
4 TraesCS4A01G056600 chr4A 88.623 501 50 4 805 1302 47709029 47709525 1.080000e-168 603.0
5 TraesCS4A01G056600 chr4A 85.610 549 56 11 759 1302 47736064 47736594 3.080000e-154 555.0
6 TraesCS4A01G056600 chr4A 100.000 50 0 0 597 646 47708803 47708852 2.900000e-15 93.5
7 TraesCS4A01G056600 chr4B 90.758 1569 96 14 1177 2738 513451083 513452609 0.000000e+00 2049.0
8 TraesCS4A01G056600 chr4B 88.873 1402 118 23 729 2121 512797963 512796591 0.000000e+00 1690.0
9 TraesCS4A01G056600 chr4B 81.770 1514 134 63 709 2160 513079433 513078000 0.000000e+00 1136.0
10 TraesCS4A01G056600 chr4B 92.820 571 23 8 83 646 513449909 513450468 0.000000e+00 811.0
11 TraesCS4A01G056600 chr4B 88.705 664 60 8 642 1302 513450515 513451166 0.000000e+00 797.0
12 TraesCS4A01G056600 chr4D 89.372 1496 128 15 642 2121 416146754 416145274 0.000000e+00 1853.0
13 TraesCS4A01G056600 chr4D 89.963 1335 88 21 896 2200 416577811 416579129 0.000000e+00 1681.0
14 TraesCS4A01G056600 chr4D 86.686 1367 129 27 709 2045 416429758 416428415 0.000000e+00 1467.0
15 TraesCS4A01G056600 chr4D 89.901 1010 67 15 1194 2200 416643072 416644049 0.000000e+00 1267.0
16 TraesCS4A01G056600 chr4D 93.323 629 42 0 1177 1805 416694199 416694827 0.000000e+00 929.0
17 TraesCS4A01G056600 chr4D 91.564 569 32 7 83 646 416577004 416577561 0.000000e+00 771.0
18 TraesCS4A01G056600 chr4D 91.388 569 33 7 83 646 416147358 416146801 0.000000e+00 765.0
19 TraesCS4A01G056600 chr4D 88.704 602 53 9 704 1302 416642303 416642892 0.000000e+00 721.0
20 TraesCS4A01G056600 chr4D 88.704 602 53 9 704 1302 416693630 416694219 0.000000e+00 721.0
21 TraesCS4A01G056600 chr4D 89.883 257 12 10 2323 2576 416695160 416695405 4.400000e-83 318.0
22 TraesCS4A01G056600 chr4D 89.024 246 20 3 684 929 416423059 416422821 5.730000e-77 298.0
23 TraesCS4A01G056600 chr4D 92.718 206 15 0 642 847 416577608 416577813 5.730000e-77 298.0
24 TraesCS4A01G056600 chr4D 90.000 190 17 2 2060 2248 416694978 416695166 7.570000e-61 244.0
25 TraesCS4A01G056600 chr4D 94.505 91 5 0 2648 2738 416695438 416695528 1.020000e-29 141.0
26 TraesCS4A01G056600 chr4D 93.220 59 4 0 2089 2147 416688697 416688755 1.350000e-13 87.9
27 TraesCS4A01G056600 chr6A 89.643 560 35 8 83 638 26094848 26094308 0.000000e+00 691.0
28 TraesCS4A01G056600 chr6A 88.750 560 40 8 83 638 26028454 26027914 0.000000e+00 664.0
29 TraesCS4A01G056600 chr6A 90.244 164 9 2 351 514 188431790 188431946 9.940000e-50 207.0
30 TraesCS4A01G056600 chr6A 89.634 164 10 2 351 514 414044469 414044625 4.620000e-48 202.0
31 TraesCS4A01G056600 chr6A 97.436 39 1 0 474 512 361775399 361775437 1.760000e-07 67.6
32 TraesCS4A01G056600 chr6A 97.436 39 1 0 474 512 581688603 581688565 1.760000e-07 67.6
33 TraesCS4A01G056600 chr7A 89.107 560 37 9 83 638 646297915 646298454 0.000000e+00 675.0
34 TraesCS4A01G056600 chr7A 93.730 319 17 2 83 398 123685402 123685720 2.470000e-130 475.0
35 TraesCS4A01G056600 chr7A 86.538 260 13 7 381 638 660698189 660697950 1.620000e-67 267.0
36 TraesCS4A01G056600 chr7A 91.304 161 7 2 354 514 490929172 490929019 2.140000e-51 213.0
37 TraesCS4A01G056600 chr7A 96.341 82 3 0 1 82 85260328 85260247 4.760000e-28 135.0
38 TraesCS4A01G056600 chr1A 93.103 319 19 2 83 398 535521641 535521959 5.340000e-127 464.0
39 TraesCS4A01G056600 chr1A 88.636 220 10 5 422 638 70750008 70750215 1.260000e-63 254.0
40 TraesCS4A01G056600 chr1A 90.683 161 8 2 354 514 439679362 439679209 9.940000e-50 207.0
41 TraesCS4A01G056600 chr3A 86.923 260 12 7 381 638 244516570 244516809 3.470000e-69 272.0
42 TraesCS4A01G056600 chr3A 95.181 83 4 0 1 83 588516369 588516287 6.150000e-27 132.0
43 TraesCS4A01G056600 chr3A 93.902 82 5 0 1 82 13366443 13366362 1.030000e-24 124.0
44 TraesCS4A01G056600 chr3A 92.941 85 5 1 3 86 544423334 544423418 3.700000e-24 122.0
45 TraesCS4A01G056600 chr2A 85.824 261 13 9 381 638 491175909 491176148 3.500000e-64 255.0
46 TraesCS4A01G056600 chrUn 93.478 92 5 1 1 91 362714051 362714142 4.760000e-28 135.0
47 TraesCS4A01G056600 chrUn 92.632 95 6 1 1 94 405290136 405290042 4.760000e-28 135.0
48 TraesCS4A01G056600 chr2B 96.341 82 3 0 1 82 634082880 634082799 4.760000e-28 135.0
49 TraesCS4A01G056600 chr6D 92.941 85 5 1 1 84 382208184 382208100 3.700000e-24 122.0
50 TraesCS4A01G056600 chr5B 92.857 84 6 0 1 84 633679620 633679703 3.700000e-24 122.0


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 TraesCS4A01G056600 chr4A 47454068 47456805 2737 True 5057.000000 5057 100.0000 1 2738 1 chr4A.!!$R1 2737
1 TraesCS4A01G056600 chr4A 47650087 47650858 771 False 1003.000000 1003 90.2190 1154 1923 1 chr4A.!!$F1 769
2 TraesCS4A01G056600 chr4A 47708334 47710596 2262 False 693.375000 1288 91.0960 83 2272 4 chr4A.!!$F3 2189
3 TraesCS4A01G056600 chr4A 47736064 47736594 530 False 555.000000 555 85.6100 759 1302 1 chr4A.!!$F2 543
4 TraesCS4A01G056600 chr4B 512796591 512797963 1372 True 1690.000000 1690 88.8730 729 2121 1 chr4B.!!$R1 1392
5 TraesCS4A01G056600 chr4B 513449909 513452609 2700 False 1219.000000 2049 90.7610 83 2738 3 chr4B.!!$F1 2655
6 TraesCS4A01G056600 chr4B 513078000 513079433 1433 True 1136.000000 1136 81.7700 709 2160 1 chr4B.!!$R2 1451
7 TraesCS4A01G056600 chr4D 416428415 416429758 1343 True 1467.000000 1467 86.6860 709 2045 1 chr4D.!!$R2 1336
8 TraesCS4A01G056600 chr4D 416145274 416147358 2084 True 1309.000000 1853 90.3800 83 2121 2 chr4D.!!$R3 2038
9 TraesCS4A01G056600 chr4D 416642303 416644049 1746 False 994.000000 1267 89.3025 704 2200 2 chr4D.!!$F3 1496
10 TraesCS4A01G056600 chr4D 416577004 416579129 2125 False 916.666667 1681 91.4150 83 2200 3 chr4D.!!$F2 2117
11 TraesCS4A01G056600 chr4D 416693630 416695528 1898 False 470.600000 929 91.2830 704 2738 5 chr4D.!!$F4 2034
12 TraesCS4A01G056600 chr6A 26094308 26094848 540 True 691.000000 691 89.6430 83 638 1 chr6A.!!$R2 555
13 TraesCS4A01G056600 chr6A 26027914 26028454 540 True 664.000000 664 88.7500 83 638 1 chr6A.!!$R1 555
14 TraesCS4A01G056600 chr7A 646297915 646298454 539 False 675.000000 675 89.1070 83 638 1 chr7A.!!$F2 555

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
884 997 0.093026 GTCACGCGGCGATATTATGC 59.907 55.0 30.94 8.05 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 2627 0.179234 TGTTCAGGCGACAACCTTCA 59.821 50.0 0.0 0.0 38.26 3.02 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 2.526873 AGAGGCCGGGTGTGTTCT 60.527 61.111 2.18 0.00 0.00 3.01
18 19 2.047179 GAGGCCGGGTGTGTTCTC 60.047 66.667 2.18 0.00 0.00 2.87
19 20 2.847234 AGGCCGGGTGTGTTCTCA 60.847 61.111 2.18 0.00 0.00 3.27
20 21 2.185310 GAGGCCGGGTGTGTTCTCAT 62.185 60.000 2.18 0.00 0.00 2.90
21 22 1.303317 GGCCGGGTGTGTTCTCATT 60.303 57.895 2.18 0.00 0.00 2.57
22 23 1.586154 GGCCGGGTGTGTTCTCATTG 61.586 60.000 2.18 0.00 0.00 2.82
23 24 0.889186 GCCGGGTGTGTTCTCATTGT 60.889 55.000 2.18 0.00 0.00 2.71
24 25 0.874390 CCGGGTGTGTTCTCATTGTG 59.126 55.000 0.00 0.00 0.00 3.33
25 26 1.593196 CGGGTGTGTTCTCATTGTGT 58.407 50.000 0.00 0.00 0.00 3.72
26 27 1.946768 CGGGTGTGTTCTCATTGTGTT 59.053 47.619 0.00 0.00 0.00 3.32
27 28 2.357637 CGGGTGTGTTCTCATTGTGTTT 59.642 45.455 0.00 0.00 0.00 2.83
28 29 3.705604 GGGTGTGTTCTCATTGTGTTTG 58.294 45.455 0.00 0.00 0.00 2.93
29 30 3.130340 GGGTGTGTTCTCATTGTGTTTGT 59.870 43.478 0.00 0.00 0.00 2.83
30 31 4.336993 GGGTGTGTTCTCATTGTGTTTGTA 59.663 41.667 0.00 0.00 0.00 2.41
31 32 5.009610 GGGTGTGTTCTCATTGTGTTTGTAT 59.990 40.000 0.00 0.00 0.00 2.29
32 33 6.142817 GGTGTGTTCTCATTGTGTTTGTATC 58.857 40.000 0.00 0.00 0.00 2.24
33 34 6.142817 GTGTGTTCTCATTGTGTTTGTATCC 58.857 40.000 0.00 0.00 0.00 2.59
34 35 6.017109 GTGTGTTCTCATTGTGTTTGTATCCT 60.017 38.462 0.00 0.00 0.00 3.24
35 36 6.545666 TGTGTTCTCATTGTGTTTGTATCCTT 59.454 34.615 0.00 0.00 0.00 3.36
36 37 7.068103 TGTGTTCTCATTGTGTTTGTATCCTTT 59.932 33.333 0.00 0.00 0.00 3.11
37 38 7.920682 GTGTTCTCATTGTGTTTGTATCCTTTT 59.079 33.333 0.00 0.00 0.00 2.27
38 39 7.920151 TGTTCTCATTGTGTTTGTATCCTTTTG 59.080 33.333 0.00 0.00 0.00 2.44
39 40 7.815840 TCTCATTGTGTTTGTATCCTTTTGA 57.184 32.000 0.00 0.00 0.00 2.69
40 41 8.408043 TCTCATTGTGTTTGTATCCTTTTGAT 57.592 30.769 0.00 0.00 37.49 2.57
41 42 8.298854 TCTCATTGTGTTTGTATCCTTTTGATG 58.701 33.333 0.00 0.00 34.76 3.07
42 43 6.867816 TCATTGTGTTTGTATCCTTTTGATGC 59.132 34.615 0.00 0.00 36.68 3.91
43 44 6.403866 TTGTGTTTGTATCCTTTTGATGCT 57.596 33.333 0.00 0.00 37.04 3.79
44 45 6.403866 TGTGTTTGTATCCTTTTGATGCTT 57.596 33.333 0.00 0.00 37.04 3.91
45 46 6.446318 TGTGTTTGTATCCTTTTGATGCTTC 58.554 36.000 0.00 0.00 37.04 3.86
46 47 6.040278 TGTGTTTGTATCCTTTTGATGCTTCA 59.960 34.615 0.00 0.00 37.04 3.02
47 48 7.092716 GTGTTTGTATCCTTTTGATGCTTCAT 58.907 34.615 2.75 0.00 37.04 2.57
48 49 7.599998 GTGTTTGTATCCTTTTGATGCTTCATT 59.400 33.333 2.75 0.00 37.04 2.57
49 50 8.149647 TGTTTGTATCCTTTTGATGCTTCATTT 58.850 29.630 2.75 0.00 37.04 2.32
50 51 8.992073 GTTTGTATCCTTTTGATGCTTCATTTT 58.008 29.630 2.75 0.00 37.04 1.82
51 52 8.537049 TTGTATCCTTTTGATGCTTCATTTTG 57.463 30.769 2.75 0.00 37.04 2.44
52 53 7.894708 TGTATCCTTTTGATGCTTCATTTTGA 58.105 30.769 2.75 0.00 37.04 2.69
53 54 8.030692 TGTATCCTTTTGATGCTTCATTTTGAG 58.969 33.333 2.75 0.00 37.04 3.02
54 55 6.409524 TCCTTTTGATGCTTCATTTTGAGT 57.590 33.333 2.75 0.00 0.00 3.41
55 56 6.449698 TCCTTTTGATGCTTCATTTTGAGTC 58.550 36.000 2.75 0.00 0.00 3.36
56 57 6.040729 TCCTTTTGATGCTTCATTTTGAGTCA 59.959 34.615 2.75 0.00 0.00 3.41
57 58 6.702723 CCTTTTGATGCTTCATTTTGAGTCAA 59.297 34.615 0.08 0.08 0.00 3.18
58 59 7.386848 CCTTTTGATGCTTCATTTTGAGTCAAT 59.613 33.333 6.36 0.00 0.00 2.57
59 60 9.414295 CTTTTGATGCTTCATTTTGAGTCAATA 57.586 29.630 6.36 1.98 0.00 1.90
60 61 9.761504 TTTTGATGCTTCATTTTGAGTCAATAA 57.238 25.926 6.36 4.84 0.00 1.40
61 62 9.761504 TTTGATGCTTCATTTTGAGTCAATAAA 57.238 25.926 6.36 0.00 0.00 1.40
62 63 8.975410 TGATGCTTCATTTTGAGTCAATAAAG 57.025 30.769 6.36 9.01 0.00 1.85
63 64 8.579006 TGATGCTTCATTTTGAGTCAATAAAGT 58.421 29.630 6.36 0.00 0.00 2.66
64 65 8.976986 ATGCTTCATTTTGAGTCAATAAAGTC 57.023 30.769 6.36 5.78 0.00 3.01
65 66 7.370383 TGCTTCATTTTGAGTCAATAAAGTCC 58.630 34.615 6.36 0.00 0.00 3.85
66 67 7.014134 TGCTTCATTTTGAGTCAATAAAGTCCA 59.986 33.333 6.36 0.00 0.00 4.02
67 68 7.327032 GCTTCATTTTGAGTCAATAAAGTCCAC 59.673 37.037 6.36 0.00 0.00 4.02
68 69 7.214467 TCATTTTGAGTCAATAAAGTCCACC 57.786 36.000 6.36 0.00 0.00 4.61
69 70 6.208599 TCATTTTGAGTCAATAAAGTCCACCC 59.791 38.462 6.36 0.00 0.00 4.61
70 71 4.993705 TTGAGTCAATAAAGTCCACCCT 57.006 40.909 0.08 0.00 0.00 4.34
71 72 4.993705 TGAGTCAATAAAGTCCACCCTT 57.006 40.909 0.00 0.00 0.00 3.95
72 73 5.319043 TGAGTCAATAAAGTCCACCCTTT 57.681 39.130 0.00 0.00 38.23 3.11
73 74 6.442541 TGAGTCAATAAAGTCCACCCTTTA 57.557 37.500 0.00 0.00 40.24 1.85
74 75 7.027874 TGAGTCAATAAAGTCCACCCTTTAT 57.972 36.000 0.00 0.00 45.19 1.40
75 76 7.110155 TGAGTCAATAAAGTCCACCCTTTATC 58.890 38.462 6.63 0.00 43.46 1.75
76 77 6.113411 AGTCAATAAAGTCCACCCTTTATCG 58.887 40.000 6.63 0.00 43.46 2.92
77 78 6.070424 AGTCAATAAAGTCCACCCTTTATCGA 60.070 38.462 6.63 0.00 43.46 3.59
78 79 6.596497 GTCAATAAAGTCCACCCTTTATCGAA 59.404 38.462 6.63 0.00 43.46 3.71
79 80 7.120138 GTCAATAAAGTCCACCCTTTATCGAAA 59.880 37.037 6.63 0.00 43.46 3.46
80 81 7.666388 TCAATAAAGTCCACCCTTTATCGAAAA 59.334 33.333 6.63 0.00 43.46 2.29
81 82 8.301002 CAATAAAGTCCACCCTTTATCGAAAAA 58.699 33.333 6.63 0.00 43.46 1.94
205 206 1.507562 TGTCAATGTACGGTGCACAG 58.492 50.000 20.43 18.06 0.00 3.66
210 212 2.080286 ATGTACGGTGCACAGACTTC 57.920 50.000 24.13 10.42 0.00 3.01
254 256 2.770164 ACTCAGACATTACAGGTGGC 57.230 50.000 0.00 0.00 0.00 5.01
286 289 2.748532 AGTAGTCACAGTAGAAGCCGTC 59.251 50.000 0.00 0.00 0.00 4.79
356 360 6.093219 CAGGGAACAGAGACTGATAATTTGTG 59.907 42.308 5.76 0.00 35.18 3.33
391 395 9.520515 AAGAAAAGAAAGGAATTACTAGCATGA 57.479 29.630 0.00 0.00 0.00 3.07
549 554 2.635714 TGCAACACATGAGCTATCTGG 58.364 47.619 0.00 0.00 0.00 3.86
550 555 1.332997 GCAACACATGAGCTATCTGGC 59.667 52.381 0.00 0.00 0.00 4.85
551 556 2.635714 CAACACATGAGCTATCTGGCA 58.364 47.619 0.00 0.00 34.17 4.92
554 559 2.172082 ACACATGAGCTATCTGGCACAT 59.828 45.455 0.00 0.00 42.43 3.21
555 560 3.389002 ACACATGAGCTATCTGGCACATA 59.611 43.478 0.00 0.00 40.44 2.29
556 561 3.995048 CACATGAGCTATCTGGCACATAG 59.005 47.826 0.00 5.51 40.44 2.23
557 562 2.827800 TGAGCTATCTGGCACATAGC 57.172 50.000 22.50 22.50 46.32 2.97
561 566 3.892918 GCTATCTGGCACATAGCAAAG 57.107 47.619 24.29 0.00 45.59 2.77
562 567 2.031333 GCTATCTGGCACATAGCAAAGC 60.031 50.000 24.29 4.58 45.59 3.51
563 568 4.547342 GCTATCTGGCACATAGCAAAGCA 61.547 47.826 24.29 0.00 45.59 3.91
564 569 5.988462 GCTATCTGGCACATAGCAAAGCAA 61.988 45.833 24.29 0.00 45.59 3.91
565 570 7.229646 GCTATCTGGCACATAGCAAAGCAAT 62.230 44.000 24.29 0.00 45.59 3.56
566 571 8.612823 GCTATCTGGCACATAGCAAAGCAATT 62.613 42.308 24.29 0.00 45.59 2.32
567 572 9.332719 GCTATCTGGCACATAGCAAAGCAATTA 62.333 40.741 24.29 0.00 45.59 1.40
571 576 4.747810 GCACATAGCAAAGCAATTAACCT 58.252 39.130 0.00 0.00 44.79 3.50
572 577 5.890334 GCACATAGCAAAGCAATTAACCTA 58.110 37.500 0.00 0.00 44.79 3.08
573 578 6.329496 GCACATAGCAAAGCAATTAACCTAA 58.671 36.000 0.00 0.00 44.79 2.69
574 579 6.811170 GCACATAGCAAAGCAATTAACCTAAA 59.189 34.615 0.00 0.00 44.79 1.85
575 580 7.009540 GCACATAGCAAAGCAATTAACCTAAAG 59.990 37.037 0.00 0.00 44.79 1.85
576 581 8.028938 CACATAGCAAAGCAATTAACCTAAAGT 58.971 33.333 0.00 0.00 0.00 2.66
577 582 8.028938 ACATAGCAAAGCAATTAACCTAAAGTG 58.971 33.333 0.00 0.00 0.00 3.16
578 583 5.783111 AGCAAAGCAATTAACCTAAAGTGG 58.217 37.500 0.00 0.00 0.00 4.00
579 584 5.304357 AGCAAAGCAATTAACCTAAAGTGGT 59.696 36.000 0.00 0.00 43.11 4.16
580 585 5.405269 GCAAAGCAATTAACCTAAAGTGGTG 59.595 40.000 0.00 0.00 40.73 4.17
581 586 6.737346 GCAAAGCAATTAACCTAAAGTGGTGA 60.737 38.462 0.00 0.00 40.73 4.02
582 587 6.575162 AAGCAATTAACCTAAAGTGGTGAG 57.425 37.500 0.00 0.00 40.73 3.51
583 588 5.876357 AGCAATTAACCTAAAGTGGTGAGA 58.124 37.500 0.00 0.00 40.73 3.27
584 589 6.485171 AGCAATTAACCTAAAGTGGTGAGAT 58.515 36.000 0.00 0.00 40.73 2.75
585 590 6.599638 AGCAATTAACCTAAAGTGGTGAGATC 59.400 38.462 0.00 0.00 40.73 2.75
586 591 6.374333 GCAATTAACCTAAAGTGGTGAGATCA 59.626 38.462 0.00 0.00 40.73 2.92
587 592 7.626452 GCAATTAACCTAAAGTGGTGAGATCAC 60.626 40.741 4.33 4.33 45.72 3.06
681 783 4.965814 TGATCTCAGAAGTTTGAACTGCT 58.034 39.130 0.00 0.00 45.98 4.24
706 808 3.005367 TGAACTGAATGCGTGACAGACTA 59.995 43.478 16.74 3.59 35.85 2.59
753 855 1.302431 CGTTGTGTCATGGGCTCCA 60.302 57.895 0.00 0.00 38.19 3.86
776 878 4.719369 AACTCGGAGGCGTGCGTC 62.719 66.667 19.59 6.01 38.89 5.19
811 913 0.387878 CGACGCCATGATAGAGCTCC 60.388 60.000 10.93 0.00 0.00 4.70
884 997 0.093026 GTCACGCGGCGATATTATGC 59.907 55.000 30.94 8.05 0.00 3.14
995 1125 4.003788 CGGCCAACTCCAGACGGT 62.004 66.667 2.24 0.00 0.00 4.83
1022 1152 2.586357 GCTCGCATCCGGGTTCTC 60.586 66.667 0.00 0.00 37.25 2.87
1146 1282 4.189188 CACGAGGAGTACGCCCCG 62.189 72.222 17.60 17.60 0.00 5.73
1169 1305 4.514577 CCCTTCGCCGCTCACGAT 62.515 66.667 0.00 0.00 43.93 3.73
1172 1308 1.355563 CTTCGCCGCTCACGATCTA 59.644 57.895 0.00 0.00 43.93 1.98
1190 1470 1.749634 CTACAAGGACTACACTCCGGG 59.250 57.143 0.00 0.00 35.20 5.73
1209 1489 2.363925 AGCCCGGACTACACTCCC 60.364 66.667 0.73 0.00 0.00 4.30
1245 1729 2.437281 CACTCCATCAAGCCCAGACTAT 59.563 50.000 0.00 0.00 0.00 2.12
1250 1734 3.900601 CCATCAAGCCCAGACTATACTCT 59.099 47.826 0.00 0.00 0.00 3.24
1602 2107 3.379445 CCGGACTACACGCCCAGT 61.379 66.667 0.00 0.00 0.00 4.00
1656 2161 0.887836 ACTCGACCACGTCTACAGCA 60.888 55.000 0.00 0.00 40.69 4.41
1781 2296 5.163673 GGAGCAAAACAGATTGGATTCTCTC 60.164 44.000 0.00 0.00 0.00 3.20
1821 2336 6.338214 TGCTATGCATTTGTTTGTTCCTTA 57.662 33.333 3.54 0.00 31.71 2.69
1868 2391 9.129209 TCACGAATCGATGAATATTATCTGAAC 57.871 33.333 10.55 0.00 0.00 3.18
1869 2392 9.133627 CACGAATCGATGAATATTATCTGAACT 57.866 33.333 10.55 0.00 0.00 3.01
1883 2416 7.750229 TTATCTGAACTGAGCTTTTGTTGAT 57.250 32.000 4.98 5.56 0.00 2.57
1958 2499 3.118542 TCTGTTTCTCATCATCGATGCG 58.881 45.455 20.81 13.70 39.63 4.73
2025 2570 4.082408 CCAGCAATTGTCATGTTCTGTGAT 60.082 41.667 7.40 0.00 0.00 3.06
2055 2600 7.946381 TGTACTGATGTCTGAGAGAAGTATT 57.054 36.000 0.00 0.00 0.00 1.89
2057 2602 8.807118 TGTACTGATGTCTGAGAGAAGTATTTT 58.193 33.333 0.00 0.00 0.00 1.82
2065 2615 9.219603 TGTCTGAGAGAAGTATTTTTATGGTTG 57.780 33.333 0.00 0.00 0.00 3.77
2066 2616 8.178313 GTCTGAGAGAAGTATTTTTATGGTTGC 58.822 37.037 0.00 0.00 0.00 4.17
2067 2617 8.103305 TCTGAGAGAAGTATTTTTATGGTTGCT 58.897 33.333 0.00 0.00 0.00 3.91
2068 2618 8.268850 TGAGAGAAGTATTTTTATGGTTGCTC 57.731 34.615 0.00 0.00 0.00 4.26
2069 2619 8.103305 TGAGAGAAGTATTTTTATGGTTGCTCT 58.897 33.333 0.00 0.00 0.00 4.09
2070 2620 8.499403 AGAGAAGTATTTTTATGGTTGCTCTC 57.501 34.615 0.00 0.00 0.00 3.20
2071 2621 8.325046 AGAGAAGTATTTTTATGGTTGCTCTCT 58.675 33.333 0.00 0.00 0.00 3.10
2072 2622 8.273780 AGAAGTATTTTTATGGTTGCTCTCTG 57.726 34.615 0.00 0.00 0.00 3.35
2073 2623 8.103305 AGAAGTATTTTTATGGTTGCTCTCTGA 58.897 33.333 0.00 0.00 0.00 3.27
2074 2624 8.635765 AAGTATTTTTATGGTTGCTCTCTGAA 57.364 30.769 0.00 0.00 0.00 3.02
2075 2625 8.635765 AGTATTTTTATGGTTGCTCTCTGAAA 57.364 30.769 0.00 0.00 0.00 2.69
2076 2626 9.247861 AGTATTTTTATGGTTGCTCTCTGAAAT 57.752 29.630 0.00 0.00 0.00 2.17
2077 2627 9.860898 GTATTTTTATGGTTGCTCTCTGAAATT 57.139 29.630 0.00 0.00 0.00 1.82
2078 2628 8.767478 ATTTTTATGGTTGCTCTCTGAAATTG 57.233 30.769 0.00 0.00 0.00 2.32
2079 2629 7.523293 TTTTATGGTTGCTCTCTGAAATTGA 57.477 32.000 0.00 0.00 0.00 2.57
2080 2630 7.523293 TTTATGGTTGCTCTCTGAAATTGAA 57.477 32.000 0.00 0.00 0.00 2.69
2233 2812 5.873712 ACATGTCAAAATTGTGCTTGTTTGA 59.126 32.000 0.00 0.00 37.58 2.69
2297 2876 2.211468 TAGGTCTCCCGCTGAGCTGA 62.211 60.000 1.78 0.00 41.57 4.26
2300 2879 1.607756 TCTCCCGCTGAGCTGAAGT 60.608 57.895 1.78 0.00 41.18 3.01
2307 2886 1.433534 GCTGAGCTGAAGTACACACC 58.566 55.000 0.00 0.00 0.00 4.16
2310 2889 1.977854 TGAGCTGAAGTACACACCCAT 59.022 47.619 0.00 0.00 0.00 4.00
2315 2894 1.628340 TGAAGTACACACCCATGGAGG 59.372 52.381 15.22 7.23 37.03 4.30
2350 2929 0.517316 GACACTCAACAACCCGATGC 59.483 55.000 0.00 0.00 0.00 3.91
2369 2948 3.413327 TGCCCAATTAGCAAAGTACGAA 58.587 40.909 0.02 0.00 37.28 3.85
2401 2983 5.981315 GGCATTCATATCACAAGGATGTTTG 59.019 40.000 0.00 0.00 37.82 2.93
2508 3090 7.611213 AATACACTGTACTATTGTTTCAGCC 57.389 36.000 10.27 0.00 33.55 4.85
2525 3107 4.901868 TCAGCCTACGTATCAACCTTTTT 58.098 39.130 0.00 0.00 0.00 1.94
2526 3108 4.933400 TCAGCCTACGTATCAACCTTTTTC 59.067 41.667 0.00 0.00 0.00 2.29
2530 3112 1.461897 ACGTATCAACCTTTTTCGCCG 59.538 47.619 0.00 0.00 0.00 6.46
2574 3156 2.571653 TCAGTAAGGAGGGTGATGTTGG 59.428 50.000 0.00 0.00 0.00 3.77
2590 3172 4.447138 TGTTGGTTGGGAATTCTAGTGT 57.553 40.909 5.23 0.00 0.00 3.55
2604 3186 5.656213 TTCTAGTGTTACTTACTCAGGGC 57.344 43.478 0.00 0.00 0.00 5.19
2612 3194 0.744771 CTTACTCAGGGCCCGAAAGC 60.745 60.000 18.44 0.00 0.00 3.51
2625 3207 3.746492 GCCCGAAAGCCACAGTTATATAG 59.254 47.826 0.00 0.00 0.00 1.31
2626 3208 4.742743 GCCCGAAAGCCACAGTTATATAGT 60.743 45.833 0.00 0.00 0.00 2.12
2627 3209 5.510179 GCCCGAAAGCCACAGTTATATAGTA 60.510 44.000 0.00 0.00 0.00 1.82
2629 3211 6.590292 CCCGAAAGCCACAGTTATATAGTATG 59.410 42.308 0.00 0.00 0.00 2.39
2630 3212 6.590292 CCGAAAGCCACAGTTATATAGTATGG 59.410 42.308 0.00 0.00 0.00 2.74
2631 3213 7.152645 CGAAAGCCACAGTTATATAGTATGGT 58.847 38.462 0.00 0.00 0.00 3.55
2632 3214 7.656137 CGAAAGCCACAGTTATATAGTATGGTT 59.344 37.037 0.00 0.00 0.00 3.67
2633 3215 8.904099 AAAGCCACAGTTATATAGTATGGTTC 57.096 34.615 0.00 0.00 0.00 3.62
2634 3216 7.612065 AGCCACAGTTATATAGTATGGTTCA 57.388 36.000 0.00 0.00 0.00 3.18
2635 3217 7.442656 AGCCACAGTTATATAGTATGGTTCAC 58.557 38.462 0.00 0.00 0.00 3.18
2636 3218 6.649557 GCCACAGTTATATAGTATGGTTCACC 59.350 42.308 0.00 0.00 0.00 4.02
2637 3219 7.472945 GCCACAGTTATATAGTATGGTTCACCT 60.473 40.741 0.00 0.00 36.82 4.00
2638 3220 7.872993 CCACAGTTATATAGTATGGTTCACCTG 59.127 40.741 0.00 0.00 36.82 4.00
2639 3221 8.421784 CACAGTTATATAGTATGGTTCACCTGT 58.578 37.037 0.00 0.00 36.82 4.00
2640 3222 8.639761 ACAGTTATATAGTATGGTTCACCTGTC 58.360 37.037 0.00 0.00 36.82 3.51
2641 3223 8.638873 CAGTTATATAGTATGGTTCACCTGTCA 58.361 37.037 0.00 0.00 36.82 3.58
2642 3224 8.639761 AGTTATATAGTATGGTTCACCTGTCAC 58.360 37.037 0.00 0.00 36.82 3.67
2643 3225 4.755266 ATAGTATGGTTCACCTGTCACC 57.245 45.455 0.00 0.00 36.82 4.02
2644 3226 2.621070 AGTATGGTTCACCTGTCACCT 58.379 47.619 0.00 0.00 36.82 4.00
2645 3227 2.303022 AGTATGGTTCACCTGTCACCTG 59.697 50.000 0.00 0.00 36.82 4.00
2646 3228 1.140312 ATGGTTCACCTGTCACCTGT 58.860 50.000 0.00 0.00 36.82 4.00
2711 3293 2.032675 GCAGGGCTTCGATCTTCATTTC 59.967 50.000 0.00 0.00 0.00 2.17
2723 3305 5.630680 CGATCTTCATTTCCACCAACAAAAG 59.369 40.000 0.00 0.00 0.00 2.27
2730 3312 4.497473 TTCCACCAACAAAAGAATAGCG 57.503 40.909 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.526873 AGAACACACCCGGCCTCT 60.527 61.111 0.00 0.00 0.00 3.69
1 2 2.047179 GAGAACACACCCGGCCTC 60.047 66.667 0.00 0.00 0.00 4.70
2 3 1.779061 AATGAGAACACACCCGGCCT 61.779 55.000 0.00 0.00 0.00 5.19
3 4 1.303317 AATGAGAACACACCCGGCC 60.303 57.895 0.00 0.00 0.00 6.13
4 5 0.889186 ACAATGAGAACACACCCGGC 60.889 55.000 0.00 0.00 0.00 6.13
5 6 0.874390 CACAATGAGAACACACCCGG 59.126 55.000 0.00 0.00 0.00 5.73
6 7 1.593196 ACACAATGAGAACACACCCG 58.407 50.000 0.00 0.00 0.00 5.28
7 8 3.130340 ACAAACACAATGAGAACACACCC 59.870 43.478 0.00 0.00 0.00 4.61
8 9 4.370364 ACAAACACAATGAGAACACACC 57.630 40.909 0.00 0.00 0.00 4.16
9 10 6.017109 AGGATACAAACACAATGAGAACACAC 60.017 38.462 0.00 0.00 41.41 3.82
10 11 6.061441 AGGATACAAACACAATGAGAACACA 58.939 36.000 0.00 0.00 41.41 3.72
11 12 6.560253 AGGATACAAACACAATGAGAACAC 57.440 37.500 0.00 0.00 41.41 3.32
12 13 7.581213 AAAGGATACAAACACAATGAGAACA 57.419 32.000 0.00 0.00 41.41 3.18
13 14 8.134895 TCAAAAGGATACAAACACAATGAGAAC 58.865 33.333 0.00 0.00 41.41 3.01
14 15 8.231692 TCAAAAGGATACAAACACAATGAGAA 57.768 30.769 0.00 0.00 41.41 2.87
15 16 7.815840 TCAAAAGGATACAAACACAATGAGA 57.184 32.000 0.00 0.00 41.41 3.27
16 17 7.062605 GCATCAAAAGGATACAAACACAATGAG 59.937 37.037 0.00 0.00 41.41 2.90
17 18 6.867816 GCATCAAAAGGATACAAACACAATGA 59.132 34.615 0.00 0.00 41.41 2.57
18 19 6.869913 AGCATCAAAAGGATACAAACACAATG 59.130 34.615 0.00 0.00 41.41 2.82
19 20 6.996509 AGCATCAAAAGGATACAAACACAAT 58.003 32.000 0.00 0.00 41.41 2.71
20 21 6.403866 AGCATCAAAAGGATACAAACACAA 57.596 33.333 0.00 0.00 41.41 3.33
21 22 6.040278 TGAAGCATCAAAAGGATACAAACACA 59.960 34.615 0.00 0.00 33.95 3.72
22 23 6.446318 TGAAGCATCAAAAGGATACAAACAC 58.554 36.000 0.00 0.00 33.95 3.32
23 24 6.647334 TGAAGCATCAAAAGGATACAAACA 57.353 33.333 0.00 0.00 33.95 2.83
24 25 8.538409 AAATGAAGCATCAAAAGGATACAAAC 57.462 30.769 0.00 0.00 39.49 2.93
25 26 8.991026 CAAAATGAAGCATCAAAAGGATACAAA 58.009 29.630 0.00 0.00 39.49 2.83
26 27 8.366401 TCAAAATGAAGCATCAAAAGGATACAA 58.634 29.630 0.00 0.00 39.49 2.41
27 28 7.894708 TCAAAATGAAGCATCAAAAGGATACA 58.105 30.769 0.00 0.00 39.49 2.29
28 29 8.031277 ACTCAAAATGAAGCATCAAAAGGATAC 58.969 33.333 0.00 0.00 39.49 2.24
29 30 8.125978 ACTCAAAATGAAGCATCAAAAGGATA 57.874 30.769 0.00 0.00 39.49 2.59
30 31 7.001099 ACTCAAAATGAAGCATCAAAAGGAT 57.999 32.000 0.00 0.00 39.49 3.24
31 32 6.040729 TGACTCAAAATGAAGCATCAAAAGGA 59.959 34.615 0.00 0.00 39.49 3.36
32 33 6.218019 TGACTCAAAATGAAGCATCAAAAGG 58.782 36.000 0.00 0.00 39.49 3.11
33 34 7.703298 TTGACTCAAAATGAAGCATCAAAAG 57.297 32.000 0.00 0.00 39.49 2.27
34 35 9.761504 TTATTGACTCAAAATGAAGCATCAAAA 57.238 25.926 0.00 0.00 39.49 2.44
35 36 9.761504 TTTATTGACTCAAAATGAAGCATCAAA 57.238 25.926 0.00 0.00 39.49 2.69
36 37 9.414295 CTTTATTGACTCAAAATGAAGCATCAA 57.586 29.630 0.00 0.00 39.49 2.57
37 38 8.579006 ACTTTATTGACTCAAAATGAAGCATCA 58.421 29.630 0.00 0.00 35.25 3.07
38 39 8.976986 ACTTTATTGACTCAAAATGAAGCATC 57.023 30.769 0.00 0.00 35.25 3.91
39 40 8.031277 GGACTTTATTGACTCAAAATGAAGCAT 58.969 33.333 0.00 0.00 35.25 3.79
40 41 7.014134 TGGACTTTATTGACTCAAAATGAAGCA 59.986 33.333 0.00 0.00 35.25 3.91
41 42 7.327032 GTGGACTTTATTGACTCAAAATGAAGC 59.673 37.037 0.00 0.00 35.25 3.86
42 43 7.809806 GGTGGACTTTATTGACTCAAAATGAAG 59.190 37.037 0.00 1.51 36.93 3.02
43 44 7.255801 GGGTGGACTTTATTGACTCAAAATGAA 60.256 37.037 0.00 0.00 0.00 2.57
44 45 6.208599 GGGTGGACTTTATTGACTCAAAATGA 59.791 38.462 0.00 0.00 0.00 2.57
45 46 6.209391 AGGGTGGACTTTATTGACTCAAAATG 59.791 38.462 0.00 0.00 0.00 2.32
46 47 6.314917 AGGGTGGACTTTATTGACTCAAAAT 58.685 36.000 0.00 0.00 0.00 1.82
47 48 5.701224 AGGGTGGACTTTATTGACTCAAAA 58.299 37.500 0.00 0.00 0.00 2.44
48 49 5.319043 AGGGTGGACTTTATTGACTCAAA 57.681 39.130 0.00 0.00 0.00 2.69
49 50 4.993705 AGGGTGGACTTTATTGACTCAA 57.006 40.909 0.00 0.00 0.00 3.02
50 51 4.993705 AAGGGTGGACTTTATTGACTCA 57.006 40.909 0.00 0.00 0.00 3.41
79 80 8.669243 GCTCAGTAGCTAATACATTCAGTTTTT 58.331 33.333 0.00 0.00 45.85 1.94
80 81 8.202745 GCTCAGTAGCTAATACATTCAGTTTT 57.797 34.615 0.00 0.00 45.85 2.43
81 82 7.778470 GCTCAGTAGCTAATACATTCAGTTT 57.222 36.000 0.00 0.00 45.85 2.66
182 183 4.257731 TGTGCACCGTACATTGACATATT 58.742 39.130 15.69 0.00 0.00 1.28
193 194 1.137513 GTGAAGTCTGTGCACCGTAC 58.862 55.000 15.69 9.71 0.00 3.67
197 198 1.668419 AACAGTGAAGTCTGTGCACC 58.332 50.000 15.69 0.00 46.25 5.01
205 206 8.812329 GTTACTGATGATGATAACAGTGAAGTC 58.188 37.037 0.00 0.00 42.37 3.01
210 212 9.546909 GTTTTGTTACTGATGATGATAACAGTG 57.453 33.333 0.00 0.00 42.37 3.66
373 377 7.800092 AGAGATGTCATGCTAGTAATTCCTTT 58.200 34.615 0.00 0.00 0.00 3.11
376 380 7.812191 CAGTAGAGATGTCATGCTAGTAATTCC 59.188 40.741 0.00 0.00 0.00 3.01
391 395 6.162079 CACATGTTCAGTTCAGTAGAGATGT 58.838 40.000 0.00 0.00 0.00 3.06
430 435 5.463286 TGTTCAACATCAGACATCATTTGC 58.537 37.500 0.00 0.00 0.00 3.68
431 436 7.933728 TTTGTTCAACATCAGACATCATTTG 57.066 32.000 0.00 0.00 0.00 2.32
432 437 7.601130 CCATTTGTTCAACATCAGACATCATTT 59.399 33.333 0.00 0.00 0.00 2.32
433 438 7.094631 CCATTTGTTCAACATCAGACATCATT 58.905 34.615 0.00 0.00 0.00 2.57
434 439 6.627243 CCATTTGTTCAACATCAGACATCAT 58.373 36.000 0.00 0.00 0.00 2.45
435 440 5.565242 GCCATTTGTTCAACATCAGACATCA 60.565 40.000 0.00 0.00 0.00 3.07
436 441 4.860907 GCCATTTGTTCAACATCAGACATC 59.139 41.667 0.00 0.00 0.00 3.06
437 442 4.281435 TGCCATTTGTTCAACATCAGACAT 59.719 37.500 0.00 0.00 0.00 3.06
507 512 5.674569 GCATTTGCCATGGCTATTATAGACG 60.675 44.000 35.53 15.93 42.51 4.18
549 554 4.747810 AGGTTAATTGCTTTGCTATGTGC 58.252 39.130 0.00 0.00 43.25 4.57
550 555 8.028938 ACTTTAGGTTAATTGCTTTGCTATGTG 58.971 33.333 0.00 0.00 0.00 3.21
551 556 8.028938 CACTTTAGGTTAATTGCTTTGCTATGT 58.971 33.333 0.00 0.00 0.00 2.29
554 559 6.492087 ACCACTTTAGGTTAATTGCTTTGCTA 59.508 34.615 0.00 0.00 39.34 3.49
555 560 5.304357 ACCACTTTAGGTTAATTGCTTTGCT 59.696 36.000 0.00 0.00 39.34 3.91
556 561 5.405269 CACCACTTTAGGTTAATTGCTTTGC 59.595 40.000 0.00 0.00 40.77 3.68
557 562 6.744112 TCACCACTTTAGGTTAATTGCTTTG 58.256 36.000 0.00 0.00 40.77 2.77
558 563 6.775629 TCTCACCACTTTAGGTTAATTGCTTT 59.224 34.615 0.00 0.00 40.77 3.51
559 564 6.303839 TCTCACCACTTTAGGTTAATTGCTT 58.696 36.000 0.00 0.00 40.77 3.91
560 565 5.876357 TCTCACCACTTTAGGTTAATTGCT 58.124 37.500 0.00 0.00 40.77 3.91
561 566 6.374333 TGATCTCACCACTTTAGGTTAATTGC 59.626 38.462 0.00 0.00 40.77 3.56
562 567 7.390440 TGTGATCTCACCACTTTAGGTTAATTG 59.610 37.037 7.81 0.00 45.88 2.32
563 568 7.458397 TGTGATCTCACCACTTTAGGTTAATT 58.542 34.615 7.81 0.00 45.88 1.40
564 569 7.016153 TGTGATCTCACCACTTTAGGTTAAT 57.984 36.000 7.81 0.00 45.88 1.40
565 570 6.428083 TGTGATCTCACCACTTTAGGTTAA 57.572 37.500 7.81 0.00 45.88 2.01
566 571 6.428083 TTGTGATCTCACCACTTTAGGTTA 57.572 37.500 7.81 0.00 45.88 2.85
567 572 4.974645 TGTGATCTCACCACTTTAGGTT 57.025 40.909 7.81 0.00 45.88 3.50
568 573 4.974645 TTGTGATCTCACCACTTTAGGT 57.025 40.909 7.81 0.00 45.88 3.08
569 574 7.607991 ACTTAATTGTGATCTCACCACTTTAGG 59.392 37.037 7.81 4.41 45.88 2.69
570 575 8.553459 ACTTAATTGTGATCTCACCACTTTAG 57.447 34.615 7.81 5.04 45.88 1.85
571 576 8.154203 TGACTTAATTGTGATCTCACCACTTTA 58.846 33.333 7.81 0.00 45.88 1.85
572 577 6.998074 TGACTTAATTGTGATCTCACCACTTT 59.002 34.615 7.81 0.20 45.88 2.66
573 578 6.533730 TGACTTAATTGTGATCTCACCACTT 58.466 36.000 7.81 2.16 45.88 3.16
574 579 6.114187 TGACTTAATTGTGATCTCACCACT 57.886 37.500 7.81 0.00 45.88 4.00
575 580 6.992063 ATGACTTAATTGTGATCTCACCAC 57.008 37.500 7.81 0.00 45.88 4.16
576 581 6.763135 GCTATGACTTAATTGTGATCTCACCA 59.237 38.462 7.81 0.00 45.88 4.17
577 582 6.763135 TGCTATGACTTAATTGTGATCTCACC 59.237 38.462 7.81 0.00 45.88 4.02
578 583 7.776933 TGCTATGACTTAATTGTGATCTCAC 57.223 36.000 3.34 3.34 46.59 3.51
579 584 8.791327 TTTGCTATGACTTAATTGTGATCTCA 57.209 30.769 0.00 0.00 0.00 3.27
580 585 7.854916 GCTTTGCTATGACTTAATTGTGATCTC 59.145 37.037 0.00 0.00 0.00 2.75
581 586 7.337689 TGCTTTGCTATGACTTAATTGTGATCT 59.662 33.333 0.00 0.00 0.00 2.75
582 587 7.475015 TGCTTTGCTATGACTTAATTGTGATC 58.525 34.615 0.00 0.00 0.00 2.92
583 588 7.395190 TGCTTTGCTATGACTTAATTGTGAT 57.605 32.000 0.00 0.00 0.00 3.06
584 589 6.816134 TGCTTTGCTATGACTTAATTGTGA 57.184 33.333 0.00 0.00 0.00 3.58
585 590 8.470040 AATTGCTTTGCTATGACTTAATTGTG 57.530 30.769 0.00 0.00 0.00 3.33
588 593 9.586435 GGTTAATTGCTTTGCTATGACTTAATT 57.414 29.630 0.00 0.00 0.00 1.40
589 594 8.971073 AGGTTAATTGCTTTGCTATGACTTAAT 58.029 29.630 0.00 0.00 0.00 1.40
590 595 8.348285 AGGTTAATTGCTTTGCTATGACTTAA 57.652 30.769 0.00 0.00 0.00 1.85
591 596 7.938140 AGGTTAATTGCTTTGCTATGACTTA 57.062 32.000 0.00 0.00 0.00 2.24
592 597 6.840780 AGGTTAATTGCTTTGCTATGACTT 57.159 33.333 0.00 0.00 0.00 3.01
593 598 7.938140 TTAGGTTAATTGCTTTGCTATGACT 57.062 32.000 0.00 0.00 0.00 3.41
594 599 8.244113 ACTTTAGGTTAATTGCTTTGCTATGAC 58.756 33.333 0.00 0.00 0.00 3.06
595 600 8.243426 CACTTTAGGTTAATTGCTTTGCTATGA 58.757 33.333 0.00 0.00 0.00 2.15
681 783 2.802247 CTGTCACGCATTCAGTTCAAGA 59.198 45.455 0.00 0.00 0.00 3.02
706 808 1.745489 GGAACGAGCAATCCGGCTT 60.745 57.895 0.00 0.00 45.99 4.35
753 855 3.382832 CGCCTCCGAGTTCACCCT 61.383 66.667 0.00 0.00 36.29 4.34
995 1125 4.471908 ATGCGAGCGCCATGGTCA 62.472 61.111 14.67 2.77 45.52 4.02
1169 1305 2.619849 CCCGGAGTGTAGTCCTTGTAGA 60.620 54.545 0.73 0.00 34.00 2.59
1172 1308 0.903454 CCCCGGAGTGTAGTCCTTGT 60.903 60.000 0.73 0.00 34.00 3.16
1190 1470 2.424733 GGAGTGTAGTCCGGGCTCC 61.425 68.421 14.54 0.00 38.89 4.70
1209 1489 4.849329 GTGTAGTCGGGGCTCGCG 62.849 72.222 0.00 0.00 41.10 5.87
1245 1729 4.435970 TCGGGGCTCGCCAGAGTA 62.436 66.667 0.00 0.00 46.03 2.59
1306 1811 0.601558 GAAGTGTACTCCAGCGACCA 59.398 55.000 0.00 0.00 0.00 4.02
1509 2014 2.734591 GCGTCAGACACCACCAGA 59.265 61.111 0.41 0.00 0.00 3.86
1543 2048 2.331194 AGTTGACGGTGTGTAATACGC 58.669 47.619 0.00 0.00 39.09 4.42
1781 2296 6.132056 GCATAGCAATTCGAGATTTACACAG 58.868 40.000 0.00 0.00 0.00 3.66
1821 2336 6.757010 CGTGAGTAATACTACAAGATTTGCCT 59.243 38.462 0.00 0.00 0.00 4.75
1868 2391 3.120095 TCGCATGATCAACAAAAGCTCAG 60.120 43.478 0.00 0.00 0.00 3.35
1869 2392 2.813172 TCGCATGATCAACAAAAGCTCA 59.187 40.909 0.00 0.00 0.00 4.26
1938 2479 3.118542 TCGCATCGATGATGAGAAACAG 58.881 45.455 29.20 6.15 43.57 3.16
1958 2499 7.976826 TCAAATCAAATAGGCAATTGCAATTC 58.023 30.769 30.32 15.43 44.36 2.17
2025 2570 5.711976 TCTCTCAGACATCAGTACATCACAA 59.288 40.000 0.00 0.00 0.00 3.33
2055 2600 7.523293 TCAATTTCAGAGAGCAACCATAAAA 57.477 32.000 0.00 0.00 0.00 1.52
2057 2602 6.151648 CCTTCAATTTCAGAGAGCAACCATAA 59.848 38.462 0.00 0.00 0.00 1.90
2065 2615 4.377841 CGACAACCTTCAATTTCAGAGAGC 60.378 45.833 0.00 0.00 0.00 4.09
2066 2616 4.377841 GCGACAACCTTCAATTTCAGAGAG 60.378 45.833 0.00 0.00 0.00 3.20
2067 2617 3.498397 GCGACAACCTTCAATTTCAGAGA 59.502 43.478 0.00 0.00 0.00 3.10
2068 2618 3.365364 GGCGACAACCTTCAATTTCAGAG 60.365 47.826 0.00 0.00 0.00 3.35
2069 2619 2.552315 GGCGACAACCTTCAATTTCAGA 59.448 45.455 0.00 0.00 0.00 3.27
2070 2620 2.554032 AGGCGACAACCTTCAATTTCAG 59.446 45.455 0.00 0.00 36.28 3.02
2071 2621 2.293122 CAGGCGACAACCTTCAATTTCA 59.707 45.455 0.00 0.00 38.26 2.69
2072 2622 2.552315 TCAGGCGACAACCTTCAATTTC 59.448 45.455 0.00 0.00 38.26 2.17
2073 2623 2.582052 TCAGGCGACAACCTTCAATTT 58.418 42.857 0.00 0.00 38.26 1.82
2074 2624 2.270352 TCAGGCGACAACCTTCAATT 57.730 45.000 0.00 0.00 38.26 2.32
2075 2625 1.880027 GTTCAGGCGACAACCTTCAAT 59.120 47.619 0.00 0.00 38.26 2.57
2076 2626 1.305201 GTTCAGGCGACAACCTTCAA 58.695 50.000 0.00 0.00 38.26 2.69
2077 2627 0.179234 TGTTCAGGCGACAACCTTCA 59.821 50.000 0.00 0.00 38.26 3.02
2078 2628 1.523758 ATGTTCAGGCGACAACCTTC 58.476 50.000 0.00 0.00 38.26 3.46
2079 2629 1.981256 AATGTTCAGGCGACAACCTT 58.019 45.000 0.00 0.00 38.26 3.50
2080 2630 1.981256 AAATGTTCAGGCGACAACCT 58.019 45.000 0.00 0.00 42.30 3.50
2233 2812 2.264005 TACAGAACGGGCACACATTT 57.736 45.000 0.00 0.00 0.00 2.32
2297 2876 0.328258 GCCTCCATGGGTGTGTACTT 59.672 55.000 13.02 0.00 36.00 2.24
2300 2879 1.136961 TTGGCCTCCATGGGTGTGTA 61.137 55.000 13.02 0.00 36.00 2.90
2315 2894 2.669569 TCTCAACTGGCGCTTGGC 60.670 61.111 7.64 0.00 42.51 4.52
2350 2929 6.128007 ACAATCTTCGTACTTTGCTAATTGGG 60.128 38.462 0.00 0.00 0.00 4.12
2369 2948 4.795469 TGTGATATGAATGCCCACAATCT 58.205 39.130 0.00 0.00 35.16 2.40
2483 3065 8.537016 AGGCTGAAACAATAGTACAGTGTATTA 58.463 33.333 6.21 7.13 33.44 0.98
2488 3070 5.288712 CGTAGGCTGAAACAATAGTACAGTG 59.711 44.000 0.00 0.00 35.86 3.66
2500 3082 3.858247 AGGTTGATACGTAGGCTGAAAC 58.142 45.455 0.08 0.00 0.00 2.78
2508 3090 3.241868 CGGCGAAAAAGGTTGATACGTAG 60.242 47.826 0.00 0.00 0.00 3.51
2530 3112 4.630940 ACGACTTCTAGTAGTCTAGCACAC 59.369 45.833 22.48 0.51 41.89 3.82
2557 3139 2.041081 CCAACCAACATCACCCTCCTTA 59.959 50.000 0.00 0.00 0.00 2.69
2574 3156 8.092687 TGAGTAAGTAACACTAGAATTCCCAAC 58.907 37.037 0.65 0.00 0.00 3.77
2590 3172 1.941377 TTCGGGCCCTGAGTAAGTAA 58.059 50.000 22.43 0.00 0.00 2.24
2604 3186 4.957296 ACTATATAACTGTGGCTTTCGGG 58.043 43.478 0.00 0.00 0.00 5.14
2612 3194 7.872993 CAGGTGAACCATACTATATAACTGTGG 59.127 40.741 1.62 0.00 38.89 4.17
2625 3207 2.038557 ACAGGTGACAGGTGAACCATAC 59.961 50.000 1.62 0.00 38.89 2.39
2626 3208 2.038426 CACAGGTGACAGGTGAACCATA 59.962 50.000 1.62 0.00 39.43 2.74
2627 3209 1.140312 ACAGGTGACAGGTGAACCAT 58.860 50.000 1.62 0.00 38.89 3.55
2629 3211 0.180406 ACACAGGTGACAGGTGAACC 59.820 55.000 11.90 0.00 39.43 3.62
2630 3212 1.670811 CAACACAGGTGACAGGTGAAC 59.329 52.381 11.90 0.00 39.43 3.18
2631 3213 1.557371 TCAACACAGGTGACAGGTGAA 59.443 47.619 11.90 0.00 39.43 3.18
2632 3214 1.134521 GTCAACACAGGTGACAGGTGA 60.135 52.381 10.12 0.00 39.43 4.02
2633 3215 1.299541 GTCAACACAGGTGACAGGTG 58.700 55.000 10.12 4.61 41.82 4.00
2634 3216 0.908910 TGTCAACACAGGTGACAGGT 59.091 50.000 13.41 0.00 37.61 4.00
2635 3217 2.260844 ATGTCAACACAGGTGACAGG 57.739 50.000 20.76 0.00 44.35 4.00
2636 3218 3.205338 TCAATGTCAACACAGGTGACAG 58.795 45.455 20.76 10.23 44.35 3.51
2637 3219 3.274095 TCAATGTCAACACAGGTGACA 57.726 42.857 18.87 18.87 45.07 3.58
2638 3220 3.120546 CGATCAATGTCAACACAGGTGAC 60.121 47.826 8.19 8.19 34.76 3.67
2639 3221 3.066380 CGATCAATGTCAACACAGGTGA 58.934 45.455 6.40 0.00 35.41 4.02
2640 3222 2.807967 ACGATCAATGTCAACACAGGTG 59.192 45.455 0.00 0.00 35.41 4.00
2641 3223 2.807967 CACGATCAATGTCAACACAGGT 59.192 45.455 0.00 0.00 35.41 4.00
2642 3224 3.066380 TCACGATCAATGTCAACACAGG 58.934 45.455 0.00 0.00 35.41 4.00
2643 3225 3.989817 TCTCACGATCAATGTCAACACAG 59.010 43.478 0.00 0.00 35.41 3.66
2644 3226 3.988819 TCTCACGATCAATGTCAACACA 58.011 40.909 0.00 0.00 36.78 3.72
2645 3227 4.627035 TCATCTCACGATCAATGTCAACAC 59.373 41.667 0.00 0.00 0.00 3.32
2646 3228 4.819769 TCATCTCACGATCAATGTCAACA 58.180 39.130 0.00 0.00 0.00 3.33
2711 3293 2.228822 AGCGCTATTCTTTTGTTGGTGG 59.771 45.455 8.99 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.