Multiple sequence alignment - TraesCS6A01G368400

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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 TraesCS6A01G368400 chr6A 100.000 3049 0 0 309 3357 594651575 594654623 0.000000e+00 5631.0
1 TraesCS6A01G368400 chr6A 93.015 1990 107 18 1172 3147 594608683 594610654 0.000000e+00 2876.0
2 TraesCS6A01G368400 chr6A 90.552 942 41 10 460 1389 594607961 594608866 0.000000e+00 1203.0
3 TraesCS6A01G368400 chr6A 100.000 106 0 0 1 106 594651267 594651372 2.930000e-46 196.0
4 TraesCS6A01G368400 chr6A 96.226 106 4 0 1 106 5075283 5075178 1.370000e-39 174.0
5 TraesCS6A01G368400 chr6A 100.000 74 0 0 3648 3721 594654914 594654987 1.800000e-28 137.0
6 TraesCS6A01G368400 chr6A 97.297 37 0 1 392 427 594607836 594607872 1.120000e-05 62.1
7 TraesCS6A01G368400 chr6B 89.023 2724 206 44 460 3147 679567922 679565256 0.000000e+00 3288.0
8 TraesCS6A01G368400 chr6B 87.206 1829 175 39 1341 3147 679552167 679550376 0.000000e+00 2026.0
9 TraesCS6A01G368400 chr6B 83.333 1512 163 41 470 1941 679397062 679398524 0.000000e+00 1314.0
10 TraesCS6A01G368400 chr6B 87.679 349 22 6 460 787 679568563 679568215 1.620000e-103 387.0
11 TraesCS6A01G368400 chr6B 90.299 134 12 1 1023 1156 679561646 679561514 1.370000e-39 174.0
12 TraesCS6A01G368400 chr6B 87.368 95 7 2 334 427 679568134 679568044 1.830000e-18 104.0
13 TraesCS6A01G368400 chr6D 86.494 2362 209 53 514 2788 448594507 448596845 0.000000e+00 2494.0
14 TraesCS6A01G368400 chr6D 85.676 1487 144 31 1329 2788 448563894 448565338 0.000000e+00 1502.0
15 TraesCS6A01G368400 chr6D 84.054 1179 144 22 1634 2796 448579823 448580973 0.000000e+00 1096.0
16 TraesCS6A01G368400 chr6D 88.556 900 75 18 460 1346 448577376 448578260 0.000000e+00 1066.0
17 TraesCS6A01G368400 chr6D 83.828 606 62 12 720 1318 448563120 448563696 9.090000e-151 544.0
18 TraesCS6A01G368400 chr6D 87.205 297 35 2 1244 1539 448579407 448579701 5.950000e-88 335.0
19 TraesCS6A01G368400 chr6D 86.222 225 18 5 3145 3357 98626191 98626414 8.040000e-57 231.0
20 TraesCS6A01G368400 chr6D 95.789 95 3 1 334 427 448577191 448577285 6.440000e-33 152.0
21 TraesCS6A01G368400 chr6D 97.297 74 2 0 3648 3721 12477961 12477888 3.900000e-25 126.0
22 TraesCS6A01G368400 chr6D 97.297 74 2 0 3648 3721 405122759 405122832 3.900000e-25 126.0
23 TraesCS6A01G368400 chrUn 83.487 1193 149 30 1623 2795 79404540 79405704 0.000000e+00 1068.0
24 TraesCS6A01G368400 chrUn 82.634 1048 139 26 1765 2795 79378408 79379429 0.000000e+00 887.0
25 TraesCS6A01G368400 chrUn 91.269 607 50 2 1262 1868 472326635 472326032 0.000000e+00 824.0
26 TraesCS6A01G368400 chrUn 92.308 416 29 2 1453 1868 477372278 477372690 4.140000e-164 588.0
27 TraesCS6A01G368400 chrUn 78.031 965 154 29 1746 2696 294343963 294344883 4.200000e-154 555.0
28 TraesCS6A01G368400 chrUn 90.840 131 11 1 1023 1153 276954021 276954150 1.370000e-39 174.0
29 TraesCS6A01G368400 chrUn 97.297 74 2 0 3648 3721 36306166 36306239 3.900000e-25 126.0
30 TraesCS6A01G368400 chrUn 97.297 74 2 0 3648 3721 356096540 356096467 3.900000e-25 126.0
31 TraesCS6A01G368400 chrUn 97.297 74 2 0 3648 3721 356142002 356141929 3.900000e-25 126.0
32 TraesCS6A01G368400 chr1D 89.140 221 12 6 3149 3357 424533699 424533919 7.920000e-67 265.0
33 TraesCS6A01G368400 chr1D 85.784 204 24 4 3155 3357 8898137 8898336 1.050000e-50 211.0
34 TraesCS6A01G368400 chr1D 85.465 172 21 3 3187 3357 81377344 81377512 3.820000e-40 176.0
35 TraesCS6A01G368400 chr1D 97.297 74 2 0 3648 3721 486635291 486635218 3.900000e-25 126.0
36 TraesCS6A01G368400 chr1D 97.297 74 2 0 3648 3721 491370706 491370633 3.900000e-25 126.0
37 TraesCS6A01G368400 chr3B 88.532 218 13 6 3148 3353 763180563 763180780 1.720000e-63 254.0
38 TraesCS6A01G368400 chr3B 88.235 221 14 6 3148 3356 763794136 763793916 1.720000e-63 254.0
39 TraesCS6A01G368400 chr5D 87.838 222 15 2 3148 3357 493624161 493623940 2.220000e-62 250.0
40 TraesCS6A01G368400 chr5D 86.878 221 17 6 3149 3357 2089565 2089785 1.730000e-58 237.0
41 TraesCS6A01G368400 chr7A 91.160 181 16 0 1045 1225 602927666 602927486 2.870000e-61 246.0
42 TraesCS6A01G368400 chr7A 86.878 221 17 8 3149 3357 524840873 524840653 1.730000e-58 237.0
43 TraesCS6A01G368400 chr7A 99.057 106 1 0 1 106 708423543 708423648 1.360000e-44 191.0
44 TraesCS6A01G368400 chr7A 96.262 107 3 1 1 106 726931111 726931005 1.370000e-39 174.0
45 TraesCS6A01G368400 chr7A 93.519 108 5 1 1 106 62583455 62583562 3.850000e-35 159.0
46 TraesCS6A01G368400 chr7A 87.681 138 12 4 3148 3280 150122315 150122452 4.980000e-34 156.0
47 TraesCS6A01G368400 chr7D 87.671 219 15 2 3149 3355 112314396 112314178 1.030000e-60 244.0
48 TraesCS6A01G368400 chr7D 86.425 221 18 4 3149 3357 36958844 36958624 8.040000e-57 231.0
49 TraesCS6A01G368400 chr7D 86.667 210 24 3 3149 3357 548918309 548918515 2.890000e-56 230.0
50 TraesCS6A01G368400 chr7D 85.714 175 13 6 3145 3307 69375535 69375361 1.370000e-39 174.0
51 TraesCS6A01G368400 chr7D 93.333 45 3 0 2967 3011 469846501 469846545 2.400000e-07 67.6
52 TraesCS6A01G368400 chr4A 84.615 221 22 5 3149 3357 647253846 647253626 3.770000e-50 209.0
53 TraesCS6A01G368400 chr4A 92.857 42 2 1 3009 3049 662253607 662253648 4.010000e-05 60.2
54 TraesCS6A01G368400 chr5B 83.700 227 23 4 3144 3357 539700399 539700624 6.300000e-48 202.0
55 TraesCS6A01G368400 chr2B 83.258 221 25 6 3149 3357 135084020 135083800 3.790000e-45 193.0
56 TraesCS6A01G368400 chr2B 98.649 74 1 0 3648 3721 41608349 41608422 8.390000e-27 132.0
57 TraesCS6A01G368400 chr2A 98.113 106 2 0 1 106 720316052 720315947 6.350000e-43 185.0
58 TraesCS6A01G368400 chr5A 96.226 106 4 0 1 106 568050090 568049985 1.370000e-39 174.0
59 TraesCS6A01G368400 chr3A 85.227 176 14 5 3149 3312 704962387 704962212 1.780000e-38 171.0
60 TraesCS6A01G368400 chr1A 95.283 106 3 1 1 106 558439383 558439280 2.300000e-37 167.0
61 TraesCS6A01G368400 chr1A 93.396 106 4 1 1 106 541074959 541074857 1.790000e-33 154.0
62 TraesCS6A01G368400 chr7B 93.396 106 5 2 1 106 516913882 516913985 4.980000e-34 156.0
63 TraesCS6A01G368400 chr1B 98.649 74 1 0 3648 3721 681520916 681520843 8.390000e-27 132.0


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 TraesCS6A01G368400 chr6A 594651267 594654987 3720 False 1988.000000 5631 100.000000 1 3721 3 chr6A.!!$F2 3720
1 TraesCS6A01G368400 chr6A 594607836 594610654 2818 False 1380.366667 2876 93.621333 392 3147 3 chr6A.!!$F1 2755
2 TraesCS6A01G368400 chr6B 679550376 679552167 1791 True 2026.000000 2026 87.206000 1341 3147 1 chr6B.!!$R1 1806
3 TraesCS6A01G368400 chr6B 679397062 679398524 1462 False 1314.000000 1314 83.333000 470 1941 1 chr6B.!!$F1 1471
4 TraesCS6A01G368400 chr6B 679561514 679568563 7049 True 988.250000 3288 88.592250 334 3147 4 chr6B.!!$R2 2813
5 TraesCS6A01G368400 chr6D 448594507 448596845 2338 False 2494.000000 2494 86.494000 514 2788 1 chr6D.!!$F3 2274
6 TraesCS6A01G368400 chr6D 448563120 448565338 2218 False 1023.000000 1502 84.752000 720 2788 2 chr6D.!!$F4 2068
7 TraesCS6A01G368400 chr6D 448577191 448580973 3782 False 662.250000 1096 88.901000 334 2796 4 chr6D.!!$F5 2462
8 TraesCS6A01G368400 chrUn 79404540 79405704 1164 False 1068.000000 1068 83.487000 1623 2795 1 chrUn.!!$F3 1172
9 TraesCS6A01G368400 chrUn 79378408 79379429 1021 False 887.000000 887 82.634000 1765 2795 1 chrUn.!!$F2 1030
10 TraesCS6A01G368400 chrUn 472326032 472326635 603 True 824.000000 824 91.269000 1262 1868 1 chrUn.!!$R3 606
11 TraesCS6A01G368400 chrUn 294343963 294344883 920 False 555.000000 555 78.031000 1746 2696 1 chrUn.!!$F5 950

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
56 57 0.107800 CACGACGGAGAGAGGGTAGA 60.108 60.0 0.00 0.0 0.00 2.59 F
331 332 0.320697 GGTTGTACCGAAGCAGACCT 59.679 55.0 0.00 0.0 0.00 3.85 F
1421 3184 1.505477 GACTCGCGGTCGGCTACTAT 61.505 60.0 6.13 0.0 40.44 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 3575 0.179089 GGACATCAGCGCATGAGACT 60.179 55.000 11.47 0.0 42.53 3.24 R
1995 3788 1.068588 GTGTGTGCACCAGAGAGTGTA 59.931 52.381 15.69 0.0 40.04 2.90 R
3227 5062 0.034477 CCATCCGGTTGGGCTTTAGT 60.034 55.000 22.04 0.0 35.24 2.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.072598 CGTGATCAACGCAGGTCG 58.927 61.111 0.00 0.00 46.99 4.79
45 46 0.725686 TTTTTGTTTCGCACGACGGA 59.274 45.000 0.00 0.00 43.89 4.69
46 47 0.302288 TTTTGTTTCGCACGACGGAG 59.698 50.000 0.00 0.00 43.89 4.63
48 49 0.937699 TTGTTTCGCACGACGGAGAG 60.938 55.000 0.00 0.00 43.89 3.20
49 50 1.081641 GTTTCGCACGACGGAGAGA 60.082 57.895 0.00 0.00 43.89 3.10
50 51 1.066114 GTTTCGCACGACGGAGAGAG 61.066 60.000 0.00 0.00 43.89 3.20
52 53 4.180946 CGCACGACGGAGAGAGGG 62.181 72.222 0.00 0.00 38.44 4.30
54 55 1.748122 GCACGACGGAGAGAGGGTA 60.748 63.158 0.00 0.00 0.00 3.69
56 57 0.107800 CACGACGGAGAGAGGGTAGA 60.108 60.000 0.00 0.00 0.00 2.59
57 58 0.838608 ACGACGGAGAGAGGGTAGAT 59.161 55.000 0.00 0.00 0.00 1.98
58 59 1.231221 CGACGGAGAGAGGGTAGATG 58.769 60.000 0.00 0.00 0.00 2.90
60 61 0.820074 ACGGAGAGAGGGTAGATGCG 60.820 60.000 0.00 0.00 0.00 4.73
61 62 0.535328 CGGAGAGAGGGTAGATGCGA 60.535 60.000 0.00 0.00 0.00 5.10
63 64 0.596082 GAGAGAGGGTAGATGCGAGC 59.404 60.000 0.00 0.00 0.00 5.03
64 65 0.825840 AGAGAGGGTAGATGCGAGCC 60.826 60.000 0.00 0.00 34.52 4.70
65 66 2.136196 GAGAGGGTAGATGCGAGCCG 62.136 65.000 0.00 0.00 39.54 5.52
66 67 3.214250 GAGGGTAGATGCGAGCCGG 62.214 68.421 0.00 0.00 39.54 6.13
67 68 4.971125 GGGTAGATGCGAGCCGGC 62.971 72.222 21.89 21.89 0.00 6.13
68 69 4.971125 GGTAGATGCGAGCCGGCC 62.971 72.222 26.15 14.23 0.00 6.13
73 74 4.664677 ATGCGAGCCGGCCGTATC 62.665 66.667 29.37 19.79 0.00 2.24
105 106 2.201022 CGCTCGGCCCTACCTGTAT 61.201 63.158 0.00 0.00 35.61 2.29
330 331 2.836944 GGTTGTACCGAAGCAGACC 58.163 57.895 0.00 0.00 0.00 3.85
331 332 0.320697 GGTTGTACCGAAGCAGACCT 59.679 55.000 0.00 0.00 0.00 3.85
332 333 1.672145 GGTTGTACCGAAGCAGACCTC 60.672 57.143 0.00 0.00 0.00 3.85
367 464 4.455533 GTGTAATGCAGGTCAATCACTCAA 59.544 41.667 0.00 0.00 0.00 3.02
441 568 4.600547 TCCAATATCTCATGCTCATTCCCT 59.399 41.667 0.00 0.00 0.00 4.20
492 679 3.619038 GCTTGAACGAGCTAGCTGTTAAT 59.381 43.478 24.99 5.87 39.57 1.40
577 776 4.504596 TGCGGCCCATCCATGACC 62.505 66.667 0.00 0.00 34.01 4.02
600 799 2.508526 AGTTCACCACTGATCCAAAGC 58.491 47.619 0.00 0.00 32.83 3.51
614 813 1.669115 AAAGCGTGCGTGCTCATCT 60.669 52.632 2.72 0.00 46.60 2.90
632 831 2.907634 TCTAGGAAAACGTGTGTGCAA 58.092 42.857 0.00 0.00 0.00 4.08
644 843 1.815003 TGTGCAATCGATCGGCAGG 60.815 57.895 20.95 4.02 38.38 4.85
775 1003 8.679100 CAATAACAAAACATTCCCCGATTAGTA 58.321 33.333 0.00 0.00 0.00 1.82
1375 3105 2.294078 GCACACCTAGCCCTCCACT 61.294 63.158 0.00 0.00 0.00 4.00
1379 3109 3.854669 CCTAGCCCTCCACTGCCG 61.855 72.222 0.00 0.00 0.00 5.69
1421 3184 1.505477 GACTCGCGGTCGGCTACTAT 61.505 60.000 6.13 0.00 40.44 2.12
1539 3302 1.968493 ACTGCTTCGTCAGGGTAAGAA 59.032 47.619 6.93 0.00 38.36 2.52
1606 3394 8.596293 TGTCATGAAATATATGTAGGCTGATGA 58.404 33.333 0.00 0.00 0.00 2.92
1607 3395 9.610705 GTCATGAAATATATGTAGGCTGATGAT 57.389 33.333 0.00 0.00 0.00 2.45
1608 3396 9.609346 TCATGAAATATATGTAGGCTGATGATG 57.391 33.333 0.00 0.00 0.00 3.07
1671 3464 2.089201 TCCGTGCTTCTCGATCAAGTA 58.911 47.619 6.22 0.00 0.00 2.24
1782 3575 2.338015 GGAGTGTGGGAGCGACGTA 61.338 63.158 0.00 0.00 0.00 3.57
1905 3698 4.213270 GGACGTGTGTCTTTCATGAATGAA 59.787 41.667 21.74 11.83 44.83 2.57
1995 3788 1.215647 GACTGCCGACGAGATGGTT 59.784 57.895 0.00 0.00 0.00 3.67
2142 3935 1.168714 GCAAGTCAGACAATGGGACC 58.831 55.000 2.66 0.00 31.99 4.46
2614 4433 5.491973 CATTTTGTTTTTCAACTTCGCCTG 58.508 37.500 0.00 0.00 35.61 4.85
2645 4468 6.096846 AGTTGTTGTACAAGAATTTGCTCCTT 59.903 34.615 19.77 0.00 39.00 3.36
2699 4523 2.380084 TCTTGCCGTGTTCCTATGTC 57.620 50.000 0.00 0.00 0.00 3.06
2871 4705 0.252375 ATGCATGGAAAAGGCCCACT 60.252 50.000 0.00 0.00 36.36 4.00
2896 4730 5.700373 ACAACATGCAACCATCCATTTAAAC 59.300 36.000 0.00 0.00 0.00 2.01
2900 4734 5.543507 TGCAACCATCCATTTAAACAAGT 57.456 34.783 0.00 0.00 0.00 3.16
2901 4735 5.923204 TGCAACCATCCATTTAAACAAGTT 58.077 33.333 0.00 0.00 0.00 2.66
3149 4984 8.783660 ACTAAGTAGATGATCTCCAATAACCA 57.216 34.615 0.00 0.00 0.00 3.67
3150 4985 8.643324 ACTAAGTAGATGATCTCCAATAACCAC 58.357 37.037 0.00 0.00 0.00 4.16
3152 4987 8.783660 AAGTAGATGATCTCCAATAACCACTA 57.216 34.615 0.00 0.00 0.00 2.74
3153 4988 8.415950 AGTAGATGATCTCCAATAACCACTAG 57.584 38.462 0.00 0.00 0.00 2.57
3155 4990 9.298250 GTAGATGATCTCCAATAACCACTAGTA 57.702 37.037 0.00 0.00 0.00 1.82
3156 4991 8.415950 AGATGATCTCCAATAACCACTAGTAG 57.584 38.462 0.00 0.00 0.00 2.57
3157 4992 8.228206 AGATGATCTCCAATAACCACTAGTAGA 58.772 37.037 3.59 0.00 0.00 2.59
3158 4993 8.783660 ATGATCTCCAATAACCACTAGTAGAA 57.216 34.615 3.59 0.00 0.00 2.10
3161 4996 9.886132 GATCTCCAATAACCACTAGTAGAAAAA 57.114 33.333 3.59 0.00 0.00 1.94
3162 4997 9.892130 ATCTCCAATAACCACTAGTAGAAAAAG 57.108 33.333 3.59 0.00 0.00 2.27
3163 4998 8.319146 TCTCCAATAACCACTAGTAGAAAAAGG 58.681 37.037 3.59 0.00 0.00 3.11
3164 4999 6.882678 TCCAATAACCACTAGTAGAAAAAGGC 59.117 38.462 3.59 0.00 0.00 4.35
3165 5000 6.657541 CCAATAACCACTAGTAGAAAAAGGCA 59.342 38.462 3.59 0.00 0.00 4.75
3166 5001 7.361799 CCAATAACCACTAGTAGAAAAAGGCAC 60.362 40.741 3.59 0.00 0.00 5.01
3168 5003 5.242795 ACCACTAGTAGAAAAAGGCACAT 57.757 39.130 3.59 0.00 0.00 3.21
3170 5005 6.068670 ACCACTAGTAGAAAAAGGCACATTT 58.931 36.000 3.59 0.00 0.00 2.32
3171 5006 6.016276 ACCACTAGTAGAAAAAGGCACATTTG 60.016 38.462 3.59 0.00 0.00 2.32
3172 5007 6.016276 CCACTAGTAGAAAAAGGCACATTTGT 60.016 38.462 3.59 0.00 0.00 2.83
3175 5010 3.751479 AGAAAAAGGCACATTTGTCCC 57.249 42.857 0.00 0.00 28.13 4.46
3176 5011 2.035832 AGAAAAAGGCACATTTGTCCCG 59.964 45.455 0.00 0.00 28.13 5.14
3177 5012 0.678950 AAAAGGCACATTTGTCCCGG 59.321 50.000 0.00 0.00 0.00 5.73
3179 5014 0.469144 AAGGCACATTTGTCCCGGTT 60.469 50.000 0.00 0.00 0.00 4.44
3180 5015 0.893727 AGGCACATTTGTCCCGGTTC 60.894 55.000 0.00 0.00 0.00 3.62
3181 5016 1.584495 GCACATTTGTCCCGGTTCC 59.416 57.895 0.00 0.00 0.00 3.62
3182 5017 1.175983 GCACATTTGTCCCGGTTCCA 61.176 55.000 0.00 0.00 0.00 3.53
3183 5018 0.881118 CACATTTGTCCCGGTTCCAG 59.119 55.000 0.00 0.00 0.00 3.86
3184 5019 0.768622 ACATTTGTCCCGGTTCCAGA 59.231 50.000 0.00 0.00 0.00 3.86
3185 5020 1.354368 ACATTTGTCCCGGTTCCAGAT 59.646 47.619 0.00 0.00 0.00 2.90
3187 5022 0.608035 TTTGTCCCGGTTCCAGATGC 60.608 55.000 0.00 0.00 0.00 3.91
3188 5023 2.124695 GTCCCGGTTCCAGATGCC 60.125 66.667 0.00 0.00 0.00 4.40
3189 5024 3.407967 TCCCGGTTCCAGATGCCC 61.408 66.667 0.00 0.00 0.00 5.36
3190 5025 3.727258 CCCGGTTCCAGATGCCCA 61.727 66.667 0.00 0.00 0.00 5.36
3191 5026 2.597340 CCGGTTCCAGATGCCCAT 59.403 61.111 0.00 0.00 0.00 4.00
3192 5027 1.076777 CCGGTTCCAGATGCCCATT 60.077 57.895 0.00 0.00 0.00 3.16
3197 5032 1.478105 GTTCCAGATGCCCATTTGTCC 59.522 52.381 0.00 0.00 0.00 4.02
3198 5033 1.002069 TCCAGATGCCCATTTGTCCT 58.998 50.000 0.00 0.00 0.00 3.85
3199 5034 1.108776 CCAGATGCCCATTTGTCCTG 58.891 55.000 0.00 0.00 0.00 3.86
3200 5035 1.108776 CAGATGCCCATTTGTCCTGG 58.891 55.000 0.00 0.00 0.00 4.45
3202 5037 1.077663 AGATGCCCATTTGTCCTGGTT 59.922 47.619 0.00 0.00 31.44 3.67
3204 5039 0.482446 TGCCCATTTGTCCTGGTTCT 59.518 50.000 0.00 0.00 31.44 3.01
3206 5041 2.290896 TGCCCATTTGTCCTGGTTCTAG 60.291 50.000 0.00 0.00 31.44 2.43
3207 5042 2.026262 GCCCATTTGTCCTGGTTCTAGA 60.026 50.000 0.00 0.00 31.44 2.43
3209 5044 4.010349 CCCATTTGTCCTGGTTCTAGAAC 58.990 47.826 24.73 24.73 40.45 3.01
3222 5057 2.743553 TCTAGAACCGGGACTAAAGGG 58.256 52.381 6.32 0.00 0.00 3.95
3223 5058 2.043526 TCTAGAACCGGGACTAAAGGGT 59.956 50.000 6.32 0.00 0.00 4.34
3224 5059 1.273759 AGAACCGGGACTAAAGGGTC 58.726 55.000 6.32 0.00 41.88 4.46
3225 5060 0.108472 GAACCGGGACTAAAGGGTCG 60.108 60.000 6.32 0.00 37.12 4.79
3226 5061 1.547472 AACCGGGACTAAAGGGTCGG 61.547 60.000 6.32 0.00 42.69 4.79
3227 5062 1.683365 CCGGGACTAAAGGGTCGGA 60.683 63.158 0.00 0.00 39.83 4.55
3229 5064 0.969409 CGGGACTAAAGGGTCGGACT 60.969 60.000 8.23 0.00 37.12 3.85
3231 5066 2.460669 GGGACTAAAGGGTCGGACTAA 58.539 52.381 8.23 0.00 37.12 2.24
3232 5067 2.833943 GGGACTAAAGGGTCGGACTAAA 59.166 50.000 8.23 0.00 37.12 1.85
3233 5068 3.118847 GGGACTAAAGGGTCGGACTAAAG 60.119 52.174 8.23 2.22 37.12 1.85
3234 5069 3.519579 GACTAAAGGGTCGGACTAAAGC 58.480 50.000 8.23 0.00 0.00 3.51
3238 5073 0.838987 AGGGTCGGACTAAAGCCCAA 60.839 55.000 8.23 0.00 41.67 4.12
3241 5076 1.017701 GTCGGACTAAAGCCCAACCG 61.018 60.000 0.00 0.00 41.39 4.44
3242 5077 1.743995 CGGACTAAAGCCCAACCGG 60.744 63.158 0.00 0.00 37.28 5.28
3243 5078 1.681076 GGACTAAAGCCCAACCGGA 59.319 57.895 9.46 0.00 0.00 5.14
3245 5080 1.379527 GACTAAAGCCCAACCGGATG 58.620 55.000 9.46 6.59 0.00 3.51
3246 5081 0.034477 ACTAAAGCCCAACCGGATGG 60.034 55.000 23.39 23.39 40.35 3.51
3247 5082 1.379309 TAAAGCCCAACCGGATGGC 60.379 57.895 24.80 22.61 45.70 4.40
3252 5087 1.817941 CCCAACCGGATGGCTTACG 60.818 63.158 24.80 7.38 39.26 3.18
3253 5088 1.219664 CCAACCGGATGGCTTACGA 59.780 57.895 18.83 0.00 39.70 3.43
3255 5090 0.725117 CAACCGGATGGCTTACGAAC 59.275 55.000 9.46 0.00 39.70 3.95
3256 5091 0.392060 AACCGGATGGCTTACGAACC 60.392 55.000 9.46 0.00 39.70 3.62
3257 5092 1.881252 CCGGATGGCTTACGAACCG 60.881 63.158 6.57 0.00 40.03 4.44
3258 5093 1.881252 CGGATGGCTTACGAACCGG 60.881 63.158 0.00 0.00 37.28 5.28
3259 5094 1.523032 GGATGGCTTACGAACCGGG 60.523 63.158 6.32 0.00 0.00 5.73
3261 5096 0.808847 GATGGCTTACGAACCGGGAC 60.809 60.000 6.32 0.00 0.00 4.46
3262 5097 1.546589 ATGGCTTACGAACCGGGACA 61.547 55.000 6.32 0.00 0.00 4.02
3263 5098 1.447314 GGCTTACGAACCGGGACAG 60.447 63.158 6.32 0.00 0.00 3.51
3265 5100 0.175073 GCTTACGAACCGGGACAGAT 59.825 55.000 6.32 0.00 0.00 2.90
3266 5101 1.922570 CTTACGAACCGGGACAGATG 58.077 55.000 6.32 0.00 0.00 2.90
3267 5102 0.533491 TTACGAACCGGGACAGATGG 59.467 55.000 6.32 0.00 0.00 3.51
3268 5103 1.324740 TACGAACCGGGACAGATGGG 61.325 60.000 6.32 0.00 0.00 4.00
3269 5104 2.590092 GAACCGGGACAGATGGGG 59.410 66.667 6.32 0.00 0.00 4.96
3270 5105 3.699134 GAACCGGGACAGATGGGGC 62.699 68.421 6.32 0.00 0.00 5.80
3272 5107 3.866582 CCGGGACAGATGGGGCTC 61.867 72.222 0.00 0.00 0.00 4.70
3304 5139 4.527583 GGCGAGCTCAGGCAGGAG 62.528 72.222 21.15 2.20 41.70 3.69
3305 5140 4.527583 GCGAGCTCAGGCAGGAGG 62.528 72.222 15.40 0.00 41.70 4.30
3307 5142 4.173924 GAGCTCAGGCAGGAGGGC 62.174 72.222 9.40 0.00 41.70 5.19
3316 5151 1.979155 GCAGGAGGGCCTTTTGTCC 60.979 63.158 7.89 3.59 43.90 4.02
3318 5153 2.907179 AGGAGGGCCTTTTGTCCCG 61.907 63.158 7.89 0.00 43.90 5.14
3322 5157 2.570284 GGGCCTTTTGTCCCGGTTG 61.570 63.158 0.84 0.00 32.00 3.77
3323 5158 2.570284 GGCCTTTTGTCCCGGTTGG 61.570 63.158 0.00 0.00 0.00 3.77
3325 5160 0.537828 GCCTTTTGTCCCGGTTGGTA 60.538 55.000 0.00 0.00 34.77 3.25
3327 5162 1.610038 CCTTTTGTCCCGGTTGGTAAC 59.390 52.381 0.00 0.00 34.77 2.50
3339 5174 4.384599 GGTAACACCAACCGGGAC 57.615 61.111 6.32 0.00 38.42 4.46
3340 5175 1.451072 GGTAACACCAACCGGGACA 59.549 57.895 6.32 0.00 38.42 4.02
3341 5176 0.179023 GGTAACACCAACCGGGACAA 60.179 55.000 6.32 0.00 38.42 3.18
3342 5177 1.677942 GTAACACCAACCGGGACAAA 58.322 50.000 6.32 0.00 41.15 2.83
3343 5178 2.022934 GTAACACCAACCGGGACAAAA 58.977 47.619 6.32 0.00 41.15 2.44
3344 5179 1.558233 AACACCAACCGGGACAAAAA 58.442 45.000 6.32 0.00 41.15 1.94
3676 7780 8.521170 TTGTGTTAGCTAGCTAATAGAGAGAA 57.479 34.615 33.67 16.19 40.18 2.87
3679 7783 8.073768 GTGTTAGCTAGCTAATAGAGAGAAGTG 58.926 40.741 33.67 0.00 40.18 3.16
3680 7784 7.993758 TGTTAGCTAGCTAATAGAGAGAAGTGA 59.006 37.037 33.67 9.35 40.18 3.41
3683 7787 5.768164 GCTAGCTAATAGAGAGAAGTGACCT 59.232 44.000 7.70 0.00 32.76 3.85
3684 7788 6.072673 GCTAGCTAATAGAGAGAAGTGACCTC 60.073 46.154 7.70 0.00 32.76 3.85
3685 7789 6.013554 AGCTAATAGAGAGAAGTGACCTCT 57.986 41.667 0.00 0.00 43.16 3.69
3695 7799 5.588648 AGAGAAGTGACCTCTCTTATCTTCG 59.411 44.000 7.89 0.00 42.04 3.79
3698 7802 3.129638 AGTGACCTCTCTTATCTTCGTGC 59.870 47.826 0.00 0.00 0.00 5.34
3700 7804 3.764434 TGACCTCTCTTATCTTCGTGCTT 59.236 43.478 0.00 0.00 0.00 3.91
3703 7807 3.118956 CCTCTCTTATCTTCGTGCTTGGT 60.119 47.826 0.00 0.00 0.00 3.67
3704 7808 4.109050 CTCTCTTATCTTCGTGCTTGGTC 58.891 47.826 0.00 0.00 0.00 4.02
3705 7809 2.854777 CTCTTATCTTCGTGCTTGGTCG 59.145 50.000 0.00 0.00 0.00 4.79
3706 7810 2.490509 TCTTATCTTCGTGCTTGGTCGA 59.509 45.455 0.00 0.00 0.00 4.20
3708 7812 0.732880 ATCTTCGTGCTTGGTCGACG 60.733 55.000 9.92 0.00 35.82 5.12
3709 7813 3.000080 CTTCGTGCTTGGTCGACGC 62.000 63.158 9.92 8.25 35.82 5.19
3710 7814 3.493830 TTCGTGCTTGGTCGACGCT 62.494 57.895 9.92 0.00 35.82 5.07
3711 7815 2.126618 CGTGCTTGGTCGACGCTA 60.127 61.111 9.92 0.00 0.00 4.26
3712 7816 2.434134 CGTGCTTGGTCGACGCTAC 61.434 63.158 9.92 7.70 0.00 3.58
3713 7817 2.126618 TGCTTGGTCGACGCTACG 60.127 61.111 9.92 0.00 0.00 3.51
3714 7818 2.126580 GCTTGGTCGACGCTACGT 60.127 61.111 9.92 0.00 45.10 3.57
3716 7820 0.248377 GCTTGGTCGACGCTACGTAT 60.248 55.000 9.92 0.00 41.37 3.06
3718 7822 2.539547 GCTTGGTCGACGCTACGTATTA 60.540 50.000 9.92 0.00 41.37 0.98
3719 7823 3.851105 GCTTGGTCGACGCTACGTATTAT 60.851 47.826 9.92 0.00 41.37 1.28
3720 7824 4.611355 GCTTGGTCGACGCTACGTATTATA 60.611 45.833 9.92 0.00 41.37 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.725686 TCCGTCGTGCGAAACAAAAA 59.274 45.000 0.00 0.00 44.77 1.94
28 29 0.528033 TCTCCGTCGTGCGAAACAAA 60.528 50.000 0.00 0.00 44.77 2.83
31 32 1.066114 CTCTCTCCGTCGTGCGAAAC 61.066 60.000 0.00 0.00 44.77 2.78
32 33 1.209383 CTCTCTCCGTCGTGCGAAA 59.791 57.895 0.00 0.00 44.77 3.46
33 34 2.687805 CCTCTCTCCGTCGTGCGAA 61.688 63.158 0.00 0.00 44.77 4.70
34 35 3.125573 CCTCTCTCCGTCGTGCGA 61.126 66.667 3.95 0.00 44.77 5.10
35 36 4.180946 CCCTCTCTCCGTCGTGCG 62.181 72.222 0.00 0.00 40.95 5.34
37 38 0.107800 TCTACCCTCTCTCCGTCGTG 60.108 60.000 0.00 0.00 0.00 4.35
38 39 0.838608 ATCTACCCTCTCTCCGTCGT 59.161 55.000 0.00 0.00 0.00 4.34
39 40 1.231221 CATCTACCCTCTCTCCGTCG 58.769 60.000 0.00 0.00 0.00 5.12
41 42 0.820074 CGCATCTACCCTCTCTCCGT 60.820 60.000 0.00 0.00 0.00 4.69
42 43 0.535328 TCGCATCTACCCTCTCTCCG 60.535 60.000 0.00 0.00 0.00 4.63
43 44 1.243902 CTCGCATCTACCCTCTCTCC 58.756 60.000 0.00 0.00 0.00 3.71
45 46 0.825840 GGCTCGCATCTACCCTCTCT 60.826 60.000 0.00 0.00 0.00 3.10
46 47 1.663173 GGCTCGCATCTACCCTCTC 59.337 63.158 0.00 0.00 0.00 3.20
48 49 2.336809 CGGCTCGCATCTACCCTC 59.663 66.667 0.00 0.00 0.00 4.30
49 50 3.227276 CCGGCTCGCATCTACCCT 61.227 66.667 0.00 0.00 0.00 4.34
50 51 4.971125 GCCGGCTCGCATCTACCC 62.971 72.222 22.15 0.00 0.00 3.69
56 57 4.664677 GATACGGCCGGCTCGCAT 62.665 66.667 31.76 24.23 0.00 4.73
312 313 0.320697 AGGTCTGCTTCGGTACAACC 59.679 55.000 0.00 0.00 34.05 3.77
313 314 1.000506 TGAGGTCTGCTTCGGTACAAC 59.999 52.381 0.00 0.00 0.00 3.32
315 316 1.557099 ATGAGGTCTGCTTCGGTACA 58.443 50.000 0.00 0.00 0.00 2.90
316 317 5.241064 TCTTATATGAGGTCTGCTTCGGTAC 59.759 44.000 0.00 0.00 0.00 3.34
317 318 5.382616 TCTTATATGAGGTCTGCTTCGGTA 58.617 41.667 0.00 0.00 0.00 4.02
319 320 4.279671 ACTCTTATATGAGGTCTGCTTCGG 59.720 45.833 17.35 0.00 38.32 4.30
320 321 5.446143 ACTCTTATATGAGGTCTGCTTCG 57.554 43.478 17.35 0.00 38.32 3.79
321 322 6.478344 CACAACTCTTATATGAGGTCTGCTTC 59.522 42.308 17.35 0.00 38.32 3.86
322 323 6.070538 ACACAACTCTTATATGAGGTCTGCTT 60.071 38.462 17.35 2.07 38.32 3.91
324 325 5.665459 ACACAACTCTTATATGAGGTCTGC 58.335 41.667 17.35 0.00 38.32 4.26
325 326 9.254133 CATTACACAACTCTTATATGAGGTCTG 57.746 37.037 17.35 12.27 38.32 3.51
326 327 7.928706 GCATTACACAACTCTTATATGAGGTCT 59.071 37.037 17.35 0.00 38.32 3.85
327 328 7.710907 TGCATTACACAACTCTTATATGAGGTC 59.289 37.037 17.35 0.75 38.32 3.85
328 329 7.564793 TGCATTACACAACTCTTATATGAGGT 58.435 34.615 17.35 9.97 38.32 3.85
330 331 7.712639 ACCTGCATTACACAACTCTTATATGAG 59.287 37.037 12.81 12.81 39.78 2.90
331 332 7.564793 ACCTGCATTACACAACTCTTATATGA 58.435 34.615 0.00 0.00 0.00 2.15
332 333 7.495606 TGACCTGCATTACACAACTCTTATATG 59.504 37.037 0.00 0.00 0.00 1.78
367 464 2.022129 GTCGTGCAGCGCTAACTGT 61.022 57.895 10.99 0.00 39.96 3.55
441 568 4.158579 ACAACTCGATGATGAGCTCAACTA 59.841 41.667 22.50 10.41 39.68 2.24
451 578 2.998670 AGCAGTTGACAACTCGATGATG 59.001 45.455 18.02 7.41 40.46 3.07
492 679 8.472413 AGTTGTCAACTAGTAACAGACTAACAA 58.528 33.333 16.74 10.45 40.23 2.83
600 799 0.179137 TTCCTAGATGAGCACGCACG 60.179 55.000 0.00 0.00 0.00 5.34
614 813 2.222213 CGATTGCACACACGTTTTCCTA 59.778 45.455 0.00 0.00 0.00 2.94
644 843 1.032114 CAAGGCGGGAGAATGGGAAC 61.032 60.000 0.00 0.00 0.00 3.62
1074 1331 1.035923 GCGATGAGAGTCAGGATGGA 58.964 55.000 0.00 0.00 36.16 3.41
1379 3109 3.468140 GTCGGTGGGCTAGGGGTC 61.468 72.222 0.00 0.00 0.00 4.46
1394 3157 1.737008 GACCGCGAGTCCTTTGGTC 60.737 63.158 8.23 0.00 41.98 4.02
1421 3184 1.219124 GCGAGGGCATGACTTCTGA 59.781 57.895 9.27 0.00 39.62 3.27
1606 3394 2.030363 CCATTAAACACCACACGCACAT 60.030 45.455 0.00 0.00 0.00 3.21
1607 3395 1.335182 CCATTAAACACCACACGCACA 59.665 47.619 0.00 0.00 0.00 4.57
1608 3396 1.335496 ACCATTAAACACCACACGCAC 59.665 47.619 0.00 0.00 0.00 5.34
1671 3464 3.580319 GGTGGGCTGTTGGGGTCT 61.580 66.667 0.00 0.00 0.00 3.85
1782 3575 0.179089 GGACATCAGCGCATGAGACT 60.179 55.000 11.47 0.00 42.53 3.24
1905 3698 2.391130 TGGCAGGTTGGGGAGTGTT 61.391 57.895 0.00 0.00 0.00 3.32
1995 3788 1.068588 GTGTGTGCACCAGAGAGTGTA 59.931 52.381 15.69 0.00 40.04 2.90
2142 3935 2.881266 CTGCACCACCGTGTTGTCG 61.881 63.158 0.00 0.00 42.39 4.35
2447 4241 4.722194 TGTTGAAAAACTAGCGATGATGC 58.278 39.130 0.00 0.00 0.00 3.91
2585 4400 5.544136 AGTTGAAAAACAAAATGCCACAC 57.456 34.783 0.00 0.00 40.36 3.82
2614 4433 8.268738 GCAAATTCTTGTACAACAACTTTCATC 58.731 33.333 3.59 0.00 33.96 2.92
2686 4510 7.596749 AACAATAGAAAGACATAGGAACACG 57.403 36.000 0.00 0.00 0.00 4.49
2864 4698 0.243636 GTTGCATGTTGTAGTGGGCC 59.756 55.000 0.00 0.00 0.00 5.80
2871 4705 6.596309 TTAAATGGATGGTTGCATGTTGTA 57.404 33.333 0.00 0.00 33.70 2.41
3133 4968 8.783660 TTCTACTAGTGGTTATTGGAGATCAT 57.216 34.615 5.39 0.00 0.00 2.45
3143 4978 6.775708 TGTGCCTTTTTCTACTAGTGGTTAT 58.224 36.000 5.39 0.00 0.00 1.89
3147 4982 6.016276 ACAAATGTGCCTTTTTCTACTAGTGG 60.016 38.462 5.39 1.87 0.00 4.00
3149 4984 6.206829 GGACAAATGTGCCTTTTTCTACTAGT 59.793 38.462 0.00 0.00 0.00 2.57
3150 4985 6.612306 GGACAAATGTGCCTTTTTCTACTAG 58.388 40.000 0.00 0.00 0.00 2.57
3152 4987 5.453567 GGACAAATGTGCCTTTTTCTACT 57.546 39.130 0.00 0.00 0.00 2.57
3163 4998 1.175983 TGGAACCGGGACAAATGTGC 61.176 55.000 6.32 0.00 35.50 4.57
3164 4999 0.881118 CTGGAACCGGGACAAATGTG 59.119 55.000 6.32 0.00 0.00 3.21
3165 5000 0.768622 TCTGGAACCGGGACAAATGT 59.231 50.000 6.32 0.00 0.00 2.71
3166 5001 1.745087 CATCTGGAACCGGGACAAATG 59.255 52.381 6.32 0.00 0.00 2.32
3168 5003 0.608035 GCATCTGGAACCGGGACAAA 60.608 55.000 6.32 0.00 0.00 2.83
3170 5005 2.668632 GCATCTGGAACCGGGACA 59.331 61.111 6.32 0.00 0.00 4.02
3171 5006 2.124695 GGCATCTGGAACCGGGAC 60.125 66.667 6.32 0.00 0.00 4.46
3172 5007 3.407967 GGGCATCTGGAACCGGGA 61.408 66.667 6.32 0.00 0.00 5.14
3175 5010 0.457035 CAAATGGGCATCTGGAACCG 59.543 55.000 0.00 0.00 0.00 4.44
3176 5011 1.478105 GACAAATGGGCATCTGGAACC 59.522 52.381 0.00 0.00 0.00 3.62
3177 5012 1.478105 GGACAAATGGGCATCTGGAAC 59.522 52.381 0.00 0.00 0.00 3.62
3179 5014 1.002069 AGGACAAATGGGCATCTGGA 58.998 50.000 0.00 0.00 0.00 3.86
3180 5015 1.108776 CAGGACAAATGGGCATCTGG 58.891 55.000 0.00 0.00 0.00 3.86
3181 5016 1.108776 CCAGGACAAATGGGCATCTG 58.891 55.000 0.00 0.00 33.94 2.90
3182 5017 0.706433 ACCAGGACAAATGGGCATCT 59.294 50.000 0.00 0.00 42.48 2.90
3183 5018 1.478105 GAACCAGGACAAATGGGCATC 59.522 52.381 0.00 0.00 42.48 3.91
3184 5019 1.077663 AGAACCAGGACAAATGGGCAT 59.922 47.619 0.00 0.00 42.48 4.40
3185 5020 0.482446 AGAACCAGGACAAATGGGCA 59.518 50.000 0.00 0.00 42.48 5.36
3187 5022 4.010349 GTTCTAGAACCAGGACAAATGGG 58.990 47.826 22.74 0.00 42.48 4.00
3200 5035 3.118847 CCCTTTAGTCCCGGTTCTAGAAC 60.119 52.174 24.73 24.73 40.45 3.01
3202 5037 2.043526 ACCCTTTAGTCCCGGTTCTAGA 59.956 50.000 0.00 0.00 0.00 2.43
3204 5039 2.460669 GACCCTTTAGTCCCGGTTCTA 58.539 52.381 0.00 0.00 0.00 2.10
3206 5041 0.108472 CGACCCTTTAGTCCCGGTTC 60.108 60.000 0.00 0.00 32.91 3.62
3207 5042 1.547472 CCGACCCTTTAGTCCCGGTT 61.547 60.000 0.00 0.00 32.91 4.44
3209 5044 1.683365 TCCGACCCTTTAGTCCCGG 60.683 63.158 0.00 0.00 38.41 5.73
3210 5045 0.969409 AGTCCGACCCTTTAGTCCCG 60.969 60.000 0.00 0.00 32.91 5.14
3211 5046 2.149973 TAGTCCGACCCTTTAGTCCC 57.850 55.000 0.00 0.00 32.91 4.46
3212 5047 3.678252 GCTTTAGTCCGACCCTTTAGTCC 60.678 52.174 0.00 0.00 32.91 3.85
3213 5048 3.519579 GCTTTAGTCCGACCCTTTAGTC 58.480 50.000 0.00 0.00 0.00 2.59
3214 5049 2.235650 GGCTTTAGTCCGACCCTTTAGT 59.764 50.000 0.00 0.00 0.00 2.24
3215 5050 2.419713 GGGCTTTAGTCCGACCCTTTAG 60.420 54.545 0.00 0.00 37.59 1.85
3216 5051 1.556451 GGGCTTTAGTCCGACCCTTTA 59.444 52.381 0.00 0.00 37.59 1.85
3220 5055 0.675837 GTTGGGCTTTAGTCCGACCC 60.676 60.000 9.26 0.00 46.18 4.46
3223 5058 1.294138 CGGTTGGGCTTTAGTCCGA 59.706 57.895 0.00 0.00 44.44 4.55
3224 5059 1.743995 CCGGTTGGGCTTTAGTCCG 60.744 63.158 0.00 0.00 44.44 4.79
3225 5060 0.255033 ATCCGGTTGGGCTTTAGTCC 59.745 55.000 0.00 0.00 41.09 3.85
3226 5061 1.379527 CATCCGGTTGGGCTTTAGTC 58.620 55.000 0.00 0.00 35.24 2.59
3227 5062 0.034477 CCATCCGGTTGGGCTTTAGT 60.034 55.000 22.04 0.00 35.24 2.24
3229 5064 1.379309 GCCATCCGGTTGGGCTTTA 60.379 57.895 28.73 0.00 44.32 1.85
3234 5069 1.817941 CGTAAGCCATCCGGTTGGG 60.818 63.158 28.73 17.11 37.24 4.12
3238 5073 1.219935 GGTTCGTAAGCCATCCGGT 59.780 57.895 0.00 0.00 37.18 5.28
3241 5076 1.523032 CCCGGTTCGTAAGCCATCC 60.523 63.158 0.00 0.00 37.18 3.51
3242 5077 0.808847 GTCCCGGTTCGTAAGCCATC 60.809 60.000 0.00 0.00 37.18 3.51
3243 5078 1.219935 GTCCCGGTTCGTAAGCCAT 59.780 57.895 0.00 0.00 37.18 4.40
3245 5080 1.447314 CTGTCCCGGTTCGTAAGCC 60.447 63.158 0.00 0.00 37.18 4.35
3246 5081 0.175073 ATCTGTCCCGGTTCGTAAGC 59.825 55.000 0.00 0.00 37.18 3.09
3247 5082 1.470979 CCATCTGTCCCGGTTCGTAAG 60.471 57.143 0.00 0.00 0.00 2.34
3248 5083 0.533491 CCATCTGTCCCGGTTCGTAA 59.467 55.000 0.00 0.00 0.00 3.18
3252 5087 2.590092 CCCCATCTGTCCCGGTTC 59.410 66.667 0.00 0.00 0.00 3.62
3253 5088 3.728373 GCCCCATCTGTCCCGGTT 61.728 66.667 0.00 0.00 0.00 4.44
3255 5090 3.866582 GAGCCCCATCTGTCCCGG 61.867 72.222 0.00 0.00 0.00 5.73
3256 5091 3.866582 GGAGCCCCATCTGTCCCG 61.867 72.222 0.00 0.00 0.00 5.14
3257 5092 2.692368 TGGAGCCCCATCTGTCCC 60.692 66.667 0.00 0.00 37.58 4.46
3258 5093 2.592308 GTGGAGCCCCATCTGTCC 59.408 66.667 0.00 0.00 45.68 4.02
3259 5094 2.187946 CGTGGAGCCCCATCTGTC 59.812 66.667 0.00 0.00 45.68 3.51
3261 5096 2.124983 CACGTGGAGCCCCATCTG 60.125 66.667 7.95 0.00 45.68 2.90
3262 5097 3.402681 CCACGTGGAGCCCCATCT 61.403 66.667 31.31 0.00 45.68 2.90
3263 5098 3.682292 GACCACGTGGAGCCCCATC 62.682 68.421 40.21 21.39 45.68 3.51
3287 5122 4.527583 CTCCTGCCTGAGCTCGCC 62.528 72.222 9.64 0.00 40.80 5.54
3288 5123 4.527583 CCTCCTGCCTGAGCTCGC 62.528 72.222 9.64 7.98 40.80 5.03
3289 5124 3.847602 CCCTCCTGCCTGAGCTCG 61.848 72.222 9.64 3.88 40.80 5.03
3290 5125 4.173924 GCCCTCCTGCCTGAGCTC 62.174 72.222 6.82 6.82 40.80 4.09
3298 5133 1.979155 GGACAAAAGGCCCTCCTGC 60.979 63.158 0.00 0.00 43.40 4.85
3299 5134 1.304464 GGGACAAAAGGCCCTCCTG 60.304 63.158 0.00 0.00 43.40 3.86
3302 5137 2.361230 CCGGGACAAAAGGCCCTC 60.361 66.667 4.64 0.00 42.40 4.30
3304 5139 2.203582 AACCGGGACAAAAGGCCC 60.204 61.111 6.32 0.00 41.11 5.80
3305 5140 2.570284 CCAACCGGGACAAAAGGCC 61.570 63.158 6.32 0.00 40.01 5.19
3307 5142 1.610038 GTTACCAACCGGGACAAAAGG 59.390 52.381 6.32 0.00 41.15 3.11
3308 5143 2.033675 GTGTTACCAACCGGGACAAAAG 59.966 50.000 6.32 0.00 41.15 2.27
3311 5146 0.179023 GGTGTTACCAACCGGGACAA 60.179 55.000 6.32 0.00 38.42 3.18
3312 5147 1.451072 GGTGTTACCAACCGGGACA 59.549 57.895 6.32 0.00 38.42 4.02
3313 5148 4.384599 GGTGTTACCAACCGGGAC 57.615 61.111 6.32 0.00 38.42 4.46
3322 5157 0.179023 TTGTCCCGGTTGGTGTTACC 60.179 55.000 0.00 0.00 39.22 2.85
3323 5158 1.677942 TTTGTCCCGGTTGGTGTTAC 58.322 50.000 0.00 0.00 34.77 2.50
3325 5160 1.558233 TTTTTGTCCCGGTTGGTGTT 58.442 45.000 0.00 0.00 34.77 3.32
3649 5484 9.794719 TCTCTCTATTAGCTAGCTAACACAATA 57.205 33.333 33.80 22.82 40.76 1.90
3650 5485 8.698973 TCTCTCTATTAGCTAGCTAACACAAT 57.301 34.615 33.80 22.92 40.76 2.71
3654 5489 7.993758 TCACTTCTCTCTATTAGCTAGCTAACA 59.006 37.037 33.80 24.62 40.76 2.41
3656 5491 7.446013 GGTCACTTCTCTCTATTAGCTAGCTAA 59.554 40.741 33.35 33.35 41.95 3.09
3658 5493 5.768164 GGTCACTTCTCTCTATTAGCTAGCT 59.232 44.000 23.12 23.12 0.00 3.32
3661 5496 7.144234 AGAGGTCACTTCTCTCTATTAGCTA 57.856 40.000 0.00 0.00 36.99 3.32
3662 5497 6.013554 AGAGGTCACTTCTCTCTATTAGCT 57.986 41.667 0.00 0.00 36.99 3.32
3676 7780 3.129638 GCACGAAGATAAGAGAGGTCACT 59.870 47.826 0.00 0.00 0.00 3.41
3679 7783 4.109050 CAAGCACGAAGATAAGAGAGGTC 58.891 47.826 0.00 0.00 0.00 3.85
3680 7784 3.118956 CCAAGCACGAAGATAAGAGAGGT 60.119 47.826 0.00 0.00 0.00 3.85
3683 7787 3.427638 CGACCAAGCACGAAGATAAGAGA 60.428 47.826 0.00 0.00 0.00 3.10
3684 7788 2.854777 CGACCAAGCACGAAGATAAGAG 59.145 50.000 0.00 0.00 0.00 2.85
3685 7789 2.490509 TCGACCAAGCACGAAGATAAGA 59.509 45.455 0.00 0.00 35.62 2.10
3689 7793 0.732880 CGTCGACCAAGCACGAAGAT 60.733 55.000 10.58 0.00 39.48 2.40
3692 7796 2.132517 TAGCGTCGACCAAGCACGAA 62.133 55.000 10.58 0.00 40.12 3.85
3695 7799 2.434134 CGTAGCGTCGACCAAGCAC 61.434 63.158 10.58 7.92 0.00 4.40
3698 7802 2.184385 AATACGTAGCGTCGACCAAG 57.816 50.000 10.58 0.00 41.54 3.61


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

AutoCloner maintained by Alex Coulton.