Multiple sequence alignment - TraesCS3A01G281400

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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 TraesCS3A01G281400 chr3A 100.000 2753 0 0 847 3599 510180381 510183133 0.000000e+00 5084.0
1 TraesCS3A01G281400 chr3A 100.000 507 0 0 1 507 510179535 510180041 0.000000e+00 937.0
2 TraesCS3A01G281400 chr3A 97.297 111 3 0 1677 1787 221571434 221571544 4.740000e-44 189.0
3 TraesCS3A01G281400 chr3A 94.167 120 6 1 1677 1795 256934689 256934808 7.940000e-42 182.0
4 TraesCS3A01G281400 chr3A 96.078 51 2 0 1 51 420812328 420812278 2.300000e-12 84.2
5 TraesCS3A01G281400 chr3A 87.879 66 5 3 1736 1799 38429406 38429470 1.390000e-09 75.0
6 TraesCS3A01G281400 chr3D 92.544 1824 82 25 1792 3599 389212392 389214177 0.000000e+00 2566.0
7 TraesCS3A01G281400 chr3D 93.548 837 34 9 847 1679 389211565 389212385 0.000000e+00 1229.0
8 TraesCS3A01G281400 chr3D 84.848 198 20 4 96 284 389210442 389210638 1.320000e-44 191.0
9 TraesCS3A01G281400 chr3D 78.947 152 24 6 3314 3463 580652859 580653004 2.960000e-16 97.1
10 TraesCS3A01G281400 chr3D 96.154 52 2 0 1 52 386715109 386715058 6.400000e-13 86.1
11 TraesCS3A01G281400 chr3B 91.412 1048 52 24 1792 2821 506965343 506966370 0.000000e+00 1402.0
12 TraesCS3A01G281400 chr3B 90.095 838 49 16 847 1679 506964528 506965336 0.000000e+00 1057.0
13 TraesCS3A01G281400 chr3B 91.161 758 45 8 2815 3560 506968578 506969325 0.000000e+00 1009.0
14 TraesCS3A01G281400 chr3B 88.309 479 50 3 847 1325 506919579 506920051 1.450000e-158 569.0
15 TraesCS3A01G281400 chr3B 97.297 111 3 0 1674 1784 15806627 15806517 4.740000e-44 189.0
16 TraesCS3A01G281400 chr3B 79.891 184 29 2 129 304 778215171 778215354 1.050000e-25 128.0
17 TraesCS3A01G281400 chr3B 96.000 75 3 0 401 475 506964362 506964436 4.880000e-24 122.0
18 TraesCS3A01G281400 chr3B 93.333 75 5 0 401 475 506919419 506919493 1.060000e-20 111.0
19 TraesCS3A01G281400 chr3B 78.488 172 29 8 3314 3480 35215452 35215284 4.910000e-19 106.0
20 TraesCS3A01G281400 chr3B 78.488 172 29 8 3314 3480 35291636 35291468 4.910000e-19 106.0
21 TraesCS3A01G281400 chr3B 92.958 71 5 0 298 368 506962755 506962825 1.770000e-18 104.0
22 TraesCS3A01G281400 chr3B 91.781 73 5 1 296 368 506918953 506919024 2.290000e-17 100.0
23 TraesCS3A01G281400 chr3B 97.826 46 1 0 1 46 331410276 331410321 2.980000e-11 80.5
24 TraesCS3A01G281400 chr3B 92.593 54 2 1 1 54 589601953 589602004 3.850000e-10 76.8
25 TraesCS3A01G281400 chr3B 94.444 36 1 1 473 507 506964461 506964496 2.000000e-03 54.7
26 TraesCS3A01G281400 chr5D 86.000 200 19 3 113 304 73770161 73769963 4.710000e-49 206.0
27 TraesCS3A01G281400 chr5D 90.566 53 5 0 54 106 344988700 344988648 1.790000e-08 71.3
28 TraesCS3A01G281400 chr2A 98.165 109 2 0 1675 1783 138184413 138184305 1.320000e-44 191.0
29 TraesCS3A01G281400 chr2A 86.400 125 13 3 1677 1799 71629223 71629101 2.250000e-27 134.0
30 TraesCS3A01G281400 chrUn 87.500 168 16 5 3314 3478 116432601 116432766 4.740000e-44 189.0
31 TraesCS3A01G281400 chrUn 77.533 227 38 6 83 298 98340428 98340204 1.360000e-24 124.0
32 TraesCS3A01G281400 chrUn 90.196 51 5 0 56 106 1070475 1070425 2.320000e-07 67.6
33 TraesCS3A01G281400 chrUn 88.889 54 6 0 53 106 300086095 300086148 2.320000e-07 67.6
34 TraesCS3A01G281400 chrUn 90.196 51 5 0 56 106 304177492 304177442 2.320000e-07 67.6
35 TraesCS3A01G281400 chrUn 80.000 85 11 5 3397 3477 168632008 168632090 1.400000e-04 58.4
36 TraesCS3A01G281400 chr6A 91.367 139 8 4 1677 1815 477910772 477910906 1.710000e-43 187.0
37 TraesCS3A01G281400 chr6A 94.000 50 3 0 56 105 544178257 544178208 3.850000e-10 76.8
38 TraesCS3A01G281400 chr2D 96.460 113 4 0 1675 1787 530300975 530301087 1.710000e-43 187.0
39 TraesCS3A01G281400 chr2D 79.042 167 27 6 3314 3474 34261057 34261221 1.370000e-19 108.0
40 TraesCS3A01G281400 chr2D 97.826 46 1 0 1 46 596613822 596613867 2.980000e-11 80.5
41 TraesCS3A01G281400 chr2D 90.196 51 5 0 56 106 544204856 544204806 2.320000e-07 67.6
42 TraesCS3A01G281400 chr2D 88.889 54 6 0 53 106 565935532 565935585 2.320000e-07 67.6
43 TraesCS3A01G281400 chr5A 94.915 118 5 1 1676 1793 442722831 442722947 2.210000e-42 183.0
44 TraesCS3A01G281400 chr5A 94.215 121 6 1 1677 1797 525715638 525715519 2.210000e-42 183.0
45 TraesCS3A01G281400 chr5A 85.156 128 16 3 1673 1799 378505860 378505735 1.050000e-25 128.0
46 TraesCS3A01G281400 chr6B 93.333 120 8 0 1665 1784 705508854 705508973 1.030000e-40 178.0
47 TraesCS3A01G281400 chr7D 85.714 168 19 5 3314 3478 296509658 296509823 4.780000e-39 172.0
48 TraesCS3A01G281400 chr7D 86.232 138 15 4 1676 1810 118368078 118368214 2.900000e-31 147.0
49 TraesCS3A01G281400 chr7D 96.000 50 2 0 1 50 105333913 105333962 8.280000e-12 82.4
50 TraesCS3A01G281400 chr7D 79.825 114 19 3 3314 3423 552951402 552951515 2.980000e-11 80.5
51 TraesCS3A01G281400 chr1B 84.940 166 23 2 3310 3473 669757308 669757143 2.220000e-37 167.0
52 TraesCS3A01G281400 chr1B 82.051 156 20 2 113 260 656923068 656922913 3.770000e-25 126.0
53 TraesCS3A01G281400 chr1B 80.337 178 20 5 135 304 152031756 152031926 1.760000e-23 121.0
54 TraesCS3A01G281400 chr1B 88.525 61 7 0 1 61 685503554 685503494 1.390000e-09 75.0
55 TraesCS3A01G281400 chr5B 81.633 196 18 10 113 298 328114809 328114996 2.900000e-31 147.0
56 TraesCS3A01G281400 chr5B 97.959 49 1 0 1 49 321266117 321266069 6.400000e-13 86.1
57 TraesCS3A01G281400 chr2B 86.400 125 16 1 1676 1800 10219957 10220080 6.270000e-28 135.0
58 TraesCS3A01G281400 chr2B 78.537 205 28 7 113 304 731334177 731334378 1.760000e-23 121.0
59 TraesCS3A01G281400 chr1D 86.555 119 15 1 1676 1794 73738891 73739008 2.920000e-26 130.0
60 TraesCS3A01G281400 chr1D 86.842 114 15 0 1677 1790 277881673 277881786 1.050000e-25 128.0
61 TraesCS3A01G281400 chr4A 78.495 186 28 8 129 304 590203302 590203485 1.060000e-20 111.0
62 TraesCS3A01G281400 chr4A 78.030 132 20 3 141 264 681681526 681681396 1.390000e-09 75.0
63 TraesCS3A01G281400 chr1A 74.721 269 48 11 56 304 50834618 50834350 6.360000e-18 102.0
64 TraesCS3A01G281400 chr1A 77.297 185 33 5 129 304 20875880 20876064 2.290000e-17 100.0
65 TraesCS3A01G281400 chr4B 76.471 170 32 4 134 295 611008016 611008185 6.400000e-13 86.1
66 TraesCS3A01G281400 chr4D 97.826 46 1 0 1 46 15880284 15880329 2.980000e-11 80.5
67 TraesCS3A01G281400 chr7B 82.418 91 13 3 1712 1801 324392686 324392774 3.850000e-10 76.8


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 TraesCS3A01G281400 chr3A 510179535 510183133 3598 False 3010.500000 5084 100.000000 1 3599 2 chr3A.!!$F4 3598
1 TraesCS3A01G281400 chr3D 389210442 389214177 3735 False 1328.666667 2566 90.313333 96 3599 3 chr3D.!!$F2 3503
2 TraesCS3A01G281400 chr3B 506962755 506969325 6570 False 624.783333 1402 92.678333 298 3560 6 chr3B.!!$F5 3262
3 TraesCS3A01G281400 chr3B 506918953 506920051 1098 False 260.000000 569 91.141000 296 1325 3 chr3B.!!$F4 1029

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
915 2840 0.035439 CATAGCGACCCACCCAAACT 60.035 55.0 0.0 0.0 0.0 2.66 F
1690 3623 0.108281 GTTGCTACTCCCTCCGTTCC 60.108 60.0 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 3699 0.178926 TGGTACTCCCTCCGTTCCAA 60.179 55.0 0.0 0.0 30.28 3.53 R
3578 7757 0.819259 TGTCTCTGTTGTTGCAGCCC 60.819 55.0 0.0 0.0 36.49 5.19 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
18 19 2.523440 TGGAGACCCAACAACGTCT 58.477 52.632 0.00 0.00 42.02 4.18
19 20 1.707106 TGGAGACCCAACAACGTCTA 58.293 50.000 0.00 0.00 39.44 2.59
20 21 1.342174 TGGAGACCCAACAACGTCTAC 59.658 52.381 0.00 0.00 39.44 2.59
21 22 1.342174 GGAGACCCAACAACGTCTACA 59.658 52.381 0.00 0.00 39.40 2.74
22 23 2.224113 GGAGACCCAACAACGTCTACAA 60.224 50.000 0.00 0.00 39.40 2.41
23 24 3.057734 GAGACCCAACAACGTCTACAAG 58.942 50.000 0.00 0.00 39.44 3.16
24 25 2.696707 AGACCCAACAACGTCTACAAGA 59.303 45.455 0.00 0.00 37.58 3.02
25 26 3.133362 AGACCCAACAACGTCTACAAGAA 59.867 43.478 0.00 0.00 37.58 2.52
26 27 3.872771 GACCCAACAACGTCTACAAGAAA 59.127 43.478 0.00 0.00 0.00 2.52
27 28 4.263435 ACCCAACAACGTCTACAAGAAAA 58.737 39.130 0.00 0.00 0.00 2.29
28 29 4.701171 ACCCAACAACGTCTACAAGAAAAA 59.299 37.500 0.00 0.00 0.00 1.94
29 30 5.163693 ACCCAACAACGTCTACAAGAAAAAG 60.164 40.000 0.00 0.00 0.00 2.27
30 31 5.270853 CCAACAACGTCTACAAGAAAAAGG 58.729 41.667 0.00 0.00 0.00 3.11
31 32 5.163693 CCAACAACGTCTACAAGAAAAAGGT 60.164 40.000 0.00 0.00 0.00 3.50
32 33 6.319399 CAACAACGTCTACAAGAAAAAGGTT 58.681 36.000 0.00 0.00 0.00 3.50
33 34 5.875930 ACAACGTCTACAAGAAAAAGGTTG 58.124 37.500 0.00 0.00 38.45 3.77
34 35 5.413523 ACAACGTCTACAAGAAAAAGGTTGT 59.586 36.000 6.17 6.17 40.17 3.32
35 36 5.479716 ACGTCTACAAGAAAAAGGTTGTG 57.520 39.130 0.00 0.00 37.46 3.33
36 37 4.939439 ACGTCTACAAGAAAAAGGTTGTGT 59.061 37.500 0.00 0.00 37.46 3.72
37 38 6.108015 ACGTCTACAAGAAAAAGGTTGTGTA 58.892 36.000 0.00 0.00 37.46 2.90
38 39 6.257193 ACGTCTACAAGAAAAAGGTTGTGTAG 59.743 38.462 0.00 0.00 39.72 2.74
39 40 6.257193 CGTCTACAAGAAAAAGGTTGTGTAGT 59.743 38.462 8.12 0.00 39.49 2.73
40 41 7.436080 CGTCTACAAGAAAAAGGTTGTGTAGTA 59.564 37.037 8.12 0.00 39.49 1.82
41 42 8.762426 GTCTACAAGAAAAAGGTTGTGTAGTAG 58.238 37.037 8.12 0.00 39.49 2.57
42 43 8.698210 TCTACAAGAAAAAGGTTGTGTAGTAGA 58.302 33.333 8.12 0.00 39.49 2.59
43 44 7.549615 ACAAGAAAAAGGTTGTGTAGTAGAC 57.450 36.000 0.00 0.00 35.55 2.59
44 45 7.107542 ACAAGAAAAAGGTTGTGTAGTAGACA 58.892 34.615 0.00 0.00 35.55 3.41
45 46 7.773690 ACAAGAAAAAGGTTGTGTAGTAGACAT 59.226 33.333 0.29 0.00 41.14 3.06
46 47 8.621286 CAAGAAAAAGGTTGTGTAGTAGACATT 58.379 33.333 0.29 0.00 41.14 2.71
47 48 9.841295 AAGAAAAAGGTTGTGTAGTAGACATTA 57.159 29.630 0.29 0.00 41.14 1.90
48 49 9.269453 AGAAAAAGGTTGTGTAGTAGACATTAC 57.731 33.333 0.29 0.00 41.14 1.89
49 50 8.967664 AAAAAGGTTGTGTAGTAGACATTACA 57.032 30.769 0.29 0.00 41.14 2.41
50 51 9.569122 AAAAAGGTTGTGTAGTAGACATTACAT 57.431 29.630 0.29 0.00 41.14 2.29
51 52 9.569122 AAAAGGTTGTGTAGTAGACATTACATT 57.431 29.630 0.29 0.00 41.14 2.71
52 53 8.773404 AAGGTTGTGTAGTAGACATTACATTC 57.227 34.615 0.29 0.00 41.14 2.67
53 54 7.033791 AGGTTGTGTAGTAGACATTACATTCG 58.966 38.462 0.29 0.00 41.14 3.34
54 55 7.031372 GGTTGTGTAGTAGACATTACATTCGA 58.969 38.462 0.29 0.00 41.14 3.71
55 56 7.705325 GGTTGTGTAGTAGACATTACATTCGAT 59.295 37.037 0.29 0.00 41.14 3.59
56 57 9.084164 GTTGTGTAGTAGACATTACATTCGATT 57.916 33.333 0.29 0.00 41.14 3.34
57 58 8.851960 TGTGTAGTAGACATTACATTCGATTC 57.148 34.615 0.00 0.00 41.14 2.52
58 59 8.463607 TGTGTAGTAGACATTACATTCGATTCA 58.536 33.333 0.00 0.00 41.14 2.57
59 60 9.464714 GTGTAGTAGACATTACATTCGATTCAT 57.535 33.333 0.00 0.00 41.14 2.57
60 61 9.678941 TGTAGTAGACATTACATTCGATTCATC 57.321 33.333 0.00 0.00 31.20 2.92
71 72 2.635141 CGATTCATCGGCTCGAAAAG 57.365 50.000 0.98 0.00 45.93 2.27
87 88 7.482654 CTCGAAAAGCATCCTTGTATATGAA 57.517 36.000 0.00 0.00 0.00 2.57
88 89 7.482654 TCGAAAAGCATCCTTGTATATGAAG 57.517 36.000 0.00 0.00 0.00 3.02
89 90 6.483307 TCGAAAAGCATCCTTGTATATGAAGG 59.517 38.462 8.45 8.45 41.36 3.46
90 91 6.260936 CGAAAAGCATCCTTGTATATGAAGGT 59.739 38.462 12.70 1.96 40.88 3.50
91 92 6.949352 AAAGCATCCTTGTATATGAAGGTG 57.051 37.500 12.70 11.40 40.88 4.00
92 93 4.392940 AGCATCCTTGTATATGAAGGTGC 58.607 43.478 20.61 20.61 42.17 5.01
93 94 4.103785 AGCATCCTTGTATATGAAGGTGCT 59.896 41.667 22.68 22.68 44.38 4.40
94 95 4.453819 GCATCCTTGTATATGAAGGTGCTC 59.546 45.833 20.74 8.32 40.59 4.26
95 96 4.689612 TCCTTGTATATGAAGGTGCTCC 57.310 45.455 12.70 0.00 40.88 4.70
97 98 4.345257 TCCTTGTATATGAAGGTGCTCCTC 59.655 45.833 7.99 2.79 44.35 3.71
98 99 4.503991 CCTTGTATATGAAGGTGCTCCTCC 60.504 50.000 7.99 0.00 44.35 4.30
99 100 3.653164 TGTATATGAAGGTGCTCCTCCA 58.347 45.455 7.99 0.93 44.35 3.86
100 101 3.643320 TGTATATGAAGGTGCTCCTCCAG 59.357 47.826 7.99 0.00 44.35 3.86
101 102 2.254152 TATGAAGGTGCTCCTCCAGT 57.746 50.000 7.99 0.00 44.35 4.00
102 103 1.366319 ATGAAGGTGCTCCTCCAGTT 58.634 50.000 7.99 0.00 44.35 3.16
103 104 0.687354 TGAAGGTGCTCCTCCAGTTC 59.313 55.000 7.99 2.13 44.35 3.01
104 105 0.980423 GAAGGTGCTCCTCCAGTTCT 59.020 55.000 7.99 0.00 44.35 3.01
105 106 1.349357 GAAGGTGCTCCTCCAGTTCTT 59.651 52.381 7.99 0.00 44.35 2.52
106 107 1.439543 AGGTGCTCCTCCAGTTCTTT 58.560 50.000 0.18 0.00 40.58 2.52
107 108 1.349357 AGGTGCTCCTCCAGTTCTTTC 59.651 52.381 0.18 0.00 40.58 2.62
108 109 1.072331 GGTGCTCCTCCAGTTCTTTCA 59.928 52.381 0.00 0.00 0.00 2.69
109 110 2.290577 GGTGCTCCTCCAGTTCTTTCAT 60.291 50.000 0.00 0.00 0.00 2.57
110 111 3.055094 GGTGCTCCTCCAGTTCTTTCATA 60.055 47.826 0.00 0.00 0.00 2.15
111 112 3.935828 GTGCTCCTCCAGTTCTTTCATAC 59.064 47.826 0.00 0.00 0.00 2.39
118 119 3.582647 TCCAGTTCTTTCATACTGCCTCA 59.417 43.478 0.00 0.00 40.28 3.86
127 128 1.607801 ATACTGCCTCAGCGACTGCA 61.608 55.000 2.45 0.00 46.23 4.41
137 138 0.244994 AGCGACTGCAGAAGACGATT 59.755 50.000 23.35 9.23 45.25 3.34
147 148 1.611977 AGAAGACGATTGTGGACGACA 59.388 47.619 0.00 0.00 0.00 4.35
148 149 2.231478 AGAAGACGATTGTGGACGACAT 59.769 45.455 0.00 0.00 33.40 3.06
184 185 5.045869 ACAAGATTCTCCCGGAGTGAAATTA 60.046 40.000 14.36 0.00 32.06 1.40
189 190 6.555463 TTCTCCCGGAGTGAAATTATAGTT 57.445 37.500 14.36 0.00 0.00 2.24
197 198 9.158233 CCGGAGTGAAATTATAGTTTTACTTCA 57.842 33.333 18.26 1.47 37.83 3.02
264 273 6.073765 GGTGACATTGTGTGTACTCTTTGTAG 60.074 42.308 0.00 0.00 42.36 2.74
268 277 4.233123 TGTGTGTACTCTTTGTAGTCCG 57.767 45.455 0.00 0.00 0.00 4.79
273 282 6.697019 GTGTGTACTCTTTGTAGTCCGTTTTA 59.303 38.462 0.00 0.00 0.00 1.52
274 283 6.697019 TGTGTACTCTTTGTAGTCCGTTTTAC 59.303 38.462 0.00 0.00 0.00 2.01
275 284 6.920210 GTGTACTCTTTGTAGTCCGTTTTACT 59.080 38.462 0.00 0.00 0.00 2.24
277 286 8.629158 TGTACTCTTTGTAGTCCGTTTTACTAA 58.371 33.333 0.00 0.00 31.48 2.24
278 287 9.631452 GTACTCTTTGTAGTCCGTTTTACTAAT 57.369 33.333 0.00 0.00 31.48 1.73
281 650 9.199982 CTCTTTGTAGTCCGTTTTACTAATGAA 57.800 33.333 0.00 0.00 31.48 2.57
283 652 9.590088 CTTTGTAGTCCGTTTTACTAATGAAAC 57.410 33.333 0.00 0.00 31.48 2.78
286 655 9.926158 TGTAGTCCGTTTTACTAATGAAACATA 57.074 29.630 0.00 0.00 34.72 2.29
324 697 3.916035 ACTCTATGTCCTGATGTGGCTA 58.084 45.455 0.00 0.00 0.00 3.93
406 2303 2.244436 CTTGTGCCGGTCAAGCATCG 62.244 60.000 21.63 6.14 43.29 3.84
414 2311 1.375908 GTCAAGCATCGGCACTCCA 60.376 57.895 0.00 0.00 44.61 3.86
425 2322 1.188219 GGCACTCCAGAGTCCTGACA 61.188 60.000 0.00 0.00 43.02 3.58
915 2840 0.035439 CATAGCGACCCACCCAAACT 60.035 55.000 0.00 0.00 0.00 2.66
1199 3124 3.112205 GCCGGATCTGCCACCTCAT 62.112 63.158 5.05 0.00 35.94 2.90
1389 3318 2.174349 GCTGCTCGCTTGTTTCCG 59.826 61.111 0.00 0.00 35.14 4.30
1487 3419 2.671682 GTGTGGCTTCTCCCTCCC 59.328 66.667 0.00 0.00 0.00 4.30
1594 3526 6.266131 TCTGAATGGCTATAGGGTCAAAAT 57.734 37.500 1.04 0.00 0.00 1.82
1600 3532 8.641498 AATGGCTATAGGGTCAAAATTCTATG 57.359 34.615 1.04 0.00 0.00 2.23
1650 3583 1.127951 GGGCAACACGAACAGTTATCG 59.872 52.381 0.00 0.00 45.47 2.92
1653 3586 2.664568 GCAACACGAACAGTTATCGCTA 59.335 45.455 0.00 0.00 43.88 4.26
1679 3612 3.412386 CCACTTAGCCAAAGTTGCTACT 58.588 45.455 0.00 0.00 46.61 2.57
1680 3613 3.437049 CCACTTAGCCAAAGTTGCTACTC 59.563 47.826 0.07 0.00 46.61 2.59
1681 3614 3.437049 CACTTAGCCAAAGTTGCTACTCC 59.563 47.826 0.07 0.00 46.61 3.85
1682 3615 2.781681 TAGCCAAAGTTGCTACTCCC 57.218 50.000 0.07 0.00 40.23 4.30
1684 3617 1.003696 AGCCAAAGTTGCTACTCCCTC 59.996 52.381 0.07 0.00 37.28 4.30
1685 3618 1.950954 GCCAAAGTTGCTACTCCCTCC 60.951 57.143 0.07 0.00 31.99 4.30
1686 3619 1.676014 CCAAAGTTGCTACTCCCTCCG 60.676 57.143 0.07 0.00 31.99 4.63
1687 3620 1.002087 CAAAGTTGCTACTCCCTCCGT 59.998 52.381 0.07 0.00 31.99 4.69
1688 3621 1.349067 AAGTTGCTACTCCCTCCGTT 58.651 50.000 0.07 0.00 31.99 4.44
1689 3622 0.896226 AGTTGCTACTCCCTCCGTTC 59.104 55.000 0.00 0.00 0.00 3.95
1690 3623 0.108281 GTTGCTACTCCCTCCGTTCC 60.108 60.000 0.00 0.00 0.00 3.62
1691 3624 1.601419 TTGCTACTCCCTCCGTTCCG 61.601 60.000 0.00 0.00 0.00 4.30
1692 3625 1.751927 GCTACTCCCTCCGTTCCGA 60.752 63.158 0.00 0.00 0.00 4.55
1693 3626 1.318158 GCTACTCCCTCCGTTCCGAA 61.318 60.000 0.00 0.00 0.00 4.30
1694 3627 1.400737 CTACTCCCTCCGTTCCGAAT 58.599 55.000 0.00 0.00 0.00 3.34
1695 3628 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
1696 3629 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
1697 3630 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
1698 3631 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
1699 3632 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
1700 3633 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1701 3634 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1702 3635 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1703 3636 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
1704 3637 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
1705 3638 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
1706 3639 2.347452 CGTTCCGAATTACTTGTCGCAT 59.653 45.455 0.00 0.00 35.93 4.73
1707 3640 3.670203 GTTCCGAATTACTTGTCGCATG 58.330 45.455 0.00 0.00 35.93 4.06
1708 3641 2.967362 TCCGAATTACTTGTCGCATGT 58.033 42.857 0.00 4.39 35.93 3.21
1709 3642 4.112716 TCCGAATTACTTGTCGCATGTA 57.887 40.909 0.00 2.87 35.93 2.29
1710 3643 4.689071 TCCGAATTACTTGTCGCATGTAT 58.311 39.130 0.00 0.00 35.93 2.29
1711 3644 4.506288 TCCGAATTACTTGTCGCATGTATG 59.494 41.667 0.00 0.00 35.93 2.39
1712 3645 4.318760 CCGAATTACTTGTCGCATGTATGG 60.319 45.833 0.00 4.42 35.93 2.74
1713 3646 4.506288 CGAATTACTTGTCGCATGTATGGA 59.494 41.667 0.00 0.00 0.00 3.41
1714 3647 5.177511 CGAATTACTTGTCGCATGTATGGAT 59.822 40.000 0.00 0.00 0.00 3.41
1715 3648 5.929697 ATTACTTGTCGCATGTATGGATG 57.070 39.130 0.00 0.00 0.00 3.51
1716 3649 3.266510 ACTTGTCGCATGTATGGATGT 57.733 42.857 0.00 0.00 0.00 3.06
1717 3650 4.400529 ACTTGTCGCATGTATGGATGTA 57.599 40.909 0.00 0.00 0.00 2.29
1718 3651 4.960938 ACTTGTCGCATGTATGGATGTAT 58.039 39.130 0.00 0.00 0.00 2.29
1719 3652 4.991056 ACTTGTCGCATGTATGGATGTATC 59.009 41.667 0.00 0.00 0.00 2.24
1720 3653 4.871933 TGTCGCATGTATGGATGTATCT 57.128 40.909 0.00 0.00 0.00 1.98
1721 3654 5.975693 TGTCGCATGTATGGATGTATCTA 57.024 39.130 0.00 0.00 0.00 1.98
1722 3655 5.954335 TGTCGCATGTATGGATGTATCTAG 58.046 41.667 0.00 0.00 0.00 2.43
1723 3656 5.710099 TGTCGCATGTATGGATGTATCTAGA 59.290 40.000 0.00 0.00 0.00 2.43
1724 3657 6.378280 TGTCGCATGTATGGATGTATCTAGAT 59.622 38.462 10.73 10.73 0.00 1.98
1725 3658 6.694844 GTCGCATGTATGGATGTATCTAGATG 59.305 42.308 15.79 0.00 0.00 2.90
1726 3659 6.378280 TCGCATGTATGGATGTATCTAGATGT 59.622 38.462 15.79 1.25 0.00 3.06
1727 3660 7.556275 TCGCATGTATGGATGTATCTAGATGTA 59.444 37.037 15.79 4.44 0.00 2.29
1728 3661 8.355913 CGCATGTATGGATGTATCTAGATGTAT 58.644 37.037 15.79 9.11 0.00 2.29
1755 3688 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
1756 3689 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
1757 3690 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
1758 3691 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
1759 3692 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
1760 3693 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
1761 3694 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
1762 3695 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
1763 3696 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
1764 3697 3.935203 ACATCCATTTCTGCGACAAGTAG 59.065 43.478 0.00 0.00 0.00 2.57
1765 3698 3.678056 TCCATTTCTGCGACAAGTAGT 57.322 42.857 0.00 0.00 34.00 2.73
1766 3699 4.002906 TCCATTTCTGCGACAAGTAGTT 57.997 40.909 0.00 0.00 34.00 2.24
1767 3700 4.385825 TCCATTTCTGCGACAAGTAGTTT 58.614 39.130 0.00 0.00 34.00 2.66
1768 3701 4.213270 TCCATTTCTGCGACAAGTAGTTTG 59.787 41.667 0.00 0.00 42.68 2.93
1769 3702 4.466828 CATTTCTGCGACAAGTAGTTTGG 58.533 43.478 0.00 0.00 41.25 3.28
1770 3703 3.462483 TTCTGCGACAAGTAGTTTGGA 57.538 42.857 0.00 0.00 41.25 3.53
1771 3704 3.462483 TCTGCGACAAGTAGTTTGGAA 57.538 42.857 0.00 0.00 41.25 3.53
1772 3705 3.128349 TCTGCGACAAGTAGTTTGGAAC 58.872 45.455 0.00 0.00 41.25 3.62
1773 3706 1.862201 TGCGACAAGTAGTTTGGAACG 59.138 47.619 0.00 0.00 41.25 3.95
1774 3707 1.193874 GCGACAAGTAGTTTGGAACGG 59.806 52.381 0.00 0.00 41.25 4.44
1775 3708 2.746269 CGACAAGTAGTTTGGAACGGA 58.254 47.619 0.00 0.00 41.25 4.69
1776 3709 2.729882 CGACAAGTAGTTTGGAACGGAG 59.270 50.000 0.00 0.00 41.25 4.63
1777 3710 3.064931 GACAAGTAGTTTGGAACGGAGG 58.935 50.000 0.00 0.00 41.25 4.30
1778 3711 2.224450 ACAAGTAGTTTGGAACGGAGGG 60.224 50.000 0.00 0.00 41.25 4.30
1779 3712 2.019807 AGTAGTTTGGAACGGAGGGA 57.980 50.000 0.00 0.00 36.23 4.20
1780 3713 1.900486 AGTAGTTTGGAACGGAGGGAG 59.100 52.381 0.00 0.00 36.23 4.30
1781 3714 1.622312 GTAGTTTGGAACGGAGGGAGT 59.378 52.381 0.00 0.00 36.23 3.85
1782 3715 2.019807 AGTTTGGAACGGAGGGAGTA 57.980 50.000 0.00 0.00 36.23 2.59
1783 3716 1.622312 AGTTTGGAACGGAGGGAGTAC 59.378 52.381 0.00 0.00 36.23 2.73
1784 3717 0.978907 TTTGGAACGGAGGGAGTACC 59.021 55.000 0.00 0.00 40.67 3.34
1785 3718 0.178926 TTGGAACGGAGGGAGTACCA 60.179 55.000 0.00 0.00 43.89 3.25
1786 3719 0.613853 TGGAACGGAGGGAGTACCAG 60.614 60.000 0.00 0.00 43.89 4.00
1787 3720 0.324091 GGAACGGAGGGAGTACCAGA 60.324 60.000 0.00 0.00 43.89 3.86
1788 3721 1.104630 GAACGGAGGGAGTACCAGAG 58.895 60.000 0.00 0.00 43.89 3.35
1789 3722 0.702902 AACGGAGGGAGTACCAGAGA 59.297 55.000 0.00 0.00 43.89 3.10
1790 3723 0.702902 ACGGAGGGAGTACCAGAGAA 59.297 55.000 0.00 0.00 43.89 2.87
1895 3828 6.494893 TTGAAATGACGATTTAGGTTGGAG 57.505 37.500 0.00 0.00 31.58 3.86
1901 3834 2.268298 CGATTTAGGTTGGAGTGGACG 58.732 52.381 0.00 0.00 0.00 4.79
1914 3847 2.140717 AGTGGACGTTCGGAAAATGTC 58.859 47.619 9.35 9.35 0.00 3.06
1941 3876 4.625800 GCTTGGTAGCCACCTCAG 57.374 61.111 2.16 0.00 45.98 3.35
1957 3892 6.511416 CCACCTCAGTATAGAATCTCTTGTG 58.489 44.000 0.00 0.00 0.00 3.33
2122 4064 0.178938 TGGCTTCCCTTTGGCATTGA 60.179 50.000 0.00 0.00 33.80 2.57
2192 4135 3.432890 GGCTGGGTCAAATCAACCAAAAA 60.433 43.478 0.00 0.00 38.62 1.94
2214 4157 1.004200 CCGTAGGCGAACCAAACCT 60.004 57.895 0.00 0.00 46.14 3.50
2218 4161 2.807392 CGTAGGCGAACCAAACCTTTTA 59.193 45.455 0.00 0.00 41.33 1.52
2220 4163 2.657143 AGGCGAACCAAACCTTTTACA 58.343 42.857 0.00 0.00 39.06 2.41
2221 4164 3.227614 AGGCGAACCAAACCTTTTACAT 58.772 40.909 0.00 0.00 39.06 2.29
2253 4196 8.721478 TCAGTTAGCATTTTTCTTAGCAACTAG 58.279 33.333 0.00 0.00 31.84 2.57
2285 4228 4.154918 CAGGGTCTCTGCAGTTATTCAAAC 59.845 45.833 14.67 1.89 36.60 2.93
2367 4310 5.126396 AGTGGCTAAGAAATGCAAAACTC 57.874 39.130 0.00 0.00 0.00 3.01
2475 4418 1.322538 ATGGGCGAAGAATGGCAACC 61.323 55.000 0.00 0.00 30.88 3.77
2681 4624 2.849942 TCACAACACAGTTCCTCATGG 58.150 47.619 0.00 0.00 0.00 3.66
2903 7067 2.034179 CGATGGTATGCTCCTTACGACA 59.966 50.000 0.00 0.00 0.00 4.35
2917 7081 7.254488 GCTCCTTACGACATTTCTTCCTTATTC 60.254 40.741 0.00 0.00 0.00 1.75
3036 7200 5.043189 CAAAGATTTGGACTCCGGTAAAC 57.957 43.478 0.00 0.00 34.59 2.01
3044 7209 7.527568 TTTGGACTCCGGTAAACATTTTATT 57.472 32.000 0.00 0.00 0.00 1.40
3127 7292 3.520569 TCAGCTTCCAAGTTTTTGTTGC 58.479 40.909 0.00 0.00 32.21 4.17
3328 7505 6.400568 CAAGTGTATTACTCCCTCCGTTTTA 58.599 40.000 0.00 0.00 39.18 1.52
3353 7531 8.941995 AAATATAGGCCCTTTTAGAGATTTCC 57.058 34.615 0.00 0.00 0.00 3.13
3375 7553 2.972713 ACAGGGACTATATGCGGATGTT 59.027 45.455 0.00 0.00 36.02 2.71
3381 7559 6.098409 AGGGACTATATGCGGATGTTTATAGG 59.902 42.308 0.00 0.00 36.02 2.57
3391 7569 8.039603 TGCGGATGTTTATAGGCATATTTTAG 57.960 34.615 0.00 0.00 0.00 1.85
3394 7572 8.391106 CGGATGTTTATAGGCATATTTTAGAGC 58.609 37.037 0.00 0.00 0.00 4.09
3400 7578 9.635520 TTTATAGGCATATTTTAGAGCGTAGAC 57.364 33.333 0.00 0.00 31.92 2.59
3420 7599 7.488150 CGTAGACTCACTCATTTTGCTTGTATA 59.512 37.037 0.00 0.00 0.00 1.47
3466 7645 6.449830 AAGGGCTTATATTTAGGAACGGAT 57.550 37.500 0.00 0.00 0.00 4.18
3478 7657 4.635699 AGGAACGGATGAAGTACCTTTT 57.364 40.909 0.00 0.00 0.00 2.27
3489 7668 9.622004 GGATGAAGTACCTTTTAACTTTTAAGC 57.378 33.333 0.00 0.00 36.10 3.09
3512 7691 4.540824 GTGAAATGAAACAGACCTCAAGC 58.459 43.478 0.00 0.00 0.00 4.01
3528 7707 1.864711 CAAGCTCCAAACGAGACGAAA 59.135 47.619 0.00 0.00 41.63 3.46
3533 7712 3.125316 GCTCCAAACGAGACGAAATGAAT 59.875 43.478 0.00 0.00 41.63 2.57
3562 7741 5.006386 AGATCTTTCCAACAAGACATGGAC 58.994 41.667 0.00 0.00 45.14 4.02
3578 7757 0.179189 GGACGCTTCGAAATGCTTGG 60.179 55.000 0.00 0.00 0.00 3.61
3580 7759 1.137404 CGCTTCGAAATGCTTGGGG 59.863 57.895 0.00 0.00 0.00 4.96
3595 7774 1.228245 GGGGCTGCAACAACAGAGA 60.228 57.895 0.50 0.00 40.25 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.342174 GTAGACGTTGTTGGGTCTCCA 59.658 52.381 0.00 0.00 42.27 3.86
1 2 1.342174 TGTAGACGTTGTTGGGTCTCC 59.658 52.381 0.00 0.00 42.27 3.71
2 3 2.806608 TGTAGACGTTGTTGGGTCTC 57.193 50.000 0.00 0.00 42.27 3.36
3 4 2.696707 TCTTGTAGACGTTGTTGGGTCT 59.303 45.455 0.00 0.00 45.06 3.85
4 5 3.102052 TCTTGTAGACGTTGTTGGGTC 57.898 47.619 0.00 0.00 0.00 4.46
6 7 4.886247 TTTTCTTGTAGACGTTGTTGGG 57.114 40.909 0.00 0.00 0.00 4.12
7 8 5.163693 ACCTTTTTCTTGTAGACGTTGTTGG 60.164 40.000 0.00 0.00 0.00 3.77
8 9 5.875930 ACCTTTTTCTTGTAGACGTTGTTG 58.124 37.500 0.00 0.00 0.00 3.33
9 10 6.072342 ACAACCTTTTTCTTGTAGACGTTGTT 60.072 34.615 0.00 0.00 38.41 2.83
10 11 5.413523 ACAACCTTTTTCTTGTAGACGTTGT 59.586 36.000 0.00 0.00 37.16 3.32
11 12 5.737290 CACAACCTTTTTCTTGTAGACGTTG 59.263 40.000 0.00 0.00 35.40 4.10
12 13 5.413523 ACACAACCTTTTTCTTGTAGACGTT 59.586 36.000 0.00 0.00 0.00 3.99
13 14 4.939439 ACACAACCTTTTTCTTGTAGACGT 59.061 37.500 0.00 0.00 0.00 4.34
14 15 5.479716 ACACAACCTTTTTCTTGTAGACG 57.520 39.130 0.00 0.00 0.00 4.18
15 16 7.549615 ACTACACAACCTTTTTCTTGTAGAC 57.450 36.000 12.31 0.00 39.06 2.59
16 17 8.698210 TCTACTACACAACCTTTTTCTTGTAGA 58.302 33.333 12.31 0.00 39.06 2.59
17 18 8.762426 GTCTACTACACAACCTTTTTCTTGTAG 58.238 37.037 5.27 5.27 41.37 2.74
18 19 8.259411 TGTCTACTACACAACCTTTTTCTTGTA 58.741 33.333 0.00 0.00 31.43 2.41
19 20 7.107542 TGTCTACTACACAACCTTTTTCTTGT 58.892 34.615 0.00 0.00 31.43 3.16
20 21 7.548196 TGTCTACTACACAACCTTTTTCTTG 57.452 36.000 0.00 0.00 31.43 3.02
21 22 8.747538 AATGTCTACTACACAACCTTTTTCTT 57.252 30.769 0.00 0.00 42.09 2.52
22 23 9.269453 GTAATGTCTACTACACAACCTTTTTCT 57.731 33.333 0.00 0.00 42.09 2.52
23 24 9.048446 TGTAATGTCTACTACACAACCTTTTTC 57.952 33.333 0.00 0.00 42.09 2.29
24 25 8.967664 TGTAATGTCTACTACACAACCTTTTT 57.032 30.769 0.00 0.00 42.09 1.94
25 26 9.569122 AATGTAATGTCTACTACACAACCTTTT 57.431 29.630 0.00 0.00 42.09 2.27
26 27 9.216117 GAATGTAATGTCTACTACACAACCTTT 57.784 33.333 0.00 0.00 42.09 3.11
27 28 7.544566 CGAATGTAATGTCTACTACACAACCTT 59.455 37.037 0.00 0.00 42.09 3.50
28 29 7.033791 CGAATGTAATGTCTACTACACAACCT 58.966 38.462 0.00 0.00 42.09 3.50
29 30 7.031372 TCGAATGTAATGTCTACTACACAACC 58.969 38.462 0.00 0.00 42.09 3.77
30 31 8.630278 ATCGAATGTAATGTCTACTACACAAC 57.370 34.615 0.00 0.00 42.09 3.32
31 32 9.297586 GAATCGAATGTAATGTCTACTACACAA 57.702 33.333 0.00 0.00 42.09 3.33
32 33 8.463607 TGAATCGAATGTAATGTCTACTACACA 58.536 33.333 0.00 0.00 42.09 3.72
33 34 8.851960 TGAATCGAATGTAATGTCTACTACAC 57.148 34.615 0.00 0.00 42.09 2.90
34 35 9.678941 GATGAATCGAATGTAATGTCTACTACA 57.321 33.333 0.00 0.00 43.86 2.74
51 52 3.615489 GCTTTTCGAGCCGATGAATCGA 61.615 50.000 14.07 0.00 46.50 3.59
52 53 1.332377 GCTTTTCGAGCCGATGAATCG 60.332 52.381 5.72 5.72 46.01 3.34
53 54 2.375324 GCTTTTCGAGCCGATGAATC 57.625 50.000 0.00 0.00 46.01 2.52
63 64 7.307632 CCTTCATATACAAGGATGCTTTTCGAG 60.308 40.741 0.00 0.00 42.94 4.04
64 65 6.483307 CCTTCATATACAAGGATGCTTTTCGA 59.517 38.462 0.00 0.00 42.94 3.71
65 66 6.260936 ACCTTCATATACAAGGATGCTTTTCG 59.739 38.462 16.18 0.00 42.94 3.46
66 67 7.420800 CACCTTCATATACAAGGATGCTTTTC 58.579 38.462 16.18 0.00 42.94 2.29
67 68 6.183360 GCACCTTCATATACAAGGATGCTTTT 60.183 38.462 16.18 0.00 42.94 2.27
68 69 5.300286 GCACCTTCATATACAAGGATGCTTT 59.700 40.000 16.18 0.00 42.94 3.51
69 70 4.823989 GCACCTTCATATACAAGGATGCTT 59.176 41.667 16.18 0.00 42.94 3.91
70 71 4.103785 AGCACCTTCATATACAAGGATGCT 59.896 41.667 21.67 21.67 44.63 3.79
71 72 4.392940 AGCACCTTCATATACAAGGATGC 58.607 43.478 16.18 18.16 42.94 3.91
72 73 4.999950 GGAGCACCTTCATATACAAGGATG 59.000 45.833 16.18 11.97 42.94 3.51
73 74 4.910304 AGGAGCACCTTCATATACAAGGAT 59.090 41.667 16.18 4.90 45.36 3.24
74 75 4.298626 AGGAGCACCTTCATATACAAGGA 58.701 43.478 16.18 0.00 45.36 3.36
75 76 4.696479 AGGAGCACCTTCATATACAAGG 57.304 45.455 0.00 9.81 45.36 3.61
76 77 4.101585 TGGAGGAGCACCTTCATATACAAG 59.898 45.833 7.14 0.00 46.01 3.16
77 78 4.037222 TGGAGGAGCACCTTCATATACAA 58.963 43.478 7.14 0.00 46.01 2.41
78 79 3.653164 TGGAGGAGCACCTTCATATACA 58.347 45.455 7.14 0.00 46.01 2.29
88 89 1.072331 TGAAAGAACTGGAGGAGCACC 59.928 52.381 0.00 0.00 0.00 5.01
89 90 2.550830 TGAAAGAACTGGAGGAGCAC 57.449 50.000 0.00 0.00 0.00 4.40
90 91 3.840666 AGTATGAAAGAACTGGAGGAGCA 59.159 43.478 0.00 0.00 0.00 4.26
91 92 4.187694 CAGTATGAAAGAACTGGAGGAGC 58.812 47.826 0.00 0.00 39.69 4.70
92 93 4.187694 GCAGTATGAAAGAACTGGAGGAG 58.812 47.826 4.79 0.00 42.72 3.69
93 94 3.055094 GGCAGTATGAAAGAACTGGAGGA 60.055 47.826 4.79 0.00 42.72 3.71
94 95 3.054802 AGGCAGTATGAAAGAACTGGAGG 60.055 47.826 4.79 0.00 42.72 4.30
95 96 4.187694 GAGGCAGTATGAAAGAACTGGAG 58.812 47.826 4.79 0.00 42.72 3.86
96 97 3.582647 TGAGGCAGTATGAAAGAACTGGA 59.417 43.478 4.79 0.00 42.72 3.86
97 98 3.937706 CTGAGGCAGTATGAAAGAACTGG 59.062 47.826 4.79 0.00 42.72 4.00
98 99 3.373439 GCTGAGGCAGTATGAAAGAACTG 59.627 47.826 0.00 0.00 44.79 3.16
99 100 3.604582 GCTGAGGCAGTATGAAAGAACT 58.395 45.455 0.00 0.00 39.69 3.01
100 101 2.349886 CGCTGAGGCAGTATGAAAGAAC 59.650 50.000 0.00 0.00 39.69 3.01
101 102 2.233676 TCGCTGAGGCAGTATGAAAGAA 59.766 45.455 0.00 0.00 39.69 2.52
102 103 1.824852 TCGCTGAGGCAGTATGAAAGA 59.175 47.619 0.00 0.00 39.69 2.52
103 104 1.929836 GTCGCTGAGGCAGTATGAAAG 59.070 52.381 0.00 0.00 39.69 2.62
104 105 1.550524 AGTCGCTGAGGCAGTATGAAA 59.449 47.619 0.00 0.00 39.69 2.69
105 106 1.134995 CAGTCGCTGAGGCAGTATGAA 60.135 52.381 1.18 0.00 38.60 2.57
106 107 0.457443 CAGTCGCTGAGGCAGTATGA 59.543 55.000 1.18 0.00 38.60 2.15
107 108 1.150567 GCAGTCGCTGAGGCAGTATG 61.151 60.000 10.46 0.00 38.60 2.39
108 109 1.142748 GCAGTCGCTGAGGCAGTAT 59.857 57.895 10.46 0.00 38.60 2.12
109 110 2.218037 CTGCAGTCGCTGAGGCAGTA 62.218 60.000 5.25 0.00 46.47 2.74
110 111 3.586461 CTGCAGTCGCTGAGGCAGT 62.586 63.158 5.25 0.00 46.47 4.40
111 112 2.814341 CTGCAGTCGCTGAGGCAG 60.814 66.667 5.25 13.50 46.47 4.85
118 119 0.244994 AATCGTCTTCTGCAGTCGCT 59.755 50.000 14.67 4.04 39.64 4.93
127 128 1.611977 TGTCGTCCACAATCGTCTTCT 59.388 47.619 0.00 0.00 29.30 2.85
137 138 0.105224 ACACCGAAATGTCGTCCACA 59.895 50.000 4.25 0.00 46.21 4.17
147 148 1.909700 ATCTTGTGCCACACCGAAAT 58.090 45.000 0.00 0.00 32.73 2.17
148 149 1.606668 GAATCTTGTGCCACACCGAAA 59.393 47.619 0.00 0.00 32.73 3.46
152 153 1.168714 GGAGAATCTTGTGCCACACC 58.831 55.000 0.00 0.00 31.33 4.16
154 155 0.321564 CGGGAGAATCTTGTGCCACA 60.322 55.000 0.00 0.00 31.05 4.17
227 236 3.949754 ACAATGTCACCATAAGAGCCATG 59.050 43.478 0.00 0.00 0.00 3.66
231 240 3.753272 ACACACAATGTCACCATAAGAGC 59.247 43.478 0.00 0.00 36.54 4.09
247 256 3.633525 ACGGACTACAAAGAGTACACACA 59.366 43.478 0.00 0.00 29.81 3.72
264 273 9.485591 CACATATGTTTCATTAGTAAAACGGAC 57.514 33.333 5.37 0.00 38.03 4.79
312 685 0.106335 CTCCAGCTAGCCACATCAGG 59.894 60.000 12.13 2.59 0.00 3.86
324 697 4.031129 CTGGCAGCACCTCCAGCT 62.031 66.667 0.00 0.00 42.79 4.24
414 2311 1.957562 CCGACGTTGTCAGGACTCT 59.042 57.895 1.30 0.00 31.51 3.24
425 2322 3.276846 GGCTGTGTTGCCGACGTT 61.277 61.111 0.00 0.00 43.74 3.99
1405 3334 1.338337 AGCTAGCATACACTACGGCAG 59.662 52.381 18.83 0.00 0.00 4.85
1594 3526 7.347222 TGAAGCTTTCCCCTCTATAACATAGAA 59.653 37.037 0.00 0.00 0.00 2.10
1600 3532 5.129650 ACTCTGAAGCTTTCCCCTCTATAAC 59.870 44.000 0.00 0.00 0.00 1.89
1650 3583 4.200092 ACTTTGGCTAAGTGGCTAATAGC 58.800 43.478 13.46 3.17 45.33 2.97
1686 3619 3.124636 ACATGCGACAAGTAATTCGGAAC 59.875 43.478 0.00 0.00 39.13 3.62
1687 3620 3.331150 ACATGCGACAAGTAATTCGGAA 58.669 40.909 0.00 0.00 39.13 4.30
1688 3621 2.967362 ACATGCGACAAGTAATTCGGA 58.033 42.857 0.00 0.00 40.02 4.55
1689 3622 4.318760 CCATACATGCGACAAGTAATTCGG 60.319 45.833 0.00 0.00 35.73 4.30
1690 3623 4.506288 TCCATACATGCGACAAGTAATTCG 59.494 41.667 0.00 0.00 38.31 3.34
1691 3624 5.984233 TCCATACATGCGACAAGTAATTC 57.016 39.130 0.00 0.00 0.00 2.17
1692 3625 5.822519 ACATCCATACATGCGACAAGTAATT 59.177 36.000 0.00 0.00 0.00 1.40
1693 3626 5.368145 ACATCCATACATGCGACAAGTAAT 58.632 37.500 0.00 0.00 0.00 1.89
1694 3627 4.765273 ACATCCATACATGCGACAAGTAA 58.235 39.130 0.00 0.00 0.00 2.24
1695 3628 4.400529 ACATCCATACATGCGACAAGTA 57.599 40.909 0.00 0.00 0.00 2.24
1696 3629 3.266510 ACATCCATACATGCGACAAGT 57.733 42.857 0.00 0.00 0.00 3.16
1697 3630 5.233225 AGATACATCCATACATGCGACAAG 58.767 41.667 0.00 0.00 0.00 3.16
1698 3631 5.213891 AGATACATCCATACATGCGACAA 57.786 39.130 0.00 0.00 0.00 3.18
1699 3632 4.871933 AGATACATCCATACATGCGACA 57.128 40.909 0.00 0.00 0.00 4.35
1700 3633 6.196079 TCTAGATACATCCATACATGCGAC 57.804 41.667 0.00 0.00 0.00 5.19
1701 3634 6.378280 ACATCTAGATACATCCATACATGCGA 59.622 38.462 4.54 0.00 0.00 5.10
1702 3635 6.567959 ACATCTAGATACATCCATACATGCG 58.432 40.000 4.54 0.00 0.00 4.73
1729 3662 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
1730 3663 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
1731 3664 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
1732 3665 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
1733 3666 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
1734 3667 6.183360 TGTCGCAGAAATGGATGTATCTAGAA 60.183 38.462 0.00 0.00 39.69 2.10
1735 3668 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
1736 3669 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
1737 3670 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
1738 3671 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
1739 3672 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
1740 3673 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
1741 3674 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
1742 3675 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
1743 3676 3.935203 ACTACTTGTCGCAGAAATGGATG 59.065 43.478 0.00 0.00 39.69 3.51
1744 3677 4.207891 ACTACTTGTCGCAGAAATGGAT 57.792 40.909 0.00 0.00 39.69 3.41
1745 3678 3.678056 ACTACTTGTCGCAGAAATGGA 57.322 42.857 0.00 0.00 39.69 3.41
1746 3679 4.466828 CAAACTACTTGTCGCAGAAATGG 58.533 43.478 0.00 0.00 39.69 3.16
1747 3680 4.213270 TCCAAACTACTTGTCGCAGAAATG 59.787 41.667 0.00 0.00 39.69 2.32
1748 3681 4.385825 TCCAAACTACTTGTCGCAGAAAT 58.614 39.130 0.00 0.00 39.69 2.17
1749 3682 3.799366 TCCAAACTACTTGTCGCAGAAA 58.201 40.909 0.00 0.00 39.69 2.52
1750 3683 3.462483 TCCAAACTACTTGTCGCAGAA 57.538 42.857 0.00 0.00 39.69 3.02
1751 3684 3.128349 GTTCCAAACTACTTGTCGCAGA 58.872 45.455 0.00 0.00 32.65 4.26
1752 3685 2.096909 CGTTCCAAACTACTTGTCGCAG 60.097 50.000 0.00 0.00 32.65 5.18
1753 3686 1.862201 CGTTCCAAACTACTTGTCGCA 59.138 47.619 0.00 0.00 32.65 5.10
1754 3687 1.193874 CCGTTCCAAACTACTTGTCGC 59.806 52.381 0.00 0.00 32.65 5.19
1755 3688 2.729882 CTCCGTTCCAAACTACTTGTCG 59.270 50.000 0.00 0.00 32.65 4.35
1756 3689 3.064931 CCTCCGTTCCAAACTACTTGTC 58.935 50.000 0.00 0.00 32.65 3.18
1757 3690 2.224450 CCCTCCGTTCCAAACTACTTGT 60.224 50.000 0.00 0.00 32.65 3.16
1758 3691 2.038033 TCCCTCCGTTCCAAACTACTTG 59.962 50.000 0.00 0.00 34.52 3.16
1759 3692 2.302157 CTCCCTCCGTTCCAAACTACTT 59.698 50.000 0.00 0.00 0.00 2.24
1760 3693 1.900486 CTCCCTCCGTTCCAAACTACT 59.100 52.381 0.00 0.00 0.00 2.57
1761 3694 1.622312 ACTCCCTCCGTTCCAAACTAC 59.378 52.381 0.00 0.00 0.00 2.73
1762 3695 2.019807 ACTCCCTCCGTTCCAAACTA 57.980 50.000 0.00 0.00 0.00 2.24
1763 3696 1.622312 GTACTCCCTCCGTTCCAAACT 59.378 52.381 0.00 0.00 0.00 2.66
1764 3697 1.338484 GGTACTCCCTCCGTTCCAAAC 60.338 57.143 0.00 0.00 0.00 2.93
1765 3698 0.978907 GGTACTCCCTCCGTTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
1766 3699 0.178926 TGGTACTCCCTCCGTTCCAA 60.179 55.000 0.00 0.00 30.28 3.53
1767 3700 0.613853 CTGGTACTCCCTCCGTTCCA 60.614 60.000 0.00 0.00 32.07 3.53
1768 3701 0.324091 TCTGGTACTCCCTCCGTTCC 60.324 60.000 0.00 0.00 0.00 3.62
1769 3702 1.104630 CTCTGGTACTCCCTCCGTTC 58.895 60.000 0.00 0.00 0.00 3.95
1770 3703 0.702902 TCTCTGGTACTCCCTCCGTT 59.297 55.000 0.00 0.00 0.00 4.44
1771 3704 0.702902 TTCTCTGGTACTCCCTCCGT 59.297 55.000 0.00 0.00 0.00 4.69
1772 3705 1.064611 TCTTCTCTGGTACTCCCTCCG 60.065 57.143 0.00 0.00 0.00 4.63
1773 3706 2.242708 TCTCTTCTCTGGTACTCCCTCC 59.757 54.545 0.00 0.00 0.00 4.30
1774 3707 3.655615 TCTCTTCTCTGGTACTCCCTC 57.344 52.381 0.00 0.00 0.00 4.30
1775 3708 4.264623 ACATTCTCTTCTCTGGTACTCCCT 60.265 45.833 0.00 0.00 0.00 4.20
1776 3709 4.027437 ACATTCTCTTCTCTGGTACTCCC 58.973 47.826 0.00 0.00 0.00 4.30
1777 3710 5.221165 GCTACATTCTCTTCTCTGGTACTCC 60.221 48.000 0.00 0.00 0.00 3.85
1778 3711 5.504994 CGCTACATTCTCTTCTCTGGTACTC 60.505 48.000 0.00 0.00 0.00 2.59
1779 3712 4.336993 CGCTACATTCTCTTCTCTGGTACT 59.663 45.833 0.00 0.00 0.00 2.73
1780 3713 4.335874 TCGCTACATTCTCTTCTCTGGTAC 59.664 45.833 0.00 0.00 0.00 3.34
1781 3714 4.524053 TCGCTACATTCTCTTCTCTGGTA 58.476 43.478 0.00 0.00 0.00 3.25
1782 3715 3.357203 TCGCTACATTCTCTTCTCTGGT 58.643 45.455 0.00 0.00 0.00 4.00
1783 3716 4.278170 AGATCGCTACATTCTCTTCTCTGG 59.722 45.833 0.00 0.00 0.00 3.86
1784 3717 5.437289 AGATCGCTACATTCTCTTCTCTG 57.563 43.478 0.00 0.00 0.00 3.35
1785 3718 5.735922 GCAAGATCGCTACATTCTCTTCTCT 60.736 44.000 0.00 0.00 0.00 3.10
1786 3719 4.444056 GCAAGATCGCTACATTCTCTTCTC 59.556 45.833 0.00 0.00 0.00 2.87
1787 3720 4.099266 AGCAAGATCGCTACATTCTCTTCT 59.901 41.667 0.00 0.00 41.55 2.85
1788 3721 4.367450 AGCAAGATCGCTACATTCTCTTC 58.633 43.478 0.00 0.00 41.55 2.87
1789 3722 4.399004 AGCAAGATCGCTACATTCTCTT 57.601 40.909 0.00 0.00 41.55 2.85
1790 3723 4.099266 AGAAGCAAGATCGCTACATTCTCT 59.901 41.667 0.00 0.00 42.89 3.10
1831 3764 0.605319 TGGCCAAACCTAAGACGCTG 60.605 55.000 0.61 0.00 40.22 5.18
1895 3828 2.096417 CAGACATTTTCCGAACGTCCAC 60.096 50.000 0.00 0.00 0.00 4.02
1901 3834 1.539827 CACCCCAGACATTTTCCGAAC 59.460 52.381 0.00 0.00 0.00 3.95
1914 3847 2.946947 CTACCAAGCAACACCCCAG 58.053 57.895 0.00 0.00 0.00 4.45
1964 3899 2.335316 TAACCCTTCCACACACACAC 57.665 50.000 0.00 0.00 0.00 3.82
1965 3900 3.218453 CAATAACCCTTCCACACACACA 58.782 45.455 0.00 0.00 0.00 3.72
1966 3901 3.219281 ACAATAACCCTTCCACACACAC 58.781 45.455 0.00 0.00 0.00 3.82
1967 3902 3.482436 GACAATAACCCTTCCACACACA 58.518 45.455 0.00 0.00 0.00 3.72
1968 3903 2.817844 GGACAATAACCCTTCCACACAC 59.182 50.000 0.00 0.00 0.00 3.82
1969 3904 2.714250 AGGACAATAACCCTTCCACACA 59.286 45.455 0.00 0.00 0.00 3.72
1970 3905 3.081804 CAGGACAATAACCCTTCCACAC 58.918 50.000 0.00 0.00 0.00 3.82
1971 3906 2.983192 TCAGGACAATAACCCTTCCACA 59.017 45.455 0.00 0.00 0.00 4.17
1972 3907 3.713826 TCAGGACAATAACCCTTCCAC 57.286 47.619 0.00 0.00 0.00 4.02
2156 4098 2.091885 ACCCAGCCAAGAGAAAAAGACA 60.092 45.455 0.00 0.00 0.00 3.41
2164 4107 1.704628 TGATTTGACCCAGCCAAGAGA 59.295 47.619 0.00 0.00 0.00 3.10
2192 4135 1.808343 GTTTGGTTCGCCTACGGATTT 59.192 47.619 0.00 0.00 40.63 2.17
2193 4136 1.445871 GTTTGGTTCGCCTACGGATT 58.554 50.000 0.00 0.00 40.63 3.01
2198 4141 3.565063 TGTAAAAGGTTTGGTTCGCCTAC 59.435 43.478 0.00 0.00 38.36 3.18
2241 4184 3.835978 TGGTAGTTGGCTAGTTGCTAAGA 59.164 43.478 0.00 0.00 42.76 2.10
2253 4196 0.250513 CAGAGACCCTGGTAGTTGGC 59.749 60.000 0.00 0.00 39.23 4.52
2285 4228 8.886719 TGATACAAGATTGTTAAAGCATGAGAG 58.113 33.333 3.14 0.00 42.35 3.20
2367 4310 3.782046 ACAGCGCCTGTGTAGTAATTAG 58.218 45.455 2.29 0.00 43.63 1.73
2451 4394 1.434696 CATTCTTCGCCCATGCCAC 59.565 57.895 0.00 0.00 0.00 5.01
2475 4418 0.469331 TCTCTACCATAGCCCCGGTG 60.469 60.000 0.00 0.00 36.69 4.94
2691 4634 3.075882 ACCCAGATGGACAATTTTGAGGA 59.924 43.478 0.00 0.00 37.39 3.71
2692 4635 3.434309 ACCCAGATGGACAATTTTGAGG 58.566 45.455 0.00 0.00 37.39 3.86
2903 7067 9.343539 GCAGTGGTTATAGAATAAGGAAGAAAT 57.656 33.333 0.00 0.00 0.00 2.17
2917 7081 3.470709 CCCATGTCAGCAGTGGTTATAG 58.529 50.000 0.00 0.00 0.00 1.31
3036 7200 8.619146 AATGTTGCACATCGTCTAATAAAATG 57.381 30.769 0.00 0.00 37.97 2.32
3044 7209 3.261580 CCAGAATGTTGCACATCGTCTA 58.738 45.455 0.00 0.00 37.97 2.59
3127 7292 2.953648 ACCCGTAAGTTTTCCTGGTTTG 59.046 45.455 0.00 0.00 0.00 2.93
3279 7444 2.171448 CCAGAGGAGGTGGGAATAAGTG 59.829 54.545 0.00 0.00 0.00 3.16
3328 7505 8.511126 TGGAAATCTCTAAAAGGGCCTATATTT 58.489 33.333 6.41 6.71 0.00 1.40
3353 7531 2.300152 ACATCCGCATATAGTCCCTGTG 59.700 50.000 0.00 0.00 0.00 3.66
3375 7553 9.021807 AGTCTACGCTCTAAAATATGCCTATAA 57.978 33.333 0.00 0.00 0.00 0.98
3381 7559 6.210078 AGTGAGTCTACGCTCTAAAATATGC 58.790 40.000 0.00 0.00 36.51 3.14
3391 7569 3.061429 GCAAAATGAGTGAGTCTACGCTC 59.939 47.826 0.00 0.00 44.55 5.03
3394 7572 4.449068 ACAAGCAAAATGAGTGAGTCTACG 59.551 41.667 0.00 0.00 0.00 3.51
3400 7578 9.539825 AGACTATATACAAGCAAAATGAGTGAG 57.460 33.333 0.00 0.00 0.00 3.51
3437 7616 9.503399 CGTTCCTAAATATAAGCCCTTTAAGAT 57.497 33.333 0.00 0.00 0.00 2.40
3478 7657 8.399425 TCTGTTTCATTTCACGCTTAAAAGTTA 58.601 29.630 0.00 0.00 0.00 2.24
3489 7668 4.776743 CTTGAGGTCTGTTTCATTTCACG 58.223 43.478 0.00 0.00 0.00 4.35
3501 7680 1.151668 CGTTTGGAGCTTGAGGTCTG 58.848 55.000 9.75 0.00 41.88 3.51
3512 7691 4.928661 ATTCATTTCGTCTCGTTTGGAG 57.071 40.909 0.00 0.00 44.58 3.86
3562 7741 1.137404 CCCCAAGCATTTCGAAGCG 59.863 57.895 0.00 0.00 35.48 4.68
3578 7757 0.819259 TGTCTCTGTTGTTGCAGCCC 60.819 55.000 0.00 0.00 36.49 5.19


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

AutoCloner maintained by Alex Coulton.