Multiple sequence alignment - TraesCS4A01G334800

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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 TraesCS4A01G334800 chr4A 100.000 5532 0 0 1 5532 617860609 617855078 0.000000e+00 10216.0
1 TraesCS4A01G334800 chr4A 87.143 770 58 19 1801 2553 617858297 617857552 0.000000e+00 835.0
2 TraesCS4A01G334800 chr4A 87.126 769 60 18 2313 3058 617858809 617858057 0.000000e+00 835.0
3 TraesCS4A01G334800 chr4A 99.636 275 1 0 4969 5243 617855586 617855312 2.300000e-138 503.0
4 TraesCS4A01G334800 chr4A 99.636 275 1 0 5024 5298 617855641 617855367 2.300000e-138 503.0
5 TraesCS4A01G334800 chr4A 99.545 220 1 0 4969 5188 617855531 617855312 8.630000e-108 401.0
6 TraesCS4A01G334800 chr4A 99.545 220 1 0 5079 5298 617855641 617855422 8.630000e-108 401.0
7 TraesCS4A01G334800 chr4A 99.394 165 1 0 4969 5133 617855476 617855312 3.240000e-77 300.0
8 TraesCS4A01G334800 chr4A 99.394 165 1 0 5134 5298 617855641 617855477 3.240000e-77 300.0
9 TraesCS4A01G334800 chr4A 99.091 110 1 0 4969 5078 617855421 617855312 1.220000e-46 198.0
10 TraesCS4A01G334800 chr4A 99.091 110 1 0 5189 5298 617855641 617855532 1.220000e-46 198.0
11 TraesCS4A01G334800 chr4A 98.182 55 1 0 4969 5023 617855366 617855312 4.560000e-16 97.1
12 TraesCS4A01G334800 chr4A 98.182 55 1 0 5244 5298 617855641 617855587 4.560000e-16 97.1
13 TraesCS4A01G334800 chr4A 97.619 42 1 0 2701 2742 617857484 617857443 7.690000e-09 73.1
14 TraesCS4A01G334800 chr4A 97.619 42 1 0 3126 3167 617857909 617857868 7.690000e-09 73.1
15 TraesCS4A01G334800 chr5B 88.219 1477 84 28 2403 3864 701546874 701548275 0.000000e+00 1681.0
16 TraesCS4A01G334800 chr5B 84.196 1468 104 54 457 1852 701545465 701546876 0.000000e+00 1308.0
17 TraesCS4A01G334800 chr5B 93.912 772 41 4 3872 4638 701548339 701549109 0.000000e+00 1160.0
18 TraesCS4A01G334800 chr5B 89.879 494 29 11 1891 2383 701546874 701547347 2.830000e-172 616.0
19 TraesCS4A01G334800 chr5B 97.238 181 5 0 4659 4839 701549095 701549275 1.940000e-79 307.0
20 TraesCS4A01G334800 chr5B 80.563 391 28 17 1 374 701544594 701544953 1.980000e-64 257.0
21 TraesCS4A01G334800 chr5D 85.825 1425 67 44 6 1351 549885817 549887185 0.000000e+00 1387.0
22 TraesCS4A01G334800 chr5D 94.034 771 42 2 3872 4638 549889350 549890120 0.000000e+00 1166.0
23 TraesCS4A01G334800 chr5D 84.631 1015 76 25 2390 3380 549887631 549888589 0.000000e+00 937.0
24 TraesCS4A01G334800 chr5D 81.944 864 66 38 1878 2703 549887631 549888442 0.000000e+00 649.0
25 TraesCS4A01G334800 chr5D 88.528 462 28 9 1389 1835 549887177 549887628 2.270000e-148 536.0
26 TraesCS4A01G334800 chr5D 96.685 181 5 1 4659 4839 549890106 549890285 3.240000e-77 300.0
27 TraesCS4A01G334800 chr5D 100.000 29 0 0 4922 4950 57174470 57174442 3.000000e-03 54.7
28 TraesCS4A01G334800 chr2B 93.414 577 33 2 4065 4638 329465004 329464430 0.000000e+00 850.0
29 TraesCS4A01G334800 chr2B 93.878 196 10 2 5333 5528 45139720 45139527 1.510000e-75 294.0
30 TraesCS4A01G334800 chr2B 95.028 181 9 0 4659 4839 329464444 329464264 9.070000e-73 285.0
31 TraesCS4A01G334800 chr2B 96.269 134 4 1 5399 5532 687476377 687476245 9.330000e-53 219.0
32 TraesCS4A01G334800 chr2B 98.438 64 1 0 5469 5532 743323451 743323514 4.530000e-21 113.0
33 TraesCS4A01G334800 chr2B 91.667 60 4 1 5469 5528 321957953 321958011 1.280000e-11 82.4
34 TraesCS4A01G334800 chr1A 89.835 364 27 6 2010 2371 34289414 34289769 5.050000e-125 459.0
35 TraesCS4A01G334800 chr1A 83.820 377 26 13 2514 2877 34289414 34289768 5.340000e-85 326.0
36 TraesCS4A01G334800 chr1A 82.386 176 20 6 2052 2220 34291794 34291965 5.780000e-30 143.0
37 TraesCS4A01G334800 chr1A 95.312 64 3 0 5469 5532 140370133 140370070 9.800000e-18 102.0
38 TraesCS4A01G334800 chrUn 94.416 197 10 1 5333 5529 119059935 119060130 9.010000e-78 302.0
39 TraesCS4A01G334800 chr1B 96.875 64 2 0 5469 5532 634151292 634151355 2.110000e-19 108.0
40 TraesCS4A01G334800 chr4D 98.333 60 1 0 5469 5528 373658391 373658450 7.580000e-19 106.0
41 TraesCS4A01G334800 chr7A 94.545 55 2 1 5474 5528 652468548 652468601 3.550000e-12 84.2


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 TraesCS4A01G334800 chr4A 617855078 617860609 5531 True 10216.000000 10216 100.000000 1 5532 1 chr4A.!!$R1 5531
1 TraesCS4A01G334800 chr4A 617855312 617858809 3497 True 343.885714 835 97.228786 1801 5298 14 chr4A.!!$R2 3497
2 TraesCS4A01G334800 chr5B 701544594 701549275 4681 False 888.166667 1681 89.001167 1 4839 6 chr5B.!!$F1 4838
3 TraesCS4A01G334800 chr5D 549885817 549890285 4468 False 829.166667 1387 88.607833 6 4839 6 chr5D.!!$F1 4833
4 TraesCS4A01G334800 chr2B 329464264 329465004 740 True 567.500000 850 94.221000 4065 4839 2 chr2B.!!$R3 774
5 TraesCS4A01G334800 chr1A 34289414 34291965 2551 False 309.333333 459 85.347000 2010 2877 3 chr1A.!!$F1 867

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
119 131 0.178961 GGGAGGTCCAGCAAAGGTTT 60.179 55.0 0.0 0.0 37.91 3.27 F
1293 1813 0.395686 CATCCCTCATCGGTCAGCAT 59.604 55.0 0.0 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1366 1888 0.109342 GGTAGCTAGCACCATGCCAT 59.891 55.0 23.37 2.65 46.52 4.40 R
4659 7368 6.708885 ACATCCATCCATATCACCATAAGT 57.291 37.5 0.00 0.00 0.00 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
65 76 8.270030 ACAAAAAGATGAGATGAGATCATACCA 58.730 33.333 0.00 0.00 37.52 3.25
68 79 8.718158 AAAGATGAGATGAGATCATACCAGTA 57.282 34.615 0.00 0.00 37.52 2.74
70 81 7.237255 AGATGAGATGAGATCATACCAGTACA 58.763 38.462 0.00 0.00 37.52 2.90
71 82 7.894897 AGATGAGATGAGATCATACCAGTACAT 59.105 37.037 0.00 0.00 37.52 2.29
102 114 3.169512 ACCCATCTACAAAAGGTTGGG 57.830 47.619 4.28 4.28 46.58 4.12
103 115 2.719705 ACCCATCTACAAAAGGTTGGGA 59.280 45.455 12.54 0.00 45.22 4.37
104 116 3.245264 ACCCATCTACAAAAGGTTGGGAG 60.245 47.826 12.54 0.00 45.22 4.30
105 117 3.356290 CCATCTACAAAAGGTTGGGAGG 58.644 50.000 0.00 0.00 39.22 4.30
106 118 3.245264 CCATCTACAAAAGGTTGGGAGGT 60.245 47.826 0.00 0.00 39.22 3.85
107 119 3.782656 TCTACAAAAGGTTGGGAGGTC 57.217 47.619 0.00 0.00 39.22 3.85
108 120 2.374170 TCTACAAAAGGTTGGGAGGTCC 59.626 50.000 0.00 0.00 39.22 4.46
109 121 0.930726 ACAAAAGGTTGGGAGGTCCA 59.069 50.000 0.00 0.00 45.43 4.02
116 128 3.170362 TGGGAGGTCCAGCAAAGG 58.830 61.111 0.00 0.00 41.46 3.11
117 129 1.774217 TGGGAGGTCCAGCAAAGGT 60.774 57.895 0.00 0.00 41.46 3.50
118 130 1.360393 TGGGAGGTCCAGCAAAGGTT 61.360 55.000 0.00 0.00 41.46 3.50
119 131 0.178961 GGGAGGTCCAGCAAAGGTTT 60.179 55.000 0.00 0.00 37.91 3.27
120 132 0.961753 GGAGGTCCAGCAAAGGTTTG 59.038 55.000 0.00 0.00 37.31 2.93
121 133 0.961753 GAGGTCCAGCAAAGGTTTGG 59.038 55.000 4.67 0.00 38.57 3.28
122 134 1.115326 AGGTCCAGCAAAGGTTTGGC 61.115 55.000 4.67 0.00 38.57 4.52
123 135 1.007387 GTCCAGCAAAGGTTTGGCG 60.007 57.895 4.67 0.00 38.57 5.69
124 136 1.152860 TCCAGCAAAGGTTTGGCGA 60.153 52.632 4.67 0.00 38.57 5.54
125 137 0.539438 TCCAGCAAAGGTTTGGCGAT 60.539 50.000 4.67 0.00 38.57 4.58
152 164 3.963374 TGCTCATAAGTAGCACTCCATCT 59.037 43.478 0.00 0.00 44.78 2.90
202 214 7.711772 GGAGACCTTTATTTAGCCTAAAGTCTC 59.288 40.741 22.76 22.76 39.25 3.36
203 215 7.566569 AGACCTTTATTTAGCCTAAAGTCTCC 58.433 38.462 9.17 0.00 35.39 3.71
244 258 7.451501 TCAAGCACATTGTGAATTAATCTCA 57.548 32.000 20.77 0.00 40.05 3.27
248 262 8.206325 AGCACATTGTGAATTAATCTCACTAG 57.794 34.615 20.77 15.86 43.03 2.57
282 296 9.206870 AGCACACTTTATCATTTTTGTTAATGG 57.793 29.630 0.00 0.00 36.41 3.16
443 485 2.197324 GCCAAACCACACTCCCCA 59.803 61.111 0.00 0.00 0.00 4.96
445 487 1.530655 CCAAACCACACTCCCCACC 60.531 63.158 0.00 0.00 0.00 4.61
639 1103 1.002502 CGAGGTGGGGGTTTCTTCC 60.003 63.158 0.00 0.00 0.00 3.46
657 1130 2.546899 TCCTCCTTCCCGAAGAATGAA 58.453 47.619 6.01 0.00 40.79 2.57
901 1405 4.415332 TCGCGCCGTGGAAGAGAC 62.415 66.667 0.00 0.00 0.00 3.36
905 1409 4.452733 GCCGTGGAAGAGACCCGG 62.453 72.222 0.00 0.00 42.37 5.73
906 1410 2.995574 CCGTGGAAGAGACCCGGT 60.996 66.667 0.00 0.00 38.23 5.28
907 1411 2.572284 CGTGGAAGAGACCCGGTC 59.428 66.667 9.81 9.81 0.00 4.79
917 1421 2.591198 ACCCGGTCGGTTGTTGTT 59.409 55.556 8.67 0.00 45.36 2.83
941 1449 0.896479 TGAAAAGCCCCGCCCTTAAC 60.896 55.000 0.00 0.00 0.00 2.01
986 1494 0.852777 CGACATCCGGTTAATCTGCG 59.147 55.000 0.00 0.00 33.91 5.18
989 1497 0.861837 CATCCGGTTAATCTGCGAGC 59.138 55.000 0.00 0.00 0.00 5.03
990 1498 0.597637 ATCCGGTTAATCTGCGAGCG 60.598 55.000 0.00 0.00 0.00 5.03
992 1500 2.871427 CGGTTAATCTGCGAGCGGC 61.871 63.158 0.00 0.00 43.96 6.53
993 1501 2.534903 GGTTAATCTGCGAGCGGCC 61.535 63.158 0.00 0.00 42.61 6.13
1204 1724 1.070445 GCCATCGTCAGGATCCAGG 59.930 63.158 15.82 5.75 31.28 4.45
1292 1812 1.825341 CATCCCTCATCGGTCAGCA 59.175 57.895 0.00 0.00 0.00 4.41
1293 1813 0.395686 CATCCCTCATCGGTCAGCAT 59.604 55.000 0.00 0.00 0.00 3.79
1294 1814 0.395686 ATCCCTCATCGGTCAGCATG 59.604 55.000 0.00 0.00 37.54 4.06
1314 1836 4.952262 TGCCTTCTTTCTTCGATTCATG 57.048 40.909 0.00 0.00 0.00 3.07
1325 1847 5.661458 TCTTCGATTCATGTTCTTACTCCC 58.339 41.667 0.00 0.00 0.00 4.30
1360 1882 4.467795 TGCCTCTGCTACTAGTTCTTGATT 59.532 41.667 0.00 0.00 38.71 2.57
1365 1887 6.102663 TCTGCTACTAGTTCTTGATTTGCTC 58.897 40.000 0.00 0.00 0.00 4.26
1366 1888 5.793817 TGCTACTAGTTCTTGATTTGCTCA 58.206 37.500 0.00 0.00 0.00 4.26
1369 1891 6.238320 GCTACTAGTTCTTGATTTGCTCATGG 60.238 42.308 0.00 0.00 32.72 3.66
1384 1906 1.202687 TCATGGCATGGTGCTAGCTAC 60.203 52.381 26.15 12.05 44.28 3.58
1392 1914 2.816411 TGGTGCTAGCTACCAACTACT 58.184 47.619 26.68 0.00 44.79 2.57
1393 1915 2.758979 TGGTGCTAGCTACCAACTACTC 59.241 50.000 26.68 7.48 44.79 2.59
1394 1916 2.101082 GGTGCTAGCTACCAACTACTCC 59.899 54.545 23.37 5.25 38.12 3.85
1395 1917 3.025262 GTGCTAGCTACCAACTACTCCT 58.975 50.000 17.23 0.00 0.00 3.69
1396 1918 4.205587 GTGCTAGCTACCAACTACTCCTA 58.794 47.826 17.23 0.00 0.00 2.94
1397 1919 4.828387 GTGCTAGCTACCAACTACTCCTAT 59.172 45.833 17.23 0.00 0.00 2.57
1398 1920 5.048573 GTGCTAGCTACCAACTACTCCTATC 60.049 48.000 17.23 0.00 0.00 2.08
1459 1984 3.249189 TGAAGGGGCCGAGCAACT 61.249 61.111 0.00 0.00 0.00 3.16
1460 1985 2.747855 GAAGGGGCCGAGCAACTG 60.748 66.667 0.00 0.00 0.00 3.16
1486 2011 5.246307 AGTTAGCAACCACTAGTCATTTCC 58.754 41.667 0.00 0.00 0.00 3.13
1500 2025 0.734889 ATTTCCGATGCTTTCGCCTG 59.265 50.000 4.38 0.00 46.71 4.85
1502 2027 0.605319 TTCCGATGCTTTCGCCTGTT 60.605 50.000 4.38 0.00 46.71 3.16
1650 2184 7.600752 GCAGTCCATTCTAGGAGTATGTAAATC 59.399 40.741 0.00 0.00 39.32 2.17
1672 2218 3.367932 CACACGTTATGGACTACAAGCAG 59.632 47.826 0.00 0.00 0.00 4.24
1736 2282 3.444742 TGAAGGTGCCATTTTAGATGCTG 59.555 43.478 0.00 0.00 0.00 4.41
1744 2290 4.923281 GCCATTTTAGATGCTGTTTTCGTT 59.077 37.500 0.00 0.00 0.00 3.85
4638 7347 6.954684 TCCCCTCTCTAACTTATGGTGATATC 59.045 42.308 0.00 0.00 0.00 1.63
4639 7348 6.155393 CCCCTCTCTAACTTATGGTGATATCC 59.845 46.154 0.00 0.00 0.00 2.59
4640 7349 6.155393 CCCTCTCTAACTTATGGTGATATCCC 59.845 46.154 0.00 1.87 0.00 3.85
4641 7350 6.155393 CCTCTCTAACTTATGGTGATATCCCC 59.845 46.154 0.00 0.00 0.00 4.81
4642 7351 6.023603 TCTCTAACTTATGGTGATATCCCCC 58.976 44.000 1.38 1.90 0.00 5.40
5302 8013 4.883354 GGCGAGGAAGGGCATGGG 62.883 72.222 0.00 0.00 0.00 4.00
5303 8014 3.797353 GCGAGGAAGGGCATGGGA 61.797 66.667 0.00 0.00 0.00 4.37
5304 8015 2.507944 CGAGGAAGGGCATGGGAG 59.492 66.667 0.00 0.00 0.00 4.30
5305 8016 2.066393 CGAGGAAGGGCATGGGAGA 61.066 63.158 0.00 0.00 0.00 3.71
5306 8017 1.414061 CGAGGAAGGGCATGGGAGAT 61.414 60.000 0.00 0.00 0.00 2.75
5307 8018 0.110104 GAGGAAGGGCATGGGAGATG 59.890 60.000 0.00 0.00 0.00 2.90
5308 8019 1.530183 GGAAGGGCATGGGAGATGC 60.530 63.158 0.00 0.00 43.85 3.91
5309 8020 1.895707 GAAGGGCATGGGAGATGCG 60.896 63.158 0.00 0.00 45.41 4.73
5310 8021 3.426309 AAGGGCATGGGAGATGCGG 62.426 63.158 0.00 0.00 45.41 5.69
5311 8022 3.877450 GGGCATGGGAGATGCGGA 61.877 66.667 0.00 0.00 45.41 5.54
5312 8023 2.192979 GGCATGGGAGATGCGGAA 59.807 61.111 0.00 0.00 45.41 4.30
5313 8024 1.453745 GGCATGGGAGATGCGGAAA 60.454 57.895 0.00 0.00 45.41 3.13
5314 8025 0.825010 GGCATGGGAGATGCGGAAAT 60.825 55.000 0.00 0.00 45.41 2.17
5315 8026 0.595095 GCATGGGAGATGCGGAAATC 59.405 55.000 0.00 0.00 35.17 2.17
5316 8027 0.870393 CATGGGAGATGCGGAAATCG 59.130 55.000 0.00 0.00 42.76 3.34
5317 8028 0.758734 ATGGGAGATGCGGAAATCGA 59.241 50.000 0.00 0.00 42.43 3.59
5318 8029 0.179084 TGGGAGATGCGGAAATCGAC 60.179 55.000 0.00 0.00 42.43 4.20
5319 8030 1.215655 GGGAGATGCGGAAATCGACG 61.216 60.000 0.00 0.00 42.43 5.12
5325 8036 2.125269 CGGAAATCGACGCCCCTT 60.125 61.111 0.00 0.00 42.43 3.95
5326 8037 1.743995 CGGAAATCGACGCCCCTTT 60.744 57.895 0.00 0.00 42.43 3.11
5327 8038 1.702491 CGGAAATCGACGCCCCTTTC 61.702 60.000 0.00 0.00 42.43 2.62
5328 8039 0.392595 GGAAATCGACGCCCCTTTCT 60.393 55.000 6.82 0.00 0.00 2.52
5329 8040 1.450025 GAAATCGACGCCCCTTTCTT 58.550 50.000 0.00 0.00 0.00 2.52
5330 8041 1.810755 GAAATCGACGCCCCTTTCTTT 59.189 47.619 0.00 0.00 0.00 2.52
5331 8042 1.450025 AATCGACGCCCCTTTCTTTC 58.550 50.000 0.00 0.00 0.00 2.62
5332 8043 0.613777 ATCGACGCCCCTTTCTTTCT 59.386 50.000 0.00 0.00 0.00 2.52
5333 8044 0.395312 TCGACGCCCCTTTCTTTCTT 59.605 50.000 0.00 0.00 0.00 2.52
5334 8045 0.517316 CGACGCCCCTTTCTTTCTTG 59.483 55.000 0.00 0.00 0.00 3.02
5335 8046 1.605753 GACGCCCCTTTCTTTCTTGT 58.394 50.000 0.00 0.00 0.00 3.16
5336 8047 2.774687 GACGCCCCTTTCTTTCTTGTA 58.225 47.619 0.00 0.00 0.00 2.41
5337 8048 2.742589 GACGCCCCTTTCTTTCTTGTAG 59.257 50.000 0.00 0.00 0.00 2.74
5338 8049 2.105993 ACGCCCCTTTCTTTCTTGTAGT 59.894 45.455 0.00 0.00 0.00 2.73
5339 8050 2.484264 CGCCCCTTTCTTTCTTGTAGTG 59.516 50.000 0.00 0.00 0.00 2.74
5340 8051 3.487372 GCCCCTTTCTTTCTTGTAGTGT 58.513 45.455 0.00 0.00 0.00 3.55
5341 8052 3.889538 GCCCCTTTCTTTCTTGTAGTGTT 59.110 43.478 0.00 0.00 0.00 3.32
5342 8053 4.341235 GCCCCTTTCTTTCTTGTAGTGTTT 59.659 41.667 0.00 0.00 0.00 2.83
5343 8054 5.163447 GCCCCTTTCTTTCTTGTAGTGTTTT 60.163 40.000 0.00 0.00 0.00 2.43
5344 8055 6.040054 GCCCCTTTCTTTCTTGTAGTGTTTTA 59.960 38.462 0.00 0.00 0.00 1.52
5345 8056 7.423199 CCCCTTTCTTTCTTGTAGTGTTTTAC 58.577 38.462 0.00 0.00 0.00 2.01
5346 8057 7.284716 CCCCTTTCTTTCTTGTAGTGTTTTACT 59.715 37.037 0.00 0.00 43.56 2.24
5347 8058 9.333724 CCCTTTCTTTCTTGTAGTGTTTTACTA 57.666 33.333 0.00 0.00 40.89 1.82
5367 8078 9.672086 TTTACTAATTCTTGATTGAACAAACGG 57.328 29.630 0.00 0.00 0.00 4.44
5368 8079 7.504924 ACTAATTCTTGATTGAACAAACGGA 57.495 32.000 0.00 0.00 0.00 4.69
5369 8080 7.360361 ACTAATTCTTGATTGAACAAACGGAC 58.640 34.615 0.00 0.00 0.00 4.79
5370 8081 6.391227 AATTCTTGATTGAACAAACGGACT 57.609 33.333 0.00 0.00 0.00 3.85
5371 8082 7.504924 AATTCTTGATTGAACAAACGGACTA 57.495 32.000 0.00 0.00 0.00 2.59
5372 8083 5.917541 TCTTGATTGAACAAACGGACTAC 57.082 39.130 0.00 0.00 0.00 2.73
5373 8084 5.607477 TCTTGATTGAACAAACGGACTACT 58.393 37.500 0.00 0.00 0.00 2.57
5374 8085 6.751157 TCTTGATTGAACAAACGGACTACTA 58.249 36.000 0.00 0.00 0.00 1.82
5375 8086 6.643770 TCTTGATTGAACAAACGGACTACTAC 59.356 38.462 0.00 0.00 0.00 2.73
5376 8087 6.092955 TGATTGAACAAACGGACTACTACT 57.907 37.500 0.00 0.00 0.00 2.57
5377 8088 5.924254 TGATTGAACAAACGGACTACTACTG 59.076 40.000 0.00 0.00 0.00 2.74
5378 8089 3.645884 TGAACAAACGGACTACTACTGC 58.354 45.455 0.00 0.00 0.00 4.40
5379 8090 3.319972 TGAACAAACGGACTACTACTGCT 59.680 43.478 0.00 0.00 0.00 4.24
5380 8091 3.572604 ACAAACGGACTACTACTGCTC 57.427 47.619 0.00 0.00 0.00 4.26
5381 8092 2.889045 ACAAACGGACTACTACTGCTCA 59.111 45.455 0.00 0.00 0.00 4.26
5382 8093 3.319972 ACAAACGGACTACTACTGCTCAA 59.680 43.478 0.00 0.00 0.00 3.02
5383 8094 4.021368 ACAAACGGACTACTACTGCTCAAT 60.021 41.667 0.00 0.00 0.00 2.57
5384 8095 5.184479 ACAAACGGACTACTACTGCTCAATA 59.816 40.000 0.00 0.00 0.00 1.90
5385 8096 6.127423 ACAAACGGACTACTACTGCTCAATAT 60.127 38.462 0.00 0.00 0.00 1.28
5386 8097 6.466885 AACGGACTACTACTGCTCAATATT 57.533 37.500 0.00 0.00 0.00 1.28
5387 8098 6.466885 ACGGACTACTACTGCTCAATATTT 57.533 37.500 0.00 0.00 0.00 1.40
5388 8099 7.578310 ACGGACTACTACTGCTCAATATTTA 57.422 36.000 0.00 0.00 0.00 1.40
5389 8100 7.424001 ACGGACTACTACTGCTCAATATTTAC 58.576 38.462 0.00 0.00 0.00 2.01
5390 8101 7.067859 ACGGACTACTACTGCTCAATATTTACA 59.932 37.037 0.00 0.00 0.00 2.41
5391 8102 7.378995 CGGACTACTACTGCTCAATATTTACAC 59.621 40.741 0.00 0.00 0.00 2.90
5392 8103 8.195436 GGACTACTACTGCTCAATATTTACACA 58.805 37.037 0.00 0.00 0.00 3.72
5393 8104 9.751542 GACTACTACTGCTCAATATTTACACAT 57.248 33.333 0.00 0.00 0.00 3.21
5412 8123 9.890629 TTACACATTAATAGCTGATTCTTCTGT 57.109 29.630 0.00 0.00 0.00 3.41
5413 8124 8.430801 ACACATTAATAGCTGATTCTTCTGTC 57.569 34.615 0.00 0.00 0.00 3.51
5414 8125 8.043113 ACACATTAATAGCTGATTCTTCTGTCA 58.957 33.333 0.00 0.00 0.00 3.58
5415 8126 9.053840 CACATTAATAGCTGATTCTTCTGTCAT 57.946 33.333 0.00 0.00 0.00 3.06
5416 8127 9.624373 ACATTAATAGCTGATTCTTCTGTCATT 57.376 29.630 0.00 0.00 0.00 2.57
5418 8129 8.668510 TTAATAGCTGATTCTTCTGTCATTCC 57.331 34.615 0.00 0.00 0.00 3.01
5419 8130 4.564782 AGCTGATTCTTCTGTCATTCCA 57.435 40.909 0.00 0.00 0.00 3.53
5420 8131 5.113446 AGCTGATTCTTCTGTCATTCCAT 57.887 39.130 0.00 0.00 0.00 3.41
5421 8132 5.507637 AGCTGATTCTTCTGTCATTCCATT 58.492 37.500 0.00 0.00 0.00 3.16
5422 8133 5.589452 AGCTGATTCTTCTGTCATTCCATTC 59.411 40.000 0.00 0.00 0.00 2.67
5423 8134 5.589452 GCTGATTCTTCTGTCATTCCATTCT 59.411 40.000 0.00 0.00 0.00 2.40
5424 8135 6.238429 GCTGATTCTTCTGTCATTCCATTCTC 60.238 42.308 0.00 0.00 0.00 2.87
5425 8136 6.118170 TGATTCTTCTGTCATTCCATTCTCC 58.882 40.000 0.00 0.00 0.00 3.71
5426 8137 5.768980 TTCTTCTGTCATTCCATTCTCCT 57.231 39.130 0.00 0.00 0.00 3.69
5427 8138 5.768980 TCTTCTGTCATTCCATTCTCCTT 57.231 39.130 0.00 0.00 0.00 3.36
5428 8139 5.494724 TCTTCTGTCATTCCATTCTCCTTG 58.505 41.667 0.00 0.00 0.00 3.61
5429 8140 5.249163 TCTTCTGTCATTCCATTCTCCTTGA 59.751 40.000 0.00 0.00 0.00 3.02
5430 8141 5.095145 TCTGTCATTCCATTCTCCTTGAG 57.905 43.478 0.00 0.00 0.00 3.02
5431 8142 4.779489 TCTGTCATTCCATTCTCCTTGAGA 59.221 41.667 0.00 0.00 36.86 3.27
5432 8143 5.095145 TGTCATTCCATTCTCCTTGAGAG 57.905 43.478 0.00 0.00 39.98 3.20
5443 8154 4.943142 CTCCTTGAGAGATTGAGTTTGC 57.057 45.455 0.00 0.00 46.50 3.68
5444 8155 4.577875 CTCCTTGAGAGATTGAGTTTGCT 58.422 43.478 0.00 0.00 46.50 3.91
5445 8156 4.573900 TCCTTGAGAGATTGAGTTTGCTC 58.426 43.478 0.00 0.00 41.97 4.26
5446 8157 3.688673 CCTTGAGAGATTGAGTTTGCTCC 59.311 47.826 0.00 0.00 40.95 4.70
5447 8158 4.565236 CCTTGAGAGATTGAGTTTGCTCCT 60.565 45.833 0.00 0.00 40.95 3.69
5448 8159 4.630644 TGAGAGATTGAGTTTGCTCCTT 57.369 40.909 0.00 0.00 40.95 3.36
5449 8160 4.573900 TGAGAGATTGAGTTTGCTCCTTC 58.426 43.478 0.00 0.00 40.95 3.46
5450 8161 4.040829 TGAGAGATTGAGTTTGCTCCTTCA 59.959 41.667 0.00 0.00 40.95 3.02
5451 8162 4.577875 AGAGATTGAGTTTGCTCCTTCAG 58.422 43.478 0.00 0.00 40.95 3.02
5452 8163 4.285517 AGAGATTGAGTTTGCTCCTTCAGA 59.714 41.667 0.00 0.00 40.95 3.27
5453 8164 5.045724 AGAGATTGAGTTTGCTCCTTCAGAT 60.046 40.000 0.00 0.00 40.95 2.90
5454 8165 5.184711 AGATTGAGTTTGCTCCTTCAGATC 58.815 41.667 0.00 0.00 40.95 2.75
5455 8166 2.964740 TGAGTTTGCTCCTTCAGATCG 58.035 47.619 0.00 0.00 40.95 3.69
5456 8167 2.300152 TGAGTTTGCTCCTTCAGATCGT 59.700 45.455 0.00 0.00 40.95 3.73
5457 8168 2.926838 GAGTTTGCTCCTTCAGATCGTC 59.073 50.000 0.00 0.00 35.76 4.20
5458 8169 2.300152 AGTTTGCTCCTTCAGATCGTCA 59.700 45.455 0.00 0.00 0.00 4.35
5459 8170 2.370281 TTGCTCCTTCAGATCGTCAC 57.630 50.000 0.00 0.00 0.00 3.67
5460 8171 1.256812 TGCTCCTTCAGATCGTCACA 58.743 50.000 0.00 0.00 0.00 3.58
5461 8172 1.067565 TGCTCCTTCAGATCGTCACAC 60.068 52.381 0.00 0.00 0.00 3.82
5462 8173 1.737363 GCTCCTTCAGATCGTCACACC 60.737 57.143 0.00 0.00 0.00 4.16
5463 8174 1.546029 CTCCTTCAGATCGTCACACCA 59.454 52.381 0.00 0.00 0.00 4.17
5464 8175 2.167281 CTCCTTCAGATCGTCACACCAT 59.833 50.000 0.00 0.00 0.00 3.55
5465 8176 2.567169 TCCTTCAGATCGTCACACCATT 59.433 45.455 0.00 0.00 0.00 3.16
5466 8177 3.007940 TCCTTCAGATCGTCACACCATTT 59.992 43.478 0.00 0.00 0.00 2.32
5467 8178 3.753272 CCTTCAGATCGTCACACCATTTT 59.247 43.478 0.00 0.00 0.00 1.82
5468 8179 4.935205 CCTTCAGATCGTCACACCATTTTA 59.065 41.667 0.00 0.00 0.00 1.52
5469 8180 5.163854 CCTTCAGATCGTCACACCATTTTAC 60.164 44.000 0.00 0.00 0.00 2.01
5470 8181 4.888917 TCAGATCGTCACACCATTTTACA 58.111 39.130 0.00 0.00 0.00 2.41
5471 8182 5.487433 TCAGATCGTCACACCATTTTACAT 58.513 37.500 0.00 0.00 0.00 2.29
5472 8183 5.351189 TCAGATCGTCACACCATTTTACATG 59.649 40.000 0.00 0.00 0.00 3.21
5473 8184 4.635765 AGATCGTCACACCATTTTACATGG 59.364 41.667 0.00 0.00 44.54 3.66
5474 8185 2.486203 TCGTCACACCATTTTACATGGC 59.514 45.455 0.00 0.00 42.82 4.40
5475 8186 2.227626 CGTCACACCATTTTACATGGCA 59.772 45.455 0.00 0.00 42.82 4.92
5476 8187 3.304996 CGTCACACCATTTTACATGGCAA 60.305 43.478 0.00 0.00 42.82 4.52
5477 8188 4.617995 CGTCACACCATTTTACATGGCAAT 60.618 41.667 0.00 0.00 42.82 3.56
5478 8189 5.237048 GTCACACCATTTTACATGGCAATT 58.763 37.500 0.00 0.00 42.82 2.32
5479 8190 6.393990 GTCACACCATTTTACATGGCAATTA 58.606 36.000 0.00 0.00 42.82 1.40
5480 8191 7.041107 GTCACACCATTTTACATGGCAATTAT 58.959 34.615 0.00 0.00 42.82 1.28
5481 8192 7.548780 GTCACACCATTTTACATGGCAATTATT 59.451 33.333 0.00 0.00 42.82 1.40
5482 8193 8.099537 TCACACCATTTTACATGGCAATTATTT 58.900 29.630 0.00 0.00 42.82 1.40
5483 8194 8.728833 CACACCATTTTACATGGCAATTATTTT 58.271 29.630 0.00 0.00 42.82 1.82
5484 8195 9.294614 ACACCATTTTACATGGCAATTATTTTT 57.705 25.926 0.00 0.00 42.82 1.94
5509 8220 9.953565 TTTGTTGGCATCTATAGTAGTTTTAGT 57.046 29.630 0.00 0.00 0.00 2.24
5510 8221 9.953565 TTGTTGGCATCTATAGTAGTTTTAGTT 57.046 29.630 0.00 0.00 0.00 2.24
5511 8222 9.378551 TGTTGGCATCTATAGTAGTTTTAGTTG 57.621 33.333 0.00 0.00 0.00 3.16
5512 8223 8.336080 GTTGGCATCTATAGTAGTTTTAGTTGC 58.664 37.037 0.00 11.36 37.69 4.17
5513 8224 7.561251 TGGCATCTATAGTAGTTTTAGTTGCA 58.439 34.615 16.88 0.00 39.07 4.08
5514 8225 7.494625 TGGCATCTATAGTAGTTTTAGTTGCAC 59.505 37.037 16.88 11.06 39.07 4.57
5515 8226 7.494625 GGCATCTATAGTAGTTTTAGTTGCACA 59.505 37.037 16.88 0.00 39.07 4.57
5516 8227 8.328864 GCATCTATAGTAGTTTTAGTTGCACAC 58.671 37.037 0.00 0.00 38.04 3.82
5517 8228 9.366216 CATCTATAGTAGTTTTAGTTGCACACA 57.634 33.333 0.00 0.00 0.00 3.72
5522 8233 9.720769 ATAGTAGTTTTAGTTGCACACATAGTT 57.279 29.630 0.00 0.00 0.00 2.24
5523 8234 7.861630 AGTAGTTTTAGTTGCACACATAGTTG 58.138 34.615 0.00 0.00 0.00 3.16
5524 8235 6.693315 AGTTTTAGTTGCACACATAGTTGT 57.307 33.333 0.00 0.00 36.15 3.32
5525 8236 7.095695 AGTTTTAGTTGCACACATAGTTGTT 57.904 32.000 0.00 0.00 32.34 2.83
5526 8237 7.543756 AGTTTTAGTTGCACACATAGTTGTTT 58.456 30.769 0.00 0.00 32.34 2.83
5527 8238 8.032451 AGTTTTAGTTGCACACATAGTTGTTTT 58.968 29.630 0.00 0.00 32.34 2.43
5528 8239 7.979115 TTTAGTTGCACACATAGTTGTTTTC 57.021 32.000 0.00 0.00 32.34 2.29
5529 8240 5.574891 AGTTGCACACATAGTTGTTTTCA 57.425 34.783 0.00 0.00 32.34 2.69
5530 8241 5.581605 AGTTGCACACATAGTTGTTTTCAG 58.418 37.500 0.00 0.00 32.34 3.02
5531 8242 5.125417 AGTTGCACACATAGTTGTTTTCAGT 59.875 36.000 0.00 0.00 32.34 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 76 8.648693 GTAGATGGGTAGAATTACCAATGTACT 58.351 37.037 15.82 4.55 46.75 2.73
82 93 2.719705 TCCCAACCTTTTGTAGATGGGT 59.280 45.455 8.39 0.00 44.71 4.51
102 114 0.961753 CCAAACCTTTGCTGGACCTC 59.038 55.000 0.00 0.00 36.86 3.85
103 115 1.115326 GCCAAACCTTTGCTGGACCT 61.115 55.000 0.00 0.00 36.86 3.85
104 116 1.367471 GCCAAACCTTTGCTGGACC 59.633 57.895 0.00 0.00 36.86 4.46
105 117 1.007387 CGCCAAACCTTTGCTGGAC 60.007 57.895 0.00 0.00 36.86 4.02
106 118 0.539438 ATCGCCAAACCTTTGCTGGA 60.539 50.000 0.00 0.00 36.86 3.86
107 119 0.388907 CATCGCCAAACCTTTGCTGG 60.389 55.000 0.00 0.00 36.86 4.85
108 120 1.010419 GCATCGCCAAACCTTTGCTG 61.010 55.000 0.00 0.00 36.86 4.41
109 121 1.290009 GCATCGCCAAACCTTTGCT 59.710 52.632 0.00 0.00 36.86 3.91
110 122 0.390209 ATGCATCGCCAAACCTTTGC 60.390 50.000 0.00 0.00 36.86 3.68
111 123 1.727880 CAATGCATCGCCAAACCTTTG 59.272 47.619 0.00 0.00 37.90 2.77
112 124 1.940752 GCAATGCATCGCCAAACCTTT 60.941 47.619 0.00 0.00 0.00 3.11
113 125 0.390209 GCAATGCATCGCCAAACCTT 60.390 50.000 0.00 0.00 0.00 3.50
114 126 1.216178 GCAATGCATCGCCAAACCT 59.784 52.632 0.00 0.00 0.00 3.50
115 127 0.803380 GAGCAATGCATCGCCAAACC 60.803 55.000 5.87 0.00 0.00 3.27
116 128 0.109179 TGAGCAATGCATCGCCAAAC 60.109 50.000 5.87 0.00 0.00 2.93
117 129 0.818938 ATGAGCAATGCATCGCCAAA 59.181 45.000 5.87 0.00 0.00 3.28
118 130 1.677942 TATGAGCAATGCATCGCCAA 58.322 45.000 5.87 0.00 0.00 4.52
119 131 1.605232 CTTATGAGCAATGCATCGCCA 59.395 47.619 5.87 4.61 0.00 5.69
120 132 1.605710 ACTTATGAGCAATGCATCGCC 59.394 47.619 5.87 0.00 0.00 5.54
121 133 3.666374 GCTACTTATGAGCAATGCATCGC 60.666 47.826 8.35 0.00 39.84 4.58
122 134 3.495753 TGCTACTTATGAGCAATGCATCG 59.504 43.478 8.35 0.00 46.71 3.84
150 162 4.082081 CCACATGCATGCTTAAGGAAAAGA 60.082 41.667 26.53 0.00 0.00 2.52
152 164 3.055963 CCCACATGCATGCTTAAGGAAAA 60.056 43.478 26.53 0.00 0.00 2.29
187 199 6.151144 GCAAATCTTGGAGACTTTAGGCTAAA 59.849 38.462 18.11 18.11 0.00 1.85
202 214 2.964174 TGCCGCTGCAAATCTTGG 59.036 55.556 0.00 0.00 46.66 3.61
244 258 8.621532 TGATAAAGTGTGCTTTTCATTCTAGT 57.378 30.769 0.00 0.00 41.78 2.57
251 265 8.715191 ACAAAAATGATAAAGTGTGCTTTTCA 57.285 26.923 0.00 3.61 41.78 2.69
360 375 7.715686 CCAGTACTACTCTTTTCTTTTGGACTT 59.284 37.037 0.00 0.00 0.00 3.01
374 389 2.921834 TTCCCAGCCAGTACTACTCT 57.078 50.000 0.00 0.00 0.00 3.24
375 390 3.031736 TCATTCCCAGCCAGTACTACTC 58.968 50.000 0.00 0.00 0.00 2.59
383 406 1.453379 CCTGCTCATTCCCAGCCAG 60.453 63.158 0.00 0.00 35.89 4.85
417 440 4.299796 TGGTTTGGCCCCCTCTGC 62.300 66.667 0.00 0.00 36.04 4.26
418 441 2.283173 GTGGTTTGGCCCCCTCTG 60.283 66.667 0.00 0.00 36.04 3.35
419 442 2.780924 TGTGGTTTGGCCCCCTCT 60.781 61.111 0.00 0.00 36.04 3.69
431 454 4.525028 TGGGGTGGGGAGTGTGGT 62.525 66.667 0.00 0.00 0.00 4.16
443 485 4.677151 GGGGGAGTGGAGTGGGGT 62.677 72.222 0.00 0.00 0.00 4.95
539 992 2.427540 GATCACGGGAGGATGGAGCG 62.428 65.000 0.00 0.00 0.00 5.03
595 1059 1.683319 GCCAAGAACCAATCCTCCTCC 60.683 57.143 0.00 0.00 0.00 4.30
639 1103 4.517285 TCAATTCATTCTTCGGGAAGGAG 58.483 43.478 8.46 0.21 43.98 3.69
657 1130 4.080919 GCTAAAAGGGGGAAGCAAATCAAT 60.081 41.667 0.00 0.00 35.05 2.57
719 1192 2.672874 CCTGCGAATCGAATCAAGTCAA 59.327 45.455 6.91 0.00 0.00 3.18
772 1272 3.003480 CGGGGAGATTCAACTTCAACTC 58.997 50.000 0.00 0.00 0.00 3.01
901 1405 2.255881 GGAACAACAACCGACCGGG 61.256 63.158 13.43 0.00 43.62 5.73
902 1406 3.336566 GGAACAACAACCGACCGG 58.663 61.111 6.94 6.94 42.03 5.28
996 1504 4.923942 AGCAGCGGGATCATGGCG 62.924 66.667 0.00 0.00 0.00 5.69
1204 1724 1.450312 CGATCTTGTGGCCCCTGTC 60.450 63.158 0.00 0.00 0.00 3.51
1292 1812 4.946157 ACATGAATCGAAGAAAGAAGGCAT 59.054 37.500 0.00 0.00 43.58 4.40
1293 1813 4.326826 ACATGAATCGAAGAAAGAAGGCA 58.673 39.130 0.00 0.00 43.58 4.75
1294 1814 4.954092 ACATGAATCGAAGAAAGAAGGC 57.046 40.909 0.00 0.00 43.58 4.35
1314 1836 1.071699 TGGTGCTGTGGGAGTAAGAAC 59.928 52.381 0.00 0.00 0.00 3.01
1344 1866 6.238320 CCATGAGCAAATCAAGAACTAGTAGC 60.238 42.308 0.00 0.00 42.53 3.58
1345 1867 6.238320 GCCATGAGCAAATCAAGAACTAGTAG 60.238 42.308 0.00 0.00 42.53 2.57
1346 1868 5.586243 GCCATGAGCAAATCAAGAACTAGTA 59.414 40.000 0.00 0.00 42.53 1.82
1365 1887 1.233019 GTAGCTAGCACCATGCCATG 58.767 55.000 18.83 0.00 46.52 3.66
1366 1888 0.109342 GGTAGCTAGCACCATGCCAT 59.891 55.000 23.37 2.65 46.52 4.40
1369 1891 1.017387 GTTGGTAGCTAGCACCATGC 58.983 55.000 28.23 22.12 45.32 4.06
1374 1896 3.025262 AGGAGTAGTTGGTAGCTAGCAC 58.975 50.000 24.64 18.39 32.83 4.40
1384 1906 7.391275 GCTAACTAGTAGGATAGGAGTAGTTGG 59.609 44.444 0.00 9.40 40.42 3.77
1388 1910 8.952278 CAATGCTAACTAGTAGGATAGGAGTAG 58.048 40.741 0.00 0.00 39.79 2.57
1389 1911 7.889073 CCAATGCTAACTAGTAGGATAGGAGTA 59.111 40.741 0.00 0.00 39.79 2.59
1390 1912 6.722129 CCAATGCTAACTAGTAGGATAGGAGT 59.278 42.308 0.00 2.03 39.79 3.85
1391 1913 6.153680 CCCAATGCTAACTAGTAGGATAGGAG 59.846 46.154 0.00 0.00 39.79 3.69
1392 1914 6.017192 CCCAATGCTAACTAGTAGGATAGGA 58.983 44.000 0.00 5.64 39.79 2.94
1393 1915 6.017192 TCCCAATGCTAACTAGTAGGATAGG 58.983 44.000 0.00 6.25 39.79 2.57
1394 1916 7.726033 ATCCCAATGCTAACTAGTAGGATAG 57.274 40.000 0.00 5.19 39.79 2.08
1395 1917 8.399529 ACTATCCCAATGCTAACTAGTAGGATA 58.600 37.037 0.00 2.51 39.79 2.59
1396 1918 7.179338 CACTATCCCAATGCTAACTAGTAGGAT 59.821 40.741 0.00 0.00 42.31 3.24
1397 1919 6.493802 CACTATCCCAATGCTAACTAGTAGGA 59.506 42.308 0.00 0.00 34.24 2.94
1398 1920 6.295349 CCACTATCCCAATGCTAACTAGTAGG 60.295 46.154 0.00 0.00 0.00 3.18
1460 1985 4.451629 TGACTAGTGGTTGCTAACTAGC 57.548 45.455 0.00 1.59 46.51 3.42
1463 1988 5.246307 GGAAATGACTAGTGGTTGCTAACT 58.754 41.667 0.00 0.00 0.00 2.24
1500 2025 6.608610 ACAACACTTTTCTGTACTTGACAAC 58.391 36.000 0.00 0.00 37.70 3.32
1502 2027 6.811253 AACAACACTTTTCTGTACTTGACA 57.189 33.333 0.00 0.00 36.35 3.58
1544 2074 9.170734 ACCTAATAGCAGATACATTGCATATTG 57.829 33.333 0.00 0.00 43.92 1.90
1568 2098 6.279882 CACAATCTTGAGAGAGGATAGAACC 58.720 44.000 0.00 0.00 34.85 3.62
1612 2146 3.637911 ATGGACTGCAAATTACCGGTA 57.362 42.857 11.16 11.16 0.00 4.02
1650 2184 3.322369 TGCTTGTAGTCCATAACGTGTG 58.678 45.455 0.00 0.00 0.00 3.82
1672 2218 3.255642 TCACAACCTAAGCAGCAAATTCC 59.744 43.478 0.00 0.00 0.00 3.01
4655 7364 8.863086 CATCCATCCATATCACCATAAGTTTTT 58.137 33.333 0.00 0.00 0.00 1.94
4656 7365 8.006564 ACATCCATCCATATCACCATAAGTTTT 58.993 33.333 0.00 0.00 0.00 2.43
4657 7366 7.529555 ACATCCATCCATATCACCATAAGTTT 58.470 34.615 0.00 0.00 0.00 2.66
4658 7367 7.095183 ACATCCATCCATATCACCATAAGTT 57.905 36.000 0.00 0.00 0.00 2.66
4659 7368 6.708885 ACATCCATCCATATCACCATAAGT 57.291 37.500 0.00 0.00 0.00 2.24
4660 7369 7.855375 AGTACATCCATCCATATCACCATAAG 58.145 38.462 0.00 0.00 0.00 1.73
4661 7370 7.679881 AGAGTACATCCATCCATATCACCATAA 59.320 37.037 0.00 0.00 0.00 1.90
4662 7371 7.124750 CAGAGTACATCCATCCATATCACCATA 59.875 40.741 0.00 0.00 0.00 2.74
4663 7372 6.028131 AGAGTACATCCATCCATATCACCAT 58.972 40.000 0.00 0.00 0.00 3.55
4664 7373 5.246883 CAGAGTACATCCATCCATATCACCA 59.753 44.000 0.00 0.00 0.00 4.17
4665 7374 5.247110 ACAGAGTACATCCATCCATATCACC 59.753 44.000 0.00 0.00 0.00 4.02
4666 7375 6.162079 CACAGAGTACATCCATCCATATCAC 58.838 44.000 0.00 0.00 0.00 3.06
4667 7376 5.279657 GCACAGAGTACATCCATCCATATCA 60.280 44.000 0.00 0.00 0.00 2.15
4668 7377 5.046735 AGCACAGAGTACATCCATCCATATC 60.047 44.000 0.00 0.00 0.00 1.63
4669 7378 4.842948 AGCACAGAGTACATCCATCCATAT 59.157 41.667 0.00 0.00 0.00 1.78
4670 7379 4.226384 AGCACAGAGTACATCCATCCATA 58.774 43.478 0.00 0.00 0.00 2.74
4671 7380 3.044156 AGCACAGAGTACATCCATCCAT 58.956 45.455 0.00 0.00 0.00 3.41
4672 7381 2.432146 GAGCACAGAGTACATCCATCCA 59.568 50.000 0.00 0.00 0.00 3.41
5298 8009 0.758734 TCGATTTCCGCATCTCCCAT 59.241 50.000 0.00 0.00 38.37 4.00
5299 8010 0.179084 GTCGATTTCCGCATCTCCCA 60.179 55.000 0.00 0.00 38.37 4.37
5300 8011 1.215655 CGTCGATTTCCGCATCTCCC 61.216 60.000 0.00 0.00 38.37 4.30
5301 8012 2.217112 CGTCGATTTCCGCATCTCC 58.783 57.895 0.00 0.00 38.37 3.71
5308 8019 1.702491 GAAAGGGGCGTCGATTTCCG 61.702 60.000 0.00 0.00 40.25 4.30
5309 8020 0.392595 AGAAAGGGGCGTCGATTTCC 60.393 55.000 10.78 0.00 33.16 3.13
5310 8021 1.450025 AAGAAAGGGGCGTCGATTTC 58.550 50.000 7.31 7.31 32.95 2.17
5311 8022 1.810755 GAAAGAAAGGGGCGTCGATTT 59.189 47.619 0.00 0.00 0.00 2.17
5312 8023 1.003233 AGAAAGAAAGGGGCGTCGATT 59.997 47.619 0.00 0.00 0.00 3.34
5313 8024 0.613777 AGAAAGAAAGGGGCGTCGAT 59.386 50.000 0.00 0.00 0.00 3.59
5314 8025 0.395312 AAGAAAGAAAGGGGCGTCGA 59.605 50.000 0.00 0.00 0.00 4.20
5315 8026 0.517316 CAAGAAAGAAAGGGGCGTCG 59.483 55.000 0.00 0.00 0.00 5.12
5316 8027 1.605753 ACAAGAAAGAAAGGGGCGTC 58.394 50.000 0.00 0.00 0.00 5.19
5317 8028 2.105993 ACTACAAGAAAGAAAGGGGCGT 59.894 45.455 0.00 0.00 0.00 5.68
5318 8029 2.484264 CACTACAAGAAAGAAAGGGGCG 59.516 50.000 0.00 0.00 0.00 6.13
5319 8030 3.487372 ACACTACAAGAAAGAAAGGGGC 58.513 45.455 0.00 0.00 0.00 5.80
5320 8031 6.465439 AAAACACTACAAGAAAGAAAGGGG 57.535 37.500 0.00 0.00 0.00 4.79
5321 8032 8.221965 AGTAAAACACTACAAGAAAGAAAGGG 57.778 34.615 0.00 0.00 34.98 3.95
5341 8052 9.672086 CCGTTTGTTCAATCAAGAATTAGTAAA 57.328 29.630 0.00 0.00 0.00 2.01
5342 8053 9.058174 TCCGTTTGTTCAATCAAGAATTAGTAA 57.942 29.630 0.00 0.00 0.00 2.24
5343 8054 8.500773 GTCCGTTTGTTCAATCAAGAATTAGTA 58.499 33.333 0.00 0.00 0.00 1.82
5344 8055 7.228706 AGTCCGTTTGTTCAATCAAGAATTAGT 59.771 33.333 0.00 0.00 0.00 2.24
5345 8056 7.584987 AGTCCGTTTGTTCAATCAAGAATTAG 58.415 34.615 0.00 0.00 0.00 1.73
5346 8057 7.504924 AGTCCGTTTGTTCAATCAAGAATTA 57.495 32.000 0.00 0.00 0.00 1.40
5347 8058 6.391227 AGTCCGTTTGTTCAATCAAGAATT 57.609 33.333 0.00 0.00 0.00 2.17
5348 8059 6.710744 AGTAGTCCGTTTGTTCAATCAAGAAT 59.289 34.615 0.00 0.00 0.00 2.40
5349 8060 6.053005 AGTAGTCCGTTTGTTCAATCAAGAA 58.947 36.000 0.00 0.00 0.00 2.52
5350 8061 5.607477 AGTAGTCCGTTTGTTCAATCAAGA 58.393 37.500 0.00 0.00 0.00 3.02
5351 8062 5.924475 AGTAGTCCGTTTGTTCAATCAAG 57.076 39.130 0.00 0.00 0.00 3.02
5352 8063 6.422701 CAGTAGTAGTCCGTTTGTTCAATCAA 59.577 38.462 0.00 0.00 0.00 2.57
5353 8064 5.924254 CAGTAGTAGTCCGTTTGTTCAATCA 59.076 40.000 0.00 0.00 0.00 2.57
5354 8065 5.163982 GCAGTAGTAGTCCGTTTGTTCAATC 60.164 44.000 0.00 0.00 0.00 2.67
5355 8066 4.689345 GCAGTAGTAGTCCGTTTGTTCAAT 59.311 41.667 0.00 0.00 0.00 2.57
5356 8067 4.053295 GCAGTAGTAGTCCGTTTGTTCAA 58.947 43.478 0.00 0.00 0.00 2.69
5357 8068 3.319972 AGCAGTAGTAGTCCGTTTGTTCA 59.680 43.478 0.00 0.00 0.00 3.18
5358 8069 3.910648 AGCAGTAGTAGTCCGTTTGTTC 58.089 45.455 0.00 0.00 0.00 3.18
5359 8070 3.319972 TGAGCAGTAGTAGTCCGTTTGTT 59.680 43.478 0.00 0.00 0.00 2.83
5360 8071 2.889045 TGAGCAGTAGTAGTCCGTTTGT 59.111 45.455 0.00 0.00 0.00 2.83
5361 8072 3.570926 TGAGCAGTAGTAGTCCGTTTG 57.429 47.619 0.00 0.00 0.00 2.93
5362 8073 4.803098 ATTGAGCAGTAGTAGTCCGTTT 57.197 40.909 0.00 0.00 0.00 3.60
5363 8074 6.466885 AATATTGAGCAGTAGTAGTCCGTT 57.533 37.500 0.00 0.00 0.00 4.44
5364 8075 6.466885 AAATATTGAGCAGTAGTAGTCCGT 57.533 37.500 0.00 0.00 0.00 4.69
5365 8076 7.378995 GTGTAAATATTGAGCAGTAGTAGTCCG 59.621 40.741 0.00 0.00 0.00 4.79
5366 8077 8.195436 TGTGTAAATATTGAGCAGTAGTAGTCC 58.805 37.037 0.00 0.00 0.00 3.85
5367 8078 9.751542 ATGTGTAAATATTGAGCAGTAGTAGTC 57.248 33.333 0.00 0.00 0.00 2.59
5386 8097 9.890629 ACAGAAGAATCAGCTATTAATGTGTAA 57.109 29.630 0.00 0.00 0.00 2.41
5387 8098 9.534565 GACAGAAGAATCAGCTATTAATGTGTA 57.465 33.333 0.00 0.00 0.00 2.90
5388 8099 8.043113 TGACAGAAGAATCAGCTATTAATGTGT 58.957 33.333 0.00 0.00 0.00 3.72
5389 8100 8.429493 TGACAGAAGAATCAGCTATTAATGTG 57.571 34.615 0.00 0.00 0.00 3.21
5390 8101 9.624373 AATGACAGAAGAATCAGCTATTAATGT 57.376 29.630 0.00 0.00 0.00 2.71
5392 8103 9.282569 GGAATGACAGAAGAATCAGCTATTAAT 57.717 33.333 0.00 0.00 0.00 1.40
5393 8104 8.267183 TGGAATGACAGAAGAATCAGCTATTAA 58.733 33.333 0.00 0.00 0.00 1.40
5394 8105 7.795047 TGGAATGACAGAAGAATCAGCTATTA 58.205 34.615 0.00 0.00 0.00 0.98
5395 8106 6.656902 TGGAATGACAGAAGAATCAGCTATT 58.343 36.000 0.00 0.00 0.00 1.73
5396 8107 6.244552 TGGAATGACAGAAGAATCAGCTAT 57.755 37.500 0.00 0.00 0.00 2.97
5397 8108 5.682234 TGGAATGACAGAAGAATCAGCTA 57.318 39.130 0.00 0.00 0.00 3.32
5398 8109 4.564782 TGGAATGACAGAAGAATCAGCT 57.435 40.909 0.00 0.00 0.00 4.24
5399 8110 5.589452 AGAATGGAATGACAGAAGAATCAGC 59.411 40.000 0.00 0.00 0.00 4.26
5400 8111 6.260493 GGAGAATGGAATGACAGAAGAATCAG 59.740 42.308 0.00 0.00 0.00 2.90
5401 8112 6.069789 AGGAGAATGGAATGACAGAAGAATCA 60.070 38.462 0.00 0.00 0.00 2.57
5402 8113 6.355747 AGGAGAATGGAATGACAGAAGAATC 58.644 40.000 0.00 0.00 0.00 2.52
5403 8114 6.324601 AGGAGAATGGAATGACAGAAGAAT 57.675 37.500 0.00 0.00 0.00 2.40
5404 8115 5.768980 AGGAGAATGGAATGACAGAAGAA 57.231 39.130 0.00 0.00 0.00 2.52
5405 8116 5.249163 TCAAGGAGAATGGAATGACAGAAGA 59.751 40.000 0.00 0.00 0.00 2.87
5406 8117 5.494724 TCAAGGAGAATGGAATGACAGAAG 58.505 41.667 0.00 0.00 0.00 2.85
5407 8118 5.249163 TCTCAAGGAGAATGGAATGACAGAA 59.751 40.000 0.00 0.00 35.59 3.02
5408 8119 4.779489 TCTCAAGGAGAATGGAATGACAGA 59.221 41.667 0.00 0.00 35.59 3.41
5409 8120 5.095145 TCTCAAGGAGAATGGAATGACAG 57.905 43.478 0.00 0.00 35.59 3.51
5410 8121 4.779489 TCTCTCAAGGAGAATGGAATGACA 59.221 41.667 0.00 0.00 46.85 3.58
5411 8122 5.350504 TCTCTCAAGGAGAATGGAATGAC 57.649 43.478 0.00 0.00 46.85 3.06
5419 8130 8.276800 GAGCAAACTCAATCTCTCAAGGAGAAT 61.277 40.741 0.00 0.00 46.46 2.40
5420 8131 7.017945 GAGCAAACTCAATCTCTCAAGGAGAA 61.018 42.308 0.00 0.00 46.46 2.87
5421 8132 5.568423 GAGCAAACTCAATCTCTCAAGGAGA 60.568 44.000 0.00 0.00 46.90 3.71
5422 8133 4.577875 AGCAAACTCAATCTCTCAAGGAG 58.422 43.478 0.00 0.00 43.12 3.69
5423 8134 4.564406 GGAGCAAACTCAATCTCTCAAGGA 60.564 45.833 0.00 0.00 45.42 3.36
5424 8135 3.688673 GGAGCAAACTCAATCTCTCAAGG 59.311 47.826 0.00 0.00 45.42 3.61
5425 8136 4.577875 AGGAGCAAACTCAATCTCTCAAG 58.422 43.478 0.00 0.00 45.42 3.02
5426 8137 4.630644 AGGAGCAAACTCAATCTCTCAA 57.369 40.909 0.00 0.00 45.42 3.02
5427 8138 4.040829 TGAAGGAGCAAACTCAATCTCTCA 59.959 41.667 0.00 0.00 45.42 3.27
5428 8139 4.573900 TGAAGGAGCAAACTCAATCTCTC 58.426 43.478 0.00 0.00 45.42 3.20
5429 8140 4.285517 TCTGAAGGAGCAAACTCAATCTCT 59.714 41.667 0.00 0.00 45.42 3.10
5430 8141 4.573900 TCTGAAGGAGCAAACTCAATCTC 58.426 43.478 0.00 0.00 45.42 2.75
5431 8142 4.630644 TCTGAAGGAGCAAACTCAATCT 57.369 40.909 0.00 0.00 45.42 2.40
5432 8143 4.033817 CGATCTGAAGGAGCAAACTCAATC 59.966 45.833 0.00 0.00 45.42 2.67
5433 8144 3.937706 CGATCTGAAGGAGCAAACTCAAT 59.062 43.478 0.00 0.00 45.42 2.57
5434 8145 3.244215 ACGATCTGAAGGAGCAAACTCAA 60.244 43.478 0.00 0.00 45.42 3.02
5435 8146 2.300152 ACGATCTGAAGGAGCAAACTCA 59.700 45.455 0.00 0.00 45.42 3.41
5436 8147 2.926838 GACGATCTGAAGGAGCAAACTC 59.073 50.000 0.00 0.00 42.66 3.01
5437 8148 2.300152 TGACGATCTGAAGGAGCAAACT 59.700 45.455 0.00 0.00 0.00 2.66
5438 8149 2.413453 GTGACGATCTGAAGGAGCAAAC 59.587 50.000 0.00 0.00 0.00 2.93
5439 8150 2.037121 TGTGACGATCTGAAGGAGCAAA 59.963 45.455 0.00 0.00 0.00 3.68
5440 8151 1.618343 TGTGACGATCTGAAGGAGCAA 59.382 47.619 0.00 0.00 0.00 3.91
5441 8152 1.067565 GTGTGACGATCTGAAGGAGCA 60.068 52.381 0.00 0.00 0.00 4.26
5442 8153 1.634702 GTGTGACGATCTGAAGGAGC 58.365 55.000 0.00 0.00 0.00 4.70
5443 8154 1.546029 TGGTGTGACGATCTGAAGGAG 59.454 52.381 0.00 0.00 0.00 3.69
5444 8155 1.627864 TGGTGTGACGATCTGAAGGA 58.372 50.000 0.00 0.00 0.00 3.36
5445 8156 2.680312 ATGGTGTGACGATCTGAAGG 57.320 50.000 0.00 0.00 0.00 3.46
5446 8157 5.408299 TGTAAAATGGTGTGACGATCTGAAG 59.592 40.000 0.00 0.00 0.00 3.02
5447 8158 5.301555 TGTAAAATGGTGTGACGATCTGAA 58.698 37.500 0.00 0.00 0.00 3.02
5448 8159 4.888917 TGTAAAATGGTGTGACGATCTGA 58.111 39.130 0.00 0.00 0.00 3.27
5449 8160 5.447683 CCATGTAAAATGGTGTGACGATCTG 60.448 44.000 0.00 0.00 34.56 2.90
5450 8161 4.635765 CCATGTAAAATGGTGTGACGATCT 59.364 41.667 0.00 0.00 34.56 2.75
5451 8162 4.730613 GCCATGTAAAATGGTGTGACGATC 60.731 45.833 6.25 0.00 41.17 3.69
5452 8163 3.128589 GCCATGTAAAATGGTGTGACGAT 59.871 43.478 6.25 0.00 41.17 3.73
5453 8164 2.486203 GCCATGTAAAATGGTGTGACGA 59.514 45.455 6.25 0.00 41.17 4.20
5454 8165 2.227626 TGCCATGTAAAATGGTGTGACG 59.772 45.455 6.25 0.00 41.17 4.35
5455 8166 3.932545 TGCCATGTAAAATGGTGTGAC 57.067 42.857 6.25 0.00 41.17 3.67
5456 8167 5.480642 AATTGCCATGTAAAATGGTGTGA 57.519 34.783 6.25 0.00 41.17 3.58
5457 8168 7.846644 AATAATTGCCATGTAAAATGGTGTG 57.153 32.000 6.25 0.00 41.17 3.82
5458 8169 8.860780 AAAATAATTGCCATGTAAAATGGTGT 57.139 26.923 6.25 0.00 41.17 4.16
5483 8194 9.953565 ACTAAAACTACTATAGATGCCAACAAA 57.046 29.630 6.78 0.00 0.00 2.83
5484 8195 9.953565 AACTAAAACTACTATAGATGCCAACAA 57.046 29.630 6.78 0.00 0.00 2.83
5485 8196 9.378551 CAACTAAAACTACTATAGATGCCAACA 57.621 33.333 6.78 0.00 0.00 3.33
5486 8197 8.336080 GCAACTAAAACTACTATAGATGCCAAC 58.664 37.037 6.78 0.00 38.66 3.77
5487 8198 8.044309 TGCAACTAAAACTACTATAGATGCCAA 58.956 33.333 6.78 0.00 41.81 4.52
5488 8199 7.494625 GTGCAACTAAAACTACTATAGATGCCA 59.505 37.037 6.78 0.00 41.81 4.92
5489 8200 7.494625 TGTGCAACTAAAACTACTATAGATGCC 59.505 37.037 6.78 4.71 41.81 4.40
5490 8201 8.328864 GTGTGCAACTAAAACTACTATAGATGC 58.671 37.037 6.78 7.16 42.42 3.91
5491 8202 9.366216 TGTGTGCAACTAAAACTACTATAGATG 57.634 33.333 6.78 1.07 38.04 2.90
5496 8207 9.720769 AACTATGTGTGCAACTAAAACTACTAT 57.279 29.630 0.00 0.00 38.04 2.12
5497 8208 8.984764 CAACTATGTGTGCAACTAAAACTACTA 58.015 33.333 0.00 0.00 38.04 1.82
5498 8209 7.497909 ACAACTATGTGTGCAACTAAAACTACT 59.502 33.333 0.00 0.00 38.69 2.57
5499 8210 7.636326 ACAACTATGTGTGCAACTAAAACTAC 58.364 34.615 0.00 0.00 38.69 2.73
5500 8211 7.795482 ACAACTATGTGTGCAACTAAAACTA 57.205 32.000 0.00 0.00 38.69 2.24
5501 8212 6.693315 ACAACTATGTGTGCAACTAAAACT 57.307 33.333 0.00 0.00 38.69 2.66
5502 8213 7.749539 AAACAACTATGTGTGCAACTAAAAC 57.250 32.000 0.00 0.00 40.46 2.43
5503 8214 8.029522 TGAAAACAACTATGTGTGCAACTAAAA 58.970 29.630 0.00 0.00 40.46 1.52
5504 8215 7.539436 TGAAAACAACTATGTGTGCAACTAAA 58.461 30.769 0.00 0.00 40.46 1.85
5505 8216 7.089770 TGAAAACAACTATGTGTGCAACTAA 57.910 32.000 0.00 0.00 40.46 2.24
5506 8217 6.317642 ACTGAAAACAACTATGTGTGCAACTA 59.682 34.615 0.00 0.00 40.46 2.24
5507 8218 5.125417 ACTGAAAACAACTATGTGTGCAACT 59.875 36.000 0.00 0.00 40.46 3.16
5508 8219 5.339990 ACTGAAAACAACTATGTGTGCAAC 58.660 37.500 0.00 0.00 40.46 4.17
5509 8220 5.574891 ACTGAAAACAACTATGTGTGCAA 57.425 34.783 0.00 0.00 40.46 4.08


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

AutoCloner maintained by Alex Coulton.