Multiple sequence alignment - TraesCS3A01G068600

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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 TraesCS3A01G068600 chr3A 100.000 3416 0 0 1 3416 41063235 41066650 0.000000e+00 6309.0
1 TraesCS3A01G068600 chr3A 88.258 2095 223 15 317 2405 41616045 41618122 0.000000e+00 2484.0
2 TraesCS3A01G068600 chr3A 87.370 1544 179 12 873 2405 41354953 41356491 0.000000e+00 1757.0
3 TraesCS3A01G068600 chr3A 95.753 777 31 1 2640 3416 41538623 41539397 0.000000e+00 1251.0
4 TraesCS3A01G068600 chr3A 92.868 687 46 1 2640 3323 41610824 41611510 0.000000e+00 994.0
5 TraesCS3A01G068600 chr3A 88.417 777 87 2 2640 3416 41618114 41618887 0.000000e+00 933.0
6 TraesCS3A01G068600 chr3A 90.544 349 26 3 317 658 41367649 41367997 4.020000e-124 455.0
7 TraesCS3A01G068600 chr3A 87.310 394 40 5 317 707 41198582 41198968 3.130000e-120 442.0
8 TraesCS3A01G068600 chr3A 87.558 217 23 2 317 530 41236515 41236730 7.320000e-62 248.0
9 TraesCS3A01G068600 chr3A 92.857 84 5 1 1 84 41230408 41230490 1.660000e-23 121.0
10 TraesCS3A01G068600 chr3A 81.098 164 15 7 10 157 41198185 41198348 2.150000e-22 117.0
11 TraesCS3A01G068600 chr3A 98.333 60 1 0 239 298 41198536 41198595 4.660000e-19 106.0
12 TraesCS3A01G068600 chr3B 89.825 1710 158 12 703 2405 51248800 51250500 0.000000e+00 2180.0
13 TraesCS3A01G068600 chr3B 88.218 1706 189 10 703 2405 51915687 51917383 0.000000e+00 2026.0
14 TraesCS3A01G068600 chr3B 89.000 1500 154 10 913 2405 52777842 52776347 0.000000e+00 1845.0
15 TraesCS3A01G068600 chr3B 89.859 1420 139 5 988 2405 52853726 52852310 0.000000e+00 1820.0
16 TraesCS3A01G068600 chr3B 88.562 1495 163 7 914 2404 52426243 52427733 0.000000e+00 1807.0
17 TraesCS3A01G068600 chr3B 89.474 1406 145 3 1001 2405 51243343 51244746 0.000000e+00 1773.0
18 TraesCS3A01G068600 chr3B 94.171 772 45 0 2640 3411 52852318 52851547 0.000000e+00 1177.0
19 TraesCS3A01G068600 chr3B 93.540 774 50 0 2640 3413 51960214 51960987 0.000000e+00 1153.0
20 TraesCS3A01G068600 chr3B 93.750 704 44 0 2708 3411 52415613 52416316 0.000000e+00 1057.0
21 TraesCS3A01G068600 chr3B 89.867 829 69 7 541 1368 52414801 52415615 0.000000e+00 1051.0
22 TraesCS3A01G068600 chr3B 88.031 777 90 1 2640 3416 51244738 51245511 0.000000e+00 917.0
23 TraesCS3A01G068600 chr3B 87.193 773 96 2 2640 3412 51926507 51927276 0.000000e+00 876.0
24 TraesCS3A01G068600 chr3B 82.474 388 53 10 317 699 52413514 52413891 3.290000e-85 326.0
25 TraesCS3A01G068600 chr3B 87.449 247 19 6 317 551 51802293 51802539 1.210000e-69 274.0
26 TraesCS3A01G068600 chr3B 85.537 242 28 3 317 551 52545780 52546021 2.630000e-61 246.0
27 TraesCS3A01G068600 chr3B 88.304 171 11 7 553 723 51911561 51911722 2.690000e-46 196.0
28 TraesCS3A01G068600 chr3B 91.489 94 8 0 205 298 51909812 51909905 2.770000e-26 130.0
29 TraesCS3A01G068600 chr3B 92.857 84 5 1 1 84 51247725 51247807 1.660000e-23 121.0
30 TraesCS3A01G068600 chr3B 87.500 96 10 2 205 299 51801145 51801239 3.600000e-20 110.0
31 TraesCS3A01G068600 chr3B 93.243 74 5 0 317 390 52426160 52426233 3.600000e-20 110.0
32 TraesCS3A01G068600 chr3B 90.244 82 7 1 3 84 52544967 52545047 4.660000e-19 106.0
33 TraesCS3A01G068600 chr3B 93.548 62 4 0 660 721 51915030 51915091 3.630000e-15 93.5
34 TraesCS3A01G068600 chr3B 93.333 60 4 0 96 155 51788507 51788566 4.700000e-14 89.8
35 TraesCS3A01G068600 chr3B 100.000 33 0 0 319 351 51248333 51248365 1.020000e-05 62.1
36 TraesCS3A01G068600 chr3D 87.412 1557 176 14 862 2405 30006562 30008111 0.000000e+00 1772.0
37 TraesCS3A01G068600 chr3D 91.763 692 48 7 2640 3328 29972227 29972912 0.000000e+00 953.0
38 TraesCS3A01G068600 chr1B 99.163 239 2 0 2401 2639 41524727 41524965 6.770000e-117 431.0
39 TraesCS3A01G068600 chr1B 99.149 235 2 0 2405 2639 3046876 3047110 1.130000e-114 424.0
40 TraesCS3A01G068600 chr1B 98.739 238 3 0 2406 2643 492367138 492366901 1.130000e-114 424.0
41 TraesCS3A01G068600 chr1B 99.145 234 2 0 2406 2639 332571106 332570873 4.080000e-114 422.0
42 TraesCS3A01G068600 chr1B 99.145 234 2 0 2406 2639 577212096 577212329 4.080000e-114 422.0
43 TraesCS3A01G068600 chr4A 97.200 250 7 0 2395 2644 242383583 242383832 1.130000e-114 424.0
44 TraesCS3A01G068600 chr5B 99.145 234 2 0 2406 2639 23670562 23670795 4.080000e-114 422.0
45 TraesCS3A01G068600 chr2B 99.145 234 2 0 2406 2639 675522821 675522588 4.080000e-114 422.0
46 TraesCS3A01G068600 chr2B 95.019 261 7 6 2399 2656 623578328 623578585 4.100000e-109 405.0


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 TraesCS3A01G068600 chr3A 41063235 41066650 3415 False 6309.000000 6309 100.000000 1 3416 1 chr3A.!!$F1 3415
1 TraesCS3A01G068600 chr3A 41354953 41356491 1538 False 1757.000000 1757 87.370000 873 2405 1 chr3A.!!$F4 1532
2 TraesCS3A01G068600 chr3A 41616045 41618887 2842 False 1708.500000 2484 88.337500 317 3416 2 chr3A.!!$F9 3099
3 TraesCS3A01G068600 chr3A 41538623 41539397 774 False 1251.000000 1251 95.753000 2640 3416 1 chr3A.!!$F6 776
4 TraesCS3A01G068600 chr3A 41610824 41611510 686 False 994.000000 994 92.868000 2640 3323 1 chr3A.!!$F7 683
5 TraesCS3A01G068600 chr3A 41198185 41198968 783 False 221.666667 442 88.913667 10 707 3 chr3A.!!$F8 697
6 TraesCS3A01G068600 chr3B 52776347 52777842 1495 True 1845.000000 1845 89.000000 913 2405 1 chr3B.!!$R1 1492
7 TraesCS3A01G068600 chr3B 52851547 52853726 2179 True 1498.500000 1820 92.015000 988 3411 2 chr3B.!!$R2 2423
8 TraesCS3A01G068600 chr3B 51960214 51960987 773 False 1153.000000 1153 93.540000 2640 3413 1 chr3B.!!$F3 773
9 TraesCS3A01G068600 chr3B 51243343 51250500 7157 False 1010.620000 2180 92.037400 1 3416 5 chr3B.!!$F4 3415
10 TraesCS3A01G068600 chr3B 52426160 52427733 1573 False 958.500000 1807 90.902500 317 2404 2 chr3B.!!$F8 2087
11 TraesCS3A01G068600 chr3B 51926507 51927276 769 False 876.000000 876 87.193000 2640 3412 1 chr3B.!!$F2 772
12 TraesCS3A01G068600 chr3B 52413514 52416316 2802 False 811.333333 1057 88.697000 317 3411 3 chr3B.!!$F7 3094
13 TraesCS3A01G068600 chr3B 51909812 51917383 7571 False 611.375000 2026 90.389750 205 2405 4 chr3B.!!$F6 2200
14 TraesCS3A01G068600 chr3D 30006562 30008111 1549 False 1772.000000 1772 87.412000 862 2405 1 chr3D.!!$F2 1543
15 TraesCS3A01G068600 chr3D 29972227 29972912 685 False 953.000000 953 91.763000 2640 3328 1 chr3D.!!$F1 688

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
123 4522 0.034186 TGCTATTGGACCAGGCAAGG 60.034 55.0 13.86 0.0 0.00 3.61 F
531 8779 0.307760 AGCTTGCGACTTTGGTTTCG 59.692 50.0 0.00 0.0 38.31 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 12039 0.868406 GGCTCAACAAGAGTGGAACG 59.132 55.0 0.00 0.00 46.47 3.95 R
2479 13039 1.319541 TGGTCAAATTTCGGCCGAAA 58.680 45.0 44.99 44.99 46.37 3.46 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
71 4460 1.546029 TCTACTGCTGTGTGGTAGCTG 59.454 52.381 6.48 0.00 43.24 4.24
73 4462 2.032528 TGCTGTGTGGTAGCTGGC 59.967 61.111 0.00 0.00 41.66 4.85
74 4463 2.747855 GCTGTGTGGTAGCTGGCC 60.748 66.667 0.00 0.00 38.14 5.36
75 4464 2.749682 CTGTGTGGTAGCTGGCCA 59.250 61.111 4.71 4.71 0.00 5.36
91 4490 3.019964 CCACTACTGTTGCTTGGCA 57.980 52.632 0.00 0.00 36.47 4.92
123 4522 0.034186 TGCTATTGGACCAGGCAAGG 60.034 55.000 13.86 0.00 0.00 3.61
128 4527 1.792757 TTGGACCAGGCAAGGCATCT 61.793 55.000 0.00 0.00 0.00 2.90
129 4528 1.452833 GGACCAGGCAAGGCATCTC 60.453 63.158 0.00 0.00 0.00 2.75
130 4529 1.452833 GACCAGGCAAGGCATCTCC 60.453 63.158 0.00 0.00 0.00 3.71
133 4532 1.035932 CCAGGCAAGGCATCTCCAAG 61.036 60.000 0.00 0.00 37.29 3.61
146 4545 4.810491 GCATCTCCAAGTCTCAGAAATCTC 59.190 45.833 0.00 0.00 0.00 2.75
157 4556 7.509546 AGTCTCAGAAATCTCAAGGTTTTGTA 58.490 34.615 0.00 0.00 35.73 2.41
158 4557 8.160106 AGTCTCAGAAATCTCAAGGTTTTGTAT 58.840 33.333 0.00 0.00 35.73 2.29
159 4558 8.787852 GTCTCAGAAATCTCAAGGTTTTGTATT 58.212 33.333 0.00 0.00 35.73 1.89
160 4559 8.786898 TCTCAGAAATCTCAAGGTTTTGTATTG 58.213 33.333 0.00 0.00 35.73 1.90
162 4561 7.231317 TCAGAAATCTCAAGGTTTTGTATTGCT 59.769 33.333 0.00 0.00 35.73 3.91
163 4562 7.869429 CAGAAATCTCAAGGTTTTGTATTGCTT 59.131 33.333 0.00 0.00 35.73 3.91
164 4563 7.869429 AGAAATCTCAAGGTTTTGTATTGCTTG 59.131 33.333 0.00 0.00 35.73 4.01
165 4564 5.452078 TCTCAAGGTTTTGTATTGCTTGG 57.548 39.130 0.00 0.00 35.73 3.61
166 4565 3.988819 TCAAGGTTTTGTATTGCTTGGC 58.011 40.909 0.00 0.00 35.73 4.52
177 4576 5.804639 TGTATTGCTTGGCTCTTCTTCTTA 58.195 37.500 0.00 0.00 0.00 2.10
178 4577 5.877012 TGTATTGCTTGGCTCTTCTTCTTAG 59.123 40.000 0.00 0.00 0.00 2.18
179 4578 4.623932 TTGCTTGGCTCTTCTTCTTAGA 57.376 40.909 0.00 0.00 0.00 2.10
180 4579 4.623932 TGCTTGGCTCTTCTTCTTAGAA 57.376 40.909 0.00 0.00 38.06 2.10
182 4581 5.564550 TGCTTGGCTCTTCTTCTTAGAAAT 58.435 37.500 0.00 0.00 39.80 2.17
186 4596 5.738909 TGGCTCTTCTTCTTAGAAATGGAG 58.261 41.667 0.00 5.06 39.80 3.86
192 4602 6.874134 TCTTCTTCTTAGAAATGGAGGTTTCG 59.126 38.462 0.00 0.00 41.74 3.46
193 4604 4.935808 TCTTCTTAGAAATGGAGGTTTCGC 59.064 41.667 0.00 0.00 41.74 4.70
224 4698 7.338710 TCTTTGTGGCTTATCAGTTTAGCTAT 58.661 34.615 0.00 0.00 35.30 2.97
232 4706 6.866248 GCTTATCAGTTTAGCTATCCTCTGTC 59.134 42.308 0.00 0.00 32.26 3.51
284 5107 2.618709 GCACTTCTGGCACTACTTTGTT 59.381 45.455 0.00 0.00 0.00 2.83
285 5108 3.066760 GCACTTCTGGCACTACTTTGTTT 59.933 43.478 0.00 0.00 0.00 2.83
286 5109 4.440112 GCACTTCTGGCACTACTTTGTTTT 60.440 41.667 0.00 0.00 0.00 2.43
287 5110 5.036737 CACTTCTGGCACTACTTTGTTTTG 58.963 41.667 0.00 0.00 0.00 2.44
288 5111 4.705023 ACTTCTGGCACTACTTTGTTTTGT 59.295 37.500 0.00 0.00 0.00 2.83
289 5112 5.185056 ACTTCTGGCACTACTTTGTTTTGTT 59.815 36.000 0.00 0.00 0.00 2.83
290 5113 5.243426 TCTGGCACTACTTTGTTTTGTTC 57.757 39.130 0.00 0.00 0.00 3.18
291 5114 4.702612 TCTGGCACTACTTTGTTTTGTTCA 59.297 37.500 0.00 0.00 0.00 3.18
292 5115 4.739195 TGGCACTACTTTGTTTTGTTCAC 58.261 39.130 0.00 0.00 0.00 3.18
293 5116 4.461081 TGGCACTACTTTGTTTTGTTCACT 59.539 37.500 0.00 0.00 0.00 3.41
294 5117 5.648526 TGGCACTACTTTGTTTTGTTCACTA 59.351 36.000 0.00 0.00 0.00 2.74
295 5118 6.183360 TGGCACTACTTTGTTTTGTTCACTAG 60.183 38.462 0.00 0.00 0.00 2.57
296 5119 6.183360 GGCACTACTTTGTTTTGTTCACTAGT 60.183 38.462 0.00 0.00 0.00 2.57
297 5120 7.248437 GCACTACTTTGTTTTGTTCACTAGTT 58.752 34.615 0.00 0.00 0.00 2.24
298 5121 7.753580 GCACTACTTTGTTTTGTTCACTAGTTT 59.246 33.333 0.00 0.00 0.00 2.66
299 5122 9.620660 CACTACTTTGTTTTGTTCACTAGTTTT 57.379 29.630 0.00 0.00 0.00 2.43
386 5250 1.005924 AGCATGGTTTTCCCCTGGTAG 59.994 52.381 0.00 0.00 39.73 3.18
390 5254 1.854280 TGGTTTTCCCCTGGTAGTTGT 59.146 47.619 0.00 0.00 39.73 3.32
432 8672 6.409704 TCTATTGTGATTCTAGCTTGCACTT 58.590 36.000 0.00 0.00 0.00 3.16
433 8673 4.754372 TTGTGATTCTAGCTTGCACTTG 57.246 40.909 0.00 0.00 0.00 3.16
457 8697 5.447413 GGCCTTGCGAGATCTTTAAAACTAC 60.447 44.000 1.22 0.00 0.00 2.73
461 8701 4.860907 TGCGAGATCTTTAAAACTACCGAC 59.139 41.667 0.00 0.00 0.00 4.79
462 8702 5.100943 GCGAGATCTTTAAAACTACCGACT 58.899 41.667 0.00 0.00 0.00 4.18
480 8724 3.330267 GACTGGCTAGAAGACTGGTTTG 58.670 50.000 3.17 0.00 0.00 2.93
491 8735 7.563888 AGAAGACTGGTTTGTAAGGTAAAAC 57.436 36.000 0.00 0.00 35.89 2.43
531 8779 0.307760 AGCTTGCGACTTTGGTTTCG 59.692 50.000 0.00 0.00 38.31 3.46
859 11404 5.582950 AATATAAATGGCAGCCCACTAGA 57.417 39.130 9.64 0.00 45.77 2.43
910 11458 7.985184 ACTTTCGAAGCATGTTATCATACCTTA 59.015 33.333 0.00 0.00 32.47 2.69
917 11465 7.823665 AGCATGTTATCATACCTTATGCATTG 58.176 34.615 3.54 0.00 41.22 2.82
938 11486 7.596248 GCATTGATTTTCAGCTTTCAGTTTCTA 59.404 33.333 0.00 0.00 0.00 2.10
982 11534 1.650242 TTTTGGGTGGACCTCTGGCA 61.650 55.000 0.00 0.00 41.11 4.92
986 11538 2.359230 GTGGACCTCTGGCACTGC 60.359 66.667 0.00 0.00 0.00 4.40
991 11543 1.152963 ACCTCTGGCACTGCGTTTT 60.153 52.632 0.00 0.00 0.00 2.43
1059 11611 6.744537 GTGTCAATAAGTTGCAAGATGTCATC 59.255 38.462 0.00 4.52 35.26 2.92
1114 11667 1.602311 AGAGCTCACAAAACTGCTGG 58.398 50.000 17.77 0.00 35.76 4.85
1152 11705 6.690704 ATTCAGTGTTGTATATACGATGCG 57.309 37.500 6.09 0.00 0.00 4.73
1175 11728 3.142174 AGAAAAGGAGGACAAAAGAGCG 58.858 45.455 0.00 0.00 0.00 5.03
1326 11879 2.819608 TGCATGTAAAGGCCTTTCAGTC 59.180 45.455 33.64 22.24 34.23 3.51
1456 12009 6.323203 TCAACAGTAGTACACAACCTACTC 57.677 41.667 2.52 0.00 31.10 2.59
1467 12020 2.268298 CAACCTACTCGAAATGGTCCG 58.732 52.381 3.80 0.00 31.64 4.79
1486 12039 4.567159 GTCCGACATCCAAACTGATAAGAC 59.433 45.833 0.00 0.00 0.00 3.01
1493 12046 4.312443 TCCAAACTGATAAGACGTTCCAC 58.688 43.478 0.00 0.00 0.00 4.02
1494 12047 4.039973 TCCAAACTGATAAGACGTTCCACT 59.960 41.667 0.00 0.00 0.00 4.00
1599 12152 8.494016 AATACAAGTCTTACAAGCTTGGTATC 57.506 34.615 29.18 15.12 40.84 2.24
1718 12271 6.821160 TGTGTTTCACAAGACTACAATGAAGA 59.179 34.615 0.00 0.00 41.69 2.87
1804 12357 0.607489 GCTCCAGAGGAAGCTTGCAA 60.607 55.000 20.82 0.00 0.00 4.08
1900 12460 7.701539 TTAAGACCTGCATTACATGAAACAT 57.298 32.000 0.00 0.00 0.00 2.71
1905 12465 5.889853 ACCTGCATTACATGAAACATCATCT 59.110 36.000 0.00 0.00 0.00 2.90
1947 12507 5.961843 CACACGAGATGATCAAATTACAAGC 59.038 40.000 0.00 0.00 0.00 4.01
1961 12521 6.903883 AATTACAAGCAGAATAGGTGTACG 57.096 37.500 0.00 0.00 0.00 3.67
2010 12570 0.343372 TAGAGGTGGGATGGGAGCTT 59.657 55.000 0.00 0.00 0.00 3.74
2035 12595 4.142609 TGGAGGAGTATGAACATTGAGC 57.857 45.455 0.00 0.00 0.00 4.26
2047 12607 6.698008 TGAACATTGAGCAAGAGAAAGAAA 57.302 33.333 0.00 0.00 0.00 2.52
2049 12609 8.394971 TGAACATTGAGCAAGAGAAAGAAATA 57.605 30.769 0.00 0.00 0.00 1.40
2052 12612 8.345724 ACATTGAGCAAGAGAAAGAAATACAT 57.654 30.769 0.00 0.00 0.00 2.29
2125 12685 1.164411 TGCAATCAAGGTTACCGCTG 58.836 50.000 0.00 0.00 0.00 5.18
2196 12756 2.093711 GGGCAAATATGTTGGTTCCCAC 60.094 50.000 0.00 0.00 30.78 4.61
2227 12787 6.015519 GCTCTCTGATGAAATAGAAGGAGCTA 60.016 42.308 0.00 0.00 37.83 3.32
2235 12795 9.585099 GATGAAATAGAAGGAGCTATGTATCTG 57.415 37.037 0.00 0.00 31.69 2.90
2252 12812 4.959560 ATCTGAGCTATGATGAGTTGCT 57.040 40.909 0.00 0.00 36.63 3.91
2293 12853 9.073475 AGTGTTTCCTTTATTGTGCTTTGTATA 57.927 29.630 0.00 0.00 0.00 1.47
2385 12945 3.777522 AGCAAGGCCAACTACTAGAAGAT 59.222 43.478 5.01 0.00 0.00 2.40
2405 12965 9.720769 AGAAGATATAGCAGAAGAGTACTACTC 57.279 37.037 8.02 8.02 45.38 2.59
2421 12981 8.073355 AGTACTACTCAGTGTTTTGATTTTCG 57.927 34.615 0.00 0.00 36.14 3.46
2422 12982 6.920569 ACTACTCAGTGTTTTGATTTTCGT 57.079 33.333 0.00 0.00 32.25 3.85
2423 12983 7.316544 ACTACTCAGTGTTTTGATTTTCGTT 57.683 32.000 0.00 0.00 32.25 3.85
2424 12984 7.758495 ACTACTCAGTGTTTTGATTTTCGTTT 58.242 30.769 0.00 0.00 32.25 3.60
2425 12985 8.241367 ACTACTCAGTGTTTTGATTTTCGTTTT 58.759 29.630 0.00 0.00 32.25 2.43
2426 12986 7.276953 ACTCAGTGTTTTGATTTTCGTTTTG 57.723 32.000 0.00 0.00 0.00 2.44
2427 12987 6.866248 ACTCAGTGTTTTGATTTTCGTTTTGT 59.134 30.769 0.00 0.00 0.00 2.83
2428 12988 7.043454 TCAGTGTTTTGATTTTCGTTTTGTG 57.957 32.000 0.00 0.00 0.00 3.33
2429 12989 6.863645 TCAGTGTTTTGATTTTCGTTTTGTGA 59.136 30.769 0.00 0.00 0.00 3.58
2430 12990 7.543868 TCAGTGTTTTGATTTTCGTTTTGTGAT 59.456 29.630 0.00 0.00 0.00 3.06
2431 12991 8.167985 CAGTGTTTTGATTTTCGTTTTGTGATT 58.832 29.630 0.00 0.00 0.00 2.57
2432 12992 8.716909 AGTGTTTTGATTTTCGTTTTGTGATTT 58.283 25.926 0.00 0.00 0.00 2.17
2433 12993 9.323963 GTGTTTTGATTTTCGTTTTGTGATTTT 57.676 25.926 0.00 0.00 0.00 1.82
2434 12994 9.884465 TGTTTTGATTTTCGTTTTGTGATTTTT 57.116 22.222 0.00 0.00 0.00 1.94
2437 12997 9.965748 TTTGATTTTCGTTTTGTGATTTTTCTC 57.034 25.926 0.00 0.00 0.00 2.87
2438 12998 7.826636 TGATTTTCGTTTTGTGATTTTTCTCG 58.173 30.769 0.00 0.00 0.00 4.04
2439 12999 5.613964 TTTCGTTTTGTGATTTTTCTCGC 57.386 34.783 0.00 0.00 0.00 5.03
2440 13000 3.623863 TCGTTTTGTGATTTTTCTCGCC 58.376 40.909 0.00 0.00 0.00 5.54
2441 13001 2.724174 CGTTTTGTGATTTTTCTCGCCC 59.276 45.455 0.00 0.00 0.00 6.13
2442 13002 3.550030 CGTTTTGTGATTTTTCTCGCCCT 60.550 43.478 0.00 0.00 0.00 5.19
2443 13003 4.319911 CGTTTTGTGATTTTTCTCGCCCTA 60.320 41.667 0.00 0.00 0.00 3.53
2444 13004 5.154222 GTTTTGTGATTTTTCTCGCCCTAG 58.846 41.667 0.00 0.00 0.00 3.02
2445 13005 2.985896 TGTGATTTTTCTCGCCCTAGG 58.014 47.619 0.06 0.06 0.00 3.02
2446 13006 1.671328 GTGATTTTTCTCGCCCTAGGC 59.329 52.381 2.05 0.00 46.75 3.93
2464 13024 1.934463 CCGAGATGGCCGAATTTCG 59.066 57.895 11.81 11.81 40.07 3.46
2481 13041 8.959761 CGAATTTCGGTCGTTTTTAAAAATTT 57.040 26.923 16.02 0.00 36.00 1.82
2482 13042 9.073266 CGAATTTCGGTCGTTTTTAAAAATTTC 57.927 29.630 16.02 9.25 36.00 2.17
2483 13043 8.959761 AATTTCGGTCGTTTTTAAAAATTTCG 57.040 26.923 16.02 14.40 0.00 3.46
2484 13044 6.493697 TTCGGTCGTTTTTAAAAATTTCGG 57.506 33.333 16.02 12.42 0.00 4.30
2485 13045 4.440431 TCGGTCGTTTTTAAAAATTTCGGC 59.560 37.500 16.02 15.29 0.00 5.54
2486 13046 4.375205 CGGTCGTTTTTAAAAATTTCGGCC 60.375 41.667 24.70 24.70 36.74 6.13
2487 13047 4.375205 GGTCGTTTTTAAAAATTTCGGCCG 60.375 41.667 22.12 22.12 32.60 6.13
2488 13048 4.440431 GTCGTTTTTAAAAATTTCGGCCGA 59.560 37.500 27.28 27.28 0.00 5.54
2489 13049 5.039333 TCGTTTTTAAAAATTTCGGCCGAA 58.961 33.333 35.81 35.81 0.00 4.30
2490 13050 5.517770 TCGTTTTTAAAAATTTCGGCCGAAA 59.482 32.000 44.99 44.99 46.37 3.46
2498 13058 1.319541 TTTCGGCCGAAATTTGACCA 58.680 45.000 41.63 22.96 38.95 4.02
2499 13059 1.319541 TTCGGCCGAAATTTGACCAA 58.680 45.000 37.13 11.77 0.00 3.67
2500 13060 1.319541 TCGGCCGAAATTTGACCAAA 58.680 45.000 28.99 0.00 34.46 3.28
2501 13061 1.889829 TCGGCCGAAATTTGACCAAAT 59.110 42.857 28.99 2.38 42.35 2.32
2558 13118 7.656707 ATTTCTCAAATTTGACCAATTTCGG 57.343 32.000 16.91 4.55 42.28 4.30
2559 13119 4.555262 TCTCAAATTTGACCAATTTCGGC 58.445 39.130 16.91 0.00 42.28 5.54
2560 13120 3.312828 TCAAATTTGACCAATTTCGGCG 58.687 40.909 16.91 0.00 42.28 6.46
2561 13121 2.362169 AATTTGACCAATTTCGGCGG 57.638 45.000 7.21 0.00 30.09 6.13
2562 13122 1.540267 ATTTGACCAATTTCGGCGGA 58.460 45.000 7.21 0.00 0.00 5.54
2563 13123 1.319541 TTTGACCAATTTCGGCGGAA 58.680 45.000 1.65 1.65 0.00 4.30
2564 13124 0.878416 TTGACCAATTTCGGCGGAAG 59.122 50.000 6.80 0.00 32.80 3.46
2565 13125 0.035598 TGACCAATTTCGGCGGAAGA 59.964 50.000 6.80 0.00 32.80 2.87
2566 13126 1.339631 TGACCAATTTCGGCGGAAGAT 60.340 47.619 6.80 0.00 32.80 2.40
2567 13127 2.093394 TGACCAATTTCGGCGGAAGATA 60.093 45.455 6.80 0.00 32.80 1.98
2568 13128 2.544267 GACCAATTTCGGCGGAAGATAG 59.456 50.000 6.80 0.00 32.80 2.08
2569 13129 2.169769 ACCAATTTCGGCGGAAGATAGA 59.830 45.455 6.80 0.00 32.80 1.98
2570 13130 3.181454 ACCAATTTCGGCGGAAGATAGAT 60.181 43.478 6.80 0.00 32.80 1.98
2571 13131 3.815401 CCAATTTCGGCGGAAGATAGATT 59.185 43.478 6.80 1.49 32.80 2.40
2572 13132 4.275936 CCAATTTCGGCGGAAGATAGATTT 59.724 41.667 6.80 0.00 32.80 2.17
2573 13133 5.444122 CAATTTCGGCGGAAGATAGATTTC 58.556 41.667 6.80 0.00 32.80 2.17
2574 13134 2.417339 TCGGCGGAAGATAGATTTCG 57.583 50.000 7.21 0.00 0.00 3.46
2575 13135 0.784778 CGGCGGAAGATAGATTTCGC 59.215 55.000 0.00 3.57 0.00 4.70
2576 13136 1.149148 GGCGGAAGATAGATTTCGCC 58.851 55.000 14.76 14.76 37.21 5.54
2577 13137 1.149148 GCGGAAGATAGATTTCGCCC 58.851 55.000 0.68 0.00 0.00 6.13
2578 13138 1.270358 GCGGAAGATAGATTTCGCCCT 60.270 52.381 0.68 0.00 0.00 5.19
2579 13139 2.029290 GCGGAAGATAGATTTCGCCCTA 60.029 50.000 0.68 0.00 0.00 3.53
2580 13140 3.839293 CGGAAGATAGATTTCGCCCTAG 58.161 50.000 0.00 0.00 0.00 3.02
2581 13141 3.367498 CGGAAGATAGATTTCGCCCTAGG 60.367 52.174 0.06 0.06 0.00 3.02
2582 13142 3.591023 GAAGATAGATTTCGCCCTAGGC 58.409 50.000 2.05 0.00 46.75 3.93
2601 13161 1.512926 CCGAGATGGCCTAAATTCGG 58.487 55.000 16.20 16.20 41.15 4.30
2602 13162 0.868406 CGAGATGGCCTAAATTCGGC 59.132 55.000 3.32 9.61 46.83 5.54
2609 13169 2.401017 GCCTAAATTCGGCCGAAATC 57.599 50.000 41.31 19.43 41.73 2.17
2610 13170 1.001706 GCCTAAATTCGGCCGAAATCC 60.002 52.381 41.31 22.63 41.73 3.01
2611 13171 2.294074 CCTAAATTCGGCCGAAATCCA 58.706 47.619 41.31 25.16 37.69 3.41
2612 13172 2.884639 CCTAAATTCGGCCGAAATCCAT 59.115 45.455 41.31 24.03 37.69 3.41
2613 13173 3.317993 CCTAAATTCGGCCGAAATCCATT 59.682 43.478 41.31 28.12 37.69 3.16
2614 13174 3.885724 AAATTCGGCCGAAATCCATTT 57.114 38.095 41.31 31.56 37.69 2.32
2615 13175 3.885724 AATTCGGCCGAAATCCATTTT 57.114 38.095 41.31 26.70 37.69 1.82
2616 13176 3.885724 ATTCGGCCGAAATCCATTTTT 57.114 38.095 41.31 20.98 37.69 1.94
2635 13195 5.638660 TTTTTACGGCCGAAATTCAAAAC 57.361 34.783 35.90 0.00 0.00 2.43
2636 13196 2.993449 TACGGCCGAAATTCAAAACC 57.007 45.000 35.90 0.00 0.00 3.27
2637 13197 0.315886 ACGGCCGAAATTCAAAACCC 59.684 50.000 35.90 0.00 0.00 4.11
2638 13198 0.601057 CGGCCGAAATTCAAAACCCT 59.399 50.000 24.07 0.00 0.00 4.34
2680 13240 0.617535 TCGGAATCTCCTCCAGCCAA 60.618 55.000 0.00 0.00 34.91 4.52
2690 13250 4.975147 TCTCCTCCAGCCAAATAGGATAAA 59.025 41.667 0.00 0.00 41.22 1.40
2698 13258 7.619302 TCCAGCCAAATAGGATAAATTTTGACT 59.381 33.333 0.00 0.00 41.22 3.41
3141 13704 4.890158 TGATCTGCACAGTCTTCCTTTA 57.110 40.909 0.00 0.00 0.00 1.85
3199 13762 9.558396 TTGATCTTTTTGGCACAGAAATAAATT 57.442 25.926 0.00 0.00 41.55 1.82
3364 13927 7.581213 TCTCTTGTTAAATTGGAAAGAGCAA 57.419 32.000 12.32 0.00 42.25 3.91
3367 13930 7.781056 TCTTGTTAAATTGGAAAGAGCAACTT 58.219 30.769 0.00 0.00 40.98 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 4460 1.866853 GCCAAGCAACAGTAGTGGCC 61.867 60.000 0.00 0.00 46.34 5.36
73 4462 0.593128 GTGCCAAGCAACAGTAGTGG 59.407 55.000 1.92 0.00 41.47 4.00
74 4463 1.597742 AGTGCCAAGCAACAGTAGTG 58.402 50.000 0.00 0.00 41.47 2.74
75 4464 1.949525 CAAGTGCCAAGCAACAGTAGT 59.050 47.619 0.00 0.00 41.47 2.73
76 4465 1.949525 ACAAGTGCCAAGCAACAGTAG 59.050 47.619 0.00 0.00 41.47 2.57
77 4466 2.051334 ACAAGTGCCAAGCAACAGTA 57.949 45.000 0.00 0.00 41.47 2.74
78 4467 2.051334 TACAAGTGCCAAGCAACAGT 57.949 45.000 0.00 0.00 41.47 3.55
91 4490 2.947652 CCAATAGCAGCAGCATACAAGT 59.052 45.455 3.17 0.00 45.49 3.16
123 4522 4.768583 AGATTTCTGAGACTTGGAGATGC 58.231 43.478 0.00 0.00 0.00 3.91
128 4527 4.594920 ACCTTGAGATTTCTGAGACTTGGA 59.405 41.667 0.00 0.00 0.00 3.53
129 4528 4.904241 ACCTTGAGATTTCTGAGACTTGG 58.096 43.478 0.00 0.00 0.00 3.61
130 4529 6.874288 AAACCTTGAGATTTCTGAGACTTG 57.126 37.500 0.00 0.00 0.00 3.16
133 4532 6.625873 ACAAAACCTTGAGATTTCTGAGAC 57.374 37.500 0.00 0.00 36.33 3.36
146 4545 3.989817 GAGCCAAGCAATACAAAACCTTG 59.010 43.478 0.00 0.00 38.61 3.61
157 4556 5.171339 TCTAAGAAGAAGAGCCAAGCAAT 57.829 39.130 0.00 0.00 0.00 3.56
158 4557 4.623932 TCTAAGAAGAAGAGCCAAGCAA 57.376 40.909 0.00 0.00 0.00 3.91
159 4558 4.623932 TTCTAAGAAGAAGAGCCAAGCA 57.376 40.909 0.00 0.00 36.80 3.91
160 4559 5.163673 CCATTTCTAAGAAGAAGAGCCAAGC 60.164 44.000 0.00 0.00 42.60 4.01
162 4561 6.126863 TCCATTTCTAAGAAGAAGAGCCAA 57.873 37.500 0.00 0.00 42.60 4.52
163 4562 5.338708 CCTCCATTTCTAAGAAGAAGAGCCA 60.339 44.000 0.00 0.00 42.60 4.75
164 4563 5.122519 CCTCCATTTCTAAGAAGAAGAGCC 58.877 45.833 0.00 0.00 42.60 4.70
165 4564 5.739959 ACCTCCATTTCTAAGAAGAAGAGC 58.260 41.667 0.00 0.00 42.60 4.09
166 4565 7.064016 CGAAACCTCCATTTCTAAGAAGAAGAG 59.936 40.741 0.00 0.00 42.60 2.85
186 4596 2.351738 CCACAAAGATCAAGGCGAAACC 60.352 50.000 0.00 0.00 39.61 3.27
192 4602 3.696051 TGATAAGCCACAAAGATCAAGGC 59.304 43.478 0.00 0.00 45.54 4.35
193 4604 4.946157 ACTGATAAGCCACAAAGATCAAGG 59.054 41.667 0.00 0.00 0.00 3.61
201 4612 6.542370 GGATAGCTAAACTGATAAGCCACAAA 59.458 38.462 0.00 0.00 36.92 2.83
304 5127 4.695217 AGTGAACAAAGCGTCTCAAAAA 57.305 36.364 0.00 0.00 0.00 1.94
305 5128 4.873827 ACTAGTGAACAAAGCGTCTCAAAA 59.126 37.500 0.00 0.00 0.00 2.44
306 5129 4.439057 ACTAGTGAACAAAGCGTCTCAAA 58.561 39.130 0.00 0.00 0.00 2.69
307 5130 4.054780 ACTAGTGAACAAAGCGTCTCAA 57.945 40.909 0.00 0.00 0.00 3.02
308 5131 3.728076 ACTAGTGAACAAAGCGTCTCA 57.272 42.857 0.00 0.00 0.00 3.27
309 5132 3.184581 CCAACTAGTGAACAAAGCGTCTC 59.815 47.826 0.00 0.00 0.00 3.36
310 5133 3.131396 CCAACTAGTGAACAAAGCGTCT 58.869 45.455 0.00 0.00 0.00 4.18
311 5134 2.870411 ACCAACTAGTGAACAAAGCGTC 59.130 45.455 0.00 0.00 0.00 5.19
312 5135 2.870411 GACCAACTAGTGAACAAAGCGT 59.130 45.455 0.00 0.00 0.00 5.07
313 5136 2.869801 TGACCAACTAGTGAACAAAGCG 59.130 45.455 0.00 0.00 0.00 4.68
314 5137 4.893424 TTGACCAACTAGTGAACAAAGC 57.107 40.909 0.00 0.00 0.00 3.51
315 5138 9.003658 AGATTATTGACCAACTAGTGAACAAAG 57.996 33.333 0.00 0.00 0.00 2.77
432 8672 2.779755 TTAAAGATCTCGCAAGGCCA 57.220 45.000 5.01 0.00 38.47 5.36
433 8673 3.440522 AGTTTTAAAGATCTCGCAAGGCC 59.559 43.478 0.00 0.00 38.47 5.19
457 8697 0.457851 CCAGTCTTCTAGCCAGTCGG 59.542 60.000 0.00 0.00 0.00 4.79
461 8701 3.409026 ACAAACCAGTCTTCTAGCCAG 57.591 47.619 0.00 0.00 0.00 4.85
462 8702 4.262894 CCTTACAAACCAGTCTTCTAGCCA 60.263 45.833 0.00 0.00 0.00 4.75
491 8735 2.753452 TCTCTGAAGTACGGTAGCAAGG 59.247 50.000 0.00 0.00 0.00 3.61
672 10605 5.699458 CCACACCGAACTACTACTGAAAATT 59.301 40.000 0.00 0.00 0.00 1.82
840 11385 3.048600 TCTCTAGTGGGCTGCCATTTAT 58.951 45.455 22.05 3.72 0.00 1.40
859 11404 4.636206 GGACAAGGCTCACGAAATTTATCT 59.364 41.667 0.00 0.00 0.00 1.98
910 11458 5.790593 ACTGAAAGCTGAAAATCAATGCAT 58.209 33.333 0.00 0.00 37.60 3.96
917 11465 9.468532 AATGTTAGAAACTGAAAGCTGAAAATC 57.531 29.630 0.00 0.00 37.60 2.17
958 11510 1.133792 AGAGGTCCACCCAAAACACTG 60.134 52.381 0.00 0.00 36.42 3.66
986 11538 1.202177 CCGCCATGGATCAGAAAAACG 60.202 52.381 18.40 4.92 42.00 3.60
991 11543 1.998444 ATGGCCGCCATGGATCAGAA 61.998 55.000 24.52 0.00 43.39 3.02
1059 11611 3.553096 GGATTAGTACAGCCTCATCCGTG 60.553 52.174 0.00 0.00 28.40 4.94
1071 11623 4.233521 TCTTCCACCCCTAGGATTAGTACA 59.766 45.833 11.48 0.00 34.56 2.90
1072 11624 4.812653 TCTTCCACCCCTAGGATTAGTAC 58.187 47.826 11.48 0.00 34.56 2.73
1114 11667 3.927142 CACTGAATTAGTTCCACTCGTCC 59.073 47.826 0.00 0.00 37.60 4.79
1152 11705 3.504134 GCTCTTTTGTCCTCCTTTTCTCC 59.496 47.826 0.00 0.00 0.00 3.71
1326 11879 5.916883 CACTATGTTGCAAAAACAAGAGGAG 59.083 40.000 0.00 0.00 33.42 3.69
1428 11981 6.047231 AGGTTGTGTACTACTGTTGAAAGTC 58.953 40.000 0.00 0.00 0.00 3.01
1456 12009 1.732941 TTGGATGTCGGACCATTTCG 58.267 50.000 5.55 0.00 36.02 3.46
1467 12020 5.063564 GGAACGTCTTATCAGTTTGGATGTC 59.936 44.000 0.00 0.00 0.00 3.06
1486 12039 0.868406 GGCTCAACAAGAGTGGAACG 59.132 55.000 0.00 0.00 46.47 3.95
1599 12152 1.512926 CAACTCCTCCAGTTCCAACG 58.487 55.000 0.00 0.00 44.14 4.10
1718 12271 6.224584 CGAAGAACCTCCTTAAGAAGAGTTT 58.775 40.000 3.36 0.00 0.00 2.66
1731 12284 3.877508 CACCAATATTCCGAAGAACCTCC 59.122 47.826 0.00 0.00 33.97 4.30
1740 12293 3.274095 TGATGCACACCAATATTCCGA 57.726 42.857 0.00 0.00 0.00 4.55
1804 12357 7.423844 AGAAACTCTTCCCTTCAATTGTTTT 57.576 32.000 5.13 0.00 31.28 2.43
1859 12413 6.208994 AGGTCTTAATAGATCCGTCCATACAC 59.791 42.308 0.00 0.00 31.42 2.90
1900 12460 7.126573 TGTGGTTACCAATATTACTCCAGATGA 59.873 37.037 5.33 0.00 34.18 2.92
1905 12465 5.187381 TCGTGTGGTTACCAATATTACTCCA 59.813 40.000 5.33 0.00 34.18 3.86
1947 12507 4.828939 TGGGTATACCGTACACCTATTCTG 59.171 45.833 15.80 0.00 44.64 3.02
1961 12521 5.061920 GAGATCAACTCGATGGGTATACC 57.938 47.826 13.99 13.99 35.84 2.73
2010 12570 6.373005 TCAATGTTCATACTCCTCCAAAGA 57.627 37.500 0.00 0.00 0.00 2.52
2049 12609 9.308000 TCAATCCCTGTGTTTCTTAAATTATGT 57.692 29.630 0.00 0.00 0.00 2.29
2052 12612 9.753674 ATCTCAATCCCTGTGTTTCTTAAATTA 57.246 29.630 0.00 0.00 0.00 1.40
2140 12700 4.261825 CCACTCATTCTCCGTTAGATCTCC 60.262 50.000 0.00 0.00 33.05 3.71
2196 12756 7.254829 CCTTCTATTTCATCAGAGAGCATGTTG 60.255 40.741 0.00 0.00 0.00 3.33
2227 12787 6.014413 AGCAACTCATCATAGCTCAGATACAT 60.014 38.462 0.00 0.00 0.00 2.29
2235 12795 2.558378 TGCAGCAACTCATCATAGCTC 58.442 47.619 0.00 0.00 32.35 4.09
2252 12812 2.238942 ACACTGTTTCAGACGATGCA 57.761 45.000 3.70 0.00 35.18 3.96
2293 12853 7.445121 TCATGCCGAATGATAGAATCTTTAGT 58.555 34.615 0.00 0.00 40.50 2.24
2385 12945 7.566569 ACACTGAGTAGTACTCTTCTGCTATA 58.433 38.462 26.60 6.47 45.27 1.31
2405 12965 7.043454 TCACAAAACGAAAATCAAAACACTG 57.957 32.000 0.00 0.00 0.00 3.66
2406 12966 7.826260 ATCACAAAACGAAAATCAAAACACT 57.174 28.000 0.00 0.00 0.00 3.55
2407 12967 8.873242 AAATCACAAAACGAAAATCAAAACAC 57.127 26.923 0.00 0.00 0.00 3.32
2408 12968 9.884465 AAAAATCACAAAACGAAAATCAAAACA 57.116 22.222 0.00 0.00 0.00 2.83
2411 12971 9.965748 GAGAAAAATCACAAAACGAAAATCAAA 57.034 25.926 0.00 0.00 0.00 2.69
2412 12972 8.317460 CGAGAAAAATCACAAAACGAAAATCAA 58.683 29.630 0.00 0.00 0.00 2.57
2413 12973 7.514435 GCGAGAAAAATCACAAAACGAAAATCA 60.514 33.333 0.00 0.00 0.00 2.57
2414 12974 6.780961 GCGAGAAAAATCACAAAACGAAAATC 59.219 34.615 0.00 0.00 0.00 2.17
2415 12975 6.292114 GGCGAGAAAAATCACAAAACGAAAAT 60.292 34.615 0.00 0.00 0.00 1.82
2416 12976 5.004916 GGCGAGAAAAATCACAAAACGAAAA 59.995 36.000 0.00 0.00 0.00 2.29
2417 12977 4.501198 GGCGAGAAAAATCACAAAACGAAA 59.499 37.500 0.00 0.00 0.00 3.46
2418 12978 4.039032 GGCGAGAAAAATCACAAAACGAA 58.961 39.130 0.00 0.00 0.00 3.85
2419 12979 3.549221 GGGCGAGAAAAATCACAAAACGA 60.549 43.478 0.00 0.00 0.00 3.85
2420 12980 2.724174 GGGCGAGAAAAATCACAAAACG 59.276 45.455 0.00 0.00 0.00 3.60
2421 12981 3.977427 AGGGCGAGAAAAATCACAAAAC 58.023 40.909 0.00 0.00 0.00 2.43
2422 12982 4.217550 CCTAGGGCGAGAAAAATCACAAAA 59.782 41.667 0.00 0.00 0.00 2.44
2423 12983 3.756434 CCTAGGGCGAGAAAAATCACAAA 59.244 43.478 0.00 0.00 0.00 2.83
2424 12984 3.343617 CCTAGGGCGAGAAAAATCACAA 58.656 45.455 0.00 0.00 0.00 3.33
2425 12985 2.939640 GCCTAGGGCGAGAAAAATCACA 60.940 50.000 11.72 0.00 39.62 3.58
2426 12986 1.671328 GCCTAGGGCGAGAAAAATCAC 59.329 52.381 11.72 0.00 39.62 3.06
2427 12987 2.038387 GCCTAGGGCGAGAAAAATCA 57.962 50.000 11.72 0.00 39.62 2.57
2446 13006 1.934463 CGAAATTCGGCCATCTCGG 59.066 57.895 7.61 0.00 36.00 4.63
2456 13016 8.959761 AAATTTTTAAAAACGACCGAAATTCG 57.040 26.923 15.35 8.62 42.36 3.34
2457 13017 9.073266 CGAAATTTTTAAAAACGACCGAAATTC 57.927 29.630 15.35 8.09 0.00 2.17
2458 13018 8.057156 CCGAAATTTTTAAAAACGACCGAAATT 58.943 29.630 15.35 0.63 0.00 1.82
2459 13019 7.557285 CCGAAATTTTTAAAAACGACCGAAAT 58.443 30.769 15.35 0.00 0.00 2.17
2460 13020 6.507614 GCCGAAATTTTTAAAAACGACCGAAA 60.508 34.615 15.35 0.00 0.00 3.46
2461 13021 5.051841 GCCGAAATTTTTAAAAACGACCGAA 60.052 36.000 15.35 0.00 0.00 4.30
2462 13022 4.440431 GCCGAAATTTTTAAAAACGACCGA 59.560 37.500 15.35 0.00 0.00 4.69
2463 13023 4.375205 GGCCGAAATTTTTAAAAACGACCG 60.375 41.667 15.35 14.74 0.00 4.79
2464 13024 4.375205 CGGCCGAAATTTTTAAAAACGACC 60.375 41.667 24.07 14.43 0.00 4.79
2465 13025 4.440431 TCGGCCGAAATTTTTAAAAACGAC 59.560 37.500 28.99 7.56 0.00 4.34
2466 13026 4.604976 TCGGCCGAAATTTTTAAAAACGA 58.395 34.783 28.99 14.06 0.00 3.85
2467 13027 4.950654 TCGGCCGAAATTTTTAAAAACG 57.049 36.364 28.99 13.78 0.00 3.60
2479 13039 1.319541 TGGTCAAATTTCGGCCGAAA 58.680 45.000 44.99 44.99 46.37 3.46
2480 13040 1.319541 TTGGTCAAATTTCGGCCGAA 58.680 45.000 35.81 35.81 0.00 4.30
2481 13041 1.319541 TTTGGTCAAATTTCGGCCGA 58.680 45.000 27.28 27.28 0.00 5.54
2482 13042 2.362169 ATTTGGTCAAATTTCGGCCG 57.638 45.000 22.12 22.12 37.74 6.13
2524 13084 8.672815 GGTCAAATTTGAGAAATTTTGGTCAAA 58.327 29.630 21.05 18.75 46.01 2.69
2525 13085 7.826252 TGGTCAAATTTGAGAAATTTTGGTCAA 59.174 29.630 21.05 7.23 46.01 3.18
2526 13086 7.334090 TGGTCAAATTTGAGAAATTTTGGTCA 58.666 30.769 21.05 3.51 46.01 4.02
2527 13087 7.784633 TGGTCAAATTTGAGAAATTTTGGTC 57.215 32.000 21.05 4.97 46.01 4.02
2528 13088 8.750515 ATTGGTCAAATTTGAGAAATTTTGGT 57.249 26.923 21.05 0.80 46.01 3.67
2531 13091 9.934190 CGAAATTGGTCAAATTTGAGAAATTTT 57.066 25.926 30.89 22.60 46.01 1.82
2532 13092 8.558700 CCGAAATTGGTCAAATTTGAGAAATTT 58.441 29.630 30.86 30.86 46.29 1.82
2533 13093 7.307930 GCCGAAATTGGTCAAATTTGAGAAATT 60.308 33.333 21.05 22.40 46.29 1.82
2534 13094 6.147656 GCCGAAATTGGTCAAATTTGAGAAAT 59.852 34.615 21.05 18.58 46.29 2.17
2535 13095 5.465056 GCCGAAATTGGTCAAATTTGAGAAA 59.535 36.000 21.05 17.28 46.29 2.52
2536 13096 4.987912 GCCGAAATTGGTCAAATTTGAGAA 59.012 37.500 21.05 16.20 46.29 2.87
2537 13097 4.555262 GCCGAAATTGGTCAAATTTGAGA 58.445 39.130 21.05 10.65 46.29 3.27
2538 13098 3.364621 CGCCGAAATTGGTCAAATTTGAG 59.635 43.478 21.05 7.43 46.29 3.02
2539 13099 3.312828 CGCCGAAATTGGTCAAATTTGA 58.687 40.909 16.91 16.91 46.29 2.69
2540 13100 2.411409 CCGCCGAAATTGGTCAAATTTG 59.589 45.455 12.15 12.15 46.29 2.32
2542 13102 1.889829 TCCGCCGAAATTGGTCAAATT 59.110 42.857 0.00 0.00 40.32 1.82
2543 13103 1.540267 TCCGCCGAAATTGGTCAAAT 58.460 45.000 0.00 0.00 0.00 2.32
2544 13104 1.268352 CTTCCGCCGAAATTGGTCAAA 59.732 47.619 0.00 0.00 0.00 2.69
2545 13105 0.878416 CTTCCGCCGAAATTGGTCAA 59.122 50.000 0.00 0.00 0.00 3.18
2546 13106 0.035598 TCTTCCGCCGAAATTGGTCA 59.964 50.000 0.00 0.00 0.00 4.02
2547 13107 1.379527 ATCTTCCGCCGAAATTGGTC 58.620 50.000 0.00 0.00 0.00 4.02
2548 13108 2.169769 TCTATCTTCCGCCGAAATTGGT 59.830 45.455 0.00 0.00 0.00 3.67
2549 13109 2.833794 TCTATCTTCCGCCGAAATTGG 58.166 47.619 0.00 0.00 0.00 3.16
2550 13110 5.424121 AAATCTATCTTCCGCCGAAATTG 57.576 39.130 0.00 0.00 0.00 2.32
2551 13111 4.211374 CGAAATCTATCTTCCGCCGAAATT 59.789 41.667 0.00 0.00 0.00 1.82
2552 13112 3.741344 CGAAATCTATCTTCCGCCGAAAT 59.259 43.478 0.00 0.00 0.00 2.17
2553 13113 3.120792 CGAAATCTATCTTCCGCCGAAA 58.879 45.455 0.00 0.00 0.00 3.46
2554 13114 2.739292 CGAAATCTATCTTCCGCCGAA 58.261 47.619 0.00 0.00 0.00 4.30
2555 13115 1.602165 GCGAAATCTATCTTCCGCCGA 60.602 52.381 0.00 0.00 0.00 5.54
2556 13116 0.784778 GCGAAATCTATCTTCCGCCG 59.215 55.000 0.00 0.00 0.00 6.46
2557 13117 1.149148 GGCGAAATCTATCTTCCGCC 58.851 55.000 7.84 7.84 36.26 6.13
2558 13118 1.149148 GGGCGAAATCTATCTTCCGC 58.851 55.000 0.00 0.00 0.00 5.54
2559 13119 2.821991 AGGGCGAAATCTATCTTCCG 57.178 50.000 0.00 0.00 0.00 4.30
2560 13120 3.617775 GCCTAGGGCGAAATCTATCTTCC 60.618 52.174 11.72 0.00 39.62 3.46
2561 13121 3.591023 GCCTAGGGCGAAATCTATCTTC 58.409 50.000 11.72 0.00 39.62 2.87
2562 13122 3.686916 GCCTAGGGCGAAATCTATCTT 57.313 47.619 11.72 0.00 39.62 2.40
2582 13142 1.512926 CCGAATTTAGGCCATCTCGG 58.487 55.000 5.01 11.40 39.79 4.63
2591 13151 2.294074 TGGATTTCGGCCGAATTTAGG 58.706 47.619 38.89 1.93 33.79 2.69
2592 13152 4.568152 AATGGATTTCGGCCGAATTTAG 57.432 40.909 38.89 2.81 33.79 1.85
2593 13153 4.993029 AAATGGATTTCGGCCGAATTTA 57.007 36.364 38.89 25.97 33.79 1.40
2594 13154 3.885724 AAATGGATTTCGGCCGAATTT 57.114 38.095 38.89 30.43 33.79 1.82
2595 13155 3.885724 AAAATGGATTTCGGCCGAATT 57.114 38.095 38.89 34.04 33.79 2.17
2596 13156 3.885724 AAAAATGGATTTCGGCCGAAT 57.114 38.095 38.89 27.72 33.79 3.34
2613 13173 4.507021 GGTTTTGAATTTCGGCCGTAAAAA 59.493 37.500 27.15 18.89 0.00 1.94
2614 13174 4.049869 GGTTTTGAATTTCGGCCGTAAAA 58.950 39.130 27.15 19.68 0.00 1.52
2615 13175 3.552478 GGGTTTTGAATTTCGGCCGTAAA 60.552 43.478 27.15 22.80 0.00 2.01
2616 13176 2.030096 GGGTTTTGAATTTCGGCCGTAA 60.030 45.455 27.15 23.35 0.00 3.18
2617 13177 1.540707 GGGTTTTGAATTTCGGCCGTA 59.459 47.619 27.15 14.12 0.00 4.02
2618 13178 0.315886 GGGTTTTGAATTTCGGCCGT 59.684 50.000 27.15 5.04 0.00 5.68
2619 13179 0.601057 AGGGTTTTGAATTTCGGCCG 59.399 50.000 22.12 22.12 0.00 6.13
2620 13180 2.823747 ACTAGGGTTTTGAATTTCGGCC 59.176 45.455 0.00 0.00 0.00 6.13
2621 13181 4.698780 AGTACTAGGGTTTTGAATTTCGGC 59.301 41.667 0.00 0.00 0.00 5.54
2622 13182 7.101700 AGTAGTACTAGGGTTTTGAATTTCGG 58.898 38.462 1.87 0.00 0.00 4.30
2623 13183 9.080915 GTAGTAGTACTAGGGTTTTGAATTTCG 57.919 37.037 10.38 0.00 30.12 3.46
2624 13184 9.080915 CGTAGTAGTACTAGGGTTTTGAATTTC 57.919 37.037 18.34 0.00 34.06 2.17
2625 13185 8.806146 TCGTAGTAGTACTAGGGTTTTGAATTT 58.194 33.333 23.27 0.00 37.23 1.82
2626 13186 8.353423 TCGTAGTAGTACTAGGGTTTTGAATT 57.647 34.615 23.27 0.00 37.23 2.17
2627 13187 7.416101 GCTCGTAGTAGTACTAGGGTTTTGAAT 60.416 40.741 23.27 0.00 37.23 2.57
2628 13188 6.127897 GCTCGTAGTAGTACTAGGGTTTTGAA 60.128 42.308 23.27 7.38 37.23 2.69
2629 13189 5.355350 GCTCGTAGTAGTACTAGGGTTTTGA 59.645 44.000 23.27 7.94 37.23 2.69
2630 13190 5.356470 AGCTCGTAGTAGTACTAGGGTTTTG 59.644 44.000 23.27 13.02 37.23 2.44
2631 13191 5.504853 AGCTCGTAGTAGTACTAGGGTTTT 58.495 41.667 23.27 9.47 37.23 2.43
2632 13192 5.109500 AGCTCGTAGTAGTACTAGGGTTT 57.891 43.478 23.27 10.80 37.23 3.27
2633 13193 4.769345 AGCTCGTAGTAGTACTAGGGTT 57.231 45.455 23.27 13.01 37.23 4.11
2634 13194 5.878406 TTAGCTCGTAGTAGTACTAGGGT 57.122 43.478 23.27 17.01 37.23 4.34
2635 13195 7.382110 TGTATTAGCTCGTAGTAGTACTAGGG 58.618 42.308 23.27 16.83 37.23 3.53
2636 13196 9.086336 GATGTATTAGCTCGTAGTAGTACTAGG 57.914 40.741 19.55 19.55 37.78 3.02
2637 13197 8.797215 CGATGTATTAGCTCGTAGTAGTACTAG 58.203 40.741 10.38 5.63 30.12 2.57
2638 13198 7.757173 CCGATGTATTAGCTCGTAGTAGTACTA 59.243 40.741 5.90 5.90 0.00 1.82
2680 13240 9.920946 TTCAGCCTAGTCAAAATTTATCCTATT 57.079 29.630 0.00 0.00 0.00 1.73
2690 13250 5.726980 TTTGCATTCAGCCTAGTCAAAAT 57.273 34.783 0.00 0.00 44.83 1.82
3141 13704 0.111061 TGCACAAGAGGGTCATTGCT 59.889 50.000 0.00 0.00 0.00 3.91
3199 13762 3.194620 TCCCTATGCCTTTTGGAACCTA 58.805 45.455 0.00 0.00 44.07 3.08
3364 13927 5.408604 GCACTGTATTTGTACTGCAGTAAGT 59.591 40.000 27.61 20.98 38.21 2.24
3367 13930 5.147330 AGCACTGTATTTGTACTGCAGTA 57.853 39.130 22.67 22.67 38.21 2.74


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

AutoCloner maintained by Alex Coulton.