Multiple sequence alignment - TraesCS1A01G199200

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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 TraesCS1A01G199200 chr1A 100.000 3317 0 0 1 3317 357788186 357791502 0.000000e+00 6126.0
1 TraesCS1A01G199200 chr1A 83.716 436 48 11 13 442 312612582 312612164 1.120000e-104 390.0
2 TraesCS1A01G199200 chr1A 100.000 69 0 0 3188 3256 357810879 357810947 9.660000e-26 128.0
3 TraesCS1A01G199200 chr1A 81.098 164 21 7 684 842 542720985 542721143 4.490000e-24 122.0
4 TraesCS1A01G199200 chr1A 100.000 60 0 0 3258 3317 567884485 567884544 9.730000e-21 111.0
5 TraesCS1A01G199200 chr1D 92.202 1462 58 18 967 2388 286642999 286644444 0.000000e+00 2017.0
6 TraesCS1A01G199200 chr1D 91.413 757 31 15 2459 3187 286644441 286645191 0.000000e+00 1007.0
7 TraesCS1A01G199200 chr1D 81.540 883 89 29 13 842 360358635 360359496 0.000000e+00 660.0
8 TraesCS1A01G199200 chr1D 77.556 802 128 30 76 844 464251163 464250381 1.410000e-118 436.0
9 TraesCS1A01G199200 chr1D 87.407 135 9 4 842 968 286642574 286642708 7.410000e-32 148.0
10 TraesCS1A01G199200 chr3B 98.819 847 6 1 1 843 159519538 159518692 0.000000e+00 1506.0
11 TraesCS1A01G199200 chr3B 83.916 429 46 11 13 435 739027868 739028279 4.010000e-104 388.0
12 TraesCS1A01G199200 chr3B 92.727 110 5 1 2074 2183 806016260 806016366 4.430000e-34 156.0
13 TraesCS1A01G199200 chr3B 100.000 67 0 0 3188 3254 73626133 73626067 1.250000e-24 124.0
14 TraesCS1A01G199200 chr3B 98.529 68 1 0 3250 3317 789061107 789061174 1.620000e-23 121.0
15 TraesCS1A01G199200 chr3B 98.507 67 1 0 3188 3254 73623036 73622970 5.810000e-23 119.0
16 TraesCS1A01G199200 chr3B 90.141 71 6 1 504 573 739028398 739028468 1.270000e-14 91.6
17 TraesCS1A01G199200 chr7B 95.564 834 35 2 11 843 363191291 363190459 0.000000e+00 1334.0
18 TraesCS1A01G199200 chr7B 81.109 884 82 33 13 843 376804294 376805145 2.170000e-176 628.0
19 TraesCS1A01G199200 chr7B 85.965 57 6 1 1638 1694 480856865 480856811 3.570000e-05 60.2
20 TraesCS1A01G199200 chrUn 94.598 833 44 1 11 842 153246990 153246158 0.000000e+00 1288.0
21 TraesCS1A01G199200 chr2A 85.080 878 90 13 8 849 669437044 669436172 0.000000e+00 857.0
22 TraesCS1A01G199200 chr2A 100.000 69 0 0 3188 3256 596410156 596410088 9.660000e-26 128.0
23 TraesCS1A01G199200 chr4B 83.819 686 64 19 193 843 626765795 626766468 2.830000e-170 608.0
24 TraesCS1A01G199200 chr2D 82.468 462 45 13 2 433 218270388 218270843 4.040000e-99 372.0
25 TraesCS1A01G199200 chr2D 81.319 273 38 8 480 745 274410047 274410313 3.350000e-50 209.0
26 TraesCS1A01G199200 chr2D 80.247 162 26 3 684 842 616125146 616125304 2.090000e-22 117.0
27 TraesCS1A01G199200 chr3A 82.529 435 44 12 13 441 616497320 616496912 1.460000e-93 353.0
28 TraesCS1A01G199200 chr3A 80.606 165 20 10 684 842 726680208 726680050 2.090000e-22 117.0
29 TraesCS1A01G199200 chr3A 100.000 60 0 0 3258 3317 741617417 741617476 9.730000e-21 111.0
30 TraesCS1A01G199200 chr5D 86.806 288 28 5 565 842 54719910 54720197 2.480000e-81 313.0
31 TraesCS1A01G199200 chr5D 84.194 310 31 3 143 435 54716017 54716325 5.420000e-73 285.0
32 TraesCS1A01G199200 chr7D 86.786 280 23 4 504 769 572186279 572186558 1.930000e-77 300.0
33 TraesCS1A01G199200 chr7D 95.385 65 3 0 3187 3251 313881184 313881248 1.630000e-18 104.0
34 TraesCS1A01G199200 chr7A 97.059 68 2 0 3186 3253 728231001 728231068 7.520000e-22 115.0
35 TraesCS1A01G199200 chr7A 97.015 67 2 0 3188 3254 728235675 728235741 2.700000e-21 113.0
36 TraesCS1A01G199200 chr5B 100.000 62 0 0 3256 3317 540483378 540483439 7.520000e-22 115.0
37 TraesCS1A01G199200 chr5B 98.333 60 1 0 3258 3317 530678225 530678284 4.530000e-19 106.0
38 TraesCS1A01G199200 chr1B 100.000 62 0 0 3256 3317 664606000 664605939 7.520000e-22 115.0
39 TraesCS1A01G199200 chr1B 100.000 58 0 0 3258 3315 196871039 196871096 1.260000e-19 108.0
40 TraesCS1A01G199200 chr1B 98.305 59 1 0 2713 2771 388874723 388874781 1.630000e-18 104.0
41 TraesCS1A01G199200 chr6D 97.015 67 2 0 3188 3254 73789919 73789853 2.700000e-21 113.0
42 TraesCS1A01G199200 chr2B 98.413 63 1 0 3255 3317 655824250 655824312 9.730000e-21 111.0
43 TraesCS1A01G199200 chr4D 95.588 68 3 0 3187 3254 163745497 163745564 3.500000e-20 110.0
44 TraesCS1A01G199200 chr4A 98.305 59 1 0 3259 3317 17335880 17335822 1.630000e-18 104.0


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 TraesCS1A01G199200 chr1A 357788186 357791502 3316 False 6126.000000 6126 100.000000 1 3317 1 chr1A.!!$F1 3316
1 TraesCS1A01G199200 chr1D 286642574 286645191 2617 False 1057.333333 2017 90.340667 842 3187 3 chr1D.!!$F2 2345
2 TraesCS1A01G199200 chr1D 360358635 360359496 861 False 660.000000 660 81.540000 13 842 1 chr1D.!!$F1 829
3 TraesCS1A01G199200 chr1D 464250381 464251163 782 True 436.000000 436 77.556000 76 844 1 chr1D.!!$R1 768
4 TraesCS1A01G199200 chr3B 159518692 159519538 846 True 1506.000000 1506 98.819000 1 843 1 chr3B.!!$R1 842
5 TraesCS1A01G199200 chr3B 739027868 739028468 600 False 239.800000 388 87.028500 13 573 2 chr3B.!!$F3 560
6 TraesCS1A01G199200 chr7B 363190459 363191291 832 True 1334.000000 1334 95.564000 11 843 1 chr7B.!!$R1 832
7 TraesCS1A01G199200 chr7B 376804294 376805145 851 False 628.000000 628 81.109000 13 843 1 chr7B.!!$F1 830
8 TraesCS1A01G199200 chrUn 153246158 153246990 832 True 1288.000000 1288 94.598000 11 842 1 chrUn.!!$R1 831
9 TraesCS1A01G199200 chr2A 669436172 669437044 872 True 857.000000 857 85.080000 8 849 1 chr2A.!!$R2 841
10 TraesCS1A01G199200 chr4B 626765795 626766468 673 False 608.000000 608 83.819000 193 843 1 chr4B.!!$F1 650
11 TraesCS1A01G199200 chr5D 54716017 54720197 4180 False 299.000000 313 85.500000 143 842 2 chr5D.!!$F1 699

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
824 4434 0.10576 TTGCCCAGGCTCCAGAAAAA 60.106 50.0 10.58 0.0 42.51 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2565 6536 0.034059 CGAGGCTGTTCTGGTTCTGT 59.966 55.0 0.0 0.0 0.0 3.41 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.406060 CTGATACGCACACGCACGC 62.406 63.158 0.00 0.00 45.53 5.34
54 56 5.865013 TGTTAATCGATGTTTCTGTTCGCTA 59.135 36.000 0.00 0.00 33.08 4.26
824 4434 0.105760 TTGCCCAGGCTCCAGAAAAA 60.106 50.000 10.58 0.00 42.51 1.94
872 4482 4.460873 GCACCAAAGCGCGCCTAC 62.461 66.667 30.33 6.80 0.00 3.18
896 4506 2.514592 CGACCAGCCATCGCCAAT 60.515 61.111 0.00 0.00 34.57 3.16
897 4507 2.114670 CGACCAGCCATCGCCAATT 61.115 57.895 0.00 0.00 34.57 2.32
908 4518 0.746204 TCGCCAATTCGCCATTGCTA 60.746 50.000 2.46 0.00 41.10 3.49
912 4522 2.571212 CCAATTCGCCATTGCTACCTA 58.429 47.619 2.46 0.00 41.10 3.08
913 4523 2.948979 CCAATTCGCCATTGCTACCTAA 59.051 45.455 2.46 0.00 41.10 2.69
914 4524 3.003689 CCAATTCGCCATTGCTACCTAAG 59.996 47.826 2.46 0.00 41.10 2.18
916 4526 3.343941 TTCGCCATTGCTACCTAAGTT 57.656 42.857 0.00 0.00 34.43 2.66
917 4527 4.475051 TTCGCCATTGCTACCTAAGTTA 57.525 40.909 0.00 0.00 34.43 2.24
918 4528 4.054780 TCGCCATTGCTACCTAAGTTAG 57.945 45.455 2.65 2.65 34.43 2.34
919 4529 2.544267 CGCCATTGCTACCTAAGTTAGC 59.456 50.000 4.22 0.00 37.35 3.09
920 4530 2.879026 GCCATTGCTACCTAAGTTAGCC 59.121 50.000 4.22 0.00 36.09 3.93
922 4532 3.877508 CCATTGCTACCTAAGTTAGCCAC 59.122 47.826 4.22 0.00 36.09 5.01
951 4569 3.760035 AGTCGCCGCCAAGACGAT 61.760 61.111 0.00 0.00 41.86 3.73
981 4891 2.507992 CGAGAGCCAGAGCAACCG 60.508 66.667 0.00 0.00 43.56 4.44
984 4894 1.882989 GAGAGCCAGAGCAACCGAGT 61.883 60.000 0.00 0.00 43.56 4.18
1065 4975 1.447838 CTACCGCAACGTCTGGCAT 60.448 57.895 7.45 0.00 0.00 4.40
1078 4988 1.610967 TGGCATACCGACCTCACCA 60.611 57.895 0.00 0.00 39.70 4.17
1079 4989 1.195442 TGGCATACCGACCTCACCAA 61.195 55.000 0.00 0.00 39.70 3.67
1106 5016 1.754234 AGGCGGATTTCCCATGTGC 60.754 57.895 0.00 0.00 34.14 4.57
1116 5026 4.431416 TTTCCCATGTGCGTATCCTATT 57.569 40.909 0.00 0.00 0.00 1.73
1119 5029 3.646162 TCCCATGTGCGTATCCTATTCTT 59.354 43.478 0.00 0.00 0.00 2.52
1133 5043 8.994170 GTATCCTATTCTTCCAACTTATGAAGC 58.006 37.037 0.00 0.00 0.00 3.86
1139 5053 5.178797 TCTTCCAACTTATGAAGCAGTAGC 58.821 41.667 0.00 0.00 42.56 3.58
1177 5092 3.643792 AGATATGCCAGGACCTGACTTAC 59.356 47.826 23.77 9.32 32.44 2.34
1184 5099 4.461198 CCAGGACCTGACTTACTTTTTGT 58.539 43.478 23.77 0.00 32.44 2.83
1188 5103 5.104485 AGGACCTGACTTACTTTTTGTGTCT 60.104 40.000 0.00 0.00 0.00 3.41
1198 5113 9.758651 ACTTACTTTTTGTGTCTTTTTGTTCTT 57.241 25.926 0.00 0.00 0.00 2.52
1255 5170 0.741221 GAGTGGGCACTGTTCCGATC 60.741 60.000 0.00 0.00 42.66 3.69
1259 5174 1.617947 GGGCACTGTTCCGATCCTCT 61.618 60.000 0.00 0.00 0.00 3.69
1278 5209 3.225177 CTGGATCCCAGCTGATGAATT 57.775 47.619 17.39 0.00 45.13 2.17
1286 5217 5.569355 TCCCAGCTGATGAATTCTAACAAA 58.431 37.500 17.39 0.00 0.00 2.83
1287 5218 6.189859 TCCCAGCTGATGAATTCTAACAAAT 58.810 36.000 17.39 0.00 0.00 2.32
1288 5219 6.095860 TCCCAGCTGATGAATTCTAACAAATG 59.904 38.462 17.39 5.87 0.00 2.32
1306 5237 7.985634 ACAAATGTGTATCTGTTTTGTGTTC 57.014 32.000 0.00 0.00 38.64 3.18
1388 5327 2.301870 ACATGTCGAGGTGAGGCTTAAA 59.698 45.455 0.00 0.00 0.00 1.52
1392 5331 3.751175 TGTCGAGGTGAGGCTTAAATTTG 59.249 43.478 0.00 0.00 0.00 2.32
1396 5335 5.354234 TCGAGGTGAGGCTTAAATTTGATTC 59.646 40.000 0.00 0.00 0.00 2.52
1426 5368 8.110860 AGTATTTCCTTTGATTTGTACTGGTG 57.889 34.615 0.00 0.00 0.00 4.17
1452 5394 3.676093 TCTCTGTTCTTCAGTCTCGCTA 58.324 45.455 0.00 0.00 43.97 4.26
1483 5425 1.338337 CTCTGTCGGCGTTCCAGATAT 59.662 52.381 20.42 0.00 34.90 1.63
1604 5553 2.834549 TCTTCTACCTCTTGGCCTCTTG 59.165 50.000 3.32 0.00 36.63 3.02
1612 5561 3.442977 CCTCTTGGCCTCTTGATTTTCAG 59.557 47.826 3.32 0.00 0.00 3.02
1631 5580 2.611292 CAGCTCTGATCAACCGGATTTC 59.389 50.000 9.46 0.00 36.00 2.17
1736 5685 2.923655 CGACAACTGCATCATCGTACTT 59.076 45.455 0.00 0.00 0.00 2.24
1737 5686 4.102649 CGACAACTGCATCATCGTACTTA 58.897 43.478 0.00 0.00 0.00 2.24
1738 5687 4.027621 CGACAACTGCATCATCGTACTTAC 60.028 45.833 0.00 0.00 0.00 2.34
1739 5688 4.181578 ACAACTGCATCATCGTACTTACC 58.818 43.478 0.00 0.00 0.00 2.85
1740 5689 4.180817 CAACTGCATCATCGTACTTACCA 58.819 43.478 0.00 0.00 0.00 3.25
1741 5690 3.782046 ACTGCATCATCGTACTTACCAC 58.218 45.455 0.00 0.00 0.00 4.16
1742 5691 3.123804 CTGCATCATCGTACTTACCACC 58.876 50.000 0.00 0.00 0.00 4.61
1743 5692 2.498078 TGCATCATCGTACTTACCACCA 59.502 45.455 0.00 0.00 0.00 4.17
1744 5693 3.133901 TGCATCATCGTACTTACCACCAT 59.866 43.478 0.00 0.00 0.00 3.55
1745 5694 3.741344 GCATCATCGTACTTACCACCATC 59.259 47.826 0.00 0.00 0.00 3.51
1757 5706 0.464373 CCACCATCACCTCATTCCCG 60.464 60.000 0.00 0.00 0.00 5.14
1762 5711 1.630126 ATCACCTCATTCCCGCTGCT 61.630 55.000 0.00 0.00 0.00 4.24
1764 5713 0.107456 CACCTCATTCCCGCTGCTAT 59.893 55.000 0.00 0.00 0.00 2.97
1765 5714 0.394565 ACCTCATTCCCGCTGCTATC 59.605 55.000 0.00 0.00 0.00 2.08
1766 5715 0.683973 CCTCATTCCCGCTGCTATCT 59.316 55.000 0.00 0.00 0.00 1.98
1781 5730 5.560953 GCTGCTATCTTCGTTTCACAACTTT 60.561 40.000 0.00 0.00 0.00 2.66
1785 5734 4.014847 TCTTCGTTTCACAACTTTGCAG 57.985 40.909 0.00 0.00 0.00 4.41
1791 5740 4.432712 GTTTCACAACTTTGCAGGTGATT 58.567 39.130 0.00 0.00 40.69 2.57
1793 5742 6.215845 GTTTCACAACTTTGCAGGTGATTAT 58.784 36.000 0.00 0.00 40.69 1.28
1794 5743 7.367285 GTTTCACAACTTTGCAGGTGATTATA 58.633 34.615 0.00 0.00 40.69 0.98
1795 5744 7.517614 TTCACAACTTTGCAGGTGATTATAA 57.482 32.000 0.00 0.00 40.69 0.98
1796 5745 6.908825 TCACAACTTTGCAGGTGATTATAAC 58.091 36.000 0.00 0.00 40.69 1.89
1798 5747 7.230510 TCACAACTTTGCAGGTGATTATAACTT 59.769 33.333 0.00 0.00 40.69 2.66
1800 5749 8.512138 ACAACTTTGCAGGTGATTATAACTTAC 58.488 33.333 0.00 0.00 40.69 2.34
1809 5758 7.711339 CAGGTGATTATAACTTACCTCTGAACC 59.289 40.741 12.02 0.00 39.63 3.62
1819 5768 1.235724 CCTCTGAACCCGTTTTGGTC 58.764 55.000 0.00 0.00 37.76 4.02
1906 5855 1.811266 CATCGTCGGCAACCAGGAG 60.811 63.158 0.00 0.00 0.00 3.69
1946 5895 1.377366 GATCTCCTGCGTCTCCGACA 61.377 60.000 0.00 0.00 35.63 4.35
1965 5914 1.131883 CACGGTCTACTGGACGTAAGG 59.868 57.143 0.00 0.00 45.35 2.69
2003 5952 1.969923 CCCAGGCCATTTGAAGAAACA 59.030 47.619 5.01 0.00 0.00 2.83
2066 6015 1.599071 CTGTATGCAGGTAATGGCACG 59.401 52.381 2.35 0.00 43.75 5.34
2074 6023 1.644786 GGTAATGGCACGCGAGCTTT 61.645 55.000 26.94 21.41 34.17 3.51
2083 6032 2.097349 GCGAGCTTTGCTTCGCTC 59.903 61.111 20.20 10.37 44.73 5.03
2096 6045 2.032178 GCTTCGCTCAAACAACTGAAGT 59.968 45.455 0.00 0.00 36.19 3.01
2103 6052 6.092944 TCGCTCAAACAACTGAAGTTTTCTTA 59.907 34.615 0.00 0.00 40.61 2.10
2155 6104 0.586802 CTGACACGGCGATCGATCTA 59.413 55.000 21.57 0.00 42.43 1.98
2202 6151 1.208293 GTGGAGATGGACAAGAGGGAC 59.792 57.143 0.00 0.00 0.00 4.46
2253 6202 1.213733 CTCCGATGCAGCAGATGTCG 61.214 60.000 1.53 8.84 0.00 4.35
2388 6337 9.149225 GATCAAGTAGCTGATATTATGTTCCTG 57.851 37.037 0.00 0.00 36.15 3.86
2389 6338 8.023021 TCAAGTAGCTGATATTATGTTCCTGT 57.977 34.615 0.00 0.00 0.00 4.00
2391 6340 9.113838 CAAGTAGCTGATATTATGTTCCTGTTT 57.886 33.333 0.00 0.00 0.00 2.83
2392 6341 8.668510 AGTAGCTGATATTATGTTCCTGTTTG 57.331 34.615 0.00 0.00 0.00 2.93
2394 6343 9.542462 GTAGCTGATATTATGTTCCTGTTTGTA 57.458 33.333 0.00 0.00 0.00 2.41
2396 6345 9.060347 AGCTGATATTATGTTCCTGTTTGTATG 57.940 33.333 0.00 0.00 0.00 2.39
2397 6346 7.805071 GCTGATATTATGTTCCTGTTTGTATGC 59.195 37.037 0.00 0.00 0.00 3.14
2398 6347 8.165239 TGATATTATGTTCCTGTTTGTATGCC 57.835 34.615 0.00 0.00 0.00 4.40
2399 6348 7.777440 TGATATTATGTTCCTGTTTGTATGCCA 59.223 33.333 0.00 0.00 0.00 4.92
2400 6349 8.710749 ATATTATGTTCCTGTTTGTATGCCAT 57.289 30.769 0.00 0.00 0.00 4.40
2401 6350 6.849085 TTATGTTCCTGTTTGTATGCCATT 57.151 33.333 0.00 0.00 0.00 3.16
2402 6351 4.517952 TGTTCCTGTTTGTATGCCATTG 57.482 40.909 0.00 0.00 0.00 2.82
2403 6352 3.894427 TGTTCCTGTTTGTATGCCATTGT 59.106 39.130 0.00 0.00 0.00 2.71
2404 6353 4.236935 GTTCCTGTTTGTATGCCATTGTG 58.763 43.478 0.00 0.00 0.00 3.33
2405 6354 3.760738 TCCTGTTTGTATGCCATTGTGA 58.239 40.909 0.00 0.00 0.00 3.58
2406 6355 3.505680 TCCTGTTTGTATGCCATTGTGAC 59.494 43.478 0.00 0.00 0.00 3.67
2407 6356 3.507233 CCTGTTTGTATGCCATTGTGACT 59.493 43.478 0.00 0.00 0.00 3.41
2408 6357 4.022068 CCTGTTTGTATGCCATTGTGACTT 60.022 41.667 0.00 0.00 0.00 3.01
2409 6358 4.869215 TGTTTGTATGCCATTGTGACTTG 58.131 39.130 0.00 0.00 0.00 3.16
2410 6359 4.582240 TGTTTGTATGCCATTGTGACTTGA 59.418 37.500 0.00 0.00 0.00 3.02
2411 6360 5.243507 TGTTTGTATGCCATTGTGACTTGAT 59.756 36.000 0.00 0.00 0.00 2.57
2412 6361 5.981088 TTGTATGCCATTGTGACTTGATT 57.019 34.783 0.00 0.00 0.00 2.57
2413 6362 5.981088 TGTATGCCATTGTGACTTGATTT 57.019 34.783 0.00 0.00 0.00 2.17
2414 6363 6.343716 TGTATGCCATTGTGACTTGATTTT 57.656 33.333 0.00 0.00 0.00 1.82
2415 6364 6.757237 TGTATGCCATTGTGACTTGATTTTT 58.243 32.000 0.00 0.00 0.00 1.94
2439 6388 7.707624 TTTTTGAGAGGCATTATGACTTGAT 57.292 32.000 0.61 0.00 34.53 2.57
2440 6389 7.707624 TTTTGAGAGGCATTATGACTTGATT 57.292 32.000 0.61 0.00 34.53 2.57
2441 6390 7.707624 TTTGAGAGGCATTATGACTTGATTT 57.292 32.000 0.61 0.00 34.53 2.17
2442 6391 8.806429 TTTGAGAGGCATTATGACTTGATTTA 57.194 30.769 0.61 0.00 34.53 1.40
2443 6392 8.985315 TTGAGAGGCATTATGACTTGATTTAT 57.015 30.769 0.61 0.00 34.53 1.40
2444 6393 8.387190 TGAGAGGCATTATGACTTGATTTATG 57.613 34.615 0.61 0.00 34.53 1.90
2445 6394 8.212995 TGAGAGGCATTATGACTTGATTTATGA 58.787 33.333 0.61 0.00 34.53 2.15
2446 6395 8.618702 AGAGGCATTATGACTTGATTTATGAG 57.381 34.615 0.61 0.00 34.53 2.90
2447 6396 8.216423 AGAGGCATTATGACTTGATTTATGAGT 58.784 33.333 0.61 0.00 34.53 3.41
2448 6397 8.162878 AGGCATTATGACTTGATTTATGAGTG 57.837 34.615 0.00 0.00 24.46 3.51
2449 6398 7.776969 AGGCATTATGACTTGATTTATGAGTGT 59.223 33.333 0.00 0.00 24.46 3.55
2450 6399 7.859377 GGCATTATGACTTGATTTATGAGTGTG 59.141 37.037 0.00 0.00 0.00 3.82
2451 6400 8.400947 GCATTATGACTTGATTTATGAGTGTGT 58.599 33.333 0.00 0.00 0.00 3.72
2456 6405 8.902540 TGACTTGATTTATGAGTGTGTAAACT 57.097 30.769 0.00 0.00 0.00 2.66
2457 6406 8.773645 TGACTTGATTTATGAGTGTGTAAACTG 58.226 33.333 0.00 0.00 0.00 3.16
2458 6407 8.677148 ACTTGATTTATGAGTGTGTAAACTGT 57.323 30.769 0.00 0.00 0.00 3.55
2459 6408 8.774586 ACTTGATTTATGAGTGTGTAAACTGTC 58.225 33.333 0.00 0.00 0.00 3.51
2460 6409 7.667043 TGATTTATGAGTGTGTAAACTGTCC 57.333 36.000 0.00 0.00 0.00 4.02
2461 6410 7.450074 TGATTTATGAGTGTGTAAACTGTCCT 58.550 34.615 0.00 0.00 0.00 3.85
2462 6411 7.602644 TGATTTATGAGTGTGTAAACTGTCCTC 59.397 37.037 0.00 0.00 0.00 3.71
2463 6412 3.746045 TGAGTGTGTAAACTGTCCTCC 57.254 47.619 0.00 0.00 0.00 4.30
2464 6413 3.305720 TGAGTGTGTAAACTGTCCTCCT 58.694 45.455 0.00 0.00 0.00 3.69
2465 6414 3.069586 TGAGTGTGTAAACTGTCCTCCTG 59.930 47.826 0.00 0.00 0.00 3.86
2466 6415 3.039011 AGTGTGTAAACTGTCCTCCTGT 58.961 45.455 0.00 0.00 0.00 4.00
2467 6416 3.454812 AGTGTGTAAACTGTCCTCCTGTT 59.545 43.478 0.00 0.00 36.86 3.16
2468 6417 4.652421 AGTGTGTAAACTGTCCTCCTGTTA 59.348 41.667 0.00 0.00 34.50 2.41
2506 6455 1.064389 GGCTTGGGGTCAGCTTAGAAT 60.064 52.381 0.00 0.00 0.00 2.40
2509 6458 3.511540 GCTTGGGGTCAGCTTAGAATTTT 59.488 43.478 0.00 0.00 0.00 1.82
2510 6459 4.619160 GCTTGGGGTCAGCTTAGAATTTTG 60.619 45.833 0.00 0.00 0.00 2.44
2511 6460 4.112634 TGGGGTCAGCTTAGAATTTTGT 57.887 40.909 0.00 0.00 0.00 2.83
2512 6461 4.079253 TGGGGTCAGCTTAGAATTTTGTC 58.921 43.478 0.00 0.00 0.00 3.18
2513 6462 4.079253 GGGGTCAGCTTAGAATTTTGTCA 58.921 43.478 0.00 0.00 0.00 3.58
2514 6463 4.706962 GGGGTCAGCTTAGAATTTTGTCAT 59.293 41.667 0.00 0.00 0.00 3.06
2515 6464 5.885912 GGGGTCAGCTTAGAATTTTGTCATA 59.114 40.000 0.00 0.00 0.00 2.15
2516 6465 6.547510 GGGGTCAGCTTAGAATTTTGTCATAT 59.452 38.462 0.00 0.00 0.00 1.78
2565 6536 7.592885 AGCAATCTACGTAGGGAATTTACTA 57.407 36.000 22.01 0.00 0.00 1.82
2570 6541 8.757982 ATCTACGTAGGGAATTTACTACAGAA 57.242 34.615 22.01 0.00 39.55 3.02
2571 6542 7.989826 TCTACGTAGGGAATTTACTACAGAAC 58.010 38.462 22.01 0.00 39.55 3.01
2580 6551 6.128254 GGAATTTACTACAGAACCAGAACAGC 60.128 42.308 0.00 0.00 0.00 4.40
2595 6566 3.260884 AGAACAGCCTCGTCATAAAAGGA 59.739 43.478 0.00 0.00 31.44 3.36
2650 6621 3.444742 CCCAGCATGATAAAGCAAACTCA 59.555 43.478 0.00 0.00 39.69 3.41
2651 6622 4.082081 CCCAGCATGATAAAGCAAACTCAA 60.082 41.667 0.00 0.00 39.69 3.02
2653 6624 5.575606 CCAGCATGATAAAGCAAACTCAAAG 59.424 40.000 0.00 0.00 39.69 2.77
2660 6633 1.986882 AGCAAACTCAAAGTCCCAGG 58.013 50.000 0.00 0.00 0.00 4.45
2694 6667 5.036117 AGAGTTTCCTCAGTGCTTTGTTA 57.964 39.130 0.00 0.00 40.40 2.41
2764 6737 3.699067 CAGAGCTTTGGTGTTTGTTCTG 58.301 45.455 0.00 0.00 33.08 3.02
2819 6792 7.630924 ACGTTTGAGTCTACTTTCATTCTTTG 58.369 34.615 0.00 0.00 0.00 2.77
2857 6835 7.278875 TGAAAATCACATGGCCTTTAAAGTTT 58.721 30.769 14.03 4.04 0.00 2.66
2861 6839 2.560981 ACATGGCCTTTAAAGTTTCCCG 59.439 45.455 14.03 8.30 0.00 5.14
2865 6843 3.569277 TGGCCTTTAAAGTTTCCCGTAAC 59.431 43.478 14.03 0.00 0.00 2.50
2869 6847 5.733091 GCCTTTAAAGTTTCCCGTAACGTTT 60.733 40.000 5.91 0.00 33.06 3.60
2871 6849 5.809719 TTAAAGTTTCCCGTAACGTTTGT 57.190 34.783 5.91 0.00 33.06 2.83
2908 6886 5.163301 GGAGGAGTATTTGTTAGGCTGATCA 60.163 44.000 0.00 0.00 0.00 2.92
2923 6901 3.243101 GCTGATCACTGCAAATCCAGATG 60.243 47.826 2.23 0.00 40.01 2.90
2941 6919 0.329261 TGTCCTTTCCATCCAGCTGG 59.671 55.000 27.87 27.87 37.66 4.85
3013 6991 2.181975 ACTGAAAATGGCCCATGGAAG 58.818 47.619 15.22 0.00 0.00 3.46
3128 7106 3.140707 TGCCCCATCAGTCCAATTATCAT 59.859 43.478 0.00 0.00 0.00 2.45
3163 7141 2.852449 TGTATCCCCTTCCTCATGCTTT 59.148 45.455 0.00 0.00 0.00 3.51
3164 7142 4.044308 TGTATCCCCTTCCTCATGCTTTA 58.956 43.478 0.00 0.00 0.00 1.85
3165 7143 3.584733 ATCCCCTTCCTCATGCTTTAC 57.415 47.619 0.00 0.00 0.00 2.01
3186 7164 4.884257 CACACACAGTGTTGTTTTGAAC 57.116 40.909 2.45 0.00 45.08 3.18
3187 7165 4.545610 CACACACAGTGTTGTTTTGAACT 58.454 39.130 2.45 0.00 45.08 3.01
3188 7166 4.382457 CACACACAGTGTTGTTTTGAACTG 59.618 41.667 2.45 0.00 45.08 3.16
3189 7167 4.277174 ACACACAGTGTTGTTTTGAACTGA 59.723 37.500 2.45 0.00 45.08 3.41
3190 7168 5.218885 CACACAGTGTTGTTTTGAACTGAA 58.781 37.500 2.45 0.00 42.09 3.02
3191 7169 5.689514 CACACAGTGTTGTTTTGAACTGAAA 59.310 36.000 2.45 0.00 42.09 2.69
3192 7170 5.920273 ACACAGTGTTGTTTTGAACTGAAAG 59.080 36.000 0.00 1.57 42.09 2.62
3193 7171 4.923281 ACAGTGTTGTTTTGAACTGAAAGC 59.077 37.500 8.54 0.00 42.09 3.51
3194 7172 4.922692 CAGTGTTGTTTTGAACTGAAAGCA 59.077 37.500 0.00 0.00 42.09 3.91
3195 7173 7.280031 ACAGTGTTGTTTTGAACTGAAAGCAG 61.280 38.462 8.54 0.00 42.09 4.24
3196 7174 4.327087 GTGTTGTTTTGAACTGAAAGCAGG 59.673 41.667 0.00 0.00 46.60 4.85
3197 7175 4.219507 TGTTGTTTTGAACTGAAAGCAGGA 59.780 37.500 0.00 0.00 46.60 3.86
3198 7176 5.167845 GTTGTTTTGAACTGAAAGCAGGAA 58.832 37.500 0.00 0.00 46.60 3.36
3199 7177 5.596836 TGTTTTGAACTGAAAGCAGGAAT 57.403 34.783 0.00 0.00 46.60 3.01
3200 7178 5.350633 TGTTTTGAACTGAAAGCAGGAATG 58.649 37.500 0.00 0.00 46.60 2.67
3201 7179 5.126869 TGTTTTGAACTGAAAGCAGGAATGA 59.873 36.000 0.00 0.00 46.60 2.57
3202 7180 5.443185 TTTGAACTGAAAGCAGGAATGAG 57.557 39.130 0.00 0.00 46.60 2.90
3203 7181 3.415212 TGAACTGAAAGCAGGAATGAGG 58.585 45.455 0.00 0.00 46.60 3.86
3204 7182 3.181440 TGAACTGAAAGCAGGAATGAGGT 60.181 43.478 0.00 0.00 46.60 3.85
3205 7183 3.515602 ACTGAAAGCAGGAATGAGGTT 57.484 42.857 0.00 0.00 46.60 3.50
3206 7184 3.416156 ACTGAAAGCAGGAATGAGGTTC 58.584 45.455 0.00 0.00 46.60 3.62
3207 7185 3.181440 ACTGAAAGCAGGAATGAGGTTCA 60.181 43.478 0.00 0.00 46.60 3.18
3208 7186 3.822735 CTGAAAGCAGGAATGAGGTTCAA 59.177 43.478 0.00 0.00 38.64 2.69
3209 7187 3.569701 TGAAAGCAGGAATGAGGTTCAAC 59.430 43.478 0.00 0.00 38.64 3.18
3210 7188 2.957402 AGCAGGAATGAGGTTCAACA 57.043 45.000 0.00 0.00 38.64 3.33
3211 7189 2.508526 AGCAGGAATGAGGTTCAACAC 58.491 47.619 0.00 0.00 38.64 3.32
3212 7190 2.158623 AGCAGGAATGAGGTTCAACACA 60.159 45.455 0.00 0.00 38.64 3.72
3213 7191 2.030805 GCAGGAATGAGGTTCAACACAC 60.031 50.000 0.00 0.00 38.64 3.82
3214 7192 3.480470 CAGGAATGAGGTTCAACACACT 58.520 45.455 0.00 0.00 38.64 3.55
3215 7193 3.885297 CAGGAATGAGGTTCAACACACTT 59.115 43.478 0.00 0.00 38.64 3.16
3216 7194 4.339247 CAGGAATGAGGTTCAACACACTTT 59.661 41.667 0.00 0.00 38.64 2.66
3217 7195 4.339247 AGGAATGAGGTTCAACACACTTTG 59.661 41.667 0.00 0.00 38.64 2.77
3218 7196 3.715628 ATGAGGTTCAACACACTTTGC 57.284 42.857 0.00 0.00 0.00 3.68
3219 7197 2.441410 TGAGGTTCAACACACTTTGCA 58.559 42.857 0.00 0.00 0.00 4.08
3220 7198 3.023119 TGAGGTTCAACACACTTTGCAT 58.977 40.909 0.00 0.00 0.00 3.96
3221 7199 3.446873 TGAGGTTCAACACACTTTGCATT 59.553 39.130 0.00 0.00 0.00 3.56
3222 7200 4.642437 TGAGGTTCAACACACTTTGCATTA 59.358 37.500 0.00 0.00 0.00 1.90
3223 7201 5.186996 AGGTTCAACACACTTTGCATTAG 57.813 39.130 0.00 0.00 0.00 1.73
3224 7202 3.735746 GGTTCAACACACTTTGCATTAGC 59.264 43.478 0.00 0.00 42.57 3.09
3225 7203 3.641437 TCAACACACTTTGCATTAGCC 57.359 42.857 0.00 0.00 41.13 3.93
3226 7204 2.954989 TCAACACACTTTGCATTAGCCA 59.045 40.909 0.00 0.00 41.13 4.75
3227 7205 3.573538 TCAACACACTTTGCATTAGCCAT 59.426 39.130 0.00 0.00 41.13 4.40
3228 7206 3.855689 ACACACTTTGCATTAGCCATC 57.144 42.857 0.00 0.00 41.13 3.51
3229 7207 3.424703 ACACACTTTGCATTAGCCATCT 58.575 40.909 0.00 0.00 41.13 2.90
3230 7208 3.192001 ACACACTTTGCATTAGCCATCTG 59.808 43.478 0.00 0.00 41.13 2.90
3231 7209 3.441222 CACACTTTGCATTAGCCATCTGA 59.559 43.478 0.00 0.00 41.13 3.27
3232 7210 3.693085 ACACTTTGCATTAGCCATCTGAG 59.307 43.478 0.00 0.00 41.13 3.35
3233 7211 3.066342 CACTTTGCATTAGCCATCTGAGG 59.934 47.826 0.00 0.00 41.13 3.86
3234 7212 2.353357 TTGCATTAGCCATCTGAGGG 57.647 50.000 3.51 3.51 41.13 4.30
3245 7223 4.872664 GCCATCTGAGGGCGTATATATAC 58.127 47.826 18.30 12.18 42.39 1.47
3246 7224 4.341235 GCCATCTGAGGGCGTATATATACA 59.659 45.833 18.30 1.54 42.39 2.29
3247 7225 5.508153 GCCATCTGAGGGCGTATATATACAG 60.508 48.000 18.30 14.24 42.39 2.74
3248 7226 5.594725 CCATCTGAGGGCGTATATATACAGT 59.405 44.000 20.24 3.92 32.87 3.55
3249 7227 6.096987 CCATCTGAGGGCGTATATATACAGTT 59.903 42.308 20.24 5.14 32.87 3.16
3250 7228 7.284716 CCATCTGAGGGCGTATATATACAGTTA 59.715 40.741 20.24 3.49 32.87 2.24
3251 7229 7.621428 TCTGAGGGCGTATATATACAGTTAC 57.379 40.000 20.24 10.19 32.87 2.50
3252 7230 7.170277 TCTGAGGGCGTATATATACAGTTACA 58.830 38.462 20.24 13.30 32.87 2.41
3253 7231 7.336176 TCTGAGGGCGTATATATACAGTTACAG 59.664 40.741 20.24 19.59 32.87 2.74
3254 7232 7.170277 TGAGGGCGTATATATACAGTTACAGA 58.830 38.462 20.24 0.00 32.87 3.41
3255 7233 7.666804 TGAGGGCGTATATATACAGTTACAGAA 59.333 37.037 20.24 0.00 32.87 3.02
3256 7234 8.413309 AGGGCGTATATATACAGTTACAGAAA 57.587 34.615 20.24 0.00 32.87 2.52
3257 7235 8.521176 AGGGCGTATATATACAGTTACAGAAAG 58.479 37.037 20.24 3.47 32.87 2.62
3258 7236 7.758528 GGGCGTATATATACAGTTACAGAAAGG 59.241 40.741 20.24 3.30 32.87 3.11
3259 7237 7.758528 GGCGTATATATACAGTTACAGAAAGGG 59.241 40.741 20.24 2.94 32.87 3.95
3260 7238 8.517878 GCGTATATATACAGTTACAGAAAGGGA 58.482 37.037 20.24 0.00 32.87 4.20
3266 7244 9.975218 ATATACAGTTACAGAAAGGGAAATGTT 57.025 29.630 0.00 0.00 32.84 2.71
3267 7245 6.635030 ACAGTTACAGAAAGGGAAATGTTC 57.365 37.500 0.00 0.00 26.36 3.18
3276 7254 3.644861 GGAAATGTTCCCAGACGGT 57.355 52.632 0.00 0.00 44.30 4.83
3277 7255 1.165270 GGAAATGTTCCCAGACGGTG 58.835 55.000 0.00 0.00 44.30 4.94
3278 7256 0.521735 GAAATGTTCCCAGACGGTGC 59.478 55.000 0.00 0.00 0.00 5.01
3279 7257 0.179004 AAATGTTCCCAGACGGTGCA 60.179 50.000 0.00 0.00 0.00 4.57
3280 7258 0.889186 AATGTTCCCAGACGGTGCAC 60.889 55.000 8.80 8.80 0.00 4.57
3281 7259 2.668550 GTTCCCAGACGGTGCACC 60.669 66.667 26.78 26.78 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.277601 ACATCGATTAACAAACAACCGAG 57.722 39.130 0.00 0.00 0.00 4.63
54 56 2.443016 AGGAGGAGGCGAGCGATT 60.443 61.111 0.00 0.00 0.00 3.34
872 4482 1.154205 CGATGGCTGGTCGCTTAAGG 61.154 60.000 4.29 0.00 39.13 2.69
883 4493 2.025156 GCGAATTGGCGATGGCTG 59.975 61.111 0.00 0.00 39.81 4.85
919 4529 3.655810 GACTGCGAGGGAGCTGTGG 62.656 68.421 6.24 0.00 46.70 4.17
920 4530 2.125753 GACTGCGAGGGAGCTGTG 60.126 66.667 6.24 0.00 46.70 3.66
968 4586 2.345244 CACTCGGTTGCTCTGGCT 59.655 61.111 0.00 0.00 39.59 4.75
969 4587 3.426568 GCACTCGGTTGCTCTGGC 61.427 66.667 2.29 0.00 39.59 4.85
970 4588 3.114616 CGCACTCGGTTGCTCTGG 61.115 66.667 7.44 0.00 40.62 3.86
971 4589 3.782244 GCGCACTCGGTTGCTCTG 61.782 66.667 0.30 0.00 40.62 3.35
1065 4975 2.652530 GCGTTGGTGAGGTCGGTA 59.347 61.111 0.00 0.00 0.00 4.02
1106 5016 9.197694 CTTCATAAGTTGGAAGAATAGGATACG 57.802 37.037 11.62 0.00 42.39 3.06
1116 5026 5.178797 GCTACTGCTTCATAAGTTGGAAGA 58.821 41.667 18.13 6.99 42.39 2.87
1139 5053 9.512435 CTGGCATATCTTAAGAAATCAAAACAG 57.488 33.333 9.71 7.19 0.00 3.16
1153 5067 3.928754 AGTCAGGTCCTGGCATATCTTA 58.071 45.455 25.26 0.00 38.73 2.10
1162 5076 4.275936 CACAAAAAGTAAGTCAGGTCCTGG 59.724 45.833 19.11 0.53 31.51 4.45
1177 5092 7.889589 AGGAAGAACAAAAAGACACAAAAAG 57.110 32.000 0.00 0.00 0.00 2.27
1184 5099 6.534793 GCATCAAAAGGAAGAACAAAAAGACA 59.465 34.615 0.00 0.00 0.00 3.41
1188 5103 6.534793 GTCTGCATCAAAAGGAAGAACAAAAA 59.465 34.615 0.00 0.00 0.00 1.94
1259 5174 2.781757 AGAATTCATCAGCTGGGATCCA 59.218 45.455 15.13 0.00 0.00 3.41
1278 5209 8.898761 ACACAAAACAGATACACATTTGTTAGA 58.101 29.630 0.00 0.00 40.98 2.10
1286 5217 7.229306 ACATCAGAACACAAAACAGATACACAT 59.771 33.333 0.00 0.00 0.00 3.21
1287 5218 6.542005 ACATCAGAACACAAAACAGATACACA 59.458 34.615 0.00 0.00 0.00 3.72
1288 5219 6.959361 ACATCAGAACACAAAACAGATACAC 58.041 36.000 0.00 0.00 0.00 2.90
1306 5237 0.886490 GGGCCGCTGGATAACATCAG 60.886 60.000 0.00 0.00 0.00 2.90
1404 5343 5.304101 TGCACCAGTACAAATCAAAGGAAAT 59.696 36.000 0.00 0.00 0.00 2.17
1452 5394 0.179100 CCGACAGAGACGCATGGATT 60.179 55.000 0.00 0.00 0.00 3.01
1604 5553 3.064545 CCGGTTGATCAGAGCTGAAAATC 59.935 47.826 4.06 2.51 43.58 2.17
1612 5561 1.943340 GGAAATCCGGTTGATCAGAGC 59.057 52.381 0.00 0.00 31.61 4.09
1736 5685 1.843851 GGGAATGAGGTGATGGTGGTA 59.156 52.381 0.00 0.00 0.00 3.25
1737 5686 0.625849 GGGAATGAGGTGATGGTGGT 59.374 55.000 0.00 0.00 0.00 4.16
1738 5687 0.464373 CGGGAATGAGGTGATGGTGG 60.464 60.000 0.00 0.00 0.00 4.61
1739 5688 1.097547 GCGGGAATGAGGTGATGGTG 61.098 60.000 0.00 0.00 0.00 4.17
1740 5689 1.224592 GCGGGAATGAGGTGATGGT 59.775 57.895 0.00 0.00 0.00 3.55
1741 5690 0.816825 CAGCGGGAATGAGGTGATGG 60.817 60.000 0.00 0.00 38.02 3.51
1742 5691 1.442526 GCAGCGGGAATGAGGTGATG 61.443 60.000 0.00 0.00 38.02 3.07
1743 5692 1.153086 GCAGCGGGAATGAGGTGAT 60.153 57.895 0.00 0.00 38.02 3.06
1744 5693 0.975556 TAGCAGCGGGAATGAGGTGA 60.976 55.000 0.00 0.00 38.02 4.02
1745 5694 0.107456 ATAGCAGCGGGAATGAGGTG 59.893 55.000 0.00 0.00 38.72 4.00
1757 5706 3.433615 AGTTGTGAAACGAAGATAGCAGC 59.566 43.478 0.00 0.00 42.39 5.25
1762 5711 5.277779 CCTGCAAAGTTGTGAAACGAAGATA 60.278 40.000 0.00 0.00 42.39 1.98
1764 5713 3.181501 CCTGCAAAGTTGTGAAACGAAGA 60.182 43.478 0.00 0.00 42.39 2.87
1765 5714 3.108144 CCTGCAAAGTTGTGAAACGAAG 58.892 45.455 0.00 0.00 42.39 3.79
1766 5715 2.490115 ACCTGCAAAGTTGTGAAACGAA 59.510 40.909 0.00 0.00 42.39 3.85
1781 5730 6.382859 TCAGAGGTAAGTTATAATCACCTGCA 59.617 38.462 16.16 0.00 39.71 4.41
1785 5734 6.990939 GGGTTCAGAGGTAAGTTATAATCACC 59.009 42.308 5.41 5.41 0.00 4.02
1791 5740 6.610075 AAACGGGTTCAGAGGTAAGTTATA 57.390 37.500 0.00 0.00 0.00 0.98
1793 5742 4.961438 AAACGGGTTCAGAGGTAAGTTA 57.039 40.909 0.00 0.00 0.00 2.24
1794 5743 3.851458 AAACGGGTTCAGAGGTAAGTT 57.149 42.857 0.00 0.00 0.00 2.66
1795 5744 3.473625 CAAAACGGGTTCAGAGGTAAGT 58.526 45.455 0.00 0.00 0.00 2.24
1796 5745 2.812011 CCAAAACGGGTTCAGAGGTAAG 59.188 50.000 0.00 0.00 0.00 2.34
1798 5747 1.770061 ACCAAAACGGGTTCAGAGGTA 59.230 47.619 0.00 0.00 38.19 3.08
1800 5749 1.235724 GACCAAAACGGGTTCAGAGG 58.764 55.000 0.00 0.00 42.53 3.69
1809 5758 3.416490 ACGCAGTGACCAAAACGG 58.584 55.556 0.00 0.00 42.51 4.44
1839 5788 3.915575 GCTGGAGGCAGAACATGG 58.084 61.111 0.00 0.00 41.35 3.66
1946 5895 1.457346 CCTTACGTCCAGTAGACCGT 58.543 55.000 0.00 0.00 43.08 4.83
1965 5914 1.066502 GGGGAAGAAGTCAGAGAGTGC 60.067 57.143 0.00 0.00 0.00 4.40
2003 5952 7.439381 ACAAATTCATGCAGTTCAGAAAGAAT 58.561 30.769 0.00 0.00 38.76 2.40
2083 6032 9.586435 AAGGAATAAGAAAACTTCAGTTGTTTG 57.414 29.630 0.00 0.00 38.44 2.93
2096 6045 9.912634 GTTCAATGTCATCAAGGAATAAGAAAA 57.087 29.630 0.00 0.00 0.00 2.29
2103 6052 6.491062 TCAAGTGTTCAATGTCATCAAGGAAT 59.509 34.615 0.00 0.00 0.00 3.01
2253 6202 2.736236 ATCGGCTGATCGATGCGC 60.736 61.111 0.54 0.00 46.52 6.09
2308 6257 3.521727 AGATCCCACAGAACTACCTGTT 58.478 45.455 0.00 0.00 44.32 3.16
2326 6275 3.064324 GCAACGGCAGCCCAAGAT 61.064 61.111 5.63 0.00 40.72 2.40
2388 6337 5.119931 TCAAGTCACAATGGCATACAAAC 57.880 39.130 0.00 0.00 0.00 2.93
2389 6338 5.981088 ATCAAGTCACAATGGCATACAAA 57.019 34.783 0.00 0.00 0.00 2.83
2391 6340 5.981088 AAATCAAGTCACAATGGCATACA 57.019 34.783 0.00 0.00 0.00 2.29
2415 6364 7.707624 ATCAAGTCATAATGCCTCTCAAAAA 57.292 32.000 0.00 0.00 0.00 1.94
2416 6365 7.707624 AATCAAGTCATAATGCCTCTCAAAA 57.292 32.000 0.00 0.00 0.00 2.44
2417 6366 7.707624 AAATCAAGTCATAATGCCTCTCAAA 57.292 32.000 0.00 0.00 0.00 2.69
2418 6367 8.843262 CATAAATCAAGTCATAATGCCTCTCAA 58.157 33.333 0.00 0.00 0.00 3.02
2419 6368 8.212995 TCATAAATCAAGTCATAATGCCTCTCA 58.787 33.333 0.00 0.00 0.00 3.27
2420 6369 8.613060 TCATAAATCAAGTCATAATGCCTCTC 57.387 34.615 0.00 0.00 0.00 3.20
2421 6370 8.216423 ACTCATAAATCAAGTCATAATGCCTCT 58.784 33.333 0.00 0.00 0.00 3.69
2422 6371 8.288208 CACTCATAAATCAAGTCATAATGCCTC 58.712 37.037 0.00 0.00 0.00 4.70
2423 6372 7.776969 ACACTCATAAATCAAGTCATAATGCCT 59.223 33.333 0.00 0.00 0.00 4.75
2424 6373 7.859377 CACACTCATAAATCAAGTCATAATGCC 59.141 37.037 0.00 0.00 0.00 4.40
2425 6374 8.400947 ACACACTCATAAATCAAGTCATAATGC 58.599 33.333 0.00 0.00 0.00 3.56
2430 6379 9.507329 AGTTTACACACTCATAAATCAAGTCAT 57.493 29.630 0.00 0.00 0.00 3.06
2431 6380 8.773645 CAGTTTACACACTCATAAATCAAGTCA 58.226 33.333 0.00 0.00 0.00 3.41
2432 6381 8.774586 ACAGTTTACACACTCATAAATCAAGTC 58.225 33.333 0.00 0.00 0.00 3.01
2433 6382 8.677148 ACAGTTTACACACTCATAAATCAAGT 57.323 30.769 0.00 0.00 0.00 3.16
2434 6383 8.230486 GGACAGTTTACACACTCATAAATCAAG 58.770 37.037 0.00 0.00 0.00 3.02
2435 6384 7.936847 AGGACAGTTTACACACTCATAAATCAA 59.063 33.333 0.00 0.00 0.00 2.57
2436 6385 7.450074 AGGACAGTTTACACACTCATAAATCA 58.550 34.615 0.00 0.00 0.00 2.57
2437 6386 7.064728 GGAGGACAGTTTACACACTCATAAATC 59.935 40.741 0.00 0.00 0.00 2.17
2438 6387 6.879458 GGAGGACAGTTTACACACTCATAAAT 59.121 38.462 0.00 0.00 0.00 1.40
2439 6388 6.042781 AGGAGGACAGTTTACACACTCATAAA 59.957 38.462 0.00 0.00 0.00 1.40
2440 6389 5.542635 AGGAGGACAGTTTACACACTCATAA 59.457 40.000 0.00 0.00 0.00 1.90
2441 6390 5.047306 CAGGAGGACAGTTTACACACTCATA 60.047 44.000 0.00 0.00 0.00 2.15
2442 6391 3.904339 AGGAGGACAGTTTACACACTCAT 59.096 43.478 0.00 0.00 0.00 2.90
2443 6392 3.069586 CAGGAGGACAGTTTACACACTCA 59.930 47.826 0.00 0.00 0.00 3.41
2444 6393 3.069729 ACAGGAGGACAGTTTACACACTC 59.930 47.826 0.00 0.00 0.00 3.51
2445 6394 3.039011 ACAGGAGGACAGTTTACACACT 58.961 45.455 0.00 0.00 0.00 3.55
2446 6395 3.470645 ACAGGAGGACAGTTTACACAC 57.529 47.619 0.00 0.00 0.00 3.82
2447 6396 5.818678 ATAACAGGAGGACAGTTTACACA 57.181 39.130 0.00 0.00 0.00 3.72
2448 6397 6.932947 ACTATAACAGGAGGACAGTTTACAC 58.067 40.000 0.00 0.00 0.00 2.90
2449 6398 8.289939 CTACTATAACAGGAGGACAGTTTACA 57.710 38.462 0.00 0.00 30.52 2.41
2460 6409 6.984474 TCAAAATTCGCCTACTATAACAGGAG 59.016 38.462 3.88 1.09 34.56 3.69
2461 6410 6.880484 TCAAAATTCGCCTACTATAACAGGA 58.120 36.000 3.88 0.00 33.42 3.86
2462 6411 6.202954 CCTCAAAATTCGCCTACTATAACAGG 59.797 42.308 0.00 0.00 34.85 4.00
2463 6412 6.292919 GCCTCAAAATTCGCCTACTATAACAG 60.293 42.308 0.00 0.00 0.00 3.16
2464 6413 5.526111 GCCTCAAAATTCGCCTACTATAACA 59.474 40.000 0.00 0.00 0.00 2.41
2465 6414 5.758784 AGCCTCAAAATTCGCCTACTATAAC 59.241 40.000 0.00 0.00 0.00 1.89
2466 6415 5.925509 AGCCTCAAAATTCGCCTACTATAA 58.074 37.500 0.00 0.00 0.00 0.98
2467 6416 5.546621 AGCCTCAAAATTCGCCTACTATA 57.453 39.130 0.00 0.00 0.00 1.31
2468 6417 4.423625 AGCCTCAAAATTCGCCTACTAT 57.576 40.909 0.00 0.00 0.00 2.12
2538 6509 8.648693 AGTAAATTCCCTACGTAGATTGCTATT 58.351 33.333 24.15 11.46 0.00 1.73
2551 6522 7.179076 TCTGGTTCTGTAGTAAATTCCCTAC 57.821 40.000 7.28 7.28 35.25 3.18
2554 6525 6.235664 TGTTCTGGTTCTGTAGTAAATTCCC 58.764 40.000 0.00 0.00 0.00 3.97
2565 6536 0.034059 CGAGGCTGTTCTGGTTCTGT 59.966 55.000 0.00 0.00 0.00 3.41
2570 6541 1.557099 TATGACGAGGCTGTTCTGGT 58.443 50.000 0.00 0.00 0.00 4.00
2571 6542 2.672961 TTATGACGAGGCTGTTCTGG 57.327 50.000 0.00 0.00 0.00 3.86
2580 6551 3.702045 AGGTCTCTCCTTTTATGACGAGG 59.298 47.826 0.00 0.00 45.67 4.63
2595 6566 2.817258 CGTGACAGAAGAAGAGGTCTCT 59.183 50.000 0.00 0.00 42.75 3.10
2650 6621 1.661463 TGCATCTCTCCTGGGACTTT 58.339 50.000 0.00 0.00 0.00 2.66
2651 6622 1.661463 TTGCATCTCTCCTGGGACTT 58.339 50.000 0.00 0.00 0.00 3.01
2653 6624 2.026822 TCTTTTGCATCTCTCCTGGGAC 60.027 50.000 0.00 0.00 0.00 4.46
2723 6696 5.080337 TCTGCTCAAGAGGAAAGACTTCTA 58.920 41.667 0.00 0.00 33.79 2.10
2764 6737 1.374758 CTGGTTGGCTCTCCACGAC 60.375 63.158 0.00 0.00 43.33 4.34
2784 6757 9.543783 AAAGTAGACTCAAACGTAAGATCTTTT 57.456 29.630 14.36 0.00 43.62 2.27
2857 6835 6.128336 CCAAAATGTATACAAACGTTACGGGA 60.128 38.462 10.14 0.00 0.00 5.14
2861 6839 7.583230 TCCACCAAAATGTATACAAACGTTAC 58.417 34.615 10.14 0.00 0.00 2.50
2865 6843 5.413213 TCCTCCACCAAAATGTATACAAACG 59.587 40.000 10.14 0.00 0.00 3.60
2869 6847 5.772393 ACTCCTCCACCAAAATGTATACA 57.228 39.130 8.27 8.27 0.00 2.29
2871 6849 8.333235 ACAAATACTCCTCCACCAAAATGTATA 58.667 33.333 0.00 0.00 0.00 1.47
2908 6886 3.446442 AAGGACATCTGGATTTGCAGT 57.554 42.857 0.00 0.00 0.00 4.40
2923 6901 0.394899 CCCAGCTGGATGGAAAGGAC 60.395 60.000 34.91 0.00 43.57 3.85
2991 6969 2.178580 TCCATGGGCCATTTTCAGTTC 58.821 47.619 18.46 0.00 0.00 3.01
3013 6991 4.061596 CCTCTGTTGACCTTTCTGAACTC 58.938 47.826 0.00 0.00 0.00 3.01
3128 7106 4.102524 AGGGGATACAATATTGTTCTCGCA 59.897 41.667 28.86 15.30 42.35 5.10
3165 7143 4.382457 CAGTTCAAAACAACACTGTGTGTG 59.618 41.667 15.11 15.84 46.79 3.82
3177 7155 5.126869 TCATTCCTGCTTTCAGTTCAAAACA 59.873 36.000 0.00 0.00 38.66 2.83
3178 7156 5.591099 TCATTCCTGCTTTCAGTTCAAAAC 58.409 37.500 0.00 0.00 38.66 2.43
3182 7160 3.181440 ACCTCATTCCTGCTTTCAGTTCA 60.181 43.478 0.00 0.00 38.66 3.18
3183 7161 3.416156 ACCTCATTCCTGCTTTCAGTTC 58.584 45.455 0.00 0.00 38.66 3.01
3185 7163 3.181440 TGAACCTCATTCCTGCTTTCAGT 60.181 43.478 0.00 0.00 38.66 3.41
3186 7164 3.415212 TGAACCTCATTCCTGCTTTCAG 58.585 45.455 0.00 0.00 40.02 3.02
3187 7165 3.507162 TGAACCTCATTCCTGCTTTCA 57.493 42.857 0.00 0.00 36.36 2.69
3188 7166 3.569701 TGTTGAACCTCATTCCTGCTTTC 59.430 43.478 0.00 0.00 36.36 2.62
3189 7167 3.319122 GTGTTGAACCTCATTCCTGCTTT 59.681 43.478 0.00 0.00 36.36 3.51
3190 7168 2.887152 GTGTTGAACCTCATTCCTGCTT 59.113 45.455 0.00 0.00 36.36 3.91
3191 7169 2.158623 TGTGTTGAACCTCATTCCTGCT 60.159 45.455 0.00 0.00 36.36 4.24
3192 7170 2.030805 GTGTGTTGAACCTCATTCCTGC 60.031 50.000 0.00 0.00 36.36 4.85
3193 7171 3.480470 AGTGTGTTGAACCTCATTCCTG 58.520 45.455 0.00 0.00 36.36 3.86
3194 7172 3.864789 AGTGTGTTGAACCTCATTCCT 57.135 42.857 0.00 0.00 36.36 3.36
3195 7173 4.610945 CAAAGTGTGTTGAACCTCATTCC 58.389 43.478 0.00 0.00 36.36 3.01
3196 7174 4.044426 GCAAAGTGTGTTGAACCTCATTC 58.956 43.478 0.00 0.00 37.88 2.67
3197 7175 3.446873 TGCAAAGTGTGTTGAACCTCATT 59.553 39.130 0.00 0.00 0.00 2.57
3198 7176 3.023119 TGCAAAGTGTGTTGAACCTCAT 58.977 40.909 0.00 0.00 0.00 2.90
3199 7177 2.441410 TGCAAAGTGTGTTGAACCTCA 58.559 42.857 0.00 0.00 0.00 3.86
3200 7178 3.715628 ATGCAAAGTGTGTTGAACCTC 57.284 42.857 0.00 0.00 0.00 3.85
3201 7179 4.499696 GCTAATGCAAAGTGTGTTGAACCT 60.500 41.667 0.00 0.00 39.41 3.50
3202 7180 3.735746 GCTAATGCAAAGTGTGTTGAACC 59.264 43.478 0.00 0.00 39.41 3.62
3203 7181 3.735746 GGCTAATGCAAAGTGTGTTGAAC 59.264 43.478 0.00 0.00 41.91 3.18
3204 7182 3.382865 TGGCTAATGCAAAGTGTGTTGAA 59.617 39.130 0.00 0.00 41.91 2.69
3205 7183 2.954989 TGGCTAATGCAAAGTGTGTTGA 59.045 40.909 0.00 0.00 41.91 3.18
3206 7184 3.367992 TGGCTAATGCAAAGTGTGTTG 57.632 42.857 0.00 0.00 41.91 3.33
3207 7185 3.828451 AGATGGCTAATGCAAAGTGTGTT 59.172 39.130 0.00 0.00 41.91 3.32
3208 7186 3.192001 CAGATGGCTAATGCAAAGTGTGT 59.808 43.478 0.00 0.00 41.91 3.72
3209 7187 3.441222 TCAGATGGCTAATGCAAAGTGTG 59.559 43.478 0.00 0.00 41.91 3.82
3210 7188 3.689347 TCAGATGGCTAATGCAAAGTGT 58.311 40.909 0.00 0.00 41.91 3.55
3211 7189 3.066342 CCTCAGATGGCTAATGCAAAGTG 59.934 47.826 0.00 0.00 41.91 3.16
3212 7190 3.285484 CCTCAGATGGCTAATGCAAAGT 58.715 45.455 0.00 0.00 41.91 2.66
3213 7191 2.621998 CCCTCAGATGGCTAATGCAAAG 59.378 50.000 0.00 0.00 41.91 2.77
3214 7192 2.658285 CCCTCAGATGGCTAATGCAAA 58.342 47.619 0.00 0.00 41.91 3.68
3215 7193 1.751733 GCCCTCAGATGGCTAATGCAA 60.752 52.381 9.41 0.00 45.70 4.08
3216 7194 0.179009 GCCCTCAGATGGCTAATGCA 60.179 55.000 9.41 0.00 45.70 3.96
3217 7195 2.638744 GCCCTCAGATGGCTAATGC 58.361 57.895 9.41 0.00 45.70 3.56
3223 7201 4.341235 TGTATATATACGCCCTCAGATGGC 59.659 45.833 16.29 6.65 45.70 4.40
3224 7202 5.594725 ACTGTATATATACGCCCTCAGATGG 59.405 44.000 16.29 0.00 36.06 3.51
3225 7203 6.701145 ACTGTATATATACGCCCTCAGATG 57.299 41.667 16.29 1.95 36.06 2.90
3226 7204 7.832685 TGTAACTGTATATATACGCCCTCAGAT 59.167 37.037 16.29 6.22 36.06 2.90
3227 7205 7.170277 TGTAACTGTATATATACGCCCTCAGA 58.830 38.462 16.29 0.00 36.06 3.27
3228 7206 7.336176 TCTGTAACTGTATATATACGCCCTCAG 59.664 40.741 16.29 18.23 36.06 3.35
3229 7207 7.170277 TCTGTAACTGTATATATACGCCCTCA 58.830 38.462 16.29 11.79 36.06 3.86
3230 7208 7.621428 TCTGTAACTGTATATATACGCCCTC 57.379 40.000 16.29 8.58 36.06 4.30
3231 7209 8.413309 TTTCTGTAACTGTATATATACGCCCT 57.587 34.615 16.29 5.45 36.06 5.19
3232 7210 7.758528 CCTTTCTGTAACTGTATATATACGCCC 59.241 40.741 16.29 5.12 36.06 6.13
3233 7211 7.758528 CCCTTTCTGTAACTGTATATATACGCC 59.241 40.741 16.29 4.83 36.06 5.68
3234 7212 8.517878 TCCCTTTCTGTAACTGTATATATACGC 58.482 37.037 16.29 6.40 36.06 4.42
3240 7218 9.975218 AACATTTCCCTTTCTGTAACTGTATAT 57.025 29.630 0.00 0.00 0.00 0.86
3241 7219 9.444600 GAACATTTCCCTTTCTGTAACTGTATA 57.555 33.333 0.00 0.00 0.00 1.47
3242 7220 7.393515 GGAACATTTCCCTTTCTGTAACTGTAT 59.606 37.037 0.00 0.00 44.30 2.29
3243 7221 6.713450 GGAACATTTCCCTTTCTGTAACTGTA 59.287 38.462 0.00 0.00 44.30 2.74
3244 7222 5.535030 GGAACATTTCCCTTTCTGTAACTGT 59.465 40.000 0.00 0.00 44.30 3.55
3245 7223 6.013842 GGAACATTTCCCTTTCTGTAACTG 57.986 41.667 0.00 0.00 44.30 3.16
3259 7237 0.521735 GCACCGTCTGGGAACATTTC 59.478 55.000 0.00 0.00 41.51 2.17
3260 7238 0.179004 TGCACCGTCTGGGAACATTT 60.179 50.000 0.00 0.00 41.51 2.32
3261 7239 0.889186 GTGCACCGTCTGGGAACATT 60.889 55.000 5.22 0.00 41.51 2.71
3262 7240 1.302511 GTGCACCGTCTGGGAACAT 60.303 57.895 5.22 0.00 41.51 2.71
3263 7241 2.110213 GTGCACCGTCTGGGAACA 59.890 61.111 5.22 0.00 40.75 3.18
3264 7242 2.668550 GGTGCACCGTCTGGGAAC 60.669 66.667 22.49 0.00 40.75 3.62


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

AutoCloner maintained by Alex Coulton.