Multiple sequence alignment - TraesCS5D01G455400

Loading Multiple Alignment...

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 TraesCS5D01G455400 chr5D 100.000 4710 0 0 1 4710 502545164 502549873 0.000000e+00 8698
1 TraesCS5D01G455400 chr5D 83.654 208 21 8 523 728 502537276 502537472 2.890000e-42 183
2 TraesCS5D01G455400 chr5D 82.212 208 24 8 523 728 502365064 502365260 2.920000e-37 167
3 TraesCS5D01G455400 chr5A 91.327 2675 129 36 303 2925 631260263 631262886 0.000000e+00 3559
4 TraesCS5D01G455400 chr5A 94.453 649 27 6 2925 3573 631263057 631263696 0.000000e+00 990
5 TraesCS5D01G455400 chr5A 83.935 554 42 27 3969 4502 631264222 631264748 1.970000e-133 486
6 TraesCS5D01G455400 chr5A 92.177 294 20 2 3632 3922 631263928 631264221 3.390000e-111 412
7 TraesCS5D01G455400 chr5A 91.667 120 10 0 150 269 631260142 631260261 2.920000e-37 167
8 TraesCS5D01G455400 chr5B 92.775 2076 75 22 39 2053 626193090 626195151 0.000000e+00 2933
9 TraesCS5D01G455400 chr5B 91.858 872 66 4 2050 2920 626195350 626196217 0.000000e+00 1212
10 TraesCS5D01G455400 chr5B 83.314 881 83 34 3636 4474 626197625 626198483 0.000000e+00 754
11 TraesCS5D01G455400 chr5B 93.051 331 14 5 1876 2198 596618626 596618297 4.260000e-130 475
12 TraesCS5D01G455400 chr5B 92.966 327 14 5 1880 2198 614667572 614667247 7.140000e-128 468
13 TraesCS5D01G455400 chr5B 80.403 694 71 24 308 965 631365995 631366659 7.140000e-128 468
14 TraesCS5D01G455400 chr5B 90.421 261 18 2 1554 1808 547960637 547960896 2.100000e-88 337
15 TraesCS5D01G455400 chr5B 97.414 116 3 0 1 116 626193007 626193122 1.030000e-46 198
16 TraesCS5D01G455400 chr5B 84.135 208 20 8 523 728 626140807 626141003 6.220000e-44 189
17 TraesCS5D01G455400 chr5B 82.775 209 21 9 523 728 626085107 626085303 6.270000e-39 172
18 TraesCS5D01G455400 chr5B 81.818 209 24 8 523 728 626107150 626107347 3.770000e-36 163
19 TraesCS5D01G455400 chr5B 81.250 208 26 7 523 728 631378855 631379051 6.310000e-34 156
20 TraesCS5D01G455400 chr5B 79.904 209 27 9 523 728 631354383 631354579 6.360000e-29 139
21 TraesCS5D01G455400 chr5B 85.321 109 16 0 1 109 631365681 631365789 3.850000e-21 113
22 TraesCS5D01G455400 chr2A 89.403 670 37 15 2925 3573 374124015 374124671 0.000000e+00 813
23 TraesCS5D01G455400 chr1D 88.203 551 33 17 3044 3573 308872854 308872315 3.090000e-176 628
24 TraesCS5D01G455400 chr7B 93.051 331 14 5 1876 2198 300116888 300117217 4.260000e-130 475
25 TraesCS5D01G455400 chr7B 93.051 331 14 6 1876 2198 358899119 358899448 4.260000e-130 475
26 TraesCS5D01G455400 chr7B 92.749 331 15 5 1876 2198 324179873 324180202 1.980000e-128 470
27 TraesCS5D01G455400 chr7B 90.536 317 24 2 1498 1808 358898094 358898410 9.430000e-112 414
28 TraesCS5D01G455400 chr4A 93.051 331 14 5 1876 2198 660179139 660178810 4.260000e-130 475
29 TraesCS5D01G455400 chr4A 92.749 331 15 5 1876 2198 692644306 692644635 1.980000e-128 470
30 TraesCS5D01G455400 chr3B 93.051 331 14 5 1876 2198 740874476 740874147 4.260000e-130 475
31 TraesCS5D01G455400 chr1B 92.749 331 13 6 1876 2198 4907553 4907226 7.140000e-128 468


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 TraesCS5D01G455400 chr5D 502545164 502549873 4709 False 8698.00 8698 100.00000 1 4710 1 chr5D.!!$F3 4709
1 TraesCS5D01G455400 chr5A 631260142 631264748 4606 False 1122.80 3559 90.71180 150 4502 5 chr5A.!!$F1 4352
2 TraesCS5D01G455400 chr5B 626193007 626198483 5476 False 1274.25 2933 91.34025 1 4474 4 chr5B.!!$F7 4473
3 TraesCS5D01G455400 chr5B 631365681 631366659 978 False 290.50 468 82.86200 1 965 2 chr5B.!!$F8 964
4 TraesCS5D01G455400 chr2A 374124015 374124671 656 False 813.00 813 89.40300 2925 3573 1 chr2A.!!$F1 648
5 TraesCS5D01G455400 chr1D 308872315 308872854 539 True 628.00 628 88.20300 3044 3573 1 chr1D.!!$R1 529
6 TraesCS5D01G455400 chr7B 358898094 358899448 1354 False 444.50 475 91.79350 1498 2198 2 chr7B.!!$F3 700

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
542 587 0.107643 TTGGCGTCTGTTCATCCACA 59.892 50.0 0.0 0.0 0.00 4.17 F
1796 1916 0.718343 GCAATGCTCGTCTCTGTGTC 59.282 55.0 0.0 0.0 0.00 3.67 F
3153 4348 0.179059 TGTGATGTCAAGCACCGTGT 60.179 50.0 0.0 0.0 42.18 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2144 3145 1.199097 CAGAATTGCGTACACCCAACC 59.801 52.381 0.00 0.00 0.00 3.77 R
3359 4990 0.463295 TCTACTAGACGGGCAGACGG 60.463 60.000 0.00 0.00 38.39 4.79 R
4038 5929 0.111253 ACTGAGTTTTCCAGGCCAGG 59.889 55.000 8.15 8.15 36.03 4.45 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
88 89 2.846918 GTGATTCGCTATCGCCGC 59.153 61.111 0.95 0.00 37.72 6.53
188 232 1.572689 TAGAGACCCTCGTGCCTCCT 61.573 60.000 0.00 0.00 35.36 3.69
223 267 1.730612 GCCTGCAAAAGTCGTAGGTAC 59.269 52.381 0.00 0.00 38.41 3.34
294 338 7.391786 GCGGTTTTTCTTTCTTTCTTTCTTTC 58.608 34.615 0.00 0.00 0.00 2.62
304 348 4.511826 TCTTTCTTTCTTTCTTGCGAGGAC 59.488 41.667 0.00 0.00 0.00 3.85
306 350 2.035449 TCTTTCTTTCTTGCGAGGACGA 59.965 45.455 0.00 0.00 42.66 4.20
357 402 9.352784 GTCCTAGATCTCGAGAAATCATTTATG 57.647 37.037 20.91 0.00 0.00 1.90
515 560 7.319646 CAAGCAACTCAGAGAGAAGTATACTT 58.680 38.462 18.05 18.05 39.23 2.24
542 587 0.107643 TTGGCGTCTGTTCATCCACA 59.892 50.000 0.00 0.00 0.00 4.17
952 1052 2.294127 ACCATCCCAGAGAGAATTCCCT 60.294 50.000 0.65 0.00 0.00 4.20
961 1062 4.222588 CAGAGAGAATTCCCTCAGACAACT 59.777 45.833 18.07 0.00 35.68 3.16
1227 1328 2.046023 TTCCTGCTGGGCATGACG 60.046 61.111 10.07 0.00 38.13 4.35
1796 1916 0.718343 GCAATGCTCGTCTCTGTGTC 59.282 55.000 0.00 0.00 0.00 3.67
1871 1991 6.471146 AGTTGAATCTGAACTGCATCTAAGT 58.529 36.000 0.00 0.00 32.30 2.24
1872 1992 6.370994 AGTTGAATCTGAACTGCATCTAAGTG 59.629 38.462 0.00 0.00 32.30 3.16
1874 1994 6.233434 TGAATCTGAACTGCATCTAAGTGTT 58.767 36.000 0.00 0.00 0.00 3.32
1915 2699 2.218987 GCTAATCGCGCTTAGGAGAAAC 59.781 50.000 25.89 8.86 30.80 2.78
1959 2746 0.956633 ACAGCAATTGTCTGCCAGTG 59.043 50.000 21.99 2.61 43.73 3.66
1993 2785 1.093972 CATTGCTGGCATCGGTTGTA 58.906 50.000 0.00 0.00 0.00 2.41
2144 3145 0.816018 TGGTGGCCGTTGTTGTACTG 60.816 55.000 0.00 0.00 0.00 2.74
2194 3196 1.523515 TGTGTCATGTGTAACGTTCGC 59.476 47.619 2.82 4.19 42.39 4.70
2245 3247 4.472691 TCGCAAGCAATCTGTATTATGC 57.527 40.909 0.00 0.00 39.06 3.14
2250 3252 6.444633 GCAAGCAATCTGTATTATGCAATCT 58.555 36.000 0.00 0.00 41.18 2.40
2252 3254 8.077991 GCAAGCAATCTGTATTATGCAATCTAA 58.922 33.333 0.00 0.00 41.18 2.10
2284 3286 6.183360 GCTTATTGTAGCATTCATCCCAACTT 60.183 38.462 0.00 0.00 40.89 2.66
2344 3355 9.699410 ATCAAATCTTCTGTCATATTTTGGGTA 57.301 29.630 0.00 0.00 0.00 3.69
2382 3393 3.434984 GTCAAGTGCATCCTGAGAAACTC 59.565 47.826 0.00 0.00 0.00 3.01
2399 3410 2.888212 ACTCTCCTTTCTCAGCTCTGT 58.112 47.619 0.00 0.00 0.00 3.41
2440 3452 9.750125 CTGTATAGCATTACTCTGTATTGTTGA 57.250 33.333 0.00 0.00 0.00 3.18
2481 3493 5.050490 TCTTCTGTACTGAAGAACTTGCAC 58.950 41.667 31.44 0.00 46.32 4.57
2483 3495 3.123804 CTGTACTGAAGAACTTGCACGT 58.876 45.455 0.00 0.00 0.00 4.49
2486 3498 1.064060 ACTGAAGAACTTGCACGTTGC 59.936 47.619 13.95 5.49 45.29 4.17
2504 3516 5.351465 ACGTTGCATCTACACTTATCTTTGG 59.649 40.000 0.00 0.00 0.00 3.28
2505 3517 5.351465 CGTTGCATCTACACTTATCTTTGGT 59.649 40.000 0.00 0.00 0.00 3.67
2506 3518 6.533723 CGTTGCATCTACACTTATCTTTGGTA 59.466 38.462 0.00 0.00 0.00 3.25
2508 3520 8.893727 GTTGCATCTACACTTATCTTTGGTATT 58.106 33.333 0.00 0.00 0.00 1.89
2509 3521 8.437360 TGCATCTACACTTATCTTTGGTATTG 57.563 34.615 0.00 0.00 0.00 1.90
2512 3526 8.755941 CATCTACACTTATCTTTGGTATTGTCG 58.244 37.037 0.00 0.00 0.00 4.35
2519 3533 9.314321 ACTTATCTTTGGTATTGTCGTCATTAG 57.686 33.333 0.00 0.00 0.00 1.73
2549 3563 8.664669 AACTTTTATGGTGGGTGAGAAAATAT 57.335 30.769 0.00 0.00 0.00 1.28
2559 3573 7.305474 GTGGGTGAGAAAATATTAACACTGTG 58.695 38.462 6.19 6.19 0.00 3.66
2591 3605 4.976224 TTATCGTCAGTCTTCCGATTCA 57.024 40.909 8.31 0.00 41.22 2.57
2771 3785 2.542411 CGATGATCTGATCGTCTGCACA 60.542 50.000 28.07 6.17 41.95 4.57
2875 3889 3.927142 CGTGAGTCCTCAAAAGGTATGTC 59.073 47.826 0.00 0.00 43.82 3.06
2878 3892 3.935828 GAGTCCTCAAAAGGTATGTCTGC 59.064 47.826 0.00 0.00 43.82 4.26
2891 3905 4.513318 GGTATGTCTGCTATTCCTTCTTGC 59.487 45.833 0.00 0.00 0.00 4.01
2898 3912 7.147655 TGTCTGCTATTCCTTCTTGCTTATACT 60.148 37.037 0.00 0.00 0.00 2.12
2900 3914 8.361139 TCTGCTATTCCTTCTTGCTTATACTAC 58.639 37.037 0.00 0.00 0.00 2.73
2901 3915 8.018537 TGCTATTCCTTCTTGCTTATACTACA 57.981 34.615 0.00 0.00 0.00 2.74
2902 3916 8.482943 TGCTATTCCTTCTTGCTTATACTACAA 58.517 33.333 0.00 0.00 0.00 2.41
2909 3923 9.330063 CCTTCTTGCTTATACTACAATCATTCA 57.670 33.333 0.00 0.00 0.00 2.57
2920 3934 4.297299 ACAATCATTCATTGATCGTGCC 57.703 40.909 1.36 0.00 44.51 5.01
2930 4125 5.639757 TCATTGATCGTGCCAATTTAGTTG 58.360 37.500 0.00 0.00 37.57 3.16
2951 4146 3.439825 TGTAGCAGTATGGCATGTTTGTG 59.560 43.478 10.98 1.39 35.86 3.33
3029 4224 2.351447 GGGTTTTCCGACTAAGCAAAGC 60.351 50.000 0.00 0.00 41.82 3.51
3057 4252 8.526147 CACCTTCTCCAGTTTATCATTTCAAAT 58.474 33.333 0.00 0.00 0.00 2.32
3122 4317 7.764901 ACGTGGTCTTATTCTAATCCTTTTCTC 59.235 37.037 0.00 0.00 0.00 2.87
3153 4348 0.179059 TGTGATGTCAAGCACCGTGT 60.179 50.000 0.00 0.00 42.18 4.49
3188 4393 3.817647 GAGCAAAAGAGTGAGTGTCCATT 59.182 43.478 0.00 0.00 0.00 3.16
3341 4618 5.006552 GTCAGTCTAGCTCAGAATGCATTTC 59.993 44.000 14.33 7.05 46.61 2.17
3387 5018 3.499157 GCCCGTCTAGTAGATCAGTAGTG 59.501 52.174 2.51 0.00 32.68 2.74
3388 5019 4.706035 CCCGTCTAGTAGATCAGTAGTGT 58.294 47.826 2.51 0.00 32.68 3.55
3565 5229 6.654793 TTTGTTTTGTTTAGCATGGTTCAC 57.345 33.333 1.12 0.65 0.00 3.18
3573 5237 8.744568 TTGTTTAGCATGGTTCACATATGATA 57.255 30.769 10.38 0.00 37.84 2.15
3574 5238 8.153479 TGTTTAGCATGGTTCACATATGATAC 57.847 34.615 10.38 4.08 37.84 2.24
3576 5240 7.967890 TTAGCATGGTTCACATATGATACAG 57.032 36.000 10.38 0.56 37.84 2.74
3577 5241 4.758674 AGCATGGTTCACATATGATACAGC 59.241 41.667 10.38 9.00 37.84 4.40
3578 5242 4.083110 GCATGGTTCACATATGATACAGCC 60.083 45.833 10.38 4.54 37.84 4.85
3579 5243 4.085357 TGGTTCACATATGATACAGCCC 57.915 45.455 10.38 0.69 33.85 5.19
3580 5244 3.181445 TGGTTCACATATGATACAGCCCC 60.181 47.826 10.38 0.00 33.85 5.80
3581 5245 3.181445 GGTTCACATATGATACAGCCCCA 60.181 47.826 10.38 0.00 33.85 4.96
3582 5246 4.507335 GGTTCACATATGATACAGCCCCAT 60.507 45.833 10.38 0.00 33.85 4.00
3583 5247 4.999469 TCACATATGATACAGCCCCATT 57.001 40.909 10.38 0.00 0.00 3.16
3584 5248 4.654915 TCACATATGATACAGCCCCATTG 58.345 43.478 10.38 0.00 0.00 2.82
3586 5250 5.309282 TCACATATGATACAGCCCCATTGTA 59.691 40.000 10.38 0.00 35.66 2.41
3587 5251 6.003326 CACATATGATACAGCCCCATTGTAA 58.997 40.000 10.38 0.00 34.92 2.41
3588 5252 6.149973 CACATATGATACAGCCCCATTGTAAG 59.850 42.308 10.38 0.00 34.92 2.34
3615 5339 3.932710 TGGATACAGCGATGTTTGAACTC 59.067 43.478 13.34 0.00 46.17 3.01
3616 5340 4.184629 GGATACAGCGATGTTTGAACTCT 58.815 43.478 13.34 0.00 0.00 3.24
3617 5341 4.268884 GGATACAGCGATGTTTGAACTCTC 59.731 45.833 13.34 0.00 0.00 3.20
3618 5342 2.417719 ACAGCGATGTTTGAACTCTCC 58.582 47.619 0.00 0.00 0.00 3.71
3619 5343 2.037772 ACAGCGATGTTTGAACTCTCCT 59.962 45.455 0.00 0.00 0.00 3.69
3621 5345 3.499918 CAGCGATGTTTGAACTCTCCTTT 59.500 43.478 0.00 0.00 0.00 3.11
3622 5346 4.690748 CAGCGATGTTTGAACTCTCCTTTA 59.309 41.667 0.00 0.00 0.00 1.85
3627 5351 6.866770 CGATGTTTGAACTCTCCTTTAGTACA 59.133 38.462 0.00 0.00 0.00 2.90
3629 5353 7.962964 TGTTTGAACTCTCCTTTAGTACATG 57.037 36.000 0.00 0.00 0.00 3.21
3630 5354 6.934645 TGTTTGAACTCTCCTTTAGTACATGG 59.065 38.462 0.00 0.00 0.00 3.66
3774 5645 3.818787 GGGCTGCGCATCTGGTTG 61.819 66.667 12.24 0.00 0.00 3.77
3785 5669 3.242969 CGCATCTGGTTGATTCATTGGAG 60.243 47.826 0.00 0.00 32.05 3.86
3793 5677 6.604171 TGGTTGATTCATTGGAGCTATACAT 58.396 36.000 0.00 0.00 0.00 2.29
3854 5740 4.571919 TCCCGTTCTTGTGTATAAAGTGG 58.428 43.478 0.00 0.00 0.00 4.00
3876 5762 7.994334 AGTGGTATAGATTAATTTAAACCGGCA 59.006 33.333 0.00 0.00 0.00 5.69
3908 5795 6.199342 GCGAAAGACTGGAGAGATGTTTATAC 59.801 42.308 0.00 0.00 0.00 1.47
4038 5929 6.105333 GGAGATAGTGCTGTCCATGAATATC 58.895 44.000 0.00 0.00 0.00 1.63
4078 5969 1.610624 GGACTCATTCCTCGGTTGCAA 60.611 52.381 0.00 0.00 41.95 4.08
4105 5996 3.258372 TCTGGAAGTAGCACTTGGTGTAG 59.742 47.826 6.31 0.00 38.80 2.74
4107 5998 4.154176 TGGAAGTAGCACTTGGTGTAGTA 58.846 43.478 6.31 0.00 38.80 1.82
4157 6055 4.323868 CCGACTACGTCTGATTTGACTTTC 59.676 45.833 0.00 0.00 37.88 2.62
4165 6063 4.750098 GTCTGATTTGACTTTCAGGACGAA 59.250 41.667 0.00 0.00 39.84 3.85
4171 6069 3.664107 TGACTTTCAGGACGAAGAATGG 58.336 45.455 0.00 0.00 34.32 3.16
4193 6100 4.082354 GGTTCTTAGCGAAAGAGTAGTGGA 60.082 45.833 4.97 0.00 44.95 4.02
4194 6101 4.966965 TCTTAGCGAAAGAGTAGTGGAG 57.033 45.455 0.92 0.00 39.36 3.86
4205 6112 7.879160 CGAAAGAGTAGTGGAGGTAGTATATCT 59.121 40.741 0.00 0.00 32.18 1.98
4222 6129 3.788227 ATCTGTTCAACAGGGCACTTA 57.212 42.857 17.71 0.00 45.94 2.24
4223 6130 3.788227 TCTGTTCAACAGGGCACTTAT 57.212 42.857 17.71 0.00 45.94 1.73
4224 6131 3.411446 TCTGTTCAACAGGGCACTTATG 58.589 45.455 17.71 0.00 45.94 1.90
4228 6149 3.616956 TCAACAGGGCACTTATGAGAG 57.383 47.619 0.00 0.00 0.00 3.20
4229 6150 2.237143 TCAACAGGGCACTTATGAGAGG 59.763 50.000 0.00 0.00 0.00 3.69
4247 6168 0.958822 GGCTGACGGTTGTTTTGGAT 59.041 50.000 0.00 0.00 0.00 3.41
4254 6175 4.454161 TGACGGTTGTTTTGGATCATACTG 59.546 41.667 0.00 0.00 0.00 2.74
4255 6176 3.756434 ACGGTTGTTTTGGATCATACTGG 59.244 43.478 0.00 0.00 0.00 4.00
4256 6177 3.756434 CGGTTGTTTTGGATCATACTGGT 59.244 43.478 0.00 0.00 0.00 4.00
4257 6178 4.938832 CGGTTGTTTTGGATCATACTGGTA 59.061 41.667 0.00 0.00 0.00 3.25
4258 6179 5.413213 CGGTTGTTTTGGATCATACTGGTAA 59.587 40.000 0.00 0.00 0.00 2.85
4259 6180 6.617879 GGTTGTTTTGGATCATACTGGTAAC 58.382 40.000 0.00 0.00 0.00 2.50
4260 6181 6.433093 GGTTGTTTTGGATCATACTGGTAACT 59.567 38.462 0.00 0.00 37.61 2.24
4261 6182 7.039993 GGTTGTTTTGGATCATACTGGTAACTT 60.040 37.037 0.00 0.00 37.61 2.66
4262 6183 7.447374 TGTTTTGGATCATACTGGTAACTTG 57.553 36.000 0.00 0.00 37.61 3.16
4263 6184 6.432783 TGTTTTGGATCATACTGGTAACTTGG 59.567 38.462 0.00 0.00 37.61 3.61
4264 6185 5.772393 TTGGATCATACTGGTAACTTGGT 57.228 39.130 0.00 0.00 37.61 3.67
4265 6186 6.877668 TTGGATCATACTGGTAACTTGGTA 57.122 37.500 0.00 0.00 37.61 3.25
4266 6187 6.877668 TGGATCATACTGGTAACTTGGTAA 57.122 37.500 0.00 0.00 37.61 2.85
4282 6203 3.857052 TGGTAAGTAAGCATCTTGTCCG 58.143 45.455 0.00 0.00 0.00 4.79
4285 6206 3.678056 AAGTAAGCATCTTGTCCGTGA 57.322 42.857 0.00 0.00 0.00 4.35
4290 6214 1.639298 GCATCTTGTCCGTGACTGGC 61.639 60.000 5.77 0.00 33.15 4.85
4298 6222 3.857854 CGTGACTGGCGCTGCATC 61.858 66.667 7.64 0.58 0.00 3.91
4306 6230 3.885521 GCGCTGCATCTTCTGGCC 61.886 66.667 0.00 0.00 0.00 5.36
4312 6236 0.745486 TGCATCTTCTGGCCATCACG 60.745 55.000 5.51 0.00 0.00 4.35
4319 6243 1.855295 TCTGGCCATCACGGTACTTA 58.145 50.000 5.51 0.00 36.97 2.24
4348 6272 0.895100 GGCAGACCAGGCATTCACAA 60.895 55.000 0.00 0.00 35.26 3.33
4388 6312 0.875059 GTTTTCAGCCAGGAACTCGG 59.125 55.000 0.00 0.00 34.60 4.63
4393 6317 2.125350 GCCAGGAACTCGGCAGAG 60.125 66.667 12.66 12.66 46.65 3.35
4395 6319 2.172483 GCCAGGAACTCGGCAGAGAA 62.172 60.000 21.22 0.00 46.65 2.87
4406 6330 1.618343 CGGCAGAGAATTTTGGGGTTT 59.382 47.619 0.00 0.00 0.00 3.27
4408 6332 2.416747 GCAGAGAATTTTGGGGTTTGC 58.583 47.619 0.00 0.00 0.00 3.68
4470 6394 2.490903 GCTGATGAATGAGTGCCAACTT 59.509 45.455 0.00 0.00 36.52 2.66
4474 6398 4.828939 TGATGAATGAGTGCCAACTTCTTT 59.171 37.500 0.00 0.00 36.52 2.52
4475 6399 5.302568 TGATGAATGAGTGCCAACTTCTTTT 59.697 36.000 0.00 0.00 36.52 2.27
4503 6434 8.508883 TTTTTGAGTAACTACTGCTGGTAAAA 57.491 30.769 0.00 0.00 36.50 1.52
4504 6435 8.508883 TTTTGAGTAACTACTGCTGGTAAAAA 57.491 30.769 0.00 0.00 36.50 1.94
4505 6436 8.685838 TTTGAGTAACTACTGCTGGTAAAAAT 57.314 30.769 0.00 0.00 36.50 1.82
4506 6437 8.685838 TTGAGTAACTACTGCTGGTAAAAATT 57.314 30.769 0.00 0.00 36.50 1.82
4507 6438 8.685838 TGAGTAACTACTGCTGGTAAAAATTT 57.314 30.769 0.00 0.00 36.50 1.82
4508 6439 8.564574 TGAGTAACTACTGCTGGTAAAAATTTG 58.435 33.333 0.00 0.00 36.50 2.32
4509 6440 8.459911 AGTAACTACTGCTGGTAAAAATTTGT 57.540 30.769 0.00 0.00 34.72 2.83
4510 6441 8.565416 AGTAACTACTGCTGGTAAAAATTTGTC 58.435 33.333 0.00 0.00 34.72 3.18
4511 6442 7.582667 AACTACTGCTGGTAAAAATTTGTCT 57.417 32.000 0.00 0.00 0.00 3.41
4512 6443 7.203255 ACTACTGCTGGTAAAAATTTGTCTC 57.797 36.000 0.00 0.00 0.00 3.36
4513 6444 6.770785 ACTACTGCTGGTAAAAATTTGTCTCA 59.229 34.615 0.00 0.00 0.00 3.27
4514 6445 6.655078 ACTGCTGGTAAAAATTTGTCTCAT 57.345 33.333 0.00 0.00 0.00 2.90
4515 6446 7.759489 ACTGCTGGTAAAAATTTGTCTCATA 57.241 32.000 0.00 0.00 0.00 2.15
4516 6447 7.593825 ACTGCTGGTAAAAATTTGTCTCATAC 58.406 34.615 0.00 0.00 0.00 2.39
4517 6448 7.448469 ACTGCTGGTAAAAATTTGTCTCATACT 59.552 33.333 0.00 0.00 0.00 2.12
4518 6449 7.816640 TGCTGGTAAAAATTTGTCTCATACTC 58.183 34.615 0.00 0.00 0.00 2.59
4519 6450 7.446931 TGCTGGTAAAAATTTGTCTCATACTCA 59.553 33.333 0.00 0.00 0.00 3.41
4520 6451 8.462016 GCTGGTAAAAATTTGTCTCATACTCAT 58.538 33.333 0.00 0.00 0.00 2.90
4521 6452 9.994432 CTGGTAAAAATTTGTCTCATACTCATC 57.006 33.333 0.00 0.00 0.00 2.92
4522 6453 9.739276 TGGTAAAAATTTGTCTCATACTCATCT 57.261 29.630 0.00 0.00 0.00 2.90
4526 6457 7.636150 AAATTTGTCTCATACTCATCTTGGG 57.364 36.000 0.00 0.00 0.00 4.12
4527 6458 3.827008 TGTCTCATACTCATCTTGGGC 57.173 47.619 0.00 0.00 0.00 5.36
4528 6459 3.378512 TGTCTCATACTCATCTTGGGCT 58.621 45.455 0.00 0.00 0.00 5.19
4529 6460 3.386078 TGTCTCATACTCATCTTGGGCTC 59.614 47.826 0.00 0.00 0.00 4.70
4530 6461 2.968574 TCTCATACTCATCTTGGGCTCC 59.031 50.000 0.00 0.00 0.00 4.70
4531 6462 2.971330 CTCATACTCATCTTGGGCTCCT 59.029 50.000 0.00 0.00 0.00 3.69
4532 6463 2.702478 TCATACTCATCTTGGGCTCCTG 59.298 50.000 0.00 0.00 0.00 3.86
4533 6464 1.500474 TACTCATCTTGGGCTCCTGG 58.500 55.000 0.00 0.00 0.00 4.45
4534 6465 1.153005 CTCATCTTGGGCTCCTGGC 60.153 63.158 0.00 0.00 40.90 4.85
4535 6466 1.617536 TCATCTTGGGCTCCTGGCT 60.618 57.895 0.00 0.00 41.46 4.75
4536 6467 1.153005 CATCTTGGGCTCCTGGCTC 60.153 63.158 0.00 0.00 42.93 4.70
4537 6468 2.739996 ATCTTGGGCTCCTGGCTCG 61.740 63.158 0.00 0.00 46.29 5.03
4538 6469 4.479993 CTTGGGCTCCTGGCTCGG 62.480 72.222 0.00 0.00 46.29 4.63
4550 6481 2.421739 GCTCGGGCCGTCACATAT 59.578 61.111 27.32 0.00 0.00 1.78
4551 6482 1.663739 GCTCGGGCCGTCACATATA 59.336 57.895 27.32 2.13 0.00 0.86
4552 6483 0.388649 GCTCGGGCCGTCACATATAG 60.389 60.000 27.32 14.20 0.00 1.31
4553 6484 0.959553 CTCGGGCCGTCACATATAGT 59.040 55.000 27.32 0.00 0.00 2.12
4554 6485 1.340248 CTCGGGCCGTCACATATAGTT 59.660 52.381 27.32 0.00 0.00 2.24
4555 6486 1.338973 TCGGGCCGTCACATATAGTTC 59.661 52.381 27.32 0.00 0.00 3.01
4556 6487 1.340248 CGGGCCGTCACATATAGTTCT 59.660 52.381 19.97 0.00 0.00 3.01
4557 6488 2.223971 CGGGCCGTCACATATAGTTCTT 60.224 50.000 19.97 0.00 0.00 2.52
4558 6489 3.391049 GGGCCGTCACATATAGTTCTTC 58.609 50.000 0.00 0.00 0.00 2.87
4559 6490 3.181469 GGGCCGTCACATATAGTTCTTCA 60.181 47.826 0.00 0.00 0.00 3.02
4560 6491 3.802685 GGCCGTCACATATAGTTCTTCAC 59.197 47.826 0.00 0.00 0.00 3.18
4561 6492 3.802685 GCCGTCACATATAGTTCTTCACC 59.197 47.826 0.00 0.00 0.00 4.02
4562 6493 4.042398 CCGTCACATATAGTTCTTCACCG 58.958 47.826 0.00 0.00 0.00 4.94
4563 6494 4.439700 CCGTCACATATAGTTCTTCACCGT 60.440 45.833 0.00 0.00 0.00 4.83
4564 6495 5.220912 CCGTCACATATAGTTCTTCACCGTA 60.221 44.000 0.00 0.00 0.00 4.02
4565 6496 6.260377 CGTCACATATAGTTCTTCACCGTAA 58.740 40.000 0.00 0.00 0.00 3.18
4566 6497 6.916387 CGTCACATATAGTTCTTCACCGTAAT 59.084 38.462 0.00 0.00 0.00 1.89
4567 6498 8.071967 CGTCACATATAGTTCTTCACCGTAATA 58.928 37.037 0.00 0.00 0.00 0.98
4568 6499 9.740239 GTCACATATAGTTCTTCACCGTAATAA 57.260 33.333 0.00 0.00 0.00 1.40
4576 6507 7.368833 AGTTCTTCACCGTAATAATATCTCCG 58.631 38.462 0.00 0.00 0.00 4.63
4577 6508 6.889301 TCTTCACCGTAATAATATCTCCGT 57.111 37.500 0.00 0.00 0.00 4.69
4578 6509 6.906659 TCTTCACCGTAATAATATCTCCGTC 58.093 40.000 0.00 0.00 0.00 4.79
4579 6510 5.287170 TCACCGTAATAATATCTCCGTCG 57.713 43.478 0.00 0.00 0.00 5.12
4580 6511 4.996758 TCACCGTAATAATATCTCCGTCGA 59.003 41.667 0.00 0.00 0.00 4.20
4581 6512 5.469760 TCACCGTAATAATATCTCCGTCGAA 59.530 40.000 0.00 0.00 0.00 3.71
4582 6513 6.017192 TCACCGTAATAATATCTCCGTCGAAA 60.017 38.462 0.00 0.00 0.00 3.46
4583 6514 6.638063 CACCGTAATAATATCTCCGTCGAAAA 59.362 38.462 0.00 0.00 0.00 2.29
4584 6515 7.167968 CACCGTAATAATATCTCCGTCGAAAAA 59.832 37.037 0.00 0.00 0.00 1.94
4599 6530 3.633361 AAAAAGAGGCAGCGCTACT 57.367 47.368 10.99 12.22 0.00 2.57
4607 6538 3.121030 CAGCGCTACTGGTGTGCC 61.121 66.667 10.99 0.00 43.19 5.01
4608 6539 4.394712 AGCGCTACTGGTGTGCCC 62.395 66.667 8.99 0.00 41.34 5.36
4609 6540 4.697756 GCGCTACTGGTGTGCCCA 62.698 66.667 0.00 0.00 42.51 5.36
4616 6547 3.625897 TGGTGTGCCCAGGTCTCG 61.626 66.667 0.00 0.00 38.72 4.04
4618 6549 4.008933 GTGTGCCCAGGTCTCGCT 62.009 66.667 0.00 0.00 0.00 4.93
4619 6550 3.241530 TGTGCCCAGGTCTCGCTT 61.242 61.111 0.00 0.00 0.00 4.68
4620 6551 1.911269 TGTGCCCAGGTCTCGCTTA 60.911 57.895 0.00 0.00 0.00 3.09
4621 6552 1.264749 TGTGCCCAGGTCTCGCTTAT 61.265 55.000 0.00 0.00 0.00 1.73
4622 6553 0.750850 GTGCCCAGGTCTCGCTTATA 59.249 55.000 0.00 0.00 0.00 0.98
4623 6554 1.040646 TGCCCAGGTCTCGCTTATAG 58.959 55.000 0.00 0.00 0.00 1.31
4624 6555 0.319986 GCCCAGGTCTCGCTTATAGC 60.320 60.000 0.00 0.00 38.02 2.97
4636 6567 3.528009 GCTTATAGCGAGACAAATGGC 57.472 47.619 0.00 0.00 0.00 4.40
4637 6568 3.134458 GCTTATAGCGAGACAAATGGCT 58.866 45.455 0.00 0.00 37.96 4.75
4638 6569 3.059325 GCTTATAGCGAGACAAATGGCTG 60.059 47.826 0.00 0.00 35.69 4.85
4639 6570 1.303309 ATAGCGAGACAAATGGCTGC 58.697 50.000 0.00 0.00 35.69 5.25
4640 6571 0.744414 TAGCGAGACAAATGGCTGCC 60.744 55.000 12.87 12.87 35.69 4.85
4641 6572 2.042831 GCGAGACAAATGGCTGCCT 61.043 57.895 21.03 2.27 30.09 4.75
4642 6573 1.986575 GCGAGACAAATGGCTGCCTC 61.987 60.000 21.03 8.54 30.09 4.70
4643 6574 1.699656 CGAGACAAATGGCTGCCTCG 61.700 60.000 21.03 14.55 37.72 4.63
4644 6575 1.986575 GAGACAAATGGCTGCCTCGC 61.987 60.000 21.03 6.55 30.09 5.03
4645 6576 3.386867 GACAAATGGCTGCCTCGCG 62.387 63.158 21.03 0.00 0.00 5.87
4646 6577 4.842091 CAAATGGCTGCCTCGCGC 62.842 66.667 21.03 0.00 38.31 6.86
4656 6587 3.470567 CCTCGCGCGTGAGAACAC 61.471 66.667 42.44 8.66 42.88 3.32
4657 6588 2.429236 CTCGCGCGTGAGAACACT 60.429 61.111 39.29 0.00 43.99 3.55
4658 6589 1.154282 CTCGCGCGTGAGAACACTA 60.154 57.895 39.29 8.57 43.99 2.74
4659 6590 1.396543 CTCGCGCGTGAGAACACTAC 61.397 60.000 39.29 2.63 43.99 2.73
4660 6591 1.728074 CGCGCGTGAGAACACTACA 60.728 57.895 24.19 0.00 43.99 2.74
4661 6592 1.071019 CGCGCGTGAGAACACTACAT 61.071 55.000 24.19 0.00 43.99 2.29
4662 6593 0.366871 GCGCGTGAGAACACTACATG 59.633 55.000 8.43 0.00 43.99 3.21
4663 6594 0.992072 CGCGTGAGAACACTACATGG 59.008 55.000 0.00 0.00 43.99 3.66
4664 6595 1.402325 CGCGTGAGAACACTACATGGA 60.402 52.381 0.00 0.00 43.99 3.41
4665 6596 2.263077 GCGTGAGAACACTACATGGAG 58.737 52.381 2.41 2.41 43.99 3.86
4666 6597 2.352814 GCGTGAGAACACTACATGGAGT 60.353 50.000 4.17 4.17 43.99 3.85
4667 6598 3.502920 CGTGAGAACACTACATGGAGTC 58.497 50.000 7.91 0.00 43.99 3.36
4668 6599 3.502920 GTGAGAACACTACATGGAGTCG 58.497 50.000 7.91 6.79 42.99 4.18
4669 6600 2.492088 TGAGAACACTACATGGAGTCGG 59.508 50.000 7.91 0.00 0.00 4.79
4670 6601 2.492484 GAGAACACTACATGGAGTCGGT 59.508 50.000 7.91 0.68 0.00 4.69
4671 6602 2.492484 AGAACACTACATGGAGTCGGTC 59.508 50.000 7.91 12.07 0.00 4.79
4699 6630 4.115279 CAGTAGGCATGCTGGTCG 57.885 61.111 18.92 0.00 35.67 4.79
4700 6631 1.219124 CAGTAGGCATGCTGGTCGT 59.781 57.895 18.92 0.00 35.67 4.34
4701 6632 0.807667 CAGTAGGCATGCTGGTCGTC 60.808 60.000 18.92 0.00 35.67 4.20
4702 6633 1.878522 GTAGGCATGCTGGTCGTCG 60.879 63.158 18.92 0.00 0.00 5.12
4703 6634 2.348104 TAGGCATGCTGGTCGTCGT 61.348 57.895 18.92 0.00 0.00 4.34
4704 6635 2.557059 TAGGCATGCTGGTCGTCGTG 62.557 60.000 18.92 0.00 0.00 4.35
4705 6636 4.152625 GCATGCTGGTCGTCGTGC 62.153 66.667 11.37 0.00 37.94 5.34
4706 6637 2.433145 CATGCTGGTCGTCGTGCT 60.433 61.111 0.00 0.00 0.00 4.40
4707 6638 2.433145 ATGCTGGTCGTCGTGCTG 60.433 61.111 0.00 0.00 0.00 4.41
4708 6639 2.931068 ATGCTGGTCGTCGTGCTGA 61.931 57.895 0.00 0.00 0.00 4.26
4709 6640 2.355837 GCTGGTCGTCGTGCTGAA 60.356 61.111 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.059264 GGCGACGAGAAAAAGATGACG 59.941 52.381 0.00 0.00 0.00 4.35
88 89 2.124983 CGTGGGAGGAGCACATGG 60.125 66.667 0.00 0.00 33.09 3.66
188 232 4.400529 TGCAGGCATTAAATCTAGACGA 57.599 40.909 0.00 0.00 0.00 4.20
246 290 2.954020 GATCGCGCACCAATCTCGGA 62.954 60.000 8.75 0.00 0.00 4.55
357 402 1.661463 TCCTGATAGGATGGCCCATC 58.339 55.000 15.71 15.71 40.06 3.51
515 560 7.172532 GTGGATGAACAGACGCCAATAATATTA 59.827 37.037 0.00 0.00 0.00 0.98
531 576 1.699083 TGCTCCTTCTGTGGATGAACA 59.301 47.619 0.00 0.00 35.30 3.18
542 587 0.550914 TGTTGGGTTGTGCTCCTTCT 59.449 50.000 0.00 0.00 0.00 2.85
546 591 1.620822 ATCTTGTTGGGTTGTGCTCC 58.379 50.000 0.00 0.00 0.00 4.70
721 807 1.442017 GTGTTCGCGGAAATGGTGC 60.442 57.895 6.13 0.00 0.00 5.01
722 808 1.154488 CGTGTTCGCGGAAATGGTG 60.154 57.895 6.13 0.00 0.00 4.17
723 809 3.249999 CGTGTTCGCGGAAATGGT 58.750 55.556 6.13 0.00 0.00 3.55
859 947 0.375803 CTGTGCGCGGGGTTAATAAC 59.624 55.000 8.83 0.00 0.00 1.89
952 1052 1.968493 GGTGGACTGGTAGTTGTCTGA 59.032 52.381 0.00 0.00 34.01 3.27
1796 1916 2.159627 AGCAAAACTAGCAATTCGACGG 59.840 45.455 0.00 0.00 0.00 4.79
1871 1991 6.434028 AGCATTCCAAAAGCACTAATCTAACA 59.566 34.615 0.00 0.00 0.00 2.41
1872 1992 6.856895 AGCATTCCAAAAGCACTAATCTAAC 58.143 36.000 0.00 0.00 0.00 2.34
1874 1994 8.752005 ATTAGCATTCCAAAAGCACTAATCTA 57.248 30.769 0.00 0.00 0.00 1.98
1915 2699 6.096705 TGCATTGTGGGGAAATAATCTAAGTG 59.903 38.462 0.00 0.00 0.00 3.16
1993 2785 2.511218 ACTTGTATCTGGGCCATGTGAT 59.489 45.455 6.72 9.51 0.00 3.06
2144 3145 1.199097 CAGAATTGCGTACACCCAACC 59.801 52.381 0.00 0.00 0.00 3.77
2194 3196 2.038295 ACAGTTTGGGAGAGCTCAAGAG 59.962 50.000 17.77 0.00 35.54 2.85
2245 3247 5.779529 ACAATAAGCCCAGCATTAGATTG 57.220 39.130 0.00 0.00 0.00 2.67
2250 3252 4.163441 TGCTACAATAAGCCCAGCATTA 57.837 40.909 0.00 0.00 42.05 1.90
2252 3254 2.734755 TGCTACAATAAGCCCAGCAT 57.265 45.000 0.00 0.00 42.05 3.79
2284 3286 8.243961 TGATGATTCCTTACCAACAAAAGAAA 57.756 30.769 0.00 0.00 0.00 2.52
2344 3355 5.163513 CACTTGACAGCACTTTGAAAAGTT 58.836 37.500 5.70 0.00 46.52 2.66
2382 3393 3.509575 ACTGTACAGAGCTGAGAAAGGAG 59.490 47.826 29.30 0.00 0.00 3.69
2399 3410 2.704464 TACAGCCTAGCTCGACTGTA 57.296 50.000 9.86 9.86 42.97 2.74
2481 3493 5.351465 ACCAAAGATAAGTGTAGATGCAACG 59.649 40.000 0.00 0.00 0.00 4.10
2483 3495 8.892723 CAATACCAAAGATAAGTGTAGATGCAA 58.107 33.333 0.00 0.00 0.00 4.08
2486 3498 8.755941 CGACAATACCAAAGATAAGTGTAGATG 58.244 37.037 0.00 0.00 0.00 2.90
2492 3504 6.961359 TGACGACAATACCAAAGATAAGTG 57.039 37.500 0.00 0.00 0.00 3.16
2504 3516 7.813852 AAGTTCAGACTAATGACGACAATAC 57.186 36.000 0.00 0.00 34.21 1.89
2505 3517 8.827177 AAAAGTTCAGACTAATGACGACAATA 57.173 30.769 0.00 0.00 34.21 1.90
2506 3518 7.730364 AAAAGTTCAGACTAATGACGACAAT 57.270 32.000 0.00 0.00 34.21 2.71
2508 3520 7.330946 CCATAAAAGTTCAGACTAATGACGACA 59.669 37.037 0.00 0.00 34.21 4.35
2509 3521 7.331193 ACCATAAAAGTTCAGACTAATGACGAC 59.669 37.037 0.00 0.00 34.21 4.34
2512 3526 7.148239 CCCACCATAAAAGTTCAGACTAATGAC 60.148 40.741 0.00 0.00 34.21 3.06
2519 3533 4.394729 TCACCCACCATAAAAGTTCAGAC 58.605 43.478 0.00 0.00 0.00 3.51
2549 3563 8.067784 CGATAAAAGAAAGAAGCACAGTGTTAA 58.932 33.333 1.61 0.00 0.00 2.01
2559 3573 6.713792 AGACTGACGATAAAAGAAAGAAGC 57.286 37.500 0.00 0.00 0.00 3.86
2570 3584 4.976224 TGAATCGGAAGACTGACGATAA 57.024 40.909 13.04 4.79 45.50 1.75
2591 3605 1.675641 GTGCAACGGGGCAGAGAAT 60.676 57.895 3.33 0.00 45.96 2.40
2621 3635 1.245376 TGTGGTAGTGGATCGCACGA 61.245 55.000 0.00 0.00 0.00 4.35
2875 3889 8.144478 TGTAGTATAAGCAAGAAGGAATAGCAG 58.856 37.037 0.00 0.00 0.00 4.24
2909 3923 5.643379 ACAACTAAATTGGCACGATCAAT 57.357 34.783 0.00 0.00 43.20 2.57
2920 3934 6.435430 TGCCATACTGCTACAACTAAATTG 57.565 37.500 0.00 0.00 44.60 2.32
2930 4125 3.689161 TCACAAACATGCCATACTGCTAC 59.311 43.478 0.00 0.00 0.00 3.58
2951 4146 4.817517 TCGCCGATTCCCTATCTAAAATC 58.182 43.478 0.00 0.00 0.00 2.17
3029 4224 2.972625 TGATAAACTGGAGAAGGTGCG 58.027 47.619 0.00 0.00 0.00 5.34
3057 4252 8.022550 CACAAATCATTACTGCACAAGTTGATA 58.977 33.333 10.54 0.00 35.98 2.15
3122 4317 5.678132 TTGACATCACAGTCATGTTTCTG 57.322 39.130 0.00 11.48 46.90 3.02
3153 4348 8.091449 TCACTCTTTTGCTCCAAAAACTTAAAA 58.909 29.630 4.88 0.00 41.77 1.52
3188 4393 4.697828 TGAGCTGGCGTGTTATTTTATCAA 59.302 37.500 0.00 0.00 0.00 2.57
3341 4618 0.665369 GGTACCCGTCTTGTCGTGTG 60.665 60.000 0.00 0.00 0.00 3.82
3359 4990 0.463295 TCTACTAGACGGGCAGACGG 60.463 60.000 0.00 0.00 38.39 4.79
3388 5019 2.111255 AGGGAGGGTGTGTACTGAAGTA 59.889 50.000 0.00 0.00 0.00 2.24
3472 5136 1.002366 CGTGTCCTAATGAGCAGCAC 58.998 55.000 0.00 0.00 0.00 4.40
3539 5203 8.821894 GTGAACCATGCTAAACAAAACAAAATA 58.178 29.630 0.00 0.00 0.00 1.40
3565 5229 6.240894 ACTTACAATGGGGCTGTATCATATG 58.759 40.000 0.00 0.00 0.00 1.78
3573 5237 3.620488 CATGTACTTACAATGGGGCTGT 58.380 45.455 0.00 0.00 39.99 4.40
3574 5238 2.951642 CCATGTACTTACAATGGGGCTG 59.048 50.000 1.96 0.00 39.99 4.85
3576 5240 3.290948 TCCATGTACTTACAATGGGGC 57.709 47.619 8.80 0.00 39.99 5.80
3577 5241 5.935945 TGTATCCATGTACTTACAATGGGG 58.064 41.667 8.80 6.02 39.99 4.96
3578 5242 5.470098 GCTGTATCCATGTACTTACAATGGG 59.530 44.000 8.80 7.79 39.99 4.00
3579 5243 5.177511 CGCTGTATCCATGTACTTACAATGG 59.822 44.000 3.31 3.31 39.99 3.16
3580 5244 5.983118 TCGCTGTATCCATGTACTTACAATG 59.017 40.000 0.00 0.00 39.99 2.82
3581 5245 6.156748 TCGCTGTATCCATGTACTTACAAT 57.843 37.500 0.00 0.00 39.99 2.71
3582 5246 5.585820 TCGCTGTATCCATGTACTTACAA 57.414 39.130 0.00 0.00 39.99 2.41
3583 5247 5.068591 ACATCGCTGTATCCATGTACTTACA 59.931 40.000 0.00 0.00 35.61 2.41
3584 5248 5.529791 ACATCGCTGTATCCATGTACTTAC 58.470 41.667 0.00 0.00 32.49 2.34
3586 5250 4.672587 ACATCGCTGTATCCATGTACTT 57.327 40.909 0.00 0.00 32.49 2.24
3587 5251 4.672587 AACATCGCTGTATCCATGTACT 57.327 40.909 0.00 0.00 33.36 2.73
3588 5252 4.808895 TCAAACATCGCTGTATCCATGTAC 59.191 41.667 0.00 0.00 33.36 2.90
3764 5635 3.490419 GCTCCAATGAATCAACCAGATGC 60.490 47.826 0.00 0.00 36.96 3.91
3774 5645 7.426929 AAACGATGTATAGCTCCAATGAATC 57.573 36.000 0.00 0.00 0.00 2.52
3785 5669 6.647067 AGAAGCCAGAATAAACGATGTATAGC 59.353 38.462 0.00 0.00 0.00 2.97
3793 5677 2.304761 ACCCAGAAGCCAGAATAAACGA 59.695 45.455 0.00 0.00 0.00 3.85
3821 5705 0.831307 AGAACGGGATCCTAGTTGCC 59.169 55.000 23.94 14.09 0.00 4.52
3876 5762 0.888619 TCCAGTCTTTCGCACGATCT 59.111 50.000 0.00 0.00 0.00 2.75
3889 5776 9.522804 CTGTAAAGTATAAACATCTCTCCAGTC 57.477 37.037 0.00 0.00 0.00 3.51
3908 5795 9.938670 CATACTTAGCACTACTAGTCTGTAAAG 57.061 37.037 0.00 6.95 30.79 1.85
4038 5929 0.111253 ACTGAGTTTTCCAGGCCAGG 59.889 55.000 8.15 8.15 36.03 4.45
4078 5969 3.118112 CCAAGTGCTACTTCCAGATGGAT 60.118 47.826 1.61 0.00 44.98 3.41
4105 5996 8.437742 CAGACATTTTGCTTCCATTTTCAATAC 58.562 33.333 0.00 0.00 0.00 1.89
4107 5998 7.172019 GTCAGACATTTTGCTTCCATTTTCAAT 59.828 33.333 0.00 0.00 0.00 2.57
4157 6055 3.619038 GCTAAGAACCATTCTTCGTCCTG 59.381 47.826 7.08 0.00 46.62 3.86
4165 6063 5.153950 ACTCTTTCGCTAAGAACCATTCT 57.846 39.130 2.23 0.00 42.19 2.40
4171 6069 5.056894 TCCACTACTCTTTCGCTAAGAAC 57.943 43.478 2.23 0.00 42.19 3.01
4178 6076 2.754002 ACTACCTCCACTACTCTTTCGC 59.246 50.000 0.00 0.00 0.00 4.70
4179 6077 7.879160 AGATATACTACCTCCACTACTCTTTCG 59.121 40.741 0.00 0.00 0.00 3.46
4181 6079 8.504409 ACAGATATACTACCTCCACTACTCTTT 58.496 37.037 0.00 0.00 0.00 2.52
4182 6080 8.048016 ACAGATATACTACCTCCACTACTCTT 57.952 38.462 0.00 0.00 0.00 2.85
4205 6112 3.072330 TCTCATAAGTGCCCTGTTGAACA 59.928 43.478 0.00 0.00 0.00 3.18
4222 6129 0.687354 AACAACCGTCAGCCTCTCAT 59.313 50.000 0.00 0.00 0.00 2.90
4223 6130 0.468226 AAACAACCGTCAGCCTCTCA 59.532 50.000 0.00 0.00 0.00 3.27
4224 6131 1.264288 CAAAACAACCGTCAGCCTCTC 59.736 52.381 0.00 0.00 0.00 3.20
4228 6149 0.958822 ATCCAAAACAACCGTCAGCC 59.041 50.000 0.00 0.00 0.00 4.85
4229 6150 1.606668 TGATCCAAAACAACCGTCAGC 59.393 47.619 0.00 0.00 0.00 4.26
4247 6168 7.038870 TGCTTACTTACCAAGTTACCAGTATGA 60.039 37.037 0.00 0.00 42.81 2.15
4254 6175 6.653740 ACAAGATGCTTACTTACCAAGTTACC 59.346 38.462 0.00 0.00 42.81 2.85
4255 6176 7.148457 GGACAAGATGCTTACTTACCAAGTTAC 60.148 40.741 0.00 0.00 42.81 2.50
4256 6177 6.877322 GGACAAGATGCTTACTTACCAAGTTA 59.123 38.462 0.00 0.00 42.81 2.24
4257 6178 5.705905 GGACAAGATGCTTACTTACCAAGTT 59.294 40.000 0.00 0.00 42.81 2.66
4258 6179 5.246307 GGACAAGATGCTTACTTACCAAGT 58.754 41.667 0.00 0.00 45.40 3.16
4259 6180 4.330074 CGGACAAGATGCTTACTTACCAAG 59.670 45.833 0.00 0.00 0.00 3.61
4260 6181 4.250464 CGGACAAGATGCTTACTTACCAA 58.750 43.478 0.00 0.00 0.00 3.67
4261 6182 3.259876 ACGGACAAGATGCTTACTTACCA 59.740 43.478 0.00 0.00 0.00 3.25
4262 6183 3.617263 CACGGACAAGATGCTTACTTACC 59.383 47.826 0.00 0.00 0.00 2.85
4263 6184 4.326548 GTCACGGACAAGATGCTTACTTAC 59.673 45.833 0.00 0.00 32.09 2.34
4264 6185 4.219944 AGTCACGGACAAGATGCTTACTTA 59.780 41.667 6.78 0.00 34.60 2.24
4265 6186 3.006967 AGTCACGGACAAGATGCTTACTT 59.993 43.478 6.78 0.00 34.60 2.24
4266 6187 2.563179 AGTCACGGACAAGATGCTTACT 59.437 45.455 6.78 0.00 34.60 2.24
4282 6203 1.975363 GAAGATGCAGCGCCAGTCAC 61.975 60.000 2.29 0.00 0.00 3.67
4285 6206 1.744368 CAGAAGATGCAGCGCCAGT 60.744 57.895 2.29 0.00 0.00 4.00
4290 6214 1.783031 GATGGCCAGAAGATGCAGCG 61.783 60.000 13.05 0.00 0.00 5.18
4298 6222 0.537188 AGTACCGTGATGGCCAGAAG 59.463 55.000 13.05 2.21 43.94 2.85
4306 6230 1.404391 ACGAGGCTAAGTACCGTGATG 59.596 52.381 0.00 0.00 31.85 3.07
4312 6236 3.754766 CCCAACGAGGCTAAGTACC 57.245 57.895 0.00 0.00 35.39 3.34
4366 6290 2.031682 CGAGTTCCTGGCTGAAAACTTG 60.032 50.000 11.37 10.81 32.34 3.16
4388 6312 2.416747 GCAAACCCCAAAATTCTCTGC 58.583 47.619 0.00 0.00 0.00 4.26
4389 6313 2.610232 CCGCAAACCCCAAAATTCTCTG 60.610 50.000 0.00 0.00 0.00 3.35
4390 6314 1.618343 CCGCAAACCCCAAAATTCTCT 59.382 47.619 0.00 0.00 0.00 3.10
4391 6315 1.343142 ACCGCAAACCCCAAAATTCTC 59.657 47.619 0.00 0.00 0.00 2.87
4392 6316 1.069978 CACCGCAAACCCCAAAATTCT 59.930 47.619 0.00 0.00 0.00 2.40
4393 6317 1.069358 TCACCGCAAACCCCAAAATTC 59.931 47.619 0.00 0.00 0.00 2.17
4395 6319 1.069978 CTTCACCGCAAACCCCAAAAT 59.930 47.619 0.00 0.00 0.00 1.82
4399 6323 1.104577 GTTCTTCACCGCAAACCCCA 61.105 55.000 0.00 0.00 0.00 4.96
4406 6330 0.976641 ATCCTCTGTTCTTCACCGCA 59.023 50.000 0.00 0.00 0.00 5.69
4408 6332 1.276421 ACCATCCTCTGTTCTTCACCG 59.724 52.381 0.00 0.00 0.00 4.94
4483 6414 8.565416 ACAAATTTTTACCAGCAGTAGTTACTC 58.435 33.333 0.00 0.00 33.46 2.59
4496 6427 9.739276 AGATGAGTATGAGACAAATTTTTACCA 57.261 29.630 0.00 0.00 0.00 3.25
4502 6433 6.096001 GCCCAAGATGAGTATGAGACAAATTT 59.904 38.462 0.00 0.00 0.00 1.82
4503 6434 5.591877 GCCCAAGATGAGTATGAGACAAATT 59.408 40.000 0.00 0.00 0.00 1.82
4504 6435 5.104193 AGCCCAAGATGAGTATGAGACAAAT 60.104 40.000 0.00 0.00 0.00 2.32
4505 6436 4.225942 AGCCCAAGATGAGTATGAGACAAA 59.774 41.667 0.00 0.00 0.00 2.83
4506 6437 3.776969 AGCCCAAGATGAGTATGAGACAA 59.223 43.478 0.00 0.00 0.00 3.18
4507 6438 3.378512 AGCCCAAGATGAGTATGAGACA 58.621 45.455 0.00 0.00 0.00 3.41
4508 6439 3.244044 GGAGCCCAAGATGAGTATGAGAC 60.244 52.174 0.00 0.00 0.00 3.36
4509 6440 2.968574 GGAGCCCAAGATGAGTATGAGA 59.031 50.000 0.00 0.00 0.00 3.27
4510 6441 2.971330 AGGAGCCCAAGATGAGTATGAG 59.029 50.000 0.00 0.00 0.00 2.90
4511 6442 2.702478 CAGGAGCCCAAGATGAGTATGA 59.298 50.000 0.00 0.00 0.00 2.15
4512 6443 2.224475 CCAGGAGCCCAAGATGAGTATG 60.224 54.545 0.00 0.00 0.00 2.39
4513 6444 2.053244 CCAGGAGCCCAAGATGAGTAT 58.947 52.381 0.00 0.00 0.00 2.12
4514 6445 1.500474 CCAGGAGCCCAAGATGAGTA 58.500 55.000 0.00 0.00 0.00 2.59
4515 6446 1.919600 GCCAGGAGCCCAAGATGAGT 61.920 60.000 0.00 0.00 34.35 3.41
4516 6447 1.153005 GCCAGGAGCCCAAGATGAG 60.153 63.158 0.00 0.00 34.35 2.90
4517 6448 1.617536 AGCCAGGAGCCCAAGATGA 60.618 57.895 0.00 0.00 45.47 2.92
4518 6449 1.153005 GAGCCAGGAGCCCAAGATG 60.153 63.158 0.00 0.00 45.47 2.90
4519 6450 2.739996 CGAGCCAGGAGCCCAAGAT 61.740 63.158 0.00 0.00 45.47 2.40
4520 6451 3.393970 CGAGCCAGGAGCCCAAGA 61.394 66.667 0.00 0.00 45.47 3.02
4521 6452 4.479993 CCGAGCCAGGAGCCCAAG 62.480 72.222 0.00 0.00 45.47 3.61
4533 6464 0.388649 CTATATGTGACGGCCCGAGC 60.389 60.000 11.71 1.20 38.76 5.03
4534 6465 0.959553 ACTATATGTGACGGCCCGAG 59.040 55.000 11.71 0.00 0.00 4.63
4535 6466 1.338973 GAACTATATGTGACGGCCCGA 59.661 52.381 11.71 0.00 0.00 5.14
4536 6467 1.340248 AGAACTATATGTGACGGCCCG 59.660 52.381 0.00 0.00 0.00 6.13
4537 6468 3.181469 TGAAGAACTATATGTGACGGCCC 60.181 47.826 0.00 0.00 0.00 5.80
4538 6469 3.802685 GTGAAGAACTATATGTGACGGCC 59.197 47.826 0.00 0.00 0.00 6.13
4539 6470 3.802685 GGTGAAGAACTATATGTGACGGC 59.197 47.826 0.00 0.00 0.00 5.68
4540 6471 4.042398 CGGTGAAGAACTATATGTGACGG 58.958 47.826 0.00 0.00 0.00 4.79
4541 6472 4.669318 ACGGTGAAGAACTATATGTGACG 58.331 43.478 0.00 0.00 0.00 4.35
4542 6473 9.740239 TTATTACGGTGAAGAACTATATGTGAC 57.260 33.333 0.00 0.00 0.00 3.67
4550 6481 8.509690 CGGAGATATTATTACGGTGAAGAACTA 58.490 37.037 0.00 0.00 0.00 2.24
4551 6482 7.014038 ACGGAGATATTATTACGGTGAAGAACT 59.986 37.037 0.00 0.00 0.00 3.01
4552 6483 7.144000 ACGGAGATATTATTACGGTGAAGAAC 58.856 38.462 0.00 0.00 0.00 3.01
4553 6484 7.281040 ACGGAGATATTATTACGGTGAAGAA 57.719 36.000 0.00 0.00 0.00 2.52
4554 6485 6.347969 CGACGGAGATATTATTACGGTGAAGA 60.348 42.308 0.00 0.00 0.00 2.87
4555 6486 5.793952 CGACGGAGATATTATTACGGTGAAG 59.206 44.000 0.00 0.00 0.00 3.02
4556 6487 5.469760 TCGACGGAGATATTATTACGGTGAA 59.530 40.000 0.00 0.00 0.00 3.18
4557 6488 4.996758 TCGACGGAGATATTATTACGGTGA 59.003 41.667 0.00 0.00 0.00 4.02
4558 6489 5.287170 TCGACGGAGATATTATTACGGTG 57.713 43.478 0.00 0.00 0.00 4.94
4559 6490 5.947228 TTCGACGGAGATATTATTACGGT 57.053 39.130 0.00 0.00 0.00 4.83
4560 6491 7.627585 TTTTTCGACGGAGATATTATTACGG 57.372 36.000 0.00 0.00 0.00 4.02
4581 6512 1.160137 CAGTAGCGCTGCCTCTTTTT 58.840 50.000 22.90 0.00 38.52 1.94
4582 6513 0.674895 CCAGTAGCGCTGCCTCTTTT 60.675 55.000 22.90 0.00 43.71 2.27
4583 6514 1.078848 CCAGTAGCGCTGCCTCTTT 60.079 57.895 22.90 0.00 43.71 2.52
4584 6515 2.286523 ACCAGTAGCGCTGCCTCTT 61.287 57.895 22.90 0.00 43.71 2.85
4585 6516 2.681778 ACCAGTAGCGCTGCCTCT 60.682 61.111 22.90 10.19 43.71 3.69
4586 6517 2.510238 CACCAGTAGCGCTGCCTC 60.510 66.667 22.90 7.89 43.71 4.70
4587 6518 3.314331 ACACCAGTAGCGCTGCCT 61.314 61.111 22.90 13.20 43.71 4.75
4588 6519 3.121030 CACACCAGTAGCGCTGCC 61.121 66.667 22.90 10.77 43.71 4.85
4589 6520 3.793144 GCACACCAGTAGCGCTGC 61.793 66.667 22.90 20.66 43.71 5.25
4590 6521 3.121030 GGCACACCAGTAGCGCTG 61.121 66.667 22.90 5.37 44.63 5.18
4591 6522 4.394712 GGGCACACCAGTAGCGCT 62.395 66.667 17.26 17.26 39.85 5.92
4592 6523 4.697756 TGGGCACACCAGTAGCGC 62.698 66.667 0.00 0.00 46.80 5.92
4601 6532 2.167398 TAAGCGAGACCTGGGCACAC 62.167 60.000 0.47 0.00 0.00 3.82
4602 6533 1.264749 ATAAGCGAGACCTGGGCACA 61.265 55.000 0.47 0.00 0.00 4.57
4603 6534 0.750850 TATAAGCGAGACCTGGGCAC 59.249 55.000 0.47 0.00 0.00 5.01
4604 6535 1.040646 CTATAAGCGAGACCTGGGCA 58.959 55.000 0.47 0.00 0.00 5.36
4605 6536 0.319986 GCTATAAGCGAGACCTGGGC 60.320 60.000 0.00 0.00 0.00 5.36
4606 6537 3.896317 GCTATAAGCGAGACCTGGG 57.104 57.895 0.00 0.00 0.00 4.45
4616 6547 3.059325 CAGCCATTTGTCTCGCTATAAGC 60.059 47.826 0.00 0.00 38.02 3.09
4617 6548 3.059325 GCAGCCATTTGTCTCGCTATAAG 60.059 47.826 0.00 0.00 0.00 1.73
4618 6549 2.872245 GCAGCCATTTGTCTCGCTATAA 59.128 45.455 0.00 0.00 0.00 0.98
4619 6550 2.483876 GCAGCCATTTGTCTCGCTATA 58.516 47.619 0.00 0.00 0.00 1.31
4620 6551 1.303309 GCAGCCATTTGTCTCGCTAT 58.697 50.000 0.00 0.00 0.00 2.97
4621 6552 0.744414 GGCAGCCATTTGTCTCGCTA 60.744 55.000 6.55 0.00 0.00 4.26
4622 6553 2.042831 GGCAGCCATTTGTCTCGCT 61.043 57.895 6.55 0.00 0.00 4.93
4623 6554 1.986575 GAGGCAGCCATTTGTCTCGC 61.987 60.000 15.80 0.00 39.71 5.03
4624 6555 2.093216 GAGGCAGCCATTTGTCTCG 58.907 57.895 15.80 0.00 39.71 4.04
4625 6556 1.986575 GCGAGGCAGCCATTTGTCTC 61.987 60.000 15.80 0.00 44.41 3.36
4626 6557 2.042831 GCGAGGCAGCCATTTGTCT 61.043 57.895 15.80 0.00 35.29 3.41
4627 6558 2.486966 GCGAGGCAGCCATTTGTC 59.513 61.111 15.80 0.11 0.00 3.18
4628 6559 3.434319 CGCGAGGCAGCCATTTGT 61.434 61.111 15.80 0.00 0.00 2.83
4629 6560 4.842091 GCGCGAGGCAGCCATTTG 62.842 66.667 15.80 1.42 42.87 2.32
4639 6570 3.470567 GTGTTCTCACGCGCGAGG 61.471 66.667 39.36 27.01 34.79 4.63
4647 6578 3.502920 CGACTCCATGTAGTGTTCTCAC 58.497 50.000 0.00 0.00 44.15 3.51
4648 6579 2.492088 CCGACTCCATGTAGTGTTCTCA 59.508 50.000 0.00 0.00 0.00 3.27
4649 6580 2.492484 ACCGACTCCATGTAGTGTTCTC 59.508 50.000 0.00 0.00 0.00 2.87
4650 6581 2.492484 GACCGACTCCATGTAGTGTTCT 59.508 50.000 0.00 0.00 0.00 3.01
4651 6582 2.416972 GGACCGACTCCATGTAGTGTTC 60.417 54.545 0.00 0.00 39.21 3.18
4652 6583 1.549170 GGACCGACTCCATGTAGTGTT 59.451 52.381 0.00 0.00 39.21 3.32
4653 6584 1.183549 GGACCGACTCCATGTAGTGT 58.816 55.000 0.00 0.00 39.21 3.55
4654 6585 1.135139 CAGGACCGACTCCATGTAGTG 59.865 57.143 0.00 0.00 42.46 2.74
4655 6586 1.475403 CAGGACCGACTCCATGTAGT 58.525 55.000 0.00 0.00 42.46 2.73
4656 6587 0.747255 CCAGGACCGACTCCATGTAG 59.253 60.000 2.34 0.00 42.46 2.74
4657 6588 1.327690 GCCAGGACCGACTCCATGTA 61.328 60.000 0.00 0.00 42.46 2.29
4658 6589 2.660064 GCCAGGACCGACTCCATGT 61.660 63.158 0.00 0.00 42.46 3.21
4659 6590 2.187946 GCCAGGACCGACTCCATG 59.812 66.667 0.00 0.00 42.46 3.66
4660 6591 3.083997 GGCCAGGACCGACTCCAT 61.084 66.667 0.00 0.00 42.46 3.41
4682 6613 0.807667 GACGACCAGCATGCCTACTG 60.808 60.000 15.66 5.81 31.97 2.74
4683 6614 1.517832 GACGACCAGCATGCCTACT 59.482 57.895 15.66 0.00 31.97 2.57
4684 6615 1.878522 CGACGACCAGCATGCCTAC 60.879 63.158 15.66 2.86 31.97 3.18
4685 6616 2.348104 ACGACGACCAGCATGCCTA 61.348 57.895 15.66 0.00 31.97 3.93
4686 6617 3.695606 ACGACGACCAGCATGCCT 61.696 61.111 15.66 0.00 31.97 4.75
4687 6618 3.490759 CACGACGACCAGCATGCC 61.491 66.667 15.66 0.00 31.97 4.40
4688 6619 4.152625 GCACGACGACCAGCATGC 62.153 66.667 10.51 10.51 31.97 4.06
4689 6620 2.433145 AGCACGACGACCAGCATG 60.433 61.111 0.00 0.00 0.00 4.06
4690 6621 2.433145 CAGCACGACGACCAGCAT 60.433 61.111 0.00 0.00 0.00 3.79
4691 6622 3.145422 TTCAGCACGACGACCAGCA 62.145 57.895 0.00 0.00 0.00 4.41
4692 6623 2.355837 TTCAGCACGACGACCAGC 60.356 61.111 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.