Multiple sequence alignment - TraesCS2A01G541500

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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 TraesCS2A01G541500 chr2A 100.000 5090 0 0 1 5090 752876082 752870993 0.000000e+00 9400.0
1 TraesCS2A01G541500 chr2D 89.234 2703 178 44 1613 4279 621069949 621067324 0.000000e+00 3275.0
2 TraesCS2A01G541500 chr2D 86.429 899 54 30 760 1611 621070862 621069985 0.000000e+00 922.0
3 TraesCS2A01G541500 chr2D 84.014 563 63 18 4533 5084 621067033 621066487 2.720000e-142 516.0
4 TraesCS2A01G541500 chr2D 88.050 159 10 5 760 915 621087626 621087474 4.050000e-41 180.0
5 TraesCS2A01G541500 chr2B 89.910 2230 111 55 760 2929 761995894 761993719 0.000000e+00 2767.0
6 TraesCS2A01G541500 chr2B 85.656 1234 131 17 2989 4207 761993570 761992368 0.000000e+00 1256.0
7 TraesCS2A01G541500 chr2B 85.619 904 79 24 972 1868 762002967 762002108 0.000000e+00 902.0
8 TraesCS2A01G541500 chr2B 82.677 381 29 24 4735 5090 761992014 761991646 2.300000e-78 303.0
9 TraesCS2A01G541500 chr2B 91.045 134 12 0 3824 3957 46099778 46099645 1.130000e-41 182.0
10 TraesCS2A01G541500 chr6A 97.105 760 20 2 1 759 71095019 71094261 0.000000e+00 1280.0
11 TraesCS2A01G541500 chr6A 87.685 812 70 16 1128 1925 429226675 429227470 0.000000e+00 918.0
12 TraesCS2A01G541500 chr1A 96.859 764 19 3 1 760 13808028 13807266 0.000000e+00 1273.0
13 TraesCS2A01G541500 chr1A 96.466 764 20 5 1 759 34342447 34343208 0.000000e+00 1254.0
14 TraesCS2A01G541500 chr1A 96.184 760 27 2 1 759 566066705 566065947 0.000000e+00 1242.0
15 TraesCS2A01G541500 chr4A 96.715 761 20 3 3 759 628889107 628889866 0.000000e+00 1262.0
16 TraesCS2A01G541500 chr4A 80.779 385 46 9 3826 4206 671017938 671017578 5.020000e-70 276.0
17 TraesCS2A01G541500 chr4A 91.209 91 8 0 4796 4886 671017111 671017021 1.920000e-24 124.0
18 TraesCS2A01G541500 chr5A 96.199 763 24 3 1 759 697641471 697642232 0.000000e+00 1243.0
19 TraesCS2A01G541500 chr7A 95.812 764 26 4 1 760 658690443 658689682 0.000000e+00 1229.0
20 TraesCS2A01G541500 chr7A 95.157 764 30 5 1 760 576419574 576420334 0.000000e+00 1199.0
21 TraesCS2A01G541500 chr7D 94.902 765 33 4 1 760 445248646 445249409 0.000000e+00 1192.0
22 TraesCS2A01G541500 chr7D 83.750 640 59 20 1033 1664 569306513 569307115 9.570000e-157 564.0
23 TraesCS2A01G541500 chr5D 83.594 640 62 20 1033 1664 23023642 23023038 1.240000e-155 560.0
24 TraesCS2A01G541500 chr5D 83.438 640 64 19 1034 1664 31939611 31939005 1.600000e-154 556.0
25 TraesCS2A01G541500 chr6D 83.125 640 64 21 1033 1664 367273319 367272716 1.250000e-150 544.0
26 TraesCS2A01G541500 chr6D 86.869 99 9 2 1584 1679 857043 857140 1.940000e-19 108.0
27 TraesCS2A01G541500 chr3B 83.711 485 57 11 1190 1664 215293674 215293202 6.050000e-119 438.0
28 TraesCS2A01G541500 chr3B 83.299 485 58 12 1190 1664 215400391 215399920 4.710000e-115 425.0
29 TraesCS2A01G541500 chr3B 95.556 90 4 0 1048 1137 88358421 88358510 1.480000e-30 145.0
30 TraesCS2A01G541500 chr3B 88.571 105 10 2 1029 1131 221631973 221631869 5.350000e-25 126.0
31 TraesCS2A01G541500 chr3B 89.691 97 8 2 1029 1124 215293805 215293710 6.920000e-24 122.0
32 TraesCS2A01G541500 chr3B 90.909 44 4 0 4427 4470 115807349 115807392 5.500000e-05 60.2
33 TraesCS2A01G541500 chr6B 82.571 459 58 13 1215 1664 76966048 76965603 7.990000e-103 385.0
34 TraesCS2A01G541500 chr6B 82.188 320 26 11 1048 1367 269744386 269744098 3.940000e-61 246.0
35 TraesCS2A01G541500 chr1B 82.262 389 40 14 3824 4207 666189075 666188711 4.950000e-80 309.0
36 TraesCS2A01G541500 chr1B 85.246 61 7 2 4795 4854 666188252 666188193 1.530000e-05 62.1
37 TraesCS2A01G541500 chr1D 87.879 99 8 2 1584 1679 10885274 10885371 4.170000e-21 113.0
38 TraesCS2A01G541500 chr4D 95.556 45 2 0 4426 4470 489195114 489195158 7.070000e-09 73.1


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 TraesCS2A01G541500 chr2A 752870993 752876082 5089 True 9400 9400 100.000 1 5090 1 chr2A.!!$R1 5089
1 TraesCS2A01G541500 chr2D 621066487 621070862 4375 True 1571 3275 86.559 760 5084 3 chr2D.!!$R2 4324
2 TraesCS2A01G541500 chr2B 761991646 761995894 4248 True 1442 2767 86.081 760 5090 3 chr2B.!!$R3 4330
3 TraesCS2A01G541500 chr2B 762002108 762002967 859 True 902 902 85.619 972 1868 1 chr2B.!!$R2 896
4 TraesCS2A01G541500 chr6A 71094261 71095019 758 True 1280 1280 97.105 1 759 1 chr6A.!!$R1 758
5 TraesCS2A01G541500 chr6A 429226675 429227470 795 False 918 918 87.685 1128 1925 1 chr6A.!!$F1 797
6 TraesCS2A01G541500 chr1A 13807266 13808028 762 True 1273 1273 96.859 1 760 1 chr1A.!!$R1 759
7 TraesCS2A01G541500 chr1A 34342447 34343208 761 False 1254 1254 96.466 1 759 1 chr1A.!!$F1 758
8 TraesCS2A01G541500 chr1A 566065947 566066705 758 True 1242 1242 96.184 1 759 1 chr1A.!!$R2 758
9 TraesCS2A01G541500 chr4A 628889107 628889866 759 False 1262 1262 96.715 3 759 1 chr4A.!!$F1 756
10 TraesCS2A01G541500 chr5A 697641471 697642232 761 False 1243 1243 96.199 1 759 1 chr5A.!!$F1 758
11 TraesCS2A01G541500 chr7A 658689682 658690443 761 True 1229 1229 95.812 1 760 1 chr7A.!!$R1 759
12 TraesCS2A01G541500 chr7A 576419574 576420334 760 False 1199 1199 95.157 1 760 1 chr7A.!!$F1 759
13 TraesCS2A01G541500 chr7D 445248646 445249409 763 False 1192 1192 94.902 1 760 1 chr7D.!!$F1 759
14 TraesCS2A01G541500 chr7D 569306513 569307115 602 False 564 564 83.750 1033 1664 1 chr7D.!!$F2 631
15 TraesCS2A01G541500 chr5D 23023038 23023642 604 True 560 560 83.594 1033 1664 1 chr5D.!!$R1 631
16 TraesCS2A01G541500 chr5D 31939005 31939611 606 True 556 556 83.438 1034 1664 1 chr5D.!!$R2 630
17 TraesCS2A01G541500 chr6D 367272716 367273319 603 True 544 544 83.125 1033 1664 1 chr6D.!!$R1 631
18 TraesCS2A01G541500 chr3B 215293202 215293805 603 True 280 438 86.701 1029 1664 2 chr3B.!!$R3 635

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
568 576 0.171007 CGTTCGTTAGCCGTTAGGGA 59.829 55.000 0.0 0.0 38.47 4.20 F
1154 1200 1.406539 CCCGCCCAGATCAAATCAAAG 59.593 52.381 0.0 0.0 0.00 2.77 F
1744 1884 0.611714 TGGAACTACTTTCGCCCCTC 59.388 55.000 0.0 0.0 34.67 4.30 F
3186 3465 1.003118 ACACATTACTGGGACATGCGT 59.997 47.619 0.0 0.0 38.20 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1658 0.182299 TGCATTCAGTCACCACCACA 59.818 50.0 0.00 0.00 0.00 4.17 R
2558 2715 2.217510 TGTCCAGACTCCAGAGTACC 57.782 55.0 0.00 0.00 42.66 3.34 R
3629 3916 0.723414 CCACTTATGTGCAGCACTCG 59.277 55.0 25.83 13.37 42.54 4.18 R
4408 4866 0.035056 GGTCAAGCATGCCACTACCT 60.035 55.0 15.66 0.00 0.00 3.08 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
568 576 0.171007 CGTTCGTTAGCCGTTAGGGA 59.829 55.000 0.00 0.00 38.47 4.20
639 648 2.738643 CGGCTAACTGGACGATCAACAT 60.739 50.000 0.00 0.00 40.66 2.71
718 727 4.764050 TTGAAAGTGGTAGTTCTGTGGA 57.236 40.909 0.00 0.00 0.00 4.02
1154 1200 1.406539 CCCGCCCAGATCAAATCAAAG 59.593 52.381 0.00 0.00 0.00 2.77
1155 1201 2.094675 CCGCCCAGATCAAATCAAAGT 58.905 47.619 0.00 0.00 0.00 2.66
1335 1393 2.276740 CCTGTTCCATCCCCTGCC 59.723 66.667 0.00 0.00 0.00 4.85
1341 1399 4.201122 CCATCCCCTGCCCTGCTC 62.201 72.222 0.00 0.00 0.00 4.26
1381 1449 2.557056 CTGTCTTCGGGTTCAGAGTGTA 59.443 50.000 0.00 0.00 0.00 2.90
1449 1518 3.317711 CGCTGTATCTGAATGGAGAGAGT 59.682 47.826 0.00 0.00 0.00 3.24
1464 1533 1.552337 GAGAGTCAGGGAGTGATGCAA 59.448 52.381 0.00 0.00 37.56 4.08
1506 1575 6.322712 TGCTGAACCCTAATTAGTTTGTTTGT 59.677 34.615 11.50 0.00 0.00 2.83
1581 1657 4.644498 CAATTTTGTTTCAGAATGCCCCT 58.356 39.130 0.00 0.00 34.76 4.79
1582 1658 4.980339 ATTTTGTTTCAGAATGCCCCTT 57.020 36.364 0.00 0.00 34.76 3.95
1618 1732 2.405892 GCAAGTGCACCAAGTTACAG 57.594 50.000 14.63 0.00 41.59 2.74
1631 1755 7.066284 GCACCAAGTTACAGTCTAATTGATGAT 59.934 37.037 0.00 0.00 0.00 2.45
1632 1756 8.950210 CACCAAGTTACAGTCTAATTGATGATT 58.050 33.333 0.00 0.00 0.00 2.57
1710 1850 6.070656 TGTTGAATTTCTTTGGTGATCCTCT 58.929 36.000 0.00 0.00 34.23 3.69
1722 1862 4.593206 TGGTGATCCTCTGTTTAGTTGAGT 59.407 41.667 0.00 0.00 34.23 3.41
1744 1884 0.611714 TGGAACTACTTTCGCCCCTC 59.388 55.000 0.00 0.00 34.67 4.30
1761 1901 3.134804 CCCCTCACCTGACTAGTAAATGG 59.865 52.174 0.00 0.00 0.00 3.16
1766 1906 6.380274 CCTCACCTGACTAGTAAATGGTAAGA 59.620 42.308 0.00 0.00 0.00 2.10
1809 1949 4.415881 TTTGAAGTCAGACTACTTGCCA 57.584 40.909 2.64 0.00 39.78 4.92
1819 1974 5.470098 TCAGACTACTTGCCATTTTCAACTC 59.530 40.000 0.00 0.00 0.00 3.01
1852 2007 7.385205 CCCCTTTCATGTACTACGATTATCAAG 59.615 40.741 0.00 0.00 0.00 3.02
1869 2024 2.569853 TCAAGGGAAGTCCGCTTTATGA 59.430 45.455 0.00 0.00 44.46 2.15
1934 2089 5.936686 ATGTCATTATGCTGTACATCTGC 57.063 39.130 0.00 0.00 40.38 4.26
1951 2106 7.426929 ACATCTGCACTGTTTCTTAAGTTAG 57.573 36.000 1.63 0.19 0.00 2.34
1980 2135 8.552034 GGTAATTCTCTCTTTGGATGATTTACG 58.448 37.037 0.00 0.00 31.34 3.18
2173 2328 3.407698 TGTAATGTGCATTTCTCGGTGT 58.592 40.909 2.56 0.00 32.50 4.16
2191 2346 5.902051 GGTGTACGACTTATAGAAATGCC 57.098 43.478 0.00 0.00 0.00 4.40
2431 2588 5.298989 TGGTGTGTTTATAACAGTGGAGT 57.701 39.130 0.00 0.00 43.10 3.85
2482 2639 5.108385 ACAGTTAGAAACATTTGCTTCCG 57.892 39.130 0.00 0.00 0.00 4.30
2524 2681 1.600663 GCGGATCGACTACCTGATGTG 60.601 57.143 0.00 0.00 0.00 3.21
2531 2688 2.736719 CGACTACCTGATGTGCCTTCAG 60.737 54.545 9.65 9.65 40.25 3.02
2782 2941 8.193953 ACTGTGATCCAAACCTTTTTCAATAT 57.806 30.769 0.00 0.00 0.00 1.28
2963 3237 9.019656 TGTTCTTATAAACATTGGCTGTAACAT 57.980 29.630 0.00 0.00 36.98 2.71
2974 3248 9.929180 ACATTGGCTGTAACATATATACTACAG 57.071 33.333 19.79 19.79 42.66 2.74
2975 3249 9.929180 CATTGGCTGTAACATATATACTACAGT 57.071 33.333 22.42 9.71 42.07 3.55
2976 3250 9.929180 ATTGGCTGTAACATATATACTACAGTG 57.071 33.333 22.42 9.68 42.07 3.66
2977 3251 8.700439 TGGCTGTAACATATATACTACAGTGA 57.300 34.615 22.42 13.40 42.07 3.41
2978 3252 8.793592 TGGCTGTAACATATATACTACAGTGAG 58.206 37.037 22.42 9.00 42.07 3.51
2979 3253 8.794553 GGCTGTAACATATATACTACAGTGAGT 58.205 37.037 22.42 0.00 42.07 3.41
3008 3282 9.482627 GGATTAATACTGAGTTAGGATGTGAAG 57.517 37.037 0.00 0.00 27.50 3.02
3099 3378 8.514330 TTAATATCACGGCTGGTTTTCTATTT 57.486 30.769 0.00 0.00 0.00 1.40
3100 3379 9.616156 TTAATATCACGGCTGGTTTTCTATTTA 57.384 29.630 0.00 0.00 0.00 1.40
3185 3464 1.737838 ACACATTACTGGGACATGCG 58.262 50.000 0.00 0.00 38.20 4.73
3186 3465 1.003118 ACACATTACTGGGACATGCGT 59.997 47.619 0.00 0.00 38.20 5.24
3188 3467 2.866156 CACATTACTGGGACATGCGTAG 59.134 50.000 0.00 0.00 38.20 3.51
3250 3529 4.202441 AGGAACTCCATGATTGAAATCCG 58.798 43.478 0.00 0.00 38.89 4.18
3252 3531 5.104527 AGGAACTCCATGATTGAAATCCGTA 60.105 40.000 0.00 0.00 38.89 4.02
3272 3551 5.809051 CCGTACTAAAGTTCCTGTTACATCC 59.191 44.000 0.00 0.00 0.00 3.51
3449 3728 3.636300 GCACCACCTGGATATGCATAAAA 59.364 43.478 11.13 0.00 35.51 1.52
3468 3753 7.361286 GCATAAAAGCAAAAGTGTAGTAGCTCT 60.361 37.037 0.00 0.00 0.00 4.09
3473 3758 4.201763 GCAAAAGTGTAGTAGCTCTGATGC 60.202 45.833 0.00 0.00 0.00 3.91
3476 3761 3.360867 AGTGTAGTAGCTCTGATGCTGT 58.639 45.455 10.54 3.00 43.87 4.40
3488 3773 7.278135 AGCTCTGATGCTGTCATTTATTTAGA 58.722 34.615 1.65 0.00 42.33 2.10
3489 3774 7.772292 AGCTCTGATGCTGTCATTTATTTAGAA 59.228 33.333 1.65 0.00 42.33 2.10
3490 3775 8.566260 GCTCTGATGCTGTCATTTATTTAGAAT 58.434 33.333 0.00 0.00 35.97 2.40
3509 3794 2.868964 TAGCACCCTCCTCCAACTAT 57.131 50.000 0.00 0.00 0.00 2.12
3555 3840 2.285026 CGACATAGTTTCGCCGTGATTG 60.285 50.000 0.00 0.00 0.00 2.67
3579 3866 5.508224 GTGCGTATTCTCCGAATTTTGAAAG 59.492 40.000 0.00 0.00 0.00 2.62
3581 3868 6.093495 TGCGTATTCTCCGAATTTTGAAAGAT 59.907 34.615 0.00 0.00 0.00 2.40
3600 3887 8.049117 TGAAAGATATGCTAAACTTCCTGTCAT 58.951 33.333 0.00 0.00 0.00 3.06
3603 3890 3.138884 TGCTAAACTTCCTGTCATGCA 57.861 42.857 0.00 0.00 0.00 3.96
3611 3898 3.244665 ACTTCCTGTCATGCATCAGTTCA 60.245 43.478 12.86 1.52 0.00 3.18
3613 3900 3.538591 TCCTGTCATGCATCAGTTCATC 58.461 45.455 12.86 0.00 0.00 2.92
3629 3916 6.417327 CAGTTCATCTGAATCAAATACGAGC 58.583 40.000 0.00 0.00 46.27 5.03
3635 3922 2.603110 TGAATCAAATACGAGCGAGTGC 59.397 45.455 0.00 0.00 43.24 4.40
3693 3980 4.647564 AGAATCCATTCTGACACCAACT 57.352 40.909 0.79 0.00 44.91 3.16
3701 3988 5.335426 CCATTCTGACACCAACTCTCAATTG 60.335 44.000 0.00 0.00 0.00 2.32
3708 4001 3.879295 CACCAACTCTCAATTGTCAGTGT 59.121 43.478 5.13 0.91 0.00 3.55
3716 4009 6.820656 ACTCTCAATTGTCAGTGTTATCATCC 59.179 38.462 5.13 0.00 0.00 3.51
3729 4022 5.126061 GTGTTATCATCCTGCAAACCTGAAT 59.874 40.000 0.00 0.00 0.00 2.57
3745 4038 3.449737 CCTGAATGATGAAACCTGCCAAT 59.550 43.478 0.00 0.00 0.00 3.16
3749 4042 5.951148 TGAATGATGAAACCTGCCAATCTTA 59.049 36.000 0.00 0.00 0.00 2.10
3762 4055 6.599244 CCTGCCAATCTTATGTTACTTTCAGA 59.401 38.462 0.00 0.00 0.00 3.27
3885 4178 3.130160 CGCCCCTTCAGCAAGCTC 61.130 66.667 0.00 0.00 0.00 4.09
3890 4183 1.451067 CCCTTCAGCAAGCTCAGAAG 58.549 55.000 12.64 12.64 37.74 2.85
3927 4220 2.977178 CACGCCTCCAAGAGCTCT 59.023 61.111 11.45 11.45 0.00 4.09
3954 4247 2.677228 CCACTTCCCGGCAAGGAT 59.323 61.111 10.56 0.00 45.00 3.24
3975 4268 3.862991 GAGGCCCCCTCGGTTAGC 61.863 72.222 0.00 0.00 41.08 3.09
3981 4274 4.157120 CCCTCGGTTAGCGGGGTG 62.157 72.222 21.58 9.24 41.24 4.61
3982 4275 3.387947 CCTCGGTTAGCGGGGTGT 61.388 66.667 15.26 0.00 0.00 4.16
3983 4276 2.183555 CTCGGTTAGCGGGGTGTC 59.816 66.667 3.46 0.00 0.00 3.67
3984 4277 2.283388 TCGGTTAGCGGGGTGTCT 60.283 61.111 3.46 0.00 0.00 3.41
3985 4278 2.125673 CGGTTAGCGGGGTGTCTG 60.126 66.667 0.00 0.00 0.00 3.51
3995 4288 1.172812 GGGGTGTCTGTCAACAAGGC 61.173 60.000 0.00 0.00 35.04 4.35
3996 4289 0.179018 GGGTGTCTGTCAACAAGGCT 60.179 55.000 0.00 0.00 35.04 4.58
4094 4387 0.463204 GCAGGCTGCAGATGACTCTA 59.537 55.000 33.33 0.00 44.26 2.43
4116 4409 1.799544 TAGAAAGAAAACGCGGGGTC 58.200 50.000 12.47 3.81 0.00 4.46
4123 4416 0.464916 AAAACGCGGGGTCTTGAAGT 60.465 50.000 12.47 0.00 0.00 3.01
4124 4417 1.164041 AAACGCGGGGTCTTGAAGTG 61.164 55.000 12.47 0.00 0.00 3.16
4129 4422 1.512926 CGGGGTCTTGAAGTGAACAG 58.487 55.000 0.00 0.00 0.00 3.16
4139 4432 2.995939 TGAAGTGAACAGTCGATGATGC 59.004 45.455 0.00 0.00 0.00 3.91
4150 4443 1.572085 CGATGATGCGCCTGGGAATC 61.572 60.000 4.18 0.00 0.00 2.52
4182 4483 9.713740 CAAAGATGCTAAGATGATGTTAGTTTC 57.286 33.333 10.52 7.93 31.22 2.78
4183 4484 7.706281 AGATGCTAAGATGATGTTAGTTTCG 57.294 36.000 10.52 0.00 31.22 3.46
4195 4497 2.004583 TAGTTTCGAATGGACTGGCG 57.995 50.000 10.54 0.00 0.00 5.69
4245 4578 3.692101 CGGTGGTGGATAATTTTGTAGCA 59.308 43.478 0.00 0.00 0.00 3.49
4276 4611 4.978083 AAACCTGCTGCTTGATTGATAG 57.022 40.909 0.00 0.00 0.00 2.08
4277 4612 3.641434 ACCTGCTGCTTGATTGATAGT 57.359 42.857 0.00 0.00 0.00 2.12
4278 4613 4.760530 ACCTGCTGCTTGATTGATAGTA 57.239 40.909 0.00 0.00 0.00 1.82
4297 4754 0.320697 AAGTAACAGACGGGGCTGAC 59.679 55.000 8.86 0.00 39.20 3.51
4319 4776 3.209410 GCACCATAGTCCTGAAATCCTG 58.791 50.000 0.00 0.00 0.00 3.86
4379 4837 1.267532 GCTCGTCGCCATATTTGTGTG 60.268 52.381 0.00 0.00 0.00 3.82
4392 4850 6.458751 CCATATTTGTGTGTGGATAACTCAGC 60.459 42.308 0.00 0.00 33.11 4.26
4408 4866 2.749839 GCATGCGGTTGCCTGGTA 60.750 61.111 0.00 0.00 41.78 3.25
4409 4867 2.764314 GCATGCGGTTGCCTGGTAG 61.764 63.158 0.00 0.00 41.78 3.18
4410 4868 2.114670 CATGCGGTTGCCTGGTAGG 61.115 63.158 0.00 0.00 41.78 3.18
4411 4869 2.602676 ATGCGGTTGCCTGGTAGGT 61.603 57.895 0.00 0.00 41.78 3.08
4412 4870 1.268992 ATGCGGTTGCCTGGTAGGTA 61.269 55.000 0.00 0.00 41.78 3.08
4422 4880 0.833287 CTGGTAGGTAGTGGCATGCT 59.167 55.000 18.92 0.00 0.00 3.79
4426 4884 2.280628 GTAGGTAGTGGCATGCTTGAC 58.719 52.381 18.92 11.88 0.00 3.18
4427 4885 0.035056 AGGTAGTGGCATGCTTGACC 60.035 55.000 18.92 18.41 0.00 4.02
4428 4886 0.035056 GGTAGTGGCATGCTTGACCT 60.035 55.000 18.92 8.74 0.00 3.85
4429 4887 1.373570 GTAGTGGCATGCTTGACCTC 58.626 55.000 18.92 1.15 0.00 3.85
4431 4889 2.046023 TGGCATGCTTGACCTCCG 60.046 61.111 18.92 0.00 0.00 4.63
4432 4890 2.045926 GGCATGCTTGACCTCCGT 60.046 61.111 18.92 0.00 0.00 4.69
4433 4891 1.675641 GGCATGCTTGACCTCCGTT 60.676 57.895 18.92 0.00 0.00 4.44
4434 4892 1.648467 GGCATGCTTGACCTCCGTTC 61.648 60.000 18.92 0.00 0.00 3.95
4435 4893 1.970917 GCATGCTTGACCTCCGTTCG 61.971 60.000 11.37 0.00 0.00 3.95
4436 4894 0.389817 CATGCTTGACCTCCGTTCGA 60.390 55.000 0.00 0.00 0.00 3.71
4437 4895 0.320374 ATGCTTGACCTCCGTTCGAA 59.680 50.000 0.00 0.00 0.00 3.71
4438 4896 0.105224 TGCTTGACCTCCGTTCGAAA 59.895 50.000 0.00 0.00 0.00 3.46
4439 4897 1.223187 GCTTGACCTCCGTTCGAAAA 58.777 50.000 0.00 0.00 0.00 2.29
4440 4898 1.600485 GCTTGACCTCCGTTCGAAAAA 59.400 47.619 0.00 0.00 0.00 1.94
4441 4899 2.349532 GCTTGACCTCCGTTCGAAAAAG 60.350 50.000 0.00 0.00 0.00 2.27
4442 4900 1.223187 TGACCTCCGTTCGAAAAAGC 58.777 50.000 0.00 0.00 0.00 3.51
4443 4901 1.202604 TGACCTCCGTTCGAAAAAGCT 60.203 47.619 0.00 0.00 0.00 3.74
4444 4902 1.871676 GACCTCCGTTCGAAAAAGCTT 59.128 47.619 0.00 0.00 0.00 3.74
4445 4903 1.602377 ACCTCCGTTCGAAAAAGCTTG 59.398 47.619 0.00 0.00 0.00 4.01
4446 4904 1.602377 CCTCCGTTCGAAAAAGCTTGT 59.398 47.619 0.00 0.00 0.00 3.16
4447 4905 2.349532 CCTCCGTTCGAAAAAGCTTGTC 60.350 50.000 0.00 0.00 0.00 3.18
4448 4906 2.544267 CTCCGTTCGAAAAAGCTTGTCT 59.456 45.455 0.00 0.00 0.00 3.41
4449 4907 2.542595 TCCGTTCGAAAAAGCTTGTCTC 59.457 45.455 0.00 0.00 0.00 3.36
4450 4908 2.544267 CCGTTCGAAAAAGCTTGTCTCT 59.456 45.455 0.00 0.00 0.00 3.10
4451 4909 3.002348 CCGTTCGAAAAAGCTTGTCTCTT 59.998 43.478 0.00 0.00 0.00 2.85
4452 4910 4.210537 CCGTTCGAAAAAGCTTGTCTCTTA 59.789 41.667 0.00 0.00 0.00 2.10
4453 4911 5.277154 CCGTTCGAAAAAGCTTGTCTCTTAA 60.277 40.000 0.00 0.00 0.00 1.85
4454 4912 6.189567 CGTTCGAAAAAGCTTGTCTCTTAAA 58.810 36.000 0.00 0.00 0.00 1.52
4455 4913 6.851330 CGTTCGAAAAAGCTTGTCTCTTAAAT 59.149 34.615 0.00 0.00 0.00 1.40
4456 4914 7.149288 CGTTCGAAAAAGCTTGTCTCTTAAATG 60.149 37.037 0.00 0.00 0.00 2.32
4457 4915 6.668323 TCGAAAAAGCTTGTCTCTTAAATGG 58.332 36.000 0.00 0.00 0.00 3.16
4458 4916 6.485313 TCGAAAAAGCTTGTCTCTTAAATGGA 59.515 34.615 0.00 0.00 0.00 3.41
4459 4917 7.174946 TCGAAAAAGCTTGTCTCTTAAATGGAT 59.825 33.333 0.00 0.00 0.00 3.41
4460 4918 7.272084 CGAAAAAGCTTGTCTCTTAAATGGATG 59.728 37.037 0.00 0.00 0.00 3.51
4461 4919 7.530426 AAAAGCTTGTCTCTTAAATGGATGT 57.470 32.000 0.00 0.00 0.00 3.06
4462 4920 6.506500 AAGCTTGTCTCTTAAATGGATGTG 57.493 37.500 0.00 0.00 0.00 3.21
4463 4921 5.564550 AGCTTGTCTCTTAAATGGATGTGT 58.435 37.500 0.00 0.00 0.00 3.72
4464 4922 5.645497 AGCTTGTCTCTTAAATGGATGTGTC 59.355 40.000 0.00 0.00 0.00 3.67
4465 4923 5.645497 GCTTGTCTCTTAAATGGATGTGTCT 59.355 40.000 0.00 0.00 0.00 3.41
4466 4924 6.818644 GCTTGTCTCTTAAATGGATGTGTCTA 59.181 38.462 0.00 0.00 0.00 2.59
4467 4925 7.010923 GCTTGTCTCTTAAATGGATGTGTCTAG 59.989 40.741 0.00 0.00 0.00 2.43
4468 4926 6.341316 TGTCTCTTAAATGGATGTGTCTAGC 58.659 40.000 0.00 0.00 0.00 3.42
4469 4927 6.070824 TGTCTCTTAAATGGATGTGTCTAGCA 60.071 38.462 0.00 0.00 0.00 3.49
4470 4928 6.478344 GTCTCTTAAATGGATGTGTCTAGCAG 59.522 42.308 0.00 0.00 0.00 4.24
4471 4929 6.381133 TCTCTTAAATGGATGTGTCTAGCAGA 59.619 38.462 0.00 0.00 0.00 4.26
4472 4930 6.341316 TCTTAAATGGATGTGTCTAGCAGAC 58.659 40.000 8.75 8.75 45.26 3.51
4473 4931 4.833478 AAATGGATGTGTCTAGCAGACT 57.167 40.909 14.60 0.00 45.27 3.24
4474 4932 5.939764 AAATGGATGTGTCTAGCAGACTA 57.060 39.130 14.60 6.93 45.27 2.59
4475 4933 5.528043 AATGGATGTGTCTAGCAGACTAG 57.472 43.478 14.60 0.00 45.27 2.57
4476 4934 2.690497 TGGATGTGTCTAGCAGACTAGC 59.310 50.000 14.60 8.42 45.27 3.42
4477 4935 2.690497 GGATGTGTCTAGCAGACTAGCA 59.310 50.000 14.60 11.61 45.27 3.49
4478 4936 3.490078 GGATGTGTCTAGCAGACTAGCAC 60.490 52.174 14.60 14.95 45.27 4.40
4479 4937 2.796557 TGTGTCTAGCAGACTAGCACT 58.203 47.619 19.04 0.00 45.27 4.40
4480 4938 3.951663 TGTGTCTAGCAGACTAGCACTA 58.048 45.455 19.04 9.82 45.27 2.74
4481 4939 4.332828 TGTGTCTAGCAGACTAGCACTAA 58.667 43.478 19.04 6.49 45.27 2.24
4482 4940 4.156190 TGTGTCTAGCAGACTAGCACTAAC 59.844 45.833 19.04 5.93 45.27 2.34
4483 4941 4.396790 GTGTCTAGCAGACTAGCACTAACT 59.603 45.833 14.60 0.00 45.27 2.24
4484 4942 5.010933 TGTCTAGCAGACTAGCACTAACTT 58.989 41.667 14.60 0.00 45.27 2.66
4485 4943 5.106118 TGTCTAGCAGACTAGCACTAACTTG 60.106 44.000 14.60 0.00 45.27 3.16
4486 4944 5.124138 GTCTAGCAGACTAGCACTAACTTGA 59.876 44.000 8.50 0.00 44.83 3.02
4487 4945 5.888724 TCTAGCAGACTAGCACTAACTTGAT 59.111 40.000 0.00 0.00 44.83 2.57
4488 4946 4.753233 AGCAGACTAGCACTAACTTGATG 58.247 43.478 0.00 0.00 36.85 3.07
4489 4947 3.308323 GCAGACTAGCACTAACTTGATGC 59.692 47.826 0.00 0.00 39.74 3.91
4498 4956 6.718454 GCACTAACTTGATGCTAGATATGG 57.282 41.667 0.00 0.00 36.40 2.74
4499 4957 5.641209 GCACTAACTTGATGCTAGATATGGG 59.359 44.000 0.00 0.00 36.40 4.00
4500 4958 6.519043 GCACTAACTTGATGCTAGATATGGGA 60.519 42.308 0.00 0.00 36.40 4.37
4501 4959 6.870965 CACTAACTTGATGCTAGATATGGGAC 59.129 42.308 0.00 0.00 0.00 4.46
4514 4972 3.935371 TGGGACAAGCTTTTTGGGA 57.065 47.368 0.00 0.00 31.92 4.37
4515 4973 1.703411 TGGGACAAGCTTTTTGGGAG 58.297 50.000 0.00 0.00 31.92 4.30
4516 4974 0.969149 GGGACAAGCTTTTTGGGAGG 59.031 55.000 0.00 0.00 0.00 4.30
4517 4975 0.969149 GGACAAGCTTTTTGGGAGGG 59.031 55.000 0.00 0.00 0.00 4.30
4518 4976 1.480498 GGACAAGCTTTTTGGGAGGGA 60.480 52.381 0.00 0.00 0.00 4.20
4519 4977 1.889170 GACAAGCTTTTTGGGAGGGAG 59.111 52.381 0.00 0.00 0.00 4.30
4520 4978 1.260544 CAAGCTTTTTGGGAGGGAGG 58.739 55.000 0.00 0.00 0.00 4.30
4521 4979 0.115152 AAGCTTTTTGGGAGGGAGGG 59.885 55.000 0.00 0.00 0.00 4.30
4522 4980 0.776080 AGCTTTTTGGGAGGGAGGGA 60.776 55.000 0.00 0.00 0.00 4.20
4523 4981 0.323816 GCTTTTTGGGAGGGAGGGAG 60.324 60.000 0.00 0.00 0.00 4.30
4575 5045 2.094390 GGTCACAGCCGTACAGATGTTA 60.094 50.000 0.00 0.00 0.00 2.41
4586 5056 1.135373 ACAGATGTTAGAGTCACGGCG 60.135 52.381 4.80 4.80 0.00 6.46
4630 5102 4.087892 CCACCTCCCACTCTGCCG 62.088 72.222 0.00 0.00 0.00 5.69
4640 5112 2.978010 CTCTGCCGCAACCCGTTT 60.978 61.111 0.00 0.00 34.38 3.60
4647 5119 4.639171 GCAACCCGTTTGGCACCG 62.639 66.667 0.00 0.00 37.83 4.94
4648 5120 3.972276 CAACCCGTTTGGCACCGG 61.972 66.667 15.86 15.86 43.82 5.28
4709 5181 0.458543 CACTAGCGATCAACCAGCGT 60.459 55.000 0.00 0.00 35.78 5.07
4714 5186 3.499737 GATCAACCAGCGTGGCCG 61.500 66.667 0.00 0.00 42.67 6.13
4882 5375 2.025418 CCCGCGCGAATATACCCAC 61.025 63.158 34.63 0.00 0.00 4.61
4883 5376 2.025418 CCGCGCGAATATACCCACC 61.025 63.158 34.63 0.00 0.00 4.61
4884 5377 1.300311 CGCGCGAATATACCCACCA 60.300 57.895 28.94 0.00 0.00 4.17
4885 5378 1.554042 CGCGCGAATATACCCACCAC 61.554 60.000 28.94 0.00 0.00 4.16
4886 5379 1.554042 GCGCGAATATACCCACCACG 61.554 60.000 12.10 0.00 0.00 4.94
4887 5380 0.942410 CGCGAATATACCCACCACGG 60.942 60.000 0.00 0.00 0.00 4.94
4888 5381 1.226030 GCGAATATACCCACCACGGC 61.226 60.000 0.00 0.00 0.00 5.68
4889 5382 0.105224 CGAATATACCCACCACGGCA 59.895 55.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
592 600 2.463752 ACCGCTTAACTGACAGGGATA 58.536 47.619 7.51 0.00 0.00 2.59
746 755 4.021807 TGTCTACTGCCGAGTATTTGACAA 60.022 41.667 0.00 0.00 35.78 3.18
765 774 4.100279 ACCGGATTCTTTTTCCTTGTCT 57.900 40.909 9.46 0.00 0.00 3.41
969 987 3.592814 CGCTCGCTCGGTGGGATA 61.593 66.667 0.00 0.00 37.01 2.59
1154 1200 1.594331 GCGTCAGGGATGGGATTAAC 58.406 55.000 0.00 0.00 0.00 2.01
1155 1201 0.105964 CGCGTCAGGGATGGGATTAA 59.894 55.000 0.00 0.00 34.11 1.40
1192 1238 2.096496 GCATCAAAACCAGATCACGAGG 59.904 50.000 0.00 0.00 0.00 4.63
1350 1418 0.866061 CCGAAGACAGCATACGGACG 60.866 60.000 0.00 0.00 45.31 4.79
1397 1465 8.925161 TTGTTGAAGACAAAAAGGTAATCAAG 57.075 30.769 0.00 0.00 44.95 3.02
1449 1518 2.439409 CACAATTGCATCACTCCCTGA 58.561 47.619 5.05 0.00 0.00 3.86
1506 1575 5.825679 GTGTGCCCAATGGTATTACATAAGA 59.174 40.000 0.00 0.00 0.00 2.10
1522 1597 0.187117 TTCCAATTGAGGTGTGCCCA 59.813 50.000 7.12 0.00 34.66 5.36
1581 1657 1.317613 GCATTCAGTCACCACCACAA 58.682 50.000 0.00 0.00 0.00 3.33
1582 1658 0.182299 TGCATTCAGTCACCACCACA 59.818 50.000 0.00 0.00 0.00 4.17
1679 1819 8.961294 TCACCAAAGAAATTCAACATTTCAAT 57.039 26.923 9.40 0.00 39.71 2.57
1693 1833 6.601332 ACTAAACAGAGGATCACCAAAGAAA 58.399 36.000 0.00 0.00 37.82 2.52
1710 1850 6.646267 AGTAGTTCCACAACTCAACTAAACA 58.354 36.000 0.00 0.00 42.27 2.83
1722 1862 1.543871 GGGGCGAAAGTAGTTCCACAA 60.544 52.381 0.00 0.00 31.99 3.33
1744 1884 9.449719 AATTTCTTACCATTTACTAGTCAGGTG 57.550 33.333 14.98 5.11 0.00 4.00
1761 1901 5.772521 AGCACACATGTTGGAATTTCTTAC 58.227 37.500 0.00 0.00 0.00 2.34
1766 1906 7.714377 TCAAATTAAGCACACATGTTGGAATTT 59.286 29.630 0.00 0.76 31.30 1.82
1775 1915 6.580041 GTCTGACTTCAAATTAAGCACACATG 59.420 38.462 0.00 0.00 0.00 3.21
1809 1949 2.587307 AGGGGGCCTATGAGTTGAAAAT 59.413 45.455 0.84 0.00 28.47 1.82
1819 1974 2.443255 AGTACATGAAAGGGGGCCTATG 59.557 50.000 0.84 2.00 31.13 2.23
1852 2007 1.300481 GCTCATAAAGCGGACTTCCC 58.700 55.000 0.00 0.00 42.21 3.97
1869 2024 4.470334 ACCAACATGAACAAAAACAGCT 57.530 36.364 0.00 0.00 0.00 4.24
1951 2106 7.872113 ATCATCCAAAGAGAGAATTACCAAC 57.128 36.000 0.00 0.00 0.00 3.77
2191 2346 5.724328 TGTCAAGAGTCTAACTGCCTATTG 58.276 41.667 0.00 0.00 0.00 1.90
2396 2553 5.947228 AAACACACCATAACTCATCACAG 57.053 39.130 0.00 0.00 0.00 3.66
2431 2588 5.680619 AGTTGTGACCATCAGAGTGTAAAA 58.319 37.500 0.00 0.00 0.00 1.52
2482 2639 4.142881 GCCGTCTAGAATGAAACAGGAAAC 60.143 45.833 0.00 0.00 0.00 2.78
2551 2708 4.956700 CCAGACTCCAGAGTACCTATTCAA 59.043 45.833 0.00 0.00 42.66 2.69
2558 2715 2.217510 TGTCCAGACTCCAGAGTACC 57.782 55.000 0.00 0.00 42.66 3.34
2563 2720 3.903714 TCAAAGATTGTCCAGACTCCAGA 59.096 43.478 0.00 0.00 0.00 3.86
2564 2721 4.277515 TCAAAGATTGTCCAGACTCCAG 57.722 45.455 0.00 0.00 0.00 3.86
2565 2722 4.916041 ATCAAAGATTGTCCAGACTCCA 57.084 40.909 0.00 0.00 0.00 3.86
2566 2723 9.566432 AAATATATCAAAGATTGTCCAGACTCC 57.434 33.333 0.00 0.00 0.00 3.85
2885 3044 4.277672 GGCATGTTGATCAGCATTGACTAT 59.722 41.667 21.03 0.00 35.83 2.12
2886 3045 3.628942 GGCATGTTGATCAGCATTGACTA 59.371 43.478 21.03 0.00 35.83 2.59
2968 3242 9.696572 TCAGTATTAATCCTAACTCACTGTAGT 57.303 33.333 9.44 0.00 34.99 2.73
2970 3244 9.696572 ACTCAGTATTAATCCTAACTCACTGTA 57.303 33.333 9.44 0.00 34.99 2.74
2971 3245 8.596781 ACTCAGTATTAATCCTAACTCACTGT 57.403 34.615 9.44 0.00 34.99 3.55
2974 3248 9.968870 CCTAACTCAGTATTAATCCTAACTCAC 57.031 37.037 0.00 0.00 0.00 3.51
2975 3249 9.931698 TCCTAACTCAGTATTAATCCTAACTCA 57.068 33.333 0.00 0.00 0.00 3.41
2980 3254 9.877222 TCACATCCTAACTCAGTATTAATCCTA 57.123 33.333 0.00 0.00 0.00 2.94
2981 3255 8.783660 TCACATCCTAACTCAGTATTAATCCT 57.216 34.615 0.00 0.00 0.00 3.24
2982 3256 9.482627 CTTCACATCCTAACTCAGTATTAATCC 57.517 37.037 0.00 0.00 0.00 3.01
2983 3257 9.482627 CCTTCACATCCTAACTCAGTATTAATC 57.517 37.037 0.00 0.00 0.00 1.75
2984 3258 7.934120 GCCTTCACATCCTAACTCAGTATTAAT 59.066 37.037 0.00 0.00 0.00 1.40
2985 3259 7.272978 GCCTTCACATCCTAACTCAGTATTAA 58.727 38.462 0.00 0.00 0.00 1.40
2986 3260 6.183360 GGCCTTCACATCCTAACTCAGTATTA 60.183 42.308 0.00 0.00 0.00 0.98
2987 3261 5.396884 GGCCTTCACATCCTAACTCAGTATT 60.397 44.000 0.00 0.00 0.00 1.89
3064 3338 5.696270 CAGCCGTGATATTAAATACTGCAGA 59.304 40.000 23.35 4.31 0.00 4.26
3065 3339 5.106948 CCAGCCGTGATATTAAATACTGCAG 60.107 44.000 13.48 13.48 0.00 4.41
3066 3340 4.754618 CCAGCCGTGATATTAAATACTGCA 59.245 41.667 0.00 0.00 0.00 4.41
3067 3341 4.755123 ACCAGCCGTGATATTAAATACTGC 59.245 41.667 0.00 0.00 0.00 4.40
3068 3342 6.861065 AACCAGCCGTGATATTAAATACTG 57.139 37.500 0.00 0.00 0.00 2.74
3084 3363 4.017126 AGCAGGTAAATAGAAAACCAGCC 58.983 43.478 4.72 0.00 44.36 4.85
3100 3379 3.963428 CTACACTAAGTTGGAGCAGGT 57.037 47.619 0.00 0.00 0.00 4.00
3185 3464 4.921515 TCACAGCAAAACTATGTCGTCTAC 59.078 41.667 0.00 0.00 0.00 2.59
3186 3465 5.128992 TCACAGCAAAACTATGTCGTCTA 57.871 39.130 0.00 0.00 0.00 2.59
3188 3467 4.627467 AGATCACAGCAAAACTATGTCGTC 59.373 41.667 0.00 0.00 0.00 4.20
3239 3518 7.333672 ACAGGAACTTTAGTACGGATTTCAATC 59.666 37.037 0.00 0.00 34.60 2.67
3242 3521 6.105397 ACAGGAACTTTAGTACGGATTTCA 57.895 37.500 0.00 0.00 34.60 2.69
3250 3529 6.624423 TCGGATGTAACAGGAACTTTAGTAC 58.376 40.000 0.00 0.00 34.60 2.73
3252 3531 5.245526 ACTCGGATGTAACAGGAACTTTAGT 59.754 40.000 0.00 0.00 34.60 2.24
3301 3580 4.978099 AGTAAATAGCCTATGTGCAGCAT 58.022 39.130 0.00 6.93 41.42 3.79
3394 3673 3.763360 CAGGGTATTCAAAACCAGATGCA 59.237 43.478 0.00 0.00 38.87 3.96
3449 3728 4.873746 TCAGAGCTACTACACTTTTGCT 57.126 40.909 0.00 0.00 0.00 3.91
3468 3753 9.341078 TGCTATTCTAAATAAATGACAGCATCA 57.659 29.630 0.00 0.00 43.13 3.07
3473 3758 8.682936 AGGGTGCTATTCTAAATAAATGACAG 57.317 34.615 0.00 0.00 0.00 3.51
3476 3761 8.045720 AGGAGGGTGCTATTCTAAATAAATGA 57.954 34.615 0.00 0.00 0.00 2.57
3488 3773 1.972588 AGTTGGAGGAGGGTGCTATT 58.027 50.000 0.00 0.00 0.00 1.73
3489 3774 2.868964 TAGTTGGAGGAGGGTGCTAT 57.131 50.000 0.00 0.00 0.00 2.97
3490 3775 2.868964 ATAGTTGGAGGAGGGTGCTA 57.131 50.000 0.00 0.00 0.00 3.49
3492 3777 2.551071 GCATATAGTTGGAGGAGGGTGC 60.551 54.545 0.00 0.00 0.00 5.01
3509 3794 1.212441 TGCATGTCCCAGTGATGCATA 59.788 47.619 11.93 0.00 45.76 3.14
3555 3840 4.593597 TCAAAATTCGGAGAATACGCAC 57.406 40.909 0.00 0.00 45.90 5.34
3559 3844 9.387123 GCATATCTTTCAAAATTCGGAGAATAC 57.613 33.333 0.00 0.00 45.90 1.89
3579 3866 5.528690 TGCATGACAGGAAGTTTAGCATATC 59.471 40.000 0.00 0.00 0.00 1.63
3581 3868 4.842574 TGCATGACAGGAAGTTTAGCATA 58.157 39.130 0.00 0.00 0.00 3.14
3611 3898 4.742167 CACTCGCTCGTATTTGATTCAGAT 59.258 41.667 0.00 0.00 0.00 2.90
3613 3900 3.302092 GCACTCGCTCGTATTTGATTCAG 60.302 47.826 0.00 0.00 34.30 3.02
3629 3916 0.723414 CCACTTATGTGCAGCACTCG 59.277 55.000 25.83 13.37 42.54 4.18
3635 3922 1.003580 ACCAGGACCACTTATGTGCAG 59.996 52.381 3.24 0.00 42.54 4.41
3693 3980 6.820152 CAGGATGATAACACTGACAATTGAGA 59.180 38.462 13.59 0.00 39.69 3.27
3701 3988 4.142600 GGTTTGCAGGATGATAACACTGAC 60.143 45.833 0.00 0.00 39.69 3.51
3708 4001 5.508567 TCATTCAGGTTTGCAGGATGATAA 58.491 37.500 0.00 0.00 39.69 1.75
3716 4009 4.021719 AGGTTTCATCATTCAGGTTTGCAG 60.022 41.667 0.00 0.00 0.00 4.41
3729 4022 5.263599 ACATAAGATTGGCAGGTTTCATCA 58.736 37.500 0.00 0.00 0.00 3.07
3745 4038 6.097839 AGGGCGTATCTGAAAGTAACATAAGA 59.902 38.462 0.00 0.00 33.76 2.10
3749 4042 4.442706 CAGGGCGTATCTGAAAGTAACAT 58.557 43.478 0.00 0.00 34.36 2.71
3789 4082 1.324740 CGATCCTCCGGGTGTACCAA 61.325 60.000 0.00 0.00 40.22 3.67
3885 4178 0.035881 TGCTCCTGAACCTGCTTCTG 59.964 55.000 0.00 0.00 0.00 3.02
3890 4183 2.328099 CGGTTGCTCCTGAACCTGC 61.328 63.158 0.00 0.00 40.77 4.85
3892 4185 2.750350 CCGGTTGCTCCTGAACCT 59.250 61.111 0.00 0.00 40.77 3.50
3967 4260 2.283388 AGACACCCCGCTAACCGA 60.283 61.111 0.00 0.00 40.02 4.69
3968 4261 2.125673 CAGACACCCCGCTAACCG 60.126 66.667 0.00 0.00 0.00 4.44
3969 4262 1.079336 GACAGACACCCCGCTAACC 60.079 63.158 0.00 0.00 0.00 2.85
3970 4263 0.034337 TTGACAGACACCCCGCTAAC 59.966 55.000 0.00 0.00 0.00 2.34
3971 4264 0.034337 GTTGACAGACACCCCGCTAA 59.966 55.000 0.00 0.00 0.00 3.09
3972 4265 1.116536 TGTTGACAGACACCCCGCTA 61.117 55.000 0.00 0.00 0.00 4.26
3973 4266 1.978455 TTGTTGACAGACACCCCGCT 61.978 55.000 0.00 0.00 0.00 5.52
3974 4267 1.507141 CTTGTTGACAGACACCCCGC 61.507 60.000 0.00 0.00 0.00 6.13
3975 4268 0.884704 CCTTGTTGACAGACACCCCG 60.885 60.000 0.00 0.00 0.00 5.73
3976 4269 1.172812 GCCTTGTTGACAGACACCCC 61.173 60.000 0.00 0.00 0.00 4.95
3977 4270 0.179018 AGCCTTGTTGACAGACACCC 60.179 55.000 0.00 0.00 0.00 4.61
3978 4271 1.230324 GAGCCTTGTTGACAGACACC 58.770 55.000 0.00 0.00 0.00 4.16
3979 4272 1.869767 CTGAGCCTTGTTGACAGACAC 59.130 52.381 0.00 0.00 0.00 3.67
3980 4273 1.202687 CCTGAGCCTTGTTGACAGACA 60.203 52.381 0.00 0.00 0.00 3.41
3981 4274 1.517242 CCTGAGCCTTGTTGACAGAC 58.483 55.000 0.00 0.00 0.00 3.51
3982 4275 0.397941 CCCTGAGCCTTGTTGACAGA 59.602 55.000 0.00 0.00 0.00 3.41
3983 4276 1.239968 GCCCTGAGCCTTGTTGACAG 61.240 60.000 0.00 0.00 34.35 3.51
3984 4277 1.228245 GCCCTGAGCCTTGTTGACA 60.228 57.895 0.00 0.00 34.35 3.58
3985 4278 2.328099 CGCCCTGAGCCTTGTTGAC 61.328 63.158 0.00 0.00 38.78 3.18
4094 4387 3.151554 ACCCCGCGTTTTCTTTCTAATT 58.848 40.909 4.92 0.00 0.00 1.40
4116 4409 4.435253 GCATCATCGACTGTTCACTTCAAG 60.435 45.833 0.00 0.00 0.00 3.02
4123 4416 1.083806 GGCGCATCATCGACTGTTCA 61.084 55.000 10.83 0.00 33.99 3.18
4124 4417 1.638467 GGCGCATCATCGACTGTTC 59.362 57.895 10.83 0.00 33.99 3.18
4129 4422 2.923426 TTCCCAGGCGCATCATCGAC 62.923 60.000 10.83 0.00 37.86 4.20
4139 4432 4.918201 GCCCTCGATTCCCAGGCG 62.918 72.222 0.00 0.00 33.18 5.52
4176 4477 1.404986 CCGCCAGTCCATTCGAAACTA 60.405 52.381 0.00 0.00 0.00 2.24
4177 4478 0.673644 CCGCCAGTCCATTCGAAACT 60.674 55.000 0.00 0.00 0.00 2.66
4182 4483 1.811266 CTGACCGCCAGTCCATTCG 60.811 63.158 0.00 0.00 45.68 3.34
4183 4484 2.109126 GCTGACCGCCAGTCCATTC 61.109 63.158 5.21 0.00 45.68 2.67
4222 4555 3.942748 GCTACAAAATTATCCACCACCGA 59.057 43.478 0.00 0.00 0.00 4.69
4245 4578 1.339151 GCAGCAGGTTTAGTGGCTAGT 60.339 52.381 0.00 0.00 34.25 2.57
4276 4611 1.547372 TCAGCCCCGTCTGTTACTTAC 59.453 52.381 0.00 0.00 35.63 2.34
4277 4612 1.547372 GTCAGCCCCGTCTGTTACTTA 59.453 52.381 0.00 0.00 35.63 2.24
4278 4613 0.320697 GTCAGCCCCGTCTGTTACTT 59.679 55.000 0.00 0.00 35.63 2.24
4297 4754 2.158900 AGGATTTCAGGACTATGGTGCG 60.159 50.000 0.00 0.00 38.85 5.34
4303 4760 2.398588 TCGCCAGGATTTCAGGACTAT 58.601 47.619 0.00 0.00 0.00 2.12
4379 4837 0.940126 CCGCATGCTGAGTTATCCAC 59.060 55.000 17.13 0.00 0.00 4.02
4408 4866 0.035056 GGTCAAGCATGCCACTACCT 60.035 55.000 15.66 0.00 0.00 3.08
4409 4867 0.035056 AGGTCAAGCATGCCACTACC 60.035 55.000 15.66 16.54 0.00 3.18
4410 4868 1.373570 GAGGTCAAGCATGCCACTAC 58.626 55.000 15.66 7.78 0.00 2.73
4411 4869 0.253044 GGAGGTCAAGCATGCCACTA 59.747 55.000 15.66 0.00 0.00 2.74
4412 4870 1.001641 GGAGGTCAAGCATGCCACT 60.002 57.895 15.66 5.46 0.00 4.00
4422 4880 1.600485 GCTTTTTCGAACGGAGGTCAA 59.400 47.619 0.00 0.00 0.00 3.18
4426 4884 1.602377 ACAAGCTTTTTCGAACGGAGG 59.398 47.619 0.00 0.00 0.00 4.30
4427 4885 2.544267 AGACAAGCTTTTTCGAACGGAG 59.456 45.455 0.00 0.00 0.00 4.63
4428 4886 2.542595 GAGACAAGCTTTTTCGAACGGA 59.457 45.455 0.00 0.00 0.00 4.69
4429 4887 2.544267 AGAGACAAGCTTTTTCGAACGG 59.456 45.455 0.00 0.00 0.00 4.44
4431 4889 7.113544 CCATTTAAGAGACAAGCTTTTTCGAAC 59.886 37.037 0.00 0.00 0.00 3.95
4432 4890 7.012894 TCCATTTAAGAGACAAGCTTTTTCGAA 59.987 33.333 0.00 0.00 0.00 3.71
4433 4891 6.485313 TCCATTTAAGAGACAAGCTTTTTCGA 59.515 34.615 0.00 0.00 0.00 3.71
4434 4892 6.668323 TCCATTTAAGAGACAAGCTTTTTCG 58.332 36.000 0.00 0.00 0.00 3.46
4435 4893 8.084684 ACATCCATTTAAGAGACAAGCTTTTTC 58.915 33.333 0.00 0.00 0.00 2.29
4436 4894 7.869429 CACATCCATTTAAGAGACAAGCTTTTT 59.131 33.333 0.00 0.00 0.00 1.94
4437 4895 7.014615 ACACATCCATTTAAGAGACAAGCTTTT 59.985 33.333 0.00 0.00 0.00 2.27
4438 4896 6.491403 ACACATCCATTTAAGAGACAAGCTTT 59.509 34.615 0.00 0.00 0.00 3.51
4439 4897 6.006449 ACACATCCATTTAAGAGACAAGCTT 58.994 36.000 0.00 0.00 0.00 3.74
4440 4898 5.564550 ACACATCCATTTAAGAGACAAGCT 58.435 37.500 0.00 0.00 0.00 3.74
4441 4899 5.645497 AGACACATCCATTTAAGAGACAAGC 59.355 40.000 0.00 0.00 0.00 4.01
4442 4900 7.010923 GCTAGACACATCCATTTAAGAGACAAG 59.989 40.741 0.00 0.00 0.00 3.16
4443 4901 6.818644 GCTAGACACATCCATTTAAGAGACAA 59.181 38.462 0.00 0.00 0.00 3.18
4444 4902 6.070824 TGCTAGACACATCCATTTAAGAGACA 60.071 38.462 0.00 0.00 0.00 3.41
4445 4903 6.341316 TGCTAGACACATCCATTTAAGAGAC 58.659 40.000 0.00 0.00 0.00 3.36
4446 4904 6.381133 TCTGCTAGACACATCCATTTAAGAGA 59.619 38.462 0.00 0.00 0.00 3.10
4447 4905 6.478344 GTCTGCTAGACACATCCATTTAAGAG 59.522 42.308 10.30 0.00 44.45 2.85
4448 4906 6.341316 GTCTGCTAGACACATCCATTTAAGA 58.659 40.000 10.30 0.00 44.45 2.10
4449 4907 6.595772 GTCTGCTAGACACATCCATTTAAG 57.404 41.667 10.30 0.00 44.45 1.85
4462 4920 5.124138 TCAAGTTAGTGCTAGTCTGCTAGAC 59.876 44.000 5.89 7.88 45.77 2.59
4463 4921 5.254115 TCAAGTTAGTGCTAGTCTGCTAGA 58.746 41.667 5.89 0.00 45.77 2.43
4464 4922 5.568685 TCAAGTTAGTGCTAGTCTGCTAG 57.431 43.478 0.00 0.00 45.68 3.42
4465 4923 5.679894 GCATCAAGTTAGTGCTAGTCTGCTA 60.680 44.000 4.81 0.00 36.02 3.49
4466 4924 4.753233 CATCAAGTTAGTGCTAGTCTGCT 58.247 43.478 0.00 0.00 0.00 4.24
4467 4925 3.308323 GCATCAAGTTAGTGCTAGTCTGC 59.692 47.826 4.81 0.00 36.02 4.26
4468 4926 4.753233 AGCATCAAGTTAGTGCTAGTCTG 58.247 43.478 11.30 0.00 46.54 3.51
4473 4931 7.310052 CCCATATCTAGCATCAAGTTAGTGCTA 60.310 40.741 16.22 16.22 46.54 3.49
4475 4933 5.641209 CCCATATCTAGCATCAAGTTAGTGC 59.359 44.000 4.02 4.02 39.10 4.40
4476 4934 6.870965 GTCCCATATCTAGCATCAAGTTAGTG 59.129 42.308 0.00 0.00 33.25 2.74
4477 4935 6.554982 TGTCCCATATCTAGCATCAAGTTAGT 59.445 38.462 0.00 0.00 33.25 2.24
4478 4936 6.997655 TGTCCCATATCTAGCATCAAGTTAG 58.002 40.000 0.00 0.00 32.79 2.34
4479 4937 6.994421 TGTCCCATATCTAGCATCAAGTTA 57.006 37.500 0.00 0.00 0.00 2.24
4480 4938 5.894298 TGTCCCATATCTAGCATCAAGTT 57.106 39.130 0.00 0.00 0.00 2.66
4481 4939 5.744300 GCTTGTCCCATATCTAGCATCAAGT 60.744 44.000 0.00 0.00 34.31 3.16
4482 4940 4.694509 GCTTGTCCCATATCTAGCATCAAG 59.305 45.833 0.00 0.00 33.93 3.02
4483 4941 4.349048 AGCTTGTCCCATATCTAGCATCAA 59.651 41.667 0.00 0.00 35.57 2.57
4484 4942 3.906218 AGCTTGTCCCATATCTAGCATCA 59.094 43.478 0.00 0.00 35.57 3.07
4485 4943 4.550076 AGCTTGTCCCATATCTAGCATC 57.450 45.455 0.00 0.00 35.57 3.91
4486 4944 4.989875 AAGCTTGTCCCATATCTAGCAT 57.010 40.909 0.00 0.00 35.57 3.79
4487 4945 4.778213 AAAGCTTGTCCCATATCTAGCA 57.222 40.909 0.00 0.00 35.57 3.49
4488 4946 5.221126 CCAAAAAGCTTGTCCCATATCTAGC 60.221 44.000 0.00 0.00 33.93 3.42
4489 4947 5.300286 CCCAAAAAGCTTGTCCCATATCTAG 59.700 44.000 0.00 0.00 0.00 2.43
4490 4948 5.044476 TCCCAAAAAGCTTGTCCCATATCTA 60.044 40.000 0.00 0.00 0.00 1.98
4491 4949 4.026052 CCCAAAAAGCTTGTCCCATATCT 58.974 43.478 0.00 0.00 0.00 1.98
4492 4950 4.023291 TCCCAAAAAGCTTGTCCCATATC 58.977 43.478 0.00 0.00 0.00 1.63
4493 4951 4.026052 CTCCCAAAAAGCTTGTCCCATAT 58.974 43.478 0.00 0.00 0.00 1.78
4494 4952 3.430453 CTCCCAAAAAGCTTGTCCCATA 58.570 45.455 0.00 0.00 0.00 2.74
4495 4953 2.250924 CTCCCAAAAAGCTTGTCCCAT 58.749 47.619 0.00 0.00 0.00 4.00
4496 4954 1.703411 CTCCCAAAAAGCTTGTCCCA 58.297 50.000 0.00 0.00 0.00 4.37
4497 4955 0.969149 CCTCCCAAAAAGCTTGTCCC 59.031 55.000 0.00 0.00 0.00 4.46
4498 4956 0.969149 CCCTCCCAAAAAGCTTGTCC 59.031 55.000 0.00 0.00 0.00 4.02
4499 4957 1.889170 CTCCCTCCCAAAAAGCTTGTC 59.111 52.381 0.00 0.00 0.00 3.18
4500 4958 1.481242 CCTCCCTCCCAAAAAGCTTGT 60.481 52.381 0.00 0.00 0.00 3.16
4501 4959 1.260544 CCTCCCTCCCAAAAAGCTTG 58.739 55.000 0.00 0.00 0.00 4.01
4502 4960 0.115152 CCCTCCCTCCCAAAAAGCTT 59.885 55.000 0.00 0.00 0.00 3.74
4503 4961 0.776080 TCCCTCCCTCCCAAAAAGCT 60.776 55.000 0.00 0.00 0.00 3.74
4504 4962 0.323816 CTCCCTCCCTCCCAAAAAGC 60.324 60.000 0.00 0.00 0.00 3.51
4505 4963 1.076438 ACTCCCTCCCTCCCAAAAAG 58.924 55.000 0.00 0.00 0.00 2.27
4506 4964 2.275466 CTACTCCCTCCCTCCCAAAAA 58.725 52.381 0.00 0.00 0.00 1.94
4507 4965 1.153565 ACTACTCCCTCCCTCCCAAAA 59.846 52.381 0.00 0.00 0.00 2.44
4508 4966 0.797579 ACTACTCCCTCCCTCCCAAA 59.202 55.000 0.00 0.00 0.00 3.28
4509 4967 0.797579 AACTACTCCCTCCCTCCCAA 59.202 55.000 0.00 0.00 0.00 4.12
4510 4968 0.338814 GAACTACTCCCTCCCTCCCA 59.661 60.000 0.00 0.00 0.00 4.37
4511 4969 0.398806 GGAACTACTCCCTCCCTCCC 60.399 65.000 0.00 0.00 38.44 4.30
4512 4970 0.756070 CGGAACTACTCCCTCCCTCC 60.756 65.000 0.00 0.00 41.87 4.30
4513 4971 0.258194 TCGGAACTACTCCCTCCCTC 59.742 60.000 0.00 0.00 41.87 4.30
4514 4972 0.935194 ATCGGAACTACTCCCTCCCT 59.065 55.000 0.00 0.00 41.87 4.20
4515 4973 1.041437 CATCGGAACTACTCCCTCCC 58.959 60.000 0.00 0.00 41.87 4.30
4516 4974 1.682323 GACATCGGAACTACTCCCTCC 59.318 57.143 0.00 0.00 41.87 4.30
4517 4975 1.334243 CGACATCGGAACTACTCCCTC 59.666 57.143 0.00 0.00 41.87 4.30
4518 4976 1.064906 TCGACATCGGAACTACTCCCT 60.065 52.381 0.73 0.00 41.87 4.20
4519 4977 1.386533 TCGACATCGGAACTACTCCC 58.613 55.000 0.73 0.00 41.87 4.30
4520 4978 3.270962 GATCGACATCGGAACTACTCC 57.729 52.381 0.73 0.00 41.40 3.85
4555 5025 2.080286 AACATCTGTACGGCTGTGAC 57.920 50.000 11.76 3.47 0.00 3.67
4561 5031 3.436496 GTGACTCTAACATCTGTACGGC 58.564 50.000 0.00 0.00 0.00 5.68
4564 5034 3.436496 GCCGTGACTCTAACATCTGTAC 58.564 50.000 0.00 0.00 0.00 2.90
4575 5045 0.317160 TCAACATTCGCCGTGACTCT 59.683 50.000 0.00 0.00 0.00 3.24
4586 5056 1.459592 CCACGAACTCGGTCAACATTC 59.540 52.381 3.88 0.00 44.95 2.67
4622 5094 3.767630 AAACGGGTTGCGGCAGAGT 62.768 57.895 1.67 0.00 0.00 3.24
4625 5097 4.341502 CCAAACGGGTTGCGGCAG 62.342 66.667 1.67 0.00 35.74 4.85
4630 5102 4.639171 CGGTGCCAAACGGGTTGC 62.639 66.667 0.00 0.00 39.65 4.17
4774 5247 3.069318 GGACGGAGGAGGCGAAGT 61.069 66.667 0.00 0.00 0.00 3.01
4834 5327 2.968697 GGGGCGTTTTGTCGTCGT 60.969 61.111 0.00 0.00 36.22 4.34
4885 5378 4.676951 AATGGTGGGGTGGTGCCG 62.677 66.667 0.00 0.00 38.44 5.69
4886 5379 2.679996 GAATGGTGGGGTGGTGCC 60.680 66.667 0.00 0.00 0.00 5.01
4887 5380 2.679996 GGAATGGTGGGGTGGTGC 60.680 66.667 0.00 0.00 0.00 5.01
4888 5381 2.037208 GGGAATGGTGGGGTGGTG 59.963 66.667 0.00 0.00 0.00 4.17
4889 5382 3.272847 GGGGAATGGTGGGGTGGT 61.273 66.667 0.00 0.00 0.00 4.16
4922 5425 4.008933 AGTGTGTGCGAGAGGGGC 62.009 66.667 0.00 0.00 0.00 5.80
4924 5427 2.740055 GCAGTGTGTGCGAGAGGG 60.740 66.667 0.00 0.00 43.99 4.30
5049 5572 2.371259 GGAGGGAGTGGGAGGAAGC 61.371 68.421 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.