Multiple sequence alignment - TraesCS2A01G566700

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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 TraesCS2A01G566700 chr2A 100.000 3643 0 0 1 3643 765763686 765760044 0.000000e+00 6728.0
1 TraesCS2A01G566700 chr2A 77.011 1231 129 91 66 1235 765800623 765799486 6.830000e-157 564.0
2 TraesCS2A01G566700 chr2A 86.913 298 22 9 56 348 765786152 765785867 5.870000e-83 318.0
3 TraesCS2A01G566700 chr2A 85.388 219 25 3 420 638 765785726 765785515 1.700000e-53 220.0
4 TraesCS2A01G566700 chr2A 93.878 49 2 1 3480 3527 183218621 183218573 5.050000e-09 73.1
5 TraesCS2A01G566700 chr2D 90.369 2357 113 56 368 2686 640299848 640297568 0.000000e+00 2990.0
6 TraesCS2A01G566700 chr2D 82.111 559 51 26 66 598 640360424 640359889 2.010000e-117 433.0
7 TraesCS2A01G566700 chr2D 88.701 354 26 8 4 348 640300282 640299934 1.560000e-113 420.0
8 TraesCS2A01G566700 chr2D 79.701 670 66 32 62 701 640311408 640310779 1.560000e-113 420.0
9 TraesCS2A01G566700 chr2D 86.282 277 24 8 366 638 640315774 640315508 4.600000e-74 289.0
10 TraesCS2A01G566700 chr2D 86.772 189 10 7 165 348 640316030 640315852 2.870000e-46 196.0
11 TraesCS2A01G566700 chr2D 87.654 81 10 0 1345 1425 386248904 386248984 1.080000e-15 95.3
12 TraesCS2A01G566700 chr2D 79.091 110 19 3 1119 1226 114554859 114554752 5.050000e-09 73.1
13 TraesCS2A01G566700 chr2D 80.220 91 15 2 2816 2904 31947921 31947832 8.440000e-07 65.8
14 TraesCS2A01G566700 chr2D 100.000 28 0 0 1683 1710 610165027 610165054 7.000000e-03 52.8
15 TraesCS2A01G566700 chr2B 95.548 1123 32 12 1767 2873 801162961 801164081 0.000000e+00 1781.0
16 TraesCS2A01G566700 chr2B 87.997 1333 64 37 370 1673 801161630 801162895 0.000000e+00 1487.0
17 TraesCS2A01G566700 chr2B 91.071 336 20 7 21 348 801161215 801161548 2.580000e-121 446.0
18 TraesCS2A01G566700 chr2B 85.028 354 25 14 4 347 801158063 801158398 5.830000e-88 335.0
19 TraesCS2A01G566700 chr2B 87.023 262 24 4 366 623 801158477 801158732 1.660000e-73 287.0
20 TraesCS2A01G566700 chr2B 82.335 334 32 14 3042 3371 801164243 801164553 7.760000e-67 265.0
21 TraesCS2A01G566700 chr2B 90.000 180 14 3 94 270 801152098 801152276 2.830000e-56 230.0
22 TraesCS2A01G566700 chr2B 74.623 729 75 54 4 714 801059038 801059674 1.700000e-53 220.0
23 TraesCS2A01G566700 chr2B 96.226 106 4 0 2907 3012 801164076 801164181 1.340000e-39 174.0
24 TraesCS2A01G566700 chr2B 88.235 119 6 5 55 173 801144163 801144273 6.350000e-28 135.0
25 TraesCS2A01G566700 chr2B 87.654 81 10 0 1345 1425 457109354 457109434 1.080000e-15 95.3
26 TraesCS2A01G566700 chr5B 88.750 80 9 0 1345 1424 90507725 90507804 8.330000e-17 99.0
27 TraesCS2A01G566700 chr5B 93.333 45 3 0 3481 3525 683524941 683524985 2.350000e-07 67.6
28 TraesCS2A01G566700 chr5A 88.095 84 9 1 1345 1427 78157977 78158060 8.330000e-17 99.0
29 TraesCS2A01G566700 chr3A 81.081 111 14 5 3423 3527 705124834 705124943 8.380000e-12 82.4
30 TraesCS2A01G566700 chr7D 80.769 104 16 4 3425 3527 636515998 636515898 1.080000e-10 78.7
31 TraesCS2A01G566700 chr4B 73.707 232 45 16 3423 3643 112866884 112867110 3.900000e-10 76.8
32 TraesCS2A01G566700 chr1B 78.862 123 19 7 3408 3527 416831072 416830954 3.900000e-10 76.8
33 TraesCS2A01G566700 chr3B 93.750 48 2 1 3481 3527 71565409 71565362 1.810000e-08 71.3
34 TraesCS2A01G566700 chr6D 91.667 48 4 0 3480 3527 445790965 445791012 2.350000e-07 67.6
35 TraesCS2A01G566700 chr3D 93.182 44 2 1 2816 2859 275561482 275561524 3.040000e-06 63.9
36 TraesCS2A01G566700 chr6B 100.000 32 0 0 3481 3512 498525100 498525131 3.930000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G566700 chr2A 765760044 765763686 3642 True 6728.000000 6728 100.000000 1 3643 1 chr2A.!!$R2 3642
1 TraesCS2A01G566700 chr2A 765799486 765800623 1137 True 564.000000 564 77.011000 66 1235 1 chr2A.!!$R3 1169
2 TraesCS2A01G566700 chr2A 765785515 765786152 637 True 269.000000 318 86.150500 56 638 2 chr2A.!!$R4 582
3 TraesCS2A01G566700 chr2D 640297568 640300282 2714 True 1705.000000 2990 89.535000 4 2686 2 chr2D.!!$R5 2682
4 TraesCS2A01G566700 chr2D 640359889 640360424 535 True 433.000000 433 82.111000 66 598 1 chr2D.!!$R4 532
5 TraesCS2A01G566700 chr2D 640310779 640311408 629 True 420.000000 420 79.701000 62 701 1 chr2D.!!$R3 639
6 TraesCS2A01G566700 chr2D 640315508 640316030 522 True 242.500000 289 86.527000 165 638 2 chr2D.!!$R6 473
7 TraesCS2A01G566700 chr2B 801158063 801164553 6490 False 682.142857 1781 89.318286 4 3371 7 chr2B.!!$F5 3367
8 TraesCS2A01G566700 chr2B 801059038 801059674 636 False 220.000000 220 74.623000 4 714 1 chr2B.!!$F2 710

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
560 3851 0.169009 GAAAGCAACACGGCCATCTC 59.831 55.0 2.24 0.0 0.00 2.75 F
1278 4639 0.035152 TTCATCTTCATGCGTGGGCT 60.035 50.0 5.98 0.0 40.82 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 5130 0.519519 CGACTGCACGCCCAATTAAA 59.480 50.0 0.00 0.0 0.0 1.52 R
2894 6291 0.391661 GGAAACAGAGGCTCGCATGA 60.392 55.0 9.22 0.0 0.0 3.07 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
75 76 2.123251 ATCGGATCTGACGGGGCT 60.123 61.111 6.33 0.00 0.00 5.19
109 110 3.125316 GCCTGACTGACGGATTTAACAAG 59.875 47.826 0.00 0.00 0.00 3.16
188 192 4.616181 ATGTTTCTAATTACCGTGCTGC 57.384 40.909 0.00 0.00 0.00 5.25
241 245 2.820973 TGGCAAACAAGGCAAGGC 59.179 55.556 0.00 0.00 41.47 4.35
261 265 3.448660 GGCCTGATTTTTCATAGCAACCT 59.551 43.478 0.00 0.00 0.00 3.50
263 267 4.866486 GCCTGATTTTTCATAGCAACCTTG 59.134 41.667 0.00 0.00 0.00 3.61
400 3677 5.793817 TCTCTGCTTTTAGTTAGTGATGCA 58.206 37.500 0.00 0.00 0.00 3.96
401 3678 6.409704 TCTCTGCTTTTAGTTAGTGATGCAT 58.590 36.000 0.00 0.00 0.00 3.96
402 3679 6.881065 TCTCTGCTTTTAGTTAGTGATGCATT 59.119 34.615 0.00 0.00 0.00 3.56
403 3680 7.065085 TCTCTGCTTTTAGTTAGTGATGCATTC 59.935 37.037 0.00 0.00 0.00 2.67
404 3681 6.654582 TCTGCTTTTAGTTAGTGATGCATTCA 59.345 34.615 0.00 0.00 0.00 2.57
405 3682 7.337689 TCTGCTTTTAGTTAGTGATGCATTCAT 59.662 33.333 0.00 0.00 36.54 2.57
493 3777 2.368439 TCAGGTATCTGTTGGCATTGC 58.632 47.619 2.20 0.00 41.59 3.56
505 3793 3.624305 GCATTGCTGCTCTGTCATG 57.376 52.632 0.16 0.00 45.32 3.07
526 3817 1.095600 GCACTGCCCTTTAGCCTAAC 58.904 55.000 0.00 0.00 0.00 2.34
528 3819 0.624254 ACTGCCCTTTAGCCTAACCC 59.376 55.000 0.00 0.00 0.00 4.11
552 3843 0.871722 TTCATCCCGAAAGCAACACG 59.128 50.000 0.00 0.00 0.00 4.49
557 3848 2.625823 CCGAAAGCAACACGGCCAT 61.626 57.895 2.24 0.00 40.19 4.40
558 3849 1.154225 CGAAAGCAACACGGCCATC 60.154 57.895 2.24 0.00 0.00 3.51
559 3850 1.577328 CGAAAGCAACACGGCCATCT 61.577 55.000 2.24 0.00 0.00 2.90
560 3851 0.169009 GAAAGCAACACGGCCATCTC 59.831 55.000 2.24 0.00 0.00 2.75
575 3869 7.328737 CACGGCCATCTCTTAATTGTACTATAC 59.671 40.741 2.24 0.00 0.00 1.47
577 3871 7.328737 CGGCCATCTCTTAATTGTACTATACAC 59.671 40.741 2.24 0.00 38.63 2.90
598 3892 7.678947 ACACACTCATTAATTCAAAGAGGAG 57.321 36.000 5.13 0.00 0.00 3.69
677 3973 7.334844 AGAAAGTTTCCTTTTTCCTAGTGTG 57.665 36.000 12.05 0.00 40.98 3.82
678 3974 5.515797 AAGTTTCCTTTTTCCTAGTGTGC 57.484 39.130 0.00 0.00 0.00 4.57
711 4018 3.475575 TGTACATCAGACAGCAAAGCAA 58.524 40.909 0.00 0.00 0.00 3.91
712 4019 3.499537 TGTACATCAGACAGCAAAGCAAG 59.500 43.478 0.00 0.00 0.00 4.01
740 4047 5.034365 AGTGCACTTTACACTTGTGGTGC 62.034 47.826 15.25 18.81 46.01 5.01
822 4133 1.467920 CCCCTCAGCTTGATTCCAAC 58.532 55.000 0.00 0.00 0.00 3.77
834 4145 1.270550 GATTCCAACCAGTGCAAGGTG 59.729 52.381 12.44 1.93 39.86 4.00
849 4160 4.583489 TGCAAGGTGCTATACTACTACTCC 59.417 45.833 1.43 0.00 45.31 3.85
851 4162 5.507650 GCAAGGTGCTATACTACTACTCCAC 60.508 48.000 0.00 0.00 40.96 4.02
852 4163 5.384145 AGGTGCTATACTACTACTCCACA 57.616 43.478 0.00 0.00 0.00 4.17
853 4164 5.763355 AGGTGCTATACTACTACTCCACAA 58.237 41.667 0.00 0.00 0.00 3.33
1039 4383 0.108233 CTGTTCTCCTCTGCTCTGCC 60.108 60.000 0.00 0.00 0.00 4.85
1040 4384 1.153667 GTTCTCCTCTGCTCTGCCG 60.154 63.158 0.00 0.00 0.00 5.69
1041 4385 1.304464 TTCTCCTCTGCTCTGCCGA 60.304 57.895 0.00 0.00 0.00 5.54
1042 4386 0.900182 TTCTCCTCTGCTCTGCCGAA 60.900 55.000 0.00 0.00 0.00 4.30
1043 4387 1.153667 CTCCTCTGCTCTGCCGAAC 60.154 63.158 0.00 0.00 0.00 3.95
1044 4388 1.881903 CTCCTCTGCTCTGCCGAACA 61.882 60.000 0.00 0.00 0.00 3.18
1047 4391 0.390866 CTCTGCTCTGCCGAACACAT 60.391 55.000 0.00 0.00 0.00 3.21
1052 4396 0.247460 CTCTGCCGAACACATCTGGA 59.753 55.000 0.00 0.00 0.00 3.86
1098 4452 4.676723 CGAGAGAGAGATCCAAAGTCAACC 60.677 50.000 0.00 0.00 0.00 3.77
1099 4453 4.163427 AGAGAGAGATCCAAAGTCAACCA 58.837 43.478 0.00 0.00 0.00 3.67
1100 4454 4.782156 AGAGAGAGATCCAAAGTCAACCAT 59.218 41.667 0.00 0.00 0.00 3.55
1101 4455 5.096443 AGAGAGATCCAAAGTCAACCATC 57.904 43.478 0.00 0.00 0.00 3.51
1244 4605 1.141657 AGCGAGGATACAGGGTACGTA 59.858 52.381 0.00 0.00 41.41 3.57
1253 4614 1.269206 ACAGGGTACGTACGTGTGTTG 60.269 52.381 30.25 22.59 0.00 3.33
1269 4630 4.217118 GTGTGTTGCTTCCTTCATCTTCAT 59.783 41.667 0.00 0.00 0.00 2.57
1270 4631 4.216902 TGTGTTGCTTCCTTCATCTTCATG 59.783 41.667 0.00 0.00 0.00 3.07
1271 4632 3.192001 TGTTGCTTCCTTCATCTTCATGC 59.808 43.478 0.00 0.00 0.00 4.06
1272 4633 2.011947 TGCTTCCTTCATCTTCATGCG 58.988 47.619 0.00 0.00 0.00 4.73
1273 4634 2.012673 GCTTCCTTCATCTTCATGCGT 58.987 47.619 0.00 0.00 0.00 5.24
1274 4635 2.223203 GCTTCCTTCATCTTCATGCGTG 60.223 50.000 0.00 0.00 0.00 5.34
1275 4636 2.028420 TCCTTCATCTTCATGCGTGG 57.972 50.000 5.98 0.00 0.00 4.94
1276 4637 1.019673 CCTTCATCTTCATGCGTGGG 58.980 55.000 5.98 0.00 0.00 4.61
1277 4638 0.379669 CTTCATCTTCATGCGTGGGC 59.620 55.000 5.98 0.00 40.52 5.36
1278 4639 0.035152 TTCATCTTCATGCGTGGGCT 60.035 50.000 5.98 0.00 40.82 5.19
1279 4640 0.745486 TCATCTTCATGCGTGGGCTG 60.745 55.000 5.98 2.14 40.82 4.85
1280 4641 1.452651 ATCTTCATGCGTGGGCTGG 60.453 57.895 5.98 0.00 40.82 4.85
1281 4642 2.898920 ATCTTCATGCGTGGGCTGGG 62.899 60.000 5.98 0.00 40.82 4.45
1334 4695 1.266718 GAATCTTGCTCGGTTGCAACA 59.733 47.619 29.55 10.57 46.43 3.33
1337 4698 1.199624 CTTGCTCGGTTGCAACAAAC 58.800 50.000 29.55 16.25 46.43 2.93
1411 4772 1.378514 GCACCCCAACATCATCCGT 60.379 57.895 0.00 0.00 0.00 4.69
1612 4973 1.000163 GACCTCAAGCTCGAGAACACA 60.000 52.381 18.75 0.00 34.79 3.72
1676 5037 2.542550 TCGGATACTCAAAGGTCCCAA 58.457 47.619 0.00 0.00 0.00 4.12
1677 5038 2.907696 TCGGATACTCAAAGGTCCCAAA 59.092 45.455 0.00 0.00 0.00 3.28
1678 5039 3.521937 TCGGATACTCAAAGGTCCCAAAT 59.478 43.478 0.00 0.00 0.00 2.32
1680 5041 4.207955 GGATACTCAAAGGTCCCAAATCC 58.792 47.826 0.00 0.00 0.00 3.01
1681 5042 4.079730 GGATACTCAAAGGTCCCAAATCCT 60.080 45.833 0.00 0.00 35.34 3.24
1697 5073 5.280934 CCAAATCCTTTCTTCTTCCTCCTCT 60.281 44.000 0.00 0.00 0.00 3.69
1698 5074 5.434182 AATCCTTTCTTCTTCCTCCTCTG 57.566 43.478 0.00 0.00 0.00 3.35
1699 5075 3.863086 TCCTTTCTTCTTCCTCCTCTGT 58.137 45.455 0.00 0.00 0.00 3.41
1701 5077 4.660771 TCCTTTCTTCTTCCTCCTCTGTTT 59.339 41.667 0.00 0.00 0.00 2.83
1702 5078 5.000591 CCTTTCTTCTTCCTCCTCTGTTTC 58.999 45.833 0.00 0.00 0.00 2.78
1710 5086 5.245075 TCTTCCTCCTCTGTTTCTTCTTCTC 59.755 44.000 0.00 0.00 0.00 2.87
1714 5090 5.065704 TCCTCTGTTTCTTCTTCTCATCG 57.934 43.478 0.00 0.00 0.00 3.84
1725 5101 3.033909 TCTTCTCATCGATCATGGTGGT 58.966 45.455 0.00 0.00 32.64 4.16
1727 5103 3.459232 TCTCATCGATCATGGTGGTTC 57.541 47.619 0.00 0.00 32.64 3.62
1728 5104 3.033909 TCTCATCGATCATGGTGGTTCT 58.966 45.455 0.00 0.00 32.64 3.01
1729 5105 3.129109 CTCATCGATCATGGTGGTTCTG 58.871 50.000 0.00 0.00 32.64 3.02
1730 5106 2.765699 TCATCGATCATGGTGGTTCTGA 59.234 45.455 0.00 0.00 32.64 3.27
1736 5112 3.407424 TCATGGTGGTTCTGAGTTCTG 57.593 47.619 0.00 0.00 0.00 3.02
1740 5116 1.605712 GGTGGTTCTGAGTTCTGACCG 60.606 57.143 0.00 0.00 0.00 4.79
1754 5130 4.808414 TCTGACCGAGAACATCAAATCT 57.192 40.909 0.00 0.00 0.00 2.40
1755 5131 5.152623 TCTGACCGAGAACATCAAATCTT 57.847 39.130 0.00 0.00 0.00 2.40
1756 5132 5.551233 TCTGACCGAGAACATCAAATCTTT 58.449 37.500 0.00 0.00 0.00 2.52
1757 5133 6.697395 TCTGACCGAGAACATCAAATCTTTA 58.303 36.000 0.00 0.00 0.00 1.85
1758 5134 7.158697 TCTGACCGAGAACATCAAATCTTTAA 58.841 34.615 0.00 0.00 0.00 1.52
1759 5135 7.824289 TCTGACCGAGAACATCAAATCTTTAAT 59.176 33.333 0.00 0.00 0.00 1.40
1764 5140 6.473455 CGAGAACATCAAATCTTTAATTGGGC 59.527 38.462 0.00 0.00 0.00 5.36
1911 5287 0.926174 CGCTCTACGTGATGCTCGTC 60.926 60.000 0.00 0.00 41.72 4.20
1959 5335 0.106419 ACCCCAAGAACTTCCGCAAA 60.106 50.000 0.00 0.00 0.00 3.68
2664 6060 4.394920 TGTTCAAATCTCTTTATGTCCGGC 59.605 41.667 0.00 0.00 0.00 6.13
2687 6083 5.950380 CCAATGTGGAATGCATACTTGCCT 61.950 45.833 0.00 0.00 43.95 4.75
2791 6187 2.445453 TTGACGAGCAAAACGTTGAC 57.555 45.000 0.00 0.00 43.97 3.18
2794 6190 1.011684 CGAGCAAAACGTTGACGCA 60.012 52.632 16.29 0.00 44.43 5.24
2873 6270 7.848223 TCACATATAAGTCCATCACTGTTTG 57.152 36.000 0.00 0.00 34.56 2.93
2874 6271 7.619965 TCACATATAAGTCCATCACTGTTTGA 58.380 34.615 0.00 0.00 39.11 2.69
2875 6272 8.267183 TCACATATAAGTCCATCACTGTTTGAT 58.733 33.333 0.00 0.00 46.75 2.57
2876 6273 8.554528 CACATATAAGTCCATCACTGTTTGATC 58.445 37.037 0.00 0.00 43.68 2.92
2877 6274 8.489489 ACATATAAGTCCATCACTGTTTGATCT 58.511 33.333 0.00 0.00 43.68 2.75
2878 6275 9.987272 CATATAAGTCCATCACTGTTTGATCTA 57.013 33.333 0.00 0.00 43.68 1.98
2881 6278 9.911788 ATAAGTCCATCACTGTTTGATCTATTT 57.088 29.630 0.00 0.00 43.68 1.40
2882 6279 7.621428 AGTCCATCACTGTTTGATCTATTTG 57.379 36.000 0.00 0.00 43.68 2.32
2883 6280 6.600822 AGTCCATCACTGTTTGATCTATTTGG 59.399 38.462 0.00 0.00 43.68 3.28
2884 6281 5.887598 TCCATCACTGTTTGATCTATTTGGG 59.112 40.000 0.00 0.00 43.68 4.12
2885 6282 5.450965 CCATCACTGTTTGATCTATTTGGGC 60.451 44.000 0.00 0.00 43.68 5.36
2886 6283 4.922206 TCACTGTTTGATCTATTTGGGCT 58.078 39.130 0.00 0.00 0.00 5.19
2887 6284 5.324409 TCACTGTTTGATCTATTTGGGCTT 58.676 37.500 0.00 0.00 0.00 4.35
2888 6285 5.183713 TCACTGTTTGATCTATTTGGGCTTG 59.816 40.000 0.00 0.00 0.00 4.01
2889 6286 5.183713 CACTGTTTGATCTATTTGGGCTTGA 59.816 40.000 0.00 0.00 0.00 3.02
2890 6287 5.954150 ACTGTTTGATCTATTTGGGCTTGAT 59.046 36.000 0.00 0.00 0.00 2.57
2891 6288 6.438425 ACTGTTTGATCTATTTGGGCTTGATT 59.562 34.615 0.00 0.00 0.00 2.57
2892 6289 7.038799 ACTGTTTGATCTATTTGGGCTTGATTT 60.039 33.333 0.00 0.00 0.00 2.17
2893 6290 7.678837 TGTTTGATCTATTTGGGCTTGATTTT 58.321 30.769 0.00 0.00 0.00 1.82
2894 6291 8.156165 TGTTTGATCTATTTGGGCTTGATTTTT 58.844 29.630 0.00 0.00 0.00 1.94
2895 6292 8.659491 GTTTGATCTATTTGGGCTTGATTTTTC 58.341 33.333 0.00 0.00 0.00 2.29
2896 6293 7.479352 TGATCTATTTGGGCTTGATTTTTCA 57.521 32.000 0.00 0.00 0.00 2.69
2897 6294 8.081517 TGATCTATTTGGGCTTGATTTTTCAT 57.918 30.769 0.00 0.00 0.00 2.57
2898 6295 7.982919 TGATCTATTTGGGCTTGATTTTTCATG 59.017 33.333 0.00 0.00 0.00 3.07
2899 6296 6.108015 TCTATTTGGGCTTGATTTTTCATGC 58.892 36.000 5.54 5.54 39.24 4.06
2900 6297 2.367030 TGGGCTTGATTTTTCATGCG 57.633 45.000 7.49 0.00 40.37 4.73
2901 6298 1.891811 TGGGCTTGATTTTTCATGCGA 59.108 42.857 7.49 0.00 40.37 5.10
2902 6299 2.094597 TGGGCTTGATTTTTCATGCGAG 60.095 45.455 7.49 0.00 40.37 5.03
2903 6300 1.922545 GGCTTGATTTTTCATGCGAGC 59.077 47.619 7.49 0.00 40.37 5.03
2904 6301 1.922545 GCTTGATTTTTCATGCGAGCC 59.077 47.619 0.00 0.00 32.80 4.70
2905 6302 2.416431 GCTTGATTTTTCATGCGAGCCT 60.416 45.455 0.00 0.00 32.80 4.58
2906 6303 3.432782 CTTGATTTTTCATGCGAGCCTC 58.567 45.455 0.00 0.00 0.00 4.70
2907 6304 2.715046 TGATTTTTCATGCGAGCCTCT 58.285 42.857 0.00 0.00 0.00 3.69
2908 6305 2.421073 TGATTTTTCATGCGAGCCTCTG 59.579 45.455 0.00 0.00 0.00 3.35
2909 6306 1.896220 TTTTTCATGCGAGCCTCTGT 58.104 45.000 0.00 0.00 0.00 3.41
2910 6307 1.896220 TTTTCATGCGAGCCTCTGTT 58.104 45.000 0.00 0.00 0.00 3.16
2911 6308 1.896220 TTTCATGCGAGCCTCTGTTT 58.104 45.000 0.00 0.00 0.00 2.83
2912 6309 1.442769 TTCATGCGAGCCTCTGTTTC 58.557 50.000 0.00 0.00 0.00 2.78
2913 6310 0.391661 TCATGCGAGCCTCTGTTTCC 60.392 55.000 0.00 0.00 0.00 3.13
2914 6311 1.448540 ATGCGAGCCTCTGTTTCCG 60.449 57.895 0.00 0.00 0.00 4.30
2982 6379 3.186409 GCTGTCATTGTCTCTGCGTTTTA 59.814 43.478 0.00 0.00 0.00 1.52
3014 6411 3.330192 TGGCACTCCAGGTTGTGT 58.670 55.556 13.99 0.00 37.47 3.72
3015 6412 1.148273 TGGCACTCCAGGTTGTGTC 59.852 57.895 11.36 11.36 37.47 3.67
3016 6413 1.344953 TGGCACTCCAGGTTGTGTCT 61.345 55.000 16.72 0.00 39.30 3.41
3017 6414 0.886490 GGCACTCCAGGTTGTGTCTG 60.886 60.000 13.99 0.00 36.06 3.51
3018 6415 1.510480 GCACTCCAGGTTGTGTCTGC 61.510 60.000 13.99 0.59 36.63 4.26
3022 6419 2.281070 CAGGTTGTGTCTGCGCCT 60.281 61.111 4.18 0.00 0.00 5.52
3035 6432 2.165437 TCTGCGCCTGTTTTTCTTTTGT 59.835 40.909 4.18 0.00 0.00 2.83
3036 6433 2.535331 TGCGCCTGTTTTTCTTTTGTC 58.465 42.857 4.18 0.00 0.00 3.18
3037 6434 1.516864 GCGCCTGTTTTTCTTTTGTCG 59.483 47.619 0.00 0.00 0.00 4.35
3038 6435 2.793237 GCGCCTGTTTTTCTTTTGTCGA 60.793 45.455 0.00 0.00 0.00 4.20
3040 6437 3.486875 CGCCTGTTTTTCTTTTGTCGACT 60.487 43.478 17.92 0.00 0.00 4.18
3082 6517 5.106078 GGCATCATTGTCCATTTGCATTTTT 60.106 36.000 0.00 0.00 0.00 1.94
3093 6528 7.603784 GTCCATTTGCATTTTTAAGTCCTTCAT 59.396 33.333 0.00 0.00 0.00 2.57
3094 6529 7.603404 TCCATTTGCATTTTTAAGTCCTTCATG 59.397 33.333 0.00 0.00 0.00 3.07
3115 6550 3.010420 GCCAGGAGCAACTAAGTAAAGG 58.990 50.000 0.00 0.00 42.97 3.11
3116 6551 3.010420 CCAGGAGCAACTAAGTAAAGGC 58.990 50.000 0.00 0.00 0.00 4.35
3117 6552 3.307762 CCAGGAGCAACTAAGTAAAGGCT 60.308 47.826 0.00 0.00 0.00 4.58
3118 6553 3.686726 CAGGAGCAACTAAGTAAAGGCTG 59.313 47.826 0.00 0.00 0.00 4.85
3120 6555 3.074412 GAGCAACTAAGTAAAGGCTGCA 58.926 45.455 0.50 0.00 33.93 4.41
3121 6556 2.814336 AGCAACTAAGTAAAGGCTGCAC 59.186 45.455 0.50 0.00 33.93 4.57
3122 6557 2.412847 GCAACTAAGTAAAGGCTGCACG 60.413 50.000 0.50 0.00 32.57 5.34
3129 6564 2.884639 AGTAAAGGCTGCACGTTCATTT 59.115 40.909 0.50 0.00 0.00 2.32
3136 6571 4.037446 AGGCTGCACGTTCATTTCTTTTAA 59.963 37.500 0.50 0.00 0.00 1.52
3137 6572 4.923281 GGCTGCACGTTCATTTCTTTTAAT 59.077 37.500 0.50 0.00 0.00 1.40
3139 6574 6.073819 GGCTGCACGTTCATTTCTTTTAATTT 60.074 34.615 0.50 0.00 0.00 1.82
3141 6576 8.484008 GCTGCACGTTCATTTCTTTTAATTTTA 58.516 29.630 0.00 0.00 0.00 1.52
3155 6590 9.280174 TCTTTTAATTTTATATACCAGGAGGCG 57.720 33.333 0.00 0.00 39.06 5.52
3156 6591 7.989416 TTTAATTTTATATACCAGGAGGCGG 57.011 36.000 0.00 0.00 39.06 6.13
3157 6592 5.578157 AATTTTATATACCAGGAGGCGGT 57.422 39.130 0.00 0.00 40.73 5.68
3158 6593 4.345859 TTTTATATACCAGGAGGCGGTG 57.654 45.455 0.00 0.00 37.33 4.94
3159 6594 1.933021 TATATACCAGGAGGCGGTGG 58.067 55.000 0.00 1.77 37.33 4.61
3160 6595 1.481056 ATATACCAGGAGGCGGTGGC 61.481 60.000 0.00 0.00 37.33 5.01
3161 6596 2.599139 TATACCAGGAGGCGGTGGCT 62.599 60.000 0.00 0.00 42.48 4.75
3167 6602 4.021925 GAGGCGGTGGCTGGACTT 62.022 66.667 0.00 0.00 38.98 3.01
3225 6660 9.583530 TTGTAACTTCGTGTAAAATAACATTCG 57.416 29.630 0.00 0.00 0.00 3.34
3258 6693 7.769044 GTCATATTATCAGCGGGGTAATATGTT 59.231 37.037 26.36 7.03 43.10 2.71
3259 6694 7.768582 TCATATTATCAGCGGGGTAATATGTTG 59.231 37.037 26.36 14.69 43.10 3.33
3267 6702 6.932400 CAGCGGGGTAATATGTTGTTCTATTA 59.068 38.462 0.00 0.00 0.00 0.98
3270 6705 8.623030 GCGGGGTAATATGTTGTTCTATTAAAA 58.377 33.333 0.00 0.00 0.00 1.52
3301 6736 8.418662 ACAATGTACTACAACAGTCTACAGAAA 58.581 33.333 0.00 0.00 38.80 2.52
3400 6835 9.598517 AAACATGCATTAAAAATATACCTGGTG 57.401 29.630 10.23 0.00 0.00 4.17
3401 6836 8.305046 ACATGCATTAAAAATATACCTGGTGT 57.695 30.769 10.23 5.27 0.00 4.16
3402 6837 9.415008 ACATGCATTAAAAATATACCTGGTGTA 57.585 29.630 10.23 7.81 0.00 2.90
3440 6875 8.856490 AGACTTGTGTATTTGAAAATGTTGAC 57.144 30.769 0.00 0.00 0.00 3.18
3441 6876 7.920682 AGACTTGTGTATTTGAAAATGTTGACC 59.079 33.333 0.00 0.00 0.00 4.02
3442 6877 7.781056 ACTTGTGTATTTGAAAATGTTGACCT 58.219 30.769 0.00 0.00 0.00 3.85
3443 6878 8.257306 ACTTGTGTATTTGAAAATGTTGACCTT 58.743 29.630 0.00 0.00 0.00 3.50
3444 6879 8.417780 TTGTGTATTTGAAAATGTTGACCTTG 57.582 30.769 0.00 0.00 0.00 3.61
3445 6880 7.776107 TGTGTATTTGAAAATGTTGACCTTGA 58.224 30.769 0.00 0.00 0.00 3.02
3446 6881 8.253810 TGTGTATTTGAAAATGTTGACCTTGAA 58.746 29.630 0.00 0.00 0.00 2.69
3447 6882 9.260002 GTGTATTTGAAAATGTTGACCTTGAAT 57.740 29.630 0.00 0.00 0.00 2.57
3448 6883 9.829507 TGTATTTGAAAATGTTGACCTTGAATT 57.170 25.926 0.00 0.00 0.00 2.17
3450 6885 8.961294 ATTTGAAAATGTTGACCTTGAATTCA 57.039 26.923 3.38 3.38 0.00 2.57
3451 6886 8.783833 TTTGAAAATGTTGACCTTGAATTCAA 57.216 26.923 19.45 19.45 33.79 2.69
3452 6887 8.783833 TTGAAAATGTTGACCTTGAATTCAAA 57.216 26.923 20.82 5.70 33.58 2.69
3453 6888 8.783833 TGAAAATGTTGACCTTGAATTCAAAA 57.216 26.923 20.82 10.16 33.58 2.44
3454 6889 9.224267 TGAAAATGTTGACCTTGAATTCAAAAA 57.776 25.926 20.82 10.71 33.58 1.94
3542 6977 4.686191 AAAAATTCACATGCACAGGGAA 57.314 36.364 8.00 8.00 0.00 3.97
3543 6978 4.686191 AAAATTCACATGCACAGGGAAA 57.314 36.364 9.46 0.00 0.00 3.13
3544 6979 4.895668 AAATTCACATGCACAGGGAAAT 57.104 36.364 9.46 0.00 0.00 2.17
3545 6980 4.460948 AATTCACATGCACAGGGAAATC 57.539 40.909 9.46 0.00 0.00 2.17
3546 6981 2.885135 TCACATGCACAGGGAAATCT 57.115 45.000 0.00 0.00 0.00 2.40
3547 6982 3.998913 TCACATGCACAGGGAAATCTA 57.001 42.857 0.00 0.00 0.00 1.98
3548 6983 4.508551 TCACATGCACAGGGAAATCTAT 57.491 40.909 0.00 0.00 0.00 1.98
3549 6984 4.858850 TCACATGCACAGGGAAATCTATT 58.141 39.130 0.00 0.00 0.00 1.73
3550 6985 5.263599 TCACATGCACAGGGAAATCTATTT 58.736 37.500 0.00 0.00 0.00 1.40
3551 6986 5.716228 TCACATGCACAGGGAAATCTATTTT 59.284 36.000 0.00 0.00 0.00 1.82
3552 6987 5.808540 CACATGCACAGGGAAATCTATTTTG 59.191 40.000 0.00 0.00 0.00 2.44
3553 6988 5.481473 ACATGCACAGGGAAATCTATTTTGT 59.519 36.000 0.00 0.00 0.00 2.83
3554 6989 5.389859 TGCACAGGGAAATCTATTTTGTG 57.610 39.130 11.67 11.67 38.27 3.33
3555 6990 4.832266 TGCACAGGGAAATCTATTTTGTGT 59.168 37.500 15.12 6.55 37.87 3.72
3556 6991 6.007076 TGCACAGGGAAATCTATTTTGTGTA 58.993 36.000 15.12 10.71 37.87 2.90
3557 6992 6.491745 TGCACAGGGAAATCTATTTTGTGTAA 59.508 34.615 15.12 6.47 37.87 2.41
3558 6993 6.806739 GCACAGGGAAATCTATTTTGTGTAAC 59.193 38.462 15.12 2.31 37.87 2.50
3559 6994 7.021196 CACAGGGAAATCTATTTTGTGTAACG 58.979 38.462 9.21 0.00 42.39 3.18
3560 6995 6.938030 ACAGGGAAATCTATTTTGTGTAACGA 59.062 34.615 0.00 0.00 42.39 3.85
3561 6996 7.446013 ACAGGGAAATCTATTTTGTGTAACGAA 59.554 33.333 0.00 0.00 42.39 3.85
3562 6997 7.962918 CAGGGAAATCTATTTTGTGTAACGAAG 59.037 37.037 0.00 0.00 42.14 3.79
3563 6998 7.881232 AGGGAAATCTATTTTGTGTAACGAAGA 59.119 33.333 0.00 0.00 42.14 2.87
3564 6999 8.508875 GGGAAATCTATTTTGTGTAACGAAGAA 58.491 33.333 0.00 0.00 42.14 2.52
3576 7011 9.754382 TTGTGTAACGAAGAATAGTAGAAAAGT 57.246 29.630 0.00 0.00 42.39 2.66
3577 7012 9.188588 TGTGTAACGAAGAATAGTAGAAAAGTG 57.811 33.333 0.00 0.00 42.39 3.16
3578 7013 9.189723 GTGTAACGAAGAATAGTAGAAAAGTGT 57.810 33.333 0.00 0.00 0.00 3.55
3579 7014 9.403110 TGTAACGAAGAATAGTAGAAAAGTGTC 57.597 33.333 0.00 0.00 0.00 3.67
3580 7015 9.403110 GTAACGAAGAATAGTAGAAAAGTGTCA 57.597 33.333 0.00 0.00 0.00 3.58
3581 7016 8.882415 AACGAAGAATAGTAGAAAAGTGTCAA 57.118 30.769 0.00 0.00 0.00 3.18
3582 7017 8.882415 ACGAAGAATAGTAGAAAAGTGTCAAA 57.118 30.769 0.00 0.00 0.00 2.69
3583 7018 9.321562 ACGAAGAATAGTAGAAAAGTGTCAAAA 57.678 29.630 0.00 0.00 0.00 2.44
3624 7059 8.614469 ACAAAGAAACAAAATGAAAACAAGGA 57.386 26.923 0.00 0.00 0.00 3.36
3625 7060 9.061435 ACAAAGAAACAAAATGAAAACAAGGAA 57.939 25.926 0.00 0.00 0.00 3.36
3626 7061 9.890352 CAAAGAAACAAAATGAAAACAAGGAAA 57.110 25.926 0.00 0.00 0.00 3.13
3628 7063 9.891828 AAGAAACAAAATGAAAACAAGGAAAAC 57.108 25.926 0.00 0.00 0.00 2.43
3629 7064 9.061435 AGAAACAAAATGAAAACAAGGAAAACA 57.939 25.926 0.00 0.00 0.00 2.83
3630 7065 9.670719 GAAACAAAATGAAAACAAGGAAAACAA 57.329 25.926 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.351541 CCATAACAAGGCCAACTGTAGTAGTA 60.352 42.308 5.01 0.00 39.18 1.82
1 2 5.488341 CATAACAAGGCCAACTGTAGTAGT 58.512 41.667 5.01 0.00 42.89 2.73
2 3 4.876107 CCATAACAAGGCCAACTGTAGTAG 59.124 45.833 5.01 0.00 0.00 2.57
75 76 4.448210 GTCAGTCAGGCCGGATATTTTTA 58.552 43.478 9.39 0.00 0.00 1.52
100 101 8.053355 CCCTAACATAACCTCTCCTTGTTAAAT 58.947 37.037 0.00 0.00 33.70 1.40
109 110 1.070289 CGCCCCTAACATAACCTCTCC 59.930 57.143 0.00 0.00 0.00 3.71
188 192 1.416373 CGTCCAGCAGATGATCGATG 58.584 55.000 0.54 0.00 32.76 3.84
241 245 6.029346 ACAAGGTTGCTATGAAAAATCAGG 57.971 37.500 0.00 0.00 0.00 3.86
253 257 4.353777 AGATCTAGTGGACAAGGTTGCTA 58.646 43.478 0.00 0.00 0.00 3.49
367 3575 7.961325 AACTAAAAGCAGAGAAGAAAGAGAG 57.039 36.000 0.00 0.00 0.00 3.20
368 3576 8.643324 ACTAACTAAAAGCAGAGAAGAAAGAGA 58.357 33.333 0.00 0.00 0.00 3.10
503 3791 0.394899 GGCTAAAGGGCAGTGCTCAT 60.395 55.000 19.27 0.93 40.53 2.90
504 3792 1.002134 GGCTAAAGGGCAGTGCTCA 60.002 57.895 19.27 0.00 40.53 4.26
505 3793 0.541863 TAGGCTAAAGGGCAGTGCTC 59.458 55.000 16.11 11.96 43.56 4.26
526 3817 1.453155 CTTTCGGGATGAACTGTGGG 58.547 55.000 0.00 0.00 35.97 4.61
528 3819 1.522668 TGCTTTCGGGATGAACTGTG 58.477 50.000 0.00 0.00 35.97 3.66
552 3843 8.148351 TGTGTATAGTACAATTAAGAGATGGCC 58.852 37.037 0.00 0.00 40.93 5.36
575 3869 7.065563 CCTCTCCTCTTTGAATTAATGAGTGTG 59.934 40.741 0.00 0.00 38.33 3.82
577 3871 6.541641 CCCTCTCCTCTTTGAATTAATGAGTG 59.458 42.308 0.00 0.00 38.33 3.51
598 3892 2.568623 TGTTGAAGAAAGCTCCCCTC 57.431 50.000 0.00 0.00 0.00 4.30
677 3973 3.123050 TGATGTACATCTACATGCACGC 58.877 45.455 30.67 6.61 42.66 5.34
678 3974 4.442403 GTCTGATGTACATCTACATGCACG 59.558 45.833 30.67 11.72 42.66 5.34
711 4018 4.408182 AGTGTAAAGTGCACTGTTCTCT 57.592 40.909 22.49 15.81 44.52 3.10
712 4019 4.332819 ACAAGTGTAAAGTGCACTGTTCTC 59.667 41.667 22.49 13.66 45.36 2.87
740 4047 1.167155 GCAGCAGCCTCATGGATCTG 61.167 60.000 0.00 0.00 33.32 2.90
834 4145 6.696441 ACACTTGTGGAGTAGTAGTATAGC 57.304 41.667 5.72 0.00 36.65 2.97
849 4160 7.119699 ACCACTAATCAATCACATACACTTGTG 59.880 37.037 0.00 0.00 46.70 3.33
851 4162 7.615582 ACCACTAATCAATCACATACACTTG 57.384 36.000 0.00 0.00 0.00 3.16
852 4163 7.987458 CCTACCACTAATCAATCACATACACTT 59.013 37.037 0.00 0.00 0.00 3.16
853 4164 7.344612 TCCTACCACTAATCAATCACATACACT 59.655 37.037 0.00 0.00 0.00 3.55
873 4191 1.477014 GGCTGGCCAAGTTATCCTACC 60.477 57.143 7.01 0.00 35.81 3.18
986 4330 2.319438 AGGAGGAGGAGATAAACAGGGT 59.681 50.000 0.00 0.00 0.00 4.34
993 4337 5.742562 AGAAGAAGAGGAGGAGGAGATAA 57.257 43.478 0.00 0.00 0.00 1.75
1039 4383 3.319137 TCCTTCTTCCAGATGTGTTCG 57.681 47.619 0.00 0.00 0.00 3.95
1040 4384 4.006319 CCTTCCTTCTTCCAGATGTGTTC 58.994 47.826 0.00 0.00 0.00 3.18
1041 4385 3.652869 TCCTTCCTTCTTCCAGATGTGTT 59.347 43.478 0.00 0.00 0.00 3.32
1042 4386 3.251484 TCCTTCCTTCTTCCAGATGTGT 58.749 45.455 0.00 0.00 0.00 3.72
1043 4387 3.988976 TCCTTCCTTCTTCCAGATGTG 57.011 47.619 0.00 0.00 0.00 3.21
1044 4388 3.265479 CCTTCCTTCCTTCTTCCAGATGT 59.735 47.826 0.00 0.00 0.00 3.06
1047 4391 3.177228 CTCCTTCCTTCCTTCTTCCAGA 58.823 50.000 0.00 0.00 0.00 3.86
1052 4396 1.552792 CGAGCTCCTTCCTTCCTTCTT 59.447 52.381 8.47 0.00 0.00 2.52
1098 4452 2.228925 TGCCTGATCTCTCTCTCGATG 58.771 52.381 0.00 0.00 0.00 3.84
1099 4453 2.655090 TGCCTGATCTCTCTCTCGAT 57.345 50.000 0.00 0.00 0.00 3.59
1100 4454 2.228925 CATGCCTGATCTCTCTCTCGA 58.771 52.381 0.00 0.00 0.00 4.04
1101 4455 1.270274 CCATGCCTGATCTCTCTCTCG 59.730 57.143 0.00 0.00 0.00 4.04
1244 4605 1.873591 GATGAAGGAAGCAACACACGT 59.126 47.619 0.00 0.00 0.00 4.49
1253 4614 2.012673 ACGCATGAAGATGAAGGAAGC 58.987 47.619 0.00 0.00 0.00 3.86
1277 4638 2.987282 TACACACGCACACAGCCCAG 62.987 60.000 0.00 0.00 41.38 4.45
1278 4639 2.390306 ATACACACGCACACAGCCCA 62.390 55.000 0.00 0.00 41.38 5.36
1279 4640 1.671054 ATACACACGCACACAGCCC 60.671 57.895 0.00 0.00 41.38 5.19
1280 4641 1.227999 ACATACACACGCACACAGCC 61.228 55.000 0.00 0.00 41.38 4.85
1281 4642 0.586319 AACATACACACGCACACAGC 59.414 50.000 0.00 0.00 40.87 4.40
1282 4643 2.286563 TCAAACATACACACGCACACAG 59.713 45.455 0.00 0.00 0.00 3.66
1283 4644 2.280628 TCAAACATACACACGCACACA 58.719 42.857 0.00 0.00 0.00 3.72
1284 4645 3.059257 TGATCAAACATACACACGCACAC 60.059 43.478 0.00 0.00 0.00 3.82
1285 4646 3.134458 TGATCAAACATACACACGCACA 58.866 40.909 0.00 0.00 0.00 4.57
1286 4647 3.804518 TGATCAAACATACACACGCAC 57.195 42.857 0.00 0.00 0.00 5.34
1320 4681 1.315981 TGGTTTGTTGCAACCGAGCA 61.316 50.000 26.14 23.96 43.99 4.26
1411 4772 0.843309 TGAGCACCACCTCCTTGAAA 59.157 50.000 0.00 0.00 0.00 2.69
1676 5037 4.849235 ACAGAGGAGGAAGAAGAAAGGATT 59.151 41.667 0.00 0.00 0.00 3.01
1677 5038 4.434195 ACAGAGGAGGAAGAAGAAAGGAT 58.566 43.478 0.00 0.00 0.00 3.24
1678 5039 3.863086 ACAGAGGAGGAAGAAGAAAGGA 58.137 45.455 0.00 0.00 0.00 3.36
1680 5041 5.863965 AGAAACAGAGGAGGAAGAAGAAAG 58.136 41.667 0.00 0.00 0.00 2.62
1681 5042 5.896073 AGAAACAGAGGAGGAAGAAGAAA 57.104 39.130 0.00 0.00 0.00 2.52
1697 5073 5.814188 CCATGATCGATGAGAAGAAGAAACA 59.186 40.000 0.54 0.00 33.31 2.83
1698 5074 5.814705 ACCATGATCGATGAGAAGAAGAAAC 59.185 40.000 0.54 0.00 33.31 2.78
1699 5075 5.814188 CACCATGATCGATGAGAAGAAGAAA 59.186 40.000 0.54 0.00 33.31 2.52
1701 5077 4.202192 CCACCATGATCGATGAGAAGAAGA 60.202 45.833 0.54 0.00 33.31 2.87
1702 5078 4.056740 CCACCATGATCGATGAGAAGAAG 58.943 47.826 0.54 0.00 33.31 2.85
1710 5086 3.129109 CTCAGAACCACCATGATCGATG 58.871 50.000 0.54 0.00 0.00 3.84
1714 5090 3.937706 CAGAACTCAGAACCACCATGATC 59.062 47.826 0.00 0.00 0.00 2.92
1736 5112 7.698130 CCAATTAAAGATTTGATGTTCTCGGTC 59.302 37.037 0.00 0.00 0.00 4.79
1740 5116 6.473455 CGCCCAATTAAAGATTTGATGTTCTC 59.527 38.462 0.00 0.00 0.00 2.87
1747 5123 3.256879 TGCACGCCCAATTAAAGATTTGA 59.743 39.130 0.00 0.00 0.00 2.69
1748 5124 3.583806 TGCACGCCCAATTAAAGATTTG 58.416 40.909 0.00 0.00 0.00 2.32
1749 5125 3.258123 ACTGCACGCCCAATTAAAGATTT 59.742 39.130 0.00 0.00 0.00 2.17
1750 5126 2.825532 ACTGCACGCCCAATTAAAGATT 59.174 40.909 0.00 0.00 0.00 2.40
1751 5127 2.423538 GACTGCACGCCCAATTAAAGAT 59.576 45.455 0.00 0.00 0.00 2.40
1752 5128 1.810151 GACTGCACGCCCAATTAAAGA 59.190 47.619 0.00 0.00 0.00 2.52
1753 5129 1.465689 CGACTGCACGCCCAATTAAAG 60.466 52.381 0.00 0.00 0.00 1.85
1754 5130 0.519519 CGACTGCACGCCCAATTAAA 59.480 50.000 0.00 0.00 0.00 1.52
1755 5131 0.604243 ACGACTGCACGCCCAATTAA 60.604 50.000 0.00 0.00 36.70 1.40
1756 5132 1.004320 ACGACTGCACGCCCAATTA 60.004 52.632 0.00 0.00 36.70 1.40
1757 5133 2.281484 ACGACTGCACGCCCAATT 60.281 55.556 0.00 0.00 36.70 2.32
1758 5134 2.742372 GACGACTGCACGCCCAAT 60.742 61.111 0.00 0.00 36.70 3.16
1794 5170 2.652530 GTGCCCACCGTCGACTTA 59.347 61.111 14.70 0.00 0.00 2.24
1902 5278 4.266070 TAGCCGCCGACGAGCATC 62.266 66.667 7.25 0.00 43.93 3.91
1959 5335 2.108976 ATGATCCGCGCGATGGTT 59.891 55.556 34.63 9.85 0.00 3.67
2655 6051 0.621082 TTCCACATTGGCCGGACATA 59.379 50.000 13.08 1.80 37.47 2.29
2873 6270 7.042254 GCATGAAAAATCAAGCCCAAATAGATC 60.042 37.037 0.00 0.00 0.00 2.75
2874 6271 6.764560 GCATGAAAAATCAAGCCCAAATAGAT 59.235 34.615 0.00 0.00 0.00 1.98
2875 6272 6.108015 GCATGAAAAATCAAGCCCAAATAGA 58.892 36.000 0.00 0.00 0.00 1.98
2876 6273 5.005971 CGCATGAAAAATCAAGCCCAAATAG 59.994 40.000 0.00 0.00 31.45 1.73
2877 6274 4.869297 CGCATGAAAAATCAAGCCCAAATA 59.131 37.500 0.00 0.00 31.45 1.40
2878 6275 3.685756 CGCATGAAAAATCAAGCCCAAAT 59.314 39.130 0.00 0.00 31.45 2.32
2879 6276 3.065655 CGCATGAAAAATCAAGCCCAAA 58.934 40.909 0.00 0.00 31.45 3.28
2880 6277 2.298446 TCGCATGAAAAATCAAGCCCAA 59.702 40.909 0.00 0.00 31.45 4.12
2881 6278 1.891811 TCGCATGAAAAATCAAGCCCA 59.108 42.857 0.00 0.00 31.45 5.36
2882 6279 2.533266 CTCGCATGAAAAATCAAGCCC 58.467 47.619 0.00 0.00 31.45 5.19
2883 6280 1.922545 GCTCGCATGAAAAATCAAGCC 59.077 47.619 0.00 0.00 31.45 4.35
2884 6281 1.922545 GGCTCGCATGAAAAATCAAGC 59.077 47.619 0.00 0.00 0.00 4.01
2885 6282 3.128242 AGAGGCTCGCATGAAAAATCAAG 59.872 43.478 9.22 0.00 0.00 3.02
2886 6283 3.084039 AGAGGCTCGCATGAAAAATCAA 58.916 40.909 9.22 0.00 0.00 2.57
2887 6284 2.421073 CAGAGGCTCGCATGAAAAATCA 59.579 45.455 9.22 0.00 0.00 2.57
2888 6285 2.421424 ACAGAGGCTCGCATGAAAAATC 59.579 45.455 9.22 0.00 0.00 2.17
2889 6286 2.440409 ACAGAGGCTCGCATGAAAAAT 58.560 42.857 9.22 0.00 0.00 1.82
2890 6287 1.896220 ACAGAGGCTCGCATGAAAAA 58.104 45.000 9.22 0.00 0.00 1.94
2891 6288 1.896220 AACAGAGGCTCGCATGAAAA 58.104 45.000 9.22 0.00 0.00 2.29
2892 6289 1.806542 GAAACAGAGGCTCGCATGAAA 59.193 47.619 9.22 0.00 0.00 2.69
2893 6290 1.442769 GAAACAGAGGCTCGCATGAA 58.557 50.000 9.22 0.00 0.00 2.57
2894 6291 0.391661 GGAAACAGAGGCTCGCATGA 60.392 55.000 9.22 0.00 0.00 3.07
2895 6292 1.699656 CGGAAACAGAGGCTCGCATG 61.700 60.000 9.22 4.71 0.00 4.06
2896 6293 1.448540 CGGAAACAGAGGCTCGCAT 60.449 57.895 9.22 0.00 0.00 4.73
2897 6294 2.048222 CGGAAACAGAGGCTCGCA 60.048 61.111 9.22 0.00 0.00 5.10
2898 6295 2.815647 CCGGAAACAGAGGCTCGC 60.816 66.667 9.22 0.00 0.00 5.03
2899 6296 1.446272 GACCGGAAACAGAGGCTCG 60.446 63.158 9.46 6.83 0.00 5.03
2900 6297 1.446272 CGACCGGAAACAGAGGCTC 60.446 63.158 9.46 6.34 0.00 4.70
2901 6298 1.878656 CTCGACCGGAAACAGAGGCT 61.879 60.000 9.46 0.00 0.00 4.58
2902 6299 1.446272 CTCGACCGGAAACAGAGGC 60.446 63.158 9.46 0.00 0.00 4.70
2903 6300 1.446272 GCTCGACCGGAAACAGAGG 60.446 63.158 9.46 0.00 0.00 3.69
2904 6301 1.801913 CGCTCGACCGGAAACAGAG 60.802 63.158 9.46 10.09 0.00 3.35
2905 6302 2.257371 CGCTCGACCGGAAACAGA 59.743 61.111 9.46 0.00 0.00 3.41
2906 6303 2.049433 ACGCTCGACCGGAAACAG 60.049 61.111 9.46 0.00 0.00 3.16
2907 6304 2.049802 GACGCTCGACCGGAAACA 60.050 61.111 9.46 0.00 0.00 2.83
2908 6305 2.808321 GGACGCTCGACCGGAAAC 60.808 66.667 9.46 0.00 0.00 2.78
2909 6306 4.409218 CGGACGCTCGACCGGAAA 62.409 66.667 21.47 0.00 46.37 3.13
2914 6311 3.735029 AGACACGGACGCTCGACC 61.735 66.667 5.01 0.00 0.00 4.79
2966 6363 5.067283 ACCAAAAGTAAAACGCAGAGACAAT 59.933 36.000 0.00 0.00 0.00 2.71
2982 6379 1.883926 GTGCCATAACGGACCAAAAGT 59.116 47.619 0.00 0.00 36.56 2.66
3006 6403 2.281070 CAGGCGCAGACACAACCT 60.281 61.111 10.83 0.00 39.87 3.50
3012 6409 1.388547 AAGAAAAACAGGCGCAGACA 58.611 45.000 10.83 0.00 39.87 3.41
3013 6410 2.492019 AAAGAAAAACAGGCGCAGAC 57.508 45.000 10.83 0.00 0.00 3.51
3014 6411 2.165437 ACAAAAGAAAAACAGGCGCAGA 59.835 40.909 10.83 0.00 0.00 4.26
3015 6412 2.535574 GACAAAAGAAAAACAGGCGCAG 59.464 45.455 10.83 3.04 0.00 5.18
3016 6413 2.535331 GACAAAAGAAAAACAGGCGCA 58.465 42.857 10.83 0.00 0.00 6.09
3017 6414 1.516864 CGACAAAAGAAAAACAGGCGC 59.483 47.619 0.00 0.00 0.00 6.53
3018 6415 2.781646 GTCGACAAAAGAAAAACAGGCG 59.218 45.455 11.55 0.00 0.00 5.52
3022 6419 4.938832 TCTCCAGTCGACAAAAGAAAAACA 59.061 37.500 19.50 0.00 0.00 2.83
3035 6432 5.300539 CCTCTCATTTTATCTCTCCAGTCGA 59.699 44.000 0.00 0.00 0.00 4.20
3036 6433 5.527951 CCTCTCATTTTATCTCTCCAGTCG 58.472 45.833 0.00 0.00 0.00 4.18
3037 6434 5.163364 TGCCTCTCATTTTATCTCTCCAGTC 60.163 44.000 0.00 0.00 0.00 3.51
3038 6435 4.718774 TGCCTCTCATTTTATCTCTCCAGT 59.281 41.667 0.00 0.00 0.00 4.00
3040 6437 5.367644 TGATGCCTCTCATTTTATCTCTCCA 59.632 40.000 0.00 0.00 35.05 3.86
3082 6517 1.210478 GCTCCTGGCATGAAGGACTTA 59.790 52.381 12.32 0.00 38.96 2.24
3094 6529 3.010420 CCTTTACTTAGTTGCTCCTGGC 58.990 50.000 0.00 0.00 42.22 4.85
3103 6538 3.121738 ACGTGCAGCCTTTACTTAGTT 57.878 42.857 0.00 0.00 0.00 2.24
3109 6544 2.989422 AATGAACGTGCAGCCTTTAC 57.011 45.000 1.02 0.00 0.00 2.01
3110 6545 3.146066 AGAAATGAACGTGCAGCCTTTA 58.854 40.909 1.02 0.00 0.00 1.85
3111 6546 1.956477 AGAAATGAACGTGCAGCCTTT 59.044 42.857 1.02 0.00 0.00 3.11
3112 6547 1.609208 AGAAATGAACGTGCAGCCTT 58.391 45.000 1.02 0.00 0.00 4.35
3113 6548 1.609208 AAGAAATGAACGTGCAGCCT 58.391 45.000 1.02 0.00 0.00 4.58
3115 6550 6.452244 AATTAAAAGAAATGAACGTGCAGC 57.548 33.333 1.02 0.00 0.00 5.25
3129 6564 9.280174 CGCCTCCTGGTATATAAAATTAAAAGA 57.720 33.333 0.00 0.00 35.27 2.52
3136 6571 4.263331 CCACCGCCTCCTGGTATATAAAAT 60.263 45.833 0.00 0.00 37.72 1.82
3137 6572 3.071892 CCACCGCCTCCTGGTATATAAAA 59.928 47.826 0.00 0.00 37.72 1.52
3139 6574 2.253610 CCACCGCCTCCTGGTATATAA 58.746 52.381 0.00 0.00 37.72 0.98
3141 6576 1.481056 GCCACCGCCTCCTGGTATAT 61.481 60.000 0.00 0.00 37.72 0.86
3142 6577 2.138179 GCCACCGCCTCCTGGTATA 61.138 63.158 0.00 0.00 37.72 1.47
3143 6578 3.480133 GCCACCGCCTCCTGGTAT 61.480 66.667 0.00 0.00 37.72 2.73
3150 6585 3.553095 AAAGTCCAGCCACCGCCTC 62.553 63.158 0.00 0.00 34.57 4.70
3151 6586 2.640581 AAAAAGTCCAGCCACCGCCT 62.641 55.000 0.00 0.00 34.57 5.52
3152 6587 2.200337 AAAAAGTCCAGCCACCGCC 61.200 57.895 0.00 0.00 34.57 6.13
3153 6588 3.443588 AAAAAGTCCAGCCACCGC 58.556 55.556 0.00 0.00 0.00 5.68
3199 6634 9.583530 CGAATGTTATTTTACACGAAGTTACAA 57.416 29.630 0.00 0.00 41.61 2.41
3203 6638 9.749490 CATACGAATGTTATTTTACACGAAGTT 57.251 29.630 0.00 0.00 41.61 2.66
3205 6640 7.372396 GGCATACGAATGTTATTTTACACGAAG 59.628 37.037 0.00 0.00 35.38 3.79
3208 6643 6.946508 GGCATACGAATGTTATTTTACACG 57.053 37.500 0.00 0.00 35.38 4.49
3225 6660 3.551890 CCGCTGATAATATGACGGCATAC 59.448 47.826 14.56 0.86 39.65 2.39
3270 6705 9.257651 GTAGACTGTTGTAGTACATTGTTCTTT 57.742 33.333 3.28 0.00 40.53 2.52
3271 6706 8.418662 TGTAGACTGTTGTAGTACATTGTTCTT 58.581 33.333 3.28 0.00 40.53 2.52
3279 6714 7.283807 TCAGTTTCTGTAGACTGTTGTAGTACA 59.716 37.037 0.00 0.00 42.90 2.90
3414 6849 9.944663 GTCAACATTTTCAAATACACAAGTCTA 57.055 29.630 0.00 0.00 0.00 2.59
3415 6850 7.920682 GGTCAACATTTTCAAATACACAAGTCT 59.079 33.333 0.00 0.00 0.00 3.24
3416 6851 7.920682 AGGTCAACATTTTCAAATACACAAGTC 59.079 33.333 0.00 0.00 0.00 3.01
3417 6852 7.781056 AGGTCAACATTTTCAAATACACAAGT 58.219 30.769 0.00 0.00 0.00 3.16
3418 6853 8.542132 CAAGGTCAACATTTTCAAATACACAAG 58.458 33.333 0.00 0.00 0.00 3.16
3419 6854 8.253810 TCAAGGTCAACATTTTCAAATACACAA 58.746 29.630 0.00 0.00 0.00 3.33
3420 6855 7.776107 TCAAGGTCAACATTTTCAAATACACA 58.224 30.769 0.00 0.00 0.00 3.72
3421 6856 8.641499 TTCAAGGTCAACATTTTCAAATACAC 57.359 30.769 0.00 0.00 0.00 2.90
3422 6857 9.829507 AATTCAAGGTCAACATTTTCAAATACA 57.170 25.926 0.00 0.00 0.00 2.29
3425 6860 8.961294 TGAATTCAAGGTCAACATTTTCAAAT 57.039 26.923 5.45 0.00 0.00 2.32
3426 6861 8.783833 TTGAATTCAAGGTCAACATTTTCAAA 57.216 26.923 16.91 0.00 27.87 2.69
3427 6862 8.783833 TTTGAATTCAAGGTCAACATTTTCAA 57.216 26.923 19.64 0.00 37.15 2.69
3428 6863 8.783833 TTTTGAATTCAAGGTCAACATTTTCA 57.216 26.923 19.64 0.00 37.15 2.69
3521 6956 4.686191 TTCCCTGTGCATGTGAATTTTT 57.314 36.364 0.00 0.00 0.00 1.94
3522 6957 4.686191 TTTCCCTGTGCATGTGAATTTT 57.314 36.364 0.00 0.00 0.00 1.82
3523 6958 4.529377 AGATTTCCCTGTGCATGTGAATTT 59.471 37.500 0.00 0.00 0.00 1.82
3524 6959 4.091549 AGATTTCCCTGTGCATGTGAATT 58.908 39.130 0.00 0.00 0.00 2.17
3525 6960 3.705051 AGATTTCCCTGTGCATGTGAAT 58.295 40.909 0.00 0.00 0.00 2.57
3526 6961 3.159213 AGATTTCCCTGTGCATGTGAA 57.841 42.857 0.00 0.00 0.00 3.18
3527 6962 2.885135 AGATTTCCCTGTGCATGTGA 57.115 45.000 0.00 0.00 0.00 3.58
3528 6963 5.587388 AAATAGATTTCCCTGTGCATGTG 57.413 39.130 0.00 0.00 0.00 3.21
3529 6964 5.481473 ACAAAATAGATTTCCCTGTGCATGT 59.519 36.000 0.00 0.00 0.00 3.21
3530 6965 5.808540 CACAAAATAGATTTCCCTGTGCATG 59.191 40.000 0.00 0.00 32.61 4.06
3531 6966 5.481473 ACACAAAATAGATTTCCCTGTGCAT 59.519 36.000 14.11 0.00 38.56 3.96
3532 6967 4.832266 ACACAAAATAGATTTCCCTGTGCA 59.168 37.500 14.11 0.00 38.56 4.57
3533 6968 5.391312 ACACAAAATAGATTTCCCTGTGC 57.609 39.130 14.11 0.00 38.56 4.57
3534 6969 7.021196 CGTTACACAAAATAGATTTCCCTGTG 58.979 38.462 13.17 13.17 39.80 3.66
3535 6970 6.938030 TCGTTACACAAAATAGATTTCCCTGT 59.062 34.615 0.00 0.00 0.00 4.00
3536 6971 7.372451 TCGTTACACAAAATAGATTTCCCTG 57.628 36.000 0.00 0.00 0.00 4.45
3537 6972 7.881232 TCTTCGTTACACAAAATAGATTTCCCT 59.119 33.333 0.00 0.00 0.00 4.20
3538 6973 8.036273 TCTTCGTTACACAAAATAGATTTCCC 57.964 34.615 0.00 0.00 0.00 3.97
3550 6985 9.754382 ACTTTTCTACTATTCTTCGTTACACAA 57.246 29.630 0.00 0.00 0.00 3.33
3551 6986 9.188588 CACTTTTCTACTATTCTTCGTTACACA 57.811 33.333 0.00 0.00 0.00 3.72
3552 6987 9.189723 ACACTTTTCTACTATTCTTCGTTACAC 57.810 33.333 0.00 0.00 0.00 2.90
3553 6988 9.403110 GACACTTTTCTACTATTCTTCGTTACA 57.597 33.333 0.00 0.00 0.00 2.41
3554 6989 9.403110 TGACACTTTTCTACTATTCTTCGTTAC 57.597 33.333 0.00 0.00 0.00 2.50
3555 6990 9.970395 TTGACACTTTTCTACTATTCTTCGTTA 57.030 29.630 0.00 0.00 0.00 3.18
3556 6991 8.882415 TTGACACTTTTCTACTATTCTTCGTT 57.118 30.769 0.00 0.00 0.00 3.85
3557 6992 8.882415 TTTGACACTTTTCTACTATTCTTCGT 57.118 30.769 0.00 0.00 0.00 3.85
3598 7033 9.061435 TCCTTGTTTTCATTTTGTTTCTTTGTT 57.939 25.926 0.00 0.00 0.00 2.83
3599 7034 8.614469 TCCTTGTTTTCATTTTGTTTCTTTGT 57.386 26.923 0.00 0.00 0.00 2.83
3600 7035 9.890352 TTTCCTTGTTTTCATTTTGTTTCTTTG 57.110 25.926 0.00 0.00 0.00 2.77
3602 7037 9.891828 GTTTTCCTTGTTTTCATTTTGTTTCTT 57.108 25.926 0.00 0.00 0.00 2.52
3603 7038 9.061435 TGTTTTCCTTGTTTTCATTTTGTTTCT 57.939 25.926 0.00 0.00 0.00 2.52
3604 7039 9.670719 TTGTTTTCCTTGTTTTCATTTTGTTTC 57.329 25.926 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.