Multiple sequence alignment - TraesCS6B01G060100

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 TraesCS6B01G060100 chr6B 100.000 5120 0 0 1 5120 39753725 39758844 0.000000e+00 9455.0
1 TraesCS6B01G060100 chr6B 88.658 1446 151 10 1846 3288 39433802 39435237 0.000000e+00 1749.0
2 TraesCS6B01G060100 chr6B 86.111 612 77 3 1022 1629 39193132 39193739 0.000000e+00 652.0
3 TraesCS6B01G060100 chr6B 86.269 386 36 10 1 383 39361513 39361142 2.220000e-108 403.0
4 TraesCS6B01G060100 chr6B 81.627 381 36 18 3931 4292 39425914 39426279 8.390000e-73 285.0
5 TraesCS6B01G060100 chr6B 82.507 343 28 15 4804 5120 39429030 39429366 6.530000e-69 272.0
6 TraesCS6B01G060100 chr6B 85.315 143 10 4 379 521 39343928 39343797 2.490000e-28 137.0
7 TraesCS6B01G060100 chr6B 94.253 87 4 1 558 643 39343633 39343547 1.160000e-26 132.0
8 TraesCS6B01G060100 chr6B 87.963 108 13 0 179 286 715854983 715854876 1.500000e-25 128.0
9 TraesCS6B01G060100 chr6D 91.275 2258 184 8 1676 3928 24364711 24362462 0.000000e+00 3066.0
10 TraesCS6B01G060100 chr6D 91.000 2089 174 10 1846 3928 24429895 24431975 0.000000e+00 2804.0
11 TraesCS6B01G060100 chr6D 89.249 2065 205 14 1871 3928 24403007 24405061 0.000000e+00 2567.0
12 TraesCS6B01G060100 chr6D 87.822 2094 233 16 1846 3928 24334871 24332789 0.000000e+00 2435.0
13 TraesCS6B01G060100 chr6D 85.653 2098 277 18 1846 3928 24298559 24296471 0.000000e+00 2185.0
14 TraesCS6B01G060100 chr6D 85.495 2089 281 19 1846 3925 24391334 24393409 0.000000e+00 2159.0
15 TraesCS6B01G060100 chr6D 86.425 1930 248 12 2006 3928 24353404 24351482 0.000000e+00 2100.0
16 TraesCS6B01G060100 chr6D 91.393 1371 107 5 2562 3928 24339996 24338633 0.000000e+00 1868.0
17 TraesCS6B01G060100 chr6D 87.847 1152 96 16 723 1848 24358499 24357366 0.000000e+00 1312.0
18 TraesCS6B01G060100 chr6D 90.194 979 55 17 677 1631 24349250 24348289 0.000000e+00 1238.0
19 TraesCS6B01G060100 chr6D 90.122 982 56 17 674 1631 24390074 24391038 0.000000e+00 1238.0
20 TraesCS6B01G060100 chr6D 95.806 620 20 3 4035 4654 24362282 24361669 0.000000e+00 996.0
21 TraesCS6B01G060100 chr6D 85.917 774 90 12 1080 1848 24299424 24298665 0.000000e+00 808.0
22 TraesCS6B01G060100 chr6D 86.229 777 70 24 1080 1848 24402183 24402930 0.000000e+00 808.0
23 TraesCS6B01G060100 chr6D 91.507 471 31 3 80 550 24389581 24390042 1.550000e-179 640.0
24 TraesCS6B01G060100 chr6D 84.514 607 65 17 1243 1848 24225995 24226573 1.600000e-159 573.0
25 TraesCS6B01G060100 chr6D 83.871 558 81 8 1080 1631 24365277 24364723 1.630000e-144 523.0
26 TraesCS6B01G060100 chr6D 90.332 331 12 7 4808 5120 24361670 24361342 2.850000e-112 416.0
27 TraesCS6B01G060100 chr6D 80.460 609 62 28 3934 4523 24355197 24354627 3.690000e-111 412.0
28 TraesCS6B01G060100 chr6D 89.552 268 23 5 4035 4301 24338453 24338190 8.210000e-88 335.0
29 TraesCS6B01G060100 chr6D 89.552 268 23 4 4035 4301 24432155 24432418 8.210000e-88 335.0
30 TraesCS6B01G060100 chr6D 90.837 251 14 3 2 247 24359219 24358973 1.370000e-85 327.0
31 TraesCS6B01G060100 chr6D 84.661 339 37 7 4043 4372 24351302 24350970 1.780000e-84 324.0
32 TraesCS6B01G060100 chr6D 84.545 330 28 10 4804 5115 24295694 24295370 6.440000e-79 305.0
33 TraesCS6B01G060100 chr6D 89.952 209 11 3 4171 4378 24296227 24296028 1.410000e-65 261.0
34 TraesCS6B01G060100 chr6D 91.813 171 14 0 1678 1848 24335147 24334977 6.630000e-59 239.0
35 TraesCS6B01G060100 chr6D 97.059 136 3 1 558 693 24358634 24358500 1.430000e-55 228.0
36 TraesCS6B01G060100 chr6D 97.037 135 2 2 4675 4807 126108254 126108388 5.160000e-55 226.0
37 TraesCS6B01G060100 chr6D 88.268 179 9 5 4128 4304 24323386 24323218 2.420000e-48 204.0
38 TraesCS6B01G060100 chr6D 85.311 177 15 1 4481 4657 24295914 24295749 6.820000e-39 172.0
39 TraesCS6B01G060100 chr6D 90.698 129 10 2 4780 4907 24405822 24405949 2.450000e-38 171.0
40 TraesCS6B01G060100 chr6D 91.667 120 9 1 4787 4906 24322872 24322754 1.140000e-36 165.0
41 TraesCS6B01G060100 chr6D 90.741 108 7 2 3934 4038 24338593 24338486 1.920000e-29 141.0
42 TraesCS6B01G060100 chr6D 90.741 108 7 2 3934 4038 24362422 24362315 1.920000e-29 141.0
43 TraesCS6B01G060100 chr6D 90.090 111 8 2 3931 4038 24432012 24432122 1.920000e-29 141.0
44 TraesCS6B01G060100 chr6D 95.402 87 3 1 558 643 24349585 24349499 2.490000e-28 137.0
45 TraesCS6B01G060100 chr6D 78.000 250 32 13 3934 4166 24296431 24296188 8.940000e-28 135.0
46 TraesCS6B01G060100 chr6D 79.630 216 19 12 3934 4131 24332749 24332541 1.160000e-26 132.0
47 TraesCS6B01G060100 chr6D 86.735 98 11 1 3934 4031 24351442 24351347 1.950000e-19 108.0
48 TraesCS6B01G060100 chr6D 89.744 78 8 0 4295 4372 24338169 24338092 3.260000e-17 100.0
49 TraesCS6B01G060100 chr6D 87.209 86 9 2 4933 5018 24350357 24350274 4.220000e-16 97.1
50 TraesCS6B01G060100 chr6D 92.063 63 5 0 4310 4372 24432454 24432516 7.060000e-14 89.8
51 TraesCS6B01G060100 chr6D 100.000 29 0 0 4654 4682 24337765 24337737 3.000000e-03 54.7
52 TraesCS6B01G060100 chr6D 100.000 29 0 0 4654 4682 24432843 24432871 3.000000e-03 54.7
53 TraesCS6B01G060100 chr6D 100.000 28 0 0 1 28 24389515 24389542 9.000000e-03 52.8
54 TraesCS6B01G060100 chr6A 89.943 2088 200 5 1846 3928 23443232 23441150 0.000000e+00 2684.0
55 TraesCS6B01G060100 chr6A 88.027 2230 206 19 1846 4038 23023902 23026107 0.000000e+00 2582.0
56 TraesCS6B01G060100 chr6A 85.755 2092 277 15 1846 3928 22816879 22818958 0.000000e+00 2193.0
57 TraesCS6B01G060100 chr6A 92.365 1336 73 10 538 1848 23444669 23443338 0.000000e+00 1875.0
58 TraesCS6B01G060100 chr6A 87.332 1113 112 6 759 1848 22815667 22816773 0.000000e+00 1247.0
59 TraesCS6B01G060100 chr6A 88.953 860 87 5 3073 3928 22988236 22989091 0.000000e+00 1055.0
60 TraesCS6B01G060100 chr6A 84.922 829 108 11 1022 1848 22690823 22691636 0.000000e+00 822.0
61 TraesCS6B01G060100 chr6A 87.963 648 41 15 2 647 22815049 22815661 0.000000e+00 730.0
62 TraesCS6B01G060100 chr6A 84.010 763 53 31 3931 4654 22989128 22989860 0.000000e+00 669.0
63 TraesCS6B01G060100 chr6A 87.013 539 42 14 1 538 23445282 23444771 2.660000e-162 582.0
64 TraesCS6B01G060100 chr6A 81.424 323 39 15 4804 5120 22989918 22990225 1.420000e-60 244.0
65 TraesCS6B01G060100 chr6A 89.714 175 16 2 1675 1848 23023623 23023796 6.670000e-54 222.0
66 TraesCS6B01G060100 chr6A 79.063 363 46 23 4037 4372 23440972 23440613 6.670000e-54 222.0
67 TraesCS6B01G060100 chr6A 91.875 160 10 2 4043 4202 23026146 23026302 2.400000e-53 220.0
68 TraesCS6B01G060100 chr6A 96.694 121 3 1 602 721 27148138 27148018 3.130000e-47 200.0
69 TraesCS6B01G060100 chr6A 80.342 234 18 11 4295 4507 22824069 22824295 8.880000e-33 152.0
70 TraesCS6B01G060100 chrUn 83.934 2247 286 41 1846 4038 278293165 278295390 0.000000e+00 2080.0
71 TraesCS6B01G060100 chrUn 87.673 1736 154 24 2340 4038 284476489 284474777 0.000000e+00 1965.0
72 TraesCS6B01G060100 chrUn 91.018 167 10 4 4043 4209 284474738 284474577 2.400000e-53 220.0
73 TraesCS6B01G060100 chrUn 96.970 33 1 0 4650 4682 278295676 278295708 7.160000e-04 56.5
74 TraesCS6B01G060100 chr4D 95.302 149 4 3 4674 4821 614659 614513 3.080000e-57 233.0
75 TraesCS6B01G060100 chr4D 97.692 130 3 0 4681 4810 311194977 311194848 1.860000e-54 224.0
76 TraesCS6B01G060100 chr4D 98.425 127 2 0 4681 4807 391290297 391290423 1.860000e-54 224.0
77 TraesCS6B01G060100 chr5D 97.692 130 3 0 4681 4810 183634084 183633955 1.860000e-54 224.0
78 TraesCS6B01G060100 chr2D 97.692 130 3 0 4681 4810 330148291 330148162 1.860000e-54 224.0
79 TraesCS6B01G060100 chr2B 97.692 130 3 0 4678 4807 677806507 677806378 1.860000e-54 224.0
80 TraesCS6B01G060100 chr1D 98.425 127 2 0 4681 4807 127143276 127143402 1.860000e-54 224.0
81 TraesCS6B01G060100 chr3D 95.620 137 5 1 4681 4817 335367446 335367311 8.630000e-53 219.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G060100 chr6B 39753725 39758844 5119 False 9455.000000 9455 100.000000 1 5120 1 chr6B.!!$F3 5119
1 TraesCS6B01G060100 chr6B 39433802 39435237 1435 False 1749.000000 1749 88.658000 1846 3288 1 chr6B.!!$F2 1442
2 TraesCS6B01G060100 chr6B 39193132 39193739 607 False 652.000000 652 86.111000 1022 1629 1 chr6B.!!$F1 607
3 TraesCS6B01G060100 chr6B 39425914 39429366 3452 False 278.500000 285 82.067000 3931 5120 2 chr6B.!!$F4 1189
4 TraesCS6B01G060100 chr6D 24402183 24405949 3766 False 1182.000000 2567 88.725333 1080 4907 3 chr6D.!!$F4 3827
5 TraesCS6B01G060100 chr6D 24389515 24393409 3894 False 1022.450000 2159 91.781000 1 3925 4 chr6D.!!$F3 3924
6 TraesCS6B01G060100 chr6D 24348289 24365277 16988 True 761.673333 3066 89.256933 2 5120 15 chr6D.!!$R4 5118
7 TraesCS6B01G060100 chr6D 24429895 24432871 2976 False 684.900000 2804 92.541000 1846 4682 5 chr6D.!!$F5 2836
8 TraesCS6B01G060100 chr6D 24332541 24339996 7455 True 663.087500 2435 90.086875 1678 4682 8 chr6D.!!$R3 3004
9 TraesCS6B01G060100 chr6D 24295370 24299424 4054 True 644.333333 2185 84.896333 1080 5115 6 chr6D.!!$R1 4035
10 TraesCS6B01G060100 chr6D 24225995 24226573 578 False 573.000000 573 84.514000 1243 1848 1 chr6D.!!$F1 605
11 TraesCS6B01G060100 chr6A 22815049 22818958 3909 False 1390.000000 2193 87.016667 2 3928 3 chr6A.!!$F3 3926
12 TraesCS6B01G060100 chr6A 23440613 23445282 4669 True 1340.750000 2684 87.096000 1 4372 4 chr6A.!!$R2 4371
13 TraesCS6B01G060100 chr6A 23023623 23026302 2679 False 1008.000000 2582 89.872000 1675 4202 3 chr6A.!!$F5 2527
14 TraesCS6B01G060100 chr6A 22690823 22691636 813 False 822.000000 822 84.922000 1022 1848 1 chr6A.!!$F1 826
15 TraesCS6B01G060100 chr6A 22988236 22990225 1989 False 656.000000 1055 84.795667 3073 5120 3 chr6A.!!$F4 2047
16 TraesCS6B01G060100 chrUn 284474577 284476489 1912 True 1092.500000 1965 89.345500 2340 4209 2 chrUn.!!$R1 1869
17 TraesCS6B01G060100 chrUn 278293165 278295708 2543 False 1068.250000 2080 90.452000 1846 4682 2 chrUn.!!$F1 2836

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
156 6225 0.034283 AGGTCCTCTACGTCCTCCAC 60.034 60.000 0.0 0.0 0.00 4.02 F
286 6359 1.142748 GGAGCAGAGCAGTACGCAT 59.857 57.895 11.3 0.0 46.13 4.73 F
2160 11902 0.031716 ACCTGAGCTGGCTGGATCTA 60.032 55.000 0.0 0.0 0.00 1.98 F
2161 11903 0.392336 CCTGAGCTGGCTGGATCTAC 59.608 60.000 0.0 0.0 0.00 2.59 F
3780 17299 0.415830 TGATGGGTCTCTGGGTGGTA 59.584 55.000 0.0 0.0 0.00 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1122 7347 0.543277 TCTGGATGCAGGCTAGTTGG 59.457 55.000 14.84 0.0 0.00 3.77 R
2237 11982 0.616891 GACCCCGTCCAGGTTGTTAT 59.383 55.000 0.00 0.0 37.88 1.89 R
3541 17045 1.071699 GTTGTAGGACAGGTTCAGGCA 59.928 52.381 0.00 0.0 0.00 4.75 R
3861 17380 1.136828 TCCAGGTAACAGCCACTTGT 58.863 50.000 0.00 0.0 41.41 3.16 R
4682 21031 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.0 0.00 4.30 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
146 6215 1.353358 TCGAGGTCACAAGGTCCTCTA 59.647 52.381 8.47 0.00 43.73 2.43
153 6222 1.473278 CACAAGGTCCTCTACGTCCTC 59.527 57.143 0.00 0.00 0.00 3.71
154 6223 1.104630 CAAGGTCCTCTACGTCCTCC 58.895 60.000 0.00 0.00 0.00 4.30
155 6224 0.702902 AAGGTCCTCTACGTCCTCCA 59.297 55.000 0.00 0.00 0.00 3.86
156 6225 0.034283 AGGTCCTCTACGTCCTCCAC 60.034 60.000 0.00 0.00 0.00 4.02
286 6359 1.142748 GGAGCAGAGCAGTACGCAT 59.857 57.895 11.30 0.00 46.13 4.73
294 6367 3.679980 CAGAGCAGTACGCATGTTAGTTT 59.320 43.478 11.30 0.00 46.13 2.66
315 6389 1.973281 CAGGCAGCGAACACCCAAT 60.973 57.895 0.00 0.00 0.00 3.16
351 6425 7.319646 TCTGTTCACAACTAATGCAAACTTTT 58.680 30.769 0.00 0.00 31.42 2.27
403 6477 2.224843 CGGATGGATGGGGATTCATCAA 60.225 50.000 5.82 0.00 43.82 2.57
417 6491 7.667219 GGGGATTCATCAATTACTCACACATAT 59.333 37.037 0.00 0.00 0.00 1.78
418 6492 8.509690 GGGATTCATCAATTACTCACACATATG 58.490 37.037 0.00 0.00 0.00 1.78
419 6493 8.509690 GGATTCATCAATTACTCACACATATGG 58.490 37.037 7.80 0.00 0.00 2.74
420 6494 9.276590 GATTCATCAATTACTCACACATATGGA 57.723 33.333 7.80 0.00 0.00 3.41
603 6797 1.620323 AGTGGCTTTGAATTCCAAGCC 59.380 47.619 38.23 38.23 43.33 4.35
656 6851 5.220416 GCTAACATAAACATCGACACCAGAC 60.220 44.000 0.00 0.00 0.00 3.51
721 6916 1.730501 AGAGCACACATCAACATCGG 58.269 50.000 0.00 0.00 0.00 4.18
786 6981 6.318648 CAGGATTGCTAGTAACCAAAGCATAA 59.681 38.462 12.27 0.00 45.09 1.90
853 7048 1.242076 ATGCAACTTCACTGTCCAGC 58.758 50.000 0.00 0.00 0.00 4.85
873 7068 5.481105 CAGCTGCTTTAATCAAATCCCAAA 58.519 37.500 0.00 0.00 0.00 3.28
882 7100 3.517296 TCAAATCCCAAACCTGCTACA 57.483 42.857 0.00 0.00 0.00 2.74
886 7104 3.959495 ATCCCAAACCTGCTACATCAT 57.041 42.857 0.00 0.00 0.00 2.45
889 7107 5.387113 TCCCAAACCTGCTACATCATATT 57.613 39.130 0.00 0.00 0.00 1.28
917 7135 4.087182 ACGGACAAGAGAGAAACTCCATA 58.913 43.478 0.00 0.00 45.96 2.74
1000 7220 5.537188 TGCTTTAATTAAACAGCAACCAGG 58.463 37.500 18.07 3.12 0.00 4.45
1093 7318 6.037786 TCCTACACCAAGAAGAACACATAG 57.962 41.667 0.00 0.00 0.00 2.23
1109 7334 3.441222 CACATAGTCATGGCAAAAGCAGA 59.559 43.478 0.00 0.00 36.39 4.26
1122 7347 0.671781 AAGCAGACATGGACACGCTC 60.672 55.000 0.00 0.00 0.00 5.03
1201 7429 0.738762 CACAGAGGACACATCTGCCG 60.739 60.000 12.23 2.20 46.64 5.69
1213 7441 0.107897 ATCTGCCGTGCGTCCAAATA 60.108 50.000 0.00 0.00 0.00 1.40
1440 7668 3.775316 AGGTACTAGCAGGCAACATAAGT 59.225 43.478 0.00 0.00 36.02 2.24
1492 7720 4.320641 GGTATCTCGACCTCAGCTACAATC 60.321 50.000 0.00 0.00 36.47 2.67
1542 7770 2.550277 TGGGTTCTCTCCATCAGCTA 57.450 50.000 0.00 0.00 0.00 3.32
1637 7865 6.374417 ACAGTACCTAAATCTTGACACCAT 57.626 37.500 0.00 0.00 0.00 3.55
1772 11406 3.498397 AGTACAATTGTTCACTGGCTTCG 59.502 43.478 17.78 0.00 0.00 3.79
1809 11443 3.131396 TCCAACTCTGAAAGTTCTTCGC 58.869 45.455 0.00 0.00 45.28 4.70
1814 11448 5.153950 ACTCTGAAAGTTCTTCGCCTTAT 57.846 39.130 0.00 0.00 33.03 1.73
1816 11450 4.504858 TCTGAAAGTTCTTCGCCTTATCC 58.495 43.478 0.00 0.00 33.76 2.59
1832 11466 5.075493 CCTTATCCATTGCCAGCTTAGAAT 58.925 41.667 0.00 0.00 0.00 2.40
1889 11631 0.465460 TATGGCCCGTTTCCAGATGC 60.465 55.000 0.00 0.00 36.98 3.91
1958 11700 2.024080 ACCTTGTGGGCATGATACCATT 60.024 45.455 0.00 0.00 39.30 3.16
1959 11701 3.033184 CCTTGTGGGCATGATACCATTT 58.967 45.455 0.00 0.00 39.30 2.32
2058 11800 2.607635 CCATCGATTACCCAGTTGTTCG 59.392 50.000 0.00 0.00 0.00 3.95
2067 11809 2.014128 CCCAGTTGTTCGCGGAATAAT 58.986 47.619 6.13 0.00 0.00 1.28
2089 11831 5.401531 TCTACAATGGTTGTCTCTACACC 57.598 43.478 0.00 0.00 44.12 4.16
2115 11857 0.913451 ATCTGACTGGAAGCCTGCCT 60.913 55.000 0.00 0.00 37.60 4.75
2122 11864 1.137872 CTGGAAGCCTGCCTACTACAG 59.862 57.143 0.00 0.00 34.82 2.74
2160 11902 0.031716 ACCTGAGCTGGCTGGATCTA 60.032 55.000 0.00 0.00 0.00 1.98
2161 11903 0.392336 CCTGAGCTGGCTGGATCTAC 59.608 60.000 0.00 0.00 0.00 2.59
2163 11905 0.826715 TGAGCTGGCTGGATCTACAC 59.173 55.000 0.00 0.00 0.00 2.90
2237 11982 8.380099 ACAACTAATGATGTTGGACCTTAGTTA 58.620 33.333 10.71 0.00 46.28 2.24
2584 12333 8.437742 CAACAATGGAATTTATGAGAGCAAAAC 58.562 33.333 0.00 0.00 31.22 2.43
2647 12396 2.551270 AGCTTCCCATCACTCTAACCA 58.449 47.619 0.00 0.00 0.00 3.67
2718 12467 2.049156 GCGCCAGGGCTTGAAAAC 60.049 61.111 8.91 0.00 39.32 2.43
2821 12570 8.964476 TCTATCAAGAAATAACCTCAATGGAC 57.036 34.615 0.00 0.00 39.71 4.02
2871 12620 3.504906 CCAGCACAAACATGACAGATCTT 59.495 43.478 0.00 0.00 0.00 2.40
2893 12648 8.131455 TCTTAGCATTGTTAATCTAAGCTTCG 57.869 34.615 0.00 0.00 38.41 3.79
3063 12818 7.118060 TGAGATCCAATATGTTTCATGGTCAA 58.882 34.615 0.00 0.00 34.50 3.18
3133 12888 6.716628 CCTTGCATACAACAATATATCAGGGT 59.283 38.462 0.00 0.00 0.00 4.34
3180 12935 3.056607 GCACAGGCATGATACAAAAAGGT 60.057 43.478 4.84 0.00 40.72 3.50
3186 12941 5.481473 AGGCATGATACAAAAAGGTGACAAT 59.519 36.000 0.00 0.00 0.00 2.71
3195 12950 7.111247 ACAAAAAGGTGACAATTCTGATGAA 57.889 32.000 0.00 0.00 36.54 2.57
3199 12954 6.966534 AAGGTGACAATTCTGATGAACTTT 57.033 33.333 0.00 0.00 34.71 2.66
3200 12955 6.966534 AGGTGACAATTCTGATGAACTTTT 57.033 33.333 0.00 0.00 34.71 2.27
3206 12961 8.298854 TGACAATTCTGATGAACTTTTGTATGG 58.701 33.333 0.00 0.00 34.80 2.74
3214 12969 9.166173 CTGATGAACTTTTGTATGGATTCACTA 57.834 33.333 0.00 0.00 0.00 2.74
3215 12970 9.166173 TGATGAACTTTTGTATGGATTCACTAG 57.834 33.333 0.00 0.00 0.00 2.57
3227 12982 3.307762 GGATTCACTAGTGGAACAAGGCT 60.308 47.826 22.48 0.00 44.16 4.58
3232 16736 4.578928 TCACTAGTGGAACAAGGCTTTTTC 59.421 41.667 22.48 16.00 44.16 2.29
3253 16757 6.419484 TTCCTGAGAATGAACTAGTTGACA 57.581 37.500 14.14 6.13 0.00 3.58
3258 16762 5.120674 TGAGAATGAACTAGTTGACAATGCG 59.879 40.000 14.14 0.00 0.00 4.73
3261 16765 3.064207 TGAACTAGTTGACAATGCGGAC 58.936 45.455 14.14 0.00 0.00 4.79
3263 16767 2.688507 ACTAGTTGACAATGCGGACAG 58.311 47.619 0.00 0.00 0.00 3.51
3308 16812 6.657541 GGTCAAGAGAGACTATATACAGGAGG 59.342 46.154 0.00 0.00 38.57 4.30
3541 17045 1.067283 CGGCTCTCACATCACTGAGTT 60.067 52.381 0.00 0.00 39.08 3.01
3575 17079 5.047021 TGTCCTACAACAATCTGAGAGGAAG 60.047 44.000 0.00 0.00 35.31 3.46
3616 17120 1.305201 GCAAACACTCGAAGACCCAA 58.695 50.000 0.00 0.00 0.00 4.12
3681 17188 3.206964 TGTAAATTGTTCGTCACAGCCA 58.793 40.909 0.00 0.00 36.48 4.75
3780 17299 0.415830 TGATGGGTCTCTGGGTGGTA 59.584 55.000 0.00 0.00 0.00 3.25
3861 17380 6.061441 CAGCCTGTATGATTGGGTTTATGTA 58.939 40.000 0.00 0.00 0.00 2.29
3929 17449 4.659111 AGAAGCTGAGATGAGATGACTG 57.341 45.455 0.00 0.00 0.00 3.51
3932 17487 5.834742 AGAAGCTGAGATGAGATGACTGTAT 59.165 40.000 0.00 0.00 0.00 2.29
4015 17577 9.529823 AACTATTCAGGATATGTATTCGAGGTA 57.470 33.333 0.00 0.00 0.00 3.08
4019 17581 7.158099 TCAGGATATGTATTCGAGGTACATG 57.842 40.000 24.37 14.90 41.50 3.21
4116 17715 9.460019 TGAATGTGTCAATTAATATTCCAGTGA 57.540 29.630 0.00 0.00 31.51 3.41
4149 17752 3.770263 ACAAGTCATGCACATGTATGC 57.230 42.857 10.27 0.00 46.32 3.14
4165 17770 2.858622 TGCATTCTAGGTGCACTGC 58.141 52.632 17.98 17.40 46.76 4.40
4225 17831 2.028748 GCATGCCATCAACTGAGGTTTT 60.029 45.455 6.36 0.00 32.73 2.43
4347 20455 4.934356 TCAAATGGCAAAGATAAGGAGGT 58.066 39.130 0.00 0.00 0.00 3.85
4391 20521 8.365647 AGAATGAAGCTGATTCTGATTTTGTTT 58.634 29.630 16.77 0.00 38.48 2.83
4401 20547 1.767681 TGATTTTGTTTTGGCCTGGCT 59.232 42.857 19.68 0.00 0.00 4.75
4494 20646 4.890499 AGAGGTCTCTATGGAAAGAGGA 57.110 45.455 0.00 0.00 42.78 3.71
4496 20648 4.480537 AGAGGTCTCTATGGAAAGAGGAGA 59.519 45.833 0.00 0.00 42.78 3.71
4558 20748 3.527253 TCATGCCCCCATATCCGATTTAT 59.473 43.478 0.00 0.00 0.00 1.40
4581 20782 5.008619 AGATGACATAGACTGCTCACTTG 57.991 43.478 0.00 0.00 0.00 3.16
4582 20783 4.708909 AGATGACATAGACTGCTCACTTGA 59.291 41.667 0.00 0.00 0.00 3.02
4583 20784 4.179926 TGACATAGACTGCTCACTTGAC 57.820 45.455 0.00 0.00 0.00 3.18
4584 20785 3.056536 TGACATAGACTGCTCACTTGACC 60.057 47.826 0.00 0.00 0.00 4.02
4585 20786 2.899900 ACATAGACTGCTCACTTGACCA 59.100 45.455 0.00 0.00 0.00 4.02
4586 20787 3.257393 CATAGACTGCTCACTTGACCAC 58.743 50.000 0.00 0.00 0.00 4.16
4587 20788 1.418334 AGACTGCTCACTTGACCACT 58.582 50.000 0.00 0.00 0.00 4.00
4588 20789 2.598565 AGACTGCTCACTTGACCACTA 58.401 47.619 0.00 0.00 0.00 2.74
4589 20790 2.297597 AGACTGCTCACTTGACCACTAC 59.702 50.000 0.00 0.00 0.00 2.73
4590 20791 2.297597 GACTGCTCACTTGACCACTACT 59.702 50.000 0.00 0.00 0.00 2.57
4591 20792 2.700897 ACTGCTCACTTGACCACTACTT 59.299 45.455 0.00 0.00 0.00 2.24
4596 20797 4.024809 GCTCACTTGACCACTACTTCAAAC 60.025 45.833 0.00 0.00 31.41 2.93
4613 20814 2.810852 CAAACCTTCAGCTCTCTTGGAC 59.189 50.000 0.00 0.00 0.00 4.02
4615 20816 1.622811 ACCTTCAGCTCTCTTGGACTG 59.377 52.381 0.00 0.00 0.00 3.51
4682 21031 5.263968 TGTCTGCCTCTGCTTTATAGTAC 57.736 43.478 0.00 0.00 38.71 2.73
4683 21032 4.956700 TGTCTGCCTCTGCTTTATAGTACT 59.043 41.667 0.00 0.00 38.71 2.73
4684 21033 5.067936 TGTCTGCCTCTGCTTTATAGTACTC 59.932 44.000 0.00 0.00 38.71 2.59
4685 21034 4.585162 TCTGCCTCTGCTTTATAGTACTCC 59.415 45.833 0.00 0.00 38.71 3.85
4686 21035 3.641906 TGCCTCTGCTTTATAGTACTCCC 59.358 47.826 0.00 0.00 38.71 4.30
4687 21036 3.898741 GCCTCTGCTTTATAGTACTCCCT 59.101 47.826 0.00 0.00 33.53 4.20
4688 21037 4.021807 GCCTCTGCTTTATAGTACTCCCTC 60.022 50.000 0.00 0.00 33.53 4.30
4689 21038 4.525100 CCTCTGCTTTATAGTACTCCCTCC 59.475 50.000 0.00 0.00 0.00 4.30
4690 21039 4.142790 TCTGCTTTATAGTACTCCCTCCG 58.857 47.826 0.00 0.00 0.00 4.63
4691 21040 3.890147 CTGCTTTATAGTACTCCCTCCGT 59.110 47.826 0.00 0.00 0.00 4.69
4692 21041 3.887716 TGCTTTATAGTACTCCCTCCGTC 59.112 47.826 0.00 0.00 0.00 4.79
4693 21042 3.255395 GCTTTATAGTACTCCCTCCGTCC 59.745 52.174 0.00 0.00 0.00 4.79
4694 21043 3.515602 TTATAGTACTCCCTCCGTCCC 57.484 52.381 0.00 0.00 0.00 4.46
4695 21044 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
4696 21045 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
4697 21046 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
4698 21047 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
4699 21048 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
4700 21049 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
4701 21050 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
4702 21051 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
4703 21052 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
4704 21053 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
4705 21054 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
4706 21055 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
4707 21056 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
4708 21057 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
4709 21058 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
4710 21059 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
4711 21060 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
4712 21061 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
4713 21062 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
4714 21063 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
4715 21064 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
4716 21065 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
4717 21066 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
4718 21067 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
4725 21074 9.569167 TTCTTGTCTTAGATTTGTCTACATACG 57.431 33.333 0.00 0.00 0.00 3.06
4726 21075 8.188799 TCTTGTCTTAGATTTGTCTACATACGG 58.811 37.037 0.00 0.00 0.00 4.02
4727 21076 7.634671 TGTCTTAGATTTGTCTACATACGGA 57.365 36.000 0.00 0.00 0.00 4.69
4728 21077 8.234136 TGTCTTAGATTTGTCTACATACGGAT 57.766 34.615 0.00 0.00 0.00 4.18
4729 21078 8.135529 TGTCTTAGATTTGTCTACATACGGATG 58.864 37.037 5.94 5.94 39.16 3.51
4731 21080 9.346005 TCTTAGATTTGTCTACATACGGATGTA 57.654 33.333 19.32 19.32 44.77 2.29
4734 21083 8.410673 AGATTTGTCTACATACGGATGTATCT 57.589 34.615 20.64 16.58 45.42 1.98
4735 21084 9.516546 AGATTTGTCTACATACGGATGTATCTA 57.483 33.333 20.64 11.01 45.42 1.98
4739 21088 8.857694 TGTCTACATACGGATGTATCTATTCA 57.142 34.615 20.64 10.60 45.42 2.57
4740 21089 8.727910 TGTCTACATACGGATGTATCTATTCAC 58.272 37.037 20.64 9.33 45.42 3.18
4741 21090 8.727910 GTCTACATACGGATGTATCTATTCACA 58.272 37.037 20.64 0.00 45.42 3.58
4742 21091 9.462606 TCTACATACGGATGTATCTATTCACAT 57.537 33.333 20.64 0.00 45.42 3.21
4745 21094 9.778741 ACATACGGATGTATCTATTCACATTTT 57.221 29.630 12.79 0.00 44.77 1.82
4749 21098 9.261180 ACGGATGTATCTATTCACATTTTAGTG 57.739 33.333 0.00 0.00 40.85 2.74
4750 21099 9.261180 CGGATGTATCTATTCACATTTTAGTGT 57.739 33.333 0.00 0.00 40.37 3.55
4762 21111 8.642908 TCACATTTTAGTGTTAGATACATCCG 57.357 34.615 0.00 0.00 39.39 4.18
4763 21112 8.255206 TCACATTTTAGTGTTAGATACATCCGT 58.745 33.333 0.00 0.00 39.39 4.69
4764 21113 9.524106 CACATTTTAGTGTTAGATACATCCGTA 57.476 33.333 0.00 0.00 39.39 4.02
4799 21148 9.720769 AATCTAAGACAAGAATTTTAAGACGGA 57.279 29.630 0.00 0.00 0.00 4.69
4800 21149 8.758633 TCTAAGACAAGAATTTTAAGACGGAG 57.241 34.615 0.00 0.00 0.00 4.63
4801 21150 6.803154 AAGACAAGAATTTTAAGACGGAGG 57.197 37.500 0.00 0.00 0.00 4.30
4802 21151 5.246307 AGACAAGAATTTTAAGACGGAGGG 58.754 41.667 0.00 0.00 0.00 4.30
4803 21152 5.012768 AGACAAGAATTTTAAGACGGAGGGA 59.987 40.000 0.00 0.00 0.00 4.20
4804 21153 5.246307 ACAAGAATTTTAAGACGGAGGGAG 58.754 41.667 0.00 0.00 0.00 4.30
4805 21154 5.221864 ACAAGAATTTTAAGACGGAGGGAGT 60.222 40.000 0.00 0.00 0.00 3.85
4806 21155 6.013984 ACAAGAATTTTAAGACGGAGGGAGTA 60.014 38.462 0.00 0.00 0.00 2.59
4822 21171 6.867293 GGAGGGAGTAGTATAATAAAGCAACG 59.133 42.308 0.00 0.00 0.00 4.10
4928 21371 4.096984 GTGCAGGGAAAATATGAGTTCAGG 59.903 45.833 0.00 0.00 0.00 3.86
4931 21392 5.509498 CAGGGAAAATATGAGTTCAGGGAA 58.491 41.667 0.00 0.00 0.00 3.97
5027 21490 0.685097 GTGCAGAGTTAGGGTCCACA 59.315 55.000 0.00 0.00 0.00 4.17
5062 21531 2.945008 TCCAATATTGTGCTGCTGCTAC 59.055 45.455 17.00 12.91 40.48 3.58
5074 21543 3.388308 CTGCTGCTACCTTACTATGCTG 58.612 50.000 0.00 0.00 0.00 4.41
5078 21547 4.122776 CTGCTACCTTACTATGCTGGTTG 58.877 47.826 0.00 0.00 34.33 3.77
5080 21549 4.120589 GCTACCTTACTATGCTGGTTGAC 58.879 47.826 0.00 0.00 34.33 3.18
5081 21550 4.382685 GCTACCTTACTATGCTGGTTGACA 60.383 45.833 0.00 0.00 34.33 3.58
5082 21551 4.634012 ACCTTACTATGCTGGTTGACAA 57.366 40.909 0.00 0.00 0.00 3.18
5084 21553 4.943705 ACCTTACTATGCTGGTTGACAATG 59.056 41.667 0.00 0.00 0.00 2.82
5100 21569 4.216902 TGACAATGATGCAGAACCTGAAAG 59.783 41.667 0.00 0.00 32.44 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 6121 2.286523 CCTGCTGGACGAACTCCCT 61.287 63.158 2.92 0.00 38.49 4.20
123 6192 0.898789 GGACCTTGTGACCTCGAGGA 60.899 60.000 37.69 14.23 40.48 3.71
146 6215 1.838073 GAATGGTGGGTGGAGGACGT 61.838 60.000 0.00 0.00 0.00 4.34
153 6222 1.344114 CAACAAAGGAATGGTGGGTGG 59.656 52.381 0.00 0.00 34.30 4.61
154 6223 2.818130 CAACAAAGGAATGGTGGGTG 57.182 50.000 0.00 0.00 34.30 4.61
286 6359 1.202710 TCGCTGCCTGGAAAACTAACA 60.203 47.619 0.00 0.00 0.00 2.41
294 6367 2.281484 GGTGTTCGCTGCCTGGAA 60.281 61.111 0.00 0.00 0.00 3.53
328 6402 7.319646 AGAAAAGTTTGCATTAGTTGTGAACA 58.680 30.769 0.00 0.00 0.00 3.18
338 6412 5.974751 GTCACCGAAAGAAAAGTTTGCATTA 59.025 36.000 0.00 0.00 0.00 1.90
339 6413 4.803613 GTCACCGAAAGAAAAGTTTGCATT 59.196 37.500 0.00 0.00 0.00 3.56
351 6425 6.987992 AGTTTATGTAACTTGTCACCGAAAGA 59.012 34.615 0.00 0.00 44.73 2.52
403 6477 6.479006 CCATCCATCCATATGTGTGAGTAAT 58.521 40.000 1.24 0.00 0.00 1.89
417 6491 0.935942 AAGCCAATCCCATCCATCCA 59.064 50.000 0.00 0.00 0.00 3.41
418 6492 1.625511 GAAGCCAATCCCATCCATCC 58.374 55.000 0.00 0.00 0.00 3.51
419 6493 1.242076 CGAAGCCAATCCCATCCATC 58.758 55.000 0.00 0.00 0.00 3.51
420 6494 3.426903 CGAAGCCAATCCCATCCAT 57.573 52.632 0.00 0.00 0.00 3.41
603 6797 2.872038 GCACACTAACAAGGACTCTGGG 60.872 54.545 0.00 0.00 0.00 4.45
656 6851 5.556915 TCCATTGGTCACTAACAAGTTAGG 58.443 41.667 20.50 11.60 45.06 2.69
757 6952 6.203723 GCTTTGGTTACTAGCAATCCTGATAG 59.796 42.308 0.00 0.00 45.32 2.08
758 6953 6.055588 GCTTTGGTTACTAGCAATCCTGATA 58.944 40.000 0.00 0.00 41.06 2.15
853 7048 5.870978 CAGGTTTGGGATTTGATTAAAGCAG 59.129 40.000 0.45 0.00 33.97 4.24
873 7068 5.296780 CGTTTTGGAATATGATGTAGCAGGT 59.703 40.000 0.00 0.00 0.00 4.00
889 7107 6.196649 GAGTTTCTCTCTTGTCCGTTTTGGA 61.197 44.000 0.00 0.00 41.34 3.53
917 7135 1.341285 TGCAGGCTTGTATCCATGCTT 60.341 47.619 0.00 0.00 40.57 3.91
1000 7220 2.446435 TGCCTGCCAAGATAAAAGTCC 58.554 47.619 0.00 0.00 0.00 3.85
1065 7286 4.081862 TGTTCTTCTTGGTGTAGGATACCG 60.082 45.833 0.00 0.00 42.12 4.02
1093 7318 2.602878 CATGTCTGCTTTTGCCATGAC 58.397 47.619 0.00 0.00 46.87 3.06
1122 7347 0.543277 TCTGGATGCAGGCTAGTTGG 59.457 55.000 14.84 0.00 0.00 3.77
1201 7429 2.286025 GGACCGTATTATTTGGACGCAC 59.714 50.000 0.00 0.00 35.28 5.34
1440 7668 2.920524 TGTAAACCAAGCAACGAGGAA 58.079 42.857 0.00 0.00 0.00 3.36
1492 7720 4.165779 GGTATTTGCATCTTGTCAAACCG 58.834 43.478 0.00 0.00 35.34 4.44
1772 11406 1.210155 GGAAGCATGTTCACCACGC 59.790 57.895 0.00 0.00 0.00 5.34
1809 11443 4.090761 TCTAAGCTGGCAATGGATAAGG 57.909 45.455 0.00 0.00 0.00 2.69
1814 11448 3.885297 GCTAATTCTAAGCTGGCAATGGA 59.115 43.478 0.00 0.00 37.01 3.41
1816 11450 3.005155 GGGCTAATTCTAAGCTGGCAATG 59.995 47.826 0.00 0.00 39.97 2.82
1832 11466 6.826231 CGAGATATCTAGAGAATCAGGGCTAA 59.174 42.308 4.89 0.00 37.82 3.09
2058 11800 5.527582 AGACAACCATTGTAGATTATTCCGC 59.472 40.000 0.00 0.00 45.52 5.54
2067 11809 4.836175 TGGTGTAGAGACAACCATTGTAGA 59.164 41.667 0.00 0.00 43.19 2.59
2089 11831 2.227388 GGCTTCCAGTCAGATTGTTGTG 59.773 50.000 0.00 0.00 0.00 3.33
2122 11864 7.010645 GCTCAGGTTACTTAATCTTTCTACTGC 59.989 40.741 0.00 0.00 0.00 4.40
2139 11881 0.833287 GATCCAGCCAGCTCAGGTTA 59.167 55.000 0.00 0.00 0.00 2.85
2160 11902 2.091541 CCTGTGAGTTTGTTGTGGTGT 58.908 47.619 0.00 0.00 0.00 4.16
2161 11903 2.091541 ACCTGTGAGTTTGTTGTGGTG 58.908 47.619 0.00 0.00 0.00 4.17
2163 11905 2.364632 TGACCTGTGAGTTTGTTGTGG 58.635 47.619 0.00 0.00 0.00 4.17
2237 11982 0.616891 GACCCCGTCCAGGTTGTTAT 59.383 55.000 0.00 0.00 37.88 1.89
2584 12333 6.071728 AGCTGGTTAGAACTGAAATCCATTTG 60.072 38.462 0.00 0.00 0.00 2.32
2821 12570 3.355378 TGACTGGGCAATCAGTAATTGG 58.645 45.455 6.58 0.00 46.76 3.16
2871 12620 6.578944 TCCGAAGCTTAGATTAACAATGCTA 58.421 36.000 8.29 0.00 0.00 3.49
3133 12888 7.012327 GCAGTTAACAATAGATCTTGGTATGCA 59.988 37.037 8.61 0.00 35.68 3.96
3176 12931 6.966534 AAAGTTCATCAGAATTGTCACCTT 57.033 33.333 0.00 0.00 35.92 3.50
3178 12933 6.507023 ACAAAAGTTCATCAGAATTGTCACC 58.493 36.000 0.00 0.00 32.03 4.02
3180 12935 8.298854 CCATACAAAAGTTCATCAGAATTGTCA 58.701 33.333 0.00 0.00 36.45 3.58
3186 12941 8.514594 GTGAATCCATACAAAAGTTCATCAGAA 58.485 33.333 0.00 0.00 0.00 3.02
3195 12950 7.016153 TCCACTAGTGAATCCATACAAAAGT 57.984 36.000 24.68 0.00 0.00 2.66
3199 12954 6.367374 TGTTCCACTAGTGAATCCATACAA 57.633 37.500 24.68 0.23 0.00 2.41
3200 12955 6.367374 TTGTTCCACTAGTGAATCCATACA 57.633 37.500 24.68 12.81 0.00 2.29
3206 12961 3.944087 AGCCTTGTTCCACTAGTGAATC 58.056 45.455 24.68 13.11 0.00 2.52
3214 12969 2.695147 CAGGAAAAAGCCTTGTTCCACT 59.305 45.455 24.94 5.83 42.81 4.00
3215 12970 2.693074 TCAGGAAAAAGCCTTGTTCCAC 59.307 45.455 24.94 2.79 42.81 4.02
3227 12982 7.773224 TGTCAACTAGTTCATTCTCAGGAAAAA 59.227 33.333 4.77 0.00 34.90 1.94
3232 16736 6.402983 GCATTGTCAACTAGTTCATTCTCAGG 60.403 42.308 4.77 0.00 0.00 3.86
3253 16757 2.918571 CAGTGACACTGTCCGCATT 58.081 52.632 24.73 0.00 41.19 3.56
3263 16767 5.813672 TGACCTTTTGTAAGTACAGTGACAC 59.186 40.000 0.00 0.00 37.52 3.67
3265 16769 6.759827 TCTTGACCTTTTGTAAGTACAGTGAC 59.240 38.462 0.00 0.00 37.52 3.67
3489 16993 3.347216 AGGGATTTCACCAGACAAATCG 58.653 45.455 0.00 0.00 39.12 3.34
3541 17045 1.071699 GTTGTAGGACAGGTTCAGGCA 59.928 52.381 0.00 0.00 0.00 4.75
3575 17079 4.142381 GCAGTTGATTTCCAGTTGGTATCC 60.142 45.833 0.00 0.00 36.34 2.59
3616 17120 6.605594 CCGGGGTTGCCAATATAAATATATGT 59.394 38.462 0.00 0.00 0.00 2.29
3681 17188 3.425659 GTTTTCTCCTGGAATTGGCTCT 58.574 45.455 0.00 0.00 33.53 4.09
3780 17299 6.043243 TCCTCTTGAACAAGAAGGTACAGAAT 59.957 38.462 16.29 0.00 45.75 2.40
3861 17380 1.136828 TCCAGGTAACAGCCACTTGT 58.863 50.000 0.00 0.00 41.41 3.16
3994 17556 7.602753 CATGTACCTCGAATACATATCCTGAA 58.397 38.462 17.32 0.00 40.51 3.02
4010 17572 1.486310 TCAGTCCATGGCATGTACCTC 59.514 52.381 24.80 10.64 0.00 3.85
4015 17577 2.651455 CAATCTCAGTCCATGGCATGT 58.349 47.619 24.80 4.97 0.00 3.21
4019 17581 1.386533 CACCAATCTCAGTCCATGGC 58.613 55.000 6.96 2.00 34.45 4.40
4116 17715 6.094048 GTGCATGACTTGTTCCAGTACAATAT 59.906 38.462 0.00 0.00 37.39 1.28
4149 17752 2.293677 TACGCAGTGCACCTAGAATG 57.706 50.000 16.83 5.08 45.73 2.67
4164 17769 3.001330 GTGCATGACTAGTTCCAATACGC 59.999 47.826 0.00 0.00 0.00 4.42
4165 17770 4.180817 TGTGCATGACTAGTTCCAATACG 58.819 43.478 0.00 0.00 0.00 3.06
4305 20413 0.733150 GTTTTGCCCGAGGTATCAGC 59.267 55.000 0.00 0.00 0.00 4.26
4347 20455 0.953471 CTTGCCATCACCGGTTTCGA 60.953 55.000 2.97 0.00 39.00 3.71
4391 20521 1.141657 CTATTGCTCTAGCCAGGCCAA 59.858 52.381 8.22 5.05 41.18 4.52
4401 20547 5.483937 TGGGTTCTTCTCAACTATTGCTCTA 59.516 40.000 0.00 0.00 0.00 2.43
4472 20624 5.672653 TCTCCTCTTTCCATAGAGACCTCTA 59.327 44.000 8.98 8.98 43.54 2.43
4473 20625 4.480537 TCTCCTCTTTCCATAGAGACCTCT 59.519 45.833 4.81 4.81 43.54 3.69
4494 20646 6.823689 ACGGTTATATGCAAAAACAGAGATCT 59.176 34.615 13.41 0.00 0.00 2.75
4496 20648 7.250569 CAACGGTTATATGCAAAAACAGAGAT 58.749 34.615 13.41 1.38 0.00 2.75
4558 20748 5.888161 TCAAGTGAGCAGTCTATGTCATCTA 59.112 40.000 0.00 0.00 0.00 1.98
4581 20782 3.498777 GCTGAAGGTTTGAAGTAGTGGTC 59.501 47.826 0.00 0.00 0.00 4.02
4582 20783 3.136626 AGCTGAAGGTTTGAAGTAGTGGT 59.863 43.478 0.00 0.00 0.00 4.16
4583 20784 3.744660 AGCTGAAGGTTTGAAGTAGTGG 58.255 45.455 0.00 0.00 0.00 4.00
4584 20785 4.636249 AGAGCTGAAGGTTTGAAGTAGTG 58.364 43.478 0.00 0.00 0.00 2.74
4585 20786 4.591072 AGAGAGCTGAAGGTTTGAAGTAGT 59.409 41.667 0.00 0.00 0.00 2.73
4586 20787 5.146010 AGAGAGCTGAAGGTTTGAAGTAG 57.854 43.478 0.00 0.00 0.00 2.57
4587 20788 5.300752 CAAGAGAGCTGAAGGTTTGAAGTA 58.699 41.667 0.00 0.00 0.00 2.24
4588 20789 4.133078 CAAGAGAGCTGAAGGTTTGAAGT 58.867 43.478 0.00 0.00 0.00 3.01
4589 20790 3.501445 CCAAGAGAGCTGAAGGTTTGAAG 59.499 47.826 0.00 0.00 0.00 3.02
4590 20791 3.136443 TCCAAGAGAGCTGAAGGTTTGAA 59.864 43.478 0.00 0.00 0.00 2.69
4591 20792 2.705658 TCCAAGAGAGCTGAAGGTTTGA 59.294 45.455 0.00 0.00 0.00 2.69
4596 20797 1.622811 ACAGTCCAAGAGAGCTGAAGG 59.377 52.381 0.00 0.00 31.76 3.46
4613 20814 2.917933 TGGTCAGACTGAACCAAACAG 58.082 47.619 17.86 0.00 40.68 3.16
4615 20816 3.632145 ACAATGGTCAGACTGAACCAAAC 59.368 43.478 22.45 6.14 31.76 2.93
4682 21031 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
4683 21032 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
4684 21033 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
4685 21034 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
4686 21035 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
4687 21036 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
4688 21037 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
4689 21038 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
4690 21039 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
4691 21040 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
4692 21041 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
4699 21048 9.569167 CGTATGTAGACAAATCTAAGACAAGAA 57.431 33.333 0.00 0.00 39.20 2.52
4700 21049 8.188799 CCGTATGTAGACAAATCTAAGACAAGA 58.811 37.037 0.00 0.00 39.20 3.02
4701 21050 8.188799 TCCGTATGTAGACAAATCTAAGACAAG 58.811 37.037 0.00 0.00 39.20 3.16
4702 21051 8.058667 TCCGTATGTAGACAAATCTAAGACAA 57.941 34.615 0.00 0.00 39.20 3.18
4703 21052 7.634671 TCCGTATGTAGACAAATCTAAGACA 57.365 36.000 0.00 0.00 39.20 3.41
4704 21053 8.136165 ACATCCGTATGTAGACAAATCTAAGAC 58.864 37.037 0.00 0.00 44.66 3.01
4705 21054 8.234136 ACATCCGTATGTAGACAAATCTAAGA 57.766 34.615 0.00 0.00 44.66 2.10
4723 21072 9.261180 CACTAAAATGTGAATAGATACATCCGT 57.739 33.333 0.00 0.00 40.12 4.69
4724 21073 9.261180 ACACTAAAATGTGAATAGATACATCCG 57.739 33.333 1.47 0.00 40.12 4.18
4736 21085 9.093970 CGGATGTATCTAACACTAAAATGTGAA 57.906 33.333 1.47 0.00 42.09 3.18
4737 21086 8.255206 ACGGATGTATCTAACACTAAAATGTGA 58.745 33.333 1.47 0.00 42.09 3.58
4738 21087 8.420374 ACGGATGTATCTAACACTAAAATGTG 57.580 34.615 0.00 0.00 42.09 3.21
4773 21122 9.720769 TCCGTCTTAAAATTCTTGTCTTAGATT 57.279 29.630 0.00 0.00 0.00 2.40
4774 21123 9.372369 CTCCGTCTTAAAATTCTTGTCTTAGAT 57.628 33.333 0.00 0.00 0.00 1.98
4775 21124 7.817962 CCTCCGTCTTAAAATTCTTGTCTTAGA 59.182 37.037 0.00 0.00 0.00 2.10
4776 21125 7.064728 CCCTCCGTCTTAAAATTCTTGTCTTAG 59.935 40.741 0.00 0.00 0.00 2.18
4777 21126 6.877322 CCCTCCGTCTTAAAATTCTTGTCTTA 59.123 38.462 0.00 0.00 0.00 2.10
4778 21127 5.705905 CCCTCCGTCTTAAAATTCTTGTCTT 59.294 40.000 0.00 0.00 0.00 3.01
4779 21128 5.012768 TCCCTCCGTCTTAAAATTCTTGTCT 59.987 40.000 0.00 0.00 0.00 3.41
4780 21129 5.243207 TCCCTCCGTCTTAAAATTCTTGTC 58.757 41.667 0.00 0.00 0.00 3.18
4781 21130 5.221864 ACTCCCTCCGTCTTAAAATTCTTGT 60.222 40.000 0.00 0.00 0.00 3.16
4782 21131 5.246307 ACTCCCTCCGTCTTAAAATTCTTG 58.754 41.667 0.00 0.00 0.00 3.02
4783 21132 5.500546 ACTCCCTCCGTCTTAAAATTCTT 57.499 39.130 0.00 0.00 0.00 2.52
4784 21133 5.720520 ACTACTCCCTCCGTCTTAAAATTCT 59.279 40.000 0.00 0.00 0.00 2.40
4785 21134 5.975282 ACTACTCCCTCCGTCTTAAAATTC 58.025 41.667 0.00 0.00 0.00 2.17
4786 21135 7.672122 ATACTACTCCCTCCGTCTTAAAATT 57.328 36.000 0.00 0.00 0.00 1.82
4787 21136 8.773033 TTATACTACTCCCTCCGTCTTAAAAT 57.227 34.615 0.00 0.00 0.00 1.82
4788 21137 8.773033 ATTATACTACTCCCTCCGTCTTAAAA 57.227 34.615 0.00 0.00 0.00 1.52
4789 21138 9.866655 TTATTATACTACTCCCTCCGTCTTAAA 57.133 33.333 0.00 0.00 0.00 1.52
4790 21139 9.866655 TTTATTATACTACTCCCTCCGTCTTAA 57.133 33.333 0.00 0.00 0.00 1.85
4791 21140 9.512588 CTTTATTATACTACTCCCTCCGTCTTA 57.487 37.037 0.00 0.00 0.00 2.10
4792 21141 7.039853 GCTTTATTATACTACTCCCTCCGTCTT 60.040 40.741 0.00 0.00 0.00 3.01
4793 21142 6.433716 GCTTTATTATACTACTCCCTCCGTCT 59.566 42.308 0.00 0.00 0.00 4.18
4794 21143 6.208204 TGCTTTATTATACTACTCCCTCCGTC 59.792 42.308 0.00 0.00 0.00 4.79
4795 21144 6.073314 TGCTTTATTATACTACTCCCTCCGT 58.927 40.000 0.00 0.00 0.00 4.69
4796 21145 6.585695 TGCTTTATTATACTACTCCCTCCG 57.414 41.667 0.00 0.00 0.00 4.63
4797 21146 6.867293 CGTTGCTTTATTATACTACTCCCTCC 59.133 42.308 0.00 0.00 0.00 4.30
4798 21147 7.432059 ACGTTGCTTTATTATACTACTCCCTC 58.568 38.462 0.00 0.00 0.00 4.30
4799 21148 7.357429 ACGTTGCTTTATTATACTACTCCCT 57.643 36.000 0.00 0.00 0.00 4.20
4800 21149 9.702494 AATACGTTGCTTTATTATACTACTCCC 57.298 33.333 0.00 0.00 0.00 4.30
4822 21171 2.035832 ACAGCACTTGGGTTGCAAATAC 59.964 45.455 0.00 0.00 0.00 1.89
4928 21371 7.786178 AAAGAGGTTAACAAAGCAAATTTCC 57.214 32.000 8.10 0.00 0.00 3.13
5027 21490 2.448582 TTGGACCGCACCTCCAAGT 61.449 57.895 3.19 0.00 41.92 3.16
5040 21509 1.747355 AGCAGCAGCACAATATTGGAC 59.253 47.619 19.37 10.60 45.49 4.02
5062 21531 5.185454 TCATTGTCAACCAGCATAGTAAGG 58.815 41.667 0.00 0.00 0.00 2.69
5074 21543 2.821969 AGGTTCTGCATCATTGTCAACC 59.178 45.455 0.00 0.00 32.42 3.77
5078 21547 4.456911 TCTTTCAGGTTCTGCATCATTGTC 59.543 41.667 0.00 0.00 0.00 3.18
5080 21549 5.340803 CATCTTTCAGGTTCTGCATCATTG 58.659 41.667 0.00 0.00 0.00 2.82
5081 21550 4.142227 GCATCTTTCAGGTTCTGCATCATT 60.142 41.667 0.00 0.00 0.00 2.57
5082 21551 3.380637 GCATCTTTCAGGTTCTGCATCAT 59.619 43.478 0.00 0.00 0.00 2.45
5084 21553 3.015327 AGCATCTTTCAGGTTCTGCATC 58.985 45.455 0.00 0.00 32.18 3.91


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

AutoCloner maintained by Alex Coulton.