Multiple sequence alignment - TraesCS3A01G082500

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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 TraesCS3A01G082500 chr3A 100.000 2879 0 0 1 2879 53295041 53292163 0.000000e+00 5317.0
1 TraesCS3A01G082500 chr3A 92.904 606 34 7 2281 2879 725187352 725186749 0.000000e+00 872.0
2 TraesCS3A01G082500 chr3A 92.051 629 35 8 2258 2879 745512309 745511689 0.000000e+00 870.0
3 TraesCS3A01G082500 chr3A 87.912 91 11 0 2165 2255 490628180 490628270 1.090000e-19 108.0
4 TraesCS3A01G082500 chr3B 88.804 920 78 16 1 904 65339856 65338946 0.000000e+00 1105.0
5 TraesCS3A01G082500 chr3B 93.750 656 41 0 1185 1840 65336266 65335611 0.000000e+00 985.0
6 TraesCS3A01G082500 chr3B 94.737 171 8 1 1989 2158 65335555 65335385 6.120000e-67 265.0
7 TraesCS3A01G082500 chr3B 95.536 112 4 1 984 1095 65338789 65338679 8.200000e-41 178.0
8 TraesCS3A01G082500 chr3B 89.474 95 9 1 2165 2259 811753616 811753523 5.040000e-23 119.0
9 TraesCS3A01G082500 chr3B 88.660 97 6 2 1095 1186 65336403 65336307 2.340000e-21 113.0
10 TraesCS3A01G082500 chr3D 95.994 649 23 3 1194 1840 42396168 42396815 0.000000e+00 1051.0
11 TraesCS3A01G082500 chr3D 95.175 456 9 5 460 904 42395273 42395726 0.000000e+00 708.0
12 TraesCS3A01G082500 chr3D 87.708 480 47 12 1 475 42394772 42395244 1.510000e-152 549.0
13 TraesCS3A01G082500 chr3D 97.326 187 5 0 984 1170 42395881 42396067 4.630000e-83 318.0
14 TraesCS3A01G082500 chr3D 93.567 171 10 1 1989 2158 42396877 42397047 1.320000e-63 254.0
15 TraesCS3A01G082500 chr6D 94.472 615 34 0 1226 1840 18534339 18534953 0.000000e+00 948.0
16 TraesCS3A01G082500 chr6D 93.028 459 16 5 460 904 18533105 18533561 0.000000e+00 656.0
17 TraesCS3A01G082500 chr6D 85.374 629 71 12 1218 1840 455496883 455496270 1.460000e-177 632.0
18 TraesCS3A01G082500 chr6D 96.552 203 7 0 984 1186 18533711 18533913 1.280000e-88 337.0
19 TraesCS3A01G082500 chr6D 88.476 269 14 5 485 736 455497820 455497552 2.790000e-80 309.0
20 TraesCS3A01G082500 chr6D 91.477 176 15 0 729 904 455497383 455497208 2.870000e-60 243.0
21 TraesCS3A01G082500 chr6D 92.715 151 10 1 2009 2158 18534995 18535145 1.740000e-52 217.0
22 TraesCS3A01G082500 chr6D 88.701 177 11 1 987 1163 455497049 455496882 1.050000e-49 207.0
23 TraesCS3A01G082500 chr6D 92.308 65 5 0 992 1056 455498479 455498543 3.050000e-15 93.5
24 TraesCS3A01G082500 chr6D 100.000 29 0 0 1195 1223 319701444 319701472 1.000000e-03 54.7
25 TraesCS3A01G082500 chr6D 94.118 34 2 0 199 232 429480317 429480350 5.000000e-03 52.8
26 TraesCS3A01G082500 chr1A 93.157 643 32 6 2248 2879 517644670 517644029 0.000000e+00 933.0
27 TraesCS3A01G082500 chr1A 91.538 650 40 8 2243 2879 386380003 386380650 0.000000e+00 881.0
28 TraesCS3A01G082500 chr1A 93.939 132 8 0 1844 1975 27289565 27289696 1.750000e-47 200.0
29 TraesCS3A01G082500 chr6A 93.207 633 34 6 2256 2879 581810753 581810121 0.000000e+00 922.0
30 TraesCS3A01G082500 chr6A 85.315 429 27 12 508 903 602163148 602162723 7.420000e-111 411.0
31 TraesCS3A01G082500 chr6A 92.308 65 5 0 992 1056 602164936 602165000 3.050000e-15 93.5
32 TraesCS3A01G082500 chr5A 92.947 638 34 6 2252 2879 399434632 399435268 0.000000e+00 918.0
33 TraesCS3A01G082500 chr5A 92.722 632 37 5 2256 2879 606836049 606835419 0.000000e+00 904.0
34 TraesCS3A01G082500 chr5A 88.406 69 7 1 2165 2233 320796876 320796809 6.610000e-12 82.4
35 TraesCS3A01G082500 chr2A 92.868 631 35 7 2258 2879 394263917 394263288 0.000000e+00 907.0
36 TraesCS3A01G082500 chr2A 95.276 127 6 0 1849 1975 293062987 293062861 4.860000e-48 202.0
37 TraesCS3A01G082500 chr2A 90.604 149 12 2 1838 1986 727783178 727783324 2.260000e-46 196.0
38 TraesCS3A01G082500 chr1B 91.108 641 42 10 2252 2879 516964957 516964319 0.000000e+00 854.0
39 TraesCS3A01G082500 chr1B 94.656 131 7 0 1845 1975 102142258 102142128 1.350000e-48 204.0
40 TraesCS3A01G082500 chr1B 90.789 152 12 2 1845 1996 669017048 669017197 4.860000e-48 202.0
41 TraesCS3A01G082500 chr1B 100.000 30 0 0 1192 1221 688379591 688379562 4.010000e-04 56.5
42 TraesCS3A01G082500 chr6B 85.095 577 74 8 1267 1840 692719315 692718748 1.920000e-161 579.0
43 TraesCS3A01G082500 chr6B 86.147 462 37 18 460 904 692639046 692638595 9.340000e-130 473.0
44 TraesCS3A01G082500 chr6B 92.737 179 13 0 1662 1840 692638358 692638180 2.850000e-65 259.0
45 TraesCS3A01G082500 chr6B 83.333 180 13 9 988 1163 692720660 692720494 1.790000e-32 150.0
46 TraesCS3A01G082500 chr6B 93.151 73 5 0 987 1059 692638436 692638364 1.090000e-19 108.0
47 TraesCS3A01G082500 chr6B 85.227 88 10 3 1990 2075 692718717 692718631 1.420000e-13 87.9
48 TraesCS3A01G082500 chr6B 80.303 132 10 8 530 651 692721307 692721182 5.110000e-13 86.1
49 TraesCS3A01G082500 chr7A 95.276 127 6 0 1849 1975 729886497 729886623 4.860000e-48 202.0
50 TraesCS3A01G082500 chr5B 93.284 134 9 0 1842 1975 82212307 82212174 6.290000e-47 198.0
51 TraesCS3A01G082500 chr4A 93.798 129 8 0 1847 1975 165056665 165056537 8.140000e-46 195.0
52 TraesCS3A01G082500 chr2B 90.604 149 9 4 1849 1996 411977593 411977449 2.930000e-45 193.0
53 TraesCS3A01G082500 chr2B 97.297 37 1 0 1185 1221 33851511 33851547 2.390000e-06 63.9
54 TraesCS3A01G082500 chr2B 97.297 37 1 0 1185 1221 33861120 33861156 2.390000e-06 63.9
55 TraesCS3A01G082500 chr2B 92.500 40 3 0 1183 1222 639969522 639969561 1.110000e-04 58.4
56 TraesCS3A01G082500 chr4D 92.105 38 3 0 1185 1222 80223060 80223097 1.000000e-03 54.7
57 TraesCS3A01G082500 chr4B 100.000 28 0 0 1194 1221 409939592 409939565 5.000000e-03 52.8


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 TraesCS3A01G082500 chr3A 53292163 53295041 2878 True 5317.00 5317 100.000000 1 2879 1 chr3A.!!$R1 2878
1 TraesCS3A01G082500 chr3A 725186749 725187352 603 True 872.00 872 92.904000 2281 2879 1 chr3A.!!$R2 598
2 TraesCS3A01G082500 chr3A 745511689 745512309 620 True 870.00 870 92.051000 2258 2879 1 chr3A.!!$R3 621
3 TraesCS3A01G082500 chr3B 65335385 65339856 4471 True 529.20 1105 92.297400 1 2158 5 chr3B.!!$R2 2157
4 TraesCS3A01G082500 chr3D 42394772 42397047 2275 False 576.00 1051 93.954000 1 2158 5 chr3D.!!$F1 2157
5 TraesCS3A01G082500 chr6D 18533105 18535145 2040 False 539.50 948 94.191750 460 2158 4 chr6D.!!$F4 1698
6 TraesCS3A01G082500 chr6D 455496270 455497820 1550 True 347.75 632 88.507000 485 1840 4 chr6D.!!$R1 1355
7 TraesCS3A01G082500 chr1A 517644029 517644670 641 True 933.00 933 93.157000 2248 2879 1 chr1A.!!$R1 631
8 TraesCS3A01G082500 chr1A 386380003 386380650 647 False 881.00 881 91.538000 2243 2879 1 chr1A.!!$F2 636
9 TraesCS3A01G082500 chr6A 581810121 581810753 632 True 922.00 922 93.207000 2256 2879 1 chr6A.!!$R1 623
10 TraesCS3A01G082500 chr5A 399434632 399435268 636 False 918.00 918 92.947000 2252 2879 1 chr5A.!!$F1 627
11 TraesCS3A01G082500 chr5A 606835419 606836049 630 True 904.00 904 92.722000 2256 2879 1 chr5A.!!$R2 623
12 TraesCS3A01G082500 chr2A 394263288 394263917 629 True 907.00 907 92.868000 2258 2879 1 chr2A.!!$R2 621
13 TraesCS3A01G082500 chr1B 516964319 516964957 638 True 854.00 854 91.108000 2252 2879 1 chr1B.!!$R2 627
14 TraesCS3A01G082500 chr6B 692638180 692639046 866 True 280.00 473 90.678333 460 1840 3 chr6B.!!$R1 1380
15 TraesCS3A01G082500 chr6B 692718631 692721307 2676 True 225.75 579 83.489500 530 2075 4 chr6B.!!$R2 1545

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
438 443 1.143183 CGCTACAGTACCCCGCAAT 59.857 57.895 0.0 0.0 0.0 3.56 F
1084 1613 1.064505 CCCAAGCTAATGATGCACACG 59.935 52.381 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 5989 0.827925 TCGACTGTCTCCCAGCAACT 60.828 55.0 6.21 0.0 45.68 3.16 R
2013 6495 0.922626 ATTCTCCTTTCCAGCTCCCC 59.077 55.0 0.00 0.0 0.00 4.81 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
144 145 6.347270 TGTGCACAGATTCAAAAATTGTTG 57.653 33.333 17.42 1.55 0.00 3.33
150 151 9.749490 GCACAGATTCAAAAATTGTTGATATTG 57.251 29.630 11.86 11.83 37.36 1.90
438 443 1.143183 CGCTACAGTACCCCGCAAT 59.857 57.895 0.00 0.00 0.00 3.56
689 828 5.381174 AGTTCACAATTCCACATCACATG 57.619 39.130 0.00 0.00 0.00 3.21
772 1087 1.283181 GATATCGCTCACGTCGCCT 59.717 57.895 0.00 0.00 41.18 5.52
922 1450 6.826741 AGCCGCCTTAAATATCTTCTTTTGTA 59.173 34.615 0.00 0.00 0.00 2.41
923 1451 6.910972 GCCGCCTTAAATATCTTCTTTTGTAC 59.089 38.462 0.00 0.00 0.00 2.90
924 1452 7.201705 GCCGCCTTAAATATCTTCTTTTGTACT 60.202 37.037 0.00 0.00 0.00 2.73
925 1453 8.336080 CCGCCTTAAATATCTTCTTTTGTACTC 58.664 37.037 0.00 0.00 0.00 2.59
926 1454 8.336080 CGCCTTAAATATCTTCTTTTGTACTCC 58.664 37.037 0.00 0.00 0.00 3.85
927 1455 8.622157 GCCTTAAATATCTTCTTTTGTACTCCC 58.378 37.037 0.00 0.00 0.00 4.30
936 1464 8.672823 TCTTCTTTTGTACTCCCTCTTTAAAC 57.327 34.615 0.00 0.00 0.00 2.01
948 1476 9.397280 ACTCCCTCTTTAAACTAATATGAAAGC 57.603 33.333 0.00 0.00 0.00 3.51
949 1477 8.433421 TCCCTCTTTAAACTAATATGAAAGCG 57.567 34.615 0.00 0.00 0.00 4.68
950 1478 8.044908 TCCCTCTTTAAACTAATATGAAAGCGT 58.955 33.333 0.00 0.00 0.00 5.07
951 1479 8.674607 CCCTCTTTAAACTAATATGAAAGCGTT 58.325 33.333 0.00 0.00 0.00 4.84
952 1480 9.490663 CCTCTTTAAACTAATATGAAAGCGTTG 57.509 33.333 0.00 0.00 0.00 4.10
954 1482 9.820229 TCTTTAAACTAATATGAAAGCGTTGTG 57.180 29.630 0.00 0.00 0.00 3.33
955 1483 9.820229 CTTTAAACTAATATGAAAGCGTTGTGA 57.180 29.630 0.00 0.00 0.00 3.58
957 1485 9.820229 TTAAACTAATATGAAAGCGTTGTGAAG 57.180 29.630 0.00 0.00 0.00 3.02
958 1486 7.435068 AACTAATATGAAAGCGTTGTGAAGT 57.565 32.000 0.00 0.00 0.00 3.01
959 1487 7.435068 ACTAATATGAAAGCGTTGTGAAGTT 57.565 32.000 0.00 0.00 0.00 2.66
960 1488 7.871853 ACTAATATGAAAGCGTTGTGAAGTTT 58.128 30.769 0.00 0.00 0.00 2.66
961 1489 8.349983 ACTAATATGAAAGCGTTGTGAAGTTTT 58.650 29.630 0.00 0.00 0.00 2.43
962 1490 9.180678 CTAATATGAAAGCGTTGTGAAGTTTTT 57.819 29.630 0.00 0.00 0.00 1.94
964 1492 9.691362 AATATGAAAGCGTTGTGAAGTTTTTAT 57.309 25.926 0.00 0.00 0.00 1.40
967 1495 9.691362 ATGAAAGCGTTGTGAAGTTTTTATATT 57.309 25.926 0.00 0.00 0.00 1.28
1084 1613 1.064505 CCCAAGCTAATGATGCACACG 59.935 52.381 0.00 0.00 0.00 4.49
1116 3921 1.839747 TGTAGGTTCAGTGCCGGGT 60.840 57.895 2.18 0.00 0.00 5.28
1163 3976 4.201970 CGAGCAGTTCCCAACTTTGTTTAA 60.202 41.667 0.00 0.00 40.46 1.52
1187 4487 4.264352 TGCTCCCTCTGTCCCAAAATAAAT 60.264 41.667 0.00 0.00 0.00 1.40
1192 4492 8.728596 TCCCTCTGTCCCAAAATAAATTTAAA 57.271 30.769 1.21 0.00 0.00 1.52
1212 4512 7.527568 TTAAAACACTTATTTTGGGACGGAT 57.472 32.000 0.00 0.00 33.80 4.18
1334 5773 2.353579 GCGCCTTTTACCGTTACATGAT 59.646 45.455 0.00 0.00 0.00 2.45
1337 5776 4.272504 CGCCTTTTACCGTTACATGATCAT 59.727 41.667 1.18 1.18 0.00 2.45
1345 5784 6.363577 ACCGTTACATGATCATCACAATTC 57.636 37.500 4.86 0.00 0.00 2.17
1358 5797 6.039616 TCATCACAATTCAATCACATGCATG 58.960 36.000 25.09 25.09 0.00 4.06
1442 5883 4.160736 TCGAGATATGTGCCAAGATACG 57.839 45.455 0.00 0.00 0.00 3.06
1548 5989 3.253188 CGTTTCAAGAAGCCTCATTTGGA 59.747 43.478 0.00 0.00 0.00 3.53
1560 6001 1.704628 TCATTTGGAGTTGCTGGGAGA 59.295 47.619 0.00 0.00 0.00 3.71
1718 6159 0.320946 TTCCCACGTAAGAAAGCCGG 60.321 55.000 0.00 0.00 43.62 6.13
1840 6281 2.715749 TGTCTGGGGCATTGTGATAG 57.284 50.000 0.00 0.00 0.00 2.08
1841 6282 1.915489 TGTCTGGGGCATTGTGATAGT 59.085 47.619 0.00 0.00 0.00 2.12
1842 6283 3.111484 TGTCTGGGGCATTGTGATAGTA 58.889 45.455 0.00 0.00 0.00 1.82
1843 6284 3.521531 TGTCTGGGGCATTGTGATAGTAA 59.478 43.478 0.00 0.00 0.00 2.24
1844 6285 4.130118 GTCTGGGGCATTGTGATAGTAAG 58.870 47.826 0.00 0.00 0.00 2.34
1845 6286 4.037222 TCTGGGGCATTGTGATAGTAAGA 58.963 43.478 0.00 0.00 0.00 2.10
1846 6287 4.473196 TCTGGGGCATTGTGATAGTAAGAA 59.527 41.667 0.00 0.00 0.00 2.52
1847 6288 4.780815 TGGGGCATTGTGATAGTAAGAAG 58.219 43.478 0.00 0.00 0.00 2.85
1848 6289 4.227300 TGGGGCATTGTGATAGTAAGAAGT 59.773 41.667 0.00 0.00 0.00 3.01
1849 6290 5.427157 TGGGGCATTGTGATAGTAAGAAGTA 59.573 40.000 0.00 0.00 0.00 2.24
1850 6291 5.758784 GGGGCATTGTGATAGTAAGAAGTAC 59.241 44.000 0.00 0.00 0.00 2.73
1851 6292 6.408206 GGGGCATTGTGATAGTAAGAAGTACT 60.408 42.308 0.00 0.00 45.42 2.73
1852 6293 6.702282 GGGCATTGTGATAGTAAGAAGTACTC 59.298 42.308 0.00 0.00 42.37 2.59
1853 6294 6.702282 GGCATTGTGATAGTAAGAAGTACTCC 59.298 42.308 0.00 0.00 42.37 3.85
1854 6295 6.702282 GCATTGTGATAGTAAGAAGTACTCCC 59.298 42.308 0.00 0.00 42.37 4.30
1855 6296 7.418025 GCATTGTGATAGTAAGAAGTACTCCCT 60.418 40.741 0.00 0.00 42.37 4.20
1856 6297 7.642082 TTGTGATAGTAAGAAGTACTCCCTC 57.358 40.000 0.00 0.00 42.37 4.30
1857 6298 6.127793 TGTGATAGTAAGAAGTACTCCCTCC 58.872 44.000 0.00 0.00 42.37 4.30
1858 6299 5.239087 GTGATAGTAAGAAGTACTCCCTCCG 59.761 48.000 0.00 0.00 42.37 4.63
1859 6300 3.735720 AGTAAGAAGTACTCCCTCCGT 57.264 47.619 0.00 0.00 38.84 4.69
1860 6301 4.044946 AGTAAGAAGTACTCCCTCCGTT 57.955 45.455 0.00 0.00 38.84 4.44
1861 6302 4.414677 AGTAAGAAGTACTCCCTCCGTTT 58.585 43.478 0.00 0.00 38.84 3.60
1862 6303 3.957591 AAGAAGTACTCCCTCCGTTTC 57.042 47.619 0.00 0.00 0.00 2.78
1863 6304 1.817447 AGAAGTACTCCCTCCGTTTCG 59.183 52.381 0.00 0.00 0.00 3.46
1864 6305 1.815003 GAAGTACTCCCTCCGTTTCGA 59.185 52.381 0.00 0.00 0.00 3.71
1865 6306 1.915141 AGTACTCCCTCCGTTTCGAA 58.085 50.000 0.00 0.00 0.00 3.71
1866 6307 2.454538 AGTACTCCCTCCGTTTCGAAT 58.545 47.619 0.00 0.00 0.00 3.34
1867 6308 2.830321 AGTACTCCCTCCGTTTCGAATT 59.170 45.455 0.00 0.00 0.00 2.17
1868 6309 4.019174 AGTACTCCCTCCGTTTCGAATTA 58.981 43.478 0.00 0.00 0.00 1.40
1869 6310 3.242549 ACTCCCTCCGTTTCGAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
1870 6311 2.830321 ACTCCCTCCGTTTCGAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
1871 6312 3.260128 ACTCCCTCCGTTTCGAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
1872 6313 3.592059 TCCCTCCGTTTCGAATTACTTG 58.408 45.455 0.00 0.00 0.00 3.16
1873 6314 3.007182 TCCCTCCGTTTCGAATTACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
1874 6315 3.370061 CCCTCCGTTTCGAATTACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
1875 6316 4.243270 CCTCCGTTTCGAATTACTTGTCT 58.757 43.478 0.00 0.00 0.00 3.41
1876 6317 4.689345 CCTCCGTTTCGAATTACTTGTCTT 59.311 41.667 0.00 0.00 0.00 3.01
1877 6318 5.389516 CCTCCGTTTCGAATTACTTGTCTTG 60.390 44.000 0.00 0.00 0.00 3.02
1878 6319 5.291178 TCCGTTTCGAATTACTTGTCTTGA 58.709 37.500 0.00 0.00 0.00 3.02
1879 6320 5.754406 TCCGTTTCGAATTACTTGTCTTGAA 59.246 36.000 0.00 0.00 0.00 2.69
1880 6321 6.425721 TCCGTTTCGAATTACTTGTCTTGAAT 59.574 34.615 0.00 0.00 0.00 2.57
1881 6322 7.041644 TCCGTTTCGAATTACTTGTCTTGAATT 60.042 33.333 0.00 0.00 0.00 2.17
1882 6323 7.589954 CCGTTTCGAATTACTTGTCTTGAATTT 59.410 33.333 0.00 0.00 0.00 1.82
1883 6324 8.409690 CGTTTCGAATTACTTGTCTTGAATTTG 58.590 33.333 0.00 0.00 0.00 2.32
1884 6325 9.233232 GTTTCGAATTACTTGTCTTGAATTTGT 57.767 29.630 0.00 0.00 0.00 2.83
1885 6326 9.445786 TTTCGAATTACTTGTCTTGAATTTGTC 57.554 29.630 0.00 0.00 0.00 3.18
1886 6327 8.378172 TCGAATTACTTGTCTTGAATTTGTCT 57.622 30.769 0.00 0.00 0.00 3.41
1887 6328 9.483916 TCGAATTACTTGTCTTGAATTTGTCTA 57.516 29.630 0.00 0.00 0.00 2.59
1888 6329 9.746711 CGAATTACTTGTCTTGAATTTGTCTAG 57.253 33.333 0.00 0.00 0.00 2.43
1893 6334 8.467402 ACTTGTCTTGAATTTGTCTAGATACG 57.533 34.615 0.00 0.00 39.77 3.06
1894 6335 7.545965 ACTTGTCTTGAATTTGTCTAGATACGG 59.454 37.037 0.00 0.00 39.77 4.02
1895 6336 7.165460 TGTCTTGAATTTGTCTAGATACGGA 57.835 36.000 0.00 0.00 39.77 4.69
1896 6337 7.782049 TGTCTTGAATTTGTCTAGATACGGAT 58.218 34.615 0.00 0.00 39.77 4.18
1897 6338 7.706607 TGTCTTGAATTTGTCTAGATACGGATG 59.293 37.037 0.00 0.00 39.77 3.51
1898 6339 7.707035 GTCTTGAATTTGTCTAGATACGGATGT 59.293 37.037 0.00 0.00 39.77 3.06
1899 6340 8.909923 TCTTGAATTTGTCTAGATACGGATGTA 58.090 33.333 0.00 0.00 33.79 2.29
1900 6341 9.698309 CTTGAATTTGTCTAGATACGGATGTAT 57.302 33.333 0.00 0.00 43.97 2.29
1916 6357 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
1917 6358 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
1918 6359 7.327275 CGGATGTATCTAGACTCATTTTAGTGC 59.673 40.741 11.25 0.00 0.00 4.40
1919 6360 8.364142 GGATGTATCTAGACTCATTTTAGTGCT 58.636 37.037 11.25 0.00 0.00 4.40
1928 6369 8.950208 AGACTCATTTTAGTGCTAAATACCTC 57.050 34.615 5.37 0.00 35.27 3.85
1929 6370 7.988028 AGACTCATTTTAGTGCTAAATACCTCC 59.012 37.037 5.37 0.00 35.27 4.30
1930 6371 6.761714 ACTCATTTTAGTGCTAAATACCTCCG 59.238 38.462 5.37 0.00 35.27 4.63
1931 6372 6.646267 TCATTTTAGTGCTAAATACCTCCGT 58.354 36.000 5.37 0.00 35.27 4.69
1932 6373 7.784037 TCATTTTAGTGCTAAATACCTCCGTA 58.216 34.615 5.37 0.00 35.27 4.02
1933 6374 8.426489 TCATTTTAGTGCTAAATACCTCCGTAT 58.574 33.333 5.37 0.00 36.72 3.06
1934 6375 8.495949 CATTTTAGTGCTAAATACCTCCGTATG 58.504 37.037 5.37 0.82 35.29 2.39
1935 6376 6.720112 TTAGTGCTAAATACCTCCGTATGT 57.280 37.500 0.00 0.00 35.29 2.29
1936 6377 7.822161 TTAGTGCTAAATACCTCCGTATGTA 57.178 36.000 0.00 0.00 35.29 2.29
1937 6378 6.328641 AGTGCTAAATACCTCCGTATGTAG 57.671 41.667 3.92 3.92 42.39 2.74
1938 6379 6.066690 AGTGCTAAATACCTCCGTATGTAGA 58.933 40.000 10.40 0.00 42.20 2.59
1939 6380 6.016443 AGTGCTAAATACCTCCGTATGTAGAC 60.016 42.308 10.40 6.74 42.20 2.59
1940 6381 5.829391 TGCTAAATACCTCCGTATGTAGACA 59.171 40.000 10.40 6.25 42.20 3.41
1941 6382 6.321945 TGCTAAATACCTCCGTATGTAGACAA 59.678 38.462 10.40 0.00 42.20 3.18
1942 6383 7.147863 TGCTAAATACCTCCGTATGTAGACAAA 60.148 37.037 10.40 0.00 42.20 2.83
1943 6384 7.871463 GCTAAATACCTCCGTATGTAGACAAAT 59.129 37.037 10.40 0.00 42.20 2.32
1944 6385 9.408069 CTAAATACCTCCGTATGTAGACAAATC 57.592 37.037 2.51 0.00 42.20 2.17
1945 6386 4.667519 ACCTCCGTATGTAGACAAATCC 57.332 45.455 0.00 0.00 0.00 3.01
1946 6387 4.028131 ACCTCCGTATGTAGACAAATCCA 58.972 43.478 0.00 0.00 0.00 3.41
1947 6388 4.468510 ACCTCCGTATGTAGACAAATCCAA 59.531 41.667 0.00 0.00 0.00 3.53
1948 6389 5.046159 ACCTCCGTATGTAGACAAATCCAAA 60.046 40.000 0.00 0.00 0.00 3.28
1949 6390 5.878116 CCTCCGTATGTAGACAAATCCAAAA 59.122 40.000 0.00 0.00 0.00 2.44
1950 6391 6.183360 CCTCCGTATGTAGACAAATCCAAAAC 60.183 42.308 0.00 0.00 0.00 2.43
1951 6392 6.231951 TCCGTATGTAGACAAATCCAAAACA 58.768 36.000 0.00 0.00 0.00 2.83
1952 6393 6.711194 TCCGTATGTAGACAAATCCAAAACAA 59.289 34.615 0.00 0.00 0.00 2.83
1953 6394 7.021196 CCGTATGTAGACAAATCCAAAACAAG 58.979 38.462 0.00 0.00 0.00 3.16
1954 6395 7.308348 CCGTATGTAGACAAATCCAAAACAAGT 60.308 37.037 0.00 0.00 0.00 3.16
1955 6396 8.714179 CGTATGTAGACAAATCCAAAACAAGTA 58.286 33.333 0.00 0.00 0.00 2.24
1959 6400 9.959749 TGTAGACAAATCCAAAACAAGTAATTC 57.040 29.630 0.00 0.00 0.00 2.17
1960 6401 9.113876 GTAGACAAATCCAAAACAAGTAATTCG 57.886 33.333 0.00 0.00 0.00 3.34
1961 6402 7.145323 AGACAAATCCAAAACAAGTAATTCGG 58.855 34.615 0.00 0.00 0.00 4.30
1962 6403 7.013846 AGACAAATCCAAAACAAGTAATTCGGA 59.986 33.333 0.00 0.00 0.00 4.55
1963 6404 7.493367 ACAAATCCAAAACAAGTAATTCGGAA 58.507 30.769 0.00 0.00 0.00 4.30
1964 6405 7.436970 ACAAATCCAAAACAAGTAATTCGGAAC 59.563 33.333 0.00 0.00 0.00 3.62
1965 6406 6.642707 ATCCAAAACAAGTAATTCGGAACA 57.357 33.333 0.00 0.00 0.00 3.18
1966 6407 6.067263 TCCAAAACAAGTAATTCGGAACAG 57.933 37.500 0.00 0.00 0.00 3.16
1967 6408 5.823570 TCCAAAACAAGTAATTCGGAACAGA 59.176 36.000 0.00 0.00 0.00 3.41
1968 6409 6.017440 TCCAAAACAAGTAATTCGGAACAGAG 60.017 38.462 0.00 0.00 0.00 3.35
2013 6495 5.245531 AGCATTTCGTACCATATACCATGG 58.754 41.667 11.19 11.19 44.54 3.66
2021 6503 1.283029 CCATATACCATGGGGGAGCTG 59.717 57.143 18.09 5.57 41.15 4.24
2043 6525 6.405176 GCTGGAAAGGAGAATTTATTGGACTG 60.405 42.308 0.00 0.00 0.00 3.51
2160 6643 9.755122 AATGTATCTTTAATAGGGAATAAGGCC 57.245 33.333 0.00 0.00 0.00 5.19
2161 6644 8.520119 TGTATCTTTAATAGGGAATAAGGCCT 57.480 34.615 0.00 0.00 0.00 5.19
2162 6645 8.955794 TGTATCTTTAATAGGGAATAAGGCCTT 58.044 33.333 24.18 24.18 0.00 4.35
2168 6651 8.950007 TTAATAGGGAATAAGGCCTTATTTGG 57.050 34.615 38.76 0.00 43.52 3.28
2169 6652 4.899898 AGGGAATAAGGCCTTATTTGGT 57.100 40.909 38.76 26.85 43.52 3.67
2170 6653 5.220872 AGGGAATAAGGCCTTATTTGGTT 57.779 39.130 38.76 24.91 43.52 3.67
2171 6654 5.599751 AGGGAATAAGGCCTTATTTGGTTT 58.400 37.500 38.76 24.29 43.52 3.27
2172 6655 6.747931 AGGGAATAAGGCCTTATTTGGTTTA 58.252 36.000 38.76 15.57 43.52 2.01
2173 6656 7.370238 AGGGAATAAGGCCTTATTTGGTTTAT 58.630 34.615 38.76 22.48 43.52 1.40
2174 6657 8.516198 AGGGAATAAGGCCTTATTTGGTTTATA 58.484 33.333 38.76 14.37 43.52 0.98
2175 6658 9.150028 GGGAATAAGGCCTTATTTGGTTTATAA 57.850 33.333 38.76 14.18 43.52 0.98
2180 6663 8.854237 AAGGCCTTATTTGGTTTATAAATCCT 57.146 30.769 18.87 0.00 0.00 3.24
2181 6664 9.945633 AAGGCCTTATTTGGTTTATAAATCCTA 57.054 29.630 18.87 2.34 0.00 2.94
2217 6700 9.886132 TTAATCCCAACTTATAAGTCTCAAGTC 57.114 33.333 18.28 0.00 38.57 3.01
2218 6701 7.741554 ATCCCAACTTATAAGTCTCAAGTCT 57.258 36.000 18.28 0.00 38.57 3.24
2219 6702 7.554959 TCCCAACTTATAAGTCTCAAGTCTT 57.445 36.000 18.28 0.00 38.57 3.01
2220 6703 7.974504 TCCCAACTTATAAGTCTCAAGTCTTT 58.025 34.615 18.28 0.00 38.57 2.52
2221 6704 9.096823 TCCCAACTTATAAGTCTCAAGTCTTTA 57.903 33.333 18.28 0.00 38.57 1.85
2222 6705 9.720769 CCCAACTTATAAGTCTCAAGTCTTTAA 57.279 33.333 18.28 0.00 38.57 1.52
2230 6713 7.569639 AAGTCTCAAGTCTTTAAAAAGTCCC 57.430 36.000 2.58 0.00 37.31 4.46
2231 6714 6.901300 AGTCTCAAGTCTTTAAAAAGTCCCT 58.099 36.000 2.58 0.00 37.31 4.20
2232 6715 8.030913 AGTCTCAAGTCTTTAAAAAGTCCCTA 57.969 34.615 2.58 0.00 37.31 3.53
2233 6716 7.932491 AGTCTCAAGTCTTTAAAAAGTCCCTAC 59.068 37.037 2.58 0.00 37.31 3.18
2234 6717 7.713942 GTCTCAAGTCTTTAAAAAGTCCCTACA 59.286 37.037 2.58 0.00 37.31 2.74
2235 6718 8.437575 TCTCAAGTCTTTAAAAAGTCCCTACAT 58.562 33.333 2.58 0.00 37.31 2.29
2236 6719 8.391075 TCAAGTCTTTAAAAAGTCCCTACATG 57.609 34.615 2.58 0.00 37.31 3.21
2237 6720 7.996644 TCAAGTCTTTAAAAAGTCCCTACATGT 59.003 33.333 2.69 2.69 37.31 3.21
2238 6721 8.630037 CAAGTCTTTAAAAAGTCCCTACATGTT 58.370 33.333 2.30 0.00 37.31 2.71
2239 6722 8.762481 AGTCTTTAAAAAGTCCCTACATGTTT 57.238 30.769 2.30 0.00 37.31 2.83
2240 6723 8.630037 AGTCTTTAAAAAGTCCCTACATGTTTG 58.370 33.333 2.30 0.00 37.31 2.93
2241 6724 7.865889 GTCTTTAAAAAGTCCCTACATGTTTGG 59.134 37.037 2.30 7.15 37.31 3.28
2242 6725 7.562088 TCTTTAAAAAGTCCCTACATGTTTGGT 59.438 33.333 2.30 0.00 37.31 3.67
2243 6726 7.663043 TTAAAAAGTCCCTACATGTTTGGTT 57.337 32.000 2.30 0.00 0.00 3.67
2244 6727 5.784578 AAAAGTCCCTACATGTTTGGTTC 57.215 39.130 2.30 3.85 0.00 3.62
2245 6728 4.724279 AAGTCCCTACATGTTTGGTTCT 57.276 40.909 2.30 5.94 0.00 3.01
2246 6729 4.724279 AGTCCCTACATGTTTGGTTCTT 57.276 40.909 2.30 0.00 0.00 2.52
2276 6759 3.665675 GAGCATCTCCAACGGCCGT 62.666 63.158 28.70 28.70 0.00 5.68
2307 6790 3.544567 CGCGCGGGGTAACGTAAC 61.545 66.667 24.84 0.00 35.98 2.50
2309 6792 1.737735 GCGCGGGGTAACGTAACTT 60.738 57.895 8.83 0.00 35.98 2.66
2312 6795 2.333014 CGCGGGGTAACGTAACTTTTA 58.667 47.619 0.00 0.00 35.98 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 9.487790 TCCAAACATTCCTTTTTCAAATATGAC 57.512 29.630 0.00 0.00 34.61 3.06
105 106 8.729805 TCTGTGCACAAAATTTTAAAATCCTT 57.270 26.923 21.98 7.89 0.00 3.36
117 118 7.987649 ACAATTTTTGAATCTGTGCACAAAAT 58.012 26.923 21.98 17.59 40.29 1.82
124 125 9.749490 CAATATCAACAATTTTTGAATCTGTGC 57.251 29.630 10.87 0.00 38.95 4.57
291 294 8.296000 CCCAAACAGTTTCTTTGAAAATTTTGT 58.704 29.630 8.47 0.00 31.32 2.83
316 319 3.626217 ACCAAGAACGTTCTTTGAAGACC 59.374 43.478 35.50 8.39 44.70 3.85
369 373 5.765677 TGATAACATGTTTCGGAAAAGGTGA 59.234 36.000 17.78 0.00 0.00 4.02
378 382 5.511377 CGGTCAATTTGATAACATGTTTCGG 59.489 40.000 17.78 0.00 0.00 4.30
385 389 4.675146 GCAGCACGGTCAATTTGATAACAT 60.675 41.667 1.78 0.00 0.00 2.71
454 459 2.483877 TGCCTATTTGACGCTTGAAGTG 59.516 45.455 3.88 3.88 0.00 3.16
455 460 2.484264 GTGCCTATTTGACGCTTGAAGT 59.516 45.455 0.00 0.00 0.00 3.01
456 461 2.159517 GGTGCCTATTTGACGCTTGAAG 60.160 50.000 0.00 0.00 0.00 3.02
457 462 1.810151 GGTGCCTATTTGACGCTTGAA 59.190 47.619 0.00 0.00 0.00 2.69
615 685 0.835941 CTGGAGCTTGGAGGTGCTAT 59.164 55.000 0.00 0.00 39.91 2.97
922 1450 9.397280 GCTTTCATATTAGTTTAAAGAGGGAGT 57.603 33.333 0.00 0.00 30.44 3.85
923 1451 8.552034 CGCTTTCATATTAGTTTAAAGAGGGAG 58.448 37.037 0.00 0.00 30.44 4.30
924 1452 8.044908 ACGCTTTCATATTAGTTTAAAGAGGGA 58.955 33.333 0.00 0.00 33.13 4.20
925 1453 8.209917 ACGCTTTCATATTAGTTTAAAGAGGG 57.790 34.615 0.00 0.00 33.13 4.30
926 1454 9.490663 CAACGCTTTCATATTAGTTTAAAGAGG 57.509 33.333 0.00 0.00 33.13 3.69
932 1460 8.995220 ACTTCACAACGCTTTCATATTAGTTTA 58.005 29.630 0.00 0.00 0.00 2.01
933 1461 7.871853 ACTTCACAACGCTTTCATATTAGTTT 58.128 30.769 0.00 0.00 0.00 2.66
935 1463 7.435068 AACTTCACAACGCTTTCATATTAGT 57.565 32.000 0.00 0.00 0.00 2.24
936 1464 8.728088 AAAACTTCACAACGCTTTCATATTAG 57.272 30.769 0.00 0.00 0.00 1.73
941 1469 9.691362 AATATAAAAACTTCACAACGCTTTCAT 57.309 25.926 0.00 0.00 0.00 2.57
965 1493 8.887717 ACGTACGTATTCTCTCTGTAAACTAAT 58.112 33.333 21.41 0.00 0.00 1.73
966 1494 8.256611 ACGTACGTATTCTCTCTGTAAACTAA 57.743 34.615 21.41 0.00 0.00 2.24
967 1495 7.834068 ACGTACGTATTCTCTCTGTAAACTA 57.166 36.000 21.41 0.00 0.00 2.24
968 1496 6.734104 ACGTACGTATTCTCTCTGTAAACT 57.266 37.500 21.41 0.00 0.00 2.66
969 1497 6.237149 GCAACGTACGTATTCTCTCTGTAAAC 60.237 42.308 23.12 0.00 0.00 2.01
970 1498 5.796935 GCAACGTACGTATTCTCTCTGTAAA 59.203 40.000 23.12 0.00 0.00 2.01
971 1499 5.106594 TGCAACGTACGTATTCTCTCTGTAA 60.107 40.000 23.12 3.90 0.00 2.41
972 1500 4.392754 TGCAACGTACGTATTCTCTCTGTA 59.607 41.667 23.12 10.16 0.00 2.74
973 1501 3.189910 TGCAACGTACGTATTCTCTCTGT 59.810 43.478 23.12 0.00 0.00 3.41
974 1502 3.754955 TGCAACGTACGTATTCTCTCTG 58.245 45.455 23.12 14.32 0.00 3.35
975 1503 3.731264 GCTGCAACGTACGTATTCTCTCT 60.731 47.826 23.12 0.00 0.00 3.10
976 1504 2.530700 GCTGCAACGTACGTATTCTCTC 59.469 50.000 23.12 6.43 0.00 3.20
977 1505 2.527100 GCTGCAACGTACGTATTCTCT 58.473 47.619 23.12 0.97 0.00 3.10
978 1506 1.252015 CGCTGCAACGTACGTATTCTC 59.748 52.381 23.12 10.22 0.00 2.87
979 1507 1.265568 CGCTGCAACGTACGTATTCT 58.734 50.000 23.12 2.29 0.00 2.40
980 1508 0.314021 GCGCTGCAACGTACGTATTC 60.314 55.000 23.12 13.73 34.88 1.75
981 1509 1.009903 TGCGCTGCAACGTACGTATT 61.010 50.000 23.12 3.61 34.76 1.89
982 1510 0.804544 ATGCGCTGCAACGTACGTAT 60.805 50.000 23.12 9.26 43.62 3.06
1059 1588 2.953648 TGCATCATTAGCTTGGGTGATG 59.046 45.455 18.32 18.32 46.60 3.07
1084 1613 0.874607 CCTACACGTATCAAGGGCGC 60.875 60.000 0.00 0.00 0.00 6.53
1116 3921 3.704061 ACCTTTTGCCTCTTTTGCTGTAA 59.296 39.130 0.00 0.00 0.00 2.41
1163 3976 1.075601 TTTTGGGACAGAGGGAGCAT 58.924 50.000 0.00 0.00 42.39 3.79
1187 4487 7.344095 TCCGTCCCAAAATAAGTGTTTTAAA 57.656 32.000 0.00 0.00 30.56 1.52
1192 4492 3.761752 CCATCCGTCCCAAAATAAGTGTT 59.238 43.478 0.00 0.00 0.00 3.32
1263 5695 8.521170 AAAGTTTTAAATAGAGGACTATGGCC 57.479 34.615 0.00 0.00 39.04 5.36
1294 5726 3.430236 GCGCAAGGGCCACTAATTAATTT 60.430 43.478 6.18 0.00 36.38 1.82
1334 5773 5.646577 TGCATGTGATTGAATTGTGATGA 57.353 34.783 0.00 0.00 0.00 2.92
1337 5776 5.394224 ACATGCATGTGATTGAATTGTGA 57.606 34.783 30.92 0.00 40.03 3.58
1358 5797 4.681025 TGTCGAAAACGTACATAGGAACAC 59.319 41.667 0.00 0.00 0.00 3.32
1442 5883 4.516698 TGTTTTGAGAGAGCATGTTTCTCC 59.483 41.667 19.42 13.84 41.58 3.71
1548 5989 0.827925 TCGACTGTCTCCCAGCAACT 60.828 55.000 6.21 0.00 45.68 3.16
1718 6159 2.438434 CCACCTCCATCCAACCGC 60.438 66.667 0.00 0.00 0.00 5.68
1840 6281 4.673841 CGAAACGGAGGGAGTACTTCTTAC 60.674 50.000 0.01 0.00 0.00 2.34
1841 6282 3.441572 CGAAACGGAGGGAGTACTTCTTA 59.558 47.826 0.01 0.00 0.00 2.10
1842 6283 2.230750 CGAAACGGAGGGAGTACTTCTT 59.769 50.000 0.01 0.00 0.00 2.52
1843 6284 1.817447 CGAAACGGAGGGAGTACTTCT 59.183 52.381 0.01 0.06 0.00 2.85
1844 6285 1.815003 TCGAAACGGAGGGAGTACTTC 59.185 52.381 0.00 0.00 0.00 3.01
1845 6286 1.915141 TCGAAACGGAGGGAGTACTT 58.085 50.000 0.00 0.00 0.00 2.24
1846 6287 1.915141 TTCGAAACGGAGGGAGTACT 58.085 50.000 0.00 0.00 0.00 2.73
1847 6288 2.955477 ATTCGAAACGGAGGGAGTAC 57.045 50.000 0.00 0.00 0.00 2.73
1848 6289 4.019174 AGTAATTCGAAACGGAGGGAGTA 58.981 43.478 0.00 0.00 0.00 2.59
1849 6290 2.830321 AGTAATTCGAAACGGAGGGAGT 59.170 45.455 0.00 0.00 0.00 3.85
1850 6291 3.521947 AGTAATTCGAAACGGAGGGAG 57.478 47.619 0.00 0.00 0.00 4.30
1851 6292 3.007182 ACAAGTAATTCGAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
1852 6293 3.332034 ACAAGTAATTCGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
1853 6294 4.243270 AGACAAGTAATTCGAAACGGAGG 58.757 43.478 0.00 0.00 0.00 4.30
1854 6295 5.404366 TCAAGACAAGTAATTCGAAACGGAG 59.596 40.000 0.00 0.00 0.00 4.63
1855 6296 5.291178 TCAAGACAAGTAATTCGAAACGGA 58.709 37.500 0.00 0.00 0.00 4.69
1856 6297 5.585500 TCAAGACAAGTAATTCGAAACGG 57.415 39.130 0.00 0.00 0.00 4.44
1857 6298 8.409690 CAAATTCAAGACAAGTAATTCGAAACG 58.590 33.333 0.00 0.00 0.00 3.60
1858 6299 9.233232 ACAAATTCAAGACAAGTAATTCGAAAC 57.767 29.630 0.00 0.00 0.00 2.78
1859 6300 9.445786 GACAAATTCAAGACAAGTAATTCGAAA 57.554 29.630 0.00 0.00 0.00 3.46
1860 6301 8.836413 AGACAAATTCAAGACAAGTAATTCGAA 58.164 29.630 0.00 0.00 0.00 3.71
1861 6302 8.378172 AGACAAATTCAAGACAAGTAATTCGA 57.622 30.769 0.00 0.00 0.00 3.71
1862 6303 9.746711 CTAGACAAATTCAAGACAAGTAATTCG 57.253 33.333 0.00 0.00 0.00 3.34
1867 6308 9.569167 CGTATCTAGACAAATTCAAGACAAGTA 57.431 33.333 0.00 0.00 0.00 2.24
1868 6309 7.545965 CCGTATCTAGACAAATTCAAGACAAGT 59.454 37.037 0.00 0.00 0.00 3.16
1869 6310 7.759886 TCCGTATCTAGACAAATTCAAGACAAG 59.240 37.037 0.00 0.00 0.00 3.16
1870 6311 7.608153 TCCGTATCTAGACAAATTCAAGACAA 58.392 34.615 0.00 0.00 0.00 3.18
1871 6312 7.165460 TCCGTATCTAGACAAATTCAAGACA 57.835 36.000 0.00 0.00 0.00 3.41
1872 6313 7.707035 ACATCCGTATCTAGACAAATTCAAGAC 59.293 37.037 0.00 0.00 0.00 3.01
1873 6314 7.782049 ACATCCGTATCTAGACAAATTCAAGA 58.218 34.615 0.00 0.00 0.00 3.02
1874 6315 9.698309 ATACATCCGTATCTAGACAAATTCAAG 57.302 33.333 0.00 0.00 32.66 3.02
1890 6331 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
1891 6332 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
1892 6333 7.327275 GCACTAAAATGAGTCTAGATACATCCG 59.673 40.741 12.66 6.68 0.00 4.18
1893 6334 8.364142 AGCACTAAAATGAGTCTAGATACATCC 58.636 37.037 12.66 0.00 0.00 3.51
1903 6344 7.988028 GGAGGTATTTAGCACTAAAATGAGTCT 59.012 37.037 6.92 0.95 38.38 3.24
1904 6345 7.042658 CGGAGGTATTTAGCACTAAAATGAGTC 60.043 40.741 6.92 2.06 38.38 3.36
1905 6346 6.761714 CGGAGGTATTTAGCACTAAAATGAGT 59.238 38.462 6.92 0.00 38.38 3.41
1906 6347 6.761714 ACGGAGGTATTTAGCACTAAAATGAG 59.238 38.462 6.92 0.00 38.38 2.90
1907 6348 6.646267 ACGGAGGTATTTAGCACTAAAATGA 58.354 36.000 6.92 0.00 38.38 2.57
1908 6349 6.920569 ACGGAGGTATTTAGCACTAAAATG 57.079 37.500 6.92 0.00 38.38 2.32
1909 6350 8.208903 ACATACGGAGGTATTTAGCACTAAAAT 58.791 33.333 6.92 0.00 37.24 1.82
1910 6351 7.558604 ACATACGGAGGTATTTAGCACTAAAA 58.441 34.615 6.92 0.00 37.24 1.52
1911 6352 7.116075 ACATACGGAGGTATTTAGCACTAAA 57.884 36.000 5.37 5.37 37.24 1.85
1912 6353 6.720112 ACATACGGAGGTATTTAGCACTAA 57.280 37.500 0.00 0.00 37.24 2.24
1913 6354 7.173907 GTCTACATACGGAGGTATTTAGCACTA 59.826 40.741 0.00 0.00 38.45 2.74
1914 6355 6.016443 GTCTACATACGGAGGTATTTAGCACT 60.016 42.308 0.00 0.00 38.45 4.40
1915 6356 6.148264 GTCTACATACGGAGGTATTTAGCAC 58.852 44.000 0.00 1.35 38.45 4.40
1916 6357 5.829391 TGTCTACATACGGAGGTATTTAGCA 59.171 40.000 0.00 3.29 38.45 3.49
1917 6358 6.323203 TGTCTACATACGGAGGTATTTAGC 57.677 41.667 0.00 0.00 38.45 3.09
1918 6359 9.408069 GATTTGTCTACATACGGAGGTATTTAG 57.592 37.037 0.00 2.51 39.29 1.85
1919 6360 8.362639 GGATTTGTCTACATACGGAGGTATTTA 58.637 37.037 0.00 0.00 37.24 1.40
1920 6361 7.147620 TGGATTTGTCTACATACGGAGGTATTT 60.148 37.037 0.00 0.00 37.24 1.40
1921 6362 6.325545 TGGATTTGTCTACATACGGAGGTATT 59.674 38.462 0.00 0.00 37.24 1.89
1922 6363 5.836898 TGGATTTGTCTACATACGGAGGTAT 59.163 40.000 0.00 0.00 39.96 2.73
1923 6364 5.202765 TGGATTTGTCTACATACGGAGGTA 58.797 41.667 0.00 0.00 0.00 3.08
1924 6365 4.028131 TGGATTTGTCTACATACGGAGGT 58.972 43.478 0.00 0.00 0.00 3.85
1925 6366 4.665833 TGGATTTGTCTACATACGGAGG 57.334 45.455 0.00 0.00 0.00 4.30
1926 6367 6.370442 TGTTTTGGATTTGTCTACATACGGAG 59.630 38.462 0.00 0.00 0.00 4.63
1927 6368 6.231951 TGTTTTGGATTTGTCTACATACGGA 58.768 36.000 0.00 0.00 0.00 4.69
1928 6369 6.489127 TGTTTTGGATTTGTCTACATACGG 57.511 37.500 0.00 0.00 0.00 4.02
1929 6370 7.581476 ACTTGTTTTGGATTTGTCTACATACG 58.419 34.615 0.00 0.00 0.00 3.06
1933 6374 9.959749 GAATTACTTGTTTTGGATTTGTCTACA 57.040 29.630 0.00 0.00 0.00 2.74
1934 6375 9.113876 CGAATTACTTGTTTTGGATTTGTCTAC 57.886 33.333 0.00 0.00 0.00 2.59
1935 6376 8.293867 CCGAATTACTTGTTTTGGATTTGTCTA 58.706 33.333 0.00 0.00 0.00 2.59
1936 6377 7.013846 TCCGAATTACTTGTTTTGGATTTGTCT 59.986 33.333 0.00 0.00 31.71 3.41
1937 6378 7.142680 TCCGAATTACTTGTTTTGGATTTGTC 58.857 34.615 0.00 0.00 31.71 3.18
1938 6379 7.045126 TCCGAATTACTTGTTTTGGATTTGT 57.955 32.000 0.00 0.00 31.71 2.83
1939 6380 7.436673 TGTTCCGAATTACTTGTTTTGGATTTG 59.563 33.333 0.00 0.00 35.73 2.32
1940 6381 7.493367 TGTTCCGAATTACTTGTTTTGGATTT 58.507 30.769 0.00 0.00 35.73 2.17
1941 6382 7.013846 TCTGTTCCGAATTACTTGTTTTGGATT 59.986 33.333 0.00 0.00 35.73 3.01
1942 6383 6.488683 TCTGTTCCGAATTACTTGTTTTGGAT 59.511 34.615 0.00 0.00 35.73 3.41
1943 6384 5.823570 TCTGTTCCGAATTACTTGTTTTGGA 59.176 36.000 0.00 0.00 34.28 3.53
1944 6385 6.067263 TCTGTTCCGAATTACTTGTTTTGG 57.933 37.500 0.00 0.00 0.00 3.28
1945 6386 6.017440 TCCTCTGTTCCGAATTACTTGTTTTG 60.017 38.462 0.00 0.00 0.00 2.44
1946 6387 6.059484 TCCTCTGTTCCGAATTACTTGTTTT 58.941 36.000 0.00 0.00 0.00 2.43
1947 6388 5.617252 TCCTCTGTTCCGAATTACTTGTTT 58.383 37.500 0.00 0.00 0.00 2.83
1948 6389 5.223449 TCCTCTGTTCCGAATTACTTGTT 57.777 39.130 0.00 0.00 0.00 2.83
1949 6390 4.884668 TCCTCTGTTCCGAATTACTTGT 57.115 40.909 0.00 0.00 0.00 3.16
1950 6391 5.238583 ACTTCCTCTGTTCCGAATTACTTG 58.761 41.667 0.00 0.00 0.00 3.16
1951 6392 5.485209 ACTTCCTCTGTTCCGAATTACTT 57.515 39.130 0.00 0.00 0.00 2.24
1952 6393 6.600882 TTACTTCCTCTGTTCCGAATTACT 57.399 37.500 0.00 0.00 0.00 2.24
1953 6394 5.291371 GCTTACTTCCTCTGTTCCGAATTAC 59.709 44.000 0.00 0.00 0.00 1.89
1954 6395 5.046878 TGCTTACTTCCTCTGTTCCGAATTA 60.047 40.000 0.00 0.00 0.00 1.40
1955 6396 4.254492 GCTTACTTCCTCTGTTCCGAATT 58.746 43.478 0.00 0.00 0.00 2.17
1956 6397 3.260884 TGCTTACTTCCTCTGTTCCGAAT 59.739 43.478 0.00 0.00 0.00 3.34
1957 6398 2.631062 TGCTTACTTCCTCTGTTCCGAA 59.369 45.455 0.00 0.00 0.00 4.30
1958 6399 2.244695 TGCTTACTTCCTCTGTTCCGA 58.755 47.619 0.00 0.00 0.00 4.55
1959 6400 2.737252 GTTGCTTACTTCCTCTGTTCCG 59.263 50.000 0.00 0.00 0.00 4.30
1960 6401 3.740115 TGTTGCTTACTTCCTCTGTTCC 58.260 45.455 0.00 0.00 0.00 3.62
1961 6402 5.751243 TTTGTTGCTTACTTCCTCTGTTC 57.249 39.130 0.00 0.00 0.00 3.18
1962 6403 5.885912 TCTTTTGTTGCTTACTTCCTCTGTT 59.114 36.000 0.00 0.00 0.00 3.16
1963 6404 5.437060 TCTTTTGTTGCTTACTTCCTCTGT 58.563 37.500 0.00 0.00 0.00 3.41
1964 6405 6.038714 AGTTCTTTTGTTGCTTACTTCCTCTG 59.961 38.462 0.00 0.00 0.00 3.35
1965 6406 6.122964 AGTTCTTTTGTTGCTTACTTCCTCT 58.877 36.000 0.00 0.00 0.00 3.69
1966 6407 6.378710 AGTTCTTTTGTTGCTTACTTCCTC 57.621 37.500 0.00 0.00 0.00 3.71
1967 6408 6.017026 GCTAGTTCTTTTGTTGCTTACTTCCT 60.017 38.462 0.00 0.00 0.00 3.36
1968 6409 6.143496 GCTAGTTCTTTTGTTGCTTACTTCC 58.857 40.000 0.00 0.00 0.00 3.46
2013 6495 0.922626 ATTCTCCTTTCCAGCTCCCC 59.077 55.000 0.00 0.00 0.00 4.81
2021 6503 7.468141 AACAGTCCAATAAATTCTCCTTTCC 57.532 36.000 0.00 0.00 0.00 3.13
2043 6525 6.919721 TGGCCTCATTCTATGTAACAAAAAC 58.080 36.000 3.32 0.00 0.00 2.43
2145 6628 6.933894 ACCAAATAAGGCCTTATTCCCTATT 58.066 36.000 38.59 25.04 42.91 1.73
2191 6674 9.886132 GACTTGAGACTTATAAGTTGGGATTAA 57.114 33.333 18.96 7.57 39.88 1.40
2192 6675 9.268282 AGACTTGAGACTTATAAGTTGGGATTA 57.732 33.333 18.96 2.08 39.88 1.75
2193 6676 8.152023 AGACTTGAGACTTATAAGTTGGGATT 57.848 34.615 18.96 3.86 39.88 3.01
2194 6677 7.741554 AGACTTGAGACTTATAAGTTGGGAT 57.258 36.000 18.96 4.56 39.88 3.85
2195 6678 7.554959 AAGACTTGAGACTTATAAGTTGGGA 57.445 36.000 18.96 6.15 39.88 4.37
2196 6679 9.720769 TTAAAGACTTGAGACTTATAAGTTGGG 57.279 33.333 18.96 10.37 39.88 4.12
2204 6687 9.286170 GGGACTTTTTAAAGACTTGAGACTTAT 57.714 33.333 9.09 0.00 39.31 1.73
2205 6688 8.491958 AGGGACTTTTTAAAGACTTGAGACTTA 58.508 33.333 9.09 0.00 39.31 2.24
2206 6689 7.347252 AGGGACTTTTTAAAGACTTGAGACTT 58.653 34.615 9.09 0.00 39.31 3.01
2207 6690 6.901300 AGGGACTTTTTAAAGACTTGAGACT 58.099 36.000 9.09 0.00 39.31 3.24
2208 6691 7.713942 TGTAGGGACTTTTTAAAGACTTGAGAC 59.286 37.037 9.09 1.64 41.75 3.36
2209 6692 7.798071 TGTAGGGACTTTTTAAAGACTTGAGA 58.202 34.615 9.09 0.00 41.75 3.27
2210 6693 8.507249 CATGTAGGGACTTTTTAAAGACTTGAG 58.493 37.037 9.09 0.00 41.75 3.02
2211 6694 7.996644 ACATGTAGGGACTTTTTAAAGACTTGA 59.003 33.333 9.09 0.00 41.75 3.02
2212 6695 8.166422 ACATGTAGGGACTTTTTAAAGACTTG 57.834 34.615 9.09 7.10 41.75 3.16
2213 6696 8.762481 AACATGTAGGGACTTTTTAAAGACTT 57.238 30.769 9.09 1.62 41.75 3.01
2214 6697 8.630037 CAAACATGTAGGGACTTTTTAAAGACT 58.370 33.333 9.09 6.64 41.75 3.24
2215 6698 7.865889 CCAAACATGTAGGGACTTTTTAAAGAC 59.134 37.037 9.55 3.03 41.75 3.01
2216 6699 7.562088 ACCAAACATGTAGGGACTTTTTAAAGA 59.438 33.333 19.48 0.00 41.75 2.52
2217 6700 7.722363 ACCAAACATGTAGGGACTTTTTAAAG 58.278 34.615 19.48 0.80 41.75 1.85
2218 6701 7.663043 ACCAAACATGTAGGGACTTTTTAAA 57.337 32.000 19.48 0.00 41.75 1.52
2219 6702 7.562088 AGAACCAAACATGTAGGGACTTTTTAA 59.438 33.333 19.48 0.00 41.75 1.52
2220 6703 7.064229 AGAACCAAACATGTAGGGACTTTTTA 58.936 34.615 19.48 0.00 41.75 1.52
2221 6704 5.897250 AGAACCAAACATGTAGGGACTTTTT 59.103 36.000 19.48 5.69 41.75 1.94
2222 6705 5.454966 AGAACCAAACATGTAGGGACTTTT 58.545 37.500 19.48 6.31 41.75 2.27
2223 6706 5.061721 AGAACCAAACATGTAGGGACTTT 57.938 39.130 19.48 6.62 41.75 2.66
2224 6707 4.724279 AGAACCAAACATGTAGGGACTT 57.276 40.909 19.48 6.91 41.75 3.01
2225 6708 4.104102 TGAAGAACCAAACATGTAGGGACT 59.896 41.667 19.48 14.38 46.37 3.85
2226 6709 4.394729 TGAAGAACCAAACATGTAGGGAC 58.605 43.478 19.48 12.78 0.00 4.46
2227 6710 4.349636 TCTGAAGAACCAAACATGTAGGGA 59.650 41.667 19.48 4.86 0.00 4.20
2228 6711 4.651778 TCTGAAGAACCAAACATGTAGGG 58.348 43.478 18.43 15.73 0.00 3.53
2229 6712 6.824305 AATCTGAAGAACCAAACATGTAGG 57.176 37.500 14.04 14.04 0.00 3.18
2235 6718 8.730680 GCTCTTATAAATCTGAAGAACCAAACA 58.269 33.333 0.00 0.00 0.00 2.83
2236 6719 8.730680 TGCTCTTATAAATCTGAAGAACCAAAC 58.269 33.333 0.00 0.00 0.00 2.93
2237 6720 8.862325 TGCTCTTATAAATCTGAAGAACCAAA 57.138 30.769 0.00 0.00 0.00 3.28
2238 6721 9.113838 GATGCTCTTATAAATCTGAAGAACCAA 57.886 33.333 0.00 0.00 0.00 3.67
2239 6722 8.489489 AGATGCTCTTATAAATCTGAAGAACCA 58.511 33.333 0.00 0.00 0.00 3.67
2240 6723 8.900983 AGATGCTCTTATAAATCTGAAGAACC 57.099 34.615 0.00 0.00 0.00 3.62
2241 6724 8.987890 GGAGATGCTCTTATAAATCTGAAGAAC 58.012 37.037 2.75 0.00 29.59 3.01
2242 6725 8.708378 TGGAGATGCTCTTATAAATCTGAAGAA 58.292 33.333 2.75 0.00 29.59 2.52
2243 6726 8.255111 TGGAGATGCTCTTATAAATCTGAAGA 57.745 34.615 2.75 0.00 29.59 2.87
2244 6727 8.772705 GTTGGAGATGCTCTTATAAATCTGAAG 58.227 37.037 2.75 0.00 29.59 3.02
2245 6728 7.439356 CGTTGGAGATGCTCTTATAAATCTGAA 59.561 37.037 2.75 0.00 29.59 3.02
2246 6729 6.925718 CGTTGGAGATGCTCTTATAAATCTGA 59.074 38.462 2.75 0.00 29.59 3.27
2302 6785 1.698714 CCCCCGCGCTAAAAGTTACG 61.699 60.000 5.56 0.00 0.00 3.18
2303 6786 2.092374 CCCCCGCGCTAAAAGTTAC 58.908 57.895 5.56 0.00 0.00 2.50
2304 6787 4.621832 CCCCCGCGCTAAAAGTTA 57.378 55.556 5.56 0.00 0.00 2.24
2432 6925 1.881252 CGCGCCGCACTTTATAGGT 60.881 57.895 10.75 0.00 0.00 3.08
2740 7239 1.741770 GAAGTTCATCTGGCCGCGT 60.742 57.895 4.92 0.00 0.00 6.01


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

AutoCloner maintained by Alex Coulton.