Multiple sequence alignment - TraesCS3A01G221600

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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 TraesCS3A01G221600 chr3A 100.000 2318 0 0 1 2318 411277259 411274942 0.000000e+00 4281
1 TraesCS3A01G221600 chr3A 90.074 806 79 1 540 1344 732918471 732917666 0.000000e+00 1044
2 TraesCS3A01G221600 chr3A 92.140 229 14 3 1850 2076 193873439 193873213 1.030000e-83 320
3 TraesCS3A01G221600 chr3D 94.341 1343 64 2 1 1343 305482565 305483895 0.000000e+00 2049
4 TraesCS3A01G221600 chr3D 89.552 1340 135 5 3 1342 141196093 141194759 0.000000e+00 1694
5 TraesCS3A01G221600 chr3D 87.786 1269 139 2 77 1345 590178519 590177267 0.000000e+00 1471
6 TraesCS3A01G221600 chr3D 91.897 506 36 2 1348 1848 316813162 316813667 0.000000e+00 702
7 TraesCS3A01G221600 chr3D 86.640 247 14 5 1844 2076 168501130 168501371 2.960000e-64 255
8 TraesCS3A01G221600 chr3D 83.333 228 29 9 1852 2076 263331924 263331703 3.910000e-48 202
9 TraesCS3A01G221600 chr3D 81.340 209 29 10 1846 2051 263332121 263331920 6.630000e-36 161
10 TraesCS3A01G221600 chr6D 82.589 1344 230 4 3 1344 25818609 25817268 0.000000e+00 1182
11 TraesCS3A01G221600 chr6D 95.154 227 10 1 1850 2076 79968750 79968975 7.880000e-95 357
12 TraesCS3A01G221600 chr7D 86.125 973 130 3 374 1345 542133347 542132379 0.000000e+00 1044
13 TraesCS3A01G221600 chr7D 80.148 1350 253 13 1 1344 615563354 615562014 0.000000e+00 994
14 TraesCS3A01G221600 chr7D 82.182 999 174 4 348 1344 606676919 606677915 0.000000e+00 856
15 TraesCS3A01G221600 chr3B 79.941 1351 249 15 5 1346 815977145 815975808 0.000000e+00 974
16 TraesCS3A01G221600 chr3B 85.902 305 23 9 1523 1807 402456716 402456412 8.050000e-80 307
17 TraesCS3A01G221600 chr6B 87.589 846 96 5 1 846 52063174 52064010 0.000000e+00 972
18 TraesCS3A01G221600 chr2B 78.238 1351 271 21 5 1343 43118244 43119583 0.000000e+00 845
19 TraesCS3A01G221600 chr2B 93.827 243 15 0 2076 2318 277308025 277307783 1.310000e-97 366
20 TraesCS3A01G221600 chr2A 91.852 405 31 2 4 408 616197906 616198308 4.320000e-157 564
21 TraesCS3A01G221600 chr2A 94.606 241 11 2 2076 2316 30350544 30350782 2.810000e-99 372
22 TraesCS3A01G221600 chr2A 93.852 244 15 0 2071 2314 757200355 757200112 3.640000e-98 368
23 TraesCS3A01G221600 chr5A 95.851 241 10 0 2074 2314 486754604 486754364 7.770000e-105 390
24 TraesCS3A01G221600 chr5A 93.450 229 12 2 1850 2076 510196420 510196647 1.030000e-88 337
25 TraesCS3A01G221600 chr5A 80.242 248 28 11 1849 2076 500630314 500630068 1.420000e-37 167
26 TraesCS3A01G221600 chr7A 95.397 239 10 1 2076 2314 5448929 5448692 1.680000e-101 379
27 TraesCS3A01G221600 chrUn 94.239 243 14 0 2076 2318 4345580 4345822 2.810000e-99 372
28 TraesCS3A01G221600 chrUn 94.239 243 14 0 2076 2318 131818872 131818630 2.810000e-99 372
29 TraesCS3A01G221600 chrUn 94.239 243 14 0 2076 2318 378239920 378240162 2.810000e-99 372
30 TraesCS3A01G221600 chr7B 93.827 243 15 0 2076 2318 63057830 63057588 1.310000e-97 366
31 TraesCS3A01G221600 chr5B 89.873 237 9 7 1841 2076 397294966 397294744 8.100000e-75 291


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 TraesCS3A01G221600 chr3A 411274942 411277259 2317 True 4281 4281 100.000 1 2318 1 chr3A.!!$R2 2317
1 TraesCS3A01G221600 chr3A 732917666 732918471 805 True 1044 1044 90.074 540 1344 1 chr3A.!!$R3 804
2 TraesCS3A01G221600 chr3D 305482565 305483895 1330 False 2049 2049 94.341 1 1343 1 chr3D.!!$F2 1342
3 TraesCS3A01G221600 chr3D 141194759 141196093 1334 True 1694 1694 89.552 3 1342 1 chr3D.!!$R1 1339
4 TraesCS3A01G221600 chr3D 590177267 590178519 1252 True 1471 1471 87.786 77 1345 1 chr3D.!!$R2 1268
5 TraesCS3A01G221600 chr3D 316813162 316813667 505 False 702 702 91.897 1348 1848 1 chr3D.!!$F3 500
6 TraesCS3A01G221600 chr6D 25817268 25818609 1341 True 1182 1182 82.589 3 1344 1 chr6D.!!$R1 1341
7 TraesCS3A01G221600 chr7D 542132379 542133347 968 True 1044 1044 86.125 374 1345 1 chr7D.!!$R1 971
8 TraesCS3A01G221600 chr7D 615562014 615563354 1340 True 994 994 80.148 1 1344 1 chr7D.!!$R2 1343
9 TraesCS3A01G221600 chr7D 606676919 606677915 996 False 856 856 82.182 348 1344 1 chr7D.!!$F1 996
10 TraesCS3A01G221600 chr3B 815975808 815977145 1337 True 974 974 79.941 5 1346 1 chr3B.!!$R2 1341
11 TraesCS3A01G221600 chr6B 52063174 52064010 836 False 972 972 87.589 1 846 1 chr6B.!!$F1 845
12 TraesCS3A01G221600 chr2B 43118244 43119583 1339 False 845 845 78.238 5 1343 1 chr2B.!!$F1 1338

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
985 993 0.107508 CAATGATCCACTGGAGGCGT 60.108 55.0 3.62 0.0 34.05 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2293 2306 0.03779 GAGAAGAGAGCCGTGTTGCT 60.038 55.0 0.0 0.0 46.37 3.91 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
247 248 2.229543 GCCACATGTGATCACAATGTGT 59.770 45.455 36.42 30.89 45.41 3.72
363 366 2.330216 ACAGCTTGGAGAGTGGTTACT 58.670 47.619 0.00 0.00 40.66 2.24
419 422 1.401018 GCATTTGGCTACACGTTCACC 60.401 52.381 0.00 0.00 40.25 4.02
481 484 1.673923 CCTTGATCGCTTGCACTCAGA 60.674 52.381 0.00 0.00 0.00 3.27
537 540 2.035066 GCCGCTTCCTAACGATAACCTA 59.965 50.000 0.00 0.00 0.00 3.08
633 637 8.785329 TTATTATGCTGATTTGGCGTATATGA 57.215 30.769 0.00 0.00 32.26 2.15
636 640 4.195416 TGCTGATTTGGCGTATATGACAA 58.805 39.130 9.26 9.26 34.30 3.18
662 666 2.315925 AATGACATCTACCACGGCAG 57.684 50.000 0.00 0.00 0.00 4.85
829 833 1.319614 GCCTATTTTGCCTTGGCCGA 61.320 55.000 9.35 0.00 37.81 5.54
985 993 0.107508 CAATGATCCACTGGAGGCGT 60.108 55.000 3.62 0.00 34.05 5.68
1042 1050 4.503817 CCATCCAACACTCAAACTCTCTGA 60.504 45.833 0.00 0.00 0.00 3.27
1081 1089 1.471676 CCTCGGAAGCGTTATCTTGCT 60.472 52.381 0.00 0.00 44.97 3.91
1099 1107 0.036952 CTTGTCCACGGATGCTCTGT 60.037 55.000 0.00 0.00 36.16 3.41
1294 1302 1.079750 GACTTGTGGCCTCTCGACC 60.080 63.158 3.32 0.00 0.00 4.79
1307 1315 3.495377 CCTCTCGACCGTAACTCTATGAG 59.505 52.174 0.00 0.00 35.52 2.90
1395 1403 8.782533 AACAGTTAATTTTTAGCTTTCTCACG 57.217 30.769 0.00 0.00 0.00 4.35
1397 1405 7.078228 CAGTTAATTTTTAGCTTTCTCACGCT 58.922 34.615 0.00 0.00 40.15 5.07
1403 1411 2.246719 AGCTTTCTCACGCTTCAACT 57.753 45.000 0.00 0.00 31.17 3.16
1404 1412 2.565841 AGCTTTCTCACGCTTCAACTT 58.434 42.857 0.00 0.00 31.17 2.66
1405 1413 2.945668 AGCTTTCTCACGCTTCAACTTT 59.054 40.909 0.00 0.00 31.17 2.66
1411 1419 4.380531 TCTCACGCTTCAACTTTCATTCT 58.619 39.130 0.00 0.00 0.00 2.40
1418 1426 5.922544 CGCTTCAACTTTCATTCTCCATTTT 59.077 36.000 0.00 0.00 0.00 1.82
1419 1427 6.421801 CGCTTCAACTTTCATTCTCCATTTTT 59.578 34.615 0.00 0.00 0.00 1.94
1442 1450 2.613506 CCCCGAACCAAACACGCTC 61.614 63.158 0.00 0.00 0.00 5.03
1443 1451 2.613506 CCCGAACCAAACACGCTCC 61.614 63.158 0.00 0.00 0.00 4.70
1444 1452 2.613506 CCGAACCAAACACGCTCCC 61.614 63.158 0.00 0.00 0.00 4.30
1464 1472 1.886222 CGCATAGGGAGAGGGAGAGAG 60.886 61.905 0.00 0.00 0.00 3.20
1496 1504 2.127708 AGGCTTTAGGTGGAATCCGAT 58.872 47.619 0.00 0.00 0.00 4.18
1529 1537 1.520120 CGATCTCACCTGCATGCGT 60.520 57.895 14.09 2.34 0.00 5.24
1545 1553 1.870055 GCGTTGTAGTCTCACCCCGA 61.870 60.000 0.00 0.00 0.00 5.14
1607 1615 2.926200 CCGAAGGCTGCAATATAGATCG 59.074 50.000 0.50 0.00 46.14 3.69
1630 1638 0.539207 TGTGCCATGGCTTGCTTGTA 60.539 50.000 35.53 11.81 42.51 2.41
1657 1665 1.320507 GACCGTGAGACCCTAGATCC 58.679 60.000 0.00 0.00 0.00 3.36
1686 1694 1.000506 AGTAGCAAGGTGTACGGTGTG 59.999 52.381 0.00 0.00 0.00 3.82
1768 1781 2.954684 CGTCACAGGCCCTGGCTTA 61.955 63.158 16.70 0.00 41.60 3.09
1777 1790 1.934220 GCCCTGGCTTACGCTTTTCC 61.934 60.000 0.00 0.00 38.26 3.13
1784 1797 0.989890 CTTACGCTTTTCCGACGAGG 59.010 55.000 0.00 0.00 42.97 4.63
1796 1809 2.573869 ACGAGGCAGTGGATCGTG 59.426 61.111 0.00 0.00 46.99 4.35
1806 1819 1.377594 TGGATCGTGCTGCAATGCT 60.378 52.632 2.77 0.00 0.00 3.79
1808 1821 0.248377 GGATCGTGCTGCAATGCTTC 60.248 55.000 2.77 0.00 0.00 3.86
1828 1841 5.059710 GCTTCGCATTACTTTTGTTGTGATC 59.940 40.000 0.00 0.00 32.04 2.92
1835 1848 8.507249 GCATTACTTTTGTTGTGATCTCTTACT 58.493 33.333 0.00 0.00 0.00 2.24
1848 1861 8.955388 TGTGATCTCTTACTGATATGAGCTATC 58.045 37.037 0.00 0.00 37.36 2.08
1849 1862 9.177608 GTGATCTCTTACTGATATGAGCTATCT 57.822 37.037 0.00 0.00 37.67 1.98
1853 1866 9.884636 TCTCTTACTGATATGAGCTATCTACTC 57.115 37.037 0.00 0.00 37.67 2.59
1854 1867 9.109393 CTCTTACTGATATGAGCTATCTACTCC 57.891 40.741 0.00 0.00 37.67 3.85
1855 1868 8.050325 TCTTACTGATATGAGCTATCTACTCCC 58.950 40.741 0.00 0.00 37.67 4.30
1856 1869 6.401537 ACTGATATGAGCTATCTACTCCCT 57.598 41.667 0.00 0.00 37.67 4.20
1857 1870 6.423182 ACTGATATGAGCTATCTACTCCCTC 58.577 44.000 0.00 0.00 37.67 4.30
1858 1871 6.217487 ACTGATATGAGCTATCTACTCCCTCT 59.783 42.308 0.00 0.00 37.67 3.69
1859 1872 6.422333 TGATATGAGCTATCTACTCCCTCTG 58.578 44.000 0.00 0.00 37.67 3.35
1860 1873 4.740154 ATGAGCTATCTACTCCCTCTGT 57.260 45.455 0.00 0.00 32.98 3.41
1861 1874 4.528076 TGAGCTATCTACTCCCTCTGTT 57.472 45.455 0.00 0.00 32.98 3.16
1862 1875 4.873010 TGAGCTATCTACTCCCTCTGTTT 58.127 43.478 0.00 0.00 32.98 2.83
1863 1876 4.890581 TGAGCTATCTACTCCCTCTGTTTC 59.109 45.833 0.00 0.00 32.98 2.78
1864 1877 4.873010 AGCTATCTACTCCCTCTGTTTCA 58.127 43.478 0.00 0.00 0.00 2.69
1865 1878 4.892934 AGCTATCTACTCCCTCTGTTTCAG 59.107 45.833 0.00 0.00 0.00 3.02
1866 1879 4.890581 GCTATCTACTCCCTCTGTTTCAGA 59.109 45.833 0.00 0.00 38.25 3.27
1867 1880 5.361285 GCTATCTACTCCCTCTGTTTCAGAA 59.639 44.000 1.22 0.00 40.18 3.02
1868 1881 6.127310 GCTATCTACTCCCTCTGTTTCAGAAA 60.127 42.308 0.00 0.00 40.18 2.52
1869 1882 6.882768 ATCTACTCCCTCTGTTTCAGAAAT 57.117 37.500 0.00 0.00 40.18 2.17
1870 1883 7.979786 ATCTACTCCCTCTGTTTCAGAAATA 57.020 36.000 0.00 0.00 40.18 1.40
1871 1884 7.411486 TCTACTCCCTCTGTTTCAGAAATAG 57.589 40.000 12.37 12.37 40.18 1.73
1872 1885 6.954684 TCTACTCCCTCTGTTTCAGAAATAGT 59.045 38.462 16.76 3.23 40.18 2.12
1873 1886 6.441088 ACTCCCTCTGTTTCAGAAATAGTT 57.559 37.500 16.76 0.00 40.18 2.24
1874 1887 6.234177 ACTCCCTCTGTTTCAGAAATAGTTG 58.766 40.000 16.76 11.74 40.18 3.16
1875 1888 6.183361 ACTCCCTCTGTTTCAGAAATAGTTGT 60.183 38.462 16.76 8.72 40.18 3.32
1876 1889 6.231211 TCCCTCTGTTTCAGAAATAGTTGTC 58.769 40.000 16.76 0.00 40.18 3.18
1877 1890 5.120830 CCCTCTGTTTCAGAAATAGTTGTCG 59.879 44.000 16.76 4.33 40.18 4.35
1878 1891 5.389935 CCTCTGTTTCAGAAATAGTTGTCGC 60.390 44.000 16.76 0.00 40.18 5.19
1879 1892 5.297547 TCTGTTTCAGAAATAGTTGTCGCT 58.702 37.500 16.76 0.00 37.57 4.93
1880 1893 5.177511 TCTGTTTCAGAAATAGTTGTCGCTG 59.822 40.000 16.76 0.00 37.57 5.18
1881 1894 4.213270 TGTTTCAGAAATAGTTGTCGCTGG 59.787 41.667 0.00 0.00 0.00 4.85
1882 1895 3.953712 TCAGAAATAGTTGTCGCTGGA 57.046 42.857 0.00 0.00 0.00 3.86
1883 1896 3.849911 TCAGAAATAGTTGTCGCTGGAG 58.150 45.455 0.00 0.00 0.00 3.86
1884 1897 2.932614 CAGAAATAGTTGTCGCTGGAGG 59.067 50.000 0.00 0.00 0.00 4.30
1885 1898 2.567615 AGAAATAGTTGTCGCTGGAGGT 59.432 45.455 0.00 0.00 0.00 3.85
1886 1899 3.008049 AGAAATAGTTGTCGCTGGAGGTT 59.992 43.478 0.00 0.00 0.00 3.50
1887 1900 3.418684 AATAGTTGTCGCTGGAGGTTT 57.581 42.857 0.00 0.00 0.00 3.27
1888 1901 2.450609 TAGTTGTCGCTGGAGGTTTC 57.549 50.000 0.00 0.00 0.00 2.78
1889 1902 0.759346 AGTTGTCGCTGGAGGTTTCT 59.241 50.000 0.00 0.00 0.00 2.52
1890 1903 1.968493 AGTTGTCGCTGGAGGTTTCTA 59.032 47.619 0.00 0.00 0.00 2.10
1891 1904 2.028930 AGTTGTCGCTGGAGGTTTCTAG 60.029 50.000 0.00 0.00 35.20 2.43
1892 1905 1.629043 TGTCGCTGGAGGTTTCTAGT 58.371 50.000 0.00 0.00 34.62 2.57
1893 1906 1.968493 TGTCGCTGGAGGTTTCTAGTT 59.032 47.619 0.00 0.00 34.62 2.24
1894 1907 2.029290 TGTCGCTGGAGGTTTCTAGTTC 60.029 50.000 0.00 0.00 34.62 3.01
1895 1908 2.029290 GTCGCTGGAGGTTTCTAGTTCA 60.029 50.000 0.00 0.00 34.62 3.18
1896 1909 2.631062 TCGCTGGAGGTTTCTAGTTCAA 59.369 45.455 0.00 0.00 34.62 2.69
1897 1910 2.737252 CGCTGGAGGTTTCTAGTTCAAC 59.263 50.000 0.00 0.00 34.62 3.18
1898 1911 3.555168 CGCTGGAGGTTTCTAGTTCAACT 60.555 47.826 0.00 0.00 34.62 3.16
1899 1912 4.390264 GCTGGAGGTTTCTAGTTCAACTT 58.610 43.478 0.00 0.00 34.62 2.66
1900 1913 4.822350 GCTGGAGGTTTCTAGTTCAACTTT 59.178 41.667 0.00 0.00 34.62 2.66
1901 1914 5.049336 GCTGGAGGTTTCTAGTTCAACTTTC 60.049 44.000 0.00 0.00 34.62 2.62
1902 1915 5.054477 TGGAGGTTTCTAGTTCAACTTTCG 58.946 41.667 0.00 0.00 0.00 3.46
1903 1916 4.083961 GGAGGTTTCTAGTTCAACTTTCGC 60.084 45.833 0.00 0.00 0.00 4.70
1904 1917 3.493503 AGGTTTCTAGTTCAACTTTCGCG 59.506 43.478 0.00 0.00 0.00 5.87
1905 1918 3.246936 GGTTTCTAGTTCAACTTTCGCGT 59.753 43.478 5.77 0.00 0.00 6.01
1906 1919 4.445385 GGTTTCTAGTTCAACTTTCGCGTA 59.555 41.667 5.77 0.00 0.00 4.42
1907 1920 5.388164 GGTTTCTAGTTCAACTTTCGCGTAG 60.388 44.000 5.77 7.77 0.00 3.51
1908 1921 4.494350 TCTAGTTCAACTTTCGCGTAGT 57.506 40.909 5.77 8.49 0.00 2.73
1909 1922 5.611796 TCTAGTTCAACTTTCGCGTAGTA 57.388 39.130 14.98 0.96 0.00 1.82
1910 1923 5.385617 TCTAGTTCAACTTTCGCGTAGTAC 58.614 41.667 14.98 10.70 0.00 2.73
1911 1924 3.968649 AGTTCAACTTTCGCGTAGTACA 58.031 40.909 14.98 4.58 0.00 2.90
1912 1925 3.979495 AGTTCAACTTTCGCGTAGTACAG 59.021 43.478 14.98 9.64 0.00 2.74
1913 1926 3.902261 TCAACTTTCGCGTAGTACAGA 57.098 42.857 14.98 11.29 0.00 3.41
1914 1927 4.227512 TCAACTTTCGCGTAGTACAGAA 57.772 40.909 14.98 2.86 0.00 3.02
1915 1928 4.609947 TCAACTTTCGCGTAGTACAGAAA 58.390 39.130 14.98 15.70 0.00 2.52
1916 1929 5.224888 TCAACTTTCGCGTAGTACAGAAAT 58.775 37.500 16.46 5.48 32.97 2.17
1917 1930 6.380995 TCAACTTTCGCGTAGTACAGAAATA 58.619 36.000 16.46 2.33 32.97 1.40
1918 1931 7.031372 TCAACTTTCGCGTAGTACAGAAATAT 58.969 34.615 16.46 9.00 32.97 1.28
1919 1932 7.219535 TCAACTTTCGCGTAGTACAGAAATATC 59.780 37.037 16.46 0.00 32.97 1.63
1920 1933 5.975939 ACTTTCGCGTAGTACAGAAATATCC 59.024 40.000 16.46 0.00 32.97 2.59
1921 1934 5.762825 TTCGCGTAGTACAGAAATATCCT 57.237 39.130 5.77 0.00 0.00 3.24
1922 1935 5.354054 TCGCGTAGTACAGAAATATCCTC 57.646 43.478 5.77 0.00 0.00 3.71
1923 1936 4.084171 TCGCGTAGTACAGAAATATCCTCG 60.084 45.833 5.77 0.00 0.00 4.63
1924 1937 3.913163 GCGTAGTACAGAAATATCCTCGC 59.087 47.826 0.38 0.00 0.00 5.03
1925 1938 4.320348 GCGTAGTACAGAAATATCCTCGCT 60.320 45.833 0.38 0.00 36.68 4.93
1926 1939 5.759963 CGTAGTACAGAAATATCCTCGCTT 58.240 41.667 0.38 0.00 0.00 4.68
1927 1940 6.207213 CGTAGTACAGAAATATCCTCGCTTT 58.793 40.000 0.38 0.00 0.00 3.51
1928 1941 6.360148 CGTAGTACAGAAATATCCTCGCTTTC 59.640 42.308 0.38 0.00 0.00 2.62
1929 1942 5.602628 AGTACAGAAATATCCTCGCTTTCC 58.397 41.667 0.00 0.00 30.84 3.13
1930 1943 4.487714 ACAGAAATATCCTCGCTTTCCA 57.512 40.909 0.00 0.00 30.84 3.53
1931 1944 4.843728 ACAGAAATATCCTCGCTTTCCAA 58.156 39.130 0.00 0.00 30.84 3.53
1932 1945 5.440610 ACAGAAATATCCTCGCTTTCCAAT 58.559 37.500 0.00 0.00 30.84 3.16
1933 1946 5.888161 ACAGAAATATCCTCGCTTTCCAATT 59.112 36.000 0.00 0.00 30.84 2.32
1934 1947 6.378280 ACAGAAATATCCTCGCTTTCCAATTT 59.622 34.615 0.00 0.00 30.84 1.82
1935 1948 7.093771 ACAGAAATATCCTCGCTTTCCAATTTT 60.094 33.333 0.00 0.00 30.84 1.82
1936 1949 7.221452 CAGAAATATCCTCGCTTTCCAATTTTG 59.779 37.037 0.00 0.00 30.84 2.44
1937 1950 6.530019 AATATCCTCGCTTTCCAATTTTGT 57.470 33.333 0.00 0.00 0.00 2.83
1938 1951 3.915437 TCCTCGCTTTCCAATTTTGTC 57.085 42.857 0.00 0.00 0.00 3.18
1939 1952 2.556622 TCCTCGCTTTCCAATTTTGTCC 59.443 45.455 0.00 0.00 0.00 4.02
1940 1953 2.558359 CCTCGCTTTCCAATTTTGTCCT 59.442 45.455 0.00 0.00 0.00 3.85
1941 1954 3.366374 CCTCGCTTTCCAATTTTGTCCTC 60.366 47.826 0.00 0.00 0.00 3.71
1942 1955 2.225491 TCGCTTTCCAATTTTGTCCTCG 59.775 45.455 0.00 0.00 0.00 4.63
1943 1956 2.328473 GCTTTCCAATTTTGTCCTCGC 58.672 47.619 0.00 0.00 0.00 5.03
1944 1957 2.926586 GCTTTCCAATTTTGTCCTCGCC 60.927 50.000 0.00 0.00 0.00 5.54
1945 1958 0.878416 TTCCAATTTTGTCCTCGCCG 59.122 50.000 0.00 0.00 0.00 6.46
1946 1959 0.958382 TCCAATTTTGTCCTCGCCGG 60.958 55.000 0.00 0.00 0.00 6.13
1947 1960 1.154035 CAATTTTGTCCTCGCCGGC 60.154 57.895 19.07 19.07 0.00 6.13
1948 1961 2.340328 AATTTTGTCCTCGCCGGCC 61.340 57.895 23.46 6.80 0.00 6.13
1949 1962 2.764637 AATTTTGTCCTCGCCGGCCT 62.765 55.000 23.46 0.00 0.00 5.19
1950 1963 2.764637 ATTTTGTCCTCGCCGGCCTT 62.765 55.000 23.46 0.00 0.00 4.35
1951 1964 3.894547 TTTGTCCTCGCCGGCCTTC 62.895 63.158 23.46 7.82 0.00 3.46
1964 1977 4.785512 CCTTCGCACTCGCTCGCT 62.786 66.667 0.00 0.00 35.30 4.93
1965 1978 3.243892 CTTCGCACTCGCTCGCTC 61.244 66.667 0.00 0.00 35.30 5.03
1966 1979 3.953444 CTTCGCACTCGCTCGCTCA 62.953 63.158 0.00 0.00 35.30 4.26
1967 1980 4.760840 TCGCACTCGCTCGCTCAC 62.761 66.667 0.00 0.00 35.30 3.51
1968 1981 4.767841 CGCACTCGCTCGCTCACT 62.768 66.667 0.00 0.00 35.30 3.41
1969 1982 2.878520 GCACTCGCTCGCTCACTC 60.879 66.667 0.00 0.00 34.30 3.51
1970 1983 2.563427 CACTCGCTCGCTCACTCA 59.437 61.111 0.00 0.00 0.00 3.41
1971 1984 1.799519 CACTCGCTCGCTCACTCAC 60.800 63.158 0.00 0.00 0.00 3.51
1972 1985 1.969064 ACTCGCTCGCTCACTCACT 60.969 57.895 0.00 0.00 0.00 3.41
1973 1986 1.226267 CTCGCTCGCTCACTCACTC 60.226 63.158 0.00 0.00 0.00 3.51
1974 1987 2.575525 CGCTCGCTCACTCACTCG 60.576 66.667 0.00 0.00 0.00 4.18
1975 1988 2.878520 GCTCGCTCACTCACTCGC 60.879 66.667 0.00 0.00 0.00 5.03
1976 1989 2.202544 CTCGCTCACTCACTCGCC 60.203 66.667 0.00 0.00 0.00 5.54
1977 1990 3.691744 CTCGCTCACTCACTCGCCC 62.692 68.421 0.00 0.00 0.00 6.13
1978 1991 4.056125 CGCTCACTCACTCGCCCA 62.056 66.667 0.00 0.00 0.00 5.36
1979 1992 2.125753 GCTCACTCACTCGCCCAG 60.126 66.667 0.00 0.00 0.00 4.45
1980 1993 2.125753 CTCACTCACTCGCCCAGC 60.126 66.667 0.00 0.00 0.00 4.85
1981 1994 3.655810 CTCACTCACTCGCCCAGCC 62.656 68.421 0.00 0.00 0.00 4.85
1992 2005 3.052082 CCCAGCCGCACTCACTTG 61.052 66.667 0.00 0.00 0.00 3.16
1993 2006 3.730761 CCAGCCGCACTCACTTGC 61.731 66.667 0.00 0.00 39.28 4.01
1994 2007 2.667536 CAGCCGCACTCACTTGCT 60.668 61.111 0.00 0.00 40.62 3.91
1995 2008 2.358003 AGCCGCACTCACTTGCTC 60.358 61.111 0.00 0.00 40.62 4.26
1996 2009 3.782244 GCCGCACTCACTTGCTCG 61.782 66.667 0.00 0.00 40.62 5.03
1997 2010 2.356313 CCGCACTCACTTGCTCGT 60.356 61.111 0.00 0.00 40.62 4.18
1998 2011 2.661566 CCGCACTCACTTGCTCGTG 61.662 63.158 0.29 0.29 40.62 4.35
1999 2012 2.553268 GCACTCACTTGCTCGTGC 59.447 61.111 1.71 1.71 44.73 5.34
2000 2013 1.958205 GCACTCACTTGCTCGTGCT 60.958 57.895 11.19 0.00 46.70 4.40
2001 2014 1.895280 GCACTCACTTGCTCGTGCTC 61.895 60.000 11.19 0.00 46.70 4.26
2002 2015 0.319383 CACTCACTTGCTCGTGCTCT 60.319 55.000 11.19 0.00 40.48 4.09
2003 2016 0.038709 ACTCACTTGCTCGTGCTCTC 60.039 55.000 11.19 0.00 40.48 3.20
2004 2017 0.243365 CTCACTTGCTCGTGCTCTCT 59.757 55.000 11.19 0.00 40.48 3.10
2005 2018 0.242286 TCACTTGCTCGTGCTCTCTC 59.758 55.000 11.19 0.00 40.48 3.20
2006 2019 1.069924 CACTTGCTCGTGCTCTCTCG 61.070 60.000 11.19 0.00 40.48 4.04
2007 2020 2.126307 TTGCTCGTGCTCTCTCGC 60.126 61.111 11.19 0.00 40.48 5.03
2008 2021 3.953444 TTGCTCGTGCTCTCTCGCG 62.953 63.158 11.19 0.00 40.48 5.87
2010 2023 4.172772 CTCGTGCTCTCTCGCGCT 62.173 66.667 5.56 0.00 39.55 5.92
2011 2024 3.675482 CTCGTGCTCTCTCGCGCTT 62.675 63.158 5.56 0.00 39.55 4.68
2012 2025 3.243892 CGTGCTCTCTCGCGCTTC 61.244 66.667 5.56 0.00 38.23 3.86
2013 2026 2.180518 GTGCTCTCTCGCGCTTCT 59.819 61.111 5.56 0.00 37.43 2.85
2014 2027 1.871789 GTGCTCTCTCGCGCTTCTC 60.872 63.158 5.56 0.00 37.43 2.87
2015 2028 2.650602 GCTCTCTCGCGCTTCTCG 60.651 66.667 5.56 0.00 42.12 4.04
2039 2052 4.491409 GCCGGCCTTCCCCTTCTC 62.491 72.222 18.11 0.00 0.00 2.87
2040 2053 4.162690 CCGGCCTTCCCCTTCTCG 62.163 72.222 0.00 0.00 0.00 4.04
2041 2054 4.840005 CGGCCTTCCCCTTCTCGC 62.840 72.222 0.00 0.00 0.00 5.03
2042 2055 4.491409 GGCCTTCCCCTTCTCGCC 62.491 72.222 0.00 0.00 0.00 5.54
2043 2056 3.403558 GCCTTCCCCTTCTCGCCT 61.404 66.667 0.00 0.00 0.00 5.52
2044 2057 2.586792 CCTTCCCCTTCTCGCCTG 59.413 66.667 0.00 0.00 0.00 4.85
2045 2058 2.124942 CTTCCCCTTCTCGCCTGC 60.125 66.667 0.00 0.00 0.00 4.85
2046 2059 3.689002 CTTCCCCTTCTCGCCTGCC 62.689 68.421 0.00 0.00 0.00 4.85
2047 2060 4.722535 TCCCCTTCTCGCCTGCCT 62.723 66.667 0.00 0.00 0.00 4.75
2048 2061 4.168291 CCCCTTCTCGCCTGCCTC 62.168 72.222 0.00 0.00 0.00 4.70
2049 2062 4.168291 CCCTTCTCGCCTGCCTCC 62.168 72.222 0.00 0.00 0.00 4.30
2050 2063 4.168291 CCTTCTCGCCTGCCTCCC 62.168 72.222 0.00 0.00 0.00 4.30
2051 2064 4.168291 CTTCTCGCCTGCCTCCCC 62.168 72.222 0.00 0.00 0.00 4.81
2052 2065 4.722535 TTCTCGCCTGCCTCCCCT 62.723 66.667 0.00 0.00 0.00 4.79
2089 2102 1.759881 CCTCAGGGCATCTCCATCC 59.240 63.158 0.00 0.00 36.21 3.51
2090 2103 1.370437 CTCAGGGCATCTCCATCCG 59.630 63.158 0.00 0.00 36.21 4.18
2091 2104 2.281345 CAGGGCATCTCCATCCGC 60.281 66.667 0.00 0.00 36.21 5.54
2092 2105 3.933722 AGGGCATCTCCATCCGCG 61.934 66.667 0.00 0.00 36.21 6.46
2096 2109 4.996434 CATCTCCATCCGCGCCCC 62.996 72.222 0.00 0.00 0.00 5.80
2113 2126 2.941025 CCAGGAAGGCCTCCCCAA 60.941 66.667 22.02 0.00 46.81 4.12
2114 2127 2.547595 CCAGGAAGGCCTCCCCAAA 61.548 63.158 22.02 0.00 46.81 3.28
2115 2128 1.304464 CAGGAAGGCCTCCCCAAAC 60.304 63.158 22.02 2.76 46.81 2.93
2116 2129 2.361230 GGAAGGCCTCCCCAAACG 60.361 66.667 5.23 0.00 38.44 3.60
2117 2130 2.434774 GAAGGCCTCCCCAAACGT 59.565 61.111 5.23 0.00 35.39 3.99
2118 2131 1.228459 GAAGGCCTCCCCAAACGTT 60.228 57.895 5.23 0.00 35.39 3.99
2119 2132 0.826256 GAAGGCCTCCCCAAACGTTT 60.826 55.000 5.23 7.96 35.39 3.60
2120 2133 0.397957 AAGGCCTCCCCAAACGTTTT 60.398 50.000 11.66 0.00 35.39 2.43
2121 2134 0.397957 AGGCCTCCCCAAACGTTTTT 60.398 50.000 11.66 0.00 35.39 1.94
2137 2150 2.960659 TTTTTGCGTCGGCGTCGA 60.961 55.556 28.81 8.66 44.10 4.20
2145 2158 3.465753 TCGGCGTCGAAAAATCGG 58.534 55.556 10.97 0.00 43.03 4.18
2146 2159 2.276430 CGGCGTCGAAAAATCGGC 60.276 61.111 1.44 8.59 44.41 5.54
2147 2160 2.099638 GGCGTCGAAAAATCGGCC 59.900 61.111 7.57 0.00 42.65 6.13
2148 2161 2.099638 GCGTCGAAAAATCGGCCC 59.900 61.111 0.00 0.00 33.73 5.80
2149 2162 2.682876 GCGTCGAAAAATCGGCCCA 61.683 57.895 0.00 0.00 33.73 5.36
2150 2163 1.423845 CGTCGAAAAATCGGCCCAG 59.576 57.895 0.00 0.00 33.73 4.45
2151 2164 1.296056 CGTCGAAAAATCGGCCCAGT 61.296 55.000 0.00 0.00 33.73 4.00
2152 2165 0.446616 GTCGAAAAATCGGCCCAGTC 59.553 55.000 0.00 0.00 0.00 3.51
2153 2166 1.017177 TCGAAAAATCGGCCCAGTCG 61.017 55.000 0.00 0.00 0.00 4.18
2154 2167 1.136774 GAAAAATCGGCCCAGTCGC 59.863 57.895 0.00 0.00 0.00 5.19
2155 2168 2.577763 GAAAAATCGGCCCAGTCGCG 62.578 60.000 0.00 0.00 0.00 5.87
2173 2186 3.420482 CCCCCAGGAGCCCGATTT 61.420 66.667 0.00 0.00 33.47 2.17
2174 2187 2.683475 CCCCAGGAGCCCGATTTT 59.317 61.111 0.00 0.00 0.00 1.82
2175 2188 1.453928 CCCCAGGAGCCCGATTTTC 60.454 63.158 0.00 0.00 0.00 2.29
2176 2189 1.819632 CCCAGGAGCCCGATTTTCG 60.820 63.158 0.00 0.00 40.07 3.46
2177 2190 2.472909 CCAGGAGCCCGATTTTCGC 61.473 63.158 0.00 0.00 38.82 4.70
2178 2191 2.124695 AGGAGCCCGATTTTCGCC 60.125 61.111 0.00 0.00 38.82 5.54
2179 2192 3.573491 GGAGCCCGATTTTCGCCG 61.573 66.667 0.00 0.00 38.82 6.46
2180 2193 3.573491 GAGCCCGATTTTCGCCGG 61.573 66.667 0.00 0.00 44.94 6.13
2181 2194 4.404098 AGCCCGATTTTCGCCGGT 62.404 61.111 1.90 0.00 43.93 5.28
2182 2195 3.872728 GCCCGATTTTCGCCGGTC 61.873 66.667 1.90 0.00 43.93 4.79
2183 2196 2.125269 CCCGATTTTCGCCGGTCT 60.125 61.111 1.90 0.00 43.93 3.85
2184 2197 2.461110 CCCGATTTTCGCCGGTCTG 61.461 63.158 1.90 0.00 43.93 3.51
2185 2198 2.461110 CCGATTTTCGCCGGTCTGG 61.461 63.158 1.90 0.00 40.78 3.86
2186 2199 2.461110 CGATTTTCGCCGGTCTGGG 61.461 63.158 1.90 0.00 38.63 4.45
2196 2209 3.668386 GGTCTGGGCCGAAAACAG 58.332 61.111 0.00 0.00 0.00 3.16
2197 2210 2.626780 GGTCTGGGCCGAAAACAGC 61.627 63.158 0.00 0.00 32.42 4.40
2198 2211 2.668212 TCTGGGCCGAAAACAGCG 60.668 61.111 0.00 0.00 32.42 5.18
2199 2212 4.404654 CTGGGCCGAAAACAGCGC 62.405 66.667 0.00 0.00 41.90 5.92
2305 2318 4.077188 GCGTCAGCAACACGGCTC 62.077 66.667 4.55 0.00 43.68 4.70
2306 2319 2.356313 CGTCAGCAACACGGCTCT 60.356 61.111 0.00 0.00 43.68 4.09
2307 2320 2.375766 CGTCAGCAACACGGCTCTC 61.376 63.158 0.00 0.00 43.68 3.20
2308 2321 1.005630 GTCAGCAACACGGCTCTCT 60.006 57.895 0.00 0.00 43.68 3.10
2309 2322 0.601311 GTCAGCAACACGGCTCTCTT 60.601 55.000 0.00 0.00 43.68 2.85
2310 2323 0.319900 TCAGCAACACGGCTCTCTTC 60.320 55.000 0.00 0.00 43.68 2.87
2311 2324 0.320247 CAGCAACACGGCTCTCTTCT 60.320 55.000 0.00 0.00 43.68 2.85
2312 2325 0.037790 AGCAACACGGCTCTCTTCTC 60.038 55.000 0.00 0.00 41.05 2.87
2313 2326 1.347817 GCAACACGGCTCTCTTCTCG 61.348 60.000 0.00 0.00 0.00 4.04
2314 2327 0.734253 CAACACGGCTCTCTTCTCGG 60.734 60.000 0.00 0.00 0.00 4.63
2315 2328 2.202676 CACGGCTCTCTTCTCGGC 60.203 66.667 0.00 0.00 0.00 5.54
2316 2329 2.361865 ACGGCTCTCTTCTCGGCT 60.362 61.111 0.00 0.00 0.00 5.52
2317 2330 2.411290 CGGCTCTCTTCTCGGCTC 59.589 66.667 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.884774 AGCCACCCGGTTCAAGCA 61.885 61.111 0.00 0.00 33.28 3.91
247 248 3.777087 TGGAAGATCCATTTGCAAAGGA 58.223 40.909 24.45 24.00 42.67 3.36
330 333 6.715280 TCTCCAAGCTGTAATCTTCATCTTT 58.285 36.000 0.00 0.00 0.00 2.52
363 366 1.687660 TGTTGAGTAGCCAACGTACCA 59.312 47.619 0.00 0.00 46.89 3.25
419 422 1.908793 ACCCCACAGAGAGGACACG 60.909 63.158 0.00 0.00 0.00 4.49
537 540 6.073314 CCATTCCTTCCCATTATCAATGAGT 58.927 40.000 0.46 0.00 41.46 3.41
633 637 6.474427 CGTGGTAGATGTCATTACGTATTTGT 59.526 38.462 0.00 0.00 0.00 2.83
636 640 5.526115 CCGTGGTAGATGTCATTACGTATT 58.474 41.667 0.00 0.00 0.00 1.89
814 818 1.665442 GTGTCGGCCAAGGCAAAAT 59.335 52.632 13.87 0.00 44.11 1.82
901 905 5.604650 CCTCACTATTCCTTAGAACCATCCT 59.395 44.000 0.00 0.00 33.97 3.24
985 993 3.809279 CCTTGCATCATCGCATGTAGTTA 59.191 43.478 0.00 0.00 42.62 2.24
1042 1050 3.559069 AGGAATCCGATTGCAACATCAT 58.441 40.909 14.31 0.00 32.49 2.45
1081 1089 0.320683 CACAGAGCATCCGTGGACAA 60.321 55.000 0.00 0.00 33.66 3.18
1099 1107 1.153046 GGCCATAAGCTAACCGCCA 60.153 57.895 0.00 0.00 43.05 5.69
1178 1186 4.688021 GGCAACTCTATTCTGAGAACGAT 58.312 43.478 0.00 0.00 37.50 3.73
1294 1302 6.828502 TTATTGCAAGCTCATAGAGTTACG 57.171 37.500 4.94 0.00 31.39 3.18
1307 1315 5.168569 GGTAAAGGGAGTTTTATTGCAAGC 58.831 41.667 4.94 0.00 0.00 4.01
1348 1356 9.586435 CTGTTTGATTAGAGGAAACAAAAGTTT 57.414 29.630 0.00 0.00 40.32 2.66
1349 1357 8.749354 ACTGTTTGATTAGAGGAAACAAAAGTT 58.251 29.630 0.00 0.00 40.32 2.66
1350 1358 8.293699 ACTGTTTGATTAGAGGAAACAAAAGT 57.706 30.769 0.00 0.00 40.32 2.66
1374 1382 7.589954 TGAAGCGTGAGAAAGCTAAAAATTAAC 59.410 33.333 0.00 0.00 43.78 2.01
1379 1387 5.065988 AGTTGAAGCGTGAGAAAGCTAAAAA 59.934 36.000 0.00 0.00 43.78 1.94
1383 1391 3.386768 AGTTGAAGCGTGAGAAAGCTA 57.613 42.857 0.00 0.00 43.78 3.32
1395 1403 7.719778 AAAAATGGAGAATGAAAGTTGAAGC 57.280 32.000 0.00 0.00 0.00 3.86
1403 1411 7.179338 TCGGGGAATTAAAAATGGAGAATGAAA 59.821 33.333 0.00 0.00 0.00 2.69
1404 1412 6.665680 TCGGGGAATTAAAAATGGAGAATGAA 59.334 34.615 0.00 0.00 0.00 2.57
1405 1413 6.191315 TCGGGGAATTAAAAATGGAGAATGA 58.809 36.000 0.00 0.00 0.00 2.57
1411 1419 4.417437 TGGTTCGGGGAATTAAAAATGGA 58.583 39.130 0.00 0.00 0.00 3.41
1418 1426 2.553172 CGTGTTTGGTTCGGGGAATTAA 59.447 45.455 0.00 0.00 0.00 1.40
1419 1427 2.152830 CGTGTTTGGTTCGGGGAATTA 58.847 47.619 0.00 0.00 0.00 1.40
1443 1451 0.897863 CTCTCCCTCTCCCTATGCGG 60.898 65.000 0.00 0.00 0.00 5.69
1444 1452 0.111446 TCTCTCCCTCTCCCTATGCG 59.889 60.000 0.00 0.00 0.00 4.73
1464 1472 5.059833 CACCTAAAGCCTATGGTCAATCTC 58.940 45.833 0.00 0.00 0.00 2.75
1529 1537 0.178955 TGGTCGGGGTGAGACTACAA 60.179 55.000 0.00 0.00 38.58 2.41
1545 1553 1.205417 GCAATGGTTTATGCAGCTGGT 59.795 47.619 17.12 0.00 42.12 4.00
1630 1638 2.305927 AGGGTCTCACGGTCATGAATTT 59.694 45.455 0.00 0.00 0.00 1.82
1657 1665 8.139989 ACCGTACACCTTGCTACTAATAATAAG 58.860 37.037 0.00 0.00 0.00 1.73
1686 1694 0.031585 GCGGGGGTTTGAACAAGTTC 59.968 55.000 6.01 6.01 39.91 3.01
1700 1708 2.202932 CGGTTGATCAGAGCGGGG 60.203 66.667 16.51 0.00 34.64 5.73
1768 1781 2.737376 GCCTCGTCGGAAAAGCGT 60.737 61.111 0.00 0.00 33.16 5.07
1777 1790 2.278206 CGATCCACTGCCTCGTCG 60.278 66.667 0.00 0.00 0.00 5.12
1806 1819 6.204688 AGAGATCACAACAAAAGTAATGCGAA 59.795 34.615 0.00 0.00 0.00 4.70
1808 1821 5.931532 AGAGATCACAACAAAAGTAATGCG 58.068 37.500 0.00 0.00 0.00 4.73
1828 1841 9.109393 GGAGTAGATAGCTCATATCAGTAAGAG 57.891 40.741 0.00 0.00 42.51 2.85
1835 1848 6.012069 ACAGAGGGAGTAGATAGCTCATATCA 60.012 42.308 0.00 0.00 42.51 2.15
1848 1861 7.176589 ACTATTTCTGAAACAGAGGGAGTAG 57.823 40.000 14.84 7.53 41.75 2.57
1849 1862 7.016268 ACAACTATTTCTGAAACAGAGGGAGTA 59.984 37.037 14.84 0.00 41.75 2.59
1850 1863 6.183361 ACAACTATTTCTGAAACAGAGGGAGT 60.183 38.462 14.84 3.60 41.75 3.85
1851 1864 6.234177 ACAACTATTTCTGAAACAGAGGGAG 58.766 40.000 14.84 3.07 41.75 4.30
1852 1865 6.187727 ACAACTATTTCTGAAACAGAGGGA 57.812 37.500 14.84 0.00 41.75 4.20
1853 1866 5.120830 CGACAACTATTTCTGAAACAGAGGG 59.879 44.000 14.84 6.37 41.75 4.30
1854 1867 5.389935 GCGACAACTATTTCTGAAACAGAGG 60.390 44.000 14.84 8.52 41.75 3.69
1855 1868 5.406780 AGCGACAACTATTTCTGAAACAGAG 59.593 40.000 14.84 10.31 41.75 3.35
1856 1869 5.177511 CAGCGACAACTATTTCTGAAACAGA 59.822 40.000 14.84 0.00 38.87 3.41
1857 1870 5.377358 CAGCGACAACTATTTCTGAAACAG 58.623 41.667 6.87 6.87 0.00 3.16
1858 1871 4.213270 CCAGCGACAACTATTTCTGAAACA 59.787 41.667 4.73 0.00 0.00 2.83
1859 1872 4.451096 TCCAGCGACAACTATTTCTGAAAC 59.549 41.667 4.73 0.00 0.00 2.78
1860 1873 4.637276 TCCAGCGACAACTATTTCTGAAA 58.363 39.130 5.15 5.15 0.00 2.69
1861 1874 4.245660 CTCCAGCGACAACTATTTCTGAA 58.754 43.478 0.00 0.00 0.00 3.02
1862 1875 3.368427 CCTCCAGCGACAACTATTTCTGA 60.368 47.826 0.00 0.00 0.00 3.27
1863 1876 2.932614 CCTCCAGCGACAACTATTTCTG 59.067 50.000 0.00 0.00 0.00 3.02
1864 1877 2.567615 ACCTCCAGCGACAACTATTTCT 59.432 45.455 0.00 0.00 0.00 2.52
1865 1878 2.973945 ACCTCCAGCGACAACTATTTC 58.026 47.619 0.00 0.00 0.00 2.17
1866 1879 3.418684 AACCTCCAGCGACAACTATTT 57.581 42.857 0.00 0.00 0.00 1.40
1867 1880 3.008049 AGAAACCTCCAGCGACAACTATT 59.992 43.478 0.00 0.00 0.00 1.73
1868 1881 2.567615 AGAAACCTCCAGCGACAACTAT 59.432 45.455 0.00 0.00 0.00 2.12
1869 1882 1.968493 AGAAACCTCCAGCGACAACTA 59.032 47.619 0.00 0.00 0.00 2.24
1870 1883 0.759346 AGAAACCTCCAGCGACAACT 59.241 50.000 0.00 0.00 0.00 3.16
1871 1884 2.288886 ACTAGAAACCTCCAGCGACAAC 60.289 50.000 0.00 0.00 0.00 3.32
1872 1885 1.968493 ACTAGAAACCTCCAGCGACAA 59.032 47.619 0.00 0.00 0.00 3.18
1873 1886 1.629043 ACTAGAAACCTCCAGCGACA 58.371 50.000 0.00 0.00 0.00 4.35
1874 1887 2.029290 TGAACTAGAAACCTCCAGCGAC 60.029 50.000 0.00 0.00 0.00 5.19
1875 1888 2.244695 TGAACTAGAAACCTCCAGCGA 58.755 47.619 0.00 0.00 0.00 4.93
1876 1889 2.737252 GTTGAACTAGAAACCTCCAGCG 59.263 50.000 0.00 0.00 0.00 5.18
1877 1890 4.009370 AGTTGAACTAGAAACCTCCAGC 57.991 45.455 0.00 0.00 0.00 4.85
1878 1891 5.177696 CGAAAGTTGAACTAGAAACCTCCAG 59.822 44.000 0.00 0.00 0.00 3.86
1879 1892 5.054477 CGAAAGTTGAACTAGAAACCTCCA 58.946 41.667 0.00 0.00 0.00 3.86
1880 1893 4.083961 GCGAAAGTTGAACTAGAAACCTCC 60.084 45.833 0.00 0.00 0.00 4.30
1881 1894 4.376109 CGCGAAAGTTGAACTAGAAACCTC 60.376 45.833 0.00 0.00 0.00 3.85
1882 1895 3.493503 CGCGAAAGTTGAACTAGAAACCT 59.506 43.478 0.00 0.00 0.00 3.50
1883 1896 3.246936 ACGCGAAAGTTGAACTAGAAACC 59.753 43.478 15.93 0.00 0.00 3.27
1884 1897 4.448363 ACGCGAAAGTTGAACTAGAAAC 57.552 40.909 15.93 0.00 0.00 2.78
1885 1898 5.284079 ACTACGCGAAAGTTGAACTAGAAA 58.716 37.500 15.93 0.00 0.00 2.52
1886 1899 4.863491 ACTACGCGAAAGTTGAACTAGAA 58.137 39.130 15.93 0.00 0.00 2.10
1887 1900 4.494350 ACTACGCGAAAGTTGAACTAGA 57.506 40.909 15.93 0.00 0.00 2.43
1888 1901 5.149273 TGTACTACGCGAAAGTTGAACTAG 58.851 41.667 15.93 1.83 0.00 2.57
1889 1902 5.049474 TCTGTACTACGCGAAAGTTGAACTA 60.049 40.000 15.93 0.00 0.00 2.24
1890 1903 3.968649 TGTACTACGCGAAAGTTGAACT 58.031 40.909 15.93 0.00 0.00 3.01
1891 1904 3.976942 TCTGTACTACGCGAAAGTTGAAC 59.023 43.478 15.93 11.42 0.00 3.18
1892 1905 4.227512 TCTGTACTACGCGAAAGTTGAA 57.772 40.909 15.93 4.40 0.00 2.69
1893 1906 3.902261 TCTGTACTACGCGAAAGTTGA 57.098 42.857 15.93 11.66 0.00 3.18
1894 1907 4.959631 TTTCTGTACTACGCGAAAGTTG 57.040 40.909 15.93 9.67 0.00 3.16
1895 1908 6.474751 GGATATTTCTGTACTACGCGAAAGTT 59.525 38.462 15.93 1.52 0.00 2.66
1896 1909 5.975939 GGATATTTCTGTACTACGCGAAAGT 59.024 40.000 15.93 18.30 0.00 2.66
1897 1910 6.207213 AGGATATTTCTGTACTACGCGAAAG 58.793 40.000 15.93 12.73 0.00 2.62
1898 1911 6.140303 AGGATATTTCTGTACTACGCGAAA 57.860 37.500 15.93 0.00 0.00 3.46
1899 1912 5.559608 CGAGGATATTTCTGTACTACGCGAA 60.560 44.000 15.93 0.00 0.00 4.70
1900 1913 4.084171 CGAGGATATTTCTGTACTACGCGA 60.084 45.833 15.93 0.00 0.00 5.87
1901 1914 4.149617 CGAGGATATTTCTGTACTACGCG 58.850 47.826 3.53 3.53 0.00 6.01
1902 1915 3.913163 GCGAGGATATTTCTGTACTACGC 59.087 47.826 0.00 0.00 35.06 4.42
1903 1916 5.359716 AGCGAGGATATTTCTGTACTACG 57.640 43.478 0.00 0.00 0.00 3.51
1904 1917 6.641723 GGAAAGCGAGGATATTTCTGTACTAC 59.358 42.308 0.00 0.00 34.19 2.73
1905 1918 6.322969 TGGAAAGCGAGGATATTTCTGTACTA 59.677 38.462 0.00 0.00 34.19 1.82
1906 1919 5.128827 TGGAAAGCGAGGATATTTCTGTACT 59.871 40.000 0.00 0.00 34.19 2.73
1907 1920 5.357257 TGGAAAGCGAGGATATTTCTGTAC 58.643 41.667 0.00 0.00 34.19 2.90
1908 1921 5.607939 TGGAAAGCGAGGATATTTCTGTA 57.392 39.130 0.00 0.00 34.19 2.74
1909 1922 4.487714 TGGAAAGCGAGGATATTTCTGT 57.512 40.909 0.00 0.00 34.19 3.41
1910 1923 6.382869 AATTGGAAAGCGAGGATATTTCTG 57.617 37.500 0.00 0.00 34.19 3.02
1911 1924 7.093771 ACAAAATTGGAAAGCGAGGATATTTCT 60.094 33.333 0.00 0.00 34.19 2.52
1912 1925 7.035612 ACAAAATTGGAAAGCGAGGATATTTC 58.964 34.615 0.00 0.00 33.20 2.17
1913 1926 6.935167 ACAAAATTGGAAAGCGAGGATATTT 58.065 32.000 0.00 0.00 0.00 1.40
1914 1927 6.405842 GGACAAAATTGGAAAGCGAGGATATT 60.406 38.462 0.00 0.00 0.00 1.28
1915 1928 5.067805 GGACAAAATTGGAAAGCGAGGATAT 59.932 40.000 0.00 0.00 0.00 1.63
1916 1929 4.398044 GGACAAAATTGGAAAGCGAGGATA 59.602 41.667 0.00 0.00 0.00 2.59
1917 1930 3.193479 GGACAAAATTGGAAAGCGAGGAT 59.807 43.478 0.00 0.00 0.00 3.24
1918 1931 2.556622 GGACAAAATTGGAAAGCGAGGA 59.443 45.455 0.00 0.00 0.00 3.71
1919 1932 2.558359 AGGACAAAATTGGAAAGCGAGG 59.442 45.455 0.00 0.00 0.00 4.63
1920 1933 3.667960 CGAGGACAAAATTGGAAAGCGAG 60.668 47.826 0.00 0.00 0.00 5.03
1921 1934 2.225491 CGAGGACAAAATTGGAAAGCGA 59.775 45.455 0.00 0.00 0.00 4.93
1922 1935 2.584791 CGAGGACAAAATTGGAAAGCG 58.415 47.619 0.00 0.00 0.00 4.68
1923 1936 2.328473 GCGAGGACAAAATTGGAAAGC 58.672 47.619 0.00 0.00 0.00 3.51
1924 1937 2.668279 CGGCGAGGACAAAATTGGAAAG 60.668 50.000 0.00 0.00 0.00 2.62
1925 1938 1.268352 CGGCGAGGACAAAATTGGAAA 59.732 47.619 0.00 0.00 0.00 3.13
1926 1939 0.878416 CGGCGAGGACAAAATTGGAA 59.122 50.000 0.00 0.00 0.00 3.53
1927 1940 0.958382 CCGGCGAGGACAAAATTGGA 60.958 55.000 9.30 0.00 45.00 3.53
1928 1941 1.506262 CCGGCGAGGACAAAATTGG 59.494 57.895 9.30 0.00 45.00 3.16
1929 1942 1.154035 GCCGGCGAGGACAAAATTG 60.154 57.895 12.58 0.00 45.00 2.32
1930 1943 3.274067 GCCGGCGAGGACAAAATT 58.726 55.556 12.58 0.00 45.00 1.82
1952 1965 2.878520 GAGTGAGCGAGCGAGTGC 60.879 66.667 0.00 0.00 43.24 4.40
1953 1966 1.799519 GTGAGTGAGCGAGCGAGTG 60.800 63.158 0.00 0.00 0.00 3.51
1954 1967 1.917782 GAGTGAGTGAGCGAGCGAGT 61.918 60.000 0.00 0.00 0.00 4.18
1955 1968 1.226267 GAGTGAGTGAGCGAGCGAG 60.226 63.158 0.00 0.00 0.00 5.03
1956 1969 2.871099 GAGTGAGTGAGCGAGCGA 59.129 61.111 0.00 0.00 0.00 4.93
1957 1970 2.575525 CGAGTGAGTGAGCGAGCG 60.576 66.667 0.00 0.00 0.00 5.03
1958 1971 2.878520 GCGAGTGAGTGAGCGAGC 60.879 66.667 0.00 0.00 0.00 5.03
1959 1972 2.202544 GGCGAGTGAGTGAGCGAG 60.203 66.667 0.00 0.00 0.00 5.03
1960 1973 3.749064 GGGCGAGTGAGTGAGCGA 61.749 66.667 0.00 0.00 0.00 4.93
1961 1974 3.978723 CTGGGCGAGTGAGTGAGCG 62.979 68.421 0.00 0.00 0.00 5.03
1962 1975 2.125753 CTGGGCGAGTGAGTGAGC 60.126 66.667 0.00 0.00 0.00 4.26
1963 1976 2.125753 GCTGGGCGAGTGAGTGAG 60.126 66.667 0.00 0.00 0.00 3.51
1964 1977 3.695606 GGCTGGGCGAGTGAGTGA 61.696 66.667 0.00 0.00 0.00 3.41
1975 1988 3.052082 CAAGTGAGTGCGGCTGGG 61.052 66.667 0.00 0.00 0.00 4.45
1976 1989 3.730761 GCAAGTGAGTGCGGCTGG 61.731 66.667 0.00 0.00 34.21 4.85
1983 1996 0.319383 AGAGCACGAGCAAGTGAGTG 60.319 55.000 14.53 2.94 44.43 3.51
1984 1997 0.038709 GAGAGCACGAGCAAGTGAGT 60.039 55.000 14.53 1.93 44.43 3.41
1985 1998 0.243365 AGAGAGCACGAGCAAGTGAG 59.757 55.000 14.53 0.00 44.43 3.51
1986 1999 0.242286 GAGAGAGCACGAGCAAGTGA 59.758 55.000 14.53 0.00 44.43 3.41
1987 2000 1.069924 CGAGAGAGCACGAGCAAGTG 61.070 60.000 7.77 7.14 45.49 3.16
1988 2001 1.211449 CGAGAGAGCACGAGCAAGT 59.789 57.895 7.77 0.00 45.49 3.16
1989 2002 2.157701 GCGAGAGAGCACGAGCAAG 61.158 63.158 7.77 0.00 45.49 4.01
1990 2003 2.126307 GCGAGAGAGCACGAGCAA 60.126 61.111 7.77 0.00 45.49 3.91
1991 2004 4.467062 CGCGAGAGAGCACGAGCA 62.467 66.667 0.00 0.00 45.49 4.26
2022 2035 4.491409 GAGAAGGGGAAGGCCGGC 62.491 72.222 21.18 21.18 33.83 6.13
2023 2036 4.162690 CGAGAAGGGGAAGGCCGG 62.163 72.222 0.00 0.00 33.83 6.13
2024 2037 4.840005 GCGAGAAGGGGAAGGCCG 62.840 72.222 0.00 0.00 33.83 6.13
2025 2038 4.491409 GGCGAGAAGGGGAAGGCC 62.491 72.222 0.00 0.00 0.00 5.19
2026 2039 3.403558 AGGCGAGAAGGGGAAGGC 61.404 66.667 0.00 0.00 0.00 4.35
2027 2040 2.586792 CAGGCGAGAAGGGGAAGG 59.413 66.667 0.00 0.00 0.00 3.46
2028 2041 2.124942 GCAGGCGAGAAGGGGAAG 60.125 66.667 0.00 0.00 0.00 3.46
2029 2042 3.717294 GGCAGGCGAGAAGGGGAA 61.717 66.667 0.00 0.00 0.00 3.97
2030 2043 4.722535 AGGCAGGCGAGAAGGGGA 62.723 66.667 0.00 0.00 0.00 4.81
2031 2044 4.168291 GAGGCAGGCGAGAAGGGG 62.168 72.222 0.00 0.00 0.00 4.79
2032 2045 4.168291 GGAGGCAGGCGAGAAGGG 62.168 72.222 0.00 0.00 0.00 3.95
2033 2046 4.168291 GGGAGGCAGGCGAGAAGG 62.168 72.222 0.00 0.00 0.00 3.46
2034 2047 4.168291 GGGGAGGCAGGCGAGAAG 62.168 72.222 0.00 0.00 0.00 2.85
2035 2048 4.722535 AGGGGAGGCAGGCGAGAA 62.723 66.667 0.00 0.00 0.00 2.87
2071 2084 1.759881 GGATGGAGATGCCCTGAGG 59.240 63.158 0.00 0.00 34.97 3.86
2072 2085 1.370437 CGGATGGAGATGCCCTGAG 59.630 63.158 0.00 0.00 34.97 3.35
2073 2086 2.811514 GCGGATGGAGATGCCCTGA 61.812 63.158 0.00 0.00 34.97 3.86
2074 2087 2.281345 GCGGATGGAGATGCCCTG 60.281 66.667 0.00 0.00 34.97 4.45
2075 2088 3.933722 CGCGGATGGAGATGCCCT 61.934 66.667 0.00 0.00 34.97 5.19
2079 2092 4.996434 GGGGCGCGGATGGAGATG 62.996 72.222 8.83 0.00 0.00 2.90
2096 2109 2.547595 TTTGGGGAGGCCTTCCTGG 61.548 63.158 30.10 0.00 44.46 4.45
2097 2110 1.304464 GTTTGGGGAGGCCTTCCTG 60.304 63.158 30.10 0.00 44.46 3.86
2099 2112 2.361230 CGTTTGGGGAGGCCTTCC 60.361 66.667 23.75 23.75 46.00 3.46
2100 2113 0.826256 AAACGTTTGGGGAGGCCTTC 60.826 55.000 13.81 3.67 0.00 3.46
2101 2114 0.397957 AAAACGTTTGGGGAGGCCTT 60.398 50.000 15.46 0.00 0.00 4.35
2102 2115 0.397957 AAAAACGTTTGGGGAGGCCT 60.398 50.000 15.46 3.86 0.00 5.19
2103 2116 2.129620 AAAAACGTTTGGGGAGGCC 58.870 52.632 15.46 0.00 0.00 5.19
2120 2133 2.033328 TTTCGACGCCGACGCAAAAA 62.033 50.000 3.70 0.00 45.50 1.94
2121 2134 2.033328 TTTTCGACGCCGACGCAAAA 62.033 50.000 4.41 9.03 45.50 2.44
2122 2135 2.033328 TTTTTCGACGCCGACGCAAA 62.033 50.000 3.70 3.21 45.50 3.68
2123 2136 1.833434 ATTTTTCGACGCCGACGCAA 61.833 50.000 3.70 0.00 45.50 4.85
2124 2137 2.217964 GATTTTTCGACGCCGACGCA 62.218 55.000 3.70 0.00 45.50 5.24
2125 2138 1.576867 GATTTTTCGACGCCGACGC 60.577 57.895 3.70 0.00 45.50 5.19
2126 2139 1.294938 CGATTTTTCGACGCCGACG 60.295 57.895 1.88 1.88 45.50 5.12
2127 2140 1.058284 CCGATTTTTCGACGCCGAC 59.942 57.895 0.00 0.00 45.50 4.79
2128 2141 2.732670 GCCGATTTTTCGACGCCGA 61.733 57.895 0.00 0.00 43.96 5.54
2129 2142 2.276430 GCCGATTTTTCGACGCCG 60.276 61.111 0.00 0.00 34.64 6.46
2130 2143 2.099638 GGCCGATTTTTCGACGCC 59.900 61.111 0.00 0.00 34.44 5.68
2131 2144 2.099638 GGGCCGATTTTTCGACGC 59.900 61.111 0.00 0.00 34.64 5.19
2132 2145 1.296056 ACTGGGCCGATTTTTCGACG 61.296 55.000 0.00 0.00 34.64 5.12
2133 2146 0.446616 GACTGGGCCGATTTTTCGAC 59.553 55.000 0.00 0.00 34.64 4.20
2134 2147 1.017177 CGACTGGGCCGATTTTTCGA 61.017 55.000 0.00 0.00 34.64 3.71
2135 2148 1.423845 CGACTGGGCCGATTTTTCG 59.576 57.895 0.00 0.00 0.00 3.46
2136 2149 1.136774 GCGACTGGGCCGATTTTTC 59.863 57.895 0.00 0.00 0.00 2.29
2137 2150 2.686816 CGCGACTGGGCCGATTTTT 61.687 57.895 0.00 0.00 0.00 1.94
2138 2151 3.124921 CGCGACTGGGCCGATTTT 61.125 61.111 0.00 0.00 0.00 1.82
2156 2169 2.911221 GAAAATCGGGCTCCTGGGGG 62.911 65.000 0.00 0.00 0.00 5.40
2157 2170 1.453928 GAAAATCGGGCTCCTGGGG 60.454 63.158 0.00 0.00 0.00 4.96
2158 2171 1.819632 CGAAAATCGGGCTCCTGGG 60.820 63.158 0.00 0.00 36.00 4.45
2159 2172 2.472909 GCGAAAATCGGGCTCCTGG 61.473 63.158 1.64 0.00 40.84 4.45
2160 2173 2.472909 GGCGAAAATCGGGCTCCTG 61.473 63.158 1.64 0.00 40.84 3.86
2161 2174 2.124695 GGCGAAAATCGGGCTCCT 60.125 61.111 1.64 0.00 40.84 3.69
2162 2175 3.573491 CGGCGAAAATCGGGCTCC 61.573 66.667 0.00 0.00 40.84 4.70
2163 2176 3.573491 CCGGCGAAAATCGGGCTC 61.573 66.667 9.30 0.00 42.32 4.70
2168 2181 2.461110 CCCAGACCGGCGAAAATCG 61.461 63.158 9.30 0.00 43.89 3.34
2169 2182 2.761195 GCCCAGACCGGCGAAAATC 61.761 63.158 9.30 0.00 39.64 2.17
2170 2183 2.750237 GCCCAGACCGGCGAAAAT 60.750 61.111 9.30 0.00 39.64 1.82
2179 2192 2.626780 GCTGTTTTCGGCCCAGACC 61.627 63.158 9.85 0.00 45.68 3.85
2180 2193 2.954611 GCTGTTTTCGGCCCAGAC 59.045 61.111 9.85 0.00 45.68 3.51
2258 2271 1.483424 CGGCTTTTTCGCGCCAAAAA 61.483 50.000 21.56 21.56 46.62 1.94
2259 2272 1.946650 CGGCTTTTTCGCGCCAAAA 60.947 52.632 8.92 8.92 46.62 2.44
2260 2273 2.354072 CGGCTTTTTCGCGCCAAA 60.354 55.556 0.00 0.00 46.62 3.28
2261 2274 4.992294 GCGGCTTTTTCGCGCCAA 62.992 61.111 0.00 0.00 46.62 4.52
2288 2301 4.077188 GAGCCGTGTTGCTGACGC 62.077 66.667 0.00 0.00 42.95 5.19
2289 2302 2.356313 AGAGCCGTGTTGCTGACG 60.356 61.111 0.00 0.00 42.95 4.35
2290 2303 0.601311 AAGAGAGCCGTGTTGCTGAC 60.601 55.000 0.00 0.00 42.95 3.51
2291 2304 0.319900 GAAGAGAGCCGTGTTGCTGA 60.320 55.000 0.00 0.00 42.95 4.26
2292 2305 0.320247 AGAAGAGAGCCGTGTTGCTG 60.320 55.000 0.00 0.00 42.95 4.41
2293 2306 0.037790 GAGAAGAGAGCCGTGTTGCT 60.038 55.000 0.00 0.00 46.37 3.91
2294 2307 1.347817 CGAGAAGAGAGCCGTGTTGC 61.348 60.000 0.00 0.00 0.00 4.17
2295 2308 0.734253 CCGAGAAGAGAGCCGTGTTG 60.734 60.000 0.00 0.00 0.00 3.33
2296 2309 1.587054 CCGAGAAGAGAGCCGTGTT 59.413 57.895 0.00 0.00 0.00 3.32
2297 2310 2.995872 GCCGAGAAGAGAGCCGTGT 61.996 63.158 0.00 0.00 0.00 4.49
2298 2311 2.202676 GCCGAGAAGAGAGCCGTG 60.203 66.667 0.00 0.00 0.00 4.94
2299 2312 2.361865 AGCCGAGAAGAGAGCCGT 60.362 61.111 0.00 0.00 0.00 5.68
2300 2313 2.411290 GAGCCGAGAAGAGAGCCG 59.589 66.667 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.