Multiple sequence alignment - TraesCS5B01G418400

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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 TraesCS5B01G418400 chr5B 100.000 1276 0 0 950 2225 594735589 594734314 0.000000e+00 2357.0
1 TraesCS5B01G418400 chr5B 100.000 369 0 0 1 369 594736538 594736170 0.000000e+00 682.0
2 TraesCS5B01G418400 chr5A 85.332 859 60 37 980 1804 605098660 605097834 0.000000e+00 828.0
3 TraesCS5B01G418400 chr5A 87.302 189 12 5 107 286 605099144 605098959 2.900000e-49 206.0
4 TraesCS5B01G418400 chr5A 86.420 81 8 2 2129 2209 605097660 605097583 3.940000e-13 86.1
5 TraesCS5B01G418400 chr5D 85.098 765 57 38 988 1724 483643594 483642859 0.000000e+00 728.0
6 TraesCS5B01G418400 chr5D 93.333 270 11 5 103 369 483643969 483643704 2.070000e-105 392.0
7 TraesCS5B01G418400 chr5D 92.157 51 2 2 20 70 60554555 60554507 1.100000e-08 71.3
8 TraesCS5B01G418400 chr4B 97.701 174 4 0 1839 2012 123497919 123497746 1.290000e-77 300.0
9 TraesCS5B01G418400 chr3B 94.271 192 11 0 1832 2023 758070449 758070258 6.010000e-76 294.0
10 TraesCS5B01G418400 chr3B 90.909 55 5 0 9 63 89855043 89855097 8.520000e-10 75.0
11 TraesCS5B01G418400 chr2B 94.180 189 9 2 1832 2019 801141533 801141346 1.010000e-73 287.0
12 TraesCS5B01G418400 chr1B 95.506 178 6 2 1836 2012 317418582 317418406 1.300000e-72 283.0
13 TraesCS5B01G418400 chr1B 95.745 47 1 1 18 63 629809685 629809639 8.520000e-10 75.0
14 TraesCS5B01G418400 chr1D 93.617 188 10 2 1836 2022 299766036 299766222 1.680000e-71 279.0
15 TraesCS5B01G418400 chr7B 93.158 190 12 1 1838 2027 662001629 662001441 6.050000e-71 278.0
16 TraesCS5B01G418400 chr7B 92.670 191 12 2 1832 2021 466970713 466970902 7.830000e-70 274.0
17 TraesCS5B01G418400 chr7B 92.670 191 12 2 1832 2021 523238639 523238828 7.830000e-70 274.0
18 TraesCS5B01G418400 chr3D 92.147 191 15 0 1826 2016 554130415 554130605 1.010000e-68 270.0


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 TraesCS5B01G418400 chr5B 594734314 594736538 2224 True 1519.500000 2357 100.000000 1 2225 2 chr5B.!!$R1 2224
1 TraesCS5B01G418400 chr5A 605097583 605099144 1561 True 373.366667 828 86.351333 107 2209 3 chr5A.!!$R1 2102
2 TraesCS5B01G418400 chr5D 483642859 483643969 1110 True 560.000000 728 89.215500 103 1724 2 chr5D.!!$R2 1621

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
985 999 0.392193 AGTCAAGCTCAAGCATCCGG 60.392 55.0 4.59 0.0 45.16 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 2025 0.036388 CGTGTGTCCTAACATGGGCT 60.036 55.0 0.0 0.0 37.81 5.19 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
17 18 4.072088 GGAAACCGAGTGCACGCG 62.072 66.667 32.26 32.26 38.87 6.01
18 19 3.335534 GAAACCGAGTGCACGCGT 61.336 61.111 34.95 22.84 37.46 6.01
19 20 3.558282 GAAACCGAGTGCACGCGTG 62.558 63.158 34.95 34.01 37.46 5.34
35 36 4.314440 TGCGACCGGCTGAAGCTT 62.314 61.111 0.00 0.00 44.05 3.74
36 37 3.491652 GCGACCGGCTGAAGCTTC 61.492 66.667 19.89 19.89 41.70 3.86
37 38 3.181967 CGACCGGCTGAAGCTTCG 61.182 66.667 21.11 16.15 41.70 3.79
38 39 2.815647 GACCGGCTGAAGCTTCGG 60.816 66.667 27.83 27.83 46.50 4.30
73 74 4.650545 GTGAAACGTTTACGCCATAGAA 57.349 40.909 14.65 0.00 44.43 2.10
74 75 4.634991 GTGAAACGTTTACGCCATAGAAG 58.365 43.478 14.65 0.00 44.43 2.85
75 76 4.386652 GTGAAACGTTTACGCCATAGAAGA 59.613 41.667 14.65 0.00 44.43 2.87
76 77 5.063060 GTGAAACGTTTACGCCATAGAAGAT 59.937 40.000 14.65 0.00 44.43 2.40
77 78 5.062934 TGAAACGTTTACGCCATAGAAGATG 59.937 40.000 14.65 0.00 44.43 2.90
78 79 4.380841 ACGTTTACGCCATAGAAGATGA 57.619 40.909 1.60 0.00 44.43 2.92
79 80 4.945246 ACGTTTACGCCATAGAAGATGAT 58.055 39.130 1.60 0.00 44.43 2.45
80 81 4.745125 ACGTTTACGCCATAGAAGATGATG 59.255 41.667 1.60 0.00 44.43 3.07
81 82 4.745125 CGTTTACGCCATAGAAGATGATGT 59.255 41.667 0.00 0.00 0.00 3.06
82 83 5.918576 CGTTTACGCCATAGAAGATGATGTA 59.081 40.000 0.00 0.00 0.00 2.29
83 84 6.129168 CGTTTACGCCATAGAAGATGATGTAC 60.129 42.308 0.00 0.00 0.00 2.90
84 85 6.650427 TTACGCCATAGAAGATGATGTACT 57.350 37.500 0.00 0.00 0.00 2.73
85 86 5.127693 ACGCCATAGAAGATGATGTACTC 57.872 43.478 0.00 0.00 0.00 2.59
86 87 4.021894 ACGCCATAGAAGATGATGTACTCC 60.022 45.833 0.00 0.00 0.00 3.85
87 88 4.219507 CGCCATAGAAGATGATGTACTCCT 59.780 45.833 0.00 0.00 0.00 3.69
88 89 5.416013 CGCCATAGAAGATGATGTACTCCTA 59.584 44.000 0.00 0.00 0.00 2.94
89 90 6.623986 CGCCATAGAAGATGATGTACTCCTAC 60.624 46.154 0.00 0.00 0.00 3.18
90 91 6.209589 GCCATAGAAGATGATGTACTCCTACA 59.790 42.308 0.00 0.00 37.28 2.74
91 92 7.598278 CCATAGAAGATGATGTACTCCTACAC 58.402 42.308 0.00 0.00 35.63 2.90
92 93 7.450014 CCATAGAAGATGATGTACTCCTACACT 59.550 40.741 0.00 0.00 35.63 3.55
93 94 8.855110 CATAGAAGATGATGTACTCCTACACTT 58.145 37.037 0.00 0.00 35.63 3.16
94 95 7.106439 AGAAGATGATGTACTCCTACACTTG 57.894 40.000 0.00 0.00 35.63 3.16
95 96 6.665680 AGAAGATGATGTACTCCTACACTTGT 59.334 38.462 0.00 0.00 35.63 3.16
96 97 7.834681 AGAAGATGATGTACTCCTACACTTGTA 59.165 37.037 0.00 0.00 35.63 2.41
97 98 7.956328 AGATGATGTACTCCTACACTTGTAA 57.044 36.000 0.00 0.00 35.63 2.41
98 99 8.362464 AGATGATGTACTCCTACACTTGTAAA 57.638 34.615 0.00 0.00 35.63 2.01
99 100 8.251721 AGATGATGTACTCCTACACTTGTAAAC 58.748 37.037 0.00 0.00 35.63 2.01
100 101 6.694447 TGATGTACTCCTACACTTGTAAACC 58.306 40.000 0.00 0.00 35.63 3.27
101 102 6.495872 TGATGTACTCCTACACTTGTAAACCT 59.504 38.462 0.00 0.00 35.63 3.50
114 115 2.035704 TGTAAACCTTGAAGGCGACGTA 59.964 45.455 11.96 0.00 39.63 3.57
178 181 0.457681 CGTTGCCCCCAAATTAAGCG 60.458 55.000 0.00 0.00 31.68 4.68
271 283 1.078143 GCCTTCTTCCGCACCATCT 60.078 57.895 0.00 0.00 0.00 2.90
317 329 3.218453 CATGTCCCCCGTGCATATAAAA 58.782 45.455 0.00 0.00 0.00 1.52
319 331 2.240160 TGTCCCCCGTGCATATAAAACT 59.760 45.455 0.00 0.00 0.00 2.66
984 998 0.725686 CAGTCAAGCTCAAGCATCCG 59.274 55.000 4.59 0.00 45.16 4.18
985 999 0.392193 AGTCAAGCTCAAGCATCCGG 60.392 55.000 4.59 0.00 45.16 5.14
988 1002 4.845580 AGCTCAAGCATCCGGGCG 62.846 66.667 0.00 0.00 45.16 6.13
1045 1090 2.874701 CTGCCCTTCATATTCTTCACCG 59.125 50.000 0.00 0.00 0.00 4.94
1228 1273 3.872728 CCGACGCCGTCTGATCGA 61.873 66.667 16.07 0.00 36.70 3.59
1252 1322 3.243267 GGAGCGTTGGTGTTGTTGTTTAT 60.243 43.478 0.00 0.00 0.00 1.40
1264 1334 5.643777 TGTTGTTGTTTATTGGGTTTGGTTG 59.356 36.000 0.00 0.00 0.00 3.77
1265 1335 5.677319 TGTTGTTTATTGGGTTTGGTTGA 57.323 34.783 0.00 0.00 0.00 3.18
1267 1337 6.653989 TGTTGTTTATTGGGTTTGGTTGATT 58.346 32.000 0.00 0.00 0.00 2.57
1268 1338 7.792032 TGTTGTTTATTGGGTTTGGTTGATTA 58.208 30.769 0.00 0.00 0.00 1.75
1269 1339 8.432805 TGTTGTTTATTGGGTTTGGTTGATTAT 58.567 29.630 0.00 0.00 0.00 1.28
1270 1340 9.278978 GTTGTTTATTGGGTTTGGTTGATTATT 57.721 29.630 0.00 0.00 0.00 1.40
1272 1342 9.930693 TGTTTATTGGGTTTGGTTGATTATTAC 57.069 29.630 0.00 0.00 0.00 1.89
1273 1343 9.373603 GTTTATTGGGTTTGGTTGATTATTACC 57.626 33.333 0.00 0.00 34.93 2.85
1274 1344 5.646577 TTGGGTTTGGTTGATTATTACCG 57.353 39.130 0.00 0.00 37.23 4.02
1275 1345 4.017808 TGGGTTTGGTTGATTATTACCGG 58.982 43.478 0.00 0.00 37.23 5.28
1276 1346 3.382227 GGGTTTGGTTGATTATTACCGGG 59.618 47.826 6.32 0.00 37.23 5.73
1277 1347 4.018490 GGTTTGGTTGATTATTACCGGGT 58.982 43.478 6.32 4.46 37.23 5.28
1278 1348 4.142337 GGTTTGGTTGATTATTACCGGGTG 60.142 45.833 10.66 0.00 37.23 4.61
1279 1349 3.284793 TGGTTGATTATTACCGGGTGG 57.715 47.619 10.66 0.00 42.84 4.61
1289 1359 4.183858 CCGGGTGGTGTGGTGTGT 62.184 66.667 0.00 0.00 0.00 3.72
1290 1360 2.590575 CGGGTGGTGTGGTGTGTC 60.591 66.667 0.00 0.00 0.00 3.67
1291 1361 2.203294 GGGTGGTGTGGTGTGTCC 60.203 66.667 0.00 0.00 0.00 4.02
1308 1378 1.407979 GTCCCCGTGTACATGGAGTAG 59.592 57.143 31.83 16.58 39.90 2.57
1309 1379 1.006281 TCCCCGTGTACATGGAGTAGT 59.994 52.381 31.83 0.00 39.90 2.73
1310 1380 2.241941 TCCCCGTGTACATGGAGTAGTA 59.758 50.000 31.83 10.03 39.90 1.82
1332 1402 4.630894 ATTTGTTGCTCGTTTCTTGTGA 57.369 36.364 0.00 0.00 0.00 3.58
1339 1409 2.032808 GCTCGTTTCTTGTGAGGTGTTC 60.033 50.000 0.00 0.00 0.00 3.18
1354 1424 2.484889 GTGTTCACTGTGAAGGAGGAC 58.515 52.381 22.61 11.65 37.00 3.85
1361 1431 1.264749 TGTGAAGGAGGACGGGATGG 61.265 60.000 0.00 0.00 0.00 3.51
1367 1437 0.760945 GGAGGACGGGATGGTGATCT 60.761 60.000 0.00 0.00 0.00 2.75
1369 1439 1.050988 AGGACGGGATGGTGATCTGG 61.051 60.000 0.00 0.00 0.00 3.86
1370 1440 1.338136 GGACGGGATGGTGATCTGGT 61.338 60.000 0.00 0.00 0.00 4.00
1411 1481 4.389992 CACAGTTGCGTTTCTATGAGATGT 59.610 41.667 0.00 0.00 0.00 3.06
1432 1514 8.285394 AGATGTGCAAATCGATGTAATGAATAC 58.715 33.333 11.28 0.00 34.92 1.89
1433 1515 7.552458 TGTGCAAATCGATGTAATGAATACT 57.448 32.000 0.00 0.00 35.42 2.12
1434 1516 7.408910 TGTGCAAATCGATGTAATGAATACTG 58.591 34.615 0.00 0.00 35.42 2.74
1435 1517 7.065683 TGTGCAAATCGATGTAATGAATACTGT 59.934 33.333 0.00 0.00 35.42 3.55
1436 1518 8.547894 GTGCAAATCGATGTAATGAATACTGTA 58.452 33.333 0.00 0.00 35.42 2.74
1467 1553 4.393680 GTGATAATCAACCGTTGCTTGGTA 59.606 41.667 10.01 0.00 39.29 3.25
1477 1564 3.119673 CCGTTGCTTGGTATGTATGCAAA 60.120 43.478 0.00 0.00 43.72 3.68
1478 1565 4.480541 CGTTGCTTGGTATGTATGCAAAA 58.519 39.130 0.00 0.00 43.72 2.44
1497 1584 1.909700 ATTTGCTTTCTCGGGCTTGA 58.090 45.000 0.00 0.00 0.00 3.02
1499 1586 1.237285 TTGCTTTCTCGGGCTTGAGC 61.237 55.000 0.00 0.00 41.14 4.26
1503 1597 0.615331 TTTCTCGGGCTTGAGCTGAT 59.385 50.000 0.00 0.00 41.70 2.90
1569 1663 4.917906 AGTCAAGCAAAAGGAGGAGTAT 57.082 40.909 0.00 0.00 0.00 2.12
1581 1675 7.996758 AAAGGAGGAGTATAGATTCAGGAAA 57.003 36.000 0.00 0.00 0.00 3.13
1582 1676 7.996758 AAGGAGGAGTATAGATTCAGGAAAA 57.003 36.000 0.00 0.00 0.00 2.29
1596 1690 8.482128 AGATTCAGGAAAACTAGATAGAGTTGG 58.518 37.037 0.00 0.00 39.62 3.77
1641 1744 1.327507 GTTTTCGATGCAAGGCGAAC 58.672 50.000 18.02 8.37 44.98 3.95
1654 1770 1.349688 AGGCGAACTGGACACCAAATA 59.650 47.619 0.00 0.00 30.80 1.40
1695 1811 5.302568 TCACTGATTTTGCACATTTCTTCCT 59.697 36.000 0.00 0.00 0.00 3.36
1712 1828 8.436046 TTTCTTCCTCAAATGTTCCAAAAATG 57.564 30.769 0.00 0.00 0.00 2.32
1713 1829 7.358770 TCTTCCTCAAATGTTCCAAAAATGA 57.641 32.000 0.00 0.00 0.00 2.57
1714 1830 7.965718 TCTTCCTCAAATGTTCCAAAAATGAT 58.034 30.769 0.00 0.00 0.00 2.45
1724 1840 2.760092 TCCAAAAATGATAGCACCAGGC 59.240 45.455 0.00 0.00 45.30 4.85
1771 1887 0.250727 TTTCCAGAAACCGGGCTGAG 60.251 55.000 19.05 11.18 34.06 3.35
1795 1911 8.340618 AGTTCTTCAGATATTTTTGCTGCTAA 57.659 30.769 0.00 0.00 0.00 3.09
1812 1928 9.698309 TTGCTGCTAACAGTAATAATATCTCTC 57.302 33.333 0.00 0.00 42.66 3.20
1814 1930 9.868277 GCTGCTAACAGTAATAATATCTCTCAT 57.132 33.333 0.00 0.00 46.30 2.90
1823 1939 9.664332 AGTAATAATATCTCTCATGGTGATTGC 57.336 33.333 0.00 0.00 31.60 3.56
1824 1940 9.664332 GTAATAATATCTCTCATGGTGATTGCT 57.336 33.333 0.00 0.00 31.60 3.91
1827 1943 6.676990 ATATCTCTCATGGTGATTGCTACA 57.323 37.500 0.00 0.00 31.60 2.74
1828 1944 4.397481 TCTCTCATGGTGATTGCTACAG 57.603 45.455 0.00 0.00 0.00 2.74
1829 1945 3.771479 TCTCTCATGGTGATTGCTACAGT 59.229 43.478 0.00 0.00 0.00 3.55
1830 1946 4.956075 TCTCTCATGGTGATTGCTACAGTA 59.044 41.667 0.00 0.00 0.00 2.74
1831 1947 5.600069 TCTCTCATGGTGATTGCTACAGTAT 59.400 40.000 0.00 0.00 0.00 2.12
1832 1948 6.777580 TCTCTCATGGTGATTGCTACAGTATA 59.222 38.462 0.00 0.00 0.00 1.47
1833 1949 7.452813 TCTCTCATGGTGATTGCTACAGTATAT 59.547 37.037 0.00 0.00 0.00 0.86
1834 1950 7.606349 TCTCATGGTGATTGCTACAGTATATC 58.394 38.462 0.00 0.00 0.00 1.63
1835 1951 7.452813 TCTCATGGTGATTGCTACAGTATATCT 59.547 37.037 0.00 0.00 0.00 1.98
1837 1953 8.432013 TCATGGTGATTGCTACAGTATATCTTT 58.568 33.333 0.00 0.00 0.00 2.52
1838 1954 9.710900 CATGGTGATTGCTACAGTATATCTTTA 57.289 33.333 0.00 0.00 0.00 1.85
1839 1955 9.935241 ATGGTGATTGCTACAGTATATCTTTAG 57.065 33.333 0.00 0.00 31.65 1.85
1840 1956 8.367911 TGGTGATTGCTACAGTATATCTTTAGG 58.632 37.037 0.00 0.00 29.82 2.69
1841 1957 7.819900 GGTGATTGCTACAGTATATCTTTAGGG 59.180 40.741 0.00 0.00 29.82 3.53
1843 1959 8.807118 TGATTGCTACAGTATATCTTTAGGGAG 58.193 37.037 0.00 0.00 29.82 4.30
1845 1961 9.824216 ATTGCTACAGTATATCTTTAGGGAGTA 57.176 33.333 0.00 0.00 29.82 2.59
1846 1962 8.632906 TGCTACAGTATATCTTTAGGGAGTAC 57.367 38.462 0.00 0.00 29.82 2.73
1847 1963 7.668886 TGCTACAGTATATCTTTAGGGAGTACC 59.331 40.741 0.00 0.00 40.67 3.34
1863 1979 7.842887 GGGAGTACCTAGAACTCATCTAAAT 57.157 40.000 20.28 0.00 44.25 1.40
1865 1981 7.506261 GGGAGTACCTAGAACTCATCTAAATGA 59.494 40.741 20.28 0.00 44.25 2.57
1888 2004 8.311395 TGAGATATAGTTTGGTCTCATTCACT 57.689 34.615 0.16 0.00 41.40 3.41
1889 2005 8.762645 TGAGATATAGTTTGGTCTCATTCACTT 58.237 33.333 0.16 0.00 41.40 3.16
1890 2006 9.606631 GAGATATAGTTTGGTCTCATTCACTTT 57.393 33.333 0.00 0.00 37.60 2.66
1891 2007 9.388506 AGATATAGTTTGGTCTCATTCACTTTG 57.611 33.333 0.00 0.00 0.00 2.77
1892 2008 9.383519 GATATAGTTTGGTCTCATTCACTTTGA 57.616 33.333 0.00 0.00 0.00 2.69
1893 2009 9.739276 ATATAGTTTGGTCTCATTCACTTTGAA 57.261 29.630 0.00 0.00 41.09 2.69
1894 2010 6.773976 AGTTTGGTCTCATTCACTTTGAAA 57.226 33.333 0.00 0.00 40.12 2.69
1895 2011 7.169158 AGTTTGGTCTCATTCACTTTGAAAA 57.831 32.000 0.00 0.00 40.12 2.29
1896 2012 7.035612 AGTTTGGTCTCATTCACTTTGAAAAC 58.964 34.615 0.00 0.00 40.12 2.43
1897 2013 6.522625 TTGGTCTCATTCACTTTGAAAACA 57.477 33.333 0.00 0.00 40.12 2.83
1898 2014 6.522625 TGGTCTCATTCACTTTGAAAACAA 57.477 33.333 0.00 0.00 40.12 2.83
1899 2015 6.563422 TGGTCTCATTCACTTTGAAAACAAG 58.437 36.000 0.00 0.00 40.12 3.16
1900 2016 6.376864 TGGTCTCATTCACTTTGAAAACAAGA 59.623 34.615 0.00 0.00 40.12 3.02
1901 2017 7.093988 TGGTCTCATTCACTTTGAAAACAAGAA 60.094 33.333 0.00 0.00 40.12 2.52
1902 2018 7.922811 GGTCTCATTCACTTTGAAAACAAGAAT 59.077 33.333 0.00 0.00 40.12 2.40
1903 2019 9.950680 GTCTCATTCACTTTGAAAACAAGAATA 57.049 29.630 0.00 0.00 40.12 1.75
1911 2027 9.334693 CACTTTGAAAACAAGAATAGATACAGC 57.665 33.333 0.00 0.00 0.00 4.40
1912 2028 8.515414 ACTTTGAAAACAAGAATAGATACAGCC 58.485 33.333 0.00 0.00 0.00 4.85
1913 2029 7.391148 TTGAAAACAAGAATAGATACAGCCC 57.609 36.000 0.00 0.00 0.00 5.19
1914 2030 6.480763 TGAAAACAAGAATAGATACAGCCCA 58.519 36.000 0.00 0.00 0.00 5.36
1915 2031 7.118723 TGAAAACAAGAATAGATACAGCCCAT 58.881 34.615 0.00 0.00 0.00 4.00
1916 2032 6.949352 AAACAAGAATAGATACAGCCCATG 57.051 37.500 0.00 0.00 0.00 3.66
1917 2033 5.636903 ACAAGAATAGATACAGCCCATGT 57.363 39.130 0.00 0.00 46.45 3.21
1918 2034 6.006275 ACAAGAATAGATACAGCCCATGTT 57.994 37.500 0.00 0.00 39.96 2.71
1919 2035 7.136822 ACAAGAATAGATACAGCCCATGTTA 57.863 36.000 0.00 0.00 39.96 2.41
1920 2036 7.220030 ACAAGAATAGATACAGCCCATGTTAG 58.780 38.462 0.00 0.00 39.96 2.34
1921 2037 6.365970 AGAATAGATACAGCCCATGTTAGG 57.634 41.667 0.00 0.00 39.96 2.69
1922 2038 6.084738 AGAATAGATACAGCCCATGTTAGGA 58.915 40.000 0.00 0.00 39.96 2.94
1923 2039 5.746990 ATAGATACAGCCCATGTTAGGAC 57.253 43.478 0.00 0.00 39.96 3.85
1924 2040 3.384168 AGATACAGCCCATGTTAGGACA 58.616 45.455 0.00 0.00 39.96 4.02
1925 2041 3.134804 AGATACAGCCCATGTTAGGACAC 59.865 47.826 0.00 0.00 39.96 3.67
1926 2042 1.064003 ACAGCCCATGTTAGGACACA 58.936 50.000 0.00 0.00 39.96 3.72
1927 2043 1.271379 ACAGCCCATGTTAGGACACAC 60.271 52.381 0.00 0.00 39.96 3.82
1928 2044 0.036388 AGCCCATGTTAGGACACACG 60.036 55.000 0.00 0.00 38.91 4.49
1929 2045 1.644786 GCCCATGTTAGGACACACGC 61.645 60.000 0.00 0.00 38.91 5.34
1930 2046 0.321210 CCCATGTTAGGACACACGCA 60.321 55.000 0.00 0.00 38.91 5.24
1931 2047 1.678728 CCCATGTTAGGACACACGCAT 60.679 52.381 0.00 0.00 38.91 4.73
1932 2048 1.665679 CCATGTTAGGACACACGCATC 59.334 52.381 0.00 0.00 38.91 3.91
1933 2049 2.621338 CATGTTAGGACACACGCATCT 58.379 47.619 0.00 0.00 38.91 2.90
1934 2050 2.831685 TGTTAGGACACACGCATCTT 57.168 45.000 0.00 0.00 0.00 2.40
1935 2051 3.945981 TGTTAGGACACACGCATCTTA 57.054 42.857 0.00 0.00 0.00 2.10
1936 2052 4.465632 TGTTAGGACACACGCATCTTAT 57.534 40.909 0.00 0.00 0.00 1.73
1937 2053 5.585820 TGTTAGGACACACGCATCTTATA 57.414 39.130 0.00 0.00 0.00 0.98
1938 2054 5.588240 TGTTAGGACACACGCATCTTATAG 58.412 41.667 0.00 0.00 0.00 1.31
1939 2055 3.099267 AGGACACACGCATCTTATAGC 57.901 47.619 0.00 0.00 0.00 2.97
1940 2056 2.430694 AGGACACACGCATCTTATAGCA 59.569 45.455 0.00 0.00 0.00 3.49
1941 2057 3.070159 AGGACACACGCATCTTATAGCAT 59.930 43.478 0.00 0.00 0.00 3.79
1942 2058 3.430218 GGACACACGCATCTTATAGCATC 59.570 47.826 0.00 0.00 0.00 3.91
1943 2059 4.051237 GACACACGCATCTTATAGCATCA 58.949 43.478 0.00 0.00 0.00 3.07
1944 2060 3.804325 ACACACGCATCTTATAGCATCAC 59.196 43.478 0.00 0.00 0.00 3.06
1945 2061 3.803778 CACACGCATCTTATAGCATCACA 59.196 43.478 0.00 0.00 0.00 3.58
1946 2062 4.450080 CACACGCATCTTATAGCATCACAT 59.550 41.667 0.00 0.00 0.00 3.21
1947 2063 4.687948 ACACGCATCTTATAGCATCACATC 59.312 41.667 0.00 0.00 0.00 3.06
1948 2064 4.092529 CACGCATCTTATAGCATCACATCC 59.907 45.833 0.00 0.00 0.00 3.51
1949 2065 4.248058 CGCATCTTATAGCATCACATCCA 58.752 43.478 0.00 0.00 0.00 3.41
1950 2066 4.692155 CGCATCTTATAGCATCACATCCAA 59.308 41.667 0.00 0.00 0.00 3.53
1951 2067 5.353400 CGCATCTTATAGCATCACATCCAAT 59.647 40.000 0.00 0.00 0.00 3.16
1952 2068 6.552629 GCATCTTATAGCATCACATCCAATG 58.447 40.000 0.00 0.00 0.00 2.82
1953 2069 6.404403 GCATCTTATAGCATCACATCCAATGG 60.404 42.308 0.00 0.00 33.60 3.16
1954 2070 6.191657 TCTTATAGCATCACATCCAATGGT 57.808 37.500 0.00 0.00 37.39 3.55
1955 2071 6.604171 TCTTATAGCATCACATCCAATGGTT 58.396 36.000 0.00 0.00 35.41 3.67
1956 2072 7.744733 TCTTATAGCATCACATCCAATGGTTA 58.255 34.615 0.00 0.00 35.41 2.85
1957 2073 8.385491 TCTTATAGCATCACATCCAATGGTTAT 58.615 33.333 0.00 0.00 35.41 1.89
1958 2074 9.671279 CTTATAGCATCACATCCAATGGTTATA 57.329 33.333 0.00 0.00 35.41 0.98
1960 2076 8.938801 ATAGCATCACATCCAATGGTTATAAA 57.061 30.769 0.00 0.00 35.41 1.40
1961 2077 7.658525 AGCATCACATCCAATGGTTATAAAA 57.341 32.000 0.00 0.00 29.73 1.52
1962 2078 7.719483 AGCATCACATCCAATGGTTATAAAAG 58.281 34.615 0.00 0.00 29.73 2.27
1963 2079 6.925165 GCATCACATCCAATGGTTATAAAAGG 59.075 38.462 0.00 0.00 33.60 3.11
1964 2080 7.417797 GCATCACATCCAATGGTTATAAAAGGT 60.418 37.037 0.00 0.00 33.60 3.50
1965 2081 7.403312 TCACATCCAATGGTTATAAAAGGTG 57.597 36.000 0.00 0.00 33.60 4.00
1966 2082 7.178573 TCACATCCAATGGTTATAAAAGGTGA 58.821 34.615 0.00 0.00 33.60 4.02
1967 2083 7.671819 TCACATCCAATGGTTATAAAAGGTGAA 59.328 33.333 0.00 0.00 33.60 3.18
1968 2084 8.477256 CACATCCAATGGTTATAAAAGGTGAAT 58.523 33.333 0.00 0.00 33.60 2.57
1969 2085 8.477256 ACATCCAATGGTTATAAAAGGTGAATG 58.523 33.333 0.00 0.00 33.60 2.67
1970 2086 8.694540 CATCCAATGGTTATAAAAGGTGAATGA 58.305 33.333 0.00 0.00 0.00 2.57
1971 2087 8.292444 TCCAATGGTTATAAAAGGTGAATGAG 57.708 34.615 0.00 0.00 0.00 2.90
1972 2088 8.112822 TCCAATGGTTATAAAAGGTGAATGAGA 58.887 33.333 0.00 0.00 0.00 3.27
1973 2089 8.190784 CCAATGGTTATAAAAGGTGAATGAGAC 58.809 37.037 0.00 0.00 0.00 3.36
1974 2090 7.881775 ATGGTTATAAAAGGTGAATGAGACC 57.118 36.000 0.00 0.00 0.00 3.85
1975 2091 6.785076 TGGTTATAAAAGGTGAATGAGACCA 58.215 36.000 0.00 0.00 35.76 4.02
1976 2092 7.235079 TGGTTATAAAAGGTGAATGAGACCAA 58.765 34.615 0.00 0.00 35.76 3.67
1977 2093 7.726291 TGGTTATAAAAGGTGAATGAGACCAAA 59.274 33.333 0.00 0.00 35.76 3.28
1978 2094 8.749354 GGTTATAAAAGGTGAATGAGACCAAAT 58.251 33.333 0.00 0.00 35.76 2.32
1985 2101 9.927081 AAAGGTGAATGAGACCAAATTATATCT 57.073 29.630 0.00 0.00 35.76 1.98
1986 2102 9.566432 AAGGTGAATGAGACCAAATTATATCTC 57.434 33.333 0.00 6.03 38.46 2.75
2057 2184 9.675464 ATGGAGATTGCACATATTTTGATTTTT 57.325 25.926 0.00 0.00 0.00 1.94
2070 2203 7.797121 ATTTTGATTTTTCCCTCTGGTACAT 57.203 32.000 0.00 0.00 38.20 2.29
2077 2210 1.278985 TCCCTCTGGTACATGCACAAG 59.721 52.381 0.00 0.00 38.20 3.16
2092 2225 2.481952 GCACAAGCAAAAACCAACACAA 59.518 40.909 0.00 0.00 41.58 3.33
2094 2227 3.745458 CACAAGCAAAAACCAACACAACT 59.255 39.130 0.00 0.00 0.00 3.16
2095 2228 3.993736 ACAAGCAAAAACCAACACAACTC 59.006 39.130 0.00 0.00 0.00 3.01
2096 2229 4.244862 CAAGCAAAAACCAACACAACTCT 58.755 39.130 0.00 0.00 0.00 3.24
2097 2230 4.110036 AGCAAAAACCAACACAACTCTC 57.890 40.909 0.00 0.00 0.00 3.20
2098 2231 3.509575 AGCAAAAACCAACACAACTCTCA 59.490 39.130 0.00 0.00 0.00 3.27
2099 2232 4.160252 AGCAAAAACCAACACAACTCTCAT 59.840 37.500 0.00 0.00 0.00 2.90
2102 2235 3.297134 AACCAACACAACTCTCATGGT 57.703 42.857 0.00 0.00 42.70 3.55
2103 2236 4.431416 AACCAACACAACTCTCATGGTA 57.569 40.909 0.00 0.00 40.13 3.25
2104 2237 4.431416 ACCAACACAACTCTCATGGTAA 57.569 40.909 0.00 0.00 39.29 2.85
2105 2238 4.985538 ACCAACACAACTCTCATGGTAAT 58.014 39.130 0.00 0.00 39.29 1.89
2106 2239 6.121776 ACCAACACAACTCTCATGGTAATA 57.878 37.500 0.00 0.00 39.29 0.98
2107 2240 6.539173 ACCAACACAACTCTCATGGTAATAA 58.461 36.000 0.00 0.00 39.29 1.40
2108 2241 7.175104 ACCAACACAACTCTCATGGTAATAAT 58.825 34.615 0.00 0.00 39.29 1.28
2109 2242 8.325787 ACCAACACAACTCTCATGGTAATAATA 58.674 33.333 0.00 0.00 39.29 0.98
2110 2243 8.612619 CCAACACAACTCTCATGGTAATAATAC 58.387 37.037 0.00 0.00 0.00 1.89
2205 2338 3.127548 CGATTGCAATCAGCTAACCACTT 59.872 43.478 32.72 0.00 45.94 3.16
2206 2339 4.666237 GATTGCAATCAGCTAACCACTTC 58.334 43.478 30.15 2.99 45.94 3.01
2207 2340 3.423539 TGCAATCAGCTAACCACTTCT 57.576 42.857 0.00 0.00 45.94 2.85
2208 2341 3.076621 TGCAATCAGCTAACCACTTCTG 58.923 45.455 0.00 0.00 45.94 3.02
2209 2342 3.244526 TGCAATCAGCTAACCACTTCTGA 60.245 43.478 0.00 0.00 45.94 3.27
2210 2343 3.753272 GCAATCAGCTAACCACTTCTGAA 59.247 43.478 0.00 0.00 38.81 3.02
2211 2344 4.142730 GCAATCAGCTAACCACTTCTGAAG 60.143 45.833 15.59 15.59 38.81 3.02
2212 2345 5.240891 CAATCAGCTAACCACTTCTGAAGA 58.759 41.667 23.36 0.11 38.81 2.87
2213 2346 4.258702 TCAGCTAACCACTTCTGAAGAC 57.741 45.455 23.36 4.42 33.17 3.01
2214 2347 3.898123 TCAGCTAACCACTTCTGAAGACT 59.102 43.478 23.36 7.32 33.17 3.24
2215 2348 4.345257 TCAGCTAACCACTTCTGAAGACTT 59.655 41.667 23.36 12.60 33.17 3.01
2216 2349 4.450419 CAGCTAACCACTTCTGAAGACTTG 59.550 45.833 23.36 11.30 0.00 3.16
2217 2350 4.101741 AGCTAACCACTTCTGAAGACTTGT 59.898 41.667 23.36 11.13 0.00 3.16
2218 2351 4.449405 GCTAACCACTTCTGAAGACTTGTC 59.551 45.833 23.36 3.98 0.00 3.18
2219 2352 4.762289 AACCACTTCTGAAGACTTGTCT 57.238 40.909 23.36 0.00 0.00 3.41
2220 2353 4.762289 ACCACTTCTGAAGACTTGTCTT 57.238 40.909 23.36 14.94 0.00 3.01
2221 2354 4.446371 ACCACTTCTGAAGACTTGTCTTG 58.554 43.478 23.36 8.60 0.00 3.02
2222 2355 3.812053 CCACTTCTGAAGACTTGTCTTGG 59.188 47.826 23.36 13.44 0.00 3.61
2223 2356 4.446371 CACTTCTGAAGACTTGTCTTGGT 58.554 43.478 23.36 8.21 0.00 3.67
2224 2357 4.878397 CACTTCTGAAGACTTGTCTTGGTT 59.122 41.667 23.36 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.072088 CGCGTGCACTCGGTTTCC 62.072 66.667 21.05 0.00 0.00 3.13
1 2 3.335534 ACGCGTGCACTCGGTTTC 61.336 61.111 30.28 3.68 0.00 2.78
2 3 3.636043 CACGCGTGCACTCGGTTT 61.636 61.111 30.28 9.50 0.00 3.27
18 19 4.314440 AAGCTTCAGCCGGTCGCA 62.314 61.111 1.90 0.00 43.38 5.10
19 20 3.491652 GAAGCTTCAGCCGGTCGC 61.492 66.667 21.67 0.00 43.38 5.19
20 21 3.181967 CGAAGCTTCAGCCGGTCG 61.182 66.667 25.47 6.53 43.38 4.79
21 22 2.815647 CCGAAGCTTCAGCCGGTC 60.816 66.667 25.47 0.00 43.38 4.79
52 53 4.386652 TCTTCTATGGCGTAAACGTTTCAC 59.613 41.667 18.42 12.68 42.22 3.18
53 54 4.558178 TCTTCTATGGCGTAAACGTTTCA 58.442 39.130 18.42 9.74 42.22 2.69
54 55 5.290158 TCATCTTCTATGGCGTAAACGTTTC 59.710 40.000 18.42 8.47 42.22 2.78
55 56 5.172934 TCATCTTCTATGGCGTAAACGTTT 58.827 37.500 18.90 18.90 42.22 3.60
56 57 4.751060 TCATCTTCTATGGCGTAAACGTT 58.249 39.130 0.00 0.00 42.22 3.99
57 58 4.380841 TCATCTTCTATGGCGTAAACGT 57.619 40.909 4.24 0.00 42.22 3.99
58 59 4.745125 ACATCATCTTCTATGGCGTAAACG 59.255 41.667 0.00 0.00 43.27 3.60
59 60 6.924060 AGTACATCATCTTCTATGGCGTAAAC 59.076 38.462 0.00 0.00 0.00 2.01
60 61 7.050970 AGTACATCATCTTCTATGGCGTAAA 57.949 36.000 0.00 0.00 0.00 2.01
61 62 6.294564 GGAGTACATCATCTTCTATGGCGTAA 60.295 42.308 0.00 0.00 0.00 3.18
62 63 5.183331 GGAGTACATCATCTTCTATGGCGTA 59.817 44.000 0.00 0.00 0.00 4.42
63 64 4.021894 GGAGTACATCATCTTCTATGGCGT 60.022 45.833 0.00 0.00 0.00 5.68
64 65 4.219507 AGGAGTACATCATCTTCTATGGCG 59.780 45.833 0.00 0.00 0.00 5.69
65 66 5.736951 AGGAGTACATCATCTTCTATGGC 57.263 43.478 0.00 0.00 0.00 4.40
66 67 7.450014 AGTGTAGGAGTACATCATCTTCTATGG 59.550 40.741 0.00 0.00 41.29 2.74
67 68 8.402798 AGTGTAGGAGTACATCATCTTCTATG 57.597 38.462 0.00 0.00 41.29 2.23
68 69 8.855110 CAAGTGTAGGAGTACATCATCTTCTAT 58.145 37.037 0.00 0.00 41.29 1.98
69 70 7.834681 ACAAGTGTAGGAGTACATCATCTTCTA 59.165 37.037 0.00 0.00 41.29 2.10
70 71 6.665680 ACAAGTGTAGGAGTACATCATCTTCT 59.334 38.462 0.00 0.00 41.29 2.85
71 72 6.868622 ACAAGTGTAGGAGTACATCATCTTC 58.131 40.000 0.00 0.00 41.29 2.87
72 73 6.859112 ACAAGTGTAGGAGTACATCATCTT 57.141 37.500 0.00 0.00 41.29 2.40
73 74 7.956328 TTACAAGTGTAGGAGTACATCATCT 57.044 36.000 0.00 0.00 41.29 2.90
74 75 7.491696 GGTTTACAAGTGTAGGAGTACATCATC 59.508 40.741 0.00 0.00 41.29 2.92
75 76 7.180408 AGGTTTACAAGTGTAGGAGTACATCAT 59.820 37.037 0.00 0.00 41.29 2.45
76 77 6.495872 AGGTTTACAAGTGTAGGAGTACATCA 59.504 38.462 0.00 0.00 41.29 3.07
77 78 6.932947 AGGTTTACAAGTGTAGGAGTACATC 58.067 40.000 0.00 0.00 41.29 3.06
78 79 6.930068 AGGTTTACAAGTGTAGGAGTACAT 57.070 37.500 0.00 0.00 41.29 2.29
79 80 6.324512 TCAAGGTTTACAAGTGTAGGAGTACA 59.675 38.462 0.00 0.00 36.78 2.90
80 81 6.752168 TCAAGGTTTACAAGTGTAGGAGTAC 58.248 40.000 0.00 0.00 0.00 2.73
81 82 6.982160 TCAAGGTTTACAAGTGTAGGAGTA 57.018 37.500 0.00 0.00 0.00 2.59
82 83 5.881923 TCAAGGTTTACAAGTGTAGGAGT 57.118 39.130 0.00 0.00 0.00 3.85
83 84 5.701290 CCTTCAAGGTTTACAAGTGTAGGAG 59.299 44.000 0.00 0.00 30.60 3.69
84 85 5.617252 CCTTCAAGGTTTACAAGTGTAGGA 58.383 41.667 0.00 0.00 30.60 2.94
85 86 4.215613 GCCTTCAAGGTTTACAAGTGTAGG 59.784 45.833 5.03 0.00 37.80 3.18
86 87 4.084013 CGCCTTCAAGGTTTACAAGTGTAG 60.084 45.833 5.03 0.00 37.80 2.74
87 88 3.810941 CGCCTTCAAGGTTTACAAGTGTA 59.189 43.478 5.03 0.00 37.80 2.90
88 89 2.616842 CGCCTTCAAGGTTTACAAGTGT 59.383 45.455 5.03 0.00 37.80 3.55
89 90 2.875933 TCGCCTTCAAGGTTTACAAGTG 59.124 45.455 5.03 0.00 37.80 3.16
90 91 2.876550 GTCGCCTTCAAGGTTTACAAGT 59.123 45.455 5.03 0.00 37.80 3.16
91 92 2.096417 CGTCGCCTTCAAGGTTTACAAG 60.096 50.000 5.03 0.00 37.80 3.16
92 93 1.868498 CGTCGCCTTCAAGGTTTACAA 59.132 47.619 5.03 0.00 37.80 2.41
93 94 1.202557 ACGTCGCCTTCAAGGTTTACA 60.203 47.619 5.03 0.00 37.80 2.41
94 95 1.505425 ACGTCGCCTTCAAGGTTTAC 58.495 50.000 5.03 0.17 37.80 2.01
95 96 2.927871 GCTACGTCGCCTTCAAGGTTTA 60.928 50.000 5.03 0.00 37.80 2.01
96 97 1.792006 CTACGTCGCCTTCAAGGTTT 58.208 50.000 5.03 0.00 37.80 3.27
97 98 0.669625 GCTACGTCGCCTTCAAGGTT 60.670 55.000 5.03 0.00 37.80 3.50
98 99 1.080025 GCTACGTCGCCTTCAAGGT 60.080 57.895 5.03 0.00 37.80 3.50
99 100 1.078759 CAGCTACGTCGCCTTCAAGG 61.079 60.000 8.64 0.00 38.80 3.61
100 101 0.109272 TCAGCTACGTCGCCTTCAAG 60.109 55.000 8.64 0.00 0.00 3.02
101 102 0.315886 TTCAGCTACGTCGCCTTCAA 59.684 50.000 8.64 0.00 0.00 2.69
178 181 3.670377 GGTGACCGTTGGCTTGGC 61.670 66.667 0.00 0.00 0.00 4.52
224 232 0.819259 TGGAAGCTTGTGGAGTGTGC 60.819 55.000 2.10 0.00 0.00 4.57
225 233 1.233019 CTGGAAGCTTGTGGAGTGTG 58.767 55.000 2.10 0.00 0.00 3.82
226 234 3.713902 CTGGAAGCTTGTGGAGTGT 57.286 52.632 2.10 0.00 0.00 3.55
263 275 1.092345 GCGGAGGAGAAAGATGGTGC 61.092 60.000 0.00 0.00 0.00 5.01
271 283 2.264794 GAAGCGGCGGAGGAGAAA 59.735 61.111 9.78 0.00 0.00 2.52
291 303 2.192979 CACGGGGGACATGGATGG 59.807 66.667 0.00 0.00 0.00 3.51
964 978 0.450983 GGATGCTTGAGCTTGACTGC 59.549 55.000 4.44 0.00 42.66 4.40
984 998 2.446802 ATTCTCCTCCTCCCGCCC 60.447 66.667 0.00 0.00 0.00 6.13
985 999 2.812619 CCATTCTCCTCCTCCCGCC 61.813 68.421 0.00 0.00 0.00 6.13
988 1002 0.624795 AACCCCATTCTCCTCCTCCC 60.625 60.000 0.00 0.00 0.00 4.30
991 1005 0.252742 ACGAACCCCATTCTCCTCCT 60.253 55.000 0.00 0.00 34.88 3.69
997 1038 1.002134 CCAGCACGAACCCCATTCT 60.002 57.895 0.00 0.00 34.88 2.40
1119 1164 2.494918 GGCGTGCCGTAGATCTGT 59.505 61.111 5.18 0.00 0.00 3.41
1195 1240 2.677848 GGGGCCCTCCTTCTTCAC 59.322 66.667 24.38 0.00 35.33 3.18
1228 1273 0.667993 CAACAACACCAACGCTCCAT 59.332 50.000 0.00 0.00 0.00 3.41
1252 1322 4.463186 CCGGTAATAATCAACCAAACCCAA 59.537 41.667 0.00 0.00 35.35 4.12
1264 1334 2.092807 ACCACACCACCCGGTAATAATC 60.093 50.000 0.00 0.00 46.94 1.75
1265 1335 1.917568 ACCACACCACCCGGTAATAAT 59.082 47.619 0.00 0.00 46.94 1.28
1267 1337 0.614294 CACCACACCACCCGGTAATA 59.386 55.000 0.00 0.00 46.94 0.98
1268 1338 1.377229 CACCACACCACCCGGTAAT 59.623 57.895 0.00 0.00 46.94 1.89
1269 1339 2.071262 ACACCACACCACCCGGTAA 61.071 57.895 0.00 0.00 46.94 2.85
1270 1340 2.446227 ACACCACACCACCCGGTA 60.446 61.111 0.00 0.00 46.94 4.02
1272 1342 4.183858 ACACACCACACCACCCGG 62.184 66.667 0.00 0.00 38.77 5.73
1273 1343 2.590575 GACACACCACACCACCCG 60.591 66.667 0.00 0.00 0.00 5.28
1274 1344 2.203294 GGACACACCACACCACCC 60.203 66.667 0.00 0.00 38.79 4.61
1275 1345 2.203294 GGGACACACCACACCACC 60.203 66.667 0.00 0.00 41.20 4.61
1276 1346 2.203294 GGGGACACACCACACCAC 60.203 66.667 0.00 0.00 42.69 4.16
1277 1347 3.867783 CGGGGACACACCACACCA 61.868 66.667 0.00 0.00 43.50 4.17
1278 1348 3.868985 ACGGGGACACACCACACC 61.869 66.667 0.00 0.00 43.50 4.16
1279 1349 2.030490 TACACGGGGACACACCACAC 62.030 60.000 0.00 0.00 43.50 3.82
1280 1350 1.761271 TACACGGGGACACACCACA 60.761 57.895 0.00 0.00 43.50 4.17
1281 1351 1.301165 GTACACGGGGACACACCAC 60.301 63.158 0.00 0.00 41.20 4.16
1282 1352 1.122632 ATGTACACGGGGACACACCA 61.123 55.000 3.86 0.00 41.20 4.17
1283 1353 0.672401 CATGTACACGGGGACACACC 60.672 60.000 3.86 0.00 38.08 4.16
1284 1354 0.672401 CCATGTACACGGGGACACAC 60.672 60.000 3.86 0.00 0.00 3.82
1285 1355 0.832559 TCCATGTACACGGGGACACA 60.833 55.000 3.86 0.00 0.00 3.72
1286 1356 0.108329 CTCCATGTACACGGGGACAC 60.108 60.000 3.86 0.00 0.00 3.67
1287 1357 0.543410 ACTCCATGTACACGGGGACA 60.543 55.000 16.28 4.46 0.00 4.02
1288 1358 1.407979 CTACTCCATGTACACGGGGAC 59.592 57.143 16.28 0.00 0.00 4.46
1289 1359 1.006281 ACTACTCCATGTACACGGGGA 59.994 52.381 16.28 13.16 0.00 4.81
1290 1360 1.481871 ACTACTCCATGTACACGGGG 58.518 55.000 6.23 6.23 0.00 5.73
1291 1361 4.931661 ATTACTACTCCATGTACACGGG 57.068 45.455 8.35 8.58 0.00 5.28
1308 1378 5.968848 TCACAAGAAACGAGCAACAAATTAC 59.031 36.000 0.00 0.00 0.00 1.89
1309 1379 6.125327 TCACAAGAAACGAGCAACAAATTA 57.875 33.333 0.00 0.00 0.00 1.40
1310 1380 4.992688 TCACAAGAAACGAGCAACAAATT 58.007 34.783 0.00 0.00 0.00 1.82
1332 1402 1.417890 CCTCCTTCACAGTGAACACCT 59.582 52.381 12.24 0.00 32.21 4.00
1339 1409 1.185618 TCCCGTCCTCCTTCACAGTG 61.186 60.000 0.00 0.00 0.00 3.66
1354 1424 0.462581 CACACCAGATCACCATCCCG 60.463 60.000 0.00 0.00 0.00 5.14
1361 1431 4.456911 ACAAATCATCACACACCAGATCAC 59.543 41.667 0.00 0.00 0.00 3.06
1367 1437 4.216042 GTGATCACAAATCATCACACACCA 59.784 41.667 21.07 0.00 45.64 4.17
1411 1481 7.552458 ACAGTATTCATTACATCGATTTGCA 57.448 32.000 0.00 0.00 32.87 4.08
1432 1514 8.879759 ACGGTTGATTATCACAAACTAATACAG 58.120 33.333 0.00 0.00 33.42 2.74
1433 1515 8.780846 ACGGTTGATTATCACAAACTAATACA 57.219 30.769 0.00 0.00 33.42 2.29
1434 1516 9.485591 CAACGGTTGATTATCACAAACTAATAC 57.514 33.333 15.66 0.00 33.42 1.89
1435 1517 8.178964 GCAACGGTTGATTATCACAAACTAATA 58.821 33.333 24.20 0.00 33.42 0.98
1436 1518 7.027161 GCAACGGTTGATTATCACAAACTAAT 58.973 34.615 24.20 0.00 33.42 1.73
1477 1564 2.229784 CTCAAGCCCGAGAAAGCAAATT 59.770 45.455 0.00 0.00 34.79 1.82
1478 1565 1.815003 CTCAAGCCCGAGAAAGCAAAT 59.185 47.619 0.00 0.00 34.79 2.32
1490 1577 1.772836 ATTCCAATCAGCTCAAGCCC 58.227 50.000 0.00 0.00 43.38 5.19
1497 1584 3.512724 CAGAAACCCAATTCCAATCAGCT 59.487 43.478 0.00 0.00 0.00 4.24
1499 1586 5.186409 ACATCAGAAACCCAATTCCAATCAG 59.814 40.000 0.00 0.00 0.00 2.90
1503 1597 4.478203 TCACATCAGAAACCCAATTCCAA 58.522 39.130 0.00 0.00 0.00 3.53
1581 1675 2.409570 GGGGCCCAACTCTATCTAGTT 58.590 52.381 26.86 0.00 40.33 2.24
1582 1676 1.414685 GGGGGCCCAACTCTATCTAGT 60.415 57.143 26.86 0.00 35.81 2.57
1596 1690 0.471022 TCAAGGAGTTTTTGGGGGCC 60.471 55.000 0.00 0.00 0.00 5.80
1607 1710 4.714632 TCGAAAACCATTCTTCAAGGAGT 58.285 39.130 0.00 0.00 0.00 3.85
1608 1711 5.634896 CATCGAAAACCATTCTTCAAGGAG 58.365 41.667 0.00 0.00 0.00 3.69
1641 1744 2.726821 AGTGCCATATTTGGTGTCCAG 58.273 47.619 4.00 0.00 45.57 3.86
1654 1770 0.824595 TGAGTTGCTGCAAGTGCCAT 60.825 50.000 26.07 3.90 41.18 4.40
1664 1780 3.047796 GTGCAAAATCAGTGAGTTGCTG 58.952 45.455 29.86 18.23 35.43 4.41
1665 1781 2.689471 TGTGCAAAATCAGTGAGTTGCT 59.311 40.909 29.86 8.36 0.00 3.91
1666 1782 3.082698 TGTGCAAAATCAGTGAGTTGC 57.917 42.857 26.30 26.30 0.00 4.17
1695 1811 6.873076 GGTGCTATCATTTTTGGAACATTTGA 59.127 34.615 0.00 0.00 39.30 2.69
1712 1828 0.106708 TTCCATCGCCTGGTGCTATC 59.893 55.000 1.39 0.00 46.08 2.08
1713 1829 0.546122 TTTCCATCGCCTGGTGCTAT 59.454 50.000 1.39 0.00 46.08 2.97
1714 1830 0.107703 CTTTCCATCGCCTGGTGCTA 60.108 55.000 1.39 0.00 46.08 3.49
1724 1840 2.128035 GATACTGTCCGCTTTCCATCG 58.872 52.381 0.00 0.00 0.00 3.84
1735 1851 5.768164 TCTGGAAACCAAAAAGATACTGTCC 59.232 40.000 0.00 0.00 30.80 4.02
1771 1887 8.023128 TGTTAGCAGCAAAAATATCTGAAGAAC 58.977 33.333 0.00 0.00 0.00 3.01
1804 1920 6.269538 ACTGTAGCAATCACCATGAGAGATAT 59.730 38.462 0.00 0.00 0.00 1.63
1806 1922 4.408270 ACTGTAGCAATCACCATGAGAGAT 59.592 41.667 0.00 0.00 0.00 2.75
1807 1923 3.771479 ACTGTAGCAATCACCATGAGAGA 59.229 43.478 0.00 0.00 0.00 3.10
1808 1924 4.134379 ACTGTAGCAATCACCATGAGAG 57.866 45.455 0.00 0.00 0.00 3.20
1809 1925 5.876651 ATACTGTAGCAATCACCATGAGA 57.123 39.130 0.00 0.00 0.00 3.27
1810 1926 7.609960 AGATATACTGTAGCAATCACCATGAG 58.390 38.462 0.00 0.00 0.00 2.90
1811 1927 7.544804 AGATATACTGTAGCAATCACCATGA 57.455 36.000 0.00 0.00 0.00 3.07
1812 1928 8.613060 AAAGATATACTGTAGCAATCACCATG 57.387 34.615 9.09 0.00 0.00 3.66
1814 1930 8.367911 CCTAAAGATATACTGTAGCAATCACCA 58.632 37.037 9.09 0.00 35.64 4.17
1816 1932 8.585881 TCCCTAAAGATATACTGTAGCAATCAC 58.414 37.037 9.09 0.00 35.64 3.06
1817 1933 8.721133 TCCCTAAAGATATACTGTAGCAATCA 57.279 34.615 9.09 0.00 35.64 2.57
1821 1937 7.668886 GGTACTCCCTAAAGATATACTGTAGCA 59.331 40.741 0.00 0.00 35.64 3.49
1830 1946 8.734763 TGAGTTCTAGGTACTCCCTAAAGATAT 58.265 37.037 17.72 0.00 45.40 1.63
1831 1947 8.110743 TGAGTTCTAGGTACTCCCTAAAGATA 57.889 38.462 17.72 0.64 45.40 1.98
1832 1948 6.982899 TGAGTTCTAGGTACTCCCTAAAGAT 58.017 40.000 17.72 0.00 45.40 2.40
1833 1949 6.398655 TGAGTTCTAGGTACTCCCTAAAGA 57.601 41.667 17.72 1.70 45.40 2.52
1834 1950 7.064229 AGATGAGTTCTAGGTACTCCCTAAAG 58.936 42.308 17.72 0.00 45.40 1.85
1835 1951 6.982899 AGATGAGTTCTAGGTACTCCCTAAA 58.017 40.000 17.72 5.09 45.40 1.85
1837 1953 7.702807 TTAGATGAGTTCTAGGTACTCCCTA 57.297 40.000 17.72 15.68 45.40 3.53
1838 1954 7.507616 CATTTAGATGAGTTCTAGGTACTCCCT 59.492 40.741 17.72 16.34 41.02 4.20
1839 1955 7.506261 TCATTTAGATGAGTTCTAGGTACTCCC 59.494 40.741 17.72 12.05 41.02 4.30
1840 1956 8.466617 TCATTTAGATGAGTTCTAGGTACTCC 57.533 38.462 17.72 8.04 41.02 3.85
1865 1981 9.388506 CAAAGTGAATGAGACCAAACTATATCT 57.611 33.333 0.00 0.00 0.00 1.98
1866 1982 9.383519 TCAAAGTGAATGAGACCAAACTATATC 57.616 33.333 0.00 0.00 0.00 1.63
1868 1984 9.567776 TTTCAAAGTGAATGAGACCAAACTATA 57.432 29.630 0.00 0.00 36.11 1.31
1869 1985 8.463930 TTTCAAAGTGAATGAGACCAAACTAT 57.536 30.769 0.00 0.00 36.11 2.12
1870 1986 7.873719 TTTCAAAGTGAATGAGACCAAACTA 57.126 32.000 0.00 0.00 36.11 2.24
1871 1987 6.773976 TTTCAAAGTGAATGAGACCAAACT 57.226 33.333 0.00 0.00 36.11 2.66
1872 1988 6.811170 TGTTTTCAAAGTGAATGAGACCAAAC 59.189 34.615 0.00 0.00 36.11 2.93
1873 1989 6.929625 TGTTTTCAAAGTGAATGAGACCAAA 58.070 32.000 0.00 0.00 36.11 3.28
1874 1990 6.522625 TGTTTTCAAAGTGAATGAGACCAA 57.477 33.333 0.00 0.00 36.11 3.67
1875 1991 6.376864 TCTTGTTTTCAAAGTGAATGAGACCA 59.623 34.615 0.00 0.00 39.47 4.02
1876 1992 6.795399 TCTTGTTTTCAAAGTGAATGAGACC 58.205 36.000 0.00 0.00 39.47 3.85
1877 1993 8.862550 ATTCTTGTTTTCAAAGTGAATGAGAC 57.137 30.769 0.00 0.00 39.47 3.36
1885 2001 9.334693 GCTGTATCTATTCTTGTTTTCAAAGTG 57.665 33.333 0.00 0.00 39.47 3.16
1886 2002 8.515414 GGCTGTATCTATTCTTGTTTTCAAAGT 58.485 33.333 0.00 0.00 39.47 2.66
1887 2003 7.970614 GGGCTGTATCTATTCTTGTTTTCAAAG 59.029 37.037 0.00 0.00 39.47 2.77
1888 2004 7.450014 TGGGCTGTATCTATTCTTGTTTTCAAA 59.550 33.333 0.00 0.00 39.47 2.69
1889 2005 6.945435 TGGGCTGTATCTATTCTTGTTTTCAA 59.055 34.615 0.00 0.00 38.21 2.69
1890 2006 6.480763 TGGGCTGTATCTATTCTTGTTTTCA 58.519 36.000 0.00 0.00 0.00 2.69
1891 2007 7.067494 ACATGGGCTGTATCTATTCTTGTTTTC 59.933 37.037 0.00 0.00 35.91 2.29
1892 2008 6.891908 ACATGGGCTGTATCTATTCTTGTTTT 59.108 34.615 0.00 0.00 35.91 2.43
1893 2009 6.426587 ACATGGGCTGTATCTATTCTTGTTT 58.573 36.000 0.00 0.00 35.91 2.83
1894 2010 6.006275 ACATGGGCTGTATCTATTCTTGTT 57.994 37.500 0.00 0.00 35.91 2.83
1895 2011 5.636903 ACATGGGCTGTATCTATTCTTGT 57.363 39.130 0.00 0.00 35.91 3.16
1896 2012 6.652481 CCTAACATGGGCTGTATCTATTCTTG 59.348 42.308 0.00 0.00 36.98 3.02
1897 2013 6.558775 TCCTAACATGGGCTGTATCTATTCTT 59.441 38.462 0.00 0.00 36.98 2.52
1898 2014 6.014156 GTCCTAACATGGGCTGTATCTATTCT 60.014 42.308 0.00 0.00 36.98 2.40
1899 2015 6.166982 GTCCTAACATGGGCTGTATCTATTC 58.833 44.000 0.00 0.00 36.98 1.75
1900 2016 5.606749 TGTCCTAACATGGGCTGTATCTATT 59.393 40.000 0.00 0.00 36.98 1.73
1901 2017 5.012148 GTGTCCTAACATGGGCTGTATCTAT 59.988 44.000 0.00 0.00 36.98 1.98
1902 2018 4.344102 GTGTCCTAACATGGGCTGTATCTA 59.656 45.833 0.00 0.00 36.98 1.98
1903 2019 3.134804 GTGTCCTAACATGGGCTGTATCT 59.865 47.826 0.00 0.00 36.98 1.98
1904 2020 3.118408 TGTGTCCTAACATGGGCTGTATC 60.118 47.826 0.00 0.00 36.98 2.24
1905 2021 2.843730 TGTGTCCTAACATGGGCTGTAT 59.156 45.455 0.00 0.00 36.98 2.29
1906 2022 2.027561 GTGTGTCCTAACATGGGCTGTA 60.028 50.000 0.00 0.00 36.98 2.74
1907 2023 1.064003 TGTGTCCTAACATGGGCTGT 58.936 50.000 0.00 0.00 40.84 4.40
1908 2024 1.453155 GTGTGTCCTAACATGGGCTG 58.547 55.000 0.00 0.00 37.81 4.85
1909 2025 0.036388 CGTGTGTCCTAACATGGGCT 60.036 55.000 0.00 0.00 37.81 5.19
1910 2026 1.644786 GCGTGTGTCCTAACATGGGC 61.645 60.000 0.00 0.00 37.81 5.36
1911 2027 0.321210 TGCGTGTGTCCTAACATGGG 60.321 55.000 0.00 0.00 37.81 4.00
1912 2028 1.665679 GATGCGTGTGTCCTAACATGG 59.334 52.381 0.00 0.00 37.81 3.66
1913 2029 2.621338 AGATGCGTGTGTCCTAACATG 58.379 47.619 0.00 0.00 37.81 3.21
1914 2030 3.334583 AAGATGCGTGTGTCCTAACAT 57.665 42.857 0.00 0.00 37.81 2.71
1915 2031 2.831685 AAGATGCGTGTGTCCTAACA 57.168 45.000 0.00 0.00 0.00 2.41
1916 2032 4.444720 GCTATAAGATGCGTGTGTCCTAAC 59.555 45.833 0.00 0.00 0.00 2.34
1917 2033 4.098807 TGCTATAAGATGCGTGTGTCCTAA 59.901 41.667 0.00 0.00 0.00 2.69
1918 2034 3.634910 TGCTATAAGATGCGTGTGTCCTA 59.365 43.478 0.00 0.00 0.00 2.94
1919 2035 2.430694 TGCTATAAGATGCGTGTGTCCT 59.569 45.455 0.00 0.00 0.00 3.85
1920 2036 2.821546 TGCTATAAGATGCGTGTGTCC 58.178 47.619 0.00 0.00 0.00 4.02
1921 2037 4.051237 TGATGCTATAAGATGCGTGTGTC 58.949 43.478 0.00 0.00 0.00 3.67
1922 2038 3.804325 GTGATGCTATAAGATGCGTGTGT 59.196 43.478 0.00 0.00 0.00 3.72
1923 2039 3.803778 TGTGATGCTATAAGATGCGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
1924 2040 4.058721 TGTGATGCTATAAGATGCGTGT 57.941 40.909 0.00 0.00 0.00 4.49
1925 2041 4.092529 GGATGTGATGCTATAAGATGCGTG 59.907 45.833 0.00 0.00 0.00 5.34
1926 2042 4.248859 GGATGTGATGCTATAAGATGCGT 58.751 43.478 0.00 0.00 0.00 5.24
1927 2043 4.248058 TGGATGTGATGCTATAAGATGCG 58.752 43.478 0.00 0.00 0.00 4.73
1928 2044 6.404403 CCATTGGATGTGATGCTATAAGATGC 60.404 42.308 0.00 0.00 0.00 3.91
1929 2045 6.657966 ACCATTGGATGTGATGCTATAAGATG 59.342 38.462 10.37 0.00 0.00 2.90
1930 2046 6.787170 ACCATTGGATGTGATGCTATAAGAT 58.213 36.000 10.37 0.00 0.00 2.40
1931 2047 6.191657 ACCATTGGATGTGATGCTATAAGA 57.808 37.500 10.37 0.00 0.00 2.10
1932 2048 6.889301 AACCATTGGATGTGATGCTATAAG 57.111 37.500 10.37 0.00 0.00 1.73
1935 2051 8.938801 TTTATAACCATTGGATGTGATGCTAT 57.061 30.769 10.37 0.00 0.00 2.97
1936 2052 8.759481 TTTTATAACCATTGGATGTGATGCTA 57.241 30.769 10.37 0.00 0.00 3.49
1937 2053 7.201938 CCTTTTATAACCATTGGATGTGATGCT 60.202 37.037 10.37 0.00 0.00 3.79
1938 2054 6.925165 CCTTTTATAACCATTGGATGTGATGC 59.075 38.462 10.37 0.00 0.00 3.91
1939 2055 7.922278 CACCTTTTATAACCATTGGATGTGATG 59.078 37.037 10.37 0.00 0.00 3.07
1940 2056 7.838696 TCACCTTTTATAACCATTGGATGTGAT 59.161 33.333 10.37 0.00 0.00 3.06
1941 2057 7.178573 TCACCTTTTATAACCATTGGATGTGA 58.821 34.615 10.37 3.03 0.00 3.58
1942 2058 7.403312 TCACCTTTTATAACCATTGGATGTG 57.597 36.000 10.37 0.57 0.00 3.21
1943 2059 8.477256 CATTCACCTTTTATAACCATTGGATGT 58.523 33.333 10.37 0.00 0.00 3.06
1944 2060 8.694540 TCATTCACCTTTTATAACCATTGGATG 58.305 33.333 10.37 0.00 0.00 3.51
1945 2061 8.837099 TCATTCACCTTTTATAACCATTGGAT 57.163 30.769 10.37 0.00 0.00 3.41
1946 2062 8.112822 TCTCATTCACCTTTTATAACCATTGGA 58.887 33.333 10.37 0.00 0.00 3.53
1947 2063 8.190784 GTCTCATTCACCTTTTATAACCATTGG 58.809 37.037 0.00 0.00 0.00 3.16
1948 2064 8.190784 GGTCTCATTCACCTTTTATAACCATTG 58.809 37.037 0.00 0.00 0.00 2.82
1949 2065 7.893302 TGGTCTCATTCACCTTTTATAACCATT 59.107 33.333 0.00 0.00 34.66 3.16
1950 2066 7.410174 TGGTCTCATTCACCTTTTATAACCAT 58.590 34.615 0.00 0.00 34.66 3.55
1951 2067 6.785076 TGGTCTCATTCACCTTTTATAACCA 58.215 36.000 0.00 0.00 34.66 3.67
1952 2068 7.696992 TTGGTCTCATTCACCTTTTATAACC 57.303 36.000 0.00 0.00 34.66 2.85
1959 2075 9.927081 AGATATAATTTGGTCTCATTCACCTTT 57.073 29.630 0.00 0.00 34.66 3.11
1960 2076 9.566432 GAGATATAATTTGGTCTCATTCACCTT 57.434 33.333 8.11 0.00 37.60 3.50
1961 2077 8.717717 TGAGATATAATTTGGTCTCATTCACCT 58.282 33.333 10.50 0.00 41.40 4.00
1962 2078 8.908786 TGAGATATAATTTGGTCTCATTCACC 57.091 34.615 10.50 0.00 41.40 4.02
1990 2106 9.973450 GATATCAGTTTTGCTAGAACTCATCTA 57.027 33.333 0.00 0.00 39.71 1.98
1991 2107 8.703743 AGATATCAGTTTTGCTAGAACTCATCT 58.296 33.333 5.32 0.62 42.48 2.90
1992 2108 8.885494 AGATATCAGTTTTGCTAGAACTCATC 57.115 34.615 5.32 0.00 35.26 2.92
1993 2109 9.678260 AAAGATATCAGTTTTGCTAGAACTCAT 57.322 29.630 5.32 0.00 35.26 2.90
1998 2114 9.905713 ACCATAAAGATATCAGTTTTGCTAGAA 57.094 29.630 5.32 0.00 0.00 2.10
2057 2184 1.278985 CTTGTGCATGTACCAGAGGGA 59.721 52.381 11.66 0.00 38.05 4.20
2077 2210 3.843999 TGAGAGTTGTGTTGGTTTTTGC 58.156 40.909 0.00 0.00 0.00 3.68
2084 2217 7.630242 ATTATTACCATGAGAGTTGTGTTGG 57.370 36.000 0.00 0.00 0.00 3.77
2109 2242 9.691362 GAACTGTGTTTACAAAATTATCATGGT 57.309 29.630 0.00 0.00 36.14 3.55
2110 2243 9.689976 TGAACTGTGTTTACAAAATTATCATGG 57.310 29.630 0.00 0.00 36.14 3.66
2151 2284 9.859427 CAAACAACATCATGGATTTACACTTAT 57.141 29.630 0.00 0.00 0.00 1.73
2152 2285 8.303156 CCAAACAACATCATGGATTTACACTTA 58.697 33.333 0.00 0.00 34.82 2.24
2158 2291 7.158021 GGAAACCAAACAACATCATGGATTTA 58.842 34.615 0.00 0.00 36.75 1.40
2164 2297 4.235939 TCGGAAACCAAACAACATCATG 57.764 40.909 0.00 0.00 0.00 3.07
2168 2301 3.181471 TGCAATCGGAAACCAAACAACAT 60.181 39.130 0.00 0.00 0.00 2.71
2171 2304 3.526931 TTGCAATCGGAAACCAAACAA 57.473 38.095 0.00 0.00 0.00 2.83
2172 2305 3.068732 TGATTGCAATCGGAAACCAAACA 59.931 39.130 29.23 9.49 38.26 2.83
2173 2306 3.648009 TGATTGCAATCGGAAACCAAAC 58.352 40.909 29.23 7.10 38.26 2.93
2174 2307 3.860378 GCTGATTGCAATCGGAAACCAAA 60.860 43.478 40.02 18.22 43.06 3.28
2175 2308 2.352617 GCTGATTGCAATCGGAAACCAA 60.353 45.455 40.02 18.84 43.06 3.67


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

AutoCloner maintained by Alex Coulton.