Multiple sequence alignment - TraesCS2B01G109200

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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 TraesCS2B01G109200 chr2B 100.000 2885 0 0 1 2885 70746041 70743157 0.000000e+00 5328.0
1 TraesCS2B01G109200 chr2B 91.107 1563 138 1 7 1568 733990454 733988892 0.000000e+00 2115.0
2 TraesCS2B01G109200 chr2B 88.644 1180 133 1 738 1916 239418282 239417103 0.000000e+00 1435.0
3 TraesCS2B01G109200 chr2B 78.625 1469 301 10 9 1470 91001686 91000224 0.000000e+00 961.0
4 TraesCS2B01G109200 chr2B 80.039 511 102 0 9 519 614231796 614232306 2.100000e-101 379.0
5 TraesCS2B01G109200 chr2B 85.507 138 18 2 2236 2371 593770067 593769930 3.000000e-30 143.0
6 TraesCS2B01G109200 chr2B 72.727 319 73 14 270 581 602215537 602215226 8.510000e-16 95.3
7 TraesCS2B01G109200 chr4B 92.749 1917 135 4 1 1916 491788639 491790552 0.000000e+00 2767.0
8 TraesCS2B01G109200 chr4B 89.706 68 7 0 2086 2153 157940403 157940470 1.420000e-13 87.9
9 TraesCS2B01G109200 chr4B 88.889 63 5 2 2087 2148 384389718 384389779 3.080000e-10 76.8
10 TraesCS2B01G109200 chr4B 86.765 68 9 0 2086 2153 405274489 405274422 3.080000e-10 76.8
11 TraesCS2B01G109200 chr5A 92.599 1743 128 1 176 1917 680485378 680487120 0.000000e+00 2503.0
12 TraesCS2B01G109200 chr7A 92.204 1706 132 1 1 1705 563324517 563326222 0.000000e+00 2412.0
13 TraesCS2B01G109200 chr1B 92.606 1393 101 2 431 1821 62019246 62020638 0.000000e+00 2001.0
14 TraesCS2B01G109200 chr5D 92.761 1188 85 1 729 1915 538532437 538531250 0.000000e+00 1716.0
15 TraesCS2B01G109200 chr2D 79.435 1911 378 11 9 1912 633507954 633506052 0.000000e+00 1338.0
16 TraesCS2B01G109200 chr2D 91.830 306 23 2 2572 2877 497626669 497626366 2.660000e-115 425.0
17 TraesCS2B01G109200 chr4A 78.478 1919 397 15 7 1916 741787805 741785894 0.000000e+00 1242.0
18 TraesCS2B01G109200 chr4A 93.636 330 20 1 1586 1915 610824664 610824992 2.580000e-135 492.0
19 TraesCS2B01G109200 chr4A 93.421 304 17 3 2571 2874 486245323 486245023 5.670000e-122 448.0
20 TraesCS2B01G109200 chr2A 92.915 621 44 0 1294 1914 102342554 102341934 0.000000e+00 904.0
21 TraesCS2B01G109200 chr6A 92.834 307 21 1 2571 2877 488167584 488167279 7.340000e-121 444.0
22 TraesCS2B01G109200 chr3A 92.763 304 17 1 2571 2874 573454882 573455180 4.410000e-118 435.0
23 TraesCS2B01G109200 chr3A 89.604 202 20 1 2369 2569 573454431 573454632 3.690000e-64 255.0
24 TraesCS2B01G109200 chr3A 85.870 184 24 2 2203 2385 198509575 198509757 8.160000e-46 195.0
25 TraesCS2B01G109200 chr3A 87.050 139 18 0 1918 2056 596101252 596101114 1.070000e-34 158.0
26 TraesCS2B01G109200 chr5B 91.582 297 19 3 2571 2867 130421187 130421477 3.460000e-109 405.0
27 TraesCS2B01G109200 chr5B 90.759 303 27 1 2571 2873 60148173 60148474 1.240000e-108 403.0
28 TraesCS2B01G109200 chr5B 92.347 196 14 1 2369 2563 60147722 60147917 7.870000e-71 278.0
29 TraesCS2B01G109200 chr5B 90.547 201 18 1 2369 2568 130420736 130420936 6.130000e-67 265.0
30 TraesCS2B01G109200 chr5B 86.029 136 19 0 1922 2057 182802308 182802173 2.320000e-31 147.0
31 TraesCS2B01G109200 chr6D 90.523 306 27 2 2571 2874 215529040 215528735 1.240000e-108 403.0
32 TraesCS2B01G109200 chr6D 94.388 196 10 1 2369 2563 460659168 460659363 1.680000e-77 300.0
33 TraesCS2B01G109200 chr6D 86.429 140 19 0 1918 2057 161925279 161925140 1.380000e-33 154.0
34 TraesCS2B01G109200 chr6D 89.623 106 10 1 2369 2474 234290490 234290386 1.800000e-27 134.0
35 TraesCS2B01G109200 chr6D 84.348 115 15 3 1918 2031 49199891 49199779 3.040000e-20 110.0
36 TraesCS2B01G109200 chr6D 84.348 115 15 3 1918 2031 280840280 280840392 3.040000e-20 110.0
37 TraesCS2B01G109200 chr6B 90.132 304 25 2 2571 2874 188255236 188254938 9.690000e-105 390.0
38 TraesCS2B01G109200 chr6B 86.765 136 18 0 1922 2057 383134346 383134481 4.980000e-33 152.0
39 TraesCS2B01G109200 chr4D 88.502 287 32 1 2086 2371 109538823 109539109 2.130000e-91 346.0
40 TraesCS2B01G109200 chr4D 88.732 142 15 1 2225 2365 452617983 452618124 3.820000e-39 172.0
41 TraesCS2B01G109200 chr4D 85.714 140 20 0 1918 2057 81091842 81091703 6.440000e-32 148.0
42 TraesCS2B01G109200 chr4D 85.217 115 14 3 1918 2031 63067924 63068036 6.530000e-22 115.0
43 TraesCS2B01G109200 chr7B 94.521 219 12 0 2650 2868 295017025 295017243 3.560000e-89 339.0
44 TraesCS2B01G109200 chr7D 90.050 201 19 1 2369 2568 209555039 209554839 2.850000e-65 259.0
45 TraesCS2B01G109200 chr3D 89.362 141 13 2 1918 2057 248129623 248129484 2.950000e-40 176.0
46 TraesCS2B01G109200 chr1D 90.000 60 4 2 2284 2342 197211018 197211076 3.080000e-10 76.8


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 TraesCS2B01G109200 chr2B 70743157 70746041 2884 True 5328.0 5328 100.0000 1 2885 1 chr2B.!!$R1 2884
1 TraesCS2B01G109200 chr2B 733988892 733990454 1562 True 2115.0 2115 91.1070 7 1568 1 chr2B.!!$R6 1561
2 TraesCS2B01G109200 chr2B 239417103 239418282 1179 True 1435.0 1435 88.6440 738 1916 1 chr2B.!!$R3 1178
3 TraesCS2B01G109200 chr2B 91000224 91001686 1462 True 961.0 961 78.6250 9 1470 1 chr2B.!!$R2 1461
4 TraesCS2B01G109200 chr2B 614231796 614232306 510 False 379.0 379 80.0390 9 519 1 chr2B.!!$F1 510
5 TraesCS2B01G109200 chr4B 491788639 491790552 1913 False 2767.0 2767 92.7490 1 1916 1 chr4B.!!$F3 1915
6 TraesCS2B01G109200 chr5A 680485378 680487120 1742 False 2503.0 2503 92.5990 176 1917 1 chr5A.!!$F1 1741
7 TraesCS2B01G109200 chr7A 563324517 563326222 1705 False 2412.0 2412 92.2040 1 1705 1 chr7A.!!$F1 1704
8 TraesCS2B01G109200 chr1B 62019246 62020638 1392 False 2001.0 2001 92.6060 431 1821 1 chr1B.!!$F1 1390
9 TraesCS2B01G109200 chr5D 538531250 538532437 1187 True 1716.0 1716 92.7610 729 1915 1 chr5D.!!$R1 1186
10 TraesCS2B01G109200 chr2D 633506052 633507954 1902 True 1338.0 1338 79.4350 9 1912 1 chr2D.!!$R2 1903
11 TraesCS2B01G109200 chr4A 741785894 741787805 1911 True 1242.0 1242 78.4780 7 1916 1 chr4A.!!$R2 1909
12 TraesCS2B01G109200 chr2A 102341934 102342554 620 True 904.0 904 92.9150 1294 1914 1 chr2A.!!$R1 620
13 TraesCS2B01G109200 chr3A 573454431 573455180 749 False 345.0 435 91.1835 2369 2874 2 chr3A.!!$F2 505
14 TraesCS2B01G109200 chr5B 60147722 60148474 752 False 340.5 403 91.5530 2369 2873 2 chr5B.!!$F1 504
15 TraesCS2B01G109200 chr5B 130420736 130421477 741 False 335.0 405 91.0645 2369 2867 2 chr5B.!!$F2 498

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
610 611 0.25589 GCCCAAGCAGGAAGGTGATA 59.744 55.0 0.0 0.0 41.22 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 1958 0.03213 CATACATCTCCGGGTCGTGG 59.968 60.0 0.0 0.0 0.0 4.94 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
178 179 1.972795 GCCATCCCATTGTATGCCATT 59.027 47.619 0.00 0.00 0.00 3.16
194 195 3.243035 TGCCATTCTTGTGTTCAAACTCG 60.243 43.478 0.00 0.00 32.87 4.18
229 230 4.873259 TGCAACGCAATAACTTCTGCTATA 59.127 37.500 0.00 0.00 34.76 1.31
383 384 0.874390 GAAACAATGCTGGCGACTGA 59.126 50.000 0.00 0.00 0.00 3.41
404 405 1.135139 TCGCAGAGCCAGAATCACTAC 59.865 52.381 0.00 0.00 0.00 2.73
417 418 4.155462 AGAATCACTACGTGCGAGAGTTTA 59.845 41.667 0.00 0.00 32.98 2.01
610 611 0.255890 GCCCAAGCAGGAAGGTGATA 59.744 55.000 0.00 0.00 41.22 2.15
890 893 8.596781 ACCATATTGTCTTCAAGTACTAGTCT 57.403 34.615 0.00 0.00 36.97 3.24
899 902 6.492429 TCTTCAAGTACTAGTCTAGTTTGGCA 59.508 38.462 17.59 7.24 40.14 4.92
1127 1130 1.410083 GCTCCCCACCATAAATGAGCA 60.410 52.381 0.00 0.00 43.50 4.26
1162 1165 1.205055 GGAGGGATCTTCGGTCCTTT 58.795 55.000 0.00 0.00 36.00 3.11
1260 1263 4.320870 CGGTTTGGTATATATGGTGGGAC 58.679 47.826 0.00 0.00 0.00 4.46
1298 1301 0.329596 GGTGAGCCCATTCAGGAACT 59.670 55.000 0.00 0.00 41.22 3.01
1307 1310 4.347607 CCCATTCAGGAACTTGGAAGATT 58.652 43.478 3.74 0.00 41.22 2.40
1428 1431 5.409826 GGGATTTGTTAGCCTCAATATCGAG 59.590 44.000 0.00 0.00 0.00 4.04
1560 1563 4.444081 ACGGCCGAGGCTAGAGGT 62.444 66.667 35.90 0.68 41.60 3.85
1594 1597 1.040339 GGTTCTGGCAAACACCACCA 61.040 55.000 12.37 0.00 35.33 4.17
1625 1628 0.755698 GTGGAGATCAGGGCGGACTA 60.756 60.000 0.00 0.00 0.00 2.59
1723 1726 9.456797 GTACTTTCTTGTGTCGTAATTTTATCG 57.543 33.333 0.00 0.00 0.00 2.92
1733 1736 7.629845 GTGTCGTAATTTTATCGCTGTTAGTTC 59.370 37.037 0.00 0.00 0.00 3.01
1806 1809 1.007154 GGAGCCCTCGCGAACTATC 60.007 63.158 11.33 6.38 41.18 2.08
1872 1875 5.354234 CACAAACGATGTAGCCCTATTTTCT 59.646 40.000 0.00 0.00 41.46 2.52
1933 1936 5.500645 AAAAAGAGAGGAAAAACGACCTG 57.499 39.130 0.00 0.00 36.57 4.00
1934 1937 4.417426 AAAGAGAGGAAAAACGACCTGA 57.583 40.909 0.00 0.00 36.57 3.86
1935 1938 4.417426 AAGAGAGGAAAAACGACCTGAA 57.583 40.909 0.00 0.00 36.57 3.02
1936 1939 4.625607 AGAGAGGAAAAACGACCTGAAT 57.374 40.909 0.00 0.00 36.57 2.57
1937 1940 5.740290 AGAGAGGAAAAACGACCTGAATA 57.260 39.130 0.00 0.00 36.57 1.75
1938 1941 6.301169 AGAGAGGAAAAACGACCTGAATAT 57.699 37.500 0.00 0.00 36.57 1.28
1939 1942 6.712276 AGAGAGGAAAAACGACCTGAATATT 58.288 36.000 0.00 0.00 36.57 1.28
1940 1943 6.595716 AGAGAGGAAAAACGACCTGAATATTG 59.404 38.462 0.00 0.00 36.57 1.90
1941 1944 6.472887 AGAGGAAAAACGACCTGAATATTGA 58.527 36.000 0.00 0.00 36.57 2.57
1942 1945 7.112779 AGAGGAAAAACGACCTGAATATTGAT 58.887 34.615 0.00 0.00 36.57 2.57
1943 1946 7.611855 AGAGGAAAAACGACCTGAATATTGATT 59.388 33.333 0.00 0.00 36.57 2.57
1944 1947 7.538575 AGGAAAAACGACCTGAATATTGATTG 58.461 34.615 0.00 0.00 34.99 2.67
1945 1948 6.751888 GGAAAAACGACCTGAATATTGATTGG 59.248 38.462 0.00 0.00 0.00 3.16
1946 1949 6.834168 AAAACGACCTGAATATTGATTGGT 57.166 33.333 0.00 0.00 0.00 3.67
1947 1950 6.436843 AAACGACCTGAATATTGATTGGTC 57.563 37.500 12.23 12.23 35.89 4.02
1948 1951 5.097742 ACGACCTGAATATTGATTGGTCA 57.902 39.130 17.98 0.61 37.73 4.02
1950 1953 5.943416 ACGACCTGAATATTGATTGGTCAAA 59.057 36.000 17.98 0.00 46.67 2.69
1951 1954 6.603201 ACGACCTGAATATTGATTGGTCAAAT 59.397 34.615 17.98 7.11 46.67 2.32
1952 1955 7.134815 CGACCTGAATATTGATTGGTCAAATC 58.865 38.462 17.98 0.00 46.67 2.17
1953 1956 7.352079 ACCTGAATATTGATTGGTCAAATCC 57.648 36.000 0.00 0.00 46.67 3.01
1954 1957 6.896860 ACCTGAATATTGATTGGTCAAATCCA 59.103 34.615 0.00 0.00 46.67 3.41
1955 1958 7.147846 ACCTGAATATTGATTGGTCAAATCCAC 60.148 37.037 0.00 0.00 46.67 4.02
1956 1959 7.111247 TGAATATTGATTGGTCAAATCCACC 57.889 36.000 0.00 0.00 46.67 4.61
1957 1960 6.666980 TGAATATTGATTGGTCAAATCCACCA 59.333 34.615 0.00 0.00 46.67 4.17
1958 1961 4.806640 ATTGATTGGTCAAATCCACCAC 57.193 40.909 0.00 0.00 46.67 4.16
1959 1962 2.158559 TGATTGGTCAAATCCACCACG 58.841 47.619 0.00 0.00 43.93 4.94
1960 1963 2.224646 TGATTGGTCAAATCCACCACGA 60.225 45.455 0.00 0.00 43.93 4.35
1961 1964 1.600023 TTGGTCAAATCCACCACGAC 58.400 50.000 0.00 0.00 43.93 4.34
1962 1965 0.250553 TGGTCAAATCCACCACGACC 60.251 55.000 0.00 0.00 45.24 4.79
1963 1966 0.958876 GGTCAAATCCACCACGACCC 60.959 60.000 0.00 0.00 40.25 4.46
1964 1967 1.004320 TCAAATCCACCACGACCCG 60.004 57.895 0.00 0.00 0.00 5.28
1965 1968 2.038269 CAAATCCACCACGACCCGG 61.038 63.158 0.00 0.00 0.00 5.73
1966 1969 2.218454 AAATCCACCACGACCCGGA 61.218 57.895 0.73 0.00 0.00 5.14
1967 1970 2.180159 AAATCCACCACGACCCGGAG 62.180 60.000 0.73 0.00 0.00 4.63
1968 1971 3.595428 ATCCACCACGACCCGGAGA 62.595 63.158 0.73 0.00 0.00 3.71
1969 1972 2.873557 ATCCACCACGACCCGGAGAT 62.874 60.000 0.73 0.00 0.00 2.75
1970 1973 2.184322 CACCACGACCCGGAGATG 59.816 66.667 0.73 0.00 0.00 2.90
1971 1974 2.283676 ACCACGACCCGGAGATGT 60.284 61.111 0.73 0.00 0.00 3.06
1972 1975 1.000521 ACCACGACCCGGAGATGTA 60.001 57.895 0.73 0.00 0.00 2.29
1973 1976 0.396695 ACCACGACCCGGAGATGTAT 60.397 55.000 0.73 0.00 0.00 2.29
1974 1977 0.032130 CCACGACCCGGAGATGTATG 59.968 60.000 0.73 0.00 0.00 2.39
1975 1978 0.597637 CACGACCCGGAGATGTATGC 60.598 60.000 0.73 0.00 0.00 3.14
1976 1979 1.040893 ACGACCCGGAGATGTATGCA 61.041 55.000 0.73 0.00 0.00 3.96
1977 1980 0.319040 CGACCCGGAGATGTATGCAG 60.319 60.000 0.73 0.00 0.00 4.41
1978 1981 0.753262 GACCCGGAGATGTATGCAGT 59.247 55.000 0.73 0.00 0.00 4.40
1979 1982 0.753262 ACCCGGAGATGTATGCAGTC 59.247 55.000 0.73 0.00 0.00 3.51
1980 1983 0.319040 CCCGGAGATGTATGCAGTCG 60.319 60.000 0.73 0.00 0.00 4.18
1981 1984 0.385751 CCGGAGATGTATGCAGTCGT 59.614 55.000 0.00 0.00 0.00 4.34
1982 1985 1.600663 CCGGAGATGTATGCAGTCGTC 60.601 57.143 0.00 0.00 0.00 4.20
1983 1986 1.759994 GGAGATGTATGCAGTCGTCG 58.240 55.000 0.00 0.00 0.00 5.12
1984 1987 1.124462 GAGATGTATGCAGTCGTCGC 58.876 55.000 0.00 0.00 0.00 5.19
1985 1988 0.455815 AGATGTATGCAGTCGTCGCA 59.544 50.000 0.00 0.00 44.94 5.10
1991 1994 3.030209 TGCAGTCGTCGCATAGAAC 57.970 52.632 0.00 0.00 33.55 3.01
1992 1995 0.526211 TGCAGTCGTCGCATAGAACT 59.474 50.000 0.00 0.00 33.55 3.01
1993 1996 0.917259 GCAGTCGTCGCATAGAACTG 59.083 55.000 5.41 5.41 39.52 3.16
1994 1997 1.550065 CAGTCGTCGCATAGAACTGG 58.450 55.000 2.45 0.00 35.24 4.00
1995 1998 0.456221 AGTCGTCGCATAGAACTGGG 59.544 55.000 0.00 0.00 0.00 4.45
1996 1999 0.527817 GTCGTCGCATAGAACTGGGG 60.528 60.000 0.00 0.00 0.00 4.96
1997 2000 1.883084 CGTCGCATAGAACTGGGGC 60.883 63.158 0.00 0.00 0.00 5.80
1999 2002 3.272334 CGCATAGAACTGGGGCGC 61.272 66.667 0.00 0.00 41.27 6.53
2000 2003 2.124736 GCATAGAACTGGGGCGCA 60.125 61.111 10.83 3.57 0.00 6.09
2001 2004 1.526917 GCATAGAACTGGGGCGCAT 60.527 57.895 10.83 0.00 0.00 4.73
2002 2005 1.510480 GCATAGAACTGGGGCGCATC 61.510 60.000 10.83 0.25 0.00 3.91
2003 2006 0.107456 CATAGAACTGGGGCGCATCT 59.893 55.000 10.83 8.79 0.00 2.90
2004 2007 0.107456 ATAGAACTGGGGCGCATCTG 59.893 55.000 10.83 7.15 0.00 2.90
2005 2008 2.593468 TAGAACTGGGGCGCATCTGC 62.593 60.000 10.83 0.00 37.78 4.26
2013 2016 3.403277 GCGCATCTGCCACAGTAG 58.597 61.111 0.30 0.00 37.91 2.57
2014 2017 2.817423 GCGCATCTGCCACAGTAGC 61.817 63.158 0.30 0.05 37.91 3.58
2015 2018 1.448365 CGCATCTGCCACAGTAGCA 60.448 57.895 12.06 0.00 38.82 3.49
2016 2019 1.699656 CGCATCTGCCACAGTAGCAC 61.700 60.000 12.06 0.00 36.01 4.40
2017 2020 1.699656 GCATCTGCCACAGTAGCACG 61.700 60.000 0.00 0.00 36.01 5.34
2018 2021 1.448540 ATCTGCCACAGTAGCACGC 60.449 57.895 0.00 0.00 36.01 5.34
2019 2022 2.859273 ATCTGCCACAGTAGCACGCC 62.859 60.000 0.00 0.00 36.01 5.68
2020 2023 3.596066 CTGCCACAGTAGCACGCCT 62.596 63.158 0.00 0.00 36.01 5.52
2021 2024 3.121030 GCCACAGTAGCACGCCTG 61.121 66.667 0.00 0.00 34.82 4.85
2022 2025 2.434884 CCACAGTAGCACGCCTGG 60.435 66.667 0.00 0.00 32.90 4.45
2023 2026 2.343758 CACAGTAGCACGCCTGGT 59.656 61.111 0.00 0.00 32.90 4.00
2024 2027 1.738099 CACAGTAGCACGCCTGGTC 60.738 63.158 0.00 0.00 32.90 4.02
2025 2028 2.507102 CAGTAGCACGCCTGGTCG 60.507 66.667 8.60 8.60 0.00 4.79
2026 2029 3.760035 AGTAGCACGCCTGGTCGG 61.760 66.667 13.50 5.47 0.00 4.79
2036 2039 4.803426 CTGGTCGGCCTCTGCGAC 62.803 72.222 7.97 2.05 39.02 5.19
2038 2041 4.803426 GGTCGGCCTCTGCGACAG 62.803 72.222 13.22 0.00 40.43 3.51
2039 2042 4.803426 GTCGGCCTCTGCGACAGG 62.803 72.222 0.00 0.00 39.32 4.00
2044 2047 3.609703 CCTCTGCGACAGGCTACT 58.390 61.111 6.95 0.00 44.05 2.57
2045 2048 1.893786 CCTCTGCGACAGGCTACTT 59.106 57.895 6.95 0.00 44.05 2.24
2046 2049 0.179124 CCTCTGCGACAGGCTACTTC 60.179 60.000 6.95 0.00 44.05 3.01
2047 2050 0.528017 CTCTGCGACAGGCTACTTCA 59.472 55.000 6.95 0.00 44.05 3.02
2048 2051 0.243907 TCTGCGACAGGCTACTTCAC 59.756 55.000 6.95 0.00 44.05 3.18
2049 2052 0.244994 CTGCGACAGGCTACTTCACT 59.755 55.000 0.00 0.00 44.05 3.41
2050 2053 0.679505 TGCGACAGGCTACTTCACTT 59.320 50.000 0.00 0.00 44.05 3.16
2051 2054 1.336887 TGCGACAGGCTACTTCACTTC 60.337 52.381 0.00 0.00 44.05 3.01
2052 2055 1.618861 CGACAGGCTACTTCACTTCG 58.381 55.000 0.00 0.00 0.00 3.79
2053 2056 1.351153 GACAGGCTACTTCACTTCGC 58.649 55.000 0.00 0.00 0.00 4.70
2054 2057 0.037232 ACAGGCTACTTCACTTCGCC 60.037 55.000 0.00 0.00 40.99 5.54
2055 2058 1.078759 CAGGCTACTTCACTTCGCCG 61.079 60.000 0.00 0.00 45.16 6.46
2056 2059 2.453638 GGCTACTTCACTTCGCCGC 61.454 63.158 0.00 0.00 0.00 6.53
2057 2060 2.453638 GCTACTTCACTTCGCCGCC 61.454 63.158 0.00 0.00 0.00 6.13
2058 2061 1.215647 CTACTTCACTTCGCCGCCT 59.784 57.895 0.00 0.00 0.00 5.52
2059 2062 0.802607 CTACTTCACTTCGCCGCCTC 60.803 60.000 0.00 0.00 0.00 4.70
2060 2063 2.221906 TACTTCACTTCGCCGCCTCC 62.222 60.000 0.00 0.00 0.00 4.30
2061 2064 4.735132 TTCACTTCGCCGCCTCCG 62.735 66.667 0.00 0.00 0.00 4.63
2070 2073 4.069232 CCGCCTCCGTGCTTCTCA 62.069 66.667 0.00 0.00 0.00 3.27
2071 2074 2.507992 CGCCTCCGTGCTTCTCAG 60.508 66.667 0.00 0.00 0.00 3.35
2072 2075 2.125350 GCCTCCGTGCTTCTCAGG 60.125 66.667 0.00 0.00 0.00 3.86
2073 2076 2.125350 CCTCCGTGCTTCTCAGGC 60.125 66.667 0.00 0.00 0.00 4.85
2074 2077 2.654079 CCTCCGTGCTTCTCAGGCT 61.654 63.158 0.00 0.00 0.00 4.58
2075 2078 1.447489 CTCCGTGCTTCTCAGGCTG 60.447 63.158 8.58 8.58 0.00 4.85
2076 2079 3.123620 CCGTGCTTCTCAGGCTGC 61.124 66.667 10.34 0.00 0.00 5.25
2077 2080 3.123620 CGTGCTTCTCAGGCTGCC 61.124 66.667 11.65 11.65 0.00 4.85
2078 2081 2.350514 GTGCTTCTCAGGCTGCCT 59.649 61.111 17.22 17.22 0.00 4.75
2079 2082 1.744741 GTGCTTCTCAGGCTGCCTC 60.745 63.158 20.49 7.07 0.00 4.70
2080 2083 2.511145 GCTTCTCAGGCTGCCTCG 60.511 66.667 20.49 14.53 0.00 4.63
2081 2084 2.511145 CTTCTCAGGCTGCCTCGC 60.511 66.667 20.49 0.00 0.00 5.03
2082 2085 4.441695 TTCTCAGGCTGCCTCGCG 62.442 66.667 20.49 8.33 0.00 5.87
2084 2087 3.826754 CTCAGGCTGCCTCGCGTA 61.827 66.667 20.49 1.12 0.00 4.42
2085 2088 3.764810 CTCAGGCTGCCTCGCGTAG 62.765 68.421 20.49 6.67 0.00 3.51
2117 2120 4.463879 CCGCTGCTCCAGACCAGG 62.464 72.222 0.00 0.00 32.44 4.45
2119 2122 3.715097 GCTGCTCCAGACCAGGCT 61.715 66.667 0.00 0.00 32.44 4.58
2120 2123 2.583520 CTGCTCCAGACCAGGCTC 59.416 66.667 0.00 0.00 32.44 4.70
2121 2124 3.005539 TGCTCCAGACCAGGCTCC 61.006 66.667 0.00 0.00 0.00 4.70
2122 2125 4.154347 GCTCCAGACCAGGCTCCG 62.154 72.222 0.00 0.00 0.00 4.63
2123 2126 4.154347 CTCCAGACCAGGCTCCGC 62.154 72.222 0.00 0.00 0.00 5.54
2165 2168 4.807039 GCTTCCGAGCGCCCGTAA 62.807 66.667 11.25 0.00 39.48 3.18
2166 2169 2.884207 CTTCCGAGCGCCCGTAAC 60.884 66.667 11.25 0.00 0.00 2.50
2167 2170 4.440127 TTCCGAGCGCCCGTAACC 62.440 66.667 11.25 0.00 0.00 2.85
2175 2178 4.029809 GCCCGTAACCAGCCACCT 62.030 66.667 0.00 0.00 0.00 4.00
2176 2179 2.267961 CCCGTAACCAGCCACCTC 59.732 66.667 0.00 0.00 0.00 3.85
2177 2180 2.291043 CCCGTAACCAGCCACCTCT 61.291 63.158 0.00 0.00 0.00 3.69
2178 2181 0.974010 CCCGTAACCAGCCACCTCTA 60.974 60.000 0.00 0.00 0.00 2.43
2179 2182 1.120530 CCGTAACCAGCCACCTCTAT 58.879 55.000 0.00 0.00 0.00 1.98
2180 2183 1.068741 CCGTAACCAGCCACCTCTATC 59.931 57.143 0.00 0.00 0.00 2.08
2181 2184 1.269102 CGTAACCAGCCACCTCTATCG 60.269 57.143 0.00 0.00 0.00 2.92
2182 2185 0.750850 TAACCAGCCACCTCTATCGC 59.249 55.000 0.00 0.00 0.00 4.58
2183 2186 1.972660 AACCAGCCACCTCTATCGCC 61.973 60.000 0.00 0.00 0.00 5.54
2184 2187 2.028190 CAGCCACCTCTATCGCCG 59.972 66.667 0.00 0.00 0.00 6.46
2185 2188 3.917760 AGCCACCTCTATCGCCGC 61.918 66.667 0.00 0.00 0.00 6.53
2187 2190 4.647615 CCACCTCTATCGCCGCGG 62.648 72.222 24.05 24.05 0.00 6.46
2188 2191 4.647615 CACCTCTATCGCCGCGGG 62.648 72.222 29.38 17.41 0.00 6.13
2206 2209 4.821589 CCGCTTCCGCTGAGACCC 62.822 72.222 0.00 0.00 0.00 4.46
2209 2212 4.821589 CTTCCGCTGAGACCCGCC 62.822 72.222 0.00 0.00 0.00 6.13
2230 2233 3.880846 CCGGCTGCGAATTGCCTC 61.881 66.667 3.32 0.00 46.42 4.70
2231 2234 3.880846 CGGCTGCGAATTGCCTCC 61.881 66.667 3.32 0.00 46.42 4.30
2232 2235 3.880846 GGCTGCGAATTGCCTCCG 61.881 66.667 0.00 0.00 45.26 4.63
2239 2242 4.740822 AATTGCCTCCGCCGCCTT 62.741 61.111 0.00 0.00 0.00 4.35
2245 2248 3.838271 CTCCGCCGCCTTGAGCTA 61.838 66.667 0.00 0.00 40.39 3.32
2246 2249 4.143333 TCCGCCGCCTTGAGCTAC 62.143 66.667 0.00 0.00 40.39 3.58
2258 2261 2.818132 AGCTACCGCTGCAGGATC 59.182 61.111 17.12 0.00 46.86 3.36
2259 2262 2.659897 GCTACCGCTGCAGGATCG 60.660 66.667 17.12 10.59 34.73 3.69
2260 2263 2.659897 CTACCGCTGCAGGATCGC 60.660 66.667 17.12 0.00 34.73 4.58
2261 2264 4.221422 TACCGCTGCAGGATCGCC 62.221 66.667 17.12 0.00 34.73 5.54
2269 2272 4.899239 CAGGATCGCCGGTGCTCC 62.899 72.222 26.87 26.87 39.96 4.70
2280 2283 4.373116 GTGCTCCGTCCGCCTTCA 62.373 66.667 0.00 0.00 0.00 3.02
2281 2284 3.621805 TGCTCCGTCCGCCTTCAA 61.622 61.111 0.00 0.00 0.00 2.69
2282 2285 3.119096 GCTCCGTCCGCCTTCAAC 61.119 66.667 0.00 0.00 0.00 3.18
2283 2286 2.434359 CTCCGTCCGCCTTCAACC 60.434 66.667 0.00 0.00 0.00 3.77
2284 2287 2.920912 TCCGTCCGCCTTCAACCT 60.921 61.111 0.00 0.00 0.00 3.50
2285 2288 2.032071 CCGTCCGCCTTCAACCTT 59.968 61.111 0.00 0.00 0.00 3.50
2286 2289 1.186917 TCCGTCCGCCTTCAACCTTA 61.187 55.000 0.00 0.00 0.00 2.69
2287 2290 1.017701 CCGTCCGCCTTCAACCTTAC 61.018 60.000 0.00 0.00 0.00 2.34
2288 2291 0.320073 CGTCCGCCTTCAACCTTACA 60.320 55.000 0.00 0.00 0.00 2.41
2289 2292 1.874739 CGTCCGCCTTCAACCTTACAA 60.875 52.381 0.00 0.00 0.00 2.41
2290 2293 1.804748 GTCCGCCTTCAACCTTACAAG 59.195 52.381 0.00 0.00 0.00 3.16
2291 2294 1.418637 TCCGCCTTCAACCTTACAAGT 59.581 47.619 0.00 0.00 0.00 3.16
2292 2295 1.804748 CCGCCTTCAACCTTACAAGTC 59.195 52.381 0.00 0.00 0.00 3.01
2293 2296 1.459592 CGCCTTCAACCTTACAAGTCG 59.540 52.381 0.00 0.00 0.00 4.18
2294 2297 1.197036 GCCTTCAACCTTACAAGTCGC 59.803 52.381 0.00 0.00 0.00 5.19
2295 2298 1.804748 CCTTCAACCTTACAAGTCGCC 59.195 52.381 0.00 0.00 0.00 5.54
2296 2299 2.489971 CTTCAACCTTACAAGTCGCCA 58.510 47.619 0.00 0.00 0.00 5.69
2297 2300 2.851263 TCAACCTTACAAGTCGCCAT 57.149 45.000 0.00 0.00 0.00 4.40
2298 2301 2.422597 TCAACCTTACAAGTCGCCATG 58.577 47.619 0.00 0.00 0.00 3.66
2299 2302 1.135689 CAACCTTACAAGTCGCCATGC 60.136 52.381 0.00 0.00 0.00 4.06
2300 2303 0.036164 ACCTTACAAGTCGCCATGCA 59.964 50.000 0.00 0.00 0.00 3.96
2301 2304 1.340017 ACCTTACAAGTCGCCATGCAT 60.340 47.619 0.00 0.00 0.00 3.96
2302 2305 1.064505 CCTTACAAGTCGCCATGCATG 59.935 52.381 20.19 20.19 0.00 4.06
2303 2306 2.009051 CTTACAAGTCGCCATGCATGA 58.991 47.619 28.31 5.25 0.00 3.07
2304 2307 1.368641 TACAAGTCGCCATGCATGAC 58.631 50.000 28.31 16.20 0.00 3.06
2305 2308 1.308069 ACAAGTCGCCATGCATGACC 61.308 55.000 28.31 16.45 33.09 4.02
2306 2309 1.028330 CAAGTCGCCATGCATGACCT 61.028 55.000 28.31 13.81 33.09 3.85
2307 2310 1.028330 AAGTCGCCATGCATGACCTG 61.028 55.000 28.31 12.10 33.09 4.00
2315 2318 3.194719 GCATGACCTGCCTTGCTC 58.805 61.111 0.00 0.00 45.66 4.26
2316 2319 2.413142 GCATGACCTGCCTTGCTCC 61.413 63.158 0.00 0.00 45.66 4.70
2317 2320 2.110967 CATGACCTGCCTTGCTCCG 61.111 63.158 0.00 0.00 0.00 4.63
2318 2321 3.984193 ATGACCTGCCTTGCTCCGC 62.984 63.158 0.00 0.00 0.00 5.54
2322 2325 4.711949 CTGCCTTGCTCCGCCACT 62.712 66.667 0.00 0.00 0.00 4.00
2325 2328 4.711949 CCTTGCTCCGCCACTGCT 62.712 66.667 0.00 0.00 34.43 4.24
2326 2329 3.123620 CTTGCTCCGCCACTGCTC 61.124 66.667 0.00 0.00 34.43 4.26
2327 2330 3.602513 CTTGCTCCGCCACTGCTCT 62.603 63.158 0.00 0.00 34.43 4.09
2328 2331 3.889134 TTGCTCCGCCACTGCTCTG 62.889 63.158 0.00 0.00 34.43 3.35
2329 2332 4.074526 GCTCCGCCACTGCTCTGA 62.075 66.667 0.00 0.00 34.43 3.27
2330 2333 2.659016 CTCCGCCACTGCTCTGAA 59.341 61.111 0.00 0.00 34.43 3.02
2331 2334 1.220206 CTCCGCCACTGCTCTGAAT 59.780 57.895 0.00 0.00 34.43 2.57
2332 2335 0.392193 CTCCGCCACTGCTCTGAATT 60.392 55.000 0.00 0.00 34.43 2.17
2333 2336 0.674581 TCCGCCACTGCTCTGAATTG 60.675 55.000 0.00 0.00 34.43 2.32
2334 2337 1.136147 CGCCACTGCTCTGAATTGC 59.864 57.895 0.00 0.00 34.43 3.56
2335 2338 1.509923 GCCACTGCTCTGAATTGCC 59.490 57.895 0.00 0.00 33.53 4.52
2336 2339 0.964358 GCCACTGCTCTGAATTGCCT 60.964 55.000 0.00 0.00 33.53 4.75
2337 2340 0.809385 CCACTGCTCTGAATTGCCTG 59.191 55.000 0.00 0.00 0.00 4.85
2338 2341 0.809385 CACTGCTCTGAATTGCCTGG 59.191 55.000 0.00 0.00 0.00 4.45
2339 2342 0.694771 ACTGCTCTGAATTGCCTGGA 59.305 50.000 0.00 0.00 0.00 3.86
2340 2343 1.339824 ACTGCTCTGAATTGCCTGGAG 60.340 52.381 0.00 0.00 0.00 3.86
2341 2344 0.679002 TGCTCTGAATTGCCTGGAGC 60.679 55.000 0.00 0.00 46.41 4.70
2342 2345 1.382692 GCTCTGAATTGCCTGGAGCC 61.383 60.000 0.00 0.00 42.20 4.70
2343 2346 1.078214 TCTGAATTGCCTGGAGCCG 60.078 57.895 0.00 0.00 42.71 5.52
2344 2347 2.751436 TGAATTGCCTGGAGCCGC 60.751 61.111 0.00 0.00 42.71 6.53
2345 2348 3.521796 GAATTGCCTGGAGCCGCC 61.522 66.667 0.00 0.00 42.71 6.13
2362 2365 3.809013 CCCTGCCGGGTTATGCCT 61.809 66.667 4.74 0.00 46.12 4.75
2363 2366 2.516930 CCTGCCGGGTTATGCCTG 60.517 66.667 2.18 0.00 43.41 4.85
2374 2377 0.913934 TTATGCCTGGACTCTGCCCA 60.914 55.000 0.00 0.00 0.00 5.36
2440 2443 1.372087 CCTTCATCGCTGCCTTGACC 61.372 60.000 0.00 0.00 0.00 4.02
2457 2460 3.805928 CCAGTACTGGTGCTCCCA 58.194 61.111 30.57 0.00 45.53 4.37
2474 2477 4.329545 AGCGTGCCGGTTCACCAT 62.330 61.111 1.90 0.00 32.22 3.55
2569 2573 1.402968 CGGTCTTAAGCCGCTAGTGTA 59.597 52.381 20.22 0.00 42.82 2.90
2589 2841 3.147553 AGCCTGAAGAAAGGAAAGGTC 57.852 47.619 0.00 0.00 40.02 3.85
2663 2915 5.851693 AGGGATGGATGTGGATTAAGTCATA 59.148 40.000 0.00 0.00 0.00 2.15
2674 2926 7.748847 GTGGATTAAGTCATAATTCACGTTGT 58.251 34.615 3.99 0.00 45.85 3.32
2752 3004 4.758674 CCGATGCATCAGGTGATATCTTTT 59.241 41.667 25.70 0.00 32.63 2.27
2755 3007 6.347483 CGATGCATCAGGTGATATCTTTTCTG 60.347 42.308 25.70 6.57 32.63 3.02
2759 3011 7.443272 TGCATCAGGTGATATCTTTTCTGTATG 59.557 37.037 3.98 11.18 32.63 2.39
2803 3055 5.107453 CGTCTGAGAACAATTACTTGGACAC 60.107 44.000 0.00 0.00 36.64 3.67
2874 3126 1.521681 GGGTATGGAGCACGCACTC 60.522 63.158 0.00 0.00 35.86 3.51
2875 3127 1.878522 GGTATGGAGCACGCACTCG 60.879 63.158 0.00 0.00 37.57 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.729881 TGGGGGCAGTCCTAAATACTTATT 59.270 41.667 0.00 0.00 35.33 1.40
178 179 4.162812 GTTTTGCGAGTTTGAACACAAGA 58.837 39.130 0.00 0.00 0.00 3.02
194 195 1.055338 GCGTTGCAGATCTGTTTTGC 58.945 50.000 23.38 17.82 38.30 3.68
229 230 2.348472 TCTCCCCACCAAAACTGAGAT 58.652 47.619 0.00 0.00 0.00 2.75
383 384 0.829333 AGTGATTCTGGCTCTGCGAT 59.171 50.000 0.00 0.00 0.00 4.58
404 405 1.135660 TGCTCTCTAAACTCTCGCACG 60.136 52.381 0.00 0.00 0.00 5.34
417 418 9.118300 CACCATCTAGAAAATATTTTGCTCTCT 57.882 33.333 17.98 10.71 0.00 3.10
435 436 7.217200 GGTGCAATTAAGTAGATCACCATCTA 58.783 38.462 0.00 0.00 40.18 1.98
610 611 6.070424 TGAGAACAATATTACCTCTTCGGGTT 60.070 38.462 10.38 0.00 40.48 4.11
838 841 5.849510 TCTTTGTCTCAACTTTCGTCCATA 58.150 37.500 0.00 0.00 0.00 2.74
890 893 3.569194 TCCAAAGAGTGTGCCAAACTA 57.431 42.857 0.00 0.00 0.00 2.24
899 902 5.241728 GGTATTTGAAGCTTCCAAAGAGTGT 59.758 40.000 23.42 10.51 37.00 3.55
978 981 0.535335 GTCGATTGGCCAGTACTCCA 59.465 55.000 5.11 0.00 0.00 3.86
1031 1034 4.371786 GCGAATACTCTCACAATCCATGA 58.628 43.478 0.00 0.00 0.00 3.07
1127 1130 1.344763 CCTCCAACTCAGTTTCGGACT 59.655 52.381 0.00 0.00 39.89 3.85
1162 1165 1.202867 TGGCATTAGCAACAGGTCACA 60.203 47.619 0.00 0.00 44.61 3.58
1260 1263 0.530650 CATGGGTGAATCTCCGTCGG 60.531 60.000 4.39 4.39 0.00 4.79
1298 1301 2.669878 GCTTGGGCCAATCTTCCAA 58.330 52.632 21.25 0.00 38.13 3.53
1428 1431 3.314635 CACTATCAGCATCAAAAGAGGCC 59.685 47.826 0.00 0.00 31.50 5.19
1470 1473 1.762957 CCTGTGGAGTCCCGTATGATT 59.237 52.381 6.74 0.00 34.29 2.57
1560 1563 0.620556 GAACCAGCCCATCCTTGAGA 59.379 55.000 0.00 0.00 0.00 3.27
1594 1597 0.403271 ATCTCCACCTTGTTGCAGCT 59.597 50.000 1.17 0.00 0.00 4.24
1723 1726 2.162408 GGCAATGACTGGAACTAACAGC 59.838 50.000 0.00 0.00 39.55 4.40
1733 1736 0.918983 TTCCCTAGGGCAATGACTGG 59.081 55.000 24.42 0.00 34.68 4.00
1806 1809 3.414700 GCCTCGTTCTGCCACACG 61.415 66.667 0.00 0.00 37.77 4.49
1872 1875 6.072008 CCATCATGGCGGTTTATATTTCATGA 60.072 38.462 0.00 0.00 42.05 3.07
1917 1920 6.472887 TCAATATTCAGGTCGTTTTTCCTCT 58.527 36.000 0.00 0.00 30.91 3.69
1918 1921 6.737254 TCAATATTCAGGTCGTTTTTCCTC 57.263 37.500 0.00 0.00 30.91 3.71
1919 1922 7.362920 CCAATCAATATTCAGGTCGTTTTTCCT 60.363 37.037 0.00 0.00 33.96 3.36
1920 1923 6.751888 CCAATCAATATTCAGGTCGTTTTTCC 59.248 38.462 0.00 0.00 0.00 3.13
1921 1924 7.312899 ACCAATCAATATTCAGGTCGTTTTTC 58.687 34.615 0.00 0.00 0.00 2.29
1922 1925 7.040062 TGACCAATCAATATTCAGGTCGTTTTT 60.040 33.333 15.09 0.00 46.45 1.94
1923 1926 6.432783 TGACCAATCAATATTCAGGTCGTTTT 59.567 34.615 15.09 0.00 46.45 2.43
1924 1927 5.943416 TGACCAATCAATATTCAGGTCGTTT 59.057 36.000 15.09 0.00 46.45 3.60
1925 1928 5.496556 TGACCAATCAATATTCAGGTCGTT 58.503 37.500 15.09 0.00 46.45 3.85
1926 1929 5.097742 TGACCAATCAATATTCAGGTCGT 57.902 39.130 15.09 0.00 46.45 4.34
1927 1930 6.435430 TTTGACCAATCAATATTCAGGTCG 57.565 37.500 15.09 0.00 46.45 4.79
1928 1931 7.068593 TGGATTTGACCAATCAATATTCAGGTC 59.931 37.037 14.00 14.00 44.36 3.85
1929 1932 6.896860 TGGATTTGACCAATCAATATTCAGGT 59.103 34.615 2.04 0.00 44.36 4.00
1930 1933 7.205297 GTGGATTTGACCAATCAATATTCAGG 58.795 38.462 2.04 0.00 44.36 3.86
1931 1934 7.147863 TGGTGGATTTGACCAATCAATATTCAG 60.148 37.037 2.04 0.00 44.36 3.02
1932 1935 6.666980 TGGTGGATTTGACCAATCAATATTCA 59.333 34.615 2.04 0.00 44.36 2.57
1933 1936 6.980397 GTGGTGGATTTGACCAATCAATATTC 59.020 38.462 0.00 0.00 45.17 1.75
1934 1937 6.405731 CGTGGTGGATTTGACCAATCAATATT 60.406 38.462 0.00 0.00 45.17 1.28
1935 1938 5.067674 CGTGGTGGATTTGACCAATCAATAT 59.932 40.000 0.00 0.00 45.17 1.28
1936 1939 4.397730 CGTGGTGGATTTGACCAATCAATA 59.602 41.667 0.00 0.00 45.17 1.90
1937 1940 3.193267 CGTGGTGGATTTGACCAATCAAT 59.807 43.478 0.00 0.00 45.17 2.57
1938 1941 2.556189 CGTGGTGGATTTGACCAATCAA 59.444 45.455 0.00 0.00 45.17 2.57
1939 1942 2.158559 CGTGGTGGATTTGACCAATCA 58.841 47.619 0.00 0.00 45.17 2.57
1940 1943 2.161609 GTCGTGGTGGATTTGACCAATC 59.838 50.000 0.00 0.00 45.17 2.67
1941 1944 2.159382 GTCGTGGTGGATTTGACCAAT 58.841 47.619 0.00 0.00 45.17 3.16
1942 1945 1.600023 GTCGTGGTGGATTTGACCAA 58.400 50.000 0.00 0.00 45.17 3.67
1943 1946 0.250553 GGTCGTGGTGGATTTGACCA 60.251 55.000 4.90 0.00 46.55 4.02
1944 1947 0.958876 GGGTCGTGGTGGATTTGACC 60.959 60.000 1.12 1.12 46.58 4.02
1945 1948 1.296056 CGGGTCGTGGTGGATTTGAC 61.296 60.000 0.00 0.00 0.00 3.18
1946 1949 1.004320 CGGGTCGTGGTGGATTTGA 60.004 57.895 0.00 0.00 0.00 2.69
1947 1950 2.038269 CCGGGTCGTGGTGGATTTG 61.038 63.158 0.00 0.00 0.00 2.32
1948 1951 2.180159 CTCCGGGTCGTGGTGGATTT 62.180 60.000 0.00 0.00 0.00 2.17
1949 1952 2.605295 TCCGGGTCGTGGTGGATT 60.605 61.111 0.00 0.00 0.00 3.01
1950 1953 2.873557 ATCTCCGGGTCGTGGTGGAT 62.874 60.000 0.00 0.00 0.00 3.41
1951 1954 3.595428 ATCTCCGGGTCGTGGTGGA 62.595 63.158 0.00 0.00 0.00 4.02
1952 1955 3.075005 ATCTCCGGGTCGTGGTGG 61.075 66.667 0.00 0.00 0.00 4.61
1953 1956 1.317431 TACATCTCCGGGTCGTGGTG 61.317 60.000 0.00 0.00 0.00 4.17
1954 1957 0.396695 ATACATCTCCGGGTCGTGGT 60.397 55.000 0.00 0.00 0.00 4.16
1955 1958 0.032130 CATACATCTCCGGGTCGTGG 59.968 60.000 0.00 0.00 0.00 4.94
1956 1959 0.597637 GCATACATCTCCGGGTCGTG 60.598 60.000 0.00 0.00 0.00 4.35
1957 1960 1.040893 TGCATACATCTCCGGGTCGT 61.041 55.000 0.00 0.00 0.00 4.34
1958 1961 0.319040 CTGCATACATCTCCGGGTCG 60.319 60.000 0.00 0.00 0.00 4.79
1959 1962 0.753262 ACTGCATACATCTCCGGGTC 59.247 55.000 0.00 0.00 0.00 4.46
1960 1963 0.753262 GACTGCATACATCTCCGGGT 59.247 55.000 0.00 0.00 0.00 5.28
1961 1964 0.319040 CGACTGCATACATCTCCGGG 60.319 60.000 0.00 0.00 0.00 5.73
1962 1965 0.385751 ACGACTGCATACATCTCCGG 59.614 55.000 0.00 0.00 0.00 5.14
1963 1966 1.759994 GACGACTGCATACATCTCCG 58.240 55.000 0.00 0.00 0.00 4.63
1964 1967 1.759994 CGACGACTGCATACATCTCC 58.240 55.000 0.00 0.00 0.00 3.71
1965 1968 1.124462 GCGACGACTGCATACATCTC 58.876 55.000 0.00 0.00 0.00 2.75
1966 1969 0.455815 TGCGACGACTGCATACATCT 59.544 50.000 0.00 0.00 37.44 2.90
1967 1970 2.957871 TGCGACGACTGCATACATC 58.042 52.632 0.00 0.00 37.44 3.06
1974 1977 0.917259 CAGTTCTATGCGACGACTGC 59.083 55.000 0.00 0.00 32.36 4.40
1975 1978 1.550065 CCAGTTCTATGCGACGACTG 58.450 55.000 0.00 1.79 37.92 3.51
1976 1979 0.456221 CCCAGTTCTATGCGACGACT 59.544 55.000 0.00 0.00 0.00 4.18
1977 1980 0.527817 CCCCAGTTCTATGCGACGAC 60.528 60.000 0.00 0.00 0.00 4.34
1978 1981 1.813859 CCCCAGTTCTATGCGACGA 59.186 57.895 0.00 0.00 0.00 4.20
1979 1982 1.883084 GCCCCAGTTCTATGCGACG 60.883 63.158 0.00 0.00 0.00 5.12
1980 1983 4.126524 GCCCCAGTTCTATGCGAC 57.873 61.111 0.00 0.00 0.00 5.19
1983 1986 1.510480 GATGCGCCCCAGTTCTATGC 61.510 60.000 4.18 0.00 0.00 3.14
1984 1987 0.107456 AGATGCGCCCCAGTTCTATG 59.893 55.000 4.18 0.00 0.00 2.23
1985 1988 0.107456 CAGATGCGCCCCAGTTCTAT 59.893 55.000 4.18 0.00 0.00 1.98
1986 1989 1.522092 CAGATGCGCCCCAGTTCTA 59.478 57.895 4.18 0.00 0.00 2.10
1987 1990 2.270205 CAGATGCGCCCCAGTTCT 59.730 61.111 4.18 0.00 0.00 3.01
1988 1991 3.512516 GCAGATGCGCCCCAGTTC 61.513 66.667 4.18 0.00 0.00 3.01
1996 1999 2.817423 GCTACTGTGGCAGATGCGC 61.817 63.158 11.52 0.00 43.26 6.09
1997 2000 1.448365 TGCTACTGTGGCAGATGCG 60.448 57.895 15.17 0.00 43.26 4.73
1998 2001 1.699656 CGTGCTACTGTGGCAGATGC 61.700 60.000 19.51 6.74 40.54 3.91
1999 2002 1.699656 GCGTGCTACTGTGGCAGATG 61.700 60.000 19.51 12.88 40.54 2.90
2000 2003 1.448540 GCGTGCTACTGTGGCAGAT 60.449 57.895 19.51 0.00 40.54 2.90
2001 2004 2.048222 GCGTGCTACTGTGGCAGA 60.048 61.111 19.51 0.00 40.54 4.26
2002 2005 3.121030 GGCGTGCTACTGTGGCAG 61.121 66.667 19.51 13.77 40.54 4.85
2003 2006 3.625897 AGGCGTGCTACTGTGGCA 61.626 61.111 15.17 15.17 37.36 4.92
2004 2007 3.121030 CAGGCGTGCTACTGTGGC 61.121 66.667 9.40 9.40 0.00 5.01
2005 2008 2.434884 CCAGGCGTGCTACTGTGG 60.435 66.667 0.00 0.00 32.90 4.17
2006 2009 1.738099 GACCAGGCGTGCTACTGTG 60.738 63.158 0.00 0.00 32.90 3.66
2007 2010 2.657237 GACCAGGCGTGCTACTGT 59.343 61.111 0.00 0.00 32.90 3.55
2008 2011 2.507102 CGACCAGGCGTGCTACTG 60.507 66.667 0.00 0.00 34.54 2.74
2009 2012 3.760035 CCGACCAGGCGTGCTACT 61.760 66.667 0.00 0.00 0.00 2.57
2019 2022 4.803426 GTCGCAGAGGCCGACCAG 62.803 72.222 0.00 0.00 36.95 4.00
2021 2024 4.803426 CTGTCGCAGAGGCCGACC 62.803 72.222 10.84 0.00 40.43 4.79
2022 2025 4.803426 CCTGTCGCAGAGGCCGAC 62.803 72.222 0.00 6.96 41.05 4.79
2027 2030 0.179124 GAAGTAGCCTGTCGCAGAGG 60.179 60.000 8.20 1.72 41.38 3.69
2028 2031 0.528017 TGAAGTAGCCTGTCGCAGAG 59.472 55.000 8.20 1.16 41.38 3.35
2029 2032 0.243907 GTGAAGTAGCCTGTCGCAGA 59.756 55.000 8.20 0.00 41.38 4.26
2030 2033 0.244994 AGTGAAGTAGCCTGTCGCAG 59.755 55.000 0.52 0.52 41.38 5.18
2031 2034 0.679505 AAGTGAAGTAGCCTGTCGCA 59.320 50.000 0.00 0.00 41.38 5.10
2032 2035 1.351153 GAAGTGAAGTAGCCTGTCGC 58.649 55.000 0.00 0.00 37.98 5.19
2033 2036 1.618861 CGAAGTGAAGTAGCCTGTCG 58.381 55.000 0.00 0.00 0.00 4.35
2034 2037 1.351153 GCGAAGTGAAGTAGCCTGTC 58.649 55.000 0.00 0.00 0.00 3.51
2035 2038 0.037232 GGCGAAGTGAAGTAGCCTGT 60.037 55.000 0.00 0.00 44.06 4.00
2036 2039 1.078759 CGGCGAAGTGAAGTAGCCTG 61.079 60.000 0.00 0.00 45.16 4.85
2037 2040 1.215647 CGGCGAAGTGAAGTAGCCT 59.784 57.895 0.00 0.00 45.16 4.58
2038 2041 2.453638 GCGGCGAAGTGAAGTAGCC 61.454 63.158 12.98 0.00 44.00 3.93
2039 2042 2.453638 GGCGGCGAAGTGAAGTAGC 61.454 63.158 12.98 0.00 0.00 3.58
2040 2043 0.802607 GAGGCGGCGAAGTGAAGTAG 60.803 60.000 12.98 0.00 0.00 2.57
2041 2044 1.214589 GAGGCGGCGAAGTGAAGTA 59.785 57.895 12.98 0.00 0.00 2.24
2042 2045 2.048127 GAGGCGGCGAAGTGAAGT 60.048 61.111 12.98 0.00 0.00 3.01
2043 2046 2.815647 GGAGGCGGCGAAGTGAAG 60.816 66.667 12.98 0.00 0.00 3.02
2044 2047 4.735132 CGGAGGCGGCGAAGTGAA 62.735 66.667 12.98 0.00 0.00 3.18
2053 2056 3.997064 CTGAGAAGCACGGAGGCGG 62.997 68.421 0.00 0.00 39.27 6.13
2054 2057 2.507992 CTGAGAAGCACGGAGGCG 60.508 66.667 0.00 0.00 39.27 5.52
2055 2058 2.125350 CCTGAGAAGCACGGAGGC 60.125 66.667 0.00 0.00 0.00 4.70
2056 2059 2.125350 GCCTGAGAAGCACGGAGG 60.125 66.667 0.00 0.00 0.00 4.30
2057 2060 1.447489 CAGCCTGAGAAGCACGGAG 60.447 63.158 0.00 0.00 0.00 4.63
2058 2061 2.659016 CAGCCTGAGAAGCACGGA 59.341 61.111 0.00 0.00 0.00 4.69
2059 2062 3.123620 GCAGCCTGAGAAGCACGG 61.124 66.667 0.00 0.00 0.00 4.94
2060 2063 3.123620 GGCAGCCTGAGAAGCACG 61.124 66.667 3.29 0.00 0.00 5.34
2061 2064 1.744741 GAGGCAGCCTGAGAAGCAC 60.745 63.158 22.26 0.00 31.76 4.40
2062 2065 2.667418 GAGGCAGCCTGAGAAGCA 59.333 61.111 22.26 0.00 31.76 3.91
2063 2066 2.511145 CGAGGCAGCCTGAGAAGC 60.511 66.667 22.26 1.30 31.76 3.86
2064 2067 2.511145 GCGAGGCAGCCTGAGAAG 60.511 66.667 22.26 5.89 31.76 2.85
2065 2068 4.441695 CGCGAGGCAGCCTGAGAA 62.442 66.667 22.26 0.00 31.76 2.87
2067 2070 3.764810 CTACGCGAGGCAGCCTGAG 62.765 68.421 22.26 14.18 31.76 3.35
2068 2071 3.826754 CTACGCGAGGCAGCCTGA 61.827 66.667 22.26 0.00 31.76 3.86
2104 2107 3.005539 GGAGCCTGGTCTGGAGCA 61.006 66.667 2.52 2.52 37.27 4.26
2105 2108 4.154347 CGGAGCCTGGTCTGGAGC 62.154 72.222 0.00 0.00 0.00 4.70
2148 2151 4.807039 TTACGGGCGCTCGGAAGC 62.807 66.667 35.52 0.90 45.56 3.86
2149 2152 2.884207 GTTACGGGCGCTCGGAAG 60.884 66.667 35.52 6.47 33.20 3.46
2150 2153 4.440127 GGTTACGGGCGCTCGGAA 62.440 66.667 35.52 31.33 0.00 4.30
2159 2162 0.974010 TAGAGGTGGCTGGTTACGGG 60.974 60.000 0.00 0.00 0.00 5.28
2160 2163 1.068741 GATAGAGGTGGCTGGTTACGG 59.931 57.143 0.00 0.00 0.00 4.02
2161 2164 1.269102 CGATAGAGGTGGCTGGTTACG 60.269 57.143 0.00 0.00 39.76 3.18
2162 2165 1.538419 GCGATAGAGGTGGCTGGTTAC 60.538 57.143 0.00 0.00 39.76 2.50
2163 2166 0.750850 GCGATAGAGGTGGCTGGTTA 59.249 55.000 0.00 0.00 39.76 2.85
2164 2167 1.522569 GCGATAGAGGTGGCTGGTT 59.477 57.895 0.00 0.00 39.76 3.67
2165 2168 2.435693 GGCGATAGAGGTGGCTGGT 61.436 63.158 0.00 0.00 39.76 4.00
2166 2169 2.423446 GGCGATAGAGGTGGCTGG 59.577 66.667 0.00 0.00 39.76 4.85
2167 2170 2.028190 CGGCGATAGAGGTGGCTG 59.972 66.667 0.00 0.00 39.76 4.85
2168 2171 3.917760 GCGGCGATAGAGGTGGCT 61.918 66.667 12.98 0.00 39.76 4.75
2170 2173 4.647615 CCGCGGCGATAGAGGTGG 62.648 72.222 25.92 0.00 39.76 4.61
2171 2174 4.647615 CCCGCGGCGATAGAGGTG 62.648 72.222 25.92 3.82 39.76 4.00
2192 2195 4.821589 GGCGGGTCTCAGCGGAAG 62.822 72.222 0.00 0.00 0.00 3.46
2242 2245 2.659897 CGATCCTGCAGCGGTAGC 60.660 66.667 8.66 0.00 45.58 3.58
2243 2246 2.659897 GCGATCCTGCAGCGGTAG 60.660 66.667 8.66 0.00 34.15 3.18
2244 2247 4.221422 GGCGATCCTGCAGCGGTA 62.221 66.667 8.66 0.00 36.28 4.02
2263 2266 3.876589 TTGAAGGCGGACGGAGCAC 62.877 63.158 0.00 0.00 36.08 4.40
2264 2267 3.621805 TTGAAGGCGGACGGAGCA 61.622 61.111 0.00 0.00 36.08 4.26
2265 2268 3.119096 GTTGAAGGCGGACGGAGC 61.119 66.667 0.00 0.00 0.00 4.70
2266 2269 2.434359 GGTTGAAGGCGGACGGAG 60.434 66.667 0.00 0.00 0.00 4.63
2267 2270 1.186917 TAAGGTTGAAGGCGGACGGA 61.187 55.000 0.00 0.00 0.00 4.69
2268 2271 1.017701 GTAAGGTTGAAGGCGGACGG 61.018 60.000 0.00 0.00 0.00 4.79
2269 2272 0.320073 TGTAAGGTTGAAGGCGGACG 60.320 55.000 0.00 0.00 0.00 4.79
2270 2273 1.804748 CTTGTAAGGTTGAAGGCGGAC 59.195 52.381 0.00 0.00 0.00 4.79
2271 2274 1.418637 ACTTGTAAGGTTGAAGGCGGA 59.581 47.619 0.00 0.00 0.00 5.54
2272 2275 1.804748 GACTTGTAAGGTTGAAGGCGG 59.195 52.381 0.00 0.00 0.00 6.13
2273 2276 1.459592 CGACTTGTAAGGTTGAAGGCG 59.540 52.381 0.00 0.00 41.51 5.52
2274 2277 1.197036 GCGACTTGTAAGGTTGAAGGC 59.803 52.381 0.00 0.00 0.00 4.35
2275 2278 1.804748 GGCGACTTGTAAGGTTGAAGG 59.195 52.381 0.00 0.00 0.00 3.46
2276 2279 2.489971 TGGCGACTTGTAAGGTTGAAG 58.510 47.619 0.00 0.00 0.00 3.02
2277 2280 2.623878 TGGCGACTTGTAAGGTTGAA 57.376 45.000 0.00 0.00 0.00 2.69
2278 2281 2.422597 CATGGCGACTTGTAAGGTTGA 58.577 47.619 0.00 0.00 0.00 3.18
2279 2282 1.135689 GCATGGCGACTTGTAAGGTTG 60.136 52.381 5.98 0.00 37.77 3.77
2280 2283 1.165270 GCATGGCGACTTGTAAGGTT 58.835 50.000 5.98 0.00 37.77 3.50
2281 2284 0.036164 TGCATGGCGACTTGTAAGGT 59.964 50.000 5.98 0.00 37.77 3.50
2282 2285 1.064505 CATGCATGGCGACTTGTAAGG 59.935 52.381 19.40 0.00 37.77 2.69
2283 2286 2.009051 TCATGCATGGCGACTTGTAAG 58.991 47.619 25.97 0.00 37.77 2.34
2284 2287 1.737236 GTCATGCATGGCGACTTGTAA 59.263 47.619 25.97 0.00 37.77 2.41
2285 2288 1.368641 GTCATGCATGGCGACTTGTA 58.631 50.000 25.97 1.11 37.77 2.41
2286 2289 1.308069 GGTCATGCATGGCGACTTGT 61.308 55.000 25.97 0.00 37.77 3.16
2287 2290 1.028330 AGGTCATGCATGGCGACTTG 61.028 55.000 25.97 0.00 38.46 3.16
2288 2291 1.028330 CAGGTCATGCATGGCGACTT 61.028 55.000 25.97 11.03 31.93 3.01
2289 2292 1.450848 CAGGTCATGCATGGCGACT 60.451 57.895 25.97 14.98 31.93 4.18
2290 2293 3.104766 CAGGTCATGCATGGCGAC 58.895 61.111 25.97 16.55 31.93 5.19
2299 2302 2.110967 CGGAGCAAGGCAGGTCATG 61.111 63.158 10.54 0.00 37.74 3.07
2300 2303 2.270205 CGGAGCAAGGCAGGTCAT 59.730 61.111 10.54 0.00 37.74 3.06
2317 2320 0.964358 AGGCAATTCAGAGCAGTGGC 60.964 55.000 0.00 0.00 41.61 5.01
2318 2321 0.809385 CAGGCAATTCAGAGCAGTGG 59.191 55.000 0.00 0.00 0.00 4.00
2319 2322 0.809385 CCAGGCAATTCAGAGCAGTG 59.191 55.000 0.00 0.00 0.00 3.66
2320 2323 0.694771 TCCAGGCAATTCAGAGCAGT 59.305 50.000 0.00 0.00 0.00 4.40
2321 2324 1.380524 CTCCAGGCAATTCAGAGCAG 58.619 55.000 0.00 0.00 0.00 4.24
2322 2325 3.564262 CTCCAGGCAATTCAGAGCA 57.436 52.632 0.00 0.00 0.00 4.26
2323 2326 2.105124 GCTCCAGGCAATTCAGAGC 58.895 57.895 0.00 0.00 42.74 4.09
2324 2327 1.094073 CGGCTCCAGGCAATTCAGAG 61.094 60.000 0.57 0.00 44.01 3.35
2325 2328 1.078214 CGGCTCCAGGCAATTCAGA 60.078 57.895 0.57 0.00 44.01 3.27
2326 2329 2.768492 GCGGCTCCAGGCAATTCAG 61.768 63.158 0.57 0.00 44.01 3.02
2327 2330 2.751436 GCGGCTCCAGGCAATTCA 60.751 61.111 0.57 0.00 44.01 2.57
2328 2331 3.521796 GGCGGCTCCAGGCAATTC 61.522 66.667 0.00 0.00 44.01 2.17
2346 2349 2.516930 CAGGCATAACCCGGCAGG 60.517 66.667 0.00 0.00 40.58 4.85
2347 2350 2.516930 CCAGGCATAACCCGGCAG 60.517 66.667 0.00 0.00 40.58 4.85
2348 2351 3.012119 TCCAGGCATAACCCGGCA 61.012 61.111 0.00 0.00 40.58 5.69
2349 2352 2.516225 GTCCAGGCATAACCCGGC 60.516 66.667 0.00 0.00 40.58 6.13
2350 2353 1.146263 GAGTCCAGGCATAACCCGG 59.854 63.158 0.00 0.00 40.58 5.73
2351 2354 0.179073 CAGAGTCCAGGCATAACCCG 60.179 60.000 0.00 0.00 40.58 5.28
2352 2355 0.464554 GCAGAGTCCAGGCATAACCC 60.465 60.000 0.00 0.00 40.58 4.11
2353 2356 0.464554 GGCAGAGTCCAGGCATAACC 60.465 60.000 2.34 0.00 39.61 2.85
2354 2357 0.464554 GGGCAGAGTCCAGGCATAAC 60.465 60.000 8.66 0.00 0.00 1.89
2355 2358 0.913934 TGGGCAGAGTCCAGGCATAA 60.914 55.000 8.66 0.00 29.54 1.90
2356 2359 1.306911 TGGGCAGAGTCCAGGCATA 60.307 57.895 8.66 0.00 29.54 3.14
2357 2360 2.611800 TGGGCAGAGTCCAGGCAT 60.612 61.111 8.66 0.00 29.54 4.40
2358 2361 3.640407 GTGGGCAGAGTCCAGGCA 61.640 66.667 8.66 0.00 38.31 4.75
2359 2362 3.196207 TTGTGGGCAGAGTCCAGGC 62.196 63.158 0.00 0.00 38.31 4.85
2360 2363 1.002868 CTTGTGGGCAGAGTCCAGG 60.003 63.158 0.00 0.00 38.31 4.45
2361 2364 1.673665 GCTTGTGGGCAGAGTCCAG 60.674 63.158 0.00 0.00 38.31 3.86
2362 2365 2.431683 GCTTGTGGGCAGAGTCCA 59.568 61.111 0.00 0.00 33.55 4.02
2363 2366 2.743928 CGCTTGTGGGCAGAGTCC 60.744 66.667 0.00 0.00 0.00 3.85
2374 2377 3.411517 AGCTATGGGGGCGCTTGT 61.412 61.111 7.64 0.00 34.52 3.16
2461 2464 2.203408 TGCAATGGTGAACCGGCA 60.203 55.556 0.00 8.63 39.43 5.69
2563 2567 5.280011 CCTTTCCTTTCTTCAGGCTACACTA 60.280 44.000 0.00 0.00 33.35 2.74
2569 2573 2.551071 CGACCTTTCCTTTCTTCAGGCT 60.551 50.000 0.00 0.00 33.35 4.58
2589 2841 0.179073 AATCGTCCAATCAGCTCCCG 60.179 55.000 0.00 0.00 0.00 5.14
2663 2915 1.754226 AGCCCAACAACAACGTGAATT 59.246 42.857 0.00 0.00 0.00 2.17
2755 3007 9.716507 ACGAATTAACATGCTGATAAAACATAC 57.283 29.630 0.00 0.00 0.00 2.39
2759 3011 8.175069 TCAGACGAATTAACATGCTGATAAAAC 58.825 33.333 0.00 0.00 0.00 2.43
2803 3055 8.181573 ACAATTGTCCTGCTAAACAATATTACG 58.818 33.333 4.92 0.00 43.45 3.18


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

AutoCloner maintained by Alex Coulton.