Multiple sequence alignment - TraesCS1A01G404900

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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 TraesCS1A01G404900 chr1A 100.000 2270 0 0 1 2270 568265066 568267335 0.000000e+00 4193.0
1 TraesCS1A01G404900 chr1A 87.013 616 54 13 833 1433 568327856 568328460 0.000000e+00 671.0
2 TraesCS1A01G404900 chr1A 82.013 606 63 30 95 676 568327020 568327603 7.340000e-130 473.0
3 TraesCS1A01G404900 chr1A 92.520 254 17 1 2019 2270 568334078 568334331 1.660000e-96 363.0
4 TraesCS1A01G404900 chr1A 83.896 385 45 6 1891 2266 568399455 568399831 3.590000e-93 351.0
5 TraesCS1A01G404900 chr1A 93.182 220 15 0 615 834 568327609 568327828 7.820000e-85 324.0
6 TraesCS1A01G404900 chr1A 81.931 404 45 7 1889 2270 568377871 568378268 1.310000e-82 316.0
7 TraesCS1A01G404900 chr1A 89.773 176 10 3 1405 1576 568383827 568383998 3.800000e-53 219.0
8 TraesCS1A01G404900 chr1A 97.619 42 1 0 1804 1845 568122629 568122670 3.130000e-09 73.1
9 TraesCS1A01G404900 chr1D 90.108 1567 59 26 76 1590 473960280 473961802 0.000000e+00 1947.0
10 TraesCS1A01G404900 chr1D 87.068 665 46 15 937 1576 473879765 473880414 0.000000e+00 715.0
11 TraesCS1A01G404900 chr1D 91.919 396 20 3 1804 2190 473961799 473962191 5.510000e-151 544.0
12 TraesCS1A01G404900 chr1D 87.805 246 17 8 1889 2134 473997879 473998111 2.220000e-70 276.0
13 TraesCS1A01G404900 chr1D 89.655 174 12 3 1405 1576 473966396 473966565 1.370000e-52 217.0
14 TraesCS1A01G404900 chr1D 87.978 183 14 4 1395 1576 473987712 473987887 2.280000e-50 209.0
15 TraesCS1A01G404900 chr1D 95.238 42 2 0 1804 1845 473872699 473872740 1.460000e-07 67.6
16 TraesCS1A01G404900 chr1D 100.000 28 0 0 139 166 473871440 473871467 4.000000e-03 52.8
17 TraesCS1A01G404900 chr1B 87.597 1540 116 31 83 1590 659285141 659286637 0.000000e+00 1716.0
18 TraesCS1A01G404900 chr1B 88.842 1192 77 24 439 1590 659033231 659034406 0.000000e+00 1413.0
19 TraesCS1A01G404900 chr1B 83.667 1500 139 46 83 1520 659181600 659183055 0.000000e+00 1315.0
20 TraesCS1A01G404900 chr1B 94.024 753 33 2 838 1590 659294564 659295304 0.000000e+00 1131.0
21 TraesCS1A01G404900 chr1B 92.129 775 37 9 838 1590 659002557 659003329 0.000000e+00 1072.0
22 TraesCS1A01G404900 chr1B 93.517 617 25 3 977 1590 659073582 659074186 0.000000e+00 904.0
23 TraesCS1A01G404900 chr1B 91.554 592 35 10 838 1429 658969034 658969610 0.000000e+00 802.0
24 TraesCS1A01G404900 chr1B 93.525 417 20 2 1861 2270 659295349 659295765 4.140000e-172 614.0
25 TraesCS1A01G404900 chr1B 93.462 413 24 2 1861 2270 659034451 659034863 5.360000e-171 610.0
26 TraesCS1A01G404900 chr1B 85.786 598 50 14 260 834 658968414 658968999 3.230000e-168 601.0
27 TraesCS1A01G404900 chr1B 93.012 415 23 3 1861 2270 659074231 659074644 3.230000e-168 601.0
28 TraesCS1A01G404900 chr1B 92.927 410 29 0 1861 2270 658969791 658970200 4.170000e-167 597.0
29 TraesCS1A01G404900 chr1B 92.927 410 29 0 1861 2270 659003374 659003783 4.170000e-167 597.0
30 TraesCS1A01G404900 chr1B 93.956 364 18 3 1861 2221 659286682 659287044 4.260000e-152 547.0
31 TraesCS1A01G404900 chr1B 79.515 742 68 39 141 834 659072736 659073441 3.440000e-123 451.0
32 TraesCS1A01G404900 chr1B 79.180 610 63 34 83 655 659293811 659294393 4.610000e-97 364.0
33 TraesCS1A01G404900 chr1B 94.776 134 6 1 701 834 659294395 659294527 8.220000e-50 207.0
34 TraesCS1A01G404900 chr1B 89.474 95 10 0 838 932 659073472 659073566 1.100000e-23 121.0
35 TraesCS1A01G404900 chr6B 99.123 228 2 0 1578 1805 438408589 438408362 5.840000e-111 411.0
36 TraesCS1A01G404900 chr6B 97.727 220 5 0 1587 1806 23231971 23231752 1.650000e-101 379.0
37 TraesCS1A01G404900 chr7B 99.545 220 1 0 1586 1805 138662135 138662354 3.510000e-108 401.0
38 TraesCS1A01G404900 chr7B 98.636 220 3 0 1586 1805 411545883 411546102 7.600000e-105 390.0
39 TraesCS1A01G404900 chr7B 89.017 173 14 2 1405 1576 65395670 65395838 2.280000e-50 209.0
40 TraesCS1A01G404900 chrUn 98.649 222 3 0 1586 1807 311485933 311486154 5.880000e-106 394.0
41 TraesCS1A01G404900 chr5B 98.206 223 4 0 1586 1808 26029886 26029664 7.600000e-105 390.0
42 TraesCS1A01G404900 chr5A 98.630 219 3 0 1587 1805 675426312 675426094 2.730000e-104 388.0
43 TraesCS1A01G404900 chr2B 98.630 219 3 0 1587 1805 144647535 144647317 2.730000e-104 388.0
44 TraesCS1A01G404900 chr4B 96.537 231 6 1 1580 1808 12236571 12236801 4.580000e-102 381.0


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 TraesCS1A01G404900 chr1A 568265066 568267335 2269 False 4193.000000 4193 100.000000 1 2270 1 chr1A.!!$F2 2269
1 TraesCS1A01G404900 chr1A 568327020 568328460 1440 False 489.333333 671 87.402667 95 1433 3 chr1A.!!$F7 1338
2 TraesCS1A01G404900 chr1D 473960280 473962191 1911 False 1245.500000 1947 91.013500 76 2190 2 chr1D.!!$F6 2114
3 TraesCS1A01G404900 chr1D 473879765 473880414 649 False 715.000000 715 87.068000 937 1576 1 chr1D.!!$F1 639
4 TraesCS1A01G404900 chr1B 659181600 659183055 1455 False 1315.000000 1315 83.667000 83 1520 1 chr1B.!!$F1 1437
5 TraesCS1A01G404900 chr1B 659285141 659287044 1903 False 1131.500000 1716 90.776500 83 2221 2 chr1B.!!$F6 2138
6 TraesCS1A01G404900 chr1B 659033231 659034863 1632 False 1011.500000 1413 91.152000 439 2270 2 chr1B.!!$F4 1831
7 TraesCS1A01G404900 chr1B 659002557 659003783 1226 False 834.500000 1072 92.528000 838 2270 2 chr1B.!!$F3 1432
8 TraesCS1A01G404900 chr1B 658968414 658970200 1786 False 666.666667 802 90.089000 260 2270 3 chr1B.!!$F2 2010
9 TraesCS1A01G404900 chr1B 659293811 659295765 1954 False 579.000000 1131 90.376250 83 2270 4 chr1B.!!$F7 2187
10 TraesCS1A01G404900 chr1B 659072736 659074644 1908 False 519.250000 904 88.879500 141 2270 4 chr1B.!!$F5 2129

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
56 57 0.036388 TAACTGAGCTGGAAAGGGCG 60.036 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 2105 0.100682 GCGCAGTTCTAGGTCATCGA 59.899 55.0 0.3 0.0 0.0 3.59 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
21 22 1.386533 AGGATGTGCAATGCTACAGC 58.613 50.000 14.38 14.38 42.50 4.40
22 23 1.064906 AGGATGTGCAATGCTACAGCT 60.065 47.619 19.29 5.30 42.66 4.24
23 24 2.171237 AGGATGTGCAATGCTACAGCTA 59.829 45.455 19.29 0.00 42.66 3.32
24 25 2.547211 GGATGTGCAATGCTACAGCTAG 59.453 50.000 19.29 0.00 42.66 3.42
25 26 1.372582 TGTGCAATGCTACAGCTAGC 58.627 50.000 6.62 6.62 45.19 3.42
26 27 1.065926 TGTGCAATGCTACAGCTAGCT 60.066 47.619 12.68 12.68 45.20 3.32
27 28 1.329906 GTGCAATGCTACAGCTAGCTG 59.670 52.381 37.27 37.27 45.20 4.24
40 41 4.922719 CAGCTAGCTGGTGTAGTAGTAAC 58.077 47.826 33.06 0.00 40.17 2.50
41 42 4.641094 CAGCTAGCTGGTGTAGTAGTAACT 59.359 45.833 33.06 0.00 40.17 2.24
42 43 4.641094 AGCTAGCTGGTGTAGTAGTAACTG 59.359 45.833 18.57 0.00 36.36 3.16
43 44 4.639310 GCTAGCTGGTGTAGTAGTAACTGA 59.361 45.833 7.70 0.00 36.36 3.41
44 45 5.220892 GCTAGCTGGTGTAGTAGTAACTGAG 60.221 48.000 7.70 0.00 36.36 3.35
45 46 3.444388 AGCTGGTGTAGTAGTAACTGAGC 59.556 47.826 0.00 0.00 36.36 4.26
46 47 3.444388 GCTGGTGTAGTAGTAACTGAGCT 59.556 47.826 0.00 0.00 36.36 4.09
47 48 4.675671 GCTGGTGTAGTAGTAACTGAGCTG 60.676 50.000 0.00 0.00 36.36 4.24
48 49 3.762288 TGGTGTAGTAGTAACTGAGCTGG 59.238 47.826 0.00 0.00 36.36 4.85
49 50 4.015084 GGTGTAGTAGTAACTGAGCTGGA 58.985 47.826 0.00 0.00 36.36 3.86
50 51 4.461781 GGTGTAGTAGTAACTGAGCTGGAA 59.538 45.833 0.00 0.00 36.36 3.53
51 52 5.047519 GGTGTAGTAGTAACTGAGCTGGAAA 60.048 44.000 0.00 0.00 36.36 3.13
52 53 6.094061 GTGTAGTAGTAACTGAGCTGGAAAG 58.906 44.000 0.00 0.00 36.36 2.62
53 54 4.810191 AGTAGTAACTGAGCTGGAAAGG 57.190 45.455 0.00 0.00 33.57 3.11
54 55 3.515901 AGTAGTAACTGAGCTGGAAAGGG 59.484 47.826 0.00 0.00 33.57 3.95
55 56 1.003696 AGTAACTGAGCTGGAAAGGGC 59.996 52.381 0.00 0.00 0.00 5.19
56 57 0.036388 TAACTGAGCTGGAAAGGGCG 60.036 55.000 0.00 0.00 0.00 6.13
57 58 3.130160 CTGAGCTGGAAAGGGCGC 61.130 66.667 0.00 0.00 0.00 6.53
58 59 3.907260 CTGAGCTGGAAAGGGCGCA 62.907 63.158 10.83 0.00 36.85 6.09
59 60 2.439156 GAGCTGGAAAGGGCGCAT 60.439 61.111 10.83 0.00 0.00 4.73
60 61 2.439156 AGCTGGAAAGGGCGCATC 60.439 61.111 10.83 0.00 0.00 3.91
61 62 3.521796 GCTGGAAAGGGCGCATCC 61.522 66.667 10.83 15.92 0.00 3.51
62 63 3.204827 CTGGAAAGGGCGCATCCG 61.205 66.667 10.83 10.39 35.96 4.18
74 75 3.281395 CATCCGCGCATGCATCCA 61.281 61.111 19.57 0.00 42.97 3.41
125 126 1.333931 GTATCATCGCGAGTGAGTGGA 59.666 52.381 16.66 3.58 0.00 4.02
298 337 6.881602 ACCTGAGAGAATATGTTTTGGAGTTC 59.118 38.462 0.00 0.00 0.00 3.01
396 450 9.507329 AGAACACAGTACAGATTCATTTACAAT 57.493 29.630 0.00 0.00 0.00 2.71
809 996 0.868406 GCGAGAACCTTGTTGTCCTG 59.132 55.000 0.00 0.00 0.00 3.86
827 1014 2.616510 CCTGTCCTCAGCCACCTTTTAG 60.617 54.545 0.00 0.00 40.09 1.85
834 1021 0.539669 AGCCACCTTTTAGCCCACAC 60.540 55.000 0.00 0.00 0.00 3.82
869 1097 5.130145 CCTATAAATAGCAGCCCTCATAGCT 59.870 44.000 0.00 0.00 42.70 3.32
885 1113 6.351371 CCTCATAGCTAAGAGAGACACCAAAA 60.351 42.308 24.11 0.00 33.74 2.44
896 1124 2.900546 AGACACCAAAACAAACCACCAA 59.099 40.909 0.00 0.00 0.00 3.67
905 1133 3.018423 ACAAACCACCAAAGCTTCTCT 57.982 42.857 0.00 0.00 0.00 3.10
934 1162 3.710209 AGGACTTCCTCAATTCCACAG 57.290 47.619 0.00 0.00 44.77 3.66
996 1233 5.019470 AGTAGAACATCACATCTCACCTGA 58.981 41.667 0.00 0.00 0.00 3.86
1041 1278 4.704103 AGCACCTCCCCGAGCTCA 62.704 66.667 15.40 0.00 30.05 4.26
1059 1296 0.318441 CAGACTCGGAGTGGAGCAAA 59.682 55.000 16.72 0.00 37.57 3.68
1107 1344 3.194719 GCCTACTACGGCGTGAGT 58.805 61.111 24.86 21.90 40.79 3.41
1493 1837 0.324614 TGACGACTGGCACCATGAAT 59.675 50.000 0.00 0.00 0.00 2.57
1583 1934 8.143193 TCATAGCACAATCAGACAAACAAATTT 58.857 29.630 0.00 0.00 0.00 1.82
1586 1937 5.754890 GCACAATCAGACAAACAAATTTCCT 59.245 36.000 0.00 0.00 0.00 3.36
1587 1938 6.922957 GCACAATCAGACAAACAAATTTCCTA 59.077 34.615 0.00 0.00 0.00 2.94
1588 1939 7.096065 GCACAATCAGACAAACAAATTTCCTAC 60.096 37.037 0.00 0.00 0.00 3.18
1589 1940 8.137437 CACAATCAGACAAACAAATTTCCTACT 58.863 33.333 0.00 0.00 0.00 2.57
1590 1941 9.349713 ACAATCAGACAAACAAATTTCCTACTA 57.650 29.630 0.00 0.00 0.00 1.82
1591 1942 9.612620 CAATCAGACAAACAAATTTCCTACTAC 57.387 33.333 0.00 0.00 0.00 2.73
1592 1943 7.739498 TCAGACAAACAAATTTCCTACTACC 57.261 36.000 0.00 0.00 0.00 3.18
1593 1944 7.514721 TCAGACAAACAAATTTCCTACTACCT 58.485 34.615 0.00 0.00 0.00 3.08
1594 1945 7.660208 TCAGACAAACAAATTTCCTACTACCTC 59.340 37.037 0.00 0.00 0.00 3.85
1595 1946 6.940867 AGACAAACAAATTTCCTACTACCTCC 59.059 38.462 0.00 0.00 0.00 4.30
1596 1947 5.704053 ACAAACAAATTTCCTACTACCTCCG 59.296 40.000 0.00 0.00 0.00 4.63
1597 1948 5.494390 AACAAATTTCCTACTACCTCCGT 57.506 39.130 0.00 0.00 0.00 4.69
1598 1949 5.082251 ACAAATTTCCTACTACCTCCGTC 57.918 43.478 0.00 0.00 0.00 4.79
1599 1950 4.081254 ACAAATTTCCTACTACCTCCGTCC 60.081 45.833 0.00 0.00 0.00 4.79
1600 1951 2.149973 TTTCCTACTACCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
1601 1952 0.107017 TTCCTACTACCTCCGTCCCG 60.107 60.000 0.00 0.00 0.00 5.14
1612 1963 3.953201 CCGTCCCGGTGTATAAGTC 57.047 57.895 0.00 0.00 42.73 3.01
1613 1964 1.105457 CCGTCCCGGTGTATAAGTCA 58.895 55.000 0.00 0.00 42.73 3.41
1614 1965 1.684983 CCGTCCCGGTGTATAAGTCAT 59.315 52.381 0.00 0.00 42.73 3.06
1615 1966 2.101917 CCGTCCCGGTGTATAAGTCATT 59.898 50.000 0.00 0.00 42.73 2.57
1616 1967 3.378339 CGTCCCGGTGTATAAGTCATTC 58.622 50.000 0.00 0.00 0.00 2.67
1617 1968 3.378339 GTCCCGGTGTATAAGTCATTCG 58.622 50.000 0.00 0.00 0.00 3.34
1618 1969 2.132762 CCCGGTGTATAAGTCATTCGC 58.867 52.381 0.00 0.00 0.00 4.70
1619 1970 1.784856 CCGGTGTATAAGTCATTCGCG 59.215 52.381 0.00 0.00 0.00 5.87
1620 1971 2.456989 CGGTGTATAAGTCATTCGCGT 58.543 47.619 5.77 0.00 0.00 6.01
1621 1972 3.548616 CCGGTGTATAAGTCATTCGCGTA 60.549 47.826 5.77 0.00 0.00 4.42
1622 1973 3.662645 CGGTGTATAAGTCATTCGCGTAG 59.337 47.826 5.77 0.00 0.00 3.51
1623 1974 4.604976 GGTGTATAAGTCATTCGCGTAGT 58.395 43.478 5.77 0.00 0.00 2.73
1624 1975 5.039333 GGTGTATAAGTCATTCGCGTAGTT 58.961 41.667 5.77 2.59 0.00 2.24
1625 1976 5.172771 GGTGTATAAGTCATTCGCGTAGTTC 59.827 44.000 5.77 0.00 0.00 3.01
1626 1977 5.970023 GTGTATAAGTCATTCGCGTAGTTCT 59.030 40.000 5.77 0.00 0.00 3.01
1627 1978 7.128331 GTGTATAAGTCATTCGCGTAGTTCTA 58.872 38.462 5.77 0.00 0.00 2.10
1628 1979 7.320797 GTGTATAAGTCATTCGCGTAGTTCTAG 59.679 40.741 5.77 0.00 0.00 2.43
1629 1980 3.694535 AGTCATTCGCGTAGTTCTAGG 57.305 47.619 5.77 0.00 0.00 3.02
1630 1981 3.015327 AGTCATTCGCGTAGTTCTAGGT 58.985 45.455 5.77 0.00 0.00 3.08
1631 1982 3.065095 AGTCATTCGCGTAGTTCTAGGTC 59.935 47.826 5.77 0.00 0.00 3.85
1632 1983 2.031314 TCATTCGCGTAGTTCTAGGTCG 59.969 50.000 5.77 5.99 0.00 4.79
1633 1984 1.725641 TTCGCGTAGTTCTAGGTCGA 58.274 50.000 5.77 11.56 0.00 4.20
1634 1985 1.945387 TCGCGTAGTTCTAGGTCGAT 58.055 50.000 5.77 0.00 0.00 3.59
1635 1986 3.097877 TCGCGTAGTTCTAGGTCGATA 57.902 47.619 5.77 0.00 0.00 2.92
1636 1987 3.457234 TCGCGTAGTTCTAGGTCGATAA 58.543 45.455 5.77 0.00 0.00 1.75
1637 1988 4.060900 TCGCGTAGTTCTAGGTCGATAAT 58.939 43.478 5.77 0.00 0.00 1.28
1638 1989 4.512944 TCGCGTAGTTCTAGGTCGATAATT 59.487 41.667 5.77 0.00 0.00 1.40
1639 1990 5.008019 TCGCGTAGTTCTAGGTCGATAATTT 59.992 40.000 5.77 0.00 0.00 1.82
1640 1991 6.202762 TCGCGTAGTTCTAGGTCGATAATTTA 59.797 38.462 5.77 0.00 0.00 1.40
1641 1992 6.852853 CGCGTAGTTCTAGGTCGATAATTTAA 59.147 38.462 0.00 0.00 0.00 1.52
1642 1993 7.149224 CGCGTAGTTCTAGGTCGATAATTTAAC 60.149 40.741 0.00 0.00 0.00 2.01
1643 1994 7.859875 GCGTAGTTCTAGGTCGATAATTTAACT 59.140 37.037 0.00 0.00 0.00 2.24
1700 2051 6.764877 ATATTTAGAAACTACATCCGCGTG 57.235 37.500 4.92 0.00 0.00 5.34
1701 2052 2.572191 TAGAAACTACATCCGCGTGG 57.428 50.000 9.28 9.28 0.00 4.94
1711 2062 3.733236 TCCGCGTGGAAATCTAGTG 57.267 52.632 17.09 0.00 42.85 2.74
1712 2063 1.179152 TCCGCGTGGAAATCTAGTGA 58.821 50.000 17.09 0.00 42.85 3.41
1713 2064 1.754803 TCCGCGTGGAAATCTAGTGAT 59.245 47.619 17.09 0.00 42.85 3.06
1714 2065 2.953648 TCCGCGTGGAAATCTAGTGATA 59.046 45.455 17.09 0.00 42.85 2.15
1715 2066 3.572682 TCCGCGTGGAAATCTAGTGATAT 59.427 43.478 17.09 0.00 42.85 1.63
1716 2067 4.763279 TCCGCGTGGAAATCTAGTGATATA 59.237 41.667 17.09 0.00 42.85 0.86
1717 2068 4.857588 CCGCGTGGAAATCTAGTGATATAC 59.142 45.833 10.20 0.00 37.49 1.47
1718 2069 4.553815 CGCGTGGAAATCTAGTGATATACG 59.446 45.833 0.00 0.00 32.81 3.06
1719 2070 5.458891 GCGTGGAAATCTAGTGATATACGT 58.541 41.667 0.00 0.00 32.54 3.57
1720 2071 5.919141 GCGTGGAAATCTAGTGATATACGTT 59.081 40.000 0.00 0.00 32.54 3.99
1721 2072 6.420008 GCGTGGAAATCTAGTGATATACGTTT 59.580 38.462 0.00 0.00 32.54 3.60
1722 2073 7.358187 GCGTGGAAATCTAGTGATATACGTTTC 60.358 40.741 0.00 0.00 32.54 2.78
1723 2074 7.646526 CGTGGAAATCTAGTGATATACGTTTCA 59.353 37.037 0.00 0.00 31.70 2.69
1724 2075 9.477484 GTGGAAATCTAGTGATATACGTTTCAT 57.523 33.333 0.00 0.00 31.70 2.57
1762 2113 9.831737 CATATTTAATTCCTCAAATCGATGACC 57.168 33.333 0.00 0.00 0.00 4.02
1763 2114 9.799106 ATATTTAATTCCTCAAATCGATGACCT 57.201 29.630 0.00 0.00 0.00 3.85
1765 2116 8.662781 TTTAATTCCTCAAATCGATGACCTAG 57.337 34.615 0.00 0.00 0.00 3.02
1766 2117 6.485830 AATTCCTCAAATCGATGACCTAGA 57.514 37.500 0.00 0.00 0.00 2.43
1767 2118 5.932619 TTCCTCAAATCGATGACCTAGAA 57.067 39.130 0.00 0.00 0.00 2.10
1768 2119 5.263968 TCCTCAAATCGATGACCTAGAAC 57.736 43.478 0.00 0.00 0.00 3.01
1769 2120 4.956700 TCCTCAAATCGATGACCTAGAACT 59.043 41.667 0.00 0.00 0.00 3.01
1770 2121 5.046529 CCTCAAATCGATGACCTAGAACTG 58.953 45.833 0.00 0.00 0.00 3.16
1771 2122 4.433615 TCAAATCGATGACCTAGAACTGC 58.566 43.478 0.00 0.00 0.00 4.40
1772 2123 2.783828 ATCGATGACCTAGAACTGCG 57.216 50.000 0.00 0.00 0.00 5.18
1773 2124 0.100682 TCGATGACCTAGAACTGCGC 59.899 55.000 0.00 0.00 0.00 6.09
1774 2125 1.202973 CGATGACCTAGAACTGCGCG 61.203 60.000 0.00 0.00 0.00 6.86
1775 2126 0.100682 GATGACCTAGAACTGCGCGA 59.899 55.000 12.10 0.00 0.00 5.87
1776 2127 0.530744 ATGACCTAGAACTGCGCGAA 59.469 50.000 12.10 0.00 0.00 4.70
1777 2128 0.530744 TGACCTAGAACTGCGCGAAT 59.469 50.000 12.10 0.00 0.00 3.34
1778 2129 0.924090 GACCTAGAACTGCGCGAATG 59.076 55.000 12.10 0.10 0.00 2.67
1779 2130 0.530744 ACCTAGAACTGCGCGAATGA 59.469 50.000 12.10 0.00 0.00 2.57
1780 2131 0.924090 CCTAGAACTGCGCGAATGAC 59.076 55.000 12.10 0.00 0.00 3.06
1781 2132 1.469940 CCTAGAACTGCGCGAATGACT 60.470 52.381 12.10 5.49 0.00 3.41
1782 2133 2.263077 CTAGAACTGCGCGAATGACTT 58.737 47.619 12.10 0.00 0.00 3.01
1783 2134 2.363788 AGAACTGCGCGAATGACTTA 57.636 45.000 12.10 0.00 0.00 2.24
1784 2135 2.893637 AGAACTGCGCGAATGACTTAT 58.106 42.857 12.10 0.00 0.00 1.73
1785 2136 4.041740 AGAACTGCGCGAATGACTTATA 57.958 40.909 12.10 0.00 0.00 0.98
1786 2137 3.797256 AGAACTGCGCGAATGACTTATAC 59.203 43.478 12.10 0.00 0.00 1.47
1787 2138 3.159353 ACTGCGCGAATGACTTATACA 57.841 42.857 12.10 0.00 0.00 2.29
1788 2139 2.858344 ACTGCGCGAATGACTTATACAC 59.142 45.455 12.10 0.00 0.00 2.90
1789 2140 2.198406 TGCGCGAATGACTTATACACC 58.802 47.619 12.10 0.00 0.00 4.16
1790 2141 1.525619 GCGCGAATGACTTATACACCC 59.474 52.381 12.10 0.00 0.00 4.61
1791 2142 1.784856 CGCGAATGACTTATACACCCG 59.215 52.381 0.00 0.00 0.00 5.28
1792 2143 2.132762 GCGAATGACTTATACACCCGG 58.867 52.381 0.00 0.00 0.00 5.73
1793 2144 2.223876 GCGAATGACTTATACACCCGGA 60.224 50.000 0.73 0.00 0.00 5.14
1794 2145 3.378339 CGAATGACTTATACACCCGGAC 58.622 50.000 0.73 0.00 0.00 4.79
1795 2146 3.378339 GAATGACTTATACACCCGGACG 58.622 50.000 0.73 0.00 0.00 4.79
1796 2147 1.105457 TGACTTATACACCCGGACGG 58.895 55.000 0.73 3.25 37.81 4.79
1797 2148 1.340893 TGACTTATACACCCGGACGGA 60.341 52.381 13.13 0.00 37.50 4.69
1798 2149 1.336125 GACTTATACACCCGGACGGAG 59.664 57.143 13.13 6.96 37.50 4.63
1799 2150 0.672342 CTTATACACCCGGACGGAGG 59.328 60.000 13.13 6.21 37.50 4.30
1828 2179 4.605640 TCCAAAGAAAAAGCTTGGATGG 57.394 40.909 0.00 3.76 0.00 3.51
1844 2195 3.265221 TGGATGGATCTTGCAGTCTTTCT 59.735 43.478 0.00 0.00 0.00 2.52
1990 2359 3.065371 CCAGTGGACAGTGAACAAAGTTC 59.935 47.826 1.68 3.05 33.67 3.01
1993 2362 5.235186 CAGTGGACAGTGAACAAAGTTCTAG 59.765 44.000 10.79 4.07 33.67 2.43
1997 2366 6.882140 TGGACAGTGAACAAAGTTCTAGAAAA 59.118 34.615 6.78 0.00 0.00 2.29
2018 2387 8.722422 AGAAAATAGATCTCTTAAGAATGGGCT 58.278 33.333 6.63 3.01 34.49 5.19
2075 2445 9.627123 CATTGGTTAGAATAACAGGAAGGAATA 57.373 33.333 2.42 0.00 0.00 1.75
2159 2533 6.276847 AGATTCTCGTCTACATTCATGAACC 58.723 40.000 11.07 0.00 0.00 3.62
2160 2534 5.400066 TTCTCGTCTACATTCATGAACCA 57.600 39.130 11.07 0.00 0.00 3.67
2161 2535 4.998788 TCTCGTCTACATTCATGAACCAG 58.001 43.478 11.07 8.24 0.00 4.00
2170 2544 6.017400 ACATTCATGAACCAGATGTTGTTC 57.983 37.500 11.07 0.25 40.94 3.18
2179 2553 6.150976 TGAACCAGATGTTGTTCATTATGTCC 59.849 38.462 5.50 0.00 44.24 4.02
2181 2555 5.882557 ACCAGATGTTGTTCATTATGTCCTC 59.117 40.000 0.00 0.00 36.83 3.71
2198 2572 1.525619 CCTCGAACCAAGTCGTCAAAC 59.474 52.381 0.00 0.00 41.80 2.93
2244 2618 9.915629 TGTGTTTGTGTTATTTGTAAGAAGTTT 57.084 25.926 0.00 0.00 0.00 2.66
2256 2630 8.685838 TTTGTAAGAAGTTTTACCTGTAGCAT 57.314 30.769 0.00 0.00 33.56 3.79
2264 2638 5.983118 AGTTTTACCTGTAGCATTTTGTTGC 59.017 36.000 0.00 0.00 43.09 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.289002 GCTGTAGCATTGCACATCCTAC 59.711 50.000 11.91 4.13 41.59 3.18
1 2 2.171237 AGCTGTAGCATTGCACATCCTA 59.829 45.455 11.91 0.00 45.16 2.94
2 3 1.064906 AGCTGTAGCATTGCACATCCT 60.065 47.619 11.91 9.21 45.16 3.24
3 4 1.386533 AGCTGTAGCATTGCACATCC 58.613 50.000 11.91 7.41 45.16 3.51
4 5 3.874400 CTAGCTGTAGCATTGCACATC 57.126 47.619 11.91 8.77 45.16 3.06
15 16 4.200874 ACTACTACACCAGCTAGCTGTAG 58.799 47.826 36.14 31.62 42.15 2.74
16 17 4.232188 ACTACTACACCAGCTAGCTGTA 57.768 45.455 36.14 24.30 42.15 2.74
17 18 3.088789 ACTACTACACCAGCTAGCTGT 57.911 47.619 36.14 24.47 42.15 4.40
18 19 4.641094 AGTTACTACTACACCAGCTAGCTG 59.359 45.833 33.58 33.58 37.01 4.24
19 20 4.641094 CAGTTACTACTACACCAGCTAGCT 59.359 45.833 12.68 12.68 31.96 3.32
20 21 4.639310 TCAGTTACTACTACACCAGCTAGC 59.361 45.833 6.62 6.62 31.96 3.42
21 22 5.220892 GCTCAGTTACTACTACACCAGCTAG 60.221 48.000 0.00 0.00 31.96 3.42
22 23 4.639310 GCTCAGTTACTACTACACCAGCTA 59.361 45.833 0.00 0.00 31.96 3.32
23 24 3.444388 GCTCAGTTACTACTACACCAGCT 59.556 47.826 0.00 0.00 31.96 4.24
24 25 3.444388 AGCTCAGTTACTACTACACCAGC 59.556 47.826 0.00 0.00 31.96 4.85
25 26 4.142359 CCAGCTCAGTTACTACTACACCAG 60.142 50.000 0.00 0.00 31.96 4.00
26 27 3.762288 CCAGCTCAGTTACTACTACACCA 59.238 47.826 0.00 0.00 31.96 4.17
27 28 4.015084 TCCAGCTCAGTTACTACTACACC 58.985 47.826 0.00 0.00 31.96 4.16
28 29 5.640189 TTCCAGCTCAGTTACTACTACAC 57.360 43.478 0.00 0.00 31.96 2.90
29 30 5.185249 CCTTTCCAGCTCAGTTACTACTACA 59.815 44.000 0.00 0.00 31.96 2.74
30 31 5.394333 CCCTTTCCAGCTCAGTTACTACTAC 60.394 48.000 0.00 0.00 31.96 2.73
31 32 4.710375 CCCTTTCCAGCTCAGTTACTACTA 59.290 45.833 0.00 0.00 31.96 1.82
32 33 3.515901 CCCTTTCCAGCTCAGTTACTACT 59.484 47.826 0.00 0.00 34.00 2.57
33 34 3.863041 CCCTTTCCAGCTCAGTTACTAC 58.137 50.000 0.00 0.00 0.00 2.73
34 35 2.236395 GCCCTTTCCAGCTCAGTTACTA 59.764 50.000 0.00 0.00 0.00 1.82
35 36 1.003696 GCCCTTTCCAGCTCAGTTACT 59.996 52.381 0.00 0.00 0.00 2.24
36 37 1.454201 GCCCTTTCCAGCTCAGTTAC 58.546 55.000 0.00 0.00 0.00 2.50
37 38 0.036388 CGCCCTTTCCAGCTCAGTTA 60.036 55.000 0.00 0.00 0.00 2.24
38 39 1.302832 CGCCCTTTCCAGCTCAGTT 60.303 57.895 0.00 0.00 0.00 3.16
39 40 2.348998 CGCCCTTTCCAGCTCAGT 59.651 61.111 0.00 0.00 0.00 3.41
40 41 3.130160 GCGCCCTTTCCAGCTCAG 61.130 66.667 0.00 0.00 0.00 3.35
41 42 3.272364 ATGCGCCCTTTCCAGCTCA 62.272 57.895 4.18 0.00 0.00 4.26
42 43 2.439156 ATGCGCCCTTTCCAGCTC 60.439 61.111 4.18 0.00 0.00 4.09
43 44 2.439156 GATGCGCCCTTTCCAGCT 60.439 61.111 4.18 0.00 0.00 4.24
44 45 3.521796 GGATGCGCCCTTTCCAGC 61.522 66.667 4.18 0.00 0.00 4.85
45 46 3.204827 CGGATGCGCCCTTTCCAG 61.205 66.667 4.18 0.00 0.00 3.86
57 58 3.249973 CTGGATGCATGCGCGGATG 62.250 63.158 32.97 32.97 42.97 3.51
58 59 2.743126 ATCTGGATGCATGCGCGGAT 62.743 55.000 14.09 7.52 42.97 4.18
59 60 2.946172 AATCTGGATGCATGCGCGGA 62.946 55.000 14.09 5.00 42.97 5.54
60 61 2.453773 GAATCTGGATGCATGCGCGG 62.454 60.000 14.09 6.52 42.97 6.46
61 62 1.082300 GAATCTGGATGCATGCGCG 60.082 57.895 14.09 0.00 42.97 6.86
62 63 1.285023 GGAATCTGGATGCATGCGC 59.715 57.895 14.09 0.00 39.24 6.09
63 64 0.591659 CTGGAATCTGGATGCATGCG 59.408 55.000 14.09 8.54 0.00 4.73
64 65 1.880675 CTCTGGAATCTGGATGCATGC 59.119 52.381 11.82 11.82 0.00 4.06
65 66 1.880675 GCTCTGGAATCTGGATGCATG 59.119 52.381 2.46 0.00 0.00 4.06
66 67 1.493446 TGCTCTGGAATCTGGATGCAT 59.507 47.619 0.00 0.00 0.00 3.96
67 68 0.913924 TGCTCTGGAATCTGGATGCA 59.086 50.000 0.00 0.00 0.00 3.96
68 69 1.134159 AGTGCTCTGGAATCTGGATGC 60.134 52.381 0.00 0.00 0.00 3.91
69 70 2.802415 CGAGTGCTCTGGAATCTGGATG 60.802 54.545 0.00 0.00 0.00 3.51
70 71 1.411977 CGAGTGCTCTGGAATCTGGAT 59.588 52.381 0.00 0.00 0.00 3.41
71 72 0.820226 CGAGTGCTCTGGAATCTGGA 59.180 55.000 0.00 0.00 0.00 3.86
72 73 0.809241 GCGAGTGCTCTGGAATCTGG 60.809 60.000 1.65 0.00 38.39 3.86
73 74 0.809241 GGCGAGTGCTCTGGAATCTG 60.809 60.000 1.65 0.00 42.25 2.90
74 75 1.519719 GGCGAGTGCTCTGGAATCT 59.480 57.895 1.65 0.00 42.25 2.40
125 126 0.111061 TCATCACCAGGCAGCAGTTT 59.889 50.000 0.00 0.00 0.00 2.66
237 254 2.057137 ATTATTGTCAGCGTGGCCAT 57.943 45.000 9.72 0.00 0.00 4.40
427 484 2.941480 CCCCAGCTTGCTATTCTTCAT 58.059 47.619 0.00 0.00 0.00 2.57
444 511 0.395586 TGTGTGCATATTCTGGCCCC 60.396 55.000 0.00 0.00 0.00 5.80
508 587 1.098050 AATTTCCTGGCTAAGCTGCG 58.902 50.000 0.00 0.00 0.00 5.18
809 996 1.454201 GCTAAAAGGTGGCTGAGGAC 58.546 55.000 0.00 0.00 0.00 3.85
827 1014 4.366684 CCCTGGGAAGGTGTGGGC 62.367 72.222 7.01 0.00 0.00 5.36
834 1021 3.308473 GCTATTTATAGGCCCTGGGAAGG 60.308 52.174 19.27 0.00 0.00 3.46
869 1097 5.355910 GTGGTTTGTTTTGGTGTCTCTCTTA 59.644 40.000 0.00 0.00 0.00 2.10
885 1113 3.018423 AGAGAAGCTTTGGTGGTTTGT 57.982 42.857 0.00 0.00 0.00 2.83
896 1124 4.285775 AGTCCTTTGCTCTTAGAGAAGCTT 59.714 41.667 14.14 0.00 32.21 3.74
926 1154 1.852157 TGGGGTGCTCCTGTGGAAT 60.852 57.895 4.53 0.00 35.33 3.01
932 1160 4.729918 GTGCCTGGGGTGCTCCTG 62.730 72.222 4.53 0.00 35.33 3.86
934 1162 4.284550 TTGTGCCTGGGGTGCTCC 62.285 66.667 0.00 0.00 0.00 4.70
996 1233 0.974383 ACGACCCGGAAGACATCTTT 59.026 50.000 0.73 0.00 36.11 2.52
1041 1278 1.048601 TTTTGCTCCACTCCGAGTCT 58.951 50.000 0.00 0.00 32.11 3.24
1342 1600 5.308825 AGCAGACAAATACAGCAGTAACTT 58.691 37.500 0.00 0.00 33.13 2.66
1493 1837 6.947464 AGCAGTTTGGCTTATAGAGAGTTAA 58.053 36.000 0.00 0.00 42.71 2.01
1596 1947 3.378339 CGAATGACTTATACACCGGGAC 58.622 50.000 6.32 0.00 0.00 4.46
1597 1948 2.223876 GCGAATGACTTATACACCGGGA 60.224 50.000 6.32 0.00 0.00 5.14
1598 1949 2.132762 GCGAATGACTTATACACCGGG 58.867 52.381 6.32 0.00 0.00 5.73
1599 1950 1.784856 CGCGAATGACTTATACACCGG 59.215 52.381 0.00 0.00 0.00 5.28
1600 1951 2.456989 ACGCGAATGACTTATACACCG 58.543 47.619 15.93 0.00 0.00 4.94
1601 1952 4.604976 ACTACGCGAATGACTTATACACC 58.395 43.478 15.93 0.00 0.00 4.16
1602 1953 5.970023 AGAACTACGCGAATGACTTATACAC 59.030 40.000 15.93 0.00 0.00 2.90
1603 1954 6.127810 AGAACTACGCGAATGACTTATACA 57.872 37.500 15.93 0.00 0.00 2.29
1604 1955 6.796072 CCTAGAACTACGCGAATGACTTATAC 59.204 42.308 15.93 0.00 0.00 1.47
1605 1956 6.484643 ACCTAGAACTACGCGAATGACTTATA 59.515 38.462 15.93 0.00 0.00 0.98
1606 1957 5.298777 ACCTAGAACTACGCGAATGACTTAT 59.701 40.000 15.93 0.00 0.00 1.73
1607 1958 4.637534 ACCTAGAACTACGCGAATGACTTA 59.362 41.667 15.93 0.00 0.00 2.24
1608 1959 3.442977 ACCTAGAACTACGCGAATGACTT 59.557 43.478 15.93 0.00 0.00 3.01
1609 1960 3.015327 ACCTAGAACTACGCGAATGACT 58.985 45.455 15.93 9.07 0.00 3.41
1610 1961 3.361414 GACCTAGAACTACGCGAATGAC 58.639 50.000 15.93 0.66 0.00 3.06
1611 1962 2.031314 CGACCTAGAACTACGCGAATGA 59.969 50.000 15.93 0.00 0.00 2.57
1612 1963 2.031314 TCGACCTAGAACTACGCGAATG 59.969 50.000 15.93 4.47 0.00 2.67
1613 1964 2.283298 TCGACCTAGAACTACGCGAAT 58.717 47.619 15.93 0.00 0.00 3.34
1614 1965 1.725641 TCGACCTAGAACTACGCGAA 58.274 50.000 15.93 0.00 0.00 4.70
1615 1966 1.945387 ATCGACCTAGAACTACGCGA 58.055 50.000 15.93 0.00 0.00 5.87
1616 1967 3.867055 TTATCGACCTAGAACTACGCG 57.133 47.619 3.53 3.53 0.00 6.01
1617 1968 7.859875 AGTTAAATTATCGACCTAGAACTACGC 59.140 37.037 0.00 0.00 0.00 4.42
1674 2025 9.563898 CACGCGGATGTAGTTTCTAAATATATA 57.436 33.333 12.47 0.00 0.00 0.86
1675 2026 7.544566 CCACGCGGATGTAGTTTCTAAATATAT 59.455 37.037 12.47 0.00 0.00 0.86
1676 2027 6.864685 CCACGCGGATGTAGTTTCTAAATATA 59.135 38.462 12.47 0.00 0.00 0.86
1677 2028 5.694910 CCACGCGGATGTAGTTTCTAAATAT 59.305 40.000 12.47 0.00 0.00 1.28
1678 2029 5.045215 CCACGCGGATGTAGTTTCTAAATA 58.955 41.667 12.47 0.00 0.00 1.40
1679 2030 3.869246 CCACGCGGATGTAGTTTCTAAAT 59.131 43.478 12.47 0.00 0.00 1.40
1680 2031 3.056678 TCCACGCGGATGTAGTTTCTAAA 60.057 43.478 12.47 0.00 35.91 1.85
1681 2032 2.492881 TCCACGCGGATGTAGTTTCTAA 59.507 45.455 12.47 0.00 35.91 2.10
1682 2033 2.093890 TCCACGCGGATGTAGTTTCTA 58.906 47.619 12.47 0.00 35.91 2.10
1683 2034 0.892755 TCCACGCGGATGTAGTTTCT 59.107 50.000 12.47 0.00 35.91 2.52
1684 2035 1.717194 TTCCACGCGGATGTAGTTTC 58.283 50.000 12.47 0.00 42.41 2.78
1685 2036 2.172851 TTTCCACGCGGATGTAGTTT 57.827 45.000 12.47 0.00 42.41 2.66
1686 2037 2.093658 AGATTTCCACGCGGATGTAGTT 60.094 45.455 12.47 0.00 42.41 2.24
1687 2038 1.480954 AGATTTCCACGCGGATGTAGT 59.519 47.619 12.47 0.00 42.41 2.73
1688 2039 2.225068 AGATTTCCACGCGGATGTAG 57.775 50.000 12.47 0.00 42.41 2.74
1689 2040 2.691526 ACTAGATTTCCACGCGGATGTA 59.308 45.455 12.47 0.00 42.41 2.29
1690 2041 1.480954 ACTAGATTTCCACGCGGATGT 59.519 47.619 12.47 0.00 42.41 3.06
1691 2042 1.860950 CACTAGATTTCCACGCGGATG 59.139 52.381 12.47 0.00 42.41 3.51
1692 2043 1.754803 TCACTAGATTTCCACGCGGAT 59.245 47.619 12.47 0.00 42.41 4.18
1693 2044 1.179152 TCACTAGATTTCCACGCGGA 58.821 50.000 12.47 0.00 40.60 5.54
1694 2045 2.225068 ATCACTAGATTTCCACGCGG 57.775 50.000 12.47 0.00 0.00 6.46
1695 2046 4.553815 CGTATATCACTAGATTTCCACGCG 59.446 45.833 3.53 3.53 35.67 6.01
1696 2047 5.458891 ACGTATATCACTAGATTTCCACGC 58.541 41.667 0.00 0.00 35.67 5.34
1697 2048 7.646526 TGAAACGTATATCACTAGATTTCCACG 59.353 37.037 0.00 2.04 35.67 4.94
1698 2049 8.867112 TGAAACGTATATCACTAGATTTCCAC 57.133 34.615 0.00 0.00 35.67 4.02
1736 2087 9.831737 GGTCATCGATTTGAGGAATTAAATATG 57.168 33.333 0.00 0.00 39.46 1.78
1737 2088 9.799106 AGGTCATCGATTTGAGGAATTAAATAT 57.201 29.630 0.00 0.00 39.46 1.28
1739 2090 9.277783 CTAGGTCATCGATTTGAGGAATTAAAT 57.722 33.333 0.00 0.00 39.46 1.40
1740 2091 8.482943 TCTAGGTCATCGATTTGAGGAATTAAA 58.517 33.333 0.00 0.00 39.46 1.52
1741 2092 8.018537 TCTAGGTCATCGATTTGAGGAATTAA 57.981 34.615 0.00 0.00 39.46 1.40
1742 2093 7.597288 TCTAGGTCATCGATTTGAGGAATTA 57.403 36.000 0.00 0.00 39.46 1.40
1743 2094 6.485830 TCTAGGTCATCGATTTGAGGAATT 57.514 37.500 0.00 0.00 39.46 2.17
1744 2095 6.098982 AGTTCTAGGTCATCGATTTGAGGAAT 59.901 38.462 0.00 0.00 39.46 3.01
1745 2096 5.422331 AGTTCTAGGTCATCGATTTGAGGAA 59.578 40.000 0.00 0.00 39.46 3.36
1746 2097 4.956700 AGTTCTAGGTCATCGATTTGAGGA 59.043 41.667 0.00 0.00 34.44 3.71
1747 2098 5.046529 CAGTTCTAGGTCATCGATTTGAGG 58.953 45.833 0.00 0.00 0.00 3.86
1748 2099 4.505922 GCAGTTCTAGGTCATCGATTTGAG 59.494 45.833 0.00 0.00 0.00 3.02
1749 2100 4.433615 GCAGTTCTAGGTCATCGATTTGA 58.566 43.478 0.00 0.00 0.00 2.69
1750 2101 3.243877 CGCAGTTCTAGGTCATCGATTTG 59.756 47.826 0.00 0.00 0.00 2.32
1751 2102 3.448686 CGCAGTTCTAGGTCATCGATTT 58.551 45.455 0.00 0.00 0.00 2.17
1752 2103 2.799917 GCGCAGTTCTAGGTCATCGATT 60.800 50.000 0.30 0.00 0.00 3.34
1753 2104 1.269309 GCGCAGTTCTAGGTCATCGAT 60.269 52.381 0.30 0.00 0.00 3.59
1754 2105 0.100682 GCGCAGTTCTAGGTCATCGA 59.899 55.000 0.30 0.00 0.00 3.59
1755 2106 1.202973 CGCGCAGTTCTAGGTCATCG 61.203 60.000 8.75 0.00 0.00 3.84
1756 2107 0.100682 TCGCGCAGTTCTAGGTCATC 59.899 55.000 8.75 0.00 0.00 2.92
1757 2108 0.530744 TTCGCGCAGTTCTAGGTCAT 59.469 50.000 8.75 0.00 0.00 3.06
1758 2109 0.530744 ATTCGCGCAGTTCTAGGTCA 59.469 50.000 8.75 0.00 0.00 4.02
1759 2110 0.924090 CATTCGCGCAGTTCTAGGTC 59.076 55.000 8.75 0.00 0.00 3.85
1760 2111 0.530744 TCATTCGCGCAGTTCTAGGT 59.469 50.000 8.75 0.00 0.00 3.08
1761 2112 0.924090 GTCATTCGCGCAGTTCTAGG 59.076 55.000 8.75 0.00 0.00 3.02
1762 2113 1.914634 AGTCATTCGCGCAGTTCTAG 58.085 50.000 8.75 0.00 0.00 2.43
1763 2114 2.363788 AAGTCATTCGCGCAGTTCTA 57.636 45.000 8.75 0.00 0.00 2.10
1764 2115 2.363788 TAAGTCATTCGCGCAGTTCT 57.636 45.000 8.75 0.00 0.00 3.01
1765 2116 3.550275 TGTATAAGTCATTCGCGCAGTTC 59.450 43.478 8.75 0.00 0.00 3.01
1766 2117 3.306166 GTGTATAAGTCATTCGCGCAGTT 59.694 43.478 8.75 0.00 0.00 3.16
1767 2118 2.858344 GTGTATAAGTCATTCGCGCAGT 59.142 45.455 8.75 0.00 0.00 4.40
1768 2119 2.218759 GGTGTATAAGTCATTCGCGCAG 59.781 50.000 8.75 0.00 0.00 5.18
1769 2120 2.198406 GGTGTATAAGTCATTCGCGCA 58.802 47.619 8.75 0.00 0.00 6.09
1770 2121 1.525619 GGGTGTATAAGTCATTCGCGC 59.474 52.381 0.00 0.00 0.00 6.86
1771 2122 1.784856 CGGGTGTATAAGTCATTCGCG 59.215 52.381 0.00 0.00 0.00 5.87
1772 2123 2.132762 CCGGGTGTATAAGTCATTCGC 58.867 52.381 0.00 0.00 0.00 4.70
1773 2124 3.378339 GTCCGGGTGTATAAGTCATTCG 58.622 50.000 0.00 0.00 0.00 3.34
1774 2125 3.378339 CGTCCGGGTGTATAAGTCATTC 58.622 50.000 0.00 0.00 0.00 2.67
1775 2126 2.101917 CCGTCCGGGTGTATAAGTCATT 59.898 50.000 0.00 0.00 0.00 2.57
1776 2127 1.684983 CCGTCCGGGTGTATAAGTCAT 59.315 52.381 0.00 0.00 0.00 3.06
1777 2128 1.105457 CCGTCCGGGTGTATAAGTCA 58.895 55.000 0.00 0.00 0.00 3.41
1778 2129 1.336125 CTCCGTCCGGGTGTATAAGTC 59.664 57.143 0.00 0.00 37.00 3.01
1779 2130 1.396653 CTCCGTCCGGGTGTATAAGT 58.603 55.000 0.00 0.00 37.00 2.24
1780 2131 0.672342 CCTCCGTCCGGGTGTATAAG 59.328 60.000 0.00 0.00 37.00 1.73
1781 2132 0.756442 CCCTCCGTCCGGGTGTATAA 60.756 60.000 0.00 0.00 36.91 0.98
1782 2133 1.152694 CCCTCCGTCCGGGTGTATA 60.153 63.158 0.00 0.00 36.91 1.47
1783 2134 2.443390 CCCTCCGTCCGGGTGTAT 60.443 66.667 0.00 0.00 36.91 2.29
1784 2135 3.650298 CTCCCTCCGTCCGGGTGTA 62.650 68.421 0.00 0.00 42.56 2.90
1786 2137 3.650298 TACTCCCTCCGTCCGGGTG 62.650 68.421 0.00 0.00 42.56 4.61
1787 2138 3.341629 TACTCCCTCCGTCCGGGT 61.342 66.667 0.00 0.00 42.56 5.28
1788 2139 2.832201 GTACTCCCTCCGTCCGGG 60.832 72.222 0.00 0.00 43.38 5.73
1789 2140 1.379576 AAGTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
1790 2141 1.382692 GGAAGTACTCCCTCCGTCCG 61.383 65.000 0.00 0.00 38.44 4.79
1791 2142 0.324091 TGGAAGTACTCCCTCCGTCC 60.324 60.000 0.00 0.00 44.69 4.79
1792 2143 1.553706 TTGGAAGTACTCCCTCCGTC 58.446 55.000 0.00 0.00 44.69 4.79
1793 2144 1.900486 CTTTGGAAGTACTCCCTCCGT 59.100 52.381 0.00 0.00 44.69 4.69
1794 2145 2.176889 TCTTTGGAAGTACTCCCTCCG 58.823 52.381 0.00 0.00 44.69 4.63
1795 2146 4.635699 TTTCTTTGGAAGTACTCCCTCC 57.364 45.455 0.00 2.18 44.69 4.30
1796 2147 5.048643 GCTTTTTCTTTGGAAGTACTCCCTC 60.049 44.000 0.00 0.00 44.69 4.30
1797 2148 4.827835 GCTTTTTCTTTGGAAGTACTCCCT 59.172 41.667 0.00 0.00 44.69 4.20
1798 2149 4.827835 AGCTTTTTCTTTGGAAGTACTCCC 59.172 41.667 0.00 0.00 44.69 4.30
1799 2150 6.209361 CAAGCTTTTTCTTTGGAAGTACTCC 58.791 40.000 0.00 0.00 45.64 3.85
1800 2151 6.039382 TCCAAGCTTTTTCTTTGGAAGTACTC 59.961 38.462 0.00 0.00 32.61 2.59
1801 2152 5.891551 TCCAAGCTTTTTCTTTGGAAGTACT 59.108 36.000 0.00 0.00 32.61 2.73
1802 2153 6.144078 TCCAAGCTTTTTCTTTGGAAGTAC 57.856 37.500 0.00 0.00 32.61 2.73
1993 2362 8.782144 CAGCCCATTCTTAAGAGATCTATTTTC 58.218 37.037 8.09 0.00 0.00 2.29
1997 2366 7.237263 ACATCAGCCCATTCTTAAGAGATCTAT 59.763 37.037 5.12 0.00 0.00 1.98
2018 2387 3.198635 CCTTGCTTCCTCCTAGAACATCA 59.801 47.826 0.00 0.00 0.00 3.07
2075 2445 6.605471 TGTCCACACAATAGACAATACTCT 57.395 37.500 0.00 0.00 37.58 3.24
2159 2533 5.812127 TCGAGGACATAATGAACAACATCTG 59.188 40.000 0.00 0.00 38.38 2.90
2160 2534 5.977635 TCGAGGACATAATGAACAACATCT 58.022 37.500 0.00 0.00 38.38 2.90
2161 2535 6.456988 GGTTCGAGGACATAATGAACAACATC 60.457 42.308 5.85 0.00 40.42 3.06
2170 2544 3.551890 CGACTTGGTTCGAGGACATAATG 59.448 47.826 0.00 0.00 41.78 1.90
2176 2550 0.313043 TGACGACTTGGTTCGAGGAC 59.687 55.000 0.00 0.00 41.78 3.85
2177 2551 1.034356 TTGACGACTTGGTTCGAGGA 58.966 50.000 0.00 0.00 41.78 3.71
2179 2553 2.198406 TGTTTGACGACTTGGTTCGAG 58.802 47.619 0.00 0.00 41.78 4.04
2181 2555 3.392769 TTTGTTTGACGACTTGGTTCG 57.607 42.857 0.00 0.00 44.87 3.95
2244 2618 4.148838 AGGCAACAAAATGCTACAGGTAA 58.851 39.130 0.00 0.00 45.68 2.85


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

AutoCloner maintained by Alex Coulton.