Multiple sequence alignment - TraesCS3D01G169400

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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 TraesCS3D01G169400 chr3D 100.000 2948 0 0 1 2948 147337016 147334069 0.000000e+00 5445.0
1 TraesCS3D01G169400 chr3D 98.439 1409 15 5 497 1900 149543743 149545149 0.000000e+00 2473.0
2 TraesCS3D01G169400 chr3D 98.369 1410 14 6 494 1900 149204582 149205985 0.000000e+00 2468.0
3 TraesCS3D01G169400 chr3D 96.862 733 13 5 2218 2948 149206018 149206742 0.000000e+00 1218.0
4 TraesCS3D01G169400 chr3D 97.180 461 12 1 14 474 149204143 149204602 0.000000e+00 778.0
5 TraesCS3D01G169400 chr3D 96.203 474 18 0 1 474 149543286 149543759 0.000000e+00 776.0
6 TraesCS3D01G169400 chr3D 97.458 236 5 1 2218 2453 149545183 149545417 4.580000e-108 401.0
7 TraesCS3D01G169400 chr3D 94.470 217 11 1 1891 2106 456103790 456103574 1.690000e-87 333.0
8 TraesCS3D01G169400 chr3D 86.220 254 12 11 2654 2887 149767851 149767601 1.360000e-63 254.0
9 TraesCS3D01G169400 chr3D 94.048 84 5 0 2584 2667 149768549 149768466 8.580000e-26 128.0
10 TraesCS3D01G169400 chr3A 94.027 1105 39 9 790 1894 166923254 166924331 0.000000e+00 1650.0
11 TraesCS3D01G169400 chr3A 90.329 1003 72 12 899 1886 159831904 159832896 0.000000e+00 1291.0
12 TraesCS3D01G169400 chr3A 86.770 257 11 11 2651 2887 181106999 181107252 6.260000e-67 265.0
13 TraesCS3D01G169400 chr3A 87.712 236 13 2 2218 2453 166924371 166924590 8.100000e-66 261.0
14 TraesCS3D01G169400 chr3A 92.857 84 6 0 2584 2667 181106313 181106396 3.990000e-24 122.0
15 TraesCS3D01G169400 chr3B 93.744 1023 51 4 864 1886 221912358 221913367 0.000000e+00 1522.0
16 TraesCS3D01G169400 chr3B 92.669 1023 66 5 864 1886 215385072 215386085 0.000000e+00 1465.0
17 TraesCS3D01G169400 chr3B 92.864 1023 50 8 864 1886 221979838 221980837 0.000000e+00 1463.0
18 TraesCS3D01G169400 chr3B 91.748 1030 66 6 864 1893 215104678 215105688 0.000000e+00 1413.0
19 TraesCS3D01G169400 chr3B 91.683 1022 48 9 868 1886 215572008 215572995 0.000000e+00 1382.0
20 TraesCS3D01G169400 chr3B 91.033 1026 67 8 864 1886 215310446 215311449 0.000000e+00 1362.0
21 TraesCS3D01G169400 chr3B 88.661 1023 67 15 864 1886 221457757 221458730 0.000000e+00 1201.0
22 TraesCS3D01G169400 chr3B 93.023 602 28 9 2297 2887 215573078 215573676 0.000000e+00 867.0
23 TraesCS3D01G169400 chr3B 84.310 478 52 15 16 471 215383982 215384458 2.080000e-121 446.0
24 TraesCS3D01G169400 chr3B 83.857 477 54 15 16 471 215308508 215308982 1.620000e-117 433.0
25 TraesCS3D01G169400 chr3B 83.716 479 53 7 16 471 221456683 221457159 2.100000e-116 429.0
26 TraesCS3D01G169400 chr3B 83.613 476 56 14 16 471 221978928 221979401 7.550000e-116 427.0
27 TraesCS3D01G169400 chr3B 90.184 326 25 5 1900 2219 641981826 641982150 4.540000e-113 418.0
28 TraesCS3D01G169400 chr3B 93.220 236 14 2 2218 2453 221750133 221750366 2.170000e-91 346.0
29 TraesCS3D01G169400 chr3B 86.349 315 29 11 2297 2607 221980920 221981224 6.090000e-87 331.0
30 TraesCS3D01G169400 chr3B 86.032 315 30 11 2297 2607 221913450 221913754 2.830000e-85 326.0
31 TraesCS3D01G169400 chr3B 91.525 236 17 3 2218 2453 215114812 215115044 3.670000e-84 322.0
32 TraesCS3D01G169400 chr3B 84.444 315 32 12 2297 2607 215386168 215386469 7.990000e-76 294.0
33 TraesCS3D01G169400 chr3B 91.139 158 13 1 314 471 221748577 221748733 2.300000e-51 213.0
34 TraesCS3D01G169400 chr3B 89.375 160 7 6 497 654 215571536 215571687 3.000000e-45 193.0
35 TraesCS3D01G169400 chr3B 89.024 164 7 8 494 654 221748716 221748871 3.000000e-45 193.0
36 TraesCS3D01G169400 chr3B 88.415 164 9 8 494 654 221457142 221457298 3.880000e-44 189.0
37 TraesCS3D01G169400 chr3B 88.485 165 8 7 494 654 221911904 221912061 3.880000e-44 189.0
38 TraesCS3D01G169400 chr3B 88.415 164 9 8 494 654 221979384 221979540 3.880000e-44 189.0
39 TraesCS3D01G169400 chr3B 88.415 164 8 8 494 654 215384441 215384596 1.400000e-43 187.0
40 TraesCS3D01G169400 chr3B 85.890 163 6 5 648 793 215571813 215571975 1.090000e-34 158.0
41 TraesCS3D01G169400 chr3B 86.928 153 2 7 648 786 221912177 221912325 3.930000e-34 156.0
42 TraesCS3D01G169400 chr3B 86.275 153 3 7 648 786 221979657 221979805 1.830000e-32 150.0
43 TraesCS3D01G169400 chr3B 94.624 93 4 1 648 739 215309240 215309332 3.060000e-30 143.0
44 TraesCS3D01G169400 chr3B 92.473 93 7 0 379 471 221911829 221911921 1.840000e-27 134.0
45 TraesCS3D01G169400 chr3B 95.946 74 2 1 816 888 221749108 221749181 5.160000e-23 119.0
46 TraesCS3D01G169400 chr3B 87.629 97 11 1 307 403 90168107 90168202 8.640000e-21 111.0
47 TraesCS3D01G169400 chr3B 93.421 76 4 1 648 722 221748991 221749066 8.640000e-21 111.0
48 TraesCS3D01G169400 chr3B 90.123 81 8 0 2374 2454 221981263 221981343 4.020000e-19 106.0
49 TraesCS3D01G169400 chr3B 90.123 81 7 1 2374 2454 215386508 215386587 1.450000e-18 104.0
50 TraesCS3D01G169400 chr3B 88.889 81 9 0 2374 2454 221913793 221913873 1.870000e-17 100.0
51 TraesCS3D01G169400 chr3B 87.654 81 10 0 2374 2454 221467156 221467236 8.700000e-16 95.3
52 TraesCS3D01G169400 chr6D 90.991 333 18 8 1900 2220 427750502 427750834 3.490000e-119 438.0
53 TraesCS3D01G169400 chr6D 96.135 207 8 0 1900 2106 30010308 30010102 3.640000e-89 339.0
54 TraesCS3D01G169400 chr6D 97.321 112 3 0 2111 2222 461429015 461429126 1.080000e-44 191.0
55 TraesCS3D01G169400 chr4D 95.305 213 9 1 1898 2110 479368631 479368420 1.310000e-88 337.0
56 TraesCS3D01G169400 chr4D 95.763 118 4 1 2111 2227 378490320 378490203 3.880000e-44 189.0
57 TraesCS3D01G169400 chr2D 95.694 209 9 0 1898 2106 638443946 638443738 1.310000e-88 337.0
58 TraesCS3D01G169400 chr2D 94.860 214 10 1 1897 2110 335144308 335144520 1.690000e-87 333.0
59 TraesCS3D01G169400 chr2D 94.836 213 10 1 1898 2110 645056031 645055820 6.090000e-87 331.0
60 TraesCS3D01G169400 chr2D 97.297 111 3 0 2111 2221 645055775 645055665 3.880000e-44 189.0
61 TraesCS3D01G169400 chr5D 95.261 211 10 0 1896 2106 255469899 255469689 4.710000e-88 335.0
62 TraesCS3D01G169400 chr5D 95.726 117 5 0 2111 2227 268929687 268929571 3.880000e-44 189.0
63 TraesCS3D01G169400 chr5D 97.297 111 3 0 2111 2221 522063489 522063599 3.880000e-44 189.0
64 TraesCS3D01G169400 chr1D 92.208 231 16 2 1894 2122 468804445 468804675 2.830000e-85 326.0
65 TraesCS3D01G169400 chr1D 93.496 123 7 1 2111 2233 461047687 461047808 6.490000e-42 182.0
66 TraesCS3D01G169400 chr7D 97.297 111 3 0 2111 2221 28783389 28783279 3.880000e-44 189.0
67 TraesCS3D01G169400 chr5A 78.279 244 43 5 205 438 10540656 10540899 6.580000e-32 148.0
68 TraesCS3D01G169400 chr4B 82.456 114 17 3 307 419 2688924 2689035 2.420000e-16 97.1
69 TraesCS3D01G169400 chr1A 86.957 69 8 1 307 374 577568783 577568851 3.150000e-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 TraesCS3D01G169400 chr3D 147334069 147337016 2947 True 5445.000000 5445 100.000000 1 2948 1 chr3D.!!$R1 2947
1 TraesCS3D01G169400 chr3D 149204143 149206742 2599 False 1488.000000 2468 97.470333 14 2948 3 chr3D.!!$F1 2934
2 TraesCS3D01G169400 chr3D 149543286 149545417 2131 False 1216.666667 2473 97.366667 1 2453 3 chr3D.!!$F2 2452
3 TraesCS3D01G169400 chr3A 159831904 159832896 992 False 1291.000000 1291 90.329000 899 1886 1 chr3A.!!$F1 987
4 TraesCS3D01G169400 chr3A 166923254 166924590 1336 False 955.500000 1650 90.869500 790 2453 2 chr3A.!!$F2 1663
5 TraesCS3D01G169400 chr3B 215104678 215105688 1010 False 1413.000000 1413 91.748000 864 1893 1 chr3B.!!$F2 1029
6 TraesCS3D01G169400 chr3B 215571536 215573676 2140 False 650.000000 1382 89.992750 497 2887 4 chr3B.!!$F8 2390
7 TraesCS3D01G169400 chr3B 215308508 215311449 2941 False 646.000000 1362 89.838000 16 1886 3 chr3B.!!$F6 1870
8 TraesCS3D01G169400 chr3B 221456683 221458730 2047 False 606.333333 1201 86.930667 16 1886 3 chr3B.!!$F9 1870
9 TraesCS3D01G169400 chr3B 215383982 215386587 2605 False 499.200000 1465 87.992200 16 2607 5 chr3B.!!$F7 2591
10 TraesCS3D01G169400 chr3B 221978928 221981343 2415 False 444.333333 1463 87.939833 16 2607 6 chr3B.!!$F12 2591
11 TraesCS3D01G169400 chr3B 221911829 221913873 2044 False 404.500000 1522 89.425167 379 2607 6 chr3B.!!$F11 2228

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
508 534 1.25084 GCAGGGAAATGCCGAGGTTT 61.251 55.0 0.0 0.0 40.43 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 3658 0.031449 TTCTGATCACACGTGTGCGA 59.969 50.0 37.7 27.03 45.25 5.1 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
78 80 3.567670 AAAATGCAAAGAAAACACGCG 57.432 38.095 3.53 3.53 0.00 6.01
80 82 1.268113 ATGCAAAGAAAACACGCGCG 61.268 50.000 30.96 30.96 0.00 6.86
477 503 7.923414 GGAGAATGCCGAGGTTTATTATTAT 57.077 36.000 0.00 0.00 0.00 1.28
478 504 8.336801 GGAGAATGCCGAGGTTTATTATTATT 57.663 34.615 0.00 0.00 0.00 1.40
479 505 9.444600 GGAGAATGCCGAGGTTTATTATTATTA 57.555 33.333 0.00 0.00 0.00 0.98
502 528 3.603144 TTTTTGCAGGGAAATGCCG 57.397 47.368 0.00 0.00 45.91 5.69
507 533 1.678970 GCAGGGAAATGCCGAGGTT 60.679 57.895 0.00 0.00 40.43 3.50
508 534 1.250840 GCAGGGAAATGCCGAGGTTT 61.251 55.000 0.00 0.00 40.43 3.27
509 535 1.953311 GCAGGGAAATGCCGAGGTTTA 60.953 52.381 0.00 0.00 40.43 2.01
1194 2780 1.012486 GCAGGTACGTTCGTCCCAAG 61.012 60.000 9.39 3.14 0.00 3.61
1260 2846 3.054503 CAGGAGGACGTCGACGGT 61.055 66.667 37.89 24.74 44.95 4.83
1894 3495 1.098869 GAGCAGAGGAGACGTGATGA 58.901 55.000 0.00 0.00 0.00 2.92
1908 3509 2.336667 GTGATGAACGGGGCAAATTTG 58.663 47.619 14.03 14.03 0.00 2.32
1909 3510 2.029470 GTGATGAACGGGGCAAATTTGA 60.029 45.455 22.31 0.00 0.00 2.69
1910 3511 2.029470 TGATGAACGGGGCAAATTTGAC 60.029 45.455 22.31 19.34 34.70 3.18
1911 3512 1.403814 TGAACGGGGCAAATTTGACA 58.596 45.000 25.05 0.55 38.18 3.58
1912 3513 1.757118 TGAACGGGGCAAATTTGACAA 59.243 42.857 25.05 0.95 38.18 3.18
1913 3514 2.168521 TGAACGGGGCAAATTTGACAAA 59.831 40.909 25.05 2.48 38.18 2.83
1914 3515 3.181461 TGAACGGGGCAAATTTGACAAAT 60.181 39.130 25.05 7.62 38.18 2.32
1915 3516 3.483808 ACGGGGCAAATTTGACAAATT 57.516 38.095 25.05 18.41 42.62 1.82
1928 3529 9.559958 AAATTTGACAAATTTGAGCTATAGACG 57.440 29.630 29.31 0.00 46.30 4.18
1929 3530 7.899178 TTTGACAAATTTGAGCTATAGACGA 57.101 32.000 24.64 0.00 0.00 4.20
1930 3531 7.899178 TTGACAAATTTGAGCTATAGACGAA 57.101 32.000 24.64 3.47 0.00 3.85
1931 3532 7.899178 TGACAAATTTGAGCTATAGACGAAA 57.101 32.000 24.64 0.00 0.00 3.46
1932 3533 8.492673 TGACAAATTTGAGCTATAGACGAAAT 57.507 30.769 24.64 1.17 0.00 2.17
1933 3534 8.604035 TGACAAATTTGAGCTATAGACGAAATC 58.396 33.333 24.64 6.30 0.00 2.17
1934 3535 8.492673 ACAAATTTGAGCTATAGACGAAATCA 57.507 30.769 24.64 0.00 0.00 2.57
1935 3536 8.946085 ACAAATTTGAGCTATAGACGAAATCAA 58.054 29.630 24.64 1.12 0.00 2.57
1936 3537 9.773328 CAAATTTGAGCTATAGACGAAATCAAA 57.227 29.630 13.08 9.32 38.92 2.69
1939 3540 8.716646 TTTGAGCTATAGACGAAATCAAATCA 57.283 30.769 3.21 0.00 32.07 2.57
1940 3541 7.700322 TGAGCTATAGACGAAATCAAATCAC 57.300 36.000 3.21 0.00 0.00 3.06
1941 3542 7.264947 TGAGCTATAGACGAAATCAAATCACA 58.735 34.615 3.21 0.00 0.00 3.58
1942 3543 7.436376 TGAGCTATAGACGAAATCAAATCACAG 59.564 37.037 3.21 0.00 0.00 3.66
1943 3544 7.492524 AGCTATAGACGAAATCAAATCACAGA 58.507 34.615 3.21 0.00 0.00 3.41
1944 3545 7.981789 AGCTATAGACGAAATCAAATCACAGAA 59.018 33.333 3.21 0.00 0.00 3.02
1945 3546 8.768955 GCTATAGACGAAATCAAATCACAGAAT 58.231 33.333 3.21 0.00 0.00 2.40
1947 3548 8.722480 ATAGACGAAATCAAATCACAGAATGA 57.278 30.769 0.00 0.00 43.13 2.57
1948 3549 7.439157 AGACGAAATCAAATCACAGAATGAA 57.561 32.000 0.00 0.00 41.93 2.57
1949 3550 7.301054 AGACGAAATCAAATCACAGAATGAAC 58.699 34.615 0.00 0.00 41.93 3.18
1950 3551 7.173907 AGACGAAATCAAATCACAGAATGAACT 59.826 33.333 0.00 0.00 41.93 3.01
1951 3552 8.322906 ACGAAATCAAATCACAGAATGAACTA 57.677 30.769 0.00 0.00 41.93 2.24
1952 3553 8.950210 ACGAAATCAAATCACAGAATGAACTAT 58.050 29.630 0.00 0.00 41.93 2.12
1953 3554 9.430838 CGAAATCAAATCACAGAATGAACTATC 57.569 33.333 0.00 0.00 41.93 2.08
1954 3555 9.727627 GAAATCAAATCACAGAATGAACTATCC 57.272 33.333 0.00 0.00 41.93 2.59
1955 3556 6.908870 TCAAATCACAGAATGAACTATCCG 57.091 37.500 0.00 0.00 41.93 4.18
1956 3557 6.406370 TCAAATCACAGAATGAACTATCCGT 58.594 36.000 0.00 0.00 41.93 4.69
1957 3558 7.552459 TCAAATCACAGAATGAACTATCCGTA 58.448 34.615 0.00 0.00 41.93 4.02
1958 3559 8.038351 TCAAATCACAGAATGAACTATCCGTAA 58.962 33.333 0.00 0.00 41.93 3.18
1959 3560 8.664798 CAAATCACAGAATGAACTATCCGTAAA 58.335 33.333 0.00 0.00 41.93 2.01
1960 3561 8.786826 AATCACAGAATGAACTATCCGTAAAA 57.213 30.769 0.00 0.00 41.93 1.52
1961 3562 7.591006 TCACAGAATGAACTATCCGTAAAAC 57.409 36.000 0.00 0.00 39.69 2.43
1962 3563 7.383687 TCACAGAATGAACTATCCGTAAAACT 58.616 34.615 0.00 0.00 39.69 2.66
1963 3564 8.525316 TCACAGAATGAACTATCCGTAAAACTA 58.475 33.333 0.00 0.00 39.69 2.24
1964 3565 9.314321 CACAGAATGAACTATCCGTAAAACTAT 57.686 33.333 0.00 0.00 39.69 2.12
1965 3566 9.886132 ACAGAATGAACTATCCGTAAAACTATT 57.114 29.630 0.00 0.00 39.69 1.73
1970 3571 8.176814 TGAACTATCCGTAAAACTATTTCACG 57.823 34.615 0.00 0.00 0.00 4.35
1971 3572 6.579491 ACTATCCGTAAAACTATTTCACGC 57.421 37.500 0.00 0.00 30.82 5.34
1972 3573 3.976468 TCCGTAAAACTATTTCACGCG 57.024 42.857 3.53 3.53 30.82 6.01
1973 3574 2.667481 TCCGTAAAACTATTTCACGCGG 59.333 45.455 12.47 0.00 34.24 6.46
1974 3575 2.424341 CGTAAAACTATTTCACGCGGC 58.576 47.619 12.47 0.00 0.00 6.53
1975 3576 2.093152 CGTAAAACTATTTCACGCGGCT 59.907 45.455 12.47 0.00 0.00 5.52
1976 3577 2.611974 AAAACTATTTCACGCGGCTG 57.388 45.000 12.47 0.00 0.00 4.85
1977 3578 1.803334 AAACTATTTCACGCGGCTGA 58.197 45.000 12.47 2.44 0.00 4.26
1978 3579 1.076332 AACTATTTCACGCGGCTGAC 58.924 50.000 12.47 0.00 0.00 3.51
1979 3580 0.246635 ACTATTTCACGCGGCTGACT 59.753 50.000 12.47 0.00 0.00 3.41
1980 3581 1.337823 ACTATTTCACGCGGCTGACTT 60.338 47.619 12.47 0.00 0.00 3.01
1981 3582 1.732259 CTATTTCACGCGGCTGACTTT 59.268 47.619 12.47 0.00 0.00 2.66
1982 3583 0.951558 ATTTCACGCGGCTGACTTTT 59.048 45.000 12.47 0.00 0.00 2.27
1983 3584 0.736053 TTTCACGCGGCTGACTTTTT 59.264 45.000 12.47 0.00 0.00 1.94
1997 3598 4.220413 TTTTTGTGTGACGCCCGA 57.780 50.000 0.00 0.00 0.00 5.14
1998 3599 1.722677 TTTTTGTGTGACGCCCGAC 59.277 52.632 0.00 0.00 0.00 4.79
1999 3600 1.025113 TTTTTGTGTGACGCCCGACA 61.025 50.000 0.00 0.00 0.00 4.35
2000 3601 1.707239 TTTTGTGTGACGCCCGACAC 61.707 55.000 14.47 14.47 42.40 3.67
2001 3602 4.934942 TGTGTGACGCCCGACACG 62.935 66.667 15.80 0.00 44.55 4.49
2002 3603 4.634133 GTGTGACGCCCGACACGA 62.634 66.667 15.80 5.46 42.06 4.35
2003 3604 3.902086 TGTGACGCCCGACACGAA 61.902 61.111 15.80 0.31 42.06 3.85
2004 3605 3.103911 GTGACGCCCGACACGAAG 61.104 66.667 7.43 0.00 32.16 3.79
2005 3606 4.351938 TGACGCCCGACACGAAGG 62.352 66.667 0.00 0.00 0.00 3.46
2013 3614 3.712881 GACACGAAGGCGCCACAC 61.713 66.667 31.54 17.81 42.48 3.82
2014 3615 4.235762 ACACGAAGGCGCCACACT 62.236 61.111 31.54 9.96 42.48 3.55
2015 3616 2.048597 CACGAAGGCGCCACACTA 60.049 61.111 31.54 0.00 42.48 2.74
2016 3617 2.048503 ACGAAGGCGCCACACTAC 60.049 61.111 31.54 11.50 42.48 2.73
2017 3618 2.048597 CGAAGGCGCCACACTACA 60.049 61.111 31.54 0.00 0.00 2.74
2018 3619 2.380410 CGAAGGCGCCACACTACAC 61.380 63.158 31.54 8.98 0.00 2.90
2019 3620 1.004918 GAAGGCGCCACACTACACT 60.005 57.895 31.54 0.00 0.00 3.55
2020 3621 1.291877 GAAGGCGCCACACTACACTG 61.292 60.000 31.54 0.00 0.00 3.66
2021 3622 2.030562 GGCGCCACACTACACTGT 59.969 61.111 24.80 0.00 0.00 3.55
2022 3623 2.317609 GGCGCCACACTACACTGTG 61.318 63.158 24.80 6.19 41.19 3.66
2023 3624 2.954753 GCGCCACACTACACTGTGC 61.955 63.158 7.90 0.00 40.33 4.57
2024 3625 1.594021 CGCCACACTACACTGTGCA 60.594 57.895 7.90 0.00 40.33 4.57
2025 3626 1.157257 CGCCACACTACACTGTGCAA 61.157 55.000 7.90 0.00 40.33 4.08
2026 3627 1.238439 GCCACACTACACTGTGCAAT 58.762 50.000 7.90 0.00 40.33 3.56
2027 3628 1.069022 GCCACACTACACTGTGCAATG 60.069 52.381 7.90 6.00 40.33 2.82
2028 3629 1.069022 CCACACTACACTGTGCAATGC 60.069 52.381 7.90 0.00 40.33 3.56
2029 3630 1.069022 CACACTACACTGTGCAATGCC 60.069 52.381 7.90 0.00 41.30 4.40
2030 3631 1.202806 ACACTACACTGTGCAATGCCT 60.203 47.619 7.90 0.00 41.30 4.75
2031 3632 1.466167 CACTACACTGTGCAATGCCTC 59.534 52.381 7.90 0.00 0.00 4.70
2032 3633 1.072173 ACTACACTGTGCAATGCCTCA 59.928 47.619 7.90 1.21 0.00 3.86
2033 3634 1.466167 CTACACTGTGCAATGCCTCAC 59.534 52.381 7.90 0.00 0.00 3.51
2034 3635 0.466007 ACACTGTGCAATGCCTCACA 60.466 50.000 7.90 0.00 40.50 3.58
2037 3638 3.656457 TGTGCAATGCCTCACAGAT 57.344 47.368 1.53 0.00 38.18 2.90
2038 3639 2.785540 TGTGCAATGCCTCACAGATA 57.214 45.000 1.53 0.00 38.18 1.98
2039 3640 2.635714 TGTGCAATGCCTCACAGATAG 58.364 47.619 1.53 0.00 38.18 2.08
2040 3641 1.945394 GTGCAATGCCTCACAGATAGG 59.055 52.381 1.53 0.00 37.17 2.57
2046 3647 3.875838 CCTCACAGATAGGCGCTAC 57.124 57.895 7.64 0.00 0.00 3.58
2047 3648 1.032794 CCTCACAGATAGGCGCTACA 58.967 55.000 7.64 0.00 0.00 2.74
2048 3649 1.269309 CCTCACAGATAGGCGCTACAC 60.269 57.143 7.64 0.00 0.00 2.90
2089 3690 7.870954 ACGTGTGATCAGAAAATTACTAAGTCA 59.129 33.333 0.00 0.00 0.00 3.41
2091 3692 9.209175 GTGTGATCAGAAAATTACTAAGTCAGT 57.791 33.333 0.00 0.00 41.62 3.41
2096 3697 9.890629 ATCAGAAAATTACTAAGTCAGTATGCA 57.109 29.630 0.00 0.00 39.51 3.96
2099 3700 6.589830 AAATTACTAAGTCAGTATGCAGCG 57.410 37.500 0.00 0.00 39.51 5.18
2100 3701 4.713824 TTACTAAGTCAGTATGCAGCGT 57.286 40.909 0.00 0.00 39.51 5.07
2104 3705 1.177401 AGTCAGTATGCAGCGTCTGA 58.823 50.000 10.46 10.87 34.76 3.27
2107 3708 2.561547 TCAGTATGCAGCGTCTGAGCT 61.562 52.381 10.46 0.00 41.62 4.09
2113 3714 2.969016 AGCGTCTGAGCTCCAGTG 59.031 61.111 12.15 7.36 45.67 3.66
2114 3715 2.813042 GCGTCTGAGCTCCAGTGC 60.813 66.667 12.15 12.64 43.38 4.40
2115 3716 2.653115 CGTCTGAGCTCCAGTGCA 59.347 61.111 12.15 0.00 43.38 4.57
2116 3717 1.445754 CGTCTGAGCTCCAGTGCAG 60.446 63.158 12.15 0.88 43.38 4.41
2117 3718 1.741032 GTCTGAGCTCCAGTGCAGC 60.741 63.158 12.15 0.00 43.38 5.25
2118 3719 2.814341 CTGAGCTCCAGTGCAGCG 60.814 66.667 12.15 0.00 42.14 5.18
2123 3724 4.383861 CTCCAGTGCAGCGCCTGA 62.384 66.667 12.27 4.47 32.44 3.86
2124 3725 4.383861 TCCAGTGCAGCGCCTGAG 62.384 66.667 12.27 3.90 32.44 3.35
2125 3726 4.383861 CCAGTGCAGCGCCTGAGA 62.384 66.667 12.27 0.00 32.44 3.27
2126 3727 2.814341 CAGTGCAGCGCCTGAGAG 60.814 66.667 2.29 0.00 32.44 3.20
2127 3728 4.756458 AGTGCAGCGCCTGAGAGC 62.756 66.667 2.29 0.00 39.42 4.09
2136 3737 3.150335 CCTGAGAGCTAGGCGCCA 61.150 66.667 31.54 14.00 40.39 5.69
2137 3738 2.105930 CTGAGAGCTAGGCGCCAC 59.894 66.667 31.54 17.93 40.39 5.01
2138 3739 2.679996 TGAGAGCTAGGCGCCACA 60.680 61.111 31.54 15.42 40.39 4.17
2139 3740 2.025767 CTGAGAGCTAGGCGCCACAT 62.026 60.000 31.54 11.17 40.39 3.21
2140 3741 1.593750 GAGAGCTAGGCGCCACATG 60.594 63.158 31.54 16.03 40.39 3.21
2141 3742 2.187946 GAGCTAGGCGCCACATGT 59.812 61.111 31.54 10.27 40.39 3.21
2142 3743 1.884926 GAGCTAGGCGCCACATGTC 60.885 63.158 31.54 14.49 40.39 3.06
2143 3744 2.125147 GCTAGGCGCCACATGTCA 60.125 61.111 31.54 2.99 0.00 3.58
2144 3745 2.176273 GCTAGGCGCCACATGTCAG 61.176 63.158 31.54 13.82 0.00 3.51
2145 3746 2.125147 TAGGCGCCACATGTCAGC 60.125 61.111 31.54 0.59 0.00 4.26
2151 3752 3.792047 CCACATGTCAGCCGCGTG 61.792 66.667 4.92 0.00 0.00 5.34
2152 3753 2.738139 CACATGTCAGCCGCGTGA 60.738 61.111 4.92 0.00 0.00 4.35
2153 3754 2.030412 ACATGTCAGCCGCGTGAA 59.970 55.556 4.92 0.00 0.00 3.18
2154 3755 1.596752 ACATGTCAGCCGCGTGAAA 60.597 52.632 4.92 0.00 0.00 2.69
2155 3756 0.955428 ACATGTCAGCCGCGTGAAAT 60.955 50.000 4.92 0.19 0.00 2.17
2156 3757 1.006086 CATGTCAGCCGCGTGAAATA 58.994 50.000 4.92 0.00 0.00 1.40
2157 3758 1.004610 CATGTCAGCCGCGTGAAATAG 60.005 52.381 4.92 0.00 0.00 1.73
2158 3759 0.037697 TGTCAGCCGCGTGAAATAGT 60.038 50.000 4.92 0.00 0.00 2.12
2159 3760 1.076332 GTCAGCCGCGTGAAATAGTT 58.924 50.000 4.92 0.00 0.00 2.24
2160 3761 1.463444 GTCAGCCGCGTGAAATAGTTT 59.537 47.619 4.92 0.00 0.00 2.66
2161 3762 1.730064 TCAGCCGCGTGAAATAGTTTC 59.270 47.619 4.92 0.00 40.08 2.78
2162 3763 1.463056 CAGCCGCGTGAAATAGTTTCA 59.537 47.619 4.92 1.24 46.68 2.69
2175 3776 8.408043 TGAAATAGTTTCATGGACAGTTCATT 57.592 30.769 0.00 0.00 44.21 2.57
2176 3777 8.514594 TGAAATAGTTTCATGGACAGTTCATTC 58.485 33.333 0.00 0.00 44.21 2.67
2177 3778 8.641498 AAATAGTTTCATGGACAGTTCATTCT 57.359 30.769 0.00 0.00 0.00 2.40
2178 3779 5.954296 AGTTTCATGGACAGTTCATTCTG 57.046 39.130 0.00 0.00 40.80 3.02
2180 3781 5.240183 AGTTTCATGGACAGTTCATTCTGTG 59.760 40.000 4.06 0.00 46.81 3.66
2181 3782 4.622260 TCATGGACAGTTCATTCTGTGA 57.378 40.909 4.06 0.00 46.81 3.58
2182 3783 5.169992 TCATGGACAGTTCATTCTGTGAT 57.830 39.130 4.06 0.00 46.81 3.06
2183 3784 5.563592 TCATGGACAGTTCATTCTGTGATT 58.436 37.500 4.06 0.00 46.81 2.57
2184 3785 6.005823 TCATGGACAGTTCATTCTGTGATTT 58.994 36.000 4.06 0.00 46.81 2.17
2185 3786 5.694231 TGGACAGTTCATTCTGTGATTTG 57.306 39.130 4.06 0.00 46.81 2.32
2186 3787 5.375773 TGGACAGTTCATTCTGTGATTTGA 58.624 37.500 4.06 0.00 46.81 2.69
2187 3788 6.005823 TGGACAGTTCATTCTGTGATTTGAT 58.994 36.000 4.06 0.00 46.81 2.57
2188 3789 6.491062 TGGACAGTTCATTCTGTGATTTGATT 59.509 34.615 4.06 0.00 46.81 2.57
2189 3790 7.014518 TGGACAGTTCATTCTGTGATTTGATTT 59.985 33.333 4.06 0.00 46.81 2.17
2190 3791 7.540055 GGACAGTTCATTCTGTGATTTGATTTC 59.460 37.037 4.06 0.00 46.81 2.17
2191 3792 7.080099 ACAGTTCATTCTGTGATTTGATTTCG 58.920 34.615 0.00 0.00 45.40 3.46
2192 3793 7.080099 CAGTTCATTCTGTGATTTGATTTCGT 58.920 34.615 0.00 0.00 36.54 3.85
2193 3794 7.269937 CAGTTCATTCTGTGATTTGATTTCGTC 59.730 37.037 0.00 0.00 36.54 4.20
2194 3795 7.173907 AGTTCATTCTGTGATTTGATTTCGTCT 59.826 33.333 0.00 0.00 36.54 4.18
2195 3796 8.443160 GTTCATTCTGTGATTTGATTTCGTCTA 58.557 33.333 0.00 0.00 36.54 2.59
2196 3797 8.722480 TCATTCTGTGATTTGATTTCGTCTAT 57.278 30.769 0.00 0.00 0.00 1.98
2197 3798 9.816354 TCATTCTGTGATTTGATTTCGTCTATA 57.184 29.630 0.00 0.00 0.00 1.31
2199 3800 8.648557 TTCTGTGATTTGATTTCGTCTATAGG 57.351 34.615 0.00 0.00 0.00 2.57
2200 3801 7.782049 TCTGTGATTTGATTTCGTCTATAGGT 58.218 34.615 0.00 0.00 0.00 3.08
2201 3802 7.921214 TCTGTGATTTGATTTCGTCTATAGGTC 59.079 37.037 0.00 0.00 0.00 3.85
2202 3803 7.552459 TGTGATTTGATTTCGTCTATAGGTCA 58.448 34.615 0.00 0.00 0.00 4.02
2203 3804 8.038351 TGTGATTTGATTTCGTCTATAGGTCAA 58.962 33.333 0.00 0.00 0.00 3.18
2204 3805 8.879759 GTGATTTGATTTCGTCTATAGGTCAAA 58.120 33.333 0.00 7.93 38.14 2.69
2205 3806 9.613428 TGATTTGATTTCGTCTATAGGTCAAAT 57.387 29.630 17.06 17.06 43.48 2.32
2209 3810 8.786826 TGATTTCGTCTATAGGTCAAATTTGT 57.213 30.769 17.47 1.67 0.00 2.83
2210 3811 8.879759 TGATTTCGTCTATAGGTCAAATTTGTC 58.120 33.333 17.47 12.07 0.00 3.18
2211 3812 8.786826 ATTTCGTCTATAGGTCAAATTTGTCA 57.213 30.769 17.47 0.00 0.00 3.58
2212 3813 8.610248 TTTCGTCTATAGGTCAAATTTGTCAA 57.390 30.769 17.47 5.31 0.00 3.18
2213 3814 8.610248 TTCGTCTATAGGTCAAATTTGTCAAA 57.390 30.769 17.47 0.00 0.00 2.69
2214 3815 8.786826 TCGTCTATAGGTCAAATTTGTCAAAT 57.213 30.769 17.47 4.91 0.00 2.32
2215 3816 9.226606 TCGTCTATAGGTCAAATTTGTCAAATT 57.773 29.630 16.26 16.26 42.62 1.82
2347 3948 2.632028 TCCTAGCCATCAGAATCAGAGC 59.368 50.000 0.00 0.00 0.00 4.09
2506 4108 2.740055 GCACTGAGCACGACCAGG 60.740 66.667 0.00 0.00 44.79 4.45
2854 4522 4.320057 CCTGAGACAACAGCAAATTCAGAC 60.320 45.833 0.50 0.00 36.67 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 80 0.596341 ATGAACCGGTTTTTGTGCGC 60.596 50.000 23.22 6.35 0.00 6.09
80 82 1.864082 CCAATGAACCGGTTTTTGTGC 59.136 47.619 28.04 15.59 0.00 4.57
185 190 0.253044 ACGCTAGGCCAATCACATGT 59.747 50.000 5.01 0.00 0.00 3.21
409 435 3.645268 AATCACGAGCCCAAGCCCC 62.645 63.158 0.00 0.00 41.25 5.80
484 510 1.000731 CTCGGCATTTCCCTGCAAAAA 59.999 47.619 0.00 0.00 44.12 1.94
485 511 0.602562 CTCGGCATTTCCCTGCAAAA 59.397 50.000 0.00 0.00 44.12 2.44
486 512 1.250154 CCTCGGCATTTCCCTGCAAA 61.250 55.000 0.00 0.00 44.12 3.68
487 513 1.678635 CCTCGGCATTTCCCTGCAA 60.679 57.895 0.00 0.00 44.12 4.08
488 514 2.045045 CCTCGGCATTTCCCTGCA 60.045 61.111 0.00 0.00 44.12 4.41
489 515 1.250840 AAACCTCGGCATTTCCCTGC 61.251 55.000 0.00 0.00 41.53 4.85
490 516 2.122783 TAAACCTCGGCATTTCCCTG 57.877 50.000 0.00 0.00 0.00 4.45
491 517 3.382083 AATAAACCTCGGCATTTCCCT 57.618 42.857 0.00 0.00 0.00 4.20
492 518 3.004419 GCTAATAAACCTCGGCATTTCCC 59.996 47.826 0.00 0.00 0.00 3.97
493 519 3.004419 GGCTAATAAACCTCGGCATTTCC 59.996 47.826 0.00 0.00 0.00 3.13
494 520 3.883489 AGGCTAATAAACCTCGGCATTTC 59.117 43.478 0.00 0.00 0.00 2.17
495 521 3.898482 AGGCTAATAAACCTCGGCATTT 58.102 40.909 0.00 0.00 0.00 2.32
502 528 4.317671 TGTCGCTAGGCTAATAAACCTC 57.682 45.455 0.00 0.00 37.50 3.85
507 533 4.583073 TGACTGATGTCGCTAGGCTAATAA 59.417 41.667 0.00 0.00 45.70 1.40
508 534 4.142038 TGACTGATGTCGCTAGGCTAATA 58.858 43.478 0.00 0.00 45.70 0.98
509 535 2.959030 TGACTGATGTCGCTAGGCTAAT 59.041 45.455 0.00 0.00 45.70 1.73
1260 2846 2.044352 TCGCCGAGATCCACTCCA 60.044 61.111 0.00 0.00 42.18 3.86
1295 2881 2.256461 CTGCCTTCAACCAAGCGC 59.744 61.111 0.00 0.00 0.00 5.92
1894 3495 2.990066 TTTGTCAAATTTGCCCCGTT 57.010 40.000 13.54 0.00 0.00 4.44
1903 3504 8.946085 TCGTCTATAGCTCAAATTTGTCAAATT 58.054 29.630 16.26 16.26 42.62 1.82
1904 3505 8.492673 TCGTCTATAGCTCAAATTTGTCAAAT 57.507 30.769 17.47 4.91 0.00 2.32
1905 3506 7.899178 TCGTCTATAGCTCAAATTTGTCAAA 57.101 32.000 17.47 0.00 0.00 2.69
1908 3509 8.604035 TGATTTCGTCTATAGCTCAAATTTGTC 58.396 33.333 17.47 10.77 0.00 3.18
1909 3510 8.492673 TGATTTCGTCTATAGCTCAAATTTGT 57.507 30.769 17.47 1.67 0.00 2.83
1910 3511 9.773328 TTTGATTTCGTCTATAGCTCAAATTTG 57.227 29.630 12.15 12.15 0.00 2.32
1913 3514 9.330063 TGATTTGATTTCGTCTATAGCTCAAAT 57.670 29.630 14.59 14.59 41.80 2.32
1914 3515 8.604035 GTGATTTGATTTCGTCTATAGCTCAAA 58.396 33.333 0.00 4.01 36.09 2.69
1915 3516 7.763985 TGTGATTTGATTTCGTCTATAGCTCAA 59.236 33.333 0.00 0.00 0.00 3.02
1916 3517 7.264947 TGTGATTTGATTTCGTCTATAGCTCA 58.735 34.615 0.00 0.00 0.00 4.26
1917 3518 7.649705 TCTGTGATTTGATTTCGTCTATAGCTC 59.350 37.037 0.00 0.00 0.00 4.09
1918 3519 7.492524 TCTGTGATTTGATTTCGTCTATAGCT 58.507 34.615 0.00 0.00 0.00 3.32
1919 3520 7.700322 TCTGTGATTTGATTTCGTCTATAGC 57.300 36.000 0.00 0.00 0.00 2.97
1921 3522 9.816354 TCATTCTGTGATTTGATTTCGTCTATA 57.184 29.630 0.00 0.00 0.00 1.31
1922 3523 8.722480 TCATTCTGTGATTTGATTTCGTCTAT 57.278 30.769 0.00 0.00 0.00 1.98
1923 3524 8.443160 GTTCATTCTGTGATTTGATTTCGTCTA 58.557 33.333 0.00 0.00 36.54 2.59
1924 3525 7.173907 AGTTCATTCTGTGATTTGATTTCGTCT 59.826 33.333 0.00 0.00 36.54 4.18
1925 3526 7.301054 AGTTCATTCTGTGATTTGATTTCGTC 58.699 34.615 0.00 0.00 36.54 4.20
1926 3527 7.206981 AGTTCATTCTGTGATTTGATTTCGT 57.793 32.000 0.00 0.00 36.54 3.85
1927 3528 9.430838 GATAGTTCATTCTGTGATTTGATTTCG 57.569 33.333 0.00 0.00 36.54 3.46
1928 3529 9.727627 GGATAGTTCATTCTGTGATTTGATTTC 57.272 33.333 0.00 0.00 36.54 2.17
1929 3530 8.400947 CGGATAGTTCATTCTGTGATTTGATTT 58.599 33.333 0.00 0.00 36.54 2.17
1930 3531 7.554118 ACGGATAGTTCATTCTGTGATTTGATT 59.446 33.333 0.00 0.00 36.54 2.57
1931 3532 7.050377 ACGGATAGTTCATTCTGTGATTTGAT 58.950 34.615 0.00 0.00 36.54 2.57
1932 3533 6.406370 ACGGATAGTTCATTCTGTGATTTGA 58.594 36.000 0.00 0.00 36.54 2.69
1933 3534 6.668541 ACGGATAGTTCATTCTGTGATTTG 57.331 37.500 0.00 0.00 36.54 2.32
1934 3535 8.786826 TTTACGGATAGTTCATTCTGTGATTT 57.213 30.769 0.00 0.00 36.54 2.17
1935 3536 8.665685 GTTTTACGGATAGTTCATTCTGTGATT 58.334 33.333 0.00 0.00 36.54 2.57
1936 3537 8.041323 AGTTTTACGGATAGTTCATTCTGTGAT 58.959 33.333 0.00 0.00 36.54 3.06
1937 3538 7.383687 AGTTTTACGGATAGTTCATTCTGTGA 58.616 34.615 0.00 0.00 33.60 3.58
1938 3539 7.596749 AGTTTTACGGATAGTTCATTCTGTG 57.403 36.000 0.00 0.00 33.60 3.66
1939 3540 9.886132 AATAGTTTTACGGATAGTTCATTCTGT 57.114 29.630 0.00 0.00 35.66 3.41
1944 3545 8.814235 CGTGAAATAGTTTTACGGATAGTTCAT 58.186 33.333 10.64 0.00 45.34 2.57
1945 3546 8.176814 CGTGAAATAGTTTTACGGATAGTTCA 57.823 34.615 10.64 0.00 45.34 3.18
1955 3556 3.123959 TCAGCCGCGTGAAATAGTTTTAC 59.876 43.478 4.92 0.00 0.00 2.01
1956 3557 3.123959 GTCAGCCGCGTGAAATAGTTTTA 59.876 43.478 4.92 0.00 0.00 1.52
1957 3558 2.095919 GTCAGCCGCGTGAAATAGTTTT 60.096 45.455 4.92 0.00 0.00 2.43
1958 3559 1.463444 GTCAGCCGCGTGAAATAGTTT 59.537 47.619 4.92 0.00 0.00 2.66
1959 3560 1.076332 GTCAGCCGCGTGAAATAGTT 58.924 50.000 4.92 0.00 0.00 2.24
1960 3561 0.246635 AGTCAGCCGCGTGAAATAGT 59.753 50.000 4.92 0.00 0.00 2.12
1961 3562 1.359848 AAGTCAGCCGCGTGAAATAG 58.640 50.000 4.92 0.00 0.00 1.73
1962 3563 1.803334 AAAGTCAGCCGCGTGAAATA 58.197 45.000 4.92 0.00 0.00 1.40
1963 3564 0.951558 AAAAGTCAGCCGCGTGAAAT 59.048 45.000 4.92 0.00 0.00 2.17
1964 3565 0.736053 AAAAAGTCAGCCGCGTGAAA 59.264 45.000 4.92 0.00 0.00 2.69
1965 3566 2.399856 AAAAAGTCAGCCGCGTGAA 58.600 47.368 4.92 0.00 0.00 3.18
1966 3567 4.134623 AAAAAGTCAGCCGCGTGA 57.865 50.000 4.92 0.00 0.00 4.35
1980 3581 1.025113 TGTCGGGCGTCACACAAAAA 61.025 50.000 0.00 0.00 0.00 1.94
1981 3582 1.449778 TGTCGGGCGTCACACAAAA 60.450 52.632 0.00 0.00 0.00 2.44
1982 3583 2.174969 GTGTCGGGCGTCACACAAA 61.175 57.895 5.81 0.00 42.20 2.83
1983 3584 2.586635 GTGTCGGGCGTCACACAA 60.587 61.111 5.81 0.00 42.20 3.33
1984 3585 4.934942 CGTGTCGGGCGTCACACA 62.935 66.667 10.72 0.00 42.67 3.72
1985 3586 4.634133 TCGTGTCGGGCGTCACAC 62.634 66.667 0.75 0.75 39.70 3.82
1986 3587 3.834447 CTTCGTGTCGGGCGTCACA 62.834 63.158 0.00 0.00 34.69 3.58
1987 3588 3.103911 CTTCGTGTCGGGCGTCAC 61.104 66.667 0.00 0.00 0.00 3.67
1988 3589 4.351938 CCTTCGTGTCGGGCGTCA 62.352 66.667 0.00 0.00 0.00 4.35
1996 3597 2.758770 TAGTGTGGCGCCTTCGTGTC 62.759 60.000 29.70 10.72 38.14 3.67
1997 3598 2.863346 TAGTGTGGCGCCTTCGTGT 61.863 57.895 29.70 9.85 38.14 4.49
1998 3599 2.048597 TAGTGTGGCGCCTTCGTG 60.049 61.111 29.70 0.00 38.14 4.35
1999 3600 2.048503 GTAGTGTGGCGCCTTCGT 60.049 61.111 29.70 12.53 38.14 3.85
2000 3601 2.048597 TGTAGTGTGGCGCCTTCG 60.049 61.111 29.70 0.00 39.07 3.79
2001 3602 1.004918 AGTGTAGTGTGGCGCCTTC 60.005 57.895 29.70 20.58 0.00 3.46
2002 3603 1.301716 CAGTGTAGTGTGGCGCCTT 60.302 57.895 29.70 13.03 0.00 4.35
2003 3604 2.343758 CAGTGTAGTGTGGCGCCT 59.656 61.111 29.70 9.99 0.00 5.52
2004 3605 2.030562 ACAGTGTAGTGTGGCGCC 59.969 61.111 22.73 22.73 0.00 6.53
2005 3606 2.954753 GCACAGTGTAGTGTGGCGC 61.955 63.158 18.52 0.00 46.73 6.53
2006 3607 1.157257 TTGCACAGTGTAGTGTGGCG 61.157 55.000 18.52 0.00 46.73 5.69
2007 3608 1.069022 CATTGCACAGTGTAGTGTGGC 60.069 52.381 18.52 12.34 46.73 5.01
2008 3609 1.069022 GCATTGCACAGTGTAGTGTGG 60.069 52.381 18.52 5.92 46.73 4.17
2010 3611 1.202806 AGGCATTGCACAGTGTAGTGT 60.203 47.619 14.25 0.00 41.52 3.55
2011 3612 1.466167 GAGGCATTGCACAGTGTAGTG 59.534 52.381 11.39 9.44 42.37 2.74
2012 3613 1.072173 TGAGGCATTGCACAGTGTAGT 59.928 47.619 11.39 0.00 0.00 2.73
2013 3614 1.466167 GTGAGGCATTGCACAGTGTAG 59.534 52.381 11.39 0.00 35.19 2.74
2014 3615 1.202746 TGTGAGGCATTGCACAGTGTA 60.203 47.619 11.39 0.00 39.86 2.90
2015 3616 0.466007 TGTGAGGCATTGCACAGTGT 60.466 50.000 11.39 0.00 39.86 3.55
2016 3617 2.333291 TGTGAGGCATTGCACAGTG 58.667 52.632 11.39 0.00 39.86 3.66
2017 3618 4.905240 TGTGAGGCATTGCACAGT 57.095 50.000 11.39 0.00 39.86 3.55
2019 3620 2.635714 CTATCTGTGAGGCATTGCACA 58.364 47.619 11.39 7.29 42.25 4.57
2020 3621 1.945394 CCTATCTGTGAGGCATTGCAC 59.055 52.381 11.39 4.64 35.63 4.57
2021 3622 2.336945 CCTATCTGTGAGGCATTGCA 57.663 50.000 11.39 0.00 0.00 4.08
2028 3629 1.032794 TGTAGCGCCTATCTGTGAGG 58.967 55.000 2.29 0.00 37.12 3.86
2029 3630 1.598183 CGTGTAGCGCCTATCTGTGAG 60.598 57.143 2.29 0.00 0.00 3.51
2030 3631 0.380733 CGTGTAGCGCCTATCTGTGA 59.619 55.000 2.29 0.00 0.00 3.58
2031 3632 0.380733 TCGTGTAGCGCCTATCTGTG 59.619 55.000 2.29 0.00 41.07 3.66
2032 3633 0.381089 GTCGTGTAGCGCCTATCTGT 59.619 55.000 2.29 0.00 41.07 3.41
2033 3634 0.317938 GGTCGTGTAGCGCCTATCTG 60.318 60.000 2.29 0.00 41.07 2.90
2034 3635 0.750546 TGGTCGTGTAGCGCCTATCT 60.751 55.000 2.29 0.00 41.07 1.98
2035 3636 0.317938 CTGGTCGTGTAGCGCCTATC 60.318 60.000 2.29 0.00 41.07 2.08
2036 3637 1.734137 CTGGTCGTGTAGCGCCTAT 59.266 57.895 2.29 0.00 41.07 2.57
2037 3638 3.060020 GCTGGTCGTGTAGCGCCTA 62.060 63.158 2.29 0.00 41.07 3.93
2038 3639 4.436998 GCTGGTCGTGTAGCGCCT 62.437 66.667 2.29 0.00 41.07 5.52
2056 3657 0.663269 TCTGATCACACGTGTGCGAC 60.663 55.000 37.70 29.00 45.25 5.19
2057 3658 0.031449 TTCTGATCACACGTGTGCGA 59.969 50.000 37.70 27.03 45.25 5.10
2058 3659 0.858583 TTTCTGATCACACGTGTGCG 59.141 50.000 37.70 25.53 45.25 5.34
2059 3660 3.542712 ATTTTCTGATCACACGTGTGC 57.457 42.857 37.70 26.75 45.25 4.57
2060 3661 6.228273 AGTAATTTTCTGATCACACGTGTG 57.772 37.500 37.04 37.04 46.91 3.82
2061 3662 7.656137 ACTTAGTAATTTTCTGATCACACGTGT 59.344 33.333 17.22 17.22 0.00 4.49
2062 3663 8.018677 ACTTAGTAATTTTCTGATCACACGTG 57.981 34.615 15.48 15.48 0.00 4.49
2063 3664 7.870954 TGACTTAGTAATTTTCTGATCACACGT 59.129 33.333 0.00 0.00 0.00 4.49
2064 3665 8.239681 TGACTTAGTAATTTTCTGATCACACG 57.760 34.615 0.00 0.00 0.00 4.49
2065 3666 9.209175 ACTGACTTAGTAATTTTCTGATCACAC 57.791 33.333 0.00 0.00 38.04 3.82
2070 3671 9.890629 TGCATACTGACTTAGTAATTTTCTGAT 57.109 29.630 0.00 0.00 44.64 2.90
2071 3672 9.371136 CTGCATACTGACTTAGTAATTTTCTGA 57.629 33.333 0.00 0.00 44.64 3.27
2072 3673 8.119226 GCTGCATACTGACTTAGTAATTTTCTG 58.881 37.037 0.00 0.00 44.64 3.02
2073 3674 7.010552 CGCTGCATACTGACTTAGTAATTTTCT 59.989 37.037 0.00 0.00 44.64 2.52
2074 3675 7.119997 CGCTGCATACTGACTTAGTAATTTTC 58.880 38.462 0.00 0.00 44.64 2.29
2075 3676 6.594159 ACGCTGCATACTGACTTAGTAATTTT 59.406 34.615 0.00 0.00 44.64 1.82
2076 3677 6.106673 ACGCTGCATACTGACTTAGTAATTT 58.893 36.000 0.00 0.00 44.64 1.82
2077 3678 5.661458 ACGCTGCATACTGACTTAGTAATT 58.339 37.500 0.00 0.00 44.64 1.40
2078 3679 5.067936 AGACGCTGCATACTGACTTAGTAAT 59.932 40.000 0.00 0.00 44.64 1.89
2079 3680 4.398358 AGACGCTGCATACTGACTTAGTAA 59.602 41.667 0.00 0.00 44.64 2.24
2080 3681 3.945921 AGACGCTGCATACTGACTTAGTA 59.054 43.478 0.00 0.00 45.50 1.82
2083 3684 2.752903 TCAGACGCTGCATACTGACTTA 59.247 45.455 13.51 0.00 35.01 2.24
2084 3685 1.546029 TCAGACGCTGCATACTGACTT 59.454 47.619 13.51 0.00 35.01 3.01
2089 3690 0.102120 GAGCTCAGACGCTGCATACT 59.898 55.000 9.40 0.00 41.08 2.12
2091 3692 1.439228 GGAGCTCAGACGCTGCATA 59.561 57.895 17.19 0.00 46.17 3.14
2096 3697 2.969016 CACTGGAGCTCAGACGCT 59.031 61.111 17.19 0.00 46.18 5.07
2099 3700 1.741032 GCTGCACTGGAGCTCAGAC 60.741 63.158 17.19 9.33 46.18 3.51
2100 3701 2.661399 GCTGCACTGGAGCTCAGA 59.339 61.111 17.19 0.00 46.18 3.27
2107 3708 4.383861 CTCAGGCGCTGCACTGGA 62.384 66.667 17.69 7.17 35.47 3.86
2110 3711 4.756458 GCTCTCAGGCGCTGCACT 62.756 66.667 7.64 0.00 0.00 4.40
2112 3713 3.070576 TAGCTCTCAGGCGCTGCA 61.071 61.111 7.64 0.00 37.05 4.41
2113 3714 2.279385 CTAGCTCTCAGGCGCTGC 60.279 66.667 7.64 2.66 37.05 5.25
2114 3715 2.416678 CCTAGCTCTCAGGCGCTG 59.583 66.667 7.64 3.67 37.05 5.18
2127 3728 2.176273 GCTGACATGTGGCGCCTAG 61.176 63.158 29.70 16.58 0.00 3.02
2128 3729 2.125147 GCTGACATGTGGCGCCTA 60.125 61.111 29.70 17.50 0.00 3.93
2134 3735 3.792047 CACGCGGCTGACATGTGG 61.792 66.667 12.47 0.00 0.00 4.17
2135 3736 1.840630 TTTCACGCGGCTGACATGTG 61.841 55.000 12.47 0.00 0.00 3.21
2136 3737 0.955428 ATTTCACGCGGCTGACATGT 60.955 50.000 12.47 0.00 0.00 3.21
2137 3738 1.004610 CTATTTCACGCGGCTGACATG 60.005 52.381 12.47 0.00 0.00 3.21
2138 3739 1.290203 CTATTTCACGCGGCTGACAT 58.710 50.000 12.47 7.33 0.00 3.06
2139 3740 0.037697 ACTATTTCACGCGGCTGACA 60.038 50.000 12.47 0.00 0.00 3.58
2140 3741 1.076332 AACTATTTCACGCGGCTGAC 58.924 50.000 12.47 0.00 0.00 3.51
2141 3742 1.730064 GAAACTATTTCACGCGGCTGA 59.270 47.619 12.47 2.44 39.45 4.26
2142 3743 1.463056 TGAAACTATTTCACGCGGCTG 59.537 47.619 12.47 0.00 44.21 4.85
2143 3744 1.803334 TGAAACTATTTCACGCGGCT 58.197 45.000 12.47 0.00 44.21 5.52
2151 3752 8.734386 AGAATGAACTGTCCATGAAACTATTTC 58.266 33.333 0.00 0.00 40.08 2.17
2152 3753 8.517878 CAGAATGAACTGTCCATGAAACTATTT 58.482 33.333 0.00 0.00 39.69 1.40
2153 3754 7.667219 ACAGAATGAACTGTCCATGAAACTATT 59.333 33.333 0.00 0.00 46.36 1.73
2154 3755 7.170965 ACAGAATGAACTGTCCATGAAACTAT 58.829 34.615 0.00 0.00 46.36 2.12
2155 3756 6.533730 ACAGAATGAACTGTCCATGAAACTA 58.466 36.000 0.00 0.00 46.36 2.24
2156 3757 5.380043 ACAGAATGAACTGTCCATGAAACT 58.620 37.500 0.00 0.00 46.36 2.66
2157 3758 5.695851 ACAGAATGAACTGTCCATGAAAC 57.304 39.130 0.00 0.00 46.36 2.78
2167 3768 7.080099 ACGAAATCAAATCACAGAATGAACTG 58.920 34.615 0.00 0.00 41.93 3.16
2168 3769 7.173907 AGACGAAATCAAATCACAGAATGAACT 59.826 33.333 0.00 0.00 41.93 3.01
2169 3770 7.301054 AGACGAAATCAAATCACAGAATGAAC 58.699 34.615 0.00 0.00 41.93 3.18
2170 3771 7.439157 AGACGAAATCAAATCACAGAATGAA 57.561 32.000 0.00 0.00 41.93 2.57
2171 3772 8.722480 ATAGACGAAATCAAATCACAGAATGA 57.278 30.769 0.00 0.00 43.13 2.57
2173 3774 9.265901 CCTATAGACGAAATCAAATCACAGAAT 57.734 33.333 0.00 0.00 0.00 2.40
2174 3775 8.258007 ACCTATAGACGAAATCAAATCACAGAA 58.742 33.333 0.00 0.00 0.00 3.02
2175 3776 7.782049 ACCTATAGACGAAATCAAATCACAGA 58.218 34.615 0.00 0.00 0.00 3.41
2176 3777 7.706607 TGACCTATAGACGAAATCAAATCACAG 59.293 37.037 0.00 0.00 0.00 3.66
2177 3778 7.552459 TGACCTATAGACGAAATCAAATCACA 58.448 34.615 0.00 0.00 0.00 3.58
2178 3779 8.420374 TTGACCTATAGACGAAATCAAATCAC 57.580 34.615 0.00 0.00 0.00 3.06
2179 3780 9.613428 ATTTGACCTATAGACGAAATCAAATCA 57.387 29.630 0.00 0.00 39.78 2.57
2183 3784 9.226606 ACAAATTTGACCTATAGACGAAATCAA 57.773 29.630 24.64 0.00 0.00 2.57
2184 3785 8.786826 ACAAATTTGACCTATAGACGAAATCA 57.213 30.769 24.64 0.00 0.00 2.57
2185 3786 8.879759 TGACAAATTTGACCTATAGACGAAATC 58.120 33.333 24.64 6.30 0.00 2.17
2186 3787 8.786826 TGACAAATTTGACCTATAGACGAAAT 57.213 30.769 24.64 0.00 0.00 2.17
2187 3788 8.610248 TTGACAAATTTGACCTATAGACGAAA 57.390 30.769 24.64 2.44 0.00 3.46
2188 3789 8.610248 TTTGACAAATTTGACCTATAGACGAA 57.390 30.769 24.64 3.11 0.00 3.85
2189 3790 8.786826 ATTTGACAAATTTGACCTATAGACGA 57.213 30.769 24.64 0.00 0.00 4.20
2190 3791 9.840427 AAATTTGACAAATTTGACCTATAGACG 57.160 29.630 29.31 0.00 46.30 4.18
2203 3804 4.002316 CCCATCGGCAAATTTGACAAATT 58.998 39.130 23.49 18.41 42.62 1.82
2204 3805 3.260380 TCCCATCGGCAAATTTGACAAAT 59.740 39.130 23.49 13.14 35.35 2.32
2205 3806 2.630098 TCCCATCGGCAAATTTGACAAA 59.370 40.909 23.49 11.38 35.35 2.83
2206 3807 2.029470 GTCCCATCGGCAAATTTGACAA 60.029 45.455 23.49 5.88 35.35 3.18
2207 3808 1.543802 GTCCCATCGGCAAATTTGACA 59.456 47.619 23.49 11.20 35.35 3.58
2208 3809 1.135112 GGTCCCATCGGCAAATTTGAC 60.135 52.381 22.31 18.50 0.00 3.18
2209 3810 1.181786 GGTCCCATCGGCAAATTTGA 58.818 50.000 22.31 1.15 0.00 2.69
2210 3811 0.175531 GGGTCCCATCGGCAAATTTG 59.824 55.000 14.03 14.03 0.00 2.32
2211 3812 1.319614 CGGGTCCCATCGGCAAATTT 61.320 55.000 9.12 0.00 0.00 1.82
2212 3813 1.752694 CGGGTCCCATCGGCAAATT 60.753 57.895 9.12 0.00 0.00 1.82
2213 3814 2.124320 CGGGTCCCATCGGCAAAT 60.124 61.111 9.12 0.00 0.00 2.32
2214 3815 3.642503 ACGGGTCCCATCGGCAAA 61.643 61.111 9.12 0.00 0.00 3.68
2215 3816 4.402528 CACGGGTCCCATCGGCAA 62.403 66.667 9.12 0.00 0.00 4.52
2244 3845 0.955428 TCATTCAGTTGCTCCACGCC 60.955 55.000 0.00 0.00 38.05 5.68
2303 3904 5.539048 ACGATTAACACTAACAACTGAGCT 58.461 37.500 0.00 0.00 0.00 4.09
2530 4132 4.592942 AGGCATTTGTGCTCTTATCTCAA 58.407 39.130 0.07 0.00 34.73 3.02
2669 4329 5.535333 AGAAATTTGCAGACAAGGAATGTG 58.465 37.500 0.00 0.00 44.12 3.21
2737 4397 9.045223 GCCATTTATCTTTCTTTTTGTTGAACT 57.955 29.630 0.00 0.00 0.00 3.01
2854 4522 6.824305 ATGTAAGAGTTTGACAGGAAATGG 57.176 37.500 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.