Multiple sequence alignment - TraesCS6D01G320300

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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 TraesCS6D01G320300 chr6D 100.000 2819 0 0 1 2819 428459993 428457175 0.000000e+00 5206.0
1 TraesCS6D01G320300 chr6D 97.748 222 5 0 1975 2196 467948713 467948934 1.580000e-102 383.0
2 TraesCS6D01G320300 chr6D 84.173 139 17 4 2064 2199 49268024 49267888 2.280000e-26 130.0
3 TraesCS6D01G320300 chr4A 97.592 1329 31 1 1 1329 213405156 213403829 0.000000e+00 2276.0
4 TraesCS6D01G320300 chr4A 97.065 1329 39 0 1 1329 74606577 74605249 0.000000e+00 2239.0
5 TraesCS6D01G320300 chr4A 96.532 519 16 2 1331 1849 74605199 74604683 0.000000e+00 857.0
6 TraesCS6D01G320300 chr4A 96.844 507 14 2 1344 1850 213403777 213403273 0.000000e+00 846.0
7 TraesCS6D01G320300 chr4A 84.722 144 21 1 2155 2297 9539661 9539518 2.930000e-30 143.0
8 TraesCS6D01G320300 chr4A 85.366 123 18 0 2668 2790 9539301 9539179 8.200000e-26 128.0
9 TraesCS6D01G320300 chr7B 97.068 1330 37 2 1 1329 259716694 259715366 0.000000e+00 2239.0
10 TraesCS6D01G320300 chr7B 95.577 520 21 2 1331 1850 259715316 259714799 0.000000e+00 832.0
11 TraesCS6D01G320300 chr2D 92.754 828 55 5 1994 2819 585067893 585068717 0.000000e+00 1192.0
12 TraesCS6D01G320300 chr2D 87.638 453 36 5 1408 1851 608375417 608375858 2.510000e-140 508.0
13 TraesCS6D01G320300 chr2D 87.342 158 16 4 2148 2303 616050620 616050465 8.020000e-41 178.0
14 TraesCS6D01G320300 chr2D 97.619 42 1 0 2458 2499 2590153 2590194 3.900000e-09 73.1
15 TraesCS6D01G320300 chr3D 95.541 740 31 2 2081 2819 449734871 449734133 0.000000e+00 1182.0
16 TraesCS6D01G320300 chr3D 96.000 400 16 0 2420 2819 316555375 316554976 0.000000e+00 651.0
17 TraesCS6D01G320300 chr3D 92.470 332 10 7 2148 2477 553316641 553316959 7.120000e-126 460.0
18 TraesCS6D01G320300 chr3D 96.124 258 9 1 1368 1624 55749893 55750150 1.210000e-113 420.0
19 TraesCS6D01G320300 chr3D 93.548 248 15 1 1605 1851 55752220 55752467 4.440000e-98 368.0
20 TraesCS6D01G320300 chr1D 92.280 829 58 6 1994 2819 443750581 443751406 0.000000e+00 1171.0
21 TraesCS6D01G320300 chr1D 95.918 49 2 0 1803 1851 59965237 59965285 2.330000e-11 80.5
22 TraesCS6D01G320300 chr1D 73.707 232 45 15 1973 2196 471080140 471079917 3.010000e-10 76.8
23 TraesCS6D01G320300 chr7D 97.121 521 13 2 1331 1851 198617228 198616710 0.000000e+00 878.0
24 TraesCS6D01G320300 chr7D 97.561 328 8 0 1002 1329 198617605 198617278 1.900000e-156 562.0
25 TraesCS6D01G320300 chr7D 94.805 231 11 1 1975 2205 364110206 364110435 2.670000e-95 359.0
26 TraesCS6D01G320300 chr3B 96.378 497 18 0 834 1330 462888646 462888150 0.000000e+00 819.0
27 TraesCS6D01G320300 chr3B 95.032 463 22 1 1390 1852 462887555 462887094 0.000000e+00 726.0
28 TraesCS6D01G320300 chr3B 89.764 127 10 3 2179 2303 8766245 8766120 2.910000e-35 159.0
29 TraesCS6D01G320300 chr3B 87.500 88 7 4 1331 1416 462888101 462888016 6.430000e-17 99.0
30 TraesCS6D01G320300 chr2B 87.750 400 34 2 1407 1802 741499194 741499582 1.190000e-123 453.0
31 TraesCS6D01G320300 chr2B 88.213 263 31 0 2557 2819 707253834 707254096 5.860000e-82 315.0
32 TraesCS6D01G320300 chr2B 91.765 170 12 2 2397 2566 707253381 707253548 4.690000e-58 235.0
33 TraesCS6D01G320300 chr2B 87.975 158 15 4 2148 2303 616947665 616947510 1.720000e-42 183.0
34 TraesCS6D01G320300 chr2B 93.750 48 3 0 2458 2505 546783910 546783863 3.900000e-09 73.1
35 TraesCS6D01G320300 chr5D 95.671 231 9 1 1975 2205 509226864 509226635 1.230000e-98 370.0
36 TraesCS6D01G320300 chr5D 84.545 110 15 2 2540 2647 44956947 44956838 1.070000e-19 108.0
37 TraesCS6D01G320300 chr1B 88.889 153 14 3 2049 2199 68949697 68949546 4.800000e-43 185.0
38 TraesCS6D01G320300 chr1B 91.667 48 4 0 2458 2505 10151886 10151933 1.810000e-07 67.6
39 TraesCS6D01G320300 chr5A 88.148 135 16 0 2683 2817 672724390 672724524 8.080000e-36 161.0
40 TraesCS6D01G320300 chr5B 85.350 157 20 3 2148 2303 376523739 376523893 2.910000e-35 159.0
41 TraesCS6D01G320300 chr5B 91.781 73 6 0 2002 2074 505696679 505696751 4.970000e-18 102.0
42 TraesCS6D01G320300 chr5B 90.000 70 7 0 2005 2074 606712624 606712555 1.080000e-14 91.6
43 TraesCS6D01G320300 chr5B 90.000 70 7 0 2005 2074 606732617 606732548 1.080000e-14 91.6
44 TraesCS6D01G320300 chr5B 100.000 39 0 0 2752 2790 10583410 10583448 3.900000e-09 73.1
45 TraesCS6D01G320300 chr5B 93.750 48 3 0 2743 2790 685600927 685600880 3.900000e-09 73.1
46 TraesCS6D01G320300 chrUn 91.667 48 4 0 2458 2505 303457357 303457404 1.810000e-07 67.6
47 TraesCS6D01G320300 chr3A 100.000 34 0 0 1041 1074 9371227 9371194 2.340000e-06 63.9


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 TraesCS6D01G320300 chr6D 428457175 428459993 2818 True 5206.0 5206 100.0000 1 2819 1 chr6D.!!$R2 2818
1 TraesCS6D01G320300 chr4A 213403273 213405156 1883 True 1561.0 2276 97.2180 1 1850 2 chr4A.!!$R3 1849
2 TraesCS6D01G320300 chr4A 74604683 74606577 1894 True 1548.0 2239 96.7985 1 1849 2 chr4A.!!$R2 1848
3 TraesCS6D01G320300 chr7B 259714799 259716694 1895 True 1535.5 2239 96.3225 1 1850 2 chr7B.!!$R1 1849
4 TraesCS6D01G320300 chr2D 585067893 585068717 824 False 1192.0 1192 92.7540 1994 2819 1 chr2D.!!$F2 825
5 TraesCS6D01G320300 chr3D 449734133 449734871 738 True 1182.0 1182 95.5410 2081 2819 1 chr3D.!!$R2 738
6 TraesCS6D01G320300 chr3D 55749893 55752467 2574 False 394.0 420 94.8360 1368 1851 2 chr3D.!!$F2 483
7 TraesCS6D01G320300 chr1D 443750581 443751406 825 False 1171.0 1171 92.2800 1994 2819 1 chr1D.!!$F2 825
8 TraesCS6D01G320300 chr7D 198616710 198617605 895 True 720.0 878 97.3410 1002 1851 2 chr7D.!!$R1 849
9 TraesCS6D01G320300 chr3B 462887094 462888646 1552 True 548.0 819 92.9700 834 1852 3 chr3B.!!$R2 1018
10 TraesCS6D01G320300 chr2B 707253381 707254096 715 False 275.0 315 89.9890 2397 2819 2 chr2B.!!$F2 422

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
652 654 1.273381 TGGAGGACCTCATTAACCCGA 60.273 52.381 23.06 0.0 37.04 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 4520 0.101759 GGCTAGTTCGACCGCACATA 59.898 55.0 0.0 0.0 0.0 2.29 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
376 378 1.514087 CAAGCATGGCGCATCCTTT 59.486 52.632 10.83 0.00 46.13 3.11
459 461 2.826777 TAGCAGCCAAGCCAAGAGCC 62.827 60.000 0.00 0.00 45.47 4.70
460 462 2.282674 CAGCCAAGCCAAGAGCCA 60.283 61.111 0.00 0.00 45.47 4.75
555 557 6.012113 TGGAAATGGTCAGAACATCAAGATT 58.988 36.000 0.00 0.00 0.00 2.40
607 609 2.342648 GCCGACCCAGTTCGACTT 59.657 61.111 0.00 0.00 41.78 3.01
652 654 1.273381 TGGAGGACCTCATTAACCCGA 60.273 52.381 23.06 0.00 37.04 5.14
873 875 2.305928 ACCAGCACTGCAACAATTACA 58.694 42.857 3.30 0.00 0.00 2.41
967 969 5.794687 TTGGAGATTTACACATAACAGCG 57.205 39.130 0.00 0.00 0.00 5.18
1093 1095 3.754586 TTTGCAAGGGCCTGCTGGT 62.755 57.895 22.57 0.00 43.07 4.00
1315 1317 7.471539 GCAGCCTACATATCCTTCAGTTTACTA 60.472 40.741 0.00 0.00 0.00 1.82
1528 2065 1.895707 GCCCGAGATGCTGGAATGG 60.896 63.158 0.00 0.00 0.00 3.16
1744 4371 2.171237 TCTATGGAACCTGGTGCTCATG 59.829 50.000 15.26 8.27 0.00 3.07
1844 4471 5.239525 GGAATCTATGTTTCCCCGATCAAAG 59.760 44.000 0.00 0.00 37.29 2.77
1872 4499 9.696917 AAAAACTTAGCCAAATCATGAACTAAG 57.303 29.630 20.05 20.05 43.73 2.18
1873 4500 6.442513 ACTTAGCCAAATCATGAACTAAGC 57.557 37.500 20.84 12.99 42.90 3.09
1874 4501 5.358160 ACTTAGCCAAATCATGAACTAAGCC 59.642 40.000 20.84 3.35 42.90 4.35
1875 4502 3.973425 AGCCAAATCATGAACTAAGCCT 58.027 40.909 0.00 0.00 0.00 4.58
1876 4503 3.698040 AGCCAAATCATGAACTAAGCCTG 59.302 43.478 0.00 0.00 0.00 4.85
1877 4504 3.696051 GCCAAATCATGAACTAAGCCTGA 59.304 43.478 0.00 0.00 0.00 3.86
1878 4505 4.439289 GCCAAATCATGAACTAAGCCTGAC 60.439 45.833 0.00 0.00 0.00 3.51
1879 4506 4.946157 CCAAATCATGAACTAAGCCTGACT 59.054 41.667 0.00 0.00 0.00 3.41
1880 4507 5.065731 CCAAATCATGAACTAAGCCTGACTC 59.934 44.000 0.00 0.00 0.00 3.36
1881 4508 5.426689 AATCATGAACTAAGCCTGACTCA 57.573 39.130 0.00 0.00 0.00 3.41
1882 4509 4.890158 TCATGAACTAAGCCTGACTCAA 57.110 40.909 0.00 0.00 0.00 3.02
1883 4510 5.227569 TCATGAACTAAGCCTGACTCAAA 57.772 39.130 0.00 0.00 0.00 2.69
1884 4511 4.997395 TCATGAACTAAGCCTGACTCAAAC 59.003 41.667 0.00 0.00 0.00 2.93
1885 4512 3.390135 TGAACTAAGCCTGACTCAAACG 58.610 45.455 0.00 0.00 0.00 3.60
1886 4513 2.457366 ACTAAGCCTGACTCAAACGG 57.543 50.000 0.00 0.00 0.00 4.44
1887 4514 1.692519 ACTAAGCCTGACTCAAACGGT 59.307 47.619 0.00 0.00 0.00 4.83
1888 4515 2.104281 ACTAAGCCTGACTCAAACGGTT 59.896 45.455 0.00 0.00 0.00 4.44
1889 4516 2.922740 AAGCCTGACTCAAACGGTTA 57.077 45.000 0.00 0.00 0.00 2.85
1890 4517 2.457366 AGCCTGACTCAAACGGTTAG 57.543 50.000 0.00 0.00 0.00 2.34
1891 4518 1.002087 AGCCTGACTCAAACGGTTAGG 59.998 52.381 0.00 0.00 41.52 2.69
1892 4519 1.270678 GCCTGACTCAAACGGTTAGGT 60.271 52.381 1.12 0.00 40.94 3.08
1893 4520 2.809299 GCCTGACTCAAACGGTTAGGTT 60.809 50.000 1.12 0.00 40.94 3.50
1894 4521 3.555586 GCCTGACTCAAACGGTTAGGTTA 60.556 47.826 1.12 0.00 40.94 2.85
1895 4522 4.828829 CCTGACTCAAACGGTTAGGTTAT 58.171 43.478 0.00 0.00 36.23 1.89
1896 4523 4.630069 CCTGACTCAAACGGTTAGGTTATG 59.370 45.833 0.00 0.00 36.23 1.90
1897 4524 5.217978 TGACTCAAACGGTTAGGTTATGT 57.782 39.130 0.00 0.00 0.00 2.29
1898 4525 4.992319 TGACTCAAACGGTTAGGTTATGTG 59.008 41.667 0.00 0.00 0.00 3.21
1899 4526 3.749609 ACTCAAACGGTTAGGTTATGTGC 59.250 43.478 0.00 0.00 0.00 4.57
1900 4527 2.737783 TCAAACGGTTAGGTTATGTGCG 59.262 45.455 0.00 0.00 0.00 5.34
1901 4528 1.729284 AACGGTTAGGTTATGTGCGG 58.271 50.000 0.00 0.00 0.00 5.69
1902 4529 0.609662 ACGGTTAGGTTATGTGCGGT 59.390 50.000 0.00 0.00 0.00 5.68
1903 4530 1.283736 CGGTTAGGTTATGTGCGGTC 58.716 55.000 0.00 0.00 0.00 4.79
1904 4531 1.283736 GGTTAGGTTATGTGCGGTCG 58.716 55.000 0.00 0.00 0.00 4.79
1905 4532 1.135024 GGTTAGGTTATGTGCGGTCGA 60.135 52.381 0.00 0.00 0.00 4.20
1906 4533 2.609350 GTTAGGTTATGTGCGGTCGAA 58.391 47.619 0.00 0.00 0.00 3.71
1907 4534 2.282701 TAGGTTATGTGCGGTCGAAC 57.717 50.000 0.00 0.00 0.00 3.95
1908 4535 0.606604 AGGTTATGTGCGGTCGAACT 59.393 50.000 0.00 0.00 0.00 3.01
1909 4536 1.820519 AGGTTATGTGCGGTCGAACTA 59.179 47.619 0.00 0.00 0.00 2.24
1910 4537 2.159282 AGGTTATGTGCGGTCGAACTAG 60.159 50.000 0.00 0.00 0.00 2.57
1911 4538 1.587034 GTTATGTGCGGTCGAACTAGC 59.413 52.381 0.00 0.00 0.00 3.42
1912 4539 0.101759 TATGTGCGGTCGAACTAGCC 59.898 55.000 0.00 0.00 0.00 3.93
1913 4540 2.508663 GTGCGGTCGAACTAGCCC 60.509 66.667 0.00 0.00 0.00 5.19
1914 4541 2.678934 TGCGGTCGAACTAGCCCT 60.679 61.111 0.00 0.00 0.00 5.19
1915 4542 2.280552 TGCGGTCGAACTAGCCCTT 61.281 57.895 0.00 0.00 0.00 3.95
1916 4543 1.810030 GCGGTCGAACTAGCCCTTG 60.810 63.158 0.00 0.00 0.00 3.61
1917 4544 1.153628 CGGTCGAACTAGCCCTTGG 60.154 63.158 0.00 0.00 0.00 3.61
1941 4568 7.585286 GCATTGTTGCTCATAATTTTCTGAA 57.415 32.000 0.00 0.00 45.77 3.02
1942 4569 8.193250 GCATTGTTGCTCATAATTTTCTGAAT 57.807 30.769 0.00 0.00 45.77 2.57
1943 4570 8.662141 GCATTGTTGCTCATAATTTTCTGAATT 58.338 29.630 0.00 0.00 45.77 2.17
1961 4588 9.965824 TTCTGAATTTATTTCAAACTTCCTGAC 57.034 29.630 0.00 0.00 43.64 3.51
1962 4589 9.130661 TCTGAATTTATTTCAAACTTCCTGACA 57.869 29.630 0.00 0.00 43.64 3.58
1963 4590 9.748708 CTGAATTTATTTCAAACTTCCTGACAA 57.251 29.630 0.00 0.00 43.64 3.18
1970 4597 7.504924 TTTCAAACTTCCTGACAATATTCGT 57.495 32.000 0.00 0.00 0.00 3.85
1971 4598 7.504924 TTCAAACTTCCTGACAATATTCGTT 57.495 32.000 0.00 0.00 0.00 3.85
1972 4599 7.129109 TCAAACTTCCTGACAATATTCGTTC 57.871 36.000 0.00 0.00 0.00 3.95
1973 4600 6.708502 TCAAACTTCCTGACAATATTCGTTCA 59.291 34.615 0.00 0.00 0.00 3.18
1974 4601 7.227711 TCAAACTTCCTGACAATATTCGTTCAA 59.772 33.333 0.00 0.00 0.00 2.69
1975 4602 7.687941 AACTTCCTGACAATATTCGTTCAAT 57.312 32.000 0.00 0.00 0.00 2.57
1976 4603 7.308782 ACTTCCTGACAATATTCGTTCAATC 57.691 36.000 0.00 0.00 0.00 2.67
1977 4604 6.316390 ACTTCCTGACAATATTCGTTCAATCC 59.684 38.462 0.00 0.00 0.00 3.01
1978 4605 5.739959 TCCTGACAATATTCGTTCAATCCA 58.260 37.500 0.00 0.00 0.00 3.41
1979 4606 5.817296 TCCTGACAATATTCGTTCAATCCAG 59.183 40.000 0.00 0.00 0.00 3.86
1980 4607 5.008019 CCTGACAATATTCGTTCAATCCAGG 59.992 44.000 0.00 0.00 0.00 4.45
1981 4608 5.739959 TGACAATATTCGTTCAATCCAGGA 58.260 37.500 0.00 0.00 0.00 3.86
1982 4609 6.176896 TGACAATATTCGTTCAATCCAGGAA 58.823 36.000 0.00 0.00 0.00 3.36
1983 4610 6.828273 TGACAATATTCGTTCAATCCAGGAAT 59.172 34.615 0.00 0.00 34.13 3.01
1984 4611 7.990314 TGACAATATTCGTTCAATCCAGGAATA 59.010 33.333 0.00 0.00 36.15 1.75
1985 4612 8.746052 ACAATATTCGTTCAATCCAGGAATAA 57.254 30.769 0.00 0.00 35.62 1.40
1986 4613 8.840321 ACAATATTCGTTCAATCCAGGAATAAG 58.160 33.333 0.00 0.00 35.62 1.73
1987 4614 8.840321 CAATATTCGTTCAATCCAGGAATAAGT 58.160 33.333 0.00 0.00 35.62 2.24
1990 4617 8.608844 ATTCGTTCAATCCAGGAATAAGTATC 57.391 34.615 0.00 0.00 29.12 2.24
1991 4618 7.361457 TCGTTCAATCCAGGAATAAGTATCT 57.639 36.000 0.00 0.00 0.00 1.98
1992 4619 8.473358 TCGTTCAATCCAGGAATAAGTATCTA 57.527 34.615 0.00 0.00 0.00 1.98
1998 4625 5.334421 TCCAGGAATAAGTATCTAGGGAGC 58.666 45.833 0.00 0.00 0.00 4.70
1999 4626 5.076598 TCCAGGAATAAGTATCTAGGGAGCT 59.923 44.000 0.00 0.00 0.00 4.09
2022 4649 0.395586 GAGCCTCCTCAGAGCTCAGA 60.396 60.000 17.77 12.99 40.29 3.27
2024 4651 2.003658 GCCTCCTCAGAGCTCAGACG 62.004 65.000 17.77 7.63 38.96 4.18
2025 4652 0.393673 CCTCCTCAGAGCTCAGACGA 60.394 60.000 17.77 11.65 38.96 4.20
2026 4653 1.458398 CTCCTCAGAGCTCAGACGAA 58.542 55.000 17.77 0.00 32.13 3.85
2027 4654 2.023673 CTCCTCAGAGCTCAGACGAAT 58.976 52.381 17.77 0.00 32.13 3.34
2028 4655 2.020720 TCCTCAGAGCTCAGACGAATC 58.979 52.381 17.77 0.00 0.00 2.52
2041 4668 2.782615 GAATCCGGCCGTTCGTTG 59.217 61.111 26.12 7.54 0.00 4.10
2042 4669 3.376914 GAATCCGGCCGTTCGTTGC 62.377 63.158 26.12 2.46 0.00 4.17
2055 4682 1.509787 CGTTGCGTTCGCTTGATGG 60.510 57.895 17.63 0.00 0.00 3.51
2056 4683 1.866237 GTTGCGTTCGCTTGATGGA 59.134 52.632 17.63 0.00 0.00 3.41
2064 4691 1.095228 TCGCTTGATGGATTTCCGGC 61.095 55.000 0.00 0.00 39.43 6.13
2067 4694 2.063541 CTTGATGGATTTCCGGCCGC 62.064 60.000 22.85 5.16 39.43 6.53
2085 4712 1.907739 CCGGATCTTGCTCTGGGAA 59.092 57.895 0.00 0.00 37.93 3.97
2098 4725 1.132977 TCTGGGAAGATATGGGCCGTA 60.133 52.381 8.15 8.15 0.00 4.02
2118 4745 6.300354 CGTAGGATCAAAGTGAAAACACTT 57.700 37.500 9.38 9.38 46.26 3.16
2121 4748 6.382869 AGGATCAAAGTGAAAACACTTCTG 57.617 37.500 14.45 13.86 43.83 3.02
2186 4813 0.475044 GTAATTCCCATACCCCGCCA 59.525 55.000 0.00 0.00 0.00 5.69
2206 4833 1.941377 AGGGCATTTGCAGGAATTCA 58.059 45.000 7.93 0.00 44.36 2.57
2313 4940 0.252742 ATTCTCCCCTTCTCCACCGT 60.253 55.000 0.00 0.00 0.00 4.83
2317 4944 1.686110 CCCCTTCTCCACCGTAGCT 60.686 63.158 0.00 0.00 0.00 3.32
2352 4979 2.997584 CGTCCTCCTCTCCTCCCCA 61.998 68.421 0.00 0.00 0.00 4.96
2400 5027 1.686052 CTTAGCTGCTCTCCCCACTAG 59.314 57.143 4.91 0.00 0.00 2.57
2647 5569 1.192146 CCGACCAAGGTCTTCTCCCA 61.192 60.000 16.57 0.00 42.54 4.37
2650 5572 2.537143 GACCAAGGTCTTCTCCCACTA 58.463 52.381 11.94 0.00 41.57 2.74
2689 5611 4.671590 TGTCGCCGACAGGAGGGA 62.672 66.667 17.22 0.00 37.67 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
376 378 6.072230 CGAGCACAAAGAGATGATAGATCCTA 60.072 42.308 0.00 0.00 0.00 2.94
383 385 4.176271 CACACGAGCACAAAGAGATGATA 58.824 43.478 0.00 0.00 0.00 2.15
459 461 8.736788 TACTTCGCCAAGTGTAGGAAATCCTG 62.737 46.154 12.29 0.00 44.00 3.86
460 462 6.087123 ACTTCGCCAAGTGTAGGAAATCCT 62.087 45.833 7.23 7.23 44.54 3.24
652 654 1.140852 CATGTCCCACATACCGGTCAT 59.859 52.381 12.40 2.15 36.53 3.06
873 875 1.064758 TGTGAAGTGGTCTGGCTTGTT 60.065 47.619 0.00 0.00 0.00 2.83
967 969 1.636988 ATGTTAGTTCGTAGCGGCAC 58.363 50.000 1.45 0.00 0.00 5.01
1093 1095 0.901827 TCTTCTAGGATTGCCGCACA 59.098 50.000 0.00 0.00 39.96 4.57
1315 1317 2.108952 AATCTGAGCCCTTCAGGTGTTT 59.891 45.455 4.51 0.00 46.68 2.83
1528 2065 0.526211 GTTTCAAAGATGACCCGGCC 59.474 55.000 0.00 0.00 34.61 6.13
1744 4371 0.887387 ACCGTACCATGCCACAACAC 60.887 55.000 0.00 0.00 0.00 3.32
1851 4478 5.591877 AGGCTTAGTTCATGATTTGGCTAAG 59.408 40.000 17.57 17.57 40.38 2.18
1852 4479 5.357878 CAGGCTTAGTTCATGATTTGGCTAA 59.642 40.000 0.00 0.93 0.00 3.09
1853 4480 4.883585 CAGGCTTAGTTCATGATTTGGCTA 59.116 41.667 0.00 0.00 0.00 3.93
1854 4481 3.698040 CAGGCTTAGTTCATGATTTGGCT 59.302 43.478 0.00 0.78 0.00 4.75
1855 4482 3.696051 TCAGGCTTAGTTCATGATTTGGC 59.304 43.478 0.00 0.00 0.00 4.52
1856 4483 4.946157 AGTCAGGCTTAGTTCATGATTTGG 59.054 41.667 0.00 0.00 0.00 3.28
1857 4484 5.645067 TGAGTCAGGCTTAGTTCATGATTTG 59.355 40.000 0.00 0.00 0.00 2.32
1858 4485 5.809001 TGAGTCAGGCTTAGTTCATGATTT 58.191 37.500 0.00 0.00 0.00 2.17
1859 4486 5.426689 TGAGTCAGGCTTAGTTCATGATT 57.573 39.130 0.00 0.00 0.00 2.57
1860 4487 5.426689 TTGAGTCAGGCTTAGTTCATGAT 57.573 39.130 0.00 0.00 0.00 2.45
1861 4488 4.890158 TTGAGTCAGGCTTAGTTCATGA 57.110 40.909 0.00 0.00 0.00 3.07
1862 4489 4.143030 CGTTTGAGTCAGGCTTAGTTCATG 60.143 45.833 0.00 0.00 0.00 3.07
1863 4490 3.997021 CGTTTGAGTCAGGCTTAGTTCAT 59.003 43.478 0.00 0.00 0.00 2.57
1864 4491 3.390135 CGTTTGAGTCAGGCTTAGTTCA 58.610 45.455 0.00 0.00 0.00 3.18
1865 4492 2.737252 CCGTTTGAGTCAGGCTTAGTTC 59.263 50.000 0.00 0.00 0.00 3.01
1866 4493 2.104281 ACCGTTTGAGTCAGGCTTAGTT 59.896 45.455 0.00 0.00 0.00 2.24
1867 4494 1.692519 ACCGTTTGAGTCAGGCTTAGT 59.307 47.619 0.00 0.00 0.00 2.24
1868 4495 2.457366 ACCGTTTGAGTCAGGCTTAG 57.543 50.000 0.00 0.00 0.00 2.18
1869 4496 2.922740 AACCGTTTGAGTCAGGCTTA 57.077 45.000 0.00 0.00 0.00 3.09
1870 4497 2.550208 CCTAACCGTTTGAGTCAGGCTT 60.550 50.000 0.00 0.00 0.00 4.35
1871 4498 1.002087 CCTAACCGTTTGAGTCAGGCT 59.998 52.381 0.00 0.00 0.00 4.58
1872 4499 1.270678 ACCTAACCGTTTGAGTCAGGC 60.271 52.381 0.00 0.00 0.00 4.85
1873 4500 2.833631 ACCTAACCGTTTGAGTCAGG 57.166 50.000 0.00 0.00 0.00 3.86
1874 4501 5.120208 CACATAACCTAACCGTTTGAGTCAG 59.880 44.000 0.00 0.00 0.00 3.51
1875 4502 4.992319 CACATAACCTAACCGTTTGAGTCA 59.008 41.667 0.00 0.00 0.00 3.41
1876 4503 4.142966 GCACATAACCTAACCGTTTGAGTC 60.143 45.833 0.00 0.00 0.00 3.36
1877 4504 3.749609 GCACATAACCTAACCGTTTGAGT 59.250 43.478 0.00 0.00 0.00 3.41
1878 4505 3.181524 CGCACATAACCTAACCGTTTGAG 60.182 47.826 0.00 0.00 0.00 3.02
1879 4506 2.737783 CGCACATAACCTAACCGTTTGA 59.262 45.455 0.00 0.00 0.00 2.69
1880 4507 2.159626 CCGCACATAACCTAACCGTTTG 60.160 50.000 0.00 0.00 0.00 2.93
1881 4508 2.078392 CCGCACATAACCTAACCGTTT 58.922 47.619 0.00 0.00 0.00 3.60
1882 4509 1.002315 ACCGCACATAACCTAACCGTT 59.998 47.619 0.00 0.00 0.00 4.44
1883 4510 0.609662 ACCGCACATAACCTAACCGT 59.390 50.000 0.00 0.00 0.00 4.83
1884 4511 1.283736 GACCGCACATAACCTAACCG 58.716 55.000 0.00 0.00 0.00 4.44
1885 4512 1.135024 TCGACCGCACATAACCTAACC 60.135 52.381 0.00 0.00 0.00 2.85
1886 4513 2.282701 TCGACCGCACATAACCTAAC 57.717 50.000 0.00 0.00 0.00 2.34
1887 4514 2.231964 AGTTCGACCGCACATAACCTAA 59.768 45.455 0.00 0.00 0.00 2.69
1888 4515 1.820519 AGTTCGACCGCACATAACCTA 59.179 47.619 0.00 0.00 0.00 3.08
1889 4516 0.606604 AGTTCGACCGCACATAACCT 59.393 50.000 0.00 0.00 0.00 3.50
1890 4517 2.190981 CTAGTTCGACCGCACATAACC 58.809 52.381 0.00 0.00 0.00 2.85
1891 4518 1.587034 GCTAGTTCGACCGCACATAAC 59.413 52.381 0.00 0.00 0.00 1.89
1892 4519 1.470285 GGCTAGTTCGACCGCACATAA 60.470 52.381 0.00 0.00 0.00 1.90
1893 4520 0.101759 GGCTAGTTCGACCGCACATA 59.898 55.000 0.00 0.00 0.00 2.29
1894 4521 1.153628 GGCTAGTTCGACCGCACAT 60.154 57.895 0.00 0.00 0.00 3.21
1895 4522 2.260434 GGCTAGTTCGACCGCACA 59.740 61.111 0.00 0.00 0.00 4.57
1896 4523 2.502692 AAGGGCTAGTTCGACCGCAC 62.503 60.000 0.00 0.00 37.08 5.34
1897 4524 2.280552 AAGGGCTAGTTCGACCGCA 61.281 57.895 0.00 0.00 37.08 5.69
1898 4525 1.810030 CAAGGGCTAGTTCGACCGC 60.810 63.158 0.00 0.00 37.08 5.68
1899 4526 1.153628 CCAAGGGCTAGTTCGACCG 60.154 63.158 0.00 0.00 37.08 4.79
1900 4527 1.449778 GCCAAGGGCTAGTTCGACC 60.450 63.158 0.00 0.00 46.69 4.79
1901 4528 4.203618 GCCAAGGGCTAGTTCGAC 57.796 61.111 0.00 0.00 46.69 4.20
1944 4571 9.226606 ACGAATATTGTCAGGAAGTTTGAAATA 57.773 29.630 0.00 0.00 0.00 1.40
1945 4572 8.110860 ACGAATATTGTCAGGAAGTTTGAAAT 57.889 30.769 0.00 0.00 0.00 2.17
1946 4573 7.504924 ACGAATATTGTCAGGAAGTTTGAAA 57.495 32.000 0.00 0.00 0.00 2.69
1947 4574 7.227711 TGAACGAATATTGTCAGGAAGTTTGAA 59.772 33.333 0.00 0.00 0.00 2.69
1948 4575 6.708502 TGAACGAATATTGTCAGGAAGTTTGA 59.291 34.615 0.00 0.00 0.00 2.69
1949 4576 6.898041 TGAACGAATATTGTCAGGAAGTTTG 58.102 36.000 0.00 0.00 0.00 2.93
1950 4577 7.504924 TTGAACGAATATTGTCAGGAAGTTT 57.495 32.000 0.00 0.00 0.00 2.66
1951 4578 7.148239 GGATTGAACGAATATTGTCAGGAAGTT 60.148 37.037 0.00 0.00 0.00 2.66
1952 4579 6.316390 GGATTGAACGAATATTGTCAGGAAGT 59.684 38.462 0.00 0.00 0.00 3.01
1953 4580 6.316140 TGGATTGAACGAATATTGTCAGGAAG 59.684 38.462 0.00 0.00 0.00 3.46
1954 4581 6.176896 TGGATTGAACGAATATTGTCAGGAA 58.823 36.000 0.00 0.00 0.00 3.36
1955 4582 5.739959 TGGATTGAACGAATATTGTCAGGA 58.260 37.500 0.00 0.00 0.00 3.86
1956 4583 5.008019 CCTGGATTGAACGAATATTGTCAGG 59.992 44.000 0.00 0.00 0.00 3.86
1957 4584 5.817296 TCCTGGATTGAACGAATATTGTCAG 59.183 40.000 0.00 0.00 0.00 3.51
1958 4585 5.739959 TCCTGGATTGAACGAATATTGTCA 58.260 37.500 0.00 0.00 0.00 3.58
1959 4586 6.677781 TTCCTGGATTGAACGAATATTGTC 57.322 37.500 0.00 0.00 0.00 3.18
1960 4587 8.746052 TTATTCCTGGATTGAACGAATATTGT 57.254 30.769 0.00 0.00 0.00 2.71
1961 4588 8.840321 ACTTATTCCTGGATTGAACGAATATTG 58.160 33.333 0.00 0.00 0.00 1.90
1962 4589 8.980481 ACTTATTCCTGGATTGAACGAATATT 57.020 30.769 0.00 0.00 0.00 1.28
1964 4591 9.706691 GATACTTATTCCTGGATTGAACGAATA 57.293 33.333 0.00 0.00 0.00 1.75
1965 4592 8.432805 AGATACTTATTCCTGGATTGAACGAAT 58.567 33.333 0.00 0.00 0.00 3.34
1966 4593 7.792032 AGATACTTATTCCTGGATTGAACGAA 58.208 34.615 0.00 0.00 0.00 3.85
1967 4594 7.361457 AGATACTTATTCCTGGATTGAACGA 57.639 36.000 0.00 0.00 0.00 3.85
1968 4595 7.815068 CCTAGATACTTATTCCTGGATTGAACG 59.185 40.741 0.00 0.00 0.00 3.95
1969 4596 8.097662 CCCTAGATACTTATTCCTGGATTGAAC 58.902 40.741 0.00 0.00 0.00 3.18
1970 4597 8.016652 TCCCTAGATACTTATTCCTGGATTGAA 58.983 37.037 0.00 0.00 0.00 2.69
1971 4598 7.544650 TCCCTAGATACTTATTCCTGGATTGA 58.455 38.462 0.00 0.00 0.00 2.57
1972 4599 7.580495 GCTCCCTAGATACTTATTCCTGGATTG 60.580 44.444 0.00 0.00 0.00 2.67
1973 4600 6.442244 GCTCCCTAGATACTTATTCCTGGATT 59.558 42.308 0.00 0.00 0.00 3.01
1974 4601 5.961421 GCTCCCTAGATACTTATTCCTGGAT 59.039 44.000 0.00 0.00 0.00 3.41
1975 4602 5.076598 AGCTCCCTAGATACTTATTCCTGGA 59.923 44.000 0.00 0.00 0.00 3.86
1976 4603 5.337788 AGCTCCCTAGATACTTATTCCTGG 58.662 45.833 0.00 0.00 0.00 4.45
1977 4604 5.420739 GGAGCTCCCTAGATACTTATTCCTG 59.579 48.000 23.19 0.00 0.00 3.86
1978 4605 5.585894 GGAGCTCCCTAGATACTTATTCCT 58.414 45.833 23.19 0.00 0.00 3.36
1979 4606 5.925506 GGAGCTCCCTAGATACTTATTCC 57.074 47.826 23.19 0.00 0.00 3.01
1998 4625 1.827789 CTCTGAGGAGGCTCGGGAG 60.828 68.421 8.69 8.96 36.03 4.30
1999 4626 2.277072 CTCTGAGGAGGCTCGGGA 59.723 66.667 8.69 3.13 36.03 5.14
2002 4629 1.727511 CTGAGCTCTGAGGAGGCTCG 61.728 65.000 16.19 0.00 41.31 5.03
2006 4633 0.393673 TCGTCTGAGCTCTGAGGAGG 60.394 60.000 30.47 20.11 39.80 4.30
2009 4636 1.066908 GGATTCGTCTGAGCTCTGAGG 59.933 57.143 27.75 27.75 0.00 3.86
2024 4651 2.782615 CAACGAACGGCCGGATTC 59.217 61.111 31.76 23.09 0.00 2.52
2025 4652 3.428282 GCAACGAACGGCCGGATT 61.428 61.111 31.76 16.36 0.00 3.01
2036 4663 1.491127 CATCAAGCGAACGCAACGA 59.509 52.632 20.66 13.38 44.88 3.85
2037 4664 1.509787 CCATCAAGCGAACGCAACG 60.510 57.895 20.66 8.74 44.88 4.10
2039 4666 1.164411 AATCCATCAAGCGAACGCAA 58.836 45.000 20.66 6.68 44.88 4.85
2041 4668 1.531883 GGAAATCCATCAAGCGAACGC 60.532 52.381 11.31 11.31 37.40 4.84
2042 4669 1.267532 CGGAAATCCATCAAGCGAACG 60.268 52.381 0.00 0.00 35.14 3.95
2043 4670 1.064060 CCGGAAATCCATCAAGCGAAC 59.936 52.381 0.00 0.00 35.14 3.95
2044 4671 1.378531 CCGGAAATCCATCAAGCGAA 58.621 50.000 0.00 0.00 35.14 4.70
2064 4691 2.587194 CAGAGCAAGATCCGGCGG 60.587 66.667 22.51 22.51 34.54 6.13
2067 4694 0.179062 CTTCCCAGAGCAAGATCCGG 60.179 60.000 0.00 0.00 0.00 5.14
2074 4701 1.143684 GCCCATATCTTCCCAGAGCAA 59.856 52.381 0.00 0.00 30.36 3.91
2075 4702 0.767375 GCCCATATCTTCCCAGAGCA 59.233 55.000 0.00 0.00 30.36 4.26
2078 4705 0.399949 ACGGCCCATATCTTCCCAGA 60.400 55.000 0.00 0.00 0.00 3.86
2079 4706 1.276421 CTACGGCCCATATCTTCCCAG 59.724 57.143 0.00 0.00 0.00 4.45
2085 4712 2.623418 TGATCCTACGGCCCATATCT 57.377 50.000 0.00 0.00 0.00 1.98
2088 4715 2.104111 CACTTTGATCCTACGGCCCATA 59.896 50.000 0.00 0.00 0.00 2.74
2089 4716 1.134098 CACTTTGATCCTACGGCCCAT 60.134 52.381 0.00 0.00 0.00 4.00
2112 4739 5.106396 GCAGACTATTCATTGCAGAAGTGTT 60.106 40.000 0.00 0.00 36.59 3.32
2113 4740 4.394300 GCAGACTATTCATTGCAGAAGTGT 59.606 41.667 0.00 0.00 36.59 3.55
2114 4741 4.634883 AGCAGACTATTCATTGCAGAAGTG 59.365 41.667 0.00 0.00 38.97 3.16
2118 4745 4.442612 GGAGAGCAGACTATTCATTGCAGA 60.443 45.833 0.00 0.00 38.97 4.26
2121 4748 3.559242 GTGGAGAGCAGACTATTCATTGC 59.441 47.826 0.00 0.00 36.83 3.56
2186 4813 2.027837 GTGAATTCCTGCAAATGCCCTT 60.028 45.455 2.27 0.00 41.18 3.95
2313 4940 4.529219 CCATGGCGGCGACAGCTA 62.529 66.667 24.18 0.00 44.37 3.32
2352 4979 1.810606 CTCGGCGCTGGGAGATGTAT 61.811 60.000 11.83 0.00 31.90 2.29
2509 5136 2.365105 GGGGTGAGGGATGGACGA 60.365 66.667 0.00 0.00 0.00 4.20
2561 5483 1.231641 GCTCCTCCTCCTCTGCCTA 59.768 63.158 0.00 0.00 0.00 3.93
2631 5553 2.158143 AGTAGTGGGAGAAGACCTTGGT 60.158 50.000 0.00 0.00 0.00 3.67
2647 5569 3.812019 CGCGCGACCCAGAGTAGT 61.812 66.667 28.94 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.