Multiple sequence alignment - TraesCS7D01G163900

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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 TraesCS7D01G163900 chr7D 100.000 2764 0 0 1 2764 113427734 113424971 0.000000e+00 5105.0
1 TraesCS7D01G163900 chr7D 85.806 155 13 5 2380 2529 113372492 113372342 3.690000e-34 156.0
2 TraesCS7D01G163900 chr7B 93.814 1374 61 11 563 1917 72997732 72996364 0.000000e+00 2045.0
3 TraesCS7D01G163900 chr7B 82.500 400 34 16 2392 2764 72984710 72984320 4.440000e-83 318.0
4 TraesCS7D01G163900 chr7B 82.973 370 36 11 1999 2358 72996366 72996014 2.670000e-80 309.0
5 TraesCS7D01G163900 chr7B 86.275 153 14 5 2380 2529 72981282 72981134 2.850000e-35 159.0
6 TraesCS7D01G163900 chr7B 80.180 111 8 8 1 110 72998597 72998500 1.370000e-08 71.3
7 TraesCS7D01G163900 chr7A 90.698 1333 95 17 533 1843 118449410 118448085 0.000000e+00 1748.0
8 TraesCS7D01G163900 chr7A 86.872 716 58 11 2002 2702 118447975 118447281 0.000000e+00 769.0
9 TraesCS7D01G163900 chr7A 84.567 473 54 10 76 529 118450052 118449580 4.200000e-123 451.0
10 TraesCS7D01G163900 chr3A 79.608 255 46 6 1444 1695 549620191 549620442 7.870000e-41 178.0
11 TraesCS7D01G163900 chr4D 96.552 87 3 0 1909 1995 478671943 478671857 7.980000e-31 145.0
12 TraesCS7D01G163900 chr1A 95.556 90 4 0 1906 1995 439847010 439847099 7.980000e-31 145.0
13 TraesCS7D01G163900 chr4B 98.750 80 1 0 1916 1995 106975942 106975863 2.870000e-30 143.0
14 TraesCS7D01G163900 chr6D 93.617 94 3 1 1915 2005 249956967 249956874 1.340000e-28 137.0
15 TraesCS7D01G163900 chr6D 93.478 92 5 1 1913 2004 185190092 185190002 4.800000e-28 135.0
16 TraesCS7D01G163900 chr2D 94.444 90 4 1 1907 1995 14895266 14895355 1.340000e-28 137.0
17 TraesCS7D01G163900 chr2D 93.617 94 3 3 1902 1995 270850352 270850262 1.340000e-28 137.0
18 TraesCS7D01G163900 chr2D 97.500 80 2 0 1916 1995 341665860 341665939 1.340000e-28 137.0
19 TraesCS7D01G163900 chr1D 94.382 89 5 0 1907 1995 216728489 216728401 1.340000e-28 137.0


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 TraesCS7D01G163900 chr7D 113424971 113427734 2763 True 5105.000000 5105 100.000000 1 2764 1 chr7D.!!$R2 2763
1 TraesCS7D01G163900 chr7B 72996014 72998597 2583 True 808.433333 2045 85.655667 1 2358 3 chr7B.!!$R2 2357
2 TraesCS7D01G163900 chr7B 72981134 72984710 3576 True 238.500000 318 84.387500 2380 2764 2 chr7B.!!$R1 384
3 TraesCS7D01G163900 chr7A 118447281 118450052 2771 True 989.333333 1748 87.379000 76 2702 3 chr7A.!!$R1 2626

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
389 604 0.537188 GAGAATCCCAGCGTCTCCAA 59.463 55.0 0.0 0.0 33.16 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2235 2702 0.169009 GATTCACCCGAGCACTTTGC 59.831 55.0 0.0 0.0 45.46 3.68 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
60 62 9.607333 AGATATCTGAATGTTTCCCTAGATACA 57.393 33.333 3.89 0.00 38.17 2.29
61 63 9.868277 GATATCTGAATGTTTCCCTAGATACAG 57.132 37.037 0.00 0.00 37.38 2.74
62 64 7.921041 ATCTGAATGTTTCCCTAGATACAGA 57.079 36.000 0.00 0.00 37.38 3.41
63 65 7.921041 TCTGAATGTTTCCCTAGATACAGAT 57.079 36.000 0.00 0.00 37.38 2.90
64 66 9.607333 ATCTGAATGTTTCCCTAGATACAGATA 57.393 33.333 0.00 0.00 37.38 1.98
65 67 8.861086 TCTGAATGTTTCCCTAGATACAGATAC 58.139 37.037 0.00 0.00 37.38 2.24
66 68 8.547481 TGAATGTTTCCCTAGATACAGATACA 57.453 34.615 0.00 0.00 37.38 2.29
67 69 8.642432 TGAATGTTTCCCTAGATACAGATACAG 58.358 37.037 0.00 0.00 37.38 2.74
97 99 2.965831 TCCCTAGATCAGGTGGAAATCG 59.034 50.000 9.47 0.00 43.80 3.34
105 107 1.303282 GGTGGAAATCGCCTTCCCT 59.697 57.895 11.48 0.00 43.78 4.20
113 272 0.911769 ATCGCCTTCCCTGAATGTGA 59.088 50.000 0.00 0.00 33.04 3.58
115 274 0.804989 CGCCTTCCCTGAATGTGAAC 59.195 55.000 0.00 0.00 0.00 3.18
144 303 6.494893 TCCAAAATGAACTATCCAGAAACG 57.505 37.500 0.00 0.00 0.00 3.60
155 314 1.518572 CAGAAACGATCCGGTCCCG 60.519 63.158 0.00 6.34 39.44 5.14
185 344 2.413837 GTCGGGAAATATCGACCATGG 58.586 52.381 11.19 11.19 46.79 3.66
189 384 4.101274 TCGGGAAATATCGACCATGGTTTA 59.899 41.667 20.85 10.83 0.00 2.01
254 449 2.037901 TGCAATCACAACCACCACAAT 58.962 42.857 0.00 0.00 0.00 2.71
259 454 4.751767 ATCACAACCACCACAATTTTGT 57.248 36.364 0.00 0.00 43.36 2.83
270 483 6.488683 CCACCACAATTTTGTCTTAGTTCCTA 59.511 38.462 0.00 0.00 39.91 2.94
275 488 8.836413 CACAATTTTGTCTTAGTTCCTAGTGAA 58.164 33.333 0.00 0.00 39.91 3.18
291 506 7.831753 TCCTAGTGAACAGAGTTCTTTATCAG 58.168 38.462 10.79 1.37 0.00 2.90
389 604 0.537188 GAGAATCCCAGCGTCTCCAA 59.463 55.000 0.00 0.00 33.16 3.53
397 612 1.238439 CAGCGTCTCCAACAACCATT 58.762 50.000 0.00 0.00 0.00 3.16
409 624 4.827284 CCAACAACCATTAAGAGTCAACCT 59.173 41.667 0.00 0.00 0.00 3.50
412 627 7.308589 CCAACAACCATTAAGAGTCAACCTAAG 60.309 40.741 0.00 0.00 0.00 2.18
416 631 7.074653 ACCATTAAGAGTCAACCTAAGTCAA 57.925 36.000 0.00 0.00 0.00 3.18
417 632 7.690256 ACCATTAAGAGTCAACCTAAGTCAAT 58.310 34.615 0.00 0.00 0.00 2.57
431 646 8.177119 ACCTAAGTCAATCAAATAGTGCAAAA 57.823 30.769 0.00 0.00 0.00 2.44
461 676 3.981212 AGGCCAAATTGCTAAGTATGGT 58.019 40.909 5.01 0.00 0.00 3.55
529 746 1.828595 TCAACAAGTCCTAGCCGCATA 59.171 47.619 0.00 0.00 0.00 3.14
530 747 2.235155 TCAACAAGTCCTAGCCGCATAA 59.765 45.455 0.00 0.00 0.00 1.90
531 748 2.311124 ACAAGTCCTAGCCGCATAAC 57.689 50.000 0.00 0.00 0.00 1.89
636 1020 3.983044 ACCATTCCAGTGTCTACTTCC 57.017 47.619 0.00 0.00 34.07 3.46
644 1028 5.338632 TCCAGTGTCTACTTCCCTCAAATA 58.661 41.667 0.00 0.00 34.07 1.40
688 1072 8.854117 AGAAGATGTAAATGATAAATTGGAGCC 58.146 33.333 0.00 0.00 0.00 4.70
692 1076 6.559810 TGTAAATGATAAATTGGAGCCGTTG 58.440 36.000 0.00 0.00 0.00 4.10
715 1099 8.974408 GTTGGTTATGTTTTTAAGGATGTCAAC 58.026 33.333 0.00 0.00 0.00 3.18
874 1269 6.015095 TGGGACAACATAACATATTGTTTGCA 60.015 34.615 0.00 0.00 37.29 4.08
1025 1432 0.902531 ACATCAGAACCGGTACAGGG 59.097 55.000 16.82 8.76 35.02 4.45
1188 1595 6.760298 TGCACTTTGTTGATAGATCATCTCTC 59.240 38.462 0.00 0.00 36.56 3.20
1311 1718 0.399949 TGGTGATCGCCCCCTTATCT 60.400 55.000 22.48 0.00 0.00 1.98
1317 1724 0.550914 TCGCCCCCTTATCTGCAAAT 59.449 50.000 0.00 0.00 0.00 2.32
1375 1782 3.309682 ACCGTTAGATTCGATGTTGCATG 59.690 43.478 0.00 0.00 0.00 4.06
1403 1810 3.403038 TCAGTTAAGAGAACAGCAAGCC 58.597 45.455 0.00 0.00 0.00 4.35
1585 1992 0.932123 CGCCACATCGAGACGATCAG 60.932 60.000 3.65 0.56 45.19 2.90
1586 1993 0.101399 GCCACATCGAGACGATCAGT 59.899 55.000 3.65 0.00 45.19 3.41
1622 2029 4.629523 GTCCCGCCCACCACGAAA 62.630 66.667 0.00 0.00 0.00 3.46
1777 2184 2.987821 CTGTCTAGCTGATGCGATGATG 59.012 50.000 0.00 0.00 45.42 3.07
1783 2190 1.509703 CTGATGCGATGATGGGTCAG 58.490 55.000 0.00 0.00 37.87 3.51
1785 2192 1.224075 GATGCGATGATGGGTCAGTG 58.776 55.000 0.00 0.00 37.87 3.66
1817 2231 7.603024 AGGTGTTTATGCTTAGTACTTGAGTTC 59.397 37.037 0.00 0.00 0.00 3.01
1850 2295 2.038387 ACATCTGGGTGTTTATCGGC 57.962 50.000 0.00 0.00 0.00 5.54
1921 2372 7.636150 TGTTACTGTAGTAGATGTTACTCCC 57.364 40.000 0.00 0.00 0.00 4.30
1922 2373 7.408543 TGTTACTGTAGTAGATGTTACTCCCT 58.591 38.462 0.00 0.00 0.00 4.20
1923 2374 7.555554 TGTTACTGTAGTAGATGTTACTCCCTC 59.444 40.741 0.00 0.00 0.00 4.30
1924 2375 5.447757 ACTGTAGTAGATGTTACTCCCTCC 58.552 45.833 0.00 0.00 0.00 4.30
1925 2376 4.458397 TGTAGTAGATGTTACTCCCTCCG 58.542 47.826 0.00 0.00 0.00 4.63
1926 2377 3.666345 AGTAGATGTTACTCCCTCCGT 57.334 47.619 0.00 0.00 0.00 4.69
1927 2378 3.553904 AGTAGATGTTACTCCCTCCGTC 58.446 50.000 0.00 0.00 0.00 4.79
1928 2379 1.777941 AGATGTTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
1929 2380 0.751452 GATGTTACTCCCTCCGTCCC 59.249 60.000 0.00 0.00 0.00 4.46
1930 2381 0.042131 ATGTTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
1931 2382 0.042131 TGTTACTCCCTCCGTCCCAT 59.958 55.000 0.00 0.00 0.00 4.00
1932 2383 1.288633 TGTTACTCCCTCCGTCCCATA 59.711 52.381 0.00 0.00 0.00 2.74
1933 2384 2.292389 TGTTACTCCCTCCGTCCCATAA 60.292 50.000 0.00 0.00 0.00 1.90
1934 2385 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
1935 2386 4.154942 GTTACTCCCTCCGTCCCATAATA 58.845 47.826 0.00 0.00 0.00 0.98
1936 2387 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1937 2388 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1938 2389 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
1939 2390 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
1940 2391 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
1941 2392 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
1942 2393 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
1943 2394 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
1944 2395 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
1945 2396 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
1946 2397 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
1947 2398 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
1948 2399 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
1975 2426 6.787085 ACTAGTGTAGTGTCAAAAATGCTC 57.213 37.500 0.00 0.00 37.69 4.26
1976 2427 6.525629 ACTAGTGTAGTGTCAAAAATGCTCT 58.474 36.000 0.00 0.00 37.69 4.09
1977 2428 6.992715 ACTAGTGTAGTGTCAAAAATGCTCTT 59.007 34.615 0.00 0.00 37.69 2.85
1978 2429 8.148351 ACTAGTGTAGTGTCAAAAATGCTCTTA 58.852 33.333 0.00 0.00 37.69 2.10
1979 2430 7.986085 AGTGTAGTGTCAAAAATGCTCTTAT 57.014 32.000 0.00 0.00 0.00 1.73
1981 2432 9.672673 AGTGTAGTGTCAAAAATGCTCTTATAT 57.327 29.630 0.00 0.00 0.00 0.86
1987 2438 9.683069 GTGTCAAAAATGCTCTTATATTATGGG 57.317 33.333 0.00 0.00 0.00 4.00
1988 2439 9.639563 TGTCAAAAATGCTCTTATATTATGGGA 57.360 29.630 0.00 0.00 0.00 4.37
1989 2440 9.899226 GTCAAAAATGCTCTTATATTATGGGAC 57.101 33.333 0.00 0.00 0.00 4.46
2006 2457 3.965347 TGGGACAGAGGTACTTATTAGGC 59.035 47.826 0.00 0.00 41.55 3.93
2023 2474 3.342926 AGGCCATAGAGACTGAGGAAT 57.657 47.619 5.01 0.00 0.00 3.01
2026 2477 3.389329 GGCCATAGAGACTGAGGAATTGA 59.611 47.826 0.00 0.00 0.00 2.57
2031 2483 7.687837 GCCATAGAGACTGAGGAATTGATGTTA 60.688 40.741 0.00 0.00 0.00 2.41
2041 2493 4.936891 GGAATTGATGTTATTCCAGCCAC 58.063 43.478 9.20 0.00 46.72 5.01
2043 2495 5.450965 GGAATTGATGTTATTCCAGCCACAG 60.451 44.000 9.20 0.00 46.72 3.66
2044 2496 3.719268 TGATGTTATTCCAGCCACAGT 57.281 42.857 0.00 0.00 0.00 3.55
2045 2497 3.346315 TGATGTTATTCCAGCCACAGTG 58.654 45.455 0.00 0.00 0.00 3.66
2046 2498 2.949177 TGTTATTCCAGCCACAGTGT 57.051 45.000 0.00 0.00 0.00 3.55
2047 2499 3.222173 TGTTATTCCAGCCACAGTGTT 57.778 42.857 0.00 0.00 0.00 3.32
2083 2541 2.358957 TGGATGAATCTGCTTCCGTTG 58.641 47.619 0.00 0.00 35.47 4.10
2084 2542 2.290260 TGGATGAATCTGCTTCCGTTGT 60.290 45.455 0.00 0.00 35.47 3.32
2085 2543 2.749621 GGATGAATCTGCTTCCGTTGTT 59.250 45.455 0.00 0.00 32.49 2.83
2086 2544 3.191371 GGATGAATCTGCTTCCGTTGTTT 59.809 43.478 0.00 0.00 32.49 2.83
2087 2545 3.896648 TGAATCTGCTTCCGTTGTTTC 57.103 42.857 0.00 0.00 32.49 2.78
2088 2546 3.476552 TGAATCTGCTTCCGTTGTTTCT 58.523 40.909 0.00 0.00 32.49 2.52
2089 2547 3.498397 TGAATCTGCTTCCGTTGTTTCTC 59.502 43.478 0.00 0.00 32.49 2.87
2090 2548 2.910688 TCTGCTTCCGTTGTTTCTCT 57.089 45.000 0.00 0.00 0.00 3.10
2091 2549 3.194005 TCTGCTTCCGTTGTTTCTCTT 57.806 42.857 0.00 0.00 0.00 2.85
2105 2563 7.587757 CGTTGTTTCTCTTCTGAATTTTACTGG 59.412 37.037 0.00 0.00 0.00 4.00
2110 2568 5.882557 TCTCTTCTGAATTTTACTGGGATGC 59.117 40.000 0.00 0.00 0.00 3.91
2132 2592 0.401356 TGCAAATGACTCCAGCTGGA 59.599 50.000 33.04 33.04 43.08 3.86
2140 2600 1.153939 CTCCAGCTGGAACTCGTCG 60.154 63.158 34.30 18.20 44.91 5.12
2209 2676 0.179116 CTGCACTGTCAGGATCGGAG 60.179 60.000 4.53 0.00 0.00 4.63
2212 2679 0.463204 CACTGTCAGGATCGGAGCAT 59.537 55.000 4.53 0.00 0.00 3.79
2217 2684 0.904649 TCAGGATCGGAGCATTGTGT 59.095 50.000 0.00 0.00 0.00 3.72
2221 2688 1.398390 GGATCGGAGCATTGTGTGAAC 59.602 52.381 0.00 0.00 0.00 3.18
2230 2697 1.326245 CATTGTGTGAACGTGACGTGT 59.674 47.619 12.85 1.44 39.99 4.49
2232 2699 0.802994 TGTGTGAACGTGACGTGTCC 60.803 55.000 12.85 4.89 39.99 4.02
2235 2702 2.732094 GAACGTGACGTGTCCCGG 60.732 66.667 12.85 0.00 39.99 5.73
2246 2713 3.423154 GTCCCGGCAAAGTGCTCG 61.423 66.667 0.00 2.60 44.28 5.03
2342 2809 2.028930 GGATTCAGTTCAGTCACCGTCT 60.029 50.000 0.00 0.00 0.00 4.18
2351 2818 1.671379 GTCACCGTCTTGGCCTTCC 60.671 63.158 3.32 0.00 43.94 3.46
2360 2841 0.393537 CTTGGCCTTCCTGCTACCAG 60.394 60.000 3.32 0.00 38.85 4.00
2371 2852 3.460648 GCTACCAGCAGTAACAGGG 57.539 57.895 0.00 0.00 41.89 4.45
2392 2873 0.239082 CGTTTTGGTTTCGTAGCCCC 59.761 55.000 0.00 0.00 0.00 5.80
2394 2875 0.185416 TTTTGGTTTCGTAGCCCCCA 59.815 50.000 0.00 0.00 0.00 4.96
2395 2876 0.537828 TTTGGTTTCGTAGCCCCCAC 60.538 55.000 0.00 0.00 0.00 4.61
2450 2939 1.222115 GGTGCAGTGTTGACTCGTCC 61.222 60.000 0.00 0.00 0.00 4.79
2490 2979 2.049063 ACTCCAGCGCGTCAGAAC 60.049 61.111 8.43 0.00 0.00 3.01
2537 3026 4.473444 ACTCCAAGAAAATGCAGGAAAGA 58.527 39.130 0.00 0.00 0.00 2.52
2581 3070 8.869109 AGTTGGAATATTTCAACCAAAATCAGA 58.131 29.630 28.54 0.00 42.71 3.27
2583 3072 8.648698 TGGAATATTTCAACCAAAATCAGAGA 57.351 30.769 0.00 0.00 31.50 3.10
2617 3125 2.689983 GAGAGAGAGAGAGAGGCCTTTG 59.310 54.545 6.77 0.00 0.00 2.77
2618 3126 2.311542 AGAGAGAGAGAGAGGCCTTTGA 59.688 50.000 6.77 0.00 0.00 2.69
2619 3127 2.689983 GAGAGAGAGAGAGGCCTTTGAG 59.310 54.545 6.77 0.00 0.00 3.02
2620 3128 2.042979 AGAGAGAGAGAGGCCTTTGAGT 59.957 50.000 6.77 0.00 0.00 3.41
2621 3129 2.831526 GAGAGAGAGAGGCCTTTGAGTT 59.168 50.000 6.77 0.00 0.00 3.01
2640 3149 2.051345 GAGGTGTTTTGCGGCGTG 60.051 61.111 9.37 0.00 0.00 5.34
2680 3189 7.706179 CGCAAATAAATGGTGAACCTGATAATT 59.294 33.333 0.37 0.00 36.82 1.40
2681 3190 8.819974 GCAAATAAATGGTGAACCTGATAATTG 58.180 33.333 0.37 2.78 36.82 2.32
2683 3192 5.343307 AAATGGTGAACCTGATAATTGCC 57.657 39.130 0.37 0.00 36.82 4.52
2707 3220 9.214957 GCCCAAATAATAAAAACAAAAGTAGCT 57.785 29.630 0.00 0.00 0.00 3.32
2713 3226 9.946165 ATAATAAAAACAAAAGTAGCTATCGCC 57.054 29.630 0.00 0.00 36.60 5.54
2729 3242 4.965119 ATCGCCTTTTCATCTTTACACC 57.035 40.909 0.00 0.00 0.00 4.16
2732 3245 2.727916 GCCTTTTCATCTTTACACCGCG 60.728 50.000 0.00 0.00 0.00 6.46
2737 3250 3.306917 TCATCTTTACACCGCGAAAGA 57.693 42.857 19.11 19.11 43.78 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 9.607333 TGTATCTAGGGAAACATTCAGATATCT 57.393 33.333 0.00 0.00 30.20 1.98
41 43 8.547481 TGTATCTGTATCTAGGGAAACATTCA 57.453 34.615 0.00 0.00 0.00 2.57
42 44 8.643324 ACTGTATCTGTATCTAGGGAAACATTC 58.357 37.037 0.00 0.00 0.00 2.67
57 59 9.347777 TCTAGGGAAGGATATACTGTATCTGTA 57.652 37.037 3.09 0.00 0.00 2.74
58 60 8.233349 TCTAGGGAAGGATATACTGTATCTGT 57.767 38.462 3.09 0.00 0.00 3.41
59 61 9.349713 GATCTAGGGAAGGATATACTGTATCTG 57.650 40.741 3.09 0.00 0.00 2.90
60 62 9.074715 TGATCTAGGGAAGGATATACTGTATCT 57.925 37.037 3.09 0.00 0.00 1.98
61 63 9.349713 CTGATCTAGGGAAGGATATACTGTATC 57.650 40.741 3.09 0.00 0.00 2.24
62 64 8.285891 CCTGATCTAGGGAAGGATATACTGTAT 58.714 40.741 5.53 5.53 43.33 2.29
63 65 7.644062 CCTGATCTAGGGAAGGATATACTGTA 58.356 42.308 0.00 0.00 43.33 2.74
64 66 6.498538 CCTGATCTAGGGAAGGATATACTGT 58.501 44.000 0.00 0.00 43.33 3.55
97 99 2.206576 AGTTCACATTCAGGGAAGGC 57.793 50.000 0.00 0.00 41.18 4.35
144 303 0.528470 GATCAGATCGGGACCGGATC 59.472 60.000 26.80 26.80 40.25 3.36
155 314 5.098893 CGATATTTCCCGACAGATCAGATC 58.901 45.833 1.64 1.64 0.00 2.75
185 344 4.003648 CACAGAAGTCATCCCACCTAAAC 58.996 47.826 0.00 0.00 0.00 2.01
189 384 0.987294 CCACAGAAGTCATCCCACCT 59.013 55.000 0.00 0.00 0.00 4.00
270 483 8.738645 AAAACTGATAAAGAACTCTGTTCACT 57.261 30.769 12.16 2.41 33.93 3.41
275 488 9.262358 GTGTCTAAAACTGATAAAGAACTCTGT 57.738 33.333 0.00 0.00 0.00 3.41
329 544 4.274978 TCATGGATGCATGTCATGAAACT 58.725 39.130 26.90 0.00 42.65 2.66
338 553 6.548251 TCATTTAGTCATTCATGGATGCATGT 59.452 34.615 24.37 8.76 33.92 3.21
358 573 5.619220 GCTGGGATTCTCATACTCTCATTT 58.381 41.667 0.00 0.00 0.00 2.32
389 604 6.838382 ACTTAGGTTGACTCTTAATGGTTGT 58.162 36.000 0.00 0.00 0.00 3.32
412 627 9.624697 TTCTACATTTTGCACTATTTGATTGAC 57.375 29.630 0.00 0.00 0.00 3.18
416 631 9.643693 CCTTTTCTACATTTTGCACTATTTGAT 57.356 29.630 0.00 0.00 0.00 2.57
417 632 7.598493 GCCTTTTCTACATTTTGCACTATTTGA 59.402 33.333 0.00 0.00 0.00 2.69
431 646 6.211384 ACTTAGCAATTTGGCCTTTTCTACAT 59.789 34.615 3.32 0.00 0.00 2.29
441 656 3.699038 TCACCATACTTAGCAATTTGGCC 59.301 43.478 0.00 0.00 0.00 5.36
461 676 3.701205 TTTGAGCTCCAATGCTAGTCA 57.299 42.857 12.15 0.00 44.17 3.41
509 726 0.613260 ATGCGGCTAGGACTTGTTGA 59.387 50.000 0.00 0.00 0.00 3.18
520 737 3.267483 GAAGACCAAAGTTATGCGGCTA 58.733 45.455 0.00 0.00 0.00 3.93
522 739 1.810151 TGAAGACCAAAGTTATGCGGC 59.190 47.619 0.00 0.00 0.00 6.53
529 746 7.173907 CACATTCTGTATCTGAAGACCAAAGTT 59.826 37.037 0.00 0.00 0.00 2.66
530 747 6.652481 CACATTCTGTATCTGAAGACCAAAGT 59.348 38.462 0.00 0.00 0.00 2.66
531 748 6.652481 ACACATTCTGTATCTGAAGACCAAAG 59.348 38.462 0.00 0.00 0.00 2.77
555 939 9.712305 AACCTGATGTTACTATCATTATAGCAC 57.288 33.333 0.00 0.00 39.01 4.40
593 977 7.502226 TGGTAAGGCAATATGAGGTAATCAAAG 59.498 37.037 0.00 0.00 42.53 2.77
602 986 4.728772 TGGAATGGTAAGGCAATATGAGG 58.271 43.478 0.00 0.00 0.00 3.86
606 990 5.103940 AGACACTGGAATGGTAAGGCAATAT 60.104 40.000 0.00 0.00 0.00 1.28
616 1000 2.572104 GGGAAGTAGACACTGGAATGGT 59.428 50.000 0.00 0.00 34.36 3.55
636 1020 8.980481 AATAGGGTCAAATGTACTATTTGAGG 57.020 34.615 22.64 6.84 45.30 3.86
644 1028 8.993424 ACATCTTCTAATAGGGTCAAATGTACT 58.007 33.333 0.00 0.00 0.00 2.73
688 1072 7.364200 TGACATCCTTAAAAACATAACCAACG 58.636 34.615 0.00 0.00 0.00 4.10
692 1076 7.325097 CACGTTGACATCCTTAAAAACATAACC 59.675 37.037 0.00 0.00 0.00 2.85
715 1099 1.915614 GCACTGCATGAGGGAACACG 61.916 60.000 0.00 0.00 0.00 4.49
788 1182 5.532779 AGAGAATGATACGTCTGCATCTGTA 59.467 40.000 0.00 0.00 0.00 2.74
1188 1595 2.295253 AAAGAATGACGTCGCTAGGG 57.705 50.000 11.62 0.00 0.00 3.53
1311 1718 0.614415 CCTTGGCCAGGGTATTTGCA 60.614 55.000 25.60 0.00 39.39 4.08
1375 1782 4.094146 GCTGTTCTCTTAACTGATTCAGGC 59.906 45.833 17.66 3.43 35.51 4.85
1403 1810 2.049156 TGTGCTGGAACGAGAGCG 60.049 61.111 0.00 0.00 44.79 5.03
1409 1816 0.249447 TGTCAGTCTGTGCTGGAACG 60.249 55.000 0.00 0.00 37.12 3.95
1412 1819 2.104622 TGAAATGTCAGTCTGTGCTGGA 59.895 45.455 0.00 0.00 37.12 3.86
1519 1926 4.695993 TGTTCATGGCTGGCGCGA 62.696 61.111 12.10 0.00 36.88 5.87
1585 1992 0.804989 CAGGGAAATGCCGAGTTGAC 59.195 55.000 0.00 0.00 37.63 3.18
1586 1993 0.322456 CCAGGGAAATGCCGAGTTGA 60.322 55.000 0.00 0.00 37.63 3.18
1777 2184 0.180406 ACACCTGAACACACTGACCC 59.820 55.000 0.00 0.00 0.00 4.46
1783 2190 4.568152 AAGCATAAACACCTGAACACAC 57.432 40.909 0.00 0.00 0.00 3.82
1785 2192 5.941948 ACTAAGCATAAACACCTGAACAC 57.058 39.130 0.00 0.00 0.00 3.32
1817 2231 0.957395 AGATGTTGGCGGCACAGAAG 60.957 55.000 12.92 0.00 0.00 2.85
1850 2295 3.595173 TGTTGGGTCAATACAGACATCG 58.405 45.455 0.00 0.00 40.29 3.84
1917 2368 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
1918 2369 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
1919 2370 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
1920 2371 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
1921 2372 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
1922 2373 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
1923 2374 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
1924 2375 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
1952 2403 6.525629 AGAGCATTTTTGACACTACACTAGT 58.474 36.000 0.00 0.00 40.28 2.57
1953 2404 7.426929 AAGAGCATTTTTGACACTACACTAG 57.573 36.000 0.00 0.00 0.00 2.57
1955 2406 7.986085 ATAAGAGCATTTTTGACACTACACT 57.014 32.000 0.00 0.00 0.00 3.55
1961 2412 9.683069 CCCATAATATAAGAGCATTTTTGACAC 57.317 33.333 0.00 0.00 0.00 3.67
1962 2413 9.639563 TCCCATAATATAAGAGCATTTTTGACA 57.360 29.630 0.00 0.00 0.00 3.58
1963 2414 9.899226 GTCCCATAATATAAGAGCATTTTTGAC 57.101 33.333 0.00 0.00 0.00 3.18
1964 2415 9.639563 TGTCCCATAATATAAGAGCATTTTTGA 57.360 29.630 0.00 0.00 0.00 2.69
1965 2416 9.903682 CTGTCCCATAATATAAGAGCATTTTTG 57.096 33.333 0.00 0.00 0.00 2.44
1966 2417 9.866655 TCTGTCCCATAATATAAGAGCATTTTT 57.133 29.630 0.00 0.00 0.00 1.94
1967 2418 9.512588 CTCTGTCCCATAATATAAGAGCATTTT 57.487 33.333 0.00 0.00 0.00 1.82
1968 2419 8.105829 CCTCTGTCCCATAATATAAGAGCATTT 58.894 37.037 0.00 0.00 0.00 2.32
1969 2420 7.238514 ACCTCTGTCCCATAATATAAGAGCATT 59.761 37.037 0.00 0.00 0.00 3.56
1970 2421 6.732862 ACCTCTGTCCCATAATATAAGAGCAT 59.267 38.462 0.00 0.00 0.00 3.79
1971 2422 6.084738 ACCTCTGTCCCATAATATAAGAGCA 58.915 40.000 0.00 0.00 0.00 4.26
1972 2423 6.613153 ACCTCTGTCCCATAATATAAGAGC 57.387 41.667 0.00 0.00 0.00 4.09
1973 2424 8.887264 AGTACCTCTGTCCCATAATATAAGAG 57.113 38.462 0.00 0.00 0.00 2.85
1979 2430 9.543231 CCTAATAAGTACCTCTGTCCCATAATA 57.457 37.037 0.00 0.00 0.00 0.98
1980 2431 7.038231 GCCTAATAAGTACCTCTGTCCCATAAT 60.038 40.741 0.00 0.00 0.00 1.28
1981 2432 6.269307 GCCTAATAAGTACCTCTGTCCCATAA 59.731 42.308 0.00 0.00 0.00 1.90
1982 2433 5.778750 GCCTAATAAGTACCTCTGTCCCATA 59.221 44.000 0.00 0.00 0.00 2.74
1983 2434 4.593634 GCCTAATAAGTACCTCTGTCCCAT 59.406 45.833 0.00 0.00 0.00 4.00
1984 2435 3.965347 GCCTAATAAGTACCTCTGTCCCA 59.035 47.826 0.00 0.00 0.00 4.37
1985 2436 3.324268 GGCCTAATAAGTACCTCTGTCCC 59.676 52.174 0.00 0.00 0.00 4.46
1986 2437 3.965347 TGGCCTAATAAGTACCTCTGTCC 59.035 47.826 3.32 0.00 0.00 4.02
1987 2438 5.810080 ATGGCCTAATAAGTACCTCTGTC 57.190 43.478 3.32 0.00 0.00 3.51
1988 2439 6.621394 TCTATGGCCTAATAAGTACCTCTGT 58.379 40.000 3.32 0.00 0.00 3.41
1989 2440 6.948886 TCTCTATGGCCTAATAAGTACCTCTG 59.051 42.308 3.32 0.00 0.00 3.35
1990 2441 6.949463 GTCTCTATGGCCTAATAAGTACCTCT 59.051 42.308 3.32 0.00 0.00 3.69
1991 2442 6.949463 AGTCTCTATGGCCTAATAAGTACCTC 59.051 42.308 3.32 0.00 0.00 3.85
1992 2443 6.722129 CAGTCTCTATGGCCTAATAAGTACCT 59.278 42.308 3.32 0.00 0.00 3.08
1993 2444 6.720288 TCAGTCTCTATGGCCTAATAAGTACC 59.280 42.308 3.32 0.00 0.00 3.34
1994 2445 7.094118 CCTCAGTCTCTATGGCCTAATAAGTAC 60.094 44.444 3.32 0.00 0.00 2.73
1995 2446 6.948886 CCTCAGTCTCTATGGCCTAATAAGTA 59.051 42.308 3.32 0.00 0.00 2.24
1996 2447 5.777732 CCTCAGTCTCTATGGCCTAATAAGT 59.222 44.000 3.32 0.00 0.00 2.24
1997 2448 6.013379 TCCTCAGTCTCTATGGCCTAATAAG 58.987 44.000 3.32 0.00 0.00 1.73
1998 2449 5.965486 TCCTCAGTCTCTATGGCCTAATAA 58.035 41.667 3.32 0.00 0.00 1.40
1999 2450 5.600669 TCCTCAGTCTCTATGGCCTAATA 57.399 43.478 3.32 0.00 0.00 0.98
2000 2451 4.477536 TCCTCAGTCTCTATGGCCTAAT 57.522 45.455 3.32 0.00 0.00 1.73
2006 2457 6.172136 ACATCAATTCCTCAGTCTCTATGG 57.828 41.667 0.00 0.00 0.00 2.74
2023 2474 3.758023 CACTGTGGCTGGAATAACATCAA 59.242 43.478 0.00 0.00 0.00 2.57
2026 2477 3.439857 ACACTGTGGCTGGAATAACAT 57.560 42.857 13.09 0.00 0.00 2.71
2031 2483 3.439857 ACATAACACTGTGGCTGGAAT 57.560 42.857 13.09 0.00 0.00 3.01
2083 2541 7.745620 TCCCAGTAAAATTCAGAAGAGAAAC 57.254 36.000 0.00 0.00 0.00 2.78
2084 2542 7.094205 GCATCCCAGTAAAATTCAGAAGAGAAA 60.094 37.037 0.00 0.00 0.00 2.52
2085 2543 6.375455 GCATCCCAGTAAAATTCAGAAGAGAA 59.625 38.462 0.00 0.00 0.00 2.87
2086 2544 5.882557 GCATCCCAGTAAAATTCAGAAGAGA 59.117 40.000 0.00 0.00 0.00 3.10
2087 2545 5.884792 AGCATCCCAGTAAAATTCAGAAGAG 59.115 40.000 0.00 0.00 0.00 2.85
2088 2546 5.819991 AGCATCCCAGTAAAATTCAGAAGA 58.180 37.500 0.00 0.00 0.00 2.87
2089 2547 6.521151 AAGCATCCCAGTAAAATTCAGAAG 57.479 37.500 0.00 0.00 0.00 2.85
2090 2548 6.690530 CAAAGCATCCCAGTAAAATTCAGAA 58.309 36.000 0.00 0.00 0.00 3.02
2091 2549 5.336690 GCAAAGCATCCCAGTAAAATTCAGA 60.337 40.000 0.00 0.00 0.00 3.27
2105 2563 2.231964 TGGAGTCATTTGCAAAGCATCC 59.768 45.455 18.19 19.54 38.76 3.51
2110 2568 2.352421 CCAGCTGGAGTCATTTGCAAAG 60.352 50.000 29.88 9.78 37.39 2.77
2132 2592 2.048127 GCCTCTTGCCGACGAGTT 60.048 61.111 0.00 0.00 0.00 3.01
2140 2600 3.949842 AAGAGAATTTTGCCTCTTGCC 57.050 42.857 6.39 0.00 45.13 4.52
2209 2676 0.303493 ACGTCACGTTCACACAATGC 59.697 50.000 0.00 0.00 36.35 3.56
2212 2679 0.993532 GACACGTCACGTTCACACAA 59.006 50.000 0.00 0.00 38.32 3.33
2230 2697 4.697756 CCGAGCACTTTGCCGGGA 62.698 66.667 15.94 0.00 46.52 5.14
2235 2702 0.169009 GATTCACCCGAGCACTTTGC 59.831 55.000 0.00 0.00 45.46 3.68
2236 2703 1.466167 CTGATTCACCCGAGCACTTTG 59.534 52.381 0.00 0.00 0.00 2.77
2246 2713 2.427506 GTCACAGGTTCTGATTCACCC 58.572 52.381 1.59 0.00 35.18 4.61
2342 2809 1.685224 CTGGTAGCAGGAAGGCCAA 59.315 57.895 14.29 0.00 36.29 4.52
2360 2841 1.265905 CCAAAACGTCCCTGTTACTGC 59.734 52.381 0.00 0.00 0.00 4.40
2371 2852 1.069703 GGGCTACGAAACCAAAACGTC 60.070 52.381 0.00 0.00 40.61 4.34
2392 2873 2.518349 AACCGTGTGGCCTTGTGG 60.518 61.111 3.32 3.45 39.70 4.17
2394 2875 2.274104 ACAACCGTGTGGCCTTGT 59.726 55.556 3.32 1.44 39.70 3.16
2450 2939 3.671928 GGACACGATTATCCGTTTATCCG 59.328 47.826 0.00 0.00 41.29 4.18
2490 2979 8.355806 GTTTCATTTACTCGCAAAAATACGAAG 58.644 33.333 0.00 0.00 37.94 3.79
2537 3026 3.508845 ACTATAATTTCATGGCCGCCT 57.491 42.857 11.61 0.00 0.00 5.52
2579 3068 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2580 3069 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2581 3070 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2583 3072 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2617 3125 1.864029 GCCGCAAAACACCTCAAACTC 60.864 52.381 0.00 0.00 0.00 3.01
2618 3126 0.102300 GCCGCAAAACACCTCAAACT 59.898 50.000 0.00 0.00 0.00 2.66
2619 3127 1.206115 CGCCGCAAAACACCTCAAAC 61.206 55.000 0.00 0.00 0.00 2.93
2620 3128 1.064946 CGCCGCAAAACACCTCAAA 59.935 52.632 0.00 0.00 0.00 2.69
2621 3129 2.115911 ACGCCGCAAAACACCTCAA 61.116 52.632 0.00 0.00 0.00 3.02
2640 3149 6.879188 TTTATTTGCGATTCGGAATTTTCC 57.121 33.333 13.83 0.00 44.05 3.13
2659 3168 6.041979 GGGCAATTATCAGGTTCACCATTTAT 59.958 38.462 0.00 0.00 38.89 1.40
2680 3189 8.994170 GCTACTTTTGTTTTTATTATTTGGGCA 58.006 29.630 0.00 0.00 0.00 5.36
2681 3190 9.214957 AGCTACTTTTGTTTTTATTATTTGGGC 57.785 29.630 0.00 0.00 0.00 5.36
2707 3220 4.569162 CGGTGTAAAGATGAAAAGGCGATA 59.431 41.667 0.00 0.00 0.00 2.92
2713 3226 4.398549 TTCGCGGTGTAAAGATGAAAAG 57.601 40.909 6.13 0.00 0.00 2.27
2729 3242 1.323534 CCCACGTAATTCTCTTTCGCG 59.676 52.381 0.00 0.00 0.00 5.87
2732 3245 2.418976 GGTGCCCACGTAATTCTCTTTC 59.581 50.000 0.00 0.00 0.00 2.62
2737 3250 1.349688 TGAAGGTGCCCACGTAATTCT 59.650 47.619 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.