Multiple sequence alignment - TraesCS1D01G105800

Loading Multiple Alignment...

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 TraesCS1D01G105800 chr1D 100.000 2717 0 0 1 2717 97908441 97911157 0.000000e+00 5018.0
1 TraesCS1D01G105800 chr1D 83.433 670 81 12 101 762 192969186 192968539 1.800000e-166 595.0
2 TraesCS1D01G105800 chr1D 86.189 391 47 6 2330 2717 15303502 15303888 1.500000e-112 416.0
3 TraesCS1D01G105800 chr1A 90.628 2102 154 20 1 2080 93366116 93368196 0.000000e+00 2750.0
4 TraesCS1D01G105800 chr1A 87.335 379 39 9 2328 2704 561623116 561622745 2.500000e-115 425.0
5 TraesCS1D01G105800 chr1B 93.285 1787 69 22 856 2632 155439509 155437764 0.000000e+00 2588.0
6 TraesCS1D01G105800 chr1B 85.340 382 44 10 2331 2709 521657073 521656701 4.240000e-103 385.0
7 TraesCS1D01G105800 chr3D 88.129 775 78 8 1 762 381824725 381823952 0.000000e+00 909.0
8 TraesCS1D01G105800 chr3D 85.658 767 96 8 2 762 70311928 70312686 0.000000e+00 795.0
9 TraesCS1D01G105800 chr3D 86.929 635 71 4 140 762 376540026 376540660 0.000000e+00 702.0
10 TraesCS1D01G105800 chr3D 100.000 30 0 0 1927 1956 553932128 553932099 3.780000e-04 56.5
11 TraesCS1D01G105800 chr3B 87.113 776 83 11 1 762 552250756 552251528 0.000000e+00 863.0
12 TraesCS1D01G105800 chr7D 86.710 775 87 7 1 762 295602195 295602966 0.000000e+00 846.0
13 TraesCS1D01G105800 chr7D 86.028 773 91 11 3 762 475586729 475587497 0.000000e+00 813.0
14 TraesCS1D01G105800 chr7D 100.000 30 0 0 1927 1956 234553697 234553726 3.780000e-04 56.5
15 TraesCS1D01G105800 chr5D 86.563 774 89 7 1 762 269745569 269746339 0.000000e+00 839.0
16 TraesCS1D01G105800 chr5D 86.546 773 87 8 3 762 337947424 337946656 0.000000e+00 835.0
17 TraesCS1D01G105800 chr5D 86.316 380 46 6 2328 2705 421490635 421491010 2.520000e-110 409.0
18 TraesCS1D01G105800 chr5D 100.000 29 0 0 1927 1955 534008275 534008303 1.000000e-03 54.7
19 TraesCS1D01G105800 chr4B 86.047 774 95 7 1 762 183455766 183456538 0.000000e+00 819.0
20 TraesCS1D01G105800 chr4B 86.005 393 44 10 2330 2717 577027292 577027678 7.000000e-111 411.0
21 TraesCS1D01G105800 chr4D 85.677 775 96 7 1 762 132574804 132575576 0.000000e+00 802.0
22 TraesCS1D01G105800 chr2D 85.457 777 94 11 1 762 242913730 242914502 0.000000e+00 791.0
23 TraesCS1D01G105800 chr2D 89.212 584 49 7 1 571 312421229 312420647 0.000000e+00 717.0
24 TraesCS1D01G105800 chr2D 85.242 393 46 12 2330 2717 401530452 401530837 7.050000e-106 394.0
25 TraesCS1D01G105800 chr2A 85.419 775 97 10 1 762 549870585 549871356 0.000000e+00 791.0
26 TraesCS1D01G105800 chr3A 83.551 766 88 16 1 760 357304340 357305073 0.000000e+00 682.0
27 TraesCS1D01G105800 chr3A 85.897 390 46 9 2332 2717 328930973 328930589 9.060000e-110 407.0
28 TraesCS1D01G105800 chr2B 92.048 415 33 0 1 415 399367394 399367808 3.900000e-163 584.0
29 TraesCS1D01G105800 chr2B 100.000 29 0 0 1927 1955 468704986 468705014 1.000000e-03 54.7
30 TraesCS1D01G105800 chr6B 87.158 366 39 7 2329 2692 118891084 118891443 2.520000e-110 409.0
31 TraesCS1D01G105800 chr5B 85.979 378 44 8 2329 2704 133899830 133900200 1.960000e-106 396.0
32 TraesCS1D01G105800 chr6D 95.556 45 1 1 1912 1956 457634751 457634708 1.350000e-08 71.3
33 TraesCS1D01G105800 chr4A 100.000 32 0 0 1927 1958 603947621 603947652 2.920000e-05 60.2
34 TraesCS1D01G105800 chr7B 100.000 30 0 0 1927 1956 206509245 206509274 3.780000e-04 56.5


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 TraesCS1D01G105800 chr1D 97908441 97911157 2716 False 5018 5018 100.000 1 2717 1 chr1D.!!$F2 2716
1 TraesCS1D01G105800 chr1D 192968539 192969186 647 True 595 595 83.433 101 762 1 chr1D.!!$R1 661
2 TraesCS1D01G105800 chr1A 93366116 93368196 2080 False 2750 2750 90.628 1 2080 1 chr1A.!!$F1 2079
3 TraesCS1D01G105800 chr1B 155437764 155439509 1745 True 2588 2588 93.285 856 2632 1 chr1B.!!$R1 1776
4 TraesCS1D01G105800 chr3D 381823952 381824725 773 True 909 909 88.129 1 762 1 chr3D.!!$R1 761
5 TraesCS1D01G105800 chr3D 70311928 70312686 758 False 795 795 85.658 2 762 1 chr3D.!!$F1 760
6 TraesCS1D01G105800 chr3D 376540026 376540660 634 False 702 702 86.929 140 762 1 chr3D.!!$F2 622
7 TraesCS1D01G105800 chr3B 552250756 552251528 772 False 863 863 87.113 1 762 1 chr3B.!!$F1 761
8 TraesCS1D01G105800 chr7D 295602195 295602966 771 False 846 846 86.710 1 762 1 chr7D.!!$F2 761
9 TraesCS1D01G105800 chr7D 475586729 475587497 768 False 813 813 86.028 3 762 1 chr7D.!!$F3 759
10 TraesCS1D01G105800 chr5D 269745569 269746339 770 False 839 839 86.563 1 762 1 chr5D.!!$F1 761
11 TraesCS1D01G105800 chr5D 337946656 337947424 768 True 835 835 86.546 3 762 1 chr5D.!!$R1 759
12 TraesCS1D01G105800 chr4B 183455766 183456538 772 False 819 819 86.047 1 762 1 chr4B.!!$F1 761
13 TraesCS1D01G105800 chr4D 132574804 132575576 772 False 802 802 85.677 1 762 1 chr4D.!!$F1 761
14 TraesCS1D01G105800 chr2D 242913730 242914502 772 False 791 791 85.457 1 762 1 chr2D.!!$F1 761
15 TraesCS1D01G105800 chr2D 312420647 312421229 582 True 717 717 89.212 1 571 1 chr2D.!!$R1 570
16 TraesCS1D01G105800 chr2A 549870585 549871356 771 False 791 791 85.419 1 762 1 chr2A.!!$F1 761
17 TraesCS1D01G105800 chr3A 357304340 357305073 733 False 682 682 83.551 1 760 1 chr3A.!!$F1 759

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
204 211 0.108377 TGGCTAGTACACACATGGCG 60.108 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2209 0.523966 TCCGGTTTATTTGGCTTGCG 59.476 50.0 0.0 0.0 0.0 4.85 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
20 21 3.591835 GCCGTGTGTGTTGTGGGG 61.592 66.667 0.00 0.00 0.00 4.96
123 126 7.304735 TGTCATTGCATACAGAACAACAATAC 58.695 34.615 0.00 0.00 0.00 1.89
166 173 8.934023 AAGGACTTGATTTCATAACCAAACTA 57.066 30.769 0.00 0.00 0.00 2.24
202 209 1.555075 AGGTGGCTAGTACACACATGG 59.445 52.381 17.52 0.00 40.54 3.66
204 211 0.108377 TGGCTAGTACACACATGGCG 60.108 55.000 0.00 0.00 0.00 5.69
228 235 2.289274 TGCACACACCAAAGTATGTTCG 59.711 45.455 0.00 0.00 28.81 3.95
229 236 2.289547 GCACACACCAAAGTATGTTCGT 59.710 45.455 0.00 0.00 28.81 3.85
253 260 9.274065 CGTAAATGCCTAGAAAACTCAAATAAC 57.726 33.333 0.00 0.00 0.00 1.89
408 419 1.651737 TTCCCTCTCGGAACCATGAA 58.348 50.000 0.00 0.00 46.27 2.57
416 427 3.513912 TCTCGGAACCATGAAGCTTCTTA 59.486 43.478 26.09 8.50 0.00 2.10
424 435 7.121907 GGAACCATGAAGCTTCTTAAGAGAAAT 59.878 37.037 26.09 6.19 41.19 2.17
438 460 9.774413 TCTTAAGAGAAATTCCGATTTATACCC 57.226 33.333 0.00 0.00 35.65 3.69
442 464 8.996651 AGAGAAATTCCGATTTATACCCAAAT 57.003 30.769 0.00 0.00 35.65 2.32
502 527 6.152492 TGTTGTGCCATGTCATAACATAATGT 59.848 34.615 14.02 0.00 44.41 2.71
585 610 8.321353 TCTGAATGTTTACTATCAAGTGGACAT 58.679 33.333 0.00 0.00 40.93 3.06
598 623 1.412710 GTGGACATCGCCTTGGATAGA 59.587 52.381 0.00 0.00 0.00 1.98
606 632 4.553330 TCGCCTTGGATAGACTTTTTCT 57.447 40.909 0.00 0.00 38.51 2.52
607 633 4.906618 TCGCCTTGGATAGACTTTTTCTT 58.093 39.130 0.00 0.00 35.55 2.52
631 658 5.139727 TGTGGGTCTCAAATGTCAGAATTT 58.860 37.500 0.00 0.00 0.00 1.82
682 709 9.629878 TTCTTATTAAGAATTACGGCCCATTTA 57.370 29.630 13.62 0.00 42.31 1.40
683 710 9.629878 TCTTATTAAGAATTACGGCCCATTTAA 57.370 29.630 3.60 0.00 33.83 1.52
712 739 9.415008 TGCTAGCTGAAAATAAATTTATGGGTA 57.585 29.630 17.23 8.49 0.00 3.69
716 743 9.474313 AGCTGAAAATAAATTTATGGGTACTGA 57.526 29.630 11.42 0.00 0.00 3.41
720 747 6.628919 AATAAATTTATGGGTACTGACGGC 57.371 37.500 11.42 0.00 0.00 5.68
753 781 5.484173 TTGCGGATTCTATGATGAACAAC 57.516 39.130 0.00 0.00 0.00 3.32
785 813 5.743636 ACAGGCAAACAAACAATATCCAT 57.256 34.783 0.00 0.00 0.00 3.41
839 867 2.029073 AACTGGGTCAGTCACGCG 59.971 61.111 3.53 3.53 44.62 6.01
862 890 2.033151 GTGTTTCTTCACCCGTTTCTCG 60.033 50.000 0.00 0.00 39.52 4.04
896 924 3.498777 GCCTTTCACAGAAGTACCAACTC 59.501 47.826 0.00 0.00 33.75 3.01
905 933 3.580458 AGAAGTACCAACTCATCAGCAGT 59.420 43.478 0.00 0.00 33.75 4.40
1228 1261 1.304962 TCCTCACCAGGAAGCGCTA 60.305 57.895 12.05 0.00 46.84 4.26
1239 1272 1.946475 GAAGCGCTAAGTCGGACCCT 61.946 60.000 12.05 0.00 0.00 4.34
1380 1413 2.342279 CAGACGGACGGGAAAGCA 59.658 61.111 0.00 0.00 0.00 3.91
1440 1473 4.344865 TTGCCGCTGTTCCTCCCC 62.345 66.667 0.00 0.00 0.00 4.81
1491 1524 0.599558 ACGCGTACCACATGTACTGT 59.400 50.000 11.67 0.00 46.36 3.55
1518 1551 4.794439 CAGCGCGTCACCGATGGA 62.794 66.667 8.43 0.00 40.58 3.41
1575 1608 1.141019 GCTCATCACCTTCGGCGTA 59.859 57.895 6.85 0.00 0.00 4.42
1587 1620 2.789917 GGCGTAGACGAGCTCGAA 59.210 61.111 40.58 22.58 43.02 3.71
1867 1903 4.892345 TGGTTGATCACATTTGGTCTGAAA 59.108 37.500 0.00 0.00 33.50 2.69
1942 1978 4.517453 CCGATTCTTGAACTAAAACCACCA 59.483 41.667 0.00 0.00 0.00 4.17
1950 1986 7.558444 TCTTGAACTAAAACCACCACACTTATT 59.442 33.333 0.00 0.00 0.00 1.40
1951 1987 7.648039 TGAACTAAAACCACCACACTTATTT 57.352 32.000 0.00 0.00 0.00 1.40
1952 1988 8.068892 TGAACTAAAACCACCACACTTATTTT 57.931 30.769 0.00 0.00 0.00 1.82
1953 1989 7.976734 TGAACTAAAACCACCACACTTATTTTG 59.023 33.333 0.00 0.00 0.00 2.44
1954 1990 6.811954 ACTAAAACCACCACACTTATTTTGG 58.188 36.000 0.00 0.00 36.39 3.28
1955 1991 5.941555 AAAACCACCACACTTATTTTGGA 57.058 34.783 0.00 0.00 34.24 3.53
1956 1992 5.941555 AAACCACCACACTTATTTTGGAA 57.058 34.783 0.00 0.00 34.24 3.53
1957 1993 6.493189 AAACCACCACACTTATTTTGGAAT 57.507 33.333 0.00 0.00 34.24 3.01
1996 2032 1.331447 CCTCGTTTTCGGTTTCGGTTT 59.669 47.619 0.00 0.00 44.25 3.27
2004 2040 6.563753 CGTTTTCGGTTTCGGTTTATTAGACA 60.564 38.462 0.00 0.00 39.94 3.41
2168 2209 9.476202 GGTTAAATTGTCAATTTAGGGATATGC 57.524 33.333 23.31 11.70 42.45 3.14
2198 2239 8.700973 AGCCAAATAAACCGGAAAATATGTAAT 58.299 29.630 9.46 0.00 0.00 1.89
2256 2297 8.442384 TGTTGAAAAGAAAAGAGTTCAATTTGC 58.558 29.630 1.46 0.00 40.85 3.68
2257 2298 7.538303 TGAAAAGAAAAGAGTTCAATTTGCC 57.462 32.000 0.00 0.00 0.00 4.52
2261 2302 5.758924 AGAAAAGAGTTCAATTTGCCGTAC 58.241 37.500 0.00 0.00 0.00 3.67
2270 2311 4.255301 TCAATTTGCCGTACGGATAAACT 58.745 39.130 37.62 22.66 37.50 2.66
2271 2312 5.417811 TCAATTTGCCGTACGGATAAACTA 58.582 37.500 37.62 19.96 37.50 2.24
2272 2313 5.291614 TCAATTTGCCGTACGGATAAACTAC 59.708 40.000 37.62 17.21 37.50 2.73
2273 2314 4.454728 TTTGCCGTACGGATAAACTACT 57.545 40.909 37.62 0.00 37.50 2.57
2274 2315 3.698029 TGCCGTACGGATAAACTACTC 57.302 47.619 37.62 15.73 37.50 2.59
2275 2316 2.032054 TGCCGTACGGATAAACTACTCG 59.968 50.000 37.62 6.72 37.50 4.18
2276 2317 2.644078 CCGTACGGATAAACTACTCGC 58.356 52.381 30.64 0.00 37.50 5.03
2277 2318 2.603173 CCGTACGGATAAACTACTCGCC 60.603 54.545 30.64 0.00 37.50 5.54
2278 2319 2.032054 CGTACGGATAAACTACTCGCCA 59.968 50.000 7.57 0.00 0.00 5.69
2279 2320 3.304257 CGTACGGATAAACTACTCGCCAT 60.304 47.826 7.57 0.00 0.00 4.40
2280 2321 4.083855 CGTACGGATAAACTACTCGCCATA 60.084 45.833 7.57 0.00 0.00 2.74
2281 2322 4.234530 ACGGATAAACTACTCGCCATAC 57.765 45.455 0.00 0.00 0.00 2.39
2282 2323 3.887716 ACGGATAAACTACTCGCCATACT 59.112 43.478 0.00 0.00 0.00 2.12
2283 2324 5.065914 ACGGATAAACTACTCGCCATACTA 58.934 41.667 0.00 0.00 0.00 1.82
2284 2325 5.180868 ACGGATAAACTACTCGCCATACTAG 59.819 44.000 0.00 0.00 0.00 2.57
2285 2326 5.391736 CGGATAAACTACTCGCCATACTAGG 60.392 48.000 0.00 0.00 0.00 3.02
2286 2327 5.709164 GGATAAACTACTCGCCATACTAGGA 59.291 44.000 0.00 0.00 0.00 2.94
2287 2328 6.377712 GGATAAACTACTCGCCATACTAGGAT 59.622 42.308 0.00 0.00 0.00 3.24
2295 2336 2.353803 CGCCATACTAGGATTAGTGGCC 60.354 54.545 11.05 0.00 42.14 5.36
2305 2346 2.174854 GGATTAGTGGCCTGGTGGTTAT 59.825 50.000 3.32 0.00 35.27 1.89
2331 2372 3.257375 TGAGCAGTACGTTTGGTCATACT 59.743 43.478 22.65 4.37 45.15 2.12
2342 2383 6.070995 ACGTTTGGTCATACTAGAAGGATTGA 60.071 38.462 0.00 0.00 0.00 2.57
2347 2388 4.979197 GTCATACTAGAAGGATTGAGCGTG 59.021 45.833 0.00 0.00 0.00 5.34
2348 2389 2.301577 ACTAGAAGGATTGAGCGTGC 57.698 50.000 0.00 0.00 0.00 5.34
2349 2390 1.827969 ACTAGAAGGATTGAGCGTGCT 59.172 47.619 0.00 0.00 0.00 4.40
2350 2391 2.234908 ACTAGAAGGATTGAGCGTGCTT 59.765 45.455 0.00 0.00 0.00 3.91
2351 2392 2.191128 AGAAGGATTGAGCGTGCTTT 57.809 45.000 0.00 0.00 0.00 3.51
2352 2393 1.808945 AGAAGGATTGAGCGTGCTTTG 59.191 47.619 0.00 0.00 0.00 2.77
2353 2394 0.242017 AAGGATTGAGCGTGCTTTGC 59.758 50.000 0.00 0.00 0.00 3.68
2355 2396 0.455633 GGATTGAGCGTGCTTTGCTG 60.456 55.000 2.67 0.00 44.18 4.41
2356 2397 1.069378 GATTGAGCGTGCTTTGCTGC 61.069 55.000 2.67 0.00 44.18 5.25
2636 2677 9.608718 AGCTAATACCTCTTATATCTTGGAACT 57.391 33.333 0.00 0.00 0.00 3.01
2637 2678 9.646427 GCTAATACCTCTTATATCTTGGAACTG 57.354 37.037 0.00 0.00 0.00 3.16
2641 2682 7.921041 ACCTCTTATATCTTGGAACTGATGA 57.079 36.000 0.00 0.00 0.00 2.92
2642 2683 8.324191 ACCTCTTATATCTTGGAACTGATGAA 57.676 34.615 0.00 0.00 0.00 2.57
2643 2684 8.772250 ACCTCTTATATCTTGGAACTGATGAAA 58.228 33.333 0.00 0.00 0.00 2.69
2644 2685 9.790344 CCTCTTATATCTTGGAACTGATGAAAT 57.210 33.333 0.00 0.00 0.00 2.17
2656 2697 8.250332 TGGAACTGATGAAATATTTAGTTTGGC 58.750 33.333 12.94 4.05 0.00 4.52
2657 2698 8.250332 GGAACTGATGAAATATTTAGTTTGGCA 58.750 33.333 12.94 1.91 0.00 4.92
2658 2699 9.294030 GAACTGATGAAATATTTAGTTTGGCAG 57.706 33.333 12.94 10.32 0.00 4.85
2659 2700 7.775120 ACTGATGAAATATTTAGTTTGGCAGG 58.225 34.615 0.00 0.00 0.00 4.85
2660 2701 7.397192 ACTGATGAAATATTTAGTTTGGCAGGT 59.603 33.333 0.00 0.00 0.00 4.00
2661 2702 7.546358 TGATGAAATATTTAGTTTGGCAGGTG 58.454 34.615 0.00 0.00 0.00 4.00
2662 2703 6.279513 TGAAATATTTAGTTTGGCAGGTGG 57.720 37.500 0.00 0.00 0.00 4.61
2663 2704 5.186797 TGAAATATTTAGTTTGGCAGGTGGG 59.813 40.000 0.00 0.00 0.00 4.61
2664 2705 1.937191 ATTTAGTTTGGCAGGTGGGG 58.063 50.000 0.00 0.00 0.00 4.96
2665 2706 0.178947 TTTAGTTTGGCAGGTGGGGG 60.179 55.000 0.00 0.00 0.00 5.40
2666 2707 1.068943 TTAGTTTGGCAGGTGGGGGA 61.069 55.000 0.00 0.00 0.00 4.81
2667 2708 1.068943 TAGTTTGGCAGGTGGGGGAA 61.069 55.000 0.00 0.00 0.00 3.97
2668 2709 1.458588 GTTTGGCAGGTGGGGGAAA 60.459 57.895 0.00 0.00 0.00 3.13
2669 2710 0.835971 GTTTGGCAGGTGGGGGAAAT 60.836 55.000 0.00 0.00 0.00 2.17
2670 2711 0.835543 TTTGGCAGGTGGGGGAAATG 60.836 55.000 0.00 0.00 0.00 2.32
2671 2712 1.734420 TTGGCAGGTGGGGGAAATGA 61.734 55.000 0.00 0.00 0.00 2.57
2672 2713 1.311059 GGCAGGTGGGGGAAATGAT 59.689 57.895 0.00 0.00 0.00 2.45
2673 2714 0.555769 GGCAGGTGGGGGAAATGATA 59.444 55.000 0.00 0.00 0.00 2.15
2674 2715 1.479389 GGCAGGTGGGGGAAATGATAG 60.479 57.143 0.00 0.00 0.00 2.08
2675 2716 1.494721 GCAGGTGGGGGAAATGATAGA 59.505 52.381 0.00 0.00 0.00 1.98
2676 2717 2.487986 GCAGGTGGGGGAAATGATAGAG 60.488 54.545 0.00 0.00 0.00 2.43
2677 2718 1.777272 AGGTGGGGGAAATGATAGAGC 59.223 52.381 0.00 0.00 0.00 4.09
2678 2719 1.543429 GGTGGGGGAAATGATAGAGCG 60.543 57.143 0.00 0.00 0.00 5.03
2679 2720 1.141053 GTGGGGGAAATGATAGAGCGT 59.859 52.381 0.00 0.00 0.00 5.07
2680 2721 1.140852 TGGGGGAAATGATAGAGCGTG 59.859 52.381 0.00 0.00 0.00 5.34
2681 2722 1.141053 GGGGGAAATGATAGAGCGTGT 59.859 52.381 0.00 0.00 0.00 4.49
2682 2723 2.421529 GGGGGAAATGATAGAGCGTGTT 60.422 50.000 0.00 0.00 0.00 3.32
2683 2724 3.279434 GGGGAAATGATAGAGCGTGTTT 58.721 45.455 0.00 0.00 0.00 2.83
2684 2725 3.694566 GGGGAAATGATAGAGCGTGTTTT 59.305 43.478 0.00 0.00 0.00 2.43
2685 2726 4.879545 GGGGAAATGATAGAGCGTGTTTTA 59.120 41.667 0.00 0.00 0.00 1.52
2686 2727 5.220796 GGGGAAATGATAGAGCGTGTTTTAC 60.221 44.000 0.00 0.00 0.00 2.01
2687 2728 5.585047 GGGAAATGATAGAGCGTGTTTTACT 59.415 40.000 0.00 0.00 0.00 2.24
2688 2729 6.093633 GGGAAATGATAGAGCGTGTTTTACTT 59.906 38.462 0.00 0.00 0.00 2.24
2689 2730 7.361799 GGGAAATGATAGAGCGTGTTTTACTTT 60.362 37.037 0.00 0.00 0.00 2.66
2690 2731 8.021396 GGAAATGATAGAGCGTGTTTTACTTTT 58.979 33.333 0.00 0.00 0.00 2.27
2692 2733 9.821662 AAATGATAGAGCGTGTTTTACTTTTAC 57.178 29.630 0.00 0.00 0.00 2.01
2693 2734 8.773404 ATGATAGAGCGTGTTTTACTTTTACT 57.227 30.769 0.00 0.00 0.00 2.24
2694 2735 8.597662 TGATAGAGCGTGTTTTACTTTTACTT 57.402 30.769 0.00 0.00 0.00 2.24
2695 2736 9.695526 TGATAGAGCGTGTTTTACTTTTACTTA 57.304 29.630 0.00 0.00 0.00 2.24
2716 2757 8.213518 ACTTATATAATGCGGCTATTTGATGG 57.786 34.615 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.146898 ACAATTGTATACCAGCAAACGTTTC 58.853 36.000 11.37 6.47 0.00 2.78
76 77 1.108776 GCACACGGACCATACTAGGA 58.891 55.000 0.00 0.00 0.00 2.94
164 171 6.772716 AGCCACCTATGTAATTGGATGTTTAG 59.227 38.462 0.00 0.00 42.13 1.85
166 173 5.518865 AGCCACCTATGTAATTGGATGTTT 58.481 37.500 0.00 0.00 42.13 2.83
202 209 0.457681 ACTTTGGTGTGTGCAAACGC 60.458 50.000 12.37 12.37 0.00 4.84
204 211 4.040445 ACATACTTTGGTGTGTGCAAAC 57.960 40.909 0.00 0.00 44.14 2.93
253 260 8.040132 TCAGGGTTCATTTTGCCTTTTTATATG 58.960 33.333 0.00 0.00 0.00 1.78
254 261 8.144862 TCAGGGTTCATTTTGCCTTTTTATAT 57.855 30.769 0.00 0.00 0.00 0.86
408 419 7.929941 AAATCGGAATTTCTCTTAAGAAGCT 57.070 32.000 6.63 0.00 42.36 3.74
416 427 8.817092 TTTGGGTATAAATCGGAATTTCTCTT 57.183 30.769 0.00 0.00 36.49 2.85
424 435 8.005388 TGGGATAAATTTGGGTATAAATCGGAA 58.995 33.333 0.00 0.00 30.33 4.30
498 523 6.647895 GCCTGAAAATCATGAAACTTGACATT 59.352 34.615 0.00 0.00 0.00 2.71
502 527 4.518590 TCGCCTGAAAATCATGAAACTTGA 59.481 37.500 0.00 0.00 0.00 3.02
585 610 4.553330 AGAAAAAGTCTATCCAAGGCGA 57.447 40.909 0.00 0.00 33.56 5.54
598 623 5.993748 TTTGAGACCCACAAAGAAAAAGT 57.006 34.783 0.00 0.00 34.03 2.66
606 632 4.163441 TCTGACATTTGAGACCCACAAA 57.837 40.909 0.00 0.00 40.62 2.83
607 633 3.855255 TCTGACATTTGAGACCCACAA 57.145 42.857 0.00 0.00 0.00 3.33
631 658 5.922053 AGCTGCATGATAGTGACAGATTTA 58.078 37.500 1.02 0.00 0.00 1.40
685 712 8.927411 ACCCATAAATTTATTTTCAGCTAGCAT 58.073 29.630 18.83 3.43 0.00 3.79
702 729 1.202604 CGGCCGTCAGTACCCATAAAT 60.203 52.381 19.50 0.00 0.00 1.40
706 733 4.157120 GCGGCCGTCAGTACCCAT 62.157 66.667 28.70 0.00 0.00 4.00
712 739 0.249398 AATTCTTAGCGGCCGTCAGT 59.751 50.000 28.70 11.79 0.00 3.41
716 743 1.800681 GCAAATTCTTAGCGGCCGT 59.199 52.632 28.70 16.08 0.00 5.68
744 772 5.277058 GCCTGTATTGAGATCGTTGTTCATC 60.277 44.000 0.00 0.00 0.00 2.92
753 781 4.944962 TTGTTTGCCTGTATTGAGATCG 57.055 40.909 0.00 0.00 0.00 3.69
785 813 3.449746 AGCAGGCCCAAAACTAACATA 57.550 42.857 0.00 0.00 0.00 2.29
797 825 0.328258 TGGTAGAGAAAAGCAGGCCC 59.672 55.000 0.00 0.00 0.00 5.80
833 861 1.205657 GTGAAGAAACACTCGCGTGA 58.794 50.000 13.36 0.00 43.97 4.35
839 867 3.203716 AGAAACGGGTGAAGAAACACTC 58.796 45.455 0.00 0.00 40.22 3.51
862 890 2.203294 AAAGGCGTGGGTGTGGAC 60.203 61.111 0.00 0.00 0.00 4.02
896 924 1.904852 GACACGTGGCACTGCTGATG 61.905 60.000 18.77 6.68 0.00 3.07
905 933 2.243957 CGCTTCTTGACACGTGGCA 61.244 57.895 23.03 23.03 0.00 4.92
1249 1282 3.803082 CTCGAACGCGTCCGGGTA 61.803 66.667 20.01 0.00 40.45 3.69
1380 1413 3.782443 GGAACCACGGCGGAGGAT 61.782 66.667 24.28 14.47 38.63 3.24
1423 1456 4.344865 GGGGAGGAACAGCGGCAA 62.345 66.667 1.45 0.00 0.00 4.52
1518 1551 1.228154 GAACAGCACCCCGACCTTT 60.228 57.895 0.00 0.00 0.00 3.11
1575 1608 3.816524 CGGCCTTCGAGCTCGTCT 61.817 66.667 33.33 0.00 42.43 4.18
1867 1903 6.786967 AGCCAAAAATCATCTAAGCAGAAT 57.213 33.333 0.00 0.00 33.50 2.40
1942 1978 8.869109 TCTGATCCAAAATTCCAAAATAAGTGT 58.131 29.630 0.00 0.00 0.00 3.55
1950 1986 6.546484 ACTCTCTCTGATCCAAAATTCCAAA 58.454 36.000 0.00 0.00 0.00 3.28
1951 1987 6.131972 ACTCTCTCTGATCCAAAATTCCAA 57.868 37.500 0.00 0.00 0.00 3.53
1952 1988 5.768980 ACTCTCTCTGATCCAAAATTCCA 57.231 39.130 0.00 0.00 0.00 3.53
1953 1989 6.052360 GGTACTCTCTCTGATCCAAAATTCC 58.948 44.000 0.00 0.00 0.00 3.01
1954 1990 6.883744 AGGTACTCTCTCTGATCCAAAATTC 58.116 40.000 0.00 0.00 0.00 2.17
1955 1991 6.882768 AGGTACTCTCTCTGATCCAAAATT 57.117 37.500 0.00 0.00 0.00 1.82
1996 2032 9.612066 TTATTCTGAATGTGTGCATGTCTAATA 57.388 29.630 13.01 0.00 35.15 0.98
2004 2040 8.089597 TCAAATTGTTATTCTGAATGTGTGCAT 58.910 29.630 13.01 0.00 36.80 3.96
2116 2157 9.119418 CAATATGACACAAGTAACATATCCCAA 57.881 33.333 0.00 0.00 35.69 4.12
2168 2209 0.523966 TCCGGTTTATTTGGCTTGCG 59.476 50.000 0.00 0.00 0.00 4.85
2214 2255 9.357652 TCTTTTCAACAAAGAAATTGAACTCTG 57.642 29.630 0.00 0.00 42.87 3.35
2256 2297 2.603173 GGCGAGTAGTTTATCCGTACGG 60.603 54.545 28.66 28.66 0.00 4.02
2257 2298 2.032054 TGGCGAGTAGTTTATCCGTACG 59.968 50.000 8.69 8.69 0.00 3.67
2261 2302 4.500603 AGTATGGCGAGTAGTTTATCCG 57.499 45.455 0.00 0.00 0.00 4.18
2270 2311 5.008331 CCACTAATCCTAGTATGGCGAGTA 58.992 45.833 0.00 0.00 36.14 2.59
2271 2312 3.827302 CCACTAATCCTAGTATGGCGAGT 59.173 47.826 0.00 0.00 36.14 4.18
2272 2313 3.367498 GCCACTAATCCTAGTATGGCGAG 60.367 52.174 0.00 0.00 37.48 5.03
2273 2314 2.561419 GCCACTAATCCTAGTATGGCGA 59.439 50.000 0.00 0.00 37.48 5.54
2274 2315 2.353803 GGCCACTAATCCTAGTATGGCG 60.354 54.545 0.00 0.00 43.52 5.69
2275 2316 2.907042 AGGCCACTAATCCTAGTATGGC 59.093 50.000 5.01 4.46 42.58 4.40
2276 2317 3.261897 CCAGGCCACTAATCCTAGTATGG 59.738 52.174 5.01 0.00 36.14 2.74
2277 2318 3.904339 ACCAGGCCACTAATCCTAGTATG 59.096 47.826 5.01 0.00 36.14 2.39
2278 2319 3.904339 CACCAGGCCACTAATCCTAGTAT 59.096 47.826 5.01 0.00 36.14 2.12
2279 2320 3.305720 CACCAGGCCACTAATCCTAGTA 58.694 50.000 5.01 0.00 36.14 1.82
2280 2321 2.119495 CACCAGGCCACTAATCCTAGT 58.881 52.381 5.01 0.00 39.04 2.57
2281 2322 1.417890 CCACCAGGCCACTAATCCTAG 59.582 57.143 5.01 0.00 0.00 3.02
2282 2323 1.274184 ACCACCAGGCCACTAATCCTA 60.274 52.381 5.01 0.00 39.06 2.94
2283 2324 0.550147 ACCACCAGGCCACTAATCCT 60.550 55.000 5.01 0.00 39.06 3.24
2284 2325 0.331616 AACCACCAGGCCACTAATCC 59.668 55.000 5.01 0.00 39.06 3.01
2285 2326 3.577805 ATAACCACCAGGCCACTAATC 57.422 47.619 5.01 0.00 39.06 1.75
2286 2327 4.045022 ACTATAACCACCAGGCCACTAAT 58.955 43.478 5.01 0.00 39.06 1.73
2287 2328 3.456842 ACTATAACCACCAGGCCACTAA 58.543 45.455 5.01 0.00 39.06 2.24
2295 2336 4.207891 ACTGCTCAACTATAACCACCAG 57.792 45.455 0.00 0.00 0.00 4.00
2305 2346 3.068448 TGACCAAACGTACTGCTCAACTA 59.932 43.478 0.00 0.00 0.00 2.24
2331 2372 3.002791 CAAAGCACGCTCAATCCTTCTA 58.997 45.455 0.00 0.00 0.00 2.10
2342 2383 3.585990 AACGCAGCAAAGCACGCT 61.586 55.556 0.00 0.00 41.47 5.07
2347 2388 1.226945 ACCAACAACGCAGCAAAGC 60.227 52.632 0.00 0.00 0.00 3.51
2348 2389 0.179140 ACACCAACAACGCAGCAAAG 60.179 50.000 0.00 0.00 0.00 2.77
2349 2390 0.244994 AACACCAACAACGCAGCAAA 59.755 45.000 0.00 0.00 0.00 3.68
2350 2391 0.457509 CAACACCAACAACGCAGCAA 60.458 50.000 0.00 0.00 0.00 3.91
2351 2392 1.138459 CAACACCAACAACGCAGCA 59.862 52.632 0.00 0.00 0.00 4.41
2352 2393 0.457681 AACAACACCAACAACGCAGC 60.458 50.000 0.00 0.00 0.00 5.25
2353 2394 1.267365 CAACAACACCAACAACGCAG 58.733 50.000 0.00 0.00 0.00 5.18
2354 2395 0.109086 CCAACAACACCAACAACGCA 60.109 50.000 0.00 0.00 0.00 5.24
2355 2396 0.804156 CCCAACAACACCAACAACGC 60.804 55.000 0.00 0.00 0.00 4.84
2356 2397 0.528470 ACCCAACAACACCAACAACG 59.472 50.000 0.00 0.00 0.00 4.10
2488 2529 9.683069 ATGATGAATTAGAAAATACCGATTTGC 57.317 29.630 0.00 0.00 35.38 3.68
2632 2673 9.294030 CTGCCAAACTAAATATTTCATCAGTTC 57.706 33.333 12.33 4.25 0.00 3.01
2633 2674 8.253113 CCTGCCAAACTAAATATTTCATCAGTT 58.747 33.333 3.39 6.15 0.00 3.16
2634 2675 7.397192 ACCTGCCAAACTAAATATTTCATCAGT 59.603 33.333 3.39 0.00 0.00 3.41
2635 2676 7.703621 CACCTGCCAAACTAAATATTTCATCAG 59.296 37.037 3.39 0.00 0.00 2.90
2636 2677 7.363705 CCACCTGCCAAACTAAATATTTCATCA 60.364 37.037 3.39 0.00 0.00 3.07
2637 2678 6.980397 CCACCTGCCAAACTAAATATTTCATC 59.020 38.462 3.39 0.00 0.00 2.92
2638 2679 6.127083 CCCACCTGCCAAACTAAATATTTCAT 60.127 38.462 3.39 0.00 0.00 2.57
2639 2680 5.186797 CCCACCTGCCAAACTAAATATTTCA 59.813 40.000 3.39 0.00 0.00 2.69
2640 2681 5.395214 CCCCACCTGCCAAACTAAATATTTC 60.395 44.000 3.39 0.00 0.00 2.17
2641 2682 4.469586 CCCCACCTGCCAAACTAAATATTT 59.530 41.667 5.89 5.89 0.00 1.40
2642 2683 4.030216 CCCCACCTGCCAAACTAAATATT 58.970 43.478 0.00 0.00 0.00 1.28
2643 2684 3.629796 CCCCCACCTGCCAAACTAAATAT 60.630 47.826 0.00 0.00 0.00 1.28
2644 2685 2.291930 CCCCCACCTGCCAAACTAAATA 60.292 50.000 0.00 0.00 0.00 1.40
2645 2686 1.552254 CCCCCACCTGCCAAACTAAAT 60.552 52.381 0.00 0.00 0.00 1.40
2646 2687 0.178947 CCCCCACCTGCCAAACTAAA 60.179 55.000 0.00 0.00 0.00 1.85
2647 2688 1.068943 TCCCCCACCTGCCAAACTAA 61.069 55.000 0.00 0.00 0.00 2.24
2648 2689 1.068943 TTCCCCCACCTGCCAAACTA 61.069 55.000 0.00 0.00 0.00 2.24
2649 2690 1.955458 TTTCCCCCACCTGCCAAACT 61.955 55.000 0.00 0.00 0.00 2.66
2650 2691 0.835971 ATTTCCCCCACCTGCCAAAC 60.836 55.000 0.00 0.00 0.00 2.93
2651 2692 0.835543 CATTTCCCCCACCTGCCAAA 60.836 55.000 0.00 0.00 0.00 3.28
2652 2693 1.229145 CATTTCCCCCACCTGCCAA 60.229 57.895 0.00 0.00 0.00 4.52
2653 2694 1.517538 ATCATTTCCCCCACCTGCCA 61.518 55.000 0.00 0.00 0.00 4.92
2654 2695 0.555769 TATCATTTCCCCCACCTGCC 59.444 55.000 0.00 0.00 0.00 4.85
2655 2696 1.494721 TCTATCATTTCCCCCACCTGC 59.505 52.381 0.00 0.00 0.00 4.85
2656 2697 2.487986 GCTCTATCATTTCCCCCACCTG 60.488 54.545 0.00 0.00 0.00 4.00
2657 2698 1.777272 GCTCTATCATTTCCCCCACCT 59.223 52.381 0.00 0.00 0.00 4.00
2658 2699 1.543429 CGCTCTATCATTTCCCCCACC 60.543 57.143 0.00 0.00 0.00 4.61
2659 2700 1.141053 ACGCTCTATCATTTCCCCCAC 59.859 52.381 0.00 0.00 0.00 4.61
2660 2701 1.140852 CACGCTCTATCATTTCCCCCA 59.859 52.381 0.00 0.00 0.00 4.96
2661 2702 1.141053 ACACGCTCTATCATTTCCCCC 59.859 52.381 0.00 0.00 0.00 5.40
2662 2703 2.622064 ACACGCTCTATCATTTCCCC 57.378 50.000 0.00 0.00 0.00 4.81
2663 2704 4.965119 AAAACACGCTCTATCATTTCCC 57.035 40.909 0.00 0.00 0.00 3.97
2664 2705 6.663944 AGTAAAACACGCTCTATCATTTCC 57.336 37.500 0.00 0.00 0.00 3.13
2665 2706 8.950403 AAAAGTAAAACACGCTCTATCATTTC 57.050 30.769 0.00 0.00 0.00 2.17
2666 2707 9.821662 GTAAAAGTAAAACACGCTCTATCATTT 57.178 29.630 0.00 0.00 0.00 2.32
2667 2708 9.216117 AGTAAAAGTAAAACACGCTCTATCATT 57.784 29.630 0.00 0.00 0.00 2.57
2668 2709 8.773404 AGTAAAAGTAAAACACGCTCTATCAT 57.227 30.769 0.00 0.00 0.00 2.45
2669 2710 8.597662 AAGTAAAAGTAAAACACGCTCTATCA 57.402 30.769 0.00 0.00 0.00 2.15
2690 2731 9.325198 CCATCAAATAGCCGCATTATATAAGTA 57.675 33.333 1.02 0.00 0.00 2.24
2691 2732 8.213518 CCATCAAATAGCCGCATTATATAAGT 57.786 34.615 1.02 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.