Multiple sequence alignment - TraesCS3B01G228300

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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 TraesCS3B01G228300 chr3B 100.000 2531 0 0 1 2531 330377995 330380525 0 4674
1 TraesCS3B01G228300 chr3B 94.425 1991 82 12 565 2531 19701235 19703220 0 3035
2 TraesCS3B01G228300 chr3B 92.951 1986 82 22 567 2531 792939418 792941366 0 2839
3 TraesCS3B01G228300 chr3B 94.170 1458 55 4 566 2005 594400317 594398872 0 2194
4 TraesCS3B01G228300 chr1B 95.320 1987 70 5 566 2531 581717562 581715578 0 3133
5 TraesCS3B01G228300 chr1B 94.607 1984 81 12 567 2531 520844119 520842143 0 3048
6 TraesCS3B01G228300 chr1B 94.227 1559 58 5 564 2104 154580591 154582135 0 2351
7 TraesCS3B01G228300 chr7B 94.869 1988 78 5 564 2531 720989193 720987210 0 3085
8 TraesCS3B01G228300 chr7B 94.615 1987 81 8 567 2531 677862790 677860808 0 3053
9 TraesCS3B01G228300 chr7B 94.544 1961 82 7 591 2531 708943230 708941275 0 3005
10 TraesCS3B01G228300 chr4A 94.909 1984 77 6 567 2531 705529252 705527274 0 3083
11 TraesCS3B01G228300 chr4A 91.000 500 37 5 1 498 466684847 466685340 0 667
12 TraesCS3B01G228300 chr2B 94.718 1988 81 7 566 2531 492636664 492638649 0 3068
13 TraesCS3B01G228300 chr2B 94.183 1994 83 11 557 2531 596962061 596964040 0 3009
14 TraesCS3B01G228300 chr2B 90.476 504 46 2 1 502 117256808 117256305 0 664
15 TraesCS3B01G228300 chr5B 94.705 1983 85 3 567 2531 497276165 497278145 0 3062
16 TraesCS3B01G228300 chr5B 94.618 1988 81 7 565 2531 46530254 46528272 0 3055
17 TraesCS3B01G228300 chr5B 94.269 1710 72 7 564 2252 682395999 682394295 0 2591
18 TraesCS3B01G228300 chr5B 93.716 1639 68 9 558 2178 317969007 317970628 0 2423
19 TraesCS3B01G228300 chr5B 90.258 503 45 4 1 501 381725637 381726137 0 654
20 TraesCS3B01G228300 chr6B 93.096 898 42 3 559 1437 634724983 634725879 0 1297
21 TraesCS3B01G228300 chr6B 90.607 511 45 3 1 509 277575831 277576340 0 675
22 TraesCS3B01G228300 chr7D 91.165 498 41 3 6 501 297158732 297158236 0 673
23 TraesCS3B01G228300 chr3D 90.419 501 46 2 1 499 226664371 226663871 0 658
24 TraesCS3B01G228300 chr3D 90.258 503 46 3 1 501 226714393 226713892 0 654
25 TraesCS3B01G228300 chr2D 90.258 503 47 2 1 501 449045023 449044521 0 656
26 TraesCS3B01G228300 chr5D 90.079 504 44 6 1 501 130610218 130609718 0 649


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 TraesCS3B01G228300 chr3B 330377995 330380525 2530 False 4674 4674 100.000 1 2531 1 chr3B.!!$F2 2530
1 TraesCS3B01G228300 chr3B 19701235 19703220 1985 False 3035 3035 94.425 565 2531 1 chr3B.!!$F1 1966
2 TraesCS3B01G228300 chr3B 792939418 792941366 1948 False 2839 2839 92.951 567 2531 1 chr3B.!!$F3 1964
3 TraesCS3B01G228300 chr3B 594398872 594400317 1445 True 2194 2194 94.170 566 2005 1 chr3B.!!$R1 1439
4 TraesCS3B01G228300 chr1B 581715578 581717562 1984 True 3133 3133 95.320 566 2531 1 chr1B.!!$R2 1965
5 TraesCS3B01G228300 chr1B 520842143 520844119 1976 True 3048 3048 94.607 567 2531 1 chr1B.!!$R1 1964
6 TraesCS3B01G228300 chr1B 154580591 154582135 1544 False 2351 2351 94.227 564 2104 1 chr1B.!!$F1 1540
7 TraesCS3B01G228300 chr7B 720987210 720989193 1983 True 3085 3085 94.869 564 2531 1 chr7B.!!$R3 1967
8 TraesCS3B01G228300 chr7B 677860808 677862790 1982 True 3053 3053 94.615 567 2531 1 chr7B.!!$R1 1964
9 TraesCS3B01G228300 chr7B 708941275 708943230 1955 True 3005 3005 94.544 591 2531 1 chr7B.!!$R2 1940
10 TraesCS3B01G228300 chr4A 705527274 705529252 1978 True 3083 3083 94.909 567 2531 1 chr4A.!!$R1 1964
11 TraesCS3B01G228300 chr2B 492636664 492638649 1985 False 3068 3068 94.718 566 2531 1 chr2B.!!$F1 1965
12 TraesCS3B01G228300 chr2B 596962061 596964040 1979 False 3009 3009 94.183 557 2531 1 chr2B.!!$F2 1974
13 TraesCS3B01G228300 chr2B 117256305 117256808 503 True 664 664 90.476 1 502 1 chr2B.!!$R1 501
14 TraesCS3B01G228300 chr5B 497276165 497278145 1980 False 3062 3062 94.705 567 2531 1 chr5B.!!$F3 1964
15 TraesCS3B01G228300 chr5B 46528272 46530254 1982 True 3055 3055 94.618 565 2531 1 chr5B.!!$R1 1966
16 TraesCS3B01G228300 chr5B 682394295 682395999 1704 True 2591 2591 94.269 564 2252 1 chr5B.!!$R2 1688
17 TraesCS3B01G228300 chr5B 317969007 317970628 1621 False 2423 2423 93.716 558 2178 1 chr5B.!!$F1 1620
18 TraesCS3B01G228300 chr5B 381725637 381726137 500 False 654 654 90.258 1 501 1 chr5B.!!$F2 500
19 TraesCS3B01G228300 chr6B 634724983 634725879 896 False 1297 1297 93.096 559 1437 1 chr6B.!!$F2 878
20 TraesCS3B01G228300 chr6B 277575831 277576340 509 False 675 675 90.607 1 509 1 chr6B.!!$F1 508
21 TraesCS3B01G228300 chr3D 226663871 226664371 500 True 658 658 90.419 1 499 1 chr3D.!!$R1 498
22 TraesCS3B01G228300 chr3D 226713892 226714393 501 True 654 654 90.258 1 501 1 chr3D.!!$R2 500
23 TraesCS3B01G228300 chr2D 449044521 449045023 502 True 656 656 90.258 1 501 1 chr2D.!!$R1 500
24 TraesCS3B01G228300 chr5D 130609718 130610218 500 True 649 649 90.079 1 501 1 chr5D.!!$R1 500

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
873 883 1.188219 ACCACACCGACAGAGAGCAT 61.188 55.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2546 0.103937 AAACACCACAAACCCATGCG 59.896 50.0 0.0 0.0 0.0 4.73 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
38 39 5.661056 ATCATTTCGGTCTACTTGTCTCA 57.339 39.130 0.00 0.00 0.00 3.27
78 79 5.888901 ACATGATCATTGCCTTGGATATCT 58.111 37.500 5.16 0.00 0.00 1.98
127 128 6.909550 TTGGCCAACAATAATTTGTCTACT 57.090 33.333 16.05 0.00 45.30 2.57
174 176 4.373156 AGCCTCTTGTGAAAACTATGGT 57.627 40.909 0.00 0.00 0.00 3.55
180 182 1.979308 TGTGAAAACTATGGTCCCCGA 59.021 47.619 0.00 0.00 0.00 5.14
317 321 3.517901 TCGTAACCATTGAGGGATTGACT 59.482 43.478 0.00 0.00 43.89 3.41
329 333 2.664015 GGATTGACTACCCCTCTACGT 58.336 52.381 0.00 0.00 0.00 3.57
392 396 6.993308 TGTTTACATAGTGTTGCTTGGTTCTA 59.007 34.615 0.00 0.00 0.00 2.10
416 420 6.415573 ACTACTGGATTGATAACCTTGGTTC 58.584 40.000 8.46 0.00 0.00 3.62
506 510 3.441572 GCAACTCACAAGTAGCATCCATT 59.558 43.478 0.00 0.00 33.48 3.16
507 511 4.437930 GCAACTCACAAGTAGCATCCATTC 60.438 45.833 0.00 0.00 33.48 2.67
508 512 4.558226 ACTCACAAGTAGCATCCATTCA 57.442 40.909 0.00 0.00 32.59 2.57
509 513 4.256920 ACTCACAAGTAGCATCCATTCAC 58.743 43.478 0.00 0.00 32.59 3.18
510 514 3.609853 TCACAAGTAGCATCCATTCACC 58.390 45.455 0.00 0.00 0.00 4.02
511 515 3.264193 TCACAAGTAGCATCCATTCACCT 59.736 43.478 0.00 0.00 0.00 4.00
512 516 3.624861 CACAAGTAGCATCCATTCACCTC 59.375 47.826 0.00 0.00 0.00 3.85
513 517 3.521126 ACAAGTAGCATCCATTCACCTCT 59.479 43.478 0.00 0.00 0.00 3.69
514 518 4.716784 ACAAGTAGCATCCATTCACCTCTA 59.283 41.667 0.00 0.00 0.00 2.43
515 519 5.367937 ACAAGTAGCATCCATTCACCTCTAT 59.632 40.000 0.00 0.00 0.00 1.98
516 520 6.554982 ACAAGTAGCATCCATTCACCTCTATA 59.445 38.462 0.00 0.00 0.00 1.31
517 521 7.236432 ACAAGTAGCATCCATTCACCTCTATAT 59.764 37.037 0.00 0.00 0.00 0.86
518 522 7.805083 AGTAGCATCCATTCACCTCTATATT 57.195 36.000 0.00 0.00 0.00 1.28
519 523 7.846066 AGTAGCATCCATTCACCTCTATATTC 58.154 38.462 0.00 0.00 0.00 1.75
520 524 6.692849 AGCATCCATTCACCTCTATATTCA 57.307 37.500 0.00 0.00 0.00 2.57
521 525 7.083062 AGCATCCATTCACCTCTATATTCAA 57.917 36.000 0.00 0.00 0.00 2.69
522 526 7.520798 AGCATCCATTCACCTCTATATTCAAA 58.479 34.615 0.00 0.00 0.00 2.69
523 527 7.446625 AGCATCCATTCACCTCTATATTCAAAC 59.553 37.037 0.00 0.00 0.00 2.93
524 528 7.229306 GCATCCATTCACCTCTATATTCAAACA 59.771 37.037 0.00 0.00 0.00 2.83
525 529 9.123902 CATCCATTCACCTCTATATTCAAACAA 57.876 33.333 0.00 0.00 0.00 2.83
526 530 9.699410 ATCCATTCACCTCTATATTCAAACAAA 57.301 29.630 0.00 0.00 0.00 2.83
527 531 9.699410 TCCATTCACCTCTATATTCAAACAAAT 57.301 29.630 0.00 0.00 0.00 2.32
528 532 9.956720 CCATTCACCTCTATATTCAAACAAATC 57.043 33.333 0.00 0.00 0.00 2.17
873 883 1.188219 ACCACACCGACAGAGAGCAT 61.188 55.000 0.00 0.00 0.00 3.79
956 966 2.512515 CGGTGGGAAGCTAGCTGC 60.513 66.667 20.16 17.54 43.29 5.25
979 989 3.567797 GCTCGGCGGCATTGAGAC 61.568 66.667 14.98 4.40 31.31 3.36
1073 1083 3.784701 GAAGATGCCTGTCTTCGTCTA 57.215 47.619 7.55 0.00 43.15 2.59
1219 1229 3.561725 GGGATCTTTGAGCAATCGGTTAG 59.438 47.826 0.00 0.00 0.00 2.34
1311 1321 3.072211 TGAACTGCAAGAAGAGCATGAG 58.928 45.455 0.00 0.00 41.82 2.90
1383 1411 2.732282 CGAAGCACGCACTGATAGAGAA 60.732 50.000 0.00 0.00 34.51 2.87
1539 1567 5.796424 ATGGAAAGGCATGAATTATGGAC 57.204 39.130 0.00 0.00 37.26 4.02
1847 1881 1.999648 TGGAAAATGTGCCTCAGCTT 58.000 45.000 0.00 0.00 40.80 3.74
2065 2452 1.367346 TTGACATGGGTAGGGAAGCA 58.633 50.000 0.00 0.00 0.00 3.91
2066 2453 1.367346 TGACATGGGTAGGGAAGCAA 58.633 50.000 0.00 0.00 0.00 3.91
2067 2454 1.922447 TGACATGGGTAGGGAAGCAAT 59.078 47.619 0.00 0.00 0.00 3.56
2068 2455 2.301346 GACATGGGTAGGGAAGCAATG 58.699 52.381 0.00 0.00 41.94 2.82
2069 2456 1.640670 ACATGGGTAGGGAAGCAATGT 59.359 47.619 0.00 0.00 43.91 2.71
2070 2457 2.849943 ACATGGGTAGGGAAGCAATGTA 59.150 45.455 0.00 0.00 46.27 2.29
2071 2458 3.463329 ACATGGGTAGGGAAGCAATGTAT 59.537 43.478 0.00 0.00 46.27 2.29
2072 2459 4.663120 ACATGGGTAGGGAAGCAATGTATA 59.337 41.667 0.00 0.00 46.27 1.47
2073 2460 4.699925 TGGGTAGGGAAGCAATGTATAC 57.300 45.455 0.00 0.00 0.00 1.47
2074 2461 4.041464 TGGGTAGGGAAGCAATGTATACA 58.959 43.478 8.27 8.27 0.00 2.29
2075 2462 4.663120 TGGGTAGGGAAGCAATGTATACAT 59.337 41.667 12.75 12.75 38.41 2.29
2076 2463 5.847265 TGGGTAGGGAAGCAATGTATACATA 59.153 40.000 18.56 0.00 35.10 2.29
2077 2464 6.013725 TGGGTAGGGAAGCAATGTATACATAG 60.014 42.308 18.56 1.16 35.10 2.23
2078 2465 6.013639 GGGTAGGGAAGCAATGTATACATAGT 60.014 42.308 18.56 1.39 35.10 2.12
2079 2466 6.874134 GGTAGGGAAGCAATGTATACATAGTG 59.126 42.308 18.56 14.66 35.10 2.74
2080 2467 6.747414 AGGGAAGCAATGTATACATAGTGA 57.253 37.500 18.56 0.00 35.10 3.41
2081 2468 6.763355 AGGGAAGCAATGTATACATAGTGAG 58.237 40.000 18.56 7.98 35.10 3.51
2082 2469 6.554982 AGGGAAGCAATGTATACATAGTGAGA 59.445 38.462 18.56 0.00 35.10 3.27
2083 2470 6.647067 GGGAAGCAATGTATACATAGTGAGAC 59.353 42.308 18.56 7.13 35.10 3.36
2084 2471 7.437748 GGAAGCAATGTATACATAGTGAGACT 58.562 38.462 18.56 4.92 35.10 3.24
2085 2472 7.596995 GGAAGCAATGTATACATAGTGAGACTC 59.403 40.741 18.56 8.64 35.10 3.36
2086 2473 7.831691 AGCAATGTATACATAGTGAGACTCT 57.168 36.000 18.56 4.29 35.10 3.24
2087 2474 7.656412 AGCAATGTATACATAGTGAGACTCTG 58.344 38.462 18.56 10.01 35.10 3.35
2088 2475 7.503902 AGCAATGTATACATAGTGAGACTCTGA 59.496 37.037 18.56 0.00 35.10 3.27
2089 2476 8.138074 GCAATGTATACATAGTGAGACTCTGAA 58.862 37.037 18.56 0.00 35.10 3.02
2096 2483 7.897575 ACATAGTGAGACTCTGAAATTTGTC 57.102 36.000 3.68 0.00 0.00 3.18
2097 2484 7.445121 ACATAGTGAGACTCTGAAATTTGTCA 58.555 34.615 3.68 0.00 32.41 3.58
2098 2485 7.933577 ACATAGTGAGACTCTGAAATTTGTCAA 59.066 33.333 3.68 0.00 32.41 3.18
2099 2486 8.777413 CATAGTGAGACTCTGAAATTTGTCAAA 58.223 33.333 3.68 0.00 32.41 2.69
2100 2487 7.630242 AGTGAGACTCTGAAATTTGTCAAAA 57.370 32.000 1.31 0.00 32.41 2.44
2101 2488 8.055279 AGTGAGACTCTGAAATTTGTCAAAAA 57.945 30.769 1.31 0.00 32.41 1.94
2121 2508 4.703379 AAAATGAAGGGTGGAAAATGCA 57.297 36.364 0.00 0.00 0.00 3.96
2122 2509 3.683365 AATGAAGGGTGGAAAATGCAC 57.317 42.857 0.00 0.00 38.03 4.57
2123 2510 2.079170 TGAAGGGTGGAAAATGCACA 57.921 45.000 4.42 0.00 40.73 4.57
2124 2511 2.392662 TGAAGGGTGGAAAATGCACAA 58.607 42.857 4.42 0.00 40.73 3.33
2125 2512 2.768527 TGAAGGGTGGAAAATGCACAAA 59.231 40.909 4.42 0.00 40.73 2.83
2126 2513 3.198635 TGAAGGGTGGAAAATGCACAAAA 59.801 39.130 4.42 0.00 40.73 2.44
2127 2514 3.922171 AGGGTGGAAAATGCACAAAAA 57.078 38.095 4.42 0.00 40.73 1.94
2142 2529 2.658422 AAAAATGCTGCGGCTGGG 59.342 55.556 20.27 0.00 39.59 4.45
2143 2530 2.946346 AAAAATGCTGCGGCTGGGG 61.946 57.895 20.27 0.00 39.59 4.96
2144 2531 3.884704 AAAATGCTGCGGCTGGGGA 62.885 57.895 20.27 0.00 39.59 4.81
2152 2539 4.452733 CGGCTGGGGACTCGAACC 62.453 72.222 0.28 0.28 0.00 3.62
2159 2546 1.295746 GGGACTCGAACCCAAGACC 59.704 63.158 18.78 1.90 46.05 3.85
2160 2547 1.080025 GGACTCGAACCCAAGACCG 60.080 63.158 0.00 0.00 0.00 4.79
2161 2548 1.737008 GACTCGAACCCAAGACCGC 60.737 63.158 0.00 0.00 0.00 5.68
2162 2549 2.342279 CTCGAACCCAAGACCGCA 59.658 61.111 0.00 0.00 0.00 5.69
2163 2550 1.079127 CTCGAACCCAAGACCGCAT 60.079 57.895 0.00 0.00 0.00 4.73
2164 2551 1.361668 CTCGAACCCAAGACCGCATG 61.362 60.000 0.00 0.00 0.00 4.06
2165 2552 2.398554 CGAACCCAAGACCGCATGG 61.399 63.158 0.00 0.00 42.84 3.66
2175 2562 2.650196 CCGCATGGGTTTGTGGTG 59.350 61.111 9.14 0.00 41.43 4.17
2176 2563 2.199652 CCGCATGGGTTTGTGGTGT 61.200 57.895 9.14 0.00 41.43 4.16
2177 2564 1.739049 CGCATGGGTTTGTGGTGTT 59.261 52.632 0.68 0.00 0.00 3.32
2178 2565 0.103937 CGCATGGGTTTGTGGTGTTT 59.896 50.000 0.68 0.00 0.00 2.83
2179 2566 1.338337 CGCATGGGTTTGTGGTGTTTA 59.662 47.619 0.68 0.00 0.00 2.01
2180 2567 2.606795 CGCATGGGTTTGTGGTGTTTAG 60.607 50.000 0.68 0.00 0.00 1.85
2181 2568 2.288763 GCATGGGTTTGTGGTGTTTAGG 60.289 50.000 0.00 0.00 0.00 2.69
2182 2569 2.074729 TGGGTTTGTGGTGTTTAGGG 57.925 50.000 0.00 0.00 0.00 3.53
2183 2570 0.677288 GGGTTTGTGGTGTTTAGGGC 59.323 55.000 0.00 0.00 0.00 5.19
2184 2571 1.699730 GGTTTGTGGTGTTTAGGGCT 58.300 50.000 0.00 0.00 0.00 5.19
2185 2572 1.339929 GGTTTGTGGTGTTTAGGGCTG 59.660 52.381 0.00 0.00 0.00 4.85
2186 2573 1.036707 TTTGTGGTGTTTAGGGCTGC 58.963 50.000 0.00 0.00 0.00 5.25
2187 2574 1.169661 TTGTGGTGTTTAGGGCTGCG 61.170 55.000 0.00 0.00 0.00 5.18
2188 2575 2.671619 TGGTGTTTAGGGCTGCGC 60.672 61.111 8.86 8.86 0.00 6.09
2189 2576 2.359975 GGTGTTTAGGGCTGCGCT 60.360 61.111 22.98 22.98 0.00 5.92
2190 2577 2.690778 GGTGTTTAGGGCTGCGCTG 61.691 63.158 27.01 10.04 0.00 5.18
2191 2578 2.359850 TGTTTAGGGCTGCGCTGG 60.360 61.111 27.01 6.50 0.00 4.85
2192 2579 2.359975 GTTTAGGGCTGCGCTGGT 60.360 61.111 27.01 5.85 0.00 4.00
2193 2580 1.078708 GTTTAGGGCTGCGCTGGTA 60.079 57.895 27.01 10.98 0.00 3.25
2194 2581 0.675522 GTTTAGGGCTGCGCTGGTAA 60.676 55.000 27.01 15.70 0.00 2.85
2195 2582 0.675522 TTTAGGGCTGCGCTGGTAAC 60.676 55.000 27.01 0.00 0.00 2.50
2196 2583 2.530958 TTAGGGCTGCGCTGGTAACC 62.531 60.000 27.01 8.16 0.00 2.85
2202 2589 2.585247 GCGCTGGTAACCGCTAGG 60.585 66.667 0.00 0.00 46.14 3.02
2203 2590 3.072486 GCGCTGGTAACCGCTAGGA 62.072 63.158 0.00 0.00 46.14 2.94
2204 2591 1.226888 CGCTGGTAACCGCTAGGAC 60.227 63.158 0.00 0.00 41.02 3.85
2205 2592 1.895238 GCTGGTAACCGCTAGGACA 59.105 57.895 0.00 0.00 41.02 4.02
2206 2593 0.179108 GCTGGTAACCGCTAGGACAG 60.179 60.000 0.00 0.00 41.02 3.51
2207 2594 1.471119 CTGGTAACCGCTAGGACAGA 58.529 55.000 0.00 0.00 41.02 3.41
2208 2595 2.032620 CTGGTAACCGCTAGGACAGAT 58.967 52.381 0.00 0.00 41.02 2.90
2209 2596 1.754803 TGGTAACCGCTAGGACAGATG 59.245 52.381 0.00 0.00 41.02 2.90
2210 2597 1.068741 GGTAACCGCTAGGACAGATGG 59.931 57.143 0.00 0.00 41.02 3.51
2211 2598 0.750850 TAACCGCTAGGACAGATGGC 59.249 55.000 0.00 0.00 41.02 4.40
2212 2599 1.264749 AACCGCTAGGACAGATGGCA 61.265 55.000 0.00 0.00 41.02 4.92
2213 2600 1.264749 ACCGCTAGGACAGATGGCAA 61.265 55.000 0.00 0.00 41.02 4.52
2214 2601 0.531532 CCGCTAGGACAGATGGCAAG 60.532 60.000 0.00 0.00 41.02 4.01
2215 2602 0.461548 CGCTAGGACAGATGGCAAGA 59.538 55.000 0.00 0.00 0.00 3.02
2216 2603 1.537776 CGCTAGGACAGATGGCAAGAG 60.538 57.143 0.00 0.00 0.00 2.85
2217 2604 1.484240 GCTAGGACAGATGGCAAGAGT 59.516 52.381 0.00 0.00 0.00 3.24
2218 2605 2.093235 GCTAGGACAGATGGCAAGAGTT 60.093 50.000 0.00 0.00 0.00 3.01
2219 2606 3.620966 GCTAGGACAGATGGCAAGAGTTT 60.621 47.826 0.00 0.00 0.00 2.66
2220 2607 2.787994 AGGACAGATGGCAAGAGTTTG 58.212 47.619 0.00 0.00 37.36 2.93
2221 2608 2.373169 AGGACAGATGGCAAGAGTTTGA 59.627 45.455 0.00 0.00 36.36 2.69
2222 2609 2.485814 GGACAGATGGCAAGAGTTTGAC 59.514 50.000 0.00 0.00 43.00 3.18
2228 2615 1.620822 GGCAAGAGTTTGACATGGGT 58.379 50.000 0.00 0.00 42.21 4.51
2229 2616 2.790433 GGCAAGAGTTTGACATGGGTA 58.210 47.619 0.00 0.00 42.21 3.69
2230 2617 2.749621 GGCAAGAGTTTGACATGGGTAG 59.250 50.000 0.00 0.00 42.21 3.18
2231 2618 2.749621 GCAAGAGTTTGACATGGGTAGG 59.250 50.000 0.00 0.00 36.36 3.18
2232 2619 3.347216 CAAGAGTTTGACATGGGTAGGG 58.653 50.000 0.00 0.00 36.36 3.53
2233 2620 2.915869 AGAGTTTGACATGGGTAGGGA 58.084 47.619 0.00 0.00 0.00 4.20
2234 2621 3.256704 AGAGTTTGACATGGGTAGGGAA 58.743 45.455 0.00 0.00 0.00 3.97
2235 2622 3.264450 AGAGTTTGACATGGGTAGGGAAG 59.736 47.826 0.00 0.00 0.00 3.46
2314 2877 2.393768 GCACATGCGTGAGAGTGGG 61.394 63.158 14.17 0.00 46.80 4.61
2368 2931 4.929211 GGTTGGAAGGTTGAAAATGTATGC 59.071 41.667 0.00 0.00 0.00 3.14
2438 3001 2.749621 GAGTGGCACTTGGTTTAGGATG 59.250 50.000 22.98 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.464222 TGAGACAAGTAGACCGAAATGATTT 58.536 36.000 0.00 0.00 0.00 2.17
38 39 6.378280 TGATCATGTATATAGGCATCACGTCT 59.622 38.462 0.00 0.00 0.00 4.18
127 128 7.722363 TCTCTCATAAAAATAGCATACGGTGA 58.278 34.615 0.00 0.00 0.00 4.02
174 176 7.345653 AGCATATGATAGAAAATAGATCGGGGA 59.654 37.037 6.97 0.00 0.00 4.81
317 321 2.980541 CCCAACACGTAGAGGGGTA 58.019 57.895 9.83 0.00 37.66 3.69
329 333 4.081420 ACAACAAATACTTGCAACCCAACA 60.081 37.500 0.00 0.00 35.84 3.33
392 396 6.388619 AACCAAGGTTATCAATCCAGTAGT 57.611 37.500 1.91 0.00 36.46 2.73
416 420 9.853177 AAAGATAAGTATTTCCCTCAGTTATGG 57.147 33.333 0.00 0.00 0.00 2.74
444 448 7.786943 TGAAGAGGAGAGGATAATGAAGTACAT 59.213 37.037 0.00 0.00 41.45 2.29
560 564 8.491134 GGGCAAAAGGATAATTAACCCTTAAAT 58.509 33.333 17.67 8.77 39.21 1.40
561 565 7.680739 AGGGCAAAAGGATAATTAACCCTTAAA 59.319 33.333 17.67 0.00 42.56 1.52
562 566 7.193338 AGGGCAAAAGGATAATTAACCCTTAA 58.807 34.615 17.67 0.00 42.56 1.85
860 870 1.875813 GCGTCATGCTCTCTGTCGG 60.876 63.158 0.00 0.00 41.73 4.79
964 974 4.467084 GGGTCTCAATGCCGCCGA 62.467 66.667 0.00 0.00 0.00 5.54
1054 1064 3.068873 GGATAGACGAAGACAGGCATCTT 59.931 47.826 3.91 3.91 41.74 2.40
1089 1099 0.036306 AAACCCTCCGATCAACGCTT 59.964 50.000 0.00 0.00 41.07 4.68
1219 1229 1.195448 CTGCATGAACACGGAACAGAC 59.805 52.381 0.00 0.00 0.00 3.51
1311 1321 1.548986 GTAGCATGCGCAACCATTTC 58.451 50.000 17.11 0.00 42.27 2.17
1539 1567 8.862074 TCATGCAATTTCAAGATTACAAATTCG 58.138 29.630 0.00 0.00 29.17 3.34
1774 1808 9.498307 CGGTGTATTTGAATTGGATTACTTAAC 57.502 33.333 0.00 0.00 0.00 2.01
1847 1881 5.935789 GGCACTAGGTGTAAACATCTACAAA 59.064 40.000 0.00 0.00 38.47 2.83
1987 2024 0.107116 AAACACCACTAACCCACGCA 60.107 50.000 0.00 0.00 0.00 5.24
2070 2457 9.593134 GACAAATTTCAGAGTCTCACTATGTAT 57.407 33.333 1.94 0.00 38.49 2.29
2071 2458 8.585018 TGACAAATTTCAGAGTCTCACTATGTA 58.415 33.333 1.94 0.00 38.49 2.29
2072 2459 7.445121 TGACAAATTTCAGAGTCTCACTATGT 58.555 34.615 1.94 0.00 38.49 2.29
2073 2460 7.895975 TGACAAATTTCAGAGTCTCACTATG 57.104 36.000 1.94 0.00 38.70 2.23
2074 2461 8.908786 TTTGACAAATTTCAGAGTCTCACTAT 57.091 30.769 1.94 0.00 32.41 2.12
2075 2462 8.731275 TTTTGACAAATTTCAGAGTCTCACTA 57.269 30.769 0.50 0.00 32.41 2.74
2076 2463 7.630242 TTTTGACAAATTTCAGAGTCTCACT 57.370 32.000 0.50 0.00 32.41 3.41
2099 2486 4.821260 GTGCATTTTCCACCCTTCATTTTT 59.179 37.500 0.00 0.00 0.00 1.94
2100 2487 4.141528 TGTGCATTTTCCACCCTTCATTTT 60.142 37.500 0.00 0.00 32.30 1.82
2101 2488 3.390639 TGTGCATTTTCCACCCTTCATTT 59.609 39.130 0.00 0.00 32.30 2.32
2102 2489 2.971330 TGTGCATTTTCCACCCTTCATT 59.029 40.909 0.00 0.00 32.30 2.57
2103 2490 2.607499 TGTGCATTTTCCACCCTTCAT 58.393 42.857 0.00 0.00 32.30 2.57
2104 2491 2.079170 TGTGCATTTTCCACCCTTCA 57.921 45.000 0.00 0.00 32.30 3.02
2105 2492 3.467374 TTTGTGCATTTTCCACCCTTC 57.533 42.857 0.00 0.00 32.30 3.46
2106 2493 3.922171 TTTTGTGCATTTTCCACCCTT 57.078 38.095 0.00 0.00 32.30 3.95
2107 2494 3.922171 TTTTTGTGCATTTTCCACCCT 57.078 38.095 0.00 0.00 32.30 4.34
2125 2512 2.658422 CCCAGCCGCAGCATTTTT 59.342 55.556 0.00 0.00 43.56 1.94
2126 2513 3.384532 CCCCAGCCGCAGCATTTT 61.385 61.111 0.00 0.00 43.56 1.82
2127 2514 4.365111 TCCCCAGCCGCAGCATTT 62.365 61.111 0.00 0.00 43.56 2.32
2135 2522 4.452733 GGTTCGAGTCCCCAGCCG 62.453 72.222 0.00 0.00 0.00 5.52
2136 2523 4.097361 GGGTTCGAGTCCCCAGCC 62.097 72.222 14.49 1.09 40.88 4.85
2137 2524 3.319198 TGGGTTCGAGTCCCCAGC 61.319 66.667 20.23 0.00 46.06 4.85
2140 2527 1.295746 GTCTTGGGTTCGAGTCCCC 59.704 63.158 20.23 15.12 44.00 4.81
2141 2528 1.295746 GGTCTTGGGTTCGAGTCCC 59.704 63.158 17.46 17.46 44.81 4.46
2142 2529 1.080025 CGGTCTTGGGTTCGAGTCC 60.080 63.158 0.82 0.82 31.75 3.85
2143 2530 1.737008 GCGGTCTTGGGTTCGAGTC 60.737 63.158 0.00 0.00 0.00 3.36
2144 2531 1.827399 ATGCGGTCTTGGGTTCGAGT 61.827 55.000 0.00 0.00 0.00 4.18
2145 2532 1.079127 ATGCGGTCTTGGGTTCGAG 60.079 57.895 0.00 0.00 0.00 4.04
2146 2533 1.375396 CATGCGGTCTTGGGTTCGA 60.375 57.895 0.00 0.00 0.00 3.71
2147 2534 2.398554 CCATGCGGTCTTGGGTTCG 61.399 63.158 0.00 0.00 34.75 3.95
2148 2535 2.046285 CCCATGCGGTCTTGGGTTC 61.046 63.158 12.27 0.00 46.96 3.62
2149 2536 2.035626 CCCATGCGGTCTTGGGTT 59.964 61.111 12.27 0.00 46.96 4.11
2158 2545 1.743321 AACACCACAAACCCATGCGG 61.743 55.000 0.00 0.00 37.81 5.69
2159 2546 0.103937 AAACACCACAAACCCATGCG 59.896 50.000 0.00 0.00 0.00 4.73
2160 2547 2.288763 CCTAAACACCACAAACCCATGC 60.289 50.000 0.00 0.00 0.00 4.06
2161 2548 2.298729 CCCTAAACACCACAAACCCATG 59.701 50.000 0.00 0.00 0.00 3.66
2162 2549 2.604139 CCCTAAACACCACAAACCCAT 58.396 47.619 0.00 0.00 0.00 4.00
2163 2550 2.030045 GCCCTAAACACCACAAACCCA 61.030 52.381 0.00 0.00 0.00 4.51
2164 2551 0.677288 GCCCTAAACACCACAAACCC 59.323 55.000 0.00 0.00 0.00 4.11
2165 2552 1.339929 CAGCCCTAAACACCACAAACC 59.660 52.381 0.00 0.00 0.00 3.27
2166 2553 1.269569 GCAGCCCTAAACACCACAAAC 60.270 52.381 0.00 0.00 0.00 2.93
2167 2554 1.036707 GCAGCCCTAAACACCACAAA 58.963 50.000 0.00 0.00 0.00 2.83
2168 2555 1.169661 CGCAGCCCTAAACACCACAA 61.170 55.000 0.00 0.00 0.00 3.33
2169 2556 1.599518 CGCAGCCCTAAACACCACA 60.600 57.895 0.00 0.00 0.00 4.17
2170 2557 3.263941 CGCAGCCCTAAACACCAC 58.736 61.111 0.00 0.00 0.00 4.16
2187 2574 0.179108 CTGTCCTAGCGGTTACCAGC 60.179 60.000 1.13 6.16 0.00 4.85
2188 2575 1.471119 TCTGTCCTAGCGGTTACCAG 58.529 55.000 1.13 0.00 0.00 4.00
2189 2576 1.754803 CATCTGTCCTAGCGGTTACCA 59.245 52.381 1.13 0.00 0.00 3.25
2190 2577 1.068741 CCATCTGTCCTAGCGGTTACC 59.931 57.143 0.00 0.00 0.00 2.85
2191 2578 1.538419 GCCATCTGTCCTAGCGGTTAC 60.538 57.143 0.00 0.00 0.00 2.50
2192 2579 0.750850 GCCATCTGTCCTAGCGGTTA 59.249 55.000 0.00 0.00 0.00 2.85
2193 2580 1.264749 TGCCATCTGTCCTAGCGGTT 61.265 55.000 0.00 0.00 0.00 4.44
2194 2581 1.264749 TTGCCATCTGTCCTAGCGGT 61.265 55.000 0.00 0.00 0.00 5.68
2195 2582 0.531532 CTTGCCATCTGTCCTAGCGG 60.532 60.000 0.00 0.00 0.00 5.52
2196 2583 0.461548 TCTTGCCATCTGTCCTAGCG 59.538 55.000 0.00 0.00 0.00 4.26
2197 2584 1.484240 ACTCTTGCCATCTGTCCTAGC 59.516 52.381 0.00 0.00 0.00 3.42
2198 2585 3.902881 AACTCTTGCCATCTGTCCTAG 57.097 47.619 0.00 0.00 0.00 3.02
2199 2586 3.582647 TCAAACTCTTGCCATCTGTCCTA 59.417 43.478 0.00 0.00 32.14 2.94
2200 2587 2.373169 TCAAACTCTTGCCATCTGTCCT 59.627 45.455 0.00 0.00 32.14 3.85
2201 2588 2.485814 GTCAAACTCTTGCCATCTGTCC 59.514 50.000 0.00 0.00 32.14 4.02
2202 2589 3.141398 TGTCAAACTCTTGCCATCTGTC 58.859 45.455 0.00 0.00 32.14 3.51
2203 2590 3.213206 TGTCAAACTCTTGCCATCTGT 57.787 42.857 0.00 0.00 32.14 3.41
2204 2591 3.119602 CCATGTCAAACTCTTGCCATCTG 60.120 47.826 0.00 0.00 28.75 2.90
2205 2592 3.087031 CCATGTCAAACTCTTGCCATCT 58.913 45.455 0.00 0.00 28.75 2.90
2206 2593 2.165030 CCCATGTCAAACTCTTGCCATC 59.835 50.000 0.00 0.00 28.75 3.51
2207 2594 2.173519 CCCATGTCAAACTCTTGCCAT 58.826 47.619 0.00 0.00 31.37 4.40
2208 2595 1.133513 ACCCATGTCAAACTCTTGCCA 60.134 47.619 0.00 0.00 32.14 4.92
2209 2596 1.620822 ACCCATGTCAAACTCTTGCC 58.379 50.000 0.00 0.00 32.14 4.52
2210 2597 2.749621 CCTACCCATGTCAAACTCTTGC 59.250 50.000 0.00 0.00 32.14 4.01
2211 2598 3.009033 TCCCTACCCATGTCAAACTCTTG 59.991 47.826 0.00 0.00 0.00 3.02
2212 2599 3.256704 TCCCTACCCATGTCAAACTCTT 58.743 45.455 0.00 0.00 0.00 2.85
2213 2600 2.915869 TCCCTACCCATGTCAAACTCT 58.084 47.619 0.00 0.00 0.00 3.24
2214 2601 3.610911 CTTCCCTACCCATGTCAAACTC 58.389 50.000 0.00 0.00 0.00 3.01
2215 2602 2.308866 CCTTCCCTACCCATGTCAAACT 59.691 50.000 0.00 0.00 0.00 2.66
2216 2603 2.307686 TCCTTCCCTACCCATGTCAAAC 59.692 50.000 0.00 0.00 0.00 2.93
2217 2604 2.638325 TCCTTCCCTACCCATGTCAAA 58.362 47.619 0.00 0.00 0.00 2.69
2218 2605 2.352561 TCCTTCCCTACCCATGTCAA 57.647 50.000 0.00 0.00 0.00 3.18
2219 2606 2.352561 TTCCTTCCCTACCCATGTCA 57.647 50.000 0.00 0.00 0.00 3.58
2220 2607 2.509964 ACATTCCTTCCCTACCCATGTC 59.490 50.000 0.00 0.00 0.00 3.06
2221 2608 2.573463 ACATTCCTTCCCTACCCATGT 58.427 47.619 0.00 0.00 0.00 3.21
2222 2609 5.309543 TGTATACATTCCTTCCCTACCCATG 59.690 44.000 0.08 0.00 0.00 3.66
2223 2610 5.482580 TGTATACATTCCTTCCCTACCCAT 58.517 41.667 0.08 0.00 0.00 4.00
2224 2611 4.898268 TGTATACATTCCTTCCCTACCCA 58.102 43.478 0.08 0.00 0.00 4.51
2225 2612 6.729569 ACTATGTATACATTCCTTCCCTACCC 59.270 42.308 22.90 0.00 37.76 3.69
2226 2613 7.453752 TCACTATGTATACATTCCTTCCCTACC 59.546 40.741 22.90 0.00 37.76 3.18
2227 2614 8.418597 TCACTATGTATACATTCCTTCCCTAC 57.581 38.462 22.90 0.00 37.76 3.18
2228 2615 8.453681 TCTCACTATGTATACATTCCTTCCCTA 58.546 37.037 22.90 1.65 37.76 3.53
2229 2616 7.233757 GTCTCACTATGTATACATTCCTTCCCT 59.766 40.741 22.90 0.00 37.76 4.20
2230 2617 7.233757 AGTCTCACTATGTATACATTCCTTCCC 59.766 40.741 22.90 7.85 37.76 3.97
2231 2618 8.085296 CAGTCTCACTATGTATACATTCCTTCC 58.915 40.741 22.90 7.16 37.76 3.46
2232 2619 8.634444 ACAGTCTCACTATGTATACATTCCTTC 58.366 37.037 22.90 8.75 37.76 3.46
2233 2620 8.417106 CACAGTCTCACTATGTATACATTCCTT 58.583 37.037 22.90 2.38 37.76 3.36
2234 2621 7.780271 TCACAGTCTCACTATGTATACATTCCT 59.220 37.037 22.90 2.77 37.76 3.36
2235 2622 7.941919 TCACAGTCTCACTATGTATACATTCC 58.058 38.462 22.90 4.76 37.76 3.01
2314 2877 5.854431 TTTCAGTGCAAAACAAAGGAAAC 57.146 34.783 0.00 0.00 0.00 2.78
2368 2931 0.390124 AAACCATGTGGCAGTGCAAG 59.610 50.000 18.61 0.00 39.32 4.01


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

AutoCloner maintained by Alex Coulton.