Multiple sequence alignment - TraesCS2A01G320900

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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 TraesCS2A01G320900 chr2A 100.000 5149 0 0 1 5149 550538271 550543419 0.000000e+00 9509
1 TraesCS2A01G320900 chr2A 83.487 757 86 25 1874 2617 723566176 723566906 0.000000e+00 669
2 TraesCS2A01G320900 chr2D 90.368 4506 266 70 22 4420 436368182 436372626 0.000000e+00 5762
3 TraesCS2A01G320900 chr2D 95.349 301 13 1 4591 4891 436373237 436373536 1.300000e-130 477
4 TraesCS2A01G320900 chr2D 99.612 258 1 0 4892 5149 436373494 436373751 6.030000e-129 472
5 TraesCS2A01G320900 chr2D 89.674 184 18 1 4420 4602 436372887 436373070 3.100000e-57 233
6 TraesCS2A01G320900 chr2B 92.437 3702 195 41 111 3744 514866347 514862663 0.000000e+00 5206
7 TraesCS2A01G320900 chr2B 89.425 643 40 14 3784 4420 514862665 514862045 0.000000e+00 785
8 TraesCS2A01G320900 chr2B 92.708 480 32 3 4415 4891 514861652 514861173 0.000000e+00 689
9 TraesCS2A01G320900 chr2B 98.062 258 3 1 4892 5149 514861215 514860960 1.020000e-121 448
10 TraesCS2A01G320900 chr2B 85.530 387 37 12 127 495 30332839 30333224 2.250000e-103 387
11 TraesCS2A01G320900 chr7D 83.752 757 85 24 1874 2617 31965561 31964830 0.000000e+00 682
12 TraesCS2A01G320900 chr4A 83.223 757 88 27 1874 2617 417625545 417626275 0.000000e+00 658
13 TraesCS2A01G320900 chr6B 80.116 689 86 21 1932 2616 520243070 520243711 2.810000e-127 466
14 TraesCS2A01G320900 chr5B 83.459 399 34 17 127 495 649446145 649446541 4.940000e-90 342
15 TraesCS2A01G320900 chr3A 87.047 193 18 4 2160 2352 633293933 633293748 1.450000e-50 211
16 TraesCS2A01G320900 chr3D 84.974 193 22 4 2160 2352 491795702 491795517 6.810000e-44 189


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 TraesCS2A01G320900 chr2A 550538271 550543419 5148 False 9509 9509 100.00000 1 5149 1 chr2A.!!$F1 5148
1 TraesCS2A01G320900 chr2A 723566176 723566906 730 False 669 669 83.48700 1874 2617 1 chr2A.!!$F2 743
2 TraesCS2A01G320900 chr2D 436368182 436373751 5569 False 1736 5762 93.75075 22 5149 4 chr2D.!!$F1 5127
3 TraesCS2A01G320900 chr2B 514860960 514866347 5387 True 1782 5206 93.15800 111 5149 4 chr2B.!!$R1 5038
4 TraesCS2A01G320900 chr7D 31964830 31965561 731 True 682 682 83.75200 1874 2617 1 chr7D.!!$R1 743
5 TraesCS2A01G320900 chr4A 417625545 417626275 730 False 658 658 83.22300 1874 2617 1 chr4A.!!$F1 743
6 TraesCS2A01G320900 chr6B 520243070 520243711 641 False 466 466 80.11600 1932 2616 1 chr6B.!!$F1 684

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
99 100 1.110442 TTGGCAATATTGGAAGGGCG 58.890 50.000 17.02 0.0 0.00 6.13 F
498 508 1.123928 GGATCGAATCAGACCACCCT 58.876 55.000 0.00 0.0 0.00 4.34 F
1830 1887 0.326264 ATCAGCTCAAAAGGCTCGGT 59.674 50.000 0.00 0.0 38.03 4.69 F
2357 2432 0.255890 ACACAAACAGAGGCCACACT 59.744 50.000 5.01 0.0 0.00 3.55 F
2426 2504 1.077716 GGTTATTGCTCACCGGCCT 60.078 57.895 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 1498 2.775384 AGTAAATCACCTTGCCCGGATA 59.225 45.455 0.73 0.00 0.00 2.59 R
2357 2432 1.808343 CAATCAGCAACAGCAGCTACA 59.192 47.619 0.00 0.00 41.14 2.74 R
3051 3132 0.036010 CCTGAATTCCAGCCTCACGT 60.036 55.000 2.27 0.00 41.57 4.49 R
3804 3924 0.105142 ACTACACCTGTGGGTCCTGT 60.105 55.000 1.91 0.00 45.41 4.00 R
4325 4451 0.986992 CGGCAAAGGAGTTACGTACG 59.013 55.000 15.01 15.01 0.00 3.67 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
99 100 1.110442 TTGGCAATATTGGAAGGGCG 58.890 50.000 17.02 0.00 0.00 6.13
103 104 3.153919 GGCAATATTGGAAGGGCGAATA 58.846 45.455 17.02 0.00 32.74 1.75
108 109 6.231211 CAATATTGGAAGGGCGAATACTAGT 58.769 40.000 7.62 0.00 31.28 2.57
113 114 5.448654 TGGAAGGGCGAATACTAGTTAGTA 58.551 41.667 0.00 1.77 42.43 1.82
168 173 7.063074 GGAGCATCAAGAACAAATGAAGAATTG 59.937 37.037 0.00 0.00 36.25 2.32
175 180 7.647907 AGAACAAATGAAGAATTGCACAATC 57.352 32.000 0.00 0.00 0.00 2.67
195 204 3.671716 TCACAGTCTAGAGCTCGTAACA 58.328 45.455 8.37 0.00 0.00 2.41
208 217 3.553508 GCTCGTAACACTGTGGGTTTCTA 60.554 47.826 13.09 0.00 0.00 2.10
311 320 3.334583 AAGTAGCCTGAAATTCGAGCA 57.665 42.857 9.24 0.00 0.00 4.26
321 331 5.335897 CCTGAAATTCGAGCATGAAAAAGGA 60.336 40.000 0.00 0.00 0.00 3.36
325 335 6.382869 AATTCGAGCATGAAAAAGGATAGG 57.617 37.500 0.00 0.00 0.00 2.57
494 504 1.269778 GCATCGGATCGAATCAGACCA 60.270 52.381 0.00 0.00 39.99 4.02
498 508 1.123928 GGATCGAATCAGACCACCCT 58.876 55.000 0.00 0.00 0.00 4.34
649 659 2.203195 AACAGCTTGTGCGCCAGA 60.203 55.556 4.18 0.00 45.42 3.86
798 818 1.740025 GATTTTCCCGTGAGCAGAAGG 59.260 52.381 0.00 0.00 0.00 3.46
837 858 7.381678 GCCTATACTAGTTTACATTCTGGTTCG 59.618 40.741 0.00 0.00 0.00 3.95
851 872 4.345288 TCTGGTTCGACGTGTATTAATCG 58.655 43.478 0.00 0.00 35.91 3.34
943 965 4.436998 CAGACACCGACCGAGCCC 62.437 72.222 0.00 0.00 0.00 5.19
944 966 4.988716 AGACACCGACCGAGCCCA 62.989 66.667 0.00 0.00 0.00 5.36
945 967 3.998672 GACACCGACCGAGCCCAA 61.999 66.667 0.00 0.00 0.00 4.12
1504 1526 5.068198 CGGGCAAGGTGATTTACTACTACTA 59.932 44.000 0.00 0.00 0.00 1.82
1582 1604 6.566079 ATTGAATCCTTCCTATGTGACTGA 57.434 37.500 0.00 0.00 0.00 3.41
1585 1607 6.778821 TGAATCCTTCCTATGTGACTGAAAA 58.221 36.000 0.00 0.00 0.00 2.29
1586 1608 7.405292 TGAATCCTTCCTATGTGACTGAAAAT 58.595 34.615 0.00 0.00 0.00 1.82
1587 1609 7.890127 TGAATCCTTCCTATGTGACTGAAAATT 59.110 33.333 0.00 0.00 0.00 1.82
1589 1611 6.542821 TCCTTCCTATGTGACTGAAAATTGT 58.457 36.000 0.00 0.00 0.00 2.71
1666 1717 8.831715 TGATCTCTGCGCATAAAAATCTAATA 57.168 30.769 12.24 0.00 0.00 0.98
1685 1742 1.103398 AGCCACAGGTTGTGTTGAGC 61.103 55.000 8.25 4.66 46.45 4.26
1692 1749 3.002791 CAGGTTGTGTTGAGCGATGTAT 58.997 45.455 0.00 0.00 0.00 2.29
1694 1751 3.055819 AGGTTGTGTTGAGCGATGTATCT 60.056 43.478 0.00 0.00 0.00 1.98
1706 1763 8.030744 TGAGCGATGTATCTATACAAGTACTC 57.969 38.462 6.89 11.00 45.40 2.59
1726 1783 8.940952 AGTACTCTTATCATTTTGACTGCTTTC 58.059 33.333 0.00 0.00 0.00 2.62
1731 1788 9.376075 TCTTATCATTTTGACTGCTTTCTAGAG 57.624 33.333 0.00 0.00 0.00 2.43
1739 1796 5.555017 TGACTGCTTTCTAGAGATGCTTTT 58.445 37.500 12.59 1.06 0.00 2.27
1740 1797 5.410746 TGACTGCTTTCTAGAGATGCTTTTG 59.589 40.000 12.59 5.69 0.00 2.44
1754 1811 9.860898 AGAGATGCTTTTGAAAATGTATTTACC 57.139 29.630 0.00 0.00 0.00 2.85
1755 1812 8.687824 AGATGCTTTTGAAAATGTATTTACCG 57.312 30.769 0.00 0.00 0.00 4.02
1761 1818 9.289303 CTTTTGAAAATGTATTTACCGATCTGG 57.711 33.333 0.00 2.55 46.41 3.86
1763 1820 7.786178 TGAAAATGTATTTACCGATCTGGAG 57.214 36.000 10.05 0.00 42.00 3.86
1830 1887 0.326264 ATCAGCTCAAAAGGCTCGGT 59.674 50.000 0.00 0.00 38.03 4.69
1880 1937 5.105063 GCCCAAGAAACTATTTCATCTTGC 58.895 41.667 8.47 0.00 44.61 4.01
1994 2058 1.444933 TGGGTGGGACTTTCATGTCT 58.555 50.000 0.00 0.00 37.16 3.41
2000 2071 4.394729 GTGGGACTTTCATGTCTTTACCA 58.605 43.478 0.00 0.00 37.16 3.25
2152 2223 5.357878 AGACGTAAGGGTCGTTCAACATATA 59.642 40.000 0.00 0.00 41.64 0.86
2158 2229 6.187727 AGGGTCGTTCAACATATATCCATT 57.812 37.500 0.00 0.00 0.00 3.16
2180 2251 7.201714 CCATTCTTCTTGGTTGCATTTGAAAAA 60.202 33.333 0.00 0.00 0.00 1.94
2208 2279 6.465035 CCCCTGTTATTTTTCCCATGAAACAA 60.465 38.462 0.00 0.00 40.12 2.83
2357 2432 0.255890 ACACAAACAGAGGCCACACT 59.744 50.000 5.01 0.00 0.00 3.55
2384 2459 4.114073 CTGCTGTTGCTGATTGTTTTTCA 58.886 39.130 0.00 0.00 40.01 2.69
2426 2504 1.077716 GGTTATTGCTCACCGGCCT 60.078 57.895 0.00 0.00 0.00 5.19
2427 2505 1.376609 GGTTATTGCTCACCGGCCTG 61.377 60.000 0.00 0.00 0.00 4.85
2443 2521 2.685388 GGCCTGCTAATTCCTCTTGTTC 59.315 50.000 0.00 0.00 0.00 3.18
2448 2526 6.558909 CCTGCTAATTCCTCTTGTTCAATTC 58.441 40.000 0.00 0.00 0.00 2.17
2468 2546 4.998671 TCATTTCCTTGTTGCTTGAACA 57.001 36.364 0.00 0.00 43.11 3.18
2473 2551 3.476552 TCCTTGTTGCTTGAACAGTAGG 58.523 45.455 0.00 0.00 45.43 3.18
2476 2554 4.498009 CCTTGTTGCTTGAACAGTAGGTTG 60.498 45.833 0.00 0.00 45.43 3.77
2477 2555 2.948979 TGTTGCTTGAACAGTAGGTTGG 59.051 45.455 0.00 0.00 39.78 3.77
2479 2557 4.131596 GTTGCTTGAACAGTAGGTTGGTA 58.868 43.478 0.00 0.00 40.63 3.25
2480 2558 4.002906 TGCTTGAACAGTAGGTTGGTAG 57.997 45.455 0.00 0.00 40.63 3.18
2481 2559 2.742589 GCTTGAACAGTAGGTTGGTAGC 59.257 50.000 0.00 0.00 40.63 3.58
2483 2561 4.579869 CTTGAACAGTAGGTTGGTAGCAT 58.420 43.478 0.00 0.00 40.63 3.79
2484 2562 4.202245 TGAACAGTAGGTTGGTAGCATC 57.798 45.455 0.00 0.00 40.63 3.91
2486 2564 3.895232 ACAGTAGGTTGGTAGCATCAG 57.105 47.619 0.00 0.00 0.00 2.90
2508 2587 3.902881 ATGAGGTGTCTTCTAGCTTGG 57.097 47.619 0.00 0.00 0.00 3.61
2509 2588 2.889512 TGAGGTGTCTTCTAGCTTGGA 58.110 47.619 0.00 0.00 0.00 3.53
2536 2615 3.670625 ACTTGCGCAGTTGTCCTAATAA 58.329 40.909 11.31 0.00 27.32 1.40
2800 2881 6.598753 TCAGTCTTTCGGTTCTAAAGTTTG 57.401 37.500 0.00 0.00 35.79 2.93
2899 2980 6.712547 GCTAGTGGATATTGTAGCAAGGATTT 59.287 38.462 0.00 0.00 38.23 2.17
2958 3039 3.337909 TCCAGAGAGATATCCCTATGCCA 59.662 47.826 3.48 0.00 0.00 4.92
2970 3051 3.054655 TCCCTATGCCACTTGTTACTTCC 60.055 47.826 0.00 0.00 0.00 3.46
2976 3057 2.140717 CCACTTGTTACTTCCGGTGTC 58.859 52.381 0.00 0.00 0.00 3.67
3051 3132 4.644498 TGAAATGCAGAGATGTCAGAACA 58.356 39.130 0.00 0.00 40.38 3.18
3082 3163 4.479158 TGGAATTCAGGTAAATATGGGGC 58.521 43.478 7.93 0.00 0.00 5.80
3108 3189 1.198637 GAAGTCACTGCCATGTGCTTC 59.801 52.381 15.24 15.24 40.27 3.86
3120 3201 6.798482 TGCCATGTGCTTCTAATTGATTAAG 58.202 36.000 7.54 0.00 42.00 1.85
3126 3207 9.851686 ATGTGCTTCTAATTGATTAAGGATGTA 57.148 29.630 0.00 0.00 0.00 2.29
3273 3354 4.279145 AGGATACACGACAGGTACTCAAT 58.721 43.478 0.00 0.00 35.00 2.57
3275 3356 6.069331 AGGATACACGACAGGTACTCAATAT 58.931 40.000 0.00 0.00 35.00 1.28
3278 3359 5.502153 ACACGACAGGTACTCAATATCTC 57.498 43.478 0.00 0.00 34.60 2.75
3280 3361 3.564644 ACGACAGGTACTCAATATCTCGG 59.435 47.826 0.00 0.00 34.60 4.63
3281 3362 3.813724 CGACAGGTACTCAATATCTCGGA 59.186 47.826 0.00 0.00 34.60 4.55
3299 3399 5.071653 TCTCGGATGGGATGTGAAAATATGA 59.928 40.000 0.00 0.00 0.00 2.15
3314 3415 9.132521 GTGAAAATATGATATGGTTTATGCTGC 57.867 33.333 0.00 0.00 0.00 5.25
3315 3416 8.858094 TGAAAATATGATATGGTTTATGCTGCA 58.142 29.630 4.13 4.13 0.00 4.41
3321 3422 6.541907 TGATATGGTTTATGCTGCATTCCTA 58.458 36.000 21.56 13.61 0.00 2.94
3331 3432 3.570975 TGCTGCATTCCTAAATAGGCATG 59.429 43.478 12.93 12.93 45.90 4.06
3332 3433 3.057033 GCTGCATTCCTAAATAGGCATGG 60.057 47.826 17.19 6.26 44.14 3.66
3349 3450 6.585416 AGGCATGGATTTTTCCAATGTAATC 58.415 36.000 0.00 0.00 43.83 1.75
3360 3464 9.434420 TTTTTCCAATGTAATCATGGTCAATTC 57.566 29.630 0.00 0.00 34.19 2.17
3375 3479 4.530553 GGTCAATTCCCTTTTACATGGGTT 59.469 41.667 0.00 0.00 43.74 4.11
3445 3551 9.628746 GTTTCACTTGTACCAAGAAAGTTTTAA 57.371 29.630 10.73 0.00 31.88 1.52
3473 3579 3.118992 TCTGCTTGTATAGTGTGCTCCTG 60.119 47.826 0.00 0.00 0.00 3.86
3486 3592 2.093764 GTGCTCCTGAGATTGCTACTGT 60.094 50.000 0.00 0.00 0.00 3.55
3504 3610 6.018669 GCTACTGTTGCATAGAGTTTATCACC 60.019 42.308 9.31 0.00 31.84 4.02
3505 3611 5.804639 ACTGTTGCATAGAGTTTATCACCA 58.195 37.500 5.58 0.00 0.00 4.17
3508 3614 3.808728 TGCATAGAGTTTATCACCAGGC 58.191 45.455 0.00 0.00 0.00 4.85
3510 3616 3.744660 CATAGAGTTTATCACCAGGCCC 58.255 50.000 0.00 0.00 0.00 5.80
3615 3728 2.046285 GGCCGCAATGTTACAGGCT 61.046 57.895 12.07 0.00 46.44 4.58
3662 3775 4.801330 TGTCCGTGAACTTCATGTCTAT 57.199 40.909 9.65 0.00 31.62 1.98
3704 3817 1.429463 GTCGTGATGCGGAGAAACTT 58.571 50.000 0.00 0.00 41.72 2.66
3736 3849 6.310711 CAGGTTAATCTCTTACTCGAACAACC 59.689 42.308 0.00 0.00 31.97 3.77
3743 3856 4.055360 TCTTACTCGAACAACCATGTGTG 58.945 43.478 0.00 0.00 40.46 3.82
3757 3877 3.495983 CCATGTGTGGTAGTTGTCCTCAA 60.496 47.826 0.00 0.00 40.83 3.02
3768 3888 7.092891 TGGTAGTTGTCCTCAAATGATCATACT 60.093 37.037 9.04 7.82 35.20 2.12
3769 3889 7.439655 GGTAGTTGTCCTCAAATGATCATACTC 59.560 40.741 9.04 1.14 35.20 2.59
3780 3900 7.603784 TCAAATGATCATACTCGGAATACATGG 59.396 37.037 9.04 0.00 0.00 3.66
3790 3910 2.368439 GGAATACATGGCTGTGCTCAA 58.632 47.619 0.00 0.00 36.79 3.02
3857 3977 6.381481 TGAATGAATACTTGCTAAGCATGG 57.619 37.500 0.00 0.00 38.76 3.66
3862 3982 1.442769 ACTTGCTAAGCATGGTCACG 58.557 50.000 0.00 0.00 38.76 4.35
3878 3998 3.309954 GGTCACGCTTAGGCTTTTATCAG 59.690 47.826 0.00 0.00 36.09 2.90
3879 3999 3.933332 GTCACGCTTAGGCTTTTATCAGT 59.067 43.478 0.00 0.00 36.09 3.41
3893 4013 7.367285 GCTTTTATCAGTGTGTAATTGTTGGA 58.633 34.615 0.00 0.00 0.00 3.53
3894 4014 7.538678 GCTTTTATCAGTGTGTAATTGTTGGAG 59.461 37.037 0.00 0.00 0.00 3.86
3896 4016 7.905604 TTATCAGTGTGTAATTGTTGGAGAG 57.094 36.000 0.00 0.00 0.00 3.20
3899 4019 2.488153 GTGTGTAATTGTTGGAGAGCCC 59.512 50.000 0.00 0.00 0.00 5.19
3903 4023 1.826385 AATTGTTGGAGAGCCCTTCG 58.174 50.000 0.00 0.00 35.38 3.79
3919 4039 4.261197 GCCCTTCGCAGTTAATTATTCAGG 60.261 45.833 0.00 0.00 37.47 3.86
3921 4041 5.220854 CCCTTCGCAGTTAATTATTCAGGTG 60.221 44.000 0.00 0.00 0.00 4.00
3927 4047 6.681178 CGCAGTTAATTATTCAGGTGTTTACG 59.319 38.462 0.00 0.00 0.00 3.18
3934 4054 2.093306 TCAGGTGTTTACGATGGCTG 57.907 50.000 0.00 0.00 0.00 4.85
3939 4059 2.343101 GTGTTTACGATGGCTGTGCTA 58.657 47.619 0.00 0.00 0.00 3.49
4001 4122 6.651859 CACCATTTTCAGGGGTATGGGACA 62.652 50.000 0.00 0.00 41.45 4.02
4052 4173 4.112634 CTCGTAAGGAGCATCGATCAAAA 58.887 43.478 0.00 0.00 35.63 2.44
4142 4263 4.523083 GGCCTTACATGGTCAAATGTCTA 58.477 43.478 0.00 0.00 41.09 2.59
4159 4280 9.102757 CAAATGTCTAGCATAGTGTATTTCAGT 57.897 33.333 0.92 0.00 40.38 3.41
4181 4302 1.069568 TCAAACGGCACTTGTATTGCG 60.070 47.619 0.00 0.00 41.18 4.85
4262 4386 8.802856 GTTATTTTGAAAATTTTGTGTTTGCCC 58.197 29.630 8.47 0.00 0.00 5.36
4271 4395 2.727123 TGTGTTTGCCCTCTTCAGAA 57.273 45.000 0.00 0.00 0.00 3.02
4273 4397 4.365514 TGTGTTTGCCCTCTTCAGAATA 57.634 40.909 0.00 0.00 0.00 1.75
4323 4449 2.689471 GCAGAATGGTGTAATCCATGCA 59.311 45.455 6.49 0.00 46.14 3.96
4324 4450 3.130869 GCAGAATGGTGTAATCCATGCAA 59.869 43.478 6.49 0.00 46.14 4.08
4325 4451 4.675510 CAGAATGGTGTAATCCATGCAAC 58.324 43.478 6.49 0.00 46.14 4.17
4326 4452 3.378112 AGAATGGTGTAATCCATGCAACG 59.622 43.478 6.49 0.00 46.14 4.10
4327 4453 2.192664 TGGTGTAATCCATGCAACGT 57.807 45.000 0.00 0.00 33.42 3.99
4353 4492 2.699954 ACTCCTTTGCCGAATACACAG 58.300 47.619 0.00 0.00 0.00 3.66
4374 4513 7.545965 ACACAGGACGATTTAGTTATTTGAGAG 59.454 37.037 0.00 0.00 0.00 3.20
4427 4980 1.676006 CACATTTCCCTTACCCGCATC 59.324 52.381 0.00 0.00 0.00 3.91
4467 5020 2.287248 GCTGTCCAGTTTGTTGAGAAGC 60.287 50.000 0.00 0.00 0.00 3.86
4473 5026 4.021456 TCCAGTTTGTTGAGAAGCTATCGA 60.021 41.667 0.00 0.00 0.00 3.59
4478 5031 6.809196 AGTTTGTTGAGAAGCTATCGAAGTAG 59.191 38.462 0.00 0.00 0.00 2.57
4516 5071 5.402867 GTGCGAAGATTATTACAGGAGTAGC 59.597 44.000 0.00 0.00 0.00 3.58
4521 5076 5.415961 AGATTATTACAGGAGTAGCCCCAT 58.584 41.667 0.00 0.00 37.37 4.00
4581 5137 1.008361 CATTGGTTTTTCAGGCGCGG 61.008 55.000 8.83 0.00 0.00 6.46
4598 5332 2.030893 CGCGGGTATCGTGGAGTTTATA 60.031 50.000 0.00 0.00 44.78 0.98
4667 5401 4.473196 TGCCAGAAAGGAATACATACTGGA 59.527 41.667 13.37 0.00 43.91 3.86
4706 5440 9.276590 CATCCTTAATCTAACAGCATAATGTGA 57.723 33.333 0.00 0.00 32.52 3.58
4712 5446 6.493189 TCTAACAGCATAATGTGATACCCA 57.507 37.500 0.00 0.00 32.52 4.51
4714 5448 5.835113 AACAGCATAATGTGATACCCAAC 57.165 39.130 0.00 0.00 32.52 3.77
4718 5452 5.525745 CAGCATAATGTGATACCCAACGTAA 59.474 40.000 0.00 0.00 0.00 3.18
4885 5619 9.442047 AGAAGAAACCAATGAGTAGAAACTATG 57.558 33.333 0.00 0.00 35.56 2.23
4886 5620 9.220767 GAAGAAACCAATGAGTAGAAACTATGT 57.779 33.333 0.00 0.00 35.56 2.29
4887 5621 9.574516 AAGAAACCAATGAGTAGAAACTATGTT 57.425 29.630 0.00 0.00 35.56 2.71
5079 5813 7.713073 TGCATAATGACGAGTAAAATGATGGTA 59.287 33.333 0.00 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 1.398692 TTCGCCCTTCCAATATTGCC 58.601 50.000 10.11 0.00 0.00 4.52
91 92 4.933505 ACTAACTAGTATTCGCCCTTCC 57.066 45.455 0.00 0.00 34.13 3.46
131 132 4.067896 TCTTGATGCTCCTGTTGTTTCTC 58.932 43.478 0.00 0.00 0.00 2.87
168 173 3.186119 GAGCTCTAGACTGTGATTGTGC 58.814 50.000 6.43 0.00 0.00 4.57
175 180 3.437395 AGTGTTACGAGCTCTAGACTGTG 59.563 47.826 12.85 0.00 0.00 3.66
195 204 1.446016 AGCCCTTAGAAACCCACAGT 58.554 50.000 0.00 0.00 0.00 3.55
234 243 6.620877 TCTAACATAGTTTGACCACTCCAT 57.379 37.500 0.00 0.00 0.00 3.41
244 253 6.129168 GCCGTCGATACATCTAACATAGTTTG 60.129 42.308 0.00 0.00 0.00 2.93
311 320 2.777692 TCTCCGGCCTATCCTTTTTCAT 59.222 45.455 0.00 0.00 0.00 2.57
321 331 0.485099 AGTGGATCTCTCCGGCCTAT 59.515 55.000 0.00 0.00 45.37 2.57
325 335 1.040339 AGTGAGTGGATCTCTCCGGC 61.040 60.000 0.00 6.43 45.37 6.13
474 484 1.269778 TGGTCTGATTCGATCCGATGC 60.270 52.381 0.00 0.00 35.23 3.91
494 504 3.062639 CGTGGGTCGGTTTAGGGT 58.937 61.111 0.00 0.00 35.71 4.34
820 841 3.739300 CACGTCGAACCAGAATGTAAACT 59.261 43.478 0.00 0.00 0.00 2.66
837 858 1.519758 CGGTGCCGATTAATACACGTC 59.480 52.381 4.35 0.00 42.83 4.34
929 950 4.309950 GTTGGGCTCGGTCGGTGT 62.310 66.667 0.00 0.00 0.00 4.16
943 965 1.608283 GGAGGGACGAAACTGGAGTTG 60.608 57.143 0.00 0.00 38.44 3.16
944 966 0.685660 GGAGGGACGAAACTGGAGTT 59.314 55.000 0.00 0.00 40.50 3.01
945 967 1.533469 CGGAGGGACGAAACTGGAGT 61.533 60.000 0.00 0.00 35.47 3.85
1476 1498 2.775384 AGTAAATCACCTTGCCCGGATA 59.225 45.455 0.73 0.00 0.00 2.59
1569 1591 6.533730 AGACACAATTTTCAGTCACATAGGA 58.466 36.000 0.00 0.00 33.56 2.94
1582 1604 6.469782 AACAGTCCAATGAGACACAATTTT 57.530 33.333 5.04 0.00 39.34 1.82
1585 1607 7.765695 AATTAACAGTCCAATGAGACACAAT 57.234 32.000 5.04 0.00 39.34 2.71
1586 1608 7.936847 ACTAATTAACAGTCCAATGAGACACAA 59.063 33.333 5.04 0.00 39.34 3.33
1587 1609 7.387673 CACTAATTAACAGTCCAATGAGACACA 59.612 37.037 5.04 0.00 39.34 3.72
1589 1611 6.371548 GCACTAATTAACAGTCCAATGAGACA 59.628 38.462 5.04 0.00 39.34 3.41
1651 1702 7.277174 ACCTGTGGCTATTAGATTTTTATGC 57.723 36.000 0.00 0.00 0.00 3.14
1655 1706 6.924111 CACAACCTGTGGCTATTAGATTTTT 58.076 36.000 0.00 0.00 44.27 1.94
1706 1763 9.376075 TCTCTAGAAAGCAGTCAAAATGATAAG 57.624 33.333 0.00 0.00 0.00 1.73
1731 1788 8.682128 TCGGTAAATACATTTTCAAAAGCATC 57.318 30.769 0.00 0.00 0.00 3.91
1739 1796 7.335627 ACTCCAGATCGGTAAATACATTTTCA 58.664 34.615 3.97 0.00 35.57 2.69
1740 1797 7.787725 ACTCCAGATCGGTAAATACATTTTC 57.212 36.000 3.97 0.00 35.57 2.29
1754 1811 3.310774 CCTACAATTGCAACTCCAGATCG 59.689 47.826 0.00 0.00 0.00 3.69
1755 1812 4.265073 ACCTACAATTGCAACTCCAGATC 58.735 43.478 0.00 0.00 0.00 2.75
1830 1887 4.439057 GACAAACCTTATCCGCACTATGA 58.561 43.478 0.00 0.00 0.00 2.15
1880 1937 6.853720 AGATTGAGCATGAAATCACTCAAAG 58.146 36.000 15.92 0.00 43.15 2.77
1933 1990 9.736023 CCTGCAAAAGAGTATATTTGAATTACC 57.264 33.333 2.66 0.00 38.50 2.85
1994 2058 8.902540 AATAATCACGATAATCAGCTGGTAAA 57.097 30.769 15.13 0.00 0.00 2.01
2000 2071 8.837788 TGATGAAATAATCACGATAATCAGCT 57.162 30.769 0.00 0.00 41.93 4.24
2152 2223 5.246656 TCAAATGCAACCAAGAAGAATGGAT 59.753 36.000 0.00 0.00 40.56 3.41
2180 2251 5.598754 TCATGGGAAAAATAACAGGGGATT 58.401 37.500 0.00 0.00 0.00 3.01
2181 2252 5.219468 TCATGGGAAAAATAACAGGGGAT 57.781 39.130 0.00 0.00 0.00 3.85
2183 2254 5.012561 TGTTTCATGGGAAAAATAACAGGGG 59.987 40.000 0.00 0.00 44.18 4.79
2270 2344 5.352284 CGGGTACATCCATAAGATAGCATC 58.648 45.833 0.00 0.00 38.11 3.91
2357 2432 1.808343 CAATCAGCAACAGCAGCTACA 59.192 47.619 0.00 0.00 41.14 2.74
2426 2504 7.707624 ATGAATTGAACAAGAGGAATTAGCA 57.292 32.000 0.00 0.00 0.00 3.49
2427 2505 8.992835 AAATGAATTGAACAAGAGGAATTAGC 57.007 30.769 0.00 0.00 0.00 3.09
2443 2521 6.258287 TGTTCAAGCAACAAGGAAATGAATTG 59.742 34.615 0.00 0.00 42.35 2.32
2448 2526 4.685924 ACTGTTCAAGCAACAAGGAAATG 58.314 39.130 0.00 0.00 44.71 2.32
2468 2546 4.716784 TCATTCTGATGCTACCAACCTACT 59.283 41.667 0.00 0.00 33.14 2.57
2473 2551 3.624861 CACCTCATTCTGATGCTACCAAC 59.375 47.826 0.00 0.00 33.14 3.77
2476 2554 3.133721 AGACACCTCATTCTGATGCTACC 59.866 47.826 0.00 0.00 33.14 3.18
2477 2555 4.399004 AGACACCTCATTCTGATGCTAC 57.601 45.455 0.00 0.00 33.14 3.58
2479 2557 3.518705 AGAAGACACCTCATTCTGATGCT 59.481 43.478 0.00 0.00 32.19 3.79
2480 2558 3.871485 AGAAGACACCTCATTCTGATGC 58.129 45.455 0.00 0.00 32.19 3.91
2481 2559 5.049167 GCTAGAAGACACCTCATTCTGATG 58.951 45.833 0.00 0.00 35.09 3.07
2483 2561 4.348486 AGCTAGAAGACACCTCATTCTGA 58.652 43.478 0.00 0.00 35.09 3.27
2484 2562 4.734398 AGCTAGAAGACACCTCATTCTG 57.266 45.455 0.00 0.00 35.09 3.02
2486 2564 4.081420 TCCAAGCTAGAAGACACCTCATTC 60.081 45.833 0.00 0.00 0.00 2.67
2508 2587 3.485877 GGACAACTGCGCAAGTCATAATC 60.486 47.826 27.62 13.64 38.56 1.75
2509 2588 2.420022 GGACAACTGCGCAAGTCATAAT 59.580 45.455 27.62 7.25 38.56 1.28
2786 2865 5.529791 TCTCACTCTCAAACTTTAGAACCG 58.470 41.667 0.00 0.00 0.00 4.44
2958 3039 1.682854 TCGACACCGGAAGTAACAAGT 59.317 47.619 9.46 0.00 36.24 3.16
2970 3051 1.271656 AGGTTACCTTTCTCGACACCG 59.728 52.381 0.00 0.00 37.07 4.94
2976 3057 1.068474 CACGCAGGTTACCTTTCTCG 58.932 55.000 0.00 5.91 0.00 4.04
3051 3132 0.036010 CCTGAATTCCAGCCTCACGT 60.036 55.000 2.27 0.00 41.57 4.49
3120 3201 6.825721 ACAACAAGAAAGATGAGGATACATCC 59.174 38.462 0.00 0.00 45.20 3.51
3126 3207 4.660168 AGCACAACAAGAAAGATGAGGAT 58.340 39.130 0.00 0.00 0.00 3.24
3134 3215 3.378112 TGTGGAGAAGCACAACAAGAAAG 59.622 43.478 0.00 0.00 0.00 2.62
3135 3216 3.128589 GTGTGGAGAAGCACAACAAGAAA 59.871 43.478 0.00 0.00 35.81 2.52
3273 3354 5.567037 ATTTTCACATCCCATCCGAGATA 57.433 39.130 0.00 0.00 0.00 1.98
3275 3356 3.931907 ATTTTCACATCCCATCCGAGA 57.068 42.857 0.00 0.00 0.00 4.04
3278 3359 7.201758 CCATATCATATTTTCACATCCCATCCG 60.202 40.741 0.00 0.00 0.00 4.18
3280 3361 8.585471 ACCATATCATATTTTCACATCCCATC 57.415 34.615 0.00 0.00 0.00 3.51
3281 3362 8.961293 AACCATATCATATTTTCACATCCCAT 57.039 30.769 0.00 0.00 0.00 4.00
3299 3399 7.838079 TTTAGGAATGCAGCATAAACCATAT 57.162 32.000 20.86 9.03 0.00 1.78
3315 3416 7.568366 TGGAAAAATCCATGCCTATTTAGGAAT 59.432 33.333 7.84 0.00 42.74 3.01
3321 3422 6.961042 ACATTGGAAAAATCCATGCCTATTT 58.039 32.000 0.00 0.00 39.86 1.40
3331 3432 7.555087 TGACCATGATTACATTGGAAAAATCC 58.445 34.615 0.00 0.00 34.15 3.01
3332 3433 9.603921 ATTGACCATGATTACATTGGAAAAATC 57.396 29.630 0.00 0.00 34.15 2.17
3349 3450 5.663456 CCATGTAAAAGGGAATTGACCATG 58.337 41.667 0.00 0.00 0.00 3.66
3395 3499 4.216411 ACAAGGCAATAACTACGTGGAT 57.784 40.909 5.70 0.00 0.00 3.41
3398 3502 3.500680 ACCAACAAGGCAATAACTACGTG 59.499 43.478 0.00 0.00 43.14 4.49
3401 3505 5.918576 GTGAAACCAACAAGGCAATAACTAC 59.081 40.000 0.00 0.00 43.14 2.73
3445 3551 4.872691 GCACACTATACAAGCAGAACAGAT 59.127 41.667 0.00 0.00 0.00 2.90
3473 3579 5.355596 ACTCTATGCAACAGTAGCAATCTC 58.644 41.667 0.00 0.00 46.27 2.75
3486 3592 4.199310 GCCTGGTGATAAACTCTATGCAA 58.801 43.478 0.00 0.00 0.00 4.08
3504 3610 2.826674 TCAAAAGGATAAGGGGCCTG 57.173 50.000 0.84 0.00 34.00 4.85
3505 3611 3.134471 AGATCAAAAGGATAAGGGGCCT 58.866 45.455 0.84 0.00 36.00 5.19
3508 3614 3.316308 CGCAAGATCAAAAGGATAAGGGG 59.684 47.826 0.00 0.00 36.00 4.79
3615 3728 1.075050 ACACCTCCCTACGAGTTCAGA 59.925 52.381 0.00 0.00 36.82 3.27
3674 3787 0.391528 CATCACGACCATGCACAGGA 60.392 55.000 13.62 0.00 0.00 3.86
3695 3808 2.932261 ACCTGGTGTTGAAGTTTCTCC 58.068 47.619 0.00 0.00 0.00 3.71
3704 3817 6.571731 CGAGTAAGAGATTAACCTGGTGTTGA 60.572 42.308 0.00 0.00 37.83 3.18
3736 3849 3.401033 TGAGGACAACTACCACACATG 57.599 47.619 0.00 0.00 0.00 3.21
3743 3856 7.275920 AGTATGATCATTTGAGGACAACTACC 58.724 38.462 14.65 0.00 35.63 3.18
3751 3864 5.869649 TTCCGAGTATGATCATTTGAGGA 57.130 39.130 14.65 14.64 0.00 3.71
3757 3877 5.877012 GCCATGTATTCCGAGTATGATCATT 59.123 40.000 14.65 0.00 0.00 2.57
3768 3888 0.541392 AGCACAGCCATGTATTCCGA 59.459 50.000 0.00 0.00 37.65 4.55
3769 3889 0.940126 GAGCACAGCCATGTATTCCG 59.060 55.000 0.00 0.00 37.65 4.30
3802 3922 1.420138 CTACACCTGTGGGTCCTGTTT 59.580 52.381 1.91 0.00 45.41 2.83
3803 3923 1.056660 CTACACCTGTGGGTCCTGTT 58.943 55.000 1.91 0.00 45.41 3.16
3804 3924 0.105142 ACTACACCTGTGGGTCCTGT 60.105 55.000 1.91 0.00 45.41 4.00
3805 3925 1.933021 TACTACACCTGTGGGTCCTG 58.067 55.000 1.91 0.00 45.41 3.86
3816 3936 8.942338 TTCATTCAATCACTGTATACTACACC 57.058 34.615 4.17 0.00 34.46 4.16
3824 3944 8.743085 AGCAAGTATTCATTCAATCACTGTAT 57.257 30.769 0.00 0.00 0.00 2.29
3833 3953 6.377996 ACCATGCTTAGCAAGTATTCATTCAA 59.622 34.615 12.08 0.00 43.62 2.69
3857 3977 3.933332 ACTGATAAAAGCCTAAGCGTGAC 59.067 43.478 0.00 0.00 46.67 3.67
3862 3982 6.737254 TTACACACTGATAAAAGCCTAAGC 57.263 37.500 0.00 0.00 40.32 3.09
3867 3987 6.586082 CCAACAATTACACACTGATAAAAGCC 59.414 38.462 0.00 0.00 0.00 4.35
3878 3998 2.488153 GGGCTCTCCAACAATTACACAC 59.512 50.000 0.00 0.00 35.00 3.82
3879 3999 2.375174 AGGGCTCTCCAACAATTACACA 59.625 45.455 0.00 0.00 38.24 3.72
3893 4013 2.789409 AATTAACTGCGAAGGGCTCT 57.211 45.000 0.00 0.00 44.05 4.09
3894 4014 4.574828 TGAATAATTAACTGCGAAGGGCTC 59.425 41.667 0.00 0.00 44.05 4.70
3896 4016 4.261197 CCTGAATAATTAACTGCGAAGGGC 60.261 45.833 0.00 0.00 43.96 5.19
3899 4019 6.422776 ACACCTGAATAATTAACTGCGAAG 57.577 37.500 0.00 0.00 0.00 3.79
3903 4023 7.745015 TCGTAAACACCTGAATAATTAACTGC 58.255 34.615 0.00 0.00 0.00 4.40
3919 4039 1.156736 AGCACAGCCATCGTAAACAC 58.843 50.000 0.00 0.00 0.00 3.32
3921 4041 2.618053 AGTAGCACAGCCATCGTAAAC 58.382 47.619 0.00 0.00 0.00 2.01
3927 4047 4.065321 ACAATCTAGTAGCACAGCCATC 57.935 45.455 0.00 0.00 0.00 3.51
3934 4054 4.331168 CCAGCTGAAACAATCTAGTAGCAC 59.669 45.833 17.39 0.00 32.42 4.40
3939 4059 3.710209 AGCCAGCTGAAACAATCTAGT 57.290 42.857 17.39 0.00 0.00 2.57
4001 4122 2.500910 CTCTGCTTCTTCCATCAGGAGT 59.499 50.000 0.00 0.00 46.74 3.85
4052 4173 1.611673 CCTGAGATGACGGCCAGTTTT 60.612 52.381 2.24 0.00 0.00 2.43
4142 4263 7.224753 CCGTTTGATACTGAAATACACTATGCT 59.775 37.037 0.00 0.00 0.00 3.79
4159 4280 3.181515 CGCAATACAAGTGCCGTTTGATA 60.182 43.478 0.00 0.00 38.86 2.15
4262 4386 6.801377 CGCTGCTATAACTCTATTCTGAAGAG 59.199 42.308 5.70 5.70 44.99 2.85
4271 4395 7.393796 AGGTGTAATACGCTGCTATAACTCTAT 59.606 37.037 3.85 0.00 0.00 1.98
4273 4397 5.535406 AGGTGTAATACGCTGCTATAACTCT 59.465 40.000 3.85 0.00 0.00 3.24
4323 4449 2.407090 GGCAAAGGAGTTACGTACGTT 58.593 47.619 27.92 8.78 0.00 3.99
4324 4450 1.666888 CGGCAAAGGAGTTACGTACGT 60.667 52.381 25.98 25.98 0.00 3.57
4325 4451 0.986992 CGGCAAAGGAGTTACGTACG 59.013 55.000 15.01 15.01 0.00 3.67
4326 4452 2.352503 TCGGCAAAGGAGTTACGTAC 57.647 50.000 0.00 0.00 0.00 3.67
4327 4453 3.598019 ATTCGGCAAAGGAGTTACGTA 57.402 42.857 0.00 0.00 0.00 3.57
4353 4492 6.702282 CCCTCTCTCAAATAACTAAATCGTCC 59.298 42.308 0.00 0.00 0.00 4.79
4516 5071 0.175760 CTACGGAGTGTGACATGGGG 59.824 60.000 0.00 0.00 45.73 4.96
4521 5076 1.179174 AGCTGCTACGGAGTGTGACA 61.179 55.000 0.00 0.00 45.73 3.58
4564 5120 2.725008 CCGCGCCTGAAAAACCAA 59.275 55.556 0.00 0.00 0.00 3.67
4566 5122 1.310216 ATACCCGCGCCTGAAAAACC 61.310 55.000 0.00 0.00 0.00 3.27
4581 5137 6.700520 CCAGAAACTATAAACTCCACGATACC 59.299 42.308 0.00 0.00 0.00 2.73
4598 5332 6.899393 TCAATTATTCTTGTGCCAGAAACT 57.101 33.333 0.00 0.00 36.36 2.66
4633 5367 2.892852 CCTTTCTGGCAAAATCACTCCA 59.107 45.455 0.00 0.00 0.00 3.86
4706 5440 7.806409 AAAAAGTAACTGTTACGTTGGGTAT 57.194 32.000 25.12 11.75 41.01 2.73
4899 5633 9.892130 ATTTTCTACTCATCGGTTTCTTCTAAT 57.108 29.630 0.00 0.00 0.00 1.73
4902 5636 9.319143 CATATTTTCTACTCATCGGTTTCTTCT 57.681 33.333 0.00 0.00 0.00 2.85
4903 5637 9.099454 ACATATTTTCTACTCATCGGTTTCTTC 57.901 33.333 0.00 0.00 0.00 2.87
4904 5638 9.449719 AACATATTTTCTACTCATCGGTTTCTT 57.550 29.630 0.00 0.00 0.00 2.52
5079 5813 6.208204 CCCATTTCTTTGTTCTCTGTGATCTT 59.792 38.462 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.