Multiple sequence alignment - TraesCS1D01G094600

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 TraesCS1D01G094600 chr1D 100.000 5741 0 0 1 5741 80442921 80448661 0.000000e+00 10602
1 TraesCS1D01G094600 chr1D 89.480 808 82 3 1 807 465832425 465831620 0.000000e+00 1018
2 TraesCS1D01G094600 chr1D 90.378 291 17 9 5346 5635 80540943 80541223 7.030000e-99 372
3 TraesCS1D01G094600 chr1D 91.286 241 17 3 5380 5620 80537068 80537304 5.550000e-85 326
4 TraesCS1D01G094600 chr1D 99.010 101 1 0 3747 3847 80446565 80446665 1.270000e-41 182
5 TraesCS1D01G094600 chr1D 99.010 101 1 0 3645 3745 80446667 80446767 1.270000e-41 182
6 TraesCS1D01G094600 chr1D 91.954 87 7 0 5655 5741 80537384 80537470 7.810000e-24 122
7 TraesCS1D01G094600 chr1B 95.788 2944 86 16 835 3745 132933636 132936574 0.000000e+00 4715
8 TraesCS1D01G094600 chr1B 93.095 1564 71 20 4209 5741 132937049 132938606 0.000000e+00 2255
9 TraesCS1D01G094600 chr1B 95.257 759 36 0 1 759 132910565 132911323 0.000000e+00 1203
10 TraesCS1D01G094600 chr1B 94.286 665 38 0 143 807 132911699 132912363 0.000000e+00 1018
11 TraesCS1D01G094600 chr1B 86.757 808 104 3 1 807 441673160 441672355 0.000000e+00 896
12 TraesCS1D01G094600 chr1B 96.721 427 11 2 3747 4170 132936474 132936900 0.000000e+00 708
13 TraesCS1D01G094600 chr1B 90.449 356 27 4 5393 5741 133032480 133032835 4.050000e-126 462
14 TraesCS1D01G094600 chr1B 94.672 244 12 1 808 1051 132911456 132911698 1.510000e-100 377
15 TraesCS1D01G094600 chr1B 90.441 272 19 5 5364 5635 133075644 133075908 9.150000e-93 351
16 TraesCS1D01G094600 chr1A 95.212 2945 96 16 833 3745 99014167 99017098 0.000000e+00 4615
17 TraesCS1D01G094600 chr1A 91.416 1398 83 13 4373 5741 99017576 99018965 0.000000e+00 1882
18 TraesCS1D01G094600 chr1A 96.187 577 19 2 3747 4323 99017001 99017574 0.000000e+00 941
19 TraesCS1D01G094600 chr1A 85.067 375 40 11 5380 5741 99048754 99049125 9.090000e-98 368
20 TraesCS1D01G094600 chr1A 88.660 291 27 5 5346 5635 99071059 99071344 3.290000e-92 350
21 TraesCS1D01G094600 chr4B 86.108 799 109 1 9 807 76563431 76564227 0.000000e+00 859
22 TraesCS1D01G094600 chr5A 85.874 807 97 5 1 807 614410431 614409642 0.000000e+00 843
23 TraesCS1D01G094600 chr5D 86.545 550 70 4 1 548 369656843 369657390 2.290000e-168 603
24 TraesCS1D01G094600 chr5B 90.314 382 22 5 2519 2899 692360566 692360933 2.400000e-133 486
25 TraesCS1D01G094600 chrUn 88.158 380 27 9 2521 2899 47692020 47691658 2.460000e-118 436
26 TraesCS1D01G094600 chr3B 77.893 579 112 14 234 804 369282340 369282910 4.260000e-91 346
27 TraesCS1D01G094600 chr7B 93.204 206 14 0 5404 5609 95337271 95337476 2.600000e-78 303
28 TraesCS1D01G094600 chr2A 75.854 439 78 16 1074 1489 775689423 775688990 1.260000e-46 198
29 TraesCS1D01G094600 chr7D 78.277 267 46 9 3120 3377 13676383 13676120 1.660000e-35 161


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 TraesCS1D01G094600 chr1D 80442921 80448661 5740 False 3655.333333 10602 99.340000 1 5741 3 chr1D.!!$F1 5740
1 TraesCS1D01G094600 chr1D 465831620 465832425 805 True 1018.000000 1018 89.480000 1 807 1 chr1D.!!$R1 806
2 TraesCS1D01G094600 chr1D 80537068 80541223 4155 False 273.333333 372 91.206000 5346 5741 3 chr1D.!!$F2 395
3 TraesCS1D01G094600 chr1B 132933636 132938606 4970 False 2559.333333 4715 95.201333 835 5741 3 chr1B.!!$F4 4906
4 TraesCS1D01G094600 chr1B 441672355 441673160 805 True 896.000000 896 86.757000 1 807 1 chr1B.!!$R1 806
5 TraesCS1D01G094600 chr1B 132910565 132912363 1798 False 866.000000 1203 94.738333 1 1051 3 chr1B.!!$F3 1050
6 TraesCS1D01G094600 chr1A 99014167 99018965 4798 False 2479.333333 4615 94.271667 833 5741 3 chr1A.!!$F3 4908
7 TraesCS1D01G094600 chr4B 76563431 76564227 796 False 859.000000 859 86.108000 9 807 1 chr4B.!!$F1 798
8 TraesCS1D01G094600 chr5A 614409642 614410431 789 True 843.000000 843 85.874000 1 807 1 chr5A.!!$R1 806
9 TraesCS1D01G094600 chr5D 369656843 369657390 547 False 603.000000 603 86.545000 1 548 1 chr5D.!!$F1 547
10 TraesCS1D01G094600 chr3B 369282340 369282910 570 False 346.000000 346 77.893000 234 804 1 chr3B.!!$F1 570

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
880 987 0.323542 TCGTCCTCCTCTTCCCTCAC 60.324 60.0 0.00 0.0 0.00 3.51 F
1446 1557 0.171231 CCAAGATCACGCTCGAGACA 59.829 55.0 18.75 0.0 0.00 3.41 F
2309 2453 2.037772 AGGCTAGATTCCGCAGTAATGG 59.962 50.0 0.00 0.0 0.00 3.16 F
3739 3886 0.035439 ATTGTGCCCGGTAGGTTCAG 60.035 55.0 0.00 0.0 38.26 3.02 F
3742 3889 0.108472 GTGCCCGGTAGGTTCAGTAC 60.108 60.0 0.00 0.0 38.26 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2348 2492 0.393537 AAAGCAGAGGGGAATCAGCG 60.394 55.000 0.00 0.0 36.86 5.18 R
2798 2942 3.648009 TCAAACGCAATTTTCCCATCAC 58.352 40.909 0.00 0.0 0.00 3.06 R
3822 3969 0.035439 CTGAACCTACCGGGCACAAT 60.035 55.000 6.32 0.0 39.10 2.71 R
4569 4852 0.032615 ACGGCTCCAGAGGAAGATCT 60.033 55.000 0.00 0.0 0.00 2.75 R
5254 5565 0.538584 TGCTTGCGTCCTCATCTGAT 59.461 50.000 0.00 0.0 0.00 2.90 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
71 72 4.619227 ACGCCCAAGTGGACACGG 62.619 66.667 0.00 0.00 37.39 4.94
402 403 3.507103 TCGAATTTGGACGTCGGATAA 57.493 42.857 9.92 1.23 35.51 1.75
473 474 1.266178 TCAAGAGGAGGACAATGCGA 58.734 50.000 0.00 0.00 0.00 5.10
506 507 2.098607 GTGTAGTGCGTGTATGCTAGGA 59.901 50.000 0.00 0.00 35.36 2.94
675 676 2.436109 GGCCCTCTGGAAGCAACA 59.564 61.111 0.00 0.00 0.00 3.33
691 692 2.780993 CAACACAACGCGAGAGTTTTT 58.219 42.857 15.93 0.85 30.96 1.94
816 921 2.811431 CGTTTTGTGAGAGCCATTGGTA 59.189 45.455 4.26 0.00 0.00 3.25
817 922 3.364964 CGTTTTGTGAGAGCCATTGGTAC 60.365 47.826 4.26 0.00 0.00 3.34
819 924 3.719268 TTGTGAGAGCCATTGGTACAT 57.281 42.857 4.26 0.00 39.30 2.29
823 928 3.873952 GTGAGAGCCATTGGTACATTCTC 59.126 47.826 4.26 9.60 39.30 2.87
824 929 3.126831 GAGAGCCATTGGTACATTCTCG 58.873 50.000 4.26 0.00 39.30 4.04
827 932 2.238646 AGCCATTGGTACATTCTCGGAA 59.761 45.455 4.26 0.00 39.30 4.30
880 987 0.323542 TCGTCCTCCTCTTCCCTCAC 60.324 60.000 0.00 0.00 0.00 3.51
1446 1557 0.171231 CCAAGATCACGCTCGAGACA 59.829 55.000 18.75 0.00 0.00 3.41
1510 1621 8.318876 CGGTATAGATCGTAGTTTTTGTTCTTG 58.681 37.037 0.00 0.00 0.00 3.02
1540 1654 4.021632 TGCATTGAATTGGATTTTGGACGA 60.022 37.500 0.00 0.00 0.00 4.20
1716 1831 7.122055 AGTTCGATGAGTTGACTCTTAGAATCT 59.878 37.037 18.37 15.25 40.72 2.40
1817 1933 9.170584 GCTGTCTTTTTGTATCTTCTTTTGTAC 57.829 33.333 0.00 0.00 0.00 2.90
1877 2001 6.821031 TGAGTAGTTTCAGTCTTACCTCTC 57.179 41.667 0.00 0.00 0.00 3.20
2112 2247 8.706322 TCTTGGCTGTGATATGTTACTATAGA 57.294 34.615 6.78 0.00 0.00 1.98
2113 2248 9.314133 TCTTGGCTGTGATATGTTACTATAGAT 57.686 33.333 6.78 0.00 0.00 1.98
2114 2249 9.363763 CTTGGCTGTGATATGTTACTATAGATG 57.636 37.037 6.78 0.00 0.00 2.90
2115 2250 7.840931 TGGCTGTGATATGTTACTATAGATGG 58.159 38.462 6.78 0.00 0.00 3.51
2116 2251 7.673926 TGGCTGTGATATGTTACTATAGATGGA 59.326 37.037 6.78 0.00 0.00 3.41
2118 2253 8.194104 GCTGTGATATGTTACTATAGATGGAGG 58.806 40.741 6.78 0.00 0.00 4.30
2299 2443 5.810080 ACAGTATACCAAGGCTAGATTCC 57.190 43.478 0.00 0.00 0.00 3.01
2309 2453 2.037772 AGGCTAGATTCCGCAGTAATGG 59.962 50.000 0.00 0.00 0.00 3.16
2348 2492 9.638239 TTACCTTCTTGCAATTCATTATTTCAC 57.362 29.630 0.00 0.00 0.00 3.18
2372 2516 2.095461 GATTCCCCTCTGCTTTGGTTC 58.905 52.381 0.00 0.00 0.00 3.62
2764 2908 4.597507 AGAATGTGTTAAGGGTGGAAGAGA 59.402 41.667 0.00 0.00 0.00 3.10
2798 2942 0.326264 CCTGGACTTCCACTCAAGGG 59.674 60.000 0.00 0.00 42.01 3.95
3052 3196 4.276926 CAGATTATTTCTGGCCTGGCTTAC 59.723 45.833 19.68 2.17 46.89 2.34
3733 3880 4.235731 GGGAATTGTGCCCGGTAG 57.764 61.111 0.00 0.00 35.50 3.18
3734 3881 1.453197 GGGAATTGTGCCCGGTAGG 60.453 63.158 0.00 0.00 35.50 3.18
3735 3882 1.301954 GGAATTGTGCCCGGTAGGT 59.698 57.895 0.00 0.00 38.26 3.08
3736 3883 0.323087 GGAATTGTGCCCGGTAGGTT 60.323 55.000 0.00 0.00 38.26 3.50
3737 3884 1.092348 GAATTGTGCCCGGTAGGTTC 58.908 55.000 0.00 0.00 38.26 3.62
3738 3885 0.402504 AATTGTGCCCGGTAGGTTCA 59.597 50.000 0.00 0.00 38.26 3.18
3739 3886 0.035439 ATTGTGCCCGGTAGGTTCAG 60.035 55.000 0.00 0.00 38.26 3.02
3740 3887 1.412453 TTGTGCCCGGTAGGTTCAGT 61.412 55.000 0.00 0.00 38.26 3.41
3741 3888 0.542467 TGTGCCCGGTAGGTTCAGTA 60.542 55.000 0.00 0.00 38.26 2.74
3742 3889 0.108472 GTGCCCGGTAGGTTCAGTAC 60.108 60.000 0.00 0.00 38.26 2.73
3743 3890 0.251922 TGCCCGGTAGGTTCAGTACT 60.252 55.000 0.00 0.00 38.26 2.73
3744 3891 0.175073 GCCCGGTAGGTTCAGTACTG 59.825 60.000 17.17 17.17 38.26 2.74
3745 3892 1.553706 CCCGGTAGGTTCAGTACTGT 58.446 55.000 21.99 5.87 35.12 3.55
3746 3893 1.203994 CCCGGTAGGTTCAGTACTGTG 59.796 57.143 21.99 0.00 35.12 3.66
3747 3894 1.891150 CCGGTAGGTTCAGTACTGTGT 59.109 52.381 21.99 8.23 0.00 3.72
3748 3895 2.094854 CCGGTAGGTTCAGTACTGTGTC 60.095 54.545 21.99 12.96 0.00 3.67
3749 3896 2.818432 CGGTAGGTTCAGTACTGTGTCT 59.182 50.000 21.99 17.77 0.00 3.41
3750 3897 3.255149 CGGTAGGTTCAGTACTGTGTCTT 59.745 47.826 21.99 12.13 0.00 3.01
3751 3898 4.557205 GGTAGGTTCAGTACTGTGTCTTG 58.443 47.826 21.99 0.00 0.00 3.02
3752 3899 3.113260 AGGTTCAGTACTGTGTCTTGC 57.887 47.619 21.99 6.22 0.00 4.01
3753 3900 2.434336 AGGTTCAGTACTGTGTCTTGCA 59.566 45.455 21.99 0.00 0.00 4.08
3754 3901 3.118408 AGGTTCAGTACTGTGTCTTGCAA 60.118 43.478 21.99 0.00 0.00 4.08
3755 3902 3.815401 GGTTCAGTACTGTGTCTTGCAAT 59.185 43.478 21.99 0.00 0.00 3.56
3756 3903 4.319766 GGTTCAGTACTGTGTCTTGCAATG 60.320 45.833 21.99 0.00 0.00 2.82
3757 3904 4.335400 TCAGTACTGTGTCTTGCAATGA 57.665 40.909 21.99 0.00 0.00 2.57
3758 3905 4.898320 TCAGTACTGTGTCTTGCAATGAT 58.102 39.130 21.99 0.00 0.00 2.45
3759 3906 4.692155 TCAGTACTGTGTCTTGCAATGATG 59.308 41.667 21.99 0.00 0.00 3.07
3760 3907 4.692155 CAGTACTGTGTCTTGCAATGATGA 59.308 41.667 15.06 0.00 0.00 2.92
3761 3908 5.353400 CAGTACTGTGTCTTGCAATGATGAT 59.647 40.000 15.06 0.00 0.00 2.45
3762 3909 5.942236 AGTACTGTGTCTTGCAATGATGATT 59.058 36.000 0.00 0.00 0.00 2.57
3763 3910 7.064966 CAGTACTGTGTCTTGCAATGATGATTA 59.935 37.037 15.06 0.00 0.00 1.75
3764 3911 7.772292 AGTACTGTGTCTTGCAATGATGATTAT 59.228 33.333 0.00 0.00 0.00 1.28
3765 3912 7.400599 ACTGTGTCTTGCAATGATGATTATT 57.599 32.000 0.00 0.00 0.00 1.40
3766 3913 7.478322 ACTGTGTCTTGCAATGATGATTATTC 58.522 34.615 0.00 0.00 0.00 1.75
3767 3914 6.798482 TGTGTCTTGCAATGATGATTATTCC 58.202 36.000 0.00 0.00 0.00 3.01
3768 3915 6.377712 TGTGTCTTGCAATGATGATTATTCCA 59.622 34.615 0.00 0.00 0.00 3.53
3769 3916 6.694411 GTGTCTTGCAATGATGATTATTCCAC 59.306 38.462 0.00 0.00 0.00 4.02
3770 3917 6.377712 TGTCTTGCAATGATGATTATTCCACA 59.622 34.615 0.00 0.00 0.00 4.17
3771 3918 6.916387 GTCTTGCAATGATGATTATTCCACAG 59.084 38.462 0.00 0.00 0.00 3.66
3772 3919 6.604396 TCTTGCAATGATGATTATTCCACAGT 59.396 34.615 0.00 0.00 0.00 3.55
3773 3920 6.778834 TGCAATGATGATTATTCCACAGTT 57.221 33.333 0.00 0.00 0.00 3.16
3774 3921 6.798482 TGCAATGATGATTATTCCACAGTTC 58.202 36.000 0.00 0.00 0.00 3.01
3775 3922 6.377712 TGCAATGATGATTATTCCACAGTTCA 59.622 34.615 0.00 0.00 0.00 3.18
3776 3923 7.093858 TGCAATGATGATTATTCCACAGTTCAA 60.094 33.333 0.00 0.00 0.00 2.69
3777 3924 7.924412 GCAATGATGATTATTCCACAGTTCAAT 59.076 33.333 0.00 0.00 0.00 2.57
3778 3925 9.811995 CAATGATGATTATTCCACAGTTCAATT 57.188 29.630 0.00 0.00 0.00 2.32
3789 3936 6.446318 TCCACAGTTCAATTTTTGTATCTGC 58.554 36.000 0.00 0.00 32.16 4.26
3790 3937 6.265196 TCCACAGTTCAATTTTTGTATCTGCT 59.735 34.615 0.00 0.00 32.16 4.24
3791 3938 6.925165 CCACAGTTCAATTTTTGTATCTGCTT 59.075 34.615 0.00 0.00 32.16 3.91
3792 3939 7.439056 CCACAGTTCAATTTTTGTATCTGCTTT 59.561 33.333 0.00 0.00 32.16 3.51
3793 3940 8.482429 CACAGTTCAATTTTTGTATCTGCTTTC 58.518 33.333 0.00 0.00 32.16 2.62
3794 3941 8.196771 ACAGTTCAATTTTTGTATCTGCTTTCA 58.803 29.630 0.00 0.00 32.16 2.69
3795 3942 9.199982 CAGTTCAATTTTTGTATCTGCTTTCAT 57.800 29.630 0.00 0.00 0.00 2.57
3820 3967 7.687941 ATTCTTTGTTAAGTATGACAGTGGG 57.312 36.000 0.00 0.00 32.98 4.61
3821 3968 6.428083 TCTTTGTTAAGTATGACAGTGGGA 57.572 37.500 0.00 0.00 32.98 4.37
3822 3969 6.833041 TCTTTGTTAAGTATGACAGTGGGAA 58.167 36.000 0.00 0.00 32.98 3.97
3823 3970 7.458397 TCTTTGTTAAGTATGACAGTGGGAAT 58.542 34.615 0.00 0.00 32.98 3.01
3824 3971 7.942341 TCTTTGTTAAGTATGACAGTGGGAATT 59.058 33.333 0.00 0.00 32.98 2.17
3825 3972 7.447374 TTGTTAAGTATGACAGTGGGAATTG 57.553 36.000 0.00 0.00 0.00 2.32
3826 3973 6.539173 TGTTAAGTATGACAGTGGGAATTGT 58.461 36.000 0.00 0.00 0.00 2.71
3827 3974 6.429692 TGTTAAGTATGACAGTGGGAATTGTG 59.570 38.462 0.00 0.00 0.00 3.33
3828 3975 3.347216 AGTATGACAGTGGGAATTGTGC 58.653 45.455 0.00 0.00 0.00 4.57
3829 3976 1.549203 ATGACAGTGGGAATTGTGCC 58.451 50.000 0.00 0.00 35.31 5.01
3830 3977 0.539438 TGACAGTGGGAATTGTGCCC 60.539 55.000 0.00 0.00 46.22 5.36
4207 4482 1.140312 ACACCAGGATGTCTGTTGGT 58.860 50.000 0.00 0.00 44.44 3.67
4285 4560 0.719465 GTAGTTGCGTCATCCCAACG 59.281 55.000 0.00 0.00 44.45 4.10
4305 4580 2.292016 CGTGCAGTATGGTTTTGGTTCA 59.708 45.455 0.00 0.00 35.86 3.18
4327 4606 7.175347 TCACTAAACACTAGCAATCTGAGAT 57.825 36.000 0.00 0.00 0.00 2.75
4328 4607 7.261325 TCACTAAACACTAGCAATCTGAGATC 58.739 38.462 0.00 0.00 0.00 2.75
4379 4658 7.710907 GCATCCTTTTATTTTGGTAATCTTCCC 59.289 37.037 0.00 0.00 0.00 3.97
4457 4740 4.778534 ACTTGCATTCTCATGTTCTTGG 57.221 40.909 0.00 0.00 32.28 3.61
4459 4742 2.799017 TGCATTCTCATGTTCTTGGCT 58.201 42.857 0.00 0.00 32.28 4.75
4463 4746 4.733815 GCATTCTCATGTTCTTGGCTGATG 60.734 45.833 0.00 0.00 32.28 3.07
4470 4753 4.829064 TGTTCTTGGCTGATGTTGTAAC 57.171 40.909 0.00 0.00 0.00 2.50
4474 4757 3.814842 TCTTGGCTGATGTTGTAACTGTG 59.185 43.478 0.00 0.00 0.00 3.66
4485 4768 5.773575 TGTTGTAACTGTGAAGAGCTCTAG 58.226 41.667 18.59 13.22 0.00 2.43
4553 4836 3.740832 TGACTGCGTAACATCTTGTTCTG 59.259 43.478 0.00 0.00 40.22 3.02
4707 4990 3.069300 AGAACATCAGAGATGTCATCCCG 59.931 47.826 12.53 0.00 0.00 5.14
4714 4997 0.541863 AGATGTCATCCCGTTCCCAC 59.458 55.000 9.29 0.00 0.00 4.61
4745 5028 1.208165 AGGGCCGATCTTTGAAGGGT 61.208 55.000 0.00 0.00 0.00 4.34
4797 5082 4.143473 CGTCAATTACACTTTCGTTAGCGT 60.143 41.667 0.00 0.00 39.49 5.07
4805 5090 4.142643 ACACTTTCGTTAGCGTTTTTGGAA 60.143 37.500 0.00 0.00 39.49 3.53
4806 5091 4.973663 CACTTTCGTTAGCGTTTTTGGAAT 59.026 37.500 0.00 0.00 39.49 3.01
4818 5103 0.885196 TTTGGAATAGTGTTGGCCGC 59.115 50.000 0.00 0.00 0.00 6.53
4864 5149 5.681543 CGCATGCTGATATCATTTGATATGC 59.318 40.000 17.13 13.99 45.07 3.14
4891 5176 4.515191 GTGTCTTGGCTTGTTGTGATTCTA 59.485 41.667 0.00 0.00 0.00 2.10
4896 5181 7.168135 GTCTTGGCTTGTTGTGATTCTAAAAAG 59.832 37.037 0.00 0.00 0.00 2.27
5042 5329 4.696479 AGATGCCTTAGTTACATGGAGG 57.304 45.455 0.00 0.00 0.00 4.30
5043 5330 4.298626 AGATGCCTTAGTTACATGGAGGA 58.701 43.478 0.00 0.00 0.00 3.71
5044 5331 4.721776 AGATGCCTTAGTTACATGGAGGAA 59.278 41.667 0.00 0.00 0.00 3.36
5059 5350 4.766375 TGGAGGAAGATGTTAAATCGGTC 58.234 43.478 0.00 0.00 0.00 4.79
5233 5544 6.583912 AAAAACATCATAGTACGACGATGG 57.416 37.500 14.99 0.07 39.64 3.51
5254 5565 2.060004 GATCCGGACTGCATCGTCGA 62.060 60.000 6.12 0.00 34.75 4.20
5259 5570 0.382158 GGACTGCATCGTCGATCAGA 59.618 55.000 26.98 8.63 34.75 3.27
5261 5572 2.049959 GACTGCATCGTCGATCAGATG 58.950 52.381 26.98 18.22 45.06 2.90
5436 5748 3.617143 GAAGGTGTACGGGTGGGCC 62.617 68.421 0.00 0.00 0.00 5.80
5622 5934 4.091549 TCTTCGGTACACCTACTTCCATT 58.908 43.478 0.00 0.00 0.00 3.16
5641 5972 4.021192 CCATTATCCTCTCTTCTCTGGAGC 60.021 50.000 0.00 0.00 31.59 4.70
5653 5984 0.603569 TCTGGAGCAGGAACGAGTTC 59.396 55.000 7.40 7.40 38.80 3.01
5656 5987 1.270305 TGGAGCAGGAACGAGTTCTTG 60.270 52.381 19.52 19.52 45.79 3.02
5669 6000 6.473397 ACGAGTTCTTGACAATCTGAAATC 57.527 37.500 6.20 6.20 32.43 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 2.551032 CCGTCCTTTTGTTTGTAGTCCC 59.449 50.000 0.00 0.00 0.00 4.46
366 367 2.616330 CGATGTTGCACCGCCAACT 61.616 57.895 11.36 0.89 44.12 3.16
402 403 1.381056 AGACCATGCCTCGCTCTCT 60.381 57.895 0.00 0.00 0.00 3.10
488 489 3.446161 ACTTTCCTAGCATACACGCACTA 59.554 43.478 0.00 0.00 0.00 2.74
506 507 3.784338 CAAAGATGTTGTGCCACACTTT 58.216 40.909 0.00 0.88 35.11 2.66
566 567 2.299867 GCCACCAATCCAACAAGTGATT 59.700 45.455 0.00 0.00 0.00 2.57
675 676 1.005347 CGTGAAAAACTCTCGCGTTGT 60.005 47.619 5.77 0.23 40.89 3.32
691 692 3.142951 CAATTGTTGGTTAGTCCCGTGA 58.857 45.455 0.00 0.00 34.77 4.35
770 771 0.401395 AAACCTCCTCCACCCAGTCA 60.401 55.000 0.00 0.00 0.00 3.41
839 944 2.579201 CTCCACAGCCGTCGGATT 59.421 61.111 17.49 0.00 0.00 3.01
880 987 4.609018 CCGGTGGATAGGCTGCGG 62.609 72.222 0.00 0.00 0.00 5.69
1356 1467 1.134367 CGCTCCACCTTCAACTCGATA 59.866 52.381 0.00 0.00 0.00 2.92
1510 1621 7.413657 CCAAAATCCAATTCAATGCATGAGAAC 60.414 37.037 14.83 0.00 39.77 3.01
1540 1654 2.488153 TCACTCGACATTCTCACGACAT 59.512 45.455 0.00 0.00 32.72 3.06
1553 1667 6.042777 TCTGGTTTCATATGAATCACTCGAC 58.957 40.000 18.61 11.47 33.54 4.20
1716 1831 5.252547 TGGCATTACTATCAAGAAACTGCA 58.747 37.500 0.00 0.00 0.00 4.41
1817 1933 4.860907 GCACAAATGAAGCAAGATTACCAG 59.139 41.667 0.00 0.00 0.00 4.00
1877 2001 3.375922 GGGGAATTGCAAAATGAATGCTG 59.624 43.478 1.71 0.00 44.14 4.41
2030 2156 5.041191 ACTAATGCCTCCCATTAACAGAG 57.959 43.478 0.00 0.00 43.76 3.35
2032 2158 7.823745 ATTAACTAATGCCTCCCATTAACAG 57.176 36.000 0.00 0.00 43.76 3.16
2044 2179 2.287608 GCGGCCTGAATTAACTAATGCC 60.288 50.000 0.00 0.00 31.41 4.40
2112 2247 8.095452 AGTAAATCAAGACATAACTCCTCCAT 57.905 34.615 0.00 0.00 0.00 3.41
2113 2248 7.496346 AGTAAATCAAGACATAACTCCTCCA 57.504 36.000 0.00 0.00 0.00 3.86
2214 2355 7.917505 CCAGCTTTTCATCAACTATATTTCACC 59.082 37.037 0.00 0.00 0.00 4.02
2299 2443 6.377327 ACATATTTCTTTCCCATTACTGCG 57.623 37.500 0.00 0.00 0.00 5.18
2309 2453 7.826690 TGCAAGAAGGTAACATATTTCTTTCC 58.173 34.615 0.00 0.00 37.68 3.13
2348 2492 0.393537 AAAGCAGAGGGGAATCAGCG 60.394 55.000 0.00 0.00 36.86 5.18
2372 2516 7.061752 AGCAAGTGTTAAGCTAATTCTTACG 57.938 36.000 0.00 0.00 36.73 3.18
2764 2908 3.974642 AGTCCAGGTTTCAACTTAGACCT 59.025 43.478 0.00 0.00 43.06 3.85
2798 2942 3.648009 TCAAACGCAATTTTCCCATCAC 58.352 40.909 0.00 0.00 0.00 3.06
3088 3232 7.147811 GGTTCATTAAGGCCAACATTAATACCA 60.148 37.037 5.01 0.00 33.76 3.25
3637 3784 4.906065 TCATCATTGCAAGACTATTGCC 57.094 40.909 4.94 0.00 44.32 4.52
3707 3854 2.620367 GGGCACAATTCCCACTGTCATA 60.620 50.000 0.00 0.00 43.37 2.15
3729 3876 4.557205 CAAGACACAGTACTGAACCTACC 58.443 47.826 29.30 10.18 0.00 3.18
3730 3877 3.988517 GCAAGACACAGTACTGAACCTAC 59.011 47.826 29.30 12.92 0.00 3.18
3731 3878 3.639561 TGCAAGACACAGTACTGAACCTA 59.360 43.478 29.30 5.00 0.00 3.08
3732 3879 2.434336 TGCAAGACACAGTACTGAACCT 59.566 45.455 29.30 17.51 0.00 3.50
3733 3880 2.833794 TGCAAGACACAGTACTGAACC 58.166 47.619 29.30 15.69 0.00 3.62
3734 3881 4.511454 TCATTGCAAGACACAGTACTGAAC 59.489 41.667 29.30 17.68 0.00 3.18
3735 3882 4.702831 TCATTGCAAGACACAGTACTGAA 58.297 39.130 29.30 10.60 0.00 3.02
3736 3883 4.335400 TCATTGCAAGACACAGTACTGA 57.665 40.909 29.30 3.63 0.00 3.41
3737 3884 4.692155 TCATCATTGCAAGACACAGTACTG 59.308 41.667 21.44 21.44 0.00 2.74
3738 3885 4.898320 TCATCATTGCAAGACACAGTACT 58.102 39.130 4.94 0.00 0.00 2.73
3739 3886 5.808042 ATCATCATTGCAAGACACAGTAC 57.192 39.130 4.94 0.00 0.00 2.73
3740 3887 8.510243 AATAATCATCATTGCAAGACACAGTA 57.490 30.769 4.94 0.00 0.00 2.74
3741 3888 7.400599 AATAATCATCATTGCAAGACACAGT 57.599 32.000 4.94 0.00 0.00 3.55
3742 3889 6.916387 GGAATAATCATCATTGCAAGACACAG 59.084 38.462 4.94 0.00 0.00 3.66
3743 3890 6.377712 TGGAATAATCATCATTGCAAGACACA 59.622 34.615 4.94 0.00 31.75 3.72
3744 3891 6.694411 GTGGAATAATCATCATTGCAAGACAC 59.306 38.462 4.94 0.00 35.80 3.67
3745 3892 6.377712 TGTGGAATAATCATCATTGCAAGACA 59.622 34.615 4.94 0.00 35.80 3.41
3746 3893 6.798482 TGTGGAATAATCATCATTGCAAGAC 58.202 36.000 4.94 0.00 35.80 3.01
3747 3894 6.604396 ACTGTGGAATAATCATCATTGCAAGA 59.396 34.615 4.94 3.10 35.80 3.02
3748 3895 6.802608 ACTGTGGAATAATCATCATTGCAAG 58.197 36.000 4.94 0.00 35.80 4.01
3749 3896 6.778834 ACTGTGGAATAATCATCATTGCAA 57.221 33.333 0.00 0.00 35.80 4.08
3750 3897 6.377712 TGAACTGTGGAATAATCATCATTGCA 59.622 34.615 0.00 0.00 32.16 4.08
3751 3898 6.798482 TGAACTGTGGAATAATCATCATTGC 58.202 36.000 0.00 0.00 0.00 3.56
3752 3899 9.811995 AATTGAACTGTGGAATAATCATCATTG 57.188 29.630 0.00 0.00 0.00 2.82
3763 3910 7.599998 GCAGATACAAAAATTGAACTGTGGAAT 59.400 33.333 0.00 0.00 34.30 3.01
3764 3911 6.922957 GCAGATACAAAAATTGAACTGTGGAA 59.077 34.615 0.00 0.00 34.30 3.53
3765 3912 6.265196 AGCAGATACAAAAATTGAACTGTGGA 59.735 34.615 0.00 0.00 34.30 4.02
3766 3913 6.449698 AGCAGATACAAAAATTGAACTGTGG 58.550 36.000 0.00 0.00 34.30 4.17
3767 3914 7.935338 AAGCAGATACAAAAATTGAACTGTG 57.065 32.000 0.00 0.00 34.30 3.66
3768 3915 8.196771 TGAAAGCAGATACAAAAATTGAACTGT 58.803 29.630 0.00 0.00 34.30 3.55
3769 3916 8.578308 TGAAAGCAGATACAAAAATTGAACTG 57.422 30.769 0.00 0.00 34.60 3.16
3794 3941 9.396022 CCCACTGTCATACTTAACAAAGAATAT 57.604 33.333 0.00 0.00 0.00 1.28
3795 3942 8.598916 TCCCACTGTCATACTTAACAAAGAATA 58.401 33.333 0.00 0.00 0.00 1.75
3796 3943 7.458397 TCCCACTGTCATACTTAACAAAGAAT 58.542 34.615 0.00 0.00 0.00 2.40
3797 3944 6.833041 TCCCACTGTCATACTTAACAAAGAA 58.167 36.000 0.00 0.00 0.00 2.52
3798 3945 6.428083 TCCCACTGTCATACTTAACAAAGA 57.572 37.500 0.00 0.00 0.00 2.52
3799 3946 7.687941 ATTCCCACTGTCATACTTAACAAAG 57.312 36.000 0.00 0.00 0.00 2.77
3800 3947 7.504238 ACAATTCCCACTGTCATACTTAACAAA 59.496 33.333 0.00 0.00 0.00 2.83
3801 3948 7.001674 ACAATTCCCACTGTCATACTTAACAA 58.998 34.615 0.00 0.00 0.00 2.83
3802 3949 6.429692 CACAATTCCCACTGTCATACTTAACA 59.570 38.462 0.00 0.00 0.00 2.41
3803 3950 6.622896 GCACAATTCCCACTGTCATACTTAAC 60.623 42.308 0.00 0.00 0.00 2.01
3804 3951 5.414454 GCACAATTCCCACTGTCATACTTAA 59.586 40.000 0.00 0.00 0.00 1.85
3805 3952 4.941263 GCACAATTCCCACTGTCATACTTA 59.059 41.667 0.00 0.00 0.00 2.24
3806 3953 3.758554 GCACAATTCCCACTGTCATACTT 59.241 43.478 0.00 0.00 0.00 2.24
3807 3954 3.347216 GCACAATTCCCACTGTCATACT 58.653 45.455 0.00 0.00 0.00 2.12
3808 3955 2.423538 GGCACAATTCCCACTGTCATAC 59.576 50.000 0.00 0.00 0.00 2.39
3809 3956 2.620367 GGGCACAATTCCCACTGTCATA 60.620 50.000 0.00 0.00 43.37 2.15
3810 3957 1.549203 GGCACAATTCCCACTGTCAT 58.451 50.000 0.00 0.00 0.00 3.06
3811 3958 0.539438 GGGCACAATTCCCACTGTCA 60.539 55.000 0.00 0.00 43.37 3.58
3812 3959 1.586154 CGGGCACAATTCCCACTGTC 61.586 60.000 1.89 0.00 44.11 3.51
3813 3960 1.603455 CGGGCACAATTCCCACTGT 60.603 57.895 1.89 0.00 44.11 3.55
3814 3961 2.342650 CCGGGCACAATTCCCACTG 61.343 63.158 0.00 0.00 44.11 3.66
3815 3962 1.493854 TACCGGGCACAATTCCCACT 61.494 55.000 6.32 0.00 44.11 4.00
3816 3963 1.001887 TACCGGGCACAATTCCCAC 60.002 57.895 6.32 0.00 44.11 4.61
3817 3964 1.301623 CTACCGGGCACAATTCCCA 59.698 57.895 6.32 0.00 44.11 4.37
3818 3965 1.453197 CCTACCGGGCACAATTCCC 60.453 63.158 6.32 0.00 40.43 3.97
3819 3966 0.323087 AACCTACCGGGCACAATTCC 60.323 55.000 6.32 0.00 39.10 3.01
3820 3967 1.092348 GAACCTACCGGGCACAATTC 58.908 55.000 6.32 0.00 39.10 2.17
3821 3968 0.402504 TGAACCTACCGGGCACAATT 59.597 50.000 6.32 0.00 39.10 2.32
3822 3969 0.035439 CTGAACCTACCGGGCACAAT 60.035 55.000 6.32 0.00 39.10 2.71
3823 3970 1.373435 CTGAACCTACCGGGCACAA 59.627 57.895 6.32 0.00 39.10 3.33
3824 3971 0.542467 TACTGAACCTACCGGGCACA 60.542 55.000 6.32 0.00 39.10 4.57
3825 3972 0.108472 GTACTGAACCTACCGGGCAC 60.108 60.000 6.32 0.00 39.10 5.01
3826 3973 0.251922 AGTACTGAACCTACCGGGCA 60.252 55.000 6.32 0.00 39.10 5.36
3827 3974 0.175073 CAGTACTGAACCTACCGGGC 59.825 60.000 18.45 0.00 39.10 6.13
3828 3975 1.843368 TCAGTACTGAACCTACCGGG 58.157 55.000 23.24 0.00 36.53 5.73
3829 3976 3.446161 TGAATCAGTACTGAACCTACCGG 59.554 47.826 28.43 0.00 43.58 5.28
3830 3977 4.713824 TGAATCAGTACTGAACCTACCG 57.286 45.455 28.43 0.00 43.58 4.02
4101 4251 4.221703 ACTCTCTAACAACAGGGTGATCAG 59.778 45.833 0.00 0.00 0.00 2.90
4207 4482 6.923508 CAGTGTTCAACAGTATCAGACACTAA 59.076 38.462 0.00 0.00 34.65 2.24
4285 4560 3.317993 AGTGAACCAAAACCATACTGCAC 59.682 43.478 0.00 0.00 0.00 4.57
4305 4580 7.175347 TGATCTCAGATTGCTAGTGTTTAGT 57.825 36.000 0.00 0.00 0.00 2.24
4457 4740 4.377841 GCTCTTCACAGTTACAACATCAGC 60.378 45.833 0.00 0.00 0.00 4.26
4459 4742 4.960938 AGCTCTTCACAGTTACAACATCA 58.039 39.130 0.00 0.00 0.00 3.07
4463 4746 6.015027 TCTAGAGCTCTTCACAGTTACAAC 57.985 41.667 23.84 0.00 0.00 3.32
4470 4753 9.677567 GTATTCTTTATCTAGAGCTCTTCACAG 57.322 37.037 23.84 13.35 0.00 3.66
4510 4793 5.645497 GTCAGCTCACAGGTCATAAAGAAAT 59.355 40.000 0.00 0.00 0.00 2.17
4553 4836 3.150767 AGATCTGCGTCCAGTATCCTAC 58.849 50.000 0.00 0.00 40.09 3.18
4569 4852 0.032615 ACGGCTCCAGAGGAAGATCT 60.033 55.000 0.00 0.00 0.00 2.75
4707 4990 2.502577 CCGGGGTATCGTGGGAAC 59.497 66.667 0.00 0.00 0.00 3.62
4797 5082 2.288518 GCGGCCAACACTATTCCAAAAA 60.289 45.455 2.24 0.00 0.00 1.94
4805 5090 4.483243 CCGGGCGGCCAACACTAT 62.483 66.667 29.19 0.00 0.00 2.12
4818 5103 7.654568 TGCGTATATATATCAATCTAACCGGG 58.345 38.462 6.32 0.00 0.00 5.73
4864 5149 0.588252 CAACAAGCCAAGACACGAGG 59.412 55.000 0.00 0.00 0.00 4.63
4891 5176 9.696917 CATAAAACAAGCCTGATACTTCTTTTT 57.303 29.630 0.00 0.00 30.91 1.94
4979 5264 1.683385 GGCATAAGATCCAAACAGGGC 59.317 52.381 0.00 0.00 38.24 5.19
5042 5329 5.420409 AGGTGAGACCGATTTAACATCTTC 58.580 41.667 0.00 0.00 44.90 2.87
5043 5330 5.422214 AGGTGAGACCGATTTAACATCTT 57.578 39.130 0.00 0.00 44.90 2.40
5044 5331 5.420409 GAAGGTGAGACCGATTTAACATCT 58.580 41.667 0.00 0.00 44.90 2.90
5059 5350 1.656652 CTATTGTGGGCGAAGGTGAG 58.343 55.000 0.00 0.00 0.00 3.51
5233 5544 2.029666 CGATGCAGTCCGGATCCC 59.970 66.667 7.81 0.00 39.20 3.85
5254 5565 0.538584 TGCTTGCGTCCTCATCTGAT 59.461 50.000 0.00 0.00 0.00 2.90
5259 5570 0.671781 GTCACTGCTTGCGTCCTCAT 60.672 55.000 0.00 0.00 0.00 2.90
5261 5572 2.375766 CGTCACTGCTTGCGTCCTC 61.376 63.158 0.00 0.00 0.00 3.71
5460 5772 2.527624 TCCTCCAGGCACAGCAGT 60.528 61.111 0.00 0.00 34.44 4.40
5622 5934 3.436325 CCTGCTCCAGAGAAGAGAGGATA 60.436 52.174 4.06 0.00 36.10 2.59
5641 5972 4.151335 CAGATTGTCAAGAACTCGTTCCTG 59.849 45.833 6.20 4.36 40.33 3.86
5653 5984 4.378770 CGTGTGGGATTTCAGATTGTCAAG 60.379 45.833 0.00 0.00 0.00 3.02
5656 5987 2.159517 GCGTGTGGGATTTCAGATTGTC 60.160 50.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.