Multiple sequence alignment - TraesCS1A01G009800

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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 TraesCS1A01G009800 chr1A 100.000 5055 0 0 1 5055 6073023 6067969 0.000000e+00 9335.0
1 TraesCS1A01G009800 chr1A 84.378 1037 104 27 311 1314 16478994 16477983 0.000000e+00 965.0
2 TraesCS1A01G009800 chr1B 95.686 4172 139 17 914 5055 38593105 38588945 0.000000e+00 6669.0
3 TraesCS1A01G009800 chr1B 95.779 687 27 2 183 869 38593804 38593120 0.000000e+00 1107.0
4 TraesCS1A01G009800 chr1B 82.108 911 122 24 4176 5047 17627242 17628150 0.000000e+00 741.0
5 TraesCS1A01G009800 chr1B 92.029 276 15 3 35 310 24704957 24704689 1.030000e-101 381.0
6 TraesCS1A01G009800 chr3A 97.668 2916 58 2 969 3875 93565698 93568612 0.000000e+00 5000.0
7 TraesCS1A01G009800 chr3A 96.386 581 14 1 338 911 93565122 93565702 0.000000e+00 950.0
8 TraesCS1A01G009800 chr3A 85.403 918 94 26 4176 5055 508450 509365 0.000000e+00 917.0
9 TraesCS1A01G009800 chr3A 97.143 175 5 0 3876 4050 93568645 93568819 3.830000e-76 296.0
10 TraesCS1A01G009800 chr3A 85.849 106 13 2 1851 1955 345577706 345577602 1.490000e-20 111.0
11 TraesCS1A01G009800 chr7A 97.531 2916 62 2 969 3875 84693273 84696187 0.000000e+00 4977.0
12 TraesCS1A01G009800 chr7A 96.651 657 13 1 2953 3600 47816943 47817599 0.000000e+00 1083.0
13 TraesCS1A01G009800 chr7A 96.213 581 15 1 338 911 84692697 84693277 0.000000e+00 944.0
14 TraesCS1A01G009800 chr7A 98.561 278 4 0 3598 3875 47819268 47819545 4.550000e-135 492.0
15 TraesCS1A01G009800 chr7A 97.714 175 4 0 3876 4050 47819578 47819752 8.220000e-78 302.0
16 TraesCS1A01G009800 chr7A 96.000 175 7 0 3876 4050 84696220 84696394 8.280000e-73 285.0
17 TraesCS1A01G009800 chr7A 88.889 99 8 3 3479 3574 60726548 60726450 8.890000e-23 119.0
18 TraesCS1A01G009800 chr4A 97.351 1699 35 2 2187 3875 636118429 636116731 0.000000e+00 2880.0
19 TraesCS1A01G009800 chr4A 97.398 1230 26 4 969 2193 636122051 636120823 0.000000e+00 2089.0
20 TraesCS1A01G009800 chr4A 84.282 1037 105 27 311 1314 598523317 598522306 0.000000e+00 959.0
21 TraesCS1A01G009800 chr4A 96.041 581 13 2 339 909 636122629 636122049 0.000000e+00 937.0
22 TraesCS1A01G009800 chr4A 80.989 910 133 24 4176 5047 735073911 735073004 0.000000e+00 686.0
23 TraesCS1A01G009800 chr4A 80.351 911 124 31 4176 5047 712118204 712117310 1.530000e-179 640.0
24 TraesCS1A01G009800 chr4A 97.143 175 5 0 3876 4050 636116698 636116524 3.830000e-76 296.0
25 TraesCS1A01G009800 chr4A 88.889 99 8 3 3479 3574 673443981 673443883 8.890000e-23 119.0
26 TraesCS1A01G009800 chr4A 100.000 37 0 0 1 37 34540602 34540638 9.080000e-08 69.4
27 TraesCS1A01G009800 chr5B 93.883 1455 75 7 52 1496 315245700 315244250 0.000000e+00 2182.0
28 TraesCS1A01G009800 chr5B 82.443 917 112 25 4175 5047 611996040 611995129 0.000000e+00 756.0
29 TraesCS1A01G009800 chr5B 93.116 276 12 3 35 310 641167380 641167648 1.020000e-106 398.0
30 TraesCS1A01G009800 chr7D 85.069 1748 165 38 1938 3624 111372089 111373801 0.000000e+00 1694.0
31 TraesCS1A01G009800 chr7D 85.047 642 67 15 740 1355 29885041 29884403 1.190000e-175 627.0
32 TraesCS1A01G009800 chr7D 89.493 276 27 1 311 586 29885473 29885200 1.040000e-91 348.0
33 TraesCS1A01G009800 chr7D 84.195 329 28 12 3332 3636 111396041 111396369 1.060000e-76 298.0
34 TraesCS1A01G009800 chr7D 88.889 99 8 3 3479 3574 56942229 56942131 8.890000e-23 119.0
35 TraesCS1A01G009800 chr7D 100.000 37 0 0 1 37 553500923 553500887 9.080000e-08 69.4
36 TraesCS1A01G009800 chr3D 85.157 1051 88 30 317 1329 528127682 528126662 0.000000e+00 1014.0
37 TraesCS1A01G009800 chr3D 84.930 1002 92 25 330 1297 553220834 553219858 0.000000e+00 959.0
38 TraesCS1A01G009800 chr3D 89.538 650 59 8 2437 3082 462274460 462273816 0.000000e+00 815.0
39 TraesCS1A01G009800 chr3D 81.928 913 120 27 4178 5047 310717186 310716276 0.000000e+00 730.0
40 TraesCS1A01G009800 chr3D 94.118 51 3 0 2246 2296 462274511 462274461 1.510000e-10 78.7
41 TraesCS1A01G009800 chr2B 89.530 659 59 9 2429 3082 557344745 557345398 0.000000e+00 826.0
42 TraesCS1A01G009800 chr2B 93.478 276 11 3 35 310 178450872 178451140 2.190000e-108 403.0
43 TraesCS1A01G009800 chr2B 100.000 37 0 0 1 37 734794780 734794816 9.080000e-08 69.4
44 TraesCS1A01G009800 chr2B 95.238 42 2 0 2246 2287 557344702 557344743 3.270000e-07 67.6
45 TraesCS1A01G009800 chr3B 89.378 659 59 10 2429 3082 817429020 817429672 0.000000e+00 819.0
46 TraesCS1A01G009800 chr3B 86.982 676 85 3 4373 5047 616188293 616187620 0.000000e+00 758.0
47 TraesCS1A01G009800 chr3B 81.407 199 28 7 4179 4371 545810109 545809914 2.440000e-33 154.0
48 TraesCS1A01G009800 chr2D 87.888 677 80 2 4373 5047 467998985 467999661 0.000000e+00 795.0
49 TraesCS1A01G009800 chr2D 82.217 911 121 19 4176 5047 566710182 566709274 0.000000e+00 747.0
50 TraesCS1A01G009800 chr2D 94.492 236 10 1 65 300 401947279 401947511 1.340000e-95 361.0
51 TraesCS1A01G009800 chr2D 100.000 37 0 0 1 37 548451945 548451909 9.080000e-08 69.4
52 TraesCS1A01G009800 chr1D 81.928 913 120 26 4176 5047 178234420 178235328 0.000000e+00 730.0
53 TraesCS1A01G009800 chr1D 81.659 916 116 39 4177 5046 12305380 12304471 0.000000e+00 713.0
54 TraesCS1A01G009800 chr1D 85.759 639 65 15 740 1355 115569822 115569187 0.000000e+00 652.0
55 TraesCS1A01G009800 chr6D 85.460 674 96 2 4373 5045 10687343 10688015 0.000000e+00 701.0
56 TraesCS1A01G009800 chr6D 85.156 640 66 15 740 1355 454644693 454644059 3.320000e-176 628.0
57 TraesCS1A01G009800 chr6D 89.531 277 26 2 311 586 454645126 454644852 1.040000e-91 348.0
58 TraesCS1A01G009800 chr6D 89.474 95 9 1 1861 1955 86946031 86946124 8.890000e-23 119.0
59 TraesCS1A01G009800 chr5A 84.066 728 109 7 4322 5047 307214446 307213724 0.000000e+00 695.0
60 TraesCS1A01G009800 chr6A 94.928 276 10 2 35 310 60564549 60564820 3.620000e-116 429.0
61 TraesCS1A01G009800 chr2A 94.937 237 11 1 74 310 560736951 560736716 2.220000e-98 370.0
62 TraesCS1A01G009800 chr2A 90.580 276 22 3 35 310 314855121 314855392 3.720000e-96 363.0
63 TraesCS1A01G009800 chr6B 84.444 180 23 5 1170 1345 712293793 712293971 6.730000e-39 172.0
64 TraesCS1A01G009800 chr6B 89.744 78 7 1 1878 1955 164861486 164861562 1.160000e-16 99.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G009800 chr1A 6067969 6073023 5054 True 9335.000000 9335 100.000000 1 5055 1 chr1A.!!$R1 5054
1 TraesCS1A01G009800 chr1A 16477983 16478994 1011 True 965.000000 965 84.378000 311 1314 1 chr1A.!!$R2 1003
2 TraesCS1A01G009800 chr1B 38588945 38593804 4859 True 3888.000000 6669 95.732500 183 5055 2 chr1B.!!$R2 4872
3 TraesCS1A01G009800 chr1B 17627242 17628150 908 False 741.000000 741 82.108000 4176 5047 1 chr1B.!!$F1 871
4 TraesCS1A01G009800 chr3A 93565122 93568819 3697 False 2082.000000 5000 97.065667 338 4050 3 chr3A.!!$F2 3712
5 TraesCS1A01G009800 chr3A 508450 509365 915 False 917.000000 917 85.403000 4176 5055 1 chr3A.!!$F1 879
6 TraesCS1A01G009800 chr7A 84692697 84696394 3697 False 2068.666667 4977 96.581333 338 4050 3 chr7A.!!$F2 3712
7 TraesCS1A01G009800 chr7A 47816943 47819752 2809 False 625.666667 1083 97.642000 2953 4050 3 chr7A.!!$F1 1097
8 TraesCS1A01G009800 chr4A 636116524 636122629 6105 True 1550.500000 2880 96.983250 339 4050 4 chr4A.!!$R5 3711
9 TraesCS1A01G009800 chr4A 598522306 598523317 1011 True 959.000000 959 84.282000 311 1314 1 chr4A.!!$R1 1003
10 TraesCS1A01G009800 chr4A 735073004 735073911 907 True 686.000000 686 80.989000 4176 5047 1 chr4A.!!$R4 871
11 TraesCS1A01G009800 chr4A 712117310 712118204 894 True 640.000000 640 80.351000 4176 5047 1 chr4A.!!$R3 871
12 TraesCS1A01G009800 chr5B 315244250 315245700 1450 True 2182.000000 2182 93.883000 52 1496 1 chr5B.!!$R1 1444
13 TraesCS1A01G009800 chr5B 611995129 611996040 911 True 756.000000 756 82.443000 4175 5047 1 chr5B.!!$R2 872
14 TraesCS1A01G009800 chr7D 111372089 111373801 1712 False 1694.000000 1694 85.069000 1938 3624 1 chr7D.!!$F1 1686
15 TraesCS1A01G009800 chr7D 29884403 29885473 1070 True 487.500000 627 87.270000 311 1355 2 chr7D.!!$R3 1044
16 TraesCS1A01G009800 chr3D 528126662 528127682 1020 True 1014.000000 1014 85.157000 317 1329 1 chr3D.!!$R2 1012
17 TraesCS1A01G009800 chr3D 553219858 553220834 976 True 959.000000 959 84.930000 330 1297 1 chr3D.!!$R3 967
18 TraesCS1A01G009800 chr3D 310716276 310717186 910 True 730.000000 730 81.928000 4178 5047 1 chr3D.!!$R1 869
19 TraesCS1A01G009800 chr3D 462273816 462274511 695 True 446.850000 815 91.828000 2246 3082 2 chr3D.!!$R4 836
20 TraesCS1A01G009800 chr2B 557344702 557345398 696 False 446.800000 826 92.384000 2246 3082 2 chr2B.!!$F3 836
21 TraesCS1A01G009800 chr3B 817429020 817429672 652 False 819.000000 819 89.378000 2429 3082 1 chr3B.!!$F1 653
22 TraesCS1A01G009800 chr3B 616187620 616188293 673 True 758.000000 758 86.982000 4373 5047 1 chr3B.!!$R2 674
23 TraesCS1A01G009800 chr2D 467998985 467999661 676 False 795.000000 795 87.888000 4373 5047 1 chr2D.!!$F2 674
24 TraesCS1A01G009800 chr2D 566709274 566710182 908 True 747.000000 747 82.217000 4176 5047 1 chr2D.!!$R2 871
25 TraesCS1A01G009800 chr1D 178234420 178235328 908 False 730.000000 730 81.928000 4176 5047 1 chr1D.!!$F1 871
26 TraesCS1A01G009800 chr1D 12304471 12305380 909 True 713.000000 713 81.659000 4177 5046 1 chr1D.!!$R1 869
27 TraesCS1A01G009800 chr1D 115569187 115569822 635 True 652.000000 652 85.759000 740 1355 1 chr1D.!!$R2 615
28 TraesCS1A01G009800 chr6D 10687343 10688015 672 False 701.000000 701 85.460000 4373 5045 1 chr6D.!!$F1 672
29 TraesCS1A01G009800 chr6D 454644059 454645126 1067 True 488.000000 628 87.343500 311 1355 2 chr6D.!!$R1 1044
30 TraesCS1A01G009800 chr5A 307213724 307214446 722 True 695.000000 695 84.066000 4322 5047 1 chr5A.!!$R1 725

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
157 158 0.034089 CCACCCTTCTCCCCATTGTC 60.034 60.0 0.00 0.0 0.00 3.18 F
1020 1172 0.397564 TGAGCACACTGGAGCAATCA 59.602 50.0 0.00 0.0 32.55 2.57 F
1925 2125 2.104572 GAGGTGGACAGTGCTCAGCA 62.105 60.0 0.00 0.0 35.60 4.41 F
2449 5075 0.601046 ATCGTGGATGCGCCTATGTG 60.601 55.0 4.18 0.0 37.63 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1153 1305 1.271652 TGCATTTAGTCGGCTTTCCCA 60.272 47.619 0.00 0.00 0.00 4.37 R
2435 5061 0.179073 ACAGTCACATAGGCGCATCC 60.179 55.000 10.83 0.00 0.00 3.51 R
2888 5517 1.383523 GCAGGTCCTTGCTCCAATAC 58.616 55.000 0.00 0.00 40.89 1.89 R
4147 8516 1.138859 CCTATGCTGGGACGTCAATCA 59.861 52.381 18.91 11.17 0.00 2.57 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
23 24 5.541845 TGATAGATATTTCACTGGGAAGCG 58.458 41.667 0.00 0.00 36.72 4.68
24 25 5.304357 TGATAGATATTTCACTGGGAAGCGA 59.696 40.000 0.00 0.00 36.72 4.93
25 26 4.487714 AGATATTTCACTGGGAAGCGAA 57.512 40.909 0.00 0.00 36.72 4.70
26 27 4.192317 AGATATTTCACTGGGAAGCGAAC 58.808 43.478 0.00 0.00 36.72 3.95
27 28 2.568623 ATTTCACTGGGAAGCGAACT 57.431 45.000 0.00 0.00 36.72 3.01
28 29 1.878953 TTTCACTGGGAAGCGAACTC 58.121 50.000 0.00 0.00 36.72 3.01
29 30 0.756294 TTCACTGGGAAGCGAACTCA 59.244 50.000 0.00 0.00 0.00 3.41
30 31 0.318441 TCACTGGGAAGCGAACTCAG 59.682 55.000 6.25 6.25 41.14 3.35
31 32 0.671781 CACTGGGAAGCGAACTCAGG 60.672 60.000 11.14 0.00 39.84 3.86
32 33 0.832135 ACTGGGAAGCGAACTCAGGA 60.832 55.000 11.14 0.00 39.84 3.86
33 34 0.321671 CTGGGAAGCGAACTCAGGAA 59.678 55.000 0.00 0.00 32.80 3.36
34 35 0.321671 TGGGAAGCGAACTCAGGAAG 59.678 55.000 0.00 0.00 0.00 3.46
35 36 0.608640 GGGAAGCGAACTCAGGAAGA 59.391 55.000 0.00 0.00 0.00 2.87
36 37 1.673329 GGGAAGCGAACTCAGGAAGAC 60.673 57.143 0.00 0.00 0.00 3.01
37 38 1.673329 GGAAGCGAACTCAGGAAGACC 60.673 57.143 0.00 0.00 0.00 3.85
38 39 0.038159 AAGCGAACTCAGGAAGACCG 60.038 55.000 0.00 0.00 41.83 4.79
39 40 2.095252 GCGAACTCAGGAAGACCGC 61.095 63.158 0.00 0.00 41.83 5.68
40 41 1.587054 CGAACTCAGGAAGACCGCT 59.413 57.895 0.00 0.00 41.83 5.52
41 42 0.456995 CGAACTCAGGAAGACCGCTC 60.457 60.000 0.00 0.00 41.83 5.03
42 43 0.892063 GAACTCAGGAAGACCGCTCT 59.108 55.000 0.00 0.00 41.83 4.09
43 44 2.093106 GAACTCAGGAAGACCGCTCTA 58.907 52.381 0.00 0.00 41.83 2.43
44 45 2.445682 ACTCAGGAAGACCGCTCTAT 57.554 50.000 0.00 0.00 41.83 1.98
45 46 2.741145 ACTCAGGAAGACCGCTCTATT 58.259 47.619 0.00 0.00 41.83 1.73
46 47 2.691011 ACTCAGGAAGACCGCTCTATTC 59.309 50.000 0.00 0.00 41.83 1.75
47 48 2.032620 TCAGGAAGACCGCTCTATTCC 58.967 52.381 0.00 0.00 41.29 3.01
48 49 1.069358 CAGGAAGACCGCTCTATTCCC 59.931 57.143 0.00 0.00 41.81 3.97
49 50 0.393448 GGAAGACCGCTCTATTCCCC 59.607 60.000 0.00 0.00 36.08 4.81
50 51 1.415200 GAAGACCGCTCTATTCCCCT 58.585 55.000 0.00 0.00 0.00 4.79
51 52 1.341852 GAAGACCGCTCTATTCCCCTC 59.658 57.143 0.00 0.00 0.00 4.30
52 53 0.558712 AGACCGCTCTATTCCCCTCT 59.441 55.000 0.00 0.00 0.00 3.69
53 54 0.963225 GACCGCTCTATTCCCCTCTC 59.037 60.000 0.00 0.00 0.00 3.20
54 55 0.470268 ACCGCTCTATTCCCCTCTCC 60.470 60.000 0.00 0.00 0.00 3.71
55 56 0.178947 CCGCTCTATTCCCCTCTCCT 60.179 60.000 0.00 0.00 0.00 3.69
56 57 1.253100 CGCTCTATTCCCCTCTCCTC 58.747 60.000 0.00 0.00 0.00 3.71
57 58 1.639722 GCTCTATTCCCCTCTCCTCC 58.360 60.000 0.00 0.00 0.00 4.30
58 59 1.829666 GCTCTATTCCCCTCTCCTCCC 60.830 61.905 0.00 0.00 0.00 4.30
59 60 0.483328 TCTATTCCCCTCTCCTCCCG 59.517 60.000 0.00 0.00 0.00 5.14
82 83 4.496336 GCGCTGCCCCCATCTCTT 62.496 66.667 0.00 0.00 0.00 2.85
88 89 2.381941 GCCCCCATCTCTTGCTCCT 61.382 63.158 0.00 0.00 0.00 3.69
94 95 2.790791 ATCTCTTGCTCCTCCGCCG 61.791 63.158 0.00 0.00 0.00 6.46
157 158 0.034089 CCACCCTTCTCCCCATTGTC 60.034 60.000 0.00 0.00 0.00 3.18
176 177 1.790387 GGATCCGCTTGCATATCGC 59.210 57.895 0.00 0.00 42.89 4.58
403 406 2.152016 GGTAAGCTCTTTTTGTCCGCT 58.848 47.619 0.00 0.00 0.00 5.52
799 935 6.309737 GGTAGTTAGATGTCGTAAGGTGTTTG 59.690 42.308 0.00 0.00 38.47 2.93
1020 1172 0.397564 TGAGCACACTGGAGCAATCA 59.602 50.000 0.00 0.00 32.55 2.57
1069 1221 7.360575 ACGAATAGTGTGATTAAACCAGAAC 57.639 36.000 0.00 0.00 0.00 3.01
1088 1240 6.204882 CCAGAACTAGGAACAAGTTTCGATTT 59.795 38.462 0.00 0.00 37.31 2.17
1153 1305 8.101419 GGGAAGTTGGATTCGGTATTAGATATT 58.899 37.037 0.00 0.00 0.00 1.28
1614 1814 3.932289 GGACCACGACTGTCAACG 58.068 61.111 8.73 0.00 34.36 4.10
1640 1840 4.389077 GTCACCGTATTCTTTGAGGAACAG 59.611 45.833 0.00 0.00 0.00 3.16
1654 1854 3.490348 AGGAACAGAAACAATCCAGGTG 58.510 45.455 0.00 0.00 34.30 4.00
1925 2125 2.104572 GAGGTGGACAGTGCTCAGCA 62.105 60.000 0.00 0.00 35.60 4.41
2430 5056 6.409234 CCTGTGGGTTTATCTATGCTCCTTTA 60.409 42.308 0.00 0.00 0.00 1.85
2435 5061 6.369065 GGGTTTATCTATGCTCCTTTATCGTG 59.631 42.308 0.00 0.00 0.00 4.35
2449 5075 0.601046 ATCGTGGATGCGCCTATGTG 60.601 55.000 4.18 0.00 37.63 3.21
2674 5302 9.886132 ACGTACTAAATTATTGTTGAGGATCTT 57.114 29.630 0.00 0.00 34.92 2.40
2707 5336 2.711542 CAGTTGAAGATTACGCCCCTT 58.288 47.619 0.00 0.00 0.00 3.95
2795 5424 0.733729 TTCCGTTTGTTTGGTGGACG 59.266 50.000 0.00 0.00 0.00 4.79
2963 5592 6.428295 TGGTAAAATAGGGGTGGAAAGTATG 58.572 40.000 0.00 0.00 0.00 2.39
3185 5818 3.375299 GCCATGCTAGGTTTCTTAGTGTG 59.625 47.826 0.00 0.00 0.00 3.82
3389 6022 2.353704 CCGCATGAAACCAGAGTGAGTA 60.354 50.000 0.00 0.00 0.00 2.59
3450 6112 1.804601 GTTTCGTCGTTCCATCCCTT 58.195 50.000 0.00 0.00 0.00 3.95
3603 7938 4.019321 AGCTAATTCAGAGGTTAGGCAACA 60.019 41.667 0.00 0.00 36.29 3.33
3649 7984 2.621998 AGCCACATTAGCAAGCATCATC 59.378 45.455 0.00 0.00 0.00 2.92
3821 8156 5.183140 GGCATAATGTTAGGTGTCTGTTTGT 59.817 40.000 0.00 0.00 0.00 2.83
3896 8265 8.582657 TTCTCTAAGCTACATGAGTTACTCTT 57.417 34.615 13.86 4.38 0.00 2.85
3897 8266 8.582657 TCTCTAAGCTACATGAGTTACTCTTT 57.417 34.615 13.86 0.00 0.00 2.52
3937 8306 4.202121 GGCAGTGTGCTACTTGCTATACTA 60.202 45.833 0.00 0.00 44.28 1.82
3960 8329 9.952030 ACTAGCTAAGCTTAATTTTCTTCTTCT 57.048 29.630 7.74 0.00 40.44 2.85
4106 8475 4.836825 TCATCCTGAAACCTGAATCTCAC 58.163 43.478 0.00 0.00 0.00 3.51
4111 8480 5.013495 TCCTGAAACCTGAATCTCACAGATT 59.987 40.000 0.00 0.00 46.84 2.40
4147 8516 6.790319 AGACAATTAGGGTTAATTCCACACT 58.210 36.000 0.00 0.00 37.38 3.55
4150 8519 7.182060 ACAATTAGGGTTAATTCCACACTGAT 58.818 34.615 3.21 0.00 37.38 2.90
4151 8520 7.673926 ACAATTAGGGTTAATTCCACACTGATT 59.326 33.333 3.21 4.09 37.38 2.57
4242 8614 2.365105 CCCCCAGCGTCTTCCCTA 60.365 66.667 0.00 0.00 0.00 3.53
4253 8625 2.091665 CGTCTTCCCTACCCTAACCCTA 60.092 54.545 0.00 0.00 0.00 3.53
4256 8628 3.604312 TCTTCCCTACCCTAACCCTACTT 59.396 47.826 0.00 0.00 0.00 2.24
4259 8631 2.022722 CCCTACCCTAACCCTACTTCCA 60.023 54.545 0.00 0.00 0.00 3.53
4967 9397 2.975536 CGCCACCGTTCCTTCCTA 59.024 61.111 0.00 0.00 0.00 2.94
4996 9426 3.038428 GGTATTCCCCTTCCCCACT 57.962 57.895 0.00 0.00 0.00 4.00
5009 9439 3.524606 CCACTCCCGTCCGCGTAT 61.525 66.667 4.92 0.00 36.15 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.304357 TCGCTTCCCAGTGAAATATCTATCA 59.696 40.000 0.00 0.00 36.56 2.15
2 3 5.808366 TCGCTTCCCAGTGAAATATCTAT 57.192 39.130 0.00 0.00 36.56 1.98
3 4 5.607939 TTCGCTTCCCAGTGAAATATCTA 57.392 39.130 0.00 0.00 44.85 1.98
4 5 4.487714 TTCGCTTCCCAGTGAAATATCT 57.512 40.909 0.00 0.00 44.85 1.98
10 11 0.756294 TGAGTTCGCTTCCCAGTGAA 59.244 50.000 0.00 0.00 45.48 3.18
11 12 0.318441 CTGAGTTCGCTTCCCAGTGA 59.682 55.000 0.00 0.00 37.79 3.41
12 13 0.671781 CCTGAGTTCGCTTCCCAGTG 60.672 60.000 0.00 0.00 0.00 3.66
13 14 0.832135 TCCTGAGTTCGCTTCCCAGT 60.832 55.000 0.00 0.00 0.00 4.00
14 15 0.321671 TTCCTGAGTTCGCTTCCCAG 59.678 55.000 0.00 0.00 0.00 4.45
15 16 0.321671 CTTCCTGAGTTCGCTTCCCA 59.678 55.000 0.00 0.00 0.00 4.37
16 17 0.608640 TCTTCCTGAGTTCGCTTCCC 59.391 55.000 0.00 0.00 0.00 3.97
17 18 1.673329 GGTCTTCCTGAGTTCGCTTCC 60.673 57.143 0.00 0.00 0.00 3.46
18 19 1.715993 GGTCTTCCTGAGTTCGCTTC 58.284 55.000 0.00 0.00 0.00 3.86
19 20 0.038159 CGGTCTTCCTGAGTTCGCTT 60.038 55.000 0.00 0.00 0.00 4.68
20 21 1.587054 CGGTCTTCCTGAGTTCGCT 59.413 57.895 0.00 0.00 0.00 4.93
21 22 2.095252 GCGGTCTTCCTGAGTTCGC 61.095 63.158 0.00 0.00 39.23 4.70
22 23 0.456995 GAGCGGTCTTCCTGAGTTCG 60.457 60.000 7.51 0.00 0.00 3.95
23 24 0.892063 AGAGCGGTCTTCCTGAGTTC 59.108 55.000 12.24 0.00 0.00 3.01
24 25 2.217510 TAGAGCGGTCTTCCTGAGTT 57.782 50.000 23.90 0.00 33.84 3.01
25 26 2.445682 ATAGAGCGGTCTTCCTGAGT 57.554 50.000 23.90 0.00 33.84 3.41
26 27 2.035321 GGAATAGAGCGGTCTTCCTGAG 59.965 54.545 23.90 0.00 33.84 3.35
27 28 2.032620 GGAATAGAGCGGTCTTCCTGA 58.967 52.381 23.90 4.22 33.84 3.86
28 29 1.069358 GGGAATAGAGCGGTCTTCCTG 59.931 57.143 26.43 0.00 32.20 3.86
29 30 1.415200 GGGAATAGAGCGGTCTTCCT 58.585 55.000 26.43 12.38 32.20 3.36
30 31 0.393448 GGGGAATAGAGCGGTCTTCC 59.607 60.000 23.90 22.72 33.84 3.46
31 32 1.341852 GAGGGGAATAGAGCGGTCTTC 59.658 57.143 23.90 14.85 33.84 2.87
32 33 1.062810 AGAGGGGAATAGAGCGGTCTT 60.063 52.381 23.90 5.31 33.84 3.01
33 34 0.558712 AGAGGGGAATAGAGCGGTCT 59.441 55.000 22.31 22.31 36.75 3.85
34 35 0.963225 GAGAGGGGAATAGAGCGGTC 59.037 60.000 6.48 6.48 0.00 4.79
35 36 0.470268 GGAGAGGGGAATAGAGCGGT 60.470 60.000 0.00 0.00 0.00 5.68
36 37 0.178947 AGGAGAGGGGAATAGAGCGG 60.179 60.000 0.00 0.00 0.00 5.52
37 38 1.253100 GAGGAGAGGGGAATAGAGCG 58.747 60.000 0.00 0.00 0.00 5.03
38 39 1.639722 GGAGGAGAGGGGAATAGAGC 58.360 60.000 0.00 0.00 0.00 4.09
39 40 1.549037 CGGGAGGAGAGGGGAATAGAG 60.549 61.905 0.00 0.00 0.00 2.43
40 41 0.483328 CGGGAGGAGAGGGGAATAGA 59.517 60.000 0.00 0.00 0.00 1.98
41 42 0.483328 TCGGGAGGAGAGGGGAATAG 59.517 60.000 0.00 0.00 0.00 1.73
42 43 1.167943 ATCGGGAGGAGAGGGGAATA 58.832 55.000 0.00 0.00 0.00 1.75
43 44 0.472734 CATCGGGAGGAGAGGGGAAT 60.473 60.000 0.00 0.00 0.00 3.01
44 45 1.075226 CATCGGGAGGAGAGGGGAA 60.075 63.158 0.00 0.00 0.00 3.97
45 46 2.609339 CATCGGGAGGAGAGGGGA 59.391 66.667 0.00 0.00 0.00 4.81
46 47 3.237741 GCATCGGGAGGAGAGGGG 61.238 72.222 0.00 0.00 0.00 4.79
47 48 3.610669 CGCATCGGGAGGAGAGGG 61.611 72.222 0.00 0.00 0.00 4.30
48 49 3.610669 CCGCATCGGGAGGAGAGG 61.611 72.222 0.00 0.00 44.15 3.69
157 158 1.959899 GCGATATGCAAGCGGATCCG 61.960 60.000 30.03 30.03 45.45 4.18
176 177 2.046700 TTCGCCGCCTAACCTTGG 60.047 61.111 0.00 0.00 0.00 3.61
327 328 1.410850 CCTCCATCCTACCATGCCGT 61.411 60.000 0.00 0.00 0.00 5.68
403 406 6.071051 GGTTTGTAAAAATCAATAGAGGGGCA 60.071 38.462 0.00 0.00 0.00 5.36
602 728 0.107654 CTCACCTTTCCGTCCATCCC 60.108 60.000 0.00 0.00 0.00 3.85
612 741 0.733223 GACGAGACGGCTCACCTTTC 60.733 60.000 20.47 2.03 41.36 2.62
799 935 6.743172 GCAACGTTTCTCTTATCTGAAATTCC 59.257 38.462 0.00 0.00 35.13 3.01
1020 1172 3.713826 TCCTCGGCAAACTTCCTTATT 57.286 42.857 0.00 0.00 0.00 1.40
1069 1221 6.142817 CCAACAAATCGAAACTTGTTCCTAG 58.857 40.000 16.35 8.78 42.41 3.02
1088 1240 2.125310 CGTATGCCTCGCCCAACA 60.125 61.111 0.00 0.00 0.00 3.33
1153 1305 1.271652 TGCATTTAGTCGGCTTTCCCA 60.272 47.619 0.00 0.00 0.00 4.37
1614 1814 2.629051 CTCAAAGAATACGGTGACCCC 58.371 52.381 0.00 0.00 0.00 4.95
1640 1840 3.319755 CAATGCACACCTGGATTGTTTC 58.680 45.455 0.00 0.00 46.14 2.78
1654 1854 7.412137 AAATTCAGAAAAGTTAGCAATGCAC 57.588 32.000 8.35 0.00 0.00 4.57
1925 2125 7.607607 TGAAACTAATACTCAATGTGACTGCAT 59.392 33.333 0.00 0.00 0.00 3.96
2149 2372 6.126940 TGTTGGGAAGGAAATCAAATCAAACA 60.127 34.615 0.00 0.00 0.00 2.83
2430 5056 0.601046 CACATAGGCGCATCCACGAT 60.601 55.000 10.83 0.00 37.29 3.73
2435 5061 0.179073 ACAGTCACATAGGCGCATCC 60.179 55.000 10.83 0.00 0.00 3.51
2449 5075 8.950208 AGCAGAGGAACTAAATAATTACAGTC 57.050 34.615 0.00 0.00 41.55 3.51
2471 5097 3.921104 ACCTGAGATCATCCTAGAAGCA 58.079 45.455 0.00 0.00 0.00 3.91
2674 5302 9.109393 GTAATCTTCAACTGCAATGATTACCTA 57.891 33.333 16.63 0.00 39.50 3.08
2707 5336 9.577110 GCAAGTTTGAAAATGAGAATGATGATA 57.423 29.630 0.00 0.00 0.00 2.15
2888 5517 1.383523 GCAGGTCCTTGCTCCAATAC 58.616 55.000 0.00 0.00 40.89 1.89
2963 5592 3.846360 CCACGGCTAACATACCTATAGC 58.154 50.000 0.00 0.00 40.98 2.97
3167 5800 5.677319 ATAGCACACTAAGAAACCTAGCA 57.323 39.130 0.00 0.00 30.45 3.49
3185 5818 4.462483 TCAGGGTCAAACATTCCAAATAGC 59.538 41.667 0.00 0.00 0.00 2.97
3389 6022 5.593909 TGATCAAATGCCCGTCTTTCATTAT 59.406 36.000 0.00 0.00 30.98 1.28
3450 6112 1.975680 GTGGGTAAGGTCAGTTCAGGA 59.024 52.381 0.00 0.00 0.00 3.86
3649 7984 8.931385 AAGCCAGCAAACATTTAGTTATATTG 57.069 30.769 0.00 0.00 40.26 1.90
3821 8156 7.243604 AGACCAATTATTTTCAGCAATTCCA 57.756 32.000 0.00 0.00 0.00 3.53
3909 8278 1.927174 CAAGTAGCACACTGCCGATAC 59.073 52.381 0.00 0.00 46.52 2.24
3937 8306 9.072375 ACAAGAAGAAGAAAATTAAGCTTAGCT 57.928 29.630 0.00 0.00 42.56 3.32
3960 8329 9.500785 TCATTTCACTTATCTACATGTTCACAA 57.499 29.630 2.30 0.00 0.00 3.33
4111 8480 7.451731 ACCCTAATTGTCTATCAATGAAGGA 57.548 36.000 16.73 0.00 44.61 3.36
4147 8516 1.138859 CCTATGCTGGGACGTCAATCA 59.861 52.381 18.91 11.17 0.00 2.57
4150 8519 1.220749 GCCTATGCTGGGACGTCAA 59.779 57.895 18.91 3.79 33.53 3.18
4151 8520 2.900273 GCCTATGCTGGGACGTCA 59.100 61.111 18.91 0.00 33.53 4.35
4242 8614 1.898542 CGGTGGAAGTAGGGTTAGGGT 60.899 57.143 0.00 0.00 0.00 4.34
4545 8965 3.764466 AGAAGCCGCACCTCCTCG 61.764 66.667 0.00 0.00 0.00 4.63
4744 9170 4.883354 GGGAGCAGCCGGGAATGG 62.883 72.222 2.18 0.00 37.63 3.16
4967 9397 3.821306 GGAATACCCGATGCCCTTT 57.179 52.632 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.