Multiple sequence alignment - TraesCS4A01G327700

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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 TraesCS4A01G327700 chr4A 100.000 4199 0 0 1 4199 613999876 613995678 0.000000e+00 7755.0
1 TraesCS4A01G327700 chr4A 96.243 3487 96 9 1 3456 519797069 519800551 0.000000e+00 5681.0
2 TraesCS4A01G327700 chr4A 95.481 686 23 6 3218 3897 519800453 519801136 0.000000e+00 1088.0
3 TraesCS4A01G327700 chr2B 96.234 3930 96 17 1 3897 527661434 527665344 0.000000e+00 6390.0
4 TraesCS4A01G327700 chr2B 76.528 916 163 34 28 905 493399396 493398495 1.780000e-123 453.0
5 TraesCS4A01G327700 chr2A 96.741 2946 77 6 527 3456 717806061 717809003 0.000000e+00 4891.0
6 TraesCS4A01G327700 chr2A 98.177 1481 22 5 2419 3897 181790140 181788663 0.000000e+00 2580.0
7 TraesCS4A01G327700 chr2A 94.953 634 26 4 3269 3897 717809275 717809907 0.000000e+00 989.0
8 TraesCS4A01G327700 chr2A 94.460 361 14 4 3218 3573 717808905 717809264 6.140000e-153 551.0
9 TraesCS4A01G327700 chr5A 90.349 2984 238 26 13 2968 556697897 556700858 0.000000e+00 3869.0
10 TraesCS4A01G327700 chr5A 90.221 2986 239 30 13 2968 709482184 709479222 0.000000e+00 3847.0
11 TraesCS4A01G327700 chr5A 90.080 2984 245 27 13 2968 465388459 465391419 0.000000e+00 3823.0
12 TraesCS4A01G327700 chr5A 90.614 2866 219 25 13 2851 556702812 556705654 0.000000e+00 3757.0
13 TraesCS4A01G327700 chr5A 89.461 408 34 3 9 407 553373679 553373272 1.350000e-139 507.0
14 TraesCS4A01G327700 chr5A 78.752 753 86 35 2871 3578 553373274 553372551 1.790000e-118 436.0
15 TraesCS4A01G327700 chr7A 90.349 2984 235 33 13 2968 60710799 60707841 0.000000e+00 3866.0
16 TraesCS4A01G327700 chr7A 90.248 2984 240 27 13 2968 689399054 689396094 0.000000e+00 3851.0
17 TraesCS4A01G327700 chr3A 97.400 2269 43 5 1513 3767 57503927 57501661 0.000000e+00 3849.0
18 TraesCS4A01G327700 chr3A 97.828 1519 31 2 1 1518 57513945 57512428 0.000000e+00 2621.0
19 TraesCS4A01G327700 chr3A 88.208 1730 165 26 9 1719 110461830 110460121 0.000000e+00 2028.0
20 TraesCS4A01G327700 chr3A 79.797 2752 468 65 25 2736 144697908 144700611 0.000000e+00 1921.0
21 TraesCS4A01G327700 chr3D 88.344 2977 278 36 13 2968 611423409 611426337 0.000000e+00 3511.0
22 TraesCS4A01G327700 chr3D 88.791 2373 214 25 13 2361 611435520 611437864 0.000000e+00 2861.0
23 TraesCS4A01G327700 chr1B 95.992 2071 74 6 806 2875 112757390 112755328 0.000000e+00 3356.0
24 TraesCS4A01G327700 chr1B 94.325 793 27 8 2607 3383 25833650 25834440 0.000000e+00 1199.0
25 TraesCS4A01G327700 chr1B 94.413 698 27 10 3218 3905 112754672 112753977 0.000000e+00 1062.0
26 TraesCS4A01G327700 chr1B 95.439 570 10 5 2903 3456 112755070 112754501 0.000000e+00 894.0
27 TraesCS4A01G327700 chr1B 91.086 617 43 6 3287 3897 25834270 25834880 0.000000e+00 824.0
28 TraesCS4A01G327700 chr1B 98.131 214 4 0 1 214 112757603 112757390 1.430000e-99 374.0
29 TraesCS4A01G327700 chr6A 88.141 1678 168 14 13 1666 316458853 316460523 0.000000e+00 1967.0
30 TraesCS4A01G327700 chr5B 88.073 1157 111 12 13 1144 320401357 320402511 0.000000e+00 1347.0
31 TraesCS4A01G327700 chr5B 88.725 408 37 3 9 407 532863573 532863166 1.360000e-134 490.0
32 TraesCS4A01G327700 chr1A 94.451 793 26 11 2607 3383 19985874 19986664 0.000000e+00 1205.0
33 TraesCS4A01G327700 chr1A 90.113 617 48 7 3287 3897 19986495 19987104 0.000000e+00 789.0
34 TraesCS4A01G327700 chr1A 91.150 452 34 5 3449 3897 19973961 19974409 3.590000e-170 608.0
35 TraesCS4A01G327700 chr7D 91.277 791 46 10 2556 3327 476751797 476752583 0.000000e+00 1057.0
36 TraesCS4A01G327700 chr4B 87.417 906 87 12 13 894 16676663 16677565 0.000000e+00 1016.0
37 TraesCS4A01G327700 chr5D 89.706 408 33 3 9 407 438355857 438355450 2.900000e-141 512.0
38 TraesCS4A01G327700 chr5D 79.017 753 84 36 2871 3578 438355452 438354729 8.280000e-122 448.0
39 TraesCS4A01G327700 chr7B 92.157 51 3 1 3941 3991 92906588 92906539 2.090000e-08 71.3
40 TraesCS4A01G327700 chr6B 97.143 35 1 0 3943 3977 127312308 127312274 4.530000e-05 60.2


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 TraesCS4A01G327700 chr4A 613995678 613999876 4198 True 7755.000000 7755 100.000000 1 4199 1 chr4A.!!$R1 4198
1 TraesCS4A01G327700 chr4A 519797069 519801136 4067 False 3384.500000 5681 95.862000 1 3897 2 chr4A.!!$F1 3896
2 TraesCS4A01G327700 chr2B 527661434 527665344 3910 False 6390.000000 6390 96.234000 1 3897 1 chr2B.!!$F1 3896
3 TraesCS4A01G327700 chr2B 493398495 493399396 901 True 453.000000 453 76.528000 28 905 1 chr2B.!!$R1 877
4 TraesCS4A01G327700 chr2A 181788663 181790140 1477 True 2580.000000 2580 98.177000 2419 3897 1 chr2A.!!$R1 1478
5 TraesCS4A01G327700 chr2A 717806061 717809907 3846 False 2143.666667 4891 95.384667 527 3897 3 chr2A.!!$F1 3370
6 TraesCS4A01G327700 chr5A 709479222 709482184 2962 True 3847.000000 3847 90.221000 13 2968 1 chr5A.!!$R1 2955
7 TraesCS4A01G327700 chr5A 465388459 465391419 2960 False 3823.000000 3823 90.080000 13 2968 1 chr5A.!!$F1 2955
8 TraesCS4A01G327700 chr5A 556697897 556705654 7757 False 3813.000000 3869 90.481500 13 2968 2 chr5A.!!$F2 2955
9 TraesCS4A01G327700 chr5A 553372551 553373679 1128 True 471.500000 507 84.106500 9 3578 2 chr5A.!!$R2 3569
10 TraesCS4A01G327700 chr7A 60707841 60710799 2958 True 3866.000000 3866 90.349000 13 2968 1 chr7A.!!$R1 2955
11 TraesCS4A01G327700 chr7A 689396094 689399054 2960 True 3851.000000 3851 90.248000 13 2968 1 chr7A.!!$R2 2955
12 TraesCS4A01G327700 chr3A 57501661 57503927 2266 True 3849.000000 3849 97.400000 1513 3767 1 chr3A.!!$R1 2254
13 TraesCS4A01G327700 chr3A 57512428 57513945 1517 True 2621.000000 2621 97.828000 1 1518 1 chr3A.!!$R2 1517
14 TraesCS4A01G327700 chr3A 110460121 110461830 1709 True 2028.000000 2028 88.208000 9 1719 1 chr3A.!!$R3 1710
15 TraesCS4A01G327700 chr3A 144697908 144700611 2703 False 1921.000000 1921 79.797000 25 2736 1 chr3A.!!$F1 2711
16 TraesCS4A01G327700 chr3D 611423409 611426337 2928 False 3511.000000 3511 88.344000 13 2968 1 chr3D.!!$F1 2955
17 TraesCS4A01G327700 chr3D 611435520 611437864 2344 False 2861.000000 2861 88.791000 13 2361 1 chr3D.!!$F2 2348
18 TraesCS4A01G327700 chr1B 112753977 112757603 3626 True 1421.500000 3356 95.993750 1 3905 4 chr1B.!!$R1 3904
19 TraesCS4A01G327700 chr1B 25833650 25834880 1230 False 1011.500000 1199 92.705500 2607 3897 2 chr1B.!!$F1 1290
20 TraesCS4A01G327700 chr6A 316458853 316460523 1670 False 1967.000000 1967 88.141000 13 1666 1 chr6A.!!$F1 1653
21 TraesCS4A01G327700 chr5B 320401357 320402511 1154 False 1347.000000 1347 88.073000 13 1144 1 chr5B.!!$F1 1131
22 TraesCS4A01G327700 chr1A 19985874 19987104 1230 False 997.000000 1205 92.282000 2607 3897 2 chr1A.!!$F2 1290
23 TraesCS4A01G327700 chr7D 476751797 476752583 786 False 1057.000000 1057 91.277000 2556 3327 1 chr7D.!!$F1 771
24 TraesCS4A01G327700 chr4B 16676663 16677565 902 False 1016.000000 1016 87.417000 13 894 1 chr4B.!!$F1 881
25 TraesCS4A01G327700 chr5D 438354729 438355857 1128 True 480.000000 512 84.361500 9 3578 2 chr5D.!!$R1 3569

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
740 818 6.428465 TCAGCATGCAATCAAACATGAATTTT 59.572 30.769 21.98 0.0 45.23 1.82 F
1322 1411 3.784338 TCTTTGCTTTGAAACCTTGCAG 58.216 40.909 0.00 0.0 35.02 4.41 F
2009 2105 4.160252 GCCCCACATAATGAACAAGTTGAT 59.840 41.667 10.54 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2238 0.476771 AAGGAAGGCCGGAAACTTGA 59.523 50.000 5.05 0.0 39.96 3.02 R
2367 2463 1.656652 CACAACCCTTATGCCTCTCG 58.343 55.000 0.00 0.0 0.00 4.04 R
3908 4965 3.057526 GTGTGCCAACAATAAGGAACTCC 60.058 47.826 0.00 0.0 35.90 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
340 347 7.232910 TGATTATTGCATATTGTGATCCCTCA 58.767 34.615 0.00 0.00 0.00 3.86
740 818 6.428465 TCAGCATGCAATCAAACATGAATTTT 59.572 30.769 21.98 0.00 45.23 1.82
960 1047 7.030768 TCTCTTTTTAAGGTGAACAAAAACCG 58.969 34.615 0.00 0.00 41.61 4.44
1201 1289 4.866486 GGGATAGCAGCTTTGACAATTTTG 59.134 41.667 0.00 0.00 0.00 2.44
1205 1293 7.975616 GGATAGCAGCTTTGACAATTTTGATAA 59.024 33.333 0.00 0.00 0.00 1.75
1322 1411 3.784338 TCTTTGCTTTGAAACCTTGCAG 58.216 40.909 0.00 0.00 35.02 4.41
1654 1743 8.735315 TGTCAAACTTCAAGAAAAAGTATCACA 58.265 29.630 0.00 0.00 35.96 3.58
1655 1744 9.736023 GTCAAACTTCAAGAAAAAGTATCACAT 57.264 29.630 0.00 0.00 35.96 3.21
1845 1940 5.280113 GGTGGACTATGTAACCAACAACCTA 60.280 44.000 0.00 0.00 42.70 3.08
1920 2016 4.662278 ACTTAATGGACAAGCTTAGGCAA 58.338 39.130 0.00 0.00 41.70 4.52
2001 2097 9.606631 TTATTAATTTTGCCCCACATAATGAAC 57.393 29.630 0.00 0.00 31.28 3.18
2009 2105 4.160252 GCCCCACATAATGAACAAGTTGAT 59.840 41.667 10.54 0.00 0.00 2.57
2142 2238 6.318648 ACAACACATGTTCTTGTAGACAATGT 59.681 34.615 14.44 0.00 40.06 2.71
2397 2493 5.279456 GCATAAGGGTTGTGGTGAGAAAAAT 60.279 40.000 0.00 0.00 0.00 1.82
3076 3424 2.015587 CAAGGAAGATGGAGCTTGCTC 58.984 52.381 13.69 13.69 44.37 4.26
3378 4024 3.845178 GCCACTTTTGGGTTGCTAATAC 58.155 45.455 0.00 0.00 44.15 1.89
3384 4030 5.475564 ACTTTTGGGTTGCTAATACGATGTT 59.524 36.000 0.00 0.00 0.00 2.71
3551 4602 2.287644 GGCAAATTTGAAAGGTGTGTGC 59.712 45.455 22.31 2.02 0.00 4.57
3723 4779 8.312896 TGTGAATGATTTTGATCACAAATTGG 57.687 30.769 13.50 0.00 46.51 3.16
3897 4954 7.254488 GCGAGTGTTAAATAAGGAATTCTCTCC 60.254 40.741 5.23 0.00 35.51 3.71
3898 4955 7.764443 CGAGTGTTAAATAAGGAATTCTCTCCA 59.236 37.037 5.23 0.00 38.02 3.86
3901 4958 9.841880 GTGTTAAATAAGGAATTCTCTCCAAAC 57.158 33.333 5.23 3.80 38.02 2.93
3906 4963 9.593565 AAATAAGGAATTCTCTCCAAACTTTCT 57.406 29.630 5.23 0.00 38.02 2.52
3908 4965 6.890979 AGGAATTCTCTCCAAACTTTCTTG 57.109 37.500 5.23 0.00 38.02 3.02
3923 4980 7.898014 AACTTTCTTGGAGTTCCTTATTGTT 57.102 32.000 0.00 0.00 32.04 2.83
3924 4981 7.277174 ACTTTCTTGGAGTTCCTTATTGTTG 57.723 36.000 0.00 0.00 36.82 3.33
3925 4982 6.265422 ACTTTCTTGGAGTTCCTTATTGTTGG 59.735 38.462 0.00 0.00 36.82 3.77
3926 4983 4.079253 TCTTGGAGTTCCTTATTGTTGGC 58.921 43.478 0.00 0.00 36.82 4.52
3927 4984 3.517296 TGGAGTTCCTTATTGTTGGCA 57.483 42.857 0.00 0.00 36.82 4.92
3928 4985 3.153919 TGGAGTTCCTTATTGTTGGCAC 58.846 45.455 0.00 0.00 36.82 5.01
3929 4986 3.153919 GGAGTTCCTTATTGTTGGCACA 58.846 45.455 0.00 0.00 0.00 4.57
3931 4988 3.821033 GAGTTCCTTATTGTTGGCACACT 59.179 43.478 0.00 0.00 39.29 3.55
3932 4989 4.215109 AGTTCCTTATTGTTGGCACACTT 58.785 39.130 0.00 0.00 39.29 3.16
3933 4990 4.037923 AGTTCCTTATTGTTGGCACACTTG 59.962 41.667 0.00 0.00 39.29 3.16
3934 4991 3.826524 TCCTTATTGTTGGCACACTTGA 58.173 40.909 0.00 0.00 39.29 3.02
3938 4995 6.491745 TCCTTATTGTTGGCACACTTGAAATA 59.508 34.615 0.00 0.00 39.29 1.40
3940 4997 4.582701 TTGTTGGCACACTTGAAATAGG 57.417 40.909 0.00 0.00 39.29 2.57
3942 4999 4.211125 TGTTGGCACACTTGAAATAGGAA 58.789 39.130 0.00 0.00 39.29 3.36
3944 5001 6.007076 TGTTGGCACACTTGAAATAGGAATA 58.993 36.000 0.00 0.00 39.29 1.75
3945 5002 6.663093 TGTTGGCACACTTGAAATAGGAATAT 59.337 34.615 0.00 0.00 39.29 1.28
3946 5003 7.831690 TGTTGGCACACTTGAAATAGGAATATA 59.168 33.333 0.00 0.00 39.29 0.86
3948 5005 7.573710 TGGCACACTTGAAATAGGAATATACT 58.426 34.615 0.00 0.00 0.00 2.12
3949 5006 7.715249 TGGCACACTTGAAATAGGAATATACTC 59.285 37.037 0.00 0.00 0.00 2.59
3950 5007 7.173390 GGCACACTTGAAATAGGAATATACTCC 59.827 40.741 0.00 0.00 35.51 3.85
3953 5010 9.004231 ACACTTGAAATAGGAATATACTCCCTT 57.996 33.333 0.00 0.00 35.95 3.95
3955 5012 8.368668 ACTTGAAATAGGAATATACTCCCTTCG 58.631 37.037 0.00 0.00 35.95 3.79
3956 5013 7.850935 TGAAATAGGAATATACTCCCTTCGT 57.149 36.000 0.00 0.00 35.95 3.85
3960 5017 4.553678 AGGAATATACTCCCTTCGTTCCA 58.446 43.478 0.00 0.00 36.87 3.53
3961 5018 5.155905 AGGAATATACTCCCTTCGTTCCAT 58.844 41.667 0.00 0.00 36.87 3.41
3962 5019 6.320518 AGGAATATACTCCCTTCGTTCCATA 58.679 40.000 0.00 0.00 36.87 2.74
3963 5020 6.960542 AGGAATATACTCCCTTCGTTCCATAT 59.039 38.462 0.00 0.00 36.87 1.78
3964 5021 7.458170 AGGAATATACTCCCTTCGTTCCATATT 59.542 37.037 0.00 0.00 36.87 1.28
3965 5022 8.755977 GGAATATACTCCCTTCGTTCCATATTA 58.244 37.037 0.00 0.00 35.05 0.98
3966 5023 9.804758 GAATATACTCCCTTCGTTCCATATTAG 57.195 37.037 0.00 0.00 0.00 1.73
3967 5024 8.896722 ATATACTCCCTTCGTTCCATATTAGT 57.103 34.615 0.00 0.00 0.00 2.24
3968 5025 5.952347 ACTCCCTTCGTTCCATATTAGTT 57.048 39.130 0.00 0.00 0.00 2.24
3969 5026 5.671493 ACTCCCTTCGTTCCATATTAGTTG 58.329 41.667 0.00 0.00 0.00 3.16
3971 5028 5.667466 TCCCTTCGTTCCATATTAGTTGTC 58.333 41.667 0.00 0.00 0.00 3.18
3972 5029 4.506654 CCCTTCGTTCCATATTAGTTGTCG 59.493 45.833 0.00 0.00 0.00 4.35
3974 5031 5.579511 CCTTCGTTCCATATTAGTTGTCGTT 59.420 40.000 0.00 0.00 0.00 3.85
3975 5032 6.397831 TTCGTTCCATATTAGTTGTCGTTG 57.602 37.500 0.00 0.00 0.00 4.10
3977 5034 6.157904 TCGTTCCATATTAGTTGTCGTTGAA 58.842 36.000 0.00 0.00 0.00 2.69
3978 5035 6.645827 TCGTTCCATATTAGTTGTCGTTGAAA 59.354 34.615 0.00 0.00 0.00 2.69
3980 5037 7.569774 CGTTCCATATTAGTTGTCGTTGAAACA 60.570 37.037 0.00 0.00 0.00 2.83
3981 5038 7.915293 TCCATATTAGTTGTCGTTGAAACAT 57.085 32.000 0.00 0.00 0.00 2.71
3982 5039 9.438228 TTCCATATTAGTTGTCGTTGAAACATA 57.562 29.630 0.00 0.00 0.00 2.29
3983 5040 9.607988 TCCATATTAGTTGTCGTTGAAACATAT 57.392 29.630 0.00 0.00 0.00 1.78
3984 5041 9.650371 CCATATTAGTTGTCGTTGAAACATATG 57.350 33.333 0.00 0.00 30.23 1.78
3989 5046 9.647797 TTAGTTGTCGTTGAAACATATGTATCT 57.352 29.630 9.21 0.00 0.00 1.98
4022 7063 9.817809 TTTTAGTGCTAGGTATATCTGTTTGAG 57.182 33.333 0.00 0.00 0.00 3.02
4024 7065 4.681942 GTGCTAGGTATATCTGTTTGAGCG 59.318 45.833 0.00 0.00 0.00 5.03
4025 7066 4.583073 TGCTAGGTATATCTGTTTGAGCGA 59.417 41.667 0.00 0.00 0.00 4.93
4026 7067 4.918583 GCTAGGTATATCTGTTTGAGCGAC 59.081 45.833 0.00 0.00 0.00 5.19
4027 7068 5.507482 GCTAGGTATATCTGTTTGAGCGACA 60.507 44.000 0.00 0.00 0.00 4.35
4028 7069 5.339008 AGGTATATCTGTTTGAGCGACAA 57.661 39.130 0.00 0.00 36.65 3.18
4029 7070 5.109903 AGGTATATCTGTTTGAGCGACAAC 58.890 41.667 0.00 0.00 38.29 3.32
4030 7071 5.105310 AGGTATATCTGTTTGAGCGACAACT 60.105 40.000 0.00 0.00 38.29 3.16
4032 7073 2.595124 TCTGTTTGAGCGACAACTGA 57.405 45.000 0.00 0.82 38.29 3.41
4034 7075 4.251543 TCTGTTTGAGCGACAACTGATA 57.748 40.909 0.00 0.00 38.29 2.15
4035 7076 3.987868 TCTGTTTGAGCGACAACTGATAC 59.012 43.478 0.00 0.00 38.29 2.24
4036 7077 2.729360 TGTTTGAGCGACAACTGATACG 59.271 45.455 0.00 0.00 38.29 3.06
4037 7078 2.717580 TTGAGCGACAACTGATACGT 57.282 45.000 0.00 0.00 33.18 3.57
4040 7081 3.495193 TGAGCGACAACTGATACGTAAC 58.505 45.455 0.00 0.00 0.00 2.50
4042 7083 4.103357 GAGCGACAACTGATACGTAACAT 58.897 43.478 5.96 0.00 0.00 2.71
4043 7084 5.163733 TGAGCGACAACTGATACGTAACATA 60.164 40.000 5.96 0.00 0.00 2.29
4044 7085 5.271625 AGCGACAACTGATACGTAACATAG 58.728 41.667 5.96 0.00 0.00 2.23
4045 7086 4.440103 GCGACAACTGATACGTAACATAGG 59.560 45.833 5.96 1.82 0.00 2.57
4046 7087 4.974275 CGACAACTGATACGTAACATAGGG 59.026 45.833 5.96 0.00 0.00 3.53
4047 7088 5.220912 CGACAACTGATACGTAACATAGGGA 60.221 44.000 5.96 0.00 0.00 4.20
4050 7091 6.830324 ACAACTGATACGTAACATAGGGAGTA 59.170 38.462 5.96 0.00 0.00 2.59
4051 7092 7.504911 ACAACTGATACGTAACATAGGGAGTAT 59.495 37.037 5.96 0.00 0.00 2.12
4052 7093 7.684937 ACTGATACGTAACATAGGGAGTATC 57.315 40.000 5.96 6.49 40.20 2.24
4053 7094 7.229308 ACTGATACGTAACATAGGGAGTATCA 58.771 38.462 5.96 13.27 44.34 2.15
4056 7097 9.085645 TGATACGTAACATAGGGAGTATCAATT 57.914 33.333 12.02 0.00 43.90 2.32
4060 7101 9.924650 ACGTAACATAGGGAGTATCAATTAATC 57.075 33.333 0.00 0.00 36.25 1.75
4069 7110 6.784031 GGAGTATCAATTAATCCCAGGTCAT 58.216 40.000 0.00 0.00 38.82 3.06
4073 7114 8.949421 AGTATCAATTAATCCCAGGTCATAAGT 58.051 33.333 0.00 0.00 0.00 2.24
4074 7115 9.574516 GTATCAATTAATCCCAGGTCATAAGTT 57.425 33.333 0.00 0.00 0.00 2.66
4077 7118 6.715347 ATTAATCCCAGGTCATAAGTTTGC 57.285 37.500 0.00 0.00 0.00 3.68
4080 7121 4.046286 TCCCAGGTCATAAGTTTGCAAT 57.954 40.909 0.00 0.00 0.00 3.56
4081 7122 4.016444 TCCCAGGTCATAAGTTTGCAATC 58.984 43.478 0.00 0.00 0.00 2.67
4082 7123 4.019174 CCCAGGTCATAAGTTTGCAATCT 58.981 43.478 0.00 1.10 0.00 2.40
4083 7124 4.142315 CCCAGGTCATAAGTTTGCAATCTG 60.142 45.833 10.72 0.00 0.00 2.90
4084 7125 4.418392 CAGGTCATAAGTTTGCAATCTGC 58.582 43.478 10.72 0.00 45.29 4.26
4137 7178 7.726033 ATGATAGGTCATAGGTTACAGATCC 57.274 40.000 0.00 0.00 43.18 3.36
4138 7179 6.017192 TGATAGGTCATAGGTTACAGATCCC 58.983 44.000 0.00 0.00 0.00 3.85
4139 7180 4.280789 AGGTCATAGGTTACAGATCCCA 57.719 45.455 0.00 0.00 0.00 4.37
4140 7181 4.631234 AGGTCATAGGTTACAGATCCCAA 58.369 43.478 0.00 0.00 0.00 4.12
4141 7182 4.409247 AGGTCATAGGTTACAGATCCCAAC 59.591 45.833 0.00 0.00 0.00 3.77
4142 7183 4.409247 GGTCATAGGTTACAGATCCCAACT 59.591 45.833 0.00 0.00 0.00 3.16
4143 7184 5.601313 GGTCATAGGTTACAGATCCCAACTA 59.399 44.000 0.00 0.00 0.00 2.24
4144 7185 6.270231 GGTCATAGGTTACAGATCCCAACTAT 59.730 42.308 0.00 0.00 0.00 2.12
4146 7187 8.867097 GTCATAGGTTACAGATCCCAACTATTA 58.133 37.037 0.00 0.00 0.00 0.98
4147 7188 9.090103 TCATAGGTTACAGATCCCAACTATTAG 57.910 37.037 0.00 0.00 0.00 1.73
4149 7190 7.362802 AGGTTACAGATCCCAACTATTAGAC 57.637 40.000 0.00 0.00 0.00 2.59
4150 7191 7.133483 AGGTTACAGATCCCAACTATTAGACT 58.867 38.462 0.00 0.00 0.00 3.24
4159 8859 6.046593 TCCCAACTATTAGACTATTTGTGCG 58.953 40.000 0.00 0.00 0.00 5.34
4160 8860 5.277345 CCCAACTATTAGACTATTTGTGCGC 60.277 44.000 0.00 0.00 0.00 6.09
4162 8862 6.017934 CCAACTATTAGACTATTTGTGCGCAT 60.018 38.462 15.91 0.00 0.00 4.73
4166 8866 6.624352 ATTAGACTATTTGTGCGCATTGAT 57.376 33.333 15.91 10.46 0.00 2.57
4167 8867 4.282950 AGACTATTTGTGCGCATTGATG 57.717 40.909 15.91 5.52 0.00 3.07
4182 8882 2.978156 TGATGCTTGGGTCTTCCTTT 57.022 45.000 0.00 0.00 36.20 3.11
4187 8887 0.969149 CTTGGGTCTTCCTTTTGCCC 59.031 55.000 0.00 0.00 39.73 5.36
4188 8888 0.825840 TTGGGTCTTCCTTTTGCCCG 60.826 55.000 0.00 0.00 42.10 6.13
4189 8889 1.228459 GGGTCTTCCTTTTGCCCGT 60.228 57.895 0.00 0.00 0.00 5.28
4190 8890 1.241990 GGGTCTTCCTTTTGCCCGTC 61.242 60.000 0.00 0.00 0.00 4.79
4191 8891 0.250770 GGTCTTCCTTTTGCCCGTCT 60.251 55.000 0.00 0.00 0.00 4.18
4192 8892 0.875059 GTCTTCCTTTTGCCCGTCTG 59.125 55.000 0.00 0.00 0.00 3.51
4195 8895 2.162681 CTTCCTTTTGCCCGTCTGAAT 58.837 47.619 0.00 0.00 0.00 2.57
4196 8896 1.533625 TCCTTTTGCCCGTCTGAATG 58.466 50.000 0.00 0.00 0.00 2.67
4198 8898 1.613437 CCTTTTGCCCGTCTGAATGTT 59.387 47.619 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
340 347 2.836981 GGTGATAGGCTCATATGGCTCT 59.163 50.000 13.60 11.58 42.90 4.09
740 818 8.651389 AGGTGTACTATACTCGGTGTTATACTA 58.349 37.037 0.00 0.00 0.00 1.82
960 1047 4.701765 ACTAGAGCAATCATGACCACATC 58.298 43.478 0.00 0.00 34.15 3.06
1205 1293 7.875971 AGAGATTTCAACTTGCGATTTAAACT 58.124 30.769 0.00 0.00 0.00 2.66
1235 1323 4.694760 TCAATCTGCACTATGCTACCAT 57.305 40.909 2.02 0.00 45.31 3.55
1280 1369 8.633561 CAAAGAAGAACCTTCTAAACCTGATTT 58.366 33.333 9.36 0.00 36.28 2.17
1281 1370 7.255625 GCAAAGAAGAACCTTCTAAACCTGATT 60.256 37.037 9.36 0.00 36.28 2.57
1322 1411 3.879892 GCAACCACTAAGGAATCCATCTC 59.120 47.826 0.61 0.00 41.22 2.75
1592 1681 6.569127 TGCATTCCCTATGTTTTACCTCTA 57.431 37.500 0.00 0.00 36.57 2.43
1654 1743 8.917088 CCAAAGATGGTCATCAAATACCTTTAT 58.083 33.333 12.75 0.00 42.18 1.40
1655 1744 7.341769 CCCAAAGATGGTCATCAAATACCTTTA 59.658 37.037 12.75 0.00 46.01 1.85
2001 2097 6.426328 ACTCTCTACTCTTTGCAATCAACTTG 59.574 38.462 0.00 0.00 37.94 3.16
2009 2105 7.226720 CCAAGTTTAACTCTCTACTCTTTGCAA 59.773 37.037 0.00 0.00 0.00 4.08
2142 2238 0.476771 AAGGAAGGCCGGAAACTTGA 59.523 50.000 5.05 0.00 39.96 3.02
2367 2463 1.656652 CACAACCCTTATGCCTCTCG 58.343 55.000 0.00 0.00 0.00 4.04
2397 2493 3.339547 GTGCTGGCCACTTTTCCTA 57.660 52.632 0.00 0.00 41.35 2.94
3076 3424 5.577945 CCATCGGATTGTTTTGATCCTTTTG 59.422 40.000 2.07 0.00 40.76 2.44
3378 4024 6.147164 ACATTACTAAGTCCACACAAACATCG 59.853 38.462 0.00 0.00 0.00 3.84
3384 4030 7.672240 TCACATACATTACTAAGTCCACACAA 58.328 34.615 0.00 0.00 0.00 3.33
3719 4774 5.155905 AGACGATCTTACCCCTAATCCAAT 58.844 41.667 0.00 0.00 0.00 3.16
3723 4779 6.579865 TGAAAAGACGATCTTACCCCTAATC 58.420 40.000 0.00 0.00 35.27 1.75
3897 4954 7.716612 ACAATAAGGAACTCCAAGAAAGTTTG 58.283 34.615 0.00 0.00 38.49 2.93
3898 4955 7.898014 ACAATAAGGAACTCCAAGAAAGTTT 57.102 32.000 0.00 0.00 38.49 2.66
3901 4958 6.681777 CCAACAATAAGGAACTCCAAGAAAG 58.318 40.000 0.00 0.00 38.49 2.62
3905 4962 3.826157 TGCCAACAATAAGGAACTCCAAG 59.174 43.478 0.00 0.00 38.49 3.61
3906 4963 3.572255 GTGCCAACAATAAGGAACTCCAA 59.428 43.478 0.00 0.00 38.49 3.53
3908 4965 3.057526 GTGTGCCAACAATAAGGAACTCC 60.058 47.826 0.00 0.00 35.90 3.85
3910 4967 3.832527 AGTGTGCCAACAATAAGGAACT 58.167 40.909 0.00 0.00 38.33 3.01
3911 4968 4.037446 TCAAGTGTGCCAACAATAAGGAAC 59.963 41.667 0.00 0.00 38.27 3.62
3912 4969 4.211125 TCAAGTGTGCCAACAATAAGGAA 58.789 39.130 0.00 0.00 38.27 3.36
3914 4971 4.582701 TTCAAGTGTGCCAACAATAAGG 57.417 40.909 0.00 0.00 38.27 2.69
3915 4972 6.808212 CCTATTTCAAGTGTGCCAACAATAAG 59.192 38.462 0.00 0.00 38.27 1.73
3916 4973 6.491745 TCCTATTTCAAGTGTGCCAACAATAA 59.508 34.615 0.00 0.00 38.27 1.40
3918 4975 4.832266 TCCTATTTCAAGTGTGCCAACAAT 59.168 37.500 0.00 0.00 38.27 2.71
3919 4976 4.211125 TCCTATTTCAAGTGTGCCAACAA 58.789 39.130 0.00 0.00 38.27 2.83
3923 4980 7.573710 AGTATATTCCTATTTCAAGTGTGCCA 58.426 34.615 0.00 0.00 0.00 4.92
3924 4981 7.173390 GGAGTATATTCCTATTTCAAGTGTGCC 59.827 40.741 7.02 0.00 34.27 5.01
3925 4982 7.173390 GGGAGTATATTCCTATTTCAAGTGTGC 59.827 40.741 13.49 0.00 37.40 4.57
3926 4983 8.432805 AGGGAGTATATTCCTATTTCAAGTGTG 58.567 37.037 13.49 0.00 37.40 3.82
3927 4984 8.568617 AGGGAGTATATTCCTATTTCAAGTGT 57.431 34.615 13.49 0.00 37.40 3.55
3928 4985 9.495572 GAAGGGAGTATATTCCTATTTCAAGTG 57.504 37.037 13.49 0.00 37.40 3.16
3929 4986 8.368668 CGAAGGGAGTATATTCCTATTTCAAGT 58.631 37.037 13.49 0.00 37.40 3.16
3931 4988 8.258850 ACGAAGGGAGTATATTCCTATTTCAA 57.741 34.615 13.49 0.00 37.40 2.69
3932 4989 7.850935 ACGAAGGGAGTATATTCCTATTTCA 57.149 36.000 13.49 0.00 37.40 2.69
3933 4990 7.818446 GGAACGAAGGGAGTATATTCCTATTTC 59.182 40.741 13.49 12.83 37.40 2.17
3934 4991 7.291651 TGGAACGAAGGGAGTATATTCCTATTT 59.708 37.037 13.49 6.59 37.40 1.40
3938 4995 4.553678 TGGAACGAAGGGAGTATATTCCT 58.446 43.478 13.49 0.55 37.40 3.36
3940 4997 9.804758 CTAATATGGAACGAAGGGAGTATATTC 57.195 37.037 0.00 0.00 0.00 1.75
3942 4999 8.896722 ACTAATATGGAACGAAGGGAGTATAT 57.103 34.615 0.00 0.00 0.00 0.86
3944 5001 7.070821 ACAACTAATATGGAACGAAGGGAGTAT 59.929 37.037 0.00 0.00 0.00 2.12
3945 5002 6.381994 ACAACTAATATGGAACGAAGGGAGTA 59.618 38.462 0.00 0.00 0.00 2.59
3946 5003 5.189145 ACAACTAATATGGAACGAAGGGAGT 59.811 40.000 0.00 0.00 0.00 3.85
3948 5005 5.667466 GACAACTAATATGGAACGAAGGGA 58.333 41.667 0.00 0.00 0.00 4.20
3949 5006 4.506654 CGACAACTAATATGGAACGAAGGG 59.493 45.833 0.00 0.00 0.00 3.95
3950 5007 5.107133 ACGACAACTAATATGGAACGAAGG 58.893 41.667 0.00 0.00 0.00 3.46
3953 5010 5.712004 TCAACGACAACTAATATGGAACGA 58.288 37.500 0.00 0.00 0.00 3.85
3955 5012 7.577979 TGTTTCAACGACAACTAATATGGAAC 58.422 34.615 0.00 0.00 0.00 3.62
3956 5013 7.731882 TGTTTCAACGACAACTAATATGGAA 57.268 32.000 0.00 0.00 0.00 3.53
3963 5020 9.647797 AGATACATATGTTTCAACGACAACTAA 57.352 29.630 23.00 0.00 0.00 2.24
3965 5022 9.647797 TTAGATACATATGTTTCAACGACAACT 57.352 29.630 23.00 6.74 0.00 3.16
3983 5040 9.953565 ACCTAGCACTAAAAACATTTAGATACA 57.046 29.630 13.61 0.00 37.80 2.29
3993 7034 9.953565 AAACAGATATACCTAGCACTAAAAACA 57.046 29.630 0.00 0.00 0.00 2.83
3996 7037 9.817809 CTCAAACAGATATACCTAGCACTAAAA 57.182 33.333 0.00 0.00 0.00 1.52
4000 7041 5.508153 CGCTCAAACAGATATACCTAGCACT 60.508 44.000 0.00 0.00 0.00 4.40
4001 7042 4.681942 CGCTCAAACAGATATACCTAGCAC 59.318 45.833 0.00 0.00 0.00 4.40
4002 7043 4.583073 TCGCTCAAACAGATATACCTAGCA 59.417 41.667 0.00 0.00 0.00 3.49
4007 7048 5.005779 CAGTTGTCGCTCAAACAGATATACC 59.994 44.000 0.00 0.00 37.81 2.73
4008 7049 5.805486 TCAGTTGTCGCTCAAACAGATATAC 59.195 40.000 0.00 0.00 37.81 1.47
4011 7052 4.251543 TCAGTTGTCGCTCAAACAGATA 57.748 40.909 0.00 0.00 37.81 1.98
4020 7061 3.495193 TGTTACGTATCAGTTGTCGCTC 58.505 45.455 2.17 0.00 0.00 5.03
4021 7062 3.564235 TGTTACGTATCAGTTGTCGCT 57.436 42.857 2.17 0.00 0.00 4.93
4022 7063 4.440103 CCTATGTTACGTATCAGTTGTCGC 59.560 45.833 11.67 0.00 0.00 5.19
4024 7065 6.140303 TCCCTATGTTACGTATCAGTTGTC 57.860 41.667 11.67 0.00 0.00 3.18
4025 7066 5.655532 ACTCCCTATGTTACGTATCAGTTGT 59.344 40.000 11.67 0.00 0.00 3.32
4026 7067 6.145338 ACTCCCTATGTTACGTATCAGTTG 57.855 41.667 11.67 4.94 0.00 3.16
4027 7068 7.722728 TGATACTCCCTATGTTACGTATCAGTT 59.277 37.037 11.67 0.00 38.62 3.16
4028 7069 7.229308 TGATACTCCCTATGTTACGTATCAGT 58.771 38.462 11.67 6.01 38.62 3.41
4029 7070 7.683437 TGATACTCCCTATGTTACGTATCAG 57.317 40.000 11.67 0.27 38.62 2.90
4030 7071 8.645814 ATTGATACTCCCTATGTTACGTATCA 57.354 34.615 8.70 8.70 40.53 2.15
4034 7075 9.924650 GATTAATTGATACTCCCTATGTTACGT 57.075 33.333 0.00 0.00 0.00 3.57
4035 7076 9.367444 GGATTAATTGATACTCCCTATGTTACG 57.633 37.037 0.00 0.00 29.19 3.18
4036 7077 9.668497 GGGATTAATTGATACTCCCTATGTTAC 57.332 37.037 1.44 0.00 45.72 2.50
4045 7086 6.187727 TGACCTGGGATTAATTGATACTCC 57.812 41.667 0.00 0.00 33.59 3.85
4046 7087 9.442047 CTTATGACCTGGGATTAATTGATACTC 57.558 37.037 0.00 0.00 0.00 2.59
4047 7088 8.949421 ACTTATGACCTGGGATTAATTGATACT 58.051 33.333 0.00 0.00 0.00 2.12
4050 7091 8.917088 CAAACTTATGACCTGGGATTAATTGAT 58.083 33.333 0.00 0.00 0.00 2.57
4051 7092 7.147915 GCAAACTTATGACCTGGGATTAATTGA 60.148 37.037 0.00 0.00 0.00 2.57
4052 7093 6.980397 GCAAACTTATGACCTGGGATTAATTG 59.020 38.462 0.00 0.00 0.00 2.32
4053 7094 6.667414 TGCAAACTTATGACCTGGGATTAATT 59.333 34.615 0.00 0.00 0.00 1.40
4056 7097 5.186256 TGCAAACTTATGACCTGGGATTA 57.814 39.130 0.00 0.00 0.00 1.75
4058 7099 3.737559 TGCAAACTTATGACCTGGGAT 57.262 42.857 0.00 0.00 0.00 3.85
4060 7101 4.019174 AGATTGCAAACTTATGACCTGGG 58.981 43.478 1.71 0.00 0.00 4.45
4062 7103 4.418392 GCAGATTGCAAACTTATGACCTG 58.582 43.478 6.47 3.37 44.26 4.00
4063 7104 4.708726 GCAGATTGCAAACTTATGACCT 57.291 40.909 6.47 0.00 44.26 3.85
4075 7116 8.580720 TTTTAGGTATAAAACTTGCAGATTGCA 58.419 29.630 0.00 0.00 42.17 4.08
4112 7153 7.839705 GGGATCTGTAACCTATGACCTATCATA 59.160 40.741 0.00 0.00 44.11 2.15
4114 7155 6.017192 GGGATCTGTAACCTATGACCTATCA 58.983 44.000 0.00 0.00 39.83 2.15
4115 7156 6.017192 TGGGATCTGTAACCTATGACCTATC 58.983 44.000 0.00 0.00 0.00 2.08
4116 7157 5.977533 TGGGATCTGTAACCTATGACCTAT 58.022 41.667 0.00 0.00 0.00 2.57
4117 7158 5.412617 TGGGATCTGTAACCTATGACCTA 57.587 43.478 0.00 0.00 0.00 3.08
4118 7159 4.280789 TGGGATCTGTAACCTATGACCT 57.719 45.455 0.00 0.00 0.00 3.85
4119 7160 4.409247 AGTTGGGATCTGTAACCTATGACC 59.591 45.833 0.00 0.00 0.00 4.02
4120 7161 5.615925 AGTTGGGATCTGTAACCTATGAC 57.384 43.478 0.00 0.00 0.00 3.06
4121 7162 7.931015 AATAGTTGGGATCTGTAACCTATGA 57.069 36.000 0.00 0.00 0.00 2.15
4122 7163 9.090103 TCTAATAGTTGGGATCTGTAACCTATG 57.910 37.037 0.00 0.00 0.00 2.23
4123 7164 9.091220 GTCTAATAGTTGGGATCTGTAACCTAT 57.909 37.037 0.00 0.00 0.00 2.57
4124 7165 8.287350 AGTCTAATAGTTGGGATCTGTAACCTA 58.713 37.037 0.00 0.00 0.00 3.08
4126 7167 7.362802 AGTCTAATAGTTGGGATCTGTAACC 57.637 40.000 0.00 0.00 0.00 2.85
4130 7171 8.993424 ACAAATAGTCTAATAGTTGGGATCTGT 58.007 33.333 3.22 0.00 35.57 3.41
4131 7172 9.265901 CACAAATAGTCTAATAGTTGGGATCTG 57.734 37.037 3.22 0.00 36.49 2.90
4132 7173 7.934120 GCACAAATAGTCTAATAGTTGGGATCT 59.066 37.037 4.29 0.00 36.49 2.75
4134 7175 6.706270 CGCACAAATAGTCTAATAGTTGGGAT 59.294 38.462 4.29 0.00 36.49 3.85
4136 7177 5.277345 GCGCACAAATAGTCTAATAGTTGGG 60.277 44.000 0.30 0.00 37.24 4.12
4137 7178 5.293324 TGCGCACAAATAGTCTAATAGTTGG 59.707 40.000 5.66 0.00 35.57 3.77
4138 7179 6.344572 TGCGCACAAATAGTCTAATAGTTG 57.655 37.500 5.66 0.00 36.91 3.16
4139 7180 7.279981 TCAATGCGCACAAATAGTCTAATAGTT 59.720 33.333 14.90 0.00 0.00 2.24
4140 7181 6.761242 TCAATGCGCACAAATAGTCTAATAGT 59.239 34.615 14.90 0.00 0.00 2.12
4141 7182 7.177498 TCAATGCGCACAAATAGTCTAATAG 57.823 36.000 14.90 0.00 0.00 1.73
4142 7183 7.575365 CATCAATGCGCACAAATAGTCTAATA 58.425 34.615 14.90 0.00 0.00 0.98
4143 7184 6.432936 CATCAATGCGCACAAATAGTCTAAT 58.567 36.000 14.90 0.00 0.00 1.73
4144 7185 5.730289 GCATCAATGCGCACAAATAGTCTAA 60.730 40.000 14.90 0.00 44.67 2.10
4146 7187 3.488047 GCATCAATGCGCACAAATAGTCT 60.488 43.478 14.90 0.00 44.67 3.24
4147 7188 2.785477 GCATCAATGCGCACAAATAGTC 59.215 45.455 14.90 0.00 44.67 2.59
4159 8859 1.135721 GGAAGACCCAAGCATCAATGC 59.864 52.381 6.88 6.88 43.80 3.56
4160 8860 2.731572 AGGAAGACCCAAGCATCAATG 58.268 47.619 0.00 0.00 37.41 2.82
4162 8862 2.978156 AAGGAAGACCCAAGCATCAA 57.022 45.000 0.00 0.00 37.41 2.57
4166 8866 1.039856 GCAAAAGGAAGACCCAAGCA 58.960 50.000 0.00 0.00 37.41 3.91
4167 8867 0.318441 GGCAAAAGGAAGACCCAAGC 59.682 55.000 0.00 0.00 37.41 4.01
4168 8868 0.969149 GGGCAAAAGGAAGACCCAAG 59.031 55.000 0.00 0.00 40.52 3.61
4169 8869 0.825840 CGGGCAAAAGGAAGACCCAA 60.826 55.000 0.00 0.00 40.87 4.12
4172 8872 0.250770 AGACGGGCAAAAGGAAGACC 60.251 55.000 0.00 0.00 0.00 3.85
4175 8875 1.604604 TTCAGACGGGCAAAAGGAAG 58.395 50.000 0.00 0.00 0.00 3.46
4177 8877 1.202879 ACATTCAGACGGGCAAAAGGA 60.203 47.619 0.00 0.00 0.00 3.36
4178 8878 1.247567 ACATTCAGACGGGCAAAAGG 58.752 50.000 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.