Multiple sequence alignment - TraesCS4D01G207400

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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 TraesCS4D01G207400 chr4D 100.000 4259 0 0 1 4259 355813011 355817269 0.000000e+00 7866.0
1 TraesCS4D01G207400 chr4D 96.147 545 17 2 3719 4259 368860627 368860083 0.000000e+00 887.0
2 TraesCS4D01G207400 chr4D 96.283 538 17 1 3718 4252 313883329 313883866 0.000000e+00 880.0
3 TraesCS4D01G207400 chr4D 79.646 226 29 14 150 362 499409959 499409738 3.430000e-31 147.0
4 TraesCS4D01G207400 chr4D 98.000 50 1 0 3421 3470 63212500 63212451 2.110000e-13 87.9
5 TraesCS4D01G207400 chr4B 93.562 3386 127 39 2 3349 439310981 439314313 0.000000e+00 4961.0
6 TraesCS4D01G207400 chr4B 81.675 191 21 12 186 366 642363933 642363747 3.430000e-31 147.0
7 TraesCS4D01G207400 chr4A 96.475 2468 71 7 864 3318 109433764 109431300 0.000000e+00 4061.0
8 TraesCS4D01G207400 chr4A 95.669 254 4 3 3069 3318 109431088 109430838 6.630000e-108 401.0
9 TraesCS4D01G207400 chr4A 87.866 239 19 8 3467 3699 109430833 109430599 5.430000e-69 272.0
10 TraesCS4D01G207400 chr4A 88.500 200 16 7 3467 3663 109431295 109431100 7.120000e-58 235.0
11 TraesCS4D01G207400 chr6D 94.312 545 16 5 3719 4256 451768897 451769433 0.000000e+00 821.0
12 TraesCS4D01G207400 chr6D 92.308 65 3 2 3318 3381 469536315 469536378 1.630000e-14 91.6
13 TraesCS4D01G207400 chr6D 97.917 48 1 0 3421 3468 94635896 94635943 2.730000e-12 84.2
14 TraesCS4D01G207400 chr2D 93.934 544 17 4 3720 4259 568247337 568247868 0.000000e+00 808.0
15 TraesCS4D01G207400 chr2D 91.768 328 17 3 3933 4259 625170877 625170559 8.400000e-122 448.0
16 TraesCS4D01G207400 chr2D 77.031 357 54 23 1 343 605112611 605112269 3.380000e-41 180.0
17 TraesCS4D01G207400 chr2D 85.714 98 9 3 3325 3421 9340566 9340473 9.750000e-17 99.0
18 TraesCS4D01G207400 chr7B 93.028 545 24 5 3719 4259 697091501 697092035 0.000000e+00 784.0
19 TraesCS4D01G207400 chr7B 74.171 422 70 29 1 407 467977154 467976757 5.740000e-29 139.0
20 TraesCS4D01G207400 chr7B 83.929 112 7 5 3311 3421 6079428 6079529 3.510000e-16 97.1
21 TraesCS4D01G207400 chr3A 92.883 548 21 6 3719 4259 33141646 33141110 0.000000e+00 780.0
22 TraesCS4D01G207400 chr7A 92.857 546 24 6 3719 4259 211722148 211722683 0.000000e+00 778.0
23 TraesCS4D01G207400 chr7A 89.071 549 47 7 3723 4259 547148158 547148705 0.000000e+00 669.0
24 TraesCS4D01G207400 chr7A 81.132 212 20 18 166 362 63441334 63441540 7.380000e-33 152.0
25 TraesCS4D01G207400 chrUn 89.818 550 38 7 3719 4259 98273191 98273731 0.000000e+00 689.0
26 TraesCS4D01G207400 chr6A 83.651 367 48 9 1 362 15790421 15790780 6.820000e-88 335.0
27 TraesCS4D01G207400 chr7D 83.380 355 39 16 2 345 521767711 521767366 1.150000e-80 311.0
28 TraesCS4D01G207400 chr7D 94.545 55 3 0 3417 3471 37793271 37793217 7.590000e-13 86.1
29 TraesCS4D01G207400 chr7D 97.917 48 1 0 3420 3467 450004461 450004414 2.730000e-12 84.2
30 TraesCS4D01G207400 chr7D 85.714 70 2 3 3352 3421 498292319 498292258 2.750000e-07 67.6
31 TraesCS4D01G207400 chr2B 77.449 439 68 23 97 518 29013186 29012762 2.560000e-57 233.0
32 TraesCS4D01G207400 chr2B 93.651 63 4 0 3313 3375 691994791 691994729 1.260000e-15 95.3
33 TraesCS4D01G207400 chr2B 87.342 79 4 5 3301 3375 159893104 159893180 7.590000e-13 86.1
34 TraesCS4D01G207400 chr5D 85.463 227 27 6 202 427 472998417 472998638 9.210000e-57 231.0
35 TraesCS4D01G207400 chr5D 82.407 108 9 7 3317 3421 255376069 255376169 7.590000e-13 86.1
36 TraesCS4D01G207400 chr5D 81.333 75 14 0 248 322 397996866 397996792 1.280000e-05 62.1
37 TraesCS4D01G207400 chr5D 78.218 101 16 6 243 341 540270853 540270757 4.600000e-05 60.2
38 TraesCS4D01G207400 chr5A 77.892 389 42 27 6 362 90631494 90631870 7.220000e-48 202.0
39 TraesCS4D01G207400 chr5A 78.455 246 36 14 179 411 680205070 680204829 1.230000e-30 145.0
40 TraesCS4D01G207400 chr5B 76.871 294 47 14 84 366 473864795 473864512 3.430000e-31 147.0
41 TraesCS4D01G207400 chr1D 86.364 110 8 5 3318 3421 319371400 319371292 3.480000e-21 113.0
42 TraesCS4D01G207400 chr3D 83.459 133 7 4 3322 3454 126957750 126957867 4.500000e-20 110.0
43 TraesCS4D01G207400 chr3D 91.139 79 5 1 3388 3464 322067109 322067187 5.820000e-19 106.0
44 TraesCS4D01G207400 chr3B 89.873 79 6 1 3390 3468 601102352 601102428 2.710000e-17 100.0
45 TraesCS4D01G207400 chr3B 89.474 76 5 1 3392 3464 764120545 764120470 4.530000e-15 93.5
46 TraesCS4D01G207400 chr1A 90.541 74 7 0 244 317 329584919 329584992 9.750000e-17 99.0
47 TraesCS4D01G207400 chr1A 88.095 84 7 1 3390 3470 83819900 83819817 3.510000e-16 97.1
48 TraesCS4D01G207400 chr6B 94.737 57 2 1 3416 3471 46919909 46919965 2.110000e-13 87.9
49 TraesCS4D01G207400 chr2A 87.342 79 4 5 3301 3375 106806937 106807013 7.590000e-13 86.1


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 TraesCS4D01G207400 chr4D 355813011 355817269 4258 False 7866.00 7866 100.0000 1 4259 1 chr4D.!!$F2 4258
1 TraesCS4D01G207400 chr4D 368860083 368860627 544 True 887.00 887 96.1470 3719 4259 1 chr4D.!!$R2 540
2 TraesCS4D01G207400 chr4D 313883329 313883866 537 False 880.00 880 96.2830 3718 4252 1 chr4D.!!$F1 534
3 TraesCS4D01G207400 chr4B 439310981 439314313 3332 False 4961.00 4961 93.5620 2 3349 1 chr4B.!!$F1 3347
4 TraesCS4D01G207400 chr4A 109430599 109433764 3165 True 1242.25 4061 92.1275 864 3699 4 chr4A.!!$R1 2835
5 TraesCS4D01G207400 chr6D 451768897 451769433 536 False 821.00 821 94.3120 3719 4256 1 chr6D.!!$F2 537
6 TraesCS4D01G207400 chr2D 568247337 568247868 531 False 808.00 808 93.9340 3720 4259 1 chr2D.!!$F1 539
7 TraesCS4D01G207400 chr7B 697091501 697092035 534 False 784.00 784 93.0280 3719 4259 1 chr7B.!!$F2 540
8 TraesCS4D01G207400 chr3A 33141110 33141646 536 True 780.00 780 92.8830 3719 4259 1 chr3A.!!$R1 540
9 TraesCS4D01G207400 chr7A 211722148 211722683 535 False 778.00 778 92.8570 3719 4259 1 chr7A.!!$F2 540
10 TraesCS4D01G207400 chr7A 547148158 547148705 547 False 669.00 669 89.0710 3723 4259 1 chr7A.!!$F3 536
11 TraesCS4D01G207400 chrUn 98273191 98273731 540 False 689.00 689 89.8180 3719 4259 1 chrUn.!!$F1 540

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
829 846 0.318120 AACTCTGCAAAAATGGGCCG 59.682 50.0 0.00 0.0 0.00 6.13 F
1679 1717 0.466007 TGCCAGCTTGCTCAAGTCAA 60.466 50.0 11.53 0.0 40.45 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 1931 0.098376 GTACCACTCTGCCGACTACG 59.902 60.0 0.00 0.0 39.43 3.51 R
3644 4152 0.248012 TGCCTTTATTCTCGGCGTGA 59.752 50.0 6.85 7.3 46.67 4.35 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
83 84 7.820044 AAATTGTTAGTCAAGCGTTTGAAAA 57.180 28.000 16.65 11.01 44.49 2.29
84 85 7.820044 AATTGTTAGTCAAGCGTTTGAAAAA 57.180 28.000 16.65 10.67 44.49 1.94
136 137 9.941325 TGTAATCAAGCATTTGGAAAATGTTAT 57.059 25.926 12.82 0.00 34.97 1.89
197 198 7.053316 TGATGAAAAACCTTTGATCATGTGT 57.947 32.000 0.00 0.00 39.37 3.72
198 199 8.175925 TGATGAAAAACCTTTGATCATGTGTA 57.824 30.769 0.00 0.00 39.37 2.90
280 292 6.576551 TCAAGCGTTTGGAAAATGTTAAAC 57.423 33.333 12.29 0.00 34.97 2.01
524 539 8.023050 TGTGTTGGAAAAGTTTTAAACATGTG 57.977 30.769 22.30 0.00 32.33 3.21
586 602 9.594478 GAGGATTAAAACCAAAAGAAACAAAGA 57.406 29.630 5.15 0.00 0.00 2.52
595 611 6.169800 CCAAAAGAAACAAAGAAAACCCAGA 58.830 36.000 0.00 0.00 0.00 3.86
596 612 6.652900 CCAAAAGAAACAAAGAAAACCCAGAA 59.347 34.615 0.00 0.00 0.00 3.02
597 613 7.174080 CCAAAAGAAACAAAGAAAACCCAGAAA 59.826 33.333 0.00 0.00 0.00 2.52
598 614 8.563732 CAAAAGAAACAAAGAAAACCCAGAAAA 58.436 29.630 0.00 0.00 0.00 2.29
599 615 8.862325 AAAGAAACAAAGAAAACCCAGAAAAT 57.138 26.923 0.00 0.00 0.00 1.82
600 616 7.848223 AGAAACAAAGAAAACCCAGAAAATG 57.152 32.000 0.00 0.00 0.00 2.32
601 617 7.619965 AGAAACAAAGAAAACCCAGAAAATGA 58.380 30.769 0.00 0.00 0.00 2.57
602 618 8.100164 AGAAACAAAGAAAACCCAGAAAATGAA 58.900 29.630 0.00 0.00 0.00 2.57
603 619 8.628630 AAACAAAGAAAACCCAGAAAATGAAA 57.371 26.923 0.00 0.00 0.00 2.69
604 620 8.628630 AACAAAGAAAACCCAGAAAATGAAAA 57.371 26.923 0.00 0.00 0.00 2.29
605 621 8.039603 ACAAAGAAAACCCAGAAAATGAAAAC 57.960 30.769 0.00 0.00 0.00 2.43
676 693 7.976135 TCAGAGAAGAGAAAAGAAATGAAGG 57.024 36.000 0.00 0.00 0.00 3.46
700 717 9.658799 AGGAAAAGAAAAAGAAGAAGGAAAAAG 57.341 29.630 0.00 0.00 0.00 2.27
781 798 1.884235 ACAGAGAAAGCCGGTGAAAG 58.116 50.000 1.90 0.00 0.00 2.62
782 799 1.416401 ACAGAGAAAGCCGGTGAAAGA 59.584 47.619 1.90 0.00 0.00 2.52
783 800 2.158813 ACAGAGAAAGCCGGTGAAAGAA 60.159 45.455 1.90 0.00 0.00 2.52
784 801 2.224314 CAGAGAAAGCCGGTGAAAGAAC 59.776 50.000 1.90 0.00 0.00 3.01
785 802 1.535896 GAGAAAGCCGGTGAAAGAACC 59.464 52.381 1.90 0.00 36.82 3.62
790 807 2.104170 AGCCGGTGAAAGAACCAAAAA 58.896 42.857 1.90 0.00 40.53 1.94
829 846 0.318120 AACTCTGCAAAAATGGGCCG 59.682 50.000 0.00 0.00 0.00 6.13
879 897 1.469308 AGAACTGTCGGTCTCGCTTAG 59.531 52.381 0.00 0.00 36.13 2.18
1166 1195 1.162698 GAAAAGTGCCGGGTACTTCC 58.837 55.000 27.23 18.87 37.49 3.46
1210 1239 1.139058 TCCTCCGATTTTAGGCTCTGC 59.861 52.381 0.00 0.00 32.55 4.26
1337 1366 3.045601 ACAACCTCAACCTCTTGATCG 57.954 47.619 0.00 0.00 35.78 3.69
1376 1405 7.472543 AGTAGCAGCTAAAATACCAAATTTCG 58.527 34.615 2.87 0.00 0.00 3.46
1377 1406 5.102313 AGCAGCTAAAATACCAAATTTCGC 58.898 37.500 0.00 0.00 0.00 4.70
1597 1635 3.728864 GCTTGTATGAAACGGCTGTCATG 60.729 47.826 9.54 1.78 36.00 3.07
1679 1717 0.466007 TGCCAGCTTGCTCAAGTCAA 60.466 50.000 11.53 0.00 40.45 3.18
1853 1891 3.578282 AGACAAAGGTAAGCCCATTTTGG 59.422 43.478 0.00 0.00 33.96 3.28
1892 1931 3.751175 TGAACATGTTCGATTTCCCAGTC 59.249 43.478 28.55 6.28 42.28 3.51
1931 1970 5.297776 GGTACTGATTGTGCTTCATATGCTT 59.702 40.000 0.00 0.00 0.00 3.91
1932 1971 5.244785 ACTGATTGTGCTTCATATGCTTG 57.755 39.130 0.00 0.00 0.00 4.01
1940 1979 6.172630 TGTGCTTCATATGCTTGTCTTAAGA 58.827 36.000 0.00 0.00 0.00 2.10
2256 2295 7.815068 ACTATTTGTGATTGCGGAGATATCTAC 59.185 37.037 4.89 4.78 0.00 2.59
2306 2345 3.901570 TTGGGGAGCAGCCATAATATT 57.098 42.857 0.00 0.00 38.95 1.28
2396 2435 1.669265 GCCGGGTTTTGTACTCTATGC 59.331 52.381 2.18 0.00 0.00 3.14
2411 2450 5.784177 ACTCTATGCGATTGTATACCTTGG 58.216 41.667 0.00 0.00 0.00 3.61
2418 2457 3.550275 CGATTGTATACCTTGGTGTGACG 59.450 47.826 2.03 0.00 0.00 4.35
2423 2462 3.973206 ATACCTTGGTGTGACGATTGA 57.027 42.857 2.03 0.00 0.00 2.57
2518 2560 4.454728 TTGACTGGCAGCATTTAATTCC 57.545 40.909 15.89 0.00 0.00 3.01
2597 2639 7.535139 TGCACCTTCTAATTTTGCAGTAATAC 58.465 34.615 0.00 0.00 38.25 1.89
2811 2853 3.007940 TCTCATTTCTGAAGCTTTCCGGA 59.992 43.478 0.00 0.00 0.00 5.14
3016 3058 2.746362 CAAGGAAGCAGTCAAGGATGTC 59.254 50.000 0.00 0.00 0.00 3.06
3019 3061 2.266554 GAAGCAGTCAAGGATGTCGAG 58.733 52.381 0.00 0.00 0.00 4.04
3329 3836 5.799827 ACTTCTCTGCATATTACTCCCTC 57.200 43.478 0.00 0.00 0.00 4.30
3330 3837 5.463154 ACTTCTCTGCATATTACTCCCTCT 58.537 41.667 0.00 0.00 0.00 3.69
3339 3846 5.631481 GCATATTACTCCCTCTGTCCCAAAA 60.631 44.000 0.00 0.00 0.00 2.44
3340 3847 6.605119 CATATTACTCCCTCTGTCCCAAAAT 58.395 40.000 0.00 0.00 0.00 1.82
3342 3849 6.652205 ATTACTCCCTCTGTCCCAAAATAA 57.348 37.500 0.00 0.00 0.00 1.40
3343 3850 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
3344 3851 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
3345 3852 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
3346 3853 3.913799 TCCCTCTGTCCCAAAATAAGTGA 59.086 43.478 0.00 0.00 0.00 3.41
3347 3854 4.010349 CCCTCTGTCCCAAAATAAGTGAC 58.990 47.826 0.00 0.00 0.00 3.67
3348 3855 4.263506 CCCTCTGTCCCAAAATAAGTGACT 60.264 45.833 0.00 0.00 0.00 3.41
3349 3856 4.938226 CCTCTGTCCCAAAATAAGTGACTC 59.062 45.833 0.00 0.00 0.00 3.36
3350 3857 5.513094 CCTCTGTCCCAAAATAAGTGACTCA 60.513 44.000 0.00 0.00 0.00 3.41
3351 3858 5.935945 TCTGTCCCAAAATAAGTGACTCAA 58.064 37.500 0.00 0.00 0.00 3.02
3352 3859 5.763204 TCTGTCCCAAAATAAGTGACTCAAC 59.237 40.000 0.00 0.00 0.00 3.18
3353 3860 5.690865 TGTCCCAAAATAAGTGACTCAACT 58.309 37.500 0.00 0.00 0.00 3.16
3354 3861 6.126409 TGTCCCAAAATAAGTGACTCAACTT 58.874 36.000 0.00 0.00 42.89 2.66
3355 3862 6.605594 TGTCCCAAAATAAGTGACTCAACTTT 59.394 34.615 0.00 0.00 40.77 2.66
3356 3863 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
3357 3864 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
3358 3865 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
3359 3866 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
3360 3867 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
3367 3874 9.880157 AAGTGACTCAACTTTGTACTAAAGTTA 57.120 29.630 23.56 15.88 45.57 2.24
3368 3875 9.530633 AGTGACTCAACTTTGTACTAAAGTTAG 57.469 33.333 23.56 21.61 45.57 2.34
3369 3876 9.525409 GTGACTCAACTTTGTACTAAAGTTAGA 57.475 33.333 23.56 21.14 45.57 2.10
3372 3879 9.880157 ACTCAACTTTGTACTAAAGTTAGAACA 57.120 29.630 23.56 12.21 45.57 3.18
3416 3923 8.788325 AAAGTTAGTACAAAGTTGAGTCACTT 57.212 30.769 0.00 0.00 38.74 3.16
3417 3924 9.880157 AAAGTTAGTACAAAGTTGAGTCACTTA 57.120 29.630 0.00 0.00 35.87 2.24
3453 3960 9.965824 AGTACAAAGTTGAGTCATTTATTTTGG 57.034 29.630 12.94 0.78 0.00 3.28
3454 3961 9.959749 GTACAAAGTTGAGTCATTTATTTTGGA 57.040 29.630 12.94 4.81 0.00 3.53
3456 3963 9.533253 ACAAAGTTGAGTCATTTATTTTGGAAG 57.467 29.630 12.94 0.00 0.00 3.46
3457 3964 8.981647 CAAAGTTGAGTCATTTATTTTGGAAGG 58.018 33.333 0.00 0.00 0.00 3.46
3458 3965 7.232118 AGTTGAGTCATTTATTTTGGAAGGG 57.768 36.000 0.00 0.00 0.00 3.95
3459 3966 7.010160 AGTTGAGTCATTTATTTTGGAAGGGA 58.990 34.615 0.00 0.00 0.00 4.20
3460 3967 7.177392 AGTTGAGTCATTTATTTTGGAAGGGAG 59.823 37.037 0.00 0.00 0.00 4.30
3461 3968 5.951747 TGAGTCATTTATTTTGGAAGGGAGG 59.048 40.000 0.00 0.00 0.00 4.30
3462 3969 5.272402 AGTCATTTATTTTGGAAGGGAGGG 58.728 41.667 0.00 0.00 0.00 4.30
3463 3970 5.016245 AGTCATTTATTTTGGAAGGGAGGGA 59.984 40.000 0.00 0.00 0.00 4.20
3464 3971 5.360999 GTCATTTATTTTGGAAGGGAGGGAG 59.639 44.000 0.00 0.00 0.00 4.30
3465 3972 5.016245 TCATTTATTTTGGAAGGGAGGGAGT 59.984 40.000 0.00 0.00 0.00 3.85
3466 3973 6.218730 TCATTTATTTTGGAAGGGAGGGAGTA 59.781 38.462 0.00 0.00 0.00 2.59
3467 3974 5.446260 TTATTTTGGAAGGGAGGGAGTAC 57.554 43.478 0.00 0.00 0.00 2.73
3468 3975 2.735259 TTTGGAAGGGAGGGAGTACT 57.265 50.000 0.00 0.00 0.00 2.73
3469 3976 2.735259 TTGGAAGGGAGGGAGTACTT 57.265 50.000 0.00 0.00 0.00 2.24
3470 3977 1.952621 TGGAAGGGAGGGAGTACTTG 58.047 55.000 0.00 0.00 0.00 3.16
3471 3978 1.435563 TGGAAGGGAGGGAGTACTTGA 59.564 52.381 0.00 0.00 0.00 3.02
3472 3979 2.045885 TGGAAGGGAGGGAGTACTTGAT 59.954 50.000 0.00 0.00 0.00 2.57
3473 3980 3.273886 TGGAAGGGAGGGAGTACTTGATA 59.726 47.826 0.00 0.00 0.00 2.15
3521 4029 1.337703 TGCAGTTGGTGAATTGCACTC 59.662 47.619 1.30 0.00 46.50 3.51
3524 4032 2.485426 CAGTTGGTGAATTGCACTCGAT 59.515 45.455 0.00 0.00 46.86 3.59
3525 4033 2.744202 AGTTGGTGAATTGCACTCGATC 59.256 45.455 0.00 0.00 46.86 3.69
3532 4040 5.700832 GGTGAATTGCACTCGATCCATATTA 59.299 40.000 0.00 0.00 46.86 0.98
3533 4041 6.372659 GGTGAATTGCACTCGATCCATATTAT 59.627 38.462 0.00 0.00 46.86 1.28
3535 4043 7.747799 GTGAATTGCACTCGATCCATATTATTG 59.252 37.037 0.00 0.00 44.27 1.90
3536 4044 7.445096 TGAATTGCACTCGATCCATATTATTGT 59.555 33.333 0.00 0.00 0.00 2.71
3537 4045 7.750229 ATTGCACTCGATCCATATTATTGTT 57.250 32.000 0.00 0.00 0.00 2.83
3538 4046 6.544038 TGCACTCGATCCATATTATTGTTG 57.456 37.500 0.00 0.00 0.00 3.33
3574 4082 6.751425 CAGTAACACATGAAGCACTTGAAAAA 59.249 34.615 0.00 0.00 0.00 1.94
3575 4083 6.751888 AGTAACACATGAAGCACTTGAAAAAC 59.248 34.615 0.00 0.00 0.00 2.43
3593 4101 3.740044 AACGTCACTTGAATTATGGCG 57.260 42.857 0.00 0.00 46.51 5.69
3625 4133 1.006043 TCCGATGAGGTCTTGACTCCT 59.994 52.381 0.61 0.00 41.99 3.69
3635 4143 2.095466 GTCTTGACTCCTGTCTCTGTCG 60.095 54.545 0.00 0.00 43.29 4.35
3636 4144 0.598562 TTGACTCCTGTCTCTGTCGC 59.401 55.000 0.00 0.00 43.29 5.19
3638 4146 1.579084 GACTCCTGTCTCTGTCGCGT 61.579 60.000 5.77 0.00 39.94 6.01
3644 4152 0.952280 TGTCTCTGTCGCGTCTTCTT 59.048 50.000 5.77 0.00 0.00 2.52
3657 4165 2.477357 CGTCTTCTTCACGCCGAGAATA 60.477 50.000 0.00 0.00 0.00 1.75
3658 4166 3.508762 GTCTTCTTCACGCCGAGAATAA 58.491 45.455 0.00 0.00 0.00 1.40
3689 4200 1.947456 CGAATAGCAAGTTTAGGGGCC 59.053 52.381 0.00 0.00 0.00 5.80
3699 4210 6.070995 AGCAAGTTTAGGGGCCTTTTATTAAC 60.071 38.462 0.84 0.00 0.00 2.01
3700 4211 6.070995 GCAAGTTTAGGGGCCTTTTATTAACT 60.071 38.462 0.84 1.14 0.00 2.24
3701 4212 7.123098 GCAAGTTTAGGGGCCTTTTATTAACTA 59.877 37.037 0.84 0.00 0.00 2.24
3702 4213 8.683615 CAAGTTTAGGGGCCTTTTATTAACTAG 58.316 37.037 0.84 0.00 0.00 2.57
3703 4214 6.832384 AGTTTAGGGGCCTTTTATTAACTAGC 59.168 38.462 0.84 0.00 0.00 3.42
3704 4215 4.873724 AGGGGCCTTTTATTAACTAGCA 57.126 40.909 0.84 0.00 0.00 3.49
3705 4216 4.533815 AGGGGCCTTTTATTAACTAGCAC 58.466 43.478 0.84 0.00 0.00 4.40
3706 4217 4.017867 AGGGGCCTTTTATTAACTAGCACA 60.018 41.667 0.84 0.00 0.00 4.57
3707 4218 4.893524 GGGGCCTTTTATTAACTAGCACAT 59.106 41.667 0.84 0.00 0.00 3.21
3708 4219 6.066032 GGGGCCTTTTATTAACTAGCACATA 58.934 40.000 0.84 0.00 0.00 2.29
3709 4220 6.719829 GGGGCCTTTTATTAACTAGCACATAT 59.280 38.462 0.84 0.00 0.00 1.78
3710 4221 7.309194 GGGGCCTTTTATTAACTAGCACATATG 60.309 40.741 0.84 0.00 0.00 1.78
3763 4274 2.280552 GGTAGCACAGGACACCGGA 61.281 63.158 9.46 0.00 0.00 5.14
3805 4317 3.925261 ACCTATAGAGCCCACATACCT 57.075 47.619 0.00 0.00 0.00 3.08
3977 4501 3.118454 GCTCCACGCTGCGCTTTA 61.118 61.111 23.51 4.35 35.14 1.85
4115 4651 0.038744 CTGCATCAGTCCCCAAACCT 59.961 55.000 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
228 240 7.119553 AGCATTTTTCAAACACTTGTTCAACAT 59.880 29.630 0.00 0.00 37.25 2.71
652 669 7.739825 TCCTTCATTTCTTTTCTCTTCTCTGA 58.260 34.615 0.00 0.00 0.00 3.27
771 788 2.588027 TTTTTGGTTCTTTCACCGGC 57.412 45.000 0.00 0.00 40.09 6.13
812 829 1.216178 CCGGCCCATTTTTGCAGAG 59.784 57.895 0.00 0.00 0.00 3.35
829 846 0.391966 GGGTCTACAGTAATCGGGCC 59.608 60.000 0.00 0.00 0.00 5.80
833 850 3.351020 CGAAGGGGTCTACAGTAATCG 57.649 52.381 0.00 0.00 0.00 3.34
910 928 4.140599 AGAGCTGCTCGCGAAGGG 62.141 66.667 22.77 0.00 45.59 3.95
989 1014 1.260538 ATCGACCAGGAGAGCTGCAA 61.261 55.000 1.02 0.00 0.00 4.08
1184 1213 2.202566 CCTAAAATCGGAGGAGCGAAC 58.797 52.381 0.00 0.00 34.46 3.95
1210 1239 4.200283 GCGAGAGGGAGTCAGCGG 62.200 72.222 0.00 0.00 0.00 5.52
1212 1241 3.844090 GGGCGAGAGGGAGTCAGC 61.844 72.222 0.00 0.00 0.00 4.26
1337 1366 2.473816 TGCTACTCGCACAAGCATATC 58.526 47.619 0.00 0.00 45.47 1.63
1376 1405 3.721035 AGCAAGACCAATCAAAAACAGC 58.279 40.909 0.00 0.00 0.00 4.40
1377 1406 3.976942 CGAGCAAGACCAATCAAAAACAG 59.023 43.478 0.00 0.00 0.00 3.16
1422 1451 1.562575 GCACCCTGGACGTGTAAACG 61.563 60.000 3.26 3.26 39.31 3.60
1434 1463 0.392998 GGACCATGTAGTGCACCCTG 60.393 60.000 14.63 5.92 0.00 4.45
1543 1573 6.714810 TCAGAACATAACAGCAACCACTATTT 59.285 34.615 0.00 0.00 0.00 1.40
1597 1635 5.283247 CCGCTCGTCGATTATAATGTTCTAC 59.717 44.000 1.78 0.00 41.67 2.59
1892 1931 0.098376 GTACCACTCTGCCGACTACG 59.902 60.000 0.00 0.00 39.43 3.51
1931 1970 8.306313 TCAGCTATAACTGGAATCTTAAGACA 57.694 34.615 7.48 0.52 38.26 3.41
1932 1971 9.601217 TTTCAGCTATAACTGGAATCTTAAGAC 57.399 33.333 7.48 0.00 38.26 3.01
1961 2000 8.918202 TGTTCCTTCAGAATAGCTTTCTTAAA 57.082 30.769 0.00 0.00 36.69 1.52
2017 2056 2.277084 GCGGAAGACAATACCGTTGAT 58.723 47.619 0.00 0.00 46.95 2.57
2062 2101 3.695060 TGAGTAAGCTAAGGAGACCTTCG 59.305 47.826 6.30 2.27 43.57 3.79
2256 2295 0.870393 AAGACACACGAGCTGCAATG 59.130 50.000 1.02 0.00 0.00 2.82
2306 2345 4.825085 GGTGGTTCAAAAGTATCCAACTCA 59.175 41.667 0.00 0.00 37.50 3.41
2396 2435 3.550275 CGTCACACCAAGGTATACAATCG 59.450 47.826 5.01 0.00 0.00 3.34
2411 2450 7.955864 GGAGTTTTATTTACTCAATCGTCACAC 59.044 37.037 0.00 0.00 43.00 3.82
2518 2560 8.886719 TCAACTAGCATCTTAATGACATTTCTG 58.113 33.333 5.89 1.06 34.61 3.02
2666 2708 1.987855 CCGCCTTGGGTCACTCCTA 60.988 63.158 0.00 0.00 36.25 2.94
2811 2853 8.706322 ACAATAAGAGGACTTGGTTAATTTGT 57.294 30.769 0.00 0.00 37.53 2.83
3016 3058 2.169789 CATGCGGCAGAAGTCCTCG 61.170 63.158 9.25 0.00 0.00 4.63
3019 3061 1.503542 CAACATGCGGCAGAAGTCC 59.496 57.895 9.25 0.00 0.00 3.85
3175 3221 5.178623 CCATCTACAAAAACGCAGTCAAGTA 59.821 40.000 0.00 0.00 45.00 2.24
3182 3228 3.425193 GCAAACCATCTACAAAAACGCAG 59.575 43.478 0.00 0.00 0.00 5.18
3184 3230 3.376540 TGCAAACCATCTACAAAAACGC 58.623 40.909 0.00 0.00 0.00 4.84
3329 3836 5.765182 AGTTGAGTCACTTATTTTGGGACAG 59.235 40.000 0.00 0.00 42.39 3.51
3330 3837 5.690865 AGTTGAGTCACTTATTTTGGGACA 58.309 37.500 0.00 0.00 0.00 4.02
3340 3847 9.880157 AACTTTAGTACAAAGTTGAGTCACTTA 57.120 29.630 23.48 0.00 45.58 2.24
3342 3849 9.530633 CTAACTTTAGTACAAAGTTGAGTCACT 57.469 33.333 27.85 13.98 46.41 3.41
3343 3850 9.525409 TCTAACTTTAGTACAAAGTTGAGTCAC 57.475 33.333 27.85 0.00 46.41 3.67
3346 3853 9.880157 TGTTCTAACTTTAGTACAAAGTTGAGT 57.120 29.630 27.85 15.55 46.41 3.41
3390 3897 9.880157 AAGTGACTCAACTTTGTACTAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
3391 3898 8.788325 AAGTGACTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
3427 3934 9.965824 CCAAAATAAATGACTCAACTTTGTACT 57.034 29.630 0.00 0.00 0.00 2.73
3428 3935 9.959749 TCCAAAATAAATGACTCAACTTTGTAC 57.040 29.630 0.00 0.00 0.00 2.90
3430 3937 9.533253 CTTCCAAAATAAATGACTCAACTTTGT 57.467 29.630 0.00 0.00 0.00 2.83
3431 3938 8.981647 CCTTCCAAAATAAATGACTCAACTTTG 58.018 33.333 0.00 0.00 0.00 2.77
3432 3939 8.150296 CCCTTCCAAAATAAATGACTCAACTTT 58.850 33.333 0.00 0.00 0.00 2.66
3433 3940 7.508977 TCCCTTCCAAAATAAATGACTCAACTT 59.491 33.333 0.00 0.00 0.00 2.66
3434 3941 7.010160 TCCCTTCCAAAATAAATGACTCAACT 58.990 34.615 0.00 0.00 0.00 3.16
3435 3942 7.227049 TCCCTTCCAAAATAAATGACTCAAC 57.773 36.000 0.00 0.00 0.00 3.18
3436 3943 6.437162 CCTCCCTTCCAAAATAAATGACTCAA 59.563 38.462 0.00 0.00 0.00 3.02
3437 3944 5.951747 CCTCCCTTCCAAAATAAATGACTCA 59.048 40.000 0.00 0.00 0.00 3.41
3438 3945 5.360999 CCCTCCCTTCCAAAATAAATGACTC 59.639 44.000 0.00 0.00 0.00 3.36
3439 3946 5.016245 TCCCTCCCTTCCAAAATAAATGACT 59.984 40.000 0.00 0.00 0.00 3.41
3440 3947 5.269189 TCCCTCCCTTCCAAAATAAATGAC 58.731 41.667 0.00 0.00 0.00 3.06
3441 3948 5.016245 ACTCCCTCCCTTCCAAAATAAATGA 59.984 40.000 0.00 0.00 0.00 2.57
3442 3949 5.272402 ACTCCCTCCCTTCCAAAATAAATG 58.728 41.667 0.00 0.00 0.00 2.32
3443 3950 5.552430 ACTCCCTCCCTTCCAAAATAAAT 57.448 39.130 0.00 0.00 0.00 1.40
3444 3951 5.554350 AGTACTCCCTCCCTTCCAAAATAAA 59.446 40.000 0.00 0.00 0.00 1.40
3445 3952 5.105853 AGTACTCCCTCCCTTCCAAAATAA 58.894 41.667 0.00 0.00 0.00 1.40
3446 3953 4.706616 AGTACTCCCTCCCTTCCAAAATA 58.293 43.478 0.00 0.00 0.00 1.40
3447 3954 3.542604 AGTACTCCCTCCCTTCCAAAAT 58.457 45.455 0.00 0.00 0.00 1.82
3448 3955 2.999928 AGTACTCCCTCCCTTCCAAAA 58.000 47.619 0.00 0.00 0.00 2.44
3449 3956 2.642807 CAAGTACTCCCTCCCTTCCAAA 59.357 50.000 0.00 0.00 0.00 3.28
3450 3957 2.158066 TCAAGTACTCCCTCCCTTCCAA 60.158 50.000 0.00 0.00 0.00 3.53
3451 3958 1.435563 TCAAGTACTCCCTCCCTTCCA 59.564 52.381 0.00 0.00 0.00 3.53
3452 3959 2.249309 TCAAGTACTCCCTCCCTTCC 57.751 55.000 0.00 0.00 0.00 3.46
3453 3960 5.952347 TTTATCAAGTACTCCCTCCCTTC 57.048 43.478 0.00 0.00 0.00 3.46
3454 3961 6.713731 TTTTTATCAAGTACTCCCTCCCTT 57.286 37.500 0.00 0.00 0.00 3.95
3492 3999 4.566545 TTCACCAACTGCACACAAATAG 57.433 40.909 0.00 0.00 0.00 1.73
3494 4001 4.121317 CAATTCACCAACTGCACACAAAT 58.879 39.130 0.00 0.00 0.00 2.32
3521 4029 8.397906 ACAGAAACACAACAATAATATGGATCG 58.602 33.333 0.00 0.00 0.00 3.69
3524 4032 7.040132 TGCACAGAAACACAACAATAATATGGA 60.040 33.333 0.00 0.00 0.00 3.41
3525 4033 7.089538 TGCACAGAAACACAACAATAATATGG 58.910 34.615 0.00 0.00 0.00 2.74
3532 4040 5.105957 TGTTACTGCACAGAAACACAACAAT 60.106 36.000 4.31 0.00 0.00 2.71
3533 4041 4.216472 TGTTACTGCACAGAAACACAACAA 59.784 37.500 4.31 0.00 0.00 2.83
3535 4043 4.095610 GTGTTACTGCACAGAAACACAAC 58.904 43.478 17.44 0.25 39.07 3.32
3536 4044 3.753797 TGTGTTACTGCACAGAAACACAA 59.246 39.130 20.54 10.44 43.54 3.33
3537 4045 3.339141 TGTGTTACTGCACAGAAACACA 58.661 40.909 19.60 19.60 43.54 3.72
3574 4082 2.006888 CCGCCATAATTCAAGTGACGT 58.993 47.619 0.00 0.00 0.00 4.34
3575 4083 1.268032 GCCGCCATAATTCAAGTGACG 60.268 52.381 0.00 0.00 0.00 4.35
3608 4116 3.518634 GACAGGAGTCAAGACCTCATC 57.481 52.381 0.00 0.00 44.34 2.92
3625 4133 0.952280 AAGAAGACGCGACAGAGACA 59.048 50.000 15.93 0.00 0.00 3.41
3636 4144 0.386858 TTCTCGGCGTGAAGAAGACG 60.387 55.000 19.17 0.00 39.87 4.18
3638 4146 3.861276 TTATTCTCGGCGTGAAGAAGA 57.139 42.857 25.52 13.91 0.00 2.87
3644 4152 0.248012 TGCCTTTATTCTCGGCGTGA 59.752 50.000 6.85 7.30 46.67 4.35
3657 4165 4.760204 ACTTGCTATTCGTAAGTTGCCTTT 59.240 37.500 0.00 0.00 44.71 3.11
3658 4166 4.324267 ACTTGCTATTCGTAAGTTGCCTT 58.676 39.130 0.00 0.00 44.71 4.35
3671 4182 3.757947 AAGGCCCCTAAACTTGCTATT 57.242 42.857 0.00 0.00 0.00 1.73
3679 4190 6.604396 TGCTAGTTAATAAAAGGCCCCTAAAC 59.396 38.462 0.00 0.00 0.00 2.01
3703 4214 3.424300 CTGGCACGGGCATATGTG 58.576 61.111 13.89 0.00 43.71 3.21
3977 4501 1.607467 GTCAAGGGCACAAGGGCAT 60.607 57.895 0.00 0.00 45.66 4.40
4115 4651 1.153369 GCTGAGGCAGACCGCATTA 60.153 57.895 0.00 0.00 45.48 1.90


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

AutoCloner maintained by Alex Coulton.