Multiple sequence alignment - TraesCS3A01G239000

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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 TraesCS3A01G239000 chr3A 100.000 3495 0 0 1 3495 447494288 447497782 0.000000e+00 6455
1 TraesCS3A01G239000 chr3A 87.734 856 92 10 1 848 221723299 221724149 0.000000e+00 987
2 TraesCS3A01G239000 chr3A 87.601 863 88 16 1 852 415913712 415914566 0.000000e+00 983
3 TraesCS3A01G239000 chr3D 98.053 2414 39 4 848 3260 331014735 331017141 0.000000e+00 4191
4 TraesCS3A01G239000 chr3D 96.269 134 5 0 2698 2831 422517661 422517794 1.630000e-53 220
5 TraesCS3A01G239000 chr3D 92.466 146 10 1 3250 3394 405859334 405859189 1.270000e-49 207
6 TraesCS3A01G239000 chr3D 97.222 108 3 0 3388 3495 331017137 331017244 2.140000e-42 183
7 TraesCS3A01G239000 chr3B 97.732 1852 39 3 848 2697 429970358 429972208 0.000000e+00 3184
8 TraesCS3A01G239000 chr3B 94.977 438 13 2 2831 3260 429972191 429972627 0.000000e+00 678
9 TraesCS3A01G239000 chr5A 88.615 852 88 7 1 847 622786552 622785705 0.000000e+00 1027
10 TraesCS3A01G239000 chr5A 87.972 848 94 7 1 847 171034115 171034955 0.000000e+00 994
11 TraesCS3A01G239000 chr1D 88.187 855 91 10 1 850 267967355 267966506 0.000000e+00 1011
12 TraesCS3A01G239000 chr6D 87.953 855 92 7 1 850 66138834 66137986 0.000000e+00 998
13 TraesCS3A01G239000 chr6D 87.515 857 94 7 1 850 66309842 66308992 0.000000e+00 977
14 TraesCS3A01G239000 chr2A 87.558 860 91 12 1 848 227468733 227469588 0.000000e+00 981
15 TraesCS3A01G239000 chr2A 94.815 135 7 0 3260 3394 607520258 607520124 9.830000e-51 211
16 TraesCS3A01G239000 chr2A 92.908 141 10 0 3260 3400 777043166 777043026 4.570000e-49 206
17 TraesCS3A01G239000 chr7A 87.441 852 100 5 1 848 293610104 293609256 0.000000e+00 974
18 TraesCS3A01G239000 chr7A 96.992 133 4 0 2698 2830 83784967 83784835 1.260000e-54 224
19 TraesCS3A01G239000 chr7B 97.761 134 3 0 2698 2831 639088021 639087888 7.540000e-57 231
20 TraesCS3A01G239000 chr4A 97.727 132 3 0 2699 2830 475420656 475420525 9.760000e-56 228
21 TraesCS3A01G239000 chr4A 94.444 144 8 0 3251 3394 227083681 227083824 4.540000e-54 222
22 TraesCS3A01G239000 chr4A 95.620 137 4 2 2697 2831 200090435 200090571 5.870000e-53 219
23 TraesCS3A01G239000 chr7D 97.015 134 4 0 2698 2831 567733384 567733251 3.510000e-55 226
24 TraesCS3A01G239000 chr7D 94.161 137 6 2 3255 3390 564074975 564074840 1.270000e-49 207
25 TraesCS3A01G239000 chr5B 96.992 133 4 0 2698 2830 574956578 574956446 1.260000e-54 224
26 TraesCS3A01G239000 chr2B 96.992 133 4 0 2698 2830 660461555 660461423 1.260000e-54 224
27 TraesCS3A01G239000 chr5D 92.617 149 6 5 3250 3394 396236372 396236519 3.530000e-50 209
28 TraesCS3A01G239000 chr4B 94.161 137 8 0 3254 3390 403331550 403331414 3.530000e-50 209
29 TraesCS3A01G239000 chr1B 93.617 141 6 3 3252 3390 176763756 176763617 1.270000e-49 207
30 TraesCS3A01G239000 chr4D 93.478 138 9 0 3253 3390 294777733 294777870 4.570000e-49 206


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 TraesCS3A01G239000 chr3A 447494288 447497782 3494 False 6455 6455 100.0000 1 3495 1 chr3A.!!$F3 3494
1 TraesCS3A01G239000 chr3A 221723299 221724149 850 False 987 987 87.7340 1 848 1 chr3A.!!$F1 847
2 TraesCS3A01G239000 chr3A 415913712 415914566 854 False 983 983 87.6010 1 852 1 chr3A.!!$F2 851
3 TraesCS3A01G239000 chr3D 331014735 331017244 2509 False 2187 4191 97.6375 848 3495 2 chr3D.!!$F2 2647
4 TraesCS3A01G239000 chr3B 429970358 429972627 2269 False 1931 3184 96.3545 848 3260 2 chr3B.!!$F1 2412
5 TraesCS3A01G239000 chr5A 622785705 622786552 847 True 1027 1027 88.6150 1 847 1 chr5A.!!$R1 846
6 TraesCS3A01G239000 chr5A 171034115 171034955 840 False 994 994 87.9720 1 847 1 chr5A.!!$F1 846
7 TraesCS3A01G239000 chr1D 267966506 267967355 849 True 1011 1011 88.1870 1 850 1 chr1D.!!$R1 849
8 TraesCS3A01G239000 chr6D 66137986 66138834 848 True 998 998 87.9530 1 850 1 chr6D.!!$R1 849
9 TraesCS3A01G239000 chr6D 66308992 66309842 850 True 977 977 87.5150 1 850 1 chr6D.!!$R2 849
10 TraesCS3A01G239000 chr2A 227468733 227469588 855 False 981 981 87.5580 1 848 1 chr2A.!!$F1 847
11 TraesCS3A01G239000 chr7A 293609256 293610104 848 True 974 974 87.4410 1 848 1 chr7A.!!$R2 847

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
418 429 0.318441 GTTGCTTTGCTCCCCCTTTC 59.682 55.0 0.0 0.0 0.0 2.62 F
792 828 0.759436 TCCCGTAAGCCCCTGATCTC 60.759 60.0 0.0 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 1845 1.599047 CTGCTGGTTGTCCGATCCT 59.401 57.895 0.0 0.0 36.3 3.24 R
2677 2714 1.004440 GCCGACAAGCTGACCTTCT 60.004 57.895 0.0 0.0 0.0 2.85 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
28 29 8.208224 TGCAGGGAAGTTTATCTATTCGAATAA 58.792 33.333 18.08 10.10 0.00 1.40
59 60 1.065998 CGGTAAAAGGATGACCCGGAA 60.066 52.381 0.73 0.00 40.87 4.30
68 69 4.035112 AGGATGACCCGGAATTGTACTTA 58.965 43.478 0.73 0.00 40.87 2.24
77 78 6.183360 ACCCGGAATTGTACTTAGACCTTATC 60.183 42.308 0.73 0.00 0.00 1.75
241 242 6.098124 AGCTACTCTCTTCTACATGCTTCAAT 59.902 38.462 0.00 0.00 0.00 2.57
285 286 6.368779 AGTCTTCGATAGGACTAGCTATCT 57.631 41.667 12.43 0.00 40.49 1.98
287 288 6.212791 AGTCTTCGATAGGACTAGCTATCTCT 59.787 42.308 12.43 0.00 40.49 3.10
299 300 9.379791 GGACTAGCTATCTCTCTCTTATTCTAC 57.620 40.741 0.00 0.00 0.00 2.59
313 314 8.622157 TCTCTTATTCTACCATTCTGTAGTTCG 58.378 37.037 0.00 0.00 39.39 3.95
316 317 5.733620 TTCTACCATTCTGTAGTTCGGTT 57.266 39.130 0.00 0.00 39.39 4.44
321 322 4.062293 CCATTCTGTAGTTCGGTTCACAA 58.938 43.478 0.00 0.00 0.00 3.33
385 394 6.456501 AGATCTTTACTTGCGAGTACTTTGT 58.543 36.000 13.64 0.00 38.07 2.83
418 429 0.318441 GTTGCTTTGCTCCCCCTTTC 59.682 55.000 0.00 0.00 0.00 2.62
498 519 1.742880 TCGACGACGACCCCTACTG 60.743 63.158 5.75 0.00 43.81 2.74
499 520 2.037136 CGACGACGACCCCTACTGT 61.037 63.158 0.00 0.00 42.66 3.55
611 643 2.304470 TGTATCCCAGTTTGTGCTAGCA 59.696 45.455 14.93 14.93 0.00 3.49
635 670 7.384932 GCAATCTTATGGCAACTTGTTTAACTT 59.615 33.333 0.00 0.00 37.61 2.66
636 671 9.906660 CAATCTTATGGCAACTTGTTTAACTTA 57.093 29.630 0.00 0.00 37.61 2.24
645 680 7.167468 GGCAACTTGTTTAACTTAATGTCTGTG 59.833 37.037 0.00 0.00 0.00 3.66
646 681 7.700656 GCAACTTGTTTAACTTAATGTCTGTGT 59.299 33.333 0.00 0.00 0.00 3.72
702 737 2.621526 TCGAGCTTATGTATTCGAGCCA 59.378 45.455 0.00 0.00 37.18 4.75
782 818 8.870879 GTTATGTTATGATATCTTCCCGTAAGC 58.129 37.037 3.98 0.00 34.97 3.09
792 828 0.759436 TCCCGTAAGCCCCTGATCTC 60.759 60.000 0.00 0.00 0.00 2.75
807 843 6.154534 CCCCTGATCTCGGTCATACATATTTA 59.845 42.308 0.00 0.00 0.00 1.40
867 904 3.657398 ATGTGCTCAAAGGGATGATGA 57.343 42.857 0.00 0.00 0.00 2.92
897 934 4.331992 AGATGCTCTCACATTTGTCAATCG 59.668 41.667 0.00 0.00 0.00 3.34
908 945 3.454042 TTGTCAATCGCATCTCAAACG 57.546 42.857 0.00 0.00 0.00 3.60
947 984 0.964860 CGCCCAATCAATCACCACCA 60.965 55.000 0.00 0.00 0.00 4.17
995 1032 2.407846 ATCGCACGATACCTGCTCGG 62.408 60.000 3.23 0.00 40.37 4.63
1021 1058 1.068816 CCGTTCGTTCAAAATCCCACC 60.069 52.381 0.00 0.00 0.00 4.61
1808 1845 4.258543 CCTCGGTGAAGCCTAACAATAAA 58.741 43.478 0.00 0.00 34.25 1.40
2119 2156 8.352942 GTTGTGGAGATAATCTGTTTCTTGTTT 58.647 33.333 0.00 0.00 0.00 2.83
2478 2515 2.615447 CAATTACATCACTGCCGCAGAT 59.385 45.455 27.12 8.33 35.18 2.90
2525 2562 3.502211 CCGTTTAGCTTTCTTGATGTGGT 59.498 43.478 0.00 0.00 0.00 4.16
2753 2790 2.041620 AGAAATGTAGGGAAAGGCTGCA 59.958 45.455 0.50 0.00 0.00 4.41
2773 2810 3.244112 GCATACTATAGACCCAAAGCGGT 60.244 47.826 6.78 0.00 39.49 5.68
3083 3128 8.791675 ACATGATACATACTGACTCTGTCTATG 58.208 37.037 0.00 3.23 33.15 2.23
3183 3228 6.118170 ACTCAAGGATAATTGACCACTCATG 58.882 40.000 5.72 0.00 35.40 3.07
3260 3305 3.095163 ATCTGCCAGCCCCCTGAG 61.095 66.667 0.00 0.00 41.77 3.35
3271 3316 2.673523 CCCTGAGGGCCTGTTCAG 59.326 66.667 12.95 12.98 40.35 3.02
3272 3317 2.227036 CCCTGAGGGCCTGTTCAGT 61.227 63.158 12.95 0.00 39.30 3.41
3273 3318 1.763770 CCTGAGGGCCTGTTCAGTT 59.236 57.895 12.95 0.00 39.30 3.16
3274 3319 0.607489 CCTGAGGGCCTGTTCAGTTG 60.607 60.000 12.95 0.00 39.30 3.16
3275 3320 0.397941 CTGAGGGCCTGTTCAGTTGA 59.602 55.000 12.95 0.00 36.82 3.18
3276 3321 0.108585 TGAGGGCCTGTTCAGTTGAC 59.891 55.000 12.95 0.00 0.00 3.18
3277 3322 0.108585 GAGGGCCTGTTCAGTTGACA 59.891 55.000 12.95 0.00 0.00 3.58
3278 3323 0.109342 AGGGCCTGTTCAGTTGACAG 59.891 55.000 4.50 0.00 0.00 3.51
3282 3327 2.638480 CCTGTTCAGTTGACAGGGAA 57.362 50.000 14.03 0.00 45.29 3.97
3283 3328 2.930950 CCTGTTCAGTTGACAGGGAAA 58.069 47.619 14.03 0.00 45.29 3.13
3284 3329 3.287222 CCTGTTCAGTTGACAGGGAAAA 58.713 45.455 14.03 0.00 45.29 2.29
3285 3330 3.891366 CCTGTTCAGTTGACAGGGAAAAT 59.109 43.478 14.03 0.00 45.29 1.82
3286 3331 5.070001 CCTGTTCAGTTGACAGGGAAAATA 58.930 41.667 14.03 0.00 45.29 1.40
3287 3332 5.182001 CCTGTTCAGTTGACAGGGAAAATAG 59.818 44.000 14.03 0.00 45.29 1.73
3288 3333 5.935945 TGTTCAGTTGACAGGGAAAATAGA 58.064 37.500 0.00 0.00 0.00 1.98
3289 3334 6.361433 TGTTCAGTTGACAGGGAAAATAGAA 58.639 36.000 0.00 0.00 0.00 2.10
3290 3335 6.486657 TGTTCAGTTGACAGGGAAAATAGAAG 59.513 38.462 0.00 0.00 0.00 2.85
3291 3336 5.560724 TCAGTTGACAGGGAAAATAGAAGG 58.439 41.667 0.00 0.00 0.00 3.46
3292 3337 4.702131 CAGTTGACAGGGAAAATAGAAGGG 59.298 45.833 0.00 0.00 0.00 3.95
3293 3338 4.354087 AGTTGACAGGGAAAATAGAAGGGT 59.646 41.667 0.00 0.00 0.00 4.34
3294 3339 5.077564 GTTGACAGGGAAAATAGAAGGGTT 58.922 41.667 0.00 0.00 0.00 4.11
3295 3340 5.333566 TGACAGGGAAAATAGAAGGGTTT 57.666 39.130 0.00 0.00 0.00 3.27
3296 3341 5.076873 TGACAGGGAAAATAGAAGGGTTTG 58.923 41.667 0.00 0.00 0.00 2.93
3297 3342 4.416516 ACAGGGAAAATAGAAGGGTTTGG 58.583 43.478 0.00 0.00 0.00 3.28
3298 3343 3.195610 CAGGGAAAATAGAAGGGTTTGGC 59.804 47.826 0.00 0.00 0.00 4.52
3299 3344 3.169908 GGGAAAATAGAAGGGTTTGGCA 58.830 45.455 0.00 0.00 0.00 4.92
3300 3345 3.195610 GGGAAAATAGAAGGGTTTGGCAG 59.804 47.826 0.00 0.00 0.00 4.85
3301 3346 3.195610 GGAAAATAGAAGGGTTTGGCAGG 59.804 47.826 0.00 0.00 0.00 4.85
3302 3347 2.532250 AATAGAAGGGTTTGGCAGGG 57.468 50.000 0.00 0.00 0.00 4.45
3303 3348 1.681229 ATAGAAGGGTTTGGCAGGGA 58.319 50.000 0.00 0.00 0.00 4.20
3304 3349 1.681229 TAGAAGGGTTTGGCAGGGAT 58.319 50.000 0.00 0.00 0.00 3.85
3305 3350 0.786435 AGAAGGGTTTGGCAGGGATT 59.214 50.000 0.00 0.00 0.00 3.01
3306 3351 0.897621 GAAGGGTTTGGCAGGGATTG 59.102 55.000 0.00 0.00 0.00 2.67
3307 3352 0.545071 AAGGGTTTGGCAGGGATTGG 60.545 55.000 0.00 0.00 0.00 3.16
3314 3359 2.605299 GCAGGGATTGGCAGGGAT 59.395 61.111 0.00 0.00 0.00 3.85
3315 3360 1.075748 GCAGGGATTGGCAGGGATT 60.076 57.895 0.00 0.00 0.00 3.01
3316 3361 0.185901 GCAGGGATTGGCAGGGATTA 59.814 55.000 0.00 0.00 0.00 1.75
3317 3362 1.820877 GCAGGGATTGGCAGGGATTAG 60.821 57.143 0.00 0.00 0.00 1.73
3318 3363 1.776667 CAGGGATTGGCAGGGATTAGA 59.223 52.381 0.00 0.00 0.00 2.10
3319 3364 1.777272 AGGGATTGGCAGGGATTAGAC 59.223 52.381 0.00 0.00 0.00 2.59
3320 3365 1.202940 GGGATTGGCAGGGATTAGACC 60.203 57.143 0.00 0.00 0.00 3.85
3331 3376 4.403585 GGGATTAGACCCTGTACAAGTC 57.596 50.000 14.91 14.91 45.90 3.01
3332 3377 3.773119 GGGATTAGACCCTGTACAAGTCA 59.227 47.826 21.55 7.87 45.90 3.41
3333 3378 4.224370 GGGATTAGACCCTGTACAAGTCAA 59.776 45.833 21.55 15.42 45.90 3.18
3334 3379 5.280317 GGGATTAGACCCTGTACAAGTCAAA 60.280 44.000 21.55 10.74 45.90 2.69
3335 3380 6.235664 GGATTAGACCCTGTACAAGTCAAAA 58.764 40.000 21.55 16.53 32.82 2.44
3336 3381 6.148976 GGATTAGACCCTGTACAAGTCAAAAC 59.851 42.308 21.55 12.73 32.82 2.43
3337 3382 3.816994 AGACCCTGTACAAGTCAAAACC 58.183 45.455 21.55 1.66 32.82 3.27
3338 3383 3.458487 AGACCCTGTACAAGTCAAAACCT 59.542 43.478 21.55 3.75 32.82 3.50
3339 3384 3.813724 GACCCTGTACAAGTCAAAACCTC 59.186 47.826 16.92 0.00 0.00 3.85
3340 3385 3.146847 CCCTGTACAAGTCAAAACCTCC 58.853 50.000 0.00 0.00 0.00 4.30
3341 3386 3.181443 CCCTGTACAAGTCAAAACCTCCT 60.181 47.826 0.00 0.00 0.00 3.69
3342 3387 4.065789 CCTGTACAAGTCAAAACCTCCTC 58.934 47.826 0.00 0.00 0.00 3.71
3343 3388 4.065789 CTGTACAAGTCAAAACCTCCTCC 58.934 47.826 0.00 0.00 0.00 4.30
3344 3389 3.456644 TGTACAAGTCAAAACCTCCTCCA 59.543 43.478 0.00 0.00 0.00 3.86
3345 3390 3.662759 ACAAGTCAAAACCTCCTCCAA 57.337 42.857 0.00 0.00 0.00 3.53
3346 3391 4.184649 ACAAGTCAAAACCTCCTCCAAT 57.815 40.909 0.00 0.00 0.00 3.16
3347 3392 4.145052 ACAAGTCAAAACCTCCTCCAATC 58.855 43.478 0.00 0.00 0.00 2.67
3348 3393 3.441500 AGTCAAAACCTCCTCCAATCC 57.558 47.619 0.00 0.00 0.00 3.01
3349 3394 2.716424 AGTCAAAACCTCCTCCAATCCA 59.284 45.455 0.00 0.00 0.00 3.41
3350 3395 2.820197 GTCAAAACCTCCTCCAATCCAC 59.180 50.000 0.00 0.00 0.00 4.02
3351 3396 2.171003 CAAAACCTCCTCCAATCCACC 58.829 52.381 0.00 0.00 0.00 4.61
3352 3397 0.704664 AAACCTCCTCCAATCCACCC 59.295 55.000 0.00 0.00 0.00 4.61
3353 3398 1.214992 AACCTCCTCCAATCCACCCC 61.215 60.000 0.00 0.00 0.00 4.95
3354 3399 1.619363 CCTCCTCCAATCCACCCCA 60.619 63.158 0.00 0.00 0.00 4.96
3355 3400 1.214305 CCTCCTCCAATCCACCCCAA 61.214 60.000 0.00 0.00 0.00 4.12
3356 3401 0.929244 CTCCTCCAATCCACCCCAAT 59.071 55.000 0.00 0.00 0.00 3.16
3357 3402 0.926293 TCCTCCAATCCACCCCAATC 59.074 55.000 0.00 0.00 0.00 2.67
3358 3403 0.106015 CCTCCAATCCACCCCAATCC 60.106 60.000 0.00 0.00 0.00 3.01
3359 3404 0.106015 CTCCAATCCACCCCAATCCC 60.106 60.000 0.00 0.00 0.00 3.85
3360 3405 1.075301 CCAATCCACCCCAATCCCC 60.075 63.158 0.00 0.00 0.00 4.81
3361 3406 1.075301 CAATCCACCCCAATCCCCC 60.075 63.158 0.00 0.00 0.00 5.40
3362 3407 1.230956 AATCCACCCCAATCCCCCT 60.231 57.895 0.00 0.00 0.00 4.79
3363 3408 1.593166 AATCCACCCCAATCCCCCTG 61.593 60.000 0.00 0.00 0.00 4.45
3364 3409 2.823662 ATCCACCCCAATCCCCCTGT 62.824 60.000 0.00 0.00 0.00 4.00
3365 3410 2.360191 CACCCCAATCCCCCTGTG 59.640 66.667 0.00 0.00 0.00 3.66
3366 3411 2.212761 ACCCCAATCCCCCTGTGA 59.787 61.111 0.00 0.00 0.00 3.58
3367 3412 1.930656 ACCCCAATCCCCCTGTGAG 60.931 63.158 0.00 0.00 0.00 3.51
3368 3413 2.693871 CCCCAATCCCCCTGTGAGG 61.694 68.421 0.00 0.00 34.30 3.86
3369 3414 1.619363 CCCAATCCCCCTGTGAGGA 60.619 63.158 0.00 0.00 37.67 3.71
3370 3415 1.639635 CCCAATCCCCCTGTGAGGAG 61.640 65.000 0.00 0.00 37.67 3.69
3371 3416 1.639635 CCAATCCCCCTGTGAGGAGG 61.640 65.000 0.00 0.00 37.67 4.30
3372 3417 0.916358 CAATCCCCCTGTGAGGAGGT 60.916 60.000 0.00 0.00 37.67 3.85
3373 3418 0.916358 AATCCCCCTGTGAGGAGGTG 60.916 60.000 0.00 0.00 37.67 4.00
3374 3419 2.125066 ATCCCCCTGTGAGGAGGTGT 62.125 60.000 0.00 0.00 37.67 4.16
3375 3420 1.080354 CCCCCTGTGAGGAGGTGTA 59.920 63.158 0.00 0.00 37.67 2.90
3376 3421 0.546747 CCCCCTGTGAGGAGGTGTAA 60.547 60.000 0.00 0.00 37.67 2.41
3377 3422 0.613777 CCCCTGTGAGGAGGTGTAAC 59.386 60.000 0.00 0.00 37.67 2.50
3378 3423 0.613777 CCCTGTGAGGAGGTGTAACC 59.386 60.000 0.00 0.00 45.56 2.85
3390 3435 2.681152 GTGTAACCGAACAAAGCCTG 57.319 50.000 0.00 0.00 0.00 4.85
3391 3436 2.215196 GTGTAACCGAACAAAGCCTGA 58.785 47.619 0.00 0.00 0.00 3.86
3410 3455 5.121811 CCTGAAGTAGTTCCAGGATCAATG 58.878 45.833 17.34 0.00 34.98 2.82
3420 3465 3.055167 TCCAGGATCAATGTTCATCGTGT 60.055 43.478 0.00 0.00 34.48 4.49
3479 3524 1.262417 TCATTCAGGGTGTACGCAGA 58.738 50.000 8.97 0.09 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 6.017192 TCTGGTTCTAGTTGTGATAAGGTCT 58.983 40.000 0.00 0.00 0.00 3.85
115 116 2.290071 CCGGGTTGTATCTGGAACTTGT 60.290 50.000 0.00 0.00 32.49 3.16
241 242 0.107703 CGCTTCTGGCAACCTCCATA 60.108 55.000 0.00 0.00 41.91 2.74
285 286 9.702253 AACTACAGAATGGTAGAATAAGAGAGA 57.298 33.333 7.30 0.00 42.68 3.10
287 288 8.622157 CGAACTACAGAATGGTAGAATAAGAGA 58.378 37.037 7.30 0.00 42.68 3.10
299 300 3.659786 TGTGAACCGAACTACAGAATGG 58.340 45.455 0.00 0.00 43.62 3.16
313 314 6.827586 TGAAATGGGTAGTATTTGTGAACC 57.172 37.500 0.00 0.00 0.00 3.62
316 317 8.821686 ATCAATGAAATGGGTAGTATTTGTGA 57.178 30.769 0.00 0.00 0.00 3.58
321 322 9.881773 ATTGGTATCAATGAAATGGGTAGTATT 57.118 29.630 0.00 0.00 41.62 1.89
355 364 5.403246 ACTCGCAAGTAAAGATCTACACTG 58.597 41.667 9.31 2.74 32.59 3.66
366 375 7.149973 ACTCATACAAAGTACTCGCAAGTAAA 58.850 34.615 0.00 0.00 39.66 2.01
369 378 5.135508 ACTCATACAAAGTACTCGCAAGT 57.864 39.130 0.00 0.00 39.66 3.16
385 394 4.242475 CAAAGCAACCGTGAGTACTCATA 58.758 43.478 27.54 3.64 42.18 2.15
418 429 3.433740 GCAACCAGGTATAGAAAGGGAGG 60.434 52.174 0.00 0.00 0.00 4.30
498 519 1.028130 GTAGTAGGCACCCTCGGTAC 58.972 60.000 0.00 0.00 34.61 3.34
499 520 0.921896 AGTAGTAGGCACCCTCGGTA 59.078 55.000 0.00 0.00 34.61 4.02
635 670 9.836864 AGCAATAATATCTGAACACAGACATTA 57.163 29.630 11.50 11.50 41.25 1.90
636 671 8.743085 AGCAATAATATCTGAACACAGACATT 57.257 30.769 8.42 8.42 42.34 2.71
702 737 1.978455 TTACAAGCCGGGGCATCGAT 61.978 55.000 12.97 0.00 44.88 3.59
707 742 3.482436 CTTTATATTACAAGCCGGGGCA 58.518 45.455 12.97 0.00 44.88 5.36
759 795 6.407202 GGCTTACGGGAAGATATCATAACAT 58.593 40.000 3.58 0.00 37.33 2.71
764 800 2.572104 GGGGCTTACGGGAAGATATCAT 59.428 50.000 3.58 0.00 37.33 2.45
779 815 0.692419 ATGACCGAGATCAGGGGCTT 60.692 55.000 9.11 0.60 30.44 4.35
782 818 1.704641 TGTATGACCGAGATCAGGGG 58.295 55.000 11.27 4.03 30.46 4.79
826 862 2.530701 TGTGACGCCCCCAATTTAAAT 58.469 42.857 0.00 0.00 0.00 1.40
827 863 1.996798 TGTGACGCCCCCAATTTAAA 58.003 45.000 0.00 0.00 0.00 1.52
834 870 2.282110 CACATTGTGACGCCCCCA 60.282 61.111 11.45 0.00 35.23 4.96
897 934 2.099062 CTGCGCCGTTTGAGATGC 59.901 61.111 4.18 0.00 0.00 3.91
947 984 4.273318 GTTATGAAGGAATCCTGCCAACT 58.727 43.478 0.90 0.00 32.13 3.16
958 995 3.802329 GCGATCCGATGGTTATGAAGGAA 60.802 47.826 0.00 0.00 0.00 3.36
995 1032 3.425758 GGATTTTGAACGAACGGTGGATC 60.426 47.826 0.00 0.00 0.00 3.36
1021 1058 3.823330 CCCCCTTCGGTCGTCTCG 61.823 72.222 0.00 0.00 0.00 4.04
1808 1845 1.599047 CTGCTGGTTGTCCGATCCT 59.401 57.895 0.00 0.00 36.30 3.24
2119 2156 6.858993 GCGTCAACAAACTAATTATCCACAAA 59.141 34.615 0.00 0.00 0.00 2.83
2478 2515 7.870445 GGGACATGCATTTACTAACTTCAAAAA 59.130 33.333 0.00 0.00 0.00 1.94
2677 2714 1.004440 GCCGACAAGCTGACCTTCT 60.004 57.895 0.00 0.00 0.00 2.85
2773 2810 2.284405 GTCCGGGGAAGGGTCTGA 60.284 66.667 0.00 0.00 0.00 3.27
2882 2919 9.362539 CAGCATTTCAGCAAGTAAATAAAGAAT 57.637 29.630 0.00 0.00 36.85 2.40
3023 3068 7.384932 ACAAGCTAAAGTTAAATGATGTTTGCC 59.615 33.333 0.00 0.00 0.00 4.52
3083 3128 8.572185 GTTTATAGGCCACTTAGTAGTAGTACC 58.428 40.741 5.01 0.00 31.96 3.34
3260 3305 0.890996 CCTGTCAACTGAACAGGCCC 60.891 60.000 9.20 0.00 43.58 5.80
3261 3306 2.633860 CCTGTCAACTGAACAGGCC 58.366 57.895 9.20 0.00 43.58 5.19
3264 3309 5.997746 TCTATTTTCCCTGTCAACTGAACAG 59.002 40.000 0.00 0.00 0.00 3.16
3265 3310 5.935945 TCTATTTTCCCTGTCAACTGAACA 58.064 37.500 0.00 0.00 0.00 3.18
3266 3311 6.072452 CCTTCTATTTTCCCTGTCAACTGAAC 60.072 42.308 0.00 0.00 0.00 3.18
3267 3312 6.003950 CCTTCTATTTTCCCTGTCAACTGAA 58.996 40.000 0.00 0.00 0.00 3.02
3268 3313 5.514834 CCCTTCTATTTTCCCTGTCAACTGA 60.515 44.000 0.00 0.00 0.00 3.41
3269 3314 4.702131 CCCTTCTATTTTCCCTGTCAACTG 59.298 45.833 0.00 0.00 0.00 3.16
3270 3315 4.354087 ACCCTTCTATTTTCCCTGTCAACT 59.646 41.667 0.00 0.00 0.00 3.16
3271 3316 4.663334 ACCCTTCTATTTTCCCTGTCAAC 58.337 43.478 0.00 0.00 0.00 3.18
3272 3317 5.333566 AACCCTTCTATTTTCCCTGTCAA 57.666 39.130 0.00 0.00 0.00 3.18
3273 3318 5.076873 CAAACCCTTCTATTTTCCCTGTCA 58.923 41.667 0.00 0.00 0.00 3.58
3274 3319 4.462834 CCAAACCCTTCTATTTTCCCTGTC 59.537 45.833 0.00 0.00 0.00 3.51
3275 3320 4.416516 CCAAACCCTTCTATTTTCCCTGT 58.583 43.478 0.00 0.00 0.00 4.00
3276 3321 3.195610 GCCAAACCCTTCTATTTTCCCTG 59.804 47.826 0.00 0.00 0.00 4.45
3277 3322 3.181412 TGCCAAACCCTTCTATTTTCCCT 60.181 43.478 0.00 0.00 0.00 4.20
3278 3323 3.169908 TGCCAAACCCTTCTATTTTCCC 58.830 45.455 0.00 0.00 0.00 3.97
3279 3324 3.195610 CCTGCCAAACCCTTCTATTTTCC 59.804 47.826 0.00 0.00 0.00 3.13
3280 3325 3.195610 CCCTGCCAAACCCTTCTATTTTC 59.804 47.826 0.00 0.00 0.00 2.29
3281 3326 3.173151 CCCTGCCAAACCCTTCTATTTT 58.827 45.455 0.00 0.00 0.00 1.82
3282 3327 2.381961 TCCCTGCCAAACCCTTCTATTT 59.618 45.455 0.00 0.00 0.00 1.40
3283 3328 2.000048 TCCCTGCCAAACCCTTCTATT 59.000 47.619 0.00 0.00 0.00 1.73
3284 3329 1.681229 TCCCTGCCAAACCCTTCTAT 58.319 50.000 0.00 0.00 0.00 1.98
3285 3330 1.681229 ATCCCTGCCAAACCCTTCTA 58.319 50.000 0.00 0.00 0.00 2.10
3286 3331 0.786435 AATCCCTGCCAAACCCTTCT 59.214 50.000 0.00 0.00 0.00 2.85
3287 3332 0.897621 CAATCCCTGCCAAACCCTTC 59.102 55.000 0.00 0.00 0.00 3.46
3288 3333 0.545071 CCAATCCCTGCCAAACCCTT 60.545 55.000 0.00 0.00 0.00 3.95
3289 3334 1.079073 CCAATCCCTGCCAAACCCT 59.921 57.895 0.00 0.00 0.00 4.34
3290 3335 2.659063 GCCAATCCCTGCCAAACCC 61.659 63.158 0.00 0.00 0.00 4.11
3291 3336 1.891722 CTGCCAATCCCTGCCAAACC 61.892 60.000 0.00 0.00 0.00 3.27
3292 3337 1.593265 CTGCCAATCCCTGCCAAAC 59.407 57.895 0.00 0.00 0.00 2.93
3293 3338 1.610086 CCTGCCAATCCCTGCCAAA 60.610 57.895 0.00 0.00 0.00 3.28
3294 3339 2.037687 CCTGCCAATCCCTGCCAA 59.962 61.111 0.00 0.00 0.00 4.52
3295 3340 4.064768 CCCTGCCAATCCCTGCCA 62.065 66.667 0.00 0.00 0.00 4.92
3296 3341 2.594365 AATCCCTGCCAATCCCTGCC 62.594 60.000 0.00 0.00 0.00 4.85
3297 3342 0.185901 TAATCCCTGCCAATCCCTGC 59.814 55.000 0.00 0.00 0.00 4.85
3298 3343 1.776667 TCTAATCCCTGCCAATCCCTG 59.223 52.381 0.00 0.00 0.00 4.45
3299 3344 1.777272 GTCTAATCCCTGCCAATCCCT 59.223 52.381 0.00 0.00 0.00 4.20
3300 3345 1.202940 GGTCTAATCCCTGCCAATCCC 60.203 57.143 0.00 0.00 0.00 3.85
3301 3346 1.202940 GGGTCTAATCCCTGCCAATCC 60.203 57.143 0.00 0.00 43.85 3.01
3302 3347 2.278332 GGGTCTAATCCCTGCCAATC 57.722 55.000 0.00 0.00 43.85 2.67
3311 3356 5.416271 TTGACTTGTACAGGGTCTAATCC 57.584 43.478 22.56 5.81 0.00 3.01
3312 3357 6.148976 GGTTTTGACTTGTACAGGGTCTAATC 59.851 42.308 22.56 19.62 0.00 1.75
3313 3358 6.002082 GGTTTTGACTTGTACAGGGTCTAAT 58.998 40.000 22.56 0.00 0.00 1.73
3314 3359 5.131475 AGGTTTTGACTTGTACAGGGTCTAA 59.869 40.000 22.56 19.69 0.00 2.10
3315 3360 4.657039 AGGTTTTGACTTGTACAGGGTCTA 59.343 41.667 22.56 16.41 0.00 2.59
3316 3361 3.458487 AGGTTTTGACTTGTACAGGGTCT 59.542 43.478 22.56 0.51 0.00 3.85
3317 3362 3.813724 GAGGTTTTGACTTGTACAGGGTC 59.186 47.826 18.25 18.25 0.00 4.46
3318 3363 3.434596 GGAGGTTTTGACTTGTACAGGGT 60.435 47.826 10.04 6.60 0.00 4.34
3319 3364 3.146847 GGAGGTTTTGACTTGTACAGGG 58.853 50.000 10.04 3.34 0.00 4.45
3320 3365 4.065789 GAGGAGGTTTTGACTTGTACAGG 58.934 47.826 2.98 2.98 0.00 4.00
3321 3366 4.065789 GGAGGAGGTTTTGACTTGTACAG 58.934 47.826 0.00 0.00 0.00 2.74
3322 3367 3.456644 TGGAGGAGGTTTTGACTTGTACA 59.543 43.478 0.00 0.00 0.00 2.90
3323 3368 4.081322 TGGAGGAGGTTTTGACTTGTAC 57.919 45.455 0.00 0.00 0.00 2.90
3324 3369 4.781775 TTGGAGGAGGTTTTGACTTGTA 57.218 40.909 0.00 0.00 0.00 2.41
3325 3370 3.662759 TTGGAGGAGGTTTTGACTTGT 57.337 42.857 0.00 0.00 0.00 3.16
3326 3371 3.507622 GGATTGGAGGAGGTTTTGACTTG 59.492 47.826 0.00 0.00 0.00 3.16
3327 3372 3.140144 TGGATTGGAGGAGGTTTTGACTT 59.860 43.478 0.00 0.00 0.00 3.01
3328 3373 2.716424 TGGATTGGAGGAGGTTTTGACT 59.284 45.455 0.00 0.00 0.00 3.41
3329 3374 2.820197 GTGGATTGGAGGAGGTTTTGAC 59.180 50.000 0.00 0.00 0.00 3.18
3330 3375 2.225017 GGTGGATTGGAGGAGGTTTTGA 60.225 50.000 0.00 0.00 0.00 2.69
3331 3376 2.171003 GGTGGATTGGAGGAGGTTTTG 58.829 52.381 0.00 0.00 0.00 2.44
3332 3377 1.077169 GGGTGGATTGGAGGAGGTTTT 59.923 52.381 0.00 0.00 0.00 2.43
3333 3378 0.704664 GGGTGGATTGGAGGAGGTTT 59.295 55.000 0.00 0.00 0.00 3.27
3334 3379 1.214992 GGGGTGGATTGGAGGAGGTT 61.215 60.000 0.00 0.00 0.00 3.50
3335 3380 1.619669 GGGGTGGATTGGAGGAGGT 60.620 63.158 0.00 0.00 0.00 3.85
3336 3381 1.214305 TTGGGGTGGATTGGAGGAGG 61.214 60.000 0.00 0.00 0.00 4.30
3337 3382 0.929244 ATTGGGGTGGATTGGAGGAG 59.071 55.000 0.00 0.00 0.00 3.69
3338 3383 0.926293 GATTGGGGTGGATTGGAGGA 59.074 55.000 0.00 0.00 0.00 3.71
3339 3384 0.106015 GGATTGGGGTGGATTGGAGG 60.106 60.000 0.00 0.00 0.00 4.30
3340 3385 0.106015 GGGATTGGGGTGGATTGGAG 60.106 60.000 0.00 0.00 0.00 3.86
3341 3386 1.589399 GGGGATTGGGGTGGATTGGA 61.589 60.000 0.00 0.00 0.00 3.53
3342 3387 1.075301 GGGGATTGGGGTGGATTGG 60.075 63.158 0.00 0.00 0.00 3.16
3343 3388 1.075301 GGGGGATTGGGGTGGATTG 60.075 63.158 0.00 0.00 0.00 2.67
3344 3389 1.230956 AGGGGGATTGGGGTGGATT 60.231 57.895 0.00 0.00 0.00 3.01
3345 3390 2.014550 CAGGGGGATTGGGGTGGAT 61.015 63.158 0.00 0.00 0.00 3.41
3346 3391 2.616893 CAGGGGGATTGGGGTGGA 60.617 66.667 0.00 0.00 0.00 4.02
3347 3392 2.946650 ACAGGGGGATTGGGGTGG 60.947 66.667 0.00 0.00 0.00 4.61
3348 3393 2.215451 CTCACAGGGGGATTGGGGTG 62.215 65.000 0.00 0.00 0.00 4.61
3349 3394 1.930656 CTCACAGGGGGATTGGGGT 60.931 63.158 0.00 0.00 0.00 4.95
3350 3395 2.693871 CCTCACAGGGGGATTGGGG 61.694 68.421 0.00 0.00 0.00 4.96
3351 3396 1.619363 TCCTCACAGGGGGATTGGG 60.619 63.158 0.00 0.00 35.59 4.12
3352 3397 1.918253 CTCCTCACAGGGGGATTGG 59.082 63.158 0.00 0.00 35.59 3.16
3358 3403 0.613777 GTTACACCTCCTCACAGGGG 59.386 60.000 0.00 0.00 43.56 4.79
3359 3404 0.613777 GGTTACACCTCCTCACAGGG 59.386 60.000 0.00 0.00 37.96 4.45
3360 3405 0.246635 CGGTTACACCTCCTCACAGG 59.753 60.000 0.00 0.00 35.66 4.00
3361 3406 1.254026 TCGGTTACACCTCCTCACAG 58.746 55.000 0.00 0.00 35.66 3.66
3362 3407 1.342174 GTTCGGTTACACCTCCTCACA 59.658 52.381 0.00 0.00 35.66 3.58
3363 3408 1.342174 TGTTCGGTTACACCTCCTCAC 59.658 52.381 0.00 0.00 35.66 3.51
3364 3409 1.707106 TGTTCGGTTACACCTCCTCA 58.293 50.000 0.00 0.00 35.66 3.86
3365 3410 2.825861 TTGTTCGGTTACACCTCCTC 57.174 50.000 0.00 0.00 35.66 3.71
3366 3411 2.809299 GCTTTGTTCGGTTACACCTCCT 60.809 50.000 0.00 0.00 35.66 3.69
3367 3412 1.534163 GCTTTGTTCGGTTACACCTCC 59.466 52.381 0.00 0.00 35.66 4.30
3368 3413 1.534163 GGCTTTGTTCGGTTACACCTC 59.466 52.381 0.00 0.00 35.66 3.85
3369 3414 1.142262 AGGCTTTGTTCGGTTACACCT 59.858 47.619 0.00 0.00 35.66 4.00
3370 3415 1.265905 CAGGCTTTGTTCGGTTACACC 59.734 52.381 0.00 0.00 34.05 4.16
3371 3416 2.215196 TCAGGCTTTGTTCGGTTACAC 58.785 47.619 0.00 0.00 0.00 2.90
3372 3417 2.623878 TCAGGCTTTGTTCGGTTACA 57.376 45.000 0.00 0.00 0.00 2.41
3373 3418 2.876550 ACTTCAGGCTTTGTTCGGTTAC 59.123 45.455 0.00 0.00 0.00 2.50
3374 3419 3.202829 ACTTCAGGCTTTGTTCGGTTA 57.797 42.857 0.00 0.00 0.00 2.85
3375 3420 2.052782 ACTTCAGGCTTTGTTCGGTT 57.947 45.000 0.00 0.00 0.00 4.44
3376 3421 2.104281 ACTACTTCAGGCTTTGTTCGGT 59.896 45.455 0.00 0.00 0.00 4.69
3377 3422 2.767505 ACTACTTCAGGCTTTGTTCGG 58.232 47.619 0.00 0.00 0.00 4.30
3378 3423 3.186613 GGAACTACTTCAGGCTTTGTTCG 59.813 47.826 5.56 0.00 34.83 3.95
3379 3424 4.134563 TGGAACTACTTCAGGCTTTGTTC 58.865 43.478 3.60 3.60 33.70 3.18
3380 3425 4.137543 CTGGAACTACTTCAGGCTTTGTT 58.862 43.478 0.00 0.00 0.00 2.83
3381 3426 3.496870 CCTGGAACTACTTCAGGCTTTGT 60.497 47.826 0.00 0.00 0.00 2.83
3382 3427 3.077359 CCTGGAACTACTTCAGGCTTTG 58.923 50.000 0.00 0.00 0.00 2.77
3383 3428 2.979678 TCCTGGAACTACTTCAGGCTTT 59.020 45.455 0.00 0.00 33.32 3.51
3384 3429 2.621070 TCCTGGAACTACTTCAGGCTT 58.379 47.619 0.00 0.00 33.32 4.35
3385 3430 2.327325 TCCTGGAACTACTTCAGGCT 57.673 50.000 0.00 0.00 33.32 4.58
3386 3431 2.501723 TGATCCTGGAACTACTTCAGGC 59.498 50.000 0.00 0.00 33.32 4.85
3387 3432 4.826274 TTGATCCTGGAACTACTTCAGG 57.174 45.455 0.00 0.00 0.00 3.86
3388 3433 5.738909 ACATTGATCCTGGAACTACTTCAG 58.261 41.667 0.00 0.00 0.00 3.02
3389 3434 5.762179 ACATTGATCCTGGAACTACTTCA 57.238 39.130 0.00 0.00 0.00 3.02
3390 3435 6.173339 TGAACATTGATCCTGGAACTACTTC 58.827 40.000 0.00 1.26 0.00 3.01
3391 3436 6.126863 TGAACATTGATCCTGGAACTACTT 57.873 37.500 0.00 0.00 0.00 2.24
3410 3455 3.921021 CCAGTCTAAGACACACGATGAAC 59.079 47.826 0.00 0.00 34.60 3.18
3420 3465 3.072476 CAGGGGAAAACCAGTCTAAGACA 59.928 47.826 0.00 0.00 42.91 3.41


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

AutoCloner maintained by Alex Coulton.