Multiple sequence alignment - TraesCS7B01G035900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G035900 chr7B 100.000 5338 0 0 1 5338 34826053 34820716 0.000000e+00 9858
1 TraesCS7B01G035900 chr7B 80.373 1233 166 42 2773 3960 34498925 34497724 0.000000e+00 867
2 TraesCS7B01G035900 chr7B 79.160 1238 166 53 2773 3960 34517953 34516758 0.000000e+00 773
3 TraesCS7B01G035900 chr7B 79.749 716 90 33 3265 3952 34516075 34515387 8.100000e-128 468
4 TraesCS7B01G035900 chr7B 81.863 408 38 17 3999 4400 34516821 34516444 1.440000e-80 311
5 TraesCS7B01G035900 chr7B 80.244 410 43 18 3999 4400 34497787 34497408 1.890000e-69 274
6 TraesCS7B01G035900 chr7B 92.174 115 9 0 3897 4011 34822106 34821992 4.280000e-36 163
7 TraesCS7B01G035900 chr7B 92.174 115 9 0 3948 4062 34822157 34822043 4.280000e-36 163
8 TraesCS7B01G035900 chr7D 94.687 2748 105 18 1649 4376 85209418 85206692 0.000000e+00 4228
9 TraesCS7B01G035900 chr7D 97.078 1369 39 1 284 1651 85210827 85209459 0.000000e+00 2305
10 TraesCS7B01G035900 chr7D 89.913 922 83 6 4426 5338 604359294 604360214 0.000000e+00 1179
11 TraesCS7B01G035900 chr7D 82.007 817 115 19 2773 3572 84804898 84804097 0.000000e+00 665
12 TraesCS7B01G035900 chr7D 87.196 453 45 8 3 450 85211134 85210690 2.220000e-138 503
13 TraesCS7B01G035900 chr7D 81.865 386 37 12 3999 4375 84803423 84803062 1.450000e-75 294
14 TraesCS7B01G035900 chr7A 90.656 1509 90 26 2573 4061 86229476 86227999 0.000000e+00 1958
15 TraesCS7B01G035900 chr7A 92.926 1032 66 3 621 1651 86231379 86230354 0.000000e+00 1495
16 TraesCS7B01G035900 chr7A 92.190 653 35 10 1909 2545 86230114 86229462 0.000000e+00 909
17 TraesCS7B01G035900 chr7A 89.442 502 37 9 3905 4400 86228104 86227613 2.110000e-173 619
18 TraesCS7B01G035900 chr7A 87.004 454 50 7 1 450 86231867 86231419 2.220000e-138 503
19 TraesCS7B01G035900 chr7A 77.472 617 84 29 3381 3960 85965697 85965099 8.630000e-83 318
20 TraesCS7B01G035900 chr7A 92.857 210 12 3 1649 1858 86230313 86230107 8.690000e-78 302
21 TraesCS7B01G035900 chr7A 81.016 374 30 17 4007 4376 85965154 85964818 5.300000e-65 259
22 TraesCS7B01G035900 chr7A 92.982 114 8 0 3948 4061 86228163 86228050 3.310000e-37 167
23 TraesCS7B01G035900 chr7A 94.393 107 6 0 3905 4011 86228053 86227947 1.190000e-36 165
24 TraesCS7B01G035900 chr1D 89.979 938 86 5 4409 5338 341843754 341844691 0.000000e+00 1205
25 TraesCS7B01G035900 chr1D 92.442 172 11 2 455 625 463382071 463381901 1.490000e-60 244
26 TraesCS7B01G035900 chr2B 89.798 941 88 5 4406 5338 782157700 782158640 0.000000e+00 1199
27 TraesCS7B01G035900 chr2D 90.294 917 81 6 4426 5338 605295309 605294397 0.000000e+00 1194
28 TraesCS7B01G035900 chr2D 92.899 169 11 1 457 624 611551049 611551217 1.490000e-60 244
29 TraesCS7B01G035900 chr2D 91.379 174 15 0 453 626 87407531 87407358 6.910000e-59 239
30 TraesCS7B01G035900 chr5D 89.479 941 88 8 4407 5338 402696087 402695149 0.000000e+00 1179
31 TraesCS7B01G035900 chr6B 89.434 937 89 7 4409 5336 701353486 701352551 0.000000e+00 1173
32 TraesCS7B01G035900 chr3D 89.967 917 81 9 4426 5338 22038454 22037545 0.000000e+00 1173
33 TraesCS7B01G035900 chr3D 92.308 169 12 1 452 620 537154696 537154863 6.910000e-59 239
34 TraesCS7B01G035900 chr3D 90.805 174 16 0 453 626 459077263 459077436 3.210000e-57 233
35 TraesCS7B01G035900 chr6D 89.267 941 89 8 4408 5338 390489811 390490749 0.000000e+00 1168
36 TraesCS7B01G035900 chr6D 93.293 164 10 1 459 621 65394436 65394273 1.920000e-59 241
37 TraesCS7B01G035900 chrUn 88.995 945 93 8 4403 5338 50350155 50349213 0.000000e+00 1158
38 TraesCS7B01G035900 chr4A 93.252 163 11 0 459 621 517406632 517406470 1.920000e-59 241
39 TraesCS7B01G035900 chr5A 92.216 167 11 2 459 624 369191145 369191310 8.940000e-58 235


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 TraesCS7B01G035900 chr7B 34820716 34826053 5337 True 9858.000000 9858 100.000000 1 5338 1 chr7B.!!$R1 5337
1 TraesCS7B01G035900 chr7B 34497408 34498925 1517 True 570.500000 867 80.308500 2773 4400 2 chr7B.!!$R2 1627
2 TraesCS7B01G035900 chr7B 34515387 34517953 2566 True 517.333333 773 80.257333 2773 4400 3 chr7B.!!$R3 1627
3 TraesCS7B01G035900 chr7D 85206692 85211134 4442 True 2345.333333 4228 92.987000 3 4376 3 chr7D.!!$R2 4373
4 TraesCS7B01G035900 chr7D 604359294 604360214 920 False 1179.000000 1179 89.913000 4426 5338 1 chr7D.!!$F1 912
5 TraesCS7B01G035900 chr7D 84803062 84804898 1836 True 479.500000 665 81.936000 2773 4375 2 chr7D.!!$R1 1602
6 TraesCS7B01G035900 chr7A 86227613 86231867 4254 True 764.750000 1958 91.556250 1 4400 8 chr7A.!!$R2 4399
7 TraesCS7B01G035900 chr7A 85964818 85965697 879 True 288.500000 318 79.244000 3381 4376 2 chr7A.!!$R1 995
8 TraesCS7B01G035900 chr1D 341843754 341844691 937 False 1205.000000 1205 89.979000 4409 5338 1 chr1D.!!$F1 929
9 TraesCS7B01G035900 chr2B 782157700 782158640 940 False 1199.000000 1199 89.798000 4406 5338 1 chr2B.!!$F1 932
10 TraesCS7B01G035900 chr2D 605294397 605295309 912 True 1194.000000 1194 90.294000 4426 5338 1 chr2D.!!$R2 912
11 TraesCS7B01G035900 chr5D 402695149 402696087 938 True 1179.000000 1179 89.479000 4407 5338 1 chr5D.!!$R1 931
12 TraesCS7B01G035900 chr6B 701352551 701353486 935 True 1173.000000 1173 89.434000 4409 5336 1 chr6B.!!$R1 927
13 TraesCS7B01G035900 chr3D 22037545 22038454 909 True 1173.000000 1173 89.967000 4426 5338 1 chr3D.!!$R1 912
14 TraesCS7B01G035900 chr6D 390489811 390490749 938 False 1168.000000 1168 89.267000 4408 5338 1 chr6D.!!$F1 930
15 TraesCS7B01G035900 chrUn 50349213 50350155 942 True 1158.000000 1158 88.995000 4403 5338 1 chrUn.!!$R1 935

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
246 249 1.047002 TCCAAACATGGCCAACTTGG 58.953 50.000 26.71 26.71 41.55 3.61 F
1097 1159 1.956636 GCAGCCAGAACCCATCATTGA 60.957 52.381 0.00 0.00 0.00 2.57 F
1110 1172 1.077501 CATTGACGCCCACCCAGAT 60.078 57.895 0.00 0.00 0.00 2.90 F
1113 1175 1.561769 TTGACGCCCACCCAGATGAT 61.562 55.000 0.00 0.00 0.00 2.45 F
1924 2029 1.606668 GTGTGTTGGAATTCCTCGCAA 59.393 47.619 25.81 12.58 34.82 4.85 F
3544 3728 1.612462 CCTCTGATTGCAGCTTCACCA 60.612 52.381 0.00 0.00 42.01 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1106 1168 0.107508 ACCTTCGTGGGCATCATCTG 60.108 55.000 2.69 0.00 41.11 2.90 R
1905 2010 1.974265 TTGCGAGGAATTCCAACACA 58.026 45.000 26.22 15.88 38.89 3.72 R
2857 2995 3.274281 AAAACAGGAAATGTGGGGGAT 57.726 42.857 0.00 0.00 43.00 3.85 R
2953 3094 4.855340 TCCTGAAACCATGGATTCCTTAC 58.145 43.478 26.67 7.68 0.00 2.34 R
3891 4459 0.895559 CCTTCCAAAGACCACCTGCC 60.896 60.000 0.00 0.00 0.00 4.85 R
4485 5215 0.179134 CTCACGAACCGGGACTGATC 60.179 60.000 6.32 0.00 32.99 2.92 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
104 107 4.555262 CATTTTTATCCACGCCTTGTTGT 58.445 39.130 0.00 0.00 0.00 3.32
118 121 2.565046 TGTTGTCATGAGGATGCACA 57.435 45.000 0.00 0.00 0.00 4.57
134 137 9.455847 GAGGATGCACAATTACTATGAAAAATC 57.544 33.333 0.00 0.00 0.00 2.17
135 138 8.416329 AGGATGCACAATTACTATGAAAAATCC 58.584 33.333 0.00 0.00 0.00 3.01
216 219 2.804440 ACCCCTCTAACCTATCCCTCAT 59.196 50.000 0.00 0.00 0.00 2.90
217 220 3.177228 CCCCTCTAACCTATCCCTCATG 58.823 54.545 0.00 0.00 0.00 3.07
246 249 1.047002 TCCAAACATGGCCAACTTGG 58.953 50.000 26.71 26.71 41.55 3.61
454 515 4.475051 TTGCCATCTTTGGATTTGGATG 57.525 40.909 0.00 0.00 46.92 3.51
484 545 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
523 584 7.118245 CCACTACGAACTACATACGGATGTATA 59.882 40.741 20.64 9.08 45.42 1.47
563 624 8.682936 AGTGTTGATTCACTCATTTTACTTCT 57.317 30.769 0.00 0.00 44.07 2.85
926 988 5.904362 AAAGCTCTGGGTTTGTTCATATC 57.096 39.130 0.00 0.00 40.95 1.63
934 996 5.996644 TGGGTTTGTTCATATCTTCGGTAT 58.003 37.500 0.00 0.00 0.00 2.73
989 1051 5.707242 TTTCTGGTTGTTGTTGTTGTGTA 57.293 34.783 0.00 0.00 0.00 2.90
1004 1066 3.981071 TGTGTAGAGAGGTGAAATGGG 57.019 47.619 0.00 0.00 0.00 4.00
1077 1139 2.176273 CAAGAGCCCGCTTCATCCG 61.176 63.158 0.00 0.00 0.00 4.18
1084 1146 3.570638 CGCTTCATCCGCAGCCAG 61.571 66.667 0.00 0.00 31.82 4.85
1097 1159 1.956636 GCAGCCAGAACCCATCATTGA 60.957 52.381 0.00 0.00 0.00 2.57
1106 1168 2.120909 CCATCATTGACGCCCACCC 61.121 63.158 0.00 0.00 0.00 4.61
1110 1172 1.077501 CATTGACGCCCACCCAGAT 60.078 57.895 0.00 0.00 0.00 2.90
1113 1175 1.561769 TTGACGCCCACCCAGATGAT 61.562 55.000 0.00 0.00 0.00 2.45
1284 1346 3.106986 GCCGCCAGCTATCTTCCCA 62.107 63.158 0.00 0.00 38.99 4.37
1507 1569 1.741770 CAGCGGGAGTTGGCAGTAC 60.742 63.158 0.00 0.00 37.43 2.73
1665 1770 6.097554 TCAAGTTGACCTTTTAGGAATGCAAA 59.902 34.615 0.08 0.00 37.67 3.68
1666 1771 6.670695 AGTTGACCTTTTAGGAATGCAAAT 57.329 33.333 0.00 0.00 37.67 2.32
1668 1773 8.189119 AGTTGACCTTTTAGGAATGCAAATAA 57.811 30.769 0.00 0.00 37.67 1.40
1669 1774 8.306761 AGTTGACCTTTTAGGAATGCAAATAAG 58.693 33.333 0.00 0.00 37.67 1.73
1896 2001 8.431593 CAATTGGTGGTTTATTTCGTTACAATG 58.568 33.333 0.00 0.00 0.00 2.82
1905 2010 9.567848 GTTTATTTCGTTACAATGATTCATGGT 57.432 29.630 11.38 11.38 32.23 3.55
1913 2018 4.151121 ACAATGATTCATGGTGTGTTGGA 58.849 39.130 5.86 0.00 0.00 3.53
1924 2029 1.606668 GTGTGTTGGAATTCCTCGCAA 59.393 47.619 25.81 12.58 34.82 4.85
1936 2041 3.695830 TCCTCGCAAAAGTATTCCTGT 57.304 42.857 0.00 0.00 0.00 4.00
2055 2172 8.810427 CAATGGTTTCTAATTTGAAATGGATCG 58.190 33.333 16.27 3.41 38.09 3.69
2056 2173 7.461182 TGGTTTCTAATTTGAAATGGATCGT 57.539 32.000 16.27 0.00 38.09 3.73
2251 2370 7.948357 AGTGGTGGTTCCTTTTAGAAAAATAC 58.052 34.615 0.00 0.00 37.07 1.89
2525 2645 6.152661 TCAAAAGTTGTTTCATTGACTCCACT 59.847 34.615 0.00 0.00 0.00 4.00
2857 2995 3.391296 AGTTTGAAGAGAGCTTGGTGGTA 59.609 43.478 0.00 0.00 33.61 3.25
3083 3224 3.686760 GCAACCAGCTTCTTCCCC 58.313 61.111 0.00 0.00 41.15 4.81
3175 3320 8.700722 TTTGCTGGTATGCTTTACAAATTATG 57.299 30.769 0.00 0.00 0.00 1.90
3197 3342 6.418057 TGTTTCAGCTCCAACCAAATTAAT 57.582 33.333 2.71 0.00 0.00 1.40
3266 3449 9.679661 TGTCTAATTGTTTCCTTTATCAGCATA 57.320 29.630 0.00 0.00 0.00 3.14
3269 3452 9.817365 CTAATTGTTTCCTTTATCAGCATATCG 57.183 33.333 0.00 0.00 0.00 2.92
3270 3453 5.673337 TGTTTCCTTTATCAGCATATCGC 57.327 39.130 0.00 0.00 42.91 4.58
3271 3454 5.122519 TGTTTCCTTTATCAGCATATCGCA 58.877 37.500 0.00 0.00 46.13 5.10
3272 3455 5.588246 TGTTTCCTTTATCAGCATATCGCAA 59.412 36.000 0.00 0.00 46.13 4.85
3273 3456 5.929697 TTCCTTTATCAGCATATCGCAAG 57.070 39.130 0.00 0.00 46.13 4.01
3274 3457 4.318332 TCCTTTATCAGCATATCGCAAGG 58.682 43.478 0.00 0.00 46.13 3.61
3275 3458 4.040339 TCCTTTATCAGCATATCGCAAGGA 59.960 41.667 9.68 9.68 42.49 3.36
3276 3459 4.756642 CCTTTATCAGCATATCGCAAGGAA 59.243 41.667 0.00 0.00 46.13 3.36
3277 3460 5.239306 CCTTTATCAGCATATCGCAAGGAAA 59.761 40.000 0.00 0.00 46.13 3.13
3278 3461 6.238731 CCTTTATCAGCATATCGCAAGGAAAA 60.239 38.462 0.00 0.00 46.13 2.29
3279 3462 4.558538 ATCAGCATATCGCAAGGAAAAC 57.441 40.909 0.00 0.00 46.13 2.43
3280 3463 3.342719 TCAGCATATCGCAAGGAAAACA 58.657 40.909 0.00 0.00 46.13 2.83
3281 3464 3.947196 TCAGCATATCGCAAGGAAAACAT 59.053 39.130 0.00 0.00 46.13 2.71
3282 3465 5.122519 TCAGCATATCGCAAGGAAAACATA 58.877 37.500 0.00 0.00 46.13 2.29
3283 3466 5.588246 TCAGCATATCGCAAGGAAAACATAA 59.412 36.000 0.00 0.00 46.13 1.90
3284 3467 5.682862 CAGCATATCGCAAGGAAAACATAAC 59.317 40.000 0.00 0.00 46.13 1.89
3285 3468 4.670621 GCATATCGCAAGGAAAACATAACG 59.329 41.667 0.00 0.00 41.79 3.18
3544 3728 1.612462 CCTCTGATTGCAGCTTCACCA 60.612 52.381 0.00 0.00 42.01 4.17
3599 3810 6.431234 ACATGCTTCTAAAAGACCAACTAAGG 59.569 38.462 0.00 0.00 34.14 2.69
3686 4236 3.198872 GCTATGTGTGCTTCCTAAGTCC 58.801 50.000 0.00 0.00 0.00 3.85
3730 4280 4.055360 GTGTGCTGCCATACGATATACAA 58.945 43.478 0.00 0.00 0.00 2.41
3814 4382 4.519730 TGTTAGGGAAATGGTACCGTTTTG 59.480 41.667 28.56 0.00 35.54 2.44
3832 4400 3.383546 TTGCGAAAACGCACATCTATC 57.616 42.857 16.42 0.00 45.06 2.08
3833 4401 2.616960 TGCGAAAACGCACATCTATCT 58.383 42.857 13.05 0.00 40.19 1.98
3834 4402 3.776340 TGCGAAAACGCACATCTATCTA 58.224 40.909 13.05 0.00 40.19 1.98
3835 4403 4.368315 TGCGAAAACGCACATCTATCTAT 58.632 39.130 13.05 0.00 40.19 1.98
3836 4404 4.444388 TGCGAAAACGCACATCTATCTATC 59.556 41.667 13.05 0.00 40.19 2.08
3841 4409 2.814336 ACGCACATCTATCTATCGCAGA 59.186 45.455 0.00 0.00 45.75 4.26
3849 4417 6.432472 ACATCTATCTATCGCAGATGAGAACA 59.568 38.462 15.63 0.00 45.58 3.18
3891 4459 1.337354 TGCATTTTGCTGTGCTGATGG 60.337 47.619 0.75 0.00 45.31 3.51
3916 4484 1.754226 GTGGTCTTTGGAAGGTTTGCA 59.246 47.619 0.00 0.00 0.00 4.08
3975 4591 0.529378 GGAAGGTTTGCAGCTGATGG 59.471 55.000 20.43 0.00 0.00 3.51
4010 4728 1.379916 CAGGATGTGGCCAGTGGAA 59.620 57.895 15.20 0.00 0.00 3.53
4012 4730 1.136329 AGGATGTGGCCAGTGGAAGT 61.136 55.000 15.20 0.00 0.00 3.01
4016 4734 2.738587 TGTGGCCAGTGGAAGTTTTA 57.261 45.000 15.20 0.00 0.00 1.52
4028 4746 5.471456 AGTGGAAGTTTTACAGCTGATGAAG 59.529 40.000 23.35 0.00 0.00 3.02
4087 4805 0.460311 ATGCTACTACACCGACTGCC 59.540 55.000 0.00 0.00 0.00 4.85
4107 4825 2.232452 CCGCTCCGAATGAATCCTCTAT 59.768 50.000 0.00 0.00 0.00 1.98
4112 4830 5.615289 CTCCGAATGAATCCTCTATTGGTT 58.385 41.667 0.00 0.00 0.00 3.67
4135 4853 2.092699 AGGAAGCCCATCAAACTAGAGC 60.093 50.000 0.00 0.00 33.88 4.09
4176 4894 3.782523 ACCAGCTTCCTATTTCCAGATGA 59.217 43.478 0.00 0.00 0.00 2.92
4177 4895 4.141528 ACCAGCTTCCTATTTCCAGATGAG 60.142 45.833 0.00 0.00 0.00 2.90
4184 4902 5.770919 TCCTATTTCCAGATGAGAGTCAGA 58.229 41.667 0.00 0.00 0.00 3.27
4200 4921 8.634444 TGAGAGTCAGATTAAATACCTAGCTTC 58.366 37.037 0.00 0.00 0.00 3.86
4230 4951 8.353423 TCCTAGCTTCAAATGCTTATTTTTCT 57.647 30.769 0.00 0.00 41.46 2.52
4295 5016 8.239681 TGAACTTTTCAGTCTCGTTATATGTG 57.760 34.615 0.00 0.00 34.08 3.21
4296 5017 8.085909 TGAACTTTTCAGTCTCGTTATATGTGA 58.914 33.333 0.00 0.00 34.08 3.58
4298 5019 8.412608 ACTTTTCAGTCTCGTTATATGTGATG 57.587 34.615 0.00 0.00 0.00 3.07
4300 5021 9.516314 CTTTTCAGTCTCGTTATATGTGATGTA 57.484 33.333 0.00 0.00 0.00 2.29
4302 5023 9.463443 TTTCAGTCTCGTTATATGTGATGTATG 57.537 33.333 0.00 0.00 0.00 2.39
4303 5024 7.593825 TCAGTCTCGTTATATGTGATGTATGG 58.406 38.462 0.00 0.00 0.00 2.74
4397 5122 2.330440 TCATGGTCATATTGCGCACT 57.670 45.000 11.12 7.82 0.00 4.40
4398 5123 2.212652 TCATGGTCATATTGCGCACTC 58.787 47.619 11.12 0.00 0.00 3.51
4399 5124 2.158914 TCATGGTCATATTGCGCACTCT 60.159 45.455 11.12 0.00 0.00 3.24
4401 5126 3.535280 TGGTCATATTGCGCACTCTTA 57.465 42.857 11.12 0.00 0.00 2.10
4402 5127 3.867857 TGGTCATATTGCGCACTCTTAA 58.132 40.909 11.12 0.00 0.00 1.85
4403 5128 4.450976 TGGTCATATTGCGCACTCTTAAT 58.549 39.130 11.12 1.50 0.00 1.40
4404 5129 4.511454 TGGTCATATTGCGCACTCTTAATC 59.489 41.667 11.12 0.00 0.00 1.75
4415 5140 5.274718 CGCACTCTTAATCTACCACTAGTG 58.725 45.833 16.34 16.34 36.92 2.74
4434 5164 1.228459 GAAAACGGGGGTTGAGGCT 60.228 57.895 0.00 0.00 0.00 4.58
4570 5302 3.349122 ACCCTTTGGTCCCGGTTT 58.651 55.556 0.00 0.00 43.06 3.27
4577 5309 0.547075 TTGGTCCCGGTTTCAGACAA 59.453 50.000 0.00 0.00 31.99 3.18
4593 5325 0.768622 ACAAGAACCGGGACCAATGA 59.231 50.000 6.32 0.00 0.00 2.57
4640 5372 2.035626 CCGGTTGGTGGCTGGAAT 59.964 61.111 0.00 0.00 34.35 3.01
4684 5416 2.297880 GTCCCGGTTTTAGCCACAAATT 59.702 45.455 0.00 0.00 0.00 1.82
4695 5427 7.696992 TTTAGCCACAAATTAGGACTAAAGG 57.303 36.000 0.00 0.00 33.11 3.11
4718 5450 1.414099 GGCCTATATATACCCCCGCCT 60.414 57.143 0.00 0.00 32.31 5.52
4724 5456 2.402557 ATATACCCCCGCCTCTGCCT 62.403 60.000 0.00 0.00 0.00 4.75
4760 5492 2.368221 TGCTTTGTTATTTTGGCCAGCT 59.632 40.909 5.11 0.00 0.00 4.24
4823 5555 6.218019 CACATGAGGTGTTCAATGAAATGTT 58.782 36.000 0.00 0.00 42.75 2.71
4829 5561 5.069516 AGGTGTTCAATGAAATGTTTGAGCT 59.930 36.000 0.00 0.00 35.07 4.09
4831 5563 7.039504 AGGTGTTCAATGAAATGTTTGAGCTAT 60.040 33.333 0.00 0.00 35.07 2.97
4915 5647 0.396435 TTGGCGGTCTGTCATGTCTT 59.604 50.000 0.00 0.00 27.93 3.01
4920 5652 1.273606 CGGTCTGTCATGTCTTGTCCT 59.726 52.381 0.00 0.00 0.00 3.85
4931 5669 0.112606 TCTTGTCCTCGTCCTCACCT 59.887 55.000 0.00 0.00 0.00 4.00
4932 5670 0.969894 CTTGTCCTCGTCCTCACCTT 59.030 55.000 0.00 0.00 0.00 3.50
4965 5704 2.176273 GCTGATCTTGTCGCGGCAT 61.176 57.895 16.97 0.00 0.00 4.40
4987 5726 0.535102 CCGTGGTGAGCCTCTTGTTT 60.535 55.000 0.00 0.00 35.27 2.83
5252 5995 4.401202 GGTATGTGAACCGGAAATTCCAAT 59.599 41.667 9.46 0.88 35.91 3.16
5256 5999 3.189702 GTGAACCGGAAATTCCAATCGAA 59.810 43.478 9.46 0.00 35.91 3.71
5266 6009 6.094881 GGAAATTCCAATCGAACCTATTGTCA 59.905 38.462 7.23 0.00 36.28 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 107 6.829849 TCATAGTAATTGTGCATCCTCATGA 58.170 36.000 0.00 0.00 30.57 3.07
118 121 8.980481 ACCTGATCGGATTTTTCATAGTAATT 57.020 30.769 2.08 0.00 36.31 1.40
173 176 2.093447 GTGGTTACCATGCACTCTAGCT 60.093 50.000 7.58 0.00 35.28 3.32
177 180 1.271379 GGTGTGGTTACCATGCACTCT 60.271 52.381 19.81 0.00 40.54 3.24
216 219 4.252073 GCCATGTTTGGATTTACATTGCA 58.748 39.130 0.00 0.00 46.92 4.08
217 220 3.622612 GGCCATGTTTGGATTTACATTGC 59.377 43.478 0.00 0.00 46.92 3.56
454 515 5.859205 TTTAGGAACGGAGGGAGTAATAC 57.141 43.478 0.00 0.00 0.00 1.89
484 545 6.622549 AGTTCGTAGTGGAATCTCTAACAAG 58.377 40.000 0.00 0.00 0.00 3.16
523 584 9.725019 TGAATCAACACTCTAAAACATGTCTAT 57.275 29.630 0.00 0.00 0.00 1.98
563 624 9.797642 TTAGATATTCCACTACGGACTACATAA 57.202 33.333 0.00 0.00 46.36 1.90
593 654 5.444663 ACCTCCGTTCCTAAATATACGTC 57.555 43.478 0.00 0.00 32.45 4.34
799 861 3.915437 CCATTTTGTGGTGGTGACTAC 57.085 47.619 0.00 0.00 43.44 2.73
989 1051 2.476199 CTCCTCCCATTTCACCTCTCT 58.524 52.381 0.00 0.00 0.00 3.10
1004 1066 3.866582 CCGACATGGCCCCTCCTC 61.867 72.222 0.00 0.00 35.26 3.71
1077 1139 0.458669 CAATGATGGGTTCTGGCTGC 59.541 55.000 0.00 0.00 0.00 5.25
1084 1146 0.679640 TGGGCGTCAATGATGGGTTC 60.680 55.000 4.48 0.00 0.00 3.62
1097 1159 2.591753 CATCATCTGGGTGGGCGT 59.408 61.111 0.00 0.00 0.00 5.68
1106 1168 0.107508 ACCTTCGTGGGCATCATCTG 60.108 55.000 2.69 0.00 41.11 2.90
1110 1172 1.220749 GCTACCTTCGTGGGCATCA 59.779 57.895 2.69 0.00 41.11 3.07
1113 1175 4.752879 GCGCTACCTTCGTGGGCA 62.753 66.667 0.00 0.00 41.11 5.36
1172 1234 1.662446 GGCACATGCACAACACTGC 60.662 57.895 6.15 0.00 44.36 4.40
1174 1236 2.035421 CAGGCACATGCACAACACT 58.965 52.632 6.15 0.00 44.36 3.55
1468 1530 1.728971 CTTCTTGCTAGTTGTGGAGCG 59.271 52.381 0.00 0.00 41.83 5.03
1479 1541 1.219124 CTCCCGCTGCTTCTTGCTA 59.781 57.895 0.00 0.00 43.37 3.49
1665 1770 8.738645 AGCGAGAAAGGTCATATTTTTCTTAT 57.261 30.769 0.86 0.00 40.27 1.73
1666 1771 9.314321 CTAGCGAGAAAGGTCATATTTTTCTTA 57.686 33.333 0.86 0.00 40.27 2.10
1668 1773 7.331791 ACTAGCGAGAAAGGTCATATTTTTCT 58.668 34.615 0.00 0.00 42.21 2.52
1669 1774 7.541122 ACTAGCGAGAAAGGTCATATTTTTC 57.459 36.000 0.00 0.00 0.00 2.29
1896 2001 4.463891 AGGAATTCCAACACACCATGAATC 59.536 41.667 26.22 0.00 38.89 2.52
1905 2010 1.974265 TTGCGAGGAATTCCAACACA 58.026 45.000 26.22 15.88 38.89 3.72
1913 2018 5.010282 ACAGGAATACTTTTGCGAGGAATT 58.990 37.500 0.00 0.00 0.00 2.17
1955 2060 7.509318 TGAGCCTATAAACAGTACACATCCTAT 59.491 37.037 0.00 0.00 0.00 2.57
2296 2416 4.153655 CGTTAAGTAGGGGAAACTTTGCTC 59.846 45.833 0.00 0.00 38.18 4.26
2857 2995 3.274281 AAAACAGGAAATGTGGGGGAT 57.726 42.857 0.00 0.00 43.00 3.85
2879 3017 5.266788 TGGAAGAGACGGGAAAGATAGTAA 58.733 41.667 0.00 0.00 0.00 2.24
2953 3094 4.855340 TCCTGAAACCATGGATTCCTTAC 58.145 43.478 26.67 7.68 0.00 2.34
3083 3224 7.029563 GCAAACCTCATAAATAACAGTTCCAG 58.970 38.462 0.00 0.00 0.00 3.86
3118 3262 4.160439 TCCAGTGTACAGATTCCAAGCTAG 59.840 45.833 0.00 0.00 0.00 3.42
3175 3320 7.826690 TCTATTAATTTGGTTGGAGCTGAAAC 58.173 34.615 0.00 0.00 0.00 2.78
3197 3342 9.421806 CACATTTCATTTTGCTTTACCATTCTA 57.578 29.630 0.00 0.00 0.00 2.10
3266 3449 4.759516 AACGTTATGTTTTCCTTGCGAT 57.240 36.364 0.00 0.00 37.59 4.58
3277 3460 3.949113 ACCAGAACCACAAACGTTATGTT 59.051 39.130 0.00 2.74 44.59 2.71
3278 3461 3.547746 ACCAGAACCACAAACGTTATGT 58.452 40.909 0.00 5.76 31.94 2.29
3279 3462 3.813166 AGACCAGAACCACAAACGTTATG 59.187 43.478 0.00 3.11 33.30 1.90
3280 3463 4.081322 AGACCAGAACCACAAACGTTAT 57.919 40.909 0.00 0.00 0.00 1.89
3281 3464 3.547054 AGACCAGAACCACAAACGTTA 57.453 42.857 0.00 0.00 0.00 3.18
3282 3465 2.413310 AGACCAGAACCACAAACGTT 57.587 45.000 0.00 0.00 0.00 3.99
3283 3466 2.285977 GAAGACCAGAACCACAAACGT 58.714 47.619 0.00 0.00 0.00 3.99
3284 3467 1.602377 GGAAGACCAGAACCACAAACG 59.398 52.381 0.00 0.00 35.97 3.60
3285 3468 2.650322 TGGAAGACCAGAACCACAAAC 58.350 47.619 0.00 0.00 41.77 2.93
3544 3728 5.568620 AGTGAAAGATGGTAACCTGAACT 57.431 39.130 0.00 0.00 0.00 3.01
3832 4400 4.318618 GCACAATGTTCTCATCTGCGATAG 60.319 45.833 0.00 0.00 32.13 2.08
3833 4401 3.557185 GCACAATGTTCTCATCTGCGATA 59.443 43.478 0.00 0.00 32.13 2.92
3834 4402 2.353889 GCACAATGTTCTCATCTGCGAT 59.646 45.455 0.00 0.00 32.13 4.58
3835 4403 1.733912 GCACAATGTTCTCATCTGCGA 59.266 47.619 0.00 0.00 32.13 5.10
3836 4404 1.736126 AGCACAATGTTCTCATCTGCG 59.264 47.619 0.00 0.00 40.04 5.18
3841 4409 4.298103 AGAGGAAGCACAATGTTCTCAT 57.702 40.909 0.00 0.00 35.59 2.90
3849 4417 5.717119 CAAAGCATTAAGAGGAAGCACAAT 58.283 37.500 0.00 0.00 0.00 2.71
3880 4448 2.044555 CACCTGCCCATCAGCACAG 61.045 63.158 0.00 0.00 41.50 3.66
3891 4459 0.895559 CCTTCCAAAGACCACCTGCC 60.896 60.000 0.00 0.00 0.00 4.85
3916 4484 5.432680 TGATCTCCTCTTTTTCATCAGCT 57.567 39.130 0.00 0.00 0.00 4.24
3975 4591 5.942826 ACATCCTGTTTGATCTCCTCTTTTC 59.057 40.000 0.00 0.00 0.00 2.29
4010 4728 5.936956 CCTCTTCTTCATCAGCTGTAAAACT 59.063 40.000 14.67 0.00 0.00 2.66
4012 4730 6.014242 TCTCCTCTTCTTCATCAGCTGTAAAA 60.014 38.462 14.67 5.50 0.00 1.52
4016 4734 3.439154 TCTCCTCTTCTTCATCAGCTGT 58.561 45.455 14.67 0.00 0.00 4.40
4028 4746 4.874966 CACATCCTGTTTGATCTCCTCTTC 59.125 45.833 0.00 0.00 0.00 2.87
4053 4771 1.649321 AGCATCTGGAGTTCCACTGA 58.351 50.000 0.00 0.00 42.01 3.41
4068 4786 0.460311 GGCAGTCGGTGTAGTAGCAT 59.540 55.000 0.00 0.00 0.00 3.79
4087 4805 3.584406 ATAGAGGATTCATTCGGAGCG 57.416 47.619 0.00 0.00 0.00 5.03
4107 4825 0.776810 TGATGGGCTTCCTGAACCAA 59.223 50.000 0.00 0.00 36.44 3.67
4112 4830 3.181329 TCTAGTTTGATGGGCTTCCTGA 58.819 45.455 0.00 0.00 0.00 3.86
4135 4853 1.080569 GTTGAATGTGCAAGCCGGG 60.081 57.895 2.18 0.00 0.00 5.73
4176 4894 8.776061 AGAAGCTAGGTATTTAATCTGACTCT 57.224 34.615 0.00 0.00 0.00 3.24
4177 4895 7.806014 CGAGAAGCTAGGTATTTAATCTGACTC 59.194 40.741 0.00 0.00 0.00 3.36
4200 4921 9.062132 AAATAAGCATTTGAAGCTAGGAGCGAG 62.062 40.741 0.00 0.00 42.53 5.03
4230 4951 4.337555 AGCTAAGCGTTCGGAAATAGTAGA 59.662 41.667 0.00 0.00 0.00 2.59
4295 5016 0.773644 ACATCCAGGGGCCATACATC 59.226 55.000 4.39 0.00 0.00 3.06
4296 5017 0.479815 CACATCCAGGGGCCATACAT 59.520 55.000 4.39 0.00 0.00 2.29
4298 5019 1.151450 CCACATCCAGGGGCCATAC 59.849 63.158 4.39 0.00 30.89 2.39
4415 5140 2.273179 GCCTCAACCCCCGTTTTCC 61.273 63.158 0.00 0.00 0.00 3.13
4422 5147 1.700186 CTTATCCTAGCCTCAACCCCC 59.300 57.143 0.00 0.00 0.00 5.40
4434 5164 3.521937 CCGGGATTAATGCCCTTATCCTA 59.478 47.826 19.28 0.00 43.72 2.94
4485 5215 0.179134 CTCACGAACCGGGACTGATC 60.179 60.000 6.32 0.00 32.99 2.92
4570 5302 0.761323 TGGTCCCGGTTCTTGTCTGA 60.761 55.000 0.00 0.00 0.00 3.27
4577 5309 1.299976 GCTCATTGGTCCCGGTTCT 59.700 57.895 0.00 0.00 0.00 3.01
4640 5372 1.452801 GGACAACCTTTGGTCCCGA 59.547 57.895 0.00 0.00 46.29 5.14
4684 5416 5.898346 ATATAGGCCTCCCTTTAGTCCTA 57.102 43.478 9.68 0.00 42.87 2.94
4695 5427 2.606378 CGGGGGTATATATAGGCCTCC 58.394 57.143 9.68 1.03 38.27 4.30
4718 5450 1.601759 GGCTCTGTTTGCAGGCAGA 60.602 57.895 17.51 17.51 42.78 4.26
4724 5456 3.435590 GCAGTGGCTCTGTTTGCA 58.564 55.556 17.02 0.00 45.23 4.08
4743 5475 2.036992 CCACAGCTGGCCAAAATAACAA 59.963 45.455 19.93 0.00 0.00 2.83
4748 5480 0.901580 CTCCCACAGCTGGCCAAAAT 60.902 55.000 19.93 0.00 36.00 1.82
4760 5492 0.182537 CACCACAAACCTCTCCCACA 59.817 55.000 0.00 0.00 0.00 4.17
4831 5563 9.220767 GAGCTTCAAAAGGAGAAAGATTAAGTA 57.779 33.333 0.00 0.00 0.00 2.24
4848 5580 3.631250 AGTTTGGACAAGGAGCTTCAAA 58.369 40.909 0.00 0.00 0.00 2.69
4850 5582 2.487265 GGAGTTTGGACAAGGAGCTTCA 60.487 50.000 0.00 0.00 0.00 3.02
4915 5647 1.241990 CGAAGGTGAGGACGAGGACA 61.242 60.000 0.00 0.00 0.00 4.02
4920 5652 0.675837 ATCGACGAAGGTGAGGACGA 60.676 55.000 0.00 0.00 0.00 4.20
5121 5864 4.963318 ACCACATCCGAATCATAGACAT 57.037 40.909 0.00 0.00 0.00 3.06
5306 6049 9.996554 TCCTCCTTAATTCTTTTCAATTTTTCC 57.003 29.630 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.