Multiple sequence alignment - TraesCS5D01G125000

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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 TraesCS5D01G125000 chr5D 100.000 9418 0 0 1 9418 190787066 190777649 0 17392
1 TraesCS5D01G125000 chr5D 91.928 3630 247 30 2565 6157 419886478 419890098 0 5038
2 TraesCS5D01G125000 chr5D 93.835 2141 120 10 1 2134 419883787 419885922 0 3212
3 TraesCS5D01G125000 chr5D 93.654 2143 116 10 1 2134 211807145 211805014 0 3186
4 TraesCS5D01G125000 chr7A 91.253 7340 533 58 2147 9418 315499598 315492300 0 9897
5 TraesCS5D01G125000 chr7A 94.118 4454 226 14 4979 9418 265357248 265361679 0 6741
6 TraesCS5D01G125000 chr7A 93.511 4315 251 23 5121 9418 458659525 458655223 0 6390
7 TraesCS5D01G125000 chr7A 90.428 3458 289 29 2565 5991 583018310 583021756 0 4514
8 TraesCS5D01G125000 chr7A 89.905 2110 185 14 2565 4662 245449157 245447064 0 2691
9 TraesCS5D01G125000 chr7A 88.956 661 58 11 2147 2796 370644035 370643379 0 802
10 TraesCS5D01G125000 chr2D 92.220 6915 429 44 2565 9418 273052375 273059241 0 9688
11 TraesCS5D01G125000 chr2D 95.537 5871 222 18 3560 9418 412328867 412334709 0 9354
12 TraesCS5D01G125000 chr2D 94.904 4317 195 16 5115 9418 259244709 259240405 0 6730
13 TraesCS5D01G125000 chr2D 94.860 2140 93 9 1 2134 412324988 412327116 0 3326
14 TraesCS5D01G125000 chr2D 94.621 2138 99 7 1 2132 220751790 220749663 0 3297
15 TraesCS5D01G125000 chr2D 94.494 2143 107 8 1 2134 184185667 184183527 0 3293
16 TraesCS5D01G125000 chr3D 95.715 5904 203 20 3560 9418 323152052 323157950 0 9455
17 TraesCS5D01G125000 chr3D 95.571 5871 223 16 3560 9418 395859353 395865198 0 9367
18 TraesCS5D01G125000 chr3D 94.393 2140 104 8 1 2134 323148094 323150223 0 3273
19 TraesCS5D01G125000 chr3D 94.303 509 22 6 2144 2649 428367497 428368001 0 773
20 TraesCS5D01G125000 chr1D 94.183 4315 209 24 5117 9416 88010003 88005716 0 6540
21 TraesCS5D01G125000 chr1D 95.715 4037 150 16 5394 9418 371719382 371723407 0 6475
22 TraesCS5D01G125000 chr1D 91.933 3632 243 35 2565 6157 238006670 238010290 0 5038
23 TraesCS5D01G125000 chr1D 96.053 2660 84 10 1 2649 371712775 371715424 0 4311
24 TraesCS5D01G125000 chr1D 95.152 2661 102 16 1 2649 238004022 238006667 0 4174
25 TraesCS5D01G125000 chr5A 93.087 3978 250 23 5115 9076 154815318 154811350 0 5799
26 TraesCS5D01G125000 chr5A 90.264 606 48 9 2144 2741 133806400 133807002 0 782
27 TraesCS5D01G125000 chr7D 95.389 3600 154 12 5827 9418 291611850 291615445 0 5718
28 TraesCS5D01G125000 chr7D 91.936 3621 245 26 2565 6157 370468613 370465012 0 5025
29 TraesCS5D01G125000 chr7D 94.104 1747 74 10 786 2526 234445163 234446886 0 2628
30 TraesCS5D01G125000 chr7D 94.327 617 28 5 1909 2520 234392247 234392861 0 939
31 TraesCS5D01G125000 chr1A 91.404 3618 277 21 2566 6157 379609039 379612648 0 4927
32 TraesCS5D01G125000 chr4D 91.573 2670 190 24 1 2649 154420756 154423411 0 3651
33 TraesCS5D01G125000 chr4D 94.587 2143 95 12 1 2134 144585664 144583534 0 3295
34 TraesCS5D01G125000 chr4D 93.529 510 24 8 2144 2649 285434928 285434424 0 750
35 TraesCS5D01G125000 chr3A 90.948 2541 192 20 2147 4662 217246948 217244421 0 3384
36 TraesCS5D01G125000 chr3A 93.324 2142 127 12 1 2134 217249132 217246999 0 3149
37 TraesCS5D01G125000 chr6A 89.738 2368 206 20 2144 4481 446425258 446427618 0 2992
38 TraesCS5D01G125000 chr6A 91.098 1977 133 21 7452 9418 446429725 446431668 0 2636
39 TraesCS5D01G125000 chr6A 90.649 1433 115 12 7993 9418 589838075 589836655 0 1886


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 TraesCS5D01G125000 chr5D 190777649 190787066 9417 True 17392.0 17392 100.0000 1 9418 1 chr5D.!!$R1 9417
1 TraesCS5D01G125000 chr5D 419883787 419890098 6311 False 4125.0 5038 92.8815 1 6157 2 chr5D.!!$F1 6156
2 TraesCS5D01G125000 chr5D 211805014 211807145 2131 True 3186.0 3186 93.6540 1 2134 1 chr5D.!!$R2 2133
3 TraesCS5D01G125000 chr7A 315492300 315499598 7298 True 9897.0 9897 91.2530 2147 9418 1 chr7A.!!$R2 7271
4 TraesCS5D01G125000 chr7A 265357248 265361679 4431 False 6741.0 6741 94.1180 4979 9418 1 chr7A.!!$F1 4439
5 TraesCS5D01G125000 chr7A 458655223 458659525 4302 True 6390.0 6390 93.5110 5121 9418 1 chr7A.!!$R4 4297
6 TraesCS5D01G125000 chr7A 583018310 583021756 3446 False 4514.0 4514 90.4280 2565 5991 1 chr7A.!!$F2 3426
7 TraesCS5D01G125000 chr7A 245447064 245449157 2093 True 2691.0 2691 89.9050 2565 4662 1 chr7A.!!$R1 2097
8 TraesCS5D01G125000 chr7A 370643379 370644035 656 True 802.0 802 88.9560 2147 2796 1 chr7A.!!$R3 649
9 TraesCS5D01G125000 chr2D 273052375 273059241 6866 False 9688.0 9688 92.2200 2565 9418 1 chr2D.!!$F1 6853
10 TraesCS5D01G125000 chr2D 259240405 259244709 4304 True 6730.0 6730 94.9040 5115 9418 1 chr2D.!!$R3 4303
11 TraesCS5D01G125000 chr2D 412324988 412334709 9721 False 6340.0 9354 95.1985 1 9418 2 chr2D.!!$F2 9417
12 TraesCS5D01G125000 chr2D 220749663 220751790 2127 True 3297.0 3297 94.6210 1 2132 1 chr2D.!!$R2 2131
13 TraesCS5D01G125000 chr2D 184183527 184185667 2140 True 3293.0 3293 94.4940 1 2134 1 chr2D.!!$R1 2133
14 TraesCS5D01G125000 chr3D 395859353 395865198 5845 False 9367.0 9367 95.5710 3560 9418 1 chr3D.!!$F1 5858
15 TraesCS5D01G125000 chr3D 323148094 323157950 9856 False 6364.0 9455 95.0540 1 9418 2 chr3D.!!$F3 9417
16 TraesCS5D01G125000 chr3D 428367497 428368001 504 False 773.0 773 94.3030 2144 2649 1 chr3D.!!$F2 505
17 TraesCS5D01G125000 chr1D 88005716 88010003 4287 True 6540.0 6540 94.1830 5117 9416 1 chr1D.!!$R1 4299
18 TraesCS5D01G125000 chr1D 371712775 371723407 10632 False 5393.0 6475 95.8840 1 9418 2 chr1D.!!$F2 9417
19 TraesCS5D01G125000 chr1D 238004022 238010290 6268 False 4606.0 5038 93.5425 1 6157 2 chr1D.!!$F1 6156
20 TraesCS5D01G125000 chr5A 154811350 154815318 3968 True 5799.0 5799 93.0870 5115 9076 1 chr5A.!!$R1 3961
21 TraesCS5D01G125000 chr5A 133806400 133807002 602 False 782.0 782 90.2640 2144 2741 1 chr5A.!!$F1 597
22 TraesCS5D01G125000 chr7D 291611850 291615445 3595 False 5718.0 5718 95.3890 5827 9418 1 chr7D.!!$F3 3591
23 TraesCS5D01G125000 chr7D 370465012 370468613 3601 True 5025.0 5025 91.9360 2565 6157 1 chr7D.!!$R1 3592
24 TraesCS5D01G125000 chr7D 234445163 234446886 1723 False 2628.0 2628 94.1040 786 2526 1 chr7D.!!$F2 1740
25 TraesCS5D01G125000 chr7D 234392247 234392861 614 False 939.0 939 94.3270 1909 2520 1 chr7D.!!$F1 611
26 TraesCS5D01G125000 chr1A 379609039 379612648 3609 False 4927.0 4927 91.4040 2566 6157 1 chr1A.!!$F1 3591
27 TraesCS5D01G125000 chr4D 154420756 154423411 2655 False 3651.0 3651 91.5730 1 2649 1 chr4D.!!$F1 2648
28 TraesCS5D01G125000 chr4D 144583534 144585664 2130 True 3295.0 3295 94.5870 1 2134 1 chr4D.!!$R1 2133
29 TraesCS5D01G125000 chr4D 285434424 285434928 504 True 750.0 750 93.5290 2144 2649 1 chr4D.!!$R2 505
30 TraesCS5D01G125000 chr3A 217244421 217249132 4711 True 3266.5 3384 92.1360 1 4662 2 chr3A.!!$R1 4661
31 TraesCS5D01G125000 chr6A 446425258 446431668 6410 False 2814.0 2992 90.4180 2144 9418 2 chr6A.!!$F1 7274
32 TraesCS5D01G125000 chr6A 589836655 589838075 1420 True 1886.0 1886 90.6490 7993 9418 1 chr6A.!!$R1 1425

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
976 991 1.352017 TGAACATGAGGGTGCACAGAT 59.648 47.619 20.43 2.91 0.00 2.90 F
1797 1845 0.762418 TTGACAGTGTTGGGGACGAT 59.238 50.000 0.00 0.00 0.00 3.73 F
2592 2726 2.203153 ACCCCTGACACGTGCAAC 60.203 61.111 17.22 8.24 0.00 4.17 F
2809 3070 0.878416 GACGCACTGCAAAATACCCA 59.122 50.000 1.11 0.00 0.00 4.51 F
4403 5550 0.874390 CTTCCGCTTGTGCTTGCTAA 59.126 50.000 0.00 0.00 36.97 3.09 F
4404 5551 1.266718 CTTCCGCTTGTGCTTGCTAAA 59.733 47.619 0.00 0.00 36.97 1.85 F
6181 8350 0.872388 ACCTCAACGAACGATTTGGC 59.128 50.000 0.14 0.00 0.00 4.52 F
6946 9137 0.181350 GAAGGCGATGGTGGAGGAAT 59.819 55.000 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2659 2907 0.400213 TGGAAGAAGCAACCGTCCAT 59.600 50.000 0.00 0.0 37.29 3.41 R
2768 3026 2.763215 GGGATGTGTGGGAGGCAA 59.237 61.111 0.00 0.0 0.00 4.52 R
4370 5517 0.237498 CGGAAGGAAAACGAAGGCAC 59.763 55.000 0.00 0.0 0.00 5.01 R
4434 5582 3.886505 TCATACTGGTTCAACCCAACAAC 59.113 43.478 3.42 0.0 37.50 3.32 R
5447 7483 0.179145 GCGTGCGCTCTAGGTTTAGA 60.179 55.000 9.73 0.0 38.26 2.10 R
6290 8472 2.100584 TGAAATTTGGTGTCACAGTGGC 59.899 45.455 5.12 0.0 0.00 5.01 R
7100 9291 1.303888 ACCTCGTCGGCCTTGTCTA 60.304 57.895 0.00 0.0 35.61 2.59 R
8861 11129 2.496899 ATGTTGTCCTCGGCTGAAAT 57.503 45.000 0.00 0.0 0.00 2.17 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
86 87 1.602323 GGTGGCCATGTGGAACGAA 60.602 57.895 9.72 0.00 42.39 3.85
151 152 3.243839 GCCAAAATGACATCCACACAACT 60.244 43.478 0.00 0.00 0.00 3.16
190 194 6.220930 ACTATGTGCTCAAGAACTTCGTAAA 58.779 36.000 0.00 0.00 0.00 2.01
536 543 1.585006 GGCGACAGAGACGGAAGAA 59.415 57.895 0.00 0.00 0.00 2.52
582 589 2.645802 ACAACCCGCAAAAACTGTCTA 58.354 42.857 0.00 0.00 0.00 2.59
817 832 4.792057 GCATGATGCAGACAATTAAGGCTC 60.792 45.833 13.36 0.00 44.26 4.70
819 834 2.877097 TGCAGACAATTAAGGCTCCA 57.123 45.000 0.00 0.00 0.00 3.86
843 858 4.649674 AGCGTTCCAGAGAAATACATCCTA 59.350 41.667 0.00 0.00 32.58 2.94
845 860 5.234543 GCGTTCCAGAGAAATACATCCTAAC 59.765 44.000 0.00 0.00 32.58 2.34
902 917 6.718454 ACATTCAACAGAAATGACTTGAGGAT 59.282 34.615 3.06 0.00 37.51 3.24
976 991 1.352017 TGAACATGAGGGTGCACAGAT 59.648 47.619 20.43 2.91 0.00 2.90
1365 1384 3.184581 GGAAGAGTAAGACACAAGCAACG 59.815 47.826 0.00 0.00 0.00 4.10
1366 1385 3.728076 AGAGTAAGACACAAGCAACGA 57.272 42.857 0.00 0.00 0.00 3.85
1367 1386 4.054780 AGAGTAAGACACAAGCAACGAA 57.945 40.909 0.00 0.00 0.00 3.85
1368 1387 4.439057 AGAGTAAGACACAAGCAACGAAA 58.561 39.130 0.00 0.00 0.00 3.46
1369 1388 4.508124 AGAGTAAGACACAAGCAACGAAAG 59.492 41.667 0.00 0.00 0.00 2.62
1370 1389 2.475200 AAGACACAAGCAACGAAAGC 57.525 45.000 0.00 0.00 0.00 3.51
1371 1390 1.378531 AGACACAAGCAACGAAAGCA 58.621 45.000 0.00 0.00 0.00 3.91
1372 1391 1.331756 AGACACAAGCAACGAAAGCAG 59.668 47.619 0.00 0.00 0.00 4.24
1373 1392 1.064060 GACACAAGCAACGAAAGCAGT 59.936 47.619 0.00 0.00 0.00 4.40
1458 1504 1.229625 TCTCAGGGTGAGGGCATGT 60.230 57.895 4.14 0.00 44.39 3.21
1466 1512 1.490490 GGTGAGGGCATGTGGATTCTA 59.510 52.381 0.00 0.00 0.00 2.10
1491 1537 4.439057 ACGTCGTGAGCAACCATAATTAT 58.561 39.130 0.00 0.00 0.00 1.28
1501 1547 4.792380 GCAACCATAATTATCGCACATGCA 60.792 41.667 4.49 0.00 42.21 3.96
1669 1717 1.003233 GTGGGCAAGGAGGTCAGTC 60.003 63.158 0.00 0.00 0.00 3.51
1703 1751 1.072331 ACAGGGCAAGGTACAGACTTG 59.928 52.381 6.11 6.11 46.15 3.16
1797 1845 0.762418 TTGACAGTGTTGGGGACGAT 59.238 50.000 0.00 0.00 0.00 3.73
1989 2041 7.856145 ATGAGGAAACATATCAGAAACACTC 57.144 36.000 0.00 0.00 0.00 3.51
1996 2048 8.827177 AAACATATCAGAAACACTCTCGTTAA 57.173 30.769 0.00 0.00 29.07 2.01
2250 2343 3.181438 TGGCATAGTAACCAAACACACCT 60.181 43.478 0.00 0.00 31.46 4.00
2520 2652 9.357161 ACTGGTATTTGGTAAGTTCAATTACAA 57.643 29.630 0.00 0.00 37.38 2.41
2592 2726 2.203153 ACCCCTGACACGTGCAAC 60.203 61.111 17.22 8.24 0.00 4.17
2659 2907 3.065648 GCGACAGTAAAAACCCTTTGACA 59.934 43.478 0.00 0.00 29.11 3.58
2809 3070 0.878416 GACGCACTGCAAAATACCCA 59.122 50.000 1.11 0.00 0.00 4.51
3101 3368 1.738099 CGAACCAGACAAGGCCGAG 60.738 63.158 0.00 0.00 32.10 4.63
3186 3453 1.281899 GCACTACACCAGCGAAGATC 58.718 55.000 0.00 0.00 0.00 2.75
4058 5203 3.255642 CCCCAACAAGTTCATCGACATTT 59.744 43.478 0.00 0.00 0.00 2.32
4059 5204 4.261994 CCCCAACAAGTTCATCGACATTTT 60.262 41.667 0.00 0.00 0.00 1.82
4154 5301 5.361857 CCCATTCTACAAAGGCATGAAGAAT 59.638 40.000 0.00 0.00 34.80 2.40
4288 5435 4.801330 TCGACTACATCACAGATGGTTT 57.199 40.909 11.29 0.00 0.00 3.27
4370 5517 3.006217 TGGGATGAAGATACATCAGAGCG 59.994 47.826 0.00 0.00 45.68 5.03
4401 5548 2.263741 CCTTCCGCTTGTGCTTGCT 61.264 57.895 0.00 0.00 36.97 3.91
4402 5549 0.955428 CCTTCCGCTTGTGCTTGCTA 60.955 55.000 0.00 0.00 36.97 3.49
4403 5550 0.874390 CTTCCGCTTGTGCTTGCTAA 59.126 50.000 0.00 0.00 36.97 3.09
4404 5551 1.266718 CTTCCGCTTGTGCTTGCTAAA 59.733 47.619 0.00 0.00 36.97 1.85
4434 5582 8.627487 TGTTGTTTCAAATTAGTAGTTTGCTG 57.373 30.769 12.08 0.00 36.69 4.41
4468 5617 4.400529 ACCAGTATGATTATGTCGTGCA 57.599 40.909 0.00 0.00 39.69 4.57
4897 6912 9.026121 AGAATGACAGTACTAGTACACTTGATT 57.974 33.333 29.87 19.36 38.48 2.57
4943 6959 8.642020 CAATAAAAAGTACAAAGAAGCATCAGC 58.358 33.333 0.00 0.00 42.56 4.26
5066 7086 2.569404 GACACCAGAAGACCCTTGAGAT 59.431 50.000 0.00 0.00 0.00 2.75
5198 7219 5.185249 TGGTGGAGTCAAGTACTAGATTCAC 59.815 44.000 0.00 1.52 39.07 3.18
5349 7385 3.513438 GAGAGAGAGCGAGCGCCA 61.513 66.667 11.66 0.00 43.17 5.69
5371 7407 4.041740 TGTATAAGCGCTCAGGTAAGTG 57.958 45.455 12.06 0.00 0.00 3.16
5374 7410 4.730949 ATAAGCGCTCAGGTAAGTGTTA 57.269 40.909 12.06 0.00 0.00 2.41
5447 7483 2.353958 TCGACTAGCGAGGTGGGT 59.646 61.111 0.00 0.00 45.59 4.51
5484 7520 3.342627 GCACGCCGCACTACACAA 61.343 61.111 0.00 0.00 41.79 3.33
5559 7597 1.967066 CAAACACCCCACCAATAAGCA 59.033 47.619 0.00 0.00 0.00 3.91
5577 7615 5.652994 AAGCACAGTTAAACAAACCAGAA 57.347 34.783 0.00 0.00 39.03 3.02
5929 8004 8.378172 TCTGACAAGTTCAACTACTAAAATGG 57.622 34.615 0.00 0.00 32.21 3.16
6181 8350 0.872388 ACCTCAACGAACGATTTGGC 59.128 50.000 0.14 0.00 0.00 4.52
6212 8394 2.038813 CAATCCCCCAACCCACCC 59.961 66.667 0.00 0.00 0.00 4.61
6213 8395 2.455532 AATCCCCCAACCCACCCA 60.456 61.111 0.00 0.00 0.00 4.51
6214 8396 2.100983 AATCCCCCAACCCACCCAA 61.101 57.895 0.00 0.00 0.00 4.12
6215 8397 1.679969 AATCCCCCAACCCACCCAAA 61.680 55.000 0.00 0.00 0.00 3.28
6216 8398 1.679969 ATCCCCCAACCCACCCAAAA 61.680 55.000 0.00 0.00 0.00 2.44
6217 8399 1.384643 CCCCCAACCCACCCAAAAA 60.385 57.895 0.00 0.00 0.00 1.94
6290 8472 0.946221 GAACAGTCAGGCCACTCACG 60.946 60.000 5.01 0.00 0.00 4.35
6405 8588 9.712359 GAATACAAAAACTATAAAGGCCTAACG 57.288 33.333 5.16 0.00 0.00 3.18
6762 8950 1.688187 GGACCCCCACGACTACCAT 60.688 63.158 0.00 0.00 0.00 3.55
6946 9137 0.181350 GAAGGCGATGGTGGAGGAAT 59.819 55.000 0.00 0.00 0.00 3.01
7000 9191 1.072806 ACAAGAGCAGCAACCTCATCA 59.927 47.619 0.00 0.00 0.00 3.07
7100 9291 0.251354 ATCATCTGCACCAGCGAACT 59.749 50.000 0.00 0.00 46.23 3.01
7517 9760 7.652909 TGCACCAAATTAATTTCTGAACTTGAG 59.347 33.333 10.53 0.00 0.00 3.02
7534 9777 6.658188 ACTTGAGGTACTAGCATAGATTCC 57.342 41.667 0.00 0.00 42.77 3.01
7536 9779 4.726583 TGAGGTACTAGCATAGATTCCGT 58.273 43.478 0.00 0.00 42.77 4.69
7544 9787 6.451393 ACTAGCATAGATTCCGTTCTTGATC 58.549 40.000 0.00 0.00 42.77 2.92
7885 10130 7.986320 AGTTTCTGAACTAGATTCATCCATGAG 59.014 37.037 0.00 0.00 46.37 2.90
7940 10191 4.495422 TCGCTTGTAAAACCAAAAAGCAA 58.505 34.783 6.52 0.00 42.63 3.91
7989 10241 8.467402 AGACTAATCTTTAAATGTGTGTCTCG 57.533 34.615 7.19 0.00 0.00 4.04
8032 10284 2.097825 CAAAGAATTCCTGCAGGAGGG 58.902 52.381 33.16 15.67 46.36 4.30
8195 10448 2.125269 GCCGATGTTGTAGGCGGT 60.125 61.111 0.00 0.00 45.22 5.68
8347 10607 3.745975 TCATGGAAGACAATCGACAACAC 59.254 43.478 0.00 0.00 0.00 3.32
8410 10670 1.202582 CTACTACCACTGCAGCTTCGT 59.797 52.381 15.27 7.21 0.00 3.85
8448 10708 0.870393 AGTCTGCATTCGTGTTGCTG 59.130 50.000 0.00 7.65 40.77 4.41
8815 11081 9.618890 TTAGACATTTACGGTAGTACTATCACT 57.381 33.333 13.53 0.26 31.60 3.41
9089 11359 6.087952 CACATTCCATAAAACATTGACACACG 59.912 38.462 0.00 0.00 0.00 4.49
9185 11457 3.565307 ACATTGCCTTGAGAAGAACCAA 58.435 40.909 0.00 0.00 0.00 3.67
9223 11496 7.210174 AGAAGGTCAAAACTAAATCAAAAGGC 58.790 34.615 0.00 0.00 0.00 4.35
9254 11527 4.274950 TCGACCAAGGAGAAAAATCACAAC 59.725 41.667 0.00 0.00 0.00 3.32
9291 11564 1.357137 TCAGCCCACATTGACCAGTA 58.643 50.000 0.00 0.00 0.00 2.74
9306 11579 4.246458 GACCAGTAAGGCACTAGTTTCAG 58.754 47.826 0.00 0.00 43.14 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 2.560542 GGCTGATATCCATCTCTCACGT 59.439 50.000 0.00 0.00 31.93 4.49
151 152 5.105187 AGCACATAGTTCATGCTCTCACTTA 60.105 40.000 0.00 0.00 46.68 2.24
190 194 3.306780 CCGGTGTAGGTTTTGTCTCTCAT 60.307 47.826 0.00 0.00 0.00 2.90
237 241 3.152341 CTGTCTGCCTCCTTGTTTTGAT 58.848 45.455 0.00 0.00 0.00 2.57
536 543 0.250166 GCACGAGGTACTTTGTGGGT 60.250 55.000 22.82 0.00 42.67 4.51
612 619 1.460689 TTTCTCCCACGGGGTCTGT 60.461 57.895 1.28 0.00 44.74 3.41
817 832 3.334691 TGTATTTCTCTGGAACGCTTGG 58.665 45.455 0.00 0.00 0.00 3.61
819 834 4.080863 AGGATGTATTTCTCTGGAACGCTT 60.081 41.667 0.00 0.00 0.00 4.68
843 858 1.435577 GGCGTTTGGTGTATCTCGTT 58.564 50.000 0.00 0.00 0.00 3.85
845 860 1.418342 CGGGCGTTTGGTGTATCTCG 61.418 60.000 0.00 0.00 0.00 4.04
902 917 2.823924 TGCCTTGTTTGACGCTACTA 57.176 45.000 0.00 0.00 0.00 1.82
1227 1243 4.320567 CCATCAAGCTCATGATCTTGCATC 60.321 45.833 27.05 0.00 37.96 3.91
1365 1384 1.929482 GCTGCTGCTTTCACTGCTTTC 60.929 52.381 8.53 0.00 35.70 2.62
1366 1385 0.031721 GCTGCTGCTTTCACTGCTTT 59.968 50.000 8.53 0.00 35.70 3.51
1367 1386 1.658673 GCTGCTGCTTTCACTGCTT 59.341 52.632 8.53 0.00 35.70 3.91
1368 1387 2.266627 GGCTGCTGCTTTCACTGCT 61.267 57.895 15.64 0.00 39.59 4.24
1369 1388 2.079020 TTGGCTGCTGCTTTCACTGC 62.079 55.000 15.64 0.00 39.59 4.40
1370 1389 0.386476 TTTGGCTGCTGCTTTCACTG 59.614 50.000 15.64 0.00 39.59 3.66
1371 1390 1.113788 TTTTGGCTGCTGCTTTCACT 58.886 45.000 15.64 0.00 39.59 3.41
1372 1391 1.862827 CTTTTTGGCTGCTGCTTTCAC 59.137 47.619 15.64 0.00 39.59 3.18
1373 1392 1.807377 GCTTTTTGGCTGCTGCTTTCA 60.807 47.619 15.64 2.20 39.59 2.69
1405 1451 1.930371 GCCAAATTCCACACGCTTGAC 60.930 52.381 0.00 0.00 0.00 3.18
1413 1459 1.605165 GTCCGGGCCAAATTCCACA 60.605 57.895 4.39 0.00 0.00 4.17
1458 1504 2.670229 GCTCACGACGTTGTAGAATCCA 60.670 50.000 8.44 0.00 0.00 3.41
1466 1512 0.531974 ATGGTTGCTCACGACGTTGT 60.532 50.000 1.48 1.48 0.00 3.32
1491 1537 2.738139 CGGAGTGTGCATGTGCGA 60.738 61.111 0.00 0.00 45.83 5.10
1501 1547 2.046892 GCCATCTGTGCGGAGTGT 60.047 61.111 0.00 0.00 0.00 3.55
1669 1717 1.205064 CCTGTTTCTGTTCAGCGCG 59.795 57.895 0.00 0.00 0.00 6.86
1797 1845 4.024893 GCTTCATCGTCAGTTTCAGTTTCA 60.025 41.667 0.00 0.00 0.00 2.69
1861 1909 0.546598 CTCCTAACTGGCCCCGAATT 59.453 55.000 0.00 0.00 35.26 2.17
2338 2450 6.767524 TCGCATTTTGGTTGAGGTAATTAT 57.232 33.333 0.00 0.00 0.00 1.28
2520 2652 4.042809 TGGTACTTGGACTGGTGATTGAAT 59.957 41.667 0.00 0.00 0.00 2.57
2592 2726 4.348863 ACTTATCAGCTGCTTATCCCAG 57.651 45.455 9.47 0.72 0.00 4.45
2659 2907 0.400213 TGGAAGAAGCAACCGTCCAT 59.600 50.000 0.00 0.00 37.29 3.41
2768 3026 2.763215 GGGATGTGTGGGAGGCAA 59.237 61.111 0.00 0.00 0.00 4.52
2809 3070 3.779183 TGAGGCAGAGATGGAAGAGAAAT 59.221 43.478 0.00 0.00 0.00 2.17
3186 3453 3.089838 TGCCATCTGGGGAGGTTG 58.910 61.111 0.00 0.00 37.04 3.77
3318 3587 8.324306 AGTCTGATGAAATTTTCAGGATACAGA 58.676 33.333 16.34 18.23 43.98 3.41
3499 3770 7.907389 TGGATCAAGTTCAGAAACTACACTAT 58.093 34.615 0.00 0.00 45.07 2.12
3554 3826 8.562892 ACTACATCAAGTTCAGAAACATCTTTG 58.437 33.333 0.00 0.00 37.88 2.77
3689 3965 5.126779 TGTTGTATGTTCTGCTTTGGTACA 58.873 37.500 0.00 0.00 0.00 2.90
4081 5228 3.938289 AGGAGTCGTACTCTTTTCCAC 57.062 47.619 12.62 0.00 44.46 4.02
4154 5301 3.064207 GTCTTCCTGCGTGTTGATGTTA 58.936 45.455 0.00 0.00 0.00 2.41
4255 5402 7.670364 TGTGATGTAGTCGATTATGATCCATT 58.330 34.615 0.00 0.00 0.00 3.16
4288 5435 1.000731 CCCGCTCTTTTGCAAATTCCA 59.999 47.619 13.65 0.00 0.00 3.53
4370 5517 0.237498 CGGAAGGAAAACGAAGGCAC 59.763 55.000 0.00 0.00 0.00 5.01
4434 5582 3.886505 TCATACTGGTTCAACCCAACAAC 59.113 43.478 3.42 0.00 37.50 3.32
4468 5617 6.959639 AGTAAACTTGTTCAACCATGACAT 57.040 33.333 0.00 0.00 34.61 3.06
5349 7385 4.099573 ACACTTACCTGAGCGCTTATACAT 59.900 41.667 13.26 0.00 0.00 2.29
5371 7407 3.255149 TCACTGGTCGAACTCCTCTTAAC 59.745 47.826 0.33 0.00 0.00 2.01
5374 7410 1.889829 CTCACTGGTCGAACTCCTCTT 59.110 52.381 0.33 0.00 0.00 2.85
5447 7483 0.179145 GCGTGCGCTCTAGGTTTAGA 60.179 55.000 9.73 0.00 38.26 2.10
5559 7597 3.066203 CGCCTTCTGGTTTGTTTAACTGT 59.934 43.478 0.00 0.00 36.93 3.55
5577 7615 3.306472 TTATATTTCTTTGCCCCGCCT 57.694 42.857 0.00 0.00 0.00 5.52
6181 8350 5.381757 TGGGGGATTGAGATTATTTTACGG 58.618 41.667 0.00 0.00 0.00 4.02
6273 8455 2.737180 CGTGAGTGGCCTGACTGT 59.263 61.111 3.32 0.00 0.00 3.55
6290 8472 2.100584 TGAAATTTGGTGTCACAGTGGC 59.899 45.455 5.12 0.00 0.00 5.01
6432 8615 4.335594 AGTTGTTGCTCAAAACTGGTACTC 59.664 41.667 0.00 0.00 37.81 2.59
6540 8723 4.465632 AGGTGACGTATGCTTTGTGATA 57.534 40.909 0.00 0.00 0.00 2.15
6712 8898 1.893808 CTTGTGGCAACCGCTCAGT 60.894 57.895 0.00 0.00 38.60 3.41
6713 8899 2.620112 CCTTGTGGCAACCGCTCAG 61.620 63.158 0.00 0.00 38.60 3.35
6714 8900 2.594303 CCTTGTGGCAACCGCTCA 60.594 61.111 0.00 0.00 38.60 4.26
6715 8901 3.365265 CCCTTGTGGCAACCGCTC 61.365 66.667 0.00 0.00 38.60 5.03
6721 8908 0.685785 TTTGCAGTCCCTTGTGGCAA 60.686 50.000 0.00 0.00 42.15 4.52
6757 8945 2.769195 GGGGGCGTGGGTATGGTA 60.769 66.667 0.00 0.00 0.00 3.25
6975 9166 0.884704 GGTTGCTGCTCTTGTCCGAA 60.885 55.000 0.00 0.00 0.00 4.30
7100 9291 1.303888 ACCTCGTCGGCCTTGTCTA 60.304 57.895 0.00 0.00 35.61 2.59
7517 9760 5.708877 AGAACGGAATCTATGCTAGTACC 57.291 43.478 0.00 0.00 0.00 3.34
7831 10076 9.406828 GTACACAAAGTCCTGAAATTAAATTCC 57.593 33.333 0.85 0.00 0.00 3.01
8032 10284 5.116069 ACCGACAAATGTGTACAATTTCC 57.884 39.130 0.00 1.13 38.41 3.13
8195 10448 3.431626 CGCTGTAGAATGGGTGGATTACA 60.432 47.826 0.00 0.00 0.00 2.41
8347 10607 2.710096 AATATCCCAACCTGTCACGG 57.290 50.000 0.00 0.00 0.00 4.94
8410 10670 3.949754 GACTTTCATGCATCTTCATCCCA 59.050 43.478 0.00 0.00 0.00 4.37
8861 11129 2.496899 ATGTTGTCCTCGGCTGAAAT 57.503 45.000 0.00 0.00 0.00 2.17
9204 11476 9.077885 ACTGATAGCCTTTTGATTTAGTTTTGA 57.922 29.630 0.00 0.00 0.00 2.69
9223 11496 4.720649 TTCTCCTTGGTCGAACTGATAG 57.279 45.455 0.33 0.00 0.00 2.08
9254 11527 4.446719 GGCTGATGCTTCTGTTTTCTTTTG 59.553 41.667 8.05 0.00 39.59 2.44
9291 11564 3.877508 GTGTTGTCTGAAACTAGTGCCTT 59.122 43.478 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.