Multiple sequence alignment - TraesCS2A01G034100

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 TraesCS2A01G034100 chr2A 100.000 2288 0 0 1 2288 15078734 15076447 0.000000e+00 4226
1 TraesCS2A01G034100 chr2A 92.523 1538 52 14 788 2286 15100150 15098637 0.000000e+00 2145
2 TraesCS2A01G034100 chr2A 92.523 1538 52 15 788 2286 15115936 15114423 0.000000e+00 2145
3 TraesCS2A01G034100 chr2A 96.465 792 21 3 1 791 15116755 15115970 0.000000e+00 1301
4 TraesCS2A01G034100 chr2A 96.731 520 15 1 1 520 15101120 15100603 0.000000e+00 865
5 TraesCS2A01G034100 chr2A 96.731 520 15 1 1 520 15120824 15120307 0.000000e+00 865
6 TraesCS2A01G034100 chr2A 86.479 710 67 16 1393 2078 15070218 15069514 0.000000e+00 752
7 TraesCS2A01G034100 chr2A 95.582 249 6 2 544 791 15100428 15100184 5.920000e-106 394
8 TraesCS2A01G034100 chr2A 86.166 253 35 0 344 596 671337204 671336952 8.050000e-70 274
9 TraesCS2A01G034100 chr2A 83.607 183 23 2 584 763 15112337 15112159 5.060000e-37 165
10 TraesCS2A01G034100 chr2A 83.060 183 24 2 584 763 15096550 15096372 2.350000e-35 159
11 TraesCS2A01G034100 chr2A 97.561 82 2 0 1902 1983 15128279 15128198 8.520000e-30 141
12 TraesCS2A01G034100 chr2A 83.459 133 15 5 2006 2136 15069696 15069569 1.440000e-22 117
13 TraesCS2A01G034100 chr2D 89.283 2286 127 43 12 2248 12979566 12977350 0.000000e+00 2756
14 TraesCS2A01G034100 chr2D 93.246 1525 68 17 788 2288 13067232 13065719 0.000000e+00 2213
15 TraesCS2A01G034100 chr2D 87.126 1336 122 31 788 2087 13055946 13054625 0.000000e+00 1469
16 TraesCS2A01G034100 chr2D 94.836 794 32 4 1 791 13068053 13067266 0.000000e+00 1230
17 TraesCS2A01G034100 chr2D 86.611 239 32 0 344 582 530480586 530480824 4.850000e-67 265
18 TraesCS2A01G034100 chr2D 78.378 222 41 7 125 345 13063830 13063615 1.100000e-28 137
19 TraesCS2A01G034100 chr2D 83.916 143 19 4 204 345 12975222 12975083 1.430000e-27 134
20 TraesCS2A01G034100 chr7B 86.831 243 27 4 344 582 75149787 75150028 1.350000e-67 267
21 TraesCS2A01G034100 chr4B 85.020 247 37 0 344 590 357958296 357958050 3.770000e-63 252


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 TraesCS2A01G034100 chr2A 15076447 15078734 2287 True 4226.000000 4226 100.0000 1 2288 1 chr2A.!!$R1 2287
1 TraesCS2A01G034100 chr2A 15112159 15120824 8665 True 1119.000000 2145 92.3315 1 2286 4 chr2A.!!$R6 2285
2 TraesCS2A01G034100 chr2A 15096372 15101120 4748 True 890.750000 2145 91.9740 1 2286 4 chr2A.!!$R5 2285
3 TraesCS2A01G034100 chr2A 15069514 15070218 704 True 434.500000 752 84.9690 1393 2136 2 chr2A.!!$R4 743
4 TraesCS2A01G034100 chr2D 13054625 13055946 1321 True 1469.000000 1469 87.1260 788 2087 1 chr2D.!!$R1 1299
5 TraesCS2A01G034100 chr2D 12975083 12979566 4483 True 1445.000000 2756 86.5995 12 2248 2 chr2D.!!$R2 2236
6 TraesCS2A01G034100 chr2D 13063615 13068053 4438 True 1193.333333 2213 88.8200 1 2288 3 chr2D.!!$R3 2287

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
667 4740 0.753262 GTCGCCTGGACACTGGATAT 59.247 55.0 0.0 0.0 45.36 1.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 6401 2.357952 GAGTTCAACGCCAAACCTTTCT 59.642 45.455 0.0 0.0 0.0 2.52 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
132 135 7.390718 CACAGCTAAGGTCCAGTAAAAATAGTT 59.609 37.037 0.00 0.00 0.00 2.24
279 282 9.620259 AAGAGAGATAGGTTAATCCATTCAAAC 57.380 33.333 0.00 0.00 39.02 2.93
582 4654 2.865119 TTAAAAAGGACGGGAGGGAC 57.135 50.000 0.00 0.00 0.00 4.46
650 4723 2.165845 AGTGTATTAGCAGGACGTGGTC 59.834 50.000 2.65 0.00 38.14 4.02
665 4738 2.982130 GTCGCCTGGACACTGGAT 59.018 61.111 0.00 0.00 45.36 3.41
666 4739 2.199117 GTCGCCTGGACACTGGATA 58.801 57.895 0.00 0.00 45.36 2.59
667 4740 0.753262 GTCGCCTGGACACTGGATAT 59.247 55.000 0.00 0.00 45.36 1.63
840 4956 3.888930 TCGCATTTTCTCCTCCTTTTGTT 59.111 39.130 0.00 0.00 0.00 2.83
913 5031 9.866655 TTCATTGGCTCTCTATAAATACCAAAT 57.133 29.630 0.00 0.00 39.02 2.32
973 5096 3.620488 AGCCAATACACACACCAATAGG 58.380 45.455 0.00 0.00 42.21 2.57
1012 5135 2.226962 AGCATCAATGGCTTCTGGTT 57.773 45.000 0.00 0.00 38.81 3.67
1062 5185 0.040058 TGCTGGCCATCCTGTTCATT 59.960 50.000 5.51 0.00 34.18 2.57
1464 5587 4.565564 GGAGCGTACGTATGTTGAGAATTT 59.434 41.667 17.90 0.00 0.00 1.82
1511 5652 1.300620 GCTGCCAGTCACGTGTACA 60.301 57.895 16.51 6.96 0.00 2.90
1694 5837 6.152379 CGTCACTGCAGCTTCTATATATTGA 58.848 40.000 15.27 2.11 0.00 2.57
1778 5925 1.034838 GTGGGTGGTGAGTTGTGCAA 61.035 55.000 0.00 0.00 0.00 4.08
1816 5963 5.794894 TCTTGTTTCCTAGCTCTACTTTGG 58.205 41.667 0.00 0.00 0.00 3.28
1908 6055 1.541233 GGTGGCTCGATTCCTGTATGG 60.541 57.143 5.59 0.00 37.10 2.74
1980 6149 9.114952 TGTTGTGTAGTCATGACTGAAATAAAA 57.885 29.630 33.76 17.08 42.52 1.52
2045 6232 1.335132 TAGTGAATCACGCCCCCTCC 61.335 60.000 7.83 0.00 39.64 4.30
2127 6315 3.627123 TGAGGAAACATATGCAATGGACG 59.373 43.478 1.58 0.00 0.00 4.79
2131 6320 3.763097 AACATATGCAATGGACGTGTG 57.237 42.857 1.58 0.00 0.00 3.82
2145 6334 4.338400 TGGACGTGTGATGAAGATAGTAGG 59.662 45.833 0.00 0.00 0.00 3.18
2163 6354 5.238583 AGTAGGAACCATTTTTCGACAGAG 58.761 41.667 0.00 0.00 0.00 3.35
2164 6355 4.351874 AGGAACCATTTTTCGACAGAGA 57.648 40.909 0.00 0.00 0.00 3.10
2210 6401 9.337396 ACTATATTGACTGTTTCTGTTGTTTGA 57.663 29.630 0.00 0.00 0.00 2.69
2250 6441 2.746277 GTACCAGCCAAGGCACCG 60.746 66.667 14.40 2.28 44.88 4.94
2259 6450 1.600023 CCAAGGCACCGAAGTACAAA 58.400 50.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.516698 AGCTGTAATTAATTGGCATCCTCG 59.483 41.667 11.05 0.25 0.00 4.63
132 135 5.892119 ACTGAAGGTCGGAGATAAGTTATCA 59.108 40.000 22.00 1.66 40.67 2.15
279 282 7.864379 AGATGTTTTGTGCAGAAACAGAAATAG 59.136 33.333 24.22 0.00 46.49 1.73
574 4646 4.412528 ACCATTTCTGTTATAGTCCCTCCC 59.587 45.833 0.00 0.00 0.00 4.30
582 4654 7.537306 CGTTTTTCCACACCATTTCTGTTATAG 59.463 37.037 0.00 0.00 0.00 1.31
650 4723 4.462834 TCTTATATATCCAGTGTCCAGGCG 59.537 45.833 0.00 0.00 0.00 5.52
840 4956 2.519771 TCTAGTTAGCCTCCCGTTGA 57.480 50.000 0.00 0.00 0.00 3.18
1012 5135 2.354103 CGGCAACCATCTTCTTCTGAGA 60.354 50.000 0.00 0.00 0.00 3.27
1293 5416 3.079578 CTGAAGAAGCTGCAATCTGGAA 58.920 45.455 1.02 0.00 0.00 3.53
1464 5587 1.070786 GAGCTGTGACCGGGAAACA 59.929 57.895 6.32 6.15 0.00 2.83
1511 5652 4.400251 CCAGCAATACATGTGGAAGTCATT 59.600 41.667 9.11 0.00 34.19 2.57
1518 5659 5.015515 TCATTTTCCAGCAATACATGTGGA 58.984 37.500 9.11 2.08 37.41 4.02
1550 5693 6.915300 CCAAATGACGAAACAGACAAATACAA 59.085 34.615 0.00 0.00 0.00 2.41
1712 5857 5.337330 GGATAAGTTGGTGCACTAGTACACT 60.337 44.000 22.50 8.16 36.99 3.55
1878 6025 2.418368 TCGAGCCACCAATAAATGCT 57.582 45.000 0.00 0.00 34.40 3.79
1908 6055 6.313905 GTCGTTCCATTACATGATCCATATCC 59.686 42.308 0.00 0.00 0.00 2.59
1982 6151 6.899393 TTGCATATGTTTCCTCAGTCTTTT 57.101 33.333 4.29 0.00 0.00 2.27
1987 6156 4.858850 TCCATTGCATATGTTTCCTCAGT 58.141 39.130 4.29 0.00 0.00 3.41
2086 6273 4.023193 CCTCAGCCTTCGTATTTGTTGTTT 60.023 41.667 0.00 0.00 0.00 2.83
2127 6315 6.222038 TGGTTCCTACTATCTTCATCACAC 57.778 41.667 0.00 0.00 0.00 3.82
2131 6320 8.552034 CGAAAAATGGTTCCTACTATCTTCATC 58.448 37.037 0.00 0.00 0.00 2.92
2145 6334 5.924475 TTCTCTCTGTCGAAAAATGGTTC 57.076 39.130 0.00 0.00 0.00 3.62
2194 6385 5.954335 ACCTTTCTCAAACAACAGAAACAG 58.046 37.500 0.00 0.00 34.39 3.16
2210 6401 2.357952 GAGTTCAACGCCAAACCTTTCT 59.642 45.455 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.