Multiple sequence alignment - TraesCS4B01G010600

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 TraesCS4B01G010600 chr4B 100.000 2919 0 0 1 2919 7100721 7103639 0.000000e+00 5391
1 TraesCS4B01G010600 chr4B 95.895 1291 52 1 1630 2919 424430841 424432131 0.000000e+00 2089
2 TraesCS4B01G010600 chr4B 93.445 656 37 5 1 653 525519041 525518389 0.000000e+00 968
3 TraesCS4B01G010600 chr4B 87.840 699 71 8 1 697 275868056 275868742 0.000000e+00 808
4 TraesCS4B01G010600 chr4B 91.329 173 15 0 697 869 576736086 576735914 1.350000e-58 237
5 TraesCS4B01G010600 chr2B 93.638 2955 135 34 1 2919 692693934 692690997 0.000000e+00 4366
6 TraesCS4B01G010600 chr7A 93.324 2936 133 24 1 2919 730332306 730329417 0.000000e+00 4277
7 TraesCS4B01G010600 chr7A 93.086 2936 139 23 1 2919 730379574 730376686 0.000000e+00 4239
8 TraesCS4B01G010600 chr7A 91.622 2041 118 13 1 2014 654048952 654050966 0.000000e+00 2772
9 TraesCS4B01G010600 chr7A 96.272 912 32 1 2010 2919 654052708 654053619 0.000000e+00 1495
10 TraesCS4B01G010600 chr7A 89.915 704 52 10 1 701 661554795 661555482 0.000000e+00 889
11 TraesCS4B01G010600 chr4A 93.323 2591 138 18 353 2919 670764585 670767164 0.000000e+00 3794
12 TraesCS4B01G010600 chr3A 95.900 1683 57 3 1238 2919 21307079 21308750 0.000000e+00 2715
13 TraesCS4B01G010600 chr3A 95.000 160 8 0 710 869 689948249 689948090 4.830000e-63 252
14 TraesCS4B01G010600 chr2A 95.781 1683 60 2 1238 2919 746144550 746142878 0.000000e+00 2704
15 TraesCS4B01G010600 chr2A 95.425 1683 66 2 1238 2919 22312388 22310716 0.000000e+00 2671
16 TraesCS4B01G010600 chr2A 92.824 655 43 4 1 653 704438436 704437784 0.000000e+00 946
17 TraesCS4B01G010600 chr2A 93.750 160 10 0 710 869 111083346 111083187 1.050000e-59 241
18 TraesCS4B01G010600 chr5A 94.003 1484 71 5 991 2456 437594021 437592538 0.000000e+00 2231
19 TraesCS4B01G010600 chr5A 93.151 657 38 6 1 653 547494113 547493460 0.000000e+00 957
20 TraesCS4B01G010600 chr5A 92.409 303 19 3 691 991 437449048 437449348 2.080000e-116 429
21 TraesCS4B01G010600 chr5A 89.773 176 18 0 691 866 433438117 433438292 2.930000e-55 226
22 TraesCS4B01G010600 chr1D 87.374 1291 113 30 868 2130 462746505 462745237 0.000000e+00 1435
23 TraesCS4B01G010600 chr1B 86.345 1201 116 23 869 2050 637833316 637832145 0.000000e+00 1266
24 TraesCS4B01G010600 chr1A 84.885 1171 114 29 967 2130 554534929 554533815 0.000000e+00 1123
25 TraesCS4B01G010600 chr5B 91.926 706 42 5 1 704 258566575 258565883 0.000000e+00 974
26 TraesCS4B01G010600 chrUn 91.880 702 39 6 1 697 62995641 62996329 0.000000e+00 965
27 TraesCS4B01G010600 chr6A 89.804 716 51 13 1 701 546014564 546015272 0.000000e+00 898
28 TraesCS4B01G010600 chr4D 89.831 177 17 1 697 873 289985850 289986025 2.930000e-55 226


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 TraesCS4B01G010600 chr4B 7100721 7103639 2918 False 5391.0 5391 100.000 1 2919 1 chr4B.!!$F1 2918
1 TraesCS4B01G010600 chr4B 424430841 424432131 1290 False 2089.0 2089 95.895 1630 2919 1 chr4B.!!$F3 1289
2 TraesCS4B01G010600 chr4B 525518389 525519041 652 True 968.0 968 93.445 1 653 1 chr4B.!!$R1 652
3 TraesCS4B01G010600 chr4B 275868056 275868742 686 False 808.0 808 87.840 1 697 1 chr4B.!!$F2 696
4 TraesCS4B01G010600 chr2B 692690997 692693934 2937 True 4366.0 4366 93.638 1 2919 1 chr2B.!!$R1 2918
5 TraesCS4B01G010600 chr7A 730329417 730332306 2889 True 4277.0 4277 93.324 1 2919 1 chr7A.!!$R1 2918
6 TraesCS4B01G010600 chr7A 730376686 730379574 2888 True 4239.0 4239 93.086 1 2919 1 chr7A.!!$R2 2918
7 TraesCS4B01G010600 chr7A 654048952 654053619 4667 False 2133.5 2772 93.947 1 2919 2 chr7A.!!$F2 2918
8 TraesCS4B01G010600 chr7A 661554795 661555482 687 False 889.0 889 89.915 1 701 1 chr7A.!!$F1 700
9 TraesCS4B01G010600 chr4A 670764585 670767164 2579 False 3794.0 3794 93.323 353 2919 1 chr4A.!!$F1 2566
10 TraesCS4B01G010600 chr3A 21307079 21308750 1671 False 2715.0 2715 95.900 1238 2919 1 chr3A.!!$F1 1681
11 TraesCS4B01G010600 chr2A 746142878 746144550 1672 True 2704.0 2704 95.781 1238 2919 1 chr2A.!!$R4 1681
12 TraesCS4B01G010600 chr2A 22310716 22312388 1672 True 2671.0 2671 95.425 1238 2919 1 chr2A.!!$R1 1681
13 TraesCS4B01G010600 chr2A 704437784 704438436 652 True 946.0 946 92.824 1 653 1 chr2A.!!$R3 652
14 TraesCS4B01G010600 chr5A 437592538 437594021 1483 True 2231.0 2231 94.003 991 2456 1 chr5A.!!$R1 1465
15 TraesCS4B01G010600 chr5A 547493460 547494113 653 True 957.0 957 93.151 1 653 1 chr5A.!!$R2 652
16 TraesCS4B01G010600 chr1D 462745237 462746505 1268 True 1435.0 1435 87.374 868 2130 1 chr1D.!!$R1 1262
17 TraesCS4B01G010600 chr1B 637832145 637833316 1171 True 1266.0 1266 86.345 869 2050 1 chr1B.!!$R1 1181
18 TraesCS4B01G010600 chr1A 554533815 554534929 1114 True 1123.0 1123 84.885 967 2130 1 chr1A.!!$R1 1163
19 TraesCS4B01G010600 chr5B 258565883 258566575 692 True 974.0 974 91.926 1 704 1 chr5B.!!$R1 703
20 TraesCS4B01G010600 chrUn 62995641 62996329 688 False 965.0 965 91.880 1 697 1 chrUn.!!$F1 696
21 TraesCS4B01G010600 chr6A 546014564 546015272 708 False 898.0 898 89.804 1 701 1 chr6A.!!$F1 700

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
801 856 0.034896 GTCCCCACATCGCCGAATAT 59.965 55.0 0.0 0.0 0.0 1.28 F
1282 1391 0.108963 CGGTTGTTGTAGGGGTTGGA 59.891 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 1932 1.490574 ACTCTGCATACTCCCTGTCC 58.509 55.0 0.00 0.00 0.0 4.02 R
2100 3987 1.889545 AAAGAAGCACCTGACAGAGC 58.110 50.0 3.32 7.87 0.0 4.09 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
50 51 9.137459 TGGAAAACTTTTGGTGTTTCTATGATA 57.863 29.630 0.00 0.00 36.72 2.15
170 175 4.368315 GGCGGAAATTTGTCTTTTTCACT 58.632 39.130 0.00 0.00 34.29 3.41
418 424 5.005682 GTGAAAATTTGTGTGGTGCTCTTTC 59.994 40.000 0.00 0.00 0.00 2.62
581 618 2.965147 TCTGCATCCCACATCGATCTAA 59.035 45.455 0.00 0.00 0.00 2.10
739 794 2.430921 GTGTCCACGAGCTCCACG 60.431 66.667 8.47 0.00 0.00 4.94
801 856 0.034896 GTCCCCACATCGCCGAATAT 59.965 55.000 0.00 0.00 0.00 1.28
952 1023 4.974438 TCCCCACTCCACCGCCTT 62.974 66.667 0.00 0.00 0.00 4.35
1020 1101 1.561643 TGGAGAACCTGATCTCGCTT 58.438 50.000 0.00 0.00 45.54 4.68
1103 1184 4.668151 CCTCTGGGACTCGCTACT 57.332 61.111 0.00 0.00 33.58 2.57
1154 1235 2.590114 CCCCGTCCGTTTTCTCCCT 61.590 63.158 0.00 0.00 0.00 4.20
1162 1243 1.889530 CGTTTTCTCCCTCCTCCGCT 61.890 60.000 0.00 0.00 0.00 5.52
1167 1248 1.153989 CTCCCTCCTCCGCTGGATA 59.846 63.158 0.00 0.00 35.30 2.59
1190 1271 2.959484 GCCCCAGCTGTGTCTGCTA 61.959 63.158 13.81 0.00 36.55 3.49
1196 1277 2.168106 CCAGCTGTGTCTGCTAGATCTT 59.832 50.000 13.81 0.00 36.55 2.40
1282 1391 0.108963 CGGTTGTTGTAGGGGTTGGA 59.891 55.000 0.00 0.00 0.00 3.53
1340 1449 7.282585 TCTTCTGCTATATAGTTTGGTTGCAT 58.717 34.615 11.38 0.00 0.00 3.96
1422 1555 6.885922 ACTATTACCACTTGGGATCAACTAC 58.114 40.000 0.00 0.00 41.15 2.73
1555 1689 4.188462 CAATTACCAGATGCGGTTCTGTA 58.812 43.478 9.45 1.90 41.30 2.74
1670 1806 5.692115 TCAGGTATGGTTATTCAAGCAGA 57.308 39.130 0.00 0.00 44.81 4.26
1765 1902 3.632080 ATTGTCACCCGTCGCCCA 61.632 61.111 0.00 0.00 0.00 5.36
1795 1932 3.152341 GCAACTCCATAGGATTGATGGG 58.848 50.000 1.97 0.00 43.58 4.00
1890 2027 7.665559 TCTTTGTCTTATTTCCAAGTGCTATGT 59.334 33.333 0.00 0.00 0.00 2.29
1893 2033 6.030228 GTCTTATTTCCAAGTGCTATGTTGC 58.970 40.000 0.00 0.00 0.00 4.17
2190 4077 6.185399 CCGTTAAACAAGCATCTATTCTTCG 58.815 40.000 0.00 0.00 0.00 3.79
2197 4084 6.582636 ACAAGCATCTATTCTTCGTGGAATA 58.417 36.000 10.53 10.53 37.20 1.75
2209 4096 9.613428 ATTCTTCGTGGAATATTTGTCTATCAA 57.387 29.630 4.39 0.00 34.59 2.57
2613 4500 0.480690 TTGTTAAGAGGGCCCTGCAA 59.519 50.000 34.59 21.62 0.00 4.08
2682 4569 5.909621 ATCAATACAGCTGACATGCTTTT 57.090 34.783 23.35 0.00 41.98 2.27
2887 4774 2.806434 ACAGCTCAATGCCACCAAATA 58.194 42.857 0.00 0.00 44.23 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 175 7.229907 GGTGTAAAAAGTTTTGATCCACCTCTA 59.770 37.037 20.61 0.64 35.50 2.43
264 269 7.812669 GTGAAGGAACTACCAAATAATTGTTGG 59.187 37.037 17.03 17.03 45.37 3.77
717 760 1.666011 GAGCTCGTGGACACCTTCA 59.334 57.895 0.00 0.00 0.00 3.02
739 794 3.157252 TCGATGCAGAGGGGAGCC 61.157 66.667 0.00 0.00 0.00 4.70
783 838 0.034756 CATATTCGGCGATGTGGGGA 59.965 55.000 11.76 0.00 0.00 4.81
797 852 2.224066 CGACGGGGAAGAAGCTCATATT 60.224 50.000 0.00 0.00 0.00 1.28
801 856 2.646175 CCGACGGGGAAGAAGCTCA 61.646 63.158 5.81 0.00 38.47 4.26
862 925 1.021390 CGAGCTGTGGATGGTTGGAC 61.021 60.000 0.00 0.00 0.00 4.02
866 929 1.078848 GCTCGAGCTGTGGATGGTT 60.079 57.895 29.88 0.00 38.21 3.67
916 979 1.152922 GGGAGGGAGACGAGACGAT 60.153 63.158 0.00 0.00 0.00 3.73
1020 1101 0.165727 CGCGTTGCAGCTTATTGACA 59.834 50.000 0.00 0.00 34.40 3.58
1103 1184 2.431771 CGACGACGGCAATGGACA 60.432 61.111 0.00 0.00 35.72 4.02
1154 1235 3.471620 GCCATATCCAGCGGAGGA 58.528 61.111 3.76 1.06 43.01 3.71
1162 1243 4.269523 GCTGGGGCGCCATATCCA 62.270 66.667 30.85 24.37 0.00 3.41
1282 1391 0.749454 CAGCGGCCCAAATCTAGCTT 60.749 55.000 0.00 0.00 32.05 3.74
1402 1523 3.055675 CCGTAGTTGATCCCAAGTGGTAA 60.056 47.826 0.00 0.00 36.65 2.85
1422 1555 1.081509 CGTGAAACAACATGCCCCG 60.082 57.895 0.00 0.00 35.74 5.73
1555 1689 5.759763 GCCAAAGGAGTTCAAATGTCAAAAT 59.240 36.000 0.00 0.00 0.00 1.82
1670 1806 2.288395 CGCCAAAATGGACAAGCTCTTT 60.288 45.455 0.00 0.00 40.96 2.52
1765 1902 2.026822 CCTATGGAGTTGCAGAACCAGT 60.027 50.000 12.02 5.29 35.84 4.00
1795 1932 1.490574 ACTCTGCATACTCCCTGTCC 58.509 55.000 0.00 0.00 0.00 4.02
1890 2027 8.398878 TGCATCAATCTTAATATCATCAGCAA 57.601 30.769 0.00 0.00 0.00 3.91
2100 3987 1.889545 AAAGAAGCACCTGACAGAGC 58.110 50.000 3.32 7.87 0.00 4.09
2136 4023 8.409371 CAATCAGTACTGCTATCTCTAACAGAA 58.591 37.037 18.45 0.00 33.62 3.02
2157 4044 4.135306 TGCTTGTTTAACGGGTACAATCA 58.865 39.130 0.00 0.00 31.96 2.57
2197 4084 8.432013 TGCCATCATACTAGTTGATAGACAAAT 58.568 33.333 15.61 0.00 40.36 2.32
2266 4153 6.864165 GCCATTAGTTCGTTTTAACATGGAAA 59.136 34.615 10.06 0.00 36.04 3.13
2443 4330 7.367285 CAAAATTAGACAGGGAAACGAAATGA 58.633 34.615 0.00 0.00 0.00 2.57
2682 4569 5.342806 CAATCACTGCACGTAAAAGAAGA 57.657 39.130 0.00 0.00 0.00 2.87
2858 4745 2.490903 GGCATTGAGCTGTTGACAGAAT 59.509 45.455 14.98 3.46 46.59 2.40


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

AutoCloner maintained by Alex Coulton.