Multiple sequence alignment - TraesCS6A01G089900

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 TraesCS6A01G089900 chr6A 100.000 2724 0 0 1 2724 58005818 58003095 0.000000e+00 5031
1 TraesCS6A01G089900 chr6A 86.675 1591 174 27 530 2095 90085498 90087075 0.000000e+00 1729
2 TraesCS6A01G089900 chr6A 97.235 651 14 1 1 651 10051840 10051194 0.000000e+00 1099
3 TraesCS6A01G089900 chr3B 96.409 2701 93 3 26 2724 802583629 802586327 0.000000e+00 4447
4 TraesCS6A01G089900 chr3B 86.641 262 27 3 2094 2349 32013573 32013832 1.600000e-72 283
5 TraesCS6A01G089900 chr5B 91.727 1523 122 4 486 2005 607045038 607046559 0.000000e+00 2111
6 TraesCS6A01G089900 chr5B 91.088 1526 129 5 486 2005 607101873 607103397 0.000000e+00 2058
7 TraesCS6A01G089900 chr5B 92.295 610 38 3 2123 2724 607103653 607104261 0.000000e+00 857
8 TraesCS6A01G089900 chr5B 92.397 605 39 2 2126 2724 607046820 607047423 0.000000e+00 856
9 TraesCS6A01G089900 chr5B 95.381 433 19 1 1 433 607044603 607045034 0.000000e+00 688
10 TraesCS6A01G089900 chr5B 95.150 433 20 1 1 433 607101438 607101869 0.000000e+00 682
11 TraesCS6A01G089900 chr4D 88.959 1422 147 8 682 2095 150016632 150018051 0.000000e+00 1748
12 TraesCS6A01G089900 chr4D 91.801 622 43 3 2109 2724 278204575 278203956 0.000000e+00 859
13 TraesCS6A01G089900 chr4D 92.411 593 37 3 2138 2724 150018166 150018756 0.000000e+00 839
14 TraesCS6A01G089900 chr1A 87.054 1568 173 20 558 2098 336239204 336237640 0.000000e+00 1744
15 TraesCS6A01G089900 chr1A 98.464 651 10 0 1 651 336239858 336239208 0.000000e+00 1147
16 TraesCS6A01G089900 chr1A 97.542 651 15 1 1 651 320287784 320287135 0.000000e+00 1112
17 TraesCS6A01G089900 chr1A 91.814 623 43 3 2108 2724 336237527 336236907 0.000000e+00 861
18 TraesCS6A01G089900 chr7A 88.260 1431 141 17 558 1963 6709564 6710992 0.000000e+00 1687
19 TraesCS6A01G089900 chr7A 88.144 1417 157 10 687 2098 148015624 148014214 0.000000e+00 1676
20 TraesCS6A01G089900 chr7A 97.067 682 20 0 1 682 518745521 518744840 0.000000e+00 1149
21 TraesCS6A01G089900 chr7A 97.696 651 14 1 1 651 6708911 6709560 0.000000e+00 1118
22 TraesCS6A01G089900 chr7A 92.135 623 41 3 2108 2724 6746060 6746680 0.000000e+00 872
23 TraesCS6A01G089900 chr5A 89.794 1264 124 5 687 1947 605326610 605325349 0.000000e+00 1615
24 TraesCS6A01G089900 chr6D 92.951 610 34 3 2123 2724 341372685 341373293 0.000000e+00 880
25 TraesCS6A01G089900 chr7D 88.768 641 39 9 2092 2724 15629421 15628806 0.000000e+00 754
26 TraesCS6A01G089900 chr7B 95.381 433 20 0 1 433 664313417 664313849 0.000000e+00 689
27 TraesCS6A01G089900 chr7B 96.629 356 12 0 486 841 664313853 664314208 2.340000e-165 592
28 TraesCS6A01G089900 chr6B 97.312 372 9 1 398 768 48105843 48105472 4.950000e-177 630


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 TraesCS6A01G089900 chr6A 58003095 58005818 2723 True 5031.000000 5031 100.000000 1 2724 1 chr6A.!!$R2 2723
1 TraesCS6A01G089900 chr6A 90085498 90087075 1577 False 1729.000000 1729 86.675000 530 2095 1 chr6A.!!$F1 1565
2 TraesCS6A01G089900 chr6A 10051194 10051840 646 True 1099.000000 1099 97.235000 1 651 1 chr6A.!!$R1 650
3 TraesCS6A01G089900 chr3B 802583629 802586327 2698 False 4447.000000 4447 96.409000 26 2724 1 chr3B.!!$F2 2698
4 TraesCS6A01G089900 chr5B 607044603 607047423 2820 False 1218.333333 2111 93.168333 1 2724 3 chr5B.!!$F1 2723
5 TraesCS6A01G089900 chr5B 607101438 607104261 2823 False 1199.000000 2058 92.844333 1 2724 3 chr5B.!!$F2 2723
6 TraesCS6A01G089900 chr4D 150016632 150018756 2124 False 1293.500000 1748 90.685000 682 2724 2 chr4D.!!$F1 2042
7 TraesCS6A01G089900 chr4D 278203956 278204575 619 True 859.000000 859 91.801000 2109 2724 1 chr4D.!!$R1 615
8 TraesCS6A01G089900 chr1A 336236907 336239858 2951 True 1250.666667 1744 92.444000 1 2724 3 chr1A.!!$R2 2723
9 TraesCS6A01G089900 chr1A 320287135 320287784 649 True 1112.000000 1112 97.542000 1 651 1 chr1A.!!$R1 650
10 TraesCS6A01G089900 chr7A 148014214 148015624 1410 True 1676.000000 1676 88.144000 687 2098 1 chr7A.!!$R1 1411
11 TraesCS6A01G089900 chr7A 6708911 6710992 2081 False 1402.500000 1687 92.978000 1 1963 2 chr7A.!!$F2 1962
12 TraesCS6A01G089900 chr7A 518744840 518745521 681 True 1149.000000 1149 97.067000 1 682 1 chr7A.!!$R2 681
13 TraesCS6A01G089900 chr7A 6746060 6746680 620 False 872.000000 872 92.135000 2108 2724 1 chr7A.!!$F1 616
14 TraesCS6A01G089900 chr5A 605325349 605326610 1261 True 1615.000000 1615 89.794000 687 1947 1 chr5A.!!$R1 1260
15 TraesCS6A01G089900 chr6D 341372685 341373293 608 False 880.000000 880 92.951000 2123 2724 1 chr6D.!!$F1 601
16 TraesCS6A01G089900 chr7D 15628806 15629421 615 True 754.000000 754 88.768000 2092 2724 1 chr7D.!!$R1 632
17 TraesCS6A01G089900 chr7B 664313417 664314208 791 False 640.500000 689 96.005000 1 841 2 chr7B.!!$F1 840

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
107 108 1.618837 TGGTCGGCTTATATCAGGCTC 59.381 52.381 8.64 2.46 37.2 4.70 F
1023 1169 3.191162 TGGATGAATTGAGCAAAGAACGG 59.809 43.478 0.00 0.00 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1237 1383 0.395312 TGAAGGTTTCCCCTCGTGAC 59.605 55.0 0.0 0.0 45.47 3.67 R
1971 2124 2.362397 TGAGATACATTCGTGCTCCTCC 59.638 50.0 0.0 0.0 30.84 4.30 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
107 108 1.618837 TGGTCGGCTTATATCAGGCTC 59.381 52.381 8.64 2.46 37.20 4.70
142 143 9.109393 GAAATATGTATGTTACAGAGGCTTTGA 57.891 33.333 12.54 0.00 42.77 2.69
331 332 8.651589 TCAGATTCCAGTATACCTATTCGAAT 57.348 34.615 16.15 16.15 0.00 3.34
506 507 3.973425 ACAGATTTTTGCCTAGCTCCAT 58.027 40.909 0.00 0.00 0.00 3.41
858 1003 6.874134 ACTACACGCTTGAATAATCAGTTTCT 59.126 34.615 0.00 0.00 36.78 2.52
919 1064 3.686726 AGCAGCGGTTGAAGAAAGAATAG 59.313 43.478 0.00 0.00 0.00 1.73
951 1096 7.761704 TGTCAAATCTATTGTAGAGAAGAGTGC 59.238 37.037 0.00 0.00 38.38 4.40
969 1114 5.649831 AGAGTGCCTTCAATTTTGATCCTAC 59.350 40.000 0.00 0.00 37.00 3.18
1022 1168 4.424061 TGGATGAATTGAGCAAAGAACG 57.576 40.909 0.00 0.00 0.00 3.95
1023 1169 3.191162 TGGATGAATTGAGCAAAGAACGG 59.809 43.478 0.00 0.00 0.00 4.44
1237 1383 2.672961 TCAGTCCGGCTACAGATTTG 57.327 50.000 0.00 0.00 0.00 2.32
1380 1526 5.547465 TGGTGACGATGTTGAAGTATTTCT 58.453 37.500 0.00 0.00 34.31 2.52
1526 1672 4.213564 CCTAAGAGAGGCAAAGACACAT 57.786 45.455 0.00 0.00 38.96 3.21
1555 1701 6.240894 TGAAGATCTGGTTGCTGTTAGAAAT 58.759 36.000 0.00 0.00 0.00 2.17
1558 1704 5.879223 AGATCTGGTTGCTGTTAGAAATGAG 59.121 40.000 0.00 0.00 0.00 2.90
1760 1913 4.408921 TCTGAAAGGAGAAAGAGTTGACCA 59.591 41.667 0.00 0.00 0.00 4.02
1869 2022 9.967346 TCGTTCTAGGTATTTTCATCTGAATAG 57.033 33.333 0.00 0.00 33.54 1.73
1971 2124 6.252967 TGTGCACTGTACCATGAATAAAAG 57.747 37.500 19.41 0.00 0.00 2.27
2058 2264 8.637986 ACTATGTTTCCTTTCATAAAAGCACAA 58.362 29.630 0.00 0.00 40.53 3.33
2139 2453 2.352960 GCTGCACTAGTTGATAGTTGCC 59.647 50.000 0.00 0.00 42.30 4.52
2349 2671 5.990996 TCAGCAATTTGATCCCTTTTTGAAC 59.009 36.000 0.00 0.00 0.00 3.18
2430 2752 7.944554 CCCCACTTGGAATATCAACTATATGTT 59.055 37.037 0.00 0.00 36.97 2.71
2456 2778 3.620488 GTCAATATTGGAGCCAACCTGA 58.380 45.455 15.36 5.09 38.88 3.86
2508 2831 6.435430 TGCGAATAAAGTTATGAAGTGCAT 57.565 33.333 0.00 0.00 41.08 3.96
2683 3006 3.016736 GCCTTTGGTTGCATCTAGCTTA 58.983 45.455 0.00 0.00 45.94 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 7.048512 GGTAACCAAGCATCAACTTAGATAGT 58.951 38.462 0.00 0.00 39.32 2.12
481 482 5.188948 TGGAGCTAGGCAAAAATCTGTAGTA 59.811 40.000 0.00 0.00 0.00 1.82
652 745 2.826725 AGACAAGGACCCTACTCGAAAG 59.173 50.000 0.00 0.00 0.00 2.62
858 1003 7.984422 TGAGAAACAATGAAATTAGCTCTCA 57.016 32.000 0.00 0.00 32.46 3.27
956 1101 8.592809 TGGCATTTTTGTAGTAGGATCAAAATT 58.407 29.630 0.00 0.00 39.59 1.82
957 1102 8.133024 TGGCATTTTTGTAGTAGGATCAAAAT 57.867 30.769 0.00 0.00 39.59 1.82
969 1114 5.757320 TCAATGGTTGTTGGCATTTTTGTAG 59.243 36.000 0.00 0.00 0.00 2.74
1022 1168 2.680339 GCTTTGTATCTCCACTTCTGCC 59.320 50.000 0.00 0.00 0.00 4.85
1023 1169 3.604582 AGCTTTGTATCTCCACTTCTGC 58.395 45.455 0.00 0.00 0.00 4.26
1157 1303 1.305930 CCCTCCGCTGTTTTACCTGC 61.306 60.000 0.00 0.00 0.00 4.85
1237 1383 0.395312 TGAAGGTTTCCCCTCGTGAC 59.605 55.000 0.00 0.00 45.47 3.67
1284 1430 7.280205 CAGGTAATGTTGGACTAGGTGAATTAC 59.720 40.741 0.00 1.48 0.00 1.89
1291 1437 3.182152 AGCAGGTAATGTTGGACTAGGT 58.818 45.455 0.00 0.00 0.00 3.08
1380 1526 5.992829 TCCATACGTTCTGCTCTTTTAACAA 59.007 36.000 0.00 0.00 0.00 2.83
1425 1571 2.102420 AGTGTGTTCATGTCTTCCGTCA 59.898 45.455 0.00 0.00 0.00 4.35
1426 1572 2.755650 AGTGTGTTCATGTCTTCCGTC 58.244 47.619 0.00 0.00 0.00 4.79
1526 1672 3.264947 CAGCAACCAGATCTTCAATCGA 58.735 45.455 0.00 0.00 0.00 3.59
1555 1701 6.121776 TCCACATAAGTTTTAAGCTCCTCA 57.878 37.500 0.00 0.00 0.00 3.86
1558 1704 6.374333 TCACATCCACATAAGTTTTAAGCTCC 59.626 38.462 0.00 0.00 0.00 4.70
1971 2124 2.362397 TGAGATACATTCGTGCTCCTCC 59.638 50.000 0.00 0.00 30.84 4.30
2058 2264 7.094631 GGCGGAACTAACAAAATTTAAAGGAT 58.905 34.615 0.00 0.00 0.00 3.24
2380 2702 7.412853 GGATGCAAAATACAGAAGTGATGTAG 58.587 38.462 0.00 0.00 36.63 2.74
2430 2752 3.464720 TGGCTCCAATATTGACCCAAA 57.535 42.857 17.23 0.00 0.00 3.28
2456 2778 2.820178 GGGGGAGAACAATGGTTTGAT 58.180 47.619 0.00 0.00 37.36 2.57
2508 2831 9.612066 TCAAACTGATATTGTCATAGCATGTTA 57.388 29.630 0.00 0.00 35.97 2.41
2530 2853 7.773489 TCACATTACCCAATTGAATCTCAAA 57.227 32.000 7.12 0.00 40.12 2.69
2683 3006 4.345859 TTCAGGTACCATTTGAACGAGT 57.654 40.909 15.94 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.