Multiple sequence alignment - TraesCS5A01G118100

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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 TraesCS5A01G118100 chr5A 100.000 2204 0 0 1 2204 241765085 241762882 0.000000e+00 4071.0
1 TraesCS5A01G118100 chr5A 96.069 1908 57 7 1 1901 241757617 241755721 0.000000e+00 3092.0
2 TraesCS5A01G118100 chr5A 90.612 490 36 5 4 486 45615877 45616363 1.840000e-180 641.0
3 TraesCS5A01G118100 chr5A 90.947 486 31 7 9 486 104498520 104498040 1.840000e-180 641.0
4 TraesCS5A01G118100 chr5A 90.515 485 37 4 9 486 361250864 361251346 1.110000e-177 632.0
5 TraesCS5A01G118100 chr5A 90.204 490 37 6 4 486 45623798 45624283 1.440000e-176 628.0
6 TraesCS5A01G118100 chr5A 82.377 488 73 11 1685 2167 302104377 302104856 1.570000e-111 412.0
7 TraesCS5A01G118100 chr7A 95.422 1551 60 4 655 2204 586293467 586295007 0.000000e+00 2460.0
8 TraesCS5A01G118100 chr7A 92.874 1656 87 14 470 2122 104340591 104338964 0.000000e+00 2375.0
9 TraesCS5A01G118100 chr7A 94.363 1437 67 7 468 1900 104325843 104324417 0.000000e+00 2193.0
10 TraesCS5A01G118100 chr7A 96.306 785 28 1 1004 1788 586301147 586301930 0.000000e+00 1288.0
11 TraesCS5A01G118100 chr7A 90.558 985 69 11 920 1900 200364420 200363456 0.000000e+00 1282.0
12 TraesCS5A01G118100 chr7A 91.173 861 63 5 646 1505 104347442 104346594 0.000000e+00 1157.0
13 TraesCS5A01G118100 chr7A 90.302 794 67 9 1330 2118 200472851 200472063 0.000000e+00 1031.0
14 TraesCS5A01G118100 chr7A 88.757 507 33 15 445 945 586300658 586301146 1.130000e-167 599.0
15 TraesCS5A01G118100 chr7A 87.260 416 48 5 921 1335 200476968 200476557 9.210000e-129 470.0
16 TraesCS5A01G118100 chr4A 92.490 972 67 6 934 1900 326014056 326013086 0.000000e+00 1386.0
17 TraesCS5A01G118100 chr4A 89.244 595 56 8 1614 2204 139859380 139859970 0.000000e+00 737.0
18 TraesCS5A01G118100 chr1A 95.251 758 34 2 1144 1900 252020713 252021469 0.000000e+00 1199.0
19 TraesCS5A01G118100 chr1A 90.702 484 36 5 10 486 262017352 262016871 8.580000e-179 636.0
20 TraesCS5A01G118100 chr1B 87.234 752 83 13 1459 2204 444626088 444625344 0.000000e+00 845.0
21 TraesCS5A01G118100 chr6A 91.525 472 33 4 20 486 325639575 325639106 0.000000e+00 643.0
22 TraesCS5A01G118100 chr6A 90.309 485 40 3 9 486 351500045 351500529 1.440000e-176 628.0
23 TraesCS5A01G118100 chr2A 90.329 486 37 5 9 486 81308024 81308507 1.440000e-176 628.0
24 TraesCS5A01G118100 chr2A 83.784 74 7 5 584 656 210054011 210054080 5.080000e-07 65.8
25 TraesCS5A01G118100 chr3A 86.123 454 58 3 1751 2202 150636061 150636511 3.290000e-133 484.0
26 TraesCS5A01G118100 chr7D 80.651 522 80 17 1695 2204 581904058 581904570 3.430000e-103 385.0
27 TraesCS5A01G118100 chr2B 82.692 416 58 13 1759 2167 313564403 313564811 7.480000e-95 357.0


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 TraesCS5A01G118100 chr5A 241762882 241765085 2203 True 4071.0 4071 100.0000 1 2204 1 chr5A.!!$R3 2203
1 TraesCS5A01G118100 chr5A 241755721 241757617 1896 True 3092.0 3092 96.0690 1 1901 1 chr5A.!!$R2 1900
2 TraesCS5A01G118100 chr7A 586293467 586295007 1540 False 2460.0 2460 95.4220 655 2204 1 chr7A.!!$F1 1549
3 TraesCS5A01G118100 chr7A 104338964 104340591 1627 True 2375.0 2375 92.8740 470 2122 1 chr7A.!!$R2 1652
4 TraesCS5A01G118100 chr7A 104324417 104325843 1426 True 2193.0 2193 94.3630 468 1900 1 chr7A.!!$R1 1432
5 TraesCS5A01G118100 chr7A 200363456 200364420 964 True 1282.0 1282 90.5580 920 1900 1 chr7A.!!$R4 980
6 TraesCS5A01G118100 chr7A 104346594 104347442 848 True 1157.0 1157 91.1730 646 1505 1 chr7A.!!$R3 859
7 TraesCS5A01G118100 chr7A 586300658 586301930 1272 False 943.5 1288 92.5315 445 1788 2 chr7A.!!$F2 1343
8 TraesCS5A01G118100 chr7A 200472063 200476968 4905 True 750.5 1031 88.7810 921 2118 2 chr7A.!!$R5 1197
9 TraesCS5A01G118100 chr4A 326013086 326014056 970 True 1386.0 1386 92.4900 934 1900 1 chr4A.!!$R1 966
10 TraesCS5A01G118100 chr4A 139859380 139859970 590 False 737.0 737 89.2440 1614 2204 1 chr4A.!!$F1 590
11 TraesCS5A01G118100 chr1A 252020713 252021469 756 False 1199.0 1199 95.2510 1144 1900 1 chr1A.!!$F1 756
12 TraesCS5A01G118100 chr1B 444625344 444626088 744 True 845.0 845 87.2340 1459 2204 1 chr1B.!!$R1 745
13 TraesCS5A01G118100 chr7D 581904058 581904570 512 False 385.0 385 80.6510 1695 2204 1 chr7D.!!$F1 509

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
820 858 1.074395 TGGTCAGGGGTGTGTGGTA 60.074 57.895 0.0 0.0 0.0 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 5685 3.031736 TCCACCTCTTAAATCTCGGGAG 58.968 50.0 0.0 0.0 0.0 4.3 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
34 35 1.334689 GGAAGGTTGCGTGTTTGCTAC 60.335 52.381 0.00 0.00 39.41 3.58
63 64 2.737376 GTGGCGGACGAACAGACC 60.737 66.667 0.00 0.00 0.00 3.85
91 92 1.325640 CGGATTCGTCTCGTCGTTCTA 59.674 52.381 0.00 0.00 0.00 2.10
105 106 4.151798 GTCGTTCTAAGCAACTTTCATGC 58.848 43.478 0.00 0.00 44.15 4.06
106 107 3.812609 TCGTTCTAAGCAACTTTCATGCA 59.187 39.130 0.00 0.00 46.22 3.96
129 130 8.609176 TGCATAAAGTATTTTCATCCGAGTTAC 58.391 33.333 0.00 0.00 40.09 2.50
277 278 9.975218 AGACTATTTACCCAAACAATTAGACAT 57.025 29.630 0.00 0.00 0.00 3.06
368 369 3.847081 AGTACTAATCTAGGCCAGGGAC 58.153 50.000 5.01 0.00 0.00 4.46
407 408 4.947147 AACCGGCCACACGCATGT 62.947 61.111 0.00 0.00 40.80 3.21
479 487 1.220529 ATGCAGAACACACACTCACG 58.779 50.000 0.00 0.00 0.00 4.35
656 694 1.783284 CAGAACGCAGTAGAGCAACA 58.217 50.000 0.00 0.00 45.00 3.33
659 697 3.187227 CAGAACGCAGTAGAGCAACAAAT 59.813 43.478 0.00 0.00 45.00 2.32
812 850 2.603776 GAGGACGTGGTCAGGGGT 60.604 66.667 0.00 0.00 33.68 4.95
813 851 2.923035 AGGACGTGGTCAGGGGTG 60.923 66.667 0.00 0.00 33.68 4.61
814 852 3.239253 GGACGTGGTCAGGGGTGT 61.239 66.667 0.00 0.00 33.68 4.16
815 853 2.030562 GACGTGGTCAGGGGTGTG 59.969 66.667 0.00 0.00 32.09 3.82
816 854 2.766651 ACGTGGTCAGGGGTGTGT 60.767 61.111 0.00 0.00 0.00 3.72
817 855 2.280797 CGTGGTCAGGGGTGTGTG 60.281 66.667 0.00 0.00 0.00 3.82
818 856 2.113139 GTGGTCAGGGGTGTGTGG 59.887 66.667 0.00 0.00 0.00 4.17
819 857 2.367648 TGGTCAGGGGTGTGTGGT 60.368 61.111 0.00 0.00 0.00 4.16
820 858 1.074395 TGGTCAGGGGTGTGTGGTA 60.074 57.895 0.00 0.00 0.00 3.25
825 863 4.323477 GGGGTGTGTGGTAGCGCA 62.323 66.667 11.47 3.59 0.00 6.09
912 951 2.668632 GCTGGTGGTTCGATGGGA 59.331 61.111 0.00 0.00 0.00 4.37
972 1011 2.418910 CGTGGATGAGCTCGAGGGT 61.419 63.158 15.58 0.00 0.00 4.34
988 1028 1.381076 GGTTTGGGGATGGTCGGAA 59.619 57.895 0.00 0.00 0.00 4.30
1131 1171 1.371558 GGACAACTCCTCCAACGCT 59.628 57.895 0.00 0.00 33.07 5.07
1142 1182 2.654877 CAACGCTGGGGACTACGT 59.345 61.111 0.00 0.00 42.81 3.57
1186 1226 1.019278 ACACAACCACATCGCGATCC 61.019 55.000 20.85 0.00 0.00 3.36
1441 5193 1.202290 GCATTGGGCCATAAGTGAACG 60.202 52.381 7.26 0.00 36.11 3.95
1922 5682 8.697507 ACAAATCTCCTTCACTACAAGAAATT 57.302 30.769 0.00 0.00 0.00 1.82
1962 5722 3.328050 AGGTGGAGTAAGAGGGAAAGTTG 59.672 47.826 0.00 0.00 0.00 3.16
2001 5761 2.996621 CAGATCTTCACGGTCTTGGTTC 59.003 50.000 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 1.043224 GAGACGAATCCGAATACGCG 58.957 55.000 3.53 3.53 39.50 6.01
91 92 9.492973 AAAATACTTTATGCATGAAAGTTGCTT 57.507 25.926 25.52 18.16 43.03 3.91
281 282 9.181061 GACATGTAGGCCCTTTTAAATAAGTTA 57.819 33.333 0.00 0.00 0.00 2.24
407 408 1.375853 GCTCCTGTGTGTGTGTGCAA 61.376 55.000 0.00 0.00 0.00 4.08
440 443 1.583451 GTGTGTGTGCGTGCAGTTG 60.583 57.895 0.00 0.00 0.00 3.16
479 487 1.062002 GTGTGTGTAGTGTGTGTGTGC 59.938 52.381 0.00 0.00 0.00 4.57
605 643 2.871022 TGCGTACTACTGCTAGCTAGTC 59.129 50.000 21.62 14.14 0.00 2.59
656 694 3.976701 CTCTCGCCCCCGTGCATTT 62.977 63.158 0.00 0.00 35.54 2.32
690 728 3.826754 CGCCTCCTGCTGTCGCTA 61.827 66.667 0.00 0.00 38.05 4.26
812 850 2.656646 CTCCTGCGCTACCACACA 59.343 61.111 9.73 0.00 0.00 3.72
813 851 2.815647 GCTCCTGCGCTACCACAC 60.816 66.667 9.73 0.00 0.00 3.82
838 876 1.951130 CTTGTGCTCACTGCGTCGT 60.951 57.895 1.47 0.00 46.63 4.34
897 936 1.060729 TTTCTCCCATCGAACCACCA 58.939 50.000 0.00 0.00 0.00 4.17
912 951 4.183916 TCCTCTGGTTTCCCCTATTTTCT 58.816 43.478 0.00 0.00 0.00 2.52
972 1011 0.326927 GAGTTCCGACCATCCCCAAA 59.673 55.000 0.00 0.00 0.00 3.28
1131 1171 2.440796 CGGCCTACGTAGTCCCCA 60.441 66.667 20.73 0.00 43.93 4.96
1186 1226 1.130613 CTCAAAAACGAGCTCGCGG 59.869 57.895 34.83 19.30 44.43 6.46
1441 5193 3.653835 AAGGGGATAGAAAAGAGCACC 57.346 47.619 0.00 0.00 0.00 5.01
1922 5682 4.081087 CCACCTCTTAAATCTCGGGAGAAA 60.081 45.833 2.00 0.00 41.36 2.52
1925 5685 3.031736 TCCACCTCTTAAATCTCGGGAG 58.968 50.000 0.00 0.00 0.00 4.30
1962 5722 7.829378 AGATCTGTTAGAATTTCGTAACCAC 57.171 36.000 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.