Multiple sequence alignment - TraesCS7D01G461400

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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 TraesCS7D01G461400 chr7D 100.000 2546 0 0 1 2546 577662023 577659478 0.000000e+00 4702
1 TraesCS7D01G461400 chr7D 95.323 1732 62 13 825 2546 63995616 63997338 0.000000e+00 2732
2 TraesCS7D01G461400 chr3D 95.494 1731 61 12 825 2546 475106907 475108629 0.000000e+00 2748
3 TraesCS7D01G461400 chr7A 94.634 1733 74 13 825 2546 36946426 36948150 0.000000e+00 2667
4 TraesCS7D01G461400 chr7A 95.647 827 35 1 1 826 188820667 188819841 0.000000e+00 1327
5 TraesCS7D01G461400 chr2A 94.667 1725 73 13 826 2539 677413379 677411663 0.000000e+00 2658
6 TraesCS7D01G461400 chr2A 94.515 1732 80 12 825 2546 677958243 677956517 0.000000e+00 2658
7 TraesCS7D01G461400 chr2A 94.467 1735 76 14 825 2546 744582255 744583982 0.000000e+00 2654
8 TraesCS7D01G461400 chr2A 93.955 1737 84 12 825 2546 213959291 213957561 0.000000e+00 2606
9 TraesCS7D01G461400 chr2A 92.900 831 52 4 1 825 712865511 712866340 0.000000e+00 1201
10 TraesCS7D01G461400 chr2A 93.159 497 13 3 353 829 643449889 643449394 0.000000e+00 710
11 TraesCS7D01G461400 chr2A 90.931 419 18 4 1 417 29215855 29215455 1.720000e-151 545
12 TraesCS7D01G461400 chr5B 93.905 1739 80 16 825 2546 3449946 3448217 0.000000e+00 2601
13 TraesCS7D01G461400 chr5A 93.941 1733 82 16 825 2546 689446281 689444561 0.000000e+00 2597
14 TraesCS7D01G461400 chr5D 97.101 828 21 2 1 825 45879068 45878241 0.000000e+00 1393
15 TraesCS7D01G461400 chr5D 94.451 829 41 5 1 825 74487878 74488705 0.000000e+00 1271
16 TraesCS7D01G461400 chr1D 96.856 827 23 3 1 825 238761170 238761995 0.000000e+00 1380
17 TraesCS7D01G461400 chr1D 92.889 450 25 3 825 1270 437479112 437479558 0.000000e+00 647
18 TraesCS7D01G461400 chr2D 96.372 827 27 3 1 825 553141214 553142039 0.000000e+00 1358
19 TraesCS7D01G461400 chr6D 95.284 827 37 2 1 825 141663843 141663017 0.000000e+00 1310
20 TraesCS7D01G461400 chr4B 92.823 836 49 5 1 825 60714420 60713585 0.000000e+00 1201
21 TraesCS7D01G461400 chr4D 90.074 816 60 16 1 811 9364039 9363240 0.000000e+00 1038
22 TraesCS7D01G461400 chrUn 91.391 151 9 2 825 971 93726284 93726134 1.190000e-48 204
23 TraesCS7D01G461400 chrUn 91.216 148 8 3 825 971 463206233 463206090 2.000000e-46 196
24 TraesCS7D01G461400 chrUn 91.608 143 9 2 825 966 175762339 175762479 7.190000e-46 195
25 TraesCS7D01G461400 chrUn 90.541 148 9 3 825 971 87140553 87140696 9.300000e-45 191
26 TraesCS7D01G461400 chrUn 90.541 148 9 3 825 971 412767122 412767265 9.300000e-45 191
27 TraesCS7D01G461400 chrUn 89.865 148 10 3 825 971 43129302 43129159 4.330000e-43 185
28 TraesCS7D01G461400 chrUn 88.514 148 16 1 825 971 60558937 60559084 7.240000e-41 178


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 TraesCS7D01G461400 chr7D 577659478 577662023 2545 True 4702 4702 100.000 1 2546 1 chr7D.!!$R1 2545
1 TraesCS7D01G461400 chr7D 63995616 63997338 1722 False 2732 2732 95.323 825 2546 1 chr7D.!!$F1 1721
2 TraesCS7D01G461400 chr3D 475106907 475108629 1722 False 2748 2748 95.494 825 2546 1 chr3D.!!$F1 1721
3 TraesCS7D01G461400 chr7A 36946426 36948150 1724 False 2667 2667 94.634 825 2546 1 chr7A.!!$F1 1721
4 TraesCS7D01G461400 chr7A 188819841 188820667 826 True 1327 1327 95.647 1 826 1 chr7A.!!$R1 825
5 TraesCS7D01G461400 chr2A 677411663 677413379 1716 True 2658 2658 94.667 826 2539 1 chr2A.!!$R4 1713
6 TraesCS7D01G461400 chr2A 677956517 677958243 1726 True 2658 2658 94.515 825 2546 1 chr2A.!!$R5 1721
7 TraesCS7D01G461400 chr2A 744582255 744583982 1727 False 2654 2654 94.467 825 2546 1 chr2A.!!$F2 1721
8 TraesCS7D01G461400 chr2A 213957561 213959291 1730 True 2606 2606 93.955 825 2546 1 chr2A.!!$R2 1721
9 TraesCS7D01G461400 chr2A 712865511 712866340 829 False 1201 1201 92.900 1 825 1 chr2A.!!$F1 824
10 TraesCS7D01G461400 chr5B 3448217 3449946 1729 True 2601 2601 93.905 825 2546 1 chr5B.!!$R1 1721
11 TraesCS7D01G461400 chr5A 689444561 689446281 1720 True 2597 2597 93.941 825 2546 1 chr5A.!!$R1 1721
12 TraesCS7D01G461400 chr5D 45878241 45879068 827 True 1393 1393 97.101 1 825 1 chr5D.!!$R1 824
13 TraesCS7D01G461400 chr5D 74487878 74488705 827 False 1271 1271 94.451 1 825 1 chr5D.!!$F1 824
14 TraesCS7D01G461400 chr1D 238761170 238761995 825 False 1380 1380 96.856 1 825 1 chr1D.!!$F1 824
15 TraesCS7D01G461400 chr2D 553141214 553142039 825 False 1358 1358 96.372 1 825 1 chr2D.!!$F1 824
16 TraesCS7D01G461400 chr6D 141663017 141663843 826 True 1310 1310 95.284 1 825 1 chr6D.!!$R1 824
17 TraesCS7D01G461400 chr4B 60713585 60714420 835 True 1201 1201 92.823 1 825 1 chr4B.!!$R1 824
18 TraesCS7D01G461400 chr4D 9363240 9364039 799 True 1038 1038 90.074 1 811 1 chr4D.!!$R1 810

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
920 947 2.358125 CGGCGGTGACCACAATGA 60.358 61.111 1.11 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2301 2358 0.590984 CGCGTGTGCAAACATTCACA 60.591 50.0 8.0 0.0 42.97 3.58 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
723 736 4.219725 AGTTGTTGTAGGTTTTGTGCTTGT 59.780 37.500 0.00 0.0 0.00 3.16
919 946 2.668212 ACGGCGGTGACCACAATG 60.668 61.111 13.24 0.0 0.00 2.82
920 947 2.358125 CGGCGGTGACCACAATGA 60.358 61.111 1.11 0.0 0.00 2.57
966 997 3.774528 CTAGCTGTGGAGGGCGCA 61.775 66.667 10.83 0.0 0.00 6.09
1273 1304 3.507162 TTCTTTGGGTTGATGCTCTGA 57.493 42.857 0.00 0.0 0.00 3.27
1426 1458 2.421424 GCTGTTGAGCTTAGGATGTTGG 59.579 50.000 0.00 0.0 42.52 3.77
1625 1660 9.877178 ATGTTGGTCAAAGTTGTTTAAATGTTA 57.123 25.926 0.00 0.0 0.00 2.41
1626 1661 9.706691 TGTTGGTCAAAGTTGTTTAAATGTTAA 57.293 25.926 0.00 0.0 0.00 2.01
1654 1694 6.625873 AGAAGAAGAAGTGACCAACATTTC 57.374 37.500 0.00 0.0 42.81 2.17
1763 1807 1.115326 AGGTTGCTCTTGGGCCAAAC 61.115 55.000 21.28 14.6 0.00 2.93
1848 1895 4.082081 TCGGGTCTCTTGCGTATTTTTCTA 60.082 41.667 0.00 0.0 0.00 2.10
1921 1968 8.909708 TTTCGTGGAAGCTAATTGAATTATTG 57.090 30.769 0.00 0.0 0.00 1.90
2204 2257 1.599797 GTGGTGTTTAGGGCTGCGT 60.600 57.895 0.00 0.0 0.00 5.24
2223 2276 0.899720 TTGGTAACCGCTAGGACAGG 59.100 55.000 0.00 0.0 41.02 4.00
2276 2329 6.239064 GGAAGGTATACATAGTGAGACTGTGG 60.239 46.154 5.01 0.0 40.99 4.17
2439 2498 3.978672 ACTTGGTTTAGGGTTAGAGTGGT 59.021 43.478 0.00 0.0 0.00 4.16
2527 2590 2.610859 GGGCTTCTCACCCCCTCA 60.611 66.667 0.00 0.0 42.01 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
523 533 0.664761 CACCCTTGCGGATGCTAATG 59.335 55.000 0.00 0.00 43.34 1.90
890 917 3.812019 CGCCGTGCTCTCTACCGT 61.812 66.667 0.00 0.00 0.00 4.83
893 920 2.202623 CACCGCCGTGCTCTCTAC 60.203 66.667 0.00 0.00 32.04 2.59
894 921 2.360726 TCACCGCCGTGCTCTCTA 60.361 61.111 0.00 0.00 40.04 2.43
917 944 2.564771 CGTGCTCTCTCTCTCTCTCAT 58.435 52.381 0.00 0.00 0.00 2.90
918 945 1.406751 CCGTGCTCTCTCTCTCTCTCA 60.407 57.143 0.00 0.00 0.00 3.27
919 946 1.299541 CCGTGCTCTCTCTCTCTCTC 58.700 60.000 0.00 0.00 0.00 3.20
920 947 0.748005 GCCGTGCTCTCTCTCTCTCT 60.748 60.000 0.00 0.00 0.00 3.10
966 997 4.162690 GGGGATCTCAACGCCGCT 62.163 66.667 0.00 0.00 0.00 5.52
1273 1304 5.243981 CAGTTCATTCATCAGAGTCTTGGT 58.756 41.667 0.00 0.00 0.00 3.67
1391 1422 2.893489 TCAACAGCTAGCTCTCTGTCAA 59.107 45.455 16.15 8.93 42.19 3.18
1426 1458 5.153950 TCTTCAAGCTTCCTAACCTTCTC 57.846 43.478 0.00 0.00 0.00 2.87
1627 1662 6.834168 TGTTGGTCACTTCTTCTTCTTTTT 57.166 33.333 0.00 0.00 0.00 1.94
1628 1663 7.410120 AATGTTGGTCACTTCTTCTTCTTTT 57.590 32.000 0.00 0.00 0.00 2.27
1632 1668 6.377327 TGAAATGTTGGTCACTTCTTCTTC 57.623 37.500 0.00 0.00 33.99 2.87
1763 1807 0.814457 ACTTGGCTCTACGCTCTGAG 59.186 55.000 0.00 0.00 39.13 3.35
1899 1946 6.264832 TGCAATAATTCAATTAGCTTCCACG 58.735 36.000 0.00 0.00 0.00 4.94
1921 1968 3.942130 ACCTTAATTGTTTGGCTCTGC 57.058 42.857 0.00 0.00 0.00 4.26
2204 2257 0.899720 CCTGTCCTAGCGGTTACCAA 59.100 55.000 1.13 0.00 0.00 3.67
2223 2276 1.270550 CCCATGTCAAAGTCTTGCCAC 59.729 52.381 0.00 0.00 32.14 5.01
2301 2358 0.590984 CGCGTGTGCAAACATTCACA 60.591 50.000 8.00 0.00 42.97 3.58


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

AutoCloner maintained by Alex Coulton.