Multiple sequence alignment - TraesCS7A01G019700

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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 TraesCS7A01G019700 chr7A 100.000 2423 0 0 1 2423 8061903 8064325 0.000000e+00 4475
1 TraesCS7A01G019700 chr7A 97.644 2250 34 7 176 2423 8182754 8184986 0.000000e+00 3843
2 TraesCS7A01G019700 chr7A 96.552 783 21 6 84 863 8224530 8225309 0.000000e+00 1291
3 TraesCS7A01G019700 chr7A 96.034 580 23 0 861 1440 7967566 7968145 0.000000e+00 944
4 TraesCS7A01G019700 chr7A 95.345 580 27 0 861 1440 8106784 8107363 0.000000e+00 922
5 TraesCS7A01G019700 chr7A 93.735 431 26 1 963 1392 7938374 7938804 0.000000e+00 645
6 TraesCS7A01G019700 chr7A 89.684 475 48 1 965 1439 8105522 8105995 2.660000e-169 604
7 TraesCS7A01G019700 chr2D 98.169 983 18 0 1441 2423 86971014 86971996 0.000000e+00 1716
8 TraesCS7A01G019700 chr2D 90.856 689 48 13 1 680 301732850 301732168 0.000000e+00 909
9 TraesCS7A01G019700 chr2D 90.566 689 53 8 1 681 408445781 408446465 0.000000e+00 902
10 TraesCS7A01G019700 chr1D 97.976 988 19 1 1437 2423 30148741 30147754 0.000000e+00 1712
11 TraesCS7A01G019700 chr6D 98.067 983 19 0 1441 2423 446336825 446337807 0.000000e+00 1711
12 TraesCS7A01G019700 chr6D 97.870 986 21 0 1438 2423 189558284 189559269 0.000000e+00 1705
13 TraesCS7A01G019700 chr6D 97.778 990 19 3 1435 2423 54051987 54052974 0.000000e+00 1703
14 TraesCS7A01G019700 chr5D 98.067 983 19 0 1441 2423 450651983 450651001 0.000000e+00 1711
15 TraesCS7A01G019700 chr5D 97.970 985 19 1 1440 2423 307447621 307446637 0.000000e+00 1707
16 TraesCS7A01G019700 chr5D 90.843 688 52 7 1 681 238725429 238726112 0.000000e+00 911
17 TraesCS7A01G019700 chr5A 97.970 985 20 0 1439 2423 137527442 137526458 0.000000e+00 1709
18 TraesCS7A01G019700 chr3D 91.304 690 46 11 1 681 17027368 17028052 0.000000e+00 929
19 TraesCS7A01G019700 chr3D 90.462 692 50 11 1 681 424337636 424338322 0.000000e+00 898
20 TraesCS7A01G019700 chr4D 90.936 684 46 13 1 673 128117558 128118236 0.000000e+00 905
21 TraesCS7A01G019700 chr4D 90.816 686 49 13 1 681 322889044 322889720 0.000000e+00 905
22 TraesCS7A01G019700 chr7D 92.662 477 34 1 963 1439 7172964 7173439 0.000000e+00 686
23 TraesCS7A01G019700 chr7D 91.631 466 34 5 979 1440 7186997 7187461 7.300000e-180 640
24 TraesCS7A01G019700 chrUn 91.102 472 39 2 965 1433 51234622 51234151 9.450000e-179 636
25 TraesCS7A01G019700 chrUn 91.102 472 39 2 965 1433 289094185 289094656 9.450000e-179 636


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 TraesCS7A01G019700 chr7A 8061903 8064325 2422 False 4475 4475 100.0000 1 2423 1 chr7A.!!$F3 2422
1 TraesCS7A01G019700 chr7A 8182754 8184986 2232 False 3843 3843 97.6440 176 2423 1 chr7A.!!$F4 2247
2 TraesCS7A01G019700 chr7A 8224530 8225309 779 False 1291 1291 96.5520 84 863 1 chr7A.!!$F5 779
3 TraesCS7A01G019700 chr7A 7967566 7968145 579 False 944 944 96.0340 861 1440 1 chr7A.!!$F2 579
4 TraesCS7A01G019700 chr7A 8105522 8107363 1841 False 763 922 92.5145 861 1440 2 chr7A.!!$F6 579
5 TraesCS7A01G019700 chr2D 86971014 86971996 982 False 1716 1716 98.1690 1441 2423 1 chr2D.!!$F1 982
6 TraesCS7A01G019700 chr2D 301732168 301732850 682 True 909 909 90.8560 1 680 1 chr2D.!!$R1 679
7 TraesCS7A01G019700 chr2D 408445781 408446465 684 False 902 902 90.5660 1 681 1 chr2D.!!$F2 680
8 TraesCS7A01G019700 chr1D 30147754 30148741 987 True 1712 1712 97.9760 1437 2423 1 chr1D.!!$R1 986
9 TraesCS7A01G019700 chr6D 446336825 446337807 982 False 1711 1711 98.0670 1441 2423 1 chr6D.!!$F3 982
10 TraesCS7A01G019700 chr6D 189558284 189559269 985 False 1705 1705 97.8700 1438 2423 1 chr6D.!!$F2 985
11 TraesCS7A01G019700 chr6D 54051987 54052974 987 False 1703 1703 97.7780 1435 2423 1 chr6D.!!$F1 988
12 TraesCS7A01G019700 chr5D 450651001 450651983 982 True 1711 1711 98.0670 1441 2423 1 chr5D.!!$R2 982
13 TraesCS7A01G019700 chr5D 307446637 307447621 984 True 1707 1707 97.9700 1440 2423 1 chr5D.!!$R1 983
14 TraesCS7A01G019700 chr5D 238725429 238726112 683 False 911 911 90.8430 1 681 1 chr5D.!!$F1 680
15 TraesCS7A01G019700 chr5A 137526458 137527442 984 True 1709 1709 97.9700 1439 2423 1 chr5A.!!$R1 984
16 TraesCS7A01G019700 chr3D 17027368 17028052 684 False 929 929 91.3040 1 681 1 chr3D.!!$F1 680
17 TraesCS7A01G019700 chr3D 424337636 424338322 686 False 898 898 90.4620 1 681 1 chr3D.!!$F2 680
18 TraesCS7A01G019700 chr4D 128117558 128118236 678 False 905 905 90.9360 1 673 1 chr4D.!!$F1 672
19 TraesCS7A01G019700 chr4D 322889044 322889720 676 False 905 905 90.8160 1 681 1 chr4D.!!$F2 680

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
144 155 0.103608 TTTCCCCTTTCCCCCTCTCA 60.104 55.000 0.0 0.0 0.00 3.27 F
400 421 2.356913 CATCACCGTCACCACGCA 60.357 61.111 0.0 0.0 45.29 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1018 1421 1.139734 TCATCCAGAAGACGCGCTC 59.860 57.895 5.73 2.87 0.00 5.03 R
2098 2504 1.481772 TGATGCTCATCGTGATGACCA 59.518 47.619 8.43 9.07 42.42 4.02 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
144 155 0.103608 TTTCCCCTTTCCCCCTCTCA 60.104 55.000 0.00 0.00 0.00 3.27
290 310 3.181427 ACCCCAAAGGCACAACAGTTATA 60.181 43.478 0.00 0.00 40.58 0.98
400 421 2.356913 CATCACCGTCACCACGCA 60.357 61.111 0.00 0.00 45.29 5.24
450 471 3.456280 CTCTGCTGGATCAAGAGTTAGC 58.544 50.000 0.00 0.00 0.00 3.09
681 705 6.438741 TGAAATTACATGCTACATTCCCCAAA 59.561 34.615 0.00 0.00 0.00 3.28
847 871 7.684317 TCAATAGATTGGTGGGTTGATACTA 57.316 36.000 2.52 0.00 38.30 1.82
882 1285 2.768344 CCCCAGGCGGTCCACTAT 60.768 66.667 0.00 0.00 33.74 2.12
1018 1421 3.451556 ATGAGGCTCGACGGCATGG 62.452 63.158 10.42 0.00 41.46 3.66
1627 2030 6.464222 AGTATATACAACAGTGCGCCATTAT 58.536 36.000 15.18 0.00 0.00 1.28
1893 2299 7.870509 AATATAGACAGCACACATCAACAAT 57.129 32.000 0.00 0.00 0.00 2.71
2031 2437 5.970317 TTGTATTACAAGTCTCGAGACCA 57.030 39.130 35.83 23.07 45.85 4.02
2098 2504 4.029520 ACCATCACATAGAAGAGAGCTGT 58.970 43.478 0.00 0.00 0.00 4.40
2101 2507 3.435275 TCACATAGAAGAGAGCTGTGGT 58.565 45.455 0.00 0.00 38.16 4.16
2102 2508 3.445450 TCACATAGAAGAGAGCTGTGGTC 59.555 47.826 0.00 0.00 38.16 4.02
2103 2509 3.194329 CACATAGAAGAGAGCTGTGGTCA 59.806 47.826 0.00 0.00 34.88 4.02
2104 2510 4.029520 ACATAGAAGAGAGCTGTGGTCAT 58.970 43.478 0.00 0.00 31.89 3.06
2105 2511 4.099266 ACATAGAAGAGAGCTGTGGTCATC 59.901 45.833 0.00 0.00 31.89 2.92
2106 2512 2.533916 AGAAGAGAGCTGTGGTCATCA 58.466 47.619 0.00 0.00 31.89 3.07
2107 2513 2.233431 AGAAGAGAGCTGTGGTCATCAC 59.767 50.000 0.00 0.00 46.23 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.374762 CCTTCCTCCCTCTCTCCACTATT 60.375 52.174 0.00 0.00 0.00 1.73
400 421 3.575351 GAGTTCCGCCAGCACGACT 62.575 63.158 0.00 0.00 34.06 4.18
450 471 0.452987 TTAACCTCGATGACGTCCCG 59.547 55.000 14.12 16.31 40.69 5.14
681 705 0.951558 CACGGCACTGGTTAGCTTTT 59.048 50.000 0.00 0.00 0.00 2.27
847 871 2.043227 GGGCCTATCTCTTGTAGCACT 58.957 52.381 0.84 0.00 0.00 4.40
882 1285 3.283684 CCGCCCGTTCAAGTTGCA 61.284 61.111 0.00 0.00 0.00 4.08
904 1307 2.111878 GTCTGGGTGTGCTGCTGT 59.888 61.111 0.00 0.00 0.00 4.40
1018 1421 1.139734 TCATCCAGAAGACGCGCTC 59.860 57.895 5.73 2.87 0.00 5.03
2031 2437 5.815740 ACTTGTAATGTGAAGACAAACTCGT 59.184 36.000 0.00 0.00 35.11 4.18
2098 2504 1.481772 TGATGCTCATCGTGATGACCA 59.518 47.619 8.43 9.07 42.42 4.02


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

AutoCloner maintained by Alex Coulton.