Multiple sequence alignment - TraesCS7B01G307400

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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 TraesCS7B01G307400 chr7B 100.000 2375 0 0 1 2375 551234904 551237278 0.000000e+00 4386
1 TraesCS7B01G307400 chr7B 94.982 1395 55 6 1 1390 615589527 615588143 0.000000e+00 2174
2 TraesCS7B01G307400 chr7B 91.236 696 55 4 1684 2375 623127409 623126716 0.000000e+00 942
3 TraesCS7B01G307400 chr4B 93.397 2408 107 14 1 2365 505003611 505001213 0.000000e+00 3518
4 TraesCS7B01G307400 chr4B 95.161 620 30 0 1 620 263059837 263059218 0.000000e+00 979
5 TraesCS7B01G307400 chr5A 94.875 1405 55 7 1 1400 345653531 345652139 0.000000e+00 2180
6 TraesCS7B01G307400 chr5A 88.648 1524 108 34 1 1488 235675060 235676554 0.000000e+00 1796
7 TraesCS7B01G307400 chr7A 94.733 1405 59 6 1 1400 578424337 578422943 0.000000e+00 2170
8 TraesCS7B01G307400 chr7A 94.793 1402 57 6 1 1397 734442712 734444102 0.000000e+00 2170
9 TraesCS7B01G307400 chr7A 93.504 1447 74 7 1 1440 639853100 639851667 0.000000e+00 2134
10 TraesCS7B01G307400 chr7A 89.324 843 77 11 1538 2375 56075357 56076191 0.000000e+00 1046
11 TraesCS7B01G307400 chr1A 93.681 1456 67 10 1 1447 539843250 539841811 0.000000e+00 2156
12 TraesCS7B01G307400 chr4A 94.942 1384 54 6 1 1378 549634099 549635472 0.000000e+00 2154
13 TraesCS7B01G307400 chr4A 94.684 1392 57 7 1 1385 490349415 490350796 0.000000e+00 2145
14 TraesCS7B01G307400 chr4A 93.734 782 34 4 1 777 29674125 29673354 0.000000e+00 1158
15 TraesCS7B01G307400 chr3B 92.730 1513 73 8 1 1502 753431312 753429826 0.000000e+00 2150
16 TraesCS7B01G307400 chr3B 91.974 760 51 8 1538 2294 753429857 753429105 0.000000e+00 1057
17 TraesCS7B01G307400 chr3B 95.968 620 25 0 1 620 751890872 751890253 0.000000e+00 1007
18 TraesCS7B01G307400 chr3B 95.323 620 29 0 1 620 557721153 557721772 0.000000e+00 985
19 TraesCS7B01G307400 chr3B 89.809 157 9 4 1538 1692 318305222 318305373 6.700000e-46 195
20 TraesCS7B01G307400 chr2B 94.089 1421 61 7 1 1403 539886114 539887529 0.000000e+00 2137
21 TraesCS7B01G307400 chr2A 94.831 890 34 3 1 885 15511930 15511048 0.000000e+00 1378
22 TraesCS7B01G307400 chr2A 88.599 842 70 13 1538 2375 610790700 610791519 0.000000e+00 1000
23 TraesCS7B01G307400 chr2A 89.382 744 70 9 1634 2375 442545695 442544959 0.000000e+00 928
24 TraesCS7B01G307400 chr5B 94.527 877 42 3 553 1428 291680763 291679892 0.000000e+00 1349
25 TraesCS7B01G307400 chr5B 90.448 848 50 17 1538 2375 117472397 117473223 0.000000e+00 1088
26 TraesCS7B01G307400 chr3D 93.378 891 49 6 540 1428 37627663 37628545 0.000000e+00 1310
27 TraesCS7B01G307400 chr3D 92.128 686 47 7 1694 2375 330463353 330462671 0.000000e+00 961
28 TraesCS7B01G307400 chr6D 90.421 856 55 13 1538 2375 297170001 297169155 0.000000e+00 1101
29 TraesCS7B01G307400 chr5D 89.148 857 68 13 1538 2374 384510621 384509770 0.000000e+00 1044
30 TraesCS7B01G307400 chr5D 88.798 857 73 15 1538 2375 401784063 401784915 0.000000e+00 1029
31 TraesCS7B01G307400 chr5D 89.617 809 70 11 1572 2375 140951691 140950892 0.000000e+00 1016
32 TraesCS7B01G307400 chr5D 87.256 871 73 17 1538 2375 29766180 29765315 0.000000e+00 959
33 TraesCS7B01G307400 chr7D 88.591 859 73 16 1538 2375 51237378 51236524 0.000000e+00 1020


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 TraesCS7B01G307400 chr7B 551234904 551237278 2374 False 4386.0 4386 100.000 1 2375 1 chr7B.!!$F1 2374
1 TraesCS7B01G307400 chr7B 615588143 615589527 1384 True 2174.0 2174 94.982 1 1390 1 chr7B.!!$R1 1389
2 TraesCS7B01G307400 chr7B 623126716 623127409 693 True 942.0 942 91.236 1684 2375 1 chr7B.!!$R2 691
3 TraesCS7B01G307400 chr4B 505001213 505003611 2398 True 3518.0 3518 93.397 1 2365 1 chr4B.!!$R2 2364
4 TraesCS7B01G307400 chr4B 263059218 263059837 619 True 979.0 979 95.161 1 620 1 chr4B.!!$R1 619
5 TraesCS7B01G307400 chr5A 345652139 345653531 1392 True 2180.0 2180 94.875 1 1400 1 chr5A.!!$R1 1399
6 TraesCS7B01G307400 chr5A 235675060 235676554 1494 False 1796.0 1796 88.648 1 1488 1 chr5A.!!$F1 1487
7 TraesCS7B01G307400 chr7A 578422943 578424337 1394 True 2170.0 2170 94.733 1 1400 1 chr7A.!!$R1 1399
8 TraesCS7B01G307400 chr7A 734442712 734444102 1390 False 2170.0 2170 94.793 1 1397 1 chr7A.!!$F2 1396
9 TraesCS7B01G307400 chr7A 639851667 639853100 1433 True 2134.0 2134 93.504 1 1440 1 chr7A.!!$R2 1439
10 TraesCS7B01G307400 chr7A 56075357 56076191 834 False 1046.0 1046 89.324 1538 2375 1 chr7A.!!$F1 837
11 TraesCS7B01G307400 chr1A 539841811 539843250 1439 True 2156.0 2156 93.681 1 1447 1 chr1A.!!$R1 1446
12 TraesCS7B01G307400 chr4A 549634099 549635472 1373 False 2154.0 2154 94.942 1 1378 1 chr4A.!!$F2 1377
13 TraesCS7B01G307400 chr4A 490349415 490350796 1381 False 2145.0 2145 94.684 1 1385 1 chr4A.!!$F1 1384
14 TraesCS7B01G307400 chr4A 29673354 29674125 771 True 1158.0 1158 93.734 1 777 1 chr4A.!!$R1 776
15 TraesCS7B01G307400 chr3B 753429105 753431312 2207 True 1603.5 2150 92.352 1 2294 2 chr3B.!!$R2 2293
16 TraesCS7B01G307400 chr3B 751890253 751890872 619 True 1007.0 1007 95.968 1 620 1 chr3B.!!$R1 619
17 TraesCS7B01G307400 chr3B 557721153 557721772 619 False 985.0 985 95.323 1 620 1 chr3B.!!$F2 619
18 TraesCS7B01G307400 chr2B 539886114 539887529 1415 False 2137.0 2137 94.089 1 1403 1 chr2B.!!$F1 1402
19 TraesCS7B01G307400 chr2A 15511048 15511930 882 True 1378.0 1378 94.831 1 885 1 chr2A.!!$R1 884
20 TraesCS7B01G307400 chr2A 610790700 610791519 819 False 1000.0 1000 88.599 1538 2375 1 chr2A.!!$F1 837
21 TraesCS7B01G307400 chr2A 442544959 442545695 736 True 928.0 928 89.382 1634 2375 1 chr2A.!!$R2 741
22 TraesCS7B01G307400 chr5B 291679892 291680763 871 True 1349.0 1349 94.527 553 1428 1 chr5B.!!$R1 875
23 TraesCS7B01G307400 chr5B 117472397 117473223 826 False 1088.0 1088 90.448 1538 2375 1 chr5B.!!$F1 837
24 TraesCS7B01G307400 chr3D 37627663 37628545 882 False 1310.0 1310 93.378 540 1428 1 chr3D.!!$F1 888
25 TraesCS7B01G307400 chr3D 330462671 330463353 682 True 961.0 961 92.128 1694 2375 1 chr3D.!!$R1 681
26 TraesCS7B01G307400 chr6D 297169155 297170001 846 True 1101.0 1101 90.421 1538 2375 1 chr6D.!!$R1 837
27 TraesCS7B01G307400 chr5D 384509770 384510621 851 True 1044.0 1044 89.148 1538 2374 1 chr5D.!!$R3 836
28 TraesCS7B01G307400 chr5D 401784063 401784915 852 False 1029.0 1029 88.798 1538 2375 1 chr5D.!!$F1 837
29 TraesCS7B01G307400 chr5D 140950892 140951691 799 True 1016.0 1016 89.617 1572 2375 1 chr5D.!!$R2 803
30 TraesCS7B01G307400 chr5D 29765315 29766180 865 True 959.0 959 87.256 1538 2375 1 chr5D.!!$R1 837
31 TraesCS7B01G307400 chr7D 51236524 51237378 854 True 1020.0 1020 88.591 1538 2375 1 chr7D.!!$R1 837

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
119 120 1.746861 CGGATGGTGAATGGCAAGCTA 60.747 52.381 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1600 1712 1.49049 AGTGCTTCCAGGTTCACAAGA 59.51 47.619 9.87 0.0 32.25 3.02 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
119 120 1.746861 CGGATGGTGAATGGCAAGCTA 60.747 52.381 0.00 0.00 0.00 3.32
357 360 6.438108 AGAACTTTTCTCTAGAGACCTTACCC 59.562 42.308 22.25 9.02 37.14 3.69
462 465 2.587247 GGGTGAGGAGCTGTCTGCA 61.587 63.158 0.00 0.00 45.94 4.41
524 527 2.427506 GTTTTCGGAGCCAGTCAAGAT 58.572 47.619 0.00 0.00 0.00 2.40
598 634 6.689554 TGCTGTTTGATGCTTTGATGATTTA 58.310 32.000 0.00 0.00 0.00 1.40
620 656 2.585330 TGCTGTTTGATTCAGAGCCAA 58.415 42.857 10.28 0.00 35.20 4.52
690 726 8.721478 GTTCAACAAAGATATCAGAACTTGCTA 58.279 33.333 5.32 0.00 33.16 3.49
847 919 1.822506 TGTCTCCAGGTCACTAGTCG 58.177 55.000 0.00 0.00 0.00 4.18
1065 1138 5.104374 ACAAAGTCTGCTGTTGAAATTGTG 58.896 37.500 0.41 0.00 0.00 3.33
1270 1343 4.405680 TCAAGATGAAGGCGGAAGAATCTA 59.594 41.667 0.00 0.00 0.00 1.98
1520 1614 4.965814 TGCATCTTATGATCTGGGAGAAC 58.034 43.478 0.00 0.00 0.00 3.01
1524 1618 3.389329 TCTTATGATCTGGGAGAACCTGC 59.611 47.826 0.00 0.00 41.11 4.85
1536 1630 1.140452 AGAACCTGCGATCTGATGCAT 59.860 47.619 0.00 0.00 40.89 3.96
1597 1709 0.179018 GGGAGCACTTGTGAACCTGT 60.179 55.000 4.79 0.00 0.00 4.00
1600 1712 2.498167 GAGCACTTGTGAACCTGTGAT 58.502 47.619 4.79 0.00 32.72 3.06
1614 1728 2.038952 CCTGTGATCTTGTGAACCTGGA 59.961 50.000 0.00 0.00 0.00 3.86
1821 1980 3.947834 CGAGGCCCAAACAAGAATTAGAT 59.052 43.478 0.00 0.00 0.00 1.98
1933 2097 6.738832 AATTCGAACTAGACTAAAAAGGCC 57.261 37.500 0.00 0.00 0.00 5.19
1934 2098 4.877378 TCGAACTAGACTAAAAAGGCCA 57.123 40.909 5.01 0.00 0.00 5.36
1953 2117 2.566724 CCATGGCCCAAAACAATAGTGT 59.433 45.455 0.00 0.00 40.75 3.55
1997 2167 5.984695 AAAAGGCTCCATTCCTAGAAAAC 57.015 39.130 0.00 0.00 32.65 2.43
2015 2186 9.487790 CTAGAAAACAAAAGGCCAAATTATTGA 57.512 29.630 5.01 0.00 38.94 2.57
2018 2189 5.488262 ACAAAAGGCCAAATTATTGAGCT 57.512 34.783 5.01 0.00 38.94 4.09
2028 2199 4.729552 AATTATTGAGCTAGGCCCATGA 57.270 40.909 0.00 0.00 0.00 3.07
2110 2289 2.674754 GGCTGAAATGGACCGGGA 59.325 61.111 6.32 0.00 0.00 5.14
2133 2312 9.586435 GGGATGATTCTATTTTACAACCTTTTG 57.414 33.333 0.00 0.00 38.83 2.44
2145 2324 5.432885 ACAACCTTTTGATTTGGTCGTAG 57.567 39.130 0.00 0.00 36.48 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 2.119495 GGTAGACCACATCTCCACCAT 58.881 52.381 0.00 0.00 36.43 3.55
357 360 8.454106 AGAAATGTTATTCAACGAGGATCAAAG 58.546 33.333 0.00 0.00 37.48 2.77
422 425 6.106673 CCCTTACGCTCTTCTTTCTGAAATA 58.893 40.000 2.88 0.00 33.79 1.40
462 465 3.323691 GGGTGGCCTTAAACAAGTCAATT 59.676 43.478 3.32 0.00 0.00 2.32
524 527 5.453339 GGCATGGAGTGACTTACTATAGCAA 60.453 44.000 0.00 0.00 40.53 3.91
598 634 3.159472 TGGCTCTGAATCAAACAGCATT 58.841 40.909 9.74 0.00 35.61 3.56
822 860 1.421268 AGTGACCTGGAGACATGCAAA 59.579 47.619 0.00 0.00 41.51 3.68
847 919 9.979270 CACACAAAATCTATACAAGAAGATGAC 57.021 33.333 0.00 0.00 37.89 3.06
1065 1138 2.550830 TGGTCTTGAGCACTTCTTCC 57.449 50.000 0.00 0.00 0.00 3.46
1222 1295 2.094597 CCGCCAATTCTTCTTGCATCAA 60.095 45.455 0.00 0.00 0.00 2.57
1270 1343 2.633657 CTTGTCGCGTGCAGCTTT 59.366 55.556 5.77 0.00 45.59 3.51
1520 1614 1.880271 AAGATGCATCAGATCGCAGG 58.120 50.000 27.81 0.00 42.37 4.85
1597 1709 2.106338 TGCTTCCAGGTTCACAAGATCA 59.894 45.455 0.00 0.00 0.00 2.92
1600 1712 1.490490 AGTGCTTCCAGGTTCACAAGA 59.510 47.619 9.87 0.00 32.25 3.02
1614 1728 3.067180 CCATCACAAGTTCACAAGTGCTT 59.933 43.478 0.00 0.00 32.25 3.91
1933 2097 3.959535 ACACTATTGTTTTGGGCCATG 57.040 42.857 7.26 0.93 28.43 3.66
1934 2098 4.672899 AGTACACTATTGTTTTGGGCCAT 58.327 39.130 7.26 0.00 37.15 4.40
1997 2167 6.044682 CCTAGCTCAATAATTTGGCCTTTTG 58.955 40.000 3.32 0.00 32.61 2.44
2015 2186 2.039613 GCTTATCTTCATGGGCCTAGCT 59.960 50.000 4.53 0.00 0.00 3.32
2018 2189 4.518278 TTTGCTTATCTTCATGGGCCTA 57.482 40.909 4.53 0.00 0.00 3.93
2145 2324 1.740025 GGCAAGCTGATGTGGTAGAAC 59.260 52.381 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.