Multiple sequence alignment - TraesCS6A01G253800

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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 TraesCS6A01G253800 chr6A 100.000 2411 0 0 1 2411 469918912 469921322 0.000000e+00 4453.0
1 TraesCS6A01G253800 chr6A 93.347 962 61 3 1450 2411 578835499 578834541 0.000000e+00 1419.0
2 TraesCS6A01G253800 chr6A 73.501 717 172 15 99 806 500131395 500132102 3.080000e-64 255.0
3 TraesCS6A01G253800 chr2A 98.051 1437 20 2 1 1437 16659639 16661067 0.000000e+00 2492.0
4 TraesCS6A01G253800 chr2A 94.185 963 52 4 1450 2411 509042797 509043756 0.000000e+00 1465.0
5 TraesCS6A01G253800 chr2A 94.111 951 54 2 1462 2411 163458761 163459710 0.000000e+00 1445.0
6 TraesCS6A01G253800 chr2A 93.340 976 62 3 1437 2411 63748064 63747091 0.000000e+00 1439.0
7 TraesCS6A01G253800 chr2A 93.340 976 61 4 1437 2411 79633897 79634869 0.000000e+00 1439.0
8 TraesCS6A01G253800 chr1A 94.357 957 51 3 1456 2411 286826714 286827668 0.000000e+00 1465.0
9 TraesCS6A01G253800 chr7A 92.778 997 67 5 1418 2411 298396659 298395665 0.000000e+00 1437.0
10 TraesCS6A01G253800 chr7A 75.709 1445 318 29 6 1437 711304297 711305721 0.000000e+00 693.0
11 TraesCS6A01G253800 chr3A 93.040 977 64 4 1437 2411 551603201 551602227 0.000000e+00 1424.0
12 TraesCS6A01G253800 chr3A 93.458 963 58 4 1452 2411 670872397 670873357 0.000000e+00 1424.0
13 TraesCS6A01G253800 chr3B 75.950 1447 319 25 1 1437 7283115 7281688 0.000000e+00 717.0
14 TraesCS6A01G253800 chr1B 75.259 1447 330 24 1 1437 183211214 183212642 0.000000e+00 664.0
15 TraesCS6A01G253800 chr5A 74.351 1310 309 24 138 1437 40717056 40718348 1.270000e-147 532.0
16 TraesCS6A01G253800 chr2D 74.670 1137 258 24 312 1437 413689697 413688580 6.030000e-131 477.0
17 TraesCS6A01G253800 chr6B 72.846 1451 355 33 1 1437 21180226 21181651 6.070000e-126 460.0
18 TraesCS6A01G253800 chr3D 74.468 799 188 15 6 796 26121737 26120947 4.970000e-87 331.0
19 TraesCS6A01G253800 chr3D 97.778 45 1 0 1393 1437 456592210 456592166 7.150000e-11 78.7
20 TraesCS6A01G253800 chr5D 97.541 122 3 0 1311 1432 112342653 112342532 2.430000e-50 209.0


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 TraesCS6A01G253800 chr6A 469918912 469921322 2410 False 4453 4453 100.000 1 2411 1 chr6A.!!$F1 2410
1 TraesCS6A01G253800 chr6A 578834541 578835499 958 True 1419 1419 93.347 1450 2411 1 chr6A.!!$R1 961
2 TraesCS6A01G253800 chr6A 500131395 500132102 707 False 255 255 73.501 99 806 1 chr6A.!!$F2 707
3 TraesCS6A01G253800 chr2A 16659639 16661067 1428 False 2492 2492 98.051 1 1437 1 chr2A.!!$F1 1436
4 TraesCS6A01G253800 chr2A 509042797 509043756 959 False 1465 1465 94.185 1450 2411 1 chr2A.!!$F4 961
5 TraesCS6A01G253800 chr2A 163458761 163459710 949 False 1445 1445 94.111 1462 2411 1 chr2A.!!$F3 949
6 TraesCS6A01G253800 chr2A 63747091 63748064 973 True 1439 1439 93.340 1437 2411 1 chr2A.!!$R1 974
7 TraesCS6A01G253800 chr2A 79633897 79634869 972 False 1439 1439 93.340 1437 2411 1 chr2A.!!$F2 974
8 TraesCS6A01G253800 chr1A 286826714 286827668 954 False 1465 1465 94.357 1456 2411 1 chr1A.!!$F1 955
9 TraesCS6A01G253800 chr7A 298395665 298396659 994 True 1437 1437 92.778 1418 2411 1 chr7A.!!$R1 993
10 TraesCS6A01G253800 chr7A 711304297 711305721 1424 False 693 693 75.709 6 1437 1 chr7A.!!$F1 1431
11 TraesCS6A01G253800 chr3A 551602227 551603201 974 True 1424 1424 93.040 1437 2411 1 chr3A.!!$R1 974
12 TraesCS6A01G253800 chr3A 670872397 670873357 960 False 1424 1424 93.458 1452 2411 1 chr3A.!!$F1 959
13 TraesCS6A01G253800 chr3B 7281688 7283115 1427 True 717 717 75.950 1 1437 1 chr3B.!!$R1 1436
14 TraesCS6A01G253800 chr1B 183211214 183212642 1428 False 664 664 75.259 1 1437 1 chr1B.!!$F1 1436
15 TraesCS6A01G253800 chr5A 40717056 40718348 1292 False 532 532 74.351 138 1437 1 chr5A.!!$F1 1299
16 TraesCS6A01G253800 chr2D 413688580 413689697 1117 True 477 477 74.670 312 1437 1 chr2D.!!$R1 1125
17 TraesCS6A01G253800 chr6B 21180226 21181651 1425 False 460 460 72.846 1 1437 1 chr6B.!!$F1 1436
18 TraesCS6A01G253800 chr3D 26120947 26121737 790 True 331 331 74.468 6 796 1 chr3D.!!$R1 790

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
841 845 1.915141 AAGGCAAGATGGTGAGTTGG 58.085 50.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2213 2224 0.968901 ACCCCAAGCTCGTATCGACA 60.969 55.0 0.0 0.0 0.0 4.35 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
85 86 2.708861 ACCATCCTATCGCCCAATAACA 59.291 45.455 0.00 0.0 0.00 2.41
495 496 9.515226 AGAAACCACTAATATTTGTTTGCTCTA 57.485 29.630 0.00 0.0 29.89 2.43
653 656 5.164620 TCACTTCCTGAATCAATGCACTA 57.835 39.130 0.00 0.0 0.00 2.74
685 689 2.094894 GCTTCCAGTGATCATGACGTTG 59.905 50.000 0.00 0.0 0.00 4.10
834 838 6.067217 AGATGTAGTTAAAGGCAAGATGGT 57.933 37.500 0.00 0.0 0.00 3.55
835 839 5.882557 AGATGTAGTTAAAGGCAAGATGGTG 59.117 40.000 0.00 0.0 0.00 4.17
836 840 5.235850 TGTAGTTAAAGGCAAGATGGTGA 57.764 39.130 0.00 0.0 0.00 4.02
837 841 5.245531 TGTAGTTAAAGGCAAGATGGTGAG 58.754 41.667 0.00 0.0 0.00 3.51
838 842 4.373156 AGTTAAAGGCAAGATGGTGAGT 57.627 40.909 0.00 0.0 0.00 3.41
839 843 4.729868 AGTTAAAGGCAAGATGGTGAGTT 58.270 39.130 0.00 0.0 0.00 3.01
840 844 4.520492 AGTTAAAGGCAAGATGGTGAGTTG 59.480 41.667 0.00 0.0 0.00 3.16
841 845 1.915141 AAGGCAAGATGGTGAGTTGG 58.085 50.000 0.00 0.0 0.00 3.77
1234 1238 2.419297 GCCATCGTTGGAGAGATCAAGT 60.419 50.000 16.83 0.0 46.92 3.16
1522 1529 1.034838 TCTCCTCGAGCTGCCTCTTC 61.035 60.000 6.99 0.0 35.90 2.87
1665 1672 6.773638 AGACTCCTGCGGATATTATTTGATT 58.226 36.000 0.00 0.0 0.00 2.57
1722 1729 3.165875 GCATCAGGGGCTACTGTCTATA 58.834 50.000 9.02 0.0 39.48 1.31
1723 1730 3.772025 GCATCAGGGGCTACTGTCTATAT 59.228 47.826 9.02 0.0 39.48 0.86
1896 1905 2.847234 TCCCAGCAGGTTGTCCGT 60.847 61.111 0.00 0.0 39.05 4.69
1957 1966 4.821935 CTTTTGGAAGGGAGCCGT 57.178 55.556 0.00 0.0 0.00 5.68
2321 2332 9.113838 TCTAGTATCCGAATACTTACGACTTTT 57.886 33.333 0.00 0.0 44.62 2.27
2350 2363 2.289532 GGCCCTGAGCAGACACTCT 61.290 63.158 0.00 0.0 46.50 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.705002 TTGGGCGATAGGATGGTGGG 61.705 60.000 0.00 0.0 0.00 4.61
495 496 3.909995 TGTATCCTCGGATTCCATTCCAT 59.090 43.478 3.41 0.0 35.34 3.41
685 689 2.663852 ACGTGCCAGTTACGCCAC 60.664 61.111 0.00 0.0 44.87 5.01
834 838 1.472552 CCGTTCACAGTCACCAACTCA 60.473 52.381 0.00 0.0 35.45 3.41
835 839 1.217882 CCGTTCACAGTCACCAACTC 58.782 55.000 0.00 0.0 35.45 3.01
836 840 0.814010 GCCGTTCACAGTCACCAACT 60.814 55.000 0.00 0.0 39.44 3.16
837 841 1.647084 GCCGTTCACAGTCACCAAC 59.353 57.895 0.00 0.0 0.00 3.77
838 842 1.525077 GGCCGTTCACAGTCACCAA 60.525 57.895 0.00 0.0 0.00 3.67
839 843 2.110213 GGCCGTTCACAGTCACCA 59.890 61.111 0.00 0.0 0.00 4.17
840 844 2.110213 TGGCCGTTCACAGTCACC 59.890 61.111 0.00 0.0 0.00 4.02
841 845 2.594962 CGTGGCCGTTCACAGTCAC 61.595 63.158 0.00 0.0 37.50 3.67
1234 1238 1.228245 GACCAAGTGCAAGGAGCCA 60.228 57.895 7.99 0.0 44.83 4.75
1274 1278 9.827411 GAGCAACTTTATTTTTACTCCTACAAG 57.173 33.333 0.00 0.0 0.00 3.16
1501 1508 0.613292 AGAGGCAGCTCGAGGAGAAA 60.613 55.000 15.58 0.0 0.00 2.52
1522 1529 4.767255 AAGGAGCTCGGCCTTGCG 62.767 66.667 7.83 0.0 43.84 4.85
1547 1554 2.050144 ACTGAAGCAGGACCTTGAAGA 58.950 47.619 0.00 0.0 35.51 2.87
1593 1600 1.073897 GCTTCACTGCTGACCCCTT 59.926 57.895 0.00 0.0 0.00 3.95
1596 1603 1.673665 CAGGCTTCACTGCTGACCC 60.674 63.158 0.00 0.0 0.00 4.46
1665 1672 5.547465 TCACAAAGAAAAGCCGAATAGAGA 58.453 37.500 0.00 0.0 0.00 3.10
1896 1905 3.087343 TCTGTCCATCCAGAGGCAA 57.913 52.632 0.00 0.0 36.57 4.52
2004 2013 1.003233 GGCTCCAAGTTCGGCTCTT 60.003 57.895 0.00 0.0 0.00 2.85
2083 2093 2.998949 GAGCCGGGGGAGACAATT 59.001 61.111 2.18 0.0 0.00 2.32
2154 2165 1.337071 GATAGCGATCCACTTCCGACA 59.663 52.381 0.00 0.0 0.00 4.35
2213 2224 0.968901 ACCCCAAGCTCGTATCGACA 60.969 55.000 0.00 0.0 0.00 4.35


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

AutoCloner maintained by Alex Coulton.