Multiple sequence alignment - TraesCS7A01G286000

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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 TraesCS7A01G286000 chr7A 100.000 2695 0 0 1 2695 332593353 332596047 0 4977
1 TraesCS7A01G286000 chr7A 92.484 2701 189 10 1 2693 536527889 536530583 0 3851
2 TraesCS7A01G286000 chr1A 93.532 2690 164 7 1 2687 53596679 53599361 0 3995
3 TraesCS7A01G286000 chr1A 93.175 2696 180 3 1 2693 387992703 387990009 0 3956
4 TraesCS7A01G286000 chr2A 93.291 2698 175 5 1 2694 417240761 417243456 0 3975
5 TraesCS7A01G286000 chr2A 92.545 2696 184 5 2 2694 165090645 165087964 0 3849
6 TraesCS7A01G286000 chr2A 92.182 2699 204 5 1 2694 567303882 567306578 0 3808
7 TraesCS7A01G286000 chr5A 93.289 2697 176 4 2 2694 350641594 350644289 0 3973
8 TraesCS7A01G286000 chr3A 92.128 2693 204 6 1 2690 570932880 570935567 0 3792
9 TraesCS7A01G286000 chr4A 91.954 2697 210 6 1 2694 66436583 66439275 0 3771


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 TraesCS7A01G286000 chr7A 332593353 332596047 2694 False 4977 4977 100.000 1 2695 1 chr7A.!!$F1 2694
1 TraesCS7A01G286000 chr7A 536527889 536530583 2694 False 3851 3851 92.484 1 2693 1 chr7A.!!$F2 2692
2 TraesCS7A01G286000 chr1A 53596679 53599361 2682 False 3995 3995 93.532 1 2687 1 chr1A.!!$F1 2686
3 TraesCS7A01G286000 chr1A 387990009 387992703 2694 True 3956 3956 93.175 1 2693 1 chr1A.!!$R1 2692
4 TraesCS7A01G286000 chr2A 417240761 417243456 2695 False 3975 3975 93.291 1 2694 1 chr2A.!!$F1 2693
5 TraesCS7A01G286000 chr2A 165087964 165090645 2681 True 3849 3849 92.545 2 2694 1 chr2A.!!$R1 2692
6 TraesCS7A01G286000 chr2A 567303882 567306578 2696 False 3808 3808 92.182 1 2694 1 chr2A.!!$F2 2693
7 TraesCS7A01G286000 chr5A 350641594 350644289 2695 False 3973 3973 93.289 2 2694 1 chr5A.!!$F1 2692
8 TraesCS7A01G286000 chr3A 570932880 570935567 2687 False 3792 3792 92.128 1 2690 1 chr3A.!!$F1 2689
9 TraesCS7A01G286000 chr4A 66436583 66439275 2692 False 3771 3771 91.954 1 2694 1 chr4A.!!$F1 2693

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
122 127 0.970427 TCACCGCATCTACCTCTGCA 60.970 55.000 0.0 0.00 38.30 4.41 F
292 298 1.139734 CTGTATCCAGCGCGACTGT 59.860 57.895 22.7 12.13 45.68 3.55 F
1545 1558 1.302033 CGAAGCAGCCCAAGACTGT 60.302 57.895 0.0 0.00 37.47 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 1342 0.247460 CTCTTCATCCGAGTGCCACA 59.753 55.000 0.0 0.0 0.00 4.17 R
1560 1579 0.685785 TGCAGCCTTTGGTGGTTTCA 60.686 50.000 0.0 0.0 40.37 2.69 R
2456 2476 3.494254 TCGTGCCCCCACTGGTTT 61.494 61.111 0.0 0.0 39.86 3.27 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
122 127 0.970427 TCACCGCATCTACCTCTGCA 60.970 55.000 0.00 0.00 38.30 4.41
164 169 2.107750 CTCGATCCGCTGCCATGT 59.892 61.111 0.00 0.00 0.00 3.21
177 182 1.704628 TGCCATGTGGAAGGAGAAGAA 59.295 47.619 2.55 0.00 37.39 2.52
243 249 3.071206 GAGGACCAGCCAGAGCGA 61.071 66.667 0.00 0.00 46.67 4.93
292 298 1.139734 CTGTATCCAGCGCGACTGT 59.860 57.895 22.70 12.13 45.68 3.55
310 316 5.392767 ACTGTATTCACTCGACAATCAGT 57.607 39.130 0.00 0.00 0.00 3.41
424 432 2.357517 AGTGCGTTCTCCTTGCCG 60.358 61.111 0.00 0.00 0.00 5.69
425 433 2.665185 GTGCGTTCTCCTTGCCGT 60.665 61.111 0.00 0.00 0.00 5.68
436 444 1.660575 CTTGCCGTTCACGTCGACT 60.661 57.895 14.70 0.00 37.74 4.18
439 447 3.458579 CCGTTCACGTCGACTGCG 61.459 66.667 14.70 10.01 37.74 5.18
515 525 1.850345 TCAACTCCACCACTTTTCCCT 59.150 47.619 0.00 0.00 0.00 4.20
608 618 5.128919 GGGTCTCTTCAAGCACATATTCAT 58.871 41.667 0.00 0.00 0.00 2.57
919 932 3.289062 TCCAACTCGTCCGCGACA 61.289 61.111 8.23 0.00 42.81 4.35
1246 1259 6.799925 TCTTTCTTTTGTTCGTTGTCTTTCAC 59.200 34.615 0.00 0.00 0.00 3.18
1273 1286 7.123247 GCCCTTATTGATATGTATTCAATGCCT 59.877 37.037 8.71 0.00 35.87 4.75
1329 1342 4.457496 CGGTGGCGAGAGTGGCAT 62.457 66.667 0.00 0.00 46.76 4.40
1424 1437 1.625818 GCAGAGAAAGGAGGTCCAAGA 59.374 52.381 0.00 0.00 38.89 3.02
1444 1457 2.915659 ACTCACGACCCGGCAAGA 60.916 61.111 0.00 0.00 0.00 3.02
1454 1467 4.323477 CGGCAAGAACCCCCGACA 62.323 66.667 0.00 0.00 44.55 4.35
1486 1499 1.403679 CCAACGTGGCAGTCTTCAAAA 59.596 47.619 0.00 0.00 0.00 2.44
1507 1520 2.416432 CCCTCGGACGTCTTCTCCC 61.416 68.421 16.46 0.00 0.00 4.30
1545 1558 1.302033 CGAAGCAGCCCAAGACTGT 60.302 57.895 0.00 0.00 37.47 3.55
1700 1720 4.919168 CAGAACGTAACCGACTGAATGTTA 59.081 41.667 0.00 0.00 40.95 2.41
1750 1770 1.602237 CACCCGCCAGTACCAAGAT 59.398 57.895 0.00 0.00 0.00 2.40
1776 1796 2.505819 AGATGGAAGATGCGGTTACCTT 59.494 45.455 0.00 0.00 0.00 3.50
1821 1841 8.023128 CGTGATCTTGTTCTTGATTATTTGGTT 58.977 33.333 0.00 0.00 0.00 3.67
1892 1912 5.178797 CCCACTCAATGTTATCGAACTTCT 58.821 41.667 0.00 0.00 36.45 2.85
1946 1966 0.608582 AGGAGCAAGAAAGCAGCAGG 60.609 55.000 0.00 0.00 36.85 4.85
1971 1991 4.202121 GGCAAGATATCACAGTCGGAACTA 60.202 45.833 5.32 0.00 33.25 2.24
1977 1997 1.534163 TCACAGTCGGAACTAGTGACG 59.466 52.381 11.92 11.92 37.99 4.35
2008 2028 1.211703 TCCAATAGCCCGAAGATGCAA 59.788 47.619 0.00 0.00 0.00 4.08
2015 2035 1.808133 GCCCGAAGATGCAAGTAGAGG 60.808 57.143 0.00 0.00 0.00 3.69
2052 2072 0.608130 TCCCAGTGTCGAGTGAATGG 59.392 55.000 0.00 0.00 0.00 3.16
2057 2077 1.552337 AGTGTCGAGTGAATGGCTCAT 59.448 47.619 0.00 0.00 36.14 2.90
2164 2184 5.256474 CCTTCTTCACCACCTATCATGTTT 58.744 41.667 0.00 0.00 0.00 2.83
2262 2282 2.808202 CGACAATAGCCAGGCTGCTTAT 60.808 50.000 25.59 6.39 42.75 1.73
2285 2305 4.482684 CAGCGCGGCTCTTCGAGA 62.483 66.667 8.83 0.00 36.40 4.04
2356 2376 9.494271 GATATGCTACTTGAATATTGTCCTTCA 57.506 33.333 0.00 0.00 27.09 3.02
2384 2404 7.981789 ACAATCTCTTATTGTCTGCTTCGAATA 59.018 33.333 0.00 0.00 37.69 1.75
2456 2476 2.467880 GGTCTGGTTGAGTGGGATCTA 58.532 52.381 0.00 0.00 0.00 1.98
2604 2625 1.649321 TGCTGAGTGGGATCTGAACT 58.351 50.000 0.00 0.00 0.00 3.01
2694 2715 1.477295 CGGGGTCTGAGTACTTCTTCC 59.523 57.143 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.008933 GTGGCTGACTCGTGGGCT 62.009 66.667 0.00 0.00 0.00 5.19
164 169 0.693049 GCCACCTTCTTCTCCTTCCA 59.307 55.000 0.00 0.00 0.00 3.53
177 182 4.988598 CACGCTCCAACGCCACCT 62.989 66.667 0.00 0.00 36.19 4.00
243 249 1.668101 GCCGGACCTCGATGAAGACT 61.668 60.000 5.05 0.00 42.43 3.24
310 316 2.287103 CAGGTCGTCGATATCGTCTTGA 59.713 50.000 23.61 14.25 40.80 3.02
424 432 3.103911 CCCGCAGTCGACGTGAAC 61.104 66.667 18.15 0.00 38.10 3.18
425 433 2.632136 AAACCCGCAGTCGACGTGAA 62.632 55.000 18.15 0.00 38.10 3.18
436 444 1.460273 GGAGGCAAAGAAAACCCGCA 61.460 55.000 0.00 0.00 0.00 5.69
439 447 0.471022 TGGGGAGGCAAAGAAAACCC 60.471 55.000 0.00 0.00 37.20 4.11
608 618 0.309922 GACCGTCTGAGAACGACACA 59.690 55.000 6.12 0.00 45.37 3.72
919 932 2.897699 GGTCCATACCGGTCACTCT 58.102 57.895 12.40 0.00 35.62 3.24
1028 1041 0.760945 GACATCCTCCGGGTGGATCT 60.761 60.000 24.24 15.34 45.33 2.75
1048 1061 2.867855 GCTCCACCGTGTCCTCACA 61.868 63.158 0.00 0.00 44.02 3.58
1246 1259 6.968904 GCATTGAATACATATCAATAAGGGCG 59.031 38.462 1.80 0.00 43.72 6.13
1273 1286 2.470990 TCTTGCTCCTGCTCTCCATTA 58.529 47.619 0.00 0.00 40.48 1.90
1315 1328 2.046988 CACATGCCACTCTCGCCA 60.047 61.111 0.00 0.00 0.00 5.69
1329 1342 0.247460 CTCTTCATCCGAGTGCCACA 59.753 55.000 0.00 0.00 0.00 4.17
1424 1437 2.989055 CTTGCCGGGTCGTGAGTGTT 62.989 60.000 2.18 0.00 0.00 3.32
1444 1457 2.754375 GTCACCATGTCGGGGGTT 59.246 61.111 0.00 0.00 39.52 4.11
1486 1499 1.668101 GAGAAGACGTCCGAGGGCAT 61.668 60.000 13.01 0.00 0.00 4.40
1560 1579 0.685785 TGCAGCCTTTGGTGGTTTCA 60.686 50.000 0.00 0.00 40.37 2.69
1750 1770 0.755079 CCGCATCTTCCATCTCCTCA 59.245 55.000 0.00 0.00 0.00 3.86
1776 1796 4.062293 CACGAGAATTGTACCTTGGTTGA 58.938 43.478 0.00 0.00 0.00 3.18
1782 1802 5.794894 ACAAGATCACGAGAATTGTACCTT 58.205 37.500 12.77 0.00 36.53 3.50
1821 1841 7.093814 CCCAAGTGAATCACCAGAATTTAATCA 60.094 37.037 10.12 0.00 34.49 2.57
1892 1912 4.677673 ATCACGTCTTCATCATCATCCA 57.322 40.909 0.00 0.00 0.00 3.41
1946 1966 2.159099 TCCGACTGTGATATCTTGCCAC 60.159 50.000 3.98 0.00 0.00 5.01
1959 1979 0.879765 CCGTCACTAGTTCCGACTGT 59.120 55.000 11.51 0.00 36.60 3.55
1971 1991 2.253610 TGGACTATTGGTTCCGTCACT 58.746 47.619 0.00 0.00 0.00 3.41
1977 1997 3.487372 GGGCTATTGGACTATTGGTTCC 58.513 50.000 0.00 0.00 0.00 3.62
2008 2028 5.810080 ACAAAAGTTACAGAGCCTCTACT 57.190 39.130 0.00 0.00 0.00 2.57
2015 2035 3.630312 TGGGACAACAAAAGTTACAGAGC 59.370 43.478 0.00 0.00 31.92 4.09
2052 2072 1.268437 GGTACAGTCGACGGTATGAGC 60.268 57.143 27.21 15.71 0.00 4.26
2057 2077 1.003839 ACGGGTACAGTCGACGGTA 60.004 57.895 22.20 22.20 22.90 4.02
2164 2184 1.218047 CATCCGACTGGCTTTCCGA 59.782 57.895 0.00 0.00 34.14 4.55
2285 2305 4.706842 AGTCAACTTACCTGGACATTGT 57.293 40.909 0.00 0.00 32.79 2.71
2356 2376 7.492524 TCGAAGCAGACAATAAGAGATTGTAT 58.507 34.615 3.03 0.00 41.76 2.29
2456 2476 3.494254 TCGTGCCCCCACTGGTTT 61.494 61.111 0.00 0.00 39.86 3.27
2604 2625 4.028490 CTTGGCGTGCCCCCACTA 62.028 66.667 8.69 0.00 39.86 2.74


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

AutoCloner maintained by Alex Coulton.