Multiple sequence alignment - TraesCS1A01G237800

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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 TraesCS1A01G237800 chr1A 100.000 3074 0 0 1 3074 423674609 423677682 0.000000e+00 5677
1 TraesCS1A01G237800 chr1D 93.655 1450 72 12 862 2293 323871246 323872693 0.000000e+00 2150
2 TraesCS1A01G237800 chr1B 95.408 1263 50 3 862 2119 436075444 436076703 0.000000e+00 2004
3 TraesCS1A01G237800 chr1B 95.408 1263 50 3 862 2119 436146910 436148169 0.000000e+00 2004
4 TraesCS1A01G237800 chr1B 88.043 92 1 4 2162 2253 436076703 436076784 1.950000e-17 100
5 TraesCS1A01G237800 chr1B 88.043 92 1 4 2162 2253 436148169 436148250 1.950000e-17 100
6 TraesCS1A01G237800 chr7B 98.266 865 12 3 1 863 48115714 48114851 0.000000e+00 1511
7 TraesCS1A01G237800 chr4A 98.152 866 13 3 1 864 301819537 301818673 0.000000e+00 1507
8 TraesCS1A01G237800 chr6B 98.150 865 13 3 1 863 77661736 77660873 0.000000e+00 1506
9 TraesCS1A01G237800 chr6B 97.924 867 14 4 1 864 275928263 275927398 0.000000e+00 1498
10 TraesCS1A01G237800 chr6B 97.806 866 15 4 1 863 584056508 584057372 0.000000e+00 1491
11 TraesCS1A01G237800 chr3A 97.921 866 15 3 1 864 140958870 140958006 0.000000e+00 1496
12 TraesCS1A01G237800 chr3A 96.169 783 26 3 2294 3074 50933058 50932278 0.000000e+00 1277
13 TraesCS1A01G237800 chr3A 96.051 785 28 3 2291 3074 679688012 679687230 0.000000e+00 1275
14 TraesCS1A01G237800 chr5B 97.917 864 15 3 1 862 446985525 446984663 0.000000e+00 1493
15 TraesCS1A01G237800 chr2B 97.688 865 16 4 1 863 384106278 384105416 0.000000e+00 1483
16 TraesCS1A01G237800 chr2B 97.688 865 17 3 1 863 518586112 518585249 0.000000e+00 1483
17 TraesCS1A01G237800 chr2A 96.169 783 28 2 2292 3074 701034724 701035504 0.000000e+00 1279
18 TraesCS1A01G237800 chr5A 95.949 790 27 5 2286 3074 705798280 705797495 0.000000e+00 1277
19 TraesCS1A01G237800 chr5A 96.164 782 26 4 2295 3074 610723409 610722630 0.000000e+00 1275
20 TraesCS1A01G237800 chr5A 95.449 791 32 4 2285 3074 650251772 650252559 0.000000e+00 1258
21 TraesCS1A01G237800 chr5A 95.107 797 34 5 2281 3074 578693553 578692759 0.000000e+00 1251
22 TraesCS1A01G237800 chr7A 95.807 787 31 2 2288 3074 679033665 679032881 0.000000e+00 1269
23 TraesCS1A01G237800 chr7A 95.812 788 30 3 2287 3074 710708484 710707700 0.000000e+00 1269
24 TraesCS1A01G237800 chrUn 94.645 747 32 3 1378 2119 376896767 376896024 0.000000e+00 1151
25 TraesCS1A01G237800 chrUn 88.043 92 1 4 2162 2253 376896024 376895943 1.950000e-17 100


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 TraesCS1A01G237800 chr1A 423674609 423677682 3073 False 5677.0 5677 100.0000 1 3074 1 chr1A.!!$F1 3073
1 TraesCS1A01G237800 chr1D 323871246 323872693 1447 False 2150.0 2150 93.6550 862 2293 1 chr1D.!!$F1 1431
2 TraesCS1A01G237800 chr1B 436075444 436076784 1340 False 1052.0 2004 91.7255 862 2253 2 chr1B.!!$F1 1391
3 TraesCS1A01G237800 chr1B 436146910 436148250 1340 False 1052.0 2004 91.7255 862 2253 2 chr1B.!!$F2 1391
4 TraesCS1A01G237800 chr7B 48114851 48115714 863 True 1511.0 1511 98.2660 1 863 1 chr7B.!!$R1 862
5 TraesCS1A01G237800 chr4A 301818673 301819537 864 True 1507.0 1507 98.1520 1 864 1 chr4A.!!$R1 863
6 TraesCS1A01G237800 chr6B 77660873 77661736 863 True 1506.0 1506 98.1500 1 863 1 chr6B.!!$R1 862
7 TraesCS1A01G237800 chr6B 275927398 275928263 865 True 1498.0 1498 97.9240 1 864 1 chr6B.!!$R2 863
8 TraesCS1A01G237800 chr6B 584056508 584057372 864 False 1491.0 1491 97.8060 1 863 1 chr6B.!!$F1 862
9 TraesCS1A01G237800 chr3A 140958006 140958870 864 True 1496.0 1496 97.9210 1 864 1 chr3A.!!$R2 863
10 TraesCS1A01G237800 chr3A 50932278 50933058 780 True 1277.0 1277 96.1690 2294 3074 1 chr3A.!!$R1 780
11 TraesCS1A01G237800 chr3A 679687230 679688012 782 True 1275.0 1275 96.0510 2291 3074 1 chr3A.!!$R3 783
12 TraesCS1A01G237800 chr5B 446984663 446985525 862 True 1493.0 1493 97.9170 1 862 1 chr5B.!!$R1 861
13 TraesCS1A01G237800 chr2B 384105416 384106278 862 True 1483.0 1483 97.6880 1 863 1 chr2B.!!$R1 862
14 TraesCS1A01G237800 chr2B 518585249 518586112 863 True 1483.0 1483 97.6880 1 863 1 chr2B.!!$R2 862
15 TraesCS1A01G237800 chr2A 701034724 701035504 780 False 1279.0 1279 96.1690 2292 3074 1 chr2A.!!$F1 782
16 TraesCS1A01G237800 chr5A 705797495 705798280 785 True 1277.0 1277 95.9490 2286 3074 1 chr5A.!!$R3 788
17 TraesCS1A01G237800 chr5A 610722630 610723409 779 True 1275.0 1275 96.1640 2295 3074 1 chr5A.!!$R2 779
18 TraesCS1A01G237800 chr5A 650251772 650252559 787 False 1258.0 1258 95.4490 2285 3074 1 chr5A.!!$F1 789
19 TraesCS1A01G237800 chr5A 578692759 578693553 794 True 1251.0 1251 95.1070 2281 3074 1 chr5A.!!$R1 793
20 TraesCS1A01G237800 chr7A 679032881 679033665 784 True 1269.0 1269 95.8070 2288 3074 1 chr7A.!!$R1 786
21 TraesCS1A01G237800 chr7A 710707700 710708484 784 True 1269.0 1269 95.8120 2287 3074 1 chr7A.!!$R2 787
22 TraesCS1A01G237800 chrUn 376895943 376896767 824 True 625.5 1151 91.3440 1378 2253 2 chrUn.!!$R1 875

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
849 855 0.105504 AAAGTCAGGCCTTGGCCTTT 60.106 50.0 28.93 18.61 38.27 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2563 2596 0.033796 CCATGGCAACCAGAGATGGT 60.034 55.0 0.0 0.0 45.55 3.55 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
590 593 1.133009 ACTAAGGAGCCTGATCGGGAT 60.133 52.381 25.54 19.48 0.00 3.85
755 760 4.640201 TGTATCATGCTTGCTTAGGTTTCC 59.360 41.667 0.00 0.00 0.00 3.13
805 811 2.494471 CTGTGAACCTGTGGTATCCGTA 59.506 50.000 0.00 0.00 33.12 4.02
808 814 2.898612 TGAACCTGTGGTATCCGTAACA 59.101 45.455 0.00 0.00 33.12 2.41
849 855 0.105504 AAAGTCAGGCCTTGGCCTTT 60.106 50.000 28.93 18.61 38.27 3.11
988 994 1.007271 CCGCTGCCGAGTATAGTGG 60.007 63.158 0.00 0.00 35.95 4.00
1004 1010 3.185246 AGTGGGTAGAGATGAAATGCG 57.815 47.619 0.00 0.00 0.00 4.73
1009 1015 0.464036 TAGAGATGAAATGCGGCCGT 59.536 50.000 28.70 6.29 0.00 5.68
1202 1208 3.760035 CCCCGACACCAGAGACGG 61.760 72.222 0.00 0.00 44.16 4.79
1400 1409 3.202097 TGTGTCATGTGTGTGGTAACTG 58.798 45.455 0.00 0.00 37.61 3.16
1417 1426 5.811100 GGTAACTGCAACTGGAGTAGTATTC 59.189 44.000 4.16 0.00 46.21 1.75
1431 1442 0.530870 GTATTCTCTGGCGGCAGGTC 60.531 60.000 35.20 16.78 0.00 3.85
1489 1500 1.514678 TTCCATGCTGGTGACAACGC 61.515 55.000 1.11 1.11 42.06 4.84
1680 1691 5.717178 AGAACAGTATAGAAGCAACTCCTCA 59.283 40.000 0.00 0.00 0.00 3.86
1709 1723 1.135141 CAGAGGAGACAGCAGCACTAC 60.135 57.143 0.00 0.00 0.00 2.73
1753 1770 2.740981 CAACAGGAGTCTGCAGATTCAC 59.259 50.000 32.44 23.48 44.59 3.18
1763 1780 0.099436 GCAGATTCACATCCAACGGC 59.901 55.000 0.00 0.00 0.00 5.68
1768 1785 1.234821 TTCACATCCAACGGCAGAAC 58.765 50.000 0.00 0.00 0.00 3.01
1801 1818 2.281208 GTACCACCGGCACAGCAA 60.281 61.111 0.00 0.00 0.00 3.91
1825 1842 8.304596 CAACTAGAAGTGAAAGTGGTAGTATCA 58.695 37.037 0.00 0.00 0.00 2.15
1833 1850 6.001460 TGAAAGTGGTAGTATCAGTTTTGGG 58.999 40.000 15.75 0.00 37.74 4.12
1891 1908 3.054503 GCAGCAGGTGGAGTGCAG 61.055 66.667 0.86 0.00 43.82 4.41
1923 1940 1.301009 GGATACTGCTACCGCTGGC 60.301 63.158 0.00 0.00 39.17 4.85
2065 2082 4.290985 TCCTGGGTTCATGGTTCAGAATTA 59.709 41.667 0.00 0.00 0.00 1.40
2231 2248 8.958060 ACAGATGTACTCCATATTACCAGTAT 57.042 34.615 0.00 0.00 32.56 2.12
2269 2302 5.599999 AGAATAACGAGGCAGTAATGTCT 57.400 39.130 0.00 0.00 0.00 3.41
2279 2312 4.457257 AGGCAGTAATGTCTCAAGAAAAGC 59.543 41.667 0.00 0.00 0.00 3.51
2282 2315 4.153117 CAGTAATGTCTCAAGAAAAGCGCT 59.847 41.667 2.64 2.64 0.00 5.92
2283 2316 3.820777 AATGTCTCAAGAAAAGCGCTC 57.179 42.857 12.06 0.00 0.00 5.03
2309 2342 4.772886 AATAAGGGTCCGAATAACTGCT 57.227 40.909 0.00 0.00 0.00 4.24
2320 2353 3.323243 GAATAACTGCTACACGTGTGGT 58.677 45.455 30.83 19.28 34.19 4.16
2432 2465 4.579384 CCGGTGTGTGGCAACCCT 62.579 66.667 0.00 0.00 0.00 4.34
2492 2525 3.136123 CGACCTAGCCGTTCCCGA 61.136 66.667 0.00 0.00 35.63 5.14
2558 2591 4.430765 CGAACCCCGACCTCCGTG 62.431 72.222 0.00 0.00 41.76 4.94
2625 2658 1.826054 CTCCCACCGCAAACCACAA 60.826 57.895 0.00 0.00 0.00 3.33
2669 2702 2.845345 CCACTCCAACCCAGCCCTT 61.845 63.158 0.00 0.00 0.00 3.95
2741 2776 6.157645 TCTCATCCTTAAGGCTGAAAATCTCT 59.842 38.462 24.40 0.00 39.54 3.10
2805 2842 5.448496 GCATGGTTCAGTGTATATTCGCAAA 60.448 40.000 0.00 0.00 0.00 3.68
2809 2846 6.150307 TGGTTCAGTGTATATTCGCAAATTGT 59.850 34.615 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
590 593 2.611800 ATGAGCAGGTCCAGGGCA 60.612 61.111 0.00 0.00 0.00 5.36
755 760 3.771577 AACCACACAGAGGAGTTAAGG 57.228 47.619 0.00 0.00 0.00 2.69
988 994 1.230324 GGCCGCATTTCATCTCTACC 58.770 55.000 0.00 0.00 0.00 3.18
1009 1015 2.125952 CTGCAGCACCATCGACGA 60.126 61.111 0.00 0.00 0.00 4.20
1041 1047 2.873288 GTTACTCCGGCGACTCGT 59.127 61.111 9.30 1.77 0.00 4.18
1129 1135 2.849120 CTTCTGCTGCTGGACGAGGG 62.849 65.000 6.69 0.00 0.00 4.30
1202 1208 5.821995 CACCTCCTACTACTAGTCCTGTTAC 59.178 48.000 0.00 0.00 0.00 2.50
1400 1409 4.688021 CCAGAGAATACTACTCCAGTTGC 58.312 47.826 0.00 0.00 38.80 4.17
1417 1426 2.125350 GAAGACCTGCCGCCAGAG 60.125 66.667 0.00 0.00 41.77 3.35
1431 1442 1.829222 ACATACCCGTACACCCTGAAG 59.171 52.381 0.00 0.00 0.00 3.02
1668 1679 0.603569 ACGTCGATGAGGAGTTGCTT 59.396 50.000 12.58 0.00 0.00 3.91
1680 1691 2.281517 CTGTCTCCTCTGTACGTCGAT 58.718 52.381 0.00 0.00 0.00 3.59
1709 1723 0.179089 CTGCTGGTACCTGCTGCTAG 60.179 60.000 34.87 23.76 40.75 3.42
1753 1770 1.308069 CCTGGTTCTGCCGTTGGATG 61.308 60.000 0.00 0.00 41.21 3.51
1763 1780 4.766375 ACCGTTAATATCACCTGGTTCTG 58.234 43.478 0.00 0.00 0.00 3.02
1768 1785 4.374399 GTGGTACCGTTAATATCACCTGG 58.626 47.826 7.57 0.00 28.91 4.45
1801 1818 7.670559 ACTGATACTACCACTTTCACTTCTAGT 59.329 37.037 0.00 0.00 0.00 2.57
1825 1842 1.137594 TCGTCCCATCCCCCAAAACT 61.138 55.000 0.00 0.00 0.00 2.66
1833 1850 2.317149 CTTCCAGCTCGTCCCATCCC 62.317 65.000 0.00 0.00 0.00 3.85
1923 1940 2.149803 TACTCGTTCCCACTGCACCG 62.150 60.000 0.00 0.00 0.00 4.94
1983 2000 1.002868 CTGCCTGTACCTTGCAGCT 60.003 57.895 13.30 0.00 45.09 4.24
2087 2104 1.938585 TCTTCGTGGAGGGATTGACT 58.061 50.000 0.00 0.00 0.00 3.41
2094 2111 5.539048 ACGATAAATATTCTTCGTGGAGGG 58.461 41.667 19.11 0.00 42.66 4.30
2309 2342 0.527113 CCGTCCATACCACACGTGTA 59.473 55.000 22.90 6.47 0.00 2.90
2355 2388 4.419921 GGCCGGTTCCCGTCCATT 62.420 66.667 1.90 0.00 45.15 3.16
2492 2525 1.152226 GAGGGGATGGATCGGAGGT 60.152 63.158 0.00 0.00 0.00 3.85
2558 2591 1.450312 CAACCAGAGATGGTCGGCC 60.450 63.158 0.00 0.00 42.20 6.13
2563 2596 0.033796 CCATGGCAACCAGAGATGGT 60.034 55.000 0.00 0.00 45.55 3.55
2604 2637 2.203294 GGTTTGCGGTGGGAGTGT 60.203 61.111 0.00 0.00 0.00 3.55
2669 2702 5.163509 CCTGGTTTTAGATGATCGTCTCTGA 60.164 44.000 20.75 6.15 0.00 3.27
2741 2776 2.225382 TGGACCCAGTACAAGATCGA 57.775 50.000 0.00 0.00 0.00 3.59
2805 2842 1.977854 TGGTGTACTCTGCCTGACAAT 59.022 47.619 0.00 0.00 0.00 2.71
2809 2846 2.103373 GATCTGGTGTACTCTGCCTGA 58.897 52.381 0.00 1.97 35.32 3.86
2890 2927 7.463618 AGGGATTCCTACTCATCCATTTCATAT 59.536 37.037 2.01 0.00 42.75 1.78
2928 2967 6.464180 CCCTTCATTCCAAAAATTGTCCTTCA 60.464 38.462 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.