Multiple sequence alignment - TraesCS1A01G269700

Loading Multiple Alignment...

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 TraesCS1A01G269700 chr1A 100.000 2255 0 0 1 2255 463957836 463960090 0.000000e+00 4165.0
1 TraesCS1A01G269700 chr1A 79.472 682 111 26 769 1430 463923794 463924466 7.340000e-125 457.0
2 TraesCS1A01G269700 chr1B 94.857 1575 73 2 689 2255 488473826 488475400 0.000000e+00 2453.0
3 TraesCS1A01G269700 chr1D 93.812 1616 74 13 665 2255 365082092 365083706 0.000000e+00 2407.0
4 TraesCS1A01G269700 chr1D 95.890 657 19 6 1 655 78058734 78058084 0.000000e+00 1057.0
5 TraesCS1A01G269700 chr1D 96.875 32 0 1 636 666 78058078 78058047 4.000000e-03 52.8
6 TraesCS1A01G269700 chr7D 96.090 665 20 4 1 664 177094971 177094312 0.000000e+00 1079.0
7 TraesCS1A01G269700 chr7D 85.284 299 40 3 1735 2031 89311902 89312198 2.810000e-79 305.0
8 TraesCS1A01G269700 chr4D 96.313 651 14 7 1 649 497459993 497460635 0.000000e+00 1061.0
9 TraesCS1A01G269700 chr3A 95.994 649 20 4 1 649 37311749 37311107 0.000000e+00 1050.0
10 TraesCS1A01G269700 chr3A 80.687 699 117 17 778 1467 632041222 632040533 5.520000e-146 527.0
11 TraesCS1A01G269700 chr3A 77.609 594 105 23 799 1375 632295260 632294678 3.590000e-88 335.0
12 TraesCS1A01G269700 chr3A 85.030 334 39 9 1735 2064 632040298 632039972 1.670000e-86 329.0
13 TraesCS1A01G269700 chr3B 80.830 699 116 18 778 1467 651427238 651426549 1.190000e-147 532.0
14 TraesCS1A01G269700 chr3B 85.030 334 39 9 1735 2064 651426305 651425979 1.670000e-86 329.0
15 TraesCS1A01G269700 chr3B 84.431 334 41 9 1735 2064 489350608 489350282 3.610000e-83 318.0
16 TraesCS1A01G269700 chr4B 80.321 686 119 16 790 1467 46934226 46933549 2.580000e-139 505.0
17 TraesCS1A01G269700 chr4B 85.382 301 36 7 1735 2031 46933305 46933009 2.810000e-79 305.0
18 TraesCS1A01G269700 chr4B 89.655 58 6 0 779 836 672128282 672128339 8.640000e-10 75.0
19 TraesCS1A01G269700 chr3D 77.867 750 152 14 724 1466 488902978 488903720 9.500000e-124 453.0
20 TraesCS1A01G269700 chr3D 77.778 621 110 23 772 1375 488893876 488894485 7.660000e-95 357.0
21 TraesCS1A01G269700 chr3D 84.731 334 40 9 1735 2064 488951035 488951361 7.770000e-85 324.0
22 TraesCS1A01G269700 chrUn 84.091 396 45 13 1 386 105221261 105220874 1.270000e-97 366.0
23 TraesCS1A01G269700 chrUn 84.091 396 45 13 1 386 105267385 105266998 1.270000e-97 366.0
24 TraesCS1A01G269700 chrUn 84.348 115 13 2 535 649 105266843 105266734 8.520000e-20 108.0
25 TraesCS1A01G269700 chr7A 83.077 390 39 18 1 375 448452820 448453197 1.670000e-86 329.0
26 TraesCS1A01G269700 chr2B 85.030 334 39 9 1735 2064 254627112 254627438 1.670000e-86 329.0
27 TraesCS1A01G269700 chr2B 79.087 263 38 11 117 375 784728772 784729021 4.980000e-37 165.0
28 TraesCS1A01G269700 chr4A 82.322 379 55 9 1 376 724408742 724409111 3.610000e-83 318.0


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 TraesCS1A01G269700 chr1A 463957836 463960090 2254 False 4165.0 4165 100.0000 1 2255 1 chr1A.!!$F2 2254
1 TraesCS1A01G269700 chr1A 463923794 463924466 672 False 457.0 457 79.4720 769 1430 1 chr1A.!!$F1 661
2 TraesCS1A01G269700 chr1B 488473826 488475400 1574 False 2453.0 2453 94.8570 689 2255 1 chr1B.!!$F1 1566
3 TraesCS1A01G269700 chr1D 365082092 365083706 1614 False 2407.0 2407 93.8120 665 2255 1 chr1D.!!$F1 1590
4 TraesCS1A01G269700 chr1D 78058047 78058734 687 True 554.9 1057 96.3825 1 666 2 chr1D.!!$R1 665
5 TraesCS1A01G269700 chr7D 177094312 177094971 659 True 1079.0 1079 96.0900 1 664 1 chr7D.!!$R1 663
6 TraesCS1A01G269700 chr4D 497459993 497460635 642 False 1061.0 1061 96.3130 1 649 1 chr4D.!!$F1 648
7 TraesCS1A01G269700 chr3A 37311107 37311749 642 True 1050.0 1050 95.9940 1 649 1 chr3A.!!$R1 648
8 TraesCS1A01G269700 chr3A 632039972 632041222 1250 True 428.0 527 82.8585 778 2064 2 chr3A.!!$R3 1286
9 TraesCS1A01G269700 chr3A 632294678 632295260 582 True 335.0 335 77.6090 799 1375 1 chr3A.!!$R2 576
10 TraesCS1A01G269700 chr3B 651425979 651427238 1259 True 430.5 532 82.9300 778 2064 2 chr3B.!!$R2 1286
11 TraesCS1A01G269700 chr4B 46933009 46934226 1217 True 405.0 505 82.8515 790 2031 2 chr4B.!!$R1 1241
12 TraesCS1A01G269700 chr3D 488902978 488903720 742 False 453.0 453 77.8670 724 1466 1 chr3D.!!$F2 742
13 TraesCS1A01G269700 chr3D 488893876 488894485 609 False 357.0 357 77.7780 772 1375 1 chr3D.!!$F1 603
14 TraesCS1A01G269700 chrUn 105266734 105267385 651 True 237.0 366 84.2195 1 649 2 chrUn.!!$R2 648

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
437 457 1.133025 CCATTTCTTTACTGCGGCCAG 59.867 52.381 2.24 0.0 44.8 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1612 0.165944 GAATGCAAGAACCCGACGTG 59.834 55.0 0.0 0.0 0.0 4.49 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
40 42 2.593026 AGGGTTTCGGCAATCTGAAAA 58.407 42.857 1.35 0.00 45.97 2.29
437 457 1.133025 CCATTTCTTTACTGCGGCCAG 59.867 52.381 2.24 0.00 44.80 4.85
586 621 7.336931 CGCTTTATATAGGCCAAAACATAGGAT 59.663 37.037 5.01 0.00 0.00 3.24
666 727 6.228258 ACTGAGATTTAGCAGTTCCGTTTAA 58.772 36.000 0.00 0.00 42.33 1.52
670 731 6.704310 AGATTTAGCAGTTCCGTTTAACCTA 58.296 36.000 0.00 0.00 0.00 3.08
679 740 3.036091 TCCGTTTAACCTATGCCTAGCT 58.964 45.455 0.00 0.00 0.00 3.32
710 771 3.007635 ACTGCTAATTCTAACCAACGGC 58.992 45.455 0.00 0.00 0.00 5.68
716 777 1.234615 TTCTAACCAACGGCAGCTGC 61.235 55.000 30.88 30.88 41.14 5.25
1479 1551 0.670546 CCGCGTTTCTGATCACCACT 60.671 55.000 4.92 0.00 0.00 4.00
1488 1560 1.267574 TGATCACCACTCCCTGCTCC 61.268 60.000 0.00 0.00 0.00 4.70
1520 1594 2.224113 CCTGAGCACTGCAAATTTTGGT 60.224 45.455 10.96 0.00 0.00 3.67
1545 1619 1.526887 GCATATCAATGTCCACGTCGG 59.473 52.381 0.00 0.00 35.38 4.79
1576 1662 1.733041 CATCGACCGAACACGCTGT 60.733 57.895 0.00 0.00 0.00 4.40
1585 1671 1.062002 CGAACACGCTGTCAAACACTT 59.938 47.619 0.00 0.00 0.00 3.16
1586 1672 2.705154 GAACACGCTGTCAAACACTTC 58.295 47.619 0.00 0.00 0.00 3.01
1609 1699 1.332144 TTACCTGTATTCCGGCGCCT 61.332 55.000 26.68 8.22 0.00 5.52
1610 1700 2.023414 TACCTGTATTCCGGCGCCTG 62.023 60.000 26.68 19.63 0.00 4.85
1624 1714 3.041940 CCTGTGTTGCGGGTCGAC 61.042 66.667 7.13 7.13 38.84 4.20
1626 1716 4.953868 TGTGTTGCGGGTCGACGG 62.954 66.667 9.92 5.12 31.43 4.79
1645 1735 0.530650 GCCTTCATGCGAATCGGAGA 60.531 55.000 4.35 0.00 45.75 3.71
1671 1761 3.745803 GGACTCGACTTCCGCCGT 61.746 66.667 0.00 0.00 38.37 5.68
1672 1762 2.202453 GACTCGACTTCCGCCGTC 60.202 66.667 0.00 0.00 38.37 4.79
1782 2070 1.080434 GAGCAAGAAGACGGCGAGT 60.080 57.895 16.62 0.00 0.00 4.18
2105 2393 0.458889 CTGCATTTGTGATTGCCGGG 60.459 55.000 2.18 0.00 38.08 5.73
2215 2511 3.678072 GTCTCGTGAATCAAACATCGGAA 59.322 43.478 0.00 0.00 0.00 4.30
2236 2532 6.514048 CGGAAAAAGAAGAGCAGAGTGAAATT 60.514 38.462 0.00 0.00 0.00 1.82
2237 2533 6.640092 GGAAAAAGAAGAGCAGAGTGAAATTG 59.360 38.462 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
337 346 7.201732 CCTCTATCTCTCTGTTCTTTCTCTGTC 60.202 44.444 0.00 0.00 0.00 3.51
487 507 2.203922 TGGGCTGGACAGGTGCTA 60.204 61.111 1.01 0.00 0.00 3.49
586 621 3.134574 AGATTCGTGTTGGGTGCTTTA 57.865 42.857 0.00 0.00 0.00 1.85
666 727 2.953284 TACTCGAGCTAGGCATAGGT 57.047 50.000 13.61 10.27 42.40 3.08
670 731 4.336993 GCAGTATATACTCGAGCTAGGCAT 59.663 45.833 13.61 0.24 33.46 4.40
679 740 9.511272 TGGTTAGAATTAGCAGTATATACTCGA 57.489 33.333 12.62 2.44 33.46 4.04
716 777 1.079503 GTACAAGAAGAAGGCAGCGG 58.920 55.000 0.00 0.00 0.00 5.52
717 778 2.086054 AGTACAAGAAGAAGGCAGCG 57.914 50.000 0.00 0.00 0.00 5.18
744 805 0.311790 TGTACGTCTTCTTCGCCGTT 59.688 50.000 0.00 0.00 34.95 4.44
1479 1551 2.043852 GACGAGGAGGAGCAGGGA 60.044 66.667 0.00 0.00 0.00 4.20
1488 1560 2.041115 TGCTCAGGTCGACGAGGAG 61.041 63.158 18.36 18.91 0.00 3.69
1520 1594 4.260985 ACGTGGACATTGATATGCTTTCA 58.739 39.130 0.00 0.00 35.03 2.69
1528 1602 1.187974 ACCCGACGTGGACATTGATA 58.812 50.000 0.00 0.00 42.00 2.15
1536 1610 2.029964 GCAAGAACCCGACGTGGA 59.970 61.111 0.00 0.00 42.00 4.02
1538 1612 0.165944 GAATGCAAGAACCCGACGTG 59.834 55.000 0.00 0.00 0.00 4.49
1545 1619 1.401905 GGTCGATGGAATGCAAGAACC 59.598 52.381 0.00 0.00 0.00 3.62
1576 1662 7.118680 GGAATACAGGTAATTCGAAGTGTTTGA 59.881 37.037 8.63 0.00 0.00 2.69
1585 1671 2.544277 CGCCGGAATACAGGTAATTCGA 60.544 50.000 5.05 0.00 33.97 3.71
1586 1672 1.790623 CGCCGGAATACAGGTAATTCG 59.209 52.381 5.05 0.00 33.97 3.34
1609 1699 4.953868 CCGTCGACCCGCAACACA 62.954 66.667 10.58 0.00 0.00 3.72
1617 1707 2.511600 CATGAAGGCCGTCGACCC 60.512 66.667 14.24 6.34 0.00 4.46
1624 1714 2.628106 CGATTCGCATGAAGGCCG 59.372 61.111 0.00 0.00 37.57 6.13
1626 1716 0.530650 TCTCCGATTCGCATGAAGGC 60.531 55.000 0.00 0.00 37.57 4.35
1627 1717 1.202463 AGTCTCCGATTCGCATGAAGG 60.202 52.381 0.00 0.00 37.57 3.46
1645 1735 1.122019 AAGTCGAGTCCCCTTGCAGT 61.122 55.000 0.00 0.00 0.00 4.40
1760 2048 3.181967 CCGTCTTCTTGCTCGGCG 61.182 66.667 0.00 0.00 36.68 6.46
2105 2393 1.066908 CTCTCTCGACATTGCTCTCCC 59.933 57.143 0.00 0.00 0.00 4.30
2215 2511 5.527033 GCAATTTCACTCTGCTCTTCTTTT 58.473 37.500 0.00 0.00 33.20 2.27


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

AutoCloner maintained by Alex Coulton.