Multiple sequence alignment - TraesCS6D01G206500

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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 TraesCS6D01G206500 chr6D 100.000 2672 0 0 1 2672 292058265 292055594 0.000000e+00 4935.0
1 TraesCS6D01G206500 chr6D 92.100 1962 119 20 742 2672 118595477 118593521 0.000000e+00 2732.0
2 TraesCS6D01G206500 chr6D 91.001 1978 120 22 742 2672 431922488 431920522 0.000000e+00 2614.0
3 TraesCS6D01G206500 chr6D 94.715 1419 65 6 549 1965 67757676 67756266 0.000000e+00 2196.0
4 TraesCS6D01G206500 chr6D 92.975 726 36 1 1960 2670 67730354 67729629 0.000000e+00 1044.0
5 TraesCS6D01G206500 chr6D 86.944 697 46 18 1 657 431923116 431922425 0.000000e+00 741.0
6 TraesCS6D01G206500 chr6D 100.000 42 0 0 616 657 292057502 292057461 7.930000e-11 78.7
7 TraesCS6D01G206500 chr3D 93.982 2725 82 18 1 2672 537586540 537583845 0.000000e+00 4048.0
8 TraesCS6D01G206500 chr3D 92.672 1965 96 24 742 2671 263230638 263232589 0.000000e+00 2787.0
9 TraesCS6D01G206500 chr3D 92.112 1965 116 16 742 2672 610706428 610708387 0.000000e+00 2734.0
10 TraesCS6D01G206500 chr3D 91.908 1965 120 15 742 2672 500625017 500623058 0.000000e+00 2712.0
11 TraesCS6D01G206500 chr3D 90.937 1953 106 26 742 2672 55375276 55377179 0.000000e+00 2560.0
12 TraesCS6D01G206500 chr3D 86.486 407 23 14 265 657 263230313 263230701 4.110000e-113 418.0
13 TraesCS6D01G206500 chr7D 92.981 1966 97 13 742 2672 475989326 475987367 0.000000e+00 2828.0
14 TraesCS6D01G206500 chr7D 91.849 1963 123 22 742 2672 135380153 135382110 0.000000e+00 2704.0
15 TraesCS6D01G206500 chr7D 86.202 674 69 14 1 656 59511042 59511709 0.000000e+00 708.0
16 TraesCS6D01G206500 chr7D 86.283 678 61 19 1 656 135379548 135380215 0.000000e+00 708.0
17 TraesCS6D01G206500 chr7D 85.755 695 47 12 1 657 475989943 475989263 0.000000e+00 688.0
18 TraesCS6D01G206500 chr7D 83.900 677 69 20 1 656 607582842 607582185 6.320000e-171 610.0
19 TraesCS6D01G206500 chr6A 92.472 1966 110 11 742 2672 569587466 569585504 0.000000e+00 2776.0
20 TraesCS6D01G206500 chr5A 92.304 1962 111 13 742 2672 484593619 484595571 0.000000e+00 2750.0
21 TraesCS6D01G206500 chr5A 91.404 1966 127 13 742 2672 43173350 43175308 0.000000e+00 2656.0
22 TraesCS6D01G206500 chr5A 84.218 678 65 27 1 656 49891895 49891238 2.920000e-174 621.0
23 TraesCS6D01G206500 chr5A 77.977 613 85 26 81 656 294239792 294239193 3.290000e-89 339.0
24 TraesCS6D01G206500 chr5D 91.874 1969 117 21 742 2672 333234400 333236363 0.000000e+00 2710.0
25 TraesCS6D01G206500 chr5D 85.778 675 69 14 1 656 545975107 545974441 0.000000e+00 689.0
26 TraesCS6D01G206500 chr5D 83.923 678 68 21 1 656 424137162 424137820 6.320000e-171 610.0
27 TraesCS6D01G206500 chr2A 91.764 1967 120 15 742 2672 378392539 378390579 0.000000e+00 2697.0
28 TraesCS6D01G206500 chr3A 91.833 1959 117 26 742 2672 80406562 80404619 0.000000e+00 2691.0
29 TraesCS6D01G206500 chr4D 92.118 1903 110 12 806 2672 47156018 47157916 0.000000e+00 2647.0
30 TraesCS6D01G206500 chr1D 92.781 1496 70 11 1211 2672 96084964 96083473 0.000000e+00 2130.0
31 TraesCS6D01G206500 chr1D 87.749 702 37 17 1 657 96103285 96102588 0.000000e+00 774.0
32 TraesCS6D01G206500 chr1D 86.982 676 61 14 1 656 479088291 479087623 0.000000e+00 736.0
33 TraesCS6D01G206500 chr1D 85.988 678 65 16 1 656 218906178 218906847 0.000000e+00 699.0
34 TraesCS6D01G206500 chr1D 80.195 616 67 29 81 656 10804055 10803455 6.880000e-111 411.0
35 TraesCS6D01G206500 chr4A 90.570 1071 62 8 1628 2672 527691591 527692648 0.000000e+00 1382.0
36 TraesCS6D01G206500 chr7A 89.790 715 47 10 1984 2672 18860844 18861558 0.000000e+00 893.0
37 TraesCS6D01G206500 chr7A 90.950 674 38 13 1 657 18859032 18859699 0.000000e+00 885.0
38 TraesCS6D01G206500 chr5B 84.853 614 58 23 67 655 369249211 369248608 1.070000e-163 586.0
39 TraesCS6D01G206500 chr4B 85.689 573 51 21 103 655 212081512 212080951 2.310000e-160 575.0
40 TraesCS6D01G206500 chr4B 85.340 573 53 21 103 655 212139437 212138876 4.990000e-157 564.0
41 TraesCS6D01G206500 chr4B 84.991 573 55 21 103 655 212110288 212109727 1.080000e-153 553.0
42 TraesCS6D01G206500 chr2D 89.189 407 20 14 265 656 407907836 407908233 1.110000e-133 486.0
43 TraesCS6D01G206500 chr2D 85.819 409 34 12 265 656 526250925 526250524 1.910000e-111 412.0
44 TraesCS6D01G206500 chr6B 86.165 412 32 13 265 656 420671253 420671659 3.180000e-114 422.0
45 TraesCS6D01G206500 chr2B 81.481 270 34 15 316 578 698309047 698309307 9.690000e-50 207.0


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 TraesCS6D01G206500 chr6D 292055594 292058265 2671 True 2506.85 4935 100.0000 1 2672 2 chr6D.!!$R4 2671
1 TraesCS6D01G206500 chr6D 118593521 118595477 1956 True 2732.00 2732 92.1000 742 2672 1 chr6D.!!$R3 1930
2 TraesCS6D01G206500 chr6D 67756266 67757676 1410 True 2196.00 2196 94.7150 549 1965 1 chr6D.!!$R2 1416
3 TraesCS6D01G206500 chr6D 431920522 431923116 2594 True 1677.50 2614 88.9725 1 2672 2 chr6D.!!$R5 2671
4 TraesCS6D01G206500 chr6D 67729629 67730354 725 True 1044.00 1044 92.9750 1960 2670 1 chr6D.!!$R1 710
5 TraesCS6D01G206500 chr3D 537583845 537586540 2695 True 4048.00 4048 93.9820 1 2672 1 chr3D.!!$R2 2671
6 TraesCS6D01G206500 chr3D 610706428 610708387 1959 False 2734.00 2734 92.1120 742 2672 1 chr3D.!!$F2 1930
7 TraesCS6D01G206500 chr3D 500623058 500625017 1959 True 2712.00 2712 91.9080 742 2672 1 chr3D.!!$R1 1930
8 TraesCS6D01G206500 chr3D 55375276 55377179 1903 False 2560.00 2560 90.9370 742 2672 1 chr3D.!!$F1 1930
9 TraesCS6D01G206500 chr3D 263230313 263232589 2276 False 1602.50 2787 89.5790 265 2671 2 chr3D.!!$F3 2406
10 TraesCS6D01G206500 chr7D 475987367 475989943 2576 True 1758.00 2828 89.3680 1 2672 2 chr7D.!!$R2 2671
11 TraesCS6D01G206500 chr7D 135379548 135382110 2562 False 1706.00 2704 89.0660 1 2672 2 chr7D.!!$F2 2671
12 TraesCS6D01G206500 chr7D 59511042 59511709 667 False 708.00 708 86.2020 1 656 1 chr7D.!!$F1 655
13 TraesCS6D01G206500 chr7D 607582185 607582842 657 True 610.00 610 83.9000 1 656 1 chr7D.!!$R1 655
14 TraesCS6D01G206500 chr6A 569585504 569587466 1962 True 2776.00 2776 92.4720 742 2672 1 chr6A.!!$R1 1930
15 TraesCS6D01G206500 chr5A 484593619 484595571 1952 False 2750.00 2750 92.3040 742 2672 1 chr5A.!!$F2 1930
16 TraesCS6D01G206500 chr5A 43173350 43175308 1958 False 2656.00 2656 91.4040 742 2672 1 chr5A.!!$F1 1930
17 TraesCS6D01G206500 chr5A 49891238 49891895 657 True 621.00 621 84.2180 1 656 1 chr5A.!!$R1 655
18 TraesCS6D01G206500 chr5A 294239193 294239792 599 True 339.00 339 77.9770 81 656 1 chr5A.!!$R2 575
19 TraesCS6D01G206500 chr5D 333234400 333236363 1963 False 2710.00 2710 91.8740 742 2672 1 chr5D.!!$F1 1930
20 TraesCS6D01G206500 chr5D 545974441 545975107 666 True 689.00 689 85.7780 1 656 1 chr5D.!!$R1 655
21 TraesCS6D01G206500 chr5D 424137162 424137820 658 False 610.00 610 83.9230 1 656 1 chr5D.!!$F2 655
22 TraesCS6D01G206500 chr2A 378390579 378392539 1960 True 2697.00 2697 91.7640 742 2672 1 chr2A.!!$R1 1930
23 TraesCS6D01G206500 chr3A 80404619 80406562 1943 True 2691.00 2691 91.8330 742 2672 1 chr3A.!!$R1 1930
24 TraesCS6D01G206500 chr4D 47156018 47157916 1898 False 2647.00 2647 92.1180 806 2672 1 chr4D.!!$F1 1866
25 TraesCS6D01G206500 chr1D 96083473 96084964 1491 True 2130.00 2130 92.7810 1211 2672 1 chr1D.!!$R2 1461
26 TraesCS6D01G206500 chr1D 96102588 96103285 697 True 774.00 774 87.7490 1 657 1 chr1D.!!$R3 656
27 TraesCS6D01G206500 chr1D 479087623 479088291 668 True 736.00 736 86.9820 1 656 1 chr1D.!!$R4 655
28 TraesCS6D01G206500 chr1D 218906178 218906847 669 False 699.00 699 85.9880 1 656 1 chr1D.!!$F1 655
29 TraesCS6D01G206500 chr1D 10803455 10804055 600 True 411.00 411 80.1950 81 656 1 chr1D.!!$R1 575
30 TraesCS6D01G206500 chr4A 527691591 527692648 1057 False 1382.00 1382 90.5700 1628 2672 1 chr4A.!!$F1 1044
31 TraesCS6D01G206500 chr7A 18859032 18861558 2526 False 889.00 893 90.3700 1 2672 2 chr7A.!!$F1 2671
32 TraesCS6D01G206500 chr5B 369248608 369249211 603 True 586.00 586 84.8530 67 655 1 chr5B.!!$R1 588
33 TraesCS6D01G206500 chr4B 212080951 212081512 561 True 575.00 575 85.6890 103 655 1 chr4B.!!$R1 552
34 TraesCS6D01G206500 chr4B 212138876 212139437 561 True 564.00 564 85.3400 103 655 1 chr4B.!!$R3 552
35 TraesCS6D01G206500 chr4B 212109727 212110288 561 True 553.00 553 84.9910 103 655 1 chr4B.!!$R2 552

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
134 144 1.270550 CATCCTGGCCAACTGAAACAC 59.729 52.381 7.01 0.0 0.0 3.32 F
150 160 3.721087 AACACCTATGCTAGCCAACTT 57.279 42.857 13.29 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1184 1272 1.194781 AGACACCACTACAGGGGCAG 61.195 60.000 0.0 0.0 34.56 4.85 R
1903 2040 1.743252 GCACACTGGACTGCCTAGC 60.743 63.158 0.0 0.0 34.31 3.42 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
34 35 8.102676 TCCTGAACATGAATTCTGAGTGAATAA 58.897 33.333 7.05 0.00 43.99 1.40
88 89 1.935873 CATGTATCGTGGCCAACTGAG 59.064 52.381 7.24 0.00 0.00 3.35
134 144 1.270550 CATCCTGGCCAACTGAAACAC 59.729 52.381 7.01 0.00 0.00 3.32
150 160 3.721087 AACACCTATGCTAGCCAACTT 57.279 42.857 13.29 0.00 0.00 2.66
161 171 5.009631 TGCTAGCCAACTTAACACATTGAT 58.990 37.500 13.29 0.00 0.00 2.57
228 263 7.001674 TCTAGCCAAAACCAAAAATCTGTAGA 58.998 34.615 0.00 0.00 0.00 2.59
706 780 6.368516 GCCACAATTGTGCAAACTAACATAAT 59.631 34.615 29.42 0.00 44.34 1.28
1059 1146 5.308759 TGAGCTTCCTCATGATATGGATCAA 59.691 40.000 3.19 0.00 42.98 2.57
1184 1272 2.690778 GGCAGTCATCAACCCGTGC 61.691 63.158 0.00 0.00 0.00 5.34
1607 1742 4.537688 TGAGGAAATGGAAGATGAACCTCT 59.462 41.667 0.00 0.00 41.89 3.69
1631 1766 2.303890 TCTTTGCTGAAGATGAGGCTGA 59.696 45.455 0.00 0.00 39.44 4.26
1637 1772 9.946140 CTTTGCTGAAGATGAGGCTGATCCTAA 62.946 44.444 10.48 0.00 40.77 2.69
1903 2040 5.493809 TCCCTTACAGAATTAAGTTTCCCG 58.506 41.667 0.00 0.00 0.00 5.14
2145 2308 1.266175 GTGCAGCTGGATATGTGCATC 59.734 52.381 17.12 0.00 46.93 3.91
2495 2675 4.461081 ACCAACATGTACAATATGCCGTTT 59.539 37.500 0.00 0.00 0.00 3.60
2546 2726 2.093869 CCAATCTTTCATGCTGGGTTGG 60.094 50.000 8.48 8.48 0.00 3.77
2581 2761 1.067354 GGAGTTGGCATCAAGCTTTGG 60.067 52.381 0.00 0.00 44.79 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 1.601419 ATGCATGCTCAGTTGGCCAC 61.601 55.000 20.33 0.00 0.00 5.01
88 89 1.270274 TCAGTTGGACAACATGCATGC 59.730 47.619 26.53 11.82 43.47 4.06
134 144 4.513442 TGTGTTAAGTTGGCTAGCATAGG 58.487 43.478 18.24 0.00 39.70 2.57
150 160 6.319911 TGTTCAGTTGGACAATCAATGTGTTA 59.680 34.615 0.00 0.00 44.12 2.41
161 171 2.288334 GCATGCATGTTCAGTTGGACAA 60.288 45.455 26.79 0.00 0.00 3.18
228 263 7.803724 AGTTTATTTGTCTTTTCGCTATCGTT 58.196 30.769 0.00 0.00 36.96 3.85
899 981 5.713792 TCAAAGAGTGTTTCAAACAACCA 57.286 34.783 4.02 0.00 44.16 3.67
985 1070 9.696917 GAGATCAAGCATTTCTTTTTCCTTTTA 57.303 29.630 0.00 0.00 31.27 1.52
1059 1146 1.547820 TGTGGCATGTTGTGTTGTTGT 59.452 42.857 0.00 0.00 0.00 3.32
1184 1272 1.194781 AGACACCACTACAGGGGCAG 61.195 60.000 0.00 0.00 34.56 4.85
1623 1758 7.437713 TCTTTTCTTATTAGGATCAGCCTCA 57.562 36.000 0.00 0.00 46.97 3.86
1637 1772 6.356190 CGCGTTTTCGTTTCTTCTTTTCTTAT 59.644 34.615 0.00 0.00 46.03 1.73
1903 2040 1.743252 GCACACTGGACTGCCTAGC 60.743 63.158 0.00 0.00 34.31 3.42
2190 2353 5.870978 CAGATCCATAATGCATCATACGTCA 59.129 40.000 0.00 0.00 0.00 4.35
2269 2447 4.020218 CACCCTCCTTTGTGTCATCTCTAA 60.020 45.833 0.00 0.00 0.00 2.10
2427 2607 0.390603 CAATCGTGGTACGCCTCCAA 60.391 55.000 0.00 0.00 42.21 3.53
2495 2675 0.179234 TTATTCCGATGAAGGGCGCA 59.821 50.000 10.83 0.00 33.05 6.09
2546 2726 4.704833 TCCTGCCTCACAAGCGCC 62.705 66.667 2.29 0.00 0.00 6.53
2550 2730 1.239968 GCCAACTCCTGCCTCACAAG 61.240 60.000 0.00 0.00 0.00 3.16
2581 2761 1.087501 GAATGCTCGGAAGACCCAAC 58.912 55.000 0.00 0.00 35.39 3.77


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

AutoCloner maintained by Alex Coulton.