Multiple sequence alignment - TraesCS6D01G120500

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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 TraesCS6D01G120500 chr6D 100.000 2348 0 0 1 2348 85544567 85546914 0.000000e+00 4337.0
1 TraesCS6D01G120500 chr6D 97.259 1642 36 6 1 1637 84682979 84681342 0.000000e+00 2774.0
2 TraesCS6D01G120500 chr6B 95.095 1162 43 6 1 1159 161350390 161349240 0.000000e+00 1818.0
3 TraesCS6D01G120500 chr6B 82.941 170 18 7 1472 1637 161348896 161348734 2.430000e-30 143.0
4 TraesCS6D01G120500 chr6A 92.880 955 41 9 687 1635 101912752 101911819 0.000000e+00 1362.0
5 TraesCS6D01G120500 chr6A 94.978 697 23 3 1 695 101929746 101929060 0.000000e+00 1083.0
6 TraesCS6D01G120500 chr1A 87.537 674 51 11 1661 2317 584882254 584882911 0.000000e+00 749.0
7 TraesCS6D01G120500 chr1A 81.780 708 103 19 1661 2347 504066724 504066022 9.420000e-159 569.0
8 TraesCS6D01G120500 chr3A 89.897 584 49 3 1661 2244 697625247 697624674 0.000000e+00 743.0
9 TraesCS6D01G120500 chr3A 88.462 104 12 0 2245 2348 538020267 538020370 2.450000e-25 126.0
10 TraesCS6D01G120500 chr3B 84.145 719 76 12 1666 2348 666807530 666808246 0.000000e+00 662.0
11 TraesCS6D01G120500 chr3B 83.404 705 93 15 1664 2348 27473641 27474341 1.180000e-177 632.0
12 TraesCS6D01G120500 chr3B 86.908 359 43 4 1666 2022 15032313 15031957 1.310000e-107 399.0
13 TraesCS6D01G120500 chr4D 90.724 442 26 5 1921 2348 403568259 403567819 2.020000e-160 575.0
14 TraesCS6D01G120500 chr4D 90.441 408 23 2 1957 2348 25429023 25429430 7.430000e-145 523.0
15 TraesCS6D01G120500 chr4D 92.735 234 16 1 1666 1899 403568861 403568629 1.040000e-88 337.0
16 TraesCS6D01G120500 chr7D 81.277 705 93 21 1664 2346 603907960 603908647 3.430000e-148 534.0
17 TraesCS6D01G120500 chr7D 83.929 560 57 16 1663 2218 601584982 601585512 2.690000e-139 505.0
18 TraesCS6D01G120500 chr1D 83.031 607 76 15 1762 2348 216720673 216720074 2.070000e-145 525.0
19 TraesCS6D01G120500 chr1D 80.460 696 84 28 1666 2339 27593892 27593227 3.510000e-133 484.0
20 TraesCS6D01G120500 chr1D 85.938 320 29 4 1661 1980 415689371 415689674 6.260000e-86 327.0
21 TraesCS6D01G120500 chr1D 84.091 264 21 9 2099 2348 415690018 415690274 3.900000e-58 235.0
22 TraesCS6D01G120500 chr1D 79.503 322 53 11 1721 2032 75933343 75933025 1.410000e-52 217.0
23 TraesCS6D01G120500 chr7A 82.951 305 33 11 2061 2348 93124835 93125137 8.330000e-65 257.0
24 TraesCS6D01G120500 chr5A 86.878 221 27 1 497 715 426349684 426349904 1.800000e-61 246.0
25 TraesCS6D01G120500 chr5A 77.336 428 62 25 1 398 426349015 426349437 1.090000e-53 220.0
26 TraesCS6D01G120500 chr5B 77.313 454 68 23 1 425 386540583 386540136 3.900000e-58 235.0
27 TraesCS6D01G120500 chr5B 91.935 124 10 0 1668 1791 512252971 512253094 8.630000e-40 174.0
28 TraesCS6D01G120500 chr5B 87.736 106 10 3 2245 2348 17584935 17584831 1.140000e-23 121.0
29 TraesCS6D01G120500 chr1B 81.604 212 37 1 504 713 588486404 588486193 8.630000e-40 174.0
30 TraesCS6D01G120500 chr1B 82.759 87 15 0 975 1061 576052104 576052018 6.960000e-11 78.7
31 TraesCS6D01G120500 chr2B 88.462 104 12 0 2245 2348 210341882 210341985 2.450000e-25 126.0
32 TraesCS6D01G120500 chr4B 87.500 104 13 0 2245 2348 18787350 18787453 1.140000e-23 121.0
33 TraesCS6D01G120500 chr3D 76.923 221 36 14 1666 1876 590876134 590875919 6.860000e-21 111.0
34 TraesCS6D01G120500 chr7B 90.476 42 3 1 833 874 637364517 637364557 1.000000e-03 54.7


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 TraesCS6D01G120500 chr6D 85544567 85546914 2347 False 4337.0 4337 100.0000 1 2348 1 chr6D.!!$F1 2347
1 TraesCS6D01G120500 chr6D 84681342 84682979 1637 True 2774.0 2774 97.2590 1 1637 1 chr6D.!!$R1 1636
2 TraesCS6D01G120500 chr6B 161348734 161350390 1656 True 980.5 1818 89.0180 1 1637 2 chr6B.!!$R1 1636
3 TraesCS6D01G120500 chr6A 101911819 101912752 933 True 1362.0 1362 92.8800 687 1635 1 chr6A.!!$R1 948
4 TraesCS6D01G120500 chr6A 101929060 101929746 686 True 1083.0 1083 94.9780 1 695 1 chr6A.!!$R2 694
5 TraesCS6D01G120500 chr1A 584882254 584882911 657 False 749.0 749 87.5370 1661 2317 1 chr1A.!!$F1 656
6 TraesCS6D01G120500 chr1A 504066022 504066724 702 True 569.0 569 81.7800 1661 2347 1 chr1A.!!$R1 686
7 TraesCS6D01G120500 chr3A 697624674 697625247 573 True 743.0 743 89.8970 1661 2244 1 chr3A.!!$R1 583
8 TraesCS6D01G120500 chr3B 666807530 666808246 716 False 662.0 662 84.1450 1666 2348 1 chr3B.!!$F2 682
9 TraesCS6D01G120500 chr3B 27473641 27474341 700 False 632.0 632 83.4040 1664 2348 1 chr3B.!!$F1 684
10 TraesCS6D01G120500 chr4D 403567819 403568861 1042 True 456.0 575 91.7295 1666 2348 2 chr4D.!!$R1 682
11 TraesCS6D01G120500 chr7D 603907960 603908647 687 False 534.0 534 81.2770 1664 2346 1 chr7D.!!$F2 682
12 TraesCS6D01G120500 chr7D 601584982 601585512 530 False 505.0 505 83.9290 1663 2218 1 chr7D.!!$F1 555
13 TraesCS6D01G120500 chr1D 216720074 216720673 599 True 525.0 525 83.0310 1762 2348 1 chr1D.!!$R3 586
14 TraesCS6D01G120500 chr1D 27593227 27593892 665 True 484.0 484 80.4600 1666 2339 1 chr1D.!!$R1 673
15 TraesCS6D01G120500 chr1D 415689371 415690274 903 False 281.0 327 85.0145 1661 2348 2 chr1D.!!$F1 687
16 TraesCS6D01G120500 chr5A 426349015 426349904 889 False 233.0 246 82.1070 1 715 2 chr5A.!!$F1 714

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
776 966 4.072839 AGTGATGTGACTGAGACGACTAA 58.927 43.478 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 1927 2.015726 GAGGAGGGAGGGAGGGAGA 61.016 68.421 0.0 0.0 0.0 3.71 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
660 845 4.564406 GGCTTTCGATCAGGATGGTGATAT 60.564 45.833 0.00 0.00 37.29 1.63
776 966 4.072839 AGTGATGTGACTGAGACGACTAA 58.927 43.478 0.00 0.00 0.00 2.24
777 967 4.155099 AGTGATGTGACTGAGACGACTAAG 59.845 45.833 0.00 0.00 0.00 2.18
845 1036 4.345257 ACAGTCCTAGAGCTCACTGAAAAA 59.655 41.667 28.89 1.69 38.90 1.94
1022 1213 4.492494 TGCAAGGTGACTATGATGTCAT 57.508 40.909 0.68 0.68 46.77 3.06
1104 1295 1.518572 GACGATGACCCGCGTGATT 60.519 57.895 4.92 0.00 41.34 2.57
1122 1313 2.974698 GCGCAGTTGCTGGAGTGT 60.975 61.111 0.30 0.00 39.32 3.55
1415 1617 5.758784 GCTCGGAGGCTTTAATTATGTAACT 59.241 40.000 7.20 0.00 0.00 2.24
1556 1821 3.501349 TCATGCTATCCTACTGAGGTCC 58.499 50.000 0.00 0.00 44.19 4.46
1576 1841 2.431454 CCTTCCTTCACTGCTTCTTCC 58.569 52.381 0.00 0.00 0.00 3.46
1577 1842 2.039613 CCTTCCTTCACTGCTTCTTCCT 59.960 50.000 0.00 0.00 0.00 3.36
1578 1843 3.261897 CCTTCCTTCACTGCTTCTTCCTA 59.738 47.826 0.00 0.00 0.00 2.94
1637 1902 2.496070 TGTACATGAGTCTTCTTCCGGG 59.504 50.000 0.00 0.00 0.00 5.73
1638 1903 1.938585 ACATGAGTCTTCTTCCGGGA 58.061 50.000 0.00 0.00 0.00 5.14
1639 1904 2.257207 ACATGAGTCTTCTTCCGGGAA 58.743 47.619 9.52 9.52 0.00 3.97
1640 1905 2.234908 ACATGAGTCTTCTTCCGGGAAG 59.765 50.000 27.38 27.38 42.72 3.46
1641 1906 2.304221 TGAGTCTTCTTCCGGGAAGA 57.696 50.000 30.78 30.78 45.45 2.87
1644 1909 3.468552 TCTTCTTCCGGGAAGACCA 57.531 52.632 33.48 21.87 46.54 4.02
1645 1910 1.724545 TCTTCTTCCGGGAAGACCAA 58.275 50.000 33.48 20.83 46.54 3.67
1646 1911 2.051692 TCTTCTTCCGGGAAGACCAAA 58.948 47.619 33.48 20.51 46.54 3.28
1647 1912 2.038557 TCTTCTTCCGGGAAGACCAAAG 59.961 50.000 33.48 27.17 46.54 2.77
1648 1913 0.036306 TCTTCCGGGAAGACCAAAGC 59.964 55.000 30.78 0.00 42.78 3.51
1649 1914 0.036875 CTTCCGGGAAGACCAAAGCT 59.963 55.000 28.97 0.00 41.71 3.74
1650 1915 0.036306 TTCCGGGAAGACCAAAGCTC 59.964 55.000 5.09 0.00 40.22 4.09
1651 1916 1.125093 TCCGGGAAGACCAAAGCTCA 61.125 55.000 0.00 0.00 40.22 4.26
1652 1917 0.250727 CCGGGAAGACCAAAGCTCAA 60.251 55.000 0.00 0.00 40.22 3.02
1653 1918 0.875059 CGGGAAGACCAAAGCTCAAC 59.125 55.000 0.00 0.00 40.22 3.18
1654 1919 1.813862 CGGGAAGACCAAAGCTCAACA 60.814 52.381 0.00 0.00 40.22 3.33
1655 1920 1.882623 GGGAAGACCAAAGCTCAACAG 59.117 52.381 0.00 0.00 39.85 3.16
1656 1921 2.487265 GGGAAGACCAAAGCTCAACAGA 60.487 50.000 0.00 0.00 39.85 3.41
1657 1922 3.214328 GGAAGACCAAAGCTCAACAGAA 58.786 45.455 0.00 0.00 35.97 3.02
1658 1923 3.823304 GGAAGACCAAAGCTCAACAGAAT 59.177 43.478 0.00 0.00 35.97 2.40
1659 1924 5.003804 GGAAGACCAAAGCTCAACAGAATA 58.996 41.667 0.00 0.00 35.97 1.75
1660 1925 5.123027 GGAAGACCAAAGCTCAACAGAATAG 59.877 44.000 0.00 0.00 35.97 1.73
1661 1926 4.583871 AGACCAAAGCTCAACAGAATAGG 58.416 43.478 0.00 0.00 0.00 2.57
1662 1927 4.042187 AGACCAAAGCTCAACAGAATAGGT 59.958 41.667 0.00 0.00 0.00 3.08
1663 1928 4.327680 ACCAAAGCTCAACAGAATAGGTC 58.672 43.478 0.00 0.00 0.00 3.85
1664 1929 4.042187 ACCAAAGCTCAACAGAATAGGTCT 59.958 41.667 0.00 0.00 36.88 3.85
1679 1944 2.133201 TCTCCCTCCCTCCCTCCT 59.867 66.667 0.00 0.00 0.00 3.69
2218 3077 4.332543 TCGGCCACCCTCCCTCTT 62.333 66.667 2.24 0.00 0.00 2.85
2331 3210 1.360393 TGGGCCACTTCTCCACCTTT 61.360 55.000 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 185 1.143684 CCATGTACTCCCCATCCTTGG 59.856 57.143 0.00 0.00 43.23 3.61
546 731 1.078708 CGGTGTATGAAAGGCGGGT 60.079 57.895 0.00 0.00 0.00 5.28
644 829 8.255111 TGGATACATATATCACCATCCTGATC 57.745 38.462 10.52 0.00 46.17 2.92
761 951 2.227194 TGTGCTTAGTCGTCTCAGTCA 58.773 47.619 0.00 0.00 0.00 3.41
845 1036 2.341257 CAAAGCTGTACACATCGCTCT 58.659 47.619 7.70 0.00 31.30 4.09
1022 1213 4.351938 CGACCTTCCACACGCCGA 62.352 66.667 0.00 0.00 0.00 5.54
1122 1313 1.178276 GGCTCTCCTCGAGTTCAAGA 58.822 55.000 12.31 7.65 41.98 3.02
1300 1491 1.854227 GTTGACGCCCTGCTATAGTC 58.146 55.000 0.84 0.00 0.00 2.59
1304 1495 2.186903 CCGTTGACGCCCTGCTAT 59.813 61.111 0.00 0.00 38.18 2.97
1415 1617 9.650714 ATGATCAATCCCTCAAAATAGAAATGA 57.349 29.630 0.00 0.00 0.00 2.57
1556 1821 2.039613 AGGAAGAAGCAGTGAAGGAAGG 59.960 50.000 0.00 0.00 0.00 3.46
1637 1902 5.123027 CCTATTCTGTTGAGCTTTGGTCTTC 59.877 44.000 0.00 0.00 0.00 2.87
1638 1903 5.006386 CCTATTCTGTTGAGCTTTGGTCTT 58.994 41.667 0.00 0.00 0.00 3.01
1639 1904 4.042187 ACCTATTCTGTTGAGCTTTGGTCT 59.958 41.667 0.00 0.00 0.00 3.85
1640 1905 4.327680 ACCTATTCTGTTGAGCTTTGGTC 58.672 43.478 0.00 0.00 0.00 4.02
1641 1906 4.042187 AGACCTATTCTGTTGAGCTTTGGT 59.958 41.667 0.00 0.00 31.12 3.67
1642 1907 4.583871 AGACCTATTCTGTTGAGCTTTGG 58.416 43.478 0.00 0.00 31.12 3.28
1643 1908 4.633565 GGAGACCTATTCTGTTGAGCTTTG 59.366 45.833 0.00 0.00 33.22 2.77
1644 1909 4.837972 GGAGACCTATTCTGTTGAGCTTT 58.162 43.478 0.00 0.00 33.22 3.51
1645 1910 4.479786 GGAGACCTATTCTGTTGAGCTT 57.520 45.455 0.00 0.00 33.22 3.74
1661 1926 2.284151 GGAGGGAGGGAGGGAGAC 59.716 72.222 0.00 0.00 0.00 3.36
1662 1927 2.015726 GAGGAGGGAGGGAGGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
1663 1928 2.612251 GAGGAGGGAGGGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
1664 1929 3.036959 GGAGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1782 2064 4.421479 CGACGACCAGGCTTCGCT 62.421 66.667 8.43 0.00 40.24 4.93
2057 2692 2.636412 CCAGAGACCACGGCGAGAA 61.636 63.158 16.62 0.00 0.00 2.87
2097 2758 4.767255 GGGAGCAGCTCACCACCG 62.767 72.222 24.09 0.00 31.08 4.94
2126 2984 3.948719 GCCACCCAACCACGAGGA 61.949 66.667 5.68 0.00 38.69 3.71
2257 3130 2.048503 CCGAAACCGAGTTCCGCT 60.049 61.111 0.00 0.00 36.84 5.52


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

AutoCloner maintained by Alex Coulton.