Multiple sequence alignment - TraesCS7D01G415400

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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 TraesCS7D01G415400 chr7D 100.000 2287 0 0 1 2287 533932811 533935097 0.000000e+00 4224.0
1 TraesCS7D01G415400 chr7D 92.125 1727 118 12 1 1714 463975826 463974105 0.000000e+00 2420.0
2 TraesCS7D01G415400 chr7D 92.005 1726 117 13 1 1709 107722767 107721046 0.000000e+00 2403.0
3 TraesCS7D01G415400 chr7D 90.888 1734 133 13 1 1720 432740539 432738817 0.000000e+00 2303.0
4 TraesCS7D01G415400 chr4B 92.361 1728 112 14 1 1714 551784716 551786437 0.000000e+00 2442.0
5 TraesCS7D01G415400 chr4B 91.836 1727 123 12 1 1714 551730108 551731829 0.000000e+00 2392.0
6 TraesCS7D01G415400 chr3D 92.366 1716 107 12 4 1716 113913345 113911651 0.000000e+00 2422.0
7 TraesCS7D01G415400 chr3D 92.130 1728 108 21 1 1713 449746635 449748349 0.000000e+00 2412.0
8 TraesCS7D01G415400 chr3D 90.105 1142 93 10 592 1718 515988397 515987261 0.000000e+00 1465.0
9 TraesCS7D01G415400 chr1D 91.887 1738 114 17 1 1718 482488459 482486729 0.000000e+00 2403.0
10 TraesCS7D01G415400 chr1D 92.084 859 51 10 877 1718 429021017 429021875 0.000000e+00 1194.0
11 TraesCS7D01G415400 chr1D 84.054 370 35 8 1932 2285 422687588 422687227 3.640000e-88 335.0
12 TraesCS7D01G415400 chr3A 91.696 1734 121 11 1 1720 418765656 418763932 0.000000e+00 2383.0
13 TraesCS7D01G415400 chr4D 91.493 1728 117 15 4 1715 493971102 493969389 0.000000e+00 2350.0
14 TraesCS7D01G415400 chr4D 90.888 1734 124 17 1 1717 116524553 116522837 0.000000e+00 2296.0
15 TraesCS7D01G415400 chr4D 91.027 1003 53 10 730 1717 508925407 508926387 0.000000e+00 1319.0
16 TraesCS7D01G415400 chr4D 91.345 855 59 8 877 1717 442391428 442392281 0.000000e+00 1155.0
17 TraesCS7D01G415400 chr2D 91.092 1740 110 19 1 1720 591013980 591015694 0.000000e+00 2313.0
18 TraesCS7D01G415400 chr1B 89.781 1732 148 17 1 1717 192470107 192468390 0.000000e+00 2191.0
19 TraesCS7D01G415400 chr4A 92.218 1452 87 13 1 1434 418072972 418071529 0.000000e+00 2032.0
20 TraesCS7D01G415400 chr6A 87.966 590 42 9 1714 2287 21058563 21059139 0.000000e+00 669.0
21 TraesCS7D01G415400 chr6D 86.640 494 41 6 1714 2191 10017180 10016696 7.240000e-145 523.0
22 TraesCS7D01G415400 chr6D 92.982 57 2 2 2229 2284 10016707 10016652 5.240000e-12 82.4
23 TraesCS7D01G415400 chr7A 92.735 234 9 4 2059 2285 613643410 613643642 4.710000e-87 331.0
24 TraesCS7D01G415400 chr5A 76.036 338 55 15 1736 2062 7826394 7826716 3.930000e-33 152.0
25 TraesCS7D01G415400 chr6B 83.030 165 18 7 1714 1878 281322847 281323001 8.520000e-30 141.0


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 TraesCS7D01G415400 chr7D 533932811 533935097 2286 False 4224.0 4224 100.000 1 2287 1 chr7D.!!$F1 2286
1 TraesCS7D01G415400 chr7D 463974105 463975826 1721 True 2420.0 2420 92.125 1 1714 1 chr7D.!!$R3 1713
2 TraesCS7D01G415400 chr7D 107721046 107722767 1721 True 2403.0 2403 92.005 1 1709 1 chr7D.!!$R1 1708
3 TraesCS7D01G415400 chr7D 432738817 432740539 1722 True 2303.0 2303 90.888 1 1720 1 chr7D.!!$R2 1719
4 TraesCS7D01G415400 chr4B 551784716 551786437 1721 False 2442.0 2442 92.361 1 1714 1 chr4B.!!$F2 1713
5 TraesCS7D01G415400 chr4B 551730108 551731829 1721 False 2392.0 2392 91.836 1 1714 1 chr4B.!!$F1 1713
6 TraesCS7D01G415400 chr3D 113911651 113913345 1694 True 2422.0 2422 92.366 4 1716 1 chr3D.!!$R1 1712
7 TraesCS7D01G415400 chr3D 449746635 449748349 1714 False 2412.0 2412 92.130 1 1713 1 chr3D.!!$F1 1712
8 TraesCS7D01G415400 chr3D 515987261 515988397 1136 True 1465.0 1465 90.105 592 1718 1 chr3D.!!$R2 1126
9 TraesCS7D01G415400 chr1D 482486729 482488459 1730 True 2403.0 2403 91.887 1 1718 1 chr1D.!!$R2 1717
10 TraesCS7D01G415400 chr1D 429021017 429021875 858 False 1194.0 1194 92.084 877 1718 1 chr1D.!!$F1 841
11 TraesCS7D01G415400 chr3A 418763932 418765656 1724 True 2383.0 2383 91.696 1 1720 1 chr3A.!!$R1 1719
12 TraesCS7D01G415400 chr4D 493969389 493971102 1713 True 2350.0 2350 91.493 4 1715 1 chr4D.!!$R2 1711
13 TraesCS7D01G415400 chr4D 116522837 116524553 1716 True 2296.0 2296 90.888 1 1717 1 chr4D.!!$R1 1716
14 TraesCS7D01G415400 chr4D 508925407 508926387 980 False 1319.0 1319 91.027 730 1717 1 chr4D.!!$F2 987
15 TraesCS7D01G415400 chr4D 442391428 442392281 853 False 1155.0 1155 91.345 877 1717 1 chr4D.!!$F1 840
16 TraesCS7D01G415400 chr2D 591013980 591015694 1714 False 2313.0 2313 91.092 1 1720 1 chr2D.!!$F1 1719
17 TraesCS7D01G415400 chr1B 192468390 192470107 1717 True 2191.0 2191 89.781 1 1717 1 chr1B.!!$R1 1716
18 TraesCS7D01G415400 chr4A 418071529 418072972 1443 True 2032.0 2032 92.218 1 1434 1 chr4A.!!$R1 1433
19 TraesCS7D01G415400 chr6A 21058563 21059139 576 False 669.0 669 87.966 1714 2287 1 chr6A.!!$F1 573
20 TraesCS7D01G415400 chr6D 10016652 10017180 528 True 302.7 523 89.811 1714 2284 2 chr6D.!!$R1 570

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
753 765 0.174389 TGCAGATCGAGGAGAGCAAC 59.826 55.0 0.0 0.0 37.82 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 1671 0.248289 GCAGCCTCAAATGCACCATT 59.752 50.0 0.0 0.0 42.11 3.16 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
37 38 3.067106 GCCTTCGTCTTCTTGTTCATCA 58.933 45.455 0.00 0.00 0.00 3.07
44 45 2.146342 CTTCTTGTTCATCACCGTGCT 58.854 47.619 0.00 0.00 0.00 4.40
123 127 2.521950 CCTAGCTCTGGCGCCCTA 60.522 66.667 26.77 16.68 44.37 3.53
327 333 1.519234 GATGTCGACTGCCATCGCA 60.519 57.895 17.92 4.55 44.78 5.10
470 476 0.670546 CTCGAACTTGGTGCGGTCAT 60.671 55.000 0.00 0.00 34.96 3.06
541 547 0.899717 GGTTGGCATTGGAGCTGGAA 60.900 55.000 0.00 0.00 34.17 3.53
581 587 3.432378 GAGAGGAGGAAGGTTGACAGTA 58.568 50.000 0.00 0.00 0.00 2.74
641 650 3.933332 GTGAGTAAATATAGGGGCGATGC 59.067 47.826 0.00 0.00 0.00 3.91
706 718 4.036144 GCTCTTCAATAAGCCATGAACTCC 59.964 45.833 0.00 0.00 32.46 3.85
712 724 0.674895 AAGCCATGAACTCCGTGCTC 60.675 55.000 0.00 0.00 0.00 4.26
753 765 0.174389 TGCAGATCGAGGAGAGCAAC 59.826 55.000 0.00 0.00 37.82 4.17
819 831 2.492773 GCCCCTTCATCCAATGCCG 61.493 63.158 0.00 0.00 0.00 5.69
1012 1029 1.464198 ATCCCCATGCCCCTAGACC 60.464 63.158 0.00 0.00 0.00 3.85
1223 1241 3.111838 CAAGGTCATCATCTTCGACGAG 58.888 50.000 0.00 0.00 0.00 4.18
1327 1373 6.927416 TCCTAAGTACTTTCGAGTTTATGCA 58.073 36.000 14.49 0.00 0.00 3.96
1404 1450 5.755375 TGCTATTAAGTAGTTGATGCTCTGC 59.245 40.000 0.00 0.00 32.72 4.26
1473 1521 4.024048 GTGTGTTGGTAACCTCATCAACTG 60.024 45.833 0.00 0.00 39.87 3.16
1477 1525 1.282157 GGTAACCTCATCAACTGGCCT 59.718 52.381 3.32 0.00 0.00 5.19
1511 1560 2.483877 CACACCAGACGTTGCATACAAT 59.516 45.455 0.00 0.00 38.27 2.71
1553 1603 2.094675 GTCCACTAACATGCAGGCAAT 58.905 47.619 0.00 0.00 0.00 3.56
1621 1671 3.583806 CAGACAACCAAACAACTTGCAA 58.416 40.909 0.00 0.00 33.27 4.08
1730 1780 1.858091 CCCTAGAAGCATAGCACACG 58.142 55.000 0.00 0.00 0.00 4.49
1830 1880 2.203153 GCGACCAGTGTGGGTGTT 60.203 61.111 0.00 0.00 43.37 3.32
1838 1888 1.226945 GTGTGGGTGTTGCTGTTGC 60.227 57.895 0.00 0.00 40.20 4.17
1857 1907 1.377072 CGTCCATGTGGCCATGTCA 60.377 57.895 9.72 1.82 45.83 3.58
1888 1938 0.536233 AGTTGGTATGCGTTGCACCA 60.536 50.000 0.00 0.00 43.04 4.17
1905 1955 3.367743 ACCTCGTGGAAGCGCGTA 61.368 61.111 11.17 0.00 37.04 4.42
1908 1958 4.764336 TCGTGGAAGCGCGTACGG 62.764 66.667 18.39 8.37 40.57 4.02
1917 1967 4.602259 CGCGTACGGGGCATCCAT 62.602 66.667 23.33 0.00 34.97 3.41
1923 1973 4.569180 CGGGGCATCCATTCCGCT 62.569 66.667 0.00 0.00 35.95 5.52
1945 1995 2.127251 GCATCGATCAGTATTGCGACA 58.873 47.619 0.00 0.00 35.44 4.35
1997 2047 2.506217 CGGCAGCACGACGTACAT 60.506 61.111 0.00 0.00 43.08 2.29
2008 2058 0.316524 GACGTACATCTCGGTACCGC 60.317 60.000 29.64 12.38 40.37 5.68
2032 2082 3.102972 ACTCACACTAGCCATGTCAGAT 58.897 45.455 0.00 0.00 0.00 2.90
2045 2095 2.437180 CAGATGGCGGCTGCTTGA 60.437 61.111 18.85 1.86 42.25 3.02
2071 2121 1.284982 GGCGTACTGAGCTGTGTGTG 61.285 60.000 0.00 0.00 34.52 3.82
2077 2127 1.136305 ACTGAGCTGTGTGTGTACGTT 59.864 47.619 0.00 0.00 0.00 3.99
2155 2220 0.687354 GCCGGGAGATACATGGTCAT 59.313 55.000 2.18 0.00 0.00 3.06
2213 2279 1.066918 AAGGACGACAGACGCGTTT 59.933 52.632 15.53 4.14 46.94 3.60
2214 2280 1.213094 AAGGACGACAGACGCGTTTG 61.213 55.000 26.25 26.25 46.94 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 127 4.790962 CCGGTGCAGATGCCAGCT 62.791 66.667 1.72 0.00 41.18 4.24
340 346 1.649664 CTGAAGACGCTGATTCCTGG 58.350 55.000 0.00 0.00 0.00 4.45
470 476 2.997315 CCTCGGGTGGTCAGCTGA 60.997 66.667 13.74 13.74 41.42 4.26
541 547 0.678395 CCATCGCCATGAGCTCTAGT 59.322 55.000 16.19 0.00 40.39 2.57
581 587 0.252927 CCCACCCCCTCTCTTCTCTT 60.253 60.000 0.00 0.00 0.00 2.85
641 650 2.754552 CTGTCACTCTTCTCCTCCTCTG 59.245 54.545 0.00 0.00 0.00 3.35
706 718 2.125753 GGAGTCAGGCAGAGCACG 60.126 66.667 0.00 0.00 0.00 5.34
712 724 2.422479 CACAATTCATGGAGTCAGGCAG 59.578 50.000 0.00 0.00 0.00 4.85
753 765 3.461773 ACCTCCGTGCCCATCTCG 61.462 66.667 0.00 0.00 0.00 4.04
819 831 3.050275 GGCAGCACAACCTCGTCC 61.050 66.667 0.00 0.00 0.00 4.79
976 993 0.250467 ATGCACTCAAGCTTCGGTGT 60.250 50.000 21.75 7.63 34.99 4.16
1223 1241 0.038166 TGACCACCTCAATGCCTTCC 59.962 55.000 0.00 0.00 0.00 3.46
1404 1450 2.737783 GCATAAGCAGAGCAGAGCATAG 59.262 50.000 0.00 0.00 41.58 2.23
1473 1521 1.626825 TGTGTGGTAACCTCTTAGGCC 59.373 52.381 0.00 0.00 39.63 5.19
1477 1525 3.322828 GTCTGGTGTGTGGTAACCTCTTA 59.677 47.826 0.00 0.00 37.36 2.10
1553 1603 0.751277 CCACACTGCCTGGTGTTTGA 60.751 55.000 4.79 0.00 46.71 2.69
1621 1671 0.248289 GCAGCCTCAAATGCACCATT 59.752 50.000 0.00 0.00 42.11 3.16
1739 1789 2.880890 GGCTGCCTTCGATATTTCATGT 59.119 45.455 12.43 0.00 0.00 3.21
1784 1834 2.664851 TGCGTGCGCTACTTGCTT 60.665 55.556 17.49 0.00 42.51 3.91
1830 1880 2.112928 ACATGGACGGCAACAGCA 59.887 55.556 0.00 0.00 0.00 4.41
1857 1907 1.617322 TACCAACTCTCTGTCTGCGT 58.383 50.000 0.00 0.00 0.00 5.24
1869 1919 0.536233 TGGTGCAACGCATACCAACT 60.536 50.000 0.00 0.00 41.91 3.16
1870 1920 0.386731 GTGGTGCAACGCATACCAAC 60.387 55.000 11.22 0.00 41.91 3.77
1888 1938 3.367743 TACGCGCTTCCACGAGGT 61.368 61.111 5.73 0.00 37.15 3.85
1905 1955 4.875713 GCGGAATGGATGCCCCGT 62.876 66.667 10.44 0.00 43.51 5.28
1908 1958 2.908940 CCAGCGGAATGGATGCCC 60.909 66.667 0.00 0.00 43.57 5.36
1913 1963 2.043604 ATCGATGCCAGCGGAATGGA 62.044 55.000 1.22 3.47 43.57 3.41
1914 1964 1.572085 GATCGATGCCAGCGGAATGG 61.572 60.000 0.54 0.00 43.72 3.16
1915 1965 0.881600 TGATCGATGCCAGCGGAATG 60.882 55.000 0.54 0.00 0.00 2.67
1916 1966 0.602106 CTGATCGATGCCAGCGGAAT 60.602 55.000 0.54 0.00 0.00 3.01
1917 1967 1.227350 CTGATCGATGCCAGCGGAA 60.227 57.895 0.54 0.00 0.00 4.30
1923 1973 1.068434 TCGCAATACTGATCGATGCCA 59.932 47.619 0.54 0.00 33.55 4.92
1997 2047 2.753043 GAGTGGGCGGTACCGAGA 60.753 66.667 37.62 16.92 42.83 4.04
2008 2058 0.615331 ACATGGCTAGTGTGAGTGGG 59.385 55.000 0.00 0.00 0.00 4.61
2032 2082 3.057548 CACATCAAGCAGCCGCCA 61.058 61.111 0.00 0.00 39.83 5.69
2045 2095 2.184322 CTCAGTACGCCGGCACAT 59.816 61.111 28.98 13.96 0.00 3.21
2052 2102 1.006102 ACACACAGCTCAGTACGCC 60.006 57.895 0.00 0.00 0.00 5.68
2077 2127 4.717877 ACTTCTCACCATTCACAACATGA 58.282 39.130 0.00 0.00 34.65 3.07
2155 2220 0.537653 TGTCTTTCACGTGGTCACCA 59.462 50.000 17.00 0.00 0.00 4.17
2213 2279 1.761174 GTGGAGTCTTGCTTCCCCA 59.239 57.895 0.00 0.00 0.00 4.96
2214 2280 1.376037 CGTGGAGTCTTGCTTCCCC 60.376 63.158 0.00 0.00 0.00 4.81
2248 2314 2.360475 GCCCAAGTCCCTGCAGTC 60.360 66.667 13.81 2.83 0.00 3.51


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

AutoCloner maintained by Alex Coulton.