Multiple sequence alignment - TraesCS6D01G215700

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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 TraesCS6D01G215700 chr6D 100.000 2288 0 0 1 2288 305745352 305747639 0 4226
1 TraesCS6D01G215700 chr6D 93.788 1642 91 4 1 1632 450905947 450907587 0 2457
2 TraesCS6D01G215700 chr6D 94.360 656 35 2 1633 2288 374720408 374719755 0 1005
3 TraesCS6D01G215700 chr6D 94.216 657 37 1 1633 2288 238297905 238297249 0 1002
4 TraesCS6D01G215700 chr7D 93.215 1636 95 11 4 1624 463975839 463974205 0 2392
5 TraesCS6D01G215700 chr7D 94.144 666 39 0 1623 2288 249092124 249092789 0 1014
6 TraesCS6D01G215700 chr7D 94.512 656 35 1 1633 2288 381644373 381645027 0 1011
7 TraesCS6D01G215700 chr7D 94.360 656 36 1 1633 2288 520670949 520670295 0 1005
8 TraesCS6D01G215700 chr7B 92.996 1642 101 9 1 1632 150842099 150843736 0 2383
9 TraesCS6D01G215700 chr4B 92.896 1647 102 7 1 1632 551784700 551786346 0 2379
10 TraesCS6D01G215700 chr4B 92.410 1647 110 7 1 1632 551730092 551731738 0 2335
11 TraesCS6D01G215700 chr1D 92.545 1650 99 11 4 1632 482488472 482486826 0 2344
12 TraesCS6D01G215700 chr2D 92.853 1623 89 13 1 1601 591013964 591015581 0 2329
13 TraesCS6D01G215700 chr4A 92.298 1636 116 4 4 1632 19185951 19184319 0 2314
14 TraesCS6D01G215700 chr2A 92.251 1639 116 4 1 1632 504065938 504067572 0 2313
15 TraesCS6D01G215700 chr3D 94.907 648 32 1 1641 2288 544087857 544088503 0 1013
16 TraesCS6D01G215700 chr3D 94.360 656 35 1 1633 2288 506210441 506211094 0 1005
17 TraesCS6D01G215700 chr4D 94.251 661 37 1 1629 2288 408079984 408079324 0 1009
18 TraesCS6D01G215700 chr4D 94.360 656 34 1 1633 2288 22931989 22931337 0 1003


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 TraesCS6D01G215700 chr6D 305745352 305747639 2287 False 4226 4226 100.000 1 2288 1 chr6D.!!$F1 2287
1 TraesCS6D01G215700 chr6D 450905947 450907587 1640 False 2457 2457 93.788 1 1632 1 chr6D.!!$F2 1631
2 TraesCS6D01G215700 chr6D 374719755 374720408 653 True 1005 1005 94.360 1633 2288 1 chr6D.!!$R2 655
3 TraesCS6D01G215700 chr6D 238297249 238297905 656 True 1002 1002 94.216 1633 2288 1 chr6D.!!$R1 655
4 TraesCS6D01G215700 chr7D 463974205 463975839 1634 True 2392 2392 93.215 4 1624 1 chr7D.!!$R1 1620
5 TraesCS6D01G215700 chr7D 249092124 249092789 665 False 1014 1014 94.144 1623 2288 1 chr7D.!!$F1 665
6 TraesCS6D01G215700 chr7D 381644373 381645027 654 False 1011 1011 94.512 1633 2288 1 chr7D.!!$F2 655
7 TraesCS6D01G215700 chr7D 520670295 520670949 654 True 1005 1005 94.360 1633 2288 1 chr7D.!!$R2 655
8 TraesCS6D01G215700 chr7B 150842099 150843736 1637 False 2383 2383 92.996 1 1632 1 chr7B.!!$F1 1631
9 TraesCS6D01G215700 chr4B 551784700 551786346 1646 False 2379 2379 92.896 1 1632 1 chr4B.!!$F2 1631
10 TraesCS6D01G215700 chr4B 551730092 551731738 1646 False 2335 2335 92.410 1 1632 1 chr4B.!!$F1 1631
11 TraesCS6D01G215700 chr1D 482486826 482488472 1646 True 2344 2344 92.545 4 1632 1 chr1D.!!$R1 1628
12 TraesCS6D01G215700 chr2D 591013964 591015581 1617 False 2329 2329 92.853 1 1601 1 chr2D.!!$F1 1600
13 TraesCS6D01G215700 chr4A 19184319 19185951 1632 True 2314 2314 92.298 4 1632 1 chr4A.!!$R1 1628
14 TraesCS6D01G215700 chr2A 504065938 504067572 1634 False 2313 2313 92.251 1 1632 1 chr2A.!!$F1 1631
15 TraesCS6D01G215700 chr3D 544087857 544088503 646 False 1013 1013 94.907 1641 2288 1 chr3D.!!$F2 647
16 TraesCS6D01G215700 chr3D 506210441 506211094 653 False 1005 1005 94.360 1633 2288 1 chr3D.!!$F1 655
17 TraesCS6D01G215700 chr4D 408079324 408079984 660 True 1009 1009 94.251 1629 2288 1 chr4D.!!$R2 659
18 TraesCS6D01G215700 chr4D 22931337 22931989 652 True 1003 1003 94.360 1633 2288 1 chr4D.!!$R1 655

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
107 111 0.036388 GGAGGTGAGGTCGATTTGCA 60.036 55.0 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 1919 0.664761 CGGACCCGATAGCTTAACGA 59.335 55.0 1.54 0.0 42.83 3.85 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
92 96 4.180946 CGTCGCTGTCGGAGGAGG 62.181 72.222 0.00 0.00 36.13 4.30
103 107 1.038130 CGGAGGAGGTGAGGTCGATT 61.038 60.000 0.00 0.00 0.00 3.34
107 111 0.036388 GGAGGTGAGGTCGATTTGCA 60.036 55.000 0.00 0.00 0.00 4.08
274 282 1.700186 ACTTGGACCACTTCTTCCTCC 59.300 52.381 0.00 0.00 32.55 4.30
507 518 1.341156 CGAGGAAGAAGGCCCTCCAT 61.341 60.000 0.00 0.00 44.66 3.41
515 526 0.474184 AAGGCCCTCCATCCAATACG 59.526 55.000 0.00 0.00 33.74 3.06
585 596 2.969262 GGAGAGGAGGAAGGTTGATAGG 59.031 54.545 0.00 0.00 0.00 2.57
639 651 3.651423 GGGCAGGGTGAGTAAATATAGGT 59.349 47.826 0.00 0.00 0.00 3.08
641 653 4.102681 GGCAGGGTGAGTAAATATAGGTGT 59.897 45.833 0.00 0.00 0.00 4.16
739 753 3.678289 CCTGACTCCATGAATTGTGTGA 58.322 45.455 0.00 0.00 0.00 3.58
864 884 0.601558 CCGAGGAAGAACCGAAGACA 59.398 55.000 0.00 0.00 44.74 3.41
868 888 2.824341 GAGGAAGAACCGAAGACACCTA 59.176 50.000 0.00 0.00 44.74 3.08
942 962 4.164981 ACTACAACCACTACCATGAGGAA 58.835 43.478 0.00 0.00 38.69 3.36
966 986 1.251251 GCCCAACTCACTTCTGCAAT 58.749 50.000 0.00 0.00 0.00 3.56
1014 1035 0.846427 TCCCCATGCTCCTGGACTTT 60.846 55.000 0.00 0.00 38.69 2.66
1110 1131 4.722193 CTGATGAACGGCAGGGTT 57.278 55.556 0.00 0.00 0.00 4.11
1175 1196 2.700371 TCAAGATCGGCTACATGGTGAT 59.300 45.455 0.00 0.00 0.00 3.06
1242 1263 0.740868 ACGATGGCATTGAGGTCGTG 60.741 55.000 21.46 0.00 43.07 4.35
1293 1315 2.687566 ACCAAGGACTAGGGCCGG 60.688 66.667 0.00 0.00 0.00 6.13
1324 1346 6.897986 TCCTTCCTAAGTACTATCGAGTCTT 58.102 40.000 0.00 0.00 37.10 3.01
1334 1362 8.789825 AGTACTATCGAGTCTTCTTTGAACTA 57.210 34.615 0.00 0.00 37.10 2.24
1727 1762 7.714813 TGTACATCCATGACGATTTTATGACAT 59.285 33.333 0.00 0.00 0.00 3.06
1759 1794 4.611943 AGTCATACATGTGATGTCGTAGC 58.388 43.478 9.11 0.00 43.67 3.58
1767 1802 2.296190 TGTGATGTCGTAGCAGTGTTCT 59.704 45.455 0.00 0.00 0.00 3.01
2030 2065 9.946140 GACAGATGTCATCCACTCATTGGACAT 62.946 44.444 9.29 4.90 45.49 3.06
2038 2073 1.012086 CTCATTGGACATGAGGCACG 58.988 55.000 0.00 0.00 41.24 5.34
2124 2159 4.139859 TGACTTGGTCAAAAGGTAACGA 57.860 40.909 0.00 0.00 39.78 3.85
2135 2170 4.382320 GTAACGAGCCGGCCCACA 62.382 66.667 26.15 1.23 0.00 4.17
2226 2261 4.283722 CCTATCGGAATTAAGCCCAGTAGT 59.716 45.833 0.00 0.00 0.00 2.73
2271 2306 0.958876 CCAGCCCGTTGTAACTTCCC 60.959 60.000 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.371558 GAAGGCCAACCACTCGACT 59.628 57.895 5.01 0.00 39.06 4.18
92 96 0.865769 ACGTTGCAAATCGACCTCAC 59.134 50.000 15.44 0.00 0.00 3.51
103 107 3.037249 GGCCGTCGTACGTTGCAA 61.037 61.111 16.05 0.00 40.58 4.08
107 111 4.729856 GCCAGGCCGTCGTACGTT 62.730 66.667 16.05 0.00 40.58 3.99
274 282 1.599992 GTCTCCGACGACACTAAACG 58.400 55.000 0.00 0.00 34.11 3.60
310 318 1.002366 GCAGTCGACATCATTCGCTT 58.998 50.000 19.50 0.00 38.95 4.68
507 518 0.254747 CCTTCCCTTGGCGTATTGGA 59.745 55.000 0.00 0.00 0.00 3.53
515 526 2.283894 CCAACCCCTTCCCTTGGC 60.284 66.667 0.00 0.00 0.00 4.52
559 570 0.336737 ACCTTCCTCCTCTCCATCGT 59.663 55.000 0.00 0.00 0.00 3.73
585 596 0.689412 CCACCCCCTCTCTTCTCTCC 60.689 65.000 0.00 0.00 0.00 3.71
639 651 2.043664 ACTCTTCCTCCTCTCCATCACA 59.956 50.000 0.00 0.00 0.00 3.58
641 653 2.313041 TCACTCTTCCTCCTCTCCATCA 59.687 50.000 0.00 0.00 0.00 3.07
739 753 3.295093 TCTCATTGCTCTCCTCGATCTT 58.705 45.455 0.00 0.00 0.00 2.40
864 884 1.291272 GTCGTCGCCAACCTTAGGT 59.709 57.895 0.00 0.00 37.65 3.08
868 888 2.049433 CTCGTCGTCGCCAACCTT 60.049 61.111 0.00 0.00 36.96 3.50
942 962 1.004044 CAGAAGTGAGTTGGGCCATCT 59.996 52.381 16.89 16.89 0.00 2.90
966 986 0.955428 GCTTCGGTGCAAGGATGACA 60.955 55.000 0.00 0.00 0.00 3.58
1004 1024 2.054799 AGTGCTTGGTAAAGTCCAGGA 58.945 47.619 0.00 0.00 38.80 3.86
1014 1035 1.225376 CCGCAACGAAGTGCTTGGTA 61.225 55.000 0.26 0.00 45.00 3.25
1051 1072 0.817634 CAGCCGGTGTTGTTCCTGAA 60.818 55.000 1.90 0.00 0.00 3.02
1118 1139 1.571773 ATAGGTGGCCCAACCCTGAC 61.572 60.000 8.63 0.00 41.54 3.51
1175 1196 0.687354 GGGAGTGAGGAGCTTGAACA 59.313 55.000 0.00 0.00 0.00 3.18
1242 1263 3.744559 TGCTTCCCGCACTTGTTC 58.255 55.556 0.00 0.00 45.47 3.18
1293 1315 1.485480 GTACTTAGGAAGGAGGTGCCC 59.515 57.143 0.00 0.00 37.37 5.36
1324 1346 8.952278 ACGCATAAACCATAAATAGTTCAAAGA 58.048 29.630 0.00 0.00 0.00 2.52
1334 1362 6.919721 ACAGTTCAACGCATAAACCATAAAT 58.080 32.000 0.00 0.00 0.00 1.40
1531 1566 1.145571 TAGTGGACAAACCCAAGGCT 58.854 50.000 0.00 0.00 38.06 4.58
1750 1785 4.157840 TGTCATAGAACACTGCTACGACAT 59.842 41.667 0.00 0.00 36.49 3.06
1863 1898 2.234913 GACCCGTTACGGTGGATGCT 62.235 60.000 22.78 0.00 46.80 3.79
1884 1919 0.664761 CGGACCCGATAGCTTAACGA 59.335 55.000 1.54 0.00 42.83 3.85
1957 1992 5.195940 TCCTCTGGCCAATGAGAATTTTAG 58.804 41.667 20.76 5.06 32.44 1.85
2038 2073 2.724690 GCCACATGTCGACGTATCATAC 59.275 50.000 10.54 0.00 0.00 2.39
2226 2261 3.489636 TGGACGGCCCAGATGAAA 58.510 55.556 3.83 0.00 40.82 2.69


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

AutoCloner maintained by Alex Coulton.