Multiple sequence alignment - TraesCS4A01G238900

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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 TraesCS4A01G238900 chr4A 100.000 2612 0 0 1 2612 548068145 548065534 0 4824
1 TraesCS4A01G238900 chr4A 95.893 2021 58 11 1 1998 327032450 327030432 0 3249
2 TraesCS4A01G238900 chr4A 96.085 613 20 3 2000 2609 109518787 109519398 0 996
3 TraesCS4A01G238900 chr4A 95.425 612 26 1 2000 2609 610974366 610974977 0 974
4 TraesCS4A01G238900 chr5A 95.680 2014 62 17 1 1998 67811357 67813361 0 3214
5 TraesCS4A01G238900 chr7A 94.475 2027 79 11 1 1998 647036509 647038531 0 3092
6 TraesCS4A01G238900 chr7A 96.585 615 19 1 2000 2612 247698591 247697977 0 1018
7 TraesCS4A01G238900 chrUn 93.990 2030 73 20 1 1996 284016945 284018959 0 3027
8 TraesCS4A01G238900 chrUn 95.752 1789 66 5 1 1787 343664190 343662410 0 2874
9 TraesCS4A01G238900 chrUn 95.432 613 24 3 2000 2609 315543713 315544324 0 974
10 TraesCS4A01G238900 chr3A 87.229 2028 208 28 1 1990 312256810 312254796 0 2263
11 TraesCS4A01G238900 chr3A 87.925 1913 191 22 1 1883 299413645 299415547 0 2217
12 TraesCS4A01G238900 chr3A 87.925 1913 190 22 1 1883 299367343 299369244 0 2215
13 TraesCS4A01G238900 chr3A 89.956 1603 118 24 431 1998 144041533 144039939 0 2028
14 TraesCS4A01G238900 chr3A 97.792 770 15 2 1 769 550669200 550668432 0 1327
15 TraesCS4A01G238900 chr6B 87.162 2033 197 38 1 1996 513262039 513264044 0 2250
16 TraesCS4A01G238900 chr6B 94.309 615 33 1 2000 2612 120529667 120529053 0 941
17 TraesCS4A01G238900 chr2A 86.706 2031 210 30 1 1996 396600350 396598345 0 2200
18 TraesCS4A01G238900 chr2A 95.779 616 22 3 2000 2612 396595812 396595198 0 990
19 TraesCS4A01G238900 chr1D 89.582 1603 121 25 431 1998 238779106 238780697 0 1993
20 TraesCS4A01G238900 chr2D 88.689 1609 133 27 431 1998 302505699 302504099 0 1917
21 TraesCS4A01G238900 chr6D 84.841 1603 180 37 431 1996 137230441 137232017 0 1555
22 TraesCS4A01G238900 chr7B 95.942 616 21 3 2000 2612 258331644 258331030 0 996
23 TraesCS4A01G238900 chr6A 95.922 613 21 3 2000 2609 254276245 254276856 0 990
24 TraesCS4A01G238900 chr4B 94.290 613 35 0 2000 2612 359841754 359841142 0 939


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 TraesCS4A01G238900 chr4A 548065534 548068145 2611 True 4824 4824 100.0000 1 2612 1 chr4A.!!$R2 2611
1 TraesCS4A01G238900 chr4A 327030432 327032450 2018 True 3249 3249 95.8930 1 1998 1 chr4A.!!$R1 1997
2 TraesCS4A01G238900 chr4A 109518787 109519398 611 False 996 996 96.0850 2000 2609 1 chr4A.!!$F1 609
3 TraesCS4A01G238900 chr4A 610974366 610974977 611 False 974 974 95.4250 2000 2609 1 chr4A.!!$F2 609
4 TraesCS4A01G238900 chr5A 67811357 67813361 2004 False 3214 3214 95.6800 1 1998 1 chr5A.!!$F1 1997
5 TraesCS4A01G238900 chr7A 647036509 647038531 2022 False 3092 3092 94.4750 1 1998 1 chr7A.!!$F1 1997
6 TraesCS4A01G238900 chr7A 247697977 247698591 614 True 1018 1018 96.5850 2000 2612 1 chr7A.!!$R1 612
7 TraesCS4A01G238900 chrUn 284016945 284018959 2014 False 3027 3027 93.9900 1 1996 1 chrUn.!!$F1 1995
8 TraesCS4A01G238900 chrUn 343662410 343664190 1780 True 2874 2874 95.7520 1 1787 1 chrUn.!!$R1 1786
9 TraesCS4A01G238900 chrUn 315543713 315544324 611 False 974 974 95.4320 2000 2609 1 chrUn.!!$F2 609
10 TraesCS4A01G238900 chr3A 312254796 312256810 2014 True 2263 2263 87.2290 1 1990 1 chr3A.!!$R2 1989
11 TraesCS4A01G238900 chr3A 299413645 299415547 1902 False 2217 2217 87.9250 1 1883 1 chr3A.!!$F2 1882
12 TraesCS4A01G238900 chr3A 299367343 299369244 1901 False 2215 2215 87.9250 1 1883 1 chr3A.!!$F1 1882
13 TraesCS4A01G238900 chr3A 144039939 144041533 1594 True 2028 2028 89.9560 431 1998 1 chr3A.!!$R1 1567
14 TraesCS4A01G238900 chr3A 550668432 550669200 768 True 1327 1327 97.7920 1 769 1 chr3A.!!$R3 768
15 TraesCS4A01G238900 chr6B 513262039 513264044 2005 False 2250 2250 87.1620 1 1996 1 chr6B.!!$F1 1995
16 TraesCS4A01G238900 chr6B 120529053 120529667 614 True 941 941 94.3090 2000 2612 1 chr6B.!!$R1 612
17 TraesCS4A01G238900 chr2A 396595198 396600350 5152 True 1595 2200 91.2425 1 2612 2 chr2A.!!$R1 2611
18 TraesCS4A01G238900 chr1D 238779106 238780697 1591 False 1993 1993 89.5820 431 1998 1 chr1D.!!$F1 1567
19 TraesCS4A01G238900 chr2D 302504099 302505699 1600 True 1917 1917 88.6890 431 1998 1 chr2D.!!$R1 1567
20 TraesCS4A01G238900 chr6D 137230441 137232017 1576 False 1555 1555 84.8410 431 1996 1 chr6D.!!$F1 1565
21 TraesCS4A01G238900 chr7B 258331030 258331644 614 True 996 996 95.9420 2000 2612 1 chr7B.!!$R1 612
22 TraesCS4A01G238900 chr6A 254276245 254276856 611 False 990 990 95.9220 2000 2609 1 chr6A.!!$F1 609
23 TraesCS4A01G238900 chr4B 359841142 359841754 612 True 939 939 94.2900 2000 2612 1 chr4B.!!$R1 612

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
764 779 0.31836 CGAGTGTGGCACAAGTCGTA 60.318 55.0 30.87 6.49 44.16 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 4698 0.179067 TGTGCGTTCGGAGTTTCCTT 60.179 50.0 0.0 0.0 33.3 3.36 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
194 195 0.465705 CTATGGAGCACCGTGACCAT 59.534 55.000 24.03 24.03 44.03 3.55
413 424 2.026641 AGCTACGGCGAGGTAATGTAA 58.973 47.619 16.62 0.00 44.37 2.41
499 514 2.365635 ACTGCCCCATCCGCTAGT 60.366 61.111 0.00 0.00 0.00 2.57
682 697 5.415701 TGAAGATTTTAGCCATGTTCTCACC 59.584 40.000 0.00 0.00 0.00 4.02
727 742 4.037208 GGTGACCTCTTCGATTTATCCGTA 59.963 45.833 0.00 0.00 0.00 4.02
764 779 0.318360 CGAGTGTGGCACAAGTCGTA 60.318 55.000 30.87 6.49 44.16 3.43
989 1018 1.484653 TCATGACGGTTGTATCAGGGG 59.515 52.381 0.00 0.00 0.00 4.79
991 1020 1.646912 TGACGGTTGTATCAGGGGAA 58.353 50.000 0.00 0.00 0.00 3.97
1420 1450 0.662374 CGCCAGTTTGCAGAAGCTTG 60.662 55.000 2.10 0.00 42.74 4.01
1479 1509 5.124645 GCTCATCAATCTGAACTGAAGGAT 58.875 41.667 0.00 0.00 0.00 3.24
1614 1647 0.975040 ACTGGCGAGCTCCTTGAGAT 60.975 55.000 8.47 0.00 0.00 2.75
1692 1733 7.286316 CCCTTTGAATCATTTTAGGCTCAGTAT 59.714 37.037 0.00 0.00 0.00 2.12
1993 2083 4.599047 TTTTGTGCCCCAGTTTATCTTG 57.401 40.909 0.00 0.00 0.00 3.02
1994 2084 2.969821 TGTGCCCCAGTTTATCTTGT 57.030 45.000 0.00 0.00 0.00 3.16
1995 2085 4.374689 TTGTGCCCCAGTTTATCTTGTA 57.625 40.909 0.00 0.00 0.00 2.41
1998 2088 4.202524 TGTGCCCCAGTTTATCTTGTAAGT 60.203 41.667 0.00 0.00 0.00 2.24
2014 4634 5.459110 TGTAAGTCATTTTAACGATCGCC 57.541 39.130 16.60 0.00 0.00 5.54
2055 4675 5.687166 ATTTGGATGCCATTCTTTGTGAT 57.313 34.783 0.00 0.00 31.53 3.06
2058 4678 4.087907 TGGATGCCATTCTTTGTGATCAA 58.912 39.130 0.00 0.00 0.00 2.57
2119 4739 7.094720 GCACATTTCATGGGATTCATTTTCAAA 60.095 33.333 0.00 0.00 35.01 2.69
2129 4749 8.600668 TGGGATTCATTTTCAAATTATGTTCCA 58.399 29.630 0.00 0.00 30.89 3.53
2183 4803 5.175859 TCATATGGTCCTCTTCACGTTTTC 58.824 41.667 2.13 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 4.694982 CCTGATATTGTGTTGTAGTGCACA 59.305 41.667 21.04 1.84 42.95 4.57
194 195 3.055094 GCCTTCTAAGGGACTGAACATGA 60.055 47.826 10.69 0.00 46.56 3.07
413 424 3.635373 CCAGCTATGGCATTCTGTTTCAT 59.365 43.478 20.57 0.00 40.52 2.57
499 514 6.192234 GTAGATTGTCTACGTCTCTTTCCA 57.808 41.667 0.00 0.00 39.81 3.53
682 697 1.032114 GGCCATGGTCCTTTTCTCCG 61.032 60.000 14.67 0.00 0.00 4.63
727 742 1.906574 TCGCCAAAGGTACAATCCTCT 59.093 47.619 0.00 0.00 36.74 3.69
970 998 1.484653 TCCCCTGATACAACCGTCATG 59.515 52.381 0.00 0.00 0.00 3.07
989 1018 1.975363 GCAGTCCATCTGTGCGCTTC 61.975 60.000 9.73 2.14 45.23 3.86
991 1020 2.435586 GCAGTCCATCTGTGCGCT 60.436 61.111 9.73 0.00 45.23 5.92
1221 1250 3.756117 GGATCCCTTTGTGAACTCAGTT 58.244 45.455 0.00 0.00 0.00 3.16
1420 1450 1.470112 GCGCTGTTCCCTCTCTAGTTC 60.470 57.143 0.00 0.00 0.00 3.01
1479 1509 3.964688 TGTCCTGTAGACTCTTCACCAAA 59.035 43.478 0.00 0.00 46.46 3.28
1614 1647 2.942604 ACTAAGGGAAGTCTAGGCCA 57.057 50.000 5.01 0.00 0.00 5.36
1663 1704 6.153340 TGAGCCTAAAATGATTCAAAGGGAAG 59.847 38.462 0.00 0.00 39.30 3.46
1770 1811 0.307760 GTGTCAACGTCAAAGCTGGG 59.692 55.000 0.00 0.00 0.00 4.45
1990 2080 5.957796 GGCGATCGTTAAAATGACTTACAAG 59.042 40.000 17.81 0.00 0.00 3.16
1991 2081 5.640357 AGGCGATCGTTAAAATGACTTACAA 59.360 36.000 17.81 0.00 0.00 2.41
1993 2083 5.713822 AGGCGATCGTTAAAATGACTTAC 57.286 39.130 17.81 0.00 0.00 2.34
1994 2084 6.730960 AAAGGCGATCGTTAAAATGACTTA 57.269 33.333 17.81 0.00 0.00 2.24
1995 2085 5.622770 AAAGGCGATCGTTAAAATGACTT 57.377 34.783 17.81 0.00 0.00 3.01
1998 2088 6.730960 AAGTAAAGGCGATCGTTAAAATGA 57.269 33.333 17.81 0.00 0.00 2.57
2014 4634 8.348285 TCCAAATTGACCCAGATAAAGTAAAG 57.652 34.615 0.00 0.00 0.00 1.85
2058 4678 6.645306 TCCTTCGGAAAATTTCTTGGTTTTT 58.355 32.000 5.65 0.00 0.00 1.94
2078 4698 0.179067 TGTGCGTTCGGAGTTTCCTT 60.179 50.000 0.00 0.00 33.30 3.36
2129 4749 3.181493 GCAATGGTTTTCGAGCATCTGAT 60.181 43.478 0.00 0.00 45.33 2.90
2135 4755 1.952990 TCTTGCAATGGTTTTCGAGCA 59.047 42.857 0.00 0.00 40.58 4.26
2234 4854 6.252599 AGCCATGACCATAGTTTTAGATGA 57.747 37.500 0.00 0.00 0.00 2.92
2423 5043 8.978564 ATATCTGAAATACTCGTTGATGCTAG 57.021 34.615 0.00 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.