Multiple sequence alignment - TraesCS1A01G204000

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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 TraesCS1A01G204000 chr1A 100.000 2661 0 0 1 2661 365634838 365637498 0.000000e+00 4915
1 TraesCS1A01G204000 chr1A 95.680 2662 107 7 1 2661 10685401 10688055 0.000000e+00 4272
2 TraesCS1A01G204000 chr5A 96.693 2661 84 4 1 2661 33908466 33911122 0.000000e+00 4423
3 TraesCS1A01G204000 chr5A 96.658 2663 84 5 1 2661 524679157 524681816 0.000000e+00 4420
4 TraesCS1A01G204000 chr5A 95.008 2664 120 11 1 2661 169180629 169177976 0.000000e+00 4170
5 TraesCS1A01G204000 chr5A 95.006 2663 96 9 1 2661 398478062 398475435 0.000000e+00 4146
6 TraesCS1A01G204000 chr7A 95.943 2662 98 9 1 2661 675353864 675351212 0.000000e+00 4309
7 TraesCS1A01G204000 chr3A 95.833 2664 105 6 1 2661 711574757 711572097 0.000000e+00 4300
8 TraesCS1A01G204000 chr3A 94.682 2670 119 19 1 2661 32208575 32211230 0.000000e+00 4122
9 TraesCS1A01G204000 chr4A 95.804 2669 100 11 1 2661 37332169 37334833 0.000000e+00 4298
10 TraesCS1A01G204000 chr6A 97.778 360 8 0 2302 2661 494430831 494431190 2.910000e-174 621


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 TraesCS1A01G204000 chr1A 365634838 365637498 2660 False 4915 4915 100.000 1 2661 1 chr1A.!!$F2 2660
1 TraesCS1A01G204000 chr1A 10685401 10688055 2654 False 4272 4272 95.680 1 2661 1 chr1A.!!$F1 2660
2 TraesCS1A01G204000 chr5A 33908466 33911122 2656 False 4423 4423 96.693 1 2661 1 chr5A.!!$F1 2660
3 TraesCS1A01G204000 chr5A 524679157 524681816 2659 False 4420 4420 96.658 1 2661 1 chr5A.!!$F2 2660
4 TraesCS1A01G204000 chr5A 169177976 169180629 2653 True 4170 4170 95.008 1 2661 1 chr5A.!!$R1 2660
5 TraesCS1A01G204000 chr5A 398475435 398478062 2627 True 4146 4146 95.006 1 2661 1 chr5A.!!$R2 2660
6 TraesCS1A01G204000 chr7A 675351212 675353864 2652 True 4309 4309 95.943 1 2661 1 chr7A.!!$R1 2660
7 TraesCS1A01G204000 chr3A 711572097 711574757 2660 True 4300 4300 95.833 1 2661 1 chr3A.!!$R1 2660
8 TraesCS1A01G204000 chr3A 32208575 32211230 2655 False 4122 4122 94.682 1 2661 1 chr3A.!!$F1 2660
9 TraesCS1A01G204000 chr4A 37332169 37334833 2664 False 4298 4298 95.804 1 2661 1 chr4A.!!$F1 2660

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
525 528 1.424302 CAATCAGGGGGCTGATCATCT 59.576 52.381 0.0 0.0 42.63 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 1723 1.00006 CACTTGGTCCCAACATTGCTG 60.0 52.381 0.0 0.0 0.0 4.41 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
124 125 4.203226 TGTGTGAGTGCTGTAAAATGGAA 58.797 39.130 0.00 0.00 0.00 3.53
131 132 4.892934 AGTGCTGTAAAATGGAAAAGGACA 59.107 37.500 0.00 0.00 0.00 4.02
290 291 3.795688 TGCCTCCTCAATCAAAGAAGT 57.204 42.857 0.00 0.00 0.00 3.01
292 293 5.441718 TGCCTCCTCAATCAAAGAAGTAT 57.558 39.130 0.00 0.00 0.00 2.12
437 439 7.096551 CCTGAACAAGTCCAAGAAAAAGAAAA 58.903 34.615 0.00 0.00 0.00 2.29
504 507 1.920325 CTCCTCCACCTCCAGGCAA 60.920 63.158 0.00 0.00 39.32 4.52
518 521 2.353610 GGCAACAATCAGGGGGCTG 61.354 63.158 0.00 0.00 0.00 4.85
525 528 1.424302 CAATCAGGGGGCTGATCATCT 59.576 52.381 0.00 0.00 42.63 2.90
840 843 3.008049 GGGCTCATCGTCCAGGTAATTAT 59.992 47.826 0.00 0.00 37.34 1.28
929 932 2.552155 CCAAACAGGCTACCTAGTTGCA 60.552 50.000 3.74 0.00 36.13 4.08
991 995 2.945668 GACTTGTTTGTCCTGTTCTGCT 59.054 45.455 0.00 0.00 0.00 4.24
1101 1105 0.980231 GACTCAGGGGGCTCATCACT 60.980 60.000 0.00 0.00 0.00 3.41
1140 1144 5.065474 CACCGACTCCAAAACAAAAACTAGA 59.935 40.000 0.00 0.00 0.00 2.43
1172 1176 8.257306 TGACTTTAGTTGCACATATCATAGTGA 58.743 33.333 0.00 0.00 37.97 3.41
1268 1272 3.737559 TTTCATGTTCTGCCCATAGGT 57.262 42.857 0.00 0.00 34.57 3.08
1414 1419 7.706281 TGGTTGCACAATAACAAAAATACTG 57.294 32.000 0.00 0.00 0.00 2.74
1512 1517 3.306225 GCTTCTGATGATTTTGTGCCCAA 60.306 43.478 0.00 0.00 0.00 4.12
1651 1656 0.752658 CTGGTGTGTGTCCACTCAGA 59.247 55.000 2.65 0.00 41.58 3.27
1657 1662 2.158519 TGTGTGTCCACTCAGACTCCTA 60.159 50.000 0.00 0.00 42.34 2.94
1762 1771 6.363065 ACACATTCAGCATCTATGATTCCTT 58.637 36.000 0.00 0.00 0.00 3.36
1810 1819 6.801862 GGATTAGTTCATGCACTGTGTAAAAC 59.198 38.462 8.37 13.02 0.00 2.43
1816 1825 6.685527 TCATGCACTGTGTAAAACAAAGTA 57.314 33.333 9.86 0.00 44.49 2.24
2145 2161 0.034337 GGTCGTAGTTGGGCAGTTGA 59.966 55.000 0.00 0.00 0.00 3.18
2289 2307 4.221924 TGCTTATGTCCTACTGTGCAACTA 59.778 41.667 0.00 0.00 38.04 2.24
2298 2316 5.057149 CCTACTGTGCAACTACTTCTGTTT 58.943 41.667 0.00 0.00 38.04 2.83
2359 2379 6.968131 TGTGTTCTACTGCAACTCATTATC 57.032 37.500 0.00 0.00 0.00 1.75
2557 2578 8.105197 TGATGGTATATGATTGAGAAGGAATGG 58.895 37.037 0.00 0.00 0.00 3.16
2594 2615 0.250234 TTGCCGAGCTGCTTCAGTAT 59.750 50.000 2.53 0.00 33.43 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 140 1.133513 ACCTTGAGGATGTGGCAACAA 60.134 47.619 0.00 0.00 44.45 2.83
292 293 8.333984 TCGTATATCATGTTCCTCTCCCTTATA 58.666 37.037 0.00 0.00 0.00 0.98
437 439 2.542907 CCGTTGCAGCAGTCGGTTT 61.543 57.895 24.14 0.00 38.45 3.27
783 786 2.933032 TAGGGCCATTGGGAGGAGGG 62.933 65.000 6.18 0.00 35.59 4.30
784 787 1.385915 TAGGGCCATTGGGAGGAGG 60.386 63.158 6.18 0.00 35.59 4.30
840 843 3.908712 ATGGGGAGTTGGGGGCAGA 62.909 63.158 0.00 0.00 0.00 4.26
991 995 3.119319 TGAGGGTTGGCATCACCTATAA 58.881 45.455 8.20 0.00 40.22 0.98
1140 1144 4.137116 TGTGCAACTAAAGTCACTCACT 57.863 40.909 0.00 0.00 38.04 3.41
1172 1176 2.620115 CAGCATGTTCTGTTCAACTGGT 59.380 45.455 0.00 0.00 0.00 4.00
1268 1272 5.247337 TGTCATGGTACTTGGATTGTAGTCA 59.753 40.000 0.00 0.00 0.00 3.41
1445 1450 2.280552 GGGCAGTAGGACCGTCACA 61.281 63.158 0.00 0.00 32.42 3.58
1651 1656 6.821616 ATGAGGAAACAGAATCATAGGAGT 57.178 37.500 0.00 0.00 30.78 3.85
1657 1662 8.641498 AGTTACAAATGAGGAAACAGAATCAT 57.359 30.769 0.00 0.00 33.91 2.45
1710 1716 3.181467 TGGTCCCAACATTGCTGAAAAAG 60.181 43.478 0.00 0.00 0.00 2.27
1716 1723 1.000060 CACTTGGTCCCAACATTGCTG 60.000 52.381 0.00 0.00 0.00 4.41
1786 1795 7.359595 TGTTTTACACAGTGCATGAACTAATC 58.640 34.615 5.87 0.00 0.00 1.75
1810 1819 5.772521 ACAAAGGCACAAATAGCTACTTTG 58.227 37.500 20.59 20.59 42.13 2.77
1816 1825 3.665745 CCAACAAAGGCACAAATAGCT 57.334 42.857 0.00 0.00 0.00 3.32
2028 2044 3.994392 GGAAGTTGCTGAGATACGACAAA 59.006 43.478 0.00 0.00 0.00 2.83
2289 2307 4.438744 GCAGTTGCACAGTAAAACAGAAGT 60.439 41.667 0.00 0.00 41.59 3.01
2298 2316 3.751175 GGACATAAGCAGTTGCACAGTAA 59.249 43.478 6.90 0.00 45.16 2.24
2359 2379 1.731433 AAGCAGTTGCACAGTGGCAG 61.731 55.000 6.90 0.00 45.88 4.85
2557 2578 5.064707 TCGGCAAGTAAGACAATAAGCATTC 59.935 40.000 0.00 0.00 0.00 2.67
2594 2615 6.127925 GCACTTCCAGATTATTGACATTGACA 60.128 38.462 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.