Multiple sequence alignment - TraesCS6A01G233400

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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 TraesCS6A01G233400 chr6A 100.000 1095 0 0 551 1645 441435435 441434341 0.000000e+00 2023
1 TraesCS6A01G233400 chr6A 95.687 997 26 6 551 1532 410894928 410895922 0.000000e+00 1587
2 TraesCS6A01G233400 chr6A 100.000 429 0 0 1914 2342 441434072 441433644 0.000000e+00 793
3 TraesCS6A01G233400 chr6A 94.911 393 19 1 1951 2342 410895975 410896367 4.280000e-172 614
4 TraesCS6A01G233400 chr6A 100.000 225 0 0 1 225 441435985 441435761 1.290000e-112 416
5 TraesCS6A01G233400 chr6A 98.667 225 3 0 1 225 410894635 410894859 1.300000e-107 399
6 TraesCS6A01G233400 chr6B 97.536 1096 21 4 551 1645 470132075 470130985 0.000000e+00 1869
7 TraesCS6A01G233400 chr6B 98.724 392 5 0 1951 2342 470130544 470130153 0.000000e+00 697
8 TraesCS6A01G233400 chr6B 99.111 225 2 0 1 225 470132368 470132144 2.800000e-109 405
9 TraesCS6A01G233400 chr6D 95.562 1104 32 8 551 1645 304287942 304286847 0.000000e+00 1751
10 TraesCS6A01G233400 chr6D 95.641 390 17 0 1953 2342 304286434 304286045 5.490000e-176 627
11 TraesCS6A01G233400 chr6D 99.556 225 1 0 1 225 304288235 304288011 6.020000e-111 411


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 TraesCS6A01G233400 chr6A 441433644 441435985 2341 True 1077.333333 2023 100.000000 1 2342 3 chr6A.!!$R1 2341
1 TraesCS6A01G233400 chr6A 410894635 410896367 1732 False 866.666667 1587 96.421667 1 2342 3 chr6A.!!$F1 2341
2 TraesCS6A01G233400 chr6B 470130153 470132368 2215 True 990.333333 1869 98.457000 1 2342 3 chr6B.!!$R1 2341
3 TraesCS6A01G233400 chr6D 304286045 304288235 2190 True 929.666667 1751 96.919667 1 2342 3 chr6D.!!$R1 2341


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
677 678 0.251209 TGGGCGACAGACAGAGTACT 60.251 55.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2032 3.758023 CTGAACCTGCCATTTGACATGTA 59.242 43.478 0.0 0.0 0.0 2.29 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
669 670 1.886886 TTAGGTTTTGGGCGACAGAC 58.113 50.000 0.00 0.00 0.00 3.51
670 671 0.759959 TAGGTTTTGGGCGACAGACA 59.240 50.000 0.00 0.00 0.00 3.41
671 672 0.535102 AGGTTTTGGGCGACAGACAG 60.535 55.000 0.00 0.00 0.00 3.51
672 673 0.534203 GGTTTTGGGCGACAGACAGA 60.534 55.000 0.00 0.00 0.00 3.41
673 674 0.868406 GTTTTGGGCGACAGACAGAG 59.132 55.000 0.00 0.00 0.00 3.35
674 675 0.468226 TTTTGGGCGACAGACAGAGT 59.532 50.000 0.00 0.00 0.00 3.24
676 677 0.601558 TTGGGCGACAGACAGAGTAC 59.398 55.000 0.00 0.00 0.00 2.73
677 678 0.251209 TGGGCGACAGACAGAGTACT 60.251 55.000 0.00 0.00 0.00 2.73
678 679 0.452585 GGGCGACAGACAGAGTACTC 59.547 60.000 15.41 15.41 0.00 2.59
1313 1334 3.947834 GACAACTTCCTTGGGATGTATGG 59.052 47.826 5.70 2.87 38.82 2.74
1336 1357 0.931005 CAGGTTCGCTAAATCGGAGC 59.069 55.000 0.00 0.00 35.82 4.70
1337 1358 0.824759 AGGTTCGCTAAATCGGAGCT 59.175 50.000 0.00 0.00 40.58 4.09
1481 1504 1.341581 CCGAATTTCTGGCCCCCTTAA 60.342 52.381 0.00 0.00 0.00 1.85
1620 1647 3.118408 TGGAGAATGTTCCCTATTCGGTG 60.118 47.826 0.00 0.00 39.07 4.94
1638 1665 5.597806 TCGGTGTACATATGAACCTCATTC 58.402 41.667 10.38 0.00 38.26 2.67
2067 2245 5.107065 CCGCTAAAAGTTTCAGGACTACTTG 60.107 44.000 0.00 0.00 32.76 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
669 670 2.094286 CCTCTTGTGCTGGAGTACTCTG 60.094 54.545 21.88 15.54 0.00 3.35
670 671 2.175202 CCTCTTGTGCTGGAGTACTCT 58.825 52.381 21.88 0.00 0.00 3.24
671 672 2.165437 CTCCTCTTGTGCTGGAGTACTC 59.835 54.545 14.87 14.87 41.64 2.59
672 673 2.175202 CTCCTCTTGTGCTGGAGTACT 58.825 52.381 0.00 0.00 41.64 2.73
673 674 2.663826 CTCCTCTTGTGCTGGAGTAC 57.336 55.000 0.00 0.00 41.64 2.73
677 678 0.972134 CAGACTCCTCTTGTGCTGGA 59.028 55.000 0.00 0.00 0.00 3.86
678 679 0.683973 ACAGACTCCTCTTGTGCTGG 59.316 55.000 0.00 0.00 0.00 4.85
1313 1334 0.373716 CGATTTAGCGAACCTGTGGC 59.626 55.000 0.00 0.00 0.00 5.01
1336 1357 0.108898 CTTCTGGACGGCACTCAGAG 60.109 60.000 0.00 0.00 38.55 3.35
1337 1358 1.536073 CCTTCTGGACGGCACTCAGA 61.536 60.000 0.00 0.00 35.95 3.27
1481 1504 7.971722 GGTAAGTCGGCATAAATGTACAAAAAT 59.028 33.333 0.00 0.00 0.00 1.82
1570 1597 9.542462 TCTTCATAACTAAAATAATCACGGAGG 57.458 33.333 0.00 0.00 0.00 4.30
1620 1647 6.174720 TCCCAGAATGAGGTTCATATGTAC 57.825 41.667 1.90 3.04 39.69 2.90
1924 2032 3.758023 CTGAACCTGCCATTTGACATGTA 59.242 43.478 0.00 0.00 0.00 2.29
2067 2245 6.477360 GCTACCTAAACTTGATAAGTGAGAGC 59.523 42.308 0.00 0.27 41.91 4.09



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

AutoCloner maintained by Alex Coulton.