Multiple sequence alignment - TraesCS6A01G156500

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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 TraesCS6A01G156500 chr6A 100.000 2225 0 0 1 2225 145451694 145453918 0.000000e+00 4109
1 TraesCS6A01G156500 chr6A 88.629 1495 115 19 582 2045 267525410 267526880 0.000000e+00 1768
2 TraesCS6A01G156500 chr6A 94.801 577 30 0 1 577 128805619 128806195 0.000000e+00 900
3 TraesCS6A01G156500 chr4A 95.193 1477 42 8 751 2225 176448590 176447141 0.000000e+00 2307
4 TraesCS6A01G156500 chr4A 96.129 155 6 0 582 736 176449177 176449023 1.020000e-63 254
5 TraesCS6A01G156500 chr3A 96.367 1156 32 4 1075 2225 603915839 603914689 0.000000e+00 1893
6 TraesCS6A01G156500 chr3A 94.974 577 29 0 1 577 50430645 50430069 0.000000e+00 905
7 TraesCS6A01G156500 chr3A 94.589 462 19 2 623 1084 603916915 603916460 0.000000e+00 710
8 TraesCS6A01G156500 chr7A 95.494 577 25 1 1 577 631079264 631079839 0.000000e+00 920
9 TraesCS6A01G156500 chr7A 95.321 577 27 0 1 577 429071303 429071879 0.000000e+00 917
10 TraesCS6A01G156500 chr1A 95.321 577 27 0 1 577 75477840 75477264 0.000000e+00 917
11 TraesCS6A01G156500 chr1A 94.627 577 31 0 1 577 18667155 18666579 0.000000e+00 894
12 TraesCS6A01G156500 chr5A 95.147 577 28 0 1 577 425239386 425239962 0.000000e+00 911
13 TraesCS6A01G156500 chr5A 94.783 575 30 0 3 577 104510694 104511268 0.000000e+00 896
14 TraesCS6A01G156500 chr5A 94.627 577 31 0 1 577 488670584 488671160 0.000000e+00 894


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 TraesCS6A01G156500 chr6A 145451694 145453918 2224 False 4109.0 4109 100.000 1 2225 1 chr6A.!!$F2 2224
1 TraesCS6A01G156500 chr6A 267525410 267526880 1470 False 1768.0 1768 88.629 582 2045 1 chr6A.!!$F3 1463
2 TraesCS6A01G156500 chr6A 128805619 128806195 576 False 900.0 900 94.801 1 577 1 chr6A.!!$F1 576
3 TraesCS6A01G156500 chr4A 176447141 176449177 2036 True 1280.5 2307 95.661 582 2225 2 chr4A.!!$R1 1643
4 TraesCS6A01G156500 chr3A 603914689 603916915 2226 True 1301.5 1893 95.478 623 2225 2 chr3A.!!$R2 1602
5 TraesCS6A01G156500 chr3A 50430069 50430645 576 True 905.0 905 94.974 1 577 1 chr3A.!!$R1 576
6 TraesCS6A01G156500 chr7A 631079264 631079839 575 False 920.0 920 95.494 1 577 1 chr7A.!!$F2 576
7 TraesCS6A01G156500 chr7A 429071303 429071879 576 False 917.0 917 95.321 1 577 1 chr7A.!!$F1 576
8 TraesCS6A01G156500 chr1A 75477264 75477840 576 True 917.0 917 95.321 1 577 1 chr1A.!!$R2 576
9 TraesCS6A01G156500 chr1A 18666579 18667155 576 True 894.0 894 94.627 1 577 1 chr1A.!!$R1 576
10 TraesCS6A01G156500 chr5A 425239386 425239962 576 False 911.0 911 95.147 1 577 1 chr5A.!!$F2 576
11 TraesCS6A01G156500 chr5A 104510694 104511268 574 False 896.0 896 94.783 3 577 1 chr5A.!!$F1 574
12 TraesCS6A01G156500 chr5A 488670584 488671160 576 False 894.0 894 94.627 1 577 1 chr5A.!!$F3 576

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
507 509 0.903454 GTTGGGTCCTTCGAGGGAGA 60.903 60.0 17.84 0.89 35.59 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 2973 0.034337 AAAGTCCAAGAAGCGGCGTA 59.966 50.0 9.37 0.0 0.0 4.42 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
241 242 5.832539 CCCTGAGATGTATTATGAGGGTT 57.167 43.478 0.00 0.00 34.96 4.11
314 315 4.503741 TTGAATAAACTTGCTCAGGTGC 57.496 40.909 0.00 0.00 0.00 5.01
332 333 4.876107 AGGTGCTCCTGTATTATGAAAACG 59.124 41.667 6.51 0.00 43.33 3.60
416 417 4.515028 ATCAAATCTGAGAGATGGCCAA 57.485 40.909 10.96 0.00 34.65 4.52
507 509 0.903454 GTTGGGTCCTTCGAGGGAGA 60.903 60.000 17.84 0.89 35.59 3.71
553 555 7.013274 GGCAACCAGACTATAATGCTTTATCAA 59.987 37.037 8.04 0.00 34.37 2.57
577 579 9.941325 CAATCTCACTTAGCCATAGAATTCTAT 57.059 33.333 20.20 20.20 39.61 1.98
580 582 9.815306 TCTCACTTAGCCATAGAATTCTATAGT 57.185 33.333 24.24 20.13 37.07 2.12
648 651 2.203728 TGTCCCGCACCTACCTGT 60.204 61.111 0.00 0.00 0.00 4.00
739 756 4.509737 GCCGCGGTAGACCAGGAC 62.510 72.222 28.70 0.93 36.06 3.85
744 761 2.762875 GGTAGACCAGGACCCCGG 60.763 72.222 0.00 0.00 35.64 5.73
813 1249 1.893808 CCTGCTTCAACCACTGCGT 60.894 57.895 0.00 0.00 0.00 5.24
928 1364 1.452651 CACAGGCGCATTGGATCCT 60.453 57.895 14.23 0.00 0.00 3.24
955 1391 4.418328 GCCCACCCATGCACCGTA 62.418 66.667 0.00 0.00 0.00 4.02
1132 2204 1.180029 GCTGAACTTCATGTGCCCAT 58.820 50.000 0.00 0.00 0.00 4.00
1200 2272 4.513406 TTTCCTCTCCTCCTCTACTCTC 57.487 50.000 0.00 0.00 0.00 3.20
1249 2321 5.649831 GCATAATTTCCTCCTCTGTTCAAGT 59.350 40.000 0.00 0.00 0.00 3.16
1340 2415 1.074405 TGGCTGCTGGTTCTCTTCAAT 59.926 47.619 0.00 0.00 0.00 2.57
1382 2457 2.328319 GGGAGAGAGAGGATGAGCAAT 58.672 52.381 0.00 0.00 0.00 3.56
1481 2568 1.453197 CCCCGTGCTATTGTTCCCC 60.453 63.158 0.00 0.00 0.00 4.81
1756 2849 1.661480 GCACAGGAAGTTGCATGCA 59.339 52.632 18.46 18.46 33.27 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
204 205 0.609131 CAGGGTGGCGATGTTCCTTT 60.609 55.000 0.00 0.00 0.00 3.11
210 211 1.267574 ACATCTCAGGGTGGCGATGT 61.268 55.000 0.00 0.00 41.00 3.06
314 315 7.359262 TGAACACGTTTTCATAATACAGGAG 57.641 36.000 12.94 0.00 30.29 3.69
433 434 2.046988 CCAGCACTCGTGGCATGA 60.047 61.111 9.42 9.42 0.00 3.07
507 509 1.265095 CTTGTTCGTTGTGCTGAGCAT 59.735 47.619 11.58 0.00 41.91 3.79
631 633 2.203728 ACAGGTAGGTGCGGGACA 60.204 61.111 1.14 0.00 0.00 4.02
640 642 4.514577 CGCCTCCGCACAGGTAGG 62.515 72.222 0.04 0.00 41.99 3.18
739 756 4.489771 GATGGCTGTGGTCCGGGG 62.490 72.222 0.00 0.00 0.00 5.73
744 761 2.592308 GGGGAGATGGCTGTGGTC 59.408 66.667 0.00 0.00 0.00 4.02
1200 2272 3.815401 ACCCAACGATCTTGAACTTGAAG 59.185 43.478 0.00 0.00 0.00 3.02
1249 2321 0.321564 GTACTGGTGCCATGTGCTCA 60.322 55.000 7.54 0.00 42.00 4.26
1382 2457 2.116983 GAACCCAGGAGCAGCTGTCA 62.117 60.000 16.64 0.00 0.00 3.58
1481 2568 1.263217 GTGGAAGCAACAGTAACACCG 59.737 52.381 0.00 0.00 0.00 4.94
1742 2835 0.333993 ATCCCTGCATGCAACTTCCT 59.666 50.000 22.88 1.57 0.00 3.36
1880 2973 0.034337 AAAGTCCAAGAAGCGGCGTA 59.966 50.000 9.37 0.00 0.00 4.42


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

AutoCloner maintained by Alex Coulton.