Multiple sequence alignment - TraesCS4A01G286900

Loading Multiple Alignment...

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 TraesCS4A01G286900 chr4A 100.000 2982 0 0 1 2982 592336807 592333826 0 5507
1 TraesCS4A01G286900 chr4A 97.653 2982 63 2 1 2982 591292549 591295523 0 5112
2 TraesCS4A01G286900 chr4A 97.016 2983 81 2 1 2982 591346315 591349290 0 5009
3 TraesCS4A01G286900 chr4A 96.916 2983 80 5 1 2982 591415834 591418805 0 4988
4 TraesCS4A01G286900 chr4A 96.849 2983 86 3 1 2982 591673819 591676794 0 4981
5 TraesCS4A01G286900 chr4A 96.649 2984 91 3 1 2982 592363129 592360153 0 4948
6 TraesCS4A01G286900 chr4A 97.389 2068 53 1 1 2067 592928461 592926394 0 3518
7 TraesCS4A01G286900 chr4A 97.371 1978 50 2 1 1977 592310850 592308874 0 3363
8 TraesCS4A01G286900 chr4A 96.613 1978 65 2 1 1977 591285601 591283625 0 3280
9 TraesCS4A01G286900 chr4A 97.320 1418 37 1 1 1417 592639077 592637660 0 2407
10 TraesCS4A01G286900 chr4A 96.950 1377 35 1 1606 2982 592926383 592925014 0 2303
11 TraesCS4A01G286900 chr4A 97.371 913 24 0 2070 2982 592636718 592635806 0 1554
12 TraesCS4A01G286900 chr4A 97.158 915 26 0 2068 2982 592308467 592307553 0 1546
13 TraesCS4A01G286900 chr4A 96.899 903 28 0 2080 2982 591283300 591282398 0 1513
14 TraesCS4A01G286900 chr4D 90.655 1573 123 13 473 2026 10828588 10830155 0 2069


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 TraesCS4A01G286900 chr4A 592333826 592336807 2981 True 5507.0 5507 100.0000 1 2982 1 chr4A.!!$R1 2981
1 TraesCS4A01G286900 chr4A 591292549 591295523 2974 False 5112.0 5112 97.6530 1 2982 1 chr4A.!!$F1 2981
2 TraesCS4A01G286900 chr4A 591346315 591349290 2975 False 5009.0 5009 97.0160 1 2982 1 chr4A.!!$F2 2981
3 TraesCS4A01G286900 chr4A 591415834 591418805 2971 False 4988.0 4988 96.9160 1 2982 1 chr4A.!!$F3 2981
4 TraesCS4A01G286900 chr4A 591673819 591676794 2975 False 4981.0 4981 96.8490 1 2982 1 chr4A.!!$F4 2981
5 TraesCS4A01G286900 chr4A 592360153 592363129 2976 True 4948.0 4948 96.6490 1 2982 1 chr4A.!!$R2 2981
6 TraesCS4A01G286900 chr4A 592925014 592928461 3447 True 2910.5 3518 97.1695 1 2982 2 chr4A.!!$R6 2981
7 TraesCS4A01G286900 chr4A 592307553 592310850 3297 True 2454.5 3363 97.2645 1 2982 2 chr4A.!!$R4 2981
8 TraesCS4A01G286900 chr4A 591282398 591285601 3203 True 2396.5 3280 96.7560 1 2982 2 chr4A.!!$R3 2981
9 TraesCS4A01G286900 chr4A 592635806 592639077 3271 True 1980.5 2407 97.3455 1 2982 2 chr4A.!!$R5 2981
10 TraesCS4A01G286900 chr4D 10828588 10830155 1567 False 2069.0 2069 90.6550 473 2026 1 chr4D.!!$F1 1553

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
121 122 1.003928 CTAGTTTTGGCCCTAACCGGT 59.996 52.381 0.00 0.0 0.0 5.28 F
141 142 1.133199 TGAAAATTGGGCTCCTGTGGT 60.133 47.619 0.00 0.0 0.0 4.16 F
1522 1536 1.678101 TCTGCATCATCGTCGACATCT 59.322 47.619 17.16 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 1582 0.461961 GTCGATGGCCTTGAGCTAGT 59.538 55.0 3.32 0.00 43.05 2.57 R
1570 1584 0.975556 TGGTCGATGGCCTTGAGCTA 60.976 55.0 17.99 6.49 43.05 3.32 R
2572 3060 0.806868 CTTGCCGTGTCATCTTGCAT 59.193 50.0 0.00 0.00 0.00 3.96 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
121 122 1.003928 CTAGTTTTGGCCCTAACCGGT 59.996 52.381 0.00 0.00 0.00 5.28
141 142 1.133199 TGAAAATTGGGCTCCTGTGGT 60.133 47.619 0.00 0.00 0.00 4.16
295 296 6.352516 TGCCTAAAGGAATTTGCAAAGAAAA 58.647 32.000 18.19 0.00 37.39 2.29
346 347 5.872070 GGCGAGATGAGGAGGATAATAAAAG 59.128 44.000 0.00 0.00 0.00 2.27
586 587 2.035704 GTGGCCACAACATCATGTTTGA 59.964 45.455 31.23 0.00 38.77 2.69
603 604 8.423349 TCATGTTTGATTTTTCATCCTTCAAGT 58.577 29.630 0.00 0.00 0.00 3.16
796 804 6.648310 CCTTATGTCTAATCACATCTTCGCAT 59.352 38.462 0.00 0.00 38.07 4.73
1097 1111 2.213499 CCAACGCAAGACAAGAGAAGT 58.787 47.619 0.00 0.00 43.62 3.01
1352 1366 2.201927 TGCAGATCTTCGGCAGCTA 58.798 52.632 2.24 0.00 42.36 3.32
1410 1424 1.970640 GCCATTTTCAACTCCAGGGTT 59.029 47.619 0.00 0.00 0.00 4.11
1522 1536 1.678101 TCTGCATCATCGTCGACATCT 59.322 47.619 17.16 0.00 0.00 2.90
2096 2584 2.715624 CTTGAAATAGCGCCGGCC 59.284 61.111 23.46 14.23 41.24 6.13
2120 2608 1.540707 GGCCAACCGACGGAAAAATTA 59.459 47.619 23.38 0.00 0.00 1.40
2572 3060 5.520376 TCTCGCTCTCAATGATCATGTTA 57.480 39.130 9.46 0.00 0.00 2.41
2702 3190 2.936202 TGATATTCTTCCTGCAAGCCC 58.064 47.619 0.00 0.00 31.26 5.19
2898 3386 2.680312 ACATTCGAGCACTGCAGTAT 57.320 45.000 21.20 11.57 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 3.426117 CTAGCGCCGACGAACCCAT 62.426 63.158 2.29 0.00 43.93 4.00
121 122 1.133199 ACCACAGGAGCCCAATTTTCA 60.133 47.619 0.00 0.00 0.00 2.69
141 142 3.599285 AAAATCGGCCCAGTCGCGA 62.599 57.895 3.71 3.71 0.00 5.87
218 219 1.541588 GCTTGAGTTGTGGCCTTTAGG 59.458 52.381 3.32 0.00 38.53 2.69
295 296 7.342799 ACCCAAACTGAGCAATAATGTCATTAT 59.657 33.333 11.62 11.62 37.05 1.28
346 347 1.521450 CCATGCGAGCCAATCCATCC 61.521 60.000 0.00 0.00 0.00 3.51
586 587 6.923199 ATCCACACTTGAAGGATGAAAAAT 57.077 33.333 0.00 0.00 40.52 1.82
603 604 6.529084 ACCAATCCTCCAAATATATCCACA 57.471 37.500 0.00 0.00 0.00 4.17
883 891 2.089980 GTGAGCTCTTCATGCCACAAT 58.910 47.619 16.19 0.00 38.29 2.71
1097 1111 1.303480 TGCTGCACTGCCATTGCTA 60.303 52.632 8.56 0.00 40.86 3.49
1352 1366 0.545548 GGTGACCCCCTCAAGAGACT 60.546 60.000 0.00 0.00 0.00 3.24
1410 1424 2.031012 CACGCCAGAGTGAAGCCA 59.969 61.111 0.00 0.00 44.43 4.75
1433 1447 1.531602 GCACCCTGGGCTTTCTGTT 60.532 57.895 14.08 0.00 0.00 3.16
1522 1536 0.761323 TCACCGGAGTGGACCTTCAA 60.761 55.000 9.46 0.00 44.64 2.69
1568 1582 0.461961 GTCGATGGCCTTGAGCTAGT 59.538 55.000 3.32 0.00 43.05 2.57
1570 1584 0.975556 TGGTCGATGGCCTTGAGCTA 60.976 55.000 17.99 6.49 43.05 3.32
2572 3060 0.806868 CTTGCCGTGTCATCTTGCAT 59.193 50.000 0.00 0.00 0.00 3.96
2702 3190 2.154462 CTACTTTGCCAAGTGTCAGGG 58.846 52.381 13.20 0.00 43.54 4.45
2898 3386 4.516321 CAGGAACTCACAATGACATCAACA 59.484 41.667 0.00 0.00 34.60 3.33


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

AutoCloner maintained by Alex Coulton.