Multiple sequence alignment - TraesCS4D01G043800

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 TraesCS4D01G043800 chr4D 100.000 3385 0 0 1 3385 19929834 19926450 0 6252
1 TraesCS4D01G043800 chr5D 97.641 2713 57 5 1 2711 503219478 503216771 0 4649
2 TraesCS4D01G043800 chr5D 97.272 2713 67 5 1 2711 6190200 6187493 0 4593
3 TraesCS4D01G043800 chr5D 97.233 2711 69 4 2 2711 503276967 503279672 0 4586
4 TraesCS4D01G043800 chr5D 97.907 669 14 0 2717 3385 503216539 503215871 0 1158
5 TraesCS4D01G043800 chr5D 97.459 669 14 2 2717 3385 329121786 329122451 0 1138
6 TraesCS4D01G043800 chrUn 97.530 2713 59 6 1 2711 93408372 93411078 0 4632
7 TraesCS4D01G043800 chrUn 97.309 2713 66 5 1 2711 216517343 216520050 0 4599
8 TraesCS4D01G043800 chrUn 98.507 670 9 1 2717 3385 93411310 93411979 0 1181
9 TraesCS4D01G043800 chr6D 97.494 2713 62 4 1 2711 168256186 168253478 0 4628
10 TraesCS4D01G043800 chr6D 97.910 670 13 1 2717 3385 168249861 168249192 0 1158
11 TraesCS4D01G043800 chr3B 97.457 2713 62 5 1 2711 201528284 201525577 0 4621
12 TraesCS4D01G043800 chr3D 97.346 2713 61 8 1 2711 589278285 589280988 0 4601
13 TraesCS4D01G043800 chr1D 96.942 2714 74 7 1 2711 254396850 254399557 0 4543
14 TraesCS4D01G043800 chr1D 97.907 669 12 2 2717 3385 254524392 254523726 0 1157
15 TraesCS4D01G043800 chr2D 98.060 670 11 2 2717 3385 272795573 272796241 0 1164
16 TraesCS4D01G043800 chr3A 97.612 670 14 2 2717 3385 672911688 672912356 0 1147
17 TraesCS4D01G043800 chr6A 96.861 669 19 2 2717 3385 271188095 271187429 0 1118
18 TraesCS4D01G043800 chr2A 96.861 669 20 1 2717 3385 335829217 335828550 0 1118


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 TraesCS4D01G043800 chr4D 19926450 19929834 3384 True 6252.0 6252 100.0000 1 3385 1 chr4D.!!$R1 3384
1 TraesCS4D01G043800 chr5D 6187493 6190200 2707 True 4593.0 4593 97.2720 1 2711 1 chr5D.!!$R1 2710
2 TraesCS4D01G043800 chr5D 503276967 503279672 2705 False 4586.0 4586 97.2330 2 2711 1 chr5D.!!$F2 2709
3 TraesCS4D01G043800 chr5D 503215871 503219478 3607 True 2903.5 4649 97.7740 1 3385 2 chr5D.!!$R2 3384
4 TraesCS4D01G043800 chr5D 329121786 329122451 665 False 1138.0 1138 97.4590 2717 3385 1 chr5D.!!$F1 668
5 TraesCS4D01G043800 chrUn 216517343 216520050 2707 False 4599.0 4599 97.3090 1 2711 1 chrUn.!!$F1 2710
6 TraesCS4D01G043800 chrUn 93408372 93411979 3607 False 2906.5 4632 98.0185 1 3385 2 chrUn.!!$F2 3384
7 TraesCS4D01G043800 chr6D 168249192 168256186 6994 True 2893.0 4628 97.7020 1 3385 2 chr6D.!!$R1 3384
8 TraesCS4D01G043800 chr3B 201525577 201528284 2707 True 4621.0 4621 97.4570 1 2711 1 chr3B.!!$R1 2710
9 TraesCS4D01G043800 chr3D 589278285 589280988 2703 False 4601.0 4601 97.3460 1 2711 1 chr3D.!!$F1 2710
10 TraesCS4D01G043800 chr1D 254396850 254399557 2707 False 4543.0 4543 96.9420 1 2711 1 chr1D.!!$F1 2710
11 TraesCS4D01G043800 chr1D 254523726 254524392 666 True 1157.0 1157 97.9070 2717 3385 1 chr1D.!!$R1 668
12 TraesCS4D01G043800 chr2D 272795573 272796241 668 False 1164.0 1164 98.0600 2717 3385 1 chr2D.!!$F1 668
13 TraesCS4D01G043800 chr3A 672911688 672912356 668 False 1147.0 1147 97.6120 2717 3385 1 chr3A.!!$F1 668
14 TraesCS4D01G043800 chr6A 271187429 271188095 666 True 1118.0 1118 96.8610 2717 3385 1 chr6A.!!$R1 668
15 TraesCS4D01G043800 chr2A 335828550 335829217 667 True 1118.0 1118 96.8610 2717 3385 1 chr2A.!!$R1 668

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
112 113 1.533129 GGCTTAATGGTTAAAGCGCCG 60.533 52.381 2.29 0.0 28.48 6.46 F
1169 1172 1.317613 AACGGCAGCAAGTGATTGAA 58.682 45.000 0.00 0.0 0.00 2.69 F
2046 2051 0.032515 CAACCCCTTGGGGTTATCCC 60.033 60.000 34.97 0.0 42.24 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 1936 1.470458 CCTCTTACTACGGGGCGTTTC 60.470 57.143 0.0 0.0 41.54 2.78 R
2183 2189 1.176527 CATGCACGGGTTCAATTCCT 58.823 50.000 0.0 0.0 0.00 3.36 R
3074 6695 3.453424 GTTGTGCGAACCAAAAGGAATT 58.547 40.909 0.0 0.0 0.00 2.17 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
112 113 1.533129 GGCTTAATGGTTAAAGCGCCG 60.533 52.381 2.29 0.00 28.48 6.46
249 250 7.874016 TCCATACATAACGAATTGGTATGGTAC 59.126 37.037 21.76 0.00 45.91 3.34
275 276 9.650371 CATTCGTACCATAACATAAGAACAATG 57.350 33.333 0.00 0.00 0.00 2.82
341 342 5.073691 AGGGAAAGTCGATTTATGGATGGAT 59.926 40.000 0.00 0.00 0.00 3.41
343 344 6.265422 GGGAAAGTCGATTTATGGATGGATTT 59.735 38.462 0.00 0.00 0.00 2.17
448 450 5.649782 AGACAGAAATAAAGCATTGGGTG 57.350 39.130 0.00 0.00 0.00 4.61
506 508 2.304761 AGCCATCGACTACCTGGAAAAA 59.695 45.455 6.18 0.00 31.38 1.94
549 551 3.369175 TGGGCCATACAATGCATTACAA 58.631 40.909 12.53 0.60 0.00 2.41
572 574 7.392113 ACAAACGTATGATCATTACCCTTCAAA 59.608 33.333 14.65 0.00 0.00 2.69
598 600 6.342111 GGGTTATTCTGTTCCACTTCTAGAG 58.658 44.000 0.00 0.00 0.00 2.43
710 712 5.336102 ACAGGAAAGTGAAATCCAATCCAT 58.664 37.500 0.00 0.00 38.23 3.41
1025 1028 3.421844 GAAATGCCCTACCTTTGAGTGT 58.578 45.455 0.00 0.00 0.00 3.55
1045 1048 9.126151 TGAGTGTGGTTTGAACTATTGATTTAA 57.874 29.630 0.00 0.00 0.00 1.52
1169 1172 1.317613 AACGGCAGCAAGTGATTGAA 58.682 45.000 0.00 0.00 0.00 2.69
1287 1290 4.444876 CCTTGTTTCAAAGAGAGGAGGACA 60.445 45.833 0.00 0.00 0.00 4.02
1337 1340 3.917988 AGGCAAATTGAAAGCTAAGCAC 58.082 40.909 0.00 0.00 0.00 4.40
1354 1357 3.190439 AGCACTGGTAATTAAGACCCCT 58.810 45.455 6.83 0.00 35.99 4.79
1408 1411 6.269077 ACCCATAATATGTGGAAGTATCGACA 59.731 38.462 12.60 0.00 46.37 4.35
1499 1502 9.303116 GAGACCTAGGATGTAGAAGATCATAAA 57.697 37.037 17.98 0.00 0.00 1.40
1932 1936 2.224066 CGGATCTAAGTGTTGGCTAGGG 60.224 54.545 0.00 0.00 0.00 3.53
2046 2051 0.032515 CAACCCCTTGGGGTTATCCC 60.033 60.000 34.97 0.00 42.24 3.85
2109 2115 4.288531 CGATAGTTTTATCCTTCGTCGCT 58.711 43.478 0.00 0.00 33.52 4.93
2122 2128 7.263100 TCCTTCGTCGCTATAAGTAAATACA 57.737 36.000 0.00 0.00 0.00 2.29
2197 2203 0.395312 ACGACAGGAATTGAACCCGT 59.605 50.000 0.00 0.00 0.00 5.28
2364 2371 8.264347 AGAATGCCACTCTTTAAAAAGGAAAAA 58.736 29.630 2.77 0.00 36.67 1.94
2677 2686 7.310664 TCGTCGTTAACTGAATTCTGAATAGT 58.689 34.615 18.13 4.57 0.00 2.12
2887 6507 2.828520 AGAAATTCAGACCTCGAGCTCA 59.171 45.455 15.40 0.00 0.00 4.26
3216 6838 5.923733 ATAGAATCAGACTCAAGTTCCGT 57.076 39.130 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 5.303333 TGCTTAACAGGGATCATCGTACATA 59.697 40.000 0.00 0.00 0.00 2.29
96 97 2.674357 GAGTTCGGCGCTTTAACCATTA 59.326 45.455 7.64 0.00 0.00 1.90
112 113 6.475402 CCCGCAAATTTACCAATTATGAGTTC 59.525 38.462 0.00 0.00 31.89 3.01
249 250 9.650371 CATTGTTCTTATGTTATGGTACGAATG 57.350 33.333 0.00 0.00 0.00 2.67
275 276 8.973378 CCAGTATCGATAAGAATTTGAGTTCTC 58.027 37.037 6.72 0.00 37.46 2.87
448 450 5.008712 CACCTTAACACCAAAGAAGAGTTCC 59.991 44.000 0.00 0.00 0.00 3.62
549 551 6.036735 CGTTTGAAGGGTAATGATCATACGTT 59.963 38.462 9.04 10.09 40.17 3.99
572 574 3.326880 AGAAGTGGAACAGAATAACCCGT 59.673 43.478 0.00 0.00 41.80 5.28
614 616 9.616156 TTTTGCCGTATTATTAAGTATTCTCCA 57.384 29.630 0.00 0.00 0.00 3.86
710 712 5.221224 GCCGTCCATGGATCAAATTATTTCA 60.221 40.000 19.62 0.00 0.00 2.69
1073 1076 5.100259 GTGATCGATTTCTAGGTTTCGTCA 58.900 41.667 0.00 8.49 33.52 4.35
1337 1340 2.174854 CCCCAGGGGTCTTAATTACCAG 59.825 54.545 18.09 0.00 38.25 4.00
1354 1357 2.783510 GAGACATCCCTATTTTCCCCCA 59.216 50.000 0.00 0.00 0.00 4.96
1499 1502 1.959042 AATCTGCCGAATCGCTCATT 58.041 45.000 0.00 0.00 0.00 2.57
1578 1581 8.097662 TGTATATGACGATCTCTAGACAGATGT 58.902 37.037 0.00 0.00 32.94 3.06
1932 1936 1.470458 CCTCTTACTACGGGGCGTTTC 60.470 57.143 0.00 0.00 41.54 2.78
1989 1993 1.767692 GGGAGCTTTCCCTTCACCA 59.232 57.895 3.72 0.00 46.39 4.17
2046 2051 1.656095 CTAGTTCTTCTTCCAAGCGCG 59.344 52.381 0.00 0.00 0.00 6.86
2080 2085 9.570488 GACGAAGGATAAAACTATCGCTATATT 57.430 33.333 0.00 0.00 33.88 1.28
2084 2089 5.446709 CGACGAAGGATAAAACTATCGCTA 58.553 41.667 0.00 0.00 33.88 4.26
2085 2090 4.288531 CGACGAAGGATAAAACTATCGCT 58.711 43.478 0.00 0.00 33.88 4.93
2099 2105 9.616634 TTATGTATTTACTTATAGCGACGAAGG 57.383 33.333 0.00 0.00 0.00 3.46
2183 2189 1.176527 CATGCACGGGTTCAATTCCT 58.823 50.000 0.00 0.00 0.00 3.36
2364 2371 5.241662 GTGTCAGAGCTGATTACTCCTTTT 58.758 41.667 3.19 0.00 42.18 2.27
2365 2372 4.619394 CGTGTCAGAGCTGATTACTCCTTT 60.619 45.833 3.19 0.00 42.18 3.11
2711 2720 8.725148 GGCATGAGGTTCAGTATCATAAATAAG 58.275 37.037 0.00 0.00 32.51 1.73
2713 2722 7.017551 AGGGCATGAGGTTCAGTATCATAAATA 59.982 37.037 0.00 0.00 32.51 1.40
2715 2724 5.132648 AGGGCATGAGGTTCAGTATCATAAA 59.867 40.000 0.00 0.00 32.51 1.40
3074 6695 3.453424 GTTGTGCGAACCAAAAGGAATT 58.547 40.909 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.