Multiple sequence alignment - TraesCS1D01G060200

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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 TraesCS1D01G060200 chr1D 100.000 5573 0 0 1 5573 40236046 40230474 0.000000e+00 10292.0
1 TraesCS1D01G060200 chr1D 93.000 100 6 1 1 99 40230111 40230210 1.620000e-30 145.0
2 TraesCS1D01G060200 chr6D 98.597 3064 41 2 1 3062 262426333 262423270 0.000000e+00 5419.0
3 TraesCS1D01G060200 chr6D 98.150 2541 35 3 3044 5573 262423258 262420719 0.000000e+00 4421.0
4 TraesCS1D01G060200 chr6D 93.750 96 6 0 4 99 262420351 262420446 1.620000e-30 145.0
5 TraesCS1D01G060200 chr3D 98.597 3064 40 3 1 3062 29938595 29935533 0.000000e+00 5417.0
6 TraesCS1D01G060200 chr3D 97.088 2541 37 5 3044 5573 29935520 29933006 0.000000e+00 4248.0
7 TraesCS1D01G060200 chr3D 93.000 100 6 1 1 99 29932634 29932733 1.620000e-30 145.0
8 TraesCS1D01G060200 chr5D 95.699 2325 81 14 739 3060 479153055 479150747 0.000000e+00 3722.0
9 TraesCS1D01G060200 chr5D 89.281 737 45 10 98 823 479153629 479152916 0.000000e+00 893.0
10 TraesCS1D01G060200 chr5D 96.797 281 8 1 3356 3636 479150604 479150325 8.450000e-128 468.0
11 TraesCS1D01G060200 chr5D 92.000 100 7 1 1 99 479132800 479132899 7.530000e-29 139.0
12 TraesCS1D01G060200 chr5D 94.872 78 4 0 3048 3125 479150682 479150605 7.580000e-24 122.0
13 TraesCS1D01G060200 chr2D 79.835 2906 529 42 914 3804 560223194 560220331 0.000000e+00 2067.0
14 TraesCS1D01G060200 chr2D 83.607 305 39 6 4379 4673 560219646 560219343 5.500000e-70 276.0
15 TraesCS1D01G060200 chr4B 78.240 3079 561 69 914 3953 112963202 112966210 0.000000e+00 1873.0
16 TraesCS1D01G060200 chr5B 80.828 1497 251 25 914 2394 604859303 604860779 0.000000e+00 1142.0
17 TraesCS1D01G060200 chr5B 88.435 147 16 1 5428 5573 530257309 530257455 5.740000e-40 176.0
18 TraesCS1D01G060200 chr5B 87.692 65 5 3 6 68 530260792 530260729 7.740000e-09 73.1
19 TraesCS1D01G060200 chr7B 80.166 1447 261 20 914 2349 629503428 629504859 0.000000e+00 1059.0
20 TraesCS1D01G060200 chr7B 75.029 1718 359 59 921 2622 56911168 56909505 0.000000e+00 732.0
21 TraesCS1D01G060200 chr7B 73.913 1196 209 68 3552 4667 214997554 214998726 8.760000e-103 385.0
22 TraesCS1D01G060200 chr7B 75.664 678 157 7 1946 2619 426108282 426107609 1.160000e-86 331.0
23 TraesCS1D01G060200 chr3B 95.918 245 10 0 2025 2269 357218005 357217761 1.120000e-106 398.0
24 TraesCS1D01G060200 chr6A 73.073 1077 258 27 1559 2619 14155750 14154690 2.470000e-93 353.0
25 TraesCS1D01G060200 chr2A 74.901 761 161 21 1561 2312 545835756 545835017 2.500000e-83 320.0
26 TraesCS1D01G060200 chr7A 76.881 545 118 7 2079 2619 52223366 52222826 9.070000e-78 302.0


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 TraesCS1D01G060200 chr1D 40230474 40236046 5572 True 10292.00 10292 100.00000 1 5573 1 chr1D.!!$R1 5572
1 TraesCS1D01G060200 chr6D 262420719 262426333 5614 True 4920.00 5419 98.37350 1 5573 2 chr6D.!!$R1 5572
2 TraesCS1D01G060200 chr3D 29933006 29938595 5589 True 4832.50 5417 97.84250 1 5573 2 chr3D.!!$R1 5572
3 TraesCS1D01G060200 chr5D 479150325 479153629 3304 True 1301.25 3722 94.16225 98 3636 4 chr5D.!!$R1 3538
4 TraesCS1D01G060200 chr2D 560219343 560223194 3851 True 1171.50 2067 81.72100 914 4673 2 chr2D.!!$R1 3759
5 TraesCS1D01G060200 chr4B 112963202 112966210 3008 False 1873.00 1873 78.24000 914 3953 1 chr4B.!!$F1 3039
6 TraesCS1D01G060200 chr5B 604859303 604860779 1476 False 1142.00 1142 80.82800 914 2394 1 chr5B.!!$F2 1480
7 TraesCS1D01G060200 chr7B 629503428 629504859 1431 False 1059.00 1059 80.16600 914 2349 1 chr7B.!!$F2 1435
8 TraesCS1D01G060200 chr7B 56909505 56911168 1663 True 732.00 732 75.02900 921 2622 1 chr7B.!!$R1 1701
9 TraesCS1D01G060200 chr7B 214997554 214998726 1172 False 385.00 385 73.91300 3552 4667 1 chr7B.!!$F1 1115
10 TraesCS1D01G060200 chr7B 426107609 426108282 673 True 331.00 331 75.66400 1946 2619 1 chr7B.!!$R2 673
11 TraesCS1D01G060200 chr6A 14154690 14155750 1060 True 353.00 353 73.07300 1559 2619 1 chr6A.!!$R1 1060
12 TraesCS1D01G060200 chr2A 545835017 545835756 739 True 320.00 320 74.90100 1561 2312 1 chr2A.!!$R1 751
13 TraesCS1D01G060200 chr7A 52222826 52223366 540 True 302.00 302 76.88100 2079 2619 1 chr7A.!!$R1 540

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
489 491 0.038343 CATTGGGCCCTTTTCACGTG 60.038 55.000 25.70 9.94 0.00 4.49 F
504 506 2.835764 TCACGTGAAAATAGGGCTAGGT 59.164 45.455 17.62 0.00 0.00 3.08 F
848 850 4.614284 GCGCATTATGTCAACTGAATATGC 59.386 41.667 0.30 0.00 0.00 3.14 F
2151 2161 3.010027 TGGAGCAGGAATTCAACATGGTA 59.990 43.478 7.93 0.00 30.35 3.25 F
2966 2979 1.185315 CCCCTTTCCGCAAATGTGAT 58.815 50.000 0.00 0.00 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1589 1599 1.394917 CATCACCTTGTGCTACTTCGC 59.605 52.381 0.00 0.0 32.98 4.70 R
2151 2161 2.639839 TCCCAGCTTACTTCTCTTTGCT 59.360 45.455 0.00 0.0 0.00 3.91 R
2297 2307 9.341899 CTTTAGTTTTATCATCAAAAACCTCCG 57.658 33.333 7.59 0.0 44.29 4.63 R
3482 3573 1.572415 AGGCATCAGGTTCCATCCATT 59.428 47.619 0.00 0.0 0.00 3.16 R
4886 5123 0.687354 CCTGGTTCAGCTACCACTGT 59.313 55.000 4.12 0.0 43.14 3.55 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
191 193 2.024273 ACGTATCCCTCTCCTTTCCTCA 60.024 50.000 0.00 0.00 0.00 3.86
454 456 7.766738 TCTTATCCGTGTTATTTACAAGATGCA 59.233 33.333 0.00 0.00 38.34 3.96
460 462 7.243487 CGTGTTATTTACAAGATGCAGATTGT 58.757 34.615 19.58 19.58 42.15 2.71
489 491 0.038343 CATTGGGCCCTTTTCACGTG 60.038 55.000 25.70 9.94 0.00 4.49
504 506 2.835764 TCACGTGAAAATAGGGCTAGGT 59.164 45.455 17.62 0.00 0.00 3.08
555 557 6.340522 ACTTTTTCTTTGAAAGGTGATGGTG 58.659 36.000 4.94 0.00 38.20 4.17
653 655 5.869344 TGAAGCTGTAGTGTGATTCATGTAC 59.131 40.000 0.00 0.00 0.00 2.90
737 739 7.663905 ACTGAATTTGTGCAGTACATTTACCTA 59.336 33.333 0.00 0.00 43.10 3.08
848 850 4.614284 GCGCATTATGTCAACTGAATATGC 59.386 41.667 0.30 0.00 0.00 3.14
872 874 6.813152 GCCTGAATGTTTGCAGTACATTTAAT 59.187 34.615 22.45 7.75 44.05 1.40
1336 1343 7.563724 AGGGTTATTACTCCAGTTAAGTCAA 57.436 36.000 0.00 0.00 0.00 3.18
1550 1560 7.039714 TGACAGTAGTGAAGAACATGTAGATGT 60.040 37.037 4.09 0.00 45.24 3.06
1589 1599 8.148999 TGATGAGGATTTCTATGAGAGTGATTG 58.851 37.037 0.00 0.00 0.00 2.67
2151 2161 3.010027 TGGAGCAGGAATTCAACATGGTA 59.990 43.478 7.93 0.00 30.35 3.25
2835 2845 4.292186 TCTATGGGCAATAGCAAGATCC 57.708 45.455 3.86 0.00 44.61 3.36
2966 2979 1.185315 CCCCTTTCCGCAAATGTGAT 58.815 50.000 0.00 0.00 0.00 3.06
3358 3449 5.927689 GGATCTCAACATGAATAGCTCTGAG 59.072 44.000 0.00 0.00 0.00 3.35
3434 3525 1.610624 GGCACGAGAGGATTGAACCAA 60.611 52.381 0.00 0.00 0.00 3.67
3482 3573 4.278170 CAGTGGAAAACTACAAGGATTGCA 59.722 41.667 0.00 0.00 44.18 4.08
3505 3596 3.597182 TGGATGGAACCTGATGCCTATA 58.403 45.455 0.00 0.00 0.00 1.31
3690 3781 2.827800 TCTATATGTGGAGCTGCTGC 57.172 50.000 14.73 14.73 40.05 5.25
3783 3874 5.605908 AGGAGGAAGAAGATTATGCTGATCA 59.394 40.000 0.00 0.00 0.00 2.92
4436 4664 4.887071 TGGCTTCTACAATCTGTTGTTTGT 59.113 37.500 0.00 0.00 46.07 2.83
4470 4698 2.192187 TGCACATCAAGCGCCACAA 61.192 52.632 2.29 0.00 33.85 3.33
4855 5092 2.307934 AACAAATTTGTGCTTGCCGT 57.692 40.000 23.93 3.36 41.31 5.68
4886 5123 4.724602 GAGGCACGACGAGCAGCA 62.725 66.667 18.77 0.00 0.00 4.41
4890 5127 2.355126 CACGACGAGCAGCACAGT 60.355 61.111 0.00 0.00 0.00 3.55
5243 5490 6.071278 CCACTTCTACTACTTTCCTGCTACTT 60.071 42.308 0.00 0.00 0.00 2.24
5562 5809 2.814183 ATTCCTCGTCGTCGCGCTTT 62.814 55.000 5.56 0.00 36.96 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
454 456 1.541147 CAATGCCGTCCACAACAATCT 59.459 47.619 0.00 0.00 0.00 2.40
460 462 2.988684 GCCCAATGCCGTCCACAA 60.989 61.111 0.00 0.00 0.00 3.33
489 491 7.418597 CCCCAAATAAAACCTAGCCCTATTTTC 60.419 40.741 0.00 0.00 0.00 2.29
504 506 5.420739 GCTGACTGATAACCCCCAAATAAAA 59.579 40.000 0.00 0.00 0.00 1.52
555 557 1.745232 TCGATGGCCACATAACCAAC 58.255 50.000 8.16 0.00 39.96 3.77
653 655 9.778993 CATTCAGTAAACTCCATTCACATTTAG 57.221 33.333 0.00 0.00 0.00 1.85
737 739 6.318648 TCAGTTAACAGAGTCTGCACAAATTT 59.681 34.615 20.31 7.52 34.37 1.82
848 850 8.649841 CAATTAAATGTACTGCAAACATTCAGG 58.350 33.333 21.18 10.28 44.66 3.86
872 874 4.366586 TGCACGCATTCAGAAAAATTCAA 58.633 34.783 0.00 0.00 0.00 2.69
889 891 7.484641 ACATACTTTAGTTAAATGCATTGCACG 59.515 33.333 14.66 3.04 43.04 5.34
1240 1244 1.839994 CAGGGTGTCACCATGGTCTAT 59.160 52.381 25.77 0.00 45.60 1.98
1336 1343 5.188751 TGTCCACATTTTCTTTTCCCTTTGT 59.811 36.000 0.00 0.00 0.00 2.83
1550 1560 8.378565 AGAAATCCTCATCAGTTTCAACTTCTA 58.621 33.333 0.00 0.00 37.08 2.10
1589 1599 1.394917 CATCACCTTGTGCTACTTCGC 59.605 52.381 0.00 0.00 32.98 4.70
2151 2161 2.639839 TCCCAGCTTACTTCTCTTTGCT 59.360 45.455 0.00 0.00 0.00 3.91
2297 2307 9.341899 CTTTAGTTTTATCATCAAAAACCTCCG 57.658 33.333 7.59 0.00 44.29 4.63
2955 2968 7.015226 TGTTTAGAAGGATATCACATTTGCG 57.985 36.000 4.83 0.00 0.00 4.85
2966 2979 8.375506 ACTTCACTCATGTTGTTTAGAAGGATA 58.624 33.333 16.22 0.00 36.47 2.59
3110 3201 2.822707 ATTGGCAGCTCTCTTCCATT 57.177 45.000 0.00 0.00 35.57 3.16
3358 3449 4.560513 GCAGATAGCTCCCATCTCTTACAC 60.561 50.000 0.00 0.00 41.15 2.90
3434 3525 2.089980 GCACTCATGAACCATGCTCTT 58.910 47.619 11.64 0.00 41.18 2.85
3482 3573 1.572415 AGGCATCAGGTTCCATCCATT 59.428 47.619 0.00 0.00 0.00 3.16
3505 3596 4.437682 TTCCCACTTCTTCATGTCACTT 57.562 40.909 0.00 0.00 0.00 3.16
3690 3781 2.041081 TGGTGTCCCTTCTTGTTATGGG 59.959 50.000 0.00 0.00 40.95 4.00
3783 3874 4.136796 TGAACTTACAGCAGTGATGCTTT 58.863 39.130 8.62 0.00 43.52 3.51
4145 4289 2.751259 GCATCTGCATTTCTTCTGACCA 59.249 45.455 0.00 0.00 41.59 4.02
4342 4570 2.992847 TCTGTTCCTCCTGTGGTAGA 57.007 50.000 0.00 0.00 0.00 2.59
4436 4664 2.575735 TGTGCACTCCCTCCATCATTTA 59.424 45.455 19.41 0.00 0.00 1.40
4470 4698 1.562942 TCCTCCTCTGCTTGCATGAAT 59.437 47.619 3.33 0.00 0.00 2.57
4855 5092 3.385384 CCTCCTCTGACTGCGCCA 61.385 66.667 4.18 0.00 0.00 5.69
4886 5123 0.687354 CCTGGTTCAGCTACCACTGT 59.313 55.000 4.12 0.00 43.14 3.55
4890 5127 1.207488 ATGGCCTGGTTCAGCTACCA 61.207 55.000 8.11 8.11 45.73 3.25
4972 5209 1.891919 GGCTCGTTGTGTCTGGCAA 60.892 57.895 0.00 0.00 0.00 4.52
5243 5490 2.618241 GCTTGTGTGTCATCCTGTTTGA 59.382 45.455 0.00 0.00 0.00 2.69
5438 5685 6.129115 GCATGTGTGTTGTGTTATTTGCTTAG 60.129 38.462 0.00 0.00 0.00 2.18


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

AutoCloner maintained by Alex Coulton.