Multiple sequence alignment - TraesCS5B01G085200

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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 TraesCS5B01G085200 chr5B 100.000 4632 0 0 1 4632 107948149 107943518 0.000000e+00 8554.0
1 TraesCS5B01G085200 chr5B 97.443 4653 94 17 1 4632 108054052 108049404 0.000000e+00 7910.0
2 TraesCS5B01G085200 chr5A 96.671 2133 70 1 1321 3452 104147508 104149640 0.000000e+00 3544.0
3 TraesCS5B01G085200 chr5A 96.736 1195 23 5 3441 4632 104149770 104150951 0.000000e+00 1977.0
4 TraesCS5B01G085200 chr5A 91.845 466 25 10 786 1243 104147058 104147518 5.050000e-179 638.0
5 TraesCS5B01G085200 chr5A 86.486 111 8 1 691 794 104144562 104144672 1.050000e-21 115.0
6 TraesCS5B01G085200 chr1D 85.724 1534 179 27 2080 3591 45695123 45693608 0.000000e+00 1583.0
7 TraesCS5B01G085200 chr1D 81.258 795 106 19 2327 3110 46236510 46237272 1.840000e-168 603.0
8 TraesCS5B01G085200 chr1D 91.832 404 29 4 1 402 448967891 448968292 1.130000e-155 560.0
9 TraesCS5B01G085200 chr1D 77.391 460 80 18 4176 4623 45687857 45687410 7.690000e-63 252.0
10 TraesCS5B01G085200 chr4B 95.978 547 18 3 1 545 650862419 650862963 0.000000e+00 885.0
11 TraesCS5B01G085200 chr4B 96.911 518 16 0 2 519 650794103 650794620 0.000000e+00 869.0
12 TraesCS5B01G085200 chr4B 91.521 401 31 3 4 402 396636670 396636271 2.440000e-152 549.0
13 TraesCS5B01G085200 chr4B 91.176 68 2 4 1248 1314 184333986 184334050 6.380000e-14 89.8
14 TraesCS5B01G085200 chr6B 96.241 532 19 1 1 532 445887002 445887532 0.000000e+00 870.0
15 TraesCS5B01G085200 chr2A 92.697 534 34 5 4 535 240134465 240133935 0.000000e+00 765.0
16 TraesCS5B01G085200 chr2A 90.299 134 12 1 410 543 81681459 81681591 1.710000e-39 174.0
17 TraesCS5B01G085200 chr2A 90.299 134 12 1 410 543 81685893 81686025 1.710000e-39 174.0
18 TraesCS5B01G085200 chr2A 91.429 70 5 1 786 854 23484314 23484245 1.370000e-15 95.3
19 TraesCS5B01G085200 chr2A 87.013 77 7 3 1244 1318 93987731 93987806 2.970000e-12 84.2
20 TraesCS5B01G085200 chr4D 91.521 401 32 2 4 402 81168839 81168439 6.770000e-153 551.0
21 TraesCS5B01G085200 chr3A 91.521 401 30 4 4 402 609670102 609669704 2.440000e-152 549.0
22 TraesCS5B01G085200 chr3A 92.857 70 4 1 786 854 31797136 31797205 2.950000e-17 100.0
23 TraesCS5B01G085200 chr1A 83.932 585 64 14 2080 2656 45756539 45755977 2.450000e-147 532.0
24 TraesCS5B01G085200 chr4A 92.121 165 12 1 370 533 580666066 580666230 1.000000e-56 231.0
25 TraesCS5B01G085200 chr7A 89.286 140 15 0 410 549 116146737 116146598 4.760000e-40 176.0
26 TraesCS5B01G085200 chr3B 92.105 76 4 2 1247 1321 368915365 368915291 6.340000e-19 106.0
27 TraesCS5B01G085200 chr3B 92.188 64 4 1 790 852 156620428 156620365 6.380000e-14 89.8
28 TraesCS5B01G085200 chr1B 90.411 73 4 3 1250 1321 611319018 611318948 4.930000e-15 93.5
29 TraesCS5B01G085200 chr6A 90.909 66 4 2 1246 1309 39550539 39550604 2.300000e-13 87.9
30 TraesCS5B01G085200 chr2B 89.706 68 5 2 1248 1313 613917488 613917555 8.260000e-13 86.1
31 TraesCS5B01G085200 chr2B 88.571 70 5 3 1246 1314 257781276 257781343 1.070000e-11 82.4
32 TraesCS5B01G085200 chr5D 88.406 69 7 1 786 853 419036203 419036135 1.070000e-11 82.4
33 TraesCS5B01G085200 chr7B 84.615 78 11 1 1243 1320 375450429 375450505 4.970000e-10 76.8


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 TraesCS5B01G085200 chr5B 107943518 107948149 4631 True 8554.0 8554 100.0000 1 4632 1 chr5B.!!$R1 4631
1 TraesCS5B01G085200 chr5B 108049404 108054052 4648 True 7910.0 7910 97.4430 1 4632 1 chr5B.!!$R2 4631
2 TraesCS5B01G085200 chr5A 104144562 104150951 6389 False 1568.5 3544 92.9345 691 4632 4 chr5A.!!$F1 3941
3 TraesCS5B01G085200 chr1D 45693608 45695123 1515 True 1583.0 1583 85.7240 2080 3591 1 chr1D.!!$R2 1511
4 TraesCS5B01G085200 chr1D 46236510 46237272 762 False 603.0 603 81.2580 2327 3110 1 chr1D.!!$F1 783
5 TraesCS5B01G085200 chr4B 650862419 650862963 544 False 885.0 885 95.9780 1 545 1 chr4B.!!$F3 544
6 TraesCS5B01G085200 chr4B 650794103 650794620 517 False 869.0 869 96.9110 2 519 1 chr4B.!!$F2 517
7 TraesCS5B01G085200 chr6B 445887002 445887532 530 False 870.0 870 96.2410 1 532 1 chr6B.!!$F1 531
8 TraesCS5B01G085200 chr2A 240133935 240134465 530 True 765.0 765 92.6970 4 535 1 chr2A.!!$R2 531
9 TraesCS5B01G085200 chr1A 45755977 45756539 562 True 532.0 532 83.9320 2080 2656 1 chr1A.!!$R1 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
884 3307 1.210204 TCAGAGGAATTGGGCCAGCT 61.210 55.000 6.23 0.0 0.00 4.24 F
1013 3437 1.300465 CATCGATGTCCAGCGGAGG 60.300 63.158 17.50 0.0 41.05 4.30 F
1131 3555 2.744166 CGACCATCAGGCTGTCATTGAT 60.744 50.000 15.27 0.0 39.06 2.57 F
1638 4062 3.194005 ACCAACTTGTGCTATATCCCG 57.806 47.619 0.00 0.0 0.00 5.14 F
1859 4283 4.095932 TGAGTTTGATGAGCAATCTGATGC 59.904 41.667 0.00 0.0 46.78 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 4328 1.268352 TGAATGCCCGGAAAAGAAACG 59.732 47.619 0.73 0.0 0.00 3.60 R
2246 4673 1.421410 GACGTGGCGATAACCAGCAG 61.421 60.000 0.00 0.0 41.46 4.24 R
2729 5160 2.654079 CGGGAGAGGCTCTTGCACT 61.654 63.158 19.80 0.0 41.91 4.40 R
2846 5279 5.774690 AGTTGCCCAGTGAATGAAAGATAAA 59.225 36.000 0.00 0.0 0.00 1.40 R
3792 6379 2.030457 ACTTGACGTTCTCTTTTGCACG 59.970 45.455 0.00 0.0 38.62 5.34 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
251 253 8.996024 AATTTTCTATTTAAACCCACAATCCG 57.004 30.769 0.00 0.00 0.00 4.18
443 446 3.135712 AGGCCCATCGACATACAAATACA 59.864 43.478 0.00 0.00 0.00 2.29
451 454 3.629855 CGACATACAAATACATGGCCCAA 59.370 43.478 0.00 0.00 0.00 4.12
499 502 6.607004 TGAAAAGGACTAAACCAAACCAAA 57.393 33.333 0.00 0.00 0.00 3.28
609 623 7.579761 TTTTTGCAAAAGATTAGGCCAAAAT 57.420 28.000 22.78 3.89 29.47 1.82
611 625 7.579761 TTTGCAAAAGATTAGGCCAAAATTT 57.420 28.000 10.02 0.00 0.00 1.82
620 634 7.386059 AGATTAGGCCAAAATTTAGTGGTTTG 58.614 34.615 5.01 0.00 37.23 2.93
621 635 6.732896 TTAGGCCAAAATTTAGTGGTTTGA 57.267 33.333 5.01 0.00 37.23 2.69
622 636 5.823861 AGGCCAAAATTTAGTGGTTTGAT 57.176 34.783 5.01 0.00 37.23 2.57
701 717 2.287977 TTTCACTCCTCTCAGTCCGA 57.712 50.000 0.00 0.00 0.00 4.55
788 3205 3.258228 ATGCTGACTCGCTTGGCCA 62.258 57.895 0.00 0.00 0.00 5.36
881 3304 2.001803 CCTCAGAGGAATTGGGCCA 58.998 57.895 11.62 0.00 37.67 5.36
884 3307 1.210204 TCAGAGGAATTGGGCCAGCT 61.210 55.000 6.23 0.00 0.00 4.24
1013 3437 1.300465 CATCGATGTCCAGCGGAGG 60.300 63.158 17.50 0.00 41.05 4.30
1131 3555 2.744166 CGACCATCAGGCTGTCATTGAT 60.744 50.000 15.27 0.00 39.06 2.57
1638 4062 3.194005 ACCAACTTGTGCTATATCCCG 57.806 47.619 0.00 0.00 0.00 5.14
1859 4283 4.095932 TGAGTTTGATGAGCAATCTGATGC 59.904 41.667 0.00 0.00 46.78 3.91
2140 4565 5.858381 TCTCTTATATGTCACATGCTTCCC 58.142 41.667 0.00 0.00 0.00 3.97
2246 4673 4.620184 GCTGCAGTTCATTGATCTCAAAAC 59.380 41.667 16.64 0.00 39.55 2.43
2729 5160 8.372877 TGATTAATTTTTCTATCTTGCCCCAA 57.627 30.769 0.00 0.00 0.00 4.12
2846 5279 6.985117 TCTTCTTTAATGTGCAAGCTCAAAT 58.015 32.000 0.64 0.00 0.00 2.32
3280 5726 3.118847 TGTGGAATGCAGTTCAAGCAAAA 60.119 39.130 0.00 0.00 46.27 2.44
3371 5817 0.033228 CAGAGATGTGATCCGCCTCC 59.967 60.000 0.00 0.00 0.00 4.30
3792 6379 9.817365 CATATAACATGTGCATTTAGTTAGCTC 57.183 33.333 0.00 0.00 0.00 4.09
3980 6567 1.402259 CGAGCGGACTGATTAGTGAGT 59.598 52.381 0.00 0.00 37.25 3.41
4338 6928 1.610624 GGCCCTTCGAAGAACATGACA 60.611 52.381 26.61 0.00 45.90 3.58
4345 6935 5.352569 CCTTCGAAGAACATGACAATTAGCT 59.647 40.000 26.61 0.00 45.90 3.32
4379 6969 0.454600 TTATGCTCGGACGTGACCTC 59.545 55.000 0.00 0.00 0.00 3.85
4381 6971 1.938657 ATGCTCGGACGTGACCTCTG 61.939 60.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 167 7.770366 AAACCGGTGGAATAACTAAAAGAAT 57.230 32.000 8.52 0.00 0.00 2.40
240 242 4.638865 GCTAATAAAAGACGGATTGTGGGT 59.361 41.667 0.00 0.00 0.00 4.51
443 446 0.461135 CGCTAAGCAATTTGGGCCAT 59.539 50.000 7.26 0.00 0.00 4.40
451 454 9.716507 CATTTAGTTTATACACGCTAAGCAATT 57.283 29.630 0.00 0.00 0.00 2.32
551 565 3.192466 GGCTTTGGCTCATTTGCTAATG 58.808 45.455 13.83 13.83 37.82 1.90
611 625 8.938906 GGTTTACGAATTTCTATCAAACCACTA 58.061 33.333 17.26 0.00 41.83 2.74
788 3205 5.567037 TCCATCGTCCAAATCAATCCTAT 57.433 39.130 0.00 0.00 0.00 2.57
881 3304 3.615155 GAAATTCTAACAGGCTGGAGCT 58.385 45.455 20.34 2.70 41.70 4.09
884 3307 2.569853 TCGGAAATTCTAACAGGCTGGA 59.430 45.455 20.34 3.42 0.00 3.86
891 3314 6.073222 GCTTTCTTGTCTCGGAAATTCTAACA 60.073 38.462 0.00 0.00 32.15 2.41
1013 3437 0.577269 CATTTCCGTCTCCGATTCGC 59.423 55.000 0.00 0.00 35.63 4.70
1131 3555 2.161808 GTCTTCATCCTCGTCTTCGTCA 59.838 50.000 0.00 0.00 38.33 4.35
1257 3681 1.730612 GTCGGACTTAGGCCTTTTTCG 59.269 52.381 12.58 6.42 0.00 3.46
1638 4062 9.765795 AGTAGAAGCACCAACTATTATTGATAC 57.234 33.333 0.00 0.00 0.00 2.24
1859 4283 7.395190 TGAATATCAGGATTTTGGAACACAG 57.605 36.000 0.00 0.00 39.29 3.66
1904 4328 1.268352 TGAATGCCCGGAAAAGAAACG 59.732 47.619 0.73 0.00 0.00 3.60
2140 4565 6.943981 TCACGTTGACTGAGAAAACAATAAG 58.056 36.000 0.00 0.00 0.00 1.73
2246 4673 1.421410 GACGTGGCGATAACCAGCAG 61.421 60.000 0.00 0.00 41.46 4.24
2678 5107 5.279156 CCAATTCTTGCTTGCTTTACTCCTT 60.279 40.000 0.00 0.00 0.00 3.36
2729 5160 2.654079 CGGGAGAGGCTCTTGCACT 61.654 63.158 19.80 0.00 41.91 4.40
2846 5279 5.774690 AGTTGCCCAGTGAATGAAAGATAAA 59.225 36.000 0.00 0.00 0.00 1.40
3280 5726 6.413052 AGCATGAAGTATCTCAACATCAACT 58.587 36.000 0.00 0.00 31.54 3.16
3548 6135 6.005066 TGTGGAATCATGAAGATACACCAT 57.995 37.500 15.40 0.00 40.89 3.55
3605 6192 5.992217 AGTGTTCCAAGTCATGTAAACTCTC 59.008 40.000 0.00 0.00 28.55 3.20
3792 6379 2.030457 ACTTGACGTTCTCTTTTGCACG 59.970 45.455 0.00 0.00 38.62 5.34
3980 6567 8.437575 AGAAATGAAGAACTGAAGGGTTAGTAA 58.562 33.333 0.00 0.00 0.00 2.24
4215 6805 5.483685 AACTGATAACTAGCTGGTGTGAA 57.516 39.130 2.40 0.00 0.00 3.18
4338 6928 2.373224 GAGGCTTTGGCTGAGCTAATT 58.627 47.619 3.52 0.00 38.98 1.40
4345 6935 1.683011 GCATAAGGAGGCTTTGGCTGA 60.683 52.381 0.00 0.00 38.98 4.26
4379 6969 3.008375 TCTTGGGAAGGATGAGAACACAG 59.992 47.826 0.00 0.00 0.00 3.66
4381 6971 3.008485 ACTCTTGGGAAGGATGAGAACAC 59.992 47.826 0.00 0.00 0.00 3.32
4600 7190 4.100189 CCTCTCTCTGGTGGGTACTAAATG 59.900 50.000 0.00 0.00 0.00 2.32
4609 7199 1.550976 GTACAACCTCTCTCTGGTGGG 59.449 57.143 0.00 0.00 37.93 4.61


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

AutoCloner maintained by Alex Coulton.