Multiple sequence alignment - TraesCS4B01G036000

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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 TraesCS4B01G036000 chr4B 100.000 2549 0 0 1 2549 26118351 26120899 0.000000e+00 4708
1 TraesCS4B01G036000 chr4B 98.010 402 7 1 175 575 26210119 26210520 0.000000e+00 697
2 TraesCS4B01G036000 chr4B 98.010 402 7 1 175 575 26249845 26250246 0.000000e+00 697
3 TraesCS4B01G036000 chr4B 97.512 402 9 1 175 575 26168268 26168669 0.000000e+00 686
4 TraesCS4B01G036000 chr4B 97.264 402 10 1 175 575 26030288 26030689 0.000000e+00 680
5 TraesCS4B01G036000 chr4B 97.264 402 10 1 175 575 26291530 26291931 0.000000e+00 680
6 TraesCS4B01G036000 chr4B 97.015 402 11 1 175 575 26082148 26082549 0.000000e+00 675
7 TraesCS4B01G036000 chr4B 96.517 402 9 2 175 575 25989940 25990337 0.000000e+00 660
8 TraesCS4B01G036000 chr4B 99.408 169 1 0 1 169 25989711 25989879 8.860000e-80 307
9 TraesCS4B01G036000 chr4B 99.408 169 1 0 1 169 26168039 26168207 8.860000e-80 307
10 TraesCS4B01G036000 chr4B 98.817 169 2 0 1 169 26030059 26030227 4.120000e-78 302
11 TraesCS4B01G036000 chr4B 98.817 169 2 0 1 169 26209890 26210058 4.120000e-78 302
12 TraesCS4B01G036000 chr4B 98.817 169 2 0 1 169 26249616 26249784 4.120000e-78 302
13 TraesCS4B01G036000 chr4B 98.817 169 1 1 1 169 26291302 26291469 1.480000e-77 300
14 TraesCS4B01G036000 chr4B 98.225 169 3 0 1 169 26081919 26082087 1.920000e-76 296
15 TraesCS4B01G036000 chr2B 98.744 1991 21 3 562 2549 781094230 781096219 0.000000e+00 3535
16 TraesCS4B01G036000 chr2B 98.840 1982 22 1 569 2549 776449262 776447281 0.000000e+00 3531
17 TraesCS4B01G036000 chr2B 98.838 1980 21 1 572 2549 776222961 776224940 0.000000e+00 3528
18 TraesCS4B01G036000 chr2A 98.838 1980 21 1 572 2549 682509134 682507155 0.000000e+00 3528
19 TraesCS4B01G036000 chr3A 98.789 1982 23 1 569 2549 54951914 54953895 0.000000e+00 3526
20 TraesCS4B01G036000 chr3B 98.787 1979 23 1 572 2549 702857655 702855677 0.000000e+00 3520
21 TraesCS4B01G036000 chr3B 98.592 1989 24 4 564 2549 20305079 20307066 0.000000e+00 3515
22 TraesCS4B01G036000 chr3B 97.333 225 5 1 352 575 412242356 412242132 5.150000e-102 381
23 TraesCS4B01G036000 chr7A 98.641 1987 25 1 565 2549 332474961 332472975 0.000000e+00 3518
24 TraesCS4B01G036000 chr5B 98.689 1983 23 1 570 2549 641128782 641126800 0.000000e+00 3515
25 TraesCS4B01G036000 chr5B 97.881 236 2 3 341 575 393701624 393701857 3.050000e-109 405


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 TraesCS4B01G036000 chr4B 26118351 26120899 2548 False 4708.0 4708 100.0000 1 2549 1 chr4B.!!$F1 2548
1 TraesCS4B01G036000 chr4B 26209890 26210520 630 False 499.5 697 98.4135 1 575 2 chr4B.!!$F6 574
2 TraesCS4B01G036000 chr4B 26249616 26250246 630 False 499.5 697 98.4135 1 575 2 chr4B.!!$F7 574
3 TraesCS4B01G036000 chr4B 26168039 26168669 630 False 496.5 686 98.4600 1 575 2 chr4B.!!$F5 574
4 TraesCS4B01G036000 chr4B 26030059 26030689 630 False 491.0 680 98.0405 1 575 2 chr4B.!!$F3 574
5 TraesCS4B01G036000 chr4B 26291302 26291931 629 False 490.0 680 98.0405 1 575 2 chr4B.!!$F8 574
6 TraesCS4B01G036000 chr4B 26081919 26082549 630 False 485.5 675 97.6200 1 575 2 chr4B.!!$F4 574
7 TraesCS4B01G036000 chr4B 25989711 25990337 626 False 483.5 660 97.9625 1 575 2 chr4B.!!$F2 574
8 TraesCS4B01G036000 chr2B 781094230 781096219 1989 False 3535.0 3535 98.7440 562 2549 1 chr2B.!!$F2 1987
9 TraesCS4B01G036000 chr2B 776447281 776449262 1981 True 3531.0 3531 98.8400 569 2549 1 chr2B.!!$R1 1980
10 TraesCS4B01G036000 chr2B 776222961 776224940 1979 False 3528.0 3528 98.8380 572 2549 1 chr2B.!!$F1 1977
11 TraesCS4B01G036000 chr2A 682507155 682509134 1979 True 3528.0 3528 98.8380 572 2549 1 chr2A.!!$R1 1977
12 TraesCS4B01G036000 chr3A 54951914 54953895 1981 False 3526.0 3526 98.7890 569 2549 1 chr3A.!!$F1 1980
13 TraesCS4B01G036000 chr3B 702855677 702857655 1978 True 3520.0 3520 98.7870 572 2549 1 chr3B.!!$R2 1977
14 TraesCS4B01G036000 chr3B 20305079 20307066 1987 False 3515.0 3515 98.5920 564 2549 1 chr3B.!!$F1 1985
15 TraesCS4B01G036000 chr7A 332472975 332474961 1986 True 3518.0 3518 98.6410 565 2549 1 chr7A.!!$R1 1984
16 TraesCS4B01G036000 chr5B 641126800 641128782 1982 True 3515.0 3515 98.6890 570 2549 1 chr5B.!!$R1 1979

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
237 293 0.745486 CTGCAATGAGGTCATCGCCA 60.745 55.0 0.51 0.0 35.51 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 1804 0.48069 TGGCCCAAGAGCAACCTTTA 59.519 50.0 0.0 0.0 0.0 1.85 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
136 137 1.408127 GCTACCCCACACACATGCATA 60.408 52.381 0.00 0.0 0.00 3.14
169 170 2.746362 CCAGGTTCATTCAGTCAAGAGC 59.254 50.000 0.00 0.0 0.00 4.09
170 171 3.558746 CCAGGTTCATTCAGTCAAGAGCT 60.559 47.826 0.00 0.0 0.00 4.09
171 172 4.323028 CCAGGTTCATTCAGTCAAGAGCTA 60.323 45.833 0.00 0.0 0.00 3.32
173 174 5.702670 CAGGTTCATTCAGTCAAGAGCTAAA 59.297 40.000 0.00 0.0 0.00 1.85
176 232 6.597280 GGTTCATTCAGTCAAGAGCTAAAGAT 59.403 38.462 0.00 0.0 0.00 2.40
213 269 1.838715 AGATCTGGATGCTGTTGCTCT 59.161 47.619 0.00 0.0 40.48 4.09
237 293 0.745486 CTGCAATGAGGTCATCGCCA 60.745 55.000 0.51 0.0 35.51 5.69
286 342 2.829384 GGGGGTGTGTTCTCCTGCA 61.829 63.158 0.00 0.0 0.00 4.41
910 966 2.403378 GCGAGAGAGAGAGCACGGT 61.403 63.158 0.00 0.0 0.00 4.83
1041 1097 3.071206 ACCTCGCGGATGCAGAGT 61.071 61.111 6.13 0.0 42.97 3.24
1078 1134 1.957562 CCTGTCTTCGTCTGTCCGT 59.042 57.895 0.00 0.0 0.00 4.69
1085 1141 4.293648 CGTCTGTCCGTGGTGCCA 62.294 66.667 0.00 0.0 0.00 4.92
1137 1193 0.530744 CGAGGAACCAGAATCGTCCA 59.469 55.000 0.00 0.0 0.00 4.02
1272 1328 2.386661 TTCTTTGGGTCGATGCTCTC 57.613 50.000 0.00 0.0 0.00 3.20
1579 1635 9.709495 TGAAGGAATTTGTAATCTTGAAATTGG 57.291 29.630 0.00 0.0 31.10 3.16
1748 1804 2.165998 GCTCTGCCTTTCTGTCCAAAT 58.834 47.619 0.00 0.0 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
213 269 2.715046 GATGACCTCATTGCAGACCAA 58.285 47.619 0.00 0.00 36.57 3.67
237 293 4.522490 GTTCGAGAACCTGAGACGCAGT 62.522 54.545 5.44 0.00 43.33 4.40
286 342 4.285020 TCTGTAGATGACAATCCTCTGCT 58.715 43.478 2.14 0.00 37.70 4.24
549 605 6.587226 CCCTTAATCAAATGACAACACATGTG 59.413 38.462 24.25 24.25 44.12 3.21
782 838 0.890996 CTCTTTGCTGGGTCCCACAC 60.891 60.000 6.47 2.50 0.00 3.82
910 966 1.748403 CATAGCTAGCTTCCCGCCA 59.252 57.895 24.88 2.48 40.39 5.69
1085 1141 1.524621 CTTCGATCAATGCCCGCCT 60.525 57.895 0.00 0.00 0.00 5.52
1093 1149 4.020218 TGTCTGAGAAACCCTTCGATCAAT 60.020 41.667 0.00 0.00 36.61 2.57
1137 1193 0.526211 TCTCGCTGCACACGTAGAAT 59.474 50.000 0.00 0.00 0.00 2.40
1272 1328 2.897436 TCATTCATCAGAGTCTTGGCG 58.103 47.619 0.00 0.00 0.00 5.69
1748 1804 0.480690 TGGCCCAAGAGCAACCTTTA 59.519 50.000 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.