Multiple sequence alignment - TraesCS4B01G025800

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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 TraesCS4B01G025800 chr4B 100.000 2549 0 0 1 2549 18580899 18578351 0 4708
1 TraesCS4B01G025800 chr6B 97.222 1980 46 6 577 2549 660437743 660435766 0 3343
2 TraesCS4B01G025800 chr6B 96.181 576 22 0 1 576 13568678 13568103 0 942
3 TraesCS4B01G025800 chr6B 96.007 576 23 0 1 576 710043350 710042775 0 937
4 TraesCS4B01G025800 chr6B 96.007 576 23 0 1 576 712900370 712899795 0 937
5 TraesCS4B01G025800 chr6B 95.833 576 24 0 1 576 712967401 712966826 0 931
6 TraesCS4B01G025800 chr7B 97.026 1984 51 5 574 2549 552932146 552930163 0 3330
7 TraesCS4B01G025800 chr7B 96.776 1985 55 6 572 2549 552850593 552852575 0 3302
8 TraesCS4B01G025800 chr7A 97.072 1981 51 4 576 2549 701581940 701583920 0 3330
9 TraesCS4B01G025800 chr6A 97.204 1967 49 3 577 2537 617222869 617220903 0 3323
10 TraesCS4B01G025800 chr5A 96.919 1980 55 3 576 2549 459744880 459746859 0 3314
11 TraesCS4B01G025800 chr4A 97.011 1974 52 4 571 2537 36562907 36564880 0 3312
12 TraesCS4B01G025800 chr3B 96.919 1980 52 4 577 2549 379294093 379296070 0 3310
13 TraesCS4B01G025800 chr1A 96.918 1979 53 5 577 2549 22791529 22793505 0 3310
14 TraesCS4B01G025800 chr1B 96.354 576 21 0 1 576 672994541 672995116 0 948
15 TraesCS4B01G025800 chr1B 96.194 578 22 0 1 578 13218293 13217716 0 946
16 TraesCS4B01G025800 chrUn 96.007 576 23 0 1 576 87673849 87674424 0 937
17 TraesCS4B01G025800 chr2B 95.660 576 25 0 1 576 777756552 777755977 0 926
18 TraesCS4B01G025800 chr5B 95.296 574 27 0 3 576 522647554 522646981 0 911


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 TraesCS4B01G025800 chr4B 18578351 18580899 2548 True 4708 4708 100.000 1 2549 1 chr4B.!!$R1 2548
1 TraesCS4B01G025800 chr6B 660435766 660437743 1977 True 3343 3343 97.222 577 2549 1 chr6B.!!$R2 1972
2 TraesCS4B01G025800 chr6B 13568103 13568678 575 True 942 942 96.181 1 576 1 chr6B.!!$R1 575
3 TraesCS4B01G025800 chr6B 710042775 710043350 575 True 937 937 96.007 1 576 1 chr6B.!!$R3 575
4 TraesCS4B01G025800 chr6B 712899795 712900370 575 True 937 937 96.007 1 576 1 chr6B.!!$R4 575
5 TraesCS4B01G025800 chr6B 712966826 712967401 575 True 931 931 95.833 1 576 1 chr6B.!!$R5 575
6 TraesCS4B01G025800 chr7B 552930163 552932146 1983 True 3330 3330 97.026 574 2549 1 chr7B.!!$R1 1975
7 TraesCS4B01G025800 chr7B 552850593 552852575 1982 False 3302 3302 96.776 572 2549 1 chr7B.!!$F1 1977
8 TraesCS4B01G025800 chr7A 701581940 701583920 1980 False 3330 3330 97.072 576 2549 1 chr7A.!!$F1 1973
9 TraesCS4B01G025800 chr6A 617220903 617222869 1966 True 3323 3323 97.204 577 2537 1 chr6A.!!$R1 1960
10 TraesCS4B01G025800 chr5A 459744880 459746859 1979 False 3314 3314 96.919 576 2549 1 chr5A.!!$F1 1973
11 TraesCS4B01G025800 chr4A 36562907 36564880 1973 False 3312 3312 97.011 571 2537 1 chr4A.!!$F1 1966
12 TraesCS4B01G025800 chr3B 379294093 379296070 1977 False 3310 3310 96.919 577 2549 1 chr3B.!!$F1 1972
13 TraesCS4B01G025800 chr1A 22791529 22793505 1976 False 3310 3310 96.918 577 2549 1 chr1A.!!$F1 1972
14 TraesCS4B01G025800 chr1B 672994541 672995116 575 False 948 948 96.354 1 576 1 chr1B.!!$F1 575
15 TraesCS4B01G025800 chr1B 13217716 13218293 577 True 946 946 96.194 1 578 1 chr1B.!!$R1 577
16 TraesCS4B01G025800 chrUn 87673849 87674424 575 False 937 937 96.007 1 576 1 chrUn.!!$F1 575
17 TraesCS4B01G025800 chr2B 777755977 777756552 575 True 926 926 95.660 1 576 1 chr2B.!!$R1 575
18 TraesCS4B01G025800 chr5B 522646981 522647554 573 True 911 911 95.296 3 576 1 chr5B.!!$R1 573

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
417 418 0.035915 GCCTGTTTGTCTCCTCCTCC 60.036 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 1767 0.74299 TACGCTCTGAATTTGGCCCG 60.743 55.0 0.0 0.0 0.0 6.13 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
151 152 4.213564 TCAAAAGGTGTTGCATTGGTTT 57.786 36.364 0.00 0.00 0.00 3.27
203 204 7.908230 TCATAAAGCTTTTGAAAAGCAAACTG 58.092 30.769 35.33 26.67 45.64 3.16
256 257 0.442310 CAACTCCATGTAACCACGCG 59.558 55.000 3.53 3.53 0.00 6.01
405 406 1.821216 CTATGTTCCACGGCCTGTTT 58.179 50.000 0.00 0.00 0.00 2.83
417 418 0.035915 GCCTGTTTGTCTCCTCCTCC 60.036 60.000 0.00 0.00 0.00 4.30
420 421 1.827969 CTGTTTGTCTCCTCCTCCGAT 59.172 52.381 0.00 0.00 0.00 4.18
423 424 2.758979 GTTTGTCTCCTCCTCCGATGTA 59.241 50.000 0.00 0.00 0.00 2.29
491 492 2.089980 GTGCAGATTCTTGCTGACCAT 58.910 47.619 0.00 0.00 44.38 3.55
532 533 5.072741 GTGGGGATAACTTGTGCATATCAT 58.927 41.667 6.60 0.00 0.00 2.45
609 614 0.840617 TTTGCCCTCAGTGGTGTGTA 59.159 50.000 0.00 0.00 0.00 2.90
628 633 2.262423 ACTCAGTTTTGCCCTCAGAC 57.738 50.000 0.00 0.00 0.00 3.51
657 662 1.144913 TGCTCAGTTTTGCCCCTAGTT 59.855 47.619 0.00 0.00 0.00 2.24
768 773 3.426615 ACGGCCAATTTTATTCAGACCA 58.573 40.909 2.24 0.00 0.00 4.02
797 802 2.674380 GCTTGTGGGACCCAGCAG 60.674 66.667 15.52 13.94 32.34 4.24
850 855 2.295253 GCTATATAAGCGGGCGACAT 57.705 50.000 0.00 0.00 42.53 3.06
1073 1078 2.224281 TGAACATGCCTGTCTTCGTCTT 60.224 45.455 0.00 0.00 33.36 3.01
1227 1232 3.841643 GAGCAATGGGTTGATCTGTTTG 58.158 45.455 0.00 0.00 45.03 2.93
1282 1287 0.392193 CGATGCTCTGGCCAAGACTT 60.392 55.000 7.01 0.00 37.74 3.01
1293 1298 4.346730 TGGCCAAGACTTTGATGAATGAT 58.653 39.130 0.61 0.00 36.36 2.45
1321 1326 4.660168 AGAAGAGCATGAAGAATGGTTGT 58.340 39.130 0.00 0.00 46.95 3.32
1509 1514 5.772004 TGGGCATTTGTAGGTATGGTAATT 58.228 37.500 0.00 0.00 0.00 1.40
1555 1560 6.653526 TGTATGGAAAGGCATGAATTATGG 57.346 37.500 0.00 0.00 37.26 2.74
1651 1656 8.612619 GTTGAAACAAATAGAGAAGAAGTGACA 58.387 33.333 0.00 0.00 0.00 3.58
1728 1733 5.677567 TGATCAATGAAATGCAGCTCTCTA 58.322 37.500 0.00 0.00 0.00 2.43
1834 1839 2.701951 CTGCATCCAATTAGGCCCATTT 59.298 45.455 0.00 0.00 37.29 2.32
1835 1840 2.435069 TGCATCCAATTAGGCCCATTTG 59.565 45.455 0.00 0.00 37.29 2.32
1857 1862 3.991773 GGGGGTTTTCTTGCGTATTTTTC 59.008 43.478 0.00 0.00 0.00 2.29
2185 2191 1.609794 GGGACTCGAACCCAGGACT 60.610 63.158 18.78 0.00 46.05 3.85
2217 2223 1.671054 GTGTTTAGGGCTGCGCTGA 60.671 57.895 27.01 17.69 0.00 4.26
2359 2371 4.693095 TGGTTTTCCTTTGTTTTGCACTTC 59.307 37.500 0.00 0.00 41.38 3.01
2366 2378 8.553459 TTCCTTTGTTTTGCACTTCAATTTTA 57.447 26.923 0.00 0.00 34.12 1.52
2448 2460 1.276989 TGGTTTAGGGTTAGAGTGGCG 59.723 52.381 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 152 3.948719 GGGGCTTGGTCGTGTCCA 61.949 66.667 0.00 0.00 35.49 4.02
203 204 1.077930 GCCTCCGGTTTACCCCTTC 60.078 63.158 0.00 0.00 0.00 3.46
256 257 5.116882 GGGGTATCTGTTCTGTTACATCAC 58.883 45.833 0.00 0.00 0.00 3.06
328 329 9.295214 CGGCTCTACTCATTTACATATTATGAG 57.705 37.037 10.62 9.18 46.73 2.90
341 342 3.997672 GCCATCGGCTCTACTCATT 57.002 52.632 0.00 0.00 46.69 2.57
405 406 1.746171 CGTACATCGGAGGAGGAGACA 60.746 57.143 0.00 0.00 35.71 3.41
417 418 4.352039 AGCATAAAGACTCACGTACATCG 58.648 43.478 0.00 0.00 46.00 3.84
420 421 4.436986 CGAGAGCATAAAGACTCACGTACA 60.437 45.833 0.00 0.00 40.58 2.90
423 424 2.747989 TCGAGAGCATAAAGACTCACGT 59.252 45.455 9.10 0.00 44.13 4.49
491 492 2.474924 CCTTGGGAGGGACCTTTCA 58.525 57.895 0.00 0.00 39.55 2.69
532 533 0.250234 CGGCTCATCCAAGACCAGAA 59.750 55.000 0.00 0.00 34.01 3.02
609 614 1.541233 CGTCTGAGGGCAAAACTGAGT 60.541 52.381 0.00 0.00 0.00 3.41
628 633 1.710249 CAAAACTGAGCACAATTCGCG 59.290 47.619 0.00 0.00 0.00 5.87
768 773 3.286751 ACAAGCCACGCGTGCAAT 61.287 55.556 33.17 17.72 41.40 3.56
797 802 0.179140 CTCTCTGCTCAACGGCTCTC 60.179 60.000 0.00 0.00 0.00 3.20
867 872 3.616721 ACCGCCGTGCTCTCTGTT 61.617 61.111 0.00 0.00 0.00 3.16
894 899 2.705821 CCGCCGTGCTCTCTCTCTT 61.706 63.158 0.00 0.00 0.00 2.85
1054 1059 2.550830 AAGACGAAGACAGGCATGTT 57.449 45.000 5.07 0.00 40.68 2.71
1190 1195 0.389948 GCTCAAACATCCCGACGACT 60.390 55.000 0.00 0.00 0.00 4.18
1227 1232 1.200716 CATGTCACCTGCATGAACACC 59.799 52.381 0.00 0.00 44.60 4.16
1282 1287 5.066117 GCTCTTCTTGCAGATCATTCATCAA 59.934 40.000 0.00 0.00 33.29 2.57
1293 1298 3.690475 TCTTCATGCTCTTCTTGCAGA 57.310 42.857 0.00 0.00 44.04 4.26
1388 1393 2.214376 AGCTAGCTCTCTGTCAGTGT 57.786 50.000 12.68 0.00 0.00 3.55
1509 1514 4.991153 TTTCAACATTACAACCAGTGCA 57.009 36.364 0.00 0.00 0.00 4.57
1728 1733 3.297134 TTTTGGACAGAAAGGCAGAGT 57.703 42.857 0.00 0.00 0.00 3.24
1760 1765 1.305219 CGCTCTGAATTTGGCCCGAA 61.305 55.000 0.00 0.00 0.00 4.30
1762 1767 0.742990 TACGCTCTGAATTTGGCCCG 60.743 55.000 0.00 0.00 0.00 6.13
1834 1839 2.296073 AATACGCAAGAAAACCCCCA 57.704 45.000 0.00 0.00 43.62 4.96
1835 1840 3.671008 AAAATACGCAAGAAAACCCCC 57.329 42.857 0.00 0.00 43.62 5.40
1876 1881 7.922278 TCAGCATTATGATTTACTGCCAAAATC 59.078 33.333 0.00 8.00 41.60 2.17
1881 1886 6.377996 AGTTTCAGCATTATGATTTACTGCCA 59.622 34.615 0.00 0.00 33.34 4.92
1932 1937 3.149005 ACCTTAATTGTTTGGCTCCGA 57.851 42.857 0.00 0.00 0.00 4.55
1964 1969 7.346751 TGAATTGGATTAATTAACAGCTCCC 57.653 36.000 11.38 3.60 39.06 4.30
2121 2126 6.591448 GCATTTTCCACCCTTCATTTCTTTAG 59.409 38.462 0.00 0.00 0.00 1.85
2126 2131 3.996363 GTGCATTTTCCACCCTTCATTTC 59.004 43.478 0.00 0.00 0.00 2.17
2185 2191 1.251527 AAACACCACAAACCCACGCA 61.252 50.000 0.00 0.00 0.00 5.24
2217 2223 1.344763 GCCATCTGTCCTAGCGGTTAT 59.655 52.381 0.00 0.00 0.00 1.89
2301 2313 2.290641 GCAAACATTCACGGTCTCACTT 59.709 45.455 0.00 0.00 0.00 3.16
2359 2371 5.538433 TCAACCTTCCAACCCTCTAAAATTG 59.462 40.000 0.00 0.00 0.00 2.32
2366 2378 3.680777 TTTTCAACCTTCCAACCCTCT 57.319 42.857 0.00 0.00 0.00 3.69
2448 2460 6.599356 TTCCCTTTAAATCCTAAACCAAGC 57.401 37.500 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.