Multiple sequence alignment - TraesCS2A01G296600

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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 TraesCS2A01G296600 chr2A 100.000 2348 0 0 1 2348 510803664 510806011 0.000000e+00 4337
1 TraesCS2A01G296600 chr2D 96.736 2359 47 12 1 2348 376813673 376816012 0.000000e+00 3903
2 TraesCS2A01G296600 chr2B 95.089 2362 64 23 1 2348 448250708 448253031 0.000000e+00 3672
3 TraesCS2A01G296600 chr4B 95.965 2181 54 15 176 2348 640325454 640327608 0.000000e+00 3509
4 TraesCS2A01G296600 chr4B 93.048 187 4 4 1 181 640324554 640324737 4.980000e-67 265
5 TraesCS2A01G296600 chr4B 92.513 187 5 4 1 181 640329565 640329382 2.310000e-65 259


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 TraesCS2A01G296600 chr2A 510803664 510806011 2347 False 4337 4337 100.0000 1 2348 1 chr2A.!!$F1 2347
1 TraesCS2A01G296600 chr2D 376813673 376816012 2339 False 3903 3903 96.7360 1 2348 1 chr2D.!!$F1 2347
2 TraesCS2A01G296600 chr2B 448250708 448253031 2323 False 3672 3672 95.0890 1 2348 1 chr2B.!!$F1 2347
3 TraesCS2A01G296600 chr4B 640324554 640327608 3054 False 1887 3509 94.5065 1 2348 2 chr4B.!!$F1 2347

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
449 1188 0.032416 ACTACATACCCTGCCTCCGT 60.032 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 2115 1.266718 GCTTTTCTTGATGTCGGTGCA 59.733 47.619 0.0 0.0 0.0 4.57 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
189 921 4.743057 TGTGTCTATCTTCCATGTCCAG 57.257 45.455 0.00 0.00 0.00 3.86
360 1099 6.787458 TGGATTAGAGCCCTTAATATCAGTGA 59.213 38.462 0.00 0.00 0.00 3.41
381 1120 6.206829 AGTGACAAGCTTTCATTAGGGTAAAC 59.793 38.462 12.42 2.21 0.00 2.01
401 1140 4.470334 ACAGGAAAGAAAAGCAAAGCAA 57.530 36.364 0.00 0.00 0.00 3.91
402 1141 4.831107 ACAGGAAAGAAAAGCAAAGCAAA 58.169 34.783 0.00 0.00 0.00 3.68
403 1142 4.872124 ACAGGAAAGAAAAGCAAAGCAAAG 59.128 37.500 0.00 0.00 0.00 2.77
404 1143 3.873361 AGGAAAGAAAAGCAAAGCAAAGC 59.127 39.130 0.00 0.00 0.00 3.51
405 1144 3.622612 GGAAAGAAAAGCAAAGCAAAGCA 59.377 39.130 0.00 0.00 0.00 3.91
441 1180 6.015991 AGTCTAGCTGTAACTACATACCCT 57.984 41.667 0.00 0.00 35.36 4.34
449 1188 0.032416 ACTACATACCCTGCCTCCGT 60.032 55.000 0.00 0.00 0.00 4.69
546 1285 6.933514 AACACAAAATATTCAACCCATCCT 57.066 33.333 0.00 0.00 0.00 3.24
605 1344 0.442310 CCTCGGCGTTGTACAACATG 59.558 55.000 32.07 22.18 41.20 3.21
630 1369 0.916086 AGGGAGAGCGAGAGAGAGAA 59.084 55.000 0.00 0.00 0.00 2.87
631 1370 1.134098 AGGGAGAGCGAGAGAGAGAAG 60.134 57.143 0.00 0.00 0.00 2.85
632 1371 1.408266 GGGAGAGCGAGAGAGAGAAGT 60.408 57.143 0.00 0.00 0.00 3.01
640 1379 5.594926 AGCGAGAGAGAGAAGTAGTAGTAC 58.405 45.833 0.00 0.00 0.00 2.73
975 1714 7.731882 TCCATAAGTTCAACGTTTTGATGTA 57.268 32.000 0.00 0.00 41.50 2.29
981 1720 5.238432 AGTTCAACGTTTTGATGTATGCAGA 59.762 36.000 0.00 0.00 41.50 4.26
1065 1804 2.125350 CTGAACCTCTCGCTGCCC 60.125 66.667 0.00 0.00 0.00 5.36
1173 1912 3.172106 TGGTCCAACAGCCCCGAA 61.172 61.111 0.00 0.00 0.00 4.30
1292 2031 1.610102 CCTTGACTTCCTGCAGGACAG 60.610 57.143 35.26 31.15 45.39 3.51
1294 2033 0.394192 TGACTTCCTGCAGGACAGTG 59.606 55.000 35.25 27.01 45.39 3.66
1376 2115 3.225235 GAGAGGCTCCATTCGGCT 58.775 61.111 11.71 0.00 40.28 5.52
1718 2460 6.324770 TCTGAAACATCTATGATAGACAGGCA 59.675 38.462 3.96 0.00 37.69 4.75
1743 2485 1.531149 CGACTTCACACCATGAACACC 59.469 52.381 0.00 0.00 42.62 4.16
2057 2803 4.275196 CGATTGATTTCAGCATCCATCACT 59.725 41.667 0.00 0.00 29.49 3.41
2323 3071 7.806487 GCTTTGTTAAGTGTACCTTAATTGTCC 59.194 37.037 15.26 6.94 45.07 4.02
2342 3090 2.238646 TCCTGATTGGAACGGTAAGCAT 59.761 45.455 0.00 0.00 42.94 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 921 5.238583 ACAGGTTTTACTGCATCTAGACAC 58.761 41.667 0.00 0.00 42.21 3.67
360 1099 5.476945 CCTGTTTACCCTAATGAAAGCTTGT 59.523 40.000 0.00 0.00 0.00 3.16
381 1120 4.260497 GCTTTGCTTTGCTTTTCTTTCCTG 60.260 41.667 0.00 0.00 0.00 3.86
401 1140 5.979517 GCTAGACTTTTGACATGTTTTGCTT 59.020 36.000 0.00 0.00 0.00 3.91
402 1141 5.300286 AGCTAGACTTTTGACATGTTTTGCT 59.700 36.000 0.00 0.00 0.00 3.91
403 1142 5.400485 CAGCTAGACTTTTGACATGTTTTGC 59.600 40.000 0.00 0.00 0.00 3.68
404 1143 6.498304 ACAGCTAGACTTTTGACATGTTTTG 58.502 36.000 0.00 0.00 0.00 2.44
405 1144 6.699575 ACAGCTAGACTTTTGACATGTTTT 57.300 33.333 0.00 0.00 0.00 2.43
441 1180 2.668212 CAGGCGAAAACGGAGGCA 60.668 61.111 0.00 0.00 0.00 4.75
449 1188 3.906720 AGGCTATCTAACAGGCGAAAA 57.093 42.857 0.00 0.00 43.04 2.29
546 1285 1.144708 TCATGGTTGGAGAGTGGCAAA 59.855 47.619 0.00 0.00 0.00 3.68
605 1344 0.535102 CTCTCGCTCTCCCTCTCTCC 60.535 65.000 0.00 0.00 0.00 3.71
630 1369 6.126710 ACAGTGAGAGGCATAGTACTACTACT 60.127 42.308 4.31 3.32 32.84 2.57
631 1370 6.056884 ACAGTGAGAGGCATAGTACTACTAC 58.943 44.000 4.31 0.00 32.84 2.73
632 1371 6.249911 ACAGTGAGAGGCATAGTACTACTA 57.750 41.667 4.31 0.00 34.82 1.82
640 1379 2.391616 TGCAACAGTGAGAGGCATAG 57.608 50.000 0.00 0.00 0.00 2.23
954 1693 7.589395 TGCATACATCAAAACGTTGAACTTAT 58.411 30.769 0.00 0.00 46.66 1.73
955 1694 6.960468 TGCATACATCAAAACGTTGAACTTA 58.040 32.000 0.00 0.00 46.66 2.24
956 1695 5.826586 TGCATACATCAAAACGTTGAACTT 58.173 33.333 0.00 0.00 46.66 2.66
975 1714 1.061812 AGAGGTATCCCCTGTCTGCAT 60.062 52.381 0.00 0.00 46.51 3.96
981 1720 1.319947 TCCTCAGAGGTATCCCCTGT 58.680 55.000 16.65 0.00 46.51 4.00
1173 1912 3.649277 GAGCACCATGGACGTCGCT 62.649 63.158 21.47 16.86 0.00 4.93
1292 2031 3.553917 GGTGTTGTTGTTATTGTTGCCAC 59.446 43.478 0.00 0.00 0.00 5.01
1294 2033 3.786635 TGGTGTTGTTGTTATTGTTGCC 58.213 40.909 0.00 0.00 0.00 4.52
1376 2115 1.266718 GCTTTTCTTGATGTCGGTGCA 59.733 47.619 0.00 0.00 0.00 4.57
1715 2457 1.639298 GGTGTGAAGTCGCAGATGCC 61.639 60.000 0.00 0.00 40.67 4.40
1718 2460 1.276138 TCATGGTGTGAAGTCGCAGAT 59.724 47.619 0.00 0.00 37.00 2.90
1743 2485 5.009911 TGAACACAAAGGAATGAACAGATGG 59.990 40.000 0.00 0.00 0.00 3.51
2057 2803 7.855784 TGGAAGTATAATGGCAAGAGATAGA 57.144 36.000 0.00 0.00 0.00 1.98
2290 3038 7.635550 AAGGTACACTTAACAAAGCACATGCT 61.636 38.462 0.00 0.00 45.87 3.79
2323 3071 3.009723 ACATGCTTACCGTTCCAATCAG 58.990 45.455 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.