Multiple sequence alignment - TraesCS4D01G119100

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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 TraesCS4D01G119100 chr4D 100.000 2561 0 0 1 2561 100482088 100484648 0.000000e+00 4730.0
1 TraesCS4D01G119100 chr4B 95.154 2559 102 11 1 2549 142696666 142699212 0.000000e+00 4019.0
2 TraesCS4D01G119100 chr4A 94.533 2579 116 13 1 2561 476067407 476064836 0.000000e+00 3958.0
3 TraesCS4D01G119100 chr3B 75.217 460 85 24 1094 1542 592824966 592824525 9.350000e-45 191.0
4 TraesCS4D01G119100 chr3B 84.375 64 7 3 153 215 466190406 466190467 2.750000e-05 60.2
5 TraesCS4D01G119100 chr5D 85.859 99 14 0 1381 1479 409454878 409454976 3.480000e-19 106.0


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 TraesCS4D01G119100 chr4D 100482088 100484648 2560 False 4730 4730 100.000 1 2561 1 chr4D.!!$F1 2560
1 TraesCS4D01G119100 chr4B 142696666 142699212 2546 False 4019 4019 95.154 1 2549 1 chr4B.!!$F1 2548
2 TraesCS4D01G119100 chr4A 476064836 476067407 2571 True 3958 3958 94.533 1 2561 1 chr4A.!!$R1 2560

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
26 27 1.114119 TGCCACAAAATGCTGCTCCA 61.114 50.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 1763 3.025322 ACCCAAAATGACAAGGACACA 57.975 42.857 0.0 0.0 0.0 3.72 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
26 27 1.114119 TGCCACAAAATGCTGCTCCA 61.114 50.000 0.00 0.00 0.00 3.86
68 69 8.592809 TGGGTAAAATGATAAGTGCTCAATTTT 58.407 29.630 0.00 0.00 30.53 1.82
184 185 1.273606 ACACTAGTGCTCGCATGTCTT 59.726 47.619 22.90 0.00 0.00 3.01
195 196 7.698130 AGTGCTCGCATGTCTTTTAATTTATTC 59.302 33.333 0.00 0.00 0.00 1.75
220 221 7.342318 CAGACTTTCTGGCAATGTTTATTTG 57.658 36.000 0.00 0.00 40.71 2.32
238 239 8.946085 GTTTATTTGGTGAGAGATGACATTACA 58.054 33.333 0.00 0.00 0.00 2.41
252 253 8.429641 AGATGACATTACAACCGATTATAAGGT 58.570 33.333 0.00 0.00 43.68 3.50
253 254 7.780008 TGACATTACAACCGATTATAAGGTG 57.220 36.000 0.00 0.00 41.21 4.00
260 261 4.957759 ACCGATTATAAGGTGTTTGTGC 57.042 40.909 0.00 0.00 39.66 4.57
425 428 2.172717 ACCACACATCAAGCCCCTATAC 59.827 50.000 0.00 0.00 0.00 1.47
556 561 1.376553 GGCAGGAACAGAGGAGTGC 60.377 63.158 0.00 0.00 0.00 4.40
612 617 3.849951 CGGCAGACATAGCGGGGT 61.850 66.667 0.00 0.00 0.00 4.95
869 886 2.428890 TGCGCCAAGGAAAAGAAAAGAA 59.571 40.909 4.18 0.00 0.00 2.52
870 887 3.052745 GCGCCAAGGAAAAGAAAAGAAG 58.947 45.455 0.00 0.00 0.00 2.85
871 888 3.243401 GCGCCAAGGAAAAGAAAAGAAGA 60.243 43.478 0.00 0.00 0.00 2.87
1203 1222 4.827087 ATCCGCTGCGTGCTCCAG 62.827 66.667 21.59 3.49 40.11 3.86
1332 1351 2.769602 AGATACCCGTGGAGGTGTAT 57.230 50.000 0.00 0.00 41.42 2.29
1596 1615 7.099120 GGTACGGGTTTGTAATTTCTTCTAGA 58.901 38.462 0.00 0.00 0.00 2.43
1597 1616 7.767659 GGTACGGGTTTGTAATTTCTTCTAGAT 59.232 37.037 0.00 0.00 0.00 1.98
1651 1670 2.169832 TTGCTTCCTCACTAGTGTGC 57.830 50.000 21.99 17.75 43.49 4.57
1690 1709 2.319136 TTCGTATGGGTGGTACATGC 57.681 50.000 0.00 0.00 44.52 4.06
1697 1716 5.240623 CGTATGGGTGGTACATGCAAATTAT 59.759 40.000 0.00 0.00 44.52 1.28
1744 1763 2.027837 GGGCTTGATGCAAATGTTCCTT 60.028 45.455 0.00 0.00 45.15 3.36
2248 2275 2.436646 GGCCGGTCACCACTGATG 60.437 66.667 0.00 0.00 0.00 3.07
2287 2314 7.013369 ACTCCAACAGATCTTGTAAAAACCTTC 59.987 37.037 0.00 0.00 39.73 3.46
2337 2364 5.920273 CCATATAATTTGCCGGAATTGTCAC 59.080 40.000 5.05 0.00 31.96 3.67
2385 2412 9.608617 CGTAAAACTTCTTTCCCTAAAATCTTC 57.391 33.333 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.963962 AATTTGGCTGTGTGGAGCAG 59.036 50.000 0.00 0.00 41.08 4.24
26 27 2.888212 ACCCACATAATTTGGCTGTGT 58.112 42.857 0.00 0.00 38.85 3.72
220 221 3.865745 CGGTTGTAATGTCATCTCTCACC 59.134 47.826 0.00 0.00 0.00 4.02
238 239 5.007682 AGCACAAACACCTTATAATCGGTT 58.992 37.500 0.00 0.00 0.00 4.44
252 253 5.769662 AGGATTAATGAAGTCAGCACAAACA 59.230 36.000 0.00 0.00 0.00 2.83
253 254 6.259550 AGGATTAATGAAGTCAGCACAAAC 57.740 37.500 0.00 0.00 0.00 2.93
326 327 5.276726 GCCTACGGTATCTTTCGTTCATTTC 60.277 44.000 0.00 0.00 40.31 2.17
556 561 3.315470 TGGTCTCGATTTCGACTAGATGG 59.685 47.826 0.00 0.00 44.22 3.51
869 886 4.562347 GCATACATGGGAATCGAGACATCT 60.562 45.833 0.00 0.00 0.00 2.90
870 887 3.681897 GCATACATGGGAATCGAGACATC 59.318 47.826 0.00 0.00 0.00 3.06
871 888 3.071457 TGCATACATGGGAATCGAGACAT 59.929 43.478 0.00 0.00 0.00 3.06
980 999 4.697756 TGTGCCTGCGTACCAGCC 62.698 66.667 5.98 0.00 40.36 4.85
1555 1574 4.301027 CCCTGTCCGGCGCTATCC 62.301 72.222 7.64 0.00 0.00 2.59
1596 1615 7.065443 GCAACGTTTCACTTTAGTTCCCTATAT 59.935 37.037 0.00 0.00 0.00 0.86
1597 1616 6.369615 GCAACGTTTCACTTTAGTTCCCTATA 59.630 38.462 0.00 0.00 0.00 1.31
1651 1670 4.744631 CGAAAACCAAAATCAGACCAAAGG 59.255 41.667 0.00 0.00 0.00 3.11
1744 1763 3.025322 ACCCAAAATGACAAGGACACA 57.975 42.857 0.00 0.00 0.00 3.72
1786 1805 8.697507 AGTTATAAAATGGGAGAATCATGACC 57.302 34.615 0.00 0.00 36.25 4.02
2105 2131 5.811399 TGAACACAAGTTAACAAGGACAG 57.189 39.130 8.61 0.00 38.30 3.51
2202 2228 5.651530 AGATATACTTATTGGCGATGACCG 58.348 41.667 0.00 0.00 42.21 4.79
2203 2229 7.324178 AGAAGATATACTTATTGGCGATGACC 58.676 38.462 0.00 0.00 39.13 4.02
2248 2275 2.570302 TGTTGGAGTTAGTCTAAGGCCC 59.430 50.000 0.00 4.03 0.00 5.80
2287 2314 5.379732 TTCCATAAAAGCACTTTTACGGG 57.620 39.130 21.44 20.48 44.16 5.28
2316 2343 6.707440 ATGTGACAATTCCGGCAAATTATA 57.293 33.333 0.00 0.00 0.00 0.98
2337 2364 4.806247 CGGGAACTGAGAAAAGTAGCTATG 59.194 45.833 0.00 0.00 36.31 2.23
2398 2425 2.372504 TCCCAACGATGTTTAGTGGGAA 59.627 45.455 7.27 0.00 40.74 3.97
2399 2426 1.979308 TCCCAACGATGTTTAGTGGGA 59.021 47.619 5.62 5.62 41.35 4.37
2473 2500 3.238497 CACCACCTCACCGGTCCA 61.238 66.667 2.59 0.00 44.93 4.02


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

AutoCloner maintained by Alex Coulton.