Multiple sequence alignment - TraesCS2D01G090000

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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 TraesCS2D01G090000 chr2D 100.000 2378 0 0 1 2378 39721576 39719199 0.000000e+00 4392.0
1 TraesCS2D01G090000 chrUn 97.603 2378 54 3 1 2378 45100762 45098388 0.000000e+00 4072.0
2 TraesCS2D01G090000 chrUn 97.478 2379 57 3 1 2378 261513094 261515470 0.000000e+00 4058.0
3 TraesCS2D01G090000 chr5B 97.603 2378 54 3 1 2378 130609847 130607473 0.000000e+00 4072.0
4 TraesCS2D01G090000 chr5B 97.519 2378 57 2 1 2378 130614871 130612496 0.000000e+00 4063.0
5 TraesCS2D01G090000 chr5B 97.228 2381 62 2 1 2378 130568785 130571164 0.000000e+00 4028.0
6 TraesCS2D01G090000 chr3A 97.393 2378 60 2 1 2378 66030343 66032718 0.000000e+00 4047.0
7 TraesCS2D01G090000 chr7B 97.269 2380 62 2 1 2378 743033730 743036108 0.000000e+00 4032.0
8 TraesCS2D01G090000 chr2B 97.225 2378 63 3 1 2378 112869083 112866709 0.000000e+00 4023.0
9 TraesCS2D01G090000 chr2B 97.260 219 5 1 1759 1977 357428852 357429069 1.040000e-98 370.0
10 TraesCS2D01G090000 chr2B 95.918 147 6 0 1 147 407763903 407764049 3.050000e-59 239.0
11 TraesCS2D01G090000 chr2B 85.638 188 22 2 1289 1476 26467205 26467023 2.410000e-45 193.0
12 TraesCS2D01G090000 chr2B 93.590 78 5 0 2057 2134 659856537 659856614 1.490000e-22 117.0
13 TraesCS2D01G090000 chr2B 97.436 39 1 0 2303 2341 716490107 716490069 1.530000e-07 67.6


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 TraesCS2D01G090000 chr2D 39719199 39721576 2377 True 4392.0 4392 100.000 1 2378 1 chr2D.!!$R1 2377
1 TraesCS2D01G090000 chrUn 45098388 45100762 2374 True 4072.0 4072 97.603 1 2378 1 chrUn.!!$R1 2377
2 TraesCS2D01G090000 chrUn 261513094 261515470 2376 False 4058.0 4058 97.478 1 2378 1 chrUn.!!$F1 2377
3 TraesCS2D01G090000 chr5B 130607473 130614871 7398 True 4067.5 4072 97.561 1 2378 2 chr5B.!!$R1 2377
4 TraesCS2D01G090000 chr5B 130568785 130571164 2379 False 4028.0 4028 97.228 1 2378 1 chr5B.!!$F1 2377
5 TraesCS2D01G090000 chr3A 66030343 66032718 2375 False 4047.0 4047 97.393 1 2378 1 chr3A.!!$F1 2377
6 TraesCS2D01G090000 chr7B 743033730 743036108 2378 False 4032.0 4032 97.269 1 2378 1 chr7B.!!$F1 2377
7 TraesCS2D01G090000 chr2B 112866709 112869083 2374 True 4023.0 4023 97.225 1 2378 1 chr2B.!!$R2 2377

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
889 890 0.393808 ACCACACGTGCAAGTTTCCT 60.394 50.0 17.22 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 7157 0.749454 ATAGGTACTTCGTCCGGCGT 60.749 55.0 16.0 2.47 41.75 5.68 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
61 62 3.824810 CGGGAGGAGTCGGTAGTC 58.175 66.667 0.00 0.00 0.00 2.59
79 80 2.597903 GGGCACTGGATCCCTTCC 59.402 66.667 9.90 5.11 45.69 3.46
102 103 1.611977 CCTGGAGAACGTGTGACACTA 59.388 52.381 14.42 0.00 31.34 2.74
106 107 2.035576 GGAGAACGTGTGACACTAGGTT 59.964 50.000 14.42 10.40 31.34 3.50
175 176 2.030274 CCCTTTTTCGTTGCCTAGGTTG 60.030 50.000 11.31 0.00 0.00 3.77
190 191 2.109425 GGTTGCACCTTCGGAATACT 57.891 50.000 0.00 0.00 34.73 2.12
238 239 3.962718 CCCCAATCTTCACTTTATGCCAT 59.037 43.478 0.00 0.00 0.00 4.40
250 251 1.048160 TATGCCATGCCGACTCTCCA 61.048 55.000 0.00 0.00 0.00 3.86
339 340 1.604755 GCGTAGGAGATCGAGACACAT 59.395 52.381 0.00 0.00 0.00 3.21
402 403 3.345414 ACAACTACGTAGAGGGTCTCTG 58.655 50.000 28.74 13.19 41.37 3.35
423 424 8.758829 TCTCTGCAAGTCTATAAATAAGTTCCA 58.241 33.333 0.00 0.00 33.76 3.53
472 473 4.215399 CGCACCCGAACAATAATATTCCAT 59.785 41.667 0.00 0.00 36.29 3.41
505 506 8.579850 TGCACCTAAGATCAAATATTTTGAGT 57.420 30.769 8.47 0.00 0.00 3.41
512 513 7.396540 AGATCAAATATTTTGAGTCGGCTTT 57.603 32.000 8.47 0.00 0.00 3.51
543 544 7.719778 AAATTCAGACTTTCTTTTTGATGCC 57.280 32.000 0.00 0.00 0.00 4.40
721 722 1.280710 ACATCGAAATGGTACCAGCCA 59.719 47.619 21.41 1.33 43.48 4.75
889 890 0.393808 ACCACACGTGCAAGTTTCCT 60.394 50.000 17.22 0.00 0.00 3.36
902 903 0.961019 GTTTCCTTGCATGTGGCTCA 59.039 50.000 0.00 0.00 45.15 4.26
928 929 4.092821 CGTGATAACTTCTTCGGATTTGCA 59.907 41.667 0.00 0.00 0.00 4.08
992 993 4.330944 TGAGCGAACCTTTTCAGAACTA 57.669 40.909 0.00 0.00 0.00 2.24
1086 1087 1.066430 GTATCTTGTCTTGGGGCGTCA 60.066 52.381 0.00 0.00 0.00 4.35
1127 1128 1.675310 CAGACATGGCGCCCTTTCA 60.675 57.895 26.77 4.49 0.00 2.69
1226 1227 0.732571 CGGTGCAATAGAATTGGCGT 59.267 50.000 0.00 0.00 0.00 5.68
1263 1264 0.478072 ATCAGTCACCTGGGCAAACA 59.522 50.000 0.00 0.00 39.31 2.83
1404 1410 0.737219 CGTTTCTAGGACCGACCGAT 59.263 55.000 0.00 0.00 44.74 4.18
1464 1470 4.202070 TGTCGGTCGCACATTCATAATAGA 60.202 41.667 0.00 0.00 0.00 1.98
1493 1499 0.883833 CATGTGCCTTCCTGAACCAC 59.116 55.000 0.00 0.00 0.00 4.16
1517 1523 2.832778 TTCCCTTGCTCCTGCTGCA 61.833 57.895 0.88 0.88 40.48 4.41
1528 1534 1.688735 TCCTGCTGCATACGATTAGCT 59.311 47.619 1.31 0.00 37.10 3.32
1621 1627 0.250513 GGGAGCTGGGCGATAATAGG 59.749 60.000 0.00 0.00 0.00 2.57
1638 1644 2.670148 GGTCCTCCGCATCCCAAGT 61.670 63.158 0.00 0.00 0.00 3.16
1745 1751 8.554490 AGAGGTACTAAATACAACTCCATGAT 57.446 34.615 0.00 0.00 41.55 2.45
1907 1914 5.455872 AGCCTAGGTGTTATTACTGAGCTA 58.544 41.667 11.31 0.00 0.00 3.32
2075 7105 4.832248 TCACACCCACACAATCTCTATTC 58.168 43.478 0.00 0.00 0.00 1.75
2127 7157 2.759191 GATCGCTCAGCAATGATACCA 58.241 47.619 0.00 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 0.663568 GTCACACGTTCTCCAGGTCG 60.664 60.000 0.00 0.00 0.00 4.79
102 103 3.217321 GTTCACCAAACCCCAACCT 57.783 52.632 0.00 0.00 31.20 3.50
126 127 3.746045 ACTTCAACTAAAGGAGCGACA 57.254 42.857 0.00 0.00 0.00 4.35
190 191 1.956629 GAGCGAAATCCCCGTCTGGA 61.957 60.000 0.00 0.00 39.18 3.86
233 234 2.315781 GATGGAGAGTCGGCATGGCA 62.316 60.000 20.37 3.64 0.00 4.92
238 239 2.710902 CCACGATGGAGAGTCGGCA 61.711 63.158 0.00 0.00 40.96 5.69
250 251 2.844348 ACCCTTGGTCTAATTCCACGAT 59.156 45.455 0.00 0.00 34.45 3.73
339 340 2.294263 ACTTTCCCCATAGCCCTAAGGA 60.294 50.000 0.00 0.00 33.47 3.36
472 473 5.708736 TTGATCTTAGGTGCATTTCCCTA 57.291 39.130 0.00 0.00 32.08 3.53
505 506 2.222886 TGAATTTTCCACGAAAGCCGA 58.777 42.857 0.00 0.00 41.76 5.54
512 513 6.693315 AAAGAAAGTCTGAATTTTCCACGA 57.307 33.333 4.47 0.00 32.96 4.35
543 544 7.719689 AAGTTTATGTTTTTATGTGATCGCG 57.280 32.000 0.00 0.00 0.00 5.87
797 798 2.626743 GGCGCACCTCTCCTAACTATTA 59.373 50.000 10.83 0.00 0.00 0.98
861 862 3.542676 ACGTGTGGTTCTGGCCGA 61.543 61.111 0.00 0.00 0.00 5.54
889 890 1.002257 ACGGATGAGCCACATGCAA 60.002 52.632 11.93 0.00 45.52 4.08
928 929 1.067212 GTGATCGGTCCGCTAGTTCAT 59.933 52.381 6.34 0.00 0.00 2.57
992 993 1.077716 GTGGCGCCCATTCCTAACT 60.078 57.895 26.77 0.00 35.28 2.24
1114 1115 1.956477 GATAATGTGAAAGGGCGCCAT 59.044 47.619 30.85 21.35 0.00 4.40
1115 1116 1.340502 TGATAATGTGAAAGGGCGCCA 60.341 47.619 30.85 5.63 0.00 5.69
1127 1128 4.348168 AGAAAGGGCGGTAGATGATAATGT 59.652 41.667 0.00 0.00 0.00 2.71
1226 1227 6.725834 TGACTGATCCTGCCATAATATACTCA 59.274 38.462 0.00 0.00 0.00 3.41
1263 1264 4.536295 TTCTTCTTGGAGGAGGGTTTTT 57.464 40.909 0.00 0.00 0.00 1.94
1301 1302 4.335874 TCTTTCGCTCTATAGGGATATCGC 59.664 45.833 11.69 11.69 43.51 4.58
1404 1410 2.674033 GTGCATGCAGGTGAGGCA 60.674 61.111 23.41 0.00 46.66 4.75
1464 1470 0.687354 AAGGCACATGAGTCCGAACT 59.313 50.000 0.00 0.00 38.88 3.01
1517 1523 1.873903 CGCAAGGCCAGCTAATCGTAT 60.874 52.381 16.79 0.00 0.00 3.06
1598 1604 1.048601 TTATCGCCCAGCTCCCTAAG 58.951 55.000 0.00 0.00 0.00 2.18
1621 1627 1.450312 CACTTGGGATGCGGAGGAC 60.450 63.158 0.00 0.00 0.00 3.85
1745 1751 4.734398 ACACAACCTTCATTTTGCTCAA 57.266 36.364 0.00 0.00 0.00 3.02
1935 1942 2.500229 GAGGAGTAGTCGGAGGATCTG 58.500 57.143 0.00 0.00 44.94 2.90
2075 7105 4.994852 TCTGGAAATGGAGTGTTAGTTTCG 59.005 41.667 0.00 0.00 31.36 3.46
2127 7157 0.749454 ATAGGTACTTCGTCCGGCGT 60.749 55.000 16.00 2.47 41.75 5.68


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

AutoCloner maintained by Alex Coulton.