Multiple sequence alignment - TraesCS7D01G286000

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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 TraesCS7D01G286000 chr7D 100.000 2275 0 0 1 2275 307089766 307092040 0 4202
1 TraesCS7D01G286000 chrUn 98.067 2276 43 1 1 2275 257944383 257946658 0 3958
2 TraesCS7D01G286000 chrUn 97.803 2276 44 2 1 2275 233524997 233522727 0 3921
3 TraesCS7D01G286000 chr1D 97.935 2276 46 1 1 2275 212429140 212431415 0 3941
4 TraesCS7D01G286000 chr4D 97.583 2276 54 1 1 2275 123689233 123691508 0 3897
5 TraesCS7D01G286000 chr5B 97.056 2276 61 2 1 2275 713112692 713110422 0 3827
6 TraesCS7D01G286000 chr4B 96.968 2276 63 2 1 2275 495537504 495535234 0 3816
7 TraesCS7D01G286000 chr6D 96.744 2273 70 4 1 2272 283187685 283189954 0 3784


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 TraesCS7D01G286000 chr7D 307089766 307092040 2274 False 4202 4202 100.000 1 2275 1 chr7D.!!$F1 2274
1 TraesCS7D01G286000 chrUn 257944383 257946658 2275 False 3958 3958 98.067 1 2275 1 chrUn.!!$F1 2274
2 TraesCS7D01G286000 chrUn 233522727 233524997 2270 True 3921 3921 97.803 1 2275 1 chrUn.!!$R1 2274
3 TraesCS7D01G286000 chr1D 212429140 212431415 2275 False 3941 3941 97.935 1 2275 1 chr1D.!!$F1 2274
4 TraesCS7D01G286000 chr4D 123689233 123691508 2275 False 3897 3897 97.583 1 2275 1 chr4D.!!$F1 2274
5 TraesCS7D01G286000 chr5B 713110422 713112692 2270 True 3827 3827 97.056 1 2275 1 chr5B.!!$R1 2274
6 TraesCS7D01G286000 chr4B 495535234 495537504 2270 True 3816 3816 96.968 1 2275 1 chr4B.!!$R1 2274
7 TraesCS7D01G286000 chr6D 283187685 283189954 2269 False 3784 3784 96.744 1 2272 1 chr6D.!!$F1 2271

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
242 243 2.014068 GCGCTCATCCCTTGCTAAAGT 61.014 52.381 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1878 0.037734 GAATGGGTCCCGGTTCAAGT 59.962 55.0 16.99 0.0 0.0 3.16 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
74 75 2.480416 GGAGAACGAGCAGACATCGAAT 60.480 50.000 1.94 0.0 42.76 3.34
242 243 2.014068 GCGCTCATCCCTTGCTAAAGT 61.014 52.381 0.00 0.0 0.00 2.66
302 303 6.765512 TCAATCACACTGTTCATTAGTTCACA 59.234 34.615 0.00 0.0 0.00 3.58
328 329 5.728351 TTTTTCGTTCGATGTCTTGAACT 57.272 34.783 3.92 0.0 41.74 3.01
385 386 3.625897 CACTCCACGTCTGGCCCA 61.626 66.667 0.00 0.0 37.49 5.36
732 733 4.819769 TGATGTGAATGATCGTGTCTTCA 58.180 39.130 0.00 0.0 0.00 3.02
756 757 9.159364 TCAACATCAATTTCAGTCTGATTAGAG 57.841 33.333 2.68 0.0 32.48 2.43
860 861 2.892425 GCCGGACGATGAAGCCTG 60.892 66.667 5.05 0.0 0.00 4.85
1046 1047 3.216230 AGTTGGGTTGGGGTATAGAGT 57.784 47.619 0.00 0.0 0.00 3.24
1107 1108 6.698380 ACGGTTCATAGTTGGGTATGATATC 58.302 40.000 0.00 0.0 38.83 1.63
1279 1281 1.061657 TCGGATCTTCCCCTAACCCAT 60.062 52.381 0.00 0.0 31.13 4.00
1396 1398 2.883828 CGAGGCACAAGGGTCCTGT 61.884 63.158 0.00 0.0 0.00 4.00
1555 1557 0.620556 GAGGGAGGCAAGAACCATGA 59.379 55.000 0.00 0.0 0.00 3.07
1706 1708 2.746362 GGAGTACTCCGGGATATACACG 59.254 54.545 25.83 0.0 45.94 4.49
1766 1768 1.060729 TCATTTCGTGGAAGTCCCCA 58.939 50.000 0.00 0.0 34.29 4.96
1876 1878 1.453745 GATGATGAAAGGCGGGCCA 60.454 57.895 12.97 0.0 38.92 5.36
1891 1893 2.033602 CCACTTGAACCGGGACCC 59.966 66.667 6.32 0.0 0.00 4.46
2005 2007 3.744660 AGCTAATATGGCTGGCTACAAC 58.255 45.455 2.00 0.0 38.73 3.32
2207 2209 2.769663 AGCCCACATGCATCATTTGATT 59.230 40.909 0.00 0.0 31.21 2.57
2208 2210 2.869801 GCCCACATGCATCATTTGATTG 59.130 45.455 0.00 0.0 31.21 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 9.582431 ACGAGAACGAGAAATAGAAATTAATCA 57.418 29.630 0.00 0.0 42.66 2.57
96 97 3.511699 TCTTGATGACGAATTCCACGAG 58.488 45.455 0.00 0.0 34.70 4.18
242 243 2.778299 AGGAGCAAGAAAACGTATGCA 58.222 42.857 11.14 0.0 41.18 3.96
302 303 6.480524 TCAAGACATCGAACGAAAAATCAT 57.519 33.333 0.12 0.0 0.00 2.45
385 386 1.135257 CGAAGTGAGCGAGACCAAGAT 60.135 52.381 0.00 0.0 0.00 2.40
598 599 0.107214 CGGCAAGGAAGGAGGCATTA 60.107 55.000 0.00 0.0 0.00 1.90
697 698 1.469703 TCACATCAATTGAAGCAGGCG 59.530 47.619 13.09 0.0 0.00 5.52
732 733 9.902684 ATCTCTAATCAGACTGAAATTGATGTT 57.097 29.630 9.70 0.0 32.23 2.71
882 883 4.047059 GGAAGTCCGGTCGCGTCA 62.047 66.667 5.77 0.0 0.00 4.35
1068 1069 1.065928 CCGTACGAGCACATCCTCC 59.934 63.158 18.76 0.0 0.00 4.30
1107 1108 1.165270 GTTCCCAACAATCCACGAGG 58.835 55.000 0.00 0.0 0.00 4.63
1294 1296 2.249413 CTCATGCTGCGGTTCCCTCT 62.249 60.000 0.00 0.0 0.00 3.69
1339 1341 5.337491 CCCTATGACCCAAAACTCAAAATGG 60.337 44.000 0.00 0.0 0.00 3.16
1380 1382 0.400594 GTAACAGGACCCTTGTGCCT 59.599 55.000 0.00 0.0 32.35 4.75
1396 1398 1.927487 TCTTCGCACCTGGGTAGTAA 58.073 50.000 0.00 0.0 0.00 2.24
1482 1484 0.460987 GTGATCCCTTGCTCTCACGG 60.461 60.000 0.00 0.0 0.00 4.94
1555 1557 1.339151 GGACCGCCACTTCTCTGAAAT 60.339 52.381 0.00 0.0 0.00 2.17
1706 1708 1.291132 GCTCGACATTAGTTGCCCTC 58.709 55.000 0.00 0.0 0.00 4.30
1766 1768 0.908198 CTACAGCCCTTTCCTCTGCT 59.092 55.000 0.00 0.0 33.52 4.24
1876 1878 0.037734 GAATGGGTCCCGGTTCAAGT 59.962 55.000 16.99 0.0 0.00 3.16
1891 1893 4.517832 TGCTTGCTGCCTATTATGAGAATG 59.482 41.667 0.00 0.0 42.00 2.67
1955 1957 3.117322 TCCACCCTTTTGGATTTCTGACA 60.117 43.478 0.00 0.0 41.00 3.58
2005 2007 6.507900 TCGTCTCATCTTTCTTTGGCTATAG 58.492 40.000 0.00 0.0 0.00 1.31
2207 2209 0.681733 GACTGGACTGGAGTGCTTCA 59.318 55.000 0.00 0.0 37.28 3.02
2208 2210 0.389166 CGACTGGACTGGAGTGCTTC 60.389 60.000 0.00 0.0 37.28 3.86


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

AutoCloner maintained by Alex Coulton.