Multiple sequence alignment - TraesCS4A01G145000

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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 TraesCS4A01G145000 chr4A 100.000 2573 0 0 1 2573 246662580 246660008 0 4752
1 TraesCS4A01G145000 chr4A 98.165 1744 30 1 1 1744 67592139 67593880 0 3042
2 TraesCS4A01G145000 chr7D 98.452 1744 27 0 1 1744 381915337 381917080 0 3072
3 TraesCS4A01G145000 chr7D 98.337 1744 29 0 1 1744 203495358 203497101 0 3061
4 TraesCS4A01G145000 chr7D 98.280 1744 30 0 1 1744 381978403 381976660 0 3055
5 TraesCS4A01G145000 chr7D 98.323 835 12 2 1739 2573 381975978 381975146 0 1463
6 TraesCS4A01G145000 chr7D 98.206 836 11 3 1739 2573 382047864 382048696 0 1458
7 TraesCS4A01G145000 chr6D 98.394 1744 28 0 1 1744 124512883 124514626 0 3066
8 TraesCS4A01G145000 chr6D 97.964 835 15 2 1739 2573 124515308 124516140 0 1447
9 TraesCS4A01G145000 chr7B 97.826 1748 34 1 1 1744 716843191 716841444 0 3014
10 TraesCS4A01G145000 chr7B 97.654 1748 37 1 1 1744 716883432 716881685 0 2998
11 TraesCS4A01G145000 chr7B 98.323 835 12 2 1739 2573 742987226 742988058 0 1463
12 TraesCS4A01G145000 chr5A 97.826 1748 34 1 1 1744 19253500 19251753 0 3014
13 TraesCS4A01G145000 chr5A 97.764 1744 38 1 1 1744 238901412 238899670 0 3003
14 TraesCS4A01G145000 chr5A 97.849 837 14 3 1739 2573 19251067 19250233 0 1443
15 TraesCS4A01G145000 chr5A 97.608 836 18 2 1739 2573 112325176 112326010 0 1432
16 TraesCS4A01G145000 chr1A 97.964 835 15 2 1739 2573 498693441 498692609 0 1447
17 TraesCS4A01G145000 chr7A 97.962 834 12 4 1739 2571 120843373 120842544 0 1441
18 TraesCS4A01G145000 chrUn 97.727 836 16 3 1739 2573 186210642 186209809 0 1435


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 TraesCS4A01G145000 chr4A 246660008 246662580 2572 True 4752.0 4752 100.0000 1 2573 1 chr4A.!!$R1 2572
1 TraesCS4A01G145000 chr4A 67592139 67593880 1741 False 3042.0 3042 98.1650 1 1744 1 chr4A.!!$F1 1743
2 TraesCS4A01G145000 chr7D 381915337 381917080 1743 False 3072.0 3072 98.4520 1 1744 1 chr7D.!!$F2 1743
3 TraesCS4A01G145000 chr7D 203495358 203497101 1743 False 3061.0 3061 98.3370 1 1744 1 chr7D.!!$F1 1743
4 TraesCS4A01G145000 chr7D 381975146 381978403 3257 True 2259.0 3055 98.3015 1 2573 2 chr7D.!!$R1 2572
5 TraesCS4A01G145000 chr7D 382047864 382048696 832 False 1458.0 1458 98.2060 1739 2573 1 chr7D.!!$F3 834
6 TraesCS4A01G145000 chr6D 124512883 124516140 3257 False 2256.5 3066 98.1790 1 2573 2 chr6D.!!$F1 2572
7 TraesCS4A01G145000 chr7B 716841444 716843191 1747 True 3014.0 3014 97.8260 1 1744 1 chr7B.!!$R1 1743
8 TraesCS4A01G145000 chr7B 716881685 716883432 1747 True 2998.0 2998 97.6540 1 1744 1 chr7B.!!$R2 1743
9 TraesCS4A01G145000 chr7B 742987226 742988058 832 False 1463.0 1463 98.3230 1739 2573 1 chr7B.!!$F1 834
10 TraesCS4A01G145000 chr5A 238899670 238901412 1742 True 3003.0 3003 97.7640 1 1744 1 chr5A.!!$R1 1743
11 TraesCS4A01G145000 chr5A 19250233 19253500 3267 True 2228.5 3014 97.8375 1 2573 2 chr5A.!!$R2 2572
12 TraesCS4A01G145000 chr5A 112325176 112326010 834 False 1432.0 1432 97.6080 1739 2573 1 chr5A.!!$F1 834
13 TraesCS4A01G145000 chr1A 498692609 498693441 832 True 1447.0 1447 97.9640 1739 2573 1 chr1A.!!$R1 834
14 TraesCS4A01G145000 chr7A 120842544 120843373 829 True 1441.0 1441 97.9620 1739 2571 1 chr7A.!!$R1 832
15 TraesCS4A01G145000 chrUn 186209809 186210642 833 True 1435.0 1435 97.7270 1739 2573 1 chrUn.!!$R1 834

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
101 102 1.461127 CCTTGCTTGTTCTCGTACAGC 59.539 52.381 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2600 1.135915 CTGCAGAGACTACAAGCCGAT 59.864 52.381 8.42 0.0 0.0 4.18 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
101 102 1.461127 CCTTGCTTGTTCTCGTACAGC 59.539 52.381 0.00 0.0 0.00 4.40
266 267 4.210331 AGGCAACCCTTTAGATATTGCTG 58.790 43.478 7.15 0.0 44.03 4.41
456 457 9.739276 AACAACTTTCTAACATCATCCTGATAA 57.261 29.630 0.00 0.0 34.28 1.75
500 501 8.703604 TTTTTCGTTTTGTCAATATCCAACAA 57.296 26.923 0.00 0.0 0.00 2.83
537 538 8.438676 AATCGTTCCAGAACTCCTTAATAATG 57.561 34.615 8.77 0.0 39.08 1.90
588 589 8.130671 TCTCAATGCTATCATCATATGTCTCA 57.869 34.615 1.90 0.0 31.27 3.27
738 739 6.046593 TGCTCTGTATAATACTTTTCCACGG 58.953 40.000 0.00 0.0 0.00 4.94
855 860 7.996098 ACTATATAAAGTGTGCAGTTTTGGT 57.004 32.000 9.86 0.0 35.70 3.67
864 869 6.639563 AGTGTGCAGTTTTGGTTCTTTATTT 58.360 32.000 0.00 0.0 0.00 1.40
904 909 1.997311 CCTCTCCACTCCCATGCCA 60.997 63.158 0.00 0.0 0.00 4.92
951 956 3.186613 GCGATTTCCGACAAGTCTTTCTT 59.813 43.478 0.00 0.0 41.76 2.52
1199 1204 1.755621 CGGAGTGGATCATCCCTCTCA 60.756 57.143 20.65 0.0 44.47 3.27
1259 1264 3.129813 ACTCGGTATAACTCACGCATTCA 59.870 43.478 0.00 0.0 0.00 2.57
1355 1360 5.456763 GGGAGCAAGAAGTATGGGATATGTT 60.457 44.000 0.00 0.0 0.00 2.71
1481 1486 4.489810 GAAGTACGCTATGATGATCCAGG 58.510 47.826 0.00 0.0 0.00 4.45
1742 2438 7.574372 AGGATTTCCTTCCATTCTTCCTAGTAT 59.426 37.037 0.00 0.0 46.09 2.12
1936 2634 2.894879 GCAGTCGGCACACACACA 60.895 61.111 0.00 0.0 43.97 3.72
2084 2783 2.893489 CTGGAGTGCTTTAGCCCTTTTT 59.107 45.455 0.00 0.0 41.18 1.94
2187 2886 0.188342 TTTCTTGCTGGGGAAGGCTT 59.812 50.000 0.00 0.0 0.00 4.35
2287 2986 1.428219 CGGTGAGAGTCGCACGTAT 59.572 57.895 19.01 0.0 35.10 3.06
2296 2995 1.404391 AGTCGCACGTATGGTAAGGAG 59.596 52.381 0.00 0.0 0.00 3.69
2357 3057 2.597578 ACCCACCCTATTTGTTCCAC 57.402 50.000 0.00 0.0 0.00 4.02
2358 3058 1.783979 ACCCACCCTATTTGTTCCACA 59.216 47.619 0.00 0.0 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.835181 AGCAGTACTCACTAGTAAGGTAGAATT 59.165 37.037 0.00 0.00 39.90 2.17
130 131 2.919228 GGAATCATCCGCAGTTAAGGT 58.081 47.619 0.00 0.00 35.59 3.50
500 501 4.637534 TCTGGAACGATTACTACGCTAAGT 59.362 41.667 0.00 0.00 0.00 2.24
588 589 9.686683 AGTATGCAGGTTCTATTTTATTGTTCT 57.313 29.630 0.00 0.00 0.00 3.01
735 736 2.510691 CGCTAAACCATCGCCCGT 60.511 61.111 0.00 0.00 0.00 5.28
738 739 0.586802 GAATCCGCTAAACCATCGCC 59.413 55.000 0.00 0.00 0.00 5.54
855 860 7.719633 AGTGAAAGACTGGCTACAAATAAAGAA 59.280 33.333 0.00 0.00 31.75 2.52
864 869 3.803715 GCAGAAGTGAAAGACTGGCTACA 60.804 47.826 0.00 0.00 34.02 2.74
951 956 2.353803 GGTTCCGCTTCTTGCTCTAAGA 60.354 50.000 0.00 0.00 43.53 2.10
1199 1204 6.626302 TGGACAACTTCAAATCTTCGTTTTT 58.374 32.000 0.00 0.00 0.00 1.94
1259 1264 3.462982 TCGTCTGCACTTGTTTGTACAT 58.537 40.909 0.00 0.00 33.44 2.29
1355 1360 5.185635 GGATGATTGATGGAAGAAACACCAA 59.814 40.000 0.00 0.00 39.69 3.67
1509 1514 6.530019 AAATAGCGAAATTCTTGGGTCATT 57.470 33.333 0.00 0.00 0.00 2.57
1742 2438 2.764128 CCCTCCTAGGCTTCCGCA 60.764 66.667 2.96 0.00 38.10 5.69
1792 2490 5.688823 CATACGAGAAAATTGCACTTCACA 58.311 37.500 0.00 0.00 0.00 3.58
1902 2600 1.135915 CTGCAGAGACTACAAGCCGAT 59.864 52.381 8.42 0.00 0.00 4.18
1932 2630 4.408821 ATGATGGCGGGCGTGTGT 62.409 61.111 0.00 0.00 0.00 3.72
2084 2783 6.293626 GCTCAAGACAGTGATTCTTGCTTAAA 60.294 38.462 15.38 1.83 46.51 1.52
2165 2864 1.703411 CCTTCCCCAGCAAGAAAACA 58.297 50.000 0.00 0.00 0.00 2.83
2187 2886 3.118629 CCTCTCCAATCCTCGATCAAACA 60.119 47.826 0.00 0.00 0.00 2.83
2357 3057 3.900601 AGCTCCAGTAGACCCATAGATTG 59.099 47.826 0.00 0.00 0.00 2.67
2358 3058 4.206244 AGCTCCAGTAGACCCATAGATT 57.794 45.455 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.