Multiple sequence alignment - TraesCS1B01G179400

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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 TraesCS1B01G179400 chr1B 100.000 2846 0 0 1 2846 325705204 325702359 0 5256
1 TraesCS1B01G179400 chr1B 96.595 2849 92 4 1 2846 322613649 322610803 0 4719
2 TraesCS1B01G179400 chr1B 95.410 2854 121 9 1 2846 363689392 363692243 0 4536
3 TraesCS1B01G179400 chr1B 95.265 2851 128 6 1 2846 652322493 652325341 0 4510
4 TraesCS1B01G179400 chr6B 96.635 2853 88 3 1 2846 91267049 91264198 0 4730
5 TraesCS1B01G179400 chr6B 95.588 2856 112 11 1 2846 517977133 517974282 0 4564
6 TraesCS1B01G179400 chr7B 95.375 2854 118 9 1 2846 120573660 120576507 0 4527
7 TraesCS1B01G179400 chr5B 95.372 2852 120 7 1 2846 894109 891264 0 4525
8 TraesCS1B01G179400 chr4A 95.231 2852 124 9 1 2846 699077869 699080714 0 4503
9 TraesCS1B01G179400 chr3B 95.200 2854 126 8 1 2846 103077661 103080511 0 4501


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 TraesCS1B01G179400 chr1B 325702359 325705204 2845 True 5256 5256 100.000 1 2846 1 chr1B.!!$R2 2845
1 TraesCS1B01G179400 chr1B 322610803 322613649 2846 True 4719 4719 96.595 1 2846 1 chr1B.!!$R1 2845
2 TraesCS1B01G179400 chr1B 363689392 363692243 2851 False 4536 4536 95.410 1 2846 1 chr1B.!!$F1 2845
3 TraesCS1B01G179400 chr1B 652322493 652325341 2848 False 4510 4510 95.265 1 2846 1 chr1B.!!$F2 2845
4 TraesCS1B01G179400 chr6B 91264198 91267049 2851 True 4730 4730 96.635 1 2846 1 chr6B.!!$R1 2845
5 TraesCS1B01G179400 chr6B 517974282 517977133 2851 True 4564 4564 95.588 1 2846 1 chr6B.!!$R2 2845
6 TraesCS1B01G179400 chr7B 120573660 120576507 2847 False 4527 4527 95.375 1 2846 1 chr7B.!!$F1 2845
7 TraesCS1B01G179400 chr5B 891264 894109 2845 True 4525 4525 95.372 1 2846 1 chr5B.!!$R1 2845
8 TraesCS1B01G179400 chr4A 699077869 699080714 2845 False 4503 4503 95.231 1 2846 1 chr4A.!!$F1 2845
9 TraesCS1B01G179400 chr3B 103077661 103080511 2850 False 4501 4501 95.200 1 2846 1 chr3B.!!$F1 2845

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
455 459 2.030562 CGCAGTGGTTCCGGAGTT 59.969 61.111 3.34 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2074 1.008995 CGGTTGCCTTGTTCGTTGG 60.009 57.895 0.0 0.0 0.0 3.77 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
342 346 4.039357 CGTGACACCGAGGACGCT 62.039 66.667 0.00 0.00 38.29 5.07
347 351 3.062466 CACCGAGGACGCTGAGGA 61.062 66.667 0.00 0.00 38.29 3.71
350 354 2.438614 CGAGGACGCTGAGGAGGA 60.439 66.667 0.00 0.00 0.00 3.71
455 459 2.030562 CGCAGTGGTTCCGGAGTT 59.969 61.111 3.34 0.00 0.00 3.01
477 481 2.361610 CAGTGGCCCCTTCGCAAT 60.362 61.111 0.00 0.00 0.00 3.56
811 823 5.835113 AAGTATGTCAATATGGGTTGCAC 57.165 39.130 0.00 0.00 0.00 4.57
1312 1324 3.365565 GGCATTTTTCATGCAAAGCAAGG 60.366 43.478 8.96 0.00 46.21 3.61
1316 1328 4.603989 TTTTCATGCAAAGCAAGGATGA 57.396 36.364 0.00 3.75 43.62 2.92
1527 1540 0.898326 TCGAGCTCCACAAGGTAGCA 60.898 55.000 8.47 0.00 39.23 3.49
1639 1652 4.366684 GCCCCTGGGTGGAGGTTG 62.367 72.222 12.71 0.00 38.35 3.77
1650 1663 1.004440 GGAGGTTGTCAAGCGCTCT 60.004 57.895 12.06 0.00 0.00 4.09
1715 1728 0.974010 CATTGGGGCAAGCTGGATGT 60.974 55.000 0.00 0.00 0.00 3.06
1880 1893 6.017440 GTGTTATCCTGTGTGCTGAAAACTTA 60.017 38.462 0.00 0.00 0.00 2.24
2061 2074 1.403687 ATCTAGGGAGGCGCTCAACC 61.404 60.000 7.64 5.02 31.08 3.77
2203 2216 0.179018 GCCTTGGCCGGACATTATCT 60.179 55.000 13.08 0.00 0.00 1.98
2368 2381 1.339151 GGTTCTCCCAGTGCTACCTTG 60.339 57.143 0.00 0.00 0.00 3.61
2466 2479 6.363626 CGGAGCCGATTCATATAATGCTATAC 59.636 42.308 2.00 0.00 42.83 1.47
2562 2576 2.585330 TCGGCCGTACCAAGATATACA 58.415 47.619 27.15 0.00 39.03 2.29
2672 2696 8.483307 AAAAGTGCTGCATTATTTATTCAAGG 57.517 30.769 5.27 0.00 0.00 3.61
2680 2704 8.985315 TGCATTATTTATTCAAGGAGATCTGT 57.015 30.769 0.00 0.00 0.00 3.41
2709 2733 4.035091 GTGCGGAATGATACAAATAGTGCA 59.965 41.667 0.00 0.00 0.00 4.57
2840 2864 2.539081 GCCTTTGTCCCTCCCTGGT 61.539 63.158 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
342 346 2.200081 CCTTCTTGGGATTCCTCCTCA 58.800 52.381 2.01 0.00 41.74 3.86
461 465 0.394352 CTTATTGCGAAGGGGCCACT 60.394 55.000 0.00 0.00 0.00 4.00
477 481 1.290955 CGTCACGGTCTTGCCCTTA 59.709 57.895 0.00 0.00 0.00 2.69
559 563 1.006571 TGCGGTGTTCTTCCTCGAC 60.007 57.895 0.00 0.00 0.00 4.20
791 803 3.548014 GCGTGCAACCCATATTGACATAC 60.548 47.826 0.00 0.00 0.00 2.39
1077 1089 0.959553 TTTCTCGCTCTGTCCGTTCT 59.040 50.000 0.00 0.00 0.00 3.01
1316 1328 9.154847 GGGTAAGTAACACGTAATTTACATTCT 57.845 33.333 13.42 2.25 31.66 2.40
1431 1444 1.202817 GACCAGAAGACCTTCTCCGTC 59.797 57.143 9.17 12.85 46.13 4.79
1527 1540 3.004951 CCCTTCATGGCCTGCTCT 58.995 61.111 3.32 0.00 0.00 4.09
1650 1663 1.675714 CGAGCACCTTCAATACAGGCA 60.676 52.381 0.00 0.00 34.32 4.75
1715 1728 3.254060 GCGTCAGTGATTAGCTTCTTCA 58.746 45.455 0.00 0.00 0.00 3.02
1931 1944 7.040823 CCATCTCTCAGATTTAATAAACAGCCC 60.041 40.741 0.00 0.00 31.32 5.19
2061 2074 1.008995 CGGTTGCCTTGTTCGTTGG 60.009 57.895 0.00 0.00 0.00 3.77
2417 2430 6.094048 CGAATCATGTCTTGGGTCAATAGTTT 59.906 38.462 0.00 0.00 0.00 2.66
2562 2576 5.181056 TGTTCATTTACGACATGTTGCATCT 59.819 36.000 13.30 0.00 0.00 2.90
2672 2696 3.717400 TCCGCACTCATAACAGATCTC 57.283 47.619 0.00 0.00 0.00 2.75
2680 2704 7.931407 ACTATTTGTATCATTCCGCACTCATAA 59.069 33.333 0.00 0.00 0.00 1.90
2709 2733 1.351017 TCGTCCAATCCCTTGCTTTCT 59.649 47.619 0.00 0.00 0.00 2.52
2791 2815 2.567169 CACTCAGGTGGTCTCCATTACA 59.433 50.000 0.00 0.00 39.59 2.41


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

AutoCloner maintained by Alex Coulton.