Multiple sequence alignment - TraesCS1A01G091800

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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 TraesCS1A01G091800 chr1A 100.000 3026 0 0 1 3026 84287827 84284802 0.000000e+00 5589
1 TraesCS1A01G091800 chr1A 95.629 3043 74 12 1 3026 587709618 587712618 0.000000e+00 4828
2 TraesCS1A01G091800 chr1A 95.754 2944 85 17 1 2915 498220599 498217667 0.000000e+00 4708
3 TraesCS1A01G091800 chr1A 95.127 2914 88 22 1 2884 23399529 23402418 0.000000e+00 4545
4 TraesCS1A01G091800 chr4A 97.143 3045 68 8 1 3026 589100064 589097020 0.000000e+00 5123
5 TraesCS1A01G091800 chr4A 96.265 2597 68 5 1 2568 155286350 155283754 0.000000e+00 4231
6 TraesCS1A01G091800 chr7A 96.589 3049 79 7 1 3026 516843082 516846128 0.000000e+00 5031
7 TraesCS1A01G091800 chr7A 96.031 3049 98 5 1 3026 646800469 646803517 0.000000e+00 4939
8 TraesCS1A01G091800 chr5A 96.458 3049 84 6 1 3026 404492956 404496003 0.000000e+00 5011
9 TraesCS1A01G091800 chr5A 96.197 3024 65 10 1 3000 522122712 522119715 0.000000e+00 4902
10 TraesCS1A01G091800 chr5A 95.736 3049 82 9 1 3026 59605802 59608825 0.000000e+00 4867
11 TraesCS1A01G091800 chr5A 96.317 2905 57 10 1 2887 99544937 99542065 0.000000e+00 4726
12 TraesCS1A01G091800 chr6A 96.065 3024 69 10 1 3000 37846978 37849975 0.000000e+00 4879
13 TraesCS1A01G091800 chr6A 95.548 3055 81 12 1 3026 608727647 608730675 0.000000e+00 4837
14 TraesCS1A01G091800 chr6A 95.578 2940 93 16 1 2915 559145173 559148100 0.000000e+00 4674
15 TraesCS1A01G091800 chr6A 93.864 2966 138 14 1 2931 396287501 396284545 0.000000e+00 4429
16 TraesCS1A01G091800 chr2A 95.896 2924 80 19 1 2897 202056306 202059216 0.000000e+00 4698
17 TraesCS1A01G091800 chr5B 90.488 410 37 2 2617 3026 62935210 62934803 9.540000e-150 540


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 TraesCS1A01G091800 chr1A 84284802 84287827 3025 True 5589 5589 100.000 1 3026 1 chr1A.!!$R1 3025
1 TraesCS1A01G091800 chr1A 587709618 587712618 3000 False 4828 4828 95.629 1 3026 1 chr1A.!!$F2 3025
2 TraesCS1A01G091800 chr1A 498217667 498220599 2932 True 4708 4708 95.754 1 2915 1 chr1A.!!$R2 2914
3 TraesCS1A01G091800 chr1A 23399529 23402418 2889 False 4545 4545 95.127 1 2884 1 chr1A.!!$F1 2883
4 TraesCS1A01G091800 chr4A 589097020 589100064 3044 True 5123 5123 97.143 1 3026 1 chr4A.!!$R2 3025
5 TraesCS1A01G091800 chr4A 155283754 155286350 2596 True 4231 4231 96.265 1 2568 1 chr4A.!!$R1 2567
6 TraesCS1A01G091800 chr7A 516843082 516846128 3046 False 5031 5031 96.589 1 3026 1 chr7A.!!$F1 3025
7 TraesCS1A01G091800 chr7A 646800469 646803517 3048 False 4939 4939 96.031 1 3026 1 chr7A.!!$F2 3025
8 TraesCS1A01G091800 chr5A 404492956 404496003 3047 False 5011 5011 96.458 1 3026 1 chr5A.!!$F2 3025
9 TraesCS1A01G091800 chr5A 522119715 522122712 2997 True 4902 4902 96.197 1 3000 1 chr5A.!!$R2 2999
10 TraesCS1A01G091800 chr5A 59605802 59608825 3023 False 4867 4867 95.736 1 3026 1 chr5A.!!$F1 3025
11 TraesCS1A01G091800 chr5A 99542065 99544937 2872 True 4726 4726 96.317 1 2887 1 chr5A.!!$R1 2886
12 TraesCS1A01G091800 chr6A 37846978 37849975 2997 False 4879 4879 96.065 1 3000 1 chr6A.!!$F1 2999
13 TraesCS1A01G091800 chr6A 608727647 608730675 3028 False 4837 4837 95.548 1 3026 1 chr6A.!!$F3 3025
14 TraesCS1A01G091800 chr6A 559145173 559148100 2927 False 4674 4674 95.578 1 2915 1 chr6A.!!$F2 2914
15 TraesCS1A01G091800 chr6A 396284545 396287501 2956 True 4429 4429 93.864 1 2931 1 chr6A.!!$R1 2930
16 TraesCS1A01G091800 chr2A 202056306 202059216 2910 False 4698 4698 95.896 1 2897 1 chr2A.!!$F1 2896

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
668 683 0.033796 CCATGGATGTGGCTGAAGGT 60.034 55.0 5.56 0.0 31.43 3.5 F
1742 1776 0.107654 GCACGGAGTCCCTGCTATTT 60.108 55.0 21.80 0.0 41.61 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2057 0.539986 CGCCTTAACTTCCTGGCCTA 59.460 55.000 3.32 0.0 42.15 3.93 R
2804 2949 1.227823 TGCCGTGCTGTTAACTGCT 60.228 52.632 29.94 0.0 40.79 4.24 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
159 171 2.320671 TGGTCCTGCCATGCCTTAT 58.679 52.632 0.00 0.00 43.61 1.73
249 261 2.174319 GCCGAATCTGAACGCTCCC 61.174 63.158 0.00 0.00 0.00 4.30
267 279 2.031012 CTGGTGTCCGCTCTTGCA 59.969 61.111 0.00 0.00 39.64 4.08
312 324 2.257207 AGTTTCCATCTTCGGACTGGA 58.743 47.619 0.30 0.30 37.29 3.86
320 332 3.304911 TCTTCGGACTGGAGAGATGAT 57.695 47.619 0.00 0.00 0.00 2.45
646 661 0.836606 TGACTCCACTGGCAAGAACA 59.163 50.000 0.00 0.00 0.00 3.18
668 683 0.033796 CCATGGATGTGGCTGAAGGT 60.034 55.000 5.56 0.00 31.43 3.50
897 915 5.656859 TGCTTCTACTTTCTGTATGGAGCTA 59.343 40.000 0.00 0.00 34.68 3.32
964 982 7.199167 TCCTTGGTATGAAGATGAAGATGAA 57.801 36.000 0.00 0.00 0.00 2.57
1468 1502 2.650116 GGACAGGAGAAGGCAGCGA 61.650 63.158 0.00 0.00 0.00 4.93
1742 1776 0.107654 GCACGGAGTCCCTGCTATTT 60.108 55.000 21.80 0.00 41.61 1.40
1794 1828 1.517210 TTTACTTTCCCGTTGGCCGC 61.517 55.000 0.00 0.00 34.38 6.53
1812 1846 3.925913 GCCGCATTACACATGTTTGAATT 59.074 39.130 0.00 0.00 0.00 2.17
2007 2041 5.643777 CGGAGTTTCATATCTTCCACACTTT 59.356 40.000 0.00 0.00 0.00 2.66
2023 2057 5.034152 CACACTTTTTCATGTTACAGCGTT 58.966 37.500 0.00 0.00 0.00 4.84
2486 2574 0.032615 AAGAGGAGGCTCGTCCATCT 60.033 55.000 28.22 14.21 39.34 2.90
2575 2663 3.902881 ATGGAAGTGCTCTCTTGTAGG 57.097 47.619 0.00 0.00 0.00 3.18
2640 2728 4.575885 TGGTGAACTCTTACTATTGTGGC 58.424 43.478 0.00 0.00 0.00 5.01
2666 2779 8.932791 CATTTGTGTTTCCGAACTAGTAGTAAT 58.067 33.333 2.50 0.00 36.70 1.89
2819 2964 3.799035 CAGTTTAGCAGTTAACAGCACG 58.201 45.455 22.93 7.33 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.724506 AGATTACTCGTTATTACCATCTCCTCA 59.275 37.037 0.00 0.00 0.00 3.86
249 261 2.743928 GCAAGAGCGGACACCAGG 60.744 66.667 0.00 0.00 0.00 4.45
312 324 1.745653 TCGAGCGTCACAATCATCTCT 59.254 47.619 0.00 0.00 0.00 3.10
320 332 0.109272 GACATCCTCGAGCGTCACAA 60.109 55.000 17.82 0.00 0.00 3.33
405 417 3.403277 GCAATCATCTGCTCGCGT 58.597 55.556 5.77 0.00 39.34 6.01
646 661 0.994247 TTCAGCCACATCCATGGAGT 59.006 50.000 21.33 14.93 43.02 3.85
668 683 1.542472 TGCTATCGAAGACGGTCAACA 59.458 47.619 11.27 0.00 42.51 3.33
897 915 0.687757 TCCAATAGGCAGACGCTCCT 60.688 55.000 0.00 0.00 38.60 3.69
964 982 2.124860 GTGGGGCGCCGTAATTCT 60.125 61.111 22.54 0.00 0.00 2.40
1468 1502 4.202567 TGCTTGTCCCAGTCCTTTATCTTT 60.203 41.667 0.00 0.00 0.00 2.52
1643 1677 9.007901 GGGTTCTTCAAGAATATCCTCATTATG 57.992 37.037 2.39 0.00 36.50 1.90
1742 1776 6.814644 CACTTTACCACATAGTTAATCACCGA 59.185 38.462 0.00 0.00 0.00 4.69
1794 1828 8.518151 TGTTAGCAATTCAAACATGTGTAATG 57.482 30.769 0.00 0.00 0.00 1.90
1812 1846 7.148188 GGATGAGAAAGAATGAACATGTTAGCA 60.148 37.037 11.95 6.76 0.00 3.49
2007 2041 2.745281 GGCCTAACGCTGTAACATGAAA 59.255 45.455 0.00 0.00 37.74 2.69
2023 2057 0.539986 CGCCTTAACTTCCTGGCCTA 59.460 55.000 3.32 0.00 42.15 3.93
2486 2574 3.264193 TGCAGGCAATCTTCTTCTTCCTA 59.736 43.478 0.00 0.00 0.00 2.94
2575 2663 3.185797 AGTTCATCAACCTAACGAAACGC 59.814 43.478 0.00 0.00 32.22 4.84
2640 2728 6.780706 ACTACTAGTTCGGAAACACAAATG 57.219 37.500 0.00 0.00 37.88 2.32
2666 2779 7.757941 TCACATCATTTAGGACAATTCAACA 57.242 32.000 0.00 0.00 0.00 3.33
2804 2949 1.227823 TGCCGTGCTGTTAACTGCT 60.228 52.632 29.94 0.00 40.79 4.24
2842 2987 3.352447 CGCTGCATAGTACAGTGCT 57.648 52.632 19.12 0.00 41.78 4.40
2871 3017 4.994471 CTGTGAGGTGCAGCGCCA 62.994 66.667 27.03 12.93 36.32 5.69


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

AutoCloner maintained by Alex Coulton.