Multiple sequence alignment - TraesCS1A01G129000

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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 TraesCS1A01G129000 chr1A 100.000 2546 0 0 1 2546 161672752 161670207 0.000000e+00 4702.0
1 TraesCS1A01G129000 chr1A 84.615 195 27 3 1867 2059 1740280 1740473 9.300000e-45 191.0
2 TraesCS1A01G129000 chr1B 96.996 1132 27 4 742 1868 214571672 214572801 0.000000e+00 1895.0
3 TraesCS1A01G129000 chr1B 97.170 742 17 3 1 741 111360804 111361542 0.000000e+00 1251.0
4 TraesCS1A01G129000 chr1B 91.069 627 49 3 117 742 107074538 107073918 0.000000e+00 841.0
5 TraesCS1A01G129000 chr1B 95.041 121 6 0 1 121 107080023 107079903 9.300000e-45 191.0
6 TraesCS1A01G129000 chr1B 97.059 34 1 0 700 733 42077433 42077400 9.840000e-05 58.4
7 TraesCS1A01G129000 chr1D 96.806 1127 34 2 742 1868 135394685 135395809 0.000000e+00 1881.0
8 TraesCS1A01G129000 chr6B 97.301 741 16 2 1 741 563115778 563115042 0.000000e+00 1254.0
9 TraesCS1A01G129000 chr6B 93.396 742 43 3 1 741 707501011 707500275 0.000000e+00 1094.0
10 TraesCS1A01G129000 chr6B 77.818 275 51 8 1868 2138 187509537 187509269 7.290000e-36 161.0
11 TraesCS1A01G129000 chr6B 81.522 184 23 10 1864 2042 624612925 624612748 9.500000e-30 141.0
12 TraesCS1A01G129000 chr2A 95.710 746 8 3 1 746 772011044 772011765 0.000000e+00 1179.0
13 TraesCS1A01G129000 chr2A 95.013 742 21 4 1 741 719701163 719700437 0.000000e+00 1151.0
14 TraesCS1A01G129000 chr2A 96.907 582 14 2 1969 2546 203900103 203900684 0.000000e+00 972.0
15 TraesCS1A01G129000 chr2A 92.675 587 42 1 156 741 676322013 676322599 0.000000e+00 845.0
16 TraesCS1A01G129000 chr2A 93.548 155 10 0 1 155 676311848 676312002 5.480000e-57 231.0
17 TraesCS1A01G129000 chr2A 92.593 108 8 0 1869 1976 203899084 203899191 3.390000e-34 156.0
18 TraesCS1A01G129000 chr2A 82.895 152 19 5 1894 2042 773795653 773795506 2.060000e-26 130.0
19 TraesCS1A01G129000 chr2A 81.053 95 8 5 2450 2538 554097828 554097918 1.630000e-07 67.6
20 TraesCS1A01G129000 chr5D 94.609 742 36 4 1 741 382948827 382949565 0.000000e+00 1146.0
21 TraesCS1A01G129000 chr5D 81.532 222 39 2 1869 2090 6388672 6388891 5.600000e-42 182.0
22 TraesCS1A01G129000 chr3B 93.062 418 28 1 1 417 514875692 514875275 6.020000e-171 610.0
23 TraesCS1A01G129000 chr3B 92.333 300 22 1 416 714 514761118 514760819 2.340000e-115 425.0
24 TraesCS1A01G129000 chr4A 81.250 256 35 6 2291 2541 685224620 685224867 7.190000e-46 195.0
25 TraesCS1A01G129000 chr3A 79.891 184 33 4 1869 2050 136034299 136034480 5.720000e-27 132.0
26 TraesCS1A01G129000 chr7B 83.217 143 20 3 1868 2008 22538907 22538767 7.390000e-26 128.0
27 TraesCS1A01G129000 chr6A 80.337 178 23 11 1869 2042 461979509 461979678 9.560000e-25 124.0
28 TraesCS1A01G129000 chr2D 79.808 104 11 7 2450 2546 432866643 432866543 1.630000e-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 TraesCS1A01G129000 chr1A 161670207 161672752 2545 True 4702 4702 100.000 1 2546 1 chr1A.!!$R1 2545
1 TraesCS1A01G129000 chr1B 214571672 214572801 1129 False 1895 1895 96.996 742 1868 1 chr1B.!!$F2 1126
2 TraesCS1A01G129000 chr1B 111360804 111361542 738 False 1251 1251 97.170 1 741 1 chr1B.!!$F1 740
3 TraesCS1A01G129000 chr1B 107073918 107074538 620 True 841 841 91.069 117 742 1 chr1B.!!$R2 625
4 TraesCS1A01G129000 chr1D 135394685 135395809 1124 False 1881 1881 96.806 742 1868 1 chr1D.!!$F1 1126
5 TraesCS1A01G129000 chr6B 563115042 563115778 736 True 1254 1254 97.301 1 741 1 chr6B.!!$R2 740
6 TraesCS1A01G129000 chr6B 707500275 707501011 736 True 1094 1094 93.396 1 741 1 chr6B.!!$R4 740
7 TraesCS1A01G129000 chr2A 772011044 772011765 721 False 1179 1179 95.710 1 746 1 chr2A.!!$F4 745
8 TraesCS1A01G129000 chr2A 719700437 719701163 726 True 1151 1151 95.013 1 741 1 chr2A.!!$R1 740
9 TraesCS1A01G129000 chr2A 676322013 676322599 586 False 845 845 92.675 156 741 1 chr2A.!!$F3 585
10 TraesCS1A01G129000 chr2A 203899084 203900684 1600 False 564 972 94.750 1869 2546 2 chr2A.!!$F5 677
11 TraesCS1A01G129000 chr5D 382948827 382949565 738 False 1146 1146 94.609 1 741 1 chr5D.!!$F2 740

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
978 1009 0.323302 TTAGCTGCCGATCACCAACA 59.677 50.0 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 3046 2.235891 CAAAAGGGACCCACTAACCAC 58.764 52.381 14.6 0.0 0.0 4.16 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
135 136 4.007644 CTCCACCACGAGCCTGCA 62.008 66.667 0.00 0.00 0.00 4.41
558 581 3.053991 TCTGACGGGAAAGAGAGAGAGAT 60.054 47.826 0.00 0.00 0.00 2.75
606 629 4.323477 CCCCGCTGGACCGAACAA 62.323 66.667 0.00 0.00 35.39 2.83
635 658 9.016623 GCGTATTAGGATTGGTATTTTGTTTTC 57.983 33.333 0.00 0.00 0.00 2.29
682 708 0.398381 GAGGAGAGGCAGGGATGAGT 60.398 60.000 0.00 0.00 0.00 3.41
797 823 1.865788 CGCACCCCACAAACATGGAG 61.866 60.000 0.00 0.00 43.02 3.86
934 965 1.280457 CTACCCTCTCCTTGCCTTGT 58.720 55.000 0.00 0.00 0.00 3.16
941 972 2.303022 CTCTCCTTGCCTTGTCTTGGTA 59.697 50.000 0.00 0.00 0.00 3.25
978 1009 0.323302 TTAGCTGCCGATCACCAACA 59.677 50.000 0.00 0.00 0.00 3.33
1065 1096 1.491668 TGTTATCCGCCAGCTTCCTA 58.508 50.000 0.00 0.00 0.00 2.94
1564 1595 0.391661 AGACGTACCCTTGCATGCAG 60.392 55.000 21.50 12.23 0.00 4.41
1739 1770 5.701290 CCTTTGTTGAGTAGGTCTCGAAATT 59.299 40.000 0.00 0.00 45.46 1.82
1872 1903 9.130312 CTCTTATGTGTCGTTTATAATAGAGGC 57.870 37.037 0.00 0.00 0.00 4.70
1904 1935 5.416083 CGGTGGTGTCTAAACTTATCATGA 58.584 41.667 0.00 0.00 0.00 3.07
1912 1943 9.979270 GTGTCTAAACTTATCATGAATGTTCAG 57.021 33.333 0.00 1.33 41.08 3.02
1959 1990 5.591099 ACGTCGAACTGGTTCTAAAACTTA 58.409 37.500 0.00 0.00 37.44 2.24
2003 2953 6.439599 GTGCTAATCTCACATGTAGACGTAT 58.560 40.000 0.00 0.00 34.73 3.06
2014 2964 5.299531 ACATGTAGACGTATAGTGTGCTCAT 59.700 40.000 0.00 0.00 30.27 2.90
2036 2986 0.447801 GGCACTGTATTTGGCTGACG 59.552 55.000 0.00 0.00 36.62 4.35
2043 2993 1.093972 TATTTGGCTGACGTGGCATG 58.906 50.000 4.87 4.87 42.07 4.06
2061 3011 2.440247 GGGCCCGCTTGTAGCAAT 60.440 61.111 5.69 0.00 42.58 3.56
2114 3064 1.423921 CTGTGGTTAGTGGGTCCCTTT 59.576 52.381 10.00 0.00 0.00 3.11
2126 3076 4.019591 GTGGGTCCCTTTTGTCAGTATAGT 60.020 45.833 10.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
302 325 1.275856 CCTGCAGAGACTGAGAAGCTT 59.724 52.381 17.39 0.00 32.44 3.74
558 581 5.295292 CGTATTCTTCACCTCGTTACTCCTA 59.705 44.000 0.00 0.00 0.00 2.94
606 629 6.316890 ACAAAATACCAATCCTAATACGCGTT 59.683 34.615 20.78 1.73 0.00 4.84
635 658 3.574216 CTGTTTTTGGCAGCGAAAAAG 57.426 42.857 23.73 12.53 33.26 2.27
749 775 1.693606 TGACTCCTGTGCATGTCTCAA 59.306 47.619 0.00 0.00 0.00 3.02
797 823 2.923605 TTGTGTTGTTTCGTTGGTCC 57.076 45.000 0.00 0.00 0.00 4.46
883 909 2.510768 GGGTGGTGACGCTCTTATAG 57.489 55.000 0.00 0.00 38.67 1.31
934 965 2.355986 ATGGAGCGGCGTACCAAGA 61.356 57.895 24.63 7.99 37.24 3.02
941 972 2.543777 AAATATACATGGAGCGGCGT 57.456 45.000 9.37 0.00 0.00 5.68
978 1009 7.309805 GCCATAGTTTATTTTGTTGGGTCTCTT 60.310 37.037 0.00 0.00 0.00 2.85
1107 1138 3.876198 CATACGCCGGCAACCAGC 61.876 66.667 28.98 0.00 44.65 4.85
1708 1739 0.251165 TACTCAACAAAGGCAGGCCC 60.251 55.000 6.70 0.00 36.58 5.80
1739 1770 2.361085 AGAAAAAGGCCCTCCTCCTA 57.639 50.000 0.00 0.00 43.40 2.94
1846 1877 9.130312 GCCTCTATTATAAACGACACATAAGAG 57.870 37.037 0.00 0.00 0.00 2.85
1904 1935 6.639632 AGTTCATGCACTAAACTGAACATT 57.360 33.333 23.44 7.61 46.22 2.71
1939 1970 7.223387 GTCTGTTAAGTTTTAGAACCAGTTCGA 59.777 37.037 4.94 0.00 43.97 3.71
1941 1972 8.205131 TGTCTGTTAAGTTTTAGAACCAGTTC 57.795 34.615 2.19 2.19 39.78 3.01
1950 1981 8.801715 ATTTGCACATGTCTGTTAAGTTTTAG 57.198 30.769 0.00 0.00 31.62 1.85
1959 1990 3.058293 CACCGTATTTGCACATGTCTGTT 60.058 43.478 0.00 0.00 31.62 3.16
2014 2964 3.278574 GTCAGCCAAATACAGTGCCATA 58.721 45.455 0.00 0.00 0.00 2.74
2043 2993 4.733542 TTGCTACAAGCGGGCCCC 62.734 66.667 18.66 9.47 46.26 5.80
2049 2999 6.195244 GTGATAATGTTTCATTGCTACAAGCG 59.805 38.462 5.40 0.00 46.26 4.68
2096 3046 2.235891 CAAAAGGGACCCACTAACCAC 58.764 52.381 14.60 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.