Multiple sequence alignment - TraesCS1D01G011000

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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 TraesCS1D01G011000 chr1D 100.000 2833 0 0 1 2833 5543163 5540331 0 5232
1 TraesCS1D01G011000 chr1D 89.192 1980 195 15 1 1978 276766058 276764096 0 2453
2 TraesCS1D01G011000 chr2D 92.970 2731 156 16 1 2701 428619032 428616308 0 3947
3 TraesCS1D01G011000 chr2D 88.651 2846 265 26 1 2833 72324109 72326909 0 3413
4 TraesCS1D01G011000 chr2D 92.374 2190 123 24 680 2833 554135209 554137390 0 3079
5 TraesCS1D01G011000 chr4A 89.021 2851 256 38 1 2833 705688524 705685713 0 3478
6 TraesCS1D01G011000 chr4A 88.757 2873 265 29 1 2833 276813495 276810641 0 3463
7 TraesCS1D01G011000 chr4A 88.552 2175 222 18 680 2833 348506325 348504157 0 2612
8 TraesCS1D01G011000 chr6D 86.704 2843 308 42 1 2832 27287091 27289874 0 3092
9 TraesCS1D01G011000 chr6D 94.041 923 47 3 1918 2833 426957943 426958864 0 1393
10 TraesCS1D01G011000 chr7A 85.961 2842 325 45 1 2832 270264397 270261620 0 2970
11 TraesCS1D01G011000 chr1B 89.646 1893 178 17 1 1879 218450021 218451909 0 2394
12 TraesCS1D01G011000 chr5B 88.543 1990 193 23 1 1979 615661536 615663501 0 2379
13 TraesCS1D01G011000 chr5B 88.895 1828 165 19 1 1817 615633596 615635396 0 2217
14 TraesCS1D01G011000 chr4D 93.074 924 53 6 1918 2833 179918839 179917919 0 1341
15 TraesCS1D01G011000 chr2B 92.134 928 61 6 1918 2833 366589170 366590097 0 1299
16 TraesCS1D01G011000 chr3D 90.968 930 65 11 1919 2833 554274589 554275514 0 1234


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 TraesCS1D01G011000 chr1D 5540331 5543163 2832 True 5232 5232 100.000 1 2833 1 chr1D.!!$R1 2832
1 TraesCS1D01G011000 chr1D 276764096 276766058 1962 True 2453 2453 89.192 1 1978 1 chr1D.!!$R2 1977
2 TraesCS1D01G011000 chr2D 428616308 428619032 2724 True 3947 3947 92.970 1 2701 1 chr2D.!!$R1 2700
3 TraesCS1D01G011000 chr2D 72324109 72326909 2800 False 3413 3413 88.651 1 2833 1 chr2D.!!$F1 2832
4 TraesCS1D01G011000 chr2D 554135209 554137390 2181 False 3079 3079 92.374 680 2833 1 chr2D.!!$F2 2153
5 TraesCS1D01G011000 chr4A 705685713 705688524 2811 True 3478 3478 89.021 1 2833 1 chr4A.!!$R3 2832
6 TraesCS1D01G011000 chr4A 276810641 276813495 2854 True 3463 3463 88.757 1 2833 1 chr4A.!!$R1 2832
7 TraesCS1D01G011000 chr4A 348504157 348506325 2168 True 2612 2612 88.552 680 2833 1 chr4A.!!$R2 2153
8 TraesCS1D01G011000 chr6D 27287091 27289874 2783 False 3092 3092 86.704 1 2832 1 chr6D.!!$F1 2831
9 TraesCS1D01G011000 chr6D 426957943 426958864 921 False 1393 1393 94.041 1918 2833 1 chr6D.!!$F2 915
10 TraesCS1D01G011000 chr7A 270261620 270264397 2777 True 2970 2970 85.961 1 2832 1 chr7A.!!$R1 2831
11 TraesCS1D01G011000 chr1B 218450021 218451909 1888 False 2394 2394 89.646 1 1879 1 chr1B.!!$F1 1878
12 TraesCS1D01G011000 chr5B 615661536 615663501 1965 False 2379 2379 88.543 1 1979 1 chr5B.!!$F2 1978
13 TraesCS1D01G011000 chr5B 615633596 615635396 1800 False 2217 2217 88.895 1 1817 1 chr5B.!!$F1 1816
14 TraesCS1D01G011000 chr4D 179917919 179918839 920 True 1341 1341 93.074 1918 2833 1 chr4D.!!$R1 915
15 TraesCS1D01G011000 chr2B 366589170 366590097 927 False 1299 1299 92.134 1918 2833 1 chr2B.!!$F1 915
16 TraesCS1D01G011000 chr3D 554274589 554275514 925 False 1234 1234 90.968 1919 2833 1 chr3D.!!$F1 914

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
275 277 1.203100 AGCCTGTGGGAGAAGCAAATT 60.203 47.619 0.0 0.0 33.58 1.82 F
581 584 4.212425 TGTGTTACCGTCTTATTTGCACAG 59.788 41.667 0.0 0.0 31.81 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1218 1330 0.037605 ACAATCCTGTCCCGTTCGAC 60.038 55.0 0.00 0.00 0.00 4.20 R
2495 2700 0.681733 AAGTGATCACGTGGTGCTCT 59.318 50.0 19.85 8.59 31.07 4.09 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
119 120 1.440938 CTGAGGAGACGCTAGGACCG 61.441 65.000 0.00 0.00 0.00 4.79
144 146 2.936912 GCTGACCGTCCAGAGCTGT 61.937 63.158 0.00 0.00 36.29 4.40
208 210 1.542547 GGAGTTTGAACGGAGCTGGAA 60.543 52.381 0.00 0.00 0.00 3.53
271 273 1.903877 GCTAGCCTGTGGGAGAAGCA 61.904 60.000 2.29 0.00 35.02 3.91
275 277 1.203100 AGCCTGTGGGAGAAGCAAATT 60.203 47.619 0.00 0.00 33.58 1.82
434 436 6.039270 ACACAGCTTTGCAACAGAAAATACTA 59.961 34.615 0.00 0.00 0.00 1.82
437 439 5.183904 AGCTTTGCAACAGAAAATACTAGGG 59.816 40.000 0.00 0.00 0.00 3.53
581 584 4.212425 TGTGTTACCGTCTTATTTGCACAG 59.788 41.667 0.00 0.00 31.81 3.66
612 615 6.323737 AGGTAGTAGGTGCCATATAGAATGT 58.676 40.000 0.00 0.00 31.94 2.71
829 880 5.859521 TTGCCATGTTAAATGAAATGCAC 57.140 34.783 0.00 0.00 0.00 4.57
836 887 5.363101 TGTTAAATGAAATGCACTTGCCAA 58.637 33.333 0.00 0.00 41.18 4.52
837 888 5.996513 TGTTAAATGAAATGCACTTGCCAAT 59.003 32.000 0.00 0.00 41.18 3.16
839 913 7.658982 TGTTAAATGAAATGCACTTGCCAATTA 59.341 29.630 0.00 0.00 41.18 1.40
965 1072 6.832520 TTCATTTTAGATGCCTTTGCTACA 57.167 33.333 0.00 0.00 38.71 2.74
1218 1330 6.510157 CGAATACTACTACCAATGCTGCAAAG 60.510 42.308 6.36 1.65 0.00 2.77
1269 1381 9.378551 GTCACATACTAAAAGTAATGGACATGA 57.621 33.333 0.00 0.00 33.89 3.07
1275 1387 2.665649 AGTAATGGACATGAACGCGA 57.334 45.000 15.93 0.00 0.00 5.87
1290 1402 2.586079 CGATCACGCGAATGCCCT 60.586 61.111 15.93 0.00 38.08 5.19
1291 1403 1.299850 CGATCACGCGAATGCCCTA 60.300 57.895 15.93 0.00 38.08 3.53
1302 1414 3.758554 GCGAATGCCCTACCATTTCATAT 59.241 43.478 0.00 0.00 35.67 1.78
1432 1544 2.676342 ACGTTGTGTTGACCAAGAACTC 59.324 45.455 0.00 0.00 0.00 3.01
1560 1672 2.704572 CTGAAGAAGCCTTACACAGGG 58.295 52.381 0.00 0.00 44.16 4.45
1782 1900 1.393539 CGTAAGCAACATTGGAGGACG 59.606 52.381 0.00 0.00 0.00 4.79
1885 2008 7.308109 GCATCAGAATTTGAAAGAAAATGCCAA 60.308 33.333 0.00 0.00 39.77 4.52
1908 2031 5.513233 AGAATGAATGACTACAATTGCCCT 58.487 37.500 5.05 0.00 0.00 5.19
1916 2062 1.541147 CTACAATTGCCCTGTGTGTGG 59.459 52.381 5.05 0.00 0.00 4.17
1953 2099 7.255730 GCCATGTTATTTCTATTGAATCTGCCT 60.256 37.037 0.00 0.00 31.56 4.75
2114 2290 0.589708 AAAACGCAAGGTAACGGCTC 59.410 50.000 0.00 0.00 46.39 4.70
2233 2413 7.938563 TCAACTACATTTGCCATGTTTTTAC 57.061 32.000 4.09 0.00 33.76 2.01
2441 2637 9.709495 AACATAGTACACGGACATAGTTTTAAA 57.291 29.630 0.00 0.00 0.00 1.52
2495 2700 3.550820 TGTAAGGTAGGCGTTCGGTATA 58.449 45.455 0.00 0.00 0.00 1.47
2640 2846 0.251354 AGCTCGATGACCATTGCAGT 59.749 50.000 0.00 0.00 0.00 4.40
2661 2867 1.229051 TGATGACAGGGACCCGTCA 60.229 57.895 28.58 28.58 39.67 4.35
2668 2874 1.152096 AGGGACCCGTCAACCTTCT 60.152 57.895 4.40 0.00 0.00 2.85
2669 2875 0.767060 AGGGACCCGTCAACCTTCTT 60.767 55.000 4.40 0.00 0.00 2.52
2671 2877 1.235724 GGACCCGTCAACCTTCTTTG 58.764 55.000 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 0.036858 GCGTCTCCTCAGCCTTCTTT 60.037 55.000 0.00 0.00 0.00 2.52
119 120 0.868406 CTGGACGGTCAGCAAAGAAC 59.132 55.000 10.76 0.00 0.00 3.01
144 146 2.031245 CGCACAACTTGAATGCCTTGTA 60.031 45.455 0.00 0.00 35.91 2.41
208 210 8.844244 GGACTTGATATGTTTCAATCATAGCTT 58.156 33.333 0.00 0.00 35.86 3.74
271 273 1.254975 GGCCGGCACCCAGTAAATTT 61.255 55.000 30.85 0.00 0.00 1.82
275 277 2.284773 TAGGCCGGCACCCAGTAA 60.285 61.111 30.85 0.01 0.00 2.24
434 436 0.901124 CTTGCTGTAGCTCAGACCCT 59.099 55.000 14.86 0.00 46.27 4.34
437 439 1.999024 GCTTCTTGCTGTAGCTCAGAC 59.001 52.381 14.86 8.26 46.27 3.51
548 550 6.780706 AAGACGGTAACACAATTGACTTAG 57.219 37.500 13.59 0.00 0.00 2.18
559 561 4.378046 CCTGTGCAAATAAGACGGTAACAC 60.378 45.833 0.00 0.00 0.00 3.32
581 584 1.475213 GGCACCTACTACCTTCATGCC 60.475 57.143 0.00 0.00 43.89 4.40
645 649 9.113838 CTGTACTCAATGGCTACTTTTCAATAT 57.886 33.333 0.00 0.00 0.00 1.28
719 724 1.263217 GCAACTACAGTTCAACCCACG 59.737 52.381 0.00 0.00 35.83 4.94
965 1072 5.163237 ACCTTATGTTGATGTAGGCCGTAAT 60.163 40.000 0.00 0.00 0.00 1.89
1040 1151 1.396996 GCGCGCTTTATTTCTTCCTGA 59.603 47.619 26.67 0.00 0.00 3.86
1058 1169 3.864686 GCCGTGTACATGCTGGCG 61.865 66.667 9.72 1.93 35.77 5.69
1218 1330 0.037605 ACAATCCTGTCCCGTTCGAC 60.038 55.000 0.00 0.00 0.00 4.20
1275 1387 1.227556 GGTAGGGCATTCGCGTGAT 60.228 57.895 5.77 0.00 39.92 3.06
1284 1396 3.434309 GCCATATGAAATGGTAGGGCAT 58.566 45.455 3.65 0.00 44.73 4.40
1290 1402 1.070914 TCGCCGCCATATGAAATGGTA 59.929 47.619 3.65 0.00 41.17 3.25
1291 1403 0.179032 TCGCCGCCATATGAAATGGT 60.179 50.000 3.65 0.00 41.17 3.55
1302 1414 4.776322 CCAAGTCCATCGCCGCCA 62.776 66.667 0.00 0.00 0.00 5.69
1432 1544 6.566187 GCATGCTTCATCTATTAGTTCAGCAG 60.566 42.308 11.37 7.85 39.29 4.24
1560 1672 3.637273 ACTTGAGGTGCGGGGGAC 61.637 66.667 0.00 0.00 0.00 4.46
1782 1900 3.018149 TGTGACCAACAACCAAGTTACC 58.982 45.455 0.00 0.00 35.24 2.85
1885 2008 5.359009 CAGGGCAATTGTAGTCATTCATTCT 59.641 40.000 7.40 0.00 0.00 2.40
1908 2031 2.549992 GGCAGATTCAGTACCACACACA 60.550 50.000 0.00 0.00 0.00 3.72
1916 2062 7.559590 AGAAATAACATGGCAGATTCAGTAC 57.440 36.000 0.00 0.00 0.00 2.73
1953 2099 7.611467 ACATGGCAGATTCAGTAGAAATAACAA 59.389 33.333 0.00 0.00 37.29 2.83
2114 2290 4.750098 CGGTTAGCATGGTAGTTCATAAGG 59.250 45.833 4.57 0.00 0.00 2.69
2233 2413 3.590720 TTTGAATGCGTCTATGATGCG 57.409 42.857 7.18 0.00 46.39 4.73
2367 2560 1.552578 ATAGTGGTGGCGTGTGAGTA 58.447 50.000 0.00 0.00 0.00 2.59
2440 2636 6.601332 TGAGGAAGGTATCAACTTGTTCTTT 58.399 36.000 0.00 0.00 0.00 2.52
2441 2637 6.187727 TGAGGAAGGTATCAACTTGTTCTT 57.812 37.500 0.00 0.00 0.00 2.52
2457 2660 2.486472 ACATTCTGTGGCTGAGGAAG 57.514 50.000 0.00 0.00 0.00 3.46
2495 2700 0.681733 AAGTGATCACGTGGTGCTCT 59.318 50.000 19.85 8.59 31.07 4.09
2640 2846 1.125093 ACGGGTCCCTGTCATCACAA 61.125 55.000 6.29 0.00 29.82 3.33
2661 2867 5.869649 ATACCTTGCAAACAAAGAAGGTT 57.130 34.783 7.71 0.00 44.75 3.50
2668 2874 4.142138 ACGTTGGAATACCTTGCAAACAAA 60.142 37.500 0.00 0.00 43.21 2.83
2669 2875 3.381908 ACGTTGGAATACCTTGCAAACAA 59.618 39.130 0.00 0.00 43.21 2.83
2671 2877 3.243267 ACACGTTGGAATACCTTGCAAAC 60.243 43.478 0.00 0.00 43.21 2.93


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

AutoCloner maintained by Alex Coulton.