Multiple sequence alignment - TraesCS7A01G485500

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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 TraesCS7A01G485500 chr7A 100.000 2321 0 0 1 2321 676281173 676278853 0.000000e+00 4287
1 TraesCS7A01G485500 chr7A 87.943 564 42 15 5 563 316236519 316235977 1.940000e-180 641
2 TraesCS7A01G485500 chr7A 84.220 545 43 13 1785 2299 676064886 676065417 7.450000e-135 490
3 TraesCS7A01G485500 chr4A 97.966 1770 29 5 1 1764 38715658 38717426 0.000000e+00 3062
4 TraesCS7A01G485500 chr4A 86.535 557 60 10 14 564 438322338 438322885 1.190000e-167 599
5 TraesCS7A01G485500 chr5D 96.167 1774 55 8 1 1764 80213500 80215270 0.000000e+00 2887
6 TraesCS7A01G485500 chr3D 96.210 1768 60 5 1 1763 65434812 65433047 0.000000e+00 2887
7 TraesCS7A01G485500 chr1D 96.381 1575 52 4 193 1765 6255953 6254382 0.000000e+00 2588
8 TraesCS7A01G485500 chr2A 96.490 1054 31 4 1 1050 628523921 628522870 0.000000e+00 1736
9 TraesCS7A01G485500 chr2A 95.574 723 30 2 1042 1764 628522719 628521999 0.000000e+00 1157
10 TraesCS7A01G485500 chr4B 87.490 1223 111 23 573 1766 116739396 116740605 0.000000e+00 1373
11 TraesCS7A01G485500 chr2D 90.984 976 63 15 1 962 602404110 602403146 0.000000e+00 1291
12 TraesCS7A01G485500 chr2D 90.647 973 70 13 1 962 602401954 602400992 0.000000e+00 1273
13 TraesCS7A01G485500 chr2D 91.759 813 57 7 957 1768 602379641 602378838 0.000000e+00 1122
14 TraesCS7A01G485500 chr2D 95.582 679 22 3 1087 1764 25805542 25806213 0.000000e+00 1081
15 TraesCS7A01G485500 chr5B 90.389 822 66 9 780 1591 576800606 576801424 0.000000e+00 1068
16 TraesCS7A01G485500 chr5B 88.772 668 64 7 59 720 576799913 576800575 0.000000e+00 808
17 TraesCS7A01G485500 chr1B 84.826 804 77 18 956 1735 610963352 610964134 0.000000e+00 767
18 TraesCS7A01G485500 chr7D 86.316 570 53 16 1 564 279398092 279398642 4.270000e-167 597
19 TraesCS7A01G485500 chr7D 83.951 567 57 16 1781 2321 585602511 585603069 1.590000e-141 512
20 TraesCS7A01G485500 chr5A 85.213 399 47 10 564 952 46498244 46498640 1.290000e-107 399
21 TraesCS7A01G485500 chr7B 90.816 196 14 1 2108 2299 654982837 654983032 2.290000e-65 259
22 TraesCS7A01G485500 chr7B 83.858 254 25 11 1838 2084 654982600 654982844 6.450000e-56 228
23 TraesCS7A01G485500 chr7B 91.613 155 13 0 1781 1935 655109004 655108850 5.020000e-52 215


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 TraesCS7A01G485500 chr7A 676278853 676281173 2320 True 4287.0 4287 100.0000 1 2321 1 chr7A.!!$R2 2320
1 TraesCS7A01G485500 chr7A 316235977 316236519 542 True 641.0 641 87.9430 5 563 1 chr7A.!!$R1 558
2 TraesCS7A01G485500 chr7A 676064886 676065417 531 False 490.0 490 84.2200 1785 2299 1 chr7A.!!$F1 514
3 TraesCS7A01G485500 chr4A 38715658 38717426 1768 False 3062.0 3062 97.9660 1 1764 1 chr4A.!!$F1 1763
4 TraesCS7A01G485500 chr4A 438322338 438322885 547 False 599.0 599 86.5350 14 564 1 chr4A.!!$F2 550
5 TraesCS7A01G485500 chr5D 80213500 80215270 1770 False 2887.0 2887 96.1670 1 1764 1 chr5D.!!$F1 1763
6 TraesCS7A01G485500 chr3D 65433047 65434812 1765 True 2887.0 2887 96.2100 1 1763 1 chr3D.!!$R1 1762
7 TraesCS7A01G485500 chr1D 6254382 6255953 1571 True 2588.0 2588 96.3810 193 1765 1 chr1D.!!$R1 1572
8 TraesCS7A01G485500 chr2A 628521999 628523921 1922 True 1446.5 1736 96.0320 1 1764 2 chr2A.!!$R1 1763
9 TraesCS7A01G485500 chr4B 116739396 116740605 1209 False 1373.0 1373 87.4900 573 1766 1 chr4B.!!$F1 1193
10 TraesCS7A01G485500 chr2D 602400992 602404110 3118 True 1282.0 1291 90.8155 1 962 2 chr2D.!!$R2 961
11 TraesCS7A01G485500 chr2D 602378838 602379641 803 True 1122.0 1122 91.7590 957 1768 1 chr2D.!!$R1 811
12 TraesCS7A01G485500 chr2D 25805542 25806213 671 False 1081.0 1081 95.5820 1087 1764 1 chr2D.!!$F1 677
13 TraesCS7A01G485500 chr5B 576799913 576801424 1511 False 938.0 1068 89.5805 59 1591 2 chr5B.!!$F1 1532
14 TraesCS7A01G485500 chr1B 610963352 610964134 782 False 767.0 767 84.8260 956 1735 1 chr1B.!!$F1 779
15 TraesCS7A01G485500 chr7D 279398092 279398642 550 False 597.0 597 86.3160 1 564 1 chr7D.!!$F1 563
16 TraesCS7A01G485500 chr7D 585602511 585603069 558 False 512.0 512 83.9510 1781 2321 1 chr7D.!!$F2 540

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
565 584 1.532794 ATTTGGGGGCTTCGTTGCA 60.533 52.632 5.0 0.0 34.04 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 2971 1.132643 CTGACTAAACGGGACTCTCGG 59.867 57.143 2.78 0.0 0.0 4.63 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
370 387 2.847327 ATATGATCCCCTTGCTCACG 57.153 50.000 0.00 0.00 0.00 4.35
565 584 1.532794 ATTTGGGGGCTTCGTTGCA 60.533 52.632 5.00 0.00 34.04 4.08
830 859 4.689345 ACAAAACGAGATAACTACCACAGC 59.311 41.667 0.00 0.00 0.00 4.40
1116 1348 3.079578 TGTGAAGAACGAGTCGGAGTAT 58.920 45.455 18.30 0.00 0.00 2.12
1646 2829 1.521681 CAAGGGTCTTCGGGCGATC 60.522 63.158 0.00 0.00 0.00 3.69
1693 2878 8.275040 ACCTAACATACTAAATCCAGCTTTGAT 58.725 33.333 0.00 0.00 0.00 2.57
1796 2994 3.305199 CGAGAGTCCCGTTTAGTCAGTTT 60.305 47.826 0.00 0.00 0.00 2.66
1812 3010 2.718731 TTTTTGCACGCAGACCGG 59.281 55.556 0.00 0.00 42.52 5.28
1857 3055 3.945434 GGCATGGTGAGCGCGATG 61.945 66.667 12.10 4.25 0.00 3.84
1862 3060 2.891936 GGTGAGCGCGATGATGCA 60.892 61.111 12.10 0.00 34.15 3.96
1865 3063 1.153588 TGAGCGCGATGATGCAAGA 60.154 52.632 12.10 0.00 34.15 3.02
1867 3065 2.053638 GCGCGATGATGCAAGACG 60.054 61.111 12.10 0.00 34.15 4.18
1916 3114 0.601841 TTTCCGGGAGCACTCGAAAC 60.602 55.000 4.50 0.00 43.41 2.78
1930 3128 0.365523 CGAAACCACATGCTCGTACG 59.634 55.000 9.53 9.53 0.00 3.67
1933 3131 3.780693 CCACATGCTCGTACGTGG 58.219 61.111 16.05 10.51 42.72 4.94
1935 3133 1.076533 CCACATGCTCGTACGTGGTC 61.077 60.000 16.05 1.63 43.23 4.02
1938 3136 4.746951 TGCTCGTACGTGGTCGCG 62.747 66.667 16.05 0.00 41.18 5.87
1940 3138 2.572647 CTCGTACGTGGTCGCGTC 60.573 66.667 16.05 0.00 44.55 5.19
1941 3139 3.299304 CTCGTACGTGGTCGCGTCA 62.299 63.158 16.05 3.05 44.55 4.35
1942 3140 2.868331 CGTACGTGGTCGCGTCAG 60.868 66.667 12.90 5.26 44.55 3.51
1943 3141 2.503375 GTACGTGGTCGCGTCAGG 60.503 66.667 12.90 13.89 44.55 3.86
1944 3142 4.409218 TACGTGGTCGCGTCAGGC 62.409 66.667 12.90 3.76 44.55 4.85
1967 3186 3.755628 GGGAGGTACGCACGAGCA 61.756 66.667 5.50 0.00 42.27 4.26
2026 3247 6.073711 GGTCCTCTCTCTCAAAAAGTAAAACG 60.074 42.308 0.00 0.00 0.00 3.60
2027 3248 5.465724 TCCTCTCTCTCAAAAAGTAAAACGC 59.534 40.000 0.00 0.00 0.00 4.84
2040 3261 5.919272 AGTAAAACGCTTCTAAGTTGGAC 57.081 39.130 0.00 0.00 0.00 4.02
2210 3490 2.547642 GGATAGTCAGGAGAGCATGCAC 60.548 54.545 21.98 14.59 0.00 4.57
2254 3534 3.416119 TCGATAACTAGGTGCTCGTTG 57.584 47.619 12.53 0.00 0.00 4.10
2282 3611 3.727726 TGCATACCACGGACATTCATAG 58.272 45.455 0.00 0.00 0.00 2.23
2293 3622 5.111989 CGGACATTCATAGAGAACACACAT 58.888 41.667 0.00 0.00 39.49 3.21
2295 3624 6.925718 CGGACATTCATAGAGAACACACATAT 59.074 38.462 0.00 0.00 39.49 1.78
2296 3625 8.082242 CGGACATTCATAGAGAACACACATATA 58.918 37.037 0.00 0.00 39.49 0.86
2297 3626 9.935241 GGACATTCATAGAGAACACACATATAT 57.065 33.333 0.00 0.00 39.49 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
370 387 1.146637 GTCCTCATGCTCATCGATGC 58.853 55.000 20.81 10.65 0.00 3.91
565 584 1.336755 CGGTAGTTGCAGGCACTTTTT 59.663 47.619 0.00 0.00 34.60 1.94
796 824 8.357402 AGTTATCTCGTTTTGTTTTTGGCTATT 58.643 29.630 0.00 0.00 0.00 1.73
830 859 1.405105 CATTCCAAATACCCGTGGCAG 59.595 52.381 0.00 0.00 34.68 4.85
1059 1250 3.387699 TCATTGAATCTCTCCACCGCATA 59.612 43.478 0.00 0.00 0.00 3.14
1105 1296 2.563471 AAAGTGCGATACTCCGACTC 57.437 50.000 0.00 0.00 39.18 3.36
1116 1348 1.070134 ACAACTGCCTCTAAAGTGCGA 59.930 47.619 0.00 0.00 0.00 5.10
1646 2829 1.655099 GCACGTGCAATGCCATAAAAG 59.345 47.619 34.52 0.00 41.59 2.27
1746 2944 6.290294 AGAGAAACTAGTAAAACGCCCATA 57.710 37.500 0.00 0.00 0.00 2.74
1773 2971 1.132643 CTGACTAAACGGGACTCTCGG 59.867 57.143 2.78 0.00 0.00 4.63
1774 2972 1.811359 ACTGACTAAACGGGACTCTCG 59.189 52.381 0.00 0.00 0.00 4.04
1796 2994 3.959975 GCCGGTCTGCGTGCAAAA 61.960 61.111 1.90 0.00 0.00 2.44
1812 3010 4.383602 AACGGTTCGCGTGCATGC 62.384 61.111 21.27 21.27 0.00 4.06
1900 3098 2.434359 GGTTTCGAGTGCTCCCGG 60.434 66.667 0.00 0.00 0.00 5.73
1916 3114 3.780693 CCACGTACGAGCATGTGG 58.219 61.111 24.41 14.12 46.36 4.17
1948 3146 4.189188 CTCGTGCGTACCTCCCGG 62.189 72.222 0.00 0.00 0.00 5.73
1949 3147 4.849329 GCTCGTGCGTACCTCCCG 62.849 72.222 0.00 0.00 0.00 5.14
1950 3148 3.755628 TGCTCGTGCGTACCTCCC 61.756 66.667 4.84 0.00 43.34 4.30
1956 3175 2.427905 GTGTCGTGCTCGTGCGTA 60.428 61.111 8.17 0.00 43.34 4.42
1961 3180 1.732732 GCTATCTTGTGTCGTGCTCGT 60.733 52.381 8.17 0.00 38.33 4.18
1963 3182 1.923204 CTGCTATCTTGTGTCGTGCTC 59.077 52.381 0.00 0.00 0.00 4.26
1967 3186 2.171840 AGTCCTGCTATCTTGTGTCGT 58.828 47.619 0.00 0.00 0.00 4.34
2026 3247 8.324163 TCTTAAGAAATGTCCAACTTAGAAGC 57.676 34.615 1.68 0.00 0.00 3.86
2027 3248 9.712305 TCTCTTAAGAAATGTCCAACTTAGAAG 57.288 33.333 6.63 0.00 0.00 2.85
2061 3282 1.662629 CGTGTGCATCTCCAACTCATC 59.337 52.381 0.00 0.00 0.00 2.92
2172 3452 7.506114 TGACTATCCAACGCTCCTAATTAATT 58.494 34.615 5.89 5.89 0.00 1.40
2210 3490 7.271223 CGAATTGTTTAATTACTTGGACTGCTG 59.729 37.037 0.00 0.00 36.66 4.41
2254 3534 1.873591 GTCCGTGGTATGCAATCATCC 59.126 52.381 0.00 0.00 34.22 3.51


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

AutoCloner maintained by Alex Coulton.