Multiple sequence alignment - TraesCS3D01G462800

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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 TraesCS3D01G462800 chr3D 100.000 3408 0 0 1 3408 567189470 567192877 0.000000e+00 6294.0
1 TraesCS3D01G462800 chr3D 88.462 1300 126 13 1176 2463 570111895 570110608 0.000000e+00 1548.0
2 TraesCS3D01G462800 chr3D 75.505 1139 237 31 1253 2364 520318948 520317825 1.400000e-143 520.0
3 TraesCS3D01G462800 chr3D 85.263 95 12 2 985 1078 520319260 520319167 2.800000e-16 97.1
4 TraesCS3D01G462800 chr3D 82.727 110 13 3 972 1079 520153039 520153144 3.620000e-15 93.5
5 TraesCS3D01G462800 chr3D 82.569 109 14 2 971 1078 520316129 520316025 1.300000e-14 91.6
6 TraesCS3D01G462800 chr3A 95.559 1959 83 3 701 2657 701264658 701266614 0.000000e+00 3133.0
7 TraesCS3D01G462800 chr3A 89.176 1589 130 16 894 2465 702905319 702903756 0.000000e+00 1943.0
8 TraesCS3D01G462800 chr3A 76.117 1164 246 24 1234 2374 655886368 655885214 6.340000e-162 580.0
9 TraesCS3D01G462800 chr3A 74.518 1142 253 27 1234 2350 655631959 655633087 2.400000e-126 462.0
10 TraesCS3D01G462800 chr3A 80.769 416 72 4 2004 2413 702915079 702914666 5.490000e-83 318.0
11 TraesCS3D01G462800 chr3A 82.727 110 13 3 972 1079 655572400 655572505 3.620000e-15 93.5
12 TraesCS3D01G462800 chr3B 95.400 1761 76 4 707 2465 756310267 756312024 0.000000e+00 2798.0
13 TraesCS3D01G462800 chr3B 82.972 599 86 7 1311 1897 756684364 756683770 8.380000e-146 527.0
14 TraesCS3D01G462800 chr3B 75.154 1139 252 23 1234 2350 684767601 684768730 1.090000e-139 507.0
15 TraesCS3D01G462800 chr3B 80.819 537 85 8 1889 2410 756682921 756682388 4.100000e-109 405.0
16 TraesCS3D01G462800 chrUn 94.832 1761 86 4 707 2465 40974481 40972724 0.000000e+00 2743.0
17 TraesCS3D01G462800 chrUn 90.698 258 20 1 923 1180 45471337 45471590 1.170000e-89 340.0
18 TraesCS3D01G462800 chrUn 100.000 28 0 0 701 728 40977015 40976988 6.000000e-03 52.8
19 TraesCS3D01G462800 chr5B 91.121 946 78 2 2468 3408 291013170 291012226 0.000000e+00 1277.0
20 TraesCS3D01G462800 chr5B 89.641 946 87 9 2466 3408 235389353 235390290 0.000000e+00 1194.0
21 TraesCS3D01G462800 chr2D 90.928 948 80 6 2463 3408 479065140 479066083 0.000000e+00 1269.0
22 TraesCS3D01G462800 chr2D 90.021 952 79 10 2465 3408 424031408 424032351 0.000000e+00 1218.0
23 TraesCS3D01G462800 chr2D 89.884 949 81 11 2466 3407 25370680 25371620 0.000000e+00 1206.0
24 TraesCS3D01G462800 chr7D 99.148 704 3 2 1 701 596332997 596332294 0.000000e+00 1264.0
25 TraesCS3D01G462800 chr7D 98.722 704 6 2 1 701 109467132 109467835 0.000000e+00 1247.0
26 TraesCS3D01G462800 chr7D 98.584 706 6 3 1 702 498824373 498823668 0.000000e+00 1245.0
27 TraesCS3D01G462800 chr7D 89.979 948 87 8 2466 3408 235924894 235923950 0.000000e+00 1218.0
28 TraesCS3D01G462800 chr7D 89.863 947 88 7 2465 3408 146088254 146087313 0.000000e+00 1210.0
29 TraesCS3D01G462800 chr5D 99.006 704 4 2 1 701 27995702 27994999 0.000000e+00 1258.0
30 TraesCS3D01G462800 chr5D 98.864 704 5 2 1 701 517965158 517964455 0.000000e+00 1253.0
31 TraesCS3D01G462800 chr5D 98.444 707 7 3 1 703 449306069 449305363 0.000000e+00 1242.0
32 TraesCS3D01G462800 chr1D 98.864 704 5 2 1 701 288324559 288323856 0.000000e+00 1253.0
33 TraesCS3D01G462800 chr1D 98.315 712 8 3 1 709 335770533 335771243 0.000000e+00 1245.0
34 TraesCS3D01G462800 chr6D 90.622 949 80 8 2466 3408 421436379 421437324 0.000000e+00 1251.0
35 TraesCS3D01G462800 chr6D 98.722 704 6 2 1 701 56347094 56346391 0.000000e+00 1247.0
36 TraesCS3D01G462800 chr6B 89.863 947 89 7 2466 3408 166068084 166069027 0.000000e+00 1210.0
37 TraesCS3D01G462800 chr5A 77.387 1194 238 22 1234 2408 401317374 401316194 0.000000e+00 680.0


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 TraesCS3D01G462800 chr3D 567189470 567192877 3407 False 6294.000000 6294 100.000000 1 3408 1 chr3D.!!$F2 3407
1 TraesCS3D01G462800 chr3D 570110608 570111895 1287 True 1548.000000 1548 88.462000 1176 2463 1 chr3D.!!$R1 1287
2 TraesCS3D01G462800 chr3D 520316025 520319260 3235 True 236.233333 520 81.112333 971 2364 3 chr3D.!!$R2 1393
3 TraesCS3D01G462800 chr3A 701264658 701266614 1956 False 3133.000000 3133 95.559000 701 2657 1 chr3A.!!$F3 1956
4 TraesCS3D01G462800 chr3A 702903756 702905319 1563 True 1943.000000 1943 89.176000 894 2465 1 chr3A.!!$R2 1571
5 TraesCS3D01G462800 chr3A 655885214 655886368 1154 True 580.000000 580 76.117000 1234 2374 1 chr3A.!!$R1 1140
6 TraesCS3D01G462800 chr3A 655631959 655633087 1128 False 462.000000 462 74.518000 1234 2350 1 chr3A.!!$F2 1116
7 TraesCS3D01G462800 chr3B 756310267 756312024 1757 False 2798.000000 2798 95.400000 707 2465 1 chr3B.!!$F2 1758
8 TraesCS3D01G462800 chr3B 684767601 684768730 1129 False 507.000000 507 75.154000 1234 2350 1 chr3B.!!$F1 1116
9 TraesCS3D01G462800 chr3B 756682388 756684364 1976 True 466.000000 527 81.895500 1311 2410 2 chr3B.!!$R1 1099
10 TraesCS3D01G462800 chrUn 40972724 40977015 4291 True 1397.900000 2743 97.416000 701 2465 2 chrUn.!!$R1 1764
11 TraesCS3D01G462800 chr5B 291012226 291013170 944 True 1277.000000 1277 91.121000 2468 3408 1 chr5B.!!$R1 940
12 TraesCS3D01G462800 chr5B 235389353 235390290 937 False 1194.000000 1194 89.641000 2466 3408 1 chr5B.!!$F1 942
13 TraesCS3D01G462800 chr2D 479065140 479066083 943 False 1269.000000 1269 90.928000 2463 3408 1 chr2D.!!$F3 945
14 TraesCS3D01G462800 chr2D 424031408 424032351 943 False 1218.000000 1218 90.021000 2465 3408 1 chr2D.!!$F2 943
15 TraesCS3D01G462800 chr2D 25370680 25371620 940 False 1206.000000 1206 89.884000 2466 3407 1 chr2D.!!$F1 941
16 TraesCS3D01G462800 chr7D 596332294 596332997 703 True 1264.000000 1264 99.148000 1 701 1 chr7D.!!$R4 700
17 TraesCS3D01G462800 chr7D 109467132 109467835 703 False 1247.000000 1247 98.722000 1 701 1 chr7D.!!$F1 700
18 TraesCS3D01G462800 chr7D 498823668 498824373 705 True 1245.000000 1245 98.584000 1 702 1 chr7D.!!$R3 701
19 TraesCS3D01G462800 chr7D 235923950 235924894 944 True 1218.000000 1218 89.979000 2466 3408 1 chr7D.!!$R2 942
20 TraesCS3D01G462800 chr7D 146087313 146088254 941 True 1210.000000 1210 89.863000 2465 3408 1 chr7D.!!$R1 943
21 TraesCS3D01G462800 chr5D 27994999 27995702 703 True 1258.000000 1258 99.006000 1 701 1 chr5D.!!$R1 700
22 TraesCS3D01G462800 chr5D 517964455 517965158 703 True 1253.000000 1253 98.864000 1 701 1 chr5D.!!$R3 700
23 TraesCS3D01G462800 chr5D 449305363 449306069 706 True 1242.000000 1242 98.444000 1 703 1 chr5D.!!$R2 702
24 TraesCS3D01G462800 chr1D 288323856 288324559 703 True 1253.000000 1253 98.864000 1 701 1 chr1D.!!$R1 700
25 TraesCS3D01G462800 chr1D 335770533 335771243 710 False 1245.000000 1245 98.315000 1 709 1 chr1D.!!$F1 708
26 TraesCS3D01G462800 chr6D 421436379 421437324 945 False 1251.000000 1251 90.622000 2466 3408 1 chr6D.!!$F1 942
27 TraesCS3D01G462800 chr6D 56346391 56347094 703 True 1247.000000 1247 98.722000 1 701 1 chr6D.!!$R1 700
28 TraesCS3D01G462800 chr6B 166068084 166069027 943 False 1210.000000 1210 89.863000 2466 3408 1 chr6B.!!$F1 942
29 TraesCS3D01G462800 chr5A 401316194 401317374 1180 True 680.000000 680 77.387000 1234 2408 1 chr5A.!!$R1 1174

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
703 709 1.329906 CACGGGCACTCTACTAGTACG 59.670 57.143 0.0 1.98 35.76 3.67 F
1609 3502 1.348696 TCCTTGCATCTTGTCTGCTCA 59.651 47.619 0.0 0.00 40.34 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2326 5106 0.700564 AGCTGCCTTCCAAGATCCAA 59.299 50.0 0.0 0.0 0.00 3.53 R
3245 7552 0.036952 AGACATGACCGAGGCACTTG 60.037 55.0 0.0 0.0 41.55 3.16 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
383 386 6.713450 GGTTACATGTTTTAAGACCTTCTCCA 59.287 38.462 2.30 0.00 0.00 3.86
703 709 1.329906 CACGGGCACTCTACTAGTACG 59.670 57.143 0.00 1.98 35.76 3.67
705 711 2.012673 CGGGCACTCTACTAGTACGTT 58.987 52.381 0.00 0.00 35.76 3.99
741 2570 4.804108 TCATTAAAGTGCCAACAATTCGG 58.196 39.130 0.00 0.00 31.74 4.30
748 2577 1.945522 CCAACAATTCGGCGACACA 59.054 52.632 10.16 0.00 0.00 3.72
782 2611 9.515226 AAAGTCATTAAAAGGTGTCAGCTATTA 57.485 29.630 4.68 0.00 0.00 0.98
783 2612 9.686683 AAGTCATTAAAAGGTGTCAGCTATTAT 57.313 29.630 4.68 0.00 0.00 1.28
818 2647 8.037166 GGATCTCATTAAAGTGGCAAATTTTCT 58.963 33.333 0.00 0.00 0.00 2.52
821 2650 6.286758 TCATTAAAGTGGCAAATTTTCTGCA 58.713 32.000 0.00 0.00 41.78 4.41
824 2653 1.413445 AGTGGCAAATTTTCTGCAGCA 59.587 42.857 9.47 0.00 41.78 4.41
1179 3024 4.081531 CACACATGGTTGGGAGCATTTTAT 60.082 41.667 0.00 0.00 41.82 1.40
1273 3160 2.402564 CAGAAGAGGATGAAGCCCCTA 58.597 52.381 0.00 0.00 31.84 3.53
1343 3230 1.894466 CCACAAAGATGGTGATTGCCA 59.106 47.619 0.00 0.00 43.48 4.92
1609 3502 1.348696 TCCTTGCATCTTGTCTGCTCA 59.651 47.619 0.00 0.00 40.34 4.26
1612 3505 2.773993 TGCATCTTGTCTGCTCATCA 57.226 45.000 0.00 0.00 40.34 3.07
1720 3624 4.986054 TTACCTTTACAGGCTCCTGAAA 57.014 40.909 21.75 15.09 45.56 2.69
1725 3629 3.963428 TTACAGGCTCCTGAAAGTCTC 57.037 47.619 21.75 0.00 46.30 3.36
1743 3647 1.630369 CTCACAAGGAACCAGATCCCA 59.370 52.381 0.00 0.00 40.59 4.37
1882 3787 2.677228 CAGGAGGCCGGATGGTTT 59.323 61.111 5.05 0.00 37.67 3.27
2089 4869 4.675114 GGTGTAATCGACAAAGCAAAGTTG 59.325 41.667 0.00 0.00 40.66 3.16
2134 4914 4.431416 TGAACCTTCCAACAAAGAGCTA 57.569 40.909 0.00 0.00 0.00 3.32
2140 4920 4.568592 CCTTCCAACAAAGAGCTAAGGGAT 60.569 45.833 0.00 0.00 0.00 3.85
2263 5043 4.009675 GTGTGACCAGAGCCATATTTGAA 58.990 43.478 0.00 0.00 0.00 2.69
2326 5106 2.600769 AGGACCTTGGAGCGACGT 60.601 61.111 0.00 0.00 0.00 4.34
2633 6912 3.283751 GAGCCTCTACTTGACTAGCTCA 58.716 50.000 4.33 0.00 43.62 4.26
2657 6936 9.527157 TCATTGATCAAAGATGGTTAAGGTTTA 57.473 29.630 13.09 0.00 0.00 2.01
2697 6977 7.765819 TGAGTTGTCATTTGATAACGAGATCAT 59.234 33.333 12.58 0.00 46.44 2.45
2729 7009 5.426504 GAGAATGATGTGATGGACAAGACT 58.573 41.667 0.00 0.00 38.36 3.24
2731 7011 3.236632 TGATGTGATGGACAAGACTCG 57.763 47.619 0.00 0.00 38.36 4.18
2769 7049 8.677300 AGCATTATGATCGTTCAGTTTTATTGT 58.323 29.630 2.21 0.00 34.73 2.71
2808 7088 6.280643 TGTCAAATACATATTCCTCCGACTG 58.719 40.000 0.00 0.00 31.43 3.51
2826 7106 4.679106 CGACTGTGAGATTATGCAACTCCT 60.679 45.833 0.00 0.00 0.00 3.69
2914 7195 4.647399 GCTCTACAGGTATCTCTGAAGGTT 59.353 45.833 0.00 0.00 38.11 3.50
2934 7215 4.982295 GGTTTTTGTTGAGTTGGCATAGAC 59.018 41.667 0.00 0.00 0.00 2.59
2936 7217 3.500448 TTGTTGAGTTGGCATAGACCA 57.500 42.857 0.00 0.00 38.16 4.02
2965 7246 4.950475 AGGATTTGTCACTCTGAGTATCGA 59.050 41.667 10.47 0.92 38.61 3.59
2984 7265 3.893324 GAGGTATCTCTGGGCCCC 58.107 66.667 22.27 0.22 37.07 5.80
3009 7290 7.434492 CCTCGGTAATACACATCATAAGAAGT 58.566 38.462 0.00 0.00 0.00 3.01
3050 7331 8.023021 ACTAATGAGTTAGTTGCAGGATGATA 57.977 34.615 0.00 0.00 46.40 2.15
3144 7425 8.902540 AATCTCGAGCAAATAACATACCAATA 57.097 30.769 7.81 0.00 0.00 1.90
3159 7440 9.936329 AACATACCAATAGACAAAGGGAATAAT 57.064 29.630 0.00 0.00 0.00 1.28
3352 7660 8.371699 TGAATTATGTGATATGGTGACCGAATA 58.628 33.333 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
703 709 7.481798 CACTTTAATGAGCTCCGATTTTACAAC 59.518 37.037 12.15 0.00 0.00 3.32
705 711 6.403200 GCACTTTAATGAGCTCCGATTTTACA 60.403 38.462 12.15 0.00 0.00 2.41
741 2570 1.387084 GACTTTCTGATCGTGTGTCGC 59.613 52.381 0.00 0.00 39.67 5.19
743 2572 6.706055 TTAATGACTTTCTGATCGTGTGTC 57.294 37.500 0.00 0.00 0.00 3.67
748 2577 6.710744 ACACCTTTTAATGACTTTCTGATCGT 59.289 34.615 0.00 0.00 0.00 3.73
783 2612 8.686334 GCCACTTTAATGAGATCCAATTTTAGA 58.314 33.333 0.00 0.00 0.00 2.10
806 2635 2.037381 TCATGCTGCAGAAAATTTGCCA 59.963 40.909 20.43 2.18 40.81 4.92
845 2674 8.070171 CGGAATAATTGTCGCTTTAATGAGATT 58.930 33.333 0.00 0.00 0.00 2.40
887 2716 3.317149 TGGCTCGCATATATATACCCGAC 59.683 47.826 10.75 8.79 0.00 4.79
919 2748 5.897824 AGGAACCAGTTTATAGTAGCTAGCA 59.102 40.000 18.83 0.00 0.00 3.49
1096 2927 7.719633 AGGTGTCAACAACATAGTGAGTTAATT 59.280 33.333 0.36 0.00 40.80 1.40
1273 3160 2.515854 TCGAGGATAGCCGCTTCTATT 58.484 47.619 0.00 0.00 39.96 1.73
1343 3230 2.208349 AGAGGAGCACCCCAGGTT 59.792 61.111 0.00 0.00 31.02 3.50
1720 3624 2.569404 GGATCTGGTTCCTTGTGAGACT 59.431 50.000 0.00 0.00 32.68 3.24
1725 3629 1.952367 GCTGGGATCTGGTTCCTTGTG 60.952 57.143 0.00 0.00 35.97 3.33
1743 3647 1.135112 TGCTCGTCAATGTCATACGCT 60.135 47.619 3.67 0.00 36.60 5.07
1882 3787 5.045578 CAGAATCCCTCCCTACAAGAGAAAA 60.046 44.000 0.00 0.00 32.86 2.29
2089 4869 4.327680 ACACAGGCAAATAGAAAGAGTCC 58.672 43.478 0.00 0.00 0.00 3.85
2140 4920 5.837770 ATGAGCCTTCATCTTGGATGATA 57.162 39.130 10.44 2.90 39.94 2.15
2263 5043 6.837312 TCCAAAATGATGGACTATTATCGGT 58.163 36.000 0.00 0.00 44.52 4.69
2326 5106 0.700564 AGCTGCCTTCCAAGATCCAA 59.299 50.000 0.00 0.00 0.00 3.53
2541 6819 7.857734 TTCCGATCAAAACAATTCTAGCATA 57.142 32.000 0.00 0.00 0.00 3.14
2697 6977 8.316946 GTCCATCACATCATTCTCCTAATGATA 58.683 37.037 11.71 0.02 43.38 2.15
2729 7009 6.144078 TCATAATGCTAAGCTAACAGACGA 57.856 37.500 0.00 0.00 0.00 4.20
2731 7011 6.642950 ACGATCATAATGCTAAGCTAACAGAC 59.357 38.462 0.00 0.00 0.00 3.51
2769 7049 7.487484 TGTATTTGACATGAAGAAAGCAACAA 58.513 30.769 0.00 0.00 31.20 2.83
2802 7082 3.525537 AGTTGCATAATCTCACAGTCGG 58.474 45.455 0.00 0.00 0.00 4.79
2808 7088 4.142609 TCCAGGAGTTGCATAATCTCAC 57.857 45.455 0.00 0.00 0.00 3.51
2826 7106 0.399949 AGGCATTCCTCCGGTATCCA 60.400 55.000 0.00 0.00 38.72 3.41
2914 7195 4.211125 TGGTCTATGCCAACTCAACAAAA 58.789 39.130 0.00 0.00 35.25 2.44
2934 7215 6.409704 TCAGAGTGACAAATCCTAATCTTGG 58.590 40.000 0.00 0.00 0.00 3.61
2936 7217 7.251321 ACTCAGAGTGACAAATCCTAATCTT 57.749 36.000 0.91 0.00 0.00 2.40
2984 7265 7.434492 ACTTCTTATGATGTGTATTACCGAGG 58.566 38.462 0.00 0.00 30.69 4.63
3009 7290 4.821260 TCATTAGTCACTTTGCTTGCAAGA 59.179 37.500 30.39 12.25 0.00 3.02
3050 7331 7.565323 AGTCTCTTTACTCGTTCCGTAATAT 57.435 36.000 0.00 0.00 0.00 1.28
3144 7425 7.065803 CGACAACATACATTATTCCCTTTGTCT 59.934 37.037 0.00 0.00 38.65 3.41
3159 7440 5.313520 TCTTTATCGGTCGACAACATACA 57.686 39.130 18.91 2.57 0.00 2.29
3245 7552 0.036952 AGACATGACCGAGGCACTTG 60.037 55.000 0.00 0.00 41.55 3.16
3247 7554 3.213912 ATGTAGACATGACCGAGGCACT 61.214 50.000 0.00 0.00 36.76 4.40
3251 7558 4.580995 AGAACTATGTAGACATGACCGAGG 59.419 45.833 0.00 0.00 37.15 4.63
3329 7637 9.166173 CAATATTCGGTCACCATATCACATAAT 57.834 33.333 0.00 0.00 0.00 1.28
3373 7681 4.573900 GACTCCTTGTCATGTCTGTGATT 58.426 43.478 0.00 0.00 44.73 2.57


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

AutoCloner maintained by Alex Coulton.