Multiple sequence alignment - TraesCS2A01G567500

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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 TraesCS2A01G567500 chr2A 100.000 5042 0 0 1 5042 766324480 766329521 0.000000e+00 9311
1 TraesCS2A01G567500 chr2B 93.436 5073 248 36 1 5042 800191538 800186520 0.000000e+00 7444
2 TraesCS2A01G567500 chr2B 88.344 652 59 5 1 645 800232661 800232020 0.000000e+00 767
3 TraesCS2A01G567500 chr2D 96.821 4373 105 14 1 4362 641063936 641068285 0.000000e+00 7275
4 TraesCS2A01G567500 chr2D 96.810 627 18 2 4417 5042 641068700 641069325 0.000000e+00 1046
5 TraesCS2A01G567500 chr5D 83.433 839 116 13 2243 3070 368366527 368365701 0.000000e+00 758
6 TraesCS2A01G567500 chr5D 89.264 503 54 0 3577 4079 368365098 368364596 9.210000e-177 630
7 TraesCS2A01G567500 chr5A 85.061 743 101 10 2305 3041 470243372 470242634 0.000000e+00 749
8 TraesCS2A01G567500 chr5A 86.964 560 69 4 3522 4079 470226884 470226327 1.190000e-175 627
9 TraesCS2A01G567500 chr5A 86.964 560 69 4 3522 4079 470242015 470241458 1.190000e-175 627
10 TraesCS2A01G567500 chr1B 80.804 995 156 24 2041 3018 4522982 4522006 0.000000e+00 747
11 TraesCS2A01G567500 chr1B 80.444 992 161 21 2041 3018 4813572 4812600 0.000000e+00 726
12 TraesCS2A01G567500 chr1B 83.906 553 84 5 3530 4079 4207768 4208318 1.610000e-144 523
13 TraesCS2A01G567500 chr1B 83.099 568 74 15 3530 4079 3574561 3573998 9.750000e-137 497
14 TraesCS2A01G567500 chr1A 79.879 994 170 19 2041 3018 2848852 2849831 0.000000e+00 701
15 TraesCS2A01G567500 chr1A 79.635 987 171 22 2041 3013 2550269 2551239 0.000000e+00 682
16 TraesCS2A01G567500 chr1A 83.566 572 87 7 3522 4089 3463075 3462507 3.460000e-146 529
17 TraesCS2A01G567500 chr1D 79.497 995 171 23 2041 3018 799782 798804 0.000000e+00 676
18 TraesCS2A01G567500 chr1D 82.923 568 76 14 3530 4079 798210 797646 4.540000e-135 492
19 TraesCS2A01G567500 chr5B 87.143 560 67 5 3522 4079 436282397 436281841 9.210000e-177 630


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 TraesCS2A01G567500 chr2A 766324480 766329521 5041 False 9311.0 9311 100.0000 1 5042 1 chr2A.!!$F1 5041
1 TraesCS2A01G567500 chr2B 800186520 800191538 5018 True 7444.0 7444 93.4360 1 5042 1 chr2B.!!$R1 5041
2 TraesCS2A01G567500 chr2B 800232020 800232661 641 True 767.0 767 88.3440 1 645 1 chr2B.!!$R2 644
3 TraesCS2A01G567500 chr2D 641063936 641069325 5389 False 4160.5 7275 96.8155 1 5042 2 chr2D.!!$F1 5041
4 TraesCS2A01G567500 chr5D 368364596 368366527 1931 True 694.0 758 86.3485 2243 4079 2 chr5D.!!$R1 1836
5 TraesCS2A01G567500 chr5A 470241458 470243372 1914 True 688.0 749 86.0125 2305 4079 2 chr5A.!!$R2 1774
6 TraesCS2A01G567500 chr5A 470226327 470226884 557 True 627.0 627 86.9640 3522 4079 1 chr5A.!!$R1 557
7 TraesCS2A01G567500 chr1B 4522006 4522982 976 True 747.0 747 80.8040 2041 3018 1 chr1B.!!$R2 977
8 TraesCS2A01G567500 chr1B 4812600 4813572 972 True 726.0 726 80.4440 2041 3018 1 chr1B.!!$R3 977
9 TraesCS2A01G567500 chr1B 4207768 4208318 550 False 523.0 523 83.9060 3530 4079 1 chr1B.!!$F1 549
10 TraesCS2A01G567500 chr1B 3573998 3574561 563 True 497.0 497 83.0990 3530 4079 1 chr1B.!!$R1 549
11 TraesCS2A01G567500 chr1A 2848852 2849831 979 False 701.0 701 79.8790 2041 3018 1 chr1A.!!$F2 977
12 TraesCS2A01G567500 chr1A 2550269 2551239 970 False 682.0 682 79.6350 2041 3013 1 chr1A.!!$F1 972
13 TraesCS2A01G567500 chr1A 3462507 3463075 568 True 529.0 529 83.5660 3522 4089 1 chr1A.!!$R1 567
14 TraesCS2A01G567500 chr1D 797646 799782 2136 True 584.0 676 81.2100 2041 4079 2 chr1D.!!$R1 2038
15 TraesCS2A01G567500 chr5B 436281841 436282397 556 True 630.0 630 87.1430 3522 4079 1 chr5B.!!$R1 557

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
80 81 0.178947 GGATCTCATCTCCGAGGGGT 60.179 60.000 0.00 0.0 33.59 4.95 F
634 657 1.930567 CGTGGTTGAACGGTATAGGG 58.069 55.000 0.00 0.0 39.89 3.53 F
1638 1664 1.520564 GCCACGATGGTGTGCGATA 60.521 57.895 7.12 0.0 42.80 2.92 F
2038 2069 1.010793 AGAGAGAGAGAGGGAGAGGGA 59.989 57.143 0.00 0.0 0.00 4.20 F
2039 2070 2.065799 GAGAGAGAGAGGGAGAGGGAT 58.934 57.143 0.00 0.0 0.00 3.85 F
2047 2078 3.655777 GAGAGGGAGAGGGATAGAGAAGA 59.344 52.174 0.00 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1428 1.242076 AGAGTGGTGTTCTGCATTGC 58.758 50.000 0.46 0.46 0.00 3.56 R
2026 2057 3.687045 TCTTCTCTATCCCTCTCCCTCT 58.313 50.000 0.00 0.00 0.00 3.69 R
3289 3393 0.482446 TTGAACCCTTGCATCCCTGT 59.518 50.000 0.00 0.00 0.00 4.00 R
3467 3635 4.500477 GCATTCTTAAATAGTTGCAAGCCG 59.500 41.667 0.00 0.00 35.53 5.52 R
3840 4064 9.282569 GCAGATTTCTTCTCATTATAATCAGGT 57.717 33.333 0.00 0.00 29.93 4.00 R
4163 4399 1.707989 TGGGAATGACTTAAGTGGGCA 59.292 47.619 14.14 5.34 0.00 5.36 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
80 81 0.178947 GGATCTCATCTCCGAGGGGT 60.179 60.000 0.00 0.00 33.59 4.95
190 193 7.278875 ACCTTGAGGACAAAATTGCAAATAAA 58.721 30.769 1.71 0.00 38.94 1.40
205 208 4.563374 GCAAATAAAGTTGTGCCTTGGGAT 60.563 41.667 0.00 0.00 0.00 3.85
355 358 3.131396 CTGAGTGTGCCTTCGTTTAGTT 58.869 45.455 0.00 0.00 0.00 2.24
466 489 3.055530 ACACATTTGGTAGAGCTCTCTGG 60.056 47.826 22.17 6.70 40.71 3.86
490 513 4.352893 TGAGATGACCTTGGTACAGATGA 58.647 43.478 0.00 0.00 42.39 2.92
634 657 1.930567 CGTGGTTGAACGGTATAGGG 58.069 55.000 0.00 0.00 39.89 3.53
1213 1237 4.782019 TTGTGGAGTGGTTTATGCATTC 57.218 40.909 3.54 0.00 0.00 2.67
1371 1395 5.694910 TCTTTCGGAGACTTTGTATGTCAAC 59.305 40.000 0.00 0.00 36.94 3.18
1404 1428 6.252967 TGACTAACCATGCACTAACATTTG 57.747 37.500 0.00 0.00 0.00 2.32
1437 1461 8.050930 AGAACACCACTCTTTTAAGTCCTAAAA 58.949 33.333 0.00 0.00 37.18 1.52
1630 1656 2.016318 CACAATGTATGCCACGATGGT 58.984 47.619 0.00 0.00 40.46 3.55
1638 1664 1.520564 GCCACGATGGTGTGCGATA 60.521 57.895 7.12 0.00 42.80 2.92
1752 1779 6.575244 ATGATCCACCTAAACCATAGTTCA 57.425 37.500 0.00 0.00 34.19 3.18
1779 1806 3.875134 GGTTAATTATGGTCGGTGGTCAG 59.125 47.826 0.00 0.00 0.00 3.51
1807 1834 6.173339 AGACAAGGTGGTACATAATTGACAG 58.827 40.000 0.00 0.00 44.52 3.51
2001 2032 2.370281 ACGCTTCACACCTATCACAG 57.630 50.000 0.00 0.00 0.00 3.66
2035 2066 5.090139 AGATAGAGAGAGAGAGAGGGAGAG 58.910 50.000 0.00 0.00 0.00 3.20
2036 2067 2.412591 AGAGAGAGAGAGAGGGAGAGG 58.587 57.143 0.00 0.00 0.00 3.69
2038 2069 1.010793 AGAGAGAGAGAGGGAGAGGGA 59.989 57.143 0.00 0.00 0.00 4.20
2039 2070 2.065799 GAGAGAGAGAGGGAGAGGGAT 58.934 57.143 0.00 0.00 0.00 3.85
2046 2077 3.657727 AGAGAGGGAGAGGGATAGAGAAG 59.342 52.174 0.00 0.00 0.00 2.85
2047 2078 3.655777 GAGAGGGAGAGGGATAGAGAAGA 59.344 52.174 0.00 0.00 0.00 2.87
2149 2185 6.944290 ACCATATGACTTATAGCAATGCATGT 59.056 34.615 8.35 0.00 0.00 3.21
2157 2193 6.429078 ACTTATAGCAATGCATGTATGACCAG 59.571 38.462 8.35 0.00 0.00 4.00
3041 3103 7.159322 TCTTCCTAGTCAACAAGATCACTAC 57.841 40.000 0.00 0.00 0.00 2.73
3467 3635 5.985530 GCAACATGAATAGGAAAAATAGGGC 59.014 40.000 0.00 0.00 0.00 5.19
3840 4064 3.992943 CCAATGGGTAGTGGACACTTA 57.007 47.619 10.57 0.00 44.70 2.24
4044 4277 4.335416 CAGGTGGTTGTATTGGTTGAGAT 58.665 43.478 0.00 0.00 0.00 2.75
4201 4437 0.603065 CATCACGAGGACCTGTGACA 59.397 55.000 21.59 7.88 46.87 3.58
4260 4496 4.342378 GCACCATATGACTGAACCTCTCTA 59.658 45.833 3.65 0.00 0.00 2.43
4284 4520 1.133072 CCAATGGGCCATGGAACCTAT 60.133 52.381 23.01 8.79 0.00 2.57
4296 4532 6.493458 GCCATGGAACCTATGTATAAAACCAT 59.507 38.462 18.40 0.00 36.27 3.55
4363 4599 1.223487 GATAAGTGGGAAGCGGCCA 59.777 57.895 2.24 0.00 0.00 5.36
4395 4631 0.535102 CCAACTCGGTGCAAACTCCT 60.535 55.000 0.00 0.00 0.00 3.69
4396 4632 0.588252 CAACTCGGTGCAAACTCCTG 59.412 55.000 0.00 0.00 0.00 3.86
4397 4633 1.166531 AACTCGGTGCAAACTCCTGC 61.167 55.000 0.00 0.00 42.95 4.85
4458 5054 2.158755 CCATCGCAGGGAGATAAAAGGT 60.159 50.000 0.00 0.00 0.00 3.50
4460 5056 1.136305 TCGCAGGGAGATAAAAGGTCG 59.864 52.381 0.00 0.00 0.00 4.79
4476 5072 1.270550 GGTCGGGTGTCTTTAAGTCGA 59.729 52.381 0.00 0.00 0.00 4.20
4479 5075 1.723220 GGGTGTCTTTAAGTCGAGCC 58.277 55.000 0.00 0.00 0.00 4.70
4731 5327 4.288626 ACACCACTAAGAGATTGGGCTAAA 59.711 41.667 0.00 0.00 34.41 1.85
4733 5329 5.888161 CACCACTAAGAGATTGGGCTAAAAT 59.112 40.000 0.00 0.00 34.41 1.82
4734 5330 7.054124 CACCACTAAGAGATTGGGCTAAAATA 58.946 38.462 0.00 0.00 34.41 1.40
4801 5397 8.690884 TGAAAACATCATTTCACTTAAGGAACA 58.309 29.630 7.53 0.74 42.68 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 0.182061 GAGGATCTCATGGCAGGCAA 59.818 55.000 0.00 0.00 0.00 4.52
190 193 4.850193 CCATCCCAAGGCACAACT 57.150 55.556 0.00 0.00 0.00 3.16
205 208 1.491754 ACTGAGGTGATATGCATGCCA 59.508 47.619 16.68 2.24 0.00 4.92
380 383 5.046950 GGTTTCCCAATTTACCATGCACTTA 60.047 40.000 0.00 0.00 0.00 2.24
466 489 4.537135 TCTGTACCAAGGTCATCTCAAC 57.463 45.455 0.00 0.00 0.00 3.18
490 513 3.338249 CCAAATGTTCGAGAGGTCATGT 58.662 45.455 0.00 0.00 0.00 3.21
634 657 7.751768 ATGGAAATACAAGCTATTTAGGCTC 57.248 36.000 0.00 0.00 39.30 4.70
855 878 6.505044 TTAACGAGTAGTCATCTAGTGCAA 57.495 37.500 0.00 0.00 30.79 4.08
1000 1023 3.411446 TGTGTTCCTTTCGATGAAGCAT 58.589 40.909 0.00 0.00 0.00 3.79
1177 1201 6.215121 CACTCCACAAAGAATTGCATGTAAA 58.785 36.000 0.00 0.00 40.34 2.01
1178 1202 5.278907 CCACTCCACAAAGAATTGCATGTAA 60.279 40.000 0.00 0.00 40.34 2.41
1179 1203 4.218200 CCACTCCACAAAGAATTGCATGTA 59.782 41.667 0.00 0.00 40.34 2.29
1404 1428 1.242076 AGAGTGGTGTTCTGCATTGC 58.758 50.000 0.46 0.46 0.00 3.56
1437 1461 5.047519 CAGCTCTCCATGGAAATTGAAAACT 60.048 40.000 17.00 4.62 0.00 2.66
1630 1656 9.243637 GAATTTGCCTTTTATATTTATCGCACA 57.756 29.630 0.00 0.00 0.00 4.57
1752 1779 5.130350 CCACCGACCATAATTAACCTTGAT 58.870 41.667 0.00 0.00 0.00 2.57
1779 1806 5.615925 ATTATGTACCACCTTGTCTCTCC 57.384 43.478 0.00 0.00 0.00 3.71
1883 1914 4.359434 TTTGGTGTTCTGGTAGCATGTA 57.641 40.909 0.00 0.00 0.00 2.29
2026 2057 3.687045 TCTTCTCTATCCCTCTCCCTCT 58.313 50.000 0.00 0.00 0.00 3.69
2030 2061 4.798882 TGACTTCTTCTCTATCCCTCTCC 58.201 47.826 0.00 0.00 0.00 3.71
2032 2063 7.747809 AATTTGACTTCTTCTCTATCCCTCT 57.252 36.000 0.00 0.00 0.00 3.69
2035 2066 8.341892 ACAAAATTTGACTTCTTCTCTATCCC 57.658 34.615 13.19 0.00 0.00 3.85
2046 2077 6.018262 GCAGGGGTAAAACAAAATTTGACTTC 60.018 38.462 13.19 0.00 0.00 3.01
2047 2078 5.820423 GCAGGGGTAAAACAAAATTTGACTT 59.180 36.000 13.19 7.38 0.00 3.01
2157 2193 8.131731 GTCATTCCTATGCAATTAGACCTTTTC 58.868 37.037 0.00 0.00 0.00 2.29
2277 2317 6.504849 TCCTACCGGACATATATAATTGGGA 58.495 40.000 9.46 0.00 33.30 4.37
2278 2319 6.801718 TCCTACCGGACATATATAATTGGG 57.198 41.667 9.46 0.00 33.30 4.12
3138 3241 6.966021 TGTTAGAAACAAGGCATTCTGTTAC 58.034 36.000 0.00 0.00 38.72 2.50
3185 3289 7.919091 GTGTTGGACACTCGAAGAATACATATA 59.081 37.037 4.06 0.00 45.27 0.86
3252 3356 2.025981 TGCATGTCCCTCATAGTTTGCT 60.026 45.455 0.00 0.00 34.67 3.91
3289 3393 0.482446 TTGAACCCTTGCATCCCTGT 59.518 50.000 0.00 0.00 0.00 4.00
3467 3635 4.500477 GCATTCTTAAATAGTTGCAAGCCG 59.500 41.667 0.00 0.00 35.53 5.52
3840 4064 9.282569 GCAGATTTCTTCTCATTATAATCAGGT 57.717 33.333 0.00 0.00 29.93 4.00
4163 4399 1.707989 TGGGAATGACTTAAGTGGGCA 59.292 47.619 14.14 5.34 0.00 5.36
4237 4473 3.133721 AGAGAGGTTCAGTCATATGGTGC 59.866 47.826 2.13 0.00 0.00 5.01
4284 4520 9.674068 TGCACATTTACTCTATGGTTTTATACA 57.326 29.630 0.00 0.00 0.00 2.29
4415 4651 4.218417 GGTGGCATCCATATTGGTATGTTC 59.782 45.833 0.00 0.00 39.03 3.18
4458 5054 1.068055 GCTCGACTTAAAGACACCCGA 60.068 52.381 0.00 0.00 0.00 5.14
4460 5056 1.001633 TGGCTCGACTTAAAGACACCC 59.998 52.381 0.00 0.00 0.00 4.61
4476 5072 0.035439 CCCGAAAGTGGTACATGGCT 60.035 55.000 0.00 0.00 44.52 4.75
4479 5075 1.199097 GCAACCCGAAAGTGGTACATG 59.801 52.381 0.00 0.00 44.52 3.21
4734 5330 8.954350 CCTGTGAAGACTTCATCAATCTTAAAT 58.046 33.333 20.43 0.00 42.47 1.40
4753 5349 1.272490 CGACTACAAGGAGCCTGTGAA 59.728 52.381 0.00 0.00 0.00 3.18
4847 5443 0.108138 AGTTTTAGAGCTGGCGCGAT 60.108 50.000 12.10 0.00 42.32 4.58


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

AutoCloner maintained by Alex Coulton.