Multiple sequence alignment - TraesCS2A01G048100

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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 TraesCS2A01G048100 chr2A 100.000 2390 0 0 1 2390 18614299 18616688 0.000000e+00 4414
1 TraesCS2A01G048100 chr2A 86.630 2012 189 36 243 2217 18676053 18678021 0.000000e+00 2152
2 TraesCS2A01G048100 chr2A 86.880 1753 182 27 1 1730 18646967 18648694 0.000000e+00 1919
3 TraesCS2A01G048100 chr2B 94.108 1748 83 13 1 1730 29055388 29057133 0.000000e+00 2639
4 TraesCS2A01G048100 chr2B 86.881 2020 193 28 8 1988 29980237 29978251 0.000000e+00 2196
5 TraesCS2A01G048100 chr2B 88.869 1123 98 15 621 1730 28998157 28999265 0.000000e+00 1356
6 TraesCS2A01G048100 chr2B 84.492 1064 103 25 1201 2223 29869624 29868582 0.000000e+00 994
7 TraesCS2A01G048100 chr2B 85.481 978 92 30 243 1208 29871437 29870498 0.000000e+00 974
8 TraesCS2A01G048100 chr2D 86.428 2041 165 43 243 2217 17238183 17240177 0.000000e+00 2132
9 TraesCS2A01G048100 chr2D 88.850 1426 98 28 824 2217 17184007 17185403 0.000000e+00 1696
10 TraesCS2A01G048100 chr2D 89.942 1034 73 12 885 1895 17336729 17337754 0.000000e+00 1304
11 TraesCS2A01G048100 chr2D 90.000 720 49 8 1199 1895 17347191 17347910 0.000000e+00 909
12 TraesCS2A01G048100 chr2D 90.000 720 49 8 1199 1895 17356409 17357128 0.000000e+00 909
13 TraesCS2A01G048100 chr2D 86.189 782 91 10 9 780 17182863 17183637 0.000000e+00 830
14 TraesCS2A01G048100 chr2D 83.853 898 111 18 1 887 17327187 17328061 0.000000e+00 824
15 TraesCS2A01G048100 chr2D 89.776 313 24 4 885 1197 17346382 17346686 6.190000e-106 394
16 TraesCS2A01G048100 chr2D 85.366 328 20 10 1897 2217 17337942 17338248 4.960000e-82 315
17 TraesCS2A01G048100 chr2D 85.366 328 20 10 1897 2217 17348293 17348599 4.960000e-82 315
18 TraesCS2A01G048100 chr2D 85.366 328 20 10 1897 2217 17357959 17358265 4.960000e-82 315
19 TraesCS2A01G048100 chr2D 85.380 171 17 2 2220 2390 17338280 17338442 1.140000e-38 171
20 TraesCS2A01G048100 chr2D 85.380 171 17 2 2220 2390 17348631 17348793 1.140000e-38 171
21 TraesCS2A01G048100 chr2D 85.380 171 17 2 2220 2390 17358297 17358459 1.140000e-38 171
22 TraesCS2A01G048100 chrUn 85.366 328 20 10 1897 2217 384030296 384030602 4.960000e-82 315
23 TraesCS2A01G048100 chrUn 85.380 171 17 2 2220 2390 384030634 384030796 1.140000e-38 171


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 TraesCS2A01G048100 chr2A 18614299 18616688 2389 False 4414.000000 4414 100.000000 1 2390 1 chr2A.!!$F1 2389
1 TraesCS2A01G048100 chr2A 18676053 18678021 1968 False 2152.000000 2152 86.630000 243 2217 1 chr2A.!!$F3 1974
2 TraesCS2A01G048100 chr2A 18646967 18648694 1727 False 1919.000000 1919 86.880000 1 1730 1 chr2A.!!$F2 1729
3 TraesCS2A01G048100 chr2B 29055388 29057133 1745 False 2639.000000 2639 94.108000 1 1730 1 chr2B.!!$F2 1729
4 TraesCS2A01G048100 chr2B 29978251 29980237 1986 True 2196.000000 2196 86.881000 8 1988 1 chr2B.!!$R1 1980
5 TraesCS2A01G048100 chr2B 28998157 28999265 1108 False 1356.000000 1356 88.869000 621 1730 1 chr2B.!!$F1 1109
6 TraesCS2A01G048100 chr2B 29868582 29871437 2855 True 984.000000 994 84.986500 243 2223 2 chr2B.!!$R2 1980
7 TraesCS2A01G048100 chr2D 17238183 17240177 1994 False 2132.000000 2132 86.428000 243 2217 1 chr2D.!!$F1 1974
8 TraesCS2A01G048100 chr2D 17182863 17185403 2540 False 1263.000000 1696 87.519500 9 2217 2 chr2D.!!$F3 2208
9 TraesCS2A01G048100 chr2D 17327187 17328061 874 False 824.000000 824 83.853000 1 887 1 chr2D.!!$F2 886
10 TraesCS2A01G048100 chr2D 17336729 17338442 1713 False 596.666667 1304 86.896000 885 2390 3 chr2D.!!$F4 1505
11 TraesCS2A01G048100 chr2D 17356409 17358459 2050 False 465.000000 909 86.915333 1199 2390 3 chr2D.!!$F6 1191
12 TraesCS2A01G048100 chr2D 17346382 17348793 2411 False 447.250000 909 87.630500 885 2390 4 chr2D.!!$F5 1505
13 TraesCS2A01G048100 chrUn 384030296 384030796 500 False 243.000000 315 85.373000 1897 2390 2 chrUn.!!$F1 493

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
191 195 1.320507 TTTTGTTACTGGGCGGAACC 58.679 50.0 0.0 0.0 37.93 3.62 F
1150 1517 0.852777 CGTAATGAAGATCGGTGCGG 59.147 55.0 0.0 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1225 2977 0.036164 TTCTGTGGCACCGCTGTATT 59.964 50.000 16.26 0.0 0.0 1.89 R
2247 4974 1.739466 GCTGGCATTTCTCAATCGTGA 59.261 47.619 0.00 0.0 0.0 4.35 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
41 43 8.321353 TGTCATACTCTCTGAAATTAACACCAT 58.679 33.333 0.00 0.00 0.00 3.55
63 65 1.535028 GCACGACATTGTCATGTTCCA 59.465 47.619 16.61 0.00 44.22 3.53
173 175 4.279420 GCTCCCTGAAGTGAAAGTTTCATT 59.721 41.667 20.72 14.26 42.47 2.57
179 181 7.978975 CCCTGAAGTGAAAGTTTCATTTTGTTA 59.021 33.333 22.59 11.78 42.47 2.41
191 195 1.320507 TTTTGTTACTGGGCGGAACC 58.679 50.000 0.00 0.00 37.93 3.62
436 450 5.405571 AGCTAAAACTGTGTACTGAATGTCG 59.594 40.000 0.00 0.00 0.00 4.35
586 604 9.555727 AAGTGAAAGCAGTTAAGTGAATTACTA 57.444 29.630 14.64 0.00 35.38 1.82
619 641 5.705441 TCACACTTCAAATGACCATAGGTTC 59.295 40.000 0.00 0.00 35.25 3.62
726 750 6.509418 TTTGTATTTTACCACTGGAGATGC 57.491 37.500 0.71 0.00 0.00 3.91
921 1288 7.524294 AGATTGTCAAATGTGAACAAACAAC 57.476 32.000 5.39 0.00 34.87 3.32
1150 1517 0.852777 CGTAATGAAGATCGGTGCGG 59.147 55.000 0.00 0.00 0.00 5.69
1225 2977 2.470983 TGCGAACCATGAATCTCACA 57.529 45.000 0.00 0.00 0.00 3.58
1287 3039 0.036388 GCACTGATGGAAGGAACGGA 60.036 55.000 0.00 0.00 0.00 4.69
1452 3211 7.199766 CAGTTTATGTTGCTTTTACTTCCACA 58.800 34.615 0.00 0.00 0.00 4.17
1504 3269 5.126869 TCCATGTTGTCAATGTTTCTGTGTT 59.873 36.000 0.00 0.00 0.00 3.32
1517 3282 2.304092 TCTGTGTTGTCTGTCCGTAGT 58.696 47.619 0.00 0.00 0.00 2.73
1563 3340 6.667848 TCAAGTTCTCAGGAATGTACCTATCA 59.332 38.462 0.00 0.00 38.32 2.15
1594 3372 7.607607 TGCTACTGATGTACTGTTTGAATTGAT 59.392 33.333 0.00 0.00 33.04 2.57
1596 3374 7.750229 ACTGATGTACTGTTTGAATTGATGT 57.250 32.000 0.00 0.00 0.00 3.06
1597 3375 7.587629 ACTGATGTACTGTTTGAATTGATGTG 58.412 34.615 0.00 0.00 0.00 3.21
1598 3376 7.445096 ACTGATGTACTGTTTGAATTGATGTGA 59.555 33.333 0.00 0.00 0.00 3.58
1600 3378 9.447157 TGATGTACTGTTTGAATTGATGTGATA 57.553 29.630 0.00 0.00 0.00 2.15
1601 3379 9.708222 GATGTACTGTTTGAATTGATGTGATAC 57.292 33.333 0.00 0.00 0.00 2.24
1648 3441 0.963225 ATGCATTGAAGTGTGCTGCA 59.037 45.000 0.00 0.00 45.84 4.41
1669 3480 2.594592 GCACTCCCACCGCACTTT 60.595 61.111 0.00 0.00 0.00 2.66
1751 3574 4.023193 AGGTTTATGCTTGTTCCGTTTCAG 60.023 41.667 0.00 0.00 0.00 3.02
1807 3634 4.754114 GCTCTCAAGTCTGAACTCATGTTT 59.246 41.667 0.00 0.00 36.39 2.83
1830 3663 0.392706 TCCAGAAGAAAGTCGCTGCA 59.607 50.000 0.00 0.00 0.00 4.41
1855 3688 5.930837 TTTCAGGGTGAACACAAATCTTT 57.069 34.783 7.25 0.00 35.89 2.52
1857 3690 4.531854 TCAGGGTGAACACAAATCTTTCA 58.468 39.130 7.25 0.00 0.00 2.69
1865 3698 8.490355 GGTGAACACAAATCTTTCATCAAATTC 58.510 33.333 7.25 0.00 31.74 2.17
1889 3722 2.758770 AATGCAGCAAGCCTTGTGCG 62.759 55.000 19.68 6.55 46.86 5.34
2099 4786 1.287815 CAGTGTTGCCACATGCCTG 59.712 57.895 0.00 0.00 44.39 4.85
2200 4898 6.493458 AGAAACCCATAAGTAAGCAACAACAT 59.507 34.615 0.00 0.00 0.00 2.71
2217 4915 3.317603 ACATTTCGAAAAGGCCATTGG 57.682 42.857 15.66 0.00 0.00 3.16
2220 4918 4.709397 ACATTTCGAAAAGGCCATTGGATA 59.291 37.500 15.66 2.23 0.00 2.59
2230 4957 0.899720 CCATTGGATATGCCCCATGC 59.100 55.000 0.00 0.00 41.77 4.06
2242 4969 1.136891 GCCCCATGCCTGAACATTTAC 59.863 52.381 0.00 0.00 0.00 2.01
2247 4974 3.956199 CCATGCCTGAACATTTACTGGAT 59.044 43.478 0.00 0.00 0.00 3.41
2270 4997 3.002042 CACGATTGAGAAATGCCAGCTAG 59.998 47.826 0.00 0.00 0.00 3.42
2289 5016 6.847792 CAGCTAGTAAACGTCAAATGCATATG 59.152 38.462 0.00 0.00 0.00 1.78
2290 5017 6.538742 AGCTAGTAAACGTCAAATGCATATGT 59.461 34.615 0.00 0.00 0.00 2.29
2291 5018 7.065803 AGCTAGTAAACGTCAAATGCATATGTT 59.934 33.333 0.00 0.00 0.00 2.71
2292 5019 8.332464 GCTAGTAAACGTCAAATGCATATGTTA 58.668 33.333 0.00 0.00 0.00 2.41
2296 5023 9.088059 GTAAACGTCAAATGCATATGTTATACG 57.912 33.333 0.00 7.28 0.00 3.06
2297 5024 6.838198 ACGTCAAATGCATATGTTATACGT 57.162 33.333 0.00 7.89 35.27 3.57
2346 5073 9.706691 TCAACTACCTTCAGTTAACATTAGAAG 57.293 33.333 8.61 13.81 36.61 2.85
2357 5084 6.371825 AGTTAACATTAGAAGGCTGCAAGTAC 59.628 38.462 8.61 0.00 35.30 2.73
2364 5091 4.911390 AGAAGGCTGCAAGTACTACATTT 58.089 39.130 0.50 0.00 35.30 2.32
2368 5095 6.240549 AGGCTGCAAGTACTACATTTAGAT 57.759 37.500 0.50 0.00 35.30 1.98
2369 5096 6.051717 AGGCTGCAAGTACTACATTTAGATG 58.948 40.000 0.50 0.00 36.25 2.90
2374 5101 6.049149 GCAAGTACTACATTTAGATGGCAGA 58.951 40.000 0.00 0.00 37.60 4.26
2380 5107 7.383102 ACTACATTTAGATGGCAGAAAACAG 57.617 36.000 0.00 0.00 37.60 3.16
2383 5110 7.288810 ACATTTAGATGGCAGAAAACAGAAA 57.711 32.000 0.00 0.00 37.60 2.52
2384 5111 7.147976 ACATTTAGATGGCAGAAAACAGAAAC 58.852 34.615 0.00 0.00 37.60 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 65 0.326264 GGTGGTGCTGAAGAGATGGT 59.674 55.000 0.00 0.00 0.00 3.55
173 175 0.183014 TGGTTCCGCCCAGTAACAAA 59.817 50.000 0.00 0.00 36.04 2.83
179 181 2.495669 CAATATTTTGGTTCCGCCCAGT 59.504 45.455 0.00 0.00 35.49 4.00
586 604 8.321353 TGGTCATTTGAAGTGTGACTTATCTAT 58.679 33.333 4.93 0.00 38.80 1.98
619 641 6.364701 TGGTGGATTAGGTTTCTCCATTATG 58.635 40.000 0.00 0.00 40.96 1.90
726 750 1.736126 CCATATGGCATCTTGCGCTAG 59.264 52.381 12.92 12.92 46.21 3.42
921 1288 2.733227 GCAAGAATGGATGTTTGCCTCG 60.733 50.000 0.00 0.00 39.88 4.63
1001 1368 5.867903 ATTGGTTGAACTGAATGGTTTCA 57.132 34.783 0.00 0.00 39.54 2.69
1126 1493 4.443063 CGCACCGATCTTCATTACGAATAA 59.557 41.667 0.00 0.00 31.69 1.40
1150 1517 3.665745 AATCAGCCCAACAAACATGAC 57.334 42.857 0.00 0.00 0.00 3.06
1225 2977 0.036164 TTCTGTGGCACCGCTGTATT 59.964 50.000 16.26 0.00 0.00 1.89
1287 3039 0.179000 GGTGATCATTGCTCGGAGGT 59.821 55.000 7.20 0.00 0.00 3.85
1452 3211 5.290493 TCTCATGCCAAATTACTCCGTAT 57.710 39.130 0.00 0.00 0.00 3.06
1504 3269 3.939740 ATAGGGTACTACGGACAGACA 57.060 47.619 0.00 0.00 30.59 3.41
1517 3282 5.399113 TGATGGTGTGTAGCATATAGGGTA 58.601 41.667 0.00 0.00 44.54 3.69
1631 3424 2.925578 TATGCAGCACACTTCAATGC 57.074 45.000 0.00 0.00 42.39 3.56
1634 3427 2.925578 GCATATGCAGCACACTTCAA 57.074 45.000 22.84 0.00 41.59 2.69
1648 3441 1.153168 GTGCGGTGGGAGTGCATAT 60.153 57.895 0.00 0.00 41.23 1.78
1751 3574 3.551846 TCCAAAGGTGTGTTCTTTCCTC 58.448 45.455 0.00 0.00 32.72 3.71
1807 3634 3.429547 GCAGCGACTTTCTTCTGGAGATA 60.430 47.826 0.00 0.00 33.49 1.98
1830 3663 7.781324 AAGATTTGTGTTCACCCTGAAATAT 57.219 32.000 0.37 0.00 38.22 1.28
1855 3688 5.707931 TGCTGCATTTTACGAATTTGATGA 58.292 33.333 0.00 0.00 0.00 2.92
1857 3690 5.062558 GCTTGCTGCATTTTACGAATTTGAT 59.937 36.000 1.84 0.00 42.31 2.57
1865 3698 1.987770 CAAGGCTTGCTGCATTTTACG 59.012 47.619 15.25 0.00 43.70 3.18
2099 4786 7.851822 TTTTGTTCGTTGATTAGATGCTTTC 57.148 32.000 0.00 0.00 0.00 2.62
2154 4846 4.099881 TCTGGCTTTCAGCATTGTTTTTCT 59.900 37.500 0.00 0.00 44.75 2.52
2175 4867 5.830991 TGTTGTTGCTTACTTATGGGTTTCT 59.169 36.000 0.00 0.00 0.00 2.52
2200 4898 4.441356 GCATATCCAATGGCCTTTTCGAAA 60.441 41.667 6.47 6.47 0.00 3.46
2230 4957 4.503910 TCGTGATCCAGTAAATGTTCAGG 58.496 43.478 0.00 0.00 0.00 3.86
2242 4969 3.003068 GGCATTTCTCAATCGTGATCCAG 59.997 47.826 0.00 0.00 31.85 3.86
2247 4974 1.739466 GCTGGCATTTCTCAATCGTGA 59.261 47.619 0.00 0.00 0.00 4.35
2270 4997 9.088059 CGTATAACATATGCATTTGACGTTTAC 57.912 33.333 21.91 13.71 0.00 2.01
2289 5016 6.976925 ACTGTTGCTTATGGAGTACGTATAAC 59.023 38.462 0.00 0.00 0.00 1.89
2290 5017 7.104043 ACTGTTGCTTATGGAGTACGTATAA 57.896 36.000 0.00 0.00 0.00 0.98
2291 5018 6.704289 ACTGTTGCTTATGGAGTACGTATA 57.296 37.500 0.00 0.00 0.00 1.47
2292 5019 5.593679 ACTGTTGCTTATGGAGTACGTAT 57.406 39.130 0.00 0.00 0.00 3.06
2293 5020 5.649395 ACTACTGTTGCTTATGGAGTACGTA 59.351 40.000 0.00 0.00 0.00 3.57
2294 5021 3.955650 ACTGTTGCTTATGGAGTACGT 57.044 42.857 0.00 0.00 0.00 3.57
2295 5022 4.995124 ACTACTGTTGCTTATGGAGTACG 58.005 43.478 0.00 0.00 0.00 3.67
2296 5023 7.098074 AGTACTACTGTTGCTTATGGAGTAC 57.902 40.000 11.96 11.96 38.73 2.73
2297 5024 6.888088 TGAGTACTACTGTTGCTTATGGAGTA 59.112 38.462 0.00 0.00 0.00 2.59
2331 5058 5.182001 ACTTGCAGCCTTCTAATGTTAACTG 59.818 40.000 7.22 0.00 0.00 3.16
2332 5059 5.316987 ACTTGCAGCCTTCTAATGTTAACT 58.683 37.500 7.22 0.00 0.00 2.24
2346 5073 5.237344 CCATCTAAATGTAGTACTTGCAGCC 59.763 44.000 0.00 0.00 0.00 4.85
2349 5076 5.739959 TGCCATCTAAATGTAGTACTTGCA 58.260 37.500 0.00 1.04 0.00 4.08
2357 5084 7.615582 TCTGTTTTCTGCCATCTAAATGTAG 57.384 36.000 0.00 0.00 0.00 2.74
2364 5091 5.620206 TCTGTTTCTGTTTTCTGCCATCTA 58.380 37.500 0.00 0.00 0.00 1.98
2368 5095 3.620488 ACTCTGTTTCTGTTTTCTGCCA 58.380 40.909 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.