Multiple sequence alignment - TraesCS1A01G237600

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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 TraesCS1A01G237600 chr1A 100.000 2935 0 0 1 2935 423463391 423460457 0.000000e+00 5421
1 TraesCS1A01G237600 chr1A 98.027 2940 53 5 1 2935 423516357 423513418 0.000000e+00 5103
2 TraesCS1A01G237600 chr1A 94.186 2236 124 5 700 2933 423594441 423592210 0.000000e+00 3404
3 TraesCS1A01G237600 chr1A 93.875 2253 117 10 700 2932 423551372 423549121 0.000000e+00 3376
4 TraesCS1A01G237600 chr1A 93.077 2239 147 6 700 2933 424080395 424082630 0.000000e+00 3269
5 TraesCS1A01G237600 chr1A 92.908 2228 147 7 700 2920 423164229 423162006 0.000000e+00 3229
6 TraesCS1A01G237600 chr1A 92.726 2227 154 5 700 2920 424272750 424274974 0.000000e+00 3208
7 TraesCS1A01G237600 chr1A 92.594 2228 154 7 700 2920 423289740 423287517 0.000000e+00 3190
8 TraesCS1A01G237600 chr1A 92.418 2229 156 9 700 2920 423227841 423225618 0.000000e+00 3168
9 TraesCS1A01G237600 chr1A 93.021 2049 136 5 866 2909 424392568 424394614 0.000000e+00 2985
10 TraesCS1A01G237600 chr1A 92.222 720 38 6 1 702 424079644 424080363 0.000000e+00 1003
11 TraesCS1A01G237600 chr1A 91.944 720 43 6 1 706 423144504 423143786 0.000000e+00 994
12 TraesCS1A01G237600 chr1A 91.213 717 46 8 1 702 423085820 423085106 0.000000e+00 959
13 TraesCS1A01G237600 chr1A 90.629 715 48 8 1 702 424390681 424391389 0.000000e+00 931
14 TraesCS1A01G237600 chr1A 90.629 715 43 9 1 702 423290475 423289772 0.000000e+00 928
15 TraesCS1A01G237600 chr1A 90.166 722 43 13 1 706 423270184 423269475 0.000000e+00 915
16 TraesCS1A01G237600 chr1A 90.042 713 46 8 3 702 423164961 423164261 0.000000e+00 900
17 TraesCS1A01G237600 chr1A 89.474 722 45 10 1 706 423208304 423207598 0.000000e+00 883
18 TraesCS1A01G237600 chr1A 89.371 715 53 8 1 702 424272014 424272718 0.000000e+00 878
19 TraesCS1A01G237600 chr1A 89.717 671 43 9 1 659 423228581 423227925 0.000000e+00 833
20 TraesCS1A01G237600 chr1A 92.323 495 34 4 212 702 423551898 423551404 0.000000e+00 701
21 TraesCS1A01G237600 chr1A 96.571 175 6 0 700 874 424391421 424391595 1.030000e-74 291
22 TraesCS1A01G237600 chr1B 85.635 724 75 12 1 702 435811478 435812194 0.000000e+00 734
23 TraesCS1A01G237600 chr1B 84.091 572 69 14 721 1273 435369261 435368693 1.550000e-147 532


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 TraesCS1A01G237600 chr1A 423460457 423463391 2934 True 5421.000000 5421 100.0000 1 2935 1 chr1A.!!$R5 2934
1 TraesCS1A01G237600 chr1A 423513418 423516357 2939 True 5103.000000 5103 98.0270 1 2935 1 chr1A.!!$R6 2934
2 TraesCS1A01G237600 chr1A 423592210 423594441 2231 True 3404.000000 3404 94.1860 700 2933 1 chr1A.!!$R7 2233
3 TraesCS1A01G237600 chr1A 424079644 424082630 2986 False 2136.000000 3269 92.6495 1 2933 2 chr1A.!!$F1 2932
4 TraesCS1A01G237600 chr1A 423162006 423164961 2955 True 2064.500000 3229 91.4750 3 2920 2 chr1A.!!$R8 2917
5 TraesCS1A01G237600 chr1A 423287517 423290475 2958 True 2059.000000 3190 91.6115 1 2920 2 chr1A.!!$R10 2919
6 TraesCS1A01G237600 chr1A 424272014 424274974 2960 False 2043.000000 3208 91.0485 1 2920 2 chr1A.!!$F2 2919
7 TraesCS1A01G237600 chr1A 423549121 423551898 2777 True 2038.500000 3376 93.0990 212 2932 2 chr1A.!!$R11 2720
8 TraesCS1A01G237600 chr1A 423225618 423228581 2963 True 2000.500000 3168 91.0675 1 2920 2 chr1A.!!$R9 2919
9 TraesCS1A01G237600 chr1A 424390681 424394614 3933 False 1402.333333 2985 93.4070 1 2909 3 chr1A.!!$F3 2908
10 TraesCS1A01G237600 chr1A 423143786 423144504 718 True 994.000000 994 91.9440 1 706 1 chr1A.!!$R2 705
11 TraesCS1A01G237600 chr1A 423085106 423085820 714 True 959.000000 959 91.2130 1 702 1 chr1A.!!$R1 701
12 TraesCS1A01G237600 chr1A 423269475 423270184 709 True 915.000000 915 90.1660 1 706 1 chr1A.!!$R4 705
13 TraesCS1A01G237600 chr1A 423207598 423208304 706 True 883.000000 883 89.4740 1 706 1 chr1A.!!$R3 705
14 TraesCS1A01G237600 chr1B 435811478 435812194 716 False 734.000000 734 85.6350 1 702 1 chr1B.!!$F1 701
15 TraesCS1A01G237600 chr1B 435368693 435369261 568 True 532.000000 532 84.0910 721 1273 1 chr1B.!!$R1 552

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
290 292 1.261480 TGTAATGGCGGCAATTGGTT 58.739 45.000 18.31 7.99 0.00 3.67 F
358 376 4.155462 AGCATTATGATCACCGATGATTGC 59.845 41.667 15.28 5.39 46.01 3.56 F
1031 2112 6.183347 CAACCAAAAGGACATAGGAGAAGAT 58.817 40.000 0.00 0.00 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 2546 6.889177 TGAGGCATGATAACTTTCCAATAACA 59.111 34.615 0.0 0.0 0.00 2.41 R
1528 2619 8.859090 TGATCATAAAATCACAAGGAAAACACT 58.141 29.630 0.0 0.0 30.76 3.55 R
2519 3617 2.641305 AGACCACTTAGCGACGACTAT 58.359 47.619 0.0 0.0 0.00 2.12 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
290 292 1.261480 TGTAATGGCGGCAATTGGTT 58.739 45.000 18.31 7.99 0.00 3.67
346 358 5.190528 TCCCCAGGAGATTAGCATTATGATC 59.809 44.000 0.00 0.00 0.00 2.92
358 376 4.155462 AGCATTATGATCACCGATGATTGC 59.845 41.667 15.28 5.39 46.01 3.56
388 409 8.285394 ACTGTTATAGCTTGAATAATGAATGCG 58.715 33.333 0.00 0.00 0.00 4.73
1031 2112 6.183347 CAACCAAAAGGACATAGGAGAAGAT 58.817 40.000 0.00 0.00 0.00 2.40
1968 3064 7.322664 TGGGAGCATTATGAATTGTTTTTCTC 58.677 34.615 0.00 0.00 0.00 2.87
2095 3191 3.264104 TCACCGTATTGGGACGATTTTC 58.736 45.455 0.00 0.00 45.82 2.29
2189 3286 6.428083 TCTAAATCTGGAACTACACACCAA 57.572 37.500 0.00 0.00 33.14 3.67
2432 3530 4.796038 AGCTGCAGCATATTTTTGTTCT 57.204 36.364 38.24 11.97 45.16 3.01
2519 3617 4.383118 CCTTTTGGCTAGCTCTAGTGCTTA 60.383 45.833 23.23 9.49 43.74 3.09
2788 3887 3.182173 CGTGTTGAATTTTGCCATGTCAC 59.818 43.478 0.00 0.00 0.00 3.67
2820 3919 8.822855 GCATTGCATCATCATATTTTTCAAAGA 58.177 29.630 3.15 0.00 0.00 2.52
2909 4008 1.951602 TCCAGTTCTCGTTTCGTGAGA 59.048 47.619 0.00 0.00 40.59 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 170 4.089923 GCAAATTCGTGCATACTTTTGGAC 59.910 41.667 13.48 0.0 44.29 4.02
290 292 0.752743 AAGCCAAGAAGCTGTGTGCA 60.753 50.000 0.00 0.0 44.11 4.57
346 358 3.287312 ACAGTTTTGCAATCATCGGTG 57.713 42.857 0.00 0.0 0.00 4.94
587 621 7.445900 ACATAGTGTATACGAAAATGTGTCG 57.554 36.000 10.40 0.0 44.10 4.35
1049 2130 6.271857 AGTGTTGATCCAGATTAGAGCCATAT 59.728 38.462 0.00 0.0 0.00 1.78
1083 2164 3.555377 CCATCAAAAGTGCCATCAAGCAA 60.555 43.478 0.00 0.0 46.19 3.91
1455 2546 6.889177 TGAGGCATGATAACTTTCCAATAACA 59.111 34.615 0.00 0.0 0.00 2.41
1528 2619 8.859090 TGATCATAAAATCACAAGGAAAACACT 58.141 29.630 0.00 0.0 30.76 3.55
2095 3191 9.372369 TGGTAGATTTAATTTTAATTTTGCCCG 57.628 29.630 0.00 0.0 0.00 6.13
2432 3530 4.917385 ACATTGTTGTGGTAGATAGCCAA 58.083 39.130 0.00 0.0 37.81 4.52
2519 3617 2.641305 AGACCACTTAGCGACGACTAT 58.359 47.619 0.00 0.0 0.00 2.12
2721 3819 4.570772 ACGATGAATAATTGGAAGACACCG 59.429 41.667 0.00 0.0 0.00 4.94
2788 3887 2.880963 TGATGATGCAATGCACATGG 57.119 45.000 21.47 0.0 43.04 3.66
2820 3919 3.245016 TGGAGAAAGTGACCAGATGCATT 60.245 43.478 0.00 0.0 0.00 3.56
2909 4008 4.059773 TGCCTGGAATGTTTTTATCCCT 57.940 40.909 0.00 0.0 32.01 4.20


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

AutoCloner maintained by Alex Coulton.