Multiple sequence alignment - TraesCS5A01G418900

Loading Multiple Alignment...

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 TraesCS5A01G418900 chr5A 100.000 2442 0 0 1 2442 606547522 606545081 0.000000e+00 4510
1 TraesCS5A01G418900 chr5A 98.269 1329 18 3 1 1324 606630896 606629568 0.000000e+00 2322
2 TraesCS5A01G418900 chr5A 93.684 570 24 4 1881 2442 606629574 606629009 0.000000e+00 843
3 TraesCS5A01G418900 chr5D 94.548 1339 53 7 1 1324 485614497 485613164 0.000000e+00 2050
4 TraesCS5A01G418900 chr5D 92.302 1247 55 25 1 1241 485825679 485824468 0.000000e+00 1733
5 TraesCS5A01G418900 chr5D 93.683 744 31 7 584 1324 485382162 485381432 0.000000e+00 1099
6 TraesCS5A01G418900 chr5D 92.051 780 41 5 127 905 485742244 485741485 0.000000e+00 1077
7 TraesCS5A01G418900 chr5D 90.877 570 35 6 1881 2442 485381438 485380878 0.000000e+00 749
8 TraesCS5A01G418900 chr5D 90.261 575 37 8 1881 2442 485613170 485612602 0.000000e+00 734
9 TraesCS5A01G418900 chr5D 89.825 570 32 9 1881 2435 485824431 485823873 0.000000e+00 708
10 TraesCS5A01G418900 chr5D 93.396 212 14 0 4 215 485382371 485382160 5.070000e-82 315
11 TraesCS5A01G418900 chr5D 79.656 349 54 10 1972 2306 485740050 485739705 4.060000e-58 235
12 TraesCS5A01G418900 chr5D 85.946 185 19 6 1121 1303 485740338 485740159 8.910000e-45 191
13 TraesCS5A01G418900 chr5B 94.535 1226 43 8 4 1221 596937327 596936118 0.000000e+00 1871
14 TraesCS5A01G418900 chr5B 86.122 490 44 13 1881 2353 596936106 596935624 7.790000e-140 507
15 TraesCS5A01G418900 chr3D 86.402 956 96 17 1 939 560912225 560913163 0.000000e+00 1014
16 TraesCS5A01G418900 chr3A 98.378 555 9 0 1326 1880 77482357 77482911 0.000000e+00 976
17 TraesCS5A01G418900 chr3A 85.042 956 102 19 1 939 696929512 696930443 0.000000e+00 935
18 TraesCS5A01G418900 chr2B 98.346 544 8 1 1341 1883 141155955 141155412 0.000000e+00 953
19 TraesCS5A01G418900 chr2B 93.226 561 35 3 1326 1886 698003516 698002959 0.000000e+00 822
20 TraesCS5A01G418900 chr4A 95.179 560 27 0 1323 1882 628007794 628008353 0.000000e+00 885
21 TraesCS5A01G418900 chr7B 93.885 556 31 3 1326 1881 728935193 728934641 0.000000e+00 835
22 TraesCS5A01G418900 chr1B 92.559 551 38 3 1330 1880 67502828 67502281 0.000000e+00 787
23 TraesCS5A01G418900 chr6B 91.532 555 42 4 1323 1877 291256506 291257055 0.000000e+00 760
24 TraesCS5A01G418900 chr6B 96.821 346 11 0 1535 1880 13699 13354 1.630000e-161 579
25 TraesCS5A01G418900 chr6B 92.327 391 27 3 1325 1715 257599029 257598642 9.870000e-154 553
26 TraesCS5A01G418900 chrUn 91.627 418 29 4 1468 1881 117082084 117082499 7.570000e-160 573
27 TraesCS5A01G418900 chr7A 87.019 416 46 6 358 770 40421124 40420714 1.710000e-126 462
28 TraesCS5A01G418900 chr7A 94.030 67 1 1 876 939 40420710 40420644 5.560000e-17 99


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 TraesCS5A01G418900 chr5A 606545081 606547522 2441 True 4510.0 4510 100.000000 1 2442 1 chr5A.!!$R1 2441
1 TraesCS5A01G418900 chr5A 606629009 606630896 1887 True 1582.5 2322 95.976500 1 2442 2 chr5A.!!$R2 2441
2 TraesCS5A01G418900 chr5D 485612602 485614497 1895 True 1392.0 2050 92.404500 1 2442 2 chr5D.!!$R2 2441
3 TraesCS5A01G418900 chr5D 485823873 485825679 1806 True 1220.5 1733 91.063500 1 2435 2 chr5D.!!$R4 2434
4 TraesCS5A01G418900 chr5D 485380878 485382371 1493 True 721.0 1099 92.652000 4 2442 3 chr5D.!!$R1 2438
5 TraesCS5A01G418900 chr5D 485739705 485742244 2539 True 501.0 1077 85.884333 127 2306 3 chr5D.!!$R3 2179
6 TraesCS5A01G418900 chr5B 596935624 596937327 1703 True 1189.0 1871 90.328500 4 2353 2 chr5B.!!$R1 2349
7 TraesCS5A01G418900 chr3D 560912225 560913163 938 False 1014.0 1014 86.402000 1 939 1 chr3D.!!$F1 938
8 TraesCS5A01G418900 chr3A 77482357 77482911 554 False 976.0 976 98.378000 1326 1880 1 chr3A.!!$F1 554
9 TraesCS5A01G418900 chr3A 696929512 696930443 931 False 935.0 935 85.042000 1 939 1 chr3A.!!$F2 938
10 TraesCS5A01G418900 chr2B 141155412 141155955 543 True 953.0 953 98.346000 1341 1883 1 chr2B.!!$R1 542
11 TraesCS5A01G418900 chr2B 698002959 698003516 557 True 822.0 822 93.226000 1326 1886 1 chr2B.!!$R2 560
12 TraesCS5A01G418900 chr4A 628007794 628008353 559 False 885.0 885 95.179000 1323 1882 1 chr4A.!!$F1 559
13 TraesCS5A01G418900 chr7B 728934641 728935193 552 True 835.0 835 93.885000 1326 1881 1 chr7B.!!$R1 555
14 TraesCS5A01G418900 chr1B 67502281 67502828 547 True 787.0 787 92.559000 1330 1880 1 chr1B.!!$R1 550
15 TraesCS5A01G418900 chr6B 291256506 291257055 549 False 760.0 760 91.532000 1323 1877 1 chr6B.!!$F1 554

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
539 556 3.61004 TGACTAATGCCGACACATCTT 57.39 42.857 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2949 0.394565 ATCTAATCCACTCCAGCGGC 59.605 55.0 0.0 0.0 0.0 6.53 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
61 64 7.482474 TCCACAATGCATATTTAGACAATGTG 58.518 34.615 0.00 6.73 41.43 3.21
105 109 3.829026 CCAGCTGTATCTGCATAGGTAGA 59.171 47.826 13.81 0.00 40.16 2.59
539 556 3.610040 TGACTAATGCCGACACATCTT 57.390 42.857 0.00 0.00 0.00 2.40
1119 2087 1.873270 GACAACGATGGTTTGGCCCC 61.873 60.000 0.00 0.00 32.98 5.80
1179 2148 9.889128 TTTTCTGATTTGGAAACTTGATTCTTT 57.111 25.926 0.00 0.00 33.22 2.52
1643 2623 5.736616 AGGAGTTATTTAGGGGAGTGGAAAT 59.263 40.000 0.00 0.00 0.00 2.17
1788 2769 1.190984 CGCTGAATCCACATCGAATCG 59.809 52.381 0.00 0.00 32.33 3.34
1882 2863 0.878961 CGTTTCCGGCTACTATGGGC 60.879 60.000 0.00 0.00 0.00 5.36
1886 2867 2.448582 CCGGCTACTATGGGCCCAA 61.449 63.158 32.58 17.36 45.01 4.12
1967 2948 3.158676 ACTGTCCAGAACCTCACTAGAC 58.841 50.000 0.00 0.00 0.00 2.59
1968 2949 2.160205 TGTCCAGAACCTCACTAGACG 58.840 52.381 0.00 0.00 30.90 4.18
1975 2980 2.103143 CTCACTAGACGCCGCTGG 59.897 66.667 0.00 0.00 0.00 4.85
1996 3001 7.519008 CGCTGGAGTGGATTAGATAAATTTGTC 60.519 40.741 6.82 6.82 0.00 3.18
2021 3026 6.984474 CGCTTCCATCCAGAATAGTTACTTTA 59.016 38.462 0.00 0.00 0.00 1.85
2048 3056 2.200337 GCGTCTGGGCCTTTTGGTT 61.200 57.895 4.53 0.00 42.99 3.67
2112 3134 1.871126 GCAGCTGGCAAAGGGAGAAC 61.871 60.000 17.12 0.00 43.97 3.01
2128 3150 3.751698 GGAGAACACCCAAGACAATACAC 59.248 47.826 0.00 0.00 0.00 2.90
2208 3240 6.678663 CGCAACTGTATCGTTTTCTATTTCTG 59.321 38.462 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 64 5.106317 TGGAAAGAACATGCGAATAACTTCC 60.106 40.000 0.00 0.00 0.00 3.46
105 109 6.186957 TGCATACCCAAATTCTACAAGATGT 58.813 36.000 0.00 0.00 0.00 3.06
1179 2148 6.189859 ACCATCAGCAGAATCCTTGAATTAA 58.810 36.000 0.00 0.00 0.00 1.40
1371 2351 2.272797 CCTCCGACTCTCGTCCCT 59.727 66.667 0.00 0.00 38.40 4.20
1488 2468 2.596904 CGTTCCTCGTTCCATGGTAT 57.403 50.000 12.58 0.00 34.52 2.73
1643 2623 1.344065 TTTACTCTCTGCCCCGTTCA 58.656 50.000 0.00 0.00 0.00 3.18
1788 2769 0.453390 AACGAGGGTCGATTCGGTAC 59.547 55.000 17.28 0.00 43.74 3.34
1967 2948 1.592669 CTAATCCACTCCAGCGGCG 60.593 63.158 0.51 0.51 0.00 6.46
1968 2949 0.394565 ATCTAATCCACTCCAGCGGC 59.605 55.000 0.00 0.00 0.00 6.53
1975 2980 7.484035 AGCGACAAATTTATCTAATCCACTC 57.516 36.000 0.00 0.00 0.00 3.51
1996 3001 4.950050 AGTAACTATTCTGGATGGAAGCG 58.050 43.478 0.00 0.00 0.00 4.68
2048 3056 5.247564 AGGATAACTATACTGCCGGCATTTA 59.752 40.000 32.87 23.97 0.00 1.40
2112 3134 7.687941 AAATCTTAGTGTATTGTCTTGGGTG 57.312 36.000 0.00 0.00 0.00 4.61
2208 3240 5.754890 AGACCAATGTGAGATTTGCAAAAAC 59.245 36.000 17.19 13.15 0.00 2.43


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

AutoCloner maintained by Alex Coulton.