Multiple sequence alignment - TraesCS1A01G194300

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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 TraesCS1A01G194300 chr1A 100.000 2606 0 0 1 2606 351597681 351595076 0.000000e+00 4813
1 TraesCS1A01G194300 chr4D 95.554 2609 104 6 1 2606 121933817 121931218 0.000000e+00 4165
2 TraesCS1A01G194300 chr4A 94.170 2607 122 11 1 2606 275460019 275462596 0.000000e+00 3945
3 TraesCS1A01G194300 chr4A 88.582 1699 187 7 910 2606 489823433 489821740 0.000000e+00 2056
4 TraesCS1A01G194300 chr4A 84.918 915 128 6 3 912 489825941 489825032 0.000000e+00 917
5 TraesCS1A01G194300 chr2B 94.241 2153 117 5 455 2606 540314006 540311860 0.000000e+00 3282
6 TraesCS1A01G194300 chr2B 93.265 1856 121 4 589 2440 542135482 542137337 0.000000e+00 2732
7 TraesCS1A01G194300 chr2B 91.899 358 26 3 1 357 540314361 540314006 5.010000e-137 497
8 TraesCS1A01G194300 chr5A 94.339 2049 98 4 572 2606 199145815 199143771 0.000000e+00 3125
9 TraesCS1A01G194300 chr5A 74.085 2377 558 53 194 2547 31902824 31905165 0.000000e+00 924
10 TraesCS1A01G194300 chr5A 94.620 539 26 2 1 539 199146348 199145813 0.000000e+00 832
11 TraesCS1A01G194300 chr5A 72.348 2253 580 36 315 2553 122123580 122125803 0.000000e+00 669
12 TraesCS1A01G194300 chr5D 94.687 1788 93 2 819 2606 502653088 502651303 0.000000e+00 2774
13 TraesCS1A01G194300 chr5D 82.567 631 88 16 17 629 324978376 324979002 1.060000e-148 536
14 TraesCS1A01G194300 chr1B 93.884 1357 80 3 1250 2606 471525547 471524194 0.000000e+00 2043
15 TraesCS1A01G194300 chr3B 93.454 1329 79 5 1278 2606 317608174 317609494 0.000000e+00 1965
16 TraesCS1A01G194300 chr5B 81.410 979 145 16 17 989 377455623 377456570 0.000000e+00 765
17 TraesCS1A01G194300 chr3A 72.562 2205 541 58 328 2500 100049290 100047118 0.000000e+00 662


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 TraesCS1A01G194300 chr1A 351595076 351597681 2605 True 4813.0 4813 100.0000 1 2606 1 chr1A.!!$R1 2605
1 TraesCS1A01G194300 chr4D 121931218 121933817 2599 True 4165.0 4165 95.5540 1 2606 1 chr4D.!!$R1 2605
2 TraesCS1A01G194300 chr4A 275460019 275462596 2577 False 3945.0 3945 94.1700 1 2606 1 chr4A.!!$F1 2605
3 TraesCS1A01G194300 chr4A 489821740 489825941 4201 True 1486.5 2056 86.7500 3 2606 2 chr4A.!!$R1 2603
4 TraesCS1A01G194300 chr2B 542135482 542137337 1855 False 2732.0 2732 93.2650 589 2440 1 chr2B.!!$F1 1851
5 TraesCS1A01G194300 chr2B 540311860 540314361 2501 True 1889.5 3282 93.0700 1 2606 2 chr2B.!!$R1 2605
6 TraesCS1A01G194300 chr5A 199143771 199146348 2577 True 1978.5 3125 94.4795 1 2606 2 chr5A.!!$R1 2605
7 TraesCS1A01G194300 chr5A 31902824 31905165 2341 False 924.0 924 74.0850 194 2547 1 chr5A.!!$F1 2353
8 TraesCS1A01G194300 chr5A 122123580 122125803 2223 False 669.0 669 72.3480 315 2553 1 chr5A.!!$F2 2238
9 TraesCS1A01G194300 chr5D 502651303 502653088 1785 True 2774.0 2774 94.6870 819 2606 1 chr5D.!!$R1 1787
10 TraesCS1A01G194300 chr5D 324978376 324979002 626 False 536.0 536 82.5670 17 629 1 chr5D.!!$F1 612
11 TraesCS1A01G194300 chr1B 471524194 471525547 1353 True 2043.0 2043 93.8840 1250 2606 1 chr1B.!!$R1 1356
12 TraesCS1A01G194300 chr3B 317608174 317609494 1320 False 1965.0 1965 93.4540 1278 2606 1 chr3B.!!$F1 1328
13 TraesCS1A01G194300 chr5B 377455623 377456570 947 False 765.0 765 81.4100 17 989 1 chr5B.!!$F1 972
14 TraesCS1A01G194300 chr3A 100047118 100049290 2172 True 662.0 662 72.5620 328 2500 1 chr3A.!!$R1 2172

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
132 135 2.581354 GCTCTCGGCATCTGTGGT 59.419 61.111 0.0 0.0 41.35 4.16 F
247 270 2.869101 AAAAGGGAAGGAGTGAGAGC 57.131 50.000 0.0 0.0 0.00 4.09 F
1388 3029 0.887387 GCCAAACTAGCGGGTGTTGA 60.887 55.000 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1195 2836 0.109153 TCCTCATTGATGATGCCCGG 59.891 55.000 0.00 0.0 36.02 5.73 R
1438 3079 1.747709 TTTAGAGTCTCTCGGTCCCG 58.252 55.000 5.39 0.0 41.35 5.14 R
2565 4222 3.646162 ACCTTCAATTTTCCCACTTTCCC 59.354 43.478 0.00 0.0 0.00 3.97 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
132 135 2.581354 GCTCTCGGCATCTGTGGT 59.419 61.111 0.00 0.00 41.35 4.16
166 169 4.616802 GCTACGGATGAAAATGTGTTGTTG 59.383 41.667 0.00 0.00 0.00 3.33
247 270 2.869101 AAAAGGGAAGGAGTGAGAGC 57.131 50.000 0.00 0.00 0.00 4.09
589 615 3.181466 GCCGGGCCAAATGAAAATTCTAT 60.181 43.478 8.12 0.00 0.00 1.98
718 744 8.451908 AAATAAAATAAAGGCTGACGAGCTAT 57.548 30.769 0.00 0.00 45.44 2.97
939 2579 5.687166 AACATTTATCTTGGTCCGACCTA 57.313 39.130 18.54 10.23 39.58 3.08
1195 2836 4.864704 TGGTCAAATAAGTTCCCAAAGC 57.135 40.909 0.00 0.00 0.00 3.51
1388 3029 0.887387 GCCAAACTAGCGGGTGTTGA 60.887 55.000 0.00 0.00 0.00 3.18
1438 3079 0.811281 GCAGGCTGATTTACACACCC 59.189 55.000 20.86 0.00 0.00 4.61
1516 3158 0.323451 GGAAAAGTTGAGGCGGGGAT 60.323 55.000 0.00 0.00 0.00 3.85
1800 3444 3.635268 CTCTGAAGTGGGGCAGCCC 62.635 68.421 24.23 24.23 44.51 5.19
1860 3505 5.411977 GTCAGATGAGATGAATAATGCCCTG 59.588 44.000 0.00 0.00 0.00 4.45
2012 3660 2.607892 AAGAAGTGTCGCAAGCCGC 61.608 57.895 0.00 0.00 36.73 6.53
2028 3676 1.136252 GCCGCGAATACATGCACTATG 60.136 52.381 8.23 0.00 42.68 2.23
2154 3802 6.041979 ACAAGATTATATCCAAAATGGTGGCC 59.958 38.462 0.00 0.00 39.03 5.36
2336 3986 7.941238 ACTTGATATGCATAAAGCTTATGACCT 59.059 33.333 11.13 0.00 41.92 3.85
2344 3994 6.686632 GCATAAAGCTTATGACCTAGTGGAGT 60.687 42.308 15.69 0.00 41.15 3.85
2347 3997 2.103263 GCTTATGACCTAGTGGAGTGGG 59.897 54.545 0.00 0.00 37.04 4.61
2563 4220 0.318120 TGCTCTCTTGTCACATGCGA 59.682 50.000 0.00 0.00 0.00 5.10
2565 4222 1.392853 GCTCTCTTGTCACATGCGAAG 59.607 52.381 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
247 270 1.658717 CCTACGAGCATCTTCCGCG 60.659 63.158 0.00 0.00 0.00 6.46
504 530 2.964209 TCTCTTCACCAACTGACTCCT 58.036 47.619 0.00 0.00 0.00 3.69
589 615 2.355197 CATACCACGGCAGTTTCATCA 58.645 47.619 0.00 0.00 0.00 3.07
740 766 7.397221 ACCATCACTCTCTGATAAAAACATGA 58.603 34.615 0.00 0.00 37.53 3.07
887 926 1.564348 AGGCCGGATGACCATAAAACT 59.436 47.619 5.05 0.00 35.59 2.66
912 951 5.793457 GTCGGACCAAGATAAATGTTTTTCG 59.207 40.000 0.00 0.00 0.00 3.46
939 2579 4.261801 AGGCATTAGAATGTAAAGTGCGT 58.738 39.130 4.27 0.00 38.65 5.24
1195 2836 0.109153 TCCTCATTGATGATGCCCGG 59.891 55.000 0.00 0.00 36.02 5.73
1438 3079 1.747709 TTTAGAGTCTCTCGGTCCCG 58.252 55.000 5.39 0.00 41.35 5.14
1603 3247 3.511477 ACCAGTTTGCTCTTCCTCTCTA 58.489 45.455 0.00 0.00 0.00 2.43
2102 3750 8.802267 ACACAACATTACATAGGCTAATTGTTT 58.198 29.630 6.12 0.00 0.00 2.83
2104 3752 7.938140 ACACAACATTACATAGGCTAATTGT 57.062 32.000 0.00 1.81 0.00 2.71
2154 3802 2.076863 AGGAAAACCTTCAATCGAGCG 58.923 47.619 0.00 0.00 32.75 5.03
2336 3986 4.445735 CCTTCAGAAAAACCCACTCCACTA 60.446 45.833 0.00 0.00 0.00 2.74
2344 3994 4.722526 TGATCTCCTTCAGAAAAACCCA 57.277 40.909 0.00 0.00 33.62 4.51
2347 3997 7.173907 TCTCAACATGATCTCCTTCAGAAAAAC 59.826 37.037 0.00 0.00 33.62 2.43
2563 4220 4.347876 CCTTCAATTTTCCCACTTTCCCTT 59.652 41.667 0.00 0.00 0.00 3.95
2565 4222 3.646162 ACCTTCAATTTTCCCACTTTCCC 59.354 43.478 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.