Multiple sequence alignment - TraesCS5A01G415700

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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 TraesCS5A01G415700 chr5A 100.000 6138 0 0 1 6138 604816252 604810115 0.000000e+00 11335
1 TraesCS5A01G415700 chr5A 92.436 5804 318 67 405 6138 555373235 555378987 0.000000e+00 8174
2 TraesCS5A01G415700 chr5A 84.499 1716 202 41 863 2561 644504384 644506052 0.000000e+00 1637
3 TraesCS5A01G415700 chr5A 84.132 876 103 23 868 1728 644485943 644486797 0.000000e+00 815
4 TraesCS5A01G415700 chr5A 88.048 502 35 12 1 480 555354344 555354842 6.900000e-159 571
5 TraesCS5A01G415700 chr5A 87.126 435 29 13 1 412 555359390 555359820 9.320000e-128 468
6 TraesCS5A01G415700 chr4A 98.682 6145 71 8 1 6138 215126159 215132300 0.000000e+00 10890
7 TraesCS5A01G415700 chr6B 98.658 4621 60 2 1 4619 683643666 683639046 0.000000e+00 8189
8 TraesCS5A01G415700 chr6B 98.748 1517 16 3 4624 6138 683638773 683637258 0.000000e+00 2693
9 TraesCS5A01G415700 chr2D 91.547 4389 278 55 904 5245 192299025 192294683 0.000000e+00 5963
10 TraesCS5A01G415700 chr2D 87.402 508 41 12 328 821 192299731 192299233 4.150000e-156 562
11 TraesCS5A01G415700 chr2D 90.632 427 27 11 5275 5693 192294692 192294271 6.950000e-154 555
12 TraesCS5A01G415700 chr2D 85.484 434 37 17 5710 6138 192294120 192293708 4.400000e-116 429
13 TraesCS5A01G415700 chr1D 93.919 3618 184 30 862 4457 2860845 2864448 0.000000e+00 5430
14 TraesCS5A01G415700 chr1D 92.216 835 50 14 4450 5279 2873204 2874028 0.000000e+00 1168
15 TraesCS5A01G415700 chr1D 91.250 560 31 9 328 877 2860155 2860706 0.000000e+00 747
16 TraesCS5A01G415700 chr1D 92.239 451 23 8 5275 5718 2880732 2881177 4.040000e-176 628
17 TraesCS5A01G415700 chr1D 89.070 430 29 11 5710 6138 2881228 2881640 9.120000e-143 518
18 TraesCS5A01G415700 chr1D 85.135 444 38 8 1 422 2859854 2860291 4.400000e-116 429
19 TraesCS5A01G415700 chr3B 82.815 5109 647 150 865 5870 523144943 523139963 0.000000e+00 4357
20 TraesCS5A01G415700 chr3A 82.164 5175 655 160 868 5940 516786864 516781856 0.000000e+00 4196
21 TraesCS5A01G415700 chr3D 82.346 4152 537 130 1881 5940 397186097 397182050 0.000000e+00 3426
22 TraesCS5A01G415700 chr6D 89.725 2433 212 33 868 3282 439520142 439522554 0.000000e+00 3073
23 TraesCS5A01G415700 chr6D 88.181 2479 198 57 3280 5718 439541502 439543925 0.000000e+00 2867
24 TraesCS5A01G415700 chr6D 82.659 346 30 18 35 360 439519212 439519547 4.690000e-71 279
25 TraesCS5A01G415700 chr2A 83.996 2162 279 37 988 3100 571477648 571475505 0.000000e+00 2013
26 TraesCS5A01G415700 chr1A 80.160 2369 341 95 3018 5317 496060131 496062439 0.000000e+00 1652


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 TraesCS5A01G415700 chr5A 604810115 604816252 6137 True 11335.00 11335 100.000000 1 6138 1 chr5A.!!$R1 6137
1 TraesCS5A01G415700 chr5A 555373235 555378987 5752 False 8174.00 8174 92.436000 405 6138 1 chr5A.!!$F3 5733
2 TraesCS5A01G415700 chr5A 644504384 644506052 1668 False 1637.00 1637 84.499000 863 2561 1 chr5A.!!$F5 1698
3 TraesCS5A01G415700 chr5A 644485943 644486797 854 False 815.00 815 84.132000 868 1728 1 chr5A.!!$F4 860
4 TraesCS5A01G415700 chr4A 215126159 215132300 6141 False 10890.00 10890 98.682000 1 6138 1 chr4A.!!$F1 6137
5 TraesCS5A01G415700 chr6B 683637258 683643666 6408 True 5441.00 8189 98.703000 1 6138 2 chr6B.!!$R1 6137
6 TraesCS5A01G415700 chr2D 192293708 192299731 6023 True 1877.25 5963 88.766250 328 6138 4 chr2D.!!$R1 5810
7 TraesCS5A01G415700 chr1D 2859854 2864448 4594 False 2202.00 5430 90.101333 1 4457 3 chr1D.!!$F2 4456
8 TraesCS5A01G415700 chr1D 2873204 2874028 824 False 1168.00 1168 92.216000 4450 5279 1 chr1D.!!$F1 829
9 TraesCS5A01G415700 chr1D 2880732 2881640 908 False 573.00 628 90.654500 5275 6138 2 chr1D.!!$F3 863
10 TraesCS5A01G415700 chr3B 523139963 523144943 4980 True 4357.00 4357 82.815000 865 5870 1 chr3B.!!$R1 5005
11 TraesCS5A01G415700 chr3A 516781856 516786864 5008 True 4196.00 4196 82.164000 868 5940 1 chr3A.!!$R1 5072
12 TraesCS5A01G415700 chr3D 397182050 397186097 4047 True 3426.00 3426 82.346000 1881 5940 1 chr3D.!!$R1 4059
13 TraesCS5A01G415700 chr6D 439541502 439543925 2423 False 2867.00 2867 88.181000 3280 5718 1 chr6D.!!$F1 2438
14 TraesCS5A01G415700 chr6D 439519212 439522554 3342 False 1676.00 3073 86.192000 35 3282 2 chr6D.!!$F2 3247
15 TraesCS5A01G415700 chr2A 571475505 571477648 2143 True 2013.00 2013 83.996000 988 3100 1 chr2A.!!$R1 2112
16 TraesCS5A01G415700 chr1A 496060131 496062439 2308 False 1652.00 1652 80.160000 3018 5317 1 chr1A.!!$F1 2299

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
591 620 2.555757 CCTGCAGCTTTTACTTGCTCTT 59.444 45.455 8.66 0.00 37.44 2.85 F
1500 1902 0.178981 AGGGCTCCAATTGCGCATAT 60.179 50.000 12.75 4.95 44.29 1.78 F
2427 2856 0.109132 GAAGATGGCAAAAGCACCGG 60.109 55.000 0.00 0.00 0.00 5.28 F
3113 3574 1.227943 GTCACCAACTCAGCCAGCA 60.228 57.895 0.00 0.00 0.00 4.41 F
3592 4057 2.894126 AGGACGAGAAGAAGCTCAAGAA 59.106 45.455 0.00 0.00 34.56 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 2710 1.142060 TCTGGGTTGTCCGAAACATGT 59.858 47.619 0.0 0.0 37.82 3.21 R
3136 3597 1.279496 TCACTCCAATCTCCACCCAG 58.721 55.000 0.0 0.0 0.00 4.45 R
3592 4057 4.232091 TGGACTCCCTACTCTTTTCTTGT 58.768 43.478 0.0 0.0 0.00 3.16 R
5116 5941 5.104982 TGTTCAAAGGATGGAAAACAGCTTT 60.105 36.000 0.0 0.0 36.24 3.51 R
5220 6048 0.035534 TTGCATCTTCAAGGCCGCTA 60.036 50.000 0.0 0.0 0.00 4.26 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
84 85 5.983118 GGGTCGAATTTCATGAGTTTTGTTT 59.017 36.000 0.00 0.00 0.00 2.83
547 574 3.211045 GCTGTAAGTGTGGTTCCTTTGA 58.789 45.455 0.00 0.00 35.30 2.69
591 620 2.555757 CCTGCAGCTTTTACTTGCTCTT 59.444 45.455 8.66 0.00 37.44 2.85
747 797 8.540388 ACTTGATCTACAAAGCCAAATCTACTA 58.460 33.333 0.00 0.00 38.08 1.82
1006 1385 5.180367 TGATTTTTGCAGTTTCATGTCGA 57.820 34.783 0.00 0.00 0.00 4.20
1179 1559 6.002082 CACAATACCACATGATCTGATGGAT 58.998 40.000 14.31 3.93 36.04 3.41
1500 1902 0.178981 AGGGCTCCAATTGCGCATAT 60.179 50.000 12.75 4.95 44.29 1.78
1594 1996 5.650543 CTTGCAACAGTTTTAACTCCAAGT 58.349 37.500 0.00 0.00 37.08 3.16
1935 2349 3.887110 TGATATTTCCTCAAGCTGCCATG 59.113 43.478 0.00 0.00 0.00 3.66
2051 2465 3.355077 TGGGCAAACCATCATTCGT 57.645 47.368 0.00 0.00 46.80 3.85
2284 2710 4.454678 ACAGTGAAGTTGCTCAAGATCAA 58.545 39.130 0.00 0.00 0.00 2.57
2427 2856 0.109132 GAAGATGGCAAAAGCACCGG 60.109 55.000 0.00 0.00 0.00 5.28
2713 3168 3.394606 AGGTGTTCTAAGCTCTTTTGGGA 59.605 43.478 0.00 0.00 0.00 4.37
2770 3225 3.402110 CACCTACTCAAAGATGTGCACA 58.598 45.455 24.08 24.08 0.00 4.57
3081 3542 5.700402 AGGATAAAGTGGCTAGTTGTGAT 57.300 39.130 0.00 0.00 0.00 3.06
3113 3574 1.227943 GTCACCAACTCAGCCAGCA 60.228 57.895 0.00 0.00 0.00 4.41
3136 3597 9.698309 AGCACAATCAATACATACATACTACTC 57.302 33.333 0.00 0.00 0.00 2.59
3140 3601 9.645059 CAATCAATACATACATACTACTCTGGG 57.355 37.037 0.00 0.00 0.00 4.45
3592 4057 2.894126 AGGACGAGAAGAAGCTCAAGAA 59.106 45.455 0.00 0.00 34.56 2.52
3692 4157 7.254455 GCAATGTACCAGTACTATGTCATGAAC 60.254 40.741 9.24 0.00 37.00 3.18
4141 4623 5.734720 TCATGTCTTCTCCTTATGTCCAAC 58.265 41.667 0.00 0.00 0.00 3.77
5116 5941 0.250684 TGCGGAAGACCATTGCTTCA 60.251 50.000 0.00 0.00 42.68 3.02
5220 6048 2.226330 TGCATTGTAGAAGGCGTTTGT 58.774 42.857 4.73 0.00 41.91 2.83
5603 6524 1.134699 TGGCTAGAGGAAGCATGTTCG 60.135 52.381 0.00 0.00 44.64 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 2.627699 GCTCAATTGAAACCCCTGAACA 59.372 45.455 9.88 0.0 0.00 3.18
591 620 3.601435 TCTGGTTCAAAAACAGTCGACA 58.399 40.909 19.50 0.0 37.10 4.35
747 797 8.135382 TCTAGCTAGTTAAGTTTTCCTGATGT 57.865 34.615 20.10 0.0 0.00 3.06
1006 1385 4.171234 TCAGACTCCATTCCTTCTTCCTT 58.829 43.478 0.00 0.0 0.00 3.36
1179 1559 8.856103 TCAGTGTCGATATTCATAGTTATCCAA 58.144 33.333 0.00 0.0 0.00 3.53
1432 1834 3.785486 CTCGCAATGATGGTGTCTCTTA 58.215 45.455 0.00 0.0 0.00 2.10
1935 2349 4.946784 ATAGTTCAATTGGTGCTCGTTC 57.053 40.909 5.42 0.0 0.00 3.95
2284 2710 1.142060 TCTGGGTTGTCCGAAACATGT 59.858 47.619 0.00 0.0 37.82 3.21
2388 2814 4.640771 TCTGTTGGATTGCTACCTTCTT 57.359 40.909 0.00 0.0 0.00 2.52
2427 2856 2.254546 TGAACCACACACATCTCCAC 57.745 50.000 0.00 0.0 0.00 4.02
2696 3151 5.445964 ACACTTTCCCAAAAGAGCTTAGAA 58.554 37.500 4.99 0.0 43.90 2.10
3081 3542 3.929955 TGGTGACCATGCTCAATATCA 57.070 42.857 0.00 0.0 0.00 2.15
3136 3597 1.279496 TCACTCCAATCTCCACCCAG 58.721 55.000 0.00 0.0 0.00 4.45
3140 3601 1.293924 CGCATCACTCCAATCTCCAC 58.706 55.000 0.00 0.0 0.00 4.02
3592 4057 4.232091 TGGACTCCCTACTCTTTTCTTGT 58.768 43.478 0.00 0.0 0.00 3.16
3692 4157 7.326454 TCTTCATCTTCTTCATCTTGTACCTG 58.674 38.462 0.00 0.0 0.00 4.00
5116 5941 5.104982 TGTTCAAAGGATGGAAAACAGCTTT 60.105 36.000 0.00 0.0 36.24 3.51
5220 6048 0.035534 TTGCATCTTCAAGGCCGCTA 60.036 50.000 0.00 0.0 0.00 4.26
5325 6195 2.568509 CCATCCAAAAGAGCCCAACATT 59.431 45.455 0.00 0.0 0.00 2.71


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

AutoCloner maintained by Alex Coulton.