Multiple sequence alignment - TraesCS6D01G043200

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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 TraesCS6D01G043200 chr6D 100.000 2790 0 0 1 2790 17891422 17894211 0.000000e+00 5153
1 TraesCS6D01G043200 chr6B 97.451 1530 28 8 576 2094 32171659 32173188 0.000000e+00 2599
2 TraesCS6D01G043200 chr6B 91.908 1174 70 4 491 1657 32023920 32025075 0.000000e+00 1618
3 TraesCS6D01G043200 chr6B 93.424 806 47 1 858 1657 31793112 31793917 0.000000e+00 1190
4 TraesCS6D01G043200 chr6B 96.733 704 21 2 2088 2790 32173236 32173938 0.000000e+00 1171
5 TraesCS6D01G043200 chr6B 93.893 524 32 0 1020 1543 32075904 32076427 0.000000e+00 791
6 TraesCS6D01G043200 chr6B 93.321 524 35 0 1020 1543 31844248 31844771 0.000000e+00 774
7 TraesCS6D01G043200 chr6B 90.860 558 42 7 1543 2094 32087057 32087611 0.000000e+00 739
8 TraesCS6D01G043200 chr6B 90.323 558 47 6 1543 2094 31869197 31869753 0.000000e+00 725
9 TraesCS6D01G043200 chr6B 93.421 380 22 3 479 856 31783759 31784137 6.750000e-156 560
10 TraesCS6D01G043200 chr6B 88.182 440 39 11 1659 2094 31842562 31842992 1.920000e-141 512
11 TraesCS6D01G043200 chr6B 87.927 439 41 8 1659 2094 32074220 32074649 8.920000e-140 507
12 TraesCS6D01G043200 chr6B 87.528 441 46 6 2093 2529 31843054 31843489 4.150000e-138 501
13 TraesCS6D01G043200 chr6B 86.168 441 52 6 2093 2529 32074710 32075145 4.210000e-128 468
14 TraesCS6D01G043200 chr6B 91.830 306 15 4 240 545 32171369 32171664 4.300000e-113 418
15 TraesCS6D01G043200 chr6B 92.593 243 15 3 1 241 32167476 32167717 2.060000e-91 346
16 TraesCS6D01G043200 chr6B 81.514 449 49 20 1 424 31783321 31783760 3.440000e-89 339
17 TraesCS6D01G043200 chr6B 81.169 462 42 18 1 424 32023428 32023882 2.070000e-86 329
18 TraesCS6D01G043200 chr6B 87.197 289 30 6 2094 2380 32087674 32087957 3.470000e-84 322
19 TraesCS6D01G043200 chr6A 95.095 1631 55 10 479 2092 18624533 18626155 0.000000e+00 2545
20 TraesCS6D01G043200 chr6A 93.050 705 44 5 2088 2790 18626204 18626905 0.000000e+00 1026
21 TraesCS6D01G043200 chr6A 83.077 195 30 3 231 424 18624342 18624534 1.030000e-39 174
22 TraesCS6D01G043200 chr1B 79.785 559 71 21 979 1531 623505711 623505189 4.390000e-98 368
23 TraesCS6D01G043200 chr3B 86.301 219 22 3 2517 2727 779624846 779625064 6.010000e-57 231
24 TraesCS6D01G043200 chr7B 83.539 243 31 3 2516 2749 74108110 74108352 4.680000e-53 219
25 TraesCS6D01G043200 chrUn 84.444 225 25 7 2517 2731 369540874 369541098 2.180000e-51 213
26 TraesCS6D01G043200 chrUn 84.444 225 25 7 2517 2731 435144129 435144353 2.180000e-51 213
27 TraesCS6D01G043200 chr4A 84.444 225 25 7 2517 2731 687514241 687514465 2.180000e-51 213
28 TraesCS6D01G043200 chr5A 83.111 225 27 6 2518 2731 600947019 600947243 7.880000e-46 195
29 TraesCS6D01G043200 chr2D 84.694 196 29 1 2559 2754 579393429 579393623 7.880000e-46 195


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 TraesCS6D01G043200 chr6D 17891422 17894211 2789 False 5153.000000 5153 100.000000 1 2790 1 chr6D.!!$F1 2789
1 TraesCS6D01G043200 chr6B 31793112 31793917 805 False 1190.000000 1190 93.424000 858 1657 1 chr6B.!!$F1 799
2 TraesCS6D01G043200 chr6B 32167476 32173938 6462 False 1133.500000 2599 94.651750 1 2790 4 chr6B.!!$F8 2789
3 TraesCS6D01G043200 chr6B 32023428 32025075 1647 False 973.500000 1618 86.538500 1 1657 2 chr6B.!!$F5 1656
4 TraesCS6D01G043200 chr6B 31869197 31869753 556 False 725.000000 725 90.323000 1543 2094 1 chr6B.!!$F2 551
5 TraesCS6D01G043200 chr6B 31842562 31844771 2209 False 595.666667 774 89.677000 1020 2529 3 chr6B.!!$F4 1509
6 TraesCS6D01G043200 chr6B 32074220 32076427 2207 False 588.666667 791 89.329333 1020 2529 3 chr6B.!!$F6 1509
7 TraesCS6D01G043200 chr6B 32087057 32087957 900 False 530.500000 739 89.028500 1543 2380 2 chr6B.!!$F7 837
8 TraesCS6D01G043200 chr6B 31783321 31784137 816 False 449.500000 560 87.467500 1 856 2 chr6B.!!$F3 855
9 TraesCS6D01G043200 chr6A 18624342 18626905 2563 False 1248.333333 2545 90.407333 231 2790 3 chr6A.!!$F1 2559
10 TraesCS6D01G043200 chr1B 623505189 623505711 522 True 368.000000 368 79.785000 979 1531 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
907 4639 0.389948 GTCCGTGGTCCTAGCTTGTG 60.39 60.0 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2229 6051 0.251386 ACTCCTCTCTCGAAGCACCA 60.251 55.0 0.0 0.0 0.0 4.17 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
29 31 2.047655 CGTTGAACCCCTAGCGCA 60.048 61.111 11.47 0.00 0.00 6.09
38 40 2.503061 CCTAGCGCACAGAGGCAT 59.497 61.111 11.47 0.00 0.00 4.40
48 50 1.196766 ACAGAGGCATGTCCAGAGCA 61.197 55.000 8.58 0.00 37.29 4.26
109 112 1.087202 TTCACGCGATGGCACCATAC 61.087 55.000 15.93 0.00 39.92 2.39
241 270 0.539986 ATACAACTAGCCCACCACCG 59.460 55.000 0.00 0.00 0.00 4.94
401 4097 4.709690 TTTTTGCGGGGGTTCCTT 57.290 50.000 0.00 0.00 0.00 3.36
481 4177 8.720562 GGTTAAATGAATTTTCTTTGTGGATGG 58.279 33.333 0.00 0.00 0.00 3.51
482 4178 9.271828 GTTAAATGAATTTTCTTTGTGGATGGT 57.728 29.630 0.00 0.00 0.00 3.55
634 4358 7.038445 CCTTGAGTTGGACCATATCATATCTCT 60.038 40.741 9.34 0.00 0.00 3.10
856 4586 7.896811 TCAATCCAATCGCATATCTTACTACT 58.103 34.615 0.00 0.00 0.00 2.57
891 4621 1.084289 GCAAACCGTATCACAGGTCC 58.916 55.000 0.00 0.00 40.37 4.46
907 4639 0.389948 GTCCGTGGTCCTAGCTTGTG 60.390 60.000 0.00 0.00 0.00 3.33
931 4663 8.414003 GTGTATATAAGGATTCTGCCGATATGA 58.586 37.037 0.00 0.00 0.00 2.15
962 4700 2.353579 CTCATCAATCAATCACAGCGCA 59.646 45.455 11.47 0.00 0.00 6.09
1020 4758 8.952278 CACCCTCTATATATACTGAGACAAGAC 58.048 40.741 12.75 0.00 0.00 3.01
1117 4855 6.523201 GGTGTATACAATTGCTCTTTTGTTCG 59.477 38.462 7.25 0.00 37.29 3.95
1303 5043 2.280404 TAGGTCGTCCTGAGCCCGAT 62.280 60.000 11.77 0.00 46.44 4.18
1694 5440 5.273170 TGAAAGTGAAATGTTCTGCTTTCG 58.727 37.500 20.26 0.00 44.82 3.46
1963 5714 2.530177 TCATGACATCGTTCGAAGAGC 58.470 47.619 0.00 0.00 38.43 4.09
1978 5729 6.752335 TCGAAGAGCAACAAAAATCAAATG 57.248 33.333 0.00 0.00 0.00 2.32
2174 5996 5.529060 AGAAATGAGAAATCGATAGGGTTGC 59.471 40.000 0.00 0.00 0.00 4.17
2340 6162 3.492102 TTAGAACTTGAAGCTGGCTGT 57.508 42.857 0.00 0.00 0.00 4.40
2344 6166 0.179045 ACTTGAAGCTGGCTGTCGTT 60.179 50.000 0.00 0.00 0.00 3.85
2478 6300 3.717294 CGGGCTAGGTGCACCCTT 61.717 66.667 32.29 17.64 42.73 3.95
2504 6327 1.878953 TCGTCTTTCTTTCCTGCACC 58.121 50.000 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 31 1.196766 TGCTCTGGACATGCCTCTGT 61.197 55.000 7.54 0.00 37.63 3.41
77 80 1.508632 GCGTGAAGCTTTGAGGTACA 58.491 50.000 0.00 0.00 44.04 2.90
109 112 2.153817 CAGCATCCGTATTCGACATTCG 59.846 50.000 0.00 0.00 42.10 3.34
315 4008 0.379669 CAGATCTGCCACGCAAATCC 59.620 55.000 10.38 0.00 36.76 3.01
391 4086 0.898326 AACATTCGCAAGGAACCCCC 60.898 55.000 0.00 0.00 37.50 5.40
401 4097 7.487829 GGAAATATTTTTGAGCTAACATTCGCA 59.512 33.333 1.43 0.00 0.00 5.10
485 4181 9.731819 CTGATCAACGAGCTTAGTAATTACTAA 57.268 33.333 28.09 28.09 44.13 2.24
486 4182 8.900781 ACTGATCAACGAGCTTAGTAATTACTA 58.099 33.333 19.30 19.30 37.73 1.82
487 4183 7.773149 ACTGATCAACGAGCTTAGTAATTACT 58.227 34.615 21.35 21.35 40.24 2.24
601 4325 2.685897 TGGTCCAACTCAAGGAAAAACG 59.314 45.455 0.00 0.00 36.80 3.60
634 4358 7.451877 TGGTTAGCAACTAAAAATAACCATGGA 59.548 33.333 21.47 0.00 46.39 3.41
856 4586 5.109210 CGGTTTGCAGATCACAGAGTTATA 58.891 41.667 0.00 0.00 0.00 0.98
891 4621 2.961526 ATACACAAGCTAGGACCACG 57.038 50.000 0.00 0.00 0.00 4.94
907 4639 9.988815 ATTCATATCGGCAGAATCCTTATATAC 57.011 33.333 0.00 0.00 0.00 1.47
1117 4855 1.144057 CCATGACTAGGCACCCGAC 59.856 63.158 0.00 0.00 0.00 4.79
1303 5043 1.760029 TGGCCATCTTCGTATGTGCTA 59.240 47.619 0.00 0.00 0.00 3.49
1694 5440 2.490115 TCACATACACATTTTTCCGGCC 59.510 45.455 0.00 0.00 0.00 6.13
1963 5714 7.959689 TGGTATGGACATTTGATTTTTGTTG 57.040 32.000 0.00 0.00 0.00 3.33
1978 5729 3.827008 TCTGAGATGCTTGGTATGGAC 57.173 47.619 0.00 0.00 0.00 4.02
2229 6051 0.251386 ACTCCTCTCTCGAAGCACCA 60.251 55.000 0.00 0.00 0.00 4.17
2340 6162 1.137479 CCCGAATGTTAGGGCTAACGA 59.863 52.381 0.00 0.00 46.19 3.85
2470 6292 2.958818 AGACGATATCCTAAGGGTGCA 58.041 47.619 0.00 0.00 0.00 4.57
2478 6300 5.362717 TGCAGGAAAGAAAGACGATATCCTA 59.637 40.000 0.00 0.00 34.18 2.94


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

AutoCloner maintained by Alex Coulton.