Multiple sequence alignment - TraesCS6D01G220600

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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 TraesCS6D01G220600 chr6D 100.000 3510 0 0 1 3510 310889479 310885970 0.000000e+00 6482
1 TraesCS6D01G220600 chr6A 96.033 3504 98 15 30 3510 447180284 447176799 0.000000e+00 5662
2 TraesCS6D01G220600 chr6B 91.000 2511 162 27 1038 3510 515577553 515580037 0.000000e+00 3326
3 TraesCS6D01G220600 chr6B 90.930 430 22 8 620 1034 515577092 515577519 2.370000e-156 562
4 TraesCS6D01G220600 chr6B 82.555 321 25 17 2 301 515576154 515576464 1.620000e-63 254
5 TraesCS6D01G220600 chr4A 85.246 244 34 2 1410 1652 739587219 739587461 2.090000e-62 250
6 TraesCS6D01G220600 chr4A 82.422 256 34 9 1395 1641 691247036 691247289 2.740000e-51 213
7 TraesCS6D01G220600 chr7A 84.836 244 35 2 1410 1652 3859880 3859638 9.730000e-61 244
8 TraesCS6D01G220600 chr7D 84.426 244 36 2 1410 1652 4026495 4026253 4.530000e-59 239
9 TraesCS6D01G220600 chr2B 83.482 224 35 2 1416 1638 470472233 470472011 1.280000e-49 207
10 TraesCS6D01G220600 chr2A 83.036 224 36 2 1416 1638 535241934 535241712 5.940000e-48 202
11 TraesCS6D01G220600 chr4D 81.743 241 40 4 1411 1649 481912293 481912055 7.690000e-47 198
12 TraesCS6D01G220600 chr2D 82.143 224 38 2 1416 1638 398087123 398086901 1.290000e-44 191


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 TraesCS6D01G220600 chr6D 310885970 310889479 3509 True 6482.000000 6482 100.000000 1 3510 1 chr6D.!!$R1 3509
1 TraesCS6D01G220600 chr6A 447176799 447180284 3485 True 5662.000000 5662 96.033000 30 3510 1 chr6A.!!$R1 3480
2 TraesCS6D01G220600 chr6B 515576154 515580037 3883 False 1380.666667 3326 88.161667 2 3510 3 chr6B.!!$F1 3508

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
453 775 1.290134 CCTGGGAAGGAGGCTTAAGT 58.710 55.0 4.02 0.0 0.00 2.24 F
1310 1716 0.035317 TCGGCACATTCTTGTCAGCT 59.965 50.0 0.00 0.0 32.34 4.24 F
1421 1830 0.627451 TTGGCATGGAGGAGCAGAAT 59.373 50.0 0.00 0.0 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 1974 0.896226 GGCCCTTGTAGAAGACGAGT 59.104 55.000 0.19 0.0 37.83 4.18 R
2322 2756 4.147449 CTCCGCCGGCAGATGTCA 62.147 66.667 28.98 0.0 0.00 3.58 R
3024 3476 5.391416 GCCTTTTCATCTTCTTTTCTCCGAG 60.391 44.000 0.00 0.0 0.00 4.63 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
147 158 1.374252 GTGGACCTGTGGTAGTGCG 60.374 63.158 0.00 0.00 35.25 5.34
148 159 1.532078 TGGACCTGTGGTAGTGCGA 60.532 57.895 0.00 0.00 35.25 5.10
157 172 2.030096 TGTGGTAGTGCGACATACGAAA 60.030 45.455 0.00 0.00 45.77 3.46
174 190 5.061920 ACGAAAGTCTTCACTCCATAGAC 57.938 43.478 0.00 0.00 44.19 2.59
221 237 2.702478 CCTCCACATGGATTCAGCTAGA 59.298 50.000 0.00 0.00 44.46 2.43
222 238 3.244146 CCTCCACATGGATTCAGCTAGAG 60.244 52.174 0.00 0.00 44.46 2.43
223 239 2.103771 TCCACATGGATTCAGCTAGAGC 59.896 50.000 0.00 0.00 39.78 4.09
224 240 2.492012 CACATGGATTCAGCTAGAGCC 58.508 52.381 0.00 0.00 43.38 4.70
225 241 2.104451 CACATGGATTCAGCTAGAGCCT 59.896 50.000 0.00 0.00 43.38 4.58
283 304 9.391006 TGTATATCCACCTGTACAATTTTTCTC 57.609 33.333 0.00 0.00 0.00 2.87
432 754 9.257234 GCGTTAGCTTCATAAAAGGAAGTCCTC 62.257 44.444 0.00 0.00 42.67 3.71
453 775 1.290134 CCTGGGAAGGAGGCTTAAGT 58.710 55.000 4.02 0.00 0.00 2.24
473 795 9.531942 CTTAAGTGCATGCATAAATTTGGATAA 57.468 29.630 25.64 9.67 0.00 1.75
533 856 4.273318 AGCCTTTTATCTGTGTTCCCATC 58.727 43.478 0.00 0.00 0.00 3.51
572 895 5.949735 ACTACCCAAATATTGTTTGAAGCG 58.050 37.500 7.38 0.00 0.00 4.68
819 1182 6.016777 ACAAAAGCTTCTCATCCAGTTGTAAG 60.017 38.462 0.00 0.00 0.00 2.34
820 1183 4.899352 AGCTTCTCATCCAGTTGTAAGT 57.101 40.909 0.00 0.00 0.00 2.24
1222 1628 3.523157 TGGCATCCAAGAAGATTGACCTA 59.477 43.478 0.00 0.00 0.00 3.08
1301 1707 9.006215 GTAACAAACTAATTAATCGGCACATTC 57.994 33.333 0.00 0.00 0.00 2.67
1310 1716 0.035317 TCGGCACATTCTTGTCAGCT 59.965 50.000 0.00 0.00 32.34 4.24
1333 1740 3.010624 TGCAAACATGGATCACAAACG 57.989 42.857 0.00 0.00 0.00 3.60
1355 1762 3.711086 CTGAACTCATTGATCGATCGGT 58.289 45.455 20.03 8.34 0.00 4.69
1421 1830 0.627451 TTGGCATGGAGGAGCAGAAT 59.373 50.000 0.00 0.00 0.00 2.40
1511 1920 2.046217 GGGTTCTGGAAGGCGACC 60.046 66.667 0.00 0.00 33.16 4.79
1547 1956 2.018355 TCTACACCAACCACTGCCTA 57.982 50.000 0.00 0.00 0.00 3.93
1565 1974 3.024547 CCTAGTCGGAATGAGGAAGACA 58.975 50.000 0.00 0.00 34.56 3.41
1806 2222 1.405256 GCGGAGGATGGCAGATATGAG 60.405 57.143 0.00 0.00 0.00 2.90
1810 2226 2.566279 GAGGATGGCAGATATGAGCTCA 59.434 50.000 20.79 20.79 0.00 4.26
1834 2250 3.462169 TGGTTCGACGACCATGGT 58.538 55.556 19.89 19.89 44.53 3.55
1898 2314 2.033602 GGTACCAGCACCACCACC 59.966 66.667 7.15 0.00 38.55 4.61
1899 2315 2.033602 GTACCAGCACCACCACCC 59.966 66.667 0.00 0.00 0.00 4.61
1971 2405 1.360551 CGGAGCTGGAGTACCATCG 59.639 63.158 0.00 0.00 45.87 3.84
2322 2756 1.900545 GAGGCCCTGGACTACGCTTT 61.901 60.000 0.00 0.00 30.74 3.51
2448 2891 4.086706 AGTGTACAAATATAGCTGGCCC 57.913 45.455 0.00 0.00 0.00 5.80
2489 2933 8.722480 ATCATGGTATATATATGCACACACAC 57.278 34.615 12.20 0.00 0.00 3.82
2490 2934 7.675062 TCATGGTATATATATGCACACACACA 58.325 34.615 12.20 0.85 0.00 3.72
2849 3298 5.446143 AGGATACACTAGAGAATGAAGCG 57.554 43.478 0.00 0.00 41.41 4.68
2852 3301 5.861251 GGATACACTAGAGAATGAAGCGATG 59.139 44.000 0.00 0.00 0.00 3.84
3024 3476 1.680735 TCCCTTGCATTGTCACAACAC 59.319 47.619 0.00 0.00 34.35 3.32
3372 3825 8.889717 GCACAAAGCCTACAGTTAAGAATTATA 58.110 33.333 0.00 0.00 37.23 0.98
3431 3884 7.262772 TCTAGAAAGAGAACTCACGAAAACAA 58.737 34.615 4.64 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 9.717942 GTAGAGGAGATAATCAATAATGCAAGT 57.282 33.333 0.00 0.00 0.00 3.16
106 107 9.554724 CCACAATAACAAACACTAATGATACAC 57.445 33.333 0.00 0.00 0.00 2.90
116 117 4.338118 CACAGGTCCACAATAACAAACACT 59.662 41.667 0.00 0.00 0.00 3.55
147 158 4.806330 TGGAGTGAAGACTTTCGTATGTC 58.194 43.478 0.51 0.51 36.04 3.06
148 159 4.866508 TGGAGTGAAGACTTTCGTATGT 57.133 40.909 0.00 0.00 36.04 2.29
157 172 3.779444 TGTGGTCTATGGAGTGAAGACT 58.221 45.455 0.00 0.00 39.65 3.24
221 237 3.118629 TCGAAATGAGTGCATTCTAGGCT 60.119 43.478 10.82 0.00 43.71 4.58
222 238 3.198068 TCGAAATGAGTGCATTCTAGGC 58.802 45.455 10.82 0.00 43.71 3.93
223 239 4.034510 GGTTCGAAATGAGTGCATTCTAGG 59.965 45.833 10.82 0.00 43.71 3.02
224 240 4.872691 AGGTTCGAAATGAGTGCATTCTAG 59.127 41.667 10.82 0.00 43.71 2.43
225 241 4.631377 CAGGTTCGAAATGAGTGCATTCTA 59.369 41.667 10.82 0.00 43.71 2.10
303 324 2.041081 TGACCCCAAACCGAATTCATCT 59.959 45.455 6.22 0.00 0.00 2.90
333 354 7.201444 CCTTCATAGAACAAGAACGACATGTAC 60.201 40.741 0.00 0.00 30.00 2.90
401 713 4.437390 CCTTTTATGAAGCTAACGCAGGTG 60.437 45.833 0.00 0.00 39.10 4.00
432 754 0.991920 TTAAGCCTCCTTCCCAGGTG 59.008 55.000 0.00 0.00 41.69 4.00
433 755 1.290134 CTTAAGCCTCCTTCCCAGGT 58.710 55.000 0.00 0.00 41.69 4.00
434 756 1.065126 CACTTAAGCCTCCTTCCCAGG 60.065 57.143 1.29 0.00 42.50 4.45
435 757 1.680249 GCACTTAAGCCTCCTTCCCAG 60.680 57.143 1.29 0.00 32.47 4.45
436 758 0.328258 GCACTTAAGCCTCCTTCCCA 59.672 55.000 1.29 0.00 32.47 4.37
473 795 7.397192 ACAGTATCCATTTTGGCACTAGAAATT 59.603 33.333 0.00 0.00 37.47 1.82
478 800 9.155975 GATATACAGTATCCATTTTGGCACTAG 57.844 37.037 0.00 0.00 37.47 2.57
479 801 8.880244 AGATATACAGTATCCATTTTGGCACTA 58.120 33.333 0.00 0.00 37.47 2.74
533 856 8.746052 TTTGGGTAGTATGACATGGAATTAAG 57.254 34.615 0.00 0.00 0.00 1.85
819 1182 4.511826 GGGCACACTAGCTGTATATTTCAC 59.488 45.833 0.00 0.00 34.17 3.18
820 1183 4.163268 TGGGCACACTAGCTGTATATTTCA 59.837 41.667 0.00 0.00 34.17 2.69
922 1285 4.511826 GGTGTTTCAGTTGTAGTTCCTCAG 59.488 45.833 0.00 0.00 0.00 3.35
1177 1583 6.480320 CCACCTTCTTCCTCAAGTAATAATCG 59.520 42.308 0.00 0.00 0.00 3.34
1280 1686 7.826690 ACAAGAATGTGCCGATTAATTAGTTT 58.173 30.769 0.00 0.00 38.69 2.66
1301 1707 3.570926 ATGTTTGCATGAGCTGACAAG 57.429 42.857 0.00 0.00 42.74 3.16
1323 1729 4.083855 TCAATGAGTTCAGCGTTTGTGATC 60.084 41.667 0.00 0.00 0.00 2.92
1333 1740 2.474359 CCGATCGATCAATGAGTTCAGC 59.526 50.000 24.40 0.00 0.00 4.26
1355 1762 3.916359 TTACCATTAATCAGGGCACGA 57.084 42.857 0.00 0.00 0.00 4.35
1363 1770 8.072321 TGCTTAGCCAAAATTACCATTAATCA 57.928 30.769 0.29 0.00 0.00 2.57
1421 1830 2.037251 GTGGCTGAAGAAGTACCAGTCA 59.963 50.000 0.00 0.00 39.84 3.41
1547 1956 2.494073 GAGTGTCTTCCTCATTCCGACT 59.506 50.000 0.00 0.00 0.00 4.18
1565 1974 0.896226 GGCCCTTGTAGAAGACGAGT 59.104 55.000 0.19 0.00 37.83 4.18
1589 1998 1.374252 CGACTTCTGACCGTTGGGG 60.374 63.158 0.00 0.00 43.62 4.96
1834 2250 3.965258 ATGAACCCACCGCCAGCA 61.965 61.111 0.00 0.00 0.00 4.41
1870 2286 2.606519 TGGTACCCGAGCTGCCTT 60.607 61.111 10.07 0.00 0.00 4.35
1891 2307 1.228552 CAAGTTCTGGGGGTGGTGG 60.229 63.158 0.00 0.00 0.00 4.61
1892 2308 1.228552 CCAAGTTCTGGGGGTGGTG 60.229 63.158 0.00 0.00 42.17 4.17
1893 2309 3.146828 GCCAAGTTCTGGGGGTGGT 62.147 63.158 0.00 0.00 46.54 4.16
1894 2310 2.283173 GCCAAGTTCTGGGGGTGG 60.283 66.667 0.00 0.00 46.54 4.61
1899 2315 3.599285 TACGGCGCCAAGTTCTGGG 62.599 63.158 28.98 9.11 46.54 4.45
2322 2756 4.147449 CTCCGCCGGCAGATGTCA 62.147 66.667 28.98 0.00 0.00 3.58
2954 3403 7.231925 GGGAAAAAGGTAAACTGAGGAATGTAA 59.768 37.037 0.00 0.00 0.00 2.41
3024 3476 5.391416 GCCTTTTCATCTTCTTTTCTCCGAG 60.391 44.000 0.00 0.00 0.00 4.63
3372 3825 6.648310 CACACATATAGAAGATGCCGATTCTT 59.352 38.462 0.46 0.00 37.05 2.52
3431 3884 3.899980 TGATCATCAGGGTCGATCTTCAT 59.100 43.478 0.00 0.00 37.14 2.57


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

AutoCloner maintained by Alex Coulton.