Multiple sequence alignment - TraesCS6B01G071300

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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 TraesCS6B01G071300 chr6B 100.000 3015 0 0 1 3015 48079457 48082471 0 5568
1 TraesCS6B01G071300 chr3B 96.405 3032 86 8 1 3015 473235646 473238671 0 4974
2 TraesCS6B01G071300 chr3B 83.842 1442 182 28 1 1394 766341692 766343130 0 1325
3 TraesCS6B01G071300 chr7B 95.387 3035 116 8 1 3015 51883761 51886791 0 4807
4 TraesCS6B01G071300 chr7B 84.061 1443 178 29 1 1394 73167725 73169164 0 1343
5 TraesCS6B01G071300 chr4B 95.251 3032 123 8 1 3015 321541994 321545021 0 4782
6 TraesCS6B01G071300 chr4B 95.826 2204 85 6 815 3015 587099150 587101349 0 3554
7 TraesCS6B01G071300 chr4B 94.697 792 27 3 1 778 587098357 587099147 0 1216
8 TraesCS6B01G071300 chr7A 93.841 3036 123 21 1 3015 126148505 126151497 0 4512
9 TraesCS6B01G071300 chr6A 94.263 2423 96 12 1 2408 182420401 182418007 0 3664
10 TraesCS6B01G071300 chr6A 93.754 1665 69 10 1354 3015 137393776 137392144 0 2466
11 TraesCS6B01G071300 chr6A 93.183 1379 58 9 1 1361 137493500 137492140 0 1993
12 TraesCS6B01G071300 chr6A 91.566 747 52 10 2275 3015 182418174 182417433 0 1020
13 TraesCS6B01G071300 chr2A 93.482 2424 100 12 1 2408 778648748 778651129 0 3548
14 TraesCS6B01G071300 chr2A 91.120 732 56 8 2290 3015 778650974 778651702 0 983
15 TraesCS6B01G071300 chr5A 81.692 2305 307 57 209 2448 514149474 514147220 0 1812
16 TraesCS6B01G071300 chr6D 93.847 1154 46 8 1871 3015 16251411 16252548 0 1714
17 TraesCS6B01G071300 chr3A 95.105 858 28 3 1 844 153362641 153363498 0 1339
18 TraesCS6B01G071300 chr3A 93.944 611 29 5 2408 3015 644687580 644686975 0 917
19 TraesCS6B01G071300 chr5D 85.038 782 89 7 209 966 408314442 408313665 0 771


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 TraesCS6B01G071300 chr6B 48079457 48082471 3014 False 5568.0 5568 100.0000 1 3015 1 chr6B.!!$F1 3014
1 TraesCS6B01G071300 chr3B 473235646 473238671 3025 False 4974.0 4974 96.4050 1 3015 1 chr3B.!!$F1 3014
2 TraesCS6B01G071300 chr3B 766341692 766343130 1438 False 1325.0 1325 83.8420 1 1394 1 chr3B.!!$F2 1393
3 TraesCS6B01G071300 chr7B 51883761 51886791 3030 False 4807.0 4807 95.3870 1 3015 1 chr7B.!!$F1 3014
4 TraesCS6B01G071300 chr7B 73167725 73169164 1439 False 1343.0 1343 84.0610 1 1394 1 chr7B.!!$F2 1393
5 TraesCS6B01G071300 chr4B 321541994 321545021 3027 False 4782.0 4782 95.2510 1 3015 1 chr4B.!!$F1 3014
6 TraesCS6B01G071300 chr4B 587098357 587101349 2992 False 2385.0 3554 95.2615 1 3015 2 chr4B.!!$F2 3014
7 TraesCS6B01G071300 chr7A 126148505 126151497 2992 False 4512.0 4512 93.8410 1 3015 1 chr7A.!!$F1 3014
8 TraesCS6B01G071300 chr6A 137392144 137393776 1632 True 2466.0 2466 93.7540 1354 3015 1 chr6A.!!$R1 1661
9 TraesCS6B01G071300 chr6A 182417433 182420401 2968 True 2342.0 3664 92.9145 1 3015 2 chr6A.!!$R3 3014
10 TraesCS6B01G071300 chr6A 137492140 137493500 1360 True 1993.0 1993 93.1830 1 1361 1 chr6A.!!$R2 1360
11 TraesCS6B01G071300 chr2A 778648748 778651702 2954 False 2265.5 3548 92.3010 1 3015 2 chr2A.!!$F1 3014
12 TraesCS6B01G071300 chr5A 514147220 514149474 2254 True 1812.0 1812 81.6920 209 2448 1 chr5A.!!$R1 2239
13 TraesCS6B01G071300 chr6D 16251411 16252548 1137 False 1714.0 1714 93.8470 1871 3015 1 chr6D.!!$F1 1144
14 TraesCS6B01G071300 chr3A 153362641 153363498 857 False 1339.0 1339 95.1050 1 844 1 chr3A.!!$F1 843
15 TraesCS6B01G071300 chr3A 644686975 644687580 605 True 917.0 917 93.9440 2408 3015 1 chr3A.!!$R1 607
16 TraesCS6B01G071300 chr5D 408313665 408314442 777 True 771.0 771 85.0380 209 966 1 chr5D.!!$R1 757

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
525 562 0.965866 CCCACCTCGTAGTGCAGAGA 60.966 60.0 2.40 0.0 36.65 3.10 F
1186 1292 0.102844 GCACCTTGCTGAAAAGTGCA 59.897 50.0 15.63 0.0 40.96 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 1969 0.323629 CGTCACCCTCTTTGGCCTTA 59.676 55.000 3.32 0.0 0.00 2.69 R
2356 2530 1.270518 ACGAGTGTCAAGCAGAAGCAT 60.271 47.619 0.00 0.0 45.49 3.79 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
35 36 3.954200 TGAAGCTTCATCCATTGCTACA 58.046 40.909 25.16 0.00 35.09 2.74
56 57 8.202137 GCTACATAAGAAACCAGAACCTATACA 58.798 37.037 0.00 0.00 0.00 2.29
525 562 0.965866 CCCACCTCGTAGTGCAGAGA 60.966 60.000 2.40 0.00 36.65 3.10
845 904 6.381420 GCAGGACATGTATATAGACATAGGGT 59.619 42.308 12.47 7.10 37.99 4.34
858 917 1.141053 CATAGGGTTGCTAGGGGTCAC 59.859 57.143 0.00 0.00 0.00 3.67
1027 1133 2.035576 GTGGACACCTCAAGTACGTCTT 59.964 50.000 0.00 0.00 36.75 3.01
1052 1158 5.010282 TGGAAGAGGCAAGAATAAAAGGAC 58.990 41.667 0.00 0.00 0.00 3.85
1186 1292 0.102844 GCACCTTGCTGAAAAGTGCA 59.897 50.000 15.63 0.00 40.96 4.57
1229 1335 4.687901 TTCCACACATTGAGTCAAGAGA 57.312 40.909 11.91 0.00 0.00 3.10
1252 1358 6.551227 AGAGAGGCACTTTAGGACAAAATTTT 59.449 34.615 0.00 0.00 41.55 1.82
1397 1506 7.856145 ACTGAACTCCTTATTAATGCTGAAG 57.144 36.000 0.00 0.00 0.00 3.02
1542 1662 7.059788 TGCTCATTGCCTTTTTATATACCTGA 58.940 34.615 0.00 0.00 42.00 3.86
1573 1693 7.873719 TCTATCAGAGACTAAGTTCCTTCTG 57.126 40.000 0.00 0.00 0.00 3.02
1848 1969 5.948454 TCCAAGAGGCAGAGGAAGGAACT 62.948 52.174 0.00 0.00 35.15 3.01
1887 2008 2.879103 GGACCAAGTGATCCCTTTGA 57.121 50.000 0.00 0.00 0.00 2.69
1952 2073 3.699038 ACAATATGTGGGTACAATGGCAC 59.301 43.478 0.00 0.00 40.84 5.01
1953 2074 3.660970 ATATGTGGGTACAATGGCACA 57.339 42.857 0.00 0.00 40.84 4.57
2006 2127 1.134401 CCGCAAGAGGATCCTTAGCAA 60.134 52.381 24.61 0.00 43.02 3.91
2011 2132 5.346522 GCAAGAGGATCCTTAGCAAAAATG 58.653 41.667 17.42 6.08 33.66 2.32
2012 2133 5.105595 GCAAGAGGATCCTTAGCAAAAATGT 60.106 40.000 17.42 0.00 33.66 2.71
2088 2209 1.904287 TGAGGCTGCAACCGTATTTT 58.096 45.000 0.50 0.00 33.69 1.82
2138 2259 1.131883 CCTGCGCTTCCAGAAAATCTG 59.868 52.381 9.73 0.32 43.91 2.90
2213 2348 7.041098 TCCACAATCTCTTTTGCTAAACTCTTC 60.041 37.037 0.00 0.00 0.00 2.87
2250 2387 3.647636 TCTACCTCTGATTGGCTAGCTT 58.352 45.455 15.72 0.00 0.00 3.74
2356 2530 6.671190 CATTTGCAATGTCTAGTTGACTTCA 58.329 36.000 0.00 0.00 45.54 3.02
2400 2609 8.957466 CGTAGTATATGTTCCATCCAATCTCTA 58.043 37.037 0.00 0.00 0.00 2.43
2429 2638 6.698380 ACATTCGTAGTATATGTTCCATCCC 58.302 40.000 0.00 0.00 0.00 3.85
2559 2804 6.530120 TGTCTTGCTAGGTCAAGTGATTTTA 58.470 36.000 9.18 0.00 42.90 1.52
2569 2814 8.324163 AGGTCAAGTGATTTTATAGTGAACAC 57.676 34.615 0.00 0.00 0.00 3.32
2665 2911 6.818644 TGAATTAGTGGTTGTCTCTTATCTGC 59.181 38.462 0.00 0.00 0.00 4.26
2777 3025 3.519510 AGAGGAATGGTCGATGGAAAAGA 59.480 43.478 0.00 0.00 0.00 2.52
2830 3078 8.825667 TTGGACTTGCCTTACAAAATAATTTC 57.174 30.769 0.00 0.00 37.96 2.17
2834 3082 6.209788 ACTTGCCTTACAAAATAATTTCGGGA 59.790 34.615 0.00 0.00 37.96 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.416271 AGCAATGGATGAAGCTTCAAAAT 57.584 34.783 31.55 21.17 41.13 1.82
35 36 7.414222 TCGTGTATAGGTTCTGGTTTCTTAT 57.586 36.000 0.00 0.00 0.00 1.73
56 57 1.188219 ACCATCTGTGCAGTCCTCGT 61.188 55.000 0.00 0.00 0.00 4.18
222 233 4.468510 TCTTCCTTTCATAGTAGCCGGAAA 59.531 41.667 5.05 0.00 0.00 3.13
525 562 2.095213 CGTGCCGCATGTTGTAATACTT 59.905 45.455 4.27 0.00 0.00 2.24
845 904 0.178903 ACCTCAGTGACCCCTAGCAA 60.179 55.000 0.00 0.00 0.00 3.91
1027 1133 4.766891 CCTTTTATTCTTGCCTCTTCCACA 59.233 41.667 0.00 0.00 0.00 4.17
1052 1158 0.747255 ATCCTCATCCGAAGTCCACG 59.253 55.000 0.00 0.00 0.00 4.94
1186 1292 2.055299 CAGAGGTACCACAACCCGT 58.945 57.895 15.94 0.00 40.71 5.28
1199 1305 2.821378 TCAATGTGTGGAATTGCAGAGG 59.179 45.455 0.00 0.00 35.43 3.69
1229 1335 6.515832 CAAAATTTTGTCCTAAAGTGCCTCT 58.484 36.000 20.57 0.00 33.59 3.69
1252 1358 4.927425 GGATAACGTTACTTCAAGAGCACA 59.073 41.667 10.81 0.00 0.00 4.57
1542 1662 7.930865 GGAACTTAGTCTCTGATAGAAATGCAT 59.069 37.037 0.00 0.00 35.47 3.96
1848 1969 0.323629 CGTCACCCTCTTTGGCCTTA 59.676 55.000 3.32 0.00 0.00 2.69
1887 2008 6.183360 GCTATTGACATCTTGAAGCATCACTT 60.183 38.462 0.00 0.00 42.98 3.16
1987 2108 2.315925 TTGCTAAGGATCCTCTTGCG 57.684 50.000 16.52 3.14 0.00 4.85
2006 2127 9.959721 TCACTAATAGCCTTCTCTTTACATTTT 57.040 29.630 0.00 0.00 0.00 1.82
2011 2132 8.831550 CCAATTCACTAATAGCCTTCTCTTTAC 58.168 37.037 0.00 0.00 0.00 2.01
2012 2133 7.499232 GCCAATTCACTAATAGCCTTCTCTTTA 59.501 37.037 0.00 0.00 0.00 1.85
2088 2209 5.423290 TGTTCATCTGATCTGGAGCTTTAGA 59.577 40.000 3.69 3.69 0.00 2.10
2138 2259 5.952347 TTTTTAGGACATACTCCCTCCTC 57.048 43.478 0.00 0.00 40.53 3.71
2213 2348 6.700960 CAGAGGTAGATGTTATCAAAGCTGAG 59.299 42.308 0.00 0.00 34.23 3.35
2356 2530 1.270518 ACGAGTGTCAAGCAGAAGCAT 60.271 47.619 0.00 0.00 45.49 3.79
2400 2609 7.778083 TGGAACATATACTACGAATGTCAAGT 58.222 34.615 0.00 0.00 32.80 3.16
2429 2638 7.332926 ACATGTTAAGCTTGTCAAGTAGAGATG 59.667 37.037 9.86 12.71 30.78 2.90
2726 2974 3.506067 CCACACCACCCATCTTTTCTAAC 59.494 47.826 0.00 0.00 0.00 2.34
2777 3025 6.815142 GCCAATTTCAGAATCTTGCAAAGTAT 59.185 34.615 0.00 0.00 46.34 2.12
2830 3078 9.125906 CGAGATAAACTACATAATTAGTTCCCG 57.874 37.037 0.00 0.00 40.69 5.14
2970 3226 6.074676 GCACAGATTCAAACTCATCAAACAAC 60.075 38.462 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.