Multiple sequence alignment - TraesCS6B01G384100

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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 TraesCS6B01G384100 chr6B 100.000 2360 0 0 1 2360 658639348 658636989 0.000000e+00 4359
1 TraesCS6B01G384100 chr6B 90.806 881 76 3 550 1430 450591600 450592475 0.000000e+00 1173
2 TraesCS6B01G384100 chr6B 95.446 549 21 4 1 547 207988283 207987737 0.000000e+00 872
3 TraesCS6B01G384100 chr6B 94.614 557 25 4 1 555 504183128 504182575 0.000000e+00 857
4 TraesCS6B01G384100 chr5B 98.172 930 16 1 1431 2360 515110359 515109431 0.000000e+00 1622
5 TraesCS6B01G384100 chr5B 97.849 930 20 0 1431 2360 686045788 686044859 0.000000e+00 1607
6 TraesCS6B01G384100 chr5B 97.645 934 22 0 1427 2360 546794980 546794047 0.000000e+00 1604
7 TraesCS6B01G384100 chr5B 94.900 549 25 3 1 547 207903866 207904413 0.000000e+00 856
8 TraesCS6B01G384100 chr5B 94.414 555 30 1 876 1430 592063515 592064068 0.000000e+00 852
9 TraesCS6B01G384100 chr5B 82.071 792 129 8 567 1353 17684215 17683432 0.000000e+00 664
10 TraesCS6B01G384100 chr1B 98.172 930 16 1 1431 2360 336626842 336627770 0.000000e+00 1622
11 TraesCS6B01G384100 chr1B 97.959 931 19 0 1430 2360 100553411 100552481 0.000000e+00 1615
12 TraesCS6B01G384100 chr1B 97.650 936 21 1 1425 2360 684842913 684843847 0.000000e+00 1605
13 TraesCS6B01G384100 chr1B 94.900 549 24 3 1 547 568480079 568480625 0.000000e+00 856
14 TraesCS6B01G384100 chr1B 77.721 781 163 7 569 1346 593052040 593052812 3.550000e-128 468
15 TraesCS6B01G384100 chr7B 97.957 930 19 0 1431 2360 254052823 254053752 0.000000e+00 1613
16 TraesCS6B01G384100 chr7B 97.744 931 20 1 1430 2360 663291088 663290159 0.000000e+00 1602
17 TraesCS6B01G384100 chr7B 78.861 790 157 9 554 1338 87119712 87120496 2.080000e-145 525
18 TraesCS6B01G384100 chr4B 97.852 931 20 0 1430 2360 651481007 651481937 0.000000e+00 1609
19 TraesCS6B01G384100 chr4B 91.600 881 69 3 550 1430 241357879 241358754 0.000000e+00 1212
20 TraesCS6B01G384100 chr4B 90.291 824 77 3 550 1372 623489019 623489840 0.000000e+00 1075
21 TraesCS6B01G384100 chr4B 86.824 888 100 10 550 1426 418205655 418206536 0.000000e+00 976
22 TraesCS6B01G384100 chr4B 95.082 549 23 3 1 547 582882491 582883037 0.000000e+00 861
23 TraesCS6B01G384100 chr3B 95.255 548 24 2 1 547 72767641 72768187 0.000000e+00 867
24 TraesCS6B01G384100 chr3B 95.073 548 24 2 1 547 462219088 462218543 0.000000e+00 859
25 TraesCS6B01G384100 chr2B 94.756 553 25 4 1 550 216887282 216887833 0.000000e+00 857
26 TraesCS6B01G384100 chr2D 94.900 549 24 4 1 547 176013936 176014482 0.000000e+00 856
27 TraesCS6B01G384100 chr1A 78.907 787 160 6 566 1349 375465587 375466370 1.610000e-146 529
28 TraesCS6B01G384100 chr1A 72.183 568 140 16 758 1317 570372749 570373306 8.730000e-35 158
29 TraesCS6B01G384100 chr5A 81.132 106 8 11 506 601 498476709 498476606 9.050000e-10 75


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 TraesCS6B01G384100 chr6B 658636989 658639348 2359 True 4359 4359 100.000 1 2360 1 chr6B.!!$R3 2359
1 TraesCS6B01G384100 chr6B 450591600 450592475 875 False 1173 1173 90.806 550 1430 1 chr6B.!!$F1 880
2 TraesCS6B01G384100 chr6B 207987737 207988283 546 True 872 872 95.446 1 547 1 chr6B.!!$R1 546
3 TraesCS6B01G384100 chr6B 504182575 504183128 553 True 857 857 94.614 1 555 1 chr6B.!!$R2 554
4 TraesCS6B01G384100 chr5B 515109431 515110359 928 True 1622 1622 98.172 1431 2360 1 chr5B.!!$R2 929
5 TraesCS6B01G384100 chr5B 686044859 686045788 929 True 1607 1607 97.849 1431 2360 1 chr5B.!!$R4 929
6 TraesCS6B01G384100 chr5B 546794047 546794980 933 True 1604 1604 97.645 1427 2360 1 chr5B.!!$R3 933
7 TraesCS6B01G384100 chr5B 207903866 207904413 547 False 856 856 94.900 1 547 1 chr5B.!!$F1 546
8 TraesCS6B01G384100 chr5B 592063515 592064068 553 False 852 852 94.414 876 1430 1 chr5B.!!$F2 554
9 TraesCS6B01G384100 chr5B 17683432 17684215 783 True 664 664 82.071 567 1353 1 chr5B.!!$R1 786
10 TraesCS6B01G384100 chr1B 336626842 336627770 928 False 1622 1622 98.172 1431 2360 1 chr1B.!!$F1 929
11 TraesCS6B01G384100 chr1B 100552481 100553411 930 True 1615 1615 97.959 1430 2360 1 chr1B.!!$R1 930
12 TraesCS6B01G384100 chr1B 684842913 684843847 934 False 1605 1605 97.650 1425 2360 1 chr1B.!!$F4 935
13 TraesCS6B01G384100 chr1B 568480079 568480625 546 False 856 856 94.900 1 547 1 chr1B.!!$F2 546
14 TraesCS6B01G384100 chr1B 593052040 593052812 772 False 468 468 77.721 569 1346 1 chr1B.!!$F3 777
15 TraesCS6B01G384100 chr7B 254052823 254053752 929 False 1613 1613 97.957 1431 2360 1 chr7B.!!$F2 929
16 TraesCS6B01G384100 chr7B 663290159 663291088 929 True 1602 1602 97.744 1430 2360 1 chr7B.!!$R1 930
17 TraesCS6B01G384100 chr7B 87119712 87120496 784 False 525 525 78.861 554 1338 1 chr7B.!!$F1 784
18 TraesCS6B01G384100 chr4B 651481007 651481937 930 False 1609 1609 97.852 1430 2360 1 chr4B.!!$F5 930
19 TraesCS6B01G384100 chr4B 241357879 241358754 875 False 1212 1212 91.600 550 1430 1 chr4B.!!$F1 880
20 TraesCS6B01G384100 chr4B 623489019 623489840 821 False 1075 1075 90.291 550 1372 1 chr4B.!!$F4 822
21 TraesCS6B01G384100 chr4B 418205655 418206536 881 False 976 976 86.824 550 1426 1 chr4B.!!$F2 876
22 TraesCS6B01G384100 chr4B 582882491 582883037 546 False 861 861 95.082 1 547 1 chr4B.!!$F3 546
23 TraesCS6B01G384100 chr3B 72767641 72768187 546 False 867 867 95.255 1 547 1 chr3B.!!$F1 546
24 TraesCS6B01G384100 chr3B 462218543 462219088 545 True 859 859 95.073 1 547 1 chr3B.!!$R1 546
25 TraesCS6B01G384100 chr2B 216887282 216887833 551 False 857 857 94.756 1 550 1 chr2B.!!$F1 549
26 TraesCS6B01G384100 chr2D 176013936 176014482 546 False 856 856 94.900 1 547 1 chr2D.!!$F1 546
27 TraesCS6B01G384100 chr1A 375465587 375466370 783 False 529 529 78.907 566 1349 1 chr1A.!!$F1 783

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
41 42 0.321122 CTTCATCGGAGGGGCTATGC 60.321 60.0 0.0 0.0 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 1600 0.179129 ATTAGTACCGGTTCGTGGCG 60.179 55.0 15.04 0.0 0.0 5.69 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
41 42 0.321122 CTTCATCGGAGGGGCTATGC 60.321 60.000 0.00 0.0 0.00 3.14
129 130 6.927664 AGATGGGATCTCATGGATACAGAAGT 60.928 42.308 14.28 0.0 44.06 3.01
239 242 3.470888 CAGGGGCCCACGAGGTAG 61.471 72.222 27.72 0.0 38.26 3.18
305 311 2.380941 GAGTAGGGTCCAAGTCTCCTC 58.619 57.143 0.00 0.0 0.00 3.71
339 345 4.977741 TGAGAAAATCACGTTACCGAAC 57.022 40.909 0.00 0.0 37.88 3.95
612 619 7.313951 AGAGATAATTGTTGCTAAGTTCAGC 57.686 36.000 0.00 0.0 42.15 4.26
617 624 3.319137 TGTTGCTAAGTTCAGCGAGAT 57.681 42.857 0.00 0.0 44.88 2.75
679 686 3.871463 GCTTCTTGCTCAATGGAGAAGGA 60.871 47.826 0.00 0.0 44.26 3.36
789 796 4.597004 AGTCGGTCTATGAGTACTTGGAA 58.403 43.478 0.00 0.0 0.00 3.53
934 943 4.256180 GGCTGGGTAGGCCGATGG 62.256 72.222 0.00 0.0 43.29 3.51
1012 1021 4.093743 TGCTAGAGTTATGTGGAGGACAA 58.906 43.478 0.00 0.0 38.36 3.18
1053 1062 6.455647 CACTGATCGTTGCCCTAATAATCTA 58.544 40.000 0.00 0.0 0.00 1.98
1206 1215 8.267620 TGAGATCTCCTTTTGATGTGGTATAT 57.732 34.615 20.03 0.0 0.00 0.86
1372 1382 1.523258 CGATGAAGCTGGGGCAGAG 60.523 63.158 0.00 0.0 41.70 3.35
1373 1383 1.823041 GATGAAGCTGGGGCAGAGC 60.823 63.158 0.00 0.0 41.70 4.09
1386 1404 1.209019 GGCAGAGCTTCTCCATCTTCA 59.791 52.381 0.00 0.0 0.00 3.02
1578 1600 1.235724 AACCTTTAGCACTGGTTCGC 58.764 50.000 0.00 0.0 39.61 4.70
1760 1782 3.436243 TCTCCTCTGTTCTTCCCTTCTC 58.564 50.000 0.00 0.0 0.00 2.87
1787 1810 4.218265 TCGAGTTCATCACAAAATTTGCG 58.782 39.130 5.52 0.0 0.00 4.85
2245 2268 3.279434 GCCCTCGTCCTTGTTATGATTT 58.721 45.455 0.00 0.0 0.00 2.17
2297 2320 7.887996 ATTTGTTGCATTTCGTGTTTATGAT 57.112 28.000 0.00 0.0 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.237143 TGGAGGGCTTCTACATCAACAG 59.763 50.000 0.00 0.00 29.60 3.16
129 130 1.173043 CCTAATTCCACCGCTGCAAA 58.827 50.000 0.00 0.00 0.00 3.68
268 274 1.215423 ACTCCAAGAAGTGCCAAAGGT 59.785 47.619 0.00 0.00 0.00 3.50
333 339 3.294079 ACGGAATGAAACGTTCGGT 57.706 47.368 0.00 9.82 40.99 4.69
339 345 2.095919 GGACTCCAAACGGAATGAAACG 60.096 50.000 0.00 0.00 30.08 3.60
357 363 7.461107 TCGAAGAAACGAAATATCAAATGGAC 58.539 34.615 0.00 0.00 39.34 4.02
503 510 7.436118 TCTATAATTTTTGATTGCTCCATGCC 58.564 34.615 0.00 0.00 42.00 4.40
552 559 9.740239 CACACATTGAATAGAATAGGAAATTGG 57.260 33.333 0.00 0.00 0.00 3.16
612 619 4.248859 AGAAGTTCACATCCACAATCTCG 58.751 43.478 5.50 0.00 0.00 4.04
617 624 5.034852 TCTGAAGAAGTTCACATCCACAA 57.965 39.130 5.50 0.00 37.79 3.33
679 686 3.736224 CCTCACCCAGGCCTGCAT 61.736 66.667 28.39 14.38 34.56 3.96
698 705 2.549349 GGGTCGTTAGAGAGTGGCAAAA 60.549 50.000 0.00 0.00 0.00 2.44
789 796 3.073062 AGTTGCACCTAGTGATGTTCCTT 59.927 43.478 0.00 0.00 35.23 3.36
1012 1021 1.836802 AGTGCCAAAAACACACCCAAT 59.163 42.857 0.00 0.00 40.59 3.16
1372 1382 2.873472 CTGAGCATGAAGATGGAGAAGC 59.127 50.000 0.00 0.00 0.00 3.86
1373 1383 2.873472 GCTGAGCATGAAGATGGAGAAG 59.127 50.000 0.00 0.00 0.00 2.85
1403 1421 3.330720 AGAGAAAGGCCACCGGGG 61.331 66.667 6.32 0.00 40.85 5.73
1578 1600 0.179129 ATTAGTACCGGTTCGTGGCG 60.179 55.000 15.04 0.00 0.00 5.69
1760 1782 3.319137 TTTGTGATGAACTCGAGAGGG 57.681 47.619 21.68 0.00 37.84 4.30
1787 1810 4.083696 CCTGCAAATCTTGACAAATTTGGC 60.084 41.667 21.74 19.79 41.19 4.52
2171 2194 7.201342 GCACTATGTATAACAAACAACGTACGA 60.201 37.037 24.41 0.00 0.00 3.43
2297 2320 7.658525 ATGTCAACTTGATGGGCATAATTTA 57.341 32.000 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.