Multiple sequence alignment - TraesCS1A01G244000

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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 TraesCS1A01G244000 chr1A 100.000 2222 0 0 1 2222 432523268 432525489 0.000000e+00 4104
1 TraesCS1A01G244000 chr1A 93.778 675 19 2 1 675 20992381 20991730 0.000000e+00 992
2 TraesCS1A01G244000 chr5A 98.441 1539 16 3 1 1539 66823333 66824863 0.000000e+00 2702
3 TraesCS1A01G244000 chr5A 94.834 871 44 1 673 1543 601069574 601070443 0.000000e+00 1358
4 TraesCS1A01G244000 chr5A 94.919 866 44 0 673 1538 23904876 23904011 0.000000e+00 1356
5 TraesCS1A01G244000 chr6A 95.917 1543 39 3 1 1543 472969359 472970877 0.000000e+00 2479
6 TraesCS1A01G244000 chr6A 95.669 1547 42 4 1 1547 595511649 595510128 0.000000e+00 2462
7 TraesCS1A01G244000 chr7A 97.278 1102 23 2 1 1102 722569875 722570969 0.000000e+00 1862
8 TraesCS1A01G244000 chr7A 95.304 873 38 3 673 1543 677975067 677975938 0.000000e+00 1382
9 TraesCS1A01G244000 chr7A 93.185 675 23 7 1 675 609346779 609347430 0.000000e+00 970
10 TraesCS1A01G244000 chr7A 92.444 675 28 2 1 675 668556470 668555819 0.000000e+00 942
11 TraesCS1A01G244000 chr5B 95.178 871 41 1 673 1542 492816263 492815393 0.000000e+00 1375
12 TraesCS1A01G244000 chr4B 95.271 867 41 0 673 1539 604143656 604144522 0.000000e+00 1375
13 TraesCS1A01G244000 chr4B 89.489 352 14 2 1 352 564153935 564154263 7.330000e-115 424
14 TraesCS1A01G244000 chr3A 95.046 868 41 2 673 1538 11598359 11597492 0.000000e+00 1363
15 TraesCS1A01G244000 chr3A 95.046 868 41 2 673 1538 11605247 11604380 0.000000e+00 1363
16 TraesCS1A01G244000 chr3A 93.037 675 24 2 1 675 11599205 11598554 0.000000e+00 965
17 TraesCS1A01G244000 chr3A 92.889 675 25 2 1 675 11606093 11605442 0.000000e+00 959
18 TraesCS1A01G244000 chr2B 93.195 676 22 3 1 675 721722981 721723633 0.000000e+00 972
19 TraesCS1A01G244000 chr7B 89.660 677 43 10 1 674 692795222 692795874 0.000000e+00 837
20 TraesCS1A01G244000 chr2D 87.153 685 72 13 1544 2221 103170378 103169703 0.000000e+00 763
21 TraesCS1A01G244000 chr2D 85.673 698 82 13 1538 2221 9672406 9671713 0.000000e+00 719
22 TraesCS1A01G244000 chr7D 86.735 686 81 7 1540 2221 119561054 119561733 0.000000e+00 754
23 TraesCS1A01G244000 chr3D 86.735 686 76 14 1540 2215 596657077 596657757 0.000000e+00 749
24 TraesCS1A01G244000 chr3D 86.499 674 74 15 1554 2221 89631546 89632208 0.000000e+00 725
25 TraesCS1A01G244000 chr3D 85.673 691 81 14 1543 2221 566073500 566072816 0.000000e+00 712
26 TraesCS1A01G244000 chr1D 86.561 692 77 13 1540 2221 249745644 249746329 0.000000e+00 749
27 TraesCS1A01G244000 chr1D 86.026 687 80 12 1545 2221 470919993 470919313 0.000000e+00 723
28 TraesCS1A01G244000 chr6D 86.127 692 83 11 1540 2221 367927743 367928431 0.000000e+00 734
29 TraesCS1A01G244000 chr4A 90.057 352 12 2 1 352 11702131 11702459 3.390000e-118 435


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 TraesCS1A01G244000 chr1A 432523268 432525489 2221 False 4104 4104 100.0000 1 2222 1 chr1A.!!$F1 2221
1 TraesCS1A01G244000 chr1A 20991730 20992381 651 True 992 992 93.7780 1 675 1 chr1A.!!$R1 674
2 TraesCS1A01G244000 chr5A 66823333 66824863 1530 False 2702 2702 98.4410 1 1539 1 chr5A.!!$F1 1538
3 TraesCS1A01G244000 chr5A 601069574 601070443 869 False 1358 1358 94.8340 673 1543 1 chr5A.!!$F2 870
4 TraesCS1A01G244000 chr5A 23904011 23904876 865 True 1356 1356 94.9190 673 1538 1 chr5A.!!$R1 865
5 TraesCS1A01G244000 chr6A 472969359 472970877 1518 False 2479 2479 95.9170 1 1543 1 chr6A.!!$F1 1542
6 TraesCS1A01G244000 chr6A 595510128 595511649 1521 True 2462 2462 95.6690 1 1547 1 chr6A.!!$R1 1546
7 TraesCS1A01G244000 chr7A 722569875 722570969 1094 False 1862 1862 97.2780 1 1102 1 chr7A.!!$F3 1101
8 TraesCS1A01G244000 chr7A 677975067 677975938 871 False 1382 1382 95.3040 673 1543 1 chr7A.!!$F2 870
9 TraesCS1A01G244000 chr7A 609346779 609347430 651 False 970 970 93.1850 1 675 1 chr7A.!!$F1 674
10 TraesCS1A01G244000 chr7A 668555819 668556470 651 True 942 942 92.4440 1 675 1 chr7A.!!$R1 674
11 TraesCS1A01G244000 chr5B 492815393 492816263 870 True 1375 1375 95.1780 673 1542 1 chr5B.!!$R1 869
12 TraesCS1A01G244000 chr4B 604143656 604144522 866 False 1375 1375 95.2710 673 1539 1 chr4B.!!$F2 866
13 TraesCS1A01G244000 chr3A 11597492 11599205 1713 True 1164 1363 94.0415 1 1538 2 chr3A.!!$R1 1537
14 TraesCS1A01G244000 chr3A 11604380 11606093 1713 True 1161 1363 93.9675 1 1538 2 chr3A.!!$R2 1537
15 TraesCS1A01G244000 chr2B 721722981 721723633 652 False 972 972 93.1950 1 675 1 chr2B.!!$F1 674
16 TraesCS1A01G244000 chr7B 692795222 692795874 652 False 837 837 89.6600 1 674 1 chr7B.!!$F1 673
17 TraesCS1A01G244000 chr2D 103169703 103170378 675 True 763 763 87.1530 1544 2221 1 chr2D.!!$R2 677
18 TraesCS1A01G244000 chr2D 9671713 9672406 693 True 719 719 85.6730 1538 2221 1 chr2D.!!$R1 683
19 TraesCS1A01G244000 chr7D 119561054 119561733 679 False 754 754 86.7350 1540 2221 1 chr7D.!!$F1 681
20 TraesCS1A01G244000 chr3D 596657077 596657757 680 False 749 749 86.7350 1540 2215 1 chr3D.!!$F2 675
21 TraesCS1A01G244000 chr3D 89631546 89632208 662 False 725 725 86.4990 1554 2221 1 chr3D.!!$F1 667
22 TraesCS1A01G244000 chr3D 566072816 566073500 684 True 712 712 85.6730 1543 2221 1 chr3D.!!$R1 678
23 TraesCS1A01G244000 chr1D 249745644 249746329 685 False 749 749 86.5610 1540 2221 1 chr1D.!!$F1 681
24 TraesCS1A01G244000 chr1D 470919313 470919993 680 True 723 723 86.0260 1545 2221 1 chr1D.!!$R1 676
25 TraesCS1A01G244000 chr6D 367927743 367928431 688 False 734 734 86.1270 1540 2221 1 chr6D.!!$F1 681

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
31 32 4.568152 ACATGCTACAAAACTGGTGAAC 57.432 40.909 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 2135 1.213094 CGCGAGAGTCACGGTTTTGT 61.213 55.0 11.95 0.0 0.0 2.83 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
31 32 4.568152 ACATGCTACAAAACTGGTGAAC 57.432 40.909 0.00 0.00 0.00 3.18
48 49 5.945191 TGGTGAACATAGAAAGCATTCATCA 59.055 36.000 4.27 0.00 37.91 3.07
279 281 8.887036 TCATTCGAAACTGCACAAGTATATAT 57.113 30.769 0.00 0.00 38.56 0.86
588 593 9.284968 ACCCGTTTTAGATTTATAGAATCATGG 57.715 33.333 0.00 0.00 0.00 3.66
1175 1378 2.468670 GCGTGTATGATGGCGGCAA 61.469 57.895 18.31 0.00 0.00 4.52
1360 1565 5.560148 CGTGGAGTTTCATATTTTCCTTCG 58.440 41.667 0.00 0.00 0.00 3.79
1604 1810 3.598019 TTATCTCTTAACCCGTGCGTT 57.402 42.857 0.00 0.00 0.00 4.84
1605 1811 2.467566 ATCTCTTAACCCGTGCGTTT 57.532 45.000 0.00 0.00 0.00 3.60
1612 1818 4.756135 TCTTAACCCGTGCGTTTAAATCTT 59.244 37.500 0.00 0.00 0.00 2.40
1631 1837 0.308376 TAAACCGCTTTCACCGTTGC 59.692 50.000 0.00 0.00 0.00 4.17
1665 1871 6.531948 CGTCGAGATTTTCAAAACTAGATCCT 59.468 38.462 0.00 0.00 28.72 3.24
1735 1943 2.052782 AAAACTGAACCGGAAGCACT 57.947 45.000 9.46 0.00 0.00 4.40
1770 1979 1.300697 GAAAGAGGCACGTCCGTGT 60.301 57.895 19.67 2.30 46.90 4.49
2042 2264 2.477189 CGTGGAAGCAAAAACGTGACTT 60.477 45.455 0.00 0.00 0.00 3.01
2143 2373 2.293399 GTGCCTCTCACGGAAACAAAAT 59.707 45.455 0.00 0.00 35.76 1.82
2221 2465 1.883732 CCCTGACTCTCGCGAAAGA 59.116 57.895 17.91 7.21 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 9.245962 GGAAAAAGATGATGAATGCTTTCTATG 57.754 33.333 12.96 0.00 32.78 2.23
48 49 5.866207 ACTCCTTACGACAAGGAAAAAGAT 58.134 37.500 19.16 4.21 45.10 2.40
201 203 3.670625 ACATGCTGTTTAAGAACGCCTA 58.329 40.909 0.00 0.00 38.65 3.93
279 281 7.647318 CGCTATTTTGGCACATATATTTGTTCA 59.353 33.333 1.05 0.00 39.30 3.18
1360 1565 2.181021 CTGACCGTACTCCACCGC 59.819 66.667 0.00 0.00 0.00 5.68
1423 1628 7.767198 CCCACTAAAATCAATCTAACGGTTAGA 59.233 37.037 27.47 27.47 45.58 2.10
1595 1801 4.160594 GGTTTAAGATTTAAACGCACGGG 58.839 43.478 14.67 0.00 38.06 5.28
1721 1929 2.922740 AAACTAGTGCTTCCGGTTCA 57.077 45.000 0.00 0.00 0.00 3.18
1746 1955 1.439679 GACGTGCCTCTTTCGGAAAT 58.560 50.000 3.24 0.00 0.00 2.17
1770 1979 2.035449 ACGGTTGTGATTTCGTGAGAGA 59.965 45.455 0.00 0.00 43.69 3.10
1906 2123 1.487482 GGTTTTGTTTCCGCAAGAGC 58.513 50.000 0.00 0.00 43.02 4.09
1918 2135 1.213094 CGCGAGAGTCACGGTTTTGT 61.213 55.000 11.95 0.00 0.00 2.83
1980 2201 2.282674 AGAGTCACGGCCGTACCA 60.283 61.111 33.70 15.54 39.03 3.25
1983 2204 3.807538 GCGAGAGTCACGGCCGTA 61.808 66.667 33.70 16.87 0.00 4.02
2131 2361 3.463944 AGAGTCACGATTTTGTTTCCGT 58.536 40.909 0.00 0.00 35.46 4.69
2143 2373 1.209383 CCTTTCGCGAGAGTCACGA 59.791 57.895 23.28 6.50 43.69 4.35


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

AutoCloner maintained by Alex Coulton.