Multiple sequence alignment - TraesCS1A01G368300

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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 TraesCS1A01G368300 chr1A 100.000 2396 0 0 1 2396 546231385 546233780 0.000000e+00 4425
1 TraesCS1A01G368300 chr1A 89.299 542 38 13 1 531 546224576 546225108 0.000000e+00 662
2 TraesCS1A01G368300 chr7B 98.866 1675 19 0 722 2396 257652462 257654136 0.000000e+00 2988
3 TraesCS1A01G368300 chr7A 98.455 1683 24 2 716 2396 299313396 299311714 0.000000e+00 2963
4 TraesCS1A01G368300 chr5A 98.792 1656 19 1 741 2396 484830719 484832373 0.000000e+00 2946
5 TraesCS1A01G368300 chr5A 98.828 256 3 0 1 256 11310799 11311054 7.810000e-125 457
6 TraesCS1A01G368300 chr2A 98.388 1675 27 0 722 2396 166818343 166816669 0.000000e+00 2944
7 TraesCS1A01G368300 chr2A 98.776 245 3 0 1 245 770129534 770129778 1.020000e-118 436
8 TraesCS1A01G368300 chr5B 97.934 1694 24 3 713 2396 47328190 47326498 0.000000e+00 2924
9 TraesCS1A01G368300 chr5B 97.969 1674 27 1 730 2396 47323125 47321452 0.000000e+00 2896
10 TraesCS1A01G368300 chr1B 97.440 1680 29 5 717 2396 526807644 526809309 0.000000e+00 2852
11 TraesCS1A01G368300 chr1B 92.987 713 26 5 1 713 621409153 621409841 0.000000e+00 1018
12 TraesCS1A01G368300 chr1B 90.211 521 32 7 22 531 621261253 621260741 0.000000e+00 662
13 TraesCS1A01G368300 chr6B 94.926 1695 75 7 713 2396 246983347 246985041 0.000000e+00 2643
14 TraesCS1A01G368300 chr6B 94.016 1671 86 8 735 2396 420862189 420863854 0.000000e+00 2519
15 TraesCS1A01G368300 chr1D 95.053 566 12 5 1 566 451781653 451782202 0.000000e+00 876
16 TraesCS1A01G368300 chr1D 91.494 435 22 2 22 456 451636668 451637087 3.430000e-163 584
17 TraesCS1A01G368300 chr1D 95.200 125 6 0 590 714 451789628 451789752 5.220000e-47 198


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 TraesCS1A01G368300 chr1A 546231385 546233780 2395 False 4425 4425 100.0000 1 2396 1 chr1A.!!$F2 2395
1 TraesCS1A01G368300 chr1A 546224576 546225108 532 False 662 662 89.2990 1 531 1 chr1A.!!$F1 530
2 TraesCS1A01G368300 chr7B 257652462 257654136 1674 False 2988 2988 98.8660 722 2396 1 chr7B.!!$F1 1674
3 TraesCS1A01G368300 chr7A 299311714 299313396 1682 True 2963 2963 98.4550 716 2396 1 chr7A.!!$R1 1680
4 TraesCS1A01G368300 chr5A 484830719 484832373 1654 False 2946 2946 98.7920 741 2396 1 chr5A.!!$F2 1655
5 TraesCS1A01G368300 chr2A 166816669 166818343 1674 True 2944 2944 98.3880 722 2396 1 chr2A.!!$R1 1674
6 TraesCS1A01G368300 chr5B 47321452 47328190 6738 True 2910 2924 97.9515 713 2396 2 chr5B.!!$R1 1683
7 TraesCS1A01G368300 chr1B 526807644 526809309 1665 False 2852 2852 97.4400 717 2396 1 chr1B.!!$F1 1679
8 TraesCS1A01G368300 chr1B 621409153 621409841 688 False 1018 1018 92.9870 1 713 1 chr1B.!!$F2 712
9 TraesCS1A01G368300 chr1B 621260741 621261253 512 True 662 662 90.2110 22 531 1 chr1B.!!$R1 509
10 TraesCS1A01G368300 chr6B 246983347 246985041 1694 False 2643 2643 94.9260 713 2396 1 chr6B.!!$F1 1683
11 TraesCS1A01G368300 chr6B 420862189 420863854 1665 False 2519 2519 94.0160 735 2396 1 chr6B.!!$F2 1661
12 TraesCS1A01G368300 chr1D 451781653 451782202 549 False 876 876 95.0530 1 566 1 chr1D.!!$F2 565

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
595 614 1.277842 ACGACAGTGGGTTGCATCATA 59.722 47.619 0.0 0.0 33.88 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 1959 4.084171 CGCATGCGAAATCATAGTCAGAAT 60.084 41.667 35.82 0.0 42.83 2.4 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
535 554 4.036616 GGCAGTTCCTTTTTGTTACCGTAA 59.963 41.667 0.0 0.0 0.00 3.18
536 555 5.278610 GGCAGTTCCTTTTTGTTACCGTAAT 60.279 40.000 0.0 0.0 0.00 1.89
537 556 6.072563 GGCAGTTCCTTTTTGTTACCGTAATA 60.073 38.462 0.0 0.0 0.00 0.98
538 557 7.362315 GGCAGTTCCTTTTTGTTACCGTAATAT 60.362 37.037 0.0 0.0 0.00 1.28
595 614 1.277842 ACGACAGTGGGTTGCATCATA 59.722 47.619 0.0 0.0 33.88 2.15
620 639 4.500127 TGAATGCTGGCAAAATGAGAATG 58.500 39.130 0.0 0.0 0.00 2.67
623 642 2.892215 TGCTGGCAAAATGAGAATGTGA 59.108 40.909 0.0 0.0 0.00 3.58
633 652 8.553696 GCAAAATGAGAATGTGAAACTTGATTT 58.446 29.630 0.0 0.0 38.04 2.17
680 699 9.722184 GGTCTTCTGAAACTTATAAACTTACCT 57.278 33.333 0.0 0.0 0.00 3.08
704 723 8.700644 CCTATCTTTTACATGCATACTTACGTC 58.299 37.037 0.0 0.0 0.00 4.34
753 777 3.609103 AATAAATCACGCATCGCTTCC 57.391 42.857 0.0 0.0 0.00 3.46
837 861 6.231211 CAGTCCTTGTTTAAGTGGTACTCAT 58.769 40.000 0.0 0.0 31.80 2.90
1246 1281 5.960811 ACCTCACCTTCTCTTCATATTCTCA 59.039 40.000 0.0 0.0 0.00 3.27
1297 1332 0.034477 GTTCCCCATCCATCACGGTT 60.034 55.000 0.0 0.0 35.57 4.44
1781 1816 3.703001 AATCAGATCACCGTTCACCTT 57.297 42.857 0.0 0.0 0.00 3.50
1813 1848 7.908193 ACTGTTGTCTTTAACTTATTTTGCG 57.092 32.000 0.0 0.0 0.00 4.85
1923 1959 3.067461 AGCGTGTACCTTCAAATGCAAAA 59.933 39.130 0.0 0.0 0.00 2.44
1989 2025 3.000819 CTACCGAGTGCCACCCCA 61.001 66.667 0.0 0.0 0.00 4.96
2185 2228 7.607223 TCAAATTTTCAGCCCAGGATTTTTATG 59.393 33.333 0.0 0.0 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
535 554 2.637872 CCACGATCAGGGGTGGTTATAT 59.362 50.000 8.83 0.00 46.79 0.86
536 555 2.043992 CCACGATCAGGGGTGGTTATA 58.956 52.381 8.83 0.00 46.79 0.98
537 556 0.837272 CCACGATCAGGGGTGGTTAT 59.163 55.000 8.83 0.00 46.79 1.89
538 557 2.292866 CCACGATCAGGGGTGGTTA 58.707 57.895 8.83 0.00 46.79 2.85
567 586 1.227823 CCCACTGTCGTTGCCTCAA 60.228 57.895 0.00 0.00 0.00 3.02
568 587 1.978455 AACCCACTGTCGTTGCCTCA 61.978 55.000 0.00 0.00 0.00 3.86
569 588 1.227853 AACCCACTGTCGTTGCCTC 60.228 57.895 0.00 0.00 0.00 4.70
570 589 1.525995 CAACCCACTGTCGTTGCCT 60.526 57.895 4.80 0.00 33.56 4.75
571 590 3.030652 CAACCCACTGTCGTTGCC 58.969 61.111 4.80 0.00 33.56 4.52
573 592 0.238289 GATGCAACCCACTGTCGTTG 59.762 55.000 11.21 11.21 41.84 4.10
574 593 0.179032 TGATGCAACCCACTGTCGTT 60.179 50.000 0.00 0.00 0.00 3.85
595 614 3.575256 TCTCATTTTGCCAGCATTCAACT 59.425 39.130 0.00 0.00 0.00 3.16
620 639 9.581099 TGTTTTCCTTCTTAAATCAAGTTTCAC 57.419 29.630 0.00 0.00 35.58 3.18
623 642 8.463607 TCGTGTTTTCCTTCTTAAATCAAGTTT 58.536 29.630 0.00 0.00 35.58 2.66
633 652 4.635324 ACCGTTTTCGTGTTTTCCTTCTTA 59.365 37.500 0.00 0.00 42.35 2.10
636 655 3.064408 AGACCGTTTTCGTGTTTTCCTTC 59.936 43.478 0.00 0.00 42.35 3.46
704 723 5.697633 GGTAGAGAGGTAGAGATACAAGTCG 59.302 48.000 0.00 0.00 0.00 4.18
739 763 3.982372 GACCGGAAGCGATGCGTGA 62.982 63.158 9.46 0.00 41.91 4.35
753 777 4.093952 ACCAGCGACGTACGACCG 62.094 66.667 24.41 23.46 45.77 4.79
837 861 5.957910 ACGCAAAAATGAATCGTTTTTCA 57.042 30.435 19.55 0.37 39.55 2.69
1158 1193 3.300765 GGACCACCGGAGACACGT 61.301 66.667 9.46 0.00 0.00 4.49
1246 1281 1.302285 CCCAACTGCATCTCCAGCT 59.698 57.895 0.00 0.00 36.29 4.24
1297 1332 0.400213 AGAATCCCTTGACAACGGCA 59.600 50.000 0.00 0.00 0.00 5.69
1781 1816 9.754382 ATAAGTTAAAGACAACAGTACGAGAAA 57.246 29.630 0.00 0.00 0.00 2.52
1813 1848 7.765307 TGAACTGAGCATTTTATTGAGAATCC 58.235 34.615 0.00 0.00 0.00 3.01
1923 1959 4.084171 CGCATGCGAAATCATAGTCAGAAT 60.084 41.667 35.82 0.00 42.83 2.40
2185 2228 8.764524 ACTAAGAAATACTCACATCAGTCAAC 57.235 34.615 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.