Multiple sequence alignment - TraesCS6A01G191800

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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 TraesCS6A01G191800 chr6A 100.000 2162 0 0 1 2162 260116791 260114630 0 3993
1 TraesCS6A01G191800 chr6D 98.371 1412 22 1 1 1411 168254415 168255826 0 2479
2 TraesCS6A01G191800 chr3B 98.159 1412 25 1 1 1411 201526513 201527924 0 2462
3 TraesCS6A01G191800 chr5D 98.017 1412 27 1 1 1411 503278737 503277326 0 2451
4 TraesCS6A01G191800 chr5D 97.946 1412 28 1 1 1411 503217707 503219118 0 2446
5 TraesCS6A01G191800 chr5D 89.305 748 77 3 1416 2160 185825762 185826509 0 935
6 TraesCS6A01G191800 chr3A 98.016 1411 28 0 1 1411 672910518 672909108 0 2451
7 TraesCS6A01G191800 chr1A 97.946 1412 28 1 1 1411 554511737 554513148 0 2446
8 TraesCS6A01G191800 chrUn 97.875 1412 28 2 1 1411 93410142 93408732 0 2440
9 TraesCS6A01G191800 chr3D 97.875 1412 27 2 1 1411 589280053 589278644 0 2438
10 TraesCS6A01G191800 chr3D 89.157 747 78 3 1416 2159 242913548 242914294 0 928
11 TraesCS6A01G191800 chr2D 97.805 1412 30 1 1 1411 272794404 272792993 0 2435
12 TraesCS6A01G191800 chr2D 89.157 747 78 3 1416 2159 271357164 271357910 0 928
13 TraesCS6A01G191800 chr6B 90.247 728 66 5 1437 2160 389274584 389273858 0 946
14 TraesCS6A01G191800 chr6B 89.544 746 76 2 1416 2160 389270912 389270168 0 944
15 TraesCS6A01G191800 chr2A 89.424 747 76 3 1416 2160 329983370 329984115 0 939
16 TraesCS6A01G191800 chr7D 89.290 747 75 5 1416 2158 326779846 326779101 0 931
17 TraesCS6A01G191800 chr7A 89.157 747 79 2 1416 2160 347229458 347230204 0 929
18 TraesCS6A01G191800 chr1D 89.142 746 78 2 1416 2158 174170741 174169996 0 926


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 TraesCS6A01G191800 chr6A 260114630 260116791 2161 True 3993 3993 100.0000 1 2162 1 chr6A.!!$R1 2161
1 TraesCS6A01G191800 chr6D 168254415 168255826 1411 False 2479 2479 98.3710 1 1411 1 chr6D.!!$F1 1410
2 TraesCS6A01G191800 chr3B 201526513 201527924 1411 False 2462 2462 98.1590 1 1411 1 chr3B.!!$F1 1410
3 TraesCS6A01G191800 chr5D 503277326 503278737 1411 True 2451 2451 98.0170 1 1411 1 chr5D.!!$R1 1410
4 TraesCS6A01G191800 chr5D 503217707 503219118 1411 False 2446 2446 97.9460 1 1411 1 chr5D.!!$F2 1410
5 TraesCS6A01G191800 chr5D 185825762 185826509 747 False 935 935 89.3050 1416 2160 1 chr5D.!!$F1 744
6 TraesCS6A01G191800 chr3A 672909108 672910518 1410 True 2451 2451 98.0160 1 1411 1 chr3A.!!$R1 1410
7 TraesCS6A01G191800 chr1A 554511737 554513148 1411 False 2446 2446 97.9460 1 1411 1 chr1A.!!$F1 1410
8 TraesCS6A01G191800 chrUn 93408732 93410142 1410 True 2440 2440 97.8750 1 1411 1 chrUn.!!$R1 1410
9 TraesCS6A01G191800 chr3D 589278644 589280053 1409 True 2438 2438 97.8750 1 1411 1 chr3D.!!$R1 1410
10 TraesCS6A01G191800 chr3D 242913548 242914294 746 False 928 928 89.1570 1416 2159 1 chr3D.!!$F1 743
11 TraesCS6A01G191800 chr2D 272792993 272794404 1411 True 2435 2435 97.8050 1 1411 1 chr2D.!!$R1 1410
12 TraesCS6A01G191800 chr2D 271357164 271357910 746 False 928 928 89.1570 1416 2159 1 chr2D.!!$F1 743
13 TraesCS6A01G191800 chr6B 389270168 389274584 4416 True 945 946 89.8955 1416 2160 2 chr6B.!!$R1 744
14 TraesCS6A01G191800 chr2A 329983370 329984115 745 False 939 939 89.4240 1416 2160 1 chr2A.!!$F1 744
15 TraesCS6A01G191800 chr7D 326779101 326779846 745 True 931 931 89.2900 1416 2158 1 chr7D.!!$R1 742
16 TraesCS6A01G191800 chr7A 347229458 347230204 746 False 929 929 89.1570 1416 2160 1 chr7A.!!$F1 744
17 TraesCS6A01G191800 chr1D 174169996 174170741 745 True 926 926 89.1420 1416 2158 1 chr1D.!!$R1 742

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
985 988 1.447643 CGCTTATGACCTCCCCCTG 59.552 63.158 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 5591 0.323302 TTGGATTCTGGTGCAGCGTA 59.677 50.0 11.91 0.0 0.0 4.42 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
67 68 5.009911 GTGATTTCTATGTTATGCATGGCCA 59.990 40.000 8.56 8.56 38.47 5.36
175 176 7.433719 GCATACGGCTTTCTAGATGTATATGAG 59.566 40.741 0.00 0.00 40.25 2.90
488 489 6.459670 AATTAAATGTGAATAACCCGTCCC 57.540 37.500 0.00 0.00 0.00 4.46
525 526 2.665185 GCGCTTCCGGTTCTGTGT 60.665 61.111 0.00 0.00 34.32 3.72
627 628 3.689347 TCACTTGCTGCCATTACTCAAT 58.311 40.909 0.00 0.00 0.00 2.57
985 988 1.447643 CGCTTATGACCTCCCCCTG 59.552 63.158 0.00 0.00 0.00 4.45
1053 1056 3.454719 TGGTGTTGTCCATGGATCAAT 57.545 42.857 19.62 0.00 31.96 2.57
1089 1092 3.072330 TGGATTTCACTTGCCTGTCTACA 59.928 43.478 0.00 0.00 0.00 2.74
1404 1408 9.794685 GATTCTTTCCCAATAAATGAAGACTTC 57.205 33.333 8.34 8.34 0.00 3.01
1411 1415 8.163408 TCCCAATAAATGAAGACTTCTTTCTGA 58.837 33.333 16.02 6.23 36.11 3.27
1412 1416 8.796475 CCCAATAAATGAAGACTTCTTTCTGAA 58.204 33.333 16.02 4.35 36.11 3.02
1413 1417 9.617975 CCAATAAATGAAGACTTCTTTCTGAAC 57.382 33.333 16.02 0.00 36.11 3.18
1435 1440 4.584743 ACATTGTTTTCAAGAAGGGAGGAC 59.415 41.667 0.00 0.00 43.41 3.85
1456 1461 4.533815 ACGATGAGGACATGACTACCTTA 58.466 43.478 0.00 0.01 36.82 2.69
1461 1466 7.338196 CGATGAGGACATGACTACCTTAGATAT 59.662 40.741 0.00 0.00 36.82 1.63
1518 1523 7.828717 TGAGGTGATTTCTAATGCAAACTATGA 59.171 33.333 0.00 0.00 0.00 2.15
1667 1674 6.152661 TGTTGTTCAAAAAGTCCTCTCACATT 59.847 34.615 0.00 0.00 0.00 2.71
1668 1675 6.135290 TGTTCAAAAAGTCCTCTCACATTG 57.865 37.500 0.00 0.00 0.00 2.82
1716 5416 1.982660 AGTCTCTCACGTTCTGGACA 58.017 50.000 9.91 0.00 0.00 4.02
1741 5441 6.546403 ACAGATTCGGACTACACATACATACT 59.454 38.462 0.00 0.00 0.00 2.12
1745 5445 6.954487 TCGGACTACACATACATACTTGAT 57.046 37.500 0.00 0.00 0.00 2.57
1798 5501 6.007703 ACTCCGAATTGGGTGATTCTTTTTA 58.992 36.000 14.55 0.00 38.76 1.52
1859 5563 5.949354 TGGATTCACCTTAAAATTCGTCCAT 59.051 36.000 0.00 0.00 39.86 3.41
1862 5566 7.282450 GGATTCACCTTAAAATTCGTCCATAGT 59.718 37.037 0.00 0.00 35.41 2.12
1866 5570 8.095792 TCACCTTAAAATTCGTCCATAGTGTTA 58.904 33.333 0.00 0.00 0.00 2.41
1949 5653 0.770499 TTGCATCACCTCCACTTGGA 59.230 50.000 0.00 0.00 43.08 3.53
1963 5667 1.304381 TTGGACCCATGAGCCTTGC 60.304 57.895 0.00 0.00 0.00 4.01
1974 5678 1.941999 GAGCCTTGCATGACCTTGGC 61.942 60.000 0.00 2.08 40.54 4.52
1991 5695 1.074727 TGGCTTAGTTTTAGGCTGCCA 59.925 47.619 22.65 6.81 45.31 4.92
2003 5707 2.731571 GCTGCCATGGGACGTCCTA 61.732 63.158 32.52 28.49 36.20 2.94
2022 5726 4.659172 CACCTCCTTGGCCGCCAA 62.659 66.667 23.46 23.46 41.69 4.52
2030 5734 3.871850 TTGGCCGCCAACCCTTACC 62.872 63.158 21.31 0.00 38.75 2.85
2081 5785 7.339953 GCTTTTTGCTTGAGATTTGTTTAGTG 58.660 34.615 0.00 0.00 38.95 2.74
2112 5816 3.550030 GCCATTGCAACTTCGTGTACTTT 60.550 43.478 0.00 0.00 37.47 2.66
2147 5851 3.005472 CGACCAGACCAAGACTACTTTCA 59.995 47.826 0.00 0.00 33.70 2.69
2160 5864 3.456277 ACTACTTTCAGATCCCCACCATC 59.544 47.826 0.00 0.00 0.00 3.51
2161 5865 2.278245 ACTTTCAGATCCCCACCATCA 58.722 47.619 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
175 176 9.866655 ATATAAGATCCATCTGTCTAGAGATCC 57.133 37.037 11.72 0.00 36.22 3.36
424 425 5.880054 TGAAAGCTAAGCAGTGGTAATTC 57.120 39.130 0.00 0.00 0.00 2.17
488 489 2.519013 CCCCTTGTTTCAAAGAGAGGG 58.481 52.381 5.69 5.69 42.79 4.30
525 526 6.397272 AGAAGACAAAATTGTTTGAAGCACA 58.603 32.000 6.21 0.00 45.99 4.57
627 628 5.105473 CGGGATAGACCTCAACAGAAAACTA 60.105 44.000 0.00 0.00 38.98 2.24
895 898 7.025963 GGTAGAATCGTAACCATAGAATACGG 58.974 42.308 4.94 0.00 41.89 4.02
958 961 2.561419 GAGGTCATAAGCGCCTATACCA 59.439 50.000 18.62 0.00 31.89 3.25
1038 1041 7.257003 CACGAAATAAATTGATCCATGGACAA 58.743 34.615 18.99 21.81 0.00 3.18
1039 1042 6.183360 CCACGAAATAAATTGATCCATGGACA 60.183 38.462 18.99 14.43 0.00 4.02
1053 1056 7.461182 AGTGAAATCCAATCCACGAAATAAA 57.539 32.000 0.00 0.00 34.93 1.40
1395 1399 7.630242 AACAATGTTCAGAAAGAAGTCTTCA 57.370 32.000 14.97 0.00 36.78 3.02
1404 1408 7.223387 CCCTTCTTGAAAACAATGTTCAGAAAG 59.777 37.037 0.00 2.26 36.41 2.62
1411 1415 5.069119 GTCCTCCCTTCTTGAAAACAATGTT 59.931 40.000 0.00 0.00 0.00 2.71
1412 1416 4.584743 GTCCTCCCTTCTTGAAAACAATGT 59.415 41.667 0.00 0.00 0.00 2.71
1413 1417 4.320494 CGTCCTCCCTTCTTGAAAACAATG 60.320 45.833 0.00 0.00 0.00 2.82
1414 1418 3.821033 CGTCCTCCCTTCTTGAAAACAAT 59.179 43.478 0.00 0.00 0.00 2.71
1435 1440 4.822350 TCTAAGGTAGTCATGTCCTCATCG 59.178 45.833 0.00 0.00 31.15 3.84
1541 1546 6.937436 AAAGTCCGTGAAGTATTTTTGTCT 57.063 33.333 0.00 0.00 0.00 3.41
1667 1674 8.150945 ACTCTATCTTCTCTTGTGTTAAAAGCA 58.849 33.333 0.00 0.00 0.00 3.91
1668 1675 8.541133 ACTCTATCTTCTCTTGTGTTAAAAGC 57.459 34.615 0.00 0.00 0.00 3.51
1716 5416 5.854010 ATGTATGTGTAGTCCGAATCTGT 57.146 39.130 0.00 0.00 0.00 3.41
1798 5501 6.006449 AGTGCATGAAGTCTAATTTCCAAGT 58.994 36.000 0.00 0.00 0.00 3.16
1812 5516 1.962807 TGGGTTGGAAAGTGCATGAAG 59.037 47.619 0.00 0.00 0.00 3.02
1866 5570 7.277981 AGCGTAAGATTGTTTCGTCAATATCTT 59.722 33.333 0.00 0.00 38.03 2.40
1887 5591 0.323302 TTGGATTCTGGTGCAGCGTA 59.677 50.000 11.91 0.00 0.00 4.42
1949 5653 0.682209 GTCATGCAAGGCTCATGGGT 60.682 55.000 14.18 0.00 41.11 4.51
1963 5667 4.142381 GCCTAAAACTAAGCCAAGGTCATG 60.142 45.833 0.00 0.00 0.00 3.07
1974 5678 2.689983 CCCATGGCAGCCTAAAACTAAG 59.310 50.000 14.15 0.00 0.00 2.18
1991 5695 0.686769 GAGGTGGTAGGACGTCCCAT 60.687 60.000 30.82 16.27 37.41 4.00
2022 5726 8.253541 TGATCTACTTATATAGGGGTAAGGGT 57.746 38.462 0.00 0.00 33.30 4.34
2081 5785 4.382754 CGAAGTTGCAATGGCTAACTTTTC 59.617 41.667 17.97 9.78 44.12 2.29
2112 5816 1.066071 TCTGGTCGTTGGACACAAACA 60.066 47.619 0.00 0.00 45.28 2.83


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

AutoCloner maintained by Alex Coulton.