Multiple sequence alignment - TraesCS1A01G083100

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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 TraesCS1A01G083100 chr1A 100.000 3848 0 0 1 3848 66891398 66895245 0.000000e+00 7107
1 TraesCS1A01G083100 chr1D 97.618 3863 65 16 1 3848 68444967 68448817 0.000000e+00 6599
2 TraesCS1A01G083100 chr1B 95.943 3870 109 18 1 3848 109727334 109731177 0.000000e+00 6233
3 TraesCS1A01G083100 chr1B 82.955 264 28 6 3116 3371 217805927 217805673 5.000000e-54 222
4 TraesCS1A01G083100 chr3D 84.173 139 22 0 1404 1542 352367945 352367807 6.710000e-28 135
5 TraesCS1A01G083100 chr2B 84.800 125 19 0 1416 1540 152844326 152844202 4.040000e-25 126
6 TraesCS1A01G083100 chr2A 90.323 93 9 0 1416 1508 100826054 100825962 5.220000e-24 122
7 TraesCS1A01G083100 chr7A 82.482 137 20 4 1405 1539 486237282 486237148 2.430000e-22 117
8 TraesCS1A01G083100 chr2D 90.000 90 9 0 1419 1508 101872850 101872761 2.430000e-22 117
9 TraesCS1A01G083100 chr7B 82.707 133 19 4 1406 1536 452961940 452962070 8.740000e-22 115
10 TraesCS1A01G083100 chr7D 85.714 105 11 4 1406 1508 436114195 436114297 1.460000e-19 108


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 TraesCS1A01G083100 chr1A 66891398 66895245 3847 False 7107 7107 100.000 1 3848 1 chr1A.!!$F1 3847
1 TraesCS1A01G083100 chr1D 68444967 68448817 3850 False 6599 6599 97.618 1 3848 1 chr1D.!!$F1 3847
2 TraesCS1A01G083100 chr1B 109727334 109731177 3843 False 6233 6233 95.943 1 3848 1 chr1B.!!$F1 3847

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
786 796 0.405247 TTAAACCCCCACCCCCTTCT 60.405 55.0 0.0 0.0 0.0 2.85 F
1156 1172 0.039618 AAATGGGGAGGCATTCGTGT 59.960 50.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 1927 1.136147 CGGCAGCAGCATTGAAGAC 59.864 57.895 2.65 0.0 44.61 3.01 R
2903 2930 3.837731 AGAAAGAAAGGGAGACTCCAGAG 59.162 47.826 23.06 0.0 38.64 3.35 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
91 93 5.198207 TCTGTCCTGGAATACGAACATCTA 58.802 41.667 0.00 0.00 0.00 1.98
244 246 1.928868 AAATCTTCTTGCAGGTGGGG 58.071 50.000 0.00 0.00 0.00 4.96
411 417 3.750652 AGAAGTAGCTGCAGAAAAGAAGC 59.249 43.478 20.43 0.00 40.70 3.86
445 451 4.891992 AAAGACAAGGCTTCTAGTAGCA 57.108 40.909 21.19 0.00 43.02 3.49
446 452 4.464069 AAGACAAGGCTTCTAGTAGCAG 57.536 45.455 21.19 13.13 43.02 4.24
447 453 2.763448 AGACAAGGCTTCTAGTAGCAGG 59.237 50.000 21.19 12.54 43.02 4.85
730 736 1.973281 GACGAGACGTACCCCCACA 60.973 63.158 0.00 0.00 41.37 4.17
786 796 0.405247 TTAAACCCCCACCCCCTTCT 60.405 55.000 0.00 0.00 0.00 2.85
991 1002 7.230913 CCCCATATATAAGTCACTATACCCTCG 59.769 44.444 0.00 0.00 0.00 4.63
1026 1040 2.425143 TCAGCCATGGATTCCTGAAC 57.575 50.000 18.40 0.00 31.90 3.18
1062 1076 0.319728 GAGGAGACTTCTGCTGTGCA 59.680 55.000 4.82 0.00 44.95 4.57
1066 1080 0.598680 AGACTTCTGCTGTGCACGAC 60.599 55.000 13.13 7.19 33.79 4.34
1156 1172 0.039618 AAATGGGGAGGCATTCGTGT 59.960 50.000 0.00 0.00 0.00 4.49
1408 1428 1.737838 CCTCGTAAATTGCTGCAGGA 58.262 50.000 17.12 10.66 0.00 3.86
1584 1604 2.766828 AGGAGGACCCTAACAGAATTCG 59.233 50.000 0.00 0.00 45.48 3.34
1614 1634 3.423539 ACTGCAGAGCAAACCTTGATA 57.576 42.857 23.35 0.00 38.41 2.15
1615 1635 3.754965 ACTGCAGAGCAAACCTTGATAA 58.245 40.909 23.35 0.00 38.41 1.75
1616 1636 4.338879 ACTGCAGAGCAAACCTTGATAAT 58.661 39.130 23.35 0.00 38.41 1.28
1636 1656 9.431887 TGATAATAATTCAACTAATACGCCTCC 57.568 33.333 0.00 0.00 0.00 4.30
1641 1661 7.462571 AATTCAACTAATACGCCTCCTTTTT 57.537 32.000 0.00 0.00 0.00 1.94
1879 1900 1.003696 GCTGGTGCTCTAGGGAACTTT 59.996 52.381 0.00 0.00 37.87 2.66
1906 1927 2.183811 CTCAGCGAGACAGCCCAG 59.816 66.667 0.00 0.00 38.01 4.45
1994 2015 1.322442 GCCAGCAAAGGAGTTGTTCT 58.678 50.000 0.00 0.00 39.63 3.01
2244 2271 0.692476 CTCCCACCAGACAATCACCA 59.308 55.000 0.00 0.00 0.00 4.17
2746 2773 5.128919 AGCTGAGACTTGTCTCACAATTTT 58.871 37.500 24.41 8.13 41.34 1.82
2849 2876 5.242393 GGTTATAAAGATCATGCAGTGCCAT 59.758 40.000 13.72 3.36 0.00 4.40
2903 2930 5.171337 CGTCAAATTGCACAGAAAAGTACAC 59.829 40.000 0.00 0.00 0.00 2.90
3268 3296 8.047310 GTCTTAATCTTTTCCCTGTGGAGAATA 58.953 37.037 0.00 0.00 43.07 1.75
3367 3395 4.338795 ACCATCCTCAGGAGAGAGTAAA 57.661 45.455 0.00 0.00 44.98 2.01
3438 3466 4.790937 TGCAAGATGGGTAGCATATGAAA 58.209 39.130 6.97 0.00 31.05 2.69
3489 3517 0.585357 CTCAACTATGGCTGCGCATC 59.415 55.000 12.24 6.63 0.00 3.91
3497 3525 1.226773 GGCTGCGCATCATGGTTTC 60.227 57.895 12.24 0.00 0.00 2.78
3498 3526 1.226773 GCTGCGCATCATGGTTTCC 60.227 57.895 12.24 0.00 0.00 3.13
3559 3587 1.134699 TGGCTAGGAGCTCAACATTCG 60.135 52.381 17.19 0.00 41.99 3.34
3569 3597 1.811965 CTCAACATTCGGCAACCATGA 59.188 47.619 0.00 0.00 0.00 3.07
3611 3639 6.375377 GTGCTTATTTGGTTTATCACGAACA 58.625 36.000 0.00 0.00 0.00 3.18
3669 3697 3.023832 CACAACCAACCTCCAGAAAAGT 58.976 45.455 0.00 0.00 0.00 2.66
3682 3710 6.072452 CCTCCAGAAAAGTTAGCCTTTACTTG 60.072 42.308 0.00 0.00 42.62 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 93 1.492993 GGGGAGAAAGAGGTGGCACT 61.493 60.000 18.45 3.24 0.00 4.40
244 246 0.240945 CATGTGCACCTCGTTTTCCC 59.759 55.000 15.69 0.00 0.00 3.97
350 356 1.674359 CAGGGTAAAGCACACACACA 58.326 50.000 0.00 0.00 30.42 3.72
411 417 8.831715 AAGCCTTGTCTTTTTATTTATGTTGG 57.168 30.769 0.00 0.00 0.00 3.77
445 451 1.589399 CCACTCCTCCTCCTCCTCCT 61.589 65.000 0.00 0.00 0.00 3.69
446 452 1.075600 CCACTCCTCCTCCTCCTCC 60.076 68.421 0.00 0.00 0.00 4.30
447 453 0.686112 CACCACTCCTCCTCCTCCTC 60.686 65.000 0.00 0.00 0.00 3.71
730 736 2.047560 GGTTGCTTCCGGCTACGT 60.048 61.111 0.00 0.00 45.14 3.57
786 796 2.283529 GGAGGTGGTTGCGAGAGGA 61.284 63.158 0.00 0.00 0.00 3.71
991 1002 0.972471 CTGAAGGGGTGGGAAATGCC 60.972 60.000 0.00 0.00 0.00 4.40
1062 1076 3.341043 CACGCAGCTTGCAGTCGT 61.341 61.111 8.52 0.00 45.36 4.34
1066 1080 1.206072 GAACTCACGCAGCTTGCAG 59.794 57.895 8.52 0.00 45.36 4.41
1408 1428 1.898574 CTTGCCGCACCTTTGGAGT 60.899 57.895 0.00 0.00 0.00 3.85
1584 1604 2.632377 TGCTCTGCAGTTACTAATGCC 58.368 47.619 14.67 0.00 41.85 4.40
1614 1634 8.747538 AAAGGAGGCGTATTAGTTGAATTATT 57.252 30.769 0.00 0.00 0.00 1.40
1615 1635 8.747538 AAAAGGAGGCGTATTAGTTGAATTAT 57.252 30.769 0.00 0.00 0.00 1.28
1616 1636 8.570068 AAAAAGGAGGCGTATTAGTTGAATTA 57.430 30.769 0.00 0.00 0.00 1.40
1641 1661 2.978978 TGAGACCACCTTCTCATGGAAA 59.021 45.455 0.00 0.00 45.79 3.13
1762 1783 1.151899 AGTGAGGGGCTTGTGGGTA 60.152 57.895 0.00 0.00 0.00 3.69
1879 1900 1.979155 CTCGCTGAGGAGGTGACCA 60.979 63.158 3.63 0.00 0.00 4.02
1906 1927 1.136147 CGGCAGCAGCATTGAAGAC 59.864 57.895 2.65 0.00 44.61 3.01
2317 2344 3.952508 TTGCTTCCGCTGCTCCCA 61.953 61.111 0.00 0.00 36.97 4.37
2903 2930 3.837731 AGAAAGAAAGGGAGACTCCAGAG 59.162 47.826 23.06 0.00 38.64 3.35
3150 3178 5.699001 ACAAATATACGACTGCAGTTTGTCA 59.301 36.000 22.65 13.85 34.34 3.58
3268 3296 2.656560 AAGCGATCAAGTAGCTTCGT 57.343 45.000 0.00 0.00 44.12 3.85
3367 3395 1.001406 CTCCTTTTCTCTCAGCCGTGT 59.999 52.381 0.00 0.00 0.00 4.49
3419 3447 5.132648 TGAGGTTTCATATGCTACCCATCTT 59.867 40.000 17.48 4.33 35.34 2.40
3438 3466 1.956477 GTGCTCACCACAAAATGAGGT 59.044 47.619 3.61 0.00 42.11 3.85
3559 3587 2.298729 TGGCTTAAGTTTCATGGTTGCC 59.701 45.455 4.02 0.00 38.42 4.52
3569 3597 3.390967 AGCACCCAAAATGGCTTAAGTTT 59.609 39.130 4.02 0.00 35.79 2.66
3611 3639 3.259876 TCACCTAGCTCGTACCACAATTT 59.740 43.478 0.00 0.00 0.00 1.82
3702 3730 5.411977 TGTTGAACGTTGAAACCAAGTTCTA 59.588 36.000 5.00 0.00 41.05 2.10


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

AutoCloner maintained by Alex Coulton.