Multiple sequence alignment - TraesCS4A01G079300

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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 TraesCS4A01G079300 chr4A 100.000 3550 0 0 1 3550 80859005 80855456 0.000000e+00 6556.0
1 TraesCS4A01G079300 chr4D 95.405 3591 88 25 1 3550 409171105 409167551 0.000000e+00 5646.0
2 TraesCS4A01G079300 chr4B 95.017 3592 110 24 1 3550 506908641 506912205 0.000000e+00 5578.0
3 TraesCS4A01G079300 chr5D 86.614 127 17 0 1596 1722 344885063 344884937 1.330000e-29 141.0
4 TraesCS4A01G079300 chr5D 85.393 89 9 3 1596 1682 436971839 436971925 4.880000e-14 89.8
5 TraesCS4A01G079300 chr5A 89.908 109 11 0 1596 1704 447305063 447305171 1.330000e-29 141.0
6 TraesCS4A01G079300 chr7D 91.753 97 8 0 1596 1692 117792114 117792210 6.180000e-28 135.0
7 TraesCS4A01G079300 chr7B 90.722 97 9 0 1596 1692 79051426 79051522 2.880000e-26 130.0
8 TraesCS4A01G079300 chr7A 90.722 97 9 0 1596 1692 122207649 122207745 2.880000e-26 130.0
9 TraesCS4A01G079300 chr5B 85.393 89 9 3 1596 1682 531187513 531187599 4.880000e-14 89.8


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 TraesCS4A01G079300 chr4A 80855456 80859005 3549 True 6556 6556 100.000 1 3550 1 chr4A.!!$R1 3549
1 TraesCS4A01G079300 chr4D 409167551 409171105 3554 True 5646 5646 95.405 1 3550 1 chr4D.!!$R1 3549
2 TraesCS4A01G079300 chr4B 506908641 506912205 3564 False 5578 5578 95.017 1 3550 1 chr4B.!!$F1 3549

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
892 924 0.397187 CCATCTAGCAGCAGCAGGAT 59.603 55.0 3.17 3.49 45.49 3.24 F
1811 1847 0.108992 GTGCGACATTCTACCCGTCA 60.109 55.0 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 1919 0.322546 GCAGAGGGTTCCCGTTGATT 60.323 55.0 15.25 0.0 0.0 2.57 R
3357 3431 0.615850 GGGTGGCTAGCTTTCTGACT 59.384 55.0 15.72 0.0 0.0 3.41 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
81 82 3.003378 CCGTCTAGTTGCATGTAGATCGA 59.997 47.826 18.59 0.00 0.00 3.59
82 83 4.320567 CCGTCTAGTTGCATGTAGATCGAT 60.321 45.833 18.59 0.00 0.00 3.59
181 185 6.642540 GCTTAACAATAACAAGAAGCAAGCTT 59.357 34.615 7.07 7.07 39.24 3.74
192 196 5.467035 AGAAGCAAGCTTAGCTAGGATAG 57.533 43.478 19.28 0.00 42.53 2.08
202 206 6.070881 AGCTTAGCTAGGATAGTTGATGGATG 60.071 42.308 4.30 0.00 41.93 3.51
330 336 3.051081 AGAAACTAAGACAGCAGCAGG 57.949 47.619 0.00 0.00 0.00 4.85
679 695 2.026262 AGAGTGAGGGAGTGAGAGAGAC 60.026 54.545 0.00 0.00 0.00 3.36
892 924 0.397187 CCATCTAGCAGCAGCAGGAT 59.603 55.000 3.17 3.49 45.49 3.24
976 1008 1.146263 GGTACCCCATTCGCCTCAG 59.854 63.158 0.00 0.00 0.00 3.35
1042 1074 2.416747 CTCCTTTGAGCGACATGAACA 58.583 47.619 0.00 0.00 0.00 3.18
1074 1106 6.636454 TCTTCTTGCCCTTTCTATTCCTAA 57.364 37.500 0.00 0.00 0.00 2.69
1219 1255 1.085091 GCTGAGCCTGAGACATTGTG 58.915 55.000 0.00 0.00 0.00 3.33
1220 1256 1.085091 CTGAGCCTGAGACATTGTGC 58.915 55.000 0.00 0.00 0.00 4.57
1272 1308 4.104383 AGGAAATTCTGTGCCTTTCTCA 57.896 40.909 0.00 0.00 0.00 3.27
1298 1334 0.540365 CTGGTTCTGGTTGCATGGGT 60.540 55.000 0.00 0.00 0.00 4.51
1481 1517 3.630148 GACGTCCCGCATGCATCG 61.630 66.667 19.57 17.06 0.00 3.84
1811 1847 0.108992 GTGCGACATTCTACCCGTCA 60.109 55.000 0.00 0.00 0.00 4.35
2204 2240 6.317857 CGAGAACTGATTTCCCAATCTTTTC 58.682 40.000 0.00 0.00 39.81 2.29
2306 2350 5.541845 ACGTGAGTAATATGTCCATCCATG 58.458 41.667 0.00 0.00 46.88 3.66
2314 2358 7.781693 AGTAATATGTCCATCCATGAAAGCTTT 59.218 33.333 12.53 12.53 0.00 3.51
2531 2589 8.262715 TCAGATACACATTTTTATTTCTCGCA 57.737 30.769 0.00 0.00 0.00 5.10
2695 2753 4.830600 TCTTCATTTTGGTGGGAGTTTACC 59.169 41.667 0.00 0.00 37.48 2.85
3089 3158 8.457585 ACCCTATCTCTCTATCTAGAAAGCTA 57.542 38.462 0.00 0.00 0.00 3.32
3136 3205 9.462606 ACAATGTACTATTCCTAAGAAAAAGGG 57.537 33.333 0.00 0.00 35.09 3.95
3357 3431 7.663081 GCTCAAAATGATGAGTATATTCCCTGA 59.337 37.037 9.14 0.00 46.85 3.86
3538 3612 2.106566 ACTGATCAGACTAGGCAGTGG 58.893 52.381 29.27 0.00 38.30 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
181 185 5.086621 TGCATCCATCAACTATCCTAGCTA 58.913 41.667 0.00 0.00 0.00 3.32
192 196 3.428045 GCTAACCAACTGCATCCATCAAC 60.428 47.826 0.00 0.00 0.00 3.18
202 206 4.216257 TCATCTCAAAAGCTAACCAACTGC 59.784 41.667 0.00 0.00 0.00 4.40
679 695 2.035961 TCACTGAGTCTGAGGAAAACCG 59.964 50.000 3.76 0.00 0.00 4.44
892 924 2.887846 TTAGGAGGAGGTGGGGGCA 61.888 63.158 0.00 0.00 0.00 5.36
1042 1074 0.402121 GGGCAAGAAGAAGGTCTGGT 59.598 55.000 0.00 0.00 0.00 4.00
1074 1106 3.052186 AGAGCCAAGGAGAGAGAAGGTAT 60.052 47.826 0.00 0.00 0.00 2.73
1219 1255 2.096019 GCAGCTCTTTGTGAAGTACAGC 60.096 50.000 0.00 0.00 41.10 4.40
1220 1256 3.397482 AGCAGCTCTTTGTGAAGTACAG 58.603 45.455 0.00 0.00 41.10 2.74
1272 1308 1.823250 GCAACCAGAACCAGGTGGATT 60.823 52.381 2.10 0.00 39.86 3.01
1481 1517 4.097135 GCTTCTTTAATTCTTCCCTCAGGC 59.903 45.833 0.00 0.00 0.00 4.85
1802 1838 1.141019 CGTGGTCCATGACGGGTAG 59.859 63.158 4.96 0.00 32.65 3.18
1833 1869 1.419387 GAACTGCTGGCCATAGGAGAT 59.581 52.381 18.67 8.13 38.28 2.75
1883 1919 0.322546 GCAGAGGGTTCCCGTTGATT 60.323 55.000 15.25 0.00 0.00 2.57
2204 2240 5.607939 AAAAGGGTAGTTTCAACCAAAGG 57.392 39.130 0.00 0.00 38.87 3.11
2290 2334 7.779326 TCAAAGCTTTCATGGATGGACATATTA 59.221 33.333 9.23 0.00 0.00 0.98
2306 2350 4.802563 GCAAATAGCAGGATCAAAGCTTTC 59.197 41.667 9.23 0.00 44.79 2.62
2377 2421 7.970061 GTCTTGCTGCATGAAAGTTATAAATCA 59.030 33.333 18.30 0.00 33.01 2.57
2626 2684 9.890629 TGCTAGACTACAATCTGTTTTATTCAT 57.109 29.630 0.00 0.00 0.00 2.57
3053 3122 3.954904 GAGAGATAGGGTCAGCACTGTAA 59.045 47.826 0.00 0.00 0.00 2.41
3117 3186 6.616237 TCGACCCTTTTTCTTAGGAATAGT 57.384 37.500 0.00 0.00 34.56 2.12
3345 3419 6.168270 AGCTTTCTGACTCAGGGAATATAC 57.832 41.667 6.20 0.00 31.51 1.47
3357 3431 0.615850 GGGTGGCTAGCTTTCTGACT 59.384 55.000 15.72 0.00 0.00 3.41
3480 3554 6.465948 AGATATGAGCCTGACATCTCAAATC 58.534 40.000 10.42 0.00 41.96 2.17
3481 3555 6.436738 AGATATGAGCCTGACATCTCAAAT 57.563 37.500 10.42 0.93 41.96 2.32
3482 3556 5.883685 AGATATGAGCCTGACATCTCAAA 57.116 39.130 10.42 0.00 41.96 2.69
3483 3557 5.883685 AAGATATGAGCCTGACATCTCAA 57.116 39.130 10.42 3.41 41.96 3.02
3484 3558 6.496218 ACATAAGATATGAGCCTGACATCTCA 59.504 38.462 9.21 9.21 42.72 3.27
3485 3559 6.934056 ACATAAGATATGAGCCTGACATCTC 58.066 40.000 4.47 0.00 0.00 2.75
3486 3560 6.931790 ACATAAGATATGAGCCTGACATCT 57.068 37.500 4.47 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.