Multiple sequence alignment - TraesCS4D01G043400

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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 TraesCS4D01G043400 chr4D 100.000 2523 0 0 1 2523 19919422 19921944 0.000000e+00 4660.0
1 TraesCS4D01G043400 chr5D 97.666 2528 54 4 1 2523 560875403 560877930 0.000000e+00 4337.0
2 TraesCS4D01G043400 chr5D 96.988 2523 71 4 6 2523 329192891 329195413 0.000000e+00 4233.0
3 TraesCS4D01G043400 chr5D 97.591 2283 49 4 247 2523 503209088 503211370 0.000000e+00 3906.0
4 TraesCS4D01G043400 chr3B 97.546 2526 59 3 1 2523 201517612 201520137 0.000000e+00 4318.0
5 TraesCS4D01G043400 chr3B 92.135 89 5 2 2110 2196 412717359 412717271 9.480000e-25 124.0
6 TraesCS4D01G043400 chr6A 96.160 2526 90 4 1 2523 260129838 260127317 0.000000e+00 4120.0
7 TraesCS4D01G043400 chr7A 94.134 2523 114 11 5 2522 352191094 352188601 0.000000e+00 3808.0
8 TraesCS4D01G043400 chr5A 96.268 1849 63 3 1 1843 283489845 283487997 0.000000e+00 3027.0
9 TraesCS4D01G043400 chrUn 97.788 1718 33 4 811 2523 93420604 93418887 0.000000e+00 2957.0
10 TraesCS4D01G043400 chrUn 97.729 1629 32 4 488 2111 383641864 383640236 0.000000e+00 2798.0
11 TraesCS4D01G043400 chr1D 97.985 1588 29 3 1 1585 206074430 206072843 0.000000e+00 2752.0
12 TraesCS4D01G043400 chr2B 97.368 76 2 0 2448 2523 425178980 425178905 2.040000e-26 130.0
13 TraesCS4D01G043400 chr2B 98.148 54 1 0 2425 2478 86512611 86512558 7.430000e-16 95.3
14 TraesCS4D01G043400 chr2B 100.000 46 0 0 2472 2517 479543665 479543710 4.470000e-13 86.1
15 TraesCS4D01G043400 chr2A 100.000 51 0 0 2473 2523 588084960 588085010 7.430000e-16 95.3


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 TraesCS4D01G043400 chr4D 19919422 19921944 2522 False 4660 4660 100.000 1 2523 1 chr4D.!!$F1 2522
1 TraesCS4D01G043400 chr5D 560875403 560877930 2527 False 4337 4337 97.666 1 2523 1 chr5D.!!$F3 2522
2 TraesCS4D01G043400 chr5D 329192891 329195413 2522 False 4233 4233 96.988 6 2523 1 chr5D.!!$F1 2517
3 TraesCS4D01G043400 chr5D 503209088 503211370 2282 False 3906 3906 97.591 247 2523 1 chr5D.!!$F2 2276
4 TraesCS4D01G043400 chr3B 201517612 201520137 2525 False 4318 4318 97.546 1 2523 1 chr3B.!!$F1 2522
5 TraesCS4D01G043400 chr6A 260127317 260129838 2521 True 4120 4120 96.160 1 2523 1 chr6A.!!$R1 2522
6 TraesCS4D01G043400 chr7A 352188601 352191094 2493 True 3808 3808 94.134 5 2522 1 chr7A.!!$R1 2517
7 TraesCS4D01G043400 chr5A 283487997 283489845 1848 True 3027 3027 96.268 1 1843 1 chr5A.!!$R1 1842
8 TraesCS4D01G043400 chrUn 93418887 93420604 1717 True 2957 2957 97.788 811 2523 1 chrUn.!!$R1 1712
9 TraesCS4D01G043400 chrUn 383640236 383641864 1628 True 2798 2798 97.729 488 2111 1 chrUn.!!$R2 1623
10 TraesCS4D01G043400 chr1D 206072843 206074430 1587 True 2752 2752 97.985 1 1585 1 chr1D.!!$R1 1584

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
309 310 1.768275 AGATTGTGGGAGTGTGTGACA 59.232 47.619 0.0 0.0 0.00 3.58 F
490 491 1.911357 TGTCATCCATGAACAGGCTCT 59.089 47.619 0.0 0.0 38.75 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1113 1115 4.321899 CCATGCGGGTTCCCATAATAATTG 60.322 45.833 8.7 0.0 0.0 2.32 R
2040 2071 5.060506 TCATTTCTTCCTTTTCTACACGCA 58.939 37.500 0.0 0.0 0.0 5.24 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
309 310 1.768275 AGATTGTGGGAGTGTGTGACA 59.232 47.619 0.00 0.00 0.00 3.58
325 326 8.579006 AGTGTGTGACATGAATTATTGATTTGT 58.421 29.630 0.00 0.00 0.00 2.83
438 439 2.237392 AGGATAGGCAGGTTCACTTGAC 59.763 50.000 0.00 0.00 0.00 3.18
490 491 1.911357 TGTCATCCATGAACAGGCTCT 59.089 47.619 0.00 0.00 38.75 4.09
639 640 7.208080 GCAATACTATCGGAGTAAAAGAAGGA 58.792 38.462 2.78 0.00 43.96 3.36
994 996 2.600731 CTCGAGCCGGATGATGATAAC 58.399 52.381 5.05 0.00 0.00 1.89
1076 1078 8.463930 ACAAAGAAACCAGACTTAAATGATCA 57.536 30.769 0.00 0.00 0.00 2.92
1113 1115 8.863704 GCTAAATTAGCTAAAGGGATGGGACAC 61.864 44.444 17.03 0.00 45.92 3.67
1235 1238 2.159057 GCCATCAATGATTGGTGAACCC 60.159 50.000 19.41 1.98 44.56 4.11
1429 1432 1.325355 TTTCGCCGCCTAGTAGCTAT 58.675 50.000 0.00 0.00 0.00 2.97
1778 1787 4.211125 TGCTTCTCTAGAGTGTCCCATAG 58.789 47.826 19.21 6.59 0.00 2.23
2040 2071 0.324830 AACTAGCGCCCTCTTCCTCT 60.325 55.000 2.29 0.00 0.00 3.69
2062 2093 5.179368 TCTGCGTGTAGAAAAGGAAGAAATG 59.821 40.000 0.00 0.00 0.00 2.32
2107 2138 4.080299 CCTCATAAAGTGCTTCCTTAGGGT 60.080 45.833 0.00 0.00 0.00 4.34
2124 2155 9.114938 TCCTTAGGGTTTAAACTTCCATTAGTA 57.885 33.333 17.50 0.00 0.00 1.82
2258 2290 7.619698 TCCATCTTGATAGGTCTTTCTGAGTTA 59.380 37.037 0.00 0.00 0.00 2.24
2289 2321 2.360483 TCCACGATCTCTCTTGATCTGC 59.640 50.000 0.00 0.00 40.32 4.26
2313 2345 7.043565 GCAAATCAATACAGAAATCAATGGGT 58.956 34.615 0.00 0.00 0.00 4.51
2376 2408 1.202533 ACGGAAGGCGGTAAGATGATG 60.203 52.381 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.579869 CAGAGGCAGTACAAAGGTATGTT 58.420 43.478 0.00 0.00 34.75 2.71
294 295 2.254546 TTCATGTCACACACTCCCAC 57.745 50.000 0.00 0.00 0.00 4.61
309 310 8.014070 TCTGCATGGACAAATCAATAATTCAT 57.986 30.769 0.00 0.00 0.00 2.57
325 326 6.489022 CAGATCCAATTCTTTATCTGCATGGA 59.511 38.462 1.14 1.14 39.03 3.41
426 427 5.923733 AGATATTCTCGTCAAGTGAACCT 57.076 39.130 0.00 0.00 35.49 3.50
438 439 7.589587 GCGGTATGATCATAGAAGATATTCTCG 59.410 40.741 15.83 1.31 32.72 4.04
490 491 8.010697 TCCATTTCTACTCTATGGGATCTTACA 58.989 37.037 0.00 0.00 39.42 2.41
583 584 6.869913 ACAATCGATGCAAAGAAAATGAATGT 59.130 30.769 0.00 0.00 0.00 2.71
798 800 1.322442 GCTCAATATCCAAGTGGGCC 58.678 55.000 0.00 0.00 32.34 5.80
891 893 6.114187 TCAATGACTCTAGGCAAGAAAAGA 57.886 37.500 0.00 0.00 32.46 2.52
994 996 2.744202 CAAAGGAACCGGACATGAGAAG 59.256 50.000 9.46 0.00 0.00 2.85
1113 1115 4.321899 CCATGCGGGTTCCCATAATAATTG 60.322 45.833 8.70 0.00 0.00 2.32
1235 1238 4.440214 GTTGCAAACGGATCTGCG 57.560 55.556 0.00 0.00 41.63 5.18
1367 1370 9.793259 TTGACATTCTCTAGAAAAGGTATTGTT 57.207 29.630 0.00 0.00 37.61 2.83
1699 1706 9.316859 CTCGTTTTAAATCCATTGCAATTTTTC 57.683 29.630 9.83 0.00 0.00 2.29
1778 1787 7.715265 TTTCGTATGGAAGATAGAAAGCATC 57.285 36.000 0.00 0.00 35.70 3.91
1975 2006 5.138758 ACTCCACCCCTTTTTACTTTTCT 57.861 39.130 0.00 0.00 0.00 2.52
2040 2071 5.060506 TCATTTCTTCCTTTTCTACACGCA 58.939 37.500 0.00 0.00 0.00 5.24
2062 2093 7.020914 AGGCTTCTCGTAATTTGATTGATTC 57.979 36.000 0.00 0.00 0.00 2.52
2245 2277 8.417106 TGGATATCAGACATAACTCAGAAAGAC 58.583 37.037 4.83 0.00 0.00 3.01
2258 2290 5.569355 AGAGAGATCGTGGATATCAGACAT 58.431 41.667 4.83 0.00 33.30 3.06
2289 2321 9.090692 GAACCCATTGATTTCTGTATTGATTTG 57.909 33.333 0.00 0.00 0.00 2.32
2313 2345 7.097192 CACAACCTATAGCTAACTTGACAGAA 58.903 38.462 0.00 0.00 0.00 3.02
2376 2408 7.142680 GTCCTAGATACATAACTGCTCAAGAC 58.857 42.308 0.00 0.00 0.00 3.01
2422 2454 8.934023 AGAAGTAATCTCTATGGAGTTAGAGG 57.066 38.462 5.93 0.00 43.57 3.69


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

AutoCloner maintained by Alex Coulton.