Multiple sequence alignment - TraesCS3B01G564800

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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 TraesCS3B01G564800 chr3B 100.000 2573 0 0 1 2573 797597578 797595006 0.000000e+00 4752
1 TraesCS3B01G564800 chr5A 97.562 2584 52 3 1 2573 19253505 19250922 0.000000e+00 4412
2 TraesCS3B01G564800 chr5A 96.819 2578 72 3 1 2573 238901417 238898845 0.000000e+00 4298
3 TraesCS3B01G564800 chr5A 96.674 2135 61 5 445 2573 238827019 238824889 0.000000e+00 3541
4 TraesCS3B01G564800 chr6D 97.595 2578 53 2 1 2573 124512878 124515451 0.000000e+00 4409
5 TraesCS3B01G564800 chr7D 97.440 2578 57 3 1 2573 203495353 203497926 0.000000e+00 4386
6 TraesCS3B01G564800 chr7D 97.284 2577 61 2 2 2573 381978407 381975835 0.000000e+00 4362
7 TraesCS3B01G564800 chr7D 97.583 2441 50 2 1 2436 381915332 381917768 0.000000e+00 4172
8 TraesCS3B01G564800 chr4A 96.977 2580 65 7 1 2573 67592134 67594707 0.000000e+00 4320
9 TraesCS3B01G564800 chr4D 96.823 2581 70 6 1 2573 123330822 123333398 0.000000e+00 4301
10 TraesCS3B01G564800 chr2D 95.657 2579 98 5 1 2573 39526407 39528977 0.000000e+00 4130
11 TraesCS3B01G564800 chr3A 92.063 252 17 2 2322 2573 658234872 658235120 4.070000e-93 351


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 TraesCS3B01G564800 chr3B 797595006 797597578 2572 True 4752 4752 100.000 1 2573 1 chr3B.!!$R1 2572
1 TraesCS3B01G564800 chr5A 19250922 19253505 2583 True 4412 4412 97.562 1 2573 1 chr5A.!!$R1 2572
2 TraesCS3B01G564800 chr5A 238898845 238901417 2572 True 4298 4298 96.819 1 2573 1 chr5A.!!$R3 2572
3 TraesCS3B01G564800 chr5A 238824889 238827019 2130 True 3541 3541 96.674 445 2573 1 chr5A.!!$R2 2128
4 TraesCS3B01G564800 chr6D 124512878 124515451 2573 False 4409 4409 97.595 1 2573 1 chr6D.!!$F1 2572
5 TraesCS3B01G564800 chr7D 203495353 203497926 2573 False 4386 4386 97.440 1 2573 1 chr7D.!!$F1 2572
6 TraesCS3B01G564800 chr7D 381975835 381978407 2572 True 4362 4362 97.284 2 2573 1 chr7D.!!$R1 2571
7 TraesCS3B01G564800 chr7D 381915332 381917768 2436 False 4172 4172 97.583 1 2436 1 chr7D.!!$F2 2435
8 TraesCS3B01G564800 chr4A 67592134 67594707 2573 False 4320 4320 96.977 1 2573 1 chr4A.!!$F1 2572
9 TraesCS3B01G564800 chr4D 123330822 123333398 2576 False 4301 4301 96.823 1 2573 1 chr4D.!!$F1 2572
10 TraesCS3B01G564800 chr2D 39526407 39528977 2570 False 4130 4130 95.657 1 2573 1 chr2D.!!$F1 2572

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
938 948 2.3606 CCCAACCGGCGATTTCCA 60.361 61.111 9.3 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 1854 0.031178 AAGCAAGCGTTTTCAGGCTG 59.969 50.0 8.58 8.58 43.5 4.85 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
503 504 9.191995 GTCTTTTTCGTTTTGTCAATATCCAAT 57.808 29.630 0.00 0.00 0.00 3.16
553 554 9.783256 GAACTCCTTAATAATACGTGCATTTTT 57.217 29.630 0.00 0.00 0.00 1.94
611 612 8.786826 ATGTCTCGGAACAATAAAATAGAACA 57.213 30.769 0.00 0.00 31.81 3.18
668 669 5.864474 GCAGTAAGGATATGAATACGACTGG 59.136 44.000 0.00 0.00 36.24 4.00
938 948 2.360600 CCCAACCGGCGATTTCCA 60.361 61.111 9.30 0.00 0.00 3.53
959 969 5.059833 CCAACAAGTCTTTCTGCTTAGAGT 58.940 41.667 0.00 0.00 0.00 3.24
988 998 4.621460 GCGGAACCAAAATAAAGCTTTCTC 59.379 41.667 16.57 1.16 0.00 2.87
1180 1190 6.247903 GTTCAAGTTTCGATCGATATTTGCA 58.752 36.000 27.13 19.49 0.00 4.08
1199 1209 2.675583 CAGAGTGGATCATCCCTCTCA 58.324 52.381 21.01 0.00 44.86 3.27
1253 1263 5.494724 ACTGAGTACTCGGTATAACTCACA 58.505 41.667 31.58 3.90 46.57 3.58
1299 1309 5.571784 ACGAAGTAACACGAATATCTCCA 57.428 39.130 0.00 0.00 41.94 3.86
1307 1317 6.525578 AACACGAATATCTCCAGTAGTCAA 57.474 37.500 0.00 0.00 0.00 3.18
1430 1440 3.370103 GGTTTCGAGGGTCATCCATTACA 60.370 47.826 0.00 0.00 38.24 2.41
1546 1558 6.417191 TTCGCTATTTCGATTTTGCTAGTT 57.583 33.333 0.00 0.00 38.37 2.24
1567 1579 3.035363 TCTTGGGAACAGTGTAGTGACA 58.965 45.455 0.00 0.00 44.54 3.58
1588 1600 9.130312 GTGACAGATAATTCCGAATCTACATAC 57.870 37.037 0.00 0.00 31.25 2.39
2058 2070 1.006162 ACTAGTCGCCTCCTTTCCTCT 59.994 52.381 0.00 0.00 0.00 3.69
2117 2129 3.782443 GGGGAAGGCCGACGATGT 61.782 66.667 0.00 0.00 33.83 3.06
2214 2226 5.427481 TGACCTTATTTATTCTCCCGGAACT 59.573 40.000 0.73 0.00 36.70 3.01
2225 2237 1.485066 TCCCGGAACTCTAGCAAATCC 59.515 52.381 0.73 0.00 0.00 3.01
2233 2245 6.316390 CGGAACTCTAGCAAATCCAATAGTTT 59.684 38.462 0.00 0.00 0.00 2.66
2250 2262 8.950210 CCAATAGTTTCATCTGCTCTTCTTAAA 58.050 33.333 0.00 0.00 0.00 1.52
2465 2477 4.699522 GGGCCAACCGAGCGAAGT 62.700 66.667 4.39 0.00 36.48 3.01
2466 2478 2.263540 GGCCAACCGAGCGAAGTA 59.736 61.111 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
399 400 8.791327 AAGAAGAATCAAAATGGTGTGTTTTT 57.209 26.923 0.00 0.00 0.00 1.94
503 504 8.422577 TCTGGAATGATTACTATGCTAAGCTA 57.577 34.615 0.00 0.00 0.00 3.32
521 522 7.441458 GCACGTATTATTAAGGAGTTCTGGAAT 59.559 37.037 0.00 0.00 0.00 3.01
553 554 7.698506 AGCATTGAGAATGAGAAATCTTTGA 57.301 32.000 0.40 0.00 41.46 2.69
656 657 9.399797 TCTAGTAGTTTATTCCAGTCGTATTCA 57.600 33.333 0.00 0.00 0.00 2.57
741 742 0.464036 ATCCGCTAAACCATCGCTCA 59.536 50.000 0.00 0.00 0.00 4.26
796 797 4.190001 CTGCATGCTCTAGTGTTGAATCT 58.810 43.478 20.33 0.00 0.00 2.40
938 948 7.727181 TCTTACTCTAAGCAGAAAGACTTGTT 58.273 34.615 0.00 0.00 35.76 2.83
959 969 5.475564 AGCTTTATTTTGGTTCCGCTTCTTA 59.524 36.000 0.00 0.00 0.00 2.10
1062 1072 3.947196 TCCCATGTTCCGATCTTTTCATG 59.053 43.478 0.00 9.34 34.41 3.07
1180 1190 3.411454 TTGAGAGGGATGATCCACTCT 57.589 47.619 23.71 23.71 42.75 3.24
1199 1209 8.791327 ATGGACAACTTCAAATCTTTGTTTTT 57.209 26.923 2.82 0.00 39.18 1.94
1253 1263 3.375610 TGCACTTGTTTGTACACGAATGT 59.624 39.130 0.00 0.00 43.30 2.71
1299 1309 6.529220 GGCTGATGGAAATAGATTGACTACT 58.471 40.000 0.00 0.00 33.62 2.57
1307 1317 1.271597 GGCCGGCTGATGGAAATAGAT 60.272 52.381 28.56 0.00 0.00 1.98
1430 1440 5.373812 TCCACTCAGAGGAAAGTCTTTTT 57.626 39.130 1.53 0.00 30.71 1.94
1498 1508 3.075882 TCTTGGGTCATCTCAATGGGTTT 59.924 43.478 0.00 0.00 33.42 3.27
1546 1558 3.035363 TGTCACTACACTGTTCCCAAGA 58.965 45.455 0.00 0.00 0.00 3.02
1558 1570 7.348080 AGATTCGGAATTATCTGTCACTACA 57.652 36.000 4.47 0.00 33.40 2.74
1563 1575 8.021396 CGTATGTAGATTCGGAATTATCTGTCA 58.979 37.037 4.47 4.02 33.38 3.58
1567 1579 8.338072 AGACGTATGTAGATTCGGAATTATCT 57.662 34.615 4.47 1.29 35.41 1.98
1842 1854 0.031178 AAGCAAGCGTTTTCAGGCTG 59.969 50.000 8.58 8.58 43.50 4.85
1875 1887 2.222027 AGCATAGGCAATAGTTTCCGC 58.778 47.619 0.67 0.00 44.61 5.54
2058 2070 0.035534 TGGCTAAGCATCTTTCGGCA 60.036 50.000 0.00 0.00 0.00 5.69
2117 2129 0.620556 GACAGCTTCCCCCTCATTGA 59.379 55.000 0.00 0.00 0.00 2.57
2214 2226 7.012704 GCAGATGAAACTATTGGATTTGCTAGA 59.987 37.037 0.00 0.00 0.00 2.43
2250 2262 1.917872 TGGCGGCCTTTGTTCTTAAT 58.082 45.000 21.46 0.00 0.00 1.40
2315 2327 2.685380 CGGCCACTCTCCCCTTCT 60.685 66.667 2.24 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.