Multiple sequence alignment - TraesCS1B01G068900

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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 TraesCS1B01G068900 chr1B 100.000 2528 0 0 1 2528 53339674 53337147 0 4669
1 TraesCS1B01G068900 chr2D 97.128 2542 55 6 1 2525 635037260 635039800 0 4274
2 TraesCS1B01G068900 chr2D 96.394 2551 69 6 1 2528 17967194 17964644 0 4180
3 TraesCS1B01G068900 chr7B 97.011 2543 58 7 1 2525 743066305 743068847 0 4259
4 TraesCS1B01G068900 chr7A 96.933 2543 61 6 1 2528 120828848 120826308 0 4248
5 TraesCS1B01G068900 chr7A 96.857 2545 62 7 1 2528 671960568 671958025 0 4241
6 TraesCS1B01G068900 chr4D 96.964 2536 65 4 1 2525 123578592 123581126 0 4246
7 TraesCS1B01G068900 chr4D 96.777 2544 61 9 1 2525 123367642 123370183 0 4224
8 TraesCS1B01G068900 chr5A 96.860 2548 60 8 1 2528 16623275 16620728 0 4244
9 TraesCS1B01G068900 chr3B 96.892 2542 64 5 1 2528 201635803 201633263 0 4242
10 TraesCS1B01G068900 chr2A 96.893 2543 61 6 1 2525 735172799 735175341 0 4242
11 TraesCS1B01G068900 chr3D 96.892 2542 61 7 1 2525 202611946 202614486 0 4241
12 TraesCS1B01G068900 chr4B 96.311 2548 74 8 1 2528 209149607 209147060 0 4167
13 TraesCS1B01G068900 chr4A 96.085 2554 73 7 1 2528 67554917 67552365 0 4137
14 TraesCS1B01G068900 chr7D 95.753 2543 88 7 1 2528 307064894 307062357 0 4080
15 TraesCS1B01G068900 chr7D 96.047 860 15 7 1687 2528 382012479 382011621 0 1382


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 TraesCS1B01G068900 chr1B 53337147 53339674 2527 True 4669 4669 100.000 1 2528 1 chr1B.!!$R1 2527
1 TraesCS1B01G068900 chr2D 635037260 635039800 2540 False 4274 4274 97.128 1 2525 1 chr2D.!!$F1 2524
2 TraesCS1B01G068900 chr2D 17964644 17967194 2550 True 4180 4180 96.394 1 2528 1 chr2D.!!$R1 2527
3 TraesCS1B01G068900 chr7B 743066305 743068847 2542 False 4259 4259 97.011 1 2525 1 chr7B.!!$F1 2524
4 TraesCS1B01G068900 chr7A 120826308 120828848 2540 True 4248 4248 96.933 1 2528 1 chr7A.!!$R1 2527
5 TraesCS1B01G068900 chr7A 671958025 671960568 2543 True 4241 4241 96.857 1 2528 1 chr7A.!!$R2 2527
6 TraesCS1B01G068900 chr4D 123578592 123581126 2534 False 4246 4246 96.964 1 2525 1 chr4D.!!$F2 2524
7 TraesCS1B01G068900 chr4D 123367642 123370183 2541 False 4224 4224 96.777 1 2525 1 chr4D.!!$F1 2524
8 TraesCS1B01G068900 chr5A 16620728 16623275 2547 True 4244 4244 96.860 1 2528 1 chr5A.!!$R1 2527
9 TraesCS1B01G068900 chr3B 201633263 201635803 2540 True 4242 4242 96.892 1 2528 1 chr3B.!!$R1 2527
10 TraesCS1B01G068900 chr2A 735172799 735175341 2542 False 4242 4242 96.893 1 2525 1 chr2A.!!$F1 2524
11 TraesCS1B01G068900 chr3D 202611946 202614486 2540 False 4241 4241 96.892 1 2525 1 chr3D.!!$F1 2524
12 TraesCS1B01G068900 chr4B 209147060 209149607 2547 True 4167 4167 96.311 1 2528 1 chr4B.!!$R1 2527
13 TraesCS1B01G068900 chr4A 67552365 67554917 2552 True 4137 4137 96.085 1 2528 1 chr4A.!!$R1 2527
14 TraesCS1B01G068900 chr7D 307062357 307064894 2537 True 4080 4080 95.753 1 2528 1 chr7D.!!$R1 2527
15 TraesCS1B01G068900 chr7D 382011621 382012479 858 True 1382 1382 96.047 1687 2528 1 chr7D.!!$R2 841

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
959 981 0.892063 GGCGCCCCAACTTTTGATTA 59.108 50.0 18.11 0.0 0.0 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 1783 0.460459 TCCTCGCGAACAAACACACA 60.46 50.0 11.33 0.0 0.0 3.72 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
390 409 2.609747 AGACAGTTGCTCCTTCCACTA 58.390 47.619 0.00 0.00 0.00 2.74
509 528 3.181493 GCCATTCATCTTGCGTCAAATCT 60.181 43.478 0.00 0.00 0.00 2.40
821 841 4.023291 GCCCCCACTAATTCTTCATTCAA 58.977 43.478 0.00 0.00 0.00 2.69
928 950 3.350219 TGCACAGAAAGACCCCTATTC 57.650 47.619 0.00 0.00 0.00 1.75
959 981 0.892063 GGCGCCCCAACTTTTGATTA 59.108 50.000 18.11 0.00 0.00 1.75
1030 1052 8.114331 AGAACATTTCTGTGAATGCTATTTCA 57.886 30.769 0.00 0.00 39.97 2.69
1088 1110 6.601217 GGAAGCATTACTCCTCTTTTCATTCT 59.399 38.462 0.00 0.00 0.00 2.40
1116 1138 9.976511 AATTCTTCAATAAGACCGATACGATTA 57.023 29.630 0.00 0.00 41.48 1.75
1166 1188 2.352561 TTGTATCCCCCTGTTCCTCA 57.647 50.000 0.00 0.00 0.00 3.86
1408 1431 2.803155 AATCGCCGTGTCCTGCATGT 62.803 55.000 0.00 0.00 32.30 3.21
1443 1466 9.804758 CTACTATTCTATGTTCTTTCCGAAAGT 57.195 33.333 18.32 4.28 39.52 2.66
1488 1511 1.797635 GCTGAGCATCTTCTATTCGCC 59.202 52.381 0.00 0.00 34.92 5.54
1563 1586 1.750778 TCCCCCATCGTCGTAAAGTAC 59.249 52.381 0.00 0.00 0.00 2.73
1574 1597 4.156739 CGTCGTAAAGTACTAAAGGTCCCT 59.843 45.833 0.00 0.00 0.00 4.20
1576 1599 5.047731 GTCGTAAAGTACTAAAGGTCCCTGT 60.048 44.000 0.00 0.00 0.00 4.00
1760 1783 1.895866 GCTCCTAGGTGTGTGTAGGGT 60.896 57.143 9.08 0.00 37.08 4.34
1778 1801 0.315869 GTGTGTGTTTGTTCGCGAGG 60.316 55.000 9.59 0.00 0.00 4.63
1875 1900 1.426751 AGGAAACTGTACCCGACCAA 58.573 50.000 0.00 0.00 41.13 3.67
1986 2017 1.541310 TTCCTCTGTCGTTGCCGGAT 61.541 55.000 5.05 0.00 33.95 4.18
1987 2018 1.079127 CCTCTGTCGTTGCCGGATT 60.079 57.895 5.05 0.00 33.95 3.01
2063 2095 2.094390 CGACCCGTTCAGTAGAATTCCA 60.094 50.000 0.65 0.00 35.92 3.53
2120 2152 4.354208 TTGGCCCCCTTCCAAATAAATA 57.646 40.909 0.00 0.00 40.35 1.40
2232 2264 3.197664 GCAGGAAGCAGGCCTAAAT 57.802 52.632 3.98 0.00 44.79 1.40
2316 2348 1.275291 TCGAGAGTCAAGGCGGAAAAT 59.725 47.619 0.00 0.00 0.00 1.82
2453 2485 0.107268 ACCAACTACCACCGGTCAAC 59.893 55.000 2.59 0.00 37.09 3.18
2455 2487 1.619827 CCAACTACCACCGGTCAACTA 59.380 52.381 2.59 0.00 37.09 2.24
2525 2572 4.579340 AGATCAAGGCAGCATATCAGTTTG 59.421 41.667 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
509 528 4.206375 TGAAACTCTTGCATGAAAGACCA 58.794 39.130 12.45 5.66 32.75 4.02
599 619 2.093658 GGTCATAGCCAAAGTCGAAGGA 60.094 50.000 0.00 0.00 0.00 3.36
853 875 3.821886 GGTTAGGTGCACCCCTCT 58.178 61.111 32.29 16.45 35.97 3.69
928 950 2.096248 TGGGGCGCCAAATTACTAAAG 58.904 47.619 30.85 0.00 0.00 1.85
959 981 9.520204 CATTGAAAAGATTAGTTGACAACAGTT 57.480 29.630 20.08 4.05 0.00 3.16
1030 1052 7.147637 GGGACAGAGAATAGGAACACTTAGATT 60.148 40.741 0.00 0.00 0.00 2.40
1088 1110 9.976511 ATCGTATCGGTCTTATTGAAGAATTTA 57.023 29.630 0.00 0.00 43.38 1.40
1116 1138 2.851195 AGAGAAACGCACAGACCAATT 58.149 42.857 0.00 0.00 0.00 2.32
1166 1188 5.565045 GCCGTAGAAGGATCGAATTGTATCT 60.565 44.000 0.00 0.00 0.00 1.98
1389 1412 2.108514 CATGCAGGACACGGCGATT 61.109 57.895 16.62 0.00 40.93 3.34
1408 1431 9.661954 AAGAACATAGAATAGTAGAGGATCCAA 57.338 33.333 15.82 0.00 33.66 3.53
1443 1466 2.445427 CACAACATAGGGATTGGCACA 58.555 47.619 0.00 0.00 0.00 4.57
1488 1511 2.012673 CAGAGGAAAAGCTTGATCCCG 58.987 52.381 21.92 11.35 33.55 5.14
1549 1572 5.163612 GGGACCTTTAGTACTTTACGACGAT 60.164 44.000 0.00 0.00 0.00 3.73
1563 1586 3.425162 AAGCTTCACAGGGACCTTTAG 57.575 47.619 0.00 0.00 0.00 1.85
1574 1597 1.270839 CCTCTTCCCGAAAGCTTCACA 60.271 52.381 0.00 0.00 34.76 3.58
1576 1599 0.324943 CCCTCTTCCCGAAAGCTTCA 59.675 55.000 0.00 0.00 34.76 3.02
1760 1783 0.460459 TCCTCGCGAACAAACACACA 60.460 50.000 11.33 0.00 0.00 3.72
1778 1801 3.868077 CCTGACTTGACGAGGAATTCATC 59.132 47.826 10.06 10.06 0.00 2.92
1875 1900 3.428589 GCTTACGAGTTTACGTCCATCCT 60.429 47.826 0.00 0.00 45.32 3.24
1986 2017 1.416401 AGGTCTCTTCGCCAAGAACAA 59.584 47.619 0.00 0.00 38.23 2.83
1987 2018 1.048601 AGGTCTCTTCGCCAAGAACA 58.951 50.000 0.00 0.00 38.23 3.18
2063 2095 2.360165 CTGCTGCCAACAGTCTTTCTTT 59.640 45.455 0.00 0.00 46.30 2.52
2120 2152 2.196925 CGAGCTCTATCCTGCCCGT 61.197 63.158 12.85 0.00 0.00 5.28
2316 2348 6.538945 TGTCATTAGACCACTATGCTTGTA 57.461 37.500 0.00 0.00 44.33 2.41
2429 2461 0.668401 CCGGTGGTAGTTGGTCGAAC 60.668 60.000 0.00 0.00 34.40 3.95
2453 2485 7.421599 CCTATAATGATGGTAGAGTCGCATAG 58.578 42.308 0.00 0.00 0.00 2.23
2455 2487 5.127845 CCCTATAATGATGGTAGAGTCGCAT 59.872 44.000 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.