Multiple sequence alignment - TraesCS6A01G128600

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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 TraesCS6A01G128600 chr6A 100.000 2471 0 0 1 2471 100761614 100764084 0.000000e+00 4564
1 TraesCS6A01G128600 chr6A 92.857 2128 117 25 1 2102 100184450 100182332 0.000000e+00 3055
2 TraesCS6A01G128600 chr6A 97.095 1687 47 2 1 1687 100803675 100805359 0.000000e+00 2843
3 TraesCS6A01G128600 chr6A 99.178 1459 11 1 1013 2471 100809263 100810720 0.000000e+00 2627
4 TraesCS6A01G128600 chr6A 86.461 1492 188 6 1 1491 100087237 100085759 0.000000e+00 1624
5 TraesCS6A01G128600 chr6A 93.556 450 23 1 1647 2096 100805365 100805808 0.000000e+00 665
6 TraesCS6A01G128600 chr6A 92.493 373 9 4 2088 2443 100808335 100808705 1.310000e-142 516
7 TraesCS6A01G128600 chr6D 94.080 2027 92 9 1 2001 83124092 83122068 0.000000e+00 3053
8 TraesCS6A01G128600 chr6D 96.763 1668 49 4 1 1667 83541240 83542903 0.000000e+00 2776
9 TraesCS6A01G128600 chr6D 89.909 1645 106 29 849 2443 83105907 83104273 0.000000e+00 2063
10 TraesCS6A01G128600 chr6D 87.875 1468 162 10 28 1493 83057260 83055807 0.000000e+00 1711
11 TraesCS6A01G128600 chr6D 85.738 603 51 12 1647 2224 83542928 83543520 2.720000e-169 604
12 TraesCS6A01G128600 chr6B 96.386 1688 56 4 1 1687 159402708 159404391 0.000000e+00 2774
13 TraesCS6A01G128600 chr6B 94.428 1687 92 2 1 1687 158149161 158147477 0.000000e+00 2593
14 TraesCS6A01G128600 chr6B 86.745 1456 177 8 28 1481 158103219 158101778 0.000000e+00 1605
15 TraesCS6A01G128600 chr6B 91.165 532 34 6 1647 2166 158147471 158146941 0.000000e+00 710
16 TraesCS6A01G128600 chr6B 96.114 386 15 0 1647 2032 159404397 159404782 4.480000e-177 630
17 TraesCS6A01G128600 chr6B 97.491 279 5 2 2165 2443 159404945 159405221 2.220000e-130 475


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 TraesCS6A01G128600 chr6A 100761614 100764084 2470 False 4564.00 4564 100.000000 1 2471 1 chr6A.!!$F1 2470
1 TraesCS6A01G128600 chr6A 100182332 100184450 2118 True 3055.00 3055 92.857000 1 2102 1 chr6A.!!$R2 2101
2 TraesCS6A01G128600 chr6A 100803675 100810720 7045 False 1662.75 2843 95.580500 1 2471 4 chr6A.!!$F2 2470
3 TraesCS6A01G128600 chr6A 100085759 100087237 1478 True 1624.00 1624 86.461000 1 1491 1 chr6A.!!$R1 1490
4 TraesCS6A01G128600 chr6D 83122068 83124092 2024 True 3053.00 3053 94.080000 1 2001 1 chr6D.!!$R3 2000
5 TraesCS6A01G128600 chr6D 83104273 83105907 1634 True 2063.00 2063 89.909000 849 2443 1 chr6D.!!$R2 1594
6 TraesCS6A01G128600 chr6D 83055807 83057260 1453 True 1711.00 1711 87.875000 28 1493 1 chr6D.!!$R1 1465
7 TraesCS6A01G128600 chr6D 83541240 83543520 2280 False 1690.00 2776 91.250500 1 2224 2 chr6D.!!$F1 2223
8 TraesCS6A01G128600 chr6B 158146941 158149161 2220 True 1651.50 2593 92.796500 1 2166 2 chr6B.!!$R2 2165
9 TraesCS6A01G128600 chr6B 158101778 158103219 1441 True 1605.00 1605 86.745000 28 1481 1 chr6B.!!$R1 1453
10 TraesCS6A01G128600 chr6B 159402708 159405221 2513 False 1293.00 2774 96.663667 1 2443 3 chr6B.!!$F1 2442

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
51 52 0.667993 ACAACAACCTCAATGGCACG 59.332 50.0 0.0 0.0 40.22 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1637 3.037549 CAGGAGAGGCTACAAAGGAGAT 58.962 50.0 0.0 0.0 0.0 2.75 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
19 20 1.603456 TTGCTCGGTGCTGAAATTGA 58.397 45.000 3.53 0.00 43.37 2.57
48 49 1.202348 GGCTACAACAACCTCAATGGC 59.798 52.381 0.00 0.00 40.22 4.40
51 52 0.667993 ACAACAACCTCAATGGCACG 59.332 50.000 0.00 0.00 40.22 5.34
58 59 1.243342 CCTCAATGGCACGCTTCCAA 61.243 55.000 0.00 0.00 37.13 3.53
229 231 4.618635 AGGTGATCTGAAGAGATTGGAGA 58.381 43.478 0.00 0.00 39.19 3.71
447 449 2.357881 TCCTGCAGCAAGCTGACG 60.358 61.111 25.03 13.80 46.30 4.35
724 726 4.021544 TGTGTGGAAAAATACCTGATTGGC 60.022 41.667 0.00 0.00 40.22 4.52
893 895 3.483421 TGGAGATGCCAATGCTAGAATG 58.517 45.455 0.00 0.00 45.87 2.67
1362 1367 2.065799 AGTCCAGTTTCCATTGACCCT 58.934 47.619 0.00 0.00 0.00 4.34
1402 1407 3.718434 TGAGGCCATCATCTTTATGACCT 59.282 43.478 5.01 0.00 44.79 3.85
1491 1496 4.696402 TGAAACCATGTAACCGTTATCACC 59.304 41.667 0.00 0.00 0.00 4.02
1495 1500 4.081752 ACCATGTAACCGTTATCACCGTTA 60.082 41.667 0.00 0.00 0.00 3.18
1615 1620 4.511454 GCGCTCCAATGATAACTTATCACA 59.489 41.667 12.76 0.00 46.94 3.58
1667 6294 3.465871 CTCTCCTGCCTAAAGCTGATTC 58.534 50.000 0.00 0.00 42.76 2.52
1812 6439 4.202050 GCAAATCAGACCAACTTTGTGTCT 60.202 41.667 7.08 7.08 38.42 3.41
1953 6591 3.684788 CCGTGGAACCACTAATTTCAGAG 59.315 47.826 19.61 2.67 44.16 3.35
2134 6778 8.640063 AATGCAAATATATTCTAGGCATGACA 57.360 30.769 19.08 8.17 40.09 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.250762 TGAAGAGTTCATTTGGAAGCGTG 59.749 43.478 0.00 0.00 35.82 5.34
51 52 4.222114 CGTTGAAGAGTTCATTTGGAAGC 58.778 43.478 0.00 0.00 39.84 3.86
58 59 4.210537 CGTGGTTACGTTGAAGAGTTCATT 59.789 41.667 0.00 0.00 44.99 2.57
229 231 2.168106 TGTTGTGTTCCAAATGCAGCTT 59.832 40.909 0.00 0.00 34.07 3.74
400 402 1.003355 CTGGAACTGTGCCGGTGAT 60.003 57.895 5.38 0.00 0.00 3.06
447 449 3.447918 TTGTAAGATAGCCGTAGTGCC 57.552 47.619 0.00 0.00 0.00 5.01
704 706 6.321181 TGATAGCCAATCAGGTATTTTTCCAC 59.679 38.462 0.00 0.00 39.77 4.02
724 726 4.275936 CCCCAAATTCGGTAGCTTTGATAG 59.724 45.833 0.00 0.00 32.83 2.08
893 895 7.934120 AGAATACCTTTGGTGCAGTATTATCTC 59.066 37.037 6.72 0.00 35.96 2.75
1362 1367 6.069905 TGGCCTCACTACCAATCTGTTTTATA 60.070 38.462 3.32 0.00 31.46 0.98
1560 1565 7.001674 TGTGCTTTCCCTGTAGATTTTCTTTA 58.998 34.615 0.00 0.00 0.00 1.85
1632 1637 3.037549 CAGGAGAGGCTACAAAGGAGAT 58.962 50.000 0.00 0.00 0.00 2.75
1953 6591 5.941733 TGACATGAAACAGTACATGATTGC 58.058 37.500 20.56 11.06 44.28 3.56
2134 6778 4.520492 CCTGTGCTAGACATTTTTCAACCT 59.480 41.667 0.00 0.00 32.74 3.50
2371 7041 5.221362 ACGCTTGGGGGTTATAATTTTATGC 60.221 40.000 0.00 0.00 34.95 3.14


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

AutoCloner maintained by Alex Coulton.