Multiple sequence alignment - TraesCS6A01G204100

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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 TraesCS6A01G204100 chr6A 100.000 2453 0 0 1 2453 353250196 353252648 0 4530
1 TraesCS6A01G204100 chrUn 99.190 1482 12 0 1 1482 38408669 38407188 0 2671
2 TraesCS6A01G204100 chr3B 99.190 1482 12 0 1 1482 35847405 35848886 0 2671
3 TraesCS6A01G204100 chr3B 96.489 1481 52 0 1 1481 29803247 29801767 0 2447
4 TraesCS6A01G204100 chr6B 99.123 1482 13 0 1 1482 489445385 489443904 0 2665
5 TraesCS6A01G204100 chr1B 99.123 1482 13 0 1 1482 654818186 654819667 0 2665
6 TraesCS6A01G204100 chr1B 88.402 1483 172 0 1 1483 534304611 534306093 0 1786
7 TraesCS6A01G204100 chr4A 98.785 1482 17 1 1 1481 16874250 16872769 0 2636
8 TraesCS6A01G204100 chr7B 98.583 1482 20 1 1 1482 685094462 685095942 0 2619
9 TraesCS6A01G204100 chr5B 95.876 1479 61 0 1 1479 172637657 172639135 0 2394
10 TraesCS6A01G204100 chr7D 92.387 972 69 5 1481 2451 569078787 569079754 0 1380
11 TraesCS6A01G204100 chr7D 91.564 972 74 6 1481 2451 387863291 387862327 0 1334
12 TraesCS6A01G204100 chr3D 92.189 973 70 6 1481 2451 393589327 393588359 0 1371
13 TraesCS6A01G204100 chr3D 91.282 975 80 4 1481 2451 311770016 311770989 0 1325
14 TraesCS6A01G204100 chr3D 91.161 973 78 8 1481 2451 185272299 185273265 0 1314
15 TraesCS6A01G204100 chr4D 91.487 975 74 7 1481 2451 275709568 275710537 0 1332
16 TraesCS6A01G204100 chr4D 91.538 969 79 3 1481 2448 378690771 378691737 0 1332
17 TraesCS6A01G204100 chr5D 91.358 972 82 2 1481 2451 29694039 29695009 0 1328
18 TraesCS6A01G204100 chr6D 90.965 974 78 8 1481 2451 350754777 350753811 0 1303


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 TraesCS6A01G204100 chr6A 353250196 353252648 2452 False 4530 4530 100.000 1 2453 1 chr6A.!!$F1 2452
1 TraesCS6A01G204100 chrUn 38407188 38408669 1481 True 2671 2671 99.190 1 1482 1 chrUn.!!$R1 1481
2 TraesCS6A01G204100 chr3B 35847405 35848886 1481 False 2671 2671 99.190 1 1482 1 chr3B.!!$F1 1481
3 TraesCS6A01G204100 chr3B 29801767 29803247 1480 True 2447 2447 96.489 1 1481 1 chr3B.!!$R1 1480
4 TraesCS6A01G204100 chr6B 489443904 489445385 1481 True 2665 2665 99.123 1 1482 1 chr6B.!!$R1 1481
5 TraesCS6A01G204100 chr1B 654818186 654819667 1481 False 2665 2665 99.123 1 1482 1 chr1B.!!$F2 1481
6 TraesCS6A01G204100 chr1B 534304611 534306093 1482 False 1786 1786 88.402 1 1483 1 chr1B.!!$F1 1482
7 TraesCS6A01G204100 chr4A 16872769 16874250 1481 True 2636 2636 98.785 1 1481 1 chr4A.!!$R1 1480
8 TraesCS6A01G204100 chr7B 685094462 685095942 1480 False 2619 2619 98.583 1 1482 1 chr7B.!!$F1 1481
9 TraesCS6A01G204100 chr5B 172637657 172639135 1478 False 2394 2394 95.876 1 1479 1 chr5B.!!$F1 1478
10 TraesCS6A01G204100 chr7D 569078787 569079754 967 False 1380 1380 92.387 1481 2451 1 chr7D.!!$F1 970
11 TraesCS6A01G204100 chr7D 387862327 387863291 964 True 1334 1334 91.564 1481 2451 1 chr7D.!!$R1 970
12 TraesCS6A01G204100 chr3D 393588359 393589327 968 True 1371 1371 92.189 1481 2451 1 chr3D.!!$R1 970
13 TraesCS6A01G204100 chr3D 311770016 311770989 973 False 1325 1325 91.282 1481 2451 1 chr3D.!!$F2 970
14 TraesCS6A01G204100 chr3D 185272299 185273265 966 False 1314 1314 91.161 1481 2451 1 chr3D.!!$F1 970
15 TraesCS6A01G204100 chr4D 275709568 275710537 969 False 1332 1332 91.487 1481 2451 1 chr4D.!!$F1 970
16 TraesCS6A01G204100 chr4D 378690771 378691737 966 False 1332 1332 91.538 1481 2448 1 chr4D.!!$F2 967
17 TraesCS6A01G204100 chr5D 29694039 29695009 970 False 1328 1328 91.358 1481 2451 1 chr5D.!!$F1 970
18 TraesCS6A01G204100 chr6D 350753811 350754777 966 True 1303 1303 90.965 1481 2451 1 chr6D.!!$R1 970

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
230 231 0.535102 CCGGAAACAGCCACAGTTCT 60.535 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1764 0.036765 GCTGGACGTGTGATGGGTTA 60.037 55.0 0.0 0.0 0.0 2.85 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
230 231 0.535102 CCGGAAACAGCCACAGTTCT 60.535 55.000 0.00 0.00 0.00 3.01
301 302 1.439679 GTTCTTCGAGCCGGACATTT 58.560 50.000 5.05 0.00 0.00 2.32
508 509 3.199946 GGACTGGAAATCTGTATGGTCCA 59.800 47.826 0.00 0.00 40.89 4.02
749 750 5.067805 GTGAATTCAGGTCTCCAAAACAGTT 59.932 40.000 8.80 0.00 0.00 3.16
1104 1106 2.851263 TCAAGGCATGTACCGAAGTT 57.149 45.000 0.00 0.00 33.69 2.66
1539 1542 0.981183 TATTGTCACTCCGGGTTGCT 59.019 50.000 0.00 0.00 0.00 3.91
1646 1649 0.394216 TGAAATCATGGCACTCGGGG 60.394 55.000 0.00 0.00 0.00 5.73
1655 1658 2.435693 GCACTCGGGGCCTAGTGAT 61.436 63.158 30.89 3.70 44.79 3.06
1699 1702 9.624373 AAGTCATAGCAACATCAATCTTAGAAT 57.376 29.630 0.00 0.00 0.00 2.40
1700 1703 9.053840 AGTCATAGCAACATCAATCTTAGAATG 57.946 33.333 0.00 0.00 0.00 2.67
1723 1726 6.199376 TGTAGTGGATACTAGGGATCAAACA 58.801 40.000 8.63 4.85 39.96 2.83
1727 1730 6.324254 AGTGGATACTAGGGATCAAACACTAC 59.676 42.308 11.91 0.00 34.74 2.73
1745 1748 7.224522 ACACTACCAAAACTAACTCGACTAT 57.775 36.000 0.00 0.00 0.00 2.12
1761 1764 8.871629 ACTCGACTATATGGTAAATCTCATCT 57.128 34.615 0.00 0.00 0.00 2.90
1772 1775 6.157820 TGGTAAATCTCATCTAACCCATCACA 59.842 38.462 0.00 0.00 0.00 3.58
1811 1814 1.552792 TGGGATTACTCACGCATGACA 59.447 47.619 0.00 0.00 0.00 3.58
1893 1896 0.676782 CTTCGGAGCCCAAAACGGAT 60.677 55.000 0.00 0.00 36.56 4.18
1898 1901 2.745152 CGGAGCCCAAAACGGATTCTAT 60.745 50.000 0.00 0.00 36.56 1.98
1901 1904 5.070685 GGAGCCCAAAACGGATTCTATATT 58.929 41.667 0.00 0.00 36.56 1.28
1932 1935 1.671742 GAAGAACAGGAGGTGGCGA 59.328 57.895 0.00 0.00 0.00 5.54
1952 1955 0.955178 CGGCTCCGTATCATGAGACT 59.045 55.000 17.78 0.00 34.31 3.24
1973 1978 4.580167 ACTCGATGAATCCTTCTCTCTGAG 59.420 45.833 0.00 0.00 0.00 3.35
2143 2149 9.760660 CTTTATTCCAAAAGTATTCTTCGTGAG 57.239 33.333 0.00 0.00 32.81 3.51
2243 2249 4.700213 ACGGGTTAGTTCCATTCAAATCAG 59.300 41.667 0.00 0.00 0.00 2.90
2273 2279 3.711190 AGAGTCCAAAACAAGGGCAAAAT 59.289 39.130 0.00 0.00 31.65 1.82
2281 2287 4.350368 AACAAGGGCAAAATAGTTTGGG 57.650 40.909 16.64 0.00 43.73 4.12
2286 2292 3.007940 AGGGCAAAATAGTTTGGGAAAGC 59.992 43.478 16.64 1.71 43.73 3.51
2451 2459 7.383300 AGCATTCAAGTTTTCAGCAAAGATTAC 59.617 33.333 0.00 0.00 0.00 1.89
2452 2460 7.617935 GCATTCAAGTTTTCAGCAAAGATTACG 60.618 37.037 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
230 231 4.988540 CAGTATCTTCGTCCAACAGACAAA 59.011 41.667 0.00 0.00 46.69 2.83
508 509 9.282569 GATCTTCATCTTGTTAGGAGCAATAAT 57.717 33.333 0.00 0.00 0.00 1.28
1104 1106 2.158813 GGGTGTGAGAGAACCAGACAAA 60.159 50.000 0.00 0.00 38.27 2.83
1539 1542 5.066893 GTCACCTACTACGTGTTATGATCCA 59.933 44.000 0.00 0.00 32.86 3.41
1646 1649 6.183360 GCTATGCTTAATGCTTATCACTAGGC 60.183 42.308 0.00 0.00 43.37 3.93
1655 1658 7.572523 ATGACTTTGCTATGCTTAATGCTTA 57.427 32.000 0.00 0.00 43.37 3.09
1699 1702 6.097839 GTGTTTGATCCCTAGTATCCACTACA 59.902 42.308 0.00 0.00 36.14 2.74
1700 1703 6.324254 AGTGTTTGATCCCTAGTATCCACTAC 59.676 42.308 9.21 0.00 36.14 2.73
1723 1726 8.411683 CCATATAGTCGAGTTAGTTTTGGTAGT 58.588 37.037 0.00 0.00 0.00 2.73
1727 1730 9.590451 TTTACCATATAGTCGAGTTAGTTTTGG 57.410 33.333 0.00 0.86 0.00 3.28
1745 1748 8.375506 GTGATGGGTTAGATGAGATTTACCATA 58.624 37.037 0.00 0.00 36.41 2.74
1761 1764 0.036765 GCTGGACGTGTGATGGGTTA 60.037 55.000 0.00 0.00 0.00 2.85
1772 1775 1.605058 ATCGTAGGCTTGCTGGACGT 61.605 55.000 0.00 0.00 35.14 4.34
1811 1814 4.338012 TCACCAATTTCATGATGCTCACT 58.662 39.130 0.00 0.00 0.00 3.41
1893 1896 2.637872 CCTCGGGAGGGCAAATATAGAA 59.362 50.000 6.84 0.00 44.87 2.10
1973 1978 1.585297 TCACGTTCGGGGAGAAAAAC 58.415 50.000 0.00 0.00 41.10 2.43
2117 2123 9.760660 CTCACGAAGAATACTTTTGGAATAAAG 57.239 33.333 0.00 0.00 40.23 1.85
2143 2149 2.742589 GTTCTCGGAATGACCTGAAACC 59.257 50.000 0.00 0.00 36.31 3.27
2210 2216 4.955450 TGGAACTAACCCGTACTAATGCTA 59.045 41.667 0.00 0.00 0.00 3.49
2216 2222 5.999205 TTGAATGGAACTAACCCGTACTA 57.001 39.130 0.00 0.00 0.00 1.82
2220 2226 4.658063 TGATTTGAATGGAACTAACCCGT 58.342 39.130 0.00 0.00 0.00 5.28
2243 2249 5.230182 CCTTGTTTTGGACTCTAATTTGCC 58.770 41.667 0.00 0.00 0.00 4.52
2273 2279 5.652014 CCATTGTATCTGCTTTCCCAAACTA 59.348 40.000 0.00 0.00 0.00 2.24
2281 2287 7.658982 TGATATGTCTCCATTGTATCTGCTTTC 59.341 37.037 0.00 0.00 32.29 2.62
2286 2292 7.601886 GGAGTTGATATGTCTCCATTGTATCTG 59.398 40.741 10.67 0.00 44.85 2.90
2373 2379 8.909708 TCAAACAGAGTTTGTAGATGTTTTTG 57.090 30.769 18.70 0.00 40.95 2.44
2382 2388 9.950680 AACAACAATATCAAACAGAGTTTGTAG 57.049 29.630 18.70 10.04 39.73 2.74
2400 2406 6.933521 TGGCTTTACATATTTGCAACAACAAT 59.066 30.769 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.