Multiple sequence alignment - TraesCS6B01G271300

Loading Multiple Alignment...

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 TraesCS6B01G271300 chr6B 100.000 2453 0 0 1 2453 489445385 489442933 0.000000e+00 4530.0
1 TraesCS6B01G271300 chr6B 83.491 212 31 4 1483 1692 622015155 622014946 6.920000e-46 195.0
2 TraesCS6B01G271300 chr6B 85.484 186 24 3 1509 1692 621582045 621582229 8.950000e-45 191.0
3 TraesCS6B01G271300 chr6B 91.304 46 3 1 1758 1802 152708707 152708662 7.320000e-06 62.1
4 TraesCS6B01G271300 chrUn 99.326 1483 10 0 1 1483 38408669 38407187 0.000000e+00 2684.0
5 TraesCS6B01G271300 chr3B 99.325 1482 10 0 1 1482 35847405 35848886 0.000000e+00 2682.0
6 TraesCS6B01G271300 chr3B 96.624 1481 50 0 1 1481 29803247 29801767 0.000000e+00 2459.0
7 TraesCS6B01G271300 chr3B 86.275 102 12 2 1591 1692 88489246 88489147 2.580000e-20 110.0
8 TraesCS6B01G271300 chr3B 88.298 94 7 4 1599 1692 600469062 600468973 2.580000e-20 110.0
9 TraesCS6B01G271300 chr1B 99.191 1484 12 0 1 1484 654818186 654819669 0.000000e+00 2675.0
10 TraesCS6B01G271300 chr1B 88.529 1482 170 0 1 1482 534304611 534306092 0.000000e+00 1796.0
11 TraesCS6B01G271300 chr6A 99.123 1482 13 0 1 1482 353250196 353251677 0.000000e+00 2665.0
12 TraesCS6B01G271300 chr6A 89.034 766 75 9 1692 2452 470565716 470566477 0.000000e+00 941.0
13 TraesCS6B01G271300 chr4A 98.853 1482 16 1 1 1481 16874250 16872769 0.000000e+00 2641.0
14 TraesCS6B01G271300 chr7B 98.785 1482 17 1 1 1482 685094462 685095942 0.000000e+00 2636.0
15 TraesCS6B01G271300 chr7B 88.235 102 10 2 1591 1692 634169847 634169946 1.190000e-23 121.0
16 TraesCS6B01G271300 chr5B 96.078 1479 58 0 1 1479 172637657 172639135 0.000000e+00 2410.0
17 TraesCS6B01G271300 chr6D 88.163 980 83 20 1483 2453 331539807 331540762 0.000000e+00 1136.0
18 TraesCS6B01G271300 chr4B 83.962 212 30 4 1483 1692 462737502 462737293 1.490000e-47 200.0
19 TraesCS6B01G271300 chr7D 87.640 89 9 2 1605 1693 181642236 181642150 4.320000e-18 102.0


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 TraesCS6B01G271300 chr6B 489442933 489445385 2452 True 4530 4530 100.000 1 2453 1 chr6B.!!$R2 2452
1 TraesCS6B01G271300 chrUn 38407187 38408669 1482 True 2684 2684 99.326 1 1483 1 chrUn.!!$R1 1482
2 TraesCS6B01G271300 chr3B 35847405 35848886 1481 False 2682 2682 99.325 1 1482 1 chr3B.!!$F1 1481
3 TraesCS6B01G271300 chr3B 29801767 29803247 1480 True 2459 2459 96.624 1 1481 1 chr3B.!!$R1 1480
4 TraesCS6B01G271300 chr1B 654818186 654819669 1483 False 2675 2675 99.191 1 1484 1 chr1B.!!$F2 1483
5 TraesCS6B01G271300 chr1B 534304611 534306092 1481 False 1796 1796 88.529 1 1482 1 chr1B.!!$F1 1481
6 TraesCS6B01G271300 chr6A 353250196 353251677 1481 False 2665 2665 99.123 1 1482 1 chr6A.!!$F1 1481
7 TraesCS6B01G271300 chr6A 470565716 470566477 761 False 941 941 89.034 1692 2452 1 chr6A.!!$F2 760
8 TraesCS6B01G271300 chr4A 16872769 16874250 1481 True 2641 2641 98.853 1 1481 1 chr4A.!!$R1 1480
9 TraesCS6B01G271300 chr7B 685094462 685095942 1480 False 2636 2636 98.785 1 1482 1 chr7B.!!$F2 1481
10 TraesCS6B01G271300 chr5B 172637657 172639135 1478 False 2410 2410 96.078 1 1479 1 chr5B.!!$F1 1478
11 TraesCS6B01G271300 chr6D 331539807 331540762 955 False 1136 1136 88.163 1483 2453 1 chr6D.!!$F1 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
1107 1109 3.007074 TCAAGGCATGTACCGAAGTGTTA 59.993 43.478 0.0 0.0 33.69 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 2169 0.036671 GGACTGGAACCTGGGTAACG 60.037 60.0 0.0 0.0 37.6 3.18 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
1107 1109 3.007074 TCAAGGCATGTACCGAAGTGTTA 59.993 43.478 0.00 0.00 33.69 2.41
1131 1133 2.291346 TGGTTCTCTCACACCCGAGATA 60.291 50.000 0.00 0.00 41.15 1.98
1420 1422 1.347707 TCAATTCTGCTCCGGAGTGTT 59.652 47.619 31.43 16.16 0.00 3.32
1611 1619 7.899178 AACTTTTAAACCAAACACCTCAAAG 57.101 32.000 0.00 0.00 0.00 2.77
1613 1621 8.124808 ACTTTTAAACCAAACACCTCAAAGTA 57.875 30.769 0.00 0.00 31.74 2.24
1617 1625 9.945904 TTTAAACCAAACACCTCAAAGTATTTT 57.054 25.926 0.00 0.00 35.03 1.82
1665 1673 8.331931 ACCACAATATTCCTATAAGAACTCCA 57.668 34.615 0.00 0.00 0.00 3.86
1701 1709 2.095263 CCAAACGCACCCTGAACAATAG 60.095 50.000 0.00 0.00 0.00 1.73
1827 1836 2.906354 ACAATAGACCATCACGCTTCC 58.094 47.619 0.00 0.00 0.00 3.46
1833 1842 1.330655 ACCATCACGCTTCCGGAGAT 61.331 55.000 3.34 0.00 39.22 2.75
1844 1853 0.105194 TCCGGAGATAGGGATGCCAA 60.105 55.000 5.86 0.00 0.00 4.52
1845 1854 0.035458 CCGGAGATAGGGATGCCAAC 59.965 60.000 5.86 0.00 0.00 3.77
1849 1858 2.708325 GGAGATAGGGATGCCAACTTCT 59.292 50.000 5.86 1.36 0.00 2.85
1895 1904 1.202428 GGCGACGAATTCTAGGCTTCT 60.202 52.381 0.00 0.00 0.00 2.85
1902 1911 4.710375 ACGAATTCTAGGCTTCTGAAGGTA 59.290 41.667 18.38 0.00 0.00 3.08
1931 1940 1.689273 GTCGTCAGATAGGGGAGCAAT 59.311 52.381 0.00 0.00 0.00 3.56
1950 1963 4.070716 CAATGAGAACAAGAAGCCTCACT 58.929 43.478 0.00 0.00 38.32 3.41
1977 1990 0.028505 CAATGTAGCTCATGGTGCGC 59.971 55.000 0.00 0.00 36.81 6.09
2021 2034 2.684001 TAGATGCCGACGGTGAAAAT 57.316 45.000 16.73 1.93 0.00 1.82
2156 2169 0.944386 ATGACAGTGCACACGAAACC 59.056 50.000 21.04 1.23 36.20 3.27
2220 2234 7.178573 CCCTACTCCTACTAGATTGATCATGA 58.821 42.308 0.00 0.00 0.00 3.07
2249 2263 1.480954 TCTCGTATGAGGAGGTTTGGC 59.519 52.381 12.06 0.00 42.79 4.52
2266 2280 1.552792 TGGCGTACAATGGTGAGATCA 59.447 47.619 0.00 0.00 0.00 2.92
2294 2309 6.712549 TGAACACGTAATGTATCGAGACTAG 58.287 40.000 12.03 1.18 42.31 2.57
2310 2325 7.459234 TCGAGACTAGGATTATCATCTAACCA 58.541 38.462 0.00 0.00 0.00 3.67
2334 2349 5.320549 AGGCCGTGTTTATATAGGATACG 57.679 43.478 0.00 9.17 46.39 3.06
2337 2352 5.335897 GGCCGTGTTTATATAGGATACGTGA 60.336 44.000 0.00 0.00 46.39 4.35
2362 2377 6.183361 ACCTAGGGTTTAAATGGGTTTAGGTT 60.183 38.462 14.81 0.00 31.81 3.50
2438 2454 0.763652 AGTAGATAGAGGCGTCCCGA 59.236 55.000 2.06 0.00 35.76 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1010 1012 4.581824 AGTCATGAAATAAAGCCGCATCAT 59.418 37.500 0.00 0.00 0.00 2.45
1107 1109 0.898320 CGGGTGTGAGAGAACCAGAT 59.102 55.000 0.00 0.00 38.27 2.90
1420 1422 2.912956 AGTCATACAAAGCCTCCTGGAA 59.087 45.455 0.00 0.00 34.57 3.53
1484 1486 1.884235 AACCAAGCCAAGAGAAGTCG 58.116 50.000 0.00 0.00 0.00 4.18
1513 1515 1.580059 TTAGAAAGAGGCCCGACCAT 58.420 50.000 0.00 0.00 43.14 3.55
1581 1588 8.578448 AGGTGTTTGGTTTAAAAGTTACAGTA 57.422 30.769 0.00 0.00 0.00 2.74
1584 1591 7.463961 TGAGGTGTTTGGTTTAAAAGTTACA 57.536 32.000 0.00 0.00 0.00 2.41
1589 1596 9.594478 AATACTTTGAGGTGTTTGGTTTAAAAG 57.406 29.630 0.00 0.00 0.00 2.27
1658 1666 5.010617 TGGGAGCAAAGTATTTTTGGAGTTC 59.989 40.000 2.28 0.00 35.03 3.01
1665 1673 4.055360 GCGTTTGGGAGCAAAGTATTTTT 58.945 39.130 0.00 0.00 35.03 1.94
1675 1683 3.884774 AGGGTGCGTTTGGGAGCA 61.885 61.111 0.00 0.00 41.55 4.26
1798 1807 5.333798 CGTGATGGTCTATTGTTCGTGTTTT 60.334 40.000 0.00 0.00 0.00 2.43
1827 1836 1.051812 AGTTGGCATCCCTATCTCCG 58.948 55.000 0.00 0.00 0.00 4.63
1844 1853 2.373502 GGCTAAGCCCATATCCAGAAGT 59.626 50.000 0.00 0.00 44.06 3.01
1845 1854 3.064900 GGCTAAGCCCATATCCAGAAG 57.935 52.381 0.00 0.00 44.06 2.85
1902 1911 4.208746 CCCTATCTGACGACTAGGTTCTT 58.791 47.826 0.00 0.00 31.82 2.52
1914 1923 2.968574 TCTCATTGCTCCCCTATCTGAC 59.031 50.000 0.00 0.00 0.00 3.51
1918 1927 3.845781 TGTTCTCATTGCTCCCCTATC 57.154 47.619 0.00 0.00 0.00 2.08
1931 1940 2.808202 GCAGTGAGGCTTCTTGTTCTCA 60.808 50.000 0.00 0.00 34.34 3.27
1950 1963 0.605050 TGAGCTACATTGCCAACGCA 60.605 50.000 0.00 0.00 45.49 5.24
2040 2053 1.204467 CATTTTGCACAGGCCGGTAAT 59.796 47.619 8.66 1.73 40.13 1.89
2115 2128 2.867472 CCTTTTGGCTACACGCGG 59.133 61.111 12.47 1.27 40.44 6.46
2156 2169 0.036671 GGACTGGAACCTGGGTAACG 60.037 60.000 0.00 0.00 37.60 3.18
2216 2229 7.989826 TCCTCATACGAGACATATACATCATG 58.010 38.462 0.00 0.00 42.34 3.07
2220 2234 6.486056 ACCTCCTCATACGAGACATATACAT 58.514 40.000 0.00 0.00 42.34 2.29
2229 2243 1.480954 GCCAAACCTCCTCATACGAGA 59.519 52.381 0.00 0.00 42.34 4.04
2249 2263 5.831997 TCATACTGATCTCACCATTGTACG 58.168 41.667 0.00 0.00 0.00 3.67
2266 2280 7.012138 AGTCTCGATACATTACGTGTTCATACT 59.988 37.037 0.00 0.00 42.29 2.12
2294 2309 5.104900 ACGGCCTATGGTTAGATGATAATCC 60.105 44.000 0.00 0.00 0.00 3.01
2310 2325 6.604795 ACGTATCCTATATAAACACGGCCTAT 59.395 38.462 0.00 0.00 32.52 2.57
2334 2349 4.311520 ACCCATTTAAACCCTAGGTCAC 57.688 45.455 8.29 0.00 33.12 3.67
2337 2352 5.316722 ACCTAAACCCATTTAAACCCTAGGT 59.683 40.000 8.29 0.00 37.65 3.08
2362 2377 0.187117 TCTCCAAACAACCATGGCCA 59.813 50.000 13.04 8.56 36.62 5.36


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

AutoCloner maintained by Alex Coulton.