Multiple sequence alignment - TraesCS6A01G054600

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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 TraesCS6A01G054600 chr6A 100.000 2705 0 0 1 2705 28428457 28425753 0.000000e+00 4996.0
1 TraesCS6A01G054600 chr6D 94.911 1906 87 4 1 1898 27115462 27113559 0.000000e+00 2974.0
2 TraesCS6A01G054600 chr6D 99.150 353 3 0 2353 2705 27113565 27113213 1.060000e-178 636.0
3 TraesCS6A01G054600 chr6B 89.244 1906 172 14 1 1898 49417191 49419071 0.000000e+00 2353.0
4 TraesCS6A01G054600 chr6B 88.598 1912 175 20 1 1898 49761097 49759215 0.000000e+00 2283.0
5 TraesCS6A01G054600 chr6B 92.676 355 22 4 2353 2705 49419064 49419416 2.400000e-140 508.0
6 TraesCS6A01G054600 chr6B 92.676 355 22 4 2353 2705 49759221 49758869 2.400000e-140 508.0
7 TraesCS6A01G054600 chr5A 97.391 460 12 0 1895 2354 556733626 556734085 0.000000e+00 784.0
8 TraesCS6A01G054600 chr4A 94.658 468 24 1 1892 2359 57729655 57729189 0.000000e+00 725.0
9 TraesCS6A01G054600 chr5D 96.013 301 12 0 2056 2356 119378812 119379112 8.700000e-135 490.0
10 TraesCS6A01G054600 chr5D 94.410 161 9 0 1893 2053 119378597 119378757 5.780000e-62 248.0
11 TraesCS6A01G054600 chr7B 93.115 305 17 4 2056 2359 392820450 392820751 6.870000e-121 444.0
12 TraesCS6A01G054600 chr3A 87.059 85 11 0 2056 2140 688881952 688881868 2.220000e-16 97.1


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 TraesCS6A01G054600 chr6A 28425753 28428457 2704 True 4996.0 4996 100.0000 1 2705 1 chr6A.!!$R1 2704
1 TraesCS6A01G054600 chr6D 27113213 27115462 2249 True 1805.0 2974 97.0305 1 2705 2 chr6D.!!$R1 2704
2 TraesCS6A01G054600 chr6B 49417191 49419416 2225 False 1430.5 2353 90.9600 1 2705 2 chr6B.!!$F1 2704
3 TraesCS6A01G054600 chr6B 49758869 49761097 2228 True 1395.5 2283 90.6370 1 2705 2 chr6B.!!$R1 2704
4 TraesCS6A01G054600 chr5D 119378597 119379112 515 False 369.0 490 95.2115 1893 2356 2 chr5D.!!$F1 463

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
281 289 1.547223 CCCCAGCCATCTCATTCATCC 60.547 57.143 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 2221 0.178301 GGGACGAAACCCCATCTCTC 59.822 60.0 0.0 0.0 43.81 3.2 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
281 289 1.547223 CCCCAGCCATCTCATTCATCC 60.547 57.143 0.00 0.00 0.00 3.51
416 424 3.896272 TGATCATCAGGAGATCAGTGAGG 59.104 47.826 0.00 0.00 44.98 3.86
430 438 2.762887 CAGTGAGGAGAGCAATGGACTA 59.237 50.000 0.00 0.00 0.00 2.59
657 665 5.361427 GGAGGCCATAGAGAAGTTAGAAAC 58.639 45.833 5.01 0.00 0.00 2.78
881 889 4.767928 AGGTACCGGTTTTTGCAATAATCA 59.232 37.500 15.04 0.00 0.00 2.57
997 1012 7.432869 TGATAATGTTTTCAGTTCAACAAGGG 58.567 34.615 0.00 0.00 36.50 3.95
1077 1092 6.050454 CAAGCATTGCAACAAATTCTCAAA 57.950 33.333 11.91 0.00 40.39 2.69
1086 1101 6.310956 TGCAACAAATTCTCAAAGACAAACTG 59.689 34.615 0.00 0.00 0.00 3.16
1088 1103 6.773976 ACAAATTCTCAAAGACAAACTGGA 57.226 33.333 0.00 0.00 0.00 3.86
1091 1106 2.833794 TCTCAAAGACAAACTGGACCG 58.166 47.619 0.00 0.00 0.00 4.79
1140 1155 9.657419 GATGATGTTTGGGAAGATAACAAAATT 57.343 29.630 0.00 0.00 36.05 1.82
1164 1179 6.371595 AGTGAATGGGAAAATTTAATGGCA 57.628 33.333 0.00 0.00 0.00 4.92
1263 1278 5.046950 AGGTGTGATGAGAAGTAGAAAGGAC 60.047 44.000 0.00 0.00 0.00 3.85
1319 1334 8.077991 TGAAAATTGTATGCTCTTCAAGAAGTG 58.922 33.333 9.44 8.34 39.38 3.16
1328 1343 4.543692 CTCTTCAAGAAGTGTGCATTTGG 58.456 43.478 9.44 0.00 39.38 3.28
1339 1354 3.494251 GTGTGCATTTGGTGGTTTGAATC 59.506 43.478 0.00 0.00 0.00 2.52
1363 1378 4.813161 CGGAAGATTATGCACATCTCTTGT 59.187 41.667 10.07 0.00 39.91 3.16
1366 1381 6.018098 GGAAGATTATGCACATCTCTTGTCAG 60.018 42.308 10.07 0.00 36.00 3.51
1410 1425 0.472471 TTCGAGGCTGTCCTTTGGTT 59.528 50.000 0.00 0.00 44.46 3.67
1436 1451 0.464373 ATTGCAGGTGGCCATCTACG 60.464 55.000 20.77 8.82 43.89 3.51
1437 1452 1.836999 TTGCAGGTGGCCATCTACGT 61.837 55.000 20.77 0.00 43.89 3.57
1448 1463 3.493503 GGCCATCTACGTAGCAATGTAAC 59.506 47.826 18.00 8.60 0.00 2.50
1453 1468 6.144563 CCATCTACGTAGCAATGTAACTGATG 59.855 42.308 18.00 11.01 0.00 3.07
1458 1473 4.259970 CGTAGCAATGTAACTGATGAGCAC 60.260 45.833 0.00 0.00 0.00 4.40
1465 1480 3.578282 TGTAACTGATGAGCACTGGAAGA 59.422 43.478 0.00 0.00 37.43 2.87
1470 1485 4.284490 ACTGATGAGCACTGGAAGAACTTA 59.716 41.667 0.00 0.00 37.43 2.24
1471 1486 4.825422 TGATGAGCACTGGAAGAACTTAG 58.175 43.478 0.00 0.00 37.43 2.18
1473 1488 4.527509 TGAGCACTGGAAGAACTTAGAG 57.472 45.455 0.00 0.00 37.43 2.43
1503 1518 8.514594 CAATTAGAACATTTAGAAGGAAGCACA 58.485 33.333 0.00 0.00 0.00 4.57
1537 1552 2.288213 ACAACTGTTCTTCGATCGAGCA 60.288 45.455 18.54 14.11 0.00 4.26
1554 1569 3.430790 CGAGCAACCATCATCTACCTGAA 60.431 47.826 0.00 0.00 0.00 3.02
1557 1572 3.624861 GCAACCATCATCTACCTGAACAG 59.375 47.826 0.00 0.00 0.00 3.16
1599 1614 8.494433 AGATACTGTAGCATATTTCCAAAAGGA 58.506 33.333 5.81 0.00 0.00 3.36
1602 1617 6.375455 ACTGTAGCATATTTCCAAAAGGACAG 59.625 38.462 0.00 0.00 36.39 3.51
1675 1690 0.467290 GCAAACTGAAGGTGGGACCA 60.467 55.000 0.00 0.00 41.95 4.02
1697 1712 0.252881 AGGCCAGAAGACATGGGAGA 60.253 55.000 5.01 0.00 38.33 3.71
1704 1719 5.630069 GCCAGAAGACATGGGAGAAAGATAA 60.630 44.000 0.00 0.00 38.33 1.75
1709 1724 6.705863 AGACATGGGAGAAAGATAATTTGC 57.294 37.500 0.00 0.00 0.00 3.68
1710 1725 6.189859 AGACATGGGAGAAAGATAATTTGCA 58.810 36.000 0.00 0.00 0.00 4.08
1789 1804 7.761704 CAGAAATACAGCACAGAGTACTATGTT 59.238 37.037 20.22 8.92 31.96 2.71
1790 1805 7.761704 AGAAATACAGCACAGAGTACTATGTTG 59.238 37.037 20.22 18.33 37.68 3.33
1882 1897 5.121611 TGGTTTTCTGCATCATAAGTGTACG 59.878 40.000 0.00 0.00 0.00 3.67
1910 1925 2.094545 CACTTAGGGCTCATTTGGTTGC 60.095 50.000 0.00 0.00 0.00 4.17
1914 1929 0.529378 GGGCTCATTTGGTTGCTGAG 59.471 55.000 0.00 0.00 39.50 3.35
1937 1952 0.404426 GGAAAACCCAGGGTAGCAGT 59.596 55.000 13.17 0.00 33.12 4.40
1948 1963 1.668101 GGTAGCAGTCACCGGGAGAG 61.668 65.000 6.32 0.00 0.00 3.20
1958 1973 2.027192 TCACCGGGAGAGATTTTTCCTG 60.027 50.000 6.32 0.00 39.19 3.86
1968 1983 2.494870 AGATTTTTCCTGTGCTCATGGC 59.505 45.455 0.00 0.00 42.22 4.40
2028 2043 2.597340 CATCACGGGGAAGGGCAT 59.403 61.111 0.00 0.00 0.00 4.40
2043 2058 3.242011 AGGGCATGGAAGTTTGACAAAT 58.758 40.909 3.49 0.00 0.00 2.32
2053 2068 3.686016 AGTTTGACAAATATCGTGGGCT 58.314 40.909 3.49 0.00 0.00 5.19
2073 2140 1.679305 GAGGGAGCAGACGAGGTCA 60.679 63.158 0.00 0.00 37.74 4.02
2088 2155 1.005215 AGGTCATAGGCTTTGCTGCTT 59.995 47.619 0.00 0.00 0.00 3.91
2124 2191 3.758133 GAGGAGGCGAGGGGATCCA 62.758 68.421 15.23 0.00 34.08 3.41
2183 2250 3.072486 TTTCGTCCCCGATCTCCGC 62.072 63.158 0.00 0.00 43.80 5.54
2241 2308 1.841556 GCCAGGATATCCCCGTCCA 60.842 63.158 18.56 0.00 36.96 4.02
2434 2501 0.701303 GAGTTTGCGTACACTCGTCG 59.299 55.000 4.03 0.00 30.51 5.12
2550 2617 2.551032 GGTAACCAAGTTCTGTTTCCCG 59.449 50.000 0.00 0.00 0.00 5.14
2565 2632 4.035909 TGTTTCCCGAAAGAAGTTGCTAAC 59.964 41.667 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
281 289 3.941483 AGATAACCGAATGCCTTGTTCAG 59.059 43.478 0.00 0.00 0.00 3.02
416 424 2.430332 ACTCAGCTAGTCCATTGCTCTC 59.570 50.000 0.00 0.00 37.96 3.20
469 477 1.558294 TCATCAAGTGCATCCTCAGCT 59.442 47.619 0.00 0.00 0.00 4.24
657 665 2.489329 CCACCCACATCTTTAGCAACAG 59.511 50.000 0.00 0.00 0.00 3.16
727 735 4.563184 GTCTGGTATACACTTCTTTCAGCG 59.437 45.833 5.01 0.00 0.00 5.18
855 863 2.054232 TGCAAAAACCGGTACCTGAA 57.946 45.000 8.00 0.00 0.00 3.02
881 889 4.731313 AGGGTTGTCTTTCTCCAATTCT 57.269 40.909 0.00 0.00 0.00 2.40
997 1012 6.151817 ACTGCCTCCAAGATCTTTTTCATTAC 59.848 38.462 4.86 0.00 0.00 1.89
1054 1069 5.660629 TTGAGAATTTGTTGCAATGCTTG 57.339 34.783 6.82 0.00 0.00 4.01
1068 1083 4.275936 CGGTCCAGTTTGTCTTTGAGAATT 59.724 41.667 0.00 0.00 0.00 2.17
1077 1092 4.141779 ACTTTCTTACGGTCCAGTTTGTCT 60.142 41.667 0.00 0.00 0.00 3.41
1086 1101 3.041508 AGCAGAACTTTCTTACGGTCC 57.958 47.619 0.00 0.00 34.74 4.46
1088 1103 6.369065 CAGAATAAGCAGAACTTTCTTACGGT 59.631 38.462 0.00 0.00 39.97 4.83
1091 1106 7.907214 TCCAGAATAAGCAGAACTTTCTTAC 57.093 36.000 0.00 0.00 39.97 2.34
1140 1155 7.327214 GTGCCATTAAATTTTCCCATTCACTA 58.673 34.615 0.00 0.00 0.00 2.74
1164 1179 2.224670 TGTTTGGATACTCCGCAAAGGT 60.225 45.455 0.00 0.00 40.17 3.50
1301 1316 3.748048 TGCACACTTCTTGAAGAGCATAC 59.252 43.478 16.21 2.78 0.00 2.39
1319 1334 3.066380 GGATTCAAACCACCAAATGCAC 58.934 45.455 0.00 0.00 0.00 4.57
1328 1343 5.733373 GCATAATCTTCCGGATTCAAACCAC 60.733 44.000 4.15 0.00 42.96 4.16
1339 1354 4.000331 AGAGATGTGCATAATCTTCCGG 58.000 45.455 14.12 0.00 34.50 5.14
1394 1409 2.561478 TGTAACCAAAGGACAGCCTC 57.439 50.000 0.00 0.00 46.28 4.70
1410 1425 1.202989 TGGCCACCTGCAATCTTTGTA 60.203 47.619 0.00 0.00 43.89 2.41
1436 1451 4.872691 AGTGCTCATCAGTTACATTGCTAC 59.127 41.667 0.00 0.00 0.00 3.58
1437 1452 4.872124 CAGTGCTCATCAGTTACATTGCTA 59.128 41.667 0.00 0.00 0.00 3.49
1448 1463 3.331478 AGTTCTTCCAGTGCTCATCAG 57.669 47.619 0.00 0.00 0.00 2.90
1453 1468 4.461081 TCTCTCTAAGTTCTTCCAGTGCTC 59.539 45.833 0.00 0.00 0.00 4.26
1458 1473 8.744652 TCTAATTGTCTCTCTAAGTTCTTCCAG 58.255 37.037 0.00 0.00 0.00 3.86
1470 1485 9.883142 CCTTCTAAATGTTCTAATTGTCTCTCT 57.117 33.333 0.00 0.00 0.00 3.10
1471 1486 9.877178 TCCTTCTAAATGTTCTAATTGTCTCTC 57.123 33.333 0.00 0.00 0.00 3.20
1503 1518 5.784177 AGAACAGTTGTGACGATAACATCT 58.216 37.500 0.00 0.00 0.00 2.90
1537 1552 5.248640 CAACTGTTCAGGTAGATGATGGTT 58.751 41.667 4.82 0.00 0.00 3.67
1554 1569 4.981806 TCTAAAACAAAGCTGCAACTGT 57.018 36.364 1.02 0.00 0.00 3.55
1557 1572 6.438763 ACAGTATCTAAAACAAAGCTGCAAC 58.561 36.000 1.02 0.00 0.00 4.17
1599 1614 8.652290 ACTATGTCTTCCTTCTTAAACTTCTGT 58.348 33.333 0.00 0.00 0.00 3.41
1602 1617 9.490379 TTCACTATGTCTTCCTTCTTAAACTTC 57.510 33.333 0.00 0.00 0.00 3.01
1675 1690 1.428912 TCCCATGTCTTCTGGCCTTTT 59.571 47.619 3.32 0.00 32.08 2.27
1697 1712 4.248058 GCCAACTGCTGCAAATTATCTTT 58.752 39.130 3.02 0.00 36.87 2.52
1704 1719 1.042229 TCTTGCCAACTGCTGCAAAT 58.958 45.000 3.02 0.00 45.94 2.32
1709 1724 1.677576 TGACTTTCTTGCCAACTGCTG 59.322 47.619 0.00 0.00 42.00 4.41
1710 1725 2.057137 TGACTTTCTTGCCAACTGCT 57.943 45.000 0.00 0.00 42.00 4.24
1882 1897 4.489306 AATGAGCCCTAAGTGTCTAACC 57.511 45.455 0.00 0.00 0.00 2.85
1937 1952 2.027192 CAGGAAAAATCTCTCCCGGTGA 60.027 50.000 0.00 0.00 31.50 4.02
1948 1963 2.884827 GCCATGAGCACAGGAAAAATC 58.115 47.619 0.00 0.00 42.97 2.17
2028 2043 4.457603 CCCACGATATTTGTCAAACTTCCA 59.542 41.667 0.00 0.00 0.00 3.53
2043 2058 1.686325 GCTCCCTCAAGCCCACGATA 61.686 60.000 0.00 0.00 36.22 2.92
2053 2068 1.228894 ACCTCGTCTGCTCCCTCAA 60.229 57.895 0.00 0.00 0.00 3.02
2073 2140 2.238144 TCTCTCAAGCAGCAAAGCCTAT 59.762 45.455 0.00 0.00 34.23 2.57
2088 2155 0.541998 TCCAACGCCTTCCTCTCTCA 60.542 55.000 0.00 0.00 0.00 3.27
2124 2191 1.068741 AGCAAACTTCCTTCGTCTCGT 59.931 47.619 0.00 0.00 0.00 4.18
2154 2221 0.178301 GGGACGAAACCCCATCTCTC 59.822 60.000 0.00 0.00 43.81 3.20
2178 2245 0.721718 GAAAATCCACGACTGCGGAG 59.278 55.000 0.85 0.85 43.17 4.63
2183 2250 2.868253 GGGGGAAAATCCACGACTG 58.132 57.895 0.00 0.00 42.21 3.51
2202 2269 3.575630 CCCAATCCACGACATATCTACG 58.424 50.000 0.00 0.00 0.00 3.51
2205 2272 1.072331 GGCCCAATCCACGACATATCT 59.928 52.381 0.00 0.00 0.00 1.98
2241 2308 2.887152 GCAGTCAGTTTGGAAGTCCATT 59.113 45.455 0.00 0.00 46.97 3.16
2261 2328 1.302271 GGACCCCGGATTATTCGGC 60.302 63.158 6.38 0.00 45.60 5.54
2434 2501 5.819379 TGCTGACATGATAAGAATCTTCCAC 59.181 40.000 0.00 0.00 32.93 4.02
2565 2632 6.758886 AGAAAGAGATATAACGAAGGTGCTTG 59.241 38.462 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.