Multiple sequence alignment - TraesCS1D01G074200

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 TraesCS1D01G074200 chr1D 100.000 2327 0 0 1 2327 55609314 55611640 0.000000e+00 4298.0
1 TraesCS1D01G074200 chr1D 97.048 813 21 2 1517 2327 55545820 55546631 0.000000e+00 1365.0
2 TraesCS1D01G074200 chr1D 94.784 671 24 6 1 666 55545137 55545801 0.000000e+00 1035.0
3 TraesCS1D01G074200 chr4A 86.214 1973 168 63 1 1902 556780624 556782563 0.000000e+00 2041.0
4 TraesCS1D01G074200 chr4A 96.405 306 10 1 1318 1622 556804441 556804746 9.600000e-139 503.0
5 TraesCS1D01G074200 chr4A 90.066 302 20 7 2024 2324 556782929 556783221 1.300000e-102 383.0
6 TraesCS1D01G074200 chr4A 92.636 258 15 4 1649 1902 556804869 556805126 3.650000e-98 368.0
7 TraesCS1D01G074200 chr4A 83.758 314 23 12 2024 2327 556805492 556805787 2.950000e-69 272.0
8 TraesCS1D01G074200 chr4A 85.714 217 21 7 2116 2327 556783557 556783768 1.080000e-53 220.0
9 TraesCS1D01G074200 chr4A 98.182 110 2 0 1899 2008 556782664 556782773 2.360000e-45 193.0
10 TraesCS1D01G074200 chr4A 96.364 110 4 0 1899 2008 556805227 556805336 5.110000e-42 182.0
11 TraesCS1D01G074200 chr4A 100.000 34 0 0 1609 1642 738080612 738080645 1.930000e-06 63.9
12 TraesCS1D01G074200 chr4B 87.993 1674 139 26 177 1807 62869982 62868328 0.000000e+00 1921.0
13 TraesCS1D01G074200 chr4B 85.965 1767 143 51 88 1808 61522528 61524235 0.000000e+00 1792.0
14 TraesCS1D01G074200 chr4B 91.323 1187 64 10 654 1808 61536129 61537308 0.000000e+00 1585.0
15 TraesCS1D01G074200 chr4B 90.863 1193 71 8 654 1808 61324824 61323632 0.000000e+00 1565.0
16 TraesCS1D01G074200 chr4B 84.281 967 108 22 218 1183 62057043 62056120 0.000000e+00 904.0
17 TraesCS1D01G074200 chr4B 80.260 1155 142 58 391 1524 140437020 140435931 0.000000e+00 791.0
18 TraesCS1D01G074200 chr4B 78.369 1373 179 67 177 1524 139940990 139939711 0.000000e+00 782.0
19 TraesCS1D01G074200 chr4B 78.638 1175 157 62 391 1524 140234111 140232990 0.000000e+00 693.0
20 TraesCS1D01G074200 chr4B 80.126 956 118 48 1 940 61888759 61889658 0.000000e+00 647.0
21 TraesCS1D01G074200 chr4B 80.022 916 110 50 1 899 62434363 62433504 5.500000e-171 610.0
22 TraesCS1D01G074200 chr4B 87.828 419 30 12 171 587 61325235 61324836 2.710000e-129 472.0
23 TraesCS1D01G074200 chr4B 94.737 304 10 4 2024 2327 139938936 139938639 3.500000e-128 468.0
24 TraesCS1D01G074200 chr4B 95.472 265 7 4 2067 2327 139937440 139937177 3.580000e-113 418.0
25 TraesCS1D01G074200 chr4B 88.235 204 14 7 2127 2327 61494320 61494124 3.870000e-58 235.0
26 TraesCS1D01G074200 chr4B 84.878 205 21 6 2127 2327 62867885 62867687 5.070000e-47 198.0
27 TraesCS1D01G074200 chr4B 94.690 113 6 0 1899 2011 139939200 139939088 2.380000e-40 176.0
28 TraesCS1D01G074200 chr4B 93.805 113 7 0 1899 2011 61323358 61323246 1.110000e-38 171.0
29 TraesCS1D01G074200 chr4B 94.545 110 6 0 1899 2008 61524509 61524618 1.110000e-38 171.0
30 TraesCS1D01G074200 chr4B 94.545 110 6 0 1899 2008 61537582 61537691 1.110000e-38 171.0
31 TraesCS1D01G074200 chr4B 93.805 113 7 0 1899 2011 62432476 62432364 1.110000e-38 171.0
32 TraesCS1D01G074200 chr4D 93.107 943 51 6 658 1596 43151450 43150518 0.000000e+00 1369.0
33 TraesCS1D01G074200 chr4D 80.996 1626 185 75 1 1596 43077762 43076231 0.000000e+00 1177.0
34 TraesCS1D01G074200 chr4D 95.570 158 7 0 1649 1806 43150378 43150221 1.070000e-63 254.0
35 TraesCS1D01G074200 chr4D 95.000 160 8 0 1649 1808 43076029 43075870 3.840000e-63 252.0
36 TraesCS1D01G074200 chr4D 87.685 203 16 4 2127 2327 43149762 43149567 6.470000e-56 228.0
37 TraesCS1D01G074200 chr4D 93.805 113 7 0 1899 2011 43075578 43075466 1.110000e-38 171.0
38 TraesCS1D01G074200 chr3D 92.500 40 3 0 1606 1645 552610859 552610820 8.980000e-05 58.4


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 TraesCS1D01G074200 chr1D 55609314 55611640 2326 False 4298.000000 4298 100.000000 1 2327 1 chr1D.!!$F1 2326
1 TraesCS1D01G074200 chr1D 55545137 55546631 1494 False 1200.000000 1365 95.916000 1 2327 2 chr1D.!!$F2 2326
2 TraesCS1D01G074200 chr4A 556780624 556783768 3144 False 709.250000 2041 90.044000 1 2327 4 chr4A.!!$F2 2326
3 TraesCS1D01G074200 chr4A 556804441 556805787 1346 False 331.250000 503 92.290750 1318 2327 4 chr4A.!!$F3 1009
4 TraesCS1D01G074200 chr4B 62867687 62869982 2295 True 1059.500000 1921 86.435500 177 2327 2 chr4B.!!$R7 2150
5 TraesCS1D01G074200 chr4B 61522528 61524618 2090 False 981.500000 1792 90.255000 88 2008 2 chr4B.!!$F2 1920
6 TraesCS1D01G074200 chr4B 62056120 62057043 923 True 904.000000 904 84.281000 218 1183 1 chr4B.!!$R2 965
7 TraesCS1D01G074200 chr4B 61536129 61537691 1562 False 878.000000 1585 92.934000 654 2008 2 chr4B.!!$F3 1354
8 TraesCS1D01G074200 chr4B 140435931 140437020 1089 True 791.000000 791 80.260000 391 1524 1 chr4B.!!$R4 1133
9 TraesCS1D01G074200 chr4B 61323246 61325235 1989 True 736.000000 1565 90.832000 171 2011 3 chr4B.!!$R5 1840
10 TraesCS1D01G074200 chr4B 140232990 140234111 1121 True 693.000000 693 78.638000 391 1524 1 chr4B.!!$R3 1133
11 TraesCS1D01G074200 chr4B 61888759 61889658 899 False 647.000000 647 80.126000 1 940 1 chr4B.!!$F1 939
12 TraesCS1D01G074200 chr4B 139937177 139940990 3813 True 461.000000 782 90.817000 177 2327 4 chr4B.!!$R8 2150
13 TraesCS1D01G074200 chr4B 62432364 62434363 1999 True 390.500000 610 86.913500 1 2011 2 chr4B.!!$R6 2010
14 TraesCS1D01G074200 chr4D 43149567 43151450 1883 True 617.000000 1369 92.120667 658 2327 3 chr4D.!!$R2 1669
15 TraesCS1D01G074200 chr4D 43075466 43077762 2296 True 533.333333 1177 89.933667 1 2011 3 chr4D.!!$R1 2010

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
308 374 0.178903 ACTAGTCCAGGTCCAGCCAA 60.179 55.0 0.0 0.0 40.61 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1504 1694 0.388649 ACTTCTTGTAGCGTCGCCTG 60.389 55.0 14.86 0.0 0.0 4.85 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
30 31 4.202070 TGTCGAAGAAAAATGGGAAACACC 60.202 41.667 0.00 0.00 39.69 4.16
308 374 0.178903 ACTAGTCCAGGTCCAGCCAA 60.179 55.000 0.00 0.00 40.61 4.52
355 421 7.693952 AGTGCATGTTTAAATATACGGTGAAG 58.306 34.615 0.00 0.00 0.00 3.02
753 865 0.817634 CGGGCGGCAAATAGGATTGA 60.818 55.000 12.47 0.00 31.84 2.57
848 1004 7.701445 AGTCGTATTTAGCTTGTATTCTACGT 58.299 34.615 0.00 0.00 34.12 3.57
849 1005 7.642978 AGTCGTATTTAGCTTGTATTCTACGTG 59.357 37.037 0.00 0.00 34.12 4.49
924 1080 1.552792 CCCTCCGCTCTTTCTTCTTCT 59.447 52.381 0.00 0.00 0.00 2.85
925 1081 2.615869 CCTCCGCTCTTTCTTCTTCTG 58.384 52.381 0.00 0.00 0.00 3.02
975 1132 5.502544 CGCTCGATTTAGGTCTTTGATTTCC 60.503 44.000 0.00 0.00 0.00 3.13
996 1153 1.451927 GATTCATCTGCCGGTGCCA 60.452 57.895 1.90 0.00 36.33 4.92
1029 1186 0.832626 TCGACATCCATGGCATGAGT 59.167 50.000 28.43 21.52 34.77 3.41
1078 1235 0.174617 GCACTCCGGGAAGAAGAGAG 59.825 60.000 0.00 0.00 0.00 3.20
1195 1355 0.836400 TCCGGTTTCCTCTTCCTGCT 60.836 55.000 0.00 0.00 0.00 4.24
1224 1384 1.221566 CATCATGGTGACGGAGGCA 59.778 57.895 0.00 0.00 0.00 4.75
1504 1694 2.626780 GCACCTTGGGGTTTCGAGC 61.627 63.158 0.00 0.00 44.73 5.03
1569 1759 4.724399 TCAAATTACAAGTCAAGAGGCCA 58.276 39.130 5.01 0.00 0.00 5.36
1642 2001 9.549078 CTCCCTCTGTAAACTTTTATAAGATCC 57.451 37.037 0.00 0.00 35.30 3.36
2216 2973 1.388547 TTGGTGTTTGGCTGTGACTC 58.611 50.000 0.00 0.00 0.00 3.36
2217 2974 0.546122 TGGTGTTTGGCTGTGACTCT 59.454 50.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.225491 TCGATTTTCACCGGCTTTCTTG 59.775 45.455 0.00 0.00 0.00 3.02
276 341 1.135170 GGACTAGTCCGGTTTTCCTCG 60.135 57.143 25.83 0.00 40.36 4.63
277 342 2.669300 GGACTAGTCCGGTTTTCCTC 57.331 55.000 25.83 0.00 40.36 3.71
308 374 4.415881 TGCTGGTTCGGTCAATGTATAT 57.584 40.909 0.00 0.00 0.00 0.86
355 421 5.391312 AATGTTCACTGTATTGAAAGCCC 57.609 39.130 0.00 0.00 37.24 5.19
753 865 2.499685 GTGAGGCTTATCCGCGGT 59.500 61.111 27.15 15.22 40.77 5.68
848 1004 2.949644 TCGATCTGAAATACGCCTCTCA 59.050 45.455 0.00 0.00 0.00 3.27
849 1005 3.251245 TCTCGATCTGAAATACGCCTCTC 59.749 47.826 0.00 0.00 0.00 3.20
925 1081 4.742201 TCGAGCAGCAAGGACGCC 62.742 66.667 0.00 0.00 0.00 5.68
975 1132 1.889105 CACCGGCAGATGAATCGGG 60.889 63.158 0.00 0.00 45.97 5.14
996 1153 1.485124 TGTCGACACAGGCCATATCT 58.515 50.000 15.76 0.00 0.00 1.98
1005 1162 0.391528 TGCCATGGATGTCGACACAG 60.392 55.000 22.71 8.84 35.41 3.66
1008 1165 0.540923 TCATGCCATGGATGTCGACA 59.459 50.000 22.48 22.48 0.00 4.35
1063 1220 2.052690 CGGCTCTCTTCTTCCCGGA 61.053 63.158 0.73 0.00 35.54 5.14
1078 1235 4.632458 GAGATCCTCGTCGGCGGC 62.632 72.222 10.62 3.25 38.89 6.53
1504 1694 0.388649 ACTTCTTGTAGCGTCGCCTG 60.389 55.000 14.86 0.00 0.00 4.85
1569 1759 3.430042 AACTGACATTCCAGCACATCT 57.570 42.857 0.00 0.00 37.68 2.90
1662 2021 9.955102 ACTCCCTTCGTAAACTTTTATAAGATT 57.045 29.630 0.00 0.00 35.30 2.40
1680 2070 7.936496 ACAACTAGTACTAAGTACTCCCTTC 57.064 40.000 3.76 0.00 44.86 3.46


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

AutoCloner maintained by Alex Coulton.