Multiple sequence alignment - TraesCS5A01G506700

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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 TraesCS5A01G506700 chr5A 100.000 2459 0 0 1 2459 671453233 671455691 0.000000e+00 4542
1 TraesCS5A01G506700 chr5A 94.774 421 22 0 2039 2459 153573334 153572914 0.000000e+00 656
2 TraesCS5A01G506700 chr3D 93.948 2049 111 9 1 2039 305617473 305615428 0.000000e+00 3085
3 TraesCS5A01G506700 chr6D 92.454 2054 132 15 1 2039 305380436 305378391 0.000000e+00 2913
4 TraesCS5A01G506700 chr6D 92.401 2053 133 15 1 2039 257992385 257994428 0.000000e+00 2905
5 TraesCS5A01G506700 chr6D 95.227 419 19 1 2039 2457 356211255 356210838 0.000000e+00 662
6 TraesCS5A01G506700 chr5D 92.405 2054 134 14 1 2039 36562317 36564363 0.000000e+00 2909
7 TraesCS5A01G506700 chr5D 95.192 416 19 1 2044 2459 36564415 36564829 0.000000e+00 656
8 TraesCS5A01G506700 chr1B 90.772 2059 153 20 1 2039 476681642 476683683 0.000000e+00 2715
9 TraesCS5A01G506700 chr1B 94.537 421 23 0 2039 2459 609878187 609878607 0.000000e+00 651
10 TraesCS5A01G506700 chr5B 89.301 2075 166 41 1 2039 598694317 598696371 0.000000e+00 2551
11 TraesCS5A01G506700 chr2B 89.374 2061 165 22 1 2039 655693865 655691837 0.000000e+00 2543
12 TraesCS5A01G506700 chr2B 87.373 2075 170 34 1 2039 19852403 19854421 0.000000e+00 2296
13 TraesCS5A01G506700 chr2B 89.189 222 19 3 1823 2039 512424105 512423884 3.120000e-69 272
14 TraesCS5A01G506700 chr2B 89.140 221 20 4 1823 2039 658222499 658222279 3.120000e-69 272
15 TraesCS5A01G506700 chr2D 91.379 1856 135 18 1 1842 87948347 87950191 0.000000e+00 2518
16 TraesCS5A01G506700 chr2D 95.192 416 20 0 2044 2459 87950406 87950821 0.000000e+00 658
17 TraesCS5A01G506700 chr4B 89.142 2063 165 28 1 2039 15517015 15519042 0.000000e+00 2514
18 TraesCS5A01G506700 chr4B 94.774 421 22 0 2039 2459 15519089 15519509 0.000000e+00 656
19 TraesCS5A01G506700 chr3B 88.943 2062 170 27 1 2039 60567024 60569050 0.000000e+00 2492
20 TraesCS5A01G506700 chr3A 89.542 1224 93 18 846 2039 38170700 38171918 0.000000e+00 1519
21 TraesCS5A01G506700 chr3A 94.952 416 21 0 2044 2459 38171970 38172385 0.000000e+00 652
22 TraesCS5A01G506700 chr1D 95.433 416 19 0 2044 2459 383348431 383348016 0.000000e+00 664
23 TraesCS5A01G506700 chr2A 95.012 421 20 1 2039 2459 130796101 130795682 0.000000e+00 660


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 TraesCS5A01G506700 chr5A 671453233 671455691 2458 False 4542.0 4542 100.0000 1 2459 1 chr5A.!!$F1 2458
1 TraesCS5A01G506700 chr3D 305615428 305617473 2045 True 3085.0 3085 93.9480 1 2039 1 chr3D.!!$R1 2038
2 TraesCS5A01G506700 chr6D 305378391 305380436 2045 True 2913.0 2913 92.4540 1 2039 1 chr6D.!!$R1 2038
3 TraesCS5A01G506700 chr6D 257992385 257994428 2043 False 2905.0 2905 92.4010 1 2039 1 chr6D.!!$F1 2038
4 TraesCS5A01G506700 chr5D 36562317 36564829 2512 False 1782.5 2909 93.7985 1 2459 2 chr5D.!!$F1 2458
5 TraesCS5A01G506700 chr1B 476681642 476683683 2041 False 2715.0 2715 90.7720 1 2039 1 chr1B.!!$F1 2038
6 TraesCS5A01G506700 chr5B 598694317 598696371 2054 False 2551.0 2551 89.3010 1 2039 1 chr5B.!!$F1 2038
7 TraesCS5A01G506700 chr2B 655691837 655693865 2028 True 2543.0 2543 89.3740 1 2039 1 chr2B.!!$R2 2038
8 TraesCS5A01G506700 chr2B 19852403 19854421 2018 False 2296.0 2296 87.3730 1 2039 1 chr2B.!!$F1 2038
9 TraesCS5A01G506700 chr2D 87948347 87950821 2474 False 1588.0 2518 93.2855 1 2459 2 chr2D.!!$F1 2458
10 TraesCS5A01G506700 chr4B 15517015 15519509 2494 False 1585.0 2514 91.9580 1 2459 2 chr4B.!!$F1 2458
11 TraesCS5A01G506700 chr3B 60567024 60569050 2026 False 2492.0 2492 88.9430 1 2039 1 chr3B.!!$F1 2038
12 TraesCS5A01G506700 chr3A 38170700 38172385 1685 False 1085.5 1519 92.2470 846 2459 2 chr3A.!!$F1 1613

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
862 927 1.207329 GGTGATACTGGTGGGACTGTC 59.793 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
1784 1891 1.066858 GGCAAGTTGACCTCATCGAGA 60.067 52.381 7.16 0.0 0.0 4.04 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
97 102 2.409378 GCTTCACCAAATCAATGTTGCG 59.591 45.455 0.00 0.00 0.00 4.85
107 112 2.376956 TCAATGTTGCGTGCGTTTAAC 58.623 42.857 0.00 0.00 0.00 2.01
219 242 9.827198 ATGGATTTCCTGAAAATATATTGCCTA 57.173 29.630 0.00 0.00 37.70 3.93
258 281 3.626930 TGCCTGGTTATATGGTTTGGAC 58.373 45.455 0.00 0.00 0.00 4.02
372 422 1.387539 TGCTGTGTTACTTGCTTGCA 58.612 45.000 0.00 0.00 0.00 4.08
507 562 2.954318 CTGTGCTATTGGCTTGCCTATT 59.046 45.455 13.16 1.17 42.39 1.73
538 593 3.128242 GCTACTTGCTTGCATCATTCTGT 59.872 43.478 0.00 0.00 38.95 3.41
540 595 5.163723 GCTACTTGCTTGCATCATTCTGTTA 60.164 40.000 0.00 0.00 38.95 2.41
608 668 6.192773 ACAATGATTGACCTGAATGAGGAAT 58.807 36.000 12.80 0.00 46.33 3.01
609 669 6.666546 ACAATGATTGACCTGAATGAGGAATT 59.333 34.615 12.80 0.00 46.33 2.17
647 710 6.700081 TGATCCTTTGTACTATACGCAACATC 59.300 38.462 0.00 0.00 0.00 3.06
710 773 6.664816 TCCCTCTATCATGCAAAAAGTCAATT 59.335 34.615 0.00 0.00 0.00 2.32
726 789 3.499918 GTCAATTGTGCTGCTACAGAAGT 59.500 43.478 5.13 0.00 32.44 3.01
732 796 2.352960 GTGCTGCTACAGAAGTAATGGC 59.647 50.000 0.00 0.00 32.44 4.40
862 927 1.207329 GGTGATACTGGTGGGACTGTC 59.793 57.143 0.00 0.00 0.00 3.51
905 973 3.753815 TGATGATGAAGCTTGGTCACAA 58.246 40.909 2.10 0.00 34.87 3.33
1048 1118 3.418047 ACCGGGGAGTTGATAAAACAAG 58.582 45.455 6.32 0.00 0.00 3.16
1103 1173 0.462759 GATGACGGAGGGGCAGAAAG 60.463 60.000 0.00 0.00 0.00 2.62
1199 1269 9.412460 TGATGATGATAGTAAAGGCAAAAAGAT 57.588 29.630 0.00 0.00 0.00 2.40
1373 1443 2.610859 ACACCAAGGGATCCCGCT 60.611 61.111 25.48 13.88 41.95 5.52
1515 1590 3.517296 TCTTGGCCCATCAACAACTAA 57.483 42.857 0.00 0.00 0.00 2.24
1535 1610 9.462174 CAACTAACTGATTTTGCTTGAAACATA 57.538 29.630 0.00 0.00 0.00 2.29
1649 1749 3.928754 TCTGGATACTGGACTTGCCTAT 58.071 45.455 0.00 0.00 37.63 2.57
1738 1845 4.150897 TGGTGTTGACTCTAAACTTGCT 57.849 40.909 0.00 0.00 0.00 3.91
1878 2012 7.009999 TGTTTTGTGTATTTTGCTCATGTGTTC 59.990 33.333 0.00 0.00 0.00 3.18
1879 2013 6.389830 TTGTGTATTTTGCTCATGTGTTCT 57.610 33.333 0.00 0.00 0.00 3.01
1895 2029 4.020307 TGTGTTCTCTGAGGCATATTGTCA 60.020 41.667 4.59 0.00 0.00 3.58
1898 2032 6.933521 GTGTTCTCTGAGGCATATTGTCATAT 59.066 38.462 4.59 0.00 0.00 1.78
1952 2086 2.237643 TGCATTTGAGTTGCCTTGCTA 58.762 42.857 0.00 0.00 39.39 3.49
1957 2091 5.179929 GCATTTGAGTTGCCTTGCTAAAAAT 59.820 36.000 0.00 0.00 33.95 1.82
2042 2225 7.201145 ACTTCATGTCAACAGGTCGTATATAC 58.799 38.462 2.53 2.53 0.00 1.47
2067 2250 6.071952 CCACTAAGCACATTACAAACCTCAAT 60.072 38.462 0.00 0.00 0.00 2.57
2068 2251 6.803320 CACTAAGCACATTACAAACCTCAATG 59.197 38.462 0.00 0.00 36.07 2.82
2095 2278 7.542025 GCTCTTGAACAAGGATGATACAAAAT 58.458 34.615 13.46 0.00 38.88 1.82
2220 2403 0.400213 TTTTCTGGGTCGATGGTGCT 59.600 50.000 0.00 0.00 0.00 4.40
2250 2433 2.793232 GGCGTACGTGGAATCTTATCAC 59.207 50.000 17.90 0.00 0.00 3.06
2302 2485 5.073428 TGACTAACATTTACAACATGCCCA 58.927 37.500 0.00 0.00 0.00 5.36
2350 2533 2.291209 TGGGCAGTCATTCATGTTGT 57.709 45.000 0.00 0.00 0.00 3.32
2450 2633 3.386932 AGCACCCACCAACATCATAAT 57.613 42.857 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 102 9.742552 TTTCTTATTTGTTTTTGTTAAACGCAC 57.257 25.926 0.00 0.00 33.05 5.34
219 242 8.766994 ACCAGGCAAATCAAACTATATATGTT 57.233 30.769 0.00 0.00 0.00 2.71
235 258 4.464597 GTCCAAACCATATAACCAGGCAAA 59.535 41.667 0.00 0.00 0.00 3.68
258 281 6.992063 AATTCAAAGTACACTATCAGGCAG 57.008 37.500 0.00 0.00 0.00 4.85
372 422 5.740290 AGCTAGTACCACACTAAACACAT 57.260 39.130 0.00 0.00 39.28 3.21
439 493 5.393787 GGTCAATCATCTTCAACATGTGCAT 60.394 40.000 0.00 0.00 0.00 3.96
507 562 6.757897 ATGCAAGCAAGTAGCATAGTAAAA 57.242 33.333 0.00 0.00 46.27 1.52
636 699 0.541392 TCCAGCAGGATGTTGCGTAT 59.459 50.000 0.00 0.00 46.73 3.06
710 773 3.599343 CCATTACTTCTGTAGCAGCACA 58.401 45.455 0.00 0.00 0.00 4.57
726 789 0.179048 CTGCCCATCTGTCGCCATTA 60.179 55.000 0.00 0.00 0.00 1.90
732 796 0.036952 ACTTGACTGCCCATCTGTCG 60.037 55.000 0.00 0.00 43.91 4.35
833 898 1.561769 CCAGTATCACCTGGGGCACA 61.562 60.000 0.00 0.00 46.89 4.57
862 927 1.529226 TTCAGCACCAACCATTACCG 58.471 50.000 0.00 0.00 0.00 4.02
973 1043 2.031120 TGAAAAACCTGTCTGCAAGGG 58.969 47.619 7.81 0.68 0.00 3.95
1012 1082 1.173913 CCGGTTTTCACATCCTTCCC 58.826 55.000 0.00 0.00 0.00 3.97
1103 1173 3.827008 TGTCATCTAGCACAGGAATCC 57.173 47.619 0.00 0.00 0.00 3.01
1199 1269 7.490962 TTATCTCTTTTTCGTTTCTTGCTCA 57.509 32.000 0.00 0.00 0.00 4.26
1515 1590 7.811236 CAGTCATATGTTTCAAGCAAAATCAGT 59.189 33.333 1.90 0.00 0.00 3.41
1535 1610 7.972277 GTCATATGTTTGAAGCAAATCAGTCAT 59.028 33.333 1.90 0.00 35.74 3.06
1649 1749 5.392767 TTGAGCAACAAACAGGTAAACAA 57.607 34.783 0.00 0.00 35.39 2.83
1701 1808 7.544217 AGTCAACACCAAATTTGTTTTACAGAC 59.456 33.333 16.73 13.80 34.91 3.51
1703 1810 7.759433 AGAGTCAACACCAAATTTGTTTTACAG 59.241 33.333 16.73 2.48 34.91 2.74
1784 1891 1.066858 GGCAAGTTGACCTCATCGAGA 60.067 52.381 7.16 0.00 0.00 4.04
1835 1943 6.490721 CACAAAACAAACAGGGGGTAACTATA 59.509 38.462 0.00 0.00 0.00 1.31
1878 2012 6.430308 AGCAAATATGACAATATGCCTCAGAG 59.570 38.462 0.00 0.00 0.00 3.35
1879 2013 6.301486 AGCAAATATGACAATATGCCTCAGA 58.699 36.000 0.00 0.00 0.00 3.27
1991 2125 5.221501 ACAATGGTGGTCAATCCTTTTTCTG 60.222 40.000 0.00 0.00 37.07 3.02
2042 2225 4.759693 TGAGGTTTGTAATGTGCTTAGTGG 59.240 41.667 0.00 0.00 0.00 4.00
2067 2250 1.159285 CATCCTTGTTCAAGAGCGCA 58.841 50.000 11.47 0.00 0.00 6.09
2068 2251 1.442769 TCATCCTTGTTCAAGAGCGC 58.557 50.000 13.29 0.00 0.00 5.92
2095 2278 6.211584 GCAACTGTCTCTATCATATCCCCTTA 59.788 42.308 0.00 0.00 0.00 2.69
2184 2367 6.127619 CCCAGAAAATATTCTCAACCCTGTTC 60.128 42.308 0.00 0.00 44.11 3.18
2185 2368 5.716703 CCCAGAAAATATTCTCAACCCTGTT 59.283 40.000 0.00 0.00 44.11 3.16
2220 2403 1.666553 CACGTACGCCTTCCTTGCA 60.667 57.895 16.72 0.00 0.00 4.08
2302 2485 5.535783 TGTTAATCCCGATGAATGATGCAAT 59.464 36.000 0.00 0.00 0.00 3.56
2308 2491 3.118075 TGCCTGTTAATCCCGATGAATGA 60.118 43.478 0.00 0.00 0.00 2.57
2316 2499 1.455383 GCCCATGCCTGTTAATCCCG 61.455 60.000 0.00 0.00 0.00 5.14
2350 2533 2.284754 TGCCTAACAAAGCCACATCA 57.715 45.000 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.