Multiple sequence alignment - TraesCS5A01G014700

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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 TraesCS5A01G014700 chr5A 100.000 3685 0 0 1 3685 10039395 10035711 0.000000e+00 6806.0
1 TraesCS5A01G014700 chr5A 88.449 303 32 3 1988 2288 699017749 699017448 2.700000e-96 363.0
2 TraesCS5A01G014700 chr1A 96.381 3675 101 10 1 3654 308350295 308353958 0.000000e+00 6021.0
3 TraesCS5A01G014700 chr1A 94.646 2839 128 16 268 3094 292891705 292888879 0.000000e+00 4379.0
4 TraesCS5A01G014700 chr1A 88.694 628 37 13 3090 3685 292888066 292887441 0.000000e+00 736.0
5 TraesCS5A01G014700 chr1A 100.000 32 0 0 3654 3685 308355617 308355648 3.970000e-05 60.2
6 TraesCS5A01G014700 chr4A 97.038 3072 88 3 198 3266 216815610 216818681 0.000000e+00 5166.0
7 TraesCS5A01G014700 chr4A 93.350 391 8 3 3295 3685 216818679 216819051 2.480000e-156 562.0
8 TraesCS5A01G014700 chr4A 95.714 210 9 0 1 210 216811895 216812104 4.560000e-89 339.0
9 TraesCS5A01G014700 chr7D 95.677 2475 92 7 1 2470 287706430 287703966 0.000000e+00 3964.0
10 TraesCS5A01G014700 chr7D 94.774 1148 56 4 2541 3685 287703969 287702823 0.000000e+00 1784.0
11 TraesCS5A01G014700 chr2B 95.039 1814 86 4 1378 3187 63518801 63520614 0.000000e+00 2848.0
12 TraesCS5A01G014700 chr3A 88.740 1341 108 24 2345 3673 91452149 91453458 0.000000e+00 1600.0
13 TraesCS5A01G014700 chr3A 87.879 1353 119 22 2345 3685 425588076 425589395 0.000000e+00 1548.0
14 TraesCS5A01G014700 chr6A 88.450 1342 107 31 2345 3672 571276294 571274987 0.000000e+00 1576.0
15 TraesCS5A01G014700 chr6A 90.968 310 24 3 1681 1988 321271220 321270913 7.360000e-112 414.0
16 TraesCS5A01G014700 chr6A 86.207 116 16 0 3570 3685 306730404 306730519 3.860000e-25 126.0
17 TraesCS5A01G014700 chr2A 86.192 1347 164 15 2345 3685 285231428 285232758 0.000000e+00 1437.0
18 TraesCS5A01G014700 chr2A 91.733 375 31 0 1916 2290 285231030 285231404 4.220000e-144 521.0
19 TraesCS5A01G014700 chr6B 94.836 852 37 6 731 1575 708049287 708050138 0.000000e+00 1323.0
20 TraesCS5A01G014700 chr6B 91.326 611 51 2 1681 2289 329470978 329470368 0.000000e+00 833.0
21 TraesCS5A01G014700 chr6B 88.113 673 72 7 2345 3013 329470343 329469675 0.000000e+00 793.0
22 TraesCS5A01G014700 chr1D 94.830 851 38 5 731 1575 420674348 420673498 0.000000e+00 1323.0
23 TraesCS5A01G014700 chr1D 93.897 852 44 7 731 1575 78367242 78368092 0.000000e+00 1279.0
24 TraesCS5A01G014700 chr2D 94.360 851 42 5 731 1575 207541028 207541878 0.000000e+00 1301.0
25 TraesCS5A01G014700 chr7A 87.080 1161 107 27 2534 3685 501097020 501095894 0.000000e+00 1273.0
26 TraesCS5A01G014700 chr7B 93.420 851 49 6 731 1575 164689096 164689945 0.000000e+00 1254.0
27 TraesCS5A01G014700 chr1B 93.538 619 31 7 1681 2290 601127441 601126823 0.000000e+00 913.0
28 TraesCS5A01G014700 chr1B 88.696 115 11 2 3563 3677 601110398 601110286 4.960000e-29 139.0
29 TraesCS5A01G014700 chr6D 91.586 309 25 1 1681 1988 232767056 232766748 3.400000e-115 425.0
30 TraesCS5A01G014700 chr5D 92.920 113 5 3 1574 1683 483521136 483521248 1.060000e-35 161.0
31 TraesCS5A01G014700 chr4B 92.920 113 5 3 1574 1683 525412158 525412046 1.060000e-35 161.0
32 TraesCS5A01G014700 chr4B 91.964 112 6 3 1575 1683 525277690 525277579 1.770000e-33 154.0
33 TraesCS5A01G014700 chr4B 90.265 113 8 3 1574 1683 525295901 525296013 1.070000e-30 145.0


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 TraesCS5A01G014700 chr5A 10035711 10039395 3684 True 6806.000000 6806 100.000000 1 3685 1 chr5A.!!$R1 3684
1 TraesCS5A01G014700 chr1A 308350295 308355648 5353 False 3040.600000 6021 98.190500 1 3685 2 chr1A.!!$F1 3684
2 TraesCS5A01G014700 chr1A 292887441 292891705 4264 True 2557.500000 4379 91.670000 268 3685 2 chr1A.!!$R1 3417
3 TraesCS5A01G014700 chr4A 216811895 216819051 7156 False 2022.333333 5166 95.367333 1 3685 3 chr4A.!!$F1 3684
4 TraesCS5A01G014700 chr7D 287702823 287706430 3607 True 2874.000000 3964 95.225500 1 3685 2 chr7D.!!$R1 3684
5 TraesCS5A01G014700 chr2B 63518801 63520614 1813 False 2848.000000 2848 95.039000 1378 3187 1 chr2B.!!$F1 1809
6 TraesCS5A01G014700 chr3A 91452149 91453458 1309 False 1600.000000 1600 88.740000 2345 3673 1 chr3A.!!$F1 1328
7 TraesCS5A01G014700 chr3A 425588076 425589395 1319 False 1548.000000 1548 87.879000 2345 3685 1 chr3A.!!$F2 1340
8 TraesCS5A01G014700 chr6A 571274987 571276294 1307 True 1576.000000 1576 88.450000 2345 3672 1 chr6A.!!$R2 1327
9 TraesCS5A01G014700 chr2A 285231030 285232758 1728 False 979.000000 1437 88.962500 1916 3685 2 chr2A.!!$F1 1769
10 TraesCS5A01G014700 chr6B 708049287 708050138 851 False 1323.000000 1323 94.836000 731 1575 1 chr6B.!!$F1 844
11 TraesCS5A01G014700 chr6B 329469675 329470978 1303 True 813.000000 833 89.719500 1681 3013 2 chr6B.!!$R1 1332
12 TraesCS5A01G014700 chr1D 420673498 420674348 850 True 1323.000000 1323 94.830000 731 1575 1 chr1D.!!$R1 844
13 TraesCS5A01G014700 chr1D 78367242 78368092 850 False 1279.000000 1279 93.897000 731 1575 1 chr1D.!!$F1 844
14 TraesCS5A01G014700 chr2D 207541028 207541878 850 False 1301.000000 1301 94.360000 731 1575 1 chr2D.!!$F1 844
15 TraesCS5A01G014700 chr7A 501095894 501097020 1126 True 1273.000000 1273 87.080000 2534 3685 1 chr7A.!!$R1 1151
16 TraesCS5A01G014700 chr7B 164689096 164689945 849 False 1254.000000 1254 93.420000 731 1575 1 chr7B.!!$F1 844
17 TraesCS5A01G014700 chr1B 601126823 601127441 618 True 913.000000 913 93.538000 1681 2290 1 chr1B.!!$R2 609

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
476 4020 0.251916 AACGGATCCTTTGCCATCGA 59.748 50.0 10.75 0.0 0.0 3.59 F
1040 4584 1.569479 GCTGACAAGCTGTTCGGGAC 61.569 60.0 5.93 0.0 46.6 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 4986 0.033781 TCCACCCTTACAAACGACCG 59.966 55.0 0.00 0.0 0.00 4.79 R
2827 6396 0.521867 CTTCGCGTTCGATGGTCGTA 60.522 55.0 5.77 0.0 45.04 3.43 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
36 37 3.402681 CCAGGATGCCAGACCGGT 61.403 66.667 6.92 6.92 36.97 5.28
37 38 2.063979 CCAGGATGCCAGACCGGTA 61.064 63.158 7.34 0.00 36.97 4.02
99 100 2.364448 GGGAGAGAAGGAGGCCGT 60.364 66.667 0.00 0.00 0.00 5.68
242 3779 2.122413 TGGAGTGGCTGTGAGGGT 60.122 61.111 0.00 0.00 0.00 4.34
476 4020 0.251916 AACGGATCCTTTGCCATCGA 59.748 50.000 10.75 0.00 0.00 3.59
766 4310 3.574614 CTTGTGCTTTTCGTAATTGGGG 58.425 45.455 0.00 0.00 0.00 4.96
1040 4584 1.569479 GCTGACAAGCTGTTCGGGAC 61.569 60.000 5.93 0.00 46.60 4.46
1124 4668 4.822896 GTCTAGACGGAGATTACTGACCAT 59.177 45.833 7.22 0.00 0.00 3.55
1196 4740 5.535753 AAAATTTCCTTTGGGTGTCTCAG 57.464 39.130 0.00 0.00 0.00 3.35
1295 4841 3.256879 CAGAGAAGACTACTGCTGGTTCA 59.743 47.826 0.00 0.00 31.04 3.18
1322 4870 3.895041 CCCCGCCCTTTAAATATGTTCAT 59.105 43.478 0.00 0.00 0.00 2.57
1342 4890 7.121611 TGTTCATGTCTGCACATCAATCTATTT 59.878 33.333 0.00 0.00 41.69 1.40
1436 4986 5.531634 TGCAACAACAAAAATCAGAGGATC 58.468 37.500 0.00 0.00 31.88 3.36
1750 5303 6.609616 AGTTCCTTTTCCAACCAAGTTATTGA 59.390 34.615 1.48 0.00 38.83 2.57
1848 5401 3.632189 GCACTGAATTGTTGGACTGAAC 58.368 45.455 0.00 0.00 0.00 3.18
2101 5665 0.807275 TGAGTGGCGATCATGAAGCG 60.807 55.000 16.86 15.83 0.00 4.68
2202 5766 7.105588 GCCTTGGGATCAATCAAACTAAATTT 58.894 34.615 0.00 0.00 31.75 1.82
2242 5806 3.448660 AGCAAAAGGGTGAATATTCTGCC 59.551 43.478 16.24 16.31 0.00 4.85
2413 5981 0.988678 AAGGATCTACAGGGCCCCAC 60.989 60.000 21.43 1.84 0.00 4.61
2661 6229 0.034059 CCGCCCGCTTATGATCTCTT 59.966 55.000 0.00 0.00 0.00 2.85
2662 6230 1.541233 CCGCCCGCTTATGATCTCTTT 60.541 52.381 0.00 0.00 0.00 2.52
2827 6396 2.338984 GAGCCCACGACGTTCACT 59.661 61.111 0.00 0.00 0.00 3.41
2884 6453 0.030504 TCAAAGTTGTCGTCGCCGTA 59.969 50.000 0.00 0.00 35.01 4.02
3017 6587 4.657824 CCCGTGGTCTTGCGTCGT 62.658 66.667 0.00 0.00 0.00 4.34
3066 6636 4.148825 GGAGATGAGCACCGCCGT 62.149 66.667 0.00 0.00 0.00 5.68
3142 7529 3.716006 GTCCGTCGTCGTCCGTCA 61.716 66.667 0.71 0.00 37.94 4.35
3403 7791 1.377202 GGTTGCGGCAGGATCTCAA 60.377 57.895 1.67 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 4.767255 CTCCTCCACGCCACAGCC 62.767 72.222 0.00 0.0 34.57 4.85
242 3779 3.616219 GCTAGTTCCTCTCACTCTCTCA 58.384 50.000 0.00 0.0 0.00 3.27
328 3865 0.847373 TTTCCACCCACACAGCCTTA 59.153 50.000 0.00 0.0 0.00 2.69
428 3972 9.638239 GATCTATTGCAAAATTCCTGTGTTTAA 57.362 29.630 1.71 0.0 0.00 1.52
476 4020 6.538742 CGTACAACCAACATAGGATTCAGATT 59.461 38.462 0.00 0.0 0.00 2.40
621 4165 2.625790 TCAATCCCCACCTTTGTTTTCG 59.374 45.455 0.00 0.0 0.00 3.46
679 4223 3.952323 CTCCAATTGCAGTCTGATGGATT 59.048 43.478 3.32 0.0 36.45 3.01
766 4310 9.710900 AATAAATTGAATCAAAACTTGGAGACC 57.289 29.630 0.00 0.0 0.00 3.85
1040 4584 0.247460 TGTTCCTCTGCCTCGACATG 59.753 55.000 0.00 0.0 0.00 3.21
1124 4668 7.661536 ACTGAACATAGCTTAGTCCAAGATA 57.338 36.000 0.00 0.0 39.36 1.98
1196 4740 5.957842 TGTTCATGTTCCACCTGTTAATC 57.042 39.130 0.00 0.0 0.00 1.75
1295 4841 4.141018 ACATATTTAAAGGGCGGGGAAGAT 60.141 41.667 0.00 0.0 0.00 2.40
1342 4890 9.153479 CCCTGGAAAAATATCCCAAACAATATA 57.847 33.333 0.00 0.0 38.82 0.86
1436 4986 0.033781 TCCACCCTTACAAACGACCG 59.966 55.000 0.00 0.0 0.00 4.79
1546 5098 7.443302 TCTCTCCATCTCCATAAACAAATCT 57.557 36.000 0.00 0.0 0.00 2.40
1750 5303 7.630242 ATCGGTTCTGTCAAAATGAATACAT 57.370 32.000 0.00 0.0 38.50 2.29
1924 5477 7.053498 TGTATATACTTTGCAGATTGCTTGGA 58.947 34.615 13.89 0.0 45.31 3.53
2101 5665 1.045911 TTGCACCCACACCTTTTCCC 61.046 55.000 0.00 0.0 0.00 3.97
2202 5766 1.203994 GCTCCAAGTACGAGGCTACAA 59.796 52.381 0.00 0.0 0.00 2.41
2413 5981 2.293122 TGGCAGTCAAGTTCCAAAATCG 59.707 45.455 0.00 0.0 0.00 3.34
2594 6162 3.031736 CTCCTGGTCTTCCGAATTCCTA 58.968 50.000 0.00 0.0 36.30 2.94
2661 6229 5.181245 GCTACTCTGCTGAAACCACAAATAA 59.819 40.000 0.00 0.0 0.00 1.40
2662 6230 4.695455 GCTACTCTGCTGAAACCACAAATA 59.305 41.667 0.00 0.0 0.00 1.40
2827 6396 0.521867 CTTCGCGTTCGATGGTCGTA 60.522 55.000 5.77 0.0 45.04 3.43
2884 6453 2.759973 TCGAGGGCGAGGAAGCAT 60.760 61.111 0.00 0.0 42.51 3.79
3632 8057 7.766219 TCTATATTTTGTCGTAGAGCAAACC 57.234 36.000 0.00 0.0 37.30 3.27


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

AutoCloner maintained by Alex Coulton.