Multiple sequence alignment - TraesCS7A01G274000

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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 TraesCS7A01G274000 chr7A 100.000 2832 0 0 1 2832 287483931 287486762 0.000000e+00 5230
1 TraesCS7A01G274000 chr7A 96.929 1042 29 2 969 2010 287521506 287522544 0.000000e+00 1744
2 TraesCS7A01G274000 chr7A 90.598 1138 87 9 890 2010 287494133 287495267 0.000000e+00 1491
3 TraesCS7A01G274000 chr7A 82.973 1063 148 19 897 1938 287499558 287500608 0.000000e+00 929
4 TraesCS7A01G274000 chr7A 96.341 164 5 1 731 893 287521106 287521269 4.650000e-68 268
5 TraesCS7A01G274000 chr7A 88.038 209 11 4 100 300 287527551 287527753 4.720000e-58 235
6 TraesCS7A01G274000 chr7A 80.631 222 36 5 466 684 287493718 287493935 6.280000e-37 165
7 TraesCS7A01G274000 chr7A 82.941 170 21 5 137 305 287493246 287493408 2.270000e-31 147
8 TraesCS7A01G274000 chr7A 96.774 62 2 0 1 62 287477075 287477136 1.390000e-18 104
9 TraesCS7A01G274000 chr7D 94.907 1296 52 3 715 2010 264028621 264029902 0.000000e+00 2015
10 TraesCS7A01G274000 chr7D 89.052 1160 77 19 890 2010 264036519 264037667 0.000000e+00 1393
11 TraesCS7A01G274000 chr7D 94.782 824 35 2 2009 2832 631022374 631023189 0.000000e+00 1277
12 TraesCS7A01G274000 chr7D 87.411 985 119 3 890 1870 264054294 264055277 0.000000e+00 1127
13 TraesCS7A01G274000 chr7D 85.781 1069 118 12 890 1938 264056260 264057314 0.000000e+00 1101
14 TraesCS7A01G274000 chr7D 85.067 1038 135 14 911 1936 264026710 264027739 0.000000e+00 1040
15 TraesCS7A01G274000 chr7D 91.114 709 39 11 1 689 264027930 264028634 0.000000e+00 939
16 TraesCS7A01G274000 chr7D 80.387 724 57 35 8 684 264053412 264054097 3.300000e-129 472
17 TraesCS7A01G274000 chr7D 93.252 163 11 0 731 893 264054099 264054261 1.010000e-59 241
18 TraesCS7A01G274000 chr7D 83.456 272 28 7 45 305 264055556 264055821 1.310000e-58 237
19 TraesCS7A01G274000 chr7D 87.719 114 13 1 571 684 264036225 264036337 6.370000e-27 132
20 TraesCS7A01G274000 chr7D 80.319 188 20 6 130 305 264035920 264036102 2.960000e-25 126
21 TraesCS7A01G274000 chr7B 92.593 1296 71 3 715 2010 244395957 244397227 0.000000e+00 1838
22 TraesCS7A01G274000 chr7B 93.380 1133 60 5 890 2010 244406798 244407927 0.000000e+00 1663
23 TraesCS7A01G274000 chr7B 94.850 835 37 5 2001 2832 186868631 186867800 0.000000e+00 1299
24 TraesCS7A01G274000 chr7B 84.444 1035 148 11 911 1936 244393959 244394989 0.000000e+00 1007
25 TraesCS7A01G274000 chr7B 91.682 529 27 9 173 689 244395447 244395970 0.000000e+00 717
26 TraesCS7A01G274000 chr7B 84.191 272 25 8 45 305 244411145 244411409 6.060000e-62 248
27 TraesCS7A01G274000 chr7B 83.412 211 12 8 1 188 244395179 244395389 1.040000e-39 174
28 TraesCS7A01G274000 chr7B 82.873 181 14 6 137 305 244406214 244406389 2.270000e-31 147
29 TraesCS7A01G274000 chr7B 89.474 114 11 1 571 684 244406504 244406616 2.940000e-30 143
30 TraesCS7A01G274000 chr2B 95.758 825 35 0 2008 2832 461519905 461519081 0.000000e+00 1330
31 TraesCS7A01G274000 chr2B 93.552 822 51 2 2010 2831 734839433 734840252 0.000000e+00 1223
32 TraesCS7A01G274000 chr1A 95.567 812 35 1 2008 2819 23029797 23030607 0.000000e+00 1299
33 TraesCS7A01G274000 chr5B 94.909 825 40 2 2008 2832 375801883 375801061 0.000000e+00 1290
34 TraesCS7A01G274000 chr5B 94.963 814 41 0 2009 2822 711052446 711051633 0.000000e+00 1277
35 TraesCS7A01G274000 chr2D 94.431 826 45 1 2008 2832 644243446 644242621 0.000000e+00 1269
36 TraesCS7A01G274000 chr4B 93.818 825 45 4 2008 2832 81985577 81986395 0.000000e+00 1236


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 TraesCS7A01G274000 chr7A 287483931 287486762 2831 False 5230.000000 5230 100.000000 1 2832 1 chr7A.!!$F2 2831
1 TraesCS7A01G274000 chr7A 287521106 287522544 1438 False 1006.000000 1744 96.635000 731 2010 2 chr7A.!!$F6 1279
2 TraesCS7A01G274000 chr7A 287499558 287500608 1050 False 929.000000 929 82.973000 897 1938 1 chr7A.!!$F3 1041
3 TraesCS7A01G274000 chr7A 287493246 287495267 2021 False 601.000000 1491 84.723333 137 2010 3 chr7A.!!$F5 1873
4 TraesCS7A01G274000 chr7D 264026710 264029902 3192 False 1331.333333 2015 90.362667 1 2010 3 chr7D.!!$F2 2009
5 TraesCS7A01G274000 chr7D 631022374 631023189 815 False 1277.000000 1277 94.782000 2009 2832 1 chr7D.!!$F1 823
6 TraesCS7A01G274000 chr7D 264053412 264057314 3902 False 635.600000 1127 86.057400 8 1938 5 chr7D.!!$F4 1930
7 TraesCS7A01G274000 chr7D 264035920 264037667 1747 False 550.333333 1393 85.696667 130 2010 3 chr7D.!!$F3 1880
8 TraesCS7A01G274000 chr7B 186867800 186868631 831 True 1299.000000 1299 94.850000 2001 2832 1 chr7B.!!$R1 831
9 TraesCS7A01G274000 chr7B 244393959 244397227 3268 False 934.000000 1838 88.032750 1 2010 4 chr7B.!!$F1 2009
10 TraesCS7A01G274000 chr7B 244406214 244411409 5195 False 550.250000 1663 87.479500 45 2010 4 chr7B.!!$F2 1965
11 TraesCS7A01G274000 chr2B 461519081 461519905 824 True 1330.000000 1330 95.758000 2008 2832 1 chr2B.!!$R1 824
12 TraesCS7A01G274000 chr2B 734839433 734840252 819 False 1223.000000 1223 93.552000 2010 2831 1 chr2B.!!$F1 821
13 TraesCS7A01G274000 chr1A 23029797 23030607 810 False 1299.000000 1299 95.567000 2008 2819 1 chr1A.!!$F1 811
14 TraesCS7A01G274000 chr5B 375801061 375801883 822 True 1290.000000 1290 94.909000 2008 2832 1 chr5B.!!$R1 824
15 TraesCS7A01G274000 chr5B 711051633 711052446 813 True 1277.000000 1277 94.963000 2009 2822 1 chr5B.!!$R2 813
16 TraesCS7A01G274000 chr2D 644242621 644243446 825 True 1269.000000 1269 94.431000 2008 2832 1 chr2D.!!$R1 824
17 TraesCS7A01G274000 chr4B 81985577 81986395 818 False 1236.000000 1236 93.818000 2008 2832 1 chr4B.!!$F1 824

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
692 2364 0.447801 ACAAATTAGCGCTGCTTCCG 59.552 50.0 22.9 10.31 40.44 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2390 6376 1.652563 GTTGGTGTGCGGGAGAAAC 59.347 57.895 0.0 0.0 0.0 2.78 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
81 1335 5.652452 GTCTCAGGTAATTATTTGCCAAGGT 59.348 40.000 7.16 0.00 39.87 3.50
88 1342 9.875708 AGGTAATTATTTGCCAAGGTTCATATA 57.124 29.630 7.16 0.00 39.87 0.86
94 1348 7.790823 ATTTGCCAAGGTTCATATAATTTGC 57.209 32.000 0.00 0.00 0.00 3.68
95 1349 5.275067 TGCCAAGGTTCATATAATTTGCC 57.725 39.130 0.00 0.00 0.00 4.52
96 1350 4.713814 TGCCAAGGTTCATATAATTTGCCA 59.286 37.500 0.00 0.00 0.00 4.92
124 1398 1.536766 TGAAACAAGCCAGCTCGAATG 59.463 47.619 0.00 0.00 0.00 2.67
163 1437 8.795513 CCTTGTGATTATGCATTATCATTACCA 58.204 33.333 26.14 18.04 33.69 3.25
195 1552 5.292765 ACCTAATGATGCTGATGACTAACG 58.707 41.667 0.00 0.00 0.00 3.18
272 1641 7.016153 TCTTATCATGTTGTTGTACCTTCCT 57.984 36.000 0.00 0.00 0.00 3.36
273 1642 8.141298 TCTTATCATGTTGTTGTACCTTCCTA 57.859 34.615 0.00 0.00 0.00 2.94
274 1643 8.598916 TCTTATCATGTTGTTGTACCTTCCTAA 58.401 33.333 0.00 0.00 0.00 2.69
275 1644 8.556213 TTATCATGTTGTTGTACCTTCCTAAC 57.444 34.615 0.00 0.00 0.00 2.34
293 1662 7.141758 TCCTAACTCTGCTTCCAAATGATAT 57.858 36.000 0.00 0.00 0.00 1.63
308 1677 8.826710 TCCAAATGATATAATGAACTTCACGTC 58.173 33.333 0.00 0.00 0.00 4.34
363 1994 3.355378 TGGAAGGATGCACCATTAAGTG 58.645 45.455 7.86 0.00 42.04 3.16
382 2015 6.432607 AAGTGATATGTGCAATCAGAAGTG 57.567 37.500 0.00 0.00 34.12 3.16
590 2261 5.029807 TGGTTGTGTCAAGAATCTGTGTA 57.970 39.130 0.00 0.00 0.00 2.90
630 2302 2.113807 TGCTGTGGATAGCTGAGACAT 58.886 47.619 0.00 0.00 44.01 3.06
674 2346 5.814705 CAGAAGACCTCATCCTAATGTTGAC 59.185 44.000 0.00 0.00 34.32 3.18
675 2347 5.485353 AGAAGACCTCATCCTAATGTTGACA 59.515 40.000 0.00 0.00 34.32 3.58
676 2348 5.762179 AGACCTCATCCTAATGTTGACAA 57.238 39.130 0.00 0.00 34.32 3.18
677 2349 6.126863 AGACCTCATCCTAATGTTGACAAA 57.873 37.500 0.00 0.00 34.32 2.83
678 2350 6.725364 AGACCTCATCCTAATGTTGACAAAT 58.275 36.000 0.00 0.00 34.32 2.32
679 2351 7.177878 AGACCTCATCCTAATGTTGACAAATT 58.822 34.615 0.00 0.00 34.32 1.82
680 2352 8.328758 AGACCTCATCCTAATGTTGACAAATTA 58.671 33.333 0.00 0.00 34.32 1.40
681 2353 8.511604 ACCTCATCCTAATGTTGACAAATTAG 57.488 34.615 15.76 15.76 36.53 1.73
682 2354 7.067494 ACCTCATCCTAATGTTGACAAATTAGC 59.933 37.037 16.56 0.00 35.79 3.09
683 2355 7.015226 TCATCCTAATGTTGACAAATTAGCG 57.985 36.000 16.56 12.70 35.79 4.26
684 2356 5.229921 TCCTAATGTTGACAAATTAGCGC 57.770 39.130 0.00 0.00 35.79 5.92
685 2357 4.941263 TCCTAATGTTGACAAATTAGCGCT 59.059 37.500 17.26 17.26 35.79 5.92
686 2358 5.030295 CCTAATGTTGACAAATTAGCGCTG 58.970 41.667 22.90 6.03 35.79 5.18
687 2359 2.330231 TGTTGACAAATTAGCGCTGC 57.670 45.000 22.90 0.67 0.00 5.25
688 2360 1.879380 TGTTGACAAATTAGCGCTGCT 59.121 42.857 22.90 3.51 43.41 4.24
689 2361 2.293122 TGTTGACAAATTAGCGCTGCTT 59.707 40.909 22.90 10.50 40.44 3.91
690 2362 2.900122 TGACAAATTAGCGCTGCTTC 57.100 45.000 22.90 8.17 40.44 3.86
691 2363 1.468520 TGACAAATTAGCGCTGCTTCC 59.531 47.619 22.90 3.66 40.44 3.46
692 2364 0.447801 ACAAATTAGCGCTGCTTCCG 59.552 50.000 22.90 10.31 40.44 4.30
693 2365 0.447801 CAAATTAGCGCTGCTTCCGT 59.552 50.000 22.90 0.00 40.44 4.69
694 2366 1.135689 CAAATTAGCGCTGCTTCCGTT 60.136 47.619 22.90 1.21 40.44 4.44
695 2367 1.165270 AATTAGCGCTGCTTCCGTTT 58.835 45.000 22.90 0.00 40.44 3.60
696 2368 0.727398 ATTAGCGCTGCTTCCGTTTC 59.273 50.000 22.90 0.00 40.44 2.78
697 2369 0.601576 TTAGCGCTGCTTCCGTTTCA 60.602 50.000 22.90 0.00 40.44 2.69
698 2370 0.601576 TAGCGCTGCTTCCGTTTCAA 60.602 50.000 22.90 0.00 40.44 2.69
699 2371 1.008995 GCGCTGCTTCCGTTTCAAA 60.009 52.632 0.00 0.00 0.00 2.69
700 2372 0.593773 GCGCTGCTTCCGTTTCAAAA 60.594 50.000 0.00 0.00 0.00 2.44
701 2373 1.833860 CGCTGCTTCCGTTTCAAAAA 58.166 45.000 0.00 0.00 0.00 1.94
1002 2848 2.282745 GCCCAAGGCTTCAGCACT 60.283 61.111 12.01 0.00 46.69 4.40
1245 5084 2.223688 ACATCTACAGCTGCATCGAGAC 60.224 50.000 15.27 0.00 0.00 3.36
1287 5126 0.879765 CAAGTCAGCCTTTGCCAGAG 59.120 55.000 0.00 0.00 38.69 3.35
1410 5250 4.102524 TGTCCAAGAGCTCCTTTTAGTTCA 59.897 41.667 10.93 0.00 31.42 3.18
1546 5386 1.604378 GGTGGTGATGCTACTGGCT 59.396 57.895 0.00 0.00 42.39 4.75
1648 5488 2.627699 TCTTGCCTCCAAAACATTCCAC 59.372 45.455 0.00 0.00 0.00 4.02
1666 5506 2.091541 CACAGGACCAAAGTTGTGTGT 58.908 47.619 0.00 0.00 36.19 3.72
1944 5824 9.005777 CAATTTTGTCAATTTCATTTCCCTGAT 57.994 29.630 0.00 0.00 0.00 2.90
1946 5826 8.977267 TTTTGTCAATTTCATTTCCCTGATTT 57.023 26.923 0.00 0.00 0.00 2.17
2074 6002 2.951642 ACACCATACACATAGCATTGCC 59.048 45.455 4.70 0.00 0.00 4.52
2108 6036 4.252878 CACAACAAGCCCAAAAGAAAAGT 58.747 39.130 0.00 0.00 0.00 2.66
2794 9626 3.068691 TCCCGGAAGACTCGCCAG 61.069 66.667 0.73 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.997621 TCCTGTAACATCACTAGTGTAAAATC 57.002 34.615 21.99 10.74 0.00 2.17
27 1280 4.816925 GCCATTAGAGACACCATTACTTCC 59.183 45.833 0.00 0.00 0.00 3.46
81 1335 5.986741 CAGCATGCTTGGCAAATTATATGAA 59.013 36.000 19.98 0.00 43.62 2.57
88 1342 2.809696 GTTTCAGCATGCTTGGCAAATT 59.190 40.909 19.98 0.00 43.62 1.82
90 1344 1.138464 TGTTTCAGCATGCTTGGCAAA 59.862 42.857 19.98 11.71 43.62 3.68
92 1346 0.751452 TTGTTTCAGCATGCTTGGCA 59.249 45.000 19.98 11.93 44.86 4.92
93 1347 1.425412 CTTGTTTCAGCATGCTTGGC 58.575 50.000 19.98 9.32 34.76 4.52
94 1348 1.425412 GCTTGTTTCAGCATGCTTGG 58.575 50.000 19.98 8.26 39.83 3.61
95 1349 1.269883 TGGCTTGTTTCAGCATGCTTG 60.270 47.619 19.98 13.88 42.10 4.01
96 1350 1.000506 CTGGCTTGTTTCAGCATGCTT 59.999 47.619 19.98 0.00 42.10 3.91
124 1398 3.241067 TCACAAGGTTATAGGTCGTGC 57.759 47.619 0.00 0.00 0.00 5.34
163 1437 4.665009 TCAGCATCATTAGGTATTCCCCTT 59.335 41.667 0.00 0.00 35.97 3.95
273 1642 8.985315 TCATTATATCATTTGGAAGCAGAGTT 57.015 30.769 0.00 0.00 0.00 3.01
274 1643 8.844244 GTTCATTATATCATTTGGAAGCAGAGT 58.156 33.333 0.00 0.00 0.00 3.24
275 1644 9.064706 AGTTCATTATATCATTTGGAAGCAGAG 57.935 33.333 0.00 0.00 0.00 3.35
293 1662 6.856426 CAGCGATATAGACGTGAAGTTCATTA 59.144 38.462 9.18 0.90 0.00 1.90
308 1677 7.368059 TGAACATAACCAGTACAGCGATATAG 58.632 38.462 0.00 0.00 0.00 1.31
310 1679 6.156748 TGAACATAACCAGTACAGCGATAT 57.843 37.500 0.00 0.00 0.00 1.63
348 1979 5.008911 TGCACATATCACTTAATGGTGCATC 59.991 40.000 11.95 0.00 36.32 3.91
363 1994 4.274459 GGTCCACTTCTGATTGCACATATC 59.726 45.833 0.00 0.00 0.00 1.63
382 2015 1.064952 CAAGTGACGTTGGTTTGGTCC 59.935 52.381 0.00 0.00 0.00 4.46
590 2261 3.317993 GCAAGGACAACCATGTTAAGTGT 59.682 43.478 0.00 0.00 40.74 3.55
674 2346 0.447801 ACGGAAGCAGCGCTAATTTG 59.552 50.000 10.99 7.43 38.25 2.32
675 2347 1.165270 AACGGAAGCAGCGCTAATTT 58.835 45.000 10.99 4.52 38.25 1.82
676 2348 1.130561 GAAACGGAAGCAGCGCTAATT 59.869 47.619 10.99 7.98 38.25 1.40
677 2349 0.727398 GAAACGGAAGCAGCGCTAAT 59.273 50.000 10.99 0.00 38.25 1.73
678 2350 0.601576 TGAAACGGAAGCAGCGCTAA 60.602 50.000 10.99 0.00 38.25 3.09
679 2351 0.601576 TTGAAACGGAAGCAGCGCTA 60.602 50.000 10.99 0.00 38.25 4.26
680 2352 1.444119 TTTGAAACGGAAGCAGCGCT 61.444 50.000 2.64 2.64 42.56 5.92
681 2353 0.593773 TTTTGAAACGGAAGCAGCGC 60.594 50.000 0.00 0.00 0.00 5.92
682 2354 1.833860 TTTTTGAAACGGAAGCAGCG 58.166 45.000 0.00 0.00 0.00 5.18
708 2380 2.476241 GCAGCAGCGCTAATTTGTTTTT 59.524 40.909 10.99 0.00 36.40 1.94
709 2381 2.061028 GCAGCAGCGCTAATTTGTTTT 58.939 42.857 10.99 0.00 36.40 2.43
710 2382 1.000385 TGCAGCAGCGCTAATTTGTTT 60.000 42.857 10.99 0.00 46.23 2.83
711 2383 0.597568 TGCAGCAGCGCTAATTTGTT 59.402 45.000 10.99 0.00 46.23 2.83
712 2384 2.256391 TGCAGCAGCGCTAATTTGT 58.744 47.368 10.99 0.00 46.23 2.83
810 2486 3.226346 TCGTTTGATTTCGGATCTCGT 57.774 42.857 0.00 0.00 40.32 4.18
1002 2848 3.838317 AGAGAATGGTAGGCAGTGTGTTA 59.162 43.478 0.00 0.00 0.00 2.41
1134 4973 1.515020 CTCTGGAACTGCTCCTCGG 59.485 63.158 0.00 0.00 45.64 4.63
1245 5084 0.179181 GCTTGGTGTGCACATCATCG 60.179 55.000 32.16 25.12 36.77 3.84
1410 5250 3.906846 AGACACATCCTCTCCTCTTTTGT 59.093 43.478 0.00 0.00 0.00 2.83
1546 5386 1.839424 TGGTGATCTCTCTCGCTTCA 58.161 50.000 0.00 0.00 0.00 3.02
1648 5488 2.364632 TCACACACAACTTTGGTCCTG 58.635 47.619 0.00 0.00 0.00 3.86
1666 5506 1.830279 CCTGCAATTGCTCCTCTTCA 58.170 50.000 29.37 7.29 42.66 3.02
2108 6036 4.497473 CCGTTGTTGGCATTCTTTTCTA 57.503 40.909 0.00 0.00 0.00 2.10
2173 6159 3.138625 CGGTGGTGGTGTGTCTCT 58.861 61.111 0.00 0.00 0.00 3.10
2390 6376 1.652563 GTTGGTGTGCGGGAGAAAC 59.347 57.895 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.