Multiple sequence alignment - TraesCS7A01G502200

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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 TraesCS7A01G502200 chr7A 100.000 1523 0 0 1 1523 691448292 691446770 0.000000e+00 2813.0
1 TraesCS7A01G502200 chr7A 80.484 1404 225 33 1 1392 691522620 691521254 0.000000e+00 1029.0
2 TraesCS7A01G502200 chr7A 100.000 547 0 0 1814 2360 691446479 691445933 0.000000e+00 1011.0
3 TraesCS7A01G502200 chr7A 87.387 111 13 1 1283 1392 691470353 691470243 2.460000e-25 126.0
4 TraesCS7A01G502200 chr7D 95.082 1525 71 4 1 1523 599193468 599191946 0.000000e+00 2398.0
5 TraesCS7A01G502200 chr7D 92.933 283 16 4 1814 2094 599191552 599191272 2.180000e-110 409.0
6 TraesCS7A01G502200 chr4B 84.860 1539 173 18 1 1523 12840220 12841714 0.000000e+00 1496.0
7 TraesCS7A01G502200 chr4B 83.616 354 40 6 1186 1522 12872515 12872867 1.360000e-82 316.0
8 TraesCS7A01G502200 chr4B 83.333 354 41 7 1186 1522 12850614 12850966 6.330000e-81 311.0
9 TraesCS7A01G502200 chr4B 79.235 183 29 6 2118 2294 17089024 17088845 4.120000e-23 119.0
10 TraesCS7A01G502200 chr7B 94.325 793 39 5 732 1523 678645375 678644588 0.000000e+00 1210.0
11 TraesCS7A01G502200 chr7B 80.391 1382 237 28 25 1390 678664032 678662669 0.000000e+00 1020.0
12 TraesCS7A01G502200 chr7B 93.249 474 29 3 1 473 678648052 678647581 0.000000e+00 695.0
13 TraesCS7A01G502200 chr7B 93.291 313 20 1 426 737 678647586 678647274 5.940000e-126 460.0
14 TraesCS7A01G502200 chr7B 84.864 403 14 15 1972 2358 678642703 678642332 1.720000e-96 363.0
15 TraesCS7A01G502200 chr7B 94.643 168 9 0 1814 1981 678644465 678644298 6.470000e-66 261.0
16 TraesCS7A01G502200 chr1A 81.863 204 29 8 2112 2312 524282379 524282577 5.220000e-37 165.0
17 TraesCS7A01G502200 chr5B 81.122 196 27 7 2116 2305 15329350 15329159 5.260000e-32 148.0
18 TraesCS7A01G502200 chr5B 82.836 134 19 4 1207 1339 684165283 684165153 1.480000e-22 117.0
19 TraesCS7A01G502200 chr6D 79.703 202 27 12 2113 2305 148802792 148802988 1.470000e-27 134.0
20 TraesCS7A01G502200 chr2A 78.894 199 34 7 2116 2310 91143823 91143629 6.850000e-26 128.0
21 TraesCS7A01G502200 chr6B 80.220 182 24 10 2087 2260 622742738 622742561 2.460000e-25 126.0
22 TraesCS7A01G502200 chr6B 81.757 148 20 6 2116 2260 622744304 622744161 1.480000e-22 117.0
23 TraesCS7A01G502200 chr4A 71.941 474 110 20 919 1383 623398909 623399368 1.480000e-22 117.0
24 TraesCS7A01G502200 chr3A 73.851 348 50 29 1971 2299 625814628 625814953 1.490000e-17 100.0
25 TraesCS7A01G502200 chr3A 100.000 28 0 0 1971 1998 472570663 472570690 4.000000e-03 52.8
26 TraesCS7A01G502200 chr2D 81.818 110 14 5 1975 2078 430227681 430227572 1.160000e-13 87.9
27 TraesCS7A01G502200 chr3B 100.000 29 0 0 1970 1998 605650766 605650794 1.000000e-03 54.7


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 TraesCS7A01G502200 chr7A 691445933 691448292 2359 True 1912.0 2813 100.0000 1 2360 2 chr7A.!!$R3 2359
1 TraesCS7A01G502200 chr7A 691521254 691522620 1366 True 1029.0 1029 80.4840 1 1392 1 chr7A.!!$R2 1391
2 TraesCS7A01G502200 chr7D 599191272 599193468 2196 True 1403.5 2398 94.0075 1 2094 2 chr7D.!!$R1 2093
3 TraesCS7A01G502200 chr4B 12840220 12841714 1494 False 1496.0 1496 84.8600 1 1523 1 chr4B.!!$F1 1522
4 TraesCS7A01G502200 chr7B 678662669 678664032 1363 True 1020.0 1020 80.3910 25 1390 1 chr7B.!!$R1 1365
5 TraesCS7A01G502200 chr7B 678642332 678648052 5720 True 597.8 1210 92.0744 1 2358 5 chr7B.!!$R2 2357

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
356 371 0.46907 GAGATGACCAGCAGCCTGAT 59.531 55.0 0.0 0.0 41.77 2.90 F
1133 3104 0.03563 GCCATCCTCTCACAGTTGCT 60.036 55.0 0.0 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1198 3169 0.096628 CAGATGTCTTGCTCTTGCGC 59.903 55.000 0.00 0.0 43.34 6.09 R
2040 5721 3.419759 GTGTTTCCGCGCGTGGAT 61.420 61.111 39.19 0.0 38.00 3.41 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
55 56 4.363990 ACCGTGCACGCTCTCCTG 62.364 66.667 33.17 19.59 38.18 3.86
207 222 3.818787 GACGACGGCGGCTTCCTA 61.819 66.667 18.49 0.00 43.91 2.94
291 306 1.239968 GGAGGTACACCGTCGTCACT 61.240 60.000 0.00 0.00 42.08 3.41
331 346 1.137479 GCTGCCATACGTACACCCTTA 59.863 52.381 0.00 0.00 0.00 2.69
333 348 2.166870 CTGCCATACGTACACCCTTACA 59.833 50.000 0.00 0.00 0.00 2.41
356 371 0.469070 GAGATGACCAGCAGCCTGAT 59.531 55.000 0.00 0.00 41.77 2.90
384 399 0.884704 AGTGTGTGCCGATCCAACAC 60.885 55.000 11.43 11.43 34.86 3.32
403 418 2.594303 CCGTTTCAGCAGGTGCCA 60.594 61.111 0.00 0.00 43.38 4.92
566 623 0.676736 CGCAGAGACCCTATCCTTCC 59.323 60.000 0.00 0.00 0.00 3.46
567 624 1.794714 GCAGAGACCCTATCCTTCCA 58.205 55.000 0.00 0.00 0.00 3.53
622 680 2.355197 CTACCGTCATCATTGGTTGCA 58.645 47.619 0.00 0.00 37.20 4.08
623 681 1.838112 ACCGTCATCATTGGTTGCAT 58.162 45.000 0.00 0.00 29.87 3.96
784 2749 2.056906 AAACCAGCACGGCTTCCTCT 62.057 55.000 0.00 0.00 36.40 3.69
796 2761 1.001633 GCTTCCTCTGGTTCGGTAACA 59.998 52.381 0.00 0.00 37.34 2.41
847 2812 0.982852 CACCAGGATGCTCTACCCCA 60.983 60.000 0.00 0.00 31.97 4.96
873 2838 2.249139 AGCTCCTACTTCGTCAACCTT 58.751 47.619 0.00 0.00 0.00 3.50
877 2842 2.960384 TCCTACTTCGTCAACCTTGTCA 59.040 45.455 0.00 0.00 0.00 3.58
1023 2994 2.009774 GTCAAGGCTGCGTATGACATT 58.990 47.619 21.38 0.00 41.35 2.71
1067 3038 0.398098 GGTAGGAGGATCGGGGTGAA 60.398 60.000 0.00 0.00 34.37 3.18
1133 3104 0.035630 GCCATCCTCTCACAGTTGCT 60.036 55.000 0.00 0.00 0.00 3.91
1143 3114 1.520192 ACAGTTGCTGACGGTGACA 59.480 52.632 2.91 0.00 35.27 3.58
1198 3169 2.347452 ACGCCGAATAAGTTGTTCATCG 59.653 45.455 12.20 14.47 0.00 3.84
1324 3296 2.686106 GGGTCTACTTCGCCCCCA 60.686 66.667 0.00 0.00 36.46 4.96
1482 3455 3.494332 AGAATGACTTTGCAGAAGGCTT 58.506 40.909 0.00 0.00 45.15 4.35
1916 3993 1.279025 ACCATCCGGCCCATGTAAGT 61.279 55.000 0.00 0.00 34.57 2.24
1920 3997 3.283751 CATCCGGCCCATGTAAGTAAAA 58.716 45.455 0.00 0.00 0.00 1.52
1929 4006 5.133221 CCCATGTAAGTAAAATAGGCAGCT 58.867 41.667 0.00 0.00 0.00 4.24
1955 4032 1.773054 GCCGCATGAGCAGACATCAG 61.773 60.000 0.00 0.00 42.27 2.90
2040 5721 3.876589 GAACCGCCAGTTGAGCCGA 62.877 63.158 0.00 0.00 39.40 5.54
2041 5722 3.254024 AACCGCCAGTTGAGCCGAT 62.254 57.895 0.00 0.00 37.29 4.18
2069 5750 0.825410 GGAAACACCACCCCGTTTTT 59.175 50.000 0.00 0.00 35.53 1.94
2151 5848 6.203145 TGTTGATCAAGCATTTGAAAACATGG 59.797 34.615 8.80 0.00 45.82 3.66
2322 6019 8.822652 AAGAATGTAGAATGAAAGGCAAAAAG 57.177 30.769 0.00 0.00 0.00 2.27
2323 6020 8.181904 AGAATGTAGAATGAAAGGCAAAAAGA 57.818 30.769 0.00 0.00 0.00 2.52
2324 6021 8.641541 AGAATGTAGAATGAAAGGCAAAAAGAA 58.358 29.630 0.00 0.00 0.00 2.52
2325 6022 9.260002 GAATGTAGAATGAAAGGCAAAAAGAAA 57.740 29.630 0.00 0.00 0.00 2.52
2326 6023 8.593492 ATGTAGAATGAAAGGCAAAAAGAAAC 57.407 30.769 0.00 0.00 0.00 2.78
2336 6033 9.117145 GAAAGGCAAAAAGAAACAAAGAAAAAG 57.883 29.630 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.520342 CGCAAGCACTAGAGGGAGC 60.520 63.158 0.00 0.0 0.00 4.70
80 81 2.901042 GATGAGGACGGGGTGGAC 59.099 66.667 0.00 0.0 0.00 4.02
207 222 1.253100 CAATTGGCCCGTTTAGGTGT 58.747 50.000 0.00 0.0 38.74 4.16
291 306 3.968837 ATGGCCCGTCCCGACACTA 62.969 63.158 0.00 0.0 0.00 2.74
313 328 2.177734 TGTAAGGGTGTACGTATGGCA 58.822 47.619 0.00 0.0 0.00 4.92
331 346 1.681166 GCTGCTGGTCATCTCCATTGT 60.681 52.381 0.00 0.0 36.84 2.71
333 348 0.106819 GGCTGCTGGTCATCTCCATT 60.107 55.000 0.00 0.0 36.84 3.16
356 371 3.748623 GCACACACTGCATCCACA 58.251 55.556 0.00 0.0 46.29 4.17
384 399 3.365265 GCACCTGCTGAAACGGGG 61.365 66.667 0.00 0.0 40.73 5.73
594 652 4.443457 CCAATGATGACGGTAGGAATGACT 60.443 45.833 0.00 0.0 0.00 3.41
622 680 3.825160 AACTCGCGGTGGTGTGCAT 62.825 57.895 6.13 0.0 0.00 3.96
623 681 4.539083 AACTCGCGGTGGTGTGCA 62.539 61.111 6.13 0.0 0.00 4.57
784 2749 2.188062 GGGATGTTGTTACCGAACCA 57.812 50.000 0.00 0.0 34.38 3.67
873 2838 4.377708 ACGGCGCTGATGCTGACA 62.378 61.111 25.98 0.0 44.17 3.58
917 2882 4.329545 GGCGCCTGAACACCTCCA 62.330 66.667 22.15 0.0 0.00 3.86
1023 2994 3.640407 GCCAGGGTGTGCTCCAGA 61.640 66.667 0.00 0.0 0.00 3.86
1133 3104 0.529773 GAAGTGCAGTGTCACCGTCA 60.530 55.000 12.26 0.0 37.68 4.35
1198 3169 0.096628 CAGATGTCTTGCTCTTGCGC 59.903 55.000 0.00 0.0 43.34 6.09
1241 3213 2.941333 CGCCGATGATGGTGATGC 59.059 61.111 0.00 0.0 42.25 3.91
1324 3296 0.593128 GTGTCGGCATTGCAGTTCTT 59.407 50.000 11.39 0.0 0.00 2.52
1482 3455 7.406553 CAGCGGAGTCGATTAAAATGAATTTA 58.593 34.615 0.00 0.0 39.00 1.40
1916 3993 1.286501 CGTGCGAGCTGCCTATTTTA 58.713 50.000 0.00 0.0 45.60 1.52
1920 3997 4.899239 GCCGTGCGAGCTGCCTAT 62.899 66.667 0.00 0.0 45.60 2.57
2040 5721 3.419759 GTGTTTCCGCGCGTGGAT 61.420 61.111 39.19 0.0 38.00 3.41
2151 5848 9.838975 TGTTCAACATTTTGTATACATGATCAC 57.161 29.630 6.36 3.6 34.02 3.06
2314 6011 6.377780 TGCTTTTTCTTTGTTTCTTTTTGCC 58.622 32.000 0.00 0.0 0.00 4.52
2315 6012 7.850268 TTGCTTTTTCTTTGTTTCTTTTTGC 57.150 28.000 0.00 0.0 0.00 3.68
2322 6019 9.833182 TGGTTTATTTTGCTTTTTCTTTGTTTC 57.167 25.926 0.00 0.0 0.00 2.78
2325 6022 9.838975 CTTTGGTTTATTTTGCTTTTTCTTTGT 57.161 25.926 0.00 0.0 0.00 2.83
2326 6023 9.288124 CCTTTGGTTTATTTTGCTTTTTCTTTG 57.712 29.630 0.00 0.0 0.00 2.77


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

AutoCloner maintained by Alex Coulton.