Multiple sequence alignment - TraesCS7B01G065600

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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 TraesCS7B01G065600 chr7B 100.000 2372 0 0 1 2372 71247772 71245401 0 4381
1 TraesCS7B01G065600 chr1D 87.244 2391 272 21 1 2372 217012062 217009686 0 2695
2 TraesCS7B01G065600 chr1D 85.506 2401 301 31 1 2372 453131568 453133950 0 2462
3 TraesCS7B01G065600 chr5D 87.622 2351 249 21 40 2372 35280712 35278386 0 2691
4 TraesCS7B01G065600 chr5D 85.357 2397 303 36 1 2372 430529857 430532230 0 2438
5 TraesCS7B01G065600 chr3D 87.542 2360 248 28 37 2372 126392447 126394784 0 2687
6 TraesCS7B01G065600 chr2B 86.848 2395 283 23 1 2372 243358820 243361205 0 2649
7 TraesCS7B01G065600 chr7D 86.611 2390 295 19 1 2372 558450751 558453133 0 2617
8 TraesCS7B01G065600 chr2D 86.140 2381 284 29 1 2353 549979728 549982090 0 2527
9 TraesCS7B01G065600 chr4D 85.997 2371 299 22 1 2353 35486691 35489046 0 2508


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 TraesCS7B01G065600 chr7B 71245401 71247772 2371 True 4381 4381 100.000 1 2372 1 chr7B.!!$R1 2371
1 TraesCS7B01G065600 chr1D 217009686 217012062 2376 True 2695 2695 87.244 1 2372 1 chr1D.!!$R1 2371
2 TraesCS7B01G065600 chr1D 453131568 453133950 2382 False 2462 2462 85.506 1 2372 1 chr1D.!!$F1 2371
3 TraesCS7B01G065600 chr5D 35278386 35280712 2326 True 2691 2691 87.622 40 2372 1 chr5D.!!$R1 2332
4 TraesCS7B01G065600 chr5D 430529857 430532230 2373 False 2438 2438 85.357 1 2372 1 chr5D.!!$F1 2371
5 TraesCS7B01G065600 chr3D 126392447 126394784 2337 False 2687 2687 87.542 37 2372 1 chr3D.!!$F1 2335
6 TraesCS7B01G065600 chr2B 243358820 243361205 2385 False 2649 2649 86.848 1 2372 1 chr2B.!!$F1 2371
7 TraesCS7B01G065600 chr7D 558450751 558453133 2382 False 2617 2617 86.611 1 2372 1 chr7D.!!$F1 2371
8 TraesCS7B01G065600 chr2D 549979728 549982090 2362 False 2527 2527 86.140 1 2353 1 chr2D.!!$F1 2352
9 TraesCS7B01G065600 chr4D 35486691 35489046 2355 False 2508 2508 85.997 1 2353 1 chr4D.!!$F1 2352

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
938 958 0.037605 GACCCCGACGAGACACAAAT 60.038 55.0 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 2084 0.108992 GGCGACACGGTGTTGAGATA 60.109 55.0 28.35 0.0 33.58 1.98 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
75 77 2.508439 GAGCCGGATTTGCGTCGA 60.508 61.111 5.05 0.00 0.00 4.20
93 95 4.175489 CGCGGACACGAGACGGAT 62.175 66.667 0.00 0.00 42.82 4.18
117 124 2.123640 GCGCCTACTCCTCTCCCT 60.124 66.667 0.00 0.00 0.00 4.20
142 149 4.514577 CCGGTCGGTGGCAGCTAG 62.515 72.222 15.48 0.00 0.00 3.42
230 242 0.959372 ACGACGACCTCGACCTTGAT 60.959 55.000 0.00 0.00 46.14 2.57
276 288 2.264480 CGTCCGGCATGAAGACCA 59.736 61.111 0.00 0.00 0.00 4.02
296 308 2.362889 CCCTCCGGCAAAGGCAAT 60.363 61.111 0.00 0.00 43.71 3.56
349 361 3.595819 GCCAAAGAAGGCGCTGAT 58.404 55.556 7.64 0.00 46.12 2.90
389 401 2.203938 TCGGCCAAGAGGAAGGGT 60.204 61.111 2.24 0.00 36.89 4.34
464 477 1.982938 ACCACGCAGTAGGAGGTCC 60.983 63.158 0.00 0.00 41.61 4.46
470 483 0.910088 GCAGTAGGAGGTCCCCAACT 60.910 60.000 0.00 0.00 36.42 3.16
546 559 0.952497 CAGCACAGCCTCATCAACGT 60.952 55.000 0.00 0.00 0.00 3.99
649 665 4.431131 CCGGTGCCCAGCTTCCAT 62.431 66.667 0.00 0.00 0.00 3.41
744 761 0.680921 CCGTGCCCATTGACCTCAAT 60.681 55.000 0.00 0.00 46.62 2.57
752 769 2.592102 ATTGACCTCAATGCCACACT 57.408 45.000 0.00 0.00 44.22 3.55
797 814 2.504681 CGCAAGGAAACGCATGCC 60.505 61.111 13.15 0.00 36.41 4.40
814 831 2.672651 CACAGATGCCGGCCAACA 60.673 61.111 26.77 4.98 0.00 3.33
817 834 2.440796 AGATGCCGGCCAACATGG 60.441 61.111 26.77 0.36 41.55 3.66
819 836 1.453015 GATGCCGGCCAACATGGTA 60.453 57.895 26.77 0.73 40.46 3.25
844 861 2.280524 CCCGCAACCTGTTCGACA 60.281 61.111 0.00 0.00 0.00 4.35
861 881 2.282180 AAAATGTCGGCCGCTGGT 60.282 55.556 23.51 2.26 0.00 4.00
891 911 5.171339 ACTACATGCAGAACCTCATCTTT 57.829 39.130 0.00 0.00 0.00 2.52
938 958 0.037605 GACCCCGACGAGACACAAAT 60.038 55.000 0.00 0.00 0.00 2.32
947 967 1.067846 CGAGACACAAATCCAGGACGA 60.068 52.381 0.00 0.00 0.00 4.20
950 970 0.762418 ACACAAATCCAGGACGACCA 59.238 50.000 6.71 0.00 38.94 4.02
1023 1044 0.107703 GTGATCAGGTCGGCATGGAA 60.108 55.000 0.21 0.00 0.00 3.53
1039 1060 1.072505 GAACTGGACGGCTTCCCAA 59.927 57.895 7.65 0.00 45.17 4.12
1089 1110 1.889829 CAAGAGGAAGAGGACGAGTGT 59.110 52.381 0.00 0.00 0.00 3.55
1090 1111 2.296073 AGAGGAAGAGGACGAGTGTT 57.704 50.000 0.00 0.00 0.00 3.32
1169 1199 2.022129 CGAGAAAGCGCACGAAGGT 61.022 57.895 11.47 0.00 0.00 3.50
1236 1266 0.476771 TTGGACAAGACCCCAAGACC 59.523 55.000 0.00 0.00 37.50 3.85
1257 1287 0.704551 GCGCTGAACAAAAGCATTCG 59.295 50.000 0.00 0.00 40.86 3.34
1262 1292 3.423206 GCTGAACAAAAGCATTCGACTTG 59.577 43.478 0.00 0.00 40.52 3.16
1271 1301 3.411446 AGCATTCGACTTGTTGGATTCA 58.589 40.909 0.00 0.00 0.00 2.57
1295 1325 1.066573 CCACCGAGAGTTTCATGAGCT 60.067 52.381 0.00 0.00 0.00 4.09
1296 1326 2.613977 CCACCGAGAGTTTCATGAGCTT 60.614 50.000 0.00 0.00 0.00 3.74
1308 1338 7.001073 AGTTTCATGAGCTTAAGAAGTTTCCT 58.999 34.615 6.67 0.00 0.00 3.36
1325 1355 6.314917 AGTTTCCTCCTTACCAAATTGTGAT 58.685 36.000 0.00 0.00 0.00 3.06
1332 1362 1.234821 ACCAAATTGTGATCACGCGT 58.765 45.000 20.54 5.58 0.00 6.01
1333 1363 1.196808 ACCAAATTGTGATCACGCGTC 59.803 47.619 20.54 0.00 0.00 5.19
1369 1399 2.762887 TCGAAGCAATGGAGAGTGATCT 59.237 45.455 0.00 0.00 0.00 2.75
1393 1423 4.485163 ACAAGAGTGCAACAAGTTTTGTC 58.515 39.130 0.00 0.00 44.59 3.18
1455 1485 1.406539 GGCATGCAAGACAAGGTATGG 59.593 52.381 21.36 0.00 0.00 2.74
1456 1486 1.202336 GCATGCAAGACAAGGTATGGC 60.202 52.381 14.21 0.00 37.30 4.40
1459 1493 1.350684 TGCAAGACAAGGTATGGCAGA 59.649 47.619 0.00 0.00 40.75 4.26
1462 1496 3.255642 GCAAGACAAGGTATGGCAGAAAA 59.744 43.478 0.00 0.00 40.75 2.29
1466 1500 2.159382 CAAGGTATGGCAGAAAACCGT 58.841 47.619 0.00 0.00 37.09 4.83
1512 1547 2.985809 GCTTGCGTGTTCATTTGCATAA 59.014 40.909 0.00 0.00 37.17 1.90
1520 1555 6.290643 CGTGTTCATTTGCATAACATTTGTG 58.709 36.000 7.44 0.00 35.72 3.33
1521 1556 6.074409 CGTGTTCATTTGCATAACATTTGTGT 60.074 34.615 7.44 0.00 35.72 3.72
1525 1560 7.405469 TCATTTGCATAACATTTGTGTCAAC 57.595 32.000 0.00 0.00 0.00 3.18
1627 1665 4.044308 TCTCCCATTGCTTTAGGGTCATA 58.956 43.478 0.00 0.00 43.31 2.15
1641 1679 4.290942 AGGGTCATAAAAGACGAGGAGAT 58.709 43.478 0.00 0.00 39.42 2.75
1666 1704 3.595758 GCGCAATATGCCGCCCTT 61.596 61.111 0.30 0.00 41.12 3.95
1679 1718 4.137872 CCCTTAAGTCGCGCGGGA 62.138 66.667 31.69 23.01 37.05 5.14
1708 1747 2.047742 GCTATGGAGGAGGTTGGGGAT 61.048 57.143 0.00 0.00 0.00 3.85
1711 1750 1.619669 GGAGGAGGTTGGGGATGGT 60.620 63.158 0.00 0.00 0.00 3.55
1837 1879 2.355193 AAGAGAGGAGGAGCGCCAC 61.355 63.158 9.88 1.27 36.29 5.01
1849 1891 0.889186 AGCGCCACCGTTTCAAAGAT 60.889 50.000 2.29 0.00 36.67 2.40
1866 1908 2.012673 AGATGAGCAAATGAACGCCTC 58.987 47.619 0.00 0.00 0.00 4.70
1891 1933 4.566837 TGGAGATCCAAATAAGGAGGCTA 58.433 43.478 0.00 0.00 44.35 3.93
1904 1946 1.681538 GAGGCTAGAGATGGACGTGA 58.318 55.000 0.00 0.00 0.00 4.35
2010 2052 1.222115 AAAGAAGTGGCACTCGCGAC 61.222 55.000 22.31 10.13 46.35 5.19
2029 2071 1.708993 CCATGATGACCGGGGTGGAT 61.709 60.000 6.32 0.00 42.00 3.41
2042 2084 2.443255 GGGGTGGATATCATGAAGGTGT 59.557 50.000 0.00 0.00 0.00 4.16
2086 2128 1.005394 GAGGCCGTGGTTCGAGAAA 60.005 57.895 0.00 0.00 42.86 2.52
2089 2131 0.879090 GGCCGTGGTTCGAGAAAATT 59.121 50.000 0.00 0.00 42.86 1.82
2095 2137 2.814336 GTGGTTCGAGAAAATTCAGGCT 59.186 45.455 0.00 0.00 0.00 4.58
2126 2168 4.543590 AAGTTCACCGATGAGTGATCTT 57.456 40.909 10.65 10.65 45.80 2.40
2164 2209 3.505808 TTTTTGTATGCCGGCTTGC 57.494 47.368 29.70 24.99 0.00 4.01
2231 2279 1.698506 CCACCCCTTTTTGTGTGCTA 58.301 50.000 0.00 0.00 0.00 3.49
2325 2375 4.334118 AGCGCTGGCATGGTGTCA 62.334 61.111 10.39 0.00 43.41 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
258 270 2.511600 GGTCTTCATGCCGGACGG 60.512 66.667 5.05 6.35 38.57 4.79
321 333 2.951475 TTCTTTGGCTTGGTCGCGGT 62.951 55.000 6.13 0.00 0.00 5.68
365 377 4.821589 CTCTTGGCCGACTCCGCC 62.822 72.222 0.00 1.67 34.23 6.13
366 378 4.821589 CCTCTTGGCCGACTCCGC 62.822 72.222 0.00 0.00 0.00 5.54
367 379 2.564553 CTTCCTCTTGGCCGACTCCG 62.565 65.000 0.00 0.00 0.00 4.63
404 416 2.584391 GGCTTCACCCCTCGTGTCT 61.584 63.158 0.00 0.00 43.51 3.41
408 420 3.692406 GACGGCTTCACCCCTCGT 61.692 66.667 0.00 0.00 36.74 4.18
446 459 1.982938 GGACCTCCTACTGCGTGGT 60.983 63.158 0.00 0.00 0.00 4.16
585 601 4.864334 GCAGCACCATCCGAGGGG 62.864 72.222 3.73 0.00 34.24 4.79
614 630 2.736995 GGTGCAAGCTGACGCGTA 60.737 61.111 13.97 0.00 42.32 4.42
635 651 0.322456 TACACATGGAAGCTGGGCAC 60.322 55.000 0.00 0.00 0.00 5.01
649 665 3.702048 GAGGCCTGCGGGTACACA 61.702 66.667 12.00 0.00 34.45 3.72
744 761 1.835267 ACCGACTACCAGTGTGGCA 60.835 57.895 0.00 0.00 42.67 4.92
752 769 2.282674 ACGAGCCACCGACTACCA 60.283 61.111 0.00 0.00 0.00 3.25
783 800 0.537143 TCTGTGGCATGCGTTTCCTT 60.537 50.000 12.44 0.00 0.00 3.36
797 814 2.048023 ATGTTGGCCGGCATCTGTG 61.048 57.895 30.85 0.00 0.00 3.66
814 831 4.157120 GCGGGCGTCTGGTACCAT 62.157 66.667 16.75 0.00 0.00 3.55
817 834 3.116531 GTTGCGGGCGTCTGGTAC 61.117 66.667 0.00 0.00 0.00 3.34
844 861 2.282180 ACCAGCGGCCGACATTTT 60.282 55.556 33.48 3.58 0.00 1.82
861 881 3.557054 GGTTCTGCATGTAGTCCTTGTCA 60.557 47.826 10.80 0.00 0.00 3.58
865 885 2.906389 TGAGGTTCTGCATGTAGTCCTT 59.094 45.455 22.18 8.55 0.00 3.36
921 941 0.739813 GGATTTGTGTCTCGTCGGGG 60.740 60.000 0.00 0.00 0.00 5.73
968 989 2.513026 ATCGGGATCATAGCCAGCGC 62.513 60.000 0.00 0.00 0.00 5.92
991 1012 1.521457 GATCACGCATGAAGGCCGA 60.521 57.895 0.00 0.00 38.69 5.54
1039 1060 2.220133 CGTTCGAAAACTCGTGGTCAAT 59.780 45.455 0.00 0.00 32.95 2.57
1057 1078 0.899720 TCCTCTTGCCCGTATTCGTT 59.100 50.000 0.00 0.00 35.01 3.85
1062 1083 1.123928 CCTCTTCCTCTTGCCCGTAT 58.876 55.000 0.00 0.00 0.00 3.06
1113 1134 2.989253 TTGGCGAGCTCGTCCTCA 60.989 61.111 35.43 24.11 44.42 3.86
1236 1266 0.664166 AATGCTTTTGTTCAGCGCCG 60.664 50.000 2.29 0.00 40.45 6.46
1242 1272 4.630894 ACAAGTCGAATGCTTTTGTTCA 57.369 36.364 0.00 0.00 0.00 3.18
1271 1301 2.567169 TCATGAAACTCTCGGTGGACAT 59.433 45.455 0.00 0.00 0.00 3.06
1308 1338 3.438781 GCGTGATCACAATTTGGTAAGGA 59.561 43.478 24.93 0.00 0.00 3.36
1332 1362 1.004320 CGAAATGGACACCCACCGA 60.004 57.895 0.00 0.00 46.98 4.69
1333 1363 0.604243 TTCGAAATGGACACCCACCG 60.604 55.000 0.00 0.00 46.98 4.94
1362 1392 4.960938 TGTTGCACTCTTGTTAGATCACT 58.039 39.130 0.00 0.00 0.00 3.41
1369 1399 6.019779 ACAAAACTTGTTGCACTCTTGTTA 57.980 33.333 0.00 0.00 42.22 2.41
1448 1478 1.339727 GGACGGTTTTCTGCCATACCT 60.340 52.381 0.00 0.00 0.00 3.08
1455 1485 2.357952 ACAAAAGAGGACGGTTTTCTGC 59.642 45.455 0.00 0.00 0.00 4.26
1456 1486 3.377172 ACACAAAAGAGGACGGTTTTCTG 59.623 43.478 0.00 0.00 0.00 3.02
1459 1493 3.349022 TGACACAAAAGAGGACGGTTTT 58.651 40.909 0.00 0.00 0.00 2.43
1462 1496 2.104111 TGATGACACAAAAGAGGACGGT 59.896 45.455 0.00 0.00 0.00 4.83
1466 1500 5.436175 TGAACTTGATGACACAAAAGAGGA 58.564 37.500 0.00 0.00 0.00 3.71
1512 1547 3.125316 GCAAGCATGTTGACACAAATGT 58.875 40.909 10.87 0.00 43.71 2.71
1627 1665 4.319177 CCTTGAACATCTCCTCGTCTTTT 58.681 43.478 0.00 0.00 0.00 2.27
1641 1679 0.455410 GGCATATTGCGCCTTGAACA 59.545 50.000 4.18 0.00 46.21 3.18
1666 1704 3.060020 CTTCCTCCCGCGCGACTTA 62.060 63.158 34.63 12.30 0.00 2.24
1675 1713 0.394565 CCATAGCTTCCTTCCTCCCG 59.605 60.000 0.00 0.00 0.00 5.14
1679 1718 2.688477 CTCCTCCATAGCTTCCTTCCT 58.312 52.381 0.00 0.00 0.00 3.36
1685 1724 1.141858 CCCAACCTCCTCCATAGCTTC 59.858 57.143 0.00 0.00 0.00 3.86
1726 1765 2.222013 GGAGTTGGTCTTCCCCCGT 61.222 63.158 0.00 0.00 0.00 5.28
1837 1879 4.797471 TCATTTGCTCATCTTTGAAACGG 58.203 39.130 0.00 0.00 0.00 4.44
1849 1891 0.250684 TGGAGGCGTTCATTTGCTCA 60.251 50.000 0.00 0.00 0.00 4.26
1866 1908 4.660168 CCTCCTTATTTGGATCTCCATGG 58.340 47.826 4.97 4.97 46.97 3.66
1881 1923 2.175069 ACGTCCATCTCTAGCCTCCTTA 59.825 50.000 0.00 0.00 0.00 2.69
1882 1924 1.063567 ACGTCCATCTCTAGCCTCCTT 60.064 52.381 0.00 0.00 0.00 3.36
1891 1933 1.895798 TGCTTCTTCACGTCCATCTCT 59.104 47.619 0.00 0.00 0.00 3.10
1904 1946 1.920610 AGCATCTTGGCTTGCTTCTT 58.079 45.000 0.00 0.00 46.71 2.52
1957 1999 4.207281 TTGGCGGCCTCGATCTCG 62.207 66.667 21.46 0.00 39.00 4.04
1990 2032 1.205064 CGCGAGTGCCACTTCTTTG 59.795 57.895 0.00 0.00 38.08 2.77
2002 2044 1.141881 GGTCATCATGGTCGCGAGT 59.858 57.895 10.24 0.00 0.00 4.18
2010 2052 1.708993 ATCCACCCCGGTCATCATGG 61.709 60.000 0.00 0.00 35.57 3.66
2042 2084 0.108992 GGCGACACGGTGTTGAGATA 60.109 55.000 28.35 0.00 33.58 1.98
2086 2128 2.502142 TGAGCATGTCAGCCTGAATT 57.498 45.000 0.00 0.00 34.23 2.17
2089 2131 0.689055 ACTTGAGCATGTCAGCCTGA 59.311 50.000 0.00 0.00 36.21 3.86
2095 2137 1.069978 TCGGTGAACTTGAGCATGTCA 59.930 47.619 0.00 0.00 0.00 3.58
2263 2312 7.523293 AAAAATATCACCACACAGTTCATGA 57.477 32.000 0.00 0.00 0.00 3.07
2308 2357 3.848301 TTGACACCATGCCAGCGCT 62.848 57.895 2.64 2.64 35.36 5.92
2325 2375 1.460504 CAGCAGCCATGTCTCATGTT 58.539 50.000 8.57 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.