Multiple sequence alignment - TraesCS7A01G459300

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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 TraesCS7A01G459300 chr7A 100.000 2438 0 0 1 2438 654395523 654397960 0 4503
1 TraesCS7A01G459300 chr7A 95.993 2446 87 10 1 2438 618748474 618746032 0 3964
2 TraesCS7A01G459300 chr6A 96.111 2443 87 8 1 2438 474617304 474619743 0 3978
3 TraesCS7A01G459300 chr6A 96.029 2443 89 8 1 2438 73419156 73421595 0 3967
4 TraesCS7A01G459300 chr6A 95.746 2445 95 9 1 2438 106289544 106291986 0 3930
5 TraesCS7A01G459300 chr4A 95.948 2443 91 8 1 2438 81354127 81351688 0 3956
6 TraesCS7A01G459300 chr4A 95.878 2450 86 12 1 2438 482066703 482069149 0 3951
7 TraesCS7A01G459300 chr4A 95.907 2443 90 9 1 2438 501519572 501517135 0 3949
8 TraesCS7A01G459300 chr4A 95.828 2445 93 9 1 2438 6136774 6139216 0 3941
9 TraesCS7A01G459300 chr1A 95.948 2443 89 7 1 2438 101571183 101568746 0 3954


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 TraesCS7A01G459300 chr7A 654395523 654397960 2437 False 4503 4503 100.000 1 2438 1 chr7A.!!$F1 2437
1 TraesCS7A01G459300 chr7A 618746032 618748474 2442 True 3964 3964 95.993 1 2438 1 chr7A.!!$R1 2437
2 TraesCS7A01G459300 chr6A 474617304 474619743 2439 False 3978 3978 96.111 1 2438 1 chr6A.!!$F3 2437
3 TraesCS7A01G459300 chr6A 73419156 73421595 2439 False 3967 3967 96.029 1 2438 1 chr6A.!!$F1 2437
4 TraesCS7A01G459300 chr6A 106289544 106291986 2442 False 3930 3930 95.746 1 2438 1 chr6A.!!$F2 2437
5 TraesCS7A01G459300 chr4A 81351688 81354127 2439 True 3956 3956 95.948 1 2438 1 chr4A.!!$R1 2437
6 TraesCS7A01G459300 chr4A 482066703 482069149 2446 False 3951 3951 95.878 1 2438 1 chr4A.!!$F2 2437
7 TraesCS7A01G459300 chr4A 501517135 501519572 2437 True 3949 3949 95.907 1 2438 1 chr4A.!!$R2 2437
8 TraesCS7A01G459300 chr4A 6136774 6139216 2442 False 3941 3941 95.828 1 2438 1 chr4A.!!$F1 2437
9 TraesCS7A01G459300 chr1A 101568746 101571183 2437 True 3954 3954 95.948 1 2438 1 chr1A.!!$R1 2437

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
351 355 0.466372 GCTAATTGGGCCCAGTCTCC 60.466 60.000 26.87 11.27 0.0 3.71 F
669 675 1.065418 CCCCTAGCAGTCCAAATTCGT 60.065 52.381 0.00 0.00 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1229 1235 0.178992 CCAGAGGCACCAAAGGACAA 60.179 55.0 0.00 0.0 0.00 3.18 R
1504 1511 0.181587 TCTTTTTCGGCACCAGGTGA 59.818 50.0 24.96 0.0 35.23 4.02 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
38 39 6.431722 AGCTGACTTCCTCTCTATTCTAGTT 58.568 40.000 0.00 0.00 0.00 2.24
74 75 5.369409 ACTTCCCCATTAAGTACTTAGGC 57.631 43.478 14.73 0.00 35.44 3.93
119 120 3.207549 TGAGGAGAGAGGATATCCAACCA 59.792 47.826 23.81 6.94 42.19 3.67
125 127 5.222870 AGAGAGGATATCCAACCATTCTGT 58.777 41.667 23.81 11.70 38.89 3.41
351 355 0.466372 GCTAATTGGGCCCAGTCTCC 60.466 60.000 26.87 11.27 0.00 3.71
407 413 8.832735 ACCTAACCTCCAAGAAATTAACATCTA 58.167 33.333 0.00 0.00 0.00 1.98
435 441 9.467796 CTTCTAGGGTCTTGGATTAAAAGATTT 57.532 33.333 0.00 0.00 36.14 2.17
518 524 8.736097 AAACCTAATATTTTTGTCCCTTCCTT 57.264 30.769 0.00 0.00 0.00 3.36
667 673 2.058593 CCCCCTAGCAGTCCAAATTC 57.941 55.000 0.00 0.00 0.00 2.17
669 675 1.065418 CCCCTAGCAGTCCAAATTCGT 60.065 52.381 0.00 0.00 0.00 3.85
698 704 3.594134 ACTCTGTCTGCAATGAGCTTAC 58.406 45.455 0.00 0.00 45.94 2.34
941 947 2.027192 TGTTTATCCCTGCTGTCTGGAC 60.027 50.000 0.00 0.00 33.56 4.02
1010 1016 6.014669 TCCAAAAACAAATTGATGACTAGGGG 60.015 38.462 0.00 0.00 0.00 4.79
1042 1048 4.326826 GAAGAGACACATCATCAAACCCA 58.673 43.478 0.00 0.00 0.00 4.51
1164 1170 5.458595 TCTAGTCAGATTGGCTCATCCTTA 58.541 41.667 0.00 0.00 32.64 2.69
1261 1267 6.672593 TGGTGCCTCTGGAAATATAGAAATT 58.327 36.000 0.00 0.00 0.00 1.82
1284 1290 9.965902 AATTCTATGATTTTCAGTAACACCTCT 57.034 29.630 0.00 0.00 0.00 3.69
1292 1298 6.633500 TTTCAGTAACACCTCTTGGATTTG 57.367 37.500 0.00 0.00 37.04 2.32
1301 1307 0.451383 TCTTGGATTTGCATTCCGCG 59.549 50.000 0.00 0.00 46.97 6.46
1349 1355 1.208293 GAGGAACTGGGCGATTCTCTT 59.792 52.381 0.00 0.00 41.55 2.85
1350 1356 1.065854 AGGAACTGGGCGATTCTCTTG 60.066 52.381 0.00 0.00 37.18 3.02
1383 1389 2.614057 CAAGGACAAGTTGACGAGCTTT 59.386 45.455 10.54 0.00 0.00 3.51
1400 1406 4.027437 AGCTTTGTGGAAACCCTAACAAA 58.973 39.130 0.00 0.00 39.51 2.83
1420 1426 1.358152 ATCCCTCCAGAAACCGTTGA 58.642 50.000 0.00 0.00 0.00 3.18
1468 1474 2.527624 TGCTCTGTGGCTGGACCT 60.528 61.111 0.00 0.00 40.22 3.85
1504 1511 6.326843 TCAAGATCTCTGATGAAGATGATGGT 59.673 38.462 0.00 0.00 33.29 3.55
1565 1572 3.691342 CCAGCCCGGTGTCTTCGA 61.691 66.667 0.00 0.00 0.00 3.71
1568 1575 0.673644 CAGCCCGGTGTCTTCGATTT 60.674 55.000 0.00 0.00 0.00 2.17
1837 1851 5.124617 GGAGATGCTCCCTGTTTTTCTAAAG 59.875 44.000 1.97 0.00 44.36 1.85
2157 2173 0.387622 CAGCCCAGCAAAATCGTGTG 60.388 55.000 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 3.116746 TCATAGTGGAGAGGGATGCCTAA 60.117 47.826 5.42 0.00 0.00 2.69
74 75 6.268617 TCAGTTTATCATAGTGGAGAGGGATG 59.731 42.308 0.00 0.00 0.00 3.51
407 413 8.393959 TCTTTTAATCCAAGACCCTAGAAGAT 57.606 34.615 0.00 0.00 0.00 2.40
435 441 5.514834 CCAGGGTTTCAAGTCTTCCTCATAA 60.515 44.000 0.00 0.00 0.00 1.90
448 454 3.312736 AAGAAGCTTCCAGGGTTTCAA 57.687 42.857 22.81 0.00 0.00 2.69
518 524 5.894393 CAGAATCTAGAGGTCTTAGGGTTGA 59.106 44.000 6.08 0.00 0.00 3.18
664 670 5.127194 TGCAGACAGAGTAAATAGGACGAAT 59.873 40.000 0.00 0.00 0.00 3.34
667 673 4.371855 TGCAGACAGAGTAAATAGGACG 57.628 45.455 0.00 0.00 0.00 4.79
669 675 6.544928 TCATTGCAGACAGAGTAAATAGGA 57.455 37.500 0.00 0.00 0.00 2.94
698 704 4.810491 CCCAAACTTCATTGACACTTTTGG 59.190 41.667 14.79 14.79 40.71 3.28
941 947 5.951747 TGAATTTTAGGGGGAACTCTCAATG 59.048 40.000 0.00 0.00 34.38 2.82
1010 1016 6.282199 TGATGTGTCTCTTCCTAAGGTTAC 57.718 41.667 0.00 0.00 0.00 2.50
1042 1048 8.006298 TGTTCCAAGAAGTAAACACAATCAAT 57.994 30.769 0.00 0.00 0.00 2.57
1229 1235 0.178992 CCAGAGGCACCAAAGGACAA 60.179 55.000 0.00 0.00 0.00 3.18
1261 1267 7.824289 CCAAGAGGTGTTACTGAAAATCATAGA 59.176 37.037 0.00 0.00 0.00 1.98
1284 1290 1.510383 CCGCGGAATGCAAATCCAA 59.490 52.632 24.07 0.00 46.97 3.53
1292 1298 2.435938 TCAAGACCCGCGGAATGC 60.436 61.111 30.73 12.66 41.47 3.56
1301 1307 1.909302 TCCTGATCAACCTCAAGACCC 59.091 52.381 0.00 0.00 0.00 4.46
1383 1389 3.898741 GGGATTTTGTTAGGGTTTCCACA 59.101 43.478 0.00 0.00 34.83 4.17
1400 1406 1.702957 TCAACGGTTTCTGGAGGGATT 59.297 47.619 0.00 0.00 0.00 3.01
1420 1426 3.120321 TGTTTAGCCACAAGTGATCGT 57.880 42.857 0.94 0.00 0.00 3.73
1468 1474 1.819288 GAGATCTTGAGACGACCCACA 59.181 52.381 0.00 0.00 0.00 4.17
1504 1511 0.181587 TCTTTTTCGGCACCAGGTGA 59.818 50.000 24.96 0.00 35.23 4.02
1565 1572 2.615493 CCTGCGGTGACCAGTAAGAAAT 60.615 50.000 1.11 0.00 0.00 2.17
1568 1575 1.972198 CCTGCGGTGACCAGTAAGA 59.028 57.895 1.11 0.00 0.00 2.10
1960 1976 8.455682 TCGTGCCAAAATAATCTAGGTTTTTAG 58.544 33.333 0.00 0.00 0.00 1.85
1966 1982 6.827586 TTTTCGTGCCAAAATAATCTAGGT 57.172 33.333 0.00 0.00 0.00 3.08
1970 1986 6.530019 AGGATTTTCGTGCCAAAATAATCT 57.470 33.333 0.00 0.00 36.33 2.40
1975 1991 4.764823 TCACTAGGATTTTCGTGCCAAAAT 59.235 37.500 0.00 0.00 38.43 1.82
2157 2173 2.726241 GCCATTTGCACTTTCTCGAAAC 59.274 45.455 0.00 0.00 40.77 2.78
2200 2216 1.172180 ATCCATGCGGCCCGTTTATG 61.172 55.000 4.45 7.56 0.00 1.90


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

AutoCloner maintained by Alex Coulton.