Multiple sequence alignment - TraesCS7D01G075700

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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 TraesCS7D01G075700 chr7D 100.000 2465 0 0 1 2465 44766317 44768781 0.000000e+00 4553
1 TraesCS7D01G075700 chr1B 98.124 1599 30 0 1 1599 461439044 461440642 0.000000e+00 2787
2 TraesCS7D01G075700 chrUn 97.874 1599 34 0 1 1599 217906591 217908189 0.000000e+00 2765
3 TraesCS7D01G075700 chr3B 97.874 1599 34 0 1 1599 6011843 6010245 0.000000e+00 2765
4 TraesCS7D01G075700 chr3B 97.874 1599 32 1 1 1599 92297809 92296213 0.000000e+00 2763
5 TraesCS7D01G075700 chr4D 97.811 1599 35 0 1 1599 123450063 123448465 0.000000e+00 2760
6 TraesCS7D01G075700 chr2B 97.811 1599 35 0 1 1599 234542237 234540639 0.000000e+00 2760
7 TraesCS7D01G075700 chr3A 97.749 1599 36 0 1 1599 495105837 495104239 0.000000e+00 2754
8 TraesCS7D01G075700 chr7A 97.685 1598 37 0 2 1599 708281822 708280225 0.000000e+00 2747
9 TraesCS7D01G075700 chr7A 93.836 876 38 14 1596 2465 47307609 47308474 0.000000e+00 1304
10 TraesCS7D01G075700 chr6D 97.625 1600 36 2 1 1599 108484131 108485729 0.000000e+00 2743
11 TraesCS7D01G075700 chr6D 82.296 514 67 17 1909 2416 420255999 420256494 8.150000e-115 424
12 TraesCS7D01G075700 chr5D 79.100 622 77 31 1849 2465 441585761 441586334 1.790000e-101 379
13 TraesCS7D01G075700 chr5A 76.404 801 115 44 1600 2370 611998637 611999393 5.010000e-97 364


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 TraesCS7D01G075700 chr7D 44766317 44768781 2464 False 4553 4553 100.000 1 2465 1 chr7D.!!$F1 2464
1 TraesCS7D01G075700 chr1B 461439044 461440642 1598 False 2787 2787 98.124 1 1599 1 chr1B.!!$F1 1598
2 TraesCS7D01G075700 chrUn 217906591 217908189 1598 False 2765 2765 97.874 1 1599 1 chrUn.!!$F1 1598
3 TraesCS7D01G075700 chr3B 6010245 6011843 1598 True 2765 2765 97.874 1 1599 1 chr3B.!!$R1 1598
4 TraesCS7D01G075700 chr3B 92296213 92297809 1596 True 2763 2763 97.874 1 1599 1 chr3B.!!$R2 1598
5 TraesCS7D01G075700 chr4D 123448465 123450063 1598 True 2760 2760 97.811 1 1599 1 chr4D.!!$R1 1598
6 TraesCS7D01G075700 chr2B 234540639 234542237 1598 True 2760 2760 97.811 1 1599 1 chr2B.!!$R1 1598
7 TraesCS7D01G075700 chr3A 495104239 495105837 1598 True 2754 2754 97.749 1 1599 1 chr3A.!!$R1 1598
8 TraesCS7D01G075700 chr7A 708280225 708281822 1597 True 2747 2747 97.685 2 1599 1 chr7A.!!$R1 1597
9 TraesCS7D01G075700 chr7A 47307609 47308474 865 False 1304 1304 93.836 1596 2465 1 chr7A.!!$F1 869
10 TraesCS7D01G075700 chr6D 108484131 108485729 1598 False 2743 2743 97.625 1 1599 1 chr6D.!!$F1 1598
11 TraesCS7D01G075700 chr5D 441585761 441586334 573 False 379 379 79.100 1849 2465 1 chr5D.!!$F1 616
12 TraesCS7D01G075700 chr5A 611998637 611999393 756 False 364 364 76.404 1600 2370 1 chr5A.!!$F1 770

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
617 619 0.033894 GGCCCGGAAATAGAACCCAA 60.034 55.0 0.73 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1513 1515 1.133637 TGCTTTTGTAGGGTCAGGCAA 60.134 47.619 0.0 0.0 0.0 4.52 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
113 114 6.822506 GTGAACTACACTTGCTTCTTGATAC 58.177 40.000 0.00 0.00 45.13 2.24
173 174 3.010138 CCCTTCCTCCACTTTGATAACCA 59.990 47.826 0.00 0.00 0.00 3.67
238 239 1.005630 GGAGTCGCACACTTGAGCT 60.006 57.895 0.00 0.00 34.41 4.09
295 296 3.564225 CCTTAGGGCCGATTAAATCACAC 59.436 47.826 0.00 0.00 0.00 3.82
313 314 5.421277 TCACACACGAGGAACTTTTCTTTA 58.579 37.500 0.00 0.00 41.55 1.85
346 347 8.923270 TCTTTTTGATTTGAAGGGTATGTTCTT 58.077 29.630 0.00 0.00 0.00 2.52
439 440 3.228188 AGGATGACTTCTTTGTTGGCA 57.772 42.857 0.00 0.00 0.00 4.92
511 512 1.674322 CCAACGCCTCGGGAAACAT 60.674 57.895 0.00 0.00 0.00 2.71
525 526 4.310769 GGGAAACATGTCGAGATAGATGG 58.689 47.826 0.00 0.00 0.00 3.51
555 557 3.832615 TTTATCCTCTTCCTTACCGGC 57.167 47.619 0.00 0.00 0.00 6.13
617 619 0.033894 GGCCCGGAAATAGAACCCAA 60.034 55.000 0.73 0.00 0.00 4.12
643 645 5.301298 CCCCTTTCTGATCCATTCATTTCTC 59.699 44.000 0.00 0.00 32.72 2.87
720 722 1.620822 GCCCTTTTGCTCTTCCTTCA 58.379 50.000 0.00 0.00 0.00 3.02
972 974 4.562394 TCGTAAAGTTTCGTTGTTCGTTCT 59.438 37.500 0.00 0.00 40.80 3.01
1084 1086 8.802856 CATTACGAGCTCAATATATAAGAGTGC 58.197 37.037 15.40 7.50 0.00 4.40
1191 1193 1.077429 GGCTTTTGAGGAGCGGGAT 60.077 57.895 0.00 0.00 41.03 3.85
1435 1437 2.428530 GCAAAGGATTGGGGATTCAGTC 59.571 50.000 0.00 0.00 37.02 3.51
1513 1515 0.673437 CCATCAGGCAACAACGGTTT 59.327 50.000 0.00 0.00 34.21 3.27
1580 1582 0.033504 GTGAAGCCTTGGAGACGACA 59.966 55.000 0.00 0.00 0.00 4.35
1647 1649 6.633500 AAAGACGTTCATCCATTTGAGAAA 57.367 33.333 0.00 0.00 0.00 2.52
1681 1684 9.877137 GAATTTGGGAAAACATTGTGAATTTAC 57.123 29.630 0.00 0.00 0.00 2.01
1688 1691 9.701355 GGAAAACATTGTGAATTTACAAAAGTG 57.299 29.630 18.38 14.55 43.13 3.16
1767 1771 7.383843 AGTTCACGAATTTGAAAACAGTTTGTT 59.616 29.630 0.00 0.00 43.41 2.83
1791 1795 9.829637 GTTAAATTTGAAAAAGTTCACGACATC 57.170 29.630 0.00 0.00 43.52 3.06
1801 1805 8.782533 AAAAGTTCACGACATCTGAAAATAAC 57.217 30.769 0.00 0.00 29.44 1.89
1805 1809 6.864560 TCACGACATCTGAAAATAACTACG 57.135 37.500 0.00 0.00 0.00 3.51
1812 1816 8.415192 ACATCTGAAAATAACTACGCGAATTA 57.585 30.769 15.93 8.57 0.00 1.40
1813 1817 8.875803 ACATCTGAAAATAACTACGCGAATTAA 58.124 29.630 15.93 0.00 0.00 1.40
2260 2325 6.203530 TGTTCACAAATTTGCAAAAAGTGTGA 59.796 30.769 31.44 31.44 38.13 3.58
2455 2527 4.586001 AGAACTTGAACCAGAAATGTGCAT 59.414 37.500 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 1.377725 GCCCTCTGTCCCACACATG 60.378 63.158 0.00 0.00 33.23 3.21
173 174 1.296715 GCCCACTCTCCGTTCACAT 59.703 57.895 0.00 0.00 0.00 3.21
238 239 0.904865 ATTCTCCAGTCTCCCGCACA 60.905 55.000 0.00 0.00 0.00 4.57
390 391 4.141413 TGACTATTGACCATTCCATCCCTG 60.141 45.833 0.00 0.00 0.00 4.45
439 440 2.880167 GCTTTCTCTCCCCCATCGTTTT 60.880 50.000 0.00 0.00 0.00 2.43
511 512 2.297315 GGTGATGCCATCTATCTCGACA 59.703 50.000 6.21 0.00 37.17 4.35
525 526 5.196695 AGGAAGAGGATAAAAAGGTGATGC 58.803 41.667 0.00 0.00 0.00 3.91
555 557 1.462670 GAAGAAGAGAAGTGCGCCTTG 59.537 52.381 14.63 0.00 32.03 3.61
617 619 2.287584 TGAATGGATCAGAAAGGGGGT 58.712 47.619 0.00 0.00 33.04 4.95
643 645 4.113815 TGGATCCCGCCTGCTTGG 62.114 66.667 9.90 0.00 39.35 3.61
720 722 1.600916 GCCTTCGTGGAGCCAAACT 60.601 57.895 0.00 0.00 38.35 2.66
829 831 2.983879 GCCCCGGGCCATGCTATAT 61.984 63.158 18.83 0.00 44.06 0.86
830 832 3.646715 GCCCCGGGCCATGCTATA 61.647 66.667 18.83 0.00 44.06 1.31
972 974 5.421056 AGAAACATAGATAGGGTCAACGACA 59.579 40.000 0.00 0.00 33.68 4.35
1435 1437 3.060363 GCACGACCTCTTAACATTACACG 59.940 47.826 0.00 0.00 0.00 4.49
1513 1515 1.133637 TGCTTTTGTAGGGTCAGGCAA 60.134 47.619 0.00 0.00 0.00 4.52
1647 1649 8.747471 ACAATGTTTTCCCAAATTCACATTTTT 58.253 25.926 0.00 0.00 29.41 1.94
1663 1666 9.209297 GCACTTTTGTAAATTCACAATGTTTTC 57.791 29.630 0.00 0.00 38.18 2.29
1688 1691 9.455847 TTTGGCAAACATTTTACATTTTTATGC 57.544 25.926 8.93 0.00 0.00 3.14
1767 1771 9.232082 CAGATGTCGTGAACTTTTTCAAATTTA 57.768 29.630 0.00 0.00 43.52 1.40
2003 2059 8.060020 TCATTTTTGTGTGCTTTATTCGAAAG 57.940 30.769 0.00 0.00 0.00 2.62
2063 2122 5.901552 TCAATTTGTGAACCTTCTCCAAAC 58.098 37.500 0.00 0.00 34.26 2.93
2211 2276 2.018515 TCCAAACCCGTGAACTGTTTC 58.981 47.619 0.00 0.00 30.19 2.78
2414 2485 4.520492 AGTTCTGCAGGGTTTTTCTATGTG 59.480 41.667 15.13 0.00 0.00 3.21
2415 2486 4.729868 AGTTCTGCAGGGTTTTTCTATGT 58.270 39.130 15.13 0.00 0.00 2.29
2416 2487 5.241506 TCAAGTTCTGCAGGGTTTTTCTATG 59.758 40.000 15.13 0.48 0.00 2.23
2417 2488 5.385198 TCAAGTTCTGCAGGGTTTTTCTAT 58.615 37.500 15.13 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.