Multiple sequence alignment - TraesCS7D01G285600

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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 TraesCS7D01G285600 chr7D 100.000 2192 0 0 1 2192 307040062 307042253 0.000000e+00 4048
1 TraesCS7D01G285600 chr3A 97.629 2193 51 1 1 2192 495104760 495102568 0.000000e+00 3760
2 TraesCS7D01G285600 chr2B 97.629 2193 51 1 1 2192 234541160 234538968 0.000000e+00 3760
3 TraesCS7D01G285600 chr1B 97.446 2193 54 2 1 2192 619195331 619193140 0.000000e+00 3738
4 TraesCS7D01G285600 chr1A 97.446 2193 54 2 1 2192 278521194 278523385 0.000000e+00 3738
5 TraesCS7D01G285600 chrUn 97.401 2193 55 2 1 2192 217907668 217909859 0.000000e+00 3733
6 TraesCS7D01G285600 chr3B 97.401 2193 55 2 1 2192 6010766 6008575 0.000000e+00 3733
7 TraesCS7D01G285600 chr3B 97.402 2194 53 2 1 2192 92296732 92294541 0.000000e+00 3733
8 TraesCS7D01G285600 chr3B 91.275 298 26 0 1895 2192 342697320 342697617 7.290000e-110 407
9 TraesCS7D01G285600 chr4A 96.945 2193 66 1 1 2192 67519498 67521690 0.000000e+00 3677
10 TraesCS7D01G285600 chr4A 93.171 1684 104 4 1 1681 280911111 280909436 0.000000e+00 2462
11 TraesCS7D01G285600 chr2A 97.525 202 5 0 1684 1885 113953702 113953903 1.610000e-91 346


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 TraesCS7D01G285600 chr7D 307040062 307042253 2191 False 4048 4048 100.000 1 2192 1 chr7D.!!$F1 2191
1 TraesCS7D01G285600 chr3A 495102568 495104760 2192 True 3760 3760 97.629 1 2192 1 chr3A.!!$R1 2191
2 TraesCS7D01G285600 chr2B 234538968 234541160 2192 True 3760 3760 97.629 1 2192 1 chr2B.!!$R1 2191
3 TraesCS7D01G285600 chr1B 619193140 619195331 2191 True 3738 3738 97.446 1 2192 1 chr1B.!!$R1 2191
4 TraesCS7D01G285600 chr1A 278521194 278523385 2191 False 3738 3738 97.446 1 2192 1 chr1A.!!$F1 2191
5 TraesCS7D01G285600 chrUn 217907668 217909859 2191 False 3733 3733 97.401 1 2192 1 chrUn.!!$F1 2191
6 TraesCS7D01G285600 chr3B 6008575 6010766 2191 True 3733 3733 97.401 1 2192 1 chr3B.!!$R1 2191
7 TraesCS7D01G285600 chr3B 92294541 92296732 2191 True 3733 3733 97.402 1 2192 1 chr3B.!!$R2 2191
8 TraesCS7D01G285600 chr4A 67519498 67521690 2192 False 3677 3677 96.945 1 2192 1 chr4A.!!$F1 2191
9 TraesCS7D01G285600 chr4A 280909436 280911111 1675 True 2462 2462 93.171 1 1681 1 chr4A.!!$R1 1680

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
508 510 0.527817 GCCTTGGAGACGATGTACCG 60.528 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1818 0.388134 CGAAGAACCGGAAGCGAAGA 60.388 55.0 9.46 0.0 0.0 2.87 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
45 46 9.994432 ATAACTCGAATTTCAAATCATTCACTC 57.006 29.630 0.00 0.00 30.84 3.51
332 333 1.795768 ATTGGTACTGTCACTGCACG 58.204 50.000 0.00 0.00 0.00 5.34
396 397 1.201954 CGTGCGACATGAAGACATTGG 60.202 52.381 0.00 0.00 34.15 3.16
440 441 1.152963 AGGCAACAACGGTTCTGCT 60.153 52.632 18.69 7.22 34.21 4.24
502 504 0.976641 TGTGAAGCCTTGGAGACGAT 59.023 50.000 0.00 0.00 0.00 3.73
508 510 0.527817 GCCTTGGAGACGATGTACCG 60.528 60.000 0.00 0.00 0.00 4.02
768 772 6.125029 CCCATCTTTCTCCATATGAAAGTGT 58.875 40.000 3.65 0.00 46.08 3.55
1065 1069 2.045926 GGCATGGACTCCGCAAGT 60.046 61.111 0.00 0.00 42.42 3.16
1071 1075 2.741092 GACTCCGCAAGTGTCCCA 59.259 61.111 0.00 0.00 38.74 4.37
1130 1134 7.569639 AGATAAAGAAGTATGACGCTCTGTA 57.430 36.000 0.00 0.00 0.00 2.74
1132 1136 8.634444 AGATAAAGAAGTATGACGCTCTGTATT 58.366 33.333 0.00 0.00 0.00 1.89
1442 1449 3.193903 TGACCAATCGGATCTTGACGTAA 59.806 43.478 0.00 0.00 35.59 3.18
1464 1471 3.528078 ACAGTAGGTACCAGAGGAGATCA 59.472 47.826 15.94 0.00 0.00 2.92
1682 1689 0.809385 CAGGTTAAGCTCCGTCTCGA 59.191 55.000 3.68 0.00 0.00 4.04
1692 1699 2.732094 CGTCTCGAAACCGCCGTT 60.732 61.111 0.00 0.00 0.00 4.44
1712 1719 4.623171 CGTTGGGTTAGGAGTAAAGCATCT 60.623 45.833 0.00 0.00 0.00 2.90
1714 1721 4.101114 TGGGTTAGGAGTAAAGCATCTCA 58.899 43.478 0.00 0.00 32.93 3.27
1866 1873 5.486775 TGACTTCTCCCTTCTTCATTGATCT 59.513 40.000 0.00 0.00 0.00 2.75
1899 1907 1.263356 CCGTCTACCAGTTGGGAAGA 58.737 55.000 2.79 2.57 41.15 2.87
1947 1955 2.418197 GGATAACTAAGCTGACACGCCA 60.418 50.000 0.00 0.00 0.00 5.69
2041 2049 3.378427 GTGCTTCAGGATTCCAATGTACC 59.622 47.826 5.29 0.00 0.00 3.34
2183 2191 2.740506 AAGAAAAGGACCGGGAAACA 57.259 45.000 6.32 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.492383 CCATAGCATGAGTAGTTGAAGCG 59.508 47.826 0.00 0.00 0.00 4.68
214 215 5.955961 TGTGTGGAGGAATCAATATCTCA 57.044 39.130 0.00 0.00 0.00 3.27
332 333 0.904394 TCCCCAATCCTTTGCTTGCC 60.904 55.000 0.00 0.00 0.00 4.52
396 397 3.487372 GGAACTTCCCCCATATTGCTAC 58.513 50.000 0.00 0.00 0.00 3.58
440 441 2.591923 TGCATGCTTTTGTAGGGTCAA 58.408 42.857 20.33 0.00 0.00 3.18
502 504 3.686854 ACCCTAGCCCCCGGTACA 61.687 66.667 0.00 0.00 0.00 2.90
508 510 3.483869 CAGCTCACCCTAGCCCCC 61.484 72.222 0.00 0.00 43.86 5.40
704 708 1.070758 AGCACCTAACCTATGCCGATG 59.929 52.381 0.00 0.00 40.33 3.84
768 772 0.541392 ACATCTCTATGTGCCCGCAA 59.459 50.000 0.00 0.00 44.79 4.85
1026 1030 1.372499 CGTACCACCACAGGTCGTG 60.372 63.158 0.00 0.00 45.92 4.35
1065 1069 0.105194 TTCTCAGAGGGTGTGGGACA 60.105 55.000 0.00 0.00 0.00 4.02
1071 1075 3.071747 GGAGTTTCTTTCTCAGAGGGTGT 59.928 47.826 0.00 0.00 34.04 4.16
1130 1134 8.095452 AGGAACTATGACCAATAGAGTCAAAT 57.905 34.615 0.00 0.00 46.67 2.32
1132 1136 7.331026 CAAGGAACTATGACCAATAGAGTCAA 58.669 38.462 0.00 0.00 43.11 3.18
1442 1449 3.528078 TGATCTCCTCTGGTACCTACTGT 59.472 47.826 14.36 0.00 0.00 3.55
1464 1471 7.918536 ATACGGATACAGTAACGATCATAGT 57.081 36.000 13.22 0.29 0.00 2.12
1682 1689 1.601477 CCTAACCCAACGGCGGTTT 60.601 57.895 13.24 0.00 40.84 3.27
1692 1699 4.101114 TGAGATGCTTTACTCCTAACCCA 58.899 43.478 0.00 0.00 32.84 4.51
1712 1719 1.741401 CGAGATGCGCCAACCTTGA 60.741 57.895 4.18 0.00 0.00 3.02
1714 1721 1.302511 AACGAGATGCGCCAACCTT 60.303 52.632 4.18 0.00 46.04 3.50
1811 1818 0.388134 CGAAGAACCGGAAGCGAAGA 60.388 55.000 9.46 0.00 0.00 2.87
1866 1873 2.450897 ACGGTTCCCTTTCCCCCA 60.451 61.111 0.00 0.00 0.00 4.96
1899 1907 4.012374 CAAGCCACAACCTTGATGTCTAT 58.988 43.478 0.00 0.00 41.64 1.98
1947 1955 2.282040 GTGCCAGCAGCCAACTCT 60.282 61.111 0.00 0.00 42.71 3.24
2041 2049 1.874019 CGTTCTGATCCTGGACGCG 60.874 63.158 3.53 3.53 0.00 6.01
2074 2082 0.400213 AAAGAATGGGACGGCAGTGA 59.600 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.