Multiple sequence alignment - TraesCS7A01G523200

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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 TraesCS7A01G523200 chr7A 100.000 2561 0 0 1 2561 705969381 705966821 0.000000e+00 4730.0
1 TraesCS7A01G523200 chr7A 94.626 2047 67 5 1 2027 706003647 706001624 0.000000e+00 3131.0
2 TraesCS7A01G523200 chr7A 90.896 714 54 8 1302 2005 705938981 705938269 0.000000e+00 948.0
3 TraesCS7A01G523200 chr7A 96.610 531 18 0 2031 2561 706000841 706000311 0.000000e+00 881.0
4 TraesCS7A01G523200 chr7A 89.901 604 49 3 707 1308 705939614 705939021 0.000000e+00 767.0
5 TraesCS7A01G523200 chr7A 81.250 144 24 3 377 518 304878536 304878394 2.080000e-21 113.0
6 TraesCS7A01G523200 chr5D 95.556 2025 83 4 544 2561 19747672 19745648 0.000000e+00 3234.0
7 TraesCS7A01G523200 chr5D 90.138 507 21 11 1 483 19763698 19763197 1.290000e-177 632.0
8 TraesCS7A01G523200 chr7B 88.618 1520 130 20 524 2011 705465982 705464474 0.000000e+00 1808.0
9 TraesCS7A01G523200 chr7B 91.106 1248 78 16 1 1223 705520023 705518784 0.000000e+00 1659.0
10 TraesCS7A01G523200 chr7B 93.238 769 47 3 1270 2034 705518785 705518018 0.000000e+00 1127.0
11 TraesCS7A01G523200 chr7B 89.564 527 38 7 2037 2561 705517629 705517118 0.000000e+00 652.0
12 TraesCS7A01G523200 chr7B 85.542 166 21 3 543 706 176002822 176002986 1.220000e-38 171.0
13 TraesCS7A01G523200 chr7B 91.667 96 4 3 1 96 449900115 449900024 2.070000e-26 130.0
14 TraesCS7A01G523200 chrUn 91.159 1312 90 12 707 2006 92847086 92848383 0.000000e+00 1757.0
15 TraesCS7A01G523200 chr3D 89.041 146 12 4 561 706 360327321 360327462 7.280000e-41 178.0
16 TraesCS7A01G523200 chr5B 85.714 168 22 2 539 706 536228698 536228863 2.620000e-40 176.0
17 TraesCS7A01G523200 chr1A 86.145 166 17 5 544 706 181769420 181769582 9.420000e-40 174.0
18 TraesCS7A01G523200 chr1A 89.320 103 6 5 1 99 496422981 496422880 9.620000e-25 124.0
19 TraesCS7A01G523200 chr2B 85.294 170 20 4 539 706 249527581 249527415 1.220000e-38 171.0
20 TraesCS7A01G523200 chr3B 86.301 146 19 1 373 518 125530353 125530209 9.490000e-35 158.0
21 TraesCS7A01G523200 chr6B 92.233 103 4 2 1 99 7191657 7191759 2.660000e-30 143.0
22 TraesCS7A01G523200 chr6B 92.233 103 4 2 1 99 7233738 7233840 2.660000e-30 143.0
23 TraesCS7A01G523200 chr4A 87.736 106 6 2 1 99 657055144 657055249 1.610000e-22 117.0
24 TraesCS7A01G523200 chr4D 86.239 109 8 2 1 102 412929612 412929504 7.490000e-21 111.0
25 TraesCS7A01G523200 chr5A 86.792 106 4 6 1 102 533495969 533495870 2.690000e-20 110.0
26 TraesCS7A01G523200 chr7D 80.153 131 22 4 2435 2561 613918036 613917906 7.540000e-16 95.3


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 TraesCS7A01G523200 chr7A 705966821 705969381 2560 True 4730.0 4730 100.000000 1 2561 1 chr7A.!!$R2 2560
1 TraesCS7A01G523200 chr7A 706000311 706003647 3336 True 2006.0 3131 95.618000 1 2561 2 chr7A.!!$R4 2560
2 TraesCS7A01G523200 chr7A 705938269 705939614 1345 True 857.5 948 90.398500 707 2005 2 chr7A.!!$R3 1298
3 TraesCS7A01G523200 chr5D 19745648 19747672 2024 True 3234.0 3234 95.556000 544 2561 1 chr5D.!!$R1 2017
4 TraesCS7A01G523200 chr5D 19763197 19763698 501 True 632.0 632 90.138000 1 483 1 chr5D.!!$R2 482
5 TraesCS7A01G523200 chr7B 705464474 705465982 1508 True 1808.0 1808 88.618000 524 2011 1 chr7B.!!$R2 1487
6 TraesCS7A01G523200 chr7B 705517118 705520023 2905 True 1146.0 1659 91.302667 1 2561 3 chr7B.!!$R3 2560
7 TraesCS7A01G523200 chrUn 92847086 92848383 1297 False 1757.0 1757 91.159000 707 2006 1 chrUn.!!$F1 1299

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
500 529 0.37861 GCTCAAAATCCAGCGCTACC 59.621 55.0 10.99 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 1982 0.891373 AGAGTCTCGCAGCTTTAGCA 59.109 50.0 4.33 0.0 45.16 3.49 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
79 80 9.761504 CATAGATGATGATGAGTAGAAGTTGTT 57.238 33.333 0.00 0.00 37.82 2.83
500 529 0.378610 GCTCAAAATCCAGCGCTACC 59.621 55.000 10.99 0.00 0.00 3.18
903 944 9.495382 GTCACCCCTCTATATATAAGAAGGAAT 57.505 37.037 13.45 3.23 27.43 3.01
1013 1054 1.915489 TGTGGGCATGGAGAAGTACAT 59.085 47.619 0.00 0.00 0.00 2.29
1048 1089 1.776662 ACTAGCGCCACTCTGGATTA 58.223 50.000 2.29 0.00 40.96 1.75
1094 1135 6.474819 TCATGTTCAATGTAAGTAACACGG 57.525 37.500 0.00 0.00 42.09 4.94
1557 1665 1.380302 CTCCACCCTCCCACCAAAG 59.620 63.158 0.00 0.00 0.00 2.77
1627 1737 6.343716 TCTTTACGGTTGGAGTTACATGTA 57.656 37.500 0.08 0.08 0.00 2.29
1634 1744 5.356190 CGGTTGGAGTTACATGTAGAGACTA 59.644 44.000 5.56 0.00 0.00 2.59
1797 1907 1.981495 AGTCCCTCTCAAAACCCTCTG 59.019 52.381 0.00 0.00 0.00 3.35
1833 1943 5.007385 AGGTCGTGTTACTATCATGTTCC 57.993 43.478 0.00 0.00 0.00 3.62
1872 1982 1.554160 CTGTGGCACTCTTCCTCTCAT 59.446 52.381 19.83 0.00 0.00 2.90
2060 3349 8.250332 GGAACTATTCTTTTTCAATGTGCCATA 58.750 33.333 0.00 0.00 0.00 2.74
2144 3433 1.532921 CCGCAACGAGAAAAAGCAACA 60.533 47.619 0.00 0.00 0.00 3.33
2238 3527 4.042809 ACCCAGATATGGTCAGAAACAACA 59.957 41.667 5.49 0.00 0.00 3.33
2313 3602 8.159447 ACTTACTAGTACTTGTTTTTAAGGGGG 58.841 37.037 15.11 0.00 31.21 5.40
2317 3606 4.831155 AGTACTTGTTTTTAAGGGGGCTTC 59.169 41.667 0.00 0.00 31.94 3.86
2387 3678 2.832643 TGGATGGATGAAGCAATGGT 57.167 45.000 0.00 0.00 0.00 3.55
2399 3690 1.384525 GCAATGGTGCCGGTATACAA 58.615 50.000 1.90 0.00 45.68 2.41
2402 3693 2.948979 CAATGGTGCCGGTATACAATGT 59.051 45.455 1.90 0.00 0.00 2.71
2432 3723 0.113972 TTGGGTGTTCATGATGGGCA 59.886 50.000 0.00 0.00 0.00 5.36
2523 3814 0.600057 CTTCTTTTCCCCAGCAGCAC 59.400 55.000 0.00 0.00 0.00 4.40
2529 3820 3.957586 CCCCAGCAGCACCTCACA 61.958 66.667 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 8.943002 GCACATAACTCATCATCATCATCATAA 58.057 33.333 0.00 0.00 0.00 1.90
212 223 7.704899 TCATCATCGTAATAACAACTCATCGTT 59.295 33.333 0.00 0.00 35.88 3.85
230 241 8.529911 CGTCATCATAATAACTCATCATCATCG 58.470 37.037 0.00 0.00 0.00 3.84
372 401 5.880054 AATTTGAAATAGCAGTAGCACGT 57.120 34.783 0.00 0.00 45.49 4.49
375 404 7.320443 CTGGTAATTTGAAATAGCAGTAGCA 57.680 36.000 8.96 7.74 45.49 3.49
518 547 6.431198 AGCACATTTAATAACCTAACACCG 57.569 37.500 0.00 0.00 0.00 4.94
697 727 6.397272 GGAAATGCACATTTAACTCCATTCA 58.603 36.000 8.53 0.00 40.77 2.57
765 806 2.961062 CTCAGGATGCTAATTTTGGGGG 59.039 50.000 0.00 0.00 34.76 5.40
780 821 4.935205 CGTGGTGAACATTAAATCTCAGGA 59.065 41.667 0.00 0.00 0.00 3.86
903 944 2.962859 TGGAGACTGCTAGCCATATCA 58.037 47.619 13.29 0.98 0.00 2.15
1013 1054 2.864882 GCTAGTAACTGCACACGTTCCA 60.865 50.000 0.00 0.00 0.00 3.53
1048 1089 4.044426 GCAACAAAGCAAACGAGAAGAAT 58.956 39.130 0.00 0.00 0.00 2.40
1308 1408 9.612620 AGAGAATAAAAACAAATTAGAGCAACG 57.387 29.630 0.00 0.00 0.00 4.10
1583 1691 8.859517 AAAGAACAAGATATACGCTACTCTTC 57.140 34.615 0.00 0.00 0.00 2.87
1797 1907 9.538508 AGTAACACGACCTTAATTAATATGGAC 57.461 33.333 8.55 2.73 33.88 4.02
1833 1943 2.725723 CAGTGCGGTGCAAAATGTTAAG 59.274 45.455 0.00 0.00 41.47 1.85
1872 1982 0.891373 AGAGTCTCGCAGCTTTAGCA 59.109 50.000 4.33 0.00 45.16 3.49
1994 2118 1.135139 GAGGTCGACATGCTTGCTCTA 59.865 52.381 18.91 0.00 0.00 2.43
2027 2151 4.695455 TGAAAAAGAATAGTTCCGGCTGAG 59.305 41.667 0.00 0.00 0.00 3.35
2029 2153 5.371115 TTGAAAAAGAATAGTTCCGGCTG 57.629 39.130 0.00 0.00 0.00 4.85
2060 3349 3.370209 GGTATTTAGTTCAAGGTCGCCCT 60.370 47.826 0.00 0.00 45.63 5.19
2144 3433 7.125356 GGGGAGGGAATTAATATATACACGTCT 59.875 40.741 0.00 0.00 0.00 4.18
2238 3527 5.680619 TCCAGAAACCATTAGCGTGAATAT 58.319 37.500 0.00 0.00 0.00 1.28
2313 3602 1.528129 CCTGTCAAAGGTGAGGAAGC 58.472 55.000 0.00 0.00 41.74 3.86
2387 3678 2.717390 AGCAAACATTGTATACCGGCA 58.283 42.857 0.00 0.00 0.00 5.69
2399 3690 5.304101 TGAACACCCAAAGATAAGCAAACAT 59.696 36.000 0.00 0.00 0.00 2.71
2402 3693 5.538053 TCATGAACACCCAAAGATAAGCAAA 59.462 36.000 0.00 0.00 0.00 3.68
2432 3723 3.087031 CAACCAGCTGGAATCTTCACAT 58.913 45.455 39.19 9.77 38.94 3.21
2523 3814 1.405463 TGATCGATCGGTCTTGTGAGG 59.595 52.381 27.39 0.00 0.00 3.86
2529 3820 4.920640 AATGTAGTGATCGATCGGTCTT 57.079 40.909 27.39 18.10 0.00 3.01


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

AutoCloner maintained by Alex Coulton.