Multiple sequence alignment - TraesCS2A01G266300

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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 TraesCS2A01G266300 chr2A 100.000 2588 0 0 1 2588 423420401 423417814 0.000000e+00 4780.0
1 TraesCS2A01G266300 chr2A 97.802 182 4 0 1 182 772458947 772458766 5.380000e-82 315.0
2 TraesCS2A01G266300 chr2A 100.000 48 0 0 205 252 123398913 123398960 3.550000e-14 89.8
3 TraesCS2A01G266300 chr2A 95.238 42 2 0 1 42 588457716 588457675 1.660000e-07 67.6
4 TraesCS2A01G266300 chr3A 96.218 2591 87 8 1 2588 227631623 227634205 0.000000e+00 4231.0
5 TraesCS2A01G266300 chr5B 95.869 2590 101 5 1 2588 34121816 34124401 0.000000e+00 4185.0
6 TraesCS2A01G266300 chr5B 96.738 2514 69 5 1 2510 127798274 127795770 0.000000e+00 4176.0
7 TraesCS2A01G266300 chr1B 96.697 2513 71 5 1 2510 638719570 638717067 0.000000e+00 4170.0
8 TraesCS2A01G266300 chr3B 96.140 2513 90 6 1 2509 730355153 730352644 0.000000e+00 4096.0
9 TraesCS2A01G266300 chr6B 95.979 2512 91 10 1 2510 128410965 128413468 0.000000e+00 4071.0
10 TraesCS2A01G266300 chr6B 95.579 2511 105 6 1 2510 265001177 265003682 0.000000e+00 4017.0
11 TraesCS2A01G266300 chr2B 96.497 2284 75 5 230 2510 760923918 760926199 0.000000e+00 3770.0
12 TraesCS2A01G266300 chr7B 96.405 2281 79 3 232 2509 47165380 47163100 0.000000e+00 3755.0


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 TraesCS2A01G266300 chr2A 423417814 423420401 2587 True 4780 4780 100.000 1 2588 1 chr2A.!!$R1 2587
1 TraesCS2A01G266300 chr3A 227631623 227634205 2582 False 4231 4231 96.218 1 2588 1 chr3A.!!$F1 2587
2 TraesCS2A01G266300 chr5B 34121816 34124401 2585 False 4185 4185 95.869 1 2588 1 chr5B.!!$F1 2587
3 TraesCS2A01G266300 chr5B 127795770 127798274 2504 True 4176 4176 96.738 1 2510 1 chr5B.!!$R1 2509
4 TraesCS2A01G266300 chr1B 638717067 638719570 2503 True 4170 4170 96.697 1 2510 1 chr1B.!!$R1 2509
5 TraesCS2A01G266300 chr3B 730352644 730355153 2509 True 4096 4096 96.140 1 2509 1 chr3B.!!$R1 2508
6 TraesCS2A01G266300 chr6B 128410965 128413468 2503 False 4071 4071 95.979 1 2510 1 chr6B.!!$F1 2509
7 TraesCS2A01G266300 chr6B 265001177 265003682 2505 False 4017 4017 95.579 1 2510 1 chr6B.!!$F2 2509
8 TraesCS2A01G266300 chr2B 760923918 760926199 2281 False 3770 3770 96.497 230 2510 1 chr2B.!!$F1 2280
9 TraesCS2A01G266300 chr7B 47163100 47165380 2280 True 3755 3755 96.405 232 2509 1 chr7B.!!$R1 2277

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
133 134 0.542232 AAGTCAGGTCCAGTAGGCGT 60.542 55.0 0.0 0.0 33.74 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 1607 0.465097 ATGCGGCCAGATGAAGAAGG 60.465 55.0 2.24 0.0 0.0 3.46 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
133 134 0.542232 AAGTCAGGTCCAGTAGGCGT 60.542 55.000 0.00 0.00 33.74 5.68
163 164 3.493350 GCTAAGCCATTCGATCTTCCTGA 60.493 47.826 0.00 0.00 0.00 3.86
315 316 2.042230 ACCGGGCCTACCTACCTG 60.042 66.667 6.32 0.00 36.97 4.00
339 340 6.799441 TGATGACATTTATGAAAAACGAACGG 59.201 34.615 0.00 0.00 0.00 4.44
348 349 8.931905 TTATGAAAAACGAACGGTGTATTAAC 57.068 30.769 0.00 0.00 0.00 2.01
475 476 4.858692 CGCTGTTTATCCAATCCAAAACTG 59.141 41.667 0.00 0.00 35.28 3.16
476 477 5.335583 CGCTGTTTATCCAATCCAAAACTGA 60.336 40.000 7.55 0.00 34.56 3.41
770 773 9.268268 TCTTAATGACTAGTTGTTCGTTTGAAT 57.732 29.630 0.00 0.00 36.29 2.57
854 860 0.611714 AACCGACAAATCCGTAGCCT 59.388 50.000 0.00 0.00 0.00 4.58
908 914 2.553172 GGATGAATCTTCTCATGCAGCC 59.447 50.000 0.00 0.00 42.12 4.85
916 922 3.693085 TCTTCTCATGCAGCCTTTTGATC 59.307 43.478 0.00 0.00 0.00 2.92
1060 1067 8.370266 ACAACCTATATACTCCACACTTAACA 57.630 34.615 0.00 0.00 0.00 2.41
1085 1092 6.856757 AGCATTTGATAGATTATCCAACCCT 58.143 36.000 0.00 0.00 34.26 4.34
1118 1125 0.778720 TATTGGTGGGGGTTCGGTTT 59.221 50.000 0.00 0.00 0.00 3.27
1208 1215 5.559770 TCATGTGGATCTAGCTTTCAACAA 58.440 37.500 0.00 0.00 29.91 2.83
1483 1490 1.540363 GCTTAGCTAGCGCCATACCAA 60.540 52.381 9.55 0.00 40.71 3.67
1598 1607 2.548480 CCTTATTTTAGTAGGCGCCAGC 59.452 50.000 31.54 20.65 44.18 4.85
1895 1906 1.296715 CAAAGCGGGAGGTGTAGCT 59.703 57.895 0.00 0.00 42.46 3.32
2106 2119 9.631452 CTTCTGTCTTTTTCTTCTTGTTCTTTT 57.369 29.630 0.00 0.00 0.00 2.27
2266 2287 5.157770 TCTCAGGATTCCTATAACCCTGT 57.842 43.478 4.51 0.00 43.54 4.00
2349 2370 7.720515 TGGATAAACTCCTTTCGGTTCTTAAAA 59.279 33.333 0.00 0.00 45.21 1.52
2384 2405 2.034066 CTGGCTTTCCGCTTCCCA 59.966 61.111 0.00 0.00 39.13 4.37
2514 2535 0.107993 AGACCGTCGTATGACTCCGA 60.108 55.000 13.11 0.00 43.21 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 1.605457 CGAATGGCTTAGCGCATCCTA 60.605 52.381 11.47 0.0 41.67 2.94
304 305 7.303182 TCATAAATGTCATCAGGTAGGTAGG 57.697 40.000 0.00 0.0 0.00 3.18
315 316 6.799925 ACCGTTCGTTTTTCATAAATGTCATC 59.200 34.615 0.00 0.0 0.00 2.92
339 340 7.838771 AACTGATAGAAACCCGTTAATACAC 57.161 36.000 0.00 0.0 0.00 2.90
348 349 7.412672 GCTTTGTTACTAACTGATAGAAACCCG 60.413 40.741 0.00 0.0 35.47 5.28
475 476 5.121298 GTGGGTTCTACCAACTAAACGAATC 59.879 44.000 0.00 0.0 43.34 2.52
476 477 4.999311 GTGGGTTCTACCAACTAAACGAAT 59.001 41.667 0.00 0.0 43.34 3.34
770 773 4.974645 TTCTCTGCCAGTTTCTTAAGGA 57.025 40.909 1.85 0.0 0.00 3.36
814 820 6.755141 CGGTTAGTTGATTCTCGAAATAAGGA 59.245 38.462 0.00 0.0 0.00 3.36
854 860 1.686325 GGGAGGCAGCGAATCACCTA 61.686 60.000 0.00 0.0 30.95 3.08
908 914 1.473677 TGCGCCCTGAATGATCAAAAG 59.526 47.619 4.18 0.0 34.49 2.27
916 922 3.104602 CTTCGCTGCGCCCTGAATG 62.105 63.158 18.65 0.0 0.00 2.67
1060 1067 7.232127 CAGGGTTGGATAATCTATCAAATGCTT 59.768 37.037 0.00 0.0 36.91 3.91
1085 1092 5.192927 CCCACCAATAACTAAGATTGCTCA 58.807 41.667 0.00 0.0 33.70 4.26
1118 1125 5.549347 TGACTAAACAAATACCCGCTAACA 58.451 37.500 0.00 0.0 0.00 2.41
1125 1132 9.614792 ACTATCTGAATGACTAAACAAATACCC 57.385 33.333 0.00 0.0 0.00 3.69
1208 1215 7.101652 ACATCTCTCATAATGTGTTCTACGT 57.898 36.000 0.00 0.0 34.88 3.57
1483 1490 7.891183 CCAAGTCACTATGGTATCTCCTACTAT 59.109 40.741 0.00 0.0 35.82 2.12
1598 1607 0.465097 ATGCGGCCAGATGAAGAAGG 60.465 55.000 2.24 0.0 0.00 3.46
1701 1711 5.473846 CAGAAGCTACCCGATCTACAAGATA 59.526 44.000 0.00 0.0 34.53 1.98
2106 2119 1.147376 CCGGAATGGGCGTTATGGA 59.853 57.895 0.00 0.0 0.00 3.41
2349 2370 3.870299 GCCAGAAAGAGAATTTCCTCCGT 60.870 47.826 0.00 0.0 33.76 4.69
2384 2405 2.102070 TAAACATGTTCGCATCCCGT 57.898 45.000 12.39 0.0 35.23 5.28


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

AutoCloner maintained by Alex Coulton.