Multiple sequence alignment - TraesCS2D01G502000

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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 TraesCS2D01G502000 chr2D 100.000 3290 0 0 1 3290 596125970 596122681 0.000000e+00 6076.0
1 TraesCS2D01G502000 chr2A 96.294 2860 75 9 443 3290 729778472 729775632 0.000000e+00 4665.0
2 TraesCS2D01G502000 chr2A 91.807 476 8 9 1 450 729779099 729778629 4.630000e-178 634.0
3 TraesCS2D01G502000 chr2B 96.915 2755 69 9 543 3290 724554439 724551694 0.000000e+00 4602.0
4 TraesCS2D01G502000 chr2B 87.970 399 12 10 1 364 724555121 724554724 3.900000e-119 438.0
5 TraesCS2D01G502000 chr3A 82.135 431 55 14 1866 2292 501487287 501487699 1.880000e-92 350.0
6 TraesCS2D01G502000 chr7B 91.388 209 16 2 2275 2482 361656455 361656662 5.370000e-73 285.0
7 TraesCS2D01G502000 chr7B 84.956 113 17 0 1786 1898 598301599 598301487 7.460000e-22 115.0
8 TraesCS2D01G502000 chr6D 84.286 70 11 0 1866 1935 221565552 221565621 5.890000e-08 69.4


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 TraesCS2D01G502000 chr2D 596122681 596125970 3289 True 6076.0 6076 100.0000 1 3290 1 chr2D.!!$R1 3289
1 TraesCS2D01G502000 chr2A 729775632 729779099 3467 True 2649.5 4665 94.0505 1 3290 2 chr2A.!!$R1 3289
2 TraesCS2D01G502000 chr2B 724551694 724555121 3427 True 2520.0 4602 92.4425 1 3290 2 chr2B.!!$R1 3289

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
956 1174 0.034476 TGGCTTCTGTGCTCTGTCTG 59.966 55.0 0.0 0.0 0.00 3.51 F
1358 1583 0.393537 CCAGATGTTGGGAGGTCTGC 60.394 60.0 0.0 0.0 43.75 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 2037 0.099436 CTGAATTAACTGCTGGCGGC 59.901 55.0 12.43 12.43 42.22 6.53 R
2907 3135 0.804544 AACCGCGGTCATGATACACG 60.805 55.0 34.29 0.00 0.00 4.49 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
22 23 3.391965 TCACCACACAACGTATGGTAAC 58.608 45.455 11.93 0.00 45.11 2.50
52 53 2.213499 ACTTGAAGACGGTGAAAGCAG 58.787 47.619 0.00 0.00 0.00 4.24
85 99 2.864343 GCTTTGGCTTCATTGCATCATC 59.136 45.455 0.00 0.00 35.22 2.92
109 123 2.031333 GCTGCAATCGGAATCAGAATCC 60.031 50.000 0.00 0.00 0.00 3.01
110 124 2.551459 CTGCAATCGGAATCAGAATCCC 59.449 50.000 0.00 0.00 33.13 3.85
159 173 1.067749 CAGATGAGCAGAGGAGGCG 59.932 63.158 0.00 0.00 36.08 5.52
366 418 0.321996 GAGGAACACGAAGGGAAGCT 59.678 55.000 0.00 0.00 0.00 3.74
956 1174 0.034476 TGGCTTCTGTGCTCTGTCTG 59.966 55.000 0.00 0.00 0.00 3.51
1326 1551 1.352083 ATGTCTACCAGGCACAGTGT 58.648 50.000 1.61 0.00 29.65 3.55
1358 1583 0.393537 CCAGATGTTGGGAGGTCTGC 60.394 60.000 0.00 0.00 43.75 4.26
1479 1704 2.931969 CGCACTGCAAGATCATCAGTTA 59.068 45.455 10.54 0.00 38.85 2.24
1591 1816 4.009675 AGAGAATGGCGCATTAAGTTCAA 58.990 39.130 10.83 0.00 33.90 2.69
1767 1992 3.426568 GTGCGAGCTCCACTTGGC 61.427 66.667 21.27 13.24 34.44 4.52
1812 2037 6.316390 GTGTAGGTGGATCAAGGAAATTACTG 59.684 42.308 0.00 0.00 0.00 2.74
1870 2095 2.304180 AGCTGTTATGAGCAAGGTCAGT 59.696 45.455 8.04 0.02 41.83 3.41
1881 2106 2.163412 GCAAGGTCAGTTGTTGAACACA 59.837 45.455 0.00 0.00 46.43 3.72
1890 2115 5.105106 TCAGTTGTTGAACACAGAGGTTCTA 60.105 40.000 0.00 0.00 45.74 2.10
2045 2270 3.125829 GCTGATGTTCGAAGAGATGCAAA 59.874 43.478 0.00 0.00 38.43 3.68
2195 2420 5.585445 ACTTGATCTCTGCTCATGATTTCAC 59.415 40.000 0.00 0.00 0.00 3.18
2220 2445 1.386533 CCATGCAGCTAAACCCTCAG 58.613 55.000 0.00 0.00 0.00 3.35
2531 2756 0.957395 CTGCATAGGGCCCATTAGCG 60.957 60.000 27.56 13.92 43.89 4.26
2806 3031 0.246635 TTCTCTTTTCTCCCTCGGCG 59.753 55.000 0.00 0.00 0.00 6.46
2907 3135 9.950496 AATGGTAGATGTATCCATAATTGAGTC 57.050 33.333 5.00 0.00 40.52 3.36
2919 3147 6.923508 TCCATAATTGAGTCGTGTATCATGAC 59.076 38.462 12.44 12.44 46.99 3.06
2958 3186 4.276926 GTCACCTGGAGCAAATGGATTATC 59.723 45.833 0.00 0.00 0.00 1.75
2965 3193 5.357878 TGGAGCAAATGGATTATCTGTTCAC 59.642 40.000 0.00 0.00 0.00 3.18
2988 3216 8.328758 TCACAATTTTGGTATCTCATCTTACCT 58.671 33.333 0.00 0.00 38.93 3.08
3047 3275 2.094390 TCTCCGGTACAATTCCAGTTCG 60.094 50.000 0.00 0.00 0.00 3.95
3128 3356 0.611618 ACCTGAATGGGCGCATTTCA 60.612 50.000 27.38 22.79 41.11 2.69
3170 3398 2.541762 GCGAGTATGATGCCTGAACTTC 59.458 50.000 0.00 0.00 0.00 3.01
3182 3410 3.269178 CCTGAACTTCATCTTCTGCTCC 58.731 50.000 0.00 0.00 0.00 4.70
3183 3411 2.928757 CTGAACTTCATCTTCTGCTCCG 59.071 50.000 0.00 0.00 0.00 4.63
3266 3494 4.094294 TGAGCTATCGTTGCCATTTACAAC 59.906 41.667 0.00 0.00 43.15 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.826385 GTCTTCAAGTCCACATGGGG 58.174 55.000 8.05 8.05 37.22 4.96
52 53 3.741476 CAAAGCCTGCGTCCTGCC 61.741 66.667 0.00 0.00 45.60 4.85
85 99 1.944709 TCTGATTCCGATTGCAGCATG 59.055 47.619 0.00 0.00 40.87 4.06
109 123 1.266175 GCTGATCATTTGATGGCTCGG 59.734 52.381 0.00 0.00 34.37 4.63
110 124 1.070108 CGCTGATCATTTGATGGCTCG 60.070 52.381 0.00 0.00 34.37 5.03
159 173 4.776953 GTGTGCGCGCGTGATGTC 62.777 66.667 32.35 14.02 0.00 3.06
171 187 2.512745 TCGTGGGTGTGTGTGTGC 60.513 61.111 0.00 0.00 0.00 4.57
181 197 0.974383 CCCTTCTTGTAGTCGTGGGT 59.026 55.000 0.00 0.00 0.00 4.51
183 199 0.391263 GGCCCTTCTTGTAGTCGTGG 60.391 60.000 0.00 0.00 0.00 4.94
366 418 0.249398 GTCCTTGCTTCGCTCCCTTA 59.751 55.000 0.00 0.00 0.00 2.69
562 780 4.223964 GAGACGAATTGCGCCCGC 62.224 66.667 4.18 5.60 46.04 6.13
563 781 3.913573 CGAGACGAATTGCGCCCG 61.914 66.667 4.18 5.96 46.04 6.13
564 782 3.564027 CCGAGACGAATTGCGCCC 61.564 66.667 4.18 0.00 46.04 6.13
565 783 4.223964 GCCGAGACGAATTGCGCC 62.224 66.667 4.18 0.00 46.04 6.53
566 784 4.223964 GGCCGAGACGAATTGCGC 62.224 66.667 0.00 0.00 46.04 6.09
568 786 3.564027 CCGGCCGAGACGAATTGC 61.564 66.667 30.73 0.00 35.20 3.56
1095 1314 2.037136 GCGACCATTCTGCTGCTGT 61.037 57.895 0.00 0.00 0.00 4.40
1326 1551 1.160870 ATCTGGTGGTGGAGGTGGA 59.839 57.895 0.00 0.00 0.00 4.02
1358 1583 3.869473 TTCTTCGCCAACGGTCCGG 62.869 63.158 17.28 0.00 40.63 5.14
1479 1704 5.394115 GCCCATATGTTTCAACCGATCTTTT 60.394 40.000 1.24 0.00 0.00 2.27
1591 1816 4.221703 AGACACCGATCTCTTCAACTCAAT 59.778 41.667 0.00 0.00 0.00 2.57
1767 1992 4.037923 ACACTTGCTGAACAAAAGGGTATG 59.962 41.667 3.89 0.00 35.82 2.39
1812 2037 0.099436 CTGAATTAACTGCTGGCGGC 59.901 55.000 12.43 12.43 42.22 6.53
1828 2053 1.556911 GCTGAAGTGATCTTCCCCTGA 59.443 52.381 5.68 0.00 46.66 3.86
1870 2095 4.116961 CGTAGAACCTCTGTGTTCAACAA 58.883 43.478 0.00 0.00 45.62 2.83
1881 2106 1.171308 TGCGCTTACGTAGAACCTCT 58.829 50.000 9.73 0.00 42.83 3.69
1890 2115 1.463444 GTTTTCTCCATGCGCTTACGT 59.537 47.619 9.73 0.00 42.83 3.57
2007 2232 4.452455 ACATCAGCTCCTTTTAACTCAACG 59.548 41.667 0.00 0.00 0.00 4.10
2045 2270 3.172339 TGCTTGTATGATGCCCCTTTTT 58.828 40.909 0.00 0.00 0.00 1.94
2195 2420 1.672881 GGTTTAGCTGCATGGCTACAG 59.327 52.381 7.14 0.00 43.40 2.74
2220 2445 2.045536 CAGTCCTCCCCAAGCTGC 60.046 66.667 0.00 0.00 0.00 5.25
2546 2771 3.131396 CGGGACTTATGGATGTAACAGC 58.869 50.000 0.00 0.00 0.00 4.40
2806 3031 1.813513 CCCTGAACAGACACATGGAC 58.186 55.000 3.19 0.00 0.00 4.02
2907 3135 0.804544 AACCGCGGTCATGATACACG 60.805 55.000 34.29 0.00 0.00 4.49
2919 3147 0.878523 TGACAACAAGAGAACCGCGG 60.879 55.000 26.86 26.86 0.00 6.46
2958 3186 8.048534 AGATGAGATACCAAAATTGTGAACAG 57.951 34.615 0.00 0.00 0.00 3.16
3047 3275 7.175641 AGCAAAGTCCCTACATGCAATTATATC 59.824 37.037 0.00 0.00 40.93 1.63
3128 3356 4.830826 CAGCATGCATCTATCAACACAT 57.169 40.909 21.98 0.00 0.00 3.21
3170 3398 1.920574 CGTTACACGGAGCAGAAGATG 59.079 52.381 0.00 0.00 38.08 2.90
3182 3410 5.087397 TGGAACTTTTTCAAACGTTACACG 58.913 37.500 0.00 0.00 36.44 4.49
3183 3411 7.273815 TGAATGGAACTTTTTCAAACGTTACAC 59.726 33.333 0.00 0.08 41.77 2.90
3266 3494 6.787085 GAGAATACTTGGGATATGAAACGG 57.213 41.667 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.