Multiple sequence alignment - TraesCS2D01G543500

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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 TraesCS2D01G543500 chr2D 100.000 2507 0 0 1 2507 621314419 621311913 0.000000e+00 4630.0
1 TraesCS2D01G543500 chr2D 87.615 1518 134 33 604 2098 621265796 621264310 0.000000e+00 1712.0
2 TraesCS2D01G543500 chr2D 85.083 1267 150 23 786 2027 621140962 621139710 0.000000e+00 1256.0
3 TraesCS2D01G543500 chr2D 79.592 245 35 10 266 510 621150528 621150299 7.180000e-36 161.0
4 TraesCS2D01G543500 chr2D 79.904 209 27 10 309 517 621266039 621265846 3.360000e-29 139.0
5 TraesCS2D01G543500 chr2D 97.143 35 0 1 2117 2150 621263794 621263760 9.690000e-05 58.4
6 TraesCS2D01G543500 chr2A 95.317 1687 63 8 836 2507 753004611 753002926 0.000000e+00 2663.0
7 TraesCS2D01G543500 chr2A 95.723 982 35 4 836 1810 752996726 752995745 0.000000e+00 1574.0
8 TraesCS2D01G543500 chr2A 94.987 758 25 5 1 755 753005389 753004642 0.000000e+00 1177.0
9 TraesCS2D01G543500 chr2A 94.379 765 31 5 1 755 752997519 752996757 0.000000e+00 1164.0
10 TraesCS2D01G543500 chr2A 94.753 648 24 3 1869 2507 752995436 752994790 0.000000e+00 1000.0
11 TraesCS2D01G543500 chr2B 86.048 1455 155 21 598 2026 762063534 762062102 0.000000e+00 1519.0
12 TraesCS2D01G543500 chr2B 84.631 1451 162 30 604 2027 762072124 762070708 0.000000e+00 1387.0
13 TraesCS2D01G543500 chrUn 84.356 1451 166 30 604 2027 342645177 342643761 0.000000e+00 1365.0
14 TraesCS2D01G543500 chrUn 86.082 1243 137 19 814 2027 338975295 338976530 0.000000e+00 1304.0
15 TraesCS2D01G543500 chrUn 86.082 1243 137 19 814 2027 342893148 342894383 0.000000e+00 1304.0
16 TraesCS2D01G543500 chrUn 85.022 227 21 5 543 756 329049716 329049490 4.200000e-53 219.0
17 TraesCS2D01G543500 chrUn 85.022 227 21 5 543 756 338975052 338975278 4.200000e-53 219.0
18 TraesCS2D01G543500 chrUn 85.022 227 21 5 543 756 342892905 342893131 4.200000e-53 219.0
19 TraesCS2D01G543500 chrUn 85.022 227 21 5 543 756 417387460 417387686 4.200000e-53 219.0


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 TraesCS2D01G543500 chr2D 621311913 621314419 2506 True 4630.000000 4630 100.000000 1 2507 1 chr2D.!!$R3 2506
1 TraesCS2D01G543500 chr2D 621139710 621140962 1252 True 1256.000000 1256 85.083000 786 2027 1 chr2D.!!$R1 1241
2 TraesCS2D01G543500 chr2D 621263760 621266039 2279 True 636.466667 1712 88.220667 309 2150 3 chr2D.!!$R4 1841
3 TraesCS2D01G543500 chr2A 753002926 753005389 2463 True 1920.000000 2663 95.152000 1 2507 2 chr2A.!!$R2 2506
4 TraesCS2D01G543500 chr2A 752994790 752997519 2729 True 1246.000000 1574 94.951667 1 2507 3 chr2A.!!$R1 2506
5 TraesCS2D01G543500 chr2B 762062102 762063534 1432 True 1519.000000 1519 86.048000 598 2026 1 chr2B.!!$R1 1428
6 TraesCS2D01G543500 chr2B 762070708 762072124 1416 True 1387.000000 1387 84.631000 604 2027 1 chr2B.!!$R2 1423
7 TraesCS2D01G543500 chrUn 342643761 342645177 1416 True 1365.000000 1365 84.356000 604 2027 1 chrUn.!!$R2 1423
8 TraesCS2D01G543500 chrUn 338975052 338976530 1478 False 761.500000 1304 85.552000 543 2027 2 chrUn.!!$F2 1484
9 TraesCS2D01G543500 chrUn 342892905 342894383 1478 False 761.500000 1304 85.552000 543 2027 2 chrUn.!!$F3 1484

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
720 745 0.535102 AGCCCGGTCTTCACAAACTG 60.535 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 3074 0.246912 GTCGCGTTTCTTGCAGATCG 60.247 55.0 5.77 0.0 0.0 3.69 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
51 52 7.661437 TCACAACTATCAACATAGAAAGCAAGT 59.339 33.333 0.00 0.00 36.25 3.16
275 280 6.037786 CCTATTCAAGGCACGATCCTAATA 57.962 41.667 0.00 0.00 38.97 0.98
324 329 2.028484 CGTACCACGCACCTGTGT 59.972 61.111 0.00 0.00 38.20 3.72
720 745 0.535102 AGCCCGGTCTTCACAAACTG 60.535 55.000 0.00 0.00 0.00 3.16
725 750 2.483013 CCGGTCTTCACAAACTGAGTCA 60.483 50.000 0.00 0.00 0.00 3.41
756 781 1.153449 TACGTACCAGCTGCATGCC 60.153 57.895 16.68 0.00 44.23 4.40
781 810 1.136828 TGCTTGTGTTCCCACCTACT 58.863 50.000 0.00 0.00 41.09 2.57
782 811 2.331166 TGCTTGTGTTCCCACCTACTA 58.669 47.619 0.00 0.00 41.09 1.82
783 812 2.038033 TGCTTGTGTTCCCACCTACTAC 59.962 50.000 0.00 0.00 41.09 2.73
802 833 4.578928 ACTACACACAACATTCAAAGTCCC 59.421 41.667 0.00 0.00 0.00 4.46
804 835 3.960102 ACACACAACATTCAAAGTCCCAT 59.040 39.130 0.00 0.00 0.00 4.00
812 843 3.297134 TTCAAAGTCCCATATCCAGGC 57.703 47.619 0.00 0.00 0.00 4.85
832 866 0.601558 ACACGCACTCCATTCTACGT 59.398 50.000 0.00 0.00 0.00 3.57
926 977 3.826729 ACCTAAGGAAGCAAACACATTCC 59.173 43.478 0.00 0.00 42.37 3.01
1035 1094 1.153647 CATTCTCGCCGTGGCTGTA 60.154 57.895 9.55 0.00 39.32 2.74
1370 1429 2.433604 AGATCGATGTCATGTCTGGCTT 59.566 45.455 0.54 0.00 0.00 4.35
1862 1941 2.006805 ATTAGGATGCCCCCAACCCG 62.007 60.000 0.00 0.00 34.63 5.28
1876 2204 2.682856 CCAACCCGAAACATACTGGATG 59.317 50.000 0.00 0.00 41.79 3.51
1939 2268 6.237901 AGTGCCATACATGTTCTTGTTTCTA 58.762 36.000 2.30 0.00 0.00 2.10
2074 2417 2.492753 GGACCAAAATTTCCCCTGTCCT 60.493 50.000 13.17 0.00 38.18 3.85
2103 2461 4.925054 CGTCCACTGTAAAAATACCTTCGA 59.075 41.667 0.00 0.00 0.00 3.71
2174 3015 7.865889 CGCCTATTTTATTTTGAGGGAATAACC 59.134 37.037 0.00 0.00 30.86 2.85
2208 3049 3.769739 AAATGTTTTCCCTTTCCCTGC 57.230 42.857 0.00 0.00 0.00 4.85
2210 3051 0.263172 TGTTTTCCCTTTCCCTGCCA 59.737 50.000 0.00 0.00 0.00 4.92
2233 3074 2.226602 TTAACTTTGTTTTGGGCGCC 57.773 45.000 21.18 21.18 0.00 6.53
2242 3083 4.713735 TTGGGCGCCGATCTGCAA 62.714 61.111 22.54 14.99 0.00 4.08
2281 3123 0.106519 AATATGGACCAGCAGGCACC 60.107 55.000 0.00 0.00 39.06 5.01
2289 3131 0.107897 CCAGCAGGCACCGTGTATAA 60.108 55.000 0.00 0.00 0.00 0.98
2435 3277 6.731467 ACCACAAATAGTCCAAATAGACCAT 58.269 36.000 0.00 0.00 37.49 3.55
2436 3278 7.867921 ACCACAAATAGTCCAAATAGACCATA 58.132 34.615 0.00 0.00 37.49 2.74
2450 3292 6.821031 ATAGACCATAGACGTCTATCCAAC 57.179 41.667 30.66 21.50 46.01 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 7.494298 TGCTCGTCTTTTAAGCAATACATATCA 59.506 33.333 0.00 0.00 42.71 2.15
202 203 3.851403 CCAAACGAATTTCTACCATTGCG 59.149 43.478 0.00 0.00 0.00 4.85
275 280 3.062639 GGCCTGTTGCATGCCTTT 58.937 55.556 16.68 0.00 40.98 3.11
324 329 0.038251 CTGTGCAGCCGAACACTCTA 60.038 55.000 0.00 0.00 37.68 2.43
517 527 6.635030 AAGAGACCCTAAAATGTTGTTGTC 57.365 37.500 0.00 0.00 0.00 3.18
720 745 7.117236 TGGTACGTACTTGATCAAAATTGACTC 59.883 37.037 24.07 2.76 40.49 3.36
725 750 5.938125 AGCTGGTACGTACTTGATCAAAATT 59.062 36.000 24.07 0.00 0.00 1.82
756 781 1.896220 TGGGAACACAAGCAAGCTAG 58.104 50.000 0.00 0.00 33.40 3.42
781 810 4.527944 TGGGACTTTGAATGTTGTGTGTA 58.472 39.130 0.00 0.00 0.00 2.90
782 811 3.360867 TGGGACTTTGAATGTTGTGTGT 58.639 40.909 0.00 0.00 0.00 3.72
783 812 4.589216 ATGGGACTTTGAATGTTGTGTG 57.411 40.909 0.00 0.00 0.00 3.82
802 833 0.462581 AGTGCGTGTGCCTGGATATG 60.463 55.000 0.00 0.00 41.78 1.78
804 835 1.218047 GAGTGCGTGTGCCTGGATA 59.782 57.895 0.00 0.00 41.78 2.59
812 843 0.992072 CGTAGAATGGAGTGCGTGTG 59.008 55.000 0.00 0.00 0.00 3.82
832 866 0.753479 ACATGTGCGGTTGGTGGAAA 60.753 50.000 0.00 0.00 0.00 3.13
926 977 0.251916 TGTATTGGTCCTTGAGCGGG 59.748 55.000 0.00 0.00 32.15 6.13
1035 1094 1.076485 GGTGCTCAGGATGGCCATT 60.076 57.895 21.84 0.72 36.16 3.16
1430 1495 3.136123 CATTGGTGGCAGCGGAGG 61.136 66.667 12.58 1.10 0.00 4.30
1521 1588 0.955428 AAGTACACATGTGCCTGCGG 60.955 55.000 25.68 0.19 0.00 5.69
1862 1941 5.066505 AGCCGAATTTCATCCAGTATGTTTC 59.933 40.000 0.00 0.00 36.89 2.78
1876 2204 2.162319 TTTTTGCCCAGCCGAATTTC 57.838 45.000 0.00 0.00 0.00 2.17
1939 2268 0.546122 TGACTGTCCCTTGCAACACT 59.454 50.000 5.17 0.00 0.00 3.55
2047 2390 2.029380 GGGGAAATTTTGGTCCTTCACG 60.029 50.000 0.00 0.00 34.10 4.35
2074 2417 1.706995 TTTTACAGTGGACGGGGCCA 61.707 55.000 4.39 0.00 35.02 5.36
2103 2461 9.739276 TCTTGATGAATGTTCTTTACCTAATGT 57.261 29.630 0.00 0.00 0.00 2.71
2208 3049 3.559655 GCCCAAAACAAAGTTAAAGCTGG 59.440 43.478 0.00 0.00 0.00 4.85
2210 3051 3.453424 CGCCCAAAACAAAGTTAAAGCT 58.547 40.909 0.00 0.00 0.00 3.74
2233 3074 0.246912 GTCGCGTTTCTTGCAGATCG 60.247 55.000 5.77 0.00 0.00 3.69
2242 3083 1.874345 ATCCAGTCGGTCGCGTTTCT 61.874 55.000 5.77 0.00 0.00 2.52
2281 3123 4.438145 GTGAGAGCAGACGATTTATACACG 59.562 45.833 0.00 0.00 0.00 4.49
2289 3131 3.340814 AAATGGTGAGAGCAGACGATT 57.659 42.857 0.00 0.00 0.00 3.34
2414 3256 7.926555 CGTCTATGGTCTATTTGGACTATTTGT 59.073 37.037 0.00 0.00 38.19 2.83
2450 3292 2.970324 CGGACACACCCACCAACG 60.970 66.667 0.00 0.00 34.64 4.10
2460 3302 4.141981 TGAAAGTTAAGTACACCGGACACA 60.142 41.667 9.46 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.