Multiple sequence alignment - TraesCS2D01G247400

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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 TraesCS2D01G247400 chr2D 100.000 2234 0 0 1 2234 291707360 291705127 0 4126
1 TraesCS2D01G247400 chr7A 95.718 2242 85 6 1 2233 638507635 638509874 0 3598
2 TraesCS2D01G247400 chr7A 95.321 2244 91 10 1 2234 708245654 708243415 0 3550
3 TraesCS2D01G247400 chrUn 95.674 2242 87 6 1 2234 171008315 171006076 0 3594
4 TraesCS2D01G247400 chr6B 95.542 2243 88 7 1 2234 596601829 596604068 0 3578
5 TraesCS2D01G247400 chr7D 95.317 2242 90 8 1 2234 382089828 382087594 0 3544
6 TraesCS2D01G247400 chr1B 95.174 2238 98 8 4 2234 672541248 672539014 0 3526
7 TraesCS2D01G247400 chr5B 95.098 2244 98 7 1 2234 567280025 567277784 0 3524


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 TraesCS2D01G247400 chr2D 291705127 291707360 2233 True 4126 4126 100.000 1 2234 1 chr2D.!!$R1 2233
1 TraesCS2D01G247400 chr7A 638507635 638509874 2239 False 3598 3598 95.718 1 2233 1 chr7A.!!$F1 2232
2 TraesCS2D01G247400 chr7A 708243415 708245654 2239 True 3550 3550 95.321 1 2234 1 chr7A.!!$R1 2233
3 TraesCS2D01G247400 chrUn 171006076 171008315 2239 True 3594 3594 95.674 1 2234 1 chrUn.!!$R1 2233
4 TraesCS2D01G247400 chr6B 596601829 596604068 2239 False 3578 3578 95.542 1 2234 1 chr6B.!!$F1 2233
5 TraesCS2D01G247400 chr7D 382087594 382089828 2234 True 3544 3544 95.317 1 2234 1 chr7D.!!$R1 2233
6 TraesCS2D01G247400 chr1B 672539014 672541248 2234 True 3526 3526 95.174 4 2234 1 chr1B.!!$R1 2230
7 TraesCS2D01G247400 chr5B 567277784 567280025 2241 True 3524 3524 95.098 1 2234 1 chr5B.!!$R1 2233

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
642 652 0.035439 TCACTTCCCCGCCATTCTTC 60.035 55.0 0.0 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1711 0.106967 GGAGCAATCCCCCTCTGTTC 60.107 60.0 0.0 0.0 0.0 3.18 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
90 94 7.273381 CGCGGTTCATATTTCATTTTCTTCTTT 59.727 33.333 0.00 0.00 0.00 2.52
99 103 5.964958 TCATTTTCTTCTTTCAAGCCGAT 57.035 34.783 0.00 0.00 0.00 4.18
137 141 6.064846 ACAAAGCACTCACTGAATTACTTG 57.935 37.500 0.00 0.00 0.00 3.16
138 142 5.590259 ACAAAGCACTCACTGAATTACTTGT 59.410 36.000 0.00 0.00 0.00 3.16
140 144 7.282224 ACAAAGCACTCACTGAATTACTTGTTA 59.718 33.333 0.00 0.00 0.00 2.41
158 162 7.434492 ACTTGTTAAATCTCGTCTTTCTCTCA 58.566 34.615 0.00 0.00 0.00 3.27
200 204 1.320344 CCGGGTCGATCAGAGGTTCA 61.320 60.000 0.00 0.00 0.00 3.18
222 226 2.610859 GCTTCTCCCCCACCCTCA 60.611 66.667 0.00 0.00 0.00 3.86
293 298 1.137086 TCTGTTGAAGCGGATAGGAGC 59.863 52.381 0.00 0.00 0.00 4.70
296 301 2.290008 TGTTGAAGCGGATAGGAGCAAA 60.290 45.455 0.00 0.00 35.48 3.68
423 433 2.772924 CCCAGCCCCCTTGTTGAT 59.227 61.111 0.00 0.00 0.00 2.57
451 461 6.833041 TGGATATTAAGGAAGCCGTATTTCA 58.167 36.000 0.00 0.00 0.00 2.69
460 470 4.095782 GGAAGCCGTATTTCACAATAGCAA 59.904 41.667 0.00 0.00 0.00 3.91
493 503 2.432300 GCTTAGGGTGCGCCTCCTA 61.432 63.158 17.49 18.26 34.75 2.94
503 513 1.080298 CGCCTCCTACGGTCGTTTT 60.080 57.895 0.16 0.00 0.00 2.43
642 652 0.035439 TCACTTCCCCGCCATTCTTC 60.035 55.000 0.00 0.00 0.00 2.87
655 665 3.118884 GCCATTCTTCTAACCGTCACCTA 60.119 47.826 0.00 0.00 0.00 3.08
729 740 0.699399 TTTTATCGGAGCAACCCCCA 59.301 50.000 0.00 0.00 34.64 4.96
753 764 0.105194 TCCAGACCCAGGAGTTCACA 60.105 55.000 0.00 0.00 0.00 3.58
780 791 4.562789 CCGTATGAGCATTCGGTACATATG 59.437 45.833 17.10 0.00 43.75 1.78
815 826 2.367567 GAGTCAAAGGGTCACCACTACA 59.632 50.000 0.00 0.00 40.13 2.74
912 923 1.592223 CCTTCTCCGAAAGCTCCGT 59.408 57.895 7.54 0.00 0.00 4.69
940 951 2.307768 CCTATCACTAGTCTTCGGCCA 58.692 52.381 2.24 0.00 0.00 5.36
956 967 1.106285 GCCAGAGGGGTTTATTGCAG 58.894 55.000 0.00 0.00 39.65 4.41
965 976 3.007940 GGGGTTTATTGCAGAAAAAGGCT 59.992 43.478 0.00 0.00 0.00 4.58
972 983 1.172812 GCAGAAAAAGGCTGGGACGT 61.173 55.000 0.00 0.00 34.00 4.34
1075 1087 1.260544 AAAAGAGCAGACCCCATTGC 58.739 50.000 0.00 0.00 40.57 3.56
1171 1183 2.282674 CTCCCAGCCAGCAAGCAA 60.283 61.111 0.55 0.00 34.23 3.91
1215 1227 5.097742 TGGAAGTGTGGATAAATCGACAT 57.902 39.130 10.42 0.00 45.07 3.06
1317 1329 3.448686 AGATCGCATTTTAGGTCGAGTG 58.551 45.455 0.00 0.00 34.30 3.51
1371 1383 4.139786 GCATTTCAAGATGGCCTCTATCA 58.860 43.478 3.32 0.00 32.41 2.15
1379 1391 5.901413 AGATGGCCTCTATCATCTTTTCA 57.099 39.130 3.32 0.00 45.32 2.69
1419 1431 0.826062 CAAGGGGCATTTGACATCCC 59.174 55.000 0.00 0.00 38.03 3.85
1440 1452 3.338249 CGAGACAAAATCAGTCCCACAT 58.662 45.455 0.00 0.00 36.68 3.21
1477 1489 1.613255 CCCAATGGACGTAACCAGCTT 60.613 52.381 0.00 0.00 43.49 3.74
1641 1653 6.822170 AGTAGAACTTCGTTTTGAGGAGTTTT 59.178 34.615 0.00 0.00 0.00 2.43
1688 1700 2.091830 ACGACTACTCTGGGATGGATCA 60.092 50.000 0.00 0.00 0.00 2.92
1698 1710 3.459598 CTGGGATGGATCAAGGTTTAGGA 59.540 47.826 0.00 0.00 0.00 2.94
1699 1711 3.459598 TGGGATGGATCAAGGTTTAGGAG 59.540 47.826 0.00 0.00 0.00 3.69
1711 1723 2.547990 GTTTAGGAGAACAGAGGGGGA 58.452 52.381 0.00 0.00 0.00 4.81
1831 1843 2.124693 CCAGGGTTGGCGTTGTGTT 61.125 57.895 0.00 0.00 37.73 3.32
1867 1879 2.158798 GCTCCGGGCTAGAGGTAATTTT 60.159 50.000 0.00 0.00 38.06 1.82
1878 1890 7.449247 GCTAGAGGTAATTTTGATGATCTCCT 58.551 38.462 0.00 0.00 0.00 3.69
1904 1916 2.549992 CCTTTGTTCCTCGTCACCATCA 60.550 50.000 0.00 0.00 0.00 3.07
1931 1943 2.236146 ACAATAAGGAGATGCGGTGACA 59.764 45.455 0.00 0.00 0.00 3.58
1933 1945 3.845781 ATAAGGAGATGCGGTGACATT 57.154 42.857 0.00 0.00 0.00 2.71
2140 2153 1.546029 GGAACTGGCCAATTCACTTCC 59.454 52.381 26.87 15.35 0.00 3.46
2150 2163 5.452636 GGCCAATTCACTTCCAAAAACTACA 60.453 40.000 0.00 0.00 0.00 2.74
2182 2195 3.667360 AGCAGAAAAATTGGTGGCATTC 58.333 40.909 0.00 0.00 0.00 2.67
2217 2230 1.306654 CCACCCCTACTACTGCCCA 60.307 63.158 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 103 7.228507 TGAGTGCTTTGTTTTATAAGAAGAGCA 59.771 33.333 7.90 7.90 33.12 4.26
115 119 6.064846 ACAAGTAATTCAGTGAGTGCTTTG 57.935 37.500 6.53 6.79 0.00 2.77
137 141 5.003967 CGCTGAGAGAAAGACGAGATTTAAC 59.996 44.000 0.00 0.00 0.00 2.01
138 142 5.096169 CGCTGAGAGAAAGACGAGATTTAA 58.904 41.667 0.00 0.00 0.00 1.52
140 144 3.506810 CGCTGAGAGAAAGACGAGATTT 58.493 45.455 0.00 0.00 0.00 2.17
158 162 0.165944 CGTCAAAAATTCTCGGCGCT 59.834 50.000 7.64 0.00 0.00 5.92
200 204 2.759795 GTGGGGGAGAAGCAAGCT 59.240 61.111 0.00 0.00 0.00 3.74
222 226 5.103515 AGCAAGGGTTATCCATTTCATAGGT 60.104 40.000 0.00 0.00 35.40 3.08
259 263 6.331369 CTTCAACAGAAGCCCTTAAAATCA 57.669 37.500 0.00 0.00 33.07 2.57
354 364 4.449405 GCCTAGATTAGATGTTCGCCTTTC 59.551 45.833 0.00 0.00 0.00 2.62
423 433 9.802039 AAATACGGCTTCCTTAATATCCAAATA 57.198 29.630 0.00 0.00 0.00 1.40
451 461 2.234908 AGCTTCTCGGAGTTGCTATTGT 59.765 45.455 19.72 3.12 31.71 2.71
460 470 0.614979 TAAGCCCAGCTTCTCGGAGT 60.615 55.000 4.87 0.00 46.77 3.85
493 503 3.441496 TTGAGTCACTAAAACGACCGT 57.559 42.857 0.00 0.00 32.33 4.83
503 513 1.630369 AGCCAGCCAATTGAGTCACTA 59.370 47.619 7.12 0.00 0.00 2.74
565 575 3.352648 CATCGGGCGGGGATAATTATTT 58.647 45.455 0.00 0.00 0.00 1.40
569 579 1.378762 CCATCGGGCGGGGATAATT 59.621 57.895 0.00 0.00 0.00 1.40
611 621 2.108970 GGGAAGTGAAGAGTACCCGAT 58.891 52.381 0.00 0.00 0.00 4.18
642 652 3.572584 GCGGATTATAGGTGACGGTTAG 58.427 50.000 0.00 0.00 0.00 2.34
655 665 0.810031 GACACACCTGCGCGGATTAT 60.810 55.000 20.25 0.00 36.31 1.28
713 723 1.705002 CCATGGGGGTTGCTCCGATA 61.705 60.000 2.85 0.00 37.00 2.92
753 764 2.169832 CCGAATGCTCATACGGGAAT 57.830 50.000 0.00 0.00 41.41 3.01
780 791 4.991687 CCTTTGACTCTTCCACTGACTTAC 59.008 45.833 0.00 0.00 0.00 2.34
838 849 0.037232 GAACCCTCAGACGACCCTTG 60.037 60.000 0.00 0.00 0.00 3.61
912 923 2.585900 AGACTAGTGATAGGTGGTCCCA 59.414 50.000 0.00 0.00 34.66 4.37
940 951 4.528206 CCTTTTTCTGCAATAAACCCCTCT 59.472 41.667 0.00 0.00 0.00 3.69
956 967 1.524008 CCCACGTCCCAGCCTTTTTC 61.524 60.000 0.00 0.00 0.00 2.29
997 1008 1.820519 GGGCTTTGCATCTGACATTCA 59.179 47.619 0.00 0.00 0.00 2.57
1075 1087 2.567169 TGTTGTACCTCACTCCCATCTG 59.433 50.000 0.00 0.00 0.00 2.90
1171 1183 6.613271 TCCATGACTTCTAGAGGAAAGCTAAT 59.387 38.462 9.14 0.00 33.07 1.73
1238 1250 0.466963 ATTTAGGACGGTTAGGGCGG 59.533 55.000 0.00 0.00 0.00 6.13
1317 1329 0.394625 ACAGACTCCCTAGCGTCTCC 60.395 60.000 5.04 0.00 38.37 3.71
1379 1391 2.034221 GGCAAACGGGAGGCTCTT 59.966 61.111 15.23 0.00 0.00 2.85
1419 1431 2.766313 TGTGGGACTGATTTTGTCTCG 58.234 47.619 0.00 0.00 37.72 4.04
1507 1519 4.364415 AAAAAGCAACTACAAGCGTTCA 57.636 36.364 0.00 0.00 31.42 3.18
1586 1598 4.917385 TGGAAGAATTGGAAGAATCGGAA 58.083 39.130 0.00 0.00 0.00 4.30
1670 1682 3.310954 ACCTTGATCCATCCCAGAGTAGT 60.311 47.826 0.00 0.00 0.00 2.73
1688 1700 2.913617 CCCCTCTGTTCTCCTAAACCTT 59.086 50.000 0.00 0.00 0.00 3.50
1698 1710 0.915364 GAGCAATCCCCCTCTGTTCT 59.085 55.000 0.00 0.00 0.00 3.01
1699 1711 0.106967 GGAGCAATCCCCCTCTGTTC 60.107 60.000 0.00 0.00 0.00 3.18
1711 1723 3.362870 CTCCAGAAGAAAGGGAGCAAT 57.637 47.619 0.00 0.00 41.53 3.56
1755 1767 2.856864 AGATTCCCCCTTTACCGGAAAT 59.143 45.455 9.46 0.00 39.07 2.17
1867 1879 0.399091 AAGGGCCGAGGAGATCATCA 60.399 55.000 0.00 0.00 0.00 3.07
1878 1890 2.345991 CGAGGAACAAAGGGCCGA 59.654 61.111 0.00 0.00 0.00 5.54
1904 1916 5.296780 CACCGCATCTCCTTATTGTTATTGT 59.703 40.000 0.00 0.00 0.00 2.71
1931 1943 7.601705 TTTCTTTTTCCTTCTGGATGACAAT 57.398 32.000 0.00 0.00 42.81 2.71
1933 1945 6.183360 GGTTTTCTTTTTCCTTCTGGATGACA 60.183 38.462 0.00 0.00 42.81 3.58
2140 2153 8.559536 TCTGCTCAAGTTAGAATGTAGTTTTTG 58.440 33.333 0.00 0.00 0.00 2.44
2150 2163 7.869429 CACCAATTTTTCTGCTCAAGTTAGAAT 59.131 33.333 0.00 0.00 31.21 2.40
2182 2195 3.435671 GGGTGGTGAAACTTTAGATGTCG 59.564 47.826 0.00 0.00 36.74 4.35


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

AutoCloner maintained by Alex Coulton.