Multiple sequence alignment - TraesCS5D01G228200

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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 TraesCS5D01G228200 chr5D 100.000 2237 0 0 1 2237 335750417 335752653 0.000000e+00 4132
1 TraesCS5D01G228200 chr5B 93.131 1776 53 16 482 2237 393577072 393578798 0.000000e+00 2540
2 TraesCS5D01G228200 chr5B 93.229 192 8 2 271 458 393576891 393577081 6.080000e-71 278
3 TraesCS5D01G228200 chr5B 89.238 223 21 1 1 220 393576577 393576799 2.190000e-70 276
4 TraesCS5D01G228200 chr5A 93.224 856 37 11 1389 2237 436881574 436882415 0.000000e+00 1240
5 TraesCS5D01G228200 chr5A 91.639 909 28 16 482 1375 436880473 436881348 0.000000e+00 1214
6 TraesCS5D01G228200 chr5A 95.290 276 8 2 1 272 436879969 436880243 1.230000e-117 433
7 TraesCS5D01G228200 chr5A 95.477 199 6 2 271 467 436880293 436880490 4.640000e-82 315


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 TraesCS5D01G228200 chr5D 335750417 335752653 2236 False 4132.000000 4132 100.0000 1 2237 1 chr5D.!!$F1 2236
1 TraesCS5D01G228200 chr5B 393576577 393578798 2221 False 1031.333333 2540 91.8660 1 2237 3 chr5B.!!$F1 2236
2 TraesCS5D01G228200 chr5A 436879969 436882415 2446 False 800.500000 1240 93.9075 1 2237 4 chr5A.!!$F1 2236

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
780 873 0.250793 ATACAATGACCGCCGGACAA 59.749 50.0 11.71 0.0 30.61 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 2079 1.743394 GTCGGAGCCCCAAATAAGTTG 59.257 52.381 0.0 0.0 36.94 3.16 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
27 28 6.939163 CCTTTACCCTTCTCCAATCATGATAG 59.061 42.308 9.04 2.98 0.00 2.08
74 78 2.969806 GCACACGGCCACAGTGATG 61.970 63.158 19.86 12.85 41.83 3.07
90 94 3.391506 TGATGGATAGATTGCCGTCAG 57.608 47.619 0.00 0.00 43.37 3.51
93 97 1.412710 TGGATAGATTGCCGTCAGTCC 59.587 52.381 0.00 0.00 30.10 3.85
98 102 2.835701 GATTGCCGTCAGTCCGCAGA 62.836 60.000 0.00 0.00 32.60 4.26
117 121 5.456497 CGCAGATCAATTTAATTTGCACGAT 59.544 36.000 11.14 1.36 34.76 3.73
221 225 0.536006 AGAGCGCTTGTTTGGAGCTT 60.536 50.000 13.26 0.00 39.71 3.74
222 226 1.156736 GAGCGCTTGTTTGGAGCTTA 58.843 50.000 13.26 0.00 39.71 3.09
223 227 1.129437 GAGCGCTTGTTTGGAGCTTAG 59.871 52.381 13.26 0.00 39.71 2.18
224 228 0.455126 GCGCTTGTTTGGAGCTTAGC 60.455 55.000 0.00 0.00 37.99 3.09
225 229 0.874390 CGCTTGTTTGGAGCTTAGCA 59.126 50.000 7.07 0.00 37.99 3.49
226 230 1.135859 CGCTTGTTTGGAGCTTAGCAG 60.136 52.381 7.07 0.00 37.99 4.24
458 530 4.497300 CACTTGCACAATTATTTGAGGGG 58.503 43.478 4.42 0.00 36.64 4.79
459 531 4.220382 CACTTGCACAATTATTTGAGGGGA 59.780 41.667 4.42 0.00 36.64 4.81
460 532 4.463891 ACTTGCACAATTATTTGAGGGGAG 59.536 41.667 4.42 0.00 36.64 4.30
461 533 4.046286 TGCACAATTATTTGAGGGGAGT 57.954 40.909 4.42 0.00 36.64 3.85
462 534 4.415596 TGCACAATTATTTGAGGGGAGTT 58.584 39.130 4.42 0.00 36.64 3.01
463 535 4.837860 TGCACAATTATTTGAGGGGAGTTT 59.162 37.500 4.42 0.00 36.64 2.66
464 536 5.170748 GCACAATTATTTGAGGGGAGTTTG 58.829 41.667 4.42 0.00 36.64 2.93
465 537 5.170748 CACAATTATTTGAGGGGAGTTTGC 58.829 41.667 4.42 0.00 36.64 3.68
466 538 5.047092 CACAATTATTTGAGGGGAGTTTGCT 60.047 40.000 4.42 0.00 36.64 3.91
467 539 5.543790 ACAATTATTTGAGGGGAGTTTGCTT 59.456 36.000 4.42 0.00 36.64 3.91
468 540 6.043127 ACAATTATTTGAGGGGAGTTTGCTTT 59.957 34.615 4.42 0.00 36.64 3.51
469 541 7.234577 ACAATTATTTGAGGGGAGTTTGCTTTA 59.765 33.333 4.42 0.00 36.64 1.85
470 542 7.978099 ATTATTTGAGGGGAGTTTGCTTTAT 57.022 32.000 0.00 0.00 0.00 1.40
471 543 7.790782 TTATTTGAGGGGAGTTTGCTTTATT 57.209 32.000 0.00 0.00 0.00 1.40
472 544 6.686484 ATTTGAGGGGAGTTTGCTTTATTT 57.314 33.333 0.00 0.00 0.00 1.40
473 545 6.493189 TTTGAGGGGAGTTTGCTTTATTTT 57.507 33.333 0.00 0.00 0.00 1.82
474 546 6.493189 TTGAGGGGAGTTTGCTTTATTTTT 57.507 33.333 0.00 0.00 0.00 1.94
580 659 6.153756 TGATATTGATATGTACACCGAACCG 58.846 40.000 0.00 0.00 0.00 4.44
597 680 1.033574 CCGGACCAGACCAGATAGTC 58.966 60.000 0.00 0.00 37.01 2.59
610 693 2.962421 CAGATAGTCCCTCCTGAACTCC 59.038 54.545 0.00 0.00 0.00 3.85
621 704 6.447084 TCCCTCCTGAACTCCTTTTTATGTAT 59.553 38.462 0.00 0.00 0.00 2.29
653 745 4.996122 GGAGCTGAGACAATCATTAGATGG 59.004 45.833 0.00 0.00 37.28 3.51
655 747 5.366460 AGCTGAGACAATCATTAGATGGTG 58.634 41.667 0.00 0.00 38.55 4.17
661 753 7.134362 AGACAATCATTAGATGGTGATCAGT 57.866 36.000 0.00 0.00 38.55 3.41
667 759 5.129980 TCATTAGATGGTGATCAGTTGAGCT 59.870 40.000 0.00 0.00 0.00 4.09
780 873 0.250793 ATACAATGACCGCCGGACAA 59.749 50.000 11.71 0.00 30.61 3.18
910 1004 2.528818 CCCCTGCTGTGTCCCTCAA 61.529 63.158 0.00 0.00 0.00 3.02
977 1071 0.985490 CTGGGGAGGGAGAAAGGGAG 60.985 65.000 0.00 0.00 0.00 4.30
978 1072 1.396594 GGGGAGGGAGAAAGGGAGA 59.603 63.158 0.00 0.00 0.00 3.71
979 1073 0.692756 GGGGAGGGAGAAAGGGAGAG 60.693 65.000 0.00 0.00 0.00 3.20
980 1074 0.340208 GGGAGGGAGAAAGGGAGAGA 59.660 60.000 0.00 0.00 0.00 3.10
981 1075 1.691163 GGGAGGGAGAAAGGGAGAGAG 60.691 61.905 0.00 0.00 0.00 3.20
982 1076 1.691163 GGAGGGAGAAAGGGAGAGAGG 60.691 61.905 0.00 0.00 0.00 3.69
987 1081 2.666317 GAGAAAGGGAGAGAGGGAGAG 58.334 57.143 0.00 0.00 0.00 3.20
998 1092 1.846439 AGAGGGAGAGACAGAGAGAGG 59.154 57.143 0.00 0.00 0.00 3.69
1191 1285 0.180642 ACATCTGCATCCTGGAGCTG 59.819 55.000 15.75 15.04 37.83 4.24
1375 1469 1.204146 GCTCATCTCTTGTACCCCCA 58.796 55.000 0.00 0.00 0.00 4.96
1377 1471 2.472029 CTCATCTCTTGTACCCCCACT 58.528 52.381 0.00 0.00 0.00 4.00
1735 2045 4.442706 GTGTTCAACACCATAGATCCGAT 58.557 43.478 9.76 0.00 43.05 4.18
1746 2056 7.668469 ACACCATAGATCCGATACACTGTAATA 59.332 37.037 0.00 0.00 0.00 0.98
1747 2057 8.520351 CACCATAGATCCGATACACTGTAATAA 58.480 37.037 0.00 0.00 0.00 1.40
1748 2058 9.256228 ACCATAGATCCGATACACTGTAATAAT 57.744 33.333 0.00 0.00 0.00 1.28
1752 2062 7.306213 AGATCCGATACACTGTAATAATCACG 58.694 38.462 0.00 0.00 0.00 4.35
1769 2079 1.597663 CACGATAAAATCCCGGTCTGC 59.402 52.381 0.00 0.00 0.00 4.26
1791 2101 1.065418 ACTTATTTGGGGCTCCGACAG 60.065 52.381 0.00 0.00 35.24 3.51
1795 2105 0.404040 TTTGGGGCTCCGACAGAAAT 59.596 50.000 0.00 0.00 35.24 2.17
1868 2180 2.799412 CAAATAACAGCTGCCGCAAAAA 59.201 40.909 15.27 0.00 39.10 1.94
1924 2237 7.936584 TGTCAGAATTTCCGTAAAAAGTGAAT 58.063 30.769 0.00 0.00 0.00 2.57
1948 2261 8.943909 ATAGAACTTATTTTAGTCAAGGTCCG 57.056 34.615 0.00 0.00 36.80 4.79
2016 2329 3.674225 GCGAATGCGTCACATCAAA 57.326 47.368 0.00 0.00 38.34 2.69
2030 2343 4.877823 TCACATCAAACATATGCTCCAGTC 59.122 41.667 1.58 0.00 0.00 3.51
2109 2423 4.110482 GTGAAGCATCCAAGAATCAATGC 58.890 43.478 0.00 0.00 43.75 3.56
2141 2455 4.377839 TTCTCAGGTTTCTCAGCTATCG 57.622 45.455 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.557056 TGCACTCGTATAGTCCTATGCC 59.443 50.000 0.00 0.00 35.76 4.40
74 78 1.603172 CGGACTGACGGCAATCTATCC 60.603 57.143 0.00 0.00 0.00 2.59
90 94 5.004726 GTGCAAATTAAATTGATCTGCGGAC 59.995 40.000 7.46 0.00 31.84 4.79
93 97 4.792702 TCGTGCAAATTAAATTGATCTGCG 59.207 37.500 7.46 3.94 31.84 5.18
117 121 2.669569 GGTCTTCGCCAGCTTGCA 60.670 61.111 10.77 0.00 0.00 4.08
225 229 4.687215 TTCTTGCTCGCCTGCGCT 62.687 61.111 9.73 0.00 39.59 5.92
226 230 4.451652 GTTCTTGCTCGCCTGCGC 62.452 66.667 6.67 0.00 39.59 6.09
278 344 1.167851 CATTATGCCCCCTGTATGCG 58.832 55.000 0.00 0.00 0.00 4.73
472 544 9.582648 AGCAAACTCCCTTAAATACTCTAAAAA 57.417 29.630 0.00 0.00 0.00 1.94
475 547 9.662947 GTTAGCAAACTCCCTTAAATACTCTAA 57.337 33.333 0.00 0.00 32.54 2.10
476 548 9.043548 AGTTAGCAAACTCCCTTAAATACTCTA 57.956 33.333 0.00 0.00 42.42 2.43
477 549 7.919151 AGTTAGCAAACTCCCTTAAATACTCT 58.081 34.615 0.00 0.00 42.42 3.24
478 550 9.662947 TTAGTTAGCAAACTCCCTTAAATACTC 57.337 33.333 0.00 0.00 42.42 2.59
483 555 9.357161 TGATTTTAGTTAGCAAACTCCCTTAAA 57.643 29.630 0.00 0.00 42.42 1.52
484 556 8.789762 GTGATTTTAGTTAGCAAACTCCCTTAA 58.210 33.333 0.00 0.00 42.42 1.85
485 557 7.940137 TGTGATTTTAGTTAGCAAACTCCCTTA 59.060 33.333 0.00 0.00 42.42 2.69
486 558 6.775629 TGTGATTTTAGTTAGCAAACTCCCTT 59.224 34.615 0.00 0.00 42.42 3.95
487 559 6.303839 TGTGATTTTAGTTAGCAAACTCCCT 58.696 36.000 0.00 0.00 42.42 4.20
488 560 6.569179 TGTGATTTTAGTTAGCAAACTCCC 57.431 37.500 0.00 0.00 42.42 4.30
489 561 7.029563 CCATGTGATTTTAGTTAGCAAACTCC 58.970 38.462 0.00 0.00 42.42 3.85
490 562 7.029563 CCCATGTGATTTTAGTTAGCAAACTC 58.970 38.462 0.00 0.00 42.42 3.01
576 655 1.273098 ACTATCTGGTCTGGTCCGGTT 60.273 52.381 0.00 0.00 35.51 4.44
580 659 1.062810 AGGGACTATCTGGTCTGGTCC 60.063 57.143 0.00 0.00 43.86 4.46
597 680 4.923415 ACATAAAAAGGAGTTCAGGAGGG 58.077 43.478 0.00 0.00 0.00 4.30
621 704 5.768164 TGATTGTCTCAGCTCCACGTATATA 59.232 40.000 0.00 0.00 0.00 0.86
661 753 1.408702 GTTTTGCCCACTTCAGCTCAA 59.591 47.619 0.00 0.00 0.00 3.02
780 873 1.076485 GCTCCCACAGGCCATGAAT 60.076 57.895 5.01 0.00 0.00 2.57
910 1004 1.526887 CTGTGTGGAGGGTGTGTGT 59.473 57.895 0.00 0.00 0.00 3.72
977 1071 2.158755 CCTCTCTCTGTCTCTCCCTCTC 60.159 59.091 0.00 0.00 0.00 3.20
978 1072 1.846439 CCTCTCTCTGTCTCTCCCTCT 59.154 57.143 0.00 0.00 0.00 3.69
979 1073 1.133792 CCCTCTCTCTGTCTCTCCCTC 60.134 61.905 0.00 0.00 0.00 4.30
980 1074 0.926293 CCCTCTCTCTGTCTCTCCCT 59.074 60.000 0.00 0.00 0.00 4.20
981 1075 0.923358 TCCCTCTCTCTGTCTCTCCC 59.077 60.000 0.00 0.00 0.00 4.30
982 1076 2.174639 TCATCCCTCTCTCTGTCTCTCC 59.825 54.545 0.00 0.00 0.00 3.71
987 1081 2.958355 CCTTCTCATCCCTCTCTCTGTC 59.042 54.545 0.00 0.00 0.00 3.51
998 1092 1.213926 ACATGGCCTTCCTTCTCATCC 59.786 52.381 3.32 0.00 0.00 3.51
1278 1372 2.215942 AAACCTCTAACCATGGGCAC 57.784 50.000 18.09 0.00 0.00 5.01
1375 1469 4.082895 CCAGCTCACAAACGTAGTACTAGT 60.083 45.833 1.87 0.00 45.00 2.57
1377 1471 3.366679 GCCAGCTCACAAACGTAGTACTA 60.367 47.826 0.00 0.00 45.00 1.82
1545 1853 5.482175 TCCAGGAAACAGTTGAAAAGGAAAA 59.518 36.000 0.00 0.00 0.00 2.29
1729 2039 7.210718 TCGTGATTATTACAGTGTATCGGAT 57.789 36.000 3.28 0.00 0.00 4.18
1746 2056 4.127171 CAGACCGGGATTTTATCGTGATT 58.873 43.478 6.32 0.00 0.00 2.57
1747 2057 3.728845 CAGACCGGGATTTTATCGTGAT 58.271 45.455 6.32 0.00 0.00 3.06
1748 2058 2.740580 GCAGACCGGGATTTTATCGTGA 60.741 50.000 6.32 0.00 0.00 4.35
1752 2062 3.279434 AGTTGCAGACCGGGATTTTATC 58.721 45.455 6.32 0.00 0.00 1.75
1769 2079 1.743394 GTCGGAGCCCCAAATAAGTTG 59.257 52.381 0.00 0.00 36.94 3.16
1791 2101 3.988379 TCTGCCAACACTGTGAATTTC 57.012 42.857 15.86 0.35 0.00 2.17
1795 2105 3.213206 AGAATCTGCCAACACTGTGAA 57.787 42.857 15.86 0.00 0.00 3.18
1849 2159 2.810439 TTTTTGCGGCAGCTGTTATT 57.190 40.000 16.64 0.00 45.42 1.40
1924 2237 7.899973 ACGGACCTTGACTAAAATAAGTTCTA 58.100 34.615 0.00 0.00 0.00 2.10
1948 2261 3.243068 CCCACAGTTGTACTTGAAGCAAC 60.243 47.826 7.36 7.36 41.78 4.17
2030 2343 9.831737 CCTGAACTTTACTTTTCTGTCATAATG 57.168 33.333 0.00 0.00 0.00 1.90
2109 2423 6.813649 TGAGAAACCTGAGAAATATTGACGAG 59.186 38.462 0.00 0.00 0.00 4.18
2141 2455 4.156739 CCAGTCAAGACTTATTTCCTTGCC 59.843 45.833 0.00 0.00 40.20 4.52


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

AutoCloner maintained by Alex Coulton.