Multiple sequence alignment - TraesCS5A01G251500

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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 TraesCS5A01G251500 chr5A 100.000 3779 0 0 1 3779 467374084 467377862 0.000000e+00 6979
1 TraesCS5A01G251500 chr5A 94.118 119 5 2 3369 3486 308093339 308093222 3.000000e-41 180
2 TraesCS5A01G251500 chr5A 94.118 119 5 2 3369 3486 308179883 308179766 3.000000e-41 180
3 TraesCS5A01G251500 chr5D 96.072 3539 114 13 258 3779 365690184 365693714 0.000000e+00 5742
4 TraesCS5A01G251500 chr5D 93.680 269 11 3 1 269 365688845 365689107 7.610000e-107 398
5 TraesCS5A01G251500 chr5B 95.050 3394 133 11 1 3371 432150934 432154315 0.000000e+00 5304
6 TraesCS5A01G251500 chr5B 97.059 306 7 2 3474 3779 432154313 432154616 7.240000e-142 514
7 TraesCS5A01G251500 chr5B 94.118 119 4 2 3370 3488 617823369 617823484 1.080000e-40 178
8 TraesCS5A01G251500 chr7B 99.074 108 1 0 3369 3476 683101466 683101573 1.070000e-45 195
9 TraesCS5A01G251500 chr3D 98.148 108 2 0 3369 3476 536331139 536331032 4.980000e-44 189
10 TraesCS5A01G251500 chr3D 97.222 108 3 0 3369 3476 68912242 68912135 2.320000e-42 183
11 TraesCS5A01G251500 chr3D 93.333 120 6 2 3370 3488 44007437 44007319 3.880000e-40 176
12 TraesCS5A01G251500 chr4B 97.273 110 3 0 3368 3477 87405116 87405225 1.790000e-43 187


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 TraesCS5A01G251500 chr5A 467374084 467377862 3778 False 6979 6979 100.0000 1 3779 1 chr5A.!!$F1 3778
1 TraesCS5A01G251500 chr5D 365688845 365693714 4869 False 3070 5742 94.8760 1 3779 2 chr5D.!!$F1 3778
2 TraesCS5A01G251500 chr5B 432150934 432154616 3682 False 2909 5304 96.0545 1 3779 2 chr5B.!!$F2 3778

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
300 1393 0.105453 ATAGAGTGGGCGAGGGACAT 60.105 55.0 0.0 0.0 0.0 3.06 F
951 2069 0.389948 GCAGTGTTCGTGTAGAGGGG 60.390 60.0 0.0 0.0 0.0 4.79 F
1599 2717 0.521735 GTCCTGATTTTGTGCCGGTC 59.478 55.0 1.9 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1374 2492 0.037326 GCAGGAATCGTGTGTCTCCA 60.037 55.0 4.81 0.0 0.00 3.86 R
1911 3029 0.815213 CCATGATCACCGACCGCAAT 60.815 55.0 0.00 0.0 0.00 3.56 R
2903 4021 1.051008 TGATGGTCACAGTGCTCACT 58.949 50.0 0.00 0.0 43.61 3.41 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
159 164 3.705638 CACCACGTCAGTGCGCAG 61.706 66.667 12.22 0.00 46.62 5.18
184 189 1.753073 CAGTACCTAACCTACCCACCG 59.247 57.143 0.00 0.00 0.00 4.94
185 190 0.461548 GTACCTAACCTACCCACCGC 59.538 60.000 0.00 0.00 0.00 5.68
186 191 0.687427 TACCTAACCTACCCACCGCC 60.687 60.000 0.00 0.00 0.00 6.13
187 192 2.738938 CCTAACCTACCCACCGCCC 61.739 68.421 0.00 0.00 0.00 6.13
228 233 1.155390 TCCGTGACACTCTCCCCTT 59.845 57.895 3.68 0.00 0.00 3.95
231 236 1.079750 GTGACACTCTCCCCTTCGC 60.080 63.158 0.00 0.00 0.00 4.70
236 241 2.344203 ACTCTCCCCTTCGCAGTCG 61.344 63.158 0.00 0.00 0.00 4.18
264 269 3.322230 GCTACGTGCAGTACTCTACTC 57.678 52.381 0.00 0.00 42.31 2.59
300 1393 0.105453 ATAGAGTGGGCGAGGGACAT 60.105 55.000 0.00 0.00 0.00 3.06
370 1466 1.642037 CCGTGCAACTGATGAGCCTG 61.642 60.000 0.00 0.00 31.75 4.85
437 1534 1.664965 GCTATCCTTGCGCTACGGG 60.665 63.158 9.73 5.55 0.00 5.28
537 1635 2.909549 TTGGGTAAAGGGCCGGGAC 61.910 63.158 2.18 0.00 0.00 4.46
605 1703 2.363795 CCAGTGGACGCTCCCCTA 60.364 66.667 1.68 0.00 35.03 3.53
808 1916 3.785505 GCTGTAATCCACGAGCAATTTCG 60.786 47.826 0.00 0.00 45.70 3.46
817 1925 1.321743 CGAGCAATTTCGTTCTCGGAG 59.678 52.381 0.00 0.00 43.13 4.63
951 2069 0.389948 GCAGTGTTCGTGTAGAGGGG 60.390 60.000 0.00 0.00 0.00 4.79
1248 2366 2.759973 CGCCTGACCTCCCTAGCA 60.760 66.667 0.00 0.00 0.00 3.49
1263 2381 0.613853 TAGCACTCCGCCACTACCTT 60.614 55.000 0.00 0.00 44.04 3.50
1272 2390 1.889530 GCCACTACCTTGCTCTCCGT 61.890 60.000 0.00 0.00 0.00 4.69
1274 2392 0.603569 CACTACCTTGCTCTCCGTGT 59.396 55.000 0.00 0.00 0.00 4.49
1276 2394 0.737715 CTACCTTGCTCTCCGTGTGC 60.738 60.000 0.00 0.00 35.88 4.57
1278 2396 3.782244 CTTGCTCTCCGTGTGCGC 61.782 66.667 0.00 0.00 37.94 6.09
1374 2492 3.307829 CGCGTTACGTCTCACTGAT 57.692 52.632 6.63 0.00 36.87 2.90
1434 2552 1.379044 CTTTTCCTGCGGGGATGCT 60.379 57.895 12.87 0.00 44.66 3.79
1458 2576 3.033764 GCTCGCCGTGTGTTCGAA 61.034 61.111 0.00 0.00 0.00 3.71
1539 2657 4.673375 AGTGGCAGCCCCTTGCAG 62.673 66.667 9.64 0.00 45.86 4.41
1599 2717 0.521735 GTCCTGATTTTGTGCCGGTC 59.478 55.000 1.90 0.00 0.00 4.79
1689 2807 1.541588 GTCAAGGGTGGCTTTGATGAC 59.458 52.381 0.00 0.00 35.91 3.06
1783 2901 4.843331 ACAGGATCCCGCCCCCAT 62.843 66.667 8.55 0.00 0.00 4.00
1833 2951 6.467677 CATGATATCGGGTTACTCCAAGAAT 58.532 40.000 0.00 0.00 38.11 2.40
1845 2963 0.901580 CCAAGAATGGGCTTGCCAGT 60.902 55.000 14.04 0.00 43.51 4.00
1899 3017 2.044650 GCAAGGAGCATGAGCCCA 60.045 61.111 0.00 0.00 44.79 5.36
1911 3029 1.351076 TGAGCCCAGATTCTGTCACA 58.649 50.000 12.54 6.16 0.00 3.58
1935 3053 2.182842 GTCGGTGATCATGGCCTGC 61.183 63.158 3.32 0.00 0.00 4.85
1938 3056 3.945434 GTGATCATGGCCTGCGCG 61.945 66.667 3.32 0.00 35.02 6.86
2013 3131 2.373169 TGAGTGCAAGGAGGATGTTCTT 59.627 45.455 0.00 0.00 0.00 2.52
2139 3257 4.164796 TGGAGTGCATTGATCTCAGGTTAT 59.835 41.667 3.95 0.00 0.00 1.89
2184 3302 1.631405 CCATTGGCCTGTTTGAGGAA 58.369 50.000 3.32 0.00 46.33 3.36
2280 3398 3.256704 TGTGGAGAAAGGGTGGTTCTAT 58.743 45.455 0.00 0.00 35.46 1.98
2802 3920 8.680001 TGAGTTCCTTTTTGTAGTTAGGAAAAC 58.320 33.333 0.00 0.00 45.55 2.43
2804 3922 6.964807 TCCTTTTTGTAGTTAGGAAAACCC 57.035 37.500 0.00 0.00 33.98 4.11
2876 3994 2.977772 TGTCATGCATATCGTGTCCA 57.022 45.000 0.00 0.00 33.44 4.02
2889 4007 7.572910 GCATATCGTGTCCATACAATGCAATTA 60.573 37.037 0.00 0.00 42.10 1.40
2956 4074 4.279145 ACATACCAGGTTACACGAGATCT 58.721 43.478 0.00 0.00 0.00 2.75
3010 4128 5.942826 TGATTTTTGCAAACCTCCAGTTTTT 59.057 32.000 12.39 0.00 46.79 1.94
3218 4336 7.307493 TGTTCAGAAGATAAACAATCCATCG 57.693 36.000 0.00 0.00 34.90 3.84
3466 4584 8.667204 GTCTGAAACGTCTTATAAAAACAAACG 58.333 33.333 0.00 0.00 35.00 3.60
3690 4809 8.279103 GCTTATCTGAAATTATTCTCAAGACCG 58.721 37.037 0.00 0.00 36.48 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.747976 CCGGAAAGCAAAGGCCCG 61.748 66.667 0.00 0.00 42.56 6.13
159 164 2.037901 GGTAGGTTAGGTACTGAGCCC 58.962 57.143 0.00 0.00 43.75 5.19
282 1375 1.043116 CATGTCCCTCGCCCACTCTA 61.043 60.000 0.00 0.00 0.00 2.43
300 1393 3.970410 CCACAAGGAGGGCCAGCA 61.970 66.667 6.18 0.00 36.89 4.41
308 1402 2.550699 TTATGCCGGCCCACAAGGAG 62.551 60.000 26.77 0.00 38.24 3.69
309 1403 1.932156 ATTATGCCGGCCCACAAGGA 61.932 55.000 26.77 1.65 38.24 3.36
370 1466 1.227853 ACGGGTGAGCAGGACAAAC 60.228 57.895 0.00 0.00 0.00 2.93
419 1516 1.664965 CCCGTAGCGCAAGGATAGC 60.665 63.158 11.47 0.00 38.28 2.97
443 1540 3.927163 ATTCGTGGGGACGACGTGC 62.927 63.158 11.45 11.45 42.20 5.34
458 1555 1.212751 GTGGGCACGCCAAGAATTC 59.787 57.895 10.83 0.00 37.98 2.17
537 1635 0.461961 CAGGGACTCCTTTAGCTCGG 59.538 60.000 0.00 0.00 42.67 4.63
873 1982 3.796717 GCAAAAACGAAACAGAAGAAGGG 59.203 43.478 0.00 0.00 0.00 3.95
906 2016 4.853196 CCGCTGTGAGTACAAAAATGAATG 59.147 41.667 0.00 0.00 36.14 2.67
907 2017 4.759693 TCCGCTGTGAGTACAAAAATGAAT 59.240 37.500 0.00 0.00 36.14 2.57
908 2018 4.130857 TCCGCTGTGAGTACAAAAATGAA 58.869 39.130 0.00 0.00 36.14 2.57
909 2019 3.734463 TCCGCTGTGAGTACAAAAATGA 58.266 40.909 0.00 0.00 36.14 2.57
951 2069 3.028130 CCTCCCTTTCCACTCTACTCTC 58.972 54.545 0.00 0.00 0.00 3.20
1248 2366 1.889530 GAGCAAGGTAGTGGCGGAGT 61.890 60.000 0.00 0.00 0.00 3.85
1374 2492 0.037326 GCAGGAATCGTGTGTCTCCA 60.037 55.000 4.81 0.00 0.00 3.86
1383 2501 2.744202 GAGTGAATTGTGCAGGAATCGT 59.256 45.455 0.00 0.00 0.00 3.73
1458 2576 1.738099 GTCGCAGTCACGCATTCCT 60.738 57.895 0.00 0.00 0.00 3.36
1539 2657 2.127003 GCAAACAGCCGTAACGCC 60.127 61.111 0.00 0.00 37.23 5.68
1599 2717 1.734477 CGCCTTGAGGACTGTGACG 60.734 63.158 0.06 0.00 37.39 4.35
1689 2807 2.611751 TGTGGTCACAACATCTTGTTCG 59.388 45.455 0.78 0.00 38.77 3.95
1783 2901 2.916269 TCCACAGGATCACATTTACCCA 59.084 45.455 0.00 0.00 0.00 4.51
1845 2963 1.689984 TGAACAAATGCACTGCCTCA 58.310 45.000 0.00 0.00 0.00 3.86
1899 3017 2.350522 GACCGCAATGTGACAGAATCT 58.649 47.619 0.00 0.00 0.00 2.40
1911 3029 0.815213 CCATGATCACCGACCGCAAT 60.815 55.000 0.00 0.00 0.00 3.56
1953 3071 1.839354 TCCATCCATACTGCAAGCTCA 59.161 47.619 0.00 0.00 37.60 4.26
2013 3131 2.031560 GTCAATCAACGCTGTGTTCACA 59.968 45.455 3.16 5.52 39.29 3.58
2107 3225 2.234661 TCAATGCACTCCAGACTACCAG 59.765 50.000 0.00 0.00 0.00 4.00
2184 3302 1.377725 CACCCCTGCGAGCTTCATT 60.378 57.895 0.00 0.00 0.00 2.57
2217 3335 3.888930 CTGACAAAAGCCCCAAGAAAGTA 59.111 43.478 0.00 0.00 0.00 2.24
2253 3371 2.348998 CCTTTCTCCACAGCGCCT 59.651 61.111 2.29 0.00 0.00 5.52
2343 3461 3.426568 GCACGAGCAAGCAGGTCC 61.427 66.667 0.00 0.00 41.71 4.46
2493 3611 3.405831 CTCCAACTCAAAGATGTGCTGA 58.594 45.455 0.00 0.00 0.00 4.26
2802 3920 6.272324 TGAAAGTATTACAGGATATGAGGGGG 59.728 42.308 0.00 0.00 0.00 5.40
2804 3922 7.735917 TGTGAAAGTATTACAGGATATGAGGG 58.264 38.462 0.00 0.00 0.00 4.30
2856 3974 3.258971 TGGACACGATATGCATGACAA 57.741 42.857 10.16 0.00 0.00 3.18
2876 3994 8.933438 CGAATTGTATCGTAATTGCATTGTAT 57.067 30.769 0.00 0.00 38.01 2.29
2903 4021 1.051008 TGATGGTCACAGTGCTCACT 58.949 50.000 0.00 0.00 43.61 3.41
3218 4336 5.590530 TGGAACAATGCCAATACAATACC 57.409 39.130 0.00 0.00 31.92 2.73
3328 4446 4.434725 CGCACACAATCACACAATCTACTC 60.435 45.833 0.00 0.00 0.00 2.59
3339 4457 4.627467 ACTTAAGATCTCGCACACAATCAC 59.373 41.667 10.09 0.00 0.00 3.06
3391 4509 6.861572 CAGTGTCTGAATGTCTAAAACGTCTA 59.138 38.462 0.00 0.00 32.44 2.59
3466 4584 7.736893 AGTGTTTATACAATCATACTCCCTCC 58.263 38.462 0.00 0.00 35.69 4.30
3690 4809 0.380378 TTTGTCTGCCGCTCACAAAC 59.620 50.000 13.40 0.00 35.57 2.93


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

AutoCloner maintained by Alex Coulton.