Multiple sequence alignment - TraesCS1A01G120500

Loading Multiple Alignment...

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 TraesCS1A01G120500 chr1A 100.000 2411 0 0 1 2411 133125480 133127890 0.000000e+00 4453.0
1 TraesCS1A01G120500 chr1D 93.842 1900 81 12 527 2411 121308719 121310597 0.000000e+00 2828.0
2 TraesCS1A01G120500 chr1D 91.026 546 44 4 1 541 121306770 121307315 0.000000e+00 732.0
3 TraesCS1A01G120500 chr1B 94.149 1521 68 8 903 2411 184741849 184743360 0.000000e+00 2296.0
4 TraesCS1A01G120500 chr1B 89.216 102 10 1 536 636 184741576 184741677 2.520000e-25 126.0
5 TraesCS1A01G120500 chr5B 82.203 118 18 3 714 830 411092922 411093037 5.490000e-17 99.0
6 TraesCS1A01G120500 chr7D 94.286 35 2 0 790 824 593924779 593924813 1.000000e-03 54.7


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 TraesCS1A01G120500 chr1A 133125480 133127890 2410 False 4453 4453 100.0000 1 2411 1 chr1A.!!$F1 2410
1 TraesCS1A01G120500 chr1D 121306770 121310597 3827 False 1780 2828 92.4340 1 2411 2 chr1D.!!$F1 2410
2 TraesCS1A01G120500 chr1B 184741576 184743360 1784 False 1211 2296 91.6825 536 2411 2 chr1B.!!$F1 1875

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
625 2051 0.033366 TGCATCGGGGTGTATGATCG 59.967 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 3584 0.611896 ATTGCCTGTTTCCCCCTTCG 60.612 55.0 0.0 0.0 0.0 3.79 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
44 45 2.637155 GCCGAAAGCGCATTACAAC 58.363 52.632 11.47 0.00 35.83 3.32
76 77 2.357034 GACGCAACCGGAGAAGCA 60.357 61.111 9.46 0.00 39.22 3.91
81 82 2.048127 AACCGGAGAAGCAGACGC 60.048 61.111 9.46 0.00 38.99 5.19
111 112 0.647410 CGCGTTTCAGATGCTACAGG 59.353 55.000 0.00 0.00 38.16 4.00
165 166 1.439228 CATCGACTCACGGATGGCT 59.561 57.895 0.00 0.00 42.82 4.75
171 172 1.957177 GACTCACGGATGGCTAGATCA 59.043 52.381 0.00 0.00 0.00 2.92
172 173 1.683917 ACTCACGGATGGCTAGATCAC 59.316 52.381 0.00 0.00 0.00 3.06
176 177 1.004440 GGATGGCTAGATCACCGGC 60.004 63.158 0.00 0.00 0.00 6.13
215 216 4.471908 ATCACGGGCATGCTCGCA 62.472 61.111 38.47 26.10 44.98 5.10
234 235 1.889105 CAGAATCCGGGGCATCACG 60.889 63.158 0.00 0.00 0.00 4.35
286 287 4.166011 GTGCTTGCGCCATCCGTC 62.166 66.667 4.18 0.00 39.71 4.79
325 326 1.787155 GCATCAATGAGGCGTAGTACG 59.213 52.381 18.37 18.37 45.88 3.67
337 338 1.838345 CGTAGTACGACTGCATGTTCG 59.162 52.381 17.85 10.11 46.05 3.95
338 339 2.182825 GTAGTACGACTGCATGTTCGG 58.817 52.381 14.71 0.00 30.80 4.30
363 364 4.980805 GCGGCGGAGGTGAACACA 62.981 66.667 9.78 0.00 0.00 3.72
416 417 2.355363 CAACTCCACGCCGTTCGA 60.355 61.111 0.00 0.00 41.67 3.71
433 434 0.179145 CGAGTCGGGCTAACGAACAT 60.179 55.000 4.10 0.00 45.38 2.71
460 461 1.207329 GGACCTTCCACGTAGATTGCT 59.793 52.381 0.00 0.00 36.28 3.91
474 475 2.706723 AGATTGCTGAGCTCATCTCCAT 59.293 45.455 18.63 7.00 41.18 3.41
484 485 1.153369 CATCTCCATGGGCGACGTT 60.153 57.895 13.02 0.00 0.00 3.99
508 513 1.153823 CGACGGGCTCCAACAGTAG 60.154 63.158 0.00 0.00 0.00 2.57
510 515 2.240162 GACGGGCTCCAACAGTAGGG 62.240 65.000 0.00 0.00 0.00 3.53
516 521 0.107017 CTCCAACAGTAGGGCATGGG 60.107 60.000 0.00 0.00 0.00 4.00
523 529 1.147153 GTAGGGCATGGGAGCAGAC 59.853 63.158 0.00 0.00 35.83 3.51
536 542 2.815211 CAGACGTGCCCATGTCCG 60.815 66.667 15.07 3.66 45.92 4.79
615 2041 4.751098 CCAATTTTATTTGATGCATCGGGG 59.249 41.667 21.34 6.80 0.00 5.73
618 2044 2.727123 TATTTGATGCATCGGGGTGT 57.273 45.000 21.34 7.06 0.00 4.16
623 2049 1.699083 TGATGCATCGGGGTGTATGAT 59.301 47.619 21.34 0.00 0.00 2.45
625 2051 0.033366 TGCATCGGGGTGTATGATCG 59.967 55.000 0.00 0.00 0.00 3.69
626 2052 0.670546 GCATCGGGGTGTATGATCGG 60.671 60.000 0.00 0.00 0.00 4.18
642 2068 9.745880 TGTATGATCGGTTCTCTTAAAACTATC 57.254 33.333 0.00 0.00 0.00 2.08
656 2082 3.695830 AACTATCCGTGGACATGTTGT 57.304 42.857 0.00 0.00 0.00 3.32
660 2086 2.451693 CCGTGGACATGTTGTACGG 58.548 57.895 24.87 24.87 43.33 4.02
662 2088 2.004583 CGTGGACATGTTGTACGGAT 57.995 50.000 17.39 0.00 32.63 4.18
670 2096 4.265893 ACATGTTGTACGGATATTTGCCA 58.734 39.130 0.00 0.00 0.00 4.92
671 2097 4.887071 ACATGTTGTACGGATATTTGCCAT 59.113 37.500 0.00 0.00 0.00 4.40
674 2100 4.702612 TGTTGTACGGATATTTGCCATGTT 59.297 37.500 0.00 0.00 0.00 2.71
677 2103 6.274157 TGTACGGATATTTGCCATGTTTTT 57.726 33.333 0.00 0.00 0.00 1.94
700 2127 7.921786 TTGTTTTGATGTAGGACCTGATAAG 57.078 36.000 3.53 0.00 0.00 1.73
738 2165 5.371115 ACGAAAACATGACAATTCCGAAT 57.629 34.783 0.00 0.00 0.00 3.34
749 2176 7.637631 TGACAATTCCGAATATTTTGGATGA 57.362 32.000 13.84 2.97 42.75 2.92
753 2180 8.477256 ACAATTCCGAATATTTTGGATGACAAT 58.523 29.630 13.84 3.61 42.75 2.71
890 2317 5.822278 TGAAAATGTCATCGAAAAACCGAA 58.178 33.333 0.00 0.00 42.22 4.30
893 2320 3.822594 TGTCATCGAAAAACCGAATGG 57.177 42.857 0.00 0.00 42.22 3.16
949 2382 6.346096 TGTATAGTGTTGAAGATGCCCTAAC 58.654 40.000 0.00 0.00 0.00 2.34
982 2422 5.242434 GGAAGGAGAAGAGAAAGAGAAACC 58.758 45.833 0.00 0.00 0.00 3.27
983 2423 4.901197 AGGAGAAGAGAAAGAGAAACCC 57.099 45.455 0.00 0.00 0.00 4.11
1054 2494 2.528708 CCTATCTCCTCCGCCCCT 59.471 66.667 0.00 0.00 0.00 4.79
1428 2878 3.884774 TGGTTGCTCCAGGCCGTT 61.885 61.111 0.00 0.00 41.93 4.44
1429 2879 3.056328 GGTTGCTCCAGGCCGTTC 61.056 66.667 0.00 0.00 40.92 3.95
1430 2880 2.032681 GTTGCTCCAGGCCGTTCT 59.967 61.111 0.00 0.00 40.92 3.01
1431 2881 1.600916 GTTGCTCCAGGCCGTTCTT 60.601 57.895 0.00 0.00 40.92 2.52
1432 2882 1.150536 TTGCTCCAGGCCGTTCTTT 59.849 52.632 0.00 0.00 40.92 2.52
1433 2883 1.172180 TTGCTCCAGGCCGTTCTTTG 61.172 55.000 0.00 0.00 40.92 2.77
1434 2884 1.302511 GCTCCAGGCCGTTCTTTGA 60.303 57.895 0.00 0.00 34.27 2.69
1435 2885 0.678048 GCTCCAGGCCGTTCTTTGAT 60.678 55.000 0.00 0.00 34.27 2.57
1436 2886 1.089920 CTCCAGGCCGTTCTTTGATG 58.910 55.000 0.00 0.00 0.00 3.07
1459 2909 2.123342 CGCATCGAGGTCAGAGATTTC 58.877 52.381 0.00 0.00 0.00 2.17
1471 2921 5.770162 GGTCAGAGATTTCTTCTTTTGGGAA 59.230 40.000 0.00 0.00 33.74 3.97
1566 3016 6.535150 GGGAAATAAAATTAAGGCTGCACTTC 59.465 38.462 0.50 0.00 32.02 3.01
1640 3096 7.010091 GCAAATTGGTAGCATACAATTTGTACC 59.990 37.037 30.82 20.85 46.69 3.34
1846 3302 3.052186 GGAGCCAGGGAGATAGGATAGAT 60.052 52.174 0.00 0.00 0.00 1.98
2115 3581 6.439058 TCCCAAAGAAGGAGAAAAGAAAACAA 59.561 34.615 0.00 0.00 0.00 2.83
2116 3582 7.038658 TCCCAAAGAAGGAGAAAAGAAAACAAA 60.039 33.333 0.00 0.00 0.00 2.83
2117 3583 7.606073 CCCAAAGAAGGAGAAAAGAAAACAAAA 59.394 33.333 0.00 0.00 0.00 2.44
2118 3584 8.443160 CCAAAGAAGGAGAAAAGAAAACAAAAC 58.557 33.333 0.00 0.00 0.00 2.43
2119 3585 7.812309 AAGAAGGAGAAAAGAAAACAAAACG 57.188 32.000 0.00 0.00 0.00 3.60
2159 3625 2.938451 CTCGCATTTAATCAGGCTCACA 59.062 45.455 0.00 0.00 0.00 3.58
2206 3672 2.729479 ATCTGGCCAGCCTCAGTCG 61.729 63.158 28.91 1.59 36.94 4.18
2306 3772 3.874383 TTCTTTCCAGATTGACCACCA 57.126 42.857 0.00 0.00 0.00 4.17
2387 3854 1.891919 GGTCGCACCAAGCAGTCAA 60.892 57.895 1.01 0.00 46.13 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.034607 CTACTGTAGAGCGAGCCCC 58.965 63.158 9.22 0.00 0.00 5.80
20 21 0.673644 AATGCGCTTTCGGCTACTGT 60.674 50.000 9.73 0.00 39.13 3.55
63 64 2.383527 GCGTCTGCTTCTCCGGTTG 61.384 63.158 0.00 0.00 38.39 3.77
93 94 1.929836 CTCCTGTAGCATCTGAAACGC 59.070 52.381 0.00 0.00 0.00 4.84
100 101 2.168106 CACTGCTTCTCCTGTAGCATCT 59.832 50.000 0.00 0.00 43.73 2.90
111 112 2.224314 GCAAGTTGTACCACTGCTTCTC 59.776 50.000 4.48 0.00 0.00 2.87
165 166 1.363807 CATGCTCGCCGGTGATCTA 59.636 57.895 19.93 8.30 0.00 1.98
176 177 3.741063 CTTCGCGTTCGCATGCTCG 62.741 63.158 17.13 17.50 35.26 5.03
190 191 1.153369 ATGCCCGTGATGACCTTCG 60.153 57.895 0.00 0.00 0.00 3.79
215 216 1.224592 GTGATGCCCCGGATTCTGT 59.775 57.895 0.73 0.00 0.00 3.41
216 217 1.889105 CGTGATGCCCCGGATTCTG 60.889 63.158 0.73 0.00 0.00 3.02
234 235 1.953138 CATCGTCCGCTGCTCATCC 60.953 63.158 0.00 0.00 0.00 3.51
299 300 1.493950 CGCCTCATTGATGCGGAGAC 61.494 60.000 23.35 0.00 41.51 3.36
319 320 1.133598 CCCGAACATGCAGTCGTACTA 59.866 52.381 13.99 0.00 0.00 1.82
325 326 0.179000 ATCTCCCCGAACATGCAGTC 59.821 55.000 0.00 0.00 0.00 3.51
328 329 1.143838 CGATCTCCCCGAACATGCA 59.856 57.895 0.00 0.00 0.00 3.96
349 350 1.639298 GCATCTGTGTTCACCTCCGC 61.639 60.000 0.37 0.00 0.00 5.54
350 351 1.354337 CGCATCTGTGTTCACCTCCG 61.354 60.000 0.37 0.00 0.00 4.63
363 364 1.532604 TTCAGTCCGTCACCGCATCT 61.533 55.000 0.00 0.00 0.00 2.90
381 382 3.416490 CCGACGTTGGCAGTGTTT 58.584 55.556 9.42 0.00 0.00 2.83
416 417 0.892755 TCATGTTCGTTAGCCCGACT 59.107 50.000 0.00 0.00 36.42 4.18
447 448 1.134995 TGAGCTCAGCAATCTACGTGG 60.135 52.381 13.74 0.00 0.00 4.94
460 461 1.834996 GCCCATGGAGATGAGCTCA 59.165 57.895 20.79 20.79 45.81 4.26
508 513 4.101448 ACGTCTGCTCCCATGCCC 62.101 66.667 0.00 0.00 0.00 5.36
510 515 3.503363 GCACGTCTGCTCCCATGC 61.503 66.667 0.00 0.00 40.63 4.06
516 521 2.046892 ACATGGGCACGTCTGCTC 60.047 61.111 0.00 0.00 45.24 4.26
523 529 2.125147 ATGTCGGACATGGGCACG 60.125 61.111 22.09 0.00 37.45 5.34
536 542 7.939784 AAAGTTAAGGGTCTTTATCCATGTC 57.060 36.000 0.00 0.00 33.00 3.06
615 2041 7.829378 AGTTTTAAGAGAACCGATCATACAC 57.171 36.000 0.00 0.00 0.00 2.90
618 2044 8.080417 CGGATAGTTTTAAGAGAACCGATCATA 58.920 37.037 0.00 0.00 40.16 2.15
623 2049 5.404946 CACGGATAGTTTTAAGAGAACCGA 58.595 41.667 0.00 0.00 40.78 4.69
625 2051 5.579904 GTCCACGGATAGTTTTAAGAGAACC 59.420 44.000 0.00 0.00 0.00 3.62
626 2052 6.161381 TGTCCACGGATAGTTTTAAGAGAAC 58.839 40.000 0.00 0.00 0.00 3.01
642 2068 2.451693 CCGTACAACATGTCCACGG 58.548 57.895 23.20 23.20 43.33 4.94
656 2082 6.274157 ACAAAAACATGGCAAATATCCGTA 57.726 33.333 0.00 0.00 0.00 4.02
660 2086 9.332301 CATCAAAACAAAAACATGGCAAATATC 57.668 29.630 0.00 0.00 0.00 1.63
662 2088 8.218338 ACATCAAAACAAAAACATGGCAAATA 57.782 26.923 0.00 0.00 0.00 1.40
670 2096 7.069331 TCAGGTCCTACATCAAAACAAAAACAT 59.931 33.333 0.00 0.00 0.00 2.71
671 2097 6.378564 TCAGGTCCTACATCAAAACAAAAACA 59.621 34.615 0.00 0.00 0.00 2.83
674 2100 8.698973 TTATCAGGTCCTACATCAAAACAAAA 57.301 30.769 0.00 0.00 0.00 2.44
677 2103 7.016153 ACTTATCAGGTCCTACATCAAAACA 57.984 36.000 0.00 0.00 0.00 2.83
700 2127 2.921996 CGTACTTGACGCTCGGTAC 58.078 57.895 0.00 0.00 46.27 3.34
720 2147 8.310382 TCCAAAATATTCGGAATTGTCATGTTT 58.690 29.630 8.76 0.00 0.00 2.83
738 2165 9.781834 CGCTTACTAAAATTGTCATCCAAAATA 57.218 29.630 0.00 0.00 36.44 1.40
749 2176 3.687698 ACCATCGCGCTTACTAAAATTGT 59.312 39.130 5.56 0.00 0.00 2.71
753 2180 2.669434 GTCACCATCGCGCTTACTAAAA 59.331 45.455 5.56 0.00 0.00 1.52
760 2187 2.325082 GGTTGTCACCATCGCGCTT 61.325 57.895 5.56 0.00 43.61 4.68
786 2213 2.286950 GCACGAAAGTTGTCATGCTTGA 60.287 45.455 0.00 0.00 46.40 3.02
841 2268 6.314400 GTCACGTAATAGCAAATTTGGTAGGA 59.686 38.462 28.16 18.51 43.44 2.94
890 2317 0.895100 AGTGCCACAATTCGTGCCAT 60.895 50.000 0.00 0.00 44.91 4.40
893 2320 0.030638 ACAAGTGCCACAATTCGTGC 59.969 50.000 0.00 0.00 44.91 5.34
949 2382 1.192146 TTCTCCTTCCCTGTCGGTGG 61.192 60.000 0.00 0.00 0.00 4.61
1065 2505 2.036571 GTTCGTTAGGGGTTGCGGG 61.037 63.158 0.00 0.00 0.00 6.13
1067 2507 3.018840 GCGTTCGTTAGGGGTTGCG 62.019 63.158 0.00 0.00 0.00 4.85
1077 2517 2.342648 GGAGGTCTGGCGTTCGTT 59.657 61.111 0.00 0.00 0.00 3.85
1351 2791 0.625683 ATCTTGAGCCCCATGGACCT 60.626 55.000 15.22 8.71 0.00 3.85
1433 2883 0.938637 CTGACCTCGATGCGCTCATC 60.939 60.000 9.73 6.61 44.34 2.92
1434 2884 1.067084 CTGACCTCGATGCGCTCAT 59.933 57.895 9.73 0.00 35.17 2.90
1435 2885 1.997928 CTCTGACCTCGATGCGCTCA 61.998 60.000 9.73 0.22 0.00 4.26
1436 2886 1.299014 CTCTGACCTCGATGCGCTC 60.299 63.158 9.73 2.56 0.00 5.03
1459 2909 4.751600 GCCAAGATTTGTTCCCAAAAGAAG 59.248 41.667 0.00 0.00 43.43 2.85
1471 2921 4.853924 AACAAAGATCGCCAAGATTTGT 57.146 36.364 2.18 2.18 41.31 2.83
1517 2967 7.235606 CCCAATCAGAATATCCAGGAACTACTA 59.764 40.741 0.00 0.00 36.02 1.82
1566 3016 4.588899 TGTAATCTCCCACAACAGGAATG 58.411 43.478 0.00 0.00 31.49 2.67
1708 3164 5.743636 ATTGGCACAGGAACAAATTACAT 57.256 34.783 0.00 0.00 42.39 2.29
1846 3302 7.865889 CGCACCTACATATCTGAAGTTAACATA 59.134 37.037 8.61 0.00 0.00 2.29
2115 3581 0.826256 GCCTGTTTCCCCCTTCGTTT 60.826 55.000 0.00 0.00 0.00 3.60
2116 3582 1.228459 GCCTGTTTCCCCCTTCGTT 60.228 57.895 0.00 0.00 0.00 3.85
2117 3583 2.002018 TTGCCTGTTTCCCCCTTCGT 62.002 55.000 0.00 0.00 0.00 3.85
2118 3584 0.611896 ATTGCCTGTTTCCCCCTTCG 60.612 55.000 0.00 0.00 0.00 3.79
2119 3585 1.186200 GATTGCCTGTTTCCCCCTTC 58.814 55.000 0.00 0.00 0.00 3.46
2159 3625 4.365111 TGCTTGCCGGCCATCCTT 62.365 61.111 26.77 0.00 0.00 3.36
2206 3672 1.070445 CCAGATGGAGGCTCAGATGTC 59.930 57.143 17.69 6.32 37.39 3.06
2306 3772 2.884087 ATCGATCGTGGCGCTCGTTT 62.884 55.000 15.94 12.08 44.06 3.60


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

AutoCloner maintained by Alex Coulton.