Multiple sequence alignment - TraesCS4B01G121900

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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 TraesCS4B01G121900 chr4B 100.000 3592 0 0 1 3592 144746288 144749879 0.000000e+00 6634
1 TraesCS4B01G121900 chr4D 97.697 3473 57 6 1 3472 101022450 101025900 0.000000e+00 5949
2 TraesCS4B01G121900 chr4D 90.033 301 26 4 2882 3181 304305054 304304757 1.560000e-103 387
3 TraesCS4B01G121900 chr4D 90.236 297 25 4 2887 3181 502760757 502760463 5.630000e-103 385
4 TraesCS4B01G121900 chr4D 100.000 119 0 0 3474 3592 101025933 101026051 1.680000e-53 220
5 TraesCS4B01G121900 chr4A 96.768 3373 80 13 1 3355 474743520 474740159 0.000000e+00 5598
6 TraesCS4B01G121900 chr4A 97.479 119 3 0 3474 3592 474739591 474739473 1.690000e-48 204
7 TraesCS4B01G121900 chr4A 96.774 93 0 1 3380 3472 474739713 474739624 6.210000e-33 152
8 TraesCS4B01G121900 chrUn 100.000 390 0 0 2215 2604 480007594 480007983 0.000000e+00 721
9 TraesCS4B01G121900 chr7A 90.878 296 25 2 2887 3181 503428822 503428528 2.600000e-106 396
10 TraesCS4B01G121900 chr5A 90.572 297 27 1 2887 3182 287614327 287614031 3.360000e-105 392
11 TraesCS4B01G121900 chr5B 90.847 295 21 5 2890 3181 299731308 299731017 1.210000e-104 390
12 TraesCS4B01G121900 chr3B 90.000 300 29 1 2882 3180 342869636 342869935 1.560000e-103 387
13 TraesCS4B01G121900 chr2B 90.000 300 28 2 2884 3181 367687796 367688095 1.560000e-103 387


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 TraesCS4B01G121900 chr4B 144746288 144749879 3591 False 6634.000000 6634 100.0000 1 3592 1 chr4B.!!$F1 3591
1 TraesCS4B01G121900 chr4D 101022450 101026051 3601 False 3084.500000 5949 98.8485 1 3592 2 chr4D.!!$F1 3591
2 TraesCS4B01G121900 chr4A 474739473 474743520 4047 True 1984.666667 5598 97.0070 1 3592 3 chr4A.!!$R1 3591

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
379 380 0.108585 AGCACAATCGACCAGGTGTT 59.891 50.000 0.00 0.00 33.88 3.32 F
568 569 2.164827 CACTTGTACACCATGCATGCAT 59.835 45.455 27.46 27.46 37.08 3.96 F
1617 1633 1.808945 CCAAGTGCTGAGAATGTGTCC 59.191 52.381 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1206 1211 2.090999 GGATCCTACCTTCTCACCCTCT 60.091 54.545 3.84 0.00 0.00 3.69 R
1690 1706 3.244422 TGCCCATCGTATTTATCCTGGTC 60.244 47.826 0.00 0.00 0.00 4.02 R
3355 3384 0.607489 CAAAGGGAGGAGGCACTGTG 60.607 60.000 2.76 2.76 41.55 3.66 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
128 129 2.033448 TGGATCACCCACCAACGC 59.967 61.111 0.00 0.00 40.82 4.84
132 133 3.469863 ATCACCCACCAACGCGTGT 62.470 57.895 14.98 3.90 31.47 4.49
210 211 3.694535 TGGTTAACGAAATTGCAACGT 57.305 38.095 0.00 4.20 41.97 3.99
220 221 4.030529 CGAAATTGCAACGTTGAATCATCC 59.969 41.667 31.62 12.27 0.00 3.51
235 236 3.021269 TCATCCGCCGATGTGTTATAC 57.979 47.619 13.63 0.00 45.32 1.47
296 297 1.748122 CTCTGCGCTTGCCTCCATT 60.748 57.895 9.73 0.00 38.03 3.16
378 379 0.603707 CAGCACAATCGACCAGGTGT 60.604 55.000 0.00 0.00 33.88 4.16
379 380 0.108585 AGCACAATCGACCAGGTGTT 59.891 50.000 0.00 0.00 33.88 3.32
446 447 3.133014 CAGGAGGCGATGATCCGT 58.867 61.111 0.00 0.00 40.73 4.69
568 569 2.164827 CACTTGTACACCATGCATGCAT 59.835 45.455 27.46 27.46 37.08 3.96
670 671 6.661377 TGCCAATTAAGTTATCAACAAGGCTA 59.339 34.615 0.00 0.00 38.07 3.93
671 672 7.341769 TGCCAATTAAGTTATCAACAAGGCTAT 59.658 33.333 0.00 0.00 38.07 2.97
672 673 7.649306 GCCAATTAAGTTATCAACAAGGCTATG 59.351 37.037 0.00 0.00 34.59 2.23
673 674 8.686334 CCAATTAAGTTATCAACAAGGCTATGT 58.314 33.333 0.00 0.00 34.24 2.29
1206 1211 2.586245 CTCATCTCCGCCTTGCCA 59.414 61.111 0.00 0.00 0.00 4.92
1617 1633 1.808945 CCAAGTGCTGAGAATGTGTCC 59.191 52.381 0.00 0.00 0.00 4.02
2832 2850 9.774413 CCTACGTAATTCCCATTTTAGATAAGT 57.226 33.333 0.00 0.00 0.00 2.24
2906 2924 6.128172 GGTGCTGAAGTGTATATATGGATTGC 60.128 42.308 0.00 0.00 0.00 3.56
2907 2925 5.939883 TGCTGAAGTGTATATATGGATTGCC 59.060 40.000 0.00 0.00 0.00 4.52
2908 2926 6.176183 GCTGAAGTGTATATATGGATTGCCT 58.824 40.000 0.00 0.00 34.31 4.75
2909 2927 7.038373 TGCTGAAGTGTATATATGGATTGCCTA 60.038 37.037 0.00 0.00 34.31 3.93
2910 2928 7.493971 GCTGAAGTGTATATATGGATTGCCTAG 59.506 40.741 0.00 0.00 34.31 3.02
2911 2929 7.331026 TGAAGTGTATATATGGATTGCCTAGC 58.669 38.462 0.00 0.00 34.31 3.42
2912 2930 6.240549 AGTGTATATATGGATTGCCTAGCC 57.759 41.667 0.00 0.00 34.31 3.93
2913 2931 5.131142 AGTGTATATATGGATTGCCTAGCCC 59.869 44.000 0.00 0.00 34.31 5.19
2914 2932 5.131142 GTGTATATATGGATTGCCTAGCCCT 59.869 44.000 0.00 0.00 34.31 5.19
2915 2933 5.731187 TGTATATATGGATTGCCTAGCCCTT 59.269 40.000 0.00 0.00 34.31 3.95
2916 2934 5.803463 ATATATGGATTGCCTAGCCCTTT 57.197 39.130 0.00 0.00 34.31 3.11
3355 3384 2.674380 CCTTGCCCCAGCTCACAC 60.674 66.667 0.00 0.00 40.80 3.82
3472 3922 4.440663 CGAGATGACAAACTCAGCTATCCA 60.441 45.833 11.63 0.00 46.02 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.640092 GCTGAAATTCTTGAAAGGAAGAACTG 59.360 38.462 0.00 0.00 43.14 3.16
121 122 1.954146 CAGTGCTACACGCGTTGGT 60.954 57.895 10.22 8.51 43.27 3.67
128 129 2.357396 TGGCTGCAGTGCTACACG 60.357 61.111 17.60 0.89 39.64 4.49
132 133 0.036952 GAACTCTGGCTGCAGTGCTA 60.037 55.000 17.60 0.00 0.00 3.49
141 142 2.964310 ATGCGCTGGAACTCTGGCT 61.964 57.895 9.73 0.00 0.00 4.75
183 184 4.023536 TGCAATTTCGTTAACCAACCTCTC 60.024 41.667 0.00 0.00 0.00 3.20
197 198 4.030529 GGATGATTCAACGTTGCAATTTCG 59.969 41.667 23.47 4.14 0.00 3.46
199 200 3.919804 CGGATGATTCAACGTTGCAATTT 59.080 39.130 23.47 13.80 0.00 1.82
220 221 1.850640 GGCGTATAACACATCGGCG 59.149 57.895 0.00 0.00 38.83 6.46
276 277 2.359230 GGAGGCAAGCGCAGAGTT 60.359 61.111 11.47 0.00 41.24 3.01
363 364 1.227999 CGCAACACCTGGTCGATTGT 61.228 55.000 13.59 0.05 0.00 2.71
378 379 1.136584 CGTTGTTATGTACACGCGCAA 60.137 47.619 5.73 0.00 36.21 4.85
379 380 0.435388 CGTTGTTATGTACACGCGCA 59.565 50.000 5.73 0.00 36.21 6.09
422 423 2.763292 ATCGCCTCCTGCTGCTCT 60.763 61.111 0.00 0.00 38.05 4.09
568 569 1.982395 CTAGGCGTCACCCAGACCA 60.982 63.158 0.00 0.00 44.66 4.02
670 671 5.642063 CGTGGTACATCTGGAACTTTAACAT 59.358 40.000 0.00 0.00 44.52 2.71
671 672 4.992319 CGTGGTACATCTGGAACTTTAACA 59.008 41.667 0.00 0.00 44.52 2.41
672 673 4.142966 GCGTGGTACATCTGGAACTTTAAC 60.143 45.833 0.00 0.00 44.52 2.01
673 674 3.998341 GCGTGGTACATCTGGAACTTTAA 59.002 43.478 0.00 0.00 44.52 1.52
722 723 4.555262 AGGATGTTTTGCGGTGTTAATTG 58.445 39.130 0.00 0.00 0.00 2.32
818 819 3.751175 TGTAAAATGGCAGGATATAGCGC 59.249 43.478 0.00 0.00 0.00 5.92
1134 1139 0.107268 GTACAGTGTTGGGGTCGGTT 59.893 55.000 0.00 0.00 0.00 4.44
1206 1211 2.090999 GGATCCTACCTTCTCACCCTCT 60.091 54.545 3.84 0.00 0.00 3.69
1212 1217 2.292521 ACTGCAGGATCCTACCTTCTCA 60.293 50.000 19.93 3.35 38.32 3.27
1690 1706 3.244422 TGCCCATCGTATTTATCCTGGTC 60.244 47.826 0.00 0.00 0.00 4.02
2604 2622 8.611051 AACCCACTATAGAGAGTTCAGTAATT 57.389 34.615 6.78 0.00 0.00 1.40
2779 2797 7.805071 CCTGATTTGAGTTACTTGCTTACAAAG 59.195 37.037 0.00 0.00 34.74 2.77
2832 2850 8.347035 CCTTTTTCTTTTGGAATAACACGTAGA 58.653 33.333 0.00 0.00 33.53 2.59
2833 2851 8.347035 TCCTTTTTCTTTTGGAATAACACGTAG 58.653 33.333 0.00 0.00 33.53 3.51
2906 2924 2.880890 CGAAATGATGGAAAGGGCTAGG 59.119 50.000 0.00 0.00 0.00 3.02
2907 2925 2.880890 CCGAAATGATGGAAAGGGCTAG 59.119 50.000 0.00 0.00 0.00 3.42
2908 2926 2.507886 TCCGAAATGATGGAAAGGGCTA 59.492 45.455 0.00 0.00 0.00 3.93
2909 2927 1.284785 TCCGAAATGATGGAAAGGGCT 59.715 47.619 0.00 0.00 0.00 5.19
2910 2928 1.405463 GTCCGAAATGATGGAAAGGGC 59.595 52.381 0.00 0.00 35.67 5.19
2911 2929 3.004752 AGTCCGAAATGATGGAAAGGG 57.995 47.619 0.00 0.00 35.67 3.95
2912 2930 5.163513 CAAAAGTCCGAAATGATGGAAAGG 58.836 41.667 0.00 0.00 35.67 3.11
2913 2931 5.163513 CCAAAAGTCCGAAATGATGGAAAG 58.836 41.667 0.00 0.00 35.67 2.62
2914 2932 4.586841 ACCAAAAGTCCGAAATGATGGAAA 59.413 37.500 0.00 0.00 35.67 3.13
2915 2933 4.148838 ACCAAAAGTCCGAAATGATGGAA 58.851 39.130 0.00 0.00 35.67 3.53
2916 2934 3.761897 ACCAAAAGTCCGAAATGATGGA 58.238 40.909 0.00 0.00 0.00 3.41
3355 3384 0.607489 CAAAGGGAGGAGGCACTGTG 60.607 60.000 2.76 2.76 41.55 3.66
3472 3922 7.624360 TTATATGAAGCAAATTCTCCGTGTT 57.376 32.000 0.00 0.00 38.83 3.32


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

AutoCloner maintained by Alex Coulton.