Multiple sequence alignment - TraesCS6D01G275300

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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 TraesCS6D01G275300 chr6D 100.000 2653 0 0 1 2653 384292277 384289625 0.000000e+00 4900
1 TraesCS6D01G275300 chr6D 91.261 1007 80 6 1284 2289 210881653 210882652 0.000000e+00 1365
2 TraesCS6D01G275300 chr2B 95.672 2657 103 5 1 2653 241245583 241248231 0.000000e+00 4259
3 TraesCS6D01G275300 chr2B 89.864 1549 123 11 1 1534 282448252 282449781 0.000000e+00 1960
4 TraesCS6D01G275300 chr2B 89.423 1560 130 12 1 1534 609289277 609287727 0.000000e+00 1934
5 TraesCS6D01G275300 chr2B 90.068 1329 80 21 819 2107 57159289 57157973 0.000000e+00 1676
6 TraesCS6D01G275300 chr4B 94.992 2656 102 11 1 2653 159345904 159348531 0.000000e+00 4139
7 TraesCS6D01G275300 chr1A 90.945 2308 153 22 1 2289 520852863 520855133 0.000000e+00 3053
8 TraesCS6D01G275300 chr3A 90.380 2318 163 24 1 2295 703931803 703929523 0.000000e+00 2990
9 TraesCS6D01G275300 chr6A 90.091 2311 162 29 1 2289 425737613 425739878 0.000000e+00 2937
10 TraesCS6D01G275300 chr6A 96.499 914 31 1 1740 2653 391444170 391445082 0.000000e+00 1509
11 TraesCS6D01G275300 chr7A 89.461 2021 160 30 301 2289 299381037 299379038 0.000000e+00 2503
12 TraesCS6D01G275300 chr2A 92.089 1302 78 15 819 2107 405467538 405468827 0.000000e+00 1810
13 TraesCS6D01G275300 chr2A 89.165 1329 92 27 819 2107 395713084 395711768 0.000000e+00 1609
14 TraesCS6D01G275300 chr2A 90.387 957 73 7 603 1545 779969558 779970509 0.000000e+00 1240
15 TraesCS6D01G275300 chr2A 89.219 640 56 11 1653 2287 741590962 741591593 0.000000e+00 787
16 TraesCS6D01G275300 chr3B 90.315 1332 74 24 819 2107 795066634 795067953 0.000000e+00 1694
17 TraesCS6D01G275300 chr3B 93.566 917 42 6 1 909 145897409 145896502 0.000000e+00 1351
18 TraesCS6D01G275300 chr3B 87.895 190 23 0 2464 2653 780604298 780604487 9.560000e-55 224
19 TraesCS6D01G275300 chr6B 90.068 1329 80 21 819 2107 168771144 168772460 0.000000e+00 1676
20 TraesCS6D01G275300 chr5A 93.668 916 43 5 1 909 543950940 543951847 0.000000e+00 1356
21 TraesCS6D01G275300 chr5A 87.027 185 21 2 2471 2653 144288747 144288930 3.460000e-49 206


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 TraesCS6D01G275300 chr6D 384289625 384292277 2652 True 4900 4900 100.000 1 2653 1 chr6D.!!$R1 2652
1 TraesCS6D01G275300 chr6D 210881653 210882652 999 False 1365 1365 91.261 1284 2289 1 chr6D.!!$F1 1005
2 TraesCS6D01G275300 chr2B 241245583 241248231 2648 False 4259 4259 95.672 1 2653 1 chr2B.!!$F1 2652
3 TraesCS6D01G275300 chr2B 282448252 282449781 1529 False 1960 1960 89.864 1 1534 1 chr2B.!!$F2 1533
4 TraesCS6D01G275300 chr2B 609287727 609289277 1550 True 1934 1934 89.423 1 1534 1 chr2B.!!$R2 1533
5 TraesCS6D01G275300 chr2B 57157973 57159289 1316 True 1676 1676 90.068 819 2107 1 chr2B.!!$R1 1288
6 TraesCS6D01G275300 chr4B 159345904 159348531 2627 False 4139 4139 94.992 1 2653 1 chr4B.!!$F1 2652
7 TraesCS6D01G275300 chr1A 520852863 520855133 2270 False 3053 3053 90.945 1 2289 1 chr1A.!!$F1 2288
8 TraesCS6D01G275300 chr3A 703929523 703931803 2280 True 2990 2990 90.380 1 2295 1 chr3A.!!$R1 2294
9 TraesCS6D01G275300 chr6A 425737613 425739878 2265 False 2937 2937 90.091 1 2289 1 chr6A.!!$F2 2288
10 TraesCS6D01G275300 chr6A 391444170 391445082 912 False 1509 1509 96.499 1740 2653 1 chr6A.!!$F1 913
11 TraesCS6D01G275300 chr7A 299379038 299381037 1999 True 2503 2503 89.461 301 2289 1 chr7A.!!$R1 1988
12 TraesCS6D01G275300 chr2A 405467538 405468827 1289 False 1810 1810 92.089 819 2107 1 chr2A.!!$F1 1288
13 TraesCS6D01G275300 chr2A 395711768 395713084 1316 True 1609 1609 89.165 819 2107 1 chr2A.!!$R1 1288
14 TraesCS6D01G275300 chr2A 779969558 779970509 951 False 1240 1240 90.387 603 1545 1 chr2A.!!$F3 942
15 TraesCS6D01G275300 chr2A 741590962 741591593 631 False 787 787 89.219 1653 2287 1 chr2A.!!$F2 634
16 TraesCS6D01G275300 chr3B 795066634 795067953 1319 False 1694 1694 90.315 819 2107 1 chr3B.!!$F2 1288
17 TraesCS6D01G275300 chr3B 145896502 145897409 907 True 1351 1351 93.566 1 909 1 chr3B.!!$R1 908
18 TraesCS6D01G275300 chr6B 168771144 168772460 1316 False 1676 1676 90.068 819 2107 1 chr6B.!!$F1 1288
19 TraesCS6D01G275300 chr5A 543950940 543951847 907 False 1356 1356 93.668 1 909 1 chr5A.!!$F2 908

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
926 1026 1.808411 TGAGTCGCCAGGAATTTGAC 58.192 50.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2416 2597 0.096454 GATGTTAAGGTCGCGGTTGC 59.904 55.0 6.13 0.0 37.91 4.17 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
34 35 4.695217 TGTAAATTTCCCACGCTTGATC 57.305 40.909 0.00 0.00 0.00 2.92
134 139 3.813443 CATACATGGCTTTGCTAGGAGT 58.187 45.455 0.00 0.00 0.00 3.85
175 181 9.606631 GGTCTGAACTCTGAATATTATGAACTT 57.393 33.333 0.00 0.00 0.00 2.66
219 225 5.065090 CAGATCAAAATCATAGTCCACGCAA 59.935 40.000 0.00 0.00 34.07 4.85
515 603 7.544566 TCGTATTTGAAGATACAAGTTGAGGTC 59.455 37.037 10.54 4.50 33.12 3.85
564 652 3.499918 CGAACCTTCAGTTTCTGCAATCT 59.500 43.478 0.00 0.00 39.40 2.40
921 1021 2.154462 CAAAGTTGAGTCGCCAGGAAT 58.846 47.619 0.00 0.00 0.00 3.01
926 1026 1.808411 TGAGTCGCCAGGAATTTGAC 58.192 50.000 0.00 0.00 0.00 3.18
990 1090 5.450688 CCGGAGAATGTAGTCTACAAAGGAG 60.451 48.000 16.50 7.15 42.76 3.69
1026 1126 7.110155 TGGACCTGAGGTTTCTTTCATATTAC 58.890 38.462 5.21 0.00 35.25 1.89
1260 1377 6.163476 TGTTAGTCTTTGAGTACGCATCAAT 58.837 36.000 0.00 0.00 36.60 2.57
1273 1390 2.749466 CGCATCAATTGGGACCCTGTAT 60.749 50.000 13.00 0.00 40.62 2.29
1278 1395 1.595311 ATTGGGACCCTGTATGAGCA 58.405 50.000 13.00 0.00 0.00 4.26
1279 1396 0.618458 TTGGGACCCTGTATGAGCAC 59.382 55.000 13.00 0.00 0.00 4.40
1280 1397 1.271840 TGGGACCCTGTATGAGCACC 61.272 60.000 13.00 0.00 0.00 5.01
1281 1398 1.144057 GGACCCTGTATGAGCACCG 59.856 63.158 0.00 0.00 0.00 4.94
1282 1399 1.614241 GGACCCTGTATGAGCACCGT 61.614 60.000 0.00 0.00 0.00 4.83
1628 1749 9.506018 TGACTTGACAGAAATCATTCTTATGAA 57.494 29.630 0.00 0.00 43.43 2.57
1644 1765 1.007734 GAACAGGCTGACGACGTCA 60.008 57.895 27.61 27.61 40.50 4.35
1746 1867 2.086869 CTACACAAGGCCATGGTCAAG 58.913 52.381 20.74 12.89 0.00 3.02
2088 2268 1.063174 CATGCCTTCAGCTTTCGCTAC 59.937 52.381 0.00 0.00 46.99 3.58
2122 2302 2.951642 TGCTCCTTTTCAGGTGACTTTG 59.048 45.455 0.00 0.00 41.69 2.77
2123 2303 2.952310 GCTCCTTTTCAGGTGACTTTGT 59.048 45.455 0.00 0.00 41.69 2.83
2245 2426 3.576982 ACGGTCTTTGGTCACTGATTCTA 59.423 43.478 0.00 0.00 0.00 2.10
2318 2499 6.044637 ACTGTTAACTAAGGGTAAATGGTGGA 59.955 38.462 7.22 0.00 0.00 4.02
2364 2545 1.274703 ATGGCTGAACAGGGGACGAT 61.275 55.000 3.99 0.00 0.00 3.73
2416 2597 2.549282 CGTCGGCAACTTTGACCG 59.451 61.111 14.75 14.75 43.91 4.79
2503 2684 1.444119 TTGTGTTTCTGACCAGCCGC 61.444 55.000 0.00 0.00 0.00 6.53
2532 2713 2.679716 GGCAGCTCCCATTCCAGT 59.320 61.111 0.00 0.00 0.00 4.00
2566 2747 2.507992 CCTTCAGGTGAGCGAGCG 60.508 66.667 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 139 2.507886 TCAGACCTCACCAGTGGAAAAA 59.492 45.455 18.40 0.00 32.71 1.94
404 492 6.330250 ACCAATCTAGGCATGGTAAAGTCTAT 59.670 38.462 11.72 0.00 45.37 1.98
472 560 8.388103 TCAAATACGAGCTTAGCATAAAAAGTC 58.612 33.333 7.07 0.00 0.00 3.01
564 652 9.304731 CATTGAAAAATCACTCACTTTTCTTCA 57.695 29.630 7.72 0.00 39.00 3.02
921 1021 0.669619 TCCTCACACGCTACGTCAAA 59.330 50.000 0.00 0.00 38.32 2.69
926 1026 2.281762 GCTAAAATCCTCACACGCTACG 59.718 50.000 0.00 0.00 0.00 3.51
990 1090 2.295885 CTCAGGTCCATCCTTCATTGC 58.704 52.381 0.00 0.00 45.67 3.56
1032 1132 7.556633 GGCTAGTCCAATGACCTTCAAAGGA 62.557 48.000 15.63 0.00 42.81 3.36
1260 1377 0.618458 GTGCTCATACAGGGTCCCAA 59.382 55.000 11.55 0.00 0.00 4.12
1273 1390 0.885879 CAGTGTAGGTACGGTGCTCA 59.114 55.000 0.00 0.00 0.00 4.26
1278 1395 2.887151 ACCTACAGTGTAGGTACGGT 57.113 50.000 41.33 24.52 45.47 4.83
1344 1462 7.550551 ACAAATGAGATCAAATCTACGACACAT 59.449 33.333 0.00 0.00 40.38 3.21
1377 1495 1.564348 GGCCACTTCCCCATCTAAAGA 59.436 52.381 0.00 0.00 0.00 2.52
1521 1642 3.365472 CCTTGGGGGTAAAATCTTCTGG 58.635 50.000 0.00 0.00 0.00 3.86
1545 1666 7.067615 TCAGTTTGTACAGAAAAGCCATGTAAA 59.932 33.333 0.00 0.00 31.61 2.01
1628 1749 1.213013 GATGACGTCGTCAGCCTGT 59.787 57.895 28.60 14.54 46.04 4.00
1644 1765 1.338136 CCGGTGGGGCTTCAGTAGAT 61.338 60.000 0.00 0.00 0.00 1.98
2088 2268 4.978083 AAAGGAGCAGCATATGAACTTG 57.022 40.909 6.97 0.00 0.00 3.16
2318 2499 5.528320 CCAATGCTTGTCACCAAAAAGAAAT 59.472 36.000 0.00 0.00 0.00 2.17
2364 2545 0.673985 CGCCCTCATCGTAATCCTGA 59.326 55.000 0.00 0.00 0.00 3.86
2416 2597 0.096454 GATGTTAAGGTCGCGGTTGC 59.904 55.000 6.13 0.00 37.91 4.17
2566 2747 1.087501 GCTTCGGTGGAATGGAAGTC 58.912 55.000 2.46 0.00 39.42 3.01


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

AutoCloner maintained by Alex Coulton.