Multiple sequence alignment - TraesCS5A01G134900

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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 TraesCS5A01G134900 chr5A 100.000 2826 0 0 1 2826 304861626 304864451 0.000000e+00 5219.0
1 TraesCS5A01G134900 chr5A 98.276 58 1 0 2769 2826 183423160 183423103 4.980000e-18 102.0
2 TraesCS5A01G134900 chr2A 96.574 2831 74 12 1 2826 277297515 277300327 0.000000e+00 4669.0
3 TraesCS5A01G134900 chr2A 96.032 2142 75 8 689 2826 743753786 743755921 0.000000e+00 3476.0
4 TraesCS5A01G134900 chr1B 93.307 2286 123 18 552 2826 349213688 349211422 0.000000e+00 3347.0
5 TraesCS5A01G134900 chr1B 93.262 1024 57 9 1810 2826 258375181 258374163 0.000000e+00 1498.0
6 TraesCS5A01G134900 chr7D 93.080 1026 59 10 1808 2826 38563006 38564026 0.000000e+00 1491.0
7 TraesCS5A01G134900 chr7D 91.004 667 54 5 2102 2765 160034261 160034924 0.000000e+00 894.0
8 TraesCS5A01G134900 chr7D 82.432 296 32 10 833 1115 3701858 3702146 1.010000e-59 241.0
9 TraesCS5A01G134900 chr5B 92.823 1031 64 8 1803 2826 280146578 280145551 0.000000e+00 1485.0
10 TraesCS5A01G134900 chr5B 91.330 669 49 7 2102 2765 176796265 176795601 0.000000e+00 905.0
11 TraesCS5A01G134900 chr5B 95.487 554 24 1 1 554 194390570 194391122 0.000000e+00 883.0
12 TraesCS5A01G134900 chr5B 86.066 244 31 2 642 885 121830256 121830016 2.790000e-65 259.0
13 TraesCS5A01G134900 chr1D 97.834 554 12 0 1 554 42485304 42484751 0.000000e+00 957.0
14 TraesCS5A01G134900 chr1D 94.393 428 19 3 1808 2232 344155701 344156126 0.000000e+00 652.0
15 TraesCS5A01G134900 chr1D 91.498 247 19 1 639 885 225716397 225716641 3.490000e-89 339.0
16 TraesCS5A01G134900 chr4D 91.604 667 45 7 2102 2765 271270388 271269730 0.000000e+00 911.0
17 TraesCS5A01G134900 chr6B 96.209 554 21 0 1 554 211124384 211124937 0.000000e+00 907.0
18 TraesCS5A01G134900 chr7B 96.029 554 22 0 1 554 478617056 478616503 0.000000e+00 902.0
19 TraesCS5A01G134900 chr7B 89.344 244 23 1 642 885 90425572 90425332 1.270000e-78 303.0
20 TraesCS5A01G134900 chr7B 89.130 230 23 1 656 885 652655446 652655673 4.610000e-73 285.0
21 TraesCS5A01G134900 chr3B 96.029 554 22 0 1 554 370268542 370267989 0.000000e+00 902.0
22 TraesCS5A01G134900 chr3B 95.487 554 24 1 1 554 167311783 167312335 0.000000e+00 883.0
23 TraesCS5A01G134900 chr3B 92.308 65 5 0 642 706 426113745 426113809 3.000000e-15 93.5
24 TraesCS5A01G134900 chrUn 95.668 554 24 0 1 554 116801725 116801172 0.000000e+00 891.0
25 TraesCS5A01G134900 chr2B 95.315 555 25 1 1 554 222942417 222942971 0.000000e+00 880.0
26 TraesCS5A01G134900 chr4A 91.949 472 32 5 1810 2278 416920873 416920405 0.000000e+00 656.0
27 TraesCS5A01G134900 chr4A 83.000 400 40 15 836 1214 741883455 741883063 1.250000e-88 337.0
28 TraesCS5A01G134900 chr4A 95.556 45 2 0 952 996 739684207 739684251 3.910000e-09 73.1
29 TraesCS5A01G134900 chr4A 95.556 45 2 0 952 996 742078189 742078233 3.910000e-09 73.1
30 TraesCS5A01G134900 chr3D 92.339 248 15 3 639 885 132027385 132027629 1.610000e-92 350.0
31 TraesCS5A01G134900 chr6A 89.919 248 22 2 638 885 361698143 361697899 1.630000e-82 316.0
32 TraesCS5A01G134900 chr7A 84.068 295 30 9 833 1115 3585468 3585757 4.640000e-68 268.0
33 TraesCS5A01G134900 chr7A 95.652 46 2 0 951 996 2549903 2549858 1.090000e-09 75.0


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 TraesCS5A01G134900 chr5A 304861626 304864451 2825 False 5219 5219 100.000 1 2826 1 chr5A.!!$F1 2825
1 TraesCS5A01G134900 chr2A 277297515 277300327 2812 False 4669 4669 96.574 1 2826 1 chr2A.!!$F1 2825
2 TraesCS5A01G134900 chr2A 743753786 743755921 2135 False 3476 3476 96.032 689 2826 1 chr2A.!!$F2 2137
3 TraesCS5A01G134900 chr1B 349211422 349213688 2266 True 3347 3347 93.307 552 2826 1 chr1B.!!$R2 2274
4 TraesCS5A01G134900 chr1B 258374163 258375181 1018 True 1498 1498 93.262 1810 2826 1 chr1B.!!$R1 1016
5 TraesCS5A01G134900 chr7D 38563006 38564026 1020 False 1491 1491 93.080 1808 2826 1 chr7D.!!$F2 1018
6 TraesCS5A01G134900 chr7D 160034261 160034924 663 False 894 894 91.004 2102 2765 1 chr7D.!!$F3 663
7 TraesCS5A01G134900 chr5B 280145551 280146578 1027 True 1485 1485 92.823 1803 2826 1 chr5B.!!$R3 1023
8 TraesCS5A01G134900 chr5B 176795601 176796265 664 True 905 905 91.330 2102 2765 1 chr5B.!!$R2 663
9 TraesCS5A01G134900 chr5B 194390570 194391122 552 False 883 883 95.487 1 554 1 chr5B.!!$F1 553
10 TraesCS5A01G134900 chr1D 42484751 42485304 553 True 957 957 97.834 1 554 1 chr1D.!!$R1 553
11 TraesCS5A01G134900 chr4D 271269730 271270388 658 True 911 911 91.604 2102 2765 1 chr4D.!!$R1 663
12 TraesCS5A01G134900 chr6B 211124384 211124937 553 False 907 907 96.209 1 554 1 chr6B.!!$F1 553
13 TraesCS5A01G134900 chr7B 478616503 478617056 553 True 902 902 96.029 1 554 1 chr7B.!!$R2 553
14 TraesCS5A01G134900 chr3B 370267989 370268542 553 True 902 902 96.029 1 554 1 chr3B.!!$R1 553
15 TraesCS5A01G134900 chr3B 167311783 167312335 552 False 883 883 95.487 1 554 1 chr3B.!!$F1 553
16 TraesCS5A01G134900 chrUn 116801172 116801725 553 True 891 891 95.668 1 554 1 chrUn.!!$R1 553
17 TraesCS5A01G134900 chr2B 222942417 222942971 554 False 880 880 95.315 1 554 1 chr2B.!!$F1 553

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
420 422 4.357313 AAGTCCTGGGGTGTACCTATAA 57.643 45.455 0.44 0.0 40.03 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 2254 1.043816 CTCCTACGGACTGATGGCAT 58.956 55.0 0.0 0.0 0.0 4.4 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
420 422 4.357313 AAGTCCTGGGGTGTACCTATAA 57.643 45.455 0.44 0.00 40.03 0.98
805 809 9.649167 AATGTACGCAAATAGAGTAGTAAGTTT 57.351 29.630 0.00 0.00 32.98 2.66
808 812 9.994432 GTACGCAAATAGAGTAGTAAGTTTAGA 57.006 33.333 0.00 0.00 32.98 2.10
1220 1230 6.588348 TCTGCATACACATTGATAGTTTCG 57.412 37.500 0.00 0.00 0.00 3.46
1230 1240 7.174946 ACACATTGATAGTTTCGGAAATTCAGT 59.825 33.333 6.43 5.16 0.00 3.41
1295 1305 0.980754 TTAGAGCCGGCATTCCCTCA 60.981 55.000 31.54 5.93 0.00 3.86
1339 1349 5.130145 CCAGATACCTCAATGGATATCTCCC 59.870 48.000 2.05 0.00 41.29 4.30
1348 1358 7.257162 CCTCAATGGATATCTCCCCAAATAAGA 60.257 40.741 2.05 0.00 41.29 2.10
1566 1578 4.024387 TGTCTCAGCATTTTCGTAAACACC 60.024 41.667 0.00 0.00 0.00 4.16
1576 1588 1.411977 TCGTAAACACCCTTCGAACCA 59.588 47.619 0.00 0.00 0.00 3.67
1843 1856 8.668353 TCACTATGACTTGTCTTTTGCATATTC 58.332 33.333 2.35 0.00 0.00 1.75
1869 1882 7.554118 CCAGTCAGACATCATTTACTATTGGTT 59.446 37.037 2.66 0.00 0.00 3.67
1979 1992 7.442062 CAGTTTTCCCATAGCAAAAAGTTCATT 59.558 33.333 0.00 0.00 0.00 2.57
2062 2076 9.651913 AAACAAAAAGATGTTGACTGTACATTT 57.348 25.926 0.00 0.00 42.49 2.32
2097 2112 4.746535 TGTTCATACCGAAGCCTTGATA 57.253 40.909 0.00 0.00 33.09 2.15
2236 2254 1.270305 CCTTCAGCTCCACTTCGTTGA 60.270 52.381 0.00 0.00 0.00 3.18
2609 2634 2.946791 AACCCCCATGGAATTCACAT 57.053 45.000 15.22 5.75 38.00 3.21
2729 2760 5.551305 AATCTTTTCAGGTTTCTTTGGGG 57.449 39.130 0.00 0.00 0.00 4.96
2781 2812 8.397575 TGCTTGGTTACACAAATATGAAACTA 57.602 30.769 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 7.116233 CGTAAATGAACTTTTTGGGAGGATTTG 59.884 37.037 0.00 0.00 0.00 2.32
420 422 7.962964 TTCTGTCGTCACATCTTTAGAATTT 57.037 32.000 0.00 0.00 0.00 1.82
438 440 6.729187 AGTAGCACAAGAAAACAATTCTGTC 58.271 36.000 0.00 0.00 33.45 3.51
501 503 1.594833 CGCAACACACCTAGGGCTA 59.405 57.895 14.81 0.00 0.00 3.93
839 843 7.283807 AGTTGTACGTTGGACTAAAAATTTCCT 59.716 33.333 0.00 0.00 0.00 3.36
856 860 6.347079 CGTTGTCATTATCCAAAGTTGTACGT 60.347 38.462 0.00 0.00 0.00 3.57
1230 1240 8.479689 TCGGTGATTTCAACTATTTGTCCTATA 58.520 33.333 0.00 0.00 34.02 1.31
1295 1305 1.123077 TCAGCTCTGTTGACTGTGGT 58.877 50.000 0.00 0.00 33.12 4.16
1348 1358 8.692710 TGGTAGAACTGTTTCGAGTCATATATT 58.307 33.333 0.00 0.00 36.78 1.28
1566 1578 6.017440 TGTGAGTTAAGAAAATGGTTCGAAGG 60.017 38.462 0.00 0.00 0.00 3.46
1576 1588 7.665559 TGGCAGTTCTATGTGAGTTAAGAAAAT 59.334 33.333 0.00 0.00 30.24 1.82
1716 1729 3.947196 TGCTTCTCTTGTTTGCTGAGAAA 59.053 39.130 0.00 0.00 43.45 2.52
1843 1856 7.050377 ACCAATAGTAAATGATGTCTGACTGG 58.950 38.462 9.51 5.92 0.00 4.00
1869 1882 4.625742 GCAACAAGTTACTGAGATTAGCGA 59.374 41.667 0.00 0.00 0.00 4.93
2236 2254 1.043816 CTCCTACGGACTGATGGCAT 58.956 55.000 0.00 0.00 0.00 4.40
2454 2476 0.473755 TGTTGGACTGCACTGGACAT 59.526 50.000 0.00 0.00 0.00 3.06
2462 2484 3.364441 GCGGCATGTTGGACTGCA 61.364 61.111 0.00 0.00 40.18 4.41
2569 2593 8.126074 GGGGTTTTGTGTTTCATTATTTTTGTC 58.874 33.333 0.00 0.00 0.00 3.18
2609 2634 9.635404 TTTCCTTAGAACTTGTTATCTTTTCCA 57.365 29.630 0.00 0.00 0.00 3.53
2715 2746 3.229697 AGAAGTCCCCAAAGAAACCTG 57.770 47.619 0.00 0.00 0.00 4.00
2729 2760 9.262358 AGTTCATGTTCAGTAACTTTAGAAGTC 57.738 33.333 0.00 0.00 41.91 3.01


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

AutoCloner maintained by Alex Coulton.