Multiple sequence alignment - TraesCS1A01G077400

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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 TraesCS1A01G077400 chr1A 100.000 4406 0 0 1 4406 60196294 60200699 0.000000e+00 8137.0
1 TraesCS1A01G077400 chr1A 98.843 4409 43 3 1 4406 60215403 60219806 0.000000e+00 7853.0
2 TraesCS1A01G077400 chr1A 95.415 1745 75 5 1 1743 60226174 60227915 0.000000e+00 2774.0
3 TraesCS1A01G077400 chr1A 94.913 1612 59 10 2020 3613 60228401 60230007 0.000000e+00 2501.0
4 TraesCS1A01G077400 chr1A 94.775 976 43 7 3435 4406 60087628 60088599 0.000000e+00 1513.0
5 TraesCS1A01G077400 chr1A 90.409 636 55 2 751 1386 60283564 60284193 0.000000e+00 832.0
6 TraesCS1A01G077400 chr1A 93.307 508 27 5 2934 3439 60081551 60082053 0.000000e+00 743.0
7 TraesCS1A01G077400 chr1A 86.820 607 50 13 2270 2861 60080965 60081556 0.000000e+00 651.0
8 TraesCS1A01G077400 chr1A 95.217 230 11 0 1740 1969 60227942 60228171 9.010000e-97 364.0
9 TraesCS1A01G077400 chr1A 96.154 52 1 1 710 761 60283251 60283301 2.820000e-12 84.2
10 TraesCS1A01G077400 chr1D 91.280 1812 115 23 2230 4019 62235463 62237253 0.000000e+00 2431.0
11 TraesCS1A01G077400 chr1D 94.574 1032 29 6 722 1743 62318967 62319981 0.000000e+00 1570.0
12 TraesCS1A01G077400 chr1D 93.776 948 33 10 2694 3622 62321787 62322727 0.000000e+00 1400.0
13 TraesCS1A01G077400 chr1D 91.183 964 51 11 1741 2702 62320009 62320940 0.000000e+00 1279.0
14 TraesCS1A01G077400 chr1D 88.020 793 81 9 751 1539 62340895 62341677 0.000000e+00 926.0
15 TraesCS1A01G077400 chr1D 92.248 387 30 0 1000 1386 62234998 62235384 2.320000e-152 549.0
16 TraesCS1A01G077400 chr1D 91.731 387 32 0 1000 1386 62225082 62225468 5.010000e-149 538.0
17 TraesCS1A01G077400 chr1D 90.819 403 36 1 985 1386 62232099 62232501 5.010000e-149 538.0
18 TraesCS1A01G077400 chr1D 79.551 401 49 22 2084 2457 62342310 62342704 5.660000e-64 255.0
19 TraesCS1A01G077400 chr1D 86.854 213 19 7 1751 1957 62341926 62342135 3.430000e-56 230.0
20 TraesCS1A01G077400 chr1D 86.154 195 22 3 3687 3878 62326433 62326625 5.780000e-49 206.0
21 TraesCS1A01G077400 chr1D 92.537 67 4 1 864 930 62224973 62225038 1.300000e-15 95.3
22 TraesCS1A01G077400 chr1D 92.537 67 4 1 864 930 62232006 62232071 1.300000e-15 95.3
23 TraesCS1A01G077400 chr1D 92.537 67 4 1 864 930 62234889 62234954 1.300000e-15 95.3
24 TraesCS1A01G077400 chr1B 92.998 1628 85 15 2061 3667 99137326 99138945 0.000000e+00 2348.0
25 TraesCS1A01G077400 chr1B 86.928 1530 117 38 2230 3717 99076379 99077867 0.000000e+00 1640.0
26 TraesCS1A01G077400 chr1B 94.810 1002 38 2 752 1743 99136214 99137211 0.000000e+00 1550.0
27 TraesCS1A01G077400 chr1B 87.903 248 21 7 4162 4406 99080764 99081005 2.590000e-72 283.0
28 TraesCS1A01G077400 chr1B 96.923 65 2 0 1741 1805 99137239 99137303 4.660000e-20 110.0
29 TraesCS1A01G077400 chr1B 92.982 57 4 0 3790 3846 99080384 99080440 2.820000e-12 84.2
30 TraesCS1A01G077400 chr1B 100.000 29 0 0 1819 1847 99137300 99137328 2.000000e-03 54.7
31 TraesCS1A01G077400 chr4B 84.342 281 34 8 3886 4159 396704010 396703733 2.610000e-67 267.0
32 TraesCS1A01G077400 chr4A 83.391 289 42 6 3875 4160 716989262 716989547 3.380000e-66 263.0
33 TraesCS1A01G077400 chr4A 81.884 276 42 8 3893 4163 491722730 491722458 4.430000e-55 226.0
34 TraesCS1A01G077400 chr6A 84.328 268 32 8 3891 4153 506639105 506639367 2.030000e-63 254.0
35 TraesCS1A01G077400 chr5A 81.915 282 42 6 3885 4163 703149213 703148938 3.430000e-56 230.0
36 TraesCS1A01G077400 chr5A 82.781 151 21 5 4015 4163 703005264 703005411 3.580000e-26 130.0
37 TraesCS1A01G077400 chr7A 84.343 198 23 6 3892 4085 126132078 126132271 2.090000e-43 187.0
38 TraesCS1A01G077400 chr3A 89.333 75 8 0 631 705 459861177 459861251 1.300000e-15 95.3


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 TraesCS1A01G077400 chr1A 60196294 60200699 4405 False 8137.000000 8137 100.000000 1 4406 1 chr1A.!!$F2 4405
1 TraesCS1A01G077400 chr1A 60215403 60219806 4403 False 7853.000000 7853 98.843000 1 4406 1 chr1A.!!$F3 4405
2 TraesCS1A01G077400 chr1A 60226174 60230007 3833 False 1879.666667 2774 95.181667 1 3613 3 chr1A.!!$F5 3612
3 TraesCS1A01G077400 chr1A 60087628 60088599 971 False 1513.000000 1513 94.775000 3435 4406 1 chr1A.!!$F1 971
4 TraesCS1A01G077400 chr1A 60080965 60082053 1088 False 697.000000 743 90.063500 2270 3439 2 chr1A.!!$F4 1169
5 TraesCS1A01G077400 chr1A 60283251 60284193 942 False 458.100000 832 93.281500 710 1386 2 chr1A.!!$F6 676
6 TraesCS1A01G077400 chr1D 62318967 62326625 7658 False 1113.750000 1570 91.421750 722 3878 4 chr1D.!!$F3 3156
7 TraesCS1A01G077400 chr1D 62232006 62237253 5247 False 741.720000 2431 91.884200 864 4019 5 chr1D.!!$F2 3155
8 TraesCS1A01G077400 chr1D 62340895 62342704 1809 False 470.333333 926 84.808333 751 2457 3 chr1D.!!$F4 1706
9 TraesCS1A01G077400 chr1B 99136214 99138945 2731 False 1015.675000 2348 96.182750 752 3667 4 chr1B.!!$F2 2915
10 TraesCS1A01G077400 chr1B 99076379 99081005 4626 False 669.066667 1640 89.271000 2230 4406 3 chr1B.!!$F1 2176

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
775 1052 3.434319 CGCATCGGCAGCAACCTT 61.434 61.111 0.0 0.0 41.24 3.50 F
2439 5998 4.944317 GGTATAGCAGCCATTTTCCTATCC 59.056 45.833 0.0 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2480 6039 1.841663 GCACGCAACAGAACACCGAT 61.842 55.000 0.0 0.0 0.0 4.18 R
3980 14824 6.266786 GGGTGTTGGGAATTAAAAAGAAGAGA 59.733 38.462 0.0 0.0 0.0 3.10 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
775 1052 3.434319 CGCATCGGCAGCAACCTT 61.434 61.111 0.00 0.00 41.24 3.50
1469 4639 7.759489 TGTCAAACTTTATCCAGCACTTATT 57.241 32.000 0.00 0.00 0.00 1.40
2395 5954 7.829211 ACTTATTTATCAGAACTGGCTTTAGCA 59.171 33.333 3.88 0.00 44.36 3.49
2439 5998 4.944317 GGTATAGCAGCCATTTTCCTATCC 59.056 45.833 0.00 0.00 0.00 2.59
2480 6039 9.364989 GGTTTCTGCTTATAAATTGTATGCAAA 57.635 29.630 10.47 6.51 38.21 3.68
3137 7600 1.678101 GCAGGTGAAGCTTGAGTTGTT 59.322 47.619 2.10 0.00 0.00 2.83
3916 14760 4.201744 CCGTCCGGTGAAAATTGTACATAC 60.202 45.833 0.00 0.00 0.00 2.39
4029 14874 6.183360 CCAGTAAGCTAAGTGCATGTAGAAAC 60.183 42.308 10.04 5.17 45.94 2.78
4047 14892 6.875972 AGAAACTAAGGAGACCATGTGTAT 57.124 37.500 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
265 267 2.124736 TGGCGCTGGTTCCTATGC 60.125 61.111 7.64 0.00 0.00 3.14
768 1045 1.702491 GACGGCGGTATGAAGGTTGC 61.702 60.000 13.24 0.00 0.00 4.17
1287 4447 9.913310 TGTTTATGGATGTAATTCCTCATAACA 57.087 29.630 0.00 0.00 36.68 2.41
1469 4639 4.130118 GTGAAGAGGAAACTGAGCAGAAA 58.870 43.478 4.21 0.00 44.43 2.52
2395 5954 5.510430 ACCTTTCTCCTCTTGTTGAAACTT 58.490 37.500 0.00 0.00 0.00 2.66
2439 5998 4.866486 GCAGAAACCAAATAGCAAATGGAG 59.134 41.667 5.05 0.00 37.66 3.86
2480 6039 1.841663 GCACGCAACAGAACACCGAT 61.842 55.000 0.00 0.00 0.00 4.18
3018 7471 5.120986 CACAGTAATGTGGTGCACGTAATTA 59.879 40.000 15.40 11.05 37.14 1.40
3137 7600 4.019860 AGAGCCTAGAAAGCAATGTCTCAA 60.020 41.667 0.00 0.00 0.00 3.02
3980 14824 6.266786 GGGTGTTGGGAATTAAAAAGAAGAGA 59.733 38.462 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.