Multiple sequence alignment - TraesCS1B01G160300

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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 TraesCS1B01G160300 chr1B 100.000 4629 0 0 1 4629 275456243 275460871 0.000000e+00 8549.0
1 TraesCS1B01G160300 chr1B 98.558 4647 48 9 1 4629 275356238 275360883 0.000000e+00 8192.0
2 TraesCS1B01G160300 chr1B 97.512 3658 54 11 783 4422 275551979 275555617 0.000000e+00 6216.0
3 TraesCS1B01G160300 chr1B 97.001 2601 60 6 2035 4629 275671865 275674453 0.000000e+00 4355.0
4 TraesCS1B01G160300 chr1B 98.407 879 14 0 957 1835 275670422 275671300 0.000000e+00 1546.0
5 TraesCS1B01G160300 chr1B 96.044 910 28 3 1 908 275551004 275551907 0.000000e+00 1474.0
6 TraesCS1B01G160300 chr1B 94.048 252 13 1 4380 4629 275555617 275555868 9.400000e-102 381.0
7 TraesCS1B01G160300 chr1B 98.104 211 4 0 1827 2037 275671866 275671656 7.320000e-98 368.0
8 TraesCS1B01G160300 chr1A 96.223 3071 74 14 979 4028 246130450 246127401 0.000000e+00 4990.0
9 TraesCS1B01G160300 chr1A 91.104 607 41 5 4026 4629 246127332 246126736 0.000000e+00 809.0
10 TraesCS1B01G160300 chr1A 87.931 290 17 8 446 717 246131294 246131005 4.470000e-85 326.0
11 TraesCS1B01G160300 chr1A 84.861 251 25 9 181 423 472439356 472439601 1.660000e-59 241.0
12 TraesCS1B01G160300 chr1A 83.270 263 16 15 729 971 246130688 246130434 2.800000e-52 217.0
13 TraesCS1B01G160300 chr2A 82.979 1598 205 34 2115 3664 610176624 610178202 0.000000e+00 1382.0
14 TraesCS1B01G160300 chr2A 83.737 1322 164 27 2389 3664 607512930 607514246 0.000000e+00 1203.0
15 TraesCS1B01G160300 chr2A 82.599 885 94 27 992 1863 610175346 610176183 0.000000e+00 726.0
16 TraesCS1B01G160300 chr2A 84.211 437 30 13 1 422 24441738 24441326 5.620000e-104 388.0
17 TraesCS1B01G160300 chr2A 84.559 272 34 7 1016 1281 607511721 607511990 3.550000e-66 263.0
18 TraesCS1B01G160300 chr2A 81.343 134 25 0 2428 2561 138527691 138527558 4.900000e-20 110.0
19 TraesCS1B01G160300 chr2B 82.750 1600 206 35 2115 3664 545152384 545153963 0.000000e+00 1362.0
20 TraesCS1B01G160300 chr2B 80.221 1355 204 38 2428 3735 186403262 186404599 0.000000e+00 959.0
21 TraesCS1B01G160300 chr2B 84.729 884 97 21 992 1863 545151110 545151967 0.000000e+00 850.0
22 TraesCS1B01G160300 chr2B 81.445 803 124 12 1061 1858 185763768 185762986 6.530000e-178 634.0
23 TraesCS1B01G160300 chr2B 81.497 708 126 3 1061 1767 186402048 186402751 1.120000e-160 577.0
24 TraesCS1B01G160300 chr2B 85.887 248 27 6 181 422 541912033 541911788 1.650000e-64 257.0
25 TraesCS1B01G160300 chr2D 83.068 1069 163 12 2599 3659 131642728 131641670 0.000000e+00 955.0
26 TraesCS1B01G160300 chr2D 91.398 372 18 9 65 424 115107835 115107466 8.940000e-137 497.0
27 TraesCS1B01G160300 chr2D 88.087 277 28 5 1008 1281 462228830 462229104 1.610000e-84 324.0
28 TraesCS1B01G160300 chr2D 83.684 190 20 6 1681 1863 462229108 462229293 7.970000e-38 169.0
29 TraesCS1B01G160300 chr2D 81.203 133 25 0 2428 2560 131642938 131642806 1.760000e-19 108.0
30 TraesCS1B01G160300 chrUn 90.389 437 25 11 1 423 108465973 108465540 4.050000e-155 558.0
31 TraesCS1B01G160300 chrUn 84.861 251 29 6 181 423 91486766 91486517 1.290000e-60 244.0
32 TraesCS1B01G160300 chr1D 90.465 430 25 5 1 422 389353396 389353817 1.880000e-153 553.0
33 TraesCS1B01G160300 chr5A 87.269 432 31 9 1 417 701632860 701633282 5.420000e-129 472.0
34 TraesCS1B01G160300 chr5A 87.273 55 3 1 642 696 450196514 450196564 5.000000e-05 60.2
35 TraesCS1B01G160300 chr7B 87.379 412 31 10 1 392 214928619 214928209 1.960000e-123 453.0
36 TraesCS1B01G160300 chr5D 87.755 294 19 10 146 423 343509285 343508993 1.240000e-85 327.0
37 TraesCS1B01G160300 chr3B 85.200 250 24 9 181 422 30696478 30696722 1.290000e-60 244.0


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 TraesCS1B01G160300 chr1B 275456243 275460871 4628 False 8549.000000 8549 100.0000 1 4629 1 chr1B.!!$F2 4628
1 TraesCS1B01G160300 chr1B 275356238 275360883 4645 False 8192.000000 8192 98.5580 1 4629 1 chr1B.!!$F1 4628
2 TraesCS1B01G160300 chr1B 275670422 275674453 4031 False 2950.500000 4355 97.7040 957 4629 2 chr1B.!!$F4 3672
3 TraesCS1B01G160300 chr1B 275551004 275555868 4864 False 2690.333333 6216 95.8680 1 4629 3 chr1B.!!$F3 4628
4 TraesCS1B01G160300 chr1A 246126736 246131294 4558 True 1585.500000 4990 89.6320 446 4629 4 chr1A.!!$R1 4183
5 TraesCS1B01G160300 chr2A 610175346 610178202 2856 False 1054.000000 1382 82.7890 992 3664 2 chr2A.!!$F2 2672
6 TraesCS1B01G160300 chr2A 607511721 607514246 2525 False 733.000000 1203 84.1480 1016 3664 2 chr2A.!!$F1 2648
7 TraesCS1B01G160300 chr2B 545151110 545153963 2853 False 1106.000000 1362 83.7395 992 3664 2 chr2B.!!$F2 2672
8 TraesCS1B01G160300 chr2B 186402048 186404599 2551 False 768.000000 959 80.8590 1061 3735 2 chr2B.!!$F1 2674
9 TraesCS1B01G160300 chr2B 185762986 185763768 782 True 634.000000 634 81.4450 1061 1858 1 chr2B.!!$R1 797
10 TraesCS1B01G160300 chr2D 131641670 131642938 1268 True 531.500000 955 82.1355 2428 3659 2 chr2D.!!$R2 1231

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
376 378 0.921896 AGGTGGATAGGCTGCATGTT 59.078 50.000 0.5 0.0 0.0 2.71 F
661 680 2.303022 TGGCAAAAACCTGAACCAACAA 59.697 40.909 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2343 3359 1.009389 CCGCGTCCTGAAGTGAGAAC 61.009 60.000 4.92 0.0 0.00 3.01 R
3896 4973 4.640771 TTCTTGGAGTTGCTCTAACCAT 57.359 40.909 0.00 0.0 40.24 3.55 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
138 139 3.787001 GGAGCGACAGGAAGGGGG 61.787 72.222 0.00 0.0 0.00 5.40
233 234 6.303839 GCTCCCTTTATCCATTATTACACCA 58.696 40.000 0.00 0.0 0.00 4.17
250 251 2.095415 CACCAACTCGTCGTCTACATGA 60.095 50.000 0.00 0.0 0.00 3.07
376 378 0.921896 AGGTGGATAGGCTGCATGTT 59.078 50.000 0.50 0.0 0.00 2.71
387 389 7.609532 GGATAGGCTGCATGTTAAGAGAAATAT 59.390 37.037 0.50 0.0 0.00 1.28
486 488 6.882768 AGGAATCAAAGATCTAACCTGACT 57.117 37.500 0.00 0.0 0.00 3.41
586 604 6.765512 TGTGAGGTCAAATTTTTGGAAAATCC 59.234 34.615 3.38 0.0 38.66 3.01
661 680 2.303022 TGGCAAAAACCTGAACCAACAA 59.697 40.909 0.00 0.0 0.00 2.83
951 1473 7.554118 CCTGGTTAGCAATCTGAATAGAGAAAA 59.446 37.037 0.00 0.0 36.14 2.29
959 1481 8.819974 GCAATCTGAATAGAGAAAAAGAGAGAG 58.180 37.037 0.00 0.0 36.14 3.20
1959 2632 2.507484 CTTTCCAACCAGATGACTGCA 58.493 47.619 0.00 0.0 42.25 4.41
2094 3107 2.549754 GGATATGATGGTGCTGGTTTCG 59.450 50.000 0.00 0.0 0.00 3.46
2343 3359 2.995574 AGAACAGACCCGACCCCG 60.996 66.667 0.00 0.0 0.00 5.73
3896 4973 3.885724 TGGTCTGCATCGTCAAATCTA 57.114 42.857 0.00 0.0 0.00 1.98
4010 5094 6.419791 TCTCCAATAAATCCCGTAAACATGT 58.580 36.000 0.00 0.0 0.00 3.21
4256 5416 8.279361 CCTATTTTAGGGGAAGAAGTTTATGGA 58.721 37.037 0.00 0.0 42.42 3.41
4435 5640 6.366630 CAAAAACAAACGTCCACAACAAAAT 58.633 32.000 0.00 0.0 0.00 1.82
4481 5688 0.033090 CCTATAAACTCGACCGGCCC 59.967 60.000 0.00 0.0 0.00 5.80
4501 5708 3.073946 CCCCAAGTTCCCTCTTGTTTAGA 59.926 47.826 5.86 0.0 42.01 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 234 2.415625 GCCTTCATGTAGACGACGAGTT 60.416 50.000 0.00 0.00 0.00 3.01
250 251 1.061546 TTGGTAACCGAAGAGGCCTT 58.938 50.000 6.77 0.00 46.52 4.35
376 378 8.972662 TCATCCCCACTATCATATTTCTCTTA 57.027 34.615 0.00 0.00 0.00 2.10
387 389 6.849697 ACCTAAATAGTTCATCCCCACTATCA 59.150 38.462 0.00 0.00 35.54 2.15
586 604 7.062371 TGCGACAAAACCCGAAATATTTAATTG 59.938 33.333 0.00 3.77 0.00 2.32
661 680 0.469144 ACCAAACCGGCAAATGAGGT 60.469 50.000 0.00 0.00 40.50 3.85
803 1128 1.446272 CCGGCTCCACTCGTTCTTC 60.446 63.158 0.00 0.00 0.00 2.87
951 1473 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
959 1481 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1180 1712 1.759445 CAGGGACGTGATCTTCCTCAT 59.241 52.381 0.00 0.00 33.24 2.90
1959 2632 4.391683 TGATTGGCCATCATCCATGTAT 57.608 40.909 6.09 0.00 36.94 2.29
2061 3053 4.533707 ACCATCATATCCAACATCCTCGAT 59.466 41.667 0.00 0.00 0.00 3.59
2094 3107 4.321601 CCATCCGACTCACTCTTATCATCC 60.322 50.000 0.00 0.00 0.00 3.51
2343 3359 1.009389 CCGCGTCCTGAAGTGAGAAC 61.009 60.000 4.92 0.00 0.00 3.01
3896 4973 4.640771 TTCTTGGAGTTGCTCTAACCAT 57.359 40.909 0.00 0.00 40.24 3.55
4010 5094 4.871557 CGTCGTGACCCTGGAAATTTATTA 59.128 41.667 0.00 0.00 0.00 0.98
4256 5416 6.291648 TCATGAGAGCTACTTTGTCAGATT 57.708 37.500 0.00 0.00 0.00 2.40
4435 5640 8.495160 TCCTAAATATATTCCGGGTTTACAGA 57.505 34.615 0.00 0.00 0.00 3.41
4501 5708 4.202535 ACGTTTTAGGGGAAGGTCATCTTT 60.203 41.667 0.00 0.00 35.50 2.52


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

AutoCloner maintained by Alex Coulton.