Multiple sequence alignment - TraesCS5D01G448800

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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 TraesCS5D01G448800 chr5D 100.000 3857 0 0 1 3857 498174722 498170866 0.000000e+00 7123
1 TraesCS5D01G448800 chr5D 85.979 1833 214 30 1083 2880 498291199 498289375 0.000000e+00 1921
2 TraesCS5D01G448800 chr5D 100.000 837 0 0 1 837 498179359 498180195 0.000000e+00 1546
3 TraesCS5D01G448800 chr5D 88.973 1188 114 14 1739 2921 498085504 498084329 0.000000e+00 1452
4 TraesCS5D01G448800 chr5D 82.898 842 97 26 862 1663 498086464 498085630 0.000000e+00 713
5 TraesCS5D01G448800 chr5D 99.702 336 1 0 1 336 560027816 560028151 1.970000e-172 616
6 TraesCS5D01G448800 chr5D 87.611 226 25 3 118 342 522167358 522167135 3.820000e-65 259
7 TraesCS5D01G448800 chr5D 87.500 112 10 3 2966 3074 498084326 498084216 4.050000e-25 126
8 TraesCS5D01G448800 chr5B 93.363 3104 145 26 516 3599 617437138 617434076 0.000000e+00 4534
9 TraesCS5D01G448800 chr5B 85.849 1802 214 31 1099 2880 617601938 617600158 0.000000e+00 1877
10 TraesCS5D01G448800 chr5B 85.363 1790 213 36 1162 2921 617293151 617291381 0.000000e+00 1808
11 TraesCS5D01G448800 chr5B 89.474 190 6 5 334 522 617437343 617437167 1.080000e-55 228
12 TraesCS5D01G448800 chr5B 79.495 317 63 2 3524 3838 576217414 576217730 1.390000e-54 224
13 TraesCS5D01G448800 chr5B 96.386 83 3 0 1 83 331836035 331835953 1.870000e-28 137
14 TraesCS5D01G448800 chr5B 96.386 83 3 0 1 83 692646037 692645955 1.870000e-28 137
15 TraesCS5D01G448800 chr5B 96.386 83 3 0 1 83 692686064 692685982 1.870000e-28 137
16 TraesCS5D01G448800 chr5B 89.623 106 7 3 2966 3068 617291378 617291274 8.690000e-27 132
17 TraesCS5D01G448800 chr5A 92.025 2370 120 40 664 3006 622394642 622392315 0.000000e+00 3265
18 TraesCS5D01G448800 chr5A 87.145 1727 179 25 1185 2880 622460599 622458885 0.000000e+00 1919
19 TraesCS5D01G448800 chr5A 85.532 1728 207 24 1162 2858 622234297 622232582 0.000000e+00 1766
20 TraesCS5D01G448800 chr5A 89.305 374 22 11 3133 3498 622323922 622323559 1.630000e-123 453
21 TraesCS5D01G448800 chr5A 94.805 154 7 1 3129 3281 622322604 622322451 4.980000e-59 239
22 TraesCS5D01G448800 chr5A 89.529 191 6 4 333 522 622394951 622394774 3.000000e-56 230
23 TraesCS5D01G448800 chr5A 92.969 128 8 1 3116 3243 622367946 622367820 6.580000e-43 185
24 TraesCS5D01G448800 chr5A 93.023 129 5 2 2990 3114 622392149 622392021 6.580000e-43 185
25 TraesCS5D01G448800 chr1B 89.132 1279 77 23 1122 2356 569519345 569520605 0.000000e+00 1535
26 TraesCS5D01G448800 chr1B 81.839 446 39 22 605 1018 569516445 569516880 1.720000e-88 337
27 TraesCS5D01G448800 chr1B 80.000 340 63 5 3503 3839 349176744 349177081 2.980000e-61 246
28 TraesCS5D01G448800 chr3A 81.948 1047 165 21 1782 2819 20557839 20556808 0.000000e+00 865
29 TraesCS5D01G448800 chr3A 86.076 237 31 2 101 336 715510223 715510458 1.780000e-63 254
30 TraesCS5D01G448800 chr3A 84.400 250 36 3 101 349 691475145 691475392 3.850000e-60 243
31 TraesCS5D01G448800 chr3D 99.702 336 1 0 1 336 184139497 184139162 1.970000e-172 616
32 TraesCS5D01G448800 chr2D 99.120 341 3 0 1 341 478815832 478816172 7.080000e-172 614
33 TraesCS5D01G448800 chr1D 88.723 470 21 19 908 1349 420843614 420844079 2.620000e-151 545
34 TraesCS5D01G448800 chr1D 90.991 222 20 0 116 337 192594787 192595008 2.250000e-77 300
35 TraesCS5D01G448800 chr1D 79.310 261 8 15 516 737 420837509 420837762 1.440000e-29 141
36 TraesCS5D01G448800 chr1D 90.909 77 7 0 776 852 420838327 420838403 1.900000e-18 104
37 TraesCS5D01G448800 chr7B 82.196 337 58 2 3504 3838 365024461 365024797 4.880000e-74 289
38 TraesCS5D01G448800 chr6B 81.739 345 59 4 3500 3841 246940769 246940426 6.310000e-73 285
39 TraesCS5D01G448800 chr6B 88.186 237 25 3 101 336 668919273 668919039 2.930000e-71 279
40 TraesCS5D01G448800 chr4A 81.065 338 62 2 3503 3838 651361714 651362051 6.350000e-68 268
41 TraesCS5D01G448800 chr2A 80.882 340 63 2 3504 3841 198015018 198014679 2.280000e-67 267
42 TraesCS5D01G448800 chr2B 80.178 338 63 4 3504 3838 142295595 142295259 2.300000e-62 250
43 TraesCS5D01G448800 chr3B 80.060 336 61 5 3505 3838 132137539 132137208 1.070000e-60 244
44 TraesCS5D01G448800 chr4D 78.457 311 61 6 3515 3823 122193150 122193456 8.450000e-47 198
45 TraesCS5D01G448800 chr6D 96.386 83 3 0 1 83 471121536 471121618 1.870000e-28 137
46 TraesCS5D01G448800 chr1A 96.386 83 3 0 1 83 590753394 590753476 1.870000e-28 137


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 TraesCS5D01G448800 chr5D 498170866 498174722 3856 True 7123.000000 7123 100.000000 1 3857 1 chr5D.!!$R1 3856
1 TraesCS5D01G448800 chr5D 498289375 498291199 1824 True 1921.000000 1921 85.979000 1083 2880 1 chr5D.!!$R2 1797
2 TraesCS5D01G448800 chr5D 498179359 498180195 836 False 1546.000000 1546 100.000000 1 837 1 chr5D.!!$F1 836
3 TraesCS5D01G448800 chr5D 498084216 498086464 2248 True 763.666667 1452 86.457000 862 3074 3 chr5D.!!$R4 2212
4 TraesCS5D01G448800 chr5B 617434076 617437343 3267 True 2381.000000 4534 91.418500 334 3599 2 chr5B.!!$R6 3265
5 TraesCS5D01G448800 chr5B 617600158 617601938 1780 True 1877.000000 1877 85.849000 1099 2880 1 chr5B.!!$R2 1781
6 TraesCS5D01G448800 chr5B 617291274 617293151 1877 True 970.000000 1808 87.493000 1162 3068 2 chr5B.!!$R5 1906
7 TraesCS5D01G448800 chr5A 622458885 622460599 1714 True 1919.000000 1919 87.145000 1185 2880 1 chr5A.!!$R3 1695
8 TraesCS5D01G448800 chr5A 622232582 622234297 1715 True 1766.000000 1766 85.532000 1162 2858 1 chr5A.!!$R1 1696
9 TraesCS5D01G448800 chr5A 622392021 622394951 2930 True 1226.666667 3265 91.525667 333 3114 3 chr5A.!!$R5 2781
10 TraesCS5D01G448800 chr5A 622322451 622323922 1471 True 346.000000 453 92.055000 3129 3498 2 chr5A.!!$R4 369
11 TraesCS5D01G448800 chr1B 569516445 569520605 4160 False 936.000000 1535 85.485500 605 2356 2 chr1B.!!$F2 1751
12 TraesCS5D01G448800 chr3A 20556808 20557839 1031 True 865.000000 865 81.948000 1782 2819 1 chr3A.!!$R1 1037

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
964 1024 1.017387 GCAGATCAACCAATCCGACC 58.983 55.000 0.00 0.0 0.0 4.79 F
1729 4347 2.603021 AGGTGATCATACGAGCTCCAT 58.397 47.619 8.47 0.0 42.4 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 4486 1.080025 GTCGAGGAAGACCGGGTTG 60.080 63.158 6.32 0.0 41.83 3.77 R
2927 5561 1.728825 GCGTATGACGACCGTTGTACA 60.729 52.381 2.65 0.0 46.05 2.90 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
964 1024 1.017387 GCAGATCAACCAATCCGACC 58.983 55.000 0.00 0.00 0.00 4.79
1729 4347 2.603021 AGGTGATCATACGAGCTCCAT 58.397 47.619 8.47 0.00 42.40 3.41
1730 4348 2.968574 AGGTGATCATACGAGCTCCATT 59.031 45.455 8.47 0.00 42.40 3.16
1731 4349 4.152647 AGGTGATCATACGAGCTCCATTA 58.847 43.478 8.47 0.00 42.40 1.90
1857 4486 0.319211 TCAACACGTCCGTCATCCAC 60.319 55.000 0.00 0.00 0.00 4.02
1865 4494 2.345991 CGTCATCCACAACCCGGT 59.654 61.111 0.00 0.00 0.00 5.28
2332 4961 4.124351 CGCCGGAGAAGTACGCCA 62.124 66.667 5.05 0.00 38.38 5.69
2422 5051 3.900892 CGGTCGGGGAGGTCATCG 61.901 72.222 0.00 0.00 0.00 3.84
2827 5456 2.618709 GAGAAAGGGGACAACAACACAG 59.381 50.000 0.00 0.00 0.00 3.66
2884 5517 6.385843 CCTGACGGTGAATCTATCTAAGATG 58.614 44.000 0.00 0.00 44.56 2.90
3064 5890 7.011482 GTGTAAGGTATTGTGCTCCTAAATCTG 59.989 40.741 0.00 0.00 0.00 2.90
3307 6144 7.884816 TTAAGATCTTTGAGTGGTTAGTTCG 57.115 36.000 14.36 0.00 0.00 3.95
3463 6301 8.984891 TGTGGAATATTAGAAAATGTGCTTTG 57.015 30.769 0.00 0.00 0.00 2.77
3488 6326 5.431420 TTGCTTGACATACGTGACAAATT 57.569 34.783 0.00 0.00 38.99 1.82
3502 6340 5.284660 CGTGACAAATTAGATGCTTTGCTTC 59.715 40.000 0.00 0.00 36.12 3.86
3514 6352 2.352960 GCTTTGCTTCATACTCCCTTCG 59.647 50.000 0.00 0.00 0.00 3.79
3633 6471 6.688073 AAAAAGTGAAGTATCTCTCTCCCA 57.312 37.500 0.00 0.00 0.00 4.37
3634 6472 6.688073 AAAAGTGAAGTATCTCTCTCCCAA 57.312 37.500 0.00 0.00 0.00 4.12
3635 6473 5.669164 AAGTGAAGTATCTCTCTCCCAAC 57.331 43.478 0.00 0.00 0.00 3.77
3636 6474 4.941713 AGTGAAGTATCTCTCTCCCAACT 58.058 43.478 0.00 0.00 0.00 3.16
3637 6475 4.709397 AGTGAAGTATCTCTCTCCCAACTG 59.291 45.833 0.00 0.00 0.00 3.16
3638 6476 3.449018 TGAAGTATCTCTCTCCCAACTGC 59.551 47.826 0.00 0.00 0.00 4.40
3639 6477 3.396685 AGTATCTCTCTCCCAACTGCT 57.603 47.619 0.00 0.00 0.00 4.24
3640 6478 3.718723 AGTATCTCTCTCCCAACTGCTT 58.281 45.455 0.00 0.00 0.00 3.91
3641 6479 4.873010 AGTATCTCTCTCCCAACTGCTTA 58.127 43.478 0.00 0.00 0.00 3.09
3642 6480 5.463154 AGTATCTCTCTCCCAACTGCTTAT 58.537 41.667 0.00 0.00 0.00 1.73
3651 6489 4.820775 TCCCAACTGCTTATATCTCTCCT 58.179 43.478 0.00 0.00 0.00 3.69
3653 6491 5.305644 TCCCAACTGCTTATATCTCTCCTTC 59.694 44.000 0.00 0.00 0.00 3.46
3745 6741 5.248640 ACTTGTCACTAACCAATGGATCAG 58.751 41.667 6.16 2.02 0.00 2.90
3746 6742 4.220693 TGTCACTAACCAATGGATCAGG 57.779 45.455 6.16 0.00 0.00 3.86
3751 6747 1.856629 AACCAATGGATCAGGCAAGG 58.143 50.000 6.16 0.00 0.00 3.61
3756 6752 3.825014 CCAATGGATCAGGCAAGGATAAG 59.175 47.826 0.00 0.00 0.00 1.73
3781 6777 9.232473 AGTTTGTCCTAAATTCTCTACAATTCC 57.768 33.333 0.00 0.00 0.00 3.01
3785 6781 6.817140 GTCCTAAATTCTCTACAATTCCGTGT 59.183 38.462 0.00 0.00 35.43 4.49
3790 6786 5.462530 TTCTCTACAATTCCGTGTCTTCA 57.537 39.130 0.00 0.00 32.75 3.02
3795 6791 4.008074 ACAATTCCGTGTCTTCATCACT 57.992 40.909 0.00 0.00 34.14 3.41
3800 6796 1.606480 CCGTGTCTTCATCACTGTGCT 60.606 52.381 2.12 0.00 34.14 4.40
3844 6840 0.896226 GACGGAGGAAGTACTTGCCT 59.104 55.000 21.97 20.91 33.97 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
890 944 6.627287 GCTGCGGTATTTAAAGGGAAATTCTT 60.627 38.462 0.00 0.00 31.51 2.52
964 1024 3.661944 AGTGAGAGCTGTGAAGATGTTG 58.338 45.455 0.00 0.00 0.00 3.33
1289 3754 4.415332 GCACGCCGTCCTTCTCGA 62.415 66.667 0.00 0.00 0.00 4.04
1358 3823 4.864334 CCAGGCTGATCCACCCGC 62.864 72.222 17.94 0.00 37.29 6.13
1401 3875 2.741985 TCAAGGTGGATGCGCACG 60.742 61.111 14.90 0.00 0.00 5.34
1566 4058 1.066143 ACATCCATGACCTTGACGTCC 60.066 52.381 14.12 0.00 31.35 4.79
1635 4127 3.866066 GCATGCTCACCTTGTCAGTCTTA 60.866 47.826 11.37 0.00 0.00 2.10
1668 4163 2.607771 GCATGCACGTCCATGAAAAAGT 60.608 45.455 23.51 0.00 44.12 2.66
1729 4347 1.652167 TTGCGCGCCTGCATCAATAA 61.652 50.000 30.77 9.04 45.78 1.40
1730 4348 2.050639 CTTGCGCGCCTGCATCAATA 62.051 55.000 30.77 1.61 45.78 1.90
1731 4349 3.405592 CTTGCGCGCCTGCATCAAT 62.406 57.895 30.77 0.00 45.78 2.57
1857 4486 1.080025 GTCGAGGAAGACCGGGTTG 60.080 63.158 6.32 0.00 41.83 3.77
1865 4494 2.594131 TGGTGAAGAAGTCGAGGAAGA 58.406 47.619 0.00 0.00 0.00 2.87
2924 5558 2.060326 ATGACGACCGTTGTACACAG 57.940 50.000 0.00 0.00 0.00 3.66
2927 5561 1.728825 GCGTATGACGACCGTTGTACA 60.729 52.381 2.65 0.00 46.05 2.90
3064 5890 6.478016 GGCCTTTTGCTTTAATCATCTTCATC 59.522 38.462 0.00 0.00 40.92 2.92
3341 6178 2.043227 CTACCAAGTCATCCCCTCCTC 58.957 57.143 0.00 0.00 0.00 3.71
3463 6301 4.661993 TGTCACGTATGTCAAGCAAATC 57.338 40.909 0.00 0.00 0.00 2.17
3488 6326 4.410228 AGGGAGTATGAAGCAAAGCATCTA 59.590 41.667 0.00 0.00 0.00 1.98
3624 6462 5.774690 AGAGATATAAGCAGTTGGGAGAGAG 59.225 44.000 0.00 0.00 0.00 3.20
3625 6463 5.710646 AGAGATATAAGCAGTTGGGAGAGA 58.289 41.667 0.00 0.00 0.00 3.10
3626 6464 5.047377 GGAGAGATATAAGCAGTTGGGAGAG 60.047 48.000 0.00 0.00 0.00 3.20
3627 6465 4.835615 GGAGAGATATAAGCAGTTGGGAGA 59.164 45.833 0.00 0.00 0.00 3.71
3628 6466 4.837860 AGGAGAGATATAAGCAGTTGGGAG 59.162 45.833 0.00 0.00 0.00 4.30
3629 6467 4.820775 AGGAGAGATATAAGCAGTTGGGA 58.179 43.478 0.00 0.00 0.00 4.37
3630 6468 5.306678 AGAAGGAGAGATATAAGCAGTTGGG 59.693 44.000 0.00 0.00 0.00 4.12
3631 6469 6.222389 CAGAAGGAGAGATATAAGCAGTTGG 58.778 44.000 0.00 0.00 0.00 3.77
3632 6470 6.041409 TCCAGAAGGAGAGATATAAGCAGTTG 59.959 42.308 0.00 0.00 39.61 3.16
3633 6471 6.139671 TCCAGAAGGAGAGATATAAGCAGTT 58.860 40.000 0.00 0.00 39.61 3.16
3634 6472 5.710646 TCCAGAAGGAGAGATATAAGCAGT 58.289 41.667 0.00 0.00 39.61 4.40
3635 6473 6.662865 TTCCAGAAGGAGAGATATAAGCAG 57.337 41.667 0.00 0.00 46.74 4.24
3636 6474 7.437713 TTTTCCAGAAGGAGAGATATAAGCA 57.562 36.000 0.00 0.00 46.74 3.91
3683 6679 9.920946 TTAGGAAAGGAATAGATACAAGCAATT 57.079 29.630 0.00 0.00 0.00 2.32
3687 6683 7.510407 AGGTTAGGAAAGGAATAGATACAAGC 58.490 38.462 0.00 0.00 0.00 4.01
3728 6724 3.003394 TGCCTGATCCATTGGTTAGTG 57.997 47.619 1.86 0.00 0.00 2.74
3729 6725 3.624777 CTTGCCTGATCCATTGGTTAGT 58.375 45.455 1.86 0.00 0.00 2.24
3745 6741 6.775594 ATTTAGGACAAACTTATCCTTGCC 57.224 37.500 0.00 0.00 43.09 4.52
3746 6742 8.056407 AGAATTTAGGACAAACTTATCCTTGC 57.944 34.615 0.00 0.00 43.09 4.01
3756 6752 8.175716 CGGAATTGTAGAGAATTTAGGACAAAC 58.824 37.037 0.00 0.00 31.19 2.93
3775 6771 3.748048 ACAGTGATGAAGACACGGAATTG 59.252 43.478 0.00 0.00 42.25 2.32
3777 6773 3.329386 CACAGTGATGAAGACACGGAAT 58.671 45.455 0.00 0.00 42.25 3.01
3780 6776 0.792640 GCACAGTGATGAAGACACGG 59.207 55.000 4.15 0.00 42.25 4.94
3781 6777 1.458445 CAGCACAGTGATGAAGACACG 59.542 52.381 13.88 0.00 42.25 4.49
3818 6814 3.991683 AGTACTTCCTCCGTCCCTTTAT 58.008 45.455 0.00 0.00 0.00 1.40
3819 6815 3.463048 AGTACTTCCTCCGTCCCTTTA 57.537 47.619 0.00 0.00 0.00 1.85
3820 6816 2.302157 CAAGTACTTCCTCCGTCCCTTT 59.698 50.000 4.77 0.00 0.00 3.11
3821 6817 1.900486 CAAGTACTTCCTCCGTCCCTT 59.100 52.381 4.77 0.00 0.00 3.95
3822 6818 1.558233 CAAGTACTTCCTCCGTCCCT 58.442 55.000 4.77 0.00 0.00 4.20
3823 6819 0.108281 GCAAGTACTTCCTCCGTCCC 60.108 60.000 4.77 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.