Multiple sequence alignment - TraesCS2B01G462100

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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 TraesCS2B01G462100 chr2B 100.000 3637 0 0 1 3637 655686164 655689800 0 6717
1 TraesCS2B01G462100 chr2B 95.404 3655 135 13 1 3637 670335327 670331688 0 5788
2 TraesCS2B01G462100 chr2B 95.030 3662 154 14 1 3637 717665984 717669642 0 5729
3 TraesCS2B01G462100 chr2B 96.818 1823 52 5 1817 3637 655662238 655660420 0 3040
4 TraesCS2B01G462100 chr2B 95.388 1843 66 6 1 1825 655672877 655671036 0 2915
5 TraesCS2B01G462100 chr2B 95.507 1825 72 10 1820 3637 19858285 19856464 0 2907
6 TraesCS2B01G462100 chr2B 95.437 1819 80 3 1822 3637 738154128 738152310 0 2896
7 TraesCS2B01G462100 chr2B 95.056 1780 63 10 1 1758 738156229 738154453 0 2776
8 TraesCS2B01G462100 chr3B 95.221 3662 145 15 1 3637 657797759 657794103 0 5766
9 TraesCS2B01G462100 chr3B 96.185 2857 90 8 1 2843 60578767 60575916 0 4654
10 TraesCS2B01G462100 chr6D 92.508 3657 228 34 3 3635 258015828 258012194 0 5193
11 TraesCS2B01G462100 chr7D 91.202 3660 269 36 1 3637 560761668 560765297 0 4926
12 TraesCS2B01G462100 chr7B 94.983 2691 103 14 1 2670 599837549 599834870 0 4193
13 TraesCS2B01G462100 chr5D 93.863 2770 133 22 887 3637 36569154 36566403 0 4139
14 TraesCS2B01G462100 chr3D 90.260 2844 221 38 823 3637 305610572 305613388 0 3666
15 TraesCS2B01G462100 chr4B 96.434 1851 57 5 1791 3637 15522927 15521082 0 3044
16 TraesCS2B01G462100 chr4B 95.452 1825 75 8 1820 3637 603284791 603286614 0 2904
17 TraesCS2B01G462100 chr4B 96.696 1725 42 5 1 1712 15524671 15522949 0 2856
18 TraesCS2B01G462100 chr4B 94.510 1785 76 8 2 1773 603283016 603284791 0 2734


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 TraesCS2B01G462100 chr2B 655686164 655689800 3636 False 6717 6717 100.0000 1 3637 1 chr2B.!!$F1 3636
1 TraesCS2B01G462100 chr2B 670331688 670335327 3639 True 5788 5788 95.4040 1 3637 1 chr2B.!!$R4 3636
2 TraesCS2B01G462100 chr2B 717665984 717669642 3658 False 5729 5729 95.0300 1 3637 1 chr2B.!!$F2 3636
3 TraesCS2B01G462100 chr2B 655660420 655662238 1818 True 3040 3040 96.8180 1817 3637 1 chr2B.!!$R2 1820
4 TraesCS2B01G462100 chr2B 655671036 655672877 1841 True 2915 2915 95.3880 1 1825 1 chr2B.!!$R3 1824
5 TraesCS2B01G462100 chr2B 19856464 19858285 1821 True 2907 2907 95.5070 1820 3637 1 chr2B.!!$R1 1817
6 TraesCS2B01G462100 chr2B 738152310 738156229 3919 True 2836 2896 95.2465 1 3637 2 chr2B.!!$R5 3636
7 TraesCS2B01G462100 chr3B 657794103 657797759 3656 True 5766 5766 95.2210 1 3637 1 chr3B.!!$R2 3636
8 TraesCS2B01G462100 chr3B 60575916 60578767 2851 True 4654 4654 96.1850 1 2843 1 chr3B.!!$R1 2842
9 TraesCS2B01G462100 chr6D 258012194 258015828 3634 True 5193 5193 92.5080 3 3635 1 chr6D.!!$R1 3632
10 TraesCS2B01G462100 chr7D 560761668 560765297 3629 False 4926 4926 91.2020 1 3637 1 chr7D.!!$F1 3636
11 TraesCS2B01G462100 chr7B 599834870 599837549 2679 True 4193 4193 94.9830 1 2670 1 chr7B.!!$R1 2669
12 TraesCS2B01G462100 chr5D 36566403 36569154 2751 True 4139 4139 93.8630 887 3637 1 chr5D.!!$R1 2750
13 TraesCS2B01G462100 chr3D 305610572 305613388 2816 False 3666 3666 90.2600 823 3637 1 chr3D.!!$F1 2814
14 TraesCS2B01G462100 chr4B 15521082 15524671 3589 True 2950 3044 96.5650 1 3637 2 chr4B.!!$R1 3636
15 TraesCS2B01G462100 chr4B 603283016 603286614 3598 False 2819 2904 94.9810 2 3637 2 chr4B.!!$F1 3635

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
626 631 0.035056 GAGTACTGCCCAGCACCAAT 60.035 55.0 0.00 0.0 33.79 3.16 F
1414 1433 0.469892 TGTCACAGTCAGGGAGCTCA 60.470 55.0 17.19 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2505 2828 1.153756 CAACCCTTGCCTCCCAACT 59.846 57.895 0.0 0.0 0.0 3.16 R
2935 3265 1.761784 TGTGTGCTTTGAATTGCCCTT 59.238 42.857 0.0 0.0 0.0 3.95 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
105 106 3.136260 TGATGCAGTCAGCCAATGGTATA 59.864 43.478 0.00 0.00 44.83 1.47
164 165 4.060900 GAGGCTCGAGCATTAAATCATGA 58.939 43.478 36.27 0.00 44.36 3.07
202 203 0.978146 AGAGAACATCCCTCCGGTGG 60.978 60.000 15.94 15.94 0.00 4.61
218 219 2.031069 CGGTGGTATGTACGGAGATCAG 60.031 54.545 0.00 0.00 0.00 2.90
236 237 3.982516 TCAGTAGGATACAAGACCTGCT 58.017 45.455 0.00 0.00 46.26 4.24
263 264 3.826729 GCTGTAACCATGGGAAAAAGTCT 59.173 43.478 18.09 0.00 0.00 3.24
320 321 3.062763 CTGTCTGCTCAACTGTACTTGG 58.937 50.000 0.00 0.00 0.00 3.61
328 329 2.706723 TCAACTGTACTTGGCCAACCTA 59.293 45.455 16.05 3.89 36.63 3.08
529 534 1.753073 GAATGCCCAATCCAACTCCAG 59.247 52.381 0.00 0.00 0.00 3.86
596 601 3.947834 GGGACACCGAAAGATCAAATGAT 59.052 43.478 0.00 0.00 37.51 2.45
626 631 0.035056 GAGTACTGCCCAGCACCAAT 60.035 55.000 0.00 0.00 33.79 3.16
643 648 5.008613 GCACCAATTTTCGATCTAGGCATAA 59.991 40.000 0.00 0.00 0.00 1.90
695 700 3.731652 AACACATCAACATGTTGGGTG 57.268 42.857 36.04 36.04 40.66 4.61
891 896 3.077359 GTCAGGCAGCAAGATTTACAGT 58.923 45.455 0.00 0.00 0.00 3.55
910 915 4.472108 ACAGTAGTAGTAGCTCAGGAGAGT 59.528 45.833 0.00 0.00 44.00 3.24
952 957 4.133078 GAGAAGGATTATCAAGCCACCTG 58.867 47.826 0.00 0.00 40.13 4.00
1414 1433 0.469892 TGTCACAGTCAGGGAGCTCA 60.470 55.000 17.19 0.00 0.00 4.26
1431 1450 5.182760 GGAGCTCACAAACTCAATGAAGAAT 59.817 40.000 17.19 0.00 34.48 2.40
1574 1593 7.385752 AGCAACTAATAGTGTAGTTTTGCGTTA 59.614 33.333 0.00 0.00 41.38 3.18
1585 1604 9.276397 GTGTAGTTTTGCGTTACTTTCTTTTTA 57.724 29.630 0.00 0.00 0.00 1.52
1704 1737 1.068895 TCGCTTGGACCGTAAAGACAA 59.931 47.619 0.00 0.00 0.00 3.18
2047 2356 8.893727 TGCTTAAATCCAGCTTCTAGTATTTTC 58.106 33.333 0.00 0.00 38.19 2.29
2131 2447 6.872920 ACATTGACAAGACAAAGCCTAAAAA 58.127 32.000 0.00 0.00 33.44 1.94
2152 2468 7.910441 AAAAAGGCAATCATTACTGGATTTG 57.090 32.000 0.00 0.00 32.86 2.32
2300 2618 1.254026 CCAGTTCCCGTGTCTCACTA 58.746 55.000 0.00 0.00 31.34 2.74
2450 2772 8.766000 AAGCTAGCTAACTAGAAAAGTTCTTC 57.234 34.615 19.70 0.00 45.64 2.87
2495 2818 2.423185 CTGTGGTGTTTTTGCTCTGACA 59.577 45.455 0.00 0.00 0.00 3.58
2505 2828 2.908688 TGCTCTGACACTAGCAAACA 57.091 45.000 5.46 0.00 45.36 2.83
2540 2863 3.069443 GGGTTGTTCCAAATTTCAGAGCA 59.931 43.478 0.00 0.00 38.11 4.26
2728 3055 2.528127 TTTGGACTGCCGAGGGGA 60.528 61.111 0.00 0.00 36.79 4.81
2935 3265 1.573108 GGGAGATCAAGGGTGTCTGA 58.427 55.000 0.00 0.00 0.00 3.27
3482 3814 3.806949 ATTTGAAGAACCTGGGTGCTA 57.193 42.857 0.00 0.00 31.60 3.49
3625 3958 1.372307 GCAGGCCAAATTGCTGGTT 59.628 52.632 5.01 0.00 38.86 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 2.703675 CTTGCACCTTGGCCCTCTGT 62.704 60.000 0.00 0.00 0.00 3.41
164 165 5.755849 TCTCTTTCTCCTTTTTGTGTCCTT 58.244 37.500 0.00 0.00 0.00 3.36
202 203 6.877855 TGTATCCTACTGATCTCCGTACATAC 59.122 42.308 0.00 2.47 34.76 2.39
218 219 2.950309 TCGAGCAGGTCTTGTATCCTAC 59.050 50.000 0.00 0.00 32.26 3.18
236 237 1.271856 TCCCATGGTTACAGCTTCGA 58.728 50.000 11.73 0.00 0.00 3.71
263 264 3.317993 GGCTCTTAGCAACTTTTGTTCCA 59.682 43.478 0.78 0.00 44.75 3.53
328 329 3.744660 CTTCTAGAACACTTGTGGCCTT 58.255 45.455 3.32 0.00 0.00 4.35
421 423 1.427368 TGGTTGCCTTCCCACTAACAT 59.573 47.619 0.00 0.00 0.00 2.71
529 534 6.615088 TCTTTATTTGCTGAGCTGTGATTTC 58.385 36.000 5.83 0.00 0.00 2.17
626 631 7.862372 GCAAATCATTTATGCCTAGATCGAAAA 59.138 33.333 0.00 0.00 34.03 2.29
643 648 3.118884 GCAGATCTTGTGGGCAAATCATT 60.119 43.478 0.00 0.00 33.73 2.57
891 896 4.200874 GCAACTCTCCTGAGCTACTACTA 58.799 47.826 0.00 0.00 43.85 1.82
910 915 3.608796 TCTCGAATTGATGTGGATGCAA 58.391 40.909 0.00 0.00 0.00 4.08
952 957 1.200948 GAATGGTGACCTCTTGCAAGC 59.799 52.381 21.99 8.18 0.00 4.01
1414 1433 6.966534 ACCTTCATTCTTCATTGAGTTTGT 57.033 33.333 0.00 0.00 0.00 2.83
1431 1450 3.011566 TGGCTCAAGACAAAACCTTCA 57.988 42.857 0.00 0.00 0.00 3.02
1491 1510 2.037772 GAGCTTCTTTGAGTCTGGTGGA 59.962 50.000 0.00 0.00 0.00 4.02
1632 1653 4.321601 CCTTGCCGTTCAATTCCATGTTTA 60.322 41.667 0.00 0.00 33.57 2.01
1704 1737 8.762481 AAAGTAAAGAAACCATTGACTTACCT 57.238 30.769 0.00 0.00 0.00 3.08
1753 1795 7.434897 TGTGTGAGCAAAAGTTTTAGCATAAAG 59.565 33.333 18.54 1.23 0.00 1.85
1966 2273 3.243839 TGGACTGAAGAAGCAAAAATGCC 60.244 43.478 0.00 0.00 34.90 4.40
2131 2447 7.547227 GTTACAAATCCAGTAATGATTGCCTT 58.453 34.615 0.00 0.00 34.34 4.35
2152 2468 4.501921 GTCGATCCCTTATGTTCACGTTAC 59.498 45.833 0.00 0.00 0.00 2.50
2325 2643 5.929415 ACTCATTGTTTTGTTTTGGAACGTT 59.071 32.000 0.00 0.00 38.65 3.99
2450 2772 8.531530 CAGTCGAACCTAAACAAAAATTGAAAG 58.468 33.333 0.00 0.00 0.00 2.62
2495 2818 1.545651 GCCTCCCAACTGTTTGCTAGT 60.546 52.381 0.00 0.00 0.00 2.57
2505 2828 1.153756 CAACCCTTGCCTCCCAACT 59.846 57.895 0.00 0.00 0.00 3.16
2540 2863 6.770286 TTCCTTATGCTTGGAATATCCTCT 57.230 37.500 0.00 0.00 37.42 3.69
2728 3055 4.157289 CCAAGTTCTTATGCATGCAACTCT 59.843 41.667 26.68 10.93 0.00 3.24
2849 3177 5.559148 AAATGCAACAATTCCCTGGTTAA 57.441 34.783 0.00 0.00 0.00 2.01
2896 3225 5.817784 TCCCCATAATGGTCGAAAACTTAA 58.182 37.500 0.00 0.00 35.17 1.85
2935 3265 1.761784 TGTGTGCTTTGAATTGCCCTT 59.238 42.857 0.00 0.00 0.00 3.95
3482 3814 2.444388 ACAGTGGATGGCATGTATGGAT 59.556 45.455 3.81 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.