Multiple sequence alignment - TraesCS1D01G285400

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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 TraesCS1D01G285400 chr1D 100.000 2730 0 0 1 2730 383343466 383346195 0 5042
1 TraesCS1D01G285400 chr2B 91.912 2782 166 33 1 2730 717666620 717669394 0 3836
2 TraesCS1D01G285400 chr2B 95.502 956 37 6 1781 2730 655688597 655689552 0 1522
3 TraesCS1D01G285400 chr2B 95.193 957 39 6 1781 2730 655661624 655660668 0 1506
4 TraesCS1D01G285400 chr2B 95.183 955 39 6 1781 2728 670332892 670331938 0 1502
5 TraesCS1D01G285400 chr2B 94.896 960 39 8 1781 2730 19857671 19856712 0 1493
6 TraesCS1D01G285400 chr6D 95.577 1786 71 7 2 1784 258015193 258013413 0 2854
7 TraesCS1D01G285400 chr6D 95.121 1783 70 11 2 1781 305371391 305373159 0 2795
8 TraesCS1D01G285400 chr6D 97.266 951 22 4 1781 2730 258013387 258012440 0 1609
9 TraesCS1D01G285400 chr2D 95.305 1789 71 8 1 1784 87963929 87962149 0 2826
10 TraesCS1D01G285400 chr2D 97.476 951 21 3 1781 2728 87953595 87952645 0 1620
11 TraesCS1D01G285400 chr7D 93.782 1785 95 13 1 1781 560762301 560764073 0 2667
12 TraesCS1D01G285400 chr7D 95.273 952 39 6 1781 2730 560764102 560765049 0 1504
13 TraesCS1D01G285400 chr5A 91.697 1939 120 26 1 1907 693850349 693848420 0 2651
14 TraesCS1D01G285400 chr3B 93.140 1793 102 14 1 1784 60578131 60576351 0 2610
15 TraesCS1D01G285400 chr3B 92.222 1800 115 18 1 1784 657797123 657795333 0 2525
16 TraesCS1D01G285400 chr3B 94.781 958 41 7 1781 2730 657795307 657794351 0 1483
17 TraesCS1D01G285400 chr7B 92.273 1799 106 21 1 1784 599836913 599835133 0 2521
18 TraesCS1D01G285400 chr5D 98.318 951 14 2 1781 2730 36567599 36566650 0 1666


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 TraesCS1D01G285400 chr1D 383343466 383346195 2729 False 5042.0 5042 100.0000 1 2730 1 chr1D.!!$F1 2729
1 TraesCS1D01G285400 chr2B 717666620 717669394 2774 False 3836.0 3836 91.9120 1 2730 1 chr2B.!!$F2 2729
2 TraesCS1D01G285400 chr2B 655688597 655689552 955 False 1522.0 1522 95.5020 1781 2730 1 chr2B.!!$F1 949
3 TraesCS1D01G285400 chr2B 655660668 655661624 956 True 1506.0 1506 95.1930 1781 2730 1 chr2B.!!$R2 949
4 TraesCS1D01G285400 chr2B 670331938 670332892 954 True 1502.0 1502 95.1830 1781 2728 1 chr2B.!!$R3 947
5 TraesCS1D01G285400 chr2B 19856712 19857671 959 True 1493.0 1493 94.8960 1781 2730 1 chr2B.!!$R1 949
6 TraesCS1D01G285400 chr6D 305371391 305373159 1768 False 2795.0 2795 95.1210 2 1781 1 chr6D.!!$F1 1779
7 TraesCS1D01G285400 chr6D 258012440 258015193 2753 True 2231.5 2854 96.4215 2 2730 2 chr6D.!!$R1 2728
8 TraesCS1D01G285400 chr2D 87962149 87963929 1780 True 2826.0 2826 95.3050 1 1784 1 chr2D.!!$R2 1783
9 TraesCS1D01G285400 chr2D 87952645 87953595 950 True 1620.0 1620 97.4760 1781 2728 1 chr2D.!!$R1 947
10 TraesCS1D01G285400 chr7D 560762301 560765049 2748 False 2085.5 2667 94.5275 1 2730 2 chr7D.!!$F1 2729
11 TraesCS1D01G285400 chr5A 693848420 693850349 1929 True 2651.0 2651 91.6970 1 1907 1 chr5A.!!$R1 1906
12 TraesCS1D01G285400 chr3B 60576351 60578131 1780 True 2610.0 2610 93.1400 1 1784 1 chr3B.!!$R1 1783
13 TraesCS1D01G285400 chr3B 657794351 657797123 2772 True 2004.0 2525 93.5015 1 2730 2 chr3B.!!$R2 2729
14 TraesCS1D01G285400 chr7B 599835133 599836913 1780 True 2521.0 2521 92.2730 1 1784 1 chr7B.!!$R1 1783
15 TraesCS1D01G285400 chr5D 36566650 36567599 949 True 1666.0 1666 98.3180 1781 2730 1 chr5D.!!$R1 949

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
882 896 1.002430 TCAAAGAAGCTCGTGATGCCT 59.998 47.619 0.0 0.0 0.00 4.75 F
894 908 2.101415 CGTGATGCCTATCAGGTTCTCA 59.899 50.000 0.0 0.0 43.66 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1738 4.691860 TTTTTGTTTTGGAACGTCGGTA 57.308 36.364 0.0 0.0 38.65 4.02 R
2307 2398 8.354426 GTTTGAGTTGCCTGGTTATAAGTTTTA 58.646 33.333 0.0 0.0 0.00 1.52 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
86 87 3.190744 ACATTTGCAGAGCATGAGTTCAG 59.809 43.478 0.00 0.00 38.76 3.02
103 104 3.981071 TCAGGGAACTTCCAGTACATG 57.019 47.619 10.11 0.00 40.21 3.21
203 204 1.533731 AGGAAATGCGTACCAAACACG 59.466 47.619 5.14 0.00 42.24 4.49
342 343 3.507233 GCAAGAGGTCACCATTCATTGAA 59.493 43.478 0.00 0.75 0.00 2.69
526 529 1.048724 TCCCCAGGCAAGGTCTATCG 61.049 60.000 0.00 0.00 0.00 2.92
535 538 3.050619 GCAAGGTCTATCGTGTTATCCG 58.949 50.000 0.00 0.00 0.00 4.18
792 806 3.755378 AGCTCGCAAACTCAATGAAGAAT 59.245 39.130 0.00 0.00 0.00 2.40
857 871 6.893583 AGACTATAATGATGAACTTGCCACT 58.106 36.000 0.00 0.00 0.00 4.00
882 896 1.002430 TCAAAGAAGCTCGTGATGCCT 59.998 47.619 0.00 0.00 0.00 4.75
883 897 2.233676 TCAAAGAAGCTCGTGATGCCTA 59.766 45.455 0.00 0.00 0.00 3.93
894 908 2.101415 CGTGATGCCTATCAGGTTCTCA 59.899 50.000 0.00 0.00 43.66 3.27
941 957 5.554822 AGTGTAGTTTTGCGTTTCTTTCA 57.445 34.783 0.00 0.00 0.00 2.69
997 1016 6.016860 GTCCGTATTCTTTTTACACCAGGTTT 60.017 38.462 0.00 0.00 0.00 3.27
1072 1091 3.368843 GTCGAATCGTTTGGACCGTAAAT 59.631 43.478 9.49 0.00 35.29 1.40
1199 1225 2.222027 GGGGAAGTTGACAACACTCAG 58.778 52.381 20.08 0.00 0.00 3.35
1321 1354 5.277825 TCTGTTTTTGGCAAATTACTCACG 58.722 37.500 14.29 6.18 0.00 4.35
1659 1698 4.038162 GTCTCTATGGGAAGAGCATTACGT 59.962 45.833 0.00 0.00 42.36 3.57
2225 2313 5.943706 TTGTTGCATTTTTAGCATTGCAT 57.056 30.435 11.91 0.00 43.91 3.96
2372 2464 2.946990 CACCCACAAGAAACCGTAAACT 59.053 45.455 0.00 0.00 0.00 2.66
2694 2787 3.575256 TCAACCATCGTAGTACCTTGTGT 59.425 43.478 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 2.119801 ATATCGATGATTGGCTGGGC 57.880 50.000 8.54 0.00 0.00 5.36
131 132 3.517602 TCAACGTCCAACAGATAATCGG 58.482 45.455 0.00 0.00 0.00 4.18
526 529 3.192633 AGTTTGAATTGCCCGGATAACAC 59.807 43.478 0.73 0.00 0.00 3.32
535 538 7.172361 TGCTTGTAAAAATAGTTTGAATTGCCC 59.828 33.333 0.00 0.00 0.00 5.36
579 583 1.225855 TCACACTAAGCCAAGTTGCG 58.774 50.000 0.00 0.00 36.02 4.85
725 739 4.223144 GCCATATTCAATTACCCTTGGGT 58.777 43.478 16.31 16.31 0.00 4.51
762 776 1.301716 GTTTGCGAGCTCCCTGACA 60.302 57.895 8.47 0.00 0.00 3.58
792 806 3.011566 TGGCTCAAGACAAAACCTTCA 57.988 42.857 0.00 0.00 0.00 3.02
857 871 4.738124 CATCACGAGCTTCTTTGAGTCTA 58.262 43.478 0.00 0.00 0.00 2.59
882 896 5.867716 GCGTTTTCTTACTGAGAACCTGATA 59.132 40.000 0.00 0.00 43.90 2.15
883 897 4.691216 GCGTTTTCTTACTGAGAACCTGAT 59.309 41.667 0.00 0.00 43.90 2.90
894 908 1.194772 GCTGCTTCGCGTTTTCTTACT 59.805 47.619 5.77 0.00 0.00 2.24
997 1016 6.092092 CGTTCAATTCCATGTTTTGCATCTA 58.908 36.000 0.00 0.00 35.19 1.98
1191 1217 4.037208 CACAGAAAGCAATTCCTGAGTGTT 59.963 41.667 0.00 0.00 38.94 3.32
1199 1225 2.818130 TTGCCACAGAAAGCAATTCC 57.182 45.000 0.00 0.00 43.74 3.01
1321 1354 5.806089 GCACATGCAAGTTTTGTACTTAC 57.194 39.130 0.00 0.00 45.29 2.34
1356 1390 5.939883 TCTCACAAATTAAGACATGGACTGG 59.060 40.000 0.00 0.00 0.00 4.00
1659 1698 1.901948 AGCGAGACGTGGGAACTGA 60.902 57.895 0.00 0.00 0.00 3.41
1699 1738 4.691860 TTTTTGTTTTGGAACGTCGGTA 57.308 36.364 0.00 0.00 38.65 4.02
2307 2398 8.354426 GTTTGAGTTGCCTGGTTATAAGTTTTA 58.646 33.333 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.