Multiple sequence alignment - TraesCS7A01G237800

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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 TraesCS7A01G237800 chr7A 100.000 4058 0 0 1 4058 211291151 211295208 0.000000e+00 7494
1 TraesCS7A01G237800 chr6B 96.619 3046 92 3 1 3036 625642337 625639293 0.000000e+00 5044
2 TraesCS7A01G237800 chr5A 96.793 3025 85 6 1 3014 534932640 534935663 0.000000e+00 5038
3 TraesCS7A01G237800 chr3B 95.828 3068 109 9 1 3057 173887613 173890672 0.000000e+00 4939
4 TraesCS7A01G237800 chr7B 95.535 3068 107 12 1 3057 139543339 139540291 0.000000e+00 4879
5 TraesCS7A01G237800 chr7B 97.880 2641 46 2 1428 4058 743006358 743008998 0.000000e+00 4558
6 TraesCS7A01G237800 chr7D 98.145 2641 37 3 1428 4057 579030028 579032667 0.000000e+00 4595
7 TraesCS7A01G237800 chr7D 97.469 1462 33 3 1 1460 579028570 579030029 0.000000e+00 2492
8 TraesCS7A01G237800 chr1A 98.027 2636 41 2 1433 4057 112004608 112001973 0.000000e+00 4569
9 TraesCS7A01G237800 chrUn 97.917 2641 44 2 1428 4057 186191121 186188481 0.000000e+00 4562
10 TraesCS7A01G237800 chrUn 97.913 2635 44 3 1433 4057 86478354 86480987 0.000000e+00 4551
11 TraesCS7A01G237800 chr1D 97.614 2640 50 6 1428 4057 212467571 212464935 0.000000e+00 4514
12 TraesCS7A01G237800 chr4B 97.423 2639 58 2 1428 4057 209271014 209268377 0.000000e+00 4488
13 TraesCS7A01G237800 chr6D 97.384 2638 60 2 1428 4057 283153826 283151190 0.000000e+00 4481
14 TraesCS7A01G237800 chr2D 98.210 2346 41 1 1713 4057 200914854 200917199 0.000000e+00 4098
15 TraesCS7A01G237800 chr2B 94.470 2640 130 6 1428 4057 343522553 343525186 0.000000e+00 4052
16 TraesCS7A01G237800 chr2B 96.403 2335 71 5 107 2431 357429135 357431466 0.000000e+00 3834
17 TraesCS7A01G237800 chr3A 97.376 1639 34 1 1428 3057 51916454 51918092 0.000000e+00 2780
18 TraesCS7A01G237800 chr4D 97.807 1505 24 1 1428 2923 123507853 123506349 0.000000e+00 2588
19 TraesCS7A01G237800 chr4D 97.471 1463 34 3 1 1460 123738808 123737346 0.000000e+00 2494
20 TraesCS7A01G237800 chr4D 97.467 1461 35 2 1 1460 123656010 123654551 0.000000e+00 2492
21 TraesCS7A01G237800 chr4D 97.331 1461 37 2 1 1460 123509311 123507852 0.000000e+00 2481
22 TraesCS7A01G237800 chr5D 98.524 271 4 0 1428 1698 413024753 413025023 2.840000e-131 479


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 TraesCS7A01G237800 chr7A 211291151 211295208 4057 False 7494.0 7494 100.000 1 4058 1 chr7A.!!$F1 4057
1 TraesCS7A01G237800 chr6B 625639293 625642337 3044 True 5044.0 5044 96.619 1 3036 1 chr6B.!!$R1 3035
2 TraesCS7A01G237800 chr5A 534932640 534935663 3023 False 5038.0 5038 96.793 1 3014 1 chr5A.!!$F1 3013
3 TraesCS7A01G237800 chr3B 173887613 173890672 3059 False 4939.0 4939 95.828 1 3057 1 chr3B.!!$F1 3056
4 TraesCS7A01G237800 chr7B 139540291 139543339 3048 True 4879.0 4879 95.535 1 3057 1 chr7B.!!$R1 3056
5 TraesCS7A01G237800 chr7B 743006358 743008998 2640 False 4558.0 4558 97.880 1428 4058 1 chr7B.!!$F1 2630
6 TraesCS7A01G237800 chr7D 579028570 579032667 4097 False 3543.5 4595 97.807 1 4057 2 chr7D.!!$F1 4056
7 TraesCS7A01G237800 chr1A 112001973 112004608 2635 True 4569.0 4569 98.027 1433 4057 1 chr1A.!!$R1 2624
8 TraesCS7A01G237800 chrUn 186188481 186191121 2640 True 4562.0 4562 97.917 1428 4057 1 chrUn.!!$R1 2629
9 TraesCS7A01G237800 chrUn 86478354 86480987 2633 False 4551.0 4551 97.913 1433 4057 1 chrUn.!!$F1 2624
10 TraesCS7A01G237800 chr1D 212464935 212467571 2636 True 4514.0 4514 97.614 1428 4057 1 chr1D.!!$R1 2629
11 TraesCS7A01G237800 chr4B 209268377 209271014 2637 True 4488.0 4488 97.423 1428 4057 1 chr4B.!!$R1 2629
12 TraesCS7A01G237800 chr6D 283151190 283153826 2636 True 4481.0 4481 97.384 1428 4057 1 chr6D.!!$R1 2629
13 TraesCS7A01G237800 chr2D 200914854 200917199 2345 False 4098.0 4098 98.210 1713 4057 1 chr2D.!!$F1 2344
14 TraesCS7A01G237800 chr2B 343522553 343525186 2633 False 4052.0 4052 94.470 1428 4057 1 chr2B.!!$F1 2629
15 TraesCS7A01G237800 chr2B 357429135 357431466 2331 False 3834.0 3834 96.403 107 2431 1 chr2B.!!$F2 2324
16 TraesCS7A01G237800 chr3A 51916454 51918092 1638 False 2780.0 2780 97.376 1428 3057 1 chr3A.!!$F1 1629
17 TraesCS7A01G237800 chr4D 123506349 123509311 2962 True 2534.5 2588 97.569 1 2923 2 chr4D.!!$R3 2922
18 TraesCS7A01G237800 chr4D 123737346 123738808 1462 True 2494.0 2494 97.471 1 1460 1 chr4D.!!$R2 1459
19 TraesCS7A01G237800 chr4D 123654551 123656010 1459 True 2492.0 2492 97.467 1 1460 1 chr4D.!!$R1 1459

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
95 97 2.082231 CCTACGTCGTCTCTCTTCCAA 58.918 52.381 0.0 0.0 0.00 3.53 F
611 613 2.505819 GGCCCCTCTCTGATAAGTCAAA 59.494 50.000 0.0 0.0 33.05 2.69 F
1181 1186 4.054671 CTCCAAGCGTCTTATCAAGATCC 58.945 47.826 0.0 0.0 40.18 3.36 F
1642 1683 1.743394 GACCCGGCGATCAAATTCTTT 59.257 47.619 9.3 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1308 1313 1.871126 GACTTGCCTTGCTCTTGGGC 61.871 60.000 0.00 0.0 45.45 5.36 R
1420 1429 5.106357 GGCTGGAAGAGAAAAGAATCAGAAC 60.106 44.000 0.00 0.0 34.07 3.01 R
2797 2852 4.202346 TGGATAATCTGGAATGCGATGTGA 60.202 41.667 0.00 0.0 0.00 3.58 R
3315 3373 4.256920 GACATATGAATATGCCTCGCCTT 58.743 43.478 10.38 0.0 42.98 4.35 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
28 29 9.403583 ACTTTTCTAGTTGTTGTGGAAAGAATA 57.596 29.630 0.0 0.0 31.29 1.75
60 61 5.649970 TGAGTTTAAGGGGTGGTTTTCTA 57.350 39.130 0.0 0.0 0.00 2.10
95 97 2.082231 CCTACGTCGTCTCTCTTCCAA 58.918 52.381 0.0 0.0 0.00 3.53
518 520 4.713792 ATCAAGTCACCAAGAAGTTCCT 57.286 40.909 0.0 0.0 0.00 3.36
581 583 9.413048 CGTTTAGTATTCAAGTTCTTCTCTTCT 57.587 33.333 0.0 0.0 0.00 2.85
611 613 2.505819 GGCCCCTCTCTGATAAGTCAAA 59.494 50.000 0.0 0.0 33.05 2.69
1137 1142 5.780282 TCGTTCCTATCTGGACCATATTCAT 59.220 40.000 0.0 0.0 46.14 2.57
1181 1186 4.054671 CTCCAAGCGTCTTATCAAGATCC 58.945 47.826 0.0 0.0 40.18 3.36
1556 1596 7.309770 AGGATATTGGGACTCTCTATTTCAC 57.690 40.000 0.0 0.0 0.00 3.18
1642 1683 1.743394 GACCCGGCGATCAAATTCTTT 59.257 47.619 9.3 0.0 0.00 2.52
1964 2015 9.770097 TCTTCATCTATCAGGTATTTCATCAAC 57.230 33.333 0.0 0.0 0.00 3.18
2235 2288 9.029368 CATCCAGAGGTGTATATTCTCATTCTA 57.971 37.037 0.0 0.0 0.00 2.10
2339 2392 6.992715 GCCATGATAAGTATAGGTGTTCTTGT 59.007 38.462 0.0 0.0 0.00 3.16
2585 2639 3.012518 CAAACTCTGGGCTAGACATTGG 58.987 50.000 0.0 0.0 0.00 3.16
2797 2852 2.474112 TCTTAGGGCTTTCGGGTATGT 58.526 47.619 0.0 0.0 0.00 2.29
2801 2856 0.035820 GGGCTTTCGGGTATGTCACA 60.036 55.000 0.0 0.0 0.00 3.58
3315 3373 7.125204 TCCTTACTCGGGATTTCTTTATCTTCA 59.875 37.037 0.0 0.0 0.00 3.02
3365 3423 4.294970 AAGGGGGAAGTGTCTCCATTTATT 59.705 41.667 0.0 0.0 46.46 1.40
3690 3748 0.096976 GACGCAACCCGATCATTGTG 59.903 55.000 11.4 11.4 41.16 3.33
3961 4019 3.501062 CGTCCCTTCCTTACCAAAGAAAC 59.499 47.826 0.0 0.0 34.37 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.047092 CACCCCTTAAACTCATTTGCTCAAT 60.047 40.000 0.00 0.00 0.00 2.57
73 74 2.083002 GGAAGAGAGACGACGTAGGTT 58.917 52.381 0.00 0.00 0.00 3.50
95 97 4.758674 CAGACACTGATGATTGTGAGGTTT 59.241 41.667 6.54 0.00 37.59 3.27
459 461 5.247084 CAATTTGCAAAGGATGATTCCCAA 58.753 37.500 18.19 0.00 43.76 4.12
518 520 9.856162 AGAACCTTAATACTAAACCAAGTTTCA 57.144 29.630 0.00 0.00 37.01 2.69
627 629 6.811170 GCCATCGAACCAGATTTTTCATTTTA 59.189 34.615 0.00 0.00 0.00 1.52
1011 1016 4.400884 ACATCTTGTCGCATAGAAGAGAGT 59.599 41.667 2.70 1.69 40.52 3.24
1137 1142 4.883585 AGAACAGTGAAAGAATCAGTTGCA 59.116 37.500 0.00 0.00 39.78 4.08
1181 1186 2.419198 CTCCCTCATTCTCCCGCG 59.581 66.667 0.00 0.00 0.00 6.46
1308 1313 1.871126 GACTTGCCTTGCTCTTGGGC 61.871 60.000 0.00 0.00 45.45 5.36
1420 1429 5.106357 GGCTGGAAGAGAAAAGAATCAGAAC 60.106 44.000 0.00 0.00 34.07 3.01
1642 1683 8.821686 ACATTATAAAGTTGATGATTCCCACA 57.178 30.769 0.00 0.00 0.00 4.17
2339 2392 8.439971 ACATATGATGAGCCCAAACTAGAAATA 58.560 33.333 10.38 0.00 0.00 1.40
2797 2852 4.202346 TGGATAATCTGGAATGCGATGTGA 60.202 41.667 0.00 0.00 0.00 3.58
2801 2856 4.897509 TCTGGATAATCTGGAATGCGAT 57.102 40.909 0.00 0.00 0.00 4.58
3315 3373 4.256920 GACATATGAATATGCCTCGCCTT 58.743 43.478 10.38 0.00 42.98 4.35
3726 3784 5.903198 TTTGAATTGGAAATGGGAAAGGT 57.097 34.783 0.00 0.00 0.00 3.50
3822 3880 3.409570 ACCTTCTTAGGCGAAAAAGACC 58.590 45.455 0.00 0.00 46.22 3.85


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

AutoCloner maintained by Alex Coulton.