Multiple sequence alignment - TraesCS2D01G184600

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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 TraesCS2D01G184600 chr2D 100.000 2378 0 0 1 2378 129923954 129926331 0.000000e+00 4392.0
1 TraesCS2D01G184600 chr2D 97.996 449 8 1 1 449 370005446 370004999 0.000000e+00 778.0
2 TraesCS2D01G184600 chr2D 97.436 117 3 0 455 571 370002433 370002317 1.440000e-47 200.0
3 TraesCS2D01G184600 chr3D 98.111 2118 30 7 1 2111 119267595 119269709 0.000000e+00 3681.0
4 TraesCS2D01G184600 chr3D 98.420 1582 24 1 797 2378 567176552 567178132 0.000000e+00 2782.0
5 TraesCS2D01G184600 chr3D 97.996 449 8 1 1 449 133676649 133676202 0.000000e+00 778.0
6 TraesCS2D01G184600 chr3D 96.800 125 2 2 448 571 133673655 133673532 8.610000e-50 207.0
7 TraesCS2D01G184600 chr6D 96.734 1837 28 10 571 2378 56361705 56359872 0.000000e+00 3031.0
8 TraesCS2D01G184600 chr7D 99.052 1582 15 0 797 2378 55628229 55629810 0.000000e+00 2839.0
9 TraesCS2D01G184600 chr7D 98.547 1583 21 2 797 2378 141508648 141507067 0.000000e+00 2795.0
10 TraesCS2D01G184600 chr7D 98.748 799 9 1 1 798 55627404 55628202 0.000000e+00 1419.0
11 TraesCS2D01G184600 chr7D 97.788 226 4 1 571 795 141508903 141508678 2.870000e-104 388.0
12 TraesCS2D01G184600 chr5D 98.295 1584 24 3 797 2378 28009947 28008365 0.000000e+00 2772.0
13 TraesCS2D01G184600 chr5D 97.768 448 7 3 1 448 259634563 259634119 0.000000e+00 769.0
14 TraesCS2D01G184600 chr5D 97.807 228 5 0 571 798 28010202 28009975 6.160000e-106 394.0
15 TraesCS2D01G184600 chr5D 97.788 226 5 0 573 798 449317415 449317190 7.970000e-105 390.0
16 TraesCS2D01G184600 chr5D 96.800 125 3 1 448 571 259631522 259631398 8.610000e-50 207.0
17 TraesCS2D01G184600 chr1D 98.230 1582 25 3 797 2378 26578933 26580511 0.000000e+00 2763.0
18 TraesCS2D01G184600 chr1D 98.168 1583 26 2 797 2378 288338833 288337253 0.000000e+00 2760.0
19 TraesCS2D01G184600 chr1D 97.807 228 5 0 571 798 46656926 46657153 6.160000e-106 394.0
20 TraesCS2D01G184600 chr1D 97.357 227 5 1 571 797 26578679 26578904 3.710000e-103 385.0
21 TraesCS2D01G184600 chr4D 98.042 1583 27 2 797 2378 108885662 108884083 0.000000e+00 2748.0
22 TraesCS2D01G184600 chr4D 97.807 228 5 0 571 798 108885917 108885690 6.160000e-106 394.0
23 TraesCS2D01G184600 chr4D 97.368 228 6 0 571 798 505478293 505478066 2.870000e-104 388.0
24 TraesCS2D01G184600 chr3A 98.218 449 7 1 1 449 493668654 493668207 0.000000e+00 784.0
25 TraesCS2D01G184600 chr3A 96.000 125 4 1 448 571 493665643 493665519 4.010000e-48 202.0
26 TraesCS2D01G184600 chr7A 96.018 452 14 3 1 449 516118458 516118008 0.000000e+00 732.0
27 TraesCS2D01G184600 chr6B 95.604 455 13 5 1 449 711435692 711435239 0.000000e+00 723.0
28 TraesCS2D01G184600 chr6B 93.103 116 6 2 456 570 711434025 711433911 4.070000e-38 169.0
29 TraesCS2D01G184600 chr5A 95.165 455 12 6 1 449 33940682 33940232 0.000000e+00 710.0
30 TraesCS2D01G184600 chr5A 92.800 125 8 1 448 571 33939003 33938879 1.880000e-41 180.0
31 TraesCS2D01G184600 chr5A 100.000 32 0 0 540 571 546994319 546994288 2.550000e-05 60.2


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 TraesCS2D01G184600 chr2D 129923954 129926331 2377 False 4392.0 4392 100.0000 1 2378 1 chr2D.!!$F1 2377
1 TraesCS2D01G184600 chr2D 370002317 370005446 3129 True 489.0 778 97.7160 1 571 2 chr2D.!!$R1 570
2 TraesCS2D01G184600 chr3D 119267595 119269709 2114 False 3681.0 3681 98.1110 1 2111 1 chr3D.!!$F1 2110
3 TraesCS2D01G184600 chr3D 567176552 567178132 1580 False 2782.0 2782 98.4200 797 2378 1 chr3D.!!$F2 1581
4 TraesCS2D01G184600 chr3D 133673532 133676649 3117 True 492.5 778 97.3980 1 571 2 chr3D.!!$R1 570
5 TraesCS2D01G184600 chr6D 56359872 56361705 1833 True 3031.0 3031 96.7340 571 2378 1 chr6D.!!$R1 1807
6 TraesCS2D01G184600 chr7D 55627404 55629810 2406 False 2129.0 2839 98.9000 1 2378 2 chr7D.!!$F1 2377
7 TraesCS2D01G184600 chr7D 141507067 141508903 1836 True 1591.5 2795 98.1675 571 2378 2 chr7D.!!$R1 1807
8 TraesCS2D01G184600 chr5D 28008365 28010202 1837 True 1583.0 2772 98.0510 571 2378 2 chr5D.!!$R2 1807
9 TraesCS2D01G184600 chr5D 259631398 259634563 3165 True 488.0 769 97.2840 1 571 2 chr5D.!!$R3 570
10 TraesCS2D01G184600 chr1D 288337253 288338833 1580 True 2760.0 2760 98.1680 797 2378 1 chr1D.!!$R1 1581
11 TraesCS2D01G184600 chr1D 26578679 26580511 1832 False 1574.0 2763 97.7935 571 2378 2 chr1D.!!$F2 1807
12 TraesCS2D01G184600 chr4D 108884083 108885917 1834 True 1571.0 2748 97.9245 571 2378 2 chr4D.!!$R2 1807
13 TraesCS2D01G184600 chr3A 493665519 493668654 3135 True 493.0 784 97.1090 1 571 2 chr3A.!!$R1 570
14 TraesCS2D01G184600 chr6B 711433911 711435692 1781 True 446.0 723 94.3535 1 570 2 chr6B.!!$R1 569
15 TraesCS2D01G184600 chr5A 33938879 33940682 1803 True 445.0 710 93.9825 1 571 2 chr5A.!!$R2 570

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
361 368 8.792633 CACTAGGAAATCAAACCATTAGTCAAA 58.207 33.333 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 4681 2.596452 ACATGTGATGAGACGTCGTTC 58.404 47.619 10.46 9.0 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
361 368 8.792633 CACTAGGAAATCAAACCATTAGTCAAA 58.207 33.333 0.00 0.00 0.00 2.69
1861 4567 2.876955 CATGCAACCGCGACCAAT 59.123 55.556 8.23 0.00 42.97 3.16
1974 4681 6.567769 AAAACATTCGTTGCAAAGTAACAG 57.432 33.333 12.18 5.25 34.86 3.16
2000 4707 6.504398 ACGACGTCTCATCACATGTTATAAT 58.496 36.000 14.70 0.00 0.00 1.28
2288 4998 1.507140 TAGGGGATTCACAGGCGAAT 58.493 50.000 0.00 0.00 38.32 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
537 3210 5.456822 GGCTTTTGAAATATTTGCTAGAGCG 59.543 40.000 5.17 0.00 45.83 5.03
709 3384 9.158233 CACTTCTAAAATTTCCTTATACACGGA 57.842 33.333 0.00 0.00 0.00 4.69
1861 4567 2.749076 CGGTCTTTGATGGCTTGATTCA 59.251 45.455 0.00 0.00 0.00 2.57
1955 4662 4.375698 CGTTCTGTTACTTTGCAACGAATG 59.624 41.667 10.27 4.42 39.10 2.67
1957 4664 3.617706 TCGTTCTGTTACTTTGCAACGAA 59.382 39.130 10.27 0.00 41.77 3.85
1974 4681 2.596452 ACATGTGATGAGACGTCGTTC 58.404 47.619 10.46 9.00 0.00 3.95
2288 4998 6.867519 TCTCACCAGTATCATTGTTTCCTA 57.132 37.500 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.