Multiple sequence alignment - TraesCS2A01G024000

Loading Multiple Alignment...

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 TraesCS2A01G024000 chr2A 100.000 1597 0 0 1 1597 11648888 11650484 0.000000e+00 2950.0
1 TraesCS2A01G024000 chr2A 98.848 1042 6 2 556 1597 11690500 11691535 0.000000e+00 1853.0
2 TraesCS2A01G024000 chr2A 100.000 776 0 0 1776 2551 11650663 11651438 0.000000e+00 1434.0
3 TraesCS2A01G024000 chr2A 99.613 776 3 0 1776 2551 11691615 11692390 0.000000e+00 1417.0
4 TraesCS2A01G024000 chr2A 91.463 574 33 5 1 561 11665262 11665832 0.000000e+00 774.0
5 TraesCS2A01G024000 chr2A 94.595 37 1 1 190 225 621683702 621683666 3.550000e-04 56.5
6 TraesCS2A01G024000 chr2D 88.909 1623 98 24 1 1597 10985588 10987154 0.000000e+00 1925.0
7 TraesCS2A01G024000 chr2D 84.698 745 75 19 855 1580 11029930 11030654 0.000000e+00 708.0
8 TraesCS2A01G024000 chr2D 83.673 343 33 9 1260 1597 11023122 11023446 4.120000e-78 302.0
9 TraesCS2A01G024000 chr2D 90.270 185 16 2 673 855 11029863 11030047 9.120000e-60 241.0
10 TraesCS2A01G024000 chr2D 85.246 244 17 5 911 1149 11022762 11022991 1.530000e-57 233.0
11 TraesCS2A01G024000 chr2D 87.395 119 11 1 853 967 10986320 10986438 1.590000e-27 134.0
12 TraesCS2A01G024000 chr2B 89.354 789 53 12 824 1587 16828594 16829376 0.000000e+00 963.0
13 TraesCS2A01G024000 chr2B 81.842 749 94 22 853 1589 16847446 16848164 2.190000e-165 592.0
14 TraesCS2A01G024000 chrUn 84.923 849 85 18 765 1589 12174227 12175056 0.000000e+00 819.0
15 TraesCS2A01G024000 chrUn 84.362 697 66 24 911 1587 12171134 12171807 0.000000e+00 643.0
16 TraesCS2A01G024000 chrUn 86.136 339 26 9 911 1244 467992733 467993055 1.880000e-91 346.0
17 TraesCS2A01G024000 chrUn 90.000 120 10 2 737 855 12174314 12174432 1.220000e-33 154.0
18 TraesCS2A01G024000 chrUn 93.333 45 3 0 372 416 18922099 18922055 1.640000e-07 67.6
19 TraesCS2A01G024000 chr1A 85.901 383 54 0 1974 2356 544918779 544918397 2.360000e-110 409.0
20 TraesCS2A01G024000 chr1A 97.906 191 4 0 2361 2551 86400168 86400358 5.260000e-87 331.0
21 TraesCS2A01G024000 chr1A 97.409 193 5 0 2359 2551 49775084 49774892 1.890000e-86 329.0
22 TraesCS2A01G024000 chr3A 83.551 383 63 0 1974 2356 11828755 11829137 2.410000e-95 359.0
23 TraesCS2A01G024000 chr3A 90.196 204 20 0 1776 1979 676751049 676750846 1.500000e-67 267.0
24 TraesCS2A01G024000 chr7A 83.200 375 61 2 1983 2356 51829395 51829022 2.430000e-90 342.0
25 TraesCS2A01G024000 chr7A 83.288 371 60 2 1983 2352 51870612 51870243 8.740000e-90 340.0
26 TraesCS2A01G024000 chr7A 77.073 205 39 6 2075 2277 17719408 17719606 7.460000e-21 111.0
27 TraesCS2A01G024000 chr6A 97.436 195 5 0 2357 2551 396431377 396431183 1.460000e-87 333.0
28 TraesCS2A01G024000 chr6A 97.409 193 5 0 2359 2551 498822837 498823029 1.890000e-86 329.0
29 TraesCS2A01G024000 chr6A 95.455 198 7 2 2356 2551 153771928 153771731 5.300000e-82 315.0
30 TraesCS2A01G024000 chr5A 97.906 191 4 0 2361 2551 614280372 614280562 5.260000e-87 331.0
31 TraesCS2A01G024000 chr5A 96.465 198 7 0 2354 2551 614272311 614272508 6.810000e-86 327.0
32 TraesCS2A01G024000 chr4A 94.258 209 10 2 2344 2551 195796880 195797087 4.100000e-83 318.0
33 TraesCS2A01G024000 chr1B 91.589 214 17 1 1776 1988 629493822 629493609 6.900000e-76 294.0
34 TraesCS2A01G024000 chr3D 95.455 154 7 0 1826 1979 2525575 2525422 1.960000e-61 246.0
35 TraesCS2A01G024000 chr3D 92.908 141 9 1 1974 2113 2525066 2524926 1.200000e-48 204.0


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 TraesCS2A01G024000 chr2A 11648888 11651438 2550 False 2192.000000 2950 100.000000 1 2551 2 chr2A.!!$F2 2550
1 TraesCS2A01G024000 chr2A 11690500 11692390 1890 False 1635.000000 1853 99.230500 556 2551 2 chr2A.!!$F3 1995
2 TraesCS2A01G024000 chr2A 11665262 11665832 570 False 774.000000 774 91.463000 1 561 1 chr2A.!!$F1 560
3 TraesCS2A01G024000 chr2D 10985588 10987154 1566 False 1029.500000 1925 88.152000 1 1597 2 chr2D.!!$F1 1596
4 TraesCS2A01G024000 chr2D 11029863 11030654 791 False 474.500000 708 87.484000 673 1580 2 chr2D.!!$F3 907
5 TraesCS2A01G024000 chr2D 11022762 11023446 684 False 267.500000 302 84.459500 911 1597 2 chr2D.!!$F2 686
6 TraesCS2A01G024000 chr2B 16828594 16829376 782 False 963.000000 963 89.354000 824 1587 1 chr2B.!!$F1 763
7 TraesCS2A01G024000 chr2B 16847446 16848164 718 False 592.000000 592 81.842000 853 1589 1 chr2B.!!$F2 736
8 TraesCS2A01G024000 chrUn 12171134 12175056 3922 False 538.666667 819 86.428333 737 1589 3 chrUn.!!$F2 852
9 TraesCS2A01G024000 chr3D 2524926 2525575 649 True 225.000000 246 94.181500 1826 2113 2 chr3D.!!$R1 287

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
470 488 2.299013 TCTCGTGTAGGCACAGATTTGT 59.701 45.455 0.0 0.0 45.5 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 4497 5.236911 GCAACTTTGGAAGCATCAAAATTCA 59.763 36.0 0.0 0.0 34.26 2.57 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
31 32 5.049954 TCGTATACTCAAAACAAGGTTGTGC 60.050 40.000 0.56 0.0 41.31 4.57
190 192 9.275398 AGAAGTACGTGAAAAATAATAACCACA 57.725 29.630 0.00 0.0 0.00 4.17
277 288 2.583024 TTCCCCCGGTTTTTCGTAAT 57.417 45.000 0.00 0.0 0.00 1.89
470 488 2.299013 TCTCGTGTAGGCACAGATTTGT 59.701 45.455 0.00 0.0 45.50 2.83
532 550 2.928801 TGCGTCCATATATGCCAACT 57.071 45.000 7.24 0.0 0.00 3.16
533 551 4.252878 CATGCGTCCATATATGCCAACTA 58.747 43.478 7.24 0.0 0.00 2.24
557 575 5.984695 AATTTAGACCCTTTGAAGCCTTC 57.015 39.130 0.00 0.0 0.00 3.46
589 607 6.429791 TGAAAGTTTTGTGAGACGATTTCA 57.570 33.333 0.00 0.0 34.15 2.69
756 3092 9.851686 TCTTCATTAAACCATATCTAGCATTGT 57.148 29.630 0.00 0.0 0.00 2.71
801 3137 3.233507 AGGCATCACCATGTTGAAAAGT 58.766 40.909 0.00 0.0 43.14 2.66
802 3138 4.406456 AGGCATCACCATGTTGAAAAGTA 58.594 39.130 0.00 0.0 43.14 2.24
831 3167 9.798994 AGTAAATCAAGACGTTACGATAAGAAT 57.201 29.630 13.03 0.0 33.80 2.40
837 3173 9.027129 TCAAGACGTTACGATAAGAATTAATGG 57.973 33.333 13.03 0.0 32.17 3.16
880 3216 6.000219 ACCATATCTAGCATTGGCACTAAAG 59.000 40.000 0.00 0.0 44.61 1.85
884 3220 6.927294 ATCTAGCATTGGCACTAAAGTTAC 57.073 37.500 0.00 0.0 44.61 2.50
2323 5233 2.887152 GCCATGGAGTTCTTGTGTTCTT 59.113 45.455 18.40 0.0 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 9.500864 CAAATTCACAAACCTTTTTACCAAATG 57.499 29.630 0.00 0.00 0.00 2.32
345 356 4.344102 AGGCCTGCACGAAGAGTAAATATA 59.656 41.667 3.11 0.00 0.00 0.86
470 488 3.275143 TCAAAAGTGCCTCTCGTGAAAA 58.725 40.909 0.00 0.00 0.00 2.29
532 550 8.333235 TGAAGGCTTCAAAGGGTCTAAATTATA 58.667 33.333 26.78 0.00 36.59 0.98
533 551 7.182060 TGAAGGCTTCAAAGGGTCTAAATTAT 58.818 34.615 26.78 0.00 36.59 1.28
557 575 7.531871 CGTCTCACAAAACTTTCATGATAACTG 59.468 37.037 0.00 0.00 0.00 3.16
674 692 7.991084 AGACCTAGGTAATTTGTTGGTTTAC 57.009 36.000 16.29 0.00 0.00 2.01
802 3138 9.286946 CTTATCGTAACGTCTTGATTTACTTCT 57.713 33.333 0.00 0.00 0.00 2.85
815 3151 7.169035 TGCCATTAATTCTTATCGTAACGTC 57.831 36.000 0.00 0.00 0.00 4.34
821 3157 6.579666 ATGCATGCCATTAATTCTTATCGT 57.420 33.333 16.68 0.00 0.00 3.73
833 3169 8.649591 TGGTTTAAGATATTAATGCATGCCATT 58.350 29.630 16.68 16.34 45.75 3.16
880 3216 6.204882 GGTGATGCCTTATCCTAACATGTAAC 59.795 42.308 0.00 0.00 34.77 2.50
884 3220 4.717877 TGGTGATGCCTTATCCTAACATG 58.282 43.478 0.00 0.00 38.35 3.21
909 3245 4.975502 TCTTAATTTGCTTGCACGTTTCAG 59.024 37.500 0.00 0.00 0.00 3.02
1948 4497 5.236911 GCAACTTTGGAAGCATCAAAATTCA 59.763 36.000 0.00 0.00 34.26 2.57


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

AutoCloner maintained by Alex Coulton.