Multiple sequence alignment - TraesCS3B01G251400

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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 TraesCS3B01G251400 chr3B 100.000 3220 0 0 1 3220 402459556 402462775 0.000000e+00 5947
1 TraesCS3B01G251400 chr3B 98.851 3221 30 4 1 3220 793274042 793270828 0.000000e+00 5736
2 TraesCS3B01G251400 chr4A 97.677 2368 37 3 871 3220 615519669 615522036 0.000000e+00 4052
3 TraesCS3B01G251400 chr4A 98.753 882 11 0 1 882 615514847 615515728 0.000000e+00 1568
4 TraesCS3B01G251400 chr2D 97.720 1579 31 2 1 1577 547217395 547218970 0.000000e+00 2712
5 TraesCS3B01G251400 chr2D 97.049 915 25 1 1573 2485 547223938 547224852 0.000000e+00 1539
6 TraesCS3B01G251400 chr2D 97.574 742 16 2 2480 3220 547237067 547237807 0.000000e+00 1269
7 TraesCS3B01G251400 chr2D 76.729 1070 161 44 1018 2052 5327883 5326867 1.710000e-142 516
8 TraesCS3B01G251400 chr3A 95.682 1436 58 4 1593 3024 506237957 506236522 0.000000e+00 2305
9 TraesCS3B01G251400 chr3A 96.577 818 28 0 3 820 506239604 506238787 0.000000e+00 1356
10 TraesCS3B01G251400 chr3A 94.355 620 22 8 821 1440 506238559 506237953 0.000000e+00 939
11 TraesCS3B01G251400 chr6D 94.645 1438 52 5 1593 3025 27487992 27489409 0.000000e+00 2206
12 TraesCS3B01G251400 chr6D 94.756 820 31 1 1 820 27486342 27487149 0.000000e+00 1266
13 TraesCS3B01G251400 chr6D 96.469 623 22 0 818 1440 27487374 27487996 0.000000e+00 1029
14 TraesCS3B01G251400 chr5D 94.583 1440 55 7 1593 3025 554884929 554886352 0.000000e+00 2206
15 TraesCS3B01G251400 chr5D 94.878 820 30 1 1 820 554879488 554880295 0.000000e+00 1271
16 TraesCS3B01G251400 chr4D 96.878 1185 24 7 2039 3220 375716833 375718007 0.000000e+00 1971
17 TraesCS3B01G251400 chr4D 88.117 749 69 10 1028 1766 272555990 272555252 0.000000e+00 872
18 TraesCS3B01G251400 chr4D 88.448 554 51 8 1219 1766 272681829 272681283 0.000000e+00 656
19 TraesCS3B01G251400 chr6A 94.337 1236 46 3 1593 2804 521443836 521442601 0.000000e+00 1873
20 TraesCS3B01G251400 chr6A 95.366 820 32 1 1 820 521445480 521444667 0.000000e+00 1299
21 TraesCS3B01G251400 chr6A 94.222 623 24 6 821 1443 521444439 521443829 0.000000e+00 941
22 TraesCS3B01G251400 chr6A 85.497 724 81 12 69 786 390094114 390094819 0.000000e+00 734
23 TraesCS3B01G251400 chr7B 95.993 1123 44 1 2099 3220 683943732 683944854 0.000000e+00 1823
24 TraesCS3B01G251400 chr7B 96.341 820 30 0 1 820 683941524 683942343 0.000000e+00 1349
25 TraesCS3B01G251400 chr7B 95.185 623 18 7 818 1440 683942568 683943178 0.000000e+00 974
26 TraesCS3B01G251400 chr7B 95.464 507 23 0 1593 2099 683943174 683943680 0.000000e+00 809
27 TraesCS3B01G251400 chr3D 95.905 928 27 2 2099 3025 308776310 308775393 0.000000e+00 1493
28 TraesCS3B01G251400 chr3D 95.000 820 29 1 1 820 308778511 308777704 0.000000e+00 1277
29 TraesCS3B01G251400 chr3D 96.129 620 24 0 821 1440 308777476 308776857 0.000000e+00 1013
30 TraesCS3B01G251400 chr3D 93.809 533 26 4 1593 2119 308776861 308776330 0.000000e+00 795
31 TraesCS3B01G251400 chr1D 94.901 706 21 5 2516 3219 97779518 97778826 0.000000e+00 1090
32 TraesCS3B01G251400 chr6B 93.702 651 28 4 2572 3220 483508449 483507810 0.000000e+00 963
33 TraesCS3B01G251400 chr6B 85.714 952 91 21 1249 2188 522513967 522513049 0.000000e+00 963
34 TraesCS3B01G251400 chr5B 93.837 503 19 3 2720 3220 455276999 455277491 0.000000e+00 747
35 TraesCS3B01G251400 chr2A 85.457 722 74 21 931 1635 368956483 368957190 0.000000e+00 723
36 TraesCS3B01G251400 chr2A 77.747 1074 173 34 1018 2052 3966986 3965940 1.650000e-167 599


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 TraesCS3B01G251400 chr3B 402459556 402462775 3219 False 5947.000000 5947 100.000000 1 3220 1 chr3B.!!$F1 3219
1 TraesCS3B01G251400 chr3B 793270828 793274042 3214 True 5736.000000 5736 98.851000 1 3220 1 chr3B.!!$R1 3219
2 TraesCS3B01G251400 chr4A 615514847 615522036 7189 False 2810.000000 4052 98.215000 1 3220 2 chr4A.!!$F1 3219
3 TraesCS3B01G251400 chr2D 547217395 547218970 1575 False 2712.000000 2712 97.720000 1 1577 1 chr2D.!!$F1 1576
4 TraesCS3B01G251400 chr2D 547223938 547224852 914 False 1539.000000 1539 97.049000 1573 2485 1 chr2D.!!$F2 912
5 TraesCS3B01G251400 chr2D 547237067 547237807 740 False 1269.000000 1269 97.574000 2480 3220 1 chr2D.!!$F3 740
6 TraesCS3B01G251400 chr2D 5326867 5327883 1016 True 516.000000 516 76.729000 1018 2052 1 chr2D.!!$R1 1034
7 TraesCS3B01G251400 chr3A 506236522 506239604 3082 True 1533.333333 2305 95.538000 3 3024 3 chr3A.!!$R1 3021
8 TraesCS3B01G251400 chr6D 27486342 27489409 3067 False 1500.333333 2206 95.290000 1 3025 3 chr6D.!!$F1 3024
9 TraesCS3B01G251400 chr5D 554884929 554886352 1423 False 2206.000000 2206 94.583000 1593 3025 1 chr5D.!!$F2 1432
10 TraesCS3B01G251400 chr5D 554879488 554880295 807 False 1271.000000 1271 94.878000 1 820 1 chr5D.!!$F1 819
11 TraesCS3B01G251400 chr4D 375716833 375718007 1174 False 1971.000000 1971 96.878000 2039 3220 1 chr4D.!!$F1 1181
12 TraesCS3B01G251400 chr4D 272555252 272555990 738 True 872.000000 872 88.117000 1028 1766 1 chr4D.!!$R1 738
13 TraesCS3B01G251400 chr4D 272681283 272681829 546 True 656.000000 656 88.448000 1219 1766 1 chr4D.!!$R2 547
14 TraesCS3B01G251400 chr6A 521442601 521445480 2879 True 1371.000000 1873 94.641667 1 2804 3 chr6A.!!$R1 2803
15 TraesCS3B01G251400 chr6A 390094114 390094819 705 False 734.000000 734 85.497000 69 786 1 chr6A.!!$F1 717
16 TraesCS3B01G251400 chr7B 683941524 683944854 3330 False 1238.750000 1823 95.745750 1 3220 4 chr7B.!!$F1 3219
17 TraesCS3B01G251400 chr3D 308775393 308778511 3118 True 1144.500000 1493 95.210750 1 3025 4 chr3D.!!$R1 3024
18 TraesCS3B01G251400 chr1D 97778826 97779518 692 True 1090.000000 1090 94.901000 2516 3219 1 chr1D.!!$R1 703
19 TraesCS3B01G251400 chr6B 483507810 483508449 639 True 963.000000 963 93.702000 2572 3220 1 chr6B.!!$R1 648
20 TraesCS3B01G251400 chr6B 522513049 522513967 918 True 963.000000 963 85.714000 1249 2188 1 chr6B.!!$R2 939
21 TraesCS3B01G251400 chr2A 368956483 368957190 707 False 723.000000 723 85.457000 931 1635 1 chr2A.!!$F1 704
22 TraesCS3B01G251400 chr2A 3965940 3966986 1046 True 599.000000 599 77.747000 1018 2052 1 chr2A.!!$R1 1034

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
330 333 6.126863 TGATGTCTACACATTTCCCTCTTT 57.873 37.500 0.0 0.0 43.79 2.52 F
1494 5748 3.729108 TCTTCTGGGATGATGACTTCCT 58.271 45.455 0.0 0.0 39.41 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 5943 3.820467 TGTCGTTGCAGAAGAATGGAAAT 59.180 39.130 0.0 0.0 31.94 2.17 R
2561 6954 1.948611 GCAGGCTCAATAACCGTCCAA 60.949 52.381 0.0 0.0 0.00 3.53 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
245 247 7.355778 CCATTTAGTTGAGTTCAAGTTCAGAC 58.644 38.462 7.45 0.0 39.89 3.51
327 330 7.445121 TGATATGATGTCTACACATTTCCCTC 58.555 38.462 0.00 0.0 43.79 4.30
330 333 6.126863 TGATGTCTACACATTTCCCTCTTT 57.873 37.500 0.00 0.0 43.79 2.52
1494 5748 3.729108 TCTTCTGGGATGATGACTTCCT 58.271 45.455 0.00 0.0 39.41 3.36
1915 6193 3.380142 CTGTTTTTGTTCCATGTTCCCG 58.620 45.455 0.00 0.0 0.00 5.14
2474 6867 4.764050 TTCCAAGTAAGTGTTCACCTCA 57.236 40.909 0.00 0.0 0.00 3.86
2561 6954 7.884354 TGAGTATTTTGATAACGGGTTTAGGTT 59.116 33.333 0.00 0.0 0.00 3.50
3165 7574 6.584942 ACGGTTGTTTGTCTCTTTTTCTTTTC 59.415 34.615 0.00 0.0 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
245 247 3.256631 ACTGAACTAAAATGGCAGCCAAG 59.743 43.478 20.84 14.06 36.95 3.61
330 333 9.959749 GTCTGGAATTACATTACACAAAAAGAA 57.040 29.630 0.00 0.00 0.00 2.52
1677 5943 3.820467 TGTCGTTGCAGAAGAATGGAAAT 59.180 39.130 0.00 0.00 31.94 2.17
1915 6193 5.633996 TCACGTGATGAAAATTTGCAAAC 57.366 34.783 15.76 4.27 33.02 2.93
2561 6954 1.948611 GCAGGCTCAATAACCGTCCAA 60.949 52.381 0.00 0.00 0.00 3.53
3165 7574 5.039480 ACAGAGACAATTTCATTCGCAAG 57.961 39.130 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.