Multiple sequence alignment - TraesCS2A01G118500

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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 TraesCS2A01G118500 chr2A 100.000 3567 0 0 1 3567 69201673 69198107 0.000000 6588.0
1 TraesCS2A01G118500 chr2A 95.432 810 13 2 2778 3567 608888969 608888164 0.000000 1269.0
2 TraesCS2A01G118500 chr2A 96.600 647 2 1 2941 3567 738426247 738426893 0.000000 1055.0
3 TraesCS2A01G118500 chr2B 97.859 3597 41 10 1 3567 39425839 39429429 0.000000 6183.0
4 TraesCS2A01G118500 chr2B 95.804 1716 24 10 1895 3567 461104075 461105785 0.000000 2726.0
5 TraesCS2A01G118500 chr4A 97.829 3592 49 5 1 3567 446472546 446476133 0.000000 6174.0
6 TraesCS2A01G118500 chr4A 97.856 3591 43 5 1 3567 537233890 537230310 0.000000 6174.0
7 TraesCS2A01G118500 chr4A 97.447 3565 55 8 34 3567 152579841 152583400 0.000000 6047.0
8 TraesCS2A01G118500 chr4A 98.255 2980 39 3 1 2971 72015305 72018280 0.000000 5203.0
9 TraesCS2A01G118500 chr4A 100.000 32 0 0 2745 2776 72017924 72017955 0.000039 60.2
10 TraesCS2A01G118500 chr4A 100.000 32 0 0 2745 2776 152582433 152582464 0.000039 60.2
11 TraesCS2A01G118500 chr6B 97.853 3587 46 6 1 3567 663847347 663850922 0.000000 6168.0
12 TraesCS2A01G118500 chr3B 97.720 3597 46 10 1 3567 85118157 85114567 0.000000 6156.0
13 TraesCS2A01G118500 chr7A 97.586 3604 44 9 3 3567 105263516 105259917 0.000000 6133.0
14 TraesCS2A01G118500 chr7A 97.452 3610 44 9 1 3567 333071516 333075120 0.000000 6113.0
15 TraesCS2A01G118500 chr1A 97.738 3449 44 8 1 3419 58179341 58182785 0.000000 5906.0
16 TraesCS2A01G118500 chr7B 98.244 3189 48 3 34 3218 147534475 147537659 0.000000 5572.0
17 TraesCS2A01G118500 chr7B 95.946 814 9 7 2774 3567 580866380 580865571 0.000000 1299.0
18 TraesCS2A01G118500 chr7B 95.690 812 11 2 2774 3565 248271242 248270435 0.000000 1284.0
19 TraesCS2A01G118500 chr3A 96.635 1872 20 11 1733 3567 128146493 128144628 0.000000 3068.0
20 TraesCS2A01G118500 chr3A 93.243 814 9 11 2774 3567 604313001 604313788 0.000000 1157.0
21 TraesCS2A01G118500 chr5A 95.823 814 10 2 2774 3567 549966524 549967333 0.000000 1293.0
22 TraesCS2A01G118500 chr5A 95.455 814 12 6 2774 3567 76747513 76746705 0.000000 1275.0
23 TraesCS2A01G118500 chr5A 94.969 815 16 3 2774 3567 598312380 598311570 0.000000 1254.0
24 TraesCS2A01G118500 chrUn 95.332 814 14 2 2774 3567 304156105 304155296 0.000000 1271.0
25 TraesCS2A01G118500 chr5B 95.086 814 16 2 2774 3567 579533609 579534418 0.000000 1260.0
26 TraesCS2A01G118500 chr1B 94.717 814 16 3 2774 3567 500913614 500914420 0.000000 1240.0
27 TraesCS2A01G118500 chr4B 94.226 814 11 3 2774 3567 237021144 237020347 0.000000 1210.0


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 TraesCS2A01G118500 chr2A 69198107 69201673 3566 True 6588.0 6588 100.0000 1 3567 1 chr2A.!!$R1 3566
1 TraesCS2A01G118500 chr2A 608888164 608888969 805 True 1269.0 1269 95.4320 2778 3567 1 chr2A.!!$R2 789
2 TraesCS2A01G118500 chr2A 738426247 738426893 646 False 1055.0 1055 96.6000 2941 3567 1 chr2A.!!$F1 626
3 TraesCS2A01G118500 chr2B 39425839 39429429 3590 False 6183.0 6183 97.8590 1 3567 1 chr2B.!!$F1 3566
4 TraesCS2A01G118500 chr2B 461104075 461105785 1710 False 2726.0 2726 95.8040 1895 3567 1 chr2B.!!$F2 1672
5 TraesCS2A01G118500 chr4A 446472546 446476133 3587 False 6174.0 6174 97.8290 1 3567 1 chr4A.!!$F1 3566
6 TraesCS2A01G118500 chr4A 537230310 537233890 3580 True 6174.0 6174 97.8560 1 3567 1 chr4A.!!$R1 3566
7 TraesCS2A01G118500 chr4A 152579841 152583400 3559 False 3053.6 6047 98.7235 34 3567 2 chr4A.!!$F3 3533
8 TraesCS2A01G118500 chr4A 72015305 72018280 2975 False 2631.6 5203 99.1275 1 2971 2 chr4A.!!$F2 2970
9 TraesCS2A01G118500 chr6B 663847347 663850922 3575 False 6168.0 6168 97.8530 1 3567 1 chr6B.!!$F1 3566
10 TraesCS2A01G118500 chr3B 85114567 85118157 3590 True 6156.0 6156 97.7200 1 3567 1 chr3B.!!$R1 3566
11 TraesCS2A01G118500 chr7A 105259917 105263516 3599 True 6133.0 6133 97.5860 3 3567 1 chr7A.!!$R1 3564
12 TraesCS2A01G118500 chr7A 333071516 333075120 3604 False 6113.0 6113 97.4520 1 3567 1 chr7A.!!$F1 3566
13 TraesCS2A01G118500 chr1A 58179341 58182785 3444 False 5906.0 5906 97.7380 1 3419 1 chr1A.!!$F1 3418
14 TraesCS2A01G118500 chr7B 147534475 147537659 3184 False 5572.0 5572 98.2440 34 3218 1 chr7B.!!$F1 3184
15 TraesCS2A01G118500 chr7B 580865571 580866380 809 True 1299.0 1299 95.9460 2774 3567 1 chr7B.!!$R2 793
16 TraesCS2A01G118500 chr7B 248270435 248271242 807 True 1284.0 1284 95.6900 2774 3565 1 chr7B.!!$R1 791
17 TraesCS2A01G118500 chr3A 128144628 128146493 1865 True 3068.0 3068 96.6350 1733 3567 1 chr3A.!!$R1 1834
18 TraesCS2A01G118500 chr3A 604313001 604313788 787 False 1157.0 1157 93.2430 2774 3567 1 chr3A.!!$F1 793
19 TraesCS2A01G118500 chr5A 549966524 549967333 809 False 1293.0 1293 95.8230 2774 3567 1 chr5A.!!$F1 793
20 TraesCS2A01G118500 chr5A 76746705 76747513 808 True 1275.0 1275 95.4550 2774 3567 1 chr5A.!!$R1 793
21 TraesCS2A01G118500 chr5A 598311570 598312380 810 True 1254.0 1254 94.9690 2774 3567 1 chr5A.!!$R2 793
22 TraesCS2A01G118500 chrUn 304155296 304156105 809 True 1271.0 1271 95.3320 2774 3567 1 chrUn.!!$R1 793
23 TraesCS2A01G118500 chr5B 579533609 579534418 809 False 1260.0 1260 95.0860 2774 3567 1 chr5B.!!$F1 793
24 TraesCS2A01G118500 chr1B 500913614 500914420 806 False 1240.0 1240 94.7170 2774 3567 1 chr1B.!!$F1 793
25 TraesCS2A01G118500 chr4B 237020347 237021144 797 True 1210.0 1210 94.2260 2774 3567 1 chr4B.!!$R1 793

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
396 397 1.153086 GATTCTGATGGGTGGCGCT 60.153 57.895 7.64 0.0 0.00 5.92 F
693 703 1.631405 CAAATGGAGCTGGGGTTCAA 58.369 50.000 0.00 0.0 0.00 2.69 F
2151 2162 0.263468 TCACCATGAGGGGGACGATA 59.737 55.000 0.00 0.0 43.36 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 1347 2.345991 CGTGTCCACCCAATCCGT 59.654 61.111 0.00 0.0 0.0 4.69 R
2480 2557 1.066573 AGGATCCTCTTCGTGCACTTG 60.067 52.381 16.19 4.8 0.0 3.16 R
3376 3487 0.749649 CGTCAGAAGGAGAGGATGGG 59.250 60.000 0.00 0.0 0.0 4.00 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
76 77 8.995027 TTACATGCCCTAAGATTTGTCATTAT 57.005 30.769 0.00 0.0 0.00 1.28
278 279 2.284921 TGGAGGCCAGAGACCCAG 60.285 66.667 5.01 0.0 0.00 4.45
396 397 1.153086 GATTCTGATGGGTGGCGCT 60.153 57.895 7.64 0.0 0.00 5.92
693 703 1.631405 CAAATGGAGCTGGGGTTCAA 58.369 50.000 0.00 0.0 0.00 2.69
1337 1347 1.125093 TCTTTTCCAGCCTCACCCGA 61.125 55.000 0.00 0.0 0.00 5.14
1512 1522 4.439153 CCAAGCATCATTCTGCGTATGTTT 60.439 41.667 0.00 0.0 46.86 2.83
2151 2162 0.263468 TCACCATGAGGGGGACGATA 59.737 55.000 0.00 0.0 43.36 2.92
2451 2480 1.895707 GCTTGGATGATGAGGCGGG 60.896 63.158 0.00 0.0 0.00 6.13
2452 2481 1.228063 CTTGGATGATGAGGCGGGG 60.228 63.158 0.00 0.0 0.00 5.73
2453 2482 2.687418 CTTGGATGATGAGGCGGGGG 62.687 65.000 0.00 0.0 0.00 5.40
2454 2483 2.849162 GGATGATGAGGCGGGGGA 60.849 66.667 0.00 0.0 0.00 4.81
2455 2484 2.746359 GATGATGAGGCGGGGGAG 59.254 66.667 0.00 0.0 0.00 4.30
2456 2485 2.851102 ATGATGAGGCGGGGGAGG 60.851 66.667 0.00 0.0 0.00 4.30
2809 2886 9.013490 CAGTATTTTTATTATGTGAGTGCTTGC 57.987 33.333 0.00 0.0 0.00 4.01
2810 2887 8.960591 AGTATTTTTATTATGTGAGTGCTTGCT 58.039 29.630 0.00 0.0 0.00 3.91
2907 2985 0.460284 GCACTATACTGTGTGGCGCT 60.460 55.000 7.64 0.0 39.89 5.92
2968 3054 0.895530 TTAGGCGCTGCACTACTTCT 59.104 50.000 7.64 0.0 0.00 2.85
3376 3487 0.458716 CTCCTCTCGTTTCTTCCGCC 60.459 60.000 0.00 0.0 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 226 0.531974 GACACCAGTGGAGCGTTCAA 60.532 55.000 18.40 0.00 34.19 2.69
278 279 1.641577 CGGTCCGAAGATGGAAACTC 58.358 55.000 4.91 0.00 40.44 3.01
693 703 2.230750 GGTACAAGTAGGCAAGAGTCGT 59.769 50.000 0.00 0.00 0.00 4.34
1337 1347 2.345991 CGTGTCCACCCAATCCGT 59.654 61.111 0.00 0.00 0.00 4.69
2480 2557 1.066573 AGGATCCTCTTCGTGCACTTG 60.067 52.381 16.19 4.80 0.00 3.16
2809 2886 1.255667 ATTTTGGCCTCCTGCAGCAG 61.256 55.000 16.23 16.23 43.89 4.24
2810 2887 1.228956 ATTTTGGCCTCCTGCAGCA 60.229 52.632 8.66 0.00 43.89 4.41
2907 2985 2.198969 TGCAGCGCCCAATTGTTGA 61.199 52.632 2.29 0.00 0.00 3.18
2968 3054 1.957177 GTGGCTCTCTGGATCGTCATA 59.043 52.381 0.00 0.00 0.00 2.15
3376 3487 0.749649 CGTCAGAAGGAGAGGATGGG 59.250 60.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.