Multiple sequence alignment - TraesCS5A01G080200

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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 TraesCS5A01G080200 chr5A 100.000 2822 0 0 1 2822 100350420 100347599 0.000000e+00 5212
1 TraesCS5A01G080200 chr5A 96.989 2823 65 5 1 2822 663200070 663202873 0.000000e+00 4724
2 TraesCS5A01G080200 chr5A 94.595 185 8 1 2640 2822 473851675 473851491 4.600000e-73 285
3 TraesCS5A01G080200 chr7A 97.417 2826 68 3 1 2822 21044141 21041317 0.000000e+00 4809
4 TraesCS5A01G080200 chr7A 96.389 2825 69 5 1 2822 688928649 688931443 0.000000e+00 4621
5 TraesCS5A01G080200 chr1A 97.131 2823 67 6 1 2822 577613554 577610745 0.000000e+00 4752
6 TraesCS5A01G080200 chr3A 96.953 2822 70 4 2 2822 714222436 714225242 0.000000e+00 4721
7 TraesCS5A01G080200 chr3B 96.670 2823 75 6 1 2822 778356450 778353646 0.000000e+00 4674
8 TraesCS5A01G080200 chr3B 95.000 340 17 0 2 341 62349511 62349850 4.140000e-148 534
9 TraesCS5A01G080200 chr6A 96.387 2823 76 7 1 2822 562226311 562223514 0.000000e+00 4625
10 TraesCS5A01G080200 chr6A 94.762 210 7 1 2617 2822 128937973 128937764 9.750000e-85 324
11 TraesCS5A01G080200 chrUn 96.419 2262 67 3 562 2822 308012124 308009876 0.000000e+00 3716
12 TraesCS5A01G080200 chrUn 96.419 2262 67 3 562 2822 308106821 308109069 0.000000e+00 3716
13 TraesCS5A01G080200 chrUn 96.419 2262 67 3 562 2822 323644452 323646700 0.000000e+00 3716
14 TraesCS5A01G080200 chr2B 94.721 341 18 0 1 341 681388381 681388721 5.350000e-147 531
15 TraesCS5A01G080200 chr2A 88.976 381 17 13 402 765 544285812 544286184 5.550000e-122 448
16 TraesCS5A01G080200 chr5B 95.175 228 8 1 2598 2822 187563348 187563121 9.610000e-95 357
17 TraesCS5A01G080200 chr7D 93.204 206 13 1 2617 2822 569309464 569309668 4.570000e-78 302
18 TraesCS5A01G080200 chr6D 93.171 205 13 1 2617 2821 367270334 367270131 1.640000e-77 300
19 TraesCS5A01G080200 chr4A 98.246 171 3 0 2652 2822 696219824 696219994 1.640000e-77 300


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 TraesCS5A01G080200 chr5A 100347599 100350420 2821 True 5212 5212 100.000 1 2822 1 chr5A.!!$R1 2821
1 TraesCS5A01G080200 chr5A 663200070 663202873 2803 False 4724 4724 96.989 1 2822 1 chr5A.!!$F1 2821
2 TraesCS5A01G080200 chr7A 21041317 21044141 2824 True 4809 4809 97.417 1 2822 1 chr7A.!!$R1 2821
3 TraesCS5A01G080200 chr7A 688928649 688931443 2794 False 4621 4621 96.389 1 2822 1 chr7A.!!$F1 2821
4 TraesCS5A01G080200 chr1A 577610745 577613554 2809 True 4752 4752 97.131 1 2822 1 chr1A.!!$R1 2821
5 TraesCS5A01G080200 chr3A 714222436 714225242 2806 False 4721 4721 96.953 2 2822 1 chr3A.!!$F1 2820
6 TraesCS5A01G080200 chr3B 778353646 778356450 2804 True 4674 4674 96.670 1 2822 1 chr3B.!!$R1 2821
7 TraesCS5A01G080200 chr6A 562223514 562226311 2797 True 4625 4625 96.387 1 2822 1 chr6A.!!$R2 2821
8 TraesCS5A01G080200 chrUn 308009876 308012124 2248 True 3716 3716 96.419 562 2822 1 chrUn.!!$R1 2260
9 TraesCS5A01G080200 chrUn 308106821 308109069 2248 False 3716 3716 96.419 562 2822 1 chrUn.!!$F1 2260
10 TraesCS5A01G080200 chrUn 323644452 323646700 2248 False 3716 3716 96.419 562 2822 1 chrUn.!!$F2 2260

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
162 163 1.41271 GATGGACTATGTCGCCAAGGA 59.587 52.381 0.0 0.0 34.95 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 2050 1.59431 GAGGTGTGAGCTCTGGACC 59.406 63.158 16.19 16.71 39.5 4.46 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
26 27 2.126850 CGTCGTTCGAGCAGCTCA 60.127 61.111 22.49 6.83 42.86 4.26
162 163 1.412710 GATGGACTATGTCGCCAAGGA 59.587 52.381 0.00 0.00 34.95 3.36
292 295 4.310022 TCCCGGGACATTGATTTAGTTT 57.690 40.909 22.63 0.00 0.00 2.66
551 554 7.119846 GGACTGCTATTTCTTTTCTTGCTTCTA 59.880 37.037 0.00 0.00 0.00 2.10
1188 1193 3.906218 TGCCAGCTTATGACCAGATATCT 59.094 43.478 0.00 0.00 0.00 1.98
1306 1311 1.836802 GGAGGAGTGAAGAAGCCTCAT 59.163 52.381 0.00 0.00 46.84 2.90
1325 1330 0.611618 TCGTTACCGCCCTGGAACTA 60.612 55.000 0.00 0.00 42.00 2.24
1443 1448 1.404181 GCAGTGAGATCCGCAAGTACA 60.404 52.381 0.00 0.00 0.00 2.90
1497 1502 2.025887 CCATTCCAGAGGCTTGTTAGGT 60.026 50.000 0.00 0.00 0.00 3.08
1578 1583 9.470399 TCCTGTTGTGTCAACTCTTATAGTATA 57.530 33.333 12.66 0.00 37.50 1.47
1705 1710 1.196012 GGTGGGTCTCTTCGAGGATT 58.804 55.000 0.00 0.00 0.00 3.01
1756 1761 1.279496 CCTGTGGGAATGTCTCTGGA 58.721 55.000 0.00 0.00 33.58 3.86
1765 1770 1.890552 ATGTCTCTGGAGGGCATCTT 58.109 50.000 0.00 0.00 0.00 2.40
1777 1782 2.560105 AGGGCATCTTTGTCTGCTTTTC 59.440 45.455 0.00 0.00 38.45 2.29
1826 1831 9.549078 GGAACTGCTAGCTCTAATTTAACTTAT 57.451 33.333 17.23 0.00 0.00 1.73
2017 2022 5.532032 TGATGATGATGCACGTATTTGGAAT 59.468 36.000 0.00 0.00 0.00 3.01
2045 2050 5.124457 CCAGTCCATTCTCACAACCAATTAG 59.876 44.000 0.00 0.00 0.00 1.73
2211 2217 0.976641 TGCCGATTCCTGACTCTGTT 59.023 50.000 0.00 0.00 0.00 3.16
2230 2236 5.941058 TCTGTTTGTCTGTTTTGGAACTGTA 59.059 36.000 0.00 0.00 36.70 2.74
2423 2429 2.907910 CAGTACATCTGCTGTTTGCC 57.092 50.000 0.00 0.00 42.00 4.52
2635 2641 9.219603 TCTTACATTCCAAACTTGATCTTACTG 57.780 33.333 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.429236 CTGCTCGAACGACGCACT 60.429 61.111 13.73 0.00 42.26 4.40
292 295 2.575532 CCAAACCTCTCAGCTTCACAA 58.424 47.619 0.00 0.00 0.00 3.33
551 554 6.949715 ACCATGATCACCTAATTTTGCAAAT 58.050 32.000 13.65 1.10 0.00 2.32
831 835 3.461085 AGTCCCAACAATCATCAGCCTAT 59.539 43.478 0.00 0.00 0.00 2.57
958 962 7.396540 ACCTGAAGCAAAAATAGAACATAGG 57.603 36.000 0.00 0.00 0.00 2.57
1139 1144 7.466804 TGAAGGTTGAGGTTCAAATTATACCT 58.533 34.615 5.92 5.92 44.75 3.08
1188 1193 9.547279 ACCATGATAGTCCATATACATCAGTAA 57.453 33.333 0.00 0.00 33.13 2.24
1229 1234 3.146104 AGCAAAGTAGAGCACATGGTT 57.854 42.857 0.00 0.00 0.00 3.67
1325 1330 5.003804 AGATTTTACACACCGAAGAGCAAT 58.996 37.500 0.00 0.00 0.00 3.56
1390 1395 8.579682 AGCACAAAATTTACTCATTTGAGAAC 57.420 30.769 14.29 0.00 44.74 3.01
1497 1502 2.239654 CCTTGAAGTCCTGGGCAATCTA 59.760 50.000 0.00 0.00 0.00 1.98
1578 1583 8.637986 TGGTGCTTTTAGTTTACTTGATTCATT 58.362 29.630 0.00 0.00 0.00 2.57
1705 1710 1.945354 CTTAAGCCCTCTCGCCACGA 61.945 60.000 0.00 0.00 0.00 4.35
1756 1761 2.299326 AAAGCAGACAAAGATGCCCT 57.701 45.000 0.00 0.00 43.60 5.19
1765 1770 2.057137 ACAGCAGGAAAAGCAGACAA 57.943 45.000 0.00 0.00 0.00 3.18
1777 1782 5.463061 CCAAACAATCACTAAAAACAGCAGG 59.537 40.000 0.00 0.00 0.00 4.85
1826 1831 3.263425 AGCAGAAATAGGGGAACGAGAAA 59.737 43.478 0.00 0.00 0.00 2.52
2017 2022 3.260884 GGTTGTGAGAATGGACTGGACTA 59.739 47.826 0.00 0.00 0.00 2.59
2045 2050 1.594310 GAGGTGTGAGCTCTGGACC 59.406 63.158 16.19 16.71 39.50 4.46
2211 2217 7.064016 GCATTTTTACAGTTCCAAAACAGACAA 59.936 33.333 0.00 0.00 37.88 3.18


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

AutoCloner maintained by Alex Coulton.