Multiple sequence alignment - TraesCS2D01G002700

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 TraesCS2D01G002700 chr2D 100.000 2297 0 0 1 2297 2114323 2116619 0.000000e+00 4242.0
1 TraesCS2D01G002700 chr2D 92.590 1471 95 9 3 1460 2694375 2692906 0.000000e+00 2100.0
2 TraesCS2D01G002700 chr2A 96.716 1340 44 0 121 1460 2151272 2152611 0.000000e+00 2231.0
3 TraesCS2D01G002700 chr2A 96.649 1343 42 1 121 1460 2057943 2059285 0.000000e+00 2228.0
4 TraesCS2D01G002700 chr2A 97.234 976 27 0 121 1096 2020965 2021940 0.000000e+00 1653.0
5 TraesCS2D01G002700 chr2A 97.234 976 27 0 121 1096 2113062 2114037 0.000000e+00 1653.0
6 TraesCS2D01G002700 chr2A 96.707 577 19 0 319 895 1983526 1984102 0.000000e+00 961.0
7 TraesCS2D01G002700 chr2A 97.227 541 14 1 1460 2000 2152668 2153207 0.000000e+00 915.0
8 TraesCS2D01G002700 chr2A 98.400 250 3 1 1460 1709 2059342 2059590 2.710000e-119 438.0
9 TraesCS2D01G002700 chr2A 98.113 212 4 0 1789 2000 2114034 2114245 1.000000e-98 370.0
10 TraesCS2D01G002700 chr2A 97.170 212 5 1 1789 2000 2021937 2022147 7.800000e-95 357.0
11 TraesCS2D01G002700 chr2A 100.000 128 0 0 1 128 1981017 1981144 1.060000e-58 237.0
12 TraesCS2D01G002700 chr2A 100.000 128 0 0 1 128 2019067 2019194 1.060000e-58 237.0
13 TraesCS2D01G002700 chr2A 100.000 128 0 0 1 128 2056045 2056172 1.060000e-58 237.0
14 TraesCS2D01G002700 chr2A 100.000 128 0 0 1 128 2111163 2111290 1.060000e-58 237.0
15 TraesCS2D01G002700 chr2A 100.000 128 0 0 1 128 2149371 2149498 1.060000e-58 237.0
16 TraesCS2D01G002700 chrUn 97.234 976 27 0 121 1096 239592981 239593956 0.000000e+00 1653.0
17 TraesCS2D01G002700 chrUn 96.698 212 6 1 1789 2000 239593953 239594163 3.630000e-93 351.0
18 TraesCS2D01G002700 chrUn 100.000 128 0 0 1 128 239591083 239591210 1.060000e-58 237.0
19 TraesCS2D01G002700 chr2B 91.188 522 41 4 669 1186 31064162 31064682 0.000000e+00 704.0
20 TraesCS2D01G002700 chr2B 82.724 301 41 9 104 401 31061698 31061990 8.140000e-65 257.0
21 TraesCS2D01G002700 chr2B 90.361 166 16 0 1295 1460 31071754 31071919 3.840000e-53 219.0
22 TraesCS2D01G002700 chr2B 93.043 115 4 2 1182 1296 31071483 31071593 5.080000e-37 165.0
23 TraesCS2D01G002700 chr7D 88.514 592 51 10 871 1460 53775851 53776427 0.000000e+00 701.0
24 TraesCS2D01G002700 chr7D 88.596 228 26 0 1460 1687 53776482 53776709 6.250000e-71 278.0
25 TraesCS2D01G002700 chr7D 94.340 53 2 1 393 444 53752937 53752989 1.890000e-11 80.5
26 TraesCS2D01G002700 chr1B 86.552 580 64 8 1724 2296 666810421 666809849 5.390000e-176 627.0
27 TraesCS2D01G002700 chr6D 85.665 579 76 6 1724 2296 49271526 49270949 9.080000e-169 603.0
28 TraesCS2D01G002700 chr5A 85.391 575 77 6 1724 2292 695741200 695740627 7.070000e-165 590.0
29 TraesCS2D01G002700 chr4A 87.371 483 52 5 820 1301 669646149 669645675 1.550000e-151 545.0
30 TraesCS2D01G002700 chr4A 85.426 446 52 8 397 832 669648380 669647938 3.480000e-123 451.0
31 TraesCS2D01G002700 chr4A 86.842 228 29 1 1460 1687 669644827 669644601 1.050000e-63 254.0
32 TraesCS2D01G002700 chr3B 82.729 579 93 4 1724 2296 104745325 104745902 2.040000e-140 508.0
33 TraesCS2D01G002700 chr6B 82.765 528 83 5 1775 2296 469068905 469069430 4.470000e-127 464.0
34 TraesCS2D01G002700 chr1A 86.047 258 35 1 2040 2296 535238742 535238999 2.250000e-70 276.0
35 TraesCS2D01G002700 chr7A 92.308 65 4 1 1185 1249 57206403 57206466 8.740000e-15 91.6


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 TraesCS2D01G002700 chr2D 2114323 2116619 2296 False 4242.000000 4242 100.000000 1 2297 1 chr2D.!!$F1 2296
1 TraesCS2D01G002700 chr2D 2692906 2694375 1469 True 2100.000000 2100 92.590000 3 1460 1 chr2D.!!$R1 1457
2 TraesCS2D01G002700 chr2A 2149371 2153207 3836 False 1127.666667 2231 97.981000 1 2000 3 chr2A.!!$F5 1999
3 TraesCS2D01G002700 chr2A 2056045 2059590 3545 False 967.666667 2228 98.349667 1 1709 3 chr2A.!!$F3 1708
4 TraesCS2D01G002700 chr2A 2111163 2114245 3082 False 753.333333 1653 98.449000 1 2000 3 chr2A.!!$F4 1999
5 TraesCS2D01G002700 chr2A 2019067 2022147 3080 False 749.000000 1653 98.134667 1 2000 3 chr2A.!!$F2 1999
6 TraesCS2D01G002700 chr2A 1981017 1984102 3085 False 599.000000 961 98.353500 1 895 2 chr2A.!!$F1 894
7 TraesCS2D01G002700 chrUn 239591083 239594163 3080 False 747.000000 1653 97.977333 1 2000 3 chrUn.!!$F1 1999
8 TraesCS2D01G002700 chr2B 31061698 31064682 2984 False 480.500000 704 86.956000 104 1186 2 chr2B.!!$F1 1082
9 TraesCS2D01G002700 chr7D 53775851 53776709 858 False 489.500000 701 88.555000 871 1687 2 chr7D.!!$F2 816
10 TraesCS2D01G002700 chr1B 666809849 666810421 572 True 627.000000 627 86.552000 1724 2296 1 chr1B.!!$R1 572
11 TraesCS2D01G002700 chr6D 49270949 49271526 577 True 603.000000 603 85.665000 1724 2296 1 chr6D.!!$R1 572
12 TraesCS2D01G002700 chr5A 695740627 695741200 573 True 590.000000 590 85.391000 1724 2292 1 chr5A.!!$R1 568
13 TraesCS2D01G002700 chr4A 669644601 669648380 3779 True 416.666667 545 86.546333 397 1687 3 chr4A.!!$R1 1290
14 TraesCS2D01G002700 chr3B 104745325 104745902 577 False 508.000000 508 82.729000 1724 2296 1 chr3B.!!$F1 572
15 TraesCS2D01G002700 chr6B 469068905 469069430 525 False 464.000000 464 82.765000 1775 2296 1 chr6B.!!$F1 521

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
391 2586 0.320374 TGTCGTCGGGAAAGCATCTT 59.68 50.0 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 8411 0.250597 AGTAGTGTTGGCCCGGTTTC 60.251 55.0 0.0 0.0 0.0 2.78 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
128 1911 1.074296 GGCCCCATCCTCCCCTAAAT 61.074 60.000 0.00 0.00 0.00 1.40
391 2586 0.320374 TGTCGTCGGGAAAGCATCTT 59.680 50.000 0.00 0.00 0.00 2.40
873 6846 4.147701 CCAAGATTGGGCGCCTAG 57.852 61.111 28.56 7.81 44.70 3.02
1065 7039 1.893808 CGCCAGTGAGCACAAGGTT 60.894 57.895 11.87 0.00 33.19 3.50
1121 7095 6.718912 TCGATGATAGAAGATGAGTGGAAGAT 59.281 38.462 0.00 0.00 0.00 2.40
1125 7099 6.608808 TGATAGAAGATGAGTGGAAGATCACA 59.391 38.462 0.00 0.00 39.93 3.58
1624 8290 5.359756 TCATATGTGACTCGGATTTTCAGG 58.640 41.667 1.90 0.00 0.00 3.86
1695 8361 7.724287 TCATCAGTTGATTGTTTTTCAATGGA 58.276 30.769 0.00 0.00 45.49 3.41
1745 8411 2.031012 TGCGCTGTTCTCCCACTG 59.969 61.111 9.73 0.00 0.00 3.66
1892 8558 2.507339 AAACGTGAATTTGCAGGTGG 57.493 45.000 0.00 0.00 37.02 4.61
1991 8662 3.884774 GCCATCACCCCGGCCATA 61.885 66.667 2.24 0.00 42.82 2.74
2021 8692 2.331893 CGCCCCGAACAAATGCAGA 61.332 57.895 0.00 0.00 0.00 4.26
2022 8693 1.508088 GCCCCGAACAAATGCAGAG 59.492 57.895 0.00 0.00 0.00 3.35
2027 8698 2.554032 CCCGAACAAATGCAGAGTCTTT 59.446 45.455 0.00 0.00 0.00 2.52
2054 8725 1.733402 TTGCCAACAAAGACCGCCTG 61.733 55.000 0.00 0.00 31.21 4.85
2066 8737 1.096386 ACCGCCTGTTTACAAACGCA 61.096 50.000 0.74 0.00 41.74 5.24
2089 8760 1.270147 GCGCTTCCGGTGAGGTATTAT 60.270 52.381 0.00 0.00 41.99 1.28
2097 8768 5.210430 TCCGGTGAGGTATTATTACTTCCA 58.790 41.667 0.00 0.00 41.99 3.53
2098 8769 5.069516 TCCGGTGAGGTATTATTACTTCCAC 59.930 44.000 0.00 0.00 41.99 4.02
2114 8785 2.526873 ACCGCCTGTCCCTTCTGT 60.527 61.111 0.00 0.00 0.00 3.41
2258 8929 3.809832 ACTTCACCAACAAGACAAGATCG 59.190 43.478 0.00 0.00 0.00 3.69
2262 8933 4.279922 TCACCAACAAGACAAGATCGACTA 59.720 41.667 0.00 0.00 0.00 2.59
2296 8968 4.040047 TCCTCTGGAATATTTGGCAGAGA 58.960 43.478 1.80 0.00 38.63 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 1911 5.010719 ACTCAAAAACTCATCGAGTACCTCA 59.989 40.000 0.00 0.0 42.59 3.86
499 2832 3.181487 ACGAATTAACAGCCAATCCATGC 60.181 43.478 0.00 0.0 0.00 4.06
873 6846 1.881973 TGAAGCAGCAAGGTCATTCAC 59.118 47.619 0.00 0.0 0.00 3.18
1065 7039 0.895530 CAAAGGCGACCTCCTCTGTA 59.104 55.000 0.00 0.0 34.82 2.74
1121 7095 2.844946 TGAATCGAGCTTGGTTTGTGA 58.155 42.857 0.00 0.0 0.00 3.58
1125 7099 4.549458 CATGTTTGAATCGAGCTTGGTTT 58.451 39.130 0.00 0.0 0.00 3.27
1175 7150 3.306641 GCTGAGAGTGAAGTTGATGACCT 60.307 47.826 0.00 0.0 0.00 3.85
1624 8290 5.296035 GCTTACATATTGTACCAACCAGTCC 59.704 44.000 0.00 0.0 31.69 3.85
1745 8411 0.250597 AGTAGTGTTGGCCCGGTTTC 60.251 55.000 0.00 0.0 0.00 2.78
1892 8558 1.534595 CCTTGAAGTTCTGCAGTCAGC 59.465 52.381 14.67 0.0 45.96 4.26
1991 8662 0.974010 TCGGGGCGTAGTTTCTCCAT 60.974 55.000 0.00 0.0 0.00 3.41
2066 8737 4.394712 CCTCACCGGAAGCGCCTT 62.395 66.667 9.46 0.0 33.16 4.35
2079 8750 4.202284 GGCGGTGGAAGTAATAATACCTCA 60.202 45.833 0.00 0.0 32.08 3.86
2089 8760 1.675219 GGACAGGCGGTGGAAGTAA 59.325 57.895 0.00 0.0 0.00 2.24
2097 8768 1.229082 TACAGAAGGGACAGGCGGT 60.229 57.895 0.00 0.0 0.00 5.68
2098 8769 1.218316 GTACAGAAGGGACAGGCGG 59.782 63.158 0.00 0.0 0.00 6.13
2258 8929 2.625790 AGAGGACGCCATGAGAATAGTC 59.374 50.000 0.00 0.0 0.00 2.59
2262 8933 0.467384 CCAGAGGACGCCATGAGAAT 59.533 55.000 0.00 0.0 0.00 2.40


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

AutoCloner maintained by Alex Coulton.