Multiple sequence alignment - TraesCS5B01G365200

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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 TraesCS5B01G365200 chr5B 100.000 2489 0 0 1 2489 544187296 544184808 0 4597
1 TraesCS5B01G365200 chr5B 95.738 610 24 2 1881 2488 544193736 544193127 0 981
2 TraesCS5B01G365200 chr5B 95.818 550 17 4 1939 2488 544195080 544194537 0 883
3 TraesCS5B01G365200 chr1D 92.222 2507 159 18 1 2485 33122462 33124954 0 3517
4 TraesCS5B01G365200 chr1D 90.988 2519 180 19 1 2489 437994289 437996790 0 3350
5 TraesCS5B01G365200 chr1D 93.165 2297 112 21 1 2270 116466587 116468865 0 3330
6 TraesCS5B01G365200 chr1D 91.420 1317 80 13 1193 2489 33198406 33197103 0 1775
7 TraesCS5B01G365200 chr1D 92.797 597 25 7 1902 2486 33170094 33169504 0 848
8 TraesCS5B01G365200 chr1D 94.926 473 21 3 2017 2488 33111438 33110968 0 737
9 TraesCS5B01G365200 chr1D 91.860 516 34 6 1978 2488 437998607 437999119 0 713
10 TraesCS5B01G365200 chr1D 90.476 546 38 6 1947 2480 437981634 437982177 0 708
11 TraesCS5B01G365200 chr7D 92.830 2329 122 18 1 2304 558325758 558328066 0 3334
12 TraesCS5B01G365200 chr3B 93.363 2260 112 30 1 2229 808050649 808048397 0 3308
13 TraesCS5B01G365200 chr6D 91.828 2325 141 24 1 2304 19452587 19454883 0 3195
14 TraesCS5B01G365200 chr6D 91.626 2233 147 22 17 2229 349550197 349552409 0 3051
15 TraesCS5B01G365200 chr2D 91.246 2319 159 19 1 2301 38586489 38588781 0 3118
16 TraesCS5B01G365200 chr2D 90.780 2321 168 22 1 2304 38597771 38600062 0 3059
17 TraesCS5B01G365200 chr2D 93.885 1995 107 9 1 1984 536412 534422 0 2994
18 TraesCS5B01G365200 chrUn 92.836 1996 127 10 1 1983 257734169 257736161 0 2880


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 TraesCS5B01G365200 chr5B 544184808 544187296 2488 True 4597.0 4597 100.000 1 2489 1 chr5B.!!$R1 2488
1 TraesCS5B01G365200 chr5B 544193127 544195080 1953 True 932.0 981 95.778 1881 2488 2 chr5B.!!$R2 607
2 TraesCS5B01G365200 chr1D 33122462 33124954 2492 False 3517.0 3517 92.222 1 2485 1 chr1D.!!$F1 2484
3 TraesCS5B01G365200 chr1D 116466587 116468865 2278 False 3330.0 3330 93.165 1 2270 1 chr1D.!!$F2 2269
4 TraesCS5B01G365200 chr1D 437994289 437999119 4830 False 2031.5 3350 91.424 1 2489 2 chr1D.!!$F4 2488
5 TraesCS5B01G365200 chr1D 33197103 33198406 1303 True 1775.0 1775 91.420 1193 2489 1 chr1D.!!$R3 1296
6 TraesCS5B01G365200 chr1D 33169504 33170094 590 True 848.0 848 92.797 1902 2486 1 chr1D.!!$R2 584
7 TraesCS5B01G365200 chr1D 437981634 437982177 543 False 708.0 708 90.476 1947 2480 1 chr1D.!!$F3 533
8 TraesCS5B01G365200 chr7D 558325758 558328066 2308 False 3334.0 3334 92.830 1 2304 1 chr7D.!!$F1 2303
9 TraesCS5B01G365200 chr3B 808048397 808050649 2252 True 3308.0 3308 93.363 1 2229 1 chr3B.!!$R1 2228
10 TraesCS5B01G365200 chr6D 19452587 19454883 2296 False 3195.0 3195 91.828 1 2304 1 chr6D.!!$F1 2303
11 TraesCS5B01G365200 chr6D 349550197 349552409 2212 False 3051.0 3051 91.626 17 2229 1 chr6D.!!$F2 2212
12 TraesCS5B01G365200 chr2D 38586489 38588781 2292 False 3118.0 3118 91.246 1 2301 1 chr2D.!!$F1 2300
13 TraesCS5B01G365200 chr2D 38597771 38600062 2291 False 3059.0 3059 90.780 1 2304 1 chr2D.!!$F2 2303
14 TraesCS5B01G365200 chr2D 534422 536412 1990 True 2994.0 2994 93.885 1 1984 1 chr2D.!!$R1 1983
15 TraesCS5B01G365200 chrUn 257734169 257736161 1992 False 2880.0 2880 92.836 1 1983 1 chrUn.!!$F1 1982

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
233 234 3.569701 GCCCATCTTGAAGTGTTCTTTCA 59.43 43.478 0.0 0.0 33.64 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 4586 1.035139 GTGGATAATTGGCTGGCCTG 58.965 55.0 13.05 4.26 36.94 4.85 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
233 234 3.569701 GCCCATCTTGAAGTGTTCTTTCA 59.430 43.478 0.00 0.00 33.64 2.69
489 491 9.284968 GCAGGACCTTTATATGCTAAATTAAGA 57.715 33.333 0.00 0.00 34.10 2.10
635 638 4.285517 CAGATGCATCTAAGGTAGGATGGT 59.714 45.833 28.27 0.00 39.52 3.55
727 732 8.349983 GCTTCAGGAAGTTACAAATTAAAGACA 58.650 33.333 10.47 0.00 40.45 3.41
1125 1131 5.049543 GGCTCATATCAAGCTTGATGAAGTC 60.050 44.000 39.83 31.08 46.68 3.01
1168 1174 7.510549 AATTTCTGGTTCCAATATACCATCG 57.489 36.000 0.00 0.00 43.15 3.84
1497 1506 5.788450 ACTATATCCAAATGAGAAGAGGCG 58.212 41.667 0.00 0.00 0.00 5.52
1516 1525 1.000955 CGTACCTGCTTCACCAACTCT 59.999 52.381 0.00 0.00 0.00 3.24
1544 1553 0.813821 GGGAGGCATGAAGCTCAAAC 59.186 55.000 0.00 0.00 44.79 2.93
1553 1562 7.839907 AGGCATGAAGCTCAAACAATATAAAA 58.160 30.769 0.00 0.00 44.79 1.52
1644 1655 8.834465 ACAGTGAATACATAGATCAAGAAATGC 58.166 33.333 0.00 0.00 0.00 3.56
1900 1927 4.465305 CGGAGGACCTATACCCGAATATTT 59.535 45.833 12.89 0.00 42.49 1.40
1968 1996 6.633325 ATCAATCATATGGGTAGGGAAGAG 57.367 41.667 2.13 0.00 0.00 2.85
2152 4573 1.009829 CTGTATGGCCGAAGAGCAAC 58.990 55.000 0.00 0.00 0.00 4.17
2157 4578 1.214589 GGCCGAAGAGCAACGACTA 59.785 57.895 0.00 0.00 0.00 2.59
2161 4582 2.223525 GCCGAAGAGCAACGACTAGTAT 60.224 50.000 0.00 0.00 0.00 2.12
2165 4586 4.962751 CGAAGAGCAACGACTAGTATACAC 59.037 45.833 5.50 0.00 0.00 2.90
2406 4829 2.868044 GCGAAGAGAGACACAACACCAT 60.868 50.000 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 234 4.898861 TGAGCCCATTTTGTTCTACCTTTT 59.101 37.500 0.00 0.00 0.00 2.27
298 300 6.830324 TCTCCTATTTCATGACCAAGGAAATG 59.170 38.462 16.14 8.33 40.41 2.32
635 638 4.320641 GGGCTTTTGTTTTAGTATCGCACA 60.321 41.667 0.00 0.00 0.00 4.57
1125 1131 4.771590 ATTATCCAATATGCAGCGTTGG 57.228 40.909 17.09 17.09 42.91 3.77
1497 1506 2.037251 TGAGAGTTGGTGAAGCAGGTAC 59.963 50.000 0.00 0.00 0.00 3.34
1516 1525 1.139498 TCATGCCTCCCCCTTTGTGA 61.139 55.000 0.00 0.00 0.00 3.58
1794 1812 4.410099 CCATGCCCTGTTATGTCCATATT 58.590 43.478 0.00 0.00 0.00 1.28
1806 1828 4.753662 CTGCTGCCCATGCCCTGT 62.754 66.667 0.00 0.00 36.33 4.00
1941 1969 9.127560 TCTTCCCTACCCATATGATTGATAATT 57.872 33.333 3.65 0.00 0.00 1.40
2152 4573 2.287668 GCTGGCCTGTGTATACTAGTCG 60.288 54.545 11.69 0.00 0.00 4.18
2157 4578 1.285280 TTGGCTGGCCTGTGTATACT 58.715 50.000 11.69 0.00 36.94 2.12
2161 4582 2.422803 GGATAATTGGCTGGCCTGTGTA 60.423 50.000 11.69 1.10 36.94 2.90
2165 4586 1.035139 GTGGATAATTGGCTGGCCTG 58.965 55.000 13.05 4.26 36.94 4.85
2406 4829 1.605058 GCTGGTGGCTCTTCTCCGTA 61.605 60.000 0.00 0.00 38.06 4.02


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

AutoCloner maintained by Alex Coulton.