Multiple sequence alignment - TraesCS5A01G177000

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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 TraesCS5A01G177000 chr5A 100.000 2388 0 0 1 2388 374024446 374022059 0.000000e+00 4410
1 TraesCS5A01G177000 chr5A 97.070 2389 66 4 1 2387 539825675 539823289 0.000000e+00 4021
2 TraesCS5A01G177000 chr5A 96.661 569 15 3 1822 2388 595668433 595667867 0.000000e+00 942
3 TraesCS5A01G177000 chr5A 92.611 203 15 0 1 203 630722653 630722855 2.320000e-75 292
4 TraesCS5A01G177000 chr5A 95.000 80 2 2 304 381 630722938 630723017 8.960000e-25 124
5 TraesCS5A01G177000 chr7A 96.529 2391 76 7 1 2388 25224712 25222326 0.000000e+00 3949
6 TraesCS5A01G177000 chr7A 92.881 2079 130 9 1 2067 116468466 116466394 0.000000e+00 3003
7 TraesCS5A01G177000 chr6A 95.067 2392 111 6 1 2388 471275618 471273230 0.000000e+00 3757
8 TraesCS5A01G177000 chr3A 95.609 2095 86 6 1 2092 496386021 496388112 0.000000e+00 3354
9 TraesCS5A01G177000 chr3A 90.572 297 22 4 737 1032 603856526 603856235 2.880000e-104 388
10 TraesCS5A01G177000 chr3D 93.385 2071 125 9 1 2067 578589352 578591414 0.000000e+00 3055
11 TraesCS5A01G177000 chr4D 92.189 2074 133 14 1 2067 168888699 168890750 0.000000e+00 2905
12 TraesCS5A01G177000 chr2D 95.898 1731 65 5 660 2388 92462905 92464631 0.000000e+00 2798
13 TraesCS5A01G177000 chr2D 97.015 67 2 0 566 632 92462839 92462905 1.940000e-21 113
14 TraesCS5A01G177000 chr5B 95.577 1266 55 1 1124 2388 617730963 617729698 0.000000e+00 2026
15 TraesCS5A01G177000 chrUn 97.183 568 13 2 1822 2388 1841802 1842367 0.000000e+00 957
16 TraesCS5A01G177000 chr2A 97.317 559 12 2 1831 2388 191763070 191762514 0.000000e+00 946
17 TraesCS5A01G177000 chr1B 96.831 568 15 3 1822 2388 563481025 563480460 0.000000e+00 946
18 TraesCS5A01G177000 chr5D 92.947 397 26 1 1 395 61858923 61859319 5.720000e-161 577
19 TraesCS5A01G177000 chr4B 92.553 94 7 0 346 439 642751931 642751838 4.140000e-28 135


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 TraesCS5A01G177000 chr5A 374022059 374024446 2387 True 4410.0 4410 100.0000 1 2388 1 chr5A.!!$R1 2387
1 TraesCS5A01G177000 chr5A 539823289 539825675 2386 True 4021.0 4021 97.0700 1 2387 1 chr5A.!!$R2 2386
2 TraesCS5A01G177000 chr5A 595667867 595668433 566 True 942.0 942 96.6610 1822 2388 1 chr5A.!!$R3 566
3 TraesCS5A01G177000 chr7A 25222326 25224712 2386 True 3949.0 3949 96.5290 1 2388 1 chr7A.!!$R1 2387
4 TraesCS5A01G177000 chr7A 116466394 116468466 2072 True 3003.0 3003 92.8810 1 2067 1 chr7A.!!$R2 2066
5 TraesCS5A01G177000 chr6A 471273230 471275618 2388 True 3757.0 3757 95.0670 1 2388 1 chr6A.!!$R1 2387
6 TraesCS5A01G177000 chr3A 496386021 496388112 2091 False 3354.0 3354 95.6090 1 2092 1 chr3A.!!$F1 2091
7 TraesCS5A01G177000 chr3D 578589352 578591414 2062 False 3055.0 3055 93.3850 1 2067 1 chr3D.!!$F1 2066
8 TraesCS5A01G177000 chr4D 168888699 168890750 2051 False 2905.0 2905 92.1890 1 2067 1 chr4D.!!$F1 2066
9 TraesCS5A01G177000 chr2D 92462839 92464631 1792 False 1455.5 2798 96.4565 566 2388 2 chr2D.!!$F1 1822
10 TraesCS5A01G177000 chr5B 617729698 617730963 1265 True 2026.0 2026 95.5770 1124 2388 1 chr5B.!!$R1 1264
11 TraesCS5A01G177000 chrUn 1841802 1842367 565 False 957.0 957 97.1830 1822 2388 1 chrUn.!!$F1 566
12 TraesCS5A01G177000 chr2A 191762514 191763070 556 True 946.0 946 97.3170 1831 2388 1 chr2A.!!$R1 557
13 TraesCS5A01G177000 chr1B 563480460 563481025 565 True 946.0 946 96.8310 1822 2388 1 chr1B.!!$R1 566

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
139 141 1.64872 CCGCAGAAGTGTGTGTTGG 59.351 57.895 0.0 0.0 31.71 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1520 1.066605 GCGCTTCGGTCAGGTTATCTA 59.933 52.381 0.0 0.0 0.0 1.98 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
139 141 1.648720 CCGCAGAAGTGTGTGTTGG 59.351 57.895 0.00 0.00 31.71 3.77
414 419 5.635700 GGTCATCAAGTTTAGACACTCTCAC 59.364 44.000 0.00 0.00 32.79 3.51
431 436 2.349590 TCACTGCATCTGATGAAACGG 58.650 47.619 21.30 10.75 0.00 4.44
798 810 2.240493 ACCGTGCAGCCATCTAATAC 57.760 50.000 0.00 0.00 0.00 1.89
908 925 7.286546 TCCCTAATCATGTTTTGTGTTTTCAGA 59.713 33.333 0.00 0.00 0.00 3.27
930 947 5.456907 AGATCGCTATCTTAGGAGAACCTGA 60.457 44.000 0.00 0.00 41.38 3.86
931 948 6.749772 AGATCGCTATCTTAGGAGAACCTGAT 60.750 42.308 0.00 0.00 41.38 2.90
1116 1133 3.160047 CTCTGCTCCTGGGCCGAT 61.160 66.667 0.00 0.00 0.00 4.18
1239 1256 3.941483 ACACTCTGTTTTGTTGGACTGAG 59.059 43.478 8.29 8.29 43.38 3.35
1467 1490 8.918202 TTTGGTTGACTGAATTAGTACTGAAT 57.082 30.769 5.39 0.00 40.53 2.57
1839 1864 5.048782 TCACATTGGAGTTGCTATGTTTGAC 60.049 40.000 0.00 0.00 0.00 3.18
1881 1909 6.528321 ACTCATATGCTTATGCTGAGCTTAA 58.472 36.000 13.42 9.31 40.49 1.85
1922 1950 4.214119 TCTGTGTGATGAGCTTAGTTTTGC 59.786 41.667 0.00 0.00 0.00 3.68
1966 1994 7.639113 TTACTTTGTTGAATCCTGTCTTGTT 57.361 32.000 0.00 0.00 0.00 2.83
2355 2450 9.643693 CTAACCATTTTTCTTGATAACTTGCAT 57.356 29.630 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 102 4.832823 CGGCCTATTTGGGGAGATAAAAAT 59.167 41.667 0.00 0.00 36.00 1.82
293 295 2.093658 ACAAAGTACCTCGCCACTATGG 60.094 50.000 0.00 0.00 41.55 2.74
414 419 1.938577 CTCCCGTTTCATCAGATGCAG 59.061 52.381 5.41 0.00 0.00 4.41
431 436 1.950954 GCAGGGCCACTTCTTAACTCC 60.951 57.143 6.18 0.00 0.00 3.85
493 501 5.921962 AAGAAGCCCTAAATCATTTCACC 57.078 39.130 0.00 0.00 0.00 4.02
798 810 8.908678 CAGGCATCACATATTATTTGAATTTCG 58.091 33.333 0.00 0.00 0.00 3.46
908 925 4.730966 TCAGGTTCTCCTAAGATAGCGAT 58.269 43.478 0.00 0.00 43.07 4.58
930 947 3.882102 TGCTTCCCCATATAGCACAAT 57.118 42.857 0.00 0.00 39.79 2.71
931 948 3.660970 TTGCTTCCCCATATAGCACAA 57.339 42.857 0.00 0.00 43.96 3.33
1116 1133 1.729586 AGCACCTGAACCTGACCTTA 58.270 50.000 0.00 0.00 0.00 2.69
1166 1183 1.962144 CTACAGACGTTGTCGGGGT 59.038 57.895 6.64 0.84 41.29 4.95
1239 1256 5.643777 ACAAACCATTATGCTACAGTCAGTC 59.356 40.000 0.00 0.00 0.00 3.51
1290 1307 2.593956 GGACCTTGACGCCCTCCTT 61.594 63.158 0.00 0.00 0.00 3.36
1494 1517 4.558095 GCGCTTCGGTCAGGTTATCTATAA 60.558 45.833 0.00 0.00 0.00 0.98
1496 1519 2.288273 GCGCTTCGGTCAGGTTATCTAT 60.288 50.000 0.00 0.00 0.00 1.98
1497 1520 1.066605 GCGCTTCGGTCAGGTTATCTA 59.933 52.381 0.00 0.00 0.00 1.98
1922 1950 2.550830 ACAAGAAGGTGGCTACAGTG 57.449 50.000 1.52 0.00 0.00 3.66
1966 1994 9.481340 CAAATGCTAGTAGCTCATGATTAGTAA 57.519 33.333 22.34 0.00 42.97 2.24
2355 2450 3.301794 ACATGAATGAAGGCCAGCATA 57.698 42.857 5.01 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.