Multiple sequence alignment - TraesCS1D01G354200

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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 TraesCS1D01G354200 chr1D 100.000 2861 0 0 1 2861 439433649 439430789 0 5284
1 TraesCS1D01G354200 chr1D 97.564 862 19 2 1 861 416651045 416651905 0 1474
2 TraesCS1D01G354200 chr1D 97.448 862 21 1 1 861 439456493 439455632 0 1469
3 TraesCS1D01G354200 chr1D 97.332 862 22 1 1 861 17172195 17171334 0 1463
4 TraesCS1D01G354200 chr1D 97.332 862 22 1 1 861 108078122 108078983 0 1463
5 TraesCS1D01G354200 chr1D 97.225 865 23 1 2 865 224330055 224330919 0 1463
6 TraesCS1D01G354200 chr2D 97.001 2001 57 3 862 2861 497912322 497914320 0 3360
7 TraesCS1D01G354200 chr2A 94.350 2000 107 5 863 2861 102742610 102744604 0 3062
8 TraesCS1D01G354200 chr7B 86.508 1927 254 4 922 2847 68052674 68054595 0 2113
9 TraesCS1D01G354200 chr7B 83.291 1981 317 14 886 2861 70536531 70534560 0 1812
10 TraesCS1D01G354200 chr5B 85.987 1991 244 15 862 2849 537932021 537933979 0 2098
11 TraesCS1D01G354200 chr7A 84.615 1989 293 13 865 2847 295219613 295221594 0 1965
12 TraesCS1D01G354200 chr7A 86.194 833 113 2 2030 2861 653625233 653626064 0 900
13 TraesCS1D01G354200 chr7D 84.156 1925 289 12 936 2855 91693409 91695322 0 1851
14 TraesCS1D01G354200 chr7D 82.530 1929 327 10 936 2861 7485477 7487398 0 1687
15 TraesCS1D01G354200 chr5A 83.704 1933 294 19 935 2861 14247448 14245531 0 1805
16 TraesCS1D01G354200 chr6D 83.075 1932 308 15 936 2861 387799005 387800923 0 1738
17 TraesCS1D01G354200 chr5D 97.335 863 22 1 1 862 464503395 464502533 0 1465
18 TraesCS1D01G354200 chr5D 97.332 862 22 1 1 861 8973244 8974105 0 1463
19 TraesCS1D01G354200 chr5D 97.225 865 23 1 1 864 487903250 487902386 0 1463
20 TraesCS1D01G354200 chr3D 96.900 871 26 1 1 870 453954115 453953245 0 1458


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 TraesCS1D01G354200 chr1D 439430789 439433649 2860 True 5284 5284 100.000 1 2861 1 chr1D.!!$R2 2860
1 TraesCS1D01G354200 chr1D 416651045 416651905 860 False 1474 1474 97.564 1 861 1 chr1D.!!$F3 860
2 TraesCS1D01G354200 chr1D 439455632 439456493 861 True 1469 1469 97.448 1 861 1 chr1D.!!$R3 860
3 TraesCS1D01G354200 chr1D 17171334 17172195 861 True 1463 1463 97.332 1 861 1 chr1D.!!$R1 860
4 TraesCS1D01G354200 chr1D 108078122 108078983 861 False 1463 1463 97.332 1 861 1 chr1D.!!$F1 860
5 TraesCS1D01G354200 chr1D 224330055 224330919 864 False 1463 1463 97.225 2 865 1 chr1D.!!$F2 863
6 TraesCS1D01G354200 chr2D 497912322 497914320 1998 False 3360 3360 97.001 862 2861 1 chr2D.!!$F1 1999
7 TraesCS1D01G354200 chr2A 102742610 102744604 1994 False 3062 3062 94.350 863 2861 1 chr2A.!!$F1 1998
8 TraesCS1D01G354200 chr7B 68052674 68054595 1921 False 2113 2113 86.508 922 2847 1 chr7B.!!$F1 1925
9 TraesCS1D01G354200 chr7B 70534560 70536531 1971 True 1812 1812 83.291 886 2861 1 chr7B.!!$R1 1975
10 TraesCS1D01G354200 chr5B 537932021 537933979 1958 False 2098 2098 85.987 862 2849 1 chr5B.!!$F1 1987
11 TraesCS1D01G354200 chr7A 295219613 295221594 1981 False 1965 1965 84.615 865 2847 1 chr7A.!!$F1 1982
12 TraesCS1D01G354200 chr7A 653625233 653626064 831 False 900 900 86.194 2030 2861 1 chr7A.!!$F2 831
13 TraesCS1D01G354200 chr7D 91693409 91695322 1913 False 1851 1851 84.156 936 2855 1 chr7D.!!$F2 1919
14 TraesCS1D01G354200 chr7D 7485477 7487398 1921 False 1687 1687 82.530 936 2861 1 chr7D.!!$F1 1925
15 TraesCS1D01G354200 chr5A 14245531 14247448 1917 True 1805 1805 83.704 935 2861 1 chr5A.!!$R1 1926
16 TraesCS1D01G354200 chr6D 387799005 387800923 1918 False 1738 1738 83.075 936 2861 1 chr6D.!!$F1 1925
17 TraesCS1D01G354200 chr5D 464502533 464503395 862 True 1465 1465 97.335 1 862 1 chr5D.!!$R1 861
18 TraesCS1D01G354200 chr5D 8973244 8974105 861 False 1463 1463 97.332 1 861 1 chr5D.!!$F1 860
19 TraesCS1D01G354200 chr5D 487902386 487903250 864 True 1463 1463 97.225 1 864 1 chr5D.!!$R2 863
20 TraesCS1D01G354200 chr3D 453953245 453954115 870 True 1458 1458 96.900 1 870 1 chr3D.!!$R1 869

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
262 263 0.242825 TCTCGTTACCGGCAAGTCTG 59.757 55.000 0.00 0.00 33.95 3.51 F
266 267 1.070175 CGTTACCGGCAAGTCTGTTTG 60.070 52.381 0.00 0.00 0.00 2.93 F
1261 1263 0.257328 TTGGAAGAAGGTGGTGCACA 59.743 50.000 20.43 1.62 35.86 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1261 1263 0.037303 CTGAACAGCCATGGACCACT 59.963 55.000 18.4 0.0 0.00 4.00 R
1543 1545 0.706433 AATCTGCCCTCACCCACAAT 59.294 50.000 0.0 0.0 0.00 2.71 R
2543 2545 1.139853 GCCATGGAAGGGTACTCTCAG 59.860 57.143 18.4 0.0 42.11 3.35 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
73 74 6.065374 AGAACTATGTAGACATGACCGAGAT 58.935 40.000 0.00 0.00 37.15 2.75
138 139 2.394632 TGGCTCCCACATATTCTACGT 58.605 47.619 0.00 0.00 0.00 3.57
262 263 0.242825 TCTCGTTACCGGCAAGTCTG 59.757 55.000 0.00 0.00 33.95 3.51
266 267 1.070175 CGTTACCGGCAAGTCTGTTTG 60.070 52.381 0.00 0.00 0.00 2.93
602 604 4.344102 AGTGCTAAGCTAACGGAATGGATA 59.656 41.667 0.00 0.00 0.00 2.59
639 641 5.608015 TCATTCTCCTAATGATGTGATCCCA 59.392 40.000 0.00 0.00 32.21 4.37
652 654 8.715190 TGATGTGATCCCATTAATCAAATGAT 57.285 30.769 0.00 0.00 46.81 2.45
695 697 8.599624 AGGAAACATAACCATCTTTGATCAAT 57.400 30.769 9.40 0.00 0.00 2.57
913 915 1.076559 TCGGACCGGCTATCTGGAA 60.077 57.895 15.25 0.00 41.45 3.53
1021 1023 1.364626 GCTGCAACACCTGGATCTCG 61.365 60.000 0.00 0.00 0.00 4.04
1204 1206 1.074775 AAGTATAGGGAGGCGGGCA 60.075 57.895 3.78 0.00 0.00 5.36
1261 1263 0.257328 TTGGAAGAAGGTGGTGCACA 59.743 50.000 20.43 1.62 35.86 4.57
1459 1461 4.018960 TGAAAGAAATCCAGCTAGCTCCTT 60.019 41.667 16.15 5.69 0.00 3.36
1543 1545 1.046472 ACGGGTCACACCTCTGAACA 61.046 55.000 0.00 0.00 38.64 3.18
1858 1860 4.079253 AGAAGCGGGTTTTGACAATACAT 58.921 39.130 10.38 0.00 0.00 2.29
2248 2250 2.735762 GCGATCTCGTGGAGCTTAGTTT 60.736 50.000 1.14 0.00 42.22 2.66
2275 2277 7.120726 GCCTACTATCCTTTGCTTAGTTGAAAA 59.879 37.037 0.00 0.00 0.00 2.29
2315 2317 3.375922 GTGTTGAGGGTCTTCGTTTTTCA 59.624 43.478 0.00 0.00 0.00 2.69
2362 2364 0.455005 GGTAGTAGTGGTCGGAGTGC 59.545 60.000 0.00 0.00 0.00 4.40
2380 2382 4.338879 AGTGCTGGCATCTGTATCTTTTT 58.661 39.130 0.00 0.00 0.00 1.94
2463 2465 3.709987 CTTGAAACAGGGAAGCAACAAG 58.290 45.455 0.00 0.00 0.00 3.16
2464 2466 1.408702 TGAAACAGGGAAGCAACAAGC 59.591 47.619 0.00 0.00 46.19 4.01
2543 2545 0.322546 ACGATGGAAAGGTTGAGGGC 60.323 55.000 0.00 0.00 0.00 5.19
2544 2546 0.035056 CGATGGAAAGGTTGAGGGCT 60.035 55.000 0.00 0.00 0.00 5.19
2703 2706 3.537874 GGCTACCGCGGTCTGGAT 61.538 66.667 38.01 12.28 36.88 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 0.179092 GTAGGGTCCGCACGCTTAAT 60.179 55.000 0.00 0.00 43.11 1.40
262 263 5.933790 TGATGTATTACGGAACAAGCAAAC 58.066 37.500 0.00 0.00 0.00 2.93
266 267 5.753438 TGAGATGATGTATTACGGAACAAGC 59.247 40.000 0.00 0.00 0.00 4.01
269 270 6.215495 TGTGAGATGATGTATTACGGAACA 57.785 37.500 0.00 0.00 0.00 3.18
320 321 4.024048 CGGTAATGCACATCACTTAATCCC 60.024 45.833 0.00 0.00 0.00 3.85
323 324 5.670485 TCTCGGTAATGCACATCACTTAAT 58.330 37.500 0.00 0.00 0.00 1.40
602 604 8.900781 CATTAGGAGAATGATGTGATTGACTTT 58.099 33.333 0.00 0.00 0.00 2.66
652 654 5.692115 TTCCTAGCCATTGACATGAGTTA 57.308 39.130 0.00 0.00 31.07 2.24
695 697 3.087370 TGCCTCTACTTGACTAGCTCA 57.913 47.619 0.00 0.00 0.00 4.26
913 915 2.811410 TCCCGTAGATGGTACTTGTGT 58.189 47.619 0.00 0.00 0.00 3.72
1021 1023 4.025896 CACATCATCAAGCTCGTCATCTTC 60.026 45.833 0.00 0.00 0.00 2.87
1261 1263 0.037303 CTGAACAGCCATGGACCACT 59.963 55.000 18.40 0.00 0.00 4.00
1396 1398 3.367498 GCTAGTTGATCAACGACCTCTGT 60.367 47.826 28.18 13.87 45.50 3.41
1459 1461 2.550277 TCTCCCTCATAGAACAGCCA 57.450 50.000 0.00 0.00 0.00 4.75
1543 1545 0.706433 AATCTGCCCTCACCCACAAT 59.294 50.000 0.00 0.00 0.00 2.71
1820 1822 3.462021 GCTTCTTGAGATGACCGCTTAT 58.538 45.455 0.00 0.00 0.00 1.73
1858 1860 1.930204 TGTGACCTCATCCTCCTCCTA 59.070 52.381 0.00 0.00 0.00 2.94
2248 2250 5.188948 TCAACTAAGCAAAGGATAGTAGGCA 59.811 40.000 0.00 0.00 30.03 4.75
2275 2277 3.206150 ACACGACTTTTCTGCAACTGAT 58.794 40.909 0.00 0.00 0.00 2.90
2315 2317 5.543790 ACCAAAGCTGAAATCAAACCCTAAT 59.456 36.000 0.00 0.00 0.00 1.73
2362 2364 8.767478 ATTTTTCAAAAAGATACAGATGCCAG 57.233 30.769 1.08 0.00 0.00 4.85
2380 2382 4.686972 TGCAACATCAACCGAATTTTTCA 58.313 34.783 0.00 0.00 0.00 2.69
2463 2465 2.422276 AAAAGCATGAAAGACACCGC 57.578 45.000 0.00 0.00 0.00 5.68
2464 2466 3.479006 CGTAAAAGCATGAAAGACACCG 58.521 45.455 0.00 0.00 0.00 4.94
2467 2469 2.817258 CCCCGTAAAAGCATGAAAGACA 59.183 45.455 0.00 0.00 0.00 3.41
2530 2532 1.349357 ACTCTCAGCCCTCAACCTTTC 59.651 52.381 0.00 0.00 0.00 2.62
2543 2545 1.139853 GCCATGGAAGGGTACTCTCAG 59.860 57.143 18.40 0.00 42.11 3.35
2544 2546 1.204146 GCCATGGAAGGGTACTCTCA 58.796 55.000 18.40 0.00 42.11 3.27


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

AutoCloner maintained by Alex Coulton.