Multiple sequence alignment - TraesCS4A01G387100

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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 TraesCS4A01G387100 chr4A 100.000 4665 0 0 1 4665 664491798 664496462 0 8615
1 TraesCS4A01G387100 chr4A 94.847 815 40 2 3851 4665 711314528 711315340 0 1271
2 TraesCS4A01G387100 chr1B 95.672 4667 179 13 1 4665 549430159 549434804 0 7478
3 TraesCS4A01G387100 chr1B 94.572 4716 192 19 1 4665 667327784 667332486 0 7232
4 TraesCS4A01G387100 chr2B 95.406 3962 171 11 2 3959 665882557 665886511 0 6298
5 TraesCS4A01G387100 chr2B 93.988 2778 138 16 1916 4665 393862085 393864861 0 4178
6 TraesCS4A01G387100 chr2B 93.976 1909 91 3 2780 4665 559153341 559151434 0 2867
7 TraesCS4A01G387100 chr4B 94.842 4052 151 17 1 4048 657450234 657446237 0 6272
8 TraesCS4A01G387100 chr4B 94.517 3301 149 13 1 3271 66831298 66834596 0 5064
9 TraesCS4A01G387100 chr4B 95.274 3068 119 11 1622 4665 403116426 403113361 0 4839
10 TraesCS4A01G387100 chr4B 94.800 2904 117 15 12 2910 5263240 5266114 0 4495
11 TraesCS4A01G387100 chr4B 93.537 2352 99 18 2318 4665 73292429 73290127 0 3452
12 TraesCS4A01G387100 chr4B 95.293 1211 56 1 2782 3992 5266032 5267241 0 1919
13 TraesCS4A01G387100 chr4B 95.196 1124 52 2 3542 4665 66834596 66835717 0 1775
14 TraesCS4A01G387100 chr7B 94.362 3973 202 16 1 3968 549380998 549384953 0 6076
15 TraesCS4A01G387100 chr7B 94.447 3926 176 24 1 3922 637748877 637744990 0 6004
16 TraesCS4A01G387100 chr7B 96.178 811 29 2 3856 4665 637745102 637744293 0 1325
17 TraesCS4A01G387100 chr3B 93.657 4020 200 17 1 3993 71171152 71167161 0 5960
18 TraesCS4A01G387100 chr3B 95.536 2912 126 4 1 2910 543579773 543576864 0 4654
19 TraesCS4A01G387100 chr3B 94.395 1909 82 1 2782 4665 698397293 698399201 0 2909
20 TraesCS4A01G387100 chr6B 89.263 624 58 8 4043 4665 698942168 698942783 0 773


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 TraesCS4A01G387100 chr4A 664491798 664496462 4664 False 8615.0 8615 100.0000 1 4665 1 chr4A.!!$F1 4664
1 TraesCS4A01G387100 chr4A 711314528 711315340 812 False 1271.0 1271 94.8470 3851 4665 1 chr4A.!!$F2 814
2 TraesCS4A01G387100 chr1B 549430159 549434804 4645 False 7478.0 7478 95.6720 1 4665 1 chr1B.!!$F1 4664
3 TraesCS4A01G387100 chr1B 667327784 667332486 4702 False 7232.0 7232 94.5720 1 4665 1 chr1B.!!$F2 4664
4 TraesCS4A01G387100 chr2B 665882557 665886511 3954 False 6298.0 6298 95.4060 2 3959 1 chr2B.!!$F2 3957
5 TraesCS4A01G387100 chr2B 393862085 393864861 2776 False 4178.0 4178 93.9880 1916 4665 1 chr2B.!!$F1 2749
6 TraesCS4A01G387100 chr2B 559151434 559153341 1907 True 2867.0 2867 93.9760 2780 4665 1 chr2B.!!$R1 1885
7 TraesCS4A01G387100 chr4B 657446237 657450234 3997 True 6272.0 6272 94.8420 1 4048 1 chr4B.!!$R3 4047
8 TraesCS4A01G387100 chr4B 403113361 403116426 3065 True 4839.0 4839 95.2740 1622 4665 1 chr4B.!!$R2 3043
9 TraesCS4A01G387100 chr4B 73290127 73292429 2302 True 3452.0 3452 93.5370 2318 4665 1 chr4B.!!$R1 2347
10 TraesCS4A01G387100 chr4B 66831298 66835717 4419 False 3419.5 5064 94.8565 1 4665 2 chr4B.!!$F2 4664
11 TraesCS4A01G387100 chr4B 5263240 5267241 4001 False 3207.0 4495 95.0465 12 3992 2 chr4B.!!$F1 3980
12 TraesCS4A01G387100 chr7B 549380998 549384953 3955 False 6076.0 6076 94.3620 1 3968 1 chr7B.!!$F1 3967
13 TraesCS4A01G387100 chr7B 637744293 637748877 4584 True 3664.5 6004 95.3125 1 4665 2 chr7B.!!$R1 4664
14 TraesCS4A01G387100 chr3B 71167161 71171152 3991 True 5960.0 5960 93.6570 1 3993 1 chr3B.!!$R1 3992
15 TraesCS4A01G387100 chr3B 543576864 543579773 2909 True 4654.0 4654 95.5360 1 2910 1 chr3B.!!$R2 2909
16 TraesCS4A01G387100 chr3B 698397293 698399201 1908 False 2909.0 2909 94.3950 2782 4665 1 chr3B.!!$F1 1883
17 TraesCS4A01G387100 chr6B 698942168 698942783 615 False 773.0 773 89.2630 4043 4665 1 chr6B.!!$F1 622

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
739 745 0.310854 GACAAGCACCCCTTTGAACG 59.689 55.000 0.00 0.0 0.00 3.95 F
1223 1229 1.274703 ACCGCCCACAGAGGATTCAT 61.275 55.000 0.00 0.0 41.22 2.57 F
1794 1803 0.685660 GAGGAGGTCTTTCCGTTGGT 59.314 55.000 0.00 0.0 42.29 3.67 F
2033 2042 1.078426 GTGCCGGCCTACTTCATGT 60.078 57.895 26.77 0.0 0.00 3.21 F
3125 3242 1.317613 ATGCTGCAAGTTTGAACGGA 58.682 45.000 6.36 0.0 35.30 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 1773 1.055040 GACCTCCTCTATGCCTGCAT 58.945 55.000 9.87 9.87 40.19 3.96 R
2033 2042 2.290323 GCAGAAAGGGGAAGAAGCACTA 60.290 50.000 0.00 0.00 0.00 2.74 R
3262 3379 0.108898 GTCTCTCGTCATGCACAGCT 60.109 55.000 0.00 0.00 0.00 4.24 R
3393 3510 1.004161 GCTCTCTTTTCAGGGCCTTCT 59.996 52.381 1.32 0.00 0.00 2.85 R
4433 5073 2.587612 TGATGCACGTTACGCTTTTC 57.412 45.000 4.09 0.00 0.00 2.29 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
107 108 2.290768 ACATCTCATGGCAAGCTTCACT 60.291 45.455 0.00 0.00 33.60 3.41
152 153 1.141254 TGGTGTTACGGACCACACAAT 59.859 47.619 13.82 0.00 44.40 2.71
183 184 7.589395 CACATACAGCACAACAAGGTAAAATA 58.411 34.615 0.00 0.00 0.00 1.40
555 557 2.969628 AGATCTTACGCTTGTCCCTG 57.030 50.000 0.00 0.00 0.00 4.45
562 564 0.744281 ACGCTTGTCCCTGGTTTTTG 59.256 50.000 0.00 0.00 0.00 2.44
563 565 0.744281 CGCTTGTCCCTGGTTTTTGT 59.256 50.000 0.00 0.00 0.00 2.83
739 745 0.310854 GACAAGCACCCCTTTGAACG 59.689 55.000 0.00 0.00 0.00 3.95
997 1003 8.362639 AGAAAACAAACGAGTACAATAGAGGTA 58.637 33.333 0.00 0.00 0.00 3.08
1094 1100 2.698797 GGGTCATTCTCAAGACGGGATA 59.301 50.000 0.00 0.00 35.63 2.59
1223 1229 1.274703 ACCGCCCACAGAGGATTCAT 61.275 55.000 0.00 0.00 41.22 2.57
1347 1355 3.251484 AGTAGCATGCCCTACATACCAT 58.749 45.455 15.66 0.00 40.07 3.55
1357 1365 3.574396 CCCTACATACCATCTGACGTCAT 59.426 47.826 20.40 6.25 0.00 3.06
1715 1724 3.228188 AGACCTTTTTGGAGTGCATGA 57.772 42.857 0.00 0.00 39.71 3.07
1764 1773 2.804986 TACCAGGATTTCAGCATGCA 57.195 45.000 21.98 0.00 34.76 3.96
1794 1803 0.685660 GAGGAGGTCTTTCCGTTGGT 59.314 55.000 0.00 0.00 42.29 3.67
1803 1812 1.944024 CTTTCCGTTGGTAGTGCACAA 59.056 47.619 21.04 0.77 0.00 3.33
1869 1878 1.487231 CGTTCTTTGCTGACCGTCG 59.513 57.895 0.00 0.00 0.00 5.12
1938 1947 4.202430 GGTGGAGGAGTTTGAAAGGAGTTA 60.202 45.833 0.00 0.00 0.00 2.24
1939 1948 5.515008 GGTGGAGGAGTTTGAAAGGAGTTAT 60.515 44.000 0.00 0.00 0.00 1.89
2033 2042 1.078426 GTGCCGGCCTACTTCATGT 60.078 57.895 26.77 0.00 0.00 3.21
2310 2319 7.985184 AGTCAGTTGTGTTACAGTCTTATTTGA 59.015 33.333 0.00 0.00 0.00 2.69
2467 2481 1.793134 GCTTGCTCAGCTGCAGTTGT 61.793 55.000 27.01 5.04 46.27 3.32
2629 2648 4.880120 TGCATTTGCCATGTTTTCTGAAAA 59.120 33.333 11.33 11.33 41.18 2.29
2633 2652 4.339872 TGCCATGTTTTCTGAAAATGCT 57.660 36.364 17.63 4.36 32.22 3.79
2766 2790 4.092279 TGTATGGAAATGACAATGGCCAA 58.908 39.130 10.96 0.00 0.00 4.52
2821 2868 7.412853 TGTACTACAGTTGCCATGTCTAATA 57.587 36.000 0.00 0.00 32.02 0.98
3125 3242 1.317613 ATGCTGCAAGTTTGAACGGA 58.682 45.000 6.36 0.00 35.30 4.69
3255 3372 2.713154 GCCGCAGACAACAAACGT 59.287 55.556 0.00 0.00 0.00 3.99
3328 3445 3.551485 GGCATGTTGTGTTGACAAAGAAC 59.449 43.478 0.00 0.00 43.77 3.01
3581 3698 1.616159 CCGTTCCATCACAAAGGGTT 58.384 50.000 0.00 0.00 0.00 4.11
3625 3742 0.940126 CGGGATTGGAGATTCAAGCG 59.060 55.000 0.00 0.00 34.24 4.68
3691 3808 3.064324 GGGGCACTGTGACATGGC 61.064 66.667 16.72 11.21 40.53 4.40
3898 4369 9.509956 ACTAAATTTGCCATGTTAGTTGTACTA 57.490 29.630 0.00 0.00 33.98 1.82
3930 4401 4.188462 TGTTAATTGTACTGGATCTGCCG 58.812 43.478 0.00 0.00 40.66 5.69
3962 4433 3.276857 ACTGAATCTGCCATGTTAGCTG 58.723 45.455 0.00 0.00 0.00 4.24
3972 4443 4.824537 TGCCATGTTAGCTGTACTGAAAAA 59.175 37.500 3.61 0.00 0.00 1.94
3978 4449 7.083875 TGTTAGCTGTACTGAAAAATATGCC 57.916 36.000 3.61 0.00 0.00 4.40
3980 4451 7.339212 TGTTAGCTGTACTGAAAAATATGCCAT 59.661 33.333 3.61 0.00 0.00 4.40
4313 4952 7.061566 TGTACTGAATATGCCATGTTAGCTA 57.938 36.000 0.00 0.00 0.00 3.32
4334 4973 6.071728 AGCTATACTGAAAAATATGCCATGGC 60.072 38.462 30.54 30.54 42.35 4.40
4433 5073 5.634859 GCAATGTATGGGAAACAAGTTGAAG 59.365 40.000 10.54 0.00 0.00 3.02
4593 5235 5.711506 TGTCTGATGAACTACATTTGCCATT 59.288 36.000 0.00 0.00 39.56 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 7.576861 AATTGATGTGATGTATCTGCATTGA 57.423 32.000 0.00 0.00 0.00 2.57
152 153 2.290577 TGTTGTGCTGTATGTGCCCATA 60.291 45.455 0.00 0.00 32.29 2.74
555 557 5.392272 CGTAGGCCCTGTAATAACAAAAACC 60.392 44.000 0.00 0.00 34.49 3.27
562 564 5.520376 TTAGTCGTAGGCCCTGTAATAAC 57.480 43.478 0.00 0.00 0.00 1.89
563 565 5.658190 ACTTTAGTCGTAGGCCCTGTAATAA 59.342 40.000 0.00 0.00 0.00 1.40
739 745 1.008079 GAGTGTTGCCAGTGCTTGC 60.008 57.895 0.00 0.00 38.71 4.01
804 810 1.918293 ATCCCCTTGTGCCTCGTCA 60.918 57.895 0.00 0.00 0.00 4.35
990 996 3.031736 GTGGCACCTCATCTTACCTCTA 58.968 50.000 6.29 0.00 0.00 2.43
997 1003 3.658398 CCTTGTGGCACCTCATCTT 57.342 52.632 16.26 0.00 0.00 2.40
1094 1100 0.251922 TAGCTTACACCGGACAGGGT 60.252 55.000 9.46 0.75 46.96 4.34
1223 1229 0.675522 GAATTGCCTTTCGACGGGGA 60.676 55.000 0.00 0.00 0.00 4.81
1347 1355 3.119245 GCCTGTAGGTTTATGACGTCAGA 60.119 47.826 24.41 17.44 37.57 3.27
1357 1365 3.324556 ACGGTACTTTGCCTGTAGGTTTA 59.675 43.478 0.00 0.00 37.57 2.01
1764 1773 1.055040 GACCTCCTCTATGCCTGCAT 58.945 55.000 9.87 9.87 40.19 3.96
1869 1878 1.377536 GAATGCCTTGTGGAGCTCTC 58.622 55.000 14.64 8.02 34.57 3.20
1909 1918 1.487142 TCAAACTCCTCCACCGTCAAA 59.513 47.619 0.00 0.00 0.00 2.69
1938 1947 8.425237 TTGATATGTTTCAATCATGGCCATAT 57.575 30.769 20.30 9.77 32.40 1.78
1939 1948 7.506599 ACTTGATATGTTTCAATCATGGCCATA 59.493 33.333 20.30 7.65 35.20 2.74
2033 2042 2.290323 GCAGAAAGGGGAAGAAGCACTA 60.290 50.000 0.00 0.00 0.00 2.74
2179 2188 2.558313 GTGGTCGCTTCTTGCTGC 59.442 61.111 0.00 0.00 40.11 5.25
2310 2319 3.054361 CCCCTACTGCCTTCATACTTGTT 60.054 47.826 0.00 0.00 0.00 2.83
2467 2481 4.381185 GCAACTGCATTCCATTGAAGATGA 60.381 41.667 0.00 0.00 41.59 2.92
2629 2648 4.910195 TCAGGAAACATGTCAACTAGCAT 58.090 39.130 0.00 0.00 0.00 3.79
2633 2652 5.534278 TGCATTTCAGGAAACATGTCAACTA 59.466 36.000 0.00 0.00 32.51 2.24
2821 2868 6.889198 ACATTAGACATGGCAACTGTAGTAT 58.111 36.000 0.00 0.00 37.61 2.12
3091 3208 5.614324 TGCAGCATTGGTAGTAGTATTCT 57.386 39.130 0.00 0.00 0.00 2.40
3255 3372 2.752903 TCGTCATGCACAGCTAGAACTA 59.247 45.455 0.00 0.00 0.00 2.24
3262 3379 0.108898 GTCTCTCGTCATGCACAGCT 60.109 55.000 0.00 0.00 0.00 4.24
3328 3445 5.389620 CGCTTCATCAATTAGCTCAGCATAG 60.390 44.000 0.00 0.00 32.80 2.23
3393 3510 1.004161 GCTCTCTTTTCAGGGCCTTCT 59.996 52.381 1.32 0.00 0.00 2.85
3581 3698 4.122337 TGTACCTTACCTCTCTTGGACA 57.878 45.455 0.00 0.00 0.00 4.02
3625 3742 6.871492 TCCCTTTCTTTGTTTTCTTGTGTTTC 59.129 34.615 0.00 0.00 0.00 2.78
3691 3808 3.181480 ACAAAACGAAATGTCCACAAGGG 60.181 43.478 0.00 0.00 34.83 3.95
3871 4342 8.296713 AGTACAACTAACATGGCAAATTTAGTG 58.703 33.333 15.43 12.65 35.44 2.74
3898 4369 5.824624 CCAGTACAATTAACATGGCAGATCT 59.175 40.000 0.00 0.00 0.00 2.75
3930 4401 4.036262 TGGCAGATTCAGTACAAACAACAC 59.964 41.667 0.00 0.00 0.00 3.32
3962 4433 9.248291 CAAATACCATGGCATATTTTTCAGTAC 57.752 33.333 13.04 0.00 30.31 2.73
3972 4443 9.586732 ACTACATTTACAAATACCATGGCATAT 57.413 29.630 13.04 0.00 0.00 1.78
4035 4506 8.826765 AGAGTCATTCTCCCAATTTAGTTTAGA 58.173 33.333 0.00 0.00 43.71 2.10
4038 4509 7.944554 TCAAGAGTCATTCTCCCAATTTAGTTT 59.055 33.333 0.00 0.00 43.71 2.66
4039 4510 7.461749 TCAAGAGTCATTCTCCCAATTTAGTT 58.538 34.615 0.00 0.00 43.71 2.24
4334 4973 6.185852 TGTGATGCAGAGTCATTACAAATG 57.814 37.500 0.00 0.00 39.14 2.32
4433 5073 2.587612 TGATGCACGTTACGCTTTTC 57.412 45.000 4.09 0.00 0.00 2.29
4593 5235 6.517034 CGAATGCGTCTACGATGTTTTAAAAA 59.483 34.615 6.71 0.00 43.02 1.94


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

AutoCloner maintained by Alex Coulton.