Multiple sequence alignment - TraesCS3D01G400800

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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 TraesCS3D01G400800 chr3D 100.000 5458 0 0 1 5458 515702911 515697454 0.000000e+00 10080
1 TraesCS3D01G400800 chr3D 97.648 5144 109 10 1 5135 546584197 546579057 0.000000e+00 8818
2 TraesCS3D01G400800 chr3D 90.351 114 8 1 1 111 474457746 474457633 4.410000e-31 147
3 TraesCS3D01G400800 chr7D 98.591 5464 67 8 1 5458 532953510 532958969 0.000000e+00 9655
4 TraesCS3D01G400800 chr7A 82.734 2421 324 50 1 2357 522245158 522247548 0.000000e+00 2069
5 TraesCS3D01G400800 chr7A 83.068 1884 264 38 2661 4511 522256088 522257949 0.000000e+00 1661
6 TraesCS3D01G400800 chr7A 83.587 1645 231 30 2455 4082 709870745 709872367 0.000000e+00 1506
7 TraesCS3D01G400800 chr7A 82.732 1303 183 33 474 1763 709868807 709870080 0.000000e+00 1122
8 TraesCS3D01G400800 chr7A 84.549 699 105 3 4641 5337 522258193 522258890 0.000000e+00 689
9 TraesCS3D01G400800 chr7A 83.989 712 108 6 4651 5360 709873001 709873708 0.000000e+00 678
10 TraesCS3D01G400800 chr7A 83.766 308 36 8 4184 4479 709872438 709872743 4.160000e-71 279
11 TraesCS3D01G400800 chr7A 91.667 168 13 1 2500 2667 522247677 522247843 1.180000e-56 231
12 TraesCS3D01G400800 chrUn 82.533 2061 293 52 2455 4479 47721416 47719387 0.000000e+00 1749
13 TraesCS3D01G400800 chrUn 82.322 2059 300 47 2455 4479 289579531 289581559 0.000000e+00 1727
14 TraesCS3D01G400800 chrUn 82.822 1304 179 36 474 1763 289577594 289578866 0.000000e+00 1125
15 TraesCS3D01G400800 chrUn 82.745 1304 181 35 474 1763 47723354 47722081 0.000000e+00 1122
16 TraesCS3D01G400800 chrUn 83.240 716 106 10 4651 5360 47719129 47718422 0.000000e+00 645
17 TraesCS3D01G400800 chrUn 82.749 713 116 6 4651 5360 289581817 289582525 3.590000e-176 628
18 TraesCS3D01G400800 chr4A 81.945 2077 294 51 2438 4479 25201077 25203107 0.000000e+00 1683
19 TraesCS3D01G400800 chr4A 82.910 1299 186 27 474 1763 25199159 25200430 0.000000e+00 1136
20 TraesCS3D01G400800 chr4A 81.191 739 104 18 4651 5360 25203366 25204098 3.690000e-156 562
21 TraesCS3D01G400800 chr1A 81.826 1095 162 31 3199 4272 497225905 497224827 0.000000e+00 885
22 TraesCS3D01G400800 chr1A 83.469 738 98 17 2438 3170 497227082 497226364 0.000000e+00 665
23 TraesCS3D01G400800 chr1A 89.387 424 45 0 1340 1763 497228154 497227731 8.050000e-148 534
24 TraesCS3D01G400800 chr3B 87.925 265 32 0 4651 4915 615890509 615890245 4.100000e-81 313
25 TraesCS3D01G400800 chr3B 83.784 296 33 3 1 283 615905882 615905589 3.240000e-67 267
26 TraesCS3D01G400800 chr3B 87.047 193 21 4 4320 4510 615890939 615890749 1.190000e-51 215
27 TraesCS3D01G400800 chr3A 78.854 506 76 16 1 483 1120728 1121225 4.100000e-81 313
28 TraesCS3D01G400800 chr5D 82.848 309 44 6 321 623 375063198 375062893 9.010000e-68 268
29 TraesCS3D01G400800 chr5B 91.071 112 8 2 1 111 58453959 58453849 3.410000e-32 150
30 TraesCS3D01G400800 chr6B 91.667 84 7 0 761 844 567103967 567104050 3.450000e-22 117


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 TraesCS3D01G400800 chr3D 515697454 515702911 5457 True 10080.000000 10080 100.000000 1 5458 1 chr3D.!!$R2 5457
1 TraesCS3D01G400800 chr3D 546579057 546584197 5140 True 8818.000000 8818 97.648000 1 5135 1 chr3D.!!$R3 5134
2 TraesCS3D01G400800 chr7D 532953510 532958969 5459 False 9655.000000 9655 98.591000 1 5458 1 chr7D.!!$F1 5457
3 TraesCS3D01G400800 chr7A 522256088 522258890 2802 False 1175.000000 1661 83.808500 2661 5337 2 chr7A.!!$F2 2676
4 TraesCS3D01G400800 chr7A 522245158 522247843 2685 False 1150.000000 2069 87.200500 1 2667 2 chr7A.!!$F1 2666
5 TraesCS3D01G400800 chr7A 709868807 709873708 4901 False 896.250000 1506 83.518500 474 5360 4 chr7A.!!$F3 4886
6 TraesCS3D01G400800 chrUn 47718422 47723354 4932 True 1172.000000 1749 82.839333 474 5360 3 chrUn.!!$R1 4886
7 TraesCS3D01G400800 chrUn 289577594 289582525 4931 False 1160.000000 1727 82.631000 474 5360 3 chrUn.!!$F1 4886
8 TraesCS3D01G400800 chr4A 25199159 25204098 4939 False 1127.000000 1683 82.015333 474 5360 3 chr4A.!!$F1 4886
9 TraesCS3D01G400800 chr1A 497224827 497228154 3327 True 694.666667 885 84.894000 1340 4272 3 chr1A.!!$R1 2932
10 TraesCS3D01G400800 chr3B 615890245 615890939 694 True 264.000000 313 87.486000 4320 4915 2 chr3B.!!$R2 595

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
270 283 1.871408 GCACATCTATGACCAGCGGAG 60.871 57.143 1.5 0.0 0.00 4.63 F
1221 1272 3.054875 TGCTAGAGTTGAAGTCATGGCAT 60.055 43.478 0.0 0.0 0.00 4.40 F
2459 2574 9.277565 CATGTTTGCACTAAATAATACAGTCAC 57.722 33.333 0.0 0.0 0.00 3.67 F
2933 3061 4.062991 TCGAAGAGGCTTTGTTTACCTTC 58.937 43.478 0.0 0.0 32.67 3.46 F
4368 4960 0.324614 ATCACACGGCAACCTCATGA 59.675 50.000 0.0 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2190 5.014123 TGAGTATGACAGGGTGAAAAGGAAT 59.986 40.000 0.0 0.0 0.00 3.01 R
2933 3061 1.397390 GCCATCTTCTGCATTGGGGG 61.397 60.000 0.0 0.0 0.00 5.40 R
3294 3854 2.025321 AGTAAAAATGTGGAGGGGCGAT 60.025 45.455 0.0 0.0 0.00 4.58 R
4384 4976 2.380064 TGTTTGGTTCCCTTGCATCT 57.620 45.000 0.0 0.0 0.00 2.90 R
5305 6052 0.988832 AAAGTAGCCGTTGGGGATGA 59.011 50.000 0.0 0.0 38.47 2.92 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
270 283 1.871408 GCACATCTATGACCAGCGGAG 60.871 57.143 1.50 0.0 0.00 4.63
319 332 8.607459 CCCATAATTAATCATCGCTAATGACTC 58.393 37.037 1.21 0.0 47.00 3.36
905 947 5.173664 GCCATTCTTTGCTCTTATTTTGCT 58.826 37.500 0.00 0.0 0.00 3.91
991 1042 9.533831 AAATGTCAATTCCTTTTAGTGGAGTAT 57.466 29.630 0.00 0.0 34.76 2.12
997 1048 9.832445 CAATTCCTTTTAGTGGAGTATAAGCTA 57.168 33.333 0.00 0.0 34.76 3.32
1221 1272 3.054875 TGCTAGAGTTGAAGTCATGGCAT 60.055 43.478 0.00 0.0 0.00 4.40
2459 2574 9.277565 CATGTTTGCACTAAATAATACAGTCAC 57.722 33.333 0.00 0.0 0.00 3.67
2933 3061 4.062991 TCGAAGAGGCTTTGTTTACCTTC 58.937 43.478 0.00 0.0 32.67 3.46
3039 3168 8.524870 TCATGTCAATGTATGATGATCTAACG 57.475 34.615 0.00 0.0 40.97 3.18
3287 3846 7.589954 AGTTAAACATTAACGCAAGACATCAAC 59.410 33.333 7.20 0.0 43.62 3.18
3294 3854 8.817100 CATTAACGCAAGACATCAACTATTCTA 58.183 33.333 0.00 0.0 43.62 2.10
3336 3899 5.621193 ACTTGGTATATCCTAACCACATGC 58.379 41.667 0.00 0.0 45.31 4.06
3619 4193 7.014615 ACCTTTCCATATTTGCATAGTTCATCC 59.985 37.037 0.00 0.0 0.00 3.51
3990 4565 1.538634 GCAACAAACTTCATGCTGCCA 60.539 47.619 0.00 0.0 34.61 4.92
4368 4960 0.324614 ATCACACGGCAACCTCATGA 59.675 50.000 0.00 0.0 0.00 3.07
4384 4976 3.795877 TCATGATTTACGAGCTGATGCA 58.204 40.909 0.00 0.0 42.74 3.96
4642 5355 2.766313 ACTGATGAGTTTTGCTGCGTA 58.234 42.857 0.00 0.0 0.00 4.42
5305 6052 5.248640 GGTGGAGCATTATATAGCACATGT 58.751 41.667 0.00 0.0 0.00 3.21
5390 6138 1.102154 TTGATTGCCATAGCCGTTGG 58.898 50.000 0.00 0.0 38.69 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
270 283 3.665323 CGCTTGAAACACTACTGCATGAC 60.665 47.826 0.00 0.00 0.00 3.06
274 287 0.586319 GCGCTTGAAACACTACTGCA 59.414 50.000 0.00 0.00 0.00 4.41
319 332 2.224549 TCGACACGCATAAACCCAAAAG 59.775 45.455 0.00 0.00 0.00 2.27
905 947 6.057321 ACTTAGATTGGGGACGAATACAAA 57.943 37.500 0.00 0.00 0.00 2.83
991 1042 5.466819 CCGATTGATAACCATCGTAGCTTA 58.533 41.667 0.00 0.00 35.03 3.09
997 1048 3.893200 TCTACCCGATTGATAACCATCGT 59.107 43.478 5.87 0.00 35.03 3.73
1840 1927 7.736447 AAAATGTGGTCAGAAACAAAAACAA 57.264 28.000 0.00 0.00 0.00 2.83
2098 2190 5.014123 TGAGTATGACAGGGTGAAAAGGAAT 59.986 40.000 0.00 0.00 0.00 3.01
2302 2397 2.605338 GGTACCGCGAGCGAATGTAATA 60.605 50.000 19.72 0.00 42.83 0.98
2459 2574 2.706339 AGTATGCCAAGCTTCTGAGG 57.294 50.000 0.00 0.00 0.00 3.86
2933 3061 1.397390 GCCATCTTCTGCATTGGGGG 61.397 60.000 0.00 0.00 0.00 5.40
3039 3168 4.083802 GCATAATAAGTGACAAGGATCGCC 60.084 45.833 0.00 0.00 0.00 5.54
3287 3846 2.248248 TGTGGAGGGGCGATAGAATAG 58.752 52.381 0.00 0.00 39.76 1.73
3294 3854 2.025321 AGTAAAAATGTGGAGGGGCGAT 60.025 45.455 0.00 0.00 0.00 4.58
4368 4960 2.547211 GCATCTGCATCAGCTCGTAAAT 59.453 45.455 0.00 0.00 42.74 1.40
4384 4976 2.380064 TGTTTGGTTCCCTTGCATCT 57.620 45.000 0.00 0.00 0.00 2.90
4642 5355 3.754965 TGCAGATTAGTTGGAAGCAACT 58.245 40.909 0.00 0.00 46.05 3.16
5305 6052 0.988832 AAAGTAGCCGTTGGGGATGA 59.011 50.000 0.00 0.00 38.47 2.92
5390 6138 1.535028 TGGCGTGAAATGTCATGTCAC 59.465 47.619 21.83 21.83 46.04 3.67


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

AutoCloner maintained by Alex Coulton.