Multiple sequence alignment - TraesCS5D01G256200

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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 TraesCS5D01G256200 chr5D 100.000 3195 0 0 1 3195 362546609 362549803 0.000000e+00 5901.0
1 TraesCS5D01G256200 chr5B 92.683 2829 87 46 400 3186 428460887 428463637 0.000000e+00 3967.0
2 TraesCS5D01G256200 chr5B 89.928 278 24 2 65 342 428444367 428444640 3.920000e-94 355.0
3 TraesCS5D01G256200 chr5B 93.220 59 2 2 23 80 428442552 428442609 5.680000e-13 86.1
4 TraesCS5D01G256200 chr5A 92.571 2625 109 45 587 3186 463451511 463454074 0.000000e+00 3688.0
5 TraesCS5D01G256200 chr5A 85.012 407 31 17 1 382 463449514 463449915 1.390000e-103 387.0
6 TraesCS5D01G256200 chr5A 94.286 175 9 1 430 603 463449900 463450074 1.890000e-67 267.0
7 TraesCS5D01G256200 chr4A 88.129 278 27 5 1396 1670 678872400 678872674 3.070000e-85 326.0
8 TraesCS5D01G256200 chr4D 87.770 278 28 5 1396 1670 471961656 471961930 1.430000e-83 320.0
9 TraesCS5D01G256200 chr4B 86.765 272 30 5 1396 1664 593422869 593423137 6.700000e-77 298.0


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 TraesCS5D01G256200 chr5D 362546609 362549803 3194 False 5901.000000 5901 100.000 1 3195 1 chr5D.!!$F1 3194
1 TraesCS5D01G256200 chr5B 428460887 428463637 2750 False 3967.000000 3967 92.683 400 3186 1 chr5B.!!$F1 2786
2 TraesCS5D01G256200 chr5B 428442552 428444640 2088 False 220.550000 355 91.574 23 342 2 chr5B.!!$F2 319
3 TraesCS5D01G256200 chr5A 463449514 463454074 4560 False 1447.333333 3688 90.623 1 3186 3 chr5A.!!$F1 3185

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
106 1879 0.309612 GGTAACCACTGCACGTTTGG 59.690 55.0 0.0 0.0 36.39 3.28 F
746 4004 0.478507 CTCTCTCTCCCTCCCTCTCC 59.521 65.0 0.0 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 5044 2.203938 TCCTCGTCCCCCAGCTTT 60.204 61.111 0.0 0.0 0.0 3.51 R
2435 5719 0.981277 CCCTTGTCCCTATCCCGTGT 60.981 60.000 0.0 0.0 0.0 4.49 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
40 41 4.993028 TGGGTATCCTTTTGCACTAAAGT 58.007 39.130 9.45 0.00 34.11 2.66
72 74 9.042008 GGTTTTGATAGTTAGCGATTCAAGATA 57.958 33.333 0.00 0.00 0.00 1.98
106 1879 0.309612 GGTAACCACTGCACGTTTGG 59.690 55.000 0.00 0.00 36.39 3.28
121 1894 5.121768 GCACGTTTGGTACACAAGAATCTAT 59.878 40.000 0.00 0.00 40.82 1.98
137 1910 9.630098 CAAGAATCTATTAAATGTTGCAGTTGT 57.370 29.630 0.00 0.00 0.00 3.32
168 1941 4.615912 GCAATTGGTTCTATGCGTTTCAGT 60.616 41.667 7.72 0.00 0.00 3.41
215 1988 3.512033 TTTTTCTTCCAACCGTGTTGG 57.488 42.857 22.56 22.56 46.41 3.77
263 2036 4.624024 CCATCACATGTTTCAACAGAATGC 59.376 41.667 0.00 0.00 43.04 3.56
274 2047 0.951558 ACAGAATGCCGTGTTTGGAC 59.048 50.000 0.00 0.00 42.53 4.02
284 2057 3.120130 GCCGTGTTTGGACGATATTTTCA 60.120 43.478 0.00 0.00 42.10 2.69
302 2075 5.828299 TTTCAACTACACCCTTTCAACTG 57.172 39.130 0.00 0.00 0.00 3.16
319 2122 5.490159 TCAACTGCATCTCACATGTTGATA 58.510 37.500 9.14 0.00 38.81 2.15
320 2123 5.352293 TCAACTGCATCTCACATGTTGATAC 59.648 40.000 9.14 6.40 38.81 2.24
343 2146 4.847365 ACATTTTCGATCGTGTCTGATG 57.153 40.909 15.94 13.25 0.00 3.07
347 2150 3.850122 TTCGATCGTGTCTGATGTCTT 57.150 42.857 15.94 0.00 0.00 3.01
376 2179 6.614694 GGGGGTATTTTGGTAGTGAAAATT 57.385 37.500 0.00 0.00 35.25 1.82
377 2180 6.636705 GGGGGTATTTTGGTAGTGAAAATTC 58.363 40.000 0.00 0.00 35.25 2.17
378 2181 6.439375 GGGGGTATTTTGGTAGTGAAAATTCT 59.561 38.462 0.00 0.00 35.25 2.40
379 2182 7.616542 GGGGGTATTTTGGTAGTGAAAATTCTA 59.383 37.037 0.00 0.00 35.25 2.10
380 2183 8.683615 GGGGTATTTTGGTAGTGAAAATTCTAG 58.316 37.037 0.00 0.00 35.25 2.43
381 2184 9.239551 GGGTATTTTGGTAGTGAAAATTCTAGT 57.760 33.333 0.00 0.00 35.25 2.57
447 2250 8.675504 GTCTATACTAGTGAAAGTTCTAGTGCA 58.324 37.037 5.39 0.00 44.12 4.57
466 2269 5.939883 AGTGCACAAAGAATAGTAAGATGCA 59.060 36.000 21.04 0.00 38.17 3.96
554 2358 1.798079 GCCGTCTTATCAGTCCACGAC 60.798 57.143 0.00 0.00 32.08 4.34
738 3996 1.077068 CGCCTGTCTCTCTCTCCCT 60.077 63.158 0.00 0.00 0.00 4.20
744 4002 1.222567 GTCTCTCTCTCCCTCCCTCT 58.777 60.000 0.00 0.00 0.00 3.69
746 4004 0.478507 CTCTCTCTCCCTCCCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
896 4160 2.221517 CGTAAGGAAACGCGGAAGAAAA 59.778 45.455 12.47 0.00 35.87 2.29
897 4161 3.303263 CGTAAGGAAACGCGGAAGAAAAA 60.303 43.478 12.47 0.00 35.87 1.94
903 4167 4.142556 GGAAACGCGGAAGAAAAATCCATA 60.143 41.667 12.47 0.00 36.74 2.74
1127 4391 3.507233 GTGCCATCTGAATTTCTGTGGAA 59.493 43.478 19.37 11.93 0.00 3.53
1168 4432 2.609610 CGGAAACCCCTCCTCCCA 60.610 66.667 0.00 0.00 32.82 4.37
1171 4435 1.541620 GAAACCCCTCCTCCCACCT 60.542 63.158 0.00 0.00 0.00 4.00
1201 4465 1.134431 CAGCCCCAATGGTAAATTGCC 60.134 52.381 0.00 0.00 36.04 4.52
1231 4499 8.897752 CCTCTTTCTTTCTTTCTTTCTTTCTGA 58.102 33.333 0.00 0.00 0.00 3.27
1248 4516 3.599343 TCTGATGGGAATTCGTTCTGTG 58.401 45.455 0.00 0.00 0.00 3.66
1277 4545 0.741221 GGCGCGGAAATCTGAGTCTT 60.741 55.000 8.83 0.00 0.00 3.01
2169 5451 1.370587 GAGAGACTCGGTGGGAGACG 61.371 65.000 0.00 0.00 46.23 4.18
2170 5452 1.376942 GAGACTCGGTGGGAGACGA 60.377 63.158 0.00 0.00 46.23 4.20
2171 5453 1.646624 GAGACTCGGTGGGAGACGAC 61.647 65.000 0.00 0.00 46.23 4.34
2172 5454 3.036783 GACTCGGTGGGAGACGACG 62.037 68.421 0.00 0.00 46.23 5.12
2434 5718 3.565902 GCTGGACTCAAGTGTAAAAAGCT 59.434 43.478 0.00 0.00 0.00 3.74
2435 5719 4.755123 GCTGGACTCAAGTGTAAAAAGCTA 59.245 41.667 0.00 0.00 0.00 3.32
2682 5969 4.954970 CAACGTGCCTGGCCCAGT 62.955 66.667 17.53 10.51 0.00 4.00
2875 6172 2.740714 GCCGTCGAACCTGATGCAC 61.741 63.158 0.00 0.00 0.00 4.57
2876 6173 2.444624 CCGTCGAACCTGATGCACG 61.445 63.158 0.00 0.00 0.00 5.34
2877 6174 2.778679 GTCGAACCTGATGCACGC 59.221 61.111 0.00 0.00 0.00 5.34
2880 6177 2.456119 CGAACCTGATGCACGCTCC 61.456 63.158 0.00 0.00 0.00 4.70
2881 6178 2.045926 AACCTGATGCACGCTCCC 60.046 61.111 0.00 0.00 0.00 4.30
2941 6248 3.344215 CGCGGCTCTCATGATGCC 61.344 66.667 22.68 22.68 42.94 4.40
2942 6249 2.203112 GCGGCTCTCATGATGCCA 60.203 61.111 28.13 3.04 46.39 4.92
2973 6280 3.035363 GAGGCTATAGAATAGGCCCCTC 58.965 54.545 14.74 0.00 42.08 4.30
2988 6295 2.279784 CTCGCGCCTGGAGATTCC 60.280 66.667 0.00 0.00 36.96 3.01
2993 6300 2.190578 GCCTGGAGATTCCGTGGG 59.809 66.667 0.00 4.07 40.17 4.61
2994 6301 2.190578 CCTGGAGATTCCGTGGGC 59.809 66.667 0.00 0.00 40.17 5.36
2995 6302 2.669133 CCTGGAGATTCCGTGGGCA 61.669 63.158 0.00 0.00 40.17 5.36
3098 6405 0.671251 CTCGATCCAGGAGTGGTAGC 59.329 60.000 0.00 0.00 45.28 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.390387 ACTTTAGTGCAAAAGGATACCCAA 58.610 37.500 13.92 0.00 40.16 4.12
19 20 6.882678 TCTTACTTTAGTGCAAAAGGATACCC 59.117 38.462 13.92 0.00 40.16 3.69
40 41 6.534475 TCGCTAACTATCAAAACCCTCTTA 57.466 37.500 0.00 0.00 0.00 2.10
79 81 2.621055 GTGCAGTGGTTACCATTTCACA 59.379 45.455 20.43 7.22 35.28 3.58
137 1910 5.350633 GCATAGAACCAATTGCATTGCTAA 58.649 37.500 10.49 3.28 38.92 3.09
199 1972 0.179040 GACCCAACACGGTTGGAAGA 60.179 55.000 27.40 0.00 42.06 2.87
215 1988 6.681777 AGTTGAAAAATATGCAGTTGAGACC 58.318 36.000 0.00 0.00 0.00 3.85
263 2036 4.671880 TGAAAATATCGTCCAAACACGG 57.328 40.909 0.00 0.00 40.35 4.94
274 2047 7.372451 TGAAAGGGTGTAGTTGAAAATATCG 57.628 36.000 0.00 0.00 0.00 2.92
284 2057 3.290948 TGCAGTTGAAAGGGTGTAGTT 57.709 42.857 0.00 0.00 0.00 2.24
302 2075 7.488187 AATGTAGTATCAACATGTGAGATGC 57.512 36.000 19.12 17.87 40.43 3.91
319 2122 5.055642 TCAGACACGATCGAAAATGTAGT 57.944 39.130 24.34 3.75 0.00 2.73
320 2123 5.516696 ACATCAGACACGATCGAAAATGTAG 59.483 40.000 24.34 11.38 0.00 2.74
353 2156 6.439375 AGAATTTTCACTACCAAAATACCCCC 59.561 38.462 0.00 0.00 33.24 5.40
354 2157 7.476540 AGAATTTTCACTACCAAAATACCCC 57.523 36.000 0.00 0.00 33.24 4.95
420 2223 8.895737 GCACTAGAACTTTCACTAGTATAGACT 58.104 37.037 0.00 0.00 44.69 3.24
421 2224 8.675504 TGCACTAGAACTTTCACTAGTATAGAC 58.324 37.037 0.00 0.00 44.69 2.59
422 2225 8.675504 GTGCACTAGAACTTTCACTAGTATAGA 58.324 37.037 10.32 0.00 44.69 1.98
423 2226 8.459635 TGTGCACTAGAACTTTCACTAGTATAG 58.540 37.037 19.41 0.00 44.69 1.31
424 2227 8.344446 TGTGCACTAGAACTTTCACTAGTATA 57.656 34.615 19.41 0.00 44.69 1.47
425 2228 7.228314 TGTGCACTAGAACTTTCACTAGTAT 57.772 36.000 19.41 0.00 44.69 2.12
428 2231 6.701841 TCTTTGTGCACTAGAACTTTCACTAG 59.298 38.462 19.41 0.00 41.01 2.57
434 2237 9.555727 TTACTATTCTTTGTGCACTAGAACTTT 57.444 29.630 26.41 17.89 31.31 2.66
447 2250 8.470002 GGGAATTTGCATCTTACTATTCTTTGT 58.530 33.333 0.00 0.00 0.00 2.83
466 2269 5.867330 TCATGCTTCACAATTTGGGAATTT 58.133 33.333 14.21 0.59 39.34 1.82
604 3861 3.746889 CGGCAATTTGCGAGCCCA 61.747 61.111 14.83 0.00 46.21 5.36
634 3891 0.623617 GACCATGGTTAGGACCCCCT 60.624 60.000 20.85 0.00 45.92 4.79
738 3996 3.118149 GCGTTTAATAAAGGGGAGAGGGA 60.118 47.826 7.43 0.00 0.00 4.20
744 4002 2.743126 CGTGTGCGTTTAATAAAGGGGA 59.257 45.455 7.43 0.00 0.00 4.81
746 4004 2.743126 TCCGTGTGCGTTTAATAAAGGG 59.257 45.455 7.43 0.00 36.15 3.95
1168 4432 3.415087 GGCTGGCCATCTGGAGGT 61.415 66.667 5.51 0.00 37.39 3.85
1201 4465 5.534278 AGAAAGAAAGAAAGAAAGAGGGCTG 59.466 40.000 0.00 0.00 0.00 4.85
1231 4499 2.356125 CCTCCACAGAACGAATTCCCAT 60.356 50.000 0.00 0.00 35.18 4.00
1277 4545 6.403092 CCATATCTAATCAAACACGCACACAA 60.403 38.462 0.00 0.00 0.00 3.33
1730 5012 3.381590 TCCTTGATCTGTATCACACGAGG 59.618 47.826 0.00 0.00 41.87 4.63
1762 5044 2.203938 TCCTCGTCCCCCAGCTTT 60.204 61.111 0.00 0.00 0.00 3.51
2185 5467 8.739972 GCTTTCTTCACTAATCTTTTATTCCCA 58.260 33.333 0.00 0.00 0.00 4.37
2404 5688 5.546621 ACACTTGAGTCCAGCTTAACTTA 57.453 39.130 0.00 0.00 0.00 2.24
2434 5718 1.690209 CCCTTGTCCCTATCCCGTGTA 60.690 57.143 0.00 0.00 0.00 2.90
2435 5719 0.981277 CCCTTGTCCCTATCCCGTGT 60.981 60.000 0.00 0.00 0.00 4.49
2822 6116 4.210746 TGCTACTACGTACGAGAATAGCAG 59.789 45.833 27.65 18.45 38.81 4.24
2875 6172 2.175035 TTTCTTGTACCGGGGGAGCG 62.175 60.000 6.32 0.00 0.00 5.03
2876 6173 0.392595 CTTTCTTGTACCGGGGGAGC 60.393 60.000 6.32 0.00 0.00 4.70
2877 6174 1.272807 TCTTTCTTGTACCGGGGGAG 58.727 55.000 6.32 0.00 0.00 4.30
2880 6177 2.853705 TGTTTCTTTCTTGTACCGGGG 58.146 47.619 6.32 0.00 0.00 5.73
2881 6178 4.577283 TCTTTGTTTCTTTCTTGTACCGGG 59.423 41.667 6.32 0.00 0.00 5.73
2973 6280 4.514577 ACGGAATCTCCAGGCGCG 62.515 66.667 0.00 0.00 35.91 6.86
3074 6381 2.508716 ACCACTCCTGGATCGAGTAGTA 59.491 50.000 2.66 0.00 40.55 1.82
3075 6382 1.285373 ACCACTCCTGGATCGAGTAGT 59.715 52.381 3.90 0.32 40.55 2.73
3076 6383 2.060050 ACCACTCCTGGATCGAGTAG 57.940 55.000 3.90 0.00 40.55 2.57


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

AutoCloner maintained by Alex Coulton.