Multiple sequence alignment - TraesCS4D01G236000

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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 TraesCS4D01G236000 chr4D 100.000 4241 0 0 1 4241 397669585 397665345 0.000000e+00 7832
1 TraesCS4D01G236000 chr4A 89.305 4376 193 83 9 4220 55380772 55376508 0.000000e+00 5234
2 TraesCS4D01G236000 chr4B 95.346 3008 79 30 1258 4238 489650042 489647069 0.000000e+00 4723
3 TraesCS4D01G236000 chr4B 93.189 925 29 15 302 1221 489650942 489650047 0.000000e+00 1328
4 TraesCS4D01G236000 chr4B 93.624 298 12 2 1 298 489651397 489651107 5.030000e-119 438
5 TraesCS4D01G236000 chr1D 86.667 195 24 2 903 1096 444882864 444882671 9.240000e-52 215


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 TraesCS4D01G236000 chr4D 397665345 397669585 4240 True 7832 7832 100.000 1 4241 1 chr4D.!!$R1 4240
1 TraesCS4D01G236000 chr4A 55376508 55380772 4264 True 5234 5234 89.305 9 4220 1 chr4A.!!$R1 4211
2 TraesCS4D01G236000 chr4B 489647069 489651397 4328 True 2163 4723 94.053 1 4238 3 chr4B.!!$R1 4237

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
49 50 0.963225 GTGCCTACCTAGCTAGCTCC 59.037 60.0 23.26 2.84 0.00 4.70 F
1262 1511 0.522626 CGTCCGGCCGGTAAAAATTT 59.477 50.0 41.57 0.00 36.47 1.82 F
1822 2086 0.036388 CACGGGCCACATACTCAAGT 60.036 55.0 4.39 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1267 1516 1.061131 GCTTGTACGTGTGCATGCTAG 59.939 52.381 20.33 9.74 40.99 3.42 R
2896 3160 0.672401 TTGCCAGTAGTTACCGCTGC 60.672 55.000 0.00 0.00 0.00 5.25 R
3368 3656 0.584396 AATACTCTCTCTCTCGCGCG 59.416 55.000 26.76 26.76 0.00 6.86 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
26 27 3.566322 CGGTACTTTGTGGGTGAAAATGA 59.434 43.478 0.00 0.00 0.00 2.57
27 28 4.036971 CGGTACTTTGTGGGTGAAAATGAA 59.963 41.667 0.00 0.00 0.00 2.57
28 29 5.278758 CGGTACTTTGTGGGTGAAAATGAAT 60.279 40.000 0.00 0.00 0.00 2.57
29 30 5.925969 GGTACTTTGTGGGTGAAAATGAATG 59.074 40.000 0.00 0.00 0.00 2.67
37 38 3.119137 GGGTGAAAATGAATGGTGCCTAC 60.119 47.826 0.00 0.00 0.00 3.18
49 50 0.963225 GTGCCTACCTAGCTAGCTCC 59.037 60.000 23.26 2.84 0.00 4.70
228 244 1.153086 CGGAGAGGCCAATCCCAAG 60.153 63.158 18.01 3.56 35.94 3.61
242 258 1.822990 TCCCAAGCCTTACTCTACGTG 59.177 52.381 0.00 0.00 0.00 4.49
252 273 2.126618 TCTACGTGCAGTTCGGCG 60.127 61.111 0.00 0.00 36.28 6.46
280 301 2.603110 CACTGATTATTCACCCGTCACG 59.397 50.000 0.00 0.00 0.00 4.35
438 635 1.195448 CGTGCGAGATTATGCCATTCC 59.805 52.381 0.00 0.00 0.00 3.01
439 636 2.221169 GTGCGAGATTATGCCATTCCA 58.779 47.619 0.00 0.00 0.00 3.53
442 639 2.483876 CGAGATTATGCCATTCCACGT 58.516 47.619 0.00 0.00 0.00 4.49
526 724 2.433239 TCCAGCCCGGAAGAAATAGTAC 59.567 50.000 0.73 0.00 42.52 2.73
529 727 4.262079 CCAGCCCGGAAGAAATAGTACTAG 60.262 50.000 0.73 0.00 36.56 2.57
559 771 7.849322 ATTCCATTCATTCATTCCATGATGA 57.151 32.000 0.00 0.00 39.39 2.92
617 830 3.475774 CACGTACGTGCCTTCCGC 61.476 66.667 32.93 0.00 39.39 5.54
806 1028 0.992695 TCCCACGGAGAGAGAGAGAA 59.007 55.000 0.00 0.00 0.00 2.87
809 1031 1.134175 CCACGGAGAGAGAGAGAAAGC 59.866 57.143 0.00 0.00 0.00 3.51
810 1032 2.091541 CACGGAGAGAGAGAGAAAGCT 58.908 52.381 0.00 0.00 0.00 3.74
812 1034 1.405105 CGGAGAGAGAGAGAAAGCTGG 59.595 57.143 0.00 0.00 0.00 4.85
814 1036 1.136891 GAGAGAGAGAGAAAGCTGGGC 59.863 57.143 0.00 0.00 0.00 5.36
815 1037 1.194218 GAGAGAGAGAAAGCTGGGCT 58.806 55.000 0.00 0.00 42.56 5.19
924 1156 5.410924 CAACAGTGGAAAGATCGATACAGA 58.589 41.667 0.00 0.00 0.00 3.41
1159 1400 1.153549 CTGGCGCTCTCCAAGGTAC 60.154 63.158 7.64 0.00 35.36 3.34
1201 1450 3.969899 TGTAGATGCGCACATTCTCTAG 58.030 45.455 14.90 0.00 36.35 2.43
1238 1487 2.104331 GCATCTGCATGTGCCTGC 59.896 61.111 11.29 5.66 42.62 4.85
1239 1488 2.415608 GCATCTGCATGTGCCTGCT 61.416 57.895 11.29 0.00 42.75 4.24
1240 1489 1.433471 CATCTGCATGTGCCTGCTG 59.567 57.895 2.07 4.56 42.75 4.41
1241 1490 2.415608 ATCTGCATGTGCCTGCTGC 61.416 57.895 2.07 0.00 42.75 5.25
1242 1491 4.129737 CTGCATGTGCCTGCTGCC 62.130 66.667 2.07 0.00 42.75 4.85
1258 1507 4.391601 CCCGTCCGGCCGGTAAAA 62.392 66.667 41.57 22.30 46.66 1.52
1259 1508 2.358492 CCGTCCGGCCGGTAAAAA 60.358 61.111 41.57 21.87 43.07 1.94
1261 1510 1.307355 CCGTCCGGCCGGTAAAAATT 61.307 55.000 41.57 0.00 43.07 1.82
1262 1511 0.522626 CGTCCGGCCGGTAAAAATTT 59.477 50.000 41.57 0.00 36.47 1.82
1263 1512 1.466192 CGTCCGGCCGGTAAAAATTTC 60.466 52.381 41.57 19.61 36.47 2.17
1265 1514 2.164827 GTCCGGCCGGTAAAAATTTCAT 59.835 45.455 41.57 0.00 36.47 2.57
1267 1516 3.119424 TCCGGCCGGTAAAAATTTCATTC 60.119 43.478 41.57 0.00 36.47 2.67
1268 1517 3.119280 CCGGCCGGTAAAAATTTCATTCT 60.119 43.478 36.64 0.00 0.00 2.40
1431 1695 2.816672 AGCTAGTTTGCTTTTCTGAGCC 59.183 45.455 0.00 0.00 40.93 4.70
1440 1704 2.611518 CTTTTCTGAGCCGATCGACTT 58.388 47.619 18.66 0.59 0.00 3.01
1441 1705 3.770666 CTTTTCTGAGCCGATCGACTTA 58.229 45.455 18.66 6.15 0.00 2.24
1442 1706 3.861276 TTTCTGAGCCGATCGACTTAA 57.139 42.857 18.66 3.74 0.00 1.85
1822 2086 0.036388 CACGGGCCACATACTCAAGT 60.036 55.000 4.39 0.00 0.00 3.16
1953 2217 2.743928 CAGAACCTCACGCTGCCC 60.744 66.667 0.00 0.00 0.00 5.36
1977 2241 2.185608 GCGTGCTCCCTCTTCTCC 59.814 66.667 0.00 0.00 0.00 3.71
2135 2399 1.458777 ACAAGGACTCGTGGGTGGA 60.459 57.895 0.00 0.00 0.00 4.02
2464 2728 1.656652 CGTAGCTTCCACCTTCATGG 58.343 55.000 0.00 0.00 41.57 3.66
2475 2739 1.037493 CCTTCATGGTATCCGTCCGA 58.963 55.000 0.00 0.00 0.00 4.55
2911 3175 1.732259 CCAAAGCAGCGGTAACTACTG 59.268 52.381 0.00 0.00 40.34 2.74
3013 3283 0.548031 GGAAGGGCTCATGTCCATGA 59.452 55.000 9.47 9.47 44.83 3.07
3064 3343 1.715585 GACACGAATGCGGTGGATG 59.284 57.895 0.00 0.00 43.17 3.51
3354 3642 2.163613 GGTGGCGAGGTTTTGATAAAGG 59.836 50.000 0.00 0.00 0.00 3.11
3355 3643 2.163613 GTGGCGAGGTTTTGATAAAGGG 59.836 50.000 0.00 0.00 0.00 3.95
3356 3644 1.134367 GGCGAGGTTTTGATAAAGGGC 59.866 52.381 0.00 0.00 0.00 5.19
3357 3645 1.202143 GCGAGGTTTTGATAAAGGGCG 60.202 52.381 0.00 0.00 0.00 6.13
3395 3695 4.398319 GAGAGAGAGAGTATTGAGGAGGG 58.602 52.174 0.00 0.00 0.00 4.30
3462 3762 6.465894 GCTTATCATTACCCCAGATTGGTACT 60.466 42.308 0.00 0.00 38.06 2.73
3485 3785 1.242076 CACAACTCCTGGAAGCCTTG 58.758 55.000 0.00 0.14 0.00 3.61
3556 3863 9.797642 TTTATATATTCATTCACCAGAGTGCAT 57.202 29.630 0.00 0.00 44.16 3.96
3826 4151 1.939769 TTTTGATAAAGCGGCCGGGC 61.940 55.000 29.38 20.04 0.00 6.13
3827 4152 4.868116 TGATAAAGCGGCCGGGCC 62.868 66.667 28.61 28.61 46.75 5.80
3907 4232 4.492294 GTCTTGCGATTTTGCGAAGAATAC 59.508 41.667 0.00 0.00 35.41 1.89
4045 4394 4.742438 ACAAACGTCGAATAAAGCATGT 57.258 36.364 0.00 0.00 0.00 3.21
4048 4397 2.695359 ACGTCGAATAAAGCATGTGGT 58.305 42.857 0.00 0.00 0.00 4.16
4064 4414 0.178950 TGGTTTTATGGCAGCACCCA 60.179 50.000 0.00 0.00 39.65 4.51
4147 4497 6.166982 CGACCACTTCCTCTTTCTCTATTTT 58.833 40.000 0.00 0.00 0.00 1.82
4157 4507 5.144100 TCTTTCTCTATTTTGGGTTTGCCA 58.856 37.500 0.00 0.00 36.17 4.92
4211 4561 3.224884 ACGTTGGGTTTGTCAACTTTG 57.775 42.857 0.00 0.00 41.47 2.77
4220 4570 5.050567 GGGTTTGTCAACTTTGAGTAGTACG 60.051 44.000 0.00 0.00 37.98 3.67
4223 4573 7.335491 GTTTGTCAACTTTGAGTAGTACGAAG 58.665 38.462 10.58 10.58 37.98 3.79
4238 4588 5.855045 AGTACGAAGAGATTTTTCTGTGGT 58.145 37.500 0.00 0.00 0.00 4.16
4239 4589 6.989659 AGTACGAAGAGATTTTTCTGTGGTA 58.010 36.000 0.00 0.00 0.00 3.25
4240 4590 6.867293 AGTACGAAGAGATTTTTCTGTGGTAC 59.133 38.462 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.963225 GAGCTAGCTAGGTAGGCACC 59.037 60.000 24.74 12.29 46.19 5.01
37 38 1.036707 GTGTCCAGGAGCTAGCTAGG 58.963 60.000 19.38 19.35 0.00 3.02
49 50 1.927174 GTTTGGATCGATCGTGTCCAG 59.073 52.381 29.52 1.08 42.54 3.86
228 244 2.260481 GAACTGCACGTAGAGTAAGGC 58.740 52.381 0.00 0.00 0.00 4.35
231 247 1.401931 GCCGAACTGCACGTAGAGTAA 60.402 52.381 0.00 0.00 0.00 2.24
252 273 2.945668 GGTGAATAATCAGTGGCTCACC 59.054 50.000 3.48 3.48 44.28 4.02
379 575 1.235281 GGACCCAACAACTTCGCCTC 61.235 60.000 0.00 0.00 0.00 4.70
380 576 1.228154 GGACCCAACAACTTCGCCT 60.228 57.895 0.00 0.00 0.00 5.52
381 577 2.613506 CGGACCCAACAACTTCGCC 61.614 63.158 0.00 0.00 0.00 5.54
382 578 0.953960 ATCGGACCCAACAACTTCGC 60.954 55.000 0.00 0.00 0.00 4.70
438 635 1.740285 CCCTATCCCTTCGGACGTG 59.260 63.158 0.00 0.00 42.48 4.49
439 636 1.457079 CCCCTATCCCTTCGGACGT 60.457 63.158 0.00 0.00 42.48 4.34
442 639 2.090153 AGAATTCCCCTATCCCTTCGGA 60.090 50.000 0.65 0.00 44.33 4.55
814 1036 6.888430 ACATTTGACTCGTTAGCTTACAAAG 58.112 36.000 3.47 2.53 31.25 2.77
815 1037 6.854496 ACATTTGACTCGTTAGCTTACAAA 57.146 33.333 3.47 0.00 0.00 2.83
924 1156 1.638589 CTCCCTCGATCCCTCCTCTAT 59.361 57.143 0.00 0.00 0.00 1.98
971 1203 3.435186 GCCGGCTGGAAAGTGCTC 61.435 66.667 22.15 0.00 37.49 4.26
1057 1292 1.747924 GGAGGAATTCTTGAAGCAGGC 59.252 52.381 5.23 0.00 0.00 4.85
1201 1450 3.143728 GCAGGTAGAGGTAGCTAGAGAC 58.856 54.545 0.00 0.00 35.13 3.36
1258 1507 4.156556 ACGTGTGCATGCTAGAATGAAATT 59.843 37.500 20.33 0.00 40.93 1.82
1259 1508 3.691118 ACGTGTGCATGCTAGAATGAAAT 59.309 39.130 20.33 0.00 0.00 2.17
1261 1510 2.698803 ACGTGTGCATGCTAGAATGAA 58.301 42.857 20.33 0.00 0.00 2.57
1262 1511 2.385013 ACGTGTGCATGCTAGAATGA 57.615 45.000 20.33 0.00 0.00 2.57
1263 1512 2.929398 TGTACGTGTGCATGCTAGAATG 59.071 45.455 20.33 6.31 0.00 2.67
1265 1514 2.734276 TGTACGTGTGCATGCTAGAA 57.266 45.000 20.33 0.00 0.00 2.10
1267 1516 1.061131 GCTTGTACGTGTGCATGCTAG 59.939 52.381 20.33 9.74 40.99 3.42
1268 1517 1.075542 GCTTGTACGTGTGCATGCTA 58.924 50.000 20.33 5.09 40.99 3.49
1440 1704 6.087159 CACGAGCGCACGTAAGATTATTATTA 59.913 38.462 31.20 0.00 44.76 0.98
1441 1705 4.980434 ACGAGCGCACGTAAGATTATTATT 59.020 37.500 30.80 1.43 44.72 1.40
1442 1706 4.381863 CACGAGCGCACGTAAGATTATTAT 59.618 41.667 31.20 2.52 44.76 1.28
1746 2010 4.385405 AGGAGCAGCAGCACGGTC 62.385 66.667 3.17 0.00 45.49 4.79
1822 2086 4.069232 CTCGTCCTGGCCGAGCAA 62.069 66.667 14.63 0.00 44.42 3.91
1953 2217 4.457496 AGGGAGCACGCGGTGATG 62.457 66.667 12.47 0.00 35.23 3.07
1968 2232 1.153667 GAGCAGCACGGAGAAGAGG 60.154 63.158 0.00 0.00 0.00 3.69
2135 2399 3.148279 GGCAGTCGGAGGTCGGAT 61.148 66.667 0.00 0.00 39.77 4.18
2464 2728 1.636988 CAGTGGTTTCGGACGGATAC 58.363 55.000 0.00 0.00 0.00 2.24
2475 2739 4.299796 ATGCGGCCCCAGTGGTTT 62.300 61.111 8.74 0.00 36.04 3.27
2634 2898 1.365028 AGGTAGAAGGAGGCCAGGTTA 59.635 52.381 5.01 0.00 0.00 2.85
2896 3160 0.672401 TTGCCAGTAGTTACCGCTGC 60.672 55.000 0.00 0.00 0.00 5.25
2911 3175 2.093537 TTGTTTCCACCGGCATTGCC 62.094 55.000 18.10 18.10 46.75 4.52
3034 3313 3.425713 CGTGTCGCCATTGCTGCT 61.426 61.111 0.00 0.00 34.43 4.24
3064 3343 2.202730 GCTGCTCTCGCTGTCTCC 60.203 66.667 0.00 0.00 37.41 3.71
3368 3656 0.584396 AATACTCTCTCTCTCGCGCG 59.416 55.000 26.76 26.76 0.00 6.86
3370 3658 2.223144 CCTCAATACTCTCTCTCTCGCG 59.777 54.545 0.00 0.00 0.00 5.87
3372 3660 4.065088 CCTCCTCAATACTCTCTCTCTCG 58.935 52.174 0.00 0.00 0.00 4.04
3427 3727 6.152661 TGGGGTAATGATAAGCAAGAAAAGTG 59.847 38.462 0.00 0.00 0.00 3.16
3462 3762 1.271379 GGCTTCCAGGAGTTGTGCTTA 60.271 52.381 0.00 0.00 0.00 3.09
3485 3785 7.270047 TCTTATGGTGTGGCTAGTATTTACAC 58.730 38.462 0.00 0.00 40.53 2.90
3542 3849 9.440773 GATTGATAATATATGCACTCTGGTGAA 57.559 33.333 0.00 0.00 45.61 3.18
3543 3850 7.761249 CGATTGATAATATATGCACTCTGGTGA 59.239 37.037 0.00 0.00 45.61 4.02
3544 3851 7.761249 TCGATTGATAATATATGCACTCTGGTG 59.239 37.037 0.00 0.00 45.53 4.17
3545 3852 7.840931 TCGATTGATAATATATGCACTCTGGT 58.159 34.615 0.00 0.00 0.00 4.00
3683 4004 2.663196 GGGGAACAGCGCTACAGT 59.337 61.111 10.99 0.00 0.00 3.55
3826 4151 2.638154 GAGGATCGTACGCTCCGG 59.362 66.667 27.24 0.00 35.72 5.14
3827 4152 2.638154 GGAGGATCGTACGCTCCG 59.362 66.667 27.24 0.00 35.72 4.63
3828 4153 1.235948 ATCGGAGGATCGTACGCTCC 61.236 60.000 26.69 26.69 34.37 4.70
3829 4154 1.436600 TATCGGAGGATCGTACGCTC 58.563 55.000 15.17 10.87 34.37 5.03
4045 4394 0.178950 TGGGTGCTGCCATAAAACCA 60.179 50.000 6.87 0.00 39.65 3.67
4048 4397 1.255882 CACTGGGTGCTGCCATAAAA 58.744 50.000 0.00 0.00 39.65 1.52
4064 4414 6.879993 CCATATCCGAGTAGTAGTATCACACT 59.120 42.308 0.00 0.00 41.62 3.55
4078 4428 1.143073 GGCCCTTTTCCATATCCGAGT 59.857 52.381 0.00 0.00 0.00 4.18
4079 4429 1.421646 AGGCCCTTTTCCATATCCGAG 59.578 52.381 0.00 0.00 0.00 4.63
4080 4430 1.518367 AGGCCCTTTTCCATATCCGA 58.482 50.000 0.00 0.00 0.00 4.55
4157 4507 6.565234 TCACAAAAACCACACGATTACAAAT 58.435 32.000 0.00 0.00 0.00 2.32
4211 4561 7.273815 CCACAGAAAAATCTCTTCGTACTACTC 59.726 40.741 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.