Multiple sequence alignment - TraesCS4A01G446000

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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 TraesCS4A01G446000 chr4A 100.000 3559 0 0 1 3559 713792485 713788927 0 6573
1 TraesCS4A01G446000 chr2B 97.360 3560 85 9 1 3555 19851984 19855539 0 6045
2 TraesCS4A01G446000 chr2B 94.311 3586 146 30 1 3555 655694281 655690723 0 5439
3 TraesCS4A01G446000 chr2B 97.361 2160 54 3 1 2159 512426259 512424102 0 3670
4 TraesCS4A01G446000 chr2B 97.398 1345 31 4 2218 3559 658222502 658221159 0 2287
5 TraesCS4A01G446000 chr6B 97.104 3557 97 4 1 3555 353552239 353548687 0 5993
6 TraesCS4A01G446000 chr6B 97.387 2449 60 4 1 2447 319457337 319459783 0 4165
7 TraesCS4A01G446000 chr4B 97.340 3308 82 6 1 3305 603291274 603287970 0 5616
8 TraesCS4A01G446000 chr4B 94.316 3589 144 27 1 3555 15516598 15520160 0 5443
9 TraesCS4A01G446000 chr3B 93.787 3589 160 29 1 3555 60566608 60570167 0 5334
10 TraesCS4A01G446000 chr7B 96.419 2206 72 7 1 2204 599829327 599831527 0 3629
11 TraesCS4A01G446000 chr7B 97.466 1342 29 5 2218 3555 693176173 693177513 0 2285
12 TraesCS4A01G446000 chr7B 97.392 1342 31 4 2218 3555 180026082 180024741 0 2281


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 TraesCS4A01G446000 chr4A 713788927 713792485 3558 True 6573 6573 100.000 1 3559 1 chr4A.!!$R1 3558
1 TraesCS4A01G446000 chr2B 19851984 19855539 3555 False 6045 6045 97.360 1 3555 1 chr2B.!!$F1 3554
2 TraesCS4A01G446000 chr2B 655690723 655694281 3558 True 5439 5439 94.311 1 3555 1 chr2B.!!$R2 3554
3 TraesCS4A01G446000 chr2B 512424102 512426259 2157 True 3670 3670 97.361 1 2159 1 chr2B.!!$R1 2158
4 TraesCS4A01G446000 chr2B 658221159 658222502 1343 True 2287 2287 97.398 2218 3559 1 chr2B.!!$R3 1341
5 TraesCS4A01G446000 chr6B 353548687 353552239 3552 True 5993 5993 97.104 1 3555 1 chr6B.!!$R1 3554
6 TraesCS4A01G446000 chr6B 319457337 319459783 2446 False 4165 4165 97.387 1 2447 1 chr6B.!!$F1 2446
7 TraesCS4A01G446000 chr4B 603287970 603291274 3304 True 5616 5616 97.340 1 3305 1 chr4B.!!$R1 3304
8 TraesCS4A01G446000 chr4B 15516598 15520160 3562 False 5443 5443 94.316 1 3555 1 chr4B.!!$F1 3554
9 TraesCS4A01G446000 chr3B 60566608 60570167 3559 False 5334 5334 93.787 1 3555 1 chr3B.!!$F1 3554
10 TraesCS4A01G446000 chr7B 599829327 599831527 2200 False 3629 3629 96.419 1 2204 1 chr7B.!!$F1 2203
11 TraesCS4A01G446000 chr7B 693176173 693177513 1340 False 2285 2285 97.466 2218 3555 1 chr7B.!!$F2 1337
12 TraesCS4A01G446000 chr7B 180024741 180026082 1341 True 2281 2281 97.392 2218 3555 1 chr7B.!!$R1 1337

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
762 799 0.953727 GTGAATCTGGTGTGCTTGCA 59.046 50.0 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2613 2666 4.586001 CCCTGTCTTCCCCATCATATTTTG 59.414 45.833 0.0 0.0 0.0 2.44 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
105 107 7.065803 ACCTTTGTTGTATCATATTCTTCACCG 59.934 37.037 0.00 0.00 0.00 4.94
261 265 8.461222 TCAAAACATACTGAGCATATCCAAAAG 58.539 33.333 0.00 0.00 0.00 2.27
266 270 4.275810 ACTGAGCATATCCAAAAGCACAT 58.724 39.130 0.00 0.00 0.00 3.21
429 437 7.840342 AACACTAAACATGCTCTAATCTCTG 57.160 36.000 0.00 0.00 0.00 3.35
483 491 5.934625 CACTTCAAAGTAGCACTTCTATGGT 59.065 40.000 0.00 0.00 37.47 3.55
762 799 0.953727 GTGAATCTGGTGTGCTTGCA 59.046 50.000 0.00 0.00 0.00 4.08
828 865 6.202570 GCTTGCCTCAACAACATAAAAATTGA 59.797 34.615 0.00 0.00 0.00 2.57
1068 1107 4.562082 TGTACTGTACACAACATGCTACC 58.438 43.478 16.26 0.00 37.50 3.18
1101 1140 1.816074 TTGTGGCGGAATCACCTAAC 58.184 50.000 0.00 0.00 36.31 2.34
1106 1145 1.145377 CGGAATCACCTAACCCCCG 59.855 63.158 0.00 0.00 36.31 5.73
1166 1205 1.003580 GGAGACAGATGGGCAGTCAAA 59.996 52.381 0.00 0.00 35.64 2.69
1171 1210 3.021695 ACAGATGGGCAGTCAAATCATG 58.978 45.455 0.00 0.00 0.00 3.07
1240 1280 2.224402 GGGAGTGATGCTCATACCCTTC 60.224 54.545 15.83 0.53 45.88 3.46
1529 1570 1.340017 CGGAGGGGCAGAAAAGATTCA 60.340 52.381 0.00 0.00 38.06 2.57
1530 1571 2.684927 CGGAGGGGCAGAAAAGATTCAT 60.685 50.000 0.00 0.00 38.06 2.57
1557 1598 4.151258 AGATGACATTGTTGAACAAGCG 57.849 40.909 16.43 11.94 41.94 4.68
1578 1619 8.340443 CAAGCGAAAGATGATAATGAAGATGAA 58.660 33.333 0.00 0.00 0.00 2.57
1934 1975 3.255642 TGTTTCTTAGCCCATCAACAAGC 59.744 43.478 0.00 0.00 0.00 4.01
2120 2162 5.221762 TGCAAAAGTTCCTACTTGCCTAGTA 60.222 40.000 6.73 0.00 43.74 1.82
2583 2630 7.934120 AGACAGTTGCTTACTTTAAAGATCAGT 59.066 33.333 21.92 1.99 33.85 3.41
2718 2771 7.665145 TCATGATTGTATCTCCTTTGACACAAA 59.335 33.333 0.00 0.00 30.48 2.83
2851 2904 3.786048 GCTTTGATTGGCTATTCGAAACG 59.214 43.478 0.00 0.00 0.00 3.60
3085 3138 0.097674 CGCTGGAAGAATTTGAGGCG 59.902 55.000 0.00 0.00 34.07 5.52
3120 3173 5.047164 AGCTGATGATGAAGTATGAGGCTAG 60.047 44.000 0.00 0.00 0.00 3.42
3192 3245 4.288626 ACCCTTCTACTTCAAGCACCAATA 59.711 41.667 0.00 0.00 0.00 1.90
3556 3609 5.430417 TGGTTCTAGGGGCTATTTTGTCATA 59.570 40.000 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 99 3.762407 TTTCTTGGATCACGGTGAAGA 57.238 42.857 15.72 10.35 0.00 2.87
261 265 2.712057 ACAGCAGCAAGTTTATGTGC 57.288 45.000 0.00 0.00 41.22 4.57
266 270 8.450964 GTTTCATCTATTACAGCAGCAAGTTTA 58.549 33.333 0.00 0.00 0.00 2.01
429 437 5.420104 AGAATGGATTTCACTCCCAAATCAC 59.580 40.000 7.30 0.00 40.60 3.06
483 491 3.730215 TTTGGGGAAGCAAGCATACTA 57.270 42.857 0.00 0.00 0.00 1.82
662 673 6.891908 ACCATATAATCAGGCAAGTCAAACTT 59.108 34.615 0.00 0.00 39.39 2.66
762 799 1.935199 GCAAGCAAACAACACAGCAAT 59.065 42.857 0.00 0.00 0.00 3.56
847 885 7.760794 TCAATCATGTTCAACCTATGCATTTTC 59.239 33.333 3.54 0.00 0.00 2.29
993 1032 6.351202 CCTCATTTAGGTCAATCATTGCCAAA 60.351 38.462 11.87 10.21 40.94 3.28
1068 1107 1.994779 GCCACAAATTCTGCATTTCCG 59.005 47.619 0.00 0.00 32.24 4.30
1101 1140 1.768870 ACTCTTTGGATGATACGGGGG 59.231 52.381 0.00 0.00 0.00 5.40
1207 1247 0.251787 TCACTCCCAGCTGCTACAGA 60.252 55.000 8.66 0.00 32.44 3.41
1529 1570 5.706833 TGTTCAACAATGTCATCTAGCACAT 59.293 36.000 0.00 0.00 34.58 3.21
1530 1571 5.062528 TGTTCAACAATGTCATCTAGCACA 58.937 37.500 0.00 0.00 0.00 4.57
1578 1619 9.491675 CTATCATCATCAAGAAAGACAATAGCT 57.508 33.333 0.00 0.00 0.00 3.32
1934 1975 7.648908 TGACATGTTTCAAGCAAAATCAAGTAG 59.351 33.333 0.00 0.00 0.00 2.57
2482 2529 7.759433 GGTTTGTAATGTGCTTTGTGCTATAAT 59.241 33.333 0.00 0.00 43.37 1.28
2556 2603 9.424319 CTGATCTTTAAAGTAAGCAACTGTCTA 57.576 33.333 14.74 0.00 38.88 2.59
2613 2666 4.586001 CCCTGTCTTCCCCATCATATTTTG 59.414 45.833 0.00 0.00 0.00 2.44
2625 2678 4.779993 ATATTCTCAACCCTGTCTTCCC 57.220 45.455 0.00 0.00 0.00 3.97
2851 2904 4.142093 ACATTATGCATTGCCTCAAGGAAC 60.142 41.667 3.54 0.00 37.39 3.62
3085 3138 1.222936 CATCAGCTCACTCCACCCC 59.777 63.158 0.00 0.00 0.00 4.95
3174 3227 5.488341 GGAAGTATTGGTGCTTGAAGTAGA 58.512 41.667 0.00 0.00 29.89 2.59
3192 3245 2.952310 GTTGACTGCAAGAAAGGGAAGT 59.048 45.455 0.00 0.00 37.43 3.01
3317 3370 1.732117 TTTGAACCCTCCCGGACTAA 58.268 50.000 0.73 0.00 34.64 2.24


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

AutoCloner maintained by Alex Coulton.