Multiple sequence alignment - TraesCS5B01G340200

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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 TraesCS5B01G340200 chr5B 100.000 3239 0 0 1 3239 524577394 524580632 0 5982
1 TraesCS5B01G340200 chr5B 98.417 2842 44 1 399 3239 267772326 267769485 0 4998
2 TraesCS5B01G340200 chr7B 98.500 3066 44 2 175 3239 577190304 577193368 0 5406
3 TraesCS5B01G340200 chr7B 97.608 2634 60 2 555 3185 586369667 586372300 0 4512
4 TraesCS5B01G340200 chr7B 96.381 2708 72 9 540 3239 203603063 203600374 0 4434
5 TraesCS5B01G340200 chr2B 96.727 3239 66 10 1 3239 699751684 699754882 0 5358
6 TraesCS5B01G340200 chr1B 96.073 3234 104 7 10 3239 659739541 659736327 0 5247
7 TraesCS5B01G340200 chr1B 96.791 2680 61 5 564 3239 631847834 631845176 0 4449
8 TraesCS5B01G340200 chr2A 95.640 3234 106 9 10 3239 470636931 470633729 0 5158
9 TraesCS5B01G340200 chr2A 97.542 2685 57 4 564 3239 411115945 411118629 0 4584
10 TraesCS5B01G340200 chr1A 96.017 3013 97 7 10 3018 58195151 58198144 0 4878
11 TraesCS5B01G340200 chr6B 96.065 2846 89 7 10 2851 693560252 693563078 0 4614
12 TraesCS5B01G340200 chr4A 96.418 2680 72 6 564 3239 740137102 740139761 0 4396
13 TraesCS5B01G340200 chr4B 96.431 1541 37 2 1700 3239 519576577 519578100 0 2525


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 TraesCS5B01G340200 chr5B 524577394 524580632 3238 False 5982 5982 100.000 1 3239 1 chr5B.!!$F1 3238
1 TraesCS5B01G340200 chr5B 267769485 267772326 2841 True 4998 4998 98.417 399 3239 1 chr5B.!!$R1 2840
2 TraesCS5B01G340200 chr7B 577190304 577193368 3064 False 5406 5406 98.500 175 3239 1 chr7B.!!$F1 3064
3 TraesCS5B01G340200 chr7B 586369667 586372300 2633 False 4512 4512 97.608 555 3185 1 chr7B.!!$F2 2630
4 TraesCS5B01G340200 chr7B 203600374 203603063 2689 True 4434 4434 96.381 540 3239 1 chr7B.!!$R1 2699
5 TraesCS5B01G340200 chr2B 699751684 699754882 3198 False 5358 5358 96.727 1 3239 1 chr2B.!!$F1 3238
6 TraesCS5B01G340200 chr1B 659736327 659739541 3214 True 5247 5247 96.073 10 3239 1 chr1B.!!$R2 3229
7 TraesCS5B01G340200 chr1B 631845176 631847834 2658 True 4449 4449 96.791 564 3239 1 chr1B.!!$R1 2675
8 TraesCS5B01G340200 chr2A 470633729 470636931 3202 True 5158 5158 95.640 10 3239 1 chr2A.!!$R1 3229
9 TraesCS5B01G340200 chr2A 411115945 411118629 2684 False 4584 4584 97.542 564 3239 1 chr2A.!!$F1 2675
10 TraesCS5B01G340200 chr1A 58195151 58198144 2993 False 4878 4878 96.017 10 3018 1 chr1A.!!$F1 3008
11 TraesCS5B01G340200 chr6B 693560252 693563078 2826 False 4614 4614 96.065 10 2851 1 chr6B.!!$F1 2841
12 TraesCS5B01G340200 chr4A 740137102 740139761 2659 False 4396 4396 96.418 564 3239 1 chr4A.!!$F1 2675
13 TraesCS5B01G340200 chr4B 519576577 519578100 1523 False 2525 2525 96.431 1700 3239 1 chr4B.!!$F1 1539

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
27 28 2.370519 TGGATCTTTCGGTGTTCCAGAA 59.629 45.455 0.0 0.0 32.80 3.02 F
897 927 2.512896 AGGACTACTCCCGTGGATTCTA 59.487 50.000 0.0 0.0 37.25 2.10 F
1603 1637 1.078848 GAGCGTCTGCCTGTTGGAT 60.079 57.895 0.0 0.0 44.31 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1187 1217 1.664649 CACGTGAAAGCAGCTCCGA 60.665 57.895 10.9 0.0 0.00 4.55 R
2106 2158 4.021016 GGAGTCCCGATGCTTAGACAATAT 60.021 45.833 0.0 0.0 0.00 1.28 R
2986 3039 1.142465 CAAGCTCATGGCCCTATCACT 59.858 52.381 0.0 0.0 43.05 3.41 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
27 28 2.370519 TGGATCTTTCGGTGTTCCAGAA 59.629 45.455 0.00 0.0 32.80 3.02
35 36 5.934935 TTCGGTGTTCCAGAATAAGTTTC 57.065 39.130 0.00 0.0 0.00 2.78
294 295 7.880160 CCAAAAGAATTGGTAGTCATATCCA 57.120 36.000 0.00 0.0 34.92 3.41
343 357 3.914312 GGATGTGTAGTCATATCCGGTG 58.086 50.000 0.00 0.0 46.68 4.94
344 358 3.321111 GGATGTGTAGTCATATCCGGTGT 59.679 47.826 0.00 0.0 46.68 4.16
345 359 4.202223 GGATGTGTAGTCATATCCGGTGTT 60.202 45.833 0.00 0.0 46.68 3.32
346 360 4.380841 TGTGTAGTCATATCCGGTGTTC 57.619 45.455 0.00 0.0 0.00 3.18
347 361 3.764972 TGTGTAGTCATATCCGGTGTTCA 59.235 43.478 0.00 0.0 0.00 3.18
348 362 4.404394 TGTGTAGTCATATCCGGTGTTCAT 59.596 41.667 0.00 0.0 0.00 2.57
349 363 5.595133 TGTGTAGTCATATCCGGTGTTCATA 59.405 40.000 0.00 0.0 0.00 2.15
350 364 6.266786 TGTGTAGTCATATCCGGTGTTCATAT 59.733 38.462 0.00 0.0 0.00 1.78
351 365 6.807230 GTGTAGTCATATCCGGTGTTCATATC 59.193 42.308 0.00 0.0 0.00 1.63
352 366 5.407407 AGTCATATCCGGTGTTCATATCC 57.593 43.478 0.00 0.0 0.00 2.59
353 367 4.082190 AGTCATATCCGGTGTTCATATCCG 60.082 45.833 0.00 0.0 43.30 4.18
897 927 2.512896 AGGACTACTCCCGTGGATTCTA 59.487 50.000 0.00 0.0 37.25 2.10
989 1019 3.994392 GAGACGCACAGTTTCCATCTTTA 59.006 43.478 0.00 0.0 0.00 1.85
1187 1217 5.847265 AGAAGAAGAGGGAAAGGAAAGTAGT 59.153 40.000 0.00 0.0 0.00 2.73
1223 1253 7.033530 TCACGTGGATTCAAAATAACTTTGT 57.966 32.000 17.00 0.0 44.18 2.83
1227 1257 6.915300 CGTGGATTCAAAATAACTTTGTGACA 59.085 34.615 0.00 0.0 44.18 3.58
1603 1637 1.078848 GAGCGTCTGCCTGTTGGAT 60.079 57.895 0.00 0.0 44.31 3.41
2205 2258 2.766828 ACGGAAGATAAAGGACTGGGAG 59.233 50.000 0.00 0.0 0.00 4.30
2512 2565 4.517453 CCGTTCTTTACTTTCCCATTGACA 59.483 41.667 0.00 0.0 0.00 3.58
2676 2729 3.364889 TTCCTCAAGGTACATATCGCG 57.635 47.619 0.00 0.0 36.34 5.87
2962 3015 4.866508 TTCTCACTTGATTACGACACCT 57.133 40.909 0.00 0.0 0.00 4.00
2986 3039 4.083003 GCCTTGACCATATTGTTTCGTTCA 60.083 41.667 0.00 0.0 0.00 3.18
3027 3080 4.450053 TGATGATGACATGTTATTGGCGA 58.550 39.130 4.41 0.0 36.82 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.406828 CATCTCCAATTGCAATATTACATCAAG 57.593 33.333 13.39 1.28 0.00 3.02
294 295 9.770097 CCATCACAACAAGAATCATATACTACT 57.230 33.333 0.00 0.00 0.00 2.57
342 356 5.547465 GGATATGAACACCGGATATGAACA 58.453 41.667 9.46 2.74 0.00 3.18
343 357 4.625742 CGGATATGAACACCGGATATGAAC 59.374 45.833 9.46 0.00 42.48 3.18
344 358 4.816392 CGGATATGAACACCGGATATGAA 58.184 43.478 9.46 0.00 42.48 2.57
345 359 4.450082 CGGATATGAACACCGGATATGA 57.550 45.455 9.46 0.00 42.48 2.15
352 366 1.931172 GAACACCGGATATGAACACCG 59.069 52.381 9.46 0.00 45.24 4.94
353 367 2.980568 TGAACACCGGATATGAACACC 58.019 47.619 9.46 0.00 0.00 4.16
354 368 4.260212 CGAATGAACACCGGATATGAACAC 60.260 45.833 9.46 0.00 0.00 3.32
897 927 2.351276 GTGGACCGGCTGACCAAT 59.649 61.111 0.00 0.00 35.40 3.16
989 1019 0.972983 CACGGTCATCTCCCCAGTCT 60.973 60.000 0.00 0.00 0.00 3.24
1187 1217 1.664649 CACGTGAAAGCAGCTCCGA 60.665 57.895 10.90 0.00 0.00 4.55
1603 1637 4.069232 CCTGACGCTCTTCGGGCA 62.069 66.667 0.00 0.00 43.86 5.36
2106 2158 4.021016 GGAGTCCCGATGCTTAGACAATAT 60.021 45.833 0.00 0.00 0.00 1.28
2512 2565 8.458843 GTTAGCCATTCAAACATGTGTAATACT 58.541 33.333 0.00 4.09 0.00 2.12
2676 2729 5.068460 ACATAGACTGGCTCTCATAGTGAAC 59.932 44.000 0.00 0.00 0.00 3.18
2962 3015 3.417101 ACGAAACAATATGGTCAAGGCA 58.583 40.909 0.00 0.00 0.00 4.75
2986 3039 1.142465 CAAGCTCATGGCCCTATCACT 59.858 52.381 0.00 0.00 43.05 3.41
3091 3144 1.281899 GCCTCTGTTGTCATAGTCGC 58.718 55.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.