Multiple sequence alignment - TraesCS6B01G271100

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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 TraesCS6B01G271100 chr6B 100.000 3438 0 0 1 3438 489229975 489233412 0 6349
1 TraesCS6B01G271100 chr6B 93.505 3464 175 26 1 3438 247392365 247395804 0 5105
2 TraesCS6B01G271100 chr3B 96.111 3446 123 8 1 3438 603034656 603031214 0 5611
3 TraesCS6B01G271100 chr3B 95.065 3445 147 18 1 3438 300387409 300390837 0 5398
4 TraesCS6B01G271100 chr3B 95.311 3327 136 11 1 3320 129942389 129939076 0 5262
5 TraesCS6B01G271100 chr3B 91.837 686 44 4 2760 3437 402664523 402665204 0 946
6 TraesCS6B01G271100 chr2B 94.155 3456 168 16 1 3438 379155438 379158877 0 5232
7 TraesCS6B01G271100 chr2B 93.272 3463 184 27 1 3438 179064048 179067486 0 5059
8 TraesCS6B01G271100 chr4B 94.092 3453 170 23 1 3438 310225956 310222523 0 5216
9 TraesCS6B01G271100 chr4B 93.041 3449 206 24 1 3435 224372262 224375690 0 5009
10 TraesCS6B01G271100 chr1B 94.068 3456 163 29 1 3436 164401142 164397709 0 5208
11 TraesCS6B01G271100 chr1B 93.308 3452 196 22 1 3438 256706747 256710177 0 5062
12 TraesCS6B01G271100 chr5B 93.853 3449 178 23 1 3436 197387100 197390527 0 5164
13 TraesCS6B01G271100 chr5B 93.399 3454 186 25 2 3438 104504802 104501374 0 5077
14 TraesCS6B01G271100 chr7B 93.499 3461 180 25 1 3438 207971314 207974752 0 5103


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 TraesCS6B01G271100 chr6B 489229975 489233412 3437 False 6349 6349 100.000 1 3438 1 chr6B.!!$F2 3437
1 TraesCS6B01G271100 chr6B 247392365 247395804 3439 False 5105 5105 93.505 1 3438 1 chr6B.!!$F1 3437
2 TraesCS6B01G271100 chr3B 603031214 603034656 3442 True 5611 5611 96.111 1 3438 1 chr3B.!!$R2 3437
3 TraesCS6B01G271100 chr3B 300387409 300390837 3428 False 5398 5398 95.065 1 3438 1 chr3B.!!$F1 3437
4 TraesCS6B01G271100 chr3B 129939076 129942389 3313 True 5262 5262 95.311 1 3320 1 chr3B.!!$R1 3319
5 TraesCS6B01G271100 chr3B 402664523 402665204 681 False 946 946 91.837 2760 3437 1 chr3B.!!$F2 677
6 TraesCS6B01G271100 chr2B 379155438 379158877 3439 False 5232 5232 94.155 1 3438 1 chr2B.!!$F2 3437
7 TraesCS6B01G271100 chr2B 179064048 179067486 3438 False 5059 5059 93.272 1 3438 1 chr2B.!!$F1 3437
8 TraesCS6B01G271100 chr4B 310222523 310225956 3433 True 5216 5216 94.092 1 3438 1 chr4B.!!$R1 3437
9 TraesCS6B01G271100 chr4B 224372262 224375690 3428 False 5009 5009 93.041 1 3435 1 chr4B.!!$F1 3434
10 TraesCS6B01G271100 chr1B 164397709 164401142 3433 True 5208 5208 94.068 1 3436 1 chr1B.!!$R1 3435
11 TraesCS6B01G271100 chr1B 256706747 256710177 3430 False 5062 5062 93.308 1 3438 1 chr1B.!!$F1 3437
12 TraesCS6B01G271100 chr5B 197387100 197390527 3427 False 5164 5164 93.853 1 3436 1 chr5B.!!$F1 3435
13 TraesCS6B01G271100 chr5B 104501374 104504802 3428 True 5077 5077 93.399 2 3438 1 chr5B.!!$R1 3436
14 TraesCS6B01G271100 chr7B 207971314 207974752 3438 False 5103 5103 93.499 1 3438 1 chr7B.!!$F1 3437

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
658 691 0.244450 CCACCGCAAAGACATGCAAT 59.756 50.000 0.00 0.0 46.76 3.56 F
1317 1355 1.267832 TGCGTCAACGAACTTTGCTTC 60.268 47.619 6.75 0.0 43.02 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 2256 0.396556 TGGGTGGATGACGCTAGCTA 60.397 55.0 13.93 0.0 38.35 3.32 R
3194 3279 0.527817 GCTTATACACGGCACTCGCT 60.528 55.0 0.00 0.0 43.89 4.93 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
535 568 3.554544 CCGAGTACGATAGCAGAGGAGTA 60.555 52.174 0.00 0.00 42.66 2.59
538 571 4.975631 AGTACGATAGCAGAGGAGTACAT 58.024 43.478 0.00 0.00 37.49 2.29
540 573 6.531923 AGTACGATAGCAGAGGAGTACATAA 58.468 40.000 0.00 0.00 37.49 1.90
658 691 0.244450 CCACCGCAAAGACATGCAAT 59.756 50.000 0.00 0.00 46.76 3.56
664 697 2.340337 GCAAAGACATGCAATTGGGAC 58.660 47.619 7.72 0.00 45.70 4.46
692 725 6.598064 GCCAGGTAATAAGTACAACTTGACAT 59.402 38.462 2.59 0.00 39.11 3.06
708 741 6.763355 ACTTGACATGACTAGTCAGTTCAAT 58.237 36.000 32.19 24.32 45.72 2.57
779 812 1.669115 CACCCACTGAGCGGTTGAG 60.669 63.158 0.00 0.00 0.00 3.02
780 813 2.046892 CCCACTGAGCGGTTGAGG 60.047 66.667 0.00 0.00 0.00 3.86
971 1008 6.322491 ACAAAAACCAAAAACTTCTCTCTCG 58.678 36.000 0.00 0.00 0.00 4.04
972 1009 6.150474 ACAAAAACCAAAAACTTCTCTCTCGA 59.850 34.615 0.00 0.00 0.00 4.04
1115 1153 4.261909 CGAGTACACTACAACCCTCAAAGT 60.262 45.833 0.00 0.00 0.00 2.66
1317 1355 1.267832 TGCGTCAACGAACTTTGCTTC 60.268 47.619 6.75 0.00 43.02 3.86
1571 1614 5.818136 TGCGGAAGATTAAATTCTGAAGG 57.182 39.130 13.92 0.00 35.45 3.46
2196 2256 2.365617 ACGACTCCTTGACTGATGTTGT 59.634 45.455 0.00 0.00 0.00 3.32
2200 2260 3.580458 ACTCCTTGACTGATGTTGTAGCT 59.420 43.478 0.00 0.00 0.00 3.32
2294 2354 0.533531 CAGTGAGCTGCCAGACAACA 60.534 55.000 0.00 0.00 35.77 3.33
2319 2379 2.159000 TCGAGTACGCAGGAGTAGATGA 60.159 50.000 0.00 0.00 39.58 2.92
2363 2423 5.109210 GGTTCATGATCGACTACATCACAA 58.891 41.667 0.00 0.00 33.04 3.33
2454 2514 4.409901 TGGATGAAGATAACATCAGAGCCA 59.590 41.667 0.00 0.00 43.84 4.75
2548 2608 4.759693 GGTTGAACCAGTGTGATTATGTCA 59.240 41.667 9.98 0.00 38.42 3.58
2574 2634 7.264221 TGCTTGTCATGTTTGAACAAGTTTAT 58.736 30.769 19.58 0.00 43.03 1.40
2708 2770 4.041240 CGTTGTCGTTGCTCTAAAGAAG 57.959 45.455 0.00 0.00 0.00 2.85
2783 2845 4.111375 ACACTTGATCGGACAGTACATC 57.889 45.455 0.00 0.00 0.00 3.06
2918 2983 5.704515 CCAGAAGACACTTGAGAACAATCAT 59.295 40.000 0.00 0.00 35.37 2.45
3014 3081 8.379457 ACTAGAACAAAAAGTATCAGTCCAAC 57.621 34.615 0.00 0.00 0.00 3.77
3193 3278 2.352617 GCACACAGGTCAAGAGAGAGAG 60.353 54.545 0.00 0.00 0.00 3.20
3194 3279 3.153130 CACACAGGTCAAGAGAGAGAGA 58.847 50.000 0.00 0.00 0.00 3.10
3323 3408 2.372040 TAAACCCAGAGTGCACGCGT 62.372 55.000 15.14 5.58 0.00 6.01
3371 3456 0.393808 GCTATCTGGGCCGGAAAACA 60.394 55.000 21.02 4.19 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 207 3.007635 GCCTTTTGTACTGCCGACTAAT 58.992 45.455 0.00 0.00 0.00 1.73
535 568 3.596214 GTCGGTGTTGATGGAGTTATGT 58.404 45.455 0.00 0.00 0.00 2.29
538 571 1.670674 GCGTCGGTGTTGATGGAGTTA 60.671 52.381 0.00 0.00 0.00 2.24
540 573 1.374252 GCGTCGGTGTTGATGGAGT 60.374 57.895 0.00 0.00 0.00 3.85
658 691 3.332485 ACTTATTACCTGGCAAGTCCCAA 59.668 43.478 0.00 0.00 33.73 4.12
664 697 6.653320 TCAAGTTGTACTTATTACCTGGCAAG 59.347 38.462 2.11 0.00 36.03 4.01
692 725 7.656137 GGTTTTCACTATTGAACTGACTAGTCA 59.344 37.037 23.80 23.80 41.64 3.41
779 812 2.644992 CGTTTGCAGTCCCTTGCC 59.355 61.111 0.00 0.00 43.43 4.52
780 813 2.193536 ACCGTTTGCAGTCCCTTGC 61.194 57.895 0.00 0.00 44.33 4.01
971 1008 1.007387 CGGCAACTGTGGGCTTTTC 60.007 57.895 7.19 0.00 0.00 2.29
972 1009 2.498056 CCGGCAACTGTGGGCTTTT 61.498 57.895 7.19 0.00 0.00 2.27
1115 1153 3.113514 TTGCCGTGGAGCTCAACCA 62.114 57.895 15.83 5.89 34.84 3.67
1139 1177 1.216444 GTGCAGACGATCTCCAGCA 59.784 57.895 0.00 0.00 0.00 4.41
1518 1561 5.822519 TCCAAATAGTAATCCAGTGCATCAC 59.177 40.000 0.00 0.00 34.10 3.06
1571 1614 5.700846 TCAGAAACTTCACTAGTCGATCAC 58.299 41.667 0.00 0.00 35.54 3.06
2196 2256 0.396556 TGGGTGGATGACGCTAGCTA 60.397 55.000 13.93 0.00 38.35 3.32
2200 2260 1.496060 AGAATGGGTGGATGACGCTA 58.504 50.000 0.00 0.00 38.35 4.26
2294 2354 1.681538 ACTCCTGCGTACTCGATGAT 58.318 50.000 0.00 0.00 39.71 2.45
2319 2379 5.865085 ACCATGATTTGTATGCGGTATACT 58.135 37.500 15.64 0.00 41.82 2.12
2363 2423 2.116827 TTCGCATATTCCCAACCGTT 57.883 45.000 0.00 0.00 0.00 4.44
2454 2514 1.154197 GCGGAAGTAAAACGAAGGCT 58.846 50.000 0.00 0.00 0.00 4.58
2548 2608 5.266733 ACTTGTTCAAACATGACAAGCAT 57.733 34.783 18.97 3.77 40.80 3.79
2574 2634 9.190858 GCAAAACATTGTACTTGATGACATAAA 57.809 29.630 13.14 0.00 0.00 1.40
2708 2770 8.196802 TGTGTGATTAGTTGCATCATAACTAC 57.803 34.615 0.00 0.00 39.57 2.73
2884 2949 5.066375 TCAAGTGTCTTCTGGTGTCATTTTG 59.934 40.000 0.00 0.00 0.00 2.44
3014 3081 6.416415 TCTAGTACTTGACTCCTCCAGTAAG 58.584 44.000 0.00 0.00 39.81 2.34
3174 3259 3.420893 CTCTCTCTCTCTTGACCTGTGT 58.579 50.000 0.00 0.00 0.00 3.72
3193 3278 1.478137 CTTATACACGGCACTCGCTC 58.522 55.000 0.00 0.00 43.89 5.03
3194 3279 0.527817 GCTTATACACGGCACTCGCT 60.528 55.000 0.00 0.00 43.89 4.93
3323 3408 1.301401 GGCTGTGTTGTGCGTCCTA 60.301 57.895 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.