Multiple sequence alignment - TraesCS3B01G383100

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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 TraesCS3B01G383100 chr3B 100.000 3441 0 0 1 3441 603034652 603031212 0 6355
1 TraesCS3B01G383100 chr3B 95.179 3443 144 16 3 3441 300387415 300390839 0 5419
2 TraesCS3B01G383100 chr3B 92.105 684 44 5 2763 3438 402664523 402665204 0 955
3 TraesCS3B01G383100 chr6B 96.109 3444 123 8 1 3441 489229979 489233414 0 5607
4 TraesCS3B01G383100 chr6B 93.924 3456 169 17 2 3441 379095870 379092440 0 5180
5 TraesCS3B01G383100 chr6B 93.616 3462 176 24 1 3441 247392369 247395806 0 5127
6 TraesCS3B01G383100 chr1B 94.613 3453 158 12 1 3441 330756294 330759730 0 5321
7 TraesCS3B01G383100 chr1B 94.063 3453 170 22 3 3441 164401136 164397705 0 5208
8 TraesCS3B01G383100 chr1B 93.536 3450 193 19 1 3441 256706751 256710179 0 5108
9 TraesCS3B01G383100 chr4B 94.293 3452 166 19 1 3441 310225952 310222521 0 5254
10 TraesCS3B01G383100 chr4B 95.591 3243 127 8 1 3240 494405642 494408871 0 5182
11 TraesCS3B01G383100 chr4B 93.918 3453 167 21 2 3441 380783996 380787418 0 5173
12 TraesCS3B01G383100 chr4B 93.006 3446 210 21 1 3436 224372266 224375690 0 5000
13 TraesCS3B01G383100 chr5B 93.940 3449 180 19 1 3441 197387104 197390531 0 5184
14 TraesCS3B01G383100 chr5B 93.661 3455 178 25 1 3441 104504799 104501372 0 5129
15 TraesCS3B01G383100 chr7B 93.640 3459 180 23 1 3441 207971318 207974754 0 5132
16 TraesCS3B01G383100 chr2B 92.409 685 44 2 2763 3441 85869402 85868720 0 970


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 TraesCS3B01G383100 chr3B 603031212 603034652 3440 True 6355 6355 100.000 1 3441 1 chr3B.!!$R1 3440
1 TraesCS3B01G383100 chr3B 300387415 300390839 3424 False 5419 5419 95.179 3 3441 1 chr3B.!!$F1 3438
2 TraesCS3B01G383100 chr3B 402664523 402665204 681 False 955 955 92.105 2763 3438 1 chr3B.!!$F2 675
3 TraesCS3B01G383100 chr6B 489229979 489233414 3435 False 5607 5607 96.109 1 3441 1 chr6B.!!$F2 3440
4 TraesCS3B01G383100 chr6B 379092440 379095870 3430 True 5180 5180 93.924 2 3441 1 chr6B.!!$R1 3439
5 TraesCS3B01G383100 chr6B 247392369 247395806 3437 False 5127 5127 93.616 1 3441 1 chr6B.!!$F1 3440
6 TraesCS3B01G383100 chr1B 330756294 330759730 3436 False 5321 5321 94.613 1 3441 1 chr1B.!!$F2 3440
7 TraesCS3B01G383100 chr1B 164397705 164401136 3431 True 5208 5208 94.063 3 3441 1 chr1B.!!$R1 3438
8 TraesCS3B01G383100 chr1B 256706751 256710179 3428 False 5108 5108 93.536 1 3441 1 chr1B.!!$F1 3440
9 TraesCS3B01G383100 chr4B 310222521 310225952 3431 True 5254 5254 94.293 1 3441 1 chr4B.!!$R1 3440
10 TraesCS3B01G383100 chr4B 494405642 494408871 3229 False 5182 5182 95.591 1 3240 1 chr4B.!!$F3 3239
11 TraesCS3B01G383100 chr4B 380783996 380787418 3422 False 5173 5173 93.918 2 3441 1 chr4B.!!$F2 3439
12 TraesCS3B01G383100 chr4B 224372266 224375690 3424 False 5000 5000 93.006 1 3436 1 chr4B.!!$F1 3435
13 TraesCS3B01G383100 chr5B 197387104 197390531 3427 False 5184 5184 93.940 1 3441 1 chr5B.!!$F1 3440
14 TraesCS3B01G383100 chr5B 104501372 104504799 3427 True 5129 5129 93.661 1 3441 1 chr5B.!!$R1 3440
15 TraesCS3B01G383100 chr7B 207971318 207974754 3436 False 5132 5132 93.640 1 3441 1 chr7B.!!$F1 3440
16 TraesCS3B01G383100 chr2B 85868720 85869402 682 True 970 970 92.409 2763 3441 1 chr2B.!!$R1 678

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
755 781 0.110486 AGTTCTTCCACGCCACCATT 59.890 50.000 0.00 0.00 0.00 3.16 F
1008 1041 1.452833 GAGGAAGGCCATGGCAGAC 60.453 63.158 36.56 24.58 44.11 3.51 F
2314 2362 0.456221 ACCTCATCGAGTACGCAAGG 59.544 55.000 0.00 0.63 46.39 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2102 2148 0.250338 GGGTTGATCTCCATACCGGC 60.250 60.000 0.0 0.0 31.18 6.13 R
2407 2455 1.370064 GCAATAGGGGCGGTCGTAT 59.630 57.895 0.0 0.0 0.00 3.06 R
3365 3433 2.882170 GGCTATTGGGCCGTTTTCT 58.118 52.632 0.0 0.0 42.82 2.52 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
76 77 7.984050 TCCTTTTGAATGCAGTCACAAATAAAA 59.016 29.630 17.75 12.20 33.38 1.52
142 143 3.625764 TCAACCAGTAACTCAGCAACAAC 59.374 43.478 0.00 0.00 0.00 3.32
227 243 6.709018 AAGGCATAGTAAAACAAACACACT 57.291 33.333 0.00 0.00 0.00 3.55
293 315 0.255890 GCTCCTGCCAGTCCCAATTA 59.744 55.000 0.00 0.00 0.00 1.40
599 624 9.075678 GGGATAAGTAGCTGATAAGTACAACTA 57.924 37.037 0.00 0.00 0.00 2.24
691 716 6.171213 GCCAGGTAATAAGTACAACTTGACT 58.829 40.000 2.59 0.00 39.11 3.41
720 745 7.773690 ACTAGTCAGTAAAACAGTGAAAACCAT 59.226 33.333 0.00 0.00 38.35 3.55
755 781 0.110486 AGTTCTTCCACGCCACCATT 59.890 50.000 0.00 0.00 0.00 3.16
960 992 6.546972 TTTCCACTGAACAAAAACCAAAAC 57.453 33.333 0.00 0.00 0.00 2.43
1008 1041 1.452833 GAGGAAGGCCATGGCAGAC 60.453 63.158 36.56 24.58 44.11 3.51
1083 1116 1.548081 TCGACATTAACGTCCCCAGA 58.452 50.000 0.00 0.00 31.91 3.86
1368 1402 4.263462 TGGTGAGCAATCCTACTCATTTGT 60.263 41.667 0.00 0.00 44.29 2.83
1606 1644 7.920738 AGTGAAGTTTCTGAAGTTGATACAAC 58.079 34.615 6.53 6.53 0.00 3.32
2102 2148 4.604976 CAACAAAGAGAAGCTGAAGTTGG 58.395 43.478 0.00 0.00 33.45 3.77
2122 2170 1.128200 CCGGTATGGAGATCAACCCA 58.872 55.000 0.00 0.00 42.00 4.51
2228 2276 4.006989 CGTCATCCACCCATTCTACAAAA 58.993 43.478 0.00 0.00 0.00 2.44
2312 2360 1.271379 ACAACCTCATCGAGTACGCAA 59.729 47.619 0.00 0.00 39.58 4.85
2314 2362 0.456221 ACCTCATCGAGTACGCAAGG 59.544 55.000 0.00 0.63 46.39 3.61
2407 2455 3.243128 GCGGGAGGCTGAAAACTTA 57.757 52.632 0.00 0.00 39.11 2.24
2433 2481 0.537371 CGCCCCTATTGCCCCTTTAG 60.537 60.000 0.00 0.00 0.00 1.85
2645 2694 6.909550 TTGGTTTGGTAGCTTCATATGTTT 57.090 33.333 1.90 0.00 0.00 2.83
2752 2802 2.071604 CACAACGTTGTTCTGTGTCG 57.928 50.000 30.49 13.42 39.91 4.35
2774 2824 5.010314 TCGGTACAACTCAGTACACTTGATT 59.990 40.000 6.59 0.00 44.76 2.57
2780 2830 4.632153 ACTCAGTACACTTGATTGGACAC 58.368 43.478 0.00 0.00 32.02 3.67
3035 3088 3.330267 CAAGTTACTGGAGGAGTCAAGC 58.670 50.000 0.00 0.00 35.96 4.01
3132 3198 3.379445 GAACTCGAGCCCGTGGGA 61.379 66.667 13.61 0.00 37.50 4.37
3360 3428 2.944429 GCGCGGACGAGCTATCTA 59.056 61.111 8.83 0.00 43.93 1.98
3365 3433 0.889638 CGGACGAGCTATCTAGGCCA 60.890 60.000 5.01 0.00 42.67 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.636150 AAATAATAATGTCACTGCTTCAGCT 57.364 32.000 0.00 0.00 42.66 4.24
142 143 8.404765 ACTACAATTTTTCCTTTGGCATTTTTG 58.595 29.630 0.00 0.00 0.00 2.44
266 288 1.351080 ACTGGCAGGAGCAGGCATAT 61.351 55.000 20.34 0.00 44.61 1.78
293 315 7.581213 TTTTCATGTACTGATGGTGTTTCTT 57.419 32.000 0.00 0.00 32.72 2.52
599 624 2.034305 GTGGCACCGATTCGTATAGTCT 59.966 50.000 6.29 0.00 0.00 3.24
691 716 9.525409 GTTTTCACTGTTTTACTGACTAGTCTA 57.475 33.333 23.01 6.11 38.36 2.59
720 745 4.411256 AGAACTAACCGTCCAAGTGAAA 57.589 40.909 0.00 0.00 0.00 2.69
878 910 4.604156 AGGTGGAAGAGAATGGGATTTTC 58.396 43.478 0.00 0.00 0.00 2.29
960 992 1.352352 TGGGCTTTTGGAGAGAGAAGG 59.648 52.381 0.00 0.00 0.00 3.46
1063 1096 2.100916 CTCTGGGGACGTTAATGTCGAT 59.899 50.000 19.12 0.00 39.83 3.59
1083 1116 1.397692 GTAGTGTACTCGCGCTTCTCT 59.602 52.381 5.56 0.99 0.00 3.10
1142 1175 1.954362 GCTGGTGCAGACGATCTCCT 61.954 60.000 0.00 0.00 39.41 3.69
1207 1240 1.227883 TACGAAACCTGCCGCCAAA 60.228 52.632 0.00 0.00 0.00 3.28
1298 1332 2.146342 CCAAGCAGAGTTCATTGACGT 58.854 47.619 0.00 0.00 0.00 4.34
1368 1402 8.995027 ATAAAACAGATAAACCATATGCAGGA 57.005 30.769 0.00 0.00 28.26 3.86
1567 1605 7.808381 CAGAAACTTCACTAGTCGATCAACTTA 59.192 37.037 0.00 0.00 35.54 2.24
1606 1644 8.766000 ATACATCGAGTACATAGACTACTCTG 57.234 38.462 0.00 0.56 38.58 3.35
2102 2148 0.250338 GGGTTGATCTCCATACCGGC 60.250 60.000 0.00 0.00 31.18 6.13
2122 2170 4.611355 CGCTGAATGTCGATGAACTTGTTT 60.611 41.667 0.00 0.00 0.00 2.83
2228 2276 4.083643 CGTGTTGATCTTGTTCTTCATGCT 60.084 41.667 0.00 0.00 0.00 3.79
2312 2360 1.666011 CGGCATACGCATCTACCCT 59.334 57.895 0.00 0.00 41.24 4.34
2407 2455 1.370064 GCAATAGGGGCGGTCGTAT 59.630 57.895 0.00 0.00 0.00 3.06
2433 2481 4.754114 GGCTCTGATGTTATCTTCATCCAC 59.246 45.833 0.00 0.00 40.38 4.02
2538 2587 4.252878 TGACAAGCACGACATAATCACAT 58.747 39.130 0.00 0.00 0.00 3.21
2752 2802 5.408604 CCAATCAAGTGTACTGAGTTGTACC 59.591 44.000 0.00 0.00 41.34 3.34
2821 2872 3.639561 TGCATTCATAGTAGCCCTTACGA 59.360 43.478 0.00 0.00 37.35 3.43
3132 3198 3.305720 TGTGCGGATTACTAGGGATTCT 58.694 45.455 0.00 0.00 0.00 2.40
3365 3433 2.882170 GGCTATTGGGCCGTTTTCT 58.118 52.632 0.00 0.00 42.82 2.52


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

AutoCloner maintained by Alex Coulton.