Multiple sequence alignment - TraesCS3B01G210600

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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 TraesCS3B01G210600 chr3B 100.000 3434 0 0 1 3434 246996083 246992650 0.000000e+00 6342
1 TraesCS3B01G210600 chr3B 93.824 3449 196 10 1 3434 402661548 402664994 0.000000e+00 5173
2 TraesCS3B01G210600 chr5D 95.360 3448 140 11 1 3434 378825558 378822117 0.000000e+00 5463
3 TraesCS3B01G210600 chr5B 94.104 3443 190 7 1 3434 453090183 453086745 0.000000e+00 5221
4 TraesCS3B01G210600 chr6B 93.894 3439 197 7 1 3434 628277332 628273902 0.000000e+00 5175
5 TraesCS3B01G210600 chr6B 93.864 3439 198 7 1 3434 628323957 628320527 0.000000e+00 5169
6 TraesCS3B01G210600 chr2B 93.881 3448 186 13 1 3434 352032744 352036180 0.000000e+00 5175
7 TraesCS3B01G210600 chr2B 93.665 3441 207 8 1 3434 315008033 315011469 0.000000e+00 5136
8 TraesCS3B01G210600 chr7B 93.692 3440 196 15 1 3434 665789672 665793096 0.000000e+00 5131
9 TraesCS3B01G210600 chr1B 93.275 3450 205 16 1 3434 555911108 555907670 0.000000e+00 5060
10 TraesCS3B01G210600 chr3A 89.811 265 24 3 3171 3433 521370819 521371082 1.530000e-88 337


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 TraesCS3B01G210600 chr3B 246992650 246996083 3433 True 6342 6342 100.000 1 3434 1 chr3B.!!$R1 3433
1 TraesCS3B01G210600 chr3B 402661548 402664994 3446 False 5173 5173 93.824 1 3434 1 chr3B.!!$F1 3433
2 TraesCS3B01G210600 chr5D 378822117 378825558 3441 True 5463 5463 95.360 1 3434 1 chr5D.!!$R1 3433
3 TraesCS3B01G210600 chr5B 453086745 453090183 3438 True 5221 5221 94.104 1 3434 1 chr5B.!!$R1 3433
4 TraesCS3B01G210600 chr6B 628273902 628277332 3430 True 5175 5175 93.894 1 3434 1 chr6B.!!$R1 3433
5 TraesCS3B01G210600 chr6B 628320527 628323957 3430 True 5169 5169 93.864 1 3434 1 chr6B.!!$R2 3433
6 TraesCS3B01G210600 chr2B 352032744 352036180 3436 False 5175 5175 93.881 1 3434 1 chr2B.!!$F2 3433
7 TraesCS3B01G210600 chr2B 315008033 315011469 3436 False 5136 5136 93.665 1 3434 1 chr2B.!!$F1 3433
8 TraesCS3B01G210600 chr7B 665789672 665793096 3424 False 5131 5131 93.692 1 3434 1 chr7B.!!$F1 3433
9 TraesCS3B01G210600 chr1B 555907670 555911108 3438 True 5060 5060 93.275 1 3434 1 chr1B.!!$R1 3433


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
930 941 0.105760 TCCCACAAACCACCATTGCT 60.106 50.0 0.00 0.0 0.00 3.91 F
1317 1328 0.818296 AGTTATGCGTCGAGGAGCTT 59.182 50.0 9.75 5.3 0.00 3.74 F
2071 2085 1.003262 CACATTTGCCGGTTTCAGCG 61.003 55.0 1.90 0.0 39.06 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 2308 0.107361 TCCTGCGTACTCGATGAGGA 60.107 55.0 0.0 0.0 39.71 3.71 R
2325 2339 0.394938 ACCATGACTTGTACGTGGCA 59.605 50.0 0.0 0.0 45.22 4.92 R
3398 3458 0.380733 TATACACGGCGCTCACTCTG 59.619 55.0 6.9 0.0 0.00 3.35 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
224 226 8.255905 AGTCGTTAGTACAAAGGCATAGTAAAT 58.744 33.333 0.00 0.00 0.00 1.40
225 227 9.520204 GTCGTTAGTACAAAGGCATAGTAAATA 57.480 33.333 0.00 0.00 0.00 1.40
316 324 6.069440 TCCCAATTCAGAAAGACCATCAGTAT 60.069 38.462 0.00 0.00 0.00 2.12
530 538 2.120312 TCACCAGTCCAAGTACCACAA 58.880 47.619 0.00 0.00 0.00 3.33
570 578 0.541998 TCATCACCGACCCTGACACT 60.542 55.000 0.00 0.00 0.00 3.55
619 627 7.096884 AGTACAGCTTGACTATACGAATCAA 57.903 36.000 0.00 0.00 33.25 2.57
848 856 4.636435 CCACGCCCCCGACAAACT 62.636 66.667 0.00 0.00 38.29 2.66
871 879 1.211567 TCCCACAAATCCCCGTCCAT 61.212 55.000 0.00 0.00 0.00 3.41
877 885 0.916086 AAATCCCCGTCCATGCACTA 59.084 50.000 0.00 0.00 0.00 2.74
884 892 2.351350 CCCGTCCATGCACTACAAAAAC 60.351 50.000 0.00 0.00 0.00 2.43
930 941 0.105760 TCCCACAAACCACCATTGCT 60.106 50.000 0.00 0.00 0.00 3.91
1009 1020 2.514824 GGAAGGCGATGGTGGAGC 60.515 66.667 0.00 0.00 0.00 4.70
1071 1082 1.687494 GCAGCAACCTCGTCGACATC 61.687 60.000 17.16 0.00 0.00 3.06
1182 1193 3.495001 GCATACTAGAAAAGGCCGATGAC 59.505 47.826 0.00 0.00 0.00 3.06
1212 1223 1.682257 GCTCTGGAGGAAGCTTGGT 59.318 57.895 2.10 0.00 0.00 3.67
1269 1280 1.792949 GTGCACTACACCAACGAAGAG 59.207 52.381 10.32 0.00 44.02 2.85
1296 1307 1.340399 CCCAGATGGCAGCAGTCCTA 61.340 60.000 5.19 0.00 0.00 2.94
1302 1313 1.639722 TGGCAGCAGTCCTACAGTTA 58.360 50.000 0.00 0.00 0.00 2.24
1317 1328 0.818296 AGTTATGCGTCGAGGAGCTT 59.182 50.000 9.75 5.30 0.00 3.74
1340 1351 2.054458 TGGTGTACCACATCGCAGT 58.946 52.632 0.00 0.00 42.01 4.40
1425 1436 9.046296 AGTATCGTATCCTGAAAATTTCATCAC 57.954 33.333 9.02 4.43 39.30 3.06
1547 1559 6.604171 TGATGCACTGGATTACTATTTGGAT 58.396 36.000 0.00 0.00 0.00 3.41
1607 1619 7.085116 ACTAGTGTAGTTTCTCAAGTTGATCG 58.915 38.462 5.91 0.00 34.86 3.69
1679 1691 9.429359 ACTTGATGTAGTGAAGTATTTTCTGAG 57.571 33.333 0.00 0.00 32.17 3.35
1785 1798 9.563748 AAGTAAACTAAACTAGTACCAATGCAA 57.436 29.630 0.00 0.00 38.26 4.08
1803 1816 7.598118 CCAATGCAAAACATACAACATTGACTA 59.402 33.333 13.49 0.00 44.38 2.59
2071 2085 1.003262 CACATTTGCCGGTTTCAGCG 61.003 55.000 1.90 0.00 39.06 5.18
2103 2117 4.775236 ACAAAGAGAAGCTGAAGTTGTCT 58.225 39.130 0.00 0.00 0.00 3.41
2279 2293 2.636403 ACTACAAACTGTGGGGGACTAC 59.364 50.000 0.00 0.00 43.12 2.73
2294 2308 2.687200 TACCCCGCTGCCAGACAT 60.687 61.111 0.00 0.00 0.00 3.06
2375 2389 2.168521 ACTACATCACAGATGGTTCGGG 59.831 50.000 11.29 0.00 0.00 5.14
2412 2426 2.299521 GAGGCTGACCACTACTACGAT 58.700 52.381 0.00 0.00 39.06 3.73
2473 2487 2.500229 CCTGCCTTCGTTTTACTTCCA 58.500 47.619 0.00 0.00 0.00 3.53
2501 2515 5.175673 GTGCTTGCCTTTTATCTTGTTGTTC 59.824 40.000 0.00 0.00 0.00 3.18
2713 2727 6.919115 GGCTGCTCTAAAGTACTAGTTATGAC 59.081 42.308 0.00 0.00 0.00 3.06
2802 2816 3.814842 TGAGAACAATCAGCACAATTCGT 59.185 39.130 0.00 0.00 0.00 3.85
2897 2911 9.667107 TGTAGCTGCTAGAAAATTAACAAGTAT 57.333 29.630 10.13 0.00 0.00 2.12
3007 3022 9.178427 GATCGGACAGTACATAATTACTACAAC 57.822 37.037 0.00 0.00 30.76 3.32
3046 3061 1.938577 TCAGTCCGTAAGCGCTACTAG 59.061 52.381 12.05 5.44 33.53 2.57
3115 3131 4.103153 TCTGAAAATGACACCAGAAGACCT 59.897 41.667 0.00 0.00 33.26 3.85
3231 3248 9.841295 AACAAAAAGTATCAGTCCAAGTTACTA 57.159 29.630 0.00 0.00 0.00 1.82
3307 3355 4.767255 CAGTCGCAGGCCCTGACC 62.767 72.222 16.85 0.27 32.44 4.02
3317 3365 0.250640 GGCCCTGACCATGCTAGATG 60.251 60.000 0.00 0.00 0.00 2.90
3349 3397 1.300233 CCGTGAGCGAATCCCTAGC 60.300 63.158 0.00 0.00 41.33 3.42
3370 3418 4.988598 CCGCACAACGCAGGACCT 62.989 66.667 0.00 0.00 42.60 3.85
3398 3458 1.003233 GGCCCACAGGTCAAGAGAC 60.003 63.158 0.00 0.00 44.21 3.36
3403 3463 1.967066 CCACAGGTCAAGAGACAGAGT 59.033 52.381 0.00 0.00 46.80 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 0.386476 TGGTCGACAGTAGCGTTTGT 59.614 50.000 18.91 0.00 0.00 2.83
224 226 0.656785 GCGTTCACGGGTGTGTTTTA 59.343 50.000 0.81 0.00 46.49 1.52
225 227 1.430228 GCGTTCACGGGTGTGTTTT 59.570 52.632 0.81 0.00 46.49 2.43
619 627 3.016031 TGATGGCATTTTACTGTCGCAT 58.984 40.909 0.00 0.00 0.00 4.73
763 771 2.455565 AACTGCTCAGTGGGTGGCT 61.456 57.895 2.97 0.00 41.58 4.75
844 852 1.632589 GGATTTGTGGGAGGCAGTTT 58.367 50.000 0.00 0.00 0.00 2.66
848 856 2.770130 GGGGATTTGTGGGAGGCA 59.230 61.111 0.00 0.00 0.00 4.75
871 879 3.571590 AGAATGGGGTTTTTGTAGTGCA 58.428 40.909 0.00 0.00 0.00 4.57
877 885 3.922375 TGGAAGAGAATGGGGTTTTTGT 58.078 40.909 0.00 0.00 0.00 2.83
884 892 2.371510 GGAGAGATGGAAGAGAATGGGG 59.628 54.545 0.00 0.00 0.00 4.96
930 941 2.028112 GTGTGTAGTGGAGATGGAAGCA 60.028 50.000 0.00 0.00 0.00 3.91
1009 1020 3.039202 GATGCTTGGCGGACGGTTG 62.039 63.158 0.00 0.00 0.00 3.77
1166 1177 1.546923 TCACGTCATCGGCCTTTTCTA 59.453 47.619 0.00 0.00 41.85 2.10
1212 1223 1.134367 CTACGATTCGGACTCTTGCCA 59.866 52.381 11.29 0.00 0.00 4.92
1269 1280 2.308722 TGCCATCTGGGGAGGTTCC 61.309 63.158 0.00 0.00 37.04 3.62
1296 1307 0.179134 GCTCCTCGACGCATAACTGT 60.179 55.000 0.00 0.00 0.00 3.55
1302 1313 2.103042 GCAAAGCTCCTCGACGCAT 61.103 57.895 0.00 0.00 0.00 4.73
1364 1375 1.341976 ACCATACAGGGCAAATGGGTC 60.342 52.381 5.63 0.00 43.73 4.46
1367 1378 4.895297 AGATAAACCATACAGGGCAAATGG 59.105 41.667 0.00 0.00 44.76 3.16
1403 1414 6.878923 AGTGTGATGAAATTTTCAGGATACGA 59.121 34.615 16.34 3.43 43.98 3.43
1404 1415 7.076842 AGTGTGATGAAATTTTCAGGATACG 57.923 36.000 16.34 0.00 43.98 3.06
1425 1436 6.231211 AGTACATCTAGTTGGGAAACAAGTG 58.769 40.000 5.80 0.00 42.57 3.16
1607 1619 8.991026 ACATCGAGTACATAGACTACACTATTC 58.009 37.037 0.00 0.00 31.68 1.75
1644 1656 6.201044 ACTTCACTACATCAAGTTCAGAAACG 59.799 38.462 0.00 0.00 40.48 3.60
1868 1882 9.739276 ATGGATGAATGTACTTCAAAAACTAGA 57.261 29.630 0.00 0.00 46.62 2.43
1917 1931 3.877559 ACAAGCGATGAATCCATGAAGA 58.122 40.909 0.00 0.00 32.09 2.87
2071 2085 5.065218 TCAGCTTCTCTTTGTCACTTTCAAC 59.935 40.000 0.00 0.00 0.00 3.18
2079 2093 4.517285 ACAACTTCAGCTTCTCTTTGTCA 58.483 39.130 0.00 0.00 0.00 3.58
2208 2222 3.525609 TGCCTTTGTAGAATGGGTGGATA 59.474 43.478 6.66 0.00 0.00 2.59
2279 2293 4.864334 GGATGTCTGGCAGCGGGG 62.864 72.222 10.34 0.00 33.59 5.73
2294 2308 0.107361 TCCTGCGTACTCGATGAGGA 60.107 55.000 0.00 0.00 39.71 3.71
2325 2339 0.394938 ACCATGACTTGTACGTGGCA 59.605 50.000 0.00 0.00 45.22 4.92
2375 2389 1.423395 CTCCCGCTCTTTCGCATATC 58.577 55.000 0.00 0.00 0.00 1.63
2473 2487 4.342092 ACAAGATAAAAGGCAAGCACAAGT 59.658 37.500 0.00 0.00 0.00 3.16
2501 2515 8.082242 CCCAACAAGAGAAAACTACTAATTTGG 58.918 37.037 0.00 0.00 0.00 3.28
2516 2530 2.241176 ACTGGTTCAACCCAACAAGAGA 59.759 45.455 3.42 0.00 37.50 3.10
2668 2682 3.380142 CCACAACGTTCCATTCAAAAGG 58.620 45.455 0.00 0.00 0.00 3.11
2713 2727 2.941891 ACGTTGTGTGATTAGTTGCG 57.058 45.000 0.00 0.00 0.00 4.85
2802 2816 6.105333 ACTTTTGAAGCATTGTTAAGCAACA 58.895 32.000 0.00 0.00 42.93 3.33
2897 2911 9.862371 TGCTTCTTAACTTTTTCATGTTTGTAA 57.138 25.926 0.00 0.00 0.00 2.41
2907 2921 6.142958 GTGTGCTGATGCTTCTTAACTTTTTC 59.857 38.462 0.88 0.00 40.48 2.29
3007 3022 6.638468 GGACTGATGCTTCTTTGTACTTTTTG 59.362 38.462 0.88 0.00 0.00 2.44
3046 3061 5.419542 TGAGTTGTACTGATAGTGCATTCC 58.580 41.667 0.74 0.00 40.42 3.01
3179 3196 4.098416 GTTCTTGTCAGTTTTGTGTGAGC 58.902 43.478 0.00 0.00 0.00 4.26
3231 3248 7.015292 TGTTTGAATCTAGTACTTGACTCCAGT 59.985 37.037 12.15 0.00 39.81 4.00
3281 3329 2.743718 CTGCGACTGACCTTGGGT 59.256 61.111 0.00 0.00 39.44 4.51
3317 3365 2.048127 ACGGGCTCGAGTTCAAGC 60.048 61.111 15.95 0.00 40.11 4.01
3398 3458 0.380733 TATACACGGCGCTCACTCTG 59.619 55.000 6.90 0.00 0.00 3.35
3403 3463 1.587876 CGCTTATACACGGCGCTCA 60.588 57.895 6.90 0.00 42.28 4.26



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

AutoCloner maintained by Alex Coulton.