Multiple sequence alignment - TraesCS1A01G204100

Loading Multiple Alignment...

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 TraesCS1A01G204100 chr1A 100.000 3785 0 0 1 3785 365639644 365635860 0 6990
1 TraesCS1A01G204100 chr5A 96.859 3789 112 7 1 3785 524683964 524680179 0 6331
2 TraesCS1A01G204100 chr5A 96.303 3787 120 7 1 3785 33913254 33909486 0 6200
3 TraesCS1A01G204100 chr5A 95.280 3199 129 20 591 3780 169176417 169179602 0 5051
4 TraesCS1A01G204100 chr2A 96.390 3795 124 11 1 3785 733078677 733074886 0 6237
5 TraesCS1A01G204100 chr2A 96.413 3736 121 11 1 3728 614226320 614222590 0 6144
6 TraesCS1A01G204100 chr4A 96.232 3795 128 14 1 3785 37336981 37333192 0 6202
7 TraesCS1A01G204100 chr3A 96.200 3789 135 9 1 3785 711569951 711573734 0 6191
8 TraesCS1A01G204100 chr3A 94.949 3207 128 29 594 3785 32212784 32209597 0 4994
9 TraesCS1A01G204100 chr6A 95.712 3708 139 16 1 3699 531061791 531058095 0 5949
10 TraesCS1A01G204100 chr7A 95.564 3697 136 17 96 3785 675349167 675352842 0 5893
11 TraesCS1A01G204100 chr7A 94.562 2501 114 12 1 2484 634128056 634130551 0 3845
12 TraesCS1A01G204100 chr7A 95.775 1207 51 0 1 1207 722679413 722680619 0 1947


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 TraesCS1A01G204100 chr1A 365635860 365639644 3784 True 6990 6990 100.000 1 3785 1 chr1A.!!$R1 3784
1 TraesCS1A01G204100 chr5A 524680179 524683964 3785 True 6331 6331 96.859 1 3785 1 chr5A.!!$R2 3784
2 TraesCS1A01G204100 chr5A 33909486 33913254 3768 True 6200 6200 96.303 1 3785 1 chr5A.!!$R1 3784
3 TraesCS1A01G204100 chr5A 169176417 169179602 3185 False 5051 5051 95.280 591 3780 1 chr5A.!!$F1 3189
4 TraesCS1A01G204100 chr2A 733074886 733078677 3791 True 6237 6237 96.390 1 3785 1 chr2A.!!$R2 3784
5 TraesCS1A01G204100 chr2A 614222590 614226320 3730 True 6144 6144 96.413 1 3728 1 chr2A.!!$R1 3727
6 TraesCS1A01G204100 chr4A 37333192 37336981 3789 True 6202 6202 96.232 1 3785 1 chr4A.!!$R1 3784
7 TraesCS1A01G204100 chr3A 711569951 711573734 3783 False 6191 6191 96.200 1 3785 1 chr3A.!!$F1 3784
8 TraesCS1A01G204100 chr3A 32209597 32212784 3187 True 4994 4994 94.949 594 3785 1 chr3A.!!$R1 3191
9 TraesCS1A01G204100 chr6A 531058095 531061791 3696 True 5949 5949 95.712 1 3699 1 chr6A.!!$R1 3698
10 TraesCS1A01G204100 chr7A 675349167 675352842 3675 False 5893 5893 95.564 96 3785 1 chr7A.!!$F2 3689
11 TraesCS1A01G204100 chr7A 634128056 634130551 2495 False 3845 3845 94.562 1 2484 1 chr7A.!!$F1 2483
12 TraesCS1A01G204100 chr7A 722679413 722680619 1206 False 1947 1947 95.775 1 1207 1 chr7A.!!$F3 1206

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
997 1024 0.251297 CAGAGAATTGCCACACCCCA 60.251 55.0 0.0 0.0 0.00 4.96 F
2447 2496 1.731433 AAGCAGTTGCACAGTGGCAG 61.731 55.0 6.9 0.0 45.88 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2661 2719 0.034337 GGTCGTAGTTGGGCAGTTGA 59.966 55.0 0.0 0.0 0.0 3.18 R
3705 3776 0.980231 GACTCAGGGGGCTCATCACT 60.980 60.0 0.0 0.0 0.0 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
43 44 1.784358 CATCCATGGCAAACCCTCAT 58.216 50.000 6.96 0.00 33.59 2.90
174 175 4.280425 TGTGCTTCAAACTGATATGCCAAA 59.720 37.500 0.00 0.00 0.00 3.28
391 392 1.807142 GTGCCAAGTTCTGCTAGGTTC 59.193 52.381 0.00 0.00 0.00 3.62
415 416 3.582647 TGCCAACTCAGACTGGAAAGATA 59.417 43.478 1.81 0.00 34.35 1.98
464 465 2.549064 TGTGTCAGTTAGCAGCATGT 57.451 45.000 0.00 0.00 39.31 3.21
713 714 2.079158 CCAAGTCAGTGAACGATGCAT 58.921 47.619 0.00 0.00 0.00 3.96
792 794 4.098960 GTCTTATCATGGTGACGGGTTCTA 59.901 45.833 0.00 0.00 0.00 2.10
997 1024 0.251297 CAGAGAATTGCCACACCCCA 60.251 55.000 0.00 0.00 0.00 4.96
1334 1367 3.316868 GGGCTTTTAGTTGCACACTGTTA 59.683 43.478 10.59 0.00 35.97 2.41
1395 1432 5.221581 ACCCTTCGAGCTAACTTGTCTTTTA 60.222 40.000 0.00 0.00 0.00 1.52
1396 1433 5.875359 CCCTTCGAGCTAACTTGTCTTTTAT 59.125 40.000 0.00 0.00 0.00 1.40
1866 1910 3.073678 GTCCAGTTGCACATGACACATA 58.926 45.455 0.00 0.00 0.00 2.29
2212 2259 6.127925 GCACTTCCAGATTATTGACATTGACA 60.128 38.462 0.00 0.00 0.00 3.58
2249 2296 5.064707 TCGGCAAGTAAGACAATAAGCATTC 59.935 40.000 0.00 0.00 0.00 2.67
2447 2496 1.731433 AAGCAGTTGCACAGTGGCAG 61.731 55.000 6.90 0.00 45.88 4.85
2508 2559 3.751175 GGACATAAGCAGTTGCACAGTAA 59.249 43.478 6.90 0.00 45.16 2.24
2517 2568 4.438744 GCAGTTGCACAGTAAAACAGAAGT 60.439 41.667 0.00 0.00 41.59 3.01
2778 2836 3.994392 GGAAGTTGCTGAGATACGACAAA 59.006 43.478 0.00 0.00 0.00 2.83
2990 3055 3.665745 CCAACAAAGGCACAAATAGCT 57.334 42.857 0.00 0.00 0.00 3.32
2996 3061 5.772521 ACAAAGGCACAAATAGCTACTTTG 58.227 37.500 20.59 20.59 42.13 2.77
3020 3085 7.359595 TGTTTTACACAGTGCATGAACTAATC 58.640 34.615 5.87 0.00 0.00 1.75
3090 3157 1.000060 CACTTGGTCCCAACATTGCTG 60.000 52.381 0.00 0.00 0.00 4.41
3096 3163 3.181467 TGGTCCCAACATTGCTGAAAAAG 60.181 43.478 0.00 0.00 0.00 2.27
3155 3223 6.821616 ATGAGGAAACAGAATCATAGGAGT 57.178 37.500 0.00 0.00 30.78 3.85
3361 3429 2.280552 GGGCAGTAGGACCGTCACA 61.281 63.158 0.00 0.00 32.42 3.58
3538 3608 5.247337 TGTCATGGTACTTGGATTGTAGTCA 59.753 40.000 0.00 0.00 0.00 3.41
3634 3705 2.620115 CAGCATGTTCTGTTCAACTGGT 59.380 45.455 0.00 0.00 0.00 4.00
3666 3737 4.137116 TGTGCAACTAAAGTCACTCACT 57.863 40.909 0.00 0.00 38.04 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.876416 GCTTTACGCTTCTGGACCACA 60.876 52.381 0.00 0.00 35.14 4.17
174 175 1.857965 TGGCTCTCTGCTCACTACAT 58.142 50.000 0.00 0.00 42.39 2.29
391 392 0.397941 TTCCAGTCTGAGTTGGCAGG 59.602 55.000 0.00 0.00 36.55 4.85
415 416 3.306780 GCACACTGGTATCTGTAGTTGGT 60.307 47.826 0.00 0.00 0.00 3.67
464 465 2.752354 CTGTGGTGGTTTTGACTGTGAA 59.248 45.455 0.00 0.00 0.00 3.18
519 520 4.251103 TCTCTATGAGTAGGCACCTTGA 57.749 45.455 0.00 0.00 0.00 3.02
713 714 2.824489 TTGCGGCACAAACACGGA 60.824 55.556 0.05 0.00 34.56 4.69
792 794 3.698040 GAGGTCAAAAGATGGTGCATCAT 59.302 43.478 13.54 13.54 42.72 2.45
997 1024 1.672881 GCTTCTGGTTCTGCGCATATT 59.327 47.619 12.24 0.00 0.00 1.28
1079 1106 4.647564 ATGGAGACCTTTGAGATGTTGT 57.352 40.909 0.00 0.00 0.00 3.32
1422 1462 6.904626 AGAAAGCACCATACCTGATTATCTT 58.095 36.000 0.00 0.00 0.00 2.40
1555 1595 5.235850 TCAGTGGCATAACAACCTTCTTA 57.764 39.130 0.00 0.00 0.00 2.10
1866 1910 5.106157 GCAACAAGTATCTGCCAACTAACAT 60.106 40.000 0.00 0.00 0.00 2.71
2212 2259 0.250234 TTGCCGAGCTGCTTCAGTAT 59.750 50.000 2.53 0.00 33.43 2.12
2249 2296 8.105197 TGATGGTATATGATTGAGAAGGAATGG 58.895 37.037 0.00 0.00 0.00 3.16
2447 2496 6.968131 TGTGTTCTACTGCAACTCATTATC 57.032 37.500 0.00 0.00 0.00 1.75
2508 2559 5.057149 CCTACTGTGCAACTACTTCTGTTT 58.943 41.667 0.00 0.00 38.04 2.83
2517 2568 4.221924 TGCTTATGTCCTACTGTGCAACTA 59.778 41.667 0.00 0.00 38.04 2.24
2661 2719 0.034337 GGTCGTAGTTGGGCAGTTGA 59.966 55.000 0.00 0.00 0.00 3.18
2990 3055 6.685527 TCATGCACTGTGTAAAACAAAGTA 57.314 33.333 9.86 0.00 44.49 2.24
2996 3061 6.801862 GGATTAGTTCATGCACTGTGTAAAAC 59.198 38.462 8.37 13.02 0.00 2.43
3044 3109 6.363065 ACACATTCAGCATCTATGATTCCTT 58.637 36.000 0.00 0.00 0.00 3.36
3155 3223 0.752658 CTGGTGTGTGTCCACTCAGA 59.247 55.000 2.65 0.00 41.58 3.27
3294 3362 3.306225 GCTTCTGATGATTTTGTGCCCAA 60.306 43.478 0.00 0.00 0.00 4.12
3392 3460 7.706281 TGGTTGCACAATAACAAAAATACTG 57.294 32.000 0.00 0.00 0.00 2.74
3538 3608 3.737559 TTTCATGTTCTGCCCATAGGT 57.262 42.857 0.00 0.00 34.57 3.08
3634 3705 8.257306 TGACTTTAGTTGCACATATCATAGTGA 58.743 33.333 0.00 0.00 37.97 3.41
3666 3737 5.065474 CACCGACTCCAAAACAAAAACTAGA 59.935 40.000 0.00 0.00 0.00 2.43
3705 3776 0.980231 GACTCAGGGGGCTCATCACT 60.980 60.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.