Multiple sequence alignment - TraesCS4A01G412700

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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 TraesCS4A01G412700 chr4A 100.000 3410 0 0 1 3410 684433395 684429986 0.000000e+00 6298
1 TraesCS4A01G412700 chr4A 93.837 3359 160 14 92 3410 516896425 516899776 0.000000e+00 5012
2 TraesCS4A01G412700 chr4A 93.182 3359 181 12 92 3410 491871642 491868292 0.000000e+00 4891
3 TraesCS4A01G412700 chr4A 91.975 3427 207 22 42 3410 524614737 524611321 0.000000e+00 4743
4 TraesCS4A01G412700 chr3A 94.501 3346 149 13 92 3410 564411531 564408194 0.000000e+00 5127
5 TraesCS4A01G412700 chr3A 92.545 3340 214 15 92 3410 628200052 628203377 0.000000e+00 4756
6 TraesCS4A01G412700 chr3A 95.775 142 6 0 1 142 10088513 10088654 2.650000e-56 230
7 TraesCS4A01G412700 chr3A 92.949 156 10 1 2 156 379523906 379524061 3.420000e-55 226
8 TraesCS4A01G412700 chr5A 93.609 3364 167 15 92 3410 266150436 266147076 0.000000e+00 4977
9 TraesCS4A01G412700 chr5A 93.042 3363 183 18 92 3410 151458886 151455531 0.000000e+00 4867
10 TraesCS4A01G412700 chr5A 89.244 3347 290 30 92 3407 304804796 304801489 0.000000e+00 4122
11 TraesCS4A01G412700 chr5A 90.772 1062 76 5 2370 3410 155193070 155192010 0.000000e+00 1399
12 TraesCS4A01G412700 chr7A 93.214 3345 194 11 92 3410 725340218 725343555 0.000000e+00 4889
13 TraesCS4A01G412700 chr7A 91.958 1604 106 3 1830 3410 306239662 306241265 0.000000e+00 2226
14 TraesCS4A01G412700 chr7A 92.357 157 11 1 1 156 216190829 216190985 4.430000e-54 222
15 TraesCS4A01G412700 chr7A 91.720 157 12 1 1 156 429562433 429562277 2.060000e-52 217
16 TraesCS4A01G412700 chr2A 93.479 3297 188 14 138 3410 87266395 87269688 0.000000e+00 4872
17 TraesCS4A01G412700 chr2A 90.304 3321 293 15 92 3410 732785737 732789030 0.000000e+00 4322
18 TraesCS4A01G412700 chr2A 93.631 157 9 1 1 156 689115973 689115817 2.050000e-57 233
19 TraesCS4A01G412700 chr6A 93.172 3339 181 25 92 3410 66957277 66960588 0.000000e+00 4859
20 TraesCS4A01G412700 chr6A 91.054 939 51 5 2505 3410 490932029 490932967 0.000000e+00 1238
21 TraesCS4A01G412700 chr6A 92.994 157 10 1 1 156 365465675 365465519 9.520000e-56 228
22 TraesCS4A01G412700 chr1A 91.672 3446 238 27 1 3410 510739417 510742849 0.000000e+00 4728
23 TraesCS4A01G412700 chr1A 91.357 3448 258 19 1 3410 576034850 576031405 0.000000e+00 4680


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 TraesCS4A01G412700 chr4A 684429986 684433395 3409 True 6298 6298 100.000 1 3410 1 chr4A.!!$R3 3409
1 TraesCS4A01G412700 chr4A 516896425 516899776 3351 False 5012 5012 93.837 92 3410 1 chr4A.!!$F1 3318
2 TraesCS4A01G412700 chr4A 491868292 491871642 3350 True 4891 4891 93.182 92 3410 1 chr4A.!!$R1 3318
3 TraesCS4A01G412700 chr4A 524611321 524614737 3416 True 4743 4743 91.975 42 3410 1 chr4A.!!$R2 3368
4 TraesCS4A01G412700 chr3A 564408194 564411531 3337 True 5127 5127 94.501 92 3410 1 chr3A.!!$R1 3318
5 TraesCS4A01G412700 chr3A 628200052 628203377 3325 False 4756 4756 92.545 92 3410 1 chr3A.!!$F3 3318
6 TraesCS4A01G412700 chr5A 266147076 266150436 3360 True 4977 4977 93.609 92 3410 1 chr5A.!!$R3 3318
7 TraesCS4A01G412700 chr5A 151455531 151458886 3355 True 4867 4867 93.042 92 3410 1 chr5A.!!$R1 3318
8 TraesCS4A01G412700 chr5A 304801489 304804796 3307 True 4122 4122 89.244 92 3407 1 chr5A.!!$R4 3315
9 TraesCS4A01G412700 chr5A 155192010 155193070 1060 True 1399 1399 90.772 2370 3410 1 chr5A.!!$R2 1040
10 TraesCS4A01G412700 chr7A 725340218 725343555 3337 False 4889 4889 93.214 92 3410 1 chr7A.!!$F3 3318
11 TraesCS4A01G412700 chr7A 306239662 306241265 1603 False 2226 2226 91.958 1830 3410 1 chr7A.!!$F2 1580
12 TraesCS4A01G412700 chr2A 87266395 87269688 3293 False 4872 4872 93.479 138 3410 1 chr2A.!!$F1 3272
13 TraesCS4A01G412700 chr2A 732785737 732789030 3293 False 4322 4322 90.304 92 3410 1 chr2A.!!$F2 3318
14 TraesCS4A01G412700 chr6A 66957277 66960588 3311 False 4859 4859 93.172 92 3410 1 chr6A.!!$F1 3318
15 TraesCS4A01G412700 chr6A 490932029 490932967 938 False 1238 1238 91.054 2505 3410 1 chr6A.!!$F2 905
16 TraesCS4A01G412700 chr1A 510739417 510742849 3432 False 4728 4728 91.672 1 3410 1 chr1A.!!$F1 3409
17 TraesCS4A01G412700 chr1A 576031405 576034850 3445 True 4680 4680 91.357 1 3410 1 chr1A.!!$R1 3409

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
754 825 0.178929 AGGGGAAGGTCGTGAAGTCT 60.179 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2553 2640 0.31716 CTGCTGTCGTAGTGGGTTCA 59.683 55.0 0.0 0.0 0.0 3.18 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
56 57 1.005215 AGTTCCTTGAGATGCCTTGGG 59.995 52.381 0.00 0.00 0.00 4.12
90 91 4.148825 CTCCTCTTGCCGGGGTCG 62.149 72.222 2.18 0.00 0.00 4.79
202 265 1.072331 GGTCTTGTCTCCTTGGCTTGA 59.928 52.381 0.00 0.00 0.00 3.02
408 472 4.341502 CAAAACAGGGCACGGGCG 62.342 66.667 2.17 0.00 42.47 6.13
409 473 4.887190 AAAACAGGGCACGGGCGT 62.887 61.111 2.17 0.00 42.47 5.68
426 490 3.383681 TGCGCGGCCTAGGTTACA 61.384 61.111 11.31 0.00 0.00 2.41
632 697 2.187946 CGCCGCTCCCTCATCTTT 59.812 61.111 0.00 0.00 0.00 2.52
633 698 2.176273 CGCCGCTCCCTCATCTTTG 61.176 63.158 0.00 0.00 0.00 2.77
717 788 1.302832 CCTCCACCACTTCTGCCAC 60.303 63.158 0.00 0.00 0.00 5.01
754 825 0.178929 AGGGGAAGGTCGTGAAGTCT 60.179 55.000 0.00 0.00 0.00 3.24
802 873 3.516866 GAAGGAGCGGGCCGTATCC 62.517 68.421 32.28 32.28 35.94 2.59
943 1022 2.640184 CAAACGGATACCCCTTCTTCC 58.360 52.381 0.00 0.00 0.00 3.46
1013 1092 3.316868 TGCGACATCATGAATACCTACGA 59.683 43.478 0.00 0.00 0.00 3.43
1032 1111 3.181443 ACGAATTCCACCTCCTTGACTTT 60.181 43.478 0.00 0.00 0.00 2.66
1304 1383 3.905678 CACCACCCGGCGCAAAAA 61.906 61.111 10.83 0.00 34.57 1.94
1409 1488 1.818363 GGCTTGCCGGGCTTACTAC 60.818 63.158 21.46 3.68 0.00 2.73
1586 1665 3.055530 CAGGAGCTGTTCAAGTATGACCT 60.056 47.826 0.00 0.00 34.61 3.85
1613 1692 1.674057 CCGAGGTCTTCAGGTTGCT 59.326 57.895 0.00 0.00 0.00 3.91
2413 2495 4.709886 AGGAGGAAGAAGAAGAGTAAGCTC 59.290 45.833 0.00 0.00 41.94 4.09
2420 2502 5.329399 AGAAGAAGAGTAAGCTCCTCTTGA 58.671 41.667 25.25 0.00 46.73 3.02
2563 2650 3.026707 TCATCGAGGATGAACCCACTA 57.973 47.619 5.86 0.00 44.70 2.74
2736 2825 2.203907 AGCAGCCTCACCAGGAGT 60.204 61.111 0.00 0.00 43.65 3.85
2874 2981 0.696501 AGAACCCGGCACAGGTAATT 59.303 50.000 0.00 0.00 36.27 1.40
2924 3074 4.037923 TCTTGTTGGATTTTGCTTGACTCC 59.962 41.667 0.00 0.00 0.00 3.85
3266 3428 1.749634 GAGAGATCTTCGACGGGGAAA 59.250 52.381 0.00 0.00 0.00 3.13
3299 3461 0.553333 TGGGTTGATGGTGGTTGACA 59.447 50.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.075601 ACCCAAGGCATCTCAAGGAA 58.924 50.000 0.00 0.0 0.00 3.36
90 91 3.763671 CCAACCAAGGCACCTCAC 58.236 61.111 0.00 0.0 0.00 3.51
202 265 5.774690 TGGAGCCATTCAAGAACAAAGTATT 59.225 36.000 0.00 0.0 0.00 1.89
408 472 2.889018 GTAACCTAGGCCGCGCAC 60.889 66.667 9.30 0.0 0.00 5.34
409 473 3.383681 TGTAACCTAGGCCGCGCA 61.384 61.111 9.30 0.0 0.00 6.09
426 490 4.337145 GTGGATATGGAGAGAGATACGGT 58.663 47.826 0.00 0.0 0.00 4.83
632 697 1.237285 GCTCTCTTTCGGCTTTGGCA 61.237 55.000 0.00 0.0 40.87 4.92
633 698 1.237285 TGCTCTCTTTCGGCTTTGGC 61.237 55.000 0.00 0.0 37.82 4.52
943 1022 2.009774 CCCGCAGTAGAAGAACAATGG 58.990 52.381 0.00 0.0 0.00 3.16
1013 1092 4.508584 GGGTAAAGTCAAGGAGGTGGAATT 60.509 45.833 0.00 0.0 0.00 2.17
1032 1111 1.202099 TCAGAACGGCATTGGGGGTA 61.202 55.000 0.00 0.0 0.00 3.69
1586 1665 0.902531 GAAGACCTCGGGATGTTGGA 59.097 55.000 0.00 0.0 0.00 3.53
2011 2090 4.594920 TGAGGAGGAAGAAGAGTTGATGTT 59.405 41.667 0.00 0.0 0.00 2.71
2273 2352 0.894184 GGTGGTCTGAGACGACTCCA 60.894 60.000 23.59 6.2 40.30 3.86
2276 2355 2.627737 GCGGTGGTCTGAGACGACT 61.628 63.158 23.59 0.0 40.30 4.18
2306 2385 2.034066 CTTCCCTTGGCCGCTTGA 59.966 61.111 0.00 0.0 0.00 3.02
2553 2640 0.317160 CTGCTGTCGTAGTGGGTTCA 59.683 55.000 0.00 0.0 0.00 3.18
2874 2981 0.321653 GGAAGCCTTGAAGCGAAGGA 60.322 55.000 14.37 0.0 44.87 3.36
2924 3074 2.245438 GACAGCCGGAAAGGGGAGAG 62.245 65.000 5.05 0.0 41.48 3.20


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

AutoCloner maintained by Alex Coulton.