Multiple sequence alignment - TraesCS3A01G119400

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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 TraesCS3A01G119400 chr3A 100.000 3864 0 0 1 3864 92260797 92256934 0.000000e+00 7136
1 TraesCS3A01G119400 chr3A 97.071 2322 50 3 1561 3864 642858543 642860864 0.000000e+00 3895
2 TraesCS3A01G119400 chr3A 96.252 2321 70 2 1561 3864 665687138 665684818 0.000000e+00 3788
3 TraesCS3A01G119400 chr3A 97.327 2207 42 2 1675 3864 149210418 149212624 0.000000e+00 3733
4 TraesCS3A01G119400 chr3A 97.545 1548 37 1 1 1548 149208878 149210424 0.000000e+00 2647
5 TraesCS3A01G119400 chr3A 96.712 882 27 2 1 881 642856783 642857663 0.000000e+00 1467
6 TraesCS3A01G119400 chr3A 96.250 880 31 2 3 881 665688896 665688018 0.000000e+00 1441
7 TraesCS3A01G119400 chr3A 94.558 882 46 2 1 881 219227328 219226448 0.000000e+00 1362
8 TraesCS3A01G119400 chr3A 97.884 709 15 0 861 1569 642857615 642858323 0.000000e+00 1227
9 TraesCS3A01G119400 chr3A 96.884 706 22 0 864 1569 665688063 665687358 0.000000e+00 1182
10 TraesCS3A01G119400 chr6A 96.857 3882 101 6 1 3864 450320506 450324384 0.000000e+00 6473
11 TraesCS3A01G119400 chr1A 96.639 2321 59 4 1561 3864 177381625 177383943 0.000000e+00 3836
12 TraesCS3A01G119400 chr1A 96.510 2321 64 2 1561 3864 270718959 270716639 0.000000e+00 3821
13 TraesCS3A01G119400 chr1A 97.068 1569 46 0 1 1569 270720747 270719179 0.000000e+00 2643
14 TraesCS3A01G119400 chr1A 94.583 1569 54 17 3 1569 177379866 177381405 0.000000e+00 2398
15 TraesCS3A01G119400 chr5A 96.295 2321 69 2 1561 3864 685307762 685310082 0.000000e+00 3794
16 TraesCS3A01G119400 chr5A 96.022 2313 80 10 1561 3864 518788462 518786153 0.000000e+00 3751
17 TraesCS3A01G119400 chr5A 95.688 2319 58 3 1561 3864 155928681 155930972 0.000000e+00 3690
18 TraesCS3A01G119400 chr5A 96.622 1569 53 0 1 1569 685305974 685307542 0.000000e+00 2604
19 TraesCS3A01G119400 chr5A 96.145 882 33 1 1 881 155926921 155927802 0.000000e+00 1439
20 TraesCS3A01G119400 chr5A 97.872 705 15 0 865 1569 155927758 155928462 0.000000e+00 1219
21 TraesCS3A01G119400 chr7A 96.961 1678 33 3 2205 3864 271152929 271151252 0.000000e+00 2800
22 TraesCS3A01G119400 chr7A 93.394 772 22 2 3108 3864 648151658 648150901 0.000000e+00 1116
23 TraesCS3A01G119400 chr2B 92.798 972 25 9 2911 3863 761956839 761957784 0.000000e+00 1365
24 TraesCS3A01G119400 chr5B 96.034 706 28 0 864 1569 521054933 521054228 0.000000e+00 1149
25 TraesCS3A01G119400 chr5B 91.697 277 8 1 3603 3864 24166934 24166658 1.700000e-98 370
26 TraesCS3A01G119400 chr5B 91.697 277 8 1 3603 3864 577991074 577991350 1.700000e-98 370
27 TraesCS3A01G119400 chr5D 91.697 277 8 1 3603 3864 485818731 485819007 1.700000e-98 370
28 TraesCS3A01G119400 chr1B 91.697 277 8 1 3603 3864 34157188 34156912 1.700000e-98 370


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 TraesCS3A01G119400 chr3A 92256934 92260797 3863 True 7136.000000 7136 100.000000 1 3864 1 chr3A.!!$R1 3863
1 TraesCS3A01G119400 chr3A 149208878 149212624 3746 False 3190.000000 3733 97.436000 1 3864 2 chr3A.!!$F1 3863
2 TraesCS3A01G119400 chr3A 642856783 642860864 4081 False 2196.333333 3895 97.222333 1 3864 3 chr3A.!!$F2 3863
3 TraesCS3A01G119400 chr3A 665684818 665688896 4078 True 2137.000000 3788 96.462000 3 3864 3 chr3A.!!$R3 3861
4 TraesCS3A01G119400 chr3A 219226448 219227328 880 True 1362.000000 1362 94.558000 1 881 1 chr3A.!!$R2 880
5 TraesCS3A01G119400 chr6A 450320506 450324384 3878 False 6473.000000 6473 96.857000 1 3864 1 chr6A.!!$F1 3863
6 TraesCS3A01G119400 chr1A 270716639 270720747 4108 True 3232.000000 3821 96.789000 1 3864 2 chr1A.!!$R1 3863
7 TraesCS3A01G119400 chr1A 177379866 177383943 4077 False 3117.000000 3836 95.611000 3 3864 2 chr1A.!!$F1 3861
8 TraesCS3A01G119400 chr5A 518786153 518788462 2309 True 3751.000000 3751 96.022000 1561 3864 1 chr5A.!!$R1 2303
9 TraesCS3A01G119400 chr5A 685305974 685310082 4108 False 3199.000000 3794 96.458500 1 3864 2 chr5A.!!$F2 3863
10 TraesCS3A01G119400 chr5A 155926921 155930972 4051 False 2116.000000 3690 96.568333 1 3864 3 chr5A.!!$F1 3863
11 TraesCS3A01G119400 chr7A 271151252 271152929 1677 True 2800.000000 2800 96.961000 2205 3864 1 chr7A.!!$R1 1659
12 TraesCS3A01G119400 chr7A 648150901 648151658 757 True 1116.000000 1116 93.394000 3108 3864 1 chr7A.!!$R2 756
13 TraesCS3A01G119400 chr2B 761956839 761957784 945 False 1365.000000 1365 92.798000 2911 3863 1 chr2B.!!$F1 952
14 TraesCS3A01G119400 chr5B 521054228 521054933 705 True 1149.000000 1149 96.034000 864 1569 1 chr5B.!!$R2 705

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
920 976 1.366679 CTCTACTGCGACGAGTACCA 58.633 55.0 0.00 0.00 0.00 3.25 F
1749 2261 1.291184 GCACGGCTCATATATGCGCA 61.291 55.0 24.82 14.96 40.10 6.09 F
2504 3029 0.179137 GCCATTTTACGCCAGGCTTC 60.179 55.0 10.54 0.00 42.01 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2504 3029 0.106335 ATCTGGCTCGGCAGAATCTG 59.894 55.000 24.07 5.78 34.12 2.90 R
2854 3379 1.002684 GGACTGCATACCTAGTCGTCG 60.003 57.143 0.00 0.00 43.24 5.12 R
3562 4097 4.067896 ACAGAACTGTATCTTGCAGGTTG 58.932 43.478 5.62 0.00 42.90 3.77 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
316 317 1.447140 GGCGACGGTGATGCTTGTA 60.447 57.895 0.00 0.00 0.00 2.41
354 355 2.515991 CCACCAACACACAGCCGT 60.516 61.111 0.00 0.00 0.00 5.68
607 608 9.739737 TTACTCCTAAAATCCCTAATTCCTAGT 57.260 33.333 0.00 0.00 0.00 2.57
920 976 1.366679 CTCTACTGCGACGAGTACCA 58.633 55.000 0.00 0.00 0.00 3.25
1039 1095 2.125952 GCAAACTTGCGATGGGGC 60.126 61.111 0.00 0.00 45.11 5.80
1042 1098 3.860930 AAACTTGCGATGGGGCCGT 62.861 57.895 0.00 0.00 0.00 5.68
1507 1563 3.515602 ATGAAGCTTTGGAACTGAGGT 57.484 42.857 0.00 0.00 0.00 3.85
1628 2140 2.553602 GCAAGTGTGATGTCCATTCACA 59.446 45.455 2.56 2.56 41.40 3.58
1749 2261 1.291184 GCACGGCTCATATATGCGCA 61.291 55.000 24.82 14.96 40.10 6.09
1804 2316 6.183360 TGCTTGTCACTCCATAGGTTATAGTC 60.183 42.308 0.00 0.00 0.00 2.59
1812 2324 7.674348 CACTCCATAGGTTATAGTCATTCCCTA 59.326 40.741 0.00 0.00 0.00 3.53
1911 2423 5.066764 TGTGAATCTGTCATGCATGTATTGG 59.933 40.000 25.43 12.57 38.90 3.16
2114 2626 7.449247 AGGCAATATAATTGGTTGTTTTGTGT 58.551 30.769 2.11 0.00 0.00 3.72
2383 2908 2.093021 TGATCCCGATTGCTGAACATGA 60.093 45.455 0.00 0.00 0.00 3.07
2504 3029 0.179137 GCCATTTTACGCCAGGCTTC 60.179 55.000 10.54 0.00 42.01 3.86
3023 3550 2.837532 ATTCATGGCCGTTGCTTTTT 57.162 40.000 0.00 0.00 37.74 1.94
3076 3605 2.833338 TGCGTAGGTGGTTATAGGTTGT 59.167 45.455 0.00 0.00 0.00 3.32
3262 3791 4.803098 ACAACTAACCGATCTTAGCTGT 57.197 40.909 0.00 5.41 31.19 4.40
3263 3792 4.745649 ACAACTAACCGATCTTAGCTGTC 58.254 43.478 0.00 0.00 30.54 3.51
3669 4219 6.128661 TGTGTTATGCGAGATAAAGTTGTGTC 60.129 38.462 0.00 0.00 0.00 3.67
3675 4225 5.525745 TGCGAGATAAAGTTGTGTCAGAAAA 59.474 36.000 0.00 0.00 0.00 2.29
3715 4265 8.434392 TGTTATTACTGTGGGAAAGAAGTACTT 58.566 33.333 8.13 8.13 40.98 2.24
3794 4344 5.466127 TGGATTATAAAAAGGCCCTGTCT 57.534 39.130 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
607 608 7.667557 AGTATGTAGAACAGCAAGAGTAAACA 58.332 34.615 0.00 0.00 0.00 2.83
920 976 1.340991 GGTCATACCTGTGTGGGCATT 60.341 52.381 0.00 0.00 41.11 3.56
990 1046 1.808411 CACCCGACATTGTAGCAAGT 58.192 50.000 0.00 0.00 0.00 3.16
1454 1510 5.191323 ACAGAAGAGGGATGATTCAGACAAT 59.809 40.000 0.00 0.00 0.00 2.71
1507 1563 3.021695 CCAAGTAGTCAGATCCACCGTA 58.978 50.000 0.00 0.00 0.00 4.02
1675 2187 3.041940 GTCGCGGTCACCACCTTG 61.042 66.667 6.13 0.00 41.17 3.61
1749 2261 3.160679 ACTCAAAGTAATGCCCAGCTT 57.839 42.857 0.00 0.00 0.00 3.74
1804 2316 9.799106 AGAACATATAAGGAAACATAGGGAATG 57.201 33.333 0.00 0.00 41.74 2.67
2114 2626 5.655974 TGATCATGTTTAATTAGGCCAGCAA 59.344 36.000 5.01 0.00 0.00 3.91
2274 2786 8.439993 TGCTAATGTTTACTTGTCAAGTACAA 57.560 30.769 22.35 16.56 45.90 2.41
2504 3029 0.106335 ATCTGGCTCGGCAGAATCTG 59.894 55.000 24.07 5.78 34.12 2.90
2854 3379 1.002684 GGACTGCATACCTAGTCGTCG 60.003 57.143 0.00 0.00 43.24 5.12
3023 3550 9.783081 ATCAGAATGCACACATATATACTGAAA 57.217 29.630 0.00 0.00 34.62 2.69
3042 3571 4.816385 CCACCTACGCATACAAATCAGAAT 59.184 41.667 0.00 0.00 0.00 2.40
3301 3830 7.654568 TGCCATTTATGCATTATTTCTGAGAG 58.345 34.615 3.54 0.00 32.85 3.20
3562 4097 4.067896 ACAGAACTGTATCTTGCAGGTTG 58.932 43.478 5.62 0.00 42.90 3.77


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

AutoCloner maintained by Alex Coulton.