Multiple sequence alignment - TraesCS3A01G346100

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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 TraesCS3A01G346100 chr3A 100.000 3524 0 0 1 3524 595433923 595437446 0.000000e+00 6508.0
1 TraesCS3A01G346100 chr3D 94.787 3549 143 20 1 3520 453096348 453099883 0.000000e+00 5491.0
2 TraesCS3A01G346100 chr3B 94.974 2925 105 16 1 2895 595287581 595290493 0.000000e+00 4549.0
3 TraesCS3A01G346100 chr3B 92.334 287 14 4 3126 3409 595290736 595291017 5.480000e-108 401.0
4 TraesCS3A01G346100 chr3B 95.238 105 3 2 3413 3516 595291185 595291288 7.830000e-37 165.0
5 TraesCS3A01G346100 chr2A 91.786 767 44 9 359 1109 279048893 279048130 0.000000e+00 1050.0
6 TraesCS3A01G346100 chr6B 78.587 1345 270 15 989 2324 169318576 169317241 0.000000e+00 872.0
7 TraesCS3A01G346100 chr1B 80.072 828 154 8 994 1819 532173987 532173169 3.890000e-169 604.0
8 TraesCS3A01G346100 chr1A 80.457 788 147 5 1034 1819 494451584 494450802 2.340000e-166 595.0
9 TraesCS3A01G346100 chr1D 80.330 788 148 5 1034 1819 397081426 397080644 1.090000e-164 590.0
10 TraesCS3A01G346100 chr7D 100.000 28 0 0 3408 3435 424658240 424658267 6.000000e-03 52.8


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 TraesCS3A01G346100 chr3A 595433923 595437446 3523 False 6508 6508 100.000 1 3524 1 chr3A.!!$F1 3523
1 TraesCS3A01G346100 chr3D 453096348 453099883 3535 False 5491 5491 94.787 1 3520 1 chr3D.!!$F1 3519
2 TraesCS3A01G346100 chr3B 595287581 595291288 3707 False 1705 4549 94.182 1 3516 3 chr3B.!!$F1 3515
3 TraesCS3A01G346100 chr2A 279048130 279048893 763 True 1050 1050 91.786 359 1109 1 chr2A.!!$R1 750
4 TraesCS3A01G346100 chr6B 169317241 169318576 1335 True 872 872 78.587 989 2324 1 chr6B.!!$R1 1335
5 TraesCS3A01G346100 chr1B 532173169 532173987 818 True 604 604 80.072 994 1819 1 chr1B.!!$R1 825
6 TraesCS3A01G346100 chr1A 494450802 494451584 782 True 595 595 80.457 1034 1819 1 chr1A.!!$R1 785
7 TraesCS3A01G346100 chr1D 397080644 397081426 782 True 590 590 80.330 1034 1819 1 chr1D.!!$R1 785

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
275 276 1.129326 CGGTCGATTTCTATGGCGTC 58.871 55.000 0.00 0.0 0.00 5.19 F
367 368 2.034879 GCTGGCAGCGCTCTGTTTA 61.035 57.895 25.47 0.0 42.29 2.01 F
727 744 2.159282 GGGAATGCAGAAAGATGTGCTG 60.159 50.000 0.00 0.0 45.61 4.41 F
2187 2210 2.286067 CGAGCTTGATGCCGAGATTTTC 60.286 50.000 0.00 0.0 44.23 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2051 1.003233 ACAGGCTGCCTAGTGGTAAAC 59.997 52.381 22.9 0.0 35.27 2.01 R
2166 2189 1.293924 AAATCTCGGCATCAAGCTCG 58.706 50.000 0.0 0.0 44.79 5.03 R
2355 2378 2.094757 TTGGCGACCGTGACTGATGT 62.095 55.000 0.0 0.0 0.00 3.06 R
3440 3765 0.175531 TCGAATCAAGGAGCATCGCA 59.824 50.000 0.0 0.0 34.37 5.10 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
20 21 1.801309 TAAACGGCTGCCAAACCTGC 61.801 55.000 20.29 0.00 0.00 4.85
21 22 4.586235 ACGGCTGCCAAACCTGCT 62.586 61.111 20.29 0.00 0.00 4.24
22 23 4.047059 CGGCTGCCAAACCTGCTG 62.047 66.667 20.29 0.00 0.00 4.41
184 185 1.216427 AGCCAGGAAATCCCAGAATCC 59.784 52.381 0.00 0.00 37.41 3.01
190 191 2.760650 GGAAATCCCAGAATCCACCAAC 59.239 50.000 0.00 0.00 34.14 3.77
275 276 1.129326 CGGTCGATTTCTATGGCGTC 58.871 55.000 0.00 0.00 0.00 5.19
367 368 2.034879 GCTGGCAGCGCTCTGTTTA 61.035 57.895 25.47 0.00 42.29 2.01
441 442 6.067263 TGGTCGGTTTTTGAGTTAGAATTG 57.933 37.500 0.00 0.00 0.00 2.32
449 450 9.887406 GGTTTTTGAGTTAGAATTGTCGAAATA 57.113 29.630 0.00 0.00 0.00 1.40
500 501 2.787473 TGCTTCACCCAGTTATCCAG 57.213 50.000 0.00 0.00 0.00 3.86
503 504 2.619074 GCTTCACCCAGTTATCCAGCTT 60.619 50.000 0.00 0.00 0.00 3.74
587 604 4.222588 CCCAAGATTTTGCCTTAATGTCCA 59.777 41.667 0.00 0.00 32.79 4.02
598 615 2.666272 TAATGTCCACAAAGGCCACA 57.334 45.000 5.01 0.00 37.29 4.17
658 675 5.122239 CCCTGCATTACATGTATCCGTTATG 59.878 44.000 6.36 7.43 0.00 1.90
727 744 2.159282 GGGAATGCAGAAAGATGTGCTG 60.159 50.000 0.00 0.00 45.61 4.41
752 769 5.565695 CGTAACAGCAAACACTTACTTTGT 58.434 37.500 0.00 0.00 32.18 2.83
984 1004 3.063725 TGGTGTTCGTTTGTTTTACTCCG 59.936 43.478 0.00 0.00 0.00 4.63
1338 1358 3.212685 GAAGCTTAATGAGGATGCTGCT 58.787 45.455 0.00 0.00 33.96 4.24
1668 1688 6.753180 TGAGGCAAATCTGATAGAGATGTAC 58.247 40.000 0.00 0.00 40.89 2.90
1771 1791 5.942977 TCCAGATCCCAGTACTAGGATTA 57.057 43.478 21.81 7.64 43.08 1.75
1836 1856 6.200854 CAGTTGAGGTAAATGCAAAGAAAACC 59.799 38.462 0.00 0.00 0.00 3.27
2028 2051 2.434359 GGTCGCAGGGAAGAACGG 60.434 66.667 0.00 0.00 0.00 4.44
2166 2189 3.074687 AGGAAGGAAAGAAGGGGTTTCTC 59.925 47.826 0.00 0.00 45.41 2.87
2187 2210 2.286067 CGAGCTTGATGCCGAGATTTTC 60.286 50.000 0.00 0.00 44.23 2.29
2355 2378 0.677731 CGATTCTGCAAGGGGAGCAA 60.678 55.000 0.00 0.00 42.17 3.91
2361 2384 0.609957 TGCAAGGGGAGCAACATCAG 60.610 55.000 0.00 0.00 39.39 2.90
2366 2389 1.021390 GGGGAGCAACATCAGTCACG 61.021 60.000 0.00 0.00 0.00 4.35
2573 2596 2.168936 TCGTGTGTGTTTCCCTGTACTT 59.831 45.455 0.00 0.00 0.00 2.24
2696 2733 6.777580 AGTTTTGCATACTATAGGGGGAAATG 59.222 38.462 4.43 0.00 0.00 2.32
2723 2760 5.827666 TCTTGATTCCGTTTTTGAACCTTC 58.172 37.500 0.00 0.00 0.00 3.46
2740 2777 9.748708 TTGAACCTTCTTGAAATAAAATGACTG 57.251 29.630 0.00 0.00 0.00 3.51
2764 2801 3.265791 GACCAGCACCATCTAGTTCTTG 58.734 50.000 0.00 0.00 0.00 3.02
2775 2812 7.332182 CACCATCTAGTTCTTGGAGTTTCTAAC 59.668 40.741 9.63 0.00 34.52 2.34
2851 2888 5.197451 AGTTGGTAATGGTCAAAGAACACA 58.803 37.500 0.00 0.00 29.56 3.72
2878 2915 2.514160 GGGAGGATGGTTTGGAGGTATT 59.486 50.000 0.00 0.00 0.00 1.89
2956 2994 4.447138 TTCAACTGTATTTGAGGTGGGT 57.553 40.909 0.00 0.00 36.84 4.51
2959 2997 3.154827 ACTGTATTTGAGGTGGGTTGG 57.845 47.619 0.00 0.00 0.00 3.77
2971 3009 4.498493 AGGTGGGTTGGGAATGTTTAAAT 58.502 39.130 0.00 0.00 0.00 1.40
2978 3016 7.017056 TGGGTTGGGAATGTTTAAATTTCAGAT 59.983 33.333 12.93 0.00 0.00 2.90
2982 3020 5.455525 GGGAATGTTTAAATTTCAGATCGCG 59.544 40.000 0.00 0.00 0.00 5.87
3000 3038 1.550130 CGACTTGGTGGGGGAGCTAA 61.550 60.000 0.00 0.00 0.00 3.09
3006 3044 1.282382 GGTGGGGGAGCTAACTGTTA 58.718 55.000 0.00 0.00 0.00 2.41
3007 3045 1.844497 GGTGGGGGAGCTAACTGTTAT 59.156 52.381 0.00 0.00 0.00 1.89
3008 3046 2.158798 GGTGGGGGAGCTAACTGTTATC 60.159 54.545 0.00 0.00 0.00 1.75
3085 3123 5.304101 AGGATAAATGTGTTTGCTTGGTTGA 59.696 36.000 0.00 0.00 0.00 3.18
3089 3127 3.951775 TGTGTTTGCTTGGTTGAAAGT 57.048 38.095 0.00 0.00 0.00 2.66
3099 3137 1.109323 GGTTGAAAGTGGCAGCTGGT 61.109 55.000 17.12 0.00 0.00 4.00
3196 3350 2.105128 CAAGGAGGAGCTACGCCG 59.895 66.667 13.69 0.00 0.00 6.46
3259 3415 4.459685 AGTTACTGCTACTGTCTGGTAGTG 59.540 45.833 0.00 0.00 40.70 2.74
3382 3543 0.542333 TTGTGGGTTCGTGACAGGAA 59.458 50.000 6.48 6.48 0.00 3.36
3467 3793 3.259374 TGCTCCTTGATTCGAGAAGTCTT 59.741 43.478 2.22 0.00 0.00 3.01
3520 3846 3.031736 TCAGGACCCATGCTAACTACTC 58.968 50.000 0.00 0.00 0.00 2.59
3521 3847 2.103263 CAGGACCCATGCTAACTACTCC 59.897 54.545 0.00 0.00 0.00 3.85
3522 3848 1.416772 GGACCCATGCTAACTACTCCC 59.583 57.143 0.00 0.00 0.00 4.30
3523 3849 2.399580 GACCCATGCTAACTACTCCCT 58.600 52.381 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.473147 CAGAATGGAGGGAGTGCAG 57.527 57.895 0.00 0.00 0.00 4.41
137 138 0.318275 CCGCGCTCTCATACTCTTCC 60.318 60.000 5.56 0.00 0.00 3.46
138 139 0.937231 GCCGCGCTCTCATACTCTTC 60.937 60.000 5.56 0.00 0.00 2.87
139 140 1.066587 GCCGCGCTCTCATACTCTT 59.933 57.895 5.56 0.00 0.00 2.85
168 169 2.287584 TGGTGGATTCTGGGATTTCCT 58.712 47.619 0.00 0.00 36.20 3.36
169 170 2.760650 GTTGGTGGATTCTGGGATTTCC 59.239 50.000 0.00 0.00 0.00 3.13
212 213 4.398598 GCCGATTTGGTGCGCGTT 62.399 61.111 8.43 0.00 41.21 4.84
236 237 0.598680 GGATCGATCCCGTGAAGCAG 60.599 60.000 30.80 0.00 41.20 4.24
237 238 1.441729 GGATCGATCCCGTGAAGCA 59.558 57.895 30.80 0.00 41.20 3.91
329 330 3.380004 AGCAAGTAGATCTCTTCCTGTCG 59.620 47.826 0.00 0.00 0.00 4.35
449 450 7.038659 CCATCTCTTGAACTCTAGAAACGATT 58.961 38.462 0.00 0.00 0.00 3.34
492 493 1.334869 CATCCGCCAAAGCTGGATAAC 59.665 52.381 2.39 0.00 46.92 1.89
500 501 1.138247 CAAGAGCATCCGCCAAAGC 59.862 57.895 0.00 0.00 39.83 3.51
503 504 0.597568 CAAACAAGAGCATCCGCCAA 59.402 50.000 0.00 0.00 39.83 4.52
610 627 5.815740 GTGGGATTACGAGCTCTAATGAAAA 59.184 40.000 12.85 0.00 0.00 2.29
658 675 5.048852 GCCAGCCAGAAGATCAGATTAAATC 60.049 44.000 0.00 0.00 0.00 2.17
727 744 2.546789 AGTAAGTGTTTGCTGTTACGCC 59.453 45.455 0.00 0.00 31.85 5.68
752 769 2.481568 CGAAGCTCTGATCTTGTTTGCA 59.518 45.455 0.00 0.00 0.00 4.08
904 921 3.139850 CCTCATGAATGGAGCAGATGTC 58.860 50.000 0.00 0.00 0.00 3.06
962 982 3.063725 CGGAGTAAAACAAACGAACACCA 59.936 43.478 0.00 0.00 0.00 4.17
963 983 3.063861 ACGGAGTAAAACAAACGAACACC 59.936 43.478 0.00 0.00 41.94 4.16
984 1004 8.039538 TCATCCATCATATCAAGCTATCTGAAC 58.960 37.037 0.00 0.00 0.00 3.18
1164 1184 4.599047 AATCTCCCTCTTTATCTGCTCG 57.401 45.455 0.00 0.00 0.00 5.03
1668 1688 2.436417 TCCGCTTTGGAAATCCTTCTG 58.564 47.619 0.44 0.00 46.38 3.02
1771 1791 7.344352 AGCACTTCTCTTTATCCTAGAGATTGT 59.656 37.037 3.64 4.07 45.47 2.71
1836 1856 1.208614 GTGCTTTGCTTCAGGCTCG 59.791 57.895 0.00 0.00 42.39 5.03
1850 1870 1.406539 CAGCTGAAAAGGTGTTGTGCT 59.593 47.619 8.42 0.00 33.12 4.40
1882 1902 2.202987 GCATCCTGTCGAGCCTGG 60.203 66.667 0.00 0.00 0.00 4.45
2028 2051 1.003233 ACAGGCTGCCTAGTGGTAAAC 59.997 52.381 22.90 0.00 35.27 2.01
2166 2189 1.293924 AAATCTCGGCATCAAGCTCG 58.706 50.000 0.00 0.00 44.79 5.03
2355 2378 2.094757 TTGGCGACCGTGACTGATGT 62.095 55.000 0.00 0.00 0.00 3.06
2361 2384 2.586635 TGTGTTGGCGACCGTGAC 60.587 61.111 1.61 0.00 0.00 3.67
2366 2389 4.030452 GCTGCTGTGTTGGCGACC 62.030 66.667 1.61 0.00 0.00 4.79
2573 2596 6.480763 TGGTTGCAAAGAGTATGGAATTAGA 58.519 36.000 0.00 0.00 30.70 2.10
2624 2661 9.672086 GTTATACACACAAGCTTTACAATTCAA 57.328 29.630 0.00 0.00 0.00 2.69
2696 2733 5.685954 GGTTCAAAAACGGAATCAAGAGTTC 59.314 40.000 0.00 0.00 36.16 3.01
2723 2760 8.511465 CTGGTCAACAGTCATTTTATTTCAAG 57.489 34.615 0.00 0.00 42.42 3.02
2740 2777 2.770164 ACTAGATGGTGCTGGTCAAC 57.230 50.000 0.00 0.00 0.00 3.18
2775 2812 9.846248 CTCTCCTTGGAAAACAAATTACAATAG 57.154 33.333 0.00 0.00 38.91 1.73
2851 2888 2.654385 TCCAAACCATCCTCCCAGAAAT 59.346 45.455 0.00 0.00 0.00 2.17
2878 2915 5.176590 GGCGATTGAATTTTTACAAAGCACA 59.823 36.000 0.00 0.00 36.36 4.57
2944 2982 2.158173 ACATTCCCAACCCACCTCAAAT 60.158 45.455 0.00 0.00 0.00 2.32
2956 2994 6.811170 GCGATCTGAAATTTAAACATTCCCAA 59.189 34.615 11.17 1.13 0.00 4.12
2959 2997 6.194692 GTCGCGATCTGAAATTTAAACATTCC 59.805 38.462 14.06 0.00 0.00 3.01
2971 3009 1.428448 CACCAAGTCGCGATCTGAAA 58.572 50.000 14.06 0.00 0.00 2.69
2982 3020 0.035343 GTTAGCTCCCCCACCAAGTC 60.035 60.000 0.00 0.00 0.00 3.01
3000 3038 4.785346 ATTCCTGCCAGATGATAACAGT 57.215 40.909 0.00 0.00 0.00 3.55
3006 3044 8.716674 AAATTATGTAATTCCTGCCAGATGAT 57.283 30.769 0.00 0.00 35.00 2.45
3007 3045 8.000709 AGAAATTATGTAATTCCTGCCAGATGA 58.999 33.333 0.00 0.00 35.00 2.92
3008 3046 8.174733 AGAAATTATGTAATTCCTGCCAGATG 57.825 34.615 0.00 0.00 35.00 2.90
3196 3350 5.908341 AGACTAATCGGGAACTTTCATCTC 58.092 41.667 0.00 0.00 0.00 2.75
3382 3543 4.681978 GCCGGCCTCACGTTCAGT 62.682 66.667 18.11 0.00 0.00 3.41
3440 3765 0.175531 TCGAATCAAGGAGCATCGCA 59.824 50.000 0.00 0.00 34.37 5.10
3467 3793 6.773200 AGTCAGAACCGATTAGATCAGTCATA 59.227 38.462 0.00 0.00 0.00 2.15
3487 3813 3.754965 TGGGTCCTGAATCAAAAGTCAG 58.245 45.455 0.00 0.00 45.10 3.51


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

AutoCloner maintained by Alex Coulton.