Multiple sequence alignment - TraesCS2A01G347000

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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 TraesCS2A01G347000 chr2A 100.000 3962 0 0 1 3962 585215312 585211351 0.000000e+00 7317
1 TraesCS2A01G347000 chr2B 96.356 3979 112 18 1 3962 519187841 519183879 0.000000e+00 6514
2 TraesCS2A01G347000 chr2D 91.622 3533 200 37 469 3962 441576675 441573200 0.000000e+00 4796
3 TraesCS2A01G347000 chr2D 97.021 470 13 1 2 471 441577256 441576788 0.000000e+00 789
4 TraesCS2A01G347000 chr5B 87.872 874 88 8 2135 2998 19791268 19790403 0.000000e+00 1011
5 TraesCS2A01G347000 chr5B 84.736 511 41 6 762 1257 19792789 19792301 9.960000e-131 477
6 TraesCS2A01G347000 chr5B 84.365 307 36 6 7 308 19793186 19792887 1.390000e-74 291
7 TraesCS2A01G347000 chr6B 84.979 233 31 4 2730 2960 435832622 435832392 2.380000e-57 233
8 TraesCS2A01G347000 chr6A 84.979 233 31 4 2730 2960 392193952 392193722 2.380000e-57 233


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 TraesCS2A01G347000 chr2A 585211351 585215312 3961 True 7317.0 7317 100.000000 1 3962 1 chr2A.!!$R1 3961
1 TraesCS2A01G347000 chr2B 519183879 519187841 3962 True 6514.0 6514 96.356000 1 3962 1 chr2B.!!$R1 3961
2 TraesCS2A01G347000 chr2D 441573200 441577256 4056 True 2792.5 4796 94.321500 2 3962 2 chr2D.!!$R1 3960
3 TraesCS2A01G347000 chr5B 19790403 19793186 2783 True 593.0 1011 85.657667 7 2998 3 chr5B.!!$R1 2991

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
45 46 1.965414 TGAGCATTTAGTCCCCTGGA 58.035 50.0 0.0 0.0 0.0 3.86 F
1886 2175 0.252375 ACCCGTCTAGCCCACCTAAA 60.252 55.0 0.0 0.0 0.0 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 2185 3.293379 AGGGGCTAGGTGGGAGGT 61.293 66.667 0.0 0.0 0.00 3.85 R
3655 4068 1.475930 GCCTCTTGGAGTATTCTGCCC 60.476 57.143 0.0 0.0 34.57 5.36 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
45 46 1.965414 TGAGCATTTAGTCCCCTGGA 58.035 50.000 0.00 0.00 0.00 3.86
141 147 4.454678 GCCACCTCATCATCATCTAAACA 58.545 43.478 0.00 0.00 0.00 2.83
197 204 5.198207 TGGTTCTGTATTCTAGATGTCGGA 58.802 41.667 0.00 0.00 0.00 4.55
443 452 7.865385 GGCTGCAATACCGATAAAATAAAATCA 59.135 33.333 0.50 0.00 0.00 2.57
494 618 2.863740 CAGCAGCGAAATATAACACGGA 59.136 45.455 0.00 0.00 0.00 4.69
506 630 6.786967 ATATAACACGGAGAAGTACTTGGT 57.213 37.500 14.14 0.00 0.00 3.67
941 1076 6.651225 AGTTCACATCTCAAACTAAGTTAGCC 59.349 38.462 9.92 0.00 31.68 3.93
1041 1176 2.871096 TAGGACATGTTGTTGGGGAC 57.129 50.000 0.00 0.00 0.00 4.46
1246 1387 6.377146 TGAACAATATTAAGTTTGAGGAGGCC 59.623 38.462 0.00 0.00 0.00 5.19
1257 1398 1.284785 TGAGGAGGCCTATTTGGGTTG 59.715 52.381 4.42 0.00 31.76 3.77
1327 1477 6.073222 AGTCAAACTCGGCTTTACTATTTGTG 60.073 38.462 0.00 0.00 0.00 3.33
1328 1478 5.761234 TCAAACTCGGCTTTACTATTTGTGT 59.239 36.000 0.00 0.00 0.00 3.72
1354 1508 6.997239 TCTAGAAAGTAGTACGCAATCTCA 57.003 37.500 0.00 0.00 0.00 3.27
1409 1563 5.400485 CACTTCAGTTGTTACCTGTACGTAC 59.600 44.000 18.90 18.90 0.00 3.67
1590 1875 3.436704 TCTTTTCATTCGGTGATGACTGC 59.563 43.478 0.00 0.00 35.86 4.40
1600 1885 3.725895 CGGTGATGACTGCGAATCAAAAG 60.726 47.826 0.00 0.00 34.70 2.27
1619 1907 3.503827 AGTATGCACGTCATCGAGAAA 57.496 42.857 0.00 0.00 40.62 2.52
1819 2107 9.768662 AAATTTGTCTGAAAAGCATCAAGTTAT 57.231 25.926 0.00 0.00 0.00 1.89
1886 2175 0.252375 ACCCGTCTAGCCCACCTAAA 60.252 55.000 0.00 0.00 0.00 1.85
1887 2176 0.906775 CCCGTCTAGCCCACCTAAAA 59.093 55.000 0.00 0.00 0.00 1.52
1896 2185 2.891191 CCCACCTAAAAACTAGGGCA 57.109 50.000 3.00 0.00 39.00 5.36
2009 2311 2.408271 TGATGGGCACAGCTTCTTAG 57.592 50.000 5.50 0.00 33.23 2.18
2040 2342 6.321181 AGGCAAAAGTACATTTCAGAAAGTGA 59.679 34.615 1.28 0.00 0.00 3.41
2082 2386 9.976511 CAGAAATATCATATTTTGCTTCCATGT 57.023 29.630 4.08 0.00 0.00 3.21
2291 2683 5.234757 TGTGTACAATGTAACACCTCGAAAC 59.765 40.000 17.12 0.00 44.29 2.78
2553 2954 6.583562 ACTTAGGGATAAAAACTCGAGATGG 58.416 40.000 21.68 0.00 0.00 3.51
2587 2988 4.265073 AGTGCTTAGGATGCAAAGTTAGG 58.735 43.478 0.00 0.00 42.41 2.69
2589 2990 4.095036 GTGCTTAGGATGCAAAGTTAGGAC 59.905 45.833 0.00 0.00 42.41 3.85
2698 3099 9.570488 GAATTTACGTACTAGAATGAACTCACT 57.430 33.333 0.00 0.00 0.00 3.41
2811 3212 3.695830 TTTGTACTCTTCCGCCAATCT 57.304 42.857 0.00 0.00 0.00 2.40
3208 3613 4.637483 ACAATGTCACCTTGAACAACAG 57.363 40.909 0.00 0.00 0.00 3.16
3342 3747 7.516198 AGCAGAACAAAGAACTAATGATGTT 57.484 32.000 0.00 0.00 34.01 2.71
3394 3800 3.454082 AGGCTTCAGGATAACTTCAGAGG 59.546 47.826 0.00 0.00 0.00 3.69
3396 3802 3.452474 CTTCAGGATAACTTCAGAGGCG 58.548 50.000 0.00 0.00 0.00 5.52
3399 3805 3.706594 TCAGGATAACTTCAGAGGCGAAT 59.293 43.478 0.00 0.00 0.00 3.34
3400 3806 4.893524 TCAGGATAACTTCAGAGGCGAATA 59.106 41.667 0.00 0.00 0.00 1.75
3401 3807 5.362717 TCAGGATAACTTCAGAGGCGAATAA 59.637 40.000 0.00 0.00 0.00 1.40
3402 3808 5.463724 CAGGATAACTTCAGAGGCGAATAAC 59.536 44.000 0.00 0.00 0.00 1.89
3403 3809 5.128827 AGGATAACTTCAGAGGCGAATAACA 59.871 40.000 0.00 0.00 0.00 2.41
3404 3810 5.463724 GGATAACTTCAGAGGCGAATAACAG 59.536 44.000 0.00 0.00 0.00 3.16
3405 3811 3.963428 ACTTCAGAGGCGAATAACAGT 57.037 42.857 0.00 0.00 0.00 3.55
3442 3853 4.392940 ACAAGGCTGGTATATTCTGCATC 58.607 43.478 0.00 0.00 0.00 3.91
3507 3919 8.153550 AGTCTCAACTCAATCTGATGTAAAAGT 58.846 33.333 0.00 0.00 0.00 2.66
3542 3954 7.437793 TTTTACCTCACCTTGTATAAAACGG 57.562 36.000 0.00 0.00 0.00 4.44
3565 3977 6.427547 CGGTTACAAATTAGTCTGGGTTTGTA 59.572 38.462 11.85 11.85 42.70 2.41
3576 3988 1.063567 TGGGTTTGTACCAGTGCCTTT 60.064 47.619 0.00 0.00 46.96 3.11
3596 4008 3.887621 TTAAGGGTCAGAGTCCATTCG 57.112 47.619 0.00 0.00 31.40 3.34
3655 4068 6.429078 TCAATCATGTTCAAGAACTGAAGAGG 59.571 38.462 13.49 6.90 44.83 3.69
3660 4073 1.349026 TCAAGAACTGAAGAGGGGCAG 59.651 52.381 0.00 0.00 38.10 4.85
3661 4074 1.349026 CAAGAACTGAAGAGGGGCAGA 59.651 52.381 0.00 0.00 36.07 4.26
3685 4098 0.260230 TCCAAGAGGCACCCAACAAA 59.740 50.000 0.00 0.00 33.74 2.83
3766 4179 5.691754 CAGATTTTTAACGCCAGAAAAGCTT 59.308 36.000 0.00 0.00 37.02 3.74
3829 4242 5.755861 GCAGTAGTCATTCCAAGGTTAGATC 59.244 44.000 0.00 0.00 0.00 2.75
3887 4301 6.040247 CAGATGATGCTAACAATGTGCAATT 58.960 36.000 2.53 0.00 40.24 2.32
3889 4303 7.865889 CAGATGATGCTAACAATGTGCAATTAT 59.134 33.333 2.53 0.00 40.24 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 6.531503 TTGGTCTTTCAATCGAGATCTAGT 57.468 37.500 0.00 0.00 0.00 2.57
118 119 3.391506 TTAGATGATGATGAGGTGGCG 57.608 47.619 0.00 0.00 0.00 5.69
197 204 5.700373 GGTGTGTGGTTTATTTCAATGCATT 59.300 36.000 5.99 5.99 0.00 3.56
494 618 5.625150 AGCATCAAAAGACCAAGTACTTCT 58.375 37.500 4.77 0.00 0.00 2.85
506 630 8.469200 CAAATGGGATAAGTAAGCATCAAAAGA 58.531 33.333 0.00 0.00 0.00 2.52
941 1076 1.856539 ATGGGTTGGGCTCTGGACAG 61.857 60.000 0.00 0.00 0.00 3.51
994 1129 1.004277 TGCCTCCCTTGACATGGTTAC 59.996 52.381 6.62 0.00 0.00 2.50
1041 1176 4.213906 GCTTTGACAAATGGGTCCAAAATG 59.786 41.667 0.05 0.00 36.97 2.32
1289 1439 5.448496 CCGAGTTTGACTTGTGATGTTGAAA 60.448 40.000 0.00 0.00 0.00 2.69
1327 1477 7.474190 AGATTGCGTACTACTTTCTAGAAGAC 58.526 38.462 5.12 0.00 0.00 3.01
1328 1478 7.336176 TGAGATTGCGTACTACTTTCTAGAAGA 59.664 37.037 5.12 0.00 0.00 2.87
1354 1508 6.839124 TTGAAAAGCTGATGTTATGGATGT 57.161 33.333 0.00 0.00 0.00 3.06
1409 1563 6.592994 TGAGATTCTTTGCTCTCAGTGTTATG 59.407 38.462 0.00 0.00 42.17 1.90
1590 1875 4.320667 TGACGTGCATACTTTTGATTCG 57.679 40.909 0.00 0.00 0.00 3.34
1600 1885 4.738252 TGTATTTCTCGATGACGTGCATAC 59.262 41.667 0.00 0.00 37.34 2.39
1699 1987 4.778579 AGTATCGTGACTAGAGCACCTAA 58.221 43.478 12.56 2.78 32.74 2.69
1700 1988 4.418973 AGTATCGTGACTAGAGCACCTA 57.581 45.455 12.56 4.62 32.74 3.08
1896 2185 3.293379 AGGGGCTAGGTGGGAGGT 61.293 66.667 0.00 0.00 0.00 3.85
2009 2311 7.422399 TCTGAAATGTACTTTTGCCTTGTAAC 58.578 34.615 11.15 0.00 0.00 2.50
2523 2923 9.765795 CTCGAGTTTTTATCCCTAAGTAATCAT 57.234 33.333 3.62 0.00 0.00 2.45
2553 2954 6.293135 GCATCCTAAGCACTTTCTATAGTTGC 60.293 42.308 0.00 5.18 0.00 4.17
2587 2988 7.229506 AGGTATGCTATTTAGATGCCTTTTGTC 59.770 37.037 0.00 0.00 0.00 3.18
2589 2990 7.365741 CAGGTATGCTATTTAGATGCCTTTTG 58.634 38.462 0.00 0.00 0.00 2.44
2811 3212 3.066064 GTGCATATATTGTTTGCCGGACA 59.934 43.478 5.05 0.00 35.51 4.02
3109 3510 4.326826 TTCATTCTGAAAGCACCCTAGTG 58.673 43.478 0.00 0.00 39.12 2.74
3157 3562 1.771854 TCACTCCAAAAGCACCCTGTA 59.228 47.619 0.00 0.00 0.00 2.74
3192 3597 6.619801 AGATAAACTGTTGTTCAAGGTGAC 57.380 37.500 0.00 0.00 34.96 3.67
3263 3668 5.335897 GGCATCTGCTTTTTAACATGACAGA 60.336 40.000 0.00 0.00 41.70 3.41
3342 3747 6.223852 GTGAAGTGTTCTGAAGGAGTATGAA 58.776 40.000 0.00 0.00 0.00 2.57
3394 3800 4.142687 ACATGCCTGTTAACTGTTATTCGC 60.143 41.667 7.22 4.91 28.70 4.70
3396 3802 8.293867 TGTAAACATGCCTGTTAACTGTTATTC 58.706 33.333 7.84 0.00 44.83 1.75
3399 3805 7.255312 CCTTGTAAACATGCCTGTTAACTGTTA 60.255 37.037 7.84 0.00 44.83 2.41
3400 3806 6.458232 TTGTAAACATGCCTGTTAACTGTT 57.542 33.333 7.84 5.81 44.83 3.16
3401 3807 5.009610 CCTTGTAAACATGCCTGTTAACTGT 59.990 40.000 7.84 0.00 44.83 3.55
3402 3808 5.460646 CCTTGTAAACATGCCTGTTAACTG 58.539 41.667 7.84 6.33 44.83 3.16
3403 3809 4.022329 GCCTTGTAAACATGCCTGTTAACT 60.022 41.667 7.84 0.00 44.83 2.24
3404 3810 4.022329 AGCCTTGTAAACATGCCTGTTAAC 60.022 41.667 7.84 0.00 44.83 2.01
3405 3811 4.022416 CAGCCTTGTAAACATGCCTGTTAA 60.022 41.667 7.84 0.00 44.83 2.01
3507 3919 4.953579 AGGTGAGGTAAAAAGTTGCTGAAA 59.046 37.500 0.00 0.00 0.00 2.69
3522 3934 4.628963 ACCGTTTTATACAAGGTGAGGT 57.371 40.909 0.00 0.00 33.37 3.85
3542 3954 7.587629 GGTACAAACCCAGACTAATTTGTAAC 58.412 38.462 14.79 14.13 44.68 2.50
3565 3977 1.497286 TGACCCTTAAAAGGCACTGGT 59.503 47.619 3.03 0.00 45.10 4.00
3576 3988 3.170717 ACGAATGGACTCTGACCCTTAA 58.829 45.455 0.00 0.00 0.00 1.85
3596 4008 2.744494 GCATCAGAACTCCTGGATGGAC 60.744 54.545 0.00 0.00 43.12 4.02
3655 4068 1.475930 GCCTCTTGGAGTATTCTGCCC 60.476 57.143 0.00 0.00 34.57 5.36
3660 4073 1.559682 TGGGTGCCTCTTGGAGTATTC 59.440 52.381 0.00 0.00 34.57 1.75
3661 4074 1.668826 TGGGTGCCTCTTGGAGTATT 58.331 50.000 0.00 0.00 34.57 1.89
3691 4104 9.193806 AGCCAGACTTGATTAACAATGAATATT 57.806 29.630 0.00 0.00 37.88 1.28
3709 4122 3.901844 TGGAGTACAAAGTTAGCCAGACT 59.098 43.478 0.00 0.00 0.00 3.24
3766 4179 4.337836 TGTTTGTTGCTCTTGTGCTTATGA 59.662 37.500 0.00 0.00 0.00 2.15
3812 4225 6.408548 GGTGATCAGATCTAACCTTGGAATGA 60.409 42.308 11.83 0.00 0.00 2.57
3829 4242 2.026915 TCTGTGGGTGAATGGTGATCAG 60.027 50.000 0.00 0.00 0.00 2.90
3861 4275 3.379372 GCACATTGTTAGCATCATCTGGT 59.621 43.478 0.00 0.00 39.41 4.00
3887 4301 9.670442 AGGGACTGGATATCAACTTTAGTAATA 57.330 33.333 4.83 0.00 37.18 0.98
3889 4303 7.989947 AGGGACTGGATATCAACTTTAGTAA 57.010 36.000 4.83 0.00 37.18 2.24


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

AutoCloner maintained by Alex Coulton.