Multiple sequence alignment - TraesCS4D01G208100

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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 TraesCS4D01G208100 chr4D 100.000 3917 0 0 1 3917 358468036 358471952 0.000000e+00 7234.0
1 TraesCS4D01G208100 chr4D 91.837 49 3 1 3672 3719 91055487 91055439 2.530000e-07 67.6
2 TraesCS4D01G208100 chr4B 93.559 3990 118 55 21 3917 441669962 441673905 0.000000e+00 5816.0
3 TraesCS4D01G208100 chr4A 94.515 3318 109 31 639 3917 106912199 106908916 0.000000e+00 5051.0
4 TraesCS4D01G208100 chr4A 91.022 646 19 13 1 614 106912903 106912265 0.000000e+00 835.0
5 TraesCS4D01G208100 chr6B 100.000 42 0 0 3675 3716 289179293 289179334 1.170000e-10 78.7
6 TraesCS4D01G208100 chr5D 95.833 48 2 0 3667 3714 255078237 255078190 1.170000e-10 78.7
7 TraesCS4D01G208100 chr5D 95.556 45 2 0 3672 3716 563397318 563397274 5.430000e-09 73.1
8 TraesCS4D01G208100 chr5D 93.023 43 3 0 3673 3715 358219717 358219759 3.270000e-06 63.9
9 TraesCS4D01G208100 chr7D 90.909 55 3 2 3524 3576 64443109 64443163 5.430000e-09 73.1
10 TraesCS4D01G208100 chr7D 95.455 44 2 0 3674 3717 691570 691527 1.950000e-08 71.3


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 TraesCS4D01G208100 chr4D 358468036 358471952 3916 False 7234 7234 100.0000 1 3917 1 chr4D.!!$F1 3916
1 TraesCS4D01G208100 chr4B 441669962 441673905 3943 False 5816 5816 93.5590 21 3917 1 chr4B.!!$F1 3896
2 TraesCS4D01G208100 chr4A 106908916 106912903 3987 True 2943 5051 92.7685 1 3917 2 chr4A.!!$R1 3916

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
755 877 0.102481 TCGAGAGCGGAGTTTATGGC 59.898 55.0 0.0 0.0 38.28 4.40 F
783 905 0.460987 CAGAGGAAATCTCGCCGCTT 60.461 55.0 0.0 0.0 46.82 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2688 2817 1.439353 GCACATAGGATGGTGGTGCG 61.439 60.000 0.0 0.0 44.32 5.34 R
3015 3144 4.584325 CCAAAAGGTTTGATCCAGAGACAA 59.416 41.667 2.3 0.0 0.00 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
158 169 0.526211 GGCGCAAGGAGGTAAAAAGG 59.474 55.000 10.83 0.00 38.28 3.11
159 170 1.244816 GCGCAAGGAGGTAAAAAGGT 58.755 50.000 0.30 0.00 38.28 3.50
161 172 2.161012 GCGCAAGGAGGTAAAAAGGTAC 59.839 50.000 0.30 0.00 38.28 3.34
380 432 4.200283 CTGCCTCTCGCCTCGTCC 62.200 72.222 0.00 0.00 36.24 4.79
410 473 4.075793 TCAGCCGGCCTACCCTCT 62.076 66.667 26.15 0.00 0.00 3.69
438 508 3.486383 TCTAAAAGCCCAGGTCAAACTG 58.514 45.455 0.00 0.00 38.21 3.16
564 638 4.864334 CCCCGGATCTGCACCTGC 62.864 72.222 0.73 0.00 42.50 4.85
651 773 3.431725 GGCTTGGCTTCCGTTCCG 61.432 66.667 0.00 0.00 0.00 4.30
755 877 0.102481 TCGAGAGCGGAGTTTATGGC 59.898 55.000 0.00 0.00 38.28 4.40
780 902 0.807667 CACCAGAGGAAATCTCGCCG 60.808 60.000 0.00 0.00 46.82 6.46
783 905 0.460987 CAGAGGAAATCTCGCCGCTT 60.461 55.000 0.00 0.00 46.82 4.68
803 925 2.913060 CTCCGGGGATCTCGACCC 60.913 72.222 0.00 0.82 46.05 4.46
972 1101 1.826054 TGGTTGGTTGGTTGGCGAG 60.826 57.895 0.00 0.00 0.00 5.03
973 1102 2.561037 GGTTGGTTGGTTGGCGAGG 61.561 63.158 0.00 0.00 0.00 4.63
974 1103 1.527380 GTTGGTTGGTTGGCGAGGA 60.527 57.895 0.00 0.00 0.00 3.71
1083 1212 1.886222 GCCAAGGTCACCAGCAACATA 60.886 52.381 0.00 0.00 0.00 2.29
2688 2817 0.393808 TTGCGGCATCCCTTACCTTC 60.394 55.000 2.28 0.00 0.00 3.46
3015 3144 1.143684 AGCATCAGTTGTTGTGTCCCT 59.856 47.619 0.00 0.00 0.00 4.20
3089 3220 1.748493 GGAACCAAATGCGGCATCTAA 59.252 47.619 16.98 0.00 0.00 2.10
3172 3303 6.286240 ACTAGAGACTTGTGCATATTGTCA 57.714 37.500 15.55 0.00 0.00 3.58
3210 3346 4.107622 CCGGTTGTTGTTAGTATACCTCG 58.892 47.826 0.00 0.00 0.00 4.63
3423 3559 3.586470 TTGGAGCAAAGTTCCCTTGTA 57.414 42.857 0.00 0.00 33.62 2.41
3424 3560 3.586470 TGGAGCAAAGTTCCCTTGTAA 57.414 42.857 0.00 0.00 33.62 2.41
3464 3601 1.002868 ATTGCCTTGCTGCTCGTCT 60.003 52.632 0.00 0.00 0.00 4.18
3491 3628 2.591923 TGGAATACCTGTTGCTGCAAA 58.408 42.857 17.80 0.83 37.04 3.68
3603 3748 0.734889 GGATTGAAGTGACATGCCCG 59.265 55.000 0.00 0.00 0.00 6.13
3612 3757 0.322366 TGACATGCCCGCTTGAATCA 60.322 50.000 9.33 1.59 0.00 2.57
3648 3793 8.912988 TGATTCAAAATAAGTGAGTTCAACCTT 58.087 29.630 0.00 0.00 0.00 3.50
3715 3860 3.780850 ACTTATTTTGGATCGGAGGGAGT 59.219 43.478 0.00 0.00 0.00 3.85
3716 3861 2.717639 ATTTTGGATCGGAGGGAGTG 57.282 50.000 0.00 0.00 0.00 3.51
3796 3967 6.601613 TCCAACAAAGTGTACATATGATTCCC 59.398 38.462 10.38 0.00 0.00 3.97
3799 3970 7.630242 ACAAAGTGTACATATGATTCCCTTG 57.370 36.000 10.38 8.40 0.00 3.61
3858 4029 8.073768 TCAAATGACCAACGTAGAATTCTTTTC 58.926 33.333 14.36 4.30 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 2.519302 AAAACGGTGCCAGCTGCT 60.519 55.556 8.66 0.00 42.00 4.24
158 169 2.849964 GCGCCTACCCCCGTAGTAC 61.850 68.421 0.00 0.00 40.46 2.73
159 170 2.519302 GCGCCTACCCCCGTAGTA 60.519 66.667 0.00 0.00 40.46 1.82
233 260 3.941657 GAGCTTCGCGTGCCTTCCT 62.942 63.158 19.37 4.68 0.00 3.36
330 382 2.186826 GGTGTGTGGTGGTGTGCTC 61.187 63.158 0.00 0.00 0.00 4.26
332 384 1.391157 AATGGTGTGTGGTGGTGTGC 61.391 55.000 0.00 0.00 0.00 4.57
410 473 1.916181 CCTGGGCTTTTAGAGGAGGAA 59.084 52.381 0.00 0.00 0.00 3.36
559 633 0.679960 GGAATACCTTTGCGGCAGGT 60.680 55.000 16.82 16.82 46.95 4.00
669 791 2.361992 TCCTACTCCGCAGCCGAA 60.362 61.111 0.00 0.00 36.29 4.30
755 877 0.394899 GATTTCCTCTGGTGGGCCTG 60.395 60.000 4.53 0.00 35.27 4.85
780 902 3.468326 GAGATCCCCGGAGCCAAGC 62.468 68.421 0.73 0.00 0.00 4.01
783 905 4.137615 TCGAGATCCCCGGAGCCA 62.138 66.667 0.73 0.00 0.00 4.75
803 925 4.843220 ACACGTAAAGATATCTACCGGG 57.157 45.455 6.32 11.79 0.00 5.73
972 1101 1.829666 GCCTAATCCTCCTCCTCCTCC 60.830 61.905 0.00 0.00 0.00 4.30
973 1102 1.639722 GCCTAATCCTCCTCCTCCTC 58.360 60.000 0.00 0.00 0.00 3.71
974 1103 0.178947 CGCCTAATCCTCCTCCTCCT 60.179 60.000 0.00 0.00 0.00 3.69
2097 2226 2.564553 CTTCCTCCTTGACCGGCTCG 62.565 65.000 0.00 0.00 0.00 5.03
2688 2817 1.439353 GCACATAGGATGGTGGTGCG 61.439 60.000 0.00 0.00 44.32 5.34
3015 3144 4.584325 CCAAAAGGTTTGATCCAGAGACAA 59.416 41.667 2.30 0.00 0.00 3.18
3464 3601 5.588648 GCAGCAACAGGTATTCCATAACTTA 59.411 40.000 0.00 0.00 35.89 2.24
3491 3628 4.823989 GCAGCATTATGATAGGTTCCAGTT 59.176 41.667 0.00 0.00 0.00 3.16
3603 3748 5.893897 ATCAGAGGAAGTTTGATTCAAGC 57.106 39.130 5.20 5.20 0.00 4.01
3612 3757 9.354673 TCACTTATTTTGAATCAGAGGAAGTTT 57.645 29.630 1.43 0.00 0.00 2.66
3648 3793 6.125327 TGAACTTGTCGCAACTTTGAATTA 57.875 33.333 0.00 0.00 0.00 1.40
3715 3860 7.112122 ACATCAACCATTCTGCTAATTCTACA 58.888 34.615 0.00 0.00 0.00 2.74
3716 3861 7.280876 TGACATCAACCATTCTGCTAATTCTAC 59.719 37.037 0.00 0.00 0.00 2.59
3752 3902 8.925161 TGTTGGAACTTTCTACAATTTCTTTG 57.075 30.769 0.00 0.00 41.36 2.77
3758 3908 7.836842 ACACTTTGTTGGAACTTTCTACAATT 58.163 30.769 0.00 0.00 34.37 2.32
3765 3915 8.564574 TCATATGTACACTTTGTTGGAACTTTC 58.435 33.333 0.00 0.00 0.00 2.62
3819 3990 4.821260 TGGTCATTTGATACATCGGATTGG 59.179 41.667 0.00 0.00 0.00 3.16
3822 3993 4.511454 CGTTGGTCATTTGATACATCGGAT 59.489 41.667 9.14 0.00 0.00 4.18
3830 4001 8.786826 AAGAATTCTACGTTGGTCATTTGATA 57.213 30.769 8.75 0.00 0.00 2.15
3858 4029 8.994170 GGATTTTCCTAGGATTCGAATCTTTAG 58.006 37.037 31.32 28.31 33.04 1.85
3897 4069 0.107848 AACAACTAAGGGCGGGATCG 60.108 55.000 0.00 0.00 39.81 3.69


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

AutoCloner maintained by Alex Coulton.