Multiple sequence alignment - TraesCS5D01G036800

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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 TraesCS5D01G036800 chr5D 100.000 3256 0 0 1 3256 35981908 35985163 0.000000e+00 6013.0
1 TraesCS5D01G036800 chr5D 92.593 54 4 0 2101 2154 35983966 35984019 9.690000e-11 78.7
2 TraesCS5D01G036800 chr5D 92.593 54 4 0 2059 2112 35984008 35984061 9.690000e-11 78.7
3 TraesCS5D01G036800 chr5B 92.825 3303 170 21 1 3255 26914152 26917435 0.000000e+00 4724.0
4 TraesCS5D01G036800 chr5B 94.444 54 3 0 2101 2154 26916222 26916275 2.080000e-12 84.2
5 TraesCS5D01G036800 chr5A 92.663 2508 122 22 3 2474 24774478 24776959 0.000000e+00 3555.0
6 TraesCS5D01G036800 chr5A 92.395 789 39 12 2472 3256 24777210 24777981 0.000000e+00 1105.0
7 TraesCS5D01G036800 chr5A 88.828 913 79 6 2160 3055 25027696 25026790 0.000000e+00 1099.0
8 TraesCS5D01G036800 chr5A 93.431 137 9 0 3057 3193 25025288 25025152 1.530000e-48 204.0
9 TraesCS5D01G036800 chr5A 86.747 166 22 0 1968 2133 25055361 25055196 5.550000e-43 185.0
10 TraesCS5D01G036800 chr5A 91.228 57 5 0 2102 2158 25055269 25055213 9.690000e-11 78.7


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 TraesCS5D01G036800 chr5D 35981908 35985163 3255 False 2056.8 6013 95.0620 1 3256 3 chr5D.!!$F1 3255
1 TraesCS5D01G036800 chr5B 26914152 26917435 3283 False 2404.1 4724 93.6345 1 3255 2 chr5B.!!$F1 3254
2 TraesCS5D01G036800 chr5A 24774478 24777981 3503 False 2330.0 3555 92.5290 3 3256 2 chr5A.!!$F1 3253
3 TraesCS5D01G036800 chr5A 25025152 25027696 2544 True 651.5 1099 91.1295 2160 3193 2 chr5A.!!$R1 1033

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
90 91 0.811219 TTGAATCCAGCGCGATGAGG 60.811 55.0 28.29 10.7 0.0 3.86 F
1056 1065 0.615331 ATGCCGAGGAGAAGAAAGCA 59.385 50.0 0.00 0.0 0.0 3.91 F
2009 2042 0.314935 ATCTTGCCCAACAAAGCACG 59.685 50.0 0.00 0.0 39.1 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1172 1181 0.748367 GATCCTTTTCGGGTCTGGGC 60.748 60.0 0.00 0.0 40.00 5.36 R
2119 2152 0.250684 TGCAGCTTTCGGTGATTCCA 60.251 50.0 0.00 0.0 41.05 3.53 R
3026 3335 0.954452 GCCTACTGCTGTGTTTTGCT 59.046 50.0 6.48 0.0 36.87 3.91 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
23 24 1.811266 CTCAAGGGACGCCATCACG 60.811 63.158 0.00 0.00 35.00 4.35
82 83 2.787249 CGCCAGTTGAATCCAGCG 59.213 61.111 0.00 0.00 37.39 5.18
90 91 0.811219 TTGAATCCAGCGCGATGAGG 60.811 55.000 28.29 10.70 0.00 3.86
96 97 4.074526 AGCGCGATGAGGCACAGT 62.075 61.111 12.10 0.00 0.00 3.55
186 187 3.685214 CTCGCCTGTCGTCCTTCCG 62.685 68.421 0.00 0.00 39.67 4.30
260 261 5.502153 TTTAGATTCTCTAGACGTCTGCC 57.498 43.478 28.12 8.58 29.56 4.85
288 289 3.062763 AGCGTGAAACTCTGAACTGATG 58.937 45.455 0.00 0.00 25.72 3.07
302 303 8.721133 TCTGAACTGATGGGCTAATTATAGTA 57.279 34.615 0.00 0.00 0.00 1.82
338 339 2.005451 CTCCGGCATTCTTCTTCACAG 58.995 52.381 0.00 0.00 0.00 3.66
362 363 1.059098 TGAGTGGTCAAGTCCTGCAT 58.941 50.000 0.00 0.00 0.00 3.96
384 385 2.162681 GGGAATGAGTGGGTGAAGTTG 58.837 52.381 0.00 0.00 0.00 3.16
387 388 3.636764 GGAATGAGTGGGTGAAGTTGTTT 59.363 43.478 0.00 0.00 0.00 2.83
389 390 3.644966 TGAGTGGGTGAAGTTGTTTCT 57.355 42.857 0.00 0.00 36.71 2.52
508 509 1.465794 AGGTACCTCTCTTCGCTGTC 58.534 55.000 9.21 0.00 0.00 3.51
531 534 4.506255 CTTCGGCCCCACATCCCC 62.506 72.222 0.00 0.00 0.00 4.81
563 566 7.642669 TCAATCAAAGTGAACAGAAGACATTC 58.357 34.615 0.00 0.00 35.52 2.67
733 738 4.345859 TTCGTACAGAAATTGACCTGGT 57.654 40.909 0.00 0.00 35.61 4.00
734 739 3.921677 TCGTACAGAAATTGACCTGGTC 58.078 45.455 19.96 19.96 34.85 4.02
841 848 5.353938 TGTACGGAGGTAGCACAAATAATC 58.646 41.667 0.00 0.00 0.00 1.75
876 883 9.914131 ATTAGAGGCTAAGTTTTGAATTTGTTC 57.086 29.630 0.00 0.00 0.00 3.18
929 938 4.085357 TGAAGTGTTACCACAGCAAGAT 57.915 40.909 0.00 0.00 44.39 2.40
1019 1028 6.183360 GCACAGATGAGCACTAATACAAATGT 60.183 38.462 0.00 0.00 0.00 2.71
1056 1065 0.615331 ATGCCGAGGAGAAGAAAGCA 59.385 50.000 0.00 0.00 0.00 3.91
1092 1101 1.406065 CCTCATCGGAGCACCTGGAT 61.406 60.000 0.00 0.00 39.96 3.41
1172 1181 0.739813 GGACCAAACCTCGACGGATG 60.740 60.000 7.76 6.31 36.31 3.51
1371 1380 2.278142 GCGCCATTGCCATCGTTC 60.278 61.111 0.00 0.00 0.00 3.95
1431 1440 3.172106 TCACCCAAGGCAACCGGA 61.172 61.111 9.46 0.00 37.17 5.14
1564 1573 1.907240 ACCATGCACCCCCTATTAGT 58.093 50.000 0.00 0.00 0.00 2.24
1626 1636 1.443872 CGCCGTACACTGACACTCC 60.444 63.158 0.00 0.00 0.00 3.85
1661 1671 8.258708 CCTTAAATAGCTAACTACCTGTGAAGT 58.741 37.037 0.00 0.00 0.00 3.01
1729 1745 1.470285 GCGTAATCGTTCACCTAGGCA 60.470 52.381 9.30 0.00 39.49 4.75
1824 1855 7.863722 TGTTGCTTAATAATTAGAGTACCCCA 58.136 34.615 0.00 0.00 0.00 4.96
1908 1941 2.151202 TGACTTCTGGACGCATTTTCC 58.849 47.619 0.00 0.00 0.00 3.13
1915 1948 2.230992 CTGGACGCATTTTCCCAAATCA 59.769 45.455 0.00 0.00 29.41 2.57
1949 1982 1.701847 AGTGTCTTCAGATTGGCAGGT 59.298 47.619 0.00 0.00 0.00 4.00
1964 1997 1.747709 CAGGTGATGAGAAAGCCAGG 58.252 55.000 0.00 0.00 0.00 4.45
1999 2032 0.482446 AACCAACCAGATCTTGCCCA 59.518 50.000 0.00 0.00 0.00 5.36
2009 2042 0.314935 ATCTTGCCCAACAAAGCACG 59.685 50.000 0.00 0.00 39.10 5.34
2115 2148 1.094785 AATGGAATCACCGAAAGCCG 58.905 50.000 0.00 0.00 42.61 5.52
2119 2152 0.451783 GAATCACCGAAAGCCGCAAT 59.548 50.000 0.00 0.00 36.84 3.56
2120 2153 0.171007 AATCACCGAAAGCCGCAATG 59.829 50.000 0.00 0.00 36.84 2.82
2137 2170 1.098050 ATGGAATCACCGAAAGCTGC 58.902 50.000 0.00 0.00 42.61 5.25
2283 2322 2.954684 AACGGGCGCTCTCAATCCA 61.955 57.895 5.36 0.00 0.00 3.41
2502 2809 9.593134 TTTTGATTGGGATATTTGTTTTATCGG 57.407 29.630 0.00 0.00 0.00 4.18
2516 2823 5.300792 TGTTTTATCGGGGAGGCAATTTATC 59.699 40.000 0.00 0.00 0.00 1.75
2545 2852 6.620877 TGGTTGTAGTAATTCTGAGGATGT 57.379 37.500 0.00 0.00 0.00 3.06
2713 3021 7.283329 AGGACCTAATTAGGAATGTCATGTTC 58.717 38.462 33.60 17.72 46.63 3.18
2727 3035 4.256920 GTCATGTTCTCACCAGCAACTAT 58.743 43.478 0.00 0.00 0.00 2.12
2731 3039 5.330455 TGTTCTCACCAGCAACTATAGAG 57.670 43.478 6.78 0.00 0.00 2.43
2790 3098 8.950007 AAAAAGGAAGGTAGACCAATCAATAA 57.050 30.769 0.66 0.00 38.89 1.40
2880 3188 2.290960 ACAATCAGGGTTAGTGGCCTTC 60.291 50.000 3.32 0.00 0.00 3.46
2932 3240 3.214697 TGCCATCTTGTTACATTTGCG 57.785 42.857 0.00 0.00 0.00 4.85
3014 3323 6.095021 GGGAACACAAAGATACCATTAACCTC 59.905 42.308 0.00 0.00 0.00 3.85
3023 3332 3.857157 ACCATTAACCTCGGCACATAT 57.143 42.857 0.00 0.00 0.00 1.78
3024 3333 4.967084 ACCATTAACCTCGGCACATATA 57.033 40.909 0.00 0.00 0.00 0.86
3025 3334 5.499004 ACCATTAACCTCGGCACATATAT 57.501 39.130 0.00 0.00 0.00 0.86
3026 3335 6.614694 ACCATTAACCTCGGCACATATATA 57.385 37.500 0.00 0.00 0.00 0.86
3037 3346 5.236263 TCGGCACATATATAGCAAAACACAG 59.764 40.000 10.44 0.00 0.00 3.66
3125 4936 4.331356 GCACAAAGCAGGCAACAG 57.669 55.556 0.00 0.00 44.79 3.16
3170 4982 2.158769 AGCAAACTCACATCACACTGGA 60.159 45.455 0.00 0.00 0.00 3.86
3225 5037 2.581354 CACTCGGGAAGCCTCAGG 59.419 66.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 2.447887 CGTCACTGTGCCTCATCGC 61.448 63.158 2.12 0.00 0.00 4.58
94 95 1.213013 GTCATCGGAGCACGTCACT 59.787 57.895 0.78 0.00 44.69 3.41
96 97 1.212751 CTGTCATCGGAGCACGTCA 59.787 57.895 0.78 0.00 44.69 4.35
119 120 3.630892 ATCATGCAGCTCAACTCTCTT 57.369 42.857 0.00 0.00 0.00 2.85
186 187 1.444553 CGACAAGACCGGAGAGTGC 60.445 63.158 9.46 0.00 0.00 4.40
209 210 1.022735 CATTGCAGTGCTGAGGATCC 58.977 55.000 17.60 2.48 0.00 3.36
260 261 1.128136 CAGAGTTTCACGCTGATGCAG 59.872 52.381 1.73 0.00 46.88 4.41
288 289 7.284716 GGGCCAACATTATACTATAATTAGCCC 59.715 40.741 19.64 19.64 45.21 5.19
302 303 1.202927 CGGAGGATGGGCCAACATTAT 60.203 52.381 11.89 0.00 40.02 1.28
338 339 3.070018 CAGGACTTGACCACTCATCAAC 58.930 50.000 0.00 0.00 32.67 3.18
362 363 1.780309 ACTTCACCCACTCATTCCCAA 59.220 47.619 0.00 0.00 0.00 4.12
384 385 6.864165 TGTAACAGTTGGTTTGTTTGAGAAAC 59.136 34.615 0.00 0.00 40.96 2.78
387 388 5.106078 GGTGTAACAGTTGGTTTGTTTGAGA 60.106 40.000 0.00 0.00 40.96 3.27
389 390 4.082136 GGGTGTAACAGTTGGTTTGTTTGA 60.082 41.667 0.00 0.00 40.96 2.69
508 509 0.179056 ATGTGGGGCCGAAGATAACG 60.179 55.000 0.00 0.00 0.00 3.18
531 534 6.437928 TCTGTTCACTTTGATTGATTTTCCG 58.562 36.000 0.00 0.00 0.00 4.30
532 535 8.137437 TCTTCTGTTCACTTTGATTGATTTTCC 58.863 33.333 0.00 0.00 0.00 3.13
563 566 2.099098 ACCTCTTTCACCTTTGCAAACG 59.901 45.455 8.05 7.23 0.00 3.60
606 609 6.265196 TGGCAGTACAGAAAGAACAATCAAAT 59.735 34.615 0.00 0.00 0.00 2.32
733 738 7.943079 TCAGAGCATTTCATTATTTCCTTGA 57.057 32.000 0.00 0.00 0.00 3.02
734 739 9.031360 CAATCAGAGCATTTCATTATTTCCTTG 57.969 33.333 0.00 0.00 0.00 3.61
841 848 7.856145 AAACTTAGCCTCTAATTCAGACATG 57.144 36.000 0.00 0.00 0.00 3.21
876 883 6.703607 GTGTATGTAGTTCCTGATGAATGGAG 59.296 42.308 0.00 0.00 34.90 3.86
929 938 5.152623 AGATTCAAGTGGATTTGTCGAGA 57.847 39.130 0.00 0.00 0.00 4.04
1009 1018 3.258123 GGTGCAGGGTTGACATTTGTATT 59.742 43.478 0.00 0.00 0.00 1.89
1019 1028 1.434513 ATCCTTGGGTGCAGGGTTGA 61.435 55.000 0.00 0.00 31.50 3.18
1172 1181 0.748367 GATCCTTTTCGGGTCTGGGC 60.748 60.000 0.00 0.00 40.00 5.36
1371 1380 4.479993 CCTGGGCTCTGCTTCGGG 62.480 72.222 0.00 0.00 0.00 5.14
1593 1602 2.344025 ACGGCGATAACTGAAAAGTCC 58.656 47.619 16.62 0.00 0.00 3.85
1824 1855 8.958119 TCATACACTTAACTCTTCTTGTGTTT 57.042 30.769 0.00 0.00 39.09 2.83
1915 1948 4.038763 TGAAGACACTGTAAATCAGACCGT 59.961 41.667 1.79 0.00 46.27 4.83
1949 1982 0.846427 ACCCCCTGGCTTTCTCATCA 60.846 55.000 0.00 0.00 33.59 3.07
1964 1997 1.671379 GTTGTCCTTCGAGCACCCC 60.671 63.158 0.00 0.00 0.00 4.95
1999 2032 2.278531 GTTGCGCCGTGCTTTGTT 60.279 55.556 4.18 0.00 46.63 2.83
2009 2042 2.327343 TGCATGACTCAGTTGCGCC 61.327 57.895 4.18 0.00 39.23 6.53
2087 2120 1.066929 GGTGATTCCATTGCGGCTTTT 60.067 47.619 0.00 0.00 35.97 2.27
2115 2148 1.474077 AGCTTTCGGTGATTCCATTGC 59.526 47.619 0.00 0.00 35.57 3.56
2119 2152 0.250684 TGCAGCTTTCGGTGATTCCA 60.251 50.000 0.00 0.00 41.05 3.53
2120 2153 0.881118 TTGCAGCTTTCGGTGATTCC 59.119 50.000 0.00 0.00 41.05 3.01
2137 2170 3.420893 TCAGGTTTAGGTGCTTCCATTG 58.579 45.455 1.79 0.00 39.02 2.82
2204 2243 2.035321 GGGAAACATTTTTGTCGCTGGA 59.965 45.455 0.00 0.00 0.00 3.86
2283 2322 7.079451 TCTAGAGAAAGAACCAAGGTGATTT 57.921 36.000 0.00 0.00 0.00 2.17
2502 2809 5.147767 ACCAAATAGGATAAATTGCCTCCC 58.852 41.667 0.00 0.00 41.22 4.30
2516 2823 8.265055 TCCTCAGAATTACTACAACCAAATAGG 58.735 37.037 0.00 0.00 45.67 2.57
2536 2843 7.798596 ATTAAAAGCATCTACACATCCTCAG 57.201 36.000 0.00 0.00 0.00 3.35
2700 3008 2.421424 GCTGGTGAGAACATGACATTCC 59.579 50.000 0.00 0.00 0.00 3.01
2713 3021 7.981789 TGTTAATTCTCTATAGTTGCTGGTGAG 59.018 37.037 0.00 0.00 0.00 3.51
2790 3098 7.944729 AGGAAGTGTTTTATGTGCAGATTAT 57.055 32.000 0.00 0.00 0.00 1.28
2932 3240 7.970614 AGTTCAGAACACTGAGAAATTTCAAAC 59.029 33.333 19.99 11.05 40.93 2.93
2957 3266 5.828299 TGTCCTGGTTGTTGAACTAAAAG 57.172 39.130 0.00 0.00 32.15 2.27
3014 3323 5.416862 TGTGTTTTGCTATATATGTGCCG 57.583 39.130 9.17 0.00 0.00 5.69
3023 3332 3.938963 GCCTACTGCTGTGTTTTGCTATA 59.061 43.478 6.48 0.00 36.87 1.31
3024 3333 2.749621 GCCTACTGCTGTGTTTTGCTAT 59.250 45.455 6.48 0.00 36.87 2.97
3025 3334 2.151202 GCCTACTGCTGTGTTTTGCTA 58.849 47.619 6.48 0.00 36.87 3.49
3026 3335 0.954452 GCCTACTGCTGTGTTTTGCT 59.046 50.000 6.48 0.00 36.87 3.91
3052 4863 1.682854 CATGTTCCTGCCAGTGTGTTT 59.317 47.619 0.00 0.00 0.00 2.83
3055 4866 1.162698 CTCATGTTCCTGCCAGTGTG 58.837 55.000 0.00 0.00 0.00 3.82
3059 4870 1.022735 GCATCTCATGTTCCTGCCAG 58.977 55.000 0.00 0.00 0.00 4.85
3123 4934 2.636768 GGAAAAAGTCATTCCGGCTG 57.363 50.000 0.00 0.00 37.22 4.85
3170 4982 2.612721 GGAATTTTGTTGGCGGCTGAAT 60.613 45.455 11.43 0.52 0.00 2.57
3225 5037 1.210478 TGTCCAGAGCTGCTATTTCCC 59.790 52.381 0.15 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.