Multiple sequence alignment - TraesCS5D01G243200

Loading Multiple Alignment...

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 TraesCS5D01G243200 chr5D 100.000 3587 0 0 1 3587 351406410 351402824 0.000000e+00 6625
1 TraesCS5D01G243200 chr5B 90.759 3636 148 75 2 3586 412464151 412460653 0.000000e+00 4680
2 TraesCS5D01G243200 chr5A 90.587 3219 127 61 3 3166 451743661 451740564 0.000000e+00 4104
3 TraesCS5D01G243200 chr5A 91.667 240 15 4 3238 3476 451740556 451740321 9.600000e-86 327
4 TraesCS5D01G243200 chr5A 94.512 164 9 0 1059 1222 376844943 376845106 1.650000e-63 254
5 TraesCS5D01G243200 chr5A 91.071 168 8 4 2 168 451757536 451757375 1.680000e-53 220
6 TraesCS5D01G243200 chr5A 83.007 153 6 8 3454 3586 451740307 451740155 1.750000e-23 121
7 TraesCS5D01G243200 chr6A 91.393 976 42 15 817 1773 566431376 566432328 0.000000e+00 1299
8 TraesCS5D01G243200 chr6A 90.779 976 49 14 817 1773 487772223 487773176 0.000000e+00 1266
9 TraesCS5D01G243200 chr2B 89.445 919 47 21 875 1773 267900977 267901865 0.000000e+00 1114
10 TraesCS5D01G243200 chr3A 95.122 164 8 0 1059 1222 435354499 435354662 3.550000e-65 259


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 TraesCS5D01G243200 chr5D 351402824 351406410 3586 True 6625.000000 6625 100.000000 1 3587 1 chr5D.!!$R1 3586
1 TraesCS5D01G243200 chr5B 412460653 412464151 3498 True 4680.000000 4680 90.759000 2 3586 1 chr5B.!!$R1 3584
2 TraesCS5D01G243200 chr5A 451740155 451743661 3506 True 1517.333333 4104 88.420333 3 3586 3 chr5A.!!$R2 3583
3 TraesCS5D01G243200 chr6A 566431376 566432328 952 False 1299.000000 1299 91.393000 817 1773 1 chr6A.!!$F2 956
4 TraesCS5D01G243200 chr6A 487772223 487773176 953 False 1266.000000 1266 90.779000 817 1773 1 chr6A.!!$F1 956
5 TraesCS5D01G243200 chr2B 267900977 267901865 888 False 1114.000000 1114 89.445000 875 1773 1 chr2B.!!$F1 898

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
874 943 0.468029 CTCTGCTCCCTCTCCCTCTC 60.468 65.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2738 2848 0.674581 CCGCCTTGTTGCTGATCTGA 60.675 55.0 3.42 0.0 0.0 3.27 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
28 29 3.198068 CCAGTCGTTTCACTCCCATATG 58.802 50.000 0.00 0.00 0.00 1.78
29 30 3.198068 CAGTCGTTTCACTCCCATATGG 58.802 50.000 15.41 15.41 0.00 2.74
81 82 1.865865 AAGACAGCGAAAAAGCGAGA 58.134 45.000 0.00 0.00 43.00 4.04
82 83 1.423395 AGACAGCGAAAAAGCGAGAG 58.577 50.000 0.00 0.00 43.00 3.20
328 336 2.434359 CGTCCACCGGAAAGCTCC 60.434 66.667 9.46 0.00 38.52 4.70
380 388 3.573772 TTGGACGCACTCGCCTCAG 62.574 63.158 0.00 0.00 39.84 3.35
402 415 1.077501 ACCGCACCCTACGCTACTA 60.078 57.895 0.00 0.00 0.00 1.82
869 938 2.445654 CCCCTCTGCTCCCTCTCC 60.446 72.222 0.00 0.00 0.00 3.71
870 939 2.445654 CCCTCTGCTCCCTCTCCC 60.446 72.222 0.00 0.00 0.00 4.30
871 940 2.695597 CCTCTGCTCCCTCTCCCT 59.304 66.667 0.00 0.00 0.00 4.20
874 943 0.468029 CTCTGCTCCCTCTCCCTCTC 60.468 65.000 0.00 0.00 0.00 3.20
875 944 0.923729 TCTGCTCCCTCTCCCTCTCT 60.924 60.000 0.00 0.00 0.00 3.10
954 1031 2.223618 CGAGGAAGAAGAAGATCCGTCC 60.224 54.545 0.00 0.00 38.31 4.79
1116 1196 2.683933 TCCTCCTTCCAGGCGGTC 60.684 66.667 0.00 0.00 41.08 4.79
1257 1337 3.535962 CTCGCCCTGCTCCTCCTC 61.536 72.222 0.00 0.00 0.00 3.71
1456 1539 2.343758 GCGACACCAAGAGCAGGA 59.656 61.111 0.00 0.00 0.00 3.86
1873 1971 1.167851 CTCTTGCCAGCGAAATTCCA 58.832 50.000 0.00 0.00 0.00 3.53
1908 2007 4.156008 GGTCACACTGTTGTTTCCATATCC 59.844 45.833 0.00 0.00 31.66 2.59
1957 2056 6.877611 ATAACTCCAACAACAACCTTACTG 57.122 37.500 0.00 0.00 0.00 2.74
2040 2139 7.769044 AGTAGTAATAATTTGAGCAACATCGGT 59.231 33.333 0.00 0.00 0.00 4.69
2050 2149 3.411446 AGCAACATCGGTGAGAAATTCA 58.589 40.909 0.65 0.00 0.00 2.57
2067 2166 7.270047 AGAAATTCATCCATTGGTTGCTAATG 58.730 34.615 8.63 1.84 35.75 1.90
2228 2327 1.278127 CAGGGGTTCGGAATGTACACT 59.722 52.381 0.00 0.00 0.00 3.55
2267 2366 1.229853 ATCGGGGGAGTGGGACTTT 60.230 57.895 0.00 0.00 0.00 2.66
2332 2431 4.811206 TGCCGTGCAGGTACAAAT 57.189 50.000 5.57 0.00 43.70 2.32
2340 2439 6.716879 CCGTGCAGGTACAAATCGATTTGG 62.717 50.000 39.58 27.66 42.20 3.28
2358 2457 1.064017 TGGTTGGACATATTGCTCCCC 60.064 52.381 0.00 0.00 0.00 4.81
2427 2529 2.951229 ATGATGATGATCAGGCTGCA 57.049 45.000 10.34 3.09 42.01 4.41
2689 2795 1.066114 GAGTTTCAGACGACGGCGAG 61.066 60.000 22.49 6.98 41.64 5.03
2690 2796 1.371389 GTTTCAGACGACGGCGAGT 60.371 57.895 22.49 13.72 41.64 4.18
2731 2841 2.954611 CGTGCTCCGAGTCAGTGA 59.045 61.111 0.00 0.00 39.56 3.41
2738 2848 2.917933 CTCCGAGTCAGTGAGAGAGAT 58.082 52.381 0.00 0.00 0.00 2.75
2739 2849 2.872245 CTCCGAGTCAGTGAGAGAGATC 59.128 54.545 0.00 0.00 0.00 2.75
2933 3055 2.439507 AGAGTGAGCCTTTCCAGTTCAA 59.560 45.455 0.00 0.00 0.00 2.69
3026 3148 1.094785 ATACCACGAATGTGCTTGCC 58.905 50.000 0.00 0.00 45.04 4.52
3074 3202 3.941483 ACCAATCTAAATCTTGACTGCCG 59.059 43.478 0.00 0.00 0.00 5.69
3123 3251 2.491693 CCATTTTGCAACGGTAGGACAT 59.508 45.455 0.00 0.00 0.00 3.06
3141 3269 1.291459 ATGGAGATGCACATGGGGGT 61.291 55.000 0.00 0.00 0.00 4.95
3142 3270 1.307647 GGAGATGCACATGGGGGTT 59.692 57.895 0.00 0.00 0.00 4.11
3143 3271 1.039233 GGAGATGCACATGGGGGTTG 61.039 60.000 0.00 0.00 0.00 3.77
3144 3272 1.000739 AGATGCACATGGGGGTTGG 59.999 57.895 0.00 0.00 0.00 3.77
3145 3273 2.039299 ATGCACATGGGGGTTGGG 59.961 61.111 0.00 0.00 0.00 4.12
3209 3337 2.718062 TGATGTTGGCCCCTATCATCAT 59.282 45.455 15.97 2.67 39.53 2.45
3223 3357 8.634444 CCCCTATCATCATAGTAGTAGTATTGC 58.366 40.741 0.00 0.00 31.28 3.56
3323 3457 0.551377 TTCATAGCCTTGGGTCCCCA 60.551 55.000 5.13 0.00 45.63 4.96
3364 3498 1.135315 CCCACCAGAAACATGAATGCG 60.135 52.381 0.00 0.00 0.00 4.73
3400 3534 3.523157 TCATGGAGGAAATGTTAGGCTGA 59.477 43.478 0.00 0.00 0.00 4.26
3401 3535 3.634397 TGGAGGAAATGTTAGGCTGAG 57.366 47.619 0.00 0.00 0.00 3.35
3406 3540 3.026694 GGAAATGTTAGGCTGAGGCAAT 58.973 45.455 9.23 0.00 40.87 3.56
3480 3651 7.948357 CATTTTGTGGATCAGGACAATCATAT 58.052 34.615 0.00 0.00 32.27 1.78
3498 3677 5.764432 TCATATCACCAACCAATGATTCCA 58.236 37.500 0.00 0.00 36.87 3.53
3508 3697 6.040729 CCAACCAATGATTCCACTGCATTATA 59.959 38.462 0.00 0.00 31.54 0.98
3509 3698 7.256048 CCAACCAATGATTCCACTGCATTATAT 60.256 37.037 0.00 0.00 31.54 0.86
3510 3699 8.795513 CAACCAATGATTCCACTGCATTATATA 58.204 33.333 0.00 0.00 31.54 0.86
3511 3700 9.537852 AACCAATGATTCCACTGCATTATATAT 57.462 29.630 0.00 0.00 31.54 0.86
3586 3785 2.688446 TCATGGTCGCTCTTATCTTCGT 59.312 45.455 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.470821 AGTGAAACGACTGGTCTTTCG 58.529 47.619 14.46 0.00 45.86 3.46
28 29 5.517054 CGCTTTCTTCTCTGTTGTATACTCC 59.483 44.000 4.17 0.00 0.00 3.85
29 30 5.517054 CCGCTTTCTTCTCTGTTGTATACTC 59.483 44.000 4.17 0.00 0.00 2.59
31 32 4.033014 GCCGCTTTCTTCTCTGTTGTATAC 59.967 45.833 0.00 0.00 0.00 1.47
32 33 4.181578 GCCGCTTTCTTCTCTGTTGTATA 58.818 43.478 0.00 0.00 0.00 1.47
34 35 2.413837 GCCGCTTTCTTCTCTGTTGTA 58.586 47.619 0.00 0.00 0.00 2.41
81 82 1.272490 TGATGTTTTCTCGGTCGAGCT 59.728 47.619 13.48 0.00 41.71 4.09
82 83 1.656095 CTGATGTTTTCTCGGTCGAGC 59.344 52.381 14.76 4.06 41.71 5.03
170 172 4.299796 GCTGGGGGTTCCTGGCAA 62.300 66.667 0.00 0.00 35.92 4.52
179 181 3.503839 TTGGAAACGGCTGGGGGT 61.504 61.111 0.00 0.00 0.00 4.95
294 302 4.816984 GGACGGGGCGAGGAGAGA 62.817 72.222 0.00 0.00 0.00 3.10
585 633 3.945304 GATCGCGACCCGGGTGTTT 62.945 63.158 36.01 5.71 40.60 2.83
701 749 1.684049 CCTCCTCCGAACTCCTGCT 60.684 63.158 0.00 0.00 0.00 4.24
702 750 1.045911 ATCCTCCTCCGAACTCCTGC 61.046 60.000 0.00 0.00 0.00 4.85
703 751 1.036707 GATCCTCCTCCGAACTCCTG 58.963 60.000 0.00 0.00 0.00 3.86
939 1016 4.081642 TCAATTTCGGACGGATCTTCTTCT 60.082 41.667 0.00 0.00 0.00 2.85
954 1031 1.732259 CTGTCCCGTTCCTCAATTTCG 59.268 52.381 0.00 0.00 0.00 3.46
1873 1971 3.638160 ACAGTGTGACCAAATCAAAGCAT 59.362 39.130 0.00 0.00 39.72 3.79
1908 2007 3.389741 GCAATCGAACAGTTGCTGG 57.610 52.632 12.96 0.00 45.41 4.85
1967 2066 7.201767 GGCTTGAATTATTACTGCTGTGAAGAT 60.202 37.037 6.48 0.00 0.00 2.40
1968 2067 6.094048 GGCTTGAATTATTACTGCTGTGAAGA 59.906 38.462 6.48 0.00 0.00 2.87
1969 2068 6.094603 AGGCTTGAATTATTACTGCTGTGAAG 59.905 38.462 6.48 0.00 0.00 3.02
1970 2069 5.945784 AGGCTTGAATTATTACTGCTGTGAA 59.054 36.000 6.48 0.00 0.00 3.18
1971 2070 5.500234 AGGCTTGAATTATTACTGCTGTGA 58.500 37.500 6.48 0.00 0.00 3.58
1972 2071 5.824904 AGGCTTGAATTATTACTGCTGTG 57.175 39.130 6.48 0.00 0.00 3.66
1973 2072 6.884295 TGTAAGGCTTGAATTATTACTGCTGT 59.116 34.615 10.69 0.66 0.00 4.40
1974 2073 7.320443 TGTAAGGCTTGAATTATTACTGCTG 57.680 36.000 10.69 0.00 0.00 4.41
2027 2126 2.542020 TTTCTCACCGATGTTGCTCA 57.458 45.000 0.00 0.00 0.00 4.26
2028 2127 3.436704 TGAATTTCTCACCGATGTTGCTC 59.563 43.478 0.00 0.00 0.00 4.26
2040 2139 4.773674 AGCAACCAATGGATGAATTTCTCA 59.226 37.500 14.01 0.00 38.81 3.27
2050 2149 5.296780 CGTTAGACATTAGCAACCAATGGAT 59.703 40.000 6.16 0.00 37.64 3.41
2067 2166 4.796312 ACAAATTGCAACACAACGTTAGAC 59.204 37.500 0.00 0.00 42.27 2.59
2228 2327 1.935925 CTTGTCGCCGTTCCGAAAA 59.064 52.632 0.00 0.00 39.17 2.29
2252 2351 2.763902 CCAAAGTCCCACTCCCCC 59.236 66.667 0.00 0.00 0.00 5.40
2332 2431 4.269183 AGCAATATGTCCAACCAAATCGA 58.731 39.130 0.00 0.00 0.00 3.59
2340 2439 2.301346 CTGGGGAGCAATATGTCCAAC 58.699 52.381 0.00 0.00 34.14 3.77
2401 2503 5.938125 CAGCCTGATCATCATCATACAATGA 59.062 40.000 0.00 0.00 44.55 2.57
2731 2841 4.141892 CCTTGTTGCTGATCTGATCTCTCT 60.142 45.833 17.82 0.00 0.00 3.10
2738 2848 0.674581 CCGCCTTGTTGCTGATCTGA 60.675 55.000 3.42 0.00 0.00 3.27
2739 2849 1.651240 CCCGCCTTGTTGCTGATCTG 61.651 60.000 0.00 0.00 0.00 2.90
2862 2980 1.909700 TTTACAGCTTGCTGGAAGGG 58.090 50.000 23.98 1.14 31.56 3.95
2933 3055 3.849527 AGAAAGAACCAAGAAGGGCAAT 58.150 40.909 0.00 0.00 43.89 3.56
3084 3212 1.378514 GGGAATCACCGCACATGGT 60.379 57.895 0.00 0.00 45.21 3.55
3123 3251 1.508667 AACCCCCATGTGCATCTCCA 61.509 55.000 0.00 0.00 0.00 3.86
3141 3269 3.509575 CCGGAAGAAATTCACAATCCCAA 59.490 43.478 0.00 0.00 0.00 4.12
3142 3270 3.088532 CCGGAAGAAATTCACAATCCCA 58.911 45.455 0.00 0.00 0.00 4.37
3143 3271 3.089284 ACCGGAAGAAATTCACAATCCC 58.911 45.455 9.46 0.00 0.00 3.85
3144 3272 3.128764 GGACCGGAAGAAATTCACAATCC 59.871 47.826 9.46 0.00 0.00 3.01
3145 3273 4.010349 AGGACCGGAAGAAATTCACAATC 58.990 43.478 9.46 0.00 0.00 2.67
3223 3357 5.294552 GCAGCAAAGGGTACTACTAGAAATG 59.705 44.000 0.00 0.00 0.00 2.32
3228 3362 2.766828 AGGCAGCAAAGGGTACTACTAG 59.233 50.000 0.00 0.00 0.00 2.57
3229 3363 2.829023 AGGCAGCAAAGGGTACTACTA 58.171 47.619 0.00 0.00 0.00 1.82
3234 3368 1.211949 TGGATAGGCAGCAAAGGGTAC 59.788 52.381 0.00 0.00 0.00 3.34
3303 3437 3.496675 GGGACCCAAGGCTATGAAC 57.503 57.895 5.33 0.00 0.00 3.18
3364 3498 1.852965 TCCATGATTTCTTCCTCCCCC 59.147 52.381 0.00 0.00 0.00 5.40
3480 3651 3.156293 CAGTGGAATCATTGGTTGGTGA 58.844 45.455 0.00 0.00 0.00 4.02
3544 3735 7.147689 CCATGAAACATTCAGAATAATGGGGAA 60.148 37.037 0.00 0.00 43.98 3.97
3563 3754 4.112634 CGAAGATAAGAGCGACCATGAAA 58.887 43.478 0.00 0.00 0.00 2.69
3564 3755 3.130516 ACGAAGATAAGAGCGACCATGAA 59.869 43.478 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.