Multiple sequence alignment - TraesCS5A01G353500

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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 TraesCS5A01G353500 chr5A 100.000 4415 0 0 1 4415 556528112 556532526 0.000000e+00 8154.0
1 TraesCS5A01G353500 chr5D 96.434 3057 75 11 33 3065 440369000 440372046 0.000000e+00 5011.0
2 TraesCS5A01G353500 chr5D 94.853 1360 47 6 3064 4415 440372306 440373650 0.000000e+00 2102.0
3 TraesCS5A01G353500 chr5D 86.607 112 12 1 2959 3067 440372083 440372194 2.160000e-23 121.0
4 TraesCS5A01G353500 chr5D 100.000 32 0 0 1 32 440368949 440368980 4.770000e-05 60.2
5 TraesCS5A01G353500 chr5B 96.033 2874 81 11 216 3065 535703393 535706257 0.000000e+00 4645.0
6 TraesCS5A01G353500 chr5B 95.994 649 26 0 3632 4280 535707718 535708366 0.000000e+00 1055.0
7 TraesCS5A01G353500 chr5B 96.880 577 15 2 3064 3639 535706558 535707132 0.000000e+00 963.0
8 TraesCS5A01G353500 chr5B 94.975 199 10 0 33 231 535703160 535703358 3.320000e-81 313.0
9 TraesCS5A01G353500 chr5B 96.330 109 4 0 4307 4415 535708356 535708464 3.510000e-41 180.0
10 TraesCS5A01G353500 chr5B 82.877 146 22 1 2925 3067 535706289 535706434 1.290000e-25 128.0
11 TraesCS5A01G353500 chr5B 100.000 32 0 0 1 32 535703109 535703140 4.770000e-05 60.2


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 TraesCS5A01G353500 chr5A 556528112 556532526 4414 False 8154.000000 8154 100.0000 1 4415 1 chr5A.!!$F1 4414
1 TraesCS5A01G353500 chr5D 440368949 440373650 4701 False 1823.550000 5011 94.4735 1 4415 4 chr5D.!!$F1 4414
2 TraesCS5A01G353500 chr5B 535703109 535708464 5355 False 1049.171429 4645 94.7270 1 4415 7 chr5B.!!$F1 4414

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
941 1020 0.391263 CTGGACACGGTAGGGAAAGC 60.391 60.0 0.0 0.0 0.0 3.51 F
2744 2826 0.600057 GAGCAGCAAAAGTCCCCAAG 59.400 55.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2859 2950 0.322546 GGTGGATTGGGGTCTGTGTC 60.323 60.000 0.0 0.0 0.0 3.67 R
4121 5118 1.758280 CAACCCATGCAGCCATGTATT 59.242 47.619 0.0 0.0 45.9 1.89 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
41 61 4.272504 TGCTTTAGACCACACTTCTTTTCG 59.727 41.667 0.00 0.00 0.00 3.46
113 133 2.076100 CTGCTTCGTTGGCATTGTAGA 58.924 47.619 0.00 0.00 39.07 2.59
137 157 6.853490 AGTTGGAGGAGTTTAGGAGAAAATT 58.147 36.000 0.00 0.00 0.00 1.82
208 228 8.049655 TGCAGTACACATAAATATTTCTTGCA 57.950 30.769 3.39 4.39 0.00 4.08
283 353 3.993081 GAGGATCTAGATCATTGCCGTTG 59.007 47.826 29.33 0.00 39.54 4.10
293 363 5.824624 AGATCATTGCCGTTGATTTCTATGT 59.175 36.000 0.00 0.00 34.03 2.29
295 365 7.663081 AGATCATTGCCGTTGATTTCTATGTAT 59.337 33.333 0.00 0.00 34.03 2.29
394 464 5.351465 TCGAATGCACTCAATTACTCCTTTC 59.649 40.000 0.00 0.00 0.00 2.62
397 467 4.245660 TGCACTCAATTACTCCTTTCTCG 58.754 43.478 0.00 0.00 0.00 4.04
564 634 1.900498 GCATGTGGCATAGCTCCCC 60.900 63.158 0.00 0.00 43.97 4.81
693 763 3.190849 CAGGCGGCATCGTGACAG 61.191 66.667 13.08 0.00 38.89 3.51
703 773 2.030213 GCATCGTGACAGCTTTCTCATC 59.970 50.000 0.87 0.00 0.00 2.92
941 1020 0.391263 CTGGACACGGTAGGGAAAGC 60.391 60.000 0.00 0.00 0.00 3.51
969 1048 5.073691 AGGGGAAAGACAAAGAGAAAGATCA 59.926 40.000 0.00 0.00 0.00 2.92
1206 1285 5.295787 GTGTTGTTCATCCTGTTGTCTAACA 59.704 40.000 0.00 0.00 44.17 2.41
1248 1327 8.017418 TGAACTTGGGATATGTTCTTTGTTTT 57.983 30.769 0.00 0.00 41.53 2.43
1621 1700 1.941294 GAGCTCAGGATGCAGTTCATG 59.059 52.381 9.40 0.00 35.05 3.07
2047 2127 1.524621 CCACCACCGCCTCATGATC 60.525 63.158 0.00 0.00 0.00 2.92
2177 2257 4.228824 TGTCCCACTCCTACTTTACTTGT 58.771 43.478 0.00 0.00 0.00 3.16
2212 2292 6.947733 TGAACATAAACTTCTGATCCCATGTT 59.052 34.615 0.00 0.00 37.89 2.71
2284 2364 1.227102 GTGCATACTGGGCCATCCA 59.773 57.895 6.72 0.00 44.79 3.41
2449 2529 7.935755 AGTGTGGATGGTTGATCATATTCTAAG 59.064 37.037 0.00 0.00 31.91 2.18
2473 2553 6.077408 GAGACTATTAGGCTGCAGCATACTG 61.077 48.000 37.63 26.55 39.65 2.74
2497 2577 5.089970 AGTCAGCACTGAACTTGCATATA 57.910 39.130 1.05 0.00 42.83 0.86
2540 2620 8.836268 ATGCTGAATTCTCTAGAGATTCATTC 57.164 34.615 28.51 27.19 35.97 2.67
2690 2772 6.594744 TCCAGCACATGTATGAACATAGAAT 58.405 36.000 10.94 0.00 44.70 2.40
2744 2826 0.600057 GAGCAGCAAAAGTCCCCAAG 59.400 55.000 0.00 0.00 0.00 3.61
2783 2865 7.693951 CAGCATCTACACAGTTTATAAGTTTGC 59.306 37.037 0.00 0.00 0.00 3.68
2789 2871 7.510549 ACACAGTTTATAAGTTTGCAGATGT 57.489 32.000 0.00 0.00 0.00 3.06
2839 2927 8.440833 ACGCAAATAACTAATTGTGAGTCTTAC 58.559 33.333 6.11 0.00 38.91 2.34
2882 2973 4.404098 GACCCCAATCCACCGCGT 62.404 66.667 4.92 0.00 0.00 6.01
2899 2990 2.735134 CGCGTATAAACATAGAAGGGCC 59.265 50.000 0.00 0.00 0.00 5.80
2903 2994 4.995487 CGTATAAACATAGAAGGGCCTTCC 59.005 45.833 36.48 21.67 40.98 3.46
2908 2999 1.959282 CATAGAAGGGCCTTCCAATGC 59.041 52.381 36.48 16.49 40.98 3.56
2928 3019 7.342942 CAATGCATAGATATAGCACATTAGCG 58.657 38.462 0.00 0.00 41.60 4.26
2949 3040 4.047822 CGCATGTAACAAAGCAGGAAAAA 58.952 39.130 0.00 0.00 0.00 1.94
2973 3064 3.380004 CCCCAAAATAATGAAGCAGCGTA 59.620 43.478 0.00 0.00 0.00 4.42
2976 3067 6.238897 CCCCAAAATAATGAAGCAGCGTAATA 60.239 38.462 0.00 0.00 0.00 0.98
2977 3068 7.199766 CCCAAAATAATGAAGCAGCGTAATAA 58.800 34.615 0.00 0.00 0.00 1.40
2979 3070 9.248291 CCAAAATAATGAAGCAGCGTAATAAAT 57.752 29.630 0.00 0.00 0.00 1.40
3002 3093 7.687941 ATACAGTTTAAGTTTGCAGCTGTAT 57.312 32.000 16.64 0.00 41.18 2.29
3098 3494 6.849588 GGAATTAATTTTCCATCCATGTGC 57.150 37.500 1.43 0.00 43.92 4.57
3127 3524 5.970317 TTCGTCCAACATAGAGACAGTTA 57.030 39.130 0.00 0.00 0.00 2.24
3131 3528 6.015688 TCGTCCAACATAGAGACAGTTAGTTT 60.016 38.462 0.00 0.00 0.00 2.66
3190 3587 6.795399 TGGTTGTTCATCTTTCTTGTTCTTC 58.205 36.000 0.00 0.00 0.00 2.87
3312 3709 7.013369 GGAAATCAAGAACAGGTTACAGACTTT 59.987 37.037 0.00 0.00 0.00 2.66
3458 3855 6.182627 TGCTCAACATGATCTAACCAGAAAT 58.817 36.000 0.00 0.00 33.50 2.17
3616 4013 8.904099 ATATACAAATGGGCTACTTTGTACTC 57.096 34.615 16.27 0.00 45.48 2.59
3830 4822 6.801539 ATACCATTAGCAATCACCATTACG 57.198 37.500 0.00 0.00 0.00 3.18
3959 4951 3.261580 TGTCATGTTCGTCAATAGCCTG 58.738 45.455 0.00 0.00 0.00 4.85
4102 5099 3.084039 AGCTTGAAATCTCCGCATTCAA 58.916 40.909 0.00 0.00 39.89 2.69
4164 5161 3.165875 TGAAAACCAAACACAGAACCCA 58.834 40.909 0.00 0.00 0.00 4.51
4204 5201 3.694072 GCCTTTAGCACCATAATGTGTCA 59.306 43.478 0.00 0.00 42.97 3.58
4214 5211 9.353431 AGCACCATAATGTGTCATATATTTTCA 57.647 29.630 0.00 0.00 38.52 2.69
4338 5335 8.842280 TCAAAATCTACTTTTAGCCGAAGAAAA 58.158 29.630 0.00 0.00 35.27 2.29
4377 5374 9.442047 ACCACAATTTAAAAAGATGTTTCACAA 57.558 25.926 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 61 4.489306 AGCCTTACCCAATTCTCTACAC 57.511 45.455 0.00 0.00 0.00 2.90
113 133 5.906772 TTTTCTCCTAAACTCCTCCAACT 57.093 39.130 0.00 0.00 0.00 3.16
295 365 4.016444 AGAAAGCTCCTTGTGTTCAACAA 58.984 39.130 0.00 0.00 46.66 2.83
394 464 8.290325 ACAAAACTTTTAGCTTTAGATTCCGAG 58.710 33.333 0.00 0.00 0.00 4.63
397 467 9.399403 CAGACAAAACTTTTAGCTTTAGATTCC 57.601 33.333 0.00 0.00 0.00 3.01
523 593 1.404391 CTGTCTTGGGATCAGCATTGC 59.596 52.381 0.00 0.00 0.00 3.56
564 634 4.284746 AGAAGAGGACTAAAGACAAGGGTG 59.715 45.833 0.00 0.00 0.00 4.61
693 763 2.284190 GCTGTACCAGGATGAGAAAGC 58.716 52.381 0.00 0.00 39.69 3.51
703 773 4.162690 GAGGGGCGCTGTACCAGG 62.163 72.222 9.52 0.00 31.21 4.45
941 1020 3.832527 TCTCTTTGTCTTTCCCCTTTGG 58.167 45.455 0.00 0.00 0.00 3.28
969 1048 1.302832 CGCCTCCTCCTTTGTTGCT 60.303 57.895 0.00 0.00 0.00 3.91
1206 1285 3.072184 AGTTCAATCAGGACTCAGCAGTT 59.928 43.478 0.00 0.00 30.63 3.16
1248 1327 2.615493 GGCAGGAACGATTTCTCTTCCA 60.615 50.000 0.00 0.00 34.09 3.53
1351 1430 2.103263 GGTCGATTTCCAGTATCCTGCT 59.897 50.000 0.00 0.00 37.38 4.24
1621 1700 5.652452 ACAAGATTGGCTGGATTTTAGTACC 59.348 40.000 0.00 0.00 0.00 3.34
1671 1750 8.846943 TTAGCAAGACAACATCTCTAAAATCA 57.153 30.769 0.00 0.00 36.27 2.57
2047 2127 7.589958 AAGACCTAGATTATGTGTACTCTGG 57.410 40.000 0.00 0.00 0.00 3.86
2212 2292 6.373759 TGCTCTCCCATCTAATCTACAGTTA 58.626 40.000 0.00 0.00 0.00 2.24
2321 2401 6.237675 CGATGCACAAACTCTGAATAGTACTG 60.238 42.308 5.39 0.00 0.00 2.74
2419 2499 9.725019 GAATATGATCAACCATCCACACTTATA 57.275 33.333 0.00 0.00 0.00 0.98
2449 2529 2.898729 TGCTGCAGCCTAATAGTCTC 57.101 50.000 34.64 4.39 41.18 3.36
2647 2729 4.473520 CGGGGTTCGCATCCTGCT 62.474 66.667 0.00 0.00 42.25 4.24
2744 2826 1.743958 AGATGCTGCTGCTTCATTGTC 59.256 47.619 26.09 10.35 43.30 3.18
2809 2897 7.298122 ACTCACAATTAGTTATTTGCGTTCTG 58.702 34.615 0.00 0.00 0.00 3.02
2859 2950 0.322546 GGTGGATTGGGGTCTGTGTC 60.323 60.000 0.00 0.00 0.00 3.67
2861 2952 1.377202 CGGTGGATTGGGGTCTGTG 60.377 63.158 0.00 0.00 0.00 3.66
2882 2973 6.584471 TTGGAAGGCCCTTCTATGTTTATA 57.416 37.500 22.35 0.00 40.07 0.98
2899 2990 7.860918 ATGTGCTATATCTATGCATTGGAAG 57.139 36.000 3.54 0.00 39.00 3.46
2903 2994 7.342942 CGCTAATGTGCTATATCTATGCATTG 58.657 38.462 3.54 2.26 39.00 2.82
2928 3019 5.120674 GGATTTTTCCTGCTTTGTTACATGC 59.879 40.000 0.00 4.39 0.00 4.06
2949 3040 3.068590 CGCTGCTTCATTATTTTGGGGAT 59.931 43.478 0.00 0.00 0.00 3.85
2973 3064 9.410556 CAGCTGCAAACTTAAACTGTATTTATT 57.589 29.630 0.00 0.00 0.00 1.40
2976 3067 6.805713 ACAGCTGCAAACTTAAACTGTATTT 58.194 32.000 15.27 0.00 35.27 1.40
2977 3068 6.391227 ACAGCTGCAAACTTAAACTGTATT 57.609 33.333 15.27 0.00 35.27 1.89
2979 3070 8.786826 ATATACAGCTGCAAACTTAAACTGTA 57.213 30.769 15.27 0.00 41.72 2.74
3002 3093 7.817418 AACCTTTCTGCTTTACTGAACAATA 57.183 32.000 0.00 0.00 36.12 1.90
3098 3494 5.689514 GTCTCTATGTTGGACGAATCATGAG 59.310 44.000 0.09 0.00 0.00 2.90
3151 3548 2.092592 ACAACCAGTCCTCGTTTCCTTT 60.093 45.455 0.00 0.00 0.00 3.11
3152 3549 1.489230 ACAACCAGTCCTCGTTTCCTT 59.511 47.619 0.00 0.00 0.00 3.36
3153 3550 1.129058 ACAACCAGTCCTCGTTTCCT 58.871 50.000 0.00 0.00 0.00 3.36
3156 3553 2.702592 TGAACAACCAGTCCTCGTTT 57.297 45.000 0.00 0.00 0.00 3.60
3159 3556 2.751166 AGATGAACAACCAGTCCTCG 57.249 50.000 0.00 0.00 0.00 4.63
3165 3562 6.382869 AGAACAAGAAAGATGAACAACCAG 57.617 37.500 0.00 0.00 0.00 4.00
3190 3587 1.323412 AGCGCATAGGAGTCCTGTAG 58.677 55.000 22.69 13.23 34.61 2.74
3312 3709 0.337773 AGGACTCTCCAGCATCCTCA 59.662 55.000 0.00 0.00 36.89 3.86
3616 4013 7.701501 GGTAGATACAGGTAAAAGAAGACTTCG 59.298 40.741 9.53 0.00 35.05 3.79
3830 4822 9.065871 CATTTCCGAGTTGAATTTGATTAGTTC 57.934 33.333 0.00 0.00 0.00 3.01
3959 4951 6.414890 GCTATTCTTTATTTCACACGAGCTC 58.585 40.000 2.73 2.73 0.00 4.09
4121 5118 1.758280 CAACCCATGCAGCCATGTATT 59.242 47.619 0.00 0.00 45.90 1.89
4164 5161 3.740115 AGGCGCATAAATAAAGGTCGAT 58.260 40.909 10.83 0.00 0.00 3.59
4204 5201 6.815641 CAGAGGCAGACGCTATGAAAATATAT 59.184 38.462 0.00 0.00 38.60 0.86
4214 5211 3.576118 ACATATTCAGAGGCAGACGCTAT 59.424 43.478 0.00 0.00 38.60 2.97
4217 5214 2.231215 ACATATTCAGAGGCAGACGC 57.769 50.000 0.00 0.00 37.44 5.19
4288 5285 4.670896 ACCTGACACCTTTTTGAATTGG 57.329 40.909 0.00 0.00 0.00 3.16
4297 5294 5.941788 AGATTTTGACTACCTGACACCTTT 58.058 37.500 0.00 0.00 0.00 3.11
4338 5335 4.510167 AATTGTGGTAAGAGGCAGCTAT 57.490 40.909 0.00 0.00 0.00 2.97
4377 5374 9.918630 CCTGATTTTGAAAATAGATGTTGACTT 57.081 29.630 2.71 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.