Multiple sequence alignment - TraesCS1D01G033000

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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 TraesCS1D01G033000 chr1D 100.000 3215 0 0 1 3215 13252429 13255643 0.000000e+00 5938.0
1 TraesCS1D01G033000 chr1D 89.318 2228 227 7 1 2224 13262594 13264814 0.000000e+00 2785.0
2 TraesCS1D01G033000 chr1D 87.265 2230 271 10 2 2224 12551827 12549604 0.000000e+00 2532.0
3 TraesCS1D01G033000 chr1B 94.309 3251 142 10 1 3215 18867855 18871098 0.000000e+00 4939.0
4 TraesCS1D01G033000 chr1B 91.734 2226 178 4 2 2224 18118490 18116268 0.000000e+00 3086.0
5 TraesCS1D01G033000 chr1B 90.791 2226 202 3 1 2224 17896406 17894182 0.000000e+00 2972.0
6 TraesCS1D01G033000 chr1B 89.363 2228 230 7 1 2224 18683518 18685742 0.000000e+00 2795.0
7 TraesCS1D01G033000 chr1B 91.004 2012 172 6 216 2224 539872559 539870554 0.000000e+00 2704.0
8 TraesCS1D01G033000 chr1B 89.188 2081 211 12 151 2224 19075902 19073829 0.000000e+00 2584.0
9 TraesCS1D01G033000 chr1B 91.085 1907 167 3 320 2224 18093322 18091417 0.000000e+00 2577.0
10 TraesCS1D01G033000 chr1B 90.025 401 38 2 1 400 17966083 17965684 4.750000e-143 518.0
11 TraesCS1D01G033000 chr1B 94.419 215 12 0 1 215 539873092 539872878 6.650000e-87 331.0
12 TraesCS1D01G033000 chr1B 80.303 462 53 22 2760 3208 18115361 18114925 6.700000e-82 315.0
13 TraesCS1D01G033000 chr1B 85.484 248 35 1 2228 2475 539870316 539870070 1.140000e-64 257.0
14 TraesCS1D01G033000 chr1B 77.075 506 63 28 2687 3185 17963732 17963273 3.200000e-60 243.0
15 TraesCS1D01G033000 chr1B 77.200 500 45 30 2644 3116 539870071 539869614 8.970000e-56 228.0
16 TraesCS1D01G033000 chr1B 79.245 371 40 24 2839 3185 18112847 18112490 1.160000e-54 224.0
17 TraesCS1D01G033000 chr1B 80.851 282 42 10 2687 2962 18360752 18360477 9.040000e-51 211.0
18 TraesCS1D01G033000 chr1B 87.943 141 10 1 3082 3215 19072618 19072478 3.320000e-35 159.0
19 TraesCS1D01G033000 chr1B 76.724 348 44 20 2759 3096 19073099 19072779 3.320000e-35 159.0
20 TraesCS1D01G033000 chr1B 96.154 52 2 0 3065 3116 18360363 18360312 5.710000e-13 86.1
21 TraesCS1D01G033000 chr1B 93.878 49 3 0 3068 3116 18089017 18088969 1.240000e-09 75.0
22 TraesCS1D01G033000 chr1B 92.308 52 4 0 3065 3116 18688990 18689041 1.240000e-09 75.0
23 TraesCS1D01G033000 chr1A 87.719 2231 257 14 2 2224 14585065 14587286 0.000000e+00 2586.0
24 TraesCS1D01G033000 chr1A 85.926 2231 296 14 2 2224 14577726 14579946 0.000000e+00 2364.0


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 TraesCS1D01G033000 chr1D 13252429 13255643 3214 False 5938.000000 5938 100.000000 1 3215 1 chr1D.!!$F1 3214
1 TraesCS1D01G033000 chr1D 13262594 13264814 2220 False 2785.000000 2785 89.318000 1 2224 1 chr1D.!!$F2 2223
2 TraesCS1D01G033000 chr1D 12549604 12551827 2223 True 2532.000000 2532 87.265000 2 2224 1 chr1D.!!$R1 2222
3 TraesCS1D01G033000 chr1B 18867855 18871098 3243 False 4939.000000 4939 94.309000 1 3215 1 chr1B.!!$F1 3214
4 TraesCS1D01G033000 chr1B 17894182 17896406 2224 True 2972.000000 2972 90.791000 1 2224 1 chr1B.!!$R1 2223
5 TraesCS1D01G033000 chr1B 18683518 18689041 5523 False 1435.000000 2795 90.835500 1 3116 2 chr1B.!!$F2 3115
6 TraesCS1D01G033000 chr1B 18088969 18093322 4353 True 1326.000000 2577 92.481500 320 3116 2 chr1B.!!$R3 2796
7 TraesCS1D01G033000 chr1B 18112490 18118490 6000 True 1208.333333 3086 83.760667 2 3208 3 chr1B.!!$R4 3206
8 TraesCS1D01G033000 chr1B 19072478 19075902 3424 True 967.333333 2584 84.618333 151 3215 3 chr1B.!!$R6 3064
9 TraesCS1D01G033000 chr1B 539869614 539873092 3478 True 880.000000 2704 87.026750 1 3116 4 chr1B.!!$R7 3115
10 TraesCS1D01G033000 chr1B 17963273 17966083 2810 True 380.500000 518 83.550000 1 3185 2 chr1B.!!$R2 3184
11 TraesCS1D01G033000 chr1A 14585065 14587286 2221 False 2586.000000 2586 87.719000 2 2224 1 chr1A.!!$F2 2222
12 TraesCS1D01G033000 chr1A 14577726 14579946 2220 False 2364.000000 2364 85.926000 2 2224 1 chr1A.!!$F1 2222

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
783 1102 3.37422 TGCAAACATGGAAGAAGCAAG 57.626 42.857 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2728 3626 0.526211 GAAAATTGGAGCCCGACACC 59.474 55.0 0.0 0.0 0.0 4.16 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
783 1102 3.374220 TGCAAACATGGAAGAAGCAAG 57.626 42.857 0.00 0.00 0.00 4.01
1033 1352 5.531634 TCAATGAAATGCAGAAACAAGGAC 58.468 37.500 0.00 0.00 0.00 3.85
1319 1638 4.783227 AGAAGGAAGGGTAATAGAAGCACA 59.217 41.667 0.00 0.00 0.00 4.57
1366 1685 2.026822 ACAGGTGAGAGGCCTAATGTTG 60.027 50.000 4.42 2.93 34.45 3.33
1535 1854 2.480419 GGATTGATGACGGGCTTATTCG 59.520 50.000 0.00 0.00 0.00 3.34
1720 2039 6.263168 AGTTCTTGGTGGACTTTGTAGAAATG 59.737 38.462 0.00 0.00 0.00 2.32
2011 2332 7.912250 GTGCCAACTCTTATCTGTTAAATCATG 59.088 37.037 0.00 0.00 0.00 3.07
2029 2350 4.507710 TCATGTCATCAGAAGGTTACTGC 58.492 43.478 0.00 0.00 35.61 4.40
2261 2828 4.070552 GGCCGAGCCGTTCACTCT 62.071 66.667 0.00 0.00 39.62 3.24
2487 3114 8.732746 TCTAAGCCAAATTGAGGTTAGATAAC 57.267 34.615 21.05 0.00 44.10 1.89
2632 3285 2.936202 TGCAGCTTCCAGTCTTCTTTT 58.064 42.857 0.00 0.00 0.00 2.27
2645 3298 6.477688 CCAGTCTTCTTTTCACGTACAAGTTA 59.522 38.462 0.00 0.00 0.00 2.24
2657 3311 5.405571 CACGTACAAGTTATATGGATCCAGC 59.594 44.000 21.33 7.65 0.00 4.85
2728 3626 7.972832 TTATGAGGTGTACAGGTTTAGTTTG 57.027 36.000 0.00 0.00 0.00 2.93
2755 3654 3.494223 CGGGCTCCAATTTTCTTTGGTTT 60.494 43.478 3.36 0.00 45.32 3.27
2756 3655 4.460263 GGGCTCCAATTTTCTTTGGTTTT 58.540 39.130 3.36 0.00 45.32 2.43
2757 3656 4.275689 GGGCTCCAATTTTCTTTGGTTTTG 59.724 41.667 3.36 0.00 45.32 2.44
2805 3704 6.802608 AGTTTAACCCTGCAACTTTTCTTAC 58.197 36.000 0.00 0.00 0.00 2.34
2855 3759 5.302568 GGAATCACAATATCAATGGCCTCAA 59.697 40.000 3.32 0.00 0.00 3.02
2858 3762 4.398988 TCACAATATCAATGGCCTCAACAC 59.601 41.667 3.32 0.00 0.00 3.32
2998 3926 4.768968 ACGGCGGTATGACTATAATAAGGT 59.231 41.667 13.24 0.00 0.00 3.50
3187 8776 7.768807 ACAATAGTGTGCCCTAAAATTACAA 57.231 32.000 0.00 0.00 36.31 2.41
3190 8779 9.651913 CAATAGTGTGCCCTAAAATTACAAATT 57.348 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.734606 CAGCAATTCGTCGAACAGGTTA 59.265 45.455 10.39 0.00 0.00 2.85
206 207 2.917905 CCATGAGGATGCCGTAGGTGT 61.918 57.143 0.00 0.00 45.61 4.16
783 1102 3.665745 TCAAAAATTCCTGCAGCTTCC 57.334 42.857 8.66 0.00 0.00 3.46
910 1229 3.442977 AGAATGCAGTCTCTTTCCATTGC 59.557 43.478 11.63 0.00 0.00 3.56
1033 1352 2.981898 TGTGAATGCATCTGGACTCAG 58.018 47.619 0.00 0.00 42.21 3.35
1187 1506 2.163412 GCTTTCACCAAATCGCCATGTA 59.837 45.455 0.00 0.00 0.00 2.29
1333 1652 2.562738 TCTCACCTGTGTGTACCATCAG 59.437 50.000 0.00 0.00 43.26 2.90
1346 1665 2.026822 ACAACATTAGGCCTCTCACCTG 60.027 50.000 9.68 3.60 38.26 4.00
1351 1670 3.334583 TGTGACAACATTAGGCCTCTC 57.665 47.619 9.68 0.00 0.00 3.20
1378 1697 2.537401 GCAGTATCCACCGACAAGTAC 58.463 52.381 0.00 0.00 0.00 2.73
1383 1702 1.341679 ACTAGGCAGTATCCACCGACA 60.342 52.381 0.00 0.00 31.45 4.35
1535 1854 1.881973 TGTGCAGCATCTCTTTGAACC 59.118 47.619 0.00 0.00 0.00 3.62
1597 1916 3.885297 CGTCCAGCCAGAAATAATCCATT 59.115 43.478 0.00 0.00 0.00 3.16
1888 2207 7.125053 TGTCATCATTATGGTGTAGGTAACAGA 59.875 37.037 5.30 0.00 39.29 3.41
2011 2332 5.689383 TTTTGCAGTAACCTTCTGATGAC 57.311 39.130 0.00 0.00 35.20 3.06
2029 2350 5.353678 CAGCCTTGACTATCTCTCCTTTTTG 59.646 44.000 0.00 0.00 0.00 2.44
2261 2828 0.548031 CAGGCTAAGGATCCTGGCAA 59.452 55.000 29.33 12.30 44.64 4.52
2577 3222 8.430801 ACACAAGCAGATATTATTCAGACTTC 57.569 34.615 0.00 0.00 0.00 3.01
2632 3285 6.718522 TGGATCCATATAACTTGTACGTGA 57.281 37.500 11.44 0.00 0.00 4.35
2657 3311 1.743958 ACGTACAGGCTGCTACTACAG 59.256 52.381 15.89 8.45 40.80 2.74
2728 3626 0.526211 GAAAATTGGAGCCCGACACC 59.474 55.000 0.00 0.00 0.00 4.16
2755 3654 1.026182 GGTGCTGCACCGATCATCAA 61.026 55.000 33.53 0.00 44.95 2.57
2756 3655 1.450134 GGTGCTGCACCGATCATCA 60.450 57.895 33.53 0.00 44.95 3.07
2757 3656 3.414272 GGTGCTGCACCGATCATC 58.586 61.111 33.53 11.34 44.95 2.92
2805 3704 4.384056 CCTTAACACCAGCATGATCTAGG 58.616 47.826 0.00 0.00 39.69 3.02
2855 3759 8.185505 TCTTTAATTCAACTGCTAAAAACGTGT 58.814 29.630 0.00 0.00 0.00 4.49
2893 3797 1.308047 TCTGCGTCAGTTTGTGCAAT 58.692 45.000 0.00 0.00 36.82 3.56
2998 3926 5.537295 AGCTCAAAATGCATCAGCCATATAA 59.463 36.000 0.00 0.00 41.13 0.98
3187 8776 8.599624 AAAGGTATGAGATGAATGAACCAATT 57.400 30.769 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.