Multiple sequence alignment - TraesCS3B01G210500

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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 TraesCS3B01G210500 chr3B 100.000 3437 0 0 1 3437 246992191 246988755 0.000000e+00 6348
1 TraesCS3B01G210500 chr3B 93.374 3456 200 15 1 3437 355963561 355960116 0.000000e+00 5086
2 TraesCS3B01G210500 chr3B 93.910 3235 173 14 1 3216 402665452 402668681 0.000000e+00 4861
3 TraesCS3B01G210500 chr5D 95.116 3460 143 13 1 3437 378821658 378818202 0.000000e+00 5430
4 TraesCS3B01G210500 chr6B 93.864 3455 189 13 1 3437 628273443 628269994 0.000000e+00 5184
5 TraesCS3B01G210500 chr6B 93.023 3454 199 25 1 3437 628430439 628427011 0.000000e+00 5005
6 TraesCS3B01G210500 chr6B 93.460 2630 155 7 1 2615 360735325 360732698 0.000000e+00 3888
7 TraesCS3B01G210500 chr2B 93.784 3459 186 18 1 3437 352036638 352040089 0.000000e+00 5169
8 TraesCS3B01G210500 chr2B 92.822 1644 103 6 1 1631 315011927 315013568 0.000000e+00 2368
9 TraesCS3B01G210500 chr5B 93.289 3457 193 17 1 3437 160810825 160814262 0.000000e+00 5062
10 TraesCS3B01G210500 chr5B 93.512 2574 141 15 882 3437 453085068 453082503 0.000000e+00 3805
11 TraesCS3B01G210500 chr1B 94.285 3237 160 12 1 3213 425399400 425402635 0.000000e+00 4929
12 TraesCS3B01G210500 chr1B 94.076 1975 95 8 1 1960 330407838 330409805 0.000000e+00 2979
13 TraesCS3B01G210500 chr1B 97.351 151 2 2 3211 3360 112026348 112026497 4.400000e-64 255
14 TraesCS3B01G210500 chr7B 93.599 3234 184 13 1 3216 365271403 365268175 0.000000e+00 4804
15 TraesCS3B01G210500 chr7B 92.543 3232 209 15 1 3214 251468355 251465138 0.000000e+00 4604
16 TraesCS3B01G210500 chr4B 89.449 3213 269 46 54 3217 494453947 494457138 0.000000e+00 3991
17 TraesCS3B01G210500 chr4B 97.279 147 3 1 3211 3357 586178783 586178638 7.370000e-62 248
18 TraesCS3B01G210500 chr2D 95.181 83 4 0 3355 3437 184176432 184176350 7.740000e-27 132
19 TraesCS3B01G210500 chr6A 92.771 83 6 0 3355 3437 589837160 589837078 1.680000e-23 121


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 TraesCS3B01G210500 chr3B 246988755 246992191 3436 True 6348 6348 100.000 1 3437 1 chr3B.!!$R1 3436
1 TraesCS3B01G210500 chr3B 355960116 355963561 3445 True 5086 5086 93.374 1 3437 1 chr3B.!!$R2 3436
2 TraesCS3B01G210500 chr3B 402665452 402668681 3229 False 4861 4861 93.910 1 3216 1 chr3B.!!$F1 3215
3 TraesCS3B01G210500 chr5D 378818202 378821658 3456 True 5430 5430 95.116 1 3437 1 chr5D.!!$R1 3436
4 TraesCS3B01G210500 chr6B 628269994 628273443 3449 True 5184 5184 93.864 1 3437 1 chr6B.!!$R2 3436
5 TraesCS3B01G210500 chr6B 628427011 628430439 3428 True 5005 5005 93.023 1 3437 1 chr6B.!!$R3 3436
6 TraesCS3B01G210500 chr6B 360732698 360735325 2627 True 3888 3888 93.460 1 2615 1 chr6B.!!$R1 2614
7 TraesCS3B01G210500 chr2B 352036638 352040089 3451 False 5169 5169 93.784 1 3437 1 chr2B.!!$F2 3436
8 TraesCS3B01G210500 chr2B 315011927 315013568 1641 False 2368 2368 92.822 1 1631 1 chr2B.!!$F1 1630
9 TraesCS3B01G210500 chr5B 160810825 160814262 3437 False 5062 5062 93.289 1 3437 1 chr5B.!!$F1 3436
10 TraesCS3B01G210500 chr5B 453082503 453085068 2565 True 3805 3805 93.512 882 3437 1 chr5B.!!$R1 2555
11 TraesCS3B01G210500 chr1B 425399400 425402635 3235 False 4929 4929 94.285 1 3213 1 chr1B.!!$F3 3212
12 TraesCS3B01G210500 chr1B 330407838 330409805 1967 False 2979 2979 94.076 1 1960 1 chr1B.!!$F2 1959
13 TraesCS3B01G210500 chr7B 365268175 365271403 3228 True 4804 4804 93.599 1 3216 1 chr7B.!!$R2 3215
14 TraesCS3B01G210500 chr7B 251465138 251468355 3217 True 4604 4604 92.543 1 3214 1 chr7B.!!$R1 3213
15 TraesCS3B01G210500 chr4B 494453947 494457138 3191 False 3991 3991 89.449 54 3217 1 chr4B.!!$F1 3163

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
364 371 0.320771 GGCCACTCACACCACTGTAG 60.321 60.0 0.0 0.0 0.00 2.74 F
1176 1201 0.889186 CCAGCGTACCAAACAAGGCT 60.889 55.0 0.0 0.0 37.31 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 2347 0.546507 TGTGGTCTGCCCTGTCCATA 60.547 55.0 0.0 0.0 32.45 2.74 R
2913 2994 0.321564 TGAATGTTGTCCTCGGCTGG 60.322 55.0 0.0 0.0 0.00 4.85 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
77 78 6.655062 TGACAAGTTCAACTACTAAAATGCG 58.345 36.000 0.00 0.00 0.00 4.73
276 279 3.838913 CAAACCCCCACCCCACCA 61.839 66.667 0.00 0.00 0.00 4.17
363 370 0.762842 AGGCCACTCACACCACTGTA 60.763 55.000 5.01 0.00 0.00 2.74
364 371 0.320771 GGCCACTCACACCACTGTAG 60.321 60.000 0.00 0.00 0.00 2.74
523 532 3.763897 ACCAGTTTTGAGCAACAACTCTT 59.236 39.130 0.00 0.00 38.29 2.85
864 882 4.954118 TCGCCTCCCACACACCCT 62.954 66.667 0.00 0.00 0.00 4.34
944 965 2.426024 CCATTGTTGCTTCCATCTCCAG 59.574 50.000 0.00 0.00 0.00 3.86
990 1011 3.272334 CAAGCCCATAGTCGCCGC 61.272 66.667 0.00 0.00 0.00 6.53
1035 1056 2.048023 CGCCAAGCATCACCATGGT 61.048 57.895 13.00 13.00 42.81 3.55
1068 1092 2.325583 AGAGCAACAACCTCGTCAAA 57.674 45.000 0.00 0.00 34.56 2.69
1107 1131 2.319136 AGCGTGAGTACACCAAAACA 57.681 45.000 0.00 0.00 43.34 2.83
1168 1193 1.301401 GTCTGCACCAGCGTACCAA 60.301 57.895 0.00 0.00 46.23 3.67
1176 1201 0.889186 CCAGCGTACCAAACAAGGCT 60.889 55.000 0.00 0.00 37.31 4.58
1503 1531 5.581126 TGCATTTCTGAAACTGTGAAGTT 57.419 34.783 4.73 0.00 0.00 2.66
1811 1851 5.390673 GCAGCACATATATCATTGACTCTGC 60.391 44.000 0.00 0.00 35.89 4.26
1845 1885 3.401182 TGAATTTGGTGAAGCATTTGGC 58.599 40.909 0.00 0.00 45.30 4.52
1928 1976 7.042658 GGACTTTGTGTACTAGTTTCTGAACTG 60.043 40.741 0.00 0.00 45.46 3.16
2048 2104 7.233757 AGACTAGTCTTTAAATGTGTGTCTCCT 59.766 37.037 20.00 0.00 36.31 3.69
2077 2134 1.600636 CCCAAGCGCCTCAAAGACA 60.601 57.895 2.29 0.00 0.00 3.41
2140 2198 1.296715 GGAGGTGACAAGCGGATGT 59.703 57.895 0.00 0.00 35.90 3.06
2164 2222 3.339141 GACAAGTCTGGTTTGGAGATCC 58.661 50.000 0.00 0.00 0.00 3.36
2229 2287 4.561606 CCAAAGACCGACAAATACTACGAG 59.438 45.833 0.00 0.00 0.00 4.18
2285 2343 3.059325 GCATTCTACGATGGCATGAAGAC 60.059 47.826 3.81 0.00 0.00 3.01
2286 2344 3.885724 TTCTACGATGGCATGAAGACA 57.114 42.857 3.81 0.00 41.62 3.41
2289 2347 4.769688 TCTACGATGGCATGAAGACAAAT 58.230 39.130 3.81 0.00 39.98 2.32
2348 2406 1.681166 GCTGCCAGACAACCTCATCAT 60.681 52.381 0.00 0.00 0.00 2.45
2365 2423 6.127619 CCTCATCATGTACGCAGGAATAGATA 60.128 42.308 0.00 0.00 38.97 1.98
2391 2449 3.407698 TGCAACGTACAAGTCATGGAAT 58.592 40.909 0.00 0.00 0.00 3.01
2440 2498 6.357367 TGGGATATTTCAAAAGAGTAGGAGC 58.643 40.000 0.00 0.00 0.00 4.70
2473 2531 2.110213 ACTGCAACTTCGCGGGAA 59.890 55.556 14.71 14.71 42.90 3.97
2568 2640 5.885881 AGTTTGCTTTCGTTATGTTGAACA 58.114 33.333 0.00 0.00 0.00 3.18
2633 2705 6.087522 GCCTATGTCTATCAAGTACATCGTC 58.912 44.000 0.00 0.00 35.54 4.20
2966 3047 7.555639 GCATCGTGCTAATAGTAGTTAGAAG 57.444 40.000 0.00 0.00 40.96 2.85
3081 3162 6.403049 TGAACACACGGTACATTCATTCTAT 58.597 36.000 0.00 0.00 0.00 1.98
3132 3213 5.982890 ATTCACATTCCCTAAAACAGTGG 57.017 39.130 0.00 0.00 0.00 4.00
3309 3390 7.947282 AGCTAATTTAAACCAGTGCTTTAACA 58.053 30.769 3.35 0.00 0.00 2.41
3382 3464 4.648651 ACTAAGTACCGCAACAGGAAAAT 58.351 39.130 0.00 0.00 34.73 1.82
3400 3482 7.175641 CAGGAAAATCAAAGAACCATCAGTACT 59.824 37.037 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 7.510428 ACATTATATGCTTGAACTTTTTGCG 57.490 32.000 0.00 0.00 0.00 4.85
296 302 7.981789 ACTGATGTCATATGTATGTTCGAACTT 59.018 33.333 27.32 23.07 35.26 2.66
363 370 4.004982 GCATGGGTTTGAAATTTGATGCT 58.995 39.130 0.00 0.00 33.69 3.79
364 371 3.181518 CGCATGGGTTTGAAATTTGATGC 60.182 43.478 0.00 0.00 33.24 3.91
841 859 0.392863 TGTGTGGGAGGCGATTCATG 60.393 55.000 0.00 0.00 0.00 3.07
864 882 1.218875 ATTTTGCAGTGCGTCGACGA 61.219 50.000 39.74 22.22 43.02 4.20
944 965 2.362169 AGTTTGTGGTTTGTGTGCAC 57.638 45.000 10.75 10.75 0.00 4.57
990 1011 1.153289 CTCCACCATCGCCTTCCTG 60.153 63.158 0.00 0.00 0.00 3.86
1035 1056 2.595124 TGCTCTTGTTTGACGTCTCA 57.405 45.000 17.92 10.46 0.00 3.27
1092 1116 4.638421 CCTTTGAGTGTTTTGGTGTACTCA 59.362 41.667 0.00 0.00 45.45 3.41
1141 1165 1.535015 GCTGGTGCAGACGATCTCTAC 60.535 57.143 0.00 0.00 39.41 2.59
1168 1193 0.773644 ATCACCTGGTCAGCCTTGTT 59.226 50.000 0.00 0.00 35.27 2.83
1176 1201 1.985614 CCTGCTCATCACCTGGTCA 59.014 57.895 0.00 0.00 0.00 4.02
1409 1436 5.694995 AGTTCATCTCTTTGGGAAACAAGA 58.305 37.500 0.00 0.00 40.82 3.02
1503 1531 6.182627 AGATGCTAATCTGGTGAAACAATCA 58.817 36.000 0.00 0.00 41.80 2.57
1643 1683 2.474112 TGGACCTATACCACTTCACCC 58.526 52.381 0.00 0.00 32.03 4.61
1725 1765 7.010771 AGACCTATACCAGTGCTTGATACATA 58.989 38.462 0.00 0.00 0.00 2.29
1764 1804 8.856490 TGCTTGATTCAAGTTTAGTTTTCTTC 57.144 30.769 23.66 6.58 42.77 2.87
2028 2081 4.695928 GGGAGGAGACACACATTTAAAGAC 59.304 45.833 0.00 0.00 0.00 3.01
2077 2134 4.313020 ACAATTTCTTCTCCTGCAGGAT 57.687 40.909 35.11 16.47 44.46 3.24
2089 2146 6.385649 ACCGACAAATGTGTACAATTTCTT 57.614 33.333 0.00 0.00 38.41 2.52
2140 2198 2.507886 TCTCCAAACCAGACTTGTCCAA 59.492 45.455 0.00 0.00 0.00 3.53
2164 2222 1.535462 GTCGATGAAGTTGTTGGGGTG 59.465 52.381 0.00 0.00 0.00 4.61
2229 2287 1.926511 CTGCAACATCGGCCAAGGAC 61.927 60.000 2.24 0.00 0.00 3.85
2263 2321 3.059325 GTCTTCATGCCATCGTAGAATGC 60.059 47.826 0.00 0.00 43.58 3.56
2285 2343 2.301346 GGTCTGCCCTGTCCATATTTG 58.699 52.381 0.00 0.00 0.00 2.32
2286 2344 1.922447 TGGTCTGCCCTGTCCATATTT 59.078 47.619 0.00 0.00 0.00 1.40
2289 2347 0.546507 TGTGGTCTGCCCTGTCCATA 60.547 55.000 0.00 0.00 32.45 2.74
2348 2406 6.071616 TGCATATGTATCTATTCCTGCGTACA 60.072 38.462 4.29 0.00 0.00 2.90
2365 2423 4.332543 CCATGACTTGTACGTTGCATATGT 59.667 41.667 4.29 0.00 0.00 2.29
2440 2498 1.486211 CAGTGGTAGTAGGGGTCAGG 58.514 60.000 0.00 0.00 0.00 3.86
2473 2531 3.682696 TGCAGACTTTCATGCATCTTCT 58.317 40.909 0.00 0.00 46.97 2.85
2568 2640 6.707290 TGACACACATAACATAAGGTAGCTT 58.293 36.000 12.54 12.54 0.00 3.74
2633 2705 5.633830 AACTTGTTGGATGACATAAGCAG 57.366 39.130 0.00 0.00 30.87 4.24
2906 2987 1.568504 TGTCCTCGGCTGGAACTTAT 58.431 50.000 0.00 0.00 37.93 1.73
2913 2994 0.321564 TGAATGTTGTCCTCGGCTGG 60.322 55.000 0.00 0.00 0.00 4.85
2966 3047 7.486802 TTTCCTGTTGCAGTACTTAGTAAAC 57.513 36.000 0.00 0.00 0.00 2.01
3081 3162 8.584063 AGCTTCCCGTTCCTTTTTATATTTTA 57.416 30.769 0.00 0.00 0.00 1.52
3347 3428 9.583765 TTGCGGTACTTAGTAAATTTTTGTTTT 57.416 25.926 0.00 0.00 0.00 2.43
3369 3451 3.735746 GGTTCTTTGATTTTCCTGTTGCG 59.264 43.478 0.00 0.00 0.00 4.85
3382 3464 8.383175 AGGAAATAAGTACTGATGGTTCTTTGA 58.617 33.333 0.00 0.00 36.96 2.69
3400 3482 8.421784 CCTAGCATGTTAGTGACTAGGAAATAA 58.578 37.037 14.61 0.00 42.35 1.40


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

AutoCloner maintained by Alex Coulton.