Multiple sequence alignment - TraesCS7D01G302800

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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 TraesCS7D01G302800 chr7D 100.000 4353 0 0 1 4353 382946978 382942626 0.000000e+00 8039.0
1 TraesCS7D01G302800 chr7B 96.139 2383 60 13 1994 4353 377322831 377320458 0.000000e+00 3862.0
2 TraesCS7D01G302800 chr7B 96.257 1309 32 12 584 1885 377324150 377322852 0.000000e+00 2130.0
3 TraesCS7D01G302800 chr7B 92.821 599 38 4 1 598 377326477 377325883 0.000000e+00 863.0
4 TraesCS7D01G302800 chr7A 95.792 1830 38 8 713 2528 431042959 431041155 0.000000e+00 2916.0
5 TraesCS7D01G302800 chr7A 96.807 1190 31 4 2527 3711 431041055 431039868 0.000000e+00 1980.0
6 TraesCS7D01G302800 chr7A 92.557 309 22 1 1 309 431043904 431043597 4.000000e-120 442.0
7 TraesCS7D01G302800 chr7A 92.742 248 12 3 486 728 431043222 431042976 1.930000e-93 353.0
8 TraesCS7D01G302800 chr7A 88.417 259 20 2 4105 4353 431038081 431037823 1.970000e-78 303.0
9 TraesCS7D01G302800 chr7A 92.821 195 12 2 295 488 431043576 431043383 9.220000e-72 281.0
10 TraesCS7D01G302800 chr3A 95.918 49 2 0 1764 1812 484112297 484112249 3.610000e-11 80.5
11 TraesCS7D01G302800 chr3B 89.130 46 3 2 3970 4014 757740478 757740522 6.080000e-04 56.5
12 TraesCS7D01G302800 chr3B 96.774 31 1 0 3977 4007 244617029 244616999 8.000000e-03 52.8
13 TraesCS7D01G302800 chr5B 100.000 28 0 0 453 480 491100046 491100019 8.000000e-03 52.8
14 TraesCS7D01G302800 chr1D 100.000 28 0 0 453 480 381308292 381308265 8.000000e-03 52.8
15 TraesCS7D01G302800 chr1B 100.000 28 0 0 453 480 511445515 511445488 8.000000e-03 52.8
16 TraesCS7D01G302800 chr1A 73.856 153 31 7 336 480 481925717 481925566 8.000000e-03 52.8


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 TraesCS7D01G302800 chr7D 382942626 382946978 4352 True 8039.000000 8039 100.000000 1 4353 1 chr7D.!!$R1 4352
1 TraesCS7D01G302800 chr7B 377320458 377326477 6019 True 2285.000000 3862 95.072333 1 4353 3 chr7B.!!$R1 4352
2 TraesCS7D01G302800 chr7A 431037823 431043904 6081 True 1045.833333 2916 93.189333 1 4353 6 chr7A.!!$R1 4352

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
529 730 1.760613 TGGACCACCAATCTCGTATCC 59.239 52.381 0.00 0.0 43.91 2.59 F
862 2848 2.226912 GCTCATCTCTCGCCGTATACTT 59.773 50.000 0.56 0.0 0.00 2.24 F
1308 3298 3.458487 TCCTTATCTCCCCTGTTTTAGCC 59.542 47.826 0.00 0.0 0.00 3.93 F
1309 3299 3.459969 CCTTATCTCCCCTGTTTTAGCCT 59.540 47.826 0.00 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1381 3372 0.463204 ACATCACAGGGCGATCAGAG 59.537 55.000 0.0 0.0 0.00 3.35 R
2752 4855 1.344763 GTCACAGGAGCAGTAACAGGT 59.655 52.381 0.0 0.0 0.00 4.00 R
3049 5152 4.899502 ACATTGGAGCATAGCCATAGTAC 58.100 43.478 0.0 0.0 34.90 2.73 R
3501 5605 7.047271 TGTATGAGAATCGATGTGAATTTGGA 58.953 34.615 0.0 0.0 38.61 3.53 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
57 59 8.747538 ACAATGTTTACAAAAAGGTAGAGTCT 57.252 30.769 0.00 0.00 0.00 3.24
109 111 6.995511 AAATGCTCCTACAAATAAACGCTA 57.004 33.333 0.00 0.00 0.00 4.26
149 151 7.870826 TCAACGAGAAATCAGCTCAAAATTTA 58.129 30.769 0.00 0.00 32.67 1.40
153 155 8.968242 ACGAGAAATCAGCTCAAAATTTAAAAC 58.032 29.630 0.00 0.00 32.67 2.43
213 215 5.452255 ACCGATGAGTGGACTACCTAAATA 58.548 41.667 0.00 0.00 37.04 1.40
215 217 6.183360 ACCGATGAGTGGACTACCTAAATAAC 60.183 42.308 0.00 0.00 37.04 1.89
250 252 6.190346 AGGTGATCCGAGTTAGTCTATACT 57.810 41.667 0.00 0.00 38.05 2.12
326 363 9.875691 GACCATCTCAATATGCAACTATACATA 57.124 33.333 0.00 0.00 33.52 2.29
429 467 8.916654 GTTATGGTTCTCGTATCATTGATACAG 58.083 37.037 27.79 23.22 43.41 2.74
451 489 7.707104 ACAGATATAATGTTACCAAAGCAAGC 58.293 34.615 0.00 0.00 0.00 4.01
529 730 1.760613 TGGACCACCAATCTCGTATCC 59.239 52.381 0.00 0.00 43.91 2.59
531 732 2.368875 GGACCACCAATCTCGTATCCAT 59.631 50.000 0.00 0.00 35.97 3.41
610 2559 7.010160 TCCACATCATGTACTCCATATCACTA 58.990 38.462 0.00 0.00 30.71 2.74
745 2730 2.256306 TCTGGTGGCATGTCTTGACTA 58.744 47.619 0.00 0.00 32.91 2.59
862 2848 2.226912 GCTCATCTCTCGCCGTATACTT 59.773 50.000 0.56 0.00 0.00 2.24
869 2855 6.964741 TCTCTCGCCGTATACTTCTTATAG 57.035 41.667 0.56 0.00 0.00 1.31
872 2858 4.330250 TCGCCGTATACTTCTTATAGGCT 58.670 43.478 10.96 0.00 36.15 4.58
929 2917 4.889995 ACCACCAGAGGAGAAAAAGAAAAG 59.110 41.667 0.00 0.00 0.00 2.27
1291 3280 6.127563 GCGAGGTGGGATTTTTATTTTCCTTA 60.128 38.462 0.00 0.00 0.00 2.69
1304 3294 8.966155 TTTATTTTCCTTATCTCCCCTGTTTT 57.034 30.769 0.00 0.00 0.00 2.43
1306 3296 9.695155 TTATTTTCCTTATCTCCCCTGTTTTAG 57.305 33.333 0.00 0.00 0.00 1.85
1308 3298 3.458487 TCCTTATCTCCCCTGTTTTAGCC 59.542 47.826 0.00 0.00 0.00 3.93
1309 3299 3.459969 CCTTATCTCCCCTGTTTTAGCCT 59.540 47.826 0.00 0.00 0.00 4.58
1310 3300 4.658901 CCTTATCTCCCCTGTTTTAGCCTA 59.341 45.833 0.00 0.00 0.00 3.93
1311 3301 5.454897 CCTTATCTCCCCTGTTTTAGCCTAC 60.455 48.000 0.00 0.00 0.00 3.18
1341 3331 7.597743 AGATGAGATTCTTTGTTTTGTTGCATC 59.402 33.333 0.00 0.00 0.00 3.91
1472 3464 3.951775 TGTTGTGAAGGTGCAGTTTTT 57.048 38.095 0.00 0.00 0.00 1.94
1702 3694 7.921786 TTAGTTCATCACTTTGTCCCATTAG 57.078 36.000 0.00 0.00 36.88 1.73
1789 3781 4.664392 ACTCCCTCCGTCCTACAATATAG 58.336 47.826 0.00 0.00 0.00 1.31
1812 3804 7.073342 AGGATCGTTTTTCAAGCTATGTTAC 57.927 36.000 0.00 0.00 0.00 2.50
2091 4084 6.602803 TCTTTATTCTGTTGGCATTGCTGATA 59.397 34.615 8.82 0.00 0.00 2.15
3049 5152 2.159572 CCAAGCAGTTTTTCCGTATCCG 60.160 50.000 0.00 0.00 0.00 4.18
3309 5412 4.322198 GCAATCTGCTTTCCATGGAAAAGA 60.322 41.667 33.74 31.93 42.61 2.52
3392 5495 7.012989 CCTTTAATGTGTATGTAACCCTTAGCC 59.987 40.741 0.00 0.00 0.00 3.93
3394 5497 4.481368 TGTGTATGTAACCCTTAGCCAG 57.519 45.455 0.00 0.00 0.00 4.85
3501 5605 7.872113 TTTGTGTTTTGCCCTATTGATTTTT 57.128 28.000 0.00 0.00 0.00 1.94
3552 5656 4.887071 ACAGAGTTGGATTGTTGCACTTAA 59.113 37.500 0.00 0.00 0.00 1.85
3557 5661 7.986889 AGAGTTGGATTGTTGCACTTAAATTTT 59.013 29.630 0.00 0.00 0.00 1.82
3566 5670 8.375608 TGTTGCACTTAAATTTTTGCACATAT 57.624 26.923 16.90 0.00 44.44 1.78
3613 5721 3.504906 TCTCACAGGTTACCTCTACAACG 59.495 47.826 0.00 0.00 0.00 4.10
3615 5723 2.559668 CACAGGTTACCTCTACAACGGA 59.440 50.000 0.00 0.00 0.00 4.69
3616 5724 3.006110 CACAGGTTACCTCTACAACGGAA 59.994 47.826 0.00 0.00 0.00 4.30
3617 5725 3.006217 ACAGGTTACCTCTACAACGGAAC 59.994 47.826 0.00 0.00 0.00 3.62
3778 5897 8.175069 TGAAATGTATTTCGTATCTTGTTCTGC 58.825 33.333 11.48 0.00 46.92 4.26
3820 5939 6.223852 AGTGGCTTATGATTATTGTCCTACG 58.776 40.000 0.00 0.00 0.00 3.51
3842 5961 1.243342 CCGCATGTCTGCTTTCCCAA 61.243 55.000 0.00 0.00 46.65 4.12
3845 5964 0.529378 CATGTCTGCTTTCCCAAGGC 59.471 55.000 0.00 0.00 0.00 4.35
3850 5969 1.305213 TGCTTTCCCAAGGCCCATC 60.305 57.895 0.00 0.00 0.00 3.51
3963 6082 8.511321 CATTCTCGTAAGCATCTATAGACTTCT 58.489 37.037 4.10 0.00 37.18 2.85
3999 6118 2.104253 CCAACGCGCCGACCTAAAT 61.104 57.895 5.73 0.00 0.00 1.40
4032 6151 1.416243 TTATCCGTATGGGTCGGCTT 58.584 50.000 0.00 0.00 46.49 4.35
4084 6205 1.431195 ATTGCCAGTGTACCCACCCA 61.431 55.000 0.00 0.00 42.88 4.51
4125 7630 8.801299 TGGCTAATTTTCACAATTTAGACATCA 58.199 29.630 2.43 0.00 38.27 3.07
4301 7817 5.811399 TTTGAAGTTGAATGTGAGTCGTT 57.189 34.783 0.00 0.00 0.00 3.85
4323 7839 5.225899 TCAATCACGCATTTCTTGATGAG 57.774 39.130 0.00 0.00 34.38 2.90
4335 7851 6.834168 TTTCTTGATGAGATTGGGTAAACC 57.166 37.500 0.00 0.00 35.17 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 49 6.254522 AGGTACACAACATTAGACTCTACCT 58.745 40.000 0.00 0.00 0.00 3.08
57 59 7.736881 TCCCTACATTAGGTACACAACATTA 57.263 36.000 0.00 0.00 44.73 1.90
109 111 4.646945 TCTCGTTGAAAGGATGAGAGCTAT 59.353 41.667 0.00 0.00 34.98 2.97
213 215 4.096984 CGGATCACCTACTTAGTTACCGTT 59.903 45.833 0.00 0.00 33.44 4.44
215 217 3.879295 TCGGATCACCTACTTAGTTACCG 59.121 47.826 0.00 0.00 38.31 4.02
250 252 9.995003 AAGTTGGCATTGTTCTCATATTAAAAA 57.005 25.926 0.00 0.00 0.00 1.94
451 489 6.381801 GGGAATCGGTTGCAATATATTTCAG 58.618 40.000 0.59 0.00 0.00 3.02
565 767 8.044060 TGTGGATTCTTTGTATCTGTTGATTC 57.956 34.615 0.00 0.00 34.32 2.52
707 2660 4.040952 ACCAGATATTGTACAGCCTGGATC 59.959 45.833 27.01 13.41 42.69 3.36
745 2730 1.270358 GCTGGAAGTCTTCACCTTCGT 60.270 52.381 14.49 0.00 39.36 3.85
806 2792 7.872138 TCCTGGATTTTCCTTATCTGTACAAT 58.128 34.615 0.00 0.00 37.46 2.71
884 2872 2.039085 CGTCGTGTATTTATCGTCCGG 58.961 52.381 0.00 0.00 0.00 5.14
929 2917 3.694072 TGGTTGATTGATTTGATCCGTCC 59.306 43.478 0.00 0.00 0.00 4.79
1257 3246 2.743718 CCACCTCGCTTCCTGTGT 59.256 61.111 0.00 0.00 0.00 3.72
1291 3280 2.434702 CGTAGGCTAAAACAGGGGAGAT 59.565 50.000 0.00 0.00 0.00 2.75
1308 3298 5.269505 ACAAAGAATCTCATCTCCCGTAG 57.730 43.478 0.00 0.00 0.00 3.51
1309 3299 5.677319 AACAAAGAATCTCATCTCCCGTA 57.323 39.130 0.00 0.00 0.00 4.02
1310 3300 4.559862 AACAAAGAATCTCATCTCCCGT 57.440 40.909 0.00 0.00 0.00 5.28
1311 3301 5.182001 ACAAAACAAAGAATCTCATCTCCCG 59.818 40.000 0.00 0.00 0.00 5.14
1341 3331 4.274147 ACAGAGACTACACCTCCATACAG 58.726 47.826 0.00 0.00 0.00 2.74
1381 3372 0.463204 ACATCACAGGGCGATCAGAG 59.537 55.000 0.00 0.00 0.00 3.35
1418 3410 3.946402 TGCACACTACAACAAACAATCG 58.054 40.909 0.00 0.00 0.00 3.34
1472 3464 3.495331 TGCCATCTTAAAAGCCAACAGA 58.505 40.909 0.00 0.00 0.00 3.41
1702 3694 3.506067 CAGTAAACCCCCAAATCTGTCAC 59.494 47.826 0.00 0.00 0.00 3.67
1789 3781 6.741358 GTGTAACATAGCTTGAAAAACGATCC 59.259 38.462 0.00 0.00 36.32 3.36
2121 4114 6.692392 CATTCTTCAATGCAAATTCGACATG 58.308 36.000 0.00 0.00 33.19 3.21
2752 4855 1.344763 GTCACAGGAGCAGTAACAGGT 59.655 52.381 0.00 0.00 0.00 4.00
3049 5152 4.899502 ACATTGGAGCATAGCCATAGTAC 58.100 43.478 0.00 0.00 34.90 2.73
3501 5605 7.047271 TGTATGAGAATCGATGTGAATTTGGA 58.953 34.615 0.00 0.00 38.61 3.53
3577 5681 9.871238 GTAACCTGTGAGATTTATACTCAGAAA 57.129 33.333 0.00 0.00 43.58 2.52
3613 5721 2.365941 GAGTGGCCCTGATACTAGTTCC 59.634 54.545 0.00 0.00 0.00 3.62
3615 5723 3.406512 AGAGTGGCCCTGATACTAGTT 57.593 47.619 0.00 0.00 0.00 2.24
3616 5724 3.406512 AAGAGTGGCCCTGATACTAGT 57.593 47.619 0.00 0.00 0.00 2.57
3617 5725 3.964031 AGAAAGAGTGGCCCTGATACTAG 59.036 47.826 0.00 0.00 0.00 2.57
3760 5879 4.669197 GCAACGCAGAACAAGATACGAAAT 60.669 41.667 0.00 0.00 0.00 2.17
3770 5889 1.403323 TCAATGTGCAACGCAGAACAA 59.597 42.857 0.00 0.00 42.39 2.83
3778 5897 1.536766 ACTCACCATCAATGTGCAACG 59.463 47.619 0.00 0.00 42.39 4.10
3842 5961 0.178970 ACTACGTATCCGATGGGCCT 60.179 55.000 4.53 0.00 37.88 5.19
3845 5964 5.121454 GTCTTACTACTACGTATCCGATGGG 59.879 48.000 0.00 0.00 37.88 4.00
3850 5969 5.178438 GGGAAGTCTTACTACTACGTATCCG 59.822 48.000 0.00 0.00 40.83 4.18
3859 5978 4.338879 TGCGTAAGGGAAGTCTTACTACT 58.661 43.478 11.41 0.00 44.02 2.57
3864 5983 2.419574 GCCATGCGTAAGGGAAGTCTTA 60.420 50.000 0.00 0.00 38.28 2.10
3877 5996 1.210478 AGTTAGATCTTGGCCATGCGT 59.790 47.619 6.09 0.53 0.00 5.24
3938 6057 8.630054 AGAAGTCTATAGATGCTTACGAGAAT 57.370 34.615 5.57 0.00 0.00 2.40
3963 6082 4.648651 GTTGGAGTTGGCCTTAGAAGTTA 58.351 43.478 3.32 0.00 0.00 2.24
4032 6151 1.002773 GAGAACCGACAAAGCCCCTAA 59.997 52.381 0.00 0.00 0.00 2.69
4071 6190 1.846124 CCTGGTGGGTGGGTACACT 60.846 63.158 0.00 0.00 46.85 3.55
4140 7646 6.091986 TGTGCAAAGTTTCTTTTCATTTGGAC 59.908 34.615 11.95 11.95 46.18 4.02
4301 7817 4.937015 TCTCATCAAGAAATGCGTGATTGA 59.063 37.500 3.91 3.91 41.97 2.57
4323 7839 1.402325 GCTTGCACGGTTTACCCAATC 60.402 52.381 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.