Multiple sequence alignment - TraesCS7D01G300000

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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 TraesCS7D01G300000 chr7D 100.000 3799 0 0 1 3799 380143882 380147680 0.000000e+00 7016.0
1 TraesCS7D01G300000 chr7A 95.350 3828 105 30 1 3799 428808775 428812558 0.000000e+00 6015.0
2 TraesCS7D01G300000 chr7B 94.909 2298 76 17 1531 3799 375190711 375192996 0.000000e+00 3557.0
3 TraesCS7D01G300000 chr7B 97.625 1263 22 6 238 1492 375188986 375190248 0.000000e+00 2159.0
4 TraesCS7D01G300000 chr7B 99.000 200 1 1 1 200 375188425 375188623 1.300000e-94 357.0
5 TraesCS7D01G300000 chr5B 83.036 112 15 3 1301 1410 211146258 211146367 8.680000e-17 99.0
6 TraesCS7D01G300000 chr5A 82.883 111 17 2 1301 1410 214166634 214166743 8.680000e-17 99.0
7 TraesCS7D01G300000 chr4D 82.301 113 16 4 1309 1419 68053418 68053528 1.120000e-15 95.3
8 TraesCS7D01G300000 chr4B 81.982 111 20 0 1309 1419 100576667 100576777 1.120000e-15 95.3
9 TraesCS7D01G300000 chr4A 82.301 113 16 4 1309 1419 517884598 517884708 1.120000e-15 95.3
10 TraesCS7D01G300000 chr5D 82.143 112 16 3 1301 1410 200501287 200501396 4.040000e-15 93.5
11 TraesCS7D01G300000 chr1A 87.500 72 9 0 2050 2121 545009085 545009014 2.430000e-12 84.2
12 TraesCS7D01G300000 chr1A 88.889 63 7 0 2050 2112 544928216 544928278 1.130000e-10 78.7
13 TraesCS7D01G300000 chr1A 87.302 63 8 0 2044 2106 463461322 463461260 5.260000e-09 73.1
14 TraesCS7D01G300000 chr3A 83.146 89 15 0 1309 1397 476385479 476385567 8.750000e-12 82.4
15 TraesCS7D01G300000 chr1D 88.889 63 7 0 2050 2112 449660800 449660862 1.130000e-10 78.7
16 TraesCS7D01G300000 chr1D 88.889 63 7 0 2050 2112 449753055 449753117 1.130000e-10 78.7
17 TraesCS7D01G300000 chr1D 88.889 63 7 0 2050 2112 449923186 449923124 1.130000e-10 78.7
18 TraesCS7D01G300000 chr1D 86.111 72 10 0 2050 2121 449982973 449982902 1.130000e-10 78.7


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 TraesCS7D01G300000 chr7D 380143882 380147680 3798 False 7016.000000 7016 100.000 1 3799 1 chr7D.!!$F1 3798
1 TraesCS7D01G300000 chr7A 428808775 428812558 3783 False 6015.000000 6015 95.350 1 3799 1 chr7A.!!$F1 3798
2 TraesCS7D01G300000 chr7B 375188425 375192996 4571 False 2024.333333 3557 97.178 1 3799 3 chr7B.!!$F1 3798

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
192 195 1.069364 CGTTGCATGCATGTGTGTACA 60.069 47.619 26.79 12.86 41.89 2.90 F
1729 2495 0.736325 TTTTCTCTGGAGCGCGCTAC 60.736 55.000 36.22 36.22 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 2807 2.118076 CAATGTGGGCCCACCTGT 59.882 61.111 44.65 30.37 45.63 4.00 R
3467 4269 1.066787 GTCTAGCTTCCACCTGTCCAC 60.067 57.143 0.00 0.00 0.00 4.02 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
192 195 1.069364 CGTTGCATGCATGTGTGTACA 60.069 47.619 26.79 12.86 41.89 2.90
298 625 7.758076 CACAACTAGCATGATCATGTTGATTTT 59.242 33.333 29.28 17.45 37.20 1.82
375 704 2.353109 CGCTCCTCAAGATCACTGTCAA 60.353 50.000 0.00 0.00 0.00 3.18
410 739 9.993454 TCTCTAGTATCGAGCTAGTATTACAAA 57.007 33.333 19.72 4.55 37.69 2.83
955 1286 1.335324 GGAGTGTGCATTGCAGTGTTC 60.335 52.381 12.53 7.58 40.08 3.18
978 1309 1.177401 TCAGTCACTGGTCGATCTGG 58.823 55.000 4.57 0.00 31.51 3.86
1113 1444 1.351080 ATGGCTATGGCTGCTGGAGT 61.351 55.000 0.00 0.00 38.73 3.85
1263 1598 3.765511 TCTCTGGCTTGGAATTCATTTGG 59.234 43.478 7.93 0.00 0.00 3.28
1531 1870 0.821301 TGACAATGCCGCAACTTGGA 60.821 50.000 10.64 0.00 0.00 3.53
1572 2337 0.961019 TGACCTGTGCCAAATCTTGC 59.039 50.000 0.00 0.00 0.00 4.01
1585 2350 5.575957 CCAAATCTTGCTGACATACATCAC 58.424 41.667 0.00 0.00 0.00 3.06
1729 2495 0.736325 TTTTCTCTGGAGCGCGCTAC 60.736 55.000 36.22 36.22 0.00 3.58
1841 2616 3.202906 GCCATACTAGCCGTCATTTTCA 58.797 45.455 0.00 0.00 0.00 2.69
1897 2672 6.721571 ACAAATCAATGAAGTGGTACGTAG 57.278 37.500 0.00 0.00 0.00 3.51
1898 2673 5.642063 ACAAATCAATGAAGTGGTACGTAGG 59.358 40.000 0.00 0.00 0.00 3.18
1899 2674 5.670792 AATCAATGAAGTGGTACGTAGGA 57.329 39.130 0.00 0.00 0.00 2.94
1900 2675 4.713824 TCAATGAAGTGGTACGTAGGAG 57.286 45.455 0.00 0.00 0.00 3.69
1901 2676 4.084287 TCAATGAAGTGGTACGTAGGAGT 58.916 43.478 0.00 0.00 0.00 3.85
1902 2677 5.255687 TCAATGAAGTGGTACGTAGGAGTA 58.744 41.667 0.00 0.00 0.00 2.59
1998 2773 9.709495 TGACAAAAGGAAAAATTCATAGAATGG 57.291 29.630 0.00 0.00 0.00 3.16
2026 2807 4.083537 ACTGACGTAAACACGGTCGTATTA 60.084 41.667 1.97 0.00 36.67 0.98
2189 2973 1.984817 CCCACCTAACAACGGCCTA 59.015 57.895 0.00 0.00 0.00 3.93
2192 2976 1.082117 CACCTAACAACGGCCTAGCG 61.082 60.000 0.00 0.00 0.00 4.26
2301 3085 1.227060 CAGCTCGACGCCATCATCA 60.227 57.895 3.66 0.00 40.39 3.07
2369 3156 4.087892 CAGGACTCACCGCCAGGG 62.088 72.222 0.00 0.00 44.74 4.45
2408 3195 0.677288 TCTTCATGTTCGACACCGGT 59.323 50.000 0.00 0.00 36.24 5.28
2513 3300 1.675641 GCCCAGTTGCTACCACCTG 60.676 63.158 0.00 0.00 31.86 4.00
3132 3932 6.856135 TGATTGATGTATGCTGAGTGAATC 57.144 37.500 0.00 0.00 0.00 2.52
3378 4178 4.248842 CACACGGCCCTGTCACCA 62.249 66.667 4.19 0.00 0.00 4.17
3379 4179 4.250305 ACACGGCCCTGTCACCAC 62.250 66.667 0.98 0.00 0.00 4.16
3467 4269 8.519492 AAACCGTCTTTGAAAATCAATATGTG 57.481 30.769 0.00 0.00 36.11 3.21
3503 4305 5.329399 AGCTAGACCTGGTAATAGAGATGG 58.671 45.833 18.17 0.00 0.00 3.51
3505 4307 5.184287 GCTAGACCTGGTAATAGAGATGGTC 59.816 48.000 18.17 0.00 41.78 4.02
3511 4313 7.339482 ACCTGGTAATAGAGATGGTCTTTTTC 58.661 38.462 0.00 0.00 36.64 2.29
3512 4314 6.480320 CCTGGTAATAGAGATGGTCTTTTTCG 59.520 42.308 0.00 0.00 36.64 3.46
3744 4551 9.860650 TCTATAGAGCAAAGATAAGAGAGACTT 57.139 33.333 0.00 0.00 42.04 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
192 195 6.131544 CATGCATGCACATGTATATATGCT 57.868 37.500 25.37 0.00 41.20 3.79
298 625 3.244284 ACGTGCACCATAACTAACTGGAA 60.244 43.478 12.15 0.00 36.35 3.53
375 704 2.038689 TCGATACTAGAGACCGGATGCT 59.961 50.000 9.46 1.30 0.00 3.79
410 739 3.947196 TCAATGGCGCATTCTAATCACTT 59.053 39.130 10.83 0.00 31.05 3.16
921 1252 3.077359 CACACTCCCTCTCAACCAATTC 58.923 50.000 0.00 0.00 0.00 2.17
955 1286 2.687425 AGATCGACCAGTGACTGATCTG 59.313 50.000 15.33 3.29 42.97 2.90
978 1309 2.748605 CACACACCTCAGTTGAGAGAC 58.251 52.381 10.64 0.00 44.74 3.36
1263 1598 4.911033 GCATTGCACCAAAATTAAGCAAAC 59.089 37.500 3.15 0.00 46.65 2.93
1531 1870 5.057819 CAGATGAGTGATTGATAAGCAGCT 58.942 41.667 0.00 0.00 0.00 4.24
1585 2350 8.562892 CAGGATTGCTGGTAATAATCAAGTAAG 58.437 37.037 0.00 0.00 33.57 2.34
1741 2507 9.508642 AGACCTCTTAATTAACTTGGAAAAGAG 57.491 33.333 11.24 7.33 38.65 2.85
1763 2529 8.523658 TGATGTTGCATATACATAGACTAGACC 58.476 37.037 2.52 0.00 36.41 3.85
1841 2616 7.436376 GGTAGTCGTGTTCAAGTTTAACTAGTT 59.564 37.037 13.68 13.68 0.00 2.24
1897 2672 4.722361 AGCTAGCTTTGTGTAGTACTCC 57.278 45.455 12.68 0.00 0.00 3.85
1898 2673 8.380743 TCTATAGCTAGCTTTGTGTAGTACTC 57.619 38.462 24.88 0.00 0.00 2.59
1899 2674 7.040961 GCTCTATAGCTAGCTTTGTGTAGTACT 60.041 40.741 24.88 0.00 45.85 2.73
1900 2675 7.079475 GCTCTATAGCTAGCTTTGTGTAGTAC 58.921 42.308 24.88 10.03 45.85 2.73
1901 2676 7.204496 GCTCTATAGCTAGCTTTGTGTAGTA 57.796 40.000 24.88 0.74 45.85 1.82
1902 2677 6.079424 GCTCTATAGCTAGCTTTGTGTAGT 57.921 41.667 24.88 0.00 45.85 2.73
2026 2807 2.118076 CAATGTGGGCCCACCTGT 59.882 61.111 44.65 30.37 45.63 4.00
2066 2847 4.859798 CAGTAGTTCTTGATCTCGTTGTCC 59.140 45.833 0.00 0.00 0.00 4.02
2237 3021 2.434884 AACGTCGGATGCTGCAGG 60.435 61.111 17.12 0.00 0.00 4.85
2301 3085 3.958860 GGTGCTCTGGTGGTGGCT 61.959 66.667 0.00 0.00 0.00 4.75
2369 3156 2.528743 CGGGCAGTGATGCGACATC 61.529 63.158 11.42 11.42 35.24 3.06
2513 3300 4.410400 CCGTCCACCAAGGGAGGC 62.410 72.222 0.00 0.00 40.62 4.70
2651 3438 3.740495 TAGCTGCTCCCCCTCCTCG 62.740 68.421 4.91 0.00 0.00 4.63
2942 3735 5.221441 GCACCTTTGGAAAACCTCAGTATTT 60.221 40.000 0.00 0.00 0.00 1.40
2945 3738 3.219281 GCACCTTTGGAAAACCTCAGTA 58.781 45.455 0.00 0.00 0.00 2.74
2946 3739 2.031870 GCACCTTTGGAAAACCTCAGT 58.968 47.619 0.00 0.00 0.00 3.41
2947 3740 2.031120 TGCACCTTTGGAAAACCTCAG 58.969 47.619 0.00 0.00 0.00 3.35
3296 4096 6.781014 TCTTTACCTTGTCCTTAGAGAACAGA 59.219 38.462 0.00 0.00 0.00 3.41
3297 4097 6.994221 TCTTTACCTTGTCCTTAGAGAACAG 58.006 40.000 0.00 0.00 0.00 3.16
3435 4237 6.469595 TGATTTTCAAAGACGGTTTAAACACG 59.530 34.615 19.57 20.10 0.00 4.49
3467 4269 1.066787 GTCTAGCTTCCACCTGTCCAC 60.067 57.143 0.00 0.00 0.00 4.02
3503 4305 5.240121 TCTATTACCACCCACGAAAAAGAC 58.760 41.667 0.00 0.00 0.00 3.01
3505 4307 5.484715 TCTCTATTACCACCCACGAAAAAG 58.515 41.667 0.00 0.00 0.00 2.27
3511 4313 4.402056 AACATCTCTATTACCACCCACG 57.598 45.455 0.00 0.00 0.00 4.94
3512 4314 7.107542 TGTAAAACATCTCTATTACCACCCAC 58.892 38.462 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.