Multiple sequence alignment - TraesCS2D01G526200

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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 TraesCS2D01G526200 chr2D 100.000 2708 0 0 1 2708 614752573 614749866 0.000000e+00 5001.0
1 TraesCS2D01G526200 chr2D 86.139 101 8 6 7 105 326273267 326273363 1.330000e-18 104.0
2 TraesCS2D01G526200 chr2B 94.277 1625 66 15 53 1675 749106658 749105059 0.000000e+00 2460.0
3 TraesCS2D01G526200 chr2B 96.374 910 32 1 1800 2708 749104849 749103940 0.000000e+00 1496.0
4 TraesCS2D01G526200 chr2B 98.148 54 1 0 1 54 749106734 749106681 7.980000e-16 95.3
5 TraesCS2D01G526200 chr2A 89.271 1687 148 17 6 1673 745089131 745087459 0.000000e+00 2082.0
6 TraesCS2D01G526200 chr2A 86.531 1084 80 27 1675 2708 745087223 745086156 0.000000e+00 1133.0
7 TraesCS2D01G526200 chr2A 87.654 81 6 4 10 87 648030876 648030797 1.030000e-14 91.6
8 TraesCS2D01G526200 chr4B 94.286 70 3 1 10 79 425192948 425192880 3.690000e-19 106.0
9 TraesCS2D01G526200 chr6B 89.157 83 7 2 6 87 687497765 687497846 4.770000e-18 102.0
10 TraesCS2D01G526200 chr7A 86.905 84 9 2 12 94 245822622 245822704 2.870000e-15 93.5
11 TraesCS2D01G526200 chr4A 88.462 78 8 1 10 87 417811189 417811265 2.870000e-15 93.5
12 TraesCS2D01G526200 chr3A 86.905 84 8 3 6 87 699105156 699105074 1.030000e-14 91.6


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 TraesCS2D01G526200 chr2D 614749866 614752573 2707 True 5001.000000 5001 100.000000 1 2708 1 chr2D.!!$R1 2707
1 TraesCS2D01G526200 chr2B 749103940 749106734 2794 True 1350.433333 2460 96.266333 1 2708 3 chr2B.!!$R1 2707
2 TraesCS2D01G526200 chr2A 745086156 745089131 2975 True 1607.500000 2082 87.901000 6 2708 2 chr2A.!!$R2 2702

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
564 608 3.678289 TGTTGGATGTGGATGAACTCAG 58.322 45.455 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 2480 0.396435 TTGCCTCGAGGAAGCTTGAA 59.604 50.0 35.69 5.21 37.39 2.69 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
80 105 5.573380 TTCCATCAATCCCCTCTCTATTG 57.427 43.478 0.00 0.00 32.96 1.90
150 176 5.106317 GCCGTGATCATGTTAGGAAGAAAAA 60.106 40.000 13.81 0.00 0.00 1.94
180 206 6.303054 TCCTAAGATTGTTGGAACACATGAA 58.697 36.000 0.00 0.00 39.29 2.57
564 608 3.678289 TGTTGGATGTGGATGAACTCAG 58.322 45.455 0.00 0.00 0.00 3.35
618 662 9.292846 TGGATATCAATTAATGTATACGCGTAC 57.707 33.333 23.19 13.62 0.00 3.67
666 710 3.699038 TGGGCATAAGTTAGGCATTTGTC 59.301 43.478 20.11 2.70 37.17 3.18
720 764 4.157840 GGCGGTTTGGATCTACTCAAAAAT 59.842 41.667 0.00 0.00 35.08 1.82
783 827 6.213802 TGTGGATAAGGATGTACACCAACTTA 59.786 38.462 14.39 12.49 33.70 2.24
794 838 9.162764 GATGTACACCAACTTATGATGTAAACT 57.837 33.333 0.00 0.00 0.00 2.66
984 1028 6.537301 TCCCATTTGTAGTAGCAAGTATTTCG 59.463 38.462 0.00 0.00 0.00 3.46
1300 1344 2.820037 GCGAGGTGGCTAGGTTGC 60.820 66.667 0.00 0.00 0.00 4.17
1323 1367 6.101332 GCACATGGAGAATGAAATGCTAAAA 58.899 36.000 0.00 0.00 38.72 1.52
1374 1418 7.499563 CACATCAAGAAGATCCAATCTCAGAAT 59.500 37.037 0.00 0.00 39.08 2.40
1375 1419 8.053963 ACATCAAGAAGATCCAATCTCAGAATT 58.946 33.333 0.00 0.00 39.08 2.17
1520 1564 3.243359 ACATGGACATGAACCAAAGGT 57.757 42.857 18.38 13.30 41.20 3.50
1602 1646 4.565962 CCGAAGATTCATGAGACTTCACAG 59.434 45.833 27.37 18.31 38.71 3.66
1610 1654 3.213206 TGAGACTTCACAGCAACCATT 57.787 42.857 0.00 0.00 0.00 3.16
1678 1956 0.613292 AGCAACACCACAACACCCAA 60.613 50.000 0.00 0.00 0.00 4.12
1684 1962 3.637769 ACACCACAACACCCAATTTACT 58.362 40.909 0.00 0.00 0.00 2.24
1690 1968 4.515944 CACAACACCCAATTTACTTCCGTA 59.484 41.667 0.00 0.00 0.00 4.02
1696 1974 5.579511 CACCCAATTTACTTCCGTACTACAG 59.420 44.000 0.00 0.00 0.00 2.74
1745 2023 2.586425 CTCCACCACTTCAACCACAAT 58.414 47.619 0.00 0.00 0.00 2.71
1751 2029 5.358922 CACCACTTCAACCACAATTTCAAT 58.641 37.500 0.00 0.00 0.00 2.57
1765 2043 7.148018 CCACAATTTCAATACTATGCAAGTCCT 60.148 37.037 0.00 0.00 39.80 3.85
1767 2045 9.461312 ACAATTTCAATACTATGCAAGTCCTAA 57.539 29.630 0.00 0.00 39.80 2.69
1768 2046 9.722056 CAATTTCAATACTATGCAAGTCCTAAC 57.278 33.333 0.00 0.00 39.80 2.34
1770 2048 7.843490 TTCAATACTATGCAAGTCCTAACAC 57.157 36.000 0.00 0.00 39.80 3.32
1771 2049 6.941857 TCAATACTATGCAAGTCCTAACACA 58.058 36.000 0.00 0.00 39.80 3.72
1772 2050 7.390823 TCAATACTATGCAAGTCCTAACACAA 58.609 34.615 0.00 0.00 39.80 3.33
1773 2051 8.046708 TCAATACTATGCAAGTCCTAACACAAT 58.953 33.333 0.00 0.00 39.80 2.71
1774 2052 9.325198 CAATACTATGCAAGTCCTAACACAATA 57.675 33.333 0.00 0.00 39.80 1.90
1775 2053 9.899661 AATACTATGCAAGTCCTAACACAATAA 57.100 29.630 0.00 0.00 39.80 1.40
1776 2054 7.611213 ACTATGCAAGTCCTAACACAATAAC 57.389 36.000 0.00 0.00 30.33 1.89
1777 2055 7.165485 ACTATGCAAGTCCTAACACAATAACA 58.835 34.615 0.00 0.00 30.33 2.41
1778 2056 6.892658 ATGCAAGTCCTAACACAATAACAA 57.107 33.333 0.00 0.00 0.00 2.83
1779 2057 6.701145 TGCAAGTCCTAACACAATAACAAA 57.299 33.333 0.00 0.00 0.00 2.83
1874 2152 2.094597 TCCGGTGGTAATGACACTTACG 60.095 50.000 0.00 0.00 38.83 3.18
1889 2167 5.487433 ACACTTACGTCCATGAATCATTCA 58.513 37.500 1.59 1.59 45.01 2.57
1922 2200 4.202461 ACTTGTCTAATGCTCCTTTGGACA 60.202 41.667 6.12 6.12 41.13 4.02
2010 2288 1.549203 ATGGATTGTGTTGAGTGGGC 58.451 50.000 0.00 0.00 0.00 5.36
2028 2306 0.461135 GCCAATAATGCACCACCAGG 59.539 55.000 0.00 0.00 42.21 4.45
2097 2375 4.525487 ACTACTTTAGATGTCGGTTGGTGA 59.475 41.667 0.00 0.00 0.00 4.02
2120 2398 9.090692 GTGATTTCATTTGAATTACATCAAGGG 57.909 33.333 6.87 0.00 40.21 3.95
2192 2502 0.321122 AAGCTTCCTCGAGGCAACAG 60.321 55.000 27.39 18.74 37.11 3.16
2221 2531 8.412456 CACATTTCATGTTTAGGGCATTATGTA 58.588 33.333 0.00 0.00 42.70 2.29
2225 2535 7.523293 TCATGTTTAGGGCATTATGTAATGG 57.477 36.000 13.08 0.00 42.46 3.16
2504 2816 5.109210 TCGACTAGCCACAAATGATAACAG 58.891 41.667 0.00 0.00 0.00 3.16
2527 2839 4.212716 CCAATGTGAGATTCATGTGGGAT 58.787 43.478 0.00 0.00 0.00 3.85
2547 2859 5.977129 GGGATAATGGTAAGTTGAAAATGCG 59.023 40.000 0.00 0.00 0.00 4.73
2570 2882 3.001533 CACCTGCATGTGAAAACAAAAGC 59.998 43.478 16.24 0.00 38.55 3.51
2659 2993 3.602390 ACATAAAATACGCATCCGCAC 57.398 42.857 0.00 0.00 38.40 5.34
2692 3026 9.520515 ACATGTCTCCTTCAAGTTAATGTAAAT 57.479 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 0.543277 TACTGCTTGAGCCTCATGGG 59.457 55.000 9.39 0.00 41.18 4.00
96 121 4.298103 ACTTCGGTGTCTAAGAGAGGTA 57.702 45.455 0.00 0.00 0.00 3.08
97 122 3.157750 ACTTCGGTGTCTAAGAGAGGT 57.842 47.619 0.00 0.00 0.00 3.85
263 299 8.598916 TCTCATGGTTATTAGTGGACTTGTTTA 58.401 33.333 0.00 0.00 0.00 2.01
430 474 3.119814 GCTCGATCGTAGCCATCTAATCA 60.120 47.826 21.48 0.00 33.73 2.57
435 479 1.576920 CGCTCGATCGTAGCCATCT 59.423 57.895 24.16 0.00 36.60 2.90
618 662 8.087750 ACCATTAATTGTTGGCCAAATATATCG 58.912 33.333 22.47 5.67 36.44 2.92
876 920 2.376109 TGGAGATACGAGGAGGTGAAC 58.624 52.381 0.00 0.00 0.00 3.18
984 1028 4.385825 TCGGCATACTCAAATGGATAACC 58.614 43.478 0.00 0.00 0.00 2.85
1300 1344 7.201376 CGTTTTTAGCATTTCATTCTCCATGTG 60.201 37.037 0.00 0.00 34.06 3.21
1344 1388 5.651139 AGATTGGATCTTCTTGATGTGTTGG 59.349 40.000 0.00 0.00 35.76 3.77
1374 1418 2.824689 TATTTGCTGGCATCCCTGAA 57.175 45.000 0.00 0.00 32.15 3.02
1375 1419 2.824689 TTATTTGCTGGCATCCCTGA 57.175 45.000 0.00 0.00 32.15 3.86
1602 1646 0.532115 GGTGGGATGACAATGGTTGC 59.468 55.000 0.00 0.00 0.00 4.17
1610 1654 1.281867 GTGGAAGATGGTGGGATGACA 59.718 52.381 0.00 0.00 0.00 3.58
1684 1962 4.338964 TCAACAACTGACTGTAGTACGGAA 59.661 41.667 16.20 2.98 0.00 4.30
1745 2023 7.880713 TGTGTTAGGACTTGCATAGTATTGAAA 59.119 33.333 0.00 0.00 37.17 2.69
1751 2029 8.315482 TGTTATTGTGTTAGGACTTGCATAGTA 58.685 33.333 0.00 0.00 37.17 1.82
1765 2043 5.847304 TGCAATGGCTTTGTTATTGTGTTA 58.153 33.333 13.79 0.00 41.91 2.41
1767 2045 4.039004 TCTGCAATGGCTTTGTTATTGTGT 59.961 37.500 13.79 0.00 41.91 3.72
1768 2046 4.558178 TCTGCAATGGCTTTGTTATTGTG 58.442 39.130 13.79 0.20 41.91 3.33
1770 2048 4.989797 TGTTCTGCAATGGCTTTGTTATTG 59.010 37.500 13.79 2.26 41.91 1.90
1771 2049 5.212532 TGTTCTGCAATGGCTTTGTTATT 57.787 34.783 13.79 0.00 41.91 1.40
1772 2050 4.870123 TGTTCTGCAATGGCTTTGTTAT 57.130 36.364 13.79 0.00 41.91 1.89
1773 2051 4.142071 TGTTGTTCTGCAATGGCTTTGTTA 60.142 37.500 13.79 4.11 41.91 2.41
1774 2052 3.197265 GTTGTTCTGCAATGGCTTTGTT 58.803 40.909 13.79 0.00 41.91 2.83
1775 2053 2.168106 TGTTGTTCTGCAATGGCTTTGT 59.832 40.909 13.79 0.00 41.91 2.83
1776 2054 2.823984 TGTTGTTCTGCAATGGCTTTG 58.176 42.857 8.64 8.64 41.91 2.77
1777 2055 3.069872 TCATGTTGTTCTGCAATGGCTTT 59.930 39.130 0.00 0.00 41.91 3.51
1778 2056 2.629137 TCATGTTGTTCTGCAATGGCTT 59.371 40.909 0.00 0.00 41.91 4.35
1779 2057 2.230508 CTCATGTTGTTCTGCAATGGCT 59.769 45.455 0.00 0.00 41.91 4.75
1874 2152 8.449397 GTTATCATAGCTGAATGATTCATGGAC 58.551 37.037 15.46 0.00 42.63 4.02
1889 2167 7.016072 AGGAGCATTAGACAAGTTATCATAGCT 59.984 37.037 0.00 0.00 0.00 3.32
1922 2200 2.092429 TCCCTAGAATTTCATGCGCCTT 60.092 45.455 4.18 0.00 0.00 4.35
1996 2274 2.666272 TATTGGCCCACTCAACACAA 57.334 45.000 0.00 0.00 0.00 3.33
2010 2288 0.461135 GCCTGGTGGTGCATTATTGG 59.539 55.000 0.00 0.00 35.27 3.16
2170 2480 0.396435 TTGCCTCGAGGAAGCTTGAA 59.604 50.000 35.69 5.21 37.39 2.69
2172 2482 0.603707 TGTTGCCTCGAGGAAGCTTG 60.604 55.000 35.69 6.96 37.39 4.01
2182 2492 2.805671 TGAAATGTGTACTGTTGCCTCG 59.194 45.455 0.00 0.00 0.00 4.63
2312 2623 6.814644 TCAATAGAGAAAGCAAAAATGCCATG 59.185 34.615 0.00 0.00 34.90 3.66
2504 2816 2.100252 CCCACATGAATCTCACATTGGC 59.900 50.000 0.00 0.00 31.37 4.52
2527 2839 5.157781 GTGCGCATTTTCAACTTACCATTA 58.842 37.500 15.91 0.00 0.00 1.90
2547 2859 2.222007 TTGTTTTCACATGCAGGTGC 57.778 45.000 25.97 12.76 38.66 5.01
2570 2882 1.447945 TGGGTGCATATTCACACACG 58.552 50.000 6.32 0.00 44.64 4.49
2626 2960 3.919223 TTTTATGTTGGTAACGGTGGC 57.081 42.857 0.00 0.00 42.51 5.01


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

AutoCloner maintained by Alex Coulton.