Multiple sequence alignment - TraesCS7D01G388200

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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 TraesCS7D01G388200 chr7D 100.000 2201 0 0 1 2201 501901262 501899062 0.000000e+00 4065
1 TraesCS7D01G388200 chr7D 98.005 401 7 1 908 1308 501842029 501842428 0.000000e+00 695
2 TraesCS7D01G388200 chr7A 92.862 1345 40 22 1 1311 569405009 569403687 0.000000e+00 1901
3 TraesCS7D01G388200 chr7A 87.866 478 28 6 1724 2201 569403023 569402576 3.220000e-148 534
4 TraesCS7D01G388200 chr7A 85.047 321 9 11 1306 1596 569403658 569403347 7.690000e-75 291
5 TraesCS7D01G388200 chr7B 92.615 1327 35 30 5 1306 531613045 531611757 0.000000e+00 1849
6 TraesCS7D01G388200 chr7B 91.949 472 33 3 1733 2201 531611221 531610752 0.000000e+00 656
7 TraesCS7D01G388200 chr7B 85.808 458 17 19 1306 1719 531611723 531611270 2.010000e-120 442


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 TraesCS7D01G388200 chr7D 501899062 501901262 2200 True 4065.000000 4065 100.000000 1 2201 1 chr7D.!!$R1 2200
1 TraesCS7D01G388200 chr7A 569402576 569405009 2433 True 908.666667 1901 88.591667 1 2201 3 chr7A.!!$R1 2200
2 TraesCS7D01G388200 chr7B 531610752 531613045 2293 True 982.333333 1849 90.124000 5 2201 3 chr7B.!!$R1 2196

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
554 568 0.179009 ATCCAGCGACCCAATCCATG 60.179 55.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 2338 0.953727 TGGTGTTGCAGAGATTGTGC 59.046 50.0 0.0 0.0 41.59 4.57 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
59 62 2.718731 CGCACAAGACCCGCAAAA 59.281 55.556 0.00 0.00 0.00 2.44
385 399 4.203654 AGTTTCCCTTATCCGAACAGTC 57.796 45.455 0.00 0.00 0.00 3.51
386 400 3.838903 AGTTTCCCTTATCCGAACAGTCT 59.161 43.478 0.00 0.00 0.00 3.24
411 425 9.790344 CTCCTTCCTTATCTGAATTACATCATT 57.210 33.333 0.00 0.00 0.00 2.57
470 484 9.888878 AAAGCTATTTTTCTACCTTAAAACGAC 57.111 29.630 0.00 0.00 0.00 4.34
547 561 0.400213 ACTTCAAATCCAGCGACCCA 59.600 50.000 0.00 0.00 0.00 4.51
553 567 0.552848 AATCCAGCGACCCAATCCAT 59.447 50.000 0.00 0.00 0.00 3.41
554 568 0.179009 ATCCAGCGACCCAATCCATG 60.179 55.000 0.00 0.00 0.00 3.66
555 569 2.484062 CCAGCGACCCAATCCATGC 61.484 63.158 0.00 0.00 0.00 4.06
556 570 1.750018 CAGCGACCCAATCCATGCA 60.750 57.895 0.00 0.00 0.00 3.96
887 911 3.999663 CCCTCTCAACTTAAGCAAGACAG 59.000 47.826 1.29 0.00 35.60 3.51
888 912 3.434984 CCTCTCAACTTAAGCAAGACAGC 59.565 47.826 1.29 0.00 35.60 4.40
889 913 4.060900 CTCTCAACTTAAGCAAGACAGCA 58.939 43.478 1.29 0.00 35.60 4.41
890 914 4.060900 TCTCAACTTAAGCAAGACAGCAG 58.939 43.478 1.29 0.00 35.60 4.24
891 915 2.549754 TCAACTTAAGCAAGACAGCAGC 59.450 45.455 1.29 0.00 35.60 5.25
892 916 2.260844 ACTTAAGCAAGACAGCAGCA 57.739 45.000 1.29 0.00 35.60 4.41
893 917 2.149578 ACTTAAGCAAGACAGCAGCAG 58.850 47.619 1.29 0.00 35.60 4.24
894 918 0.877071 TTAAGCAAGACAGCAGCAGC 59.123 50.000 0.00 0.00 42.56 5.25
895 919 0.250424 TAAGCAAGACAGCAGCAGCA 60.250 50.000 3.17 0.00 45.49 4.41
896 920 1.516365 AAGCAAGACAGCAGCAGCAG 61.516 55.000 3.17 0.00 45.49 4.24
897 921 2.561885 CAAGACAGCAGCAGCAGC 59.438 61.111 3.17 0.46 45.49 5.25
898 922 2.112507 AAGACAGCAGCAGCAGCA 59.887 55.556 12.92 0.00 45.49 4.41
899 923 1.966972 AAGACAGCAGCAGCAGCAG 60.967 57.895 12.92 6.60 45.49 4.24
936 960 3.414700 CACGAGCTTGCCGGTGTC 61.415 66.667 1.90 0.00 0.00 3.67
959 983 1.613836 CAACTTCCAAGAAGCAGCCT 58.386 50.000 4.28 0.00 0.00 4.58
960 984 2.553028 CCAACTTCCAAGAAGCAGCCTA 60.553 50.000 4.28 0.00 0.00 3.93
961 985 2.746362 CAACTTCCAAGAAGCAGCCTAG 59.254 50.000 4.28 0.00 0.00 3.02
962 986 1.280421 ACTTCCAAGAAGCAGCCTAGG 59.720 52.381 3.67 3.67 0.00 3.02
963 987 1.280421 CTTCCAAGAAGCAGCCTAGGT 59.720 52.381 11.31 0.00 0.00 3.08
1424 1528 7.801716 TGAGCTTATGTAGTCTTTGTTGTTT 57.198 32.000 0.00 0.00 0.00 2.83
1514 1626 8.879342 AATAGTTATTTCAGAGTCGATGGAAG 57.121 34.615 0.00 0.00 0.00 3.46
1515 1627 5.112686 AGTTATTTCAGAGTCGATGGAAGC 58.887 41.667 0.00 0.00 0.00 3.86
1516 1628 3.616956 ATTTCAGAGTCGATGGAAGCA 57.383 42.857 0.00 0.00 0.00 3.91
1517 1629 3.616956 TTTCAGAGTCGATGGAAGCAT 57.383 42.857 0.00 0.00 0.00 3.79
1562 1680 4.437682 AGAGTTTGATGAACAACTCCCA 57.562 40.909 8.15 0.00 40.84 4.37
1563 1681 4.392940 AGAGTTTGATGAACAACTCCCAG 58.607 43.478 8.15 0.00 40.84 4.45
1625 1871 6.403866 AAGATGTGCAACCACTTAATTGAA 57.596 33.333 0.00 0.00 42.54 2.69
1634 1880 7.388224 TGCAACCACTTAATTGAACGTTAGATA 59.612 33.333 0.00 0.00 0.00 1.98
1663 1909 4.494091 ACGAACTTCCAGGATCATTGAT 57.506 40.909 0.00 0.00 0.00 2.57
1719 1965 9.481340 CATACACTCATATGTTGCTATGTACTT 57.519 33.333 1.90 0.00 33.85 2.24
1720 1966 9.698309 ATACACTCATATGTTGCTATGTACTTC 57.302 33.333 1.90 0.00 33.85 3.01
1722 1968 6.986231 CACTCATATGTTGCTATGTACTTCCA 59.014 38.462 1.90 0.00 32.13 3.53
1730 2047 6.156256 TGTTGCTATGTACTTCCAGGAGTAAT 59.844 38.462 0.00 0.00 34.15 1.89
1756 2073 8.648557 TCTAAATGTATACAGTTGCAGTGATC 57.351 34.615 24.72 0.00 35.62 2.92
1757 2074 8.257306 TCTAAATGTATACAGTTGCAGTGATCA 58.743 33.333 24.72 4.41 35.62 2.92
1760 2077 9.565090 AAATGTATACAGTTGCAGTGATCATAT 57.435 29.630 17.16 0.00 32.50 1.78
1817 2134 0.036010 TACTTGAGCAGGAGCAAGCC 60.036 55.000 0.00 0.00 43.99 4.35
1844 2161 8.474831 ACAAGCCTAGTGAAAATTTTACAAACT 58.525 29.630 2.75 8.06 0.00 2.66
1898 2215 5.916661 ATAAGCTCCGAAACTGAGAGTAA 57.083 39.130 0.00 0.00 31.26 2.24
2039 2356 1.242076 AGCACAATCTCTGCAACACC 58.758 50.000 0.00 0.00 37.08 4.16
2041 2358 1.542915 GCACAATCTCTGCAACACCAT 59.457 47.619 0.00 0.00 34.56 3.55
2052 2369 5.368145 TCTGCAACACCATATGTAGATTCC 58.632 41.667 1.24 0.00 42.31 3.01
2111 2430 9.319143 TGACATAAAACCAAAATGTAAACCTTG 57.681 29.630 0.00 0.00 34.09 3.61
2112 2431 9.320352 GACATAAAACCAAAATGTAAACCTTGT 57.680 29.630 0.00 0.00 34.09 3.16
2113 2432 9.320352 ACATAAAACCAAAATGTAAACCTTGTC 57.680 29.630 0.00 0.00 32.21 3.18
2114 2433 9.319143 CATAAAACCAAAATGTAAACCTTGTCA 57.681 29.630 0.00 0.00 0.00 3.58
2115 2434 9.892130 ATAAAACCAAAATGTAAACCTTGTCAA 57.108 25.926 0.00 0.00 0.00 3.18
2116 2435 8.622948 AAAACCAAAATGTAAACCTTGTCAAA 57.377 26.923 0.00 0.00 0.00 2.69
2117 2436 8.622948 AAACCAAAATGTAAACCTTGTCAAAA 57.377 26.923 0.00 0.00 0.00 2.44
2118 2437 8.800370 AACCAAAATGTAAACCTTGTCAAAAT 57.200 26.923 0.00 0.00 0.00 1.82
2119 2438 9.892130 AACCAAAATGTAAACCTTGTCAAAATA 57.108 25.926 0.00 0.00 0.00 1.40
2120 2439 9.541143 ACCAAAATGTAAACCTTGTCAAAATAG 57.459 29.630 0.00 0.00 0.00 1.73
2121 2440 9.757227 CCAAAATGTAAACCTTGTCAAAATAGA 57.243 29.630 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.052159 CCACTTGGTTGTTGCATTGTTA 57.948 40.909 0.00 0.00 0.00 2.41
15 16 2.903798 CCACTTGGTTGTTGCATTGTT 58.096 42.857 0.00 0.00 0.00 2.83
59 62 0.472471 TTGGAGCTCCGTGACCTTTT 59.528 50.000 27.43 0.00 39.43 2.27
360 374 5.240844 ACTGTTCGGATAAGGGAAACTTTTG 59.759 40.000 0.00 0.00 40.64 2.44
385 399 9.790344 AATGATGTAATTCAGATAAGGAAGGAG 57.210 33.333 0.00 0.00 0.00 3.69
509 523 9.607988 TTTGAAGTGTCGTGAATATATTATGGT 57.392 29.630 0.00 0.00 0.00 3.55
554 568 2.028763 CGAACAATCAGCAAATGCATGC 59.971 45.455 11.82 11.82 46.78 4.06
555 569 3.247442 ACGAACAATCAGCAAATGCATG 58.753 40.909 0.00 3.66 45.16 4.06
556 570 3.581024 ACGAACAATCAGCAAATGCAT 57.419 38.095 8.28 0.00 45.16 3.96
802 826 1.901085 GCTGGACGGACAGGATTCT 59.099 57.895 10.10 0.00 38.90 2.40
897 921 3.432588 GACCTGCTGCTGCTGCTG 61.433 66.667 27.67 25.97 40.48 4.41
936 960 2.030451 GCTGCTTCTTGGAAGTTGGAAG 60.030 50.000 8.73 0.00 38.42 3.46
959 983 7.065504 CCTCCTAAACTAAGCTACCTAACCTA 58.934 42.308 0.00 0.00 0.00 3.08
960 984 5.898397 CCTCCTAAACTAAGCTACCTAACCT 59.102 44.000 0.00 0.00 0.00 3.50
961 985 5.896106 TCCTCCTAAACTAAGCTACCTAACC 59.104 44.000 0.00 0.00 0.00 2.85
962 986 7.415592 TTCCTCCTAAACTAAGCTACCTAAC 57.584 40.000 0.00 0.00 0.00 2.34
963 987 6.097981 GCTTCCTCCTAAACTAAGCTACCTAA 59.902 42.308 0.00 0.00 39.51 2.69
1391 1468 2.338577 ACATAAGCTCATGCCTCCAC 57.661 50.000 0.00 0.00 40.80 4.02
1435 1539 5.186198 AGTATATGCACCTGAAAGACCAAC 58.814 41.667 0.00 0.00 34.07 3.77
1515 1627 2.619646 TGCAACTGTAGGCATATGCATG 59.380 45.455 28.07 12.79 44.36 4.06
1516 1628 2.620115 GTGCAACTGTAGGCATATGCAT 59.380 45.455 28.07 24.13 43.21 3.96
1517 1629 2.016318 GTGCAACTGTAGGCATATGCA 58.984 47.619 28.07 6.84 42.75 3.96
1562 1680 1.446272 GCTTAGAGACGCGCAACCT 60.446 57.895 5.73 0.00 0.00 3.50
1563 1681 1.014564 AAGCTTAGAGACGCGCAACC 61.015 55.000 5.73 0.00 0.00 3.77
1634 1880 7.519032 TGATCCTGGAAGTTCGTTTTTATTT 57.481 32.000 0.00 0.00 0.00 1.40
1695 1941 8.141909 GGAAGTACATAGCAACATATGAGTGTA 58.858 37.037 10.38 6.20 36.76 2.90
1730 2047 9.098355 GATCACTGCAACTGTATACATTTAGAA 57.902 33.333 5.91 0.00 0.00 2.10
1748 2065 5.082251 TGGCTCTATCATATGATCACTGC 57.918 43.478 21.42 18.85 36.05 4.40
1756 2073 7.984050 CACTAACCCTATTGGCTCTATCATATG 59.016 40.741 0.00 0.00 37.83 1.78
1757 2074 7.126421 CCACTAACCCTATTGGCTCTATCATAT 59.874 40.741 0.00 0.00 37.83 1.78
1760 2077 4.593206 CCACTAACCCTATTGGCTCTATCA 59.407 45.833 0.00 0.00 37.83 2.15
1791 2108 3.453717 TGCTCCTGCTCAAGTATCTTCAT 59.546 43.478 0.00 0.00 40.48 2.57
1817 2134 8.539674 GTTTGTAAAATTTTCACTAGGCTTGTG 58.460 33.333 20.82 20.82 36.82 3.33
1844 2161 9.187996 TGATTTTTATCCAAATATCTGAGTGCA 57.812 29.630 0.00 0.00 34.80 4.57
1882 2199 4.931661 AGTTGTTACTCTCAGTTTCGGA 57.068 40.909 0.00 0.00 0.00 4.55
1898 2215 9.533253 CAAATAAAGTTGAAATCAGGAAGTTGT 57.467 29.630 0.00 0.00 0.00 3.32
2020 2337 1.242076 GGTGTTGCAGAGATTGTGCT 58.758 50.000 0.00 0.00 41.78 4.40
2021 2338 0.953727 TGGTGTTGCAGAGATTGTGC 59.046 50.000 0.00 0.00 41.59 4.57
2022 2339 4.397103 ACATATGGTGTTGCAGAGATTGTG 59.603 41.667 7.80 0.00 38.01 3.33
2023 2340 4.592942 ACATATGGTGTTGCAGAGATTGT 58.407 39.130 7.80 0.00 38.01 2.71
2024 2341 6.051074 TCTACATATGGTGTTGCAGAGATTG 58.949 40.000 7.80 0.00 42.29 2.67
2025 2342 6.239217 TCTACATATGGTGTTGCAGAGATT 57.761 37.500 7.80 0.00 42.29 2.40
2027 2344 5.876651 ATCTACATATGGTGTTGCAGAGA 57.123 39.130 7.80 0.00 42.29 3.10
2028 2345 5.468072 GGAATCTACATATGGTGTTGCAGAG 59.532 44.000 7.80 0.00 42.29 3.35
2029 2346 5.130975 AGGAATCTACATATGGTGTTGCAGA 59.869 40.000 7.80 0.00 42.29 4.26
2030 2347 5.237996 CAGGAATCTACATATGGTGTTGCAG 59.762 44.000 7.80 0.00 42.29 4.41
2031 2348 5.104569 TCAGGAATCTACATATGGTGTTGCA 60.105 40.000 7.80 0.00 42.29 4.08
2032 2349 5.368145 TCAGGAATCTACATATGGTGTTGC 58.632 41.667 7.80 2.24 42.29 4.17
2033 2350 7.219322 TGATCAGGAATCTACATATGGTGTTG 58.781 38.462 7.80 0.00 34.70 3.33
2041 2358 9.098355 CGAAAAGTTTGATCAGGAATCTACATA 57.902 33.333 0.00 0.00 35.24 2.29
2110 2429 6.472016 TGGCAGACATAGTTCTATTTTGACA 58.528 36.000 0.00 0.00 0.00 3.58
2111 2430 6.985188 TGGCAGACATAGTTCTATTTTGAC 57.015 37.500 0.00 0.00 0.00 3.18
2115 2434 9.935241 CACTATATGGCAGACATAGTTCTATTT 57.065 33.333 13.51 0.00 44.79 1.40
2116 2435 8.535335 CCACTATATGGCAGACATAGTTCTATT 58.465 37.037 13.51 0.00 44.79 1.73
2117 2436 8.072321 CCACTATATGGCAGACATAGTTCTAT 57.928 38.462 13.51 0.00 44.79 1.98
2118 2437 7.468141 CCACTATATGGCAGACATAGTTCTA 57.532 40.000 13.51 0.00 44.79 2.10
2119 2438 6.352016 CCACTATATGGCAGACATAGTTCT 57.648 41.667 13.51 0.00 44.79 3.01


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

AutoCloner maintained by Alex Coulton.