Multiple sequence alignment - TraesCS3D01G263300

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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 TraesCS3D01G263300 chr3D 100.000 2474 0 0 1 2474 365508981 365506508 0.000000e+00 4569
1 TraesCS3D01G263300 chr3D 93.350 406 21 5 2066 2470 611864864 611865264 1.640000e-166 595
2 TraesCS3D01G263300 chr3D 93.137 408 23 5 2066 2471 369995278 369995682 5.890000e-166 593
3 TraesCS3D01G263300 chr3D 91.707 410 24 10 2066 2470 64352296 64351892 5.970000e-156 560
4 TraesCS3D01G263300 chr7A 94.570 2081 97 6 2 2068 7721960 7724038 0.000000e+00 3203
5 TraesCS3D01G263300 chr7A 93.645 2077 104 6 2 2067 727828386 727830445 0.000000e+00 3079
6 TraesCS3D01G263300 chr2A 94.321 2078 101 6 2 2067 34831000 34833072 0.000000e+00 3168
7 TraesCS3D01G263300 chr6A 94.081 2078 108 6 2 2068 94342159 94344232 0.000000e+00 3142
8 TraesCS3D01G263300 chr5A 93.867 2087 101 13 2 2071 311293668 311291592 0.000000e+00 3120
9 TraesCS3D01G263300 chr7D 95.546 1841 74 7 2 1840 203038661 203036827 0.000000e+00 2939
10 TraesCS3D01G263300 chr7D 94.740 1749 60 14 1 1737 548271620 548269892 0.000000e+00 2691
11 TraesCS3D01G263300 chr7D 90.328 548 24 8 1945 2468 505907658 505907116 0.000000e+00 691
12 TraesCS3D01G263300 chr7D 91.879 431 13 2 2066 2474 259279730 259279300 1.280000e-162 582
13 TraesCS3D01G263300 chr1D 96.145 1738 65 2 1 1737 464935403 464937139 0.000000e+00 2837
14 TraesCS3D01G263300 chr2D 95.394 1737 66 7 2 1737 142523387 142521664 0.000000e+00 2752
15 TraesCS3D01G263300 chr2D 94.840 407 19 2 2066 2471 340628645 340629050 3.470000e-178 634
16 TraesCS3D01G263300 chr2D 87.688 398 46 1 2066 2463 425889307 425889701 6.230000e-126 460
17 TraesCS3D01G263300 chr3A 94.143 1656 91 6 85 1737 658727946 658726294 0.000000e+00 2516
18 TraesCS3D01G263300 chr6B 90.262 1643 141 12 4 1634 46354155 46355790 0.000000e+00 2130
19 TraesCS3D01G263300 chr3B 90.000 1650 134 13 2 1634 741700708 741699073 0.000000e+00 2104
20 TraesCS3D01G263300 chr1A 89.140 1593 115 22 45 1634 405356358 405354821 0.000000e+00 1930
21 TraesCS3D01G263300 chr4D 96.092 563 21 1 2 563 22550430 22549868 0.000000e+00 917
22 TraesCS3D01G263300 chr6D 95.833 408 15 1 2066 2471 415756048 415756455 0.000000e+00 658
23 TraesCS3D01G263300 chr5D 93.103 406 22 3 2066 2471 279889232 279889631 7.620000e-165 590
24 TraesCS3D01G263300 chr5D 91.111 405 27 3 2066 2470 149654056 149654451 7.780000e-150 540


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 TraesCS3D01G263300 chr3D 365506508 365508981 2473 True 4569 4569 100.000 1 2474 1 chr3D.!!$R2 2473
1 TraesCS3D01G263300 chr7A 7721960 7724038 2078 False 3203 3203 94.570 2 2068 1 chr7A.!!$F1 2066
2 TraesCS3D01G263300 chr7A 727828386 727830445 2059 False 3079 3079 93.645 2 2067 1 chr7A.!!$F2 2065
3 TraesCS3D01G263300 chr2A 34831000 34833072 2072 False 3168 3168 94.321 2 2067 1 chr2A.!!$F1 2065
4 TraesCS3D01G263300 chr6A 94342159 94344232 2073 False 3142 3142 94.081 2 2068 1 chr6A.!!$F1 2066
5 TraesCS3D01G263300 chr5A 311291592 311293668 2076 True 3120 3120 93.867 2 2071 1 chr5A.!!$R1 2069
6 TraesCS3D01G263300 chr7D 203036827 203038661 1834 True 2939 2939 95.546 2 1840 1 chr7D.!!$R1 1838
7 TraesCS3D01G263300 chr7D 548269892 548271620 1728 True 2691 2691 94.740 1 1737 1 chr7D.!!$R4 1736
8 TraesCS3D01G263300 chr7D 505907116 505907658 542 True 691 691 90.328 1945 2468 1 chr7D.!!$R3 523
9 TraesCS3D01G263300 chr1D 464935403 464937139 1736 False 2837 2837 96.145 1 1737 1 chr1D.!!$F1 1736
10 TraesCS3D01G263300 chr2D 142521664 142523387 1723 True 2752 2752 95.394 2 1737 1 chr2D.!!$R1 1735
11 TraesCS3D01G263300 chr3A 658726294 658727946 1652 True 2516 2516 94.143 85 1737 1 chr3A.!!$R1 1652
12 TraesCS3D01G263300 chr6B 46354155 46355790 1635 False 2130 2130 90.262 4 1634 1 chr6B.!!$F1 1630
13 TraesCS3D01G263300 chr3B 741699073 741700708 1635 True 2104 2104 90.000 2 1634 1 chr3B.!!$R1 1632
14 TraesCS3D01G263300 chr1A 405354821 405356358 1537 True 1930 1930 89.140 45 1634 1 chr1A.!!$R1 1589
15 TraesCS3D01G263300 chr4D 22549868 22550430 562 True 917 917 96.092 2 563 1 chr4D.!!$R1 561

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
694 726 1.00225 CGTGCTACACCGTGTCAGTC 61.002 60.0 7.63 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2235 2519 1.068741 CCTAGGTCGTCCTATGTTGGC 59.931 57.143 8.93 0.0 44.3 4.52 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
71 72 4.180946 CGCGTCGCTACAGAGCCT 62.181 66.667 16.36 0.00 46.86 4.58
364 366 3.965258 AGCACCCCCGCATCAACA 61.965 61.111 0.00 0.00 0.00 3.33
565 589 4.794648 TGCATGGGTAGCCACCGC 62.795 66.667 23.80 23.80 46.86 5.68
692 724 1.733041 CCGTGCTACACCGTGTCAG 60.733 63.158 7.63 5.72 0.00 3.51
693 725 1.007734 CGTGCTACACCGTGTCAGT 60.008 57.895 7.63 0.00 0.00 3.41
694 726 1.002250 CGTGCTACACCGTGTCAGTC 61.002 60.000 7.63 0.00 0.00 3.51
695 727 1.002250 GTGCTACACCGTGTCAGTCG 61.002 60.000 7.63 0.00 0.00 4.18
696 728 2.087009 GCTACACCGTGTCAGTCGC 61.087 63.158 7.63 1.18 0.00 5.19
698 730 3.884581 TACACCGTGTCAGTCGCGC 62.885 63.158 7.63 0.00 46.95 6.86
778 828 4.308458 TAGCCACGCGCCACACTT 62.308 61.111 5.73 0.00 38.78 3.16
786 836 2.972505 CGCCACACTTTCGCTGGT 60.973 61.111 0.00 0.00 0.00 4.00
975 1036 1.958205 CCTACTGCTATGCGCTGCC 60.958 63.158 9.73 0.00 40.84 4.85
1068 1130 0.251653 AGTACGAGAAGGAGGTGGCA 60.252 55.000 0.00 0.00 0.00 4.92
1086 1148 1.638529 CAGAGAAGGTGTGGAGAGGT 58.361 55.000 0.00 0.00 0.00 3.85
1390 1462 0.690762 AGTACCTGCCCGTTTGTGAT 59.309 50.000 0.00 0.00 0.00 3.06
1395 1467 1.518325 CTGCCCGTTTGTGATGTGTA 58.482 50.000 0.00 0.00 0.00 2.90
1693 1973 7.411486 TTGTTTCCTAAGACAAATTGAACCA 57.589 32.000 0.00 0.00 33.19 3.67
1694 1974 7.411486 TGTTTCCTAAGACAAATTGAACCAA 57.589 32.000 0.00 0.00 0.00 3.67
1695 1975 8.017418 TGTTTCCTAAGACAAATTGAACCAAT 57.983 30.769 0.00 0.00 35.39 3.16
1696 1976 9.137459 TGTTTCCTAAGACAAATTGAACCAATA 57.863 29.630 0.00 0.00 32.43 1.90
1697 1977 9.974980 GTTTCCTAAGACAAATTGAACCAATAA 57.025 29.630 0.00 0.00 32.43 1.40
1701 1981 9.423061 CCTAAGACAAATTGAACCAATAAAAGG 57.577 33.333 0.00 0.00 32.43 3.11
1705 1985 9.710900 AGACAAATTGAACCAATAAAAGGAATC 57.289 29.630 0.00 0.00 32.43 2.52
1706 1986 8.532977 ACAAATTGAACCAATAAAAGGAATCG 57.467 30.769 0.00 0.00 32.43 3.34
1707 1987 8.364142 ACAAATTGAACCAATAAAAGGAATCGA 58.636 29.630 0.00 0.00 32.43 3.59
1708 1988 9.369904 CAAATTGAACCAATAAAAGGAATCGAT 57.630 29.630 0.00 0.00 32.43 3.59
1709 1989 9.942850 AAATTGAACCAATAAAAGGAATCGATT 57.057 25.926 11.20 11.20 32.43 3.34
1710 1990 8.931385 ATTGAACCAATAAAAGGAATCGATTG 57.069 30.769 16.96 0.00 31.77 2.67
1711 1991 7.695480 TGAACCAATAAAAGGAATCGATTGA 57.305 32.000 16.96 0.00 30.62 2.57
1712 1992 8.292444 TGAACCAATAAAAGGAATCGATTGAT 57.708 30.769 16.96 0.06 35.98 2.57
1714 1994 9.586435 GAACCAATAAAAGGAATCGATTGATTT 57.414 29.630 16.96 14.79 44.79 2.17
1715 1995 8.931385 ACCAATAAAAGGAATCGATTGATTTG 57.069 30.769 16.96 8.94 44.79 2.32
1716 1996 7.492344 ACCAATAAAAGGAATCGATTGATTTGC 59.508 33.333 16.96 0.00 44.79 3.68
1717 1997 7.492020 CCAATAAAAGGAATCGATTGATTTGCA 59.508 33.333 16.96 8.16 44.79 4.08
1718 1998 9.037737 CAATAAAAGGAATCGATTGATTTGCAT 57.962 29.630 16.96 9.83 44.79 3.96
1722 2002 9.603921 AAAAGGAATCGATTGATTTGCATAATT 57.396 25.926 16.96 0.00 44.79 1.40
1723 2003 9.603921 AAAGGAATCGATTGATTTGCATAATTT 57.396 25.926 16.96 2.14 44.79 1.82
1910 2191 5.880887 GGAGAGAAAAATAAACCGATGGACT 59.119 40.000 0.00 0.00 0.00 3.85
2048 2332 2.743636 GGAGACGATTCACCAACTCA 57.256 50.000 0.00 0.00 32.87 3.41
2095 2379 8.501580 GTGTTAAACCTACTGTATTCCAACTTC 58.498 37.037 0.00 0.00 0.00 3.01
2176 2460 6.526325 CACACGAAAAACAGAATCTGTCAAAA 59.474 34.615 17.02 0.00 44.62 2.44
2219 2503 4.748102 TCTGTAACTAACGCAAACTTCTGG 59.252 41.667 0.00 0.00 0.00 3.86
2225 2509 1.594331 ACGCAAACTTCTGGAACTCC 58.406 50.000 0.00 0.00 0.00 3.85
2226 2510 1.134220 ACGCAAACTTCTGGAACTCCA 60.134 47.619 0.00 0.00 45.30 3.86
2231 2515 4.566759 GCAAACTTCTGGAACTCCAAAAAC 59.433 41.667 0.00 0.00 46.97 2.43
2234 2518 4.855340 ACTTCTGGAACTCCAAAAACTCA 58.145 39.130 0.00 0.00 46.97 3.41
2235 2519 4.884164 ACTTCTGGAACTCCAAAAACTCAG 59.116 41.667 0.00 0.00 46.97 3.35
2240 2524 3.490933 GGAACTCCAAAAACTCAGCCAAC 60.491 47.826 0.00 0.00 35.64 3.77
2247 2531 4.321230 CCAAAAACTCAGCCAACATAGGAC 60.321 45.833 0.00 0.00 0.00 3.85
2302 2608 8.622157 TCACGTTCTGGTGATTTTTAACAATTA 58.378 29.630 0.00 0.00 41.76 1.40
2339 2645 6.982724 AGAAAGTTTCTGGAATTTTCTGCAAG 59.017 34.615 17.35 0.00 46.37 4.01
2436 2742 6.156949 ACATCTAACCAGAGGCTAGATCAAAA 59.843 38.462 6.10 0.00 38.57 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
364 366 1.888436 TTGAGGAAGACGGCAGCGAT 61.888 55.000 0.00 0.00 0.00 4.58
533 557 3.228759 GCAATGGGCATGGCGGAT 61.229 61.111 13.76 4.87 43.97 4.18
565 589 2.107141 GGGTCAATCCGAGGAGCG 59.893 66.667 0.00 0.00 40.47 5.03
749 799 1.003718 GTGGCTAGGGTGTGTGTCC 60.004 63.158 0.00 0.00 0.00 4.02
806 856 2.123425 AGCGAAGGGATAGGCGGA 60.123 61.111 0.00 0.00 0.00 5.54
975 1036 2.104331 CAGCGTACCAGCGGTAGG 59.896 66.667 17.45 17.45 44.11 3.18
1068 1130 2.291930 CCTACCTCTCCACACCTTCTCT 60.292 54.545 0.00 0.00 0.00 3.10
1086 1148 3.680196 ACCGCCCCAGACCTCCTA 61.680 66.667 0.00 0.00 0.00 2.94
1390 1462 7.517614 TTGCAAACTTTCCTAATCATACACA 57.482 32.000 0.00 0.00 0.00 3.72
1395 1467 9.995003 TTAACATTTGCAAACTTTCCTAATCAT 57.005 25.926 15.41 0.00 0.00 2.45
1668 1948 7.841956 TGGTTCAATTTGTCTTAGGAAACAAA 58.158 30.769 3.45 3.45 46.16 2.83
1669 1949 7.411486 TGGTTCAATTTGTCTTAGGAAACAA 57.589 32.000 0.00 0.00 29.84 2.83
1670 1950 7.411486 TTGGTTCAATTTGTCTTAGGAAACA 57.589 32.000 0.00 0.00 30.79 2.83
1671 1951 9.974980 TTATTGGTTCAATTTGTCTTAGGAAAC 57.025 29.630 0.00 0.00 35.54 2.78
1675 1955 9.423061 CCTTTTATTGGTTCAATTTGTCTTAGG 57.577 33.333 0.00 0.00 35.54 2.69
1679 1959 9.710900 GATTCCTTTTATTGGTTCAATTTGTCT 57.289 29.630 0.00 0.00 35.54 3.41
1680 1960 8.647226 CGATTCCTTTTATTGGTTCAATTTGTC 58.353 33.333 0.00 0.00 35.54 3.18
1681 1961 8.364142 TCGATTCCTTTTATTGGTTCAATTTGT 58.636 29.630 0.00 0.00 35.54 2.83
1682 1962 8.755696 TCGATTCCTTTTATTGGTTCAATTTG 57.244 30.769 0.00 0.00 35.54 2.32
1683 1963 9.942850 AATCGATTCCTTTTATTGGTTCAATTT 57.057 25.926 4.39 0.00 35.54 1.82
1684 1964 9.369904 CAATCGATTCCTTTTATTGGTTCAATT 57.630 29.630 7.92 0.00 35.54 2.32
1685 1965 8.748412 TCAATCGATTCCTTTTATTGGTTCAAT 58.252 29.630 7.92 0.00 37.80 2.57
1686 1966 8.116651 TCAATCGATTCCTTTTATTGGTTCAA 57.883 30.769 7.92 0.00 0.00 2.69
1687 1967 7.695480 TCAATCGATTCCTTTTATTGGTTCA 57.305 32.000 7.92 0.00 0.00 3.18
1688 1968 9.586435 AAATCAATCGATTCCTTTTATTGGTTC 57.414 29.630 7.92 0.00 41.12 3.62
1689 1969 9.369904 CAAATCAATCGATTCCTTTTATTGGTT 57.630 29.630 7.92 0.00 41.12 3.67
1690 1970 7.492344 GCAAATCAATCGATTCCTTTTATTGGT 59.508 33.333 7.92 0.00 41.12 3.67
1691 1971 7.492020 TGCAAATCAATCGATTCCTTTTATTGG 59.508 33.333 7.92 1.25 41.12 3.16
1692 1972 8.410030 TGCAAATCAATCGATTCCTTTTATTG 57.590 30.769 7.92 8.01 41.12 1.90
1696 1976 9.603921 AATTATGCAAATCAATCGATTCCTTTT 57.396 25.926 7.92 5.75 41.12 2.27
1697 1977 9.603921 AAATTATGCAAATCAATCGATTCCTTT 57.396 25.926 7.92 8.03 41.12 3.11
1742 2022 9.349713 ACAGATTTTCAGGAAACAAATAGTACA 57.650 29.630 0.00 0.00 0.00 2.90
1749 2029 9.883142 ACAAATAACAGATTTTCAGGAAACAAA 57.117 25.926 0.00 0.00 0.00 2.83
1750 2030 9.883142 AACAAATAACAGATTTTCAGGAAACAA 57.117 25.926 0.00 0.00 0.00 2.83
1751 2031 9.883142 AAACAAATAACAGATTTTCAGGAAACA 57.117 25.926 0.00 0.00 0.00 2.83
1753 2033 9.541143 GGAAACAAATAACAGATTTTCAGGAAA 57.459 29.630 0.00 0.00 0.00 3.13
1754 2034 8.923270 AGGAAACAAATAACAGATTTTCAGGAA 58.077 29.630 0.00 0.00 0.00 3.36
1755 2035 8.477419 AGGAAACAAATAACAGATTTTCAGGA 57.523 30.769 0.00 0.00 0.00 3.86
1910 2191 4.033251 CCACCCCCTCCCACCCTA 62.033 72.222 0.00 0.00 0.00 3.53
2048 2332 6.146760 ACACCAATCTCTACTCCTAATGGAT 58.853 40.000 0.00 0.00 42.29 3.41
2219 2503 3.130340 TGTTGGCTGAGTTTTTGGAGTTC 59.870 43.478 0.00 0.00 0.00 3.01
2225 2509 4.613622 CGTCCTATGTTGGCTGAGTTTTTG 60.614 45.833 0.00 0.00 0.00 2.44
2226 2510 3.502211 CGTCCTATGTTGGCTGAGTTTTT 59.498 43.478 0.00 0.00 0.00 1.94
2231 2515 1.471676 GGTCGTCCTATGTTGGCTGAG 60.472 57.143 0.00 0.00 0.00 3.35
2234 2518 2.032620 CTAGGTCGTCCTATGTTGGCT 58.967 52.381 8.93 0.00 44.30 4.75
2235 2519 1.068741 CCTAGGTCGTCCTATGTTGGC 59.931 57.143 8.93 0.00 44.30 4.52
2240 2524 3.753294 AATTGCCTAGGTCGTCCTATG 57.247 47.619 11.31 7.67 44.30 2.23
2247 2531 6.189677 TCAATAAACAAATTGCCTAGGTCG 57.810 37.500 11.31 0.00 36.89 4.79
2334 2640 8.750515 TTGGATGATAGTTATTTGATCTTGCA 57.249 30.769 0.00 0.00 0.00 4.08
2379 2685 8.900983 ATGTTTTAATTAGTGTTTGTGCCAAT 57.099 26.923 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.