Multiple sequence alignment - TraesCS7A01G141700

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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 TraesCS7A01G141700 chr7A 100.000 2468 0 0 1 2468 93063876 93066343 0.000000e+00 4558.0
1 TraesCS7A01G141700 chr7A 85.350 471 59 7 1000 1464 632966728 632967194 1.720000e-131 479.0
2 TraesCS7A01G141700 chr7D 90.360 2002 102 39 1 1960 91053771 91055723 0.000000e+00 2543.0
3 TraesCS7A01G141700 chr7D 87.500 336 36 5 2135 2468 91055980 91056311 1.380000e-102 383.0
4 TraesCS7A01G141700 chr7D 89.516 124 8 4 2046 2165 91055850 91055972 4.250000e-33 152.0
5 TraesCS7A01G141700 chr7B 87.177 1201 85 33 998 2165 43949109 43947945 0.000000e+00 1301.0
6 TraesCS7A01G141700 chr7B 91.387 952 61 14 1 944 43950128 43949190 0.000000e+00 1284.0
7 TraesCS7A01G141700 chr7B 89.351 817 35 23 1031 1842 43896940 43896171 0.000000e+00 979.0
8 TraesCS7A01G141700 chr7B 86.296 467 61 3 1000 1464 592357444 592357909 2.830000e-139 505.0
9 TraesCS7A01G141700 chr7B 84.971 346 36 7 2135 2468 43947937 43947596 1.090000e-88 337.0
10 TraesCS7A01G141700 chr7B 93.421 152 4 1 2323 2468 43889222 43889071 1.150000e-53 220.0
11 TraesCS7A01G141700 chr7B 91.139 79 2 3 2393 2468 43896036 43895960 4.340000e-18 102.0
12 TraesCS7A01G141700 chr7B 82.222 135 7 6 2048 2165 43897246 43897112 1.560000e-17 100.0
13 TraesCS7A01G141700 chr7B 100.000 41 0 0 2382 2422 43896061 43896021 2.630000e-10 76.8
14 TraesCS7A01G141700 chr1A 93.220 472 32 0 998 1469 364040178 364039707 0.000000e+00 695.0
15 TraesCS7A01G141700 chr1D 92.424 462 35 0 999 1460 291799253 291798792 0.000000e+00 660.0
16 TraesCS7A01G141700 chr1D 92.157 459 36 0 999 1457 291841763 291842221 0.000000e+00 649.0
17 TraesCS7A01G141700 chr1B 92.289 402 31 0 999 1400 392837550 392837951 2.750000e-159 571.0


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 TraesCS7A01G141700 chr7A 93063876 93066343 2467 False 4558.00 4558 100.000000 1 2468 1 chr7A.!!$F1 2467
1 TraesCS7A01G141700 chr7D 91053771 91056311 2540 False 1026.00 2543 89.125333 1 2468 3 chr7D.!!$F1 2467
2 TraesCS7A01G141700 chr7B 43947596 43950128 2532 True 974.00 1301 87.845000 1 2468 3 chr7B.!!$R3 2467
3 TraesCS7A01G141700 chr7B 43895960 43897246 1286 True 314.45 979 90.678000 1031 2468 4 chr7B.!!$R2 1437

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
976 1020 0.109226 CTTCGTCGAGGACCCAAGTC 60.109 60.0 7.43 0.0 42.73 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 1965 0.24445 AATCACCATGCGGCAGTTTG 59.756 50.0 9.25 1.54 34.57 2.93 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
35 36 5.885230 TCGATGCAAAGAACTCAATGATT 57.115 34.783 0.00 0.00 0.00 2.57
37 38 4.264614 CGATGCAAAGAACTCAATGATTGC 59.735 41.667 10.55 10.55 42.49 3.56
38 39 4.859304 TGCAAAGAACTCAATGATTGCT 57.141 36.364 16.33 0.00 42.59 3.91
156 157 1.053264 AGCAGCGGAATCAGGAGGAT 61.053 55.000 0.00 0.00 38.05 3.24
187 198 0.179189 CAATTTCAGCGGCCGAAGAC 60.179 55.000 33.48 11.55 0.00 3.01
208 219 1.300697 GAACAGTCGAAGGCACCGT 60.301 57.895 0.00 0.00 0.00 4.83
425 439 2.266055 GGGAGGCGTGGAGAAGTG 59.734 66.667 0.00 0.00 0.00 3.16
448 462 3.179830 CGAGTTCGAGATGGTTAGTTGG 58.820 50.000 0.00 0.00 43.02 3.77
575 589 2.287274 TTCGTCCCTCGCCATGGAA 61.287 57.895 18.40 0.73 39.67 3.53
576 590 2.202932 CGTCCCTCGCCATGGAAG 60.203 66.667 18.40 11.83 31.03 3.46
577 591 2.514824 GTCCCTCGCCATGGAAGC 60.515 66.667 18.40 0.00 31.03 3.86
578 592 2.688666 TCCCTCGCCATGGAAGCT 60.689 61.111 18.40 0.00 0.00 3.74
579 593 2.515523 CCCTCGCCATGGAAGCTG 60.516 66.667 18.40 4.91 0.00 4.24
581 595 3.207669 CTCGCCATGGAAGCTGCC 61.208 66.667 18.40 2.64 0.00 4.85
584 598 3.818787 GCCATGGAAGCTGCCGTG 61.819 66.667 24.66 24.66 43.20 4.94
586 600 3.136123 CATGGAAGCTGCCGTGGG 61.136 66.667 23.99 0.00 40.52 4.61
587 601 3.650950 ATGGAAGCTGCCGTGGGT 61.651 61.111 3.97 0.00 0.00 4.51
588 602 3.925630 ATGGAAGCTGCCGTGGGTG 62.926 63.158 3.97 0.00 0.00 4.61
599 613 2.931921 GTGGGTGGGTTGGAAGGT 59.068 61.111 0.00 0.00 0.00 3.50
796 823 2.317609 GCAGAGTTCGCGCAGGAAA 61.318 57.895 8.75 0.00 0.00 3.13
797 824 1.639298 GCAGAGTTCGCGCAGGAAAT 61.639 55.000 8.75 2.38 0.00 2.17
798 825 0.371645 CAGAGTTCGCGCAGGAAATC 59.628 55.000 14.87 14.87 40.34 2.17
799 826 1.078759 AGAGTTCGCGCAGGAAATCG 61.079 55.000 16.12 0.00 43.62 3.34
895 923 7.640597 TTCCATCTATATATAGTCCACACGG 57.359 40.000 17.44 9.70 0.00 4.94
911 939 1.595382 CGGCCCCATCGATCTCAAC 60.595 63.158 0.00 0.00 0.00 3.18
912 940 1.832912 GGCCCCATCGATCTCAACT 59.167 57.895 0.00 0.00 0.00 3.16
914 942 0.755686 GCCCCATCGATCTCAACTCT 59.244 55.000 0.00 0.00 0.00 3.24
918 947 3.492309 CCCCATCGATCTCAACTCTCAAG 60.492 52.174 0.00 0.00 0.00 3.02
922 951 3.579709 TCGATCTCAACTCTCAAGCAAC 58.420 45.455 0.00 0.00 0.00 4.17
929 958 4.887748 TCAACTCTCAAGCAACCTAGAAG 58.112 43.478 0.00 0.00 0.00 2.85
944 973 5.305585 ACCTAGAAGCTAGAGAGATCGAAG 58.694 45.833 0.00 0.00 0.00 3.79
946 975 3.820557 AGAAGCTAGAGAGATCGAAGCT 58.179 45.455 0.00 0.00 45.12 3.74
947 976 3.565482 AGAAGCTAGAGAGATCGAAGCTG 59.435 47.826 6.31 0.00 42.49 4.24
950 979 4.144297 AGCTAGAGAGATCGAAGCTGAAT 58.856 43.478 4.78 0.00 41.78 2.57
951 980 4.216257 AGCTAGAGAGATCGAAGCTGAATC 59.784 45.833 4.78 0.00 41.78 2.52
952 981 4.216257 GCTAGAGAGATCGAAGCTGAATCT 59.784 45.833 5.66 5.66 0.00 2.40
966 1010 3.241784 GCTGAATCTAAAGCTTCGTCGAG 59.758 47.826 0.00 0.00 36.47 4.04
967 1011 3.770666 TGAATCTAAAGCTTCGTCGAGG 58.229 45.455 0.00 0.00 0.00 4.63
968 1012 3.442625 TGAATCTAAAGCTTCGTCGAGGA 59.557 43.478 8.76 3.17 0.00 3.71
969 1013 2.915738 TCTAAAGCTTCGTCGAGGAC 57.084 50.000 7.43 0.00 0.00 3.85
970 1014 1.471684 TCTAAAGCTTCGTCGAGGACC 59.528 52.381 7.43 2.18 0.00 4.46
972 1016 1.469335 AAAGCTTCGTCGAGGACCCA 61.469 55.000 7.43 0.00 0.00 4.51
975 1019 1.965219 CTTCGTCGAGGACCCAAGT 59.035 57.895 7.43 0.00 0.00 3.16
976 1020 0.109226 CTTCGTCGAGGACCCAAGTC 60.109 60.000 7.43 0.00 42.73 3.01
977 1021 0.538977 TTCGTCGAGGACCCAAGTCT 60.539 55.000 7.43 0.00 43.05 3.24
978 1022 0.538977 TCGTCGAGGACCCAAGTCTT 60.539 55.000 3.17 0.00 43.05 3.01
979 1023 0.388649 CGTCGAGGACCCAAGTCTTG 60.389 60.000 5.53 5.53 43.05 3.02
980 1024 0.680061 GTCGAGGACCCAAGTCTTGT 59.320 55.000 11.61 0.00 43.05 3.16
981 1025 1.891150 GTCGAGGACCCAAGTCTTGTA 59.109 52.381 11.61 0.00 43.05 2.41
983 1027 1.067071 CGAGGACCCAAGTCTTGTACC 60.067 57.143 11.61 10.77 43.05 3.34
984 1028 2.258109 GAGGACCCAAGTCTTGTACCT 58.742 52.381 16.84 16.84 43.05 3.08
985 1029 2.234168 GAGGACCCAAGTCTTGTACCTC 59.766 54.545 22.30 22.30 43.05 3.85
986 1030 1.067071 GGACCCAAGTCTTGTACCTCG 60.067 57.143 11.61 0.00 43.05 4.63
988 1032 0.391263 CCCAAGTCTTGTACCTCGCC 60.391 60.000 11.61 0.00 0.00 5.54
989 1033 0.608640 CCAAGTCTTGTACCTCGCCT 59.391 55.000 11.61 0.00 0.00 5.52
990 1034 1.002087 CCAAGTCTTGTACCTCGCCTT 59.998 52.381 11.61 0.00 0.00 4.35
991 1035 2.550208 CCAAGTCTTGTACCTCGCCTTT 60.550 50.000 11.61 0.00 0.00 3.11
992 1036 2.457366 AGTCTTGTACCTCGCCTTTG 57.543 50.000 0.00 0.00 0.00 2.77
993 1037 1.968493 AGTCTTGTACCTCGCCTTTGA 59.032 47.619 0.00 0.00 0.00 2.69
994 1038 2.028930 AGTCTTGTACCTCGCCTTTGAG 60.029 50.000 0.00 0.00 35.70 3.02
1200 1256 1.515304 GCAGAAGGAGTCGACGCTC 60.515 63.158 18.88 9.63 34.89 5.03
1267 1323 1.900351 CTCACCGGCAAGGAGATCA 59.100 57.895 0.00 0.00 45.00 2.92
1270 1326 0.745845 CACCGGCAAGGAGATCAAGG 60.746 60.000 0.00 0.00 45.00 3.61
1471 1527 1.336056 GCGGTGCCTGCTACTAGATAC 60.336 57.143 0.00 0.00 0.00 2.24
1474 1530 3.756963 CGGTGCCTGCTACTAGATACATA 59.243 47.826 0.00 0.00 0.00 2.29
1476 1532 4.523173 GGTGCCTGCTACTAGATACATACA 59.477 45.833 0.00 0.00 0.00 2.29
1477 1533 5.336055 GGTGCCTGCTACTAGATACATACAG 60.336 48.000 0.00 0.00 0.00 2.74
1478 1534 5.241949 GTGCCTGCTACTAGATACATACAGT 59.758 44.000 0.00 0.00 0.00 3.55
1479 1535 5.473846 TGCCTGCTACTAGATACATACAGTC 59.526 44.000 0.00 0.00 0.00 3.51
1480 1536 5.708230 GCCTGCTACTAGATACATACAGTCT 59.292 44.000 0.00 0.00 0.00 3.24
1539 1599 9.387257 GCTAGGGTTTAGCTGTAGTTTTTATAA 57.613 33.333 0.00 0.00 37.56 0.98
1666 1727 3.873361 TGTAAGCTGCAATGCTGTATCTC 59.127 43.478 13.44 0.00 43.24 2.75
1687 1748 3.894427 TCTGCATCTTTTTGCTACCCAAA 59.106 39.130 0.00 0.00 43.18 3.28
1695 1757 1.604604 TTGCTACCCAAACACTGCTC 58.395 50.000 0.00 0.00 0.00 4.26
1696 1758 0.764890 TGCTACCCAAACACTGCTCT 59.235 50.000 0.00 0.00 0.00 4.09
1707 1769 0.100682 CACTGCTCTCATTGCATGCC 59.899 55.000 16.68 0.00 39.86 4.40
1708 1770 1.355563 CTGCTCTCATTGCATGCCG 59.644 57.895 16.68 3.68 39.86 5.69
1720 1782 0.590732 GCATGCCGAAATGAGAAGCG 60.591 55.000 6.36 0.00 0.00 4.68
1823 1890 5.103687 GGGAAACACTTCTTCTAGATCGAC 58.896 45.833 0.00 0.00 0.00 4.20
1824 1891 5.105675 GGGAAACACTTCTTCTAGATCGACT 60.106 44.000 0.00 0.00 0.00 4.18
1825 1892 5.802956 GGAAACACTTCTTCTAGATCGACTG 59.197 44.000 0.00 0.00 0.00 3.51
1826 1893 6.349445 GGAAACACTTCTTCTAGATCGACTGA 60.349 42.308 0.00 0.00 0.00 3.41
1838 1905 4.030134 GATCGACTGATCTTTACACCGT 57.970 45.455 0.00 0.00 46.22 4.83
1839 1906 3.482722 TCGACTGATCTTTACACCGTC 57.517 47.619 0.00 0.00 0.00 4.79
1840 1907 3.079578 TCGACTGATCTTTACACCGTCT 58.920 45.455 0.00 0.00 0.00 4.18
1841 1908 3.126514 TCGACTGATCTTTACACCGTCTC 59.873 47.826 0.00 0.00 0.00 3.36
1842 1909 3.427243 GACTGATCTTTACACCGTCTCG 58.573 50.000 0.00 0.00 0.00 4.04
1854 1921 3.519930 GTCTCGGCGTCTCCCCTC 61.520 72.222 6.85 0.00 0.00 4.30
1925 1995 2.789208 CATGGTGATTTGCGTGATGAC 58.211 47.619 0.00 0.00 0.00 3.06
1940 2010 0.179004 ATGACGTGAACCAAAGGCCA 60.179 50.000 5.01 0.00 0.00 5.36
1944 2014 0.667184 CGTGAACCAAAGGCCAATGC 60.667 55.000 5.01 0.00 0.00 3.56
1946 2016 1.892474 GTGAACCAAAGGCCAATGCTA 59.108 47.619 5.01 0.00 37.74 3.49
1947 2017 2.094545 GTGAACCAAAGGCCAATGCTAG 60.095 50.000 5.01 0.00 37.74 3.42
1960 2030 4.201990 GCCAATGCTAGGAAACTGAAGATG 60.202 45.833 0.00 0.00 43.88 2.90
1961 2031 5.188434 CCAATGCTAGGAAACTGAAGATGA 58.812 41.667 0.00 0.00 43.88 2.92
1963 2033 6.320672 CCAATGCTAGGAAACTGAAGATGAAT 59.679 38.462 0.00 0.00 43.88 2.57
2004 2157 8.070171 GTGTATTGTGAGTGTGATTTATATGGC 58.930 37.037 0.00 0.00 0.00 4.40
2005 2158 7.992608 TGTATTGTGAGTGTGATTTATATGGCT 59.007 33.333 0.00 0.00 0.00 4.75
2006 2159 7.886629 ATTGTGAGTGTGATTTATATGGCTT 57.113 32.000 0.00 0.00 0.00 4.35
2007 2160 8.978874 ATTGTGAGTGTGATTTATATGGCTTA 57.021 30.769 0.00 0.00 0.00 3.09
2008 2161 8.978874 TTGTGAGTGTGATTTATATGGCTTAT 57.021 30.769 0.00 0.00 0.00 1.73
2010 2163 9.710900 TGTGAGTGTGATTTATATGGCTTATAG 57.289 33.333 1.06 0.00 0.00 1.31
2011 2164 9.712305 GTGAGTGTGATTTATATGGCTTATAGT 57.288 33.333 1.06 0.00 0.00 2.12
2021 2174 8.842358 TTATATGGCTTATAGTAGTTGTTGCC 57.158 34.615 0.00 0.00 39.53 4.52
2022 2175 4.561500 TGGCTTATAGTAGTTGTTGCCA 57.438 40.909 0.00 0.00 45.51 4.92
2023 2176 4.513442 TGGCTTATAGTAGTTGTTGCCAG 58.487 43.478 0.00 0.00 43.29 4.85
2024 2177 3.312697 GGCTTATAGTAGTTGTTGCCAGC 59.687 47.826 0.00 0.00 38.99 4.85
2025 2178 3.312697 GCTTATAGTAGTTGTTGCCAGCC 59.687 47.826 0.00 0.00 0.00 4.85
2026 2179 4.770795 CTTATAGTAGTTGTTGCCAGCCT 58.229 43.478 0.00 0.00 0.00 4.58
2027 2180 2.472695 TAGTAGTTGTTGCCAGCCTG 57.527 50.000 0.00 0.00 0.00 4.85
2028 2181 0.250901 AGTAGTTGTTGCCAGCCTGG 60.251 55.000 6.32 6.32 41.55 4.45
2029 2182 0.537371 GTAGTTGTTGCCAGCCTGGT 60.537 55.000 13.35 0.00 40.46 4.00
2030 2183 0.184933 TAGTTGTTGCCAGCCTGGTT 59.815 50.000 13.35 0.00 40.46 3.67
2031 2184 1.109323 AGTTGTTGCCAGCCTGGTTC 61.109 55.000 13.35 3.95 40.46 3.62
2032 2185 1.076412 TTGTTGCCAGCCTGGTTCA 60.076 52.632 13.35 6.58 40.46 3.18
2033 2186 1.108727 TTGTTGCCAGCCTGGTTCAG 61.109 55.000 13.35 0.00 40.46 3.02
2034 2187 1.529244 GTTGCCAGCCTGGTTCAGT 60.529 57.895 13.35 0.00 40.46 3.41
2035 2188 1.109323 GTTGCCAGCCTGGTTCAGTT 61.109 55.000 13.35 0.00 40.46 3.16
2036 2189 1.108727 TTGCCAGCCTGGTTCAGTTG 61.109 55.000 13.35 0.00 40.46 3.16
2037 2190 1.529244 GCCAGCCTGGTTCAGTTGT 60.529 57.895 13.35 0.00 40.46 3.32
2038 2191 1.109323 GCCAGCCTGGTTCAGTTGTT 61.109 55.000 13.35 0.00 40.46 2.83
2039 2192 1.402787 CCAGCCTGGTTCAGTTGTTT 58.597 50.000 1.39 0.00 31.35 2.83
2040 2193 1.067516 CCAGCCTGGTTCAGTTGTTTG 59.932 52.381 1.39 0.00 31.35 2.93
2041 2194 0.746659 AGCCTGGTTCAGTTGTTTGC 59.253 50.000 0.00 0.00 0.00 3.68
2042 2195 0.459489 GCCTGGTTCAGTTGTTTGCA 59.541 50.000 0.00 0.00 0.00 4.08
2043 2196 1.134848 GCCTGGTTCAGTTGTTTGCAA 60.135 47.619 0.00 0.00 0.00 4.08
2044 2197 2.676463 GCCTGGTTCAGTTGTTTGCAAA 60.676 45.455 8.05 8.05 36.22 3.68
2045 2198 3.189285 CCTGGTTCAGTTGTTTGCAAAG 58.811 45.455 13.26 0.01 36.22 2.77
2053 2206 4.100529 CAGTTGTTTGCAAAGTGAGACAG 58.899 43.478 13.26 0.87 36.22 3.51
2057 2210 5.384063 TGTTTGCAAAGTGAGACAGAAAA 57.616 34.783 13.26 0.00 0.00 2.29
2065 2218 6.414987 GCAAAGTGAGACAGAAAATGTTGTAC 59.585 38.462 0.00 0.00 44.17 2.90
2066 2219 7.679638 GCAAAGTGAGACAGAAAATGTTGTACT 60.680 37.037 0.00 0.00 44.17 2.73
2067 2220 7.484035 AAGTGAGACAGAAAATGTTGTACTC 57.516 36.000 0.00 0.00 44.17 2.59
2086 2239 6.656270 TGTACTCAATGCTCTGAAATGAATGT 59.344 34.615 0.00 0.00 0.00 2.71
2115 2281 7.756722 AGTCTGAACTTTGTTCTGAATTTGTTG 59.243 33.333 17.22 0.00 28.74 3.33
2148 2314 6.058183 AGTTCTATGTTTCAGTTTGCAGAGT 58.942 36.000 0.00 0.00 0.00 3.24
2158 2366 5.733676 TCAGTTTGCAGAGTTATGCTCATA 58.266 37.500 0.14 0.00 46.63 2.15
2159 2367 5.814188 TCAGTTTGCAGAGTTATGCTCATAG 59.186 40.000 0.14 0.00 46.63 2.23
2181 2389 2.352960 GCTGAGGTGAGCCGAAAATTAG 59.647 50.000 0.00 0.00 40.50 1.73
2185 2394 4.162320 TGAGGTGAGCCGAAAATTAGAGAT 59.838 41.667 0.00 0.00 40.50 2.75
2209 2418 2.968574 TGGCTCCTGATAGTGATCCTTC 59.031 50.000 0.00 0.00 0.00 3.46
2212 2421 3.057596 GCTCCTGATAGTGATCCTTCGAG 60.058 52.174 0.00 0.00 0.00 4.04
2218 2427 4.895889 TGATAGTGATCCTTCGAGGTGAAT 59.104 41.667 0.00 0.00 36.53 2.57
2219 2428 6.068670 TGATAGTGATCCTTCGAGGTGAATA 58.931 40.000 0.00 0.00 36.53 1.75
2222 2431 5.144100 AGTGATCCTTCGAGGTGAATAGAT 58.856 41.667 0.00 0.00 36.53 1.98
2251 2460 3.471680 AGAAAGAGAGCAAACTGGACAC 58.528 45.455 0.00 0.00 0.00 3.67
2267 2477 4.127171 TGGACACTTTTACACTTCAGAGC 58.873 43.478 0.00 0.00 0.00 4.09
2271 2481 5.186198 ACACTTTTACACTTCAGAGCAACT 58.814 37.500 0.00 0.00 0.00 3.16
2304 2523 4.513318 AGACACTAGTTCAGCAAAAGCTTC 59.487 41.667 0.00 0.00 0.00 3.86
2305 2524 4.199310 ACACTAGTTCAGCAAAAGCTTCA 58.801 39.130 0.00 0.00 0.00 3.02
2306 2525 4.823989 ACACTAGTTCAGCAAAAGCTTCAT 59.176 37.500 0.00 0.00 0.00 2.57
2307 2526 5.300286 ACACTAGTTCAGCAAAAGCTTCATT 59.700 36.000 0.00 0.00 0.00 2.57
2308 2527 6.183360 ACACTAGTTCAGCAAAAGCTTCATTT 60.183 34.615 0.00 0.00 0.00 2.32
2311 2530 8.413229 ACTAGTTCAGCAAAAGCTTCATTTTTA 58.587 29.630 0.00 0.00 30.01 1.52
2312 2531 7.468922 AGTTCAGCAAAAGCTTCATTTTTAC 57.531 32.000 0.00 0.00 30.01 2.01
2313 2532 6.479990 AGTTCAGCAAAAGCTTCATTTTTACC 59.520 34.615 0.00 0.00 30.01 2.85
2314 2533 5.911752 TCAGCAAAAGCTTCATTTTTACCA 58.088 33.333 0.00 0.00 30.01 3.25
2315 2534 6.344500 TCAGCAAAAGCTTCATTTTTACCAA 58.656 32.000 0.00 0.00 30.01 3.67
2316 2535 6.257630 TCAGCAAAAGCTTCATTTTTACCAAC 59.742 34.615 0.00 0.00 30.01 3.77
2317 2536 6.036953 CAGCAAAAGCTTCATTTTTACCAACA 59.963 34.615 0.00 0.00 30.01 3.33
2318 2537 6.597280 AGCAAAAGCTTCATTTTTACCAACAA 59.403 30.769 0.00 0.00 30.01 2.83
2319 2538 6.686679 GCAAAAGCTTCATTTTTACCAACAAC 59.313 34.615 0.00 0.00 30.01 3.32
2323 2542 6.402222 AGCTTCATTTTTACCAACAACAACA 58.598 32.000 0.00 0.00 0.00 3.33
2326 2545 8.017946 GCTTCATTTTTACCAACAACAACAAAA 58.982 29.630 0.00 0.00 0.00 2.44
2380 2599 1.263484 TCATTTTGCGCGTTTTCGGTA 59.737 42.857 8.43 0.00 44.29 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.521639 AGAGCAATCATTGAGTTCTTTGCA 59.478 37.500 18.90 0.00 41.33 4.08
37 38 2.825836 GCCGGGACATTGCCAGAG 60.826 66.667 2.18 0.00 0.00 3.35
38 39 2.497792 ATTGCCGGGACATTGCCAGA 62.498 55.000 2.18 0.00 0.00 3.86
156 157 3.301706 GCTGAAATTGCGTTCCGTTTTA 58.698 40.909 0.00 0.00 0.00 1.52
187 198 0.868406 GGTGCCTTCGACTGTTCTTG 59.132 55.000 0.00 0.00 0.00 3.02
208 219 2.203640 AGGTCCGACAGAGTGCCA 60.204 61.111 0.00 0.00 0.00 4.92
409 423 2.435059 GCACTTCTCCACGCCTCC 60.435 66.667 0.00 0.00 0.00 4.30
425 439 1.134560 ACTAACCATCTCGAACTCGGC 59.865 52.381 0.00 0.00 40.29 5.54
579 593 4.589675 TTCCAACCCACCCACGGC 62.590 66.667 0.00 0.00 0.00 5.68
581 595 2.282180 CCTTCCAACCCACCCACG 60.282 66.667 0.00 0.00 0.00 4.94
582 596 1.530655 CACCTTCCAACCCACCCAC 60.531 63.158 0.00 0.00 0.00 4.61
583 597 2.931107 CACCTTCCAACCCACCCA 59.069 61.111 0.00 0.00 0.00 4.51
584 598 2.600470 GCACCTTCCAACCCACCC 60.600 66.667 0.00 0.00 0.00 4.61
585 599 1.903404 CTGCACCTTCCAACCCACC 60.903 63.158 0.00 0.00 0.00 4.61
586 600 1.152756 ACTGCACCTTCCAACCCAC 60.153 57.895 0.00 0.00 0.00 4.61
587 601 1.152777 CACTGCACCTTCCAACCCA 60.153 57.895 0.00 0.00 0.00 4.51
588 602 1.903404 CCACTGCACCTTCCAACCC 60.903 63.158 0.00 0.00 0.00 4.11
599 613 2.603473 AGCCGTACCTCCACTGCA 60.603 61.111 0.00 0.00 31.73 4.41
796 823 1.596203 CTGCGGTGCCATGATCGAT 60.596 57.895 0.00 0.00 0.00 3.59
797 824 2.202919 CTGCGGTGCCATGATCGA 60.203 61.111 0.00 0.00 0.00 3.59
798 825 3.274586 CCTGCGGTGCCATGATCG 61.275 66.667 0.00 0.00 0.00 3.69
799 826 2.687418 ATCCCTGCGGTGCCATGATC 62.687 60.000 0.00 0.00 0.00 2.92
870 898 7.682261 GCCGTGTGGACTATATATAGATGGAAG 60.682 44.444 23.70 10.35 37.49 3.46
895 923 0.755686 AGAGTTGAGATCGATGGGGC 59.244 55.000 0.54 0.00 0.00 5.80
911 939 3.608316 AGCTTCTAGGTTGCTTGAGAG 57.392 47.619 0.00 0.00 32.61 3.20
912 940 4.344978 TCTAGCTTCTAGGTTGCTTGAGA 58.655 43.478 9.55 5.92 38.15 3.27
914 942 4.344978 TCTCTAGCTTCTAGGTTGCTTGA 58.655 43.478 9.55 11.28 38.15 3.02
918 947 4.320202 CGATCTCTCTAGCTTCTAGGTTGC 60.320 50.000 0.00 0.00 0.00 4.17
922 951 4.154195 GCTTCGATCTCTCTAGCTTCTAGG 59.846 50.000 0.00 0.00 0.00 3.02
929 958 3.980646 TTCAGCTTCGATCTCTCTAGC 57.019 47.619 0.00 0.00 0.00 3.42
944 973 3.179830 TCGACGAAGCTTTAGATTCAGC 58.820 45.455 0.00 0.00 40.19 4.26
946 975 3.442625 TCCTCGACGAAGCTTTAGATTCA 59.557 43.478 0.00 0.00 40.19 2.57
947 976 3.792421 GTCCTCGACGAAGCTTTAGATTC 59.208 47.826 0.00 0.00 37.12 2.52
950 979 1.471684 GGTCCTCGACGAAGCTTTAGA 59.528 52.381 0.00 0.00 32.65 2.10
951 980 1.469423 GGGTCCTCGACGAAGCTTTAG 60.469 57.143 0.00 0.26 32.65 1.85
952 981 0.529378 GGGTCCTCGACGAAGCTTTA 59.471 55.000 0.00 0.00 32.65 1.85
959 1003 0.538977 AAGACTTGGGTCCTCGACGA 60.539 55.000 0.00 0.00 43.05 4.20
966 1010 1.067071 CGAGGTACAAGACTTGGGTCC 60.067 57.143 19.16 16.08 43.05 4.46
967 1011 1.672145 GCGAGGTACAAGACTTGGGTC 60.672 57.143 19.16 8.72 42.41 4.46
968 1012 0.320697 GCGAGGTACAAGACTTGGGT 59.679 55.000 19.16 1.97 34.12 4.51
969 1013 0.391263 GGCGAGGTACAAGACTTGGG 60.391 60.000 19.16 0.00 34.12 4.12
970 1014 0.608640 AGGCGAGGTACAAGACTTGG 59.391 55.000 19.16 1.67 34.12 3.61
972 1016 2.367567 TCAAAGGCGAGGTACAAGACTT 59.632 45.455 0.00 0.00 36.95 3.01
975 1019 2.244695 TCTCAAAGGCGAGGTACAAGA 58.755 47.619 0.00 0.00 33.59 3.02
976 1020 2.743636 TCTCAAAGGCGAGGTACAAG 57.256 50.000 0.00 0.00 33.59 3.16
977 1021 3.478857 TTTCTCAAAGGCGAGGTACAA 57.521 42.857 0.00 0.00 33.59 2.41
978 1022 3.070446 TCTTTTCTCAAAGGCGAGGTACA 59.930 43.478 0.00 0.00 40.08 2.90
979 1023 3.660865 TCTTTTCTCAAAGGCGAGGTAC 58.339 45.455 0.00 0.00 40.08 3.34
980 1024 4.253685 CATCTTTTCTCAAAGGCGAGGTA 58.746 43.478 0.00 0.00 40.08 3.08
981 1025 2.930826 TCTTTTCTCAAAGGCGAGGT 57.069 45.000 0.00 0.00 40.08 3.85
983 1027 2.485426 TGCATCTTTTCTCAAAGGCGAG 59.515 45.455 0.00 0.00 40.08 5.03
984 1028 2.485426 CTGCATCTTTTCTCAAAGGCGA 59.515 45.455 0.00 0.00 40.08 5.54
985 1029 2.485426 TCTGCATCTTTTCTCAAAGGCG 59.515 45.455 0.00 0.00 40.08 5.52
986 1030 4.398673 AGATCTGCATCTTTTCTCAAAGGC 59.601 41.667 0.00 0.00 40.08 4.35
1267 1323 0.388649 GTGTGCTCGATGTCGACCTT 60.389 55.000 14.12 0.00 44.22 3.50
1270 1326 2.152699 CGGTGTGCTCGATGTCGAC 61.153 63.158 9.11 9.11 44.22 4.20
1471 1527 5.579511 CGTAGGTAAAACCCAAGACTGTATG 59.420 44.000 0.00 0.00 39.75 2.39
1474 1530 3.642848 TCGTAGGTAAAACCCAAGACTGT 59.357 43.478 0.00 0.00 39.75 3.55
1476 1532 4.154942 TCTCGTAGGTAAAACCCAAGACT 58.845 43.478 0.00 0.00 39.75 3.24
1477 1533 4.492611 CTCTCGTAGGTAAAACCCAAGAC 58.507 47.826 0.00 0.00 39.75 3.01
1478 1534 3.056322 GCTCTCGTAGGTAAAACCCAAGA 60.056 47.826 0.00 0.00 39.75 3.02
1479 1535 3.056035 AGCTCTCGTAGGTAAAACCCAAG 60.056 47.826 0.00 0.00 39.75 3.61
1480 1536 2.901839 AGCTCTCGTAGGTAAAACCCAA 59.098 45.455 0.00 0.00 39.75 4.12
1564 1624 7.418840 AACCATTACGTAACAATGTTCGTAA 57.581 32.000 27.65 27.65 46.97 3.18
1565 1625 7.418840 AAACCATTACGTAACAATGTTCGTA 57.581 32.000 19.06 19.06 37.66 3.43
1566 1626 5.927954 AACCATTACGTAACAATGTTCGT 57.072 34.783 20.52 20.52 39.74 3.85
1707 1769 6.516478 TTCATATCTTCGCTTCTCATTTCG 57.484 37.500 0.00 0.00 0.00 3.46
1742 1805 1.067915 TCACGCAAGGCTATTTTTGGC 60.068 47.619 0.00 0.00 46.39 4.52
1823 1890 2.798680 CCGAGACGGTGTAAAGATCAG 58.201 52.381 1.80 0.00 42.73 2.90
1824 1891 2.933495 CCGAGACGGTGTAAAGATCA 57.067 50.000 1.80 0.00 42.73 2.92
1843 1910 4.131088 GTGTCCGAGGGGAGACGC 62.131 72.222 0.00 0.00 45.47 5.19
1854 1921 5.348997 GGTAGAAGAGAGATTTTTGTGTCCG 59.651 44.000 0.00 0.00 0.00 4.79
1886 1956 2.197324 GGCAGTTTGGTGGGGTGA 59.803 61.111 0.00 0.00 0.00 4.02
1887 1957 3.294493 CGGCAGTTTGGTGGGGTG 61.294 66.667 0.00 0.00 0.00 4.61
1890 1960 2.990967 ATGCGGCAGTTTGGTGGG 60.991 61.111 9.25 0.00 0.00 4.61
1891 1961 2.259204 CATGCGGCAGTTTGGTGG 59.741 61.111 9.25 0.00 0.00 4.61
1892 1962 2.259204 CCATGCGGCAGTTTGGTG 59.741 61.111 9.25 0.00 0.00 4.17
1893 1963 2.203480 ACCATGCGGCAGTTTGGT 60.203 55.556 18.51 18.51 37.64 3.67
1894 1964 1.597797 ATCACCATGCGGCAGTTTGG 61.598 55.000 17.30 17.30 34.57 3.28
1895 1965 0.244450 AATCACCATGCGGCAGTTTG 59.756 50.000 9.25 1.54 34.57 2.93
1896 1966 0.968405 AAATCACCATGCGGCAGTTT 59.032 45.000 9.25 0.22 34.57 2.66
1897 1967 0.244450 CAAATCACCATGCGGCAGTT 59.756 50.000 9.25 0.00 34.57 3.16
1925 1995 0.667184 GCATTGGCCTTTGGTTCACG 60.667 55.000 3.32 0.00 0.00 4.35
1928 1998 1.478105 CCTAGCATTGGCCTTTGGTTC 59.522 52.381 14.02 0.00 42.56 3.62
1933 2003 2.827921 CAGTTTCCTAGCATTGGCCTTT 59.172 45.455 3.32 0.00 42.56 3.11
1940 2010 9.466497 TTTATTCATCTTCAGTTTCCTAGCATT 57.534 29.630 0.00 0.00 0.00 3.56
1961 2031 9.912634 CACAATACACAGGAACTTGAATTTATT 57.087 29.630 0.00 0.00 34.60 1.40
1963 2033 8.684386 TCACAATACACAGGAACTTGAATTTA 57.316 30.769 0.00 0.00 34.60 1.40
1978 2131 8.070171 GCCATATAAATCACACTCACAATACAC 58.930 37.037 0.00 0.00 0.00 2.90
2014 2167 3.760261 ACTGAACCAGGCTGGCAACAA 62.760 52.381 33.04 13.45 42.67 2.83
2015 2168 2.283143 ACTGAACCAGGCTGGCAACA 62.283 55.000 33.04 25.73 42.67 3.33
2016 2169 1.109323 AACTGAACCAGGCTGGCAAC 61.109 55.000 33.04 22.81 42.67 4.17
2017 2170 1.108727 CAACTGAACCAGGCTGGCAA 61.109 55.000 33.04 17.42 42.67 4.52
2018 2171 1.529010 CAACTGAACCAGGCTGGCA 60.529 57.895 33.04 21.88 42.67 4.92
2019 2172 1.109323 AACAACTGAACCAGGCTGGC 61.109 55.000 33.04 18.32 42.67 4.85
2020 2173 1.067516 CAAACAACTGAACCAGGCTGG 59.932 52.381 31.62 31.62 45.02 4.85
2021 2174 1.536709 GCAAACAACTGAACCAGGCTG 60.537 52.381 7.75 7.75 35.51 4.85
2022 2175 0.746659 GCAAACAACTGAACCAGGCT 59.253 50.000 0.00 0.00 35.51 4.58
2023 2176 0.459489 TGCAAACAACTGAACCAGGC 59.541 50.000 0.00 0.00 35.51 4.85
2024 2177 2.957491 TTGCAAACAACTGAACCAGG 57.043 45.000 0.00 0.00 35.51 4.45
2025 2178 3.613737 CACTTTGCAAACAACTGAACCAG 59.386 43.478 8.05 0.00 34.87 4.00
2026 2179 3.256879 TCACTTTGCAAACAACTGAACCA 59.743 39.130 8.05 0.00 34.87 3.67
2027 2180 3.843999 TCACTTTGCAAACAACTGAACC 58.156 40.909 8.05 0.00 34.87 3.62
2028 2181 4.558860 GTCTCACTTTGCAAACAACTGAAC 59.441 41.667 8.05 4.96 34.87 3.18
2029 2182 4.217334 TGTCTCACTTTGCAAACAACTGAA 59.783 37.500 8.05 0.00 34.87 3.02
2030 2183 3.755905 TGTCTCACTTTGCAAACAACTGA 59.244 39.130 8.05 5.94 34.87 3.41
2031 2184 4.095410 TGTCTCACTTTGCAAACAACTG 57.905 40.909 8.05 0.37 34.87 3.16
2032 2185 4.009675 TCTGTCTCACTTTGCAAACAACT 58.990 39.130 8.05 0.00 34.87 3.16
2033 2186 4.355543 TCTGTCTCACTTTGCAAACAAC 57.644 40.909 8.05 3.11 34.87 3.32
2034 2187 5.384063 TTTCTGTCTCACTTTGCAAACAA 57.616 34.783 8.05 0.00 0.00 2.83
2035 2188 5.384063 TTTTCTGTCTCACTTTGCAAACA 57.616 34.783 8.05 3.36 0.00 2.83
2036 2189 5.807011 ACATTTTCTGTCTCACTTTGCAAAC 59.193 36.000 8.05 0.00 29.94 2.93
2037 2190 5.964758 ACATTTTCTGTCTCACTTTGCAAA 58.035 33.333 12.14 12.14 29.94 3.68
2038 2191 5.581126 ACATTTTCTGTCTCACTTTGCAA 57.419 34.783 0.00 0.00 29.94 4.08
2039 2192 5.105797 ACAACATTTTCTGTCTCACTTTGCA 60.106 36.000 0.00 0.00 36.98 4.08
2040 2193 5.343249 ACAACATTTTCTGTCTCACTTTGC 58.657 37.500 0.00 0.00 36.98 3.68
2041 2194 7.697691 AGTACAACATTTTCTGTCTCACTTTG 58.302 34.615 0.00 0.00 36.98 2.77
2042 2195 7.552687 TGAGTACAACATTTTCTGTCTCACTTT 59.447 33.333 0.00 0.00 36.98 2.66
2043 2196 7.047891 TGAGTACAACATTTTCTGTCTCACTT 58.952 34.615 0.00 0.00 36.98 3.16
2044 2197 6.582636 TGAGTACAACATTTTCTGTCTCACT 58.417 36.000 0.00 0.00 36.98 3.41
2045 2198 6.844696 TGAGTACAACATTTTCTGTCTCAC 57.155 37.500 0.00 0.00 36.98 3.51
2053 2206 6.902341 TCAGAGCATTGAGTACAACATTTTC 58.098 36.000 0.00 0.00 38.90 2.29
2057 2210 6.656270 TCATTTCAGAGCATTGAGTACAACAT 59.344 34.615 0.00 0.00 38.90 2.71
2065 2218 8.242053 ACTTTACATTCATTTCAGAGCATTGAG 58.758 33.333 0.00 0.00 0.00 3.02
2066 2219 8.114331 ACTTTACATTCATTTCAGAGCATTGA 57.886 30.769 0.00 0.00 0.00 2.57
2067 2220 8.242053 AGACTTTACATTCATTTCAGAGCATTG 58.758 33.333 0.00 0.00 0.00 2.82
2102 2255 2.957680 TGAGCAGGCAACAAATTCAGAA 59.042 40.909 0.00 0.00 41.41 3.02
2115 2281 3.753272 TGAAACATAGAACTTGAGCAGGC 59.247 43.478 0.00 0.00 0.00 4.85
2170 2378 3.879892 AGCCAAGATCTCTAATTTTCGGC 59.120 43.478 0.00 0.00 36.04 5.54
2172 2380 5.236047 CAGGAGCCAAGATCTCTAATTTTCG 59.764 44.000 0.00 0.00 0.00 3.46
2173 2381 6.352516 TCAGGAGCCAAGATCTCTAATTTTC 58.647 40.000 0.00 0.00 0.00 2.29
2181 2389 3.894427 TCACTATCAGGAGCCAAGATCTC 59.106 47.826 0.00 0.00 0.00 2.75
2185 2394 2.968574 GGATCACTATCAGGAGCCAAGA 59.031 50.000 0.00 0.00 39.36 3.02
2219 2428 9.294614 AGTTTGCTCTCTTTCTTTGAATTATCT 57.705 29.630 0.00 0.00 0.00 1.98
2222 2431 7.502226 TCCAGTTTGCTCTCTTTCTTTGAATTA 59.498 33.333 0.00 0.00 0.00 1.40
2231 2440 3.471680 AGTGTCCAGTTTGCTCTCTTTC 58.528 45.455 0.00 0.00 0.00 2.62
2251 2460 5.277538 GGTGAGTTGCTCTGAAGTGTAAAAG 60.278 44.000 0.00 0.00 0.00 2.27
2267 2477 1.069823 AGTGTCTGAGCTGGTGAGTTG 59.930 52.381 0.00 0.00 0.00 3.16
2271 2481 2.294449 ACTAGTGTCTGAGCTGGTGA 57.706 50.000 0.00 0.00 0.00 4.02
2344 2563 8.170553 GCGCAAAATGAAGTGAAAATGAAATAT 58.829 29.630 0.30 0.00 0.00 1.28
2377 2596 2.147958 TGAAACCGACACTTGCATACC 58.852 47.619 0.00 0.00 0.00 2.73
2380 2599 1.967319 ACTGAAACCGACACTTGCAT 58.033 45.000 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.