Multiple sequence alignment - TraesCS7A01G261400

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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 TraesCS7A01G261400 chr7A 100.000 2912 0 0 1 2912 255889373 255886462 0.000000e+00 5378
1 TraesCS7A01G261400 chr7A 97.512 1608 39 1 360 1966 32589644 32588037 0.000000e+00 2747
2 TraesCS7A01G261400 chr7A 86.457 1942 238 16 4 1928 88959661 88957728 0.000000e+00 2106
3 TraesCS7A01G261400 chr7A 86.354 1942 240 16 4 1928 722320039 722318106 0.000000e+00 2095
4 TraesCS7A01G261400 chr7A 87.089 883 100 10 1097 1966 171878764 171877883 0.000000e+00 987
5 TraesCS7A01G261400 chr6B 96.599 1970 58 4 1 1966 610805864 610807828 0.000000e+00 3258
6 TraesCS7A01G261400 chr1A 96.546 1969 60 4 1 1966 184936440 184934477 0.000000e+00 3253
7 TraesCS7A01G261400 chr7B 96.390 1967 66 4 1 1966 574510875 574512837 0.000000e+00 3234
8 TraesCS7A01G261400 chr5A 88.036 1981 218 14 1 1966 663074074 663076050 0.000000e+00 2327
9 TraesCS7A01G261400 chr5A 98.284 816 14 0 2097 2912 584030966 584031781 0.000000e+00 1430
10 TraesCS7A01G261400 chr5A 94.010 818 47 2 2097 2912 225252467 225251650 0.000000e+00 1238
11 TraesCS7A01G261400 chr5A 88.102 706 81 3 4 707 167892423 167891719 0.000000e+00 835
12 TraesCS7A01G261400 chrUn 96.509 974 33 1 1 973 445250996 445251969 0.000000e+00 1609
13 TraesCS7A01G261400 chrUn 86.275 1122 134 15 822 1929 98277487 98276372 0.000000e+00 1201
14 TraesCS7A01G261400 chrUn 86.976 883 101 10 1097 1966 386814551 386813670 0.000000e+00 981
15 TraesCS7A01G261400 chr3A 83.532 1427 187 24 8 1419 47783913 47785306 0.000000e+00 1290
16 TraesCS7A01G261400 chr4A 93.399 818 51 3 2097 2912 12650345 12651161 0.000000e+00 1208
17 TraesCS7A01G261400 chr4A 87.980 807 95 2 2097 2901 722377780 722378586 0.000000e+00 952
18 TraesCS7A01G261400 chr6A 85.498 1124 136 21 822 1929 53257554 53256442 0.000000e+00 1147
19 TraesCS7A01G261400 chr1D 87.841 806 96 2 2097 2900 74292840 74293645 0.000000e+00 944
20 TraesCS7A01G261400 chr7D 82.463 1072 152 21 876 1928 317664191 317663137 0.000000e+00 905
21 TraesCS7A01G261400 chr4B 86.503 815 108 2 2100 2912 591234397 591233583 0.000000e+00 894
22 TraesCS7A01G261400 chr3B 88.813 733 77 4 2097 2827 454701970 454702699 0.000000e+00 894
23 TraesCS7A01G261400 chr3B 92.500 160 11 1 2753 2912 250469133 250469291 8.120000e-56 228
24 TraesCS7A01G261400 chr6D 86.325 819 103 8 2097 2910 128083161 128083975 0.000000e+00 883
25 TraesCS7A01G261400 chr2B 87.731 758 89 4 2151 2906 183307630 183308385 0.000000e+00 881


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 TraesCS7A01G261400 chr7A 255886462 255889373 2911 True 5378 5378 100.000 1 2912 1 chr7A.!!$R4 2911
1 TraesCS7A01G261400 chr7A 32588037 32589644 1607 True 2747 2747 97.512 360 1966 1 chr7A.!!$R1 1606
2 TraesCS7A01G261400 chr7A 88957728 88959661 1933 True 2106 2106 86.457 4 1928 1 chr7A.!!$R2 1924
3 TraesCS7A01G261400 chr7A 722318106 722320039 1933 True 2095 2095 86.354 4 1928 1 chr7A.!!$R5 1924
4 TraesCS7A01G261400 chr7A 171877883 171878764 881 True 987 987 87.089 1097 1966 1 chr7A.!!$R3 869
5 TraesCS7A01G261400 chr6B 610805864 610807828 1964 False 3258 3258 96.599 1 1966 1 chr6B.!!$F1 1965
6 TraesCS7A01G261400 chr1A 184934477 184936440 1963 True 3253 3253 96.546 1 1966 1 chr1A.!!$R1 1965
7 TraesCS7A01G261400 chr7B 574510875 574512837 1962 False 3234 3234 96.390 1 1966 1 chr7B.!!$F1 1965
8 TraesCS7A01G261400 chr5A 663074074 663076050 1976 False 2327 2327 88.036 1 1966 1 chr5A.!!$F2 1965
9 TraesCS7A01G261400 chr5A 584030966 584031781 815 False 1430 1430 98.284 2097 2912 1 chr5A.!!$F1 815
10 TraesCS7A01G261400 chr5A 225251650 225252467 817 True 1238 1238 94.010 2097 2912 1 chr5A.!!$R2 815
11 TraesCS7A01G261400 chr5A 167891719 167892423 704 True 835 835 88.102 4 707 1 chr5A.!!$R1 703
12 TraesCS7A01G261400 chrUn 445250996 445251969 973 False 1609 1609 96.509 1 973 1 chrUn.!!$F1 972
13 TraesCS7A01G261400 chrUn 98276372 98277487 1115 True 1201 1201 86.275 822 1929 1 chrUn.!!$R1 1107
14 TraesCS7A01G261400 chrUn 386813670 386814551 881 True 981 981 86.976 1097 1966 1 chrUn.!!$R2 869
15 TraesCS7A01G261400 chr3A 47783913 47785306 1393 False 1290 1290 83.532 8 1419 1 chr3A.!!$F1 1411
16 TraesCS7A01G261400 chr4A 12650345 12651161 816 False 1208 1208 93.399 2097 2912 1 chr4A.!!$F1 815
17 TraesCS7A01G261400 chr4A 722377780 722378586 806 False 952 952 87.980 2097 2901 1 chr4A.!!$F2 804
18 TraesCS7A01G261400 chr6A 53256442 53257554 1112 True 1147 1147 85.498 822 1929 1 chr6A.!!$R1 1107
19 TraesCS7A01G261400 chr1D 74292840 74293645 805 False 944 944 87.841 2097 2900 1 chr1D.!!$F1 803
20 TraesCS7A01G261400 chr7D 317663137 317664191 1054 True 905 905 82.463 876 1928 1 chr7D.!!$R1 1052
21 TraesCS7A01G261400 chr4B 591233583 591234397 814 True 894 894 86.503 2100 2912 1 chr4B.!!$R1 812
22 TraesCS7A01G261400 chr3B 454701970 454702699 729 False 894 894 88.813 2097 2827 1 chr3B.!!$F2 730
23 TraesCS7A01G261400 chr6D 128083161 128083975 814 False 883 883 86.325 2097 2910 1 chr6D.!!$F1 813
24 TraesCS7A01G261400 chr2B 183307630 183308385 755 False 881 881 87.731 2151 2906 1 chr2B.!!$F1 755

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
117 118 1.11295 GGTTCCTCGGGGTAAGAGAG 58.887 60.0 0.0 0.0 37.93 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2065 0.10741 TCGCAAGGTCACAAGTGGTT 60.107 50.0 0.0 0.0 38.47 3.67 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
117 118 1.112950 GGTTCCTCGGGGTAAGAGAG 58.887 60.000 0.00 0.00 37.93 3.20
224 226 5.121454 GTGCTATTATCTAGTTGATGCTGGC 59.879 44.000 0.00 0.00 36.65 4.85
355 359 6.578163 TCATCAGCAAGAAATGTGATTGAA 57.422 33.333 0.00 0.00 31.61 2.69
661 665 6.073276 CCAAAAGACAAGATCGTTGATACACA 60.073 38.462 10.61 0.00 32.01 3.72
665 669 7.101652 AGACAAGATCGTTGATACACACTAT 57.898 36.000 10.61 0.00 0.00 2.12
797 801 9.683069 GTCATTTCATTCACTTTCTTGTAATGT 57.317 29.630 0.00 0.00 32.22 2.71
856 860 7.912056 TCCTACATGAGCATTTATATTCTGC 57.088 36.000 0.00 0.00 36.15 4.26
894 900 9.932207 ACACACATTTCATTGTCATATTGAAAT 57.068 25.926 6.52 6.52 44.23 2.17
933 939 2.905415 AGGAGGGCAAATTGACATCA 57.095 45.000 15.68 0.00 38.07 3.07
1032 1042 6.546428 TCTTCTTGGAAAGTAGATACTGGG 57.454 41.667 0.00 0.00 44.02 4.45
1209 1220 5.658198 TTGGATGGGATGATGAGAAGAAT 57.342 39.130 0.00 0.00 0.00 2.40
1246 1257 2.157942 AGGGAGACATATATGGGCTGGT 60.158 50.000 16.96 0.00 0.00 4.00
1537 1567 9.804977 AGGAGAATATTCCTGAATTAAATGAGG 57.195 33.333 11.92 0.00 45.84 3.86
1538 1568 9.799106 GGAGAATATTCCTGAATTAAATGAGGA 57.201 33.333 11.92 0.00 34.27 3.71
1834 1864 0.251297 TGGTGGTGATGCTGGAAAGG 60.251 55.000 0.00 0.00 0.00 3.11
1837 1867 0.178967 TGGTGATGCTGGAAAGGCAA 60.179 50.000 0.00 0.00 43.14 4.52
1976 2006 6.721571 TTTTAGCTCAGGAAACAGATAACG 57.278 37.500 0.00 0.00 0.00 3.18
1977 2007 2.622436 AGCTCAGGAAACAGATAACGC 58.378 47.619 0.00 0.00 0.00 4.84
1978 2008 2.234908 AGCTCAGGAAACAGATAACGCT 59.765 45.455 0.00 0.00 0.00 5.07
1979 2009 2.605366 GCTCAGGAAACAGATAACGCTC 59.395 50.000 0.00 0.00 0.00 5.03
1980 2010 3.190874 CTCAGGAAACAGATAACGCTCC 58.809 50.000 0.00 0.00 0.00 4.70
1981 2011 2.565391 TCAGGAAACAGATAACGCTCCA 59.435 45.455 0.00 0.00 0.00 3.86
1982 2012 3.197766 TCAGGAAACAGATAACGCTCCAT 59.802 43.478 0.00 0.00 0.00 3.41
1983 2013 4.404394 TCAGGAAACAGATAACGCTCCATA 59.596 41.667 0.00 0.00 0.00 2.74
1984 2014 4.747108 CAGGAAACAGATAACGCTCCATAG 59.253 45.833 0.00 0.00 0.00 2.23
1985 2015 4.649674 AGGAAACAGATAACGCTCCATAGA 59.350 41.667 0.00 0.00 0.00 1.98
1986 2016 4.985409 GGAAACAGATAACGCTCCATAGAG 59.015 45.833 0.00 0.00 43.57 2.43
1987 2017 5.452077 GGAAACAGATAACGCTCCATAGAGT 60.452 44.000 0.00 0.00 42.59 3.24
1996 2026 4.526970 CGCTCCATAGAGTGTCATTTTG 57.473 45.455 0.00 0.00 44.19 2.44
1997 2027 3.935203 CGCTCCATAGAGTGTCATTTTGT 59.065 43.478 0.00 0.00 44.19 2.83
1998 2028 4.033358 CGCTCCATAGAGTGTCATTTTGTC 59.967 45.833 0.00 0.00 44.19 3.18
1999 2029 4.033358 GCTCCATAGAGTGTCATTTTGTCG 59.967 45.833 0.00 0.00 42.59 4.35
2000 2030 5.400066 TCCATAGAGTGTCATTTTGTCGA 57.600 39.130 0.00 0.00 0.00 4.20
2001 2031 5.977635 TCCATAGAGTGTCATTTTGTCGAT 58.022 37.500 0.00 0.00 0.00 3.59
2002 2032 6.406370 TCCATAGAGTGTCATTTTGTCGATT 58.594 36.000 0.00 0.00 0.00 3.34
2003 2033 6.878923 TCCATAGAGTGTCATTTTGTCGATTT 59.121 34.615 0.00 0.00 0.00 2.17
2004 2034 7.390440 TCCATAGAGTGTCATTTTGTCGATTTT 59.610 33.333 0.00 0.00 0.00 1.82
2005 2035 8.023128 CCATAGAGTGTCATTTTGTCGATTTTT 58.977 33.333 0.00 0.00 0.00 1.94
2008 2038 8.154649 AGAGTGTCATTTTGTCGATTTTTAGT 57.845 30.769 0.00 0.00 0.00 2.24
2009 2039 8.621286 AGAGTGTCATTTTGTCGATTTTTAGTT 58.379 29.630 0.00 0.00 0.00 2.24
2010 2040 8.782533 AGTGTCATTTTGTCGATTTTTAGTTC 57.217 30.769 0.00 0.00 0.00 3.01
2011 2041 8.621286 AGTGTCATTTTGTCGATTTTTAGTTCT 58.379 29.630 0.00 0.00 0.00 3.01
2012 2042 8.892905 GTGTCATTTTGTCGATTTTTAGTTCTC 58.107 33.333 0.00 0.00 0.00 2.87
2013 2043 8.616942 TGTCATTTTGTCGATTTTTAGTTCTCA 58.383 29.630 0.00 0.00 0.00 3.27
2014 2044 9.612620 GTCATTTTGTCGATTTTTAGTTCTCAT 57.387 29.630 0.00 0.00 0.00 2.90
2015 2045 9.825972 TCATTTTGTCGATTTTTAGTTCTCATC 57.174 29.630 0.00 0.00 0.00 2.92
2016 2046 9.831737 CATTTTGTCGATTTTTAGTTCTCATCT 57.168 29.630 0.00 0.00 0.00 2.90
2018 2048 9.663904 TTTTGTCGATTTTTAGTTCTCATCTTG 57.336 29.630 0.00 0.00 0.00 3.02
2019 2049 7.962964 TGTCGATTTTTAGTTCTCATCTTGT 57.037 32.000 0.00 0.00 0.00 3.16
2020 2050 8.018677 TGTCGATTTTTAGTTCTCATCTTGTC 57.981 34.615 0.00 0.00 0.00 3.18
2021 2051 7.117812 TGTCGATTTTTAGTTCTCATCTTGTCC 59.882 37.037 0.00 0.00 0.00 4.02
2022 2052 6.310467 TCGATTTTTAGTTCTCATCTTGTCCG 59.690 38.462 0.00 0.00 0.00 4.79
2023 2053 5.607119 TTTTTAGTTCTCATCTTGTCCGC 57.393 39.130 0.00 0.00 0.00 5.54
2024 2054 2.561733 TAGTTCTCATCTTGTCCGCG 57.438 50.000 0.00 0.00 0.00 6.46
2025 2055 0.603569 AGTTCTCATCTTGTCCGCGT 59.396 50.000 4.92 0.00 0.00 6.01
2026 2056 1.816835 AGTTCTCATCTTGTCCGCGTA 59.183 47.619 4.92 0.00 0.00 4.42
2027 2057 1.918609 GTTCTCATCTTGTCCGCGTAC 59.081 52.381 4.92 0.00 0.00 3.67
2028 2058 0.454600 TCTCATCTTGTCCGCGTACC 59.545 55.000 4.92 0.00 0.00 3.34
2029 2059 0.527817 CTCATCTTGTCCGCGTACCC 60.528 60.000 4.92 0.00 0.00 3.69
2030 2060 1.876714 CATCTTGTCCGCGTACCCG 60.877 63.158 4.92 0.00 37.07 5.28
2040 2070 3.481661 CGTACCCGCATGAACCAC 58.518 61.111 0.00 0.00 0.00 4.16
2041 2071 1.079405 CGTACCCGCATGAACCACT 60.079 57.895 0.00 0.00 0.00 4.00
2042 2072 0.672401 CGTACCCGCATGAACCACTT 60.672 55.000 0.00 0.00 0.00 3.16
2043 2073 0.802494 GTACCCGCATGAACCACTTG 59.198 55.000 0.00 0.00 0.00 3.16
2044 2074 0.398696 TACCCGCATGAACCACTTGT 59.601 50.000 0.00 0.00 0.00 3.16
2045 2075 1.172180 ACCCGCATGAACCACTTGTG 61.172 55.000 0.00 0.00 35.06 3.33
2046 2076 0.888736 CCCGCATGAACCACTTGTGA 60.889 55.000 0.00 0.00 36.63 3.58
2047 2077 0.238289 CCGCATGAACCACTTGTGAC 59.762 55.000 0.00 0.00 36.63 3.67
2048 2078 0.238289 CGCATGAACCACTTGTGACC 59.762 55.000 0.00 0.00 36.63 4.02
2049 2079 1.609208 GCATGAACCACTTGTGACCT 58.391 50.000 0.00 0.00 0.00 3.85
2050 2080 1.956477 GCATGAACCACTTGTGACCTT 59.044 47.619 0.00 0.00 0.00 3.50
2051 2081 2.287788 GCATGAACCACTTGTGACCTTG 60.288 50.000 0.00 1.81 0.00 3.61
2052 2082 1.388547 TGAACCACTTGTGACCTTGC 58.611 50.000 1.89 0.00 0.00 4.01
2053 2083 0.307760 GAACCACTTGTGACCTTGCG 59.692 55.000 1.89 0.00 0.00 4.85
2054 2084 0.107410 AACCACTTGTGACCTTGCGA 60.107 50.000 1.89 0.00 0.00 5.10
2055 2085 0.532862 ACCACTTGTGACCTTGCGAG 60.533 55.000 1.89 0.00 0.00 5.03
2056 2086 0.249868 CCACTTGTGACCTTGCGAGA 60.250 55.000 1.22 0.00 0.00 4.04
2057 2087 1.609061 CCACTTGTGACCTTGCGAGAT 60.609 52.381 1.22 0.00 0.00 2.75
2058 2088 2.353704 CCACTTGTGACCTTGCGAGATA 60.354 50.000 1.22 0.00 0.00 1.98
2059 2089 3.525537 CACTTGTGACCTTGCGAGATAT 58.474 45.455 1.22 0.00 0.00 1.63
2060 2090 3.935203 CACTTGTGACCTTGCGAGATATT 59.065 43.478 1.22 0.00 0.00 1.28
2061 2091 5.109210 CACTTGTGACCTTGCGAGATATTA 58.891 41.667 1.22 0.00 0.00 0.98
2062 2092 5.580691 CACTTGTGACCTTGCGAGATATTAA 59.419 40.000 1.22 0.00 0.00 1.40
2063 2093 5.581085 ACTTGTGACCTTGCGAGATATTAAC 59.419 40.000 1.22 0.00 0.00 2.01
2064 2094 4.109766 TGTGACCTTGCGAGATATTAACG 58.890 43.478 1.22 0.00 0.00 3.18
2065 2095 4.142337 TGTGACCTTGCGAGATATTAACGA 60.142 41.667 1.22 0.00 0.00 3.85
2066 2096 4.206609 GTGACCTTGCGAGATATTAACGAC 59.793 45.833 1.22 0.00 0.00 4.34
2067 2097 4.142337 TGACCTTGCGAGATATTAACGACA 60.142 41.667 1.22 0.00 0.00 4.35
2068 2098 4.110482 ACCTTGCGAGATATTAACGACAC 58.890 43.478 1.22 0.00 0.00 3.67
2069 2099 4.109766 CCTTGCGAGATATTAACGACACA 58.890 43.478 1.22 0.00 0.00 3.72
2070 2100 4.026804 CCTTGCGAGATATTAACGACACAC 60.027 45.833 1.22 0.00 0.00 3.82
2071 2101 4.099380 TGCGAGATATTAACGACACACA 57.901 40.909 0.00 0.00 0.00 3.72
2072 2102 4.487019 TGCGAGATATTAACGACACACAA 58.513 39.130 0.00 0.00 0.00 3.33
2073 2103 4.924462 TGCGAGATATTAACGACACACAAA 59.076 37.500 0.00 0.00 0.00 2.83
2074 2104 5.061684 TGCGAGATATTAACGACACACAAAG 59.938 40.000 0.00 0.00 0.00 2.77
2075 2105 5.061808 GCGAGATATTAACGACACACAAAGT 59.938 40.000 0.00 0.00 0.00 2.66
2076 2106 6.400727 GCGAGATATTAACGACACACAAAGTT 60.401 38.462 0.00 0.00 0.00 2.66
2077 2107 7.201376 GCGAGATATTAACGACACACAAAGTTA 60.201 37.037 0.00 0.00 0.00 2.24
2078 2108 8.641155 CGAGATATTAACGACACACAAAGTTAA 58.359 33.333 0.00 2.74 41.40 2.01
2081 2111 8.889849 ATATTAACGACACACAAAGTTAATGC 57.110 30.769 17.46 0.00 44.50 3.56
2082 2112 4.893424 AACGACACACAAAGTTAATGCT 57.107 36.364 0.00 0.00 0.00 3.79
2083 2113 4.468095 ACGACACACAAAGTTAATGCTC 57.532 40.909 0.00 0.00 0.00 4.26
2084 2114 3.059868 ACGACACACAAAGTTAATGCTCG 60.060 43.478 0.00 0.00 0.00 5.03
2085 2115 3.059868 CGACACACAAAGTTAATGCTCGT 60.060 43.478 0.00 0.00 0.00 4.18
2086 2116 4.551990 CGACACACAAAGTTAATGCTCGTT 60.552 41.667 0.00 0.00 0.00 3.85
2087 2117 5.243426 ACACACAAAGTTAATGCTCGTTT 57.757 34.783 0.00 0.00 0.00 3.60
2088 2118 6.366315 ACACACAAAGTTAATGCTCGTTTA 57.634 33.333 0.00 0.00 0.00 2.01
2089 2119 6.966021 ACACACAAAGTTAATGCTCGTTTAT 58.034 32.000 0.00 0.00 0.00 1.40
2090 2120 6.855914 ACACACAAAGTTAATGCTCGTTTATG 59.144 34.615 0.00 0.00 0.00 1.90
2091 2121 6.305399 CACACAAAGTTAATGCTCGTTTATGG 59.695 38.462 0.00 0.00 0.00 2.74
2092 2122 5.799936 CACAAAGTTAATGCTCGTTTATGGG 59.200 40.000 0.00 0.00 0.00 4.00
2093 2123 4.632538 AAGTTAATGCTCGTTTATGGGC 57.367 40.909 0.00 0.00 0.00 5.36
2094 2124 3.616219 AGTTAATGCTCGTTTATGGGCA 58.384 40.909 0.00 0.00 39.06 5.36
2095 2125 4.207165 AGTTAATGCTCGTTTATGGGCAT 58.793 39.130 3.46 3.46 45.65 4.40
2252 2283 4.453136 TGTTAATGCCCGAACAAGACTTAC 59.547 41.667 0.00 0.00 32.74 2.34
2323 2355 7.727186 ACTTGGTATTTATGGTAGGATAGACGA 59.273 37.037 0.00 0.00 0.00 4.20
2586 2618 1.283029 CTGGAGGATGGATTGGTGTGT 59.717 52.381 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 7.462571 AACTAACATGGACCCTTTTGTATTC 57.537 36.000 0.00 0.00 0.00 1.75
224 226 5.368989 AGAAACCCTTCACAGTTCTTGTAG 58.631 41.667 0.00 0.00 38.16 2.74
308 312 4.558178 TGCAGCATGTTAAACAATTCCTG 58.442 39.130 0.00 0.00 39.31 3.86
355 359 4.473444 TCTTGAGCAATCCAAAAGTCCTT 58.527 39.130 0.00 0.00 0.00 3.36
562 566 0.659427 CGGATGATGTTTCGCTGCAT 59.341 50.000 0.00 0.00 0.00 3.96
564 568 0.302890 CTCGGATGATGTTTCGCTGC 59.697 55.000 0.00 0.00 0.00 5.25
567 571 0.652592 CCACTCGGATGATGTTTCGC 59.347 55.000 0.00 0.00 0.00 4.70
592 596 8.902540 TTTCATCAGCTAACTTGTCTCTTTAA 57.097 30.769 0.00 0.00 0.00 1.52
593 597 8.939929 CATTTCATCAGCTAACTTGTCTCTTTA 58.060 33.333 0.00 0.00 0.00 1.85
856 860 7.697352 ATGAAATGTGTGTGTACAAACAATG 57.303 32.000 20.46 0.00 46.15 2.82
894 900 6.490040 CCTCCTTTGACTTGGTTTTCTGATAA 59.510 38.462 0.00 0.00 0.00 1.75
1032 1042 3.133721 AGGTCAGATATCCAGACTTGTGC 59.866 47.826 19.50 7.85 32.98 4.57
1209 1220 5.135533 TGTCTCCCTATCTCCAGTTACCATA 59.864 44.000 0.00 0.00 0.00 2.74
1274 1285 9.390795 CAGTTGAAAATAACATGAAACAGAGAG 57.609 33.333 0.00 0.00 33.02 3.20
1536 1566 0.535102 CACCGGATGGGCTTGTATCC 60.535 60.000 9.46 0.00 40.62 2.59
1537 1567 0.535102 CCACCGGATGGGCTTGTATC 60.535 60.000 9.46 0.00 45.95 2.24
1538 1568 1.531748 CCACCGGATGGGCTTGTAT 59.468 57.895 9.46 0.00 45.95 2.29
1834 1864 5.393163 CACGCAAATTGATGAAAAGTTTTGC 59.607 36.000 5.36 7.84 43.21 3.68
1966 1996 4.402793 ACACTCTATGGAGCGTTATCTGTT 59.597 41.667 5.91 0.00 42.98 3.16
1967 1997 3.954904 ACACTCTATGGAGCGTTATCTGT 59.045 43.478 5.91 0.00 42.98 3.41
1968 1998 4.036852 TGACACTCTATGGAGCGTTATCTG 59.963 45.833 5.91 0.00 42.98 2.90
1969 1999 4.207955 TGACACTCTATGGAGCGTTATCT 58.792 43.478 5.91 0.00 42.98 1.98
1970 2000 4.569761 TGACACTCTATGGAGCGTTATC 57.430 45.455 5.91 0.00 42.98 1.75
1971 2001 5.537300 AATGACACTCTATGGAGCGTTAT 57.463 39.130 5.91 2.34 42.98 1.89
1972 2002 5.339008 AAATGACACTCTATGGAGCGTTA 57.661 39.130 5.91 0.00 42.98 3.18
1973 2003 3.895232 AATGACACTCTATGGAGCGTT 57.105 42.857 5.91 0.00 42.98 4.84
1974 2004 3.895232 AAATGACACTCTATGGAGCGT 57.105 42.857 5.91 2.21 42.98 5.07
1975 2005 3.935203 ACAAAATGACACTCTATGGAGCG 59.065 43.478 5.91 0.00 42.98 5.03
1976 2006 4.033358 CGACAAAATGACACTCTATGGAGC 59.967 45.833 5.91 0.00 42.98 4.70
1977 2007 5.410924 TCGACAAAATGACACTCTATGGAG 58.589 41.667 4.25 4.25 44.62 3.86
1978 2008 5.400066 TCGACAAAATGACACTCTATGGA 57.600 39.130 0.00 0.00 0.00 3.41
1979 2009 6.668541 AATCGACAAAATGACACTCTATGG 57.331 37.500 0.00 0.00 0.00 2.74
1980 2010 8.955061 AAAAATCGACAAAATGACACTCTATG 57.045 30.769 0.00 0.00 0.00 2.23
1982 2012 9.268268 ACTAAAAATCGACAAAATGACACTCTA 57.732 29.630 0.00 0.00 0.00 2.43
1983 2013 8.154649 ACTAAAAATCGACAAAATGACACTCT 57.845 30.769 0.00 0.00 0.00 3.24
1984 2014 8.782533 AACTAAAAATCGACAAAATGACACTC 57.217 30.769 0.00 0.00 0.00 3.51
1985 2015 8.621286 AGAACTAAAAATCGACAAAATGACACT 58.379 29.630 0.00 0.00 0.00 3.55
1986 2016 8.782533 AGAACTAAAAATCGACAAAATGACAC 57.217 30.769 0.00 0.00 0.00 3.67
1987 2017 8.616942 TGAGAACTAAAAATCGACAAAATGACA 58.383 29.630 0.00 0.00 0.00 3.58
1988 2018 9.612620 ATGAGAACTAAAAATCGACAAAATGAC 57.387 29.630 0.00 0.00 0.00 3.06
1989 2019 9.825972 GATGAGAACTAAAAATCGACAAAATGA 57.174 29.630 0.00 0.00 0.00 2.57
1990 2020 9.831737 AGATGAGAACTAAAAATCGACAAAATG 57.168 29.630 0.00 0.00 0.00 2.32
1992 2022 9.663904 CAAGATGAGAACTAAAAATCGACAAAA 57.336 29.630 0.00 0.00 0.00 2.44
1993 2023 8.836413 ACAAGATGAGAACTAAAAATCGACAAA 58.164 29.630 0.00 0.00 0.00 2.83
1994 2024 8.378172 ACAAGATGAGAACTAAAAATCGACAA 57.622 30.769 0.00 0.00 0.00 3.18
1995 2025 7.117812 GGACAAGATGAGAACTAAAAATCGACA 59.882 37.037 0.00 0.00 0.00 4.35
1996 2026 7.457060 GGACAAGATGAGAACTAAAAATCGAC 58.543 38.462 0.00 0.00 0.00 4.20
1997 2027 6.310467 CGGACAAGATGAGAACTAAAAATCGA 59.690 38.462 0.00 0.00 0.00 3.59
1998 2028 6.470160 CGGACAAGATGAGAACTAAAAATCG 58.530 40.000 0.00 0.00 0.00 3.34
1999 2029 6.251549 GCGGACAAGATGAGAACTAAAAATC 58.748 40.000 0.00 0.00 0.00 2.17
2000 2030 5.163854 CGCGGACAAGATGAGAACTAAAAAT 60.164 40.000 0.00 0.00 0.00 1.82
2001 2031 4.151689 CGCGGACAAGATGAGAACTAAAAA 59.848 41.667 0.00 0.00 0.00 1.94
2002 2032 3.678072 CGCGGACAAGATGAGAACTAAAA 59.322 43.478 0.00 0.00 0.00 1.52
2003 2033 3.250744 CGCGGACAAGATGAGAACTAAA 58.749 45.455 0.00 0.00 0.00 1.85
2004 2034 2.230508 ACGCGGACAAGATGAGAACTAA 59.769 45.455 12.47 0.00 0.00 2.24
2005 2035 1.816835 ACGCGGACAAGATGAGAACTA 59.183 47.619 12.47 0.00 0.00 2.24
2006 2036 0.603569 ACGCGGACAAGATGAGAACT 59.396 50.000 12.47 0.00 0.00 3.01
2007 2037 1.918609 GTACGCGGACAAGATGAGAAC 59.081 52.381 18.68 0.00 0.00 3.01
2008 2038 1.135199 GGTACGCGGACAAGATGAGAA 60.135 52.381 25.30 0.00 0.00 2.87
2009 2039 0.454600 GGTACGCGGACAAGATGAGA 59.545 55.000 25.30 0.00 0.00 3.27
2010 2040 0.527817 GGGTACGCGGACAAGATGAG 60.528 60.000 25.30 0.00 0.00 2.90
2011 2041 1.514087 GGGTACGCGGACAAGATGA 59.486 57.895 25.30 0.00 0.00 2.92
2012 2042 1.876714 CGGGTACGCGGACAAGATG 60.877 63.158 25.30 3.40 0.00 2.90
2013 2043 2.493030 CGGGTACGCGGACAAGAT 59.507 61.111 25.30 0.00 0.00 2.40
2023 2053 0.672401 AAGTGGTTCATGCGGGTACG 60.672 55.000 0.00 0.00 44.63 3.67
2024 2054 0.802494 CAAGTGGTTCATGCGGGTAC 59.198 55.000 0.00 0.00 0.00 3.34
2025 2055 0.398696 ACAAGTGGTTCATGCGGGTA 59.601 50.000 0.00 0.00 0.00 3.69
2026 2056 1.150536 ACAAGTGGTTCATGCGGGT 59.849 52.632 0.00 0.00 0.00 5.28
2027 2057 0.888736 TCACAAGTGGTTCATGCGGG 60.889 55.000 0.00 0.00 0.00 6.13
2028 2058 0.238289 GTCACAAGTGGTTCATGCGG 59.762 55.000 0.00 0.00 0.00 5.69
2029 2059 0.238289 GGTCACAAGTGGTTCATGCG 59.762 55.000 0.00 0.00 0.00 4.73
2030 2060 1.609208 AGGTCACAAGTGGTTCATGC 58.391 50.000 0.00 0.00 0.00 4.06
2031 2061 2.287788 GCAAGGTCACAAGTGGTTCATG 60.288 50.000 0.00 0.00 0.00 3.07
2032 2062 1.956477 GCAAGGTCACAAGTGGTTCAT 59.044 47.619 0.00 0.00 0.00 2.57
2033 2063 1.388547 GCAAGGTCACAAGTGGTTCA 58.611 50.000 0.00 0.00 0.00 3.18
2034 2064 0.307760 CGCAAGGTCACAAGTGGTTC 59.692 55.000 0.00 0.00 0.00 3.62
2035 2065 0.107410 TCGCAAGGTCACAAGTGGTT 60.107 50.000 0.00 0.00 38.47 3.67
2036 2066 0.532862 CTCGCAAGGTCACAAGTGGT 60.533 55.000 0.00 0.00 38.47 4.16
2037 2067 0.249868 TCTCGCAAGGTCACAAGTGG 60.250 55.000 0.00 0.00 38.47 4.00
2038 2068 1.800805 ATCTCGCAAGGTCACAAGTG 58.199 50.000 0.00 0.00 38.47 3.16
2039 2069 3.895232 ATATCTCGCAAGGTCACAAGT 57.105 42.857 0.00 0.00 38.47 3.16
2040 2070 5.276395 CGTTAATATCTCGCAAGGTCACAAG 60.276 44.000 0.00 0.00 38.47 3.16
2041 2071 4.565166 CGTTAATATCTCGCAAGGTCACAA 59.435 41.667 0.00 0.00 38.47 3.33
2042 2072 4.109766 CGTTAATATCTCGCAAGGTCACA 58.890 43.478 0.00 0.00 38.47 3.58
2043 2073 4.206609 GTCGTTAATATCTCGCAAGGTCAC 59.793 45.833 0.00 0.00 38.47 3.67
2044 2074 4.142337 TGTCGTTAATATCTCGCAAGGTCA 60.142 41.667 0.00 0.00 38.47 4.02
2045 2075 4.206609 GTGTCGTTAATATCTCGCAAGGTC 59.793 45.833 0.00 0.00 38.47 3.85
2046 2076 4.110482 GTGTCGTTAATATCTCGCAAGGT 58.890 43.478 0.00 0.00 38.47 3.50
2047 2077 4.026804 GTGTGTCGTTAATATCTCGCAAGG 60.027 45.833 0.00 0.00 38.47 3.61
2048 2078 4.561213 TGTGTGTCGTTAATATCTCGCAAG 59.439 41.667 0.00 0.00 0.00 4.01
2049 2079 4.487019 TGTGTGTCGTTAATATCTCGCAA 58.513 39.130 0.00 0.00 0.00 4.85
2050 2080 4.099380 TGTGTGTCGTTAATATCTCGCA 57.901 40.909 0.00 0.00 0.00 5.10
2051 2081 5.061808 ACTTTGTGTGTCGTTAATATCTCGC 59.938 40.000 0.00 0.00 0.00 5.03
2052 2082 6.627690 ACTTTGTGTGTCGTTAATATCTCG 57.372 37.500 0.00 0.00 0.00 4.04
2055 2085 8.995906 GCATTAACTTTGTGTGTCGTTAATATC 58.004 33.333 0.00 0.00 39.31 1.63
2056 2086 8.726988 AGCATTAACTTTGTGTGTCGTTAATAT 58.273 29.630 0.00 0.00 39.31 1.28
2057 2087 8.090250 AGCATTAACTTTGTGTGTCGTTAATA 57.910 30.769 0.00 0.00 39.31 0.98
2058 2088 6.966021 AGCATTAACTTTGTGTGTCGTTAAT 58.034 32.000 0.00 0.00 40.95 1.40
2059 2089 6.366315 AGCATTAACTTTGTGTGTCGTTAA 57.634 33.333 0.00 0.00 36.59 2.01
2060 2090 5.332732 CGAGCATTAACTTTGTGTGTCGTTA 60.333 40.000 0.00 0.00 0.00 3.18
2061 2091 4.551990 CGAGCATTAACTTTGTGTGTCGTT 60.552 41.667 0.00 0.00 0.00 3.85
2062 2092 3.059868 CGAGCATTAACTTTGTGTGTCGT 60.060 43.478 0.00 0.00 0.00 4.34
2063 2093 3.059868 ACGAGCATTAACTTTGTGTGTCG 60.060 43.478 0.00 0.00 0.00 4.35
2064 2094 4.468095 ACGAGCATTAACTTTGTGTGTC 57.532 40.909 0.00 0.00 0.00 3.67
2065 2095 4.893424 AACGAGCATTAACTTTGTGTGT 57.107 36.364 0.00 0.00 0.00 3.72
2066 2096 6.305399 CCATAAACGAGCATTAACTTTGTGTG 59.695 38.462 0.00 0.00 0.00 3.82
2067 2097 6.378582 CCATAAACGAGCATTAACTTTGTGT 58.621 36.000 0.00 0.00 0.00 3.72
2068 2098 5.799936 CCCATAAACGAGCATTAACTTTGTG 59.200 40.000 0.00 0.00 0.00 3.33
2069 2099 5.621329 GCCCATAAACGAGCATTAACTTTGT 60.621 40.000 0.00 0.00 0.00 2.83
2070 2100 4.798387 GCCCATAAACGAGCATTAACTTTG 59.202 41.667 0.00 0.00 0.00 2.77
2071 2101 4.461081 TGCCCATAAACGAGCATTAACTTT 59.539 37.500 0.00 0.00 0.00 2.66
2072 2102 4.013728 TGCCCATAAACGAGCATTAACTT 58.986 39.130 0.00 0.00 0.00 2.66
2073 2103 3.616219 TGCCCATAAACGAGCATTAACT 58.384 40.909 0.00 0.00 0.00 2.24
2074 2104 4.290155 CATGCCCATAAACGAGCATTAAC 58.710 43.478 0.00 0.00 43.17 2.01
2075 2105 3.317711 CCATGCCCATAAACGAGCATTAA 59.682 43.478 0.00 0.00 43.17 1.40
2076 2106 2.884012 CCATGCCCATAAACGAGCATTA 59.116 45.455 0.00 0.00 43.17 1.90
2077 2107 1.682854 CCATGCCCATAAACGAGCATT 59.317 47.619 0.00 0.00 43.17 3.56
2078 2108 1.321474 CCATGCCCATAAACGAGCAT 58.679 50.000 0.00 0.00 46.50 3.79
2079 2109 1.383456 GCCATGCCCATAAACGAGCA 61.383 55.000 0.00 0.00 40.00 4.26
2080 2110 1.360192 GCCATGCCCATAAACGAGC 59.640 57.895 0.00 0.00 0.00 5.03
2081 2111 0.664761 CTGCCATGCCCATAAACGAG 59.335 55.000 0.00 0.00 0.00 4.18
2082 2112 0.254462 TCTGCCATGCCCATAAACGA 59.746 50.000 0.00 0.00 0.00 3.85
2083 2113 1.066002 CTTCTGCCATGCCCATAAACG 59.934 52.381 0.00 0.00 0.00 3.60
2084 2114 2.378038 TCTTCTGCCATGCCCATAAAC 58.622 47.619 0.00 0.00 0.00 2.01
2085 2115 2.824689 TCTTCTGCCATGCCCATAAA 57.175 45.000 0.00 0.00 0.00 1.40
2086 2116 4.451891 TTATCTTCTGCCATGCCCATAA 57.548 40.909 0.00 0.00 0.00 1.90
2087 2117 4.451891 TTTATCTTCTGCCATGCCCATA 57.548 40.909 0.00 0.00 0.00 2.74
2088 2118 3.317455 TTTATCTTCTGCCATGCCCAT 57.683 42.857 0.00 0.00 0.00 4.00
2089 2119 2.824689 TTTATCTTCTGCCATGCCCA 57.175 45.000 0.00 0.00 0.00 5.36
2090 2120 3.195396 TGTTTTTATCTTCTGCCATGCCC 59.805 43.478 0.00 0.00 0.00 5.36
2091 2121 4.176271 GTGTTTTTATCTTCTGCCATGCC 58.824 43.478 0.00 0.00 0.00 4.40
2092 2122 4.808558 TGTGTTTTTATCTTCTGCCATGC 58.191 39.130 0.00 0.00 0.00 4.06
2093 2123 7.894376 AAATGTGTTTTTATCTTCTGCCATG 57.106 32.000 0.00 0.00 0.00 3.66
2095 2125 9.995003 AATAAAATGTGTTTTTATCTTCTGCCA 57.005 25.926 4.35 0.00 45.50 4.92
2202 2233 2.124507 CTCCAAAACCGCCTCTCCCA 62.125 60.000 0.00 0.00 0.00 4.37
2252 2283 8.150296 ACTTTCTTTTTGAGAACCCATTATTGG 58.850 33.333 0.00 0.00 43.90 3.16
2323 2355 5.023452 ACCTTTCCTTCTTGAACCAGTTTT 58.977 37.500 0.00 0.00 0.00 2.43
2586 2618 3.796717 CGCTTCTGCTGTTAATACATCGA 59.203 43.478 0.00 0.00 36.97 3.59


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

AutoCloner maintained by Alex Coulton.