Multiple sequence alignment - TraesCS2B01G330800

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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 TraesCS2B01G330800 chr2B 100.000 2225 0 0 1 2225 474908271 474906047 0.000000e+00 4109.0
1 TraesCS2B01G330800 chr2B 97.917 48 1 0 1250 1297 755374055 755374102 1.420000e-12 84.2
2 TraesCS2B01G330800 chr3D 98.386 1301 16 4 1 1297 589279724 589281023 0.000000e+00 2281.0
3 TraesCS2B01G330800 chr3D 97.222 216 6 0 2010 2225 589265133 589265348 1.260000e-97 366.0
4 TraesCS2B01G330800 chrUn 98.580 1268 12 5 1 1263 93409813 93411079 0.000000e+00 2237.0
5 TraesCS2B01G330800 chrUn 98.423 1268 15 4 1 1263 216521582 216520315 0.000000e+00 2226.0
6 TraesCS2B01G330800 chrUn 98.421 1267 16 3 1 1263 396205542 396206808 0.000000e+00 2226.0
7 TraesCS2B01G330800 chr5D 98.059 1288 21 3 1 1284 6188758 6187471 0.000000e+00 2237.0
8 TraesCS2B01G330800 chr5D 98.579 1267 14 3 1 1263 503218036 503216770 0.000000e+00 2237.0
9 TraesCS2B01G330800 chr5D 98.057 1287 22 2 1 1284 503278408 503279694 0.000000e+00 2235.0
10 TraesCS2B01G330800 chr5D 98.185 661 11 1 1292 1952 6236777 6237436 0.000000e+00 1153.0
11 TraesCS2B01G330800 chr5D 97.731 661 14 1 1292 1952 503330033 503329374 0.000000e+00 1136.0
12 TraesCS2B01G330800 chr5D 97.368 38 1 0 1260 1297 6187440 6187477 5.130000e-07 65.8
13 TraesCS2B01G330800 chr5D 97.368 38 1 0 1260 1297 432404996 432404959 5.130000e-07 65.8
14 TraesCS2B01G330800 chr1D 98.061 1289 20 4 1 1284 254398291 254399579 0.000000e+00 2237.0
15 TraesCS2B01G330800 chr1D 97.731 661 14 1 1292 1952 290506290 290505631 0.000000e+00 1136.0
16 TraesCS2B01G330800 chr1D 97.277 661 16 2 1292 1952 254476120 254475462 0.000000e+00 1120.0
17 TraesCS2B01G330800 chr1D 97.126 661 18 1 1292 1952 180357272 180357931 0.000000e+00 1114.0
18 TraesCS2B01G330800 chr1D 97.685 216 5 0 2010 2225 254383631 254383846 2.700000e-99 372.0
19 TraesCS2B01G330800 chr6D 98.423 1268 15 4 1 1263 168251946 168253213 0.000000e+00 2226.0
20 TraesCS2B01G330800 chr6D 97.222 216 6 0 2010 2225 168265129 168264914 1.260000e-97 366.0
21 TraesCS2B01G330800 chr2D 98.487 661 9 1 1292 1952 33930585 33931244 0.000000e+00 1164.0
22 TraesCS2B01G330800 chr2D 97.222 216 6 0 2010 2225 272554171 272553956 1.260000e-97 366.0
23 TraesCS2B01G330800 chr3B 98.336 661 10 1 1292 1952 201492125 201491466 0.000000e+00 1158.0
24 TraesCS2B01G330800 chr1A 98.336 661 10 1 1292 1952 554448823 554449482 0.000000e+00 1158.0
25 TraesCS2B01G330800 chr4A 97.876 659 13 1 1292 1950 141129363 141128706 0.000000e+00 1138.0
26 TraesCS2B01G330800 chr3A 97.685 216 5 0 2010 2225 66006742 66006957 2.700000e-99 372.0
27 TraesCS2B01G330800 chr3A 97.222 216 6 0 2010 2225 593313078 593312863 1.260000e-97 366.0
28 TraesCS2B01G330800 chr3A 98.039 51 1 0 1247 1297 336825433 336825483 3.040000e-14 89.8
29 TraesCS2B01G330800 chr2A 97.685 216 5 0 2010 2225 726908065 726908280 2.700000e-99 372.0
30 TraesCS2B01G330800 chr7D 97.222 216 6 0 2010 2225 77241362 77241147 1.260000e-97 366.0
31 TraesCS2B01G330800 chr7B 97.222 216 6 0 2010 2225 662724794 662724579 1.260000e-97 366.0


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 TraesCS2B01G330800 chr2B 474906047 474908271 2224 True 4109 4109 100.000 1 2225 1 chr2B.!!$R1 2224
1 TraesCS2B01G330800 chr3D 589279724 589281023 1299 False 2281 2281 98.386 1 1297 1 chr3D.!!$F2 1296
2 TraesCS2B01G330800 chrUn 93409813 93411079 1266 False 2237 2237 98.580 1 1263 1 chrUn.!!$F1 1262
3 TraesCS2B01G330800 chrUn 216520315 216521582 1267 True 2226 2226 98.423 1 1263 1 chrUn.!!$R1 1262
4 TraesCS2B01G330800 chrUn 396205542 396206808 1266 False 2226 2226 98.421 1 1263 1 chrUn.!!$F2 1262
5 TraesCS2B01G330800 chr5D 6187471 6188758 1287 True 2237 2237 98.059 1 1284 1 chr5D.!!$R1 1283
6 TraesCS2B01G330800 chr5D 503216770 503218036 1266 True 2237 2237 98.579 1 1263 1 chr5D.!!$R3 1262
7 TraesCS2B01G330800 chr5D 503278408 503279694 1286 False 2235 2235 98.057 1 1284 1 chr5D.!!$F3 1283
8 TraesCS2B01G330800 chr5D 6236777 6237436 659 False 1153 1153 98.185 1292 1952 1 chr5D.!!$F2 660
9 TraesCS2B01G330800 chr5D 503329374 503330033 659 True 1136 1136 97.731 1292 1952 1 chr5D.!!$R4 660
10 TraesCS2B01G330800 chr1D 254398291 254399579 1288 False 2237 2237 98.061 1 1284 1 chr1D.!!$F3 1283
11 TraesCS2B01G330800 chr1D 290505631 290506290 659 True 1136 1136 97.731 1292 1952 1 chr1D.!!$R2 660
12 TraesCS2B01G330800 chr1D 254475462 254476120 658 True 1120 1120 97.277 1292 1952 1 chr1D.!!$R1 660
13 TraesCS2B01G330800 chr1D 180357272 180357931 659 False 1114 1114 97.126 1292 1952 1 chr1D.!!$F1 660
14 TraesCS2B01G330800 chr6D 168251946 168253213 1267 False 2226 2226 98.423 1 1263 1 chr6D.!!$F1 1262
15 TraesCS2B01G330800 chr2D 33930585 33931244 659 False 1164 1164 98.487 1292 1952 1 chr2D.!!$F1 660
16 TraesCS2B01G330800 chr3B 201491466 201492125 659 True 1158 1158 98.336 1292 1952 1 chr3B.!!$R1 660
17 TraesCS2B01G330800 chr1A 554448823 554449482 659 False 1158 1158 98.336 1292 1952 1 chr1A.!!$F1 660
18 TraesCS2B01G330800 chr4A 141128706 141129363 657 True 1138 1138 97.876 1292 1950 1 chr4A.!!$R1 658

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
259 262 2.404559 TCAACCGATATGCCCTTAGGT 58.595 47.619 0.0 0.0 34.57 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 2179 0.028642 ATGGTAGGGGCAGAGGGAAT 60.029 55.0 0.0 0.0 0.0 3.01 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
259 262 2.404559 TCAACCGATATGCCCTTAGGT 58.595 47.619 0.00 0.00 34.57 3.08
941 947 4.833478 AAGGAGTAATCAGCTGTGACAT 57.167 40.909 14.67 0.00 34.75 3.06
968 977 5.372547 AAAACGAATCCTTTTGTAGCTCC 57.627 39.130 0.00 0.00 0.00 4.70
1036 1045 5.479124 AGAAACAATAGTAACGTGGTCCT 57.521 39.130 0.00 0.00 0.00 3.85
1062 1071 4.823989 GCATCTAGCATTCTACCCACAATT 59.176 41.667 0.00 0.00 44.79 2.32
1334 1346 3.435671 GTCACAAGCTTTATGTTAGGCGT 59.564 43.478 0.00 0.00 0.00 5.68
1461 1473 9.331282 CTTCCTACAAATTAGTGAATTAGGAGG 57.669 37.037 0.00 0.00 38.05 4.30
1952 1964 1.060308 CATCCGCGCCTTAAACGTG 59.940 57.895 0.00 4.56 40.58 4.49
1955 1967 3.795342 CGCGCCTTAAACGTGGGG 61.795 66.667 0.00 2.69 37.38 4.96
1956 1968 3.436924 GCGCCTTAAACGTGGGGG 61.437 66.667 0.00 8.72 36.87 5.40
1957 1969 2.348243 CGCCTTAAACGTGGGGGA 59.652 61.111 0.00 0.00 35.47 4.81
1958 1970 1.302671 CGCCTTAAACGTGGGGGAA 60.303 57.895 0.00 0.00 35.47 3.97
1959 1971 1.579964 CGCCTTAAACGTGGGGGAAC 61.580 60.000 0.00 0.00 35.47 3.62
1960 1972 0.251033 GCCTTAAACGTGGGGGAACT 60.251 55.000 0.00 0.00 0.00 3.01
1961 1973 1.003464 GCCTTAAACGTGGGGGAACTA 59.997 52.381 0.00 0.00 0.00 2.24
1962 1974 2.356432 GCCTTAAACGTGGGGGAACTAT 60.356 50.000 0.00 0.00 0.00 2.12
1963 1975 3.538591 CCTTAAACGTGGGGGAACTATC 58.461 50.000 0.00 0.00 0.00 2.08
1964 1976 3.538591 CTTAAACGTGGGGGAACTATCC 58.461 50.000 0.00 0.00 45.77 2.59
1977 1989 5.791367 GGAACTATCCGTTTCTTAACACC 57.209 43.478 0.00 0.00 35.56 4.16
1978 1990 5.240121 GGAACTATCCGTTTCTTAACACCA 58.760 41.667 0.00 0.00 35.56 4.17
1979 1991 5.702209 GGAACTATCCGTTTCTTAACACCAA 59.298 40.000 0.00 0.00 35.56 3.67
1980 1992 6.373495 GGAACTATCCGTTTCTTAACACCAAT 59.627 38.462 0.00 0.00 35.56 3.16
1981 1993 7.094506 GGAACTATCCGTTTCTTAACACCAATT 60.095 37.037 0.00 0.00 35.56 2.32
1982 1994 7.754851 ACTATCCGTTTCTTAACACCAATTT 57.245 32.000 0.00 0.00 33.75 1.82
1983 1995 7.813645 ACTATCCGTTTCTTAACACCAATTTC 58.186 34.615 0.00 0.00 33.75 2.17
1984 1996 6.894339 ATCCGTTTCTTAACACCAATTTCT 57.106 33.333 0.00 0.00 33.75 2.52
1985 1997 7.989416 ATCCGTTTCTTAACACCAATTTCTA 57.011 32.000 0.00 0.00 33.75 2.10
1986 1998 7.989416 TCCGTTTCTTAACACCAATTTCTAT 57.011 32.000 0.00 0.00 33.75 1.98
1987 1999 8.036273 TCCGTTTCTTAACACCAATTTCTATC 57.964 34.615 0.00 0.00 33.75 2.08
1988 2000 7.881232 TCCGTTTCTTAACACCAATTTCTATCT 59.119 33.333 0.00 0.00 33.75 1.98
1989 2001 8.512138 CCGTTTCTTAACACCAATTTCTATCTT 58.488 33.333 0.00 0.00 33.75 2.40
1990 2002 9.893305 CGTTTCTTAACACCAATTTCTATCTTT 57.107 29.630 0.00 0.00 33.75 2.52
1997 2009 8.499403 AACACCAATTTCTATCTTTCTCTAGC 57.501 34.615 0.00 0.00 0.00 3.42
1998 2010 7.051000 ACACCAATTTCTATCTTTCTCTAGCC 58.949 38.462 0.00 0.00 0.00 3.93
1999 2011 7.050377 CACCAATTTCTATCTTTCTCTAGCCA 58.950 38.462 0.00 0.00 0.00 4.75
2000 2012 7.554118 CACCAATTTCTATCTTTCTCTAGCCAA 59.446 37.037 0.00 0.00 0.00 4.52
2001 2013 7.554476 ACCAATTTCTATCTTTCTCTAGCCAAC 59.446 37.037 0.00 0.00 0.00 3.77
2002 2014 7.012799 CCAATTTCTATCTTTCTCTAGCCAACC 59.987 40.741 0.00 0.00 0.00 3.77
2003 2015 6.875972 TTTCTATCTTTCTCTAGCCAACCT 57.124 37.500 0.00 0.00 0.00 3.50
2004 2016 6.875972 TTCTATCTTTCTCTAGCCAACCTT 57.124 37.500 0.00 0.00 0.00 3.50
2005 2017 6.472686 TCTATCTTTCTCTAGCCAACCTTC 57.527 41.667 0.00 0.00 0.00 3.46
2006 2018 3.983044 TCTTTCTCTAGCCAACCTTCC 57.017 47.619 0.00 0.00 0.00 3.46
2007 2019 2.572104 TCTTTCTCTAGCCAACCTTCCC 59.428 50.000 0.00 0.00 0.00 3.97
2008 2020 0.902531 TTCTCTAGCCAACCTTCCCG 59.097 55.000 0.00 0.00 0.00 5.14
2009 2021 1.153349 CTCTAGCCAACCTTCCCGC 60.153 63.158 0.00 0.00 0.00 6.13
2010 2022 1.899437 CTCTAGCCAACCTTCCCGCA 61.899 60.000 0.00 0.00 0.00 5.69
2011 2023 1.450312 CTAGCCAACCTTCCCGCAG 60.450 63.158 0.00 0.00 0.00 5.18
2012 2024 3.622060 TAGCCAACCTTCCCGCAGC 62.622 63.158 0.00 0.00 0.00 5.25
2014 2026 3.365265 CCAACCTTCCCGCAGCAC 61.365 66.667 0.00 0.00 0.00 4.40
2015 2027 3.365265 CAACCTTCCCGCAGCACC 61.365 66.667 0.00 0.00 0.00 5.01
2016 2028 3.570212 AACCTTCCCGCAGCACCT 61.570 61.111 0.00 0.00 0.00 4.00
2017 2029 2.221299 AACCTTCCCGCAGCACCTA 61.221 57.895 0.00 0.00 0.00 3.08
2018 2030 2.185310 AACCTTCCCGCAGCACCTAG 62.185 60.000 0.00 0.00 0.00 3.02
2019 2031 2.660064 CCTTCCCGCAGCACCTAGT 61.660 63.158 0.00 0.00 0.00 2.57
2020 2032 1.327690 CCTTCCCGCAGCACCTAGTA 61.328 60.000 0.00 0.00 0.00 1.82
2021 2033 0.753262 CTTCCCGCAGCACCTAGTAT 59.247 55.000 0.00 0.00 0.00 2.12
2022 2034 0.750850 TTCCCGCAGCACCTAGTATC 59.249 55.000 0.00 0.00 0.00 2.24
2023 2035 1.113517 TCCCGCAGCACCTAGTATCC 61.114 60.000 0.00 0.00 0.00 2.59
2024 2036 1.399744 CCCGCAGCACCTAGTATCCA 61.400 60.000 0.00 0.00 0.00 3.41
2025 2037 0.681733 CCGCAGCACCTAGTATCCAT 59.318 55.000 0.00 0.00 0.00 3.41
2026 2038 1.337260 CCGCAGCACCTAGTATCCATC 60.337 57.143 0.00 0.00 0.00 3.51
2027 2039 1.667177 CGCAGCACCTAGTATCCATCG 60.667 57.143 0.00 0.00 0.00 3.84
2028 2040 1.341531 GCAGCACCTAGTATCCATCGT 59.658 52.381 0.00 0.00 0.00 3.73
2029 2041 2.224066 GCAGCACCTAGTATCCATCGTT 60.224 50.000 0.00 0.00 0.00 3.85
2030 2042 3.741388 GCAGCACCTAGTATCCATCGTTT 60.741 47.826 0.00 0.00 0.00 3.60
2031 2043 4.500887 GCAGCACCTAGTATCCATCGTTTA 60.501 45.833 0.00 0.00 0.00 2.01
2032 2044 4.982916 CAGCACCTAGTATCCATCGTTTAC 59.017 45.833 0.00 0.00 0.00 2.01
2033 2045 3.979495 GCACCTAGTATCCATCGTTTACG 59.021 47.826 0.00 0.00 41.45 3.18
2034 2046 4.543692 CACCTAGTATCCATCGTTTACGG 58.456 47.826 2.09 0.00 40.29 4.02
2035 2047 3.005155 ACCTAGTATCCATCGTTTACGGC 59.995 47.826 2.09 0.00 40.29 5.68
2036 2048 3.255149 CCTAGTATCCATCGTTTACGGCT 59.745 47.826 2.09 0.00 40.29 5.52
2037 2049 4.456911 CCTAGTATCCATCGTTTACGGCTA 59.543 45.833 2.09 0.00 40.29 3.93
2038 2050 4.500603 AGTATCCATCGTTTACGGCTAG 57.499 45.455 2.09 0.00 40.29 3.42
2039 2051 2.814280 ATCCATCGTTTACGGCTAGG 57.186 50.000 2.09 0.55 40.29 3.02
2040 2052 1.766494 TCCATCGTTTACGGCTAGGA 58.234 50.000 2.09 2.77 40.29 2.94
2041 2053 1.406539 TCCATCGTTTACGGCTAGGAC 59.593 52.381 2.09 0.00 40.29 3.85
2042 2054 1.407979 CCATCGTTTACGGCTAGGACT 59.592 52.381 2.09 0.00 40.29 3.85
2043 2055 2.620115 CCATCGTTTACGGCTAGGACTA 59.380 50.000 2.09 0.00 40.29 2.59
2044 2056 3.549625 CCATCGTTTACGGCTAGGACTAC 60.550 52.174 2.09 0.00 40.29 2.73
2045 2057 2.991250 TCGTTTACGGCTAGGACTACT 58.009 47.619 2.09 0.00 40.29 2.57
2046 2058 2.679837 TCGTTTACGGCTAGGACTACTG 59.320 50.000 2.09 0.00 40.29 2.74
2047 2059 2.223433 CGTTTACGGCTAGGACTACTGG 60.223 54.545 0.00 0.00 35.37 4.00
2048 2060 2.062971 TTACGGCTAGGACTACTGGG 57.937 55.000 0.00 0.00 0.00 4.45
2049 2061 0.184451 TACGGCTAGGACTACTGGGG 59.816 60.000 0.00 0.00 0.00 4.96
2050 2062 1.076192 CGGCTAGGACTACTGGGGT 60.076 63.158 0.00 0.00 0.00 4.95
2051 2063 1.108132 CGGCTAGGACTACTGGGGTC 61.108 65.000 0.00 0.00 0.00 4.46
2052 2064 0.262285 GGCTAGGACTACTGGGGTCT 59.738 60.000 0.00 0.00 34.47 3.85
2053 2065 1.694844 GCTAGGACTACTGGGGTCTC 58.305 60.000 0.00 0.00 34.47 3.36
2054 2066 1.215924 GCTAGGACTACTGGGGTCTCT 59.784 57.143 0.00 0.00 34.47 3.10
2055 2067 2.442502 GCTAGGACTACTGGGGTCTCTA 59.557 54.545 0.00 0.00 34.47 2.43
2056 2068 3.117587 GCTAGGACTACTGGGGTCTCTAA 60.118 52.174 0.00 0.00 34.47 2.10
2057 2069 4.448054 GCTAGGACTACTGGGGTCTCTAAT 60.448 50.000 0.00 0.00 34.47 1.73
2058 2070 4.187506 AGGACTACTGGGGTCTCTAATC 57.812 50.000 0.00 0.00 34.47 1.75
2059 2071 3.117054 AGGACTACTGGGGTCTCTAATCC 60.117 52.174 0.00 0.00 34.47 3.01
2060 2072 3.232662 GACTACTGGGGTCTCTAATCCC 58.767 54.545 0.00 0.00 42.73 3.85
2065 2077 3.951563 TGGGGTCTCTAATCCCATTTG 57.048 47.619 0.00 0.00 45.04 2.32
2066 2078 2.091885 TGGGGTCTCTAATCCCATTTGC 60.092 50.000 0.00 0.00 45.04 3.68
2067 2079 2.175715 GGGGTCTCTAATCCCATTTGCT 59.824 50.000 2.64 0.00 45.06 3.91
2068 2080 3.481453 GGGTCTCTAATCCCATTTGCTC 58.519 50.000 0.00 0.00 42.95 4.26
2069 2081 3.481453 GGTCTCTAATCCCATTTGCTCC 58.519 50.000 0.00 0.00 0.00 4.70
2070 2082 3.481453 GTCTCTAATCCCATTTGCTCCC 58.519 50.000 0.00 0.00 0.00 4.30
2071 2083 2.443255 TCTCTAATCCCATTTGCTCCCC 59.557 50.000 0.00 0.00 0.00 4.81
2072 2084 2.444766 CTCTAATCCCATTTGCTCCCCT 59.555 50.000 0.00 0.00 0.00 4.79
2073 2085 3.652869 CTCTAATCCCATTTGCTCCCCTA 59.347 47.826 0.00 0.00 0.00 3.53
2074 2086 3.652869 TCTAATCCCATTTGCTCCCCTAG 59.347 47.826 0.00 0.00 0.00 3.02
2085 2097 1.770294 CTCCCCTAGCTTTCGTCTCT 58.230 55.000 0.00 0.00 0.00 3.10
2086 2098 1.679153 CTCCCCTAGCTTTCGTCTCTC 59.321 57.143 0.00 0.00 0.00 3.20
2087 2099 1.005569 TCCCCTAGCTTTCGTCTCTCA 59.994 52.381 0.00 0.00 0.00 3.27
2088 2100 1.407258 CCCCTAGCTTTCGTCTCTCAG 59.593 57.143 0.00 0.00 0.00 3.35
2089 2101 2.096248 CCCTAGCTTTCGTCTCTCAGT 58.904 52.381 0.00 0.00 0.00 3.41
2090 2102 2.159310 CCCTAGCTTTCGTCTCTCAGTG 60.159 54.545 0.00 0.00 0.00 3.66
2091 2103 2.490115 CCTAGCTTTCGTCTCTCAGTGT 59.510 50.000 0.00 0.00 0.00 3.55
2092 2104 2.715737 AGCTTTCGTCTCTCAGTGTC 57.284 50.000 0.00 0.00 0.00 3.67
2093 2105 1.957177 AGCTTTCGTCTCTCAGTGTCA 59.043 47.619 0.00 0.00 0.00 3.58
2094 2106 2.030363 AGCTTTCGTCTCTCAGTGTCAG 60.030 50.000 0.00 0.00 0.00 3.51
2095 2107 2.287909 GCTTTCGTCTCTCAGTGTCAGT 60.288 50.000 0.00 0.00 0.00 3.41
2096 2108 3.304257 CTTTCGTCTCTCAGTGTCAGTG 58.696 50.000 0.78 0.78 0.00 3.66
2097 2109 1.968704 TCGTCTCTCAGTGTCAGTGT 58.031 50.000 7.54 0.00 0.00 3.55
2098 2110 1.874231 TCGTCTCTCAGTGTCAGTGTC 59.126 52.381 7.54 0.00 0.00 3.67
2099 2111 1.399087 CGTCTCTCAGTGTCAGTGTCG 60.399 57.143 7.54 1.26 0.00 4.35
2100 2112 1.068885 GTCTCTCAGTGTCAGTGTCGG 60.069 57.143 7.54 0.75 0.00 4.79
2101 2113 0.387878 CTCTCAGTGTCAGTGTCGGC 60.388 60.000 7.54 0.00 0.00 5.54
2102 2114 1.373497 CTCAGTGTCAGTGTCGGCC 60.373 63.158 7.54 0.00 0.00 6.13
2103 2115 2.357517 CAGTGTCAGTGTCGGCCC 60.358 66.667 0.00 0.00 0.00 5.80
2104 2116 2.842462 AGTGTCAGTGTCGGCCCA 60.842 61.111 0.00 0.00 0.00 5.36
2105 2117 2.357517 GTGTCAGTGTCGGCCCAG 60.358 66.667 0.00 0.00 0.00 4.45
2106 2118 4.314440 TGTCAGTGTCGGCCCAGC 62.314 66.667 0.00 0.00 0.00 4.85
2107 2119 4.314440 GTCAGTGTCGGCCCAGCA 62.314 66.667 0.00 0.00 0.00 4.41
2108 2120 4.007644 TCAGTGTCGGCCCAGCAG 62.008 66.667 0.00 0.00 0.00 4.24
2109 2121 4.007644 CAGTGTCGGCCCAGCAGA 62.008 66.667 0.00 0.00 0.00 4.26
2110 2122 3.699894 AGTGTCGGCCCAGCAGAG 61.700 66.667 0.00 0.00 32.90 3.35
2111 2123 4.008933 GTGTCGGCCCAGCAGAGT 62.009 66.667 0.00 0.00 32.90 3.24
2112 2124 4.007644 TGTCGGCCCAGCAGAGTG 62.008 66.667 0.00 0.00 32.90 3.51
2122 2134 3.647824 GCAGAGTGCTTTCGCTGT 58.352 55.556 0.00 0.00 40.96 4.40
2123 2135 1.944778 GCAGAGTGCTTTCGCTGTT 59.055 52.632 0.00 0.00 40.96 3.16
2124 2136 0.385223 GCAGAGTGCTTTCGCTGTTG 60.385 55.000 0.00 0.00 40.96 3.33
2125 2137 0.236711 CAGAGTGCTTTCGCTGTTGG 59.763 55.000 0.00 0.00 36.97 3.77
2126 2138 0.179045 AGAGTGCTTTCGCTGTTGGT 60.179 50.000 0.00 0.00 36.97 3.67
2127 2139 0.040958 GAGTGCTTTCGCTGTTGGTG 60.041 55.000 0.00 0.00 36.97 4.17
2128 2140 0.748005 AGTGCTTTCGCTGTTGGTGT 60.748 50.000 0.00 0.00 36.97 4.16
2129 2141 0.317020 GTGCTTTCGCTGTTGGTGTC 60.317 55.000 0.00 0.00 36.97 3.67
2130 2142 1.282875 GCTTTCGCTGTTGGTGTCC 59.717 57.895 0.00 0.00 0.00 4.02
2131 2143 1.166531 GCTTTCGCTGTTGGTGTCCT 61.167 55.000 0.00 0.00 0.00 3.85
2132 2144 1.308998 CTTTCGCTGTTGGTGTCCTT 58.691 50.000 0.00 0.00 0.00 3.36
2133 2145 1.676006 CTTTCGCTGTTGGTGTCCTTT 59.324 47.619 0.00 0.00 0.00 3.11
2134 2146 1.305201 TTCGCTGTTGGTGTCCTTTC 58.695 50.000 0.00 0.00 0.00 2.62
2135 2147 0.534203 TCGCTGTTGGTGTCCTTTCC 60.534 55.000 0.00 0.00 0.00 3.13
2136 2148 1.841663 CGCTGTTGGTGTCCTTTCCG 61.842 60.000 0.00 0.00 0.00 4.30
2137 2149 0.534203 GCTGTTGGTGTCCTTTCCGA 60.534 55.000 0.00 0.00 0.00 4.55
2138 2150 1.882352 GCTGTTGGTGTCCTTTCCGAT 60.882 52.381 0.00 0.00 0.00 4.18
2139 2151 2.076863 CTGTTGGTGTCCTTTCCGATC 58.923 52.381 0.00 0.00 0.00 3.69
2140 2152 1.697432 TGTTGGTGTCCTTTCCGATCT 59.303 47.619 0.00 0.00 0.00 2.75
2141 2153 2.289444 TGTTGGTGTCCTTTCCGATCTC 60.289 50.000 0.00 0.00 0.00 2.75
2142 2154 1.639722 TGGTGTCCTTTCCGATCTCA 58.360 50.000 0.00 0.00 0.00 3.27
2143 2155 1.974957 TGGTGTCCTTTCCGATCTCAA 59.025 47.619 0.00 0.00 0.00 3.02
2144 2156 2.571653 TGGTGTCCTTTCCGATCTCAAT 59.428 45.455 0.00 0.00 0.00 2.57
2145 2157 2.939103 GGTGTCCTTTCCGATCTCAATG 59.061 50.000 0.00 0.00 0.00 2.82
2146 2158 2.352960 GTGTCCTTTCCGATCTCAATGC 59.647 50.000 0.00 0.00 0.00 3.56
2147 2159 1.594862 GTCCTTTCCGATCTCAATGCG 59.405 52.381 0.00 0.00 0.00 4.73
2148 2160 1.207089 TCCTTTCCGATCTCAATGCGT 59.793 47.619 0.00 0.00 0.00 5.24
2149 2161 2.009774 CCTTTCCGATCTCAATGCGTT 58.990 47.619 0.00 0.00 0.00 4.84
2150 2162 2.420022 CCTTTCCGATCTCAATGCGTTT 59.580 45.455 0.00 0.00 0.00 3.60
2151 2163 3.485877 CCTTTCCGATCTCAATGCGTTTC 60.486 47.826 0.00 0.00 0.00 2.78
2152 2164 2.378445 TCCGATCTCAATGCGTTTCA 57.622 45.000 0.00 0.00 0.00 2.69
2153 2165 1.999735 TCCGATCTCAATGCGTTTCAC 59.000 47.619 0.00 0.00 0.00 3.18
2154 2166 1.062587 CCGATCTCAATGCGTTTCACC 59.937 52.381 0.00 0.00 0.00 4.02
2155 2167 1.267038 CGATCTCAATGCGTTTCACCG 60.267 52.381 0.00 0.00 0.00 4.94
2163 2175 3.411351 CGTTTCACCGCTCCACCG 61.411 66.667 0.00 0.00 0.00 4.94
2171 2183 3.497879 CGCTCCACCGGAAATTCC 58.502 61.111 9.46 0.99 0.00 3.01
2172 2184 2.112815 CGCTCCACCGGAAATTCCC 61.113 63.158 9.46 0.00 31.13 3.97
2173 2185 1.303282 GCTCCACCGGAAATTCCCT 59.697 57.895 9.46 0.00 31.13 4.20
2174 2186 0.748367 GCTCCACCGGAAATTCCCTC 60.748 60.000 9.46 0.00 31.13 4.30
2175 2187 0.912486 CTCCACCGGAAATTCCCTCT 59.088 55.000 9.46 0.00 31.13 3.69
2176 2188 0.618458 TCCACCGGAAATTCCCTCTG 59.382 55.000 9.46 0.00 31.13 3.35
2177 2189 1.032114 CCACCGGAAATTCCCTCTGC 61.032 60.000 9.46 0.00 31.13 4.26
2178 2190 1.032114 CACCGGAAATTCCCTCTGCC 61.032 60.000 9.46 0.00 31.13 4.85
2179 2191 1.453928 CCGGAAATTCCCTCTGCCC 60.454 63.158 6.42 0.00 31.13 5.36
2180 2192 1.453928 CGGAAATTCCCTCTGCCCC 60.454 63.158 6.42 0.00 31.13 5.80
2181 2193 1.926426 CGGAAATTCCCTCTGCCCCT 61.926 60.000 6.42 0.00 31.13 4.79
2182 2194 1.222567 GGAAATTCCCTCTGCCCCTA 58.777 55.000 0.00 0.00 0.00 3.53
2183 2195 1.133761 GGAAATTCCCTCTGCCCCTAC 60.134 57.143 0.00 0.00 0.00 3.18
2184 2196 0.927029 AAATTCCCTCTGCCCCTACC 59.073 55.000 0.00 0.00 0.00 3.18
2185 2197 0.253630 AATTCCCTCTGCCCCTACCA 60.254 55.000 0.00 0.00 0.00 3.25
2186 2198 0.028642 ATTCCCTCTGCCCCTACCAT 60.029 55.000 0.00 0.00 0.00 3.55
2187 2199 0.645496 TTCCCTCTGCCCCTACCATA 59.355 55.000 0.00 0.00 0.00 2.74
2188 2200 0.105142 TCCCTCTGCCCCTACCATAC 60.105 60.000 0.00 0.00 0.00 2.39
2189 2201 0.104934 CCCTCTGCCCCTACCATACT 60.105 60.000 0.00 0.00 0.00 2.12
2190 2202 1.343069 CCTCTGCCCCTACCATACTC 58.657 60.000 0.00 0.00 0.00 2.59
2191 2203 1.343069 CTCTGCCCCTACCATACTCC 58.657 60.000 0.00 0.00 0.00 3.85
2192 2204 0.639943 TCTGCCCCTACCATACTCCA 59.360 55.000 0.00 0.00 0.00 3.86
2193 2205 1.051812 CTGCCCCTACCATACTCCAG 58.948 60.000 0.00 0.00 0.00 3.86
2194 2206 1.054406 TGCCCCTACCATACTCCAGC 61.054 60.000 0.00 0.00 0.00 4.85
2195 2207 0.764752 GCCCCTACCATACTCCAGCT 60.765 60.000 0.00 0.00 0.00 4.24
2196 2208 1.807814 CCCCTACCATACTCCAGCTT 58.192 55.000 0.00 0.00 0.00 3.74
2197 2209 1.417890 CCCCTACCATACTCCAGCTTG 59.582 57.143 0.00 0.00 0.00 4.01
2198 2210 1.417890 CCCTACCATACTCCAGCTTGG 59.582 57.143 0.00 0.00 39.43 3.61
2199 2211 2.119495 CCTACCATACTCCAGCTTGGT 58.881 52.381 10.27 10.27 44.43 3.67
2200 2212 3.305720 CCTACCATACTCCAGCTTGGTA 58.694 50.000 11.34 11.34 42.35 3.25
2202 2214 2.834113 ACCATACTCCAGCTTGGTAGT 58.166 47.619 3.62 7.73 40.62 2.73
2203 2215 3.182152 ACCATACTCCAGCTTGGTAGTT 58.818 45.455 3.62 0.00 40.62 2.24
2204 2216 3.587506 ACCATACTCCAGCTTGGTAGTTT 59.412 43.478 3.62 0.00 40.62 2.66
2205 2217 4.192317 CCATACTCCAGCTTGGTAGTTTC 58.808 47.826 10.24 0.00 39.03 2.78
2206 2218 2.861147 ACTCCAGCTTGGTAGTTTCC 57.139 50.000 0.00 0.00 39.03 3.13
2207 2219 2.054799 ACTCCAGCTTGGTAGTTTCCA 58.945 47.619 0.00 0.00 39.03 3.53
2208 2220 2.224548 ACTCCAGCTTGGTAGTTTCCAC 60.225 50.000 0.00 0.00 39.03 4.02
2209 2221 1.073284 TCCAGCTTGGTAGTTTCCACC 59.927 52.381 0.00 0.00 39.03 4.61
2210 2222 1.156736 CAGCTTGGTAGTTTCCACCG 58.843 55.000 0.00 0.00 39.04 4.94
2211 2223 0.605589 AGCTTGGTAGTTTCCACCGC 60.606 55.000 0.00 0.00 39.04 5.68
2212 2224 1.583495 GCTTGGTAGTTTCCACCGCC 61.583 60.000 0.00 0.00 39.04 6.13
2213 2225 0.036306 CTTGGTAGTTTCCACCGCCT 59.964 55.000 0.00 0.00 39.04 5.52
2214 2226 0.250553 TTGGTAGTTTCCACCGCCTG 60.251 55.000 0.00 0.00 39.04 4.85
2215 2227 1.373812 GGTAGTTTCCACCGCCTGT 59.626 57.895 0.00 0.00 0.00 4.00
2216 2228 0.672711 GGTAGTTTCCACCGCCTGTC 60.673 60.000 0.00 0.00 0.00 3.51
2217 2229 0.672711 GTAGTTTCCACCGCCTGTCC 60.673 60.000 0.00 0.00 0.00 4.02
2218 2230 1.122632 TAGTTTCCACCGCCTGTCCA 61.123 55.000 0.00 0.00 0.00 4.02
2219 2231 1.527380 GTTTCCACCGCCTGTCCAA 60.527 57.895 0.00 0.00 0.00 3.53
2220 2232 1.228124 TTTCCACCGCCTGTCCAAG 60.228 57.895 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 3.635591 AGGAATCCAAATCTGCCGAATT 58.364 40.909 0.61 0.00 0.00 2.17
259 262 4.344359 TTCTATGTTATGCATGGCCGTA 57.656 40.909 10.16 2.00 38.47 4.02
326 329 6.071728 CCCTCTTTTGCAATGAGTTTCACTAT 60.072 38.462 21.02 0.00 32.43 2.12
330 333 3.960102 ACCCTCTTTTGCAATGAGTTTCA 59.040 39.130 21.02 0.00 32.43 2.69
968 977 9.525409 CCTTTTCTATCTTTGCCAATAAATGAG 57.475 33.333 0.00 0.00 0.00 2.90
1036 1045 1.699634 GGGTAGAATGCTAGATGCCCA 59.300 52.381 0.00 0.00 42.00 5.36
1062 1071 0.391793 TCGCGATTGTATGGCCAACA 60.392 50.000 10.96 13.21 0.00 3.33
1172 1181 7.523293 TCCTTTCTTGCATTTTCATAACTCA 57.477 32.000 0.00 0.00 0.00 3.41
1409 1421 9.325198 GGTACTGAACTTTTGGATTTGAATTTT 57.675 29.630 0.00 0.00 0.00 1.82
1410 1422 8.704668 AGGTACTGAACTTTTGGATTTGAATTT 58.295 29.630 0.00 0.00 37.18 1.82
1411 1423 8.250143 AGGTACTGAACTTTTGGATTTGAATT 57.750 30.769 0.00 0.00 37.18 2.17
1412 1424 7.839680 AGGTACTGAACTTTTGGATTTGAAT 57.160 32.000 0.00 0.00 37.18 2.57
1952 1964 4.194640 GTTAAGAAACGGATAGTTCCCCC 58.805 47.826 0.00 0.00 43.37 5.40
1953 1965 4.633126 GTGTTAAGAAACGGATAGTTCCCC 59.367 45.833 0.00 0.00 43.37 4.81
1954 1966 4.633126 GGTGTTAAGAAACGGATAGTTCCC 59.367 45.833 0.00 0.00 43.37 3.97
1955 1967 5.240121 TGGTGTTAAGAAACGGATAGTTCC 58.760 41.667 0.00 0.00 43.37 3.62
1956 1968 6.790285 TTGGTGTTAAGAAACGGATAGTTC 57.210 37.500 0.00 0.00 43.37 3.01
1957 1969 7.754851 AATTGGTGTTAAGAAACGGATAGTT 57.245 32.000 0.00 0.00 46.76 2.24
1958 1970 7.664318 AGAAATTGGTGTTAAGAAACGGATAGT 59.336 33.333 0.00 0.00 38.53 2.12
1959 1971 8.040716 AGAAATTGGTGTTAAGAAACGGATAG 57.959 34.615 0.00 0.00 38.53 2.08
1960 1972 7.989416 AGAAATTGGTGTTAAGAAACGGATA 57.011 32.000 0.00 0.00 38.53 2.59
1961 1973 6.894339 AGAAATTGGTGTTAAGAAACGGAT 57.106 33.333 0.00 0.00 38.53 4.18
1962 1974 7.881232 AGATAGAAATTGGTGTTAAGAAACGGA 59.119 33.333 0.00 0.00 38.53 4.69
1963 1975 8.040716 AGATAGAAATTGGTGTTAAGAAACGG 57.959 34.615 0.00 0.00 38.53 4.44
1964 1976 9.893305 AAAGATAGAAATTGGTGTTAAGAAACG 57.107 29.630 0.00 0.00 38.53 3.60
1971 1983 9.601217 GCTAGAGAAAGATAGAAATTGGTGTTA 57.399 33.333 0.00 0.00 0.00 2.41
1972 1984 7.554476 GGCTAGAGAAAGATAGAAATTGGTGTT 59.446 37.037 0.00 0.00 0.00 3.32
1973 1985 7.051000 GGCTAGAGAAAGATAGAAATTGGTGT 58.949 38.462 0.00 0.00 0.00 4.16
1974 1986 7.050377 TGGCTAGAGAAAGATAGAAATTGGTG 58.950 38.462 0.00 0.00 0.00 4.17
1975 1987 7.200434 TGGCTAGAGAAAGATAGAAATTGGT 57.800 36.000 0.00 0.00 0.00 3.67
1976 1988 7.012799 GGTTGGCTAGAGAAAGATAGAAATTGG 59.987 40.741 0.00 0.00 0.00 3.16
1977 1989 7.772757 AGGTTGGCTAGAGAAAGATAGAAATTG 59.227 37.037 0.00 0.00 0.00 2.32
1978 1990 7.866870 AGGTTGGCTAGAGAAAGATAGAAATT 58.133 34.615 0.00 0.00 0.00 1.82
1979 1991 7.444703 AGGTTGGCTAGAGAAAGATAGAAAT 57.555 36.000 0.00 0.00 0.00 2.17
1980 1992 6.875972 AGGTTGGCTAGAGAAAGATAGAAA 57.124 37.500 0.00 0.00 0.00 2.52
1981 1993 6.127026 GGAAGGTTGGCTAGAGAAAGATAGAA 60.127 42.308 0.00 0.00 0.00 2.10
1982 1994 5.364157 GGAAGGTTGGCTAGAGAAAGATAGA 59.636 44.000 0.00 0.00 0.00 1.98
1983 1995 5.454045 GGGAAGGTTGGCTAGAGAAAGATAG 60.454 48.000 0.00 0.00 0.00 2.08
1984 1996 4.409247 GGGAAGGTTGGCTAGAGAAAGATA 59.591 45.833 0.00 0.00 0.00 1.98
1985 1997 3.201045 GGGAAGGTTGGCTAGAGAAAGAT 59.799 47.826 0.00 0.00 0.00 2.40
1986 1998 2.572104 GGGAAGGTTGGCTAGAGAAAGA 59.428 50.000 0.00 0.00 0.00 2.52
1987 1999 2.678190 CGGGAAGGTTGGCTAGAGAAAG 60.678 54.545 0.00 0.00 0.00 2.62
1988 2000 1.278127 CGGGAAGGTTGGCTAGAGAAA 59.722 52.381 0.00 0.00 0.00 2.52
1989 2001 0.902531 CGGGAAGGTTGGCTAGAGAA 59.097 55.000 0.00 0.00 0.00 2.87
1990 2002 1.614241 GCGGGAAGGTTGGCTAGAGA 61.614 60.000 0.00 0.00 0.00 3.10
1991 2003 1.153349 GCGGGAAGGTTGGCTAGAG 60.153 63.158 0.00 0.00 0.00 2.43
1992 2004 1.899437 CTGCGGGAAGGTTGGCTAGA 61.899 60.000 0.00 0.00 0.00 2.43
1993 2005 1.450312 CTGCGGGAAGGTTGGCTAG 60.450 63.158 0.00 0.00 0.00 3.42
1994 2006 2.668632 CTGCGGGAAGGTTGGCTA 59.331 61.111 0.00 0.00 0.00 3.93
1997 2009 3.365265 GTGCTGCGGGAAGGTTGG 61.365 66.667 0.00 0.00 0.00 3.77
1998 2010 2.463589 TAGGTGCTGCGGGAAGGTTG 62.464 60.000 0.00 0.00 0.00 3.77
1999 2011 2.185310 CTAGGTGCTGCGGGAAGGTT 62.185 60.000 0.00 0.00 0.00 3.50
2000 2012 2.606519 TAGGTGCTGCGGGAAGGT 60.607 61.111 0.00 0.00 0.00 3.50
2001 2013 1.327690 TACTAGGTGCTGCGGGAAGG 61.328 60.000 0.00 0.00 0.00 3.46
2002 2014 0.753262 ATACTAGGTGCTGCGGGAAG 59.247 55.000 0.00 0.00 0.00 3.46
2003 2015 0.750850 GATACTAGGTGCTGCGGGAA 59.249 55.000 0.00 0.00 0.00 3.97
2004 2016 1.113517 GGATACTAGGTGCTGCGGGA 61.114 60.000 0.00 0.00 0.00 5.14
2005 2017 1.367840 GGATACTAGGTGCTGCGGG 59.632 63.158 0.00 0.00 0.00 6.13
2006 2018 0.681733 ATGGATACTAGGTGCTGCGG 59.318 55.000 0.00 0.00 37.61 5.69
2007 2019 1.667177 CGATGGATACTAGGTGCTGCG 60.667 57.143 0.00 0.00 37.61 5.18
2008 2020 1.341531 ACGATGGATACTAGGTGCTGC 59.658 52.381 0.00 0.00 37.61 5.25
2009 2021 3.735237 AACGATGGATACTAGGTGCTG 57.265 47.619 0.00 0.00 37.61 4.41
2010 2022 4.261489 CGTAAACGATGGATACTAGGTGCT 60.261 45.833 0.00 0.00 43.02 4.40
2011 2023 3.979495 CGTAAACGATGGATACTAGGTGC 59.021 47.826 0.00 0.00 43.02 5.01
2012 2024 4.543692 CCGTAAACGATGGATACTAGGTG 58.456 47.826 3.65 0.00 43.02 4.00
2013 2025 3.005155 GCCGTAAACGATGGATACTAGGT 59.995 47.826 3.65 0.00 43.02 3.08
2014 2026 3.255149 AGCCGTAAACGATGGATACTAGG 59.745 47.826 3.65 0.00 43.02 3.02
2015 2027 4.500603 AGCCGTAAACGATGGATACTAG 57.499 45.455 3.65 0.00 43.02 2.57
2016 2028 4.456911 CCTAGCCGTAAACGATGGATACTA 59.543 45.833 3.65 0.00 43.02 1.82
2017 2029 3.255149 CCTAGCCGTAAACGATGGATACT 59.745 47.826 3.65 0.00 43.02 2.12
2018 2030 3.254166 TCCTAGCCGTAAACGATGGATAC 59.746 47.826 3.65 0.00 43.02 2.24
2019 2031 3.254166 GTCCTAGCCGTAAACGATGGATA 59.746 47.826 3.65 0.00 43.02 2.59
2020 2032 2.035576 GTCCTAGCCGTAAACGATGGAT 59.964 50.000 3.65 0.00 43.02 3.41
2021 2033 1.406539 GTCCTAGCCGTAAACGATGGA 59.593 52.381 3.65 3.33 43.02 3.41
2022 2034 1.407979 AGTCCTAGCCGTAAACGATGG 59.592 52.381 3.65 1.05 43.02 3.51
2023 2035 2.865343 AGTCCTAGCCGTAAACGATG 57.135 50.000 3.65 0.00 43.02 3.84
2024 2036 3.314635 CAGTAGTCCTAGCCGTAAACGAT 59.685 47.826 3.65 0.00 43.02 3.73
2025 2037 2.679837 CAGTAGTCCTAGCCGTAAACGA 59.320 50.000 3.65 0.00 43.02 3.85
2026 2038 2.223433 CCAGTAGTCCTAGCCGTAAACG 60.223 54.545 0.00 0.00 39.44 3.60
2027 2039 2.100418 CCCAGTAGTCCTAGCCGTAAAC 59.900 54.545 0.00 0.00 0.00 2.01
2028 2040 2.381911 CCCAGTAGTCCTAGCCGTAAA 58.618 52.381 0.00 0.00 0.00 2.01
2029 2041 1.410648 CCCCAGTAGTCCTAGCCGTAA 60.411 57.143 0.00 0.00 0.00 3.18
2030 2042 0.184451 CCCCAGTAGTCCTAGCCGTA 59.816 60.000 0.00 0.00 0.00 4.02
2031 2043 1.076192 CCCCAGTAGTCCTAGCCGT 60.076 63.158 0.00 0.00 0.00 5.68
2032 2044 1.076192 ACCCCAGTAGTCCTAGCCG 60.076 63.158 0.00 0.00 0.00 5.52
2033 2045 0.262285 AGACCCCAGTAGTCCTAGCC 59.738 60.000 0.00 0.00 34.67 3.93
2034 2046 1.215924 AGAGACCCCAGTAGTCCTAGC 59.784 57.143 0.00 0.00 34.67 3.42
2035 2047 4.792513 TTAGAGACCCCAGTAGTCCTAG 57.207 50.000 0.00 0.00 34.67 3.02
2036 2048 4.106019 GGATTAGAGACCCCAGTAGTCCTA 59.894 50.000 0.00 0.00 34.67 2.94
2037 2049 3.117054 GGATTAGAGACCCCAGTAGTCCT 60.117 52.174 0.00 0.00 34.67 3.85
2038 2050 3.232662 GGATTAGAGACCCCAGTAGTCC 58.767 54.545 0.00 0.00 34.67 3.85
2039 2051 3.232662 GGGATTAGAGACCCCAGTAGTC 58.767 54.545 0.00 0.00 40.19 2.59
2040 2052 2.590611 TGGGATTAGAGACCCCAGTAGT 59.409 50.000 0.00 0.00 44.67 2.73
2041 2053 3.330126 TGGGATTAGAGACCCCAGTAG 57.670 52.381 0.00 0.00 44.67 2.57
2046 2058 2.175715 AGCAAATGGGATTAGAGACCCC 59.824 50.000 0.00 0.00 45.01 4.95
2047 2059 3.481453 GAGCAAATGGGATTAGAGACCC 58.519 50.000 0.00 0.00 45.74 4.46
2048 2060 3.481453 GGAGCAAATGGGATTAGAGACC 58.519 50.000 0.00 0.00 0.00 3.85
2049 2061 3.481453 GGGAGCAAATGGGATTAGAGAC 58.519 50.000 0.00 0.00 0.00 3.36
2050 2062 2.443255 GGGGAGCAAATGGGATTAGAGA 59.557 50.000 0.00 0.00 0.00 3.10
2051 2063 2.444766 AGGGGAGCAAATGGGATTAGAG 59.555 50.000 0.00 0.00 0.00 2.43
2052 2064 2.502745 AGGGGAGCAAATGGGATTAGA 58.497 47.619 0.00 0.00 0.00 2.10
2053 2065 4.026356 CTAGGGGAGCAAATGGGATTAG 57.974 50.000 0.00 0.00 0.00 1.73
2066 2078 1.679153 GAGAGACGAAAGCTAGGGGAG 59.321 57.143 0.00 0.00 0.00 4.30
2067 2079 1.005569 TGAGAGACGAAAGCTAGGGGA 59.994 52.381 0.00 0.00 0.00 4.81
2068 2080 1.407258 CTGAGAGACGAAAGCTAGGGG 59.593 57.143 0.00 0.00 0.00 4.79
2069 2081 2.096248 ACTGAGAGACGAAAGCTAGGG 58.904 52.381 0.00 0.00 0.00 3.53
2070 2082 2.490115 ACACTGAGAGACGAAAGCTAGG 59.510 50.000 0.00 0.00 0.00 3.02
2071 2083 3.189495 TGACACTGAGAGACGAAAGCTAG 59.811 47.826 0.00 0.00 0.00 3.42
2072 2084 3.146847 TGACACTGAGAGACGAAAGCTA 58.853 45.455 0.00 0.00 0.00 3.32
2073 2085 1.957177 TGACACTGAGAGACGAAAGCT 59.043 47.619 0.00 0.00 0.00 3.74
2074 2086 2.287909 ACTGACACTGAGAGACGAAAGC 60.288 50.000 0.00 0.00 0.00 3.51
2075 2087 3.243234 ACACTGACACTGAGAGACGAAAG 60.243 47.826 0.00 0.00 0.00 2.62
2076 2088 2.688446 ACACTGACACTGAGAGACGAAA 59.312 45.455 0.00 0.00 0.00 3.46
2077 2089 2.290916 GACACTGACACTGAGAGACGAA 59.709 50.000 0.00 0.00 0.00 3.85
2078 2090 1.874231 GACACTGACACTGAGAGACGA 59.126 52.381 0.00 0.00 0.00 4.20
2079 2091 1.399087 CGACACTGACACTGAGAGACG 60.399 57.143 0.00 0.00 0.00 4.18
2080 2092 1.068885 CCGACACTGACACTGAGAGAC 60.069 57.143 0.00 0.00 0.00 3.36
2081 2093 1.239347 CCGACACTGACACTGAGAGA 58.761 55.000 0.00 0.00 0.00 3.10
2082 2094 0.387878 GCCGACACTGACACTGAGAG 60.388 60.000 0.00 0.00 0.00 3.20
2083 2095 1.660355 GCCGACACTGACACTGAGA 59.340 57.895 0.00 0.00 0.00 3.27
2084 2096 1.373497 GGCCGACACTGACACTGAG 60.373 63.158 0.00 0.00 0.00 3.35
2085 2097 2.734591 GGCCGACACTGACACTGA 59.265 61.111 0.00 0.00 0.00 3.41
2086 2098 2.357517 GGGCCGACACTGACACTG 60.358 66.667 0.00 0.00 0.00 3.66
2087 2099 2.842462 TGGGCCGACACTGACACT 60.842 61.111 0.00 0.00 0.00 3.55
2088 2100 2.357517 CTGGGCCGACACTGACAC 60.358 66.667 0.00 0.00 0.00 3.67
2089 2101 4.314440 GCTGGGCCGACACTGACA 62.314 66.667 0.00 0.00 0.00 3.58
2090 2102 4.314440 TGCTGGGCCGACACTGAC 62.314 66.667 0.00 0.00 0.00 3.51
2091 2103 4.007644 CTGCTGGGCCGACACTGA 62.008 66.667 0.00 0.00 0.00 3.41
2092 2104 3.947132 CTCTGCTGGGCCGACACTG 62.947 68.421 0.00 0.00 0.00 3.66
2093 2105 3.699894 CTCTGCTGGGCCGACACT 61.700 66.667 0.00 0.00 0.00 3.55
2094 2106 4.008933 ACTCTGCTGGGCCGACAC 62.009 66.667 0.00 0.00 0.00 3.67
2095 2107 4.007644 CACTCTGCTGGGCCGACA 62.008 66.667 0.00 0.00 0.00 4.35
2113 2125 1.308998 AAGGACACCAACAGCGAAAG 58.691 50.000 0.00 0.00 0.00 2.62
2114 2126 1.673920 GAAAGGACACCAACAGCGAAA 59.326 47.619 0.00 0.00 0.00 3.46
2115 2127 1.305201 GAAAGGACACCAACAGCGAA 58.695 50.000 0.00 0.00 0.00 4.70
2116 2128 0.534203 GGAAAGGACACCAACAGCGA 60.534 55.000 0.00 0.00 0.00 4.93
2117 2129 1.841663 CGGAAAGGACACCAACAGCG 61.842 60.000 0.00 0.00 0.00 5.18
2118 2130 0.534203 TCGGAAAGGACACCAACAGC 60.534 55.000 0.00 0.00 0.00 4.40
2119 2131 2.076863 GATCGGAAAGGACACCAACAG 58.923 52.381 0.00 0.00 0.00 3.16
2120 2132 1.697432 AGATCGGAAAGGACACCAACA 59.303 47.619 0.00 0.00 0.00 3.33
2121 2133 2.289444 TGAGATCGGAAAGGACACCAAC 60.289 50.000 0.00 0.00 0.00 3.77
2122 2134 1.974957 TGAGATCGGAAAGGACACCAA 59.025 47.619 0.00 0.00 0.00 3.67
2123 2135 1.639722 TGAGATCGGAAAGGACACCA 58.360 50.000 0.00 0.00 0.00 4.17
2124 2136 2.762535 TTGAGATCGGAAAGGACACC 57.237 50.000 0.00 0.00 0.00 4.16
2125 2137 2.352960 GCATTGAGATCGGAAAGGACAC 59.647 50.000 0.00 0.00 0.00 3.67
2126 2138 2.632377 GCATTGAGATCGGAAAGGACA 58.368 47.619 0.00 0.00 0.00 4.02
2127 2139 1.594862 CGCATTGAGATCGGAAAGGAC 59.405 52.381 0.00 0.00 0.00 3.85
2128 2140 1.207089 ACGCATTGAGATCGGAAAGGA 59.793 47.619 0.00 0.00 0.00 3.36
2129 2141 1.656652 ACGCATTGAGATCGGAAAGG 58.343 50.000 0.00 0.00 0.00 3.11
2130 2142 3.125146 TGAAACGCATTGAGATCGGAAAG 59.875 43.478 0.00 0.00 0.00 2.62
2131 2143 3.070748 TGAAACGCATTGAGATCGGAAA 58.929 40.909 0.00 0.00 0.00 3.13
2132 2144 2.415168 GTGAAACGCATTGAGATCGGAA 59.585 45.455 0.00 0.00 0.00 4.30
2133 2145 1.999735 GTGAAACGCATTGAGATCGGA 59.000 47.619 0.00 0.00 0.00 4.55
2134 2146 1.062587 GGTGAAACGCATTGAGATCGG 59.937 52.381 0.00 0.00 38.12 4.18
2135 2147 1.267038 CGGTGAAACGCATTGAGATCG 60.267 52.381 0.00 0.00 38.12 3.69
2136 2148 2.442189 CGGTGAAACGCATTGAGATC 57.558 50.000 0.00 0.00 38.12 2.75
2146 2158 3.411351 CGGTGGAGCGGTGAAACG 61.411 66.667 0.00 0.00 38.12 3.60
2147 2159 2.999739 TTCCGGTGGAGCGGTGAAAC 63.000 60.000 16.33 0.00 31.21 2.78
2148 2160 2.326773 TTTCCGGTGGAGCGGTGAAA 62.327 55.000 16.33 8.33 31.21 2.69
2149 2161 2.119484 ATTTCCGGTGGAGCGGTGAA 62.119 55.000 16.33 12.63 31.21 3.18
2150 2162 2.119484 AATTTCCGGTGGAGCGGTGA 62.119 55.000 16.33 7.36 31.21 4.02
2151 2163 1.644786 GAATTTCCGGTGGAGCGGTG 61.645 60.000 16.33 0.00 31.21 4.94
2152 2164 1.376812 GAATTTCCGGTGGAGCGGT 60.377 57.895 16.33 0.00 31.21 5.68
2153 2165 2.112815 GGAATTTCCGGTGGAGCGG 61.113 63.158 11.05 11.05 31.21 5.52
2154 2166 2.112815 GGGAATTTCCGGTGGAGCG 61.113 63.158 9.31 0.00 37.43 5.03
2155 2167 0.748367 GAGGGAATTTCCGGTGGAGC 60.748 60.000 9.31 0.00 37.43 4.70
2156 2168 0.912486 AGAGGGAATTTCCGGTGGAG 59.088 55.000 9.31 0.00 37.43 3.86
2157 2169 0.618458 CAGAGGGAATTTCCGGTGGA 59.382 55.000 9.31 0.00 37.43 4.02
2158 2170 1.032114 GCAGAGGGAATTTCCGGTGG 61.032 60.000 9.31 1.12 37.43 4.61
2159 2171 1.032114 GGCAGAGGGAATTTCCGGTG 61.032 60.000 9.31 7.48 37.43 4.94
2160 2172 1.303282 GGCAGAGGGAATTTCCGGT 59.697 57.895 9.31 0.00 37.43 5.28
2161 2173 1.453928 GGGCAGAGGGAATTTCCGG 60.454 63.158 9.31 0.00 37.43 5.14
2162 2174 1.453928 GGGGCAGAGGGAATTTCCG 60.454 63.158 9.31 0.00 37.43 4.30
2163 2175 1.133761 GTAGGGGCAGAGGGAATTTCC 60.134 57.143 6.91 6.91 35.23 3.13
2164 2176 1.133761 GGTAGGGGCAGAGGGAATTTC 60.134 57.143 0.00 0.00 0.00 2.17
2165 2177 0.927029 GGTAGGGGCAGAGGGAATTT 59.073 55.000 0.00 0.00 0.00 1.82
2166 2178 0.253630 TGGTAGGGGCAGAGGGAATT 60.254 55.000 0.00 0.00 0.00 2.17
2167 2179 0.028642 ATGGTAGGGGCAGAGGGAAT 60.029 55.000 0.00 0.00 0.00 3.01
2168 2180 0.645496 TATGGTAGGGGCAGAGGGAA 59.355 55.000 0.00 0.00 0.00 3.97
2169 2181 0.105142 GTATGGTAGGGGCAGAGGGA 60.105 60.000 0.00 0.00 0.00 4.20
2170 2182 0.104934 AGTATGGTAGGGGCAGAGGG 60.105 60.000 0.00 0.00 0.00 4.30
2171 2183 1.343069 GAGTATGGTAGGGGCAGAGG 58.657 60.000 0.00 0.00 0.00 3.69
2172 2184 1.343069 GGAGTATGGTAGGGGCAGAG 58.657 60.000 0.00 0.00 0.00 3.35
2173 2185 0.639943 TGGAGTATGGTAGGGGCAGA 59.360 55.000 0.00 0.00 0.00 4.26
2174 2186 1.051812 CTGGAGTATGGTAGGGGCAG 58.948 60.000 0.00 0.00 0.00 4.85
2175 2187 1.054406 GCTGGAGTATGGTAGGGGCA 61.054 60.000 0.00 0.00 0.00 5.36
2176 2188 0.764752 AGCTGGAGTATGGTAGGGGC 60.765 60.000 0.00 0.00 0.00 5.80
2177 2189 1.417890 CAAGCTGGAGTATGGTAGGGG 59.582 57.143 0.00 0.00 0.00 4.79
2178 2190 1.417890 CCAAGCTGGAGTATGGTAGGG 59.582 57.143 0.00 0.00 40.96 3.53
2179 2191 2.119495 ACCAAGCTGGAGTATGGTAGG 58.881 52.381 3.62 0.00 44.11 3.18
2181 2193 3.990369 ACTACCAAGCTGGAGTATGGTA 58.010 45.455 11.34 11.34 44.11 3.25
2183 2195 3.914426 AACTACCAAGCTGGAGTATGG 57.086 47.619 8.91 3.89 40.96 2.74
2184 2196 4.192317 GGAAACTACCAAGCTGGAGTATG 58.808 47.826 8.91 0.00 40.96 2.39
2185 2197 3.844211 TGGAAACTACCAAGCTGGAGTAT 59.156 43.478 8.91 0.00 40.96 2.12
2186 2198 3.007614 GTGGAAACTACCAAGCTGGAGTA 59.992 47.826 8.91 0.64 40.96 2.59
2187 2199 2.054799 TGGAAACTACCAAGCTGGAGT 58.945 47.619 8.91 0.00 40.96 3.85
2188 2200 2.427506 GTGGAAACTACCAAGCTGGAG 58.572 52.381 8.91 0.00 40.96 3.86
2189 2201 1.073284 GGTGGAAACTACCAAGCTGGA 59.927 52.381 8.91 0.00 40.96 3.86
2190 2202 1.534729 GGTGGAAACTACCAAGCTGG 58.465 55.000 0.00 0.00 45.02 4.85
2191 2203 1.156736 CGGTGGAAACTACCAAGCTG 58.843 55.000 5.27 0.00 41.87 4.24
2192 2204 0.605589 GCGGTGGAAACTACCAAGCT 60.606 55.000 0.00 0.00 41.87 3.74
2193 2205 1.583495 GGCGGTGGAAACTACCAAGC 61.583 60.000 5.27 0.00 41.87 4.01
2194 2206 0.036306 AGGCGGTGGAAACTACCAAG 59.964 55.000 5.27 0.00 41.87 3.61
2195 2207 0.250553 CAGGCGGTGGAAACTACCAA 60.251 55.000 5.27 0.00 41.87 3.67
2196 2208 1.373435 CAGGCGGTGGAAACTACCA 59.627 57.895 5.27 0.00 38.11 3.25
2197 2209 0.672711 GACAGGCGGTGGAAACTACC 60.673 60.000 0.00 0.00 34.81 3.18
2198 2210 0.672711 GGACAGGCGGTGGAAACTAC 60.673 60.000 0.00 0.00 0.00 2.73
2199 2211 1.122632 TGGACAGGCGGTGGAAACTA 61.123 55.000 0.00 0.00 0.00 2.24
2200 2212 1.990160 TTGGACAGGCGGTGGAAACT 61.990 55.000 0.00 0.00 0.00 2.66
2201 2213 1.515521 CTTGGACAGGCGGTGGAAAC 61.516 60.000 0.00 0.00 0.00 2.78
2202 2214 1.228124 CTTGGACAGGCGGTGGAAA 60.228 57.895 0.00 0.00 0.00 3.13
2203 2215 2.429930 CTTGGACAGGCGGTGGAA 59.570 61.111 0.00 0.00 0.00 3.53
2204 2216 3.636231 CCTTGGACAGGCGGTGGA 61.636 66.667 0.00 0.00 35.13 4.02


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

AutoCloner maintained by Alex Coulton.