Multiple sequence alignment - TraesCS5D01G164200

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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 TraesCS5D01G164200 chr5D 100.000 6560 0 0 1 6560 255683665 255690224 0.000000e+00 12115.0
1 TraesCS5D01G164200 chr5D 92.877 702 42 6 99 794 359054831 359055530 0.000000e+00 1013.0
2 TraesCS5D01G164200 chr5D 84.813 428 44 11 3942 4363 170396628 170396216 1.700000e-110 411.0
3 TraesCS5D01G164200 chr5D 81.452 248 26 11 3950 4190 255686700 255686934 1.120000e-42 185.0
4 TraesCS5D01G164200 chr5D 81.377 247 28 10 3036 3270 255687614 255687854 1.120000e-42 185.0
5 TraesCS5D01G164200 chr5A 96.033 3151 84 20 810 3935 339736632 339739766 0.000000e+00 5088.0
6 TraesCS5D01G164200 chr5A 93.598 2671 92 33 3934 6560 339739848 339742483 0.000000e+00 3912.0
7 TraesCS5D01G164200 chr5A 92.833 293 18 2 2054 2343 34330295 34330003 7.860000e-114 422.0
8 TraesCS5D01G164200 chr5A 86.514 393 34 4 1468 1842 34330764 34330373 1.320000e-111 414.0
9 TraesCS5D01G164200 chr5A 86.500 200 22 5 4042 4238 105083241 105083044 1.430000e-51 215.0
10 TraesCS5D01G164200 chr5A 83.401 247 26 8 3950 4190 339738866 339739103 1.430000e-51 215.0
11 TraesCS5D01G164200 chr5A 93.939 132 5 2 3108 3236 708160247 708160378 5.190000e-46 196.0
12 TraesCS5D01G164200 chr5A 93.684 95 6 0 1966 2060 519884868 519884774 6.860000e-30 143.0
13 TraesCS5D01G164200 chr5A 93.684 95 5 1 1963 2057 355734048 355734141 2.470000e-29 141.0
14 TraesCS5D01G164200 chr5A 87.805 123 11 3 3026 3147 708160127 708160246 2.470000e-29 141.0
15 TraesCS5D01G164200 chr5B 95.731 2108 41 16 2054 4150 289563362 289565431 0.000000e+00 3349.0
16 TraesCS5D01G164200 chr5B 94.841 1861 54 15 4149 5989 289565513 289567351 0.000000e+00 2867.0
17 TraesCS5D01G164200 chr5B 95.638 1192 31 9 791 1972 289562184 289563364 0.000000e+00 1893.0
18 TraesCS5D01G164200 chr5B 95.923 466 19 0 6095 6560 289574078 289574543 0.000000e+00 756.0
19 TraesCS5D01G164200 chr5B 86.799 303 28 7 3942 4239 318136161 318135866 1.760000e-85 327.0
20 TraesCS5D01G164200 chr5B 87.793 213 22 3 3026 3236 24639515 24639725 5.080000e-61 246.0
21 TraesCS5D01G164200 chr5B 82.234 197 19 9 3036 3229 289565247 289565430 8.810000e-34 156.0
22 TraesCS5D01G164200 chr5B 92.661 109 6 2 5988 6096 289567511 289567617 8.810000e-34 156.0
23 TraesCS5D01G164200 chr3A 92.450 808 47 6 1 794 13961710 13962517 0.000000e+00 1142.0
24 TraesCS5D01G164200 chr2A 92.327 808 48 6 1 794 766828111 766828918 0.000000e+00 1136.0
25 TraesCS5D01G164200 chr2A 91.832 808 52 6 1 794 649567795 649566988 0.000000e+00 1114.0
26 TraesCS5D01G164200 chr2A 89.623 106 9 2 1953 2057 678422081 678421977 4.130000e-27 134.0
27 TraesCS5D01G164200 chr7A 92.193 807 47 8 1 792 628836303 628837108 0.000000e+00 1127.0
28 TraesCS5D01G164200 chr1A 91.584 808 54 6 1 794 491117483 491116676 0.000000e+00 1103.0
29 TraesCS5D01G164200 chr1A 91.337 808 55 7 1 794 513205762 513206568 0.000000e+00 1090.0
30 TraesCS5D01G164200 chr1A 84.706 255 36 2 1039 1293 487695579 487695328 1.090000e-62 252.0
31 TraesCS5D01G164200 chr4B 92.424 726 49 6 2 723 174044700 174043977 0.000000e+00 1031.0
32 TraesCS5D01G164200 chr4B 86.235 247 26 8 3999 4239 636711899 636711655 1.810000e-65 261.0
33 TraesCS5D01G164200 chr4B 83.974 156 20 3 3076 3228 636711902 636711749 1.910000e-30 145.0
34 TraesCS5D01G164200 chr4B 97.674 43 1 0 3942 3984 636711937 636711895 2.540000e-09 75.0
35 TraesCS5D01G164200 chr1D 93.286 700 41 4 99 792 425542977 425542278 0.000000e+00 1027.0
36 TraesCS5D01G164200 chr2D 93.939 231 5 4 1 231 7060872 7060651 2.270000e-89 340.0
37 TraesCS5D01G164200 chr2D 93.939 231 5 5 1 231 641020277 641020498 2.270000e-89 340.0
38 TraesCS5D01G164200 chr2D 94.505 91 5 0 1966 2056 353281061 353280971 2.470000e-29 141.0
39 TraesCS5D01G164200 chr4A 87.213 305 24 10 3942 4239 658780583 658780287 3.790000e-87 333.0
40 TraesCS5D01G164200 chr4A 87.213 305 24 10 3942 4239 658808209 658807913 3.790000e-87 333.0
41 TraesCS5D01G164200 chr4A 86.885 305 25 10 3942 4239 658763090 658762794 1.760000e-85 327.0
42 TraesCS5D01G164200 chr4A 90.050 201 15 5 4042 4238 66751700 66751501 8.440000e-64 255.0
43 TraesCS5D01G164200 chr4A 88.073 109 9 3 3124 3229 66751700 66751593 6.910000e-25 126.0
44 TraesCS5D01G164200 chr4A 92.857 56 4 0 4068 4123 66751760 66751705 1.520000e-11 82.4
45 TraesCS5D01G164200 chr1B 86.235 247 25 9 3999 4239 55334480 55334723 6.530000e-65 259.0
46 TraesCS5D01G164200 chr6D 87.417 151 9 5 4009 4150 427000041 427000190 1.460000e-36 165.0
47 TraesCS5D01G164200 chr6D 89.189 111 8 3 1971 2080 469536403 469536296 1.150000e-27 135.0
48 TraesCS5D01G164200 chr6D 82.857 140 11 6 3102 3229 427000051 427000189 5.380000e-21 113.0
49 TraesCS5D01G164200 chr4D 96.552 87 3 0 1971 2057 28237809 28237895 1.910000e-30 145.0
50 TraesCS5D01G164200 chr7D 92.632 95 7 0 1963 2057 10055371 10055465 3.190000e-28 137.0
51 TraesCS5D01G164200 chr7D 89.524 105 9 2 1954 2056 81910935 81911039 1.480000e-26 132.0
52 TraesCS5D01G164200 chr6B 91.089 101 6 2 1968 2065 308529201 308529301 4.130000e-27 134.0


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 TraesCS5D01G164200 chr5D 255683665 255690224 6559 False 4161.666667 12115 87.609667 1 6560 3 chr5D.!!$F2 6559
1 TraesCS5D01G164200 chr5D 359054831 359055530 699 False 1013.000000 1013 92.877000 99 794 1 chr5D.!!$F1 695
2 TraesCS5D01G164200 chr5A 339736632 339742483 5851 False 3071.666667 5088 91.010667 810 6560 3 chr5A.!!$F2 5750
3 TraesCS5D01G164200 chr5A 34330003 34330764 761 True 418.000000 422 89.673500 1468 2343 2 chr5A.!!$R3 875
4 TraesCS5D01G164200 chr5B 289562184 289567617 5433 False 1684.200000 3349 92.221000 791 6096 5 chr5B.!!$F3 5305
5 TraesCS5D01G164200 chr3A 13961710 13962517 807 False 1142.000000 1142 92.450000 1 794 1 chr3A.!!$F1 793
6 TraesCS5D01G164200 chr2A 766828111 766828918 807 False 1136.000000 1136 92.327000 1 794 1 chr2A.!!$F1 793
7 TraesCS5D01G164200 chr2A 649566988 649567795 807 True 1114.000000 1114 91.832000 1 794 1 chr2A.!!$R1 793
8 TraesCS5D01G164200 chr7A 628836303 628837108 805 False 1127.000000 1127 92.193000 1 792 1 chr7A.!!$F1 791
9 TraesCS5D01G164200 chr1A 491116676 491117483 807 True 1103.000000 1103 91.584000 1 794 1 chr1A.!!$R2 793
10 TraesCS5D01G164200 chr1A 513205762 513206568 806 False 1090.000000 1090 91.337000 1 794 1 chr1A.!!$F1 793
11 TraesCS5D01G164200 chr4B 174043977 174044700 723 True 1031.000000 1031 92.424000 2 723 1 chr4B.!!$R1 721
12 TraesCS5D01G164200 chr1D 425542278 425542977 699 True 1027.000000 1027 93.286000 99 792 1 chr1D.!!$R1 693

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
182 183 0.744414 GGCAAAGGCAGCTCGACATA 60.744 55.000 0.00 0.0 43.71 2.29 F
262 263 1.073199 CCAAAGCGAAGGAGGTGGT 59.927 57.895 0.00 0.0 0.00 4.16 F
1985 2140 1.361197 TCATGTACTCCCTCTGTCCCA 59.639 52.381 0.00 0.0 0.00 4.37 F
2673 2833 0.106967 GGGAGTTCAGGCCAAGGATC 60.107 60.000 5.01 0.0 0.00 3.36 F
3160 3325 1.342074 TGAGCTGCTTCCTACAGTGT 58.658 50.000 2.53 0.0 37.47 3.55 F
4938 5280 1.238439 ATGGTTTTGAGGTGCTGACG 58.762 50.000 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 2194 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12 R
2122 2280 0.244721 GCACATCAAGAGGCAAACCC 59.755 55.000 0.00 0.00 36.11 4.11 R
3119 3284 2.821378 TCAACCAATGGCTCTTGACATG 59.179 45.455 0.00 0.00 41.99 3.21 R
4090 4347 1.073722 TGCAGAGAAACCTGGCAGG 59.926 57.895 31.62 31.62 42.49 4.85 R
5006 5348 4.526650 AGAGAAACACCACACCAAGTTTTT 59.473 37.500 0.00 0.00 34.62 1.94 R
6234 6754 0.608640 AATCGAAGAGTGGCGTCCTT 59.391 50.000 0.00 0.00 43.63 3.36 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
26 27 2.165641 CACTTTGCATGGCATGATGTCT 59.834 45.455 30.69 6.62 38.76 3.41
182 183 0.744414 GGCAAAGGCAGCTCGACATA 60.744 55.000 0.00 0.00 43.71 2.29
262 263 1.073199 CCAAAGCGAAGGAGGTGGT 59.927 57.895 0.00 0.00 0.00 4.16
627 639 1.857837 CGGCATTTGAAACGTTGCTTT 59.142 42.857 8.00 0.00 35.46 3.51
661 676 2.046285 CGGACAGGATGGGGCAAAC 61.046 63.158 0.00 0.00 43.62 2.93
720 736 4.430765 GACACGCCCGGACACGAT 62.431 66.667 16.67 5.80 44.60 3.73
738 755 5.072741 CACGATCCCAAATCCCTATCAAAT 58.927 41.667 0.00 0.00 0.00 2.32
795 815 1.376609 GCGGTGGAGTTGGCCTTATG 61.377 60.000 3.32 0.00 0.00 1.90
797 817 1.751437 GGTGGAGTTGGCCTTATGAC 58.249 55.000 3.32 0.00 0.00 3.06
798 818 1.682087 GGTGGAGTTGGCCTTATGACC 60.682 57.143 3.32 0.00 0.00 4.02
1050 1071 3.575247 ATCCACGGCACCAACCCA 61.575 61.111 0.00 0.00 0.00 4.51
1080 1101 2.496817 GAGAAGATCGTGCGGGCT 59.503 61.111 0.00 0.00 0.00 5.19
1538 1563 5.782047 TGGAAGTATGCACTCCAAATTTTG 58.218 37.500 6.26 1.99 32.29 2.44
1539 1564 5.304101 TGGAAGTATGCACTCCAAATTTTGT 59.696 36.000 8.26 0.00 32.29 2.83
1594 1636 5.712917 GGTAGCTAGCTAGGTGTATGAGATT 59.287 44.000 30.89 0.00 35.39 2.40
1630 1674 7.417003 GGGGTATGCGGTTATTTTACTCATTTT 60.417 37.037 0.00 0.00 0.00 1.82
1631 1675 7.646526 GGGTATGCGGTTATTTTACTCATTTTC 59.353 37.037 0.00 0.00 0.00 2.29
1752 1797 6.644592 CCGCATTCAGAAAAGGTTTGATTTTA 59.355 34.615 0.00 0.00 30.22 1.52
1849 1905 3.125829 TGCTCAATTTCTCGCTGATGTTC 59.874 43.478 0.00 0.00 0.00 3.18
1850 1906 3.486542 GCTCAATTTCTCGCTGATGTTCC 60.487 47.826 0.00 0.00 0.00 3.62
1972 2127 8.984764 TCTGTTAAACACATAGTTGTCATGTAC 58.015 33.333 0.00 0.00 41.19 2.90
1973 2128 8.896320 TGTTAAACACATAGTTGTCATGTACT 57.104 30.769 0.00 0.00 41.19 2.73
1974 2129 8.984764 TGTTAAACACATAGTTGTCATGTACTC 58.015 33.333 0.00 0.00 41.19 2.59
1975 2130 8.440833 GTTAAACACATAGTTGTCATGTACTCC 58.559 37.037 0.00 0.00 41.19 3.85
1976 2131 5.086104 ACACATAGTTGTCATGTACTCCC 57.914 43.478 0.00 0.00 34.88 4.30
1977 2132 4.777896 ACACATAGTTGTCATGTACTCCCT 59.222 41.667 0.00 0.00 34.88 4.20
1978 2133 5.105310 ACACATAGTTGTCATGTACTCCCTC 60.105 44.000 0.00 0.00 34.88 4.30
1979 2134 5.127845 CACATAGTTGTCATGTACTCCCTCT 59.872 44.000 0.00 0.00 34.88 3.69
1980 2135 5.127845 ACATAGTTGTCATGTACTCCCTCTG 59.872 44.000 0.00 0.00 34.88 3.35
1981 2136 3.511477 AGTTGTCATGTACTCCCTCTGT 58.489 45.455 0.00 0.00 0.00 3.41
1982 2137 3.511934 AGTTGTCATGTACTCCCTCTGTC 59.488 47.826 0.00 0.00 0.00 3.51
1983 2138 2.457598 TGTCATGTACTCCCTCTGTCC 58.542 52.381 0.00 0.00 0.00 4.02
1984 2139 1.757699 GTCATGTACTCCCTCTGTCCC 59.242 57.143 0.00 0.00 0.00 4.46
1985 2140 1.361197 TCATGTACTCCCTCTGTCCCA 59.639 52.381 0.00 0.00 0.00 4.37
1986 2141 2.187958 CATGTACTCCCTCTGTCCCAA 58.812 52.381 0.00 0.00 0.00 4.12
1987 2142 2.409064 TGTACTCCCTCTGTCCCAAA 57.591 50.000 0.00 0.00 0.00 3.28
1988 2143 2.696775 TGTACTCCCTCTGTCCCAAAA 58.303 47.619 0.00 0.00 0.00 2.44
1989 2144 3.256704 TGTACTCCCTCTGTCCCAAAAT 58.743 45.455 0.00 0.00 0.00 1.82
1990 2145 4.431378 TGTACTCCCTCTGTCCCAAAATA 58.569 43.478 0.00 0.00 0.00 1.40
1991 2146 4.847512 TGTACTCCCTCTGTCCCAAAATAA 59.152 41.667 0.00 0.00 0.00 1.40
1992 2147 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
1993 2148 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
1994 2149 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
1995 2150 3.010138 TCCCTCTGTCCCAAAATAAGTGG 59.990 47.826 0.00 0.00 35.77 4.00
1996 2151 2.755103 CCTCTGTCCCAAAATAAGTGGC 59.245 50.000 0.00 0.00 34.56 5.01
1997 2152 3.562176 CCTCTGTCCCAAAATAAGTGGCT 60.562 47.826 0.00 0.00 34.56 4.75
1998 2153 3.686016 TCTGTCCCAAAATAAGTGGCTC 58.314 45.455 0.00 0.00 34.56 4.70
1999 2154 3.073798 TCTGTCCCAAAATAAGTGGCTCA 59.926 43.478 0.00 0.00 34.56 4.26
2000 2155 3.826157 CTGTCCCAAAATAAGTGGCTCAA 59.174 43.478 0.00 0.00 34.56 3.02
2001 2156 3.572255 TGTCCCAAAATAAGTGGCTCAAC 59.428 43.478 0.00 0.00 34.56 3.18
2002 2157 3.826729 GTCCCAAAATAAGTGGCTCAACT 59.173 43.478 0.00 0.00 34.56 3.16
2003 2158 4.280929 GTCCCAAAATAAGTGGCTCAACTT 59.719 41.667 5.53 5.53 42.89 2.66
2004 2159 4.898861 TCCCAAAATAAGTGGCTCAACTTT 59.101 37.500 5.52 0.00 40.77 2.66
2005 2160 6.015772 GTCCCAAAATAAGTGGCTCAACTTTA 60.016 38.462 5.52 0.00 40.77 1.85
2006 2161 6.723977 TCCCAAAATAAGTGGCTCAACTTTAT 59.276 34.615 5.52 0.00 40.77 1.40
2007 2162 7.891183 TCCCAAAATAAGTGGCTCAACTTTATA 59.109 33.333 5.52 0.00 40.77 0.98
2008 2163 7.973944 CCCAAAATAAGTGGCTCAACTTTATAC 59.026 37.037 5.52 0.00 40.77 1.47
2009 2164 8.739972 CCAAAATAAGTGGCTCAACTTTATACT 58.260 33.333 5.52 0.00 40.77 2.12
2012 2167 8.664211 AATAAGTGGCTCAACTTTATACTAGC 57.336 34.615 5.52 0.00 40.77 3.42
2013 2168 5.941555 AGTGGCTCAACTTTATACTAGCT 57.058 39.130 0.00 0.00 0.00 3.32
2014 2169 6.301169 AGTGGCTCAACTTTATACTAGCTT 57.699 37.500 0.00 0.00 0.00 3.74
2015 2170 6.712276 AGTGGCTCAACTTTATACTAGCTTT 58.288 36.000 0.00 0.00 0.00 3.51
2016 2171 7.848128 AGTGGCTCAACTTTATACTAGCTTTA 58.152 34.615 0.00 0.00 0.00 1.85
2017 2172 7.982354 AGTGGCTCAACTTTATACTAGCTTTAG 59.018 37.037 0.00 0.00 0.00 1.85
2018 2173 7.764901 GTGGCTCAACTTTATACTAGCTTTAGT 59.235 37.037 0.00 0.00 0.00 2.24
2019 2174 8.974238 TGGCTCAACTTTATACTAGCTTTAGTA 58.026 33.333 0.00 0.00 37.01 1.82
2020 2175 9.247126 GGCTCAACTTTATACTAGCTTTAGTAC 57.753 37.037 0.00 0.00 35.60 2.73
2021 2176 9.798994 GCTCAACTTTATACTAGCTTTAGTACA 57.201 33.333 0.00 0.00 35.60 2.90
2031 2186 9.857957 ATACTAGCTTTAGTACAAAGTTGAGTC 57.142 33.333 14.90 0.00 35.60 3.36
2032 2187 7.723324 ACTAGCTTTAGTACAAAGTTGAGTCA 58.277 34.615 14.90 0.00 0.00 3.41
2033 2188 6.846325 AGCTTTAGTACAAAGTTGAGTCAC 57.154 37.500 14.90 0.00 0.00 3.67
2034 2189 6.583562 AGCTTTAGTACAAAGTTGAGTCACT 58.416 36.000 14.90 0.00 0.00 3.41
2035 2190 7.048512 AGCTTTAGTACAAAGTTGAGTCACTT 58.951 34.615 14.90 0.00 38.74 3.16
2036 2191 8.202137 AGCTTTAGTACAAAGTTGAGTCACTTA 58.798 33.333 14.90 0.00 35.87 2.24
2037 2192 8.989980 GCTTTAGTACAAAGTTGAGTCACTTAT 58.010 33.333 14.90 0.00 35.87 1.73
2042 2197 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
2043 2198 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
2044 2199 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
2045 2200 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
2046 2201 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
2047 2202 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
2048 2203 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
2049 2204 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
2050 2205 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2051 2206 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
2052 2207 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2053 2208 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2054 2209 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
2055 2210 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2122 2280 9.448294 GACCACTAGTCAGTAATCTTAAATACG 57.552 37.037 0.00 0.00 45.55 3.06
2432 2590 2.142357 GAAGCCCCACCAAAGAACGC 62.142 60.000 0.00 0.00 0.00 4.84
2650 2809 8.876790 GTTTTTAGTACTCTGTTTACTGTGTGT 58.123 33.333 0.00 0.00 31.99 3.72
2673 2833 0.106967 GGGAGTTCAGGCCAAGGATC 60.107 60.000 5.01 0.00 0.00 3.36
2935 3098 2.338785 GCAAGAGCTTCTGGGGCAC 61.339 63.158 0.00 0.00 37.91 5.01
2970 3133 5.056480 CAGGTTCACTTGTCTTGTATCACA 58.944 41.667 0.00 0.00 0.00 3.58
3160 3325 1.342074 TGAGCTGCTTCCTACAGTGT 58.658 50.000 2.53 0.00 37.47 3.55
3349 3517 1.403249 CCTCCATTTTTCTGCCGCTTG 60.403 52.381 0.00 0.00 0.00 4.01
3509 3677 6.073112 GGTTTGCCAACGAGTTATTGTAAGTA 60.073 38.462 0.00 0.00 33.13 2.24
3579 3748 6.980978 TGAAAGTAGAAATCAGATAAGAGCCG 59.019 38.462 0.00 0.00 0.00 5.52
3709 3878 9.920946 AAGGGCATAGAAGTAATCTCATTTTTA 57.079 29.630 0.00 0.00 39.71 1.52
4001 4258 3.313274 GCAGTTGCATTGCATATTTGC 57.687 42.857 12.95 14.96 44.39 3.68
4050 4307 3.019564 GGCATGTTAATGTCAAGAGCCT 58.980 45.455 0.00 0.00 38.35 4.58
4088 4345 7.821359 GCTGCTTCCTATAGTGAATAATCATGA 59.179 37.037 0.00 0.00 38.01 3.07
4090 4347 8.097038 TGCTTCCTATAGTGAATAATCATGACC 58.903 37.037 0.00 0.00 38.01 4.02
4230 4571 6.430000 TGTTTAGTCCATGTTAAGAAGCCTTC 59.570 38.462 0.00 0.00 33.94 3.46
4280 4621 7.254590 CCGGATATAATTGCATAGCTAAGCTTC 60.255 40.741 20.60 7.18 40.44 3.86
4482 4824 2.749076 TCATGTTCATTAGCTGTGCACC 59.251 45.455 15.69 0.00 0.00 5.01
4526 4868 7.386299 ACATTGAGCTACTTTCTAAGTTCAGTG 59.614 37.037 9.13 9.13 42.81 3.66
4650 4992 4.827835 TCATATGGTGGAGACTACTGTAGC 59.172 45.833 14.55 7.77 0.00 3.58
4679 5021 5.354792 TGCGTAAAAGTAATTATGTGGGTCC 59.645 40.000 0.00 0.00 0.00 4.46
4741 5083 4.943705 TGGAAGCCTGATAGATGTTCAAAC 59.056 41.667 0.00 0.00 0.00 2.93
4938 5280 1.238439 ATGGTTTTGAGGTGCTGACG 58.762 50.000 0.00 0.00 0.00 4.35
5006 5348 9.038072 TGGTTTGAGGTTACTGACATACTTATA 57.962 33.333 0.00 0.00 0.00 0.98
5020 5362 8.788806 TGACATACTTATAAAAACTTGGTGTGG 58.211 33.333 0.00 0.00 0.00 4.17
5076 5418 7.276658 CAGTGTGTTGATTTGGTCTCTAGATAC 59.723 40.741 0.00 0.00 0.00 2.24
5227 5584 2.571757 GAGACCGTCACCGCATCA 59.428 61.111 0.40 0.00 0.00 3.07
5235 5592 1.269465 CGTCACCGCATCAGAGATGAT 60.269 52.381 10.95 0.00 0.00 2.45
5253 5610 3.014623 TGATGACTACAACCGAGATCGT 58.985 45.455 1.09 0.00 37.74 3.73
5481 5841 1.746991 GAAGAAGGGCAGCGGGAAG 60.747 63.158 0.00 0.00 0.00 3.46
5529 5889 1.645034 TAGAGATGAACAAGCTGCGC 58.355 50.000 0.00 0.00 0.00 6.09
5559 5919 2.943036 GGTTGGGACCACTGAAGTAA 57.057 50.000 0.00 0.00 45.77 2.24
5613 5973 5.049828 CCAAGCTTAAAACCAACAAAGGAG 58.950 41.667 0.00 0.00 0.00 3.69
5647 6007 7.665561 TTTTTCTTTTAACACTGCAAGCTTT 57.334 28.000 0.00 0.00 37.60 3.51
5683 6043 1.765230 TGTAACTTTGGCGGTTTGGT 58.235 45.000 0.00 0.00 0.00 3.67
5705 6065 2.746362 CTGCTTTTCTGGCTCTACCTTG 59.254 50.000 0.00 0.00 40.22 3.61
5707 6067 2.877708 GCTTTTCTGGCTCTACCTTGCT 60.878 50.000 0.00 0.00 40.22 3.91
5739 6099 7.703298 TTTTGCATTTTTCTTGAGAGACATG 57.297 32.000 0.00 0.00 0.00 3.21
5758 6118 1.280133 TGGTGAAGGCTGATGAAGGAG 59.720 52.381 0.00 0.00 0.00 3.69
5759 6119 1.556911 GGTGAAGGCTGATGAAGGAGA 59.443 52.381 0.00 0.00 0.00 3.71
5881 6241 1.012086 CGTGCCAAGATGAGATGTGG 58.988 55.000 0.00 0.00 0.00 4.17
5882 6242 1.405933 CGTGCCAAGATGAGATGTGGA 60.406 52.381 0.00 0.00 32.54 4.02
5883 6243 2.715046 GTGCCAAGATGAGATGTGGAA 58.285 47.619 0.00 0.00 32.54 3.53
5884 6244 3.285484 GTGCCAAGATGAGATGTGGAAT 58.715 45.455 0.00 0.00 32.54 3.01
5989 6349 7.226128 TCAATGATTGCTTCATACTTAGCTGAG 59.774 37.037 3.53 3.53 44.51 3.35
5990 6350 4.813161 TGATTGCTTCATACTTAGCTGAGC 59.187 41.667 5.23 0.00 38.22 4.26
5995 6515 4.981674 GCTTCATACTTAGCTGAGCTAGTG 59.018 45.833 14.49 13.44 42.34 2.74
6001 6521 7.721842 TCATACTTAGCTGAGCTAGTGTATTCT 59.278 37.037 25.44 13.25 42.34 2.40
6033 6553 7.009174 GCCGATTGAAAACAATGTAACCATTAG 59.991 37.037 0.00 0.00 39.28 1.73
6067 6587 0.250727 AGCGTTAAGGCTCCAAGCAA 60.251 50.000 16.67 0.00 44.75 3.91
6107 6627 7.148069 GGTGGATAGTGAATTCCCTAACAAAAG 60.148 40.741 2.27 0.00 0.00 2.27
6176 6696 0.535780 TGGTGAAGCTTCTGTGGCTG 60.536 55.000 26.09 0.00 40.19 4.85
6180 6700 1.970640 TGAAGCTTCTGTGGCTGTAGA 59.029 47.619 26.09 0.00 40.19 2.59
6194 6714 3.070018 GCTGTAGACTTGAGCAACACAT 58.930 45.455 0.00 0.00 32.70 3.21
6199 6719 3.341823 AGACTTGAGCAACACATCATCC 58.658 45.455 0.00 0.00 0.00 3.51
6210 6730 4.046938 ACACATCATCCGTATCACAGTC 57.953 45.455 0.00 0.00 0.00 3.51
6227 6747 1.672030 TCGGTCGGCGTAGAGAACA 60.672 57.895 6.85 0.00 0.00 3.18
6232 6752 0.520404 TCGGCGTAGAGAACAGACAC 59.480 55.000 6.85 0.00 0.00 3.67
6233 6753 0.522180 CGGCGTAGAGAACAGACACT 59.478 55.000 0.00 0.00 0.00 3.55
6234 6754 1.736126 CGGCGTAGAGAACAGACACTA 59.264 52.381 0.00 0.00 0.00 2.74
6235 6755 2.161012 CGGCGTAGAGAACAGACACTAA 59.839 50.000 0.00 0.00 0.00 2.24
6236 6756 3.728268 CGGCGTAGAGAACAGACACTAAG 60.728 52.174 0.00 0.00 0.00 2.18
6383 6904 3.365265 CAACCCTTGGACGGCAGC 61.365 66.667 0.00 0.00 0.00 5.25
6483 7004 1.217942 ACAAGACCAAAGGGAAGCCTT 59.782 47.619 0.00 0.00 38.05 4.35
6552 7073 2.031012 CAGTCCTGGTGCGCTTGA 59.969 61.111 9.73 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.974957 TCGTCCCTCACATCCTTTTGA 59.025 47.619 0.00 0.00 0.00 2.69
182 183 1.006102 CTTGACGTTGTCGGCCTCT 60.006 57.895 0.00 0.00 45.66 3.69
262 263 0.807275 CACGCTCATGATCGCAAGGA 60.807 55.000 18.25 0.00 38.47 3.36
357 358 1.399440 CGATCGGACGACCTAGTTCAA 59.601 52.381 7.38 0.00 35.09 2.69
607 617 1.486439 AAGCAACGTTTCAAATGCCG 58.514 45.000 0.00 0.00 39.59 5.69
720 736 4.231658 TGTCCATTTGATAGGGATTTGGGA 59.768 41.667 0.00 0.00 32.43 4.37
795 815 3.930229 GGCACCAAATAAAATTTCCGGTC 59.070 43.478 0.00 0.00 0.00 4.79
797 817 2.926838 CGGCACCAAATAAAATTTCCGG 59.073 45.455 0.00 0.00 0.00 5.14
798 818 2.926838 CCGGCACCAAATAAAATTTCCG 59.073 45.455 0.00 0.00 0.00 4.30
854 875 5.743636 ACCCTAGACTATAGTAGACGAGG 57.256 47.826 5.09 8.56 40.79 4.63
1050 1071 2.103153 TCTTCTCCACCAGGTTCTGT 57.897 50.000 0.00 0.00 35.89 3.41
1080 1101 5.594725 CCAGTAGTTGCTCTGGTAGATCTTA 59.405 44.000 0.00 0.00 44.19 2.10
1594 1636 1.409521 CCGCATACCCCCAAATCTGAA 60.410 52.381 0.00 0.00 0.00 3.02
1630 1674 8.034804 TGAATTCTGAAACGAATACAGATGAGA 58.965 33.333 7.05 0.00 39.78 3.27
1631 1675 8.113062 GTGAATTCTGAAACGAATACAGATGAG 58.887 37.037 7.05 0.00 39.78 2.90
1752 1797 1.067295 TGGCAGAGTTTGGGACAGAT 58.933 50.000 0.00 0.00 42.39 2.90
1849 1905 3.965292 TTAAGATGTCGCTAGTCTCGG 57.035 47.619 0.00 0.00 0.00 4.63
1850 1906 6.028368 TCTTTTTAAGATGTCGCTAGTCTCG 58.972 40.000 0.00 0.00 31.20 4.04
1972 2127 4.265073 CACTTATTTTGGGACAGAGGGAG 58.735 47.826 0.00 0.00 42.39 4.30
1973 2128 3.010138 CCACTTATTTTGGGACAGAGGGA 59.990 47.826 0.00 0.00 42.39 4.20
1974 2129 3.356290 CCACTTATTTTGGGACAGAGGG 58.644 50.000 0.00 0.00 42.39 4.30
1975 2130 2.755103 GCCACTTATTTTGGGACAGAGG 59.245 50.000 0.00 0.00 42.39 3.69
1976 2131 3.690460 AGCCACTTATTTTGGGACAGAG 58.310 45.455 0.00 0.00 42.39 3.35
1977 2132 3.073798 TGAGCCACTTATTTTGGGACAGA 59.926 43.478 0.00 0.00 42.39 3.41
1978 2133 3.420893 TGAGCCACTTATTTTGGGACAG 58.579 45.455 0.00 0.00 42.39 3.51
1979 2134 3.517296 TGAGCCACTTATTTTGGGACA 57.483 42.857 0.00 0.00 34.35 4.02
1980 2135 3.826729 AGTTGAGCCACTTATTTTGGGAC 59.173 43.478 0.00 0.00 34.35 4.46
1981 2136 4.112634 AGTTGAGCCACTTATTTTGGGA 57.887 40.909 0.00 0.00 34.35 4.37
1982 2137 4.871933 AAGTTGAGCCACTTATTTTGGG 57.128 40.909 0.00 0.00 35.10 4.12
1983 2138 8.739972 AGTATAAAGTTGAGCCACTTATTTTGG 58.260 33.333 0.00 0.00 35.87 3.28
1986 2141 9.110502 GCTAGTATAAAGTTGAGCCACTTATTT 57.889 33.333 0.00 0.00 35.87 1.40
1987 2142 8.487028 AGCTAGTATAAAGTTGAGCCACTTATT 58.513 33.333 0.00 0.00 35.87 1.40
1988 2143 8.024145 AGCTAGTATAAAGTTGAGCCACTTAT 57.976 34.615 0.00 0.00 35.87 1.73
1989 2144 7.419711 AGCTAGTATAAAGTTGAGCCACTTA 57.580 36.000 0.00 0.00 35.87 2.24
1990 2145 6.301169 AGCTAGTATAAAGTTGAGCCACTT 57.699 37.500 0.00 0.00 38.74 3.16
1991 2146 5.941555 AGCTAGTATAAAGTTGAGCCACT 57.058 39.130 0.00 0.00 0.00 4.00
1992 2147 6.986904 AAAGCTAGTATAAAGTTGAGCCAC 57.013 37.500 0.00 0.00 0.00 5.01
1993 2148 7.848128 ACTAAAGCTAGTATAAAGTTGAGCCA 58.152 34.615 0.00 0.00 36.56 4.75
1994 2149 9.247126 GTACTAAAGCTAGTATAAAGTTGAGCC 57.753 37.037 0.00 0.00 41.57 4.70
1995 2150 9.798994 TGTACTAAAGCTAGTATAAAGTTGAGC 57.201 33.333 0.00 0.00 41.57 4.26
2005 2160 9.857957 GACTCAACTTTGTACTAAAGCTAGTAT 57.142 33.333 14.06 1.74 41.57 2.12
2006 2161 8.853126 TGACTCAACTTTGTACTAAAGCTAGTA 58.147 33.333 14.06 0.00 39.23 1.82
2007 2162 7.652507 GTGACTCAACTTTGTACTAAAGCTAGT 59.347 37.037 14.06 13.80 41.43 2.57
2008 2163 7.868415 AGTGACTCAACTTTGTACTAAAGCTAG 59.132 37.037 14.06 11.78 0.00 3.42
2009 2164 7.723324 AGTGACTCAACTTTGTACTAAAGCTA 58.277 34.615 14.06 3.93 0.00 3.32
2010 2165 6.583562 AGTGACTCAACTTTGTACTAAAGCT 58.416 36.000 14.06 3.86 0.00 3.74
2011 2166 6.846325 AGTGACTCAACTTTGTACTAAAGC 57.154 37.500 14.06 0.00 0.00 3.51
2016 2171 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
2017 2172 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
2018 2173 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
2019 2174 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
2020 2175 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
2021 2176 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
2022 2177 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
2023 2178 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
2024 2179 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
2025 2180 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2026 2181 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
2027 2182 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
2028 2183 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
2029 2184 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
2030 2185 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
2031 2186 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2032 2187 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2033 2188 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2034 2189 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2035 2190 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2036 2191 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2037 2192 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
2038 2193 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
2039 2194 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
2040 2195 0.042131 AACATACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
2041 2196 1.138464 GAAACATACTCCCTCCGTCCC 59.862 57.143 0.00 0.00 0.00 4.46
2042 2197 1.829222 TGAAACATACTCCCTCCGTCC 59.171 52.381 0.00 0.00 0.00 4.79
2043 2198 2.496470 ACTGAAACATACTCCCTCCGTC 59.504 50.000 0.00 0.00 0.00 4.79
2044 2199 2.537143 ACTGAAACATACTCCCTCCGT 58.463 47.619 0.00 0.00 0.00 4.69
2045 2200 4.730949 TTACTGAAACATACTCCCTCCG 57.269 45.455 0.00 0.00 0.00 4.63
2046 2201 7.362802 ACTATTACTGAAACATACTCCCTCC 57.637 40.000 0.00 0.00 0.00 4.30
2047 2202 9.668497 AAAACTATTACTGAAACATACTCCCTC 57.332 33.333 0.00 0.00 0.00 4.30
2122 2280 0.244721 GCACATCAAGAGGCAAACCC 59.755 55.000 0.00 0.00 36.11 4.11
2414 2572 2.200337 GCGTTCTTTGGTGGGGCTT 61.200 57.895 0.00 0.00 0.00 4.35
2432 2590 1.617947 CCCTCTCCCTTTCCCTGTCG 61.618 65.000 0.00 0.00 0.00 4.35
2650 2809 1.703411 CTTGGCCTGAACTCCCAAAA 58.297 50.000 3.32 0.00 38.10 2.44
2673 2833 7.090808 GCCCTTAACCAATAAGAAAACAGAAG 58.909 38.462 0.00 0.00 43.16 2.85
2970 3133 2.939103 GTCACTGTTTCAGTCTTGTGCT 59.061 45.455 0.00 0.00 43.43 4.40
3119 3284 2.821378 TCAACCAATGGCTCTTGACATG 59.179 45.455 0.00 0.00 41.99 3.21
3349 3517 7.071014 TCATTTCAAAAACTCAAAAGGTTGC 57.929 32.000 0.00 0.00 31.03 4.17
3509 3677 3.055167 GCACATTAAGCTTTGGGGGAAAT 60.055 43.478 3.20 0.00 0.00 2.17
3562 3731 4.950050 TCCTTCGGCTCTTATCTGATTTC 58.050 43.478 0.00 0.00 0.00 2.17
3579 3748 5.106515 GCCGGAAATGAATATAAGCTCCTTC 60.107 44.000 5.05 0.00 0.00 3.46
4001 4258 7.148255 TGGCAGTAACTCTAGTATGCAAAATTG 60.148 37.037 13.55 0.00 35.28 2.32
4002 4259 6.884295 TGGCAGTAACTCTAGTATGCAAAATT 59.116 34.615 13.55 0.00 35.28 1.82
4003 4260 6.414732 TGGCAGTAACTCTAGTATGCAAAAT 58.585 36.000 13.55 0.00 35.28 1.82
4004 4261 5.800296 TGGCAGTAACTCTAGTATGCAAAA 58.200 37.500 13.55 0.00 35.28 2.44
4005 4262 5.414789 TGGCAGTAACTCTAGTATGCAAA 57.585 39.130 13.55 3.08 35.28 3.68
4006 4263 5.359756 CATGGCAGTAACTCTAGTATGCAA 58.640 41.667 13.55 6.04 35.28 4.08
4007 4264 4.202253 CCATGGCAGTAACTCTAGTATGCA 60.202 45.833 0.00 0.00 35.28 3.96
4008 4265 4.310769 CCATGGCAGTAACTCTAGTATGC 58.689 47.826 0.00 6.41 33.83 3.14
4009 4266 4.310769 GCCATGGCAGTAACTCTAGTATG 58.689 47.826 32.08 0.00 41.49 2.39
4010 4267 4.608948 GCCATGGCAGTAACTCTAGTAT 57.391 45.455 32.08 0.00 41.49 2.12
4012 4269 2.990066 GCCATGGCAGTAACTCTAGT 57.010 50.000 32.08 0.00 41.49 2.57
4050 4307 1.247567 GAAGCAGCTTGCCTACCAAA 58.752 50.000 13.91 0.00 46.52 3.28
4088 4345 1.763770 CAGAGAAACCTGGCAGGGT 59.236 57.895 35.34 29.30 36.34 4.34
4090 4347 1.073722 TGCAGAGAAACCTGGCAGG 59.926 57.895 31.62 31.62 42.49 4.85
4256 4597 8.498054 TGAAGCTTAGCTATGCAATTATATCC 57.502 34.615 27.63 7.85 38.25 2.59
4280 4621 5.047164 ACTGATCTTATCTAGGCAGAGCATG 60.047 44.000 0.00 0.00 32.73 4.06
4345 4686 9.478768 GTTTCCAAAAATAACCGATTCCTTTTA 57.521 29.630 0.00 0.00 0.00 1.52
4353 4694 9.554395 AAAAATGAGTTTCCAAAAATAACCGAT 57.446 25.926 0.00 0.00 0.00 4.18
4650 4992 6.468956 CCACATAATTACTTTTACGCAAGCAG 59.531 38.462 0.00 0.00 45.62 4.24
4679 5021 8.292444 TCTGTCCAACCCTGATAAAATATTTG 57.708 34.615 0.39 0.00 0.00 2.32
4938 5280 8.764524 AGAAACTACAGATCATTTAGTCACAC 57.235 34.615 0.00 0.00 0.00 3.82
5006 5348 4.526650 AGAGAAACACCACACCAAGTTTTT 59.473 37.500 0.00 0.00 34.62 1.94
5020 5362 4.692625 AGTGCATGTATCACAGAGAAACAC 59.307 41.667 0.00 0.00 36.93 3.32
5076 5418 5.759763 CCTGGAAAAACAAAGATCAAAAGGG 59.240 40.000 0.00 0.00 0.00 3.95
5227 5584 4.527944 TCTCGGTTGTAGTCATCATCTCT 58.472 43.478 0.00 0.00 0.00 3.10
5235 5592 2.161012 GTCACGATCTCGGTTGTAGTCA 59.839 50.000 4.44 0.00 44.95 3.41
5253 5610 4.731853 TCCCTGCCATCCCGGTCA 62.732 66.667 0.00 0.00 36.97 4.02
5418 5775 1.075970 CTCCTCCCTCGGACCATCA 60.076 63.158 0.00 0.00 0.00 3.07
5529 5889 0.600255 GTCCCAACCCTATCGATGCG 60.600 60.000 8.54 0.00 0.00 4.73
5683 6043 2.260822 AGGTAGAGCCAGAAAAGCAGA 58.739 47.619 0.00 0.00 40.61 4.26
5738 6098 1.280133 CTCCTTCATCAGCCTTCACCA 59.720 52.381 0.00 0.00 0.00 4.17
5739 6099 1.556911 TCTCCTTCATCAGCCTTCACC 59.443 52.381 0.00 0.00 0.00 4.02
5850 6210 3.016031 TCTTGGCACGATTATTGCACAT 58.984 40.909 0.00 0.00 42.12 3.21
5881 6241 7.707893 ACATGGTCAAAATGCAGCTTATTATTC 59.292 33.333 0.00 0.00 0.00 1.75
5882 6242 7.558604 ACATGGTCAAAATGCAGCTTATTATT 58.441 30.769 0.00 0.00 0.00 1.40
5883 6243 7.116075 ACATGGTCAAAATGCAGCTTATTAT 57.884 32.000 0.00 0.00 0.00 1.28
5884 6244 6.528537 ACATGGTCAAAATGCAGCTTATTA 57.471 33.333 0.00 0.00 0.00 0.98
5989 6349 5.060662 TCGGCATCATAGAATACACTAGC 57.939 43.478 0.00 0.00 0.00 3.42
5990 6350 7.315890 TCAATCGGCATCATAGAATACACTAG 58.684 38.462 0.00 0.00 0.00 2.57
5995 6515 7.639039 TGTTTTCAATCGGCATCATAGAATAC 58.361 34.615 0.00 0.00 0.00 1.89
6001 6521 6.206395 ACATTGTTTTCAATCGGCATCATA 57.794 33.333 0.00 0.00 46.18 2.15
6033 6553 2.674796 ACGCTCAAGGGATGTACTTC 57.325 50.000 0.59 0.10 0.00 3.01
6067 6587 7.961351 TCACTATCCACCACATTTTCATTTTT 58.039 30.769 0.00 0.00 0.00 1.94
6164 6684 2.072298 CAAGTCTACAGCCACAGAAGC 58.928 52.381 0.00 0.00 0.00 3.86
6176 6696 4.331168 GGATGATGTGTTGCTCAAGTCTAC 59.669 45.833 0.00 0.00 0.00 2.59
6180 6700 2.079158 CGGATGATGTGTTGCTCAAGT 58.921 47.619 0.00 0.00 0.00 3.16
6199 6719 1.585521 GCCGACCGACTGTGATACG 60.586 63.158 0.00 0.00 0.00 3.06
6210 6730 1.226323 CTGTTCTCTACGCCGACCG 60.226 63.158 0.00 0.00 44.21 4.79
6227 6747 0.889306 GAGTGGCGTCCTTAGTGTCT 59.111 55.000 0.00 0.00 0.00 3.41
6232 6752 0.809385 TCGAAGAGTGGCGTCCTTAG 59.191 55.000 0.00 0.00 0.00 2.18
6233 6753 1.471119 ATCGAAGAGTGGCGTCCTTA 58.529 50.000 0.00 0.00 43.63 2.69
6234 6754 0.608640 AATCGAAGAGTGGCGTCCTT 59.391 50.000 0.00 0.00 43.63 3.36
6235 6755 1.134560 GTAATCGAAGAGTGGCGTCCT 59.865 52.381 0.00 0.00 43.63 3.85
6236 6756 1.134560 AGTAATCGAAGAGTGGCGTCC 59.865 52.381 0.00 0.00 43.63 4.79
6456 6977 0.895559 CCTTTGGTCTTGTCCTGGGC 60.896 60.000 0.00 0.00 0.00 5.36
6525 7046 2.888863 CAGGACTGGACGCCTCTC 59.111 66.667 0.00 0.00 30.41 3.20


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

AutoCloner maintained by Alex Coulton.