Multiple sequence alignment - TraesCS5D01G196800

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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 TraesCS5D01G196800 chr5D 100.000 2174 0 0 1 2174 299972511 299974684 0.000000e+00 4015.0
1 TraesCS5D01G196800 chr5D 98.285 1283 10 3 1 1272 6253279 6254560 0.000000e+00 2237.0
2 TraesCS5D01G196800 chr5D 98.045 1279 14 4 1 1272 503339437 503338163 0.000000e+00 2213.0
3 TraesCS5D01G196800 chr5D 97.886 1277 17 3 1 1272 503313499 503312228 0.000000e+00 2200.0
4 TraesCS5D01G196800 chr5D 97.207 179 4 1 1997 2174 87962049 87962227 3.510000e-78 302.0
5 TraesCS5D01G196800 chr5D 97.207 179 4 1 1997 2174 303591756 303591578 3.510000e-78 302.0
6 TraesCS5D01G196800 chr5D 97.207 179 4 1 1997 2174 320532046 320532224 3.510000e-78 302.0
7 TraesCS5D01G196800 chr5D 96.000 50 1 1 1957 2005 477661440 477661489 1.790000e-11 80.5
8 TraesCS5D01G196800 chr3B 98.593 1279 7 4 1 1272 101924873 101923599 0.000000e+00 2252.0
9 TraesCS5D01G196800 chr3A 98.284 1282 8 5 1 1272 105556960 105558237 0.000000e+00 2233.0
10 TraesCS5D01G196800 chr5B 98.203 1280 11 4 1 1272 57515128 57516403 0.000000e+00 2226.0
11 TraesCS5D01G196800 chr7B 98.121 1277 14 3 1 1272 662755038 662756309 0.000000e+00 2217.0
12 TraesCS5D01G196800 chr1B 98.042 1277 15 3 1 1272 633716968 633715697 0.000000e+00 2211.0
13 TraesCS5D01G196800 chr1B 97.207 179 4 1 1997 2174 455975094 455974916 3.510000e-78 302.0
14 TraesCS5D01G196800 chr1D 97.961 1275 13 5 1 1272 254459405 254458141 0.000000e+00 2198.0
15 TraesCS5D01G196800 chr1D 95.840 673 27 1 1286 1957 349772956 349773628 0.000000e+00 1086.0
16 TraesCS5D01G196800 chr1D 97.790 181 4 0 1092 1272 243971382 243971202 1.620000e-81 313.0
17 TraesCS5D01G196800 chr1D 100.000 151 0 0 1122 1272 254455569 254455719 1.640000e-71 279.0
18 TraesCS5D01G196800 chr3D 95.840 673 27 1 1286 1957 108981356 108980684 0.000000e+00 1086.0
19 TraesCS5D01G196800 chr3D 97.191 178 5 0 1997 2174 437926814 437926991 3.510000e-78 302.0
20 TraesCS5D01G196800 chr6D 95.685 672 29 0 1286 1957 203035867 203035196 0.000000e+00 1081.0
21 TraesCS5D01G196800 chr6D 95.387 672 31 0 1286 1957 409200089 409199418 0.000000e+00 1070.0
22 TraesCS5D01G196800 chr6D 95.266 676 28 2 1286 1957 324632519 324633194 0.000000e+00 1068.0
23 TraesCS5D01G196800 chr6D 95.097 673 32 1 1286 1957 395052925 395053597 0.000000e+00 1059.0
24 TraesCS5D01G196800 chr6D 86.288 423 55 2 1522 1941 168747164 168747586 7.070000e-125 457.0
25 TraesCS5D01G196800 chr6D 97.191 178 5 0 1997 2174 66602272 66602095 3.510000e-78 302.0
26 TraesCS5D01G196800 chr6D 96.667 150 5 0 1123 1272 354353673 354353822 1.290000e-62 250.0
27 TraesCS5D01G196800 chr2D 95.691 673 28 1 1286 1957 281916396 281917068 0.000000e+00 1081.0
28 TraesCS5D01G196800 chr2D 97.191 178 5 0 1997 2174 298705297 298705474 3.510000e-78 302.0
29 TraesCS5D01G196800 chr2D 97.191 178 5 0 1997 2174 390494375 390494552 3.510000e-78 302.0
30 TraesCS5D01G196800 chr2D 97.191 178 5 0 1997 2174 394278238 394278415 3.510000e-78 302.0
31 TraesCS5D01G196800 chr2D 82.972 323 53 2 1602 1923 184535949 184535628 7.590000e-75 291.0
32 TraesCS5D01G196800 chr7D 95.542 673 29 1 1286 1957 453310658 453309986 0.000000e+00 1075.0
33 TraesCS5D01G196800 chr7D 95.245 673 31 1 1286 1957 502701437 502700765 0.000000e+00 1064.0
34 TraesCS5D01G196800 chr7D 89.881 336 30 4 1583 1915 195542083 195542417 1.540000e-116 429.0
35 TraesCS5D01G196800 chr7D 84.688 320 46 2 1623 1941 135656005 135655688 1.250000e-82 316.0
36 TraesCS5D01G196800 chr4A 90.455 440 40 2 1485 1923 423546457 423546019 1.450000e-161 579.0
37 TraesCS5D01G196800 chr4A 88.959 317 33 2 1625 1941 74851973 74851659 7.280000e-105 390.0
38 TraesCS5D01G196800 chr7A 88.542 288 33 0 1626 1913 626781850 626782137 1.230000e-92 350.0
39 TraesCS5D01G196800 chr4D 81.361 338 56 6 1590 1923 266102699 266103033 3.560000e-68 268.0
40 TraesCS5D01G196800 chr4D 97.959 49 0 1 1193 1240 198417968 198418016 1.380000e-12 84.2


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 TraesCS5D01G196800 chr5D 299972511 299974684 2173 False 4015 4015 100.000 1 2174 1 chr5D.!!$F3 2173
1 TraesCS5D01G196800 chr5D 6253279 6254560 1281 False 2237 2237 98.285 1 1272 1 chr5D.!!$F1 1271
2 TraesCS5D01G196800 chr5D 503338163 503339437 1274 True 2213 2213 98.045 1 1272 1 chr5D.!!$R3 1271
3 TraesCS5D01G196800 chr5D 503312228 503313499 1271 True 2200 2200 97.886 1 1272 1 chr5D.!!$R2 1271
4 TraesCS5D01G196800 chr3B 101923599 101924873 1274 True 2252 2252 98.593 1 1272 1 chr3B.!!$R1 1271
5 TraesCS5D01G196800 chr3A 105556960 105558237 1277 False 2233 2233 98.284 1 1272 1 chr3A.!!$F1 1271
6 TraesCS5D01G196800 chr5B 57515128 57516403 1275 False 2226 2226 98.203 1 1272 1 chr5B.!!$F1 1271
7 TraesCS5D01G196800 chr7B 662755038 662756309 1271 False 2217 2217 98.121 1 1272 1 chr7B.!!$F1 1271
8 TraesCS5D01G196800 chr1B 633715697 633716968 1271 True 2211 2211 98.042 1 1272 1 chr1B.!!$R2 1271
9 TraesCS5D01G196800 chr1D 254458141 254459405 1264 True 2198 2198 97.961 1 1272 1 chr1D.!!$R2 1271
10 TraesCS5D01G196800 chr1D 349772956 349773628 672 False 1086 1086 95.840 1286 1957 1 chr1D.!!$F2 671
11 TraesCS5D01G196800 chr3D 108980684 108981356 672 True 1086 1086 95.840 1286 1957 1 chr3D.!!$R1 671
12 TraesCS5D01G196800 chr6D 203035196 203035867 671 True 1081 1081 95.685 1286 1957 1 chr6D.!!$R2 671
13 TraesCS5D01G196800 chr6D 409199418 409200089 671 True 1070 1070 95.387 1286 1957 1 chr6D.!!$R3 671
14 TraesCS5D01G196800 chr6D 324632519 324633194 675 False 1068 1068 95.266 1286 1957 1 chr6D.!!$F2 671
15 TraesCS5D01G196800 chr6D 395052925 395053597 672 False 1059 1059 95.097 1286 1957 1 chr6D.!!$F4 671
16 TraesCS5D01G196800 chr2D 281916396 281917068 672 False 1081 1081 95.691 1286 1957 1 chr2D.!!$F1 671
17 TraesCS5D01G196800 chr7D 453309986 453310658 672 True 1075 1075 95.542 1286 1957 1 chr7D.!!$R2 671
18 TraesCS5D01G196800 chr7D 502700765 502701437 672 True 1064 1064 95.245 1286 1957 1 chr7D.!!$R3 671

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
322 326 1.468736 GCAGCAATAACAGAAGCAGCC 60.469 52.381 0.0 0.0 34.03 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 2090 0.107508 CCCTAGTGCACCATCACAGG 60.108 60.0 14.63 10.29 39.35 4.0 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
322 326 1.468736 GCAGCAATAACAGAAGCAGCC 60.469 52.381 0.00 0.00 34.03 4.85
873 888 4.517832 CCATGCATGAATTGAGCTAAGCTA 59.482 41.667 28.31 0.00 39.88 3.32
1272 1295 2.106683 ATTCGTGGGCGCTGCTAAC 61.107 57.895 7.64 0.00 38.14 2.34
1273 1296 2.796483 ATTCGTGGGCGCTGCTAACA 62.796 55.000 7.64 0.00 38.14 2.41
1274 1297 2.796483 TTCGTGGGCGCTGCTAACAT 62.796 55.000 7.64 0.00 38.14 2.71
1275 1298 2.793946 GTGGGCGCTGCTAACATG 59.206 61.111 7.64 0.00 0.00 3.21
1276 1299 3.133464 TGGGCGCTGCTAACATGC 61.133 61.111 7.64 0.00 0.00 4.06
1277 1300 3.892581 GGGCGCTGCTAACATGCC 61.893 66.667 7.64 5.55 43.22 4.40
1278 1301 4.241999 GGCGCTGCTAACATGCCG 62.242 66.667 7.64 0.00 37.44 5.69
1279 1302 4.894203 GCGCTGCTAACATGCCGC 62.894 66.667 0.00 0.00 39.28 6.53
1280 1303 3.197790 CGCTGCTAACATGCCGCT 61.198 61.111 0.00 0.00 40.25 5.52
1281 1304 2.406401 GCTGCTAACATGCCGCTG 59.594 61.111 0.00 0.00 39.51 5.18
1282 1305 2.108514 GCTGCTAACATGCCGCTGA 61.109 57.895 10.92 0.00 39.51 4.26
1283 1306 1.717937 CTGCTAACATGCCGCTGAC 59.282 57.895 0.00 0.00 0.00 3.51
1284 1307 2.028766 CTGCTAACATGCCGCTGACG 62.029 60.000 0.00 0.00 39.67 4.35
1459 1485 1.202698 GCCTCTTCGCATCCTTATGGT 60.203 52.381 0.00 0.00 33.38 3.55
1616 1642 1.267038 CGCGTATCACACACATCTTGC 60.267 52.381 0.00 0.00 0.00 4.01
1789 1815 0.950555 TCGCACACACCTTCATCTGC 60.951 55.000 0.00 0.00 0.00 4.26
1819 1845 4.351874 TTCTTTTGTTCCTCCTCATCGT 57.648 40.909 0.00 0.00 0.00 3.73
1840 1866 7.667043 TCGTAAACAGTTAATTGAGCTGAAT 57.333 32.000 4.81 0.00 34.60 2.57
1870 1896 2.150390 TGCATCGCACACACAACTAAT 58.850 42.857 0.00 0.00 31.71 1.73
1879 1905 5.348724 CGCACACACAACTAATATCTGAACT 59.651 40.000 0.00 0.00 0.00 3.01
1923 1951 4.104066 GCAAATGTTTTGCACCTTTTTGG 58.896 39.130 17.54 0.00 44.34 3.28
1957 1985 0.796312 CACTGTTTGCGATTACGGCT 59.204 50.000 0.00 0.00 40.15 5.52
1958 1986 1.076332 ACTGTTTGCGATTACGGCTC 58.924 50.000 0.00 0.00 40.15 4.70
1959 1987 1.337823 ACTGTTTGCGATTACGGCTCT 60.338 47.619 0.00 0.00 40.15 4.09
1960 1988 1.061131 CTGTTTGCGATTACGGCTCTG 59.939 52.381 0.00 0.00 40.15 3.35
1961 1989 1.337354 TGTTTGCGATTACGGCTCTGA 60.337 47.619 0.00 0.00 40.15 3.27
1962 1990 1.933853 GTTTGCGATTACGGCTCTGAT 59.066 47.619 0.00 0.00 40.15 2.90
1963 1991 1.852942 TTGCGATTACGGCTCTGATC 58.147 50.000 0.00 0.00 40.15 2.92
1964 1992 0.317854 TGCGATTACGGCTCTGATCG 60.318 55.000 0.00 0.00 42.99 3.69
1965 1993 0.317938 GCGATTACGGCTCTGATCGT 60.318 55.000 10.21 10.21 42.33 3.73
1966 1994 1.069432 GCGATTACGGCTCTGATCGTA 60.069 52.381 8.60 8.60 42.33 3.43
1967 1995 2.840673 CGATTACGGCTCTGATCGTAG 58.159 52.381 11.30 0.00 41.81 3.51
1968 1996 2.223611 CGATTACGGCTCTGATCGTAGT 59.776 50.000 11.30 9.61 41.81 2.73
1969 1997 3.556513 GATTACGGCTCTGATCGTAGTG 58.443 50.000 11.27 0.00 41.81 2.74
1970 1998 2.034104 TACGGCTCTGATCGTAGTGT 57.966 50.000 8.60 0.00 40.31 3.55
1971 1999 0.733729 ACGGCTCTGATCGTAGTGTC 59.266 55.000 4.74 0.00 37.88 3.67
1972 2000 0.733150 CGGCTCTGATCGTAGTGTCA 59.267 55.000 0.00 0.00 0.00 3.58
1973 2001 1.532090 CGGCTCTGATCGTAGTGTCAC 60.532 57.143 0.00 0.00 0.00 3.67
1974 2002 1.532090 GGCTCTGATCGTAGTGTCACG 60.532 57.143 0.00 0.00 43.28 4.35
1975 2003 1.130749 GCTCTGATCGTAGTGTCACGT 59.869 52.381 0.00 0.00 42.51 4.49
1976 2004 2.414293 GCTCTGATCGTAGTGTCACGTT 60.414 50.000 0.00 0.00 42.51 3.99
1977 2005 3.181513 GCTCTGATCGTAGTGTCACGTTA 60.182 47.826 0.00 0.00 42.51 3.18
1978 2006 4.579564 CTCTGATCGTAGTGTCACGTTAG 58.420 47.826 0.00 0.00 42.51 2.34
1979 2007 3.099362 CTGATCGTAGTGTCACGTTAGC 58.901 50.000 0.00 0.00 42.51 3.09
1980 2008 2.485038 TGATCGTAGTGTCACGTTAGCA 59.515 45.455 0.00 0.00 42.51 3.49
1981 2009 2.606717 TCGTAGTGTCACGTTAGCAG 57.393 50.000 0.00 0.00 42.51 4.24
1982 2010 0.982673 CGTAGTGTCACGTTAGCAGC 59.017 55.000 0.00 0.00 37.16 5.25
1983 2011 1.664874 CGTAGTGTCACGTTAGCAGCA 60.665 52.381 0.00 0.00 37.16 4.41
1984 2012 2.607187 GTAGTGTCACGTTAGCAGCAT 58.393 47.619 0.00 0.00 0.00 3.79
1985 2013 1.714794 AGTGTCACGTTAGCAGCATC 58.285 50.000 0.00 0.00 0.00 3.91
1986 2014 0.721718 GTGTCACGTTAGCAGCATCC 59.278 55.000 0.00 0.00 0.00 3.51
1987 2015 0.608130 TGTCACGTTAGCAGCATCCT 59.392 50.000 0.00 0.00 0.00 3.24
1988 2016 1.002366 GTCACGTTAGCAGCATCCTG 58.998 55.000 0.00 0.00 42.13 3.86
2011 2039 5.957910 CAGTAGTGCAATACAAGCTAGAC 57.042 43.478 24.70 0.00 0.00 2.59
2012 2040 5.410924 CAGTAGTGCAATACAAGCTAGACA 58.589 41.667 24.70 0.00 0.00 3.41
2013 2041 6.045318 CAGTAGTGCAATACAAGCTAGACAT 58.955 40.000 24.70 0.00 0.00 3.06
2014 2042 6.199908 CAGTAGTGCAATACAAGCTAGACATC 59.800 42.308 24.70 0.00 0.00 3.06
2015 2043 5.089970 AGTGCAATACAAGCTAGACATCA 57.910 39.130 0.00 0.00 0.00 3.07
2016 2044 5.678583 AGTGCAATACAAGCTAGACATCAT 58.321 37.500 0.00 0.00 0.00 2.45
2017 2045 6.820335 AGTGCAATACAAGCTAGACATCATA 58.180 36.000 0.00 0.00 0.00 2.15
2018 2046 6.703607 AGTGCAATACAAGCTAGACATCATAC 59.296 38.462 0.00 0.00 0.00 2.39
2019 2047 6.479990 GTGCAATACAAGCTAGACATCATACA 59.520 38.462 0.00 0.00 0.00 2.29
2020 2048 6.703165 TGCAATACAAGCTAGACATCATACAG 59.297 38.462 0.00 0.00 0.00 2.74
2021 2049 6.925718 GCAATACAAGCTAGACATCATACAGA 59.074 38.462 0.00 0.00 0.00 3.41
2022 2050 7.439356 GCAATACAAGCTAGACATCATACAGAA 59.561 37.037 0.00 0.00 0.00 3.02
2023 2051 8.759641 CAATACAAGCTAGACATCATACAGAAC 58.240 37.037 0.00 0.00 0.00 3.01
2024 2052 6.286240 ACAAGCTAGACATCATACAGAACA 57.714 37.500 0.00 0.00 0.00 3.18
2025 2053 6.882656 ACAAGCTAGACATCATACAGAACAT 58.117 36.000 0.00 0.00 0.00 2.71
2026 2054 6.760298 ACAAGCTAGACATCATACAGAACATG 59.240 38.462 0.00 0.00 0.00 3.21
2027 2055 5.295950 AGCTAGACATCATACAGAACATGC 58.704 41.667 0.00 0.00 0.00 4.06
2028 2056 5.052481 GCTAGACATCATACAGAACATGCA 58.948 41.667 0.00 0.00 0.00 3.96
2029 2057 5.525012 GCTAGACATCATACAGAACATGCAA 59.475 40.000 0.00 0.00 0.00 4.08
2030 2058 5.808042 AGACATCATACAGAACATGCAAC 57.192 39.130 0.00 0.00 0.00 4.17
2031 2059 4.637534 AGACATCATACAGAACATGCAACC 59.362 41.667 0.00 0.00 0.00 3.77
2032 2060 4.334552 ACATCATACAGAACATGCAACCA 58.665 39.130 0.00 0.00 0.00 3.67
2033 2061 4.156556 ACATCATACAGAACATGCAACCAC 59.843 41.667 0.00 0.00 0.00 4.16
2034 2062 3.749226 TCATACAGAACATGCAACCACA 58.251 40.909 0.00 0.00 0.00 4.17
2035 2063 4.334552 TCATACAGAACATGCAACCACAT 58.665 39.130 0.00 0.00 0.00 3.21
2036 2064 5.495640 TCATACAGAACATGCAACCACATA 58.504 37.500 0.00 0.00 0.00 2.29
2037 2065 6.121590 TCATACAGAACATGCAACCACATAT 58.878 36.000 0.00 0.00 0.00 1.78
2038 2066 7.278875 TCATACAGAACATGCAACCACATATA 58.721 34.615 0.00 0.00 0.00 0.86
2039 2067 7.772757 TCATACAGAACATGCAACCACATATAA 59.227 33.333 0.00 0.00 0.00 0.98
2040 2068 6.194796 ACAGAACATGCAACCACATATAAC 57.805 37.500 0.00 0.00 0.00 1.89
2041 2069 5.709631 ACAGAACATGCAACCACATATAACA 59.290 36.000 0.00 0.00 0.00 2.41
2042 2070 6.127925 ACAGAACATGCAACCACATATAACAG 60.128 38.462 0.00 0.00 0.00 3.16
2043 2071 5.945784 AGAACATGCAACCACATATAACAGT 59.054 36.000 0.00 0.00 0.00 3.55
2044 2072 5.565592 ACATGCAACCACATATAACAGTG 57.434 39.130 0.00 0.00 35.56 3.66
2045 2073 4.142403 ACATGCAACCACATATAACAGTGC 60.142 41.667 0.00 0.00 34.48 4.40
2046 2074 2.752354 TGCAACCACATATAACAGTGCC 59.248 45.455 0.00 0.00 34.48 5.01
2047 2075 2.752354 GCAACCACATATAACAGTGCCA 59.248 45.455 0.00 0.00 34.48 4.92
2048 2076 3.192422 GCAACCACATATAACAGTGCCAA 59.808 43.478 0.00 0.00 34.48 4.52
2049 2077 4.675146 GCAACCACATATAACAGTGCCAAG 60.675 45.833 0.00 0.00 34.48 3.61
2050 2078 4.301072 ACCACATATAACAGTGCCAAGT 57.699 40.909 0.00 0.00 34.48 3.16
2051 2079 4.662278 ACCACATATAACAGTGCCAAGTT 58.338 39.130 0.00 0.00 34.48 2.66
2052 2080 5.811190 ACCACATATAACAGTGCCAAGTTA 58.189 37.500 0.00 0.00 34.48 2.24
2053 2081 5.880332 ACCACATATAACAGTGCCAAGTTAG 59.120 40.000 0.00 0.00 34.10 2.34
2054 2082 6.112734 CCACATATAACAGTGCCAAGTTAGA 58.887 40.000 0.00 0.00 34.10 2.10
2055 2083 6.258727 CCACATATAACAGTGCCAAGTTAGAG 59.741 42.308 0.00 0.00 34.10 2.43
2056 2084 6.258727 CACATATAACAGTGCCAAGTTAGAGG 59.741 42.308 0.00 0.00 34.10 3.69
2057 2085 2.568623 AACAGTGCCAAGTTAGAGGG 57.431 50.000 0.00 0.00 0.00 4.30
2058 2086 1.729586 ACAGTGCCAAGTTAGAGGGA 58.270 50.000 0.00 0.00 0.00 4.20
2059 2087 1.625818 ACAGTGCCAAGTTAGAGGGAG 59.374 52.381 0.00 0.00 0.00 4.30
2060 2088 0.615850 AGTGCCAAGTTAGAGGGAGC 59.384 55.000 0.00 0.00 0.00 4.70
2061 2089 0.324943 GTGCCAAGTTAGAGGGAGCA 59.675 55.000 0.00 0.00 0.00 4.26
2062 2090 0.324943 TGCCAAGTTAGAGGGAGCAC 59.675 55.000 0.00 0.00 0.00 4.40
2063 2091 0.393132 GCCAAGTTAGAGGGAGCACC 60.393 60.000 0.00 0.00 40.67 5.01
2072 2100 3.081554 GGGAGCACCTGTGATGGT 58.918 61.111 0.51 0.00 41.77 3.55
2080 2108 0.615331 ACCTGTGATGGTGCACTAGG 59.385 55.000 17.98 15.76 40.14 3.02
2081 2109 0.107508 CCTGTGATGGTGCACTAGGG 60.108 60.000 17.98 5.76 39.49 3.53
2082 2110 0.904649 CTGTGATGGTGCACTAGGGA 59.095 55.000 17.98 0.00 39.49 4.20
2083 2111 1.278985 CTGTGATGGTGCACTAGGGAA 59.721 52.381 17.98 0.00 39.49 3.97
2084 2112 1.278985 TGTGATGGTGCACTAGGGAAG 59.721 52.381 17.98 0.00 39.49 3.46
2085 2113 1.555075 GTGATGGTGCACTAGGGAAGA 59.445 52.381 17.98 0.00 35.91 2.87
2086 2114 1.555075 TGATGGTGCACTAGGGAAGAC 59.445 52.381 17.98 0.00 0.00 3.01
2087 2115 0.537188 ATGGTGCACTAGGGAAGACG 59.463 55.000 17.98 0.00 0.00 4.18
2088 2116 0.830444 TGGTGCACTAGGGAAGACGT 60.830 55.000 17.98 0.00 0.00 4.34
2089 2117 0.389948 GGTGCACTAGGGAAGACGTG 60.390 60.000 17.98 0.00 0.00 4.49
2090 2118 4.187056 GCACTAGGGAAGACGTGC 57.813 61.111 0.00 0.00 44.73 5.34
2091 2119 1.592223 GCACTAGGGAAGACGTGCT 59.408 57.895 0.00 0.00 46.70 4.40
2092 2120 0.458716 GCACTAGGGAAGACGTGCTC 60.459 60.000 0.00 0.00 46.70 4.26
2093 2121 0.888619 CACTAGGGAAGACGTGCTCA 59.111 55.000 0.00 0.00 0.00 4.26
2094 2122 1.478510 CACTAGGGAAGACGTGCTCAT 59.521 52.381 0.00 0.00 0.00 2.90
2095 2123 1.751924 ACTAGGGAAGACGTGCTCATC 59.248 52.381 0.00 0.00 0.00 2.92
2096 2124 1.751351 CTAGGGAAGACGTGCTCATCA 59.249 52.381 0.00 0.00 0.00 3.07
2097 2125 1.198713 AGGGAAGACGTGCTCATCAT 58.801 50.000 0.00 0.00 0.00 2.45
2098 2126 1.137872 AGGGAAGACGTGCTCATCATC 59.862 52.381 0.00 0.00 0.00 2.92
2099 2127 1.134699 GGGAAGACGTGCTCATCATCA 60.135 52.381 0.00 0.00 0.00 3.07
2100 2128 2.621338 GGAAGACGTGCTCATCATCAA 58.379 47.619 0.00 0.00 0.00 2.57
2101 2129 2.349886 GGAAGACGTGCTCATCATCAAC 59.650 50.000 0.00 0.00 0.00 3.18
2102 2130 2.749280 AGACGTGCTCATCATCAACA 57.251 45.000 0.00 0.00 0.00 3.33
2103 2131 2.341257 AGACGTGCTCATCATCAACAC 58.659 47.619 0.00 0.00 0.00 3.32
2104 2132 2.068519 GACGTGCTCATCATCAACACA 58.931 47.619 0.00 0.00 0.00 3.72
2105 2133 2.480037 GACGTGCTCATCATCAACACAA 59.520 45.455 0.00 0.00 0.00 3.33
2106 2134 2.224079 ACGTGCTCATCATCAACACAAC 59.776 45.455 0.00 0.00 0.00 3.32
2107 2135 2.481568 CGTGCTCATCATCAACACAACT 59.518 45.455 0.00 0.00 0.00 3.16
2108 2136 3.679502 CGTGCTCATCATCAACACAACTA 59.320 43.478 0.00 0.00 0.00 2.24
2109 2137 4.330894 CGTGCTCATCATCAACACAACTAT 59.669 41.667 0.00 0.00 0.00 2.12
2110 2138 5.566623 GTGCTCATCATCAACACAACTATG 58.433 41.667 0.00 0.00 0.00 2.23
2111 2139 5.122869 GTGCTCATCATCAACACAACTATGT 59.877 40.000 0.00 0.00 41.61 2.29
2112 2140 5.706833 TGCTCATCATCAACACAACTATGTT 59.293 36.000 0.00 0.00 43.67 2.71
2123 2151 7.658179 AACACAACTATGTTGAGTGTCTATG 57.342 36.000 16.04 5.06 42.08 2.23
2124 2152 5.639506 ACACAACTATGTTGAGTGTCTATGC 59.360 40.000 16.04 0.00 38.98 3.14
2125 2153 5.639082 CACAACTATGTTGAGTGTCTATGCA 59.361 40.000 16.04 0.00 37.82 3.96
2126 2154 6.314648 CACAACTATGTTGAGTGTCTATGCAT 59.685 38.462 16.04 3.79 37.82 3.96
2127 2155 6.314648 ACAACTATGTTGAGTGTCTATGCATG 59.685 38.462 10.16 0.00 35.91 4.06
2128 2156 5.982356 ACTATGTTGAGTGTCTATGCATGT 58.018 37.500 10.16 0.00 0.00 3.21
2129 2157 5.814188 ACTATGTTGAGTGTCTATGCATGTG 59.186 40.000 10.16 2.07 0.00 3.21
2130 2158 4.006780 TGTTGAGTGTCTATGCATGTGT 57.993 40.909 10.16 0.00 0.00 3.72
2131 2159 4.388485 TGTTGAGTGTCTATGCATGTGTT 58.612 39.130 10.16 0.00 0.00 3.32
2132 2160 4.213906 TGTTGAGTGTCTATGCATGTGTTG 59.786 41.667 10.16 0.00 0.00 3.33
2133 2161 4.006780 TGAGTGTCTATGCATGTGTTGT 57.993 40.909 10.16 0.00 0.00 3.32
2134 2162 3.996363 TGAGTGTCTATGCATGTGTTGTC 59.004 43.478 10.16 0.28 0.00 3.18
2135 2163 4.248859 GAGTGTCTATGCATGTGTTGTCT 58.751 43.478 10.16 0.00 0.00 3.41
2136 2164 4.645535 AGTGTCTATGCATGTGTTGTCTT 58.354 39.130 10.16 0.00 0.00 3.01
2137 2165 4.453478 AGTGTCTATGCATGTGTTGTCTTG 59.547 41.667 10.16 0.00 0.00 3.02
2138 2166 3.189080 TGTCTATGCATGTGTTGTCTTGC 59.811 43.478 10.16 0.00 38.43 4.01
2139 2167 3.189080 GTCTATGCATGTGTTGTCTTGCA 59.811 43.478 10.16 9.04 46.70 4.08
2140 2168 3.819902 TCTATGCATGTGTTGTCTTGCAA 59.180 39.130 10.16 0.00 46.13 4.08
2141 2169 2.955477 TGCATGTGTTGTCTTGCAAA 57.045 40.000 0.00 0.00 42.51 3.68
2142 2170 3.455990 TGCATGTGTTGTCTTGCAAAT 57.544 38.095 0.00 0.00 42.51 2.32
2143 2171 3.382855 TGCATGTGTTGTCTTGCAAATC 58.617 40.909 0.00 0.00 42.51 2.17
2144 2172 3.181478 TGCATGTGTTGTCTTGCAAATCA 60.181 39.130 0.00 0.00 42.51 2.57
2145 2173 3.991773 GCATGTGTTGTCTTGCAAATCAT 59.008 39.130 0.00 0.00 39.03 2.45
2146 2174 4.090930 GCATGTGTTGTCTTGCAAATCATC 59.909 41.667 0.00 3.00 39.03 2.92
2147 2175 5.466819 CATGTGTTGTCTTGCAAATCATCT 58.533 37.500 0.00 0.00 39.03 2.90
2148 2176 5.518848 TGTGTTGTCTTGCAAATCATCTT 57.481 34.783 0.00 0.00 39.03 2.40
2149 2177 5.283294 TGTGTTGTCTTGCAAATCATCTTG 58.717 37.500 0.00 0.00 39.03 3.02
2150 2178 4.682860 GTGTTGTCTTGCAAATCATCTTGG 59.317 41.667 0.00 0.00 39.03 3.61
2151 2179 4.240096 GTTGTCTTGCAAATCATCTTGGG 58.760 43.478 0.00 0.00 39.03 4.12
2152 2180 2.827322 TGTCTTGCAAATCATCTTGGGG 59.173 45.455 0.00 0.00 0.00 4.96
2153 2181 2.167075 GTCTTGCAAATCATCTTGGGGG 59.833 50.000 0.00 0.00 0.00 5.40
2168 2196 3.656869 GGGGGTGGAGGAGTAGAAT 57.343 57.895 0.00 0.00 0.00 2.40
2169 2197 1.425694 GGGGGTGGAGGAGTAGAATC 58.574 60.000 0.00 0.00 0.00 2.52
2170 2198 1.062044 GGGGGTGGAGGAGTAGAATCT 60.062 57.143 0.00 0.00 0.00 2.40
2171 2199 2.043227 GGGGTGGAGGAGTAGAATCTG 58.957 57.143 0.00 0.00 0.00 2.90
2172 2200 2.627217 GGGGTGGAGGAGTAGAATCTGT 60.627 54.545 0.00 0.00 0.00 3.41
2173 2201 3.373877 GGGGTGGAGGAGTAGAATCTGTA 60.374 52.174 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
322 326 3.627123 TCACCATGAATCCACTAATTGCG 59.373 43.478 0.00 0.00 0.00 4.85
832 847 4.023365 GCATGGTTCCAGATAATCTGCTTC 60.023 45.833 0.00 0.00 42.98 3.86
1272 1295 3.490759 GGTCACGTCAGCGGCATG 61.491 66.667 1.45 0.00 43.45 4.06
1276 1299 1.736645 ATTTCGGTCACGTCAGCGG 60.737 57.895 11.93 0.00 43.45 5.52
1277 1300 1.006825 TCATTTCGGTCACGTCAGCG 61.007 55.000 4.12 4.12 44.93 5.18
1278 1301 0.438830 GTCATTTCGGTCACGTCAGC 59.561 55.000 0.00 0.00 41.85 4.26
1279 1302 1.068474 GGTCATTTCGGTCACGTCAG 58.932 55.000 0.00 0.00 41.85 3.51
1280 1303 0.320073 GGGTCATTTCGGTCACGTCA 60.320 55.000 0.00 0.00 41.85 4.35
1281 1304 0.320073 TGGGTCATTTCGGTCACGTC 60.320 55.000 0.00 0.00 41.85 4.34
1282 1305 0.323629 ATGGGTCATTTCGGTCACGT 59.676 50.000 0.00 0.00 41.85 4.49
1283 1306 1.006832 GATGGGTCATTTCGGTCACG 58.993 55.000 0.00 0.00 42.74 4.35
1284 1307 1.065418 AGGATGGGTCATTTCGGTCAC 60.065 52.381 0.00 0.00 0.00 3.67
1367 1390 6.787085 AACTATCAAGTTAAGTGTGCTCAC 57.213 37.500 10.92 10.92 44.26 3.51
1616 1642 8.383619 CAAGAGAACAGAAACGGTTCAATATAG 58.616 37.037 16.95 0.37 45.45 1.31
1789 1815 2.695147 AGGAACAAAAGAAACAGGCAGG 59.305 45.455 0.00 0.00 0.00 4.85
1819 1845 7.667043 ACGATTCAGCTCAATTAACTGTTTA 57.333 32.000 0.00 0.00 33.12 2.01
1870 1896 5.355071 GGATGCATCAAACACAGTTCAGATA 59.645 40.000 27.25 0.00 0.00 1.98
1879 1905 2.583024 TGGAGGATGCATCAAACACA 57.417 45.000 27.25 15.12 0.00 3.72
1923 1951 5.174943 GCAAACAGTGGTGTAAAATAACTGC 59.825 40.000 0.00 0.00 41.53 4.40
1957 1985 3.181513 GCTAACGTGACACTACGATCAGA 60.182 47.826 3.68 0.00 46.46 3.27
1958 1986 3.099362 GCTAACGTGACACTACGATCAG 58.901 50.000 3.68 0.86 46.46 2.90
1959 1987 2.485038 TGCTAACGTGACACTACGATCA 59.515 45.455 3.68 0.00 46.46 2.92
1960 1988 3.099362 CTGCTAACGTGACACTACGATC 58.901 50.000 3.68 0.00 46.46 3.69
1961 1989 2.731341 GCTGCTAACGTGACACTACGAT 60.731 50.000 3.68 0.00 46.46 3.73
1962 1990 1.400629 GCTGCTAACGTGACACTACGA 60.401 52.381 3.68 0.00 46.46 3.43
1964 1992 2.060326 TGCTGCTAACGTGACACTAC 57.940 50.000 3.68 0.00 0.00 2.73
1965 1993 2.416836 GGATGCTGCTAACGTGACACTA 60.417 50.000 3.68 0.00 0.00 2.74
1966 1994 1.673033 GGATGCTGCTAACGTGACACT 60.673 52.381 3.68 0.00 0.00 3.55
1967 1995 0.721718 GGATGCTGCTAACGTGACAC 59.278 55.000 0.00 0.00 0.00 3.67
1968 1996 0.608130 AGGATGCTGCTAACGTGACA 59.392 50.000 0.00 0.00 0.00 3.58
1969 1997 1.002366 CAGGATGCTGCTAACGTGAC 58.998 55.000 0.00 0.00 0.00 3.67
1970 1998 3.441244 CAGGATGCTGCTAACGTGA 57.559 52.632 0.00 0.00 0.00 4.35
1988 2016 4.268884 GTCTAGCTTGTATTGCACTACTGC 59.731 45.833 14.49 16.45 44.52 4.40
1989 2017 5.410924 TGTCTAGCTTGTATTGCACTACTG 58.589 41.667 14.49 8.92 0.00 2.74
1990 2018 5.661056 TGTCTAGCTTGTATTGCACTACT 57.339 39.130 14.49 0.00 0.00 2.57
1991 2019 6.042777 TGATGTCTAGCTTGTATTGCACTAC 58.957 40.000 7.25 7.25 0.00 2.73
1992 2020 6.220726 TGATGTCTAGCTTGTATTGCACTA 57.779 37.500 0.00 0.00 0.00 2.74
1993 2021 5.089970 TGATGTCTAGCTTGTATTGCACT 57.910 39.130 0.00 0.00 0.00 4.40
1994 2022 5.998454 ATGATGTCTAGCTTGTATTGCAC 57.002 39.130 0.00 0.00 0.00 4.57
1995 2023 6.581712 TGTATGATGTCTAGCTTGTATTGCA 58.418 36.000 0.00 0.00 0.00 4.08
1996 2024 6.925718 TCTGTATGATGTCTAGCTTGTATTGC 59.074 38.462 0.00 0.00 0.00 3.56
1997 2025 8.759641 GTTCTGTATGATGTCTAGCTTGTATTG 58.240 37.037 0.00 0.00 0.00 1.90
1998 2026 8.478066 TGTTCTGTATGATGTCTAGCTTGTATT 58.522 33.333 0.00 0.00 0.00 1.89
1999 2027 8.011844 TGTTCTGTATGATGTCTAGCTTGTAT 57.988 34.615 0.00 0.00 0.00 2.29
2000 2028 7.404671 TGTTCTGTATGATGTCTAGCTTGTA 57.595 36.000 0.00 0.00 0.00 2.41
2001 2029 6.286240 TGTTCTGTATGATGTCTAGCTTGT 57.714 37.500 0.00 0.00 0.00 3.16
2002 2030 6.292757 GCATGTTCTGTATGATGTCTAGCTTG 60.293 42.308 0.00 0.00 0.00 4.01
2003 2031 5.757320 GCATGTTCTGTATGATGTCTAGCTT 59.243 40.000 0.00 0.00 0.00 3.74
2004 2032 5.163374 TGCATGTTCTGTATGATGTCTAGCT 60.163 40.000 0.00 0.00 0.00 3.32
2005 2033 5.052481 TGCATGTTCTGTATGATGTCTAGC 58.948 41.667 0.00 0.00 0.00 3.42
2006 2034 6.018425 GGTTGCATGTTCTGTATGATGTCTAG 60.018 42.308 0.00 0.00 0.00 2.43
2007 2035 5.817296 GGTTGCATGTTCTGTATGATGTCTA 59.183 40.000 0.00 0.00 0.00 2.59
2008 2036 4.637534 GGTTGCATGTTCTGTATGATGTCT 59.362 41.667 0.00 0.00 0.00 3.41
2009 2037 4.395854 TGGTTGCATGTTCTGTATGATGTC 59.604 41.667 0.00 0.00 0.00 3.06
2010 2038 4.156556 GTGGTTGCATGTTCTGTATGATGT 59.843 41.667 0.00 0.00 0.00 3.06
2011 2039 4.156373 TGTGGTTGCATGTTCTGTATGATG 59.844 41.667 0.00 0.00 0.00 3.07
2012 2040 4.334552 TGTGGTTGCATGTTCTGTATGAT 58.665 39.130 0.00 0.00 0.00 2.45
2013 2041 3.749226 TGTGGTTGCATGTTCTGTATGA 58.251 40.909 0.00 0.00 0.00 2.15
2014 2042 4.707030 ATGTGGTTGCATGTTCTGTATG 57.293 40.909 0.00 0.00 0.00 2.39
2015 2043 7.555914 TGTTATATGTGGTTGCATGTTCTGTAT 59.444 33.333 0.00 0.00 0.00 2.29
2016 2044 6.881602 TGTTATATGTGGTTGCATGTTCTGTA 59.118 34.615 0.00 0.00 0.00 2.74
2017 2045 5.709631 TGTTATATGTGGTTGCATGTTCTGT 59.290 36.000 0.00 0.00 0.00 3.41
2018 2046 6.127925 ACTGTTATATGTGGTTGCATGTTCTG 60.128 38.462 0.00 0.00 0.00 3.02
2019 2047 5.945784 ACTGTTATATGTGGTTGCATGTTCT 59.054 36.000 0.00 0.00 0.00 3.01
2020 2048 6.029607 CACTGTTATATGTGGTTGCATGTTC 58.970 40.000 0.00 0.00 0.00 3.18
2021 2049 5.622007 GCACTGTTATATGTGGTTGCATGTT 60.622 40.000 0.00 0.00 34.99 2.71
2022 2050 4.142403 GCACTGTTATATGTGGTTGCATGT 60.142 41.667 0.00 0.00 34.99 3.21
2023 2051 4.353737 GCACTGTTATATGTGGTTGCATG 58.646 43.478 0.00 0.00 34.99 4.06
2024 2052 3.381272 GGCACTGTTATATGTGGTTGCAT 59.619 43.478 0.00 0.00 34.99 3.96
2025 2053 2.752354 GGCACTGTTATATGTGGTTGCA 59.248 45.455 0.00 0.00 34.99 4.08
2026 2054 2.752354 TGGCACTGTTATATGTGGTTGC 59.248 45.455 0.00 0.00 34.99 4.17
2027 2055 4.458989 ACTTGGCACTGTTATATGTGGTTG 59.541 41.667 0.00 0.00 34.99 3.77
2028 2056 4.662278 ACTTGGCACTGTTATATGTGGTT 58.338 39.130 0.00 0.00 34.99 3.67
2029 2057 4.301072 ACTTGGCACTGTTATATGTGGT 57.699 40.909 0.00 0.00 34.99 4.16
2030 2058 6.112734 TCTAACTTGGCACTGTTATATGTGG 58.887 40.000 11.18 2.16 34.99 4.17
2031 2059 6.258727 CCTCTAACTTGGCACTGTTATATGTG 59.741 42.308 11.18 0.00 37.26 3.21
2032 2060 6.349300 CCTCTAACTTGGCACTGTTATATGT 58.651 40.000 11.18 0.00 30.90 2.29
2033 2061 5.760253 CCCTCTAACTTGGCACTGTTATATG 59.240 44.000 11.18 4.16 30.90 1.78
2034 2062 5.665812 TCCCTCTAACTTGGCACTGTTATAT 59.334 40.000 11.18 0.00 30.90 0.86
2035 2063 5.027460 TCCCTCTAACTTGGCACTGTTATA 58.973 41.667 11.18 5.53 30.90 0.98
2036 2064 3.844211 TCCCTCTAACTTGGCACTGTTAT 59.156 43.478 11.18 0.00 30.90 1.89
2037 2065 3.244582 TCCCTCTAACTTGGCACTGTTA 58.755 45.455 10.54 10.54 0.00 2.41
2038 2066 2.039084 CTCCCTCTAACTTGGCACTGTT 59.961 50.000 9.51 9.51 0.00 3.16
2039 2067 1.625818 CTCCCTCTAACTTGGCACTGT 59.374 52.381 0.00 0.00 0.00 3.55
2040 2068 1.677217 GCTCCCTCTAACTTGGCACTG 60.677 57.143 0.00 0.00 0.00 3.66
2041 2069 0.615850 GCTCCCTCTAACTTGGCACT 59.384 55.000 0.00 0.00 0.00 4.40
2042 2070 0.324943 TGCTCCCTCTAACTTGGCAC 59.675 55.000 0.00 0.00 0.00 5.01
2043 2071 0.324943 GTGCTCCCTCTAACTTGGCA 59.675 55.000 0.00 0.00 0.00 4.92
2044 2072 0.393132 GGTGCTCCCTCTAACTTGGC 60.393 60.000 0.00 0.00 0.00 4.52
2045 2073 1.065854 CAGGTGCTCCCTCTAACTTGG 60.066 57.143 0.00 0.00 43.86 3.61
2046 2074 1.625818 ACAGGTGCTCCCTCTAACTTG 59.374 52.381 0.00 0.00 43.86 3.16
2047 2075 1.625818 CACAGGTGCTCCCTCTAACTT 59.374 52.381 0.00 0.00 43.86 2.66
2048 2076 1.203187 TCACAGGTGCTCCCTCTAACT 60.203 52.381 0.00 0.00 43.86 2.24
2049 2077 1.267121 TCACAGGTGCTCCCTCTAAC 58.733 55.000 0.00 0.00 43.86 2.34
2050 2078 1.833630 CATCACAGGTGCTCCCTCTAA 59.166 52.381 0.00 0.00 43.86 2.10
2051 2079 1.489481 CATCACAGGTGCTCCCTCTA 58.511 55.000 0.00 0.00 43.86 2.43
2052 2080 1.270414 CCATCACAGGTGCTCCCTCT 61.270 60.000 0.00 0.00 43.86 3.69
2053 2081 1.222936 CCATCACAGGTGCTCCCTC 59.777 63.158 0.00 0.00 43.86 4.30
2055 2083 3.081554 ACCATCACAGGTGCTCCC 58.918 61.111 0.00 0.00 41.30 4.30
2061 2089 0.615331 CCTAGTGCACCATCACAGGT 59.385 55.000 14.63 0.00 44.48 4.00
2062 2090 0.107508 CCCTAGTGCACCATCACAGG 60.108 60.000 14.63 10.29 39.35 4.00
2063 2091 0.904649 TCCCTAGTGCACCATCACAG 59.095 55.000 14.63 1.38 39.35 3.66
2064 2092 1.278985 CTTCCCTAGTGCACCATCACA 59.721 52.381 14.63 0.00 39.35 3.58
2065 2093 1.555075 TCTTCCCTAGTGCACCATCAC 59.445 52.381 14.63 0.00 37.24 3.06
2066 2094 1.555075 GTCTTCCCTAGTGCACCATCA 59.445 52.381 14.63 0.00 0.00 3.07
2067 2095 1.471676 CGTCTTCCCTAGTGCACCATC 60.472 57.143 14.63 0.00 0.00 3.51
2068 2096 0.537188 CGTCTTCCCTAGTGCACCAT 59.463 55.000 14.63 0.00 0.00 3.55
2069 2097 0.830444 ACGTCTTCCCTAGTGCACCA 60.830 55.000 14.63 0.00 0.00 4.17
2070 2098 0.389948 CACGTCTTCCCTAGTGCACC 60.390 60.000 14.63 0.00 0.00 5.01
2071 2099 3.123674 CACGTCTTCCCTAGTGCAC 57.876 57.895 9.40 9.40 0.00 4.57
2074 2102 0.888619 TGAGCACGTCTTCCCTAGTG 59.111 55.000 0.00 0.00 37.63 2.74
2075 2103 1.751924 GATGAGCACGTCTTCCCTAGT 59.248 52.381 0.00 0.00 0.00 2.57
2076 2104 1.751351 TGATGAGCACGTCTTCCCTAG 59.249 52.381 4.95 0.00 33.61 3.02
2077 2105 1.847328 TGATGAGCACGTCTTCCCTA 58.153 50.000 4.95 0.00 33.61 3.53
2078 2106 1.137872 GATGATGAGCACGTCTTCCCT 59.862 52.381 4.95 0.00 33.13 4.20
2079 2107 1.134699 TGATGATGAGCACGTCTTCCC 60.135 52.381 13.98 0.00 36.21 3.97
2080 2108 2.299993 TGATGATGAGCACGTCTTCC 57.700 50.000 13.98 1.66 36.21 3.46
2081 2109 2.995939 TGTTGATGATGAGCACGTCTTC 59.004 45.455 10.93 10.93 37.00 2.87
2082 2110 2.738846 GTGTTGATGATGAGCACGTCTT 59.261 45.455 4.95 0.00 33.61 3.01
2083 2111 2.289010 TGTGTTGATGATGAGCACGTCT 60.289 45.455 4.95 0.00 33.61 4.18
2084 2112 2.068519 TGTGTTGATGATGAGCACGTC 58.931 47.619 0.00 0.00 33.23 4.34
2085 2113 2.168326 TGTGTTGATGATGAGCACGT 57.832 45.000 0.00 0.00 33.23 4.49
2086 2114 2.481568 AGTTGTGTTGATGATGAGCACG 59.518 45.455 0.00 0.00 33.23 5.34
2087 2115 5.122869 ACATAGTTGTGTTGATGATGAGCAC 59.877 40.000 0.00 0.00 33.85 4.40
2088 2116 5.247862 ACATAGTTGTGTTGATGATGAGCA 58.752 37.500 0.00 0.00 33.85 4.26
2089 2117 5.808042 ACATAGTTGTGTTGATGATGAGC 57.192 39.130 0.00 0.00 33.85 4.26
2099 2127 6.147821 GCATAGACACTCAACATAGTTGTGTT 59.852 38.462 13.07 7.00 42.75 3.32
2100 2128 5.639506 GCATAGACACTCAACATAGTTGTGT 59.360 40.000 10.69 10.69 43.39 3.72
2101 2129 5.639082 TGCATAGACACTCAACATAGTTGTG 59.361 40.000 9.43 9.51 35.83 3.33
2102 2130 5.793817 TGCATAGACACTCAACATAGTTGT 58.206 37.500 9.43 0.00 37.82 3.32
2103 2131 6.314648 ACATGCATAGACACTCAACATAGTTG 59.685 38.462 0.00 3.58 0.00 3.16
2104 2132 6.314648 CACATGCATAGACACTCAACATAGTT 59.685 38.462 0.00 0.00 0.00 2.24
2105 2133 5.814188 CACATGCATAGACACTCAACATAGT 59.186 40.000 0.00 0.00 0.00 2.12
2106 2134 5.814188 ACACATGCATAGACACTCAACATAG 59.186 40.000 0.00 0.00 0.00 2.23
2107 2135 5.733676 ACACATGCATAGACACTCAACATA 58.266 37.500 0.00 0.00 0.00 2.29
2108 2136 4.582869 ACACATGCATAGACACTCAACAT 58.417 39.130 0.00 0.00 0.00 2.71
2109 2137 4.006780 ACACATGCATAGACACTCAACA 57.993 40.909 0.00 0.00 0.00 3.33
2110 2138 4.214119 ACAACACATGCATAGACACTCAAC 59.786 41.667 0.00 0.00 0.00 3.18
2111 2139 4.388485 ACAACACATGCATAGACACTCAA 58.612 39.130 0.00 0.00 0.00 3.02
2112 2140 3.996363 GACAACACATGCATAGACACTCA 59.004 43.478 0.00 0.00 0.00 3.41
2113 2141 4.248859 AGACAACACATGCATAGACACTC 58.751 43.478 0.00 0.00 0.00 3.51
2114 2142 4.277515 AGACAACACATGCATAGACACT 57.722 40.909 0.00 0.00 0.00 3.55
2115 2143 4.715896 CAAGACAACACATGCATAGACAC 58.284 43.478 0.00 0.00 0.00 3.67
2116 2144 3.189080 GCAAGACAACACATGCATAGACA 59.811 43.478 0.00 0.00 38.63 3.41
2117 2145 3.189080 TGCAAGACAACACATGCATAGAC 59.811 43.478 0.00 0.00 43.32 2.59
2118 2146 3.410508 TGCAAGACAACACATGCATAGA 58.589 40.909 0.00 0.00 43.32 1.98
2119 2147 3.835378 TGCAAGACAACACATGCATAG 57.165 42.857 0.00 0.00 43.32 2.23
2120 2148 4.581077 TTTGCAAGACAACACATGCATA 57.419 36.364 0.00 0.00 46.97 3.14
2121 2149 3.455990 TTTGCAAGACAACACATGCAT 57.544 38.095 0.00 0.00 46.97 3.96
2122 2150 2.955477 TTTGCAAGACAACACATGCA 57.045 40.000 0.00 0.00 46.21 3.96
2123 2151 3.382855 TGATTTGCAAGACAACACATGC 58.617 40.909 0.00 0.00 38.23 4.06
2124 2152 5.466819 AGATGATTTGCAAGACAACACATG 58.533 37.500 10.68 0.00 38.23 3.21
2125 2153 5.717078 AGATGATTTGCAAGACAACACAT 57.283 34.783 10.68 5.60 38.23 3.21
2126 2154 5.283294 CAAGATGATTTGCAAGACAACACA 58.717 37.500 10.68 1.66 38.23 3.72
2127 2155 4.682860 CCAAGATGATTTGCAAGACAACAC 59.317 41.667 10.68 6.80 38.23 3.32
2128 2156 4.262121 CCCAAGATGATTTGCAAGACAACA 60.262 41.667 10.68 4.29 38.23 3.33
2129 2157 4.240096 CCCAAGATGATTTGCAAGACAAC 58.760 43.478 10.68 8.72 38.23 3.32
2130 2158 3.258872 CCCCAAGATGATTTGCAAGACAA 59.741 43.478 10.68 0.00 36.13 3.18
2131 2159 2.827322 CCCCAAGATGATTTGCAAGACA 59.173 45.455 0.00 4.65 0.00 3.41
2132 2160 2.167075 CCCCCAAGATGATTTGCAAGAC 59.833 50.000 0.00 0.00 0.00 3.01
2133 2161 2.459644 CCCCCAAGATGATTTGCAAGA 58.540 47.619 0.00 0.00 0.00 3.02
2134 2162 2.973694 CCCCCAAGATGATTTGCAAG 57.026 50.000 0.00 0.00 0.00 4.01
2150 2178 1.062044 AGATTCTACTCCTCCACCCCC 60.062 57.143 0.00 0.00 0.00 5.40
2151 2179 2.043227 CAGATTCTACTCCTCCACCCC 58.957 57.143 0.00 0.00 0.00 4.95
2152 2180 2.753247 ACAGATTCTACTCCTCCACCC 58.247 52.381 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.