Multiple sequence alignment - TraesCS4A01G464100

Loading Multiple Alignment...

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 TraesCS4A01G464100 chr4A 100.000 4185 0 0 1 4185 728088543 728084359 0.000000e+00 7729.0
1 TraesCS4A01G464100 chr7A 88.404 2018 115 43 2216 4182 9755603 9757552 0.000000e+00 2320.0
2 TraesCS4A01G464100 chr7A 88.481 1363 97 28 688 2013 9754268 9755607 0.000000e+00 1592.0
3 TraesCS4A01G464100 chr7A 94.126 698 29 3 3 690 9753547 9754242 0.000000e+00 1051.0
4 TraesCS4A01G464100 chr7A 94.828 58 2 1 2211 2268 639221209 639221265 5.760000e-14 89.8
5 TraesCS4A01G464100 chr7D 92.033 1343 67 16 688 2013 10714477 10715796 0.000000e+00 1851.0
6 TraesCS4A01G464100 chr7D 90.275 1018 40 30 2211 3198 10715788 10716776 0.000000e+00 1277.0
7 TraesCS4A01G464100 chr7D 96.372 689 22 1 2 690 10713766 10714451 0.000000e+00 1131.0
8 TraesCS4A01G464100 chr7D 88.202 873 55 25 3332 4185 10716907 10717750 0.000000e+00 998.0
9 TraesCS4A01G464100 chr7D 81.343 402 54 11 1594 1986 63071052 63071441 1.460000e-79 307.0
10 TraesCS4A01G464100 chr7D 94.828 58 2 1 2211 2268 63071449 63071505 5.760000e-14 89.8
11 TraesCS4A01G464100 chr2B 86.740 362 22 10 1679 2021 56001853 56002207 3.050000e-101 379.0
12 TraesCS4A01G464100 chr2B 98.446 193 3 0 2022 2214 47313068 47312876 1.440000e-89 340.0
13 TraesCS4A01G464100 chr2B 93.464 153 9 1 2745 2896 510167747 510167595 4.210000e-55 226.0
14 TraesCS4A01G464100 chr1A 98.462 195 3 0 2022 2216 6671498 6671692 1.110000e-90 344.0
15 TraesCS4A01G464100 chr7B 98.446 193 3 0 2022 2214 718077356 718077164 1.440000e-89 340.0
16 TraesCS4A01G464100 chr7B 97.462 197 5 0 2020 2216 540430199 540430395 1.860000e-88 337.0
17 TraesCS4A01G464100 chr3B 98.446 193 3 0 2022 2214 141816007 141816199 1.440000e-89 340.0
18 TraesCS4A01G464100 chr3B 95.169 207 10 0 2014 2220 798661035 798660829 1.120000e-85 327.0
19 TraesCS4A01G464100 chr1B 98.446 193 3 0 2022 2214 588495068 588495260 1.440000e-89 340.0
20 TraesCS4A01G464100 chr1B 92.825 223 11 4 1995 2214 59666442 59666662 6.750000e-83 318.0
21 TraesCS4A01G464100 chr5B 95.238 210 10 0 2015 2224 546504402 546504611 2.410000e-87 333.0
22 TraesCS4A01G464100 chr1D 81.638 403 51 13 1594 1986 393065196 393065585 3.140000e-81 313.0
23 TraesCS4A01G464100 chr1D 80.597 402 57 11 1594 1986 477539023 477539412 1.470000e-74 291.0
24 TraesCS4A01G464100 chr1D 80.100 402 59 11 1594 1986 392993546 392993935 3.190000e-71 279.0
25 TraesCS4A01G464100 chr6D 81.218 394 51 13 1603 1986 435556737 435557117 3.160000e-76 296.0
26 TraesCS4A01G464100 chr6D 84.181 177 24 4 1594 1768 34894283 34894457 7.200000e-38 169.0
27 TraesCS4A01G464100 chr6D 96.552 58 1 1 2211 2268 435557125 435557181 1.240000e-15 95.3
28 TraesCS4A01G464100 chr3A 81.218 394 51 13 1603 1986 555171888 555171508 3.160000e-76 296.0


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 TraesCS4A01G464100 chr4A 728084359 728088543 4184 True 7729.000000 7729 100.0000 1 4185 1 chr4A.!!$R1 4184
1 TraesCS4A01G464100 chr7A 9753547 9757552 4005 False 1654.333333 2320 90.3370 3 4182 3 chr7A.!!$F2 4179
2 TraesCS4A01G464100 chr7D 10713766 10717750 3984 False 1314.250000 1851 91.7205 2 4185 4 chr7D.!!$F1 4183

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
531 542 0.038744 AAGAGACAGTGGGCATTGGG 59.961 55.0 0.00 0.0 0.00 4.12 F
1946 2026 0.033781 GTTGCATTGCACACCCATGT 59.966 50.0 11.66 0.0 38.71 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 2131 0.171455 ATAGCGTGCTATAGCGGAGC 59.829 55.0 22.98 22.98 45.83 4.7 R
3511 3709 1.105167 TATGAGCTCGTACGTGGGGG 61.105 60.0 16.05 3.25 0.00 5.4 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
111 112 5.933463 GCAAATCAAATCATGAGGACCAAAA 59.067 36.000 0.09 0.00 42.53 2.44
127 128 7.175104 AGGACCAAAACTATGCAATTCTTAGA 58.825 34.615 0.00 0.00 0.00 2.10
157 158 8.641498 AAAACTATGGCATATATTCCTCCTTG 57.359 34.615 7.81 0.00 0.00 3.61
194 195 4.694037 ACGTAGTTTAACCAAGAGGAATGC 59.306 41.667 0.00 0.00 37.78 3.56
224 225 6.645003 CAGTACTGTTAGTAATGCAGTTGTCA 59.355 38.462 15.06 0.00 39.45 3.58
370 381 2.102925 TCACATCTGTCACACTGAGCAA 59.897 45.455 0.00 0.00 29.63 3.91
482 493 6.730960 ATCAATGCTTTGCGATTTGATTTT 57.269 29.167 7.44 0.00 34.25 1.82
486 497 3.740321 TGCTTTGCGATTTGATTTTGACC 59.260 39.130 0.00 0.00 0.00 4.02
496 507 7.381139 GCGATTTGATTTTGACCTAAAGAAACA 59.619 33.333 0.00 0.00 0.00 2.83
506 517 6.503524 TGACCTAAAGAAACATTTTGCTCAC 58.496 36.000 0.00 0.00 0.00 3.51
531 542 0.038744 AAGAGACAGTGGGCATTGGG 59.961 55.000 0.00 0.00 0.00 4.12
535 546 0.678048 GACAGTGGGCATTGGGTCTC 60.678 60.000 0.00 0.00 0.00 3.36
589 600 9.462606 CTAAATTGTTCCTTGTAGGTCCTAAAT 57.537 33.333 0.00 0.00 36.53 1.40
703 742 2.884639 TGCTTGCCTTACTTTGTTCCTC 59.115 45.455 0.00 0.00 0.00 3.71
745 784 1.569479 GCTATTCGATTCAGCCGGGC 61.569 60.000 12.11 12.11 0.00 6.13
838 877 2.423064 CCCGGGCCATGTTTTAGCC 61.423 63.158 8.08 1.58 46.37 3.93
916 955 4.796231 CCGGACCTTCGGCTGTCG 62.796 72.222 0.00 0.00 43.71 4.35
976 1015 0.389556 CCCATCAGATCATCGAGGCG 60.390 60.000 0.00 0.00 0.00 5.52
978 1017 0.389556 CATCAGATCATCGAGGCGGG 60.390 60.000 0.00 0.00 0.00 6.13
981 1020 3.978491 GATCATCGAGGCGGGCGA 61.978 66.667 0.00 2.96 42.48 5.54
982 1021 3.905705 GATCATCGAGGCGGGCGAG 62.906 68.421 0.00 0.00 41.49 5.03
993 1032 4.200283 GGGCGAGCAGACCGAGAG 62.200 72.222 0.00 0.00 38.99 3.20
994 1033 3.134792 GGCGAGCAGACCGAGAGA 61.135 66.667 0.00 0.00 0.00 3.10
995 1034 2.701780 GGCGAGCAGACCGAGAGAA 61.702 63.158 0.00 0.00 0.00 2.87
996 1035 1.213013 GCGAGCAGACCGAGAGAAA 59.787 57.895 0.00 0.00 0.00 2.52
1164 1203 0.253044 TGCTGGCCACTGTATTCCTC 59.747 55.000 0.00 0.00 0.00 3.71
1224 1263 9.241317 CATTACTATTATCAAAAGCAAAGGCAG 57.759 33.333 0.00 0.00 44.61 4.85
1268 1307 2.211353 GCAGCTGCTAGTACCAGTAC 57.789 55.000 31.33 0.00 38.21 2.73
1332 1371 2.224018 TGCACATGAACTGGCCTTTTTC 60.224 45.455 3.32 4.39 0.00 2.29
1335 1374 4.301628 CACATGAACTGGCCTTTTTCTTC 58.698 43.478 3.32 0.00 0.00 2.87
1342 1381 5.268118 ACTGGCCTTTTTCTTCTTCTTTG 57.732 39.130 3.32 0.00 0.00 2.77
1657 1718 7.492344 AGTTTGAATTGATTCTGTTTGAACACC 59.508 33.333 5.42 0.00 37.52 4.16
1659 1720 6.738114 TGAATTGATTCTGTTTGAACACCTC 58.262 36.000 5.42 0.00 37.52 3.85
1673 1734 6.978343 TGAACACCTCTAACATTATTTCCG 57.022 37.500 0.00 0.00 0.00 4.30
1735 1804 8.429641 CCAAGACCCTAATAGCTAGTTTGATTA 58.570 37.037 0.00 0.00 0.00 1.75
1738 1807 9.160412 AGACCCTAATAGCTAGTTTGATTATGT 57.840 33.333 0.00 0.00 0.00 2.29
1739 1808 9.209175 GACCCTAATAGCTAGTTTGATTATGTG 57.791 37.037 0.00 0.00 0.00 3.21
1780 1850 7.532571 TCTGTTTTCATCAAATCTAGCACATG 58.467 34.615 0.00 0.00 0.00 3.21
1781 1851 6.623486 TGTTTTCATCAAATCTAGCACATGG 58.377 36.000 0.00 0.00 0.00 3.66
1810 1880 3.781079 TGAACTGAACCAACAGCAAAG 57.219 42.857 0.00 0.00 41.06 2.77
1946 2026 0.033781 GTTGCATTGCACACCCATGT 59.966 50.000 11.66 0.00 38.71 3.21
1976 2062 5.296780 ACAAACACAATCACTAGAACACCAG 59.703 40.000 0.00 0.00 0.00 4.00
2014 2100 9.407380 TGAATTACATCCATAATTTGTGCTACT 57.593 29.630 0.00 0.00 35.38 2.57
2015 2101 9.669353 GAATTACATCCATAATTTGTGCTACTG 57.331 33.333 0.00 0.00 35.38 2.74
2016 2102 5.505173 ACATCCATAATTTGTGCTACTGC 57.495 39.130 0.00 0.00 40.20 4.40
2017 2103 5.195940 ACATCCATAATTTGTGCTACTGCT 58.804 37.500 0.00 0.00 40.48 4.24
2018 2104 6.356556 ACATCCATAATTTGTGCTACTGCTA 58.643 36.000 0.00 0.00 40.48 3.49
2019 2105 6.484643 ACATCCATAATTTGTGCTACTGCTAG 59.515 38.462 0.00 0.00 40.48 3.42
2020 2106 5.368145 TCCATAATTTGTGCTACTGCTAGG 58.632 41.667 0.00 0.00 40.48 3.02
2021 2107 4.023707 CCATAATTTGTGCTACTGCTAGGC 60.024 45.833 0.00 0.00 40.48 3.93
2022 2108 2.787473 ATTTGTGCTACTGCTAGGCA 57.213 45.000 0.00 0.00 40.48 4.75
2026 2112 2.671145 TGCTACTGCTAGGCACTGT 58.329 52.632 0.00 0.00 37.43 3.55
2027 2113 0.976641 TGCTACTGCTAGGCACTGTT 59.023 50.000 0.00 0.00 37.43 3.16
2028 2114 1.347707 TGCTACTGCTAGGCACTGTTT 59.652 47.619 0.00 0.00 37.43 2.83
2029 2115 2.003301 GCTACTGCTAGGCACTGTTTC 58.997 52.381 0.00 0.00 41.52 2.78
2030 2116 2.612972 GCTACTGCTAGGCACTGTTTCA 60.613 50.000 0.00 0.00 41.52 2.69
2031 2117 2.638480 ACTGCTAGGCACTGTTTCAA 57.362 45.000 0.00 0.00 41.52 2.69
2032 2118 2.930950 ACTGCTAGGCACTGTTTCAAA 58.069 42.857 0.00 0.00 41.52 2.69
2033 2119 3.490348 ACTGCTAGGCACTGTTTCAAAT 58.510 40.909 0.00 0.00 41.52 2.32
2034 2120 4.651778 ACTGCTAGGCACTGTTTCAAATA 58.348 39.130 0.00 0.00 41.52 1.40
2035 2121 4.697352 ACTGCTAGGCACTGTTTCAAATAG 59.303 41.667 0.00 0.00 41.52 1.73
2036 2122 3.440173 TGCTAGGCACTGTTTCAAATAGC 59.560 43.478 0.00 0.00 41.52 2.97
2037 2123 3.181496 GCTAGGCACTGTTTCAAATAGCC 60.181 47.826 0.00 0.00 41.52 3.93
2038 2124 2.171003 AGGCACTGTTTCAAATAGCCC 58.829 47.619 0.00 0.00 41.45 5.19
2039 2125 1.135402 GGCACTGTTTCAAATAGCCCG 60.135 52.381 0.00 0.00 34.71 6.13
2040 2126 1.732405 GCACTGTTTCAAATAGCCCGC 60.732 52.381 0.00 0.00 0.00 6.13
2041 2127 1.812571 CACTGTTTCAAATAGCCCGCT 59.187 47.619 0.00 0.00 0.00 5.52
2042 2128 3.006940 CACTGTTTCAAATAGCCCGCTA 58.993 45.455 0.00 0.00 0.00 4.26
2043 2129 3.627577 CACTGTTTCAAATAGCCCGCTAT 59.372 43.478 3.31 3.31 40.63 2.97
2044 2130 4.814234 CACTGTTTCAAATAGCCCGCTATA 59.186 41.667 9.56 0.00 38.20 1.31
2045 2131 5.050091 CACTGTTTCAAATAGCCCGCTATAG 60.050 44.000 9.56 6.26 38.20 1.31
2046 2132 3.813166 TGTTTCAAATAGCCCGCTATAGC 59.187 43.478 15.09 15.09 38.20 2.97
2047 2133 4.065789 GTTTCAAATAGCCCGCTATAGCT 58.934 43.478 21.98 6.31 43.20 3.32
2048 2134 3.594603 TCAAATAGCCCGCTATAGCTC 57.405 47.619 21.98 11.04 40.56 4.09
2049 2135 2.233922 TCAAATAGCCCGCTATAGCTCC 59.766 50.000 21.98 10.06 40.56 4.70
2050 2136 0.818296 AATAGCCCGCTATAGCTCCG 59.182 55.000 21.98 10.15 40.56 4.63
2051 2137 1.668101 ATAGCCCGCTATAGCTCCGC 61.668 60.000 21.98 18.46 40.56 5.54
2052 2138 2.766306 TAGCCCGCTATAGCTCCGCT 62.766 60.000 24.41 24.41 43.41 5.52
2053 2139 2.341101 GCCCGCTATAGCTCCGCTA 61.341 63.158 21.98 0.00 45.55 4.26
2061 2147 1.579932 TAGCTCCGCTATAGCACGC 59.420 57.895 23.99 20.26 42.62 5.34
2062 2148 0.889638 TAGCTCCGCTATAGCACGCT 60.890 55.000 25.78 25.78 42.62 5.07
2063 2149 0.889638 AGCTCCGCTATAGCACGCTA 60.890 55.000 23.99 0.39 42.62 4.26
2064 2150 0.171455 GCTCCGCTATAGCACGCTAT 59.829 55.000 23.99 15.45 42.21 2.97
2065 2151 1.400846 GCTCCGCTATAGCACGCTATA 59.599 52.381 23.99 15.99 42.21 1.31
2083 2169 6.418585 GCTATAGCGTTTACAAAAGGTCTT 57.581 37.500 9.40 0.00 31.10 3.01
2084 2170 6.248631 GCTATAGCGTTTACAAAAGGTCTTG 58.751 40.000 9.40 0.00 31.10 3.02
2085 2171 3.349488 AGCGTTTACAAAAGGTCTTGC 57.651 42.857 0.00 0.00 0.00 4.01
2086 2172 2.041244 GCGTTTACAAAAGGTCTTGCG 58.959 47.619 0.00 0.00 0.00 4.85
2087 2173 2.041244 CGTTTACAAAAGGTCTTGCGC 58.959 47.619 0.00 0.00 0.00 6.09
2088 2174 2.286772 CGTTTACAAAAGGTCTTGCGCT 60.287 45.455 9.73 0.00 0.00 5.92
2089 2175 3.059461 CGTTTACAAAAGGTCTTGCGCTA 60.059 43.478 9.73 0.00 0.00 4.26
2090 2176 4.553156 CGTTTACAAAAGGTCTTGCGCTAA 60.553 41.667 9.73 0.00 0.00 3.09
2091 2177 4.742438 TTACAAAAGGTCTTGCGCTAAG 57.258 40.909 9.73 11.02 37.76 2.18
2092 2178 2.846193 ACAAAAGGTCTTGCGCTAAGA 58.154 42.857 9.73 13.31 43.01 2.10
2093 2179 2.808543 ACAAAAGGTCTTGCGCTAAGAG 59.191 45.455 18.44 10.73 45.71 2.85
2094 2180 3.067106 CAAAAGGTCTTGCGCTAAGAGA 58.933 45.455 18.44 9.99 45.71 3.10
2095 2181 2.371910 AAGGTCTTGCGCTAAGAGAC 57.628 50.000 18.44 18.59 45.71 3.36
2096 2182 1.551452 AGGTCTTGCGCTAAGAGACT 58.449 50.000 22.91 18.83 45.71 3.24
2097 2183 1.896465 AGGTCTTGCGCTAAGAGACTT 59.104 47.619 22.91 17.23 45.71 3.01
2098 2184 2.300437 AGGTCTTGCGCTAAGAGACTTT 59.700 45.455 22.91 14.31 45.71 2.66
2099 2185 2.413453 GGTCTTGCGCTAAGAGACTTTG 59.587 50.000 22.91 0.00 45.71 2.77
2100 2186 2.413453 GTCTTGCGCTAAGAGACTTTGG 59.587 50.000 18.44 0.00 45.71 3.28
2101 2187 2.037251 TCTTGCGCTAAGAGACTTTGGT 59.963 45.455 9.73 0.00 40.43 3.67
2102 2188 2.080286 TGCGCTAAGAGACTTTGGTC 57.920 50.000 9.73 0.00 42.41 4.02
2103 2189 1.337823 TGCGCTAAGAGACTTTGGTCC 60.338 52.381 9.73 0.00 43.05 4.46
2104 2190 1.337823 GCGCTAAGAGACTTTGGTCCA 60.338 52.381 0.00 0.00 43.05 4.02
2105 2191 2.870435 GCGCTAAGAGACTTTGGTCCAA 60.870 50.000 0.00 0.00 43.05 3.53
2106 2192 3.399330 CGCTAAGAGACTTTGGTCCAAA 58.601 45.455 16.26 16.26 43.05 3.28
2107 2193 3.186613 CGCTAAGAGACTTTGGTCCAAAC 59.813 47.826 13.26 4.96 43.05 2.93
2108 2194 4.134563 GCTAAGAGACTTTGGTCCAAACA 58.865 43.478 13.26 0.00 43.05 2.83
2109 2195 4.578928 GCTAAGAGACTTTGGTCCAAACAA 59.421 41.667 13.26 0.00 43.05 2.83
2110 2196 5.067283 GCTAAGAGACTTTGGTCCAAACAAA 59.933 40.000 13.26 0.00 43.05 2.83
2111 2197 6.239036 GCTAAGAGACTTTGGTCCAAACAAAT 60.239 38.462 13.26 0.00 43.05 2.32
2112 2198 5.520376 AGAGACTTTGGTCCAAACAAATG 57.480 39.130 13.26 6.01 43.05 2.32
2113 2199 5.200483 AGAGACTTTGGTCCAAACAAATGA 58.800 37.500 13.26 0.00 43.05 2.57
2114 2200 5.656416 AGAGACTTTGGTCCAAACAAATGAA 59.344 36.000 13.26 0.00 43.05 2.57
2115 2201 5.660460 AGACTTTGGTCCAAACAAATGAAC 58.340 37.500 13.26 4.31 43.05 3.18
2116 2202 5.186797 AGACTTTGGTCCAAACAAATGAACA 59.813 36.000 13.26 0.00 43.05 3.18
2117 2203 5.799213 ACTTTGGTCCAAACAAATGAACAA 58.201 33.333 13.26 0.00 37.22 2.83
2118 2204 6.234177 ACTTTGGTCCAAACAAATGAACAAA 58.766 32.000 13.26 0.00 41.86 2.83
2119 2205 6.883756 ACTTTGGTCCAAACAAATGAACAAAT 59.116 30.769 13.26 0.00 42.79 2.32
2120 2206 8.043710 ACTTTGGTCCAAACAAATGAACAAATA 58.956 29.630 13.26 0.00 42.79 1.40
2121 2207 8.970859 TTTGGTCCAAACAAATGAACAAATAT 57.029 26.923 13.26 0.00 39.91 1.28
2122 2208 8.970859 TTGGTCCAAACAAATGAACAAATATT 57.029 26.923 0.40 0.00 33.06 1.28
2123 2209 8.970859 TGGTCCAAACAAATGAACAAATATTT 57.029 26.923 0.00 0.00 0.00 1.40
2124 2210 9.401058 TGGTCCAAACAAATGAACAAATATTTT 57.599 25.926 0.00 0.00 0.00 1.82
2135 2221 7.144007 TGAACAAATATTTTAAATAGCGCGC 57.856 32.000 26.66 26.66 0.00 6.86
2136 2222 6.970043 TGAACAAATATTTTAAATAGCGCGCT 59.030 30.769 38.01 38.01 0.00 5.92
2137 2223 8.123575 TGAACAAATATTTTAAATAGCGCGCTA 58.876 29.630 39.72 39.72 0.00 4.26
2138 2224 9.113876 GAACAAATATTTTAAATAGCGCGCTAT 57.886 29.630 40.32 40.32 40.63 2.97
2140 2226 9.755064 ACAAATATTTTAAATAGCGCGCTATAG 57.245 29.630 43.81 25.10 38.20 1.31
2141 2227 8.725046 CAAATATTTTAAATAGCGCGCTATAGC 58.275 33.333 43.81 15.09 38.20 2.97
2142 2228 7.772332 ATATTTTAAATAGCGCGCTATAGCT 57.228 32.000 43.81 33.17 46.53 3.32
2143 2229 5.917541 TTTTAAATAGCGCGCTATAGCTT 57.082 34.783 43.81 35.76 44.15 3.74
2144 2230 5.511088 TTTAAATAGCGCGCTATAGCTTC 57.489 39.130 43.81 10.26 44.15 3.86
2145 2231 1.618861 AATAGCGCGCTATAGCTTCG 58.381 50.000 43.81 22.79 44.15 3.79
2148 2234 4.841029 CGCGCTATAGCTTCGCTA 57.159 55.556 21.98 0.00 45.55 4.26
2156 2242 3.474007 TAGCTTCGCTATAGCACGC 57.526 52.632 23.99 20.26 41.11 5.34
2157 2243 0.952280 TAGCTTCGCTATAGCACGCT 59.048 50.000 25.78 25.78 41.11 5.07
2158 2244 0.952280 AGCTTCGCTATAGCACGCTA 59.048 50.000 23.99 0.39 41.11 4.26
2159 2245 1.053811 GCTTCGCTATAGCACGCTAC 58.946 55.000 23.99 4.81 42.21 3.58
2160 2246 1.599667 GCTTCGCTATAGCACGCTACA 60.600 52.381 23.99 0.00 42.21 2.74
2161 2247 2.311462 CTTCGCTATAGCACGCTACAG 58.689 52.381 23.99 0.00 42.21 2.74
2162 2248 0.040336 TCGCTATAGCACGCTACAGC 60.040 55.000 23.99 17.40 43.42 4.40
2163 2249 0.317854 CGCTATAGCACGCTACAGCA 60.318 55.000 24.54 0.00 46.18 4.41
2164 2250 1.667177 CGCTATAGCACGCTACAGCAT 60.667 52.381 24.54 3.68 46.18 3.79
2165 2251 2.408050 GCTATAGCACGCTACAGCATT 58.592 47.619 21.34 0.00 45.44 3.56
2166 2252 2.802816 GCTATAGCACGCTACAGCATTT 59.197 45.455 21.34 0.00 45.44 2.32
2167 2253 3.363378 GCTATAGCACGCTACAGCATTTG 60.363 47.826 21.34 0.00 45.44 2.32
2168 2254 2.378445 TAGCACGCTACAGCATTTGA 57.622 45.000 1.61 0.00 42.21 2.69
2169 2255 1.522668 AGCACGCTACAGCATTTGAA 58.477 45.000 1.61 0.00 42.21 2.69
2170 2256 1.879380 AGCACGCTACAGCATTTGAAA 59.121 42.857 1.61 0.00 42.21 2.69
2171 2257 2.095567 AGCACGCTACAGCATTTGAAAG 60.096 45.455 1.61 0.00 42.21 2.62
2172 2258 2.095768 GCACGCTACAGCATTTGAAAGA 60.096 45.455 1.61 0.00 42.21 2.52
2173 2259 3.740590 CACGCTACAGCATTTGAAAGAG 58.259 45.455 1.61 0.00 42.21 2.85
2174 2260 2.744202 ACGCTACAGCATTTGAAAGAGG 59.256 45.455 1.61 0.00 42.21 3.69
2175 2261 2.744202 CGCTACAGCATTTGAAAGAGGT 59.256 45.455 1.61 0.00 42.21 3.85
2176 2262 3.181516 CGCTACAGCATTTGAAAGAGGTC 60.182 47.826 1.61 0.00 42.21 3.85
2177 2263 3.127721 GCTACAGCATTTGAAAGAGGTCC 59.872 47.826 0.00 0.00 41.59 4.46
2178 2264 2.154462 ACAGCATTTGAAAGAGGTCCG 58.846 47.619 0.00 0.00 0.00 4.79
2179 2265 2.224523 ACAGCATTTGAAAGAGGTCCGA 60.225 45.455 0.00 0.00 0.00 4.55
2180 2266 2.160417 CAGCATTTGAAAGAGGTCCGAC 59.840 50.000 0.00 0.00 0.00 4.79
2181 2267 1.128692 GCATTTGAAAGAGGTCCGACG 59.871 52.381 0.00 0.00 0.00 5.12
2182 2268 1.128692 CATTTGAAAGAGGTCCGACGC 59.871 52.381 0.00 0.00 0.00 5.19
2183 2269 0.391597 TTTGAAAGAGGTCCGACGCT 59.608 50.000 0.00 0.00 0.00 5.07
2184 2270 1.250328 TTGAAAGAGGTCCGACGCTA 58.750 50.000 0.00 0.00 0.00 4.26
2185 2271 1.250328 TGAAAGAGGTCCGACGCTAA 58.750 50.000 0.00 0.00 0.00 3.09
2186 2272 1.201647 TGAAAGAGGTCCGACGCTAAG 59.798 52.381 0.00 0.00 0.00 2.18
2187 2273 1.471684 GAAAGAGGTCCGACGCTAAGA 59.528 52.381 0.00 0.00 0.00 2.10
2188 2274 1.765230 AAGAGGTCCGACGCTAAGAT 58.235 50.000 0.00 0.00 0.00 2.40
2189 2275 1.025812 AGAGGTCCGACGCTAAGATG 58.974 55.000 0.00 0.00 0.00 2.90
2190 2276 0.595310 GAGGTCCGACGCTAAGATGC 60.595 60.000 0.00 0.00 0.00 3.91
2191 2277 1.038130 AGGTCCGACGCTAAGATGCT 61.038 55.000 0.00 0.00 0.00 3.79
2192 2278 0.179108 GGTCCGACGCTAAGATGCTT 60.179 55.000 0.00 0.00 0.00 3.91
2193 2279 1.066605 GGTCCGACGCTAAGATGCTTA 59.933 52.381 0.00 0.00 0.00 3.09
2194 2280 2.386249 GTCCGACGCTAAGATGCTTAG 58.614 52.381 9.30 9.30 0.00 2.18
2195 2281 1.132588 CCGACGCTAAGATGCTTAGC 58.867 55.000 22.75 22.75 42.82 3.09
2199 2285 1.202816 GCTAAGATGCTTAGCGCGC 59.797 57.895 26.66 26.66 43.27 6.86
2200 2286 1.218230 GCTAAGATGCTTAGCGCGCT 61.218 55.000 38.01 38.01 43.27 5.92
2201 2287 1.930817 GCTAAGATGCTTAGCGCGCTA 60.931 52.381 35.48 35.48 43.27 4.26
2202 2288 2.600731 CTAAGATGCTTAGCGCGCTAT 58.399 47.619 38.51 26.50 43.27 2.97
2203 2289 1.871080 AAGATGCTTAGCGCGCTATT 58.129 45.000 38.51 26.01 43.27 1.73
2204 2290 1.871080 AGATGCTTAGCGCGCTATTT 58.129 45.000 38.51 23.54 43.27 1.40
2205 2291 3.026630 AGATGCTTAGCGCGCTATTTA 57.973 42.857 38.51 26.65 43.27 1.40
2206 2292 3.390135 AGATGCTTAGCGCGCTATTTAA 58.610 40.909 38.51 25.53 43.27 1.52
2207 2293 3.807622 AGATGCTTAGCGCGCTATTTAAA 59.192 39.130 38.51 25.16 43.27 1.52
2208 2294 4.272504 AGATGCTTAGCGCGCTATTTAAAA 59.727 37.500 38.51 24.43 43.27 1.52
2209 2295 3.676540 TGCTTAGCGCGCTATTTAAAAC 58.323 40.909 38.51 22.00 43.27 2.43
2210 2296 3.372822 TGCTTAGCGCGCTATTTAAAACT 59.627 39.130 38.51 14.50 43.27 2.66
2211 2297 4.142773 TGCTTAGCGCGCTATTTAAAACTT 60.143 37.500 38.51 13.94 43.27 2.66
2212 2298 4.791676 GCTTAGCGCGCTATTTAAAACTTT 59.208 37.500 38.51 13.72 0.00 2.66
2213 2299 5.275280 GCTTAGCGCGCTATTTAAAACTTTG 60.275 40.000 38.51 15.49 0.00 2.77
2214 2300 2.914838 AGCGCGCTATTTAAAACTTTGC 59.085 40.909 35.79 0.00 0.00 3.68
2228 2314 4.826274 AACTTTGCTGCTAGGTATGAGA 57.174 40.909 0.00 0.00 0.00 3.27
2268 2354 2.587194 CGGGAGCGCCAAGATCTG 60.587 66.667 9.31 0.00 35.20 2.90
2301 2387 4.489771 CCTCACGGGGGCCATGAC 62.490 72.222 4.39 0.00 0.00 3.06
2660 2746 1.638388 CGTCTACTGCGTACGTGGGA 61.638 60.000 17.90 5.77 32.16 4.37
2661 2747 0.737219 GTCTACTGCGTACGTGGGAT 59.263 55.000 17.90 1.19 0.00 3.85
2663 2749 0.030369 CTACTGCGTACGTGGGATCC 59.970 60.000 17.90 1.92 0.00 3.36
2664 2750 1.717791 TACTGCGTACGTGGGATCCG 61.718 60.000 17.90 0.00 0.00 4.18
2677 2763 3.165559 GATCCGTCGATCCGTCAAG 57.834 57.895 0.00 0.00 39.29 3.02
2678 2764 0.317938 GATCCGTCGATCCGTCAAGG 60.318 60.000 0.00 0.00 39.29 3.61
2694 2780 3.967332 CAAGGATTGGGCTCAATTTGT 57.033 42.857 14.31 0.00 43.94 2.83
2699 2785 3.131046 GGATTGGGCTCAATTTGTTCGAT 59.869 43.478 14.31 0.00 43.08 3.59
2700 2786 3.848272 TTGGGCTCAATTTGTTCGATC 57.152 42.857 0.00 0.00 0.00 3.69
2706 2792 3.181506 GCTCAATTTGTTCGATCCCTGAC 60.182 47.826 0.00 0.00 0.00 3.51
2736 2822 2.618794 TGCAAGATTTTGATTGGGGGT 58.381 42.857 0.00 0.00 36.36 4.95
2925 3022 1.004595 GTCCGTCCGCCATTAAACTC 58.995 55.000 0.00 0.00 0.00 3.01
2933 3030 2.159382 CGCCATTAAACTCAACCCACT 58.841 47.619 0.00 0.00 0.00 4.00
2935 3032 3.421844 GCCATTAAACTCAACCCACTCT 58.578 45.455 0.00 0.00 0.00 3.24
2937 3034 4.807643 GCCATTAAACTCAACCCACTCTCT 60.808 45.833 0.00 0.00 0.00 3.10
2938 3035 4.697352 CCATTAAACTCAACCCACTCTCTG 59.303 45.833 0.00 0.00 0.00 3.35
2939 3036 5.513094 CCATTAAACTCAACCCACTCTCTGA 60.513 44.000 0.00 0.00 0.00 3.27
2940 3037 5.623956 TTAAACTCAACCCACTCTCTGAA 57.376 39.130 0.00 0.00 0.00 3.02
2990 3123 1.989165 GTGAGCTCATTCAGTGTCGAC 59.011 52.381 21.47 9.11 0.00 4.20
3135 3268 3.179939 GGCGAAGACGGTCGAAGC 61.180 66.667 13.51 13.51 43.86 3.86
3198 3331 1.140816 GTGTGACTCTGAACCGAAGC 58.859 55.000 0.00 0.00 0.00 3.86
3214 3347 1.177256 AAGCCTGAACTGCAGCAAGG 61.177 55.000 20.41 20.41 43.50 3.61
3289 3423 3.358707 TCAACACTGTACTGTACCGTG 57.641 47.619 29.14 29.14 45.61 4.94
3307 3441 3.129287 CCGTGGGAAATTTGGATGAGAAG 59.871 47.826 0.00 0.00 0.00 2.85
3352 3525 7.551974 AGAGTGAGATAAACAATGAGATGTTGG 59.448 37.037 0.00 0.00 42.49 3.77
3370 3543 2.571212 TGGTTGATGGTGTCACTCAAC 58.429 47.619 21.46 21.46 45.04 3.18
3397 3570 8.129001 TCCATCTATAATTAGGAGCCCTGATTA 58.871 37.037 15.81 15.81 43.12 1.75
3398 3571 8.772250 CCATCTATAATTAGGAGCCCTGATTAA 58.228 37.037 16.80 6.74 42.54 1.40
3402 3575 3.402628 TTAGGAGCCCTGATTAATCGC 57.597 47.619 10.80 8.14 34.61 4.58
3403 3576 0.398318 AGGAGCCCTGATTAATCGCC 59.602 55.000 10.80 5.37 29.57 5.54
3404 3577 0.108585 GGAGCCCTGATTAATCGCCA 59.891 55.000 10.80 0.00 0.00 5.69
3405 3578 1.271597 GGAGCCCTGATTAATCGCCAT 60.272 52.381 10.80 0.00 0.00 4.40
3409 3582 2.821969 GCCCTGATTAATCGCCATTCAT 59.178 45.455 10.80 0.00 0.00 2.57
3442 3615 3.369756 TCGTTCATGTCCGAATTAGCAAC 59.630 43.478 6.94 0.00 0.00 4.17
3511 3709 0.108138 CTCCATTGACGGACCCTCAC 60.108 60.000 0.00 0.00 0.00 3.51
3532 3730 1.269102 CCCCACGTACGAGCTCATAAG 60.269 57.143 24.41 7.95 0.00 1.73
3533 3731 1.404391 CCCACGTACGAGCTCATAAGT 59.596 52.381 24.41 8.68 0.00 2.24
3534 3732 2.451132 CCACGTACGAGCTCATAAGTG 58.549 52.381 23.31 23.31 32.57 3.16
3542 3740 8.016229 ACGTACGAGCTCATAAGTGATAAATAG 58.984 37.037 24.41 0.00 32.98 1.73
3578 3776 2.279120 CTCCTGCACGATCGAGGC 60.279 66.667 24.34 23.53 0.00 4.70
3866 4067 4.552365 CGGATGGCGGTGGAGCAT 62.552 66.667 0.00 0.00 39.27 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.008813 ACAGCAGAATATAGAGGCCCATG 59.991 47.826 0.00 0.00 0.00 3.66
281 292 3.243359 TCACCTGAAGAATTTGGGCTT 57.757 42.857 0.00 0.00 0.00 4.35
408 419 2.545106 GGTGGTCGTACAAAAATCGTGT 59.455 45.455 0.00 0.00 0.00 4.49
482 493 6.460953 GGTGAGCAAAATGTTTCTTTAGGTCA 60.461 38.462 0.00 0.00 0.00 4.02
486 497 7.706179 TCTTTGGTGAGCAAAATGTTTCTTTAG 59.294 33.333 11.19 0.00 0.00 1.85
496 507 4.889409 TGTCTCTTCTTTGGTGAGCAAAAT 59.111 37.500 11.19 0.00 0.00 1.82
506 517 1.202806 TGCCCACTGTCTCTTCTTTGG 60.203 52.381 0.00 0.00 0.00 3.28
531 542 4.543590 TCCCATGAGAAAGTTCTGAGAC 57.456 45.455 0.00 0.00 37.73 3.36
535 546 2.751806 GCCTTCCCATGAGAAAGTTCTG 59.248 50.000 0.00 0.00 37.73 3.02
803 842 2.107953 GGGAGAGGAGCACATCGC 59.892 66.667 0.00 0.00 42.91 4.58
840 879 2.526993 TTTTCGCACACGTGACCGG 61.527 57.895 25.01 0.00 41.18 5.28
875 914 0.394762 TGGCATCTGAAGGCATGTCC 60.395 55.000 4.96 0.00 36.56 4.02
916 955 2.698274 CCATGGTTTTTATAGGGGTGGC 59.302 50.000 2.57 0.00 0.00 5.01
976 1015 4.200283 CTCTCGGTCTGCTCGCCC 62.200 72.222 0.00 0.00 0.00 6.13
978 1017 0.388649 TTTTCTCTCGGTCTGCTCGC 60.389 55.000 0.00 0.00 0.00 5.03
996 1035 2.028748 GCATCCTGCACTCCACATTTTT 60.029 45.455 0.00 0.00 44.26 1.94
1224 1263 7.646922 GCTTTTATCACCATGATGATCTGTTTC 59.353 37.037 5.62 0.00 39.97 2.78
1263 1302 3.008330 ACGACTACTGGTGCTAGTACTG 58.992 50.000 10.95 6.90 32.19 2.74
1264 1303 3.269178 GACGACTACTGGTGCTAGTACT 58.731 50.000 10.95 0.00 32.19 2.73
1265 1304 2.030213 CGACGACTACTGGTGCTAGTAC 59.970 54.545 1.77 1.77 32.19 2.73
1266 1305 2.274437 CGACGACTACTGGTGCTAGTA 58.726 52.381 0.00 0.00 32.19 1.82
1267 1306 1.085091 CGACGACTACTGGTGCTAGT 58.915 55.000 0.00 0.00 34.71 2.57
1268 1307 1.085091 ACGACGACTACTGGTGCTAG 58.915 55.000 0.00 0.00 0.00 3.42
1272 1311 0.313043 ACCAACGACGACTACTGGTG 59.687 55.000 0.00 0.00 38.95 4.17
1482 1521 3.819188 GGGAGCAGATTGCCGAAG 58.181 61.111 0.00 0.00 46.52 3.79
1697 1764 1.273327 GGGTCTTGGTGCATTTCAAGG 59.727 52.381 19.88 8.14 40.35 3.61
1780 1850 3.674997 TGGTTCAGTTCAAGATGCTACC 58.325 45.455 0.00 0.00 0.00 3.18
1781 1851 4.515191 TGTTGGTTCAGTTCAAGATGCTAC 59.485 41.667 0.00 0.00 0.00 3.58
1810 1880 3.364664 CCGTAAAGCCGAAGTCTTTTTCC 60.365 47.826 0.00 0.00 36.87 3.13
1926 2005 0.319083 CATGGGTGTGCAATGCAACT 59.681 50.000 10.44 0.00 41.47 3.16
1946 2026 7.281999 TGTTCTAGTGATTGTGTTTGTGAATCA 59.718 33.333 0.00 0.00 34.47 2.57
1948 2028 7.417612 GTGTTCTAGTGATTGTGTTTGTGAAT 58.582 34.615 0.00 0.00 0.00 2.57
1949 2029 6.183360 GGTGTTCTAGTGATTGTGTTTGTGAA 60.183 38.462 0.00 0.00 0.00 3.18
1950 2030 5.295787 GGTGTTCTAGTGATTGTGTTTGTGA 59.704 40.000 0.00 0.00 0.00 3.58
1951 2031 5.065859 TGGTGTTCTAGTGATTGTGTTTGTG 59.934 40.000 0.00 0.00 0.00 3.33
1952 2032 5.189928 TGGTGTTCTAGTGATTGTGTTTGT 58.810 37.500 0.00 0.00 0.00 2.83
1953 2033 5.527214 TCTGGTGTTCTAGTGATTGTGTTTG 59.473 40.000 0.00 0.00 0.00 2.93
1963 2049 6.618287 TTGAATTTGTCTGGTGTTCTAGTG 57.382 37.500 0.00 0.00 0.00 2.74
1994 2080 5.195940 AGCAGTAGCACAAATTATGGATGT 58.804 37.500 0.00 0.00 45.49 3.06
2008 2094 0.976641 AACAGTGCCTAGCAGTAGCA 59.023 50.000 0.00 0.00 40.54 3.49
2009 2095 2.003301 GAAACAGTGCCTAGCAGTAGC 58.997 52.381 0.00 0.00 40.54 3.58
2010 2096 3.319137 TGAAACAGTGCCTAGCAGTAG 57.681 47.619 0.00 0.00 40.54 2.57
2011 2097 3.762407 TTGAAACAGTGCCTAGCAGTA 57.238 42.857 0.00 0.00 40.54 2.74
2012 2098 2.638480 TTGAAACAGTGCCTAGCAGT 57.362 45.000 0.00 0.00 43.59 4.40
2013 2099 4.437930 GCTATTTGAAACAGTGCCTAGCAG 60.438 45.833 0.00 0.00 40.08 4.24
2014 2100 3.440173 GCTATTTGAAACAGTGCCTAGCA 59.560 43.478 0.00 0.00 35.60 3.49
2015 2101 3.181496 GGCTATTTGAAACAGTGCCTAGC 60.181 47.826 0.00 1.84 36.32 3.42
2016 2102 3.378427 GGGCTATTTGAAACAGTGCCTAG 59.622 47.826 10.48 0.00 38.93 3.02
2017 2103 3.352648 GGGCTATTTGAAACAGTGCCTA 58.647 45.455 10.48 0.00 38.93 3.93
2018 2104 2.171003 GGGCTATTTGAAACAGTGCCT 58.829 47.619 10.48 0.00 38.93 4.75
2019 2105 1.135402 CGGGCTATTTGAAACAGTGCC 60.135 52.381 0.00 0.00 38.28 5.01
2020 2106 1.732405 GCGGGCTATTTGAAACAGTGC 60.732 52.381 0.00 0.00 0.00 4.40
2021 2107 1.812571 AGCGGGCTATTTGAAACAGTG 59.187 47.619 0.00 0.00 0.00 3.66
2022 2108 2.200373 AGCGGGCTATTTGAAACAGT 57.800 45.000 0.00 0.00 0.00 3.55
2023 2109 4.083802 GCTATAGCGGGCTATTTGAAACAG 60.084 45.833 17.49 8.76 39.65 3.16
2024 2110 3.813166 GCTATAGCGGGCTATTTGAAACA 59.187 43.478 17.49 0.00 39.65 2.83
2025 2111 4.406001 GCTATAGCGGGCTATTTGAAAC 57.594 45.455 17.49 0.05 39.65 2.78
2045 2131 0.171455 ATAGCGTGCTATAGCGGAGC 59.829 55.000 22.98 22.98 45.83 4.70
2046 2132 3.326733 CTATAGCGTGCTATAGCGGAG 57.673 52.381 27.04 13.65 46.26 4.63
2060 2146 6.248631 CAAGACCTTTTGTAAACGCTATAGC 58.751 40.000 15.09 15.09 37.78 2.97
2061 2147 6.248631 GCAAGACCTTTTGTAAACGCTATAG 58.751 40.000 0.00 0.00 0.00 1.31
2062 2148 5.163933 CGCAAGACCTTTTGTAAACGCTATA 60.164 40.000 0.00 0.00 43.02 1.31
2063 2149 4.378046 CGCAAGACCTTTTGTAAACGCTAT 60.378 41.667 0.00 0.00 43.02 2.97
2064 2150 3.059461 CGCAAGACCTTTTGTAAACGCTA 60.059 43.478 0.00 0.00 43.02 4.26
2065 2151 2.286772 CGCAAGACCTTTTGTAAACGCT 60.287 45.455 0.00 0.00 43.02 5.07
2066 2152 2.041244 CGCAAGACCTTTTGTAAACGC 58.959 47.619 0.00 0.00 43.02 4.84
2067 2153 2.041244 GCGCAAGACCTTTTGTAAACG 58.959 47.619 0.30 0.00 43.02 3.60
2068 2154 3.349488 AGCGCAAGACCTTTTGTAAAC 57.651 42.857 11.47 0.00 43.02 2.01
2069 2155 4.817464 TCTTAGCGCAAGACCTTTTGTAAA 59.183 37.500 11.47 0.00 38.39 2.01
2070 2156 4.382291 TCTTAGCGCAAGACCTTTTGTAA 58.618 39.130 11.47 0.00 38.39 2.41
2071 2157 3.994392 CTCTTAGCGCAAGACCTTTTGTA 59.006 43.478 11.47 0.00 38.39 2.41
2072 2158 2.808543 CTCTTAGCGCAAGACCTTTTGT 59.191 45.455 11.47 0.00 38.39 2.83
2073 2159 3.067106 TCTCTTAGCGCAAGACCTTTTG 58.933 45.455 11.47 4.34 38.39 2.44
2074 2160 3.067833 GTCTCTTAGCGCAAGACCTTTT 58.932 45.455 11.47 0.00 38.39 2.27
2075 2161 2.300437 AGTCTCTTAGCGCAAGACCTTT 59.700 45.455 21.13 7.34 40.21 3.11
2076 2162 1.896465 AGTCTCTTAGCGCAAGACCTT 59.104 47.619 21.13 7.87 40.21 3.50
2077 2163 1.551452 AGTCTCTTAGCGCAAGACCT 58.449 50.000 21.13 14.93 40.21 3.85
2078 2164 2.371910 AAGTCTCTTAGCGCAAGACC 57.628 50.000 21.13 13.52 40.21 3.85
2079 2165 2.413453 CCAAAGTCTCTTAGCGCAAGAC 59.587 50.000 11.47 16.26 38.39 3.01
2080 2166 2.037251 ACCAAAGTCTCTTAGCGCAAGA 59.963 45.455 11.47 15.40 41.10 3.02
2081 2167 2.413453 GACCAAAGTCTCTTAGCGCAAG 59.587 50.000 11.47 11.67 40.10 4.01
2082 2168 2.413837 GACCAAAGTCTCTTAGCGCAA 58.586 47.619 11.47 0.50 40.10 4.85
2083 2169 1.337823 GGACCAAAGTCTCTTAGCGCA 60.338 52.381 11.47 0.00 43.05 6.09
2084 2170 1.337823 TGGACCAAAGTCTCTTAGCGC 60.338 52.381 0.00 0.00 43.05 5.92
2085 2171 2.743636 TGGACCAAAGTCTCTTAGCG 57.256 50.000 0.00 0.00 43.05 4.26
2086 2172 4.134563 TGTTTGGACCAAAGTCTCTTAGC 58.865 43.478 20.14 5.76 43.05 3.09
2087 2173 6.693315 TTTGTTTGGACCAAAGTCTCTTAG 57.307 37.500 20.14 0.00 43.05 2.18
2088 2174 6.831353 TCATTTGTTTGGACCAAAGTCTCTTA 59.169 34.615 20.14 1.24 43.05 2.10
2089 2175 5.656416 TCATTTGTTTGGACCAAAGTCTCTT 59.344 36.000 20.14 1.05 43.05 2.85
2090 2176 5.200483 TCATTTGTTTGGACCAAAGTCTCT 58.800 37.500 20.14 1.91 43.05 3.10
2091 2177 5.514274 TCATTTGTTTGGACCAAAGTCTC 57.486 39.130 20.14 8.94 43.05 3.36
2092 2178 5.186797 TGTTCATTTGTTTGGACCAAAGTCT 59.813 36.000 20.14 2.95 43.05 3.24
2093 2179 5.415221 TGTTCATTTGTTTGGACCAAAGTC 58.585 37.500 20.14 10.01 42.73 3.01
2094 2180 5.413309 TGTTCATTTGTTTGGACCAAAGT 57.587 34.783 20.14 4.29 35.45 2.66
2095 2181 6.734104 TTTGTTCATTTGTTTGGACCAAAG 57.266 33.333 20.14 8.25 35.45 2.77
2096 2182 8.970859 ATATTTGTTCATTTGTTTGGACCAAA 57.029 26.923 15.89 15.89 36.34 3.28
2097 2183 8.970859 AATATTTGTTCATTTGTTTGGACCAA 57.029 26.923 1.69 1.69 0.00 3.67
2098 2184 8.970859 AAATATTTGTTCATTTGTTTGGACCA 57.029 26.923 0.00 0.00 0.00 4.02
2109 2195 8.265998 GCGCGCTATTTAAAATATTTGTTCATT 58.734 29.630 26.67 0.00 0.00 2.57
2110 2196 7.647715 AGCGCGCTATTTAAAATATTTGTTCAT 59.352 29.630 35.79 0.00 0.00 2.57
2111 2197 6.970043 AGCGCGCTATTTAAAATATTTGTTCA 59.030 30.769 35.79 0.00 0.00 3.18
2112 2198 7.376530 AGCGCGCTATTTAAAATATTTGTTC 57.623 32.000 35.79 0.00 0.00 3.18
2114 2200 9.755064 CTATAGCGCGCTATTTAAAATATTTGT 57.245 29.630 46.76 27.18 39.65 2.83
2115 2201 8.725046 GCTATAGCGCGCTATTTAAAATATTTG 58.275 33.333 46.76 26.68 39.65 2.32
2116 2202 8.822105 GCTATAGCGCGCTATTTAAAATATTT 57.178 30.769 46.76 27.75 39.65 1.40
2141 2227 2.311462 CTGTAGCGTGCTATAGCGAAG 58.689 52.381 19.55 13.65 45.83 3.79
2142 2228 2.401017 CTGTAGCGTGCTATAGCGAA 57.599 50.000 19.55 0.03 45.83 4.70
2146 2232 4.051237 TCAAATGCTGTAGCGTGCTATAG 58.949 43.478 18.06 18.06 45.83 1.31
2147 2233 4.053469 TCAAATGCTGTAGCGTGCTATA 57.947 40.909 4.68 1.34 45.83 1.31
2148 2234 2.905075 TCAAATGCTGTAGCGTGCTAT 58.095 42.857 4.68 0.00 45.83 2.97
2149 2235 2.378445 TCAAATGCTGTAGCGTGCTA 57.622 45.000 0.00 0.00 45.83 3.49
2150 2236 1.522668 TTCAAATGCTGTAGCGTGCT 58.477 45.000 0.00 0.00 45.83 4.40
2151 2237 2.095768 TCTTTCAAATGCTGTAGCGTGC 60.096 45.455 0.00 0.00 45.83 5.34
2152 2238 3.425359 CCTCTTTCAAATGCTGTAGCGTG 60.425 47.826 0.00 0.00 45.83 5.34
2153 2239 2.744202 CCTCTTTCAAATGCTGTAGCGT 59.256 45.455 0.00 0.00 45.83 5.07
2154 2240 2.744202 ACCTCTTTCAAATGCTGTAGCG 59.256 45.455 0.00 0.00 45.83 4.26
2155 2241 3.127721 GGACCTCTTTCAAATGCTGTAGC 59.872 47.826 0.00 0.00 42.50 3.58
2156 2242 3.372206 CGGACCTCTTTCAAATGCTGTAG 59.628 47.826 0.00 0.00 0.00 2.74
2157 2243 3.007506 TCGGACCTCTTTCAAATGCTGTA 59.992 43.478 0.00 0.00 0.00 2.74
2158 2244 2.154462 CGGACCTCTTTCAAATGCTGT 58.846 47.619 0.00 0.00 0.00 4.40
2159 2245 2.160417 GTCGGACCTCTTTCAAATGCTG 59.840 50.000 0.00 0.00 0.00 4.41
2160 2246 2.427506 GTCGGACCTCTTTCAAATGCT 58.572 47.619 0.00 0.00 0.00 3.79
2161 2247 1.128692 CGTCGGACCTCTTTCAAATGC 59.871 52.381 1.91 0.00 0.00 3.56
2162 2248 1.128692 GCGTCGGACCTCTTTCAAATG 59.871 52.381 1.91 0.00 0.00 2.32
2163 2249 1.002087 AGCGTCGGACCTCTTTCAAAT 59.998 47.619 1.91 0.00 0.00 2.32
2164 2250 0.391597 AGCGTCGGACCTCTTTCAAA 59.608 50.000 1.91 0.00 0.00 2.69
2165 2251 1.250328 TAGCGTCGGACCTCTTTCAA 58.750 50.000 1.91 0.00 0.00 2.69
2166 2252 1.201647 CTTAGCGTCGGACCTCTTTCA 59.798 52.381 1.91 0.00 0.00 2.69
2167 2253 1.471684 TCTTAGCGTCGGACCTCTTTC 59.528 52.381 1.91 0.00 0.00 2.62
2168 2254 1.542492 TCTTAGCGTCGGACCTCTTT 58.458 50.000 1.91 0.00 0.00 2.52
2169 2255 1.405821 CATCTTAGCGTCGGACCTCTT 59.594 52.381 1.91 0.00 0.00 2.85
2170 2256 1.025812 CATCTTAGCGTCGGACCTCT 58.974 55.000 1.91 2.89 0.00 3.69
2171 2257 0.595310 GCATCTTAGCGTCGGACCTC 60.595 60.000 1.91 0.00 0.00 3.85
2172 2258 1.038130 AGCATCTTAGCGTCGGACCT 61.038 55.000 1.91 3.67 40.15 3.85
2173 2259 0.179108 AAGCATCTTAGCGTCGGACC 60.179 55.000 1.91 0.00 40.15 4.46
2174 2260 2.386249 CTAAGCATCTTAGCGTCGGAC 58.614 52.381 0.00 0.00 40.15 4.79
2175 2261 1.269102 GCTAAGCATCTTAGCGTCGGA 60.269 52.381 18.95 0.00 38.12 4.55
2176 2262 1.132588 GCTAAGCATCTTAGCGTCGG 58.867 55.000 18.95 0.00 38.12 4.79
2189 2275 3.936661 AGTTTTAAATAGCGCGCTAAGC 58.063 40.909 40.90 27.92 43.95 3.09
2190 2276 5.275280 GCAAAGTTTTAAATAGCGCGCTAAG 60.275 40.000 40.90 16.80 31.73 2.18
2191 2277 4.555747 GCAAAGTTTTAAATAGCGCGCTAA 59.444 37.500 40.90 26.03 31.73 3.09
2192 2278 4.092816 GCAAAGTTTTAAATAGCGCGCTA 58.907 39.130 39.72 39.72 0.00 4.26
2193 2279 2.914838 GCAAAGTTTTAAATAGCGCGCT 59.085 40.909 38.01 38.01 0.00 5.92
2194 2280 2.914838 AGCAAAGTTTTAAATAGCGCGC 59.085 40.909 26.66 26.66 0.00 6.86
2195 2281 3.241333 GCAGCAAAGTTTTAAATAGCGCG 60.241 43.478 0.00 0.00 0.00 6.86
2196 2282 3.920412 AGCAGCAAAGTTTTAAATAGCGC 59.080 39.130 0.00 0.00 0.00 5.92
2197 2283 5.739161 CCTAGCAGCAAAGTTTTAAATAGCG 59.261 40.000 0.00 0.00 0.00 4.26
2198 2284 6.621613 ACCTAGCAGCAAAGTTTTAAATAGC 58.378 36.000 0.00 0.00 0.00 2.97
2199 2285 9.722056 CATACCTAGCAGCAAAGTTTTAAATAG 57.278 33.333 0.00 0.00 0.00 1.73
2200 2286 9.456147 TCATACCTAGCAGCAAAGTTTTAAATA 57.544 29.630 0.00 0.00 0.00 1.40
2201 2287 8.348285 TCATACCTAGCAGCAAAGTTTTAAAT 57.652 30.769 0.00 0.00 0.00 1.40
2202 2288 7.663905 TCTCATACCTAGCAGCAAAGTTTTAAA 59.336 33.333 0.00 0.00 0.00 1.52
2203 2289 7.119262 GTCTCATACCTAGCAGCAAAGTTTTAA 59.881 37.037 0.00 0.00 0.00 1.52
2204 2290 6.594159 GTCTCATACCTAGCAGCAAAGTTTTA 59.406 38.462 0.00 0.00 0.00 1.52
2205 2291 5.412904 GTCTCATACCTAGCAGCAAAGTTTT 59.587 40.000 0.00 0.00 0.00 2.43
2206 2292 4.938226 GTCTCATACCTAGCAGCAAAGTTT 59.062 41.667 0.00 0.00 0.00 2.66
2207 2293 4.508662 GTCTCATACCTAGCAGCAAAGTT 58.491 43.478 0.00 0.00 0.00 2.66
2208 2294 3.429547 CGTCTCATACCTAGCAGCAAAGT 60.430 47.826 0.00 0.00 0.00 2.66
2209 2295 3.119291 CGTCTCATACCTAGCAGCAAAG 58.881 50.000 0.00 0.00 0.00 2.77
2210 2296 2.738643 GCGTCTCATACCTAGCAGCAAA 60.739 50.000 0.00 0.00 0.00 3.68
2211 2297 1.202417 GCGTCTCATACCTAGCAGCAA 60.202 52.381 0.00 0.00 0.00 3.91
2212 2298 0.385751 GCGTCTCATACCTAGCAGCA 59.614 55.000 0.00 0.00 0.00 4.41
2213 2299 0.671251 AGCGTCTCATACCTAGCAGC 59.329 55.000 0.00 0.00 0.00 5.25
2214 2300 1.000827 CCAGCGTCTCATACCTAGCAG 60.001 57.143 0.00 0.00 0.00 4.24
2228 2314 4.070552 GCTCCGAACCTCCAGCGT 62.071 66.667 0.00 0.00 0.00 5.07
2301 2387 0.741221 GCCCTTGTAGAAGGTGAGCG 60.741 60.000 16.93 3.04 46.84 5.03
2329 2415 1.844289 GTGGTGGAGGTGGTGGGTA 60.844 63.158 0.00 0.00 0.00 3.69
2660 2746 0.750546 TCCTTGACGGATCGACGGAT 60.751 55.000 0.00 0.00 36.69 4.18
2661 2747 1.377594 TCCTTGACGGATCGACGGA 60.378 57.895 0.00 0.00 36.69 4.69
2673 2759 3.509442 ACAAATTGAGCCCAATCCTTGA 58.491 40.909 11.10 0.00 41.84 3.02
2676 2762 2.493278 CGAACAAATTGAGCCCAATCCT 59.507 45.455 0.00 0.00 41.84 3.24
2677 2763 2.491693 TCGAACAAATTGAGCCCAATCC 59.508 45.455 0.00 0.00 41.84 3.01
2678 2764 3.848272 TCGAACAAATTGAGCCCAATC 57.152 42.857 0.00 0.00 41.84 2.67
2680 2766 2.491693 GGATCGAACAAATTGAGCCCAA 59.508 45.455 0.00 0.00 32.10 4.12
2681 2767 2.091541 GGATCGAACAAATTGAGCCCA 58.908 47.619 0.00 0.00 32.10 5.36
2682 2768 2.851805 GGATCGAACAAATTGAGCCC 57.148 50.000 0.00 0.00 32.10 5.19
2683 2769 2.098117 CAGGGATCGAACAAATTGAGCC 59.902 50.000 0.00 0.00 37.46 4.70
2684 2770 3.009723 TCAGGGATCGAACAAATTGAGC 58.990 45.455 0.00 0.00 0.00 4.26
2685 2771 3.062639 CGTCAGGGATCGAACAAATTGAG 59.937 47.826 0.00 0.00 0.00 3.02
2686 2772 3.000041 CGTCAGGGATCGAACAAATTGA 59.000 45.455 0.00 0.00 0.00 2.57
2687 2773 3.000041 TCGTCAGGGATCGAACAAATTG 59.000 45.455 0.00 0.00 33.13 2.32
2688 2774 3.328382 TCGTCAGGGATCGAACAAATT 57.672 42.857 0.00 0.00 33.13 1.82
2689 2775 3.543680 ATCGTCAGGGATCGAACAAAT 57.456 42.857 0.00 0.00 39.45 2.32
2690 2776 3.328382 AATCGTCAGGGATCGAACAAA 57.672 42.857 0.00 0.00 39.45 2.83
2691 2777 4.459390 TTAATCGTCAGGGATCGAACAA 57.541 40.909 0.00 0.00 39.45 2.83
2692 2778 4.158949 TCTTTAATCGTCAGGGATCGAACA 59.841 41.667 0.00 0.00 39.45 3.18
2693 2779 4.679662 TCTTTAATCGTCAGGGATCGAAC 58.320 43.478 0.00 0.00 39.45 3.95
2694 2780 4.994907 TCTTTAATCGTCAGGGATCGAA 57.005 40.909 0.00 0.00 39.45 3.71
2699 2785 3.904800 TGCATCTTTAATCGTCAGGGA 57.095 42.857 0.00 0.00 0.00 4.20
2700 2786 4.191544 TCTTGCATCTTTAATCGTCAGGG 58.808 43.478 0.00 0.00 0.00 4.45
2706 2792 8.537223 CCAATCAAAATCTTGCATCTTTAATCG 58.463 33.333 0.00 0.00 32.14 3.34
2736 2822 1.907936 CCCCTGCCAAATCCAAATCAA 59.092 47.619 0.00 0.00 0.00 2.57
2925 3022 4.275936 ACGAAAAATTCAGAGAGTGGGTTG 59.724 41.667 0.00 0.00 0.00 3.77
2935 3032 4.380531 AGCACTCTGACGAAAAATTCAGA 58.619 39.130 0.00 1.58 44.80 3.27
2937 3034 4.380531 AGAGCACTCTGACGAAAAATTCA 58.619 39.130 0.00 0.00 38.75 2.57
2938 3035 4.999751 AGAGCACTCTGACGAAAAATTC 57.000 40.909 0.00 0.00 38.75 2.17
2966 3091 2.735663 GACACTGAATGAGCTCACTGTG 59.264 50.000 27.94 27.94 37.88 3.66
2990 3123 6.876257 ACATCATGTCATCATCATCAGATCAG 59.124 38.462 0.00 0.00 30.20 2.90
3034 3167 3.080641 CCCAGGATCACCAGCACA 58.919 61.111 0.00 0.00 38.94 4.57
3198 3331 1.900016 TGCCTTGCTGCAGTTCAGG 60.900 57.895 16.64 17.87 43.06 3.86
3214 3347 2.097007 TCAAAATTTCAAATGCGCGTGC 60.097 40.909 15.48 15.48 43.20 5.34
3220 3353 9.683069 TTCTCTCTAGTTCAAAATTTCAAATGC 57.317 29.630 0.00 0.00 0.00 3.56
3289 3423 5.478332 ACAACTCTTCTCATCCAAATTTCCC 59.522 40.000 0.00 0.00 0.00 3.97
3320 3473 7.763071 TCTCATTGTTTATCTCACTCTCATGTG 59.237 37.037 0.00 0.00 39.15 3.21
3336 3489 5.305128 ACCATCAACCAACATCTCATTGTTT 59.695 36.000 0.00 0.00 37.73 2.83
3340 3513 4.410099 ACACCATCAACCAACATCTCATT 58.590 39.130 0.00 0.00 0.00 2.57
3352 3525 5.044301 ATGGAGTTGAGTGACACCATCAAC 61.044 45.833 23.39 23.39 44.36 3.18
3370 3543 5.960811 TCAGGGCTCCTAATTATAGATGGAG 59.039 44.000 11.58 11.58 45.05 3.86
3397 3570 2.352651 CGACACAGAATGAATGGCGATT 59.647 45.455 0.00 0.00 45.35 3.34
3398 3571 1.935873 CGACACAGAATGAATGGCGAT 59.064 47.619 0.00 0.00 45.35 4.58
3399 3572 1.337728 ACGACACAGAATGAATGGCGA 60.338 47.619 5.60 0.00 45.35 5.54
3402 3575 2.736721 ACGAACGACACAGAATGAATGG 59.263 45.455 0.14 0.00 39.69 3.16
3403 3576 4.084589 TGAACGAACGACACAGAATGAATG 60.085 41.667 0.14 0.00 39.69 2.67
3404 3577 4.055360 TGAACGAACGACACAGAATGAAT 58.945 39.130 0.14 0.00 39.69 2.57
3405 3578 3.449632 TGAACGAACGACACAGAATGAA 58.550 40.909 0.14 0.00 39.69 2.57
3409 3582 2.792674 GACATGAACGAACGACACAGAA 59.207 45.455 0.00 0.00 0.00 3.02
3511 3709 1.105167 TATGAGCTCGTACGTGGGGG 61.105 60.000 16.05 3.25 0.00 5.40
3532 3730 1.879380 TGCGCCATGGCTATTTATCAC 59.121 47.619 33.07 11.84 39.32 3.06
3533 3731 1.879380 GTGCGCCATGGCTATTTATCA 59.121 47.619 33.07 15.83 39.32 2.15
3534 3732 1.879380 TGTGCGCCATGGCTATTTATC 59.121 47.619 33.07 16.22 39.32 1.75
3542 3740 4.722855 GTGGTTGTGCGCCATGGC 62.723 66.667 27.67 27.67 38.40 4.40
3578 3776 2.867333 CTTGCTGCTTCGCCATGCTG 62.867 60.000 0.00 0.00 0.00 4.41
3589 3787 4.749310 CGCGTCCTCCTTGCTGCT 62.749 66.667 0.00 0.00 0.00 4.24
3607 3805 2.747022 CCATGGACGTGGTGTGGA 59.253 61.111 5.56 0.00 34.46 4.02
3757 3958 4.065281 AGTGCGCGTAGTCCACCC 62.065 66.667 8.43 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.