Multiple sequence alignment - TraesCS2D01G290600

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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 TraesCS2D01G290600 chr2D 100.000 3955 0 0 1 3955 372806998 372803044 0.000000e+00 7304.0
1 TraesCS2D01G290600 chr2D 89.538 822 75 10 1 814 169947593 169946775 0.000000e+00 1031.0
2 TraesCS2D01G290600 chr2D 92.803 264 16 3 2004 2265 76002991 76002729 2.880000e-101 379.0
3 TraesCS2D01G290600 chr2D 96.216 185 7 0 1387 1571 596152359 596152543 1.790000e-78 303.0
4 TraesCS2D01G290600 chr2D 81.849 292 38 10 2995 3273 372803730 372803441 8.550000e-57 231.0
5 TraesCS2D01G290600 chr2D 81.849 292 38 10 3269 3558 372804004 372803726 8.550000e-57 231.0
6 TraesCS2D01G290600 chr2A 95.965 1710 48 5 2266 3955 504554508 504556216 0.000000e+00 2756.0
7 TraesCS2D01G290600 chr2A 94.376 1209 49 10 814 2006 504553305 504554510 0.000000e+00 1838.0
8 TraesCS2D01G290600 chr2A 83.516 273 36 7 3263 3532 504555231 504555497 3.050000e-61 246.0
9 TraesCS2D01G290600 chr2A 82.847 274 39 5 2989 3254 504555510 504555783 5.110000e-59 239.0
10 TraesCS2D01G290600 chr2A 96.296 54 2 0 3453 3506 504555777 504555830 5.440000e-14 89.8
11 TraesCS2D01G290600 chr2B 95.447 1208 40 7 814 2006 442332058 442330851 0.000000e+00 1912.0
12 TraesCS2D01G290600 chr2B 96.814 1130 32 1 2265 3390 442330854 442329725 0.000000e+00 1884.0
13 TraesCS2D01G290600 chr2B 92.833 586 19 3 3387 3955 442329627 442329048 0.000000e+00 828.0
14 TraesCS2D01G290600 chr2B 98.148 54 1 0 3453 3506 442329484 442329431 1.170000e-15 95.3
15 TraesCS2D01G290600 chr3D 93.171 820 50 5 1 815 331179618 331180436 0.000000e+00 1199.0
16 TraesCS2D01G290600 chr3D 89.281 821 79 8 1 814 114505305 114504487 0.000000e+00 1020.0
17 TraesCS2D01G290600 chr3D 92.308 39 1 1 3620 3658 66311979 66311943 2.000000e-03 54.7
18 TraesCS2D01G290600 chr4D 90.366 820 69 7 2 814 141484795 141485611 0.000000e+00 1068.0
19 TraesCS2D01G290600 chr4D 90.208 817 65 12 1 808 163686706 163687516 0.000000e+00 1051.0
20 TraesCS2D01G290600 chr4D 89.010 828 78 8 4 820 90431940 90431115 0.000000e+00 1013.0
21 TraesCS2D01G290600 chr4D 99.621 264 1 0 2002 2265 214947644 214947381 2.140000e-132 483.0
22 TraesCS2D01G290600 chr1D 89.467 826 71 11 2 814 346526847 346527669 0.000000e+00 1029.0
23 TraesCS2D01G290600 chr1D 100.000 29 0 0 3619 3647 11775355 11775327 2.000000e-03 54.7
24 TraesCS2D01G290600 chr5D 89.429 823 74 9 1 815 135839700 135840517 0.000000e+00 1026.0
25 TraesCS2D01G290600 chr5D 89.281 821 78 9 1 814 69668542 69669359 0.000000e+00 1020.0
26 TraesCS2D01G290600 chr7D 93.767 369 17 4 1353 1720 417790124 417789761 2.080000e-152 549.0
27 TraesCS2D01G290600 chr3B 92.509 267 18 2 2005 2269 77005532 77005266 8.020000e-102 381.0
28 TraesCS2D01G290600 chr3B 91.954 261 20 1 2005 2265 738505907 738505648 8.080000e-97 364.0
29 TraesCS2D01G290600 chr4A 92.748 262 18 1 2004 2265 556696195 556696455 1.040000e-100 377.0
30 TraesCS2D01G290600 chr5A 91.985 262 21 0 2004 2265 451882189 451881928 6.240000e-98 368.0
31 TraesCS2D01G290600 chr5A 92.015 263 19 2 2004 2265 566366977 566367238 6.240000e-98 368.0
32 TraesCS2D01G290600 chr3A 91.954 261 21 0 2005 2265 630924984 630925244 2.250000e-97 366.0
33 TraesCS2D01G290600 chr6A 91.011 267 24 0 2004 2270 6295014 6294748 1.040000e-95 361.0
34 TraesCS2D01G290600 chr6A 100.000 32 0 0 3617 3648 431145408 431145377 4.270000e-05 60.2
35 TraesCS2D01G290600 chr7B 96.875 32 1 0 3617 3648 714311667 714311698 2.000000e-03 54.7
36 TraesCS2D01G290600 chr6D 100.000 29 0 0 3619 3647 35662643 35662615 2.000000e-03 54.7
37 TraesCS2D01G290600 chr5B 100.000 28 0 0 3618 3645 53662215 53662188 7.000000e-03 52.8


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 TraesCS2D01G290600 chr2D 372803044 372806998 3954 True 2588.666667 7304 87.899333 1 3955 3 chr2D.!!$R3 3954
1 TraesCS2D01G290600 chr2D 169946775 169947593 818 True 1031.000000 1031 89.538000 1 814 1 chr2D.!!$R2 813
2 TraesCS2D01G290600 chr2A 504553305 504556216 2911 False 1033.760000 2756 90.600000 814 3955 5 chr2A.!!$F1 3141
3 TraesCS2D01G290600 chr2B 442329048 442332058 3010 True 1179.825000 1912 95.810500 814 3955 4 chr2B.!!$R1 3141
4 TraesCS2D01G290600 chr3D 331179618 331180436 818 False 1199.000000 1199 93.171000 1 815 1 chr3D.!!$F1 814
5 TraesCS2D01G290600 chr3D 114504487 114505305 818 True 1020.000000 1020 89.281000 1 814 1 chr3D.!!$R2 813
6 TraesCS2D01G290600 chr4D 141484795 141485611 816 False 1068.000000 1068 90.366000 2 814 1 chr4D.!!$F1 812
7 TraesCS2D01G290600 chr4D 163686706 163687516 810 False 1051.000000 1051 90.208000 1 808 1 chr4D.!!$F2 807
8 TraesCS2D01G290600 chr4D 90431115 90431940 825 True 1013.000000 1013 89.010000 4 820 1 chr4D.!!$R1 816
9 TraesCS2D01G290600 chr1D 346526847 346527669 822 False 1029.000000 1029 89.467000 2 814 1 chr1D.!!$F1 812
10 TraesCS2D01G290600 chr5D 135839700 135840517 817 False 1026.000000 1026 89.429000 1 815 1 chr5D.!!$F2 814
11 TraesCS2D01G290600 chr5D 69668542 69669359 817 False 1020.000000 1020 89.281000 1 814 1 chr5D.!!$F1 813

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
171 172 0.179127 ACGTGAGCCATGACGATCAG 60.179 55.0 11.17 0.10 38.94 2.90 F
990 1015 0.749454 GGAGCATGGTGCCACCTAAG 60.749 60.0 16.23 5.94 46.52 2.18 F
2021 2061 0.616964 GGTACTCCCTCCGGTCCTTT 60.617 60.0 0.00 0.00 0.00 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1816 0.036952 ACACACCGAGCAGAATGAGG 60.037 55.0 0.00 0.0 39.69 3.86 R
2238 2278 0.037046 TCCGGTCCTTTTTACTCCGC 60.037 55.0 0.00 0.0 39.87 5.54 R
3229 3274 0.250640 CAAGAACTCCTGCCAGCAGT 60.251 55.0 17.86 0.0 42.15 4.40 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
171 172 0.179127 ACGTGAGCCATGACGATCAG 60.179 55.000 11.17 0.10 38.94 2.90
210 211 1.721133 GCGCAACGTCCTTGTTTCG 60.721 57.895 0.30 0.00 40.60 3.46
224 225 4.201970 CCTTGTTTCGTCTTTGGTGCTAAA 60.202 41.667 0.00 0.00 0.00 1.85
289 290 4.406648 TTCCATATCAGTGCAACGAGAT 57.593 40.909 0.00 0.00 45.86 2.75
380 381 1.597663 CAGACGAAGACCGCTTTTGTT 59.402 47.619 0.00 0.00 43.32 2.83
419 421 2.252072 CTCCCCTTTCAATCGGCCGA 62.252 60.000 33.12 33.12 0.00 5.54
443 445 1.821332 GCTCCCTTCCCGCTCAATG 60.821 63.158 0.00 0.00 0.00 2.82
457 459 3.359950 GCTCAATGTTTGGGAAGAGGAT 58.640 45.455 0.00 0.00 30.85 3.24
512 521 6.519043 GCAGTAGTGGGCATCTGATCTTTATA 60.519 42.308 0.00 0.00 0.00 0.98
563 574 2.024414 GCACAAGAACACCTCAACCTT 58.976 47.619 0.00 0.00 0.00 3.50
728 743 1.677052 GTCCGCGAGATCTTAGGAAGT 59.323 52.381 8.23 0.00 32.20 3.01
740 755 1.941377 TAGGAAGTTAGGGCGTGGAA 58.059 50.000 0.00 0.00 0.00 3.53
767 786 2.159272 GAAAGAACTTCGCGCGCACT 62.159 55.000 32.61 15.71 0.00 4.40
941 965 8.759641 TGTCCATACAATTTTTGAACGATTTTG 58.240 29.630 0.00 0.00 30.91 2.44
987 1012 4.052518 GGGAGCATGGTGCCACCT 62.053 66.667 28.24 0.00 46.52 4.00
989 1014 1.302949 GGAGCATGGTGCCACCTAA 59.697 57.895 16.23 0.00 46.52 2.69
990 1015 0.749454 GGAGCATGGTGCCACCTAAG 60.749 60.000 16.23 5.94 46.52 2.18
1776 1816 2.734673 CGTCTCTTCTTGCCGCAGC 61.735 63.158 0.00 0.00 40.48 5.25
1780 1820 2.359107 CTTCTTGCCGCAGCCTCA 60.359 61.111 0.00 0.00 38.69 3.86
1993 2033 6.687105 GCAGGTATTTTGCGTATTTCTGTTAG 59.313 38.462 0.00 0.00 0.00 2.34
2010 2050 2.184579 GCGTCAGCAGGTACTCCC 59.815 66.667 0.00 0.00 44.35 4.30
2012 2052 1.810532 CGTCAGCAGGTACTCCCTC 59.189 63.158 0.00 0.00 43.86 4.30
2013 2053 1.668101 CGTCAGCAGGTACTCCCTCC 61.668 65.000 0.00 0.00 43.86 4.30
2014 2054 1.379977 TCAGCAGGTACTCCCTCCG 60.380 63.158 0.00 0.00 43.86 4.63
2015 2055 2.042843 AGCAGGTACTCCCTCCGG 60.043 66.667 0.00 0.00 43.86 5.14
2016 2056 2.363925 GCAGGTACTCCCTCCGGT 60.364 66.667 0.00 0.00 43.86 5.28
2017 2057 2.424733 GCAGGTACTCCCTCCGGTC 61.425 68.421 0.00 0.00 43.86 4.79
2018 2058 1.757340 CAGGTACTCCCTCCGGTCC 60.757 68.421 0.00 0.00 43.86 4.46
2019 2059 1.934870 AGGTACTCCCTCCGGTCCT 60.935 63.158 0.00 0.00 40.71 3.85
2020 2060 1.001376 GGTACTCCCTCCGGTCCTT 59.999 63.158 0.00 0.00 0.00 3.36
2021 2061 0.616964 GGTACTCCCTCCGGTCCTTT 60.617 60.000 0.00 0.00 0.00 3.11
2022 2062 1.273759 GTACTCCCTCCGGTCCTTTT 58.726 55.000 0.00 0.00 0.00 2.27
2023 2063 1.627329 GTACTCCCTCCGGTCCTTTTT 59.373 52.381 0.00 0.00 0.00 1.94
2024 2064 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
2025 2065 1.907255 ACTCCCTCCGGTCCTTTTTAG 59.093 52.381 0.00 0.00 0.00 1.85
2026 2066 1.907255 CTCCCTCCGGTCCTTTTTAGT 59.093 52.381 0.00 0.00 0.00 2.24
2027 2067 1.904537 TCCCTCCGGTCCTTTTTAGTC 59.095 52.381 0.00 0.00 0.00 2.59
2028 2068 1.907255 CCCTCCGGTCCTTTTTAGTCT 59.093 52.381 0.00 0.00 0.00 3.24
2029 2069 2.354805 CCCTCCGGTCCTTTTTAGTCTG 60.355 54.545 0.00 0.00 0.00 3.51
2030 2070 2.347731 CTCCGGTCCTTTTTAGTCTGC 58.652 52.381 0.00 0.00 0.00 4.26
2031 2071 1.695242 TCCGGTCCTTTTTAGTCTGCA 59.305 47.619 0.00 0.00 0.00 4.41
2032 2072 2.304761 TCCGGTCCTTTTTAGTCTGCAT 59.695 45.455 0.00 0.00 0.00 3.96
2033 2073 3.516300 TCCGGTCCTTTTTAGTCTGCATA 59.484 43.478 0.00 0.00 0.00 3.14
2034 2074 4.163458 TCCGGTCCTTTTTAGTCTGCATAT 59.837 41.667 0.00 0.00 0.00 1.78
2035 2075 5.364446 TCCGGTCCTTTTTAGTCTGCATATA 59.636 40.000 0.00 0.00 0.00 0.86
2036 2076 6.053005 CCGGTCCTTTTTAGTCTGCATATAA 58.947 40.000 0.00 0.00 0.00 0.98
2037 2077 6.202954 CCGGTCCTTTTTAGTCTGCATATAAG 59.797 42.308 0.00 0.00 0.00 1.73
2038 2078 6.761714 CGGTCCTTTTTAGTCTGCATATAAGT 59.238 38.462 0.00 0.00 0.00 2.24
2039 2079 7.280205 CGGTCCTTTTTAGTCTGCATATAAGTT 59.720 37.037 0.00 0.00 0.00 2.66
2040 2080 8.957466 GGTCCTTTTTAGTCTGCATATAAGTTT 58.043 33.333 0.00 0.00 0.00 2.66
2046 2086 7.534085 TTAGTCTGCATATAAGTTTTGTCCG 57.466 36.000 0.00 0.00 0.00 4.79
2047 2087 5.730550 AGTCTGCATATAAGTTTTGTCCGA 58.269 37.500 0.00 0.00 0.00 4.55
2048 2088 6.170506 AGTCTGCATATAAGTTTTGTCCGAA 58.829 36.000 0.00 0.00 0.00 4.30
2049 2089 6.313905 AGTCTGCATATAAGTTTTGTCCGAAG 59.686 38.462 0.00 0.00 0.00 3.79
2050 2090 6.092259 GTCTGCATATAAGTTTTGTCCGAAGT 59.908 38.462 0.00 0.00 0.00 3.01
2051 2091 6.312918 TCTGCATATAAGTTTTGTCCGAAGTC 59.687 38.462 0.00 0.00 0.00 3.01
2052 2092 5.935206 TGCATATAAGTTTTGTCCGAAGTCA 59.065 36.000 0.00 0.00 0.00 3.41
2053 2093 6.428465 TGCATATAAGTTTTGTCCGAAGTCAA 59.572 34.615 0.00 0.00 0.00 3.18
2054 2094 7.041030 TGCATATAAGTTTTGTCCGAAGTCAAA 60.041 33.333 0.00 0.00 32.75 2.69
2055 2095 7.481798 GCATATAAGTTTTGTCCGAAGTCAAAG 59.518 37.037 0.00 0.00 35.47 2.77
2056 2096 3.692791 AGTTTTGTCCGAAGTCAAAGC 57.307 42.857 0.00 0.00 35.47 3.51
2057 2097 3.013921 AGTTTTGTCCGAAGTCAAAGCA 58.986 40.909 0.00 0.00 37.28 3.91
2058 2098 3.632145 AGTTTTGTCCGAAGTCAAAGCAT 59.368 39.130 0.00 0.00 37.28 3.79
2059 2099 3.896648 TTTGTCCGAAGTCAAAGCATC 57.103 42.857 0.00 0.00 0.00 3.91
2060 2100 1.808411 TGTCCGAAGTCAAAGCATCC 58.192 50.000 0.00 0.00 0.00 3.51
2061 2101 1.087501 GTCCGAAGTCAAAGCATCCC 58.912 55.000 0.00 0.00 0.00 3.85
2062 2102 0.984230 TCCGAAGTCAAAGCATCCCT 59.016 50.000 0.00 0.00 0.00 4.20
2063 2103 2.093658 GTCCGAAGTCAAAGCATCCCTA 60.094 50.000 0.00 0.00 0.00 3.53
2064 2104 2.093658 TCCGAAGTCAAAGCATCCCTAC 60.094 50.000 0.00 0.00 0.00 3.18
2065 2105 2.093447 CCGAAGTCAAAGCATCCCTACT 60.093 50.000 0.00 0.00 0.00 2.57
2066 2106 3.600388 CGAAGTCAAAGCATCCCTACTT 58.400 45.455 0.00 0.00 0.00 2.24
2067 2107 4.003648 CGAAGTCAAAGCATCCCTACTTT 58.996 43.478 0.00 0.00 36.56 2.66
2072 2112 3.806949 AAAGCATCCCTACTTTGACCA 57.193 42.857 0.00 0.00 34.88 4.02
2073 2113 3.806949 AAGCATCCCTACTTTGACCAA 57.193 42.857 0.00 0.00 0.00 3.67
2074 2114 3.806949 AGCATCCCTACTTTGACCAAA 57.193 42.857 0.00 0.00 0.00 3.28
2075 2115 4.322057 AGCATCCCTACTTTGACCAAAT 57.678 40.909 0.00 0.00 0.00 2.32
2076 2116 4.677182 AGCATCCCTACTTTGACCAAATT 58.323 39.130 0.00 0.00 0.00 1.82
2077 2117 5.086621 AGCATCCCTACTTTGACCAAATTT 58.913 37.500 0.00 0.00 0.00 1.82
2078 2118 6.252995 AGCATCCCTACTTTGACCAAATTTA 58.747 36.000 0.00 0.00 0.00 1.40
2079 2119 6.897413 AGCATCCCTACTTTGACCAAATTTAT 59.103 34.615 0.00 0.00 0.00 1.40
2080 2120 8.058847 AGCATCCCTACTTTGACCAAATTTATA 58.941 33.333 0.00 0.00 0.00 0.98
2081 2121 8.352942 GCATCCCTACTTTGACCAAATTTATAG 58.647 37.037 0.00 0.00 0.00 1.31
2082 2122 9.627123 CATCCCTACTTTGACCAAATTTATAGA 57.373 33.333 0.00 0.00 0.00 1.98
2106 2146 9.289303 AGAAAAACGTATCAATATTCACAATGC 57.711 29.630 0.00 0.00 0.00 3.56
2107 2147 7.985634 AAAACGTATCAATATTCACAATGCC 57.014 32.000 0.00 0.00 0.00 4.40
2108 2148 6.691754 AACGTATCAATATTCACAATGCCA 57.308 33.333 0.00 0.00 0.00 4.92
2109 2149 6.691754 ACGTATCAATATTCACAATGCCAA 57.308 33.333 0.00 0.00 0.00 4.52
2110 2150 7.094508 ACGTATCAATATTCACAATGCCAAA 57.905 32.000 0.00 0.00 0.00 3.28
2111 2151 7.715657 ACGTATCAATATTCACAATGCCAAAT 58.284 30.769 0.00 0.00 0.00 2.32
2112 2152 7.862372 ACGTATCAATATTCACAATGCCAAATC 59.138 33.333 0.00 0.00 0.00 2.17
2113 2153 7.059831 CGTATCAATATTCACAATGCCAAATCG 59.940 37.037 0.00 0.00 0.00 3.34
2114 2154 5.590145 TCAATATTCACAATGCCAAATCGG 58.410 37.500 0.00 0.00 38.11 4.18
2115 2155 5.126869 TCAATATTCACAATGCCAAATCGGT 59.873 36.000 0.00 0.00 36.97 4.69
2116 2156 6.319911 TCAATATTCACAATGCCAAATCGGTA 59.680 34.615 0.00 0.00 36.97 4.02
2117 2157 6.899393 ATATTCACAATGCCAAATCGGTAT 57.101 33.333 0.00 0.00 42.87 2.73
2126 2166 6.959639 ATGCCAAATCGGTATTGTTAGATT 57.040 33.333 0.00 0.00 36.55 2.40
2127 2167 6.371809 TGCCAAATCGGTATTGTTAGATTC 57.628 37.500 0.00 0.00 36.97 2.52
2128 2168 5.883115 TGCCAAATCGGTATTGTTAGATTCA 59.117 36.000 0.00 0.00 36.97 2.57
2129 2169 6.545666 TGCCAAATCGGTATTGTTAGATTCAT 59.454 34.615 0.00 0.00 36.97 2.57
2130 2170 7.068103 TGCCAAATCGGTATTGTTAGATTCATT 59.932 33.333 0.00 0.00 36.97 2.57
2131 2171 8.564574 GCCAAATCGGTATTGTTAGATTCATTA 58.435 33.333 0.00 0.00 36.97 1.90
2132 2172 9.878599 CCAAATCGGTATTGTTAGATTCATTAC 57.121 33.333 0.00 0.00 32.79 1.89
2133 2173 9.580916 CAAATCGGTATTGTTAGATTCATTACG 57.419 33.333 0.00 0.00 32.79 3.18
2134 2174 9.537192 AAATCGGTATTGTTAGATTCATTACGA 57.463 29.630 0.00 0.00 32.79 3.43
2135 2175 9.537192 AATCGGTATTGTTAGATTCATTACGAA 57.463 29.630 0.00 0.00 38.22 3.85
2136 2176 8.929827 TCGGTATTGTTAGATTCATTACGAAA 57.070 30.769 0.00 0.00 37.12 3.46
2137 2177 9.537192 TCGGTATTGTTAGATTCATTACGAAAT 57.463 29.630 0.00 0.00 37.12 2.17
2138 2178 9.793245 CGGTATTGTTAGATTCATTACGAAATC 57.207 33.333 0.00 0.00 37.12 2.17
2149 2189 9.869844 GATTCATTACGAAATCTAGTTTCATGG 57.130 33.333 14.20 5.03 45.24 3.66
2150 2190 9.613428 ATTCATTACGAAATCTAGTTTCATGGA 57.387 29.630 14.20 8.26 45.24 3.41
2151 2191 9.443323 TTCATTACGAAATCTAGTTTCATGGAA 57.557 29.630 14.20 0.00 45.24 3.53
2152 2192 9.613428 TCATTACGAAATCTAGTTTCATGGAAT 57.387 29.630 14.20 7.43 45.24 3.01
2183 2223 9.832445 ATTCGGTATTGTAGATGTTGATACTTT 57.168 29.630 0.00 0.00 0.00 2.66
2184 2224 9.661563 TTCGGTATTGTAGATGTTGATACTTTT 57.338 29.630 0.00 0.00 0.00 2.27
2225 2265 4.494484 ACTTTGCAAAGTTTGACTTGACC 58.506 39.130 33.85 0.20 46.52 4.02
2226 2266 3.518634 TTGCAAAGTTTGACTTGACCC 57.481 42.857 19.82 0.00 38.66 4.46
2227 2267 2.451490 TGCAAAGTTTGACTTGACCCA 58.549 42.857 19.82 2.20 38.66 4.51
2228 2268 2.828520 TGCAAAGTTTGACTTGACCCAA 59.171 40.909 19.82 0.00 38.66 4.12
2229 2269 3.259374 TGCAAAGTTTGACTTGACCCAAA 59.741 39.130 19.82 0.00 38.66 3.28
2230 2270 4.081198 TGCAAAGTTTGACTTGACCCAAAT 60.081 37.500 19.82 0.00 38.66 2.32
2231 2271 4.507756 GCAAAGTTTGACTTGACCCAAATC 59.492 41.667 19.82 0.00 38.66 2.17
2232 2272 5.682212 GCAAAGTTTGACTTGACCCAAATCT 60.682 40.000 19.82 0.00 38.66 2.40
2233 2273 6.460953 GCAAAGTTTGACTTGACCCAAATCTA 60.461 38.462 19.82 0.00 38.66 1.98
2234 2274 7.488322 CAAAGTTTGACTTGACCCAAATCTAA 58.512 34.615 10.19 0.00 38.66 2.10
2235 2275 7.839680 AAGTTTGACTTGACCCAAATCTAAT 57.160 32.000 0.00 0.00 37.00 1.73
2236 2276 8.934023 AAGTTTGACTTGACCCAAATCTAATA 57.066 30.769 0.00 0.00 37.00 0.98
2237 2277 8.336801 AGTTTGACTTGACCCAAATCTAATAC 57.663 34.615 0.00 0.00 35.14 1.89
2238 2278 6.978343 TTGACTTGACCCAAATCTAATACG 57.022 37.500 0.00 0.00 0.00 3.06
2239 2279 4.873827 TGACTTGACCCAAATCTAATACGC 59.126 41.667 0.00 0.00 0.00 4.42
2240 2280 3.869246 ACTTGACCCAAATCTAATACGCG 59.131 43.478 3.53 3.53 0.00 6.01
2241 2281 2.828877 TGACCCAAATCTAATACGCGG 58.171 47.619 12.47 0.00 0.00 6.46
2242 2282 2.431419 TGACCCAAATCTAATACGCGGA 59.569 45.455 12.47 0.00 0.00 5.54
2243 2283 3.057734 GACCCAAATCTAATACGCGGAG 58.942 50.000 12.47 1.75 0.00 4.63
2244 2284 2.433239 ACCCAAATCTAATACGCGGAGT 59.567 45.455 12.47 2.60 0.00 3.85
2245 2285 3.638160 ACCCAAATCTAATACGCGGAGTA 59.362 43.478 12.47 4.11 40.03 2.59
2246 2286 4.099881 ACCCAAATCTAATACGCGGAGTAA 59.900 41.667 12.47 0.00 39.04 2.24
2247 2287 5.051816 CCCAAATCTAATACGCGGAGTAAA 58.948 41.667 12.47 0.00 39.04 2.01
2248 2288 5.524646 CCCAAATCTAATACGCGGAGTAAAA 59.475 40.000 12.47 0.00 39.04 1.52
2249 2289 6.037391 CCCAAATCTAATACGCGGAGTAAAAA 59.963 38.462 12.47 0.00 39.04 1.94
2250 2290 7.123830 CCAAATCTAATACGCGGAGTAAAAAG 58.876 38.462 12.47 0.00 39.04 2.27
2251 2291 6.839820 AATCTAATACGCGGAGTAAAAAGG 57.160 37.500 12.47 0.00 39.04 3.11
2252 2292 5.581126 TCTAATACGCGGAGTAAAAAGGA 57.419 39.130 12.47 0.00 39.04 3.36
2253 2293 5.343249 TCTAATACGCGGAGTAAAAAGGAC 58.657 41.667 12.47 0.00 39.04 3.85
2254 2294 2.368655 TACGCGGAGTAAAAAGGACC 57.631 50.000 12.47 0.00 31.26 4.46
2255 2295 0.668401 ACGCGGAGTAAAAAGGACCG 60.668 55.000 12.47 0.00 45.26 4.79
2256 2296 1.356527 CGCGGAGTAAAAAGGACCGG 61.357 60.000 0.00 0.00 43.15 5.28
2257 2297 0.037046 GCGGAGTAAAAAGGACCGGA 60.037 55.000 9.46 0.00 43.15 5.14
2258 2298 2.005560 GCGGAGTAAAAAGGACCGGAG 61.006 57.143 9.46 0.00 43.15 4.63
2383 2423 2.483714 GCGTGAAGATCCTGGCTATCAA 60.484 50.000 0.00 0.00 0.00 2.57
2435 2475 3.380004 AGAAGGTGATGAGCTTACTCGAG 59.620 47.826 11.84 11.84 46.69 4.04
2476 2516 6.458210 AGACTTTGCATTTCCAGGTAATTTG 58.542 36.000 0.00 0.00 0.00 2.32
2673 2713 3.131046 TGTTGCGAGATATCTCAAGAGCA 59.869 43.478 27.97 24.68 43.00 4.26
2735 2775 3.815856 TTTGCATGTTTTCTCCTTGCA 57.184 38.095 0.00 0.00 41.22 4.08
2786 2826 1.868251 GTCCGAGATGTGCGACGTC 60.868 63.158 5.18 5.18 34.40 4.34
2913 2953 5.163364 ACCATAGAAGGTGTGAATGCTCTAG 60.163 44.000 0.00 0.00 41.30 2.43
3051 3091 6.767524 TGGTTATGTTCAGTTGAGTTTTGT 57.232 33.333 0.00 0.00 0.00 2.83
3112 3152 9.797556 AGGTTTCATGTTGAAAAAGTTTACTAC 57.202 29.630 4.37 0.00 46.53 2.73
3179 3224 4.067896 CTGCATGTGGAGTTGTAGACTTT 58.932 43.478 0.00 0.00 39.19 2.66
3229 3274 2.031560 GTGAAGATTGTTGCGTGTGACA 59.968 45.455 0.00 0.00 0.00 3.58
3267 3312 8.543774 AGTTCTTGTGGTATGATAGTTCTGAAT 58.456 33.333 0.00 0.00 0.00 2.57
3451 3597 9.691362 TTAAAGTTAATTTTCTGAATGTGGAGC 57.309 29.630 0.00 0.00 32.01 4.70
3506 3652 6.437928 GTTTCACTGTGAAGATTGTTGCATA 58.562 36.000 21.13 1.67 37.70 3.14
3507 3653 5.868043 TCACTGTGAAGATTGTTGCATAG 57.132 39.130 8.27 0.00 0.00 2.23
3535 3681 4.253685 TGCTGGCAAGACTTATTGTAGTC 58.746 43.478 0.00 0.00 43.90 2.59
3553 3699 8.988064 TTGTAGTCATTGATTTAGTCTGAGTC 57.012 34.615 0.00 0.00 0.00 3.36
3564 3710 7.759886 TGATTTAGTCTGAGTCTAATGGTTTCG 59.240 37.037 0.26 0.00 0.00 3.46
3599 3762 6.660722 TGTTGCAACTTATTTTGTACTACCG 58.339 36.000 28.61 0.00 0.00 4.02
3702 3866 7.195374 TGCCTGATACTTTAACCTTATCAGT 57.805 36.000 17.78 3.72 44.06 3.41
3852 4016 5.067674 TCGATCCCTTTGATATTTTTGGCTG 59.932 40.000 0.00 0.00 32.41 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
210 211 0.888619 GCCCCTTTAGCACCAAAGAC 59.111 55.000 6.95 0.00 37.66 3.01
289 290 0.541063 TGCCGTCCTACTGGTCTTGA 60.541 55.000 0.00 0.00 34.23 3.02
363 364 2.140717 CCTAACAAAAGCGGTCTTCGT 58.859 47.619 0.00 0.00 41.72 3.85
400 401 1.819632 CGGCCGATTGAAAGGGGAG 60.820 63.158 24.07 0.00 0.00 4.30
419 421 2.677228 CGGGAAGGGAGCCAACAT 59.323 61.111 0.00 0.00 0.00 2.71
443 445 1.683319 GCCCTGATCCTCTTCCCAAAC 60.683 57.143 0.00 0.00 0.00 2.93
487 489 1.415659 AGATCAGATGCCCACTACTGC 59.584 52.381 0.00 0.00 0.00 4.40
512 521 9.319060 TGTATCTAAGGATCAGCTAAAGATCAT 57.681 33.333 12.97 4.70 42.84 2.45
534 543 2.884639 GGTGTTCTTGTGCTTGGTGTAT 59.115 45.455 0.00 0.00 0.00 2.29
535 544 2.092646 AGGTGTTCTTGTGCTTGGTGTA 60.093 45.455 0.00 0.00 0.00 2.90
563 574 0.417841 AGGGGAAGAACAGCCTCCTA 59.582 55.000 0.00 0.00 0.00 2.94
728 743 1.606885 CCTACCGTTCCACGCCCTAA 61.607 60.000 0.00 0.00 40.91 2.69
740 755 1.337541 GCGAAGTTCTTTCCCTACCGT 60.338 52.381 0.56 0.00 31.82 4.83
767 786 2.565834 CCCTTAAGGTTCGAACTCTGGA 59.434 50.000 26.32 11.50 0.00 3.86
962 986 1.676746 CACCATGCTCCCTTCTCATG 58.323 55.000 0.00 0.00 37.81 3.07
987 1012 4.040461 GGTGCTTCCATAGTCCATAGCTTA 59.960 45.833 0.00 0.00 35.97 3.09
989 1014 2.370189 GGTGCTTCCATAGTCCATAGCT 59.630 50.000 0.00 0.00 35.97 3.32
990 1015 2.104792 TGGTGCTTCCATAGTCCATAGC 59.895 50.000 0.00 0.00 41.93 2.97
1299 1339 4.816984 GGGACGGGGAGCTCGAGA 62.817 72.222 18.75 0.00 0.00 4.04
1548 1588 3.435186 GTTGGGCAGCCGAGAAGC 61.435 66.667 5.00 0.00 0.00 3.86
1776 1816 0.036952 ACACACCGAGCAGAATGAGG 60.037 55.000 0.00 0.00 39.69 3.86
1780 1820 1.672356 GCCACACACCGAGCAGAAT 60.672 57.895 0.00 0.00 0.00 2.40
1993 2033 2.184579 GGGAGTACCTGCTGACGC 59.815 66.667 0.00 0.00 35.85 5.19
2010 2050 2.289444 TGCAGACTAAAAAGGACCGGAG 60.289 50.000 9.46 0.00 0.00 4.63
2011 2051 1.695242 TGCAGACTAAAAAGGACCGGA 59.305 47.619 9.46 0.00 0.00 5.14
2012 2052 2.178912 TGCAGACTAAAAAGGACCGG 57.821 50.000 0.00 0.00 0.00 5.28
2013 2053 6.761714 ACTTATATGCAGACTAAAAAGGACCG 59.238 38.462 0.00 0.00 0.00 4.79
2014 2054 8.507524 AACTTATATGCAGACTAAAAAGGACC 57.492 34.615 0.00 0.00 0.00 4.46
2020 2060 8.447833 CGGACAAAACTTATATGCAGACTAAAA 58.552 33.333 0.00 0.00 0.00 1.52
2021 2061 7.820386 TCGGACAAAACTTATATGCAGACTAAA 59.180 33.333 0.00 0.00 0.00 1.85
2022 2062 7.324935 TCGGACAAAACTTATATGCAGACTAA 58.675 34.615 0.00 0.00 0.00 2.24
2023 2063 6.869695 TCGGACAAAACTTATATGCAGACTA 58.130 36.000 0.00 0.00 0.00 2.59
2024 2064 5.730550 TCGGACAAAACTTATATGCAGACT 58.269 37.500 0.00 0.00 0.00 3.24
2025 2065 6.092259 ACTTCGGACAAAACTTATATGCAGAC 59.908 38.462 0.00 0.00 0.00 3.51
2026 2066 6.170506 ACTTCGGACAAAACTTATATGCAGA 58.829 36.000 0.00 0.00 0.00 4.26
2027 2067 6.092122 TGACTTCGGACAAAACTTATATGCAG 59.908 38.462 0.00 0.00 0.00 4.41
2028 2068 5.935206 TGACTTCGGACAAAACTTATATGCA 59.065 36.000 0.00 0.00 0.00 3.96
2029 2069 6.417191 TGACTTCGGACAAAACTTATATGC 57.583 37.500 0.00 0.00 0.00 3.14
2030 2070 7.481798 GCTTTGACTTCGGACAAAACTTATATG 59.518 37.037 0.00 0.00 38.59 1.78
2031 2071 7.174253 TGCTTTGACTTCGGACAAAACTTATAT 59.826 33.333 0.00 0.00 38.59 0.86
2032 2072 6.483974 TGCTTTGACTTCGGACAAAACTTATA 59.516 34.615 0.00 0.00 38.59 0.98
2033 2073 5.298276 TGCTTTGACTTCGGACAAAACTTAT 59.702 36.000 0.00 0.00 38.59 1.73
2034 2074 4.636648 TGCTTTGACTTCGGACAAAACTTA 59.363 37.500 0.00 0.00 38.59 2.24
2035 2075 3.442273 TGCTTTGACTTCGGACAAAACTT 59.558 39.130 0.00 0.00 38.59 2.66
2036 2076 3.013921 TGCTTTGACTTCGGACAAAACT 58.986 40.909 0.00 0.00 38.59 2.66
2037 2077 3.414549 TGCTTTGACTTCGGACAAAAC 57.585 42.857 0.00 0.00 38.59 2.43
2038 2078 3.004315 GGATGCTTTGACTTCGGACAAAA 59.996 43.478 0.00 0.00 38.59 2.44
2039 2079 2.552315 GGATGCTTTGACTTCGGACAAA 59.448 45.455 0.00 0.00 37.29 2.83
2040 2080 2.151202 GGATGCTTTGACTTCGGACAA 58.849 47.619 0.00 0.00 0.00 3.18
2041 2081 1.610624 GGGATGCTTTGACTTCGGACA 60.611 52.381 0.00 0.00 0.00 4.02
2042 2082 1.087501 GGGATGCTTTGACTTCGGAC 58.912 55.000 0.00 0.00 0.00 4.79
2043 2083 0.984230 AGGGATGCTTTGACTTCGGA 59.016 50.000 0.00 0.00 0.00 4.55
2044 2084 2.093447 AGTAGGGATGCTTTGACTTCGG 60.093 50.000 0.00 0.00 0.00 4.30
2045 2085 3.252974 AGTAGGGATGCTTTGACTTCG 57.747 47.619 0.00 0.00 0.00 3.79
2052 2092 3.806949 TGGTCAAAGTAGGGATGCTTT 57.193 42.857 0.00 0.00 35.55 3.51
2053 2093 3.806949 TTGGTCAAAGTAGGGATGCTT 57.193 42.857 0.00 0.00 0.00 3.91
2054 2094 3.806949 TTTGGTCAAAGTAGGGATGCT 57.193 42.857 0.00 0.00 0.00 3.79
2055 2095 5.405935 AAATTTGGTCAAAGTAGGGATGC 57.594 39.130 2.55 0.00 33.32 3.91
2056 2096 9.627123 TCTATAAATTTGGTCAAAGTAGGGATG 57.373 33.333 0.00 0.00 33.32 3.51
2080 2120 9.289303 GCATTGTGAATATTGATACGTTTTTCT 57.711 29.630 0.00 0.00 0.00 2.52
2081 2121 8.531530 GGCATTGTGAATATTGATACGTTTTTC 58.468 33.333 0.00 0.00 0.00 2.29
2082 2122 8.031864 TGGCATTGTGAATATTGATACGTTTTT 58.968 29.630 0.00 0.00 0.00 1.94
2083 2123 7.542890 TGGCATTGTGAATATTGATACGTTTT 58.457 30.769 0.00 0.00 0.00 2.43
2084 2124 7.094508 TGGCATTGTGAATATTGATACGTTT 57.905 32.000 0.00 0.00 0.00 3.60
2085 2125 6.691754 TGGCATTGTGAATATTGATACGTT 57.308 33.333 0.00 0.00 0.00 3.99
2086 2126 6.691754 TTGGCATTGTGAATATTGATACGT 57.308 33.333 0.00 0.00 0.00 3.57
2087 2127 7.059831 CGATTTGGCATTGTGAATATTGATACG 59.940 37.037 0.00 0.00 0.00 3.06
2088 2128 7.326789 CCGATTTGGCATTGTGAATATTGATAC 59.673 37.037 0.00 0.00 0.00 2.24
2089 2129 7.014134 ACCGATTTGGCATTGTGAATATTGATA 59.986 33.333 0.00 0.00 43.94 2.15
2090 2130 6.183360 ACCGATTTGGCATTGTGAATATTGAT 60.183 34.615 0.00 0.00 43.94 2.57
2091 2131 5.126869 ACCGATTTGGCATTGTGAATATTGA 59.873 36.000 0.00 0.00 43.94 2.57
2092 2132 5.350633 ACCGATTTGGCATTGTGAATATTG 58.649 37.500 0.00 0.00 43.94 1.90
2093 2133 5.596836 ACCGATTTGGCATTGTGAATATT 57.403 34.783 0.00 0.00 43.94 1.28
2094 2134 6.899393 ATACCGATTTGGCATTGTGAATAT 57.101 33.333 0.00 0.00 43.94 1.28
2095 2135 6.502652 CAATACCGATTTGGCATTGTGAATA 58.497 36.000 7.50 0.00 43.76 1.75
2096 2136 5.350633 CAATACCGATTTGGCATTGTGAAT 58.649 37.500 7.50 0.00 43.76 2.57
2097 2137 4.742417 CAATACCGATTTGGCATTGTGAA 58.258 39.130 7.50 0.00 43.76 3.18
2098 2138 4.368874 CAATACCGATTTGGCATTGTGA 57.631 40.909 7.50 0.00 43.76 3.58
2102 2142 6.959639 ATCTAACAATACCGATTTGGCATT 57.040 33.333 0.00 0.00 43.94 3.56
2103 2143 6.545666 TGAATCTAACAATACCGATTTGGCAT 59.454 34.615 0.00 0.00 43.94 4.40
2104 2144 5.883115 TGAATCTAACAATACCGATTTGGCA 59.117 36.000 0.00 0.00 43.94 4.92
2105 2145 6.371809 TGAATCTAACAATACCGATTTGGC 57.628 37.500 0.00 0.00 43.94 4.52
2106 2146 9.878599 GTAATGAATCTAACAATACCGATTTGG 57.121 33.333 0.00 0.00 46.41 3.28
2107 2147 9.580916 CGTAATGAATCTAACAATACCGATTTG 57.419 33.333 0.00 0.00 0.00 2.32
2108 2148 9.537192 TCGTAATGAATCTAACAATACCGATTT 57.463 29.630 0.00 0.00 0.00 2.17
2109 2149 9.537192 TTCGTAATGAATCTAACAATACCGATT 57.463 29.630 0.00 0.00 0.00 3.34
2110 2150 9.537192 TTTCGTAATGAATCTAACAATACCGAT 57.463 29.630 0.00 0.00 36.22 4.18
2111 2151 8.929827 TTTCGTAATGAATCTAACAATACCGA 57.070 30.769 0.00 0.00 36.22 4.69
2112 2152 9.793245 GATTTCGTAATGAATCTAACAATACCG 57.207 33.333 0.00 0.00 36.22 4.02
2157 2197 9.832445 AAAGTATCAACATCTACAATACCGAAT 57.168 29.630 0.00 0.00 0.00 3.34
2158 2198 9.661563 AAAAGTATCAACATCTACAATACCGAA 57.338 29.630 0.00 0.00 0.00 4.30
2204 2244 3.865164 GGGTCAAGTCAAACTTTGCAAAG 59.135 43.478 32.53 32.53 36.03 2.77
2205 2245 3.259374 TGGGTCAAGTCAAACTTTGCAAA 59.741 39.130 12.14 12.14 36.03 3.68
2206 2246 2.828520 TGGGTCAAGTCAAACTTTGCAA 59.171 40.909 0.00 0.00 36.03 4.08
2207 2247 2.451490 TGGGTCAAGTCAAACTTTGCA 58.549 42.857 0.00 0.00 36.03 4.08
2208 2248 3.518634 TTGGGTCAAGTCAAACTTTGC 57.481 42.857 0.00 0.00 36.03 3.68
2209 2249 5.906073 AGATTTGGGTCAAGTCAAACTTTG 58.094 37.500 6.06 0.00 36.03 2.77
2210 2250 7.654022 TTAGATTTGGGTCAAGTCAAACTTT 57.346 32.000 6.06 0.00 36.03 2.66
2211 2251 7.839680 ATTAGATTTGGGTCAAGTCAAACTT 57.160 32.000 6.06 0.00 39.39 2.66
2212 2252 7.119262 CGTATTAGATTTGGGTCAAGTCAAACT 59.881 37.037 6.06 0.00 35.97 2.66
2213 2253 7.241376 CGTATTAGATTTGGGTCAAGTCAAAC 58.759 38.462 6.06 0.00 35.97 2.93
2214 2254 6.128117 GCGTATTAGATTTGGGTCAAGTCAAA 60.128 38.462 6.06 0.00 33.48 2.69
2215 2255 5.353123 GCGTATTAGATTTGGGTCAAGTCAA 59.647 40.000 6.06 0.58 33.48 3.18
2216 2256 4.873827 GCGTATTAGATTTGGGTCAAGTCA 59.126 41.667 6.06 0.00 33.48 3.41
2217 2257 4.025979 CGCGTATTAGATTTGGGTCAAGTC 60.026 45.833 0.00 0.00 31.63 3.01
2218 2258 3.869246 CGCGTATTAGATTTGGGTCAAGT 59.131 43.478 0.00 0.00 0.00 3.16
2219 2259 3.247648 CCGCGTATTAGATTTGGGTCAAG 59.752 47.826 4.92 0.00 0.00 3.02
2220 2260 3.118702 TCCGCGTATTAGATTTGGGTCAA 60.119 43.478 4.92 0.00 0.00 3.18
2221 2261 2.431419 TCCGCGTATTAGATTTGGGTCA 59.569 45.455 4.92 0.00 0.00 4.02
2222 2262 3.057734 CTCCGCGTATTAGATTTGGGTC 58.942 50.000 4.92 0.00 0.00 4.46
2223 2263 2.433239 ACTCCGCGTATTAGATTTGGGT 59.567 45.455 4.92 0.00 0.00 4.51
2224 2264 3.107642 ACTCCGCGTATTAGATTTGGG 57.892 47.619 4.92 0.00 0.00 4.12
2225 2265 6.592798 TTTTACTCCGCGTATTAGATTTGG 57.407 37.500 4.92 0.00 0.00 3.28
2226 2266 7.010738 TCCTTTTTACTCCGCGTATTAGATTTG 59.989 37.037 4.92 0.00 0.00 2.32
2227 2267 7.010830 GTCCTTTTTACTCCGCGTATTAGATTT 59.989 37.037 4.92 0.00 0.00 2.17
2228 2268 6.478016 GTCCTTTTTACTCCGCGTATTAGATT 59.522 38.462 4.92 0.00 0.00 2.40
2229 2269 5.981915 GTCCTTTTTACTCCGCGTATTAGAT 59.018 40.000 4.92 0.00 0.00 1.98
2230 2270 5.343249 GTCCTTTTTACTCCGCGTATTAGA 58.657 41.667 4.92 0.00 0.00 2.10
2231 2271 4.505556 GGTCCTTTTTACTCCGCGTATTAG 59.494 45.833 4.92 0.00 0.00 1.73
2232 2272 4.432712 GGTCCTTTTTACTCCGCGTATTA 58.567 43.478 4.92 0.00 0.00 0.98
2233 2273 3.264947 GGTCCTTTTTACTCCGCGTATT 58.735 45.455 4.92 0.00 0.00 1.89
2234 2274 2.736400 CGGTCCTTTTTACTCCGCGTAT 60.736 50.000 4.92 0.00 35.01 3.06
2235 2275 1.402720 CGGTCCTTTTTACTCCGCGTA 60.403 52.381 4.92 0.00 35.01 4.42
2236 2276 0.668401 CGGTCCTTTTTACTCCGCGT 60.668 55.000 4.92 0.00 35.01 6.01
2237 2277 1.356527 CCGGTCCTTTTTACTCCGCG 61.357 60.000 0.00 0.00 39.87 6.46
2238 2278 0.037046 TCCGGTCCTTTTTACTCCGC 60.037 55.000 0.00 0.00 39.87 5.54
2239 2279 1.405121 CCTCCGGTCCTTTTTACTCCG 60.405 57.143 0.00 0.00 40.72 4.63
2240 2280 1.065636 CCCTCCGGTCCTTTTTACTCC 60.066 57.143 0.00 0.00 0.00 3.85
2241 2281 1.904537 TCCCTCCGGTCCTTTTTACTC 59.095 52.381 0.00 0.00 0.00 2.59
2242 2282 1.907255 CTCCCTCCGGTCCTTTTTACT 59.093 52.381 0.00 0.00 0.00 2.24
2243 2283 1.627329 ACTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
2244 2284 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
2245 2285 1.907255 CTACTCCCTCCGGTCCTTTTT 59.093 52.381 0.00 0.00 0.00 1.94
2246 2286 1.203275 ACTACTCCCTCCGGTCCTTTT 60.203 52.381 0.00 0.00 0.00 2.27
2247 2287 0.412640 ACTACTCCCTCCGGTCCTTT 59.587 55.000 0.00 0.00 0.00 3.11
2248 2288 1.302907 TACTACTCCCTCCGGTCCTT 58.697 55.000 0.00 0.00 0.00 3.36
2249 2289 1.424684 GATACTACTCCCTCCGGTCCT 59.575 57.143 0.00 0.00 0.00 3.85
2250 2290 1.424684 AGATACTACTCCCTCCGGTCC 59.575 57.143 0.00 0.00 0.00 4.46
2251 2291 2.955342 AGATACTACTCCCTCCGGTC 57.045 55.000 0.00 0.00 0.00 4.79
2252 2292 4.803329 TTAAGATACTACTCCCTCCGGT 57.197 45.455 0.00 0.00 0.00 5.28
2253 2293 7.173722 TCTAATTAAGATACTACTCCCTCCGG 58.826 42.308 0.00 0.00 0.00 5.14
2254 2294 7.148205 GCTCTAATTAAGATACTACTCCCTCCG 60.148 44.444 0.00 0.00 32.41 4.63
2255 2295 7.670559 TGCTCTAATTAAGATACTACTCCCTCC 59.329 40.741 0.00 0.00 32.41 4.30
2256 2296 8.638629 TGCTCTAATTAAGATACTACTCCCTC 57.361 38.462 0.00 0.00 32.41 4.30
2257 2297 9.084533 CTTGCTCTAATTAAGATACTACTCCCT 57.915 37.037 0.00 0.00 32.41 4.20
2258 2298 8.862085 ACTTGCTCTAATTAAGATACTACTCCC 58.138 37.037 0.00 0.00 32.41 4.30
2263 2303 9.751542 GCTGAACTTGCTCTAATTAAGATACTA 57.248 33.333 0.00 0.00 32.41 1.82
2264 2304 8.260818 TGCTGAACTTGCTCTAATTAAGATACT 58.739 33.333 0.00 0.00 32.41 2.12
2265 2305 8.425577 TGCTGAACTTGCTCTAATTAAGATAC 57.574 34.615 0.00 0.00 32.41 2.24
2266 2306 9.448438 TTTGCTGAACTTGCTCTAATTAAGATA 57.552 29.630 0.00 0.00 32.41 1.98
2267 2307 7.928307 TTGCTGAACTTGCTCTAATTAAGAT 57.072 32.000 0.00 0.00 32.41 2.40
2268 2308 7.445402 ACTTTGCTGAACTTGCTCTAATTAAGA 59.555 33.333 0.00 0.00 0.00 2.10
2269 2309 7.536622 CACTTTGCTGAACTTGCTCTAATTAAG 59.463 37.037 0.00 0.00 0.00 1.85
2270 2310 7.228507 TCACTTTGCTGAACTTGCTCTAATTAA 59.771 33.333 0.00 0.00 0.00 1.40
2271 2311 6.710295 TCACTTTGCTGAACTTGCTCTAATTA 59.290 34.615 0.00 0.00 0.00 1.40
2272 2312 5.532406 TCACTTTGCTGAACTTGCTCTAATT 59.468 36.000 0.00 0.00 0.00 1.40
2273 2313 5.049129 GTCACTTTGCTGAACTTGCTCTAAT 60.049 40.000 0.00 0.00 0.00 1.73
2274 2314 4.273480 GTCACTTTGCTGAACTTGCTCTAA 59.727 41.667 0.00 0.00 0.00 2.10
2383 2423 4.518211 CCTTCTTGCTTGAGAACTTCACAT 59.482 41.667 0.00 0.00 34.94 3.21
2435 2475 0.326264 TCTCCAAGCAGGGAAAGCTC 59.674 55.000 0.00 0.00 42.53 4.09
2476 2516 1.597742 TGGAACAGCTCAAGTTCTGC 58.402 50.000 13.34 1.53 43.67 4.26
2673 2713 4.273480 GTGTTGCTCGCATTCCAGTATAAT 59.727 41.667 0.00 0.00 0.00 1.28
2690 2730 1.005867 CATGCCAGGGTTGTGTTGC 60.006 57.895 0.00 0.00 0.00 4.17
2930 2970 1.679559 GCCCCAAGATGTTGATGCCC 61.680 60.000 3.74 0.00 35.46 5.36
2999 3039 2.908428 GGCGCATCATGGATGGCA 60.908 61.111 10.83 0.00 40.10 4.92
3051 3091 6.631314 GCCAAAATGAGTCTGGAATCTAGAGA 60.631 42.308 0.00 0.00 31.38 3.10
3112 3152 3.957497 AGAGACACTAGCCACCTCATTAG 59.043 47.826 0.00 0.00 0.00 1.73
3150 3195 4.624015 ACAACTCCACATGCAGAAAATTG 58.376 39.130 0.00 0.00 0.00 2.32
3179 3224 7.286546 TCAAACCATTCAACTCAACCTAAATCA 59.713 33.333 0.00 0.00 0.00 2.57
3229 3274 0.250640 CAAGAACTCCTGCCAGCAGT 60.251 55.000 17.86 0.00 42.15 4.40
3267 3312 2.418609 CGCATCAGGGATGGCGATTATA 60.419 50.000 13.75 0.00 40.10 0.98
3451 3597 6.257411 CACTCAGCCTAAATCAATGACTACAG 59.743 42.308 0.00 0.00 0.00 2.74
3506 3652 1.303155 GTCTTGCCAGCAGCTTCCT 60.303 57.895 0.00 0.00 44.23 3.36
3507 3653 0.892814 AAGTCTTGCCAGCAGCTTCC 60.893 55.000 0.00 0.00 44.23 3.46
3535 3681 8.954950 ACCATTAGACTCAGACTAAATCAATG 57.045 34.615 0.54 0.00 34.28 2.82
3546 3692 3.258372 ACAGCGAAACCATTAGACTCAGA 59.742 43.478 0.00 0.00 0.00 3.27
3553 3699 5.106555 ACAATCTTCACAGCGAAACCATTAG 60.107 40.000 0.00 0.00 31.71 1.73
3564 3710 3.360249 AGTTGCAACAATCTTCACAGC 57.640 42.857 30.11 0.00 0.00 4.40
3599 3762 6.648725 AAGACATCTGTATTTCGTTACAGC 57.351 37.500 14.11 5.01 45.67 4.40


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

AutoCloner maintained by Alex Coulton.