Multiple sequence alignment - TraesCS3D01G048500

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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 TraesCS3D01G048500 chr3D 100.000 4974 0 0 1 4974 18657138 18662111 0.000000e+00 9186.0
1 TraesCS3D01G048500 chr3D 93.652 1906 90 13 2330 4217 18926509 18928401 0.000000e+00 2820.0
2 TraesCS3D01G048500 chr3D 94.210 1019 47 4 899 1909 18911024 18912038 0.000000e+00 1544.0
3 TraesCS3D01G048500 chr3D 93.706 572 34 1 2221 2790 18740563 18741134 0.000000e+00 856.0
4 TraesCS3D01G048500 chr3D 94.292 438 23 2 1475 1910 18739710 18740147 0.000000e+00 669.0
5 TraesCS3D01G048500 chr3D 91.538 390 27 2 201 590 18910468 18910851 2.640000e-147 532.0
6 TraesCS3D01G048500 chr3D 96.237 186 7 0 605 790 18910830 18911015 6.260000e-79 305.0
7 TraesCS3D01G048500 chr3D 83.014 365 23 10 1998 2323 18912020 18912384 1.350000e-75 294.0
8 TraesCS3D01G048500 chr3D 88.412 233 26 1 4477 4709 18932477 18932708 3.790000e-71 279.0
9 TraesCS3D01G048500 chr3D 95.946 74 3 0 2002 2075 18740133 18740206 2.430000e-23 121.0
10 TraesCS3D01G048500 chr3D 73.359 259 50 14 949 1201 18779002 18779247 1.480000e-10 78.7
11 TraesCS3D01G048500 chr3B 93.070 2785 158 19 2206 4974 30091651 30088886 0.000000e+00 4041.0
12 TraesCS3D01G048500 chr3B 91.959 2823 195 16 2161 4974 29592974 29590175 0.000000e+00 3927.0
13 TraesCS3D01G048500 chr3B 94.854 1885 93 2 2669 4551 30409435 30411317 0.000000e+00 2940.0
14 TraesCS3D01G048500 chr3B 94.700 1302 62 6 611 1910 29594620 29593324 0.000000e+00 2015.0
15 TraesCS3D01G048500 chr3B 88.414 1614 134 18 2473 4050 29379793 29381389 0.000000e+00 1895.0
16 TraesCS3D01G048500 chr3B 92.737 1308 66 14 605 1910 30406940 30408220 0.000000e+00 1862.0
17 TraesCS3D01G048500 chr3B 92.552 1262 71 7 650 1910 30093339 30092100 0.000000e+00 1788.0
18 TraesCS3D01G048500 chr3B 89.143 875 65 20 905 1761 29640843 29641705 0.000000e+00 1062.0
19 TraesCS3D01G048500 chr3B 81.926 1267 148 50 3741 4974 29787730 29788948 0.000000e+00 996.0
20 TraesCS3D01G048500 chr3B 90.909 539 47 2 2170 2707 30408903 30409440 0.000000e+00 723.0
21 TraesCS3D01G048500 chr3B 94.056 286 16 1 293 578 29595616 29595332 2.750000e-117 433.0
22 TraesCS3D01G048500 chr3B 94.056 286 16 1 293 578 30095679 30095395 2.750000e-117 433.0
23 TraesCS3D01G048500 chr3B 92.617 298 22 0 293 590 30406664 30406961 3.560000e-116 429.0
24 TraesCS3D01G048500 chr3B 86.972 284 34 3 3521 3802 29354645 29354363 2.890000e-82 316.0
25 TraesCS3D01G048500 chr3B 92.166 217 15 2 156 370 29640075 29640291 6.260000e-79 305.0
26 TraesCS3D01G048500 chr3B 92.994 157 11 0 156 312 30406170 30406326 3.870000e-56 230.0
27 TraesCS3D01G048500 chr3B 94.697 132 7 0 605 736 29640713 29640844 6.530000e-49 206.0
28 TraesCS3D01G048500 chr3B 90.647 139 10 2 2003 2141 30408207 30408342 1.100000e-41 182.0
29 TraesCS3D01G048500 chr3B 92.593 108 8 0 156 263 29598845 29598738 6.670000e-34 156.0
30 TraesCS3D01G048500 chr3B 98.795 83 1 0 507 589 29640651 29640733 1.120000e-31 148.0
31 TraesCS3D01G048500 chr3B 92.233 103 8 0 161 263 30098931 30098829 4.010000e-31 147.0
32 TraesCS3D01G048500 chr3B 81.928 166 16 10 1 154 118259121 118258958 1.450000e-25 128.0
33 TraesCS3D01G048500 chr3B 100.000 31 0 0 1880 1910 30092056 30092026 1.930000e-04 58.4
34 TraesCS3D01G048500 chr3A 93.971 1841 101 6 2250 4087 26195553 26197386 0.000000e+00 2776.0
35 TraesCS3D01G048500 chr3A 91.844 1594 106 12 2473 4050 26141561 26143146 0.000000e+00 2202.0
36 TraesCS3D01G048500 chr3A 95.066 1297 63 1 605 1901 26194099 26195394 0.000000e+00 2039.0
37 TraesCS3D01G048500 chr3A 88.308 325 15 5 266 590 26193819 26194120 7.870000e-98 368.0
38 TraesCS3D01G048500 chr3A 78.019 323 65 3 1358 1677 26472514 26472833 1.090000e-46 198.0
39 TraesCS3D01G048500 chr3A 82.822 163 10 13 2012 2159 26195394 26195553 4.040000e-26 130.0
40 TraesCS3D01G048500 chrUn 82.530 166 29 0 1512 1677 282462319 282462154 4.010000e-31 147.0
41 TraesCS3D01G048500 chr2A 91.837 98 8 0 2184 2281 445714585 445714682 2.410000e-28 137.0
42 TraesCS3D01G048500 chr1A 92.857 84 5 1 1 84 539751112 539751030 2.430000e-23 121.0
43 TraesCS3D01G048500 chr5A 87.379 103 12 1 2184 2286 305569598 305569497 3.150000e-22 117.0
44 TraesCS3D01G048500 chr5A 92.000 50 2 2 107 155 560479472 560479520 8.930000e-08 69.4
45 TraesCS3D01G048500 chr7D 81.560 141 24 2 2159 2299 436480874 436481012 1.130000e-21 115.0
46 TraesCS3D01G048500 chr7D 86.139 101 14 0 2183 2283 573104633 573104533 5.260000e-20 110.0
47 TraesCS3D01G048500 chr7D 80.645 124 23 1 2156 2279 28560426 28560548 1.470000e-15 95.3
48 TraesCS3D01G048500 chr7D 97.674 43 0 1 108 150 561382575 561382534 6.910000e-09 73.1
49 TraesCS3D01G048500 chr7D 97.674 43 0 1 108 150 561444074 561444033 6.910000e-09 73.1
50 TraesCS3D01G048500 chr7D 89.091 55 5 1 98 151 610587706 610587760 3.210000e-07 67.6
51 TraesCS3D01G048500 chr7A 83.168 101 17 0 2183 2283 32874604 32874704 5.300000e-15 93.5
52 TraesCS3D01G048500 chr2B 82.759 116 9 7 46 150 62379211 62379326 5.300000e-15 93.5
53 TraesCS3D01G048500 chr7B 88.333 60 6 1 92 150 511051771 511051712 2.480000e-08 71.3
54 TraesCS3D01G048500 chr4B 97.619 42 0 1 114 154 2271759 2271718 2.480000e-08 71.3
55 TraesCS3D01G048500 chr1B 91.489 47 2 2 110 154 10355093 10355139 4.160000e-06 63.9
56 TraesCS3D01G048500 chr5B 97.222 36 1 0 671 706 28755760 28755795 1.500000e-05 62.1


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 TraesCS3D01G048500 chr3D 18657138 18662111 4973 False 9186.000000 9186 100.000000 1 4974 1 chr3D.!!$F1 4973
1 TraesCS3D01G048500 chr3D 18926509 18928401 1892 False 2820.000000 2820 93.652000 2330 4217 1 chr3D.!!$F3 1887
2 TraesCS3D01G048500 chr3D 18910468 18912384 1916 False 668.750000 1544 91.249750 201 2323 4 chr3D.!!$F6 2122
3 TraesCS3D01G048500 chr3D 18739710 18741134 1424 False 548.666667 856 94.648000 1475 2790 3 chr3D.!!$F5 1315
4 TraesCS3D01G048500 chr3B 29379793 29381389 1596 False 1895.000000 1895 88.414000 2473 4050 1 chr3B.!!$F1 1577
5 TraesCS3D01G048500 chr3B 29590175 29598845 8670 True 1632.750000 3927 93.327000 156 4974 4 chr3B.!!$R3 4818
6 TraesCS3D01G048500 chr3B 30088886 30098931 10045 True 1293.480000 4041 94.382200 161 4974 5 chr3B.!!$R4 4813
7 TraesCS3D01G048500 chr3B 30406170 30411317 5147 False 1061.000000 2940 92.459667 156 4551 6 chr3B.!!$F4 4395
8 TraesCS3D01G048500 chr3B 29787730 29788948 1218 False 996.000000 996 81.926000 3741 4974 1 chr3B.!!$F2 1233
9 TraesCS3D01G048500 chr3B 29640075 29641705 1630 False 430.250000 1062 93.700250 156 1761 4 chr3B.!!$F3 1605
10 TraesCS3D01G048500 chr3A 26141561 26143146 1585 False 2202.000000 2202 91.844000 2473 4050 1 chr3A.!!$F1 1577
11 TraesCS3D01G048500 chr3A 26193819 26197386 3567 False 1328.250000 2776 90.041750 266 4087 4 chr3A.!!$F3 3821

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
60 61 0.185901 TCTTTGGGGCTTGTTCTGCT 59.814 50.0 0.00 0.00 0.00 4.24 F
61 62 0.316204 CTTTGGGGCTTGTTCTGCTG 59.684 55.0 0.00 0.00 0.00 4.41 F
62 63 0.396974 TTTGGGGCTTGTTCTGCTGT 60.397 50.0 0.00 0.00 0.00 4.40 F
118 119 0.400213 TGGATTCTTGGTCCGTTGCT 59.600 50.0 0.00 0.00 38.64 3.91 F
305 3364 0.806868 CCTGTTGCATGCAGGTGTAG 59.193 55.0 21.50 14.48 46.22 2.74 F
2081 7959 0.794229 GAACGCATGAATGTGGCACG 60.794 55.0 13.77 0.29 42.35 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1118 6906 0.678395 CGGATCAGAGATGGTGAGGG 59.322 60.000 0.00 0.0 0.00 4.30 R
1947 7765 1.102978 ACCCTATTTCATGCGGTTGC 58.897 50.000 0.00 0.0 43.20 4.17 R
1951 7769 2.218603 GGTGTACCCTATTTCATGCGG 58.781 52.381 0.00 0.0 0.00 5.69 R
1952 7770 2.912771 TGGTGTACCCTATTTCATGCG 58.087 47.619 0.00 0.0 34.29 4.73 R
2172 8617 3.138798 GGTCCGCTCGGCAGTCTA 61.139 66.667 2.96 0.0 34.68 2.59 R
4078 10642 0.531532 CGGCCATGATGAGAGACACC 60.532 60.000 2.24 0.0 0.00 4.16 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
23 24 4.741239 ACCACCCCTGAGCCGGAT 62.741 66.667 5.05 0.00 0.00 4.18
24 25 3.411517 CCACCCCTGAGCCGGATT 61.412 66.667 5.05 0.00 0.00 3.01
25 26 2.070039 CCACCCCTGAGCCGGATTA 61.070 63.158 5.05 0.00 0.00 1.75
26 27 1.447643 CACCCCTGAGCCGGATTAG 59.552 63.158 5.05 4.54 0.00 1.73
27 28 2.427753 CCCCTGAGCCGGATTAGC 59.572 66.667 5.05 0.00 0.00 3.09
28 29 2.143419 CCCCTGAGCCGGATTAGCT 61.143 63.158 5.05 0.00 45.23 3.32
53 54 5.659440 TTTTTAGCTATCTTTGGGGCTTG 57.341 39.130 0.00 0.00 36.40 4.01
54 55 4.316025 TTTAGCTATCTTTGGGGCTTGT 57.684 40.909 0.00 0.00 36.40 3.16
55 56 2.907458 AGCTATCTTTGGGGCTTGTT 57.093 45.000 0.00 0.00 0.00 2.83
56 57 2.728007 AGCTATCTTTGGGGCTTGTTC 58.272 47.619 0.00 0.00 0.00 3.18
57 58 2.310052 AGCTATCTTTGGGGCTTGTTCT 59.690 45.455 0.00 0.00 0.00 3.01
58 59 2.424956 GCTATCTTTGGGGCTTGTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
59 60 1.260544 ATCTTTGGGGCTTGTTCTGC 58.739 50.000 0.00 0.00 0.00 4.26
60 61 0.185901 TCTTTGGGGCTTGTTCTGCT 59.814 50.000 0.00 0.00 0.00 4.24
61 62 0.316204 CTTTGGGGCTTGTTCTGCTG 59.684 55.000 0.00 0.00 0.00 4.41
62 63 0.396974 TTTGGGGCTTGTTCTGCTGT 60.397 50.000 0.00 0.00 0.00 4.40
63 64 1.108727 TTGGGGCTTGTTCTGCTGTG 61.109 55.000 0.00 0.00 0.00 3.66
64 65 2.647297 GGGCTTGTTCTGCTGTGC 59.353 61.111 0.00 0.00 0.00 4.57
65 66 2.647297 GGCTTGTTCTGCTGTGCC 59.353 61.111 0.00 0.00 0.00 5.01
66 67 2.647297 GCTTGTTCTGCTGTGCCC 59.353 61.111 0.00 0.00 0.00 5.36
67 68 2.924105 GCTTGTTCTGCTGTGCCCC 61.924 63.158 0.00 0.00 0.00 5.80
68 69 1.529010 CTTGTTCTGCTGTGCCCCA 60.529 57.895 0.00 0.00 0.00 4.96
69 70 1.521450 CTTGTTCTGCTGTGCCCCAG 61.521 60.000 0.00 0.00 44.53 4.45
79 80 4.100479 TGCCCCAGCATGACTTTG 57.900 55.556 0.00 0.00 46.52 2.77
80 81 1.153524 TGCCCCAGCATGACTTTGT 59.846 52.632 0.00 0.00 46.52 2.83
81 82 1.180456 TGCCCCAGCATGACTTTGTG 61.180 55.000 0.00 0.00 46.52 3.33
82 83 1.588082 CCCCAGCATGACTTTGTGC 59.412 57.895 0.00 0.00 39.69 4.57
83 84 1.588082 CCCAGCATGACTTTGTGCC 59.412 57.895 0.00 0.00 42.20 5.01
84 85 0.896940 CCCAGCATGACTTTGTGCCT 60.897 55.000 0.00 0.00 42.20 4.75
85 86 0.963962 CCAGCATGACTTTGTGCCTT 59.036 50.000 0.00 0.00 42.20 4.35
86 87 2.161855 CCAGCATGACTTTGTGCCTTA 58.838 47.619 0.00 0.00 42.20 2.69
87 88 2.756760 CCAGCATGACTTTGTGCCTTAT 59.243 45.455 0.00 0.00 42.20 1.73
88 89 3.194116 CCAGCATGACTTTGTGCCTTATT 59.806 43.478 0.00 0.00 42.20 1.40
89 90 4.418392 CAGCATGACTTTGTGCCTTATTC 58.582 43.478 0.00 0.00 42.20 1.75
90 91 4.081406 AGCATGACTTTGTGCCTTATTCA 58.919 39.130 0.00 0.00 42.20 2.57
91 92 4.708421 AGCATGACTTTGTGCCTTATTCAT 59.292 37.500 0.00 0.00 42.20 2.57
92 93 5.887598 AGCATGACTTTGTGCCTTATTCATA 59.112 36.000 0.00 0.00 42.20 2.15
93 94 6.377996 AGCATGACTTTGTGCCTTATTCATAA 59.622 34.615 0.00 0.00 42.20 1.90
94 95 7.069085 AGCATGACTTTGTGCCTTATTCATAAT 59.931 33.333 0.00 0.00 42.20 1.28
95 96 7.168637 GCATGACTTTGTGCCTTATTCATAATG 59.831 37.037 0.00 0.00 35.35 1.90
96 97 7.701539 TGACTTTGTGCCTTATTCATAATGT 57.298 32.000 0.00 0.00 0.00 2.71
97 98 7.537715 TGACTTTGTGCCTTATTCATAATGTG 58.462 34.615 0.00 0.00 0.00 3.21
98 99 7.176515 TGACTTTGTGCCTTATTCATAATGTGT 59.823 33.333 0.00 0.00 0.00 3.72
99 100 7.895759 ACTTTGTGCCTTATTCATAATGTGTT 58.104 30.769 0.00 0.00 0.00 3.32
100 101 7.814107 ACTTTGTGCCTTATTCATAATGTGTTG 59.186 33.333 0.00 0.00 0.00 3.33
101 102 6.206395 TGTGCCTTATTCATAATGTGTTGG 57.794 37.500 0.00 0.00 0.00 3.77
102 103 5.948758 TGTGCCTTATTCATAATGTGTTGGA 59.051 36.000 0.00 0.00 0.00 3.53
103 104 6.606796 TGTGCCTTATTCATAATGTGTTGGAT 59.393 34.615 0.00 0.00 0.00 3.41
104 105 7.123997 TGTGCCTTATTCATAATGTGTTGGATT 59.876 33.333 0.00 0.00 0.00 3.01
105 106 7.649306 GTGCCTTATTCATAATGTGTTGGATTC 59.351 37.037 0.00 0.00 0.00 2.52
106 107 7.560991 TGCCTTATTCATAATGTGTTGGATTCT 59.439 33.333 0.00 0.00 0.00 2.40
107 108 8.416329 GCCTTATTCATAATGTGTTGGATTCTT 58.584 33.333 0.00 0.00 0.00 2.52
108 109 9.740239 CCTTATTCATAATGTGTTGGATTCTTG 57.260 33.333 0.00 0.00 0.00 3.02
109 110 9.740239 CTTATTCATAATGTGTTGGATTCTTGG 57.260 33.333 0.00 0.00 0.00 3.61
110 111 7.722949 ATTCATAATGTGTTGGATTCTTGGT 57.277 32.000 0.00 0.00 0.00 3.67
111 112 6.757897 TCATAATGTGTTGGATTCTTGGTC 57.242 37.500 0.00 0.00 0.00 4.02
112 113 5.652014 TCATAATGTGTTGGATTCTTGGTCC 59.348 40.000 0.00 0.00 36.26 4.46
113 114 1.890876 TGTGTTGGATTCTTGGTCCG 58.109 50.000 0.00 0.00 38.64 4.79
114 115 1.142060 TGTGTTGGATTCTTGGTCCGT 59.858 47.619 0.00 0.00 38.64 4.69
115 116 2.227194 GTGTTGGATTCTTGGTCCGTT 58.773 47.619 0.00 0.00 38.64 4.44
116 117 2.031157 GTGTTGGATTCTTGGTCCGTTG 60.031 50.000 0.00 0.00 38.64 4.10
117 118 1.068541 GTTGGATTCTTGGTCCGTTGC 60.069 52.381 0.00 0.00 38.64 4.17
118 119 0.400213 TGGATTCTTGGTCCGTTGCT 59.600 50.000 0.00 0.00 38.64 3.91
119 120 1.202879 TGGATTCTTGGTCCGTTGCTT 60.203 47.619 0.00 0.00 38.64 3.91
120 121 1.886542 GGATTCTTGGTCCGTTGCTTT 59.113 47.619 0.00 0.00 0.00 3.51
121 122 3.078837 GGATTCTTGGTCCGTTGCTTTA 58.921 45.455 0.00 0.00 0.00 1.85
122 123 3.694566 GGATTCTTGGTCCGTTGCTTTAT 59.305 43.478 0.00 0.00 0.00 1.40
123 124 4.879545 GGATTCTTGGTCCGTTGCTTTATA 59.120 41.667 0.00 0.00 0.00 0.98
124 125 5.355910 GGATTCTTGGTCCGTTGCTTTATAA 59.644 40.000 0.00 0.00 0.00 0.98
125 126 6.039382 GGATTCTTGGTCCGTTGCTTTATAAT 59.961 38.462 0.00 0.00 0.00 1.28
126 127 7.227910 GGATTCTTGGTCCGTTGCTTTATAATA 59.772 37.037 0.00 0.00 0.00 0.98
127 128 8.691661 ATTCTTGGTCCGTTGCTTTATAATAT 57.308 30.769 0.00 0.00 0.00 1.28
128 129 9.787435 ATTCTTGGTCCGTTGCTTTATAATATA 57.213 29.630 0.00 0.00 0.00 0.86
129 130 9.616156 TTCTTGGTCCGTTGCTTTATAATATAA 57.384 29.630 0.00 0.00 0.00 0.98
130 131 9.616156 TCTTGGTCCGTTGCTTTATAATATAAA 57.384 29.630 5.46 5.46 0.00 1.40
131 132 9.878599 CTTGGTCCGTTGCTTTATAATATAAAG 57.121 33.333 22.11 22.11 37.53 1.85
132 133 8.967664 TGGTCCGTTGCTTTATAATATAAAGT 57.032 30.769 25.08 0.00 37.00 2.66
133 134 8.832521 TGGTCCGTTGCTTTATAATATAAAGTG 58.167 33.333 25.08 16.07 37.00 3.16
134 135 8.287503 GGTCCGTTGCTTTATAATATAAAGTGG 58.712 37.037 25.08 21.38 37.00 4.00
135 136 8.287503 GTCCGTTGCTTTATAATATAAAGTGGG 58.712 37.037 25.08 20.78 37.00 4.61
136 137 7.446013 TCCGTTGCTTTATAATATAAAGTGGGG 59.554 37.037 25.08 21.01 37.00 4.96
137 138 7.308951 CCGTTGCTTTATAATATAAAGTGGGGG 60.309 40.741 25.08 19.24 37.00 5.40
138 139 7.446013 CGTTGCTTTATAATATAAAGTGGGGGA 59.554 37.037 25.08 6.78 37.00 4.81
139 140 9.138596 GTTGCTTTATAATATAAAGTGGGGGAA 57.861 33.333 25.08 11.16 37.00 3.97
140 141 9.716556 TTGCTTTATAATATAAAGTGGGGGAAA 57.283 29.630 25.08 11.64 37.00 3.13
141 142 9.138596 TGCTTTATAATATAAAGTGGGGGAAAC 57.861 33.333 25.08 11.77 37.00 2.78
142 143 8.582437 GCTTTATAATATAAAGTGGGGGAAACC 58.418 37.037 25.08 8.44 41.88 3.27
159 160 6.880484 GGGAAACCCTTTTTCTCAAAAGTAA 58.120 36.000 6.68 0.00 45.28 2.24
164 165 7.569639 ACCCTTTTTCTCAAAAGTAAGACTC 57.430 36.000 6.68 0.00 45.28 3.36
169 170 4.175787 TCTCAAAAGTAAGACTCGGAGC 57.824 45.455 4.58 0.00 0.00 4.70
305 3364 0.806868 CCTGTTGCATGCAGGTGTAG 59.193 55.000 21.50 14.48 46.22 2.74
313 3729 4.388485 TGCATGCAGGTGTAGTATATTGG 58.612 43.478 18.46 0.00 0.00 3.16
388 4120 4.654091 AAGAACATGTGAAACTTGGTGG 57.346 40.909 0.00 0.00 42.53 4.61
505 4238 5.306532 TGTGCGTAGTTGGTTTTGTTAAA 57.693 34.783 0.00 0.00 0.00 1.52
598 4331 9.796120 TGATAAGGCAAAATAAATACCTTTTCG 57.204 29.630 0.00 0.00 39.73 3.46
604 6392 8.766151 GGCAAAATAAATACCTTTTCGAACAAA 58.234 29.630 0.00 0.00 0.00 2.83
793 6581 1.642037 CTGCACCCACTTGATCTGCG 61.642 60.000 0.00 0.00 0.00 5.18
801 6589 1.817099 CTTGATCTGCGGCCACTCC 60.817 63.158 2.24 0.00 0.00 3.85
803 6591 2.202987 GATCTGCGGCCACTCCTG 60.203 66.667 2.24 0.00 0.00 3.86
875 6663 2.861763 TGTTAGACGTACGACGACTG 57.138 50.000 24.41 0.00 45.17 3.51
1047 6835 1.202099 TCATCGGGGTTTGGTGGCTA 61.202 55.000 0.00 0.00 0.00 3.93
1286 7082 3.693085 AGTATCTCTTACGAGGAACGCAA 59.307 43.478 0.00 0.00 46.94 4.85
1416 7212 3.009916 ACCTCAGCAACCTGAATCTCATT 59.990 43.478 0.00 0.00 46.84 2.57
1522 7333 2.203294 GGGTGGTGTTTGTCCGCT 60.203 61.111 0.00 0.00 35.96 5.52
1653 7464 2.458951 GACTACGAGCAGCTCATCAAG 58.541 52.381 22.49 14.34 0.00 3.02
1761 7574 6.659745 TCAAGTTTGTAGCTACACTAGGAA 57.340 37.500 26.02 14.33 35.64 3.36
1762 7575 7.241042 TCAAGTTTGTAGCTACACTAGGAAT 57.759 36.000 26.02 6.77 35.64 3.01
1875 7690 2.158449 CGTGGAAGCTCTGTCAATCAAC 59.842 50.000 0.00 0.00 0.00 3.18
1885 7703 3.198635 TCTGTCAATCAACTGAGATCCCC 59.801 47.826 0.00 0.00 0.00 4.81
1887 7705 3.330405 TGTCAATCAACTGAGATCCCCAA 59.670 43.478 0.00 0.00 0.00 4.12
1890 7708 5.420104 GTCAATCAACTGAGATCCCCAATTT 59.580 40.000 0.00 0.00 0.00 1.82
1891 7709 5.419788 TCAATCAACTGAGATCCCCAATTTG 59.580 40.000 0.00 0.00 0.00 2.32
1892 7710 4.656100 TCAACTGAGATCCCCAATTTGA 57.344 40.909 0.00 0.00 0.00 2.69
1893 7711 4.592942 TCAACTGAGATCCCCAATTTGAG 58.407 43.478 0.00 0.00 0.00 3.02
1894 7712 4.289410 TCAACTGAGATCCCCAATTTGAGA 59.711 41.667 0.00 0.00 0.00 3.27
1895 7713 5.044624 TCAACTGAGATCCCCAATTTGAGAT 60.045 40.000 0.00 0.00 0.00 2.75
1896 7714 5.463051 ACTGAGATCCCCAATTTGAGATT 57.537 39.130 0.00 0.00 0.00 2.40
1897 7715 6.581388 ACTGAGATCCCCAATTTGAGATTA 57.419 37.500 0.00 0.00 0.00 1.75
1898 7716 6.599445 ACTGAGATCCCCAATTTGAGATTAG 58.401 40.000 0.00 3.84 0.00 1.73
1899 7717 6.159398 ACTGAGATCCCCAATTTGAGATTAGT 59.841 38.462 0.00 4.34 0.00 2.24
1900 7718 7.348274 ACTGAGATCCCCAATTTGAGATTAGTA 59.652 37.037 0.00 0.00 0.00 1.82
1901 7719 7.509546 TGAGATCCCCAATTTGAGATTAGTAC 58.490 38.462 0.00 0.00 0.00 2.73
1902 7720 7.127186 TGAGATCCCCAATTTGAGATTAGTACA 59.873 37.037 0.00 0.00 0.00 2.90
1903 7721 8.050316 AGATCCCCAATTTGAGATTAGTACAT 57.950 34.615 0.00 0.00 0.00 2.29
1904 7722 7.941238 AGATCCCCAATTTGAGATTAGTACATG 59.059 37.037 0.00 0.00 0.00 3.21
1905 7723 7.206789 TCCCCAATTTGAGATTAGTACATGA 57.793 36.000 0.00 0.00 0.00 3.07
1906 7724 7.815383 TCCCCAATTTGAGATTAGTACATGAT 58.185 34.615 0.00 0.00 0.00 2.45
1907 7725 8.281531 TCCCCAATTTGAGATTAGTACATGATT 58.718 33.333 0.00 0.00 0.00 2.57
1908 7726 8.917088 CCCCAATTTGAGATTAGTACATGATTT 58.083 33.333 0.00 0.00 0.00 2.17
1940 7758 2.670019 GGGTTTCCCCCGCTTTATAT 57.330 50.000 0.00 0.00 45.80 0.86
1941 7759 2.953453 GGGTTTCCCCCGCTTTATATT 58.047 47.619 0.00 0.00 45.80 1.28
1942 7760 4.103013 GGGTTTCCCCCGCTTTATATTA 57.897 45.455 0.00 0.00 45.80 0.98
1943 7761 4.669700 GGGTTTCCCCCGCTTTATATTAT 58.330 43.478 0.00 0.00 45.80 1.28
1944 7762 4.461431 GGGTTTCCCCCGCTTTATATTATG 59.539 45.833 0.00 0.00 45.80 1.90
1945 7763 5.318630 GGTTTCCCCCGCTTTATATTATGA 58.681 41.667 0.00 0.00 0.00 2.15
1946 7764 5.771165 GGTTTCCCCCGCTTTATATTATGAA 59.229 40.000 0.00 0.00 0.00 2.57
1947 7765 6.072119 GGTTTCCCCCGCTTTATATTATGAAG 60.072 42.308 4.29 4.29 0.00 3.02
1948 7766 4.585879 TCCCCCGCTTTATATTATGAAGC 58.414 43.478 18.46 18.46 45.29 3.86
1957 7775 7.786305 CTTTATATTATGAAGCAACCGCATG 57.214 36.000 0.00 0.00 42.27 4.06
1958 7776 7.503521 TTTATATTATGAAGCAACCGCATGA 57.496 32.000 0.00 0.00 42.27 3.07
1959 7777 7.503521 TTATATTATGAAGCAACCGCATGAA 57.496 32.000 0.00 0.00 42.27 2.57
1960 7778 4.717233 ATTATGAAGCAACCGCATGAAA 57.283 36.364 0.00 0.00 42.27 2.69
1961 7779 4.717233 TTATGAAGCAACCGCATGAAAT 57.283 36.364 0.00 0.00 42.27 2.17
1962 7780 5.826601 TTATGAAGCAACCGCATGAAATA 57.173 34.783 0.00 0.00 42.27 1.40
1963 7781 3.763097 TGAAGCAACCGCATGAAATAG 57.237 42.857 0.00 0.00 42.27 1.73
1964 7782 2.423185 TGAAGCAACCGCATGAAATAGG 59.577 45.455 0.00 0.00 42.27 2.57
1965 7783 1.392589 AGCAACCGCATGAAATAGGG 58.607 50.000 0.00 0.00 42.27 3.53
1966 7784 1.102978 GCAACCGCATGAAATAGGGT 58.897 50.000 0.00 0.00 38.36 4.34
1967 7785 2.092646 AGCAACCGCATGAAATAGGGTA 60.093 45.455 0.00 0.00 42.27 3.69
1968 7786 2.032924 GCAACCGCATGAAATAGGGTAC 59.967 50.000 0.00 0.00 38.36 3.34
1969 7787 3.275143 CAACCGCATGAAATAGGGTACA 58.725 45.455 0.00 0.00 31.61 2.90
1970 7788 2.914059 ACCGCATGAAATAGGGTACAC 58.086 47.619 0.00 0.00 30.24 2.90
1971 7789 2.218603 CCGCATGAAATAGGGTACACC 58.781 52.381 0.00 0.00 40.67 4.16
1972 7790 2.420827 CCGCATGAAATAGGGTACACCA 60.421 50.000 0.00 0.00 43.89 4.17
1973 7791 3.275143 CGCATGAAATAGGGTACACCAA 58.725 45.455 0.00 0.00 43.89 3.67
1974 7792 3.064820 CGCATGAAATAGGGTACACCAAC 59.935 47.826 0.00 0.00 43.89 3.77
1975 7793 4.013728 GCATGAAATAGGGTACACCAACA 58.986 43.478 0.00 0.00 43.89 3.33
1976 7794 4.461081 GCATGAAATAGGGTACACCAACAA 59.539 41.667 0.00 0.00 43.89 2.83
1977 7795 5.047660 GCATGAAATAGGGTACACCAACAAA 60.048 40.000 0.00 0.00 43.89 2.83
1978 7796 6.620678 CATGAAATAGGGTACACCAACAAAG 58.379 40.000 0.00 0.00 43.89 2.77
1979 7797 5.074115 TGAAATAGGGTACACCAACAAAGG 58.926 41.667 0.00 0.00 43.89 3.11
1980 7798 5.163077 TGAAATAGGGTACACCAACAAAGGA 60.163 40.000 0.00 0.00 43.89 3.36
1981 7799 5.530176 AATAGGGTACACCAACAAAGGAT 57.470 39.130 0.00 0.00 43.89 3.24
1982 7800 3.895704 AGGGTACACCAACAAAGGATT 57.104 42.857 0.00 0.00 43.89 3.01
1983 7801 4.193240 AGGGTACACCAACAAAGGATTT 57.807 40.909 0.00 0.00 43.89 2.17
1984 7802 4.552674 AGGGTACACCAACAAAGGATTTT 58.447 39.130 0.00 0.00 43.89 1.82
1985 7803 5.707495 AGGGTACACCAACAAAGGATTTTA 58.293 37.500 0.00 0.00 43.89 1.52
1986 7804 6.137559 AGGGTACACCAACAAAGGATTTTAA 58.862 36.000 0.00 0.00 43.89 1.52
1987 7805 6.266786 AGGGTACACCAACAAAGGATTTTAAG 59.733 38.462 0.00 0.00 43.89 1.85
1988 7806 6.265876 GGGTACACCAACAAAGGATTTTAAGA 59.734 38.462 0.00 0.00 35.83 2.10
1989 7807 7.039293 GGGTACACCAACAAAGGATTTTAAGAT 60.039 37.037 0.00 0.00 35.83 2.40
1990 7808 8.364894 GGTACACCAACAAAGGATTTTAAGATT 58.635 33.333 0.00 0.00 33.45 2.40
1993 7811 9.143155 ACACCAACAAAGGATTTTAAGATTAGT 57.857 29.630 0.00 0.00 35.03 2.24
2075 7953 1.665679 GACGGATGAACGCATGAATGT 59.334 47.619 0.00 0.00 34.11 2.71
2081 7959 0.794229 GAACGCATGAATGTGGCACG 60.794 55.000 13.77 0.29 42.35 5.34
2082 7960 2.100797 CGCATGAATGTGGCACGG 59.899 61.111 13.77 0.00 34.78 4.94
2083 7961 2.397754 CGCATGAATGTGGCACGGA 61.398 57.895 13.77 0.00 34.78 4.69
2159 8282 1.605457 GGATGTCAGACGCTTGTGTGA 60.605 52.381 0.00 0.00 42.96 3.58
2285 8739 1.202698 GCGTTGGAGATGCCCTTATCT 60.203 52.381 0.00 0.00 40.02 1.98
2293 8747 7.872061 TGGAGATGCCCTTATCTTCTTTATA 57.128 36.000 0.00 0.00 37.53 0.98
2372 8828 7.819900 ACATGACATCTTAGAAACTACAGGTTC 59.180 37.037 0.00 0.00 37.12 3.62
2436 8893 1.748950 TTTGATCTGCTTATGCCGCA 58.251 45.000 0.00 0.00 38.71 5.69
2483 8940 1.824230 GGCTGTCAAATTGCCATGGTA 59.176 47.619 14.67 5.86 45.46 3.25
2561 9022 0.108186 TTCACTGCAGATGGTAGGCG 60.108 55.000 23.35 0.00 32.86 5.52
2564 9025 1.886313 CTGCAGATGGTAGGCGCAG 60.886 63.158 8.42 0.00 43.55 5.18
2618 9079 3.002791 TGGCTTCTGCTCAGAAAATACG 58.997 45.455 12.72 3.34 45.75 3.06
2897 9435 1.600107 GGGGTGCACCGACATAAGA 59.400 57.895 29.08 0.00 41.60 2.10
2932 9470 0.620556 TCATCCTCCCAAAGCAGACC 59.379 55.000 0.00 0.00 0.00 3.85
3063 9601 2.421725 TGGAGAAGGTGGATATGGCAT 58.578 47.619 4.88 4.88 0.00 4.40
3194 9732 6.656902 AGGACATCACATATCAACATTGTCT 58.343 36.000 0.00 0.00 34.23 3.41
3425 9963 8.801299 TCAAGCCTCAGAATATACTTCTAGATG 58.199 37.037 4.14 4.14 0.00 2.90
3448 9986 4.178545 AGATTTTTGTCCCAAGATTGCG 57.821 40.909 0.00 0.00 0.00 4.85
3608 10146 6.438425 TGTCTATAGCTATGGAATGATGCTCA 59.562 38.462 20.12 9.45 32.66 4.26
3893 10431 1.739067 GTTCCTTTCATGTCCCTCGG 58.261 55.000 0.00 0.00 0.00 4.63
3911 10449 0.935196 GGTCCCGTCATATTTGTCGC 59.065 55.000 0.00 0.00 33.82 5.19
4036 10581 6.475504 TCCCACTGCATTACCATTATGATAG 58.524 40.000 0.00 0.00 0.00 2.08
4090 10654 1.662629 CGTTGCATGGTGTCTCTCATC 59.337 52.381 0.00 0.00 0.00 2.92
4336 10903 3.259902 GACCTGACGACCCTACAAAATC 58.740 50.000 0.00 0.00 0.00 2.17
4424 10991 8.603242 ATCTTATCCACGAACCAAACATATAC 57.397 34.615 0.00 0.00 0.00 1.47
4503 11077 3.461085 AGTGGCCAGATCAACCATAGAAT 59.539 43.478 5.11 0.00 35.53 2.40
4667 11241 0.450983 GTTACTCTCCCTCGACACCG 59.549 60.000 0.00 0.00 37.07 4.94
4796 11390 1.153369 GTAGCTCCGGAATGCAGCA 60.153 57.895 17.13 0.00 31.98 4.41
4834 11428 1.067416 GTATCACGGCGAGATGGCA 59.933 57.895 26.37 7.09 45.16 4.92
4899 11495 2.894387 GGCAGATCAGCCGACAGC 60.894 66.667 13.94 0.00 46.12 4.40
4900 11496 3.670637 GGCAGATCAGCCGACAGCA 62.671 63.158 13.94 0.00 46.12 4.41
4918 11515 1.002134 AGCGGCCTAACACTTGCAT 60.002 52.632 0.00 0.00 0.00 3.96
4923 11520 3.314080 GCGGCCTAACACTTGCATATTTA 59.686 43.478 0.00 0.00 0.00 1.40
4941 11538 1.204146 TATGCTCTCGGCCTTTTCCT 58.796 50.000 0.00 0.00 40.92 3.36
4942 11539 1.204146 ATGCTCTCGGCCTTTTCCTA 58.796 50.000 0.00 0.00 40.92 2.94
4955 11552 4.021981 GCCTTTTCCTAGTTCACTGCAAAT 60.022 41.667 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.833151 TAATCCGGCTCAGGGGTGGT 62.833 60.000 0.00 0.00 0.00 4.16
7 8 2.044806 CTAATCCGGCTCAGGGGTGG 62.045 65.000 0.00 0.00 0.00 4.61
8 9 1.447643 CTAATCCGGCTCAGGGGTG 59.552 63.158 0.00 0.00 0.00 4.61
9 10 2.444256 GCTAATCCGGCTCAGGGGT 61.444 63.158 0.00 0.00 0.00 4.95
10 11 2.143419 AGCTAATCCGGCTCAGGGG 61.143 63.158 0.00 0.00 34.70 4.79
11 12 3.555967 AGCTAATCCGGCTCAGGG 58.444 61.111 0.00 0.00 34.70 4.45
31 32 5.083821 ACAAGCCCCAAAGATAGCTAAAAA 58.916 37.500 0.00 0.00 34.49 1.94
32 33 4.672899 ACAAGCCCCAAAGATAGCTAAAA 58.327 39.130 0.00 0.00 34.49 1.52
33 34 4.316025 ACAAGCCCCAAAGATAGCTAAA 57.684 40.909 0.00 0.00 34.49 1.85
34 35 4.018415 AGAACAAGCCCCAAAGATAGCTAA 60.018 41.667 0.00 0.00 34.49 3.09
35 36 3.523564 AGAACAAGCCCCAAAGATAGCTA 59.476 43.478 0.00 0.00 34.49 3.32
36 37 2.310052 AGAACAAGCCCCAAAGATAGCT 59.690 45.455 0.00 0.00 37.10 3.32
37 38 2.424956 CAGAACAAGCCCCAAAGATAGC 59.575 50.000 0.00 0.00 0.00 2.97
38 39 2.424956 GCAGAACAAGCCCCAAAGATAG 59.575 50.000 0.00 0.00 0.00 2.08
39 40 2.041620 AGCAGAACAAGCCCCAAAGATA 59.958 45.455 0.00 0.00 0.00 1.98
40 41 1.203100 AGCAGAACAAGCCCCAAAGAT 60.203 47.619 0.00 0.00 0.00 2.40
41 42 0.185901 AGCAGAACAAGCCCCAAAGA 59.814 50.000 0.00 0.00 0.00 2.52
42 43 0.316204 CAGCAGAACAAGCCCCAAAG 59.684 55.000 0.00 0.00 0.00 2.77
43 44 0.396974 ACAGCAGAACAAGCCCCAAA 60.397 50.000 0.00 0.00 0.00 3.28
44 45 1.108727 CACAGCAGAACAAGCCCCAA 61.109 55.000 0.00 0.00 0.00 4.12
45 46 1.529010 CACAGCAGAACAAGCCCCA 60.529 57.895 0.00 0.00 0.00 4.96
46 47 2.924105 GCACAGCAGAACAAGCCCC 61.924 63.158 0.00 0.00 0.00 5.80
47 48 2.647297 GCACAGCAGAACAAGCCC 59.353 61.111 0.00 0.00 0.00 5.19
48 49 2.647297 GGCACAGCAGAACAAGCC 59.353 61.111 0.00 0.00 34.71 4.35
49 50 2.647297 GGGCACAGCAGAACAAGC 59.353 61.111 0.00 0.00 0.00 4.01
50 51 1.521450 CTGGGGCACAGCAGAACAAG 61.521 60.000 2.59 0.00 40.97 3.16
51 52 1.529010 CTGGGGCACAGCAGAACAA 60.529 57.895 2.59 0.00 40.97 2.83
52 53 2.113774 CTGGGGCACAGCAGAACA 59.886 61.111 2.59 0.00 40.97 3.18
63 64 1.588082 CACAAAGTCATGCTGGGGC 59.412 57.895 0.00 0.00 39.26 5.80
64 65 1.588082 GCACAAAGTCATGCTGGGG 59.412 57.895 0.00 0.00 38.84 4.96
65 66 0.896940 AGGCACAAAGTCATGCTGGG 60.897 55.000 0.00 0.00 41.74 4.45
66 67 0.963962 AAGGCACAAAGTCATGCTGG 59.036 50.000 0.00 0.00 41.74 4.85
67 68 4.082625 TGAATAAGGCACAAAGTCATGCTG 60.083 41.667 0.00 0.00 41.74 4.41
68 69 4.081406 TGAATAAGGCACAAAGTCATGCT 58.919 39.130 0.00 0.00 41.74 3.79
69 70 4.439305 TGAATAAGGCACAAAGTCATGC 57.561 40.909 0.00 0.00 41.29 4.06
70 71 8.192774 ACATTATGAATAAGGCACAAAGTCATG 58.807 33.333 0.00 0.00 33.49 3.07
71 72 8.192774 CACATTATGAATAAGGCACAAAGTCAT 58.807 33.333 0.00 0.00 35.11 3.06
72 73 7.176515 ACACATTATGAATAAGGCACAAAGTCA 59.823 33.333 0.00 0.00 0.00 3.41
73 74 7.538575 ACACATTATGAATAAGGCACAAAGTC 58.461 34.615 0.00 0.00 0.00 3.01
74 75 7.466746 ACACATTATGAATAAGGCACAAAGT 57.533 32.000 0.00 0.00 0.00 2.66
75 76 7.276218 CCAACACATTATGAATAAGGCACAAAG 59.724 37.037 0.00 0.00 0.00 2.77
76 77 7.039434 TCCAACACATTATGAATAAGGCACAAA 60.039 33.333 0.00 0.00 0.00 2.83
77 78 6.435591 TCCAACACATTATGAATAAGGCACAA 59.564 34.615 0.00 0.00 0.00 3.33
78 79 5.948758 TCCAACACATTATGAATAAGGCACA 59.051 36.000 0.00 0.00 0.00 4.57
79 80 6.449635 TCCAACACATTATGAATAAGGCAC 57.550 37.500 0.00 0.00 0.00 5.01
80 81 7.560991 AGAATCCAACACATTATGAATAAGGCA 59.439 33.333 0.00 0.00 0.00 4.75
81 82 7.945134 AGAATCCAACACATTATGAATAAGGC 58.055 34.615 0.00 0.00 0.00 4.35
82 83 9.740239 CAAGAATCCAACACATTATGAATAAGG 57.260 33.333 0.00 0.00 0.00 2.69
83 84 9.740239 CCAAGAATCCAACACATTATGAATAAG 57.260 33.333 0.00 0.00 0.00 1.73
84 85 9.253832 ACCAAGAATCCAACACATTATGAATAA 57.746 29.630 0.00 0.00 0.00 1.40
85 86 8.821686 ACCAAGAATCCAACACATTATGAATA 57.178 30.769 0.00 0.00 0.00 1.75
86 87 7.147846 GGACCAAGAATCCAACACATTATGAAT 60.148 37.037 0.00 0.00 36.15 2.57
87 88 6.152661 GGACCAAGAATCCAACACATTATGAA 59.847 38.462 0.00 0.00 36.15 2.57
88 89 5.652014 GGACCAAGAATCCAACACATTATGA 59.348 40.000 0.00 0.00 36.15 2.15
89 90 5.449041 CGGACCAAGAATCCAACACATTATG 60.449 44.000 0.00 0.00 35.83 1.90
90 91 4.640201 CGGACCAAGAATCCAACACATTAT 59.360 41.667 0.00 0.00 35.83 1.28
91 92 4.006989 CGGACCAAGAATCCAACACATTA 58.993 43.478 0.00 0.00 35.83 1.90
92 93 2.819608 CGGACCAAGAATCCAACACATT 59.180 45.455 0.00 0.00 35.83 2.71
93 94 2.224769 ACGGACCAAGAATCCAACACAT 60.225 45.455 0.00 0.00 35.83 3.21
94 95 1.142060 ACGGACCAAGAATCCAACACA 59.858 47.619 0.00 0.00 35.83 3.72
95 96 1.892209 ACGGACCAAGAATCCAACAC 58.108 50.000 0.00 0.00 35.83 3.32
96 97 2.226330 CAACGGACCAAGAATCCAACA 58.774 47.619 0.00 0.00 35.83 3.33
97 98 1.068541 GCAACGGACCAAGAATCCAAC 60.069 52.381 0.00 0.00 35.83 3.77
98 99 1.202879 AGCAACGGACCAAGAATCCAA 60.203 47.619 0.00 0.00 35.83 3.53
99 100 0.400213 AGCAACGGACCAAGAATCCA 59.600 50.000 0.00 0.00 35.83 3.41
100 101 1.534729 AAGCAACGGACCAAGAATCC 58.465 50.000 0.00 0.00 0.00 3.01
101 102 4.965119 ATAAAGCAACGGACCAAGAATC 57.035 40.909 0.00 0.00 0.00 2.52
102 103 8.691661 ATATTATAAAGCAACGGACCAAGAAT 57.308 30.769 0.00 0.00 0.00 2.40
103 104 9.616156 TTATATTATAAAGCAACGGACCAAGAA 57.384 29.630 0.00 0.00 0.00 2.52
104 105 9.616156 TTTATATTATAAAGCAACGGACCAAGA 57.384 29.630 5.01 0.00 0.00 3.02
105 106 9.878599 CTTTATATTATAAAGCAACGGACCAAG 57.121 33.333 18.54 0.00 0.00 3.61
106 107 9.398538 ACTTTATATTATAAAGCAACGGACCAA 57.601 29.630 25.76 0.00 37.89 3.67
107 108 8.832521 CACTTTATATTATAAAGCAACGGACCA 58.167 33.333 25.76 0.00 37.89 4.02
108 109 8.287503 CCACTTTATATTATAAAGCAACGGACC 58.712 37.037 25.76 0.00 37.89 4.46
109 110 8.287503 CCCACTTTATATTATAAAGCAACGGAC 58.712 37.037 25.76 0.00 37.89 4.79
110 111 7.446013 CCCCACTTTATATTATAAAGCAACGGA 59.554 37.037 25.76 0.03 37.89 4.69
111 112 7.308951 CCCCCACTTTATATTATAAAGCAACGG 60.309 40.741 25.76 21.17 37.89 4.44
112 113 7.446013 TCCCCCACTTTATATTATAAAGCAACG 59.554 37.037 25.76 16.15 37.89 4.10
113 114 8.700439 TCCCCCACTTTATATTATAAAGCAAC 57.300 34.615 25.76 0.00 37.89 4.17
114 115 9.716556 TTTCCCCCACTTTATATTATAAAGCAA 57.283 29.630 25.76 12.66 37.89 3.91
115 116 9.138596 GTTTCCCCCACTTTATATTATAAAGCA 57.861 33.333 25.76 8.96 37.89 3.91
116 117 8.582437 GGTTTCCCCCACTTTATATTATAAAGC 58.418 37.037 25.76 12.65 37.89 3.51
135 136 5.353394 ACTTTTGAGAAAAAGGGTTTCCC 57.647 39.130 13.75 0.00 45.90 3.97
136 137 7.705325 GTCTTACTTTTGAGAAAAAGGGTTTCC 59.295 37.037 13.75 0.00 42.48 3.13
137 138 8.467598 AGTCTTACTTTTGAGAAAAAGGGTTTC 58.532 33.333 13.75 0.00 42.48 2.78
138 139 8.362464 AGTCTTACTTTTGAGAAAAAGGGTTT 57.638 30.769 13.75 0.00 42.48 3.27
139 140 7.201705 CGAGTCTTACTTTTGAGAAAAAGGGTT 60.202 37.037 13.75 0.00 42.48 4.11
140 141 6.260271 CGAGTCTTACTTTTGAGAAAAAGGGT 59.740 38.462 13.75 0.13 42.48 4.34
141 142 6.293462 CCGAGTCTTACTTTTGAGAAAAAGGG 60.293 42.308 13.75 5.61 42.48 3.95
142 143 6.482308 TCCGAGTCTTACTTTTGAGAAAAAGG 59.518 38.462 13.75 0.00 42.48 3.11
143 144 7.478520 TCCGAGTCTTACTTTTGAGAAAAAG 57.521 36.000 8.92 8.92 43.49 2.27
144 145 6.018180 GCTCCGAGTCTTACTTTTGAGAAAAA 60.018 38.462 0.00 0.00 0.00 1.94
145 146 5.465724 GCTCCGAGTCTTACTTTTGAGAAAA 59.534 40.000 0.00 0.00 0.00 2.29
146 147 4.989168 GCTCCGAGTCTTACTTTTGAGAAA 59.011 41.667 0.00 0.00 0.00 2.52
147 148 4.557205 GCTCCGAGTCTTACTTTTGAGAA 58.443 43.478 0.00 0.00 0.00 2.87
148 149 3.056749 GGCTCCGAGTCTTACTTTTGAGA 60.057 47.826 0.00 0.00 0.00 3.27
149 150 3.254892 GGCTCCGAGTCTTACTTTTGAG 58.745 50.000 0.00 0.00 0.00 3.02
150 151 2.028385 GGGCTCCGAGTCTTACTTTTGA 60.028 50.000 0.00 0.00 0.00 2.69
151 152 2.028020 AGGGCTCCGAGTCTTACTTTTG 60.028 50.000 0.00 0.00 0.00 2.44
152 153 2.258109 AGGGCTCCGAGTCTTACTTTT 58.742 47.619 0.00 0.00 0.00 2.27
153 154 1.939980 AGGGCTCCGAGTCTTACTTT 58.060 50.000 0.00 0.00 0.00 2.66
154 155 1.550976 CAAGGGCTCCGAGTCTTACTT 59.449 52.381 0.00 0.00 0.00 2.24
159 160 1.985116 GGTCAAGGGCTCCGAGTCT 60.985 63.158 0.00 0.00 0.00 3.24
164 165 3.612247 CTGTGGGTCAAGGGCTCCG 62.612 68.421 0.00 0.00 0.00 4.63
169 170 1.304282 CCATCCTGTGGGTCAAGGG 59.696 63.158 0.00 0.00 44.79 3.95
220 221 4.009675 TCAGGCCAGTAATTAACTTGCTG 58.990 43.478 5.01 7.98 44.40 4.41
313 3729 4.814771 ACACCGCCAGCTAATTAATCTAAC 59.185 41.667 0.00 0.00 0.00 2.34
388 4120 1.933853 CGCAGTCCAAGGTAAGCATAC 59.066 52.381 0.00 0.00 0.00 2.39
505 4238 7.998383 TGAGTATATACAGGCAACCAAATCATT 59.002 33.333 15.18 0.00 37.17 2.57
608 6396 7.340232 AGCTGACTCATTTATTTTGCCTTATCA 59.660 33.333 0.00 0.00 0.00 2.15
609 6397 7.646922 CAGCTGACTCATTTATTTTGCCTTATC 59.353 37.037 8.42 0.00 0.00 1.75
793 6581 1.648467 GAACGCAATCAGGAGTGGCC 61.648 60.000 0.00 0.00 0.00 5.36
801 6589 1.734465 GAAGACCTGGAACGCAATCAG 59.266 52.381 0.00 0.00 0.00 2.90
803 6591 1.087501 GGAAGACCTGGAACGCAATC 58.912 55.000 0.00 0.00 0.00 2.67
871 6659 4.133078 GGGAATGGAATCATCTCACAGTC 58.867 47.826 0.00 0.00 32.24 3.51
875 6663 3.582998 TGGGGAATGGAATCATCTCAC 57.417 47.619 0.00 0.00 32.24 3.51
998 6786 1.273267 ACCAGTAGACAGGAGCCATCA 60.273 52.381 0.00 0.00 0.00 3.07
1047 6835 2.573869 CCGACGAGCATCAGTGGT 59.426 61.111 0.00 0.00 39.13 4.16
1118 6906 0.678395 CGGATCAGAGATGGTGAGGG 59.322 60.000 0.00 0.00 0.00 4.30
1286 7082 2.061773 CTTCATCAACGACTCGCAAGT 58.938 47.619 0.00 0.00 38.88 3.16
1416 7212 2.852449 TCCTCCGTGCAATTGTACAAA 58.148 42.857 23.74 11.51 0.00 2.83
1522 7333 2.571757 GTCGTGATGCACTCCCGA 59.428 61.111 0.00 0.00 31.34 5.14
1761 7574 4.220382 TGCAAACAAATTAGGCACTGCTAT 59.780 37.500 0.00 0.00 41.52 2.97
1762 7575 3.571828 TGCAAACAAATTAGGCACTGCTA 59.428 39.130 0.00 0.00 41.52 3.49
1875 7690 6.599445 ACTAATCTCAAATTGGGGATCTCAG 58.401 40.000 0.00 0.00 0.00 3.35
1922 7740 9.390582 GCTTCATAATATAAAGCGGGGGAAACC 62.391 44.444 0.00 0.00 42.18 3.27
1923 7741 6.569801 GCTTCATAATATAAAGCGGGGGAAAC 60.570 42.308 0.00 0.00 36.41 2.78
1924 7742 5.475564 GCTTCATAATATAAAGCGGGGGAAA 59.524 40.000 0.00 0.00 36.41 3.13
1925 7743 5.007682 GCTTCATAATATAAAGCGGGGGAA 58.992 41.667 0.00 0.00 36.41 3.97
1926 7744 4.042311 TGCTTCATAATATAAAGCGGGGGA 59.958 41.667 3.90 0.00 46.54 4.81
1927 7745 4.331968 TGCTTCATAATATAAAGCGGGGG 58.668 43.478 3.90 0.00 46.54 5.40
1928 7746 5.335661 GGTTGCTTCATAATATAAAGCGGGG 60.336 44.000 3.90 0.00 46.54 5.73
1929 7747 5.616866 CGGTTGCTTCATAATATAAAGCGGG 60.617 44.000 3.90 0.00 46.54 6.13
1930 7748 5.382303 CGGTTGCTTCATAATATAAAGCGG 58.618 41.667 3.90 0.00 46.54 5.52
1931 7749 4.846137 GCGGTTGCTTCATAATATAAAGCG 59.154 41.667 3.90 0.00 46.54 4.68
1932 7750 5.757886 TGCGGTTGCTTCATAATATAAAGC 58.242 37.500 1.21 1.21 44.41 3.51
1933 7751 7.584108 TCATGCGGTTGCTTCATAATATAAAG 58.416 34.615 0.00 0.00 43.34 1.85
1934 7752 7.503521 TCATGCGGTTGCTTCATAATATAAA 57.496 32.000 0.00 0.00 43.34 1.40
1935 7753 7.503521 TTCATGCGGTTGCTTCATAATATAA 57.496 32.000 0.00 0.00 43.34 0.98
1936 7754 7.503521 TTTCATGCGGTTGCTTCATAATATA 57.496 32.000 0.00 0.00 43.34 0.86
1937 7755 6.389830 TTTCATGCGGTTGCTTCATAATAT 57.610 33.333 0.00 0.00 43.34 1.28
1938 7756 5.826601 TTTCATGCGGTTGCTTCATAATA 57.173 34.783 0.00 0.00 43.34 0.98
1939 7757 4.717233 TTTCATGCGGTTGCTTCATAAT 57.283 36.364 0.00 0.00 43.34 1.28
1940 7758 4.717233 ATTTCATGCGGTTGCTTCATAA 57.283 36.364 0.00 0.00 43.34 1.90
1941 7759 4.275689 CCTATTTCATGCGGTTGCTTCATA 59.724 41.667 0.00 0.00 43.34 2.15
1942 7760 3.067180 CCTATTTCATGCGGTTGCTTCAT 59.933 43.478 0.00 0.00 43.34 2.57
1943 7761 2.423185 CCTATTTCATGCGGTTGCTTCA 59.577 45.455 0.00 0.00 43.34 3.02
1944 7762 2.223572 CCCTATTTCATGCGGTTGCTTC 60.224 50.000 0.00 0.00 43.34 3.86
1945 7763 1.750778 CCCTATTTCATGCGGTTGCTT 59.249 47.619 0.00 0.00 43.34 3.91
1946 7764 1.340991 ACCCTATTTCATGCGGTTGCT 60.341 47.619 0.00 0.00 43.34 3.91
1947 7765 1.102978 ACCCTATTTCATGCGGTTGC 58.897 50.000 0.00 0.00 43.20 4.17
1948 7766 3.064820 GTGTACCCTATTTCATGCGGTTG 59.935 47.826 0.00 0.00 0.00 3.77
1949 7767 3.275999 GTGTACCCTATTTCATGCGGTT 58.724 45.455 0.00 0.00 0.00 4.44
1950 7768 2.420967 GGTGTACCCTATTTCATGCGGT 60.421 50.000 0.00 0.00 0.00 5.68
1951 7769 2.218603 GGTGTACCCTATTTCATGCGG 58.781 52.381 0.00 0.00 0.00 5.69
1952 7770 2.912771 TGGTGTACCCTATTTCATGCG 58.087 47.619 0.00 0.00 34.29 4.73
1953 7771 4.013728 TGTTGGTGTACCCTATTTCATGC 58.986 43.478 0.00 0.00 34.29 4.06
1954 7772 6.350110 CCTTTGTTGGTGTACCCTATTTCATG 60.350 42.308 0.00 0.00 34.29 3.07
1955 7773 5.714806 CCTTTGTTGGTGTACCCTATTTCAT 59.285 40.000 0.00 0.00 34.29 2.57
1956 7774 5.074115 CCTTTGTTGGTGTACCCTATTTCA 58.926 41.667 0.00 0.00 34.29 2.69
1957 7775 5.318630 TCCTTTGTTGGTGTACCCTATTTC 58.681 41.667 0.00 0.00 34.29 2.17
1958 7776 5.327737 TCCTTTGTTGGTGTACCCTATTT 57.672 39.130 0.00 0.00 34.29 1.40
1959 7777 5.530176 ATCCTTTGTTGGTGTACCCTATT 57.470 39.130 0.00 0.00 34.29 1.73
1960 7778 5.530176 AATCCTTTGTTGGTGTACCCTAT 57.470 39.130 0.00 0.00 34.29 2.57
1961 7779 5.327737 AAATCCTTTGTTGGTGTACCCTA 57.672 39.130 0.00 0.00 34.29 3.53
1962 7780 3.895704 AATCCTTTGTTGGTGTACCCT 57.104 42.857 0.00 0.00 34.29 4.34
1963 7781 4.948341 AAAATCCTTTGTTGGTGTACCC 57.052 40.909 0.00 0.00 34.29 3.69
1964 7782 7.279750 TCTTAAAATCCTTTGTTGGTGTACC 57.720 36.000 0.00 0.00 0.00 3.34
1967 7785 9.143155 ACTAATCTTAAAATCCTTTGTTGGTGT 57.857 29.630 0.00 0.00 0.00 4.16
1997 7815 9.295825 ACCAAGTCAAAATCATGTACTAATTCA 57.704 29.630 0.00 0.00 0.00 2.57
1998 7816 9.774742 GACCAAGTCAAAATCATGTACTAATTC 57.225 33.333 0.00 0.00 32.09 2.17
1999 7817 9.295825 TGACCAAGTCAAAATCATGTACTAATT 57.704 29.630 0.00 0.00 39.78 1.40
2172 8617 3.138798 GGTCCGCTCGGCAGTCTA 61.139 66.667 2.96 0.00 34.68 2.59
2177 8622 3.896133 GTATCGGTCCGCTCGGCA 61.896 66.667 6.34 0.00 34.68 5.69
2293 8747 4.660789 AGCTCAGCTGAACAAACAAAAT 57.339 36.364 18.85 0.00 37.57 1.82
2372 8828 3.378427 TCAGTAGACCGACATCACATCAG 59.622 47.826 0.00 0.00 0.00 2.90
2436 8893 5.334414 GCGCAACTAGCTATTAGAAATGCAT 60.334 40.000 0.30 0.00 42.61 3.96
2561 9022 7.315890 ACCTATCAAAATTAACTTCTTGCTGC 58.684 34.615 0.00 0.00 0.00 5.25
2618 9079 9.813080 GTATGAAAGTTTGAGACAAAGTATCAC 57.187 33.333 0.00 0.00 33.38 3.06
2754 9281 4.811557 GCATGAGACTGTGTAAACTATCCC 59.188 45.833 0.00 0.00 0.00 3.85
2897 9435 7.037297 TGGGAGGATGAGAAGACTAATCTTTTT 60.037 37.037 0.00 0.00 45.60 1.94
2932 9470 6.618287 TCTTCCATGCTTGATTTATTACCG 57.382 37.500 0.22 0.00 0.00 4.02
3194 9732 1.388547 AAGCAAAAACCGAGCAGACA 58.611 45.000 0.00 0.00 0.00 3.41
3223 9761 2.749621 CTCATAAACAAGGGCTCGCTTT 59.250 45.455 0.00 0.00 0.00 3.51
3608 10146 3.747852 TCCTTCCTCCTACCATTTCCAT 58.252 45.455 0.00 0.00 0.00 3.41
3688 10226 4.467795 ACCTGTTCTGCTACACTGTCATAT 59.532 41.667 0.00 0.00 0.00 1.78
3698 10236 4.814771 ACAAGTTTGTACCTGTTCTGCTAC 59.185 41.667 0.00 0.00 40.16 3.58
3893 10431 0.935196 GGCGACAAATATGACGGGAC 59.065 55.000 3.26 0.00 43.36 4.46
3911 10449 2.809119 TGTAACCATAACTTGTGTGCGG 59.191 45.455 0.00 0.00 0.00 5.69
3961 10499 4.650972 TCCTTTTGGCTATGGTAACAGT 57.349 40.909 0.00 0.00 46.42 3.55
4008 10551 6.610830 TCATAATGGTAATGCAGTGGGAATTT 59.389 34.615 0.00 0.00 0.00 1.82
4013 10556 6.240894 ACTATCATAATGGTAATGCAGTGGG 58.759 40.000 0.00 0.00 0.00 4.61
4078 10642 0.531532 CGGCCATGATGAGAGACACC 60.532 60.000 2.24 0.00 0.00 4.16
4090 10654 2.676121 TCAAACAGCCCGGCCATG 60.676 61.111 5.55 0.79 0.00 3.66
4219 10784 9.856488 CGTACTACGACCCTTACTTATACTATA 57.144 37.037 2.17 0.00 46.05 1.31
4234 10801 6.777526 ATCTATGACTTACGTACTACGACC 57.222 41.667 15.49 0.80 46.05 4.79
4257 10824 1.570501 TCCGAGGCCCCTAACTACTTA 59.429 52.381 0.00 0.00 0.00 2.24
4394 10961 7.613585 TGTTTGGTTCGTGGATAAGATACTTA 58.386 34.615 0.00 0.00 0.00 2.24
4424 10991 4.001652 AGAGCAATATGATCCGCTGATTG 58.998 43.478 0.00 0.00 32.25 2.67
4489 11056 6.179906 TCCCTTCTGATTCTATGGTTGATC 57.820 41.667 0.00 0.00 0.00 2.92
4503 11077 0.973632 TTAAGTGCGCTCCCTTCTGA 59.026 50.000 9.73 0.00 0.00 3.27
4746 11340 1.435515 GCGACGAAGAGCCTCTCAT 59.564 57.895 0.00 0.00 32.06 2.90
4819 11413 4.794439 CGTGCCATCTCGCCGTGA 62.794 66.667 0.00 0.00 0.00 4.35
4895 11491 2.358737 GTGTTAGGCCGCTGCTGT 60.359 61.111 0.00 0.00 37.74 4.40
4897 11493 1.672356 CAAGTGTTAGGCCGCTGCT 60.672 57.895 0.00 0.00 37.74 4.24
4899 11495 1.308069 ATGCAAGTGTTAGGCCGCTG 61.308 55.000 0.00 0.00 0.00 5.18
4900 11496 0.251916 TATGCAAGTGTTAGGCCGCT 59.748 50.000 0.00 0.00 0.00 5.52
4918 11515 4.134563 GGAAAAGGCCGAGAGCATAAATA 58.865 43.478 0.00 0.00 46.50 1.40
4923 11520 1.139853 CTAGGAAAAGGCCGAGAGCAT 59.860 52.381 0.00 0.00 46.50 3.79
4941 11538 8.715191 ATTTTTGTTTGATTTGCAGTGAACTA 57.285 26.923 0.00 0.00 0.00 2.24
4942 11539 7.614124 ATTTTTGTTTGATTTGCAGTGAACT 57.386 28.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.