Multiple sequence alignment - TraesCS6D01G245200

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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 TraesCS6D01G245200 chr6D 100.000 4907 0 0 1 4907 347157262 347152356 0.000000e+00 9062.0
1 TraesCS6D01G245200 chr6D 77.979 386 74 9 125 503 254867368 254867749 1.060000e-56 231.0
2 TraesCS6D01G245200 chr6D 94.000 50 3 0 514 563 387414712 387414663 5.270000e-10 76.8
3 TraesCS6D01G245200 chr6D 100.000 28 0 0 4177 4204 411785197 411785170 9.000000e-03 52.8
4 TraesCS6D01G245200 chr6B 93.502 4109 165 31 142 4204 533528479 533532531 0.000000e+00 6015.0
5 TraesCS6D01G245200 chr6A 92.164 2093 92 27 875 2935 496234335 496236387 0.000000e+00 2891.0
6 TraesCS6D01G245200 chr6A 90.380 1237 61 29 2977 4204 496236799 496237986 0.000000e+00 1572.0
7 TraesCS6D01G245200 chr6A 88.802 384 32 9 125 503 496211260 496211637 1.240000e-125 460.0
8 TraesCS6D01G245200 chr6A 95.082 122 6 0 1 122 137682027 137682148 5.010000e-45 193.0
9 TraesCS6D01G245200 chr6A 93.056 72 1 2 744 811 496234263 496234334 8.690000e-18 102.0
10 TraesCS6D01G245200 chr6A 97.872 47 1 0 2932 2978 496236621 496236667 1.130000e-11 82.4
11 TraesCS6D01G245200 chr4D 95.461 705 27 3 4207 4907 461002126 461002829 0.000000e+00 1120.0
12 TraesCS6D01G245200 chr4D 94.017 702 41 1 4207 4907 274757744 274757043 0.000000e+00 1062.0
13 TraesCS6D01G245200 chr2D 94.971 696 32 3 4207 4900 564661662 564660968 0.000000e+00 1088.0
14 TraesCS6D01G245200 chr2D 93.352 707 40 3 4207 4907 588812533 588811828 0.000000e+00 1038.0
15 TraesCS6D01G245200 chr3B 93.750 704 40 3 4207 4907 82876400 82877102 0.000000e+00 1053.0
16 TraesCS6D01G245200 chr3B 78.329 383 78 4 125 503 828599371 828598990 4.910000e-60 243.0
17 TraesCS6D01G245200 chr3A 93.590 702 44 1 4207 4907 115172922 115173623 0.000000e+00 1046.0
18 TraesCS6D01G245200 chr5D 93.457 703 41 5 4207 4907 105664366 105663667 0.000000e+00 1038.0
19 TraesCS6D01G245200 chr3D 93.191 705 41 7 4206 4907 403727948 403727248 0.000000e+00 1029.0
20 TraesCS6D01G245200 chr3D 93.172 703 42 5 4206 4907 288486846 288486149 0.000000e+00 1027.0
21 TraesCS6D01G245200 chrUn 78.796 382 78 3 125 503 278965489 278965108 2.270000e-63 254.0
22 TraesCS6D01G245200 chrUn 94.400 125 7 0 1 125 32314137 32314013 5.010000e-45 193.0
23 TraesCS6D01G245200 chr5A 78.796 382 78 3 125 503 31672884 31672503 2.270000e-63 254.0
24 TraesCS6D01G245200 chr5A 78.796 382 78 3 125 503 31756070 31755689 2.270000e-63 254.0
25 TraesCS6D01G245200 chr5A 78.534 382 79 3 125 503 31607102 31606721 1.050000e-61 248.0
26 TraesCS6D01G245200 chr5A 78.590 383 77 5 125 503 31960820 31960439 1.050000e-61 248.0
27 TraesCS6D01G245200 chr5A 95.161 124 6 0 1 124 386702592 386702715 3.870000e-46 196.0
28 TraesCS6D01G245200 chr5A 93.701 127 8 0 1 127 11747817 11747943 1.800000e-44 191.0
29 TraesCS6D01G245200 chr4A 97.710 131 2 1 1 131 58342649 58342778 1.780000e-54 224.0
30 TraesCS6D01G245200 chr7B 95.161 124 6 0 1 124 293130687 293130810 3.870000e-46 196.0
31 TraesCS6D01G245200 chr2A 95.161 124 6 0 1 124 775983488 775983611 3.870000e-46 196.0
32 TraesCS6D01G245200 chr2B 94.400 125 7 0 1 125 201247898 201247774 5.010000e-45 193.0
33 TraesCS6D01G245200 chr7D 94.355 124 7 0 1 124 111108135 111108258 1.800000e-44 191.0


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 TraesCS6D01G245200 chr6D 347152356 347157262 4906 True 9062.00 9062 100.000 1 4907 1 chr6D.!!$R1 4906
1 TraesCS6D01G245200 chr6B 533528479 533532531 4052 False 6015.00 6015 93.502 142 4204 1 chr6B.!!$F1 4062
2 TraesCS6D01G245200 chr6A 496234263 496237986 3723 False 1161.85 2891 93.368 744 4204 4 chr6A.!!$F3 3460
3 TraesCS6D01G245200 chr4D 461002126 461002829 703 False 1120.00 1120 95.461 4207 4907 1 chr4D.!!$F1 700
4 TraesCS6D01G245200 chr4D 274757043 274757744 701 True 1062.00 1062 94.017 4207 4907 1 chr4D.!!$R1 700
5 TraesCS6D01G245200 chr2D 564660968 564661662 694 True 1088.00 1088 94.971 4207 4900 1 chr2D.!!$R1 693
6 TraesCS6D01G245200 chr2D 588811828 588812533 705 True 1038.00 1038 93.352 4207 4907 1 chr2D.!!$R2 700
7 TraesCS6D01G245200 chr3B 82876400 82877102 702 False 1053.00 1053 93.750 4207 4907 1 chr3B.!!$F1 700
8 TraesCS6D01G245200 chr3A 115172922 115173623 701 False 1046.00 1046 93.590 4207 4907 1 chr3A.!!$F1 700
9 TraesCS6D01G245200 chr5D 105663667 105664366 699 True 1038.00 1038 93.457 4207 4907 1 chr5D.!!$R1 700
10 TraesCS6D01G245200 chr3D 403727248 403727948 700 True 1029.00 1029 93.191 4206 4907 1 chr3D.!!$R2 701
11 TraesCS6D01G245200 chr3D 288486149 288486846 697 True 1027.00 1027 93.172 4206 4907 1 chr3D.!!$R1 701

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
261 262 0.179059 TTTGTCTCGAGGCAGCACAA 60.179 50.0 20.53 15.36 0.00 3.33 F
515 517 0.468226 AAAACTCGGTGCTCCACAGA 59.532 50.0 5.52 0.00 36.35 3.41 F
1942 1969 0.179161 CCGTCTAGAAGACCGCACAG 60.179 60.0 7.30 0.00 42.12 3.66 F
2420 2475 0.321564 GGGGAACTTGGCCAATTTGC 60.322 55.0 25.76 25.76 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1727 0.169672 GAGCGGCAGAACGTACTGTA 59.830 55.0 1.45 0.0 39.73 2.74 R
2106 2156 0.176910 TGAAACCACACTCTCGCACA 59.823 50.0 0.00 0.0 0.00 4.57 R
3851 4277 0.114168 TATGGCTGCTTGGGGTTTGT 59.886 50.0 0.00 0.0 0.00 2.83 R
4337 4771 2.092914 AGGCATACTAGGGACACTTTGC 60.093 50.0 0.00 0.0 0.00 3.68 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
25 26 7.923414 AATAGTTTGAGGACCAGAATAACAC 57.077 36.000 0.00 0.00 0.00 3.32
26 27 5.304686 AGTTTGAGGACCAGAATAACACA 57.695 39.130 0.00 0.00 0.00 3.72
27 28 5.063880 AGTTTGAGGACCAGAATAACACAC 58.936 41.667 0.00 0.00 0.00 3.82
28 29 4.698201 TTGAGGACCAGAATAACACACA 57.302 40.909 0.00 0.00 0.00 3.72
29 30 4.908601 TGAGGACCAGAATAACACACAT 57.091 40.909 0.00 0.00 0.00 3.21
30 31 6.367374 TTGAGGACCAGAATAACACACATA 57.633 37.500 0.00 0.00 0.00 2.29
31 32 6.560003 TGAGGACCAGAATAACACACATAT 57.440 37.500 0.00 0.00 0.00 1.78
32 33 6.957631 TGAGGACCAGAATAACACACATATT 58.042 36.000 0.00 0.00 0.00 1.28
33 34 6.823182 TGAGGACCAGAATAACACACATATTG 59.177 38.462 0.00 0.00 0.00 1.90
34 35 5.590259 AGGACCAGAATAACACACATATTGC 59.410 40.000 0.00 0.00 0.00 3.56
35 36 5.356751 GGACCAGAATAACACACATATTGCA 59.643 40.000 0.00 0.00 0.00 4.08
36 37 6.194796 ACCAGAATAACACACATATTGCAC 57.805 37.500 0.00 0.00 0.00 4.57
37 38 5.945784 ACCAGAATAACACACATATTGCACT 59.054 36.000 0.00 0.00 0.00 4.40
38 39 6.434028 ACCAGAATAACACACATATTGCACTT 59.566 34.615 0.00 0.00 0.00 3.16
39 40 7.039784 ACCAGAATAACACACATATTGCACTTT 60.040 33.333 0.00 0.00 0.00 2.66
40 41 7.274033 CCAGAATAACACACATATTGCACTTTG 59.726 37.037 0.00 0.00 0.00 2.77
41 42 8.022550 CAGAATAACACACATATTGCACTTTGA 58.977 33.333 1.62 0.00 0.00 2.69
42 43 8.239314 AGAATAACACACATATTGCACTTTGAG 58.761 33.333 1.62 0.00 0.00 3.02
43 44 4.771590 ACACACATATTGCACTTTGAGG 57.228 40.909 1.62 0.00 0.00 3.86
44 45 4.397420 ACACACATATTGCACTTTGAGGA 58.603 39.130 1.62 0.00 0.00 3.71
45 46 4.216257 ACACACATATTGCACTTTGAGGAC 59.784 41.667 1.62 0.00 0.00 3.85
46 47 3.758554 ACACATATTGCACTTTGAGGACC 59.241 43.478 1.62 0.00 0.00 4.46
47 48 4.012374 CACATATTGCACTTTGAGGACCT 58.988 43.478 0.00 0.00 0.00 3.85
48 49 4.012374 ACATATTGCACTTTGAGGACCTG 58.988 43.478 0.00 0.00 0.00 4.00
49 50 1.915141 ATTGCACTTTGAGGACCTGG 58.085 50.000 0.00 0.00 0.00 4.45
50 51 0.843309 TTGCACTTTGAGGACCTGGA 59.157 50.000 0.00 0.00 0.00 3.86
51 52 1.067295 TGCACTTTGAGGACCTGGAT 58.933 50.000 0.00 0.00 0.00 3.41
52 53 1.271543 TGCACTTTGAGGACCTGGATG 60.272 52.381 0.00 0.00 0.00 3.51
53 54 1.003580 GCACTTTGAGGACCTGGATGA 59.996 52.381 0.00 0.00 0.00 2.92
54 55 2.704572 CACTTTGAGGACCTGGATGAC 58.295 52.381 0.00 0.00 0.00 3.06
55 56 1.276421 ACTTTGAGGACCTGGATGACG 59.724 52.381 0.00 0.00 0.00 4.35
56 57 1.550524 CTTTGAGGACCTGGATGACGA 59.449 52.381 0.00 0.00 0.00 4.20
57 58 1.866015 TTGAGGACCTGGATGACGAT 58.134 50.000 0.00 0.00 0.00 3.73
58 59 1.866015 TGAGGACCTGGATGACGATT 58.134 50.000 0.00 0.00 0.00 3.34
59 60 3.026707 TGAGGACCTGGATGACGATTA 57.973 47.619 0.00 0.00 0.00 1.75
60 61 3.576861 TGAGGACCTGGATGACGATTAT 58.423 45.455 0.00 0.00 0.00 1.28
61 62 3.574396 TGAGGACCTGGATGACGATTATC 59.426 47.826 0.00 0.00 0.00 1.75
62 63 3.574396 GAGGACCTGGATGACGATTATCA 59.426 47.826 0.00 0.00 0.00 2.15
63 64 4.163427 AGGACCTGGATGACGATTATCAT 58.837 43.478 0.00 0.00 42.15 2.45
64 65 5.333581 AGGACCTGGATGACGATTATCATA 58.666 41.667 0.00 0.00 39.48 2.15
65 66 5.420421 AGGACCTGGATGACGATTATCATAG 59.580 44.000 0.00 0.00 39.48 2.23
66 67 5.186021 GGACCTGGATGACGATTATCATAGT 59.814 44.000 0.00 0.00 39.48 2.12
67 68 6.295349 GGACCTGGATGACGATTATCATAGTT 60.295 42.308 0.00 0.00 39.48 2.24
68 69 6.692486 ACCTGGATGACGATTATCATAGTTC 58.308 40.000 0.00 0.00 39.48 3.01
69 70 5.802451 CCTGGATGACGATTATCATAGTTCG 59.198 44.000 0.00 0.00 39.48 3.95
70 71 6.349363 CCTGGATGACGATTATCATAGTTCGA 60.349 42.308 6.20 0.00 39.48 3.71
71 72 6.612306 TGGATGACGATTATCATAGTTCGAG 58.388 40.000 6.20 0.00 39.48 4.04
72 73 6.030849 GGATGACGATTATCATAGTTCGAGG 58.969 44.000 6.20 0.00 39.48 4.63
73 74 6.127980 GGATGACGATTATCATAGTTCGAGGA 60.128 42.308 6.20 0.00 39.48 3.71
74 75 5.998553 TGACGATTATCATAGTTCGAGGAC 58.001 41.667 6.20 0.00 35.64 3.85
75 76 5.048921 TGACGATTATCATAGTTCGAGGACC 60.049 44.000 6.20 0.00 35.64 4.46
76 77 5.071370 ACGATTATCATAGTTCGAGGACCT 58.929 41.667 0.00 0.00 35.64 3.85
77 78 6.236409 ACGATTATCATAGTTCGAGGACCTA 58.764 40.000 0.00 0.00 35.64 3.08
78 79 6.149142 ACGATTATCATAGTTCGAGGACCTAC 59.851 42.308 0.00 0.00 35.64 3.18
79 80 6.148976 CGATTATCATAGTTCGAGGACCTACA 59.851 42.308 0.00 0.00 33.59 2.74
80 81 7.148222 CGATTATCATAGTTCGAGGACCTACAT 60.148 40.741 0.00 0.00 33.59 2.29
81 82 5.713792 ATCATAGTTCGAGGACCTACATG 57.286 43.478 0.00 0.00 0.00 3.21
82 83 4.788679 TCATAGTTCGAGGACCTACATGA 58.211 43.478 0.00 0.00 0.00 3.07
83 84 4.579340 TCATAGTTCGAGGACCTACATGAC 59.421 45.833 0.00 0.00 0.00 3.06
84 85 2.803956 AGTTCGAGGACCTACATGACA 58.196 47.619 0.00 0.00 0.00 3.58
85 86 2.492484 AGTTCGAGGACCTACATGACAC 59.508 50.000 0.00 0.00 0.00 3.67
86 87 1.471119 TCGAGGACCTACATGACACC 58.529 55.000 0.00 0.00 0.00 4.16
87 88 1.005569 TCGAGGACCTACATGACACCT 59.994 52.381 0.00 0.41 0.00 4.00
88 89 1.405821 CGAGGACCTACATGACACCTC 59.594 57.143 0.00 9.05 40.03 3.85
89 90 2.741145 GAGGACCTACATGACACCTCT 58.259 52.381 0.00 0.00 40.20 3.69
90 91 2.428890 GAGGACCTACATGACACCTCTG 59.571 54.545 0.00 0.00 40.20 3.35
91 92 2.043115 AGGACCTACATGACACCTCTGA 59.957 50.000 0.00 0.00 0.00 3.27
92 93 2.832129 GGACCTACATGACACCTCTGAA 59.168 50.000 0.00 0.00 0.00 3.02
93 94 3.260884 GGACCTACATGACACCTCTGAAA 59.739 47.826 0.00 0.00 0.00 2.69
94 95 4.080863 GGACCTACATGACACCTCTGAAAT 60.081 45.833 0.00 0.00 0.00 2.17
95 96 5.128827 GGACCTACATGACACCTCTGAAATA 59.871 44.000 0.00 0.00 0.00 1.40
96 97 6.227298 ACCTACATGACACCTCTGAAATAG 57.773 41.667 0.00 0.00 0.00 1.73
97 98 5.721960 ACCTACATGACACCTCTGAAATAGT 59.278 40.000 0.00 0.00 0.00 2.12
98 99 6.213600 ACCTACATGACACCTCTGAAATAGTT 59.786 38.462 0.00 0.00 0.00 2.24
99 100 6.758886 CCTACATGACACCTCTGAAATAGTTC 59.241 42.308 0.00 0.00 0.00 3.01
100 101 5.171476 ACATGACACCTCTGAAATAGTTCG 58.829 41.667 0.00 0.00 36.46 3.95
101 102 5.047306 ACATGACACCTCTGAAATAGTTCGA 60.047 40.000 0.00 0.00 36.46 3.71
102 103 5.060662 TGACACCTCTGAAATAGTTCGAG 57.939 43.478 13.91 13.91 36.46 4.04
104 105 4.087182 ACACCTCTGAAATAGTTCGAGGA 58.913 43.478 31.48 16.50 46.43 3.71
105 106 4.082136 ACACCTCTGAAATAGTTCGAGGAC 60.082 45.833 31.48 1.57 46.43 3.85
106 107 3.447944 ACCTCTGAAATAGTTCGAGGACC 59.552 47.826 31.48 0.97 46.43 4.46
107 108 3.702045 CCTCTGAAATAGTTCGAGGACCT 59.298 47.826 25.82 0.00 46.43 3.85
108 109 4.888239 CCTCTGAAATAGTTCGAGGACCTA 59.112 45.833 25.82 0.00 46.43 3.08
109 110 5.536916 CCTCTGAAATAGTTCGAGGACCTAT 59.463 44.000 25.82 0.00 46.43 2.57
110 111 6.392625 TCTGAAATAGTTCGAGGACCTATG 57.607 41.667 0.00 0.00 36.46 2.23
111 112 6.127101 TCTGAAATAGTTCGAGGACCTATGA 58.873 40.000 0.00 0.00 36.46 2.15
112 113 6.778069 TCTGAAATAGTTCGAGGACCTATGAT 59.222 38.462 0.00 0.00 36.46 2.45
113 114 6.749139 TGAAATAGTTCGAGGACCTATGATG 58.251 40.000 0.00 0.00 36.46 3.07
114 115 4.792521 ATAGTTCGAGGACCTATGATGC 57.207 45.455 0.00 0.00 0.00 3.91
115 116 2.388735 AGTTCGAGGACCTATGATGCA 58.611 47.619 0.00 0.00 0.00 3.96
116 117 2.101582 AGTTCGAGGACCTATGATGCAC 59.898 50.000 0.00 0.00 0.00 4.57
117 118 2.073252 TCGAGGACCTATGATGCACT 57.927 50.000 0.00 0.00 0.00 4.40
118 119 2.388735 TCGAGGACCTATGATGCACTT 58.611 47.619 0.00 0.00 0.00 3.16
119 120 2.362397 TCGAGGACCTATGATGCACTTC 59.638 50.000 0.00 0.00 0.00 3.01
120 121 2.101415 CGAGGACCTATGATGCACTTCA 59.899 50.000 0.00 0.00 0.00 3.02
121 122 3.462021 GAGGACCTATGATGCACTTCAC 58.538 50.000 0.00 0.00 0.00 3.18
122 123 3.110705 AGGACCTATGATGCACTTCACT 58.889 45.455 0.00 0.00 0.00 3.41
123 124 3.133721 AGGACCTATGATGCACTTCACTC 59.866 47.826 0.00 0.00 0.00 3.51
124 125 3.118629 GGACCTATGATGCACTTCACTCA 60.119 47.826 0.00 0.00 0.00 3.41
125 126 3.866651 ACCTATGATGCACTTCACTCAC 58.133 45.455 0.00 0.00 0.00 3.51
126 127 3.201290 CCTATGATGCACTTCACTCACC 58.799 50.000 0.00 0.00 0.00 4.02
127 128 2.119801 ATGATGCACTTCACTCACCC 57.880 50.000 0.00 0.00 0.00 4.61
128 129 0.764271 TGATGCACTTCACTCACCCA 59.236 50.000 0.00 0.00 0.00 4.51
129 130 1.142667 TGATGCACTTCACTCACCCAA 59.857 47.619 0.00 0.00 0.00 4.12
130 131 2.229792 GATGCACTTCACTCACCCAAA 58.770 47.619 0.00 0.00 0.00 3.28
131 132 2.363306 TGCACTTCACTCACCCAAAT 57.637 45.000 0.00 0.00 0.00 2.32
132 133 3.500448 TGCACTTCACTCACCCAAATA 57.500 42.857 0.00 0.00 0.00 1.40
133 134 3.146066 TGCACTTCACTCACCCAAATAC 58.854 45.455 0.00 0.00 0.00 1.89
134 135 3.181445 TGCACTTCACTCACCCAAATACT 60.181 43.478 0.00 0.00 0.00 2.12
135 136 3.821033 GCACTTCACTCACCCAAATACTT 59.179 43.478 0.00 0.00 0.00 2.24
136 137 4.320494 GCACTTCACTCACCCAAATACTTG 60.320 45.833 0.00 0.00 0.00 3.16
137 138 4.821805 CACTTCACTCACCCAAATACTTGT 59.178 41.667 0.00 0.00 0.00 3.16
138 139 5.049405 CACTTCACTCACCCAAATACTTGTC 60.049 44.000 0.00 0.00 0.00 3.18
139 140 4.698201 TCACTCACCCAAATACTTGTCA 57.302 40.909 0.00 0.00 0.00 3.58
140 141 5.241403 TCACTCACCCAAATACTTGTCAT 57.759 39.130 0.00 0.00 0.00 3.06
152 153 2.787994 ACTTGTCATTGAGGGCTTCAG 58.212 47.619 0.00 0.00 37.07 3.02
159 160 5.128919 GTCATTGAGGGCTTCAGTCATAAT 58.871 41.667 0.00 0.00 37.07 1.28
169 170 9.866655 AGGGCTTCAGTCATAATATTCAAAATA 57.133 29.630 0.00 0.00 0.00 1.40
200 201 2.721090 GTGCATTGTCTTTCACTTTCGC 59.279 45.455 0.00 0.00 0.00 4.70
211 212 3.410631 TCACTTTCGCATTGGGACTAA 57.589 42.857 2.45 0.00 0.00 2.24
215 216 4.679654 CACTTTCGCATTGGGACTAAAAAC 59.320 41.667 2.45 0.00 0.00 2.43
243 244 4.471904 TGATTTCTCTACGCTCACCATT 57.528 40.909 0.00 0.00 0.00 3.16
246 247 3.678056 TTCTCTACGCTCACCATTTGT 57.322 42.857 0.00 0.00 0.00 2.83
248 249 2.826128 TCTCTACGCTCACCATTTGTCT 59.174 45.455 0.00 0.00 0.00 3.41
259 260 0.445436 CATTTGTCTCGAGGCAGCAC 59.555 55.000 20.53 7.05 0.00 4.40
261 262 0.179059 TTTGTCTCGAGGCAGCACAA 60.179 50.000 20.53 15.36 0.00 3.33
264 265 1.482182 TGTCTCGAGGCAGCACAATAT 59.518 47.619 17.42 0.00 0.00 1.28
340 341 4.880120 GGATCAGTGAATCATCAGCAAAGA 59.120 41.667 0.00 0.00 35.88 2.52
455 456 6.392354 CCTCGGTACACACAAGAATAAGTAA 58.608 40.000 0.00 0.00 0.00 2.24
470 471 8.715190 AGAATAAGTAAAGAGATAGAGGGTCC 57.285 38.462 0.00 0.00 0.00 4.46
513 515 2.614983 GTTTAAAACTCGGTGCTCCACA 59.385 45.455 5.52 0.00 35.86 4.17
515 517 0.468226 AAAACTCGGTGCTCCACAGA 59.532 50.000 5.52 0.00 36.35 3.41
552 554 8.000709 TGCATAATTAGATTCACCCAATTCTCT 58.999 33.333 0.00 0.00 0.00 3.10
559 561 6.986250 AGATTCACCCAATTCTCTTGAAAAC 58.014 36.000 0.00 0.00 35.63 2.43
641 643 0.517316 GTGTGGTAGCAAAAGGAGCG 59.483 55.000 0.00 0.00 37.01 5.03
663 665 3.637229 GCAGTACTAGTCCTATTCCAGCA 59.363 47.826 0.00 0.00 0.00 4.41
664 666 4.261825 GCAGTACTAGTCCTATTCCAGCAG 60.262 50.000 0.00 0.00 0.00 4.24
665 667 4.279671 CAGTACTAGTCCTATTCCAGCAGG 59.720 50.000 0.00 0.00 0.00 4.85
666 668 3.689872 ACTAGTCCTATTCCAGCAGGA 57.310 47.619 0.00 0.00 43.93 3.86
674 676 2.342279 TCCAGCAGGAAACCGTCG 59.658 61.111 0.00 0.00 42.23 5.12
675 677 2.742372 CCAGCAGGAAACCGTCGG 60.742 66.667 10.48 10.48 36.89 4.79
676 678 2.030562 CAGCAGGAAACCGTCGGT 59.969 61.111 12.23 12.23 37.65 4.69
677 679 2.027625 CAGCAGGAAACCGTCGGTC 61.028 63.158 19.16 5.91 33.12 4.79
678 680 3.110178 GCAGGAAACCGTCGGTCG 61.110 66.667 19.16 5.44 33.12 4.79
679 681 2.646719 CAGGAAACCGTCGGTCGA 59.353 61.111 19.16 0.00 42.86 4.20
680 682 1.443872 CAGGAAACCGTCGGTCGAG 60.444 63.158 19.16 2.68 42.86 4.04
681 683 2.808321 GGAAACCGTCGGTCGAGC 60.808 66.667 19.16 4.06 42.86 5.03
836 842 1.144057 CTCGTAGCCGCCCATCTTT 59.856 57.895 0.00 0.00 0.00 2.52
844 850 2.059786 CGCCCATCTTTGCCCCAAT 61.060 57.895 0.00 0.00 0.00 3.16
848 854 2.940971 GCCCATCTTTGCCCCAATTTTC 60.941 50.000 0.00 0.00 0.00 2.29
852 858 1.696884 TCTTTGCCCCAATTTTCACCC 59.303 47.619 0.00 0.00 0.00 4.61
1431 1437 1.148157 CGCACCAAGGTCGAGCTATG 61.148 60.000 18.94 16.78 0.00 2.23
1463 1471 2.437002 GTGCCGGCCCAATTCGTA 60.437 61.111 26.77 0.00 0.00 3.43
1597 1609 2.821969 GAGATGGCACTGTTTGGATTGT 59.178 45.455 0.00 0.00 0.00 2.71
1674 1686 2.499205 CACCGGCGAGCCAATCTA 59.501 61.111 9.30 0.00 35.37 1.98
1739 1751 1.812686 TACGTTCTGCCGCTCCAGTT 61.813 55.000 0.00 0.00 34.47 3.16
1742 1754 1.079127 TTCTGCCGCTCCAGTTAGC 60.079 57.895 0.00 0.00 39.21 3.09
1746 1762 1.376037 GCCGCTCCAGTTAGCACTT 60.376 57.895 0.00 0.00 42.91 3.16
1757 1773 4.381079 CCAGTTAGCACTTCTACCAGAGTC 60.381 50.000 0.00 0.00 0.00 3.36
1772 1790 5.482463 CCAGAGTCTGGCTTACAGTGGTC 62.482 56.522 26.03 0.00 45.13 4.02
1777 1795 2.033194 GGCTTACAGTGGTCGTGCC 61.033 63.158 0.00 0.00 37.90 5.01
1781 1799 0.830444 TTACAGTGGTCGTGCCCTCT 60.830 55.000 0.00 0.00 36.04 3.69
1785 1803 0.320697 AGTGGTCGTGCCCTCTAAAC 59.679 55.000 0.00 0.00 36.04 2.01
1792 1810 1.065418 CGTGCCCTCTAAACTCCCAAT 60.065 52.381 0.00 0.00 0.00 3.16
1800 1818 5.241662 CCTCTAAACTCCCAATGCTATAGC 58.758 45.833 18.18 18.18 42.50 2.97
1802 1820 5.858381 TCTAAACTCCCAATGCTATAGCTG 58.142 41.667 24.61 15.44 42.66 4.24
1803 1821 2.557920 ACTCCCAATGCTATAGCTGC 57.442 50.000 24.61 0.61 42.66 5.25
1807 1825 2.303022 TCCCAATGCTATAGCTGCCTAC 59.697 50.000 24.61 0.00 42.66 3.18
1816 1834 4.997395 GCTATAGCTGCCTACTAATTTGCA 59.003 41.667 17.75 0.00 38.21 4.08
1826 1844 8.433421 TGCCTACTAATTTGCAGTAATACTTC 57.567 34.615 0.00 0.00 0.00 3.01
1827 1845 8.265055 TGCCTACTAATTTGCAGTAATACTTCT 58.735 33.333 0.00 0.00 0.00 2.85
1879 1898 5.919272 AAAGGAAAGTCAGTAAACGCTAC 57.081 39.130 0.00 0.00 0.00 3.58
1880 1899 4.595762 AGGAAAGTCAGTAAACGCTACA 57.404 40.909 0.00 0.00 0.00 2.74
1927 1954 0.460987 CACCTCTTGATCAGCCCGTC 60.461 60.000 0.00 0.00 0.00 4.79
1941 1968 1.592400 CCCGTCTAGAAGACCGCACA 61.592 60.000 7.30 0.00 42.12 4.57
1942 1969 0.179161 CCGTCTAGAAGACCGCACAG 60.179 60.000 7.30 0.00 42.12 3.66
1993 2020 4.471548 CCTCCCCTACGAATTCTCTTCTA 58.528 47.826 3.52 0.00 0.00 2.10
2001 2028 7.982354 CCCTACGAATTCTCTTCTAAACATTCT 59.018 37.037 3.52 0.00 0.00 2.40
2029 2056 8.633075 TTCAATTTCTGTAGAGTTTTTGCTTG 57.367 30.769 0.00 0.00 0.00 4.01
2034 2061 5.061179 TCTGTAGAGTTTTTGCTTGTACCC 58.939 41.667 0.00 0.00 0.00 3.69
2070 2120 2.128035 CACGAGTTGCGACTTCTTTCT 58.872 47.619 8.34 0.00 44.57 2.52
2106 2156 5.464069 AGTTTGGGGTCTCCTGTAATTTTT 58.536 37.500 0.00 0.00 36.20 1.94
2111 2161 3.365969 GGGTCTCCTGTAATTTTTGTGCG 60.366 47.826 0.00 0.00 0.00 5.34
2120 2170 3.354089 AATTTTTGTGCGAGAGTGTGG 57.646 42.857 0.00 0.00 0.00 4.17
2195 2245 4.323417 TGGCATGAAAAGAATGTCGTAGT 58.677 39.130 0.00 0.00 32.14 2.73
2304 2354 9.295214 CAACTACATCTTCAGTTCAGTAGTATG 57.705 37.037 0.00 0.00 40.68 2.39
2420 2475 0.321564 GGGGAACTTGGCCAATTTGC 60.322 55.000 25.76 25.76 0.00 3.68
2460 2515 8.725148 CAATTAGCTTGATCTGTACTTCAAGTT 58.275 33.333 22.89 20.92 46.76 2.66
2462 2517 8.677148 TTAGCTTGATCTGTACTTCAAGTTTT 57.323 30.769 22.89 15.94 46.76 2.43
2547 2602 4.141855 ACCGAAAACGATTGTTGATGTC 57.858 40.909 0.00 0.00 38.62 3.06
3181 3606 9.823647 AGGTATGAAAGTAGATGTTGAGTATTG 57.176 33.333 0.00 0.00 0.00 1.90
3291 3716 2.499205 CATAGGAACCTCGCGCCA 59.501 61.111 0.00 0.00 0.00 5.69
3372 3797 2.370445 CCTCCCGGATTGGTGCTCT 61.370 63.158 0.73 0.00 35.15 4.09
3421 3846 6.591834 CGAGTCATTGTCTCTTGAGGTATTTT 59.408 38.462 8.85 0.00 0.00 1.82
3426 3851 3.265995 TGTCTCTTGAGGTATTTTCCCCC 59.734 47.826 0.00 0.00 0.00 5.40
3430 3855 5.016245 TCTCTTGAGGTATTTTCCCCCAAAT 59.984 40.000 0.00 0.00 0.00 2.32
3431 3856 5.660533 TCTTGAGGTATTTTCCCCCAAATT 58.339 37.500 0.00 0.00 0.00 1.82
3439 3864 7.669304 AGGTATTTTCCCCCAAATTTTGAATTG 59.331 33.333 10.72 0.00 0.00 2.32
3450 3875 8.720562 CCCAAATTTTGAATTGATTTGACCTAC 58.279 33.333 10.72 0.00 41.14 3.18
3454 3879 6.588719 TTTGAATTGATTTGACCTACCTGG 57.411 37.500 0.00 0.00 42.93 4.45
3472 3897 4.022068 ACCTGGTACACAAATTTGCATGAG 60.022 41.667 18.12 6.79 0.00 2.90
3652 4078 3.196685 AGGAGTGGTATGCTCTTCTTGTC 59.803 47.826 0.00 0.00 33.73 3.18
3684 4110 1.880340 GCTGCTCATCGAACCGAGG 60.880 63.158 10.70 0.00 39.91 4.63
3698 4124 2.977914 ACCGAGGTGATCTGTTTGATG 58.022 47.619 0.00 0.00 35.14 3.07
3742 4168 5.418310 ACGTACATTTCAACTCACTTTGG 57.582 39.130 0.00 0.00 0.00 3.28
3851 4277 0.328926 TTCAGCATCATCACCTGCCA 59.671 50.000 0.00 0.00 39.22 4.92
3951 4377 4.314440 TCGGCTTGCTGTCGCCTT 62.314 61.111 1.11 0.00 44.46 4.35
4047 4473 6.696441 AGCAAAATTCTCCTCAGATTCATC 57.304 37.500 0.00 0.00 0.00 2.92
4051 4477 7.013464 GCAAAATTCTCCTCAGATTCATCAGAT 59.987 37.037 0.00 0.00 0.00 2.90
4156 4589 5.208463 TCCTATGACGCTATACATGCAAA 57.792 39.130 0.00 0.00 0.00 3.68
4172 4605 2.220313 GCAAACAAAATGCACCATGGT 58.780 42.857 13.00 13.00 43.29 3.55
4175 4608 3.834489 AACAAAATGCACCATGGTTGA 57.166 38.095 16.84 4.62 0.00 3.18
4204 4637 0.037303 CCCGCATAGAGCCCAATCAT 59.963 55.000 0.00 0.00 41.38 2.45
4227 4660 5.467738 TCTGAAGGAAATATGCCCTAGAGA 58.532 41.667 0.00 0.49 31.36 3.10
4447 4882 4.071961 TGAACGGGATCACATCATTAGG 57.928 45.455 0.00 0.00 0.00 2.69
4478 4913 1.874129 ATGGACAAGACCCATCCGTA 58.126 50.000 0.00 0.00 40.16 4.02
4485 4920 3.262405 ACAAGACCCATCCGTAAGCTTAA 59.738 43.478 7.99 0.00 0.00 1.85
4576 5011 0.814010 ATGCAACTCCCGAATACCGC 60.814 55.000 0.00 0.00 36.84 5.68
4693 5136 4.282496 AGGATTTGTCACTCCGAGTATCT 58.718 43.478 0.00 0.00 36.62 1.98
4716 5159 2.957474 GAGGTATCTCTGGGCTCTCTT 58.043 52.381 0.00 0.00 37.07 2.85
4814 5257 3.577415 AGTAAAGAGACTTGCCGGTAACT 59.423 43.478 0.00 0.00 0.00 2.24
4870 5313 2.181125 TCTCGGGCAAGTAACATACCA 58.819 47.619 0.00 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.942341 TGTGTTATTCTGGTCCTCAAACTATTT 59.058 33.333 0.00 0.00 0.00 1.40
1 2 7.390718 GTGTGTTATTCTGGTCCTCAAACTATT 59.609 37.037 0.00 0.00 0.00 1.73
2 3 6.879458 GTGTGTTATTCTGGTCCTCAAACTAT 59.121 38.462 0.00 0.00 0.00 2.12
3 4 6.183361 TGTGTGTTATTCTGGTCCTCAAACTA 60.183 38.462 0.00 0.00 0.00 2.24
4 5 5.063880 GTGTGTTATTCTGGTCCTCAAACT 58.936 41.667 0.00 0.00 0.00 2.66
5 6 4.819630 TGTGTGTTATTCTGGTCCTCAAAC 59.180 41.667 0.00 0.00 0.00 2.93
6 7 5.042463 TGTGTGTTATTCTGGTCCTCAAA 57.958 39.130 0.00 0.00 0.00 2.69
7 8 4.698201 TGTGTGTTATTCTGGTCCTCAA 57.302 40.909 0.00 0.00 0.00 3.02
8 9 4.908601 ATGTGTGTTATTCTGGTCCTCA 57.091 40.909 0.00 0.00 0.00 3.86
9 10 6.238484 GCAATATGTGTGTTATTCTGGTCCTC 60.238 42.308 0.00 0.00 0.00 3.71
10 11 5.590259 GCAATATGTGTGTTATTCTGGTCCT 59.410 40.000 0.00 0.00 0.00 3.85
11 12 5.356751 TGCAATATGTGTGTTATTCTGGTCC 59.643 40.000 0.00 0.00 0.00 4.46
12 13 6.094048 AGTGCAATATGTGTGTTATTCTGGTC 59.906 38.462 0.00 0.00 0.00 4.02
13 14 5.945784 AGTGCAATATGTGTGTTATTCTGGT 59.054 36.000 0.00 0.00 0.00 4.00
14 15 6.441093 AGTGCAATATGTGTGTTATTCTGG 57.559 37.500 0.00 0.00 0.00 3.86
15 16 8.022550 TCAAAGTGCAATATGTGTGTTATTCTG 58.977 33.333 0.00 0.00 0.00 3.02
16 17 8.109705 TCAAAGTGCAATATGTGTGTTATTCT 57.890 30.769 0.00 0.00 0.00 2.40
17 18 7.485913 CCTCAAAGTGCAATATGTGTGTTATTC 59.514 37.037 0.00 0.00 0.00 1.75
18 19 7.176515 TCCTCAAAGTGCAATATGTGTGTTATT 59.823 33.333 0.00 0.00 0.00 1.40
19 20 6.658816 TCCTCAAAGTGCAATATGTGTGTTAT 59.341 34.615 0.00 0.00 0.00 1.89
20 21 6.000840 TCCTCAAAGTGCAATATGTGTGTTA 58.999 36.000 0.00 0.00 0.00 2.41
21 22 4.826733 TCCTCAAAGTGCAATATGTGTGTT 59.173 37.500 0.00 0.00 0.00 3.32
22 23 4.216257 GTCCTCAAAGTGCAATATGTGTGT 59.784 41.667 0.00 0.00 0.00 3.72
23 24 4.379813 GGTCCTCAAAGTGCAATATGTGTG 60.380 45.833 0.00 0.00 0.00 3.82
24 25 3.758554 GGTCCTCAAAGTGCAATATGTGT 59.241 43.478 0.00 0.00 0.00 3.72
25 26 4.012374 AGGTCCTCAAAGTGCAATATGTG 58.988 43.478 0.00 0.00 0.00 3.21
26 27 4.012374 CAGGTCCTCAAAGTGCAATATGT 58.988 43.478 0.00 0.00 0.00 2.29
27 28 3.379372 CCAGGTCCTCAAAGTGCAATATG 59.621 47.826 0.00 0.00 0.00 1.78
28 29 3.266772 TCCAGGTCCTCAAAGTGCAATAT 59.733 43.478 0.00 0.00 0.00 1.28
29 30 2.642311 TCCAGGTCCTCAAAGTGCAATA 59.358 45.455 0.00 0.00 0.00 1.90
30 31 1.425066 TCCAGGTCCTCAAAGTGCAAT 59.575 47.619 0.00 0.00 0.00 3.56
31 32 0.843309 TCCAGGTCCTCAAAGTGCAA 59.157 50.000 0.00 0.00 0.00 4.08
32 33 1.067295 ATCCAGGTCCTCAAAGTGCA 58.933 50.000 0.00 0.00 0.00 4.57
33 34 1.003580 TCATCCAGGTCCTCAAAGTGC 59.996 52.381 0.00 0.00 0.00 4.40
34 35 2.704572 GTCATCCAGGTCCTCAAAGTG 58.295 52.381 0.00 0.00 0.00 3.16
35 36 1.276421 CGTCATCCAGGTCCTCAAAGT 59.724 52.381 0.00 0.00 0.00 2.66
36 37 1.550524 TCGTCATCCAGGTCCTCAAAG 59.449 52.381 0.00 0.00 0.00 2.77
37 38 1.639722 TCGTCATCCAGGTCCTCAAA 58.360 50.000 0.00 0.00 0.00 2.69
38 39 1.866015 ATCGTCATCCAGGTCCTCAA 58.134 50.000 0.00 0.00 0.00 3.02
39 40 1.866015 AATCGTCATCCAGGTCCTCA 58.134 50.000 0.00 0.00 0.00 3.86
40 41 3.574396 TGATAATCGTCATCCAGGTCCTC 59.426 47.826 0.00 0.00 0.00 3.71
41 42 3.576861 TGATAATCGTCATCCAGGTCCT 58.423 45.455 0.00 0.00 0.00 3.85
42 43 4.543590 ATGATAATCGTCATCCAGGTCC 57.456 45.455 0.00 0.00 33.69 4.46
43 44 6.274157 ACTATGATAATCGTCATCCAGGTC 57.726 41.667 0.00 0.00 39.45 3.85
44 45 6.570571 CGAACTATGATAATCGTCATCCAGGT 60.571 42.308 0.00 0.00 39.45 4.00
45 46 5.802451 CGAACTATGATAATCGTCATCCAGG 59.198 44.000 0.00 0.00 39.45 4.45
46 47 6.612306 TCGAACTATGATAATCGTCATCCAG 58.388 40.000 7.05 0.00 39.45 3.86
47 48 6.349363 CCTCGAACTATGATAATCGTCATCCA 60.349 42.308 7.05 0.00 39.45 3.41
48 49 6.030849 CCTCGAACTATGATAATCGTCATCC 58.969 44.000 7.05 0.00 39.45 3.51
49 50 6.743627 GTCCTCGAACTATGATAATCGTCATC 59.256 42.308 7.05 0.00 39.45 2.92
50 51 6.349445 GGTCCTCGAACTATGATAATCGTCAT 60.349 42.308 7.05 0.00 41.49 3.06
51 52 5.048921 GGTCCTCGAACTATGATAATCGTCA 60.049 44.000 7.05 0.00 36.70 4.35
52 53 5.181622 AGGTCCTCGAACTATGATAATCGTC 59.818 44.000 7.05 0.00 36.70 4.20
53 54 5.071370 AGGTCCTCGAACTATGATAATCGT 58.929 41.667 7.05 0.00 36.70 3.73
54 55 5.630661 AGGTCCTCGAACTATGATAATCG 57.369 43.478 0.00 2.06 36.67 3.34
55 56 7.450124 TGTAGGTCCTCGAACTATGATAATC 57.550 40.000 0.00 0.00 34.19 1.75
56 57 7.670140 TCATGTAGGTCCTCGAACTATGATAAT 59.330 37.037 0.00 0.00 34.19 1.28
57 58 7.002276 TCATGTAGGTCCTCGAACTATGATAA 58.998 38.462 0.00 0.00 34.19 1.75
58 59 6.430308 GTCATGTAGGTCCTCGAACTATGATA 59.570 42.308 0.00 0.00 34.19 2.15
59 60 5.241949 GTCATGTAGGTCCTCGAACTATGAT 59.758 44.000 0.00 0.00 34.19 2.45
60 61 4.579340 GTCATGTAGGTCCTCGAACTATGA 59.421 45.833 0.00 0.00 34.19 2.15
61 62 4.338400 TGTCATGTAGGTCCTCGAACTATG 59.662 45.833 0.00 0.00 34.19 2.23
62 63 4.338682 GTGTCATGTAGGTCCTCGAACTAT 59.661 45.833 0.00 0.00 34.19 2.12
63 64 3.693085 GTGTCATGTAGGTCCTCGAACTA 59.307 47.826 0.00 0.00 29.72 2.24
64 65 2.492484 GTGTCATGTAGGTCCTCGAACT 59.508 50.000 0.00 0.00 32.68 3.01
65 66 2.416972 GGTGTCATGTAGGTCCTCGAAC 60.417 54.545 0.00 0.00 0.00 3.95
66 67 1.822990 GGTGTCATGTAGGTCCTCGAA 59.177 52.381 0.00 0.00 0.00 3.71
67 68 1.005569 AGGTGTCATGTAGGTCCTCGA 59.994 52.381 0.00 0.00 0.00 4.04
68 69 1.405821 GAGGTGTCATGTAGGTCCTCG 59.594 57.143 0.00 0.00 33.44 4.63
69 70 2.428890 CAGAGGTGTCATGTAGGTCCTC 59.571 54.545 0.00 13.09 40.94 3.71
70 71 2.043115 TCAGAGGTGTCATGTAGGTCCT 59.957 50.000 0.00 0.00 0.00 3.85
71 72 2.457598 TCAGAGGTGTCATGTAGGTCC 58.542 52.381 0.00 0.00 0.00 4.46
72 73 4.537135 TTTCAGAGGTGTCATGTAGGTC 57.463 45.455 0.00 0.00 0.00 3.85
73 74 5.721960 ACTATTTCAGAGGTGTCATGTAGGT 59.278 40.000 0.00 0.00 0.00 3.08
74 75 6.227298 ACTATTTCAGAGGTGTCATGTAGG 57.773 41.667 0.00 0.00 0.00 3.18
75 76 6.473778 CGAACTATTTCAGAGGTGTCATGTAG 59.526 42.308 0.00 0.00 0.00 2.74
76 77 6.152154 TCGAACTATTTCAGAGGTGTCATGTA 59.848 38.462 0.00 0.00 0.00 2.29
77 78 5.047306 TCGAACTATTTCAGAGGTGTCATGT 60.047 40.000 0.00 0.00 0.00 3.21
78 79 5.410924 TCGAACTATTTCAGAGGTGTCATG 58.589 41.667 0.00 0.00 0.00 3.07
79 80 5.394663 CCTCGAACTATTTCAGAGGTGTCAT 60.395 44.000 17.61 0.00 42.05 3.06
80 81 4.082190 CCTCGAACTATTTCAGAGGTGTCA 60.082 45.833 17.61 0.00 42.05 3.58
81 82 4.158025 TCCTCGAACTATTTCAGAGGTGTC 59.842 45.833 21.48 0.00 44.46 3.67
82 83 4.082136 GTCCTCGAACTATTTCAGAGGTGT 60.082 45.833 21.48 0.00 44.46 4.16
83 84 4.425520 GTCCTCGAACTATTTCAGAGGTG 58.574 47.826 21.48 8.06 44.46 4.00
84 85 3.447944 GGTCCTCGAACTATTTCAGAGGT 59.552 47.826 21.48 0.00 44.46 3.85
85 86 3.702045 AGGTCCTCGAACTATTTCAGAGG 59.298 47.826 18.80 18.80 44.93 3.69
86 87 4.993029 AGGTCCTCGAACTATTTCAGAG 57.007 45.455 0.00 7.31 34.68 3.35
87 88 6.127101 TCATAGGTCCTCGAACTATTTCAGA 58.873 40.000 0.00 0.00 39.24 3.27
88 89 6.392625 TCATAGGTCCTCGAACTATTTCAG 57.607 41.667 0.00 0.00 39.24 3.02
89 90 6.738731 GCATCATAGGTCCTCGAACTATTTCA 60.739 42.308 0.00 0.00 39.24 2.69
90 91 5.635700 GCATCATAGGTCCTCGAACTATTTC 59.364 44.000 0.00 0.00 39.24 2.17
91 92 5.070446 TGCATCATAGGTCCTCGAACTATTT 59.930 40.000 0.00 0.00 39.24 1.40
92 93 4.588951 TGCATCATAGGTCCTCGAACTATT 59.411 41.667 0.00 0.00 39.24 1.73
93 94 4.021894 GTGCATCATAGGTCCTCGAACTAT 60.022 45.833 0.00 0.00 42.55 2.12
94 95 3.318275 GTGCATCATAGGTCCTCGAACTA 59.682 47.826 0.00 0.00 36.22 2.24
95 96 2.101582 GTGCATCATAGGTCCTCGAACT 59.898 50.000 0.00 0.00 32.68 3.01
96 97 2.101582 AGTGCATCATAGGTCCTCGAAC 59.898 50.000 0.00 0.00 0.00 3.95
97 98 2.388735 AGTGCATCATAGGTCCTCGAA 58.611 47.619 0.00 0.00 0.00 3.71
98 99 2.073252 AGTGCATCATAGGTCCTCGA 57.927 50.000 0.00 0.00 0.00 4.04
99 100 2.101415 TGAAGTGCATCATAGGTCCTCG 59.899 50.000 0.00 0.00 0.00 4.63
100 101 3.133721 AGTGAAGTGCATCATAGGTCCTC 59.866 47.826 0.00 0.00 0.00 3.71
101 102 3.110705 AGTGAAGTGCATCATAGGTCCT 58.889 45.455 0.00 0.00 0.00 3.85
102 103 3.118629 TGAGTGAAGTGCATCATAGGTCC 60.119 47.826 0.00 0.00 0.00 4.46
103 104 3.868077 GTGAGTGAAGTGCATCATAGGTC 59.132 47.826 0.00 0.00 0.00 3.85
104 105 3.369892 GGTGAGTGAAGTGCATCATAGGT 60.370 47.826 0.00 0.00 0.00 3.08
105 106 3.201290 GGTGAGTGAAGTGCATCATAGG 58.799 50.000 0.00 0.00 0.00 2.57
106 107 3.201290 GGGTGAGTGAAGTGCATCATAG 58.799 50.000 0.00 0.00 0.00 2.23
107 108 2.571202 TGGGTGAGTGAAGTGCATCATA 59.429 45.455 0.00 0.00 0.00 2.15
108 109 1.352017 TGGGTGAGTGAAGTGCATCAT 59.648 47.619 0.00 0.00 0.00 2.45
109 110 0.764271 TGGGTGAGTGAAGTGCATCA 59.236 50.000 0.00 0.00 0.00 3.07
110 111 1.896220 TTGGGTGAGTGAAGTGCATC 58.104 50.000 0.00 0.00 0.00 3.91
111 112 2.363306 TTTGGGTGAGTGAAGTGCAT 57.637 45.000 0.00 0.00 0.00 3.96
112 113 2.363306 ATTTGGGTGAGTGAAGTGCA 57.637 45.000 0.00 0.00 0.00 4.57
113 114 3.412386 AGTATTTGGGTGAGTGAAGTGC 58.588 45.455 0.00 0.00 0.00 4.40
114 115 4.821805 ACAAGTATTTGGGTGAGTGAAGTG 59.178 41.667 2.81 0.00 38.66 3.16
115 116 5.048846 ACAAGTATTTGGGTGAGTGAAGT 57.951 39.130 2.81 0.00 38.66 3.01
116 117 5.063204 TGACAAGTATTTGGGTGAGTGAAG 58.937 41.667 2.81 0.00 38.66 3.02
117 118 5.042463 TGACAAGTATTTGGGTGAGTGAA 57.958 39.130 2.81 0.00 38.66 3.18
118 119 4.698201 TGACAAGTATTTGGGTGAGTGA 57.302 40.909 2.81 0.00 38.66 3.41
119 120 5.473162 TCAATGACAAGTATTTGGGTGAGTG 59.527 40.000 2.81 0.00 38.66 3.51
120 121 5.630121 TCAATGACAAGTATTTGGGTGAGT 58.370 37.500 2.81 0.00 38.66 3.41
121 122 5.124457 CCTCAATGACAAGTATTTGGGTGAG 59.876 44.000 2.81 8.56 38.66 3.51
122 123 5.009631 CCTCAATGACAAGTATTTGGGTGA 58.990 41.667 2.81 0.28 38.66 4.02
123 124 4.158394 CCCTCAATGACAAGTATTTGGGTG 59.842 45.833 2.81 0.00 38.66 4.61
124 125 4.344104 CCCTCAATGACAAGTATTTGGGT 58.656 43.478 2.81 0.00 38.66 4.51
125 126 3.131046 GCCCTCAATGACAAGTATTTGGG 59.869 47.826 2.81 0.00 38.66 4.12
126 127 4.019174 AGCCCTCAATGACAAGTATTTGG 58.981 43.478 2.81 0.00 38.66 3.28
127 128 5.183713 TGAAGCCCTCAATGACAAGTATTTG 59.816 40.000 0.00 0.00 40.24 2.32
128 129 5.324409 TGAAGCCCTCAATGACAAGTATTT 58.676 37.500 0.00 0.00 0.00 1.40
129 130 4.922206 TGAAGCCCTCAATGACAAGTATT 58.078 39.130 0.00 0.00 0.00 1.89
130 131 4.018960 ACTGAAGCCCTCAATGACAAGTAT 60.019 41.667 0.00 0.00 32.17 2.12
131 132 3.327757 ACTGAAGCCCTCAATGACAAGTA 59.672 43.478 0.00 0.00 32.17 2.24
132 133 2.107204 ACTGAAGCCCTCAATGACAAGT 59.893 45.455 0.00 0.00 32.17 3.16
133 134 2.746362 GACTGAAGCCCTCAATGACAAG 59.254 50.000 0.00 0.00 32.17 3.16
134 135 2.106338 TGACTGAAGCCCTCAATGACAA 59.894 45.455 0.00 0.00 32.17 3.18
135 136 1.699083 TGACTGAAGCCCTCAATGACA 59.301 47.619 0.00 0.00 32.17 3.58
136 137 2.479566 TGACTGAAGCCCTCAATGAC 57.520 50.000 0.00 0.00 32.17 3.06
137 138 4.842531 TTATGACTGAAGCCCTCAATGA 57.157 40.909 0.00 0.00 32.17 2.57
138 139 7.446319 TGAATATTATGACTGAAGCCCTCAATG 59.554 37.037 0.00 0.00 32.17 2.82
139 140 7.520798 TGAATATTATGACTGAAGCCCTCAAT 58.479 34.615 0.00 0.00 32.17 2.57
140 141 6.899089 TGAATATTATGACTGAAGCCCTCAA 58.101 36.000 0.00 0.00 32.17 3.02
179 180 2.721090 GCGAAAGTGAAAGACAATGCAC 59.279 45.455 0.00 0.00 0.00 4.57
188 189 2.554032 AGTCCCAATGCGAAAGTGAAAG 59.446 45.455 0.00 0.00 0.00 2.62
189 190 2.582052 AGTCCCAATGCGAAAGTGAAA 58.418 42.857 0.00 0.00 0.00 2.69
200 201 4.701956 AGCATCGTTTTTAGTCCCAATG 57.298 40.909 0.00 0.00 0.00 2.82
211 212 5.671329 GCGTAGAGAAATCAAGCATCGTTTT 60.671 40.000 0.00 0.00 0.00 2.43
215 216 3.119291 AGCGTAGAGAAATCAAGCATCG 58.881 45.455 0.00 0.00 0.00 3.84
243 244 0.035317 ATTGTGCTGCCTCGAGACAA 59.965 50.000 15.71 16.01 0.00 3.18
246 247 1.756538 TCATATTGTGCTGCCTCGAGA 59.243 47.619 15.71 0.00 0.00 4.04
248 249 2.689553 TTCATATTGTGCTGCCTCGA 57.310 45.000 0.00 0.00 0.00 4.04
259 260 8.729529 CTGAAAGCAGCATTAGATTCATATTG 57.270 34.615 0.00 0.00 34.95 1.90
332 333 9.932699 CAGTGATTTCTAATATTCTCTTTGCTG 57.067 33.333 0.00 0.00 0.00 4.41
340 341 8.658619 AGATGCTCCAGTGATTTCTAATATTCT 58.341 33.333 0.00 0.00 0.00 2.40
434 435 7.811236 TCTCTTTACTTATTCTTGTGTGTACCG 59.189 37.037 0.00 0.00 0.00 4.02
470 471 1.799933 ACTAGAGGATCAAGGCAGGG 58.200 55.000 0.00 0.00 37.82 4.45
513 515 6.711277 TCTAATTATGCAGTGTGTTTCCTCT 58.289 36.000 0.00 0.00 0.00 3.69
515 517 7.611467 TGAATCTAATTATGCAGTGTGTTTCCT 59.389 33.333 0.00 0.00 0.00 3.36
641 643 3.637229 TGCTGGAATAGGACTAGTACTGC 59.363 47.826 18.50 11.58 38.73 4.40
663 665 2.960170 CTCGACCGACGGTTTCCT 59.040 61.111 22.69 0.00 42.82 3.36
664 666 2.808321 GCTCGACCGACGGTTTCC 60.808 66.667 22.69 7.61 42.82 3.13
665 667 2.808321 GGCTCGACCGACGGTTTC 60.808 66.667 22.69 8.42 42.82 2.78
674 676 1.623973 CGTTTTTCTCCGGCTCGACC 61.624 60.000 0.00 0.00 0.00 4.79
675 677 1.779683 CGTTTTTCTCCGGCTCGAC 59.220 57.895 0.00 0.00 0.00 4.20
676 678 2.025418 GCGTTTTTCTCCGGCTCGA 61.025 57.895 0.00 0.00 0.00 4.04
677 679 2.474712 GCGTTTTTCTCCGGCTCG 59.525 61.111 0.00 0.00 0.00 5.03
678 680 2.868196 GGCGTTTTTCTCCGGCTC 59.132 61.111 0.00 0.00 45.06 4.70
679 681 2.999739 TTCGGCGTTTTTCTCCGGCT 63.000 55.000 6.85 0.00 46.14 5.52
680 682 2.508755 CTTCGGCGTTTTTCTCCGGC 62.509 60.000 6.85 0.00 43.65 6.13
681 683 1.495951 CTTCGGCGTTTTTCTCCGG 59.504 57.895 6.85 0.00 43.65 5.14
687 689 2.943653 CGCTCCTTCGGCGTTTTT 59.056 55.556 6.85 0.00 46.37 1.94
707 709 1.230635 CCAAACTGGCAGTGACTCCG 61.231 60.000 22.83 6.11 0.00 4.63
719 721 1.069022 CATTGTCTCCGTGCCAAACTG 60.069 52.381 0.00 0.00 0.00 3.16
792 794 1.725557 GACTCGTCGCATCTAGCCCA 61.726 60.000 0.00 0.00 41.38 5.36
793 795 1.008309 GACTCGTCGCATCTAGCCC 60.008 63.158 0.00 0.00 41.38 5.19
836 842 0.400525 TTGGGGTGAAAATTGGGGCA 60.401 50.000 0.00 0.00 0.00 5.36
844 850 0.958091 CTGTGCGATTGGGGTGAAAA 59.042 50.000 0.00 0.00 0.00 2.29
848 854 2.034066 ACCTGTGCGATTGGGGTG 59.966 61.111 0.00 0.00 0.00 4.61
1394 1400 1.400246 CGAATTGCGACACGAGCGTA 61.400 55.000 0.00 0.00 44.57 4.42
1431 1437 1.299089 GCACGGTTGAACCAAGCAC 60.299 57.895 19.23 0.00 41.25 4.40
1485 1493 0.613260 TAGAGTGCACAAATCCGCCT 59.387 50.000 21.04 5.14 0.00 5.52
1597 1609 2.930887 GCAGTGATAAGACGACCAAGCA 60.931 50.000 0.00 0.00 0.00 3.91
1661 1673 1.876156 CCAAATCTAGATTGGCTCGCC 59.124 52.381 18.61 0.00 0.00 5.54
1674 1686 3.156293 GCAAATTTTTGGGCCCAAATCT 58.844 40.909 42.99 31.29 44.14 2.40
1692 1704 0.890542 AACATTCGCAGCTCAGGCAA 60.891 50.000 0.00 0.00 41.70 4.52
1715 1727 0.169672 GAGCGGCAGAACGTACTGTA 59.830 55.000 1.45 0.00 39.73 2.74
1716 1728 1.080705 GAGCGGCAGAACGTACTGT 60.081 57.895 1.45 0.00 39.73 3.55
1739 1751 3.357203 CCAGACTCTGGTAGAAGTGCTA 58.643 50.000 16.18 0.00 45.82 3.49
1772 1790 0.323629 TTGGGAGTTTAGAGGGCACG 59.676 55.000 0.00 0.00 0.00 5.34
1777 1795 5.012561 AGCTATAGCATTGGGAGTTTAGAGG 59.987 44.000 26.07 0.00 45.16 3.69
1781 1799 4.389374 GCAGCTATAGCATTGGGAGTTTA 58.611 43.478 26.07 0.00 45.16 2.01
1785 1803 1.350351 AGGCAGCTATAGCATTGGGAG 59.650 52.381 26.07 8.03 45.16 4.30
1792 1810 4.997395 GCAAATTAGTAGGCAGCTATAGCA 59.003 41.667 26.07 2.34 45.16 3.49
1802 1820 8.552034 CAGAAGTATTACTGCAAATTAGTAGGC 58.448 37.037 4.61 0.00 32.67 3.93
1803 1821 9.601217 ACAGAAGTATTACTGCAAATTAGTAGG 57.399 33.333 4.61 0.00 37.61 3.18
1903 1930 2.419297 GGGCTGATCAAGAGGTGTACTG 60.419 54.545 0.00 0.00 0.00 2.74
1905 1932 1.471676 CGGGCTGATCAAGAGGTGTAC 60.472 57.143 0.00 0.00 0.00 2.90
1915 1942 2.025155 GTCTTCTAGACGGGCTGATCA 58.975 52.381 0.00 0.00 35.28 2.92
1927 1954 0.603569 ACACCTGTGCGGTCTTCTAG 59.396 55.000 0.00 0.00 44.93 2.43
1941 1968 0.606604 CAGCCTACCACGTAACACCT 59.393 55.000 0.00 0.00 0.00 4.00
1942 1969 0.390735 CCAGCCTACCACGTAACACC 60.391 60.000 0.00 0.00 0.00 4.16
1946 1973 0.819582 GCTACCAGCCTACCACGTAA 59.180 55.000 0.00 0.00 34.48 3.18
2001 2028 8.686334 AGCAAAAACTCTACAGAAATTGAAAGA 58.314 29.630 0.00 0.00 0.00 2.52
2046 2073 0.507358 GAAGTCGCAACTCGTGAACC 59.493 55.000 0.00 0.00 39.67 3.62
2049 2076 2.124903 GAAAGAAGTCGCAACTCGTGA 58.875 47.619 0.00 0.00 39.67 4.35
2050 2077 2.128035 AGAAAGAAGTCGCAACTCGTG 58.872 47.619 0.00 0.00 39.67 4.35
2070 2120 7.201965 GGAGACCCCAAACTTAATTTCTCAAAA 60.202 37.037 0.00 0.00 34.14 2.44
2106 2156 0.176910 TGAAACCACACTCTCGCACA 59.823 50.000 0.00 0.00 0.00 4.57
2111 2161 6.072508 TGAGCATAAAATGAAACCACACTCTC 60.073 38.462 0.00 0.00 0.00 3.20
2120 2170 6.317857 GTGGAGAGTGAGCATAAAATGAAAC 58.682 40.000 0.00 0.00 0.00 2.78
2171 2221 4.789012 ACGACATTCTTTTCATGCCATT 57.211 36.364 0.00 0.00 0.00 3.16
2195 2245 8.895141 TTAGGCAGCTATAATACCTGATAAGA 57.105 34.615 0.00 0.00 31.79 2.10
2304 2354 1.406539 CCCATGGAACTATGCTGCAAC 59.593 52.381 15.22 0.00 0.00 4.17
2400 2450 1.351076 CAAATTGGCCAAGTTCCCCT 58.649 50.000 27.36 4.57 0.00 4.79
2401 2451 0.321564 GCAAATTGGCCAAGTTCCCC 60.322 55.000 27.36 15.00 0.00 4.81
2402 2452 3.231734 GCAAATTGGCCAAGTTCCC 57.768 52.632 27.36 17.37 0.00 3.97
2420 2475 8.394971 TCAAGCTAATTGTCCATACATAATGG 57.605 34.615 0.00 0.00 45.75 3.16
2547 2602 2.358193 TACCACCGATTCCGCATCCG 62.358 60.000 0.00 0.00 0.00 4.18
2661 2716 1.450211 CTTGTCCGACAACCCCTGT 59.550 57.895 9.99 0.00 42.61 4.00
3131 3556 8.802267 CCTGATTGGACTAATTTTCTGGTTTTA 58.198 33.333 0.00 0.00 38.35 1.52
3165 3590 4.430007 TCACCGCAATACTCAACATCTAC 58.570 43.478 0.00 0.00 0.00 2.59
3181 3606 7.637709 AAAAGATTTTGTAAGATTTCACCGC 57.362 32.000 0.00 0.00 0.00 5.68
3291 3716 1.550976 GGTTTCAGTGAGTCCTCCGAT 59.449 52.381 7.99 0.00 0.00 4.18
3372 3797 4.743651 GCAATCTTGACATAATCCGAGGGA 60.744 45.833 0.00 0.00 35.55 4.20
3421 3846 6.714356 GTCAAATCAATTCAAAATTTGGGGGA 59.286 34.615 5.83 0.11 39.64 4.81
3426 3851 9.492973 AGGTAGGTCAAATCAATTCAAAATTTG 57.507 29.630 0.00 0.00 40.23 2.32
3430 3855 6.991938 CCAGGTAGGTCAAATCAATTCAAAA 58.008 36.000 0.00 0.00 0.00 2.44
3431 3856 6.588719 CCAGGTAGGTCAAATCAATTCAAA 57.411 37.500 0.00 0.00 0.00 2.69
3450 3875 4.218200 TCTCATGCAAATTTGTGTACCAGG 59.782 41.667 19.03 9.94 0.00 4.45
3454 3879 5.119931 TGGTCTCATGCAAATTTGTGTAC 57.880 39.130 19.03 12.12 0.00 2.90
3529 3955 2.104111 TCGGCCGTTTTGATATCCTGAT 59.896 45.455 27.15 0.00 0.00 2.90
3652 4078 2.029200 TGAGCAGCACAGAGAGAGAAAG 60.029 50.000 0.00 0.00 0.00 2.62
3684 4110 7.992180 ACAAAAAGAACATCAAACAGATCAC 57.008 32.000 0.00 0.00 33.72 3.06
3742 4168 6.115446 TCCATCCTGATAATCAAGACAACAC 58.885 40.000 0.00 0.00 0.00 3.32
3851 4277 0.114168 TATGGCTGCTTGGGGTTTGT 59.886 50.000 0.00 0.00 0.00 2.83
3951 4377 6.035220 CGGTAACACGAAATTATTCAGCTACA 59.965 38.462 0.00 0.00 35.15 2.74
4011 4437 6.813649 GGAGAATTTTGCTTTAGGAACCATTC 59.186 38.462 6.85 6.85 31.23 2.67
4013 4439 6.019108 AGGAGAATTTTGCTTTAGGAACCAT 58.981 36.000 0.00 0.00 0.00 3.55
4097 4530 6.780031 TCCTTTTTCTACCAATCAATCCACAA 59.220 34.615 0.00 0.00 0.00 3.33
4156 4589 2.699846 ACTCAACCATGGTGCATTTTGT 59.300 40.909 20.60 8.01 0.00 2.83
4204 4637 5.305644 GTCTCTAGGGCATATTTCCTTCAGA 59.694 44.000 0.00 0.29 34.75 3.27
4337 4771 2.092914 AGGCATACTAGGGACACTTTGC 60.093 50.000 0.00 0.00 0.00 3.68
4447 4882 4.574013 GGTCTTGTCCATCACATCATTCTC 59.426 45.833 0.00 0.00 33.90 2.87
4540 4975 7.712639 GGAGTTGCATAATCTCATAGTCAAAGA 59.287 37.037 0.00 0.00 0.00 2.52
4576 5011 2.254546 TAGCACACAAGGTGTTCCTG 57.745 50.000 0.00 0.00 45.08 3.86
4693 5136 1.856259 AGAGCCCAGAGATACCTCTCA 59.144 52.381 5.50 0.00 46.38 3.27
4711 5154 3.056179 TCGTGATGTGCATTACCAAGAGA 60.056 43.478 0.00 0.00 0.00 3.10
4716 5159 3.559655 GCTTATCGTGATGTGCATTACCA 59.440 43.478 0.00 0.00 0.00 3.25
4870 5313 8.106247 ACAACATACGTTATTCCTTTGTCATT 57.894 30.769 0.00 0.00 32.75 2.57


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

AutoCloner maintained by Alex Coulton.