Multiple sequence alignment - TraesCS3B01G521400

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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 TraesCS3B01G521400 chr3B 100.000 5610 0 0 1 5610 764692670 764698279 0.000000e+00 10360.0
1 TraesCS3B01G521400 chr3B 95.939 1379 31 13 4237 5610 764738038 764739396 0.000000e+00 2213.0
2 TraesCS3B01G521400 chr3A 92.660 2793 147 26 220 2978 710273564 710276332 0.000000e+00 3969.0
3 TraesCS3B01G521400 chr3A 93.009 1130 59 13 2977 4089 710276426 710277552 0.000000e+00 1631.0
4 TraesCS3B01G521400 chr3A 91.502 812 54 6 4326 5137 710278004 710278800 0.000000e+00 1103.0
5 TraesCS3B01G521400 chr3A 90.435 230 20 2 4094 4323 710277596 710277823 9.130000e-78 302.0
6 TraesCS3B01G521400 chr3A 93.220 59 4 0 5138 5196 710278860 710278918 2.780000e-13 87.9
7 TraesCS3B01G521400 chr3A 97.674 43 1 0 5433 5475 710332105 710332147 2.170000e-09 75.0
8 TraesCS3B01G521400 chr3A 97.368 38 0 1 29 66 552477128 552477164 4.690000e-06 63.9
9 TraesCS3B01G521400 chr3A 96.774 31 1 0 1893 1923 710275291 710275321 1.000000e-02 52.8
10 TraesCS3B01G521400 chr3D 92.634 2783 143 33 377 3141 575130483 575127745 0.000000e+00 3947.0
11 TraesCS3B01G521400 chr3D 94.265 959 43 9 3144 4093 575127673 575126718 0.000000e+00 1456.0
12 TraesCS3B01G521400 chr3D 91.655 719 49 7 4176 4891 575126645 575125935 0.000000e+00 985.0
13 TraesCS3B01G521400 chr3D 92.075 429 34 0 1067 1495 614626538 614626966 6.220000e-169 604.0
14 TraesCS3B01G521400 chr3D 88.704 301 27 2 4884 5184 575125802 575125509 1.490000e-95 361.0
15 TraesCS3B01G521400 chr3D 78.903 237 26 12 5365 5581 575125262 575125030 7.580000e-29 139.0
16 TraesCS3B01G521400 chr3D 91.398 93 7 1 5357 5449 211947649 211947558 5.900000e-25 126.0
17 TraesCS3B01G521400 chr3D 91.566 83 7 0 5353 5435 419520725 419520643 1.280000e-21 115.0
18 TraesCS3B01G521400 chrUn 100.000 435 0 0 4946 5380 476132519 476132085 0.000000e+00 804.0
19 TraesCS3B01G521400 chr4A 95.879 461 11 6 3786 4242 688787961 688788417 0.000000e+00 739.0
20 TraesCS3B01G521400 chr1D 78.809 571 118 1 1060 1627 408432331 408432901 1.140000e-101 381.0
21 TraesCS3B01G521400 chr1D 92.683 82 6 0 5357 5438 311986689 311986608 9.870000e-23 119.0
22 TraesCS3B01G521400 chr1B 78.634 571 119 1 1060 1627 549518394 549518964 5.310000e-100 375.0
23 TraesCS3B01G521400 chr1B 87.129 101 11 2 5357 5456 346658189 346658288 4.590000e-21 113.0
24 TraesCS3B01G521400 chr1A 78.284 571 121 1 1060 1627 504313411 504313981 1.150000e-96 364.0
25 TraesCS3B01G521400 chr5B 85.714 217 15 11 2 202 41942779 41942995 1.220000e-51 215.0
26 TraesCS3B01G521400 chr5B 84.821 112 15 2 1 112 84474674 84474783 1.650000e-20 111.0
27 TraesCS3B01G521400 chr4D 93.750 80 5 0 5357 5436 433364852 433364773 2.750000e-23 121.0
28 TraesCS3B01G521400 chr4D 86.076 79 11 0 28 106 358083577 358083499 1.000000e-12 86.1
29 TraesCS3B01G521400 chr2B 93.750 80 5 0 5357 5436 479990170 479990091 2.750000e-23 121.0
30 TraesCS3B01G521400 chr6A 93.671 79 5 0 5357 5435 418099796 418099874 9.870000e-23 119.0
31 TraesCS3B01G521400 chr5A 89.247 93 10 0 20 112 654062076 654061984 3.550000e-22 117.0
32 TraesCS3B01G521400 chr2A 83.654 104 15 2 8 110 163700026 163700128 4.630000e-16 97.1


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 TraesCS3B01G521400 chr3B 764692670 764698279 5609 False 10360.00 10360 100.000000 1 5610 1 chr3B.!!$F1 5609
1 TraesCS3B01G521400 chr3B 764738038 764739396 1358 False 2213.00 2213 95.939000 4237 5610 1 chr3B.!!$F2 1373
2 TraesCS3B01G521400 chr3A 710273564 710278918 5354 False 1190.95 3969 92.933333 220 5196 6 chr3A.!!$F3 4976
3 TraesCS3B01G521400 chr3D 575125030 575130483 5453 True 1377.60 3947 89.232200 377 5581 5 chr3D.!!$R3 5204
4 TraesCS3B01G521400 chr1D 408432331 408432901 570 False 381.00 381 78.809000 1060 1627 1 chr1D.!!$F1 567
5 TraesCS3B01G521400 chr1B 549518394 549518964 570 False 375.00 375 78.634000 1060 1627 1 chr1B.!!$F2 567
6 TraesCS3B01G521400 chr1A 504313411 504313981 570 False 364.00 364 78.284000 1060 1627 1 chr1A.!!$F1 567

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
938 953 0.026285 GTTCGATTGATTGCCGACCG 59.974 55.000 0.00 0.0 31.60 4.79 F
1937 1967 1.133790 GGTCTGCAGTTCATGGCAATC 59.866 52.381 14.67 0.0 39.93 2.67 F
3145 3293 0.028902 GCAGCAACCTCGTTTCGTTT 59.971 50.000 0.00 0.0 0.00 3.60 F
4192 4458 0.108992 TACATGAACTCGGTGTCGGC 60.109 55.000 0.00 0.0 36.95 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2548 2591 0.598065 AAAACATCTGTCGGCCAAGC 59.402 50.000 2.24 0.00 0.00 4.01 R
3191 3410 0.986527 TGCCATGGAGCTTCTCAGAA 59.013 50.000 18.40 0.00 31.08 3.02 R
4409 4854 0.886563 CAGAAAGGCTCCTTGGCAAG 59.113 55.000 20.31 20.31 44.55 4.01 R
5420 6172 1.633945 AGCCAAATACTCCCTCCGTTT 59.366 47.619 0.00 0.00 0.00 3.60 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
35 36 9.923143 AATAAAAAGGAGAAATAGAAAAACCGG 57.077 29.630 0.00 0.00 0.00 5.28
36 37 6.971726 AAAAGGAGAAATAGAAAAACCGGT 57.028 33.333 0.00 0.00 0.00 5.28
37 38 6.971726 AAAGGAGAAATAGAAAAACCGGTT 57.028 33.333 15.86 15.86 0.00 4.44
38 39 6.971726 AAGGAGAAATAGAAAAACCGGTTT 57.028 33.333 26.87 26.87 0.00 3.27
39 40 8.467963 AAAGGAGAAATAGAAAAACCGGTTTA 57.532 30.769 31.80 17.41 31.63 2.01
40 41 7.683437 AGGAGAAATAGAAAAACCGGTTTAG 57.317 36.000 31.80 0.00 31.63 1.85
41 42 6.657966 AGGAGAAATAGAAAAACCGGTTTAGG 59.342 38.462 31.80 0.00 31.63 2.69
42 43 6.127814 GGAGAAATAGAAAAACCGGTTTAGGG 60.128 42.308 31.80 0.00 35.02 3.53
43 44 6.545567 AGAAATAGAAAAACCGGTTTAGGGA 58.454 36.000 31.80 18.12 35.02 4.20
44 45 6.432162 AGAAATAGAAAAACCGGTTTAGGGAC 59.568 38.462 31.80 19.59 35.02 4.46
45 46 2.867624 AGAAAAACCGGTTTAGGGACC 58.132 47.619 31.80 16.49 36.31 4.46
46 47 2.444388 AGAAAAACCGGTTTAGGGACCT 59.556 45.455 31.80 18.21 37.56 3.85
47 48 3.117398 AGAAAAACCGGTTTAGGGACCTT 60.117 43.478 31.80 20.18 37.56 3.50
48 49 2.574006 AAACCGGTTTAGGGACCTTC 57.426 50.000 30.76 0.00 37.56 3.46
49 50 0.694771 AACCGGTTTAGGGACCTTCC 59.305 55.000 15.86 0.00 37.56 3.46
50 51 0.474273 ACCGGTTTAGGGACCTTCCA 60.474 55.000 0.00 0.00 38.64 3.53
51 52 0.252197 CCGGTTTAGGGACCTTCCAG 59.748 60.000 0.00 0.00 38.64 3.86
52 53 1.272807 CGGTTTAGGGACCTTCCAGA 58.727 55.000 0.00 0.00 38.64 3.86
53 54 1.626825 CGGTTTAGGGACCTTCCAGAA 59.373 52.381 0.00 0.00 38.64 3.02
54 55 2.354805 CGGTTTAGGGACCTTCCAGAAG 60.355 54.545 0.00 0.15 38.64 2.85
66 67 2.375014 TCCAGAAGGTTCCCAAAACC 57.625 50.000 0.00 0.00 40.58 3.27
67 68 0.958822 CCAGAAGGTTCCCAAAACCG 59.041 55.000 1.52 0.00 44.82 4.44
68 69 0.958822 CAGAAGGTTCCCAAAACCGG 59.041 55.000 0.00 0.00 44.82 5.28
69 70 0.554305 AGAAGGTTCCCAAAACCGGT 59.446 50.000 0.00 0.00 44.82 5.28
70 71 1.776063 AGAAGGTTCCCAAAACCGGTA 59.224 47.619 8.00 0.00 44.82 4.02
71 72 2.175284 AGAAGGTTCCCAAAACCGGTAA 59.825 45.455 8.00 0.00 44.82 2.85
72 73 2.752075 AGGTTCCCAAAACCGGTAAA 57.248 45.000 8.00 0.00 44.82 2.01
73 74 3.029483 AGGTTCCCAAAACCGGTAAAA 57.971 42.857 8.00 0.00 44.82 1.52
74 75 3.372897 AGGTTCCCAAAACCGGTAAAAA 58.627 40.909 8.00 0.00 44.82 1.94
75 76 3.132646 AGGTTCCCAAAACCGGTAAAAAC 59.867 43.478 8.00 7.07 44.82 2.43
76 77 3.456280 GTTCCCAAAACCGGTAAAAACC 58.544 45.455 8.00 0.00 0.00 3.27
77 78 2.743553 TCCCAAAACCGGTAAAAACCA 58.256 42.857 8.00 0.00 0.00 3.67
78 79 2.694109 TCCCAAAACCGGTAAAAACCAG 59.306 45.455 8.00 0.00 0.00 4.00
79 80 2.475818 CCAAAACCGGTAAAAACCAGC 58.524 47.619 8.00 0.00 0.00 4.85
80 81 2.101750 CCAAAACCGGTAAAAACCAGCT 59.898 45.455 8.00 0.00 0.00 4.24
81 82 3.120041 CAAAACCGGTAAAAACCAGCTG 58.880 45.455 8.00 6.78 0.00 4.24
82 83 2.061509 AACCGGTAAAAACCAGCTGT 57.938 45.000 8.00 0.00 0.00 4.40
83 84 1.314730 ACCGGTAAAAACCAGCTGTG 58.685 50.000 4.49 6.81 0.00 3.66
84 85 1.134037 ACCGGTAAAAACCAGCTGTGA 60.134 47.619 4.49 0.00 0.00 3.58
85 86 1.950909 CCGGTAAAAACCAGCTGTGAA 59.049 47.619 13.81 0.00 0.00 3.18
86 87 2.359531 CCGGTAAAAACCAGCTGTGAAA 59.640 45.455 13.81 0.00 0.00 2.69
87 88 3.368495 CGGTAAAAACCAGCTGTGAAAC 58.632 45.455 13.81 2.99 37.35 2.78
88 89 3.368495 GGTAAAAACCAGCTGTGAAACG 58.632 45.455 13.81 0.00 42.39 3.60
89 90 3.181494 GGTAAAAACCAGCTGTGAAACGT 60.181 43.478 13.81 0.00 42.39 3.99
90 91 2.844122 AAAACCAGCTGTGAAACGTC 57.156 45.000 13.81 0.00 42.39 4.34
91 92 2.038387 AAACCAGCTGTGAAACGTCT 57.962 45.000 13.81 0.00 42.39 4.18
92 93 2.902705 AACCAGCTGTGAAACGTCTA 57.097 45.000 13.81 0.00 42.39 2.59
93 94 2.440539 ACCAGCTGTGAAACGTCTAG 57.559 50.000 13.81 0.00 42.39 2.43
94 95 1.961394 ACCAGCTGTGAAACGTCTAGA 59.039 47.619 13.81 0.00 42.39 2.43
95 96 2.364324 ACCAGCTGTGAAACGTCTAGAA 59.636 45.455 13.81 0.00 42.39 2.10
96 97 2.989840 CCAGCTGTGAAACGTCTAGAAG 59.010 50.000 13.81 3.94 42.39 2.85
97 98 2.989840 CAGCTGTGAAACGTCTAGAAGG 59.010 50.000 5.25 0.68 42.39 3.46
98 99 2.628657 AGCTGTGAAACGTCTAGAAGGT 59.371 45.455 10.53 0.00 42.39 3.50
99 100 3.069729 AGCTGTGAAACGTCTAGAAGGTT 59.930 43.478 8.82 8.82 42.39 3.50
100 101 3.429207 GCTGTGAAACGTCTAGAAGGTTC 59.571 47.826 24.40 24.40 42.39 3.62
101 102 3.986277 TGTGAAACGTCTAGAAGGTTCC 58.014 45.455 26.90 19.88 42.39 3.62
102 103 3.243975 TGTGAAACGTCTAGAAGGTTCCC 60.244 47.826 26.90 19.37 42.39 3.97
103 104 2.967201 TGAAACGTCTAGAAGGTTCCCA 59.033 45.455 26.90 12.44 35.99 4.37
104 105 3.388676 TGAAACGTCTAGAAGGTTCCCAA 59.611 43.478 26.90 11.28 35.99 4.12
105 106 4.141665 TGAAACGTCTAGAAGGTTCCCAAA 60.142 41.667 26.90 10.97 35.99 3.28
106 107 4.426736 AACGTCTAGAAGGTTCCCAAAA 57.573 40.909 10.53 0.00 30.25 2.44
107 108 3.736720 ACGTCTAGAAGGTTCCCAAAAC 58.263 45.455 10.53 0.00 0.00 2.43
108 109 3.072211 CGTCTAGAAGGTTCCCAAAACC 58.928 50.000 0.00 0.00 40.58 3.27
109 110 3.072211 GTCTAGAAGGTTCCCAAAACCG 58.928 50.000 0.00 0.00 44.82 4.44
110 111 2.039348 TCTAGAAGGTTCCCAAAACCGG 59.961 50.000 0.00 0.00 44.82 5.28
111 112 0.848053 AGAAGGTTCCCAAAACCGGA 59.152 50.000 9.46 0.00 44.82 5.14
112 113 1.427753 AGAAGGTTCCCAAAACCGGAT 59.572 47.619 9.46 0.00 44.82 4.18
113 114 1.544246 GAAGGTTCCCAAAACCGGATG 59.456 52.381 9.46 3.78 44.82 3.51
114 115 0.251608 AGGTTCCCAAAACCGGATGG 60.252 55.000 9.46 13.68 44.82 3.51
118 119 3.287445 CCAAAACCGGATGGGCTG 58.713 61.111 9.46 0.00 40.62 4.85
131 132 3.521796 GGCTGGCCCAATTCGCTC 61.522 66.667 0.00 0.00 0.00 5.03
132 133 3.880846 GCTGGCCCAATTCGCTCG 61.881 66.667 0.00 0.00 0.00 5.03
133 134 3.880846 CTGGCCCAATTCGCTCGC 61.881 66.667 0.00 0.00 0.00 5.03
134 135 4.408821 TGGCCCAATTCGCTCGCT 62.409 61.111 0.00 0.00 0.00 4.93
135 136 2.203015 GGCCCAATTCGCTCGCTA 60.203 61.111 0.00 0.00 0.00 4.26
136 137 2.247437 GGCCCAATTCGCTCGCTAG 61.247 63.158 0.00 0.00 0.00 3.42
137 138 2.247437 GCCCAATTCGCTCGCTAGG 61.247 63.158 0.00 0.00 0.00 3.02
138 139 1.144057 CCCAATTCGCTCGCTAGGT 59.856 57.895 0.00 0.00 0.00 3.08
139 140 0.876342 CCCAATTCGCTCGCTAGGTC 60.876 60.000 0.00 0.00 0.00 3.85
140 141 1.209275 CCAATTCGCTCGCTAGGTCG 61.209 60.000 0.00 0.00 0.00 4.79
141 142 0.525668 CAATTCGCTCGCTAGGTCGT 60.526 55.000 0.00 0.00 0.00 4.34
142 143 0.248539 AATTCGCTCGCTAGGTCGTC 60.249 55.000 0.00 0.00 0.00 4.20
143 144 2.376231 ATTCGCTCGCTAGGTCGTCG 62.376 60.000 0.00 0.00 0.00 5.12
145 146 3.878519 GCTCGCTAGGTCGTCGCT 61.879 66.667 0.00 0.00 0.00 4.93
146 147 2.325166 CTCGCTAGGTCGTCGCTC 59.675 66.667 0.00 0.00 0.00 5.03
147 148 3.494454 CTCGCTAGGTCGTCGCTCG 62.494 68.421 0.00 0.00 41.41 5.03
148 149 3.862402 CGCTAGGTCGTCGCTCGT 61.862 66.667 0.00 0.00 40.80 4.18
149 150 2.023041 GCTAGGTCGTCGCTCGTC 59.977 66.667 0.00 0.00 40.80 4.20
150 151 2.462782 GCTAGGTCGTCGCTCGTCT 61.463 63.158 0.00 3.07 40.80 4.18
151 152 1.348938 CTAGGTCGTCGCTCGTCTG 59.651 63.158 0.00 0.00 40.80 3.51
152 153 1.360194 CTAGGTCGTCGCTCGTCTGT 61.360 60.000 0.00 0.00 40.80 3.41
153 154 1.632948 TAGGTCGTCGCTCGTCTGTG 61.633 60.000 0.00 0.00 40.80 3.66
154 155 3.166630 GTCGTCGCTCGTCTGTGC 61.167 66.667 0.00 0.00 40.80 4.57
160 161 2.583593 GCTCGTCTGTGCGATCCC 60.584 66.667 0.00 0.00 40.29 3.85
161 162 2.105128 CTCGTCTGTGCGATCCCC 59.895 66.667 0.00 0.00 40.29 4.81
162 163 3.432051 CTCGTCTGTGCGATCCCCC 62.432 68.421 0.00 0.00 40.29 5.40
163 164 4.873129 CGTCTGTGCGATCCCCCG 62.873 72.222 0.00 0.00 0.00 5.73
164 165 4.530857 GTCTGTGCGATCCCCCGG 62.531 72.222 0.00 0.00 0.00 5.73
170 171 4.796495 GCGATCCCCCGGCTGTTT 62.796 66.667 0.00 0.00 0.00 2.83
171 172 2.824041 CGATCCCCCGGCTGTTTG 60.824 66.667 0.00 0.00 0.00 2.93
172 173 2.674754 GATCCCCCGGCTGTTTGA 59.325 61.111 0.00 0.00 0.00 2.69
173 174 1.749258 GATCCCCCGGCTGTTTGAC 60.749 63.158 0.00 0.00 0.00 3.18
179 180 4.210447 CGGCTGTTTGACGCAAAG 57.790 55.556 5.45 0.00 41.83 2.77
180 181 1.646540 CGGCTGTTTGACGCAAAGA 59.353 52.632 5.45 4.19 41.83 2.52
181 182 0.384725 CGGCTGTTTGACGCAAAGAG 60.385 55.000 18.46 18.46 44.21 2.85
206 207 3.715628 CGATAGGATTTGCCCTTTTGG 57.284 47.619 0.00 0.00 37.74 3.28
207 208 3.287222 CGATAGGATTTGCCCTTTTGGA 58.713 45.455 0.00 0.00 44.07 3.53
208 209 3.066760 CGATAGGATTTGCCCTTTTGGAC 59.933 47.826 0.00 0.00 44.07 4.02
209 210 2.702270 AGGATTTGCCCTTTTGGACT 57.298 45.000 0.00 0.00 44.07 3.85
210 211 2.250924 AGGATTTGCCCTTTTGGACTG 58.749 47.619 0.00 0.00 44.07 3.51
211 212 1.338105 GGATTTGCCCTTTTGGACTGC 60.338 52.381 0.00 0.00 44.07 4.40
212 213 1.344114 GATTTGCCCTTTTGGACTGCA 59.656 47.619 0.00 0.00 44.07 4.41
213 214 1.198713 TTTGCCCTTTTGGACTGCAA 58.801 45.000 0.00 0.00 44.07 4.08
214 215 1.198713 TTGCCCTTTTGGACTGCAAA 58.801 45.000 0.00 0.00 39.90 3.68
215 216 0.463620 TGCCCTTTTGGACTGCAAAC 59.536 50.000 0.00 0.00 44.07 2.93
216 217 0.249868 GCCCTTTTGGACTGCAAACC 60.250 55.000 0.00 2.32 44.07 3.27
217 218 1.118838 CCCTTTTGGACTGCAAACCA 58.881 50.000 7.34 7.34 44.07 3.67
218 219 1.069049 CCCTTTTGGACTGCAAACCAG 59.931 52.381 10.66 1.92 44.07 4.00
219 220 1.538849 CCTTTTGGACTGCAAACCAGC 60.539 52.381 10.66 0.00 45.78 4.85
220 221 0.463620 TTTTGGACTGCAAACCAGCC 59.536 50.000 10.66 0.00 45.78 4.85
221 222 1.398958 TTTGGACTGCAAACCAGCCC 61.399 55.000 10.66 0.00 45.78 5.19
222 223 2.203480 GGACTGCAAACCAGCCCA 60.203 61.111 4.25 0.00 43.08 5.36
233 234 4.974721 CAGCCCAGCCCAAACGGT 62.975 66.667 0.00 0.00 0.00 4.83
250 251 1.078143 GTAAGCCTGACCCAGCCTG 60.078 63.158 0.00 0.00 0.00 4.85
261 262 1.307647 CCAGCCTGGCCTGGTATTT 59.692 57.895 27.68 10.30 45.87 1.40
271 272 1.937191 CCTGGTATTTTTGGGCCAGT 58.063 50.000 6.23 0.00 45.08 4.00
277 285 0.406361 ATTTTTGGGCCAGTCGGGTA 59.594 50.000 6.23 0.00 39.65 3.69
281 289 3.834799 GGGCCAGTCGGGTAGTCG 61.835 72.222 4.39 0.00 39.65 4.18
322 335 2.539274 TGTTTAGTTGTACGTGCCGTTC 59.461 45.455 0.00 2.00 41.54 3.95
323 336 1.407434 TTAGTTGTACGTGCCGTTCG 58.593 50.000 0.00 0.00 41.54 3.95
335 348 3.870606 CGTTCGCCGGAGTTGATT 58.129 55.556 5.05 0.00 0.00 2.57
338 351 1.463528 CGTTCGCCGGAGTTGATTTTC 60.464 52.381 5.05 0.00 0.00 2.29
343 356 4.066490 TCGCCGGAGTTGATTTTCTTTTA 58.934 39.130 5.05 0.00 0.00 1.52
344 357 4.515944 TCGCCGGAGTTGATTTTCTTTTAA 59.484 37.500 5.05 0.00 0.00 1.52
346 359 5.861787 CGCCGGAGTTGATTTTCTTTTAATT 59.138 36.000 5.05 0.00 0.00 1.40
347 360 6.033513 CGCCGGAGTTGATTTTCTTTTAATTC 59.966 38.462 5.05 0.00 0.00 2.17
348 361 7.090808 GCCGGAGTTGATTTTCTTTTAATTCT 58.909 34.615 5.05 0.00 0.00 2.40
349 362 7.273598 GCCGGAGTTGATTTTCTTTTAATTCTC 59.726 37.037 5.05 0.00 0.00 2.87
351 364 9.677567 CGGAGTTGATTTTCTTTTAATTCTCAA 57.322 29.630 0.00 0.00 0.00 3.02
416 429 4.400961 GAGGAGCACGGGCAGCTT 62.401 66.667 14.57 0.00 43.58 3.74
478 491 1.666209 ATTAATGGCGGCCACTGCAC 61.666 55.000 26.48 0.00 40.13 4.57
689 703 4.087892 CGAGCTGGAGGTGGGTGG 62.088 72.222 0.00 0.00 0.00 4.61
740 754 3.199561 CTCGCCTCGATCCGCATCA 62.200 63.158 0.00 0.00 34.61 3.07
750 764 3.067601 TCGATCCGCATCAGCTTACTTAA 59.932 43.478 0.00 0.00 39.10 1.85
763 777 0.179067 TACTTAATCTTGCGCCGGGG 60.179 55.000 15.40 15.40 0.00 5.73
843 857 2.993008 TGGATGACCAGCTCCTGC 59.007 61.111 0.00 0.00 41.77 4.85
865 879 2.245438 CTTTCTCGGGGGACTGGAGC 62.245 65.000 0.00 0.00 37.31 4.70
892 907 1.519455 CGAGGTTGGTGAGCGATCC 60.519 63.158 0.00 0.00 0.00 3.36
926 941 0.719465 CGCGCTTAAGGTGTTCGATT 59.281 50.000 5.56 0.00 0.00 3.34
938 953 0.026285 GTTCGATTGATTGCCGACCG 59.974 55.000 0.00 0.00 31.60 4.79
1491 1511 4.329545 GGCCTGCCGTCCACTGAA 62.330 66.667 0.00 0.00 0.00 3.02
1666 1687 5.474578 TGTATCTTGCTCTGTCTTTGTCT 57.525 39.130 0.00 0.00 0.00 3.41
1714 1735 2.358898 GCGTGCAATCATTTGGTATCCT 59.641 45.455 0.00 0.00 33.22 3.24
1784 1805 7.516198 AGTTATTTTCTTCTGCAGTGATTGT 57.484 32.000 14.67 5.28 0.00 2.71
1804 1825 6.844696 TTGTAACTCACTGTTTGATGAGAC 57.155 37.500 8.18 0.00 44.32 3.36
1805 1826 5.297547 TGTAACTCACTGTTTGATGAGACC 58.702 41.667 8.18 0.00 44.32 3.85
1814 1835 6.797033 CACTGTTTGATGAGACCGAAAAATAC 59.203 38.462 0.00 0.00 0.00 1.89
1825 1846 7.170998 TGAGACCGAAAAATACAGAACTTTCTC 59.829 37.037 0.00 0.00 34.74 2.87
1867 1888 9.561270 GTGAAAGCTTTATGAAAGAATACTTCC 57.439 33.333 12.68 0.00 41.02 3.46
1892 1913 7.083858 CGATCAAAGGAAAAACATGCTTAAGA 58.916 34.615 6.67 0.00 30.13 2.10
1898 1919 6.974965 AGGAAAAACATGCTTAAGACTTGAG 58.025 36.000 6.67 2.65 0.00 3.02
1900 1921 7.449704 AGGAAAAACATGCTTAAGACTTGAGAT 59.550 33.333 10.99 0.00 0.00 2.75
1902 1923 9.122613 GAAAAACATGCTTAAGACTTGAGATTC 57.877 33.333 10.99 8.93 0.00 2.52
1904 1925 6.981762 ACATGCTTAAGACTTGAGATTCTG 57.018 37.500 10.99 4.63 0.00 3.02
1905 1926 5.353678 ACATGCTTAAGACTTGAGATTCTGC 59.646 40.000 10.99 0.00 0.00 4.26
1909 1930 6.102663 GCTTAAGACTTGAGATTCTGCTGTA 58.897 40.000 10.99 0.00 0.00 2.74
1910 1931 6.255453 GCTTAAGACTTGAGATTCTGCTGTAG 59.745 42.308 10.99 0.00 0.00 2.74
1911 1932 5.736951 AAGACTTGAGATTCTGCTGTAGT 57.263 39.130 0.00 0.00 0.00 2.73
1912 1933 5.323371 AGACTTGAGATTCTGCTGTAGTC 57.677 43.478 0.00 0.00 0.00 2.59
1917 1947 6.426328 ACTTGAGATTCTGCTGTAGTCTTTTG 59.574 38.462 0.00 0.00 0.00 2.44
1937 1967 1.133790 GGTCTGCAGTTCATGGCAATC 59.866 52.381 14.67 0.00 39.93 2.67
1961 1991 2.902523 TCAGCACATGAGATTCTGCTC 58.097 47.619 0.00 0.00 37.91 4.26
2113 2144 4.097286 GCACCAACCTTCAGTTTACTCAAA 59.903 41.667 0.00 0.00 36.18 2.69
2222 2264 8.837099 ATATTTTTGTTAATCACCTGGGATGA 57.163 30.769 0.00 0.00 0.00 2.92
2258 2300 8.946085 CCAACTTGATTTTATACAGAAGTAGCA 58.054 33.333 0.00 0.00 32.86 3.49
2292 2334 6.656693 ACATCTAGGATTTGGAGTGAGTTTTG 59.343 38.462 0.00 0.00 0.00 2.44
2300 2342 7.595130 GGATTTGGAGTGAGTTTTGATGTTAAC 59.405 37.037 0.00 0.00 0.00 2.01
2333 2375 6.172630 TGCTACAAAGAGTGATTTCATAGCA 58.827 36.000 5.95 5.95 39.39 3.49
2382 2424 6.377327 AAAGACGTTTTGATCTTGACATGT 57.623 33.333 0.00 0.00 35.34 3.21
2405 2447 7.903145 TGTACTGTTGGACTCATGTACTTAAT 58.097 34.615 0.00 0.00 33.59 1.40
2450 2493 5.148502 CCTCTTGGGTATACATCACCTACT 58.851 45.833 5.01 0.00 36.25 2.57
2517 2560 2.933906 GCTAACGCCAAAGCACTATACA 59.066 45.455 0.00 0.00 39.83 2.29
2518 2561 3.560068 GCTAACGCCAAAGCACTATACAT 59.440 43.478 0.00 0.00 39.83 2.29
2548 2591 1.662629 GACGTGATGCACATCTTCTGG 59.337 52.381 11.66 0.33 38.60 3.86
2693 2736 0.887387 TTACAGCTGGCGTTCCAACC 60.887 55.000 19.93 0.00 42.91 3.77
2819 2862 2.661594 GCTAAGTTTTTGAGGCAACCG 58.338 47.619 0.00 0.00 37.17 4.44
2847 2890 4.764823 TCATTGTTTGGGATAACAGTGACC 59.235 41.667 9.64 0.00 44.58 4.02
2962 3005 5.192927 TGCTCACCCAAATAAGGACATTAG 58.807 41.667 0.00 0.00 0.00 1.73
3062 3202 5.063880 AGAATGTGTGAGTTTACTTGGTCC 58.936 41.667 0.00 0.00 0.00 4.46
3127 3275 1.403323 GGCTAGCTTGAAATCACAGGC 59.597 52.381 15.72 0.00 41.95 4.85
3142 3290 1.961277 AGGCAGCAACCTCGTTTCG 60.961 57.895 0.00 0.00 33.62 3.46
3145 3293 0.028902 GCAGCAACCTCGTTTCGTTT 59.971 50.000 0.00 0.00 0.00 3.60
3167 3386 9.113876 CGTTTTTGTCAAAAAGTATATGTCCTC 57.886 33.333 21.07 6.63 40.71 3.71
3221 3440 2.923020 GCTCCATGGCAATTTAAACACG 59.077 45.455 6.96 0.00 0.00 4.49
3227 3446 5.007136 CCATGGCAATTTAAACACGTGTTTT 59.993 36.000 41.66 26.67 45.07 2.43
3279 3498 3.913089 AGTTATTTGCCTTTTCTTGCCG 58.087 40.909 0.00 0.00 0.00 5.69
3289 3508 3.981416 CCTTTTCTTGCCGTAAAAGAAGC 59.019 43.478 13.20 0.00 42.82 3.86
3294 3513 3.065648 TCTTGCCGTAAAAGAAGCGTTTT 59.934 39.130 0.00 1.07 30.79 2.43
3295 3514 2.722071 TGCCGTAAAAGAAGCGTTTTG 58.278 42.857 5.14 0.00 31.96 2.44
3297 3516 2.717519 GCCGTAAAAGAAGCGTTTTGTC 59.282 45.455 5.14 0.00 31.96 3.18
3299 3518 4.594136 CCGTAAAAGAAGCGTTTTGTCTT 58.406 39.130 5.14 0.00 33.01 3.01
3300 3519 5.032220 CCGTAAAAGAAGCGTTTTGTCTTT 58.968 37.500 5.14 0.00 42.07 2.52
3332 3551 6.052840 CAAGGTATTTGCTACTATGTGCTG 57.947 41.667 0.00 0.00 0.00 4.41
3581 3800 0.610687 CGAAGGGAGAACTCAGGCTT 59.389 55.000 4.23 0.00 0.00 4.35
3599 3818 5.012046 CAGGCTTGATATGGGTGACAGTATA 59.988 44.000 0.00 0.00 0.00 1.47
3629 3848 4.310740 AGGGGATGATTCAGGTTATGTCT 58.689 43.478 0.00 0.00 0.00 3.41
3641 3860 5.246203 TCAGGTTATGTCTTAGCAGTGTTCT 59.754 40.000 0.00 0.00 0.00 3.01
3697 3916 8.943002 TGCTGAGCATGTCTGAATAATAATATG 58.057 33.333 1.40 0.00 31.71 1.78
3783 4006 8.525729 AATCCCTGTTATCTATAATGGTTCCT 57.474 34.615 0.00 0.00 0.00 3.36
3851 4074 5.914898 TGCACTAACTGAGTATAAGCTCA 57.085 39.130 0.00 0.00 42.56 4.26
3852 4075 6.471233 TGCACTAACTGAGTATAAGCTCAT 57.529 37.500 0.00 0.00 43.61 2.90
3856 4079 7.254252 GCACTAACTGAGTATAAGCTCATTGTG 60.254 40.741 0.00 0.00 43.61 3.33
4017 4240 9.965902 ATAGAATTCTGATAAAAAGGTCTGTGT 57.034 29.630 18.47 0.00 0.00 3.72
4018 4241 8.103948 AGAATTCTGATAAAAAGGTCTGTGTG 57.896 34.615 7.30 0.00 0.00 3.82
4019 4242 5.689383 TTCTGATAAAAAGGTCTGTGTGC 57.311 39.130 0.00 0.00 0.00 4.57
4020 4243 4.072131 TCTGATAAAAAGGTCTGTGTGCC 58.928 43.478 0.00 0.00 0.00 5.01
4058 4283 1.813513 TGGCTTGCTCTGCTTACTTC 58.186 50.000 0.00 0.00 0.00 3.01
4078 4303 5.646793 ACTTCGACTATGTACAGAGTGCTTA 59.353 40.000 26.91 9.04 32.31 3.09
4112 4378 2.500098 AGTCCATTGCCGCTTCTAGTTA 59.500 45.455 0.00 0.00 0.00 2.24
4115 4381 2.808543 CCATTGCCGCTTCTAGTTATCC 59.191 50.000 0.00 0.00 0.00 2.59
4125 4391 1.412710 TCTAGTTATCCCTTGCCAGCG 59.587 52.381 0.00 0.00 0.00 5.18
4134 4400 1.641577 CCTTGCCAGCGTAACTAGAC 58.358 55.000 0.00 0.00 0.00 2.59
4140 4406 3.121544 GCCAGCGTAACTAGACAATACC 58.878 50.000 0.00 0.00 0.00 2.73
4141 4407 3.429822 GCCAGCGTAACTAGACAATACCA 60.430 47.826 0.00 0.00 0.00 3.25
4160 4426 7.849804 ATACCATTAACTGCTAACAAGACAG 57.150 36.000 0.00 0.00 37.45 3.51
4161 4427 4.455877 ACCATTAACTGCTAACAAGACAGC 59.544 41.667 0.00 0.00 38.31 4.40
4168 4434 2.613595 TGCTAACAAGACAGCAACACAG 59.386 45.455 0.00 0.00 44.49 3.66
4169 4435 2.603173 GCTAACAAGACAGCAACACAGC 60.603 50.000 0.00 0.00 37.73 4.40
4184 4450 3.515630 ACACAGCTGATACATGAACTCG 58.484 45.455 23.35 0.00 0.00 4.18
4189 4455 2.860735 GCTGATACATGAACTCGGTGTC 59.139 50.000 0.00 0.00 0.00 3.67
4192 4458 0.108992 TACATGAACTCGGTGTCGGC 60.109 55.000 0.00 0.00 36.95 5.54
4205 4471 1.452108 GTCGGCCCAGCAGCTTATT 60.452 57.895 0.00 0.00 0.00 1.40
4276 4542 6.375945 AATCAAAAGTTGTTTGCCCATTTC 57.624 33.333 0.00 0.00 0.00 2.17
4290 4556 2.624636 CCATTTCAGGCCATGCTTTTC 58.375 47.619 5.01 0.00 0.00 2.29
4301 4567 2.419667 CATGCTTTTCCCCTTTGCTTG 58.580 47.619 0.00 0.00 0.00 4.01
4323 4589 6.194796 TGCAGCCAAATATACTCTGTTTTC 57.805 37.500 0.00 0.00 0.00 2.29
4409 4854 5.761726 TCAATACATGATCAACCATCAGCTC 59.238 40.000 0.00 0.00 45.11 4.09
4570 5015 1.361993 GATCGAGATGGCGCAGAGT 59.638 57.895 10.83 0.00 0.00 3.24
4574 5019 1.875813 GAGATGGCGCAGAGTCACG 60.876 63.158 10.83 1.53 37.24 4.35
4594 5039 1.445582 GTTCTACCGCCCGTCACTG 60.446 63.158 0.00 0.00 0.00 3.66
5403 6155 4.500837 CGTGGTTCATAGTGAAATCTCTCG 59.499 45.833 0.00 0.00 38.22 4.04
5406 6158 6.254589 GTGGTTCATAGTGAAATCTCTCGAAG 59.745 42.308 0.00 0.00 38.22 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.923143 CCGGTTTTTCTATTTCTCCTTTTTATT 57.077 29.630 0.00 0.00 0.00 1.40
10 11 9.085645 ACCGGTTTTTCTATTTCTCCTTTTTAT 57.914 29.630 0.00 0.00 0.00 1.40
11 12 8.467963 ACCGGTTTTTCTATTTCTCCTTTTTA 57.532 30.769 0.00 0.00 0.00 1.52
12 13 7.356089 ACCGGTTTTTCTATTTCTCCTTTTT 57.644 32.000 0.00 0.00 0.00 1.94
13 14 6.971726 ACCGGTTTTTCTATTTCTCCTTTT 57.028 33.333 0.00 0.00 0.00 2.27
14 15 6.971726 AACCGGTTTTTCTATTTCTCCTTT 57.028 33.333 15.86 0.00 0.00 3.11
15 16 6.971726 AAACCGGTTTTTCTATTTCTCCTT 57.028 33.333 26.87 0.00 0.00 3.36
16 17 6.657966 CCTAAACCGGTTTTTCTATTTCTCCT 59.342 38.462 35.69 10.63 34.23 3.69
17 18 6.127814 CCCTAAACCGGTTTTTCTATTTCTCC 60.128 42.308 35.69 0.00 34.23 3.71
18 19 6.656270 TCCCTAAACCGGTTTTTCTATTTCTC 59.344 38.462 35.69 0.00 34.23 2.87
19 20 6.432162 GTCCCTAAACCGGTTTTTCTATTTCT 59.568 38.462 35.69 11.84 34.23 2.52
20 21 6.349611 GGTCCCTAAACCGGTTTTTCTATTTC 60.350 42.308 35.69 18.02 34.23 2.17
21 22 5.477984 GGTCCCTAAACCGGTTTTTCTATTT 59.522 40.000 35.69 13.37 34.23 1.40
22 23 5.012239 GGTCCCTAAACCGGTTTTTCTATT 58.988 41.667 35.69 14.14 34.23 1.73
23 24 4.290459 AGGTCCCTAAACCGGTTTTTCTAT 59.710 41.667 35.69 14.91 44.49 1.98
24 25 3.652387 AGGTCCCTAAACCGGTTTTTCTA 59.348 43.478 35.69 18.09 44.49 2.10
25 26 2.444388 AGGTCCCTAAACCGGTTTTTCT 59.556 45.455 35.69 20.04 44.49 2.52
26 27 2.867624 AGGTCCCTAAACCGGTTTTTC 58.132 47.619 35.69 20.20 44.49 2.29
27 28 3.225104 GAAGGTCCCTAAACCGGTTTTT 58.775 45.455 35.69 22.17 44.49 1.94
28 29 2.489619 GGAAGGTCCCTAAACCGGTTTT 60.490 50.000 35.69 20.20 44.49 2.43
29 30 1.074405 GGAAGGTCCCTAAACCGGTTT 59.926 52.381 33.42 33.42 44.49 3.27
30 31 0.694771 GGAAGGTCCCTAAACCGGTT 59.305 55.000 15.86 15.86 44.49 4.44
31 32 0.474273 TGGAAGGTCCCTAAACCGGT 60.474 55.000 0.00 0.00 44.49 5.28
32 33 0.252197 CTGGAAGGTCCCTAAACCGG 59.748 60.000 0.00 0.00 44.49 5.28
33 34 1.272807 TCTGGAAGGTCCCTAAACCG 58.727 55.000 0.00 0.00 44.49 4.44
34 35 3.351794 CTTCTGGAAGGTCCCTAAACC 57.648 52.381 2.66 0.00 39.80 3.27
55 56 3.118847 TGGTTTTTACCGGTTTTGGGAAC 60.119 43.478 15.04 9.67 29.20 3.62
56 57 3.102204 TGGTTTTTACCGGTTTTGGGAA 58.898 40.909 15.04 0.00 0.00 3.97
57 58 2.694109 CTGGTTTTTACCGGTTTTGGGA 59.306 45.455 15.04 0.00 0.00 4.37
58 59 2.803852 GCTGGTTTTTACCGGTTTTGGG 60.804 50.000 15.04 0.00 38.40 4.12
59 60 2.101750 AGCTGGTTTTTACCGGTTTTGG 59.898 45.455 15.04 0.00 38.40 3.28
60 61 3.120041 CAGCTGGTTTTTACCGGTTTTG 58.880 45.455 15.04 0.00 38.40 2.44
61 62 2.761767 ACAGCTGGTTTTTACCGGTTTT 59.238 40.909 15.04 0.00 38.40 2.43
62 63 2.100087 CACAGCTGGTTTTTACCGGTTT 59.900 45.455 15.04 0.00 38.40 3.27
63 64 1.679153 CACAGCTGGTTTTTACCGGTT 59.321 47.619 15.04 0.00 38.40 4.44
64 65 1.134037 TCACAGCTGGTTTTTACCGGT 60.134 47.619 19.93 13.98 38.40 5.28
65 66 1.600023 TCACAGCTGGTTTTTACCGG 58.400 50.000 19.93 0.00 39.14 5.28
66 67 3.368495 GTTTCACAGCTGGTTTTTACCG 58.632 45.455 19.93 0.00 0.00 4.02
67 68 3.181494 ACGTTTCACAGCTGGTTTTTACC 60.181 43.478 19.93 0.00 0.00 2.85
68 69 4.023739 ACGTTTCACAGCTGGTTTTTAC 57.976 40.909 19.93 7.22 0.00 2.01
69 70 3.942748 AGACGTTTCACAGCTGGTTTTTA 59.057 39.130 19.93 0.00 0.00 1.52
70 71 2.752903 AGACGTTTCACAGCTGGTTTTT 59.247 40.909 19.93 0.00 0.00 1.94
71 72 2.365582 AGACGTTTCACAGCTGGTTTT 58.634 42.857 19.93 0.00 0.00 2.43
72 73 2.038387 AGACGTTTCACAGCTGGTTT 57.962 45.000 19.93 0.00 0.00 3.27
73 74 2.364324 TCTAGACGTTTCACAGCTGGTT 59.636 45.455 19.93 0.00 0.00 3.67
74 75 1.961394 TCTAGACGTTTCACAGCTGGT 59.039 47.619 19.93 4.52 0.00 4.00
75 76 2.724977 TCTAGACGTTTCACAGCTGG 57.275 50.000 19.93 7.28 0.00 4.85
76 77 2.989840 CCTTCTAGACGTTTCACAGCTG 59.010 50.000 13.48 13.48 0.00 4.24
77 78 2.628657 ACCTTCTAGACGTTTCACAGCT 59.371 45.455 0.00 0.00 0.00 4.24
78 79 3.027974 ACCTTCTAGACGTTTCACAGC 57.972 47.619 0.00 0.00 0.00 4.40
79 80 3.988517 GGAACCTTCTAGACGTTTCACAG 59.011 47.826 8.46 0.00 0.00 3.66
80 81 3.986277 GGAACCTTCTAGACGTTTCACA 58.014 45.455 8.46 0.00 0.00 3.58
101 102 2.350458 CCAGCCCATCCGGTTTTGG 61.350 63.158 0.00 7.62 0.00 3.28
102 103 3.005540 GCCAGCCCATCCGGTTTTG 62.006 63.158 0.00 0.00 0.00 2.44
103 104 2.679996 GCCAGCCCATCCGGTTTT 60.680 61.111 0.00 0.00 0.00 2.43
104 105 4.759205 GGCCAGCCCATCCGGTTT 62.759 66.667 0.00 0.00 0.00 3.27
114 115 3.521796 GAGCGAATTGGGCCAGCC 61.522 66.667 6.23 0.00 0.00 4.85
115 116 3.880846 CGAGCGAATTGGGCCAGC 61.881 66.667 6.23 6.88 0.00 4.85
116 117 2.923426 TAGCGAGCGAATTGGGCCAG 62.923 60.000 6.23 0.00 0.00 4.85
117 118 2.923426 CTAGCGAGCGAATTGGGCCA 62.923 60.000 0.00 0.00 0.00 5.36
118 119 2.203015 TAGCGAGCGAATTGGGCC 60.203 61.111 0.00 0.00 0.00 5.80
119 120 2.247437 CCTAGCGAGCGAATTGGGC 61.247 63.158 0.00 0.00 0.00 5.36
120 121 0.876342 GACCTAGCGAGCGAATTGGG 60.876 60.000 0.00 0.00 0.00 4.12
121 122 1.209275 CGACCTAGCGAGCGAATTGG 61.209 60.000 0.00 0.00 0.00 3.16
122 123 0.525668 ACGACCTAGCGAGCGAATTG 60.526 55.000 1.27 0.00 34.83 2.32
123 124 0.248539 GACGACCTAGCGAGCGAATT 60.249 55.000 1.27 0.00 34.83 2.17
124 125 1.355916 GACGACCTAGCGAGCGAAT 59.644 57.895 1.27 0.00 34.83 3.34
125 126 2.789917 GACGACCTAGCGAGCGAA 59.210 61.111 1.27 0.00 34.83 4.70
126 127 3.561213 CGACGACCTAGCGAGCGA 61.561 66.667 1.27 0.00 35.76 4.93
128 129 3.793603 GAGCGACGACCTAGCGAGC 62.794 68.421 0.00 0.00 38.16 5.03
129 130 2.325166 GAGCGACGACCTAGCGAG 59.675 66.667 0.00 0.00 35.78 5.03
130 131 3.561213 CGAGCGACGACCTAGCGA 61.561 66.667 0.00 0.00 45.77 4.93
131 132 3.770353 GACGAGCGACGACCTAGCG 62.770 68.421 12.62 0.00 45.77 4.26
132 133 2.023041 GACGAGCGACGACCTAGC 59.977 66.667 12.62 0.00 45.77 3.42
133 134 1.348938 CAGACGAGCGACGACCTAG 59.651 63.158 12.62 0.00 45.77 3.02
134 135 1.375140 ACAGACGAGCGACGACCTA 60.375 57.895 12.62 0.00 45.77 3.08
135 136 2.668889 ACAGACGAGCGACGACCT 60.669 61.111 12.62 6.74 45.77 3.85
136 137 2.502080 CACAGACGAGCGACGACC 60.502 66.667 12.62 4.86 45.77 4.79
137 138 3.166630 GCACAGACGAGCGACGAC 61.167 66.667 12.62 6.97 45.77 4.34
143 144 2.583593 GGGATCGCACAGACGAGC 60.584 66.667 4.64 0.00 46.69 5.03
144 145 2.105128 GGGGATCGCACAGACGAG 59.895 66.667 12.32 0.00 46.69 4.18
146 147 4.873129 CGGGGGATCGCACAGACG 62.873 72.222 13.04 4.53 0.00 4.18
147 148 4.530857 CCGGGGGATCGCACAGAC 62.531 72.222 13.04 0.00 0.00 3.51
153 154 4.796495 AAACAGCCGGGGGATCGC 62.796 66.667 2.18 0.06 0.00 4.58
154 155 2.824041 CAAACAGCCGGGGGATCG 60.824 66.667 2.18 0.00 0.00 3.69
155 156 1.749258 GTCAAACAGCCGGGGGATC 60.749 63.158 2.18 0.00 0.00 3.36
156 157 2.355115 GTCAAACAGCCGGGGGAT 59.645 61.111 2.18 0.00 0.00 3.85
157 158 4.323477 CGTCAAACAGCCGGGGGA 62.323 66.667 2.18 0.00 0.00 4.81
160 161 2.731587 CTTTGCGTCAAACAGCCGGG 62.732 60.000 2.18 0.00 0.00 5.73
161 162 1.370414 CTTTGCGTCAAACAGCCGG 60.370 57.895 0.00 0.00 0.00 6.13
162 163 0.384725 CTCTTTGCGTCAAACAGCCG 60.385 55.000 1.63 0.00 0.00 5.52
163 164 0.661483 GCTCTTTGCGTCAAACAGCC 60.661 55.000 16.00 4.83 38.69 4.85
164 165 2.788535 GCTCTTTGCGTCAAACAGC 58.211 52.632 13.40 13.40 37.95 4.40
174 175 0.102481 TCCTATCGGACGCTCTTTGC 59.898 55.000 0.00 0.00 33.30 3.68
175 176 2.802787 ATCCTATCGGACGCTCTTTG 57.197 50.000 0.00 0.00 43.51 2.77
176 177 3.458189 CAAATCCTATCGGACGCTCTTT 58.542 45.455 0.00 0.00 43.51 2.52
177 178 2.803492 GCAAATCCTATCGGACGCTCTT 60.803 50.000 0.00 0.00 43.51 2.85
178 179 1.269831 GCAAATCCTATCGGACGCTCT 60.270 52.381 0.00 0.00 43.51 4.09
179 180 1.140816 GCAAATCCTATCGGACGCTC 58.859 55.000 0.00 0.00 43.51 5.03
180 181 0.249911 GGCAAATCCTATCGGACGCT 60.250 55.000 0.00 0.00 43.51 5.07
181 182 1.228657 GGGCAAATCCTATCGGACGC 61.229 60.000 0.00 0.00 43.51 5.19
182 183 0.393077 AGGGCAAATCCTATCGGACG 59.607 55.000 0.00 0.00 43.51 4.79
183 184 2.640316 AAGGGCAAATCCTATCGGAC 57.360 50.000 0.00 0.00 43.51 4.79
184 185 3.287222 CAAAAGGGCAAATCCTATCGGA 58.713 45.455 0.00 0.00 45.16 4.55
185 186 2.362077 CCAAAAGGGCAAATCCTATCGG 59.638 50.000 0.00 0.00 35.80 4.18
186 187 3.066760 GTCCAAAAGGGCAAATCCTATCG 59.933 47.826 0.00 0.00 35.80 2.92
187 188 4.098501 CAGTCCAAAAGGGCAAATCCTATC 59.901 45.833 0.00 0.00 35.80 2.08
188 189 4.026052 CAGTCCAAAAGGGCAAATCCTAT 58.974 43.478 0.00 0.00 35.80 2.57
189 190 3.430453 CAGTCCAAAAGGGCAAATCCTA 58.570 45.455 0.00 0.00 35.80 2.94
190 191 2.250924 CAGTCCAAAAGGGCAAATCCT 58.749 47.619 0.00 0.00 39.17 3.24
191 192 1.338105 GCAGTCCAAAAGGGCAAATCC 60.338 52.381 0.00 0.00 36.21 3.01
192 193 1.344114 TGCAGTCCAAAAGGGCAAATC 59.656 47.619 0.00 0.00 36.21 2.17
193 194 1.422531 TGCAGTCCAAAAGGGCAAAT 58.577 45.000 0.00 0.00 36.21 2.32
194 195 1.198713 TTGCAGTCCAAAAGGGCAAA 58.801 45.000 0.00 0.00 41.05 3.68
195 196 1.134551 GTTTGCAGTCCAAAAGGGCAA 60.135 47.619 0.00 0.00 44.48 4.52
196 197 0.463620 GTTTGCAGTCCAAAAGGGCA 59.536 50.000 0.00 0.00 44.48 5.36
197 198 0.249868 GGTTTGCAGTCCAAAAGGGC 60.250 55.000 4.67 0.00 44.48 5.19
198 199 1.069049 CTGGTTTGCAGTCCAAAAGGG 59.931 52.381 11.94 0.00 44.48 3.95
199 200 1.538849 GCTGGTTTGCAGTCCAAAAGG 60.539 52.381 11.94 3.58 44.48 3.11
200 201 1.538849 GGCTGGTTTGCAGTCCAAAAG 60.539 52.381 11.94 3.87 44.48 2.27
201 202 0.463620 GGCTGGTTTGCAGTCCAAAA 59.536 50.000 11.94 0.00 44.48 2.44
202 203 1.398958 GGGCTGGTTTGCAGTCCAAA 61.399 55.000 11.94 0.00 43.55 3.28
203 204 1.832167 GGGCTGGTTTGCAGTCCAA 60.832 57.895 11.94 0.00 43.55 3.53
204 205 2.203480 GGGCTGGTTTGCAGTCCA 60.203 61.111 10.69 10.69 43.55 4.02
205 206 2.203480 TGGGCTGGTTTGCAGTCC 60.203 61.111 0.00 0.00 44.31 3.85
206 207 2.924105 GCTGGGCTGGTTTGCAGTC 61.924 63.158 0.00 0.00 34.04 3.51
207 208 2.914097 GCTGGGCTGGTTTGCAGT 60.914 61.111 0.00 0.00 34.04 4.40
208 209 3.688159 GGCTGGGCTGGTTTGCAG 61.688 66.667 0.00 0.00 34.04 4.41
211 212 2.139484 TTTGGGCTGGGCTGGTTTG 61.139 57.895 0.00 0.00 0.00 2.93
212 213 2.140138 GTTTGGGCTGGGCTGGTTT 61.140 57.895 0.00 0.00 0.00 3.27
213 214 2.524148 GTTTGGGCTGGGCTGGTT 60.524 61.111 0.00 0.00 0.00 3.67
214 215 4.974721 CGTTTGGGCTGGGCTGGT 62.975 66.667 0.00 0.00 0.00 4.00
216 217 3.561120 TACCGTTTGGGCTGGGCTG 62.561 63.158 0.00 0.00 40.62 4.85
217 218 2.764637 CTTACCGTTTGGGCTGGGCT 62.765 60.000 0.00 0.00 40.62 5.19
218 219 2.282603 TTACCGTTTGGGCTGGGC 60.283 61.111 0.00 0.00 40.62 5.36
219 220 2.340328 GCTTACCGTTTGGGCTGGG 61.340 63.158 0.00 0.00 40.62 4.45
220 221 2.340328 GGCTTACCGTTTGGGCTGG 61.340 63.158 0.00 0.00 40.62 4.85
221 222 1.303317 AGGCTTACCGTTTGGGCTG 60.303 57.895 0.00 0.00 42.76 4.85
222 223 1.303317 CAGGCTTACCGTTTGGGCT 60.303 57.895 0.00 0.00 42.76 5.19
261 262 1.833787 GACTACCCGACTGGCCCAAA 61.834 60.000 0.00 0.00 37.83 3.28
322 335 2.989422 AAAGAAAATCAACTCCGGCG 57.011 45.000 0.00 0.00 0.00 6.46
323 336 7.090808 AGAATTAAAAGAAAATCAACTCCGGC 58.909 34.615 0.00 0.00 0.00 6.13
370 383 0.877071 GGAGACGACGACTTGGTACA 59.123 55.000 0.00 0.00 0.00 2.90
371 384 0.169894 GGGAGACGACGACTTGGTAC 59.830 60.000 0.00 0.00 0.00 3.34
372 385 0.962356 GGGGAGACGACGACTTGGTA 60.962 60.000 0.00 0.00 0.00 3.25
373 386 2.273912 GGGGAGACGACGACTTGGT 61.274 63.158 0.00 0.00 0.00 3.67
374 387 2.572284 GGGGAGACGACGACTTGG 59.428 66.667 0.00 0.00 0.00 3.61
375 388 2.572284 GGGGGAGACGACGACTTG 59.428 66.667 0.00 0.00 0.00 3.16
492 505 0.541296 CATTGATGGGGGAGATGGGC 60.541 60.000 0.00 0.00 0.00 5.36
740 754 1.933853 CGGCGCAAGATTAAGTAAGCT 59.066 47.619 10.83 0.00 43.02 3.74
763 777 3.357079 CCGTTGGAGCACTGCACC 61.357 66.667 10.38 10.38 39.68 5.01
843 857 0.321653 CCAGTCCCCCGAGAAAGTTG 60.322 60.000 0.00 0.00 0.00 3.16
865 879 1.000060 TCACCAACCTCGAACCTAACG 60.000 52.381 0.00 0.00 0.00 3.18
901 916 2.434359 ACCTTAAGCGCGTGCCTC 60.434 61.111 19.02 0.00 44.31 4.70
902 917 2.742372 CACCTTAAGCGCGTGCCT 60.742 61.111 19.02 7.46 44.31 4.75
906 921 0.389426 ATCGAACACCTTAAGCGCGT 60.389 50.000 8.43 0.00 0.00 6.01
926 941 3.700970 TGCTCCGGTCGGCAATCA 61.701 61.111 14.70 0.00 35.40 2.57
1491 1511 1.533469 CCTCGAACACCTCCCTCGTT 61.533 60.000 0.00 0.00 34.27 3.85
1690 1711 2.747396 ACCAAATGATTGCACGCATT 57.253 40.000 7.26 7.26 36.35 3.56
1714 1735 5.644188 ACCAAATCAATTTCTCTCCCTCAA 58.356 37.500 0.00 0.00 0.00 3.02
1784 1805 4.279922 TCGGTCTCATCAAACAGTGAGTTA 59.720 41.667 0.00 0.00 41.92 2.24
1804 1825 6.365247 TCTCGAGAAAGTTCTGTATTTTTCGG 59.635 38.462 14.01 3.25 41.02 4.30
1805 1826 7.221287 GTCTCGAGAAAGTTCTGTATTTTTCG 58.779 38.462 18.55 4.75 41.62 3.46
1814 1835 3.983741 AGTTGGTCTCGAGAAAGTTCTG 58.016 45.455 18.55 0.00 37.73 3.02
1825 1846 4.786609 GCTTTCACTCAAAAGTTGGTCTCG 60.787 45.833 0.00 0.00 38.30 4.04
1867 1888 7.061094 GTCTTAAGCATGTTTTTCCTTTGATCG 59.939 37.037 0.00 0.00 0.00 3.69
1892 1913 5.736951 AAGACTACAGCAGAATCTCAAGT 57.263 39.130 0.00 0.00 0.00 3.16
1898 1919 5.121454 CAGACCAAAAGACTACAGCAGAATC 59.879 44.000 0.00 0.00 0.00 2.52
1900 1921 4.380531 CAGACCAAAAGACTACAGCAGAA 58.619 43.478 0.00 0.00 0.00 3.02
1902 1923 2.481952 GCAGACCAAAAGACTACAGCAG 59.518 50.000 0.00 0.00 0.00 4.24
1904 1925 2.481952 CTGCAGACCAAAAGACTACAGC 59.518 50.000 8.42 0.00 27.34 4.40
1905 1926 3.733337 ACTGCAGACCAAAAGACTACAG 58.267 45.455 23.35 0.00 37.57 2.74
1909 1930 3.281727 TGAACTGCAGACCAAAAGACT 57.718 42.857 23.35 0.00 0.00 3.24
1910 1931 3.304928 CCATGAACTGCAGACCAAAAGAC 60.305 47.826 23.35 1.34 0.00 3.01
1911 1932 2.886523 CCATGAACTGCAGACCAAAAGA 59.113 45.455 23.35 0.00 0.00 2.52
1912 1933 2.608752 GCCATGAACTGCAGACCAAAAG 60.609 50.000 23.35 10.86 0.00 2.27
1917 1947 1.133790 GATTGCCATGAACTGCAGACC 59.866 52.381 23.35 11.84 38.95 3.85
1937 1967 4.096532 AGCAGAATCTCATGTGCTGAAATG 59.903 41.667 5.52 0.00 44.55 2.32
1961 1991 7.872993 TGACAACTAATCAGACCAAAAGACTAG 59.127 37.037 0.00 0.00 0.00 2.57
2070 2101 6.488344 TGGTGCATATCTACAAAGTGTCAAAA 59.512 34.615 0.00 0.00 0.00 2.44
2113 2144 4.018490 TCAAATGCAATAGGCTGATGTGT 58.982 39.130 0.00 0.00 45.15 3.72
2199 2241 7.552050 TTCATCCCAGGTGATTAACAAAAAT 57.448 32.000 0.00 0.00 0.00 1.82
2209 2251 4.875389 ACATCAAATTCATCCCAGGTGAT 58.125 39.130 0.00 0.00 0.00 3.06
2258 2300 8.993424 ACTCCAAATCCTAGATGTACAGTTTAT 58.007 33.333 0.33 0.00 0.00 1.40
2292 2334 7.786178 TTGTAGCATACTCATGGTTAACATC 57.214 36.000 8.10 0.00 43.54 3.06
2300 2342 5.664457 TCACTCTTTGTAGCATACTCATGG 58.336 41.667 0.00 0.00 43.54 3.66
2337 2379 9.273016 TCTTTCGAGAAAATCAGAACAAATAGT 57.727 29.630 0.00 0.00 0.00 2.12
2342 2384 5.522460 ACGTCTTTCGAGAAAATCAGAACAA 59.478 36.000 0.00 0.00 42.86 2.83
2354 2396 5.175126 GTCAAGATCAAAACGTCTTTCGAGA 59.825 40.000 0.00 0.00 42.86 4.04
2355 2397 5.051039 TGTCAAGATCAAAACGTCTTTCGAG 60.051 40.000 0.00 0.00 42.86 4.04
2405 2447 5.104527 AGGTCACTATGCTAACTGCCATAAA 60.105 40.000 0.00 0.00 42.00 1.40
2517 2560 5.058490 TGTGCATCACGTCATTATCATGAT 58.942 37.500 13.81 13.81 35.68 2.45
2518 2561 4.440880 TGTGCATCACGTCATTATCATGA 58.559 39.130 0.00 0.00 37.14 3.07
2548 2591 0.598065 AAAACATCTGTCGGCCAAGC 59.402 50.000 2.24 0.00 0.00 4.01
2582 2625 8.537728 AAATTTAATTATGTGAGCCAGATGGA 57.462 30.769 2.18 0.00 37.39 3.41
2676 2719 2.594592 GGTTGGAACGCCAGCTGT 60.595 61.111 13.81 0.00 46.91 4.40
2693 2736 6.183360 GGCCTCCAAGATAGAGTATATTCTCG 60.183 46.154 0.29 0.00 39.21 4.04
2819 2862 6.091169 CACTGTTATCCCAAACAATGAAATGC 59.909 38.462 0.00 0.00 38.52 3.56
2847 2890 4.194640 CCCATAACCTCATGAGTGACAAG 58.805 47.826 21.11 7.36 0.00 3.16
2982 3120 6.095860 GGTAGGACCGTAAAAGCCAAAATTAT 59.904 38.462 0.00 0.00 0.00 1.28
3034 3173 8.372459 ACCAAGTAAACTCACACATTCTATACA 58.628 33.333 0.00 0.00 0.00 2.29
3036 3175 8.038944 GGACCAAGTAAACTCACACATTCTATA 58.961 37.037 0.00 0.00 0.00 1.31
3084 3224 3.641436 TGTCCAGACACTACTGACACAAT 59.359 43.478 0.00 0.00 39.94 2.71
3127 3275 2.468532 AAAACGAAACGAGGTTGCTG 57.531 45.000 0.00 0.00 0.00 4.41
3142 3290 9.959749 TGAGGACATATACTTTTTGACAAAAAC 57.040 29.630 19.67 9.19 35.57 2.43
3181 3400 5.163364 TGGAGCTTCTCAGAATAGATGTTCC 60.163 44.000 12.66 12.66 44.48 3.62
3191 3410 0.986527 TGCCATGGAGCTTCTCAGAA 59.013 50.000 18.40 0.00 31.08 3.02
3192 3411 0.986527 TTGCCATGGAGCTTCTCAGA 59.013 50.000 18.40 0.00 31.08 3.27
3221 3440 9.000486 GGGTATCCTAGAATAATAGCAAAACAC 58.000 37.037 0.00 0.00 0.00 3.32
3227 3446 7.246027 TCAGTGGGTATCCTAGAATAATAGCA 58.754 38.462 0.00 0.00 0.00 3.49
3332 3551 1.597742 TCTGCTTGAGCTGGAAACAC 58.402 50.000 9.54 0.00 42.66 3.32
3581 3800 6.147473 TCCCTTTATACTGTCACCCATATCA 58.853 40.000 0.00 0.00 0.00 2.15
3599 3818 3.310141 CCTGAATCATCCCCTTTCCCTTT 60.310 47.826 0.00 0.00 0.00 3.11
3629 3848 7.973944 GGAAGAAAAGAAAAAGAACACTGCTAA 59.026 33.333 0.00 0.00 0.00 3.09
3783 4006 3.964031 ACCAACAACTCCCAAGCAAAATA 59.036 39.130 0.00 0.00 0.00 1.40
3851 4074 3.575805 ACCCTGTCCAATGAAACACAAT 58.424 40.909 0.00 0.00 0.00 2.71
3852 4075 3.025322 ACCCTGTCCAATGAAACACAA 57.975 42.857 0.00 0.00 0.00 3.33
3856 4079 5.622233 GCAGAAATACCCTGTCCAATGAAAC 60.622 44.000 0.00 0.00 34.29 2.78
4017 4240 2.700722 TGCAGAATGGTAATACGGCA 57.299 45.000 0.00 0.00 35.86 5.69
4018 4241 4.094887 CCATATGCAGAATGGTAATACGGC 59.905 45.833 18.55 0.00 39.30 5.68
4019 4242 4.094887 GCCATATGCAGAATGGTAATACGG 59.905 45.833 24.42 0.21 44.87 4.02
4020 4243 4.937620 AGCCATATGCAGAATGGTAATACG 59.062 41.667 24.42 5.57 44.87 3.06
4058 4283 5.064834 TGTCTAAGCACTCTGTACATAGTCG 59.935 44.000 10.73 8.24 0.00 4.18
4078 4303 1.949799 ATGGACTCCTCAAGCTGTCT 58.050 50.000 0.00 0.00 0.00 3.41
4112 4378 1.139058 CTAGTTACGCTGGCAAGGGAT 59.861 52.381 12.95 0.00 39.59 3.85
4115 4381 1.067142 TGTCTAGTTACGCTGGCAAGG 60.067 52.381 0.00 0.00 0.00 3.61
4125 4391 8.943909 AGCAGTTAATGGTATTGTCTAGTTAC 57.056 34.615 0.00 0.00 38.04 2.50
4134 4400 8.039603 TGTCTTGTTAGCAGTTAATGGTATTG 57.960 34.615 0.00 0.00 41.36 1.90
4140 4406 5.611796 TGCTGTCTTGTTAGCAGTTAATG 57.388 39.130 0.00 0.00 44.36 1.90
4160 4426 3.438087 AGTTCATGTATCAGCTGTGTTGC 59.562 43.478 14.67 4.54 0.00 4.17
4161 4427 4.201656 CGAGTTCATGTATCAGCTGTGTTG 60.202 45.833 14.67 6.13 0.00 3.33
4168 4434 2.860735 GACACCGAGTTCATGTATCAGC 59.139 50.000 0.00 0.00 0.00 4.26
4169 4435 3.108881 CGACACCGAGTTCATGTATCAG 58.891 50.000 0.00 0.00 38.22 2.90
4189 4455 1.510480 GCTAATAAGCTGCTGGGCCG 61.510 60.000 1.35 0.00 45.85 6.13
4200 4466 5.509972 GCATCGTCGACTCTATGCTAATAAG 59.490 44.000 26.76 5.80 41.16 1.73
4205 4471 2.218603 TGCATCGTCGACTCTATGCTA 58.781 47.619 30.38 20.95 43.98 3.49
4276 4542 0.906282 AAGGGGAAAAGCATGGCCTG 60.906 55.000 3.32 0.34 0.00 4.85
4301 4567 6.442513 AGAAAACAGAGTATATTTGGCTGC 57.557 37.500 0.00 0.00 0.00 5.25
4340 4785 7.437793 TGAAAAATTTGCTCATGGAAAATCC 57.562 32.000 0.00 0.00 37.08 3.01
4361 4806 4.269183 ACTGTTCAGTGTGATGGTTTGAA 58.731 39.130 4.58 0.00 0.00 2.69
4409 4854 0.886563 CAGAAAGGCTCCTTGGCAAG 59.113 55.000 20.31 20.31 44.55 4.01
5380 6130 4.500837 CGAGAGATTTCACTATGAACCACG 59.499 45.833 0.00 0.00 35.89 4.94
5403 6155 7.656542 CCCTCCGTTTCTAAATATAAGTCCTTC 59.343 40.741 0.00 0.00 0.00 3.46
5406 6158 7.059202 TCCCTCCGTTTCTAAATATAAGTCC 57.941 40.000 0.00 0.00 0.00 3.85
5420 6172 1.633945 AGCCAAATACTCCCTCCGTTT 59.366 47.619 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.