Multiple sequence alignment - TraesCS3A01G183000

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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 TraesCS3A01G183000 chr3A 100.000 3436 0 0 1 3436 212122404 212125839 0.000000e+00 6346
1 TraesCS3A01G183000 chr3A 98.794 2901 23 2 422 3310 610424080 610421180 0.000000e+00 5153
2 TraesCS3A01G183000 chr3A 99.412 170 1 0 260 429 610424332 610424163 3.330000e-80 309
3 TraesCS3A01G183000 chr7B 99.000 2901 17 2 422 3310 204003004 204005904 0.000000e+00 5186
4 TraesCS3A01G183000 chr7B 98.235 170 3 0 260 429 204002752 204002921 7.210000e-77 298
5 TraesCS3A01G183000 chr7B 100.000 126 0 0 3311 3436 244402904 244403029 2.060000e-57 233
6 TraesCS3A01G183000 chr3B 98.931 2901 19 2 422 3310 829116709 829119609 0.000000e+00 5175
7 TraesCS3A01G183000 chr3B 98.862 2901 21 2 422 3310 813958257 813955357 0.000000e+00 5164
8 TraesCS3A01G183000 chr3B 89.179 268 20 4 1 259 252591748 252592015 3.310000e-85 326
9 TraesCS3A01G183000 chr3B 98.824 170 2 0 260 429 829116457 829116626 1.550000e-78 303
10 TraesCS3A01G183000 chr3B 98.214 168 3 0 262 429 813958507 813958340 9.330000e-76 294
11 TraesCS3A01G183000 chr3B 100.000 128 0 0 3309 3436 368603144 368603017 1.590000e-58 237
12 TraesCS3A01G183000 chr3B 100.000 126 0 0 3311 3436 126480542 126480667 2.060000e-57 233
13 TraesCS3A01G183000 chr2A 98.621 2901 28 2 422 3310 713923740 713926640 0.000000e+00 5125
14 TraesCS3A01G183000 chr2A 98.522 2504 28 1 816 3310 39363907 39361404 0.000000e+00 4410
15 TraesCS3A01G183000 chr2A 98.026 304 6 0 422 725 39364192 39363889 2.350000e-146 529
16 TraesCS3A01G183000 chr2A 99.415 171 1 0 259 429 39364445 39364275 9.260000e-81 311
17 TraesCS3A01G183000 chr2A 99.412 170 1 0 260 429 713923488 713923657 3.330000e-80 309
18 TraesCS3A01G183000 chr4A 98.276 2901 37 3 422 3310 586087826 586084927 0.000000e+00 5068
19 TraesCS3A01G183000 chr4A 98.824 170 2 0 260 429 586088078 586087909 1.550000e-78 303
20 TraesCS3A01G183000 chr7D 97.002 2902 73 4 422 3310 237548481 237551381 0.000000e+00 4865
21 TraesCS3A01G183000 chr7D 97.059 170 5 0 260 429 237548280 237548449 1.560000e-73 287
22 TraesCS3A01G183000 chr7D 90.351 114 10 1 136 248 107261151 107261264 7.680000e-32 148
23 TraesCS3A01G183000 chr5B 97.914 2397 40 2 924 3310 599616903 599614507 0.000000e+00 4141
24 TraesCS3A01G183000 chr5B 91.781 73 6 0 858 930 531864453 531864525 6.070000e-18 102
25 TraesCS3A01G183000 chr3D 89.098 266 20 3 3 259 173711332 173711597 4.280000e-84 322
26 TraesCS3A01G183000 chr3D 93.143 175 8 2 259 429 511281795 511281621 1.580000e-63 254
27 TraesCS3A01G183000 chr1B 99.237 131 1 0 3306 3436 271101099 271101229 1.590000e-58 237
28 TraesCS3A01G183000 chr1B 100.000 128 0 0 3309 3436 626041856 626041729 1.590000e-58 237
29 TraesCS3A01G183000 chr4B 100.000 126 0 0 3311 3436 240104224 240104349 2.060000e-57 233
30 TraesCS3A01G183000 chr2D 100.000 126 0 0 3311 3436 564446759 564446884 2.060000e-57 233
31 TraesCS3A01G183000 chr2B 100.000 126 0 0 3311 3436 45692136 45692011 2.060000e-57 233
32 TraesCS3A01G183000 chr6B 97.744 133 3 0 3304 3436 270873257 270873389 2.670000e-56 230
33 TraesCS3A01G183000 chr5A 80.808 198 33 4 64 260 656739564 656739757 2.140000e-32 150


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 TraesCS3A01G183000 chr3A 212122404 212125839 3435 False 6346.0 6346 100.000000 1 3436 1 chr3A.!!$F1 3435
1 TraesCS3A01G183000 chr3A 610421180 610424332 3152 True 2731.0 5153 99.103000 260 3310 2 chr3A.!!$R1 3050
2 TraesCS3A01G183000 chr7B 204002752 204005904 3152 False 2742.0 5186 98.617500 260 3310 2 chr7B.!!$F2 3050
3 TraesCS3A01G183000 chr3B 829116457 829119609 3152 False 2739.0 5175 98.877500 260 3310 2 chr3B.!!$F3 3050
4 TraesCS3A01G183000 chr3B 813955357 813958507 3150 True 2729.0 5164 98.538000 262 3310 2 chr3B.!!$R2 3048
5 TraesCS3A01G183000 chr2A 713923488 713926640 3152 False 2717.0 5125 99.016500 260 3310 2 chr2A.!!$F1 3050
6 TraesCS3A01G183000 chr2A 39361404 39364445 3041 True 1750.0 4410 98.654333 259 3310 3 chr2A.!!$R1 3051
7 TraesCS3A01G183000 chr4A 586084927 586088078 3151 True 2685.5 5068 98.550000 260 3310 2 chr4A.!!$R1 3050
8 TraesCS3A01G183000 chr7D 237548280 237551381 3101 False 2576.0 4865 97.030500 260 3310 2 chr7D.!!$F2 3050
9 TraesCS3A01G183000 chr5B 599614507 599616903 2396 True 4141.0 4141 97.914000 924 3310 1 chr5B.!!$R1 2386

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
57 58 0.032130 CCATACGGATCTGGGTCGTG 59.968 60.0 6.47 0.0 38.19 4.35 F
60 61 0.253894 TACGGATCTGGGTCGTGAGA 59.746 55.0 6.47 0.0 38.19 3.27 F
127 128 0.393448 GGGAGAAATCCCTAGGCGAC 59.607 60.0 2.05 0.0 46.39 5.19 F
131 132 0.529992 GAAATCCCTAGGCGACACCG 60.530 60.0 2.05 0.0 46.52 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 1531 3.070159 TCACCAACTCTCTCCTCTGTTTG 59.930 47.826 0.0 0.0 0.00 2.93 R
1468 1564 4.664688 ACTCCATCACAGAATTTTCCCT 57.335 40.909 0.0 0.0 0.00 4.20 R
1876 1972 5.484290 CCCTTAATCCACCTCGGTTATATCT 59.516 44.000 0.0 0.0 35.57 1.98 R
2766 2871 8.590470 CATGTCATACGAGTATAGCAATCAATC 58.410 37.037 0.0 0.0 0.00 2.67 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
19 20 0.969894 GTCGGGGATGATAGGTCAGG 59.030 60.000 0.00 0.00 37.87 3.86
20 21 0.857675 TCGGGGATGATAGGTCAGGA 59.142 55.000 0.00 0.00 37.87 3.86
21 22 1.203063 TCGGGGATGATAGGTCAGGAG 60.203 57.143 0.00 0.00 37.87 3.69
22 23 1.650528 GGGGATGATAGGTCAGGAGG 58.349 60.000 0.00 0.00 37.87 4.30
23 24 0.980423 GGGATGATAGGTCAGGAGGC 59.020 60.000 0.00 0.00 37.87 4.70
24 25 0.605589 GGATGATAGGTCAGGAGGCG 59.394 60.000 0.00 0.00 37.87 5.52
25 26 0.605589 GATGATAGGTCAGGAGGCGG 59.394 60.000 0.00 0.00 37.87 6.13
26 27 1.476007 ATGATAGGTCAGGAGGCGGC 61.476 60.000 0.00 0.00 37.87 6.53
27 28 1.834822 GATAGGTCAGGAGGCGGCT 60.835 63.158 13.09 13.09 0.00 5.52
28 29 1.811645 GATAGGTCAGGAGGCGGCTC 61.812 65.000 29.56 29.56 0.00 4.70
29 30 2.305314 ATAGGTCAGGAGGCGGCTCT 62.305 60.000 34.35 19.76 0.00 4.09
30 31 4.154347 GGTCAGGAGGCGGCTCTG 62.154 72.222 34.35 28.07 0.00 3.35
31 32 3.386237 GTCAGGAGGCGGCTCTGT 61.386 66.667 34.35 21.33 0.00 3.41
32 33 3.385384 TCAGGAGGCGGCTCTGTG 61.385 66.667 34.35 29.48 0.00 3.66
35 36 4.828925 GGAGGCGGCTCTGTGCTC 62.829 72.222 34.35 15.94 42.39 4.26
36 37 4.828925 GAGGCGGCTCTGTGCTCC 62.829 72.222 30.02 2.78 42.39 4.70
38 39 4.828925 GGCGGCTCTGTGCTCCTC 62.829 72.222 0.00 0.00 42.39 3.71
39 40 4.828925 GCGGCTCTGTGCTCCTCC 62.829 72.222 1.44 0.00 42.39 4.30
40 41 3.385384 CGGCTCTGTGCTCCTCCA 61.385 66.667 1.44 0.00 42.39 3.86
41 42 2.729479 CGGCTCTGTGCTCCTCCAT 61.729 63.158 1.44 0.00 42.39 3.41
42 43 1.395045 CGGCTCTGTGCTCCTCCATA 61.395 60.000 1.44 0.00 42.39 2.74
43 44 0.105778 GGCTCTGTGCTCCTCCATAC 59.894 60.000 1.44 0.00 42.39 2.39
44 45 0.249238 GCTCTGTGCTCCTCCATACG 60.249 60.000 0.00 0.00 38.95 3.06
45 46 0.387202 CTCTGTGCTCCTCCATACGG 59.613 60.000 0.00 0.00 0.00 4.02
46 47 0.033503 TCTGTGCTCCTCCATACGGA 60.034 55.000 0.00 0.00 39.79 4.69
47 48 1.043816 CTGTGCTCCTCCATACGGAT 58.956 55.000 0.00 0.00 41.79 4.18
48 49 1.000283 CTGTGCTCCTCCATACGGATC 60.000 57.143 0.00 0.00 41.79 3.36
49 50 1.333177 GTGCTCCTCCATACGGATCT 58.667 55.000 0.00 0.00 41.79 2.75
50 51 1.000283 GTGCTCCTCCATACGGATCTG 60.000 57.143 0.00 0.00 41.79 2.90
51 52 0.605589 GCTCCTCCATACGGATCTGG 59.394 60.000 6.47 0.00 41.79 3.86
52 53 1.261480 CTCCTCCATACGGATCTGGG 58.739 60.000 6.47 0.00 41.79 4.45
53 54 0.561184 TCCTCCATACGGATCTGGGT 59.439 55.000 6.47 0.00 41.79 4.51
54 55 0.969894 CCTCCATACGGATCTGGGTC 59.030 60.000 6.47 0.00 41.79 4.46
55 56 0.598562 CTCCATACGGATCTGGGTCG 59.401 60.000 6.47 0.00 41.79 4.79
56 57 0.106369 TCCATACGGATCTGGGTCGT 60.106 55.000 6.47 2.79 35.91 4.34
57 58 0.032130 CCATACGGATCTGGGTCGTG 59.968 60.000 6.47 0.00 38.19 4.35
58 59 1.029681 CATACGGATCTGGGTCGTGA 58.970 55.000 6.47 0.00 38.19 4.35
59 60 1.001268 CATACGGATCTGGGTCGTGAG 60.001 57.143 6.47 0.00 38.19 3.51
60 61 0.253894 TACGGATCTGGGTCGTGAGA 59.746 55.000 6.47 0.00 38.19 3.27
70 71 2.649034 TCGTGAGACTTGCCGGTC 59.351 61.111 1.90 0.00 36.56 4.79
71 72 2.432628 CGTGAGACTTGCCGGTCC 60.433 66.667 1.90 0.00 36.95 4.46
72 73 2.932234 CGTGAGACTTGCCGGTCCT 61.932 63.158 1.90 0.00 36.95 3.85
73 74 1.079750 GTGAGACTTGCCGGTCCTC 60.080 63.158 1.90 3.64 36.95 3.71
74 75 2.182030 GAGACTTGCCGGTCCTCG 59.818 66.667 1.90 0.00 36.95 4.63
75 76 2.282958 AGACTTGCCGGTCCTCGA 60.283 61.111 1.90 0.00 42.43 4.04
76 77 1.668101 GAGACTTGCCGGTCCTCGAT 61.668 60.000 1.90 0.00 42.43 3.59
77 78 1.519455 GACTTGCCGGTCCTCGATG 60.519 63.158 1.90 0.00 42.43 3.84
78 79 2.892425 CTTGCCGGTCCTCGATGC 60.892 66.667 1.90 0.00 42.43 3.91
79 80 4.812476 TTGCCGGTCCTCGATGCG 62.812 66.667 1.90 0.00 42.43 4.73
81 82 4.286320 GCCGGTCCTCGATGCGAT 62.286 66.667 1.90 0.00 42.43 4.58
82 83 2.417516 CCGGTCCTCGATGCGATT 59.582 61.111 0.00 0.00 42.43 3.34
83 84 1.951130 CCGGTCCTCGATGCGATTG 60.951 63.158 0.00 0.00 42.43 2.67
84 85 1.951130 CGGTCCTCGATGCGATTGG 60.951 63.158 0.00 0.00 42.43 3.16
85 86 1.441729 GGTCCTCGATGCGATTGGA 59.558 57.895 0.00 0.00 34.61 3.53
86 87 0.598680 GGTCCTCGATGCGATTGGAG 60.599 60.000 0.00 0.00 32.37 3.86
87 88 1.068083 TCCTCGATGCGATTGGAGC 59.932 57.895 0.00 0.00 34.61 4.70
88 89 1.068753 CCTCGATGCGATTGGAGCT 59.931 57.895 0.00 0.00 34.61 4.09
89 90 1.220169 CCTCGATGCGATTGGAGCTG 61.220 60.000 0.00 0.00 34.61 4.24
90 91 1.220169 CTCGATGCGATTGGAGCTGG 61.220 60.000 0.00 0.00 34.61 4.85
91 92 1.227350 CGATGCGATTGGAGCTGGA 60.227 57.895 0.00 0.00 35.28 3.86
92 93 1.220169 CGATGCGATTGGAGCTGGAG 61.220 60.000 0.00 0.00 35.28 3.86
93 94 0.883814 GATGCGATTGGAGCTGGAGG 60.884 60.000 0.00 0.00 35.28 4.30
94 95 1.630126 ATGCGATTGGAGCTGGAGGT 61.630 55.000 0.00 0.00 35.28 3.85
95 96 1.817099 GCGATTGGAGCTGGAGGTG 60.817 63.158 0.00 0.00 0.00 4.00
96 97 1.817099 CGATTGGAGCTGGAGGTGC 60.817 63.158 0.00 0.00 0.00 5.01
97 98 1.817099 GATTGGAGCTGGAGGTGCG 60.817 63.158 0.00 0.00 36.64 5.34
98 99 3.335356 ATTGGAGCTGGAGGTGCGG 62.335 63.158 0.00 0.00 36.64 5.69
100 101 3.474570 GGAGCTGGAGGTGCGGAT 61.475 66.667 0.00 0.00 35.28 4.18
101 102 2.586792 GAGCTGGAGGTGCGGATT 59.413 61.111 0.00 0.00 35.28 3.01
102 103 1.522580 GAGCTGGAGGTGCGGATTC 60.523 63.158 0.00 0.00 35.28 2.52
103 104 2.244117 GAGCTGGAGGTGCGGATTCA 62.244 60.000 0.00 0.00 35.28 2.57
104 105 1.377202 GCTGGAGGTGCGGATTCAA 60.377 57.895 0.00 0.00 0.00 2.69
105 106 0.960364 GCTGGAGGTGCGGATTCAAA 60.960 55.000 0.00 0.00 0.00 2.69
106 107 1.755179 CTGGAGGTGCGGATTCAAAT 58.245 50.000 0.00 0.00 0.00 2.32
107 108 1.672881 CTGGAGGTGCGGATTCAAATC 59.327 52.381 0.00 0.00 34.66 2.17
108 109 0.657840 GGAGGTGCGGATTCAAATCG 59.342 55.000 0.00 0.00 36.27 3.34
109 110 0.657840 GAGGTGCGGATTCAAATCGG 59.342 55.000 6.06 6.06 38.38 4.18
110 111 0.748005 AGGTGCGGATTCAAATCGGG 60.748 55.000 10.97 1.65 36.56 5.14
111 112 0.746563 GGTGCGGATTCAAATCGGGA 60.747 55.000 10.97 6.45 36.56 5.14
112 113 0.657840 GTGCGGATTCAAATCGGGAG 59.342 55.000 10.97 0.00 36.91 4.30
113 114 0.539518 TGCGGATTCAAATCGGGAGA 59.460 50.000 10.97 0.00 46.90 3.71
114 115 1.065782 TGCGGATTCAAATCGGGAGAA 60.066 47.619 10.97 0.00 45.37 2.87
115 116 2.014128 GCGGATTCAAATCGGGAGAAA 58.986 47.619 10.97 0.00 45.37 2.52
116 117 2.618709 GCGGATTCAAATCGGGAGAAAT 59.381 45.455 10.97 0.00 45.37 2.17
117 118 3.304057 GCGGATTCAAATCGGGAGAAATC 60.304 47.826 10.97 0.00 45.37 2.17
118 119 3.251004 CGGATTCAAATCGGGAGAAATCC 59.749 47.826 0.00 0.00 43.87 3.01
119 120 3.570125 GGATTCAAATCGGGAGAAATCCC 59.430 47.826 3.03 3.03 42.56 3.85
120 121 7.946858 CGGATTCAAATCGGGAGAAATCCCT 62.947 48.000 11.44 0.00 44.19 4.20
121 122 8.640912 CGGATTCAAATCGGGAGAAATCCCTA 62.641 46.154 11.44 0.77 44.19 3.53
126 127 2.836020 GGGAGAAATCCCTAGGCGA 58.164 57.895 2.05 2.52 46.39 5.54
127 128 0.393448 GGGAGAAATCCCTAGGCGAC 59.607 60.000 2.05 0.00 46.39 5.19
128 129 1.120530 GGAGAAATCCCTAGGCGACA 58.879 55.000 2.05 0.00 0.00 4.35
129 130 1.202545 GGAGAAATCCCTAGGCGACAC 60.203 57.143 2.05 0.00 0.00 3.67
130 131 0.831307 AGAAATCCCTAGGCGACACC 59.169 55.000 2.05 0.00 39.61 4.16
131 132 0.529992 GAAATCCCTAGGCGACACCG 60.530 60.000 2.05 0.00 46.52 4.94
132 133 1.968050 AAATCCCTAGGCGACACCGG 61.968 60.000 2.05 0.00 46.52 5.28
133 134 3.674050 ATCCCTAGGCGACACCGGT 62.674 63.158 0.00 0.00 46.52 5.28
134 135 3.834799 CCCTAGGCGACACCGGTC 61.835 72.222 2.59 0.00 46.52 4.79
162 163 4.664062 CCCATGGGCATCGTCTTT 57.336 55.556 20.41 0.00 0.00 2.52
163 164 2.886382 CCCATGGGCATCGTCTTTT 58.114 52.632 20.41 0.00 0.00 2.27
164 165 0.740737 CCCATGGGCATCGTCTTTTC 59.259 55.000 20.41 0.00 0.00 2.29
165 166 1.683011 CCCATGGGCATCGTCTTTTCT 60.683 52.381 20.41 0.00 0.00 2.52
166 167 1.672881 CCATGGGCATCGTCTTTTCTC 59.327 52.381 2.85 0.00 0.00 2.87
167 168 1.672881 CATGGGCATCGTCTTTTCTCC 59.327 52.381 0.00 0.00 0.00 3.71
168 169 0.690192 TGGGCATCGTCTTTTCTCCA 59.310 50.000 0.00 0.00 0.00 3.86
169 170 1.281867 TGGGCATCGTCTTTTCTCCAT 59.718 47.619 0.00 0.00 0.00 3.41
170 171 1.672881 GGGCATCGTCTTTTCTCCATG 59.327 52.381 0.00 0.00 0.00 3.66
171 172 1.672881 GGCATCGTCTTTTCTCCATGG 59.327 52.381 4.97 4.97 0.00 3.66
172 173 2.632377 GCATCGTCTTTTCTCCATGGA 58.368 47.619 15.27 15.27 0.00 3.41
173 174 2.611292 GCATCGTCTTTTCTCCATGGAG 59.389 50.000 32.60 32.60 43.21 3.86
184 185 4.655762 TCTCCATGGAGACGTTCATTAG 57.344 45.455 35.92 11.28 45.26 1.73
185 186 4.278310 TCTCCATGGAGACGTTCATTAGA 58.722 43.478 35.92 13.44 45.26 2.10
186 187 4.895889 TCTCCATGGAGACGTTCATTAGAT 59.104 41.667 35.92 0.00 45.26 1.98
187 188 5.010112 TCTCCATGGAGACGTTCATTAGATC 59.990 44.000 35.92 0.00 45.26 2.75
188 189 4.895889 TCCATGGAGACGTTCATTAGATCT 59.104 41.667 11.44 0.00 0.00 2.75
189 190 4.987285 CCATGGAGACGTTCATTAGATCTG 59.013 45.833 5.56 0.00 0.00 2.90
190 191 4.046938 TGGAGACGTTCATTAGATCTGC 57.953 45.455 5.18 0.00 0.00 4.26
191 192 3.701542 TGGAGACGTTCATTAGATCTGCT 59.298 43.478 5.18 0.00 0.00 4.24
192 193 4.202060 TGGAGACGTTCATTAGATCTGCTC 60.202 45.833 5.18 0.00 0.00 4.26
193 194 4.037446 GGAGACGTTCATTAGATCTGCTCT 59.963 45.833 5.18 0.00 38.06 4.09
194 195 5.239744 GGAGACGTTCATTAGATCTGCTCTA 59.760 44.000 5.18 0.00 35.28 2.43
195 196 6.067263 AGACGTTCATTAGATCTGCTCTAC 57.933 41.667 5.18 0.00 36.17 2.59
196 197 5.009210 AGACGTTCATTAGATCTGCTCTACC 59.991 44.000 5.18 0.00 36.17 3.18
197 198 4.890581 ACGTTCATTAGATCTGCTCTACCT 59.109 41.667 5.18 0.00 36.17 3.08
198 199 5.009210 ACGTTCATTAGATCTGCTCTACCTC 59.991 44.000 5.18 0.00 36.17 3.85
199 200 5.563867 CGTTCATTAGATCTGCTCTACCTCC 60.564 48.000 5.18 0.00 36.17 4.30
200 201 5.066913 TCATTAGATCTGCTCTACCTCCA 57.933 43.478 5.18 0.00 36.17 3.86
201 202 4.830046 TCATTAGATCTGCTCTACCTCCAC 59.170 45.833 5.18 0.00 36.17 4.02
202 203 2.080654 AGATCTGCTCTACCTCCACC 57.919 55.000 0.00 0.00 30.26 4.61
203 204 1.289231 AGATCTGCTCTACCTCCACCA 59.711 52.381 0.00 0.00 30.26 4.17
204 205 1.410882 GATCTGCTCTACCTCCACCAC 59.589 57.143 0.00 0.00 0.00 4.16
205 206 0.965866 TCTGCTCTACCTCCACCACG 60.966 60.000 0.00 0.00 0.00 4.94
206 207 2.184579 GCTCTACCTCCACCACGC 59.815 66.667 0.00 0.00 0.00 5.34
207 208 2.352032 GCTCTACCTCCACCACGCT 61.352 63.158 0.00 0.00 0.00 5.07
208 209 1.035932 GCTCTACCTCCACCACGCTA 61.036 60.000 0.00 0.00 0.00 4.26
209 210 1.693627 CTCTACCTCCACCACGCTAT 58.306 55.000 0.00 0.00 0.00 2.97
210 211 2.032620 CTCTACCTCCACCACGCTATT 58.967 52.381 0.00 0.00 0.00 1.73
211 212 2.431057 CTCTACCTCCACCACGCTATTT 59.569 50.000 0.00 0.00 0.00 1.40
212 213 2.167693 TCTACCTCCACCACGCTATTTG 59.832 50.000 0.00 0.00 0.00 2.32
213 214 0.690762 ACCTCCACCACGCTATTTGT 59.309 50.000 0.00 0.00 0.00 2.83
214 215 1.338769 ACCTCCACCACGCTATTTGTC 60.339 52.381 0.00 0.00 0.00 3.18
215 216 1.066143 CCTCCACCACGCTATTTGTCT 60.066 52.381 0.00 0.00 0.00 3.41
216 217 2.615493 CCTCCACCACGCTATTTGTCTT 60.615 50.000 0.00 0.00 0.00 3.01
217 218 2.673368 CTCCACCACGCTATTTGTCTTC 59.327 50.000 0.00 0.00 0.00 2.87
218 219 1.737793 CCACCACGCTATTTGTCTTCC 59.262 52.381 0.00 0.00 0.00 3.46
219 220 1.393539 CACCACGCTATTTGTCTTCCG 59.606 52.381 0.00 0.00 0.00 4.30
220 221 1.006832 CCACGCTATTTGTCTTCCGG 58.993 55.000 0.00 0.00 0.00 5.14
221 222 1.006832 CACGCTATTTGTCTTCCGGG 58.993 55.000 0.00 0.00 0.00 5.73
222 223 0.611714 ACGCTATTTGTCTTCCGGGT 59.388 50.000 0.00 0.00 0.00 5.28
223 224 1.006832 CGCTATTTGTCTTCCGGGTG 58.993 55.000 0.00 0.00 0.00 4.61
224 225 1.404986 CGCTATTTGTCTTCCGGGTGA 60.405 52.381 0.00 0.00 0.00 4.02
225 226 2.706890 GCTATTTGTCTTCCGGGTGAA 58.293 47.619 0.00 0.00 0.00 3.18
226 227 3.078837 GCTATTTGTCTTCCGGGTGAAA 58.921 45.455 0.00 0.00 31.06 2.69
227 228 3.504520 GCTATTTGTCTTCCGGGTGAAAA 59.495 43.478 0.00 0.00 31.06 2.29
228 229 4.157840 GCTATTTGTCTTCCGGGTGAAAAT 59.842 41.667 0.00 10.86 31.06 1.82
229 230 4.783764 ATTTGTCTTCCGGGTGAAAATC 57.216 40.909 0.00 0.00 31.06 2.17
230 231 2.194201 TGTCTTCCGGGTGAAAATCC 57.806 50.000 0.00 0.00 31.06 3.01
231 232 1.702957 TGTCTTCCGGGTGAAAATCCT 59.297 47.619 0.00 0.00 31.06 3.24
232 233 2.907696 TGTCTTCCGGGTGAAAATCCTA 59.092 45.455 0.00 0.00 31.06 2.94
233 234 3.328343 TGTCTTCCGGGTGAAAATCCTAA 59.672 43.478 0.00 0.00 31.06 2.69
234 235 3.688185 GTCTTCCGGGTGAAAATCCTAAC 59.312 47.826 0.00 0.00 31.06 2.34
235 236 3.585732 TCTTCCGGGTGAAAATCCTAACT 59.414 43.478 0.00 0.00 31.06 2.24
236 237 3.343941 TCCGGGTGAAAATCCTAACTG 57.656 47.619 0.00 0.00 0.00 3.16
237 238 1.743394 CCGGGTGAAAATCCTAACTGC 59.257 52.381 0.00 0.00 0.00 4.40
238 239 2.432444 CGGGTGAAAATCCTAACTGCA 58.568 47.619 0.00 0.00 0.00 4.41
239 240 2.420022 CGGGTGAAAATCCTAACTGCAG 59.580 50.000 13.48 13.48 0.00 4.41
240 241 3.421844 GGGTGAAAATCCTAACTGCAGT 58.578 45.455 15.25 15.25 0.00 4.40
241 242 4.585879 GGGTGAAAATCCTAACTGCAGTA 58.414 43.478 22.01 4.30 0.00 2.74
242 243 4.636206 GGGTGAAAATCCTAACTGCAGTAG 59.364 45.833 22.01 16.57 0.00 2.57
243 244 4.636206 GGTGAAAATCCTAACTGCAGTAGG 59.364 45.833 22.01 23.92 0.00 3.18
244 245 4.095036 GTGAAAATCCTAACTGCAGTAGGC 59.905 45.833 22.01 13.02 45.13 3.93
807 898 0.595095 GCTGTTGTTTGCAGAGGAGG 59.405 55.000 0.00 0.00 36.12 4.30
1016 1112 4.592942 CAAGACATGGGAGAAAATCAGGA 58.407 43.478 0.00 0.00 0.00 3.86
1435 1531 6.767902 TGAAGGGAATGTGATGTTAATAGCTC 59.232 38.462 0.00 0.00 0.00 4.09
1876 1972 1.923395 ATGCGTGGAAGGGGGAGAA 60.923 57.895 0.00 0.00 0.00 2.87
2766 2871 8.567948 AGTGGAATGAAGTACTTTGTTACATTG 58.432 33.333 18.86 0.00 0.00 2.82
3120 3225 3.652057 ACATTCCTCATCAACCGGATT 57.348 42.857 9.46 0.00 32.57 3.01
3310 3415 2.501723 TCTGGTCAGAAGGGATACAAGC 59.498 50.000 0.00 0.00 33.91 4.01
3311 3416 2.503356 CTGGTCAGAAGGGATACAAGCT 59.497 50.000 0.00 0.00 39.74 3.74
3312 3417 3.706594 CTGGTCAGAAGGGATACAAGCTA 59.293 47.826 0.00 0.00 39.74 3.32
3313 3418 4.298626 TGGTCAGAAGGGATACAAGCTAT 58.701 43.478 0.00 0.00 39.74 2.97
3314 3419 4.101585 TGGTCAGAAGGGATACAAGCTATG 59.898 45.833 0.00 0.00 39.74 2.23
3315 3420 4.101741 GGTCAGAAGGGATACAAGCTATGT 59.898 45.833 6.74 6.74 46.36 2.29
3316 3421 5.396884 GGTCAGAAGGGATACAAGCTATGTT 60.397 44.000 6.82 0.00 43.63 2.71
3317 3422 6.116126 GTCAGAAGGGATACAAGCTATGTTT 58.884 40.000 6.82 0.54 43.63 2.83
3318 3423 6.599638 GTCAGAAGGGATACAAGCTATGTTTT 59.400 38.462 6.82 0.00 43.63 2.43
3319 3424 7.121315 GTCAGAAGGGATACAAGCTATGTTTTT 59.879 37.037 6.82 0.00 43.63 1.94
3320 3425 8.325787 TCAGAAGGGATACAAGCTATGTTTTTA 58.674 33.333 6.82 0.00 43.63 1.52
3321 3426 8.956426 CAGAAGGGATACAAGCTATGTTTTTAA 58.044 33.333 6.82 0.00 43.63 1.52
3322 3427 9.178758 AGAAGGGATACAAGCTATGTTTTTAAG 57.821 33.333 6.82 0.00 43.63 1.85
3323 3428 7.881775 AGGGATACAAGCTATGTTTTTAAGG 57.118 36.000 6.82 0.00 43.63 2.69
3324 3429 6.321435 AGGGATACAAGCTATGTTTTTAAGGC 59.679 38.462 6.82 0.00 43.63 4.35
3325 3430 6.199393 GGATACAAGCTATGTTTTTAAGGCG 58.801 40.000 6.82 0.00 43.63 5.52
3326 3431 4.434713 ACAAGCTATGTTTTTAAGGCGG 57.565 40.909 0.00 0.00 40.06 6.13
3327 3432 3.824443 ACAAGCTATGTTTTTAAGGCGGT 59.176 39.130 0.00 0.00 40.06 5.68
3328 3433 5.005094 ACAAGCTATGTTTTTAAGGCGGTA 58.995 37.500 0.00 0.00 40.06 4.02
3329 3434 5.474189 ACAAGCTATGTTTTTAAGGCGGTAA 59.526 36.000 0.00 0.00 40.06 2.85
3330 3435 5.813080 AGCTATGTTTTTAAGGCGGTAAG 57.187 39.130 0.00 0.00 0.00 2.34
3331 3436 4.638865 AGCTATGTTTTTAAGGCGGTAAGG 59.361 41.667 0.00 0.00 0.00 2.69
3341 3446 4.570663 CGGTAAGGCGAGGCGAGG 62.571 72.222 0.00 0.00 0.00 4.63
3342 3447 4.893601 GGTAAGGCGAGGCGAGGC 62.894 72.222 0.00 0.92 0.00 4.70
3404 3509 2.879462 GGCGACGCCTTAGACACG 60.879 66.667 31.30 0.00 46.69 4.49
3405 3510 2.126580 GCGACGCCTTAGACACGT 60.127 61.111 9.14 0.00 43.83 4.49
3406 3511 2.434134 GCGACGCCTTAGACACGTG 61.434 63.158 15.48 15.48 40.69 4.49
3407 3512 2.434134 CGACGCCTTAGACACGTGC 61.434 63.158 17.22 8.74 40.69 5.34
3408 3513 1.372499 GACGCCTTAGACACGTGCA 60.372 57.895 17.22 0.00 40.69 4.57
3409 3514 0.736325 GACGCCTTAGACACGTGCAT 60.736 55.000 17.22 6.92 40.69 3.96
3410 3515 0.528924 ACGCCTTAGACACGTGCATA 59.471 50.000 17.22 5.79 38.85 3.14
3411 3516 1.136305 ACGCCTTAGACACGTGCATAT 59.864 47.619 17.22 1.25 38.85 1.78
3412 3517 2.359848 ACGCCTTAGACACGTGCATATA 59.640 45.455 17.22 0.18 38.85 0.86
3413 3518 3.005472 ACGCCTTAGACACGTGCATATAT 59.995 43.478 17.22 0.00 38.85 0.86
3414 3519 4.216902 ACGCCTTAGACACGTGCATATATA 59.783 41.667 17.22 0.00 38.85 0.86
3415 3520 5.158494 CGCCTTAGACACGTGCATATATAA 58.842 41.667 17.22 3.15 0.00 0.98
3416 3521 5.805486 CGCCTTAGACACGTGCATATATAAT 59.195 40.000 17.22 0.00 0.00 1.28
3417 3522 6.970613 CGCCTTAGACACGTGCATATATAATA 59.029 38.462 17.22 0.00 0.00 0.98
3418 3523 7.648112 CGCCTTAGACACGTGCATATATAATAT 59.352 37.037 17.22 0.00 0.00 1.28
3419 3524 9.961265 GCCTTAGACACGTGCATATATAATATA 57.039 33.333 17.22 0.00 0.00 0.86
3423 3528 8.818141 AGACACGTGCATATATAATATATGGC 57.182 34.615 17.22 12.53 33.72 4.40
3424 3529 8.421002 AGACACGTGCATATATAATATATGGCA 58.579 33.333 17.22 14.34 33.72 4.92
3425 3530 8.593492 ACACGTGCATATATAATATATGGCAG 57.407 34.615 17.22 13.68 33.72 4.85
3426 3531 7.171508 ACACGTGCATATATAATATATGGCAGC 59.828 37.037 17.22 12.22 33.72 5.25
3427 3532 6.650807 ACGTGCATATATAATATATGGCAGCC 59.349 38.462 16.42 3.66 33.72 4.85
3428 3533 6.650390 CGTGCATATATAATATATGGCAGCCA 59.350 38.462 18.99 18.99 38.19 4.75
3429 3534 7.173047 CGTGCATATATAATATATGGCAGCCAA 59.827 37.037 20.84 8.57 36.95 4.52
3430 3535 9.017509 GTGCATATATAATATATGGCAGCCAAT 57.982 33.333 20.84 15.37 36.95 3.16
3431 3536 9.590828 TGCATATATAATATATGGCAGCCAATT 57.409 29.630 20.84 16.29 36.95 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.969894 CCTGACCTATCATCCCCGAC 59.030 60.000 0.00 0.00 33.22 4.79
1 2 0.857675 TCCTGACCTATCATCCCCGA 59.142 55.000 0.00 0.00 33.22 5.14
2 3 1.261480 CTCCTGACCTATCATCCCCG 58.739 60.000 0.00 0.00 33.22 5.73
3 4 1.650528 CCTCCTGACCTATCATCCCC 58.349 60.000 0.00 0.00 33.22 4.81
4 5 0.980423 GCCTCCTGACCTATCATCCC 59.020 60.000 0.00 0.00 33.22 3.85
5 6 0.605589 CGCCTCCTGACCTATCATCC 59.394 60.000 0.00 0.00 33.22 3.51
6 7 0.605589 CCGCCTCCTGACCTATCATC 59.394 60.000 0.00 0.00 33.22 2.92
7 8 1.476007 GCCGCCTCCTGACCTATCAT 61.476 60.000 0.00 0.00 33.22 2.45
8 9 2.134287 GCCGCCTCCTGACCTATCA 61.134 63.158 0.00 0.00 0.00 2.15
9 10 1.811645 GAGCCGCCTCCTGACCTATC 61.812 65.000 0.00 0.00 31.68 2.08
10 11 1.834822 GAGCCGCCTCCTGACCTAT 60.835 63.158 0.00 0.00 31.68 2.57
11 12 2.442272 GAGCCGCCTCCTGACCTA 60.442 66.667 0.00 0.00 31.68 3.08
12 13 4.390556 AGAGCCGCCTCCTGACCT 62.391 66.667 0.00 0.00 38.96 3.85
13 14 4.154347 CAGAGCCGCCTCCTGACC 62.154 72.222 0.00 0.00 38.96 4.02
14 15 3.386237 ACAGAGCCGCCTCCTGAC 61.386 66.667 10.78 0.00 38.96 3.51
15 16 3.385384 CACAGAGCCGCCTCCTGA 61.385 66.667 10.78 0.00 38.96 3.86
25 26 0.249238 CGTATGGAGGAGCACAGAGC 60.249 60.000 0.00 0.00 46.19 4.09
26 27 0.387202 CCGTATGGAGGAGCACAGAG 59.613 60.000 0.00 0.00 37.49 3.35
27 28 0.033503 TCCGTATGGAGGAGCACAGA 60.034 55.000 0.00 0.00 40.17 3.41
28 29 2.504920 TCCGTATGGAGGAGCACAG 58.495 57.895 0.00 0.00 40.17 3.66
29 30 4.776965 TCCGTATGGAGGAGCACA 57.223 55.556 0.00 0.00 40.17 4.57
38 39 0.032130 CACGACCCAGATCCGTATGG 59.968 60.000 0.00 0.00 36.45 2.74
39 40 1.001268 CTCACGACCCAGATCCGTATG 60.001 57.143 0.00 0.00 34.91 2.39
40 41 1.133884 TCTCACGACCCAGATCCGTAT 60.134 52.381 0.00 0.00 34.91 3.06
41 42 0.253894 TCTCACGACCCAGATCCGTA 59.746 55.000 0.00 0.00 34.91 4.02
42 43 1.001269 TCTCACGACCCAGATCCGT 60.001 57.895 0.00 0.00 36.95 4.69
43 44 1.032657 AGTCTCACGACCCAGATCCG 61.033 60.000 0.00 0.00 41.16 4.18
44 45 1.134965 CAAGTCTCACGACCCAGATCC 60.135 57.143 0.00 0.00 41.16 3.36
45 46 1.737363 GCAAGTCTCACGACCCAGATC 60.737 57.143 0.00 0.00 41.16 2.75
46 47 0.247736 GCAAGTCTCACGACCCAGAT 59.752 55.000 0.00 0.00 41.16 2.90
47 48 1.666011 GCAAGTCTCACGACCCAGA 59.334 57.895 0.00 0.00 41.16 3.86
48 49 1.374758 GGCAAGTCTCACGACCCAG 60.375 63.158 0.00 0.00 41.16 4.45
49 50 2.741092 GGCAAGTCTCACGACCCA 59.259 61.111 0.00 0.00 41.16 4.51
50 51 2.432628 CGGCAAGTCTCACGACCC 60.433 66.667 0.00 0.00 41.16 4.46
51 52 2.432628 CCGGCAAGTCTCACGACC 60.433 66.667 0.00 0.00 41.16 4.79
52 53 1.733399 GACCGGCAAGTCTCACGAC 60.733 63.158 0.00 0.00 40.54 4.34
53 54 2.649034 GACCGGCAAGTCTCACGA 59.351 61.111 0.00 0.00 33.79 4.35
54 55 2.432628 GGACCGGCAAGTCTCACG 60.433 66.667 0.00 0.00 36.95 4.35
55 56 1.079750 GAGGACCGGCAAGTCTCAC 60.080 63.158 0.00 0.00 36.95 3.51
56 57 2.636412 CGAGGACCGGCAAGTCTCA 61.636 63.158 0.00 0.00 36.95 3.27
57 58 1.668101 ATCGAGGACCGGCAAGTCTC 61.668 60.000 0.00 0.44 39.14 3.36
58 59 1.682684 ATCGAGGACCGGCAAGTCT 60.683 57.895 0.00 0.00 39.14 3.24
59 60 1.519455 CATCGAGGACCGGCAAGTC 60.519 63.158 0.00 0.00 39.14 3.01
60 61 2.579201 CATCGAGGACCGGCAAGT 59.421 61.111 0.00 0.00 39.14 3.16
61 62 2.892425 GCATCGAGGACCGGCAAG 60.892 66.667 0.00 0.00 39.14 4.01
62 63 4.812476 CGCATCGAGGACCGGCAA 62.812 66.667 0.00 0.00 39.14 4.52
64 65 3.792053 AATCGCATCGAGGACCGGC 62.792 63.158 0.00 0.00 39.91 6.13
65 66 1.951130 CAATCGCATCGAGGACCGG 60.951 63.158 0.00 0.00 39.91 5.28
66 67 1.951130 CCAATCGCATCGAGGACCG 60.951 63.158 0.00 0.00 39.91 4.79
67 68 0.598680 CTCCAATCGCATCGAGGACC 60.599 60.000 0.00 0.00 39.91 4.46
68 69 1.218230 GCTCCAATCGCATCGAGGAC 61.218 60.000 0.00 0.00 39.91 3.85
69 70 1.068083 GCTCCAATCGCATCGAGGA 59.932 57.895 0.00 0.00 39.91 3.71
70 71 1.068753 AGCTCCAATCGCATCGAGG 59.931 57.895 0.00 0.00 39.91 4.63
71 72 1.220169 CCAGCTCCAATCGCATCGAG 61.220 60.000 0.00 0.00 39.91 4.04
72 73 1.227350 CCAGCTCCAATCGCATCGA 60.227 57.895 0.00 0.00 41.13 3.59
73 74 1.220169 CTCCAGCTCCAATCGCATCG 61.220 60.000 0.00 0.00 0.00 3.84
74 75 0.883814 CCTCCAGCTCCAATCGCATC 60.884 60.000 0.00 0.00 0.00 3.91
75 76 1.147824 CCTCCAGCTCCAATCGCAT 59.852 57.895 0.00 0.00 0.00 4.73
76 77 2.293318 ACCTCCAGCTCCAATCGCA 61.293 57.895 0.00 0.00 0.00 5.10
77 78 1.817099 CACCTCCAGCTCCAATCGC 60.817 63.158 0.00 0.00 0.00 4.58
78 79 1.817099 GCACCTCCAGCTCCAATCG 60.817 63.158 0.00 0.00 0.00 3.34
79 80 1.817099 CGCACCTCCAGCTCCAATC 60.817 63.158 0.00 0.00 0.00 2.67
80 81 2.270205 CGCACCTCCAGCTCCAAT 59.730 61.111 0.00 0.00 0.00 3.16
81 82 4.020617 CCGCACCTCCAGCTCCAA 62.021 66.667 0.00 0.00 0.00 3.53
83 84 2.932130 GAATCCGCACCTCCAGCTCC 62.932 65.000 0.00 0.00 0.00 4.70
84 85 1.522580 GAATCCGCACCTCCAGCTC 60.523 63.158 0.00 0.00 0.00 4.09
85 86 1.841302 TTGAATCCGCACCTCCAGCT 61.841 55.000 0.00 0.00 0.00 4.24
86 87 0.960364 TTTGAATCCGCACCTCCAGC 60.960 55.000 0.00 0.00 0.00 4.85
87 88 1.672881 GATTTGAATCCGCACCTCCAG 59.327 52.381 0.00 0.00 0.00 3.86
88 89 1.750193 GATTTGAATCCGCACCTCCA 58.250 50.000 0.00 0.00 0.00 3.86
89 90 0.657840 CGATTTGAATCCGCACCTCC 59.342 55.000 0.00 0.00 31.68 4.30
90 91 0.657840 CCGATTTGAATCCGCACCTC 59.342 55.000 0.00 0.00 31.68 3.85
91 92 0.748005 CCCGATTTGAATCCGCACCT 60.748 55.000 0.00 0.00 31.68 4.00
92 93 0.746563 TCCCGATTTGAATCCGCACC 60.747 55.000 0.00 0.00 31.68 5.01
93 94 0.657840 CTCCCGATTTGAATCCGCAC 59.342 55.000 0.00 0.00 31.68 5.34
94 95 0.539518 TCTCCCGATTTGAATCCGCA 59.460 50.000 0.00 0.00 31.68 5.69
95 96 1.663695 TTCTCCCGATTTGAATCCGC 58.336 50.000 0.00 0.00 31.68 5.54
96 97 3.251004 GGATTTCTCCCGATTTGAATCCG 59.749 47.826 0.00 0.00 35.28 4.18
97 98 4.837896 GGATTTCTCCCGATTTGAATCC 57.162 45.455 0.00 0.00 35.28 3.01
109 110 1.120530 TGTCGCCTAGGGATTTCTCC 58.879 55.000 11.72 0.00 41.26 3.71
110 111 1.202545 GGTGTCGCCTAGGGATTTCTC 60.203 57.143 11.72 0.00 0.00 2.87
111 112 0.831307 GGTGTCGCCTAGGGATTTCT 59.169 55.000 11.72 0.00 0.00 2.52
112 113 0.529992 CGGTGTCGCCTAGGGATTTC 60.530 60.000 11.72 0.00 34.25 2.17
113 114 1.520666 CGGTGTCGCCTAGGGATTT 59.479 57.895 11.72 0.00 34.25 2.17
114 115 2.432300 CCGGTGTCGCCTAGGGATT 61.432 63.158 11.72 0.00 34.25 3.01
115 116 2.838225 CCGGTGTCGCCTAGGGAT 60.838 66.667 11.72 0.00 34.25 3.85
116 117 4.371417 ACCGGTGTCGCCTAGGGA 62.371 66.667 6.12 3.19 34.25 4.20
117 118 3.834799 GACCGGTGTCGCCTAGGG 61.835 72.222 14.63 0.44 34.25 3.53
145 146 0.740737 GAAAAGACGATGCCCATGGG 59.259 55.000 27.87 27.87 38.57 4.00
146 147 1.672881 GAGAAAAGACGATGCCCATGG 59.327 52.381 4.14 4.14 0.00 3.66
147 148 1.672881 GGAGAAAAGACGATGCCCATG 59.327 52.381 0.00 0.00 0.00 3.66
148 149 1.281867 TGGAGAAAAGACGATGCCCAT 59.718 47.619 0.00 0.00 0.00 4.00
149 150 0.690192 TGGAGAAAAGACGATGCCCA 59.310 50.000 0.00 0.00 0.00 5.36
150 151 1.672881 CATGGAGAAAAGACGATGCCC 59.327 52.381 0.00 0.00 0.00 5.36
151 152 1.672881 CCATGGAGAAAAGACGATGCC 59.327 52.381 5.56 0.00 0.00 4.40
152 153 2.611292 CTCCATGGAGAAAAGACGATGC 59.389 50.000 34.54 0.00 44.53 3.91
153 154 4.128925 TCTCCATGGAGAAAAGACGATG 57.871 45.455 37.09 12.02 46.89 3.84
164 165 4.655762 TCTAATGAACGTCTCCATGGAG 57.344 45.455 32.60 32.60 43.21 3.86
165 166 4.895889 AGATCTAATGAACGTCTCCATGGA 59.104 41.667 15.27 15.27 0.00 3.41
166 167 4.987285 CAGATCTAATGAACGTCTCCATGG 59.013 45.833 4.97 4.97 0.00 3.66
167 168 4.447054 GCAGATCTAATGAACGTCTCCATG 59.553 45.833 0.00 0.00 0.00 3.66
168 169 4.343526 AGCAGATCTAATGAACGTCTCCAT 59.656 41.667 0.00 0.00 0.00 3.41
169 170 3.701542 AGCAGATCTAATGAACGTCTCCA 59.298 43.478 0.00 0.00 0.00 3.86
170 171 4.037446 AGAGCAGATCTAATGAACGTCTCC 59.963 45.833 0.00 0.00 36.10 3.71
171 172 5.181690 AGAGCAGATCTAATGAACGTCTC 57.818 43.478 0.00 0.00 36.10 3.36
172 173 5.009210 GGTAGAGCAGATCTAATGAACGTCT 59.991 44.000 0.00 0.00 42.23 4.18
173 174 5.009210 AGGTAGAGCAGATCTAATGAACGTC 59.991 44.000 0.00 0.00 42.23 4.34
174 175 4.890581 AGGTAGAGCAGATCTAATGAACGT 59.109 41.667 0.00 0.00 42.23 3.99
175 176 5.446143 AGGTAGAGCAGATCTAATGAACG 57.554 43.478 0.00 0.00 42.23 3.95
176 177 5.303078 TGGAGGTAGAGCAGATCTAATGAAC 59.697 44.000 0.00 0.00 42.23 3.18
177 178 5.303078 GTGGAGGTAGAGCAGATCTAATGAA 59.697 44.000 0.00 0.00 42.23 2.57
178 179 4.830046 GTGGAGGTAGAGCAGATCTAATGA 59.170 45.833 0.00 0.00 42.23 2.57
179 180 4.021544 GGTGGAGGTAGAGCAGATCTAATG 60.022 50.000 0.00 0.00 42.23 1.90
180 181 4.156477 GGTGGAGGTAGAGCAGATCTAAT 58.844 47.826 0.00 0.00 42.23 1.73
181 182 3.052869 TGGTGGAGGTAGAGCAGATCTAA 60.053 47.826 0.00 0.00 42.23 2.10
182 183 2.514160 TGGTGGAGGTAGAGCAGATCTA 59.486 50.000 0.00 0.00 39.64 1.98
183 184 1.289231 TGGTGGAGGTAGAGCAGATCT 59.711 52.381 0.00 0.00 42.47 2.75
184 185 1.410882 GTGGTGGAGGTAGAGCAGATC 59.589 57.143 0.00 0.00 0.00 2.75
185 186 1.490574 GTGGTGGAGGTAGAGCAGAT 58.509 55.000 0.00 0.00 0.00 2.90
186 187 0.965866 CGTGGTGGAGGTAGAGCAGA 60.966 60.000 0.00 0.00 0.00 4.26
187 188 1.513158 CGTGGTGGAGGTAGAGCAG 59.487 63.158 0.00 0.00 0.00 4.24
188 189 2.646175 GCGTGGTGGAGGTAGAGCA 61.646 63.158 0.00 0.00 0.00 4.26
189 190 1.035932 TAGCGTGGTGGAGGTAGAGC 61.036 60.000 0.00 0.00 0.00 4.09
190 191 1.693627 ATAGCGTGGTGGAGGTAGAG 58.306 55.000 0.00 0.00 0.00 2.43
191 192 2.154567 AATAGCGTGGTGGAGGTAGA 57.845 50.000 0.00 0.00 0.00 2.59
192 193 2.093658 ACAAATAGCGTGGTGGAGGTAG 60.094 50.000 0.00 0.00 0.00 3.18
193 194 1.903860 ACAAATAGCGTGGTGGAGGTA 59.096 47.619 0.00 0.00 0.00 3.08
194 195 0.690762 ACAAATAGCGTGGTGGAGGT 59.309 50.000 0.00 0.00 0.00 3.85
195 196 1.066143 AGACAAATAGCGTGGTGGAGG 60.066 52.381 0.00 0.00 0.00 4.30
196 197 2.386661 AGACAAATAGCGTGGTGGAG 57.613 50.000 0.00 0.00 0.00 3.86
197 198 2.614481 GGAAGACAAATAGCGTGGTGGA 60.614 50.000 0.00 0.00 0.00 4.02
198 199 1.737793 GGAAGACAAATAGCGTGGTGG 59.262 52.381 0.00 0.00 0.00 4.61
199 200 1.393539 CGGAAGACAAATAGCGTGGTG 59.606 52.381 0.00 0.00 0.00 4.17
200 201 1.674817 CCGGAAGACAAATAGCGTGGT 60.675 52.381 0.00 0.00 0.00 4.16
201 202 1.006832 CCGGAAGACAAATAGCGTGG 58.993 55.000 0.00 0.00 0.00 4.94
202 203 1.006832 CCCGGAAGACAAATAGCGTG 58.993 55.000 0.73 0.00 0.00 5.34
203 204 0.611714 ACCCGGAAGACAAATAGCGT 59.388 50.000 0.73 0.00 0.00 5.07
204 205 1.006832 CACCCGGAAGACAAATAGCG 58.993 55.000 0.73 0.00 0.00 4.26
205 206 2.396590 TCACCCGGAAGACAAATAGC 57.603 50.000 0.73 0.00 0.00 2.97
206 207 5.163652 GGATTTTCACCCGGAAGACAAATAG 60.164 44.000 0.73 0.00 36.72 1.73
207 208 4.703093 GGATTTTCACCCGGAAGACAAATA 59.297 41.667 0.73 0.00 36.72 1.40
208 209 3.509967 GGATTTTCACCCGGAAGACAAAT 59.490 43.478 0.73 9.00 36.72 2.32
209 210 2.888414 GGATTTTCACCCGGAAGACAAA 59.112 45.455 0.73 4.73 36.72 2.83
210 211 2.107552 AGGATTTTCACCCGGAAGACAA 59.892 45.455 0.73 0.00 36.72 3.18
211 212 1.702957 AGGATTTTCACCCGGAAGACA 59.297 47.619 0.73 0.00 36.72 3.41
212 213 2.491675 AGGATTTTCACCCGGAAGAC 57.508 50.000 0.73 0.00 36.72 3.01
213 214 3.585732 AGTTAGGATTTTCACCCGGAAGA 59.414 43.478 0.73 0.00 36.72 2.87
214 215 3.689649 CAGTTAGGATTTTCACCCGGAAG 59.310 47.826 0.73 0.00 36.72 3.46
215 216 3.681593 CAGTTAGGATTTTCACCCGGAA 58.318 45.455 0.73 0.00 0.00 4.30
216 217 2.617021 GCAGTTAGGATTTTCACCCGGA 60.617 50.000 0.73 0.00 0.00 5.14
217 218 1.743394 GCAGTTAGGATTTTCACCCGG 59.257 52.381 0.00 0.00 0.00 5.73
218 219 2.420022 CTGCAGTTAGGATTTTCACCCG 59.580 50.000 5.25 0.00 0.00 5.28
219 220 3.421844 ACTGCAGTTAGGATTTTCACCC 58.578 45.455 15.25 0.00 0.00 4.61
220 221 4.636206 CCTACTGCAGTTAGGATTTTCACC 59.364 45.833 27.06 0.00 32.87 4.02
221 222 4.095036 GCCTACTGCAGTTAGGATTTTCAC 59.905 45.833 30.59 16.19 40.77 3.18
222 223 4.261801 GCCTACTGCAGTTAGGATTTTCA 58.738 43.478 30.59 11.17 40.77 2.69
223 224 3.309954 CGCCTACTGCAGTTAGGATTTTC 59.690 47.826 30.59 18.52 41.33 2.29
224 225 3.270877 CGCCTACTGCAGTTAGGATTTT 58.729 45.455 30.59 9.11 41.33 1.82
225 226 2.420129 CCGCCTACTGCAGTTAGGATTT 60.420 50.000 30.59 9.72 41.33 2.17
226 227 1.139058 CCGCCTACTGCAGTTAGGATT 59.861 52.381 30.59 10.35 41.33 3.01
227 228 0.753262 CCGCCTACTGCAGTTAGGAT 59.247 55.000 30.59 10.97 41.33 3.24
228 229 1.956629 GCCGCCTACTGCAGTTAGGA 61.957 60.000 30.59 14.52 41.33 2.94
229 230 1.521681 GCCGCCTACTGCAGTTAGG 60.522 63.158 27.06 26.27 41.33 2.69
230 231 1.878522 CGCCGCCTACTGCAGTTAG 60.879 63.158 27.06 17.55 41.33 2.34
231 232 2.183300 CGCCGCCTACTGCAGTTA 59.817 61.111 27.06 10.10 41.33 2.24
232 233 3.691342 TCGCCGCCTACTGCAGTT 61.691 61.111 27.06 9.41 41.33 3.16
233 234 4.436998 GTCGCCGCCTACTGCAGT 62.437 66.667 25.12 25.12 41.33 4.40
246 247 4.038080 CAACAAAGGCCCCGTCGC 62.038 66.667 0.00 0.00 0.00 5.19
247 248 3.361977 CCAACAAAGGCCCCGTCG 61.362 66.667 0.00 0.00 0.00 5.12
248 249 2.989253 CCCAACAAAGGCCCCGTC 60.989 66.667 0.00 0.00 0.00 4.79
255 256 4.016444 ACACATATACAGCCCAACAAAGG 58.984 43.478 0.00 0.00 0.00 3.11
256 257 4.699735 TCACACATATACAGCCCAACAAAG 59.300 41.667 0.00 0.00 0.00 2.77
257 258 4.657013 TCACACATATACAGCCCAACAAA 58.343 39.130 0.00 0.00 0.00 2.83
807 898 2.095364 CAGCAACAACAGCATCTTCCTC 60.095 50.000 0.00 0.00 0.00 3.71
1016 1112 5.514274 TTTTTCAATTGCCTTCTCGAGTT 57.486 34.783 13.13 0.00 0.00 3.01
1435 1531 3.070159 TCACCAACTCTCTCCTCTGTTTG 59.930 47.826 0.00 0.00 0.00 2.93
1468 1564 4.664688 ACTCCATCACAGAATTTTCCCT 57.335 40.909 0.00 0.00 0.00 4.20
1876 1972 5.484290 CCCTTAATCCACCTCGGTTATATCT 59.516 44.000 0.00 0.00 35.57 1.98
2766 2871 8.590470 CATGTCATACGAGTATAGCAATCAATC 58.410 37.037 0.00 0.00 0.00 2.67
2908 3013 7.936847 TGTGACAAACTCCTTATTCACATACTT 59.063 33.333 0.00 0.00 35.65 2.24
3120 3225 1.060729 TTCCAATCACCCTTGACGGA 58.939 50.000 0.00 0.00 35.67 4.69
3310 3415 4.495184 CGCCTTACCGCCTTAAAAACATAG 60.495 45.833 0.00 0.00 0.00 2.23
3311 3416 3.374678 CGCCTTACCGCCTTAAAAACATA 59.625 43.478 0.00 0.00 0.00 2.29
3312 3417 2.162809 CGCCTTACCGCCTTAAAAACAT 59.837 45.455 0.00 0.00 0.00 2.71
3313 3418 1.536331 CGCCTTACCGCCTTAAAAACA 59.464 47.619 0.00 0.00 0.00 2.83
3314 3419 1.805943 TCGCCTTACCGCCTTAAAAAC 59.194 47.619 0.00 0.00 0.00 2.43
3315 3420 2.078392 CTCGCCTTACCGCCTTAAAAA 58.922 47.619 0.00 0.00 0.00 1.94
3316 3421 1.676615 CCTCGCCTTACCGCCTTAAAA 60.677 52.381 0.00 0.00 0.00 1.52
3317 3422 0.108041 CCTCGCCTTACCGCCTTAAA 60.108 55.000 0.00 0.00 0.00 1.52
3318 3423 1.518774 CCTCGCCTTACCGCCTTAA 59.481 57.895 0.00 0.00 0.00 1.85
3319 3424 3.085119 GCCTCGCCTTACCGCCTTA 62.085 63.158 0.00 0.00 0.00 2.69
3320 3425 4.468689 GCCTCGCCTTACCGCCTT 62.469 66.667 0.00 0.00 0.00 4.35
3324 3429 4.570663 CCTCGCCTCGCCTTACCG 62.571 72.222 0.00 0.00 0.00 4.02
3325 3430 4.893601 GCCTCGCCTCGCCTTACC 62.894 72.222 0.00 0.00 0.00 2.85
3370 3475 1.763200 GCCTCGCCTTACGCTTTAGC 61.763 60.000 0.00 0.00 43.23 3.09
3371 3476 1.480219 CGCCTCGCCTTACGCTTTAG 61.480 60.000 0.00 0.00 43.23 1.85
3372 3477 1.517694 CGCCTCGCCTTACGCTTTA 60.518 57.895 0.00 0.00 43.23 1.85
3373 3478 2.813908 CGCCTCGCCTTACGCTTT 60.814 61.111 0.00 0.00 43.23 3.51
3374 3479 3.755628 TCGCCTCGCCTTACGCTT 61.756 61.111 0.00 0.00 43.23 4.68
3375 3480 4.493747 GTCGCCTCGCCTTACGCT 62.494 66.667 0.00 0.00 43.23 5.07
3388 3493 2.126580 ACGTGTCTAAGGCGTCGC 60.127 61.111 9.22 9.22 33.22 5.19
3389 3494 2.434134 GCACGTGTCTAAGGCGTCG 61.434 63.158 18.38 0.00 36.67 5.12
3390 3495 0.736325 ATGCACGTGTCTAAGGCGTC 60.736 55.000 18.38 0.00 36.67 5.19
3391 3496 0.528924 TATGCACGTGTCTAAGGCGT 59.471 50.000 18.38 4.53 39.59 5.68
3392 3497 1.852942 ATATGCACGTGTCTAAGGCG 58.147 50.000 18.38 0.00 0.00 5.52
3393 3498 8.873215 ATATTATATATGCACGTGTCTAAGGC 57.127 34.615 18.38 0.47 0.00 4.35
3397 3502 9.908152 GCCATATATTATATATGCACGTGTCTA 57.092 33.333 20.90 9.42 32.22 2.59
3398 3503 8.421002 TGCCATATATTATATATGCACGTGTCT 58.579 33.333 20.90 7.32 32.22 3.41
3399 3504 8.587952 TGCCATATATTATATATGCACGTGTC 57.412 34.615 20.90 10.14 32.22 3.67
3400 3505 7.171508 GCTGCCATATATTATATATGCACGTGT 59.828 37.037 20.90 0.00 32.22 4.49
3401 3506 7.360353 GGCTGCCATATATTATATATGCACGTG 60.360 40.741 20.90 12.28 32.22 4.49
3402 3507 6.650807 GGCTGCCATATATTATATATGCACGT 59.349 38.462 20.90 0.00 32.22 4.49
3403 3508 6.650390 TGGCTGCCATATATTATATATGCACG 59.350 38.462 19.30 16.30 32.22 5.34
3404 3509 7.984422 TGGCTGCCATATATTATATATGCAC 57.016 36.000 19.30 16.38 32.22 4.57
3405 3510 9.590828 AATTGGCTGCCATATATTATATATGCA 57.409 29.630 24.03 19.63 31.53 3.96


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

AutoCloner maintained by Alex Coulton.