Multiple sequence alignment - TraesCS2A01G423100

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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 TraesCS2A01G423100 chr2A 100.000 3517 0 0 1 3517 678124627 678121111 0.000000e+00 6495
1 TraesCS2A01G423100 chr2A 98.741 3176 39 1 342 3517 57916518 57913344 0.000000e+00 5642
2 TraesCS2A01G423100 chr2A 96.127 3176 99 12 342 3517 672845011 672848162 0.000000e+00 5162
3 TraesCS2A01G423100 chr7A 99.089 3185 29 0 333 3517 299568835 299572019 0.000000e+00 5722
4 TraesCS2A01G423100 chr1D 98.117 3186 56 3 332 3517 283557056 283560237 0.000000e+00 5548
5 TraesCS2A01G423100 chr3B 98.017 3177 59 2 342 3517 245008829 245012002 0.000000e+00 5515
6 TraesCS2A01G423100 chr3B 98.093 2675 51 0 843 3517 259399586 259396912 0.000000e+00 4658
7 TraesCS2A01G423100 chr3B 93.978 465 27 1 353 817 259400043 259399580 0.000000e+00 702
8 TraesCS2A01G423100 chr4D 97.324 3176 64 3 342 3517 281202809 281199655 0.000000e+00 5374
9 TraesCS2A01G423100 chr1B 96.631 3176 76 12 342 3517 682092121 682088977 0.000000e+00 5243
10 TraesCS2A01G423100 chr1B 98.600 2785 39 0 342 3126 611146109 611148893 0.000000e+00 4927
11 TraesCS2A01G423100 chr4B 95.373 3177 129 11 341 3517 637596055 637599213 0.000000e+00 5036
12 TraesCS2A01G423100 chr2D 82.196 337 34 11 2 328 534736848 534736528 2.080000e-67 267
13 TraesCS2A01G423100 chr2D 86.452 155 16 3 179 328 534737353 534737199 7.810000e-37 165
14 TraesCS2A01G423100 chr2B 87.374 198 20 2 131 328 636091681 636091489 4.570000e-54 222


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 TraesCS2A01G423100 chr2A 678121111 678124627 3516 True 6495 6495 100.0000 1 3517 1 chr2A.!!$R2 3516
1 TraesCS2A01G423100 chr2A 57913344 57916518 3174 True 5642 5642 98.7410 342 3517 1 chr2A.!!$R1 3175
2 TraesCS2A01G423100 chr2A 672845011 672848162 3151 False 5162 5162 96.1270 342 3517 1 chr2A.!!$F1 3175
3 TraesCS2A01G423100 chr7A 299568835 299572019 3184 False 5722 5722 99.0890 333 3517 1 chr7A.!!$F1 3184
4 TraesCS2A01G423100 chr1D 283557056 283560237 3181 False 5548 5548 98.1170 332 3517 1 chr1D.!!$F1 3185
5 TraesCS2A01G423100 chr3B 245008829 245012002 3173 False 5515 5515 98.0170 342 3517 1 chr3B.!!$F1 3175
6 TraesCS2A01G423100 chr3B 259396912 259400043 3131 True 2680 4658 96.0355 353 3517 2 chr3B.!!$R1 3164
7 TraesCS2A01G423100 chr4D 281199655 281202809 3154 True 5374 5374 97.3240 342 3517 1 chr4D.!!$R1 3175
8 TraesCS2A01G423100 chr1B 682088977 682092121 3144 True 5243 5243 96.6310 342 3517 1 chr1B.!!$R1 3175
9 TraesCS2A01G423100 chr1B 611146109 611148893 2784 False 4927 4927 98.6000 342 3126 1 chr1B.!!$F1 2784
10 TraesCS2A01G423100 chr4B 637596055 637599213 3158 False 5036 5036 95.3730 341 3517 1 chr4B.!!$F1 3176
11 TraesCS2A01G423100 chr2D 534736528 534737353 825 True 216 267 84.3240 2 328 2 chr2D.!!$R1 326

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
60 61 0.179108 CGAATCCGGTCTTCTCCCAC 60.179 60.0 0.0 0.0 0.0 4.61 F
63 64 0.252284 ATCCGGTCTTCTCCCACAGT 60.252 55.0 0.0 0.0 0.0 3.55 F
64 65 0.406750 TCCGGTCTTCTCCCACAGTA 59.593 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2492 2.300152 GACTGACCCTCACTCATGACAA 59.700 50.000 0.0 0.0 0.0 3.18 R
2260 2741 3.388676 CCATTGTACGATTGGGGGTACTA 59.611 47.826 0.0 0.0 39.7 1.82 R
2573 3054 1.202302 CCTTCTCTATCGCAGTCGCAA 60.202 52.381 0.0 0.0 38.4 4.85 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
22 23 5.913946 TTTTCTTTCCTCTTCCTCCTCTT 57.086 39.130 0.00 0.00 0.00 2.85
23 24 5.491323 TTTCTTTCCTCTTCCTCCTCTTC 57.509 43.478 0.00 0.00 0.00 2.87
24 25 4.133526 TCTTTCCTCTTCCTCCTCTTCA 57.866 45.455 0.00 0.00 0.00 3.02
25 26 4.693420 TCTTTCCTCTTCCTCCTCTTCAT 58.307 43.478 0.00 0.00 0.00 2.57
26 27 4.714308 TCTTTCCTCTTCCTCCTCTTCATC 59.286 45.833 0.00 0.00 0.00 2.92
27 28 3.765432 TCCTCTTCCTCCTCTTCATCA 57.235 47.619 0.00 0.00 0.00 3.07
28 29 3.641046 TCCTCTTCCTCCTCTTCATCAG 58.359 50.000 0.00 0.00 0.00 2.90
29 30 3.270696 TCCTCTTCCTCCTCTTCATCAGA 59.729 47.826 0.00 0.00 0.00 3.27
30 31 3.384467 CCTCTTCCTCCTCTTCATCAGAC 59.616 52.174 0.00 0.00 0.00 3.51
31 32 4.280819 CTCTTCCTCCTCTTCATCAGACT 58.719 47.826 0.00 0.00 0.00 3.24
32 33 4.022603 TCTTCCTCCTCTTCATCAGACTG 58.977 47.826 0.00 0.00 0.00 3.51
33 34 2.744760 TCCTCCTCTTCATCAGACTGG 58.255 52.381 1.81 0.00 0.00 4.00
34 35 1.761784 CCTCCTCTTCATCAGACTGGG 59.238 57.143 1.81 0.00 0.00 4.45
35 36 1.138661 CTCCTCTTCATCAGACTGGGC 59.861 57.143 1.81 0.00 0.00 5.36
36 37 1.202330 CCTCTTCATCAGACTGGGCT 58.798 55.000 1.81 0.00 0.00 5.19
37 38 1.134461 CCTCTTCATCAGACTGGGCTG 60.134 57.143 1.81 0.00 37.24 4.85
38 39 1.554160 CTCTTCATCAGACTGGGCTGT 59.446 52.381 1.81 0.00 37.20 4.40
39 40 1.277273 TCTTCATCAGACTGGGCTGTG 59.723 52.381 1.81 2.20 37.20 3.66
40 41 0.325933 TTCATCAGACTGGGCTGTGG 59.674 55.000 1.81 0.00 37.20 4.17
41 42 1.748122 CATCAGACTGGGCTGTGGC 60.748 63.158 1.81 0.00 37.20 5.01
42 43 3.320879 ATCAGACTGGGCTGTGGCG 62.321 63.158 1.81 0.00 39.81 5.69
43 44 4.007644 CAGACTGGGCTGTGGCGA 62.008 66.667 0.00 0.00 39.81 5.54
44 45 3.241530 AGACTGGGCTGTGGCGAA 61.242 61.111 0.00 0.00 39.81 4.70
45 46 2.045926 GACTGGGCTGTGGCGAAT 60.046 61.111 0.00 0.00 39.81 3.34
46 47 2.045926 ACTGGGCTGTGGCGAATC 60.046 61.111 0.00 0.00 39.81 2.52
47 48 2.825836 CTGGGCTGTGGCGAATCC 60.826 66.667 0.00 0.00 39.81 3.01
48 49 4.776322 TGGGCTGTGGCGAATCCG 62.776 66.667 0.00 0.00 39.81 4.18
50 51 4.778143 GGCTGTGGCGAATCCGGT 62.778 66.667 0.00 0.00 39.81 5.28
51 52 3.195698 GCTGTGGCGAATCCGGTC 61.196 66.667 0.00 0.00 37.80 4.79
52 53 2.579201 CTGTGGCGAATCCGGTCT 59.421 61.111 0.00 0.00 37.80 3.85
53 54 1.079127 CTGTGGCGAATCCGGTCTT 60.079 57.895 0.00 0.00 37.80 3.01
54 55 1.079405 TGTGGCGAATCCGGTCTTC 60.079 57.895 0.00 5.38 37.80 2.87
55 56 1.218316 GTGGCGAATCCGGTCTTCT 59.782 57.895 0.00 0.00 37.80 2.85
56 57 0.806492 GTGGCGAATCCGGTCTTCTC 60.806 60.000 0.00 1.07 37.80 2.87
57 58 1.227292 GGCGAATCCGGTCTTCTCC 60.227 63.158 0.00 7.06 36.06 3.71
58 59 1.227292 GCGAATCCGGTCTTCTCCC 60.227 63.158 0.00 0.00 36.06 4.30
59 60 1.956629 GCGAATCCGGTCTTCTCCCA 61.957 60.000 0.00 0.00 36.06 4.37
60 61 0.179108 CGAATCCGGTCTTCTCCCAC 60.179 60.000 0.00 0.00 0.00 4.61
61 62 0.902531 GAATCCGGTCTTCTCCCACA 59.097 55.000 0.00 0.00 0.00 4.17
62 63 0.905357 AATCCGGTCTTCTCCCACAG 59.095 55.000 0.00 0.00 0.00 3.66
63 64 0.252284 ATCCGGTCTTCTCCCACAGT 60.252 55.000 0.00 0.00 0.00 3.55
64 65 0.406750 TCCGGTCTTCTCCCACAGTA 59.593 55.000 0.00 0.00 0.00 2.74
65 66 0.531200 CCGGTCTTCTCCCACAGTAC 59.469 60.000 0.00 0.00 0.00 2.73
66 67 1.254026 CGGTCTTCTCCCACAGTACA 58.746 55.000 0.00 0.00 0.00 2.90
67 68 1.825474 CGGTCTTCTCCCACAGTACAT 59.175 52.381 0.00 0.00 0.00 2.29
68 69 2.159226 CGGTCTTCTCCCACAGTACATC 60.159 54.545 0.00 0.00 0.00 3.06
69 70 2.832129 GGTCTTCTCCCACAGTACATCA 59.168 50.000 0.00 0.00 0.00 3.07
70 71 3.452627 GGTCTTCTCCCACAGTACATCAT 59.547 47.826 0.00 0.00 0.00 2.45
71 72 4.442192 GGTCTTCTCCCACAGTACATCATC 60.442 50.000 0.00 0.00 0.00 2.92
72 73 4.404073 GTCTTCTCCCACAGTACATCATCT 59.596 45.833 0.00 0.00 0.00 2.90
73 74 4.403752 TCTTCTCCCACAGTACATCATCTG 59.596 45.833 0.00 0.00 37.65 2.90
74 75 2.432146 TCTCCCACAGTACATCATCTGC 59.568 50.000 0.00 0.00 35.37 4.26
75 76 2.169144 CTCCCACAGTACATCATCTGCA 59.831 50.000 0.00 0.00 35.37 4.41
76 77 2.773661 TCCCACAGTACATCATCTGCAT 59.226 45.455 0.00 0.00 35.37 3.96
77 78 3.136763 CCCACAGTACATCATCTGCATC 58.863 50.000 0.00 0.00 35.37 3.91
78 79 3.136763 CCACAGTACATCATCTGCATCC 58.863 50.000 0.00 0.00 35.37 3.51
79 80 3.181457 CCACAGTACATCATCTGCATCCT 60.181 47.826 0.00 0.00 35.37 3.24
80 81 4.449131 CACAGTACATCATCTGCATCCTT 58.551 43.478 0.00 0.00 35.37 3.36
81 82 4.272748 CACAGTACATCATCTGCATCCTTG 59.727 45.833 0.00 0.00 35.37 3.61
82 83 4.080695 ACAGTACATCATCTGCATCCTTGT 60.081 41.667 0.00 0.00 35.37 3.16
83 84 4.880120 CAGTACATCATCTGCATCCTTGTT 59.120 41.667 0.00 0.00 0.00 2.83
84 85 4.880120 AGTACATCATCTGCATCCTTGTTG 59.120 41.667 0.00 0.00 0.00 3.33
85 86 3.959293 ACATCATCTGCATCCTTGTTGA 58.041 40.909 0.00 0.00 0.00 3.18
86 87 3.693085 ACATCATCTGCATCCTTGTTGAC 59.307 43.478 0.00 0.00 0.00 3.18
87 88 2.349590 TCATCTGCATCCTTGTTGACG 58.650 47.619 0.00 0.00 0.00 4.35
88 89 2.028203 TCATCTGCATCCTTGTTGACGA 60.028 45.455 0.00 0.00 0.00 4.20
89 90 1.795768 TCTGCATCCTTGTTGACGAC 58.204 50.000 0.00 0.00 0.00 4.34
90 91 1.069978 TCTGCATCCTTGTTGACGACA 59.930 47.619 0.00 0.00 36.19 4.35
91 92 1.872952 CTGCATCCTTGTTGACGACAA 59.127 47.619 8.01 8.01 45.70 3.18
103 104 2.980568 TGACGACAACCTCACAAAAGT 58.019 42.857 0.00 0.00 0.00 2.66
104 105 2.675844 TGACGACAACCTCACAAAAGTG 59.324 45.455 0.00 0.00 0.00 3.16
105 106 2.933906 GACGACAACCTCACAAAAGTGA 59.066 45.455 0.00 0.00 0.00 3.41
106 107 3.340034 ACGACAACCTCACAAAAGTGAA 58.660 40.909 0.00 0.00 32.43 3.18
107 108 3.754323 ACGACAACCTCACAAAAGTGAAA 59.246 39.130 0.00 0.00 32.43 2.69
108 109 4.095610 CGACAACCTCACAAAAGTGAAAC 58.904 43.478 0.00 0.00 32.43 2.78
109 110 4.378978 CGACAACCTCACAAAAGTGAAACA 60.379 41.667 0.00 0.00 41.43 2.83
110 111 4.805219 ACAACCTCACAAAAGTGAAACAC 58.195 39.130 0.00 0.00 41.43 3.32
111 112 4.279671 ACAACCTCACAAAAGTGAAACACA 59.720 37.500 4.75 0.00 41.43 3.72
112 113 5.047377 ACAACCTCACAAAAGTGAAACACAT 60.047 36.000 4.75 0.00 41.43 3.21
113 114 4.997565 ACCTCACAAAAGTGAAACACATG 58.002 39.130 4.75 0.00 41.43 3.21
114 115 4.704540 ACCTCACAAAAGTGAAACACATGA 59.295 37.500 0.00 0.48 41.43 3.07
115 116 5.360714 ACCTCACAAAAGTGAAACACATGAT 59.639 36.000 0.00 0.00 41.43 2.45
116 117 5.916883 CCTCACAAAAGTGAAACACATGATC 59.083 40.000 0.00 0.00 41.43 2.92
117 118 6.448207 TCACAAAAGTGAAACACATGATCA 57.552 33.333 0.00 0.00 41.43 2.92
118 119 6.497437 TCACAAAAGTGAAACACATGATCAG 58.503 36.000 0.00 0.00 41.43 2.90
119 120 6.095300 TCACAAAAGTGAAACACATGATCAGT 59.905 34.615 0.00 0.00 41.43 3.41
120 121 6.753279 CACAAAAGTGAAACACATGATCAGTT 59.247 34.615 0.00 4.93 41.43 3.16
121 122 7.914871 CACAAAAGTGAAACACATGATCAGTTA 59.085 33.333 0.00 0.00 41.43 2.24
122 123 8.465999 ACAAAAGTGAAACACATGATCAGTTAA 58.534 29.630 0.00 0.00 41.43 2.01
123 124 8.961092 CAAAAGTGAAACACATGATCAGTTAAG 58.039 33.333 0.00 1.35 41.43 1.85
124 125 7.807977 AAGTGAAACACATGATCAGTTAAGT 57.192 32.000 0.00 0.00 41.43 2.24
125 126 8.902540 AAGTGAAACACATGATCAGTTAAGTA 57.097 30.769 0.00 0.00 41.43 2.24
126 127 8.902540 AGTGAAACACATGATCAGTTAAGTAA 57.097 30.769 0.00 0.00 41.43 2.24
127 128 9.337396 AGTGAAACACATGATCAGTTAAGTAAA 57.663 29.630 0.00 0.00 41.43 2.01
128 129 9.944663 GTGAAACACATGATCAGTTAAGTAAAA 57.055 29.630 0.00 0.00 36.32 1.52
129 130 9.944663 TGAAACACATGATCAGTTAAGTAAAAC 57.055 29.630 0.00 0.00 0.00 2.43
130 131 9.944663 GAAACACATGATCAGTTAAGTAAAACA 57.055 29.630 0.00 0.00 0.00 2.83
159 160 8.819643 ACTGAAGAACTAAGACTATTGACAAC 57.180 34.615 0.00 0.00 0.00 3.32
160 161 8.643324 ACTGAAGAACTAAGACTATTGACAACT 58.357 33.333 0.00 0.00 0.00 3.16
161 162 9.482627 CTGAAGAACTAAGACTATTGACAACTT 57.517 33.333 0.00 0.00 0.00 2.66
167 168 8.480643 ACTAAGACTATTGACAACTTACATGC 57.519 34.615 0.00 0.00 0.00 4.06
168 169 8.094548 ACTAAGACTATTGACAACTTACATGCA 58.905 33.333 0.00 0.00 0.00 3.96
169 170 6.727824 AGACTATTGACAACTTACATGCAC 57.272 37.500 0.00 0.00 0.00 4.57
170 171 6.467677 AGACTATTGACAACTTACATGCACT 58.532 36.000 0.00 0.00 0.00 4.40
171 172 6.936900 AGACTATTGACAACTTACATGCACTT 59.063 34.615 0.00 0.00 0.00 3.16
172 173 8.094548 AGACTATTGACAACTTACATGCACTTA 58.905 33.333 0.00 0.00 0.00 2.24
173 174 8.256611 ACTATTGACAACTTACATGCACTTAG 57.743 34.615 0.00 0.00 0.00 2.18
174 175 5.356882 TTGACAACTTACATGCACTTAGC 57.643 39.130 0.00 0.00 45.96 3.09
175 176 3.751175 TGACAACTTACATGCACTTAGCC 59.249 43.478 0.00 0.00 44.83 3.93
176 177 4.003648 GACAACTTACATGCACTTAGCCT 58.996 43.478 0.00 0.00 44.83 4.58
177 178 4.398319 ACAACTTACATGCACTTAGCCTT 58.602 39.130 0.00 0.00 44.83 4.35
178 179 5.556915 ACAACTTACATGCACTTAGCCTTA 58.443 37.500 0.00 0.00 44.83 2.69
179 180 6.180472 ACAACTTACATGCACTTAGCCTTAT 58.820 36.000 0.00 0.00 44.83 1.73
180 181 7.335627 ACAACTTACATGCACTTAGCCTTATA 58.664 34.615 0.00 0.00 44.83 0.98
181 182 7.993183 ACAACTTACATGCACTTAGCCTTATAT 59.007 33.333 0.00 0.00 44.83 0.86
182 183 9.489084 CAACTTACATGCACTTAGCCTTATATA 57.511 33.333 0.00 0.00 44.83 0.86
192 193 8.260818 GCACTTAGCCTTATATAGATGGATGAA 58.739 37.037 3.56 0.00 37.23 2.57
205 206 8.804912 ATAGATGGATGAAAATAATCTCTGCC 57.195 34.615 0.00 0.00 0.00 4.85
206 207 6.607970 AGATGGATGAAAATAATCTCTGCCA 58.392 36.000 0.00 0.00 0.00 4.92
207 208 6.715718 AGATGGATGAAAATAATCTCTGCCAG 59.284 38.462 0.00 0.00 0.00 4.85
208 209 5.759059 TGGATGAAAATAATCTCTGCCAGT 58.241 37.500 0.00 0.00 0.00 4.00
209 210 6.899089 TGGATGAAAATAATCTCTGCCAGTA 58.101 36.000 0.00 0.00 0.00 2.74
210 211 6.767902 TGGATGAAAATAATCTCTGCCAGTAC 59.232 38.462 0.00 0.00 0.00 2.73
211 212 6.205658 GGATGAAAATAATCTCTGCCAGTACC 59.794 42.308 0.00 0.00 0.00 3.34
212 213 6.061022 TGAAAATAATCTCTGCCAGTACCA 57.939 37.500 0.00 0.00 0.00 3.25
213 214 6.480763 TGAAAATAATCTCTGCCAGTACCAA 58.519 36.000 0.00 0.00 0.00 3.67
214 215 6.374333 TGAAAATAATCTCTGCCAGTACCAAC 59.626 38.462 0.00 0.00 0.00 3.77
215 216 2.789409 AATCTCTGCCAGTACCAACC 57.211 50.000 0.00 0.00 0.00 3.77
216 217 1.656587 ATCTCTGCCAGTACCAACCA 58.343 50.000 0.00 0.00 0.00 3.67
217 218 1.429930 TCTCTGCCAGTACCAACCAA 58.570 50.000 0.00 0.00 0.00 3.67
218 219 1.771854 TCTCTGCCAGTACCAACCAAA 59.228 47.619 0.00 0.00 0.00 3.28
219 220 2.154462 CTCTGCCAGTACCAACCAAAG 58.846 52.381 0.00 0.00 0.00 2.77
220 221 1.771854 TCTGCCAGTACCAACCAAAGA 59.228 47.619 0.00 0.00 0.00 2.52
221 222 1.880027 CTGCCAGTACCAACCAAAGAC 59.120 52.381 0.00 0.00 0.00 3.01
222 223 0.872388 GCCAGTACCAACCAAAGACG 59.128 55.000 0.00 0.00 0.00 4.18
223 224 1.541670 GCCAGTACCAACCAAAGACGA 60.542 52.381 0.00 0.00 0.00 4.20
224 225 2.140717 CCAGTACCAACCAAAGACGAC 58.859 52.381 0.00 0.00 0.00 4.34
225 226 2.140717 CAGTACCAACCAAAGACGACC 58.859 52.381 0.00 0.00 0.00 4.79
226 227 1.764134 AGTACCAACCAAAGACGACCA 59.236 47.619 0.00 0.00 0.00 4.02
227 228 2.140717 GTACCAACCAAAGACGACCAG 58.859 52.381 0.00 0.00 0.00 4.00
228 229 0.834612 ACCAACCAAAGACGACCAGA 59.165 50.000 0.00 0.00 0.00 3.86
229 230 1.210967 ACCAACCAAAGACGACCAGAA 59.789 47.619 0.00 0.00 0.00 3.02
230 231 2.294074 CCAACCAAAGACGACCAGAAA 58.706 47.619 0.00 0.00 0.00 2.52
231 232 2.290641 CCAACCAAAGACGACCAGAAAG 59.709 50.000 0.00 0.00 0.00 2.62
232 233 3.202906 CAACCAAAGACGACCAGAAAGA 58.797 45.455 0.00 0.00 0.00 2.52
233 234 3.553828 ACCAAAGACGACCAGAAAGAA 57.446 42.857 0.00 0.00 0.00 2.52
234 235 3.881220 ACCAAAGACGACCAGAAAGAAA 58.119 40.909 0.00 0.00 0.00 2.52
235 236 3.877508 ACCAAAGACGACCAGAAAGAAAG 59.122 43.478 0.00 0.00 0.00 2.62
236 237 3.304057 CCAAAGACGACCAGAAAGAAAGC 60.304 47.826 0.00 0.00 0.00 3.51
237 238 3.477210 AAGACGACCAGAAAGAAAGCT 57.523 42.857 0.00 0.00 0.00 3.74
238 239 3.477210 AGACGACCAGAAAGAAAGCTT 57.523 42.857 0.00 0.00 35.37 3.74
239 240 3.394719 AGACGACCAGAAAGAAAGCTTC 58.605 45.455 0.00 0.00 31.82 3.86
240 241 3.131396 GACGACCAGAAAGAAAGCTTCA 58.869 45.455 0.00 0.00 31.82 3.02
241 242 3.134458 ACGACCAGAAAGAAAGCTTCAG 58.866 45.455 0.00 0.00 31.82 3.02
242 243 3.134458 CGACCAGAAAGAAAGCTTCAGT 58.866 45.455 0.00 0.00 31.82 3.41
243 244 3.561725 CGACCAGAAAGAAAGCTTCAGTT 59.438 43.478 0.00 0.00 31.82 3.16
244 245 4.553547 CGACCAGAAAGAAAGCTTCAGTTG 60.554 45.833 0.00 0.00 31.82 3.16
245 246 3.067320 ACCAGAAAGAAAGCTTCAGTTGC 59.933 43.478 0.00 0.00 31.82 4.17
246 247 3.317430 CCAGAAAGAAAGCTTCAGTTGCT 59.683 43.478 0.00 0.00 43.32 3.91
247 248 4.288531 CAGAAAGAAAGCTTCAGTTGCTG 58.711 43.478 0.00 4.26 41.03 4.41
248 249 3.317430 AGAAAGAAAGCTTCAGTTGCTGG 59.683 43.478 0.00 0.00 41.03 4.85
249 250 1.613836 AGAAAGCTTCAGTTGCTGGG 58.386 50.000 0.00 0.00 41.03 4.45
250 251 1.133668 AGAAAGCTTCAGTTGCTGGGT 60.134 47.619 0.00 0.00 41.03 4.51
251 252 2.106511 AGAAAGCTTCAGTTGCTGGGTA 59.893 45.455 0.00 0.00 41.03 3.69
252 253 2.887151 AAGCTTCAGTTGCTGGGTAT 57.113 45.000 0.00 0.00 41.03 2.73
253 254 2.409948 AGCTTCAGTTGCTGGGTATC 57.590 50.000 0.00 0.00 39.56 2.24
254 255 1.912043 AGCTTCAGTTGCTGGGTATCT 59.088 47.619 0.00 0.00 39.56 1.98
255 256 2.307098 AGCTTCAGTTGCTGGGTATCTT 59.693 45.455 0.00 0.00 39.56 2.40
256 257 3.084786 GCTTCAGTTGCTGGGTATCTTT 58.915 45.455 0.00 0.00 31.51 2.52
257 258 3.127721 GCTTCAGTTGCTGGGTATCTTTC 59.872 47.826 0.00 0.00 31.51 2.62
258 259 4.583871 CTTCAGTTGCTGGGTATCTTTCT 58.416 43.478 0.00 0.00 31.51 2.52
259 260 4.640771 TCAGTTGCTGGGTATCTTTCTT 57.359 40.909 0.00 0.00 31.51 2.52
260 261 4.985538 TCAGTTGCTGGGTATCTTTCTTT 58.014 39.130 0.00 0.00 31.51 2.52
261 262 5.003804 TCAGTTGCTGGGTATCTTTCTTTC 58.996 41.667 0.00 0.00 31.51 2.62
262 263 5.006386 CAGTTGCTGGGTATCTTTCTTTCT 58.994 41.667 0.00 0.00 0.00 2.52
263 264 5.006386 AGTTGCTGGGTATCTTTCTTTCTG 58.994 41.667 0.00 0.00 0.00 3.02
264 265 3.347216 TGCTGGGTATCTTTCTTTCTGC 58.653 45.455 0.00 0.00 0.00 4.26
265 266 3.244875 TGCTGGGTATCTTTCTTTCTGCA 60.245 43.478 0.00 0.00 0.00 4.41
266 267 3.758554 GCTGGGTATCTTTCTTTCTGCAA 59.241 43.478 0.00 0.00 0.00 4.08
267 268 4.379918 GCTGGGTATCTTTCTTTCTGCAAC 60.380 45.833 0.00 0.00 0.00 4.17
268 269 4.724399 TGGGTATCTTTCTTTCTGCAACA 58.276 39.130 0.00 0.00 0.00 3.33
269 270 5.324409 TGGGTATCTTTCTTTCTGCAACAT 58.676 37.500 0.00 0.00 0.00 2.71
270 271 5.415701 TGGGTATCTTTCTTTCTGCAACATC 59.584 40.000 0.00 0.00 0.00 3.06
271 272 5.649831 GGGTATCTTTCTTTCTGCAACATCT 59.350 40.000 0.00 0.00 0.00 2.90
272 273 6.404074 GGGTATCTTTCTTTCTGCAACATCTG 60.404 42.308 0.00 0.00 0.00 2.90
286 287 4.897224 CAACATCTGCAAACTATACGGTG 58.103 43.478 0.00 0.00 0.00 4.94
287 288 4.465632 ACATCTGCAAACTATACGGTGA 57.534 40.909 0.00 0.00 0.00 4.02
288 289 5.023533 ACATCTGCAAACTATACGGTGAT 57.976 39.130 0.00 0.00 0.00 3.06
289 290 5.050490 ACATCTGCAAACTATACGGTGATC 58.950 41.667 0.00 0.00 0.00 2.92
290 291 4.729227 TCTGCAAACTATACGGTGATCA 57.271 40.909 0.00 0.00 0.00 2.92
291 292 4.682787 TCTGCAAACTATACGGTGATCAG 58.317 43.478 0.00 0.00 0.00 2.90
292 293 4.159693 TCTGCAAACTATACGGTGATCAGT 59.840 41.667 0.00 0.00 0.00 3.41
293 294 4.827692 TGCAAACTATACGGTGATCAGTT 58.172 39.130 0.00 0.00 0.00 3.16
294 295 4.629634 TGCAAACTATACGGTGATCAGTTG 59.370 41.667 0.00 0.00 30.20 3.16
295 296 4.630069 GCAAACTATACGGTGATCAGTTGT 59.370 41.667 0.00 0.00 30.20 3.32
296 297 5.121768 GCAAACTATACGGTGATCAGTTGTT 59.878 40.000 0.00 0.00 30.20 2.83
297 298 6.672357 GCAAACTATACGGTGATCAGTTGTTC 60.672 42.308 0.00 0.00 30.20 3.18
298 299 5.916661 ACTATACGGTGATCAGTTGTTCT 57.083 39.130 0.00 0.00 0.00 3.01
299 300 7.400599 AACTATACGGTGATCAGTTGTTCTA 57.599 36.000 0.00 0.00 0.00 2.10
300 301 6.793349 ACTATACGGTGATCAGTTGTTCTAC 58.207 40.000 0.00 0.00 0.00 2.59
301 302 5.916661 ATACGGTGATCAGTTGTTCTACT 57.083 39.130 0.00 0.00 0.00 2.57
302 303 7.772292 ACTATACGGTGATCAGTTGTTCTACTA 59.228 37.037 0.00 0.00 0.00 1.82
303 304 5.312120 ACGGTGATCAGTTGTTCTACTAG 57.688 43.478 0.00 0.00 0.00 2.57
304 305 4.765856 ACGGTGATCAGTTGTTCTACTAGT 59.234 41.667 0.00 0.00 0.00 2.57
305 306 5.243283 ACGGTGATCAGTTGTTCTACTAGTT 59.757 40.000 0.00 0.00 0.00 2.24
306 307 5.573282 CGGTGATCAGTTGTTCTACTAGTTG 59.427 44.000 0.00 0.00 0.00 3.16
307 308 6.456501 GGTGATCAGTTGTTCTACTAGTTGT 58.543 40.000 0.00 0.00 0.00 3.32
308 309 6.929606 GGTGATCAGTTGTTCTACTAGTTGTT 59.070 38.462 0.00 0.00 0.00 2.83
309 310 7.116519 GGTGATCAGTTGTTCTACTAGTTGTTC 59.883 40.741 0.00 0.00 0.00 3.18
310 311 7.868415 GTGATCAGTTGTTCTACTAGTTGTTCT 59.132 37.037 0.00 0.00 0.00 3.01
311 312 8.082852 TGATCAGTTGTTCTACTAGTTGTTCTC 58.917 37.037 0.00 0.00 0.00 2.87
312 313 7.584122 TCAGTTGTTCTACTAGTTGTTCTCT 57.416 36.000 0.00 0.00 0.00 3.10
313 314 8.008513 TCAGTTGTTCTACTAGTTGTTCTCTT 57.991 34.615 0.00 0.00 0.00 2.85
314 315 8.475639 TCAGTTGTTCTACTAGTTGTTCTCTTT 58.524 33.333 0.00 0.00 0.00 2.52
315 316 8.543774 CAGTTGTTCTACTAGTTGTTCTCTTTG 58.456 37.037 0.00 0.00 0.00 2.77
316 317 7.711339 AGTTGTTCTACTAGTTGTTCTCTTTGG 59.289 37.037 0.00 0.00 0.00 3.28
317 318 5.989777 TGTTCTACTAGTTGTTCTCTTTGGC 59.010 40.000 0.00 0.00 0.00 4.52
318 319 6.183360 TGTTCTACTAGTTGTTCTCTTTGGCT 60.183 38.462 0.00 0.00 0.00 4.75
319 320 6.420913 TCTACTAGTTGTTCTCTTTGGCTT 57.579 37.500 0.00 0.00 0.00 4.35
320 321 6.223852 TCTACTAGTTGTTCTCTTTGGCTTG 58.776 40.000 0.00 0.00 0.00 4.01
321 322 4.781934 ACTAGTTGTTCTCTTTGGCTTGT 58.218 39.130 0.00 0.00 0.00 3.16
322 323 5.193679 ACTAGTTGTTCTCTTTGGCTTGTT 58.806 37.500 0.00 0.00 0.00 2.83
323 324 5.652452 ACTAGTTGTTCTCTTTGGCTTGTTT 59.348 36.000 0.00 0.00 0.00 2.83
324 325 5.405935 AGTTGTTCTCTTTGGCTTGTTTT 57.594 34.783 0.00 0.00 0.00 2.43
325 326 5.793817 AGTTGTTCTCTTTGGCTTGTTTTT 58.206 33.333 0.00 0.00 0.00 1.94
326 327 6.930731 AGTTGTTCTCTTTGGCTTGTTTTTA 58.069 32.000 0.00 0.00 0.00 1.52
327 328 7.382898 AGTTGTTCTCTTTGGCTTGTTTTTAA 58.617 30.769 0.00 0.00 0.00 1.52
328 329 8.040727 AGTTGTTCTCTTTGGCTTGTTTTTAAT 58.959 29.630 0.00 0.00 0.00 1.40
329 330 9.308318 GTTGTTCTCTTTGGCTTGTTTTTAATA 57.692 29.630 0.00 0.00 0.00 0.98
330 331 9.877178 TTGTTCTCTTTGGCTTGTTTTTAATAA 57.123 25.926 0.00 0.00 0.00 1.40
331 332 9.528018 TGTTCTCTTTGGCTTGTTTTTAATAAG 57.472 29.630 0.00 0.00 33.31 1.73
450 451 1.536073 CCTCTGTTCCGTGAGAGCCA 61.536 60.000 0.00 0.00 35.34 4.75
814 815 3.414700 GCAACGCTGTCAGGTCCG 61.415 66.667 1.14 0.00 0.00 4.79
939 940 3.971468 AGAGGAGAAGAGGAGTGCTAT 57.029 47.619 0.00 0.00 0.00 2.97
1468 1469 7.287950 CAAAATTGAAGAAACTGTGCATGATG 58.712 34.615 0.00 0.00 0.00 3.07
2012 2492 1.202698 GGAGGCCAGAGCGAATGTATT 60.203 52.381 5.01 0.00 41.24 1.89
2260 2741 7.766278 ACGTTAGAGAGTTTGAATGCTATCAAT 59.234 33.333 5.73 0.00 38.98 2.57
2573 3054 1.677966 CTGCTGGCATGGCTCTTGT 60.678 57.895 21.08 0.00 0.00 3.16
3197 3681 5.104817 TGACTGCAACCTATCTGATCAATCA 60.105 40.000 0.00 0.00 35.16 2.57
3202 3686 5.530171 GCAACCTATCTGATCAATCACACAT 59.470 40.000 0.00 0.00 32.50 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.369699 TGAAGAGGAGGAAGAGGAAAGAAAA 59.630 40.000 0.00 0.00 0.00 2.29
2 3 4.493618 TGAAGAGGAGGAAGAGGAAAGAA 58.506 43.478 0.00 0.00 0.00 2.52
4 5 4.469227 TGATGAAGAGGAGGAAGAGGAAAG 59.531 45.833 0.00 0.00 0.00 2.62
5 6 4.429505 TGATGAAGAGGAGGAAGAGGAAA 58.570 43.478 0.00 0.00 0.00 3.13
6 7 4.029520 CTGATGAAGAGGAGGAAGAGGAA 58.970 47.826 0.00 0.00 0.00 3.36
7 8 3.270696 TCTGATGAAGAGGAGGAAGAGGA 59.729 47.826 0.00 0.00 0.00 3.71
8 9 3.384467 GTCTGATGAAGAGGAGGAAGAGG 59.616 52.174 0.00 0.00 34.84 3.69
9 10 4.098349 CAGTCTGATGAAGAGGAGGAAGAG 59.902 50.000 0.00 0.00 34.84 2.85
10 11 4.022603 CAGTCTGATGAAGAGGAGGAAGA 58.977 47.826 0.00 0.00 34.84 2.87
11 12 3.132646 CCAGTCTGATGAAGAGGAGGAAG 59.867 52.174 0.00 0.00 34.84 3.46
12 13 3.102972 CCAGTCTGATGAAGAGGAGGAA 58.897 50.000 0.00 0.00 34.84 3.36
13 14 2.625352 CCCAGTCTGATGAAGAGGAGGA 60.625 54.545 0.00 0.00 34.84 3.71
14 15 1.761784 CCCAGTCTGATGAAGAGGAGG 59.238 57.143 0.00 0.00 34.84 4.30
15 16 1.138661 GCCCAGTCTGATGAAGAGGAG 59.861 57.143 0.00 0.00 34.84 3.69
16 17 1.198713 GCCCAGTCTGATGAAGAGGA 58.801 55.000 0.00 0.00 34.84 3.71
17 18 1.134461 CAGCCCAGTCTGATGAAGAGG 60.134 57.143 0.00 0.00 34.84 3.69
18 19 1.554160 ACAGCCCAGTCTGATGAAGAG 59.446 52.381 0.00 0.00 34.84 2.85
19 20 1.277273 CACAGCCCAGTCTGATGAAGA 59.723 52.381 0.00 0.00 37.51 2.87
20 21 1.678123 CCACAGCCCAGTCTGATGAAG 60.678 57.143 0.00 0.00 37.51 3.02
21 22 0.325933 CCACAGCCCAGTCTGATGAA 59.674 55.000 0.00 0.00 37.51 2.57
22 23 1.985614 CCACAGCCCAGTCTGATGA 59.014 57.895 0.00 0.00 37.51 2.92
23 24 1.748122 GCCACAGCCCAGTCTGATG 60.748 63.158 0.00 0.00 37.51 3.07
24 25 2.673523 GCCACAGCCCAGTCTGAT 59.326 61.111 0.00 0.00 37.51 2.90
25 26 4.007644 CGCCACAGCCCAGTCTGA 62.008 66.667 0.00 0.00 37.51 3.27
26 27 2.809861 ATTCGCCACAGCCCAGTCTG 62.810 60.000 0.00 0.00 39.86 3.51
27 28 2.527951 GATTCGCCACAGCCCAGTCT 62.528 60.000 0.00 0.00 34.57 3.24
28 29 2.045926 ATTCGCCACAGCCCAGTC 60.046 61.111 0.00 0.00 34.57 3.51
29 30 2.045926 GATTCGCCACAGCCCAGT 60.046 61.111 0.00 0.00 34.57 4.00
30 31 2.825836 GGATTCGCCACAGCCCAG 60.826 66.667 0.00 0.00 36.34 4.45
31 32 4.776322 CGGATTCGCCACAGCCCA 62.776 66.667 0.00 0.00 35.94 5.36
33 34 4.778143 ACCGGATTCGCCACAGCC 62.778 66.667 9.46 0.00 35.94 4.85
34 35 3.195698 GACCGGATTCGCCACAGC 61.196 66.667 9.46 0.00 35.94 4.40
35 36 1.079127 AAGACCGGATTCGCCACAG 60.079 57.895 9.46 0.00 35.94 3.66
36 37 1.079405 GAAGACCGGATTCGCCACA 60.079 57.895 9.46 0.00 35.94 4.17
37 38 0.806492 GAGAAGACCGGATTCGCCAC 60.806 60.000 9.46 3.66 35.94 5.01
38 39 1.515954 GAGAAGACCGGATTCGCCA 59.484 57.895 9.46 0.00 35.94 5.69
39 40 1.227292 GGAGAAGACCGGATTCGCC 60.227 63.158 23.00 23.00 39.05 5.54
40 41 1.227292 GGGAGAAGACCGGATTCGC 60.227 63.158 9.46 13.68 34.56 4.70
41 42 0.179108 GTGGGAGAAGACCGGATTCG 60.179 60.000 9.46 0.00 0.00 3.34
42 43 0.902531 TGTGGGAGAAGACCGGATTC 59.097 55.000 9.46 12.46 0.00 2.52
43 44 0.905357 CTGTGGGAGAAGACCGGATT 59.095 55.000 9.46 1.40 0.00 3.01
44 45 0.252284 ACTGTGGGAGAAGACCGGAT 60.252 55.000 9.46 0.00 0.00 4.18
45 46 0.406750 TACTGTGGGAGAAGACCGGA 59.593 55.000 9.46 0.00 0.00 5.14
46 47 0.531200 GTACTGTGGGAGAAGACCGG 59.469 60.000 0.00 0.00 0.00 5.28
47 48 1.254026 TGTACTGTGGGAGAAGACCG 58.746 55.000 0.00 0.00 0.00 4.79
48 49 2.832129 TGATGTACTGTGGGAGAAGACC 59.168 50.000 0.00 0.00 0.00 3.85
49 50 4.404073 AGATGATGTACTGTGGGAGAAGAC 59.596 45.833 0.00 0.00 0.00 3.01
50 51 4.403752 CAGATGATGTACTGTGGGAGAAGA 59.596 45.833 0.00 0.00 0.00 2.87
51 52 4.691175 CAGATGATGTACTGTGGGAGAAG 58.309 47.826 0.00 0.00 0.00 2.85
52 53 3.118629 GCAGATGATGTACTGTGGGAGAA 60.119 47.826 0.00 0.00 36.62 2.87
53 54 2.432146 GCAGATGATGTACTGTGGGAGA 59.568 50.000 0.00 0.00 36.62 3.71
54 55 2.169144 TGCAGATGATGTACTGTGGGAG 59.831 50.000 0.00 0.00 36.62 4.30
55 56 2.187100 TGCAGATGATGTACTGTGGGA 58.813 47.619 0.00 0.00 36.62 4.37
56 57 2.696989 TGCAGATGATGTACTGTGGG 57.303 50.000 0.00 0.00 36.62 4.61
57 58 3.136763 GGATGCAGATGATGTACTGTGG 58.863 50.000 0.00 0.00 36.62 4.17
58 59 4.069300 AGGATGCAGATGATGTACTGTG 57.931 45.455 0.00 0.00 36.62 3.66
59 60 4.080695 ACAAGGATGCAGATGATGTACTGT 60.081 41.667 0.00 0.00 36.62 3.55
60 61 4.449131 ACAAGGATGCAGATGATGTACTG 58.551 43.478 0.00 0.00 37.22 2.74
61 62 4.767578 ACAAGGATGCAGATGATGTACT 57.232 40.909 0.00 0.00 0.00 2.73
62 63 4.877823 TCAACAAGGATGCAGATGATGTAC 59.122 41.667 0.00 0.00 0.00 2.90
63 64 4.877823 GTCAACAAGGATGCAGATGATGTA 59.122 41.667 0.00 0.00 0.00 2.29
64 65 3.693085 GTCAACAAGGATGCAGATGATGT 59.307 43.478 0.00 0.00 0.00 3.06
65 66 3.242641 CGTCAACAAGGATGCAGATGATG 60.243 47.826 0.00 0.00 0.00 3.07
66 67 2.941064 CGTCAACAAGGATGCAGATGAT 59.059 45.455 0.00 0.00 0.00 2.45
67 68 2.028203 TCGTCAACAAGGATGCAGATGA 60.028 45.455 0.00 0.00 0.00 2.92
68 69 2.094894 GTCGTCAACAAGGATGCAGATG 59.905 50.000 0.00 0.00 0.00 2.90
69 70 2.289631 TGTCGTCAACAAGGATGCAGAT 60.290 45.455 0.00 0.00 34.03 2.90
70 71 1.069978 TGTCGTCAACAAGGATGCAGA 59.930 47.619 0.00 0.00 34.03 4.26
71 72 1.511850 TGTCGTCAACAAGGATGCAG 58.488 50.000 0.00 0.00 34.03 4.41
72 73 1.960417 TTGTCGTCAACAAGGATGCA 58.040 45.000 0.00 0.00 42.95 3.96
82 83 3.340034 ACTTTTGTGAGGTTGTCGTCAA 58.660 40.909 0.00 0.00 39.61 3.18
83 84 2.980568 ACTTTTGTGAGGTTGTCGTCA 58.019 42.857 0.00 0.00 36.34 4.35
96 97 6.455360 ACTGATCATGTGTTTCACTTTTGT 57.545 33.333 0.00 0.00 35.11 2.83
97 98 8.854979 TTAACTGATCATGTGTTTCACTTTTG 57.145 30.769 0.00 0.00 35.11 2.44
98 99 8.686334 ACTTAACTGATCATGTGTTTCACTTTT 58.314 29.630 0.00 0.00 35.11 2.27
99 100 8.225603 ACTTAACTGATCATGTGTTTCACTTT 57.774 30.769 0.00 0.00 35.11 2.66
100 101 7.807977 ACTTAACTGATCATGTGTTTCACTT 57.192 32.000 0.00 0.00 35.11 3.16
101 102 8.902540 TTACTTAACTGATCATGTGTTTCACT 57.097 30.769 0.00 0.00 35.11 3.41
102 103 9.944663 TTTTACTTAACTGATCATGTGTTTCAC 57.055 29.630 0.00 0.00 34.56 3.18
103 104 9.944663 GTTTTACTTAACTGATCATGTGTTTCA 57.055 29.630 0.00 0.00 0.00 2.69
104 105 9.944663 TGTTTTACTTAACTGATCATGTGTTTC 57.055 29.630 0.00 0.00 0.00 2.78
133 134 9.262358 GTTGTCAATAGTCTTAGTTCTTCAGTT 57.738 33.333 0.00 0.00 0.00 3.16
134 135 8.643324 AGTTGTCAATAGTCTTAGTTCTTCAGT 58.357 33.333 0.00 0.00 0.00 3.41
135 136 9.482627 AAGTTGTCAATAGTCTTAGTTCTTCAG 57.517 33.333 0.00 0.00 0.00 3.02
141 142 8.936864 GCATGTAAGTTGTCAATAGTCTTAGTT 58.063 33.333 0.00 0.00 0.00 2.24
142 143 8.094548 TGCATGTAAGTTGTCAATAGTCTTAGT 58.905 33.333 0.00 0.00 0.00 2.24
143 144 8.383619 GTGCATGTAAGTTGTCAATAGTCTTAG 58.616 37.037 0.00 0.00 0.00 2.18
144 145 8.094548 AGTGCATGTAAGTTGTCAATAGTCTTA 58.905 33.333 0.00 0.00 0.00 2.10
145 146 6.936900 AGTGCATGTAAGTTGTCAATAGTCTT 59.063 34.615 0.00 0.00 0.00 3.01
146 147 6.467677 AGTGCATGTAAGTTGTCAATAGTCT 58.532 36.000 0.00 0.00 0.00 3.24
147 148 6.727824 AGTGCATGTAAGTTGTCAATAGTC 57.272 37.500 0.00 0.00 0.00 2.59
148 149 7.148407 GCTAAGTGCATGTAAGTTGTCAATAGT 60.148 37.037 0.00 0.00 42.31 2.12
149 150 7.182761 GCTAAGTGCATGTAAGTTGTCAATAG 58.817 38.462 0.00 0.00 42.31 1.73
150 151 6.093495 GGCTAAGTGCATGTAAGTTGTCAATA 59.907 38.462 0.00 0.00 45.15 1.90
151 152 5.106157 GGCTAAGTGCATGTAAGTTGTCAAT 60.106 40.000 0.00 0.00 45.15 2.57
152 153 4.215399 GGCTAAGTGCATGTAAGTTGTCAA 59.785 41.667 0.00 0.00 45.15 3.18
153 154 3.751175 GGCTAAGTGCATGTAAGTTGTCA 59.249 43.478 0.00 0.00 45.15 3.58
154 155 4.003648 AGGCTAAGTGCATGTAAGTTGTC 58.996 43.478 0.00 0.00 45.15 3.18
155 156 4.021102 AGGCTAAGTGCATGTAAGTTGT 57.979 40.909 0.00 0.00 45.15 3.32
156 157 6.683974 ATAAGGCTAAGTGCATGTAAGTTG 57.316 37.500 0.00 0.00 45.15 3.16
157 158 9.712305 CTATATAAGGCTAAGTGCATGTAAGTT 57.288 33.333 0.00 0.00 45.15 2.66
158 159 9.090103 TCTATATAAGGCTAAGTGCATGTAAGT 57.910 33.333 0.00 0.00 45.15 2.24
160 161 9.875691 CATCTATATAAGGCTAAGTGCATGTAA 57.124 33.333 0.00 0.00 45.15 2.41
161 162 8.478066 CCATCTATATAAGGCTAAGTGCATGTA 58.522 37.037 0.00 0.00 45.15 2.29
162 163 7.180946 TCCATCTATATAAGGCTAAGTGCATGT 59.819 37.037 0.00 0.00 45.15 3.21
163 164 7.559486 TCCATCTATATAAGGCTAAGTGCATG 58.441 38.462 0.00 0.00 45.15 4.06
164 165 7.739995 TCCATCTATATAAGGCTAAGTGCAT 57.260 36.000 0.00 0.00 45.15 3.96
165 166 7.400052 TCATCCATCTATATAAGGCTAAGTGCA 59.600 37.037 0.00 0.00 45.15 4.57
166 167 7.786030 TCATCCATCTATATAAGGCTAAGTGC 58.214 38.462 0.00 0.00 41.94 4.40
179 180 9.896645 GGCAGAGATTATTTTCATCCATCTATA 57.103 33.333 0.00 0.00 0.00 1.31
180 181 8.388589 TGGCAGAGATTATTTTCATCCATCTAT 58.611 33.333 0.00 0.00 0.00 1.98
181 182 7.748677 TGGCAGAGATTATTTTCATCCATCTA 58.251 34.615 0.00 0.00 0.00 1.98
182 183 6.607970 TGGCAGAGATTATTTTCATCCATCT 58.392 36.000 0.00 0.00 0.00 2.90
192 193 5.193679 GGTTGGTACTGGCAGAGATTATTT 58.806 41.667 23.66 0.00 0.00 1.40
195 196 3.178046 TGGTTGGTACTGGCAGAGATTA 58.822 45.455 23.66 0.00 0.00 1.75
196 197 1.985159 TGGTTGGTACTGGCAGAGATT 59.015 47.619 23.66 0.12 0.00 2.40
197 198 1.656587 TGGTTGGTACTGGCAGAGAT 58.343 50.000 23.66 0.55 0.00 2.75
198 199 1.429930 TTGGTTGGTACTGGCAGAGA 58.570 50.000 23.66 5.56 0.00 3.10
199 200 2.154462 CTTTGGTTGGTACTGGCAGAG 58.846 52.381 23.66 0.00 0.00 3.35
200 201 1.771854 TCTTTGGTTGGTACTGGCAGA 59.228 47.619 23.66 1.56 0.00 4.26
201 202 1.880027 GTCTTTGGTTGGTACTGGCAG 59.120 52.381 14.16 14.16 0.00 4.85
202 203 1.812324 CGTCTTTGGTTGGTACTGGCA 60.812 52.381 0.00 0.00 0.00 4.92
203 204 0.872388 CGTCTTTGGTTGGTACTGGC 59.128 55.000 0.00 0.00 0.00 4.85
204 205 2.140717 GTCGTCTTTGGTTGGTACTGG 58.859 52.381 0.00 0.00 0.00 4.00
205 206 2.140717 GGTCGTCTTTGGTTGGTACTG 58.859 52.381 0.00 0.00 0.00 2.74
206 207 1.764134 TGGTCGTCTTTGGTTGGTACT 59.236 47.619 0.00 0.00 0.00 2.73
207 208 2.140717 CTGGTCGTCTTTGGTTGGTAC 58.859 52.381 0.00 0.00 0.00 3.34
208 209 2.040939 TCTGGTCGTCTTTGGTTGGTA 58.959 47.619 0.00 0.00 0.00 3.25
209 210 0.834612 TCTGGTCGTCTTTGGTTGGT 59.165 50.000 0.00 0.00 0.00 3.67
210 211 1.961793 TTCTGGTCGTCTTTGGTTGG 58.038 50.000 0.00 0.00 0.00 3.77
211 212 3.202906 TCTTTCTGGTCGTCTTTGGTTG 58.797 45.455 0.00 0.00 0.00 3.77
212 213 3.553828 TCTTTCTGGTCGTCTTTGGTT 57.446 42.857 0.00 0.00 0.00 3.67
213 214 3.553828 TTCTTTCTGGTCGTCTTTGGT 57.446 42.857 0.00 0.00 0.00 3.67
214 215 3.304057 GCTTTCTTTCTGGTCGTCTTTGG 60.304 47.826 0.00 0.00 0.00 3.28
215 216 3.561725 AGCTTTCTTTCTGGTCGTCTTTG 59.438 43.478 0.00 0.00 0.00 2.77
216 217 3.809905 AGCTTTCTTTCTGGTCGTCTTT 58.190 40.909 0.00 0.00 0.00 2.52
217 218 3.477210 AGCTTTCTTTCTGGTCGTCTT 57.523 42.857 0.00 0.00 0.00 3.01
218 219 3.181465 TGAAGCTTTCTTTCTGGTCGTCT 60.181 43.478 0.00 0.00 31.48 4.18
219 220 3.131396 TGAAGCTTTCTTTCTGGTCGTC 58.869 45.455 0.00 0.00 31.48 4.20
220 221 3.134458 CTGAAGCTTTCTTTCTGGTCGT 58.866 45.455 0.00 0.00 31.48 4.34
221 222 3.134458 ACTGAAGCTTTCTTTCTGGTCG 58.866 45.455 0.00 0.00 31.48 4.79
222 223 4.791088 GCAACTGAAGCTTTCTTTCTGGTC 60.791 45.833 0.00 0.00 31.48 4.02
223 224 3.067320 GCAACTGAAGCTTTCTTTCTGGT 59.933 43.478 0.00 0.00 31.48 4.00
224 225 3.317430 AGCAACTGAAGCTTTCTTTCTGG 59.683 43.478 0.00 0.00 39.87 3.86
225 226 4.288531 CAGCAACTGAAGCTTTCTTTCTG 58.711 43.478 0.00 1.01 41.14 3.02
226 227 3.317430 CCAGCAACTGAAGCTTTCTTTCT 59.683 43.478 0.00 0.00 41.14 2.52
227 228 3.551659 CCCAGCAACTGAAGCTTTCTTTC 60.552 47.826 0.00 0.00 41.14 2.62
228 229 2.363359 CCCAGCAACTGAAGCTTTCTTT 59.637 45.455 0.00 0.00 41.14 2.52
229 230 1.959282 CCCAGCAACTGAAGCTTTCTT 59.041 47.619 0.00 0.00 41.14 2.52
230 231 1.133668 ACCCAGCAACTGAAGCTTTCT 60.134 47.619 0.00 0.00 41.14 2.52
231 232 1.322442 ACCCAGCAACTGAAGCTTTC 58.678 50.000 0.00 0.00 41.14 2.62
232 233 2.656947 TACCCAGCAACTGAAGCTTT 57.343 45.000 0.00 0.00 41.14 3.51
233 234 2.307098 AGATACCCAGCAACTGAAGCTT 59.693 45.455 0.00 0.00 41.14 3.74
234 235 1.912043 AGATACCCAGCAACTGAAGCT 59.088 47.619 0.00 0.00 44.62 3.74
235 236 2.409948 AGATACCCAGCAACTGAAGC 57.590 50.000 0.00 0.00 32.44 3.86
236 237 4.583871 AGAAAGATACCCAGCAACTGAAG 58.416 43.478 0.00 0.00 32.44 3.02
237 238 4.640771 AGAAAGATACCCAGCAACTGAA 57.359 40.909 0.00 0.00 32.44 3.02
238 239 4.640771 AAGAAAGATACCCAGCAACTGA 57.359 40.909 0.00 0.00 32.44 3.41
239 240 5.006386 AGAAAGAAAGATACCCAGCAACTG 58.994 41.667 0.00 0.00 0.00 3.16
240 241 5.006386 CAGAAAGAAAGATACCCAGCAACT 58.994 41.667 0.00 0.00 0.00 3.16
241 242 4.379918 GCAGAAAGAAAGATACCCAGCAAC 60.380 45.833 0.00 0.00 0.00 4.17
242 243 3.758554 GCAGAAAGAAAGATACCCAGCAA 59.241 43.478 0.00 0.00 0.00 3.91
243 244 3.244875 TGCAGAAAGAAAGATACCCAGCA 60.245 43.478 0.00 0.00 0.00 4.41
244 245 3.347216 TGCAGAAAGAAAGATACCCAGC 58.653 45.455 0.00 0.00 0.00 4.85
245 246 4.761739 TGTTGCAGAAAGAAAGATACCCAG 59.238 41.667 0.00 0.00 0.00 4.45
246 247 4.724399 TGTTGCAGAAAGAAAGATACCCA 58.276 39.130 0.00 0.00 0.00 4.51
247 248 5.649831 AGATGTTGCAGAAAGAAAGATACCC 59.350 40.000 0.00 0.00 0.00 3.69
248 249 6.549952 CAGATGTTGCAGAAAGAAAGATACC 58.450 40.000 0.00 0.00 0.00 2.73
264 265 4.629634 TCACCGTATAGTTTGCAGATGTTG 59.370 41.667 0.00 0.00 0.00 3.33
265 266 4.827692 TCACCGTATAGTTTGCAGATGTT 58.172 39.130 0.00 0.00 0.00 2.71
266 267 4.465632 TCACCGTATAGTTTGCAGATGT 57.534 40.909 0.00 0.00 0.00 3.06
267 268 5.049828 TGATCACCGTATAGTTTGCAGATG 58.950 41.667 0.00 0.00 0.00 2.90
268 269 5.163405 ACTGATCACCGTATAGTTTGCAGAT 60.163 40.000 0.00 0.00 0.00 2.90
269 270 4.159693 ACTGATCACCGTATAGTTTGCAGA 59.840 41.667 0.00 0.00 0.00 4.26
270 271 4.433615 ACTGATCACCGTATAGTTTGCAG 58.566 43.478 0.00 0.00 0.00 4.41
271 272 4.465632 ACTGATCACCGTATAGTTTGCA 57.534 40.909 0.00 0.00 0.00 4.08
272 273 4.630069 ACAACTGATCACCGTATAGTTTGC 59.370 41.667 0.00 0.00 29.78 3.68
273 274 6.590292 AGAACAACTGATCACCGTATAGTTTG 59.410 38.462 0.00 0.00 29.78 2.93
274 275 6.698380 AGAACAACTGATCACCGTATAGTTT 58.302 36.000 0.00 0.00 29.78 2.66
275 276 6.282199 AGAACAACTGATCACCGTATAGTT 57.718 37.500 0.00 0.00 32.23 2.24
276 277 5.916661 AGAACAACTGATCACCGTATAGT 57.083 39.130 0.00 0.00 0.00 2.12
277 278 7.028926 AGTAGAACAACTGATCACCGTATAG 57.971 40.000 0.00 0.00 0.00 1.31
278 279 7.772292 ACTAGTAGAACAACTGATCACCGTATA 59.228 37.037 3.59 0.00 0.00 1.47
279 280 5.916661 AGTAGAACAACTGATCACCGTAT 57.083 39.130 0.00 0.00 0.00 3.06
280 281 5.942236 ACTAGTAGAACAACTGATCACCGTA 59.058 40.000 3.59 0.00 0.00 4.02
281 282 4.765856 ACTAGTAGAACAACTGATCACCGT 59.234 41.667 3.59 0.00 0.00 4.83
282 283 5.312120 ACTAGTAGAACAACTGATCACCG 57.688 43.478 3.59 0.00 0.00 4.94
283 284 6.456501 ACAACTAGTAGAACAACTGATCACC 58.543 40.000 3.59 0.00 0.00 4.02
284 285 7.868415 AGAACAACTAGTAGAACAACTGATCAC 59.132 37.037 3.59 0.00 0.00 3.06
285 286 7.952671 AGAACAACTAGTAGAACAACTGATCA 58.047 34.615 3.59 0.00 0.00 2.92
286 287 8.301002 AGAGAACAACTAGTAGAACAACTGATC 58.699 37.037 3.59 0.00 0.00 2.92
287 288 8.184304 AGAGAACAACTAGTAGAACAACTGAT 57.816 34.615 3.59 0.00 0.00 2.90
288 289 7.584122 AGAGAACAACTAGTAGAACAACTGA 57.416 36.000 3.59 0.00 0.00 3.41
289 290 8.543774 CAAAGAGAACAACTAGTAGAACAACTG 58.456 37.037 3.59 0.00 0.00 3.16
290 291 7.711339 CCAAAGAGAACAACTAGTAGAACAACT 59.289 37.037 3.59 0.00 0.00 3.16
291 292 7.518529 GCCAAAGAGAACAACTAGTAGAACAAC 60.519 40.741 3.59 0.00 0.00 3.32
292 293 6.482308 GCCAAAGAGAACAACTAGTAGAACAA 59.518 38.462 3.59 0.00 0.00 2.83
293 294 5.989777 GCCAAAGAGAACAACTAGTAGAACA 59.010 40.000 3.59 0.00 0.00 3.18
294 295 6.224584 AGCCAAAGAGAACAACTAGTAGAAC 58.775 40.000 3.59 0.00 0.00 3.01
295 296 6.420913 AGCCAAAGAGAACAACTAGTAGAA 57.579 37.500 3.59 0.00 0.00 2.10
296 297 6.183360 ACAAGCCAAAGAGAACAACTAGTAGA 60.183 38.462 3.59 0.00 0.00 2.59
297 298 5.992217 ACAAGCCAAAGAGAACAACTAGTAG 59.008 40.000 0.00 0.00 0.00 2.57
298 299 5.925509 ACAAGCCAAAGAGAACAACTAGTA 58.074 37.500 0.00 0.00 0.00 1.82
299 300 4.781934 ACAAGCCAAAGAGAACAACTAGT 58.218 39.130 0.00 0.00 0.00 2.57
300 301 5.757850 AACAAGCCAAAGAGAACAACTAG 57.242 39.130 0.00 0.00 0.00 2.57
301 302 6.524101 AAAACAAGCCAAAGAGAACAACTA 57.476 33.333 0.00 0.00 0.00 2.24
302 303 5.405935 AAAACAAGCCAAAGAGAACAACT 57.594 34.783 0.00 0.00 0.00 3.16
303 304 7.589574 TTAAAAACAAGCCAAAGAGAACAAC 57.410 32.000 0.00 0.00 0.00 3.32
304 305 9.877178 TTATTAAAAACAAGCCAAAGAGAACAA 57.123 25.926 0.00 0.00 0.00 2.83
305 306 9.528018 CTTATTAAAAACAAGCCAAAGAGAACA 57.472 29.630 0.00 0.00 0.00 3.18
306 307 9.529325 ACTTATTAAAAACAAGCCAAAGAGAAC 57.471 29.630 0.00 0.00 0.00 3.01
331 332 9.837525 CCTATATCGGTTCAACAGTAAGTATAC 57.162 37.037 0.00 0.00 0.00 1.47
335 336 5.452917 GGCCTATATCGGTTCAACAGTAAGT 60.453 44.000 0.00 0.00 0.00 2.24
450 451 2.290641 TGTGTCTTTCTTGGTGTGTGGT 60.291 45.455 0.00 0.00 0.00 4.16
2012 2492 2.300152 GACTGACCCTCACTCATGACAA 59.700 50.000 0.00 0.00 0.00 3.18
2260 2741 3.388676 CCATTGTACGATTGGGGGTACTA 59.611 47.826 0.00 0.00 39.70 1.82
2573 3054 1.202302 CCTTCTCTATCGCAGTCGCAA 60.202 52.381 0.00 0.00 38.40 4.85
2618 3099 7.505585 TCTCAAAAGAAACATGTCCAAACCTAT 59.494 33.333 0.00 0.00 0.00 2.57
3197 3681 3.718434 ACCCAGTATCATGGATGATGTGT 59.282 43.478 11.66 0.69 46.34 3.72
3202 3686 6.762077 TTTCATACCCAGTATCATGGATGA 57.238 37.500 0.00 0.00 43.57 2.92


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

AutoCloner maintained by Alex Coulton.