Multiple sequence alignment - TraesCS5A01G224800

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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 TraesCS5A01G224800 chr5A 100.000 2660 0 0 1 2660 439845908 439843249 0.000000e+00 4913.0
1 TraesCS5A01G224800 chr5A 81.416 113 4 2 1409 1504 439838823 439838935 2.840000e-10 76.8
2 TraesCS5A01G224800 chr3B 95.628 1098 31 10 1572 2660 805649286 805650375 0.000000e+00 1746.0
3 TraesCS5A01G224800 chr3B 94.265 959 37 8 1572 2524 13807439 13806493 0.000000e+00 1450.0
4 TraesCS5A01G224800 chr3B 92.138 954 33 12 660 1572 13808444 13807492 0.000000e+00 1308.0
5 TraesCS5A01G224800 chr3B 90.796 967 34 16 657 1572 805648272 805649234 0.000000e+00 1242.0
6 TraesCS5A01G224800 chr3B 92.037 540 29 5 1602 2138 672894424 672894952 0.000000e+00 747.0
7 TraesCS5A01G224800 chr3B 93.548 496 23 5 2172 2660 672894952 672895445 0.000000e+00 730.0
8 TraesCS5A01G224800 chr3B 93.750 288 16 2 379 665 805647939 805648225 5.260000e-117 431.0
9 TraesCS5A01G224800 chr3B 91.126 293 19 7 379 665 13808785 13808494 8.930000e-105 390.0
10 TraesCS5A01G224800 chr3B 96.774 93 3 0 2568 2660 13806490 13806398 3.550000e-34 156.0
11 TraesCS5A01G224800 chr3B 88.889 54 0 2 1410 1463 791613038 791613085 7.950000e-06 62.1
12 TraesCS5A01G224800 chr1B 94.561 956 35 6 1572 2526 12779799 12780738 0.000000e+00 1461.0
13 TraesCS5A01G224800 chr1B 90.948 939 42 17 657 1572 12778844 12779762 0.000000e+00 1223.0
14 TraesCS5A01G224800 chr1B 93.573 389 21 4 1 389 623270633 623271017 6.380000e-161 577.0
15 TraesCS5A01G224800 chr1B 93.448 290 15 3 379 665 12778509 12778797 6.800000e-116 427.0
16 TraesCS5A01G224800 chr1B 96.685 181 6 0 198 378 623242671 623242851 4.300000e-78 302.0
17 TraesCS5A01G224800 chr1B 96.774 93 3 0 2568 2660 12780738 12780830 3.550000e-34 156.0
18 TraesCS5A01G224800 chr1A 94.228 589 25 5 2081 2660 548551116 548551704 0.000000e+00 891.0
19 TraesCS5A01G224800 chr1A 94.531 512 22 2 1572 2083 548550426 548550931 0.000000e+00 785.0
20 TraesCS5A01G224800 chr1A 81.948 698 68 19 1598 2263 548416192 548416863 3.010000e-149 538.0
21 TraesCS5A01G224800 chr1A 85.574 305 29 6 2249 2551 548416878 548417169 3.330000e-79 305.0
22 TraesCS5A01G224800 chr1A 92.481 133 4 3 1786 1916 8658894 8659022 4.520000e-43 185.0
23 TraesCS5A01G224800 chr1A 90.769 130 12 0 1572 1701 8658764 8658893 9.790000e-40 174.0
24 TraesCS5A01G224800 chr2D 90.813 566 30 11 1636 2193 648420704 648421255 0.000000e+00 737.0
25 TraesCS5A01G224800 chr7B 92.537 469 24 5 2090 2550 713510751 713510286 0.000000e+00 662.0
26 TraesCS5A01G224800 chr7B 90.297 505 29 7 1572 2076 713511309 713510825 0.000000e+00 643.0
27 TraesCS5A01G224800 chr7B 93.939 66 4 0 1506 1571 713511427 713511362 1.680000e-17 100.0
28 TraesCS5A01G224800 chr2A 97.884 378 8 0 1 378 43669902 43670279 0.000000e+00 654.0
29 TraesCS5A01G224800 chr2A 98.315 178 3 0 201 378 43663208 43663385 1.990000e-81 313.0
30 TraesCS5A01G224800 chr2A 88.318 214 18 6 171 380 762400027 762400237 1.580000e-62 250.0
31 TraesCS5A01G224800 chr5D 95.026 382 11 2 1 382 45042266 45041893 6.340000e-166 593.0
32 TraesCS5A01G224800 chr5B 95.283 212 9 1 1 212 271155208 271154998 4.240000e-88 335.0
33 TraesCS5A01G224800 chr6B 93.868 212 13 0 1 212 342808068 342808279 1.190000e-83 320.0
34 TraesCS5A01G224800 chr2B 90.393 229 15 6 156 380 439913165 439913390 7.200000e-76 294.0
35 TraesCS5A01G224800 chr2B 95.556 180 7 1 201 380 439894513 439894691 1.200000e-73 287.0
36 TraesCS5A01G224800 chr2B 91.795 195 12 4 185 378 563618831 563618640 4.360000e-68 268.0
37 TraesCS5A01G224800 chr4D 97.826 46 1 0 1459 1504 23956630 23956675 2.190000e-11 80.5
38 TraesCS5A01G224800 chr4D 88.235 51 1 1 1409 1459 23956570 23956615 3.700000e-04 56.5


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 TraesCS5A01G224800 chr5A 439843249 439845908 2659 True 4913.000000 4913 100.000000 1 2660 1 chr5A.!!$R1 2659
1 TraesCS5A01G224800 chr3B 805647939 805650375 2436 False 1139.666667 1746 93.391333 379 2660 3 chr3B.!!$F3 2281
2 TraesCS5A01G224800 chr3B 13806398 13808785 2387 True 826.000000 1450 93.575750 379 2660 4 chr3B.!!$R1 2281
3 TraesCS5A01G224800 chr3B 672894424 672895445 1021 False 738.500000 747 92.792500 1602 2660 2 chr3B.!!$F2 1058
4 TraesCS5A01G224800 chr1B 12778509 12780830 2321 False 816.750000 1461 93.932750 379 2660 4 chr1B.!!$F3 2281
5 TraesCS5A01G224800 chr1A 548550426 548551704 1278 False 838.000000 891 94.379500 1572 2660 2 chr1A.!!$F3 1088
6 TraesCS5A01G224800 chr1A 548416192 548417169 977 False 421.500000 538 83.761000 1598 2551 2 chr1A.!!$F2 953
7 TraesCS5A01G224800 chr2D 648420704 648421255 551 False 737.000000 737 90.813000 1636 2193 1 chr2D.!!$F1 557
8 TraesCS5A01G224800 chr7B 713510286 713511427 1141 True 468.333333 662 92.257667 1506 2550 3 chr7B.!!$R1 1044

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
174 175 0.036732 TTCTCTGCGGCCAAATCACT 59.963 50.0 2.24 0.0 0.00 3.41 F
204 205 0.038618 AGCGTGCTGATAACGTGTGA 60.039 50.0 0.00 0.0 42.93 3.58 F
330 331 0.039527 GCCAAAACATGACCACCGAC 60.040 55.0 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 1535 0.175302 ACATGCAGGAGCTTCTCGAG 59.825 55.000 4.84 5.93 42.74 4.04 R
1613 1784 0.535335 AAGATAGGCGCAAGGTCGAA 59.465 50.000 10.83 0.00 38.28 3.71 R
2279 2729 4.422984 ACAGCCTCCTTAACCTACAACTA 58.577 43.478 0.00 0.00 0.00 2.24 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 3.782244 GCACCGCGCTTGAGAGTG 61.782 66.667 5.56 2.31 37.77 3.51
59 60 1.375396 TGGTGTGCCATAGACACGC 60.375 57.895 0.00 0.00 43.95 5.34
60 61 2.452813 GGTGTGCCATAGACACGCG 61.453 63.158 3.53 3.53 46.89 6.01
61 62 2.813474 TGTGCCATAGACACGCGC 60.813 61.111 5.73 0.00 41.03 6.86
62 63 3.564027 GTGCCATAGACACGCGCC 61.564 66.667 5.73 0.00 0.00 6.53
63 64 4.830765 TGCCATAGACACGCGCCC 62.831 66.667 5.73 0.00 0.00 6.13
65 66 4.201679 CCATAGACACGCGCCCGA 62.202 66.667 5.73 0.00 38.29 5.14
66 67 2.655364 CATAGACACGCGCCCGAG 60.655 66.667 5.73 0.00 38.29 4.63
67 68 3.900892 ATAGACACGCGCCCGAGG 61.901 66.667 5.73 0.00 38.29 4.63
75 76 4.070552 GCGCCCGAGGACTCTGTT 62.071 66.667 0.00 0.00 0.00 3.16
76 77 2.125912 CGCCCGAGGACTCTGTTG 60.126 66.667 0.00 0.00 0.00 3.33
77 78 2.435059 GCCCGAGGACTCTGTTGC 60.435 66.667 0.00 0.00 0.00 4.17
78 79 2.266055 CCCGAGGACTCTGTTGCC 59.734 66.667 0.00 0.00 0.00 4.52
79 80 2.125912 CCGAGGACTCTGTTGCCG 60.126 66.667 0.00 0.00 0.00 5.69
80 81 2.125912 CGAGGACTCTGTTGCCGG 60.126 66.667 0.00 0.00 0.00 6.13
81 82 2.636412 CGAGGACTCTGTTGCCGGA 61.636 63.158 5.05 0.00 0.00 5.14
83 84 1.228894 AGGACTCTGTTGCCGGAGA 60.229 57.895 5.05 0.00 45.48 3.71
84 85 1.216710 GGACTCTGTTGCCGGAGAG 59.783 63.158 5.05 11.40 45.48 3.20
85 86 1.446966 GACTCTGTTGCCGGAGAGC 60.447 63.158 15.86 7.06 45.48 4.09
86 87 2.125350 CTCTGTTGCCGGAGAGCC 60.125 66.667 5.05 0.00 45.48 4.70
87 88 2.922503 TCTGTTGCCGGAGAGCCA 60.923 61.111 5.05 0.00 0.00 4.75
88 89 2.743928 CTGTTGCCGGAGAGCCAC 60.744 66.667 5.05 0.00 0.00 5.01
89 90 4.680237 TGTTGCCGGAGAGCCACG 62.680 66.667 5.05 0.00 31.25 4.94
110 111 4.803426 CGGCCGTGTCTCTGCCTC 62.803 72.222 19.50 0.00 42.95 4.70
111 112 4.459089 GGCCGTGTCTCTGCCTCC 62.459 72.222 0.00 0.00 42.07 4.30
112 113 3.695606 GCCGTGTCTCTGCCTCCA 61.696 66.667 0.00 0.00 0.00 3.86
113 114 2.575993 CCGTGTCTCTGCCTCCAG 59.424 66.667 0.00 0.00 40.54 3.86
114 115 1.979155 CCGTGTCTCTGCCTCCAGA 60.979 63.158 0.00 0.00 45.54 3.86
115 116 1.326213 CCGTGTCTCTGCCTCCAGAT 61.326 60.000 0.00 0.00 46.44 2.90
116 117 0.179116 CGTGTCTCTGCCTCCAGATG 60.179 60.000 0.00 0.00 46.44 2.90
117 118 0.461693 GTGTCTCTGCCTCCAGATGC 60.462 60.000 0.00 0.00 46.44 3.91
118 119 1.227205 GTCTCTGCCTCCAGATGCG 60.227 63.158 0.00 0.00 46.44 4.73
119 120 1.380380 TCTCTGCCTCCAGATGCGA 60.380 57.895 0.00 0.00 46.44 5.10
120 121 1.067749 CTCTGCCTCCAGATGCGAG 59.932 63.158 0.00 3.80 46.44 5.03
121 122 1.380380 TCTGCCTCCAGATGCGAGA 60.380 57.895 0.00 0.00 42.98 4.04
122 123 1.067749 CTGCCTCCAGATGCGAGAG 59.932 63.158 0.00 0.00 41.77 3.20
123 124 1.380380 TGCCTCCAGATGCGAGAGA 60.380 57.895 0.00 0.00 0.00 3.10
124 125 1.363443 GCCTCCAGATGCGAGAGAG 59.637 63.158 0.00 0.00 0.00 3.20
125 126 1.363443 CCTCCAGATGCGAGAGAGC 59.637 63.158 0.00 0.00 37.71 4.09
126 127 1.363443 CTCCAGATGCGAGAGAGCC 59.637 63.158 0.00 0.00 36.02 4.70
127 128 2.027314 CCAGATGCGAGAGAGCCG 59.973 66.667 0.00 0.00 36.02 5.52
142 143 4.445545 CCGCTTCGCCGCTGTTTC 62.446 66.667 0.00 0.00 0.00 2.78
143 144 4.445545 CGCTTCGCCGCTGTTTCC 62.446 66.667 0.00 0.00 0.00 3.13
144 145 4.103103 GCTTCGCCGCTGTTTCCC 62.103 66.667 0.00 0.00 0.00 3.97
145 146 3.431725 CTTCGCCGCTGTTTCCCC 61.432 66.667 0.00 0.00 0.00 4.81
146 147 3.901797 CTTCGCCGCTGTTTCCCCT 62.902 63.158 0.00 0.00 0.00 4.79
147 148 3.485346 TTCGCCGCTGTTTCCCCTT 62.485 57.895 0.00 0.00 0.00 3.95
148 149 3.431725 CGCCGCTGTTTCCCCTTC 61.432 66.667 0.00 0.00 0.00 3.46
149 150 3.431725 GCCGCTGTTTCCCCTTCG 61.432 66.667 0.00 0.00 0.00 3.79
150 151 3.431725 CCGCTGTTTCCCCTTCGC 61.432 66.667 0.00 0.00 0.00 4.70
151 152 2.358737 CGCTGTTTCCCCTTCGCT 60.359 61.111 0.00 0.00 0.00 4.93
152 153 1.966451 CGCTGTTTCCCCTTCGCTT 60.966 57.895 0.00 0.00 0.00 4.68
153 154 1.515521 CGCTGTTTCCCCTTCGCTTT 61.516 55.000 0.00 0.00 0.00 3.51
154 155 0.241213 GCTGTTTCCCCTTCGCTTTC 59.759 55.000 0.00 0.00 0.00 2.62
155 156 1.897560 CTGTTTCCCCTTCGCTTTCT 58.102 50.000 0.00 0.00 0.00 2.52
156 157 2.230660 CTGTTTCCCCTTCGCTTTCTT 58.769 47.619 0.00 0.00 0.00 2.52
157 158 2.226674 CTGTTTCCCCTTCGCTTTCTTC 59.773 50.000 0.00 0.00 0.00 2.87
158 159 2.158667 TGTTTCCCCTTCGCTTTCTTCT 60.159 45.455 0.00 0.00 0.00 2.85
159 160 2.474410 TTCCCCTTCGCTTTCTTCTC 57.526 50.000 0.00 0.00 0.00 2.87
160 161 1.645710 TCCCCTTCGCTTTCTTCTCT 58.354 50.000 0.00 0.00 0.00 3.10
161 162 1.276421 TCCCCTTCGCTTTCTTCTCTG 59.724 52.381 0.00 0.00 0.00 3.35
162 163 1.082690 CCCTTCGCTTTCTTCTCTGC 58.917 55.000 0.00 0.00 0.00 4.26
165 166 2.781300 CGCTTTCTTCTCTGCGGC 59.219 61.111 0.00 0.00 43.97 6.53
166 167 2.744768 CGCTTTCTTCTCTGCGGCC 61.745 63.158 0.00 0.00 43.97 6.13
167 168 1.672356 GCTTTCTTCTCTGCGGCCA 60.672 57.895 2.24 0.00 0.00 5.36
168 169 1.237285 GCTTTCTTCTCTGCGGCCAA 61.237 55.000 2.24 0.00 0.00 4.52
169 170 1.238439 CTTTCTTCTCTGCGGCCAAA 58.762 50.000 2.24 0.00 0.00 3.28
170 171 1.815003 CTTTCTTCTCTGCGGCCAAAT 59.185 47.619 2.24 0.00 0.00 2.32
171 172 1.453155 TTCTTCTCTGCGGCCAAATC 58.547 50.000 2.24 0.00 0.00 2.17
172 173 0.324614 TCTTCTCTGCGGCCAAATCA 59.675 50.000 2.24 0.00 0.00 2.57
173 174 0.449388 CTTCTCTGCGGCCAAATCAC 59.551 55.000 2.24 0.00 0.00 3.06
174 175 0.036732 TTCTCTGCGGCCAAATCACT 59.963 50.000 2.24 0.00 0.00 3.41
175 176 0.391661 TCTCTGCGGCCAAATCACTC 60.392 55.000 2.24 0.00 0.00 3.51
176 177 0.392193 CTCTGCGGCCAAATCACTCT 60.392 55.000 2.24 0.00 0.00 3.24
177 178 0.391661 TCTGCGGCCAAATCACTCTC 60.392 55.000 2.24 0.00 0.00 3.20
178 179 1.699656 CTGCGGCCAAATCACTCTCG 61.700 60.000 2.24 0.00 0.00 4.04
179 180 2.464459 GCGGCCAAATCACTCTCGG 61.464 63.158 2.24 0.00 0.00 4.63
180 181 1.079127 CGGCCAAATCACTCTCGGT 60.079 57.895 2.24 0.00 0.00 4.69
181 182 0.673644 CGGCCAAATCACTCTCGGTT 60.674 55.000 2.24 0.00 0.00 4.44
182 183 1.404986 CGGCCAAATCACTCTCGGTTA 60.405 52.381 2.24 0.00 0.00 2.85
183 184 2.280628 GGCCAAATCACTCTCGGTTAG 58.719 52.381 0.00 0.00 0.00 2.34
184 185 2.280628 GCCAAATCACTCTCGGTTAGG 58.719 52.381 0.00 0.00 0.00 2.69
185 186 2.093658 GCCAAATCACTCTCGGTTAGGA 60.094 50.000 0.00 0.00 0.00 2.94
186 187 3.786635 CCAAATCACTCTCGGTTAGGAG 58.213 50.000 0.00 0.00 35.86 3.69
187 188 3.190874 CAAATCACTCTCGGTTAGGAGC 58.809 50.000 0.00 0.00 33.98 4.70
189 190 0.322277 TCACTCTCGGTTAGGAGCGT 60.322 55.000 0.00 0.00 46.27 5.07
190 191 0.179161 CACTCTCGGTTAGGAGCGTG 60.179 60.000 0.00 0.00 46.27 5.34
191 192 1.226717 CTCTCGGTTAGGAGCGTGC 60.227 63.158 0.00 0.00 46.27 5.34
192 193 1.658686 CTCTCGGTTAGGAGCGTGCT 61.659 60.000 0.00 0.00 46.27 4.40
193 194 1.517257 CTCGGTTAGGAGCGTGCTG 60.517 63.158 0.00 0.00 46.27 4.41
194 195 1.934220 CTCGGTTAGGAGCGTGCTGA 61.934 60.000 0.00 0.00 46.27 4.26
195 196 1.141881 CGGTTAGGAGCGTGCTGAT 59.858 57.895 0.00 0.00 41.58 2.90
196 197 0.384309 CGGTTAGGAGCGTGCTGATA 59.616 55.000 0.00 0.00 41.58 2.15
197 198 1.202371 CGGTTAGGAGCGTGCTGATAA 60.202 52.381 0.00 0.00 41.58 1.75
198 199 2.202566 GGTTAGGAGCGTGCTGATAAC 58.797 52.381 0.00 8.01 0.00 1.89
199 200 1.852895 GTTAGGAGCGTGCTGATAACG 59.147 52.381 0.00 0.00 43.81 3.18
200 201 1.100510 TAGGAGCGTGCTGATAACGT 58.899 50.000 0.00 0.00 42.93 3.99
201 202 0.458543 AGGAGCGTGCTGATAACGTG 60.459 55.000 0.00 0.00 42.93 4.49
202 203 0.736325 GGAGCGTGCTGATAACGTGT 60.736 55.000 0.00 0.00 42.93 4.49
203 204 0.366871 GAGCGTGCTGATAACGTGTG 59.633 55.000 0.00 0.00 42.93 3.82
204 205 0.038618 AGCGTGCTGATAACGTGTGA 60.039 50.000 0.00 0.00 42.93 3.58
205 206 0.787787 GCGTGCTGATAACGTGTGAA 59.212 50.000 0.00 0.00 42.93 3.18
206 207 1.193650 GCGTGCTGATAACGTGTGAAA 59.806 47.619 0.00 0.00 42.93 2.69
207 208 2.721797 GCGTGCTGATAACGTGTGAAAG 60.722 50.000 0.00 0.00 42.93 2.62
208 209 2.475111 CGTGCTGATAACGTGTGAAAGT 59.525 45.455 0.00 0.00 36.31 2.66
209 210 3.671459 CGTGCTGATAACGTGTGAAAGTA 59.329 43.478 0.00 0.00 36.31 2.24
210 211 4.149221 CGTGCTGATAACGTGTGAAAGTAA 59.851 41.667 0.00 0.00 36.31 2.24
211 212 5.332732 CGTGCTGATAACGTGTGAAAGTAAA 60.333 40.000 0.00 0.00 36.31 2.01
212 213 6.423862 GTGCTGATAACGTGTGAAAGTAAAA 58.576 36.000 0.00 0.00 0.00 1.52
213 214 6.908284 GTGCTGATAACGTGTGAAAGTAAAAA 59.092 34.615 0.00 0.00 0.00 1.94
214 215 6.908284 TGCTGATAACGTGTGAAAGTAAAAAC 59.092 34.615 0.00 0.00 0.00 2.43
215 216 6.084551 GCTGATAACGTGTGAAAGTAAAAACG 59.915 38.462 0.00 0.00 37.09 3.60
216 217 7.231705 TGATAACGTGTGAAAGTAAAAACGA 57.768 32.000 0.00 0.00 35.18 3.85
217 218 7.339207 TGATAACGTGTGAAAGTAAAAACGAG 58.661 34.615 0.00 0.00 35.18 4.18
218 219 5.783100 AACGTGTGAAAGTAAAAACGAGA 57.217 34.783 0.00 0.00 35.18 4.04
219 220 5.385396 ACGTGTGAAAGTAAAAACGAGAG 57.615 39.130 0.00 0.00 35.18 3.20
220 221 5.104374 ACGTGTGAAAGTAAAAACGAGAGA 58.896 37.500 0.00 0.00 35.18 3.10
221 222 5.231568 ACGTGTGAAAGTAAAAACGAGAGAG 59.768 40.000 0.00 0.00 35.18 3.20
222 223 5.332355 CGTGTGAAAGTAAAAACGAGAGAGG 60.332 44.000 0.00 0.00 33.03 3.69
223 224 5.751990 GTGTGAAAGTAAAAACGAGAGAGGA 59.248 40.000 0.00 0.00 0.00 3.71
224 225 6.424207 GTGTGAAAGTAAAAACGAGAGAGGAT 59.576 38.462 0.00 0.00 0.00 3.24
225 226 6.423905 TGTGAAAGTAAAAACGAGAGAGGATG 59.576 38.462 0.00 0.00 0.00 3.51
226 227 5.932303 TGAAAGTAAAAACGAGAGAGGATGG 59.068 40.000 0.00 0.00 0.00 3.51
227 228 5.740290 AAGTAAAAACGAGAGAGGATGGA 57.260 39.130 0.00 0.00 0.00 3.41
228 229 5.331876 AGTAAAAACGAGAGAGGATGGAG 57.668 43.478 0.00 0.00 0.00 3.86
229 230 2.682155 AAAACGAGAGAGGATGGAGC 57.318 50.000 0.00 0.00 0.00 4.70
230 231 1.561643 AAACGAGAGAGGATGGAGCA 58.438 50.000 0.00 0.00 0.00 4.26
231 232 1.561643 AACGAGAGAGGATGGAGCAA 58.438 50.000 0.00 0.00 0.00 3.91
232 233 1.561643 ACGAGAGAGGATGGAGCAAA 58.438 50.000 0.00 0.00 0.00 3.68
233 234 2.114616 ACGAGAGAGGATGGAGCAAAT 58.885 47.619 0.00 0.00 0.00 2.32
234 235 2.158986 ACGAGAGAGGATGGAGCAAATG 60.159 50.000 0.00 0.00 0.00 2.32
235 236 2.102084 CGAGAGAGGATGGAGCAAATGA 59.898 50.000 0.00 0.00 0.00 2.57
236 237 3.244146 CGAGAGAGGATGGAGCAAATGAT 60.244 47.826 0.00 0.00 0.00 2.45
237 238 4.066490 GAGAGAGGATGGAGCAAATGATG 58.934 47.826 0.00 0.00 0.00 3.07
238 239 3.147629 GAGAGGATGGAGCAAATGATGG 58.852 50.000 0.00 0.00 0.00 3.51
239 240 2.781757 AGAGGATGGAGCAAATGATGGA 59.218 45.455 0.00 0.00 0.00 3.41
240 241 3.203710 AGAGGATGGAGCAAATGATGGAA 59.796 43.478 0.00 0.00 0.00 3.53
241 242 3.294214 AGGATGGAGCAAATGATGGAAC 58.706 45.455 0.00 0.00 0.00 3.62
259 260 6.462552 TGGAACAGTTGTTTCATTGATTGA 57.537 33.333 1.85 0.00 38.53 2.57
260 261 6.871844 TGGAACAGTTGTTTCATTGATTGAA 58.128 32.000 1.85 0.00 38.53 2.69
261 262 6.979817 TGGAACAGTTGTTTCATTGATTGAAG 59.020 34.615 1.85 0.00 44.90 3.02
262 263 7.147932 TGGAACAGTTGTTTCATTGATTGAAGA 60.148 33.333 1.85 0.00 44.90 2.87
263 264 7.869429 GGAACAGTTGTTTCATTGATTGAAGAT 59.131 33.333 0.00 0.00 44.90 2.40
264 265 9.252962 GAACAGTTGTTTCATTGATTGAAGATT 57.747 29.630 0.00 0.00 44.90 2.40
265 266 8.583810 ACAGTTGTTTCATTGATTGAAGATTG 57.416 30.769 0.00 0.00 44.90 2.67
266 267 7.654520 ACAGTTGTTTCATTGATTGAAGATTGG 59.345 33.333 0.00 0.00 44.90 3.16
267 268 7.117236 CAGTTGTTTCATTGATTGAAGATTGGG 59.883 37.037 0.00 0.00 44.90 4.12
268 269 6.040209 TGTTTCATTGATTGAAGATTGGGG 57.960 37.500 0.00 0.00 44.90 4.96
269 270 5.543405 TGTTTCATTGATTGAAGATTGGGGT 59.457 36.000 0.00 0.00 44.90 4.95
270 271 6.723515 TGTTTCATTGATTGAAGATTGGGGTA 59.276 34.615 0.00 0.00 44.90 3.69
271 272 7.399765 TGTTTCATTGATTGAAGATTGGGGTAT 59.600 33.333 0.00 0.00 44.90 2.73
272 273 7.976414 TTCATTGATTGAAGATTGGGGTATT 57.024 32.000 0.00 0.00 39.44 1.89
273 274 7.976414 TCATTGATTGAAGATTGGGGTATTT 57.024 32.000 0.00 0.00 0.00 1.40
274 275 9.486123 TTCATTGATTGAAGATTGGGGTATTTA 57.514 29.630 0.00 0.00 39.44 1.40
275 276 9.659135 TCATTGATTGAAGATTGGGGTATTTAT 57.341 29.630 0.00 0.00 0.00 1.40
291 292 7.683437 GGTATTTATACCCTCATTACAAGGC 57.317 40.000 7.56 0.00 45.62 4.35
292 293 7.228590 GGTATTTATACCCTCATTACAAGGCA 58.771 38.462 7.56 0.00 45.62 4.75
293 294 7.390718 GGTATTTATACCCTCATTACAAGGCAG 59.609 40.741 7.56 0.00 45.62 4.85
294 295 5.968676 TTATACCCTCATTACAAGGCAGT 57.031 39.130 0.00 0.00 32.15 4.40
295 296 4.862641 ATACCCTCATTACAAGGCAGTT 57.137 40.909 0.00 0.00 32.15 3.16
296 297 5.968676 ATACCCTCATTACAAGGCAGTTA 57.031 39.130 0.00 0.00 32.15 2.24
297 298 3.951663 ACCCTCATTACAAGGCAGTTAC 58.048 45.455 0.00 0.00 32.15 2.50
298 299 3.329520 ACCCTCATTACAAGGCAGTTACA 59.670 43.478 0.00 0.00 32.15 2.41
299 300 4.202524 ACCCTCATTACAAGGCAGTTACAA 60.203 41.667 0.00 0.00 32.15 2.41
300 301 4.764823 CCCTCATTACAAGGCAGTTACAAA 59.235 41.667 0.00 0.00 32.15 2.83
301 302 5.106157 CCCTCATTACAAGGCAGTTACAAAG 60.106 44.000 0.00 0.00 32.15 2.77
302 303 5.705441 CCTCATTACAAGGCAGTTACAAAGA 59.295 40.000 0.00 0.00 0.00 2.52
303 304 6.206634 CCTCATTACAAGGCAGTTACAAAGAA 59.793 38.462 0.00 0.00 0.00 2.52
304 305 7.202016 TCATTACAAGGCAGTTACAAAGAAG 57.798 36.000 0.00 0.00 0.00 2.85
305 306 6.206634 TCATTACAAGGCAGTTACAAAGAAGG 59.793 38.462 0.00 0.00 0.00 3.46
306 307 2.623416 ACAAGGCAGTTACAAAGAAGGC 59.377 45.455 0.00 0.00 0.00 4.35
307 308 1.523758 AGGCAGTTACAAAGAAGGCG 58.476 50.000 0.00 0.00 0.00 5.52
308 309 0.521735 GGCAGTTACAAAGAAGGCGG 59.478 55.000 0.00 0.00 0.00 6.13
309 310 1.235724 GCAGTTACAAAGAAGGCGGT 58.764 50.000 0.00 0.00 0.00 5.68
310 311 1.607148 GCAGTTACAAAGAAGGCGGTT 59.393 47.619 0.00 0.00 0.00 4.44
311 312 2.604614 GCAGTTACAAAGAAGGCGGTTG 60.605 50.000 0.00 0.00 0.00 3.77
312 313 1.607148 AGTTACAAAGAAGGCGGTTGC 59.393 47.619 0.00 0.00 41.71 4.17
323 324 2.516486 GCGGTTGCCAAAACATGAC 58.484 52.632 0.00 0.00 33.98 3.06
324 325 0.943835 GCGGTTGCCAAAACATGACC 60.944 55.000 0.00 0.00 33.98 4.02
325 326 0.387202 CGGTTGCCAAAACATGACCA 59.613 50.000 0.00 0.00 0.00 4.02
326 327 1.864565 GGTTGCCAAAACATGACCAC 58.135 50.000 0.00 0.00 0.00 4.16
327 328 1.540146 GGTTGCCAAAACATGACCACC 60.540 52.381 0.00 0.00 0.00 4.61
328 329 0.387202 TTGCCAAAACATGACCACCG 59.613 50.000 0.00 0.00 0.00 4.94
329 330 0.466372 TGCCAAAACATGACCACCGA 60.466 50.000 0.00 0.00 0.00 4.69
330 331 0.039527 GCCAAAACATGACCACCGAC 60.040 55.000 0.00 0.00 0.00 4.79
331 332 1.313772 CCAAAACATGACCACCGACA 58.686 50.000 0.00 0.00 0.00 4.35
332 333 1.885887 CCAAAACATGACCACCGACAT 59.114 47.619 0.00 0.00 0.00 3.06
333 334 3.078097 CCAAAACATGACCACCGACATA 58.922 45.455 0.00 0.00 0.00 2.29
334 335 3.126858 CCAAAACATGACCACCGACATAG 59.873 47.826 0.00 0.00 0.00 2.23
335 336 2.024176 AACATGACCACCGACATAGC 57.976 50.000 0.00 0.00 0.00 2.97
336 337 0.901827 ACATGACCACCGACATAGCA 59.098 50.000 0.00 0.00 0.00 3.49
337 338 1.486310 ACATGACCACCGACATAGCAT 59.514 47.619 0.00 0.00 0.00 3.79
338 339 1.869132 CATGACCACCGACATAGCATG 59.131 52.381 0.00 0.00 0.00 4.06
339 340 0.177836 TGACCACCGACATAGCATGG 59.822 55.000 0.00 0.00 36.46 3.66
340 341 0.464036 GACCACCGACATAGCATGGA 59.536 55.000 0.00 0.00 34.38 3.41
341 342 1.070758 GACCACCGACATAGCATGGAT 59.929 52.381 0.00 0.00 34.38 3.41
342 343 1.490490 ACCACCGACATAGCATGGATT 59.510 47.619 0.00 0.00 34.38 3.01
343 344 2.092429 ACCACCGACATAGCATGGATTT 60.092 45.455 0.00 0.00 34.38 2.17
344 345 3.135712 ACCACCGACATAGCATGGATTTA 59.864 43.478 0.00 0.00 34.38 1.40
345 346 4.202461 ACCACCGACATAGCATGGATTTAT 60.202 41.667 0.00 0.00 34.38 1.40
346 347 5.012664 ACCACCGACATAGCATGGATTTATA 59.987 40.000 0.00 0.00 34.38 0.98
347 348 5.937540 CCACCGACATAGCATGGATTTATAA 59.062 40.000 0.00 0.00 31.69 0.98
348 349 6.599244 CCACCGACATAGCATGGATTTATAAT 59.401 38.462 0.00 0.00 31.69 1.28
349 350 7.121168 CCACCGACATAGCATGGATTTATAATT 59.879 37.037 0.00 0.00 31.69 1.40
350 351 9.161629 CACCGACATAGCATGGATTTATAATTA 57.838 33.333 0.00 0.00 33.60 1.40
351 352 9.733556 ACCGACATAGCATGGATTTATAATTAA 57.266 29.630 0.00 0.00 33.60 1.40
395 396 9.702253 TTCCTAACAGTATCTCTATCTTTGTCT 57.298 33.333 0.00 0.00 0.00 3.41
460 463 2.692368 GATGGGCAGGGTGGAGGA 60.692 66.667 0.00 0.00 0.00 3.71
621 627 2.202362 CGCTCAGACGTCGTCCTG 60.202 66.667 21.40 17.49 32.18 3.86
622 628 2.179517 GCTCAGACGTCGTCCTGG 59.820 66.667 21.40 11.73 32.18 4.45
623 629 2.179517 CTCAGACGTCGTCCTGGC 59.820 66.667 21.40 0.00 32.18 4.85
625 631 4.778415 CAGACGTCGTCCTGGCCG 62.778 72.222 21.40 0.00 32.18 6.13
665 671 1.229658 CCAGGAAGTCCCCCTCTGT 60.230 63.158 0.00 0.00 36.42 3.41
666 672 0.042731 CCAGGAAGTCCCCCTCTGTA 59.957 60.000 0.00 0.00 36.42 2.74
667 673 1.490574 CAGGAAGTCCCCCTCTGTAG 58.509 60.000 0.00 0.00 36.42 2.74
669 675 0.617820 GGAAGTCCCCCTCTGTAGCA 60.618 60.000 0.00 0.00 0.00 3.49
670 676 1.501582 GAAGTCCCCCTCTGTAGCAT 58.498 55.000 0.00 0.00 0.00 3.79
671 677 1.139853 GAAGTCCCCCTCTGTAGCATG 59.860 57.143 0.00 0.00 0.00 4.06
672 678 0.692419 AGTCCCCCTCTGTAGCATGG 60.692 60.000 0.00 0.00 0.00 3.66
731 792 4.697756 TTCAACCAGCCGCTCGGG 62.698 66.667 10.57 4.82 39.58 5.14
742 803 0.806102 CCGCTCGGGTTCACATGTAG 60.806 60.000 0.00 0.00 0.00 2.74
743 804 0.108804 CGCTCGGGTTCACATGTAGT 60.109 55.000 0.00 0.00 0.00 2.73
747 808 2.427453 CTCGGGTTCACATGTAGTAGCT 59.573 50.000 0.00 0.00 0.00 3.32
824 885 0.593128 CCCAGTCAACCTTCTTTGCG 59.407 55.000 0.00 0.00 0.00 4.85
825 886 0.040067 CCAGTCAACCTTCTTTGCGC 60.040 55.000 0.00 0.00 0.00 6.09
961 1022 2.283298 CTTCGTGGTCATGCAAGCTAT 58.717 47.619 0.00 0.00 0.00 2.97
974 1035 2.911484 CAAGCTATGACCTCCACCTTC 58.089 52.381 0.00 0.00 0.00 3.46
1057 1118 0.309612 GAACAATTTGCCGTGGACGT 59.690 50.000 0.00 0.00 37.74 4.34
1228 1295 3.277211 CTTGCTTGCTGGCGTGCAT 62.277 57.895 11.52 0.00 42.96 3.96
1288 1363 0.661020 GGTGGTTTGTGTGACGAAGG 59.339 55.000 0.00 0.00 0.00 3.46
1296 1371 2.125512 GTGACGAAGGCGATGGCT 60.126 61.111 0.00 0.00 41.24 4.75
1299 1374 1.035385 TGACGAAGGCGATGGCTAGA 61.035 55.000 0.00 0.00 37.50 2.43
1427 1519 1.303398 TCCGCAGAAGGACTCGAGT 60.303 57.895 20.18 20.18 34.92 4.18
1428 1520 1.153939 CCGCAGAAGGACTCGAGTG 60.154 63.158 25.58 8.56 0.00 3.51
1440 1535 3.140576 TCGAGTGGAGAGTCGAGAC 57.859 57.895 0.00 0.00 46.75 3.36
1504 1622 0.259065 ATGGCGTGGAGAGGAGAGTA 59.741 55.000 0.00 0.00 0.00 2.59
1550 1668 2.126424 GAGGTCGTGTCTGTCCGC 60.126 66.667 0.00 0.00 0.00 5.54
1952 2162 4.191804 AGTAGCTAGGTGATGGTCTCAT 57.808 45.455 4.27 0.00 35.97 2.90
2066 2293 6.240894 TCATGATGGTTCCTGAATATTAGGC 58.759 40.000 0.00 0.00 35.23 3.93
2078 2494 6.767902 CCTGAATATTAGGCGCCATATTGTAT 59.232 38.462 27.67 15.50 0.00 2.29
2079 2495 7.283127 CCTGAATATTAGGCGCCATATTGTATT 59.717 37.037 27.67 21.05 0.00 1.89
2157 2576 9.464714 CGCACTATTGTACTATTCTTTACAGAT 57.535 33.333 0.00 0.00 30.03 2.90
2180 2599 9.484806 AGATAAAGATCAAATGAAGGGAAACAT 57.515 29.630 0.00 0.00 34.17 2.71
2222 2643 7.962995 ATCTAAACCAGTTCTGATACTCTCA 57.037 36.000 1.00 0.00 0.00 3.27
2279 2729 9.866655 TCATTAAATTGCCTATCTTGGAATAGT 57.133 29.630 0.00 0.00 0.00 2.12
2441 2911 8.567948 GTCTGAAAAATGAACATCCTCTTTGTA 58.432 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.782244 CACTCTCAAGCGCGGTGC 61.782 66.667 13.41 5.16 46.98 5.01
6 7 3.114616 CCACTCTCAAGCGCGGTG 61.115 66.667 13.41 7.03 0.00 4.94
45 46 3.564027 GGCGCGTGTCTATGGCAC 61.564 66.667 8.43 0.00 0.00 5.01
46 47 4.830765 GGGCGCGTGTCTATGGCA 62.831 66.667 8.43 0.00 0.00 4.92
48 49 4.201679 TCGGGCGCGTGTCTATGG 62.202 66.667 23.19 0.00 0.00 2.74
49 50 2.655364 CTCGGGCGCGTGTCTATG 60.655 66.667 23.19 2.54 0.00 2.23
50 51 3.900892 CCTCGGGCGCGTGTCTAT 61.901 66.667 23.19 0.00 0.00 1.98
58 59 4.070552 AACAGAGTCCTCGGGCGC 62.071 66.667 0.00 0.00 34.09 6.53
59 60 2.125912 CAACAGAGTCCTCGGGCG 60.126 66.667 0.00 0.00 34.09 6.13
60 61 2.435059 GCAACAGAGTCCTCGGGC 60.435 66.667 0.00 0.00 34.09 6.13
61 62 2.266055 GGCAACAGAGTCCTCGGG 59.734 66.667 0.00 0.00 34.09 5.14
62 63 2.125912 CGGCAACAGAGTCCTCGG 60.126 66.667 0.00 0.00 34.09 4.63
63 64 2.125912 CCGGCAACAGAGTCCTCG 60.126 66.667 0.00 0.00 34.09 4.63
64 65 1.216710 CTCCGGCAACAGAGTCCTC 59.783 63.158 0.00 0.00 36.31 3.71
65 66 1.228894 TCTCCGGCAACAGAGTCCT 60.229 57.895 0.00 0.00 42.05 3.85
66 67 1.216710 CTCTCCGGCAACAGAGTCC 59.783 63.158 9.27 0.00 42.05 3.85
67 68 1.446966 GCTCTCCGGCAACAGAGTC 60.447 63.158 16.77 7.77 42.05 3.36
68 69 2.659610 GCTCTCCGGCAACAGAGT 59.340 61.111 16.77 0.00 42.05 3.24
69 70 2.125350 GGCTCTCCGGCAACAGAG 60.125 66.667 12.46 12.46 42.80 3.35
70 71 2.922503 TGGCTCTCCGGCAACAGA 60.923 61.111 0.00 0.00 46.25 3.41
95 96 3.655810 CTGGAGGCAGAGACACGGC 62.656 68.421 0.00 0.00 38.89 5.68
96 97 1.326213 ATCTGGAGGCAGAGACACGG 61.326 60.000 0.00 0.00 34.35 4.94
97 98 0.179116 CATCTGGAGGCAGAGACACG 60.179 60.000 0.00 0.00 34.35 4.49
98 99 0.461693 GCATCTGGAGGCAGAGACAC 60.462 60.000 2.27 0.00 38.12 3.67
99 100 1.903294 GCATCTGGAGGCAGAGACA 59.097 57.895 2.27 0.00 38.12 3.41
100 101 1.227205 CGCATCTGGAGGCAGAGAC 60.227 63.158 7.94 0.00 38.12 3.36
101 102 1.380380 TCGCATCTGGAGGCAGAGA 60.380 57.895 7.94 0.00 38.12 3.10
102 103 1.067749 CTCGCATCTGGAGGCAGAG 59.932 63.158 7.94 10.22 38.12 3.35
103 104 1.380380 TCTCGCATCTGGAGGCAGA 60.380 57.895 7.94 6.66 38.12 4.26
104 105 1.067749 CTCTCGCATCTGGAGGCAG 59.932 63.158 7.94 4.68 38.12 4.85
105 106 1.380380 TCTCTCGCATCTGGAGGCA 60.380 57.895 7.94 0.00 38.12 4.75
106 107 1.363443 CTCTCTCGCATCTGGAGGC 59.637 63.158 0.00 0.00 34.34 4.70
107 108 1.363443 GCTCTCTCGCATCTGGAGG 59.637 63.158 0.00 0.00 32.34 4.30
108 109 1.363443 GGCTCTCTCGCATCTGGAG 59.637 63.158 0.00 0.00 0.00 3.86
109 110 2.484928 CGGCTCTCTCGCATCTGGA 61.485 63.158 0.00 0.00 0.00 3.86
110 111 2.027314 CGGCTCTCTCGCATCTGG 59.973 66.667 0.00 0.00 0.00 3.86
128 129 3.431725 GGGGAAACAGCGGCGAAG 61.432 66.667 12.98 3.84 0.00 3.79
129 130 3.485346 AAGGGGAAACAGCGGCGAA 62.485 57.895 12.98 0.00 0.00 4.70
130 131 3.894547 GAAGGGGAAACAGCGGCGA 62.895 63.158 12.98 0.00 0.00 5.54
131 132 3.431725 GAAGGGGAAACAGCGGCG 61.432 66.667 0.51 0.51 0.00 6.46
132 133 3.431725 CGAAGGGGAAACAGCGGC 61.432 66.667 0.00 0.00 0.00 6.53
133 134 3.431725 GCGAAGGGGAAACAGCGG 61.432 66.667 0.00 0.00 0.00 5.52
134 135 1.515521 AAAGCGAAGGGGAAACAGCG 61.516 55.000 0.00 0.00 0.00 5.18
135 136 0.241213 GAAAGCGAAGGGGAAACAGC 59.759 55.000 0.00 0.00 0.00 4.40
136 137 1.897560 AGAAAGCGAAGGGGAAACAG 58.102 50.000 0.00 0.00 0.00 3.16
137 138 2.158667 AGAAGAAAGCGAAGGGGAAACA 60.159 45.455 0.00 0.00 0.00 2.83
138 139 2.484651 GAGAAGAAAGCGAAGGGGAAAC 59.515 50.000 0.00 0.00 0.00 2.78
139 140 2.372172 AGAGAAGAAAGCGAAGGGGAAA 59.628 45.455 0.00 0.00 0.00 3.13
140 141 1.978580 AGAGAAGAAAGCGAAGGGGAA 59.021 47.619 0.00 0.00 0.00 3.97
141 142 1.276421 CAGAGAAGAAAGCGAAGGGGA 59.724 52.381 0.00 0.00 0.00 4.81
142 143 1.731720 CAGAGAAGAAAGCGAAGGGG 58.268 55.000 0.00 0.00 0.00 4.79
143 144 1.082690 GCAGAGAAGAAAGCGAAGGG 58.917 55.000 0.00 0.00 0.00 3.95
149 150 1.237285 TTGGCCGCAGAGAAGAAAGC 61.237 55.000 0.00 0.00 0.00 3.51
150 151 1.238439 TTTGGCCGCAGAGAAGAAAG 58.762 50.000 0.00 0.00 0.00 2.62
151 152 1.812571 GATTTGGCCGCAGAGAAGAAA 59.187 47.619 0.00 0.00 0.00 2.52
152 153 1.271325 TGATTTGGCCGCAGAGAAGAA 60.271 47.619 0.00 0.00 0.00 2.52
153 154 0.324614 TGATTTGGCCGCAGAGAAGA 59.675 50.000 0.00 0.00 0.00 2.87
154 155 0.449388 GTGATTTGGCCGCAGAGAAG 59.551 55.000 0.00 0.00 0.00 2.85
155 156 0.036732 AGTGATTTGGCCGCAGAGAA 59.963 50.000 0.00 0.00 0.00 2.87
156 157 0.391661 GAGTGATTTGGCCGCAGAGA 60.392 55.000 0.00 0.00 0.00 3.10
157 158 0.392193 AGAGTGATTTGGCCGCAGAG 60.392 55.000 0.00 0.00 0.00 3.35
158 159 0.391661 GAGAGTGATTTGGCCGCAGA 60.392 55.000 0.00 0.00 0.00 4.26
159 160 1.699656 CGAGAGTGATTTGGCCGCAG 61.700 60.000 0.00 0.00 0.00 5.18
160 161 1.741401 CGAGAGTGATTTGGCCGCA 60.741 57.895 0.00 0.00 0.00 5.69
161 162 2.464459 CCGAGAGTGATTTGGCCGC 61.464 63.158 0.00 0.00 0.00 6.53
162 163 0.673644 AACCGAGAGTGATTTGGCCG 60.674 55.000 0.00 0.00 0.00 6.13
163 164 2.280628 CTAACCGAGAGTGATTTGGCC 58.719 52.381 0.00 0.00 0.00 5.36
164 165 2.093658 TCCTAACCGAGAGTGATTTGGC 60.094 50.000 0.00 0.00 0.00 4.52
165 166 3.786635 CTCCTAACCGAGAGTGATTTGG 58.213 50.000 0.00 0.00 30.97 3.28
166 167 3.190874 GCTCCTAACCGAGAGTGATTTG 58.809 50.000 0.00 0.00 32.47 2.32
167 168 2.159226 CGCTCCTAACCGAGAGTGATTT 60.159 50.000 0.00 0.00 42.05 2.17
168 169 1.405821 CGCTCCTAACCGAGAGTGATT 59.594 52.381 0.00 0.00 42.05 2.57
169 170 1.025812 CGCTCCTAACCGAGAGTGAT 58.974 55.000 0.00 0.00 42.05 3.06
170 171 0.322277 ACGCTCCTAACCGAGAGTGA 60.322 55.000 7.51 0.00 40.79 3.41
171 172 2.181584 ACGCTCCTAACCGAGAGTG 58.818 57.895 0.00 0.00 40.79 3.51
172 173 1.935327 GCACGCTCCTAACCGAGAGT 61.935 60.000 0.00 0.00 42.74 3.24
173 174 1.226717 GCACGCTCCTAACCGAGAG 60.227 63.158 0.00 0.00 35.95 3.20
174 175 1.677966 AGCACGCTCCTAACCGAGA 60.678 57.895 0.00 0.00 30.97 4.04
175 176 1.517257 CAGCACGCTCCTAACCGAG 60.517 63.158 0.00 0.00 0.00 4.63
176 177 1.320344 ATCAGCACGCTCCTAACCGA 61.320 55.000 0.00 0.00 0.00 4.69
177 178 0.384309 TATCAGCACGCTCCTAACCG 59.616 55.000 0.00 0.00 0.00 4.44
178 179 2.202566 GTTATCAGCACGCTCCTAACC 58.797 52.381 8.22 0.00 0.00 2.85
179 180 1.852895 CGTTATCAGCACGCTCCTAAC 59.147 52.381 8.97 8.97 0.00 2.34
180 181 1.475280 ACGTTATCAGCACGCTCCTAA 59.525 47.619 0.00 0.00 41.53 2.69
181 182 1.100510 ACGTTATCAGCACGCTCCTA 58.899 50.000 0.00 0.00 41.53 2.94
182 183 0.458543 CACGTTATCAGCACGCTCCT 60.459 55.000 0.00 0.00 41.53 3.69
183 184 0.736325 ACACGTTATCAGCACGCTCC 60.736 55.000 0.00 0.00 41.53 4.70
184 185 0.366871 CACACGTTATCAGCACGCTC 59.633 55.000 0.00 0.00 41.53 5.03
185 186 0.038618 TCACACGTTATCAGCACGCT 60.039 50.000 0.00 0.00 41.53 5.07
186 187 0.787787 TTCACACGTTATCAGCACGC 59.212 50.000 0.00 0.00 41.53 5.34
187 188 2.475111 ACTTTCACACGTTATCAGCACG 59.525 45.455 0.00 0.00 43.52 5.34
188 189 5.585500 TTACTTTCACACGTTATCAGCAC 57.415 39.130 0.00 0.00 0.00 4.40
189 190 6.606234 TTTTACTTTCACACGTTATCAGCA 57.394 33.333 0.00 0.00 0.00 4.41
190 191 6.084551 CGTTTTTACTTTCACACGTTATCAGC 59.915 38.462 0.00 0.00 0.00 4.26
191 192 7.339207 TCGTTTTTACTTTCACACGTTATCAG 58.661 34.615 0.00 0.00 0.00 2.90
192 193 7.222417 TCTCGTTTTTACTTTCACACGTTATCA 59.778 33.333 0.00 0.00 0.00 2.15
193 194 7.558137 TCTCGTTTTTACTTTCACACGTTATC 58.442 34.615 0.00 0.00 0.00 1.75
194 195 7.436080 TCTCTCGTTTTTACTTTCACACGTTAT 59.564 33.333 0.00 0.00 0.00 1.89
195 196 6.751425 TCTCTCGTTTTTACTTTCACACGTTA 59.249 34.615 0.00 0.00 0.00 3.18
196 197 5.577945 TCTCTCGTTTTTACTTTCACACGTT 59.422 36.000 0.00 0.00 0.00 3.99
197 198 5.104374 TCTCTCGTTTTTACTTTCACACGT 58.896 37.500 0.00 0.00 0.00 4.49
198 199 5.332355 CCTCTCTCGTTTTTACTTTCACACG 60.332 44.000 0.00 0.00 0.00 4.49
199 200 5.751990 TCCTCTCTCGTTTTTACTTTCACAC 59.248 40.000 0.00 0.00 0.00 3.82
200 201 5.909477 TCCTCTCTCGTTTTTACTTTCACA 58.091 37.500 0.00 0.00 0.00 3.58
201 202 6.128526 CCATCCTCTCTCGTTTTTACTTTCAC 60.129 42.308 0.00 0.00 0.00 3.18
202 203 5.932303 CCATCCTCTCTCGTTTTTACTTTCA 59.068 40.000 0.00 0.00 0.00 2.69
203 204 6.164176 TCCATCCTCTCTCGTTTTTACTTTC 58.836 40.000 0.00 0.00 0.00 2.62
204 205 6.110411 TCCATCCTCTCTCGTTTTTACTTT 57.890 37.500 0.00 0.00 0.00 2.66
205 206 5.725362 CTCCATCCTCTCTCGTTTTTACTT 58.275 41.667 0.00 0.00 0.00 2.24
206 207 4.382147 GCTCCATCCTCTCTCGTTTTTACT 60.382 45.833 0.00 0.00 0.00 2.24
207 208 3.866327 GCTCCATCCTCTCTCGTTTTTAC 59.134 47.826 0.00 0.00 0.00 2.01
208 209 3.513912 TGCTCCATCCTCTCTCGTTTTTA 59.486 43.478 0.00 0.00 0.00 1.52
209 210 2.303022 TGCTCCATCCTCTCTCGTTTTT 59.697 45.455 0.00 0.00 0.00 1.94
210 211 1.902508 TGCTCCATCCTCTCTCGTTTT 59.097 47.619 0.00 0.00 0.00 2.43
211 212 1.561643 TGCTCCATCCTCTCTCGTTT 58.438 50.000 0.00 0.00 0.00 3.60
212 213 1.561643 TTGCTCCATCCTCTCTCGTT 58.438 50.000 0.00 0.00 0.00 3.85
213 214 1.561643 TTTGCTCCATCCTCTCTCGT 58.438 50.000 0.00 0.00 0.00 4.18
214 215 2.102084 TCATTTGCTCCATCCTCTCTCG 59.898 50.000 0.00 0.00 0.00 4.04
215 216 3.834489 TCATTTGCTCCATCCTCTCTC 57.166 47.619 0.00 0.00 0.00 3.20
216 217 3.181442 CCATCATTTGCTCCATCCTCTCT 60.181 47.826 0.00 0.00 0.00 3.10
217 218 3.147629 CCATCATTTGCTCCATCCTCTC 58.852 50.000 0.00 0.00 0.00 3.20
218 219 2.781757 TCCATCATTTGCTCCATCCTCT 59.218 45.455 0.00 0.00 0.00 3.69
219 220 3.219176 TCCATCATTTGCTCCATCCTC 57.781 47.619 0.00 0.00 0.00 3.71
220 221 3.294214 GTTCCATCATTTGCTCCATCCT 58.706 45.455 0.00 0.00 0.00 3.24
221 222 3.025978 TGTTCCATCATTTGCTCCATCC 58.974 45.455 0.00 0.00 0.00 3.51
222 223 3.698040 ACTGTTCCATCATTTGCTCCATC 59.302 43.478 0.00 0.00 0.00 3.51
223 224 3.705051 ACTGTTCCATCATTTGCTCCAT 58.295 40.909 0.00 0.00 0.00 3.41
224 225 3.159213 ACTGTTCCATCATTTGCTCCA 57.841 42.857 0.00 0.00 0.00 3.86
225 226 3.256631 ACAACTGTTCCATCATTTGCTCC 59.743 43.478 0.00 0.00 33.36 4.70
226 227 4.510038 ACAACTGTTCCATCATTTGCTC 57.490 40.909 0.00 0.00 33.36 4.26
227 228 4.942761 AACAACTGTTCCATCATTTGCT 57.057 36.364 0.00 0.00 33.36 3.91
228 229 5.049167 TGAAACAACTGTTCCATCATTTGC 58.951 37.500 0.00 0.00 37.25 3.68
229 230 7.438757 TCAATGAAACAACTGTTCCATCATTTG 59.561 33.333 14.17 11.32 39.25 2.32
230 231 7.499292 TCAATGAAACAACTGTTCCATCATTT 58.501 30.769 14.17 3.35 39.25 2.32
231 232 7.053316 TCAATGAAACAACTGTTCCATCATT 57.947 32.000 12.20 12.20 40.64 2.57
232 233 6.653526 TCAATGAAACAACTGTTCCATCAT 57.346 33.333 0.00 0.00 31.63 2.45
233 234 6.653526 ATCAATGAAACAACTGTTCCATCA 57.346 33.333 0.00 0.00 31.63 3.07
234 235 7.147312 TCAATCAATGAAACAACTGTTCCATC 58.853 34.615 0.00 0.00 31.63 3.51
235 236 7.053316 TCAATCAATGAAACAACTGTTCCAT 57.947 32.000 0.00 0.00 34.37 3.41
236 237 6.462552 TCAATCAATGAAACAACTGTTCCA 57.537 33.333 0.00 0.00 37.25 3.53
248 249 7.976414 AATACCCCAATCTTCAATCAATGAA 57.024 32.000 0.00 0.00 45.71 2.57
249 250 7.976414 AAATACCCCAATCTTCAATCAATGA 57.024 32.000 0.00 0.00 35.85 2.57
252 253 9.362151 GGTATAAATACCCCAATCTTCAATCAA 57.638 33.333 7.80 0.00 45.62 2.57
253 254 8.934023 GGTATAAATACCCCAATCTTCAATCA 57.066 34.615 7.80 0.00 45.62 2.57
268 269 7.937394 ACTGCCTTGTAATGAGGGTATAAATAC 59.063 37.037 0.00 0.00 34.75 1.89
269 270 8.041143 ACTGCCTTGTAATGAGGGTATAAATA 57.959 34.615 0.00 0.00 34.75 1.40
270 271 6.911308 ACTGCCTTGTAATGAGGGTATAAAT 58.089 36.000 0.00 0.00 34.75 1.40
271 272 6.321821 ACTGCCTTGTAATGAGGGTATAAA 57.678 37.500 0.00 0.00 34.75 1.40
272 273 5.968676 ACTGCCTTGTAATGAGGGTATAA 57.031 39.130 0.00 0.00 34.75 0.98
273 274 5.968676 AACTGCCTTGTAATGAGGGTATA 57.031 39.130 0.00 0.00 34.75 1.47
274 275 4.862641 AACTGCCTTGTAATGAGGGTAT 57.137 40.909 0.00 0.00 34.75 2.73
275 276 4.532916 TGTAACTGCCTTGTAATGAGGGTA 59.467 41.667 0.00 0.00 34.75 3.69
276 277 3.329520 TGTAACTGCCTTGTAATGAGGGT 59.670 43.478 0.00 0.00 34.75 4.34
277 278 3.950397 TGTAACTGCCTTGTAATGAGGG 58.050 45.455 0.00 0.00 34.75 4.30
278 279 5.705441 TCTTTGTAACTGCCTTGTAATGAGG 59.295 40.000 0.00 0.00 37.35 3.86
279 280 6.801539 TCTTTGTAACTGCCTTGTAATGAG 57.198 37.500 0.00 0.00 0.00 2.90
280 281 6.206634 CCTTCTTTGTAACTGCCTTGTAATGA 59.793 38.462 0.00 0.00 0.00 2.57
281 282 6.381801 CCTTCTTTGTAACTGCCTTGTAATG 58.618 40.000 0.00 0.00 0.00 1.90
282 283 5.048013 GCCTTCTTTGTAACTGCCTTGTAAT 60.048 40.000 0.00 0.00 0.00 1.89
283 284 4.277423 GCCTTCTTTGTAACTGCCTTGTAA 59.723 41.667 0.00 0.00 0.00 2.41
284 285 3.818773 GCCTTCTTTGTAACTGCCTTGTA 59.181 43.478 0.00 0.00 0.00 2.41
285 286 2.623416 GCCTTCTTTGTAACTGCCTTGT 59.377 45.455 0.00 0.00 0.00 3.16
286 287 2.350772 CGCCTTCTTTGTAACTGCCTTG 60.351 50.000 0.00 0.00 0.00 3.61
287 288 1.880027 CGCCTTCTTTGTAACTGCCTT 59.120 47.619 0.00 0.00 0.00 4.35
288 289 1.523758 CGCCTTCTTTGTAACTGCCT 58.476 50.000 0.00 0.00 0.00 4.75
289 290 0.521735 CCGCCTTCTTTGTAACTGCC 59.478 55.000 0.00 0.00 0.00 4.85
290 291 1.235724 ACCGCCTTCTTTGTAACTGC 58.764 50.000 0.00 0.00 0.00 4.40
291 292 2.604614 GCAACCGCCTTCTTTGTAACTG 60.605 50.000 0.00 0.00 0.00 3.16
292 293 1.607148 GCAACCGCCTTCTTTGTAACT 59.393 47.619 0.00 0.00 0.00 2.24
293 294 2.046283 GCAACCGCCTTCTTTGTAAC 57.954 50.000 0.00 0.00 0.00 2.50
305 306 0.943835 GGTCATGTTTTGGCAACCGC 60.944 55.000 0.00 0.00 37.44 5.68
306 307 0.387202 TGGTCATGTTTTGGCAACCG 59.613 50.000 0.00 0.00 0.00 4.44
307 308 1.540146 GGTGGTCATGTTTTGGCAACC 60.540 52.381 0.00 0.00 46.69 3.77
308 309 1.864565 GGTGGTCATGTTTTGGCAAC 58.135 50.000 0.00 0.00 32.67 4.17
309 310 0.387202 CGGTGGTCATGTTTTGGCAA 59.613 50.000 0.00 0.00 0.00 4.52
310 311 0.466372 TCGGTGGTCATGTTTTGGCA 60.466 50.000 0.00 0.00 0.00 4.92
311 312 0.039527 GTCGGTGGTCATGTTTTGGC 60.040 55.000 0.00 0.00 0.00 4.52
312 313 1.313772 TGTCGGTGGTCATGTTTTGG 58.686 50.000 0.00 0.00 0.00 3.28
313 314 3.426159 GCTATGTCGGTGGTCATGTTTTG 60.426 47.826 0.00 0.00 0.00 2.44
314 315 2.747446 GCTATGTCGGTGGTCATGTTTT 59.253 45.455 0.00 0.00 0.00 2.43
315 316 2.290008 TGCTATGTCGGTGGTCATGTTT 60.290 45.455 0.00 0.00 0.00 2.83
316 317 1.277842 TGCTATGTCGGTGGTCATGTT 59.722 47.619 0.00 0.00 0.00 2.71
317 318 0.901827 TGCTATGTCGGTGGTCATGT 59.098 50.000 0.00 0.00 0.00 3.21
318 319 1.869132 CATGCTATGTCGGTGGTCATG 59.131 52.381 0.00 0.00 0.00 3.07
319 320 1.202687 CCATGCTATGTCGGTGGTCAT 60.203 52.381 0.00 0.00 0.00 3.06
320 321 0.177836 CCATGCTATGTCGGTGGTCA 59.822 55.000 0.00 0.00 0.00 4.02
321 322 0.464036 TCCATGCTATGTCGGTGGTC 59.536 55.000 0.00 0.00 0.00 4.02
322 323 1.131638 ATCCATGCTATGTCGGTGGT 58.868 50.000 0.00 0.00 0.00 4.16
323 324 2.260844 AATCCATGCTATGTCGGTGG 57.739 50.000 0.00 0.00 0.00 4.61
324 325 7.615582 ATTATAAATCCATGCTATGTCGGTG 57.384 36.000 0.00 0.00 0.00 4.94
325 326 9.733556 TTAATTATAAATCCATGCTATGTCGGT 57.266 29.630 0.00 0.00 0.00 4.69
369 370 9.702253 AGACAAAGATAGAGATACTGTTAGGAA 57.298 33.333 0.00 0.00 0.00 3.36
392 393 6.716934 TGATAGAAGTGGTGGAGAATAGAC 57.283 41.667 0.00 0.00 0.00 2.59
395 396 4.962362 TGCTGATAGAAGTGGTGGAGAATA 59.038 41.667 0.00 0.00 0.00 1.75
460 463 1.302033 CCGAACTCTGGCTGCTTGT 60.302 57.895 0.00 0.00 0.00 3.16
593 599 4.554363 CTGAGCGTCGTAGCGGGG 62.554 72.222 0.00 0.00 43.00 5.73
615 621 1.065928 GATAGTCACGGCCAGGACG 59.934 63.158 15.24 15.24 41.40 4.79
621 627 1.068250 GGCAGAGATAGTCACGGCC 59.932 63.158 0.00 0.00 40.31 6.13
622 628 0.390860 ATGGCAGAGATAGTCACGGC 59.609 55.000 0.00 0.00 0.00 5.68
623 629 1.871408 GCATGGCAGAGATAGTCACGG 60.871 57.143 0.00 0.00 0.00 4.94
625 631 2.364970 AGAGCATGGCAGAGATAGTCAC 59.635 50.000 0.00 0.00 0.00 3.67
626 632 2.627221 GAGAGCATGGCAGAGATAGTCA 59.373 50.000 0.00 0.00 0.00 3.41
627 633 2.029110 GGAGAGCATGGCAGAGATAGTC 60.029 54.545 0.00 0.00 0.00 2.59
670 676 2.350895 CTCCAATGGCGACCACCA 59.649 61.111 0.00 0.00 45.82 4.17
671 677 2.438434 CCTCCAATGGCGACCACC 60.438 66.667 0.00 0.00 35.80 4.61
672 678 3.134127 GCCTCCAATGGCGACCAC 61.134 66.667 0.00 0.00 43.74 4.16
698 759 1.380302 GAAGGGAAGAAGGCCAGCA 59.620 57.895 5.01 0.00 0.00 4.41
731 792 2.599082 GCGACAGCTACTACATGTGAAC 59.401 50.000 9.11 0.00 41.01 3.18
734 795 1.560923 GGCGACAGCTACTACATGTG 58.439 55.000 9.11 0.93 44.37 3.21
742 803 2.874780 CGTGACGGCGACAGCTAC 60.875 66.667 16.62 0.05 44.37 3.58
743 804 3.318539 GACGTGACGGCGACAGCTA 62.319 63.158 16.62 0.00 44.37 3.32
747 808 4.337060 CAGGACGTGACGGCGACA 62.337 66.667 16.62 12.05 34.63 4.35
938 999 2.244436 CTTGCATGACCACGAAGCCG 62.244 60.000 0.00 0.00 42.50 5.52
961 1022 2.583441 CGGCTGAAGGTGGAGGTCA 61.583 63.158 0.00 0.00 0.00 4.02
974 1035 3.842923 ATCTCCTGTCGCCGGCTG 61.843 66.667 26.68 18.23 0.00 4.85
1057 1118 1.874345 GCGAGGACAAAGGAGGACGA 61.874 60.000 0.00 0.00 0.00 4.20
1068 1129 4.361971 ACCGAGGAGGCGAGGACA 62.362 66.667 0.00 0.00 46.52 4.02
1208 1275 4.712425 CACGCCAGCAAGCAAGCC 62.712 66.667 0.00 0.00 34.23 4.35
1228 1295 0.456628 TCGTCCATTATCGCGTCCAA 59.543 50.000 5.77 0.00 0.00 3.53
1259 1334 3.868985 AAACCACCGCCGTCCTGT 61.869 61.111 0.00 0.00 0.00 4.00
1288 1363 3.606662 TCGCCCTCTAGCCATCGC 61.607 66.667 0.00 0.00 0.00 4.58
1379 1471 4.415150 CTCCACCACGCAGGCCAT 62.415 66.667 5.01 0.00 43.14 4.40
1440 1535 0.175302 ACATGCAGGAGCTTCTCGAG 59.825 55.000 4.84 5.93 42.74 4.04
1504 1622 0.668706 GCATGCGCCATCGTCTCTAT 60.669 55.000 4.18 0.00 38.14 1.98
1550 1668 2.892425 GGCCGGAGTTCTGCATCG 60.892 66.667 5.05 0.00 0.00 3.84
1584 1755 1.590792 CGAGCTCGAGATGCATGCA 60.591 57.895 32.06 25.04 43.02 3.96
1613 1784 0.535335 AAGATAGGCGCAAGGTCGAA 59.465 50.000 10.83 0.00 38.28 3.71
2233 2654 5.482163 TGACTCATACAACCAGACAATGA 57.518 39.130 0.00 0.00 0.00 2.57
2234 2655 6.748333 AATGACTCATACAACCAGACAATG 57.252 37.500 0.00 0.00 0.00 2.82
2279 2729 4.422984 ACAGCCTCCTTAACCTACAACTA 58.577 43.478 0.00 0.00 0.00 2.24
2441 2911 2.225117 CCCCTCCCAACAGAACATTCTT 60.225 50.000 0.00 0.00 34.74 2.52
2630 3105 7.112779 ACATCCATAAAGGTTTTAGGAGTGAG 58.887 38.462 0.00 0.00 39.02 3.51


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

AutoCloner maintained by Alex Coulton.