Multiple sequence alignment - TraesCS3A01G423000

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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 TraesCS3A01G423000 chr3A 100.000 4505 0 0 1 4505 664682542 664687046 0.000000e+00 8320
1 TraesCS3A01G423000 chr3A 99.831 592 1 0 3450 4041 664703085 664703676 0.000000e+00 1088
2 TraesCS3A01G423000 chr3B 91.639 4174 200 83 416 4505 701404869 701408977 0.000000e+00 5637
3 TraesCS3A01G423000 chr3D 95.226 2786 85 17 1753 4505 531044311 531047081 0.000000e+00 4364
4 TraesCS3A01G423000 chr3D 92.893 1182 56 18 577 1747 531043061 531044225 0.000000e+00 1692
5 TraesCS3A01G423000 chr3D 94.186 172 7 1 414 582 531042863 531043034 4.470000e-65 259
6 TraesCS3A01G423000 chr2B 86.452 310 37 4 1 309 39921287 39921592 7.220000e-88 335


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 TraesCS3A01G423000 chr3A 664682542 664687046 4504 False 8320 8320 100.000000 1 4505 1 chr3A.!!$F1 4504
1 TraesCS3A01G423000 chr3A 664703085 664703676 591 False 1088 1088 99.831000 3450 4041 1 chr3A.!!$F2 591
2 TraesCS3A01G423000 chr3B 701404869 701408977 4108 False 5637 5637 91.639000 416 4505 1 chr3B.!!$F1 4089
3 TraesCS3A01G423000 chr3D 531042863 531047081 4218 False 2105 4364 94.101667 414 4505 3 chr3D.!!$F1 4091

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
937 988 0.034337 AGCCGTCCGTGAGCTTTTAA 59.966 50.0 0.00 0.00 31.27 1.52 F
964 1015 0.178935 GATCAGAGGGGAGAGAGGGG 60.179 65.0 0.00 0.00 0.00 4.79 F
2511 2660 0.395724 AAATGCAGTTCGGGATCCCC 60.396 55.0 25.73 11.42 41.09 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2832 2981 0.108281 GACAAGAACTACCCCTCGGC 60.108 60.000 0.0 0.0 0.00 5.54 R
2955 3104 1.351017 GTGTCCCCATTGTTCTCCTCA 59.649 52.381 0.0 0.0 0.00 3.86 R
4431 4644 0.173255 AACACCCAAATGCTATGCGC 59.827 50.000 0.0 0.0 39.77 6.09 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
27 28 6.793505 TTTGGTGTACAAATGGGTTACTTT 57.206 33.333 0.00 0.00 43.81 2.66
28 29 6.793505 TTGGTGTACAAATGGGTTACTTTT 57.206 33.333 0.00 0.00 35.79 2.27
29 30 6.793505 TGGTGTACAAATGGGTTACTTTTT 57.206 33.333 0.00 0.00 0.00 1.94
30 31 7.893124 TGGTGTACAAATGGGTTACTTTTTA 57.107 32.000 0.00 0.00 0.00 1.52
31 32 7.942990 TGGTGTACAAATGGGTTACTTTTTAG 58.057 34.615 0.00 0.00 0.00 1.85
32 33 7.014422 TGGTGTACAAATGGGTTACTTTTTAGG 59.986 37.037 0.00 0.00 0.00 2.69
33 34 7.014518 GGTGTACAAATGGGTTACTTTTTAGGT 59.985 37.037 0.00 0.00 0.00 3.08
34 35 7.863877 GTGTACAAATGGGTTACTTTTTAGGTG 59.136 37.037 0.00 0.00 0.00 4.00
35 36 6.413783 ACAAATGGGTTACTTTTTAGGTGG 57.586 37.500 0.00 0.00 0.00 4.61
36 37 6.137559 ACAAATGGGTTACTTTTTAGGTGGA 58.862 36.000 0.00 0.00 0.00 4.02
37 38 6.612049 ACAAATGGGTTACTTTTTAGGTGGAA 59.388 34.615 0.00 0.00 0.00 3.53
38 39 7.125963 ACAAATGGGTTACTTTTTAGGTGGAAA 59.874 33.333 0.00 0.00 0.00 3.13
39 40 7.678207 AATGGGTTACTTTTTAGGTGGAAAA 57.322 32.000 0.00 0.00 0.00 2.29
40 41 6.718522 TGGGTTACTTTTTAGGTGGAAAAG 57.281 37.500 7.55 7.55 45.22 2.27
41 42 6.433441 TGGGTTACTTTTTAGGTGGAAAAGA 58.567 36.000 14.21 0.00 43.44 2.52
42 43 6.548251 TGGGTTACTTTTTAGGTGGAAAAGAG 59.452 38.462 14.21 0.00 43.44 2.85
43 44 6.774170 GGGTTACTTTTTAGGTGGAAAAGAGA 59.226 38.462 14.21 1.98 43.44 3.10
44 45 7.286087 GGGTTACTTTTTAGGTGGAAAAGAGAA 59.714 37.037 14.21 6.77 43.44 2.87
45 46 8.857098 GGTTACTTTTTAGGTGGAAAAGAGAAT 58.143 33.333 14.21 0.00 43.44 2.40
50 51 9.394477 CTTTTTAGGTGGAAAAGAGAATAAACG 57.606 33.333 3.86 0.00 43.44 3.60
51 52 8.680039 TTTTAGGTGGAAAAGAGAATAAACGA 57.320 30.769 0.00 0.00 0.00 3.85
52 53 8.680039 TTTAGGTGGAAAAGAGAATAAACGAA 57.320 30.769 0.00 0.00 0.00 3.85
53 54 6.803154 AGGTGGAAAAGAGAATAAACGAAG 57.197 37.500 0.00 0.00 0.00 3.79
54 55 6.531021 AGGTGGAAAAGAGAATAAACGAAGA 58.469 36.000 0.00 0.00 0.00 2.87
55 56 6.996282 AGGTGGAAAAGAGAATAAACGAAGAA 59.004 34.615 0.00 0.00 0.00 2.52
56 57 7.041303 AGGTGGAAAAGAGAATAAACGAAGAAC 60.041 37.037 0.00 0.00 0.00 3.01
68 69 2.579013 CGAAGAACGGCAGAAAGAAC 57.421 50.000 0.00 0.00 38.46 3.01
69 70 1.136611 CGAAGAACGGCAGAAAGAACG 60.137 52.381 0.00 0.00 38.46 3.95
70 71 1.194772 GAAGAACGGCAGAAAGAACGG 59.805 52.381 0.00 0.00 0.00 4.44
71 72 0.391597 AGAACGGCAGAAAGAACGGA 59.608 50.000 0.00 0.00 0.00 4.69
72 73 0.790814 GAACGGCAGAAAGAACGGAG 59.209 55.000 0.00 0.00 0.00 4.63
73 74 0.602905 AACGGCAGAAAGAACGGAGG 60.603 55.000 0.00 0.00 0.00 4.30
74 75 2.391389 CGGCAGAAAGAACGGAGGC 61.391 63.158 0.00 0.00 0.00 4.70
75 76 1.302511 GGCAGAAAGAACGGAGGCA 60.303 57.895 0.00 0.00 0.00 4.75
76 77 0.889186 GGCAGAAAGAACGGAGGCAA 60.889 55.000 0.00 0.00 0.00 4.52
77 78 0.519077 GCAGAAAGAACGGAGGCAAG 59.481 55.000 0.00 0.00 0.00 4.01
78 79 1.160137 CAGAAAGAACGGAGGCAAGG 58.840 55.000 0.00 0.00 0.00 3.61
79 80 0.036875 AGAAAGAACGGAGGCAAGGG 59.963 55.000 0.00 0.00 0.00 3.95
80 81 0.960861 GAAAGAACGGAGGCAAGGGG 60.961 60.000 0.00 0.00 0.00 4.79
81 82 1.423794 AAAGAACGGAGGCAAGGGGA 61.424 55.000 0.00 0.00 0.00 4.81
82 83 1.208165 AAGAACGGAGGCAAGGGGAT 61.208 55.000 0.00 0.00 0.00 3.85
83 84 0.326238 AGAACGGAGGCAAGGGGATA 60.326 55.000 0.00 0.00 0.00 2.59
84 85 0.544697 GAACGGAGGCAAGGGGATAA 59.455 55.000 0.00 0.00 0.00 1.75
85 86 0.546598 AACGGAGGCAAGGGGATAAG 59.453 55.000 0.00 0.00 0.00 1.73
86 87 1.227973 CGGAGGCAAGGGGATAAGC 60.228 63.158 0.00 0.00 0.00 3.09
87 88 1.700042 CGGAGGCAAGGGGATAAGCT 61.700 60.000 0.00 0.00 0.00 3.74
88 89 0.109532 GGAGGCAAGGGGATAAGCTC 59.890 60.000 0.00 0.00 0.00 4.09
89 90 1.135960 GAGGCAAGGGGATAAGCTCT 58.864 55.000 0.00 0.00 0.00 4.09
90 91 1.071542 GAGGCAAGGGGATAAGCTCTC 59.928 57.143 0.00 0.00 0.00 3.20
91 92 0.250081 GGCAAGGGGATAAGCTCTCG 60.250 60.000 0.00 0.00 0.00 4.04
92 93 0.466124 GCAAGGGGATAAGCTCTCGT 59.534 55.000 0.00 0.00 0.00 4.18
93 94 1.808133 GCAAGGGGATAAGCTCTCGTG 60.808 57.143 0.00 0.00 0.00 4.35
94 95 1.123928 AAGGGGATAAGCTCTCGTGG 58.876 55.000 0.00 0.00 0.00 4.94
95 96 0.760945 AGGGGATAAGCTCTCGTGGG 60.761 60.000 0.00 0.00 0.00 4.61
96 97 0.759436 GGGGATAAGCTCTCGTGGGA 60.759 60.000 0.00 0.00 0.00 4.37
97 98 0.676736 GGGATAAGCTCTCGTGGGAG 59.323 60.000 0.00 0.00 41.89 4.30
98 99 0.676736 GGATAAGCTCTCGTGGGAGG 59.323 60.000 0.00 0.00 40.85 4.30
99 100 1.404843 GATAAGCTCTCGTGGGAGGT 58.595 55.000 0.00 0.00 44.56 3.85
100 101 1.067821 GATAAGCTCTCGTGGGAGGTG 59.932 57.143 1.61 0.00 42.29 4.00
101 102 0.970937 TAAGCTCTCGTGGGAGGTGG 60.971 60.000 1.61 0.00 42.29 4.61
102 103 2.680352 GCTCTCGTGGGAGGTGGA 60.680 66.667 0.00 0.00 40.85 4.02
103 104 2.283529 GCTCTCGTGGGAGGTGGAA 61.284 63.158 0.00 0.00 40.85 3.53
104 105 1.893786 CTCTCGTGGGAGGTGGAAG 59.106 63.158 0.00 0.00 40.85 3.46
105 106 0.612174 CTCTCGTGGGAGGTGGAAGA 60.612 60.000 0.00 0.00 40.85 2.87
106 107 0.178944 TCTCGTGGGAGGTGGAAGAA 60.179 55.000 0.00 0.00 40.85 2.52
107 108 0.247736 CTCGTGGGAGGTGGAAGAAG 59.752 60.000 0.00 0.00 36.61 2.85
108 109 1.376037 CGTGGGAGGTGGAAGAAGC 60.376 63.158 0.00 0.00 0.00 3.86
109 110 1.831652 CGTGGGAGGTGGAAGAAGCT 61.832 60.000 0.00 0.00 0.00 3.74
110 111 0.322008 GTGGGAGGTGGAAGAAGCTG 60.322 60.000 0.00 0.00 0.00 4.24
111 112 1.301293 GGGAGGTGGAAGAAGCTGG 59.699 63.158 0.00 0.00 0.00 4.85
112 113 1.377856 GGAGGTGGAAGAAGCTGGC 60.378 63.158 0.00 0.00 0.00 4.85
113 114 1.743252 GAGGTGGAAGAAGCTGGCG 60.743 63.158 0.00 0.00 0.00 5.69
114 115 2.172483 GAGGTGGAAGAAGCTGGCGA 62.172 60.000 0.00 0.00 0.00 5.54
115 116 2.035442 GGTGGAAGAAGCTGGCGAC 61.035 63.158 0.00 0.00 0.00 5.19
116 117 2.035442 GTGGAAGAAGCTGGCGACC 61.035 63.158 0.00 0.00 0.00 4.79
117 118 2.815647 GGAAGAAGCTGGCGACCG 60.816 66.667 0.00 0.00 0.00 4.79
118 119 2.815647 GAAGAAGCTGGCGACCGG 60.816 66.667 0.00 0.00 0.00 5.28
119 120 4.394712 AAGAAGCTGGCGACCGGG 62.395 66.667 6.32 0.00 0.00 5.73
140 141 4.083862 GGCTGGGACCCTGTCGTC 62.084 72.222 17.97 2.15 32.65 4.20
147 148 2.928416 GACCCTGTCGTCCAAAAGG 58.072 57.895 0.00 0.00 0.00 3.11
148 149 0.108019 GACCCTGTCGTCCAAAAGGT 59.892 55.000 0.00 0.00 0.00 3.50
149 150 0.179029 ACCCTGTCGTCCAAAAGGTG 60.179 55.000 0.00 0.00 0.00 4.00
168 169 3.669354 GACGATTGTCCTAGGGCTG 57.331 57.895 15.92 4.49 39.30 4.85
169 170 0.105039 GACGATTGTCCTAGGGCTGG 59.895 60.000 15.92 3.55 39.30 4.85
170 171 0.325296 ACGATTGTCCTAGGGCTGGA 60.325 55.000 15.92 0.73 0.00 3.86
174 175 3.208335 GTCCTAGGGCTGGACGAC 58.792 66.667 5.99 0.00 43.55 4.34
175 176 1.681327 GTCCTAGGGCTGGACGACA 60.681 63.158 5.99 0.00 43.55 4.35
185 186 2.048127 GGACGACAGGCCTGTGTC 60.048 66.667 42.40 38.20 45.05 3.67
189 190 3.052081 GACAGGCCTGTGTCGTCT 58.948 61.111 42.40 17.02 45.05 4.18
190 191 1.373497 GACAGGCCTGTGTCGTCTG 60.373 63.158 42.40 12.57 45.05 3.51
191 192 2.047844 CAGGCCTGTGTCGTCTGG 60.048 66.667 25.53 0.00 0.00 3.86
192 193 3.314331 AGGCCTGTGTCGTCTGGG 61.314 66.667 3.11 0.00 0.00 4.45
193 194 4.394712 GGCCTGTGTCGTCTGGGG 62.395 72.222 0.00 0.00 0.00 4.96
195 196 4.394712 CCTGTGTCGTCTGGGGCC 62.395 72.222 0.00 0.00 0.00 5.80
196 197 4.394712 CTGTGTCGTCTGGGGCCC 62.395 72.222 18.17 18.17 0.00 5.80
234 235 2.519780 GGGACGAGGGAGAGCGAT 60.520 66.667 0.00 0.00 0.00 4.58
235 236 2.725008 GGACGAGGGAGAGCGATG 59.275 66.667 0.00 0.00 0.00 3.84
236 237 2.026879 GACGAGGGAGAGCGATGC 59.973 66.667 0.00 0.00 0.00 3.91
237 238 3.815569 GACGAGGGAGAGCGATGCG 62.816 68.421 0.00 0.00 0.00 4.73
238 239 3.586961 CGAGGGAGAGCGATGCGA 61.587 66.667 0.00 0.00 0.00 5.10
239 240 2.026879 GAGGGAGAGCGATGCGAC 59.973 66.667 0.00 0.00 0.00 5.19
240 241 3.815569 GAGGGAGAGCGATGCGACG 62.816 68.421 0.00 0.00 0.00 5.12
241 242 4.194720 GGGAGAGCGATGCGACGT 62.195 66.667 0.00 0.00 35.59 4.34
242 243 2.951745 GGAGAGCGATGCGACGTG 60.952 66.667 0.00 0.00 35.59 4.49
243 244 2.951745 GAGAGCGATGCGACGTGG 60.952 66.667 0.00 0.00 35.59 4.94
244 245 4.498520 AGAGCGATGCGACGTGGG 62.499 66.667 0.00 0.00 35.59 4.61
280 281 4.065281 CCACGTGGAGGACCGGAC 62.065 72.222 31.31 0.00 39.42 4.79
281 282 3.299977 CACGTGGAGGACCGGACA 61.300 66.667 9.46 0.00 39.42 4.02
282 283 3.300765 ACGTGGAGGACCGGACAC 61.301 66.667 9.46 8.15 39.42 3.67
283 284 4.065281 CGTGGAGGACCGGACACC 62.065 72.222 9.46 10.54 39.42 4.16
284 285 2.603776 GTGGAGGACCGGACACCT 60.604 66.667 9.46 14.14 39.42 4.00
285 286 2.603473 TGGAGGACCGGACACCTG 60.603 66.667 20.09 0.00 39.42 4.00
286 287 2.603776 GGAGGACCGGACACCTGT 60.604 66.667 20.09 2.38 36.57 4.00
287 288 2.647158 GGAGGACCGGACACCTGTC 61.647 68.421 20.09 9.82 44.04 3.51
288 289 2.989824 AGGACCGGACACCTGTCG 60.990 66.667 9.46 0.00 45.65 4.35
289 290 3.300765 GGACCGGACACCTGTCGT 61.301 66.667 9.46 0.00 45.65 4.34
290 291 2.257676 GACCGGACACCTGTCGTC 59.742 66.667 9.46 0.00 45.65 4.20
295 296 4.098847 GACACCTGTCGTCCTCCT 57.901 61.111 0.00 0.00 35.12 3.69
296 297 3.261250 GACACCTGTCGTCCTCCTA 57.739 57.895 0.00 0.00 35.12 2.94
297 298 1.765230 GACACCTGTCGTCCTCCTAT 58.235 55.000 0.00 0.00 35.12 2.57
298 299 2.928334 GACACCTGTCGTCCTCCTATA 58.072 52.381 0.00 0.00 35.12 1.31
299 300 2.879646 GACACCTGTCGTCCTCCTATAG 59.120 54.545 0.00 0.00 35.12 1.31
300 301 4.305063 GACACCTGTCGTCCTCCTATAGG 61.305 56.522 13.07 13.07 40.00 2.57
301 302 1.249407 CCTGTCGTCCTCCTATAGGC 58.751 60.000 14.50 0.00 46.10 3.93
302 303 1.249407 CTGTCGTCCTCCTATAGGCC 58.751 60.000 14.50 0.00 46.10 5.19
306 307 2.255430 GTCCTCCTATAGGCCGACG 58.745 63.158 14.50 0.00 46.10 5.12
307 308 1.074423 TCCTCCTATAGGCCGACGG 59.926 63.158 14.50 10.29 46.10 4.79
308 309 1.977544 CCTCCTATAGGCCGACGGG 60.978 68.421 17.22 5.35 38.97 5.28
326 327 2.678934 CCCCACTCGTCCTCCGAA 60.679 66.667 0.00 0.00 46.75 4.30
327 328 2.711922 CCCCACTCGTCCTCCGAAG 61.712 68.421 0.00 0.00 46.75 3.79
328 329 1.677966 CCCACTCGTCCTCCGAAGA 60.678 63.158 0.00 0.00 46.75 2.87
329 330 1.658686 CCCACTCGTCCTCCGAAGAG 61.659 65.000 2.15 2.15 46.75 2.85
330 331 0.677098 CCACTCGTCCTCCGAAGAGA 60.677 60.000 9.55 0.00 46.75 3.10
331 332 0.448593 CACTCGTCCTCCGAAGAGAC 59.551 60.000 9.55 0.00 46.75 3.36
332 333 1.020333 ACTCGTCCTCCGAAGAGACG 61.020 60.000 9.55 6.39 46.75 4.18
333 334 0.740164 CTCGTCCTCCGAAGAGACGA 60.740 60.000 12.99 12.99 46.75 4.20
334 335 0.740164 TCGTCCTCCGAAGAGACGAG 60.740 60.000 10.39 0.00 44.03 4.18
335 336 1.707239 CGTCCTCCGAAGAGACGAGG 61.707 65.000 6.81 1.53 43.39 4.63
336 337 1.749638 TCCTCCGAAGAGACGAGGC 60.750 63.158 0.00 0.00 43.39 4.70
337 338 2.776913 CCTCCGAAGAGACGAGGCC 61.777 68.421 0.00 0.00 43.39 5.19
338 339 2.035155 TCCGAAGAGACGAGGCCA 59.965 61.111 5.01 0.00 35.09 5.36
339 340 1.379977 TCCGAAGAGACGAGGCCAT 60.380 57.895 5.01 0.00 35.09 4.40
340 341 0.106868 TCCGAAGAGACGAGGCCATA 60.107 55.000 5.01 0.00 35.09 2.74
341 342 0.962489 CCGAAGAGACGAGGCCATAT 59.038 55.000 5.01 0.00 35.09 1.78
342 343 2.160205 CCGAAGAGACGAGGCCATATA 58.840 52.381 5.01 0.00 35.09 0.86
343 344 2.162608 CCGAAGAGACGAGGCCATATAG 59.837 54.545 5.01 0.00 35.09 1.31
344 345 3.075148 CGAAGAGACGAGGCCATATAGA 58.925 50.000 5.01 0.00 35.09 1.98
345 346 3.502595 CGAAGAGACGAGGCCATATAGAA 59.497 47.826 5.01 0.00 35.09 2.10
346 347 4.023107 CGAAGAGACGAGGCCATATAGAAA 60.023 45.833 5.01 0.00 35.09 2.52
347 348 5.507482 CGAAGAGACGAGGCCATATAGAAAA 60.507 44.000 5.01 0.00 35.09 2.29
348 349 6.426646 AAGAGACGAGGCCATATAGAAAAT 57.573 37.500 5.01 0.00 0.00 1.82
349 350 7.540474 AAGAGACGAGGCCATATAGAAAATA 57.460 36.000 5.01 0.00 0.00 1.40
350 351 7.540474 AGAGACGAGGCCATATAGAAAATAA 57.460 36.000 5.01 0.00 0.00 1.40
351 352 7.963532 AGAGACGAGGCCATATAGAAAATAAA 58.036 34.615 5.01 0.00 0.00 1.40
352 353 8.429641 AGAGACGAGGCCATATAGAAAATAAAA 58.570 33.333 5.01 0.00 0.00 1.52
353 354 9.220767 GAGACGAGGCCATATAGAAAATAAAAT 57.779 33.333 5.01 0.00 0.00 1.82
354 355 9.574516 AGACGAGGCCATATAGAAAATAAAATT 57.425 29.630 5.01 0.00 0.00 1.82
575 579 1.008995 CCGAACCAAAACCACAGCG 60.009 57.895 0.00 0.00 0.00 5.18
611 646 0.392060 CTAAACTACCCCGTGGCACC 60.392 60.000 12.86 0.00 33.59 5.01
635 670 1.213296 CTATTACCTGTGGGGCCAGT 58.787 55.000 4.39 0.00 39.10 4.00
637 672 1.863155 ATTACCTGTGGGGCCAGTGG 61.863 60.000 4.39 4.20 39.10 4.00
745 780 2.347490 CACCTCACTTCCCGGGTG 59.653 66.667 22.86 17.23 42.29 4.61
768 808 4.828925 GCTGCCCTGTCTCGAGCC 62.829 72.222 7.81 0.00 0.00 4.70
937 988 0.034337 AGCCGTCCGTGAGCTTTTAA 59.966 50.000 0.00 0.00 31.27 1.52
954 1005 1.500474 TAACTGCTGGGATCAGAGGG 58.500 55.000 0.00 0.00 43.49 4.30
964 1015 0.178935 GATCAGAGGGGAGAGAGGGG 60.179 65.000 0.00 0.00 0.00 4.79
1363 1426 0.819582 AATTCCATTTCTGCCTGCGG 59.180 50.000 0.00 0.00 0.00 5.69
1364 1427 1.039233 ATTCCATTTCTGCCTGCGGG 61.039 55.000 7.41 7.41 0.00 6.13
1483 1547 4.520846 CACGCGGCCGATTTGCTC 62.521 66.667 33.48 8.16 38.29 4.26
1557 1621 5.105063 GCTGATTAGAAGCCAAATTCAACC 58.895 41.667 0.00 0.00 34.45 3.77
1578 1642 1.393883 GCTAGTGCGGTTTCTGTTAGC 59.606 52.381 0.00 0.00 0.00 3.09
1588 1652 3.211045 GTTTCTGTTAGCAGGTGGTTGA 58.789 45.455 6.75 0.00 42.78 3.18
1601 1665 2.224066 GGTGGTTGAGAGTATGCGCTAT 60.224 50.000 9.73 3.00 0.00 2.97
1657 1721 1.508632 TGGAAAGTACTTCGTGCTGC 58.491 50.000 8.95 0.00 34.56 5.25
1733 1801 7.880713 AGAGGAACATAGAAGTTCTCTTTTTCC 59.119 37.037 9.12 15.73 45.52 3.13
1747 1815 6.453092 TCTCTTTTTCCGTACTAGTTGGAAG 58.547 40.000 21.58 14.45 42.36 3.46
1749 1817 6.819284 TCTTTTTCCGTACTAGTTGGAAGAA 58.181 36.000 21.58 21.44 42.36 2.52
1750 1818 6.703165 TCTTTTTCCGTACTAGTTGGAAGAAC 59.297 38.462 21.58 4.89 42.36 3.01
1751 1819 5.534207 TTTCCGTACTAGTTGGAAGAACA 57.466 39.130 21.58 10.32 42.36 3.18
1792 1940 2.349155 CGCGGTTGTTAGAGTTGTTTCC 60.349 50.000 0.00 0.00 0.00 3.13
1829 1977 7.718334 TTCTTCTCTGGAAAGGTTTTTCTTT 57.282 32.000 0.69 0.00 41.92 2.52
1839 1987 6.266786 GGAAAGGTTTTTCTTTAGGGACATGA 59.733 38.462 0.00 0.00 41.92 3.07
2000 2148 2.278332 AGGGTTTTTCTGGACAGAGC 57.722 50.000 1.92 0.00 38.88 4.09
2014 2162 3.128242 GGACAGAGCTTCATGATTGGTTG 59.872 47.826 0.00 3.41 0.00 3.77
2030 2178 5.590530 TTGGTTGTTAAGATGTGTGCTTT 57.409 34.783 0.00 0.00 0.00 3.51
2174 2323 3.616956 TGATTCTGCCGAGAATGACTT 57.383 42.857 4.13 0.00 47.00 3.01
2222 2371 4.595762 ATCTGAAAACATGCTGCAAACT 57.404 36.364 6.36 0.00 0.00 2.66
2334 2483 4.230657 CGGATAACCTCATAAAGCTCTCG 58.769 47.826 0.00 0.00 0.00 4.04
2511 2660 0.395724 AAATGCAGTTCGGGATCCCC 60.396 55.000 25.73 11.42 41.09 4.81
2712 2861 5.136105 ACTTCAAAGATGACTTCAAAGCCT 58.864 37.500 0.00 0.00 34.61 4.58
2832 2981 7.694388 TTCAACTCCAGAAATATACGAATCG 57.306 36.000 0.00 0.00 0.00 3.34
2858 3007 1.067071 GGGTAGTTCTTGTCAGGGTCG 60.067 57.143 0.00 0.00 0.00 4.79
2919 3068 1.340114 CCAGCTAAGGTTCCCAAGACC 60.340 57.143 0.00 0.00 37.44 3.85
2922 3071 3.199946 CAGCTAAGGTTCCCAAGACCATA 59.800 47.826 0.00 0.00 39.71 2.74
2955 3104 3.134442 TGCCCTTGAAACAAATGCTTTCT 59.866 39.130 0.00 0.00 0.00 2.52
2969 3118 3.415212 TGCTTTCTGAGGAGAACAATGG 58.585 45.455 0.00 0.00 37.97 3.16
3060 3209 2.028130 CAATGGCGAGGCAGATTCC 58.972 57.895 5.43 0.00 0.00 3.01
3090 3239 1.417890 CCGGTTGCTCTTATGGAGGAT 59.582 52.381 0.00 0.00 41.89 3.24
3111 3260 1.990060 TAGCAGTGAGGGGCAGTCC 60.990 63.158 0.00 0.00 0.00 3.85
3132 3281 3.978723 CTCGTCACCTGCTGAGCGG 62.979 68.421 6.22 6.22 34.23 5.52
3211 3360 0.670546 AACCATGGAGAGCACGAACG 60.671 55.000 21.47 0.00 0.00 3.95
4093 4252 2.033372 TCCGCGGGTCTGAATAATACA 58.967 47.619 27.83 0.00 0.00 2.29
4095 4254 2.223971 CCGCGGGTCTGAATAATACAGT 60.224 50.000 20.10 0.00 36.81 3.55
4134 4293 1.593196 TGCTTCCTGTCAGGTTTTCG 58.407 50.000 18.65 5.27 36.53 3.46
4137 4296 0.536460 TTCCTGTCAGGTTTTCGGGC 60.536 55.000 18.65 0.00 36.53 6.13
4141 4326 4.257654 TCAGGTTTTCGGGCGCCA 62.258 61.111 30.85 5.28 0.00 5.69
4142 4327 3.291383 CAGGTTTTCGGGCGCCAA 61.291 61.111 30.85 12.67 0.00 4.52
4179 4364 4.258543 TGAATTCCCCGTACAACTGATTC 58.741 43.478 2.27 0.00 0.00 2.52
4189 4375 1.061799 CAACTGATTCGCGTTGCTGC 61.062 55.000 5.77 0.00 34.77 5.25
4203 4389 4.496341 GCGTTGCTGCTATGATATGTTTGT 60.496 41.667 7.48 0.00 0.00 2.83
4326 4515 3.680777 TCAAAAGGAGTTTTCCCCTGT 57.319 42.857 0.00 0.00 45.24 4.00
4334 4523 3.239449 GAGTTTTCCCCTGTCCCATTTT 58.761 45.455 0.00 0.00 0.00 1.82
4400 4589 0.815615 CGGGATCAGCCAAAGTAGCC 60.816 60.000 0.00 0.00 38.95 3.93
4431 4644 3.637998 AAAAGAGAGCATGCTTGTGTG 57.362 42.857 23.61 0.00 0.00 3.82
4475 4688 4.315803 TCTTTCCGTTCACAGATTTCTCC 58.684 43.478 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.451354 AGTAACCCATTTGTACACCAAAGT 58.549 37.500 0.00 0.00 45.79 2.66
4 5 6.793505 AAAGTAACCCATTTGTACACCAAA 57.206 33.333 0.00 0.00 46.59 3.28
5 6 6.793505 AAAAGTAACCCATTTGTACACCAA 57.206 33.333 0.00 0.00 0.00 3.67
6 7 6.793505 AAAAAGTAACCCATTTGTACACCA 57.206 33.333 0.00 0.00 0.00 4.17
7 8 7.014518 ACCTAAAAAGTAACCCATTTGTACACC 59.985 37.037 0.00 0.00 0.00 4.16
8 9 7.863877 CACCTAAAAAGTAACCCATTTGTACAC 59.136 37.037 0.00 0.00 0.00 2.90
9 10 7.014422 CCACCTAAAAAGTAACCCATTTGTACA 59.986 37.037 0.00 0.00 0.00 2.90
10 11 7.231115 TCCACCTAAAAAGTAACCCATTTGTAC 59.769 37.037 0.00 0.00 0.00 2.90
11 12 7.296098 TCCACCTAAAAAGTAACCCATTTGTA 58.704 34.615 0.00 0.00 0.00 2.41
12 13 6.137559 TCCACCTAAAAAGTAACCCATTTGT 58.862 36.000 0.00 0.00 0.00 2.83
13 14 6.658188 TCCACCTAAAAAGTAACCCATTTG 57.342 37.500 0.00 0.00 0.00 2.32
14 15 7.678207 TTTCCACCTAAAAAGTAACCCATTT 57.322 32.000 0.00 0.00 0.00 2.32
15 16 7.565768 TCTTTTCCACCTAAAAAGTAACCCATT 59.434 33.333 7.88 0.00 42.00 3.16
16 17 7.070629 TCTTTTCCACCTAAAAAGTAACCCAT 58.929 34.615 7.88 0.00 42.00 4.00
17 18 6.433441 TCTTTTCCACCTAAAAAGTAACCCA 58.567 36.000 7.88 0.00 42.00 4.51
18 19 6.774170 TCTCTTTTCCACCTAAAAAGTAACCC 59.226 38.462 7.88 0.00 42.00 4.11
19 20 7.812690 TCTCTTTTCCACCTAAAAAGTAACC 57.187 36.000 7.88 0.00 42.00 2.85
24 25 9.394477 CGTTTATTCTCTTTTCCACCTAAAAAG 57.606 33.333 2.67 2.67 42.46 2.27
25 26 9.122779 TCGTTTATTCTCTTTTCCACCTAAAAA 57.877 29.630 0.00 0.00 0.00 1.94
26 27 8.680039 TCGTTTATTCTCTTTTCCACCTAAAA 57.320 30.769 0.00 0.00 0.00 1.52
27 28 8.680039 TTCGTTTATTCTCTTTTCCACCTAAA 57.320 30.769 0.00 0.00 0.00 1.85
28 29 8.152246 TCTTCGTTTATTCTCTTTTCCACCTAA 58.848 33.333 0.00 0.00 0.00 2.69
29 30 7.673180 TCTTCGTTTATTCTCTTTTCCACCTA 58.327 34.615 0.00 0.00 0.00 3.08
30 31 6.531021 TCTTCGTTTATTCTCTTTTCCACCT 58.469 36.000 0.00 0.00 0.00 4.00
31 32 6.796705 TCTTCGTTTATTCTCTTTTCCACC 57.203 37.500 0.00 0.00 0.00 4.61
32 33 6.790825 CGTTCTTCGTTTATTCTCTTTTCCAC 59.209 38.462 0.00 0.00 34.52 4.02
33 34 6.073440 CCGTTCTTCGTTTATTCTCTTTTCCA 60.073 38.462 0.00 0.00 37.94 3.53
34 35 6.304882 CCGTTCTTCGTTTATTCTCTTTTCC 58.695 40.000 0.00 0.00 37.94 3.13
35 36 5.789021 GCCGTTCTTCGTTTATTCTCTTTTC 59.211 40.000 0.00 0.00 37.94 2.29
36 37 5.237779 TGCCGTTCTTCGTTTATTCTCTTTT 59.762 36.000 0.00 0.00 37.94 2.27
37 38 4.753107 TGCCGTTCTTCGTTTATTCTCTTT 59.247 37.500 0.00 0.00 37.94 2.52
38 39 4.312443 TGCCGTTCTTCGTTTATTCTCTT 58.688 39.130 0.00 0.00 37.94 2.85
39 40 3.921677 TGCCGTTCTTCGTTTATTCTCT 58.078 40.909 0.00 0.00 37.94 3.10
40 41 3.924686 TCTGCCGTTCTTCGTTTATTCTC 59.075 43.478 0.00 0.00 37.94 2.87
41 42 3.921677 TCTGCCGTTCTTCGTTTATTCT 58.078 40.909 0.00 0.00 37.94 2.40
42 43 4.657075 TTCTGCCGTTCTTCGTTTATTC 57.343 40.909 0.00 0.00 37.94 1.75
43 44 4.753107 TCTTTCTGCCGTTCTTCGTTTATT 59.247 37.500 0.00 0.00 37.94 1.40
44 45 4.312443 TCTTTCTGCCGTTCTTCGTTTAT 58.688 39.130 0.00 0.00 37.94 1.40
45 46 3.719924 TCTTTCTGCCGTTCTTCGTTTA 58.280 40.909 0.00 0.00 37.94 2.01
46 47 2.557317 TCTTTCTGCCGTTCTTCGTTT 58.443 42.857 0.00 0.00 37.94 3.60
47 48 2.234300 TCTTTCTGCCGTTCTTCGTT 57.766 45.000 0.00 0.00 37.94 3.85
48 49 1.865340 GTTCTTTCTGCCGTTCTTCGT 59.135 47.619 0.00 0.00 37.94 3.85
49 50 1.136611 CGTTCTTTCTGCCGTTCTTCG 60.137 52.381 0.00 0.00 39.52 3.79
50 51 1.194772 CCGTTCTTTCTGCCGTTCTTC 59.805 52.381 0.00 0.00 0.00 2.87
51 52 1.202604 TCCGTTCTTTCTGCCGTTCTT 60.203 47.619 0.00 0.00 0.00 2.52
52 53 0.391597 TCCGTTCTTTCTGCCGTTCT 59.608 50.000 0.00 0.00 0.00 3.01
53 54 0.790814 CTCCGTTCTTTCTGCCGTTC 59.209 55.000 0.00 0.00 0.00 3.95
54 55 0.602905 CCTCCGTTCTTTCTGCCGTT 60.603 55.000 0.00 0.00 0.00 4.44
55 56 1.004918 CCTCCGTTCTTTCTGCCGT 60.005 57.895 0.00 0.00 0.00 5.68
56 57 2.391389 GCCTCCGTTCTTTCTGCCG 61.391 63.158 0.00 0.00 0.00 5.69
57 58 0.889186 TTGCCTCCGTTCTTTCTGCC 60.889 55.000 0.00 0.00 0.00 4.85
58 59 0.519077 CTTGCCTCCGTTCTTTCTGC 59.481 55.000 0.00 0.00 0.00 4.26
59 60 1.160137 CCTTGCCTCCGTTCTTTCTG 58.840 55.000 0.00 0.00 0.00 3.02
60 61 0.036875 CCCTTGCCTCCGTTCTTTCT 59.963 55.000 0.00 0.00 0.00 2.52
61 62 0.960861 CCCCTTGCCTCCGTTCTTTC 60.961 60.000 0.00 0.00 0.00 2.62
62 63 1.074951 CCCCTTGCCTCCGTTCTTT 59.925 57.895 0.00 0.00 0.00 2.52
63 64 1.208165 ATCCCCTTGCCTCCGTTCTT 61.208 55.000 0.00 0.00 0.00 2.52
64 65 0.326238 TATCCCCTTGCCTCCGTTCT 60.326 55.000 0.00 0.00 0.00 3.01
65 66 0.544697 TTATCCCCTTGCCTCCGTTC 59.455 55.000 0.00 0.00 0.00 3.95
66 67 0.546598 CTTATCCCCTTGCCTCCGTT 59.453 55.000 0.00 0.00 0.00 4.44
67 68 1.984288 GCTTATCCCCTTGCCTCCGT 61.984 60.000 0.00 0.00 0.00 4.69
68 69 1.227973 GCTTATCCCCTTGCCTCCG 60.228 63.158 0.00 0.00 0.00 4.63
69 70 0.109532 GAGCTTATCCCCTTGCCTCC 59.890 60.000 0.00 0.00 0.00 4.30
70 71 1.071542 GAGAGCTTATCCCCTTGCCTC 59.928 57.143 0.00 0.00 0.00 4.70
71 72 1.135960 GAGAGCTTATCCCCTTGCCT 58.864 55.000 0.00 0.00 0.00 4.75
72 73 0.250081 CGAGAGCTTATCCCCTTGCC 60.250 60.000 0.00 0.00 0.00 4.52
73 74 0.466124 ACGAGAGCTTATCCCCTTGC 59.534 55.000 0.00 0.00 0.00 4.01
74 75 1.202580 CCACGAGAGCTTATCCCCTTG 60.203 57.143 0.00 0.00 0.00 3.61
75 76 1.123928 CCACGAGAGCTTATCCCCTT 58.876 55.000 0.00 0.00 0.00 3.95
76 77 0.760945 CCCACGAGAGCTTATCCCCT 60.761 60.000 0.00 0.00 0.00 4.79
77 78 0.759436 TCCCACGAGAGCTTATCCCC 60.759 60.000 0.00 0.00 0.00 4.81
78 79 0.676736 CTCCCACGAGAGCTTATCCC 59.323 60.000 0.00 0.00 38.52 3.85
79 80 0.676736 CCTCCCACGAGAGCTTATCC 59.323 60.000 0.00 0.00 38.52 2.59
80 81 1.067821 CACCTCCCACGAGAGCTTATC 59.932 57.143 0.00 0.00 38.52 1.75
81 82 1.115467 CACCTCCCACGAGAGCTTAT 58.885 55.000 0.00 0.00 38.52 1.73
82 83 0.970937 CCACCTCCCACGAGAGCTTA 60.971 60.000 0.00 0.00 38.52 3.09
83 84 2.286523 CCACCTCCCACGAGAGCTT 61.287 63.158 0.00 0.00 38.52 3.74
84 85 2.681778 CCACCTCCCACGAGAGCT 60.682 66.667 0.00 0.00 38.52 4.09
85 86 2.232298 CTTCCACCTCCCACGAGAGC 62.232 65.000 0.00 0.00 38.52 4.09
86 87 0.612174 TCTTCCACCTCCCACGAGAG 60.612 60.000 0.00 0.00 38.52 3.20
87 88 0.178944 TTCTTCCACCTCCCACGAGA 60.179 55.000 0.00 0.00 38.52 4.04
88 89 0.247736 CTTCTTCCACCTCCCACGAG 59.752 60.000 0.00 0.00 35.72 4.18
89 90 1.827399 GCTTCTTCCACCTCCCACGA 61.827 60.000 0.00 0.00 0.00 4.35
90 91 1.376037 GCTTCTTCCACCTCCCACG 60.376 63.158 0.00 0.00 0.00 4.94
91 92 0.322008 CAGCTTCTTCCACCTCCCAC 60.322 60.000 0.00 0.00 0.00 4.61
92 93 1.492133 CCAGCTTCTTCCACCTCCCA 61.492 60.000 0.00 0.00 0.00 4.37
93 94 1.301293 CCAGCTTCTTCCACCTCCC 59.699 63.158 0.00 0.00 0.00 4.30
94 95 1.377856 GCCAGCTTCTTCCACCTCC 60.378 63.158 0.00 0.00 0.00 4.30
95 96 1.743252 CGCCAGCTTCTTCCACCTC 60.743 63.158 0.00 0.00 0.00 3.85
96 97 2.217038 TCGCCAGCTTCTTCCACCT 61.217 57.895 0.00 0.00 0.00 4.00
97 98 2.035442 GTCGCCAGCTTCTTCCACC 61.035 63.158 0.00 0.00 0.00 4.61
98 99 2.035442 GGTCGCCAGCTTCTTCCAC 61.035 63.158 0.00 0.00 0.00 4.02
99 100 2.347490 GGTCGCCAGCTTCTTCCA 59.653 61.111 0.00 0.00 0.00 3.53
100 101 2.815647 CGGTCGCCAGCTTCTTCC 60.816 66.667 0.00 0.00 0.00 3.46
101 102 2.815647 CCGGTCGCCAGCTTCTTC 60.816 66.667 0.00 0.00 0.00 2.87
102 103 4.394712 CCCGGTCGCCAGCTTCTT 62.395 66.667 0.00 0.00 0.00 2.52
123 124 4.083862 GACGACAGGGTCCCAGCC 62.084 72.222 11.55 0.00 35.59 4.85
129 130 0.108019 ACCTTTTGGACGACAGGGTC 59.892 55.000 0.00 0.00 44.07 4.46
130 131 0.179029 CACCTTTTGGACGACAGGGT 60.179 55.000 0.00 0.00 44.07 4.34
131 132 2.629002 CACCTTTTGGACGACAGGG 58.371 57.895 0.00 0.00 44.07 4.45
150 151 0.105039 CCAGCCCTAGGACAATCGTC 59.895 60.000 11.48 0.00 41.80 4.20
151 152 0.325296 TCCAGCCCTAGGACAATCGT 60.325 55.000 11.48 0.00 0.00 3.73
152 153 2.516448 TCCAGCCCTAGGACAATCG 58.484 57.895 11.48 0.00 0.00 3.34
158 159 1.379977 CTGTCGTCCAGCCCTAGGA 60.380 63.158 11.48 0.00 33.59 2.94
159 160 2.427245 CCTGTCGTCCAGCCCTAGG 61.427 68.421 0.06 0.06 40.06 3.02
160 161 3.082579 GCCTGTCGTCCAGCCCTAG 62.083 68.421 0.18 0.00 40.06 3.02
161 162 3.075005 GCCTGTCGTCCAGCCCTA 61.075 66.667 0.18 0.00 40.06 3.53
164 165 4.767255 CAGGCCTGTCGTCCAGCC 62.767 72.222 25.53 2.50 40.06 4.85
165 166 4.008933 ACAGGCCTGTCGTCCAGC 62.009 66.667 33.20 0.00 40.24 4.85
166 167 2.047844 CACAGGCCTGTCGTCCAG 60.048 66.667 35.79 19.42 42.83 3.86
167 168 2.842462 ACACAGGCCTGTCGTCCA 60.842 61.111 35.79 0.00 42.83 4.02
168 169 2.048127 GACACAGGCCTGTCGTCC 60.048 66.667 34.81 24.81 42.83 4.79
172 173 1.373497 CAGACGACACAGGCCTGTC 60.373 63.158 35.79 23.87 42.83 3.51
173 174 2.737180 CAGACGACACAGGCCTGT 59.263 61.111 33.20 33.20 46.17 4.00
174 175 2.047844 CCAGACGACACAGGCCTG 60.048 66.667 31.60 31.60 0.00 4.85
175 176 3.314331 CCCAGACGACACAGGCCT 61.314 66.667 0.00 0.00 0.00 5.19
176 177 4.394712 CCCCAGACGACACAGGCC 62.395 72.222 0.00 0.00 0.00 5.19
178 179 4.394712 GGCCCCAGACGACACAGG 62.395 72.222 0.00 0.00 0.00 4.00
179 180 4.394712 GGGCCCCAGACGACACAG 62.395 72.222 12.23 0.00 0.00 3.66
211 212 4.227134 CTCCCTCGTCCCGGCATG 62.227 72.222 0.00 0.00 0.00 4.06
212 213 4.458829 TCTCCCTCGTCCCGGCAT 62.459 66.667 0.00 0.00 0.00 4.40
217 218 2.519780 ATCGCTCTCCCTCGTCCC 60.520 66.667 0.00 0.00 0.00 4.46
218 219 2.725008 CATCGCTCTCCCTCGTCC 59.275 66.667 0.00 0.00 0.00 4.79
219 220 2.026879 GCATCGCTCTCCCTCGTC 59.973 66.667 0.00 0.00 0.00 4.20
220 221 3.893763 CGCATCGCTCTCCCTCGT 61.894 66.667 0.00 0.00 0.00 4.18
221 222 3.586961 TCGCATCGCTCTCCCTCG 61.587 66.667 0.00 0.00 0.00 4.63
222 223 2.026879 GTCGCATCGCTCTCCCTC 59.973 66.667 0.00 0.00 0.00 4.30
223 224 3.893763 CGTCGCATCGCTCTCCCT 61.894 66.667 0.00 0.00 0.00 4.20
224 225 4.194720 ACGTCGCATCGCTCTCCC 62.195 66.667 0.00 0.00 0.00 4.30
225 226 2.951745 CACGTCGCATCGCTCTCC 60.952 66.667 0.00 0.00 0.00 3.71
226 227 2.951745 CCACGTCGCATCGCTCTC 60.952 66.667 0.00 0.00 0.00 3.20
227 228 4.498520 CCCACGTCGCATCGCTCT 62.499 66.667 0.00 0.00 0.00 4.09
263 264 4.065281 GTCCGGTCCTCCACGTGG 62.065 72.222 29.26 29.26 0.00 4.94
264 265 3.299977 TGTCCGGTCCTCCACGTG 61.300 66.667 9.08 9.08 0.00 4.49
265 266 3.300765 GTGTCCGGTCCTCCACGT 61.301 66.667 0.00 0.00 0.00 4.49
266 267 4.065281 GGTGTCCGGTCCTCCACG 62.065 72.222 0.00 0.00 0.00 4.94
267 268 2.603776 AGGTGTCCGGTCCTCCAC 60.604 66.667 0.00 1.96 0.00 4.02
268 269 2.603473 CAGGTGTCCGGTCCTCCA 60.603 66.667 0.00 0.00 30.91 3.86
269 270 2.603776 ACAGGTGTCCGGTCCTCC 60.604 66.667 0.00 4.06 30.91 4.30
270 271 2.971452 GACAGGTGTCCGGTCCTC 59.029 66.667 0.00 0.00 41.62 3.71
271 272 2.989824 CGACAGGTGTCCGGTCCT 60.990 66.667 0.00 5.52 43.89 3.85
272 273 3.278592 GACGACAGGTGTCCGGTCC 62.279 68.421 0.00 2.95 43.89 4.46
273 274 2.257676 GACGACAGGTGTCCGGTC 59.742 66.667 0.00 8.57 43.46 4.79
274 275 3.300765 GGACGACAGGTGTCCGGT 61.301 66.667 0.00 0.00 45.82 5.28
278 279 1.765230 ATAGGAGGACGACAGGTGTC 58.235 55.000 0.00 0.00 41.47 3.67
279 280 2.933573 CTATAGGAGGACGACAGGTGT 58.066 52.381 0.00 0.00 0.00 4.16
281 282 4.740871 GGCCTATAGGAGGACGACAGGT 62.741 59.091 23.61 0.00 46.28 4.00
282 283 2.160432 GGCCTATAGGAGGACGACAGG 61.160 61.905 23.61 0.00 46.28 4.00
283 284 1.249407 GGCCTATAGGAGGACGACAG 58.751 60.000 23.61 0.00 46.28 3.51
284 285 3.434053 GGCCTATAGGAGGACGACA 57.566 57.895 23.61 0.00 46.28 4.35
291 292 3.682792 CCCGTCGGCCTATAGGAG 58.317 66.667 23.61 14.87 37.39 3.69
316 317 1.707239 CCTCGTCTCTTCGGAGGACG 61.707 65.000 21.71 21.71 41.84 4.79
317 318 1.995646 GCCTCGTCTCTTCGGAGGAC 61.996 65.000 10.33 4.40 42.08 3.85
318 319 1.749638 GCCTCGTCTCTTCGGAGGA 60.750 63.158 10.33 0.00 42.08 3.71
319 320 2.776913 GGCCTCGTCTCTTCGGAGG 61.777 68.421 0.00 1.99 42.08 4.30
320 321 1.388065 ATGGCCTCGTCTCTTCGGAG 61.388 60.000 3.32 0.00 43.09 4.63
321 322 0.106868 TATGGCCTCGTCTCTTCGGA 60.107 55.000 3.32 0.00 0.00 4.55
322 323 0.962489 ATATGGCCTCGTCTCTTCGG 59.038 55.000 3.32 0.00 0.00 4.30
323 324 3.075148 TCTATATGGCCTCGTCTCTTCG 58.925 50.000 3.32 0.00 0.00 3.79
324 325 5.455056 TTTCTATATGGCCTCGTCTCTTC 57.545 43.478 3.32 0.00 0.00 2.87
325 326 5.871396 TTTTCTATATGGCCTCGTCTCTT 57.129 39.130 3.32 0.00 0.00 2.85
326 327 7.540474 TTATTTTCTATATGGCCTCGTCTCT 57.460 36.000 3.32 0.00 0.00 3.10
327 328 8.603242 TTTTATTTTCTATATGGCCTCGTCTC 57.397 34.615 3.32 0.00 0.00 3.36
328 329 9.574516 AATTTTATTTTCTATATGGCCTCGTCT 57.425 29.630 3.32 0.00 0.00 4.18
536 537 2.038659 GTGGGGAAGAGAGAGAGGATG 58.961 57.143 0.00 0.00 0.00 3.51
537 538 1.062505 GGTGGGGAAGAGAGAGAGGAT 60.063 57.143 0.00 0.00 0.00 3.24
575 579 2.566529 GCTTGGGGTAAAGCGTGC 59.433 61.111 0.00 0.00 42.86 5.34
582 586 2.577563 GGGGTAGTTTAGCTTGGGGTAA 59.422 50.000 0.00 0.00 34.18 2.85
583 587 2.199208 GGGGTAGTTTAGCTTGGGGTA 58.801 52.381 0.00 0.00 0.00 3.69
586 590 0.616891 ACGGGGTAGTTTAGCTTGGG 59.383 55.000 0.00 0.00 0.00 4.12
587 591 1.677820 CCACGGGGTAGTTTAGCTTGG 60.678 57.143 0.00 0.00 0.00 3.61
589 593 0.035725 GCCACGGGGTAGTTTAGCTT 60.036 55.000 5.12 0.00 36.17 3.74
611 646 1.472728 GCCCCACAGGTAATAGACACG 60.473 57.143 0.00 0.00 38.26 4.49
617 652 0.916086 CACTGGCCCCACAGGTAATA 59.084 55.000 0.00 0.00 42.75 0.98
745 780 1.294659 CGAGACAGGGCAGCAAAGAC 61.295 60.000 0.00 0.00 0.00 3.01
768 808 1.327460 CTTCTCTCTCTCGCTCACTCG 59.673 57.143 0.00 0.00 0.00 4.18
775 815 1.676006 CCCTTCTCTTCTCTCTCTCGC 59.324 57.143 0.00 0.00 0.00 5.03
776 816 3.275617 TCCCTTCTCTTCTCTCTCTCG 57.724 52.381 0.00 0.00 0.00 4.04
824 865 1.163554 CTTGCTTCTTCCACTGGCTC 58.836 55.000 0.00 0.00 0.00 4.70
937 988 1.692042 CCCCTCTGATCCCAGCAGT 60.692 63.158 0.00 0.00 40.20 4.40
964 1015 4.468689 GCTCCCTGCGTACCACCC 62.469 72.222 0.00 0.00 0.00 4.61
1284 1344 2.667470 CTGGTAGGCTAGCACTAGGAA 58.333 52.381 21.67 0.06 33.87 3.36
1297 1359 3.930012 GGCGGCTAGGCTGGTAGG 61.930 72.222 15.11 0.00 42.90 3.18
1318 1381 0.109597 GCAGCGATTTGGTTCAGTGG 60.110 55.000 0.00 0.00 0.00 4.00
1364 1427 3.986006 TCCACAGGGACGACGCAC 61.986 66.667 4.64 0.00 38.64 5.34
1481 1545 1.823295 CTATCCCACCACCACCGAG 59.177 63.158 0.00 0.00 0.00 4.63
1483 1547 2.189521 GCTATCCCACCACCACCG 59.810 66.667 0.00 0.00 0.00 4.94
1484 1548 1.224592 CAGCTATCCCACCACCACC 59.775 63.158 0.00 0.00 0.00 4.61
1485 1549 0.328258 AACAGCTATCCCACCACCAC 59.672 55.000 0.00 0.00 0.00 4.16
1543 1607 2.228822 CACTAGCGGTTGAATTTGGCTT 59.771 45.455 2.41 0.00 35.28 4.35
1578 1642 1.645034 CGCATACTCTCAACCACCTG 58.355 55.000 0.00 0.00 0.00 4.00
1588 1652 6.516718 ACAACAAGATAATAGCGCATACTCT 58.483 36.000 11.47 1.56 0.00 3.24
1601 1665 8.892723 GTGATCACCATGATTACAACAAGATAA 58.107 33.333 15.31 0.00 41.38 1.75
1657 1721 0.400213 TGCCCCCACTGTTTGTAGAG 59.600 55.000 0.00 0.00 0.00 2.43
1733 1801 8.928270 AATTCTATGTTCTTCCAACTAGTACG 57.072 34.615 0.00 0.00 0.00 3.67
1747 1815 8.261908 GCGCAAAATCACATTAATTCTATGTTC 58.738 33.333 0.30 0.00 34.11 3.18
1749 1817 6.414694 CGCGCAAAATCACATTAATTCTATGT 59.585 34.615 8.75 1.36 36.70 2.29
1750 1818 6.129378 CCGCGCAAAATCACATTAATTCTATG 60.129 38.462 8.75 0.00 0.00 2.23
1751 1819 5.914635 CCGCGCAAAATCACATTAATTCTAT 59.085 36.000 8.75 0.00 0.00 1.98
1792 1940 9.748708 TTTCCAGAGAAGAAAATAAACACATTG 57.251 29.630 0.00 0.00 32.35 2.82
1829 1977 6.542821 ACTTTTCTTGAATGTCATGTCCCTA 58.457 36.000 0.00 0.00 0.00 3.53
1839 1987 6.266168 TGTGACACAACTTTTCTTGAATGT 57.734 33.333 5.62 0.00 0.00 2.71
2000 2148 7.539710 CACACATCTTAACAACCAATCATGAAG 59.460 37.037 0.00 0.00 0.00 3.02
2030 2178 9.856488 TGTAAACAACAAAATACTACAGCAAAA 57.144 25.926 0.00 0.00 34.29 2.44
2055 2204 9.968870 GAATGTAAGTAGGGATAGAGTTACTTG 57.031 37.037 6.12 0.00 37.07 3.16
2174 2323 0.466007 TTGCTGAGCCTGCAAAGTCA 60.466 50.000 0.23 0.00 43.24 3.41
2222 2371 3.928754 ACACTCCCATGATCTAGGCTTA 58.071 45.455 0.00 0.00 0.00 3.09
2334 2483 0.620556 ACCATGTCACCCCATCTGTC 59.379 55.000 0.00 0.00 0.00 3.51
2511 2660 1.794701 CAATCGCAGACCACCGATATG 59.205 52.381 0.00 0.00 42.74 1.78
2712 2861 1.843851 CCTGACCCCTGCTGGTATTTA 59.156 52.381 9.00 0.00 39.24 1.40
2832 2981 0.108281 GACAAGAACTACCCCTCGGC 60.108 60.000 0.00 0.00 0.00 5.54
2858 3007 1.626356 TACTGGTGCAGGATCCTGGC 61.626 60.000 36.92 28.93 43.77 4.85
2919 3068 4.780815 TCAAGGGCAGTGGTAGAAATATG 58.219 43.478 0.00 0.00 0.00 1.78
2922 3071 3.806949 TTCAAGGGCAGTGGTAGAAAT 57.193 42.857 0.00 0.00 0.00 2.17
2955 3104 1.351017 GTGTCCCCATTGTTCTCCTCA 59.649 52.381 0.00 0.00 0.00 3.86
2969 3118 3.562779 TTCGCCTTCGACGTGTCCC 62.563 63.158 0.00 0.00 45.43 4.46
3042 3191 0.749091 TGGAATCTGCCTCGCCATTG 60.749 55.000 0.00 0.00 0.00 2.82
3090 3239 1.127567 ACTGCCCCTCACTGCTACAA 61.128 55.000 0.00 0.00 0.00 2.41
3132 3281 1.135489 TCTTGATGTCTGTACCGCGAC 60.135 52.381 8.23 0.00 0.00 5.19
3211 3360 1.258445 TTCTCCCTGGAGCTCGGAAC 61.258 60.000 7.83 0.00 41.71 3.62
4075 4234 3.093717 ACTGTATTATTCAGACCCGCG 57.906 47.619 0.00 0.00 36.81 6.46
4093 4252 2.645838 TTCTTCAGCCTCAGCAAACT 57.354 45.000 0.00 0.00 43.56 2.66
4095 4254 3.379372 GCATATTCTTCAGCCTCAGCAAA 59.621 43.478 0.00 0.00 43.56 3.68
4150 4335 1.483415 GTACGGGGAATTCAGCCTGTA 59.517 52.381 14.93 14.93 0.00 2.74
4153 4338 0.988832 TTGTACGGGGAATTCAGCCT 59.011 50.000 7.93 0.00 0.00 4.58
4163 4348 1.418342 CGCGAATCAGTTGTACGGGG 61.418 60.000 0.00 0.00 34.34 5.73
4165 4350 1.065358 AACGCGAATCAGTTGTACGG 58.935 50.000 15.93 0.00 0.00 4.02
4179 4364 1.794701 ACATATCATAGCAGCAACGCG 59.205 47.619 3.53 3.53 36.85 6.01
4203 4389 2.960384 CCCCATGCATTGATAGAAAGCA 59.040 45.455 0.00 0.00 39.79 3.91
4303 4492 4.151883 CAGGGGAAAACTCCTTTTGATCA 58.848 43.478 0.00 0.00 29.21 2.92
4305 4494 4.152647 GACAGGGGAAAACTCCTTTTGAT 58.847 43.478 0.00 0.00 29.21 2.57
4326 4515 4.224594 TGCCTCATTTGCAATAAAATGGGA 59.775 37.500 9.80 2.82 46.62 4.37
4334 4523 6.286758 TGTTTTTCTTGCCTCATTTGCAATA 58.713 32.000 0.00 0.00 46.68 1.90
4431 4644 0.173255 AACACCCAAATGCTATGCGC 59.827 50.000 0.00 0.00 39.77 6.09
4475 4688 1.878088 CATTTCTCAGCCATGATCCCG 59.122 52.381 0.00 0.00 34.12 5.14


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

AutoCloner maintained by Alex Coulton.