Multiple sequence alignment - TraesCS5A01G391200

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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 TraesCS5A01G391200 chr5A 100.000 3594 0 0 1 3594 586306170 586309763 0.000000e+00 6637
1 TraesCS5A01G391200 chr5A 77.049 427 58 16 23 418 138203914 138204331 3.640000e-50 209
2 TraesCS5A01G391200 chr5D 88.761 3043 125 80 638 3594 465905164 465908075 0.000000e+00 3524
3 TraesCS5A01G391200 chr5D 92.793 222 11 5 413 629 465904904 465905125 2.080000e-82 316
4 TraesCS5A01G391200 chr5B 87.681 3044 171 85 251 3165 573141155 573144123 0.000000e+00 3356
5 TraesCS5A01G391200 chr5B 90.558 233 13 4 3166 3392 573144179 573144408 2.100000e-77 300
6 TraesCS5A01G391200 chr5B 88.462 208 12 6 3386 3592 573145563 573145759 1.290000e-59 241
7 TraesCS5A01G391200 chr1D 88.412 233 22 5 23 251 30227926 30227695 3.530000e-70 276
8 TraesCS5A01G391200 chr1D 84.519 239 29 7 24 257 86784728 86784493 2.790000e-56 230
9 TraesCS5A01G391200 chr1D 82.700 237 36 5 24 257 37961109 37961343 4.700000e-49 206
10 TraesCS5A01G391200 chr1B 79.384 422 52 19 25 416 264347561 264347977 7.650000e-67 265
11 TraesCS5A01G391200 chr7D 85.062 241 27 7 24 257 518053294 518053056 1.670000e-58 237
12 TraesCS5A01G391200 chrUn 83.898 236 30 8 26 257 50911086 50911317 6.040000e-53 219
13 TraesCS5A01G391200 chr2B 77.176 425 62 20 21 416 152499445 152499027 7.820000e-52 215
14 TraesCS5A01G391200 chr3B 82.969 229 34 5 26 251 628406714 628406488 6.080000e-48 202


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 TraesCS5A01G391200 chr5A 586306170 586309763 3593 False 6637 6637 100.000000 1 3594 1 chr5A.!!$F2 3593
1 TraesCS5A01G391200 chr5D 465904904 465908075 3171 False 1920 3524 90.777000 413 3594 2 chr5D.!!$F1 3181
2 TraesCS5A01G391200 chr5B 573141155 573145759 4604 False 1299 3356 88.900333 251 3592 3 chr5B.!!$F1 3341

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
227 228 0.178981 AATGTGGACAGTGGCAGCTT 60.179 50.0 0.0 0.0 0.0 3.74 F
1072 1149 0.109342 CTCCCCATCCAATTCCCTCG 59.891 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 1468 0.103572 GCAACCGATTCCCGCTACTA 59.896 55.0 0.0 0.0 36.84 1.82 R
2949 3101 0.030908 CGCCTAATCACGACCTCCTC 59.969 60.0 0.0 0.0 0.00 3.71 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
23 24 3.944476 CCTCTCCAGGGAACAAGTG 57.056 57.895 0.00 0.00 35.89 3.16
24 25 0.326264 CCTCTCCAGGGAACAAGTGG 59.674 60.000 0.00 0.00 35.89 4.00
25 26 0.326264 CTCTCCAGGGAACAAGTGGG 59.674 60.000 0.00 0.00 31.70 4.61
26 27 1.133809 TCTCCAGGGAACAAGTGGGG 61.134 60.000 0.00 0.00 32.51 4.96
27 28 2.142292 CTCCAGGGAACAAGTGGGGG 62.142 65.000 0.00 0.00 31.70 5.40
28 29 2.160171 CCAGGGAACAAGTGGGGGA 61.160 63.158 0.00 0.00 0.00 4.81
29 30 1.380302 CAGGGAACAAGTGGGGGAG 59.620 63.158 0.00 0.00 0.00 4.30
30 31 1.133809 CAGGGAACAAGTGGGGGAGA 61.134 60.000 0.00 0.00 0.00 3.71
31 32 1.134438 AGGGAACAAGTGGGGGAGAC 61.134 60.000 0.00 0.00 0.00 3.36
32 33 1.134438 GGGAACAAGTGGGGGAGACT 61.134 60.000 0.00 0.00 0.00 3.24
33 34 0.771755 GGAACAAGTGGGGGAGACTT 59.228 55.000 0.00 0.00 33.82 3.01
38 39 2.991250 CAAGTGGGGGAGACTTGTATG 58.009 52.381 0.00 0.00 43.55 2.39
39 40 2.571653 CAAGTGGGGGAGACTTGTATGA 59.428 50.000 0.00 0.00 43.55 2.15
40 41 2.472029 AGTGGGGGAGACTTGTATGAG 58.528 52.381 0.00 0.00 0.00 2.90
41 42 2.044492 AGTGGGGGAGACTTGTATGAGA 59.956 50.000 0.00 0.00 0.00 3.27
42 43 3.041946 GTGGGGGAGACTTGTATGAGAT 58.958 50.000 0.00 0.00 0.00 2.75
43 44 3.070302 GTGGGGGAGACTTGTATGAGATC 59.930 52.174 0.00 0.00 0.00 2.75
44 45 3.051803 TGGGGGAGACTTGTATGAGATCT 60.052 47.826 0.00 0.00 0.00 2.75
45 46 3.576550 GGGGGAGACTTGTATGAGATCTC 59.423 52.174 16.21 16.21 35.99 2.75
46 47 4.219115 GGGGAGACTTGTATGAGATCTCA 58.781 47.826 27.03 27.03 44.59 3.27
47 48 4.038642 GGGGAGACTTGTATGAGATCTCAC 59.961 50.000 27.37 16.08 43.11 3.51
48 49 4.646945 GGGAGACTTGTATGAGATCTCACA 59.353 45.833 27.37 18.49 43.11 3.58
49 50 5.304101 GGGAGACTTGTATGAGATCTCACAT 59.696 44.000 27.37 15.28 43.11 3.21
50 51 6.183360 GGGAGACTTGTATGAGATCTCACATT 60.183 42.308 27.37 14.54 43.11 2.71
51 52 7.271511 GGAGACTTGTATGAGATCTCACATTT 58.728 38.462 27.37 14.18 43.11 2.32
52 53 8.417106 GGAGACTTGTATGAGATCTCACATTTA 58.583 37.037 27.37 13.13 43.11 1.40
53 54 9.462174 GAGACTTGTATGAGATCTCACATTTAG 57.538 37.037 27.37 20.49 43.11 1.85
54 55 8.420222 AGACTTGTATGAGATCTCACATTTAGG 58.580 37.037 27.37 15.55 43.11 2.69
55 56 8.083828 ACTTGTATGAGATCTCACATTTAGGT 57.916 34.615 27.37 16.12 43.11 3.08
56 57 7.984050 ACTTGTATGAGATCTCACATTTAGGTG 59.016 37.037 27.37 13.14 43.11 4.00
57 58 7.423844 TGTATGAGATCTCACATTTAGGTGT 57.576 36.000 27.37 10.18 43.11 4.16
82 83 6.683974 ATCATGAGATCAACCCTAAAAACG 57.316 37.500 0.09 0.00 0.00 3.60
83 84 5.556915 TCATGAGATCAACCCTAAAAACGT 58.443 37.500 0.00 0.00 0.00 3.99
84 85 6.703319 TCATGAGATCAACCCTAAAAACGTA 58.297 36.000 0.00 0.00 0.00 3.57
85 86 7.335627 TCATGAGATCAACCCTAAAAACGTAT 58.664 34.615 0.00 0.00 0.00 3.06
86 87 8.479689 TCATGAGATCAACCCTAAAAACGTATA 58.520 33.333 0.00 0.00 0.00 1.47
87 88 9.273016 CATGAGATCAACCCTAAAAACGTATAT 57.727 33.333 0.00 0.00 0.00 0.86
88 89 9.847224 ATGAGATCAACCCTAAAAACGTATATT 57.153 29.630 0.00 0.00 0.00 1.28
89 90 9.675464 TGAGATCAACCCTAAAAACGTATATTT 57.325 29.630 0.00 0.00 0.00 1.40
94 95 9.941325 TCAACCCTAAAAACGTATATTTAGACA 57.059 29.630 20.98 5.84 40.10 3.41
134 135 9.890085 CTGAAATTATTTAACAACATTCATGCG 57.110 29.630 0.00 0.00 0.00 4.73
135 136 9.631452 TGAAATTATTTAACAACATTCATGCGA 57.369 25.926 0.00 0.00 0.00 5.10
137 138 7.684062 ATTATTTAACAACATTCATGCGAGC 57.316 32.000 0.00 0.00 0.00 5.03
138 139 4.764679 TTTAACAACATTCATGCGAGCT 57.235 36.364 0.00 0.00 0.00 4.09
139 140 5.871465 TTTAACAACATTCATGCGAGCTA 57.129 34.783 0.00 0.00 0.00 3.32
140 141 6.435430 TTTAACAACATTCATGCGAGCTAT 57.565 33.333 0.00 0.00 0.00 2.97
141 142 3.957671 ACAACATTCATGCGAGCTATG 57.042 42.857 0.00 0.00 0.00 2.23
142 143 3.273434 ACAACATTCATGCGAGCTATGT 58.727 40.909 0.00 0.00 0.00 2.29
143 144 3.310774 ACAACATTCATGCGAGCTATGTC 59.689 43.478 0.00 0.00 0.00 3.06
144 145 3.465742 ACATTCATGCGAGCTATGTCT 57.534 42.857 0.00 0.00 0.00 3.41
145 146 4.590850 ACATTCATGCGAGCTATGTCTA 57.409 40.909 0.00 0.00 0.00 2.59
146 147 4.302455 ACATTCATGCGAGCTATGTCTAC 58.698 43.478 0.00 0.00 0.00 2.59
147 148 4.202151 ACATTCATGCGAGCTATGTCTACA 60.202 41.667 0.00 0.00 0.00 2.74
148 149 4.385358 TTCATGCGAGCTATGTCTACAA 57.615 40.909 0.00 0.00 0.00 2.41
149 150 3.706698 TCATGCGAGCTATGTCTACAAC 58.293 45.455 0.00 0.00 0.00 3.32
150 151 3.381590 TCATGCGAGCTATGTCTACAACT 59.618 43.478 0.00 0.00 0.00 3.16
151 152 3.868757 TGCGAGCTATGTCTACAACTT 57.131 42.857 0.00 0.00 0.00 2.66
152 153 4.188247 TGCGAGCTATGTCTACAACTTT 57.812 40.909 0.00 0.00 0.00 2.66
153 154 3.926527 TGCGAGCTATGTCTACAACTTTG 59.073 43.478 0.00 0.00 0.00 2.77
154 155 4.174009 GCGAGCTATGTCTACAACTTTGA 58.826 43.478 0.00 0.00 0.00 2.69
155 156 4.625742 GCGAGCTATGTCTACAACTTTGAA 59.374 41.667 0.00 0.00 0.00 2.69
156 157 5.120208 GCGAGCTATGTCTACAACTTTGAAA 59.880 40.000 0.00 0.00 0.00 2.69
157 158 6.347402 GCGAGCTATGTCTACAACTTTGAAAA 60.347 38.462 0.00 0.00 0.00 2.29
158 159 7.572759 CGAGCTATGTCTACAACTTTGAAAAA 58.427 34.615 0.00 0.00 0.00 1.94
179 180 7.755582 AAAAACAGCTGAAAACTTGATGTAC 57.244 32.000 23.35 0.00 29.82 2.90
180 181 6.449635 AAACAGCTGAAAACTTGATGTACA 57.550 33.333 23.35 0.00 29.82 2.90
181 182 6.639632 AACAGCTGAAAACTTGATGTACAT 57.360 33.333 23.35 8.43 29.82 2.29
182 183 6.639632 ACAGCTGAAAACTTGATGTACATT 57.360 33.333 23.35 0.00 0.00 2.71
183 184 7.042797 ACAGCTGAAAACTTGATGTACATTT 57.957 32.000 23.35 0.00 0.00 2.32
184 185 8.165239 ACAGCTGAAAACTTGATGTACATTTA 57.835 30.769 23.35 0.00 0.00 1.40
185 186 8.292448 ACAGCTGAAAACTTGATGTACATTTAG 58.708 33.333 23.35 12.35 0.00 1.85
186 187 8.506437 CAGCTGAAAACTTGATGTACATTTAGA 58.494 33.333 8.42 4.05 0.00 2.10
187 188 8.725148 AGCTGAAAACTTGATGTACATTTAGAG 58.275 33.333 19.26 13.10 0.00 2.43
188 189 8.721478 GCTGAAAACTTGATGTACATTTAGAGA 58.279 33.333 19.26 1.24 0.00 3.10
194 195 9.725019 AACTTGATGTACATTTAGAGATTCACA 57.275 29.630 19.26 3.95 0.00 3.58
195 196 9.725019 ACTTGATGTACATTTAGAGATTCACAA 57.275 29.630 19.26 10.14 0.00 3.33
221 222 9.874205 AAATATAAATTTCAATGTGGACAGTGG 57.126 29.630 7.33 0.00 41.72 4.00
222 223 3.665745 AATTTCAATGTGGACAGTGGC 57.334 42.857 7.33 0.00 41.72 5.01
223 224 2.064434 TTTCAATGTGGACAGTGGCA 57.936 45.000 7.33 0.00 41.72 4.92
224 225 1.608055 TTCAATGTGGACAGTGGCAG 58.392 50.000 7.33 0.00 41.72 4.85
225 226 0.890542 TCAATGTGGACAGTGGCAGC 60.891 55.000 7.33 0.00 41.72 5.25
226 227 0.892358 CAATGTGGACAGTGGCAGCT 60.892 55.000 0.00 0.00 38.19 4.24
227 228 0.178981 AATGTGGACAGTGGCAGCTT 60.179 50.000 0.00 0.00 0.00 3.74
228 229 0.178981 ATGTGGACAGTGGCAGCTTT 60.179 50.000 0.00 0.00 0.00 3.51
229 230 1.102809 TGTGGACAGTGGCAGCTTTG 61.103 55.000 0.00 0.00 0.00 2.77
230 231 2.195567 TGGACAGTGGCAGCTTTGC 61.196 57.895 0.00 0.00 0.00 3.68
231 232 2.253452 GACAGTGGCAGCTTTGCG 59.747 61.111 0.00 0.00 35.24 4.85
232 233 2.516930 ACAGTGGCAGCTTTGCGT 60.517 55.556 0.00 0.00 35.24 5.24
233 234 2.050714 CAGTGGCAGCTTTGCGTG 60.051 61.111 0.00 0.00 35.24 5.34
234 235 2.516930 AGTGGCAGCTTTGCGTGT 60.517 55.556 0.00 0.00 35.24 4.49
235 236 1.227823 AGTGGCAGCTTTGCGTGTA 60.228 52.632 0.00 0.00 35.24 2.90
236 237 0.606401 AGTGGCAGCTTTGCGTGTAT 60.606 50.000 0.00 0.00 35.24 2.29
237 238 0.454957 GTGGCAGCTTTGCGTGTATG 60.455 55.000 0.00 0.00 35.24 2.39
238 239 1.137404 GGCAGCTTTGCGTGTATGG 59.863 57.895 0.00 0.00 35.24 2.74
239 240 1.586154 GGCAGCTTTGCGTGTATGGT 61.586 55.000 0.00 0.00 35.24 3.55
240 241 1.083489 GCAGCTTTGCGTGTATGGTA 58.917 50.000 0.00 0.00 0.00 3.25
241 242 1.202031 GCAGCTTTGCGTGTATGGTAC 60.202 52.381 0.00 0.00 0.00 3.34
242 243 2.346803 CAGCTTTGCGTGTATGGTACT 58.653 47.619 0.00 0.00 0.00 2.73
243 244 2.742053 CAGCTTTGCGTGTATGGTACTT 59.258 45.455 0.00 0.00 0.00 2.24
244 245 3.188460 CAGCTTTGCGTGTATGGTACTTT 59.812 43.478 0.00 0.00 0.00 2.66
245 246 3.188460 AGCTTTGCGTGTATGGTACTTTG 59.812 43.478 0.00 0.00 0.00 2.77
246 247 3.187637 GCTTTGCGTGTATGGTACTTTGA 59.812 43.478 0.00 0.00 0.00 2.69
247 248 4.708601 CTTTGCGTGTATGGTACTTTGAC 58.291 43.478 0.00 0.00 0.00 3.18
248 249 3.388345 TGCGTGTATGGTACTTTGACA 57.612 42.857 0.00 0.00 0.00 3.58
249 250 3.061322 TGCGTGTATGGTACTTTGACAC 58.939 45.455 9.42 9.42 37.61 3.67
256 257 5.937540 TGTATGGTACTTTGACACTTCCATG 59.062 40.000 0.00 0.00 36.01 3.66
270 271 6.173339 ACACTTCCATGAATGTAAGTCGAAT 58.827 36.000 0.00 0.00 35.18 3.34
325 327 8.855110 ACCAAACATTGATGTATGTCTACAAAA 58.145 29.630 0.00 0.00 41.09 2.44
354 356 8.674263 TTGGAAATGCTTGAACATGTATTTTT 57.326 26.923 0.00 0.00 33.41 1.94
433 435 2.883621 GGGAACGAGTCGTCCTCC 59.116 66.667 22.77 22.77 39.99 4.30
478 480 2.868044 GCAAGATATCGCGGTCCTCATT 60.868 50.000 6.13 0.00 0.00 2.57
574 581 2.194201 TTCCGGTCCATTTCTTGTCC 57.806 50.000 0.00 0.00 0.00 4.02
631 638 1.549950 CCACCCAGGGTTAAGCACAAT 60.550 52.381 9.12 0.00 31.02 2.71
635 672 2.432444 CCAGGGTTAAGCACAATTCGA 58.568 47.619 7.03 0.00 0.00 3.71
636 673 2.161609 CCAGGGTTAAGCACAATTCGAC 59.838 50.000 7.03 0.00 0.00 4.20
755 796 1.448540 CCAGCTTGCTCTACCACCG 60.449 63.158 0.00 0.00 0.00 4.94
764 805 1.471119 CTCTACCACCGCCAGTAGAA 58.529 55.000 7.71 0.00 43.21 2.10
818 859 1.592669 GTGCGGTGATCATCCTCGG 60.593 63.158 0.00 0.00 0.00 4.63
819 860 2.029666 GCGGTGATCATCCTCGGG 59.970 66.667 0.00 0.00 0.00 5.14
820 861 2.737180 CGGTGATCATCCTCGGGG 59.263 66.667 0.00 0.00 0.00 5.73
821 862 1.832608 CGGTGATCATCCTCGGGGA 60.833 63.158 6.42 6.42 46.81 4.81
843 884 1.077089 GAGAACGCCGACTAACAGCC 61.077 60.000 0.00 0.00 0.00 4.85
968 1026 0.742635 CTTCTGCCCGGCTTCTTCTC 60.743 60.000 11.61 0.00 0.00 2.87
969 1027 2.124942 CTGCCCGGCTTCTTCTCC 60.125 66.667 11.61 0.00 0.00 3.71
970 1028 2.607750 TGCCCGGCTTCTTCTCCT 60.608 61.111 11.61 0.00 0.00 3.69
971 1029 2.190488 CTGCCCGGCTTCTTCTCCTT 62.190 60.000 11.61 0.00 0.00 3.36
972 1030 1.450491 GCCCGGCTTCTTCTCCTTC 60.450 63.158 0.71 0.00 0.00 3.46
973 1031 1.904990 GCCCGGCTTCTTCTCCTTCT 61.905 60.000 0.71 0.00 0.00 2.85
1036 1099 2.470196 CGCATATATAGCCGCGTACT 57.530 50.000 4.92 4.51 42.66 2.73
1037 1100 2.373269 CGCATATATAGCCGCGTACTC 58.627 52.381 4.92 0.00 42.66 2.59
1038 1101 2.223180 CGCATATATAGCCGCGTACTCA 60.223 50.000 4.92 0.00 42.66 3.41
1072 1149 0.109342 CTCCCCATCCAATTCCCTCG 59.891 60.000 0.00 0.00 0.00 4.63
1127 1207 1.523258 CTCGCATTGCAGGGAGGAG 60.523 63.158 9.69 2.20 42.82 3.69
1128 1208 1.964608 CTCGCATTGCAGGGAGGAGA 61.965 60.000 9.69 0.00 42.82 3.71
1129 1209 1.523258 CGCATTGCAGGGAGGAGAG 60.523 63.158 9.69 0.00 0.00 3.20
1148 1228 3.843027 AGAGGACTCAATCAAGGTGATGT 59.157 43.478 1.75 0.00 37.15 3.06
1149 1229 5.026121 AGAGGACTCAATCAAGGTGATGTA 58.974 41.667 1.75 0.00 37.15 2.29
1150 1230 5.091261 AGGACTCAATCAAGGTGATGTAC 57.909 43.478 0.00 0.00 37.15 2.90
1151 1231 9.716994 GAGAGGACTCAATCAAGGTGATGTACC 62.717 48.148 1.75 0.00 44.69 3.34
1178 1258 1.546476 ACCACATCGTTGTCTCTCTCC 59.454 52.381 0.00 0.00 32.34 3.71
1186 1266 2.355716 CGTTGTCTCTCTCCCTCTCTCT 60.356 54.545 0.00 0.00 0.00 3.10
1188 1268 1.484653 TGTCTCTCTCCCTCTCTCTCG 59.515 57.143 0.00 0.00 0.00 4.04
1189 1269 1.760613 GTCTCTCTCCCTCTCTCTCGA 59.239 57.143 0.00 0.00 0.00 4.04
1190 1270 2.368875 GTCTCTCTCCCTCTCTCTCGAT 59.631 54.545 0.00 0.00 0.00 3.59
1191 1271 2.632996 TCTCTCTCCCTCTCTCTCGATC 59.367 54.545 0.00 0.00 0.00 3.69
1192 1272 1.343142 TCTCTCCCTCTCTCTCGATCG 59.657 57.143 9.36 9.36 0.00 3.69
1193 1273 1.343142 CTCTCCCTCTCTCTCGATCGA 59.657 57.143 18.32 18.32 0.00 3.59
1251 1331 5.292589 GTGGATGATTGGTTGATTTGATTGC 59.707 40.000 0.00 0.00 0.00 3.56
1298 1378 3.092081 GCGTGTGCTTTCATTCACC 57.908 52.632 0.00 0.00 38.39 4.02
1299 1379 0.310543 GCGTGTGCTTTCATTCACCA 59.689 50.000 0.00 0.00 38.39 4.17
1300 1380 1.664016 GCGTGTGCTTTCATTCACCAG 60.664 52.381 0.00 0.00 38.39 4.00
1343 1423 2.153247 GTGTGTTCTACGCTTCGAACTG 59.847 50.000 8.70 0.00 40.04 3.16
1388 1468 2.359900 CCTCTTTTGTGCCTAGCGAAT 58.640 47.619 0.00 0.00 0.00 3.34
1389 1469 3.531538 CCTCTTTTGTGCCTAGCGAATA 58.468 45.455 0.00 0.00 0.00 1.75
1390 1470 3.557595 CCTCTTTTGTGCCTAGCGAATAG 59.442 47.826 0.00 0.00 0.00 1.73
1396 1476 0.596577 TGCCTAGCGAATAGTAGCGG 59.403 55.000 0.00 0.00 38.61 5.52
1400 1480 2.492484 CCTAGCGAATAGTAGCGGGAAT 59.508 50.000 4.90 0.00 38.61 3.01
1423 1503 3.706140 GCGATCGGCAGTTGGTAG 58.294 61.111 18.30 0.00 42.87 3.18
1424 1504 1.141019 GCGATCGGCAGTTGGTAGA 59.859 57.895 18.30 0.00 42.87 2.59
1465 1546 0.790207 TCTGCTCGCGTGAAATTGAC 59.210 50.000 13.13 0.00 0.00 3.18
1467 1548 1.218875 TGCTCGCGTGAAATTGACGT 61.219 50.000 13.13 0.00 39.08 4.34
1545 1628 7.362142 GGAAAATTTCGGCTAGAATTCTGACTT 60.362 37.037 18.47 0.26 38.86 3.01
1674 1762 2.806856 GCTTCGCTCGCACATCCTG 61.807 63.158 0.00 0.00 0.00 3.86
1678 1766 0.602638 TCGCTCGCACATCCTGTTTT 60.603 50.000 0.00 0.00 0.00 2.43
1681 1769 1.135859 GCTCGCACATCCTGTTTTCTG 60.136 52.381 0.00 0.00 0.00 3.02
1710 1799 1.897398 CTGTTGGTGTCGGCGTTAGC 61.897 60.000 6.85 7.59 44.18 3.09
1733 1823 3.565764 TGAGCCTGATGGTATTCTTGG 57.434 47.619 0.00 0.00 35.27 3.61
1734 1824 2.225467 GAGCCTGATGGTATTCTTGGC 58.775 52.381 0.00 0.00 36.72 4.52
1735 1825 0.947244 GCCTGATGGTATTCTTGGCG 59.053 55.000 0.00 0.00 35.27 5.69
1736 1826 1.747206 GCCTGATGGTATTCTTGGCGT 60.747 52.381 0.00 0.00 35.27 5.68
1737 1827 1.942657 CCTGATGGTATTCTTGGCGTG 59.057 52.381 0.00 0.00 0.00 5.34
1738 1828 1.331756 CTGATGGTATTCTTGGCGTGC 59.668 52.381 0.00 0.00 0.00 5.34
1739 1829 1.065491 TGATGGTATTCTTGGCGTGCT 60.065 47.619 0.00 0.00 0.00 4.40
2377 2488 1.073964 CGCCATCATGTGATCGATCC 58.926 55.000 22.31 13.85 31.21 3.36
2386 2497 3.626028 TGTGATCGATCCATCAGTACG 57.374 47.619 22.31 0.00 33.29 3.67
2387 2498 2.287608 TGTGATCGATCCATCAGTACGC 60.288 50.000 22.31 2.45 33.29 4.42
2509 2633 3.167093 CGTACATATACACGCGCCA 57.833 52.632 5.73 0.00 0.00 5.69
2510 2634 0.774098 CGTACATATACACGCGCCAC 59.226 55.000 5.73 0.00 0.00 5.01
2511 2635 1.842720 GTACATATACACGCGCCACA 58.157 50.000 5.73 0.00 0.00 4.17
2512 2636 2.400399 GTACATATACACGCGCCACAT 58.600 47.619 5.73 0.00 0.00 3.21
2588 2713 9.331282 AGTAGAAGCCAGAATAAAATACATCAC 57.669 33.333 0.00 0.00 0.00 3.06
2589 2714 9.331282 GTAGAAGCCAGAATAAAATACATCACT 57.669 33.333 0.00 0.00 0.00 3.41
2620 2745 4.055360 GCATTCATGTGGTACTGCGTATA 58.945 43.478 0.00 0.00 0.00 1.47
2621 2746 4.084537 GCATTCATGTGGTACTGCGTATAC 60.085 45.833 0.00 0.00 0.00 1.47
2622 2747 4.994907 TTCATGTGGTACTGCGTATACT 57.005 40.909 0.56 0.00 0.00 2.12
2652 2780 9.006405 ACTACTACTAGAAACTAAGGAGGATCT 57.994 37.037 0.00 0.00 33.73 2.75
2663 2791 2.710377 AGGAGGATCTGAGATCGATCG 58.290 52.381 19.33 9.36 38.49 3.69
2664 2792 2.304470 AGGAGGATCTGAGATCGATCGA 59.696 50.000 21.86 21.86 38.49 3.59
2665 2793 3.054434 AGGAGGATCTGAGATCGATCGAT 60.054 47.826 29.76 29.76 38.49 3.59
2666 2794 3.312421 GGAGGATCTGAGATCGATCGATC 59.688 52.174 38.82 38.82 42.52 3.69
2667 2795 5.160721 GGAGGATCTGAGATCGATCGATCA 61.161 50.000 43.10 31.32 43.62 2.92
2675 2804 2.414058 ATCGATCGATCAGTGTCTGC 57.586 50.000 24.60 0.00 0.00 4.26
2685 2814 1.067565 TCAGTGTCTGCCGTCTCATTC 60.068 52.381 0.00 0.00 0.00 2.67
2701 2830 0.678048 ATTCTCAGCGCCCCACTTTC 60.678 55.000 2.29 0.00 0.00 2.62
2783 2914 2.286872 GTTGCACTCTGATCTGATGGG 58.713 52.381 2.43 0.62 0.00 4.00
2791 2922 0.034186 TGATCTGATGGGGTTGTGCC 60.034 55.000 0.00 0.00 0.00 5.01
2792 2923 0.034186 GATCTGATGGGGTTGTGCCA 60.034 55.000 0.00 0.00 39.65 4.92
2800 2931 2.564721 GGGTTGTGCCAGGCTTCAC 61.565 63.158 14.15 2.83 39.65 3.18
2810 2941 1.833630 CCAGGCTTCACTATCCTCACA 59.166 52.381 0.00 0.00 0.00 3.58
2811 2942 2.158986 CCAGGCTTCACTATCCTCACAG 60.159 54.545 0.00 0.00 0.00 3.66
2815 2946 2.695666 GCTTCACTATCCTCACAGGCTA 59.304 50.000 0.00 0.00 34.61 3.93
2816 2947 3.491792 GCTTCACTATCCTCACAGGCTAC 60.492 52.174 0.00 0.00 34.61 3.58
2842 2973 2.583593 GCGATGCCTCCGTCTGTC 60.584 66.667 0.00 0.00 0.00 3.51
2843 2974 2.105128 CGATGCCTCCGTCTGTCC 59.895 66.667 0.00 0.00 0.00 4.02
2846 2977 3.924013 ATGCCTCCGTCTGTCCCCA 62.924 63.158 0.00 0.00 0.00 4.96
2847 2978 3.775654 GCCTCCGTCTGTCCCCAG 61.776 72.222 0.00 0.00 40.25 4.45
2862 3001 2.846206 TCCCCAGAAGTGATTATGCAGT 59.154 45.455 0.00 0.00 0.00 4.40
2863 3002 2.947652 CCCCAGAAGTGATTATGCAGTG 59.052 50.000 0.00 0.00 0.00 3.66
2864 3003 3.614092 CCCAGAAGTGATTATGCAGTGT 58.386 45.455 0.00 0.00 0.00 3.55
2865 3004 4.384098 CCCCAGAAGTGATTATGCAGTGTA 60.384 45.833 0.00 0.00 0.00 2.90
2866 3005 5.371526 CCCAGAAGTGATTATGCAGTGTAT 58.628 41.667 0.00 0.00 0.00 2.29
2867 3006 5.824624 CCCAGAAGTGATTATGCAGTGTATT 59.175 40.000 0.00 0.00 0.00 1.89
2868 3007 6.992123 CCCAGAAGTGATTATGCAGTGTATTA 59.008 38.462 0.00 0.00 0.00 0.98
2904 3056 3.769536 CATGTAAAGATGGGGCGAAAAC 58.230 45.455 0.00 0.00 0.00 2.43
2949 3101 2.951745 GCGTCGAGGAGCGTCATG 60.952 66.667 9.75 0.00 41.80 3.07
2956 3108 1.000993 AGGAGCGTCATGAGGAGGT 59.999 57.895 19.26 8.27 33.92 3.85
3022 3174 1.738030 CGGGAGTAGGTGTTAAAGCGG 60.738 57.143 0.00 0.00 0.00 5.52
3026 3178 0.390209 GTAGGTGTTAAAGCGGGCGA 60.390 55.000 0.00 0.00 0.00 5.54
3045 3197 2.173669 GGTGGATGATGTGTCGCCG 61.174 63.158 0.00 0.00 0.00 6.46
3078 3241 0.322456 CGGTGGTGGGTGACATGAAT 60.322 55.000 0.00 0.00 0.00 2.57
3135 3298 1.495951 GCCGTGTCGAATTCACACC 59.504 57.895 23.52 13.79 41.04 4.16
3144 3307 4.578516 TGTCGAATTCACACCAAAACAGAT 59.421 37.500 6.22 0.00 0.00 2.90
3145 3308 4.911610 GTCGAATTCACACCAAAACAGATG 59.088 41.667 6.22 0.00 0.00 2.90
3146 3309 4.023279 TCGAATTCACACCAAAACAGATGG 60.023 41.667 6.22 0.00 43.84 3.51
3147 3310 4.023279 CGAATTCACACCAAAACAGATGGA 60.023 41.667 6.22 0.00 40.56 3.41
3169 3387 1.270550 GCCATGCAAACACAAGCTAGT 59.729 47.619 0.00 0.00 0.00 2.57
3175 3393 1.000274 CAAACACAAGCTAGTTGGGGC 60.000 52.381 10.68 0.00 44.80 5.80
3188 3406 3.044894 AGTTGGGGCCAATTTTTCTTCA 58.955 40.909 4.39 0.00 38.28 3.02
3189 3407 3.652387 AGTTGGGGCCAATTTTTCTTCAT 59.348 39.130 4.39 0.00 38.28 2.57
3195 3415 4.397420 GGCCAATTTTTCTTCATGGGTTT 58.603 39.130 0.00 0.00 0.00 3.27
3205 3425 9.898152 TTTTTCTTCATGGGTTTAAATTCAACT 57.102 25.926 0.00 0.00 0.00 3.16
3253 3474 2.436670 CGTTGTTTGTTTCGTGAGGTG 58.563 47.619 0.00 0.00 0.00 4.00
3254 3475 2.789779 CGTTGTTTGTTTCGTGAGGTGG 60.790 50.000 0.00 0.00 0.00 4.61
3255 3476 2.116827 TGTTTGTTTCGTGAGGTGGT 57.883 45.000 0.00 0.00 0.00 4.16
3281 3502 0.976641 TCAGAAGTCGCATCCACCTT 59.023 50.000 0.00 0.00 0.00 3.50
3293 3514 0.181587 TCCACCTTGCGAGGACAAAA 59.818 50.000 27.65 4.23 46.74 2.44
3302 3523 2.293122 TGCGAGGACAAAATGGTTCTTG 59.707 45.455 0.00 0.00 31.80 3.02
3415 4811 0.325272 AAGGAAAGGAGGAGGCGTTC 59.675 55.000 0.00 0.00 0.00 3.95
3430 4826 4.939368 TTCGGCGGTTGTGGGTGG 62.939 66.667 7.21 0.00 0.00 4.61
3434 4830 4.906537 GCGGTTGTGGGTGGGGTT 62.907 66.667 0.00 0.00 0.00 4.11
3547 4951 1.515954 CTCGATTGTGCCTACCGGT 59.484 57.895 13.98 13.98 0.00 5.28
3548 4952 0.742505 CTCGATTGTGCCTACCGGTA 59.257 55.000 14.95 14.95 0.00 4.02
3549 4953 0.457035 TCGATTGTGCCTACCGGTAC 59.543 55.000 11.16 3.90 45.14 3.34
3550 4954 0.529119 CGATTGTGCCTACCGGTACC 60.529 60.000 11.16 0.16 44.39 3.34
3551 4955 0.529119 GATTGTGCCTACCGGTACCG 60.529 60.000 27.68 27.68 44.39 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.326264 CCACTTGTTCCCTGGAGAGG 59.674 60.000 0.00 0.00 39.42 3.69
6 7 0.326264 CCCACTTGTTCCCTGGAGAG 59.674 60.000 0.00 0.00 0.00 3.20
7 8 1.133809 CCCCACTTGTTCCCTGGAGA 61.134 60.000 0.00 0.00 0.00 3.71
8 9 1.380302 CCCCACTTGTTCCCTGGAG 59.620 63.158 0.00 0.00 0.00 3.86
9 10 2.160171 CCCCCACTTGTTCCCTGGA 61.160 63.158 0.00 0.00 0.00 3.86
10 11 2.142292 CTCCCCCACTTGTTCCCTGG 62.142 65.000 0.00 0.00 0.00 4.45
11 12 1.133809 TCTCCCCCACTTGTTCCCTG 61.134 60.000 0.00 0.00 0.00 4.45
12 13 1.134438 GTCTCCCCCACTTGTTCCCT 61.134 60.000 0.00 0.00 0.00 4.20
13 14 1.134438 AGTCTCCCCCACTTGTTCCC 61.134 60.000 0.00 0.00 0.00 3.97
14 15 0.771755 AAGTCTCCCCCACTTGTTCC 59.228 55.000 0.00 0.00 32.65 3.62
15 16 1.897560 CAAGTCTCCCCCACTTGTTC 58.102 55.000 4.69 0.00 43.92 3.18
19 20 2.840651 CTCATACAAGTCTCCCCCACTT 59.159 50.000 0.00 0.00 34.24 3.16
20 21 2.044492 TCTCATACAAGTCTCCCCCACT 59.956 50.000 0.00 0.00 0.00 4.00
21 22 2.467880 TCTCATACAAGTCTCCCCCAC 58.532 52.381 0.00 0.00 0.00 4.61
22 23 2.940514 TCTCATACAAGTCTCCCCCA 57.059 50.000 0.00 0.00 0.00 4.96
23 24 3.576550 GAGATCTCATACAAGTCTCCCCC 59.423 52.174 18.11 0.00 31.41 5.40
24 25 4.038642 GTGAGATCTCATACAAGTCTCCCC 59.961 50.000 27.51 7.00 42.18 4.81
25 26 4.646945 TGTGAGATCTCATACAAGTCTCCC 59.353 45.833 27.51 11.04 42.18 4.30
26 27 5.843673 TGTGAGATCTCATACAAGTCTCC 57.156 43.478 27.51 11.52 42.18 3.71
27 28 9.462174 CTAAATGTGAGATCTCATACAAGTCTC 57.538 37.037 27.51 12.21 42.18 3.36
28 29 8.420222 CCTAAATGTGAGATCTCATACAAGTCT 58.580 37.037 27.51 6.92 42.18 3.24
29 30 8.200792 ACCTAAATGTGAGATCTCATACAAGTC 58.799 37.037 27.51 13.60 42.18 3.01
30 31 7.984050 CACCTAAATGTGAGATCTCATACAAGT 59.016 37.037 27.51 15.89 42.18 3.16
31 32 7.984050 ACACCTAAATGTGAGATCTCATACAAG 59.016 37.037 27.51 20.05 42.18 3.16
32 33 7.851228 ACACCTAAATGTGAGATCTCATACAA 58.149 34.615 27.51 14.34 42.18 2.41
33 34 7.423844 ACACCTAAATGTGAGATCTCATACA 57.576 36.000 27.51 21.23 42.18 2.29
58 59 6.316390 ACGTTTTTAGGGTTGATCTCATGATC 59.684 38.462 0.00 0.00 46.89 2.92
59 60 6.180472 ACGTTTTTAGGGTTGATCTCATGAT 58.820 36.000 0.00 0.00 35.26 2.45
60 61 5.556915 ACGTTTTTAGGGTTGATCTCATGA 58.443 37.500 0.00 0.00 0.00 3.07
61 62 5.880054 ACGTTTTTAGGGTTGATCTCATG 57.120 39.130 0.00 0.00 0.00 3.07
62 63 9.847224 AATATACGTTTTTAGGGTTGATCTCAT 57.153 29.630 0.00 0.00 0.00 2.90
63 64 9.675464 AAATATACGTTTTTAGGGTTGATCTCA 57.325 29.630 0.00 0.00 0.00 3.27
68 69 9.941325 TGTCTAAATATACGTTTTTAGGGTTGA 57.059 29.630 17.82 4.22 36.51 3.18
108 109 9.890085 CGCATGAATGTTGTTAAATAATTTCAG 57.110 29.630 0.00 0.00 0.00 3.02
109 110 9.631452 TCGCATGAATGTTGTTAAATAATTTCA 57.369 25.926 0.00 0.00 0.00 2.69
111 112 8.594687 GCTCGCATGAATGTTGTTAAATAATTT 58.405 29.630 0.00 0.00 0.00 1.82
112 113 7.975616 AGCTCGCATGAATGTTGTTAAATAATT 59.024 29.630 0.00 0.00 0.00 1.40
113 114 7.483307 AGCTCGCATGAATGTTGTTAAATAAT 58.517 30.769 0.00 0.00 0.00 1.28
114 115 6.851609 AGCTCGCATGAATGTTGTTAAATAA 58.148 32.000 0.00 0.00 0.00 1.40
115 116 6.435430 AGCTCGCATGAATGTTGTTAAATA 57.565 33.333 0.00 0.00 0.00 1.40
116 117 5.314923 AGCTCGCATGAATGTTGTTAAAT 57.685 34.783 0.00 0.00 0.00 1.40
117 118 4.764679 AGCTCGCATGAATGTTGTTAAA 57.235 36.364 0.00 0.00 0.00 1.52
118 119 5.353956 ACATAGCTCGCATGAATGTTGTTAA 59.646 36.000 0.00 0.00 0.00 2.01
119 120 4.875536 ACATAGCTCGCATGAATGTTGTTA 59.124 37.500 0.00 0.00 0.00 2.41
120 121 3.691118 ACATAGCTCGCATGAATGTTGTT 59.309 39.130 0.00 0.00 0.00 2.83
121 122 3.273434 ACATAGCTCGCATGAATGTTGT 58.727 40.909 0.00 0.00 0.00 3.32
122 123 3.558829 AGACATAGCTCGCATGAATGTTG 59.441 43.478 0.00 0.00 31.19 3.33
123 124 3.801698 AGACATAGCTCGCATGAATGTT 58.198 40.909 0.00 0.00 31.19 2.71
124 125 3.465742 AGACATAGCTCGCATGAATGT 57.534 42.857 0.00 0.00 33.63 2.71
125 126 4.301628 TGTAGACATAGCTCGCATGAATG 58.698 43.478 0.00 0.00 0.00 2.67
126 127 4.590850 TGTAGACATAGCTCGCATGAAT 57.409 40.909 0.00 0.00 0.00 2.57
127 128 4.112634 GTTGTAGACATAGCTCGCATGAA 58.887 43.478 0.00 0.00 0.00 2.57
128 129 3.381590 AGTTGTAGACATAGCTCGCATGA 59.618 43.478 0.00 0.00 0.00 3.07
129 130 3.711086 AGTTGTAGACATAGCTCGCATG 58.289 45.455 0.00 0.00 0.00 4.06
130 131 4.392921 AAGTTGTAGACATAGCTCGCAT 57.607 40.909 0.00 0.00 0.00 4.73
131 132 3.868757 AAGTTGTAGACATAGCTCGCA 57.131 42.857 0.00 0.00 0.00 5.10
132 133 4.174009 TCAAAGTTGTAGACATAGCTCGC 58.826 43.478 0.00 0.00 0.00 5.03
133 134 6.706055 TTTCAAAGTTGTAGACATAGCTCG 57.294 37.500 0.00 0.00 0.00 5.03
155 156 7.319646 TGTACATCAAGTTTTCAGCTGTTTTT 58.680 30.769 14.67 0.00 0.00 1.94
156 157 6.862209 TGTACATCAAGTTTTCAGCTGTTTT 58.138 32.000 14.67 0.00 0.00 2.43
157 158 6.449635 TGTACATCAAGTTTTCAGCTGTTT 57.550 33.333 14.67 0.00 0.00 2.83
158 159 6.639632 ATGTACATCAAGTTTTCAGCTGTT 57.360 33.333 14.67 0.00 0.00 3.16
159 160 6.639632 AATGTACATCAAGTTTTCAGCTGT 57.360 33.333 14.67 0.00 0.00 4.40
160 161 8.506437 TCTAAATGTACATCAAGTTTTCAGCTG 58.494 33.333 9.23 7.63 0.00 4.24
161 162 8.621532 TCTAAATGTACATCAAGTTTTCAGCT 57.378 30.769 9.23 0.00 0.00 4.24
162 163 8.721478 TCTCTAAATGTACATCAAGTTTTCAGC 58.279 33.333 9.23 0.00 0.00 4.26
168 169 9.725019 TGTGAATCTCTAAATGTACATCAAGTT 57.275 29.630 9.23 2.21 0.00 2.66
169 170 9.725019 TTGTGAATCTCTAAATGTACATCAAGT 57.275 29.630 9.23 0.00 0.00 3.16
195 196 9.874205 CCACTGTCCACATTGAAATTTATATTT 57.126 29.630 0.00 0.00 36.68 1.40
196 197 7.981225 GCCACTGTCCACATTGAAATTTATATT 59.019 33.333 0.00 0.00 0.00 1.28
197 198 7.123997 TGCCACTGTCCACATTGAAATTTATAT 59.876 33.333 0.00 0.00 0.00 0.86
198 199 6.435591 TGCCACTGTCCACATTGAAATTTATA 59.564 34.615 0.00 0.00 0.00 0.98
199 200 5.245751 TGCCACTGTCCACATTGAAATTTAT 59.754 36.000 0.00 0.00 0.00 1.40
200 201 4.586421 TGCCACTGTCCACATTGAAATTTA 59.414 37.500 0.00 0.00 0.00 1.40
201 202 3.387374 TGCCACTGTCCACATTGAAATTT 59.613 39.130 0.00 0.00 0.00 1.82
202 203 2.964464 TGCCACTGTCCACATTGAAATT 59.036 40.909 0.00 0.00 0.00 1.82
203 204 2.559668 CTGCCACTGTCCACATTGAAAT 59.440 45.455 0.00 0.00 0.00 2.17
204 205 1.955778 CTGCCACTGTCCACATTGAAA 59.044 47.619 0.00 0.00 0.00 2.69
205 206 1.608055 CTGCCACTGTCCACATTGAA 58.392 50.000 0.00 0.00 0.00 2.69
206 207 0.890542 GCTGCCACTGTCCACATTGA 60.891 55.000 0.00 0.00 0.00 2.57
207 208 0.892358 AGCTGCCACTGTCCACATTG 60.892 55.000 0.00 0.00 0.00 2.82
208 209 0.178981 AAGCTGCCACTGTCCACATT 60.179 50.000 0.00 0.00 0.00 2.71
209 210 0.178981 AAAGCTGCCACTGTCCACAT 60.179 50.000 0.00 0.00 0.00 3.21
210 211 1.102809 CAAAGCTGCCACTGTCCACA 61.103 55.000 0.00 0.00 0.00 4.17
211 212 1.656441 CAAAGCTGCCACTGTCCAC 59.344 57.895 0.00 0.00 0.00 4.02
212 213 2.195567 GCAAAGCTGCCACTGTCCA 61.196 57.895 0.00 0.00 43.26 4.02
213 214 2.647297 GCAAAGCTGCCACTGTCC 59.353 61.111 0.00 0.00 43.26 4.02
214 215 2.253452 CGCAAAGCTGCCACTGTC 59.747 61.111 0.00 0.00 46.56 3.51
215 216 2.516930 ACGCAAAGCTGCCACTGT 60.517 55.556 0.00 0.00 46.56 3.55
216 217 1.506309 TACACGCAAAGCTGCCACTG 61.506 55.000 0.00 0.00 46.56 3.66
217 218 0.606401 ATACACGCAAAGCTGCCACT 60.606 50.000 0.00 0.00 46.56 4.00
218 219 0.454957 CATACACGCAAAGCTGCCAC 60.455 55.000 0.00 0.00 46.56 5.01
219 220 1.585267 CCATACACGCAAAGCTGCCA 61.585 55.000 0.00 0.00 46.56 4.92
220 221 1.137404 CCATACACGCAAAGCTGCC 59.863 57.895 0.00 0.00 46.56 4.85
221 222 1.083489 TACCATACACGCAAAGCTGC 58.917 50.000 0.00 0.00 45.75 5.25
222 223 2.346803 AGTACCATACACGCAAAGCTG 58.653 47.619 0.00 0.00 0.00 4.24
223 224 2.762535 AGTACCATACACGCAAAGCT 57.237 45.000 0.00 0.00 0.00 3.74
224 225 3.187637 TCAAAGTACCATACACGCAAAGC 59.812 43.478 0.00 0.00 0.00 3.51
225 226 4.212425 TGTCAAAGTACCATACACGCAAAG 59.788 41.667 0.00 0.00 0.00 2.77
226 227 4.024725 GTGTCAAAGTACCATACACGCAAA 60.025 41.667 0.00 0.00 32.05 3.68
227 228 3.495377 GTGTCAAAGTACCATACACGCAA 59.505 43.478 0.00 0.00 32.05 4.85
228 229 3.061322 GTGTCAAAGTACCATACACGCA 58.939 45.455 0.00 0.00 32.05 5.24
229 230 3.323243 AGTGTCAAAGTACCATACACGC 58.677 45.455 10.77 0.74 43.96 5.34
230 231 4.387862 GGAAGTGTCAAAGTACCATACACG 59.612 45.833 10.77 0.00 43.96 4.49
231 232 5.302360 TGGAAGTGTCAAAGTACCATACAC 58.698 41.667 9.26 9.26 40.53 2.90
232 233 5.554437 TGGAAGTGTCAAAGTACCATACA 57.446 39.130 0.00 0.00 0.00 2.29
233 234 6.170506 TCATGGAAGTGTCAAAGTACCATAC 58.829 40.000 0.00 0.00 35.34 2.39
234 235 6.367374 TCATGGAAGTGTCAAAGTACCATA 57.633 37.500 0.00 0.00 35.34 2.74
235 236 5.241403 TCATGGAAGTGTCAAAGTACCAT 57.759 39.130 0.00 0.00 37.16 3.55
236 237 4.698201 TCATGGAAGTGTCAAAGTACCA 57.302 40.909 0.00 0.00 0.00 3.25
237 238 5.473504 ACATTCATGGAAGTGTCAAAGTACC 59.526 40.000 0.00 0.00 0.00 3.34
238 239 6.560253 ACATTCATGGAAGTGTCAAAGTAC 57.440 37.500 0.00 0.00 0.00 2.73
239 240 8.322906 CTTACATTCATGGAAGTGTCAAAGTA 57.677 34.615 3.81 0.00 42.51 2.24
240 241 7.206981 CTTACATTCATGGAAGTGTCAAAGT 57.793 36.000 3.81 0.00 42.51 2.66
256 257 6.273825 TCAGCTCCTAATTCGACTTACATTC 58.726 40.000 0.00 0.00 0.00 2.67
300 302 9.689976 TTTTTGTAGACATACATCAATGTTTGG 57.310 29.630 15.07 3.69 41.86 3.28
325 327 8.851541 ATACATGTTCAAGCATTTCCAAATTT 57.148 26.923 2.30 0.00 0.00 1.82
327 329 8.851541 AAATACATGTTCAAGCATTTCCAAAT 57.148 26.923 2.30 0.00 0.00 2.32
404 406 2.359975 GTTCCCGGGGCAGAGTTG 60.360 66.667 23.50 0.00 0.00 3.16
405 407 4.016706 CGTTCCCGGGGCAGAGTT 62.017 66.667 23.50 0.00 0.00 3.01
407 409 4.148825 CTCGTTCCCGGGGCAGAG 62.149 72.222 23.50 21.34 33.95 3.35
409 411 4.452733 GACTCGTTCCCGGGGCAG 62.453 72.222 23.50 13.68 44.25 4.85
484 486 6.108687 CCTAGTGCTAATCAGATGTTGTTCA 58.891 40.000 0.00 0.00 0.00 3.18
485 487 5.007136 GCCTAGTGCTAATCAGATGTTGTTC 59.993 44.000 0.00 0.00 36.87 3.18
486 488 4.878397 GCCTAGTGCTAATCAGATGTTGTT 59.122 41.667 0.00 0.00 36.87 2.83
488 490 4.445453 TGCCTAGTGCTAATCAGATGTTG 58.555 43.478 5.06 0.00 42.00 3.33
574 581 3.366440 TGATGACATGATCTGAGCTCG 57.634 47.619 9.64 4.19 0.00 5.03
693 734 3.274393 AGTGTTCTCGCACTGTGAC 57.726 52.632 12.86 0.55 46.72 3.67
764 805 4.858692 GCATTTTTCACGATGCACAGTAAT 59.141 37.500 0.00 0.00 46.03 1.89
818 859 4.144703 GTCGGCGTTCTCCCTCCC 62.145 72.222 6.85 0.00 0.00 4.30
819 860 1.318158 TTAGTCGGCGTTCTCCCTCC 61.318 60.000 6.85 0.00 0.00 4.30
820 861 0.179142 GTTAGTCGGCGTTCTCCCTC 60.179 60.000 6.85 0.00 0.00 4.30
821 862 0.896940 TGTTAGTCGGCGTTCTCCCT 60.897 55.000 6.85 0.00 0.00 4.20
968 1026 2.434331 TTGCCGGTGGGAAGAAGG 59.566 61.111 1.90 0.00 34.06 3.46
973 1031 2.747686 GAGACTTGCCGGTGGGAA 59.252 61.111 1.90 0.00 34.06 3.97
1035 1098 0.107508 AGGCGGTGTGGATGAATGAG 60.108 55.000 0.00 0.00 0.00 2.90
1036 1099 0.107703 GAGGCGGTGTGGATGAATGA 60.108 55.000 0.00 0.00 0.00 2.57
1037 1100 1.097547 GGAGGCGGTGTGGATGAATG 61.098 60.000 0.00 0.00 0.00 2.67
1038 1101 1.224592 GGAGGCGGTGTGGATGAAT 59.775 57.895 0.00 0.00 0.00 2.57
1127 1207 4.213564 ACATCACCTTGATTGAGTCCTC 57.786 45.455 0.00 0.00 34.28 3.71
1128 1208 4.080863 GGTACATCACCTTGATTGAGTCCT 60.081 45.833 0.00 0.00 44.79 3.85
1129 1209 4.192317 GGTACATCACCTTGATTGAGTCC 58.808 47.826 0.00 0.00 44.79 3.85
1148 1228 1.927487 ACGATGTGGTGGTACTGGTA 58.073 50.000 0.00 0.00 0.00 3.25
1149 1229 1.053424 AACGATGTGGTGGTACTGGT 58.947 50.000 0.00 0.00 0.00 4.00
1150 1230 1.270625 ACAACGATGTGGTGGTACTGG 60.271 52.381 0.00 0.00 38.69 4.00
1151 1231 2.066262 GACAACGATGTGGTGGTACTG 58.934 52.381 1.86 0.00 40.74 2.74
1152 1232 1.968493 AGACAACGATGTGGTGGTACT 59.032 47.619 1.86 0.00 40.74 2.73
1153 1233 2.029290 AGAGACAACGATGTGGTGGTAC 60.029 50.000 1.86 0.00 40.74 3.34
1154 1234 2.230508 GAGAGACAACGATGTGGTGGTA 59.769 50.000 1.86 0.00 40.74 3.25
1155 1235 1.000955 GAGAGACAACGATGTGGTGGT 59.999 52.381 1.86 0.00 40.74 4.16
1156 1236 1.273606 AGAGAGACAACGATGTGGTGG 59.726 52.381 1.86 0.00 40.74 4.61
1157 1237 2.600731 GAGAGAGACAACGATGTGGTG 58.399 52.381 1.86 0.00 40.74 4.17
1158 1238 1.546476 GGAGAGAGACAACGATGTGGT 59.454 52.381 1.86 0.00 40.74 4.16
1159 1239 1.134965 GGGAGAGAGACAACGATGTGG 60.135 57.143 1.86 0.00 40.74 4.17
1186 1266 3.932089 TGCATGTTTCTGATTTCGATCGA 59.068 39.130 15.15 15.15 0.00 3.59
1188 1268 6.748658 TCAAATGCATGTTTCTGATTTCGATC 59.251 34.615 0.00 0.00 0.00 3.69
1189 1269 6.623486 TCAAATGCATGTTTCTGATTTCGAT 58.377 32.000 0.00 0.00 0.00 3.59
1190 1270 6.011476 TCAAATGCATGTTTCTGATTTCGA 57.989 33.333 0.00 0.00 0.00 3.71
1191 1271 6.880822 ATCAAATGCATGTTTCTGATTTCG 57.119 33.333 0.00 0.00 0.00 3.46
1193 1273 9.158233 CCTAAATCAAATGCATGTTTCTGATTT 57.842 29.630 23.15 23.15 38.06 2.17
1251 1331 2.040544 AAGAAGGTTCGGCATGGCG 61.041 57.895 33.54 33.54 0.00 5.69
1293 1373 6.702716 AAAGAAACGGAATTAACTGGTGAA 57.297 33.333 0.00 0.00 0.00 3.18
1294 1374 6.702716 AAAAGAAACGGAATTAACTGGTGA 57.297 33.333 0.00 0.00 0.00 4.02
1295 1375 6.200097 CCAAAAAGAAACGGAATTAACTGGTG 59.800 38.462 0.00 0.00 0.00 4.17
1297 1377 6.508777 TCCAAAAAGAAACGGAATTAACTGG 58.491 36.000 0.00 0.00 0.00 4.00
1298 1378 7.167468 CACTCCAAAAAGAAACGGAATTAACTG 59.833 37.037 0.00 0.00 0.00 3.16
1299 1379 7.147966 ACACTCCAAAAAGAAACGGAATTAACT 60.148 33.333 0.00 0.00 0.00 2.24
1300 1380 6.976349 ACACTCCAAAAAGAAACGGAATTAAC 59.024 34.615 0.00 0.00 0.00 2.01
1343 1423 5.397142 AACAATTGATGAGAAGAAAGGGC 57.603 39.130 13.59 0.00 0.00 5.19
1388 1468 0.103572 GCAACCGATTCCCGCTACTA 59.896 55.000 0.00 0.00 36.84 1.82
1389 1469 1.153429 GCAACCGATTCCCGCTACT 60.153 57.895 0.00 0.00 36.84 2.57
1390 1470 2.522638 CGCAACCGATTCCCGCTAC 61.523 63.158 0.00 0.00 36.29 3.58
1424 1504 2.487762 GCAAGAGAGGAGATCGATCGAT 59.512 50.000 29.76 29.76 37.59 3.59
1465 1546 3.904136 AGAAAATGAAACAGAGGCACG 57.096 42.857 0.00 0.00 0.00 5.34
1467 1548 6.205464 CAGAGTTAGAAAATGAAACAGAGGCA 59.795 38.462 0.00 0.00 0.00 4.75
1545 1628 1.383943 ACTCCACACACACCTCCCA 60.384 57.895 0.00 0.00 0.00 4.37
1667 1755 4.916041 TCTGATCCAGAAAACAGGATGT 57.084 40.909 0.00 0.00 45.14 3.06
1678 1766 1.980765 ACCAACAGCTTCTGATCCAGA 59.019 47.619 0.29 0.00 38.87 3.86
1681 1769 2.079925 GACACCAACAGCTTCTGATCC 58.920 52.381 0.29 0.00 35.18 3.36
1696 1785 0.947180 TCAAAGCTAACGCCGACACC 60.947 55.000 0.00 0.00 36.60 4.16
1710 1799 4.337555 CCAAGAATACCATCAGGCTCAAAG 59.662 45.833 0.00 0.00 39.06 2.77
1733 1823 2.684843 CCCTTCTCTGCAAGCACGC 61.685 63.158 0.00 0.00 0.00 5.34
1734 1824 2.684843 GCCCTTCTCTGCAAGCACG 61.685 63.158 0.00 0.00 0.00 5.34
1735 1825 2.684843 CGCCCTTCTCTGCAAGCAC 61.685 63.158 0.00 0.00 0.00 4.40
1736 1826 2.359107 CGCCCTTCTCTGCAAGCA 60.359 61.111 0.00 0.00 0.00 3.91
1737 1827 2.046892 TCGCCCTTCTCTGCAAGC 60.047 61.111 0.00 0.00 0.00 4.01
1738 1828 0.321122 AACTCGCCCTTCTCTGCAAG 60.321 55.000 0.00 0.00 0.00 4.01
1739 1829 0.320771 GAACTCGCCCTTCTCTGCAA 60.321 55.000 0.00 0.00 0.00 4.08
1989 2079 4.432741 GGGCACTTGGGCTCCTCC 62.433 72.222 0.00 0.00 42.84 4.30
2043 2133 3.984193 CTTGGGCGGCTCCTCCTTG 62.984 68.421 9.56 0.00 34.39 3.61
2058 2148 3.984193 CTTGGGCGGCTCCTCCTTG 62.984 68.421 9.56 0.00 34.39 3.61
2258 2360 1.206371 GGTACTGCGGGTAGATGTTGT 59.794 52.381 0.00 0.00 0.00 3.32
2377 2488 2.353889 AGTACTGTACGGCGTACTGATG 59.646 50.000 43.02 31.76 43.29 3.07
2386 2497 0.179153 GGAACGGAGTACTGTACGGC 60.179 60.000 11.97 8.47 45.00 5.68
2387 2498 0.453390 GGGAACGGAGTACTGTACGG 59.547 60.000 11.97 0.00 45.00 4.02
2508 2632 7.517614 AGAGAGTAGGTGTATATGTGATGTG 57.482 40.000 0.00 0.00 0.00 3.21
2509 2633 8.441572 AGTAGAGAGTAGGTGTATATGTGATGT 58.558 37.037 0.00 0.00 0.00 3.06
2510 2634 8.856153 AGTAGAGAGTAGGTGTATATGTGATG 57.144 38.462 0.00 0.00 0.00 3.07
2511 2635 8.104566 GGAGTAGAGAGTAGGTGTATATGTGAT 58.895 40.741 0.00 0.00 0.00 3.06
2512 2636 7.451732 GGAGTAGAGAGTAGGTGTATATGTGA 58.548 42.308 0.00 0.00 0.00 3.58
2586 2711 4.426416 CACATGAATGCATTTGGGTAGTG 58.574 43.478 14.33 12.36 30.38 2.74
2587 2712 3.448301 CCACATGAATGCATTTGGGTAGT 59.552 43.478 14.33 4.45 44.82 2.73
2588 2713 4.049546 CCACATGAATGCATTTGGGTAG 57.950 45.455 14.33 1.75 44.82 3.18
2663 2791 0.528017 TGAGACGGCAGACACTGATC 59.472 55.000 0.00 0.00 32.44 2.92
2664 2792 1.189752 ATGAGACGGCAGACACTGAT 58.810 50.000 0.00 0.00 32.44 2.90
2665 2793 0.969149 AATGAGACGGCAGACACTGA 59.031 50.000 0.00 0.00 32.44 3.41
2666 2794 1.067283 AGAATGAGACGGCAGACACTG 60.067 52.381 0.00 0.00 34.12 3.66
2667 2795 1.203523 GAGAATGAGACGGCAGACACT 59.796 52.381 0.00 0.00 0.00 3.55
2675 2804 1.880340 GGCGCTGAGAATGAGACGG 60.880 63.158 7.64 0.00 0.00 4.79
2685 2814 1.372087 GATGAAAGTGGGGCGCTGAG 61.372 60.000 7.64 0.00 0.00 3.35
2701 2830 8.347771 ACAGCAGCACATACTAATAATTTGATG 58.652 33.333 0.00 0.00 0.00 3.07
2783 2914 0.250727 TAGTGAAGCCTGGCACAACC 60.251 55.000 22.65 9.47 38.70 3.77
2791 2922 2.158986 CCTGTGAGGATAGTGAAGCCTG 60.159 54.545 0.00 0.00 37.67 4.85
2792 2923 2.114616 CCTGTGAGGATAGTGAAGCCT 58.885 52.381 0.00 0.00 37.67 4.58
2800 2931 4.081420 ACAAAGTGTAGCCTGTGAGGATAG 60.081 45.833 0.00 0.00 36.85 2.08
2810 2941 1.806542 CATCGCAACAAAGTGTAGCCT 59.193 47.619 0.00 0.00 0.00 4.58
2811 2942 1.729149 GCATCGCAACAAAGTGTAGCC 60.729 52.381 0.00 0.00 0.00 3.93
2815 2946 0.593128 GAGGCATCGCAACAAAGTGT 59.407 50.000 0.00 0.00 0.00 3.55
2816 2947 0.109597 GGAGGCATCGCAACAAAGTG 60.110 55.000 0.00 0.00 0.00 3.16
2842 2973 2.947652 CACTGCATAATCACTTCTGGGG 59.052 50.000 0.00 0.00 0.00 4.96
2843 2974 3.614092 ACACTGCATAATCACTTCTGGG 58.386 45.455 0.00 0.00 0.00 4.45
2871 3010 6.263842 CCCATCTTTACATGCACATACAGAAT 59.736 38.462 0.00 0.00 0.00 2.40
2873 3012 5.125356 CCCATCTTTACATGCACATACAGA 58.875 41.667 0.00 0.00 0.00 3.41
2874 3013 4.276678 CCCCATCTTTACATGCACATACAG 59.723 45.833 0.00 0.00 0.00 2.74
2904 3056 1.017177 CCGTACCCATCAACCGTGTG 61.017 60.000 0.00 0.00 0.00 3.82
2949 3101 0.030908 CGCCTAATCACGACCTCCTC 59.969 60.000 0.00 0.00 0.00 3.71
2956 3108 2.883730 GTGCGCGCCTAATCACGA 60.884 61.111 30.77 2.53 0.00 4.35
3008 3160 0.108520 CTCGCCCGCTTTAACACCTA 60.109 55.000 0.00 0.00 0.00 3.08
3022 3174 0.811616 GACACATCATCCACCTCGCC 60.812 60.000 0.00 0.00 0.00 5.54
3026 3178 1.221840 GGCGACACATCATCCACCT 59.778 57.895 0.00 0.00 0.00 4.00
3078 3241 1.340991 GGTTTGCTTGGCCTCCATCTA 60.341 52.381 3.32 0.00 31.53 1.98
3119 3282 3.033185 GTTTTGGTGTGAATTCGACACG 58.967 45.455 23.06 0.00 43.95 4.49
3135 3298 1.134907 GCATGGCCTCCATCTGTTTTG 60.135 52.381 3.32 0.00 43.15 2.44
3144 3307 0.758310 TTGTGTTTGCATGGCCTCCA 60.758 50.000 3.32 0.00 38.19 3.86
3145 3308 0.037975 CTTGTGTTTGCATGGCCTCC 60.038 55.000 3.32 0.00 0.00 4.30
3146 3309 0.668401 GCTTGTGTTTGCATGGCCTC 60.668 55.000 3.32 0.00 0.00 4.70
3147 3310 1.117142 AGCTTGTGTTTGCATGGCCT 61.117 50.000 3.32 0.00 0.00 5.19
3169 3387 3.244840 CCATGAAGAAAAATTGGCCCCAA 60.245 43.478 0.00 1.67 40.47 4.12
3188 3406 8.017418 TCACTTTCAGTTGAATTTAAACCCAT 57.983 30.769 0.00 0.00 33.54 4.00
3189 3407 7.411486 TCACTTTCAGTTGAATTTAAACCCA 57.589 32.000 0.00 0.00 33.54 4.51
3195 3415 6.017109 GGTGAGCTCACTTTCAGTTGAATTTA 60.017 38.462 38.17 0.08 45.73 1.40
3203 3423 2.298729 GAGAGGTGAGCTCACTTTCAGT 59.701 50.000 38.17 23.17 45.73 3.41
3205 3425 1.270826 CGAGAGGTGAGCTCACTTTCA 59.729 52.381 38.17 6.91 45.73 2.69
3253 3474 1.066858 TGCGACTTCTGATTCTCCACC 60.067 52.381 0.00 0.00 0.00 4.61
3254 3475 2.370281 TGCGACTTCTGATTCTCCAC 57.630 50.000 0.00 0.00 0.00 4.02
3255 3476 2.159043 GGATGCGACTTCTGATTCTCCA 60.159 50.000 0.00 0.00 0.00 3.86
3281 3502 2.270352 AGAACCATTTTGTCCTCGCA 57.730 45.000 0.00 0.00 0.00 5.10
3384 3609 2.039084 TCCTTTCCTTTCACCTCTCAGC 59.961 50.000 0.00 0.00 0.00 4.26
3421 4817 2.197324 GAGCAACCCCACCCACAA 59.803 61.111 0.00 0.00 0.00 3.33
3422 4818 4.263572 CGAGCAACCCCACCCACA 62.264 66.667 0.00 0.00 0.00 4.17
3423 4819 2.798148 CTACGAGCAACCCCACCCAC 62.798 65.000 0.00 0.00 0.00 4.61
3427 4823 2.813908 CGCTACGAGCAACCCCAC 60.814 66.667 7.47 0.00 42.58 4.61
3428 4824 4.077184 CCGCTACGAGCAACCCCA 62.077 66.667 7.47 0.00 42.58 4.96
3551 4955 3.767806 GTCCCGTTCCCGTCCTCC 61.768 72.222 0.00 0.00 0.00 4.30
3553 4957 4.666253 TCGTCCCGTTCCCGTCCT 62.666 66.667 0.00 0.00 0.00 3.85
3554 4958 4.125695 CTCGTCCCGTTCCCGTCC 62.126 72.222 0.00 0.00 0.00 4.79
3555 4959 3.048941 CTCTCGTCCCGTTCCCGTC 62.049 68.421 0.00 0.00 0.00 4.79
3556 4960 3.060615 CTCTCGTCCCGTTCCCGT 61.061 66.667 0.00 0.00 0.00 5.28
3557 4961 2.749044 TCTCTCGTCCCGTTCCCG 60.749 66.667 0.00 0.00 0.00 5.14
3558 4962 1.678300 ACTCTCTCGTCCCGTTCCC 60.678 63.158 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.