Multiple sequence alignment - TraesCS4B01G323400

Loading Multiple Alignment...

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 TraesCS4B01G323400 chr4B 100.000 2312 0 0 1 2312 613904713 613907024 0.000000e+00 4270.0
1 TraesCS4B01G323400 chr4D 89.066 1317 78 37 388 1675 483180431 483179152 0.000000e+00 1574.0
2 TraesCS4B01G323400 chr5A 88.554 961 70 21 922 1863 663376284 663375345 0.000000e+00 1129.0
3 TraesCS4B01G323400 chr5A 87.576 491 31 13 188 669 663377244 663376775 2.020000e-150 542.0
4 TraesCS4B01G323400 chr5A 90.090 222 13 2 2092 2310 663374920 663374705 1.750000e-71 279.0
5 TraesCS4B01G323400 chr5A 97.468 79 0 1 1905 1981 663375105 663375027 1.440000e-27 134.0
6 TraesCS4B01G323400 chr5A 93.056 72 4 1 1997 2068 663374977 663374907 1.130000e-18 104.0
7 TraesCS4B01G323400 chr5A 77.037 135 25 5 1 132 28237129 28236998 3.190000e-09 73.1
8 TraesCS4B01G323400 chr4A 82.203 118 17 3 1 115 651346321 651346437 5.260000e-17 99.0
9 TraesCS4B01G323400 chr2B 81.667 120 19 3 1 118 621664412 621664530 1.890000e-16 97.1
10 TraesCS4B01G323400 chr2D 79.832 119 19 3 1 118 350071539 350071653 5.290000e-12 82.4
11 TraesCS4B01G323400 chr7A 79.675 123 16 7 1 118 125106442 125106560 1.900000e-11 80.5
12 TraesCS4B01G323400 chr1B 77.536 138 25 5 1 135 355154623 355154757 6.850000e-11 78.7
13 TraesCS4B01G323400 chr3B 78.689 122 20 5 1 118 617959790 617959909 2.460000e-10 76.8
14 TraesCS4B01G323400 chr1D 78.512 121 21 4 1 118 307442093 307442211 8.860000e-10 75.0
15 TraesCS4B01G323400 chr5B 77.698 139 17 11 1 132 467049780 467049911 3.190000e-09 73.1


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 TraesCS4B01G323400 chr4B 613904713 613907024 2311 False 4270.0 4270 100.0000 1 2312 1 chr4B.!!$F1 2311
1 TraesCS4B01G323400 chr4D 483179152 483180431 1279 True 1574.0 1574 89.0660 388 1675 1 chr4D.!!$R1 1287
2 TraesCS4B01G323400 chr5A 663374705 663377244 2539 True 437.6 1129 91.3488 188 2310 5 chr5A.!!$R2 2122

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
645 661 0.032615 AGGGGACAAGCCAACAACAA 60.033 50.0 0.0 0.0 38.95 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 2849 0.177836 TGGCATGCATACGTAGCAGT 59.822 50.0 21.36 9.43 46.36 4.4 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
60 61 5.957842 AAACTTCAGGTTGCGATAAATGA 57.042 34.783 0.00 0.00 38.29 2.57
61 62 6.515272 AAACTTCAGGTTGCGATAAATGAT 57.485 33.333 0.00 0.00 38.29 2.45
62 63 5.490139 ACTTCAGGTTGCGATAAATGATG 57.510 39.130 0.00 0.00 0.00 3.07
63 64 3.969117 TCAGGTTGCGATAAATGATGC 57.031 42.857 0.00 0.00 0.00 3.91
64 65 3.277715 TCAGGTTGCGATAAATGATGCA 58.722 40.909 0.00 0.00 35.15 3.96
65 66 3.065233 TCAGGTTGCGATAAATGATGCAC 59.935 43.478 0.00 0.00 37.01 4.57
66 67 3.016031 AGGTTGCGATAAATGATGCACA 58.984 40.909 0.00 0.00 37.01 4.57
67 68 3.633525 AGGTTGCGATAAATGATGCACAT 59.366 39.130 0.00 0.00 41.45 3.21
68 69 3.732219 GGTTGCGATAAATGATGCACATG 59.268 43.478 0.00 0.00 39.39 3.21
69 70 3.002708 TGCGATAAATGATGCACATGC 57.997 42.857 0.00 0.00 39.39 4.06
96 97 3.658757 GCATTTGCCACAAACCTAAGA 57.341 42.857 0.00 0.00 34.31 2.10
97 98 3.988819 GCATTTGCCACAAACCTAAGAA 58.011 40.909 0.00 0.00 34.31 2.52
98 99 3.989817 GCATTTGCCACAAACCTAAGAAG 59.010 43.478 0.00 0.00 34.31 2.85
99 100 4.261994 GCATTTGCCACAAACCTAAGAAGA 60.262 41.667 0.00 0.00 34.31 2.87
100 101 5.567423 GCATTTGCCACAAACCTAAGAAGAT 60.567 40.000 0.00 0.00 34.31 2.40
101 102 5.452078 TTTGCCACAAACCTAAGAAGATG 57.548 39.130 0.00 0.00 0.00 2.90
102 103 4.365514 TGCCACAAACCTAAGAAGATGA 57.634 40.909 0.00 0.00 0.00 2.92
103 104 4.326826 TGCCACAAACCTAAGAAGATGAG 58.673 43.478 0.00 0.00 0.00 2.90
104 105 4.041567 TGCCACAAACCTAAGAAGATGAGA 59.958 41.667 0.00 0.00 0.00 3.27
105 106 4.633565 GCCACAAACCTAAGAAGATGAGAG 59.366 45.833 0.00 0.00 0.00 3.20
106 107 5.799213 CCACAAACCTAAGAAGATGAGAGT 58.201 41.667 0.00 0.00 0.00 3.24
107 108 5.641209 CCACAAACCTAAGAAGATGAGAGTG 59.359 44.000 0.00 0.00 0.00 3.51
108 109 6.459066 CACAAACCTAAGAAGATGAGAGTGA 58.541 40.000 0.00 0.00 0.00 3.41
109 110 7.102346 CACAAACCTAAGAAGATGAGAGTGAT 58.898 38.462 0.00 0.00 0.00 3.06
110 111 7.277539 CACAAACCTAAGAAGATGAGAGTGATC 59.722 40.741 0.00 0.00 0.00 2.92
111 112 7.180051 ACAAACCTAAGAAGATGAGAGTGATCT 59.820 37.037 0.00 0.00 0.00 2.75
112 113 7.732222 AACCTAAGAAGATGAGAGTGATCTT 57.268 36.000 0.00 0.00 41.83 2.40
113 114 7.732222 ACCTAAGAAGATGAGAGTGATCTTT 57.268 36.000 0.00 0.00 39.72 2.52
114 115 7.555087 ACCTAAGAAGATGAGAGTGATCTTTG 58.445 38.462 0.00 0.00 39.72 2.77
115 116 6.479660 CCTAAGAAGATGAGAGTGATCTTTGC 59.520 42.308 0.00 0.00 39.72 3.68
116 117 5.417754 AGAAGATGAGAGTGATCTTTGCA 57.582 39.130 0.00 0.00 39.72 4.08
117 118 5.802465 AGAAGATGAGAGTGATCTTTGCAA 58.198 37.500 0.00 0.00 39.72 4.08
118 119 6.236409 AGAAGATGAGAGTGATCTTTGCAAA 58.764 36.000 12.14 12.14 39.72 3.68
119 120 6.713903 AGAAGATGAGAGTGATCTTTGCAAAA 59.286 34.615 13.84 5.01 39.72 2.44
120 121 6.251655 AGATGAGAGTGATCTTTGCAAAAC 57.748 37.500 13.84 8.43 0.00 2.43
121 122 5.766670 AGATGAGAGTGATCTTTGCAAAACA 59.233 36.000 13.84 10.72 0.00 2.83
122 123 5.428496 TGAGAGTGATCTTTGCAAAACAG 57.572 39.130 13.84 1.43 0.00 3.16
123 124 4.883585 TGAGAGTGATCTTTGCAAAACAGT 59.116 37.500 13.84 15.07 0.00 3.55
124 125 5.179045 AGAGTGATCTTTGCAAAACAGTG 57.821 39.130 13.84 0.98 0.00 3.66
125 126 3.709987 AGTGATCTTTGCAAAACAGTGC 58.290 40.909 13.84 2.67 45.15 4.40
126 127 3.382546 AGTGATCTTTGCAAAACAGTGCT 59.617 39.130 13.84 4.88 45.17 4.40
127 128 3.732721 GTGATCTTTGCAAAACAGTGCTC 59.267 43.478 13.84 3.08 45.17 4.26
128 129 3.633525 TGATCTTTGCAAAACAGTGCTCT 59.366 39.130 13.84 0.00 45.17 4.09
129 130 4.098349 TGATCTTTGCAAAACAGTGCTCTT 59.902 37.500 13.84 0.00 45.17 2.85
130 131 4.454728 TCTTTGCAAAACAGTGCTCTTT 57.545 36.364 13.84 0.00 45.17 2.52
131 132 5.574891 TCTTTGCAAAACAGTGCTCTTTA 57.425 34.783 13.84 0.00 45.17 1.85
132 133 6.147864 TCTTTGCAAAACAGTGCTCTTTAT 57.852 33.333 13.84 0.00 45.17 1.40
133 134 6.572519 TCTTTGCAAAACAGTGCTCTTTATT 58.427 32.000 13.84 0.00 45.17 1.40
134 135 6.697019 TCTTTGCAAAACAGTGCTCTTTATTC 59.303 34.615 13.84 0.00 45.17 1.75
135 136 5.772825 TGCAAAACAGTGCTCTTTATTCT 57.227 34.783 0.00 0.00 45.17 2.40
136 137 6.875948 TGCAAAACAGTGCTCTTTATTCTA 57.124 33.333 0.00 0.00 45.17 2.10
137 138 7.270757 TGCAAAACAGTGCTCTTTATTCTAA 57.729 32.000 0.00 0.00 45.17 2.10
138 139 7.138736 TGCAAAACAGTGCTCTTTATTCTAAC 58.861 34.615 0.00 0.00 45.17 2.34
139 140 7.138736 GCAAAACAGTGCTCTTTATTCTAACA 58.861 34.615 0.00 0.00 41.51 2.41
140 141 7.809806 GCAAAACAGTGCTCTTTATTCTAACAT 59.190 33.333 0.00 0.00 41.51 2.71
143 144 7.757097 ACAGTGCTCTTTATTCTAACATACG 57.243 36.000 0.00 0.00 0.00 3.06
144 145 6.757010 ACAGTGCTCTTTATTCTAACATACGG 59.243 38.462 0.00 0.00 0.00 4.02
145 146 6.757010 CAGTGCTCTTTATTCTAACATACGGT 59.243 38.462 0.00 0.00 0.00 4.83
146 147 7.277981 CAGTGCTCTTTATTCTAACATACGGTT 59.722 37.037 0.00 0.00 43.62 4.44
147 148 8.472413 AGTGCTCTTTATTCTAACATACGGTTA 58.528 33.333 0.00 0.00 40.96 2.85
148 149 9.090692 GTGCTCTTTATTCTAACATACGGTTAA 57.909 33.333 0.00 0.00 41.27 2.01
149 150 9.309516 TGCTCTTTATTCTAACATACGGTTAAG 57.690 33.333 0.00 0.00 41.27 1.85
150 151 8.274248 GCTCTTTATTCTAACATACGGTTAAGC 58.726 37.037 0.00 0.00 41.27 3.09
151 152 9.530633 CTCTTTATTCTAACATACGGTTAAGCT 57.469 33.333 2.76 0.00 41.27 3.74
154 155 9.533253 TTTATTCTAACATACGGTTAAGCTACC 57.467 33.333 2.76 0.00 41.27 3.18
155 156 6.528537 TTCTAACATACGGTTAAGCTACCA 57.471 37.500 6.48 0.00 41.27 3.25
156 157 6.528537 TCTAACATACGGTTAAGCTACCAA 57.471 37.500 6.48 0.00 41.27 3.67
157 158 6.934056 TCTAACATACGGTTAAGCTACCAAA 58.066 36.000 6.48 0.00 41.27 3.28
158 159 7.385267 TCTAACATACGGTTAAGCTACCAAAA 58.615 34.615 6.48 0.00 41.27 2.44
159 160 6.490566 AACATACGGTTAAGCTACCAAAAG 57.509 37.500 6.48 0.00 38.15 2.27
160 161 4.939439 ACATACGGTTAAGCTACCAAAAGG 59.061 41.667 6.48 0.00 38.12 3.11
161 162 3.497103 ACGGTTAAGCTACCAAAAGGT 57.503 42.857 6.48 0.00 38.12 3.50
162 163 3.143728 ACGGTTAAGCTACCAAAAGGTG 58.856 45.455 6.48 0.00 38.12 4.00
163 164 3.181452 ACGGTTAAGCTACCAAAAGGTGA 60.181 43.478 6.48 0.00 38.12 4.02
164 165 3.435671 CGGTTAAGCTACCAAAAGGTGAG 59.564 47.826 6.48 0.00 38.12 3.51
165 166 4.648651 GGTTAAGCTACCAAAAGGTGAGA 58.351 43.478 0.45 0.00 38.12 3.27
166 167 4.695928 GGTTAAGCTACCAAAAGGTGAGAG 59.304 45.833 0.45 0.00 38.12 3.20
167 168 5.306394 GTTAAGCTACCAAAAGGTGAGAGT 58.694 41.667 0.00 0.00 0.00 3.24
168 169 3.409026 AGCTACCAAAAGGTGAGAGTG 57.591 47.619 0.00 0.00 0.00 3.51
169 170 2.972713 AGCTACCAAAAGGTGAGAGTGA 59.027 45.455 0.00 0.00 0.00 3.41
170 171 3.584848 AGCTACCAAAAGGTGAGAGTGAT 59.415 43.478 0.00 0.00 0.00 3.06
171 172 4.042187 AGCTACCAAAAGGTGAGAGTGATT 59.958 41.667 0.00 0.00 0.00 2.57
172 173 4.762251 GCTACCAAAAGGTGAGAGTGATTT 59.238 41.667 0.00 0.00 0.00 2.17
173 174 5.106515 GCTACCAAAAGGTGAGAGTGATTTC 60.107 44.000 0.00 0.00 0.00 2.17
174 175 3.815401 ACCAAAAGGTGAGAGTGATTTCG 59.185 43.478 0.00 0.00 0.00 3.46
175 176 3.189287 CCAAAAGGTGAGAGTGATTTCGG 59.811 47.826 0.00 0.00 0.00 4.30
176 177 2.770164 AAGGTGAGAGTGATTTCGGG 57.230 50.000 0.00 0.00 0.00 5.14
177 178 0.250513 AGGTGAGAGTGATTTCGGGC 59.749 55.000 0.00 0.00 0.00 6.13
178 179 1.084370 GGTGAGAGTGATTTCGGGCG 61.084 60.000 0.00 0.00 0.00 6.13
179 180 1.447838 TGAGAGTGATTTCGGGCGC 60.448 57.895 0.00 0.00 0.00 6.53
180 181 2.509336 AGAGTGATTTCGGGCGCG 60.509 61.111 18.21 18.21 0.00 6.86
181 182 3.564027 GAGTGATTTCGGGCGCGG 61.564 66.667 23.74 4.77 0.00 6.46
182 183 4.077184 AGTGATTTCGGGCGCGGA 62.077 61.111 23.74 12.70 0.00 5.54
183 184 3.122323 GTGATTTCGGGCGCGGAA 61.122 61.111 20.01 20.01 0.00 4.30
184 185 2.817834 TGATTTCGGGCGCGGAAG 60.818 61.111 22.08 0.00 0.00 3.46
223 224 2.457366 AGCTACCAAACGGACTCTTG 57.543 50.000 0.00 0.00 0.00 3.02
235 236 2.419159 CGGACTCTTGATGCTGATCCAA 60.419 50.000 0.00 0.00 0.00 3.53
246 247 4.890158 TGCTGATCCAACTCAGAAACTA 57.110 40.909 5.31 0.00 44.48 2.24
248 249 3.620821 GCTGATCCAACTCAGAAACTAGC 59.379 47.826 5.31 0.00 44.48 3.42
278 279 2.359975 CGTCCAGACCCAAAGGCC 60.360 66.667 0.00 0.00 36.11 5.19
279 280 2.035783 GTCCAGACCCAAAGGCCC 59.964 66.667 0.00 0.00 36.11 5.80
290 291 1.528309 AAAGGCCCTGGTGTCGTTG 60.528 57.895 0.00 0.00 0.00 4.10
295 296 4.988598 CCTGGTGTCGTTGCCGCT 62.989 66.667 0.00 0.00 0.00 5.52
308 309 4.320456 CCGCTGGTCACTGGCACT 62.320 66.667 0.00 0.00 0.00 4.40
309 310 3.046087 CGCTGGTCACTGGCACTG 61.046 66.667 0.00 0.00 0.00 3.66
310 311 2.670934 GCTGGTCACTGGCACTGG 60.671 66.667 0.00 0.00 0.00 4.00
311 312 2.670934 CTGGTCACTGGCACTGGC 60.671 66.667 0.00 0.00 40.13 4.85
312 313 3.480679 CTGGTCACTGGCACTGGCA 62.481 63.158 5.02 5.02 43.71 4.92
313 314 2.203337 GGTCACTGGCACTGGCAA 60.203 61.111 6.75 0.00 43.71 4.52
329 342 1.970114 CAAGCAGTGGCACCTCTGG 60.970 63.158 15.27 5.36 44.61 3.86
376 389 1.061411 CATGCATGCAGAACCGTCG 59.939 57.895 26.69 2.94 0.00 5.12
377 390 1.375908 ATGCATGCAGAACCGTCGT 60.376 52.632 26.69 2.26 0.00 4.34
378 391 1.361668 ATGCATGCAGAACCGTCGTC 61.362 55.000 26.69 0.00 0.00 4.20
379 392 1.738099 GCATGCAGAACCGTCGTCT 60.738 57.895 14.21 0.00 0.00 4.18
380 393 0.457853 GCATGCAGAACCGTCGTCTA 60.458 55.000 14.21 0.00 0.00 2.59
381 394 1.269166 CATGCAGAACCGTCGTCTAC 58.731 55.000 0.00 0.00 0.00 2.59
382 395 0.172803 ATGCAGAACCGTCGTCTACC 59.827 55.000 0.00 0.00 0.00 3.18
383 396 0.892358 TGCAGAACCGTCGTCTACCT 60.892 55.000 0.00 0.00 0.00 3.08
384 397 0.179169 GCAGAACCGTCGTCTACCTC 60.179 60.000 0.00 0.00 0.00 3.85
385 398 0.450983 CAGAACCGTCGTCTACCTCC 59.549 60.000 0.00 0.00 0.00 4.30
386 399 0.037303 AGAACCGTCGTCTACCTCCA 59.963 55.000 0.00 0.00 0.00 3.86
417 430 3.677424 GCACCAAAACCAAACTGTTGCTA 60.677 43.478 0.00 0.00 33.01 3.49
424 437 3.740115 ACCAAACTGTTGCTACTCGAAT 58.260 40.909 0.00 0.00 33.01 3.34
425 438 3.746492 ACCAAACTGTTGCTACTCGAATC 59.254 43.478 0.00 0.00 33.01 2.52
426 439 3.745975 CCAAACTGTTGCTACTCGAATCA 59.254 43.478 0.00 0.00 33.01 2.57
427 440 4.213270 CCAAACTGTTGCTACTCGAATCAA 59.787 41.667 0.00 0.00 33.01 2.57
428 441 5.277779 CCAAACTGTTGCTACTCGAATCAAA 60.278 40.000 0.00 0.00 33.01 2.69
568 583 1.210478 CATTCCATCTCCCGTGAACCT 59.790 52.381 0.00 0.00 0.00 3.50
575 590 1.229368 TCCCGTGAACCTGATCCCA 60.229 57.895 0.00 0.00 0.00 4.37
645 661 0.032615 AGGGGACAAGCCAACAACAA 60.033 50.000 0.00 0.00 38.95 2.83
710 746 2.418083 CCAAGGGCCCGCATCTTTC 61.418 63.158 18.44 0.00 0.00 2.62
726 869 0.881118 TTTCGGAGAATTGCACAGCC 59.119 50.000 0.00 0.00 45.90 4.85
748 891 3.689161 CCTTAATTCCGTTGTGCTCATGA 59.311 43.478 0.00 0.00 0.00 3.07
754 897 1.541147 CCGTTGTGCTCATGACCAAAT 59.459 47.619 0.00 0.00 0.00 2.32
755 898 2.030007 CCGTTGTGCTCATGACCAAATT 60.030 45.455 0.00 0.00 0.00 1.82
756 899 3.190327 CCGTTGTGCTCATGACCAAATTA 59.810 43.478 0.00 0.00 0.00 1.40
757 900 4.406069 CGTTGTGCTCATGACCAAATTAG 58.594 43.478 0.00 0.00 0.00 1.73
818 1110 0.534412 CCACAAAGTTGCAACACCCA 59.466 50.000 30.11 0.00 0.00 4.51
843 1140 0.749454 CAAAGCCTCCCATTCCCTCG 60.749 60.000 0.00 0.00 0.00 4.63
856 1153 3.788333 TTCCCTCGTCACGGTATAAAG 57.212 47.619 0.00 0.00 0.00 1.85
857 1154 2.026641 TCCCTCGTCACGGTATAAAGG 58.973 52.381 0.00 0.00 0.00 3.11
867 1164 1.596203 GTATAAAGGACCGCGCCCC 60.596 63.158 0.00 3.27 0.00 5.80
904 1201 2.106566 TCACAAGCCACCACAACAATT 58.893 42.857 0.00 0.00 0.00 2.32
907 1204 3.989167 CACAAGCCACCACAACAATTATG 59.011 43.478 0.00 0.00 0.00 1.90
909 1206 2.246469 AGCCACCACAACAATTATGCA 58.754 42.857 0.00 0.00 0.00 3.96
911 1208 3.261390 AGCCACCACAACAATTATGCAAT 59.739 39.130 0.00 0.00 0.00 3.56
913 1210 5.046735 AGCCACCACAACAATTATGCAATTA 60.047 36.000 0.00 0.00 32.96 1.40
914 1211 5.816777 GCCACCACAACAATTATGCAATTAT 59.183 36.000 0.00 0.00 32.96 1.28
915 1212 6.315891 GCCACCACAACAATTATGCAATTATT 59.684 34.615 0.00 0.00 32.96 1.40
916 1213 7.676807 GCCACCACAACAATTATGCAATTATTG 60.677 37.037 13.89 13.89 45.88 1.90
948 1245 2.043852 ACCGATCGAGCTCCCACT 60.044 61.111 18.66 0.00 0.00 4.00
952 1249 0.318275 CGATCGAGCTCCCACTTAGC 60.318 60.000 10.26 0.00 40.40 3.09
996 1294 1.201647 GCTCGGTGTACTAGCTTGTGA 59.798 52.381 11.27 0.00 33.40 3.58
1007 1305 1.375908 GCTTGTGAGACATGGCCGA 60.376 57.895 0.00 0.00 0.00 5.54
1014 1312 2.230994 GAGACATGGCCGACAGCAGA 62.231 60.000 0.00 0.00 46.50 4.26
1015 1313 2.046892 ACATGGCCGACAGCAGAC 60.047 61.111 0.00 0.00 46.50 3.51
1049 1350 3.823330 GGCCATCCTCGTCGTCGT 61.823 66.667 0.00 0.00 38.33 4.34
1051 1352 2.022902 CCATCCTCGTCGTCGTCG 59.977 66.667 5.50 5.50 38.33 5.12
1052 1353 2.648102 CATCCTCGTCGTCGTCGC 60.648 66.667 7.01 0.00 38.33 5.19
1053 1354 2.818714 ATCCTCGTCGTCGTCGCT 60.819 61.111 7.01 0.00 38.33 4.93
1331 1649 1.379044 CCACCCTCCCAACATCTGC 60.379 63.158 0.00 0.00 0.00 4.26
1466 1790 2.076100 CTACGTACCTGTCGGTGTGTA 58.924 52.381 0.00 0.00 45.18 2.90
1467 1791 0.877071 ACGTACCTGTCGGTGTGTAG 59.123 55.000 0.00 0.00 45.18 2.74
1479 1803 2.933906 CGGTGTGTAGAAGTGTGTGTTT 59.066 45.455 0.00 0.00 0.00 2.83
1482 1810 3.000925 GTGTGTAGAAGTGTGTGTTTCCG 59.999 47.826 0.00 0.00 0.00 4.30
1536 1865 6.095580 TGTGTAACATTGCCACTACTTCAAAA 59.904 34.615 0.00 0.00 45.67 2.44
1537 1866 6.975772 GTGTAACATTGCCACTACTTCAAAAA 59.024 34.615 0.00 0.00 36.32 1.94
1585 1915 7.176515 TGCATGTGGTTTCTGTAAACAATCTAT 59.823 33.333 0.00 0.00 45.68 1.98
1593 1923 5.433526 TCTGTAAACAATCTATTTCGGGGG 58.566 41.667 0.00 0.00 0.00 5.40
1609 1939 1.958579 GGGGGTTAATTAATCCACCGC 59.041 52.381 25.42 17.89 38.23 5.68
1658 1988 3.021269 ACAGTGCTTCGTTCAATCGTA 57.979 42.857 0.00 0.00 0.00 3.43
1666 1996 5.191059 GCTTCGTTCAATCGTATCATGTTC 58.809 41.667 0.00 0.00 0.00 3.18
1772 2102 1.279496 CCAACATCTGTCCTCCTGGA 58.721 55.000 0.00 0.00 40.69 3.86
1784 2114 2.149578 CCTCCTGGAATCGATTGATGC 58.850 52.381 16.96 0.17 34.24 3.91
1785 2115 2.486013 CCTCCTGGAATCGATTGATGCA 60.486 50.000 16.96 2.15 34.24 3.96
1795 2125 7.661027 TGGAATCGATTGATGCAGTATAAATGA 59.339 33.333 16.96 0.00 34.24 2.57
1799 2129 6.424812 TCGATTGATGCAGTATAAATGACTGG 59.575 38.462 5.05 0.00 43.78 4.00
1804 2134 3.142174 GCAGTATAAATGACTGGAGCCC 58.858 50.000 5.05 0.00 43.78 5.19
1828 2158 5.566826 CGGAGGTACAATATACATCCACCAG 60.567 48.000 15.72 0.00 45.63 4.00
1835 2165 0.756903 ATACATCCACCAGGCCGTAC 59.243 55.000 0.00 0.00 33.74 3.67
1857 2187 1.597742 CTGTGGGTGTGTGAAAGAGG 58.402 55.000 0.00 0.00 0.00 3.69
1864 2358 1.065551 GTGTGTGAAAGAGGGTGTTGC 59.934 52.381 0.00 0.00 0.00 4.17
1889 2383 1.152030 TCCCCTCTTGGCAGTGACT 60.152 57.895 0.00 0.00 0.00 3.41
1890 2384 1.002868 CCCCTCTTGGCAGTGACTG 60.003 63.158 8.52 8.52 34.12 3.51
1981 2513 1.066358 TCTACGAGGACGAGAGCTTGA 60.066 52.381 0.00 0.00 42.66 3.02
1982 2514 1.944024 CTACGAGGACGAGAGCTTGAT 59.056 52.381 0.00 0.00 42.66 2.57
1984 2516 1.021202 CGAGGACGAGAGCTTGATCT 58.979 55.000 0.00 0.00 42.66 2.75
1985 2517 1.268488 CGAGGACGAGAGCTTGATCTG 60.268 57.143 0.00 0.00 42.66 2.90
1986 2518 1.748493 GAGGACGAGAGCTTGATCTGT 59.252 52.381 0.00 0.00 0.00 3.41
1987 2519 2.946329 GAGGACGAGAGCTTGATCTGTA 59.054 50.000 0.00 0.00 0.00 2.74
1988 2520 3.357203 AGGACGAGAGCTTGATCTGTAA 58.643 45.455 0.00 0.00 0.00 2.41
1989 2521 3.129638 AGGACGAGAGCTTGATCTGTAAC 59.870 47.826 0.00 0.00 0.00 2.50
1990 2522 3.440228 GACGAGAGCTTGATCTGTAACC 58.560 50.000 0.00 0.00 0.00 2.85
1991 2523 2.826128 ACGAGAGCTTGATCTGTAACCA 59.174 45.455 0.00 0.00 0.00 3.67
1992 2524 3.258372 ACGAGAGCTTGATCTGTAACCAA 59.742 43.478 0.00 0.00 0.00 3.67
2024 2590 1.599797 GGGCCGGGTTAATCCATCG 60.600 63.158 2.18 0.00 38.11 3.84
2031 2597 3.123804 CGGGTTAATCCATCGACAGAAG 58.876 50.000 5.41 0.00 38.11 2.85
2039 2605 1.638133 CATCGACAGAAGTCCAGCTG 58.362 55.000 6.78 6.78 41.87 4.24
2049 2615 4.081198 CAGAAGTCCAGCTGTCTTATCCTT 60.081 45.833 13.81 3.50 0.00 3.36
2050 2616 4.161377 AGAAGTCCAGCTGTCTTATCCTTC 59.839 45.833 13.81 11.72 0.00 3.46
2051 2617 3.445008 AGTCCAGCTGTCTTATCCTTCA 58.555 45.455 13.81 0.00 0.00 3.02
2052 2618 3.196685 AGTCCAGCTGTCTTATCCTTCAC 59.803 47.826 13.81 0.00 0.00 3.18
2053 2619 3.055819 GTCCAGCTGTCTTATCCTTCACA 60.056 47.826 13.81 0.00 0.00 3.58
2054 2620 3.582647 TCCAGCTGTCTTATCCTTCACAA 59.417 43.478 13.81 0.00 0.00 3.33
2055 2621 3.686726 CCAGCTGTCTTATCCTTCACAAC 59.313 47.826 13.81 0.00 0.00 3.32
2056 2622 4.318332 CAGCTGTCTTATCCTTCACAACA 58.682 43.478 5.25 0.00 0.00 3.33
2057 2623 4.391216 CAGCTGTCTTATCCTTCACAACAG 59.609 45.833 5.25 0.00 36.58 3.16
2058 2624 4.040952 AGCTGTCTTATCCTTCACAACAGT 59.959 41.667 0.00 0.00 36.05 3.55
2059 2625 4.153117 GCTGTCTTATCCTTCACAACAGTG 59.847 45.833 0.00 0.00 36.05 3.66
2060 2626 5.290493 TGTCTTATCCTTCACAACAGTGT 57.710 39.130 0.00 0.00 39.07 3.55
2061 2627 5.680619 TGTCTTATCCTTCACAACAGTGTT 58.319 37.500 1.64 1.64 35.07 3.32
2062 2628 5.758296 TGTCTTATCCTTCACAACAGTGTTC 59.242 40.000 5.27 0.00 35.07 3.18
2063 2629 5.179555 GTCTTATCCTTCACAACAGTGTTCC 59.820 44.000 5.27 0.00 35.07 3.62
2064 2630 1.948104 TCCTTCACAACAGTGTTCCG 58.052 50.000 5.27 0.00 35.07 4.30
2065 2631 1.208535 TCCTTCACAACAGTGTTCCGT 59.791 47.619 5.27 0.00 35.07 4.69
2066 2632 2.014128 CCTTCACAACAGTGTTCCGTT 58.986 47.619 5.27 0.00 35.07 4.44
2067 2633 2.031683 CCTTCACAACAGTGTTCCGTTC 59.968 50.000 5.27 0.00 35.07 3.95
2068 2634 2.684001 TCACAACAGTGTTCCGTTCT 57.316 45.000 5.27 0.00 35.07 3.01
2069 2635 2.980568 TCACAACAGTGTTCCGTTCTT 58.019 42.857 5.27 0.00 35.07 2.52
2070 2636 4.126208 TCACAACAGTGTTCCGTTCTTA 57.874 40.909 5.27 0.00 35.07 2.10
2071 2637 4.116961 TCACAACAGTGTTCCGTTCTTAG 58.883 43.478 5.27 0.00 35.07 2.18
2072 2638 2.870411 ACAACAGTGTTCCGTTCTTAGC 59.130 45.455 5.27 0.00 32.58 3.09
2073 2639 3.131396 CAACAGTGTTCCGTTCTTAGCT 58.869 45.455 5.27 0.00 0.00 3.32
2074 2640 3.027974 ACAGTGTTCCGTTCTTAGCTC 57.972 47.619 0.00 0.00 0.00 4.09
2075 2641 2.364324 ACAGTGTTCCGTTCTTAGCTCA 59.636 45.455 0.00 0.00 0.00 4.26
2076 2642 2.989840 CAGTGTTCCGTTCTTAGCTCAG 59.010 50.000 0.00 0.00 0.00 3.35
2077 2643 2.891580 AGTGTTCCGTTCTTAGCTCAGA 59.108 45.455 0.00 0.00 0.00 3.27
2078 2644 3.057174 AGTGTTCCGTTCTTAGCTCAGAG 60.057 47.826 0.00 0.00 0.00 3.35
2079 2645 3.057456 GTGTTCCGTTCTTAGCTCAGAGA 60.057 47.826 0.00 0.00 0.00 3.10
2080 2646 3.572682 TGTTCCGTTCTTAGCTCAGAGAA 59.427 43.478 0.00 0.00 0.00 2.87
2081 2647 4.170256 GTTCCGTTCTTAGCTCAGAGAAG 58.830 47.826 0.00 0.00 32.91 2.85
2082 2648 3.687125 TCCGTTCTTAGCTCAGAGAAGA 58.313 45.455 0.00 0.00 32.91 2.87
2083 2649 4.079970 TCCGTTCTTAGCTCAGAGAAGAA 58.920 43.478 0.00 5.94 36.97 2.52
2084 2650 4.156922 TCCGTTCTTAGCTCAGAGAAGAAG 59.843 45.833 12.52 7.13 39.28 2.85
2085 2651 4.156922 CCGTTCTTAGCTCAGAGAAGAAGA 59.843 45.833 12.52 8.95 39.28 2.87
2086 2652 5.336055 CCGTTCTTAGCTCAGAGAAGAAGAA 60.336 44.000 12.52 13.19 39.28 2.52
2087 2653 6.153067 CGTTCTTAGCTCAGAGAAGAAGAAA 58.847 40.000 17.15 5.80 39.28 2.52
2088 2654 6.642950 CGTTCTTAGCTCAGAGAAGAAGAAAA 59.357 38.462 17.15 2.12 39.28 2.29
2089 2655 7.169982 CGTTCTTAGCTCAGAGAAGAAGAAAAA 59.830 37.037 17.15 1.61 39.28 1.94
2090 2656 8.998377 GTTCTTAGCTCAGAGAAGAAGAAAAAT 58.002 33.333 17.15 0.00 39.28 1.82
2097 2663 7.172361 GCTCAGAGAAGAAGAAAAATACAGTGT 59.828 37.037 0.00 0.00 0.00 3.55
2115 2681 1.595929 TTCCGTTCAGTCGTTGGGC 60.596 57.895 0.00 0.00 0.00 5.36
2241 2810 4.969484 ACAACCTCCGATGAACTTTAGTT 58.031 39.130 0.00 0.00 41.64 2.24
2242 2811 6.105397 ACAACCTCCGATGAACTTTAGTTA 57.895 37.500 0.00 0.00 38.56 2.24
2243 2812 6.164176 ACAACCTCCGATGAACTTTAGTTAG 58.836 40.000 0.00 0.00 38.56 2.34
2244 2813 5.997384 ACCTCCGATGAACTTTAGTTAGT 57.003 39.130 0.00 0.00 38.56 2.24
2245 2814 7.039504 ACAACCTCCGATGAACTTTAGTTAGTA 60.040 37.037 0.00 0.00 38.56 1.82
2246 2815 7.098074 ACCTCCGATGAACTTTAGTTAGTAG 57.902 40.000 0.00 0.00 38.56 2.57
2280 2849 2.171237 CCTCCAGTAATCATCTGTGCCA 59.829 50.000 0.00 0.00 0.00 4.92
2287 2856 2.322355 ATCATCTGTGCCACTGCTAC 57.678 50.000 0.00 0.00 38.71 3.58
2310 2879 0.528924 TGCATGCCAGCATCAACTTC 59.471 50.000 16.68 0.00 40.11 3.01
2311 2880 0.815734 GCATGCCAGCATCAACTTCT 59.184 50.000 6.36 0.00 33.90 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 6.744112 TCATTTATCGCAACCTGAAGTTTTT 58.256 32.000 0.00 0.00 36.18 1.94
37 38 6.325919 TCATTTATCGCAACCTGAAGTTTT 57.674 33.333 0.00 0.00 36.18 2.43
38 39 5.957842 TCATTTATCGCAACCTGAAGTTT 57.042 34.783 0.00 0.00 36.18 2.66
39 40 5.677091 GCATCATTTATCGCAACCTGAAGTT 60.677 40.000 0.00 0.00 40.16 2.66
40 41 4.201950 GCATCATTTATCGCAACCTGAAGT 60.202 41.667 0.00 0.00 0.00 3.01
41 42 4.201940 TGCATCATTTATCGCAACCTGAAG 60.202 41.667 0.00 0.00 0.00 3.02
42 43 3.693578 TGCATCATTTATCGCAACCTGAA 59.306 39.130 0.00 0.00 0.00 3.02
43 44 3.065233 GTGCATCATTTATCGCAACCTGA 59.935 43.478 0.00 0.00 35.87 3.86
44 45 3.181498 TGTGCATCATTTATCGCAACCTG 60.181 43.478 0.00 0.00 35.87 4.00
45 46 3.016031 TGTGCATCATTTATCGCAACCT 58.984 40.909 0.00 0.00 35.87 3.50
46 47 3.419264 TGTGCATCATTTATCGCAACC 57.581 42.857 0.00 0.00 35.87 3.77
47 48 3.180980 GCATGTGCATCATTTATCGCAAC 59.819 43.478 0.00 0.00 41.59 4.17
48 49 3.373849 GCATGTGCATCATTTATCGCAA 58.626 40.909 0.00 0.00 41.59 4.85
49 50 3.002708 GCATGTGCATCATTTATCGCA 57.997 42.857 0.00 0.00 41.59 5.10
76 77 3.658757 TCTTAGGTTTGTGGCAAATGC 57.341 42.857 0.00 0.00 41.14 3.56
77 78 5.452078 TCTTCTTAGGTTTGTGGCAAATG 57.548 39.130 0.00 0.00 0.00 2.32
78 79 5.774690 TCATCTTCTTAGGTTTGTGGCAAAT 59.225 36.000 0.00 0.00 0.00 2.32
79 80 5.136828 TCATCTTCTTAGGTTTGTGGCAAA 58.863 37.500 0.00 0.00 0.00 3.68
80 81 4.724399 TCATCTTCTTAGGTTTGTGGCAA 58.276 39.130 0.00 0.00 0.00 4.52
81 82 4.041567 TCTCATCTTCTTAGGTTTGTGGCA 59.958 41.667 0.00 0.00 0.00 4.92
82 83 4.579869 TCTCATCTTCTTAGGTTTGTGGC 58.420 43.478 0.00 0.00 0.00 5.01
83 84 5.641209 CACTCTCATCTTCTTAGGTTTGTGG 59.359 44.000 0.00 0.00 0.00 4.17
84 85 6.459066 TCACTCTCATCTTCTTAGGTTTGTG 58.541 40.000 0.00 0.00 0.00 3.33
85 86 6.672266 TCACTCTCATCTTCTTAGGTTTGT 57.328 37.500 0.00 0.00 0.00 2.83
86 87 7.555087 AGATCACTCTCATCTTCTTAGGTTTG 58.445 38.462 0.00 0.00 0.00 2.93
87 88 7.732222 AGATCACTCTCATCTTCTTAGGTTT 57.268 36.000 0.00 0.00 0.00 3.27
88 89 7.732222 AAGATCACTCTCATCTTCTTAGGTT 57.268 36.000 0.00 0.00 36.04 3.50
89 90 7.555087 CAAAGATCACTCTCATCTTCTTAGGT 58.445 38.462 0.00 0.00 39.27 3.08
90 91 6.479660 GCAAAGATCACTCTCATCTTCTTAGG 59.520 42.308 0.00 0.00 39.27 2.69
91 92 7.040494 TGCAAAGATCACTCTCATCTTCTTAG 58.960 38.462 0.00 0.00 39.27 2.18
92 93 6.939622 TGCAAAGATCACTCTCATCTTCTTA 58.060 36.000 0.00 0.00 39.27 2.10
93 94 5.802465 TGCAAAGATCACTCTCATCTTCTT 58.198 37.500 0.00 0.00 39.27 2.52
94 95 5.417754 TGCAAAGATCACTCTCATCTTCT 57.582 39.130 0.00 0.00 39.27 2.85
95 96 6.492007 TTTGCAAAGATCACTCTCATCTTC 57.508 37.500 8.05 0.00 39.27 2.87
96 97 6.263842 TGTTTTGCAAAGATCACTCTCATCTT 59.736 34.615 12.41 0.00 41.50 2.40
97 98 5.766670 TGTTTTGCAAAGATCACTCTCATCT 59.233 36.000 12.41 0.00 31.51 2.90
98 99 6.005583 TGTTTTGCAAAGATCACTCTCATC 57.994 37.500 12.41 0.00 0.00 2.92
99 100 5.533903 ACTGTTTTGCAAAGATCACTCTCAT 59.466 36.000 12.41 0.00 0.00 2.90
100 101 4.883585 ACTGTTTTGCAAAGATCACTCTCA 59.116 37.500 12.41 0.00 0.00 3.27
101 102 5.210715 CACTGTTTTGCAAAGATCACTCTC 58.789 41.667 12.41 0.00 0.00 3.20
102 103 4.498682 GCACTGTTTTGCAAAGATCACTCT 60.499 41.667 12.41 0.00 42.49 3.24
103 104 3.732721 GCACTGTTTTGCAAAGATCACTC 59.267 43.478 12.41 0.00 42.49 3.51
104 105 3.382546 AGCACTGTTTTGCAAAGATCACT 59.617 39.130 12.41 4.63 45.62 3.41
105 106 3.709987 AGCACTGTTTTGCAAAGATCAC 58.290 40.909 12.41 8.31 45.62 3.06
106 107 3.633525 AGAGCACTGTTTTGCAAAGATCA 59.366 39.130 12.41 11.73 45.62 2.92
107 108 4.234530 AGAGCACTGTTTTGCAAAGATC 57.765 40.909 12.41 8.60 45.62 2.75
108 109 4.660789 AAGAGCACTGTTTTGCAAAGAT 57.339 36.364 12.41 0.00 45.62 2.40
109 110 4.454728 AAAGAGCACTGTTTTGCAAAGA 57.545 36.364 12.41 2.48 45.62 2.52
110 111 6.698766 AGAATAAAGAGCACTGTTTTGCAAAG 59.301 34.615 12.41 3.37 45.62 2.77
111 112 6.572519 AGAATAAAGAGCACTGTTTTGCAAA 58.427 32.000 8.05 8.05 45.62 3.68
112 113 6.147864 AGAATAAAGAGCACTGTTTTGCAA 57.852 33.333 0.00 0.00 45.62 4.08
113 114 5.772825 AGAATAAAGAGCACTGTTTTGCA 57.227 34.783 0.00 0.00 45.62 4.08
114 115 7.138736 TGTTAGAATAAAGAGCACTGTTTTGC 58.861 34.615 0.00 0.00 43.34 3.68
117 118 8.656849 CGTATGTTAGAATAAAGAGCACTGTTT 58.343 33.333 0.00 0.00 0.00 2.83
118 119 7.277981 CCGTATGTTAGAATAAAGAGCACTGTT 59.722 37.037 0.00 0.00 0.00 3.16
119 120 6.757010 CCGTATGTTAGAATAAAGAGCACTGT 59.243 38.462 0.00 0.00 0.00 3.55
120 121 6.757010 ACCGTATGTTAGAATAAAGAGCACTG 59.243 38.462 0.00 0.00 0.00 3.66
121 122 6.875076 ACCGTATGTTAGAATAAAGAGCACT 58.125 36.000 0.00 0.00 0.00 4.40
122 123 7.535489 AACCGTATGTTAGAATAAAGAGCAC 57.465 36.000 0.00 0.00 34.69 4.40
123 124 9.309516 CTTAACCGTATGTTAGAATAAAGAGCA 57.690 33.333 0.00 0.00 40.42 4.26
124 125 8.274248 GCTTAACCGTATGTTAGAATAAAGAGC 58.726 37.037 0.00 0.00 40.42 4.09
125 126 9.530633 AGCTTAACCGTATGTTAGAATAAAGAG 57.469 33.333 0.00 0.00 40.42 2.85
128 129 9.533253 GGTAGCTTAACCGTATGTTAGAATAAA 57.467 33.333 0.00 0.00 40.42 1.40
129 130 8.694540 TGGTAGCTTAACCGTATGTTAGAATAA 58.305 33.333 0.00 0.00 42.91 1.40
130 131 8.236585 TGGTAGCTTAACCGTATGTTAGAATA 57.763 34.615 0.00 0.00 42.91 1.75
131 132 7.116075 TGGTAGCTTAACCGTATGTTAGAAT 57.884 36.000 0.00 0.00 42.91 2.40
132 133 6.528537 TGGTAGCTTAACCGTATGTTAGAA 57.471 37.500 0.00 0.00 42.91 2.10
133 134 6.528537 TTGGTAGCTTAACCGTATGTTAGA 57.471 37.500 0.00 0.00 42.91 2.10
134 135 7.201582 CCTTTTGGTAGCTTAACCGTATGTTAG 60.202 40.741 0.00 0.00 42.91 2.34
135 136 6.594937 CCTTTTGGTAGCTTAACCGTATGTTA 59.405 38.462 0.00 0.00 42.91 2.41
136 137 5.413523 CCTTTTGGTAGCTTAACCGTATGTT 59.586 40.000 0.00 0.00 42.91 2.71
137 138 4.939439 CCTTTTGGTAGCTTAACCGTATGT 59.061 41.667 0.00 0.00 42.91 2.29
138 139 5.479716 CCTTTTGGTAGCTTAACCGTATG 57.520 43.478 0.00 0.00 42.91 2.39
154 155 3.189287 CCCGAAATCACTCTCACCTTTTG 59.811 47.826 0.00 0.00 0.00 2.44
155 156 3.412386 CCCGAAATCACTCTCACCTTTT 58.588 45.455 0.00 0.00 0.00 2.27
156 157 2.876079 GCCCGAAATCACTCTCACCTTT 60.876 50.000 0.00 0.00 0.00 3.11
157 158 1.339151 GCCCGAAATCACTCTCACCTT 60.339 52.381 0.00 0.00 0.00 3.50
158 159 0.250513 GCCCGAAATCACTCTCACCT 59.749 55.000 0.00 0.00 0.00 4.00
159 160 1.084370 CGCCCGAAATCACTCTCACC 61.084 60.000 0.00 0.00 0.00 4.02
160 161 1.696832 GCGCCCGAAATCACTCTCAC 61.697 60.000 0.00 0.00 0.00 3.51
161 162 1.447838 GCGCCCGAAATCACTCTCA 60.448 57.895 0.00 0.00 0.00 3.27
162 163 2.517450 CGCGCCCGAAATCACTCTC 61.517 63.158 0.00 0.00 36.29 3.20
163 164 2.509336 CGCGCCCGAAATCACTCT 60.509 61.111 0.00 0.00 36.29 3.24
164 165 3.564027 CCGCGCCCGAAATCACTC 61.564 66.667 0.00 0.00 36.29 3.51
165 166 3.599285 TTCCGCGCCCGAAATCACT 62.599 57.895 0.00 0.00 36.29 3.41
166 167 3.095898 CTTCCGCGCCCGAAATCAC 62.096 63.158 0.00 0.00 36.29 3.06
167 168 2.817834 CTTCCGCGCCCGAAATCA 60.818 61.111 0.00 0.00 36.29 2.57
168 169 4.237809 GCTTCCGCGCCCGAAATC 62.238 66.667 0.00 0.00 36.29 2.17
169 170 4.778143 AGCTTCCGCGCCCGAAAT 62.778 61.111 0.00 0.00 42.32 2.17
176 177 3.100862 GATTCCACAGCTTCCGCGC 62.101 63.158 0.00 0.00 42.32 6.86
177 178 2.464459 GGATTCCACAGCTTCCGCG 61.464 63.158 0.00 0.00 42.32 6.46
178 179 2.464459 CGGATTCCACAGCTTCCGC 61.464 63.158 9.19 0.00 43.91 5.54
179 180 3.799753 CGGATTCCACAGCTTCCG 58.200 61.111 7.81 7.81 44.37 4.30
180 181 1.084370 CGACGGATTCCACAGCTTCC 61.084 60.000 3.09 0.00 0.00 3.46
181 182 1.084370 CCGACGGATTCCACAGCTTC 61.084 60.000 8.64 0.00 0.00 3.86
182 183 1.079127 CCGACGGATTCCACAGCTT 60.079 57.895 8.64 0.00 0.00 3.74
183 184 2.283529 ACCGACGGATTCCACAGCT 61.284 57.895 23.38 0.00 0.00 4.24
184 185 2.100631 CACCGACGGATTCCACAGC 61.101 63.158 23.38 0.00 0.00 4.40
185 186 0.037697 TTCACCGACGGATTCCACAG 60.038 55.000 23.38 0.00 0.00 3.66
186 187 0.037697 CTTCACCGACGGATTCCACA 60.038 55.000 23.38 0.00 0.00 4.17
195 196 0.788391 GTTTGGTAGCTTCACCGACG 59.212 55.000 0.00 0.00 41.88 5.12
223 224 4.260170 AGTTTCTGAGTTGGATCAGCATC 58.740 43.478 0.00 0.00 45.25 3.91
235 236 6.017026 GGCTTTAGTTTTGCTAGTTTCTGAGT 60.017 38.462 0.00 0.00 0.00 3.41
246 247 1.244816 GGACGGGCTTTAGTTTTGCT 58.755 50.000 0.00 0.00 0.00 3.91
248 249 2.225727 GTCTGGACGGGCTTTAGTTTTG 59.774 50.000 0.00 0.00 0.00 2.44
294 295 2.670934 GCCAGTGCCAGTGACCAG 60.671 66.667 0.00 0.00 0.00 4.00
295 296 2.963928 CTTGCCAGTGCCAGTGACCA 62.964 60.000 0.00 0.00 36.33 4.02
308 309 4.208403 AGGTGCCACTGCTTGCCA 62.208 61.111 0.00 0.00 38.71 4.92
309 310 3.368571 GAGGTGCCACTGCTTGCC 61.369 66.667 0.00 0.00 38.71 4.52
310 311 2.282040 AGAGGTGCCACTGCTTGC 60.282 61.111 0.00 0.00 38.71 4.01
311 312 1.970114 CCAGAGGTGCCACTGCTTG 60.970 63.158 9.68 0.00 38.71 4.01
312 313 2.433446 CCAGAGGTGCCACTGCTT 59.567 61.111 9.68 0.00 38.71 3.91
313 314 3.644606 CCCAGAGGTGCCACTGCT 61.645 66.667 9.68 0.00 38.71 4.24
323 324 0.035630 CAAGAGCTTGTCCCCAGAGG 60.036 60.000 2.11 0.00 35.92 3.69
360 373 2.027073 GACGACGGTTCTGCATGCA 61.027 57.895 21.29 21.29 0.00 3.96
364 377 0.892358 AGGTAGACGACGGTTCTGCA 60.892 55.000 0.00 0.00 0.00 4.41
365 378 0.179169 GAGGTAGACGACGGTTCTGC 60.179 60.000 0.00 0.00 0.00 4.26
366 379 0.450983 GGAGGTAGACGACGGTTCTG 59.549 60.000 0.00 0.00 0.00 3.02
371 384 1.994507 CTGCTGGAGGTAGACGACGG 61.995 65.000 0.00 0.00 0.00 4.79
373 386 0.452585 GACTGCTGGAGGTAGACGAC 59.547 60.000 0.14 0.00 0.00 4.34
374 387 0.328592 AGACTGCTGGAGGTAGACGA 59.671 55.000 0.14 0.00 0.00 4.20
375 388 1.944024 CTAGACTGCTGGAGGTAGACG 59.056 57.143 0.14 0.00 0.00 4.18
376 389 1.679153 GCTAGACTGCTGGAGGTAGAC 59.321 57.143 10.64 1.47 0.00 2.59
377 390 1.285078 TGCTAGACTGCTGGAGGTAGA 59.715 52.381 10.64 0.00 0.00 2.59
378 391 1.407258 GTGCTAGACTGCTGGAGGTAG 59.593 57.143 0.14 2.61 0.00 3.18
379 392 1.475403 GTGCTAGACTGCTGGAGGTA 58.525 55.000 0.14 0.00 0.00 3.08
380 393 1.261238 GGTGCTAGACTGCTGGAGGT 61.261 60.000 0.14 0.00 0.00 3.85
381 394 1.260538 TGGTGCTAGACTGCTGGAGG 61.261 60.000 0.14 0.00 0.00 4.30
382 395 0.610174 TTGGTGCTAGACTGCTGGAG 59.390 55.000 0.00 0.00 0.00 3.86
383 396 1.055849 TTTGGTGCTAGACTGCTGGA 58.944 50.000 0.00 0.00 0.00 3.86
384 397 1.537202 GTTTTGGTGCTAGACTGCTGG 59.463 52.381 0.00 0.00 0.00 4.85
385 398 1.537202 GGTTTTGGTGCTAGACTGCTG 59.463 52.381 0.00 0.00 0.00 4.41
386 399 1.142870 TGGTTTTGGTGCTAGACTGCT 59.857 47.619 0.00 0.00 0.00 4.24
417 430 2.388232 GCCGCCGTTTGATTCGAGT 61.388 57.895 0.00 0.00 0.00 4.18
424 437 0.320858 TTGTATCAGCCGCCGTTTGA 60.321 50.000 0.00 0.00 0.00 2.69
425 438 0.519519 TTTGTATCAGCCGCCGTTTG 59.480 50.000 0.00 0.00 0.00 2.93
426 439 1.068816 GTTTTGTATCAGCCGCCGTTT 60.069 47.619 0.00 0.00 0.00 3.60
427 440 0.519961 GTTTTGTATCAGCCGCCGTT 59.480 50.000 0.00 0.00 0.00 4.44
428 441 1.303091 GGTTTTGTATCAGCCGCCGT 61.303 55.000 0.00 0.00 0.00 5.68
611 626 4.293648 CCTGTCCCGTCACGCACA 62.294 66.667 0.00 0.00 0.00 4.57
631 646 2.564947 TGAAGGTTTGTTGTTGGCTTGT 59.435 40.909 0.00 0.00 0.00 3.16
645 661 1.774894 TAGCTTGGCCCGTGAAGGTT 61.775 55.000 10.17 0.00 38.74 3.50
710 746 0.962356 AAGGGCTGTGCAATTCTCCG 60.962 55.000 0.00 0.00 0.00 4.63
718 754 0.037590 ACGGAATTAAGGGCTGTGCA 59.962 50.000 0.00 0.00 0.00 4.57
726 869 3.689161 TCATGAGCACAACGGAATTAAGG 59.311 43.478 0.00 0.00 0.00 2.69
770 913 0.250513 GGTGTCCTTGGCCAGTCTAG 59.749 60.000 5.11 0.00 0.00 2.43
828 1120 2.367202 TGACGAGGGAATGGGAGGC 61.367 63.158 0.00 0.00 0.00 4.70
837 1129 2.026641 CCTTTATACCGTGACGAGGGA 58.973 52.381 6.54 0.00 0.00 4.20
838 1130 2.026641 TCCTTTATACCGTGACGAGGG 58.973 52.381 6.54 0.00 0.00 4.30
867 1164 2.815503 TGTGAATTGTGAGTGATGGCTG 59.184 45.455 0.00 0.00 0.00 4.85
872 1169 3.254166 GTGGCTTGTGAATTGTGAGTGAT 59.746 43.478 0.00 0.00 0.00 3.06
873 1170 2.618241 GTGGCTTGTGAATTGTGAGTGA 59.382 45.455 0.00 0.00 0.00 3.41
874 1171 2.287788 GGTGGCTTGTGAATTGTGAGTG 60.288 50.000 0.00 0.00 0.00 3.51
875 1172 1.956477 GGTGGCTTGTGAATTGTGAGT 59.044 47.619 0.00 0.00 0.00 3.41
876 1173 1.955778 TGGTGGCTTGTGAATTGTGAG 59.044 47.619 0.00 0.00 0.00 3.51
904 1201 7.597369 CGGTGCTACTACTACAATAATTGCATA 59.403 37.037 0.00 0.00 0.00 3.14
907 1204 5.981315 TCGGTGCTACTACTACAATAATTGC 59.019 40.000 0.00 0.00 0.00 3.56
909 1206 6.510536 GGTCGGTGCTACTACTACAATAATT 58.489 40.000 0.00 0.00 0.00 1.40
911 1208 4.035558 CGGTCGGTGCTACTACTACAATAA 59.964 45.833 0.00 0.00 0.00 1.40
913 1210 2.357009 CGGTCGGTGCTACTACTACAAT 59.643 50.000 0.00 0.00 0.00 2.71
914 1211 1.739466 CGGTCGGTGCTACTACTACAA 59.261 52.381 0.00 0.00 0.00 2.41
915 1212 1.066215 TCGGTCGGTGCTACTACTACA 60.066 52.381 0.00 0.00 0.00 2.74
916 1213 1.656652 TCGGTCGGTGCTACTACTAC 58.343 55.000 0.00 0.00 0.00 2.73
917 1214 2.487934 GATCGGTCGGTGCTACTACTA 58.512 52.381 0.00 0.00 0.00 1.82
918 1215 1.307097 GATCGGTCGGTGCTACTACT 58.693 55.000 0.00 0.00 0.00 2.57
919 1216 0.041488 CGATCGGTCGGTGCTACTAC 60.041 60.000 11.03 0.00 44.00 2.73
920 1217 2.314256 CGATCGGTCGGTGCTACTA 58.686 57.895 11.03 0.00 44.00 1.82
948 1245 2.939103 GCTTGCTGCTTAGCTTAGCTAA 59.061 45.455 23.89 23.14 46.97 3.09
952 1249 1.063764 GCTGCTTGCTGCTTAGCTTAG 59.936 52.381 21.60 15.11 43.37 2.18
985 1283 1.065854 GGCCATGTCTCACAAGCTAGT 60.066 52.381 0.00 0.00 33.53 2.57
996 1294 2.267006 CTGCTGTCGGCCATGTCT 59.733 61.111 2.24 0.00 40.92 3.41
1034 1335 2.022902 CGACGACGACGAGGATGG 59.977 66.667 15.32 0.00 42.66 3.51
1036 1337 2.818714 AGCGACGACGACGAGGAT 60.819 61.111 22.94 0.59 42.66 3.24
1453 1777 1.340248 ACACTTCTACACACCGACAGG 59.660 52.381 0.00 0.00 45.13 4.00
1466 1790 2.277084 GACACGGAAACACACACTTCT 58.723 47.619 0.00 0.00 0.00 2.85
1467 1791 1.329599 GGACACGGAAACACACACTTC 59.670 52.381 0.00 0.00 0.00 3.01
1479 1803 3.319198 GCCAAGAGGGGACACGGA 61.319 66.667 0.00 0.00 37.04 4.69
1482 1810 1.302832 CACTGCCAAGAGGGGACAC 60.303 63.158 0.00 0.00 37.04 3.67
1505 1833 1.870402 TGGCAATGTTACACACAGACG 59.130 47.619 0.00 0.00 39.40 4.18
1536 1865 7.872163 CACATGTATAAAGTGCACACATTTT 57.128 32.000 21.04 12.97 38.95 1.82
1561 1891 9.912634 AAATAGATTGTTTACAGAAACCACATG 57.087 29.630 0.00 0.00 43.74 3.21
1585 1915 4.279982 GGTGGATTAATTAACCCCCGAAA 58.720 43.478 6.12 0.00 0.00 3.46
1593 1923 4.638865 AGTTCTGGCGGTGGATTAATTAAC 59.361 41.667 0.00 0.00 0.00 2.01
1609 1939 4.804108 CGATAAGATAGCTGGAGTTCTGG 58.196 47.826 0.00 0.00 0.00 3.86
1695 2025 9.745880 CTTTTTAGATCTAGAATACCGCTAACA 57.254 33.333 6.55 0.00 0.00 2.41
1696 2026 9.747293 ACTTTTTAGATCTAGAATACCGCTAAC 57.253 33.333 6.55 0.00 0.00 2.34
1698 2028 9.962783 GAACTTTTTAGATCTAGAATACCGCTA 57.037 33.333 6.55 0.00 0.00 4.26
1707 2037 9.950496 AGATGCTTTGAACTTTTTAGATCTAGA 57.050 29.630 2.02 0.00 0.00 2.43
1756 2086 1.759445 CGATTCCAGGAGGACAGATGT 59.241 52.381 0.00 0.00 45.73 3.06
1772 2102 8.501580 CAGTCATTTATACTGCATCAATCGATT 58.498 33.333 4.39 4.39 38.08 3.34
1784 2114 3.393800 CGGGCTCCAGTCATTTATACTG 58.606 50.000 0.00 0.00 43.26 2.74
1785 2115 2.368875 CCGGGCTCCAGTCATTTATACT 59.631 50.000 0.00 0.00 0.00 2.12
1795 2125 2.363925 GTACCTCCGGGCTCCAGT 60.364 66.667 0.00 0.00 35.63 4.00
1799 2129 2.895404 TGTATATTGTACCTCCGGGCTC 59.105 50.000 0.00 0.00 35.63 4.70
1804 2134 4.282449 TGGTGGATGTATATTGTACCTCCG 59.718 45.833 9.30 0.00 35.74 4.63
1816 2146 0.756903 GTACGGCCTGGTGGATGTAT 59.243 55.000 0.00 0.00 34.57 2.29
1842 2172 0.182775 ACACCCTCTTTCACACACCC 59.817 55.000 0.00 0.00 0.00 4.61
1864 2358 4.760047 CCAAGAGGGGACACGCGG 62.760 72.222 12.47 1.27 34.23 6.46
1873 2367 0.604780 CACAGTCACTGCCAAGAGGG 60.605 60.000 4.13 0.00 34.37 4.30
1889 2383 2.877786 CCAGCAATGTTACACAGACACA 59.122 45.455 0.00 0.00 0.00 3.72
1890 2384 2.878406 ACCAGCAATGTTACACAGACAC 59.122 45.455 0.00 0.00 0.00 3.67
1982 2514 9.938280 CCCGAAATATATAGATTTGGTTACAGA 57.062 33.333 9.98 0.00 0.00 3.41
1984 2516 7.608761 GGCCCGAAATATATAGATTTGGTTACA 59.391 37.037 9.98 0.00 0.00 2.41
1985 2517 7.201582 CGGCCCGAAATATATAGATTTGGTTAC 60.202 40.741 9.98 1.54 0.00 2.50
1986 2518 6.819649 CGGCCCGAAATATATAGATTTGGTTA 59.180 38.462 9.98 0.00 0.00 2.85
1987 2519 5.646360 CGGCCCGAAATATATAGATTTGGTT 59.354 40.000 9.98 0.00 0.00 3.67
1988 2520 5.183228 CGGCCCGAAATATATAGATTTGGT 58.817 41.667 9.98 0.00 0.00 3.67
1989 2521 4.574828 CCGGCCCGAAATATATAGATTTGG 59.425 45.833 3.71 8.68 0.00 3.28
1990 2522 4.574828 CCCGGCCCGAAATATATAGATTTG 59.425 45.833 3.71 3.43 0.00 2.32
1991 2523 4.226620 ACCCGGCCCGAAATATATAGATTT 59.773 41.667 3.71 5.03 0.00 2.17
1992 2524 3.778629 ACCCGGCCCGAAATATATAGATT 59.221 43.478 3.71 0.00 0.00 2.40
2031 2597 3.055819 TGTGAAGGATAAGACAGCTGGAC 60.056 47.826 19.93 11.75 0.00 4.02
2039 2605 5.179555 GGAACACTGTTGTGAAGGATAAGAC 59.820 44.000 0.00 0.00 46.55 3.01
2049 2615 2.684001 AGAACGGAACACTGTTGTGA 57.316 45.000 0.00 0.00 46.55 3.58
2051 2617 2.870411 GCTAAGAACGGAACACTGTTGT 59.130 45.455 0.00 0.00 37.67 3.32
2052 2618 3.131396 AGCTAAGAACGGAACACTGTTG 58.869 45.455 0.00 0.00 33.89 3.33
2053 2619 3.181469 TGAGCTAAGAACGGAACACTGTT 60.181 43.478 0.00 0.00 36.06 3.16
2054 2620 2.364324 TGAGCTAAGAACGGAACACTGT 59.636 45.455 0.00 0.00 0.00 3.55
2055 2621 2.989840 CTGAGCTAAGAACGGAACACTG 59.010 50.000 0.00 0.00 0.00 3.66
2056 2622 2.891580 TCTGAGCTAAGAACGGAACACT 59.108 45.455 0.00 0.00 0.00 3.55
2057 2623 3.057456 TCTCTGAGCTAAGAACGGAACAC 60.057 47.826 1.42 0.00 0.00 3.32
2058 2624 3.154710 TCTCTGAGCTAAGAACGGAACA 58.845 45.455 1.42 0.00 0.00 3.18
2059 2625 3.851976 TCTCTGAGCTAAGAACGGAAC 57.148 47.619 1.42 0.00 0.00 3.62
2060 2626 4.079970 TCTTCTCTGAGCTAAGAACGGAA 58.920 43.478 1.42 1.89 0.00 4.30
2061 2627 3.687125 TCTTCTCTGAGCTAAGAACGGA 58.313 45.455 1.42 0.00 0.00 4.69
2062 2628 4.156922 TCTTCTTCTCTGAGCTAAGAACGG 59.843 45.833 14.22 8.59 35.02 4.44
2063 2629 5.303747 TCTTCTTCTCTGAGCTAAGAACG 57.696 43.478 14.22 11.53 35.02 3.95
2064 2630 7.954788 TTTTCTTCTTCTCTGAGCTAAGAAC 57.045 36.000 19.42 0.00 35.02 3.01
2066 2632 9.646427 GTATTTTTCTTCTTCTCTGAGCTAAGA 57.354 33.333 0.00 0.00 0.00 2.10
2067 2633 9.429359 TGTATTTTTCTTCTTCTCTGAGCTAAG 57.571 33.333 0.00 0.00 0.00 2.18
2068 2634 9.429359 CTGTATTTTTCTTCTTCTCTGAGCTAA 57.571 33.333 0.00 0.00 0.00 3.09
2069 2635 8.589338 ACTGTATTTTTCTTCTTCTCTGAGCTA 58.411 33.333 0.00 0.00 0.00 3.32
2070 2636 7.387397 CACTGTATTTTTCTTCTTCTCTGAGCT 59.613 37.037 0.00 0.00 0.00 4.09
2071 2637 7.172361 ACACTGTATTTTTCTTCTTCTCTGAGC 59.828 37.037 0.00 0.00 0.00 4.26
2072 2638 8.600449 ACACTGTATTTTTCTTCTTCTCTGAG 57.400 34.615 0.00 0.00 0.00 3.35
2073 2639 8.964476 AACACTGTATTTTTCTTCTTCTCTGA 57.036 30.769 0.00 0.00 0.00 3.27
2074 2640 8.286097 GGAACACTGTATTTTTCTTCTTCTCTG 58.714 37.037 0.00 0.00 0.00 3.35
2075 2641 7.171678 CGGAACACTGTATTTTTCTTCTTCTCT 59.828 37.037 0.00 0.00 0.00 3.10
2076 2642 7.041984 ACGGAACACTGTATTTTTCTTCTTCTC 60.042 37.037 0.00 0.00 0.00 2.87
2077 2643 6.766467 ACGGAACACTGTATTTTTCTTCTTCT 59.234 34.615 0.00 0.00 0.00 2.85
2078 2644 6.956047 ACGGAACACTGTATTTTTCTTCTTC 58.044 36.000 0.00 0.00 0.00 2.87
2079 2645 6.937436 ACGGAACACTGTATTTTTCTTCTT 57.063 33.333 0.00 0.00 0.00 2.52
2080 2646 6.540914 TGAACGGAACACTGTATTTTTCTTCT 59.459 34.615 0.00 0.00 0.00 2.85
2081 2647 6.721321 TGAACGGAACACTGTATTTTTCTTC 58.279 36.000 0.00 0.00 0.00 2.87
2082 2648 6.317893 ACTGAACGGAACACTGTATTTTTCTT 59.682 34.615 0.00 0.00 0.00 2.52
2083 2649 5.820947 ACTGAACGGAACACTGTATTTTTCT 59.179 36.000 0.00 0.00 0.00 2.52
2084 2650 6.056428 ACTGAACGGAACACTGTATTTTTC 57.944 37.500 0.00 0.00 0.00 2.29
2085 2651 5.277154 CGACTGAACGGAACACTGTATTTTT 60.277 40.000 0.00 0.00 0.00 1.94
2086 2652 4.210537 CGACTGAACGGAACACTGTATTTT 59.789 41.667 0.00 0.00 0.00 1.82
2087 2653 3.739300 CGACTGAACGGAACACTGTATTT 59.261 43.478 0.00 0.00 0.00 1.40
2088 2654 3.243636 ACGACTGAACGGAACACTGTATT 60.244 43.478 0.00 0.00 37.61 1.89
2089 2655 2.295349 ACGACTGAACGGAACACTGTAT 59.705 45.455 0.00 0.00 37.61 2.29
2090 2656 1.677576 ACGACTGAACGGAACACTGTA 59.322 47.619 0.00 0.00 37.61 2.74
2097 2663 1.595929 GCCCAACGACTGAACGGAA 60.596 57.895 0.00 0.00 37.61 4.30
2198 2767 7.703197 GGTTGTAAAAGAAAATCCGAGTTGAAA 59.297 33.333 0.00 0.00 0.00 2.69
2199 2768 7.067737 AGGTTGTAAAAGAAAATCCGAGTTGAA 59.932 33.333 0.00 0.00 0.00 2.69
2207 2776 5.952526 TCGGAGGTTGTAAAAGAAAATCC 57.047 39.130 0.00 0.00 0.00 3.01
2214 2783 5.941948 AAGTTCATCGGAGGTTGTAAAAG 57.058 39.130 0.00 0.00 0.00 2.27
2241 2810 7.468496 ACTGGAGGTTTTCTCTCTTACTACTA 58.532 38.462 0.00 0.00 42.10 1.82
2242 2811 6.316513 ACTGGAGGTTTTCTCTCTTACTACT 58.683 40.000 0.00 0.00 42.10 2.57
2243 2812 6.593268 ACTGGAGGTTTTCTCTCTTACTAC 57.407 41.667 0.00 0.00 42.10 2.73
2244 2813 8.896722 ATTACTGGAGGTTTTCTCTCTTACTA 57.103 34.615 0.00 0.00 42.10 1.82
2245 2814 7.455008 TGATTACTGGAGGTTTTCTCTCTTACT 59.545 37.037 0.00 0.00 42.10 2.24
2246 2815 7.612677 TGATTACTGGAGGTTTTCTCTCTTAC 58.387 38.462 0.00 0.00 42.10 2.34
2280 2849 0.177836 TGGCATGCATACGTAGCAGT 59.822 50.000 21.36 9.43 46.36 4.40


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

AutoCloner maintained by Alex Coulton.