Multiple sequence alignment - TraesCS4A01G048600

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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 TraesCS4A01G048600 chr4A 100.000 3213 0 0 1 3213 39462075 39465287 0.000000e+00 5934.0
1 TraesCS4A01G048600 chr4A 100.000 28 0 0 2181 2208 738811732 738811759 6.000000e-03 52.8
2 TraesCS4A01G048600 chr4B 92.331 1343 66 16 841 2170 520935114 520933796 0.000000e+00 1875.0
3 TraesCS4A01G048600 chr4B 94.305 878 48 1 2338 3213 520933346 520932469 0.000000e+00 1343.0
4 TraesCS4A01G048600 chr4B 88.710 186 8 4 2166 2340 520933623 520933440 6.980000e-52 215.0
5 TraesCS4A01G048600 chr4B 87.719 57 7 0 723 779 117194486 117194430 2.070000e-07 67.6
6 TraesCS4A01G048600 chr4D 93.569 1244 66 9 928 2170 425283613 425282383 0.000000e+00 1842.0
7 TraesCS4A01G048600 chr4D 95.427 1006 44 2 2208 3213 425280975 425279972 0.000000e+00 1602.0
8 TraesCS4A01G048600 chr4D 82.576 396 27 14 255 618 425284988 425284603 8.660000e-81 311.0
9 TraesCS4A01G048600 chr4D 85.405 185 16 8 1 184 54673489 54673663 7.080000e-42 182.0
10 TraesCS4A01G048600 chr4D 96.610 59 2 0 841 899 425284001 425283943 7.340000e-17 99.0
11 TraesCS4A01G048600 chr4D 96.875 32 0 1 718 749 476309368 476309398 6.000000e-03 52.8
12 TraesCS4A01G048600 chr6D 89.796 196 16 2 1 196 292078872 292079063 6.880000e-62 248.0
13 TraesCS4A01G048600 chr6A 89.583 192 14 5 1 192 113535440 113535625 4.140000e-59 239.0
14 TraesCS4A01G048600 chr6A 77.509 289 38 11 316 579 504476031 504475745 7.180000e-32 148.0
15 TraesCS4A01G048600 chr5D 87.500 200 20 4 1 199 276265568 276265373 3.230000e-55 226.0
16 TraesCS4A01G048600 chr5D 91.489 47 4 0 722 768 469466546 469466592 7.440000e-07 65.8
17 TraesCS4A01G048600 chr7D 85.930 199 22 4 1 198 633593526 633593333 1.170000e-49 207.0
18 TraesCS4A01G048600 chr7D 87.395 119 12 3 467 584 64181092 64181208 2.010000e-27 134.0
19 TraesCS4A01G048600 chr7D 100.000 28 0 0 2181 2208 4870857 4870884 6.000000e-03 52.8
20 TraesCS4A01G048600 chr1D 85.859 198 21 4 1 198 399159011 399158821 1.510000e-48 204.0
21 TraesCS4A01G048600 chr2A 80.756 291 28 11 302 566 12328378 12328090 5.440000e-48 202.0
22 TraesCS4A01G048600 chr2A 79.252 294 28 22 302 566 12329159 12328870 1.180000e-39 174.0
23 TraesCS4A01G048600 chr2A 81.421 183 24 9 19 199 738967296 738967122 1.200000e-29 141.0
24 TraesCS4A01G048600 chr3B 83.756 197 25 5 4 200 421011893 421012082 2.550000e-41 180.0
25 TraesCS4A01G048600 chr2D 79.038 291 31 19 302 566 11844092 11843806 4.260000e-39 172.0
26 TraesCS4A01G048600 chr2D 76.699 309 44 15 302 585 526115465 526115160 2.580000e-31 147.0
27 TraesCS4A01G048600 chr2D 90.741 54 5 0 722 775 119282423 119282370 4.450000e-09 73.1
28 TraesCS4A01G048600 chr2B 85.294 170 18 6 4 172 10415475 10415312 5.510000e-38 169.0
29 TraesCS4A01G048600 chr5B 86.066 122 14 3 467 587 708334841 708334960 9.360000e-26 128.0
30 TraesCS4A01G048600 chr5B 74.754 305 51 16 299 579 376392414 376392716 2.620000e-21 113.0
31 TraesCS4A01G048600 chr7B 93.182 44 3 0 2165 2208 623563658 623563615 7.440000e-07 65.8
32 TraesCS4A01G048600 chr7B 97.222 36 1 0 2173 2208 623502422 623502387 9.620000e-06 62.1
33 TraesCS4A01G048600 chr7B 97.222 36 1 0 2173 2208 623520299 623520264 9.620000e-06 62.1
34 TraesCS4A01G048600 chr7B 97.222 36 1 0 2173 2208 623534966 623534931 9.620000e-06 62.1
35 TraesCS4A01G048600 chr5A 97.059 34 1 0 554 587 281060944 281060977 1.240000e-04 58.4
36 TraesCS4A01G048600 chr7A 100.000 28 0 0 723 750 94304271 94304244 6.000000e-03 52.8


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 TraesCS4A01G048600 chr4A 39462075 39465287 3212 False 5934.000000 5934 100.0000 1 3213 1 chr4A.!!$F1 3212
1 TraesCS4A01G048600 chr4B 520932469 520935114 2645 True 1144.333333 1875 91.7820 841 3213 3 chr4B.!!$R2 2372
2 TraesCS4A01G048600 chr4D 425279972 425284988 5016 True 963.500000 1842 92.0455 255 3213 4 chr4D.!!$R1 2958

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
218 219 0.032615 CTAGGGTGGTGCTCTCCTCT 60.033 60.0 0.0 0.0 0.0 3.69 F
219 220 0.033011 TAGGGTGGTGCTCTCCTCTC 60.033 60.0 0.0 0.0 0.0 3.20 F
1740 2570 0.181350 GTCAGCCCCTCCGATGATTT 59.819 55.0 0.0 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 2674 0.674895 GATGCCAGCACCTCGTTCTT 60.675 55.000 0.00 0.0 0.0 2.52 R
2036 2866 1.207329 GACACGGTGGGAGCTAGAATT 59.793 52.381 13.48 0.0 0.0 2.17 R
2829 5307 1.280457 GCCTTCCCTCTCCTCTTTGA 58.720 55.000 0.00 0.0 0.0 2.69 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
17 18 3.924507 GCCGAATCAATGCCCTGT 58.075 55.556 0.00 0.00 0.00 4.00
18 19 2.192605 GCCGAATCAATGCCCTGTT 58.807 52.632 0.00 0.00 0.00 3.16
19 20 0.532115 GCCGAATCAATGCCCTGTTT 59.468 50.000 0.00 0.00 0.00 2.83
20 21 1.066929 GCCGAATCAATGCCCTGTTTT 60.067 47.619 0.00 0.00 0.00 2.43
21 22 2.609350 CCGAATCAATGCCCTGTTTTG 58.391 47.619 0.00 0.00 0.00 2.44
22 23 1.994779 CGAATCAATGCCCTGTTTTGC 59.005 47.619 0.00 0.00 0.00 3.68
23 24 2.349590 GAATCAATGCCCTGTTTTGCC 58.650 47.619 0.00 0.00 0.00 4.52
24 25 0.247185 ATCAATGCCCTGTTTTGCCG 59.753 50.000 0.00 0.00 0.00 5.69
25 26 0.825425 TCAATGCCCTGTTTTGCCGA 60.825 50.000 0.00 0.00 0.00 5.54
26 27 0.033228 CAATGCCCTGTTTTGCCGAA 59.967 50.000 0.00 0.00 0.00 4.30
27 28 0.975887 AATGCCCTGTTTTGCCGAAT 59.024 45.000 0.00 0.00 0.00 3.34
28 29 0.975887 ATGCCCTGTTTTGCCGAATT 59.024 45.000 0.00 0.00 0.00 2.17
29 30 0.755686 TGCCCTGTTTTGCCGAATTT 59.244 45.000 0.00 0.00 0.00 1.82
30 31 1.139853 TGCCCTGTTTTGCCGAATTTT 59.860 42.857 0.00 0.00 0.00 1.82
31 32 1.530720 GCCCTGTTTTGCCGAATTTTG 59.469 47.619 0.00 0.00 0.00 2.44
32 33 2.804933 GCCCTGTTTTGCCGAATTTTGA 60.805 45.455 0.00 0.00 0.00 2.69
33 34 2.799978 CCCTGTTTTGCCGAATTTTGAC 59.200 45.455 0.00 0.00 0.00 3.18
34 35 2.799978 CCTGTTTTGCCGAATTTTGACC 59.200 45.455 0.00 0.00 0.00 4.02
35 36 2.464865 TGTTTTGCCGAATTTTGACCG 58.535 42.857 0.00 0.00 0.00 4.79
36 37 2.099263 TGTTTTGCCGAATTTTGACCGA 59.901 40.909 0.00 0.00 0.00 4.69
37 38 3.117046 GTTTTGCCGAATTTTGACCGAA 58.883 40.909 0.00 0.00 0.00 4.30
38 39 3.651803 TTTGCCGAATTTTGACCGAAT 57.348 38.095 0.00 0.00 0.00 3.34
39 40 4.768130 TTTGCCGAATTTTGACCGAATA 57.232 36.364 0.00 0.00 0.00 1.75
40 41 4.974368 TTGCCGAATTTTGACCGAATAT 57.026 36.364 0.00 0.00 0.00 1.28
41 42 4.545823 TGCCGAATTTTGACCGAATATC 57.454 40.909 0.00 0.00 0.00 1.63
42 43 3.942115 TGCCGAATTTTGACCGAATATCA 59.058 39.130 0.00 0.00 0.00 2.15
43 44 4.578516 TGCCGAATTTTGACCGAATATCAT 59.421 37.500 0.00 0.00 0.00 2.45
44 45 5.067153 TGCCGAATTTTGACCGAATATCATT 59.933 36.000 0.00 0.00 0.00 2.57
45 46 5.977129 GCCGAATTTTGACCGAATATCATTT 59.023 36.000 0.00 0.00 0.00 2.32
46 47 6.475402 GCCGAATTTTGACCGAATATCATTTT 59.525 34.615 0.00 0.00 0.00 1.82
47 48 7.305993 GCCGAATTTTGACCGAATATCATTTTC 60.306 37.037 0.00 0.00 0.00 2.29
48 49 7.700234 CCGAATTTTGACCGAATATCATTTTCA 59.300 33.333 0.00 0.00 0.00 2.69
49 50 9.071221 CGAATTTTGACCGAATATCATTTTCAA 57.929 29.630 0.00 0.00 0.00 2.69
54 55 9.703892 TTTGACCGAATATCATTTTCAAAATGT 57.296 25.926 20.03 11.46 30.60 2.71
55 56 9.703892 TTGACCGAATATCATTTTCAAAATGTT 57.296 25.926 20.03 15.15 0.00 2.71
56 57 9.703892 TGACCGAATATCATTTTCAAAATGTTT 57.296 25.926 20.03 13.15 0.00 2.83
75 76 4.821935 AAAAAGGGCGTCTGAGGG 57.178 55.556 0.00 0.00 0.00 4.30
76 77 1.603739 AAAAAGGGCGTCTGAGGGC 60.604 57.895 14.65 14.65 0.00 5.19
77 78 3.901797 AAAAGGGCGTCTGAGGGCG 62.902 63.158 16.14 0.05 0.00 6.13
105 106 4.785453 CGGCAGAGGCTGGGAACC 62.785 72.222 0.00 0.00 42.93 3.62
106 107 4.432741 GGCAGAGGCTGGGAACCC 62.433 72.222 2.46 2.46 43.21 4.11
117 118 3.467226 GGAACCCGATCGCCTCCA 61.467 66.667 10.32 0.00 0.00 3.86
118 119 2.202892 GAACCCGATCGCCTCCAC 60.203 66.667 10.32 0.00 0.00 4.02
119 120 4.143333 AACCCGATCGCCTCCACG 62.143 66.667 10.32 0.00 0.00 4.94
131 132 2.755836 CCTCCACGGCAAAAATATCG 57.244 50.000 0.00 0.00 0.00 2.92
132 133 1.268539 CCTCCACGGCAAAAATATCGC 60.269 52.381 0.00 0.00 0.00 4.58
133 134 1.670811 CTCCACGGCAAAAATATCGCT 59.329 47.619 0.00 0.00 0.00 4.93
134 135 1.400142 TCCACGGCAAAAATATCGCTG 59.600 47.619 0.00 0.00 38.04 5.18
135 136 1.533756 CCACGGCAAAAATATCGCTGG 60.534 52.381 0.00 0.00 36.31 4.85
136 137 1.132262 CACGGCAAAAATATCGCTGGT 59.868 47.619 0.00 0.00 36.31 4.00
137 138 1.816224 ACGGCAAAAATATCGCTGGTT 59.184 42.857 0.00 0.00 36.31 3.67
138 139 2.159435 ACGGCAAAAATATCGCTGGTTC 60.159 45.455 0.00 0.00 36.31 3.62
139 140 2.450160 GGCAAAAATATCGCTGGTTCG 58.550 47.619 0.00 0.00 0.00 3.95
140 141 1.846175 GCAAAAATATCGCTGGTTCGC 59.154 47.619 0.00 0.00 0.00 4.70
141 142 2.450160 CAAAAATATCGCTGGTTCGCC 58.550 47.619 0.00 0.00 37.92 5.54
142 143 1.021968 AAAATATCGCTGGTTCGCCC 58.978 50.000 0.00 0.00 36.08 6.13
143 144 0.818040 AAATATCGCTGGTTCGCCCC 60.818 55.000 0.00 0.00 36.08 5.80
144 145 2.676163 AATATCGCTGGTTCGCCCCC 62.676 60.000 0.00 0.00 36.08 5.40
163 164 3.178539 AGCGGCGCTTTTTCTAGC 58.821 55.556 31.35 0.00 33.89 3.42
164 165 2.100410 GCGGCGCTTTTTCTAGCC 59.900 61.111 26.86 0.00 45.67 3.93
165 166 2.791927 CGGCGCTTTTTCTAGCCC 59.208 61.111 7.64 0.00 46.36 5.19
166 167 2.761195 CGGCGCTTTTTCTAGCCCC 61.761 63.158 7.64 0.00 46.36 5.80
167 168 1.378646 GGCGCTTTTTCTAGCCCCT 60.379 57.895 7.64 0.00 43.54 4.79
168 169 0.965866 GGCGCTTTTTCTAGCCCCTT 60.966 55.000 7.64 0.00 43.54 3.95
169 170 0.171231 GCGCTTTTTCTAGCCCCTTG 59.829 55.000 0.00 0.00 37.90 3.61
170 171 0.811281 CGCTTTTTCTAGCCCCTTGG 59.189 55.000 0.00 0.00 37.90 3.61
172 173 1.852633 CTTTTTCTAGCCCCTTGGGG 58.147 55.000 20.18 20.18 44.57 4.96
195 196 3.746957 GGGGGCTGGAGATGTTCT 58.253 61.111 0.00 0.00 0.00 3.01
196 197 2.930935 GGGGGCTGGAGATGTTCTA 58.069 57.895 0.00 0.00 0.00 2.10
197 198 1.213296 GGGGGCTGGAGATGTTCTAA 58.787 55.000 0.00 0.00 0.00 2.10
198 199 1.141858 GGGGGCTGGAGATGTTCTAAG 59.858 57.143 0.00 0.00 0.00 2.18
199 200 1.475930 GGGGCTGGAGATGTTCTAAGC 60.476 57.143 4.04 4.04 35.81 3.09
200 201 1.488393 GGGCTGGAGATGTTCTAAGCT 59.512 52.381 10.01 0.00 36.40 3.74
201 202 2.700897 GGGCTGGAGATGTTCTAAGCTA 59.299 50.000 10.01 0.00 36.40 3.32
202 203 3.244044 GGGCTGGAGATGTTCTAAGCTAG 60.244 52.174 10.01 0.00 36.40 3.42
203 204 3.244044 GGCTGGAGATGTTCTAAGCTAGG 60.244 52.174 10.01 0.00 36.40 3.02
204 205 3.244044 GCTGGAGATGTTCTAAGCTAGGG 60.244 52.174 0.00 0.00 34.59 3.53
205 206 3.964031 CTGGAGATGTTCTAAGCTAGGGT 59.036 47.826 0.00 0.00 0.00 4.34
206 207 3.706594 TGGAGATGTTCTAAGCTAGGGTG 59.293 47.826 0.00 0.00 0.00 4.61
207 208 3.070302 GGAGATGTTCTAAGCTAGGGTGG 59.930 52.174 0.00 0.00 0.00 4.61
208 209 3.707102 GAGATGTTCTAAGCTAGGGTGGT 59.293 47.826 0.00 0.00 0.00 4.16
209 210 3.452627 AGATGTTCTAAGCTAGGGTGGTG 59.547 47.826 0.00 0.00 0.00 4.17
210 211 1.278127 TGTTCTAAGCTAGGGTGGTGC 59.722 52.381 0.00 0.00 0.00 5.01
211 212 1.555533 GTTCTAAGCTAGGGTGGTGCT 59.444 52.381 0.00 0.00 38.87 4.40
212 213 1.486211 TCTAAGCTAGGGTGGTGCTC 58.514 55.000 0.00 0.00 35.85 4.26
213 214 1.007238 TCTAAGCTAGGGTGGTGCTCT 59.993 52.381 0.00 0.00 35.85 4.09
214 215 1.410882 CTAAGCTAGGGTGGTGCTCTC 59.589 57.143 0.00 0.00 35.85 3.20
215 216 1.268283 AAGCTAGGGTGGTGCTCTCC 61.268 60.000 0.00 0.00 35.85 3.71
216 217 1.687493 GCTAGGGTGGTGCTCTCCT 60.687 63.158 0.00 0.00 0.00 3.69
217 218 1.681486 GCTAGGGTGGTGCTCTCCTC 61.681 65.000 0.00 0.00 0.00 3.71
218 219 0.032615 CTAGGGTGGTGCTCTCCTCT 60.033 60.000 0.00 0.00 0.00 3.69
219 220 0.033011 TAGGGTGGTGCTCTCCTCTC 60.033 60.000 0.00 0.00 0.00 3.20
220 221 2.363172 GGGTGGTGCTCTCCTCTCC 61.363 68.421 0.00 0.00 0.00 3.71
221 222 1.305718 GGTGGTGCTCTCCTCTCCT 60.306 63.158 0.00 0.00 0.00 3.69
222 223 0.907230 GGTGGTGCTCTCCTCTCCTT 60.907 60.000 0.00 0.00 0.00 3.36
223 224 0.980423 GTGGTGCTCTCCTCTCCTTT 59.020 55.000 0.00 0.00 0.00 3.11
224 225 1.349357 GTGGTGCTCTCCTCTCCTTTT 59.651 52.381 0.00 0.00 0.00 2.27
225 226 2.057922 TGGTGCTCTCCTCTCCTTTTT 58.942 47.619 0.00 0.00 0.00 1.94
246 247 6.737254 TTTTCCTGCTTTTATTACGAGGAG 57.263 37.500 0.00 0.00 31.34 3.69
247 248 4.402056 TCCTGCTTTTATTACGAGGAGG 57.598 45.455 4.03 4.03 46.71 4.30
248 249 3.134081 TCCTGCTTTTATTACGAGGAGGG 59.866 47.826 9.74 0.00 45.76 4.30
249 250 3.134081 CCTGCTTTTATTACGAGGAGGGA 59.866 47.826 2.60 0.00 43.07 4.20
250 251 4.202367 CCTGCTTTTATTACGAGGAGGGAT 60.202 45.833 2.60 0.00 43.07 3.85
251 252 4.703897 TGCTTTTATTACGAGGAGGGATG 58.296 43.478 0.00 0.00 0.00 3.51
252 253 3.498777 GCTTTTATTACGAGGAGGGATGC 59.501 47.826 0.00 0.00 0.00 3.91
253 254 4.703897 CTTTTATTACGAGGAGGGATGCA 58.296 43.478 0.00 0.00 0.00 3.96
262 263 2.621998 GAGGAGGGATGCATGTCATTTG 59.378 50.000 2.46 0.00 35.05 2.32
301 302 7.885297 CATGAGGTGGACAAAGAGAATTTTTA 58.115 34.615 0.00 0.00 0.00 1.52
305 306 5.470368 GTGGACAAAGAGAATTTTTAGGGC 58.530 41.667 0.00 0.00 0.00 5.19
312 313 7.728532 ACAAAGAGAATTTTTAGGGCTCCTTTA 59.271 33.333 0.00 0.00 34.61 1.85
351 352 8.792830 TTGTAGAACTTTGGAGGATTAGAATG 57.207 34.615 0.00 0.00 0.00 2.67
358 359 7.633789 ACTTTGGAGGATTAGAATGCTTAGAA 58.366 34.615 0.00 0.00 37.20 2.10
360 361 9.129532 CTTTGGAGGATTAGAATGCTTAGAAAT 57.870 33.333 0.00 0.00 37.20 2.17
361 362 9.479549 TTTGGAGGATTAGAATGCTTAGAAATT 57.520 29.630 0.00 0.00 37.20 1.82
362 363 9.479549 TTGGAGGATTAGAATGCTTAGAAATTT 57.520 29.630 0.00 0.00 37.20 1.82
401 410 9.551734 TTCATAGGACTGAATCACATAGAAATG 57.448 33.333 0.00 0.00 33.40 2.32
403 412 8.986847 CATAGGACTGAATCACATAGAAATGTC 58.013 37.037 0.00 0.00 44.70 3.06
404 413 7.192852 AGGACTGAATCACATAGAAATGTCT 57.807 36.000 0.00 0.00 44.70 3.41
405 414 7.271511 AGGACTGAATCACATAGAAATGTCTC 58.728 38.462 0.00 0.00 44.70 3.36
406 415 6.481644 GGACTGAATCACATAGAAATGTCTCC 59.518 42.308 0.00 0.00 44.70 3.71
407 416 7.192852 ACTGAATCACATAGAAATGTCTCCT 57.807 36.000 0.00 0.00 44.70 3.69
408 417 8.311395 ACTGAATCACATAGAAATGTCTCCTA 57.689 34.615 0.00 0.00 44.70 2.94
409 418 8.762645 ACTGAATCACATAGAAATGTCTCCTAA 58.237 33.333 0.00 0.00 44.70 2.69
410 419 9.258826 CTGAATCACATAGAAATGTCTCCTAAG 57.741 37.037 0.00 0.00 44.70 2.18
411 420 8.206867 TGAATCACATAGAAATGTCTCCTAAGG 58.793 37.037 0.00 0.00 44.70 2.69
426 435 9.268282 TGTCTCCTAAGGATTTCTTTGTACTAT 57.732 33.333 0.00 0.00 36.93 2.12
458 467 4.702131 GGATTTGTAGCATCCACTCAAACT 59.298 41.667 0.00 0.00 40.21 2.66
460 469 5.437289 TTTGTAGCATCCACTCAAACTTG 57.563 39.130 0.00 0.00 0.00 3.16
469 492 5.083533 TCCACTCAAACTTGTTGCATTTT 57.916 34.783 0.00 0.00 0.00 1.82
518 541 6.631763 ATCATGTAGGATTGAGATGGCATA 57.368 37.500 0.00 0.00 0.00 3.14
519 542 6.631763 TCATGTAGGATTGAGATGGCATAT 57.368 37.500 0.00 0.00 0.00 1.78
521 544 6.214005 TCATGTAGGATTGAGATGGCATATCA 59.786 38.462 20.13 20.13 0.00 2.15
541 564 9.976511 CATATCATGCCAATTCTATGTTTTTCT 57.023 29.630 0.00 0.00 0.00 2.52
585 618 3.137176 CCTATGAATCAAAGAGGCCCTCA 59.863 47.826 14.46 0.00 32.06 3.86
596 629 1.215382 GGCCCTCAAATCAAACGGC 59.785 57.895 0.00 0.00 35.60 5.68
614 647 3.243569 ACGGCCAGAAAGAAGATAGATCG 60.244 47.826 2.24 0.00 0.00 3.69
618 651 4.739137 GCCAGAAAGAAGATAGATCGTGCT 60.739 45.833 0.00 0.00 0.00 4.40
622 1120 5.534654 AGAAAGAAGATAGATCGTGCTAGCT 59.465 40.000 17.23 0.00 38.65 3.32
644 1142 5.183522 GCTATAGTAGAACTAGTGGCCGAAT 59.816 44.000 0.00 0.00 33.66 3.34
664 1162 4.789012 ATTGTTGTATGGCTTGGTTCTG 57.211 40.909 0.00 0.00 0.00 3.02
673 1171 1.145803 GCTTGGTTCTGTACACGACC 58.854 55.000 13.57 13.57 0.00 4.79
699 1197 3.135225 CGTGGAACAATGTAGTGTGGAA 58.865 45.455 0.00 0.00 44.16 3.53
701 1199 3.502211 GTGGAACAATGTAGTGTGGAAGG 59.498 47.826 0.00 0.00 44.16 3.46
719 1217 1.294780 GTAGCACTGCTGCCTGAGT 59.705 57.895 14.15 0.00 45.53 3.41
725 1223 2.419297 GCACTGCTGCCTGAGTAATACT 60.419 50.000 0.00 0.00 37.45 2.12
726 1224 3.866651 CACTGCTGCCTGAGTAATACTT 58.133 45.455 0.00 0.00 0.00 2.24
727 1225 3.868077 CACTGCTGCCTGAGTAATACTTC 59.132 47.826 0.00 0.00 0.00 3.01
728 1226 3.118592 ACTGCTGCCTGAGTAATACTTCC 60.119 47.826 0.00 0.00 0.00 3.46
729 1227 3.107601 TGCTGCCTGAGTAATACTTCCT 58.892 45.455 0.00 0.00 0.00 3.36
730 1228 3.133003 TGCTGCCTGAGTAATACTTCCTC 59.867 47.826 0.00 0.00 0.00 3.71
731 1229 3.386402 GCTGCCTGAGTAATACTTCCTCT 59.614 47.826 0.00 0.00 0.00 3.69
732 1230 4.739137 GCTGCCTGAGTAATACTTCCTCTG 60.739 50.000 0.00 0.00 0.00 3.35
733 1231 4.353777 TGCCTGAGTAATACTTCCTCTGT 58.646 43.478 0.00 0.00 0.00 3.41
734 1232 4.777896 TGCCTGAGTAATACTTCCTCTGTT 59.222 41.667 0.00 0.00 0.00 3.16
735 1233 5.248477 TGCCTGAGTAATACTTCCTCTGTTT 59.752 40.000 0.00 0.00 0.00 2.83
736 1234 5.813157 GCCTGAGTAATACTTCCTCTGTTTC 59.187 44.000 0.00 0.00 0.00 2.78
737 1235 6.574465 GCCTGAGTAATACTTCCTCTGTTTCA 60.574 42.308 0.00 0.00 0.00 2.69
738 1236 7.386851 CCTGAGTAATACTTCCTCTGTTTCAA 58.613 38.462 0.00 0.00 0.00 2.69
739 1237 7.878127 CCTGAGTAATACTTCCTCTGTTTCAAA 59.122 37.037 0.00 0.00 0.00 2.69
740 1238 9.273016 CTGAGTAATACTTCCTCTGTTTCAAAA 57.727 33.333 0.00 0.00 0.00 2.44
741 1239 9.793259 TGAGTAATACTTCCTCTGTTTCAAAAT 57.207 29.630 0.00 0.00 0.00 1.82
748 1246 8.329203 ACTTCCTCTGTTTCAAAATAGATGAC 57.671 34.615 6.69 0.00 35.92 3.06
749 1247 7.391833 ACTTCCTCTGTTTCAAAATAGATGACC 59.608 37.037 6.69 0.00 35.92 4.02
750 1248 7.020827 TCCTCTGTTTCAAAATAGATGACCT 57.979 36.000 2.91 0.00 35.92 3.85
751 1249 7.461749 TCCTCTGTTTCAAAATAGATGACCTT 58.538 34.615 2.91 0.00 35.92 3.50
752 1250 8.602424 TCCTCTGTTTCAAAATAGATGACCTTA 58.398 33.333 2.91 0.00 35.92 2.69
753 1251 9.401058 CCTCTGTTTCAAAATAGATGACCTTAT 57.599 33.333 2.91 0.00 35.92 1.73
832 1330 7.739498 TGAAAGGAGTACAAAGTATTTCACC 57.261 36.000 0.00 0.00 35.03 4.02
833 1331 7.284074 TGAAAGGAGTACAAAGTATTTCACCA 58.716 34.615 0.00 0.00 35.03 4.17
836 1334 8.528044 AAGGAGTACAAAGTATTTCACCAAAA 57.472 30.769 0.00 0.00 35.03 2.44
913 1733 0.671251 GGTGCAAACCGAACCAATCA 59.329 50.000 0.00 0.00 33.94 2.57
914 1734 1.067821 GGTGCAAACCGAACCAATCAA 59.932 47.619 0.00 0.00 33.94 2.57
915 1735 2.288763 GGTGCAAACCGAACCAATCAAT 60.289 45.455 0.00 0.00 33.94 2.57
916 1736 2.986479 GTGCAAACCGAACCAATCAATC 59.014 45.455 0.00 0.00 0.00 2.67
917 1737 2.029470 TGCAAACCGAACCAATCAATCC 60.029 45.455 0.00 0.00 0.00 3.01
918 1738 2.673893 GCAAACCGAACCAATCAATCCC 60.674 50.000 0.00 0.00 0.00 3.85
919 1739 1.847328 AACCGAACCAATCAATCCCC 58.153 50.000 0.00 0.00 0.00 4.81
920 1740 0.999712 ACCGAACCAATCAATCCCCT 59.000 50.000 0.00 0.00 0.00 4.79
921 1741 1.340991 ACCGAACCAATCAATCCCCTG 60.341 52.381 0.00 0.00 0.00 4.45
922 1742 1.064758 CCGAACCAATCAATCCCCTGA 60.065 52.381 0.00 0.00 0.00 3.86
923 1743 2.620367 CCGAACCAATCAATCCCCTGAA 60.620 50.000 0.00 0.00 0.00 3.02
924 1744 2.423538 CGAACCAATCAATCCCCTGAAC 59.576 50.000 0.00 0.00 0.00 3.18
925 1745 3.430453 GAACCAATCAATCCCCTGAACA 58.570 45.455 0.00 0.00 0.00 3.18
926 1746 3.091633 ACCAATCAATCCCCTGAACAG 57.908 47.619 0.00 0.00 0.00 3.16
951 1771 4.857251 GGCGACGGATCCAAATCT 57.143 55.556 13.41 0.00 32.12 2.40
952 1772 2.606275 GGCGACGGATCCAAATCTC 58.394 57.895 13.41 0.85 32.12 2.75
972 1792 0.462403 GCGCACGGTTCCCCTATAAA 60.462 55.000 0.30 0.00 0.00 1.40
973 1793 1.812708 GCGCACGGTTCCCCTATAAAT 60.813 52.381 0.30 0.00 0.00 1.40
986 1806 6.335934 TCCCCTATAAATATACCAGCTCCAA 58.664 40.000 0.00 0.00 0.00 3.53
1000 1824 0.320771 CTCCAAACTACGCAGGCACT 60.321 55.000 0.00 0.00 43.88 4.40
1007 1831 2.579684 CTACGCAGGCACTTCCCCTC 62.580 65.000 0.00 0.00 34.60 4.30
1014 1838 1.562672 GGCACTTCCCCTCCTGCTTA 61.563 60.000 0.00 0.00 0.00 3.09
1030 1854 4.321750 CCTGCTTATACGGTAATCACGGAT 60.322 45.833 0.00 0.00 38.63 4.18
1180 2010 1.153489 CCTCCTGCACGACATCCTG 60.153 63.158 0.00 0.00 0.00 3.86
1439 2269 4.400961 GCAGCAGGAAGACGGCCT 62.401 66.667 0.00 0.00 41.55 5.19
1503 2333 1.533338 GGTCGACATACACTACGGCTG 60.533 57.143 18.91 0.00 0.00 4.85
1506 2336 1.480219 GACATACACTACGGCTGCGC 61.480 60.000 0.00 0.00 0.00 6.09
1573 2403 4.082523 GCTACCTGCCGCCTCACA 62.083 66.667 0.00 0.00 35.15 3.58
1626 2456 2.756691 TTTCGGGCGGGATCTCGA 60.757 61.111 21.68 5.43 0.00 4.04
1700 2530 1.729470 CTGCTACGTCGCATCTCCCT 61.729 60.000 15.69 0.00 39.52 4.20
1736 2566 3.144120 CTCGTCAGCCCCTCCGATG 62.144 68.421 0.00 0.00 0.00 3.84
1738 2568 2.502492 CGTCAGCCCCTCCGATGAT 61.502 63.158 0.00 0.00 0.00 2.45
1739 2569 1.832912 GTCAGCCCCTCCGATGATT 59.167 57.895 0.00 0.00 0.00 2.57
1740 2570 0.181350 GTCAGCCCCTCCGATGATTT 59.819 55.000 0.00 0.00 0.00 2.17
1741 2571 0.469917 TCAGCCCCTCCGATGATTTC 59.530 55.000 0.00 0.00 0.00 2.17
1742 2572 0.471617 CAGCCCCTCCGATGATTTCT 59.528 55.000 0.00 0.00 0.00 2.52
1743 2573 1.694150 CAGCCCCTCCGATGATTTCTA 59.306 52.381 0.00 0.00 0.00 2.10
1752 2582 5.508153 CCTCCGATGATTTCTACTACAGGTG 60.508 48.000 0.00 0.00 0.00 4.00
1768 2598 1.605058 GGTGCTCCGCTCTTGTCCTA 61.605 60.000 0.00 0.00 0.00 2.94
1779 2609 1.201647 TCTTGTCCTAGCGTTTCCTCG 59.798 52.381 0.00 0.00 0.00 4.63
1844 2674 1.742761 CTACCCCGTCGTCACTTCTA 58.257 55.000 0.00 0.00 0.00 2.10
1876 2706 4.819761 GCATCGCTCGTCCAGGCA 62.820 66.667 0.00 0.00 0.00 4.75
1921 2751 2.743928 GAGGTGCAGCGGAACAGG 60.744 66.667 10.78 0.00 0.00 4.00
2005 2835 4.843728 TCCCCAATGTCAGAAATCTACAC 58.156 43.478 0.00 0.00 0.00 2.90
2036 2866 5.394443 GGGTTTACCACGACAGTATGTATCA 60.394 44.000 0.69 0.00 45.99 2.15
2051 2881 4.689612 TGTATCAATTCTAGCTCCCACC 57.310 45.455 0.00 0.00 0.00 4.61
2089 2921 4.821260 TGATATCGCATTGGTAGCATGTTT 59.179 37.500 0.00 0.00 0.00 2.83
2150 2982 7.402811 TGTGTAGTTCTCTGAAAATTGTACG 57.597 36.000 0.00 0.00 0.00 3.67
2180 4441 6.231951 TGTTAAAATTGTACGGATCTCCACA 58.768 36.000 0.00 0.00 35.14 4.17
2216 4595 7.298854 TGAATATAGCATCGACTTAAGTCTCG 58.701 38.462 28.30 19.28 42.66 4.04
2219 4598 2.097791 AGCATCGACTTAAGTCTCGGTC 59.902 50.000 28.30 15.55 42.66 4.79
2230 4609 3.428746 AGTCTCGGTCGATTGAGATTG 57.571 47.619 18.72 0.00 42.73 2.67
2246 4625 4.156556 TGAGATTGAGCAATCCCGAAAAAG 59.843 41.667 17.12 0.00 46.28 2.27
2294 4673 3.960102 TCAACTCCAAATTCAAAGTGCCT 59.040 39.130 0.00 0.00 0.00 4.75
2440 4916 4.100035 TGTTCACAGATCCTAGTAGCATGG 59.900 45.833 0.00 0.00 0.00 3.66
2592 5068 4.281688 ACAAGAATTTCAGGTGTTCCATGG 59.718 41.667 4.97 4.97 35.89 3.66
2599 5075 2.173519 CAGGTGTTCCATGGCTTGAAT 58.826 47.619 6.96 0.00 35.89 2.57
2683 5159 2.178912 ACGCCCAAAATCTCGAGAAA 57.821 45.000 20.91 0.00 0.00 2.52
2689 5165 3.191371 CCCAAAATCTCGAGAAAGTTGGG 59.809 47.826 35.61 35.61 42.13 4.12
2767 5245 7.094334 GGACGATTTTCTCCTTTCTTGGTATTT 60.094 37.037 0.00 0.00 0.00 1.40
2771 5249 8.727100 ATTTTCTCCTTTCTTGGTATTTCCTT 57.273 30.769 0.00 0.00 37.07 3.36
2829 5307 2.165437 TCAACAAAGTTTTTGGAGCGCT 59.835 40.909 11.27 11.27 0.00 5.92
2890 5368 0.939419 AAACGCCGTAACTCAACACC 59.061 50.000 0.00 0.00 0.00 4.16
2893 5371 1.012486 CGCCGTAACTCAACACCTCC 61.012 60.000 0.00 0.00 0.00 4.30
3057 5535 0.596577 CACGGGTCCGATGACGATAT 59.403 55.000 16.90 0.00 42.73 1.63
3098 5576 5.351458 AGAACAGAAAATGGCAAAGTGAAC 58.649 37.500 0.00 0.00 0.00 3.18
3100 5578 5.343307 ACAGAAAATGGCAAAGTGAACTT 57.657 34.783 0.00 0.00 37.91 2.66
3122 5600 7.636150 CTTGAATTAAGTTGATGGAGGACAT 57.364 36.000 0.00 0.00 44.18 3.06
3138 5616 2.866762 GGACATAAGGAACATGCGTCTC 59.133 50.000 0.00 0.00 0.00 3.36
3182 5660 3.566322 CCACGGATCTACTAGAAGGTGAG 59.434 52.174 0.00 4.04 29.75 3.51
3206 5684 1.202475 GCACGGTTGGTTGGAACATTT 60.202 47.619 0.00 0.00 39.30 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.532115 AAACAGGGCATTGATTCGGC 59.468 50.000 0.00 0.00 0.00 5.54
1 2 2.609350 CAAAACAGGGCATTGATTCGG 58.391 47.619 0.00 0.00 0.00 4.30
2 3 1.994779 GCAAAACAGGGCATTGATTCG 59.005 47.619 0.00 0.00 0.00 3.34
3 4 2.349590 GGCAAAACAGGGCATTGATTC 58.650 47.619 0.00 0.00 0.00 2.52
4 5 1.338011 CGGCAAAACAGGGCATTGATT 60.338 47.619 0.00 0.00 0.00 2.57
5 6 0.247185 CGGCAAAACAGGGCATTGAT 59.753 50.000 0.00 0.00 0.00 2.57
6 7 0.825425 TCGGCAAAACAGGGCATTGA 60.825 50.000 0.00 0.00 0.00 2.57
7 8 0.033228 TTCGGCAAAACAGGGCATTG 59.967 50.000 0.00 0.00 0.00 2.82
8 9 0.975887 ATTCGGCAAAACAGGGCATT 59.024 45.000 0.00 0.00 0.00 3.56
9 10 0.975887 AATTCGGCAAAACAGGGCAT 59.024 45.000 0.00 0.00 0.00 4.40
10 11 0.755686 AAATTCGGCAAAACAGGGCA 59.244 45.000 0.00 0.00 0.00 5.36
11 12 1.530720 CAAAATTCGGCAAAACAGGGC 59.469 47.619 0.00 0.00 0.00 5.19
12 13 2.799978 GTCAAAATTCGGCAAAACAGGG 59.200 45.455 0.00 0.00 0.00 4.45
13 14 2.799978 GGTCAAAATTCGGCAAAACAGG 59.200 45.455 0.00 0.00 0.00 4.00
14 15 2.470999 CGGTCAAAATTCGGCAAAACAG 59.529 45.455 0.00 0.00 0.00 3.16
15 16 2.099263 TCGGTCAAAATTCGGCAAAACA 59.901 40.909 0.00 0.00 0.00 2.83
16 17 2.733517 TCGGTCAAAATTCGGCAAAAC 58.266 42.857 0.00 0.00 0.00 2.43
17 18 3.438297 TTCGGTCAAAATTCGGCAAAA 57.562 38.095 0.00 0.00 0.00 2.44
18 19 3.651803 ATTCGGTCAAAATTCGGCAAA 57.348 38.095 0.00 0.00 0.00 3.68
19 20 4.396478 TGATATTCGGTCAAAATTCGGCAA 59.604 37.500 0.00 0.00 0.00 4.52
20 21 3.942115 TGATATTCGGTCAAAATTCGGCA 59.058 39.130 0.00 0.00 0.00 5.69
21 22 4.545823 TGATATTCGGTCAAAATTCGGC 57.454 40.909 0.00 0.00 0.00 5.54
22 23 7.700234 TGAAAATGATATTCGGTCAAAATTCGG 59.300 33.333 0.00 0.00 0.00 4.30
23 24 8.613613 TGAAAATGATATTCGGTCAAAATTCG 57.386 30.769 0.00 0.00 0.00 3.34
28 29 9.703892 ACATTTTGAAAATGATATTCGGTCAAA 57.296 25.926 30.75 0.00 33.10 2.69
29 30 9.703892 AACATTTTGAAAATGATATTCGGTCAA 57.296 25.926 30.75 0.00 0.00 3.18
30 31 9.703892 AAACATTTTGAAAATGATATTCGGTCA 57.296 25.926 30.75 0.00 0.00 4.02
58 59 1.603739 GCCCTCAGACGCCCTTTTT 60.604 57.895 0.00 0.00 0.00 1.94
59 60 2.034221 GCCCTCAGACGCCCTTTT 59.966 61.111 0.00 0.00 0.00 2.27
60 61 4.394712 CGCCCTCAGACGCCCTTT 62.395 66.667 0.00 0.00 0.00 3.11
88 89 4.785453 GGTTCCCAGCCTCTGCCG 62.785 72.222 0.00 0.00 38.69 5.69
89 90 4.432741 GGGTTCCCAGCCTCTGCC 62.433 72.222 2.59 0.00 37.61 4.85
90 91 4.785453 CGGGTTCCCAGCCTCTGC 62.785 72.222 8.70 0.00 38.58 4.26
91 92 2.317149 GATCGGGTTCCCAGCCTCTG 62.317 65.000 8.70 0.00 38.58 3.35
92 93 2.041265 ATCGGGTTCCCAGCCTCT 59.959 61.111 8.70 0.00 38.58 3.69
93 94 2.506472 GATCGGGTTCCCAGCCTC 59.494 66.667 8.70 0.00 38.58 4.70
94 95 3.470888 CGATCGGGTTCCCAGCCT 61.471 66.667 7.38 0.00 38.58 4.58
97 98 3.447025 GAGGCGATCGGGTTCCCAG 62.447 68.421 18.30 1.53 0.00 4.45
98 99 3.467226 GAGGCGATCGGGTTCCCA 61.467 66.667 18.30 0.00 0.00 4.37
99 100 4.237207 GGAGGCGATCGGGTTCCC 62.237 72.222 18.30 8.97 0.00 3.97
100 101 3.467226 TGGAGGCGATCGGGTTCC 61.467 66.667 18.30 9.37 0.00 3.62
101 102 2.202892 GTGGAGGCGATCGGGTTC 60.203 66.667 18.30 0.00 0.00 3.62
102 103 4.143333 CGTGGAGGCGATCGGGTT 62.143 66.667 18.30 0.00 0.00 4.11
112 113 1.268539 GCGATATTTTTGCCGTGGAGG 60.269 52.381 0.00 0.00 44.97 4.30
113 114 1.670811 AGCGATATTTTTGCCGTGGAG 59.329 47.619 0.00 0.00 35.03 3.86
114 115 1.400142 CAGCGATATTTTTGCCGTGGA 59.600 47.619 0.00 0.00 35.03 4.02
115 116 1.533756 CCAGCGATATTTTTGCCGTGG 60.534 52.381 0.00 0.00 35.03 4.94
116 117 1.132262 ACCAGCGATATTTTTGCCGTG 59.868 47.619 0.00 0.00 35.03 4.94
117 118 1.459450 ACCAGCGATATTTTTGCCGT 58.541 45.000 0.00 0.00 35.03 5.68
118 119 2.450160 GAACCAGCGATATTTTTGCCG 58.550 47.619 0.00 0.00 35.03 5.69
119 120 2.450160 CGAACCAGCGATATTTTTGCC 58.550 47.619 0.00 0.00 35.03 4.52
120 121 1.846175 GCGAACCAGCGATATTTTTGC 59.154 47.619 0.00 0.00 34.63 3.68
121 122 2.450160 GGCGAACCAGCGATATTTTTG 58.550 47.619 0.00 0.00 38.18 2.44
122 123 1.404035 GGGCGAACCAGCGATATTTTT 59.596 47.619 0.00 0.00 39.85 1.94
123 124 1.021968 GGGCGAACCAGCGATATTTT 58.978 50.000 0.00 0.00 39.85 1.82
124 125 0.818040 GGGGCGAACCAGCGATATTT 60.818 55.000 0.00 0.00 42.91 1.40
125 126 1.227853 GGGGCGAACCAGCGATATT 60.228 57.895 0.00 0.00 42.91 1.28
126 127 2.426023 GGGGCGAACCAGCGATAT 59.574 61.111 0.00 0.00 42.91 1.63
127 128 3.857038 GGGGGCGAACCAGCGATA 61.857 66.667 0.00 0.00 42.91 2.92
146 147 2.399356 GGCTAGAAAAAGCGCCGCT 61.399 57.895 5.39 5.39 43.74 5.52
147 148 2.100410 GGCTAGAAAAAGCGCCGC 59.900 61.111 2.29 0.00 43.74 6.53
148 149 2.791927 GGGCTAGAAAAAGCGCCG 59.208 61.111 2.29 0.00 46.59 6.46
151 152 0.811281 CCAAGGGGCTAGAAAAAGCG 59.189 55.000 0.00 0.00 43.74 4.68
152 153 1.186200 CCCAAGGGGCTAGAAAAAGC 58.814 55.000 0.00 0.00 41.99 3.51
178 179 1.141858 CTTAGAACATCTCCAGCCCCC 59.858 57.143 0.00 0.00 0.00 5.40
179 180 1.475930 GCTTAGAACATCTCCAGCCCC 60.476 57.143 1.71 0.00 30.56 5.80
180 181 1.488393 AGCTTAGAACATCTCCAGCCC 59.512 52.381 7.50 0.00 34.90 5.19
181 182 2.998316 AGCTTAGAACATCTCCAGCC 57.002 50.000 7.50 0.00 34.90 4.85
182 183 3.244044 CCCTAGCTTAGAACATCTCCAGC 60.244 52.174 0.00 4.17 34.68 4.85
183 184 3.964031 ACCCTAGCTTAGAACATCTCCAG 59.036 47.826 0.00 0.00 0.00 3.86
184 185 3.706594 CACCCTAGCTTAGAACATCTCCA 59.293 47.826 0.00 0.00 0.00 3.86
185 186 3.070302 CCACCCTAGCTTAGAACATCTCC 59.930 52.174 0.00 0.00 0.00 3.71
186 187 3.707102 ACCACCCTAGCTTAGAACATCTC 59.293 47.826 0.00 0.00 0.00 2.75
187 188 3.452627 CACCACCCTAGCTTAGAACATCT 59.547 47.826 0.00 0.00 0.00 2.90
188 189 3.798202 CACCACCCTAGCTTAGAACATC 58.202 50.000 0.00 0.00 0.00 3.06
189 190 2.092914 GCACCACCCTAGCTTAGAACAT 60.093 50.000 0.00 0.00 0.00 2.71
190 191 1.278127 GCACCACCCTAGCTTAGAACA 59.722 52.381 0.00 0.00 0.00 3.18
191 192 1.555533 AGCACCACCCTAGCTTAGAAC 59.444 52.381 0.00 0.00 34.37 3.01
192 193 1.831736 GAGCACCACCCTAGCTTAGAA 59.168 52.381 0.00 0.00 39.02 2.10
193 194 1.007238 AGAGCACCACCCTAGCTTAGA 59.993 52.381 0.00 0.00 39.02 2.10
194 195 1.410882 GAGAGCACCACCCTAGCTTAG 59.589 57.143 0.00 0.00 39.02 2.18
195 196 1.486211 GAGAGCACCACCCTAGCTTA 58.514 55.000 0.00 0.00 39.02 3.09
196 197 1.268283 GGAGAGCACCACCCTAGCTT 61.268 60.000 0.00 0.00 39.02 3.74
197 198 1.687493 GGAGAGCACCACCCTAGCT 60.687 63.158 0.00 0.00 42.17 3.32
198 199 1.681486 GAGGAGAGCACCACCCTAGC 61.681 65.000 0.00 0.00 0.00 3.42
199 200 0.032615 AGAGGAGAGCACCACCCTAG 60.033 60.000 0.00 0.00 0.00 3.02
200 201 0.033011 GAGAGGAGAGCACCACCCTA 60.033 60.000 0.00 0.00 0.00 3.53
201 202 1.305718 GAGAGGAGAGCACCACCCT 60.306 63.158 0.00 0.00 0.00 4.34
202 203 2.363172 GGAGAGGAGAGCACCACCC 61.363 68.421 0.00 0.00 0.00 4.61
203 204 0.907230 AAGGAGAGGAGAGCACCACC 60.907 60.000 0.00 0.00 0.00 4.61
204 205 0.980423 AAAGGAGAGGAGAGCACCAC 59.020 55.000 0.00 0.00 0.00 4.16
205 206 1.734655 AAAAGGAGAGGAGAGCACCA 58.265 50.000 0.00 0.00 0.00 4.17
206 207 2.869101 AAAAAGGAGAGGAGAGCACC 57.131 50.000 0.00 0.00 0.00 5.01
222 223 6.150474 CCTCCTCGTAATAAAAGCAGGAAAAA 59.850 38.462 0.00 0.00 29.55 1.94
223 224 5.646360 CCTCCTCGTAATAAAAGCAGGAAAA 59.354 40.000 0.00 0.00 29.55 2.29
224 225 5.183228 CCTCCTCGTAATAAAAGCAGGAAA 58.817 41.667 0.00 0.00 29.55 3.13
225 226 4.383770 CCCTCCTCGTAATAAAAGCAGGAA 60.384 45.833 0.00 0.00 29.55 3.36
226 227 3.134081 CCCTCCTCGTAATAAAAGCAGGA 59.866 47.826 0.00 0.00 0.00 3.86
227 228 3.134081 TCCCTCCTCGTAATAAAAGCAGG 59.866 47.826 0.00 0.00 0.00 4.85
228 229 4.402056 TCCCTCCTCGTAATAAAAGCAG 57.598 45.455 0.00 0.00 0.00 4.24
229 230 4.703897 CATCCCTCCTCGTAATAAAAGCA 58.296 43.478 0.00 0.00 0.00 3.91
230 231 3.498777 GCATCCCTCCTCGTAATAAAAGC 59.501 47.826 0.00 0.00 0.00 3.51
231 232 4.703897 TGCATCCCTCCTCGTAATAAAAG 58.296 43.478 0.00 0.00 0.00 2.27
232 233 4.764050 TGCATCCCTCCTCGTAATAAAA 57.236 40.909 0.00 0.00 0.00 1.52
233 234 4.102524 ACATGCATCCCTCCTCGTAATAAA 59.897 41.667 0.00 0.00 0.00 1.40
234 235 3.646162 ACATGCATCCCTCCTCGTAATAA 59.354 43.478 0.00 0.00 0.00 1.40
235 236 3.239449 ACATGCATCCCTCCTCGTAATA 58.761 45.455 0.00 0.00 0.00 0.98
236 237 2.037772 GACATGCATCCCTCCTCGTAAT 59.962 50.000 0.00 0.00 0.00 1.89
237 238 1.412710 GACATGCATCCCTCCTCGTAA 59.587 52.381 0.00 0.00 0.00 3.18
238 239 1.040646 GACATGCATCCCTCCTCGTA 58.959 55.000 0.00 0.00 0.00 3.43
239 240 0.977627 TGACATGCATCCCTCCTCGT 60.978 55.000 0.00 0.00 0.00 4.18
240 241 0.395686 ATGACATGCATCCCTCCTCG 59.604 55.000 0.00 0.00 28.85 4.63
241 242 2.621998 CAAATGACATGCATCCCTCCTC 59.378 50.000 0.00 0.00 35.78 3.71
242 243 2.662866 CAAATGACATGCATCCCTCCT 58.337 47.619 0.00 0.00 35.78 3.69
243 244 1.684983 CCAAATGACATGCATCCCTCC 59.315 52.381 0.00 0.00 35.78 4.30
244 245 1.684983 CCCAAATGACATGCATCCCTC 59.315 52.381 0.00 0.00 35.78 4.30
245 246 1.288633 TCCCAAATGACATGCATCCCT 59.711 47.619 0.00 0.00 35.78 4.20
246 247 1.779221 TCCCAAATGACATGCATCCC 58.221 50.000 0.00 0.00 35.78 3.85
247 248 4.374399 GAATTCCCAAATGACATGCATCC 58.626 43.478 0.00 0.00 35.78 3.51
248 249 4.374399 GGAATTCCCAAATGACATGCATC 58.626 43.478 14.03 0.00 33.21 3.91
249 250 4.411256 GGAATTCCCAAATGACATGCAT 57.589 40.909 14.03 0.00 34.93 3.96
250 251 3.891422 GGAATTCCCAAATGACATGCA 57.109 42.857 14.03 0.00 34.14 3.96
262 263 4.629340 ACCTCATGGCAAGGGAATTCCC 62.629 54.545 33.10 33.10 46.89 3.97
279 280 6.071896 CCCTAAAAATTCTCTTTGTCCACCTC 60.072 42.308 0.00 0.00 0.00 3.85
285 286 5.712446 AGGAGCCCTAAAAATTCTCTTTGTC 59.288 40.000 0.00 0.00 28.47 3.18
351 352 9.567917 GAATCAAACAACGAAAAATTTCTAAGC 57.432 29.630 4.54 0.00 35.07 3.09
358 359 9.191995 GTCCTATGAATCAAACAACGAAAAATT 57.808 29.630 0.00 0.00 0.00 1.82
360 361 7.860373 CAGTCCTATGAATCAAACAACGAAAAA 59.140 33.333 0.00 0.00 0.00 1.94
361 362 7.227711 TCAGTCCTATGAATCAAACAACGAAAA 59.772 33.333 0.00 0.00 0.00 2.29
362 363 6.708502 TCAGTCCTATGAATCAAACAACGAAA 59.291 34.615 0.00 0.00 0.00 3.46
365 374 6.480524 TTCAGTCCTATGAATCAAACAACG 57.519 37.500 0.00 0.00 34.31 4.10
394 403 9.672673 CAAAGAAATCCTTAGGAGACATTTCTA 57.327 33.333 21.07 0.00 39.21 2.10
397 406 9.232473 GTACAAAGAAATCCTTAGGAGACATTT 57.768 33.333 7.19 2.02 34.05 2.32
410 419 9.983804 CCTACGAAAAATAGTACAAAGAAATCC 57.016 33.333 0.00 0.00 0.00 3.01
426 435 5.941058 TGGATGCTACAAATCCTACGAAAAA 59.059 36.000 4.23 0.00 43.52 1.94
429 438 4.161565 AGTGGATGCTACAAATCCTACGAA 59.838 41.667 4.23 0.00 43.52 3.85
430 439 3.704566 AGTGGATGCTACAAATCCTACGA 59.295 43.478 4.23 0.00 43.52 3.43
432 441 5.023533 TGAGTGGATGCTACAAATCCTAC 57.976 43.478 4.23 1.75 43.52 3.18
441 450 4.787598 CAACAAGTTTGAGTGGATGCTAC 58.212 43.478 0.00 0.00 0.00 3.58
469 492 6.587206 TGGTTTGTTTGATTGCATCATAGA 57.413 33.333 0.00 0.00 39.39 1.98
521 544 9.822185 GGAATAAGAAAAACATAGAATTGGCAT 57.178 29.630 0.00 0.00 0.00 4.40
558 581 5.457342 GGGCCTCTTTGATTCATAGGATTCT 60.457 44.000 0.84 0.00 0.00 2.40
559 582 4.764308 GGGCCTCTTTGATTCATAGGATTC 59.236 45.833 0.84 0.00 0.00 2.52
561 584 3.986134 AGGGCCTCTTTGATTCATAGGAT 59.014 43.478 0.00 0.00 0.00 3.24
562 585 3.392616 GAGGGCCTCTTTGATTCATAGGA 59.607 47.826 26.44 0.85 0.00 2.94
563 586 3.137176 TGAGGGCCTCTTTGATTCATAGG 59.863 47.826 32.28 5.38 0.00 2.57
564 587 4.428294 TGAGGGCCTCTTTGATTCATAG 57.572 45.455 32.28 0.00 0.00 2.23
585 618 3.888930 TCTTCTTTCTGGCCGTTTGATTT 59.111 39.130 0.00 0.00 0.00 2.17
596 629 4.942852 AGCACGATCTATCTTCTTTCTGG 58.057 43.478 0.00 0.00 0.00 3.86
614 647 6.348704 GCCACTAGTTCTACTATAGCTAGCAC 60.349 46.154 18.83 2.50 34.21 4.40
618 651 5.012458 TCGGCCACTAGTTCTACTATAGCTA 59.988 44.000 2.24 0.00 29.08 3.32
622 1120 6.548622 ACAATTCGGCCACTAGTTCTACTATA 59.451 38.462 2.24 0.00 29.08 1.31
644 1142 3.561143 ACAGAACCAAGCCATACAACAA 58.439 40.909 0.00 0.00 0.00 2.83
673 1171 3.807622 ACACTACATTGTTCCACGACTTG 59.192 43.478 0.00 0.00 0.00 3.16
692 1190 0.035458 AGCAGTGCTACCTTCCACAC 59.965 55.000 18.11 0.00 36.99 3.82
725 1223 7.461749 AGGTCATCTATTTTGAAACAGAGGAA 58.538 34.615 1.27 0.00 30.50 3.36
726 1224 7.020827 AGGTCATCTATTTTGAAACAGAGGA 57.979 36.000 0.00 0.00 0.00 3.71
727 1225 7.693969 AAGGTCATCTATTTTGAAACAGAGG 57.306 36.000 0.00 0.00 0.00 3.69
806 1304 8.793592 GGTGAAATACTTTGTACTCCTTTCATT 58.206 33.333 0.00 0.00 34.71 2.57
807 1305 7.942341 TGGTGAAATACTTTGTACTCCTTTCAT 59.058 33.333 0.00 0.00 34.71 2.57
808 1306 7.284074 TGGTGAAATACTTTGTACTCCTTTCA 58.716 34.615 0.00 0.00 0.00 2.69
809 1307 7.739498 TGGTGAAATACTTTGTACTCCTTTC 57.261 36.000 0.00 0.00 0.00 2.62
810 1308 8.528044 TTTGGTGAAATACTTTGTACTCCTTT 57.472 30.769 0.00 0.00 0.00 3.11
811 1309 8.528044 TTTTGGTGAAATACTTTGTACTCCTT 57.472 30.769 0.00 0.00 0.00 3.36
812 1310 8.528044 TTTTTGGTGAAATACTTTGTACTCCT 57.472 30.769 0.00 0.00 0.00 3.69
836 1334 1.066454 GCACTTTGCACCGTACCTTTT 59.934 47.619 0.00 0.00 44.26 2.27
839 1337 4.058797 GCACTTTGCACCGTACCT 57.941 55.556 0.00 0.00 44.26 3.08
888 1396 1.534163 GGTTCGGTTTGCACCTTCTAC 59.466 52.381 0.00 0.00 41.64 2.59
913 1733 1.073923 GTGTCCACTGTTCAGGGGATT 59.926 52.381 23.99 0.00 0.00 3.01
914 1734 0.693049 GTGTCCACTGTTCAGGGGAT 59.307 55.000 23.99 0.00 0.00 3.85
915 1735 1.754380 CGTGTCCACTGTTCAGGGGA 61.754 60.000 18.53 18.53 0.00 4.81
916 1736 1.301716 CGTGTCCACTGTTCAGGGG 60.302 63.158 14.34 14.34 0.00 4.79
917 1737 1.301716 CCGTGTCCACTGTTCAGGG 60.302 63.158 4.82 0.00 0.00 4.45
918 1738 1.961277 GCCGTGTCCACTGTTCAGG 60.961 63.158 4.82 0.00 0.00 3.86
919 1739 2.310233 CGCCGTGTCCACTGTTCAG 61.310 63.158 0.00 0.00 0.00 3.02
920 1740 2.279851 CGCCGTGTCCACTGTTCA 60.280 61.111 0.00 0.00 0.00 3.18
921 1741 2.028484 TCGCCGTGTCCACTGTTC 59.972 61.111 0.00 0.00 0.00 3.18
922 1742 2.279918 GTCGCCGTGTCCACTGTT 60.280 61.111 0.00 0.00 0.00 3.16
923 1743 4.640855 CGTCGCCGTGTCCACTGT 62.641 66.667 0.00 0.00 0.00 3.55
926 1746 4.430765 ATCCGTCGCCGTGTCCAC 62.431 66.667 0.00 0.00 0.00 4.02
943 1763 2.813474 CCGTGCGCGAGATTTGGA 60.813 61.111 23.45 0.00 41.33 3.53
948 1768 4.814294 GGGAACCGTGCGCGAGAT 62.814 66.667 23.45 6.36 40.86 2.75
972 1792 3.386726 TGCGTAGTTTGGAGCTGGTATAT 59.613 43.478 0.00 0.00 0.00 0.86
973 1793 2.761767 TGCGTAGTTTGGAGCTGGTATA 59.238 45.455 0.00 0.00 0.00 1.47
986 1806 1.003718 GGGAAGTGCCTGCGTAGTT 60.004 57.895 0.00 0.00 36.66 2.24
1000 1824 1.343681 ACCGTATAAGCAGGAGGGGAA 60.344 52.381 0.00 0.00 0.00 3.97
1007 1831 3.005050 TCCGTGATTACCGTATAAGCAGG 59.995 47.826 7.34 7.34 0.00 4.85
1014 1838 2.095059 GCCGTATCCGTGATTACCGTAT 60.095 50.000 0.00 0.00 0.00 3.06
1240 2070 2.467826 GGTCATGAAGCGCCAGAGC 61.468 63.158 2.29 0.83 37.41 4.09
1251 2081 1.405933 CGATGTTGAGGCAGGTCATGA 60.406 52.381 0.00 0.00 0.00 3.07
1439 2269 2.577059 GCGGATCCACCTGTCGAA 59.423 61.111 13.41 0.00 36.31 3.71
1685 2515 2.831366 GCGAGGGAGATGCGACGTA 61.831 63.158 0.00 0.00 0.00 3.57
1686 2516 4.194720 GCGAGGGAGATGCGACGT 62.195 66.667 0.00 0.00 0.00 4.34
1736 2566 3.707793 CGGAGCACCTGTAGTAGAAATC 58.292 50.000 0.00 0.00 0.00 2.17
1772 2602 1.255667 AACGAGGCTAGGCGAGGAAA 61.256 55.000 11.10 0.00 0.00 3.13
1844 2674 0.674895 GATGCCAGCACCTCGTTCTT 60.675 55.000 0.00 0.00 0.00 2.52
1876 2706 7.238305 TCATCCATGTCCTTTATACAGATGGAT 59.762 37.037 11.94 11.94 43.02 3.41
1921 2751 2.359850 TGTGGCTTCATCACCCGC 60.360 61.111 0.00 0.00 34.46 6.13
2017 2847 7.342769 AGAATTGATACATACTGTCGTGGTA 57.657 36.000 0.00 0.00 0.00 3.25
2026 2856 6.014156 GGTGGGAGCTAGAATTGATACATACT 60.014 42.308 0.00 0.00 0.00 2.12
2036 2866 1.207329 GACACGGTGGGAGCTAGAATT 59.793 52.381 13.48 0.00 0.00 2.17
2051 2881 6.020984 TGCGATATCAAATTTCAAAGACACG 58.979 36.000 3.12 0.00 0.00 4.49
2089 2921 7.227355 TCCCTATAAATGGTTTTATGTGGGA 57.773 36.000 19.10 19.10 46.15 4.37
2118 2950 2.926200 CAGAGAACTACACAATCTGCCG 59.074 50.000 0.00 0.00 31.83 5.69
2150 2982 9.704098 GAGATCCGTACAATTTTAACAGAATTC 57.296 33.333 0.00 0.00 0.00 2.17
2180 4441 9.964303 GTCGATGCTATATTCATGAGATCTTAT 57.036 33.333 0.00 0.00 0.00 1.73
2216 4595 3.249559 GGATTGCTCAATCTCAATCGACC 59.750 47.826 18.63 0.45 45.69 4.79
2219 4598 2.222678 CGGGATTGCTCAATCTCAATCG 59.777 50.000 19.11 12.53 46.14 3.34
2230 4609 4.237349 TGTTTCTTTTTCGGGATTGCTC 57.763 40.909 0.00 0.00 0.00 4.26
2246 4625 3.374988 TCATGACGCAGAATCCATGTTTC 59.625 43.478 0.00 0.00 38.00 2.78
2398 4874 6.428159 GTGAACATGATAACAAAGACAGGACT 59.572 38.462 0.00 0.00 0.00 3.85
2440 4916 7.198390 TCCACGCATCTTAGTAATAACTACAC 58.802 38.462 0.00 0.00 37.94 2.90
2524 5000 6.486657 CCTGGTAGAAGACAACAAAGAAATGA 59.513 38.462 0.00 0.00 0.00 2.57
2592 5068 4.572795 GGCTGAGGAGTAAAGTATTCAAGC 59.427 45.833 0.00 0.00 0.00 4.01
2599 5075 2.895404 ACAACGGCTGAGGAGTAAAGTA 59.105 45.455 0.00 0.00 0.00 2.24
2714 5192 9.443323 TCAACTTTAATGAAAGATATGACCGAA 57.557 29.630 9.70 0.00 44.23 4.30
2717 5195 9.396022 TCCTCAACTTTAATGAAAGATATGACC 57.604 33.333 9.70 0.00 44.23 4.02
2720 5198 9.098355 TCGTCCTCAACTTTAATGAAAGATATG 57.902 33.333 9.70 5.67 44.23 1.78
2829 5307 1.280457 GCCTTCCCTCTCCTCTTTGA 58.720 55.000 0.00 0.00 0.00 2.69
2855 5333 3.317149 GGCGTTTGGAAGGTTTACTCTTT 59.683 43.478 0.00 0.00 0.00 2.52
2890 5368 4.322349 CCTTCAGGTTCTTGTACTCAGGAG 60.322 50.000 0.00 0.00 31.57 3.69
2984 5462 1.809207 CGGCATTTCCTTCGGCATT 59.191 52.632 0.00 0.00 0.00 3.56
3080 5558 5.596836 TCAAGTTCACTTTGCCATTTTCT 57.403 34.783 0.00 0.00 33.11 2.52
3098 5576 7.636150 ATGTCCTCCATCAACTTAATTCAAG 57.364 36.000 0.00 0.00 40.38 3.02
3100 5578 7.775093 CCTTATGTCCTCCATCAACTTAATTCA 59.225 37.037 0.00 0.00 34.86 2.57
3121 5599 4.471904 TTGAGAGACGCATGTTCCTTAT 57.528 40.909 0.00 0.00 0.00 1.73
3122 5600 3.953712 TTGAGAGACGCATGTTCCTTA 57.046 42.857 0.00 0.00 0.00 2.69
3138 5616 8.338259 CGTGGTTAATCTCTGGATTTATTTGAG 58.662 37.037 0.00 0.00 41.75 3.02
3182 5660 3.601685 CCAACCAACCGTGCCACC 61.602 66.667 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.