Multiple sequence alignment - TraesCS5A01G289900

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 TraesCS5A01G289900 chr5A 100.000 2596 0 0 1 2596 496537551 496534956 0.000000e+00 4795.0
1 TraesCS5A01G289900 chr5A 86.169 629 46 15 1062 1675 496175521 496174919 2.180000e-180 641.0
2 TraesCS5A01G289900 chr5A 87.895 380 39 6 298 676 496176866 496176493 8.530000e-120 440.0
3 TraesCS5A01G289900 chr5A 79.675 615 74 25 1085 1689 496204805 496204232 1.870000e-106 396.0
4 TraesCS5A01G289900 chr5A 90.037 271 16 2 758 1028 496175850 496175591 8.900000e-90 340.0
5 TraesCS5A01G289900 chr5A 85.465 172 12 6 2425 2596 119999747 119999905 1.600000e-37 167.0
6 TraesCS5A01G289900 chr5A 87.500 72 8 1 289 360 311970094 311970164 5.950000e-12 82.4
7 TraesCS5A01G289900 chr5D 84.142 2144 147 74 382 2424 394191231 394189180 0.000000e+00 1897.0
8 TraesCS5A01G289900 chr5D 75.630 833 108 53 871 1675 394549018 394548253 2.490000e-85 326.0
9 TraesCS5A01G289900 chr5D 75.630 833 108 53 871 1675 394551031 394550266 2.490000e-85 326.0
10 TraesCS5A01G289900 chr5D 80.000 255 18 17 1086 1313 394280861 394280613 9.620000e-35 158.0
11 TraesCS5A01G289900 chr5D 90.816 98 8 1 154 250 354839261 354839358 2.100000e-26 130.0
12 TraesCS5A01G289900 chr5B 86.350 1348 91 35 1042 2352 474056379 474055088 0.000000e+00 1384.0
13 TraesCS5A01G289900 chr5B 91.084 415 22 9 623 1028 474056843 474056435 4.880000e-152 547.0
14 TraesCS5A01G289900 chr5B 76.913 797 78 48 849 1584 474279253 474278502 3.180000e-94 355.0
15 TraesCS5A01G289900 chr5B 81.199 367 38 14 1088 1453 474453437 474453101 1.530000e-67 267.0
16 TraesCS5A01G289900 chr5B 87.000 200 13 8 384 573 474057054 474056858 2.020000e-51 213.0
17 TraesCS5A01G289900 chr5B 81.646 158 26 3 2 158 474059237 474059082 7.540000e-26 128.0
18 TraesCS5A01G289900 chrUn 75.630 833 108 53 871 1675 332176560 332175795 2.490000e-85 326.0
19 TraesCS5A01G289900 chr3B 90.217 184 16 2 2413 2596 136793331 136793150 3.340000e-59 239.0
20 TraesCS5A01G289900 chr6A 88.372 172 9 2 2425 2596 78006839 78006679 2.040000e-46 196.0
21 TraesCS5A01G289900 chr6A 95.000 120 6 0 2425 2544 613234148 613234029 3.410000e-44 189.0
22 TraesCS5A01G289900 chr6A 94.167 120 7 0 2425 2544 613150978 613150859 1.590000e-42 183.0
23 TraesCS5A01G289900 chr6A 94.167 120 7 0 2425 2544 613169081 613168962 1.590000e-42 183.0
24 TraesCS5A01G289900 chr6A 93.388 121 7 1 2425 2544 613188283 613188163 7.380000e-41 178.0
25 TraesCS5A01G289900 chr3D 87.222 180 9 4 2418 2596 75088374 75088208 2.640000e-45 193.0
26 TraesCS5A01G289900 chr3D 89.796 98 9 1 154 250 590751857 590751760 9.750000e-25 124.0
27 TraesCS5A01G289900 chr4A 86.782 174 12 2 2423 2596 583444294 583444132 1.590000e-42 183.0
28 TraesCS5A01G289900 chr3A 94.167 120 7 0 2425 2544 456378984 456379103 1.590000e-42 183.0
29 TraesCS5A01G289900 chr3A 86.628 172 12 2 2425 2596 745904866 745904706 2.050000e-41 180.0
30 TraesCS5A01G289900 chr4B 85.465 172 14 2 2425 2596 614117076 614117236 4.440000e-38 169.0
31 TraesCS5A01G289900 chr1A 84.884 172 15 4 2425 2596 431032854 431032694 2.070000e-36 163.0
32 TraesCS5A01G289900 chr1A 84.302 172 16 6 2425 2596 4784796 4784956 9.620000e-35 158.0
33 TraesCS5A01G289900 chr7D 84.024 169 16 2 2428 2596 159901605 159901448 4.470000e-33 152.0
34 TraesCS5A01G289900 chr7D 87.736 106 10 2 154 256 25510694 25510799 1.260000e-23 121.0
35 TraesCS5A01G289900 chr7D 90.110 91 9 0 160 250 75346882 75346792 4.540000e-23 119.0
36 TraesCS5A01G289900 chr7B 83.721 172 17 2 2425 2596 496876127 496876287 4.470000e-33 152.0
37 TraesCS5A01G289900 chr1B 82.857 175 19 4 2422 2596 457365311 457365474 2.080000e-31 147.0
38 TraesCS5A01G289900 chr1B 88.506 87 8 1 291 375 602222516 602222430 1.270000e-18 104.0
39 TraesCS5A01G289900 chr2B 89.899 99 9 1 153 250 692930759 692930857 2.710000e-25 126.0
40 TraesCS5A01G289900 chr2D 91.398 93 5 3 160 250 644282163 644282072 9.750000e-25 124.0
41 TraesCS5A01G289900 chr2D 88.660 97 11 0 154 250 605457236 605457332 4.540000e-23 119.0
42 TraesCS5A01G289900 chr2A 89.796 98 9 1 154 250 729555142 729555239 9.750000e-25 124.0
43 TraesCS5A01G289900 chr4D 89.474 95 8 2 154 247 505324778 505324871 4.540000e-23 119.0


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 TraesCS5A01G289900 chr5A 496534956 496537551 2595 True 4795.000000 4795 100.000000 1 2596 1 chr5A.!!$R2 2595
1 TraesCS5A01G289900 chr5A 496174919 496176866 1947 True 473.666667 641 88.033667 298 1675 3 chr5A.!!$R3 1377
2 TraesCS5A01G289900 chr5A 496204232 496204805 573 True 396.000000 396 79.675000 1085 1689 1 chr5A.!!$R1 604
3 TraesCS5A01G289900 chr5D 394189180 394191231 2051 True 1897.000000 1897 84.142000 382 2424 1 chr5D.!!$R1 2042
4 TraesCS5A01G289900 chr5D 394548253 394551031 2778 True 326.000000 326 75.630000 871 1675 2 chr5D.!!$R3 804
5 TraesCS5A01G289900 chr5B 474055088 474059237 4149 True 568.000000 1384 86.520000 2 2352 4 chr5B.!!$R3 2350
6 TraesCS5A01G289900 chr5B 474278502 474279253 751 True 355.000000 355 76.913000 849 1584 1 chr5B.!!$R1 735
7 TraesCS5A01G289900 chrUn 332175795 332176560 765 True 326.000000 326 75.630000 871 1675 1 chrUn.!!$R1 804

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
455 2273 0.029967 TCGCGATGCTCAGTCAGATC 59.97 55.0 3.71 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2431 7071 0.105039 GATAGGGTTGCACGGAGGAG 59.895 60.0 0.0 0.0 0.0 3.69 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
20 21 1.548719 TGGAATGTCACGACCGATTCT 59.451 47.619 9.04 0.00 29.60 2.40
25 26 2.429478 TGTCACGACCGATTCTAGTCA 58.571 47.619 0.00 0.00 33.08 3.41
27 28 3.442625 TGTCACGACCGATTCTAGTCATT 59.557 43.478 0.00 0.00 33.08 2.57
31 32 2.604855 CGACCGATTCTAGTCATTCCCG 60.605 54.545 0.00 0.00 33.08 5.14
32 33 2.361438 GACCGATTCTAGTCATTCCCGT 59.639 50.000 0.00 0.00 33.08 5.28
34 35 2.100916 CCGATTCTAGTCATTCCCGTGT 59.899 50.000 0.00 0.00 0.00 4.49
35 36 3.372954 CGATTCTAGTCATTCCCGTGTC 58.627 50.000 0.00 0.00 0.00 3.67
42 43 2.180204 CATTCCCGTGTCCATCCGC 61.180 63.158 0.00 0.00 0.00 5.54
43 44 3.400599 ATTCCCGTGTCCATCCGCC 62.401 63.158 0.00 0.00 0.00 6.13
56 57 3.690280 CCGCCGGCCAAAATGGTT 61.690 61.111 23.46 0.00 40.46 3.67
85 86 0.250727 CCACCATTGGTCGTTGAGGT 60.251 55.000 5.04 0.00 38.23 3.85
92 93 4.457603 CCATTGGTCGTTGAGGTCAATTAA 59.542 41.667 0.00 0.00 38.24 1.40
97 98 2.073816 CGTTGAGGTCAATTAACGGCT 58.926 47.619 0.00 0.00 41.37 5.52
104 105 2.007608 GTCAATTAACGGCTGGGAGAC 58.992 52.381 0.00 0.00 0.00 3.36
138 139 2.903357 CGGCCACCACTGAGCTAT 59.097 61.111 2.24 0.00 0.00 2.97
142 143 0.250234 GCCACCACTGAGCTATGACA 59.750 55.000 0.00 0.00 0.00 3.58
143 144 1.134280 GCCACCACTGAGCTATGACAT 60.134 52.381 0.00 0.00 0.00 3.06
144 145 2.681976 GCCACCACTGAGCTATGACATT 60.682 50.000 0.00 0.00 0.00 2.71
147 148 3.620374 CACCACTGAGCTATGACATTGTC 59.380 47.826 9.93 9.93 0.00 3.18
167 168 4.101448 GTGCTCGGGGGTGCTCAT 62.101 66.667 0.00 0.00 0.00 2.90
168 169 2.364973 TGCTCGGGGGTGCTCATA 60.365 61.111 0.00 0.00 0.00 2.15
169 170 2.423446 GCTCGGGGGTGCTCATAG 59.577 66.667 0.00 0.00 0.00 2.23
170 171 2.134287 GCTCGGGGGTGCTCATAGA 61.134 63.158 0.00 0.00 0.00 1.98
172 173 1.457643 TCGGGGGTGCTCATAGAGG 60.458 63.158 0.00 0.00 0.00 3.69
174 175 0.469331 CGGGGGTGCTCATAGAGGTA 60.469 60.000 0.00 0.00 0.00 3.08
176 177 1.343069 GGGGTGCTCATAGAGGTAGG 58.657 60.000 0.00 0.00 0.00 3.18
178 179 1.413227 GGGTGCTCATAGAGGTAGGGT 60.413 57.143 0.00 0.00 0.00 4.34
181 182 3.563223 GTGCTCATAGAGGTAGGGTGTA 58.437 50.000 0.00 0.00 0.00 2.90
182 183 3.318557 GTGCTCATAGAGGTAGGGTGTAC 59.681 52.174 0.00 0.00 0.00 2.90
185 186 4.744867 GCTCATAGAGGTAGGGTGTACGTA 60.745 50.000 0.00 0.00 0.00 3.57
186 187 5.558818 CTCATAGAGGTAGGGTGTACGTAT 58.441 45.833 0.00 0.00 0.00 3.06
187 188 5.311265 TCATAGAGGTAGGGTGTACGTATG 58.689 45.833 0.00 0.00 0.00 2.39
188 189 3.659183 AGAGGTAGGGTGTACGTATGT 57.341 47.619 0.00 0.00 0.00 2.29
189 190 3.285484 AGAGGTAGGGTGTACGTATGTG 58.715 50.000 0.00 0.00 0.00 3.21
191 192 1.534595 GGTAGGGTGTACGTATGTGCG 60.535 57.143 0.00 0.00 32.77 5.34
194 195 1.818060 AGGGTGTACGTATGTGCGTTA 59.182 47.619 0.00 0.00 43.04 3.18
195 196 2.230992 AGGGTGTACGTATGTGCGTTAA 59.769 45.455 0.00 0.00 43.04 2.01
196 197 3.119029 AGGGTGTACGTATGTGCGTTAAT 60.119 43.478 0.00 0.00 43.04 1.40
197 198 4.097741 AGGGTGTACGTATGTGCGTTAATA 59.902 41.667 0.00 0.00 43.04 0.98
198 199 4.984161 GGGTGTACGTATGTGCGTTAATAT 59.016 41.667 0.00 0.00 43.04 1.28
199 200 5.107760 GGGTGTACGTATGTGCGTTAATATG 60.108 44.000 0.00 0.00 43.04 1.78
200 201 5.686841 GGTGTACGTATGTGCGTTAATATGA 59.313 40.000 0.00 0.00 43.04 2.15
203 204 5.883328 ACGTATGTGCGTTAATATGAGTG 57.117 39.130 0.00 0.00 43.04 3.51
204 205 4.743151 ACGTATGTGCGTTAATATGAGTGG 59.257 41.667 0.00 0.00 43.04 4.00
206 207 3.620427 TGTGCGTTAATATGAGTGGGT 57.380 42.857 0.00 0.00 0.00 4.51
207 208 3.266636 TGTGCGTTAATATGAGTGGGTG 58.733 45.455 0.00 0.00 0.00 4.61
208 209 3.267483 GTGCGTTAATATGAGTGGGTGT 58.733 45.455 0.00 0.00 0.00 4.16
209 210 4.081586 TGTGCGTTAATATGAGTGGGTGTA 60.082 41.667 0.00 0.00 0.00 2.90
210 211 5.054477 GTGCGTTAATATGAGTGGGTGTAT 58.946 41.667 0.00 0.00 0.00 2.29
211 212 5.050363 GTGCGTTAATATGAGTGGGTGTATG 60.050 44.000 0.00 0.00 0.00 2.39
212 213 4.084013 GCGTTAATATGAGTGGGTGTATGC 60.084 45.833 0.00 0.00 0.00 3.14
214 215 2.169832 ATATGAGTGGGTGTATGCGC 57.830 50.000 0.00 0.00 0.00 6.09
215 216 0.249280 TATGAGTGGGTGTATGCGCG 60.249 55.000 0.00 0.00 0.00 6.86
216 217 2.125673 GAGTGGGTGTATGCGCGT 60.126 61.111 8.43 7.55 0.00 6.01
217 218 1.140161 GAGTGGGTGTATGCGCGTA 59.860 57.895 8.43 4.92 0.00 4.42
219 220 0.529773 AGTGGGTGTATGCGCGTATG 60.530 55.000 20.45 0.00 0.00 2.39
220 221 0.808453 GTGGGTGTATGCGCGTATGT 60.808 55.000 20.45 0.00 0.00 2.29
223 224 1.724623 GGGTGTATGCGCGTATGTATG 59.275 52.381 20.45 0.00 0.00 2.39
224 225 2.608506 GGGTGTATGCGCGTATGTATGA 60.609 50.000 20.45 0.00 0.00 2.15
225 226 2.661675 GGTGTATGCGCGTATGTATGAG 59.338 50.000 20.45 0.00 0.00 2.90
226 227 2.090658 GTGTATGCGCGTATGTATGAGC 59.909 50.000 20.45 0.00 38.31 4.26
229 230 4.228451 CGCGTATGTATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
230 231 2.506544 CGCGTATGTATGAGCGCTT 58.493 52.632 13.26 0.00 46.56 4.68
232 233 0.111089 GCGTATGTATGAGCGCTTGC 60.111 55.000 13.26 0.00 45.48 4.01
233 234 0.159554 CGTATGTATGAGCGCTTGCG 59.840 55.000 13.26 10.90 45.69 4.85
234 235 1.209128 GTATGTATGAGCGCTTGCGT 58.791 50.000 13.26 3.97 45.69 5.24
236 237 0.179100 ATGTATGAGCGCTTGCGTCT 60.179 50.000 13.26 13.17 45.69 4.18
238 239 1.078759 GTATGAGCGCTTGCGTCTGT 61.079 55.000 13.26 7.66 45.69 3.41
239 240 0.454196 TATGAGCGCTTGCGTCTGTA 59.546 50.000 13.26 6.26 45.69 2.74
240 241 1.078759 ATGAGCGCTTGCGTCTGTAC 61.079 55.000 13.26 0.00 45.69 2.90
241 242 2.432628 AGCGCTTGCGTCTGTACC 60.433 61.111 16.38 0.00 45.69 3.34
247 1456 0.782384 CTTGCGTCTGTACCGTGTTC 59.218 55.000 0.00 0.00 0.00 3.18
248 1457 0.102663 TTGCGTCTGTACCGTGTTCA 59.897 50.000 0.00 0.00 0.00 3.18
250 1459 1.269883 TGCGTCTGTACCGTGTTCAAT 60.270 47.619 0.00 0.00 0.00 2.57
379 1588 2.279935 AGAGCCGAGGGAGTATAGTG 57.720 55.000 0.00 0.00 0.00 2.74
388 2199 4.443621 GAGGGAGTATAGTGGAAACTTGC 58.556 47.826 0.00 0.00 0.00 4.01
427 2238 1.248785 ACGTGTCGGTAGCAGGACAT 61.249 55.000 6.04 0.00 44.22 3.06
455 2273 0.029967 TCGCGATGCTCAGTCAGATC 59.970 55.000 3.71 0.00 0.00 2.75
468 2286 4.343526 TCAGTCAGATCTTCTAATCAGCCC 59.656 45.833 0.00 0.00 0.00 5.19
471 2289 3.068732 TCAGATCTTCTAATCAGCCCGTG 59.931 47.826 0.00 0.00 0.00 4.94
580 2398 2.403586 GCCCGATGCAGTAAACGC 59.596 61.111 0.00 0.00 40.77 4.84
685 2517 0.173708 GAGGGAGCGTACTGACAAGG 59.826 60.000 0.00 0.00 0.00 3.61
813 3211 1.600916 GGGCCGTTCTGACAAGCTT 60.601 57.895 0.00 0.00 0.00 3.74
814 3212 1.578206 GGGCCGTTCTGACAAGCTTC 61.578 60.000 0.00 0.00 0.00 3.86
828 3226 1.227438 GCTTCGGGCGTGGCTATTA 60.227 57.895 0.00 0.00 0.00 0.98
835 3233 1.488261 GGCGTGGCTATTACTGCGTC 61.488 60.000 0.00 0.00 0.00 5.19
896 3300 1.281925 TGGGAGGAGCTTCCATTCCC 61.282 60.000 10.41 10.41 46.24 3.97
1020 5464 4.078516 GAGGTAAGTGCCGGCCGT 62.079 66.667 26.77 15.93 0.00 5.68
1034 5478 3.274393 GCCGTGCCATCACTACTAG 57.726 57.895 0.00 0.00 40.99 2.57
1058 5547 1.098050 GGCAGTGATCACCATGAACC 58.902 55.000 22.21 10.79 0.00 3.62
1151 5644 3.008704 GGAACTACAACTACCACCACCAT 59.991 47.826 0.00 0.00 0.00 3.55
1264 5784 0.322546 AATCCCACGCCCAAGAAGAC 60.323 55.000 0.00 0.00 0.00 3.01
1268 5788 2.034879 CACGCCCAAGAAGACGCAT 61.035 57.895 0.00 0.00 0.00 4.73
1274 5794 1.016130 CCAAGAAGACGCATGCGAGT 61.016 55.000 43.72 27.43 42.83 4.18
1371 5897 2.750350 GCAGCAGGTACCAGGTGT 59.250 61.111 29.88 1.53 35.33 4.16
1468 5996 2.361230 CCCCGGAAAAGGCTGTCC 60.361 66.667 0.73 7.31 0.00 4.02
1544 6088 3.550639 CGCTCTTTGTTTGGATGCAGAAA 60.551 43.478 0.00 0.00 0.00 2.52
1571 6115 3.105248 TGGATGGGATGCCTGGGG 61.105 66.667 4.35 0.00 0.00 4.96
1603 6160 4.148825 CGCCTCCTGAACCCCGAG 62.149 72.222 0.00 0.00 0.00 4.63
1606 6163 1.609501 CCTCCTGAACCCCGAGACA 60.610 63.158 0.00 0.00 0.00 3.41
1611 6168 1.003839 TGAACCCCGAGACATGTGC 60.004 57.895 1.15 0.00 0.00 4.57
1612 6169 1.745489 GAACCCCGAGACATGTGCC 60.745 63.158 1.15 0.00 0.00 5.01
1613 6170 3.605749 AACCCCGAGACATGTGCCG 62.606 63.158 1.15 6.27 0.00 5.69
1614 6171 4.838152 CCCCGAGACATGTGCCGG 62.838 72.222 22.03 22.03 41.47 6.13
1615 6172 4.082523 CCCGAGACATGTGCCGGT 62.083 66.667 24.98 0.00 40.30 5.28
1616 6173 2.509336 CCGAGACATGTGCCGGTC 60.509 66.667 21.16 0.00 37.40 4.79
1655 6234 0.317160 TCCTGCGTTCGTGTTCATCT 59.683 50.000 0.00 0.00 0.00 2.90
1666 6245 4.304110 TCGTGTTCATCTCCAGTGTTTAC 58.696 43.478 0.00 0.00 0.00 2.01
1675 6254 3.649023 TCTCCAGTGTTTACTTGCCCTTA 59.351 43.478 0.00 0.00 34.07 2.69
1676 6255 4.288626 TCTCCAGTGTTTACTTGCCCTTAT 59.711 41.667 0.00 0.00 34.07 1.73
1704 6288 8.706322 TTGGATATACTGCTATACTTCTGTCA 57.294 34.615 0.00 0.00 0.00 3.58
1735 6319 1.591248 CGAGTGTTTTGTGCGTATGC 58.409 50.000 0.00 0.00 43.20 3.14
1747 6331 1.586154 GCGTATGCCTTGGCTTGTGT 61.586 55.000 13.18 0.00 33.98 3.72
1769 6359 6.419710 GTGTCAAAATGGTTAGCAGTAAAACC 59.580 38.462 0.00 0.00 44.51 3.27
1816 6407 7.284518 GAGTTTCTACTCTCTTGTGTAATGC 57.715 40.000 0.00 0.00 45.99 3.56
1834 6425 7.332182 GTGTAATGCTGGTAAAGATATCTAGGC 59.668 40.741 5.46 5.33 0.00 3.93
1837 6428 6.439636 TGCTGGTAAAGATATCTAGGCATT 57.560 37.500 5.46 0.00 0.00 3.56
1915 6506 7.686438 AACATATTGAGTGCAACATCTTGTA 57.314 32.000 0.00 0.00 41.43 2.41
1922 6513 1.548986 GCAACATCTTGTATTGCGCC 58.451 50.000 4.18 0.00 39.36 6.53
1925 6516 3.546815 GCAACATCTTGTATTGCGCCTAG 60.547 47.826 4.18 0.00 39.36 3.02
1937 6528 2.870372 GCCTAGCAAGCACGTTGG 59.130 61.111 0.00 0.00 36.56 3.77
1943 6534 2.762535 AGCAAGCACGTTGGTATACT 57.237 45.000 2.25 0.00 45.23 2.12
1944 6535 3.880047 AGCAAGCACGTTGGTATACTA 57.120 42.857 2.25 0.00 45.23 1.82
1946 6537 4.766375 AGCAAGCACGTTGGTATACTATT 58.234 39.130 2.25 0.00 45.23 1.73
1947 6538 5.183228 AGCAAGCACGTTGGTATACTATTT 58.817 37.500 2.25 0.00 45.23 1.40
1949 6540 6.150474 AGCAAGCACGTTGGTATACTATTTTT 59.850 34.615 2.25 0.00 45.23 1.94
1950 6541 7.334921 AGCAAGCACGTTGGTATACTATTTTTA 59.665 33.333 2.25 0.00 45.23 1.52
1951 6542 8.126700 GCAAGCACGTTGGTATACTATTTTTAT 58.873 33.333 2.25 0.00 36.56 1.40
1952 6543 9.433317 CAAGCACGTTGGTATACTATTTTTATG 57.567 33.333 2.25 0.00 31.82 1.90
1954 6545 9.169592 AGCACGTTGGTATACTATTTTTATGTT 57.830 29.630 2.25 0.00 0.00 2.71
1993 6601 6.795399 TGTCAACCTGAAAAGAAATCACTTC 58.205 36.000 0.00 0.00 0.00 3.01
2048 6661 2.611292 CCGAGATTCAGAAAGATGGCAC 59.389 50.000 0.00 0.00 0.00 5.01
2103 6733 1.202615 GCATGAGCATGAGGAGCAGTA 60.203 52.381 14.27 0.00 41.20 2.74
2155 6785 6.684613 GCATTGATTCCTGCAGTTGGATAATT 60.685 38.462 13.81 0.00 38.28 1.40
2207 6843 5.127845 TGCCTACCATTTTTGTTTCAACTCA 59.872 36.000 0.00 0.00 0.00 3.41
2217 6853 3.057019 TGTTTCAACTCAACTCGATCGG 58.943 45.455 16.41 8.65 0.00 4.18
2286 6922 4.083696 GCCGCAGAGAGAGTAACTATCTAC 60.084 50.000 0.00 0.00 44.13 2.59
2350 6987 5.574188 AGAACTGGCATGGTAGAGAAAATT 58.426 37.500 0.00 0.00 0.00 1.82
2369 7006 3.121030 CTACGTGGGTGCAGCTGC 61.121 66.667 31.89 31.89 42.50 5.25
2404 7041 1.327303 CTCCAGTCTGGCTAGCTAGG 58.673 60.000 25.85 12.48 37.47 3.02
2406 7043 0.749649 CCAGTCTGGCTAGCTAGGTG 59.250 60.000 25.85 21.65 0.00 4.00
2407 7044 0.103937 CAGTCTGGCTAGCTAGGTGC 59.896 60.000 25.85 16.52 43.29 5.01
2408 7045 0.324738 AGTCTGGCTAGCTAGGTGCA 60.325 55.000 25.85 8.46 45.94 4.57
2425 7065 4.410492 GTGCAAACAACACCTCTATCAG 57.590 45.455 0.00 0.00 31.67 2.90
2435 7075 1.799933 CCTCTATCAGGCCAACTCCT 58.200 55.000 5.01 0.00 34.56 3.69
2436 7076 1.691434 CCTCTATCAGGCCAACTCCTC 59.309 57.143 5.01 0.00 34.56 3.71
2437 7077 1.691434 CTCTATCAGGCCAACTCCTCC 59.309 57.143 5.01 0.00 33.25 4.30
2438 7078 0.390860 CTATCAGGCCAACTCCTCCG 59.609 60.000 5.01 0.00 33.25 4.63
2439 7079 0.325296 TATCAGGCCAACTCCTCCGT 60.325 55.000 5.01 0.00 33.25 4.69
2440 7080 1.903877 ATCAGGCCAACTCCTCCGTG 61.904 60.000 5.01 0.00 33.25 4.94
2441 7081 4.021925 AGGCCAACTCCTCCGTGC 62.022 66.667 5.01 0.00 0.00 5.34
2442 7082 4.329545 GGCCAACTCCTCCGTGCA 62.330 66.667 0.00 0.00 0.00 4.57
2443 7083 2.281484 GCCAACTCCTCCGTGCAA 60.281 61.111 0.00 0.00 0.00 4.08
2444 7084 2.617274 GCCAACTCCTCCGTGCAAC 61.617 63.158 0.00 0.00 0.00 4.17
2445 7085 1.966451 CCAACTCCTCCGTGCAACC 60.966 63.158 0.00 0.00 0.00 3.77
2446 7086 1.966451 CAACTCCTCCGTGCAACCC 60.966 63.158 0.00 0.00 0.00 4.11
2447 7087 2.147387 AACTCCTCCGTGCAACCCT 61.147 57.895 0.00 0.00 0.00 4.34
2448 7088 0.834687 AACTCCTCCGTGCAACCCTA 60.835 55.000 0.00 0.00 0.00 3.53
2449 7089 0.617820 ACTCCTCCGTGCAACCCTAT 60.618 55.000 0.00 0.00 0.00 2.57
2450 7090 0.105039 CTCCTCCGTGCAACCCTATC 59.895 60.000 0.00 0.00 0.00 2.08
2451 7091 1.146263 CCTCCGTGCAACCCTATCC 59.854 63.158 0.00 0.00 0.00 2.59
2452 7092 1.338136 CCTCCGTGCAACCCTATCCT 61.338 60.000 0.00 0.00 0.00 3.24
2453 7093 0.179073 CTCCGTGCAACCCTATCCTG 60.179 60.000 0.00 0.00 0.00 3.86
2454 7094 0.907704 TCCGTGCAACCCTATCCTGT 60.908 55.000 0.00 0.00 0.00 4.00
2455 7095 0.462047 CCGTGCAACCCTATCCTGTC 60.462 60.000 0.00 0.00 0.00 3.51
2456 7096 0.462047 CGTGCAACCCTATCCTGTCC 60.462 60.000 0.00 0.00 0.00 4.02
2457 7097 0.462047 GTGCAACCCTATCCTGTCCG 60.462 60.000 0.00 0.00 0.00 4.79
2458 7098 1.146263 GCAACCCTATCCTGTCCGG 59.854 63.158 0.00 0.00 0.00 5.14
2459 7099 1.146263 CAACCCTATCCTGTCCGGC 59.854 63.158 0.00 0.00 0.00 6.13
2460 7100 2.070650 AACCCTATCCTGTCCGGCC 61.071 63.158 0.00 0.00 0.00 6.13
2461 7101 3.242291 CCCTATCCTGTCCGGCCC 61.242 72.222 0.00 0.00 0.00 5.80
2462 7102 3.242291 CCTATCCTGTCCGGCCCC 61.242 72.222 0.00 0.00 0.00 5.80
2463 7103 3.616721 CTATCCTGTCCGGCCCCG 61.617 72.222 0.00 0.00 39.44 5.73
2464 7104 4.468769 TATCCTGTCCGGCCCCGT 62.469 66.667 5.93 0.00 37.81 5.28
2465 7105 3.988050 TATCCTGTCCGGCCCCGTT 62.988 63.158 5.93 0.00 37.81 4.44
2470 7110 4.994471 GTCCGGCCCCGTTCGTTT 62.994 66.667 5.93 0.00 37.81 3.60
2471 7111 4.992511 TCCGGCCCCGTTCGTTTG 62.993 66.667 5.93 0.00 37.81 2.93
2472 7112 4.992511 CCGGCCCCGTTCGTTTGA 62.993 66.667 5.93 0.00 37.81 2.69
2473 7113 2.973600 CGGCCCCGTTCGTTTGAA 60.974 61.111 0.00 0.00 34.35 2.69
2474 7114 2.951458 GGCCCCGTTCGTTTGAAG 59.049 61.111 0.00 0.00 33.98 3.02
2475 7115 1.895231 GGCCCCGTTCGTTTGAAGT 60.895 57.895 0.00 0.00 33.98 3.01
2476 7116 0.603439 GGCCCCGTTCGTTTGAAGTA 60.603 55.000 0.00 0.00 33.98 2.24
2477 7117 1.228533 GCCCCGTTCGTTTGAAGTAA 58.771 50.000 0.00 0.00 33.98 2.24
2478 7118 1.603326 GCCCCGTTCGTTTGAAGTAAA 59.397 47.619 0.00 0.00 33.98 2.01
2479 7119 2.033174 GCCCCGTTCGTTTGAAGTAAAA 59.967 45.455 0.00 0.00 33.98 1.52
2480 7120 3.850740 GCCCCGTTCGTTTGAAGTAAAAG 60.851 47.826 0.00 0.00 33.98 2.27
2481 7121 3.560896 CCCCGTTCGTTTGAAGTAAAAGA 59.439 43.478 0.00 0.00 35.44 2.52
2482 7122 4.319261 CCCCGTTCGTTTGAAGTAAAAGAG 60.319 45.833 0.00 0.00 37.89 2.85
2483 7123 4.508861 CCCGTTCGTTTGAAGTAAAAGAGA 59.491 41.667 0.00 0.00 37.89 3.10
2484 7124 5.429615 CCGTTCGTTTGAAGTAAAAGAGAC 58.570 41.667 0.00 0.00 37.89 3.36
2485 7125 5.005971 CCGTTCGTTTGAAGTAAAAGAGACA 59.994 40.000 0.00 0.00 37.89 3.41
2486 7126 6.455913 CCGTTCGTTTGAAGTAAAAGAGACAA 60.456 38.462 0.00 0.00 37.89 3.18
2487 7127 6.957077 CGTTCGTTTGAAGTAAAAGAGACAAA 59.043 34.615 0.00 0.00 37.89 2.83
2488 7128 7.479291 CGTTCGTTTGAAGTAAAAGAGACAAAA 59.521 33.333 0.00 0.00 37.89 2.44
2489 7129 9.120422 GTTCGTTTGAAGTAAAAGAGACAAAAA 57.880 29.630 0.00 0.00 37.89 1.94
2522 7162 3.981308 CGGGAGCAAACGGACATT 58.019 55.556 0.00 0.00 0.00 2.71
2523 7163 2.253513 CGGGAGCAAACGGACATTT 58.746 52.632 0.00 0.00 0.00 2.32
2524 7164 0.109781 CGGGAGCAAACGGACATTTG 60.110 55.000 0.00 0.00 41.62 2.32
2525 7165 0.958822 GGGAGCAAACGGACATTTGT 59.041 50.000 0.68 0.00 40.92 2.83
2526 7166 1.068541 GGGAGCAAACGGACATTTGTC 60.069 52.381 1.99 1.99 40.92 3.18
2536 7176 2.774439 GACATTTGTCCGCTTTGTGT 57.226 45.000 0.00 0.00 39.07 3.72
2537 7177 2.650608 GACATTTGTCCGCTTTGTGTC 58.349 47.619 0.00 0.00 39.07 3.67
2538 7178 1.336755 ACATTTGTCCGCTTTGTGTCC 59.663 47.619 0.00 0.00 0.00 4.02
2539 7179 0.591170 ATTTGTCCGCTTTGTGTCCG 59.409 50.000 0.00 0.00 0.00 4.79
2540 7180 2.054140 TTTGTCCGCTTTGTGTCCGC 62.054 55.000 0.00 0.00 0.00 5.54
2541 7181 2.665185 GTCCGCTTTGTGTCCGCT 60.665 61.111 0.00 0.00 0.00 5.52
2542 7182 2.110213 TCCGCTTTGTGTCCGCTT 59.890 55.556 0.00 0.00 0.00 4.68
2543 7183 1.525077 TCCGCTTTGTGTCCGCTTT 60.525 52.632 0.00 0.00 0.00 3.51
2544 7184 1.370414 CCGCTTTGTGTCCGCTTTG 60.370 57.895 0.00 0.00 0.00 2.77
2545 7185 1.355210 CGCTTTGTGTCCGCTTTGT 59.645 52.632 0.00 0.00 0.00 2.83
2546 7186 0.929824 CGCTTTGTGTCCGCTTTGTG 60.930 55.000 0.00 0.00 0.00 3.33
2547 7187 0.100503 GCTTTGTGTCCGCTTTGTGT 59.899 50.000 0.00 0.00 0.00 3.72
2548 7188 1.859998 GCTTTGTGTCCGCTTTGTGTC 60.860 52.381 0.00 0.00 0.00 3.67
2549 7189 0.736053 TTTGTGTCCGCTTTGTGTCC 59.264 50.000 0.00 0.00 0.00 4.02
2550 7190 1.433053 TTGTGTCCGCTTTGTGTCCG 61.433 55.000 0.00 0.00 0.00 4.79
2551 7191 2.970324 TGTCCGCTTTGTGTCCGC 60.970 61.111 0.00 0.00 0.00 5.54
2552 7192 2.665185 GTCCGCTTTGTGTCCGCT 60.665 61.111 0.00 0.00 0.00 5.52
2553 7193 2.110213 TCCGCTTTGTGTCCGCTT 59.890 55.556 0.00 0.00 0.00 4.68
2554 7194 1.525077 TCCGCTTTGTGTCCGCTTT 60.525 52.632 0.00 0.00 0.00 3.51
2555 7195 1.082104 CCGCTTTGTGTCCGCTTTC 60.082 57.895 0.00 0.00 0.00 2.62
2556 7196 1.438710 CGCTTTGTGTCCGCTTTCG 60.439 57.895 0.00 0.00 0.00 3.46
2557 7197 1.827315 CGCTTTGTGTCCGCTTTCGA 61.827 55.000 0.00 0.00 38.10 3.71
2558 7198 0.384353 GCTTTGTGTCCGCTTTCGAC 60.384 55.000 0.00 0.00 38.10 4.20
2559 7199 0.234884 CTTTGTGTCCGCTTTCGACC 59.765 55.000 0.00 0.00 38.10 4.79
2560 7200 1.161563 TTTGTGTCCGCTTTCGACCC 61.162 55.000 0.00 0.00 38.10 4.46
2561 7201 2.029964 GTGTCCGCTTTCGACCCA 59.970 61.111 0.00 0.00 38.10 4.51
2562 7202 1.375523 GTGTCCGCTTTCGACCCAT 60.376 57.895 0.00 0.00 38.10 4.00
2563 7203 1.079405 TGTCCGCTTTCGACCCATC 60.079 57.895 0.00 0.00 38.10 3.51
2564 7204 1.814169 GTCCGCTTTCGACCCATCC 60.814 63.158 0.00 0.00 38.10 3.51
2565 7205 2.890474 CCGCTTTCGACCCATCCG 60.890 66.667 0.00 0.00 38.10 4.18
2566 7206 3.564027 CGCTTTCGACCCATCCGC 61.564 66.667 0.00 0.00 38.10 5.54
2567 7207 3.564027 GCTTTCGACCCATCCGCG 61.564 66.667 0.00 0.00 0.00 6.46
2568 7208 2.890474 CTTTCGACCCATCCGCGG 60.890 66.667 22.12 22.12 0.00 6.46
2577 7217 3.061848 CATCCGCGGCCCAAGTTT 61.062 61.111 23.51 0.00 0.00 2.66
2578 7218 3.061848 ATCCGCGGCCCAAGTTTG 61.062 61.111 23.51 0.00 0.00 2.93
2586 7226 3.977244 CCCAAGTTTGCGCCGCTT 61.977 61.111 11.67 3.41 0.00 4.68
2587 7227 2.027460 CCAAGTTTGCGCCGCTTT 59.973 55.556 11.67 0.00 0.00 3.51
2588 7228 1.591327 CCAAGTTTGCGCCGCTTTT 60.591 52.632 11.67 0.00 0.00 2.27
2589 7229 0.318275 CCAAGTTTGCGCCGCTTTTA 60.318 50.000 11.67 0.00 0.00 1.52
2590 7230 1.052287 CAAGTTTGCGCCGCTTTTAG 58.948 50.000 11.67 0.00 0.00 1.85
2591 7231 0.039527 AAGTTTGCGCCGCTTTTAGG 60.040 50.000 11.67 0.00 0.00 2.69
2592 7232 1.443702 GTTTGCGCCGCTTTTAGGG 60.444 57.895 11.67 0.00 0.00 3.53
2593 7233 1.899534 TTTGCGCCGCTTTTAGGGT 60.900 52.632 11.67 0.00 0.00 4.34
2594 7234 2.136196 TTTGCGCCGCTTTTAGGGTG 62.136 55.000 11.67 0.00 36.89 4.61
2595 7235 2.744709 GCGCCGCTTTTAGGGTGA 60.745 61.111 0.00 0.00 35.85 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.548719 AGAATCGGTCGTGACATTCCA 59.451 47.619 2.00 0.00 29.16 3.53
10 11 2.604855 CGGGAATGACTAGAATCGGTCG 60.605 54.545 0.00 0.00 35.45 4.79
12 13 2.100916 CACGGGAATGACTAGAATCGGT 59.899 50.000 0.00 0.00 0.00 4.69
14 15 3.372954 GACACGGGAATGACTAGAATCG 58.627 50.000 0.00 0.00 0.00 3.34
20 21 1.760613 GGATGGACACGGGAATGACTA 59.239 52.381 0.00 0.00 0.00 2.59
25 26 2.189521 GCGGATGGACACGGGAAT 59.810 61.111 0.00 0.00 0.00 3.01
34 35 3.653664 ATTTTGGCCGGCGGATGGA 62.654 57.895 33.44 11.17 0.00 3.41
35 36 3.146913 ATTTTGGCCGGCGGATGG 61.147 61.111 33.44 2.59 0.00 3.51
42 43 2.047370 GGCAACCATTTTGGCCGG 60.047 61.111 0.00 0.00 42.67 6.13
85 86 1.065709 GGTCTCCCAGCCGTTAATTGA 60.066 52.381 0.00 0.00 0.00 2.57
104 105 4.570663 GCGTCGATCGACTGGGGG 62.571 72.222 37.12 25.43 42.54 5.40
127 128 3.201290 GGACAATGTCATAGCTCAGTGG 58.799 50.000 15.86 0.00 34.60 4.00
131 132 1.831106 ACCGGACAATGTCATAGCTCA 59.169 47.619 15.86 0.00 33.68 4.26
132 133 2.205074 CACCGGACAATGTCATAGCTC 58.795 52.381 15.86 0.00 33.68 4.09
136 137 1.470805 CGAGCACCGGACAATGTCATA 60.471 52.381 15.86 0.00 33.68 2.15
138 139 1.374125 CGAGCACCGGACAATGTCA 60.374 57.895 15.86 0.00 33.68 3.58
158 159 1.343069 CCCTACCTCTATGAGCACCC 58.657 60.000 0.00 0.00 0.00 4.61
159 160 1.689273 CACCCTACCTCTATGAGCACC 59.311 57.143 0.00 0.00 0.00 5.01
160 161 2.389715 ACACCCTACCTCTATGAGCAC 58.610 52.381 0.00 0.00 0.00 4.40
161 162 2.848678 ACACCCTACCTCTATGAGCA 57.151 50.000 0.00 0.00 0.00 4.26
162 163 2.553172 CGTACACCCTACCTCTATGAGC 59.447 54.545 0.00 0.00 0.00 4.26
163 164 3.818180 ACGTACACCCTACCTCTATGAG 58.182 50.000 0.00 0.00 0.00 2.90
164 165 3.939740 ACGTACACCCTACCTCTATGA 57.060 47.619 0.00 0.00 0.00 2.15
165 166 5.048921 CACATACGTACACCCTACCTCTATG 60.049 48.000 0.00 0.00 0.00 2.23
166 167 5.068636 CACATACGTACACCCTACCTCTAT 58.931 45.833 0.00 0.00 0.00 1.98
167 168 4.454678 CACATACGTACACCCTACCTCTA 58.545 47.826 0.00 0.00 0.00 2.43
168 169 3.285484 CACATACGTACACCCTACCTCT 58.715 50.000 0.00 0.00 0.00 3.69
169 170 2.223665 GCACATACGTACACCCTACCTC 60.224 54.545 0.00 0.00 0.00 3.85
170 171 1.753073 GCACATACGTACACCCTACCT 59.247 52.381 0.00 0.00 0.00 3.08
172 173 1.133025 ACGCACATACGTACACCCTAC 59.867 52.381 0.00 0.00 46.19 3.18
174 175 2.269978 ACGCACATACGTACACCCT 58.730 52.632 0.00 0.00 46.19 4.34
182 183 4.149922 CCCACTCATATTAACGCACATACG 59.850 45.833 0.00 0.00 39.50 3.06
185 186 3.876914 CACCCACTCATATTAACGCACAT 59.123 43.478 0.00 0.00 0.00 3.21
186 187 3.266636 CACCCACTCATATTAACGCACA 58.733 45.455 0.00 0.00 0.00 4.57
187 188 3.267483 ACACCCACTCATATTAACGCAC 58.733 45.455 0.00 0.00 0.00 5.34
188 189 3.620427 ACACCCACTCATATTAACGCA 57.380 42.857 0.00 0.00 0.00 5.24
189 190 4.084013 GCATACACCCACTCATATTAACGC 60.084 45.833 0.00 0.00 0.00 4.84
191 192 4.084013 GCGCATACACCCACTCATATTAAC 60.084 45.833 0.30 0.00 0.00 2.01
192 193 4.062293 GCGCATACACCCACTCATATTAA 58.938 43.478 0.30 0.00 0.00 1.40
194 195 2.494059 GCGCATACACCCACTCATATT 58.506 47.619 0.30 0.00 0.00 1.28
195 196 1.605457 CGCGCATACACCCACTCATAT 60.605 52.381 8.75 0.00 0.00 1.78
196 197 0.249280 CGCGCATACACCCACTCATA 60.249 55.000 8.75 0.00 0.00 2.15
197 198 1.521457 CGCGCATACACCCACTCAT 60.521 57.895 8.75 0.00 0.00 2.90
198 199 1.596895 TACGCGCATACACCCACTCA 61.597 55.000 5.73 0.00 0.00 3.41
199 200 0.249322 ATACGCGCATACACCCACTC 60.249 55.000 5.73 0.00 0.00 3.51
200 201 0.529773 CATACGCGCATACACCCACT 60.530 55.000 5.73 0.00 0.00 4.00
203 204 1.724623 CATACATACGCGCATACACCC 59.275 52.381 5.73 0.00 0.00 4.61
204 205 2.661675 CTCATACATACGCGCATACACC 59.338 50.000 5.73 0.00 0.00 4.16
206 207 2.324860 GCTCATACATACGCGCATACA 58.675 47.619 5.73 0.00 0.00 2.29
207 208 1.317611 CGCTCATACATACGCGCATAC 59.682 52.381 5.73 0.00 39.11 2.39
208 209 1.613270 CGCTCATACATACGCGCATA 58.387 50.000 5.73 0.00 39.11 3.14
209 210 2.434688 CGCTCATACATACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
210 211 3.916439 CGCTCATACATACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
214 215 0.159554 CGCAAGCGCTCATACATACG 59.840 55.000 12.06 0.00 35.30 3.06
215 216 1.190323 GACGCAAGCGCTCATACATAC 59.810 52.381 12.06 0.00 44.19 2.39
216 217 1.067060 AGACGCAAGCGCTCATACATA 59.933 47.619 12.06 0.00 44.19 2.29
217 218 0.179100 AGACGCAAGCGCTCATACAT 60.179 50.000 12.06 0.00 44.19 2.29
219 220 1.078759 ACAGACGCAAGCGCTCATAC 61.079 55.000 12.06 1.58 44.19 2.39
220 221 0.454196 TACAGACGCAAGCGCTCATA 59.546 50.000 12.06 5.16 44.19 2.15
223 224 2.445438 GGTACAGACGCAAGCGCTC 61.445 63.158 12.06 11.06 44.19 5.03
224 225 2.432628 GGTACAGACGCAAGCGCT 60.433 61.111 15.09 2.64 44.19 5.92
225 226 3.838795 CGGTACAGACGCAAGCGC 61.839 66.667 15.09 0.00 44.19 5.92
226 227 2.430244 ACGGTACAGACGCAAGCG 60.430 61.111 13.50 13.50 46.03 4.68
227 228 1.219522 AACACGGTACAGACGCAAGC 61.220 55.000 0.00 0.00 45.62 4.01
229 230 0.102663 TGAACACGGTACAGACGCAA 59.897 50.000 0.00 0.00 34.00 4.85
230 231 0.102663 TTGAACACGGTACAGACGCA 59.897 50.000 0.00 0.00 34.00 5.24
232 233 4.461992 AAAATTGAACACGGTACAGACG 57.538 40.909 0.00 0.00 37.36 4.18
365 1574 4.683832 CAAGTTTCCACTATACTCCCTCG 58.316 47.826 0.00 0.00 30.68 4.63
375 1584 3.863400 GCTTCTACCGCAAGTTTCCACTA 60.863 47.826 0.00 0.00 30.68 2.74
379 1588 0.803117 GGCTTCTACCGCAAGTTTCC 59.197 55.000 0.00 0.00 0.00 3.13
388 2199 2.672961 TGACAAGATGGCTTCTACCG 57.327 50.000 3.03 0.00 33.05 4.02
455 2273 3.459232 TCATCACGGGCTGATTAGAAG 57.541 47.619 0.00 0.00 37.53 2.85
468 2286 1.016627 ATTTCCGCACCATCATCACG 58.983 50.000 0.00 0.00 0.00 4.35
471 2289 3.376859 TGTGTTATTTCCGCACCATCATC 59.623 43.478 0.00 0.00 32.62 2.92
720 2552 0.993746 GTTTGACAAAGAGCGCGCAG 60.994 55.000 35.10 18.85 0.00 5.18
721 2553 1.010125 GTTTGACAAAGAGCGCGCA 60.010 52.632 35.10 6.63 0.00 6.09
813 3211 1.440060 CAGTAATAGCCACGCCCGA 59.560 57.895 0.00 0.00 0.00 5.14
814 3212 2.244651 GCAGTAATAGCCACGCCCG 61.245 63.158 0.00 0.00 0.00 6.13
1020 5464 1.417517 CCATGGCTAGTAGTGATGGCA 59.582 52.381 13.56 0.00 39.22 4.92
1025 5469 1.482182 CACTGCCATGGCTAGTAGTGA 59.518 52.381 35.01 16.73 41.16 3.41
1028 5472 2.366590 TGATCACTGCCATGGCTAGTAG 59.633 50.000 35.53 26.23 42.51 2.57
1029 5473 2.103094 GTGATCACTGCCATGGCTAGTA 59.897 50.000 35.53 22.29 42.51 1.82
1031 5475 1.590932 GTGATCACTGCCATGGCTAG 58.409 55.000 35.53 29.73 42.51 3.42
1032 5476 0.181114 GGTGATCACTGCCATGGCTA 59.819 55.000 35.53 21.25 42.51 3.93
1033 5477 1.077212 GGTGATCACTGCCATGGCT 60.077 57.895 35.53 17.03 42.51 4.75
1034 5478 0.754217 ATGGTGATCACTGCCATGGC 60.754 55.000 30.54 30.54 41.05 4.40
1058 5547 8.621286 AGTAAAAGATAAGAAACCACAAGTGTG 58.379 33.333 4.38 4.38 45.23 3.82
1371 5897 2.571757 GTCCTCGTCGACATGCCA 59.428 61.111 17.16 0.00 32.74 4.92
1462 5990 1.741770 CCGGCAGTAACTGGACAGC 60.742 63.158 0.00 0.00 38.48 4.40
1463 5991 0.320374 TTCCGGCAGTAACTGGACAG 59.680 55.000 0.00 0.00 44.97 3.51
1468 5996 1.821216 ACCAATTCCGGCAGTAACTG 58.179 50.000 0.00 0.00 34.12 3.16
1544 6088 1.155323 ATCCCATCCACATGCTCCAT 58.845 50.000 0.00 0.00 0.00 3.41
1571 6115 2.397252 GCGACGCATGAGTTGAGC 59.603 61.111 19.85 13.91 0.00 4.26
1634 6206 0.249699 ATGAACACGAACGCAGGACA 60.250 50.000 0.00 0.00 0.00 4.02
1655 6234 4.650972 ATAAGGGCAAGTAAACACTGGA 57.349 40.909 0.00 0.00 0.00 3.86
1666 6245 6.150140 GCAGTATATCCAAGAATAAGGGCAAG 59.850 42.308 0.00 0.00 0.00 4.01
1676 6255 9.368416 ACAGAAGTATAGCAGTATATCCAAGAA 57.632 33.333 0.00 0.00 0.00 2.52
1697 6281 3.487372 TCGGAGAGAGAACTTGACAGAA 58.513 45.455 0.00 0.00 0.00 3.02
1735 6319 2.102925 ACCATTTTGACACAAGCCAAGG 59.897 45.455 0.00 0.00 0.00 3.61
1747 6331 6.716934 TGGTTTTACTGCTAACCATTTTGA 57.283 33.333 2.74 0.00 46.55 2.69
1812 6403 6.439636 TGCCTAGATATCTTTACCAGCATT 57.560 37.500 11.25 0.00 0.00 3.56
1860 6451 7.888424 ACCCACATTACACAAAAATAAGGTAC 58.112 34.615 0.00 0.00 0.00 3.34
1862 6453 6.987403 ACCCACATTACACAAAAATAAGGT 57.013 33.333 0.00 0.00 0.00 3.50
1868 6459 9.132923 TGTTATCTTACCCACATTACACAAAAA 57.867 29.630 0.00 0.00 0.00 1.94
1883 6474 8.208718 TGTTGCACTCAATATGTTATCTTACC 57.791 34.615 0.00 0.00 34.29 2.85
1919 6510 2.476051 CAACGTGCTTGCTAGGCG 59.524 61.111 0.00 0.00 0.00 5.52
1922 6513 3.782046 AGTATACCAACGTGCTTGCTAG 58.218 45.455 0.00 0.00 0.00 3.42
1925 6516 5.479716 AAATAGTATACCAACGTGCTTGC 57.520 39.130 0.00 0.00 0.00 4.01
1950 6541 8.566260 GGTTGACAGATACTCGTATAGTAACAT 58.434 37.037 0.00 0.00 43.87 2.71
1951 6542 7.772292 AGGTTGACAGATACTCGTATAGTAACA 59.228 37.037 0.00 0.00 43.87 2.41
1952 6543 8.068977 CAGGTTGACAGATACTCGTATAGTAAC 58.931 40.741 0.00 0.00 43.87 2.50
1954 6545 7.503549 TCAGGTTGACAGATACTCGTATAGTA 58.496 38.462 0.00 0.00 44.76 1.82
1955 6546 6.354938 TCAGGTTGACAGATACTCGTATAGT 58.645 40.000 0.00 0.00 42.62 2.12
1956 6547 6.862711 TCAGGTTGACAGATACTCGTATAG 57.137 41.667 0.00 0.00 0.00 1.31
1957 6548 7.634671 TTTCAGGTTGACAGATACTCGTATA 57.365 36.000 0.00 0.00 0.00 1.47
1958 6549 6.525578 TTTCAGGTTGACAGATACTCGTAT 57.474 37.500 0.00 0.00 0.00 3.06
1959 6550 5.970317 TTTCAGGTTGACAGATACTCGTA 57.030 39.130 0.00 0.00 0.00 3.43
1960 6551 4.866508 TTTCAGGTTGACAGATACTCGT 57.133 40.909 0.00 0.00 0.00 4.18
1961 6552 5.470368 TCTTTTCAGGTTGACAGATACTCG 58.530 41.667 0.00 0.00 0.00 4.18
1962 6553 7.730364 TTTCTTTTCAGGTTGACAGATACTC 57.270 36.000 0.00 0.00 0.00 2.59
1963 6554 7.939039 TGATTTCTTTTCAGGTTGACAGATACT 59.061 33.333 0.00 0.00 0.00 2.12
1964 6555 8.017946 GTGATTTCTTTTCAGGTTGACAGATAC 58.982 37.037 0.00 0.00 0.00 2.24
1993 6601 2.721274 TGCACATCAAAATTGGTCCG 57.279 45.000 0.00 0.00 0.00 4.79
2028 6637 2.611292 GGTGCCATCTTTCTGAATCTCG 59.389 50.000 0.00 0.00 0.00 4.04
2155 6785 1.134521 AGAAGCCAGTTCACAACGACA 60.135 47.619 0.00 0.00 37.67 4.35
2207 6843 2.203070 GGCATGGCCGATCGAGTT 60.203 61.111 18.66 0.00 39.62 3.01
2227 6863 2.016961 CGACAGTGTATGGCATGGC 58.983 57.895 13.29 13.29 36.31 4.40
2229 6865 0.654160 CTGCGACAGTGTATGGCATG 59.346 55.000 10.98 0.00 36.31 4.06
2230 6866 1.091771 GCTGCGACAGTGTATGGCAT 61.092 55.000 14.28 4.88 36.31 4.40
2231 6867 1.741401 GCTGCGACAGTGTATGGCA 60.741 57.895 13.50 13.50 36.31 4.92
2232 6868 2.802667 CGCTGCGACAGTGTATGGC 61.803 63.158 18.66 0.71 37.23 4.40
2233 6869 2.167219 CCGCTGCGACAGTGTATGG 61.167 63.158 25.45 0.00 39.99 2.74
2286 6922 4.214332 GCCAAGAAAAGACACAAGGTAGAG 59.786 45.833 0.00 0.00 0.00 2.43
2294 6931 6.115446 CCTATCTATGCCAAGAAAAGACACA 58.885 40.000 0.00 0.00 0.00 3.72
2350 6987 3.625897 AGCTGCACCCACGTAGCA 61.626 61.111 8.35 6.30 45.93 3.49
2369 7006 3.723554 GAGCAGTAGGTCCAAGTCG 57.276 57.895 0.00 0.00 36.27 4.18
2404 7041 3.189287 CCTGATAGAGGTGTTGTTTGCAC 59.811 47.826 0.00 0.00 37.02 4.57
2406 7043 2.162408 GCCTGATAGAGGTGTTGTTTGC 59.838 50.000 0.00 0.00 44.97 3.68
2407 7044 2.749621 GGCCTGATAGAGGTGTTGTTTG 59.250 50.000 0.00 0.00 44.97 2.93
2408 7045 2.375174 TGGCCTGATAGAGGTGTTGTTT 59.625 45.455 3.32 0.00 44.97 2.83
2424 7064 4.021925 GCACGGAGGAGTTGGCCT 62.022 66.667 3.32 0.00 42.17 5.19
2425 7065 3.842925 TTGCACGGAGGAGTTGGCC 62.843 63.158 0.00 0.00 0.00 5.36
2426 7066 2.281484 TTGCACGGAGGAGTTGGC 60.281 61.111 0.00 0.00 0.00 4.52
2427 7067 1.966451 GGTTGCACGGAGGAGTTGG 60.966 63.158 0.00 0.00 0.00 3.77
2428 7068 1.966451 GGGTTGCACGGAGGAGTTG 60.966 63.158 0.00 0.00 0.00 3.16
2429 7069 0.834687 TAGGGTTGCACGGAGGAGTT 60.835 55.000 0.00 0.00 0.00 3.01
2430 7070 0.617820 ATAGGGTTGCACGGAGGAGT 60.618 55.000 0.00 0.00 0.00 3.85
2431 7071 0.105039 GATAGGGTTGCACGGAGGAG 59.895 60.000 0.00 0.00 0.00 3.69
2432 7072 1.335132 GGATAGGGTTGCACGGAGGA 61.335 60.000 0.00 0.00 0.00 3.71
2433 7073 1.146263 GGATAGGGTTGCACGGAGG 59.854 63.158 0.00 0.00 0.00 4.30
2434 7074 0.179073 CAGGATAGGGTTGCACGGAG 60.179 60.000 0.00 0.00 0.00 4.63
2435 7075 0.907704 ACAGGATAGGGTTGCACGGA 60.908 55.000 0.00 0.00 0.00 4.69
2436 7076 0.462047 GACAGGATAGGGTTGCACGG 60.462 60.000 0.00 0.00 0.00 4.94
2437 7077 0.462047 GGACAGGATAGGGTTGCACG 60.462 60.000 0.00 0.00 0.00 5.34
2438 7078 0.462047 CGGACAGGATAGGGTTGCAC 60.462 60.000 0.00 0.00 0.00 4.57
2439 7079 1.622607 CCGGACAGGATAGGGTTGCA 61.623 60.000 0.00 0.00 45.00 4.08
2440 7080 1.146263 CCGGACAGGATAGGGTTGC 59.854 63.158 0.00 0.00 45.00 4.17
2441 7081 1.146263 GCCGGACAGGATAGGGTTG 59.854 63.158 5.05 0.00 45.00 3.77
2442 7082 2.070650 GGCCGGACAGGATAGGGTT 61.071 63.158 5.05 0.00 45.00 4.11
2443 7083 2.446036 GGCCGGACAGGATAGGGT 60.446 66.667 5.05 0.00 45.00 4.34
2444 7084 3.242291 GGGCCGGACAGGATAGGG 61.242 72.222 11.00 0.00 45.00 3.53
2445 7085 3.242291 GGGGCCGGACAGGATAGG 61.242 72.222 11.00 0.00 45.00 2.57
2446 7086 3.616721 CGGGGCCGGACAGGATAG 61.617 72.222 11.00 0.00 45.00 2.08
2447 7087 3.988050 AACGGGGCCGGACAGGATA 62.988 63.158 18.95 0.00 45.00 2.59
2453 7093 4.994471 AAACGAACGGGGCCGGAC 62.994 66.667 18.95 0.00 44.69 4.79
2454 7094 4.992511 CAAACGAACGGGGCCGGA 62.993 66.667 18.95 0.00 44.69 5.14
2455 7095 4.992511 TCAAACGAACGGGGCCGG 62.993 66.667 9.88 9.88 44.69 6.13
2456 7096 2.961669 CTTCAAACGAACGGGGCCG 61.962 63.158 0.00 0.00 46.03 6.13
2457 7097 0.603439 TACTTCAAACGAACGGGGCC 60.603 55.000 0.00 0.00 0.00 5.80
2458 7098 1.228533 TTACTTCAAACGAACGGGGC 58.771 50.000 0.00 0.00 0.00 5.80
2459 7099 3.560896 TCTTTTACTTCAAACGAACGGGG 59.439 43.478 0.00 0.00 0.00 5.73
2460 7100 4.508861 TCTCTTTTACTTCAAACGAACGGG 59.491 41.667 0.00 0.00 0.00 5.28
2461 7101 5.005971 TGTCTCTTTTACTTCAAACGAACGG 59.994 40.000 0.00 0.00 0.00 4.44
2462 7102 6.028040 TGTCTCTTTTACTTCAAACGAACG 57.972 37.500 0.00 0.00 0.00 3.95
2463 7103 8.663771 TTTTGTCTCTTTTACTTCAAACGAAC 57.336 30.769 0.00 0.00 0.00 3.95
2504 7144 1.862602 AAATGTCCGTTTGCTCCCGC 61.863 55.000 0.00 0.00 0.00 6.13
2505 7145 0.109781 CAAATGTCCGTTTGCTCCCG 60.110 55.000 0.00 0.00 32.90 5.14
2506 7146 0.958822 ACAAATGTCCGTTTGCTCCC 59.041 50.000 11.00 0.00 41.61 4.30
2507 7147 2.331809 GACAAATGTCCGTTTGCTCC 57.668 50.000 11.00 0.00 41.61 4.70
2517 7157 2.604614 GGACACAAAGCGGACAAATGTC 60.605 50.000 4.96 4.96 44.04 3.06
2518 7158 1.336755 GGACACAAAGCGGACAAATGT 59.663 47.619 0.00 0.00 0.00 2.71
2519 7159 1.662876 CGGACACAAAGCGGACAAATG 60.663 52.381 0.00 0.00 0.00 2.32
2520 7160 0.591170 CGGACACAAAGCGGACAAAT 59.409 50.000 0.00 0.00 0.00 2.32
2521 7161 2.018544 CGGACACAAAGCGGACAAA 58.981 52.632 0.00 0.00 0.00 2.83
2522 7162 2.539338 GCGGACACAAAGCGGACAA 61.539 57.895 0.00 0.00 0.00 3.18
2523 7163 2.933878 AAGCGGACACAAAGCGGACA 62.934 55.000 0.00 0.00 35.78 4.02
2524 7164 1.782028 AAAGCGGACACAAAGCGGAC 61.782 55.000 0.00 0.00 35.78 4.79
2525 7165 1.525077 AAAGCGGACACAAAGCGGA 60.525 52.632 0.00 0.00 35.78 5.54
2526 7166 1.370414 CAAAGCGGACACAAAGCGG 60.370 57.895 0.00 0.00 35.78 5.52
2527 7167 0.929824 CACAAAGCGGACACAAAGCG 60.930 55.000 0.00 0.00 35.78 4.68
2528 7168 0.100503 ACACAAAGCGGACACAAAGC 59.899 50.000 0.00 0.00 0.00 3.51
2529 7169 1.268539 GGACACAAAGCGGACACAAAG 60.269 52.381 0.00 0.00 0.00 2.77
2530 7170 0.736053 GGACACAAAGCGGACACAAA 59.264 50.000 0.00 0.00 0.00 2.83
2531 7171 1.433053 CGGACACAAAGCGGACACAA 61.433 55.000 0.00 0.00 0.00 3.33
2532 7172 1.885388 CGGACACAAAGCGGACACA 60.885 57.895 0.00 0.00 0.00 3.72
2533 7173 2.935955 CGGACACAAAGCGGACAC 59.064 61.111 0.00 0.00 0.00 3.67
2534 7174 2.933878 AAGCGGACACAAAGCGGACA 62.934 55.000 0.00 0.00 35.78 4.02
2535 7175 1.782028 AAAGCGGACACAAAGCGGAC 61.782 55.000 0.00 0.00 35.78 4.79
2536 7176 1.503818 GAAAGCGGACACAAAGCGGA 61.504 55.000 0.00 0.00 35.78 5.54
2537 7177 1.082104 GAAAGCGGACACAAAGCGG 60.082 57.895 0.00 0.00 35.78 5.52
2538 7178 1.438710 CGAAAGCGGACACAAAGCG 60.439 57.895 0.00 0.00 35.78 4.68
2539 7179 0.384353 GTCGAAAGCGGACACAAAGC 60.384 55.000 0.00 0.00 38.28 3.51
2540 7180 0.234884 GGTCGAAAGCGGACACAAAG 59.765 55.000 0.00 0.00 38.28 2.77
2541 7181 1.161563 GGGTCGAAAGCGGACACAAA 61.162 55.000 0.00 0.00 38.28 2.83
2542 7182 1.595929 GGGTCGAAAGCGGACACAA 60.596 57.895 0.00 0.00 38.28 3.33
2543 7183 2.029964 GGGTCGAAAGCGGACACA 59.970 61.111 0.00 0.00 38.28 3.72
2544 7184 1.359459 GATGGGTCGAAAGCGGACAC 61.359 60.000 0.00 0.31 38.28 3.67
2545 7185 1.079405 GATGGGTCGAAAGCGGACA 60.079 57.895 0.00 0.00 38.28 4.02
2546 7186 1.814169 GGATGGGTCGAAAGCGGAC 60.814 63.158 0.00 0.00 38.28 4.79
2547 7187 2.582436 GGATGGGTCGAAAGCGGA 59.418 61.111 0.00 0.00 38.28 5.54
2548 7188 2.890474 CGGATGGGTCGAAAGCGG 60.890 66.667 0.00 0.00 38.28 5.52
2549 7189 3.564027 GCGGATGGGTCGAAAGCG 61.564 66.667 0.00 0.00 39.35 4.68
2550 7190 3.564027 CGCGGATGGGTCGAAAGC 61.564 66.667 0.00 0.00 0.00 3.51
2551 7191 2.890474 CCGCGGATGGGTCGAAAG 60.890 66.667 24.07 0.00 0.00 2.62
2560 7200 3.061848 AAACTTGGGCCGCGGATG 61.062 61.111 33.48 13.17 0.00 3.51
2561 7201 3.061848 CAAACTTGGGCCGCGGAT 61.062 61.111 33.48 2.53 0.00 4.18
2569 7209 2.969677 AAAAGCGGCGCAAACTTGGG 62.970 55.000 35.02 2.32 43.22 4.12
2570 7210 0.318275 TAAAAGCGGCGCAAACTTGG 60.318 50.000 35.02 0.00 0.00 3.61
2571 7211 1.052287 CTAAAAGCGGCGCAAACTTG 58.948 50.000 35.02 14.96 0.00 3.16
2572 7212 0.039527 CCTAAAAGCGGCGCAAACTT 60.040 50.000 35.02 21.44 0.00 2.66
2573 7213 1.579429 CCTAAAAGCGGCGCAAACT 59.421 52.632 35.02 17.18 0.00 2.66
2574 7214 1.443702 CCCTAAAAGCGGCGCAAAC 60.444 57.895 35.02 4.02 0.00 2.93
2575 7215 1.899534 ACCCTAAAAGCGGCGCAAA 60.900 52.632 35.02 14.63 0.00 3.68
2576 7216 2.281900 ACCCTAAAAGCGGCGCAA 60.282 55.556 35.02 15.01 0.00 4.85
2577 7217 3.053291 CACCCTAAAAGCGGCGCA 61.053 61.111 35.02 12.54 0.00 6.09
2578 7218 2.744709 TCACCCTAAAAGCGGCGC 60.745 61.111 26.86 26.86 0.00 6.53


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

AutoCloner maintained by Alex Coulton.