Multiple sequence alignment - TraesCS1D01G304100

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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 TraesCS1D01G304100 chr1D 100.000 2978 0 0 1 2978 401775998 401773021 0.000000e+00 5500.0
1 TraesCS1D01G304100 chr1D 94.055 1413 70 5 830 2229 402006670 402005259 0.000000e+00 2132.0
2 TraesCS1D01G304100 chr1D 94.055 1413 70 5 830 2229 402108232 402106821 0.000000e+00 2132.0
3 TraesCS1D01G304100 chr1D 93.984 1413 71 5 830 2229 402051714 402050303 0.000000e+00 2126.0
4 TraesCS1D01G304100 chr1D 93.972 1410 71 5 830 2226 401921452 401920044 0.000000e+00 2121.0
5 TraesCS1D01G304100 chr1D 86.198 384 41 6 1765 2145 401699773 401699399 3.570000e-109 405.0
6 TraesCS1D01G304100 chr1D 88.176 296 15 9 883 1158 401700060 401699765 4.760000e-88 335.0
7 TraesCS1D01G304100 chr1D 88.571 210 17 2 430 636 402052192 402051987 6.370000e-62 248.0
8 TraesCS1D01G304100 chr1D 91.429 105 9 0 1699 1803 402123835 402123731 8.600000e-31 145.0
9 TraesCS1D01G304100 chr1D 100.000 35 0 0 2944 2978 28624692 28624726 6.890000e-07 65.8
10 TraesCS1D01G304100 chr1A 93.548 2294 94 20 616 2888 497580812 497578552 0.000000e+00 3367.0
11 TraesCS1D01G304100 chr1A 90.942 1634 97 20 642 2233 497585852 497584228 0.000000e+00 2150.0
12 TraesCS1D01G304100 chr1A 88.889 342 29 4 244 576 497581152 497580811 2.140000e-111 412.0
13 TraesCS1D01G304100 chr1A 92.553 188 14 0 1765 1952 497537384 497537197 1.360000e-68 270.0
14 TraesCS1D01G304100 chr1A 83.972 287 39 6 2230 2513 570047712 570047430 4.890000e-68 268.0
15 TraesCS1D01G304100 chr1A 85.235 149 13 4 701 842 497537809 497537663 8.600000e-31 145.0
16 TraesCS1D01G304100 chr1A 92.000 100 8 0 1699 1798 497616297 497616198 1.110000e-29 141.0
17 TraesCS1D01G304100 chr1A 87.850 107 10 1 536 639 497587956 497587850 4.030000e-24 122.0
18 TraesCS1D01G304100 chr1A 100.000 35 0 0 2906 2940 497578551 497578517 6.890000e-07 65.8
19 TraesCS1D01G304100 chr1B 91.596 1535 93 20 643 2147 539589925 539588397 0.000000e+00 2087.0
20 TraesCS1D01G304100 chr1B 80.353 397 49 16 2226 2611 343988574 343988952 1.050000e-69 274.0
21 TraesCS1D01G304100 chr1B 88.837 215 19 2 430 639 539590191 539589977 2.940000e-65 259.0
22 TraesCS1D01G304100 chr1B 87.195 164 17 4 244 405 539591648 539591487 1.820000e-42 183.0
23 TraesCS1D01G304100 chr7D 87.136 1166 124 20 983 2141 506882674 506883820 0.000000e+00 1299.0
24 TraesCS1D01G304100 chr7B 89.839 994 97 3 983 1976 535614364 535615353 0.000000e+00 1273.0
25 TraesCS1D01G304100 chr7A 83.376 391 56 7 2228 2615 694514797 694514413 1.310000e-93 353.0
26 TraesCS1D01G304100 chr5A 86.269 335 29 4 2279 2612 495877436 495877118 6.110000e-92 348.0
27 TraesCS1D01G304100 chr5A 84.570 337 41 9 2279 2611 85355021 85355350 1.030000e-84 324.0
28 TraesCS1D01G304100 chr3D 83.243 370 42 15 2259 2618 11779903 11780262 3.700000e-84 322.0
29 TraesCS1D01G304100 chr5D 83.881 335 36 8 2279 2612 393812778 393812461 1.340000e-78 303.0
30 TraesCS1D01G304100 chr2D 81.156 398 53 14 2230 2616 5420911 5421297 1.740000e-77 300.0
31 TraesCS1D01G304100 chr2D 83.333 144 22 2 2475 2618 525515443 525515302 6.700000e-27 132.0
32 TraesCS1D01G304100 chr2D 100.000 38 0 0 2941 2978 304665198 304665235 1.480000e-08 71.3
33 TraesCS1D01G304100 chr4A 87.356 261 28 4 2279 2537 729428987 729429244 8.070000e-76 294.0
34 TraesCS1D01G304100 chr4A 100.000 36 0 0 2943 2978 606802059 606802024 1.920000e-07 67.6
35 TraesCS1D01G304100 chrUn 84.722 288 34 8 2230 2513 386869011 386869292 2.260000e-71 279.0
36 TraesCS1D01G304100 chrUn 84.028 288 36 8 2230 2513 1718247 1717966 4.890000e-68 268.0
37 TraesCS1D01G304100 chrUn 84.028 288 36 8 2230 2513 449187267 449187548 4.890000e-68 268.0
38 TraesCS1D01G304100 chrUn 82.524 309 44 8 2306 2612 227613148 227612848 2.280000e-66 263.0
39 TraesCS1D01G304100 chrUn 82.524 309 44 8 2306 2612 253546140 253546440 2.280000e-66 263.0
40 TraesCS1D01G304100 chrUn 100.000 35 0 0 2944 2978 9910490 9910524 6.890000e-07 65.8
41 TraesCS1D01G304100 chr3A 80.469 384 48 16 2252 2618 25304375 25304002 4.890000e-68 268.0
42 TraesCS1D01G304100 chr6D 81.682 333 46 10 2299 2625 448916404 448916081 2.280000e-66 263.0
43 TraesCS1D01G304100 chr6D 100.000 34 0 0 2945 2978 103462904 103462871 2.480000e-06 63.9
44 TraesCS1D01G304100 chr2B 81.410 312 46 10 2220 2526 36867876 36868180 8.250000e-61 244.0
45 TraesCS1D01G304100 chr3B 81.897 116 16 4 2676 2787 795277671 795277557 3.160000e-15 93.5


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 TraesCS1D01G304100 chr1D 401773021 401775998 2977 True 5500.00 5500 100.000000 1 2978 1 chr1D.!!$R1 2977
1 TraesCS1D01G304100 chr1D 402005259 402006670 1411 True 2132.00 2132 94.055000 830 2229 1 chr1D.!!$R3 1399
2 TraesCS1D01G304100 chr1D 402106821 402108232 1411 True 2132.00 2132 94.055000 830 2229 1 chr1D.!!$R4 1399
3 TraesCS1D01G304100 chr1D 401920044 401921452 1408 True 2121.00 2121 93.972000 830 2226 1 chr1D.!!$R2 1396
4 TraesCS1D01G304100 chr1D 402050303 402052192 1889 True 1187.00 2126 91.277500 430 2229 2 chr1D.!!$R7 1799
5 TraesCS1D01G304100 chr1D 401699399 401700060 661 True 370.00 405 87.187000 883 2145 2 chr1D.!!$R6 1262
6 TraesCS1D01G304100 chr1A 497578517 497587956 9439 True 1223.36 3367 92.245800 244 2940 5 chr1A.!!$R4 2696
7 TraesCS1D01G304100 chr1A 497537197 497537809 612 True 207.50 270 88.894000 701 1952 2 chr1A.!!$R3 1251
8 TraesCS1D01G304100 chr1B 539588397 539591648 3251 True 843.00 2087 89.209333 244 2147 3 chr1B.!!$R1 1903
9 TraesCS1D01G304100 chr7D 506882674 506883820 1146 False 1299.00 1299 87.136000 983 2141 1 chr7D.!!$F1 1158
10 TraesCS1D01G304100 chr7B 535614364 535615353 989 False 1273.00 1273 89.839000 983 1976 1 chr7B.!!$F1 993

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
450 1723 0.111832 TAGGTCCTCACACCGTGTCT 59.888 55.0 0.0 0.0 41.90 3.41 F
475 1748 0.443869 CGACCAACGAAGCAATCCAG 59.556 55.0 0.0 0.0 45.77 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 5027 0.473694 TCCTCCTCAGGAAGTTGGCA 60.474 55.0 0.00 0.0 46.84 4.92 R
2237 10662 0.827507 GGCACCTGGGAGCTGAAAAA 60.828 55.0 12.19 0.0 32.43 1.94 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
33 34 4.394712 CCACGGCACCTCTCCCAC 62.395 72.222 0.00 0.00 0.00 4.61
34 35 4.394712 CACGGCACCTCTCCCACC 62.395 72.222 0.00 0.00 0.00 4.61
98 99 4.323477 CCGCTCCCCGTTGGACAA 62.323 66.667 0.00 0.00 38.61 3.18
99 100 2.742372 CGCTCCCCGTTGGACAAG 60.742 66.667 0.00 0.00 38.61 3.16
100 101 3.056328 GCTCCCCGTTGGACAAGC 61.056 66.667 0.00 0.00 38.61 4.01
101 102 2.429930 CTCCCCGTTGGACAAGCA 59.570 61.111 0.00 0.00 38.61 3.91
102 103 1.672356 CTCCCCGTTGGACAAGCAG 60.672 63.158 0.00 0.00 38.61 4.24
103 104 3.365265 CCCCGTTGGACAAGCAGC 61.365 66.667 0.00 0.00 35.39 5.25
104 105 3.365265 CCCGTTGGACAAGCAGCC 61.365 66.667 0.00 0.00 0.00 4.85
105 106 2.594303 CCGTTGGACAAGCAGCCA 60.594 61.111 0.00 0.00 0.00 4.75
106 107 2.620112 CCGTTGGACAAGCAGCCAG 61.620 63.158 0.00 0.00 35.23 4.85
107 108 2.647297 GTTGGACAAGCAGCCAGC 59.353 61.111 0.00 0.00 46.19 4.85
135 136 4.933064 CTCCGATCTCGCCGCCAC 62.933 72.222 0.00 0.00 38.18 5.01
187 188 3.127533 GCCAACGGCTCGCTCATT 61.128 61.111 0.00 0.00 46.69 2.57
188 189 2.690778 GCCAACGGCTCGCTCATTT 61.691 57.895 0.00 0.00 46.69 2.32
189 190 1.425428 CCAACGGCTCGCTCATTTC 59.575 57.895 0.00 0.00 0.00 2.17
190 191 1.059369 CAACGGCTCGCTCATTTCG 59.941 57.895 0.00 0.00 0.00 3.46
191 192 1.080093 AACGGCTCGCTCATTTCGA 60.080 52.632 0.00 0.00 34.52 3.71
192 193 0.669318 AACGGCTCGCTCATTTCGAA 60.669 50.000 0.00 0.00 35.38 3.71
193 194 0.669318 ACGGCTCGCTCATTTCGAAA 60.669 50.000 13.91 13.91 35.38 3.46
194 195 0.442310 CGGCTCGCTCATTTCGAAAA 59.558 50.000 15.66 0.00 35.38 2.29
195 196 1.786928 CGGCTCGCTCATTTCGAAAAC 60.787 52.381 15.66 4.25 35.38 2.43
196 197 1.465856 GGCTCGCTCATTTCGAAAACC 60.466 52.381 15.66 2.84 35.38 3.27
197 198 1.196808 GCTCGCTCATTTCGAAAACCA 59.803 47.619 15.66 0.71 35.38 3.67
198 199 2.839474 CTCGCTCATTTCGAAAACCAC 58.161 47.619 15.66 4.61 35.38 4.16
199 200 1.533731 TCGCTCATTTCGAAAACCACC 59.466 47.619 15.66 2.15 32.53 4.61
200 201 1.401018 CGCTCATTTCGAAAACCACCC 60.401 52.381 15.66 1.12 0.00 4.61
201 202 1.401018 GCTCATTTCGAAAACCACCCG 60.401 52.381 15.66 1.09 0.00 5.28
202 203 2.147958 CTCATTTCGAAAACCACCCGA 58.852 47.619 15.66 2.71 0.00 5.14
203 204 2.747446 CTCATTTCGAAAACCACCCGAT 59.253 45.455 15.66 0.00 32.07 4.18
204 205 3.150767 TCATTTCGAAAACCACCCGATT 58.849 40.909 15.66 0.00 32.07 3.34
205 206 3.570550 TCATTTCGAAAACCACCCGATTT 59.429 39.130 15.66 0.00 32.07 2.17
206 207 3.629438 TTTCGAAAACCACCCGATTTC 57.371 42.857 8.44 0.00 32.07 2.17
207 208 1.525941 TCGAAAACCACCCGATTTCC 58.474 50.000 0.00 0.00 31.03 3.13
208 209 1.072648 TCGAAAACCACCCGATTTCCT 59.927 47.619 0.00 0.00 31.03 3.36
209 210 1.199097 CGAAAACCACCCGATTTCCTG 59.801 52.381 0.00 0.00 31.03 3.86
210 211 1.544246 GAAAACCACCCGATTTCCTGG 59.456 52.381 0.00 0.00 0.00 4.45
211 212 0.481128 AAACCACCCGATTTCCTGGT 59.519 50.000 0.00 0.00 38.74 4.00
212 213 1.364269 AACCACCCGATTTCCTGGTA 58.636 50.000 0.00 0.00 35.90 3.25
213 214 1.364269 ACCACCCGATTTCCTGGTAA 58.636 50.000 0.00 0.00 35.14 2.85
214 215 1.920351 ACCACCCGATTTCCTGGTAAT 59.080 47.619 0.00 0.00 35.14 1.89
215 216 2.310647 ACCACCCGATTTCCTGGTAATT 59.689 45.455 0.00 0.00 35.14 1.40
216 217 2.949644 CCACCCGATTTCCTGGTAATTC 59.050 50.000 0.00 0.00 0.00 2.17
217 218 2.612212 CACCCGATTTCCTGGTAATTCG 59.388 50.000 0.00 7.72 33.97 3.34
218 219 2.502538 ACCCGATTTCCTGGTAATTCGA 59.497 45.455 17.01 0.00 35.38 3.71
219 220 3.054948 ACCCGATTTCCTGGTAATTCGAA 60.055 43.478 0.00 0.00 35.38 3.71
220 221 3.942748 CCCGATTTCCTGGTAATTCGAAA 59.057 43.478 0.00 2.29 35.38 3.46
221 222 4.396790 CCCGATTTCCTGGTAATTCGAAAA 59.603 41.667 0.00 0.00 35.38 2.29
222 223 5.448632 CCCGATTTCCTGGTAATTCGAAAAG 60.449 44.000 0.00 0.00 35.38 2.27
223 224 5.028375 CGATTTCCTGGTAATTCGAAAAGC 58.972 41.667 0.00 3.95 35.38 3.51
224 225 5.391523 CGATTTCCTGGTAATTCGAAAAGCA 60.392 40.000 0.00 8.69 35.38 3.91
225 226 4.759516 TTCCTGGTAATTCGAAAAGCAC 57.240 40.909 0.00 0.00 0.00 4.40
226 227 3.745799 TCCTGGTAATTCGAAAAGCACA 58.254 40.909 0.00 0.00 0.00 4.57
227 228 4.138290 TCCTGGTAATTCGAAAAGCACAA 58.862 39.130 0.00 0.00 0.00 3.33
228 229 4.580995 TCCTGGTAATTCGAAAAGCACAAA 59.419 37.500 0.00 0.00 0.00 2.83
229 230 5.242838 TCCTGGTAATTCGAAAAGCACAAAT 59.757 36.000 0.00 0.00 0.00 2.32
230 231 6.431543 TCCTGGTAATTCGAAAAGCACAAATA 59.568 34.615 0.00 0.00 0.00 1.40
231 232 6.526674 CCTGGTAATTCGAAAAGCACAAATAC 59.473 38.462 0.00 0.00 0.00 1.89
232 233 7.209471 TGGTAATTCGAAAAGCACAAATACT 57.791 32.000 0.00 0.00 0.00 2.12
233 234 7.302524 TGGTAATTCGAAAAGCACAAATACTC 58.697 34.615 0.00 0.00 0.00 2.59
234 235 7.041030 TGGTAATTCGAAAAGCACAAATACTCA 60.041 33.333 0.00 0.00 0.00 3.41
235 236 7.806014 GGTAATTCGAAAAGCACAAATACTCAA 59.194 33.333 0.00 0.00 0.00 3.02
236 237 9.176181 GTAATTCGAAAAGCACAAATACTCAAA 57.824 29.630 0.00 0.00 0.00 2.69
237 238 7.858052 ATTCGAAAAGCACAAATACTCAAAG 57.142 32.000 0.00 0.00 0.00 2.77
238 239 6.612247 TCGAAAAGCACAAATACTCAAAGA 57.388 33.333 0.00 0.00 0.00 2.52
239 240 7.202016 TCGAAAAGCACAAATACTCAAAGAT 57.798 32.000 0.00 0.00 0.00 2.40
240 241 7.648142 TCGAAAAGCACAAATACTCAAAGATT 58.352 30.769 0.00 0.00 0.00 2.40
241 242 8.134895 TCGAAAAGCACAAATACTCAAAGATTT 58.865 29.630 0.00 0.00 0.00 2.17
242 243 8.420189 CGAAAAGCACAAATACTCAAAGATTTC 58.580 33.333 0.00 0.00 0.00 2.17
243 244 8.593492 AAAAGCACAAATACTCAAAGATTTCC 57.407 30.769 0.00 0.00 0.00 3.13
244 245 6.272822 AGCACAAATACTCAAAGATTTCCC 57.727 37.500 0.00 0.00 0.00 3.97
245 246 5.185828 AGCACAAATACTCAAAGATTTCCCC 59.814 40.000 0.00 0.00 0.00 4.81
246 247 5.047377 GCACAAATACTCAAAGATTTCCCCA 60.047 40.000 0.00 0.00 0.00 4.96
247 248 6.351286 GCACAAATACTCAAAGATTTCCCCAT 60.351 38.462 0.00 0.00 0.00 4.00
248 249 7.614494 CACAAATACTCAAAGATTTCCCCATT 58.386 34.615 0.00 0.00 0.00 3.16
249 250 7.761249 CACAAATACTCAAAGATTTCCCCATTC 59.239 37.037 0.00 0.00 0.00 2.67
256 257 6.474630 TCAAAGATTTCCCCATTCCATTTTG 58.525 36.000 0.00 0.00 0.00 2.44
258 259 3.845398 AGATTTCCCCATTCCATTTTGCA 59.155 39.130 0.00 0.00 0.00 4.08
265 266 4.515361 CCCATTCCATTTTGCATTGCTTA 58.485 39.130 10.49 0.00 0.00 3.09
270 271 7.539366 CCATTCCATTTTGCATTGCTTAAAAAG 59.461 33.333 10.49 6.36 0.00 2.27
274 275 7.444792 TCCATTTTGCATTGCTTAAAAAGATGT 59.555 29.630 10.49 0.00 0.00 3.06
293 294 5.487488 AGATGTATTCTTCCAAGGTACCACA 59.513 40.000 15.94 5.74 0.00 4.17
295 296 4.595781 TGTATTCTTCCAAGGTACCACACT 59.404 41.667 15.94 0.00 0.00 3.55
298 299 2.897969 TCTTCCAAGGTACCACACTCTC 59.102 50.000 15.94 0.00 0.00 3.20
301 302 1.202582 CCAAGGTACCACACTCTCTCG 59.797 57.143 15.94 0.00 0.00 4.04
405 407 4.504858 CGGGTGAGAGTAGTTAATTGCTT 58.495 43.478 0.00 0.00 0.00 3.91
406 408 5.657474 CGGGTGAGAGTAGTTAATTGCTTA 58.343 41.667 0.00 0.00 0.00 3.09
407 409 6.103997 CGGGTGAGAGTAGTTAATTGCTTAA 58.896 40.000 0.00 0.00 0.00 1.85
408 410 6.761714 CGGGTGAGAGTAGTTAATTGCTTAAT 59.238 38.462 0.00 0.00 0.00 1.40
409 411 7.280205 CGGGTGAGAGTAGTTAATTGCTTAATT 59.720 37.037 0.00 0.00 0.00 1.40
416 418 9.404848 GAGTAGTTAATTGCTTAATTTAGGGGT 57.595 33.333 0.00 0.00 0.00 4.95
423 425 5.761165 TGCTTAATTTAGGGGTAAATCGC 57.239 39.130 0.00 0.00 0.00 4.58
424 426 5.442391 TGCTTAATTTAGGGGTAAATCGCT 58.558 37.500 0.00 0.00 0.00 4.93
425 427 5.298276 TGCTTAATTTAGGGGTAAATCGCTG 59.702 40.000 0.00 0.00 0.00 5.18
426 428 5.758924 CTTAATTTAGGGGTAAATCGCTGC 58.241 41.667 0.00 0.00 0.00 5.25
427 429 2.047002 TTTAGGGGTAAATCGCTGCC 57.953 50.000 0.00 0.00 0.00 4.85
428 430 0.913205 TTAGGGGTAAATCGCTGCCA 59.087 50.000 0.00 0.00 0.00 4.92
450 1723 0.111832 TAGGTCCTCACACCGTGTCT 59.888 55.000 0.00 0.00 41.90 3.41
475 1748 0.443869 CGACCAACGAAGCAATCCAG 59.556 55.000 0.00 0.00 45.77 3.86
499 1772 0.790814 GTTGTAACCTGCGAGTCAGC 59.209 55.000 0.00 0.00 41.50 4.26
505 1778 2.814341 CTGCGAGTCAGCTGGCTG 60.814 66.667 28.75 18.57 45.10 4.85
531 1806 2.159179 AGTCAAAGGCCAAACAGGTT 57.841 45.000 5.01 0.00 40.61 3.50
534 1809 2.093711 GTCAAAGGCCAAACAGGTTGTT 60.094 45.455 5.01 0.00 43.41 2.83
550 1825 6.363896 ACAGGTTGTTCAAAAGTTTGTTTACG 59.636 34.615 3.82 0.00 39.18 3.18
585 1863 2.851805 TCCATTCGACTCACTCATCG 57.148 50.000 0.00 0.00 39.72 3.84
624 1902 3.087031 CAGGAGCAACCAACAGATCATT 58.913 45.455 0.00 0.00 42.04 2.57
670 3944 8.830741 AGAGAGGGAAAAAGAGAGATAAATTCA 58.169 33.333 0.00 0.00 0.00 2.57
693 3967 9.613428 TTCACTCGATTATTGAAGGAAACATAT 57.387 29.630 0.00 0.00 0.00 1.78
730 4004 3.196685 AGTTCTAGCAGTCTCCATGTTCC 59.803 47.826 0.00 0.00 0.00 3.62
734 4008 4.962362 TCTAGCAGTCTCCATGTTCCATAA 59.038 41.667 0.00 0.00 0.00 1.90
735 4009 3.878778 AGCAGTCTCCATGTTCCATAAC 58.121 45.455 0.00 0.00 36.07 1.89
824 4133 6.403636 CCATCTAACTAACAATGTCAAGGTGC 60.404 42.308 0.00 0.00 0.00 5.01
873 4203 4.099266 GGAACCCTTGCATGCATGTATAAA 59.901 41.667 26.79 15.12 0.00 1.40
885 4216 4.103943 TGCATGTATAAATAGCCCTCCACA 59.896 41.667 0.00 0.00 0.00 4.17
886 4217 4.697352 GCATGTATAAATAGCCCTCCACAG 59.303 45.833 0.00 0.00 0.00 3.66
887 4218 5.513094 GCATGTATAAATAGCCCTCCACAGA 60.513 44.000 0.00 0.00 0.00 3.41
889 4220 3.753294 ATAAATAGCCCTCCACAGACG 57.247 47.619 0.00 0.00 0.00 4.18
891 4222 1.568504 AATAGCCCTCCACAGACGAA 58.431 50.000 0.00 0.00 0.00 3.85
892 4223 0.824759 ATAGCCCTCCACAGACGAAC 59.175 55.000 0.00 0.00 0.00 3.95
991 4328 7.784633 AATTCATTAAGAGCTAGCTTGAGAC 57.215 36.000 20.42 5.38 0.00 3.36
1410 4775 2.001361 GCGACGCAGCCTACTTCCTA 62.001 60.000 16.42 0.00 0.00 2.94
1520 4885 1.003233 ACCATTCTTCAACCTCGACCC 59.997 52.381 0.00 0.00 0.00 4.46
1629 4994 1.703438 CGTCCTTCGTCTCCGATCGT 61.703 60.000 15.09 0.00 43.80 3.73
1631 4996 1.004079 GTCCTTCGTCTCCGATCGTAC 60.004 57.143 15.09 8.27 43.80 3.67
1639 5004 4.950974 CCGATCGTACCGCCGTCG 62.951 72.222 15.09 0.00 33.96 5.12
1662 5027 2.094659 CGACATCGACGCTGGCTTT 61.095 57.895 2.68 0.00 43.02 3.51
1984 10390 3.679389 GTTGTCAACCACTGATCCATCT 58.321 45.455 4.21 0.00 36.14 2.90
1994 10400 4.637534 CCACTGATCCATCTTTGAATCGTT 59.362 41.667 0.00 0.00 0.00 3.85
2045 10452 3.632189 CACTTTAGTTTTGCACTGCCTC 58.368 45.455 0.00 0.00 35.97 4.70
2105 10516 7.268586 TGCATGTACTGTAATTGGTTGTTTTT 58.731 30.769 0.00 0.00 0.00 1.94
2283 10708 9.675464 CCTACACCCTTTATGAACAGTAAATTA 57.325 33.333 0.00 0.00 0.00 1.40
2325 10755 9.491675 TTGCAACATCAAATATGATCAAACTTT 57.508 25.926 0.00 0.00 44.53 2.66
2326 10756 8.927721 TGCAACATCAAATATGATCAAACTTTG 58.072 29.630 16.14 16.14 44.53 2.77
2327 10757 8.928733 GCAACATCAAATATGATCAAACTTTGT 58.071 29.630 19.20 8.61 44.53 2.83
2340 10770 5.101628 TCAAACTTTGTAAGTGCTTGCAAG 58.898 37.500 22.44 22.44 43.83 4.01
2349 10779 2.476821 AGTGCTTGCAAGTTTTCATGC 58.523 42.857 26.55 11.82 43.69 4.06
2357 10787 3.118482 TGCAAGTTTTCATGCCCAAAAGA 60.118 39.130 0.00 0.00 42.89 2.52
2416 10846 6.028040 CAGTGCTTGAAATTTTGAACACTG 57.972 37.500 20.86 20.86 45.21 3.66
2440 10870 8.450578 TGTTAACACTGAAATCTGAAACTCAT 57.549 30.769 3.59 0.00 0.00 2.90
2466 10896 8.758829 TGTGTACACCTTTCTCTACATGATATT 58.241 33.333 22.91 0.00 0.00 1.28
2514 10944 7.970384 TCTACAAAGTTTAGCCATATTTGACG 58.030 34.615 3.23 0.00 35.40 4.35
2524 10954 4.933400 AGCCATATTTGACGTCGTAAAGTT 59.067 37.500 11.62 0.00 0.00 2.66
2526 10956 5.731263 GCCATATTTGACGTCGTAAAGTTTC 59.269 40.000 11.62 0.00 0.00 2.78
2527 10957 6.619018 GCCATATTTGACGTCGTAAAGTTTCA 60.619 38.462 11.62 0.00 0.00 2.69
2528 10958 7.461107 CCATATTTGACGTCGTAAAGTTTCAT 58.539 34.615 11.62 0.00 0.00 2.57
2529 10959 8.597227 CCATATTTGACGTCGTAAAGTTTCATA 58.403 33.333 11.62 0.00 0.00 2.15
2533 10963 9.887406 ATTTGACGTCGTAAAGTTTCATATTTT 57.113 25.926 11.62 0.00 0.00 1.82
2534 10964 9.719279 TTTGACGTCGTAAAGTTTCATATTTTT 57.281 25.926 11.62 0.00 0.00 1.94
2746 11177 4.645667 TCGTGCATGATACATATTTCGC 57.354 40.909 3.97 0.00 0.00 4.70
2804 11236 9.414295 TGAGAAGCTGATTATTTCAATTTTGTG 57.586 29.630 0.00 0.00 32.78 3.33
2888 11323 0.687354 GACCGGCATGGACATATCCT 59.313 55.000 0.00 0.00 46.43 3.24
2889 11324 0.397941 ACCGGCATGGACATATCCTG 59.602 55.000 0.00 0.00 46.43 3.86
2890 11325 0.957395 CCGGCATGGACATATCCTGC 60.957 60.000 6.05 6.05 46.43 4.85
2891 11326 0.250424 CGGCATGGACATATCCTGCA 60.250 55.000 13.97 0.00 46.43 4.41
2892 11327 1.531423 GGCATGGACATATCCTGCAG 58.469 55.000 6.78 6.78 46.43 4.41
2893 11328 1.202855 GGCATGGACATATCCTGCAGT 60.203 52.381 13.81 0.00 46.43 4.40
2894 11329 2.149578 GCATGGACATATCCTGCAGTC 58.850 52.381 13.81 2.76 46.43 3.51
2895 11330 2.486013 GCATGGACATATCCTGCAGTCA 60.486 50.000 13.81 0.00 46.43 3.41
2896 11331 3.400255 CATGGACATATCCTGCAGTCAG 58.600 50.000 13.81 0.00 46.43 3.51
2897 11332 2.470990 TGGACATATCCTGCAGTCAGT 58.529 47.619 13.81 3.61 46.43 3.41
2898 11333 3.642141 TGGACATATCCTGCAGTCAGTA 58.358 45.455 13.81 0.11 46.43 2.74
2899 11334 4.226384 TGGACATATCCTGCAGTCAGTAT 58.774 43.478 13.81 2.56 46.43 2.12
2900 11335 5.393866 TGGACATATCCTGCAGTCAGTATA 58.606 41.667 13.81 3.05 46.43 1.47
2901 11336 5.838521 TGGACATATCCTGCAGTCAGTATAA 59.161 40.000 13.81 0.00 46.43 0.98
2902 11337 6.015095 TGGACATATCCTGCAGTCAGTATAAG 60.015 42.308 13.81 2.67 46.43 1.73
2903 11338 6.352016 ACATATCCTGCAGTCAGTATAAGG 57.648 41.667 13.81 0.00 38.66 2.69
2904 11339 5.841237 ACATATCCTGCAGTCAGTATAAGGT 59.159 40.000 13.81 3.45 38.66 3.50
2940 11375 1.880027 GTTTTCAGCCGGTCACAGATT 59.120 47.619 1.90 0.00 0.00 2.40
2941 11376 2.270352 TTTCAGCCGGTCACAGATTT 57.730 45.000 1.90 0.00 0.00 2.17
2942 11377 2.270352 TTCAGCCGGTCACAGATTTT 57.730 45.000 1.90 0.00 0.00 1.82
2943 11378 2.270352 TCAGCCGGTCACAGATTTTT 57.730 45.000 1.90 0.00 0.00 1.94
2975 11410 2.790766 AGGATGACCCTGGCCTCT 59.209 61.111 3.32 0.00 45.61 3.69
2976 11411 1.692042 AGGATGACCCTGGCCTCTG 60.692 63.158 3.32 0.00 45.61 3.35
2977 11412 2.191641 GATGACCCTGGCCTCTGC 59.808 66.667 3.32 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.394712 GTGGGAGAGGTGCCGTGG 62.395 72.222 0.00 0.00 36.82 4.94
17 18 4.394712 GGTGGGAGAGGTGCCGTG 62.395 72.222 0.00 0.00 36.82 4.94
85 86 2.429930 CTGCTTGTCCAACGGGGA 59.570 61.111 0.00 0.00 45.89 4.81
86 87 3.365265 GCTGCTTGTCCAACGGGG 61.365 66.667 0.00 0.00 38.37 5.73
87 88 3.365265 GGCTGCTTGTCCAACGGG 61.365 66.667 0.00 0.00 0.00 5.28
88 89 2.594303 TGGCTGCTTGTCCAACGG 60.594 61.111 0.00 0.00 0.00 4.44
89 90 2.949106 CTGGCTGCTTGTCCAACG 59.051 61.111 0.00 0.00 30.98 4.10
90 91 2.647297 GCTGGCTGCTTGTCCAAC 59.353 61.111 9.31 0.00 38.95 3.77
91 92 2.598394 GGCTGGCTGCTTGTCCAA 60.598 61.111 16.14 0.00 42.39 3.53
92 93 3.214190 ATGGCTGGCTGCTTGTCCA 62.214 57.895 16.14 5.58 42.39 4.02
93 94 2.362120 ATGGCTGGCTGCTTGTCC 60.362 61.111 16.14 0.00 42.39 4.02
94 95 2.413142 GGATGGCTGGCTGCTTGTC 61.413 63.158 16.14 10.97 42.39 3.18
95 96 2.362120 GGATGGCTGGCTGCTTGT 60.362 61.111 16.14 2.63 42.39 3.16
96 97 3.515286 CGGATGGCTGGCTGCTTG 61.515 66.667 16.14 0.00 42.39 4.01
118 119 4.933064 GTGGCGGCGAGATCGGAG 62.933 72.222 12.98 0.00 40.23 4.63
171 172 1.425428 GAAATGAGCGAGCCGTTGG 59.575 57.895 0.00 0.00 0.00 3.77
172 173 1.059369 CGAAATGAGCGAGCCGTTG 59.941 57.895 0.00 0.00 0.00 4.10
173 174 0.669318 TTCGAAATGAGCGAGCCGTT 60.669 50.000 0.00 0.00 39.14 4.44
174 175 0.669318 TTTCGAAATGAGCGAGCCGT 60.669 50.000 6.47 0.00 39.14 5.68
175 176 0.442310 TTTTCGAAATGAGCGAGCCG 59.558 50.000 12.12 0.00 39.14 5.52
176 177 1.465856 GGTTTTCGAAATGAGCGAGCC 60.466 52.381 12.12 0.00 39.14 4.70
177 178 1.196808 TGGTTTTCGAAATGAGCGAGC 59.803 47.619 12.12 5.86 39.14 5.03
178 179 2.412847 GGTGGTTTTCGAAATGAGCGAG 60.413 50.000 12.12 0.00 39.14 5.03
179 180 1.533731 GGTGGTTTTCGAAATGAGCGA 59.466 47.619 12.12 0.00 35.76 4.93
180 181 1.401018 GGGTGGTTTTCGAAATGAGCG 60.401 52.381 12.12 0.00 0.00 5.03
181 182 1.401018 CGGGTGGTTTTCGAAATGAGC 60.401 52.381 12.12 8.08 0.00 4.26
182 183 2.147958 TCGGGTGGTTTTCGAAATGAG 58.852 47.619 12.12 0.19 0.00 2.90
183 184 2.257691 TCGGGTGGTTTTCGAAATGA 57.742 45.000 12.12 0.00 0.00 2.57
184 185 3.569250 AATCGGGTGGTTTTCGAAATG 57.431 42.857 12.12 0.00 36.49 2.32
185 186 3.057104 GGAAATCGGGTGGTTTTCGAAAT 60.057 43.478 12.12 0.00 35.90 2.17
186 187 2.293955 GGAAATCGGGTGGTTTTCGAAA 59.706 45.455 6.47 6.47 35.90 3.46
187 188 1.881324 GGAAATCGGGTGGTTTTCGAA 59.119 47.619 0.00 0.00 35.90 3.71
188 189 1.072648 AGGAAATCGGGTGGTTTTCGA 59.927 47.619 0.00 0.00 35.90 3.71
189 190 1.199097 CAGGAAATCGGGTGGTTTTCG 59.801 52.381 0.00 0.00 35.90 3.46
190 191 1.544246 CCAGGAAATCGGGTGGTTTTC 59.456 52.381 0.00 0.00 34.83 2.29
191 192 1.133294 ACCAGGAAATCGGGTGGTTTT 60.133 47.619 0.00 0.00 40.54 2.43
192 193 0.481128 ACCAGGAAATCGGGTGGTTT 59.519 50.000 0.00 0.00 40.54 3.27
193 194 1.364269 TACCAGGAAATCGGGTGGTT 58.636 50.000 0.00 0.00 43.74 3.67
194 195 1.364269 TTACCAGGAAATCGGGTGGT 58.636 50.000 0.00 0.00 43.74 4.16
195 196 2.729028 ATTACCAGGAAATCGGGTGG 57.271 50.000 0.00 0.00 43.74 4.61
196 197 2.612212 CGAATTACCAGGAAATCGGGTG 59.388 50.000 0.00 0.00 43.74 4.61
197 198 2.502538 TCGAATTACCAGGAAATCGGGT 59.497 45.455 0.00 0.00 45.77 5.28
198 199 3.188159 TCGAATTACCAGGAAATCGGG 57.812 47.619 0.00 0.00 36.74 5.14
199 200 5.554822 TTTTCGAATTACCAGGAAATCGG 57.445 39.130 0.00 0.00 0.00 4.18
200 201 5.028375 GCTTTTCGAATTACCAGGAAATCG 58.972 41.667 0.00 0.00 0.00 3.34
201 202 5.800438 GTGCTTTTCGAATTACCAGGAAATC 59.200 40.000 0.00 0.00 0.00 2.17
202 203 5.242838 TGTGCTTTTCGAATTACCAGGAAAT 59.757 36.000 0.00 0.00 0.00 2.17
203 204 4.580995 TGTGCTTTTCGAATTACCAGGAAA 59.419 37.500 0.00 0.00 0.00 3.13
204 205 4.138290 TGTGCTTTTCGAATTACCAGGAA 58.862 39.130 0.00 0.00 0.00 3.36
205 206 3.745799 TGTGCTTTTCGAATTACCAGGA 58.254 40.909 0.00 0.00 0.00 3.86
206 207 4.497473 TTGTGCTTTTCGAATTACCAGG 57.503 40.909 0.00 0.00 0.00 4.45
207 208 7.305474 AGTATTTGTGCTTTTCGAATTACCAG 58.695 34.615 0.00 0.00 0.00 4.00
208 209 7.041030 TGAGTATTTGTGCTTTTCGAATTACCA 60.041 33.333 0.00 0.00 0.00 3.25
209 210 7.302524 TGAGTATTTGTGCTTTTCGAATTACC 58.697 34.615 0.00 0.00 0.00 2.85
210 211 8.722342 TTGAGTATTTGTGCTTTTCGAATTAC 57.278 30.769 0.00 0.00 0.00 1.89
211 212 9.393249 CTTTGAGTATTTGTGCTTTTCGAATTA 57.607 29.630 0.00 0.00 0.00 1.40
212 213 8.134895 TCTTTGAGTATTTGTGCTTTTCGAATT 58.865 29.630 0.00 0.00 0.00 2.17
213 214 7.648142 TCTTTGAGTATTTGTGCTTTTCGAAT 58.352 30.769 0.00 0.00 0.00 3.34
214 215 7.022055 TCTTTGAGTATTTGTGCTTTTCGAA 57.978 32.000 0.00 0.00 0.00 3.71
215 216 6.612247 TCTTTGAGTATTTGTGCTTTTCGA 57.388 33.333 0.00 0.00 0.00 3.71
216 217 7.858052 AATCTTTGAGTATTTGTGCTTTTCG 57.142 32.000 0.00 0.00 0.00 3.46
217 218 8.703336 GGAAATCTTTGAGTATTTGTGCTTTTC 58.297 33.333 0.00 0.00 0.00 2.29
218 219 7.657354 GGGAAATCTTTGAGTATTTGTGCTTTT 59.343 33.333 0.00 0.00 0.00 2.27
219 220 7.154656 GGGAAATCTTTGAGTATTTGTGCTTT 58.845 34.615 0.00 0.00 0.00 3.51
220 221 6.295292 GGGGAAATCTTTGAGTATTTGTGCTT 60.295 38.462 0.00 0.00 0.00 3.91
221 222 5.185828 GGGGAAATCTTTGAGTATTTGTGCT 59.814 40.000 0.00 0.00 0.00 4.40
222 223 5.047377 TGGGGAAATCTTTGAGTATTTGTGC 60.047 40.000 0.00 0.00 0.00 4.57
223 224 6.588719 TGGGGAAATCTTTGAGTATTTGTG 57.411 37.500 0.00 0.00 0.00 3.33
224 225 7.093333 GGAATGGGGAAATCTTTGAGTATTTGT 60.093 37.037 0.00 0.00 0.00 2.83
225 226 7.093377 TGGAATGGGGAAATCTTTGAGTATTTG 60.093 37.037 0.00 0.00 0.00 2.32
226 227 6.959366 TGGAATGGGGAAATCTTTGAGTATTT 59.041 34.615 0.00 0.00 0.00 1.40
227 228 6.502138 TGGAATGGGGAAATCTTTGAGTATT 58.498 36.000 0.00 0.00 0.00 1.89
228 229 6.091076 TGGAATGGGGAAATCTTTGAGTAT 57.909 37.500 0.00 0.00 0.00 2.12
229 230 5.528600 TGGAATGGGGAAATCTTTGAGTA 57.471 39.130 0.00 0.00 0.00 2.59
230 231 4.402616 TGGAATGGGGAAATCTTTGAGT 57.597 40.909 0.00 0.00 0.00 3.41
231 232 5.945144 AATGGAATGGGGAAATCTTTGAG 57.055 39.130 0.00 0.00 0.00 3.02
232 233 6.474630 CAAAATGGAATGGGGAAATCTTTGA 58.525 36.000 0.00 0.00 0.00 2.69
233 234 5.124297 GCAAAATGGAATGGGGAAATCTTTG 59.876 40.000 0.00 0.00 0.00 2.77
234 235 5.222089 TGCAAAATGGAATGGGGAAATCTTT 60.222 36.000 0.00 0.00 0.00 2.52
235 236 4.289148 TGCAAAATGGAATGGGGAAATCTT 59.711 37.500 0.00 0.00 0.00 2.40
236 237 3.845398 TGCAAAATGGAATGGGGAAATCT 59.155 39.130 0.00 0.00 0.00 2.40
237 238 4.219264 TGCAAAATGGAATGGGGAAATC 57.781 40.909 0.00 0.00 0.00 2.17
238 239 4.866327 ATGCAAAATGGAATGGGGAAAT 57.134 36.364 0.00 0.00 0.00 2.17
239 240 4.333690 CAATGCAAAATGGAATGGGGAAA 58.666 39.130 0.00 0.00 0.00 3.13
240 241 3.873020 GCAATGCAAAATGGAATGGGGAA 60.873 43.478 0.00 0.00 0.00 3.97
241 242 2.355920 GCAATGCAAAATGGAATGGGGA 60.356 45.455 0.00 0.00 0.00 4.81
242 243 2.018515 GCAATGCAAAATGGAATGGGG 58.981 47.619 0.00 0.00 0.00 4.96
243 244 2.993937 AGCAATGCAAAATGGAATGGG 58.006 42.857 8.35 0.00 0.00 4.00
244 245 6.497785 TTTAAGCAATGCAAAATGGAATGG 57.502 33.333 8.35 0.00 0.00 3.16
245 246 8.291032 TCTTTTTAAGCAATGCAAAATGGAATG 58.709 29.630 8.35 0.00 0.00 2.67
246 247 8.393671 TCTTTTTAAGCAATGCAAAATGGAAT 57.606 26.923 8.35 0.00 0.00 3.01
247 248 7.798596 TCTTTTTAAGCAATGCAAAATGGAA 57.201 28.000 8.35 0.00 0.00 3.53
248 249 7.444792 ACATCTTTTTAAGCAATGCAAAATGGA 59.555 29.630 8.35 8.29 0.00 3.41
249 250 7.586747 ACATCTTTTTAAGCAATGCAAAATGG 58.413 30.769 8.35 3.56 0.00 3.16
270 271 5.585047 GTGTGGTACCTTGGAAGAATACATC 59.415 44.000 14.36 0.00 0.00 3.06
274 275 5.091552 AGAGTGTGGTACCTTGGAAGAATA 58.908 41.667 14.36 0.00 0.00 1.75
298 299 7.911205 AGACTAAAACATACTCTTTCGATCGAG 59.089 37.037 18.54 9.21 0.00 4.04
301 302 9.355215 TGAAGACTAAAACATACTCTTTCGATC 57.645 33.333 0.00 0.00 0.00 3.69
325 326 9.349713 ACACAACCTCTAATTAAATCAAAGTGA 57.650 29.630 0.00 0.00 0.00 3.41
360 362 7.202526 CCGCACATCTCCAACAAATTATTTAT 58.797 34.615 0.00 0.00 0.00 1.40
372 374 1.191489 TCTCACCCGCACATCTCCAA 61.191 55.000 0.00 0.00 0.00 3.53
376 378 1.107114 CTACTCTCACCCGCACATCT 58.893 55.000 0.00 0.00 0.00 2.90
405 407 4.139038 GGCAGCGATTTACCCCTAAATTA 58.861 43.478 0.00 0.00 33.44 1.40
406 408 2.956333 GGCAGCGATTTACCCCTAAATT 59.044 45.455 0.00 0.00 33.44 1.82
407 409 2.092103 TGGCAGCGATTTACCCCTAAAT 60.092 45.455 0.00 0.00 35.59 1.40
408 410 1.282447 TGGCAGCGATTTACCCCTAAA 59.718 47.619 0.00 0.00 0.00 1.85
409 411 0.913205 TGGCAGCGATTTACCCCTAA 59.087 50.000 0.00 0.00 0.00 2.69
411 413 1.077716 GTGGCAGCGATTTACCCCT 60.078 57.895 0.00 0.00 0.00 4.79
412 414 0.679960 AAGTGGCAGCGATTTACCCC 60.680 55.000 0.00 0.00 0.00 4.95
414 416 1.940613 CCTAAGTGGCAGCGATTTACC 59.059 52.381 0.00 0.00 0.00 2.85
416 418 2.419574 GGACCTAAGTGGCAGCGATTTA 60.420 50.000 0.00 0.00 40.22 1.40
418 420 0.107654 GGACCTAAGTGGCAGCGATT 60.108 55.000 0.00 0.00 40.22 3.34
419 421 0.978146 AGGACCTAAGTGGCAGCGAT 60.978 55.000 0.00 0.00 40.22 4.58
421 423 1.153549 GAGGACCTAAGTGGCAGCG 60.154 63.158 0.00 0.00 40.22 5.18
422 424 0.391793 GTGAGGACCTAAGTGGCAGC 60.392 60.000 0.00 0.00 40.22 5.25
423 425 0.976641 TGTGAGGACCTAAGTGGCAG 59.023 55.000 0.00 0.00 40.22 4.85
424 426 0.685097 GTGTGAGGACCTAAGTGGCA 59.315 55.000 0.00 0.00 40.22 4.92
425 427 0.036294 GGTGTGAGGACCTAAGTGGC 60.036 60.000 0.00 0.00 40.22 5.01
426 428 0.246635 CGGTGTGAGGACCTAAGTGG 59.753 60.000 0.00 0.00 42.93 4.00
427 429 0.966920 ACGGTGTGAGGACCTAAGTG 59.033 55.000 0.00 0.00 33.35 3.16
428 430 0.966920 CACGGTGTGAGGACCTAAGT 59.033 55.000 0.00 0.00 35.23 2.24
450 1723 4.367023 CTTCGTTGGTCGGCCCGA 62.367 66.667 0.00 0.00 40.32 5.14
499 1772 3.375299 GCCTTTGACTTATGTACAGCCAG 59.625 47.826 0.33 0.00 0.00 4.85
505 1778 5.335661 CCTGTTTGGCCTTTGACTTATGTAC 60.336 44.000 3.32 0.00 0.00 2.90
531 1806 7.324135 GTGAGTTCGTAAACAAACTTTTGAACA 59.676 33.333 8.69 0.00 40.55 3.18
534 1809 6.900189 TGTGAGTTCGTAAACAAACTTTTGA 58.100 32.000 8.69 0.00 40.55 2.69
550 1825 4.560035 CGAATGGAAATGCAATGTGAGTTC 59.440 41.667 0.00 0.00 0.00 3.01
639 1917 6.353404 TCTCTCTTTTTCCCTCTCTTCTTC 57.647 41.667 0.00 0.00 0.00 2.87
640 1918 6.950860 ATCTCTCTTTTTCCCTCTCTTCTT 57.049 37.500 0.00 0.00 0.00 2.52
641 1919 8.442660 TTTATCTCTCTTTTTCCCTCTCTTCT 57.557 34.615 0.00 0.00 0.00 2.85
706 3980 5.105310 GGAACATGGAGACTGCTAGAACTAA 60.105 44.000 0.00 0.00 0.00 2.24
709 3983 3.055819 TGGAACATGGAGACTGCTAGAAC 60.056 47.826 0.00 0.00 0.00 3.01
713 3987 5.626809 GTGTTATGGAACATGGAGACTGCTA 60.627 44.000 0.00 0.00 46.98 3.49
719 3993 3.264193 AGCTGTGTTATGGAACATGGAGA 59.736 43.478 0.00 0.00 46.98 3.71
730 4004 4.436332 TGCACTGATCTAGCTGTGTTATG 58.564 43.478 0.00 0.00 39.17 1.90
734 4008 2.902523 CATGCACTGATCTAGCTGTGT 58.097 47.619 0.00 0.00 39.17 3.72
735 4009 1.598132 GCATGCACTGATCTAGCTGTG 59.402 52.381 14.21 0.00 39.72 3.66
792 4070 7.066163 TGACATTGTTAGTTAGATGGATGCTTG 59.934 37.037 0.00 0.00 0.00 4.01
793 4071 7.112122 TGACATTGTTAGTTAGATGGATGCTT 58.888 34.615 0.00 0.00 0.00 3.91
795 4073 6.925610 TGACATTGTTAGTTAGATGGATGC 57.074 37.500 0.00 0.00 0.00 3.91
824 4133 5.614308 TCCATGGTGCACTTGATAAGATAG 58.386 41.667 17.98 0.58 0.00 2.08
873 4203 0.824759 GTTCGTCTGTGGAGGGCTAT 59.175 55.000 0.00 0.00 0.00 2.97
885 4216 3.769844 AGGTGATGGAATGTAGTTCGTCT 59.230 43.478 0.00 0.00 37.73 4.18
886 4217 4.113354 GAGGTGATGGAATGTAGTTCGTC 58.887 47.826 0.00 0.00 37.73 4.20
887 4218 3.513912 TGAGGTGATGGAATGTAGTTCGT 59.486 43.478 0.00 0.00 37.73 3.85
889 4220 5.059833 GGATGAGGTGATGGAATGTAGTTC 58.940 45.833 0.00 0.00 36.04 3.01
891 4222 3.392616 GGGATGAGGTGATGGAATGTAGT 59.607 47.826 0.00 0.00 0.00 2.73
892 4223 3.392285 TGGGATGAGGTGATGGAATGTAG 59.608 47.826 0.00 0.00 0.00 2.74
991 4328 2.741985 TGCGGCCATTGTCTGTCG 60.742 61.111 2.24 0.00 0.00 4.35
1263 4628 1.992277 GGGAGGGCTCAGCTTCTCA 60.992 63.158 17.91 0.00 33.37 3.27
1309 4674 3.257561 CTTGGCCGCGTCGATCAG 61.258 66.667 4.92 0.00 0.00 2.90
1410 4775 4.914983 TGATCTTGACCTTCATCTTGCTT 58.085 39.130 0.00 0.00 0.00 3.91
1639 5004 4.194720 AGCGTCGATGTCGGAGGC 62.195 66.667 6.48 6.93 40.29 4.70
1662 5027 0.473694 TCCTCCTCAGGAAGTTGGCA 60.474 55.000 0.00 0.00 46.84 4.92
1984 10390 2.348685 CGCAACACCGTAACGATTCAAA 60.349 45.455 0.00 0.00 0.00 2.69
1994 10400 5.119898 ACGAATTAAATAACGCAACACCGTA 59.880 36.000 0.00 0.00 41.16 4.02
2045 10452 5.639506 ACGAAAATCACAAGTAGATGACCTG 59.360 40.000 0.00 0.00 0.00 4.00
2117 10530 1.404583 GCACCAATAAGCAGCCAAAGG 60.405 52.381 0.00 0.00 0.00 3.11
2236 10661 1.260544 GCACCTGGGAGCTGAAAAAT 58.739 50.000 0.00 0.00 0.00 1.82
2237 10662 0.827507 GGCACCTGGGAGCTGAAAAA 60.828 55.000 12.19 0.00 32.43 1.94
2293 10718 9.654663 TGATCATATTTGATGTTGCAAATTTCA 57.345 25.926 0.00 1.61 43.83 2.69
2297 10722 9.661563 AGTTTGATCATATTTGATGTTGCAAAT 57.338 25.926 0.00 0.00 46.79 2.32
2325 10755 4.710423 TGAAAACTTGCAAGCACTTACA 57.290 36.364 26.27 15.20 0.00 2.41
2326 10756 4.084900 GCATGAAAACTTGCAAGCACTTAC 60.085 41.667 26.27 12.96 0.00 2.34
2327 10757 4.050553 GCATGAAAACTTGCAAGCACTTA 58.949 39.130 26.27 10.74 0.00 2.24
2349 10779 4.681483 GCTCTTCGAATGTTTTCTTTTGGG 59.319 41.667 0.00 0.00 0.00 4.12
2357 10787 7.602644 TCTTGTGTATAGCTCTTCGAATGTTTT 59.397 33.333 0.00 0.00 0.00 2.43
2409 10839 7.246674 TCAGATTTCAGTGTTAACAGTGTTC 57.753 36.000 32.36 26.66 45.17 3.18
2411 10841 7.336931 AGTTTCAGATTTCAGTGTTAACAGTGT 59.663 33.333 32.36 19.83 45.17 3.55
2412 10842 7.697691 AGTTTCAGATTTCAGTGTTAACAGTG 58.302 34.615 29.80 29.80 46.05 3.66
2416 10846 8.345565 ACATGAGTTTCAGATTTCAGTGTTAAC 58.654 33.333 0.00 0.00 0.00 2.01
2440 10870 6.605471 ATCATGTAGAGAAAGGTGTACACA 57.395 37.500 26.51 3.18 29.66 3.72
2472 10902 9.435688 ACTTTGTAGATTTTTGCAAGTTTTCTT 57.564 25.926 0.00 0.00 41.31 2.52
2490 10920 7.748847 ACGTCAAATATGGCTAAACTTTGTAG 58.251 34.615 0.00 0.00 0.00 2.74
2502 10932 4.852609 ACTTTACGACGTCAAATATGGC 57.147 40.909 17.16 0.00 0.00 4.40
2591 11021 4.953940 AGAGAAAGATGTGATAGCTCCC 57.046 45.455 0.00 0.00 0.00 4.30
2715 11146 7.887996 ATGTATCATGCACGAAAAACAAATT 57.112 28.000 0.00 0.00 0.00 1.82
2716 11147 9.585099 AATATGTATCATGCACGAAAAACAAAT 57.415 25.926 0.00 0.00 0.00 2.32
2727 11158 5.050159 TCACAGCGAAATATGTATCATGCAC 60.050 40.000 0.00 0.00 0.00 4.57
2798 11230 6.667370 CATGTACAGAGCACAATACACAAAA 58.333 36.000 0.33 0.00 30.69 2.44
2804 11236 2.614057 GGGCATGTACAGAGCACAATAC 59.386 50.000 20.54 6.01 0.00 1.89
2888 11323 6.791867 AATGACTACCTTATACTGACTGCA 57.208 37.500 0.00 0.00 0.00 4.41
2889 11324 9.197694 CAATAATGACTACCTTATACTGACTGC 57.802 37.037 0.00 0.00 0.00 4.40
2890 11325 9.698309 CCAATAATGACTACCTTATACTGACTG 57.302 37.037 0.00 0.00 0.00 3.51
2891 11326 8.368668 GCCAATAATGACTACCTTATACTGACT 58.631 37.037 0.00 0.00 0.00 3.41
2892 11327 7.603024 GGCCAATAATGACTACCTTATACTGAC 59.397 40.741 0.00 0.00 0.00 3.51
2893 11328 7.524863 CGGCCAATAATGACTACCTTATACTGA 60.525 40.741 2.24 0.00 0.00 3.41
2894 11329 6.590292 CGGCCAATAATGACTACCTTATACTG 59.410 42.308 2.24 0.00 0.00 2.74
2895 11330 6.295688 CCGGCCAATAATGACTACCTTATACT 60.296 42.308 2.24 0.00 0.00 2.12
2896 11331 5.873164 CCGGCCAATAATGACTACCTTATAC 59.127 44.000 2.24 0.00 0.00 1.47
2897 11332 5.544948 ACCGGCCAATAATGACTACCTTATA 59.455 40.000 0.00 0.00 0.00 0.98
2898 11333 4.349930 ACCGGCCAATAATGACTACCTTAT 59.650 41.667 0.00 0.00 0.00 1.73
2899 11334 3.712733 ACCGGCCAATAATGACTACCTTA 59.287 43.478 0.00 0.00 0.00 2.69
2900 11335 2.508300 ACCGGCCAATAATGACTACCTT 59.492 45.455 0.00 0.00 0.00 3.50
2901 11336 2.124411 ACCGGCCAATAATGACTACCT 58.876 47.619 0.00 0.00 0.00 3.08
2902 11337 2.632987 ACCGGCCAATAATGACTACC 57.367 50.000 0.00 0.00 0.00 3.18
2903 11338 4.396790 TGAAAACCGGCCAATAATGACTAC 59.603 41.667 0.00 0.00 0.00 2.73
2904 11339 4.590918 TGAAAACCGGCCAATAATGACTA 58.409 39.130 0.00 0.00 0.00 2.59
2945 11380 6.010219 CAGGGTCATCCTCCTTTTCTAAAAA 58.990 40.000 0.00 0.00 46.12 1.94
2946 11381 5.516591 CCAGGGTCATCCTCCTTTTCTAAAA 60.517 44.000 0.00 0.00 46.12 1.52
2947 11382 4.018415 CCAGGGTCATCCTCCTTTTCTAAA 60.018 45.833 0.00 0.00 46.12 1.85
2948 11383 3.523564 CCAGGGTCATCCTCCTTTTCTAA 59.476 47.826 0.00 0.00 46.12 2.10
2949 11384 3.115390 CCAGGGTCATCCTCCTTTTCTA 58.885 50.000 0.00 0.00 46.12 2.10
2950 11385 1.918957 CCAGGGTCATCCTCCTTTTCT 59.081 52.381 0.00 0.00 46.12 2.52
2951 11386 1.683319 GCCAGGGTCATCCTCCTTTTC 60.683 57.143 0.00 0.00 46.12 2.29
2952 11387 0.332972 GCCAGGGTCATCCTCCTTTT 59.667 55.000 0.00 0.00 46.12 2.27
2953 11388 1.575447 GGCCAGGGTCATCCTCCTTT 61.575 60.000 0.00 0.00 46.12 3.11
2954 11389 2.003548 GGCCAGGGTCATCCTCCTT 61.004 63.158 0.00 0.00 46.12 3.36
2955 11390 2.367512 GGCCAGGGTCATCCTCCT 60.368 66.667 0.00 0.00 46.12 3.69
2956 11391 2.367512 AGGCCAGGGTCATCCTCC 60.368 66.667 5.01 0.00 46.12 4.30
2957 11392 1.383803 AGAGGCCAGGGTCATCCTC 60.384 63.158 5.01 2.46 46.12 3.71
2959 11394 2.914289 CAGAGGCCAGGGTCATCC 59.086 66.667 5.01 0.00 0.00 3.51
2960 11395 2.191641 GCAGAGGCCAGGGTCATC 59.808 66.667 5.01 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.