Multiple sequence alignment - TraesCS7B01G471800

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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 TraesCS7B01G471800 chr7B 100.000 2840 0 0 1 2840 727655096 727652257 0.000000e+00 5245.0
1 TraesCS7B01G471800 chr7B 82.604 845 118 18 1000 1840 727186270 727185451 0.000000e+00 719.0
2 TraesCS7B01G471800 chr7B 82.409 847 117 23 1001 1840 727392089 727392910 0.000000e+00 710.0
3 TraesCS7B01G471800 chr7B 79.219 717 125 15 1000 1712 727328230 727327534 7.120000e-131 477.0
4 TraesCS7B01G471800 chr7A 87.110 1955 180 42 889 2822 722482069 722483972 0.000000e+00 2148.0
5 TraesCS7B01G471800 chr7A 89.364 1053 93 10 652 1696 722451112 722452153 0.000000e+00 1306.0
6 TraesCS7B01G471800 chr7A 87.840 773 84 3 1222 1990 722572789 722573555 0.000000e+00 898.0
7 TraesCS7B01G471800 chr7A 79.565 827 135 20 1019 1840 722414385 722415182 6.870000e-156 560.0
8 TraesCS7B01G471800 chr7A 85.338 532 63 10 2116 2638 722577856 722578381 1.160000e-148 536.0
9 TraesCS7B01G471800 chr7A 91.884 345 24 3 887 1230 722571999 722572340 1.980000e-131 479.0
10 TraesCS7B01G471800 chr7A 79.798 693 83 36 1705 2378 722481094 722481748 4.310000e-123 451.0
11 TraesCS7B01G471800 chr7A 88.000 225 9 9 652 861 722571779 722572000 1.690000e-62 250.0
12 TraesCS7B01G471800 chr7A 88.152 211 22 2 407 617 620842426 620842219 6.080000e-62 248.0
13 TraesCS7B01G471800 chr7A 86.842 228 18 8 2615 2840 722578384 722578601 7.860000e-61 244.0
14 TraesCS7B01G471800 chr7D 84.397 1692 179 50 719 2378 627058894 627060532 0.000000e+00 1583.0
15 TraesCS7B01G471800 chr7D 88.409 1251 106 26 652 1892 627070957 627072178 0.000000e+00 1471.0
16 TraesCS7B01G471800 chr7D 89.059 914 74 17 1922 2822 627072175 627073075 0.000000e+00 1110.0
17 TraesCS7B01G471800 chr7D 84.788 848 109 14 1000 1840 626909014 626909848 0.000000e+00 833.0
18 TraesCS7B01G471800 chr7D 94.503 382 18 3 1 380 565437453 565437833 1.130000e-163 586.0
19 TraesCS7B01G471800 chr7D 80.268 745 126 11 1103 1840 626922881 626923611 2.490000e-150 542.0
20 TraesCS7B01G471800 chr7D 78.591 738 131 18 1000 1734 627024015 627024728 1.990000e-126 462.0
21 TraesCS7B01G471800 chr7D 87.963 216 24 2 401 615 203332281 203332495 1.310000e-63 254.0
22 TraesCS7B01G471800 chrUn 82.604 914 134 17 1000 1901 83608266 83609166 0.000000e+00 784.0
23 TraesCS7B01G471800 chr1A 95.276 381 17 1 1 380 576538666 576539046 1.130000e-168 603.0
24 TraesCS7B01G471800 chr5D 94.503 382 19 2 1 380 381806209 381805828 3.150000e-164 588.0
25 TraesCS7B01G471800 chr5D 89.151 212 22 1 404 615 410086527 410086737 2.170000e-66 263.0
26 TraesCS7B01G471800 chr5D 86.056 251 21 2 378 615 327236066 327236315 1.010000e-64 257.0
27 TraesCS7B01G471800 chr2D 94.723 379 18 2 1 377 204123996 204123618 3.150000e-164 588.0
28 TraesCS7B01G471800 chr2D 94.226 381 20 2 1 380 7062540 7062161 5.270000e-162 580.0
29 TraesCS7B01G471800 chr3D 94.241 382 20 2 1 380 7297144 7297525 1.470000e-162 582.0
30 TraesCS7B01G471800 chr3D 82.609 253 27 5 378 615 7299400 7299650 1.030000e-49 207.0
31 TraesCS7B01G471800 chr3D 81.923 260 26 8 378 623 362067507 362067759 1.730000e-47 200.0
32 TraesCS7B01G471800 chr6D 94.226 381 21 1 1 380 392268226 392268606 5.270000e-162 580.0
33 TraesCS7B01G471800 chr6D 85.375 253 20 4 378 615 283559042 283559292 2.190000e-61 246.0
34 TraesCS7B01G471800 chr6D 97.917 48 1 0 378 425 444127925 444127878 1.810000e-12 84.2
35 TraesCS7B01G471800 chr4D 94.241 382 19 3 1 380 387087109 387087489 5.270000e-162 580.0
36 TraesCS7B01G471800 chr4D 94.444 378 19 2 1 377 457071868 457071492 5.270000e-162 580.0
37 TraesCS7B01G471800 chr4D 87.324 213 25 2 404 615 388820502 388820713 2.830000e-60 243.0
38 TraesCS7B01G471800 chr4D 84.100 239 32 3 379 615 58948391 58948625 2.850000e-55 226.0
39 TraesCS7B01G471800 chr5B 85.656 244 27 3 378 615 146835167 146835408 1.690000e-62 250.0
40 TraesCS7B01G471800 chr2B 88.152 211 22 3 407 617 120579549 120579342 6.080000e-62 248.0
41 TraesCS7B01G471800 chr1D 84.462 251 25 2 378 615 425542527 425542278 4.730000e-58 235.0


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 TraesCS7B01G471800 chr7B 727652257 727655096 2839 True 5245.000000 5245 100.000000 1 2840 1 chr7B.!!$R3 2839
1 TraesCS7B01G471800 chr7B 727185451 727186270 819 True 719.000000 719 82.604000 1000 1840 1 chr7B.!!$R1 840
2 TraesCS7B01G471800 chr7B 727392089 727392910 821 False 710.000000 710 82.409000 1001 1840 1 chr7B.!!$F1 839
3 TraesCS7B01G471800 chr7B 727327534 727328230 696 True 477.000000 477 79.219000 1000 1712 1 chr7B.!!$R2 712
4 TraesCS7B01G471800 chr7A 722451112 722452153 1041 False 1306.000000 1306 89.364000 652 1696 1 chr7A.!!$F2 1044
5 TraesCS7B01G471800 chr7A 722481094 722483972 2878 False 1299.500000 2148 83.454000 889 2822 2 chr7A.!!$F3 1933
6 TraesCS7B01G471800 chr7A 722414385 722415182 797 False 560.000000 560 79.565000 1019 1840 1 chr7A.!!$F1 821
7 TraesCS7B01G471800 chr7A 722571779 722573555 1776 False 542.333333 898 89.241333 652 1990 3 chr7A.!!$F4 1338
8 TraesCS7B01G471800 chr7A 722577856 722578601 745 False 390.000000 536 86.090000 2116 2840 2 chr7A.!!$F5 724
9 TraesCS7B01G471800 chr7D 627058894 627060532 1638 False 1583.000000 1583 84.397000 719 2378 1 chr7D.!!$F6 1659
10 TraesCS7B01G471800 chr7D 627070957 627073075 2118 False 1290.500000 1471 88.734000 652 2822 2 chr7D.!!$F7 2170
11 TraesCS7B01G471800 chr7D 626909014 626909848 834 False 833.000000 833 84.788000 1000 1840 1 chr7D.!!$F3 840
12 TraesCS7B01G471800 chr7D 626922881 626923611 730 False 542.000000 542 80.268000 1103 1840 1 chr7D.!!$F4 737
13 TraesCS7B01G471800 chr7D 627024015 627024728 713 False 462.000000 462 78.591000 1000 1734 1 chr7D.!!$F5 734
14 TraesCS7B01G471800 chrUn 83608266 83609166 900 False 784.000000 784 82.604000 1000 1901 1 chrUn.!!$F1 901
15 TraesCS7B01G471800 chr3D 7297144 7299650 2506 False 394.500000 582 88.425000 1 615 2 chr3D.!!$F2 614

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
348 350 0.028242 CCGACGAGAAGGAGACATCG 59.972 60.0 0.0 0.0 38.51 3.84 F
385 387 0.036952 CTCCTCATGCTTGGACGTGT 60.037 55.0 0.0 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 3766 0.179032 TCGCTCAAGCACCTTTCCAA 60.179 50.000 2.5 0.0 42.21 3.53 R
2121 4426 1.742831 ACGAAACAGCAAAGCACTCAA 59.257 42.857 0.0 0.0 0.00 3.02 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
86 88 4.862823 CCCCCTCTCTCCCCCGTC 62.863 77.778 0.00 0.00 0.00 4.79
175 177 1.600916 GCCAAGGCGTCAAGGAAGT 60.601 57.895 1.58 0.00 0.00 3.01
212 214 1.517832 CGGAGGAGATCGCCAAGTT 59.482 57.895 18.44 0.00 34.79 2.66
213 215 0.807667 CGGAGGAGATCGCCAAGTTG 60.808 60.000 18.44 0.00 34.79 3.16
214 216 0.462759 GGAGGAGATCGCCAAGTTGG 60.463 60.000 18.17 18.17 41.55 3.77
215 217 0.537188 GAGGAGATCGCCAAGTTGGA 59.463 55.000 26.52 5.86 40.96 3.53
216 218 0.250513 AGGAGATCGCCAAGTTGGAC 59.749 55.000 26.52 15.20 40.96 4.02
217 219 1.084370 GGAGATCGCCAAGTTGGACG 61.084 60.000 26.52 25.05 40.96 4.79
218 220 1.696832 GAGATCGCCAAGTTGGACGC 61.697 60.000 26.52 14.95 40.96 5.19
220 222 1.970917 GATCGCCAAGTTGGACGCAG 61.971 60.000 26.52 10.24 40.96 5.18
222 224 2.250939 CGCCAAGTTGGACGCAGAA 61.251 57.895 26.52 0.00 40.96 3.02
223 225 1.576421 GCCAAGTTGGACGCAGAAG 59.424 57.895 26.52 0.00 40.96 2.85
234 236 2.781300 GCAGAAGCGGCGAAGAAG 59.219 61.111 12.98 0.00 0.00 2.85
235 237 1.738099 GCAGAAGCGGCGAAGAAGA 60.738 57.895 12.98 0.00 0.00 2.87
236 238 1.691215 GCAGAAGCGGCGAAGAAGAG 61.691 60.000 12.98 0.00 0.00 2.85
237 239 1.080995 CAGAAGCGGCGAAGAAGAGG 61.081 60.000 12.98 0.00 0.00 3.69
238 240 1.215647 GAAGCGGCGAAGAAGAGGA 59.784 57.895 12.98 0.00 0.00 3.71
241 243 2.202810 CGGCGAAGAAGAGGAGCC 60.203 66.667 0.00 0.00 44.00 4.70
242 244 2.202810 GGCGAAGAAGAGGAGCCG 60.203 66.667 0.00 0.00 38.28 5.52
243 245 2.202810 GCGAAGAAGAGGAGCCGG 60.203 66.667 0.00 0.00 0.00 6.13
244 246 2.711922 GCGAAGAAGAGGAGCCGGA 61.712 63.158 5.05 0.00 0.00 5.14
245 247 1.435515 CGAAGAAGAGGAGCCGGAG 59.564 63.158 5.05 0.00 0.00 4.63
248 250 1.326951 AAGAAGAGGAGCCGGAGAGC 61.327 60.000 5.05 0.00 0.00 4.09
249 251 2.038007 AAGAGGAGCCGGAGAGCA 59.962 61.111 5.05 0.00 34.23 4.26
251 253 2.757917 GAGGAGCCGGAGAGCAGT 60.758 66.667 5.05 0.00 34.23 4.40
252 254 2.757917 AGGAGCCGGAGAGCAGTC 60.758 66.667 5.05 0.00 34.23 3.51
253 255 4.200283 GGAGCCGGAGAGCAGTCG 62.200 72.222 5.05 0.00 34.23 4.18
255 257 3.404141 GAGCCGGAGAGCAGTCGTC 62.404 68.421 5.05 0.00 34.23 4.20
256 258 3.749064 GCCGGAGAGCAGTCGTCA 61.749 66.667 5.05 0.00 0.00 4.35
257 259 2.962569 CCGGAGAGCAGTCGTCAA 59.037 61.111 0.00 0.00 0.00 3.18
258 260 1.153939 CCGGAGAGCAGTCGTCAAG 60.154 63.158 0.00 0.00 0.00 3.02
259 261 1.153939 CGGAGAGCAGTCGTCAAGG 60.154 63.158 0.00 0.00 0.00 3.61
261 263 0.109039 GGAGAGCAGTCGTCAAGGTC 60.109 60.000 0.00 0.00 0.00 3.85
262 264 0.598562 GAGAGCAGTCGTCAAGGTCA 59.401 55.000 6.97 0.00 32.52 4.02
263 265 1.000163 GAGAGCAGTCGTCAAGGTCAA 60.000 52.381 6.97 0.00 32.52 3.18
265 267 1.728971 GAGCAGTCGTCAAGGTCAATG 59.271 52.381 0.00 0.00 0.00 2.82
266 268 0.166814 GCAGTCGTCAAGGTCAATGC 59.833 55.000 0.00 0.00 0.00 3.56
267 269 0.798776 CAGTCGTCAAGGTCAATGCC 59.201 55.000 0.00 0.00 0.00 4.40
269 271 2.032634 TCGTCAAGGTCAATGCCGC 61.033 57.895 0.00 0.00 0.00 6.53
270 272 2.877691 GTCAAGGTCAATGCCGCC 59.122 61.111 0.00 0.00 0.00 6.13
271 273 2.745884 TCAAGGTCAATGCCGCCG 60.746 61.111 0.00 0.00 0.00 6.46
272 274 4.481112 CAAGGTCAATGCCGCCGC 62.481 66.667 0.00 0.00 0.00 6.53
291 293 3.423154 GCCAAGTTCGCCACCGAG 61.423 66.667 0.00 0.00 45.35 4.63
292 294 3.423154 CCAAGTTCGCCACCGAGC 61.423 66.667 0.00 0.00 45.35 5.03
342 344 3.839432 GGGGCCGACGAGAAGGAG 61.839 72.222 0.00 0.00 0.00 3.69
343 345 2.754658 GGGCCGACGAGAAGGAGA 60.755 66.667 0.00 0.00 0.00 3.71
345 347 2.341101 GGCCGACGAGAAGGAGACA 61.341 63.158 0.00 0.00 0.00 3.41
346 348 1.668101 GGCCGACGAGAAGGAGACAT 61.668 60.000 0.00 0.00 0.00 3.06
347 349 0.248702 GCCGACGAGAAGGAGACATC 60.249 60.000 0.00 0.00 0.00 3.06
348 350 0.028242 CCGACGAGAAGGAGACATCG 59.972 60.000 0.00 0.00 38.51 3.84
349 351 0.727970 CGACGAGAAGGAGACATCGT 59.272 55.000 0.00 0.00 45.04 3.73
353 355 2.095161 ACGAGAAGGAGACATCGTCAAC 60.095 50.000 0.00 0.00 40.66 3.18
354 356 2.095212 CGAGAAGGAGACATCGTCAACA 60.095 50.000 0.00 0.00 34.60 3.33
355 357 3.611766 CGAGAAGGAGACATCGTCAACAA 60.612 47.826 0.00 0.00 34.60 2.83
357 359 4.310769 AGAAGGAGACATCGTCAACAAAG 58.689 43.478 0.00 0.00 34.60 2.77
360 362 2.096218 GGAGACATCGTCAACAAAGTGC 60.096 50.000 0.00 0.00 34.60 4.40
362 364 2.287915 AGACATCGTCAACAAAGTGCAC 59.712 45.455 9.40 9.40 34.60 4.57
363 365 1.003972 ACATCGTCAACAAAGTGCACG 60.004 47.619 12.01 0.00 0.00 5.34
364 366 0.041312 ATCGTCAACAAAGTGCACGC 60.041 50.000 12.01 0.00 0.00 5.34
365 367 1.654137 CGTCAACAAAGTGCACGCC 60.654 57.895 12.01 0.00 0.00 5.68
366 368 1.299089 GTCAACAAAGTGCACGCCC 60.299 57.895 12.01 0.00 0.00 6.13
368 370 1.008538 CAACAAAGTGCACGCCCTC 60.009 57.895 12.01 0.00 0.00 4.30
369 371 2.193536 AACAAAGTGCACGCCCTCC 61.194 57.895 12.01 0.00 0.00 4.30
371 373 2.032681 AAAGTGCACGCCCTCCTC 59.967 61.111 12.01 0.00 0.00 3.71
372 374 2.818169 AAAGTGCACGCCCTCCTCA 61.818 57.895 12.01 0.00 0.00 3.86
374 376 2.809861 AAGTGCACGCCCTCCTCATG 62.810 60.000 12.01 0.00 0.00 3.07
375 377 4.783621 TGCACGCCCTCCTCATGC 62.784 66.667 0.00 0.00 36.81 4.06
376 378 4.479993 GCACGCCCTCCTCATGCT 62.480 66.667 0.00 0.00 33.44 3.79
377 379 2.270205 CACGCCCTCCTCATGCTT 59.730 61.111 0.00 0.00 0.00 3.91
378 380 2.110967 CACGCCCTCCTCATGCTTG 61.111 63.158 0.00 0.00 0.00 4.01
380 382 3.001514 GCCCTCCTCATGCTTGGA 58.998 61.111 0.00 0.00 0.00 3.53
381 383 1.452833 GCCCTCCTCATGCTTGGAC 60.453 63.158 0.00 0.00 0.00 4.02
382 384 1.153289 CCCTCCTCATGCTTGGACG 60.153 63.158 0.00 0.00 0.00 4.79
383 385 1.599047 CCTCCTCATGCTTGGACGT 59.401 57.895 0.00 0.00 0.00 4.34
384 386 0.742281 CCTCCTCATGCTTGGACGTG 60.742 60.000 0.00 0.00 0.00 4.49
385 387 0.036952 CTCCTCATGCTTGGACGTGT 60.037 55.000 0.00 0.00 0.00 4.49
387 389 1.204704 TCCTCATGCTTGGACGTGTAG 59.795 52.381 0.00 0.00 0.00 2.74
395 397 4.814294 GGACGTGTAGGCCGCTGG 62.814 72.222 0.00 0.00 38.99 4.85
414 416 1.442520 CTTTGTTGCCGGCGTGATG 60.443 57.895 23.90 6.35 0.00 3.07
415 417 1.851021 CTTTGTTGCCGGCGTGATGA 61.851 55.000 23.90 0.00 0.00 2.92
416 418 1.448119 TTTGTTGCCGGCGTGATGAA 61.448 50.000 23.90 6.19 0.00 2.57
417 419 2.123988 TTGTTGCCGGCGTGATGAAC 62.124 55.000 23.90 19.29 0.00 3.18
419 421 1.017177 GTTGCCGGCGTGATGAACTA 61.017 55.000 23.90 0.00 0.00 2.24
420 422 0.739462 TTGCCGGCGTGATGAACTAG 60.739 55.000 23.90 0.00 0.00 2.57
421 423 1.883084 GCCGGCGTGATGAACTAGG 60.883 63.158 12.58 0.00 0.00 3.02
422 424 1.227263 CCGGCGTGATGAACTAGGG 60.227 63.158 6.01 0.00 0.00 3.53
423 425 1.883084 CGGCGTGATGAACTAGGGC 60.883 63.158 0.00 0.00 0.00 5.19
424 426 1.523938 GGCGTGATGAACTAGGGCC 60.524 63.158 0.00 0.00 0.00 5.80
426 428 0.811616 GCGTGATGAACTAGGGCCTG 60.812 60.000 18.53 8.95 0.00 4.85
427 429 0.179073 CGTGATGAACTAGGGCCTGG 60.179 60.000 18.53 17.35 0.00 4.45
428 430 0.464554 GTGATGAACTAGGGCCTGGC 60.465 60.000 18.53 11.05 0.00 4.85
429 431 0.913934 TGATGAACTAGGGCCTGGCA 60.914 55.000 22.05 8.09 0.00 4.92
430 432 0.475906 GATGAACTAGGGCCTGGCAT 59.524 55.000 22.05 13.05 0.00 4.40
433 435 1.106285 GAACTAGGGCCTGGCATTTG 58.894 55.000 22.05 10.88 0.00 2.32
434 436 0.704076 AACTAGGGCCTGGCATTTGA 59.296 50.000 22.05 0.00 0.00 2.69
435 437 0.704076 ACTAGGGCCTGGCATTTGAA 59.296 50.000 22.05 0.00 0.00 2.69
436 438 1.077005 ACTAGGGCCTGGCATTTGAAA 59.923 47.619 22.05 0.00 0.00 2.69
437 439 1.478105 CTAGGGCCTGGCATTTGAAAC 59.522 52.381 22.05 0.00 0.00 2.78
439 441 1.665442 GGCCTGGCATTTGAAACGT 59.335 52.632 22.05 0.00 0.00 3.99
444 446 2.053627 CTGGCATTTGAAACGTTGCTC 58.946 47.619 8.00 0.00 35.46 4.26
445 447 1.680735 TGGCATTTGAAACGTTGCTCT 59.319 42.857 8.00 0.00 35.46 4.09
446 448 2.100584 TGGCATTTGAAACGTTGCTCTT 59.899 40.909 8.00 0.00 35.46 2.85
447 449 3.123050 GGCATTTGAAACGTTGCTCTTT 58.877 40.909 8.00 0.00 35.46 2.52
448 450 3.555547 GGCATTTGAAACGTTGCTCTTTT 59.444 39.130 8.00 0.00 35.46 2.27
449 451 4.033932 GGCATTTGAAACGTTGCTCTTTTT 59.966 37.500 8.00 0.00 35.46 1.94
473 475 2.225068 AATAGACGCGAACAGGATGG 57.775 50.000 15.93 0.00 43.62 3.51
474 476 0.389391 ATAGACGCGAACAGGATGGG 59.611 55.000 15.93 0.00 43.62 4.00
475 477 1.672854 TAGACGCGAACAGGATGGGG 61.673 60.000 15.93 0.00 43.62 4.96
478 480 2.361104 GCGAACAGGATGGGGCAA 60.361 61.111 0.00 0.00 43.62 4.52
479 481 1.976474 GCGAACAGGATGGGGCAAA 60.976 57.895 0.00 0.00 43.62 3.68
480 482 1.883021 CGAACAGGATGGGGCAAAC 59.117 57.895 0.00 0.00 43.62 2.93
481 483 1.883021 GAACAGGATGGGGCAAACG 59.117 57.895 0.00 0.00 43.62 3.60
485 487 1.076777 AGGATGGGGCAAACGGATG 60.077 57.895 0.00 0.00 0.00 3.51
486 488 2.785425 GGATGGGGCAAACGGATGC 61.785 63.158 6.17 6.17 45.67 3.91
492 494 2.175811 GCAAACGGATGCGACCAC 59.824 61.111 15.49 0.00 36.45 4.16
493 495 2.474266 CAAACGGATGCGACCACG 59.526 61.111 15.49 0.00 42.93 4.94
531 533 3.716195 CATCCCAGGACACGCCCA 61.716 66.667 0.00 0.00 37.37 5.36
532 534 2.933287 ATCCCAGGACACGCCCAA 60.933 61.111 0.00 0.00 37.37 4.12
534 536 2.764637 ATCCCAGGACACGCCCAAAC 62.765 60.000 0.00 0.00 37.37 2.93
535 537 2.203280 CCAGGACACGCCCAAACA 60.203 61.111 0.00 0.00 37.37 2.83
536 538 2.551912 CCAGGACACGCCCAAACAC 61.552 63.158 0.00 0.00 37.37 3.32
537 539 1.525995 CAGGACACGCCCAAACACT 60.526 57.895 0.00 0.00 37.37 3.55
538 540 1.525995 AGGACACGCCCAAACACTG 60.526 57.895 0.00 0.00 37.37 3.66
539 541 2.331451 GACACGCCCAAACACTGC 59.669 61.111 0.00 0.00 0.00 4.40
540 542 3.194272 GACACGCCCAAACACTGCC 62.194 63.158 0.00 0.00 0.00 4.85
541 543 3.977244 CACGCCCAAACACTGCCC 61.977 66.667 0.00 0.00 0.00 5.36
544 546 2.604382 GCCCAAACACTGCCCCAT 60.604 61.111 0.00 0.00 0.00 4.00
545 547 2.216331 GCCCAAACACTGCCCCATT 61.216 57.895 0.00 0.00 0.00 3.16
546 548 1.672898 CCCAAACACTGCCCCATTG 59.327 57.895 0.00 0.00 0.00 2.82
547 549 1.004679 CCAAACACTGCCCCATTGC 60.005 57.895 0.00 0.00 0.00 3.56
548 550 1.474332 CCAAACACTGCCCCATTGCT 61.474 55.000 0.00 0.00 0.00 3.91
549 551 0.037975 CAAACACTGCCCCATTGCTC 60.038 55.000 0.00 0.00 0.00 4.26
551 553 0.698238 AACACTGCCCCATTGCTCTA 59.302 50.000 0.00 0.00 0.00 2.43
553 555 1.133976 ACACTGCCCCATTGCTCTATC 60.134 52.381 0.00 0.00 0.00 2.08
554 556 0.475906 ACTGCCCCATTGCTCTATCC 59.524 55.000 0.00 0.00 0.00 2.59
555 557 0.475475 CTGCCCCATTGCTCTATCCA 59.525 55.000 0.00 0.00 0.00 3.41
558 560 1.683385 GCCCCATTGCTCTATCCAAAC 59.317 52.381 0.00 0.00 0.00 2.93
560 562 1.949525 CCCATTGCTCTATCCAAACGG 59.050 52.381 0.00 0.00 0.00 4.44
561 563 2.421388 CCCATTGCTCTATCCAAACGGA 60.421 50.000 0.00 0.00 36.85 4.69
562 564 2.614057 CCATTGCTCTATCCAAACGGAC 59.386 50.000 0.00 0.00 34.62 4.79
564 566 2.672961 TGCTCTATCCAAACGGACAG 57.327 50.000 0.00 0.00 34.62 3.51
565 567 2.176045 TGCTCTATCCAAACGGACAGA 58.824 47.619 0.00 0.00 33.56 3.41
567 569 2.815478 CTCTATCCAAACGGACAGAGC 58.185 52.381 3.96 0.00 45.02 4.09
568 570 2.428890 CTCTATCCAAACGGACAGAGCT 59.571 50.000 3.96 0.00 45.02 4.09
569 571 2.427453 TCTATCCAAACGGACAGAGCTC 59.573 50.000 5.27 5.27 30.88 4.09
570 572 0.108615 ATCCAAACGGACAGAGCTCG 60.109 55.000 8.37 6.04 34.62 5.03
571 573 1.738099 CCAAACGGACAGAGCTCGG 60.738 63.158 12.66 12.66 0.00 4.63
573 575 0.108615 CAAACGGACAGAGCTCGGAT 60.109 55.000 21.22 3.83 0.00 4.18
576 578 1.471119 ACGGACAGAGCTCGGATAAA 58.529 50.000 21.22 0.00 0.00 1.40
577 579 1.822990 ACGGACAGAGCTCGGATAAAA 59.177 47.619 21.22 0.00 0.00 1.52
578 580 2.194271 CGGACAGAGCTCGGATAAAAC 58.806 52.381 21.22 4.56 0.00 2.43
579 581 2.194271 GGACAGAGCTCGGATAAAACG 58.806 52.381 21.22 0.00 0.00 3.60
580 582 2.194271 GACAGAGCTCGGATAAAACGG 58.806 52.381 21.22 0.00 0.00 4.44
581 583 1.822990 ACAGAGCTCGGATAAAACGGA 59.177 47.619 21.22 0.00 0.00 4.69
583 585 1.197910 GAGCTCGGATAAAACGGACG 58.802 55.000 0.00 0.00 0.00 4.79
584 586 0.529378 AGCTCGGATAAAACGGACGT 59.471 50.000 0.00 0.00 0.00 4.34
585 587 0.919300 GCTCGGATAAAACGGACGTC 59.081 55.000 7.13 7.13 0.00 4.34
586 588 1.553308 CTCGGATAAAACGGACGTCC 58.447 55.000 25.28 25.28 0.00 4.79
596 598 2.357881 GGACGTCCGTTTGGGGTC 60.358 66.667 20.85 0.00 37.97 4.46
597 599 2.735857 GACGTCCGTTTGGGGTCG 60.736 66.667 3.51 0.00 38.68 4.79
598 600 4.974989 ACGTCCGTTTGGGGTCGC 62.975 66.667 0.00 0.00 37.16 5.19
616 618 2.349755 GCGGTGGAGTTGGCCTTA 59.650 61.111 3.32 0.00 0.00 2.69
617 619 2.038837 GCGGTGGAGTTGGCCTTAC 61.039 63.158 3.32 1.81 0.00 2.34
620 622 0.391263 GGTGGAGTTGGCCTTACTCG 60.391 60.000 23.52 0.00 42.31 4.18
621 623 0.391263 GTGGAGTTGGCCTTACTCGG 60.391 60.000 23.52 0.00 42.31 4.63
629 631 3.663644 GCCTTACTCGGCCTTACTC 57.336 57.895 0.00 0.00 44.41 2.59
630 632 0.104487 GCCTTACTCGGCCTTACTCC 59.896 60.000 0.00 0.00 44.41 3.85
633 635 1.669999 TTACTCGGCCTTACTCCGCC 61.670 60.000 0.00 0.00 46.05 6.13
634 636 2.563013 TACTCGGCCTTACTCCGCCT 62.563 60.000 0.00 0.00 46.05 5.52
635 637 2.682494 TCGGCCTTACTCCGCCTT 60.682 61.111 0.00 0.00 46.05 4.35
637 639 2.669240 GGCCTTACTCCGCCTTGT 59.331 61.111 0.00 0.00 42.21 3.16
638 640 1.002502 GGCCTTACTCCGCCTTGTT 60.003 57.895 0.00 0.00 42.21 2.83
639 641 1.025113 GGCCTTACTCCGCCTTGTTC 61.025 60.000 0.00 0.00 42.21 3.18
642 644 2.500229 CCTTACTCCGCCTTGTTCAAA 58.500 47.619 0.00 0.00 0.00 2.69
643 645 2.484264 CCTTACTCCGCCTTGTTCAAAG 59.516 50.000 0.00 0.00 0.00 2.77
644 646 2.178912 TACTCCGCCTTGTTCAAAGG 57.821 50.000 0.00 0.00 40.39 3.11
645 647 0.537371 ACTCCGCCTTGTTCAAAGGG 60.537 55.000 6.28 0.00 37.88 3.95
646 648 0.537371 CTCCGCCTTGTTCAAAGGGT 60.537 55.000 6.28 0.00 37.88 4.34
647 649 0.766131 TCCGCCTTGTTCAAAGGGTA 59.234 50.000 6.28 0.00 37.88 3.69
648 650 1.165270 CCGCCTTGTTCAAAGGGTAG 58.835 55.000 6.28 0.00 37.88 3.18
650 652 2.500229 CGCCTTGTTCAAAGGGTAGAA 58.500 47.619 6.28 0.00 37.88 2.10
651 653 3.081804 CGCCTTGTTCAAAGGGTAGAAT 58.918 45.455 6.28 0.00 37.88 2.40
652 654 3.127030 CGCCTTGTTCAAAGGGTAGAATC 59.873 47.826 6.28 0.00 37.88 2.52
653 655 4.336280 GCCTTGTTCAAAGGGTAGAATCT 58.664 43.478 6.28 0.00 37.88 2.40
815 838 0.398381 GAGCCTCCTCCTCCTGTCAT 60.398 60.000 0.00 0.00 31.68 3.06
817 840 1.406860 GCCTCCTCCTCCTGTCATCC 61.407 65.000 0.00 0.00 0.00 3.51
818 841 0.264359 CCTCCTCCTCCTGTCATCCT 59.736 60.000 0.00 0.00 0.00 3.24
820 843 2.111613 CCTCCTCCTCCTGTCATCCTAT 59.888 54.545 0.00 0.00 0.00 2.57
821 844 3.164268 CTCCTCCTCCTGTCATCCTATG 58.836 54.545 0.00 0.00 0.00 2.23
824 847 3.570540 CTCCTCCTGTCATCCTATGTGA 58.429 50.000 0.00 0.00 0.00 3.58
850 873 3.947841 CACACGTGCAACCACCGG 61.948 66.667 17.22 0.00 38.79 5.28
861 884 1.106944 AACCACCGGTTTCCAAGCTG 61.107 55.000 2.97 0.00 44.33 4.24
865 889 2.282462 CGGTTTCCAAGCTGCCCT 60.282 61.111 0.00 0.00 0.00 5.19
868 894 2.601367 TTTCCAAGCTGCCCTGCC 60.601 61.111 0.00 0.00 0.00 4.85
904 992 6.054860 ACCCTCTGCATATATACAACATCC 57.945 41.667 0.00 0.00 0.00 3.51
918 1006 1.115467 ACATCCATCGTCTCCTCCAC 58.885 55.000 0.00 0.00 0.00 4.02
919 1007 1.114627 CATCCATCGTCTCCTCCACA 58.885 55.000 0.00 0.00 0.00 4.17
920 1008 1.115467 ATCCATCGTCTCCTCCACAC 58.885 55.000 0.00 0.00 0.00 3.82
932 1020 0.390340 CTCCACACCACCACATCTCG 60.390 60.000 0.00 0.00 0.00 4.04
950 1041 2.152016 TCGTCTCATCTCACACGTCTT 58.848 47.619 0.00 0.00 33.89 3.01
988 1079 3.696051 ACAAGCTCAAGAAGAAGCAACAA 59.304 39.130 0.00 0.00 0.00 2.83
998 1089 4.513318 AGAAGAAGCAACAACAAGAGCTAC 59.487 41.667 0.00 0.00 36.07 3.58
1072 1166 1.983119 CTTCTCCAAGCCCCGCCATA 61.983 60.000 0.00 0.00 0.00 2.74
1073 1167 2.203209 CTCCAAGCCCCGCCATAC 60.203 66.667 0.00 0.00 0.00 2.39
1092 1186 2.587194 CGCTCCATCAGCCTTCCG 60.587 66.667 0.00 0.00 46.74 4.30
1095 1189 2.285368 TCCATCAGCCTTCCGGGT 60.285 61.111 0.00 0.00 43.12 5.28
1097 1191 0.619255 TCCATCAGCCTTCCGGGTAA 60.619 55.000 0.00 0.00 39.50 2.85
1099 1193 0.810031 CATCAGCCTTCCGGGTAACG 60.810 60.000 0.00 0.00 39.50 3.18
1231 1800 3.931631 CTCCACTCCTCCCTGGCCA 62.932 68.421 4.71 4.71 35.26 5.36
1353 1923 1.000396 GGGCTTCCATGAGTGCCTT 60.000 57.895 17.71 0.00 44.36 4.35
1735 3766 3.630013 TGGAGAGGCTGCACGCTT 61.630 61.111 0.50 0.90 39.13 4.68
1741 3772 1.795170 GAGGCTGCACGCTTTGGAAA 61.795 55.000 0.50 0.00 39.13 3.13
1751 3800 1.335324 CGCTTTGGAAAGGTGCTTGAG 60.335 52.381 1.45 0.00 36.53 3.02
1918 4214 7.542534 TTACTGAACGTTACAACAAGATGTT 57.457 32.000 0.00 0.00 42.08 2.71
2015 4312 7.051623 TCTGTTTGACAACATAGTACAAGGTT 58.948 34.615 0.00 0.00 42.21 3.50
2016 4313 7.554835 TCTGTTTGACAACATAGTACAAGGTTT 59.445 33.333 0.00 0.00 42.21 3.27
2031 4328 8.406297 AGTACAAGGTTTTCTTCAATTTCTCAC 58.594 33.333 0.00 0.00 32.41 3.51
2066 4363 2.559698 TGCAGCTACCTAGTGCAAAA 57.440 45.000 2.70 0.00 44.05 2.44
2104 4409 8.523915 TTGTCCTAATATGAAACTGATGCAAT 57.476 30.769 0.00 0.00 0.00 3.56
2105 4410 8.158169 TGTCCTAATATGAAACTGATGCAATC 57.842 34.615 0.00 0.00 45.83 2.67
2121 4426 3.508402 TGCAATCACTGATCAGCATTGTT 59.492 39.130 30.45 15.35 35.78 2.83
2127 4432 4.214758 TCACTGATCAGCATTGTTTGAGTG 59.785 41.667 22.83 9.51 0.00 3.51
2133 4438 2.220133 CAGCATTGTTTGAGTGCTTTGC 59.780 45.455 0.00 0.00 46.29 3.68
2166 4472 5.045869 AGAGCTTACCTTGTGCTAACCATAA 60.046 40.000 0.00 0.00 37.16 1.90
2281 4597 1.209747 ACCCGAAGTCTATCAAAGCCC 59.790 52.381 0.00 0.00 0.00 5.19
2283 4599 2.555199 CCGAAGTCTATCAAAGCCCAG 58.445 52.381 0.00 0.00 0.00 4.45
2309 4625 6.561519 ACCATACAAGGTCAGCTATACTTT 57.438 37.500 0.00 0.00 37.28 2.66
2412 4729 2.554893 TCACCAAATTAACAAGCCGACC 59.445 45.455 0.00 0.00 0.00 4.79
2425 4742 2.858745 AGCCGACCTACAAACATGTTT 58.141 42.857 18.13 18.13 0.00 2.83
2428 4745 5.007682 AGCCGACCTACAAACATGTTTAAT 58.992 37.500 22.87 16.18 0.00 1.40
2484 4802 1.259609 TGTGGTCTCCCGTAAATCGT 58.740 50.000 0.00 0.00 37.94 3.73
2489 4807 2.424956 GGTCTCCCGTAAATCGTACAGT 59.575 50.000 0.00 0.00 37.94 3.55
2491 4809 3.855950 GTCTCCCGTAAATCGTACAGTTG 59.144 47.826 0.00 0.00 37.94 3.16
2514 4832 9.787532 GTTGTAATATGCAACTTTATCACACAT 57.212 29.630 13.20 0.00 41.94 3.21
2531 4850 2.294233 CACATTCACACCCTCAAACCAG 59.706 50.000 0.00 0.00 0.00 4.00
2544 4863 7.993183 CACCCTCAAACCAGACATACTAATTAT 59.007 37.037 0.00 0.00 0.00 1.28
2573 4892 4.847990 AGGGGTAAAATCGATACAACCA 57.152 40.909 19.06 0.00 0.00 3.67
2598 4918 4.003011 TTTTTGACCGCGCCGTCG 62.003 61.111 21.08 0.00 35.40 5.12
2615 4967 2.159612 CGTCGGTCGATCTGTTTCACTA 60.160 50.000 0.00 0.00 42.86 2.74
2650 5004 2.348362 TCGCAGCTAATCAACAATGTCG 59.652 45.455 0.00 0.00 0.00 4.35
2723 5078 7.290813 TCTAGTCATGCTAGGTTGATCTAGAA 58.709 38.462 18.22 0.00 45.55 2.10
2739 5095 5.933846 TCTAGAATCTACCTAGCCTTCCT 57.066 43.478 0.00 0.00 34.94 3.36
2752 5108 0.598680 CCTTCCTTGATCTAGGCGCG 60.599 60.000 17.41 0.00 35.15 6.86
2754 5110 0.385751 TTCCTTGATCTAGGCGCGAG 59.614 55.000 17.41 0.00 35.15 5.03
2768 5124 2.696076 CGCGAGCATGTAGTACAAAC 57.304 50.000 7.16 2.47 0.00 2.93
2769 5125 1.989864 CGCGAGCATGTAGTACAAACA 59.010 47.619 7.16 3.84 0.00 2.83
2770 5126 2.603110 CGCGAGCATGTAGTACAAACAT 59.397 45.455 7.16 7.78 38.08 2.71
2785 5141 7.045416 AGTACAAACATGACTACTGAAACACA 58.955 34.615 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 168 2.257371 CGACCGCGACTTCCTTGA 59.743 61.111 8.23 0.00 40.82 3.02
193 195 1.961180 AACTTGGCGATCTCCTCCGG 61.961 60.000 2.88 0.00 0.00 5.14
195 197 0.462759 CCAACTTGGCGATCTCCTCC 60.463 60.000 2.88 0.00 0.00 4.30
198 200 1.084370 CGTCCAACTTGGCGATCTCC 61.084 60.000 15.48 0.00 38.63 3.71
200 202 1.741770 GCGTCCAACTTGGCGATCT 60.742 57.895 21.49 0.00 38.63 2.75
201 203 1.970917 CTGCGTCCAACTTGGCGATC 61.971 60.000 21.49 10.20 38.63 3.69
203 205 2.652382 TTCTGCGTCCAACTTGGCGA 62.652 55.000 21.49 10.44 38.63 5.54
204 206 2.175184 CTTCTGCGTCCAACTTGGCG 62.175 60.000 15.97 15.97 37.47 5.69
205 207 1.576421 CTTCTGCGTCCAACTTGGC 59.424 57.895 2.52 0.00 37.47 4.52
217 219 1.691215 CTCTTCTTCGCCGCTTCTGC 61.691 60.000 0.00 0.00 0.00 4.26
218 220 1.080995 CCTCTTCTTCGCCGCTTCTG 61.081 60.000 0.00 0.00 0.00 3.02
220 222 0.804156 CTCCTCTTCTTCGCCGCTTC 60.804 60.000 0.00 0.00 0.00 3.86
222 224 2.888863 CTCCTCTTCTTCGCCGCT 59.111 61.111 0.00 0.00 0.00 5.52
223 225 2.888051 GCTCCTCTTCTTCGCCGC 60.888 66.667 0.00 0.00 0.00 6.53
225 227 2.202810 CGGCTCCTCTTCTTCGCC 60.203 66.667 0.00 0.00 37.40 5.54
227 229 1.032657 TCTCCGGCTCCTCTTCTTCG 61.033 60.000 0.00 0.00 0.00 3.79
228 230 0.744281 CTCTCCGGCTCCTCTTCTTC 59.256 60.000 0.00 0.00 0.00 2.87
231 233 2.015227 CTGCTCTCCGGCTCCTCTTC 62.015 65.000 0.00 0.00 0.00 2.87
232 234 2.038007 TGCTCTCCGGCTCCTCTT 59.962 61.111 0.00 0.00 0.00 2.85
233 235 2.441901 CTGCTCTCCGGCTCCTCT 60.442 66.667 0.00 0.00 0.00 3.69
234 236 2.757917 ACTGCTCTCCGGCTCCTC 60.758 66.667 0.00 0.00 0.00 3.71
235 237 2.757917 GACTGCTCTCCGGCTCCT 60.758 66.667 0.00 0.00 0.00 3.69
236 238 4.200283 CGACTGCTCTCCGGCTCC 62.200 72.222 0.00 0.00 0.00 4.70
237 239 3.404141 GACGACTGCTCTCCGGCTC 62.404 68.421 0.00 0.00 0.00 4.70
238 240 3.444805 GACGACTGCTCTCCGGCT 61.445 66.667 0.00 0.00 0.00 5.52
241 243 1.153939 CCTTGACGACTGCTCTCCG 60.154 63.158 0.00 0.00 0.00 4.63
242 244 0.109039 GACCTTGACGACTGCTCTCC 60.109 60.000 0.00 0.00 0.00 3.71
243 245 0.598562 TGACCTTGACGACTGCTCTC 59.401 55.000 0.00 0.00 0.00 3.20
244 246 1.040646 TTGACCTTGACGACTGCTCT 58.959 50.000 0.00 0.00 0.00 4.09
245 247 1.728971 CATTGACCTTGACGACTGCTC 59.271 52.381 0.00 0.00 0.00 4.26
248 250 0.798776 GGCATTGACCTTGACGACTG 59.201 55.000 0.00 0.00 0.00 3.51
249 251 3.233355 GGCATTGACCTTGACGACT 57.767 52.632 0.00 0.00 0.00 4.18
253 255 2.877691 GGCGGCATTGACCTTGAC 59.122 61.111 3.07 0.00 0.00 3.18
255 257 4.481112 GCGGCGGCATTGACCTTG 62.481 66.667 9.78 0.00 39.62 3.61
274 276 3.423154 CTCGGTGGCGAACTTGGC 61.423 66.667 0.00 0.00 0.00 4.52
275 277 3.423154 GCTCGGTGGCGAACTTGG 61.423 66.667 0.00 0.00 0.00 3.61
325 327 3.839432 CTCCTTCTCGTCGGCCCC 61.839 72.222 0.00 0.00 0.00 5.80
327 329 1.668101 ATGTCTCCTTCTCGTCGGCC 61.668 60.000 0.00 0.00 0.00 6.13
328 330 0.248702 GATGTCTCCTTCTCGTCGGC 60.249 60.000 0.00 0.00 0.00 5.54
329 331 0.028242 CGATGTCTCCTTCTCGTCGG 59.972 60.000 0.00 0.00 37.09 4.79
330 332 0.727970 ACGATGTCTCCTTCTCGTCG 59.272 55.000 0.00 0.00 40.00 5.12
333 335 2.095212 TGTTGACGATGTCTCCTTCTCG 60.095 50.000 0.00 0.00 37.17 4.04
334 336 3.577649 TGTTGACGATGTCTCCTTCTC 57.422 47.619 0.00 0.00 33.15 2.87
335 337 4.202264 ACTTTGTTGACGATGTCTCCTTCT 60.202 41.667 0.00 0.00 33.15 2.85
337 339 3.809832 CACTTTGTTGACGATGTCTCCTT 59.190 43.478 0.00 0.00 33.15 3.36
340 342 2.543848 TGCACTTTGTTGACGATGTCTC 59.456 45.455 0.00 0.00 33.15 3.36
341 343 2.287915 GTGCACTTTGTTGACGATGTCT 59.712 45.455 10.32 0.00 33.15 3.41
342 344 2.639751 GTGCACTTTGTTGACGATGTC 58.360 47.619 10.32 0.00 0.00 3.06
343 345 1.003972 CGTGCACTTTGTTGACGATGT 60.004 47.619 16.19 0.00 31.71 3.06
345 347 0.041312 GCGTGCACTTTGTTGACGAT 60.041 50.000 16.19 0.00 31.71 3.73
346 348 1.350319 GCGTGCACTTTGTTGACGA 59.650 52.632 16.19 0.00 31.71 4.20
347 349 1.654137 GGCGTGCACTTTGTTGACG 60.654 57.895 16.19 0.00 0.00 4.35
348 350 1.299089 GGGCGTGCACTTTGTTGAC 60.299 57.895 16.19 0.00 0.00 3.18
349 351 1.444119 GAGGGCGTGCACTTTGTTGA 61.444 55.000 16.19 0.00 0.00 3.18
353 355 2.281761 AGGAGGGCGTGCACTTTG 60.282 61.111 16.19 0.00 0.00 2.77
354 356 2.032681 GAGGAGGGCGTGCACTTT 59.967 61.111 16.19 0.00 0.00 2.66
355 357 2.596851 ATGAGGAGGGCGTGCACTT 61.597 57.895 16.19 0.00 0.00 3.16
357 359 2.821366 CATGAGGAGGGCGTGCAC 60.821 66.667 6.82 6.82 0.00 4.57
360 362 2.110967 CAAGCATGAGGAGGGCGTG 61.111 63.158 0.00 0.00 0.00 5.34
362 364 2.515523 CCAAGCATGAGGAGGGCG 60.516 66.667 0.00 0.00 0.00 6.13
363 365 1.452833 GTCCAAGCATGAGGAGGGC 60.453 63.158 0.00 0.00 33.85 5.19
364 366 1.153289 CGTCCAAGCATGAGGAGGG 60.153 63.158 0.00 0.00 36.43 4.30
365 367 0.742281 CACGTCCAAGCATGAGGAGG 60.742 60.000 15.83 15.83 43.53 4.30
366 368 0.036952 ACACGTCCAAGCATGAGGAG 60.037 55.000 0.00 0.00 33.85 3.69
368 370 1.645034 CTACACGTCCAAGCATGAGG 58.355 55.000 0.00 0.00 0.00 3.86
369 371 1.645034 CCTACACGTCCAAGCATGAG 58.355 55.000 0.00 0.00 0.00 2.90
371 373 1.369091 GGCCTACACGTCCAAGCATG 61.369 60.000 0.00 0.00 0.00 4.06
372 374 1.078426 GGCCTACACGTCCAAGCAT 60.078 57.895 0.00 0.00 0.00 3.79
374 376 2.813908 CGGCCTACACGTCCAAGC 60.814 66.667 0.00 0.00 0.00 4.01
375 377 2.813908 GCGGCCTACACGTCCAAG 60.814 66.667 0.00 0.00 0.00 3.61
376 378 3.307906 AGCGGCCTACACGTCCAA 61.308 61.111 0.00 0.00 0.00 3.53
377 379 4.063967 CAGCGGCCTACACGTCCA 62.064 66.667 0.00 0.00 0.00 4.02
378 380 4.814294 CCAGCGGCCTACACGTCC 62.814 72.222 0.00 0.00 0.00 4.79
395 397 3.267597 ATCACGCCGGCAACAAAGC 62.268 57.895 28.98 0.00 0.00 3.51
396 398 1.442520 CATCACGCCGGCAACAAAG 60.443 57.895 28.98 11.60 0.00 2.77
397 399 1.448119 TTCATCACGCCGGCAACAAA 61.448 50.000 28.98 9.55 0.00 2.83
400 402 1.017177 TAGTTCATCACGCCGGCAAC 61.017 55.000 28.98 21.22 0.00 4.17
401 403 0.739462 CTAGTTCATCACGCCGGCAA 60.739 55.000 28.98 11.85 0.00 4.52
402 404 1.153647 CTAGTTCATCACGCCGGCA 60.154 57.895 28.98 7.49 0.00 5.69
403 405 1.883084 CCTAGTTCATCACGCCGGC 60.883 63.158 19.07 19.07 0.00 6.13
404 406 1.227263 CCCTAGTTCATCACGCCGG 60.227 63.158 0.00 0.00 0.00 6.13
405 407 1.883084 GCCCTAGTTCATCACGCCG 60.883 63.158 0.00 0.00 0.00 6.46
406 408 1.523938 GGCCCTAGTTCATCACGCC 60.524 63.158 0.00 0.00 0.00 5.68
408 410 0.179073 CCAGGCCCTAGTTCATCACG 60.179 60.000 0.00 0.00 0.00 4.35
414 416 1.106285 CAAATGCCAGGCCCTAGTTC 58.894 55.000 9.64 0.00 0.00 3.01
415 417 0.704076 TCAAATGCCAGGCCCTAGTT 59.296 50.000 9.64 0.00 0.00 2.24
416 418 0.704076 TTCAAATGCCAGGCCCTAGT 59.296 50.000 9.64 0.00 0.00 2.57
417 419 1.478105 GTTTCAAATGCCAGGCCCTAG 59.522 52.381 9.64 0.00 0.00 3.02
419 421 1.535204 CGTTTCAAATGCCAGGCCCT 61.535 55.000 9.64 0.00 0.00 5.19
420 422 1.079888 CGTTTCAAATGCCAGGCCC 60.080 57.895 9.64 0.00 0.00 5.80
421 423 0.033366 AACGTTTCAAATGCCAGGCC 59.967 50.000 9.64 0.00 0.00 5.19
422 424 1.139163 CAACGTTTCAAATGCCAGGC 58.861 50.000 3.66 3.66 0.00 4.85
423 425 1.139163 GCAACGTTTCAAATGCCAGG 58.861 50.000 0.00 0.00 32.73 4.45
424 426 2.053627 GAGCAACGTTTCAAATGCCAG 58.946 47.619 0.00 0.00 39.59 4.85
426 428 2.422276 AGAGCAACGTTTCAAATGCC 57.578 45.000 0.00 0.00 39.59 4.40
427 429 4.777140 AAAAGAGCAACGTTTCAAATGC 57.223 36.364 0.00 0.00 39.06 3.56
448 450 6.402766 CCATCCTGTTCGCGTCTATTTAAAAA 60.403 38.462 5.77 0.00 0.00 1.94
449 451 5.064198 CCATCCTGTTCGCGTCTATTTAAAA 59.936 40.000 5.77 0.00 0.00 1.52
450 452 4.569162 CCATCCTGTTCGCGTCTATTTAAA 59.431 41.667 5.77 0.00 0.00 1.52
452 454 3.491964 CCCATCCTGTTCGCGTCTATTTA 60.492 47.826 5.77 0.00 0.00 1.40
454 456 1.202533 CCCATCCTGTTCGCGTCTATT 60.203 52.381 5.77 0.00 0.00 1.73
455 457 0.389391 CCCATCCTGTTCGCGTCTAT 59.611 55.000 5.77 0.00 0.00 1.98
456 458 1.672854 CCCCATCCTGTTCGCGTCTA 61.673 60.000 5.77 0.00 0.00 2.59
458 460 2.511600 CCCCATCCTGTTCGCGTC 60.512 66.667 5.77 1.06 0.00 5.19
461 463 1.976474 TTTGCCCCATCCTGTTCGC 60.976 57.895 0.00 0.00 0.00 4.70
462 464 1.883021 GTTTGCCCCATCCTGTTCG 59.117 57.895 0.00 0.00 0.00 3.95
463 465 1.595093 CCGTTTGCCCCATCCTGTTC 61.595 60.000 0.00 0.00 0.00 3.18
464 466 1.606313 CCGTTTGCCCCATCCTGTT 60.606 57.895 0.00 0.00 0.00 3.16
465 467 1.863155 ATCCGTTTGCCCCATCCTGT 61.863 55.000 0.00 0.00 0.00 4.00
466 468 1.076777 ATCCGTTTGCCCCATCCTG 60.077 57.895 0.00 0.00 0.00 3.86
468 470 2.785425 GCATCCGTTTGCCCCATCC 61.785 63.158 0.00 0.00 36.60 3.51
469 471 2.807622 GCATCCGTTTGCCCCATC 59.192 61.111 0.00 0.00 36.60 3.51
470 472 3.140141 CGCATCCGTTTGCCCCAT 61.140 61.111 1.70 0.00 39.52 4.00
473 475 3.810896 GGTCGCATCCGTTTGCCC 61.811 66.667 1.70 0.00 39.52 5.36
474 476 3.053291 TGGTCGCATCCGTTTGCC 61.053 61.111 1.70 0.00 39.52 4.52
475 477 2.175811 GTGGTCGCATCCGTTTGC 59.824 61.111 0.00 0.00 39.29 3.68
514 516 2.762969 TTTGGGCGTGTCCTGGGATG 62.763 60.000 0.00 0.00 34.39 3.51
515 517 2.534396 TTTGGGCGTGTCCTGGGAT 61.534 57.895 0.00 0.00 34.39 3.85
516 518 3.172106 TTTGGGCGTGTCCTGGGA 61.172 61.111 0.00 0.00 34.39 4.37
517 519 2.983592 GTTTGGGCGTGTCCTGGG 60.984 66.667 0.00 0.00 34.39 4.45
518 520 2.203280 TGTTTGGGCGTGTCCTGG 60.203 61.111 0.00 0.00 34.39 4.45
519 521 1.525995 AGTGTTTGGGCGTGTCCTG 60.526 57.895 0.00 0.00 34.39 3.86
520 522 1.525995 CAGTGTTTGGGCGTGTCCT 60.526 57.895 0.00 0.00 34.39 3.85
521 523 3.030652 CAGTGTTTGGGCGTGTCC 58.969 61.111 0.00 0.00 0.00 4.02
522 524 2.331451 GCAGTGTTTGGGCGTGTC 59.669 61.111 0.00 0.00 0.00 3.67
523 525 3.216292 GGCAGTGTTTGGGCGTGT 61.216 61.111 0.00 0.00 0.00 4.49
524 526 3.977244 GGGCAGTGTTTGGGCGTG 61.977 66.667 0.00 0.00 0.00 5.34
527 529 2.216331 AATGGGGCAGTGTTTGGGC 61.216 57.895 0.00 0.00 0.00 5.36
528 530 1.672898 CAATGGGGCAGTGTTTGGG 59.327 57.895 0.00 0.00 0.00 4.12
529 531 1.004679 GCAATGGGGCAGTGTTTGG 60.005 57.895 0.00 0.00 31.72 3.28
531 533 0.178953 AGAGCAATGGGGCAGTGTTT 60.179 50.000 0.00 0.00 31.72 2.83
532 534 0.698238 TAGAGCAATGGGGCAGTGTT 59.302 50.000 0.00 0.00 31.72 3.32
534 536 1.602311 GATAGAGCAATGGGGCAGTG 58.398 55.000 0.00 0.00 35.83 3.66
535 537 0.475906 GGATAGAGCAATGGGGCAGT 59.524 55.000 0.00 0.00 35.83 4.40
536 538 0.475475 TGGATAGAGCAATGGGGCAG 59.525 55.000 0.00 0.00 35.83 4.85
537 539 0.925558 TTGGATAGAGCAATGGGGCA 59.074 50.000 0.00 0.00 35.83 5.36
538 540 1.683385 GTTTGGATAGAGCAATGGGGC 59.317 52.381 0.00 0.00 0.00 5.80
539 541 1.949525 CGTTTGGATAGAGCAATGGGG 59.050 52.381 0.00 0.00 0.00 4.96
540 542 1.949525 CCGTTTGGATAGAGCAATGGG 59.050 52.381 0.00 0.00 37.49 4.00
541 543 2.917933 TCCGTTTGGATAGAGCAATGG 58.082 47.619 0.00 0.00 40.17 3.16
553 555 1.738099 CCGAGCTCTGTCCGTTTGG 60.738 63.158 12.85 0.00 0.00 3.28
554 556 0.108615 ATCCGAGCTCTGTCCGTTTG 60.109 55.000 12.85 0.00 0.00 2.93
555 557 1.471119 TATCCGAGCTCTGTCCGTTT 58.529 50.000 12.85 0.00 0.00 3.60
558 560 2.194271 GTTTTATCCGAGCTCTGTCCG 58.806 52.381 12.85 0.00 0.00 4.79
560 562 2.159282 TCCGTTTTATCCGAGCTCTGTC 60.159 50.000 12.85 0.00 0.00 3.51
561 563 1.822990 TCCGTTTTATCCGAGCTCTGT 59.177 47.619 12.85 0.00 0.00 3.41
562 564 2.194271 GTCCGTTTTATCCGAGCTCTG 58.806 52.381 12.85 5.31 0.00 3.35
564 566 1.197910 CGTCCGTTTTATCCGAGCTC 58.802 55.000 2.73 2.73 0.00 4.09
565 567 0.529378 ACGTCCGTTTTATCCGAGCT 59.471 50.000 0.00 0.00 0.00 4.09
567 569 1.553308 GGACGTCCGTTTTATCCGAG 58.447 55.000 20.85 0.00 0.00 4.63
568 570 3.719699 GGACGTCCGTTTTATCCGA 57.280 52.632 20.85 0.00 0.00 4.55
579 581 2.357881 GACCCCAAACGGACGTCC 60.358 66.667 25.28 25.28 0.00 4.79
580 582 2.735857 CGACCCCAAACGGACGTC 60.736 66.667 7.13 7.13 0.00 4.34
581 583 4.974989 GCGACCCCAAACGGACGT 62.975 66.667 0.00 0.00 34.99 4.34
598 600 3.599285 TAAGGCCAACTCCACCGCG 62.599 63.158 5.01 0.00 0.00 6.46
599 601 2.038837 GTAAGGCCAACTCCACCGC 61.039 63.158 5.01 0.00 0.00 5.68
600 602 0.391263 GAGTAAGGCCAACTCCACCG 60.391 60.000 21.84 0.00 37.91 4.94
601 603 0.391263 CGAGTAAGGCCAACTCCACC 60.391 60.000 24.73 8.15 40.24 4.61
604 606 4.934989 CCGAGTAAGGCCAACTCC 57.065 61.111 24.73 12.46 40.24 3.85
621 623 0.321298 TGAACAAGGCGGAGTAAGGC 60.321 55.000 0.00 0.00 0.00 4.35
622 624 2.178912 TTGAACAAGGCGGAGTAAGG 57.821 50.000 0.00 0.00 0.00 2.69
623 625 2.484264 CCTTTGAACAAGGCGGAGTAAG 59.516 50.000 0.00 0.00 0.00 2.34
624 626 2.500229 CCTTTGAACAAGGCGGAGTAA 58.500 47.619 0.00 0.00 0.00 2.24
628 630 0.766131 TACCCTTTGAACAAGGCGGA 59.234 50.000 9.63 0.00 36.10 5.54
629 631 1.165270 CTACCCTTTGAACAAGGCGG 58.835 55.000 0.00 0.00 36.10 6.13
630 632 2.178912 TCTACCCTTTGAACAAGGCG 57.821 50.000 0.00 0.00 36.10 5.52
631 633 4.336280 AGATTCTACCCTTTGAACAAGGC 58.664 43.478 0.00 0.00 36.10 4.35
633 635 8.792830 TGATTAGATTCTACCCTTTGAACAAG 57.207 34.615 0.00 0.00 0.00 3.16
639 641 9.442047 GGACATATGATTAGATTCTACCCTTTG 57.558 37.037 10.38 0.00 0.00 2.77
642 644 6.954684 ACGGACATATGATTAGATTCTACCCT 59.045 38.462 10.38 0.00 0.00 4.34
643 645 7.171630 ACGGACATATGATTAGATTCTACCC 57.828 40.000 10.38 0.00 0.00 3.69
644 646 6.967767 CGACGGACATATGATTAGATTCTACC 59.032 42.308 10.38 0.00 0.00 3.18
645 647 6.967767 CCGACGGACATATGATTAGATTCTAC 59.032 42.308 8.64 0.00 0.00 2.59
646 648 6.657966 ACCGACGGACATATGATTAGATTCTA 59.342 38.462 23.38 0.00 0.00 2.10
647 649 5.477291 ACCGACGGACATATGATTAGATTCT 59.523 40.000 23.38 0.00 0.00 2.40
648 650 5.573282 CACCGACGGACATATGATTAGATTC 59.427 44.000 23.38 0.00 0.00 2.52
650 652 4.082190 CCACCGACGGACATATGATTAGAT 60.082 45.833 23.38 0.00 0.00 1.98
651 653 3.254903 CCACCGACGGACATATGATTAGA 59.745 47.826 23.38 0.00 0.00 2.10
652 654 3.254903 TCCACCGACGGACATATGATTAG 59.745 47.826 23.38 0.44 0.00 1.73
653 655 3.224269 TCCACCGACGGACATATGATTA 58.776 45.455 23.38 0.00 0.00 1.75
821 844 4.088762 CGTGTGGGTGCGCATCAC 62.089 66.667 28.34 28.34 44.90 3.06
850 873 2.653115 GCAGGGCAGCTTGGAAAC 59.347 61.111 0.00 0.00 0.00 2.78
868 894 2.366167 AGGGTAGGAGGCAGCCAG 60.366 66.667 15.80 0.00 35.96 4.85
904 992 0.108615 GTGGTGTGGAGGAGACGATG 60.109 60.000 0.00 0.00 0.00 3.84
918 1006 0.603065 TGAGACGAGATGTGGTGGTG 59.397 55.000 0.00 0.00 0.00 4.17
919 1007 1.478510 GATGAGACGAGATGTGGTGGT 59.521 52.381 0.00 0.00 0.00 4.16
920 1008 1.753649 AGATGAGACGAGATGTGGTGG 59.246 52.381 0.00 0.00 0.00 4.61
932 1020 1.989165 GCAAGACGTGTGAGATGAGAC 59.011 52.381 0.00 0.00 0.00 3.36
998 1089 1.734465 GACCGAAGTTGAGAGCCATTG 59.266 52.381 0.00 0.00 0.00 2.82
1092 1186 2.686106 TGGGAGGAGGCGTTACCC 60.686 66.667 0.00 0.00 40.58 3.69
1095 1189 2.686106 GGGTGGGAGGAGGCGTTA 60.686 66.667 0.00 0.00 0.00 3.18
1231 1800 2.364961 CGGGAGGAGGAGGAGGTT 59.635 66.667 0.00 0.00 0.00 3.50
1344 1914 0.894835 TGAGCGACATAAGGCACTCA 59.105 50.000 0.00 0.00 38.49 3.41
1353 1923 2.202743 GCGTGCCTGAGCGACATA 60.203 61.111 0.00 0.00 44.31 2.29
1627 2197 4.814294 GGAAGATGACGCCGCGGT 62.814 66.667 28.70 7.71 0.00 5.68
1735 3766 0.179032 TCGCTCAAGCACCTTTCCAA 60.179 50.000 2.50 0.00 42.21 3.53
1741 3772 2.358003 GCACTCGCTCAAGCACCT 60.358 61.111 2.50 0.00 42.21 4.00
2055 4352 8.658609 CAAATTATTCCATTGTTTTGCACTAGG 58.341 33.333 0.00 0.00 0.00 3.02
2092 4397 4.142447 GCTGATCAGTGATTGCATCAGTTT 60.142 41.667 23.38 0.83 40.85 2.66
2104 4409 4.214758 CACTCAAACAATGCTGATCAGTGA 59.785 41.667 23.38 15.39 42.95 3.41
2105 4410 4.473199 CACTCAAACAATGCTGATCAGTG 58.527 43.478 23.38 16.06 45.52 3.66
2121 4426 1.742831 ACGAAACAGCAAAGCACTCAA 59.257 42.857 0.00 0.00 0.00 3.02
2127 4432 1.801178 AGCTCTACGAAACAGCAAAGC 59.199 47.619 0.00 0.00 35.46 3.51
2133 4438 4.386049 CACAAGGTAAGCTCTACGAAACAG 59.614 45.833 0.00 0.00 0.00 3.16
2166 4472 2.779430 TGCTCATCATTATGGTCACCCT 59.221 45.455 0.00 0.00 33.61 4.34
2366 4682 4.500499 AGCTTCACAATAGCTTGGAGAT 57.500 40.909 0.00 0.00 46.42 2.75
2387 4703 6.383415 GTCGGCTTGTTAATTTGGTGAATTA 58.617 36.000 0.00 0.00 38.80 1.40
2388 4704 5.227152 GTCGGCTTGTTAATTTGGTGAATT 58.773 37.500 0.00 0.00 40.88 2.17
2402 4718 2.151202 CATGTTTGTAGGTCGGCTTGT 58.849 47.619 0.00 0.00 0.00 3.16
2438 4756 7.671398 AGAACAGAGGTGTGATTAAATTGGAAT 59.329 33.333 0.00 0.00 36.84 3.01
2439 4757 7.004086 AGAACAGAGGTGTGATTAAATTGGAA 58.996 34.615 0.00 0.00 36.84 3.53
2440 4758 6.542821 AGAACAGAGGTGTGATTAAATTGGA 58.457 36.000 0.00 0.00 36.84 3.53
2441 4759 6.824305 AGAACAGAGGTGTGATTAAATTGG 57.176 37.500 0.00 0.00 36.84 3.16
2442 4760 7.592533 CACAAGAACAGAGGTGTGATTAAATTG 59.407 37.037 0.00 0.00 43.23 2.32
2505 4823 4.632327 TTGAGGGTGTGAATGTGTGATA 57.368 40.909 0.00 0.00 0.00 2.15
2514 4832 1.562008 TGTCTGGTTTGAGGGTGTGAA 59.438 47.619 0.00 0.00 0.00 3.18
2531 4850 8.218488 ACCCCTTCTTGGAATAATTAGTATGTC 58.782 37.037 0.00 0.00 38.35 3.06
2544 4863 4.644163 TCGATTTTACCCCTTCTTGGAA 57.356 40.909 0.00 0.00 38.35 3.53
2573 4892 2.353579 GGCGCGGTCAAAAACATATAGT 59.646 45.455 8.83 0.00 0.00 2.12
2598 4918 5.869888 AGTCAATTAGTGAAACAGATCGACC 59.130 40.000 0.00 0.00 41.43 4.79
2615 4967 4.510038 AGCTGCGATTTCAAAGTCAATT 57.490 36.364 0.00 0.00 0.00 2.32
2650 5004 2.436173 CAAGATTCCTAGTGTCCCCTCC 59.564 54.545 0.00 0.00 0.00 4.30
2723 5078 5.086598 AGATCAAGGAAGGCTAGGTAGAT 57.913 43.478 0.00 0.00 0.00 1.98
2739 5095 0.598419 CATGCTCGCGCCTAGATCAA 60.598 55.000 0.00 0.00 34.43 2.57
2761 5117 7.241663 TGTGTTTCAGTAGTCATGTTTGTAC 57.758 36.000 0.00 0.00 0.00 2.90
2762 5118 7.477144 CTGTGTTTCAGTAGTCATGTTTGTA 57.523 36.000 0.00 0.00 39.17 2.41
2779 5135 7.807977 ATATCAGTGTCAGAAAACTGTGTTT 57.192 32.000 12.27 0.00 43.49 2.83
2810 5168 8.342634 GCGGTTTAACATCATAGTTGATACATT 58.657 33.333 0.00 0.00 40.70 2.71


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

AutoCloner maintained by Alex Coulton.