Multiple sequence alignment - TraesCS2B01G234900

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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 TraesCS2B01G234900 chr2B 100.000 2525 0 0 742 3266 234369712 234367188 0.000000e+00 4663.0
1 TraesCS2B01G234900 chr2B 100.000 354 0 0 1 354 234370453 234370100 0.000000e+00 654.0
2 TraesCS2B01G234900 chr2B 96.498 257 1 2 98 354 234369712 234369464 5.040000e-113 418.0
3 TraesCS2B01G234900 chr2B 96.498 257 1 2 742 990 234370356 234370100 5.040000e-113 418.0
4 TraesCS2B01G234900 chr2B 82.663 398 49 10 2493 2882 286985715 286985330 5.220000e-88 335.0
5 TraesCS2B01G234900 chr2D 94.293 1682 51 18 804 2469 177461805 177460153 0.000000e+00 2532.0
6 TraesCS2B01G234900 chr2D 86.478 636 63 17 2483 3103 177460093 177459466 0.000000e+00 676.0
7 TraesCS2B01G234900 chr2D 87.313 402 39 8 2493 2885 633320460 633320858 1.790000e-122 449.0
8 TraesCS2B01G234900 chr2D 81.679 393 53 13 2493 2878 262450184 262450564 3.160000e-80 309.0
9 TraesCS2B01G234900 chr2D 92.800 125 8 1 3138 3261 177459082 177458958 2.590000e-41 180.0
10 TraesCS2B01G234900 chr2D 93.548 62 4 0 2878 2939 633320872 633320933 3.470000e-15 93.5
11 TraesCS2B01G234900 chr2A 97.813 1463 32 0 1007 2469 190319040 190317578 0.000000e+00 2525.0
12 TraesCS2B01G234900 chr2A 89.950 806 52 13 2483 3261 190317518 190316715 0.000000e+00 1013.0
13 TraesCS2B01G234900 chr6D 81.305 567 70 18 2493 3024 175718544 175717979 8.370000e-116 427.0
14 TraesCS2B01G234900 chr6B 86.047 387 51 3 2493 2877 291775816 291775431 2.340000e-111 412.0
15 TraesCS2B01G234900 chr6B 77.183 355 29 22 2714 3028 409293514 409293172 3.370000e-35 159.0
16 TraesCS2B01G234900 chr3A 90.370 270 23 3 2492 2759 555414668 555414936 5.180000e-93 351.0
17 TraesCS2B01G234900 chr3B 89.531 277 21 6 2492 2762 150947035 150946761 8.680000e-91 344.0
18 TraesCS2B01G234900 chr4B 83.806 247 29 8 2648 2885 181507806 181507562 1.180000e-54 224.0
19 TraesCS2B01G234900 chr4D 84.685 222 25 6 2672 2885 119284546 119284326 2.550000e-51 213.0
20 TraesCS2B01G234900 chr5B 82.819 227 33 5 3038 3261 212396776 212396553 7.150000e-47 198.0


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 TraesCS2B01G234900 chr2B 234367188 234370453 3265 True 1538.250000 4663 98.249000 1 3266 4 chr2B.!!$R2 3265
1 TraesCS2B01G234900 chr2D 177458958 177461805 2847 True 1129.333333 2532 91.190333 804 3261 3 chr2D.!!$R1 2457
2 TraesCS2B01G234900 chr2A 190316715 190319040 2325 True 1769.000000 2525 93.881500 1007 3261 2 chr2A.!!$R1 2254
3 TraesCS2B01G234900 chr6D 175717979 175718544 565 True 427.000000 427 81.305000 2493 3024 1 chr6D.!!$R1 531

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
246 247 0.032267 GAAAGTCGCCGGGGAGATAG 59.968 60.0 23.26 0.0 0.0 2.08 F
311 312 0.034337 TTCACTGTTCCCCTACACGC 59.966 55.0 0.00 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 1471 0.603065 CACAGACCACGAGATCCACA 59.397 55.000 0.0 0.0 0.0 4.17 R
2453 2469 1.069296 GCGCTAAGTGATGTTGTTGCA 60.069 47.619 0.0 0.0 0.0 4.08 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
25 26 7.394870 GTGAAGCAAAATTTTCACTAGAACC 57.605 36.000 11.72 0.00 45.99 3.62
26 27 6.978080 GTGAAGCAAAATTTTCACTAGAACCA 59.022 34.615 11.72 1.84 45.99 3.67
27 28 7.491048 GTGAAGCAAAATTTTCACTAGAACCAA 59.509 33.333 11.72 0.00 45.99 3.67
28 29 8.037758 TGAAGCAAAATTTTCACTAGAACCAAA 58.962 29.630 0.00 0.00 32.39 3.28
29 30 8.962884 AAGCAAAATTTTCACTAGAACCAAAT 57.037 26.923 0.00 0.00 32.39 2.32
112 113 8.964420 CGAAGCAGAATTTTAATTAGAACCAA 57.036 30.769 0.00 0.00 0.00 3.67
113 114 9.405587 CGAAGCAGAATTTTAATTAGAACCAAA 57.594 29.630 0.00 0.00 0.00 3.28
121 122 9.996554 AATTTTAATTAGAACCAAACAAGGAGG 57.003 29.630 0.00 0.00 0.00 4.30
122 123 8.770010 TTTTAATTAGAACCAAACAAGGAGGA 57.230 30.769 0.00 0.00 0.00 3.71
123 124 8.770010 TTTAATTAGAACCAAACAAGGAGGAA 57.230 30.769 0.00 0.00 0.00 3.36
124 125 8.950007 TTAATTAGAACCAAACAAGGAGGAAT 57.050 30.769 0.00 0.00 0.00 3.01
125 126 7.855784 AATTAGAACCAAACAAGGAGGAATT 57.144 32.000 0.00 0.00 0.00 2.17
126 127 6.894339 TTAGAACCAAACAAGGAGGAATTC 57.106 37.500 0.00 0.00 0.00 2.17
127 128 5.066913 AGAACCAAACAAGGAGGAATTCT 57.933 39.130 5.23 0.00 0.00 2.40
128 129 5.073428 AGAACCAAACAAGGAGGAATTCTC 58.927 41.667 5.23 1.17 41.71 2.87
129 130 3.412386 ACCAAACAAGGAGGAATTCTCG 58.588 45.455 5.23 0.00 43.34 4.04
130 131 3.181443 ACCAAACAAGGAGGAATTCTCGT 60.181 43.478 5.23 0.38 43.34 4.18
132 133 4.278419 CCAAACAAGGAGGAATTCTCGTTT 59.722 41.667 5.23 4.05 45.16 3.60
133 134 5.472137 CCAAACAAGGAGGAATTCTCGTTTA 59.528 40.000 5.23 0.00 45.16 2.01
134 135 6.151144 CCAAACAAGGAGGAATTCTCGTTTAT 59.849 38.462 5.23 0.00 45.16 1.40
135 136 6.986904 AACAAGGAGGAATTCTCGTTTATC 57.013 37.500 5.23 0.00 45.16 1.75
136 137 6.049955 ACAAGGAGGAATTCTCGTTTATCA 57.950 37.500 5.23 0.00 45.16 2.15
137 138 6.472887 ACAAGGAGGAATTCTCGTTTATCAA 58.527 36.000 5.23 0.00 45.16 2.57
138 139 6.940298 ACAAGGAGGAATTCTCGTTTATCAAA 59.060 34.615 5.23 0.00 45.16 2.69
139 140 7.447238 ACAAGGAGGAATTCTCGTTTATCAAAA 59.553 33.333 5.23 0.00 45.16 2.44
140 141 8.462016 CAAGGAGGAATTCTCGTTTATCAAAAT 58.538 33.333 5.23 0.00 45.16 1.82
141 142 9.681062 AAGGAGGAATTCTCGTTTATCAAAATA 57.319 29.630 5.23 0.00 45.16 1.40
142 143 9.681062 AGGAGGAATTCTCGTTTATCAAAATAA 57.319 29.630 5.23 0.00 43.34 1.40
234 235 3.311486 AAAGAGCCAGAGAGAAAGTCG 57.689 47.619 0.00 0.00 0.00 4.18
235 236 0.530288 AGAGCCAGAGAGAAAGTCGC 59.470 55.000 0.00 0.00 0.00 5.19
236 237 0.459411 GAGCCAGAGAGAAAGTCGCC 60.459 60.000 0.00 0.00 0.00 5.54
237 238 1.807573 GCCAGAGAGAAAGTCGCCG 60.808 63.158 0.00 0.00 0.00 6.46
238 239 1.153745 CCAGAGAGAAAGTCGCCGG 60.154 63.158 0.00 0.00 0.00 6.13
239 240 1.153745 CAGAGAGAAAGTCGCCGGG 60.154 63.158 2.18 0.00 0.00 5.73
240 241 2.184579 GAGAGAAAGTCGCCGGGG 59.815 66.667 13.31 13.31 0.00 5.73
241 242 2.283676 AGAGAAAGTCGCCGGGGA 60.284 61.111 18.63 18.63 0.00 4.81
242 243 2.184579 GAGAAAGTCGCCGGGGAG 59.815 66.667 23.26 0.00 0.00 4.30
243 244 2.283676 AGAAAGTCGCCGGGGAGA 60.284 61.111 23.26 0.00 0.00 3.71
244 245 1.677637 GAGAAAGTCGCCGGGGAGAT 61.678 60.000 23.26 11.04 0.00 2.75
245 246 0.396695 AGAAAGTCGCCGGGGAGATA 60.397 55.000 23.26 0.00 0.00 1.98
246 247 0.032267 GAAAGTCGCCGGGGAGATAG 59.968 60.000 23.26 0.00 0.00 2.08
247 248 1.400530 AAAGTCGCCGGGGAGATAGG 61.401 60.000 23.26 0.00 0.00 2.57
248 249 2.203451 GTCGCCGGGGAGATAGGA 60.203 66.667 23.26 0.00 0.00 2.94
249 250 1.831286 GTCGCCGGGGAGATAGGAA 60.831 63.158 23.26 0.00 0.00 3.36
250 251 1.831286 TCGCCGGGGAGATAGGAAC 60.831 63.158 18.63 0.00 0.00 3.62
251 252 2.868986 CGCCGGGGAGATAGGAACC 61.869 68.421 14.46 0.00 0.00 3.62
252 253 1.459730 GCCGGGGAGATAGGAACCT 60.460 63.158 2.18 0.00 0.00 3.50
253 254 1.054978 GCCGGGGAGATAGGAACCTT 61.055 60.000 2.18 0.00 0.00 3.50
254 255 0.759346 CCGGGGAGATAGGAACCTTG 59.241 60.000 0.00 0.00 0.00 3.61
255 256 1.691482 CCGGGGAGATAGGAACCTTGA 60.691 57.143 0.00 0.00 0.00 3.02
256 257 1.413077 CGGGGAGATAGGAACCTTGAC 59.587 57.143 0.00 0.00 0.00 3.18
257 258 1.769465 GGGGAGATAGGAACCTTGACC 59.231 57.143 0.00 0.00 0.00 4.02
258 259 2.629909 GGGGAGATAGGAACCTTGACCT 60.630 54.545 0.00 0.00 39.95 3.85
259 260 2.436173 GGGAGATAGGAACCTTGACCTG 59.564 54.545 0.00 0.00 37.68 4.00
260 261 2.436173 GGAGATAGGAACCTTGACCTGG 59.564 54.545 0.00 0.00 37.68 4.45
261 262 2.436173 GAGATAGGAACCTTGACCTGGG 59.564 54.545 0.00 0.00 37.68 4.45
262 263 2.197465 GATAGGAACCTTGACCTGGGT 58.803 52.381 0.00 0.00 37.68 4.51
263 264 2.127651 TAGGAACCTTGACCTGGGTT 57.872 50.000 0.00 0.00 46.97 4.11
266 267 2.640473 AACCTTGACCTGGGTTCCA 58.360 52.632 0.00 0.00 41.38 3.53
276 277 3.786495 TGGGTTCCAGACTAGAGCA 57.214 52.632 0.00 0.00 0.00 4.26
277 278 2.024176 TGGGTTCCAGACTAGAGCAA 57.976 50.000 0.00 0.00 0.00 3.91
278 279 1.902508 TGGGTTCCAGACTAGAGCAAG 59.097 52.381 0.00 0.00 0.00 4.01
279 280 1.406205 GGGTTCCAGACTAGAGCAAGC 60.406 57.143 0.00 0.00 0.00 4.01
280 281 1.552792 GGTTCCAGACTAGAGCAAGCT 59.447 52.381 0.00 0.00 0.00 3.74
281 282 2.761208 GGTTCCAGACTAGAGCAAGCTA 59.239 50.000 0.00 0.00 0.00 3.32
282 283 3.181480 GGTTCCAGACTAGAGCAAGCTAG 60.181 52.174 0.00 6.71 42.77 3.42
283 284 2.028130 TCCAGACTAGAGCAAGCTAGC 58.972 52.381 6.62 6.62 41.21 3.42
291 292 2.865492 AGCAAGCTAGCTCCTTTGC 58.135 52.632 25.08 25.08 42.18 3.68
292 293 0.327591 AGCAAGCTAGCTCCTTTGCT 59.672 50.000 28.06 28.06 42.18 3.91
293 294 1.172175 GCAAGCTAGCTCCTTTGCTT 58.828 50.000 25.14 3.88 45.22 3.91
294 295 1.132073 GCAAGCTAGCTCCTTTGCTTC 59.868 52.381 25.14 3.84 42.89 3.86
295 296 2.430465 CAAGCTAGCTCCTTTGCTTCA 58.570 47.619 19.65 0.00 42.89 3.02
296 297 2.106477 AGCTAGCTCCTTTGCTTCAC 57.894 50.000 12.68 0.00 43.74 3.18
297 298 1.627834 AGCTAGCTCCTTTGCTTCACT 59.372 47.619 12.68 0.00 43.74 3.41
298 299 1.736681 GCTAGCTCCTTTGCTTCACTG 59.263 52.381 7.70 0.00 43.74 3.66
299 300 2.873649 GCTAGCTCCTTTGCTTCACTGT 60.874 50.000 7.70 0.00 43.74 3.55
300 301 2.355010 AGCTCCTTTGCTTCACTGTT 57.645 45.000 0.00 0.00 40.93 3.16
301 302 2.225467 AGCTCCTTTGCTTCACTGTTC 58.775 47.619 0.00 0.00 40.93 3.18
302 303 1.268079 GCTCCTTTGCTTCACTGTTCC 59.732 52.381 0.00 0.00 0.00 3.62
303 304 1.882623 CTCCTTTGCTTCACTGTTCCC 59.117 52.381 0.00 0.00 0.00 3.97
304 305 0.961753 CCTTTGCTTCACTGTTCCCC 59.038 55.000 0.00 0.00 0.00 4.81
305 306 1.479389 CCTTTGCTTCACTGTTCCCCT 60.479 52.381 0.00 0.00 0.00 4.79
306 307 2.224769 CCTTTGCTTCACTGTTCCCCTA 60.225 50.000 0.00 0.00 0.00 3.53
307 308 2.561478 TTGCTTCACTGTTCCCCTAC 57.439 50.000 0.00 0.00 0.00 3.18
308 309 1.429930 TGCTTCACTGTTCCCCTACA 58.570 50.000 0.00 0.00 0.00 2.74
309 310 1.071699 TGCTTCACTGTTCCCCTACAC 59.928 52.381 0.00 0.00 0.00 2.90
310 311 1.939838 GCTTCACTGTTCCCCTACACG 60.940 57.143 0.00 0.00 0.00 4.49
311 312 0.034337 TTCACTGTTCCCCTACACGC 59.966 55.000 0.00 0.00 0.00 5.34
312 313 1.375523 CACTGTTCCCCTACACGCC 60.376 63.158 0.00 0.00 0.00 5.68
313 314 1.535687 ACTGTTCCCCTACACGCCT 60.536 57.895 0.00 0.00 0.00 5.52
314 315 0.251922 ACTGTTCCCCTACACGCCTA 60.252 55.000 0.00 0.00 0.00 3.93
315 316 0.899720 CTGTTCCCCTACACGCCTAA 59.100 55.000 0.00 0.00 0.00 2.69
316 317 1.276989 CTGTTCCCCTACACGCCTAAA 59.723 52.381 0.00 0.00 0.00 1.85
317 318 1.910671 TGTTCCCCTACACGCCTAAAT 59.089 47.619 0.00 0.00 0.00 1.40
318 319 2.093341 TGTTCCCCTACACGCCTAAATC 60.093 50.000 0.00 0.00 0.00 2.17
319 320 2.169978 GTTCCCCTACACGCCTAAATCT 59.830 50.000 0.00 0.00 0.00 2.40
320 321 2.474112 TCCCCTACACGCCTAAATCTT 58.526 47.619 0.00 0.00 0.00 2.40
321 322 3.645434 TCCCCTACACGCCTAAATCTTA 58.355 45.455 0.00 0.00 0.00 2.10
322 323 3.640029 TCCCCTACACGCCTAAATCTTAG 59.360 47.826 0.00 0.00 0.00 2.18
323 324 3.391049 CCCTACACGCCTAAATCTTAGC 58.609 50.000 0.00 0.00 0.00 3.09
324 325 3.069729 CCCTACACGCCTAAATCTTAGCT 59.930 47.826 0.00 0.00 0.00 3.32
325 326 4.299978 CCTACACGCCTAAATCTTAGCTC 58.700 47.826 0.00 0.00 0.00 4.09
326 327 2.810650 ACACGCCTAAATCTTAGCTCG 58.189 47.619 0.00 0.00 0.00 5.03
327 328 2.426024 ACACGCCTAAATCTTAGCTCGA 59.574 45.455 0.00 0.00 0.00 4.04
328 329 2.789893 CACGCCTAAATCTTAGCTCGAC 59.210 50.000 0.00 0.00 0.00 4.20
329 330 2.688958 ACGCCTAAATCTTAGCTCGACT 59.311 45.455 0.00 0.00 0.00 4.18
330 331 3.881688 ACGCCTAAATCTTAGCTCGACTA 59.118 43.478 0.00 0.00 0.00 2.59
331 332 4.220572 CGCCTAAATCTTAGCTCGACTAC 58.779 47.826 0.00 0.00 0.00 2.73
332 333 4.548494 GCCTAAATCTTAGCTCGACTACC 58.452 47.826 0.00 0.00 0.00 3.18
333 334 4.559099 GCCTAAATCTTAGCTCGACTACCC 60.559 50.000 0.00 0.00 0.00 3.69
334 335 4.583489 CCTAAATCTTAGCTCGACTACCCA 59.417 45.833 0.00 0.00 0.00 4.51
335 336 4.388378 AAATCTTAGCTCGACTACCCAC 57.612 45.455 0.00 0.00 0.00 4.61
336 337 1.760192 TCTTAGCTCGACTACCCACC 58.240 55.000 0.00 0.00 0.00 4.61
337 338 0.381089 CTTAGCTCGACTACCCACCG 59.619 60.000 0.00 0.00 0.00 4.94
338 339 0.322816 TTAGCTCGACTACCCACCGT 60.323 55.000 0.00 0.00 0.00 4.83
339 340 0.745845 TAGCTCGACTACCCACCGTC 60.746 60.000 0.00 0.00 0.00 4.79
342 343 4.487412 CGACTACCCACCGTCGGC 62.487 72.222 12.28 0.00 46.61 5.54
343 344 3.376078 GACTACCCACCGTCGGCA 61.376 66.667 12.28 0.00 0.00 5.69
344 345 3.352338 GACTACCCACCGTCGGCAG 62.352 68.421 12.28 4.04 0.00 4.85
345 346 4.143333 CTACCCACCGTCGGCAGG 62.143 72.222 12.28 14.89 0.00 4.85
766 767 8.770010 TTTTAATTAGAACCAAACAAGGAGGA 57.230 30.769 0.00 0.00 0.00 3.71
767 768 8.770010 TTTAATTAGAACCAAACAAGGAGGAA 57.230 30.769 0.00 0.00 0.00 3.36
768 769 8.950007 TTAATTAGAACCAAACAAGGAGGAAT 57.050 30.769 0.00 0.00 0.00 3.01
769 770 7.855784 AATTAGAACCAAACAAGGAGGAATT 57.144 32.000 0.00 0.00 0.00 2.17
770 771 6.894339 TTAGAACCAAACAAGGAGGAATTC 57.106 37.500 0.00 0.00 0.00 2.17
771 772 5.066913 AGAACCAAACAAGGAGGAATTCT 57.933 39.130 5.23 0.00 0.00 2.40
772 773 5.073428 AGAACCAAACAAGGAGGAATTCTC 58.927 41.667 5.23 1.17 41.71 2.87
773 774 3.412386 ACCAAACAAGGAGGAATTCTCG 58.588 45.455 5.23 0.00 43.34 4.04
774 775 3.181443 ACCAAACAAGGAGGAATTCTCGT 60.181 43.478 5.23 0.38 43.34 4.18
776 777 4.278419 CCAAACAAGGAGGAATTCTCGTTT 59.722 41.667 5.23 4.05 45.16 3.60
777 778 5.472137 CCAAACAAGGAGGAATTCTCGTTTA 59.528 40.000 5.23 0.00 45.16 2.01
778 779 6.151144 CCAAACAAGGAGGAATTCTCGTTTAT 59.849 38.462 5.23 0.00 45.16 1.40
779 780 6.986904 AACAAGGAGGAATTCTCGTTTATC 57.013 37.500 5.23 0.00 45.16 1.75
780 781 6.049955 ACAAGGAGGAATTCTCGTTTATCA 57.950 37.500 5.23 0.00 45.16 2.15
781 782 6.472887 ACAAGGAGGAATTCTCGTTTATCAA 58.527 36.000 5.23 0.00 45.16 2.57
782 783 6.940298 ACAAGGAGGAATTCTCGTTTATCAAA 59.060 34.615 5.23 0.00 45.16 2.69
783 784 7.447238 ACAAGGAGGAATTCTCGTTTATCAAAA 59.553 33.333 5.23 0.00 45.16 2.44
784 785 8.462016 CAAGGAGGAATTCTCGTTTATCAAAAT 58.538 33.333 5.23 0.00 45.16 1.82
785 786 9.681062 AAGGAGGAATTCTCGTTTATCAAAATA 57.319 29.630 5.23 0.00 45.16 1.40
786 787 9.681062 AGGAGGAATTCTCGTTTATCAAAATAA 57.319 29.630 5.23 0.00 43.34 1.40
878 879 2.184579 GAGAAACTCGCCGGGGAG 59.815 66.667 38.62 38.62 39.97 4.30
879 880 2.283676 AGAAACTCGCCGGGGAGA 60.284 61.111 44.41 17.05 37.49 3.71
880 881 1.677637 GAGAAACTCGCCGGGGAGAT 61.678 60.000 44.41 34.55 37.49 2.75
881 882 0.396695 AGAAACTCGCCGGGGAGATA 60.397 55.000 44.41 15.94 37.49 1.98
883 884 1.400530 AAACTCGCCGGGGAGATAGG 61.401 60.000 44.41 25.49 37.49 2.57
884 885 2.115480 CTCGCCGGGGAGATAGGA 59.885 66.667 38.00 8.17 36.08 2.94
885 886 1.530891 CTCGCCGGGGAGATAGGAA 60.531 63.158 38.00 7.39 36.08 3.36
886 887 1.807495 CTCGCCGGGGAGATAGGAAC 61.807 65.000 38.00 0.00 36.08 3.62
887 888 2.868986 CGCCGGGGAGATAGGAACC 61.869 68.421 14.46 0.00 0.00 3.62
888 889 1.459730 GCCGGGGAGATAGGAACCT 60.460 63.158 2.18 0.00 0.00 3.50
889 890 1.054978 GCCGGGGAGATAGGAACCTT 61.055 60.000 2.18 0.00 0.00 3.50
890 891 0.759346 CCGGGGAGATAGGAACCTTG 59.241 60.000 0.00 0.00 0.00 3.61
891 892 1.691482 CCGGGGAGATAGGAACCTTGA 60.691 57.143 0.00 0.00 0.00 3.02
892 893 1.413077 CGGGGAGATAGGAACCTTGAC 59.587 57.143 0.00 0.00 0.00 3.18
913 914 2.024176 TGGGTTCCAGACTAGAGCAA 57.976 50.000 0.00 0.00 0.00 3.91
928 929 0.327591 AGCAAGCTAGCTCCTTTGCT 59.672 50.000 28.06 28.06 42.18 3.91
933 934 1.627834 AGCTAGCTCCTTTGCTTCACT 59.372 47.619 12.68 0.00 43.74 3.41
934 935 1.736681 GCTAGCTCCTTTGCTTCACTG 59.263 52.381 7.70 0.00 43.74 3.66
935 936 2.873649 GCTAGCTCCTTTGCTTCACTGT 60.874 50.000 7.70 0.00 43.74 3.55
936 937 2.355010 AGCTCCTTTGCTTCACTGTT 57.645 45.000 0.00 0.00 40.93 3.16
937 938 2.225467 AGCTCCTTTGCTTCACTGTTC 58.775 47.619 0.00 0.00 40.93 3.18
938 939 1.268079 GCTCCTTTGCTTCACTGTTCC 59.732 52.381 0.00 0.00 0.00 3.62
939 940 1.882623 CTCCTTTGCTTCACTGTTCCC 59.117 52.381 0.00 0.00 0.00 3.97
940 941 0.961753 CCTTTGCTTCACTGTTCCCC 59.038 55.000 0.00 0.00 0.00 4.81
941 942 1.479389 CCTTTGCTTCACTGTTCCCCT 60.479 52.381 0.00 0.00 0.00 4.79
942 943 2.224769 CCTTTGCTTCACTGTTCCCCTA 60.225 50.000 0.00 0.00 0.00 3.53
943 944 2.561478 TTGCTTCACTGTTCCCCTAC 57.439 50.000 0.00 0.00 0.00 3.18
944 945 1.429930 TGCTTCACTGTTCCCCTACA 58.570 50.000 0.00 0.00 0.00 2.74
945 946 1.071699 TGCTTCACTGTTCCCCTACAC 59.928 52.381 0.00 0.00 0.00 2.90
946 947 1.939838 GCTTCACTGTTCCCCTACACG 60.940 57.143 0.00 0.00 0.00 4.49
947 948 0.034337 TTCACTGTTCCCCTACACGC 59.966 55.000 0.00 0.00 0.00 5.34
948 949 1.375523 CACTGTTCCCCTACACGCC 60.376 63.158 0.00 0.00 0.00 5.68
949 950 1.535687 ACTGTTCCCCTACACGCCT 60.536 57.895 0.00 0.00 0.00 5.52
950 951 0.251922 ACTGTTCCCCTACACGCCTA 60.252 55.000 0.00 0.00 0.00 3.93
951 952 0.899720 CTGTTCCCCTACACGCCTAA 59.100 55.000 0.00 0.00 0.00 2.69
952 953 1.276989 CTGTTCCCCTACACGCCTAAA 59.723 52.381 0.00 0.00 0.00 1.85
953 954 1.910671 TGTTCCCCTACACGCCTAAAT 59.089 47.619 0.00 0.00 0.00 1.40
954 955 2.093341 TGTTCCCCTACACGCCTAAATC 60.093 50.000 0.00 0.00 0.00 2.17
955 956 2.169978 GTTCCCCTACACGCCTAAATCT 59.830 50.000 0.00 0.00 0.00 2.40
965 966 2.688958 ACGCCTAAATCTTAGCTCGACT 59.311 45.455 0.00 0.00 0.00 4.18
979 980 3.376078 GACTACCCACCGTCGGCA 61.376 66.667 12.28 0.00 0.00 5.69
981 982 4.143333 CTACCCACCGTCGGCAGG 62.143 72.222 12.28 14.89 0.00 4.85
1011 1027 2.271821 CACATCATGACCCCGCCA 59.728 61.111 0.00 0.00 0.00 5.69
1351 1367 3.264845 GCTTCCTCCCCAACCCCA 61.265 66.667 0.00 0.00 0.00 4.96
1455 1471 1.528309 CGCCACCTCCAACACCTTT 60.528 57.895 0.00 0.00 0.00 3.11
1499 1515 4.944372 GTCCCGGCGCTACATCCG 62.944 72.222 7.64 0.00 44.89 4.18
1569 1585 3.378427 GCATGTTAGATTTCGAGCCCTTT 59.622 43.478 0.00 0.00 0.00 3.11
1633 1649 3.213206 TCAAAGTGATCTGCAAGGTGT 57.787 42.857 0.00 0.00 0.00 4.16
1660 1676 3.363178 GAAAACAAGGTTGCTGTCTTCG 58.637 45.455 0.00 0.00 0.00 3.79
1677 1693 2.795175 TCGTCTTCTCTTCACACACC 57.205 50.000 0.00 0.00 0.00 4.16
1836 1852 0.870393 AACTGCTCATGCTTGACACG 59.130 50.000 0.00 0.00 40.48 4.49
2300 2316 4.274950 TGCTACTGTAAACTTCCTTTGTGC 59.725 41.667 0.00 0.00 0.00 4.57
2383 2399 3.242011 AGTCAAACCAGGGAATGCAATT 58.758 40.909 0.00 0.00 40.93 2.32
2453 2469 8.834749 TTTTTGCACTAGTTGTTTTAAGGTTT 57.165 26.923 0.00 0.00 0.00 3.27
2595 2658 5.826643 AGAGTCCAGTCAGTTTAGAGATCT 58.173 41.667 0.00 0.00 0.00 2.75
2638 2701 2.878406 ACCGATTTGTTGGTCAAGTCTG 59.122 45.455 0.00 0.00 39.55 3.51
2767 2832 6.914665 TCCAATTTGGTATGAGATCCATCTT 58.085 36.000 14.98 0.00 39.03 2.40
2773 2838 6.947376 TGGTATGAGATCCATCTTGATGAT 57.053 37.500 11.76 4.26 37.25 2.45
2862 2927 2.997897 GAGCGGAGGACCAGGTGT 60.998 66.667 0.00 0.00 35.59 4.16
2913 3027 2.204291 TGCCCCCACCTCCAGATT 60.204 61.111 0.00 0.00 0.00 2.40
2914 3028 2.276309 CTGCCCCCACCTCCAGATTC 62.276 65.000 0.00 0.00 0.00 2.52
3025 3148 3.003173 TGTCCCCTTCTCCAGCGG 61.003 66.667 0.00 0.00 0.00 5.52
3044 3176 4.357947 GCTGTCGTGACCGCCTCA 62.358 66.667 5.23 0.00 35.84 3.86
3060 3192 0.962356 CTCAACCGCCTTCATGCCTT 60.962 55.000 0.00 0.00 0.00 4.35
3072 3204 0.896940 CATGCCTTCACCTGCCAACT 60.897 55.000 0.00 0.00 0.00 3.16
3074 3206 2.270986 GCCTTCACCTGCCAACTGG 61.271 63.158 0.00 0.00 40.61 4.00
3156 3637 3.097162 CCCCCTTCTGCCCCTACC 61.097 72.222 0.00 0.00 0.00 3.18
3186 3667 2.674420 CCTCGGATTAGGTCCTGGTTA 58.326 52.381 0.00 0.00 45.46 2.85
3219 3700 2.760374 CTTCCACAAGCTCGACTTTCT 58.240 47.619 0.00 0.00 36.04 2.52
3261 3742 6.315393 GTCAATCCTCTTGGTTCGCTAAATAA 59.685 38.462 0.00 0.00 34.23 1.40
3262 3743 6.882140 TCAATCCTCTTGGTTCGCTAAATAAA 59.118 34.615 0.00 0.00 34.23 1.40
3263 3744 7.556275 TCAATCCTCTTGGTTCGCTAAATAAAT 59.444 33.333 0.00 0.00 34.23 1.40
3264 3745 6.677781 TCCTCTTGGTTCGCTAAATAAATG 57.322 37.500 0.00 0.00 34.23 2.32
3265 3746 6.177610 TCCTCTTGGTTCGCTAAATAAATGT 58.822 36.000 0.00 0.00 34.23 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.106439 TGGTTCTAGTGAAAATTTTGCTTCA 57.894 32.000 8.47 0.00 33.52 3.02
3 4 8.419076 TTTGGTTCTAGTGAAAATTTTGCTTC 57.581 30.769 8.47 0.00 33.52 3.86
4 5 8.962884 ATTTGGTTCTAGTGAAAATTTTGCTT 57.037 26.923 8.47 0.00 33.52 3.91
11 12 9.753674 TCTTCCATATTTGGTTCTAGTGAAAAT 57.246 29.630 1.86 0.00 44.06 1.82
12 13 9.753674 ATCTTCCATATTTGGTTCTAGTGAAAA 57.246 29.630 1.86 0.00 44.06 2.29
13 14 9.753674 AATCTTCCATATTTGGTTCTAGTGAAA 57.246 29.630 1.86 0.00 44.06 2.69
14 15 9.753674 AAATCTTCCATATTTGGTTCTAGTGAA 57.246 29.630 1.86 0.00 44.06 3.18
66 67 8.440833 GCTTCGCTATTTGATTTAATACGGTAT 58.559 33.333 0.00 0.00 0.00 2.73
67 68 7.438757 TGCTTCGCTATTTGATTTAATACGGTA 59.561 33.333 0.00 0.00 0.00 4.02
68 69 6.259167 TGCTTCGCTATTTGATTTAATACGGT 59.741 34.615 0.00 0.00 0.00 4.83
69 70 6.655062 TGCTTCGCTATTTGATTTAATACGG 58.345 36.000 0.00 0.00 0.00 4.02
70 71 7.564128 TCTGCTTCGCTATTTGATTTAATACG 58.436 34.615 0.00 0.00 0.00 3.06
71 72 9.884465 ATTCTGCTTCGCTATTTGATTTAATAC 57.116 29.630 0.00 0.00 0.00 1.89
73 74 9.807649 AAATTCTGCTTCGCTATTTGATTTAAT 57.192 25.926 0.00 0.00 0.00 1.40
74 75 9.638239 AAAATTCTGCTTCGCTATTTGATTTAA 57.362 25.926 0.00 0.00 0.00 1.52
76 77 9.638239 TTAAAATTCTGCTTCGCTATTTGATTT 57.362 25.926 0.00 0.00 0.00 2.17
77 78 9.807649 ATTAAAATTCTGCTTCGCTATTTGATT 57.192 25.926 0.00 0.00 0.00 2.57
78 79 9.807649 AATTAAAATTCTGCTTCGCTATTTGAT 57.192 25.926 0.00 0.00 0.00 2.57
83 84 9.937175 GTTCTAATTAAAATTCTGCTTCGCTAT 57.063 29.630 0.00 0.00 0.00 2.97
84 85 8.395633 GGTTCTAATTAAAATTCTGCTTCGCTA 58.604 33.333 0.00 0.00 0.00 4.26
85 86 7.094377 TGGTTCTAATTAAAATTCTGCTTCGCT 60.094 33.333 0.00 0.00 0.00 4.93
86 87 7.027161 TGGTTCTAATTAAAATTCTGCTTCGC 58.973 34.615 0.00 0.00 0.00 4.70
87 88 8.964420 TTGGTTCTAATTAAAATTCTGCTTCG 57.036 30.769 0.00 0.00 0.00 3.79
95 96 9.996554 CCTCCTTGTTTGGTTCTAATTAAAATT 57.003 29.630 0.00 0.00 0.00 1.82
96 97 9.374711 TCCTCCTTGTTTGGTTCTAATTAAAAT 57.625 29.630 0.00 0.00 0.00 1.82
97 98 8.770010 TCCTCCTTGTTTGGTTCTAATTAAAA 57.230 30.769 0.00 0.00 0.00 1.52
98 99 8.770010 TTCCTCCTTGTTTGGTTCTAATTAAA 57.230 30.769 0.00 0.00 0.00 1.52
99 100 8.950007 ATTCCTCCTTGTTTGGTTCTAATTAA 57.050 30.769 0.00 0.00 0.00 1.40
100 101 8.950007 AATTCCTCCTTGTTTGGTTCTAATTA 57.050 30.769 0.00 0.00 0.00 1.40
101 102 7.730332 AGAATTCCTCCTTGTTTGGTTCTAATT 59.270 33.333 0.65 0.00 0.00 1.40
102 103 7.241628 AGAATTCCTCCTTGTTTGGTTCTAAT 58.758 34.615 0.65 0.00 0.00 1.73
103 104 6.610830 AGAATTCCTCCTTGTTTGGTTCTAA 58.389 36.000 0.65 0.00 0.00 2.10
104 105 6.200878 AGAATTCCTCCTTGTTTGGTTCTA 57.799 37.500 0.65 0.00 0.00 2.10
105 106 5.066913 AGAATTCCTCCTTGTTTGGTTCT 57.933 39.130 0.65 0.00 0.00 3.01
106 107 4.083271 CGAGAATTCCTCCTTGTTTGGTTC 60.083 45.833 0.65 0.00 38.71 3.62
107 108 3.821033 CGAGAATTCCTCCTTGTTTGGTT 59.179 43.478 0.65 0.00 38.71 3.67
108 109 3.181443 ACGAGAATTCCTCCTTGTTTGGT 60.181 43.478 0.65 0.00 38.71 3.67
109 110 3.412386 ACGAGAATTCCTCCTTGTTTGG 58.588 45.455 0.65 0.00 38.71 3.28
110 111 5.438761 AAACGAGAATTCCTCCTTGTTTG 57.561 39.130 0.65 0.00 42.35 2.93
111 112 6.940298 TGATAAACGAGAATTCCTCCTTGTTT 59.060 34.615 12.75 12.75 44.62 2.83
112 113 6.472887 TGATAAACGAGAATTCCTCCTTGTT 58.527 36.000 0.65 0.00 38.33 2.83
113 114 6.049955 TGATAAACGAGAATTCCTCCTTGT 57.950 37.500 0.65 0.00 38.71 3.16
114 115 6.985188 TTGATAAACGAGAATTCCTCCTTG 57.015 37.500 0.65 0.00 38.71 3.61
115 116 7.996098 TTTTGATAAACGAGAATTCCTCCTT 57.004 32.000 0.65 0.00 38.71 3.36
116 117 9.681062 TTATTTTGATAAACGAGAATTCCTCCT 57.319 29.630 0.65 0.00 38.71 3.69
212 213 4.061596 CGACTTTCTCTCTGGCTCTTTTT 58.938 43.478 0.00 0.00 0.00 1.94
213 214 3.658709 CGACTTTCTCTCTGGCTCTTTT 58.341 45.455 0.00 0.00 0.00 2.27
214 215 2.611722 GCGACTTTCTCTCTGGCTCTTT 60.612 50.000 0.00 0.00 0.00 2.52
215 216 1.067213 GCGACTTTCTCTCTGGCTCTT 60.067 52.381 0.00 0.00 0.00 2.85
216 217 0.530288 GCGACTTTCTCTCTGGCTCT 59.470 55.000 0.00 0.00 0.00 4.09
217 218 0.459411 GGCGACTTTCTCTCTGGCTC 60.459 60.000 0.00 0.00 0.00 4.70
218 219 1.594310 GGCGACTTTCTCTCTGGCT 59.406 57.895 0.00 0.00 0.00 4.75
219 220 1.807573 CGGCGACTTTCTCTCTGGC 60.808 63.158 0.00 0.00 0.00 4.85
220 221 1.153745 CCGGCGACTTTCTCTCTGG 60.154 63.158 9.30 0.00 0.00 3.86
221 222 1.153745 CCCGGCGACTTTCTCTCTG 60.154 63.158 9.30 0.00 0.00 3.35
222 223 2.352032 CCCCGGCGACTTTCTCTCT 61.352 63.158 9.30 0.00 0.00 3.10
223 224 2.184579 CCCCGGCGACTTTCTCTC 59.815 66.667 9.30 0.00 0.00 3.20
224 225 2.283676 TCCCCGGCGACTTTCTCT 60.284 61.111 9.30 0.00 0.00 3.10
225 226 1.677637 ATCTCCCCGGCGACTTTCTC 61.678 60.000 9.30 0.00 0.00 2.87
226 227 0.396695 TATCTCCCCGGCGACTTTCT 60.397 55.000 9.30 0.00 0.00 2.52
227 228 0.032267 CTATCTCCCCGGCGACTTTC 59.968 60.000 9.30 0.00 0.00 2.62
228 229 1.400530 CCTATCTCCCCGGCGACTTT 61.401 60.000 9.30 0.00 0.00 2.66
229 230 1.833049 CCTATCTCCCCGGCGACTT 60.833 63.158 9.30 0.00 0.00 3.01
230 231 2.203509 CCTATCTCCCCGGCGACT 60.204 66.667 9.30 0.00 0.00 4.18
231 232 1.831286 TTCCTATCTCCCCGGCGAC 60.831 63.158 9.30 0.00 0.00 5.19
232 233 1.831286 GTTCCTATCTCCCCGGCGA 60.831 63.158 9.30 0.00 0.00 5.54
233 234 2.735237 GTTCCTATCTCCCCGGCG 59.265 66.667 0.00 0.00 0.00 6.46
234 235 1.054978 AAGGTTCCTATCTCCCCGGC 61.055 60.000 0.00 0.00 0.00 6.13
235 236 0.759346 CAAGGTTCCTATCTCCCCGG 59.241 60.000 0.00 0.00 0.00 5.73
236 237 1.413077 GTCAAGGTTCCTATCTCCCCG 59.587 57.143 0.00 0.00 0.00 5.73
237 238 1.769465 GGTCAAGGTTCCTATCTCCCC 59.231 57.143 0.00 0.00 0.00 4.81
238 239 2.436173 CAGGTCAAGGTTCCTATCTCCC 59.564 54.545 0.00 0.00 32.26 4.30
239 240 2.436173 CCAGGTCAAGGTTCCTATCTCC 59.564 54.545 0.00 0.00 32.26 3.71
240 241 2.436173 CCCAGGTCAAGGTTCCTATCTC 59.564 54.545 0.00 0.00 32.26 2.75
241 242 2.225908 ACCCAGGTCAAGGTTCCTATCT 60.226 50.000 0.00 0.00 29.94 1.98
242 243 2.197465 ACCCAGGTCAAGGTTCCTATC 58.803 52.381 0.00 0.00 29.94 2.08
243 244 2.361085 ACCCAGGTCAAGGTTCCTAT 57.639 50.000 0.00 0.00 29.94 2.57
244 245 2.127651 AACCCAGGTCAAGGTTCCTA 57.872 50.000 0.00 0.00 42.85 2.94
245 246 2.960710 AACCCAGGTCAAGGTTCCT 58.039 52.632 0.00 0.00 42.85 3.36
249 250 4.430388 TGGAACCCAGGTCAAGGT 57.570 55.556 0.00 0.00 38.27 3.50
258 259 1.902508 CTTGCTCTAGTCTGGAACCCA 59.097 52.381 0.00 0.00 0.00 4.51
259 260 1.406205 GCTTGCTCTAGTCTGGAACCC 60.406 57.143 0.00 0.00 0.00 4.11
260 261 1.552792 AGCTTGCTCTAGTCTGGAACC 59.447 52.381 0.00 0.00 0.00 3.62
261 262 3.736740 GCTAGCTTGCTCTAGTCTGGAAC 60.737 52.174 13.17 0.00 38.58 3.62
262 263 2.428890 GCTAGCTTGCTCTAGTCTGGAA 59.571 50.000 13.17 0.00 38.58 3.53
263 264 2.028130 GCTAGCTTGCTCTAGTCTGGA 58.972 52.381 13.17 0.00 38.58 3.86
264 265 2.031120 AGCTAGCTTGCTCTAGTCTGG 58.969 52.381 17.30 0.00 39.34 3.86
274 275 1.132073 GAAGCAAAGGAGCTAGCTTGC 59.868 52.381 25.08 25.08 46.35 4.01
275 276 2.161211 GTGAAGCAAAGGAGCTAGCTTG 59.839 50.000 20.42 14.17 46.35 4.01
277 278 1.627834 AGTGAAGCAAAGGAGCTAGCT 59.372 47.619 19.45 19.45 45.89 3.32
278 279 1.736681 CAGTGAAGCAAAGGAGCTAGC 59.263 52.381 6.62 6.62 45.89 3.42
279 280 3.051081 ACAGTGAAGCAAAGGAGCTAG 57.949 47.619 0.00 0.00 45.89 3.42
280 281 3.403038 GAACAGTGAAGCAAAGGAGCTA 58.597 45.455 0.00 0.00 45.89 3.32
282 283 1.268079 GGAACAGTGAAGCAAAGGAGC 59.732 52.381 0.00 0.00 0.00 4.70
283 284 1.882623 GGGAACAGTGAAGCAAAGGAG 59.117 52.381 0.00 0.00 0.00 3.69
284 285 1.478654 GGGGAACAGTGAAGCAAAGGA 60.479 52.381 0.00 0.00 0.00 3.36
285 286 0.961753 GGGGAACAGTGAAGCAAAGG 59.038 55.000 0.00 0.00 0.00 3.11
286 287 1.986882 AGGGGAACAGTGAAGCAAAG 58.013 50.000 0.00 0.00 0.00 2.77
287 288 2.173782 TGTAGGGGAACAGTGAAGCAAA 59.826 45.455 0.00 0.00 0.00 3.68
288 289 1.771854 TGTAGGGGAACAGTGAAGCAA 59.228 47.619 0.00 0.00 0.00 3.91
289 290 1.071699 GTGTAGGGGAACAGTGAAGCA 59.928 52.381 0.00 0.00 0.00 3.91
290 291 1.809684 GTGTAGGGGAACAGTGAAGC 58.190 55.000 0.00 0.00 0.00 3.86
291 292 1.939838 GCGTGTAGGGGAACAGTGAAG 60.940 57.143 0.00 0.00 0.00 3.02
292 293 0.034337 GCGTGTAGGGGAACAGTGAA 59.966 55.000 0.00 0.00 0.00 3.18
293 294 1.669440 GCGTGTAGGGGAACAGTGA 59.331 57.895 0.00 0.00 0.00 3.41
294 295 1.375523 GGCGTGTAGGGGAACAGTG 60.376 63.158 0.00 0.00 0.00 3.66
295 296 0.251922 TAGGCGTGTAGGGGAACAGT 60.252 55.000 0.00 0.00 0.00 3.55
296 297 0.899720 TTAGGCGTGTAGGGGAACAG 59.100 55.000 0.00 0.00 0.00 3.16
297 298 1.350071 TTTAGGCGTGTAGGGGAACA 58.650 50.000 0.00 0.00 0.00 3.18
298 299 2.169978 AGATTTAGGCGTGTAGGGGAAC 59.830 50.000 0.00 0.00 0.00 3.62
299 300 2.474112 AGATTTAGGCGTGTAGGGGAA 58.526 47.619 0.00 0.00 0.00 3.97
300 301 2.170012 AGATTTAGGCGTGTAGGGGA 57.830 50.000 0.00 0.00 0.00 4.81
301 302 3.802675 GCTAAGATTTAGGCGTGTAGGGG 60.803 52.174 0.00 0.00 0.00 4.79
302 303 3.069729 AGCTAAGATTTAGGCGTGTAGGG 59.930 47.826 0.00 0.00 0.00 3.53
303 304 4.299978 GAGCTAAGATTTAGGCGTGTAGG 58.700 47.826 0.00 0.00 0.00 3.18
304 305 3.975670 CGAGCTAAGATTTAGGCGTGTAG 59.024 47.826 0.00 0.00 0.00 2.74
305 306 3.628942 TCGAGCTAAGATTTAGGCGTGTA 59.371 43.478 0.00 0.00 0.00 2.90
306 307 2.426024 TCGAGCTAAGATTTAGGCGTGT 59.574 45.455 0.00 0.00 0.00 4.49
307 308 2.789893 GTCGAGCTAAGATTTAGGCGTG 59.210 50.000 0.00 0.00 0.00 5.34
308 309 2.688958 AGTCGAGCTAAGATTTAGGCGT 59.311 45.455 0.00 0.00 0.00 5.68
309 310 3.357166 AGTCGAGCTAAGATTTAGGCG 57.643 47.619 0.00 0.00 0.00 5.52
310 311 4.548494 GGTAGTCGAGCTAAGATTTAGGC 58.452 47.826 0.00 0.00 0.00 3.93
311 312 4.583489 TGGGTAGTCGAGCTAAGATTTAGG 59.417 45.833 0.00 0.00 0.00 2.69
312 313 5.507650 GGTGGGTAGTCGAGCTAAGATTTAG 60.508 48.000 0.00 0.00 0.00 1.85
313 314 4.340381 GGTGGGTAGTCGAGCTAAGATTTA 59.660 45.833 0.00 0.00 0.00 1.40
314 315 3.132467 GGTGGGTAGTCGAGCTAAGATTT 59.868 47.826 0.00 0.00 0.00 2.17
315 316 2.694109 GGTGGGTAGTCGAGCTAAGATT 59.306 50.000 0.00 0.00 0.00 2.40
316 317 2.308690 GGTGGGTAGTCGAGCTAAGAT 58.691 52.381 0.00 0.00 0.00 2.40
317 318 1.760192 GGTGGGTAGTCGAGCTAAGA 58.240 55.000 0.00 0.00 0.00 2.10
318 319 0.381089 CGGTGGGTAGTCGAGCTAAG 59.619 60.000 0.00 0.00 0.00 2.18
319 320 0.322816 ACGGTGGGTAGTCGAGCTAA 60.323 55.000 0.00 0.00 0.00 3.09
320 321 0.745845 GACGGTGGGTAGTCGAGCTA 60.746 60.000 0.00 0.00 0.00 3.32
321 322 2.035312 ACGGTGGGTAGTCGAGCT 59.965 61.111 0.00 0.00 0.00 4.09
322 323 2.488820 GACGGTGGGTAGTCGAGC 59.511 66.667 0.00 0.00 0.00 5.03
326 327 3.352338 CTGCCGACGGTGGGTAGTC 62.352 68.421 16.73 0.00 33.18 2.59
327 328 3.379445 CTGCCGACGGTGGGTAGT 61.379 66.667 16.73 0.00 33.18 2.73
328 329 4.143333 CCTGCCGACGGTGGGTAG 62.143 72.222 18.03 18.03 37.07 3.18
741 742 8.770010 TCCTCCTTGTTTGGTTCTAATTAAAA 57.230 30.769 0.00 0.00 0.00 1.52
742 743 8.770010 TTCCTCCTTGTTTGGTTCTAATTAAA 57.230 30.769 0.00 0.00 0.00 1.52
743 744 8.950007 ATTCCTCCTTGTTTGGTTCTAATTAA 57.050 30.769 0.00 0.00 0.00 1.40
744 745 8.950007 AATTCCTCCTTGTTTGGTTCTAATTA 57.050 30.769 0.00 0.00 0.00 1.40
745 746 7.730332 AGAATTCCTCCTTGTTTGGTTCTAATT 59.270 33.333 0.65 0.00 0.00 1.40
746 747 7.241628 AGAATTCCTCCTTGTTTGGTTCTAAT 58.758 34.615 0.65 0.00 0.00 1.73
747 748 6.610830 AGAATTCCTCCTTGTTTGGTTCTAA 58.389 36.000 0.65 0.00 0.00 2.10
748 749 6.200878 AGAATTCCTCCTTGTTTGGTTCTA 57.799 37.500 0.65 0.00 0.00 2.10
749 750 5.066913 AGAATTCCTCCTTGTTTGGTTCT 57.933 39.130 0.65 0.00 0.00 3.01
750 751 4.083271 CGAGAATTCCTCCTTGTTTGGTTC 60.083 45.833 0.65 0.00 38.71 3.62
751 752 3.821033 CGAGAATTCCTCCTTGTTTGGTT 59.179 43.478 0.65 0.00 38.71 3.67
752 753 3.181443 ACGAGAATTCCTCCTTGTTTGGT 60.181 43.478 0.65 0.00 38.71 3.67
753 754 3.412386 ACGAGAATTCCTCCTTGTTTGG 58.588 45.455 0.65 0.00 38.71 3.28
754 755 5.438761 AAACGAGAATTCCTCCTTGTTTG 57.561 39.130 0.65 0.00 42.35 2.93
755 756 6.940298 TGATAAACGAGAATTCCTCCTTGTTT 59.060 34.615 12.75 12.75 44.62 2.83
756 757 6.472887 TGATAAACGAGAATTCCTCCTTGTT 58.527 36.000 0.65 0.00 38.33 2.83
757 758 6.049955 TGATAAACGAGAATTCCTCCTTGT 57.950 37.500 0.65 0.00 38.71 3.16
758 759 6.985188 TTGATAAACGAGAATTCCTCCTTG 57.015 37.500 0.65 0.00 38.71 3.61
759 760 7.996098 TTTTGATAAACGAGAATTCCTCCTT 57.004 32.000 0.65 0.00 38.71 3.36
760 761 9.681062 TTATTTTGATAAACGAGAATTCCTCCT 57.319 29.630 0.65 0.00 38.71 3.69
852 853 0.530288 GCGAGTTTCTCTCTGGCTCT 59.470 55.000 0.00 0.00 40.75 4.09
853 854 0.459411 GGCGAGTTTCTCTCTGGCTC 60.459 60.000 0.00 0.00 40.75 4.70
854 855 1.594310 GGCGAGTTTCTCTCTGGCT 59.406 57.895 0.00 0.00 40.75 4.75
855 856 1.807573 CGGCGAGTTTCTCTCTGGC 60.808 63.158 0.00 0.00 40.75 4.85
858 859 2.352032 CCCCGGCGAGTTTCTCTCT 61.352 63.158 9.30 0.00 40.75 3.10
865 866 1.833049 CCTATCTCCCCGGCGAGTT 60.833 63.158 15.64 10.19 0.00 3.01
867 868 1.530891 TTCCTATCTCCCCGGCGAG 60.531 63.158 9.30 10.02 0.00 5.03
878 879 2.197465 ACCCAGGTCAAGGTTCCTATC 58.803 52.381 0.00 0.00 29.94 2.08
879 880 2.361085 ACCCAGGTCAAGGTTCCTAT 57.639 50.000 0.00 0.00 29.94 2.57
880 881 2.127651 AACCCAGGTCAAGGTTCCTA 57.872 50.000 0.00 0.00 42.85 2.94
881 882 2.960710 AACCCAGGTCAAGGTTCCT 58.039 52.632 0.00 0.00 42.85 3.36
885 886 4.430388 TGGAACCCAGGTCAAGGT 57.570 55.556 0.00 0.00 38.27 3.50
910 911 1.132073 GAAGCAAAGGAGCTAGCTTGC 59.868 52.381 25.08 25.08 46.35 4.01
911 912 2.161211 GTGAAGCAAAGGAGCTAGCTTG 59.839 50.000 20.42 14.17 46.35 4.01
913 914 1.627834 AGTGAAGCAAAGGAGCTAGCT 59.372 47.619 19.45 19.45 45.89 3.32
923 924 2.173782 TGTAGGGGAACAGTGAAGCAAA 59.826 45.455 0.00 0.00 0.00 3.68
928 929 0.034337 GCGTGTAGGGGAACAGTGAA 59.966 55.000 0.00 0.00 0.00 3.18
933 934 1.350071 TTTAGGCGTGTAGGGGAACA 58.650 50.000 0.00 0.00 0.00 3.18
934 935 2.169978 AGATTTAGGCGTGTAGGGGAAC 59.830 50.000 0.00 0.00 0.00 3.62
935 936 2.474112 AGATTTAGGCGTGTAGGGGAA 58.526 47.619 0.00 0.00 0.00 3.97
936 937 2.170012 AGATTTAGGCGTGTAGGGGA 57.830 50.000 0.00 0.00 0.00 4.81
937 938 3.802675 GCTAAGATTTAGGCGTGTAGGGG 60.803 52.174 0.00 0.00 0.00 4.79
938 939 3.069729 AGCTAAGATTTAGGCGTGTAGGG 59.930 47.826 0.00 0.00 0.00 3.53
939 940 4.299978 GAGCTAAGATTTAGGCGTGTAGG 58.700 47.826 0.00 0.00 0.00 3.18
940 941 3.975670 CGAGCTAAGATTTAGGCGTGTAG 59.024 47.826 0.00 0.00 0.00 2.74
941 942 3.628942 TCGAGCTAAGATTTAGGCGTGTA 59.371 43.478 0.00 0.00 0.00 2.90
942 943 2.426024 TCGAGCTAAGATTTAGGCGTGT 59.574 45.455 0.00 0.00 0.00 4.49
943 944 2.789893 GTCGAGCTAAGATTTAGGCGTG 59.210 50.000 0.00 0.00 0.00 5.34
944 945 2.688958 AGTCGAGCTAAGATTTAGGCGT 59.311 45.455 0.00 0.00 0.00 5.68
945 946 3.357166 AGTCGAGCTAAGATTTAGGCG 57.643 47.619 0.00 0.00 0.00 5.52
946 947 4.548494 GGTAGTCGAGCTAAGATTTAGGC 58.452 47.826 0.00 0.00 0.00 3.93
947 948 4.583489 TGGGTAGTCGAGCTAAGATTTAGG 59.417 45.833 0.00 0.00 0.00 2.69
948 949 5.507650 GGTGGGTAGTCGAGCTAAGATTTAG 60.508 48.000 0.00 0.00 0.00 1.85
949 950 4.340381 GGTGGGTAGTCGAGCTAAGATTTA 59.660 45.833 0.00 0.00 0.00 1.40
950 951 3.132467 GGTGGGTAGTCGAGCTAAGATTT 59.868 47.826 0.00 0.00 0.00 2.17
951 952 2.694109 GGTGGGTAGTCGAGCTAAGATT 59.306 50.000 0.00 0.00 0.00 2.40
952 953 2.308690 GGTGGGTAGTCGAGCTAAGAT 58.691 52.381 0.00 0.00 0.00 2.40
953 954 1.760192 GGTGGGTAGTCGAGCTAAGA 58.240 55.000 0.00 0.00 0.00 2.10
954 955 0.381089 CGGTGGGTAGTCGAGCTAAG 59.619 60.000 0.00 0.00 0.00 2.18
955 956 0.322816 ACGGTGGGTAGTCGAGCTAA 60.323 55.000 0.00 0.00 0.00 3.09
981 982 3.682292 GATGTGGTGGGGGAGCGAC 62.682 68.421 0.00 0.00 0.00 5.19
1064 1080 3.324930 CCTGGAGCTGTGGAGGCA 61.325 66.667 0.00 0.00 0.00 4.75
1161 1177 1.851021 CGTGGCGAAATGAGGTGCAA 61.851 55.000 0.00 0.00 0.00 4.08
1187 1203 4.388499 GCGCGAAGGAGTGGGGAA 62.388 66.667 12.10 0.00 0.00 3.97
1455 1471 0.603065 CACAGACCACGAGATCCACA 59.397 55.000 0.00 0.00 0.00 4.17
1515 1531 1.726533 CGGAGTCCGCTAGGTCTTCC 61.727 65.000 20.50 0.00 41.17 3.46
1569 1585 1.896660 GTCACTGGCCGGAGCAAAA 60.897 57.895 21.41 0.00 42.56 2.44
1597 1613 1.790755 TTGAACGACGATTCACCCTG 58.209 50.000 0.00 0.00 38.31 4.45
1601 1617 4.386049 AGATCACTTTGAACGACGATTCAC 59.614 41.667 0.00 0.00 38.31 3.18
1633 1649 1.203523 AGCAACCTTGTTTTCGCACAA 59.796 42.857 0.00 0.00 35.33 3.33
1660 1676 1.068741 ACCGGTGTGTGAAGAGAAGAC 59.931 52.381 6.12 0.00 0.00 3.01
1677 1693 6.183360 GGTGTTGAATACTAACCCATTTACCG 60.183 42.308 0.00 0.00 0.00 4.02
1836 1852 4.361451 AATGGTGAATTTCATCTCACGC 57.639 40.909 10.84 0.00 42.40 5.34
2174 2190 3.771479 TGACACATACATCCTCTCAAGCT 59.229 43.478 0.00 0.00 0.00 3.74
2453 2469 1.069296 GCGCTAAGTGATGTTGTTGCA 60.069 47.619 0.00 0.00 0.00 4.08
2622 2685 3.644966 AGACCAGACTTGACCAACAAA 57.355 42.857 0.00 0.00 38.08 2.83
2638 2701 5.396101 GGTCGGCCCCTTTATATAATAGACC 60.396 48.000 0.00 0.00 36.84 3.85
2669 2732 7.066374 ACGACAATATTCTTCTCTGCTTTTC 57.934 36.000 0.00 0.00 0.00 2.29
2767 2832 5.059161 CCTCGATTTCTTTGCCTATCATCA 58.941 41.667 0.00 0.00 0.00 3.07
2773 2838 2.027192 ACAGCCTCGATTTCTTTGCCTA 60.027 45.455 0.00 0.00 0.00 3.93
3035 3158 4.699522 AAGGCGGTTGAGGCGGTC 62.700 66.667 0.00 0.00 41.99 4.79
3060 3192 0.257328 TGAAACCAGTTGGCAGGTGA 59.743 50.000 0.00 0.00 38.37 4.02
3098 3230 2.121042 ATGGGTTGTGGAGGGGGT 60.121 61.111 0.00 0.00 0.00 4.95
3129 3261 4.506255 GAAGGGGGTGATGGGCGG 62.506 72.222 0.00 0.00 0.00 6.13
3179 3660 2.351276 AGGCACGCCTTAACCAGG 59.649 61.111 4.27 0.00 45.70 4.45
3213 3694 3.935203 CGAACCAGCATATGTCAGAAAGT 59.065 43.478 4.29 0.00 0.00 2.66
3217 3698 1.831106 ACCGAACCAGCATATGTCAGA 59.169 47.619 4.29 0.00 0.00 3.27
3218 3699 2.205074 GACCGAACCAGCATATGTCAG 58.795 52.381 4.29 0.00 0.00 3.51
3219 3700 1.552792 TGACCGAACCAGCATATGTCA 59.447 47.619 4.29 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.