Multiple sequence alignment - TraesCS2D01G256900

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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 TraesCS2D01G256900 chr2D 100.000 2595 0 0 1 2595 312025526 312028120 0.000000e+00 4793.0
1 TraesCS2D01G256900 chr2B 97.414 928 21 3 1669 2595 379880704 379879779 0.000000e+00 1578.0
2 TraesCS2D01G256900 chr2B 89.148 857 29 13 824 1640 379881537 379880705 0.000000e+00 1009.0
3 TraesCS2D01G256900 chr2B 89.062 256 25 1 507 759 379881867 379881612 5.390000e-82 315.0
4 TraesCS2D01G256900 chr2A 91.494 1011 45 18 651 1640 425870379 425869389 0.000000e+00 1352.0
5 TraesCS2D01G256900 chr2A 95.954 519 15 2 1701 2219 425869366 425868854 0.000000e+00 837.0
6 TraesCS2D01G256900 chr2A 89.189 370 31 4 2229 2595 425867652 425867289 1.090000e-123 453.0
7 TraesCS2D01G256900 chr2A 90.854 164 15 0 2432 2595 756123917 756124080 1.210000e-53 220.0
8 TraesCS2D01G256900 chr3B 91.566 166 14 0 2430 2595 396729900 396729735 2.010000e-56 230.0
9 TraesCS2D01G256900 chr7A 90.303 165 16 0 2431 2595 35703898 35704062 1.560000e-52 217.0
10 TraesCS2D01G256900 chr7A 89.820 167 17 0 2429 2595 575454317 575454151 5.620000e-52 215.0
11 TraesCS2D01G256900 chrUn 90.244 164 16 0 2432 2595 33077082 33077245 5.620000e-52 215.0
12 TraesCS2D01G256900 chr1A 90.244 164 16 0 2432 2595 92312443 92312280 5.620000e-52 215.0
13 TraesCS2D01G256900 chr1A 90.244 164 16 0 2432 2595 241918695 241918858 5.620000e-52 215.0
14 TraesCS2D01G256900 chr1A 90.741 54 5 0 2380 2433 522484563 522484616 3.580000e-09 73.1
15 TraesCS2D01G256900 chr4D 86.250 80 7 4 1368 1443 111140464 111140543 1.650000e-12 84.2
16 TraesCS2D01G256900 chr4B 86.250 80 7 4 1368 1443 172321291 172321370 1.650000e-12 84.2
17 TraesCS2D01G256900 chr4A 86.250 80 7 4 1368 1443 465790441 465790362 1.650000e-12 84.2


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 TraesCS2D01G256900 chr2D 312025526 312028120 2594 False 4793.000000 4793 100.000000 1 2595 1 chr2D.!!$F1 2594
1 TraesCS2D01G256900 chr2B 379879779 379881867 2088 True 967.333333 1578 91.874667 507 2595 3 chr2B.!!$R1 2088
2 TraesCS2D01G256900 chr2A 425867289 425870379 3090 True 880.666667 1352 92.212333 651 2595 3 chr2A.!!$R1 1944

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
303 304 0.037017 CATTGTGGTCCGGGTGGTTA 59.963 55.0 0.0 0.0 36.3 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 3518 0.038251 TCCAGCAGCAGAGTACGTTG 60.038 55.0 0.0 0.0 0.0 4.1 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
76 77 9.863845 TTTAAGTTCAAAAATTCGAGGAAAAGT 57.136 25.926 0.00 0.00 0.00 2.66
77 78 9.863845 TTAAGTTCAAAAATTCGAGGAAAAGTT 57.136 25.926 0.00 0.00 0.00 2.66
78 79 8.771920 AAGTTCAAAAATTCGAGGAAAAGTTT 57.228 26.923 0.00 0.00 0.00 2.66
79 80 9.863845 AAGTTCAAAAATTCGAGGAAAAGTTTA 57.136 25.926 0.00 0.00 0.00 2.01
172 173 9.911138 AAAAAGTTCATCAATTTTGCAAAAAGT 57.089 22.222 27.10 15.85 0.00 2.66
173 174 9.911138 AAAAGTTCATCAATTTTGCAAAAAGTT 57.089 22.222 27.10 15.71 0.00 2.66
174 175 9.558648 AAAGTTCATCAATTTTGCAAAAAGTTC 57.441 25.926 27.10 12.52 0.00 3.01
175 176 8.266392 AGTTCATCAATTTTGCAAAAAGTTCA 57.734 26.923 27.10 6.50 0.00 3.18
176 177 8.895737 AGTTCATCAATTTTGCAAAAAGTTCAT 58.104 25.926 27.10 8.61 0.00 2.57
177 178 8.949953 GTTCATCAATTTTGCAAAAAGTTCATG 58.050 29.630 27.10 19.12 0.00 3.07
178 179 8.434733 TCATCAATTTTGCAAAAAGTTCATGA 57.565 26.923 27.10 20.85 0.00 3.07
179 180 8.890718 TCATCAATTTTGCAAAAAGTTCATGAA 58.109 25.926 27.10 3.38 0.00 2.57
180 181 9.672086 CATCAATTTTGCAAAAAGTTCATGAAT 57.328 25.926 27.10 5.17 0.00 2.57
221 222 6.978343 AAAACGAAAAAGGAAAGAAAAGGG 57.022 33.333 0.00 0.00 0.00 3.95
222 223 5.925506 AACGAAAAAGGAAAGAAAAGGGA 57.074 34.783 0.00 0.00 0.00 4.20
223 224 5.925506 ACGAAAAAGGAAAGAAAAGGGAA 57.074 34.783 0.00 0.00 0.00 3.97
224 225 6.288941 ACGAAAAAGGAAAGAAAAGGGAAA 57.711 33.333 0.00 0.00 0.00 3.13
225 226 6.703319 ACGAAAAAGGAAAGAAAAGGGAAAA 58.297 32.000 0.00 0.00 0.00 2.29
226 227 7.162761 ACGAAAAAGGAAAGAAAAGGGAAAAA 58.837 30.769 0.00 0.00 0.00 1.94
271 272 9.249053 AGGAAAGAAAGAAGAAAAAGAAGAAGT 57.751 29.630 0.00 0.00 0.00 3.01
272 273 9.295214 GGAAAGAAAGAAGAAAAAGAAGAAGTG 57.705 33.333 0.00 0.00 0.00 3.16
276 277 9.401058 AGAAAGAAGAAAAAGAAGAAGTGATCA 57.599 29.630 0.00 0.00 0.00 2.92
280 281 9.794685 AGAAGAAAAAGAAGAAGTGATCAAAAC 57.205 29.630 0.00 0.00 0.00 2.43
281 282 9.573133 GAAGAAAAAGAAGAAGTGATCAAAACA 57.427 29.630 0.00 0.00 0.00 2.83
283 284 9.525409 AGAAAAAGAAGAAGTGATCAAAACATG 57.475 29.630 0.00 0.00 0.00 3.21
284 285 7.704789 AAAAGAAGAAGTGATCAAAACATGC 57.295 32.000 0.00 0.00 0.00 4.06
285 286 6.395426 AAGAAGAAGTGATCAAAACATGCA 57.605 33.333 0.00 0.00 0.00 3.96
286 287 6.585695 AGAAGAAGTGATCAAAACATGCAT 57.414 33.333 0.00 0.00 0.00 3.96
287 288 6.989659 AGAAGAAGTGATCAAAACATGCATT 58.010 32.000 0.00 0.00 0.00 3.56
288 289 6.866770 AGAAGAAGTGATCAAAACATGCATTG 59.133 34.615 0.00 5.01 0.00 2.82
289 290 6.092955 AGAAGTGATCAAAACATGCATTGT 57.907 33.333 0.00 0.00 41.53 2.71
290 291 5.924254 AGAAGTGATCAAAACATGCATTGTG 59.076 36.000 0.00 0.00 38.99 3.33
291 292 4.562082 AGTGATCAAAACATGCATTGTGG 58.438 39.130 0.00 0.00 38.99 4.17
292 293 4.039488 AGTGATCAAAACATGCATTGTGGT 59.961 37.500 0.00 0.00 38.99 4.16
293 294 4.386652 GTGATCAAAACATGCATTGTGGTC 59.613 41.667 0.00 0.00 38.99 4.02
294 295 3.383620 TCAAAACATGCATTGTGGTCC 57.616 42.857 0.00 0.00 38.99 4.46
295 296 2.060284 CAAAACATGCATTGTGGTCCG 58.940 47.619 0.00 0.00 38.99 4.79
296 297 0.602562 AAACATGCATTGTGGTCCGG 59.397 50.000 0.00 0.00 38.99 5.14
297 298 1.250154 AACATGCATTGTGGTCCGGG 61.250 55.000 0.00 0.00 38.99 5.73
298 299 1.678635 CATGCATTGTGGTCCGGGT 60.679 57.895 0.00 0.00 0.00 5.28
299 300 1.678635 ATGCATTGTGGTCCGGGTG 60.679 57.895 0.00 0.00 0.00 4.61
300 301 3.061848 GCATTGTGGTCCGGGTGG 61.062 66.667 0.00 0.00 0.00 4.61
301 302 2.434331 CATTGTGGTCCGGGTGGT 59.566 61.111 0.00 0.00 36.30 4.16
302 303 1.228429 CATTGTGGTCCGGGTGGTT 60.228 57.895 0.00 0.00 36.30 3.67
303 304 0.037017 CATTGTGGTCCGGGTGGTTA 59.963 55.000 0.00 0.00 36.30 2.85
304 305 0.326927 ATTGTGGTCCGGGTGGTTAG 59.673 55.000 0.00 0.00 36.30 2.34
305 306 1.055551 TTGTGGTCCGGGTGGTTAGT 61.056 55.000 0.00 0.00 36.30 2.24
306 307 1.004200 GTGGTCCGGGTGGTTAGTG 60.004 63.158 0.00 0.00 36.30 2.74
307 308 2.046604 GGTCCGGGTGGTTAGTGC 60.047 66.667 0.00 0.00 36.30 4.40
308 309 2.745037 GTCCGGGTGGTTAGTGCA 59.255 61.111 0.00 0.00 36.30 4.57
309 310 1.375523 GTCCGGGTGGTTAGTGCAG 60.376 63.158 0.00 0.00 36.30 4.41
310 311 1.839747 TCCGGGTGGTTAGTGCAGT 60.840 57.895 0.00 0.00 36.30 4.40
311 312 1.072505 CCGGGTGGTTAGTGCAGTT 59.927 57.895 0.00 0.00 0.00 3.16
312 313 0.536460 CCGGGTGGTTAGTGCAGTTT 60.536 55.000 0.00 0.00 0.00 2.66
313 314 1.270947 CCGGGTGGTTAGTGCAGTTTA 60.271 52.381 0.00 0.00 0.00 2.01
314 315 2.617021 CCGGGTGGTTAGTGCAGTTTAT 60.617 50.000 0.00 0.00 0.00 1.40
315 316 2.676342 CGGGTGGTTAGTGCAGTTTATC 59.324 50.000 0.00 0.00 0.00 1.75
316 317 2.676342 GGGTGGTTAGTGCAGTTTATCG 59.324 50.000 0.00 0.00 0.00 2.92
317 318 3.592059 GGTGGTTAGTGCAGTTTATCGA 58.408 45.455 0.00 0.00 0.00 3.59
318 319 3.617263 GGTGGTTAGTGCAGTTTATCGAG 59.383 47.826 0.00 0.00 0.00 4.04
319 320 4.243270 GTGGTTAGTGCAGTTTATCGAGT 58.757 43.478 0.00 0.00 0.00 4.18
320 321 4.091509 GTGGTTAGTGCAGTTTATCGAGTG 59.908 45.833 0.00 0.00 0.00 3.51
321 322 3.062234 GGTTAGTGCAGTTTATCGAGTGC 59.938 47.826 0.00 0.00 44.40 4.40
325 326 2.145053 GCAGTTTATCGAGTGCAACG 57.855 50.000 8.02 8.02 45.86 4.10
326 327 1.724623 GCAGTTTATCGAGTGCAACGA 59.275 47.619 17.12 17.12 45.86 3.85
327 328 2.222596 GCAGTTTATCGAGTGCAACGAG 60.223 50.000 18.98 8.44 45.86 4.18
328 329 3.242518 CAGTTTATCGAGTGCAACGAGA 58.757 45.455 18.98 13.63 45.86 4.04
329 330 3.859961 CAGTTTATCGAGTGCAACGAGAT 59.140 43.478 18.98 10.65 45.86 2.75
330 331 4.027295 CAGTTTATCGAGTGCAACGAGATC 60.027 45.833 18.98 12.19 45.86 2.75
331 332 2.776312 TATCGAGTGCAACGAGATCC 57.224 50.000 18.98 0.00 45.86 3.36
332 333 1.107114 ATCGAGTGCAACGAGATCCT 58.893 50.000 18.98 3.42 45.86 3.24
333 334 0.171231 TCGAGTGCAACGAGATCCTG 59.829 55.000 12.15 0.00 45.86 3.86
334 335 0.803768 CGAGTGCAACGAGATCCTGG 60.804 60.000 8.56 0.00 45.86 4.45
335 336 0.460987 GAGTGCAACGAGATCCTGGG 60.461 60.000 0.00 0.00 45.86 4.45
336 337 1.194781 AGTGCAACGAGATCCTGGGT 61.195 55.000 0.00 0.00 45.86 4.51
337 338 0.321653 GTGCAACGAGATCCTGGGTT 60.322 55.000 0.00 0.00 0.00 4.11
338 339 0.400213 TGCAACGAGATCCTGGGTTT 59.600 50.000 0.00 0.00 0.00 3.27
339 340 1.202879 TGCAACGAGATCCTGGGTTTT 60.203 47.619 0.00 0.00 0.00 2.43
340 341 1.886542 GCAACGAGATCCTGGGTTTTT 59.113 47.619 0.00 0.00 0.00 1.94
374 375 7.861176 TTTGTTCGTAAATAGTTTGGATTGC 57.139 32.000 0.00 0.00 0.00 3.56
375 376 6.811253 TGTTCGTAAATAGTTTGGATTGCT 57.189 33.333 0.00 0.00 0.00 3.91
376 377 7.209471 TGTTCGTAAATAGTTTGGATTGCTT 57.791 32.000 0.00 0.00 0.00 3.91
377 378 8.325421 TGTTCGTAAATAGTTTGGATTGCTTA 57.675 30.769 0.00 0.00 0.00 3.09
378 379 8.231837 TGTTCGTAAATAGTTTGGATTGCTTAC 58.768 33.333 0.00 0.00 0.00 2.34
379 380 7.311364 TCGTAAATAGTTTGGATTGCTTACC 57.689 36.000 0.00 0.00 0.00 2.85
380 381 6.879993 TCGTAAATAGTTTGGATTGCTTACCA 59.120 34.615 0.00 0.00 0.00 3.25
381 382 6.964934 CGTAAATAGTTTGGATTGCTTACCAC 59.035 38.462 0.00 0.00 35.81 4.16
382 383 6.909550 AAATAGTTTGGATTGCTTACCACA 57.090 33.333 0.00 0.00 35.81 4.17
383 384 7.480760 AAATAGTTTGGATTGCTTACCACAT 57.519 32.000 0.00 0.00 35.81 3.21
384 385 8.588290 AAATAGTTTGGATTGCTTACCACATA 57.412 30.769 0.00 0.00 35.81 2.29
385 386 5.897377 AGTTTGGATTGCTTACCACATAC 57.103 39.130 0.00 0.00 35.81 2.39
386 387 5.570320 AGTTTGGATTGCTTACCACATACT 58.430 37.500 0.00 0.00 35.81 2.12
387 388 6.717289 AGTTTGGATTGCTTACCACATACTA 58.283 36.000 0.00 0.00 35.81 1.82
388 389 7.346471 AGTTTGGATTGCTTACCACATACTAT 58.654 34.615 0.00 0.00 35.81 2.12
389 390 8.491134 AGTTTGGATTGCTTACCACATACTATA 58.509 33.333 0.00 0.00 35.81 1.31
390 391 9.284968 GTTTGGATTGCTTACCACATACTATAT 57.715 33.333 0.00 0.00 35.81 0.86
391 392 9.502091 TTTGGATTGCTTACCACATACTATATC 57.498 33.333 0.00 0.00 35.81 1.63
392 393 8.201242 TGGATTGCTTACCACATACTATATCA 57.799 34.615 0.00 0.00 0.00 2.15
393 394 8.094548 TGGATTGCTTACCACATACTATATCAC 58.905 37.037 0.00 0.00 0.00 3.06
394 395 7.275779 GGATTGCTTACCACATACTATATCACG 59.724 40.741 0.00 0.00 0.00 4.35
395 396 6.644248 TGCTTACCACATACTATATCACGT 57.356 37.500 0.00 0.00 0.00 4.49
396 397 6.443792 TGCTTACCACATACTATATCACGTG 58.556 40.000 9.94 9.94 0.00 4.49
398 399 4.252971 ACCACATACTATATCACGTGGC 57.747 45.455 17.00 0.00 46.25 5.01
399 400 3.639561 ACCACATACTATATCACGTGGCA 59.360 43.478 17.00 3.90 46.25 4.92
400 401 4.100344 ACCACATACTATATCACGTGGCAA 59.900 41.667 17.00 1.48 46.25 4.52
401 402 4.686091 CCACATACTATATCACGTGGCAAG 59.314 45.833 17.00 10.69 37.68 4.01
402 403 4.686091 CACATACTATATCACGTGGCAAGG 59.314 45.833 17.00 6.47 0.00 3.61
403 404 4.587262 ACATACTATATCACGTGGCAAGGA 59.413 41.667 17.00 5.63 0.00 3.36
404 405 3.735237 ACTATATCACGTGGCAAGGAG 57.265 47.619 17.00 8.43 0.00 3.69
405 406 3.296854 ACTATATCACGTGGCAAGGAGA 58.703 45.455 17.00 2.89 0.00 3.71
406 407 3.898123 ACTATATCACGTGGCAAGGAGAT 59.102 43.478 17.00 10.09 0.00 2.75
407 408 2.890808 TATCACGTGGCAAGGAGATC 57.109 50.000 17.00 0.00 0.00 2.75
408 409 0.179000 ATCACGTGGCAAGGAGATCC 59.821 55.000 17.00 0.00 0.00 3.36
419 420 2.350863 AGGAGATCCTGGGTTTGACT 57.649 50.000 0.00 0.00 46.55 3.41
420 421 2.192263 AGGAGATCCTGGGTTTGACTC 58.808 52.381 0.00 0.00 46.55 3.36
421 422 2.192263 GGAGATCCTGGGTTTGACTCT 58.808 52.381 0.00 0.00 0.00 3.24
422 423 2.169561 GGAGATCCTGGGTTTGACTCTC 59.830 54.545 0.00 0.00 0.00 3.20
423 424 2.169561 GAGATCCTGGGTTTGACTCTCC 59.830 54.545 0.00 0.00 0.00 3.71
424 425 1.909302 GATCCTGGGTTTGACTCTCCA 59.091 52.381 0.00 0.00 0.00 3.86
425 426 1.056660 TCCTGGGTTTGACTCTCCAC 58.943 55.000 0.00 0.00 0.00 4.02
426 427 0.320771 CCTGGGTTTGACTCTCCACG 60.321 60.000 0.00 0.00 0.00 4.94
427 428 0.951040 CTGGGTTTGACTCTCCACGC 60.951 60.000 0.00 0.00 0.00 5.34
428 429 2.027625 GGGTTTGACTCTCCACGCG 61.028 63.158 3.53 3.53 0.00 6.01
429 430 2.027625 GGTTTGACTCTCCACGCGG 61.028 63.158 12.47 0.00 0.00 6.46
430 431 1.006571 GTTTGACTCTCCACGCGGA 60.007 57.895 12.47 0.00 39.79 5.54
431 432 1.006571 TTTGACTCTCCACGCGGAC 60.007 57.895 12.47 0.00 35.91 4.79
435 436 4.421479 CTCTCCACGCGGACGCTT 62.421 66.667 12.47 1.98 45.53 4.68
436 437 3.916392 CTCTCCACGCGGACGCTTT 62.916 63.158 12.47 0.00 45.53 3.51
437 438 3.041940 CTCCACGCGGACGCTTTT 61.042 61.111 12.47 0.00 45.53 2.27
438 439 2.589442 TCCACGCGGACGCTTTTT 60.589 55.556 12.47 0.00 45.53 1.94
484 485 0.528924 AAAAATCTAAACGGGCCGGC 59.471 50.000 31.78 21.18 0.00 6.13
485 486 1.317431 AAAATCTAAACGGGCCGGCC 61.317 55.000 38.57 38.57 0.00 6.13
496 497 3.752339 GCCGGCCCAGCTTGAAAG 61.752 66.667 18.11 0.00 0.00 2.62
497 498 3.064324 CCGGCCCAGCTTGAAAGG 61.064 66.667 0.00 0.00 0.00 3.11
498 499 3.064324 CGGCCCAGCTTGAAAGGG 61.064 66.667 0.00 1.56 45.68 3.95
499 500 2.118294 GGCCCAGCTTGAAAGGGT 59.882 61.111 7.83 0.00 44.69 4.34
500 501 2.278330 GGCCCAGCTTGAAAGGGTG 61.278 63.158 7.83 0.00 44.69 4.61
501 502 1.531602 GCCCAGCTTGAAAGGGTGT 60.532 57.895 7.83 0.00 44.69 4.16
502 503 1.809567 GCCCAGCTTGAAAGGGTGTG 61.810 60.000 7.83 0.00 44.69 3.82
503 504 0.468029 CCCAGCTTGAAAGGGTGTGT 60.468 55.000 0.00 0.00 37.81 3.72
504 505 0.670162 CCAGCTTGAAAGGGTGTGTG 59.330 55.000 0.00 0.00 0.00 3.82
505 506 1.392589 CAGCTTGAAAGGGTGTGTGT 58.607 50.000 0.00 0.00 0.00 3.72
512 513 4.602259 AGGGTGTGTGTGCGTCCG 62.602 66.667 0.00 0.00 0.00 4.79
538 539 3.899531 GCAAAATGCACAATAACAAACGC 59.100 39.130 0.00 0.00 44.26 4.84
545 546 2.979813 CACAATAACAAACGCCTGAAGC 59.020 45.455 0.00 0.00 38.52 3.86
562 563 5.447818 CCTGAAGCGTCAAATAGGAAATCAC 60.448 44.000 3.39 0.00 31.88 3.06
612 616 1.207089 TGGTCATTCATCCACGAGTCC 59.793 52.381 0.00 0.00 0.00 3.85
621 625 1.227527 CCACGAGTCCTGTTGCACA 60.228 57.895 0.00 0.00 0.00 4.57
622 626 0.603707 CCACGAGTCCTGTTGCACAT 60.604 55.000 0.00 0.00 0.00 3.21
647 651 4.530857 CAGGGGCGGATCGACACC 62.531 72.222 0.00 0.00 40.38 4.16
653 657 0.878961 GGCGGATCGACACCCATTAC 60.879 60.000 5.12 0.00 33.63 1.89
673 677 4.415150 CCACCGGACATGCAGCCT 62.415 66.667 9.46 0.00 0.00 4.58
718 722 0.741326 CGAGACTCGATCCACCACAT 59.259 55.000 20.25 0.00 43.74 3.21
732 736 0.888736 CCACATCCAGCCGTTTGACA 60.889 55.000 0.00 0.00 0.00 3.58
768 802 1.239296 GCCGGGAATAATTACGCCCC 61.239 60.000 15.45 11.78 37.27 5.80
776 810 2.035237 TAATTACGCCCCGAGCCAGG 62.035 60.000 0.00 0.00 38.78 4.45
828 862 2.899339 GAAGGGCCTGCGCAGATC 60.899 66.667 38.06 26.60 36.38 2.75
898 932 4.111016 CCAGCACATGTGGCAGCG 62.111 66.667 26.55 11.24 0.00 5.18
991 1036 0.250727 AATACCATCCATTCCGCCCG 60.251 55.000 0.00 0.00 0.00 6.13
997 1042 2.343475 ATCCATTCCGCCCGCATTCT 62.343 55.000 0.00 0.00 0.00 2.40
1009 1054 0.108186 CGCATTCTCCACTACCAGCA 60.108 55.000 0.00 0.00 0.00 4.41
1017 1062 3.391382 ACTACCAGCACTCCGGCC 61.391 66.667 0.00 0.00 0.00 6.13
1285 1341 7.834068 TTCTCATCTTCTTTTCTAACCGATG 57.166 36.000 0.00 0.00 0.00 3.84
1289 1345 1.365699 TCTTTTCTAACCGATGCCGC 58.634 50.000 0.00 0.00 0.00 6.53
1312 1377 1.230324 GTTTCTTGCAGAAGGTCGCT 58.770 50.000 0.00 0.00 35.37 4.93
1314 1379 0.106708 TTCTTGCAGAAGGTCGCTGT 59.893 50.000 0.00 0.00 35.81 4.40
1640 1719 3.301706 GTTTTATCGCTCGGTTTGCAAA 58.698 40.909 8.05 8.05 0.00 3.68
1641 1720 2.604969 TTATCGCTCGGTTTGCAAAC 57.395 45.000 30.09 30.09 38.17 2.93
1642 1721 0.440758 TATCGCTCGGTTTGCAAACG 59.559 50.000 30.40 25.11 39.77 3.60
1643 1722 2.182614 ATCGCTCGGTTTGCAAACGG 62.183 55.000 32.59 32.59 39.77 4.44
1644 1723 2.729491 GCTCGGTTTGCAAACGGC 60.729 61.111 33.20 29.20 45.13 5.68
1645 1724 3.030652 CTCGGTTTGCAAACGGCT 58.969 55.556 33.20 0.00 45.15 5.52
1646 1725 1.370414 CTCGGTTTGCAAACGGCTG 60.370 57.895 33.20 25.80 45.15 4.85
1647 1726 3.029735 CGGTTTGCAAACGGCTGC 61.030 61.111 30.40 17.97 45.15 5.25
1648 1727 2.661537 GGTTTGCAAACGGCTGCC 60.662 61.111 30.40 15.84 45.15 4.85
1649 1728 2.105930 GTTTGCAAACGGCTGCCA 59.894 55.556 25.35 0.00 45.15 4.92
1650 1729 1.520342 GTTTGCAAACGGCTGCCAA 60.520 52.632 25.35 0.59 45.15 4.52
1651 1730 1.227205 TTTGCAAACGGCTGCCAAG 60.227 52.632 20.29 5.70 45.15 3.61
1661 1740 2.975536 CTGCCAAGCCATGTTGGG 59.024 61.111 14.96 1.01 46.31 4.12
2212 2291 0.829333 ACCTCGCTCAGATGATGCTT 59.171 50.000 0.00 0.00 0.00 3.91
2247 3518 5.404946 TCAGTAAGTGTATAAGGTTGACGC 58.595 41.667 0.00 0.00 0.00 5.19
2248 3519 5.047872 TCAGTAAGTGTATAAGGTTGACGCA 60.048 40.000 0.00 0.00 0.00 5.24
2440 3714 5.163301 TGCACATCTAAATCCTACTCCCTTC 60.163 44.000 0.00 0.00 0.00 3.46
2446 3720 2.777459 ATCCTACTCCCTTCGTCCAT 57.223 50.000 0.00 0.00 0.00 3.41
2458 3732 4.809426 CCCTTCGTCCATGAATAAGTGTAC 59.191 45.833 0.00 0.00 0.00 2.90
2483 3757 7.773690 ACTCCTAGCTTTTGTCTTAAGTGAAAA 59.226 33.333 1.63 7.99 0.00 2.29
2531 3805 5.500234 AGGACAAAGTAGCAGCATTTATGA 58.500 37.500 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 9.863845 ACTTTTCCTCGAATTTTTGAACTTAAA 57.136 25.926 0.00 0.00 0.00 1.52
51 52 9.863845 AACTTTTCCTCGAATTTTTGAACTTAA 57.136 25.926 0.00 0.00 0.00 1.85
52 53 9.863845 AAACTTTTCCTCGAATTTTTGAACTTA 57.136 25.926 0.00 0.00 0.00 2.24
53 54 8.771920 AAACTTTTCCTCGAATTTTTGAACTT 57.228 26.923 0.00 0.00 0.00 2.66
146 147 9.911138 ACTTTTTGCAAAATTGATGAACTTTTT 57.089 22.222 24.39 0.13 0.00 1.94
147 148 9.911138 AACTTTTTGCAAAATTGATGAACTTTT 57.089 22.222 24.39 6.63 0.00 2.27
148 149 9.558648 GAACTTTTTGCAAAATTGATGAACTTT 57.441 25.926 24.39 9.33 0.00 2.66
149 150 8.728833 TGAACTTTTTGCAAAATTGATGAACTT 58.271 25.926 24.39 9.92 0.00 2.66
150 151 8.266392 TGAACTTTTTGCAAAATTGATGAACT 57.734 26.923 24.39 3.31 0.00 3.01
151 152 8.949953 CATGAACTTTTTGCAAAATTGATGAAC 58.050 29.630 24.39 11.39 0.00 3.18
152 153 8.890718 TCATGAACTTTTTGCAAAATTGATGAA 58.109 25.926 25.14 15.36 26.39 2.57
153 154 8.434733 TCATGAACTTTTTGCAAAATTGATGA 57.565 26.923 24.27 24.27 0.00 2.92
154 155 9.672086 ATTCATGAACTTTTTGCAAAATTGATG 57.328 25.926 24.39 22.77 0.00 3.07
195 196 9.104965 CCCTTTTCTTTCCTTTTTCGTTTTATT 57.895 29.630 0.00 0.00 0.00 1.40
196 197 8.479689 TCCCTTTTCTTTCCTTTTTCGTTTTAT 58.520 29.630 0.00 0.00 0.00 1.40
197 198 7.838884 TCCCTTTTCTTTCCTTTTTCGTTTTA 58.161 30.769 0.00 0.00 0.00 1.52
198 199 6.703319 TCCCTTTTCTTTCCTTTTTCGTTTT 58.297 32.000 0.00 0.00 0.00 2.43
199 200 6.288941 TCCCTTTTCTTTCCTTTTTCGTTT 57.711 33.333 0.00 0.00 0.00 3.60
200 201 5.925506 TCCCTTTTCTTTCCTTTTTCGTT 57.074 34.783 0.00 0.00 0.00 3.85
201 202 5.925506 TTCCCTTTTCTTTCCTTTTTCGT 57.074 34.783 0.00 0.00 0.00 3.85
202 203 7.603963 TTTTTCCCTTTTCTTTCCTTTTTCG 57.396 32.000 0.00 0.00 0.00 3.46
245 246 9.249053 ACTTCTTCTTTTTCTTCTTTCTTTCCT 57.751 29.630 0.00 0.00 0.00 3.36
246 247 9.295214 CACTTCTTCTTTTTCTTCTTTCTTTCC 57.705 33.333 0.00 0.00 0.00 3.13
250 251 9.401058 TGATCACTTCTTCTTTTTCTTCTTTCT 57.599 29.630 0.00 0.00 0.00 2.52
254 255 9.794685 GTTTTGATCACTTCTTCTTTTTCTTCT 57.205 29.630 0.00 0.00 0.00 2.85
255 256 9.573133 TGTTTTGATCACTTCTTCTTTTTCTTC 57.427 29.630 0.00 0.00 0.00 2.87
257 258 9.525409 CATGTTTTGATCACTTCTTCTTTTTCT 57.475 29.630 0.00 0.00 0.00 2.52
258 259 8.271487 GCATGTTTTGATCACTTCTTCTTTTTC 58.729 33.333 0.00 0.00 0.00 2.29
259 260 7.765360 TGCATGTTTTGATCACTTCTTCTTTTT 59.235 29.630 0.00 0.00 0.00 1.94
260 261 7.267128 TGCATGTTTTGATCACTTCTTCTTTT 58.733 30.769 0.00 0.00 0.00 2.27
261 262 6.808829 TGCATGTTTTGATCACTTCTTCTTT 58.191 32.000 0.00 0.00 0.00 2.52
262 263 6.395426 TGCATGTTTTGATCACTTCTTCTT 57.605 33.333 0.00 0.00 0.00 2.52
263 264 6.585695 ATGCATGTTTTGATCACTTCTTCT 57.414 33.333 0.00 0.00 0.00 2.85
264 265 6.643770 ACAATGCATGTTTTGATCACTTCTTC 59.356 34.615 0.00 0.00 40.06 2.87
265 266 6.422701 CACAATGCATGTTTTGATCACTTCTT 59.577 34.615 0.00 0.00 41.46 2.52
266 267 5.924254 CACAATGCATGTTTTGATCACTTCT 59.076 36.000 0.00 0.00 41.46 2.85
267 268 5.119588 CCACAATGCATGTTTTGATCACTTC 59.880 40.000 0.00 0.00 41.46 3.01
268 269 4.992319 CCACAATGCATGTTTTGATCACTT 59.008 37.500 0.00 0.00 41.46 3.16
269 270 4.039488 ACCACAATGCATGTTTTGATCACT 59.961 37.500 0.00 0.00 41.46 3.41
270 271 4.309099 ACCACAATGCATGTTTTGATCAC 58.691 39.130 0.00 0.00 41.46 3.06
271 272 4.558178 GACCACAATGCATGTTTTGATCA 58.442 39.130 0.00 0.00 41.46 2.92
272 273 3.928375 GGACCACAATGCATGTTTTGATC 59.072 43.478 0.00 9.32 41.46 2.92
273 274 3.614630 CGGACCACAATGCATGTTTTGAT 60.615 43.478 0.00 2.72 41.46 2.57
274 275 2.288091 CGGACCACAATGCATGTTTTGA 60.288 45.455 0.00 0.00 41.46 2.69
275 276 2.060284 CGGACCACAATGCATGTTTTG 58.940 47.619 0.00 0.00 41.46 2.44
276 277 1.000731 CCGGACCACAATGCATGTTTT 59.999 47.619 0.00 0.00 41.46 2.43
277 278 0.602562 CCGGACCACAATGCATGTTT 59.397 50.000 0.00 0.00 41.46 2.83
278 279 1.250154 CCCGGACCACAATGCATGTT 61.250 55.000 0.73 0.00 41.46 2.71
279 280 1.678635 CCCGGACCACAATGCATGT 60.679 57.895 0.73 0.00 45.34 3.21
280 281 1.678635 ACCCGGACCACAATGCATG 60.679 57.895 0.73 0.00 0.00 4.06
281 282 1.678635 CACCCGGACCACAATGCAT 60.679 57.895 0.73 0.00 0.00 3.96
282 283 2.282110 CACCCGGACCACAATGCA 60.282 61.111 0.73 0.00 0.00 3.96
283 284 3.061848 CCACCCGGACCACAATGC 61.062 66.667 0.73 0.00 0.00 3.56
284 285 0.037017 TAACCACCCGGACCACAATG 59.963 55.000 0.73 0.00 35.59 2.82
285 286 0.326927 CTAACCACCCGGACCACAAT 59.673 55.000 0.73 0.00 35.59 2.71
286 287 1.055551 ACTAACCACCCGGACCACAA 61.056 55.000 0.73 0.00 35.59 3.33
287 288 1.459921 ACTAACCACCCGGACCACA 60.460 57.895 0.73 0.00 35.59 4.17
288 289 1.004200 CACTAACCACCCGGACCAC 60.004 63.158 0.73 0.00 35.59 4.16
289 290 2.886134 GCACTAACCACCCGGACCA 61.886 63.158 0.73 0.00 35.59 4.02
290 291 2.046604 GCACTAACCACCCGGACC 60.047 66.667 0.73 0.00 35.59 4.46
291 292 1.375523 CTGCACTAACCACCCGGAC 60.376 63.158 0.73 0.00 35.59 4.79
292 293 1.412453 AACTGCACTAACCACCCGGA 61.412 55.000 0.73 0.00 35.59 5.14
293 294 0.536460 AAACTGCACTAACCACCCGG 60.536 55.000 0.00 0.00 38.77 5.73
294 295 2.172851 TAAACTGCACTAACCACCCG 57.827 50.000 0.00 0.00 0.00 5.28
295 296 2.676342 CGATAAACTGCACTAACCACCC 59.324 50.000 0.00 0.00 0.00 4.61
296 297 3.592059 TCGATAAACTGCACTAACCACC 58.408 45.455 0.00 0.00 0.00 4.61
297 298 4.091509 CACTCGATAAACTGCACTAACCAC 59.908 45.833 0.00 0.00 0.00 4.16
298 299 4.242475 CACTCGATAAACTGCACTAACCA 58.758 43.478 0.00 0.00 0.00 3.67
299 300 3.062234 GCACTCGATAAACTGCACTAACC 59.938 47.826 0.00 0.00 0.00 2.85
300 301 3.678072 TGCACTCGATAAACTGCACTAAC 59.322 43.478 0.00 0.00 34.73 2.34
301 302 3.920446 TGCACTCGATAAACTGCACTAA 58.080 40.909 0.00 0.00 34.73 2.24
302 303 3.586100 TGCACTCGATAAACTGCACTA 57.414 42.857 0.00 0.00 34.73 2.74
303 304 2.455674 TGCACTCGATAAACTGCACT 57.544 45.000 0.00 0.00 34.73 4.40
304 305 2.721797 CGTTGCACTCGATAAACTGCAC 60.722 50.000 4.72 0.00 39.32 4.57
305 306 1.459209 CGTTGCACTCGATAAACTGCA 59.541 47.619 4.72 0.00 37.86 4.41
306 307 1.724623 TCGTTGCACTCGATAAACTGC 59.275 47.619 8.76 0.00 32.30 4.40
307 308 3.242518 TCTCGTTGCACTCGATAAACTG 58.757 45.455 12.46 2.38 36.73 3.16
308 309 3.570926 TCTCGTTGCACTCGATAAACT 57.429 42.857 12.46 0.00 36.73 2.66
309 310 3.243177 GGATCTCGTTGCACTCGATAAAC 59.757 47.826 12.46 4.87 36.73 2.01
310 311 3.130516 AGGATCTCGTTGCACTCGATAAA 59.869 43.478 12.46 4.05 36.73 1.40
311 312 2.688446 AGGATCTCGTTGCACTCGATAA 59.312 45.455 12.46 6.07 36.73 1.75
312 313 2.033424 CAGGATCTCGTTGCACTCGATA 59.967 50.000 12.46 7.19 36.73 2.92
313 314 1.107114 AGGATCTCGTTGCACTCGAT 58.893 50.000 12.46 0.88 36.73 3.59
314 315 0.171231 CAGGATCTCGTTGCACTCGA 59.829 55.000 11.69 11.69 35.96 4.04
315 316 0.803768 CCAGGATCTCGTTGCACTCG 60.804 60.000 4.38 4.38 0.00 4.18
316 317 0.460987 CCCAGGATCTCGTTGCACTC 60.461 60.000 0.00 0.00 0.00 3.51
317 318 1.194781 ACCCAGGATCTCGTTGCACT 61.195 55.000 0.00 0.00 0.00 4.40
318 319 0.321653 AACCCAGGATCTCGTTGCAC 60.322 55.000 0.00 0.00 0.00 4.57
319 320 0.400213 AAACCCAGGATCTCGTTGCA 59.600 50.000 0.00 0.00 0.00 4.08
320 321 1.534729 AAAACCCAGGATCTCGTTGC 58.465 50.000 0.00 0.00 0.00 4.17
348 349 9.562583 GCAATCCAAACTATTTACGAACAAATA 57.437 29.630 0.00 0.00 30.84 1.40
349 350 8.303876 AGCAATCCAAACTATTTACGAACAAAT 58.696 29.630 0.00 0.00 32.91 2.32
350 351 7.653647 AGCAATCCAAACTATTTACGAACAAA 58.346 30.769 0.00 0.00 0.00 2.83
351 352 7.209471 AGCAATCCAAACTATTTACGAACAA 57.791 32.000 0.00 0.00 0.00 2.83
352 353 6.811253 AGCAATCCAAACTATTTACGAACA 57.189 33.333 0.00 0.00 0.00 3.18
353 354 7.695201 GGTAAGCAATCCAAACTATTTACGAAC 59.305 37.037 0.00 0.00 0.00 3.95
354 355 7.390996 TGGTAAGCAATCCAAACTATTTACGAA 59.609 33.333 0.00 0.00 0.00 3.85
355 356 6.879993 TGGTAAGCAATCCAAACTATTTACGA 59.120 34.615 0.00 0.00 0.00 3.43
356 357 6.964934 GTGGTAAGCAATCCAAACTATTTACG 59.035 38.462 0.00 0.00 35.38 3.18
357 358 7.822658 TGTGGTAAGCAATCCAAACTATTTAC 58.177 34.615 0.00 0.00 35.38 2.01
358 359 8.588290 ATGTGGTAAGCAATCCAAACTATTTA 57.412 30.769 0.00 0.00 35.38 1.40
359 360 6.909550 TGTGGTAAGCAATCCAAACTATTT 57.090 33.333 0.00 0.00 35.38 1.40
360 361 7.834181 AGTATGTGGTAAGCAATCCAAACTATT 59.166 33.333 0.00 0.00 35.38 1.73
361 362 7.346471 AGTATGTGGTAAGCAATCCAAACTAT 58.654 34.615 0.00 0.00 35.38 2.12
362 363 6.717289 AGTATGTGGTAAGCAATCCAAACTA 58.283 36.000 0.00 0.00 35.38 2.24
363 364 5.570320 AGTATGTGGTAAGCAATCCAAACT 58.430 37.500 0.00 0.00 35.38 2.66
364 365 5.897377 AGTATGTGGTAAGCAATCCAAAC 57.103 39.130 0.00 0.00 35.38 2.93
365 366 9.502091 GATATAGTATGTGGTAAGCAATCCAAA 57.498 33.333 0.00 0.00 35.38 3.28
366 367 8.655901 TGATATAGTATGTGGTAAGCAATCCAA 58.344 33.333 0.00 0.00 35.38 3.53
367 368 8.094548 GTGATATAGTATGTGGTAAGCAATCCA 58.905 37.037 0.00 0.00 0.00 3.41
368 369 7.275779 CGTGATATAGTATGTGGTAAGCAATCC 59.724 40.741 0.00 0.00 0.00 3.01
369 370 7.813148 ACGTGATATAGTATGTGGTAAGCAATC 59.187 37.037 0.00 0.00 0.00 2.67
370 371 7.598869 CACGTGATATAGTATGTGGTAAGCAAT 59.401 37.037 10.90 0.00 31.75 3.56
371 372 6.921307 CACGTGATATAGTATGTGGTAAGCAA 59.079 38.462 10.90 0.00 31.75 3.91
372 373 6.443792 CACGTGATATAGTATGTGGTAAGCA 58.556 40.000 10.90 0.00 31.75 3.91
373 374 5.862323 CCACGTGATATAGTATGTGGTAAGC 59.138 44.000 19.30 0.00 44.94 3.09
379 380 4.686091 CCTTGCCACGTGATATAGTATGTG 59.314 45.833 19.30 0.00 34.42 3.21
380 381 4.587262 TCCTTGCCACGTGATATAGTATGT 59.413 41.667 19.30 0.00 0.00 2.29
381 382 5.048013 TCTCCTTGCCACGTGATATAGTATG 60.048 44.000 19.30 1.63 0.00 2.39
382 383 5.077564 TCTCCTTGCCACGTGATATAGTAT 58.922 41.667 19.30 0.00 0.00 2.12
383 384 4.466827 TCTCCTTGCCACGTGATATAGTA 58.533 43.478 19.30 0.00 0.00 1.82
384 385 3.296854 TCTCCTTGCCACGTGATATAGT 58.703 45.455 19.30 0.00 0.00 2.12
385 386 4.489810 GATCTCCTTGCCACGTGATATAG 58.510 47.826 19.30 8.41 0.00 1.31
386 387 3.258372 GGATCTCCTTGCCACGTGATATA 59.742 47.826 19.30 0.00 0.00 0.86
387 388 2.037772 GGATCTCCTTGCCACGTGATAT 59.962 50.000 19.30 0.00 0.00 1.63
388 389 1.412710 GGATCTCCTTGCCACGTGATA 59.587 52.381 19.30 1.81 0.00 2.15
389 390 0.179000 GGATCTCCTTGCCACGTGAT 59.821 55.000 19.30 0.00 0.00 3.06
390 391 0.904865 AGGATCTCCTTGCCACGTGA 60.905 55.000 19.30 0.00 46.09 4.35
391 392 0.742281 CAGGATCTCCTTGCCACGTG 60.742 60.000 9.08 9.08 46.09 4.49
392 393 1.599047 CAGGATCTCCTTGCCACGT 59.401 57.895 0.00 0.00 46.09 4.49
393 394 1.153289 CCAGGATCTCCTTGCCACG 60.153 63.158 0.00 0.00 46.09 4.94
394 395 1.225704 CCCAGGATCTCCTTGCCAC 59.774 63.158 0.00 0.00 46.09 5.01
395 396 0.846427 AACCCAGGATCTCCTTGCCA 60.846 55.000 0.00 0.00 46.09 4.92
396 397 0.332972 AAACCCAGGATCTCCTTGCC 59.667 55.000 0.00 0.00 46.09 4.52
397 398 1.004745 TCAAACCCAGGATCTCCTTGC 59.995 52.381 0.00 0.00 46.09 4.01
398 399 2.307098 AGTCAAACCCAGGATCTCCTTG 59.693 50.000 0.00 0.00 46.09 3.61
399 400 2.573915 GAGTCAAACCCAGGATCTCCTT 59.426 50.000 0.00 0.00 46.09 3.36
401 402 2.169561 GAGAGTCAAACCCAGGATCTCC 59.830 54.545 0.00 0.00 0.00 3.71
402 403 2.169561 GGAGAGTCAAACCCAGGATCTC 59.830 54.545 0.00 0.00 0.00 2.75
403 404 2.192263 GGAGAGTCAAACCCAGGATCT 58.808 52.381 0.00 0.00 0.00 2.75
404 405 1.909302 TGGAGAGTCAAACCCAGGATC 59.091 52.381 0.00 0.00 0.00 3.36
405 406 1.630878 GTGGAGAGTCAAACCCAGGAT 59.369 52.381 0.00 0.00 0.00 3.24
406 407 1.056660 GTGGAGAGTCAAACCCAGGA 58.943 55.000 0.00 0.00 0.00 3.86
407 408 0.320771 CGTGGAGAGTCAAACCCAGG 60.321 60.000 0.00 0.00 0.00 4.45
408 409 0.951040 GCGTGGAGAGTCAAACCCAG 60.951 60.000 0.00 0.00 0.00 4.45
409 410 1.070786 GCGTGGAGAGTCAAACCCA 59.929 57.895 0.00 0.00 0.00 4.51
410 411 2.027625 CGCGTGGAGAGTCAAACCC 61.028 63.158 0.00 0.00 0.00 4.11
411 412 2.027625 CCGCGTGGAGAGTCAAACC 61.028 63.158 10.20 0.00 37.49 3.27
412 413 1.006571 TCCGCGTGGAGAGTCAAAC 60.007 57.895 15.21 0.00 40.17 2.93
413 414 3.450507 TCCGCGTGGAGAGTCAAA 58.549 55.556 15.21 0.00 40.17 2.69
465 466 0.528924 GCCGGCCCGTTTAGATTTTT 59.471 50.000 18.11 0.00 0.00 1.94
466 467 1.317431 GGCCGGCCCGTTTAGATTTT 61.317 55.000 36.64 0.00 0.00 1.82
467 468 1.751544 GGCCGGCCCGTTTAGATTT 60.752 57.895 36.64 0.00 0.00 2.17
468 469 2.124445 GGCCGGCCCGTTTAGATT 60.124 61.111 36.64 0.00 0.00 2.40
479 480 3.752339 CTTTCAAGCTGGGCCGGC 61.752 66.667 30.23 30.23 35.73 6.13
480 481 3.064324 CCTTTCAAGCTGGGCCGG 61.064 66.667 8.39 8.39 0.00 6.13
481 482 3.064324 CCCTTTCAAGCTGGGCCG 61.064 66.667 0.00 0.00 33.88 6.13
482 483 2.118294 ACCCTTTCAAGCTGGGCC 59.882 61.111 5.98 0.00 44.56 5.80
483 484 1.531602 ACACCCTTTCAAGCTGGGC 60.532 57.895 5.98 0.00 44.56 5.36
484 485 0.468029 ACACACCCTTTCAAGCTGGG 60.468 55.000 4.52 4.52 46.07 4.45
485 486 0.670162 CACACACCCTTTCAAGCTGG 59.330 55.000 0.00 0.00 0.00 4.85
486 487 1.066002 CACACACACCCTTTCAAGCTG 59.934 52.381 0.00 0.00 0.00 4.24
487 488 1.392589 CACACACACCCTTTCAAGCT 58.607 50.000 0.00 0.00 0.00 3.74
488 489 0.249031 GCACACACACCCTTTCAAGC 60.249 55.000 0.00 0.00 0.00 4.01
489 490 0.029300 CGCACACACACCCTTTCAAG 59.971 55.000 0.00 0.00 0.00 3.02
490 491 0.678366 ACGCACACACACCCTTTCAA 60.678 50.000 0.00 0.00 0.00 2.69
491 492 1.078072 ACGCACACACACCCTTTCA 60.078 52.632 0.00 0.00 0.00 2.69
492 493 1.647084 GACGCACACACACCCTTTC 59.353 57.895 0.00 0.00 0.00 2.62
493 494 1.822186 GGACGCACACACACCCTTT 60.822 57.895 0.00 0.00 0.00 3.11
494 495 2.203153 GGACGCACACACACCCTT 60.203 61.111 0.00 0.00 0.00 3.95
495 496 4.602259 CGGACGCACACACACCCT 62.602 66.667 0.00 0.00 0.00 4.34
496 497 4.903010 ACGGACGCACACACACCC 62.903 66.667 0.00 0.00 0.00 4.61
497 498 2.466140 AAACGGACGCACACACACC 61.466 57.895 0.00 0.00 0.00 4.16
498 499 1.297304 CAAACGGACGCACACACAC 60.297 57.895 0.00 0.00 0.00 3.82
499 500 3.094154 CAAACGGACGCACACACA 58.906 55.556 0.00 0.00 0.00 3.72
500 501 2.351888 GCAAACGGACGCACACAC 60.352 61.111 0.00 0.00 0.00 3.82
501 502 1.923227 TTTGCAAACGGACGCACACA 61.923 50.000 8.05 0.00 38.00 3.72
502 503 0.798771 TTTTGCAAACGGACGCACAC 60.799 50.000 12.39 0.00 38.00 3.82
503 504 0.101399 ATTTTGCAAACGGACGCACA 59.899 45.000 12.39 0.00 38.00 4.57
504 505 0.502275 CATTTTGCAAACGGACGCAC 59.498 50.000 12.39 0.00 38.00 5.34
505 506 1.211818 GCATTTTGCAAACGGACGCA 61.212 50.000 12.39 0.00 44.26 5.24
538 539 4.635765 TGATTTCCTATTTGACGCTTCAGG 59.364 41.667 0.00 0.00 31.71 3.86
545 546 5.621197 TTGGTGTGATTTCCTATTTGACG 57.379 39.130 0.00 0.00 0.00 4.35
583 584 5.540911 GTGGATGAATGACCATTTTTGTGT 58.459 37.500 0.00 0.00 38.48 3.72
586 587 5.058149 TCGTGGATGAATGACCATTTTTG 57.942 39.130 0.00 0.00 38.48 2.44
600 604 0.320683 TGCAACAGGACTCGTGGATG 60.321 55.000 3.87 3.73 0.00 3.51
630 634 4.530857 GGTGTCGATCCGCCCCTG 62.531 72.222 0.00 0.00 0.00 4.45
643 647 1.002624 CGGTGGCTGTAATGGGTGT 60.003 57.895 0.00 0.00 0.00 4.16
645 649 1.921346 TCCGGTGGCTGTAATGGGT 60.921 57.895 0.00 0.00 0.00 4.51
647 651 0.107214 ATGTCCGGTGGCTGTAATGG 60.107 55.000 0.00 0.00 0.00 3.16
653 657 3.129502 CTGCATGTCCGGTGGCTG 61.130 66.667 0.00 1.70 0.00 4.85
673 677 1.940752 GCGTGCTTACCTTACCCGAAA 60.941 52.381 0.00 0.00 0.00 3.46
718 722 0.179234 TCAACTGTCAAACGGCTGGA 59.821 50.000 0.00 0.00 0.00 3.86
732 736 1.670811 CGGCTCACAACTTGTTCAACT 59.329 47.619 0.00 0.00 0.00 3.16
828 862 1.950007 AGTCTGTCGGTGACTGTCG 59.050 57.895 2.98 0.00 42.46 4.35
923 963 2.644992 GGAGCCGTTTTGCAGGTG 59.355 61.111 0.00 0.00 0.00 4.00
991 1036 1.065854 AGTGCTGGTAGTGGAGAATGC 60.066 52.381 0.00 0.00 0.00 3.56
997 1042 1.982395 CCGGAGTGCTGGTAGTGGA 60.982 63.158 0.00 0.00 35.70 4.02
1009 1054 2.258726 GCAGTTTTTCGGCCGGAGT 61.259 57.895 27.83 9.23 0.00 3.85
1017 1062 3.603770 GGATTGAATCGTGCAGTTTTTCG 59.396 43.478 0.00 0.00 0.00 3.46
1285 1341 1.370900 CTGCAAGAAACACAGCGGC 60.371 57.895 0.00 0.00 34.07 6.53
1473 1538 1.068417 ACGCAGTGCCGACTAACAA 59.932 52.632 10.11 0.00 42.51 2.83
1643 1722 2.263540 CCAACATGGCTTGGCAGC 59.736 61.111 5.31 1.00 46.52 5.25
1644 1723 2.975536 CCCAACATGGCTTGGCAG 59.024 61.111 9.15 0.00 39.67 4.85
1652 1731 0.606401 AACGAGACAGCCCAACATGG 60.606 55.000 0.00 0.00 37.25 3.66
1653 1732 2.093306 TAACGAGACAGCCCAACATG 57.907 50.000 0.00 0.00 0.00 3.21
1654 1733 2.851263 TTAACGAGACAGCCCAACAT 57.149 45.000 0.00 0.00 0.00 2.71
1655 1734 2.851263 ATTAACGAGACAGCCCAACA 57.149 45.000 0.00 0.00 0.00 3.33
1656 1735 3.821841 CAAATTAACGAGACAGCCCAAC 58.178 45.455 0.00 0.00 0.00 3.77
1657 1736 2.227865 GCAAATTAACGAGACAGCCCAA 59.772 45.455 0.00 0.00 0.00 4.12
1658 1737 1.810151 GCAAATTAACGAGACAGCCCA 59.190 47.619 0.00 0.00 0.00 5.36
1659 1738 2.084546 AGCAAATTAACGAGACAGCCC 58.915 47.619 0.00 0.00 0.00 5.19
1660 1739 3.831715 AAGCAAATTAACGAGACAGCC 57.168 42.857 0.00 0.00 0.00 4.85
1661 1740 8.175716 ACTAATTAAGCAAATTAACGAGACAGC 58.824 33.333 0.00 0.00 39.10 4.40
1662 1741 9.690434 GACTAATTAAGCAAATTAACGAGACAG 57.310 33.333 0.00 0.00 39.10 3.51
1663 1742 9.431887 AGACTAATTAAGCAAATTAACGAGACA 57.568 29.630 0.00 0.00 39.10 3.41
2237 3508 1.068127 AGAGTACGTTGCGTCAACCTT 59.932 47.619 14.31 6.83 40.82 3.50
2247 3518 0.038251 TCCAGCAGCAGAGTACGTTG 60.038 55.000 0.00 0.00 0.00 4.10
2248 3519 0.898320 ATCCAGCAGCAGAGTACGTT 59.102 50.000 0.00 0.00 0.00 3.99
2440 3714 5.263968 AGGAGTACACTTATTCATGGACG 57.736 43.478 0.00 0.00 34.61 4.79
2446 3720 7.676947 ACAAAAGCTAGGAGTACACTTATTCA 58.323 34.615 0.00 0.00 0.00 2.57
2458 3732 7.730364 TTTCACTTAAGACAAAAGCTAGGAG 57.270 36.000 10.09 0.00 0.00 3.69
2531 3805 8.066247 AGGGGTCTAGTGATACTAATTTAGTGT 58.934 37.037 17.47 11.79 39.81 3.55


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

AutoCloner maintained by Alex Coulton.