Multiple sequence alignment - TraesCS6A01G094900

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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 TraesCS6A01G094900 chr6A 100.000 2546 0 0 1 2546 61540865 61538320 0.000000e+00 4702
1 TraesCS6A01G094900 chr6A 96.625 1689 45 6 868 2546 57901439 57903125 0.000000e+00 2793
2 TraesCS6A01G094900 chr4B 95.352 2001 81 8 542 2531 660380883 660378884 0.000000e+00 3169
3 TraesCS6A01G094900 chr4B 90.050 402 32 7 541 939 407108831 407108435 4.860000e-142 514
4 TraesCS6A01G094900 chr3A 95.000 2020 62 7 534 2546 617401015 617403002 0.000000e+00 3134
5 TraesCS6A01G094900 chr3A 96.503 1687 49 5 868 2546 735555636 735557320 0.000000e+00 2780
6 TraesCS6A01G094900 chr6B 94.638 2014 66 9 542 2546 660437743 660435763 0.000000e+00 3083
7 TraesCS6A01G094900 chr1A 94.583 2012 70 6 542 2546 22791529 22793508 0.000000e+00 3075
8 TraesCS6A01G094900 chr1A 94.772 1970 60 8 585 2546 531499961 531498027 0.000000e+00 3027
9 TraesCS6A01G094900 chr1A 90.418 407 31 7 537 940 38372359 38372760 1.730000e-146 529
10 TraesCS6A01G094900 chr5A 94.491 2015 70 8 541 2546 459744880 459746862 0.000000e+00 3068
11 TraesCS6A01G094900 chr7B 94.400 2018 70 8 540 2546 552932145 552930160 0.000000e+00 3061
12 TraesCS6A01G094900 chr7B 80.431 511 71 16 3 489 575389301 575388796 1.860000e-96 363
13 TraesCS6A01G094900 chr7A 89.245 1776 125 27 542 2288 709273716 709275454 0.000000e+00 2161
14 TraesCS6A01G094900 chr7A 90.796 402 31 5 542 940 689996369 689995971 1.340000e-147 532
15 TraesCS6A01G094900 chr6D 86.882 526 39 8 1 512 53640142 53640651 1.710000e-156 562
16 TraesCS6A01G094900 chr4A 90.617 405 30 7 541 940 603147221 603146820 4.820000e-147 531
17 TraesCS6A01G094900 chr7D 89.951 408 32 4 544 944 90563634 90563229 3.750000e-143 518
18 TraesCS6A01G094900 chr3D 88.642 405 39 6 542 942 132628046 132627645 1.060000e-133 486


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 TraesCS6A01G094900 chr6A 61538320 61540865 2545 True 4702 4702 100.000 1 2546 1 chr6A.!!$R1 2545
1 TraesCS6A01G094900 chr6A 57901439 57903125 1686 False 2793 2793 96.625 868 2546 1 chr6A.!!$F1 1678
2 TraesCS6A01G094900 chr4B 660378884 660380883 1999 True 3169 3169 95.352 542 2531 1 chr4B.!!$R2 1989
3 TraesCS6A01G094900 chr3A 617401015 617403002 1987 False 3134 3134 95.000 534 2546 1 chr3A.!!$F1 2012
4 TraesCS6A01G094900 chr3A 735555636 735557320 1684 False 2780 2780 96.503 868 2546 1 chr3A.!!$F2 1678
5 TraesCS6A01G094900 chr6B 660435763 660437743 1980 True 3083 3083 94.638 542 2546 1 chr6B.!!$R1 2004
6 TraesCS6A01G094900 chr1A 22791529 22793508 1979 False 3075 3075 94.583 542 2546 1 chr1A.!!$F1 2004
7 TraesCS6A01G094900 chr1A 531498027 531499961 1934 True 3027 3027 94.772 585 2546 1 chr1A.!!$R1 1961
8 TraesCS6A01G094900 chr5A 459744880 459746862 1982 False 3068 3068 94.491 541 2546 1 chr5A.!!$F1 2005
9 TraesCS6A01G094900 chr7B 552930160 552932145 1985 True 3061 3061 94.400 540 2546 1 chr7B.!!$R1 2006
10 TraesCS6A01G094900 chr7B 575388796 575389301 505 True 363 363 80.431 3 489 1 chr7B.!!$R2 486
11 TraesCS6A01G094900 chr7A 709273716 709275454 1738 False 2161 2161 89.245 542 2288 1 chr7A.!!$F1 1746
12 TraesCS6A01G094900 chr6D 53640142 53640651 509 False 562 562 86.882 1 512 1 chr6D.!!$F1 511

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
700 715 0.033642 GACTCGGCCCTTATAGGTGC 59.966 60.0 0.0 0.0 31.93 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 2238 1.005156 CCCCAACCGCACCAATTTG 60.005 57.895 0.0 0.0 0.0 2.32 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
19 20 3.597162 CGCGTCGGAATTAGGTCG 58.403 61.111 0.00 0.00 0.00 4.79
20 21 1.942712 CGCGTCGGAATTAGGTCGG 60.943 63.158 0.00 0.00 0.00 4.79
33 34 2.903375 AGGTCGGACTACTTCTCCTT 57.097 50.000 8.23 0.00 0.00 3.36
89 90 1.544314 GCAGGTGGCTTGATCCTATCC 60.544 57.143 0.00 0.00 40.25 2.59
91 92 1.061033 AGGTGGCTTGATCCTATCCCT 60.061 52.381 0.00 0.00 0.00 4.20
122 124 5.529430 AGATATGGCGAGATTAGTCTATCGG 59.471 44.000 4.09 0.00 33.97 4.18
214 229 2.882761 CGGTGGTGGATCTATCGTTCTA 59.117 50.000 0.00 0.00 0.00 2.10
224 239 3.716431 TCTATCGTTCTACCCCAACCTT 58.284 45.455 0.00 0.00 0.00 3.50
259 274 1.741028 TGGATCTTGGTCCACAGGAA 58.259 50.000 0.00 0.00 43.20 3.36
261 276 1.676014 GGATCTTGGTCCACAGGAACG 60.676 57.143 0.00 0.00 43.50 3.95
262 277 1.002087 GATCTTGGTCCACAGGAACGT 59.998 52.381 0.00 0.00 43.50 3.99
263 278 0.391597 TCTTGGTCCACAGGAACGTC 59.608 55.000 0.00 0.00 43.50 4.34
264 279 0.602905 CTTGGTCCACAGGAACGTCC 60.603 60.000 0.00 0.00 43.50 4.79
265 280 2.047213 TTGGTCCACAGGAACGTCCC 62.047 60.000 0.00 0.00 43.50 4.46
266 281 2.214920 GGTCCACAGGAACGTCCCT 61.215 63.158 0.00 0.00 37.19 4.20
267 282 1.292541 GTCCACAGGAACGTCCCTC 59.707 63.158 0.00 0.00 37.19 4.30
268 283 2.261671 CCACAGGAACGTCCCTCG 59.738 66.667 0.00 0.00 46.00 4.63
269 284 2.261671 CACAGGAACGTCCCTCGG 59.738 66.667 0.00 0.00 44.69 4.63
270 285 2.203596 ACAGGAACGTCCCTCGGT 60.204 61.111 0.00 0.00 44.57 4.69
274 289 2.177778 GAACGTCCCTCGGTCGAC 59.822 66.667 7.13 7.13 46.27 4.20
275 290 2.595463 AACGTCCCTCGGTCGACA 60.595 61.111 18.91 0.00 44.69 4.35
276 291 1.930908 GAACGTCCCTCGGTCGACAT 61.931 60.000 18.91 0.00 46.27 3.06
277 292 2.102357 CGTCCCTCGGTCGACATG 59.898 66.667 18.91 9.36 36.43 3.21
278 293 2.202756 GTCCCTCGGTCGACATGC 60.203 66.667 18.91 0.00 0.00 4.06
279 294 3.458163 TCCCTCGGTCGACATGCC 61.458 66.667 18.91 0.00 0.00 4.40
280 295 3.770040 CCCTCGGTCGACATGCCA 61.770 66.667 18.91 0.00 0.00 4.92
281 296 2.509336 CCTCGGTCGACATGCCAC 60.509 66.667 18.91 0.00 0.00 5.01
282 297 2.261361 CTCGGTCGACATGCCACA 59.739 61.111 18.91 0.00 0.00 4.17
283 298 1.374125 CTCGGTCGACATGCCACAA 60.374 57.895 18.91 0.00 0.00 3.33
284 299 1.626654 CTCGGTCGACATGCCACAAC 61.627 60.000 18.91 0.00 0.00 3.32
285 300 1.958715 CGGTCGACATGCCACAACA 60.959 57.895 18.91 0.00 0.00 3.33
286 301 1.502990 CGGTCGACATGCCACAACAA 61.503 55.000 18.91 0.00 0.00 2.83
287 302 0.881118 GGTCGACATGCCACAACAAT 59.119 50.000 18.91 0.00 0.00 2.71
288 303 2.080693 GGTCGACATGCCACAACAATA 58.919 47.619 18.91 0.00 0.00 1.90
289 304 2.682856 GGTCGACATGCCACAACAATAT 59.317 45.455 18.91 0.00 0.00 1.28
290 305 3.487376 GGTCGACATGCCACAACAATATG 60.487 47.826 18.91 0.00 0.00 1.78
291 306 3.126858 GTCGACATGCCACAACAATATGT 59.873 43.478 11.55 0.00 34.91 2.29
298 313 2.282701 CACAACAATATGTGCCTGGC 57.717 50.000 12.87 12.87 43.67 4.85
299 314 1.820519 CACAACAATATGTGCCTGGCT 59.179 47.619 21.03 1.67 43.67 4.75
300 315 1.820519 ACAACAATATGTGCCTGGCTG 59.179 47.619 21.03 10.95 30.82 4.85
301 316 0.819582 AACAATATGTGCCTGGCTGC 59.180 50.000 21.03 13.09 0.00 5.25
302 317 0.033796 ACAATATGTGCCTGGCTGCT 60.034 50.000 21.03 6.47 0.00 4.24
303 318 1.108776 CAATATGTGCCTGGCTGCTT 58.891 50.000 21.03 12.72 0.00 3.91
304 319 1.108776 AATATGTGCCTGGCTGCTTG 58.891 50.000 21.03 0.00 0.00 4.01
305 320 1.389609 ATATGTGCCTGGCTGCTTGC 61.390 55.000 21.03 0.47 41.94 4.01
306 321 2.767978 TATGTGCCTGGCTGCTTGCA 62.768 55.000 21.03 9.26 45.15 4.08
307 322 4.052229 GTGCCTGGCTGCTTGCAG 62.052 66.667 21.03 17.34 45.15 4.41
317 332 2.754658 GCTTGCAGCAGGCCTGAT 60.755 61.111 37.21 29.54 44.64 2.90
318 333 2.772691 GCTTGCAGCAGGCCTGATC 61.773 63.158 37.21 22.91 44.64 2.92
319 334 1.378119 CTTGCAGCAGGCCTGATCA 60.378 57.895 37.21 25.15 44.64 2.92
320 335 0.752009 CTTGCAGCAGGCCTGATCAT 60.752 55.000 37.21 15.42 44.64 2.45
321 336 0.750546 TTGCAGCAGGCCTGATCATC 60.751 55.000 37.21 20.62 44.64 2.92
322 337 2.252346 GCAGCAGGCCTGATCATCG 61.252 63.158 37.21 19.21 44.64 3.84
323 338 1.444672 CAGCAGGCCTGATCATCGA 59.555 57.895 37.21 0.00 44.64 3.59
324 339 0.879400 CAGCAGGCCTGATCATCGAC 60.879 60.000 37.21 15.66 44.64 4.20
325 340 1.047596 AGCAGGCCTGATCATCGACT 61.048 55.000 37.21 17.81 0.00 4.18
326 341 0.179062 GCAGGCCTGATCATCGACTT 60.179 55.000 37.21 0.00 0.00 3.01
327 342 1.069204 GCAGGCCTGATCATCGACTTA 59.931 52.381 37.21 0.00 0.00 2.24
328 343 2.748605 CAGGCCTGATCATCGACTTAC 58.251 52.381 29.88 0.00 0.00 2.34
329 344 2.101415 CAGGCCTGATCATCGACTTACA 59.899 50.000 29.88 0.00 0.00 2.41
330 345 2.766263 AGGCCTGATCATCGACTTACAA 59.234 45.455 3.11 0.00 0.00 2.41
331 346 3.197766 AGGCCTGATCATCGACTTACAAA 59.802 43.478 3.11 0.00 0.00 2.83
332 347 3.557595 GGCCTGATCATCGACTTACAAAG 59.442 47.826 0.00 0.00 0.00 2.77
333 348 3.001736 GCCTGATCATCGACTTACAAAGC 59.998 47.826 0.00 0.00 0.00 3.51
334 349 3.557595 CCTGATCATCGACTTACAAAGCC 59.442 47.826 0.00 0.00 0.00 4.35
335 350 4.437239 CTGATCATCGACTTACAAAGCCT 58.563 43.478 0.00 0.00 0.00 4.58
336 351 4.433615 TGATCATCGACTTACAAAGCCTC 58.566 43.478 0.00 0.00 0.00 4.70
337 352 2.876091 TCATCGACTTACAAAGCCTCG 58.124 47.619 0.00 0.00 0.00 4.63
338 353 2.230508 TCATCGACTTACAAAGCCTCGT 59.769 45.455 0.00 0.00 31.35 4.18
339 354 2.806608 TCGACTTACAAAGCCTCGTT 57.193 45.000 0.00 0.00 31.35 3.85
340 355 2.400399 TCGACTTACAAAGCCTCGTTG 58.600 47.619 0.00 0.00 31.35 4.10
341 356 1.459592 CGACTTACAAAGCCTCGTTGG 59.540 52.381 0.00 0.00 39.35 3.77
362 377 2.544685 CGATGACGCTTCTTTGGATCT 58.455 47.619 0.00 0.00 0.00 2.75
363 378 2.283617 CGATGACGCTTCTTTGGATCTG 59.716 50.000 0.00 0.00 0.00 2.90
364 379 2.099141 TGACGCTTCTTTGGATCTGG 57.901 50.000 0.00 0.00 0.00 3.86
365 380 0.729690 GACGCTTCTTTGGATCTGGC 59.270 55.000 0.00 0.00 0.00 4.85
366 381 0.036732 ACGCTTCTTTGGATCTGGCA 59.963 50.000 0.00 0.00 0.00 4.92
367 382 1.167851 CGCTTCTTTGGATCTGGCAA 58.832 50.000 0.00 0.00 0.00 4.52
368 383 1.541147 CGCTTCTTTGGATCTGGCAAA 59.459 47.619 0.00 0.00 0.00 3.68
369 384 2.415090 CGCTTCTTTGGATCTGGCAAAG 60.415 50.000 13.68 13.68 37.30 2.77
370 385 2.094338 GCTTCTTTGGATCTGGCAAAGG 60.094 50.000 17.55 8.16 36.78 3.11
371 386 2.978156 TCTTTGGATCTGGCAAAGGT 57.022 45.000 17.55 0.00 36.78 3.50
372 387 2.517959 TCTTTGGATCTGGCAAAGGTG 58.482 47.619 17.55 0.90 36.78 4.00
373 388 1.547372 CTTTGGATCTGGCAAAGGTGG 59.453 52.381 12.57 0.00 33.64 4.61
374 389 0.776810 TTGGATCTGGCAAAGGTGGA 59.223 50.000 0.00 0.00 0.00 4.02
375 390 0.329261 TGGATCTGGCAAAGGTGGAG 59.671 55.000 0.00 0.00 0.00 3.86
376 391 0.394899 GGATCTGGCAAAGGTGGAGG 60.395 60.000 0.00 0.00 0.00 4.30
377 392 1.000396 ATCTGGCAAAGGTGGAGGC 60.000 57.895 0.00 0.00 0.00 4.70
378 393 1.504275 ATCTGGCAAAGGTGGAGGCT 61.504 55.000 0.00 0.00 0.00 4.58
379 394 1.676967 CTGGCAAAGGTGGAGGCTC 60.677 63.158 5.78 5.78 0.00 4.70
380 395 2.416107 CTGGCAAAGGTGGAGGCTCA 62.416 60.000 17.69 0.00 0.00 4.26
381 396 1.228552 GGCAAAGGTGGAGGCTCAA 60.229 57.895 17.69 0.76 0.00 3.02
382 397 0.613012 GGCAAAGGTGGAGGCTCAAT 60.613 55.000 17.69 0.00 0.00 2.57
383 398 0.529378 GCAAAGGTGGAGGCTCAATG 59.471 55.000 17.69 0.98 0.00 2.82
384 399 1.915141 CAAAGGTGGAGGCTCAATGT 58.085 50.000 17.69 0.00 0.00 2.71
385 400 1.815003 CAAAGGTGGAGGCTCAATGTC 59.185 52.381 17.69 0.00 0.00 3.06
386 401 1.067295 AAGGTGGAGGCTCAATGTCA 58.933 50.000 17.69 1.17 0.00 3.58
387 402 0.326264 AGGTGGAGGCTCAATGTCAC 59.674 55.000 17.69 13.86 0.00 3.67
388 403 0.326264 GGTGGAGGCTCAATGTCACT 59.674 55.000 17.69 0.00 0.00 3.41
389 404 1.271597 GGTGGAGGCTCAATGTCACTT 60.272 52.381 17.69 0.00 0.00 3.16
390 405 2.079925 GTGGAGGCTCAATGTCACTTC 58.920 52.381 17.69 0.00 0.00 3.01
391 406 1.980765 TGGAGGCTCAATGTCACTTCT 59.019 47.619 17.69 0.00 0.00 2.85
392 407 2.289882 TGGAGGCTCAATGTCACTTCTG 60.290 50.000 17.69 0.00 0.00 3.02
393 408 2.354259 GAGGCTCAATGTCACTTCTGG 58.646 52.381 10.25 0.00 0.00 3.86
394 409 0.807496 GGCTCAATGTCACTTCTGGC 59.193 55.000 0.00 0.00 0.00 4.85
395 410 0.445436 GCTCAATGTCACTTCTGGCG 59.555 55.000 0.00 0.00 0.00 5.69
396 411 1.800805 CTCAATGTCACTTCTGGCGT 58.199 50.000 0.00 0.00 0.00 5.68
397 412 1.462283 CTCAATGTCACTTCTGGCGTG 59.538 52.381 0.00 0.00 0.00 5.34
398 413 0.110056 CAATGTCACTTCTGGCGTGC 60.110 55.000 0.00 0.00 32.54 5.34
399 414 1.568612 AATGTCACTTCTGGCGTGCG 61.569 55.000 0.00 0.00 32.54 5.34
400 415 4.077188 GTCACTTCTGGCGTGCGC 62.077 66.667 8.17 8.17 41.06 6.09
401 416 4.299547 TCACTTCTGGCGTGCGCT 62.300 61.111 16.21 0.00 41.60 5.92
402 417 3.349006 CACTTCTGGCGTGCGCTT 61.349 61.111 16.21 0.00 41.60 4.68
403 418 2.591715 ACTTCTGGCGTGCGCTTT 60.592 55.556 16.21 0.00 41.60 3.51
404 419 2.127118 CTTCTGGCGTGCGCTTTG 60.127 61.111 16.21 0.00 41.60 2.77
405 420 3.599792 CTTCTGGCGTGCGCTTTGG 62.600 63.158 16.21 4.77 41.60 3.28
416 431 3.127533 GCTTTGGCGACGCTGGAT 61.128 61.111 20.77 0.00 0.00 3.41
417 432 2.690778 GCTTTGGCGACGCTGGATT 61.691 57.895 20.77 0.00 0.00 3.01
418 433 1.875963 CTTTGGCGACGCTGGATTT 59.124 52.632 20.77 0.00 0.00 2.17
419 434 0.454957 CTTTGGCGACGCTGGATTTG 60.455 55.000 20.77 0.40 0.00 2.32
420 435 1.861542 TTTGGCGACGCTGGATTTGG 61.862 55.000 20.77 0.00 0.00 3.28
421 436 3.508840 GGCGACGCTGGATTTGGG 61.509 66.667 20.77 0.00 0.00 4.12
422 437 4.179579 GCGACGCTGGATTTGGGC 62.180 66.667 13.73 0.00 0.00 5.36
447 462 3.482783 GCTGACTTCGGCGAGTGC 61.483 66.667 10.46 7.73 38.61 4.40
448 463 2.049156 CTGACTTCGGCGAGTGCA 60.049 61.111 10.46 8.50 45.35 4.57
449 464 2.049156 TGACTTCGGCGAGTGCAG 60.049 61.111 10.46 7.29 45.35 4.41
450 465 2.811317 GACTTCGGCGAGTGCAGG 60.811 66.667 10.46 0.40 45.35 4.85
451 466 3.282745 GACTTCGGCGAGTGCAGGA 62.283 63.158 10.46 0.00 45.35 3.86
452 467 2.048222 CTTCGGCGAGTGCAGGAA 60.048 61.111 10.46 0.00 45.35 3.36
453 468 1.667830 CTTCGGCGAGTGCAGGAAA 60.668 57.895 10.46 0.00 45.35 3.13
454 469 1.227704 TTCGGCGAGTGCAGGAAAA 60.228 52.632 10.46 0.00 45.35 2.29
455 470 1.503818 TTCGGCGAGTGCAGGAAAAC 61.504 55.000 10.46 0.00 45.35 2.43
456 471 2.954611 GGCGAGTGCAGGAAAACC 59.045 61.111 0.00 0.00 45.35 3.27
457 472 1.600916 GGCGAGTGCAGGAAAACCT 60.601 57.895 0.00 0.00 45.35 3.50
458 473 0.321298 GGCGAGTGCAGGAAAACCTA 60.321 55.000 0.00 0.00 45.35 3.08
459 474 1.079503 GCGAGTGCAGGAAAACCTAG 58.920 55.000 0.00 0.00 42.15 3.02
460 475 1.726853 CGAGTGCAGGAAAACCTAGG 58.273 55.000 7.41 7.41 0.00 3.02
461 476 1.275291 CGAGTGCAGGAAAACCTAGGA 59.725 52.381 17.98 0.00 0.00 2.94
462 477 2.289444 CGAGTGCAGGAAAACCTAGGAA 60.289 50.000 17.98 0.00 0.00 3.36
463 478 3.619979 CGAGTGCAGGAAAACCTAGGAAT 60.620 47.826 17.98 0.02 0.00 3.01
464 479 4.382685 CGAGTGCAGGAAAACCTAGGAATA 60.383 45.833 17.98 0.00 0.00 1.75
465 480 5.104259 AGTGCAGGAAAACCTAGGAATAG 57.896 43.478 17.98 0.00 0.00 1.73
466 481 4.536489 AGTGCAGGAAAACCTAGGAATAGT 59.464 41.667 17.98 0.00 0.00 2.12
467 482 5.014228 AGTGCAGGAAAACCTAGGAATAGTT 59.986 40.000 17.98 1.24 0.00 2.24
468 483 5.354513 GTGCAGGAAAACCTAGGAATAGTTC 59.645 44.000 17.98 10.38 0.00 3.01
469 484 5.250774 TGCAGGAAAACCTAGGAATAGTTCT 59.749 40.000 17.98 1.03 0.00 3.01
470 485 5.586643 GCAGGAAAACCTAGGAATAGTTCTG 59.413 44.000 17.98 13.83 0.00 3.02
471 486 6.712276 CAGGAAAACCTAGGAATAGTTCTGT 58.288 40.000 17.98 1.17 0.00 3.41
472 487 7.580882 GCAGGAAAACCTAGGAATAGTTCTGTA 60.581 40.741 17.98 0.00 0.00 2.74
473 488 8.487028 CAGGAAAACCTAGGAATAGTTCTGTAT 58.513 37.037 17.98 0.00 0.00 2.29
474 489 9.059023 AGGAAAACCTAGGAATAGTTCTGTATT 57.941 33.333 17.98 0.00 0.00 1.89
475 490 9.682465 GGAAAACCTAGGAATAGTTCTGTATTT 57.318 33.333 17.98 0.00 0.00 1.40
512 527 7.044798 AGATGTCTATCTACAAAGTTTCCAGC 58.955 38.462 0.00 0.00 41.82 4.85
513 528 6.109156 TGTCTATCTACAAAGTTTCCAGCA 57.891 37.500 0.00 0.00 0.00 4.41
514 529 6.530120 TGTCTATCTACAAAGTTTCCAGCAA 58.470 36.000 0.00 0.00 0.00 3.91
515 530 6.995686 TGTCTATCTACAAAGTTTCCAGCAAA 59.004 34.615 0.00 0.00 0.00 3.68
516 531 7.173218 TGTCTATCTACAAAGTTTCCAGCAAAG 59.827 37.037 0.00 0.00 0.00 2.77
517 532 7.173390 GTCTATCTACAAAGTTTCCAGCAAAGT 59.827 37.037 0.00 0.00 0.00 2.66
518 533 5.499139 TCTACAAAGTTTCCAGCAAAGTG 57.501 39.130 0.00 0.00 0.00 3.16
519 534 4.947388 TCTACAAAGTTTCCAGCAAAGTGT 59.053 37.500 0.00 0.00 0.00 3.55
520 535 4.535526 ACAAAGTTTCCAGCAAAGTGTT 57.464 36.364 0.00 0.00 0.00 3.32
521 536 4.494484 ACAAAGTTTCCAGCAAAGTGTTC 58.506 39.130 0.00 0.00 0.00 3.18
522 537 4.021544 ACAAAGTTTCCAGCAAAGTGTTCA 60.022 37.500 0.00 0.00 0.00 3.18
523 538 5.111293 CAAAGTTTCCAGCAAAGTGTTCAT 58.889 37.500 0.00 0.00 0.00 2.57
524 539 5.343307 AAGTTTCCAGCAAAGTGTTCATT 57.657 34.783 0.00 0.00 0.00 2.57
525 540 4.685924 AGTTTCCAGCAAAGTGTTCATTG 58.314 39.130 0.00 0.00 0.00 2.82
534 549 5.379757 CAAAGTGTTCATTGCACTCAAAC 57.620 39.130 0.00 0.00 45.36 2.93
535 550 4.989279 AAGTGTTCATTGCACTCAAACT 57.011 36.364 0.00 0.00 45.36 2.66
536 551 4.297299 AGTGTTCATTGCACTCAAACTG 57.703 40.909 0.00 0.00 42.90 3.16
537 552 3.696051 AGTGTTCATTGCACTCAAACTGT 59.304 39.130 0.00 0.00 42.90 3.55
538 553 4.158394 AGTGTTCATTGCACTCAAACTGTT 59.842 37.500 0.00 0.00 42.90 3.16
588 603 5.071250 AGTGGTGTCCATGTACTCAGTTTTA 59.929 40.000 0.00 0.00 35.28 1.52
637 652 4.063967 CCTAGTCCGTGCGCACCA 62.064 66.667 33.23 18.47 0.00 4.17
641 656 2.372040 TAGTCCGTGCGCACCAACTT 62.372 55.000 33.88 22.68 0.00 2.66
694 709 1.633945 ACCTTTTGACTCGGCCCTTAT 59.366 47.619 0.00 0.00 0.00 1.73
700 715 0.033642 GACTCGGCCCTTATAGGTGC 59.966 60.000 0.00 0.00 31.93 5.01
710 725 1.038681 TTATAGGTGCGACCAGGCGA 61.039 55.000 0.00 0.00 41.95 5.54
717 732 3.069980 GCGACCAGGCGACAGAGAT 62.070 63.158 0.00 0.00 0.00 2.75
735 750 8.174733 ACAGAGATGGCCAATTTTATTCATAG 57.825 34.615 10.96 0.00 0.00 2.23
744 759 5.804473 CCAATTTTATTCATAGCGTTGCACA 59.196 36.000 0.00 0.00 0.00 4.57
841 857 3.366629 GGTGACCACAGCGAGAGA 58.633 61.111 0.00 0.00 34.87 3.10
842 858 1.214062 GGTGACCACAGCGAGAGAG 59.786 63.158 0.00 0.00 34.87 3.20
843 859 1.244697 GGTGACCACAGCGAGAGAGA 61.245 60.000 0.00 0.00 34.87 3.10
844 860 0.170116 GTGACCACAGCGAGAGAGAG 59.830 60.000 0.00 0.00 0.00 3.20
845 861 1.138671 GACCACAGCGAGAGAGAGC 59.861 63.158 0.00 0.00 0.00 4.09
846 862 1.590610 GACCACAGCGAGAGAGAGCA 61.591 60.000 0.00 0.00 35.48 4.26
847 863 0.969917 ACCACAGCGAGAGAGAGCAT 60.970 55.000 0.00 0.00 35.48 3.79
848 864 0.528033 CCACAGCGAGAGAGAGCATG 60.528 60.000 0.00 0.00 35.48 4.06
849 865 0.528033 CACAGCGAGAGAGAGCATGG 60.528 60.000 0.00 0.00 35.48 3.66
850 866 0.969917 ACAGCGAGAGAGAGCATGGT 60.970 55.000 0.00 0.00 35.48 3.55
851 867 0.528033 CAGCGAGAGAGAGCATGGTG 60.528 60.000 0.00 0.00 35.48 4.17
852 868 1.227205 GCGAGAGAGAGCATGGTGG 60.227 63.158 0.00 0.00 0.00 4.61
853 869 1.954362 GCGAGAGAGAGCATGGTGGT 61.954 60.000 0.00 0.00 0.00 4.16
854 870 0.179116 CGAGAGAGAGCATGGTGGTG 60.179 60.000 0.00 0.00 0.00 4.17
855 871 1.189752 GAGAGAGAGCATGGTGGTGA 58.810 55.000 0.00 0.00 0.00 4.02
856 872 0.901124 AGAGAGAGCATGGTGGTGAC 59.099 55.000 0.00 0.00 0.00 3.67
857 873 0.107945 GAGAGAGCATGGTGGTGACC 60.108 60.000 0.00 0.00 43.48 4.02
865 881 2.436646 GGTGGTGACCATGGCGAG 60.437 66.667 13.04 0.00 42.59 5.03
866 882 2.662596 GTGGTGACCATGGCGAGA 59.337 61.111 13.04 0.00 35.28 4.04
869 885 1.142748 GGTGACCATGGCGAGAGAG 59.857 63.158 13.04 0.00 0.00 3.20
964 1019 1.486211 GAAGCTAGTAGTGGAGGGCA 58.514 55.000 0.00 0.00 0.00 5.36
988 1043 0.902531 GGTGTTGAGATCCCCTTCGA 59.097 55.000 0.00 0.00 0.00 3.71
1117 1172 4.099633 TGATCAGAGGGTTTCTCAGACAT 58.900 43.478 0.00 0.00 44.81 3.06
1145 1201 1.189403 CAGAATCGTCCGTTCTACGC 58.811 55.000 0.00 0.00 40.91 4.42
1206 1262 2.088950 TTTCGTGGTCGGGATCTTTC 57.911 50.000 0.00 0.00 37.69 2.62
1280 1336 0.391661 GTCGATGCTCTGGCCAAGAA 60.392 55.000 7.01 2.07 37.74 2.52
1337 1393 4.183686 GCGCATGCTGCCACGAAT 62.184 61.111 17.13 0.00 41.12 3.34
1615 1679 8.974408 CCTAGTTTAAATGTTGGTTAAAGTTGC 58.026 33.333 0.00 0.00 36.19 4.17
2041 2128 1.999648 TGGAAAATGTGCCTCAGCTT 58.000 45.000 0.00 0.00 40.80 3.74
2082 2169 6.430616 CCAGGTGCCAAAATAAATGAACATTT 59.569 34.615 15.41 15.41 42.95 2.32
2146 2238 2.102252 TGAAGGGTGGAAAATGCACAAC 59.898 45.455 4.42 0.00 40.73 3.32
2159 2251 0.529555 GCACAACAAATTGGTGCGGT 60.530 50.000 11.42 0.00 39.04 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.002862 CGAGATGAAGGAGAAGTAGTCCG 59.997 52.174 0.00 0.00 39.30 4.79
19 20 3.316868 CCGAGATGAAGGAGAAGTAGTCC 59.683 52.174 0.00 0.00 0.00 3.85
20 21 3.243267 GCCGAGATGAAGGAGAAGTAGTC 60.243 52.174 0.00 0.00 0.00 2.59
89 90 3.797039 TCTCGCCATATCTGAAAACAGG 58.203 45.455 0.00 0.00 0.00 4.00
91 92 6.582636 ACTAATCTCGCCATATCTGAAAACA 58.417 36.000 0.00 0.00 0.00 2.83
122 124 3.110178 GCCACGGTAGCGACACAC 61.110 66.667 22.88 1.67 0.00 3.82
186 201 1.804326 GATCCACCACCGTCGAACG 60.804 63.158 0.00 0.00 42.11 3.95
214 229 0.178935 CCCATTGACAAGGTTGGGGT 60.179 55.000 15.14 0.00 44.29 4.95
224 239 3.903714 AGATCCACGATATCCCATTGACA 59.096 43.478 0.00 0.00 0.00 3.58
254 269 2.572284 GACCGAGGGACGTTCCTG 59.428 66.667 23.57 9.75 40.78 3.86
255 270 3.060615 CGACCGAGGGACGTTCCT 61.061 66.667 17.69 17.69 40.78 3.36
257 272 1.930908 ATGTCGACCGAGGGACGTTC 61.931 60.000 14.12 0.00 41.15 3.95
259 274 2.360852 ATGTCGACCGAGGGACGT 60.361 61.111 14.12 0.00 41.15 4.34
261 276 2.202756 GCATGTCGACCGAGGGAC 60.203 66.667 14.12 0.00 0.00 4.46
262 277 3.458163 GGCATGTCGACCGAGGGA 61.458 66.667 14.12 0.00 0.00 4.20
263 278 3.770040 TGGCATGTCGACCGAGGG 61.770 66.667 14.12 0.00 0.00 4.30
264 279 2.509336 GTGGCATGTCGACCGAGG 60.509 66.667 14.12 0.00 0.00 4.63
265 280 1.374125 TTGTGGCATGTCGACCGAG 60.374 57.895 14.12 3.79 0.00 4.63
266 281 1.666553 GTTGTGGCATGTCGACCGA 60.667 57.895 14.12 0.00 0.00 4.69
267 282 1.502990 TTGTTGTGGCATGTCGACCG 61.503 55.000 14.12 5.33 0.00 4.79
268 283 0.881118 ATTGTTGTGGCATGTCGACC 59.119 50.000 14.12 0.00 0.00 4.79
269 284 3.126858 ACATATTGTTGTGGCATGTCGAC 59.873 43.478 9.11 9.11 0.00 4.20
270 285 3.126686 CACATATTGTTGTGGCATGTCGA 59.873 43.478 0.00 0.00 42.63 4.20
271 286 3.428163 CACATATTGTTGTGGCATGTCG 58.572 45.455 0.00 0.00 42.63 4.35
272 287 3.181397 GCACATATTGTTGTGGCATGTC 58.819 45.455 6.70 0.00 45.69 3.06
273 288 3.235157 GCACATATTGTTGTGGCATGT 57.765 42.857 6.70 0.00 45.69 3.21
278 293 1.135024 GCCAGGCACATATTGTTGTGG 60.135 52.381 6.55 0.00 45.69 4.17
280 295 1.820519 CAGCCAGGCACATATTGTTGT 59.179 47.619 15.80 0.00 0.00 3.32
281 296 1.470285 GCAGCCAGGCACATATTGTTG 60.470 52.381 15.80 0.05 0.00 3.33
282 297 0.819582 GCAGCCAGGCACATATTGTT 59.180 50.000 15.80 0.00 0.00 2.83
283 298 0.033796 AGCAGCCAGGCACATATTGT 60.034 50.000 15.80 0.00 35.83 2.71
284 299 1.108776 AAGCAGCCAGGCACATATTG 58.891 50.000 15.80 2.55 35.83 1.90
285 300 1.108776 CAAGCAGCCAGGCACATATT 58.891 50.000 15.80 0.00 35.83 1.28
286 301 1.389609 GCAAGCAGCCAGGCACATAT 61.390 55.000 15.80 0.00 37.23 1.78
287 302 2.048023 GCAAGCAGCCAGGCACATA 61.048 57.895 15.80 0.00 37.23 2.29
288 303 3.379445 GCAAGCAGCCAGGCACAT 61.379 61.111 15.80 0.00 37.23 3.21
289 304 4.898765 TGCAAGCAGCCAGGCACA 62.899 61.111 15.80 0.00 44.83 4.57
290 305 4.052229 CTGCAAGCAGCCAGGCAC 62.052 66.667 15.80 5.12 44.83 5.01
301 316 0.752009 ATGATCAGGCCTGCTGCAAG 60.752 55.000 28.91 2.18 43.89 4.01
302 317 0.750546 GATGATCAGGCCTGCTGCAA 60.751 55.000 28.91 11.08 43.89 4.08
303 318 1.153025 GATGATCAGGCCTGCTGCA 60.153 57.895 28.91 23.42 43.89 4.41
304 319 2.252346 CGATGATCAGGCCTGCTGC 61.252 63.158 28.91 18.67 40.16 5.25
305 320 0.879400 GTCGATGATCAGGCCTGCTG 60.879 60.000 28.91 12.86 0.00 4.41
306 321 1.047596 AGTCGATGATCAGGCCTGCT 61.048 55.000 28.91 19.94 0.00 4.24
307 322 0.179062 AAGTCGATGATCAGGCCTGC 60.179 55.000 28.91 15.67 0.00 4.85
308 323 2.101415 TGTAAGTCGATGATCAGGCCTG 59.899 50.000 27.87 27.87 0.00 4.85
309 324 2.388735 TGTAAGTCGATGATCAGGCCT 58.611 47.619 0.00 0.00 0.00 5.19
310 325 2.890808 TGTAAGTCGATGATCAGGCC 57.109 50.000 0.09 0.00 0.00 5.19
311 326 3.001736 GCTTTGTAAGTCGATGATCAGGC 59.998 47.826 0.09 0.00 0.00 4.85
312 327 3.557595 GGCTTTGTAAGTCGATGATCAGG 59.442 47.826 0.09 0.00 0.00 3.86
313 328 4.437239 AGGCTTTGTAAGTCGATGATCAG 58.563 43.478 0.09 0.00 38.41 2.90
314 329 4.433615 GAGGCTTTGTAAGTCGATGATCA 58.566 43.478 0.00 0.00 38.41 2.92
315 330 3.487574 CGAGGCTTTGTAAGTCGATGATC 59.512 47.826 0.00 0.00 38.41 2.92
316 331 3.119101 ACGAGGCTTTGTAAGTCGATGAT 60.119 43.478 0.00 0.00 38.41 2.45
317 332 2.230508 ACGAGGCTTTGTAAGTCGATGA 59.769 45.455 0.00 0.00 38.41 2.92
318 333 2.607187 ACGAGGCTTTGTAAGTCGATG 58.393 47.619 0.00 0.00 38.41 3.84
319 334 2.993899 CAACGAGGCTTTGTAAGTCGAT 59.006 45.455 0.00 0.00 38.41 3.59
320 335 2.400399 CAACGAGGCTTTGTAAGTCGA 58.600 47.619 0.00 0.00 38.41 4.20
321 336 1.459592 CCAACGAGGCTTTGTAAGTCG 59.540 52.381 0.00 0.00 38.41 4.18
342 357 2.283617 CAGATCCAAAGAAGCGTCATCG 59.716 50.000 1.61 0.00 40.37 3.84
343 358 2.611292 CCAGATCCAAAGAAGCGTCATC 59.389 50.000 1.61 0.00 0.00 2.92
344 359 2.636830 CCAGATCCAAAGAAGCGTCAT 58.363 47.619 1.61 0.00 0.00 3.06
345 360 1.945819 GCCAGATCCAAAGAAGCGTCA 60.946 52.381 1.61 0.00 0.00 4.35
346 361 0.729690 GCCAGATCCAAAGAAGCGTC 59.270 55.000 0.00 0.00 0.00 5.19
347 362 0.036732 TGCCAGATCCAAAGAAGCGT 59.963 50.000 0.00 0.00 0.00 5.07
348 363 1.167851 TTGCCAGATCCAAAGAAGCG 58.832 50.000 0.00 0.00 0.00 4.68
353 368 1.547372 CCACCTTTGCCAGATCCAAAG 59.453 52.381 13.16 13.16 45.37 2.77
354 369 1.146774 TCCACCTTTGCCAGATCCAAA 59.853 47.619 0.00 0.00 0.00 3.28
355 370 0.776810 TCCACCTTTGCCAGATCCAA 59.223 50.000 0.00 0.00 0.00 3.53
356 371 0.329261 CTCCACCTTTGCCAGATCCA 59.671 55.000 0.00 0.00 0.00 3.41
357 372 0.394899 CCTCCACCTTTGCCAGATCC 60.395 60.000 0.00 0.00 0.00 3.36
358 373 1.034292 GCCTCCACCTTTGCCAGATC 61.034 60.000 0.00 0.00 0.00 2.75
359 374 1.000396 GCCTCCACCTTTGCCAGAT 60.000 57.895 0.00 0.00 0.00 2.90
360 375 2.129555 GAGCCTCCACCTTTGCCAGA 62.130 60.000 0.00 0.00 0.00 3.86
361 376 1.676967 GAGCCTCCACCTTTGCCAG 60.677 63.158 0.00 0.00 0.00 4.85
362 377 2.005606 TTGAGCCTCCACCTTTGCCA 62.006 55.000 0.00 0.00 0.00 4.92
363 378 0.613012 ATTGAGCCTCCACCTTTGCC 60.613 55.000 0.00 0.00 0.00 4.52
364 379 0.529378 CATTGAGCCTCCACCTTTGC 59.471 55.000 0.00 0.00 0.00 3.68
365 380 1.815003 GACATTGAGCCTCCACCTTTG 59.185 52.381 0.00 0.00 0.00 2.77
366 381 1.425066 TGACATTGAGCCTCCACCTTT 59.575 47.619 0.00 0.00 0.00 3.11
367 382 1.067295 TGACATTGAGCCTCCACCTT 58.933 50.000 0.00 0.00 0.00 3.50
368 383 0.326264 GTGACATTGAGCCTCCACCT 59.674 55.000 0.00 0.00 0.00 4.00
369 384 0.326264 AGTGACATTGAGCCTCCACC 59.674 55.000 0.00 0.00 0.00 4.61
370 385 2.079925 GAAGTGACATTGAGCCTCCAC 58.920 52.381 0.00 0.00 0.00 4.02
371 386 1.980765 AGAAGTGACATTGAGCCTCCA 59.019 47.619 0.00 0.00 0.00 3.86
372 387 2.354259 CAGAAGTGACATTGAGCCTCC 58.646 52.381 0.00 0.00 0.00 4.30
373 388 2.354259 CCAGAAGTGACATTGAGCCTC 58.646 52.381 0.00 0.00 0.00 4.70
374 389 1.612726 GCCAGAAGTGACATTGAGCCT 60.613 52.381 0.00 0.00 0.00 4.58
375 390 0.807496 GCCAGAAGTGACATTGAGCC 59.193 55.000 0.00 0.00 0.00 4.70
376 391 0.445436 CGCCAGAAGTGACATTGAGC 59.555 55.000 0.00 0.00 0.00 4.26
377 392 1.462283 CACGCCAGAAGTGACATTGAG 59.538 52.381 0.00 0.00 41.83 3.02
378 393 1.511850 CACGCCAGAAGTGACATTGA 58.488 50.000 0.00 0.00 41.83 2.57
379 394 0.110056 GCACGCCAGAAGTGACATTG 60.110 55.000 0.07 0.00 41.83 2.82
380 395 1.568612 CGCACGCCAGAAGTGACATT 61.569 55.000 0.07 0.00 41.83 2.71
381 396 2.029288 CGCACGCCAGAAGTGACAT 61.029 57.895 0.07 0.00 41.83 3.06
382 397 2.661537 CGCACGCCAGAAGTGACA 60.662 61.111 0.07 0.00 41.83 3.58
383 398 4.077188 GCGCACGCCAGAAGTGAC 62.077 66.667 0.30 0.00 41.83 3.67
384 399 3.807631 AAGCGCACGCCAGAAGTGA 62.808 57.895 11.47 0.00 41.83 3.41
385 400 2.896801 AAAGCGCACGCCAGAAGTG 61.897 57.895 11.47 0.00 43.17 3.16
386 401 2.591715 AAAGCGCACGCCAGAAGT 60.592 55.556 11.47 0.00 43.17 3.01
387 402 2.127118 CAAAGCGCACGCCAGAAG 60.127 61.111 11.47 0.00 43.17 2.85
388 403 3.659092 CCAAAGCGCACGCCAGAA 61.659 61.111 11.47 0.00 43.17 3.02
399 414 2.200170 AAATCCAGCGTCGCCAAAGC 62.200 55.000 14.86 0.00 0.00 3.51
400 415 0.454957 CAAATCCAGCGTCGCCAAAG 60.455 55.000 14.86 1.43 0.00 2.77
401 416 1.578926 CAAATCCAGCGTCGCCAAA 59.421 52.632 14.86 0.00 0.00 3.28
402 417 2.331893 CCAAATCCAGCGTCGCCAA 61.332 57.895 14.86 0.00 0.00 4.52
403 418 2.745884 CCAAATCCAGCGTCGCCA 60.746 61.111 14.86 0.00 0.00 5.69
404 419 3.508840 CCCAAATCCAGCGTCGCC 61.509 66.667 14.86 0.00 0.00 5.54
405 420 4.179579 GCCCAAATCCAGCGTCGC 62.180 66.667 9.80 9.80 0.00 5.19
406 421 3.864686 CGCCCAAATCCAGCGTCG 61.865 66.667 0.00 0.00 44.65 5.12
430 445 3.482783 GCACTCGCCGAAGTCAGC 61.483 66.667 0.00 0.00 0.00 4.26
431 446 2.049156 TGCACTCGCCGAAGTCAG 60.049 61.111 0.00 0.00 37.32 3.51
432 447 2.049156 CTGCACTCGCCGAAGTCA 60.049 61.111 0.00 0.00 37.32 3.41
433 448 2.765250 TTCCTGCACTCGCCGAAGTC 62.765 60.000 0.00 0.00 37.32 3.01
434 449 2.377628 TTTCCTGCACTCGCCGAAGT 62.378 55.000 0.00 0.00 37.32 3.01
435 450 1.227999 TTTTCCTGCACTCGCCGAAG 61.228 55.000 0.00 0.00 37.32 3.79
436 451 1.227704 TTTTCCTGCACTCGCCGAA 60.228 52.632 0.00 0.00 37.32 4.30
437 452 1.959226 GTTTTCCTGCACTCGCCGA 60.959 57.895 0.00 0.00 37.32 5.54
438 453 2.556287 GTTTTCCTGCACTCGCCG 59.444 61.111 0.00 0.00 37.32 6.46
439 454 2.954611 GGTTTTCCTGCACTCGCC 59.045 61.111 0.00 0.00 37.32 5.54
449 464 9.682465 AAATACAGAACTATTCCTAGGTTTTCC 57.318 33.333 9.08 0.00 41.05 3.13
486 501 8.198109 GCTGGAAACTTTGTAGATAGACATCTA 58.802 37.037 0.00 0.00 41.84 1.98
487 502 7.044798 GCTGGAAACTTTGTAGATAGACATCT 58.955 38.462 0.00 0.00 44.04 2.90
488 503 6.818644 TGCTGGAAACTTTGTAGATAGACATC 59.181 38.462 0.00 0.00 0.00 3.06
489 504 6.711277 TGCTGGAAACTTTGTAGATAGACAT 58.289 36.000 0.00 0.00 0.00 3.06
490 505 6.109156 TGCTGGAAACTTTGTAGATAGACA 57.891 37.500 0.00 0.00 0.00 3.41
491 506 7.173390 ACTTTGCTGGAAACTTTGTAGATAGAC 59.827 37.037 0.00 0.00 0.00 2.59
492 507 7.173218 CACTTTGCTGGAAACTTTGTAGATAGA 59.827 37.037 0.00 0.00 0.00 1.98
493 508 7.041098 ACACTTTGCTGGAAACTTTGTAGATAG 60.041 37.037 0.00 0.00 0.00 2.08
494 509 6.770785 ACACTTTGCTGGAAACTTTGTAGATA 59.229 34.615 0.00 0.00 0.00 1.98
495 510 5.594317 ACACTTTGCTGGAAACTTTGTAGAT 59.406 36.000 0.00 0.00 0.00 1.98
496 511 4.947388 ACACTTTGCTGGAAACTTTGTAGA 59.053 37.500 0.00 0.00 0.00 2.59
497 512 5.248870 ACACTTTGCTGGAAACTTTGTAG 57.751 39.130 0.00 0.00 0.00 2.74
498 513 5.184096 TGAACACTTTGCTGGAAACTTTGTA 59.816 36.000 0.00 0.00 0.00 2.41
499 514 4.021544 TGAACACTTTGCTGGAAACTTTGT 60.022 37.500 0.00 0.00 0.00 2.83
500 515 4.493547 TGAACACTTTGCTGGAAACTTTG 58.506 39.130 0.00 0.00 0.00 2.77
501 516 4.799564 TGAACACTTTGCTGGAAACTTT 57.200 36.364 0.00 0.00 0.00 2.66
502 517 5.111293 CAATGAACACTTTGCTGGAAACTT 58.889 37.500 0.00 0.00 0.00 2.66
503 518 4.685924 CAATGAACACTTTGCTGGAAACT 58.314 39.130 0.00 0.00 0.00 2.66
504 519 3.245990 GCAATGAACACTTTGCTGGAAAC 59.754 43.478 11.59 0.00 43.75 2.78
505 520 3.118847 TGCAATGAACACTTTGCTGGAAA 60.119 39.130 17.02 0.00 46.50 3.13
506 521 2.429971 TGCAATGAACACTTTGCTGGAA 59.570 40.909 17.02 0.69 46.50 3.53
507 522 2.030371 TGCAATGAACACTTTGCTGGA 58.970 42.857 17.02 0.96 46.50 3.86
508 523 2.129607 GTGCAATGAACACTTTGCTGG 58.870 47.619 17.02 0.00 46.50 4.85
509 524 3.088194 AGTGCAATGAACACTTTGCTG 57.912 42.857 17.02 0.00 46.01 4.41
516 531 4.032703 ACAGTTTGAGTGCAATGAACAC 57.967 40.909 11.18 2.80 38.35 3.32
517 532 4.717233 AACAGTTTGAGTGCAATGAACA 57.283 36.364 11.18 0.00 33.25 3.18
518 533 5.687285 CCTTAACAGTTTGAGTGCAATGAAC 59.313 40.000 0.00 0.00 33.25 3.18
519 534 5.221224 CCCTTAACAGTTTGAGTGCAATGAA 60.221 40.000 0.00 0.00 33.25 2.57
520 535 4.278170 CCCTTAACAGTTTGAGTGCAATGA 59.722 41.667 0.00 0.00 33.25 2.57
521 536 4.037923 ACCCTTAACAGTTTGAGTGCAATG 59.962 41.667 0.00 0.00 33.25 2.82
522 537 4.215109 ACCCTTAACAGTTTGAGTGCAAT 58.785 39.130 0.00 0.00 33.25 3.56
523 538 3.626930 ACCCTTAACAGTTTGAGTGCAA 58.373 40.909 0.00 0.00 0.00 4.08
524 539 3.290948 ACCCTTAACAGTTTGAGTGCA 57.709 42.857 0.00 0.00 0.00 4.57
525 540 5.761165 TTAACCCTTAACAGTTTGAGTGC 57.239 39.130 0.00 0.00 0.00 4.40
527 542 9.239551 GGATAATTAACCCTTAACAGTTTGAGT 57.760 33.333 0.24 0.00 0.00 3.41
528 543 9.462606 AGGATAATTAACCCTTAACAGTTTGAG 57.537 33.333 8.09 0.00 0.00 3.02
529 544 9.816787 AAGGATAATTAACCCTTAACAGTTTGA 57.183 29.630 16.48 0.00 38.43 2.69
533 548 8.528643 GCAAAAGGATAATTAACCCTTAACAGT 58.471 33.333 17.67 4.89 39.21 3.55
534 549 7.979537 GGCAAAAGGATAATTAACCCTTAACAG 59.020 37.037 17.67 11.45 39.21 3.16
535 550 7.093245 GGGCAAAAGGATAATTAACCCTTAACA 60.093 37.037 17.67 0.00 39.21 2.41
536 551 7.125204 AGGGCAAAAGGATAATTAACCCTTAAC 59.875 37.037 17.67 12.09 42.56 2.01
537 552 7.193338 AGGGCAAAAGGATAATTAACCCTTAA 58.807 34.615 17.67 0.00 42.56 1.85
538 553 6.747931 AGGGCAAAAGGATAATTAACCCTTA 58.252 36.000 17.67 0.00 42.56 2.69
588 603 1.742761 CACAATTCGCATCTGAGGGT 58.257 50.000 0.00 0.00 0.00 4.34
637 652 1.940613 GCAGAGTTCACGGAACAAGTT 59.059 47.619 15.94 0.00 44.11 2.66
641 656 1.300620 CGGCAGAGTTCACGGAACA 60.301 57.895 15.94 0.00 44.11 3.18
694 709 3.755628 GTCGCCTGGTCGCACCTA 61.756 66.667 5.78 0.00 39.58 3.08
700 715 1.226802 CATCTCTGTCGCCTGGTCG 60.227 63.158 0.00 0.00 0.00 4.79
710 725 7.255730 GCTATGAATAAAATTGGCCATCTCTGT 60.256 37.037 6.09 0.00 0.00 3.41
717 732 5.347342 CAACGCTATGAATAAAATTGGCCA 58.653 37.500 0.00 0.00 0.00 5.36
744 759 2.430704 CTGGGTCCCACAAGCCATGT 62.431 60.000 6.47 0.00 45.28 3.21
836 852 1.134848 GTCACCACCATGCTCTCTCTC 60.135 57.143 0.00 0.00 0.00 3.20
837 853 0.901124 GTCACCACCATGCTCTCTCT 59.099 55.000 0.00 0.00 0.00 3.10
838 854 0.107945 GGTCACCACCATGCTCTCTC 60.108 60.000 0.00 0.00 43.17 3.20
839 855 1.986413 GGTCACCACCATGCTCTCT 59.014 57.895 0.00 0.00 43.17 3.10
840 856 4.625800 GGTCACCACCATGCTCTC 57.374 61.111 0.00 0.00 43.17 3.20
848 864 2.436646 CTCGCCATGGTCACCACC 60.437 66.667 14.67 0.00 44.10 4.61
849 865 1.448540 CTCTCGCCATGGTCACCAC 60.449 63.158 14.67 0.00 35.80 4.16
850 866 1.607801 CTCTCTCGCCATGGTCACCA 61.608 60.000 14.67 0.00 38.19 4.17
851 867 1.142748 CTCTCTCGCCATGGTCACC 59.857 63.158 14.67 0.00 0.00 4.02
852 868 0.102120 CTCTCTCTCGCCATGGTCAC 59.898 60.000 14.67 0.00 0.00 3.67
853 869 0.034089 TCTCTCTCTCGCCATGGTCA 60.034 55.000 14.67 0.00 0.00 4.02
854 870 0.667993 CTCTCTCTCTCGCCATGGTC 59.332 60.000 14.67 4.79 0.00 4.02
855 871 0.257328 TCTCTCTCTCTCGCCATGGT 59.743 55.000 14.67 0.00 0.00 3.55
856 872 0.953727 CTCTCTCTCTCTCGCCATGG 59.046 60.000 7.63 7.63 0.00 3.66
857 873 0.311790 GCTCTCTCTCTCTCGCCATG 59.688 60.000 0.00 0.00 0.00 3.66
858 874 0.106769 TGCTCTCTCTCTCTCGCCAT 60.107 55.000 0.00 0.00 0.00 4.40
859 875 1.029408 GTGCTCTCTCTCTCTCGCCA 61.029 60.000 0.00 0.00 0.00 5.69
860 876 1.727467 GTGCTCTCTCTCTCTCGCC 59.273 63.158 0.00 0.00 0.00 5.54
861 877 1.351707 CGTGCTCTCTCTCTCTCGC 59.648 63.158 0.00 0.00 0.00 5.03
862 878 0.742990 ACCGTGCTCTCTCTCTCTCG 60.743 60.000 0.00 0.00 0.00 4.04
863 879 0.732571 CACCGTGCTCTCTCTCTCTC 59.267 60.000 0.00 0.00 0.00 3.20
864 880 0.679640 CCACCGTGCTCTCTCTCTCT 60.680 60.000 0.00 0.00 0.00 3.10
865 881 0.963355 ACCACCGTGCTCTCTCTCTC 60.963 60.000 0.00 0.00 0.00 3.20
866 882 1.075836 ACCACCGTGCTCTCTCTCT 59.924 57.895 0.00 0.00 0.00 3.10
869 885 1.080434 GTCACCACCGTGCTCTCTC 60.080 63.158 0.00 0.00 40.04 3.20
891 907 1.928706 GCCGTGCTCTCTCTCTCGTT 61.929 60.000 0.00 0.00 0.00 3.85
940 995 2.624557 CCTCCACTACTAGCTTCCCACT 60.625 54.545 0.00 0.00 0.00 4.00
964 1019 2.264794 GGATCTCAACACCGCCGT 59.735 61.111 0.00 0.00 0.00 5.68
971 1026 1.825474 GAGTCGAAGGGGATCTCAACA 59.175 52.381 0.00 0.00 0.00 3.33
988 1043 0.820871 GAAGACATGGAGCTCGGAGT 59.179 55.000 7.83 5.42 0.00 3.85
1100 1155 2.757868 CTCGATGTCTGAGAAACCCTCT 59.242 50.000 0.00 0.00 42.44 3.69
1117 1172 0.815734 GGACGATTCTGGTTCCTCGA 59.184 55.000 0.00 0.00 35.24 4.04
1145 1201 2.572095 TACCCCATTCTCGCTGCACG 62.572 60.000 0.00 2.79 45.62 5.34
1206 1262 4.403432 ACCAAATAGATCAACCCATTGCTG 59.597 41.667 0.00 0.00 35.63 4.41
1280 1336 6.178324 TCTTCTTGCAGTTCATTCATCAGAT 58.822 36.000 0.00 0.00 0.00 2.90
1896 1964 8.037758 TCAATTAGCTTCCACAAAAAGTTTCAA 58.962 29.630 0.00 0.00 0.00 2.69
2041 2128 1.276989 CCTGGCGTAAACCTCTACCAA 59.723 52.381 0.00 0.00 0.00 3.67
2082 2169 9.267084 GTTTTTCTCAATGTAATGCCCTTAAAA 57.733 29.630 0.00 0.00 0.00 1.52
2146 2238 1.005156 CCCCAACCGCACCAATTTG 60.005 57.895 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.