Multiple sequence alignment - TraesCS5B01G243600

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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 TraesCS5B01G243600 chr5B 100.000 2972 0 0 1 2972 423902518 423899547 0.000000e+00 5489
1 TraesCS5B01G243600 chr5D 94.783 2492 66 20 510 2972 358826059 358823603 0.000000e+00 3823
2 TraesCS5B01G243600 chr5D 82.096 983 142 28 1004 1970 403415468 403414504 0.000000e+00 809
3 TraesCS5B01G243600 chr5D 89.091 220 21 2 68 286 358826593 358826376 1.360000e-68 270
4 TraesCS5B01G243600 chr5A 94.840 2403 71 20 603 2967 459677486 459675099 0.000000e+00 3701


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 TraesCS5B01G243600 chr5B 423899547 423902518 2971 True 5489.0 5489 100.000 1 2972 1 chr5B.!!$R1 2971
1 TraesCS5B01G243600 chr5D 358823603 358826593 2990 True 2046.5 3823 91.937 68 2972 2 chr5D.!!$R2 2904
2 TraesCS5B01G243600 chr5D 403414504 403415468 964 True 809.0 809 82.096 1004 1970 1 chr5D.!!$R1 966
3 TraesCS5B01G243600 chr5A 459675099 459677486 2387 True 3701.0 3701 94.840 603 2967 1 chr5A.!!$R1 2364

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
387 389 0.096976 CGTGTCAATGATGGAACGGC 59.903 55.0 0.0 0.0 34.34 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 2370 0.959553 CACAGACTACGGTGTGGAGT 59.04 55.0 0.0 0.0 40.49 3.85 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
17 18 4.798433 TTCATGTTGCCAGCGACT 57.202 50.000 11.20 0.00 0.00 4.18
18 19 3.019964 TTCATGTTGCCAGCGACTT 57.980 47.368 11.20 2.28 0.00 3.01
19 20 2.177394 TTCATGTTGCCAGCGACTTA 57.823 45.000 11.20 0.00 0.00 2.24
20 21 1.725641 TCATGTTGCCAGCGACTTAG 58.274 50.000 11.20 1.94 0.00 2.18
21 22 0.097674 CATGTTGCCAGCGACTTAGC 59.902 55.000 11.20 0.00 37.41 3.09
28 29 2.182030 AGCGACTTAGCTCGGCAC 59.818 61.111 0.00 0.00 45.67 5.01
29 30 3.685214 AGCGACTTAGCTCGGCACG 62.685 63.158 0.00 0.00 45.67 5.34
44 45 3.405170 GGCACGTTGAGTAATGGAATG 57.595 47.619 0.00 0.00 0.00 2.67
45 46 2.747446 GGCACGTTGAGTAATGGAATGT 59.253 45.455 0.00 0.00 0.00 2.71
46 47 3.936453 GGCACGTTGAGTAATGGAATGTA 59.064 43.478 0.00 0.00 0.00 2.29
47 48 4.574828 GGCACGTTGAGTAATGGAATGTAT 59.425 41.667 0.00 0.00 0.00 2.29
48 49 5.501715 GCACGTTGAGTAATGGAATGTATG 58.498 41.667 0.00 0.00 0.00 2.39
49 50 5.504010 GCACGTTGAGTAATGGAATGTATGG 60.504 44.000 0.00 0.00 0.00 2.74
50 51 5.584649 CACGTTGAGTAATGGAATGTATGGT 59.415 40.000 0.00 0.00 0.00 3.55
51 52 6.093495 CACGTTGAGTAATGGAATGTATGGTT 59.907 38.462 0.00 0.00 0.00 3.67
52 53 6.315393 ACGTTGAGTAATGGAATGTATGGTTC 59.685 38.462 0.00 0.00 0.00 3.62
53 54 6.238374 CGTTGAGTAATGGAATGTATGGTTCC 60.238 42.308 0.00 0.00 44.32 3.62
60 61 3.963129 GGAATGTATGGTTCCAGGTTCA 58.037 45.455 0.00 0.00 43.67 3.18
61 62 4.340617 GGAATGTATGGTTCCAGGTTCAA 58.659 43.478 0.00 0.00 43.67 2.69
62 63 4.770010 GGAATGTATGGTTCCAGGTTCAAA 59.230 41.667 0.00 0.00 43.67 2.69
63 64 5.245075 GGAATGTATGGTTCCAGGTTCAAAA 59.755 40.000 0.00 0.00 43.67 2.44
64 65 6.239458 GGAATGTATGGTTCCAGGTTCAAAAA 60.239 38.462 0.00 0.00 43.67 1.94
127 128 6.926630 ACCATTATTTTAGTGCAGGGAAAA 57.073 33.333 0.00 0.00 0.00 2.29
144 145 5.828328 AGGGAAAACTAAGTTGACTCCAAAG 59.172 40.000 0.00 0.00 33.49 2.77
145 146 5.593095 GGGAAAACTAAGTTGACTCCAAAGT 59.407 40.000 0.00 0.00 38.88 2.66
162 163 4.569564 CCAAAGTTATAGTACCAAGCGGAC 59.430 45.833 0.00 0.00 35.59 4.79
173 174 3.403038 ACCAAGCGGACTGATATATTGC 58.597 45.455 0.00 0.00 35.59 3.56
178 179 4.673441 AGCGGACTGATATATTGCGATAC 58.327 43.478 0.00 0.00 0.00 2.24
180 181 4.676986 GCGGACTGATATATTGCGATACCA 60.677 45.833 0.00 0.00 0.00 3.25
204 205 7.832187 CCATTAGTGTCCAGTTTCCCTTATTAA 59.168 37.037 0.00 0.00 0.00 1.40
207 208 4.393990 GTGTCCAGTTTCCCTTATTAACCG 59.606 45.833 0.00 0.00 0.00 4.44
215 216 7.337436 CAGTTTCCCTTATTAACCGGTCAATTA 59.663 37.037 8.63 0.00 0.00 1.40
219 220 8.228035 TCCCTTATTAACCGGTCAATTATTTG 57.772 34.615 8.63 0.00 0.00 2.32
220 221 7.835181 TCCCTTATTAACCGGTCAATTATTTGT 59.165 33.333 8.63 0.00 34.32 2.83
248 250 8.757982 AGTTCATAATGAGGCAATATTTCAGT 57.242 30.769 0.00 0.00 0.00 3.41
253 255 9.976511 CATAATGAGGCAATATTTCAGTCAATT 57.023 29.630 0.00 0.00 0.00 2.32
286 288 7.145932 AGTTATGTTGCAATTCTACTTGGTC 57.854 36.000 0.59 0.00 0.00 4.02
288 290 4.098914 TGTTGCAATTCTACTTGGTCCT 57.901 40.909 0.59 0.00 0.00 3.85
289 291 4.469657 TGTTGCAATTCTACTTGGTCCTT 58.530 39.130 0.59 0.00 0.00 3.36
290 292 5.626142 TGTTGCAATTCTACTTGGTCCTTA 58.374 37.500 0.59 0.00 0.00 2.69
291 293 5.472137 TGTTGCAATTCTACTTGGTCCTTAC 59.528 40.000 0.59 0.00 0.00 2.34
292 294 5.235850 TGCAATTCTACTTGGTCCTTACA 57.764 39.130 0.00 0.00 0.00 2.41
293 295 5.001232 TGCAATTCTACTTGGTCCTTACAC 58.999 41.667 0.00 0.00 0.00 2.90
294 296 4.092968 GCAATTCTACTTGGTCCTTACACG 59.907 45.833 0.00 0.00 0.00 4.49
295 297 3.947910 TTCTACTTGGTCCTTACACGG 57.052 47.619 0.00 0.00 0.00 4.94
296 298 2.173519 TCTACTTGGTCCTTACACGGG 58.826 52.381 0.00 0.00 0.00 5.28
297 299 2.173519 CTACTTGGTCCTTACACGGGA 58.826 52.381 0.00 0.00 0.00 5.14
298 300 0.974383 ACTTGGTCCTTACACGGGAG 59.026 55.000 0.00 0.00 33.04 4.30
299 301 1.263356 CTTGGTCCTTACACGGGAGA 58.737 55.000 0.00 0.00 33.04 3.71
300 302 1.204941 CTTGGTCCTTACACGGGAGAG 59.795 57.143 0.00 0.00 33.04 3.20
301 303 0.406750 TGGTCCTTACACGGGAGAGA 59.593 55.000 0.00 0.00 33.04 3.10
302 304 1.104630 GGTCCTTACACGGGAGAGAG 58.895 60.000 0.00 0.00 33.04 3.20
303 305 0.456628 GTCCTTACACGGGAGAGAGC 59.543 60.000 0.00 0.00 33.04 4.09
304 306 0.331954 TCCTTACACGGGAGAGAGCT 59.668 55.000 0.00 0.00 0.00 4.09
305 307 0.741915 CCTTACACGGGAGAGAGCTC 59.258 60.000 5.27 5.27 40.54 4.09
316 318 3.139603 GAGAGAGCTCCTTTGACGTAC 57.860 52.381 10.93 0.00 35.01 3.67
317 319 1.469308 AGAGAGCTCCTTTGACGTACG 59.531 52.381 15.01 15.01 0.00 3.67
318 320 1.467734 GAGAGCTCCTTTGACGTACGA 59.532 52.381 24.41 0.00 0.00 3.43
319 321 1.199558 AGAGCTCCTTTGACGTACGAC 59.800 52.381 24.41 17.22 0.00 4.34
320 322 0.956633 AGCTCCTTTGACGTACGACA 59.043 50.000 24.41 20.02 0.00 4.35
321 323 1.058404 GCTCCTTTGACGTACGACAC 58.942 55.000 24.41 12.96 0.00 3.67
322 324 1.694639 CTCCTTTGACGTACGACACC 58.305 55.000 24.41 8.39 0.00 4.16
323 325 1.268899 CTCCTTTGACGTACGACACCT 59.731 52.381 24.41 0.00 0.00 4.00
324 326 1.001048 TCCTTTGACGTACGACACCTG 60.001 52.381 24.41 13.40 0.00 4.00
325 327 0.782384 CTTTGACGTACGACACCTGC 59.218 55.000 24.41 2.60 0.00 4.85
326 328 0.598158 TTTGACGTACGACACCTGCC 60.598 55.000 24.41 1.06 0.00 4.85
327 329 2.503375 GACGTACGACACCTGCCG 60.503 66.667 24.41 0.00 0.00 5.69
328 330 3.259425 GACGTACGACACCTGCCGT 62.259 63.158 24.41 0.00 42.15 5.68
329 331 2.049802 CGTACGACACCTGCCGTT 60.050 61.111 10.44 0.00 39.86 4.44
330 332 2.084681 CGTACGACACCTGCCGTTC 61.085 63.158 10.44 0.00 39.86 3.95
331 333 1.007038 GTACGACACCTGCCGTTCA 60.007 57.895 0.00 0.00 39.86 3.18
332 334 1.007336 GTACGACACCTGCCGTTCAG 61.007 60.000 0.00 0.00 42.49 3.02
333 335 2.758770 TACGACACCTGCCGTTCAGC 62.759 60.000 0.00 0.00 41.50 4.26
334 336 3.050275 GACACCTGCCGTTCAGCC 61.050 66.667 0.00 0.00 41.50 4.85
335 337 3.825160 GACACCTGCCGTTCAGCCA 62.825 63.158 0.00 0.00 41.50 4.75
336 338 3.357079 CACCTGCCGTTCAGCCAC 61.357 66.667 0.00 0.00 41.50 5.01
337 339 3.560251 ACCTGCCGTTCAGCCACT 61.560 61.111 0.00 0.00 41.50 4.00
338 340 3.052082 CCTGCCGTTCAGCCACTG 61.052 66.667 0.00 0.00 41.50 3.66
339 341 2.031012 CTGCCGTTCAGCCACTGA 59.969 61.111 0.00 0.00 38.87 3.41
340 342 2.280797 TGCCGTTCAGCCACTGAC 60.281 61.111 0.00 0.00 40.46 3.51
341 343 2.280797 GCCGTTCAGCCACTGACA 60.281 61.111 0.00 0.00 40.46 3.58
342 344 1.672356 GCCGTTCAGCCACTGACAT 60.672 57.895 0.00 0.00 40.46 3.06
343 345 1.915614 GCCGTTCAGCCACTGACATG 61.916 60.000 0.00 0.00 40.46 3.21
344 346 0.603707 CCGTTCAGCCACTGACATGT 60.604 55.000 0.00 0.00 40.46 3.21
345 347 0.514255 CGTTCAGCCACTGACATGTG 59.486 55.000 1.15 0.00 40.46 3.21
353 355 2.479566 CACTGACATGTGGGCTAAGT 57.520 50.000 1.15 0.00 34.56 2.24
354 356 2.783135 CACTGACATGTGGGCTAAGTT 58.217 47.619 1.15 0.00 34.56 2.66
355 357 2.744202 CACTGACATGTGGGCTAAGTTC 59.256 50.000 1.15 0.00 34.56 3.01
356 358 2.290323 ACTGACATGTGGGCTAAGTTCC 60.290 50.000 1.15 0.00 0.00 3.62
357 359 1.702401 TGACATGTGGGCTAAGTTCCA 59.298 47.619 1.15 0.00 0.00 3.53
358 360 2.107378 TGACATGTGGGCTAAGTTCCAA 59.893 45.455 1.15 0.00 34.47 3.53
359 361 2.749621 GACATGTGGGCTAAGTTCCAAG 59.250 50.000 1.15 0.00 34.47 3.61
360 362 1.474077 CATGTGGGCTAAGTTCCAAGC 59.526 52.381 0.00 0.00 38.03 4.01
361 363 0.605319 TGTGGGCTAAGTTCCAAGCG 60.605 55.000 0.00 0.00 39.71 4.68
362 364 1.002624 TGGGCTAAGTTCCAAGCGG 60.003 57.895 0.00 0.00 39.71 5.52
363 365 1.749258 GGGCTAAGTTCCAAGCGGG 60.749 63.158 0.00 0.00 39.71 6.13
364 366 2.407428 GGCTAAGTTCCAAGCGGGC 61.407 63.158 0.00 0.00 39.71 6.13
365 367 2.407428 GCTAAGTTCCAAGCGGGCC 61.407 63.158 0.00 0.00 36.21 5.80
366 368 1.749258 CTAAGTTCCAAGCGGGCCC 60.749 63.158 13.57 13.57 36.21 5.80
367 369 2.478335 CTAAGTTCCAAGCGGGCCCA 62.478 60.000 24.92 0.00 36.21 5.36
368 370 2.757980 TAAGTTCCAAGCGGGCCCAC 62.758 60.000 24.92 13.54 36.21 4.61
377 379 3.430862 CGGGCCCACGTGTCAATG 61.431 66.667 24.92 0.00 0.00 2.82
378 380 2.033448 GGGCCCACGTGTCAATGA 59.967 61.111 19.95 0.00 0.00 2.57
379 381 1.378514 GGGCCCACGTGTCAATGAT 60.379 57.895 19.95 0.00 0.00 2.45
380 382 1.656818 GGGCCCACGTGTCAATGATG 61.657 60.000 19.95 0.00 0.00 3.07
381 383 1.656818 GGCCCACGTGTCAATGATGG 61.657 60.000 15.65 6.83 0.00 3.51
382 384 0.676466 GCCCACGTGTCAATGATGGA 60.676 55.000 15.65 0.00 31.69 3.41
383 385 1.819928 CCCACGTGTCAATGATGGAA 58.180 50.000 15.65 0.00 31.69 3.53
384 386 1.468520 CCCACGTGTCAATGATGGAAC 59.531 52.381 15.65 0.00 31.69 3.62
385 387 1.128507 CCACGTGTCAATGATGGAACG 59.871 52.381 15.65 8.45 39.83 3.95
386 388 1.128507 CACGTGTCAATGATGGAACGG 59.871 52.381 7.58 2.42 38.94 4.44
387 389 0.096976 CGTGTCAATGATGGAACGGC 59.903 55.000 0.00 0.00 34.34 5.68
388 390 1.164411 GTGTCAATGATGGAACGGCA 58.836 50.000 0.00 0.00 0.00 5.69
389 391 1.135689 GTGTCAATGATGGAACGGCAC 60.136 52.381 0.00 0.00 0.00 5.01
390 392 0.451783 GTCAATGATGGAACGGCACC 59.548 55.000 0.00 0.00 0.00 5.01
391 393 0.679640 TCAATGATGGAACGGCACCC 60.680 55.000 0.00 0.00 0.00 4.61
392 394 0.680921 CAATGATGGAACGGCACCCT 60.681 55.000 0.00 0.00 0.00 4.34
393 395 0.916086 AATGATGGAACGGCACCCTA 59.084 50.000 0.00 0.00 0.00 3.53
394 396 0.180406 ATGATGGAACGGCACCCTAC 59.820 55.000 0.00 0.00 0.00 3.18
395 397 1.153229 GATGGAACGGCACCCTACC 60.153 63.158 0.00 0.00 0.00 3.18
401 403 4.197498 CGGCACCCTACCGTACGG 62.197 72.222 32.22 32.22 45.70 4.02
402 404 4.519437 GGCACCCTACCGTACGGC 62.519 72.222 33.62 17.32 39.32 5.68
403 405 3.762247 GCACCCTACCGTACGGCA 61.762 66.667 33.62 21.22 39.32 5.69
404 406 2.493030 CACCCTACCGTACGGCAG 59.507 66.667 33.62 29.10 39.32 4.85
405 407 2.757099 ACCCTACCGTACGGCAGG 60.757 66.667 37.11 37.11 46.18 4.85
407 409 3.534056 CCTACCGTACGGCAGGGG 61.534 72.222 36.68 26.35 43.55 4.79
408 410 2.440796 CTACCGTACGGCAGGGGA 60.441 66.667 33.62 11.31 39.32 4.81
409 411 1.831286 CTACCGTACGGCAGGGGAT 60.831 63.158 33.62 15.14 39.32 3.85
410 412 1.803366 CTACCGTACGGCAGGGGATC 61.803 65.000 33.62 0.00 39.32 3.36
411 413 3.925090 CCGTACGGCAGGGGATCC 61.925 72.222 23.44 1.92 0.00 3.36
412 414 2.838225 CGTACGGCAGGGGATCCT 60.838 66.667 12.58 0.00 46.26 3.24
413 415 2.857744 CGTACGGCAGGGGATCCTC 61.858 68.421 12.58 7.90 42.67 3.71
414 416 2.520982 TACGGCAGGGGATCCTCG 60.521 66.667 12.58 5.37 42.67 4.63
415 417 3.369410 TACGGCAGGGGATCCTCGT 62.369 63.158 12.58 15.21 42.67 4.18
416 418 3.917760 CGGCAGGGGATCCTCGTC 61.918 72.222 12.58 4.80 42.67 4.20
417 419 3.917760 GGCAGGGGATCCTCGTCG 61.918 72.222 12.58 2.84 42.67 5.12
418 420 3.148279 GCAGGGGATCCTCGTCGT 61.148 66.667 12.58 0.00 42.67 4.34
419 421 3.121019 CAGGGGATCCTCGTCGTC 58.879 66.667 12.58 0.00 42.67 4.20
420 422 2.123812 AGGGGATCCTCGTCGTCC 60.124 66.667 12.58 1.93 39.80 4.79
422 424 2.123812 GGGATCCTCGTCGTCCCT 60.124 66.667 12.58 0.00 46.59 4.20
423 425 1.757340 GGGATCCTCGTCGTCCCTT 60.757 63.158 12.58 0.00 46.59 3.95
424 426 0.466922 GGGATCCTCGTCGTCCCTTA 60.467 60.000 12.58 0.00 46.59 2.69
425 427 0.667453 GGATCCTCGTCGTCCCTTAC 59.333 60.000 3.84 0.00 0.00 2.34
426 428 1.386533 GATCCTCGTCGTCCCTTACA 58.613 55.000 0.00 0.00 0.00 2.41
427 429 1.955080 GATCCTCGTCGTCCCTTACAT 59.045 52.381 0.00 0.00 0.00 2.29
428 430 1.100510 TCCTCGTCGTCCCTTACATG 58.899 55.000 0.00 0.00 0.00 3.21
429 431 1.100510 CCTCGTCGTCCCTTACATGA 58.899 55.000 0.00 0.00 0.00 3.07
430 432 1.681793 CCTCGTCGTCCCTTACATGAT 59.318 52.381 0.00 0.00 0.00 2.45
431 433 2.543861 CCTCGTCGTCCCTTACATGATG 60.544 54.545 0.00 0.00 0.00 3.07
432 434 1.407618 TCGTCGTCCCTTACATGATGG 59.592 52.381 0.00 0.00 0.00 3.51
433 435 1.538204 CGTCGTCCCTTACATGATGGG 60.538 57.143 0.00 7.90 42.90 4.00
434 436 1.485066 GTCGTCCCTTACATGATGGGT 59.515 52.381 17.27 0.00 42.28 4.51
435 437 2.696707 GTCGTCCCTTACATGATGGGTA 59.303 50.000 17.27 6.47 42.28 3.69
436 438 2.963101 TCGTCCCTTACATGATGGGTAG 59.037 50.000 17.27 13.58 42.28 3.18
437 439 2.037251 CGTCCCTTACATGATGGGTAGG 59.963 54.545 17.27 0.24 42.28 3.18
438 440 2.372172 GTCCCTTACATGATGGGTAGGG 59.628 54.545 17.56 17.56 42.28 3.53
440 442 2.418669 CCTTACATGATGGGTAGGGGT 58.581 52.381 0.00 0.00 35.11 4.95
441 443 2.783510 CCTTACATGATGGGTAGGGGTT 59.216 50.000 0.00 0.00 35.11 4.11
442 444 3.435026 CCTTACATGATGGGTAGGGGTTG 60.435 52.174 0.00 0.00 35.11 3.77
443 445 0.926293 ACATGATGGGTAGGGGTTGG 59.074 55.000 0.00 0.00 0.00 3.77
444 446 0.185901 CATGATGGGTAGGGGTTGGG 59.814 60.000 0.00 0.00 0.00 4.12
445 447 0.998945 ATGATGGGTAGGGGTTGGGG 60.999 60.000 0.00 0.00 0.00 4.96
446 448 1.308392 GATGGGTAGGGGTTGGGGA 60.308 63.158 0.00 0.00 0.00 4.81
447 449 1.308746 ATGGGTAGGGGTTGGGGAG 60.309 63.158 0.00 0.00 0.00 4.30
448 450 2.694992 GGGTAGGGGTTGGGGAGG 60.695 72.222 0.00 0.00 0.00 4.30
449 451 2.694992 GGTAGGGGTTGGGGAGGG 60.695 72.222 0.00 0.00 0.00 4.30
450 452 2.694992 GTAGGGGTTGGGGAGGGG 60.695 72.222 0.00 0.00 0.00 4.79
451 453 4.047196 TAGGGGTTGGGGAGGGGG 62.047 72.222 0.00 0.00 0.00 5.40
499 503 7.984002 TGTGACAGAAAATAACATTGTTGTG 57.016 32.000 12.30 0.00 35.83 3.33
500 504 6.977502 TGTGACAGAAAATAACATTGTTGTGG 59.022 34.615 12.30 0.00 35.83 4.17
505 509 9.077885 ACAGAAAATAACATTGTTGTGGTAGAT 57.922 29.630 12.30 0.00 35.83 1.98
549 821 5.336150 TCTTTTTGTTTGGAATGTGCTCA 57.664 34.783 0.00 0.00 0.00 4.26
550 822 5.916318 TCTTTTTGTTTGGAATGTGCTCAT 58.084 33.333 0.00 0.00 35.59 2.90
553 825 5.987777 TTTGTTTGGAATGTGCTCATTTG 57.012 34.783 14.73 0.00 43.33 2.32
554 826 3.391965 TGTTTGGAATGTGCTCATTTGC 58.608 40.909 14.73 3.91 43.33 3.68
559 831 2.494870 GGAATGTGCTCATTTGCCTCTT 59.505 45.455 14.73 0.00 43.33 2.85
565 837 2.699846 TGCTCATTTGCCTCTTGGTTTT 59.300 40.909 0.00 0.00 35.27 2.43
569 841 5.544650 CTCATTTGCCTCTTGGTTTTCATT 58.455 37.500 0.00 0.00 35.27 2.57
570 842 5.927819 TCATTTGCCTCTTGGTTTTCATTT 58.072 33.333 0.00 0.00 35.27 2.32
571 843 5.759273 TCATTTGCCTCTTGGTTTTCATTTG 59.241 36.000 0.00 0.00 35.27 2.32
572 844 4.751767 TTGCCTCTTGGTTTTCATTTGT 57.248 36.364 0.00 0.00 35.27 2.83
573 845 4.751767 TGCCTCTTGGTTTTCATTTGTT 57.248 36.364 0.00 0.00 35.27 2.83
574 846 4.440880 TGCCTCTTGGTTTTCATTTGTTG 58.559 39.130 0.00 0.00 35.27 3.33
575 847 4.081198 TGCCTCTTGGTTTTCATTTGTTGT 60.081 37.500 0.00 0.00 35.27 3.32
576 848 4.875536 GCCTCTTGGTTTTCATTTGTTGTT 59.124 37.500 0.00 0.00 35.27 2.83
577 849 5.220643 GCCTCTTGGTTTTCATTTGTTGTTG 60.221 40.000 0.00 0.00 35.27 3.33
578 850 6.105333 CCTCTTGGTTTTCATTTGTTGTTGA 58.895 36.000 0.00 0.00 0.00 3.18
579 851 6.256321 CCTCTTGGTTTTCATTTGTTGTTGAG 59.744 38.462 0.00 0.00 0.00 3.02
580 852 6.929625 TCTTGGTTTTCATTTGTTGTTGAGA 58.070 32.000 0.00 0.00 0.00 3.27
581 853 7.035004 TCTTGGTTTTCATTTGTTGTTGAGAG 58.965 34.615 0.00 0.00 0.00 3.20
582 854 5.108517 TGGTTTTCATTTGTTGTTGAGAGC 58.891 37.500 0.00 0.00 0.00 4.09
583 855 5.105392 TGGTTTTCATTTGTTGTTGAGAGCT 60.105 36.000 0.00 0.00 0.00 4.09
584 856 5.812127 GGTTTTCATTTGTTGTTGAGAGCTT 59.188 36.000 0.00 0.00 0.00 3.74
585 857 6.313658 GGTTTTCATTTGTTGTTGAGAGCTTT 59.686 34.615 0.00 0.00 0.00 3.51
586 858 7.148423 GGTTTTCATTTGTTGTTGAGAGCTTTT 60.148 33.333 0.00 0.00 0.00 2.27
587 859 7.524294 TTTCATTTGTTGTTGAGAGCTTTTC 57.476 32.000 0.00 0.00 0.00 2.29
588 860 5.591099 TCATTTGTTGTTGAGAGCTTTTCC 58.409 37.500 0.00 0.00 0.00 3.13
664 937 4.209911 CGCACTATCATCACCAACTACATG 59.790 45.833 0.00 0.00 0.00 3.21
969 1255 3.402681 CCACATGACCCTCCGCCT 61.403 66.667 0.00 0.00 0.00 5.52
970 1256 2.187946 CACATGACCCTCCGCCTC 59.812 66.667 0.00 0.00 0.00 4.70
971 1257 3.083997 ACATGACCCTCCGCCTCC 61.084 66.667 0.00 0.00 0.00 4.30
972 1258 4.227134 CATGACCCTCCGCCTCCG 62.227 72.222 0.00 0.00 0.00 4.63
1177 1466 1.898094 GTGCAGCATCACCACCACA 60.898 57.895 0.00 0.00 0.00 4.17
1641 1930 3.391382 GCCACCTACGACCAGGCT 61.391 66.667 0.00 0.00 42.01 4.58
2077 2370 1.302366 CCATAGATCGCAAGCTGCAA 58.698 50.000 1.02 0.00 45.36 4.08
2175 2468 9.354673 GATCATTTAGTGGGGAATTTTGATCTA 57.645 33.333 0.00 0.00 0.00 1.98
2185 2478 5.833131 GGGAATTTTGATCTATGCCACCTAA 59.167 40.000 0.00 0.00 0.00 2.69
2186 2479 6.494835 GGGAATTTTGATCTATGCCACCTAAT 59.505 38.462 0.00 0.00 0.00 1.73
2187 2480 7.669722 GGGAATTTTGATCTATGCCACCTAATA 59.330 37.037 0.00 0.00 0.00 0.98
2254 2549 5.411831 TGATTCATGTGTGTTCTAGAGCT 57.588 39.130 8.15 0.00 0.00 4.09
2300 2595 7.740519 ATTTTCACTGCGCTGTTATTTATTC 57.259 32.000 18.01 0.00 0.00 1.75
2310 2605 6.702282 GCGCTGTTATTTATTCTAGACCTCTT 59.298 38.462 0.00 0.00 0.00 2.85
2364 2661 4.746535 TCGGCCAATACAGACAAAGATA 57.253 40.909 2.24 0.00 0.00 1.98
2539 2843 7.348201 CAGGATTATTCTAACTTCGCATGAAC 58.652 38.462 0.00 0.00 0.00 3.18
2540 2844 7.225538 CAGGATTATTCTAACTTCGCATGAACT 59.774 37.037 0.00 0.00 0.00 3.01
2560 2864 7.915508 TGAACTGTGTGTTGTTTAGTGATTAG 58.084 34.615 0.00 0.00 39.30 1.73
2561 2865 7.551262 TGAACTGTGTGTTGTTTAGTGATTAGT 59.449 33.333 0.00 0.00 39.30 2.24
2562 2866 8.951787 AACTGTGTGTTGTTTAGTGATTAGTA 57.048 30.769 0.00 0.00 37.52 1.82
2639 2943 5.715439 TCCCATGTTCATCTGGTAAGAAT 57.285 39.130 0.00 0.00 35.59 2.40
2794 3122 2.554032 GCAAATAGACCGCATGCCTAAT 59.446 45.455 13.15 0.00 0.00 1.73
2849 3178 1.276138 ACTGGCATGAGACATCAACGA 59.724 47.619 0.00 0.00 39.39 3.85
2850 3179 2.289631 ACTGGCATGAGACATCAACGAA 60.290 45.455 0.00 0.00 39.39 3.85
2851 3180 2.941064 CTGGCATGAGACATCAACGAAT 59.059 45.455 0.00 0.00 39.39 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.687494 CGAGCTAAGTCGCTGGCAAC 61.687 60.000 0.00 0.00 41.08 4.17
6 7 1.446099 CGAGCTAAGTCGCTGGCAA 60.446 57.895 0.00 0.00 41.08 4.52
7 8 2.181777 CGAGCTAAGTCGCTGGCA 59.818 61.111 0.00 0.00 41.08 4.92
8 9 2.583593 CCGAGCTAAGTCGCTGGC 60.584 66.667 0.00 0.00 41.08 4.85
9 10 2.583593 GCCGAGCTAAGTCGCTGG 60.584 66.667 0.00 0.00 41.08 4.85
10 11 2.161486 GTGCCGAGCTAAGTCGCTG 61.161 63.158 0.00 0.00 41.08 5.18
11 12 2.182030 GTGCCGAGCTAAGTCGCT 59.818 61.111 0.00 0.00 44.33 4.93
12 13 3.248171 CGTGCCGAGCTAAGTCGC 61.248 66.667 0.00 0.00 38.69 5.19
13 14 1.443872 AACGTGCCGAGCTAAGTCG 60.444 57.895 0.00 0.00 39.77 4.18
14 15 0.388134 TCAACGTGCCGAGCTAAGTC 60.388 55.000 0.00 0.00 0.00 3.01
15 16 0.388649 CTCAACGTGCCGAGCTAAGT 60.389 55.000 0.00 0.00 0.00 2.24
16 17 0.388649 ACTCAACGTGCCGAGCTAAG 60.389 55.000 9.21 0.00 32.21 2.18
17 18 0.883153 TACTCAACGTGCCGAGCTAA 59.117 50.000 9.21 0.00 32.21 3.09
18 19 0.883153 TTACTCAACGTGCCGAGCTA 59.117 50.000 9.21 1.05 32.21 3.32
19 20 0.246635 ATTACTCAACGTGCCGAGCT 59.753 50.000 9.21 0.00 32.21 4.09
20 21 0.370273 CATTACTCAACGTGCCGAGC 59.630 55.000 9.21 0.00 32.21 5.03
21 22 0.999406 CCATTACTCAACGTGCCGAG 59.001 55.000 8.02 8.02 35.30 4.63
22 23 0.604073 TCCATTACTCAACGTGCCGA 59.396 50.000 0.00 0.00 0.00 5.54
23 24 1.434555 TTCCATTACTCAACGTGCCG 58.565 50.000 0.00 0.00 0.00 5.69
24 25 2.747446 ACATTCCATTACTCAACGTGCC 59.253 45.455 0.00 0.00 0.00 5.01
25 26 5.501715 CATACATTCCATTACTCAACGTGC 58.498 41.667 0.00 0.00 0.00 5.34
26 27 5.584649 ACCATACATTCCATTACTCAACGTG 59.415 40.000 0.00 0.00 0.00 4.49
27 28 5.741011 ACCATACATTCCATTACTCAACGT 58.259 37.500 0.00 0.00 0.00 3.99
28 29 6.238374 GGAACCATACATTCCATTACTCAACG 60.238 42.308 0.00 0.00 44.42 4.10
29 30 7.027778 GGAACCATACATTCCATTACTCAAC 57.972 40.000 0.00 0.00 44.42 3.18
39 40 3.963129 TGAACCTGGAACCATACATTCC 58.037 45.455 0.00 0.00 45.13 3.01
40 41 5.975693 TTTGAACCTGGAACCATACATTC 57.024 39.130 0.00 0.00 0.00 2.67
41 42 6.739331 TTTTTGAACCTGGAACCATACATT 57.261 33.333 0.00 0.00 0.00 2.71
101 102 7.639113 TTCCCTGCACTAAAATAATGGTAAG 57.361 36.000 0.00 0.00 0.00 2.34
115 116 3.883489 GTCAACTTAGTTTTCCCTGCACT 59.117 43.478 0.00 0.00 0.00 4.40
121 122 5.593095 ACTTTGGAGTCAACTTAGTTTTCCC 59.407 40.000 13.85 6.61 31.78 3.97
144 145 4.644103 TCAGTCCGCTTGGTACTATAAC 57.356 45.455 0.00 0.00 0.00 1.89
145 146 8.818622 ATATATCAGTCCGCTTGGTACTATAA 57.181 34.615 0.00 0.00 0.00 0.98
162 163 8.932945 ACACTAATGGTATCGCAATATATCAG 57.067 34.615 0.00 0.00 0.00 2.90
173 174 4.809426 GGAAACTGGACACTAATGGTATCG 59.191 45.833 0.00 0.00 0.00 2.92
178 179 3.721087 AGGGAAACTGGACACTAATGG 57.279 47.619 0.00 0.00 0.00 3.16
180 181 7.832685 GGTTAATAAGGGAAACTGGACACTAAT 59.167 37.037 0.00 0.00 0.00 1.73
204 205 8.974060 ATGAACTATACAAATAATTGACCGGT 57.026 30.769 6.92 6.92 38.94 5.28
227 228 9.976511 AATTGACTGAAATATTGCCTCATTATG 57.023 29.630 0.00 0.00 0.00 1.90
246 248 5.564550 ACATAACTTCTCAGGCAATTGACT 58.435 37.500 8.40 8.40 0.00 3.41
248 250 5.335897 GCAACATAACTTCTCAGGCAATTGA 60.336 40.000 10.34 0.00 0.00 2.57
253 255 3.138884 TGCAACATAACTTCTCAGGCA 57.861 42.857 0.00 0.00 0.00 4.75
255 257 6.506500 AGAATTGCAACATAACTTCTCAGG 57.493 37.500 0.00 0.00 0.00 3.86
256 258 8.261492 AGTAGAATTGCAACATAACTTCTCAG 57.739 34.615 12.69 0.00 0.00 3.35
286 288 0.741915 GAGCTCTCTCCCGTGTAAGG 59.258 60.000 6.43 0.00 33.19 2.69
296 298 2.476519 CGTACGTCAAAGGAGCTCTCTC 60.477 54.545 14.64 0.00 38.62 3.20
297 299 1.469308 CGTACGTCAAAGGAGCTCTCT 59.531 52.381 14.64 6.28 0.00 3.10
298 300 1.467734 TCGTACGTCAAAGGAGCTCTC 59.532 52.381 16.05 3.76 0.00 3.20
299 301 1.199558 GTCGTACGTCAAAGGAGCTCT 59.800 52.381 16.05 0.00 0.00 4.09
300 302 1.068748 TGTCGTACGTCAAAGGAGCTC 60.069 52.381 16.05 4.71 0.00 4.09
301 303 0.956633 TGTCGTACGTCAAAGGAGCT 59.043 50.000 16.05 0.00 0.00 4.09
302 304 1.058404 GTGTCGTACGTCAAAGGAGC 58.942 55.000 16.51 0.16 0.00 4.70
303 305 1.268899 AGGTGTCGTACGTCAAAGGAG 59.731 52.381 16.51 0.00 0.00 3.69
304 306 1.001048 CAGGTGTCGTACGTCAAAGGA 60.001 52.381 16.51 0.00 0.00 3.36
305 307 1.415374 CAGGTGTCGTACGTCAAAGG 58.585 55.000 16.51 5.62 0.00 3.11
306 308 0.782384 GCAGGTGTCGTACGTCAAAG 59.218 55.000 16.51 10.41 0.00 2.77
307 309 0.598158 GGCAGGTGTCGTACGTCAAA 60.598 55.000 16.51 0.00 0.00 2.69
308 310 1.007038 GGCAGGTGTCGTACGTCAA 60.007 57.895 16.51 0.06 0.00 3.18
309 311 2.646719 GGCAGGTGTCGTACGTCA 59.353 61.111 16.05 13.49 0.00 4.35
310 312 2.503375 CGGCAGGTGTCGTACGTC 60.503 66.667 16.05 10.62 38.51 4.34
317 319 3.050275 GGCTGAACGGCAGGTGTC 61.050 66.667 7.91 0.00 45.03 3.67
318 320 3.872603 TGGCTGAACGGCAGGTGT 61.873 61.111 7.91 0.00 45.03 4.16
323 325 2.280797 GTCAGTGGCTGAACGGCA 60.281 61.111 7.91 0.00 42.46 5.69
324 326 1.672356 ATGTCAGTGGCTGAACGGC 60.672 57.895 0.00 0.00 42.46 5.68
325 327 0.603707 ACATGTCAGTGGCTGAACGG 60.604 55.000 0.00 0.00 42.46 4.44
326 328 0.514255 CACATGTCAGTGGCTGAACG 59.486 55.000 0.00 0.00 42.46 3.95
334 336 2.479566 ACTTAGCCCACATGTCAGTG 57.520 50.000 0.00 0.00 39.21 3.66
335 337 2.290323 GGAACTTAGCCCACATGTCAGT 60.290 50.000 0.00 0.00 0.00 3.41
336 338 2.290260 TGGAACTTAGCCCACATGTCAG 60.290 50.000 0.00 0.00 0.00 3.51
337 339 1.702401 TGGAACTTAGCCCACATGTCA 59.298 47.619 0.00 0.00 0.00 3.58
338 340 2.489938 TGGAACTTAGCCCACATGTC 57.510 50.000 0.00 0.00 0.00 3.06
339 341 2.795329 CTTGGAACTTAGCCCACATGT 58.205 47.619 0.00 0.00 31.11 3.21
340 342 1.474077 GCTTGGAACTTAGCCCACATG 59.526 52.381 0.00 0.00 32.22 3.21
341 343 1.839424 GCTTGGAACTTAGCCCACAT 58.161 50.000 0.00 0.00 32.22 3.21
342 344 0.605319 CGCTTGGAACTTAGCCCACA 60.605 55.000 0.00 0.00 34.22 4.17
343 345 1.305930 CCGCTTGGAACTTAGCCCAC 61.306 60.000 0.00 0.00 34.22 4.61
344 346 1.002624 CCGCTTGGAACTTAGCCCA 60.003 57.895 0.00 0.00 34.22 5.36
345 347 1.749258 CCCGCTTGGAACTTAGCCC 60.749 63.158 0.00 0.00 34.22 5.19
346 348 2.407428 GCCCGCTTGGAACTTAGCC 61.407 63.158 0.00 0.00 34.22 3.93
347 349 2.407428 GGCCCGCTTGGAACTTAGC 61.407 63.158 0.00 0.00 35.39 3.09
348 350 1.749258 GGGCCCGCTTGGAACTTAG 60.749 63.158 5.69 0.00 35.39 2.18
349 351 2.353573 GGGCCCGCTTGGAACTTA 59.646 61.111 5.69 0.00 35.39 2.24
350 352 3.897122 TGGGCCCGCTTGGAACTT 61.897 61.111 19.37 0.00 35.39 2.66
351 353 4.660938 GTGGGCCCGCTTGGAACT 62.661 66.667 28.79 0.00 35.39 3.01
360 362 3.430862 CATTGACACGTGGGCCCG 61.431 66.667 21.57 8.84 0.00 6.13
361 363 1.378514 ATCATTGACACGTGGGCCC 60.379 57.895 21.57 17.59 0.00 5.80
362 364 1.656818 CCATCATTGACACGTGGGCC 61.657 60.000 21.57 9.12 0.00 5.80
363 365 0.676466 TCCATCATTGACACGTGGGC 60.676 55.000 21.57 12.05 0.00 5.36
364 366 1.468520 GTTCCATCATTGACACGTGGG 59.531 52.381 21.57 8.69 0.00 4.61
365 367 1.128507 CGTTCCATCATTGACACGTGG 59.871 52.381 21.57 0.90 0.00 4.94
366 368 1.128507 CCGTTCCATCATTGACACGTG 59.871 52.381 15.48 15.48 0.00 4.49
367 369 1.438651 CCGTTCCATCATTGACACGT 58.561 50.000 0.00 0.00 0.00 4.49
368 370 0.096976 GCCGTTCCATCATTGACACG 59.903 55.000 0.00 0.00 0.00 4.49
369 371 1.135689 GTGCCGTTCCATCATTGACAC 60.136 52.381 0.00 0.00 0.00 3.67
370 372 1.164411 GTGCCGTTCCATCATTGACA 58.836 50.000 0.00 0.00 0.00 3.58
371 373 0.451783 GGTGCCGTTCCATCATTGAC 59.548 55.000 0.00 0.00 0.00 3.18
372 374 0.679640 GGGTGCCGTTCCATCATTGA 60.680 55.000 0.00 0.00 0.00 2.57
373 375 0.680921 AGGGTGCCGTTCCATCATTG 60.681 55.000 0.00 0.00 0.00 2.82
374 376 0.916086 TAGGGTGCCGTTCCATCATT 59.084 50.000 0.00 0.00 0.00 2.57
375 377 0.180406 GTAGGGTGCCGTTCCATCAT 59.820 55.000 0.00 0.00 0.00 2.45
376 378 1.600107 GTAGGGTGCCGTTCCATCA 59.400 57.895 0.00 0.00 0.00 3.07
377 379 1.153229 GGTAGGGTGCCGTTCCATC 60.153 63.158 2.38 0.00 0.00 3.51
378 380 2.995547 GGTAGGGTGCCGTTCCAT 59.004 61.111 2.38 0.00 0.00 3.41
379 381 3.697747 CGGTAGGGTGCCGTTCCA 61.698 66.667 7.23 0.00 43.84 3.53
385 387 4.519437 GCCGTACGGTAGGGTGCC 62.519 72.222 33.34 12.09 36.15 5.01
386 388 3.711541 CTGCCGTACGGTAGGGTGC 62.712 68.421 36.24 20.99 43.03 5.01
387 389 2.493030 CTGCCGTACGGTAGGGTG 59.507 66.667 36.24 17.96 43.03 4.61
391 393 1.803366 GATCCCCTGCCGTACGGTAG 61.803 65.000 36.68 36.68 45.73 3.18
392 394 1.829533 GATCCCCTGCCGTACGGTA 60.830 63.158 33.34 28.79 37.65 4.02
393 395 3.152400 GATCCCCTGCCGTACGGT 61.152 66.667 33.34 13.65 37.65 4.83
394 396 3.925090 GGATCCCCTGCCGTACGG 61.925 72.222 30.06 30.06 38.57 4.02
395 397 2.838225 AGGATCCCCTGCCGTACG 60.838 66.667 8.55 8.69 42.42 3.67
396 398 2.857744 CGAGGATCCCCTGCCGTAC 61.858 68.421 8.55 0.00 44.53 3.67
397 399 2.520982 CGAGGATCCCCTGCCGTA 60.521 66.667 8.55 0.00 44.53 4.02
398 400 4.779733 ACGAGGATCCCCTGCCGT 62.780 66.667 8.55 7.95 44.53 5.68
399 401 3.917760 GACGAGGATCCCCTGCCG 61.918 72.222 8.55 7.30 44.53 5.69
400 402 3.917760 CGACGAGGATCCCCTGCC 61.918 72.222 8.55 0.00 44.53 4.85
401 403 3.140225 GACGACGAGGATCCCCTGC 62.140 68.421 8.55 0.00 44.53 4.85
402 404 2.491022 GGACGACGAGGATCCCCTG 61.491 68.421 8.55 0.45 44.53 4.45
403 405 3.735251 GGGACGACGAGGATCCCCT 62.735 68.421 8.55 0.00 45.70 4.79
404 406 3.225061 GGGACGACGAGGATCCCC 61.225 72.222 8.55 0.00 45.70 4.81
406 408 0.667453 GTAAGGGACGACGAGGATCC 59.333 60.000 2.48 2.48 0.00 3.36
407 409 1.386533 TGTAAGGGACGACGAGGATC 58.613 55.000 0.00 0.00 0.00 3.36
408 410 1.681793 CATGTAAGGGACGACGAGGAT 59.318 52.381 0.00 0.00 0.00 3.24
409 411 1.100510 CATGTAAGGGACGACGAGGA 58.899 55.000 0.00 0.00 0.00 3.71
410 412 1.100510 TCATGTAAGGGACGACGAGG 58.899 55.000 0.00 0.00 0.00 4.63
411 413 2.543861 CCATCATGTAAGGGACGACGAG 60.544 54.545 0.00 0.00 0.00 4.18
412 414 1.407618 CCATCATGTAAGGGACGACGA 59.592 52.381 0.00 0.00 0.00 4.20
413 415 1.538204 CCCATCATGTAAGGGACGACG 60.538 57.143 12.60 0.00 45.80 5.12
414 416 1.485066 ACCCATCATGTAAGGGACGAC 59.515 52.381 21.25 0.00 45.80 4.34
415 417 1.874129 ACCCATCATGTAAGGGACGA 58.126 50.000 21.25 0.00 45.80 4.20
416 418 2.037251 CCTACCCATCATGTAAGGGACG 59.963 54.545 21.25 13.05 45.80 4.79
417 419 2.372172 CCCTACCCATCATGTAAGGGAC 59.628 54.545 21.25 0.00 45.80 4.46
418 420 2.698967 CCCCTACCCATCATGTAAGGGA 60.699 54.545 21.25 4.97 45.80 4.20
420 422 2.418669 ACCCCTACCCATCATGTAAGG 58.581 52.381 0.00 0.00 0.00 2.69
421 423 3.435026 CCAACCCCTACCCATCATGTAAG 60.435 52.174 0.00 0.00 0.00 2.34
422 424 2.512056 CCAACCCCTACCCATCATGTAA 59.488 50.000 0.00 0.00 0.00 2.41
423 425 2.131854 CCAACCCCTACCCATCATGTA 58.868 52.381 0.00 0.00 0.00 2.29
424 426 0.926293 CCAACCCCTACCCATCATGT 59.074 55.000 0.00 0.00 0.00 3.21
425 427 0.185901 CCCAACCCCTACCCATCATG 59.814 60.000 0.00 0.00 0.00 3.07
426 428 0.998945 CCCCAACCCCTACCCATCAT 60.999 60.000 0.00 0.00 0.00 2.45
427 429 1.621205 CCCCAACCCCTACCCATCA 60.621 63.158 0.00 0.00 0.00 3.07
428 430 1.308392 TCCCCAACCCCTACCCATC 60.308 63.158 0.00 0.00 0.00 3.51
429 431 1.308746 CTCCCCAACCCCTACCCAT 60.309 63.158 0.00 0.00 0.00 4.00
430 432 2.126372 CTCCCCAACCCCTACCCA 59.874 66.667 0.00 0.00 0.00 4.51
431 433 2.694992 CCTCCCCAACCCCTACCC 60.695 72.222 0.00 0.00 0.00 3.69
432 434 2.694992 CCCTCCCCAACCCCTACC 60.695 72.222 0.00 0.00 0.00 3.18
433 435 2.694992 CCCCTCCCCAACCCCTAC 60.695 72.222 0.00 0.00 0.00 3.18
434 436 4.047196 CCCCCTCCCCAACCCCTA 62.047 72.222 0.00 0.00 0.00 3.53
452 454 2.162681 CTCTTTTGATGTGTGTCCCCC 58.837 52.381 0.00 0.00 0.00 5.40
453 455 2.863809 ACTCTTTTGATGTGTGTCCCC 58.136 47.619 0.00 0.00 0.00 4.81
454 456 4.097892 ACAAACTCTTTTGATGTGTGTCCC 59.902 41.667 4.18 0.00 44.38 4.46
455 457 5.036737 CACAAACTCTTTTGATGTGTGTCC 58.963 41.667 4.18 0.00 44.38 4.02
456 458 5.739161 GTCACAAACTCTTTTGATGTGTGTC 59.261 40.000 4.18 0.00 44.38 3.67
457 459 5.182950 TGTCACAAACTCTTTTGATGTGTGT 59.817 36.000 4.18 0.00 44.38 3.72
458 460 5.639757 TGTCACAAACTCTTTTGATGTGTG 58.360 37.500 4.18 0.00 44.38 3.82
459 461 5.647658 TCTGTCACAAACTCTTTTGATGTGT 59.352 36.000 4.18 0.00 44.38 3.72
460 462 6.122850 TCTGTCACAAACTCTTTTGATGTG 57.877 37.500 4.18 0.00 44.38 3.21
461 463 6.757897 TTCTGTCACAAACTCTTTTGATGT 57.242 33.333 4.18 0.00 44.38 3.06
462 464 8.638685 ATTTTCTGTCACAAACTCTTTTGATG 57.361 30.769 4.18 0.22 44.38 3.07
464 466 9.567848 GTTATTTTCTGTCACAAACTCTTTTGA 57.432 29.630 4.18 0.00 44.38 2.69
468 470 9.520204 CAATGTTATTTTCTGTCACAAACTCTT 57.480 29.630 0.00 0.00 0.00 2.85
543 815 1.251251 ACCAAGAGGCAAATGAGCAC 58.749 50.000 0.00 0.00 39.06 4.40
549 821 5.683681 ACAAATGAAAACCAAGAGGCAAAT 58.316 33.333 0.00 0.00 39.06 2.32
550 822 5.096443 ACAAATGAAAACCAAGAGGCAAA 57.904 34.783 0.00 0.00 39.06 3.68
553 825 4.441792 ACAACAAATGAAAACCAAGAGGC 58.558 39.130 0.00 0.00 39.06 4.70
554 826 6.105333 TCAACAACAAATGAAAACCAAGAGG 58.895 36.000 0.00 0.00 42.21 3.69
559 831 5.105392 AGCTCTCAACAACAAATGAAAACCA 60.105 36.000 0.00 0.00 0.00 3.67
565 837 5.126869 TGGAAAAGCTCTCAACAACAAATGA 59.873 36.000 0.00 0.00 0.00 2.57
569 841 4.462483 ACTTGGAAAAGCTCTCAACAACAA 59.538 37.500 0.00 0.00 0.00 2.83
570 842 4.016444 ACTTGGAAAAGCTCTCAACAACA 58.984 39.130 0.00 0.00 0.00 3.33
571 843 4.639135 ACTTGGAAAAGCTCTCAACAAC 57.361 40.909 0.00 0.00 0.00 3.32
572 844 5.680619 TCTACTTGGAAAAGCTCTCAACAA 58.319 37.500 0.00 0.00 0.00 2.83
573 845 5.290493 TCTACTTGGAAAAGCTCTCAACA 57.710 39.130 0.00 0.00 0.00 3.33
574 846 5.123027 CCATCTACTTGGAAAAGCTCTCAAC 59.877 44.000 0.00 0.00 39.25 3.18
575 847 5.013079 TCCATCTACTTGGAAAAGCTCTCAA 59.987 40.000 0.00 0.00 42.82 3.02
576 848 4.532126 TCCATCTACTTGGAAAAGCTCTCA 59.468 41.667 0.00 0.00 42.82 3.27
577 849 5.091261 TCCATCTACTTGGAAAAGCTCTC 57.909 43.478 0.00 0.00 42.82 3.20
586 858 3.199442 TCCACCTTCCATCTACTTGGA 57.801 47.619 0.00 0.00 44.08 3.53
587 859 3.264450 ACTTCCACCTTCCATCTACTTGG 59.736 47.826 0.00 0.00 38.18 3.61
588 860 4.256920 CACTTCCACCTTCCATCTACTTG 58.743 47.826 0.00 0.00 0.00 3.16
631 904 5.393569 GGTGATGATAGTGCGATAGTAGCAT 60.394 44.000 5.69 5.69 46.96 3.79
632 905 4.082733 GGTGATGATAGTGCGATAGTAGCA 60.083 45.833 0.00 0.00 42.99 3.49
633 906 4.082733 TGGTGATGATAGTGCGATAGTAGC 60.083 45.833 0.00 0.00 39.35 3.58
634 907 5.629079 TGGTGATGATAGTGCGATAGTAG 57.371 43.478 0.00 0.00 39.35 2.57
635 908 5.535030 AGTTGGTGATGATAGTGCGATAGTA 59.465 40.000 0.00 0.00 39.35 1.82
636 909 4.342378 AGTTGGTGATGATAGTGCGATAGT 59.658 41.667 0.00 0.00 39.35 2.12
822 1096 1.019805 GCTGGGTCTCGCAACCTAAC 61.020 60.000 6.08 0.00 39.42 2.34
968 1254 2.355363 TGTTTCGTCGGTGCGGAG 60.355 61.111 0.00 0.00 0.00 4.63
969 1255 2.659244 GTGTTTCGTCGGTGCGGA 60.659 61.111 0.00 0.00 0.00 5.54
970 1256 3.708734 GGTGTTTCGTCGGTGCGG 61.709 66.667 0.00 0.00 0.00 5.69
971 1257 2.938823 CTGGTGTTTCGTCGGTGCG 61.939 63.158 0.00 0.00 0.00 5.34
972 1258 1.557443 CTCTGGTGTTTCGTCGGTGC 61.557 60.000 0.00 0.00 0.00 5.01
973 1259 0.031585 TCTCTGGTGTTTCGTCGGTG 59.968 55.000 0.00 0.00 0.00 4.94
1177 1466 2.743718 CTGCAGGAGGTGGTCGTT 59.256 61.111 5.57 0.00 0.00 3.85
2077 2370 0.959553 CACAGACTACGGTGTGGAGT 59.040 55.000 0.00 0.00 40.49 3.85
2175 2468 4.949856 CCAAGACAAAGTATTAGGTGGCAT 59.050 41.667 0.00 0.00 0.00 4.40
2185 2478 5.071788 TGAGGAACTGACCAAGACAAAGTAT 59.928 40.000 0.00 0.00 41.55 2.12
2186 2479 4.407621 TGAGGAACTGACCAAGACAAAGTA 59.592 41.667 0.00 0.00 41.55 2.24
2187 2480 3.199946 TGAGGAACTGACCAAGACAAAGT 59.800 43.478 0.00 0.00 41.55 2.66
2254 2549 2.039216 TGGTAAGCCTGAACCGAATTCA 59.961 45.455 6.22 2.63 45.39 2.57
2364 2661 4.922206 TGCTGATTTGTCATTTCCTACCT 58.078 39.130 0.00 0.00 0.00 3.08
2539 2843 8.589335 AGTACTAATCACTAAACAACACACAG 57.411 34.615 0.00 0.00 0.00 3.66
2540 2844 8.951787 AAGTACTAATCACTAAACAACACACA 57.048 30.769 0.00 0.00 0.00 3.72
2560 2864 5.805994 GCAGGCATATTATCTACCGAAGTAC 59.194 44.000 0.00 0.00 0.00 2.73
2561 2865 5.715279 AGCAGGCATATTATCTACCGAAGTA 59.285 40.000 0.00 0.00 0.00 2.24
2562 2866 4.528596 AGCAGGCATATTATCTACCGAAGT 59.471 41.667 0.00 0.00 0.00 3.01
2574 2878 6.918333 TTGTCAGCACTCAGCAGGCATATT 62.918 45.833 0.00 0.00 44.12 1.28
2575 2879 5.511126 TTGTCAGCACTCAGCAGGCATAT 62.511 47.826 0.00 0.00 44.12 1.78
2656 2960 1.200839 CGTCCGTTTGACTGTTCGC 59.799 57.895 0.00 0.00 42.13 4.70
2851 3180 9.374711 TGTGGACACTGGATAGTCATAATATTA 57.625 33.333 3.91 0.00 36.50 0.98


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

AutoCloner maintained by Alex Coulton.