Multiple sequence alignment - TraesCS6D01G280000

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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 TraesCS6D01G280000 chr6D 100.000 2381 0 0 1 2381 387881803 387884183 0.000000e+00 4397.0
1 TraesCS6D01G280000 chr6D 77.586 464 83 17 45 502 393927880 393927432 6.530000e-66 261.0
2 TraesCS6D01G280000 chr6D 81.089 349 32 20 956 1279 387780688 387781027 5.080000e-62 248.0
3 TraesCS6D01G280000 chr6B 92.367 773 34 10 728 1481 579094028 579094794 0.000000e+00 1077.0
4 TraesCS6D01G280000 chr6B 91.743 436 27 7 1948 2381 579355591 579356019 4.380000e-167 597.0
5 TraesCS6D01G280000 chr6B 85.560 464 27 11 1475 1909 579094899 579095351 1.300000e-122 449.0
6 TraesCS6D01G280000 chr6B 87.719 342 28 7 857 1189 578950441 578950777 1.030000e-103 387.0
7 TraesCS6D01G280000 chr6B 84.802 329 22 17 643 965 579102337 579102643 2.970000e-79 305.0
8 TraesCS6D01G280000 chr6B 91.667 156 13 0 2226 2381 579101694 579101849 1.430000e-52 217.0
9 TraesCS6D01G280000 chr6B 82.828 198 16 8 1678 1860 579353984 579354178 6.810000e-36 161.0
10 TraesCS6D01G280000 chr6A 90.141 710 33 7 643 1319 533253326 533254031 0.000000e+00 889.0
11 TraesCS6D01G280000 chr6A 94.626 428 15 2 1954 2381 533256492 533256911 0.000000e+00 656.0
12 TraesCS6D01G280000 chr6A 77.808 365 74 7 141 501 457451458 457451097 3.980000e-53 219.0
13 TraesCS6D01G280000 chr6A 88.953 172 11 3 1309 1480 533254450 533254613 3.100000e-49 206.0
14 TraesCS6D01G280000 chr6A 90.741 108 6 2 1475 1578 533254718 533254825 8.870000e-30 141.0
15 TraesCS6D01G280000 chr5D 83.600 500 65 11 3 498 372306505 372306991 1.000000e-123 453.0
16 TraesCS6D01G280000 chr5D 82.236 501 70 8 1 498 470050522 470050038 4.740000e-112 414.0
17 TraesCS6D01G280000 chr5D 79.430 491 87 9 15 498 9289509 9289026 3.790000e-88 335.0
18 TraesCS6D01G280000 chr4A 82.164 499 85 4 3 498 567224389 567224886 2.190000e-115 425.0
19 TraesCS6D01G280000 chr4D 81.783 516 79 8 3 505 324201196 324201709 3.660000e-113 418.0
20 TraesCS6D01G280000 chr4D 83.862 347 49 6 3 348 339455706 339456046 8.210000e-85 324.0
21 TraesCS6D01G280000 chr3B 78.728 503 97 8 3 500 508259755 508259258 6.350000e-86 327.0
22 TraesCS6D01G280000 chr5A 80.806 422 74 6 17 434 693653208 693653626 8.210000e-85 324.0
23 TraesCS6D01G280000 chr2D 81.433 307 45 7 21 317 372703213 372703517 8.500000e-60 241.0
24 TraesCS6D01G280000 chr2D 81.818 275 43 6 227 497 96688531 96688260 8.560000e-55 224.0
25 TraesCS6D01G280000 chr7D 82.310 277 45 4 227 500 83388659 83388384 1.100000e-58 237.0
26 TraesCS6D01G280000 chr5B 94.444 36 0 1 1329 1364 327153881 327153848 1.000000e-03 54.7
27 TraesCS6D01G280000 chr5B 94.444 36 1 1 1329 1363 327435060 327435025 1.000000e-03 54.7


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 TraesCS6D01G280000 chr6D 387881803 387884183 2380 False 4397 4397 100.00000 1 2381 1 chr6D.!!$F2 2380
1 TraesCS6D01G280000 chr6B 579094028 579095351 1323 False 763 1077 88.96350 728 1909 2 chr6B.!!$F2 1181
2 TraesCS6D01G280000 chr6B 579353984 579356019 2035 False 379 597 87.28550 1678 2381 2 chr6B.!!$F4 703
3 TraesCS6D01G280000 chr6B 579101694 579102643 949 False 261 305 88.23450 643 2381 2 chr6B.!!$F3 1738
4 TraesCS6D01G280000 chr6A 533253326 533256911 3585 False 473 889 91.11525 643 2381 4 chr6A.!!$F1 1738
5 TraesCS6D01G280000 chr4D 324201196 324201709 513 False 418 418 81.78300 3 505 1 chr4D.!!$F1 502


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
579 580 0.033642 CCATTTGTGTGTGCCATGCA 59.966 50.0 0.0 0.0 35.6 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 5088 0.102481 CAGAATGCTTGGCCTCATGC 59.898 55.0 3.32 3.62 42.34 4.06 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
93 94 2.117156 CCGCCATTGCCTTCTCCAG 61.117 63.158 0.00 0.00 0.00 3.86
94 95 2.768492 CGCCATTGCCTTCTCCAGC 61.768 63.158 0.00 0.00 0.00 4.85
115 116 2.998097 CACGGGATGACACCCCAT 59.002 61.111 5.48 0.00 46.62 4.00
120 121 1.202651 CGGGATGACACCCCATTAGAC 60.203 57.143 5.48 0.00 46.62 2.59
147 148 1.611491 GGACTGATCGGAGTCAGATCC 59.389 57.143 24.71 11.67 46.77 3.36
156 157 2.583593 GTCAGATCCGCTGTCCGC 60.584 66.667 0.00 0.00 45.14 5.54
163 164 4.529219 CCGCTGTCCGCCATGCTA 62.529 66.667 0.00 0.00 35.03 3.49
170 171 1.753078 TCCGCCATGCTAGAGACGT 60.753 57.895 0.00 0.00 0.00 4.34
172 173 1.299468 CGCCATGCTAGAGACGTCC 60.299 63.158 13.01 3.77 0.00 4.79
182 183 0.458025 AGAGACGTCCGAAAATCGCC 60.458 55.000 13.01 0.00 38.82 5.54
192 193 0.583917 GAAAATCGCCGGAGATGAGC 59.416 55.000 22.09 9.75 0.00 4.26
194 195 0.249657 AAATCGCCGGAGATGAGCTC 60.250 55.000 22.09 6.82 43.17 4.09
214 215 4.101448 GTGGCGGAGGGAGTGCAT 62.101 66.667 0.00 0.00 0.00 3.96
215 216 4.100084 TGGCGGAGGGAGTGCATG 62.100 66.667 0.00 0.00 0.00 4.06
219 220 2.669133 CGGAGGGAGTGCATGGGAA 61.669 63.158 0.00 0.00 0.00 3.97
220 221 1.691219 GGAGGGAGTGCATGGGAAA 59.309 57.895 0.00 0.00 0.00 3.13
226 227 1.457346 GAGTGCATGGGAAAGGAGTG 58.543 55.000 0.00 0.00 0.00 3.51
246 247 2.173782 TGTGAAGTGGCTAGGGTTTTGA 59.826 45.455 0.00 0.00 0.00 2.69
247 248 3.181434 TGTGAAGTGGCTAGGGTTTTGAT 60.181 43.478 0.00 0.00 0.00 2.57
251 252 0.254747 TGGCTAGGGTTTTGATCCGG 59.745 55.000 0.00 0.00 0.00 5.14
255 256 2.017049 CTAGGGTTTTGATCCGGCAAG 58.983 52.381 0.00 0.00 0.00 4.01
256 257 1.215382 GGGTTTTGATCCGGCAAGC 59.785 57.895 0.00 0.00 0.00 4.01
257 258 1.154035 GGTTTTGATCCGGCAAGCG 60.154 57.895 0.00 0.00 0.00 4.68
259 260 1.302913 TTTTGATCCGGCAAGCGGA 60.303 52.632 5.02 5.02 40.06 5.54
261 262 1.375853 TTTGATCCGGCAAGCGGATG 61.376 55.000 18.43 0.00 45.20 3.51
262 263 2.108976 GATCCGGCAAGCGGATGA 59.891 61.111 18.43 2.99 45.20 2.92
347 348 1.613317 CGCCCCATATCCGCCTCATA 61.613 60.000 0.00 0.00 0.00 2.15
348 349 0.839946 GCCCCATATCCGCCTCATAT 59.160 55.000 0.00 0.00 0.00 1.78
349 350 1.212935 GCCCCATATCCGCCTCATATT 59.787 52.381 0.00 0.00 0.00 1.28
350 351 2.357154 GCCCCATATCCGCCTCATATTT 60.357 50.000 0.00 0.00 0.00 1.40
353 354 3.054434 CCCATATCCGCCTCATATTTGGA 60.054 47.826 0.00 0.00 0.00 3.53
354 355 3.941483 CCATATCCGCCTCATATTTGGAC 59.059 47.826 0.00 0.00 0.00 4.02
355 356 4.323792 CCATATCCGCCTCATATTTGGACT 60.324 45.833 0.00 0.00 0.00 3.85
356 357 2.620251 TCCGCCTCATATTTGGACTG 57.380 50.000 0.00 0.00 0.00 3.51
357 358 1.140852 TCCGCCTCATATTTGGACTGG 59.859 52.381 0.00 0.00 0.00 4.00
359 360 2.224621 CCGCCTCATATTTGGACTGGAT 60.225 50.000 0.00 0.00 0.00 3.41
361 362 4.323792 CCGCCTCATATTTGGACTGGATAT 60.324 45.833 0.00 0.00 0.00 1.63
362 363 4.633126 CGCCTCATATTTGGACTGGATATG 59.367 45.833 0.00 0.00 35.87 1.78
363 364 5.569428 CGCCTCATATTTGGACTGGATATGA 60.569 44.000 0.00 0.00 39.29 2.15
366 367 6.378661 TCATATTTGGACTGGATATGAGGG 57.621 41.667 0.00 0.00 37.67 4.30
367 368 6.090870 TCATATTTGGACTGGATATGAGGGA 58.909 40.000 0.00 0.00 37.67 4.20
368 369 6.737131 TCATATTTGGACTGGATATGAGGGAT 59.263 38.462 0.00 0.00 37.67 3.85
371 372 1.280421 GGACTGGATATGAGGGATGCC 59.720 57.143 0.00 0.00 0.00 4.40
372 373 0.979665 ACTGGATATGAGGGATGCCG 59.020 55.000 0.00 0.00 0.00 5.69
373 374 1.269958 CTGGATATGAGGGATGCCGA 58.730 55.000 0.00 0.00 0.00 5.54
374 375 1.836166 CTGGATATGAGGGATGCCGAT 59.164 52.381 0.00 0.00 0.00 4.18
375 376 1.833630 TGGATATGAGGGATGCCGATC 59.166 52.381 0.00 0.00 0.00 3.69
376 377 1.833630 GGATATGAGGGATGCCGATCA 59.166 52.381 0.00 0.00 0.00 2.92
378 379 0.610174 TATGAGGGATGCCGATCAGC 59.390 55.000 0.00 0.00 0.00 4.26
382 383 3.928779 GGATGCCGATCAGCCCGA 61.929 66.667 0.00 0.00 45.34 5.14
383 384 2.356793 GATGCCGATCAGCCCGAG 60.357 66.667 0.00 0.00 0.00 4.63
384 385 4.615815 ATGCCGATCAGCCCGAGC 62.616 66.667 0.00 0.00 40.32 5.03
389 390 3.093278 GATCAGCCCGAGCGTTTG 58.907 61.111 0.00 0.00 46.67 2.93
390 391 1.447838 GATCAGCCCGAGCGTTTGA 60.448 57.895 0.00 0.00 46.67 2.69
391 392 1.424493 GATCAGCCCGAGCGTTTGAG 61.424 60.000 0.00 0.00 46.67 3.02
392 393 2.859273 ATCAGCCCGAGCGTTTGAGG 62.859 60.000 0.00 0.00 46.67 3.86
396 397 4.697756 CCGAGCGTTTGAGGCCCA 62.698 66.667 0.00 0.00 0.00 5.36
397 398 2.436646 CGAGCGTTTGAGGCCCAT 60.437 61.111 0.00 0.00 0.00 4.00
398 399 2.040544 CGAGCGTTTGAGGCCCATT 61.041 57.895 0.00 0.00 0.00 3.16
399 400 1.586154 CGAGCGTTTGAGGCCCATTT 61.586 55.000 0.00 0.00 0.00 2.32
400 401 0.109132 GAGCGTTTGAGGCCCATTTG 60.109 55.000 0.00 0.00 0.00 2.32
402 403 0.109132 GCGTTTGAGGCCCATTTGAG 60.109 55.000 0.00 0.00 0.00 3.02
403 404 0.527565 CGTTTGAGGCCCATTTGAGG 59.472 55.000 0.00 0.00 0.00 3.86
409 410 3.190878 GCCCATTTGAGGCGTCTG 58.809 61.111 8.06 0.00 41.41 3.51
410 411 1.675641 GCCCATTTGAGGCGTCTGT 60.676 57.895 8.06 0.00 41.41 3.41
411 412 1.244019 GCCCATTTGAGGCGTCTGTT 61.244 55.000 8.06 0.00 41.41 3.16
414 415 1.068333 CCATTTGAGGCGTCTGTTTGG 60.068 52.381 8.06 6.01 0.00 3.28
415 416 1.068333 CATTTGAGGCGTCTGTTTGGG 60.068 52.381 8.06 0.00 0.00 4.12
416 417 0.106918 TTTGAGGCGTCTGTTTGGGT 60.107 50.000 8.06 0.00 0.00 4.51
417 418 0.106918 TTGAGGCGTCTGTTTGGGTT 60.107 50.000 8.06 0.00 0.00 4.11
418 419 0.759959 TGAGGCGTCTGTTTGGGTTA 59.240 50.000 8.06 0.00 0.00 2.85
419 420 1.141254 TGAGGCGTCTGTTTGGGTTAA 59.859 47.619 8.06 0.00 0.00 2.01
420 421 2.223745 GAGGCGTCTGTTTGGGTTAAA 58.776 47.619 0.00 0.00 0.00 1.52
421 422 2.619646 GAGGCGTCTGTTTGGGTTAAAA 59.380 45.455 0.00 0.00 0.00 1.52
422 423 3.227614 AGGCGTCTGTTTGGGTTAAAAT 58.772 40.909 0.00 0.00 0.00 1.82
423 424 3.639561 AGGCGTCTGTTTGGGTTAAAATT 59.360 39.130 0.00 0.00 0.00 1.82
424 425 4.100344 AGGCGTCTGTTTGGGTTAAAATTT 59.900 37.500 0.00 0.00 0.00 1.82
425 426 4.446385 GGCGTCTGTTTGGGTTAAAATTTC 59.554 41.667 0.00 0.00 0.00 2.17
428 429 5.172411 CGTCTGTTTGGGTTAAAATTTCACG 59.828 40.000 0.00 0.00 0.00 4.35
429 430 6.267070 GTCTGTTTGGGTTAAAATTTCACGA 58.733 36.000 0.00 0.00 0.00 4.35
430 431 6.197655 GTCTGTTTGGGTTAAAATTTCACGAC 59.802 38.462 0.00 0.00 0.00 4.34
431 432 5.349809 TGTTTGGGTTAAAATTTCACGACC 58.650 37.500 0.00 0.00 0.00 4.79
432 433 5.105473 TGTTTGGGTTAAAATTTCACGACCA 60.105 36.000 11.77 6.19 0.00 4.02
433 434 4.839668 TGGGTTAAAATTTCACGACCAG 57.160 40.909 11.77 0.00 0.00 4.00
434 435 4.208746 TGGGTTAAAATTTCACGACCAGT 58.791 39.130 11.77 0.00 0.00 4.00
435 436 4.276431 TGGGTTAAAATTTCACGACCAGTC 59.724 41.667 11.77 0.00 0.00 3.51
436 437 4.276431 GGGTTAAAATTTCACGACCAGTCA 59.724 41.667 11.77 0.00 0.00 3.41
437 438 5.449304 GGTTAAAATTTCACGACCAGTCAG 58.551 41.667 0.00 0.00 0.00 3.51
438 439 5.008316 GGTTAAAATTTCACGACCAGTCAGT 59.992 40.000 0.00 0.00 0.00 3.41
440 441 7.254863 GGTTAAAATTTCACGACCAGTCAGTAA 60.255 37.037 0.00 0.00 0.00 2.24
441 442 5.668558 AAATTTCACGACCAGTCAGTAAC 57.331 39.130 0.00 0.00 0.00 2.50
442 443 2.806608 TTCACGACCAGTCAGTAACC 57.193 50.000 0.00 0.00 0.00 2.85
443 444 0.594602 TCACGACCAGTCAGTAACCG 59.405 55.000 0.00 0.00 0.00 4.44
444 445 0.594602 CACGACCAGTCAGTAACCGA 59.405 55.000 0.00 0.00 0.00 4.69
445 446 0.879765 ACGACCAGTCAGTAACCGAG 59.120 55.000 0.00 0.00 0.00 4.63
446 447 0.456312 CGACCAGTCAGTAACCGAGC 60.456 60.000 0.00 0.00 0.00 5.03
447 448 0.456312 GACCAGTCAGTAACCGAGCG 60.456 60.000 0.00 0.00 0.00 5.03
448 449 1.153823 CCAGTCAGTAACCGAGCGG 60.154 63.158 7.48 7.48 42.03 5.52
449 450 1.153823 CAGTCAGTAACCGAGCGGG 60.154 63.158 14.07 0.00 43.62 6.13
452 453 2.509336 CAGTAACCGAGCGGGCTG 60.509 66.667 14.07 13.43 40.62 4.85
453 454 4.452733 AGTAACCGAGCGGGCTGC 62.453 66.667 11.19 11.19 46.98 5.25
467 468 3.423154 CTGCCCGGACGTTTGAGC 61.423 66.667 0.73 0.00 0.00 4.26
471 472 4.675029 CCGGACGTTTGAGCGGGT 62.675 66.667 0.00 0.00 35.98 5.28
473 474 2.248835 CGGACGTTTGAGCGGGTTT 61.249 57.895 0.00 0.00 35.98 3.27
476 477 0.234884 GACGTTTGAGCGGGTTTGAG 59.765 55.000 0.00 0.00 35.98 3.02
477 478 1.164041 ACGTTTGAGCGGGTTTGAGG 61.164 55.000 0.00 0.00 35.98 3.86
478 479 1.285950 GTTTGAGCGGGTTTGAGGC 59.714 57.895 0.00 0.00 0.00 4.70
479 480 2.258013 TTTGAGCGGGTTTGAGGCG 61.258 57.895 0.00 0.00 0.00 5.52
480 481 2.668185 TTTGAGCGGGTTTGAGGCGA 62.668 55.000 0.00 0.00 0.00 5.54
481 482 3.119096 GAGCGGGTTTGAGGCGAC 61.119 66.667 0.00 0.00 0.00 5.19
482 483 4.699522 AGCGGGTTTGAGGCGACC 62.700 66.667 0.00 0.00 35.14 4.79
495 496 1.587054 GCGACCGGCTATAGATGCT 59.413 57.895 0.00 0.00 39.11 3.79
496 497 0.456995 GCGACCGGCTATAGATGCTC 60.457 60.000 0.00 0.00 39.11 4.26
497 498 1.169577 CGACCGGCTATAGATGCTCT 58.830 55.000 0.00 0.00 0.00 4.09
498 499 2.357075 CGACCGGCTATAGATGCTCTA 58.643 52.381 0.00 0.00 32.87 2.43
501 502 4.011023 GACCGGCTATAGATGCTCTAAGA 58.989 47.826 0.00 0.00 31.96 2.10
502 503 4.408276 ACCGGCTATAGATGCTCTAAGAA 58.592 43.478 0.00 0.00 31.96 2.52
503 504 4.833380 ACCGGCTATAGATGCTCTAAGAAA 59.167 41.667 0.00 0.00 31.96 2.52
504 505 5.482175 ACCGGCTATAGATGCTCTAAGAAAT 59.518 40.000 0.00 0.00 31.96 2.17
506 507 7.147983 ACCGGCTATAGATGCTCTAAGAAATAG 60.148 40.741 0.00 0.00 31.96 1.73
523 524 6.389906 AGAAATAGAAAATTTTGACTGGGCG 58.610 36.000 8.47 0.00 0.00 6.13
524 525 5.722021 AATAGAAAATTTTGACTGGGCGT 57.278 34.783 8.47 0.00 0.00 5.68
525 526 5.722021 ATAGAAAATTTTGACTGGGCGTT 57.278 34.783 8.47 0.00 0.00 4.84
527 528 3.383185 AGAAAATTTTGACTGGGCGTTGA 59.617 39.130 8.47 0.00 0.00 3.18
529 530 4.335400 AAATTTTGACTGGGCGTTGAAT 57.665 36.364 0.00 0.00 0.00 2.57
530 531 5.461032 AAATTTTGACTGGGCGTTGAATA 57.539 34.783 0.00 0.00 0.00 1.75
531 532 5.461032 AATTTTGACTGGGCGTTGAATAA 57.539 34.783 0.00 0.00 0.00 1.40
533 534 4.497473 TTTGACTGGGCGTTGAATAAAG 57.503 40.909 0.00 0.00 0.00 1.85
534 535 3.134574 TGACTGGGCGTTGAATAAAGT 57.865 42.857 0.00 0.00 0.00 2.66
535 536 2.811431 TGACTGGGCGTTGAATAAAGTG 59.189 45.455 0.00 0.00 0.00 3.16
536 537 1.539827 ACTGGGCGTTGAATAAAGTGC 59.460 47.619 0.00 0.00 0.00 4.40
537 538 0.519519 TGGGCGTTGAATAAAGTGCG 59.480 50.000 0.00 0.00 0.00 5.34
538 539 0.796870 GGGCGTTGAATAAAGTGCGC 60.797 55.000 0.00 0.00 43.46 6.09
539 540 1.125847 GGCGTTGAATAAAGTGCGCG 61.126 55.000 0.00 0.00 44.86 6.86
540 541 1.720330 GCGTTGAATAAAGTGCGCGC 61.720 55.000 27.26 27.26 35.71 6.86
541 542 0.451957 CGTTGAATAAAGTGCGCGCA 60.452 50.000 33.09 33.09 0.00 6.09
556 557 3.167945 GCATGCGACGCAAAGCAC 61.168 61.111 32.36 16.82 46.83 4.40
557 558 2.557805 CATGCGACGCAAAGCACT 59.442 55.556 28.24 6.01 46.83 4.40
558 559 1.794785 CATGCGACGCAAAGCACTG 60.795 57.895 28.24 15.47 46.83 3.66
559 560 1.960763 ATGCGACGCAAAGCACTGA 60.961 52.632 28.24 0.00 46.83 3.41
560 561 2.127609 GCGACGCAAAGCACTGAC 60.128 61.111 16.42 0.00 0.00 3.51
561 562 2.551270 CGACGCAAAGCACTGACC 59.449 61.111 0.00 0.00 0.00 4.02
563 564 1.568612 CGACGCAAAGCACTGACCAT 61.569 55.000 0.00 0.00 0.00 3.55
564 565 0.593128 GACGCAAAGCACTGACCATT 59.407 50.000 0.00 0.00 0.00 3.16
565 566 1.001378 GACGCAAAGCACTGACCATTT 60.001 47.619 0.00 0.00 0.00 2.32
566 567 1.269206 ACGCAAAGCACTGACCATTTG 60.269 47.619 0.00 0.00 36.07 2.32
567 568 1.269206 CGCAAAGCACTGACCATTTGT 60.269 47.619 0.00 0.00 35.55 2.83
568 569 2.129607 GCAAAGCACTGACCATTTGTG 58.870 47.619 0.00 0.00 35.55 3.33
569 570 2.481795 GCAAAGCACTGACCATTTGTGT 60.482 45.455 0.00 0.00 35.55 3.72
570 571 3.117794 CAAAGCACTGACCATTTGTGTG 58.882 45.455 0.00 0.00 34.52 3.82
571 572 2.057137 AGCACTGACCATTTGTGTGT 57.943 45.000 0.00 0.00 34.52 3.72
572 573 1.677576 AGCACTGACCATTTGTGTGTG 59.322 47.619 0.00 0.00 34.52 3.82
573 574 1.865248 GCACTGACCATTTGTGTGTGC 60.865 52.381 0.00 0.00 41.94 4.57
574 575 1.032014 ACTGACCATTTGTGTGTGCC 58.968 50.000 0.00 0.00 0.00 5.01
576 577 1.614903 CTGACCATTTGTGTGTGCCAT 59.385 47.619 0.00 0.00 0.00 4.40
577 578 1.340568 TGACCATTTGTGTGTGCCATG 59.659 47.619 0.00 0.00 0.00 3.66
578 579 0.033781 ACCATTTGTGTGTGCCATGC 59.966 50.000 0.00 0.00 0.00 4.06
579 580 0.033642 CCATTTGTGTGTGCCATGCA 59.966 50.000 0.00 0.00 35.60 3.96
580 581 1.338294 CCATTTGTGTGTGCCATGCAT 60.338 47.619 0.00 0.00 41.91 3.96
581 582 1.729517 CATTTGTGTGTGCCATGCATG 59.270 47.619 20.19 20.19 41.91 4.06
582 583 0.751452 TTTGTGTGTGCCATGCATGT 59.249 45.000 24.58 0.00 41.91 3.21
583 584 1.613836 TTGTGTGTGCCATGCATGTA 58.386 45.000 24.58 11.07 41.91 2.29
585 586 1.959282 TGTGTGTGCCATGCATGTAAA 59.041 42.857 24.58 6.46 41.91 2.01
586 587 2.288091 TGTGTGTGCCATGCATGTAAAC 60.288 45.455 24.58 17.68 41.91 2.01
587 588 2.030007 GTGTGTGCCATGCATGTAAACT 60.030 45.455 24.58 0.00 41.91 2.66
588 589 2.030096 TGTGTGCCATGCATGTAAACTG 60.030 45.455 24.58 9.73 41.91 3.16
589 590 2.228582 GTGTGCCATGCATGTAAACTGA 59.771 45.455 24.58 3.31 41.91 3.41
591 592 3.320256 TGTGCCATGCATGTAAACTGAAA 59.680 39.130 24.58 2.35 41.91 2.69
592 593 3.674753 GTGCCATGCATGTAAACTGAAAC 59.325 43.478 24.58 7.26 41.91 2.78
594 595 4.764308 TGCCATGCATGTAAACTGAAACTA 59.236 37.500 24.58 0.00 31.71 2.24
595 596 5.106197 TGCCATGCATGTAAACTGAAACTAG 60.106 40.000 24.58 5.77 31.71 2.57
596 597 5.123820 GCCATGCATGTAAACTGAAACTAGA 59.876 40.000 24.58 0.00 0.00 2.43
597 598 6.546395 CCATGCATGTAAACTGAAACTAGAC 58.454 40.000 24.58 0.00 0.00 2.59
598 599 6.149308 CCATGCATGTAAACTGAAACTAGACA 59.851 38.462 24.58 0.00 0.00 3.41
599 600 7.308529 CCATGCATGTAAACTGAAACTAGACAA 60.309 37.037 24.58 0.00 0.00 3.18
600 601 7.189693 TGCATGTAAACTGAAACTAGACAAG 57.810 36.000 0.00 0.00 0.00 3.16
601 602 6.989759 TGCATGTAAACTGAAACTAGACAAGA 59.010 34.615 0.00 0.00 0.00 3.02
602 603 7.042051 TGCATGTAAACTGAAACTAGACAAGAC 60.042 37.037 0.00 0.00 0.00 3.01
603 604 7.042051 GCATGTAAACTGAAACTAGACAAGACA 60.042 37.037 0.00 0.00 0.00 3.41
604 605 7.766219 TGTAAACTGAAACTAGACAAGACAC 57.234 36.000 0.00 0.00 0.00 3.67
605 606 7.324935 TGTAAACTGAAACTAGACAAGACACA 58.675 34.615 0.00 0.00 0.00 3.72
606 607 6.910536 AAACTGAAACTAGACAAGACACAG 57.089 37.500 0.00 0.00 0.00 3.66
607 608 4.950050 ACTGAAACTAGACAAGACACAGG 58.050 43.478 0.00 0.00 0.00 4.00
609 610 3.964688 TGAAACTAGACAAGACACAGGGA 59.035 43.478 0.00 0.00 0.00 4.20
610 611 4.202223 TGAAACTAGACAAGACACAGGGAC 60.202 45.833 0.00 0.00 0.00 4.46
611 612 1.887198 ACTAGACAAGACACAGGGACG 59.113 52.381 0.00 0.00 0.00 4.79
615 616 3.637273 AAGACACAGGGACGGGCC 61.637 66.667 0.00 0.00 0.00 5.80
616 617 4.640690 AGACACAGGGACGGGCCT 62.641 66.667 0.84 0.00 36.66 5.19
619 620 1.833787 GACACAGGGACGGGCCTTTA 61.834 60.000 0.84 0.00 36.66 1.85
620 621 1.205460 ACACAGGGACGGGCCTTTAT 61.205 55.000 0.84 0.00 36.66 1.40
621 622 0.034477 CACAGGGACGGGCCTTTATT 60.034 55.000 0.84 0.00 36.66 1.40
623 624 1.076513 ACAGGGACGGGCCTTTATTTT 59.923 47.619 0.84 0.00 36.66 1.82
641 642 1.996798 TTTTGGGGTACGGCAAATCA 58.003 45.000 0.00 0.00 0.00 2.57
762 771 1.331756 ACTACGCCGGAATACGTACTG 59.668 52.381 5.05 1.28 43.35 2.74
816 825 0.826715 TGAGAATCCAGGAGCGAAGG 59.173 55.000 0.00 0.00 0.00 3.46
872 881 7.254852 TCGTGCTATTTTTCAAAGTTCAAACT 58.745 30.769 0.00 0.00 42.04 2.66
913 923 2.191128 AAACGATGAAGCAGCTTCCT 57.809 45.000 28.73 21.01 39.51 3.36
914 924 1.446907 AACGATGAAGCAGCTTCCTG 58.553 50.000 28.73 20.63 39.51 3.86
1029 1050 3.142174 CCTAGCTAATTTAGTGGCAGCC 58.858 50.000 3.66 3.66 32.58 4.85
1046 1067 2.947652 CAGCCAGAAGAGAGAGAGAGAG 59.052 54.545 0.00 0.00 0.00 3.20
1138 1171 1.003839 GGTCATGGTGTTCTCGGCA 60.004 57.895 0.00 0.00 0.00 5.69
1222 1270 1.496060 TCATCCGGCAGGTGTATCTT 58.504 50.000 1.81 0.00 39.05 2.40
1271 1319 4.135153 CCTCGTGCTCGACCTGGG 62.135 72.222 6.80 3.28 41.35 4.45
1272 1320 3.062466 CTCGTGCTCGACCTGGGA 61.062 66.667 6.80 0.00 41.35 4.37
1284 1335 2.553466 CGACCTGGGACCCAAATAACAA 60.553 50.000 15.87 0.00 30.80 2.83
1323 1803 2.781595 GAAACCGGCGAGAGGAAGCA 62.782 60.000 9.30 0.00 34.54 3.91
1327 1807 1.299773 CGGCGAGAGGAAGCAGATC 60.300 63.158 0.00 0.00 34.54 2.75
1347 1827 3.400054 GCAGAGGCCGGGGTACTT 61.400 66.667 2.18 0.00 0.00 2.24
1580 2183 5.621228 CACTCTTTTGTTCTGCGTATGAAAC 59.379 40.000 0.00 0.00 0.00 2.78
1603 2206 9.654663 AAACTATTGCTCTTTTGGTAGTAGTAG 57.345 33.333 0.00 0.00 0.00 2.57
1604 2207 8.363761 ACTATTGCTCTTTTGGTAGTAGTAGT 57.636 34.615 0.00 0.00 30.03 2.73
1695 3368 7.303261 GCAAAAACTATTCCAGGTGTACTTAC 58.697 38.462 0.00 0.00 0.00 2.34
1704 3382 3.620488 CAGGTGTACTTACATGCCCAAT 58.380 45.455 0.00 0.00 38.63 3.16
1705 3383 4.016444 CAGGTGTACTTACATGCCCAATT 58.984 43.478 0.00 0.00 38.63 2.32
1716 3394 7.602265 ACTTACATGCCCAATTGAATACAAAAC 59.398 33.333 7.12 0.00 39.54 2.43
1737 3415 2.350192 CGCTAACGGTATGCAAACATGA 59.650 45.455 0.00 0.00 35.01 3.07
1738 3416 3.181515 CGCTAACGGTATGCAAACATGAA 60.182 43.478 0.00 0.00 35.01 2.57
1742 3420 3.009723 ACGGTATGCAAACATGAAGAGG 58.990 45.455 0.00 0.00 37.04 3.69
1750 3428 2.403252 AACATGAAGAGGGCCGTAAG 57.597 50.000 0.00 0.00 0.00 2.34
1845 3538 4.151689 ACGGTTACATGTCGATTTTGACTG 59.848 41.667 11.87 3.56 39.64 3.51
1863 3556 2.542595 ACTGTTCCAAAATGTCGTCGTC 59.457 45.455 0.00 0.00 0.00 4.20
1865 3558 2.798283 TGTTCCAAAATGTCGTCGTCTC 59.202 45.455 0.00 0.00 0.00 3.36
1868 4684 1.415374 CAAAATGTCGTCGTCTCGGT 58.585 50.000 0.00 0.00 0.00 4.69
1893 4709 0.546122 TCATGGGCATAGTCCACCAC 59.454 55.000 0.00 0.00 41.42 4.16
1897 4713 1.004277 TGGGCATAGTCCACCACTTTC 59.996 52.381 0.00 0.00 36.43 2.62
1986 5018 3.745723 TTGGCCTCTTCCAAGTTCC 57.254 52.632 3.32 0.00 40.92 3.62
1987 5019 0.850100 TTGGCCTCTTCCAAGTTCCA 59.150 50.000 3.32 0.00 40.92 3.53
1988 5020 0.850100 TGGCCTCTTCCAAGTTCCAA 59.150 50.000 3.32 0.00 32.18 3.53
2032 5065 2.904915 GCTTACTGTCGAAAGCAACAC 58.095 47.619 13.37 0.00 45.89 3.32
2097 5131 6.867816 TGGCAGACATGTATTTCAAAAACATC 59.132 34.615 0.00 0.00 31.60 3.06
2149 5183 0.611200 TTCCACACGTACTCCCATGG 59.389 55.000 4.14 4.14 0.00 3.66
2181 5215 8.733458 CCTCATTTTTGTGAAGACATGAGAATA 58.267 33.333 0.00 0.00 37.55 1.75
2346 5381 3.932710 CCTGCACACTAAAATTCTAGCGA 59.067 43.478 0.00 0.00 0.00 4.93
2355 5390 3.521947 AAATTCTAGCGACGCCTACTT 57.478 42.857 17.79 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.243907 CTGTCCGACACGACTCCATT 59.756 55.000 0.00 0.00 33.70 3.16
74 75 3.521796 GGAGAAGGCAATGGCGGC 61.522 66.667 0.00 0.00 42.47 6.53
115 116 2.879026 CGATCAGTCCGGATCTGTCTAA 59.121 50.000 24.21 12.16 41.21 2.10
152 153 1.725557 GACGTCTCTAGCATGGCGGA 61.726 60.000 8.70 0.00 0.00 5.54
156 157 0.738975 TTCGGACGTCTCTAGCATGG 59.261 55.000 16.46 0.00 0.00 3.66
162 163 1.202222 GGCGATTTTCGGACGTCTCTA 60.202 52.381 16.46 0.00 40.84 2.43
163 164 0.458025 GGCGATTTTCGGACGTCTCT 60.458 55.000 16.46 0.00 40.84 3.10
172 173 0.855349 CTCATCTCCGGCGATTTTCG 59.145 55.000 9.30 0.00 43.89 3.46
182 183 2.415010 CACCCGAGCTCATCTCCG 59.585 66.667 15.40 0.00 38.62 4.63
212 213 2.816087 CACTTCACACTCCTTTCCCATG 59.184 50.000 0.00 0.00 0.00 3.66
214 215 1.142870 CCACTTCACACTCCTTTCCCA 59.857 52.381 0.00 0.00 0.00 4.37
215 216 1.897560 CCACTTCACACTCCTTTCCC 58.102 55.000 0.00 0.00 0.00 3.97
219 220 1.625818 CCTAGCCACTTCACACTCCTT 59.374 52.381 0.00 0.00 0.00 3.36
220 221 1.270907 CCTAGCCACTTCACACTCCT 58.729 55.000 0.00 0.00 0.00 3.69
226 227 2.858745 TCAAAACCCTAGCCACTTCAC 58.141 47.619 0.00 0.00 0.00 3.18
256 257 4.091945 CCTCACATATATTTGCGTCATCCG 59.908 45.833 0.00 0.00 40.40 4.18
257 258 4.997395 ACCTCACATATATTTGCGTCATCC 59.003 41.667 0.00 0.00 0.00 3.51
259 260 4.686091 CGACCTCACATATATTTGCGTCAT 59.314 41.667 14.26 0.00 0.00 3.06
260 261 4.048504 CGACCTCACATATATTTGCGTCA 58.951 43.478 14.26 0.00 0.00 4.35
261 262 3.428870 CCGACCTCACATATATTTGCGTC 59.571 47.826 8.03 8.03 0.00 5.19
262 263 3.390135 CCGACCTCACATATATTTGCGT 58.610 45.455 0.00 0.00 0.00 5.24
331 332 3.054434 TCCAAATATGAGGCGGATATGGG 60.054 47.826 0.00 0.00 0.00 4.00
333 334 4.633126 CAGTCCAAATATGAGGCGGATATG 59.367 45.833 0.00 0.00 0.00 1.78
334 335 4.323792 CCAGTCCAAATATGAGGCGGATAT 60.324 45.833 0.00 0.00 0.00 1.63
335 336 3.007940 CCAGTCCAAATATGAGGCGGATA 59.992 47.826 0.00 0.00 0.00 2.59
337 338 1.140852 CCAGTCCAAATATGAGGCGGA 59.859 52.381 0.00 0.00 0.00 5.54
338 339 1.140852 TCCAGTCCAAATATGAGGCGG 59.859 52.381 0.00 0.00 0.00 6.13
339 340 2.620251 TCCAGTCCAAATATGAGGCG 57.380 50.000 0.00 0.00 0.00 5.52
340 341 5.809001 TCATATCCAGTCCAAATATGAGGC 58.191 41.667 0.00 0.00 37.43 4.70
344 345 6.378661 TCCCTCATATCCAGTCCAAATATG 57.621 41.667 0.00 0.00 35.58 1.78
347 348 4.508047 GCATCCCTCATATCCAGTCCAAAT 60.508 45.833 0.00 0.00 0.00 2.32
348 349 3.181440 GCATCCCTCATATCCAGTCCAAA 60.181 47.826 0.00 0.00 0.00 3.28
349 350 2.373169 GCATCCCTCATATCCAGTCCAA 59.627 50.000 0.00 0.00 0.00 3.53
350 351 1.980765 GCATCCCTCATATCCAGTCCA 59.019 52.381 0.00 0.00 0.00 4.02
353 354 0.979665 CGGCATCCCTCATATCCAGT 59.020 55.000 0.00 0.00 0.00 4.00
354 355 1.269958 TCGGCATCCCTCATATCCAG 58.730 55.000 0.00 0.00 0.00 3.86
355 356 1.833630 GATCGGCATCCCTCATATCCA 59.166 52.381 0.00 0.00 0.00 3.41
356 357 1.833630 TGATCGGCATCCCTCATATCC 59.166 52.381 0.00 0.00 0.00 2.59
357 358 2.741228 GCTGATCGGCATCCCTCATATC 60.741 54.545 21.88 0.00 0.00 1.63
359 360 0.610174 GCTGATCGGCATCCCTCATA 59.390 55.000 21.88 0.00 0.00 2.15
361 362 2.811514 GGCTGATCGGCATCCCTCA 61.812 63.158 27.26 0.00 38.25 3.86
362 363 2.031768 GGCTGATCGGCATCCCTC 59.968 66.667 27.26 5.67 38.25 4.30
365 366 3.873026 CTCGGGCTGATCGGCATCC 62.873 68.421 27.26 18.61 40.61 3.51
366 367 2.356793 CTCGGGCTGATCGGCATC 60.357 66.667 27.26 17.15 40.61 3.91
367 368 4.615815 GCTCGGGCTGATCGGCAT 62.616 66.667 27.26 0.00 40.61 4.40
371 372 2.509336 AAACGCTCGGGCTGATCG 60.509 61.111 17.24 17.24 41.79 3.69
372 373 1.424493 CTCAAACGCTCGGGCTGATC 61.424 60.000 5.36 0.00 36.09 2.92
373 374 1.448540 CTCAAACGCTCGGGCTGAT 60.449 57.895 5.36 0.00 36.09 2.90
374 375 2.048222 CTCAAACGCTCGGGCTGA 60.048 61.111 5.36 0.70 36.09 4.26
375 376 3.121030 CCTCAAACGCTCGGGCTG 61.121 66.667 5.36 0.78 36.09 4.85
380 381 1.586154 AAATGGGCCTCAAACGCTCG 61.586 55.000 4.53 0.00 0.00 5.03
381 382 0.109132 CAAATGGGCCTCAAACGCTC 60.109 55.000 4.53 0.00 0.00 5.03
382 383 0.539438 TCAAATGGGCCTCAAACGCT 60.539 50.000 4.53 0.00 0.00 5.07
383 384 0.109132 CTCAAATGGGCCTCAAACGC 60.109 55.000 4.53 0.00 0.00 4.84
384 385 0.527565 CCTCAAATGGGCCTCAAACG 59.472 55.000 4.53 0.00 0.00 3.60
385 386 0.247460 GCCTCAAATGGGCCTCAAAC 59.753 55.000 4.53 0.00 43.49 2.93
387 388 1.678635 CGCCTCAAATGGGCCTCAA 60.679 57.895 4.53 0.00 46.24 3.02
388 389 2.045045 CGCCTCAAATGGGCCTCA 60.045 61.111 4.53 0.00 46.24 3.86
389 390 2.044946 ACGCCTCAAATGGGCCTC 60.045 61.111 4.53 0.00 46.24 4.70
390 391 2.044946 GACGCCTCAAATGGGCCT 60.045 61.111 4.53 0.00 46.24 5.19
391 392 2.044946 AGACGCCTCAAATGGGCC 60.045 61.111 0.00 0.00 46.24 5.80
392 393 1.244019 AACAGACGCCTCAAATGGGC 61.244 55.000 0.00 0.00 45.57 5.36
393 394 1.068333 CAAACAGACGCCTCAAATGGG 60.068 52.381 0.00 0.00 0.00 4.00
395 396 1.068333 CCCAAACAGACGCCTCAAATG 60.068 52.381 0.00 0.00 0.00 2.32
396 397 1.247567 CCCAAACAGACGCCTCAAAT 58.752 50.000 0.00 0.00 0.00 2.32
397 398 0.106918 ACCCAAACAGACGCCTCAAA 60.107 50.000 0.00 0.00 0.00 2.69
398 399 0.106918 AACCCAAACAGACGCCTCAA 60.107 50.000 0.00 0.00 0.00 3.02
399 400 0.759959 TAACCCAAACAGACGCCTCA 59.240 50.000 0.00 0.00 0.00 3.86
400 401 1.886886 TTAACCCAAACAGACGCCTC 58.113 50.000 0.00 0.00 0.00 4.70
402 403 3.653539 ATTTTAACCCAAACAGACGCC 57.346 42.857 0.00 0.00 0.00 5.68
403 404 5.044558 TGAAATTTTAACCCAAACAGACGC 58.955 37.500 0.00 0.00 0.00 5.19
404 405 5.172411 CGTGAAATTTTAACCCAAACAGACG 59.828 40.000 0.00 0.00 0.00 4.18
405 406 6.197655 GTCGTGAAATTTTAACCCAAACAGAC 59.802 38.462 0.00 0.00 0.00 3.51
407 408 5.460748 GGTCGTGAAATTTTAACCCAAACAG 59.539 40.000 0.00 0.00 0.00 3.16
408 409 5.105473 TGGTCGTGAAATTTTAACCCAAACA 60.105 36.000 0.00 0.00 0.00 2.83
409 410 5.349809 TGGTCGTGAAATTTTAACCCAAAC 58.650 37.500 0.00 0.00 0.00 2.93
410 411 5.127356 ACTGGTCGTGAAATTTTAACCCAAA 59.873 36.000 0.00 0.00 0.00 3.28
411 412 4.645588 ACTGGTCGTGAAATTTTAACCCAA 59.354 37.500 0.00 0.00 0.00 4.12
414 415 5.008316 ACTGACTGGTCGTGAAATTTTAACC 59.992 40.000 0.00 0.00 0.00 2.85
415 416 6.056428 ACTGACTGGTCGTGAAATTTTAAC 57.944 37.500 0.00 0.00 0.00 2.01
416 417 7.254863 GGTTACTGACTGGTCGTGAAATTTTAA 60.255 37.037 0.00 0.00 0.00 1.52
417 418 6.203338 GGTTACTGACTGGTCGTGAAATTTTA 59.797 38.462 0.00 0.00 0.00 1.52
418 419 5.008316 GGTTACTGACTGGTCGTGAAATTTT 59.992 40.000 0.00 0.00 0.00 1.82
419 420 4.514066 GGTTACTGACTGGTCGTGAAATTT 59.486 41.667 0.00 0.00 0.00 1.82
420 421 4.062991 GGTTACTGACTGGTCGTGAAATT 58.937 43.478 7.89 0.00 0.00 1.82
421 422 3.660865 GGTTACTGACTGGTCGTGAAAT 58.339 45.455 7.89 0.00 0.00 2.17
422 423 2.544277 CGGTTACTGACTGGTCGTGAAA 60.544 50.000 7.89 0.00 0.00 2.69
423 424 1.001048 CGGTTACTGACTGGTCGTGAA 60.001 52.381 7.89 0.00 0.00 3.18
424 425 0.594602 CGGTTACTGACTGGTCGTGA 59.405 55.000 7.89 0.00 0.00 4.35
425 426 0.594602 TCGGTTACTGACTGGTCGTG 59.405 55.000 0.00 1.90 35.23 4.35
428 429 0.456312 CGCTCGGTTACTGACTGGTC 60.456 60.000 0.00 0.00 35.23 4.02
429 430 1.585006 CGCTCGGTTACTGACTGGT 59.415 57.895 0.00 0.00 35.23 4.00
430 431 1.153823 CCGCTCGGTTACTGACTGG 60.154 63.158 0.00 0.00 35.23 4.00
431 432 1.153823 CCCGCTCGGTTACTGACTG 60.154 63.158 7.59 0.00 35.87 3.51
432 433 3.003113 GCCCGCTCGGTTACTGACT 62.003 63.158 7.59 0.00 0.00 3.41
433 434 2.508663 GCCCGCTCGGTTACTGAC 60.509 66.667 7.59 0.00 0.00 3.51
434 435 2.678934 AGCCCGCTCGGTTACTGA 60.679 61.111 7.59 0.00 0.00 3.41
435 436 2.509336 CAGCCCGCTCGGTTACTG 60.509 66.667 7.59 7.97 0.00 2.74
436 437 4.452733 GCAGCCCGCTCGGTTACT 62.453 66.667 7.59 0.00 37.77 2.24
449 450 3.423154 CTCAAACGTCCGGGCAGC 61.423 66.667 6.96 0.00 0.00 5.25
456 457 1.161563 TCAAACCCGCTCAAACGTCC 61.162 55.000 0.00 0.00 0.00 4.79
459 460 1.574428 CCTCAAACCCGCTCAAACG 59.426 57.895 0.00 0.00 0.00 3.60
460 461 1.285950 GCCTCAAACCCGCTCAAAC 59.714 57.895 0.00 0.00 0.00 2.93
461 462 2.258013 CGCCTCAAACCCGCTCAAA 61.258 57.895 0.00 0.00 0.00 2.69
462 463 2.668212 CGCCTCAAACCCGCTCAA 60.668 61.111 0.00 0.00 0.00 3.02
463 464 3.621805 TCGCCTCAAACCCGCTCA 61.622 61.111 0.00 0.00 0.00 4.26
464 465 3.119096 GTCGCCTCAAACCCGCTC 61.119 66.667 0.00 0.00 0.00 5.03
465 466 4.699522 GGTCGCCTCAAACCCGCT 62.700 66.667 0.00 0.00 0.00 5.52
469 470 2.588856 ATAGCCGGTCGCCTCAAACC 62.589 60.000 1.90 0.00 38.78 3.27
470 471 0.103572 TATAGCCGGTCGCCTCAAAC 59.896 55.000 1.90 0.00 38.78 2.93
471 472 0.387929 CTATAGCCGGTCGCCTCAAA 59.612 55.000 1.90 0.00 38.78 2.69
473 474 0.251209 ATCTATAGCCGGTCGCCTCA 60.251 55.000 1.90 0.00 38.78 3.86
476 477 1.446272 GCATCTATAGCCGGTCGCC 60.446 63.158 1.90 0.00 38.78 5.54
477 478 0.456995 GAGCATCTATAGCCGGTCGC 60.457 60.000 1.90 0.00 37.98 5.19
478 479 3.704381 GAGCATCTATAGCCGGTCG 57.296 57.895 1.90 0.00 0.00 4.79
496 497 9.358872 GCCCAGTCAAAATTTTCTATTTCTTAG 57.641 33.333 0.00 0.00 0.00 2.18
497 498 8.026607 CGCCCAGTCAAAATTTTCTATTTCTTA 58.973 33.333 0.00 0.00 0.00 2.10
498 499 6.868339 CGCCCAGTCAAAATTTTCTATTTCTT 59.132 34.615 0.00 0.00 0.00 2.52
501 502 6.096673 ACGCCCAGTCAAAATTTTCTATTT 57.903 33.333 0.00 0.00 0.00 1.40
502 503 5.722021 ACGCCCAGTCAAAATTTTCTATT 57.278 34.783 0.00 0.00 0.00 1.73
503 504 5.242838 TCAACGCCCAGTCAAAATTTTCTAT 59.757 36.000 0.00 0.00 0.00 1.98
504 505 4.580995 TCAACGCCCAGTCAAAATTTTCTA 59.419 37.500 0.00 0.00 0.00 2.10
506 507 3.712187 TCAACGCCCAGTCAAAATTTTC 58.288 40.909 0.00 0.00 0.00 2.29
510 511 5.010617 ACTTTATTCAACGCCCAGTCAAAAT 59.989 36.000 0.00 0.00 0.00 1.82
512 513 3.886505 ACTTTATTCAACGCCCAGTCAAA 59.113 39.130 0.00 0.00 0.00 2.69
513 514 3.252215 CACTTTATTCAACGCCCAGTCAA 59.748 43.478 0.00 0.00 0.00 3.18
514 515 2.811431 CACTTTATTCAACGCCCAGTCA 59.189 45.455 0.00 0.00 0.00 3.41
515 516 2.414161 GCACTTTATTCAACGCCCAGTC 60.414 50.000 0.00 0.00 0.00 3.51
516 517 1.539827 GCACTTTATTCAACGCCCAGT 59.460 47.619 0.00 0.00 0.00 4.00
518 519 0.519519 CGCACTTTATTCAACGCCCA 59.480 50.000 0.00 0.00 0.00 5.36
519 520 0.796870 GCGCACTTTATTCAACGCCC 60.797 55.000 0.30 0.00 40.43 6.13
520 521 1.125847 CGCGCACTTTATTCAACGCC 61.126 55.000 8.75 0.00 43.15 5.68
523 524 1.578915 CATGCGCGCACTTTATTCAAC 59.421 47.619 39.05 0.00 0.00 3.18
524 525 1.893759 CATGCGCGCACTTTATTCAA 58.106 45.000 39.05 9.89 0.00 2.69
525 526 0.523125 GCATGCGCGCACTTTATTCA 60.523 50.000 39.05 10.81 0.00 2.57
527 528 4.382728 GCATGCGCGCACTTTATT 57.617 50.000 39.05 17.70 0.00 1.40
538 539 4.740062 TGCTTTGCGTCGCATGCG 62.740 61.111 33.61 33.61 39.74 4.73
539 540 3.167945 GTGCTTTGCGTCGCATGC 61.168 61.111 27.68 27.68 38.76 4.06
540 541 1.794785 CAGTGCTTTGCGTCGCATG 60.795 57.895 22.41 17.42 38.76 4.06
541 542 1.960763 TCAGTGCTTTGCGTCGCAT 60.961 52.632 22.41 1.06 38.76 4.73
546 547 1.032014 AAATGGTCAGTGCTTTGCGT 58.968 45.000 0.00 0.00 0.00 5.24
548 549 2.129607 CACAAATGGTCAGTGCTTTGC 58.870 47.619 0.00 0.00 33.03 3.68
551 552 2.099592 CACACACAAATGGTCAGTGCTT 59.900 45.455 0.00 0.00 36.76 3.91
552 553 1.677576 CACACACAAATGGTCAGTGCT 59.322 47.619 0.00 0.00 36.76 4.40
553 554 1.865248 GCACACACAAATGGTCAGTGC 60.865 52.381 0.00 0.00 44.76 4.40
554 555 1.269206 GGCACACACAAATGGTCAGTG 60.269 52.381 0.00 0.00 39.12 3.66
555 556 1.032014 GGCACACACAAATGGTCAGT 58.968 50.000 0.00 0.00 0.00 3.41
556 557 1.031235 TGGCACACACAAATGGTCAG 58.969 50.000 0.00 0.00 0.00 3.51
557 558 3.197664 TGGCACACACAAATGGTCA 57.802 47.368 0.00 0.00 0.00 4.02
569 570 2.512705 TCAGTTTACATGCATGGCACA 58.487 42.857 29.41 9.76 43.04 4.57
570 571 3.574284 TTCAGTTTACATGCATGGCAC 57.426 42.857 29.41 21.00 43.04 5.01
571 572 3.573538 AGTTTCAGTTTACATGCATGGCA 59.426 39.130 29.41 14.80 44.86 4.92
572 573 4.178545 AGTTTCAGTTTACATGCATGGC 57.821 40.909 29.41 16.20 0.00 4.40
573 574 6.149308 TGTCTAGTTTCAGTTTACATGCATGG 59.851 38.462 29.41 11.47 0.00 3.66
574 575 7.132694 TGTCTAGTTTCAGTTTACATGCATG 57.867 36.000 25.09 25.09 0.00 4.06
576 577 6.989759 TCTTGTCTAGTTTCAGTTTACATGCA 59.010 34.615 0.00 0.00 0.00 3.96
577 578 7.042051 TGTCTTGTCTAGTTTCAGTTTACATGC 60.042 37.037 0.00 0.00 0.00 4.06
578 579 8.276325 GTGTCTTGTCTAGTTTCAGTTTACATG 58.724 37.037 0.00 0.00 0.00 3.21
579 580 7.985184 TGTGTCTTGTCTAGTTTCAGTTTACAT 59.015 33.333 0.00 0.00 0.00 2.29
580 581 7.324935 TGTGTCTTGTCTAGTTTCAGTTTACA 58.675 34.615 0.00 0.00 0.00 2.41
581 582 7.042658 CCTGTGTCTTGTCTAGTTTCAGTTTAC 60.043 40.741 0.00 0.00 0.00 2.01
582 583 6.984474 CCTGTGTCTTGTCTAGTTTCAGTTTA 59.016 38.462 0.00 0.00 0.00 2.01
583 584 5.817816 CCTGTGTCTTGTCTAGTTTCAGTTT 59.182 40.000 0.00 0.00 0.00 2.66
585 586 4.202264 CCCTGTGTCTTGTCTAGTTTCAGT 60.202 45.833 0.00 0.00 0.00 3.41
586 587 4.039245 TCCCTGTGTCTTGTCTAGTTTCAG 59.961 45.833 0.00 0.00 0.00 3.02
587 588 3.964688 TCCCTGTGTCTTGTCTAGTTTCA 59.035 43.478 0.00 0.00 0.00 2.69
588 589 4.308265 GTCCCTGTGTCTTGTCTAGTTTC 58.692 47.826 0.00 0.00 0.00 2.78
589 590 3.243771 CGTCCCTGTGTCTTGTCTAGTTT 60.244 47.826 0.00 0.00 0.00 2.66
591 592 1.887198 CGTCCCTGTGTCTTGTCTAGT 59.113 52.381 0.00 0.00 0.00 2.57
592 593 1.202582 CCGTCCCTGTGTCTTGTCTAG 59.797 57.143 0.00 0.00 0.00 2.43
594 595 1.472662 CCCGTCCCTGTGTCTTGTCT 61.473 60.000 0.00 0.00 0.00 3.41
595 596 1.004918 CCCGTCCCTGTGTCTTGTC 60.005 63.158 0.00 0.00 0.00 3.18
596 597 3.148084 CCCGTCCCTGTGTCTTGT 58.852 61.111 0.00 0.00 0.00 3.16
597 598 2.358737 GCCCGTCCCTGTGTCTTG 60.359 66.667 0.00 0.00 0.00 3.02
598 599 3.637273 GGCCCGTCCCTGTGTCTT 61.637 66.667 0.00 0.00 0.00 3.01
599 600 4.640690 AGGCCCGTCCCTGTGTCT 62.641 66.667 0.00 0.00 32.84 3.41
600 601 1.833787 TAAAGGCCCGTCCCTGTGTC 61.834 60.000 0.00 0.00 34.80 3.67
601 602 1.205460 ATAAAGGCCCGTCCCTGTGT 61.205 55.000 0.00 0.00 34.80 3.72
602 603 0.034477 AATAAAGGCCCGTCCCTGTG 60.034 55.000 0.00 0.00 34.80 3.66
603 604 0.702316 AAATAAAGGCCCGTCCCTGT 59.298 50.000 0.00 0.00 34.80 4.00
604 605 1.847328 AAAATAAAGGCCCGTCCCTG 58.153 50.000 0.00 0.00 34.80 4.45
605 606 2.615986 AAAAATAAAGGCCCGTCCCT 57.384 45.000 0.00 0.00 36.58 4.20
621 622 2.317040 TGATTTGCCGTACCCCAAAAA 58.683 42.857 8.96 0.79 34.93 1.94
623 624 1.996798 TTGATTTGCCGTACCCCAAA 58.003 45.000 7.72 7.72 35.64 3.28
625 626 2.223803 AATTGATTTGCCGTACCCCA 57.776 45.000 0.00 0.00 0.00 4.96
627 628 3.428862 CCAGAAATTGATTTGCCGTACCC 60.429 47.826 0.00 0.00 0.00 3.69
628 629 3.192633 ACCAGAAATTGATTTGCCGTACC 59.807 43.478 0.00 0.00 0.00 3.34
629 630 4.412207 GACCAGAAATTGATTTGCCGTAC 58.588 43.478 0.00 0.00 0.00 3.67
630 631 3.442273 GGACCAGAAATTGATTTGCCGTA 59.558 43.478 0.00 0.00 0.00 4.02
631 632 2.231235 GGACCAGAAATTGATTTGCCGT 59.769 45.455 0.00 0.00 0.00 5.68
633 634 3.959535 TGGACCAGAAATTGATTTGCC 57.040 42.857 0.00 0.00 0.00 4.52
634 635 6.806388 AAATTGGACCAGAAATTGATTTGC 57.194 33.333 0.00 0.00 0.00 3.68
637 638 9.506018 CCTTTAAAATTGGACCAGAAATTGATT 57.494 29.630 0.00 0.00 0.00 2.57
639 640 8.028652 ACCTTTAAAATTGGACCAGAAATTGA 57.971 30.769 0.00 0.00 0.00 2.57
641 642 9.693739 AAAACCTTTAAAATTGGACCAGAAATT 57.306 25.926 0.00 0.00 0.00 1.82
887 896 2.223340 GCTGCTTCATCGTTTACATGGG 60.223 50.000 0.00 0.00 0.00 4.00
1029 1050 3.861840 ACGTCTCTCTCTCTCTCTTCTG 58.138 50.000 0.00 0.00 0.00 3.02
1046 1067 3.002144 GTCCGGTTATCTCTGAGTACGTC 59.998 52.174 0.00 0.00 0.00 4.34
1271 1319 1.548719 GGGGCACTTGTTATTTGGGTC 59.451 52.381 0.00 0.00 0.00 4.46
1272 1320 1.149077 AGGGGCACTTGTTATTTGGGT 59.851 47.619 0.00 0.00 0.00 4.51
1284 1335 0.618680 TGCAGACTATCAGGGGCACT 60.619 55.000 0.00 0.00 0.00 4.40
1323 1803 2.815945 CCCGGCCTCTGCATGATCT 61.816 63.158 0.00 0.00 40.13 2.75
1327 1807 3.479203 TACCCCGGCCTCTGCATG 61.479 66.667 0.00 0.00 40.13 4.06
1580 2183 9.953697 CTACTACTACTACCAAAAGAGCAATAG 57.046 37.037 0.00 0.00 0.00 1.73
1617 3290 4.713792 ACCTGAAGACTGGAGAAACATT 57.286 40.909 0.00 0.00 38.29 2.71
1695 3368 4.201705 GCGTTTTGTATTCAATTGGGCATG 60.202 41.667 5.42 0.00 33.32 4.06
1704 3382 6.535811 CATACCGTTAGCGTTTTGTATTCAA 58.464 36.000 0.00 0.00 36.15 2.69
1705 3383 5.446206 GCATACCGTTAGCGTTTTGTATTCA 60.446 40.000 0.00 0.00 36.15 2.57
1716 3394 2.350192 TCATGTTTGCATACCGTTAGCG 59.650 45.455 4.77 0.00 33.30 4.26
1764 3442 0.834612 TCCAAGTCCACCAAGTCGTT 59.165 50.000 0.00 0.00 0.00 3.85
1845 3538 2.160013 CGAGACGACGACATTTTGGAAC 60.160 50.000 0.00 0.00 35.09 3.62
1863 3556 2.107950 TGCCCATGAAAACTACCGAG 57.892 50.000 0.00 0.00 0.00 4.63
1865 3558 3.541632 ACTATGCCCATGAAAACTACCG 58.458 45.455 0.00 0.00 0.00 4.02
1868 4684 4.523083 GTGGACTATGCCCATGAAAACTA 58.477 43.478 0.00 0.00 35.91 2.24
1893 4709 6.454795 TGAAAATCCCTTGAAAATCCGAAAG 58.545 36.000 0.00 0.00 0.00 2.62
1897 4713 5.723295 ACATGAAAATCCCTTGAAAATCCG 58.277 37.500 0.00 0.00 0.00 4.18
1982 5014 4.252878 CAATAGGCATTTTGGGTTGGAAC 58.747 43.478 0.00 0.00 0.00 3.62
1983 5015 3.262915 CCAATAGGCATTTTGGGTTGGAA 59.737 43.478 12.14 0.00 38.98 3.53
1984 5016 2.836981 CCAATAGGCATTTTGGGTTGGA 59.163 45.455 12.14 0.00 38.98 3.53
1985 5017 3.264998 CCAATAGGCATTTTGGGTTGG 57.735 47.619 12.14 0.00 38.98 3.77
2008 5040 2.143122 TGCTTTCGACAGTAAGCCAAG 58.857 47.619 15.11 0.86 46.14 3.61
2010 5042 1.871039 GTTGCTTTCGACAGTAAGCCA 59.129 47.619 15.11 3.58 46.14 4.75
2054 5088 0.102481 CAGAATGCTTGGCCTCATGC 59.898 55.000 3.32 3.62 42.34 4.06
2097 5131 8.438676 AATGATTAGAAAATGTAGGGAAGACG 57.561 34.615 0.00 0.00 0.00 4.18
2149 5183 5.048504 TGTCTTCACAAAAATGAGGCTGATC 60.049 40.000 0.00 0.00 0.00 2.92
2346 5381 5.458041 TCTGTACAGTTTTAAGTAGGCGT 57.542 39.130 21.99 0.00 0.00 5.68



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

AutoCloner maintained by Alex Coulton.