Multiple sequence alignment - TraesCS4D01G289900

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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 TraesCS4D01G289900 chr4D 100.000 2658 0 0 1 2658 461211650 461214307 0.000000e+00 4909
1 TraesCS4D01G289900 chr4A 90.345 1854 109 44 722 2557 7408591 7406790 0.000000e+00 2368
2 TraesCS4D01G289900 chr4B 90.096 1666 111 37 435 2091 576194409 576196029 0.000000e+00 2113
3 TraesCS4D01G289900 chr4B 87.703 431 36 8 2230 2656 576196066 576196483 1.110000e-133 486
4 TraesCS4D01G289900 chr4B 84.504 484 60 12 997 1480 83337791 83338259 5.180000e-127 464
5 TraesCS4D01G289900 chr4B 83.300 497 58 11 997 1482 316988555 316989037 4.060000e-118 435
6 TraesCS4D01G289900 chr4B 89.474 342 22 2 17 345 576194049 576194389 1.140000e-113 420
7 TraesCS4D01G289900 chr4B 92.233 103 8 0 1742 1844 201661382 201661280 2.130000e-31 147
8 TraesCS4D01G289900 chr7B 85.841 452 51 6 1029 1479 179639061 179638622 4.010000e-128 468
9 TraesCS4D01G289900 chr6B 85.268 448 54 5 1029 1476 19453033 19453468 4.030000e-123 451
10 TraesCS4D01G289900 chr6B 93.269 104 5 2 1742 1844 505324289 505324391 4.580000e-33 152
11 TraesCS4D01G289900 chr2B 81.995 411 36 18 1074 1482 663372743 663372369 5.520000e-82 315
12 TraesCS4D01G289900 chr2B 79.725 291 19 19 1628 1906 677184429 677184691 9.780000e-40 174
13 TraesCS4D01G289900 chr5D 80.364 275 21 19 1621 1887 459348770 459348521 7.560000e-41 178
14 TraesCS4D01G289900 chr5D 93.269 104 5 2 1742 1844 249070655 249070553 4.580000e-33 152
15 TraesCS4D01G289900 chr2D 93.269 104 5 2 1742 1844 53042182 53042080 4.580000e-33 152
16 TraesCS4D01G289900 chr7D 92.308 104 6 2 1742 1844 2748720 2748618 2.130000e-31 147


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 TraesCS4D01G289900 chr4D 461211650 461214307 2657 False 4909.000000 4909 100.000 1 2658 1 chr4D.!!$F1 2657
1 TraesCS4D01G289900 chr4A 7406790 7408591 1801 True 2368.000000 2368 90.345 722 2557 1 chr4A.!!$R1 1835
2 TraesCS4D01G289900 chr4B 576194049 576196483 2434 False 1006.333333 2113 89.091 17 2656 3 chr4B.!!$F3 2639

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
140 154 0.680921 ATGCGAATCAACCCCACCAG 60.681 55.0 0.00 0.0 0.00 4.00 F
151 165 0.698238 CCCCACCAGGACATCTTCAA 59.302 55.0 0.00 0.0 38.24 2.69 F
371 385 0.888736 TCAATGGTGCAACACTCCGG 60.889 55.0 6.58 0.0 39.98 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 1394 0.251297 CAAGAACCCACCCATGCAGA 60.251 55.000 0.00 0.0 0.00 4.26 R
1369 1399 0.560688 ACAACCAAGAACCCACCCAT 59.439 50.000 0.00 0.0 0.00 4.00 R
2059 2105 1.003928 TGTGCACCTGATCTTGCTGAT 59.996 47.619 15.69 0.0 39.62 2.90 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
79 93 4.735369 TCTTACATGGAAAAGGCAAAGGA 58.265 39.130 0.00 0.00 0.00 3.36
82 96 3.509442 ACATGGAAAAGGCAAAGGATCA 58.491 40.909 0.00 0.00 0.00 2.92
94 108 4.038282 GGCAAAGGATCAATCACATATGCA 59.962 41.667 1.58 0.00 0.00 3.96
102 116 5.648178 TCAATCACATATGCAGCAAGTTT 57.352 34.783 0.00 0.00 0.00 2.66
126 140 2.480037 CTGCTAACACTGAACAATGCGA 59.520 45.455 0.00 0.00 0.00 5.10
140 154 0.680921 ATGCGAATCAACCCCACCAG 60.681 55.000 0.00 0.00 0.00 4.00
141 155 2.046285 GCGAATCAACCCCACCAGG 61.046 63.158 0.00 0.00 0.00 4.45
151 165 0.698238 CCCCACCAGGACATCTTCAA 59.302 55.000 0.00 0.00 38.24 2.69
197 211 3.184581 GTCAGAACTCAACATTGACGACC 59.815 47.826 0.00 0.00 32.90 4.79
201 215 1.148310 CTCAACATTGACGACCGCTT 58.852 50.000 0.00 0.00 32.90 4.68
202 216 1.126846 CTCAACATTGACGACCGCTTC 59.873 52.381 0.00 0.00 32.90 3.86
219 233 2.904915 CTTCGTCTTTGAAACCGAAGC 58.095 47.619 16.79 0.00 46.36 3.86
227 241 2.613026 TGAAACCGAAGCAACTGAGA 57.387 45.000 0.00 0.00 0.00 3.27
250 264 3.127791 AGAATGGTCCTCCTGATCACT 57.872 47.619 0.00 0.00 36.78 3.41
264 278 2.761767 TGATCACTTGGGCCAATTGATG 59.238 45.455 40.27 26.43 41.49 3.07
276 290 3.841643 CCAATTGATGTTCAGTTCAGGC 58.158 45.455 7.12 0.00 0.00 4.85
296 310 2.154462 CCGAAACCTGCTCTCATGTTT 58.846 47.619 0.00 0.00 41.54 2.83
319 333 1.576421 GCACTTGAAGCGGGAACTG 59.424 57.895 0.00 0.00 38.10 3.16
331 345 1.098050 GGGAACTGCTGCTTGTATGG 58.902 55.000 0.00 0.00 0.00 2.74
336 350 1.340405 ACTGCTGCTTGTATGGAAGGG 60.340 52.381 0.00 0.00 0.00 3.95
344 358 3.448660 GCTTGTATGGAAGGGATTGCTTT 59.551 43.478 0.00 0.00 0.00 3.51
345 359 4.081476 GCTTGTATGGAAGGGATTGCTTTT 60.081 41.667 0.00 0.00 0.00 2.27
346 360 5.404466 TTGTATGGAAGGGATTGCTTTTG 57.596 39.130 0.00 0.00 0.00 2.44
347 361 3.768757 TGTATGGAAGGGATTGCTTTTGG 59.231 43.478 0.00 0.00 0.00 3.28
348 362 0.975887 TGGAAGGGATTGCTTTTGGC 59.024 50.000 0.00 0.00 42.22 4.52
349 363 1.269958 GGAAGGGATTGCTTTTGGCT 58.730 50.000 0.00 0.00 42.39 4.75
350 364 1.205655 GGAAGGGATTGCTTTTGGCTC 59.794 52.381 0.00 0.00 42.39 4.70
351 365 2.174360 GAAGGGATTGCTTTTGGCTCT 58.826 47.619 0.00 0.00 42.39 4.09
352 366 2.315720 AGGGATTGCTTTTGGCTCTT 57.684 45.000 0.00 0.00 42.39 2.85
353 367 2.174360 AGGGATTGCTTTTGGCTCTTC 58.826 47.619 0.00 0.00 42.39 2.87
354 368 1.895131 GGGATTGCTTTTGGCTCTTCA 59.105 47.619 0.00 0.00 42.39 3.02
355 369 2.299867 GGGATTGCTTTTGGCTCTTCAA 59.700 45.455 0.00 0.00 42.39 2.69
356 370 3.055602 GGGATTGCTTTTGGCTCTTCAAT 60.056 43.478 0.00 0.00 42.39 2.57
357 371 3.930848 GGATTGCTTTTGGCTCTTCAATG 59.069 43.478 0.00 0.00 42.39 2.82
358 372 3.389925 TTGCTTTTGGCTCTTCAATGG 57.610 42.857 0.00 0.00 42.39 3.16
359 373 2.318908 TGCTTTTGGCTCTTCAATGGT 58.681 42.857 0.00 0.00 42.39 3.55
360 374 2.036217 TGCTTTTGGCTCTTCAATGGTG 59.964 45.455 0.00 0.00 42.39 4.17
361 375 2.680577 CTTTTGGCTCTTCAATGGTGC 58.319 47.619 0.00 0.00 0.00 5.01
362 376 1.702182 TTTGGCTCTTCAATGGTGCA 58.298 45.000 0.00 0.00 0.00 4.57
363 377 1.702182 TTGGCTCTTCAATGGTGCAA 58.298 45.000 0.00 0.00 0.00 4.08
364 378 0.961019 TGGCTCTTCAATGGTGCAAC 59.039 50.000 0.00 0.00 0.00 4.17
365 379 0.961019 GGCTCTTCAATGGTGCAACA 59.039 50.000 7.04 7.04 39.98 3.33
366 380 1.336240 GGCTCTTCAATGGTGCAACAC 60.336 52.381 6.58 0.00 39.98 3.32
367 381 1.610522 GCTCTTCAATGGTGCAACACT 59.389 47.619 6.58 0.00 39.98 3.55
368 382 2.351157 GCTCTTCAATGGTGCAACACTC 60.351 50.000 6.58 0.00 39.98 3.51
369 383 2.227388 CTCTTCAATGGTGCAACACTCC 59.773 50.000 6.58 0.00 39.98 3.85
370 384 0.950836 TTCAATGGTGCAACACTCCG 59.049 50.000 6.58 0.00 39.98 4.63
371 385 0.888736 TCAATGGTGCAACACTCCGG 60.889 55.000 6.58 0.00 39.98 5.14
376 390 1.084289 GGTGCAACACTCCGGTAATC 58.916 55.000 0.00 0.00 39.98 1.75
377 391 1.338769 GGTGCAACACTCCGGTAATCT 60.339 52.381 0.00 0.00 39.98 2.40
379 393 2.415512 GTGCAACACTCCGGTAATCTTC 59.584 50.000 0.00 0.00 36.32 2.87
390 404 5.529791 TCCGGTAATCTTCGAATCAGATTC 58.470 41.667 12.87 12.62 39.71 2.52
403 417 3.795688 TCAGATTCCTTGGAGCTTGTT 57.204 42.857 0.00 0.00 0.00 2.83
404 418 4.104383 TCAGATTCCTTGGAGCTTGTTT 57.896 40.909 0.00 0.00 0.00 2.83
405 419 3.822735 TCAGATTCCTTGGAGCTTGTTTG 59.177 43.478 0.00 0.00 0.00 2.93
406 420 3.571401 CAGATTCCTTGGAGCTTGTTTGT 59.429 43.478 0.00 0.00 0.00 2.83
407 421 4.038402 CAGATTCCTTGGAGCTTGTTTGTT 59.962 41.667 0.00 0.00 0.00 2.83
408 422 4.651045 AGATTCCTTGGAGCTTGTTTGTTT 59.349 37.500 0.00 0.00 0.00 2.83
409 423 3.799281 TCCTTGGAGCTTGTTTGTTTG 57.201 42.857 0.00 0.00 0.00 2.93
410 424 3.096092 TCCTTGGAGCTTGTTTGTTTGT 58.904 40.909 0.00 0.00 0.00 2.83
411 425 3.513515 TCCTTGGAGCTTGTTTGTTTGTT 59.486 39.130 0.00 0.00 0.00 2.83
412 426 4.020662 TCCTTGGAGCTTGTTTGTTTGTTT 60.021 37.500 0.00 0.00 0.00 2.83
413 427 4.093261 CCTTGGAGCTTGTTTGTTTGTTTG 59.907 41.667 0.00 0.00 0.00 2.93
414 428 4.264460 TGGAGCTTGTTTGTTTGTTTGT 57.736 36.364 0.00 0.00 0.00 2.83
415 429 4.636249 TGGAGCTTGTTTGTTTGTTTGTT 58.364 34.783 0.00 0.00 0.00 2.83
416 430 5.059833 TGGAGCTTGTTTGTTTGTTTGTTT 58.940 33.333 0.00 0.00 0.00 2.83
417 431 5.049818 TGGAGCTTGTTTGTTTGTTTGTTTG 60.050 36.000 0.00 0.00 0.00 2.93
418 432 5.049749 GGAGCTTGTTTGTTTGTTTGTTTGT 60.050 36.000 0.00 0.00 0.00 2.83
419 433 6.370433 AGCTTGTTTGTTTGTTTGTTTGTT 57.630 29.167 0.00 0.00 0.00 2.83
420 434 6.790282 AGCTTGTTTGTTTGTTTGTTTGTTT 58.210 28.000 0.00 0.00 0.00 2.83
421 435 6.690528 AGCTTGTTTGTTTGTTTGTTTGTTTG 59.309 30.769 0.00 0.00 0.00 2.93
422 436 6.470556 GCTTGTTTGTTTGTTTGTTTGTTTGT 59.529 30.769 0.00 0.00 0.00 2.83
423 437 7.008719 GCTTGTTTGTTTGTTTGTTTGTTTGTT 59.991 29.630 0.00 0.00 0.00 2.83
424 438 8.742554 TTGTTTGTTTGTTTGTTTGTTTGTTT 57.257 23.077 0.00 0.00 0.00 2.83
425 439 8.742554 TGTTTGTTTGTTTGTTTGTTTGTTTT 57.257 23.077 0.00 0.00 0.00 2.43
426 440 9.191995 TGTTTGTTTGTTTGTTTGTTTGTTTTT 57.808 22.222 0.00 0.00 0.00 1.94
427 441 9.453087 GTTTGTTTGTTTGTTTGTTTGTTTTTG 57.547 25.926 0.00 0.00 0.00 2.44
428 442 7.209595 TGTTTGTTTGTTTGTTTGTTTTTGC 57.790 28.000 0.00 0.00 0.00 3.68
429 443 6.021468 TGTTTGTTTGTTTGTTTGTTTTTGCG 60.021 30.769 0.00 0.00 0.00 4.85
430 444 3.968724 TGTTTGTTTGTTTGTTTTTGCGC 59.031 34.783 0.00 0.00 0.00 6.09
431 445 3.878086 TTGTTTGTTTGTTTTTGCGCA 57.122 33.333 5.66 5.66 0.00 6.09
432 446 4.410492 TTGTTTGTTTGTTTTTGCGCAT 57.590 31.818 12.75 0.00 0.00 4.73
433 447 5.530519 TTGTTTGTTTGTTTTTGCGCATA 57.469 30.435 12.75 2.60 0.00 3.14
434 448 5.725110 TGTTTGTTTGTTTTTGCGCATAT 57.275 30.435 12.75 0.00 0.00 1.78
435 449 6.111768 TGTTTGTTTGTTTTTGCGCATATT 57.888 29.167 12.75 0.00 0.00 1.28
436 450 5.961843 TGTTTGTTTGTTTTTGCGCATATTG 59.038 32.000 12.75 0.00 0.00 1.90
437 451 4.722203 TGTTTGTTTTTGCGCATATTGG 57.278 36.364 12.75 0.00 0.00 3.16
438 452 4.371786 TGTTTGTTTTTGCGCATATTGGA 58.628 34.783 12.75 0.00 0.00 3.53
439 453 4.447054 TGTTTGTTTTTGCGCATATTGGAG 59.553 37.500 12.75 0.00 0.00 3.86
440 454 2.605030 TGTTTTTGCGCATATTGGAGC 58.395 42.857 12.75 0.00 0.00 4.70
441 455 2.230992 TGTTTTTGCGCATATTGGAGCT 59.769 40.909 12.75 0.00 34.46 4.09
442 456 3.253230 GTTTTTGCGCATATTGGAGCTT 58.747 40.909 12.75 0.00 34.46 3.74
443 457 2.565210 TTTGCGCATATTGGAGCTTG 57.435 45.000 12.75 0.00 34.46 4.01
444 458 1.462616 TTGCGCATATTGGAGCTTGT 58.537 45.000 12.75 0.00 34.46 3.16
473 487 6.607004 TGCTTAAGGCTAAAGTTAGAGACT 57.393 37.500 4.29 0.00 42.39 3.24
477 491 7.388224 GCTTAAGGCTAAAGTTAGAGACTGTTT 59.612 37.037 4.29 0.00 36.97 2.83
478 492 8.603242 TTAAGGCTAAAGTTAGAGACTGTTTG 57.397 34.615 2.18 0.00 39.00 2.93
497 511 7.556635 ACTGTTTGAAGTTAGCCTCTTTAGTTT 59.443 33.333 0.00 0.00 0.00 2.66
498 512 7.703328 TGTTTGAAGTTAGCCTCTTTAGTTTG 58.297 34.615 0.00 0.00 0.00 2.93
525 539 7.013274 TGAGATAAAAAGTTTGTTGTCCAGAGG 59.987 37.037 0.00 0.00 0.00 3.69
526 540 4.736126 AAAAAGTTTGTTGTCCAGAGGG 57.264 40.909 0.00 0.00 0.00 4.30
585 599 8.643324 AACACTATTAGTGGTTAAATGGCAAAA 58.357 29.630 24.01 0.00 45.36 2.44
611 625 5.939457 TGTACACATCGAACAACAAACAAA 58.061 33.333 0.00 0.00 0.00 2.83
617 631 5.971202 ACATCGAACAACAAACAAATGTCTC 59.029 36.000 0.00 0.00 31.81 3.36
632 646 1.271652 TGTCTCGCTCTTCTCTGGACT 60.272 52.381 0.00 0.00 0.00 3.85
642 656 4.274147 TCTTCTCTGGACTAGGTGATGTC 58.726 47.826 0.00 0.00 0.00 3.06
651 665 4.355437 GACTAGGTGATGTCGTTGATCTG 58.645 47.826 0.00 0.00 0.00 2.90
653 667 2.964740 AGGTGATGTCGTTGATCTGTG 58.035 47.619 0.00 0.00 0.00 3.66
654 668 1.394917 GGTGATGTCGTTGATCTGTGC 59.605 52.381 0.00 0.00 0.00 4.57
658 672 1.738099 GTCGTTGATCTGTGCCGCT 60.738 57.895 0.00 0.00 0.00 5.52
665 679 0.935898 GATCTGTGCCGCTCTGATTG 59.064 55.000 13.85 0.00 0.00 2.67
676 690 4.274459 GCCGCTCTGATTGTAATCTTGATT 59.726 41.667 6.21 1.35 36.39 2.57
680 694 7.430502 CCGCTCTGATTGTAATCTTGATTTTTC 59.569 37.037 0.95 0.00 36.39 2.29
682 696 9.798994 GCTCTGATTGTAATCTTGATTTTTCAT 57.201 29.630 0.95 0.00 36.39 2.57
714 729 8.973835 ACAAATTCCTTATCGCGAAAATAAAA 57.026 26.923 15.24 4.18 0.00 1.52
715 730 9.581099 ACAAATTCCTTATCGCGAAAATAAAAT 57.419 25.926 15.24 6.53 0.00 1.82
762 778 2.343758 GAACAGCGCCTGAGTGGA 59.656 61.111 2.29 0.00 38.35 4.02
764 780 1.078848 AACAGCGCCTGAGTGGATC 60.079 57.895 2.29 0.00 38.35 3.36
832 848 2.906897 ACTTGGCCACCGCAAGTG 60.907 61.111 3.88 0.00 46.83 3.16
923 947 4.659529 TCGGGATAGACAGATCCATAGT 57.340 45.455 4.89 0.00 46.42 2.12
924 948 4.999310 TCGGGATAGACAGATCCATAGTT 58.001 43.478 4.89 0.00 46.42 2.24
934 958 4.133078 CAGATCCATAGTTGAAGAAGGGC 58.867 47.826 0.00 0.00 0.00 5.19
935 959 3.782523 AGATCCATAGTTGAAGAAGGGCA 59.217 43.478 0.00 0.00 0.00 5.36
936 960 3.634397 TCCATAGTTGAAGAAGGGCAG 57.366 47.619 0.00 0.00 0.00 4.85
937 961 3.181329 TCCATAGTTGAAGAAGGGCAGA 58.819 45.455 0.00 0.00 0.00 4.26
941 965 1.003355 TTGAAGAAGGGCAGAGGCG 60.003 57.895 0.00 0.00 42.47 5.52
943 967 2.607750 AAGAAGGGCAGAGGCGGA 60.608 61.111 0.00 0.00 42.47 5.54
972 998 2.910199 CGGAGCAGAGGAAATCAATCA 58.090 47.619 0.00 0.00 0.00 2.57
973 999 3.273434 CGGAGCAGAGGAAATCAATCAA 58.727 45.455 0.00 0.00 0.00 2.57
981 1007 3.941483 GAGGAAATCAATCAAGAAGGCGA 59.059 43.478 0.00 0.00 0.00 5.54
985 1011 2.680312 TCAATCAAGAAGGCGAGGAG 57.320 50.000 0.00 0.00 0.00 3.69
988 1014 1.118838 ATCAAGAAGGCGAGGAGGAG 58.881 55.000 0.00 0.00 0.00 3.69
990 1016 1.610673 AAGAAGGCGAGGAGGAGCA 60.611 57.895 0.00 0.00 34.54 4.26
1158 1186 1.963515 GTCAACAAGGCCAAGGACAAT 59.036 47.619 5.01 0.00 0.00 2.71
1346 1374 2.092753 CCCACAAGGTCTGCATCTATGT 60.093 50.000 0.00 0.00 0.00 2.29
1358 1388 3.128589 TGCATCTATGTTTTCTTTCCCGC 59.871 43.478 0.00 0.00 0.00 6.13
1359 1389 3.128589 GCATCTATGTTTTCTTTCCCGCA 59.871 43.478 0.00 0.00 0.00 5.69
1360 1390 4.380444 GCATCTATGTTTTCTTTCCCGCAA 60.380 41.667 0.00 0.00 0.00 4.85
1362 1392 4.394729 TCTATGTTTTCTTTCCCGCAACT 58.605 39.130 0.00 0.00 0.00 3.16
1363 1393 2.861462 TGTTTTCTTTCCCGCAACTG 57.139 45.000 0.00 0.00 0.00 3.16
1364 1394 2.096248 TGTTTTCTTTCCCGCAACTGT 58.904 42.857 0.00 0.00 0.00 3.55
1365 1395 2.098443 TGTTTTCTTTCCCGCAACTGTC 59.902 45.455 0.00 0.00 0.00 3.51
1366 1396 2.341846 TTTCTTTCCCGCAACTGTCT 57.658 45.000 0.00 0.00 0.00 3.41
1367 1397 1.593196 TTCTTTCCCGCAACTGTCTG 58.407 50.000 0.00 0.00 0.00 3.51
1368 1398 0.884704 TCTTTCCCGCAACTGTCTGC 60.885 55.000 5.31 5.31 39.04 4.26
1369 1399 1.153066 TTTCCCGCAACTGTCTGCA 60.153 52.632 12.87 0.00 42.77 4.41
1372 1412 2.693762 CCCGCAACTGTCTGCATGG 61.694 63.158 12.87 9.43 42.77 3.66
1389 1429 1.223501 TGGGTGGGTTCTTGGTTGTA 58.776 50.000 0.00 0.00 0.00 2.41
1394 1434 3.756963 GGTGGGTTCTTGGTTGTAGATTC 59.243 47.826 0.00 0.00 0.00 2.52
1400 1440 6.094186 GGGTTCTTGGTTGTAGATTCTGATTC 59.906 42.308 0.00 0.00 0.00 2.52
1404 1444 6.372659 TCTTGGTTGTAGATTCTGATTCTTGC 59.627 38.462 7.32 3.17 0.00 4.01
1405 1445 5.809001 TGGTTGTAGATTCTGATTCTTGCT 58.191 37.500 7.32 0.00 0.00 3.91
1406 1446 5.645067 TGGTTGTAGATTCTGATTCTTGCTG 59.355 40.000 7.32 0.00 0.00 4.41
1407 1447 5.645497 GGTTGTAGATTCTGATTCTTGCTGT 59.355 40.000 7.32 0.00 0.00 4.40
1408 1448 6.402983 GGTTGTAGATTCTGATTCTTGCTGTG 60.403 42.308 7.32 0.00 0.00 3.66
1409 1449 5.181009 TGTAGATTCTGATTCTTGCTGTGG 58.819 41.667 7.32 0.00 0.00 4.17
1410 1450 3.618351 AGATTCTGATTCTTGCTGTGGG 58.382 45.455 0.00 0.00 0.00 4.61
1411 1451 3.265221 AGATTCTGATTCTTGCTGTGGGA 59.735 43.478 0.00 0.00 0.00 4.37
1412 1452 3.726557 TTCTGATTCTTGCTGTGGGAT 57.273 42.857 0.00 0.00 0.00 3.85
1413 1453 2.995283 TCTGATTCTTGCTGTGGGATG 58.005 47.619 0.00 0.00 0.00 3.51
1414 1454 2.022195 CTGATTCTTGCTGTGGGATGG 58.978 52.381 0.00 0.00 0.00 3.51
1415 1455 1.341285 TGATTCTTGCTGTGGGATGGG 60.341 52.381 0.00 0.00 0.00 4.00
1416 1456 1.002069 ATTCTTGCTGTGGGATGGGA 58.998 50.000 0.00 0.00 0.00 4.37
1417 1457 1.002069 TTCTTGCTGTGGGATGGGAT 58.998 50.000 0.00 0.00 0.00 3.85
1418 1458 1.891933 TCTTGCTGTGGGATGGGATA 58.108 50.000 0.00 0.00 0.00 2.59
1419 1459 2.421725 TCTTGCTGTGGGATGGGATAT 58.578 47.619 0.00 0.00 0.00 1.63
1420 1460 2.107031 TCTTGCTGTGGGATGGGATATG 59.893 50.000 0.00 0.00 0.00 1.78
1421 1461 0.773014 TGCTGTGGGATGGGATATGG 59.227 55.000 0.00 0.00 0.00 2.74
1422 1462 1.067295 GCTGTGGGATGGGATATGGA 58.933 55.000 0.00 0.00 0.00 3.41
1423 1463 1.425066 GCTGTGGGATGGGATATGGAA 59.575 52.381 0.00 0.00 0.00 3.53
1424 1464 2.042162 GCTGTGGGATGGGATATGGAAT 59.958 50.000 0.00 0.00 0.00 3.01
1425 1465 3.501019 GCTGTGGGATGGGATATGGAATT 60.501 47.826 0.00 0.00 0.00 2.17
1447 1487 1.067416 GATGCAGATGTACCGCGGA 59.933 57.895 35.90 10.61 0.00 5.54
1603 1643 0.531974 TGGTGAAGCACAAGGACGAC 60.532 55.000 0.00 0.00 35.86 4.34
1775 1818 3.512329 TCGGTTGTGGACTAATAAGAGCA 59.488 43.478 0.00 0.00 0.00 4.26
1912 1956 6.455646 CGAAGTAGTAGATTTGCATCCAACAC 60.456 42.308 0.00 0.00 0.00 3.32
1913 1957 6.054860 AGTAGTAGATTTGCATCCAACACT 57.945 37.500 0.00 0.00 0.00 3.55
1914 1958 6.109359 AGTAGTAGATTTGCATCCAACACTC 58.891 40.000 0.00 0.00 0.00 3.51
1927 1971 7.123098 TGCATCCAACACTCTGATTTTCATAAT 59.877 33.333 0.00 0.00 0.00 1.28
2006 2051 8.893563 TGTTAATTTAGGATGGAACCTGAAAT 57.106 30.769 0.00 0.00 38.63 2.17
2049 2095 5.043903 TCTGTTTTCTGTCTCGACAAAGAG 58.956 41.667 1.02 1.88 41.33 2.85
2059 2105 3.193479 TCTCGACAAAGAGCAATAGAGCA 59.807 43.478 0.00 0.00 38.12 4.26
2098 2144 6.683708 GTGCACAATTGTCTTTTGAATGTTTG 59.316 34.615 13.17 0.00 0.00 2.93
2117 2163 1.202639 TGTGCCTTGCCTATACCATCG 60.203 52.381 0.00 0.00 0.00 3.84
2124 2170 4.322049 CCTTGCCTATACCATCGTAGGAAG 60.322 50.000 2.74 4.04 39.91 3.46
2125 2171 3.840991 TGCCTATACCATCGTAGGAAGT 58.159 45.455 2.74 0.00 39.91 3.01
2126 2172 4.989277 TGCCTATACCATCGTAGGAAGTA 58.011 43.478 2.74 0.00 39.91 2.24
2127 2173 5.577100 TGCCTATACCATCGTAGGAAGTAT 58.423 41.667 13.05 13.05 39.91 2.12
2128 2174 6.014647 TGCCTATACCATCGTAGGAAGTATT 58.985 40.000 13.49 3.36 39.91 1.89
2129 2175 7.177184 TGCCTATACCATCGTAGGAAGTATTA 58.823 38.462 13.49 4.04 39.91 0.98
2130 2176 7.670979 TGCCTATACCATCGTAGGAAGTATTAA 59.329 37.037 13.49 1.49 39.91 1.40
2200 2246 6.042093 TGTTTATCTCCTCTGAGTTGTCAAGT 59.958 38.462 3.66 0.00 39.75 3.16
2202 2248 7.776618 TTATCTCCTCTGAGTTGTCAAGTTA 57.223 36.000 3.66 0.00 39.75 2.24
2205 2251 3.964688 TCCTCTGAGTTGTCAAGTTACCA 59.035 43.478 3.66 0.00 30.14 3.25
2210 2256 5.029807 TGAGTTGTCAAGTTACCATGTCA 57.970 39.130 0.00 0.00 0.00 3.58
2212 2258 5.883115 TGAGTTGTCAAGTTACCATGTCAAA 59.117 36.000 0.00 0.00 0.00 2.69
2217 2263 7.340122 TGTCAAGTTACCATGTCAAATTTGA 57.660 32.000 16.91 16.91 34.20 2.69
2230 2276 8.484799 CATGTCAAATTTGATTTGTCAAGTCTG 58.515 33.333 23.05 8.04 45.95 3.51
2261 2307 4.100963 CACTGCTACCATCCTACCATTGTA 59.899 45.833 0.00 0.00 0.00 2.41
2262 2308 4.101119 ACTGCTACCATCCTACCATTGTAC 59.899 45.833 0.00 0.00 0.00 2.90
2263 2309 3.389983 TGCTACCATCCTACCATTGTACC 59.610 47.826 0.00 0.00 0.00 3.34
2264 2310 3.389983 GCTACCATCCTACCATTGTACCA 59.610 47.826 0.00 0.00 0.00 3.25
2265 2311 4.041691 GCTACCATCCTACCATTGTACCAT 59.958 45.833 0.00 0.00 0.00 3.55
2266 2312 5.456186 GCTACCATCCTACCATTGTACCATT 60.456 44.000 0.00 0.00 0.00 3.16
2267 2313 4.792068 ACCATCCTACCATTGTACCATTG 58.208 43.478 0.00 0.00 0.00 2.82
2268 2314 4.229582 ACCATCCTACCATTGTACCATTGT 59.770 41.667 0.00 0.00 0.00 2.71
2415 2464 8.226819 TGTGTTAACTTCATCATTTGTTGGTA 57.773 30.769 7.22 0.00 0.00 3.25
2459 2508 8.619546 GGAAGAGAGGTTTTCATTGATTCATAG 58.380 37.037 0.00 0.00 0.00 2.23
2489 2538 7.995289 AGAGTTTACAGAGTCATCATCTACAG 58.005 38.462 0.00 0.00 0.00 2.74
2492 2541 8.247562 AGTTTACAGAGTCATCATCTACAGAAC 58.752 37.037 0.00 0.00 0.00 3.01
2506 2555 3.753294 ACAGAACGACCAATCTCTGTT 57.247 42.857 0.00 0.00 35.22 3.16
2514 2563 4.020573 ACGACCAATCTCTGTTTGGACATA 60.021 41.667 9.31 0.00 45.35 2.29
2523 2572 1.499438 TGTTTGGACATACCCCAACCA 59.501 47.619 0.00 0.00 42.80 3.67
2530 2579 4.093743 GGACATACCCCAACCAGAAATTT 58.906 43.478 0.00 0.00 0.00 1.82
2578 2627 1.817357 CAAGCTCATGAGTTGCCTGA 58.183 50.000 23.38 0.00 0.00 3.86
2603 2652 9.887406 GATTAAACTCGACCAATTTTAGAAACA 57.113 29.630 0.00 0.00 0.00 2.83
2611 2660 6.364976 CGACCAATTTTAGAAACATTGAACCC 59.635 38.462 0.00 0.00 30.66 4.11
2614 2663 7.877612 ACCAATTTTAGAAACATTGAACCCATC 59.122 33.333 0.00 0.00 30.66 3.51
2624 2673 4.163078 ACATTGAACCCATCCAGAGTAGAG 59.837 45.833 0.00 0.00 0.00 2.43
2626 2675 3.366396 TGAACCCATCCAGAGTAGAGTC 58.634 50.000 0.00 0.00 0.00 3.36
2656 2705 5.545335 TGTTGATCTCTCCATATGTATGCCT 59.455 40.000 1.24 0.00 32.40 4.75
2657 2706 5.929058 TGATCTCTCCATATGTATGCCTC 57.071 43.478 1.24 0.00 32.40 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.470821 CACATTCCCGACTAATCCGTC 58.529 52.381 0.00 0.00 0.00 4.79
3 4 1.217882 GCACATTCCCGACTAATCCG 58.782 55.000 0.00 0.00 0.00 4.18
4 5 2.325583 TGCACATTCCCGACTAATCC 57.674 50.000 0.00 0.00 0.00 3.01
5 6 3.466836 TCATGCACATTCCCGACTAATC 58.533 45.455 0.00 0.00 0.00 1.75
7 8 3.558931 ATCATGCACATTCCCGACTAA 57.441 42.857 0.00 0.00 0.00 2.24
8 9 4.681074 TTATCATGCACATTCCCGACTA 57.319 40.909 0.00 0.00 0.00 2.59
9 10 3.558931 TTATCATGCACATTCCCGACT 57.441 42.857 0.00 0.00 0.00 4.18
10 11 3.546020 CGTTTATCATGCACATTCCCGAC 60.546 47.826 0.00 0.00 0.00 4.79
11 12 2.611751 CGTTTATCATGCACATTCCCGA 59.388 45.455 0.00 0.00 0.00 5.14
12 13 2.854424 GCGTTTATCATGCACATTCCCG 60.854 50.000 0.00 0.00 37.36 5.14
13 14 2.731217 GCGTTTATCATGCACATTCCC 58.269 47.619 0.00 0.00 37.36 3.97
14 15 2.375110 CGCGTTTATCATGCACATTCC 58.625 47.619 0.00 0.00 37.23 3.01
15 16 1.775208 GCGCGTTTATCATGCACATTC 59.225 47.619 8.43 0.00 37.23 2.67
79 93 5.847111 AACTTGCTGCATATGTGATTGAT 57.153 34.783 1.84 0.00 0.00 2.57
82 96 5.404946 GTGAAACTTGCTGCATATGTGATT 58.595 37.500 1.84 0.00 0.00 2.57
108 122 5.281693 TGATTCGCATTGTTCAGTGTTAG 57.718 39.130 0.00 0.00 0.00 2.34
126 140 1.005924 GATGTCCTGGTGGGGTTGATT 59.994 52.381 0.00 0.00 35.33 2.57
140 154 1.106285 GGTGGCCATTGAAGATGTCC 58.894 55.000 9.72 0.00 0.00 4.02
141 155 1.106285 GGGTGGCCATTGAAGATGTC 58.894 55.000 9.72 0.00 0.00 3.06
151 165 2.248374 AACCAGATGGGGTGGCCAT 61.248 57.895 9.72 0.00 41.32 4.40
165 179 1.562008 TGAGTTCTGACCAACCAACCA 59.438 47.619 0.00 0.00 0.00 3.67
197 211 0.856641 TCGGTTTCAAAGACGAAGCG 59.143 50.000 0.00 0.00 43.31 4.68
201 215 1.942677 TGCTTCGGTTTCAAAGACGA 58.057 45.000 0.00 0.00 0.00 4.20
202 216 2.031683 AGTTGCTTCGGTTTCAAAGACG 59.968 45.455 0.00 0.00 0.00 4.18
219 233 4.142049 GGAGGACCATTCTAGTCTCAGTTG 60.142 50.000 0.00 0.00 34.56 3.16
227 241 3.964031 GTGATCAGGAGGACCATTCTAGT 59.036 47.826 0.00 0.00 38.94 2.57
250 264 2.607499 ACTGAACATCAATTGGCCCAA 58.393 42.857 5.42 0.00 0.00 4.12
264 278 0.591659 GGTTTCGGCCTGAACTGAAC 59.408 55.000 15.13 8.81 35.97 3.18
276 290 1.813513 AACATGAGAGCAGGTTTCGG 58.186 50.000 0.00 0.00 45.77 4.30
296 310 2.258013 CCCGCTTCAAGTGCCGAAA 61.258 57.895 0.00 0.00 0.00 3.46
319 333 2.355010 ATCCCTTCCATACAAGCAGC 57.645 50.000 0.00 0.00 0.00 5.25
344 358 1.340889 GTTGCACCATTGAAGAGCCAA 59.659 47.619 0.00 0.00 0.00 4.52
345 359 0.961019 GTTGCACCATTGAAGAGCCA 59.039 50.000 0.00 0.00 0.00 4.75
346 360 0.961019 TGTTGCACCATTGAAGAGCC 59.039 50.000 0.00 0.00 0.00 4.70
347 361 1.610522 AGTGTTGCACCATTGAAGAGC 59.389 47.619 0.00 0.00 34.49 4.09
348 362 2.227388 GGAGTGTTGCACCATTGAAGAG 59.773 50.000 0.00 0.00 34.49 2.85
349 363 2.229792 GGAGTGTTGCACCATTGAAGA 58.770 47.619 0.00 0.00 34.49 2.87
350 364 1.069022 CGGAGTGTTGCACCATTGAAG 60.069 52.381 0.00 0.00 34.49 3.02
351 365 0.950836 CGGAGTGTTGCACCATTGAA 59.049 50.000 0.00 0.00 34.49 2.69
352 366 0.888736 CCGGAGTGTTGCACCATTGA 60.889 55.000 0.00 0.00 34.49 2.57
353 367 1.172180 ACCGGAGTGTTGCACCATTG 61.172 55.000 9.46 0.00 34.49 2.82
354 368 0.398696 TACCGGAGTGTTGCACCATT 59.601 50.000 9.46 0.00 34.49 3.16
355 369 0.398696 TTACCGGAGTGTTGCACCAT 59.601 50.000 9.46 0.00 34.49 3.55
356 370 0.398696 ATTACCGGAGTGTTGCACCA 59.601 50.000 9.46 0.00 34.49 4.17
357 371 1.084289 GATTACCGGAGTGTTGCACC 58.916 55.000 9.46 0.00 34.49 5.01
358 372 2.094762 AGATTACCGGAGTGTTGCAC 57.905 50.000 9.46 0.00 34.10 4.57
359 373 2.695359 GAAGATTACCGGAGTGTTGCA 58.305 47.619 9.46 0.00 0.00 4.08
360 374 1.659098 CGAAGATTACCGGAGTGTTGC 59.341 52.381 9.46 0.00 0.00 4.17
361 375 3.226346 TCGAAGATTACCGGAGTGTTG 57.774 47.619 9.46 0.00 0.00 3.33
362 376 3.947910 TTCGAAGATTACCGGAGTGTT 57.052 42.857 9.46 0.00 35.04 3.32
363 377 3.446161 TGATTCGAAGATTACCGGAGTGT 59.554 43.478 9.46 0.00 35.04 3.55
364 378 4.041740 TGATTCGAAGATTACCGGAGTG 57.958 45.455 9.46 0.00 35.04 3.51
365 379 3.952323 TCTGATTCGAAGATTACCGGAGT 59.048 43.478 9.46 0.00 35.04 3.85
366 380 4.569761 TCTGATTCGAAGATTACCGGAG 57.430 45.455 9.46 0.00 35.04 4.63
367 381 5.509163 GGAATCTGATTCGAAGATTACCGGA 60.509 44.000 20.72 3.53 42.94 5.14
368 382 4.686554 GGAATCTGATTCGAAGATTACCGG 59.313 45.833 20.72 0.00 42.94 5.28
369 383 5.533482 AGGAATCTGATTCGAAGATTACCG 58.467 41.667 20.72 0.00 43.40 4.02
370 384 6.203723 CCAAGGAATCTGATTCGAAGATTACC 59.796 42.308 20.72 13.82 43.40 2.85
371 385 6.986817 TCCAAGGAATCTGATTCGAAGATTAC 59.013 38.462 20.72 11.20 42.94 1.89
376 390 3.559242 GCTCCAAGGAATCTGATTCGAAG 59.441 47.826 20.72 13.45 40.17 3.79
377 391 3.198635 AGCTCCAAGGAATCTGATTCGAA 59.801 43.478 20.72 0.00 40.17 3.71
379 393 3.191078 AGCTCCAAGGAATCTGATTCG 57.809 47.619 20.72 9.70 40.17 3.34
390 404 3.525268 ACAAACAAACAAGCTCCAAGG 57.475 42.857 0.00 0.00 0.00 3.61
403 417 7.461416 CGCAAAAACAAACAAACAAACAAACAA 60.461 29.630 0.00 0.00 0.00 2.83
404 418 6.021468 CGCAAAAACAAACAAACAAACAAACA 60.021 30.769 0.00 0.00 0.00 2.83
405 419 6.332600 CGCAAAAACAAACAAACAAACAAAC 58.667 32.000 0.00 0.00 0.00 2.93
406 420 5.052370 GCGCAAAAACAAACAAACAAACAAA 60.052 32.000 0.30 0.00 0.00 2.83
407 421 4.437820 GCGCAAAAACAAACAAACAAACAA 59.562 33.333 0.30 0.00 0.00 2.83
408 422 3.968724 GCGCAAAAACAAACAAACAAACA 59.031 34.783 0.30 0.00 0.00 2.83
409 423 3.968724 TGCGCAAAAACAAACAAACAAAC 59.031 34.783 8.16 0.00 0.00 2.93
410 424 4.209452 TGCGCAAAAACAAACAAACAAA 57.791 31.818 8.16 0.00 0.00 2.83
411 425 3.878086 TGCGCAAAAACAAACAAACAA 57.122 33.333 8.16 0.00 0.00 2.83
412 426 5.725110 ATATGCGCAAAAACAAACAAACA 57.275 30.435 17.11 0.00 0.00 2.83
413 427 5.394904 CCAATATGCGCAAAAACAAACAAAC 59.605 36.000 17.11 0.00 0.00 2.93
414 428 5.294306 TCCAATATGCGCAAAAACAAACAAA 59.706 32.000 17.11 0.00 0.00 2.83
415 429 4.811024 TCCAATATGCGCAAAAACAAACAA 59.189 33.333 17.11 0.00 0.00 2.83
416 430 4.371786 TCCAATATGCGCAAAAACAAACA 58.628 34.783 17.11 0.00 0.00 2.83
417 431 4.666402 GCTCCAATATGCGCAAAAACAAAC 60.666 41.667 17.11 0.00 0.00 2.93
418 432 3.431572 GCTCCAATATGCGCAAAAACAAA 59.568 39.130 17.11 0.00 0.00 2.83
419 433 2.992543 GCTCCAATATGCGCAAAAACAA 59.007 40.909 17.11 0.00 0.00 2.83
420 434 2.230992 AGCTCCAATATGCGCAAAAACA 59.769 40.909 17.11 0.00 0.00 2.83
421 435 2.879826 AGCTCCAATATGCGCAAAAAC 58.120 42.857 17.11 0.00 0.00 2.43
422 436 3.252400 CAAGCTCCAATATGCGCAAAAA 58.748 40.909 17.11 2.95 0.00 1.94
423 437 2.230992 ACAAGCTCCAATATGCGCAAAA 59.769 40.909 17.11 6.15 0.00 2.44
424 438 1.818060 ACAAGCTCCAATATGCGCAAA 59.182 42.857 17.11 0.00 0.00 3.68
425 439 1.462616 ACAAGCTCCAATATGCGCAA 58.537 45.000 17.11 4.13 0.00 4.85
426 440 1.462616 AACAAGCTCCAATATGCGCA 58.537 45.000 14.96 14.96 0.00 6.09
427 441 3.181501 TGTTAACAAGCTCCAATATGCGC 60.182 43.478 5.64 0.00 0.00 6.09
428 442 4.614555 TGTTAACAAGCTCCAATATGCG 57.385 40.909 5.64 0.00 0.00 4.73
429 443 4.741676 GCATGTTAACAAGCTCCAATATGC 59.258 41.667 24.55 15.85 38.00 3.14
430 444 6.140303 AGCATGTTAACAAGCTCCAATATG 57.860 37.500 27.80 12.20 46.47 1.78
473 487 7.338449 ACAAACTAAAGAGGCTAACTTCAAACA 59.662 33.333 0.00 0.00 0.00 2.83
477 491 6.588204 TCACAAACTAAAGAGGCTAACTTCA 58.412 36.000 0.00 0.00 0.00 3.02
478 492 6.929606 TCTCACAAACTAAAGAGGCTAACTTC 59.070 38.462 0.00 0.00 0.00 3.01
497 511 7.338196 TCTGGACAACAAACTTTTTATCTCACA 59.662 33.333 0.00 0.00 0.00 3.58
498 512 7.703328 TCTGGACAACAAACTTTTTATCTCAC 58.297 34.615 0.00 0.00 0.00 3.51
576 590 6.691754 TCGATGTGTACATATTTTGCCATT 57.308 33.333 6.55 0.00 36.57 3.16
585 599 7.428282 TGTTTGTTGTTCGATGTGTACATAT 57.572 32.000 4.58 4.58 36.57 1.78
590 604 6.556212 ACATTTGTTTGTTGTTCGATGTGTA 58.444 32.000 0.00 0.00 0.00 2.90
611 625 1.748493 GTCCAGAGAAGAGCGAGACAT 59.252 52.381 0.00 0.00 0.00 3.06
617 631 1.403679 CACCTAGTCCAGAGAAGAGCG 59.596 57.143 0.00 0.00 0.00 5.03
632 646 3.676049 GCACAGATCAACGACATCACCTA 60.676 47.826 0.00 0.00 0.00 3.08
642 656 1.446792 AGAGCGGCACAGATCAACG 60.447 57.895 1.45 0.00 0.00 4.10
651 665 2.555199 AGATTACAATCAGAGCGGCAC 58.445 47.619 1.45 0.00 37.89 5.01
653 667 3.198068 TCAAGATTACAATCAGAGCGGC 58.802 45.455 4.85 0.00 37.89 6.53
654 668 5.998454 AATCAAGATTACAATCAGAGCGG 57.002 39.130 4.85 0.00 37.89 5.52
726 741 8.064222 CGCTGTTCAGAATATCGTTCATATTTT 58.936 33.333 3.84 0.00 37.74 1.82
729 744 5.119279 GCGCTGTTCAGAATATCGTTCATAT 59.881 40.000 0.00 0.00 0.00 1.78
731 746 3.246226 GCGCTGTTCAGAATATCGTTCAT 59.754 43.478 0.00 0.00 0.00 2.57
737 752 2.799412 CTCAGGCGCTGTTCAGAATATC 59.201 50.000 7.64 0.00 32.61 1.63
739 754 1.550524 ACTCAGGCGCTGTTCAGAATA 59.449 47.619 7.64 0.00 32.61 1.75
751 766 1.739049 GAGGAGATCCACTCAGGCG 59.261 63.158 8.87 0.00 46.54 5.52
779 795 4.241555 GGGCAGCCGTCGGATCAT 62.242 66.667 17.49 0.00 0.00 2.45
806 822 3.579302 TGGCCAAGTCAGGGGTGG 61.579 66.667 0.61 0.00 35.39 4.61
832 848 1.079057 GGAAGGCACGGGTTCTCTC 60.079 63.158 0.00 0.00 0.00 3.20
923 947 1.003355 CGCCTCTGCCCTTCTTCAA 60.003 57.895 0.00 0.00 0.00 2.69
924 948 2.665000 CGCCTCTGCCCTTCTTCA 59.335 61.111 0.00 0.00 0.00 3.02
947 973 1.977293 ATTTCCTCTGCTCCGCCTCC 61.977 60.000 0.00 0.00 0.00 4.30
949 975 1.267574 TGATTTCCTCTGCTCCGCCT 61.268 55.000 0.00 0.00 0.00 5.52
970 996 1.608717 GCTCCTCCTCGCCTTCTTGA 61.609 60.000 0.00 0.00 0.00 3.02
971 997 1.153469 GCTCCTCCTCGCCTTCTTG 60.153 63.158 0.00 0.00 0.00 3.02
972 998 0.980231 ATGCTCCTCCTCGCCTTCTT 60.980 55.000 0.00 0.00 0.00 2.52
973 999 1.382420 ATGCTCCTCCTCGCCTTCT 60.382 57.895 0.00 0.00 0.00 2.85
981 1007 3.532155 GCCGACGATGCTCCTCCT 61.532 66.667 0.00 0.00 0.00 3.69
1158 1186 1.596934 GGAGATGCGGAACCAGTCA 59.403 57.895 0.00 0.00 0.00 3.41
1336 1364 3.128589 GCGGGAAAGAAAACATAGATGCA 59.871 43.478 0.00 0.00 0.00 3.96
1340 1368 4.215399 CAGTTGCGGGAAAGAAAACATAGA 59.785 41.667 0.00 0.00 0.00 1.98
1341 1369 4.023193 ACAGTTGCGGGAAAGAAAACATAG 60.023 41.667 0.00 0.00 0.00 2.23
1342 1370 3.886505 ACAGTTGCGGGAAAGAAAACATA 59.113 39.130 0.00 0.00 0.00 2.29
1344 1372 2.096248 ACAGTTGCGGGAAAGAAAACA 58.904 42.857 0.00 0.00 0.00 2.83
1346 1374 2.357637 CAGACAGTTGCGGGAAAGAAAA 59.642 45.455 0.00 0.00 0.00 2.29
1358 1388 1.246056 CCCACCCATGCAGACAGTTG 61.246 60.000 0.00 0.00 0.00 3.16
1359 1389 1.075482 CCCACCCATGCAGACAGTT 59.925 57.895 0.00 0.00 0.00 3.16
1360 1390 1.719063 AACCCACCCATGCAGACAGT 61.719 55.000 0.00 0.00 0.00 3.55
1362 1392 1.074775 GAACCCACCCATGCAGACA 59.925 57.895 0.00 0.00 0.00 3.41
1363 1393 0.251341 AAGAACCCACCCATGCAGAC 60.251 55.000 0.00 0.00 0.00 3.51
1364 1394 0.251297 CAAGAACCCACCCATGCAGA 60.251 55.000 0.00 0.00 0.00 4.26
1365 1395 1.252904 CCAAGAACCCACCCATGCAG 61.253 60.000 0.00 0.00 0.00 4.41
1366 1396 1.228831 CCAAGAACCCACCCATGCA 60.229 57.895 0.00 0.00 0.00 3.96
1367 1397 0.831711 AACCAAGAACCCACCCATGC 60.832 55.000 0.00 0.00 0.00 4.06
1368 1398 0.968405 CAACCAAGAACCCACCCATG 59.032 55.000 0.00 0.00 0.00 3.66
1369 1399 0.560688 ACAACCAAGAACCCACCCAT 59.439 50.000 0.00 0.00 0.00 4.00
1372 1412 2.943036 TCTACAACCAAGAACCCACC 57.057 50.000 0.00 0.00 0.00 4.61
1389 1429 3.265221 TCCCACAGCAAGAATCAGAATCT 59.735 43.478 0.00 0.00 0.00 2.40
1394 1434 2.022195 CCATCCCACAGCAAGAATCAG 58.978 52.381 0.00 0.00 0.00 2.90
1400 1440 2.511659 CATATCCCATCCCACAGCAAG 58.488 52.381 0.00 0.00 0.00 4.01
1404 1444 4.393239 AATTCCATATCCCATCCCACAG 57.607 45.455 0.00 0.00 0.00 3.66
1405 1445 5.281663 CCATAATTCCATATCCCATCCCACA 60.282 44.000 0.00 0.00 0.00 4.17
1406 1446 5.044179 TCCATAATTCCATATCCCATCCCAC 60.044 44.000 0.00 0.00 0.00 4.61
1407 1447 5.114589 TCCATAATTCCATATCCCATCCCA 58.885 41.667 0.00 0.00 0.00 4.37
1408 1448 5.732331 TCCATAATTCCATATCCCATCCC 57.268 43.478 0.00 0.00 0.00 3.85
1409 1449 5.537674 GCATCCATAATTCCATATCCCATCC 59.462 44.000 0.00 0.00 0.00 3.51
1410 1450 6.131264 TGCATCCATAATTCCATATCCCATC 58.869 40.000 0.00 0.00 0.00 3.51
1411 1451 6.068676 TCTGCATCCATAATTCCATATCCCAT 60.069 38.462 0.00 0.00 0.00 4.00
1412 1452 5.253564 TCTGCATCCATAATTCCATATCCCA 59.746 40.000 0.00 0.00 0.00 4.37
1413 1453 5.759059 TCTGCATCCATAATTCCATATCCC 58.241 41.667 0.00 0.00 0.00 3.85
1414 1454 6.832384 ACATCTGCATCCATAATTCCATATCC 59.168 38.462 0.00 0.00 0.00 2.59
1415 1455 7.876936 ACATCTGCATCCATAATTCCATATC 57.123 36.000 0.00 0.00 0.00 1.63
1416 1456 7.776969 GGTACATCTGCATCCATAATTCCATAT 59.223 37.037 0.00 0.00 0.00 1.78
1417 1457 7.112122 GGTACATCTGCATCCATAATTCCATA 58.888 38.462 0.00 0.00 0.00 2.74
1418 1458 5.948162 GGTACATCTGCATCCATAATTCCAT 59.052 40.000 0.00 0.00 0.00 3.41
1419 1459 5.316167 GGTACATCTGCATCCATAATTCCA 58.684 41.667 0.00 0.00 0.00 3.53
1420 1460 4.393062 CGGTACATCTGCATCCATAATTCC 59.607 45.833 0.00 0.00 0.00 3.01
1421 1461 4.142816 GCGGTACATCTGCATCCATAATTC 60.143 45.833 0.00 0.00 46.78 2.17
1422 1462 3.753272 GCGGTACATCTGCATCCATAATT 59.247 43.478 0.00 0.00 46.78 1.40
1423 1463 3.338249 GCGGTACATCTGCATCCATAAT 58.662 45.455 0.00 0.00 46.78 1.28
1424 1464 2.766313 GCGGTACATCTGCATCCATAA 58.234 47.619 0.00 0.00 46.78 1.90
1425 1465 2.455674 GCGGTACATCTGCATCCATA 57.544 50.000 0.00 0.00 46.78 2.74
1447 1487 1.333636 CGGTGAGGCAGATCTTCCCT 61.334 60.000 7.89 9.48 0.00 4.20
1685 1725 2.009051 TGTCACTGTCAGCAACAACAG 58.991 47.619 0.00 1.17 46.61 3.16
2006 2051 6.189677 CAGACTTCTGTTAACCAACACAAA 57.810 37.500 2.48 0.00 39.75 2.83
2049 2095 3.813724 TGATCTTGCTGATGCTCTATTGC 59.186 43.478 0.00 0.00 40.48 3.56
2059 2105 1.003928 TGTGCACCTGATCTTGCTGAT 59.996 47.619 15.69 0.00 39.62 2.90
2098 2144 1.202651 ACGATGGTATAGGCAAGGCAC 60.203 52.381 0.00 0.00 0.00 5.01
2210 2256 7.729116 ACATCCAGACTTGACAAATCAAATTT 58.271 30.769 0.00 0.00 44.28 1.82
2212 2258 6.906157 ACATCCAGACTTGACAAATCAAAT 57.094 33.333 0.00 0.00 44.28 2.32
2217 2263 4.697352 GTGCTACATCCAGACTTGACAAAT 59.303 41.667 0.00 0.00 0.00 2.32
2222 2268 2.354103 GCAGTGCTACATCCAGACTTGA 60.354 50.000 8.18 0.00 0.00 3.02
2249 2295 4.919774 ACACAATGGTACAATGGTAGGA 57.080 40.909 0.00 0.00 44.80 2.94
2415 2464 7.974504 TCTCTTCCCTCAAAACAAAGTATAGT 58.025 34.615 0.00 0.00 0.00 2.12
2425 2474 4.887655 TGAAAACCTCTCTTCCCTCAAAAC 59.112 41.667 0.00 0.00 0.00 2.43
2459 2508 6.274157 TGATGACTCTGTAAACTCTCCTTC 57.726 41.667 0.00 0.00 0.00 3.46
2489 2538 3.186613 GTCCAAACAGAGATTGGTCGTTC 59.813 47.826 5.31 0.00 46.05 3.95
2492 2541 2.766313 TGTCCAAACAGAGATTGGTCG 58.234 47.619 5.31 0.00 46.05 4.79
2506 2555 1.748732 TCTGGTTGGGGTATGTCCAA 58.251 50.000 0.00 0.00 41.50 3.53
2514 2563 5.427157 ACTGTTAAAAATTTCTGGTTGGGGT 59.573 36.000 0.00 0.00 0.00 4.95
2523 2572 7.573968 AGAGTGAGCACTGTTAAAAATTTCT 57.426 32.000 8.03 0.00 42.66 2.52
2530 2579 4.873746 AGCTAGAGTGAGCACTGTTAAA 57.126 40.909 8.03 0.00 45.43 1.52
2587 2636 7.213678 TGGGTTCAATGTTTCTAAAATTGGTC 58.786 34.615 3.25 0.00 33.14 4.02
2603 2652 4.366267 ACTCTACTCTGGATGGGTTCAAT 58.634 43.478 0.00 0.00 0.00 2.57
2611 2660 5.199024 CATCCTTGACTCTACTCTGGATG 57.801 47.826 0.00 0.00 41.95 3.51
2614 2663 4.464244 TCAACATCCTTGACTCTACTCTGG 59.536 45.833 0.00 0.00 0.00 3.86
2624 2673 4.478206 TGGAGAGATCAACATCCTTGAC 57.522 45.455 0.00 0.00 32.79 3.18
2626 2675 6.531923 ACATATGGAGAGATCAACATCCTTG 58.468 40.000 7.80 0.26 32.79 3.61


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

AutoCloner maintained by Alex Coulton.