Multiple sequence alignment - TraesCS7B01G261600

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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 TraesCS7B01G261600 chr7B 100.000 4028 0 0 1 4028 482091093 482087066 0.000000e+00 7439.0
1 TraesCS7B01G261600 chr7D 97.569 3208 74 2 820 4027 459801991 459798788 0.000000e+00 5489.0
2 TraesCS7B01G261600 chr7D 93.651 315 14 2 1 309 459802420 459802106 2.190000e-127 466.0
3 TraesCS7B01G261600 chr7D 85.549 173 15 7 384 550 480048974 480049142 5.350000e-39 172.0
4 TraesCS7B01G261600 chr7D 87.654 81 8 1 674 752 459802096 459802016 4.290000e-15 93.5
5 TraesCS7B01G261600 chr7A 97.475 2693 63 2 804 3496 539712251 539714938 0.000000e+00 4591.0
6 TraesCS7B01G261600 chr7A 96.324 544 17 1 3485 4028 539715124 539715664 0.000000e+00 891.0
7 TraesCS7B01G261600 chr6A 86.062 452 52 4 2132 2582 300213760 300213319 3.640000e-130 475.0
8 TraesCS7B01G261600 chr6A 86.139 101 14 0 3005 3105 300213294 300213194 4.260000e-20 110.0
9 TraesCS7B01G261600 chr6D 89.535 172 9 4 384 553 115876838 115877002 4.080000e-50 209.0
10 TraesCS7B01G261600 chr2B 88.824 170 16 2 387 553 334937897 334937728 5.280000e-49 206.0
11 TraesCS7B01G261600 chr2B 85.380 171 17 6 387 549 82073252 82073082 1.920000e-38 171.0
12 TraesCS7B01G261600 chr1A 87.135 171 14 4 387 554 85028216 85028051 1.910000e-43 187.0
13 TraesCS7B01G261600 chr4B 86.207 174 19 4 384 553 375820620 375820792 2.470000e-42 183.0
14 TraesCS7B01G261600 chr3D 86.310 168 18 5 384 547 5368464 5368298 1.150000e-40 178.0
15 TraesCS7B01G261600 chr2A 85.465 172 22 3 384 553 311541935 311542105 4.140000e-40 176.0
16 TraesCS7B01G261600 chr6B 84.971 173 22 3 384 553 375723704 375723533 5.350000e-39 172.0


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 TraesCS7B01G261600 chr7B 482087066 482091093 4027 True 7439.000000 7439 100.0000 1 4028 1 chr7B.!!$R1 4027
1 TraesCS7B01G261600 chr7D 459798788 459802420 3632 True 2016.166667 5489 92.9580 1 4027 3 chr7D.!!$R1 4026
2 TraesCS7B01G261600 chr7A 539712251 539715664 3413 False 2741.000000 4591 96.8995 804 4028 2 chr7A.!!$F1 3224
3 TraesCS7B01G261600 chr6A 300213194 300213760 566 True 292.500000 475 86.1005 2132 3105 2 chr6A.!!$R1 973

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
870 879 0.041488 GAGACATACGCGGGACTACG 60.041 60.0 12.47 0.0 0.00 3.51 F
1896 1905 0.679505 AGTCGTTGCTAGTGCCTTCA 59.320 50.0 0.00 0.0 38.71 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2547 2556 0.738389 GCCCAAATGGTGTATGTCCG 59.262 55.000 0.0 0.0 36.04 4.79 R
3754 3959 1.134367 CTTGTGCTGATGATGGGCTTG 59.866 52.381 0.0 0.0 0.00 4.01 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
26 27 3.061601 GCGTATTTCCGTCTACGTTTAGC 60.062 47.826 0.00 0.00 41.99 3.09
35 36 3.640592 GTCTACGTTTAGCCTAGGATGC 58.359 50.000 14.75 0.12 0.00 3.91
100 101 3.312736 TTTGGTCTTTGGGCTTCTTCT 57.687 42.857 0.00 0.00 0.00 2.85
103 104 1.443802 GTCTTTGGGCTTCTTCTCCG 58.556 55.000 0.00 0.00 0.00 4.63
132 133 1.378882 GCATGGCCAGCTTCGATTCA 61.379 55.000 13.05 0.00 0.00 2.57
149 150 3.475566 TTCATTGGGAATCTAGCGAGG 57.524 47.619 0.00 0.00 0.00 4.63
216 223 2.933260 GCCGATTCACCTTCTTCTTCTC 59.067 50.000 0.00 0.00 0.00 2.87
269 276 2.509166 TCTCCTTCTGGCTTCGACTA 57.491 50.000 0.00 0.00 0.00 2.59
289 296 1.014044 GCGACTTCTCGGTCATTGCA 61.014 55.000 0.00 0.00 40.53 4.08
309 316 1.153353 CCAACAATGTTACGTCGGCT 58.847 50.000 0.00 0.00 0.00 5.52
310 317 1.127951 CCAACAATGTTACGTCGGCTC 59.872 52.381 0.00 0.00 0.00 4.70
311 318 1.795872 CAACAATGTTACGTCGGCTCA 59.204 47.619 0.00 0.00 0.00 4.26
312 319 1.710013 ACAATGTTACGTCGGCTCAG 58.290 50.000 0.00 0.00 0.00 3.35
313 320 1.000506 ACAATGTTACGTCGGCTCAGT 59.999 47.619 0.00 0.00 0.00 3.41
316 323 2.092882 GTTACGTCGGCTCAGTGGC 61.093 63.158 0.00 0.00 37.94 5.01
317 324 2.273179 TTACGTCGGCTCAGTGGCT 61.273 57.895 0.00 0.00 39.32 4.75
318 325 2.486636 TTACGTCGGCTCAGTGGCTG 62.487 60.000 0.00 6.18 39.32 4.85
319 326 4.056125 CGTCGGCTCAGTGGCTGA 62.056 66.667 10.11 10.11 44.22 4.26
321 328 2.917227 TCGGCTCAGTGGCTGACA 60.917 61.111 10.11 0.00 41.95 3.58
336 343 5.923204 TGGCTGACACAAAAATAAAATGGT 58.077 33.333 0.00 0.00 0.00 3.55
337 344 5.757320 TGGCTGACACAAAAATAAAATGGTG 59.243 36.000 0.00 0.00 0.00 4.17
338 345 5.179182 GGCTGACACAAAAATAAAATGGTGG 59.821 40.000 0.00 0.00 0.00 4.61
339 346 5.179182 GCTGACACAAAAATAAAATGGTGGG 59.821 40.000 0.00 0.00 0.00 4.61
340 347 5.059833 TGACACAAAAATAAAATGGTGGGC 58.940 37.500 0.00 0.00 0.00 5.36
341 348 4.061596 ACACAAAAATAAAATGGTGGGCG 58.938 39.130 0.00 0.00 0.00 6.13
342 349 4.061596 CACAAAAATAAAATGGTGGGCGT 58.938 39.130 0.00 0.00 0.00 5.68
343 350 4.061596 ACAAAAATAAAATGGTGGGCGTG 58.938 39.130 0.00 0.00 0.00 5.34
344 351 2.378445 AAATAAAATGGTGGGCGTGC 57.622 45.000 0.00 0.00 0.00 5.34
345 352 1.555967 AATAAAATGGTGGGCGTGCT 58.444 45.000 0.00 0.00 0.00 4.40
346 353 1.102978 ATAAAATGGTGGGCGTGCTC 58.897 50.000 0.00 0.00 0.00 4.26
347 354 0.250945 TAAAATGGTGGGCGTGCTCA 60.251 50.000 0.00 0.00 0.00 4.26
348 355 1.805428 AAAATGGTGGGCGTGCTCAC 61.805 55.000 16.42 16.42 46.11 3.51
349 356 2.697147 AAATGGTGGGCGTGCTCACT 62.697 55.000 22.92 2.76 46.08 3.41
350 357 2.697147 AATGGTGGGCGTGCTCACTT 62.697 55.000 22.92 8.96 46.08 3.16
351 358 1.836999 ATGGTGGGCGTGCTCACTTA 61.837 55.000 22.92 13.54 46.08 2.24
352 359 1.302192 GGTGGGCGTGCTCACTTAA 60.302 57.895 22.92 0.00 46.08 1.85
353 360 0.887387 GGTGGGCGTGCTCACTTAAA 60.887 55.000 22.92 0.00 46.08 1.52
354 361 0.948678 GTGGGCGTGCTCACTTAAAA 59.051 50.000 17.35 0.00 43.65 1.52
355 362 1.335496 GTGGGCGTGCTCACTTAAAAA 59.665 47.619 17.35 0.00 43.65 1.94
356 363 2.030274 GTGGGCGTGCTCACTTAAAAAT 60.030 45.455 17.35 0.00 43.65 1.82
357 364 3.189702 GTGGGCGTGCTCACTTAAAAATA 59.810 43.478 17.35 0.00 43.65 1.40
358 365 3.821600 TGGGCGTGCTCACTTAAAAATAA 59.178 39.130 0.00 0.00 0.00 1.40
359 366 4.461081 TGGGCGTGCTCACTTAAAAATAAT 59.539 37.500 0.00 0.00 0.00 1.28
360 367 5.648526 TGGGCGTGCTCACTTAAAAATAATA 59.351 36.000 0.00 0.00 0.00 0.98
361 368 6.151312 TGGGCGTGCTCACTTAAAAATAATAA 59.849 34.615 0.00 0.00 0.00 1.40
362 369 7.147983 TGGGCGTGCTCACTTAAAAATAATAAT 60.148 33.333 0.00 0.00 0.00 1.28
363 370 7.704899 GGGCGTGCTCACTTAAAAATAATAATT 59.295 33.333 0.00 0.00 0.00 1.40
364 371 9.083080 GGCGTGCTCACTTAAAAATAATAATTT 57.917 29.630 0.00 0.00 36.87 1.82
387 394 9.775854 ATTTATGGTCTATCTTCATTGAGTCTG 57.224 33.333 0.00 0.00 0.00 3.51
388 395 6.805016 ATGGTCTATCTTCATTGAGTCTGT 57.195 37.500 0.00 0.00 0.00 3.41
389 396 5.970592 TGGTCTATCTTCATTGAGTCTGTG 58.029 41.667 0.00 0.00 0.00 3.66
390 397 5.481824 TGGTCTATCTTCATTGAGTCTGTGT 59.518 40.000 0.00 0.00 0.00 3.72
391 398 6.663523 TGGTCTATCTTCATTGAGTCTGTGTA 59.336 38.462 0.00 0.00 0.00 2.90
392 399 7.148000 TGGTCTATCTTCATTGAGTCTGTGTAG 60.148 40.741 0.00 0.00 0.00 2.74
393 400 7.199766 GTCTATCTTCATTGAGTCTGTGTAGG 58.800 42.308 0.00 0.00 0.00 3.18
394 401 7.067615 GTCTATCTTCATTGAGTCTGTGTAGGA 59.932 40.741 0.00 0.00 0.00 2.94
395 402 5.392767 TCTTCATTGAGTCTGTGTAGGAC 57.607 43.478 0.00 0.00 0.00 3.85
396 403 4.832823 TCTTCATTGAGTCTGTGTAGGACA 59.167 41.667 0.00 0.00 36.29 4.02
432 439 6.798427 ACATAGTTATGTCACATCCACTCT 57.202 37.500 5.92 0.00 42.96 3.24
433 440 6.577103 ACATAGTTATGTCACATCCACTCTG 58.423 40.000 5.92 9.01 42.96 3.35
434 441 6.155221 ACATAGTTATGTCACATCCACTCTGT 59.845 38.462 12.20 12.20 42.96 3.41
435 442 5.489792 AGTTATGTCACATCCACTCTGTT 57.510 39.130 0.00 0.00 0.00 3.16
436 443 5.869579 AGTTATGTCACATCCACTCTGTTT 58.130 37.500 0.00 0.00 0.00 2.83
437 444 5.702670 AGTTATGTCACATCCACTCTGTTTG 59.297 40.000 0.00 0.00 0.00 2.93
438 445 3.558931 TGTCACATCCACTCTGTTTGT 57.441 42.857 0.00 0.00 0.00 2.83
439 446 3.205338 TGTCACATCCACTCTGTTTGTG 58.795 45.455 0.00 0.00 39.16 3.33
449 456 5.567138 CACTCTGTTTGTGGTCTCTTTTT 57.433 39.130 0.00 0.00 0.00 1.94
494 501 9.800433 TCTTGTTGTTGCATTATATATTTGTGG 57.200 29.630 0.00 0.00 0.00 4.17
495 502 8.939201 TTGTTGTTGCATTATATATTTGTGGG 57.061 30.769 0.00 0.00 0.00 4.61
496 503 8.298729 TGTTGTTGCATTATATATTTGTGGGA 57.701 30.769 0.00 0.00 0.00 4.37
497 504 8.412456 TGTTGTTGCATTATATATTTGTGGGAG 58.588 33.333 0.00 0.00 0.00 4.30
498 505 7.523293 TGTTGCATTATATATTTGTGGGAGG 57.477 36.000 0.00 0.00 0.00 4.30
499 506 7.066142 TGTTGCATTATATATTTGTGGGAGGT 58.934 34.615 0.00 0.00 0.00 3.85
500 507 7.563188 TGTTGCATTATATATTTGTGGGAGGTT 59.437 33.333 0.00 0.00 0.00 3.50
501 508 9.073475 GTTGCATTATATATTTGTGGGAGGTTA 57.927 33.333 0.00 0.00 0.00 2.85
502 509 8.862325 TGCATTATATATTTGTGGGAGGTTAG 57.138 34.615 0.00 0.00 0.00 2.34
503 510 8.664992 TGCATTATATATTTGTGGGAGGTTAGA 58.335 33.333 0.00 0.00 0.00 2.10
504 511 9.686683 GCATTATATATTTGTGGGAGGTTAGAT 57.313 33.333 0.00 0.00 0.00 1.98
508 515 4.927267 ATTTGTGGGAGGTTAGATGTGA 57.073 40.909 0.00 0.00 0.00 3.58
509 516 4.927267 TTTGTGGGAGGTTAGATGTGAT 57.073 40.909 0.00 0.00 0.00 3.06
510 517 6.575244 ATTTGTGGGAGGTTAGATGTGATA 57.425 37.500 0.00 0.00 0.00 2.15
511 518 6.575244 TTTGTGGGAGGTTAGATGTGATAT 57.425 37.500 0.00 0.00 0.00 1.63
512 519 5.808366 TGTGGGAGGTTAGATGTGATATC 57.192 43.478 0.00 0.00 0.00 1.63
513 520 4.593206 TGTGGGAGGTTAGATGTGATATCC 59.407 45.833 0.00 0.00 0.00 2.59
514 521 4.841246 GTGGGAGGTTAGATGTGATATCCT 59.159 45.833 0.00 0.00 0.00 3.24
515 522 5.308237 GTGGGAGGTTAGATGTGATATCCTT 59.692 44.000 0.00 0.00 0.00 3.36
516 523 6.497259 GTGGGAGGTTAGATGTGATATCCTTA 59.503 42.308 0.00 0.00 0.00 2.69
517 524 7.016268 GTGGGAGGTTAGATGTGATATCCTTAA 59.984 40.741 0.00 0.00 0.00 1.85
518 525 7.570982 TGGGAGGTTAGATGTGATATCCTTAAA 59.429 37.037 0.00 0.00 0.00 1.52
519 526 8.437575 GGGAGGTTAGATGTGATATCCTTAAAA 58.562 37.037 0.00 0.00 0.00 1.52
520 527 9.847224 GGAGGTTAGATGTGATATCCTTAAAAA 57.153 33.333 0.00 0.00 0.00 1.94
561 568 9.947669 TTAAACAAATTGATTTTCATTGGCTTG 57.052 25.926 0.00 0.00 0.00 4.01
562 569 6.563222 ACAAATTGATTTTCATTGGCTTGG 57.437 33.333 0.00 0.00 0.00 3.61
563 570 6.297582 ACAAATTGATTTTCATTGGCTTGGA 58.702 32.000 0.00 0.00 0.00 3.53
564 571 6.943718 ACAAATTGATTTTCATTGGCTTGGAT 59.056 30.769 0.00 0.00 0.00 3.41
565 572 6.995511 AATTGATTTTCATTGGCTTGGATG 57.004 33.333 0.00 0.00 0.00 3.51
566 573 4.475051 TGATTTTCATTGGCTTGGATGG 57.525 40.909 0.00 0.00 0.00 3.51
567 574 4.095211 TGATTTTCATTGGCTTGGATGGA 58.905 39.130 0.00 0.00 0.00 3.41
568 575 3.959535 TTTTCATTGGCTTGGATGGAC 57.040 42.857 0.00 0.00 0.00 4.02
569 576 1.851304 TTCATTGGCTTGGATGGACC 58.149 50.000 0.00 0.00 39.54 4.46
570 577 1.002069 TCATTGGCTTGGATGGACCT 58.998 50.000 0.00 0.00 39.86 3.85
571 578 1.358787 TCATTGGCTTGGATGGACCTT 59.641 47.619 0.00 0.00 39.86 3.50
572 579 2.580322 TCATTGGCTTGGATGGACCTTA 59.420 45.455 0.00 0.00 39.86 2.69
573 580 3.011144 TCATTGGCTTGGATGGACCTTAA 59.989 43.478 0.00 0.00 39.86 1.85
574 581 3.534357 TTGGCTTGGATGGACCTTAAA 57.466 42.857 0.00 0.00 39.86 1.52
575 582 3.534357 TGGCTTGGATGGACCTTAAAA 57.466 42.857 0.00 0.00 39.86 1.52
576 583 3.850752 TGGCTTGGATGGACCTTAAAAA 58.149 40.909 0.00 0.00 39.86 1.94
577 584 4.424842 TGGCTTGGATGGACCTTAAAAAT 58.575 39.130 0.00 0.00 39.86 1.82
578 585 4.466015 TGGCTTGGATGGACCTTAAAAATC 59.534 41.667 0.00 0.00 39.86 2.17
579 586 4.466015 GGCTTGGATGGACCTTAAAAATCA 59.534 41.667 0.00 0.00 39.86 2.57
580 587 5.394553 GGCTTGGATGGACCTTAAAAATCAG 60.395 44.000 0.00 0.00 39.86 2.90
581 588 5.418840 GCTTGGATGGACCTTAAAAATCAGA 59.581 40.000 0.00 0.00 39.86 3.27
582 589 6.071391 GCTTGGATGGACCTTAAAAATCAGAA 60.071 38.462 0.00 0.00 39.86 3.02
583 590 7.525360 GCTTGGATGGACCTTAAAAATCAGAAA 60.525 37.037 0.00 0.00 39.86 2.52
584 591 7.466746 TGGATGGACCTTAAAAATCAGAAAG 57.533 36.000 0.00 0.00 39.86 2.62
585 592 7.010160 TGGATGGACCTTAAAAATCAGAAAGT 58.990 34.615 0.00 0.00 39.86 2.66
586 593 7.508977 TGGATGGACCTTAAAAATCAGAAAGTT 59.491 33.333 0.00 0.00 39.86 2.66
587 594 9.020731 GGATGGACCTTAAAAATCAGAAAGTTA 57.979 33.333 0.00 0.00 35.41 2.24
632 639 5.720371 TTAAAATTCTGGGTGTGACATGG 57.280 39.130 0.00 0.00 0.00 3.66
633 640 1.549203 AATTCTGGGTGTGACATGGC 58.451 50.000 0.00 0.00 0.00 4.40
634 641 0.405198 ATTCTGGGTGTGACATGGCA 59.595 50.000 0.00 0.00 0.00 4.92
635 642 0.537143 TTCTGGGTGTGACATGGCAC 60.537 55.000 25.46 25.46 39.22 5.01
636 643 2.281414 TGGGTGTGACATGGCACG 60.281 61.111 26.22 0.00 41.63 5.34
637 644 3.737172 GGGTGTGACATGGCACGC 61.737 66.667 32.85 32.85 45.87 5.34
639 646 3.737172 GTGTGACATGGCACGCCC 61.737 66.667 31.12 15.97 42.01 6.13
652 659 3.066190 CGCCCGACACACCCTCTA 61.066 66.667 0.00 0.00 0.00 2.43
653 660 2.893398 GCCCGACACACCCTCTAG 59.107 66.667 0.00 0.00 0.00 2.43
654 661 2.722201 GCCCGACACACCCTCTAGG 61.722 68.421 0.00 0.00 43.78 3.02
663 670 4.680487 CCCTCTAGGTACGCCACT 57.320 61.111 0.00 0.00 37.19 4.00
664 671 2.416901 CCCTCTAGGTACGCCACTC 58.583 63.158 0.00 0.00 37.19 3.51
665 672 1.108132 CCCTCTAGGTACGCCACTCC 61.108 65.000 0.00 0.00 37.19 3.85
666 673 1.108132 CCTCTAGGTACGCCACTCCC 61.108 65.000 0.00 0.00 37.19 4.30
667 674 0.106619 CTCTAGGTACGCCACTCCCT 60.107 60.000 0.00 0.00 37.19 4.20
668 675 0.106819 TCTAGGTACGCCACTCCCTC 60.107 60.000 0.00 0.00 37.19 4.30
669 676 0.395311 CTAGGTACGCCACTCCCTCA 60.395 60.000 0.00 0.00 37.19 3.86
670 677 0.395311 TAGGTACGCCACTCCCTCAG 60.395 60.000 0.00 0.00 37.19 3.35
671 678 2.184579 GTACGCCACTCCCTCAGC 59.815 66.667 0.00 0.00 0.00 4.26
672 679 2.037367 TACGCCACTCCCTCAGCT 59.963 61.111 0.00 0.00 0.00 4.24
679 686 0.260230 CACTCCCTCAGCTCCTAGGA 59.740 60.000 11.98 11.98 34.58 2.94
681 688 2.109128 CACTCCCTCAGCTCCTAGGATA 59.891 54.545 13.12 0.00 34.58 2.59
682 689 2.109304 ACTCCCTCAGCTCCTAGGATAC 59.891 54.545 13.12 7.92 34.58 2.24
753 762 4.509737 GGCGAGTGCGGTAGGGAC 62.510 72.222 0.00 0.00 44.10 4.46
754 763 4.509737 GCGAGTGCGGTAGGGACC 62.510 72.222 0.00 0.00 43.03 4.46
771 780 4.141883 CGTAGGGTGACGAACGTG 57.858 61.111 4.19 0.00 45.82 4.49
772 781 1.443194 CGTAGGGTGACGAACGTGG 60.443 63.158 4.19 0.00 45.82 4.94
773 782 1.855213 CGTAGGGTGACGAACGTGGA 61.855 60.000 4.19 0.00 45.82 4.02
774 783 0.529378 GTAGGGTGACGAACGTGGAT 59.471 55.000 4.19 0.00 0.00 3.41
775 784 1.745087 GTAGGGTGACGAACGTGGATA 59.255 52.381 4.19 0.00 0.00 2.59
776 785 1.481871 AGGGTGACGAACGTGGATAT 58.518 50.000 4.19 0.00 0.00 1.63
777 786 2.658285 AGGGTGACGAACGTGGATATA 58.342 47.619 4.19 0.00 0.00 0.86
778 787 3.025978 AGGGTGACGAACGTGGATATAA 58.974 45.455 4.19 0.00 0.00 0.98
779 788 3.118542 GGGTGACGAACGTGGATATAAC 58.881 50.000 4.19 0.00 0.00 1.89
780 789 3.118542 GGTGACGAACGTGGATATAACC 58.881 50.000 4.19 0.00 0.00 2.85
781 790 3.429272 GGTGACGAACGTGGATATAACCA 60.429 47.826 4.19 0.00 37.63 3.67
782 791 4.175516 GTGACGAACGTGGATATAACCAA 58.824 43.478 2.84 0.00 41.87 3.67
796 805 7.051623 GGATATAACCAAGGACATGTGTTGTA 58.948 38.462 1.15 4.02 39.18 2.41
797 806 7.012044 GGATATAACCAAGGACATGTGTTGTAC 59.988 40.741 1.15 0.00 39.18 2.90
798 807 3.569194 ACCAAGGACATGTGTTGTACA 57.431 42.857 1.15 0.00 42.18 2.90
817 826 6.282167 TGTACACACAACGGAGAAAAATAGA 58.718 36.000 0.00 0.00 0.00 1.98
818 827 5.924475 ACACACAACGGAGAAAAATAGAG 57.076 39.130 0.00 0.00 0.00 2.43
833 842 4.468095 AATAGAGCACACACAACGAAAC 57.532 40.909 0.00 0.00 0.00 2.78
860 869 2.765108 ATCAGCAGTCGAGACATACG 57.235 50.000 5.99 0.00 0.00 3.06
870 879 0.041488 GAGACATACGCGGGACTACG 60.041 60.000 12.47 0.00 0.00 3.51
1056 1065 1.152139 CCTCCCCCTCATCCTCCTC 60.152 68.421 0.00 0.00 0.00 3.71
1695 1704 2.043450 CTCGCCCCTCTCTGGACT 60.043 66.667 0.00 0.00 38.35 3.85
1896 1905 0.679505 AGTCGTTGCTAGTGCCTTCA 59.320 50.000 0.00 0.00 38.71 3.02
2013 2022 2.823924 TTGAACAGTCGATTCGGGAA 57.176 45.000 6.18 0.00 0.00 3.97
2040 2049 3.313874 CCCTTCGATGGGCAGAGT 58.686 61.111 22.35 0.00 40.84 3.24
2046 2055 2.787473 TCGATGGGCAGAGTTTGAAT 57.213 45.000 0.00 0.00 0.00 2.57
2061 2070 6.018507 AGAGTTTGAATTTTGATTTGCACAGC 60.019 34.615 0.00 0.00 0.00 4.40
2064 2073 3.490155 TGAATTTTGATTTGCACAGCGTG 59.510 39.130 4.61 4.61 36.51 5.34
2397 2406 2.802057 GCAAACGGTCAGTGACTACAGT 60.802 50.000 22.18 14.03 32.47 3.55
2406 2415 5.279306 GGTCAGTGACTACAGTTGTAATGGA 60.279 44.000 22.18 0.00 32.47 3.41
2413 2422 3.620427 ACAGTTGTAATGGACGGCATA 57.380 42.857 0.00 0.00 0.00 3.14
2547 2556 2.159627 CGTTGATTACACTTGGAGCACC 59.840 50.000 0.00 0.00 0.00 5.01
2868 2877 5.574891 TGTATGCCATTTACATGTTGGTC 57.425 39.130 14.95 8.93 32.90 4.02
3072 3081 5.938125 GGTGGATACTACTTGAAAGCTTCAA 59.062 40.000 0.00 5.34 42.14 2.69
3243 3252 9.616156 TTCCACTTGTCTTGTAAGTTTAATGTA 57.384 29.630 0.00 0.00 36.29 2.29
3326 3335 4.202245 TGTTGACTAGCATGTTCCCTAC 57.798 45.455 0.00 0.00 0.00 3.18
3351 3360 0.179113 TCGCTGCGTGCATTCTATGA 60.179 50.000 22.48 0.00 43.06 2.15
3560 3765 8.152309 ACTATCTTTACTACTAAGTAGTGCCG 57.848 38.462 10.57 2.43 46.99 5.69
3564 3769 5.808042 TTACTACTAAGTAGTGCCGTCAG 57.192 43.478 10.57 1.94 46.99 3.51
3592 3797 6.971527 TTGTATGGTAGGATTTGTGTTACG 57.028 37.500 0.00 0.00 0.00 3.18
3600 3805 4.091549 AGGATTTGTGTTACGTAGGGAGA 58.908 43.478 0.00 0.00 0.00 3.71
3627 3832 9.755122 AAACCCTTCTTGTCTTTATATTAAGCT 57.245 29.630 0.00 0.00 0.00 3.74
3722 3927 3.515502 TGTCCTGCTGCTTGATTAGTACT 59.484 43.478 0.00 0.00 0.00 2.73
3726 3931 5.656859 TCCTGCTGCTTGATTAGTACTCTAA 59.343 40.000 0.00 0.00 39.95 2.10
3774 3979 1.134367 CAAGCCCATCATCAGCACAAG 59.866 52.381 0.00 0.00 0.00 3.16
3816 4021 9.606631 GTGAGAAATCTAAACTGTAGGAATGAT 57.393 33.333 0.00 0.00 0.00 2.45
3854 4059 5.180492 TGACAGGTTAACCAAAAAGCTATCG 59.820 40.000 26.26 2.79 32.03 2.92
3909 4114 6.293735 GGAGATTTTACGTGATGGTCAAAACA 60.294 38.462 0.00 0.00 0.00 2.83
3998 4203 6.423302 CCATATAGAACAACTGATGTCTGCTC 59.577 42.308 0.00 0.00 42.99 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.671251 GTCGTCCAGAGCATCCTAGG 59.329 60.000 0.82 0.82 33.66 3.02
51 52 5.670792 ACCATAGTTGTCCACTTTATCGA 57.329 39.130 0.00 0.00 36.88 3.59
100 101 1.815003 CCATGCATCGTTGAGCGGA 60.815 57.895 0.00 0.00 41.72 5.54
103 104 2.332362 CTGGCCATGCATCGTTGAGC 62.332 60.000 5.51 0.00 0.00 4.26
132 133 4.409247 ACTTTACCTCGCTAGATTCCCAAT 59.591 41.667 0.00 0.00 0.00 3.16
149 150 2.298163 TGACAGAACCGGGAGACTTTAC 59.702 50.000 6.32 0.00 0.00 2.01
199 200 2.237392 CCCGGAGAAGAAGAAGGTGAAT 59.763 50.000 0.73 0.00 0.00 2.57
216 223 2.717639 AGACCAAATTCTCATCCCGG 57.282 50.000 0.00 0.00 0.00 5.73
229 236 3.201353 TGGTGATGAACGAAAGACCAA 57.799 42.857 0.00 0.00 30.54 3.67
269 276 0.737715 GCAATGACCGAGAAGTCGCT 60.738 55.000 0.00 0.00 45.41 4.93
285 292 2.286477 CGACGTAACATTGTTGGTGCAA 60.286 45.455 12.30 0.00 0.00 4.08
287 294 1.399215 CCGACGTAACATTGTTGGTGC 60.399 52.381 12.30 4.42 35.31 5.01
289 296 0.869730 GCCGACGTAACATTGTTGGT 59.130 50.000 12.30 9.61 41.04 3.67
303 310 2.433318 GTCAGCCACTGAGCCGAC 60.433 66.667 0.00 0.00 41.46 4.79
309 316 5.843673 TTTATTTTTGTGTCAGCCACTGA 57.156 34.783 0.00 0.00 44.81 3.41
310 317 6.073657 CCATTTTATTTTTGTGTCAGCCACTG 60.074 38.462 0.00 0.00 44.81 3.66
311 318 5.990996 CCATTTTATTTTTGTGTCAGCCACT 59.009 36.000 0.00 0.00 44.81 4.00
312 319 5.757808 ACCATTTTATTTTTGTGTCAGCCAC 59.242 36.000 0.00 0.00 44.78 5.01
313 320 5.757320 CACCATTTTATTTTTGTGTCAGCCA 59.243 36.000 0.00 0.00 0.00 4.75
316 323 5.179182 GCCCACCATTTTATTTTTGTGTCAG 59.821 40.000 0.00 0.00 0.00 3.51
317 324 5.059833 GCCCACCATTTTATTTTTGTGTCA 58.940 37.500 0.00 0.00 0.00 3.58
318 325 4.151512 CGCCCACCATTTTATTTTTGTGTC 59.848 41.667 0.00 0.00 0.00 3.67
319 326 4.061596 CGCCCACCATTTTATTTTTGTGT 58.938 39.130 0.00 0.00 0.00 3.72
320 327 4.061596 ACGCCCACCATTTTATTTTTGTG 58.938 39.130 0.00 0.00 0.00 3.33
321 328 4.061596 CACGCCCACCATTTTATTTTTGT 58.938 39.130 0.00 0.00 0.00 2.83
322 329 3.120373 GCACGCCCACCATTTTATTTTTG 60.120 43.478 0.00 0.00 0.00 2.44
323 330 3.070748 GCACGCCCACCATTTTATTTTT 58.929 40.909 0.00 0.00 0.00 1.94
324 331 2.301583 AGCACGCCCACCATTTTATTTT 59.698 40.909 0.00 0.00 0.00 1.82
325 332 1.899142 AGCACGCCCACCATTTTATTT 59.101 42.857 0.00 0.00 0.00 1.40
326 333 1.476488 GAGCACGCCCACCATTTTATT 59.524 47.619 0.00 0.00 0.00 1.40
327 334 1.102978 GAGCACGCCCACCATTTTAT 58.897 50.000 0.00 0.00 0.00 1.40
328 335 0.250945 TGAGCACGCCCACCATTTTA 60.251 50.000 0.00 0.00 0.00 1.52
329 336 1.530419 TGAGCACGCCCACCATTTT 60.530 52.632 0.00 0.00 0.00 1.82
330 337 2.115052 TGAGCACGCCCACCATTT 59.885 55.556 0.00 0.00 0.00 2.32
331 338 2.672996 GTGAGCACGCCCACCATT 60.673 61.111 0.00 0.00 0.00 3.16
332 339 1.836999 TAAGTGAGCACGCCCACCAT 61.837 55.000 0.00 0.00 36.20 3.55
333 340 2.046009 TTAAGTGAGCACGCCCACCA 62.046 55.000 0.00 0.00 36.20 4.17
334 341 0.887387 TTTAAGTGAGCACGCCCACC 60.887 55.000 0.00 0.00 36.20 4.61
335 342 0.948678 TTTTAAGTGAGCACGCCCAC 59.051 50.000 0.00 0.00 36.20 4.61
336 343 1.681538 TTTTTAAGTGAGCACGCCCA 58.318 45.000 0.00 0.00 36.20 5.36
337 344 4.428615 TTATTTTTAAGTGAGCACGCCC 57.571 40.909 0.00 0.00 36.20 6.13
338 345 8.628882 AATTATTATTTTTAAGTGAGCACGCC 57.371 30.769 0.00 0.00 36.20 5.68
361 368 9.775854 CAGACTCAATGAAGATAGACCATAAAT 57.224 33.333 0.00 0.00 0.00 1.40
362 369 8.762645 ACAGACTCAATGAAGATAGACCATAAA 58.237 33.333 0.00 0.00 0.00 1.40
363 370 8.200120 CACAGACTCAATGAAGATAGACCATAA 58.800 37.037 0.00 0.00 0.00 1.90
364 371 7.343057 ACACAGACTCAATGAAGATAGACCATA 59.657 37.037 0.00 0.00 0.00 2.74
365 372 6.155910 ACACAGACTCAATGAAGATAGACCAT 59.844 38.462 0.00 0.00 0.00 3.55
366 373 5.481824 ACACAGACTCAATGAAGATAGACCA 59.518 40.000 0.00 0.00 0.00 4.02
367 374 5.971763 ACACAGACTCAATGAAGATAGACC 58.028 41.667 0.00 0.00 0.00 3.85
368 375 7.067615 TCCTACACAGACTCAATGAAGATAGAC 59.932 40.741 0.00 0.00 0.00 2.59
369 376 7.067615 GTCCTACACAGACTCAATGAAGATAGA 59.932 40.741 0.00 0.00 0.00 1.98
370 377 7.148000 TGTCCTACACAGACTCAATGAAGATAG 60.148 40.741 0.00 0.00 35.21 2.08
371 378 6.663523 TGTCCTACACAGACTCAATGAAGATA 59.336 38.462 0.00 0.00 35.21 1.98
372 379 5.481824 TGTCCTACACAGACTCAATGAAGAT 59.518 40.000 0.00 0.00 35.21 2.40
373 380 4.832823 TGTCCTACACAGACTCAATGAAGA 59.167 41.667 0.00 0.00 35.21 2.87
374 381 5.139435 TGTCCTACACAGACTCAATGAAG 57.861 43.478 0.00 0.00 35.21 3.02
410 417 6.577103 ACAGAGTGGATGTGACATAACTATG 58.423 40.000 23.16 23.16 39.55 2.23
411 418 6.798427 ACAGAGTGGATGTGACATAACTAT 57.202 37.500 11.93 7.54 0.00 2.12
412 419 6.605471 AACAGAGTGGATGTGACATAACTA 57.395 37.500 11.93 0.00 0.00 2.24
413 420 5.489792 AACAGAGTGGATGTGACATAACT 57.510 39.130 11.82 11.82 0.00 2.24
414 421 5.470098 ACAAACAGAGTGGATGTGACATAAC 59.530 40.000 0.00 0.07 0.00 1.89
415 422 5.469760 CACAAACAGAGTGGATGTGACATAA 59.530 40.000 0.00 0.00 39.10 1.90
416 423 4.996758 CACAAACAGAGTGGATGTGACATA 59.003 41.667 0.00 0.00 39.10 2.29
417 424 3.817084 CACAAACAGAGTGGATGTGACAT 59.183 43.478 0.00 0.00 39.10 3.06
418 425 3.205338 CACAAACAGAGTGGATGTGACA 58.795 45.455 8.01 0.00 39.10 3.58
419 426 3.885484 CACAAACAGAGTGGATGTGAC 57.115 47.619 8.01 0.00 39.10 3.67
427 434 5.567138 AAAAAGAGACCACAAACAGAGTG 57.433 39.130 0.00 0.00 36.76 3.51
468 475 9.800433 CCACAAATATATAATGCAACAACAAGA 57.200 29.630 0.00 0.00 0.00 3.02
469 476 9.033481 CCCACAAATATATAATGCAACAACAAG 57.967 33.333 0.00 0.00 0.00 3.16
470 477 8.753133 TCCCACAAATATATAATGCAACAACAA 58.247 29.630 0.00 0.00 0.00 2.83
471 478 8.298729 TCCCACAAATATATAATGCAACAACA 57.701 30.769 0.00 0.00 0.00 3.33
472 479 7.867403 CCTCCCACAAATATATAATGCAACAAC 59.133 37.037 0.00 0.00 0.00 3.32
473 480 7.563188 ACCTCCCACAAATATATAATGCAACAA 59.437 33.333 0.00 0.00 0.00 2.83
474 481 7.066142 ACCTCCCACAAATATATAATGCAACA 58.934 34.615 0.00 0.00 0.00 3.33
475 482 7.524717 ACCTCCCACAAATATATAATGCAAC 57.475 36.000 0.00 0.00 0.00 4.17
476 483 9.295825 CTAACCTCCCACAAATATATAATGCAA 57.704 33.333 0.00 0.00 0.00 4.08
477 484 8.664992 TCTAACCTCCCACAAATATATAATGCA 58.335 33.333 0.00 0.00 0.00 3.96
478 485 9.686683 ATCTAACCTCCCACAAATATATAATGC 57.313 33.333 0.00 0.00 0.00 3.56
482 489 9.387397 TCACATCTAACCTCCCACAAATATATA 57.613 33.333 0.00 0.00 0.00 0.86
483 490 8.275187 TCACATCTAACCTCCCACAAATATAT 57.725 34.615 0.00 0.00 0.00 0.86
484 491 7.684317 TCACATCTAACCTCCCACAAATATA 57.316 36.000 0.00 0.00 0.00 0.86
485 492 6.575244 TCACATCTAACCTCCCACAAATAT 57.425 37.500 0.00 0.00 0.00 1.28
486 493 6.575244 ATCACATCTAACCTCCCACAAATA 57.425 37.500 0.00 0.00 0.00 1.40
487 494 4.927267 TCACATCTAACCTCCCACAAAT 57.073 40.909 0.00 0.00 0.00 2.32
488 495 4.927267 ATCACATCTAACCTCCCACAAA 57.073 40.909 0.00 0.00 0.00 2.83
489 496 5.071788 GGATATCACATCTAACCTCCCACAA 59.928 44.000 4.83 0.00 0.00 3.33
490 497 4.593206 GGATATCACATCTAACCTCCCACA 59.407 45.833 4.83 0.00 0.00 4.17
491 498 4.841246 AGGATATCACATCTAACCTCCCAC 59.159 45.833 4.83 0.00 0.00 4.61
492 499 5.093236 AGGATATCACATCTAACCTCCCA 57.907 43.478 4.83 0.00 0.00 4.37
493 500 7.554959 TTAAGGATATCACATCTAACCTCCC 57.445 40.000 4.83 0.00 0.00 4.30
494 501 9.847224 TTTTTAAGGATATCACATCTAACCTCC 57.153 33.333 4.83 0.00 0.00 4.30
535 542 9.947669 CAAGCCAATGAAAATCAATTTGTTTAA 57.052 25.926 0.00 0.00 0.00 1.52
536 543 8.566260 CCAAGCCAATGAAAATCAATTTGTTTA 58.434 29.630 0.00 0.00 0.00 2.01
537 544 7.284944 TCCAAGCCAATGAAAATCAATTTGTTT 59.715 29.630 0.00 0.00 0.00 2.83
538 545 6.771749 TCCAAGCCAATGAAAATCAATTTGTT 59.228 30.769 0.00 0.00 0.00 2.83
539 546 6.297582 TCCAAGCCAATGAAAATCAATTTGT 58.702 32.000 0.00 0.00 0.00 2.83
540 547 6.804770 TCCAAGCCAATGAAAATCAATTTG 57.195 33.333 0.00 0.00 0.00 2.32
541 548 6.376018 CCATCCAAGCCAATGAAAATCAATTT 59.624 34.615 0.00 0.00 0.00 1.82
542 549 5.883673 CCATCCAAGCCAATGAAAATCAATT 59.116 36.000 0.00 0.00 0.00 2.32
543 550 5.190132 TCCATCCAAGCCAATGAAAATCAAT 59.810 36.000 0.00 0.00 0.00 2.57
544 551 4.531339 TCCATCCAAGCCAATGAAAATCAA 59.469 37.500 0.00 0.00 0.00 2.57
545 552 4.081531 GTCCATCCAAGCCAATGAAAATCA 60.082 41.667 0.00 0.00 0.00 2.57
546 553 4.436332 GTCCATCCAAGCCAATGAAAATC 58.564 43.478 0.00 0.00 0.00 2.17
547 554 3.198417 GGTCCATCCAAGCCAATGAAAAT 59.802 43.478 0.00 0.00 35.97 1.82
548 555 2.566724 GGTCCATCCAAGCCAATGAAAA 59.433 45.455 0.00 0.00 35.97 2.29
549 556 2.178580 GGTCCATCCAAGCCAATGAAA 58.821 47.619 0.00 0.00 35.97 2.69
550 557 1.358787 AGGTCCATCCAAGCCAATGAA 59.641 47.619 0.00 0.00 39.02 2.57
551 558 1.002069 AGGTCCATCCAAGCCAATGA 58.998 50.000 0.00 0.00 39.02 2.57
552 559 1.856629 AAGGTCCATCCAAGCCAATG 58.143 50.000 0.00 0.00 39.02 2.82
553 560 3.756082 TTAAGGTCCATCCAAGCCAAT 57.244 42.857 0.00 0.00 39.02 3.16
554 561 3.534357 TTTAAGGTCCATCCAAGCCAA 57.466 42.857 0.00 0.00 39.02 4.52
555 562 3.534357 TTTTAAGGTCCATCCAAGCCA 57.466 42.857 0.00 0.00 39.02 4.75
556 563 4.466015 TGATTTTTAAGGTCCATCCAAGCC 59.534 41.667 0.00 0.00 39.02 4.35
557 564 5.418840 TCTGATTTTTAAGGTCCATCCAAGC 59.581 40.000 0.00 0.00 39.02 4.01
558 565 7.466746 TTCTGATTTTTAAGGTCCATCCAAG 57.533 36.000 0.00 0.00 39.02 3.61
559 566 7.508977 ACTTTCTGATTTTTAAGGTCCATCCAA 59.491 33.333 0.00 0.00 39.02 3.53
560 567 7.010160 ACTTTCTGATTTTTAAGGTCCATCCA 58.990 34.615 0.00 0.00 39.02 3.41
561 568 7.468141 ACTTTCTGATTTTTAAGGTCCATCC 57.532 36.000 0.00 0.00 0.00 3.51
607 614 6.989169 CCATGTCACACCCAGAATTTTAAAAA 59.011 34.615 4.44 0.00 0.00 1.94
608 615 6.520272 CCATGTCACACCCAGAATTTTAAAA 58.480 36.000 2.51 2.51 0.00 1.52
609 616 5.510520 GCCATGTCACACCCAGAATTTTAAA 60.511 40.000 0.00 0.00 0.00 1.52
610 617 4.021544 GCCATGTCACACCCAGAATTTTAA 60.022 41.667 0.00 0.00 0.00 1.52
611 618 3.509575 GCCATGTCACACCCAGAATTTTA 59.490 43.478 0.00 0.00 0.00 1.52
612 619 2.299867 GCCATGTCACACCCAGAATTTT 59.700 45.455 0.00 0.00 0.00 1.82
613 620 1.895131 GCCATGTCACACCCAGAATTT 59.105 47.619 0.00 0.00 0.00 1.82
614 621 1.203038 TGCCATGTCACACCCAGAATT 60.203 47.619 0.00 0.00 0.00 2.17
615 622 0.405198 TGCCATGTCACACCCAGAAT 59.595 50.000 0.00 0.00 0.00 2.40
616 623 0.537143 GTGCCATGTCACACCCAGAA 60.537 55.000 1.15 0.00 36.97 3.02
617 624 1.073025 GTGCCATGTCACACCCAGA 59.927 57.895 1.15 0.00 36.97 3.86
618 625 2.327343 CGTGCCATGTCACACCCAG 61.327 63.158 7.75 0.00 36.80 4.45
619 626 2.281414 CGTGCCATGTCACACCCA 60.281 61.111 7.75 0.00 36.80 4.51
620 627 3.737172 GCGTGCCATGTCACACCC 61.737 66.667 7.75 0.00 36.80 4.61
621 628 3.737172 GGCGTGCCATGTCACACC 61.737 66.667 7.75 2.59 36.80 4.16
622 629 3.737172 GGGCGTGCCATGTCACAC 61.737 66.667 13.76 4.36 36.80 3.82
634 641 3.873679 TAGAGGGTGTGTCGGGCGT 62.874 63.158 0.00 0.00 0.00 5.68
635 642 3.064987 CTAGAGGGTGTGTCGGGCG 62.065 68.421 0.00 0.00 0.00 6.13
636 643 2.722201 CCTAGAGGGTGTGTCGGGC 61.722 68.421 0.00 0.00 0.00 6.13
637 644 3.617368 CCTAGAGGGTGTGTCGGG 58.383 66.667 0.00 0.00 0.00 5.14
646 653 1.108132 GGAGTGGCGTACCTAGAGGG 61.108 65.000 0.00 0.00 40.27 4.30
647 654 1.108132 GGGAGTGGCGTACCTAGAGG 61.108 65.000 0.00 0.00 42.17 3.69
648 655 0.106619 AGGGAGTGGCGTACCTAGAG 60.107 60.000 0.00 0.00 36.63 2.43
649 656 0.106819 GAGGGAGTGGCGTACCTAGA 60.107 60.000 0.00 0.00 36.63 2.43
650 657 0.395311 TGAGGGAGTGGCGTACCTAG 60.395 60.000 0.00 0.00 36.63 3.02
651 658 0.395311 CTGAGGGAGTGGCGTACCTA 60.395 60.000 0.00 0.00 36.63 3.08
652 659 1.682684 CTGAGGGAGTGGCGTACCT 60.683 63.158 0.00 0.00 36.63 3.08
653 660 2.893398 CTGAGGGAGTGGCGTACC 59.107 66.667 0.00 0.00 0.00 3.34
654 661 2.184579 GCTGAGGGAGTGGCGTAC 59.815 66.667 0.00 0.00 0.00 3.67
655 662 2.037367 AGCTGAGGGAGTGGCGTA 59.963 61.111 0.00 0.00 0.00 4.42
656 663 3.386237 GAGCTGAGGGAGTGGCGT 61.386 66.667 0.00 0.00 0.00 5.68
657 664 4.154347 GGAGCTGAGGGAGTGGCG 62.154 72.222 0.00 0.00 0.00 5.69
658 665 1.381872 TAGGAGCTGAGGGAGTGGC 60.382 63.158 0.00 0.00 0.00 5.01
659 666 0.758685 CCTAGGAGCTGAGGGAGTGG 60.759 65.000 1.05 0.00 0.00 4.00
660 667 0.260230 TCCTAGGAGCTGAGGGAGTG 59.740 60.000 7.62 0.00 33.27 3.51
661 668 1.240527 ATCCTAGGAGCTGAGGGAGT 58.759 55.000 18.34 0.00 33.27 3.85
662 669 2.378547 AGTATCCTAGGAGCTGAGGGAG 59.621 54.545 18.34 0.00 33.27 4.30
663 670 2.377193 GAGTATCCTAGGAGCTGAGGGA 59.623 54.545 18.34 0.00 33.27 4.20
664 671 2.802719 GAGTATCCTAGGAGCTGAGGG 58.197 57.143 18.34 0.00 33.27 4.30
698 705 3.125829 CCATGAACAGAGTTTGATGTCGG 59.874 47.826 0.00 0.00 0.00 4.79
708 715 3.679917 CGTGCTATTCCCATGAACAGAGT 60.680 47.826 0.00 0.00 32.13 3.24
752 761 1.898574 ACGTTCGTCACCCTACGGT 60.899 57.895 0.00 0.00 46.31 4.83
753 762 1.443194 CACGTTCGTCACCCTACGG 60.443 63.158 0.00 0.00 43.05 4.02
754 763 1.443194 CCACGTTCGTCACCCTACG 60.443 63.158 0.00 0.00 44.19 3.51
756 765 2.127271 TATCCACGTTCGTCACCCTA 57.873 50.000 0.00 0.00 0.00 3.53
758 767 3.118542 GTTATATCCACGTTCGTCACCC 58.881 50.000 0.00 0.00 0.00 4.61
759 768 3.118542 GGTTATATCCACGTTCGTCACC 58.881 50.000 0.00 0.00 0.00 4.02
762 771 3.800506 CCTTGGTTATATCCACGTTCGTC 59.199 47.826 1.78 0.00 37.20 4.20
763 772 3.448301 TCCTTGGTTATATCCACGTTCGT 59.552 43.478 1.78 0.00 37.20 3.85
764 773 3.800506 GTCCTTGGTTATATCCACGTTCG 59.199 47.826 1.78 0.00 37.20 3.95
765 774 4.761975 TGTCCTTGGTTATATCCACGTTC 58.238 43.478 1.78 0.00 37.20 3.95
766 775 4.829872 TGTCCTTGGTTATATCCACGTT 57.170 40.909 1.78 0.00 37.20 3.99
767 776 4.163458 ACATGTCCTTGGTTATATCCACGT 59.837 41.667 1.78 0.00 37.20 4.49
768 777 4.511454 CACATGTCCTTGGTTATATCCACG 59.489 45.833 0.00 0.98 37.20 4.94
769 778 5.437060 ACACATGTCCTTGGTTATATCCAC 58.563 41.667 0.00 0.00 37.20 4.02
770 779 5.708736 ACACATGTCCTTGGTTATATCCA 57.291 39.130 0.00 0.00 35.49 3.41
771 780 5.885912 ACAACACATGTCCTTGGTTATATCC 59.114 40.000 14.51 0.00 37.96 2.59
772 781 7.551262 TGTACAACACATGTCCTTGGTTATATC 59.449 37.037 14.51 2.32 42.70 1.63
773 782 7.398829 TGTACAACACATGTCCTTGGTTATAT 58.601 34.615 14.51 1.74 42.70 0.86
774 783 6.770542 TGTACAACACATGTCCTTGGTTATA 58.229 36.000 14.51 0.21 42.70 0.98
775 784 5.626142 TGTACAACACATGTCCTTGGTTAT 58.374 37.500 14.51 1.04 42.70 1.89
776 785 5.037383 TGTACAACACATGTCCTTGGTTA 57.963 39.130 14.51 0.58 42.70 2.85
777 786 3.892284 TGTACAACACATGTCCTTGGTT 58.108 40.909 14.51 5.46 42.70 3.67
778 787 3.569194 TGTACAACACATGTCCTTGGT 57.431 42.857 14.51 0.00 42.70 3.67
796 805 4.213482 GCTCTATTTTTCTCCGTTGTGTGT 59.787 41.667 0.00 0.00 0.00 3.72
797 806 4.213270 TGCTCTATTTTTCTCCGTTGTGTG 59.787 41.667 0.00 0.00 0.00 3.82
798 807 4.213482 GTGCTCTATTTTTCTCCGTTGTGT 59.787 41.667 0.00 0.00 0.00 3.72
799 808 4.213270 TGTGCTCTATTTTTCTCCGTTGTG 59.787 41.667 0.00 0.00 0.00 3.33
800 809 4.213482 GTGTGCTCTATTTTTCTCCGTTGT 59.787 41.667 0.00 0.00 0.00 3.32
801 810 4.213270 TGTGTGCTCTATTTTTCTCCGTTG 59.787 41.667 0.00 0.00 0.00 4.10
802 811 4.213482 GTGTGTGCTCTATTTTTCTCCGTT 59.787 41.667 0.00 0.00 0.00 4.44
817 826 3.202906 ACTATGTTTCGTTGTGTGTGCT 58.797 40.909 0.00 0.00 0.00 4.40
818 827 3.001838 TGACTATGTTTCGTTGTGTGTGC 59.998 43.478 0.00 0.00 0.00 4.57
833 842 4.041049 GTCTCGACTGCTGATTGACTATG 58.959 47.826 0.00 0.00 0.00 2.23
860 869 0.743097 AAGGATGTACGTAGTCCCGC 59.257 55.000 18.62 0.00 43.93 6.13
945 954 2.232298 CTGGGTTCAGTCGAGGCCTC 62.232 65.000 23.79 23.79 36.30 4.70
948 957 2.435059 GCTGGGTTCAGTCGAGGC 60.435 66.667 0.00 0.00 42.78 4.70
1006 1015 1.612146 GGGTTTGGGGTGGGGATTG 60.612 63.158 0.00 0.00 0.00 2.67
1291 1300 0.476611 ACAAAGGAAGGGAGGAGGCT 60.477 55.000 0.00 0.00 0.00 4.58
1368 1377 3.680786 TGGACGCTGTGGGAGACG 61.681 66.667 0.00 0.00 0.00 4.18
1381 1390 2.202756 GGCGACATCGAGGTGGAC 60.203 66.667 16.55 9.66 43.02 4.02
1695 1704 1.153369 GATGTAGCGCTCCTTGCCA 60.153 57.895 16.34 2.44 38.78 4.92
1896 1905 4.164796 TCATAATGCACTGGGATTCTGAGT 59.835 41.667 0.00 0.00 34.54 3.41
2013 2022 1.047002 CATCGAAGGGCAGATCTCCT 58.953 55.000 0.00 0.00 34.29 3.69
2040 2049 4.569966 ACGCTGTGCAAATCAAAATTCAAA 59.430 33.333 0.00 0.00 0.00 2.69
2046 2055 2.859526 TCACGCTGTGCAAATCAAAA 57.140 40.000 0.00 0.00 32.98 2.44
2061 2070 2.226674 TGAGCACTCAGAGTACTTCACG 59.773 50.000 1.67 0.00 34.14 4.35
2064 2073 5.390356 GCAAATTGAGCACTCAGAGTACTTC 60.390 44.000 1.67 2.25 41.13 3.01
2397 2406 8.678593 TTGTAATTATATGCCGTCCATTACAA 57.321 30.769 12.85 12.85 41.44 2.41
2406 2415 9.772973 TTTCTAGTCATTGTAATTATATGCCGT 57.227 29.630 5.93 0.00 0.00 5.68
2547 2556 0.738389 GCCCAAATGGTGTATGTCCG 59.262 55.000 0.00 0.00 36.04 4.79
2868 2877 2.036217 CAGCTCCTGAGAAGCCTGATAG 59.964 54.545 0.00 0.00 32.44 2.08
3072 3081 3.132824 TGTCAACTATGATCGCATCAGGT 59.867 43.478 5.33 4.35 43.53 4.00
3243 3252 3.737559 TGTATGAAGGGCAATTCAGGT 57.262 42.857 9.75 0.00 42.20 4.00
3411 3420 8.319143 ACATGTTGTAACTTGTAACACCTATC 57.681 34.615 12.77 0.00 43.02 2.08
3560 3765 2.504175 TCCTACCATACAAAGGGCTGAC 59.496 50.000 0.00 0.00 0.00 3.51
3564 3769 4.097892 CACAAATCCTACCATACAAAGGGC 59.902 45.833 0.00 0.00 0.00 5.19
3627 3832 5.569355 TCAAGGACATTATTCAGGCTTTCA 58.431 37.500 0.00 0.00 0.00 2.69
3722 3927 3.446310 TTACAATGCTCGCGGATTAGA 57.554 42.857 6.13 0.00 29.38 2.10
3726 3931 2.238942 TCATTACAATGCTCGCGGAT 57.761 45.000 6.13 0.00 36.36 4.18
3754 3959 1.134367 CTTGTGCTGATGATGGGCTTG 59.866 52.381 0.00 0.00 0.00 4.01
3774 3979 3.799366 TCTCACCGACTCTCAGTCTATC 58.201 50.000 2.32 0.00 42.92 2.08
3816 4021 5.847111 AACCTGTCATATTCTACGCTACA 57.153 39.130 0.00 0.00 0.00 2.74
3854 4059 6.638063 CCCTTTTTACCAGTAAAAACTAACGC 59.362 38.462 19.49 0.00 44.98 4.84
3909 4114 0.981183 TAAGATGGCGTCAACACCCT 59.019 50.000 9.78 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.