Multiple sequence alignment - TraesCS2D01G504200

Loading Multiple Alignment...

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 TraesCS2D01G504200 chr2D 100.000 2368 0 0 885 3252 598735280 598732913 0.000000e+00 4373.0
1 TraesCS2D01G504200 chr2D 100.000 709 0 0 1 709 598736164 598735456 0.000000e+00 1310.0
2 TraesCS2D01G504200 chr2D 97.059 34 1 0 279 312 28088271 28088238 1.260000e-04 58.4
3 TraesCS2D01G504200 chr2A 91.588 1486 92 10 998 2457 732990003 732988525 0.000000e+00 2021.0
4 TraesCS2D01G504200 chr2A 96.923 715 19 1 2538 3252 732988504 732987793 0.000000e+00 1195.0
5 TraesCS2D01G504200 chr2A 89.211 380 35 5 1 376 732997149 732996772 1.370000e-128 470.0
6 TraesCS2D01G504200 chr2A 89.130 92 6 1 905 996 732996676 732996589 9.540000e-21 111.0
7 TraesCS2D01G504200 chr2A 76.608 171 34 5 214 378 666033578 666033748 4.470000e-14 89.8
8 TraesCS2D01G504200 chr2B 91.290 1481 94 16 994 2454 727243794 727242329 0.000000e+00 1988.0
9 TraesCS2D01G504200 chr2B 90.574 1464 104 10 994 2454 727317512 727316080 0.000000e+00 1908.0
10 TraesCS2D01G504200 chr2B 94.700 717 30 5 2541 3252 727242033 727241320 0.000000e+00 1107.0
11 TraesCS2D01G504200 chr2B 84.615 377 48 6 1 375 727621650 727621282 1.840000e-97 366.0
12 TraesCS2D01G504200 chr2B 88.104 269 31 1 2567 2835 727314554 727314287 5.240000e-83 318.0
13 TraesCS2D01G504200 chr2B 90.204 245 21 1 2890 3134 727314274 727314033 1.880000e-82 316.0
14 TraesCS2D01G504200 chr2B 82.596 339 33 12 361 680 727542426 727542095 3.200000e-70 276.0
15 TraesCS2D01G504200 chr5B 75.290 259 51 11 2956 3206 682819895 682819642 9.540000e-21 111.0
16 TraesCS2D01G504200 chr3D 79.675 123 21 4 3086 3206 19037865 19037745 5.780000e-13 86.1
17 TraesCS2D01G504200 chr7D 85.333 75 9 2 201 274 442311134 442311207 3.480000e-10 76.8
18 TraesCS2D01G504200 chr1B 79.787 94 16 3 161 251 297329593 297329500 7.530000e-07 65.8


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 TraesCS2D01G504200 chr2D 598732913 598736164 3251 True 2841.500000 4373 100.000000 1 3252 2 chr2D.!!$R2 3251
1 TraesCS2D01G504200 chr2A 732987793 732990003 2210 True 1608.000000 2021 94.255500 998 3252 2 chr2A.!!$R1 2254
2 TraesCS2D01G504200 chr2A 732996589 732997149 560 True 290.500000 470 89.170500 1 996 2 chr2A.!!$R2 995
3 TraesCS2D01G504200 chr2B 727241320 727243794 2474 True 1547.500000 1988 92.995000 994 3252 2 chr2B.!!$R3 2258
4 TraesCS2D01G504200 chr2B 727314033 727317512 3479 True 847.333333 1908 89.627333 994 3134 3 chr2B.!!$R4 2140

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
372 377 0.036732 TCAGCGTTGGAGATGCCTTT 59.963 50.0 0.00 0.0 41.38 3.11 F
405 410 0.036875 GGCCCCTTCTCCATATTCGG 59.963 60.0 0.00 0.0 0.00 4.30 F
614 619 0.107703 GATCAATGTGAGGTCGGCCA 60.108 55.0 9.71 0.0 37.19 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 2255 0.341961 TGGTAGGCTGGTCCATACCT 59.658 55.0 17.42 16.71 46.91 3.08 R
2217 2286 0.809385 ATCTTCCACACGTCGACGAT 59.191 50.0 41.52 26.48 43.02 3.73 R
2387 2456 0.824109 CACCGTCTTGGATGGCTCTA 59.176 55.0 5.77 0.00 42.09 2.43 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
21 24 1.710816 CGGAGGCTATTCTTCCCTCT 58.289 55.000 5.95 0.00 43.66 3.69
22 25 2.043227 CGGAGGCTATTCTTCCCTCTT 58.957 52.381 5.95 0.00 43.66 2.85
23 26 2.224161 CGGAGGCTATTCTTCCCTCTTG 60.224 54.545 5.95 0.00 43.66 3.02
56 59 2.047844 CGGAGGCTCACAGTGGTG 60.048 66.667 17.69 0.00 46.66 4.17
64 67 3.349006 CACAGTGGTGCGGTGAGC 61.349 66.667 0.00 0.00 44.32 4.26
99 103 2.500229 GGGAAGACATGTCGTGGAAAA 58.500 47.619 19.32 0.00 34.09 2.29
100 104 2.225727 GGGAAGACATGTCGTGGAAAAC 59.774 50.000 19.32 3.35 34.09 2.43
205 209 2.442236 AATACCCTCGTCCGGTCTAA 57.558 50.000 0.00 0.00 34.66 2.10
215 219 4.823157 TCGTCCGGTCTAAATGAAAATCA 58.177 39.130 0.00 0.00 0.00 2.57
217 221 5.522460 TCGTCCGGTCTAAATGAAAATCATC 59.478 40.000 0.00 0.00 35.76 2.92
224 228 8.673711 CGGTCTAAATGAAAATCATCCAGTTTA 58.326 33.333 0.00 0.00 35.76 2.01
272 276 4.214986 TCCTCTTTGAAATGTATGCGGA 57.785 40.909 0.00 0.00 0.00 5.54
294 298 2.044946 GTTGGATGGCCGGCTCTT 60.045 61.111 28.56 14.50 36.79 2.85
296 300 4.802051 TGGATGGCCGGCTCTTGC 62.802 66.667 28.56 18.89 36.79 4.01
307 311 1.085091 GGCTCTTGCATCAGTGTCTG 58.915 55.000 0.00 0.00 41.91 3.51
316 320 2.658548 TCAGTGTCTGCGGACTGAT 58.341 52.632 25.54 9.37 42.88 2.90
324 328 2.105128 GCGGACTGATCCTCACCG 59.895 66.667 11.48 11.48 43.73 4.94
325 329 2.808315 CGGACTGATCCTCACCGG 59.192 66.667 0.00 0.00 43.73 5.28
344 348 0.742505 GTCGGTCGGATATGGTGTCA 59.257 55.000 0.00 0.00 0.00 3.58
353 358 2.025321 GGATATGGTGTCAGGTTTGGGT 60.025 50.000 0.00 0.00 0.00 4.51
364 369 1.515521 GGTTTGGGTCAGCGTTGGAG 61.516 60.000 0.00 0.00 0.00 3.86
372 377 0.036732 TCAGCGTTGGAGATGCCTTT 59.963 50.000 0.00 0.00 41.38 3.11
376 381 1.017387 CGTTGGAGATGCCTTTAGCC 58.983 55.000 0.00 0.00 42.71 3.93
378 383 2.019984 GTTGGAGATGCCTTTAGCCTG 58.980 52.381 0.00 0.00 42.71 4.85
379 384 1.583556 TGGAGATGCCTTTAGCCTGA 58.416 50.000 0.00 0.00 42.71 3.86
380 385 2.130193 TGGAGATGCCTTTAGCCTGAT 58.870 47.619 0.00 0.00 42.71 2.90
381 386 2.158711 TGGAGATGCCTTTAGCCTGATG 60.159 50.000 0.00 0.00 42.71 3.07
382 387 2.502295 GAGATGCCTTTAGCCTGATGG 58.498 52.381 0.00 0.00 42.71 3.51
384 389 2.511218 AGATGCCTTTAGCCTGATGGAA 59.489 45.455 0.00 0.00 42.71 3.53
385 390 2.128771 TGCCTTTAGCCTGATGGAAC 57.871 50.000 0.00 0.00 42.71 3.62
387 392 1.668419 CCTTTAGCCTGATGGAACGG 58.332 55.000 0.00 0.00 34.57 4.44
388 393 1.017387 CTTTAGCCTGATGGAACGGC 58.983 55.000 0.00 0.00 44.09 5.68
389 394 0.393808 TTTAGCCTGATGGAACGGCC 60.394 55.000 0.00 0.00 44.84 6.13
392 397 3.411517 CCTGATGGAACGGCCCCT 61.412 66.667 0.00 0.00 34.97 4.79
393 398 2.677228 CTGATGGAACGGCCCCTT 59.323 61.111 0.00 0.00 34.97 3.95
394 399 1.452108 CTGATGGAACGGCCCCTTC 60.452 63.158 0.00 0.99 34.97 3.46
395 400 1.915078 CTGATGGAACGGCCCCTTCT 61.915 60.000 11.90 0.00 34.97 2.85
396 401 1.153147 GATGGAACGGCCCCTTCTC 60.153 63.158 0.00 0.00 34.97 2.87
397 402 2.610532 GATGGAACGGCCCCTTCTCC 62.611 65.000 0.00 0.00 34.97 3.71
398 403 3.327404 GGAACGGCCCCTTCTCCA 61.327 66.667 0.00 0.00 0.00 3.86
399 404 2.680370 GGAACGGCCCCTTCTCCAT 61.680 63.158 0.00 0.00 0.00 3.41
400 405 1.342672 GGAACGGCCCCTTCTCCATA 61.343 60.000 0.00 0.00 0.00 2.74
401 406 0.765510 GAACGGCCCCTTCTCCATAT 59.234 55.000 0.00 0.00 0.00 1.78
402 407 1.143073 GAACGGCCCCTTCTCCATATT 59.857 52.381 0.00 0.00 0.00 1.28
403 408 0.765510 ACGGCCCCTTCTCCATATTC 59.234 55.000 0.00 0.00 0.00 1.75
404 409 0.320771 CGGCCCCTTCTCCATATTCG 60.321 60.000 0.00 0.00 0.00 3.34
405 410 0.036875 GGCCCCTTCTCCATATTCGG 59.963 60.000 0.00 0.00 0.00 4.30
406 411 0.036875 GCCCCTTCTCCATATTCGGG 59.963 60.000 0.00 0.00 0.00 5.14
407 412 1.435256 CCCCTTCTCCATATTCGGGT 58.565 55.000 0.00 0.00 0.00 5.28
408 413 1.072331 CCCCTTCTCCATATTCGGGTG 59.928 57.143 0.00 0.00 0.00 4.61
409 414 1.072331 CCCTTCTCCATATTCGGGTGG 59.928 57.143 0.00 0.00 36.82 4.61
410 415 1.768870 CCTTCTCCATATTCGGGTGGT 59.231 52.381 0.00 0.00 36.84 4.16
411 416 2.172717 CCTTCTCCATATTCGGGTGGTT 59.827 50.000 0.00 0.00 36.84 3.67
412 417 3.206150 CTTCTCCATATTCGGGTGGTTG 58.794 50.000 0.00 0.00 36.84 3.77
413 418 1.134220 TCTCCATATTCGGGTGGTTGC 60.134 52.381 0.00 0.00 36.84 4.17
414 419 0.462937 TCCATATTCGGGTGGTTGCG 60.463 55.000 0.00 0.00 36.84 4.85
415 420 1.355210 CATATTCGGGTGGTTGCGC 59.645 57.895 0.00 0.00 0.00 6.09
416 421 1.078072 ATATTCGGGTGGTTGCGCA 60.078 52.632 5.66 5.66 0.00 6.09
417 422 0.465460 ATATTCGGGTGGTTGCGCAT 60.465 50.000 12.75 0.00 0.00 4.73
418 423 1.372838 TATTCGGGTGGTTGCGCATG 61.373 55.000 12.75 0.00 0.00 4.06
421 426 4.054825 GGGTGGTTGCGCATGGTG 62.055 66.667 12.75 0.00 0.00 4.17
422 427 4.054825 GGTGGTTGCGCATGGTGG 62.055 66.667 12.75 0.00 0.00 4.61
423 428 4.054825 GTGGTTGCGCATGGTGGG 62.055 66.667 12.75 0.00 0.00 4.61
424 429 4.594854 TGGTTGCGCATGGTGGGT 62.595 61.111 12.75 0.00 32.36 4.51
425 430 3.302344 GGTTGCGCATGGTGGGTT 61.302 61.111 12.75 0.00 32.36 4.11
426 431 1.974343 GGTTGCGCATGGTGGGTTA 60.974 57.895 12.75 0.00 32.36 2.85
427 432 1.528292 GGTTGCGCATGGTGGGTTAA 61.528 55.000 12.75 0.00 32.36 2.01
428 433 0.315568 GTTGCGCATGGTGGGTTAAA 59.684 50.000 12.75 0.00 32.36 1.52
429 434 1.067213 GTTGCGCATGGTGGGTTAAAT 60.067 47.619 12.75 0.00 32.36 1.40
430 435 1.261480 TGCGCATGGTGGGTTAAATT 58.739 45.000 5.66 0.00 32.36 1.82
431 436 1.067283 TGCGCATGGTGGGTTAAATTG 60.067 47.619 5.66 0.00 32.36 2.32
432 437 1.203523 GCGCATGGTGGGTTAAATTGA 59.796 47.619 0.30 0.00 32.36 2.57
433 438 2.353208 GCGCATGGTGGGTTAAATTGAA 60.353 45.455 0.30 0.00 32.36 2.69
434 439 3.678529 GCGCATGGTGGGTTAAATTGAAT 60.679 43.478 0.30 0.00 32.36 2.57
435 440 4.440802 GCGCATGGTGGGTTAAATTGAATA 60.441 41.667 0.30 0.00 32.36 1.75
436 441 5.738783 GCGCATGGTGGGTTAAATTGAATAT 60.739 40.000 0.30 0.00 32.36 1.28
437 442 6.515862 GCGCATGGTGGGTTAAATTGAATATA 60.516 38.462 0.30 0.00 32.36 0.86
438 443 7.601856 CGCATGGTGGGTTAAATTGAATATAT 58.398 34.615 0.00 0.00 0.00 0.86
439 444 8.087750 CGCATGGTGGGTTAAATTGAATATATT 58.912 33.333 0.00 0.00 0.00 1.28
440 445 9.777297 GCATGGTGGGTTAAATTGAATATATTT 57.223 29.630 0.00 0.00 0.00 1.40
447 452 8.964150 GGGTTAAATTGAATATATTTGTGACGC 58.036 33.333 0.00 0.00 0.00 5.19
448 453 8.964150 GGTTAAATTGAATATATTTGTGACGCC 58.036 33.333 0.00 0.00 0.00 5.68
449 454 9.509855 GTTAAATTGAATATATTTGTGACGCCA 57.490 29.630 0.00 0.00 0.00 5.69
451 456 8.994429 AAATTGAATATATTTGTGACGCCAAA 57.006 26.923 0.00 0.00 38.58 3.28
452 457 8.633075 AATTGAATATATTTGTGACGCCAAAG 57.367 30.769 0.00 0.00 37.71 2.77
453 458 6.993786 TGAATATATTTGTGACGCCAAAGA 57.006 33.333 0.00 0.00 37.71 2.52
454 459 7.566760 TGAATATATTTGTGACGCCAAAGAT 57.433 32.000 0.00 7.69 39.07 2.40
455 460 8.669946 TGAATATATTTGTGACGCCAAAGATA 57.330 30.769 0.00 10.56 40.65 1.98
456 461 9.283768 TGAATATATTTGTGACGCCAAAGATAT 57.716 29.630 13.05 13.05 44.72 1.63
458 463 9.897744 AATATATTTGTGACGCCAAAGATATTG 57.102 29.630 21.84 0.00 46.69 1.90
459 464 5.895636 ATTTGTGACGCCAAAGATATTGA 57.104 34.783 2.62 0.00 37.71 2.57
460 465 5.697473 TTTGTGACGCCAAAGATATTGAA 57.303 34.783 0.00 0.00 31.06 2.69
461 466 5.895636 TTGTGACGCCAAAGATATTGAAT 57.104 34.783 0.00 0.00 0.00 2.57
462 467 5.895636 TGTGACGCCAAAGATATTGAATT 57.104 34.783 0.00 0.00 0.00 2.17
463 468 6.993786 TGTGACGCCAAAGATATTGAATTA 57.006 33.333 0.00 0.00 0.00 1.40
464 469 7.384439 TGTGACGCCAAAGATATTGAATTAA 57.616 32.000 0.00 0.00 0.00 1.40
465 470 7.821652 TGTGACGCCAAAGATATTGAATTAAA 58.178 30.769 0.00 0.00 0.00 1.52
466 471 8.300286 TGTGACGCCAAAGATATTGAATTAAAA 58.700 29.630 0.00 0.00 0.00 1.52
467 472 9.134734 GTGACGCCAAAGATATTGAATTAAAAA 57.865 29.630 0.00 0.00 0.00 1.94
488 493 4.574599 AATCGCTTGGATAATTTCAGGC 57.425 40.909 0.00 0.00 34.08 4.85
490 495 2.781945 GCTTGGATAATTTCAGGCGG 57.218 50.000 0.00 0.00 0.00 6.13
491 496 2.297701 GCTTGGATAATTTCAGGCGGA 58.702 47.619 0.00 0.00 0.00 5.54
492 497 2.687935 GCTTGGATAATTTCAGGCGGAA 59.312 45.455 0.00 0.00 0.00 4.30
502 507 4.392921 TTTCAGGCGGAAAAATTCAACA 57.607 36.364 10.41 0.00 42.37 3.33
503 508 4.599047 TTCAGGCGGAAAAATTCAACAT 57.401 36.364 0.00 0.00 30.98 2.71
504 509 4.599047 TCAGGCGGAAAAATTCAACATT 57.401 36.364 0.00 0.00 0.00 2.71
505 510 4.954875 TCAGGCGGAAAAATTCAACATTT 58.045 34.783 0.00 0.00 0.00 2.32
506 511 4.987912 TCAGGCGGAAAAATTCAACATTTC 59.012 37.500 0.00 0.00 33.38 2.17
507 512 4.152223 CAGGCGGAAAAATTCAACATTTCC 59.848 41.667 8.08 8.08 45.52 3.13
532 537 1.419381 TTTTGGAAACTGGCCCTTCC 58.581 50.000 17.51 17.51 41.37 3.46
533 538 0.471022 TTTGGAAACTGGCCCTTCCC 60.471 55.000 20.18 8.22 40.45 3.97
534 539 1.660019 TTGGAAACTGGCCCTTCCCA 61.660 55.000 20.18 10.67 40.45 4.37
535 540 1.155155 GGAAACTGGCCCTTCCCAA 59.845 57.895 14.65 0.00 35.95 4.12
536 541 0.471022 GGAAACTGGCCCTTCCCAAA 60.471 55.000 14.65 0.00 35.95 3.28
537 542 1.419381 GAAACTGGCCCTTCCCAAAA 58.581 50.000 0.00 0.00 33.73 2.44
538 543 1.765904 GAAACTGGCCCTTCCCAAAAA 59.234 47.619 0.00 0.00 33.73 1.94
561 566 3.622627 AAAAACCGGTATCGCGAAAAA 57.377 38.095 15.24 0.00 34.56 1.94
562 567 3.835378 AAAACCGGTATCGCGAAAAAT 57.165 38.095 15.24 0.00 34.56 1.82
563 568 4.943142 AAAACCGGTATCGCGAAAAATA 57.057 36.364 15.24 0.00 34.56 1.40
564 569 3.931285 AACCGGTATCGCGAAAAATAC 57.069 42.857 15.24 11.22 34.56 1.89
565 570 3.169355 ACCGGTATCGCGAAAAATACT 57.831 42.857 15.24 0.00 34.56 2.12
566 571 4.305989 ACCGGTATCGCGAAAAATACTA 57.694 40.909 15.24 0.00 34.56 1.82
567 572 4.044426 ACCGGTATCGCGAAAAATACTAC 58.956 43.478 15.24 9.19 34.56 2.73
568 573 3.426525 CCGGTATCGCGAAAAATACTACC 59.573 47.826 15.24 17.35 34.56 3.18
569 574 4.293415 CGGTATCGCGAAAAATACTACCT 58.707 43.478 23.18 3.90 0.00 3.08
570 575 4.741676 CGGTATCGCGAAAAATACTACCTT 59.258 41.667 23.18 3.72 0.00 3.50
571 576 5.332055 CGGTATCGCGAAAAATACTACCTTG 60.332 44.000 23.18 10.62 0.00 3.61
572 577 5.750067 GGTATCGCGAAAAATACTACCTTGA 59.250 40.000 15.24 0.00 0.00 3.02
573 578 5.713822 ATCGCGAAAAATACTACCTTGAC 57.286 39.130 15.24 0.00 0.00 3.18
574 579 4.558178 TCGCGAAAAATACTACCTTGACA 58.442 39.130 6.20 0.00 0.00 3.58
575 580 4.624024 TCGCGAAAAATACTACCTTGACAG 59.376 41.667 6.20 0.00 0.00 3.51
576 581 4.648970 GCGAAAAATACTACCTTGACAGC 58.351 43.478 0.00 0.00 0.00 4.40
577 582 4.392138 GCGAAAAATACTACCTTGACAGCT 59.608 41.667 0.00 0.00 0.00 4.24
578 583 5.671329 GCGAAAAATACTACCTTGACAGCTG 60.671 44.000 13.48 13.48 0.00 4.24
579 584 5.629079 AAAAATACTACCTTGACAGCTGC 57.371 39.130 15.27 7.45 0.00 5.25
580 585 4.559862 AAATACTACCTTGACAGCTGCT 57.440 40.909 15.27 0.00 0.00 4.24
581 586 3.533606 ATACTACCTTGACAGCTGCTG 57.466 47.619 27.02 27.02 37.52 4.41
582 587 0.322975 ACTACCTTGACAGCTGCTGG 59.677 55.000 31.00 16.91 35.51 4.85
583 588 0.322975 CTACCTTGACAGCTGCTGGT 59.677 55.000 31.00 21.44 35.51 4.00
584 589 1.550524 CTACCTTGACAGCTGCTGGTA 59.449 52.381 31.00 21.41 35.51 3.25
585 590 0.322975 ACCTTGACAGCTGCTGGTAG 59.677 55.000 31.00 22.64 35.51 3.18
586 591 0.610174 CCTTGACAGCTGCTGGTAGA 59.390 55.000 31.00 14.23 35.51 2.59
587 592 1.405256 CCTTGACAGCTGCTGGTAGAG 60.405 57.143 31.00 21.24 35.51 2.43
588 593 0.610174 TTGACAGCTGCTGGTAGAGG 59.390 55.000 31.00 6.97 35.51 3.69
589 594 1.153469 GACAGCTGCTGGTAGAGGC 60.153 63.158 31.00 3.37 35.51 4.70
590 595 2.202851 CAGCTGCTGGTAGAGGCG 60.203 66.667 21.71 0.00 0.00 5.52
591 596 3.465403 AGCTGCTGGTAGAGGCGG 61.465 66.667 0.00 0.00 37.83 6.13
592 597 3.461773 GCTGCTGGTAGAGGCGGA 61.462 66.667 0.00 0.00 37.02 5.54
593 598 2.811101 CTGCTGGTAGAGGCGGAG 59.189 66.667 0.00 0.00 37.02 4.63
594 599 2.759973 TGCTGGTAGAGGCGGAGG 60.760 66.667 0.00 0.00 0.00 4.30
595 600 3.541713 GCTGGTAGAGGCGGAGGG 61.542 72.222 0.00 0.00 0.00 4.30
596 601 2.279073 CTGGTAGAGGCGGAGGGA 59.721 66.667 0.00 0.00 0.00 4.20
597 602 1.152440 CTGGTAGAGGCGGAGGGAT 60.152 63.158 0.00 0.00 0.00 3.85
598 603 1.152525 TGGTAGAGGCGGAGGGATC 60.153 63.158 0.00 0.00 0.00 3.36
599 604 1.152525 GGTAGAGGCGGAGGGATCA 60.153 63.158 0.00 0.00 0.00 2.92
600 605 0.759436 GGTAGAGGCGGAGGGATCAA 60.759 60.000 0.00 0.00 0.00 2.57
601 606 1.343069 GTAGAGGCGGAGGGATCAAT 58.657 55.000 0.00 0.00 0.00 2.57
602 607 1.001406 GTAGAGGCGGAGGGATCAATG 59.999 57.143 0.00 0.00 0.00 2.82
603 608 0.692419 AGAGGCGGAGGGATCAATGT 60.692 55.000 0.00 0.00 0.00 2.71
604 609 0.533755 GAGGCGGAGGGATCAATGTG 60.534 60.000 0.00 0.00 0.00 3.21
605 610 0.982852 AGGCGGAGGGATCAATGTGA 60.983 55.000 0.00 0.00 0.00 3.58
606 611 0.533755 GGCGGAGGGATCAATGTGAG 60.534 60.000 0.00 0.00 0.00 3.51
607 612 0.533755 GCGGAGGGATCAATGTGAGG 60.534 60.000 0.00 0.00 0.00 3.86
608 613 0.833287 CGGAGGGATCAATGTGAGGT 59.167 55.000 0.00 0.00 0.00 3.85
609 614 1.202580 CGGAGGGATCAATGTGAGGTC 60.203 57.143 0.00 0.00 0.00 3.85
610 615 1.202580 GGAGGGATCAATGTGAGGTCG 60.203 57.143 0.00 0.00 0.00 4.79
611 616 0.833287 AGGGATCAATGTGAGGTCGG 59.167 55.000 0.00 0.00 0.00 4.79
612 617 0.815615 GGGATCAATGTGAGGTCGGC 60.816 60.000 0.00 0.00 0.00 5.54
613 618 0.815615 GGATCAATGTGAGGTCGGCC 60.816 60.000 0.00 0.00 0.00 6.13
614 619 0.107703 GATCAATGTGAGGTCGGCCA 60.108 55.000 9.71 0.00 37.19 5.36
615 620 0.548031 ATCAATGTGAGGTCGGCCAT 59.452 50.000 9.71 0.00 37.19 4.40
616 621 0.392863 TCAATGTGAGGTCGGCCATG 60.393 55.000 9.71 0.00 37.19 3.66
617 622 1.750399 AATGTGAGGTCGGCCATGC 60.750 57.895 9.71 0.00 37.19 4.06
618 623 2.482796 AATGTGAGGTCGGCCATGCA 62.483 55.000 9.71 3.50 37.19 3.96
619 624 2.124570 GTGAGGTCGGCCATGCAT 60.125 61.111 9.71 0.00 37.19 3.96
620 625 2.124612 TGAGGTCGGCCATGCATG 60.125 61.111 20.19 20.19 37.19 4.06
621 626 2.190313 GAGGTCGGCCATGCATGA 59.810 61.111 28.31 4.84 37.19 3.07
622 627 1.451927 GAGGTCGGCCATGCATGAA 60.452 57.895 28.31 7.55 37.19 2.57
623 628 1.001020 AGGTCGGCCATGCATGAAA 60.001 52.632 28.31 7.18 37.19 2.69
624 629 0.611618 AGGTCGGCCATGCATGAAAA 60.612 50.000 28.31 7.54 37.19 2.29
625 630 0.458370 GGTCGGCCATGCATGAAAAC 60.458 55.000 28.31 17.98 34.09 2.43
626 631 0.798009 GTCGGCCATGCATGAAAACG 60.798 55.000 28.31 22.75 0.00 3.60
629 634 1.154054 GCCATGCATGAAAACGCGA 60.154 52.632 28.31 0.00 0.00 5.87
639 644 0.794473 GAAAACGCGATTCTCCCGTT 59.206 50.000 15.93 0.00 45.84 4.44
689 701 1.135228 GCAAACAGTTTGTCGGTTGGT 60.135 47.619 23.96 0.00 42.56 3.67
697 709 2.050168 GTCGGTTGGTACGCGTCA 60.050 61.111 18.63 5.56 0.00 4.35
699 711 1.067084 TCGGTTGGTACGCGTCAAA 59.933 52.632 18.63 5.98 0.00 2.69
703 715 2.067766 GGTTGGTACGCGTCAAATACA 58.932 47.619 18.63 4.02 0.00 2.29
707 719 4.374843 TGGTACGCGTCAAATACACTAT 57.625 40.909 18.63 0.00 0.00 2.12
708 720 5.497635 TGGTACGCGTCAAATACACTATA 57.502 39.130 18.63 0.00 0.00 1.31
923 935 6.720112 AAAATACACTATAGCCCGACAGTA 57.280 37.500 0.00 0.00 0.00 2.74
1196 1208 4.069232 CCTGCCGGAGCTCGTCAA 62.069 66.667 5.05 0.00 40.80 3.18
1261 1273 1.762222 CGCCGATTTACCTGGCTTCG 61.762 60.000 0.00 0.00 46.67 3.79
1370 1408 2.250939 TGGCCGACTTCTTGTTGCG 61.251 57.895 0.00 0.00 0.00 4.85
1630 1693 4.142687 GGTCATACTTGCTTAACAATGCGT 60.143 41.667 0.00 0.00 37.72 5.24
1660 1723 1.375908 GATCTTGTGTGGCGAGGCA 60.376 57.895 0.00 0.00 0.00 4.75
1682 1745 2.974698 GAGGGCGATTCATGGCGG 60.975 66.667 0.00 0.00 31.82 6.13
1685 1748 2.974698 GGCGATTCATGGCGGGAG 60.975 66.667 0.00 0.00 31.82 4.30
1690 1753 0.462047 GATTCATGGCGGGAGTTCGT 60.462 55.000 0.00 0.00 0.00 3.85
1769 1832 0.248417 CATGGACTCGCTCGTCTCAG 60.248 60.000 2.86 0.00 34.38 3.35
1770 1833 0.393132 ATGGACTCGCTCGTCTCAGA 60.393 55.000 2.86 0.00 34.38 3.27
1771 1834 1.021920 TGGACTCGCTCGTCTCAGAG 61.022 60.000 0.00 0.00 41.03 3.35
1798 1861 1.717791 CGTCGCCCCGTATGTACTCA 61.718 60.000 0.00 0.00 0.00 3.41
1965 2028 4.148825 GCTCGACATGGGGCTCGT 62.149 66.667 0.00 0.00 0.00 4.18
1967 2030 2.678580 TCGACATGGGGCTCGTCA 60.679 61.111 0.00 0.00 0.00 4.35
1993 2056 1.071471 CGTCAAGTTCCTGTGGGCT 59.929 57.895 0.00 0.00 0.00 5.19
2085 2154 2.743928 CGACCAGCTCAAGGTGCC 60.744 66.667 0.00 0.00 40.09 5.01
2116 2185 1.149627 CGTTGGGGGTTTCCTGACA 59.850 57.895 0.00 0.00 35.33 3.58
2183 2252 4.160329 TCCGATGCTTACTCTTCCCATAT 58.840 43.478 0.00 0.00 0.00 1.78
2184 2253 5.330233 TCCGATGCTTACTCTTCCCATATA 58.670 41.667 0.00 0.00 0.00 0.86
2185 2254 5.958380 TCCGATGCTTACTCTTCCCATATAT 59.042 40.000 0.00 0.00 0.00 0.86
2186 2255 7.123383 TCCGATGCTTACTCTTCCCATATATA 58.877 38.462 0.00 0.00 0.00 0.86
2206 2275 1.435256 GGTATGGACCAGCCTACCAT 58.565 55.000 15.26 0.00 46.12 3.55
2246 2315 2.084546 GTGTGGAAGATTGGGTACAGC 58.915 52.381 0.00 0.00 0.00 4.40
2337 2406 0.390124 GAGCTCCTCTGATCTGCCAG 59.610 60.000 0.87 0.00 35.55 4.85
2345 2414 1.206610 TCTGATCTGCCAGAGAGCAAC 59.793 52.381 0.00 0.00 46.40 4.17
2464 2533 9.686683 AAGCTGTATATGATTTAACCAAGACTT 57.313 29.630 0.00 0.00 0.00 3.01
2487 2556 5.519183 TTTTTCATCCATCCCTCTCTGAA 57.481 39.130 0.00 0.00 0.00 3.02
2488 2557 5.722172 TTTTCATCCATCCCTCTCTGAAT 57.278 39.130 0.00 0.00 0.00 2.57
2489 2558 4.970860 TTCATCCATCCCTCTCTGAATC 57.029 45.455 0.00 0.00 0.00 2.52
2490 2559 3.246301 TCATCCATCCCTCTCTGAATCC 58.754 50.000 0.00 0.00 0.00 3.01
2491 2560 2.875102 TCCATCCCTCTCTGAATCCA 57.125 50.000 0.00 0.00 0.00 3.41
2492 2561 2.687297 TCCATCCCTCTCTGAATCCAG 58.313 52.381 0.00 0.00 41.74 3.86
2493 2562 2.248423 TCCATCCCTCTCTGAATCCAGA 59.752 50.000 0.00 0.00 46.48 3.86
2502 2571 3.340814 TCTGAATCCAGAACTCTTGCC 57.659 47.619 0.00 0.00 45.74 4.52
2503 2572 2.909006 TCTGAATCCAGAACTCTTGCCT 59.091 45.455 0.00 0.00 45.74 4.75
2504 2573 3.055530 TCTGAATCCAGAACTCTTGCCTC 60.056 47.826 0.00 0.00 45.74 4.70
2506 2575 3.269178 GAATCCAGAACTCTTGCCTCTG 58.731 50.000 0.00 0.00 37.03 3.35
2507 2576 2.015456 TCCAGAACTCTTGCCTCTGA 57.985 50.000 0.00 0.00 39.15 3.27
2509 2578 2.499289 TCCAGAACTCTTGCCTCTGATC 59.501 50.000 0.00 0.00 39.15 2.92
2512 2581 3.129462 CAGAACTCTTGCCTCTGATCGTA 59.871 47.826 0.00 0.00 39.15 3.43
2515 2584 2.685897 ACTCTTGCCTCTGATCGTACTC 59.314 50.000 0.00 0.00 0.00 2.59
2516 2585 1.671328 TCTTGCCTCTGATCGTACTCG 59.329 52.381 0.00 0.00 38.55 4.18
2617 4227 1.339151 GCTGAAGAACCGTGGGATTCT 60.339 52.381 0.00 0.00 36.73 2.40
2773 4383 1.300620 GTACTGCACGCACCACAGA 60.301 57.895 0.00 0.00 35.38 3.41
2908 4518 0.614979 GGTACCACTCCTGGCTCTCA 60.615 60.000 7.15 0.00 42.08 3.27
2909 4519 0.820871 GTACCACTCCTGGCTCTCAG 59.179 60.000 0.00 0.00 42.08 3.35
2910 4520 0.972983 TACCACTCCTGGCTCTCAGC 60.973 60.000 0.00 0.00 42.08 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 43 2.359230 GCACCACTGTGAGCCTCC 60.359 66.667 9.86 0.00 45.76 4.30
44 47 3.349006 CACCGCACCACTGTGAGC 61.349 66.667 9.86 11.79 45.76 4.26
64 67 0.609957 TTCCCCATGTCAGCAGCAAG 60.610 55.000 0.00 0.00 0.00 4.01
173 177 4.563976 ACGAGGGTATTTACATTTCGAACG 59.436 41.667 0.00 0.00 32.80 3.95
181 185 2.363359 GACCGGACGAGGGTATTTACAT 59.637 50.000 9.46 0.00 38.07 2.29
182 186 1.750778 GACCGGACGAGGGTATTTACA 59.249 52.381 9.46 0.00 38.07 2.41
189 193 0.822164 CATTTAGACCGGACGAGGGT 59.178 55.000 9.46 0.00 41.48 4.34
215 219 9.911788 ACTAGATGAAATTCATGTAAACTGGAT 57.088 29.630 13.82 0.00 37.20 3.41
272 276 2.671070 CCGGCCATCCAACTCTGT 59.329 61.111 2.24 0.00 0.00 3.41
294 298 1.374631 GTCCGCAGACACTGATGCA 60.375 57.895 2.81 0.00 42.68 3.96
296 300 0.244721 TCAGTCCGCAGACACTGATG 59.755 55.000 2.32 0.00 46.15 3.07
324 328 0.031721 GACACCATATCCGACCGACC 59.968 60.000 0.00 0.00 0.00 4.79
325 329 0.742505 TGACACCATATCCGACCGAC 59.257 55.000 0.00 0.00 0.00 4.79
344 348 1.528309 CCAACGCTGACCCAAACCT 60.528 57.895 0.00 0.00 0.00 3.50
353 358 0.036732 AAAGGCATCTCCAACGCTGA 59.963 50.000 0.00 0.00 37.29 4.26
364 369 2.620585 GTTCCATCAGGCTAAAGGCATC 59.379 50.000 6.30 0.00 44.01 3.91
376 381 1.452108 GAAGGGGCCGTTCCATCAG 60.452 63.158 24.88 0.00 36.21 2.90
378 383 1.153147 GAGAAGGGGCCGTTCCATC 60.153 63.158 29.80 20.17 36.21 3.51
379 384 2.680370 GGAGAAGGGGCCGTTCCAT 61.680 63.158 29.80 16.37 36.21 3.41
380 385 3.327404 GGAGAAGGGGCCGTTCCA 61.327 66.667 29.80 0.00 36.21 3.53
381 386 1.342672 TATGGAGAAGGGGCCGTTCC 61.343 60.000 29.80 20.02 0.00 3.62
382 387 0.765510 ATATGGAGAAGGGGCCGTTC 59.234 55.000 27.22 27.22 0.00 3.95
384 389 0.765510 GAATATGGAGAAGGGGCCGT 59.234 55.000 0.00 0.00 0.00 5.68
385 390 0.320771 CGAATATGGAGAAGGGGCCG 60.321 60.000 0.00 0.00 0.00 6.13
387 392 0.036875 CCCGAATATGGAGAAGGGGC 59.963 60.000 0.00 0.00 35.36 5.80
388 393 1.072331 CACCCGAATATGGAGAAGGGG 59.928 57.143 3.23 0.00 42.95 4.79
389 394 1.072331 CCACCCGAATATGGAGAAGGG 59.928 57.143 0.00 0.00 44.17 3.95
391 396 3.206150 CAACCACCCGAATATGGAGAAG 58.794 50.000 0.00 0.00 39.46 2.85
392 397 2.682563 GCAACCACCCGAATATGGAGAA 60.683 50.000 0.00 0.00 39.46 2.87
393 398 1.134220 GCAACCACCCGAATATGGAGA 60.134 52.381 0.00 0.00 39.46 3.71
394 399 1.308998 GCAACCACCCGAATATGGAG 58.691 55.000 0.00 0.00 39.46 3.86
395 400 0.462937 CGCAACCACCCGAATATGGA 60.463 55.000 0.00 0.00 39.46 3.41
396 401 2.021722 CGCAACCACCCGAATATGG 58.978 57.895 0.00 0.00 42.13 2.74
397 402 1.355210 GCGCAACCACCCGAATATG 59.645 57.895 0.30 0.00 0.00 1.78
398 403 0.465460 ATGCGCAACCACCCGAATAT 60.465 50.000 17.11 0.00 0.00 1.28
399 404 1.078072 ATGCGCAACCACCCGAATA 60.078 52.632 17.11 0.00 0.00 1.75
400 405 2.361104 ATGCGCAACCACCCGAAT 60.361 55.556 17.11 0.00 0.00 3.34
401 406 3.361158 CATGCGCAACCACCCGAA 61.361 61.111 17.11 0.00 0.00 4.30
404 409 4.054825 CACCATGCGCAACCACCC 62.055 66.667 17.11 0.00 0.00 4.61
405 410 4.054825 CCACCATGCGCAACCACC 62.055 66.667 17.11 0.00 0.00 4.61
406 411 4.054825 CCCACCATGCGCAACCAC 62.055 66.667 17.11 0.00 0.00 4.16
407 412 2.698776 TAACCCACCATGCGCAACCA 62.699 55.000 17.11 0.00 0.00 3.67
408 413 1.528292 TTAACCCACCATGCGCAACC 61.528 55.000 17.11 0.00 0.00 3.77
409 414 0.315568 TTTAACCCACCATGCGCAAC 59.684 50.000 17.11 0.00 0.00 4.17
410 415 1.261480 ATTTAACCCACCATGCGCAA 58.739 45.000 17.11 0.00 0.00 4.85
411 416 1.067283 CAATTTAACCCACCATGCGCA 60.067 47.619 14.96 14.96 0.00 6.09
412 417 1.203523 TCAATTTAACCCACCATGCGC 59.796 47.619 0.00 0.00 0.00 6.09
413 418 3.584406 TTCAATTTAACCCACCATGCG 57.416 42.857 0.00 0.00 0.00 4.73
414 419 9.777297 AAATATATTCAATTTAACCCACCATGC 57.223 29.630 0.00 0.00 0.00 4.06
421 426 8.964150 GCGTCACAAATATATTCAATTTAACCC 58.036 33.333 0.00 0.00 0.00 4.11
422 427 8.964150 GGCGTCACAAATATATTCAATTTAACC 58.036 33.333 0.00 0.00 0.00 2.85
423 428 9.509855 TGGCGTCACAAATATATTCAATTTAAC 57.490 29.630 0.00 0.00 0.00 2.01
426 431 8.994429 TTTGGCGTCACAAATATATTCAATTT 57.006 26.923 0.00 0.00 35.57 1.82
427 432 8.465999 TCTTTGGCGTCACAAATATATTCAATT 58.534 29.630 0.00 0.00 39.39 2.32
428 433 7.995289 TCTTTGGCGTCACAAATATATTCAAT 58.005 30.769 0.00 0.00 39.39 2.57
429 434 7.384439 TCTTTGGCGTCACAAATATATTCAA 57.616 32.000 0.00 0.00 39.39 2.69
430 435 6.993786 TCTTTGGCGTCACAAATATATTCA 57.006 33.333 0.00 0.00 39.39 2.57
432 437 9.897744 CAATATCTTTGGCGTCACAAATATATT 57.102 29.630 17.07 17.07 43.39 1.28
433 438 9.283768 TCAATATCTTTGGCGTCACAAATATAT 57.716 29.630 0.00 2.34 39.63 0.86
434 439 8.669946 TCAATATCTTTGGCGTCACAAATATA 57.330 30.769 0.00 0.00 39.39 0.86
435 440 7.566760 TCAATATCTTTGGCGTCACAAATAT 57.433 32.000 0.00 0.00 39.39 1.28
436 441 6.993786 TCAATATCTTTGGCGTCACAAATA 57.006 33.333 0.00 0.00 39.39 1.40
437 442 5.895636 TCAATATCTTTGGCGTCACAAAT 57.104 34.783 0.00 0.00 39.39 2.32
438 443 5.697473 TTCAATATCTTTGGCGTCACAAA 57.303 34.783 0.00 0.00 37.96 2.83
439 444 5.895636 ATTCAATATCTTTGGCGTCACAA 57.104 34.783 0.00 0.00 0.00 3.33
440 445 5.895636 AATTCAATATCTTTGGCGTCACA 57.104 34.783 0.00 0.00 0.00 3.58
441 446 8.682128 TTTTAATTCAATATCTTTGGCGTCAC 57.318 30.769 0.00 0.00 0.00 3.67
464 469 5.812127 GCCTGAAATTATCCAAGCGATTTTT 59.188 36.000 0.00 0.00 31.92 1.94
465 470 5.351458 GCCTGAAATTATCCAAGCGATTTT 58.649 37.500 0.00 0.00 31.92 1.82
466 471 4.498009 CGCCTGAAATTATCCAAGCGATTT 60.498 41.667 10.85 0.00 40.29 2.17
467 472 3.003689 CGCCTGAAATTATCCAAGCGATT 59.996 43.478 10.85 0.00 40.29 3.34
468 473 2.549754 CGCCTGAAATTATCCAAGCGAT 59.450 45.455 10.85 0.00 40.29 4.58
469 474 1.939934 CGCCTGAAATTATCCAAGCGA 59.060 47.619 10.85 0.00 40.29 4.93
470 475 1.002468 CCGCCTGAAATTATCCAAGCG 60.002 52.381 9.87 9.87 38.67 4.68
471 476 2.297701 TCCGCCTGAAATTATCCAAGC 58.702 47.619 0.00 0.00 0.00 4.01
472 477 4.981806 TTTCCGCCTGAAATTATCCAAG 57.018 40.909 0.00 0.00 38.04 3.61
473 478 5.730296 TTTTTCCGCCTGAAATTATCCAA 57.270 34.783 0.00 0.00 42.38 3.53
474 479 5.930837 ATTTTTCCGCCTGAAATTATCCA 57.069 34.783 0.00 0.00 42.38 3.41
475 480 6.337356 TGAATTTTTCCGCCTGAAATTATCC 58.663 36.000 0.00 0.00 42.38 2.59
476 481 7.330700 TGTTGAATTTTTCCGCCTGAAATTATC 59.669 33.333 0.00 0.00 42.38 1.75
477 482 7.158021 TGTTGAATTTTTCCGCCTGAAATTAT 58.842 30.769 0.00 0.00 42.38 1.28
478 483 6.516718 TGTTGAATTTTTCCGCCTGAAATTA 58.483 32.000 0.00 0.00 42.38 1.40
479 484 5.363939 TGTTGAATTTTTCCGCCTGAAATT 58.636 33.333 0.00 0.00 42.38 1.82
480 485 4.954875 TGTTGAATTTTTCCGCCTGAAAT 58.045 34.783 0.00 0.00 42.38 2.17
481 486 4.392921 TGTTGAATTTTTCCGCCTGAAA 57.607 36.364 0.00 0.00 41.18 2.69
482 487 4.599047 ATGTTGAATTTTTCCGCCTGAA 57.401 36.364 0.00 0.00 0.00 3.02
483 488 4.599047 AATGTTGAATTTTTCCGCCTGA 57.401 36.364 0.00 0.00 0.00 3.86
484 489 4.152223 GGAAATGTTGAATTTTTCCGCCTG 59.848 41.667 3.45 0.00 39.12 4.85
485 490 4.314961 GGAAATGTTGAATTTTTCCGCCT 58.685 39.130 3.45 0.00 39.12 5.52
486 491 4.661993 GGAAATGTTGAATTTTTCCGCC 57.338 40.909 3.45 0.00 39.12 6.13
512 517 1.765904 GGAAGGGCCAGTTTCCAAAAA 59.234 47.619 21.55 0.00 41.97 1.94
513 518 1.419381 GGAAGGGCCAGTTTCCAAAA 58.581 50.000 21.55 0.00 41.97 2.44
514 519 0.471022 GGGAAGGGCCAGTTTCCAAA 60.471 55.000 25.36 0.00 43.74 3.28
515 520 1.155155 GGGAAGGGCCAGTTTCCAA 59.845 57.895 25.36 0.00 43.74 3.53
516 521 1.660019 TTGGGAAGGGCCAGTTTCCA 61.660 55.000 25.36 19.80 43.74 3.53
517 522 0.471022 TTTGGGAAGGGCCAGTTTCC 60.471 55.000 19.41 19.41 41.71 3.13
518 523 1.419381 TTTTGGGAAGGGCCAGTTTC 58.581 50.000 6.18 5.13 38.95 2.78
519 524 1.886422 TTTTTGGGAAGGGCCAGTTT 58.114 45.000 6.18 0.00 38.95 2.66
520 525 3.644953 TTTTTGGGAAGGGCCAGTT 57.355 47.368 6.18 0.00 38.95 3.16
541 546 3.622627 TTTTTCGCGATACCGGTTTTT 57.377 38.095 15.04 0.00 36.06 1.94
542 547 3.835378 ATTTTTCGCGATACCGGTTTT 57.165 38.095 15.04 0.00 36.06 2.43
543 548 3.934579 AGTATTTTTCGCGATACCGGTTT 59.065 39.130 15.04 4.10 36.06 3.27
544 549 3.524541 AGTATTTTTCGCGATACCGGTT 58.475 40.909 15.04 0.00 36.06 4.44
545 550 3.169355 AGTATTTTTCGCGATACCGGT 57.831 42.857 13.98 13.98 36.06 5.28
546 551 3.426525 GGTAGTATTTTTCGCGATACCGG 59.573 47.826 10.88 0.00 36.06 5.28
547 552 4.293415 AGGTAGTATTTTTCGCGATACCG 58.707 43.478 20.97 0.00 37.00 4.02
548 553 5.750067 TCAAGGTAGTATTTTTCGCGATACC 59.250 40.000 20.08 20.08 33.02 2.73
549 554 6.254157 TGTCAAGGTAGTATTTTTCGCGATAC 59.746 38.462 10.88 9.78 0.00 2.24
550 555 6.331845 TGTCAAGGTAGTATTTTTCGCGATA 58.668 36.000 10.88 0.90 0.00 2.92
551 556 5.172934 TGTCAAGGTAGTATTTTTCGCGAT 58.827 37.500 10.88 0.00 0.00 4.58
552 557 4.558178 TGTCAAGGTAGTATTTTTCGCGA 58.442 39.130 3.71 3.71 0.00 5.87
553 558 4.724036 GCTGTCAAGGTAGTATTTTTCGCG 60.724 45.833 0.00 0.00 0.00 5.87
554 559 4.392138 AGCTGTCAAGGTAGTATTTTTCGC 59.608 41.667 0.00 0.00 30.55 4.70
555 560 5.671329 GCAGCTGTCAAGGTAGTATTTTTCG 60.671 44.000 16.64 0.00 31.35 3.46
556 561 5.412904 AGCAGCTGTCAAGGTAGTATTTTTC 59.587 40.000 16.64 0.00 31.35 2.29
557 562 5.182001 CAGCAGCTGTCAAGGTAGTATTTTT 59.818 40.000 16.64 0.00 31.35 1.94
558 563 4.697352 CAGCAGCTGTCAAGGTAGTATTTT 59.303 41.667 16.64 0.00 31.35 1.82
559 564 4.256920 CAGCAGCTGTCAAGGTAGTATTT 58.743 43.478 16.64 0.00 31.35 1.40
560 565 3.369892 CCAGCAGCTGTCAAGGTAGTATT 60.370 47.826 21.26 0.00 31.35 1.89
561 566 2.169352 CCAGCAGCTGTCAAGGTAGTAT 59.831 50.000 21.26 0.00 31.35 2.12
562 567 1.550524 CCAGCAGCTGTCAAGGTAGTA 59.449 52.381 21.26 0.00 31.35 1.82
563 568 0.322975 CCAGCAGCTGTCAAGGTAGT 59.677 55.000 21.26 0.00 31.35 2.73
564 569 0.322975 ACCAGCAGCTGTCAAGGTAG 59.677 55.000 21.26 5.62 31.35 3.18
565 570 1.550524 CTACCAGCAGCTGTCAAGGTA 59.449 52.381 21.26 18.80 31.35 3.08
566 571 0.322975 CTACCAGCAGCTGTCAAGGT 59.677 55.000 21.26 18.69 33.28 3.50
567 572 0.610174 TCTACCAGCAGCTGTCAAGG 59.390 55.000 21.26 14.03 0.00 3.61
568 573 1.405256 CCTCTACCAGCAGCTGTCAAG 60.405 57.143 21.26 14.25 0.00 3.02
569 574 0.610174 CCTCTACCAGCAGCTGTCAA 59.390 55.000 21.26 5.13 0.00 3.18
570 575 1.892819 GCCTCTACCAGCAGCTGTCA 61.893 60.000 21.26 7.30 0.00 3.58
571 576 1.153469 GCCTCTACCAGCAGCTGTC 60.153 63.158 21.26 7.83 0.00 3.51
572 577 2.985456 GCCTCTACCAGCAGCTGT 59.015 61.111 21.26 11.57 0.00 4.40
573 578 2.202851 CGCCTCTACCAGCAGCTG 60.203 66.667 16.23 16.23 0.00 4.24
574 579 3.465403 CCGCCTCTACCAGCAGCT 61.465 66.667 0.00 0.00 0.00 4.24
575 580 3.438017 CTCCGCCTCTACCAGCAGC 62.438 68.421 0.00 0.00 0.00 5.25
576 581 2.790791 CCTCCGCCTCTACCAGCAG 61.791 68.421 0.00 0.00 0.00 4.24
577 582 2.759973 CCTCCGCCTCTACCAGCA 60.760 66.667 0.00 0.00 0.00 4.41
578 583 3.541713 CCCTCCGCCTCTACCAGC 61.542 72.222 0.00 0.00 0.00 4.85
579 584 1.152440 ATCCCTCCGCCTCTACCAG 60.152 63.158 0.00 0.00 0.00 4.00
580 585 1.152525 GATCCCTCCGCCTCTACCA 60.153 63.158 0.00 0.00 0.00 3.25
581 586 0.759436 TTGATCCCTCCGCCTCTACC 60.759 60.000 0.00 0.00 0.00 3.18
582 587 1.001406 CATTGATCCCTCCGCCTCTAC 59.999 57.143 0.00 0.00 0.00 2.59
583 588 1.342074 CATTGATCCCTCCGCCTCTA 58.658 55.000 0.00 0.00 0.00 2.43
584 589 0.692419 ACATTGATCCCTCCGCCTCT 60.692 55.000 0.00 0.00 0.00 3.69
585 590 0.533755 CACATTGATCCCTCCGCCTC 60.534 60.000 0.00 0.00 0.00 4.70
586 591 0.982852 TCACATTGATCCCTCCGCCT 60.983 55.000 0.00 0.00 0.00 5.52
587 592 0.533755 CTCACATTGATCCCTCCGCC 60.534 60.000 0.00 0.00 0.00 6.13
588 593 0.533755 CCTCACATTGATCCCTCCGC 60.534 60.000 0.00 0.00 0.00 5.54
589 594 0.833287 ACCTCACATTGATCCCTCCG 59.167 55.000 0.00 0.00 0.00 4.63
590 595 1.202580 CGACCTCACATTGATCCCTCC 60.203 57.143 0.00 0.00 0.00 4.30
591 596 1.202580 CCGACCTCACATTGATCCCTC 60.203 57.143 0.00 0.00 0.00 4.30
592 597 0.833287 CCGACCTCACATTGATCCCT 59.167 55.000 0.00 0.00 0.00 4.20
593 598 0.815615 GCCGACCTCACATTGATCCC 60.816 60.000 0.00 0.00 0.00 3.85
594 599 0.815615 GGCCGACCTCACATTGATCC 60.816 60.000 0.00 0.00 0.00 3.36
595 600 0.107703 TGGCCGACCTCACATTGATC 60.108 55.000 0.00 0.00 36.63 2.92
596 601 0.548031 ATGGCCGACCTCACATTGAT 59.452 50.000 0.00 0.00 36.63 2.57
597 602 0.392863 CATGGCCGACCTCACATTGA 60.393 55.000 0.00 0.00 36.63 2.57
598 603 1.996786 GCATGGCCGACCTCACATTG 61.997 60.000 0.00 0.00 36.63 2.82
599 604 1.750399 GCATGGCCGACCTCACATT 60.750 57.895 0.00 0.00 36.63 2.71
600 605 2.124570 GCATGGCCGACCTCACAT 60.125 61.111 0.00 0.00 36.63 3.21
601 606 2.970379 ATGCATGGCCGACCTCACA 61.970 57.895 0.00 0.00 36.63 3.58
602 607 2.124570 ATGCATGGCCGACCTCAC 60.125 61.111 0.00 0.00 36.63 3.51
603 608 2.124612 CATGCATGGCCGACCTCA 60.125 61.111 19.40 0.00 36.63 3.86
604 609 1.031571 TTTCATGCATGGCCGACCTC 61.032 55.000 25.97 0.00 36.63 3.85
605 610 0.611618 TTTTCATGCATGGCCGACCT 60.612 50.000 25.97 0.00 36.63 3.85
606 611 0.458370 GTTTTCATGCATGGCCGACC 60.458 55.000 25.97 6.55 0.00 4.79
607 612 0.798009 CGTTTTCATGCATGGCCGAC 60.798 55.000 25.97 17.16 0.00 4.79
608 613 1.505807 CGTTTTCATGCATGGCCGA 59.494 52.632 25.97 4.13 0.00 5.54
609 614 2.160221 GCGTTTTCATGCATGGCCG 61.160 57.895 25.97 21.02 34.70 6.13
610 615 2.160221 CGCGTTTTCATGCATGGCC 61.160 57.895 25.97 10.60 34.13 5.36
611 616 0.526096 ATCGCGTTTTCATGCATGGC 60.526 50.000 25.97 18.91 34.13 4.40
612 617 1.847999 GAATCGCGTTTTCATGCATGG 59.152 47.619 25.97 10.93 34.13 3.66
613 618 2.780014 GAGAATCGCGTTTTCATGCATG 59.220 45.455 21.07 21.07 34.13 4.06
614 619 2.223340 GGAGAATCGCGTTTTCATGCAT 60.223 45.455 20.72 0.00 34.13 3.96
615 620 1.130373 GGAGAATCGCGTTTTCATGCA 59.870 47.619 20.72 0.00 34.13 3.96
616 621 1.531883 GGGAGAATCGCGTTTTCATGC 60.532 52.381 20.72 13.18 38.65 4.06
617 622 2.458592 GGGAGAATCGCGTTTTCATG 57.541 50.000 20.72 0.00 38.65 3.07
626 631 0.919300 GTCGTAAACGGGAGAATCGC 59.081 55.000 2.24 0.00 45.73 4.58
639 644 3.853831 TCTCCAAATAGCACGTCGTAA 57.146 42.857 0.00 0.00 0.00 3.18
899 911 5.985911 ACTGTCGGGCTATAGTGTATTTTT 58.014 37.500 0.84 0.00 0.00 1.94
900 912 5.609533 ACTGTCGGGCTATAGTGTATTTT 57.390 39.130 0.84 0.00 0.00 1.82
901 913 6.066690 TCTACTGTCGGGCTATAGTGTATTT 58.933 40.000 0.84 0.00 0.00 1.40
902 914 5.628130 TCTACTGTCGGGCTATAGTGTATT 58.372 41.667 0.84 0.00 0.00 1.89
903 915 5.238624 TCTACTGTCGGGCTATAGTGTAT 57.761 43.478 0.84 0.00 0.00 2.29
904 916 4.694760 TCTACTGTCGGGCTATAGTGTA 57.305 45.455 0.84 0.00 0.00 2.90
905 917 3.572632 TCTACTGTCGGGCTATAGTGT 57.427 47.619 0.84 0.00 0.00 3.55
906 918 3.253677 CCTTCTACTGTCGGGCTATAGTG 59.746 52.174 0.84 0.00 0.00 2.74
907 919 3.117587 ACCTTCTACTGTCGGGCTATAGT 60.118 47.826 0.84 0.00 0.00 2.12
908 920 3.488363 ACCTTCTACTGTCGGGCTATAG 58.512 50.000 0.00 0.00 0.00 1.31
909 921 3.589951 ACCTTCTACTGTCGGGCTATA 57.410 47.619 0.00 0.00 0.00 1.31
910 922 2.456073 ACCTTCTACTGTCGGGCTAT 57.544 50.000 0.00 0.00 0.00 2.97
920 932 5.972107 TCGCTAAACAGTAACCTTCTACT 57.028 39.130 0.00 0.00 32.13 2.57
923 935 3.995048 GCTTCGCTAAACAGTAACCTTCT 59.005 43.478 0.00 0.00 0.00 2.85
940 952 2.477525 GGTCACGAGTAAGTAGGCTTCG 60.478 54.545 0.00 0.00 36.22 3.79
951 963 0.328592 AGCTGGAGAGGTCACGAGTA 59.671 55.000 0.00 0.00 0.00 2.59
952 964 0.540830 AAGCTGGAGAGGTCACGAGT 60.541 55.000 0.00 0.00 0.00 4.18
954 966 1.587043 CGAAGCTGGAGAGGTCACGA 61.587 60.000 0.00 0.00 33.93 4.35
955 967 1.153939 CGAAGCTGGAGAGGTCACG 60.154 63.158 0.00 0.00 0.00 4.35
956 968 1.216710 CCGAAGCTGGAGAGGTCAC 59.783 63.158 0.00 0.00 0.00 3.67
957 969 1.228894 ACCGAAGCTGGAGAGGTCA 60.229 57.895 0.00 0.00 0.00 4.02
1195 1207 2.075355 TTGGGGATGGCGGTCAAGTT 62.075 55.000 0.00 0.00 0.00 2.66
1196 1208 2.534396 TTGGGGATGGCGGTCAAGT 61.534 57.895 0.00 0.00 0.00 3.16
1305 1317 0.972471 TTGGCAGCATCTCCTCGAGA 60.972 55.000 15.71 0.00 43.20 4.04
1497 1535 2.811317 GAGTTGGCGCTCTCACCG 60.811 66.667 7.64 0.00 32.99 4.94
1553 1595 6.747280 GCAGTATAATTGAGCAACACGAAATT 59.253 34.615 0.00 0.00 0.00 1.82
1630 1693 2.224281 ACACAAGATCGGCTGAAACTCA 60.224 45.455 0.00 0.00 0.00 3.41
1677 1740 2.967397 CACTACGAACTCCCGCCA 59.033 61.111 0.00 0.00 0.00 5.69
1682 1745 2.183555 CCGGGCACTACGAACTCC 59.816 66.667 0.00 0.00 0.00 3.85
1769 1832 4.516195 GGGCGACGAAGGCTCCTC 62.516 72.222 0.00 0.00 36.85 3.71
1789 1852 2.422803 GCAGGGGCCAATTGAGTACATA 60.423 50.000 7.12 0.00 0.00 2.29
1798 1861 2.041612 GGGATGCAGGGGCCAATT 60.042 61.111 4.39 0.00 40.13 2.32
1953 2016 2.994995 TCGTGACGAGCCCCATGT 60.995 61.111 2.39 0.00 0.00 3.21
1973 2036 2.317609 CCCACAGGAACTTGACGCG 61.318 63.158 3.53 3.53 34.60 6.01
1993 2056 3.573772 CTGCGCTTGGTCGTGGAGA 62.574 63.158 9.73 0.00 35.21 3.71
2085 2154 2.398554 CCAACGGAAGGATGGCACG 61.399 63.158 0.00 0.00 35.81 5.34
2116 2185 1.672356 GGAGTTCATGCCGCAGTGT 60.672 57.895 0.00 0.00 0.00 3.55
2158 2227 2.093658 GGGAAGAGTAAGCATCGGAACA 60.094 50.000 0.00 0.00 0.00 3.18
2183 2252 3.403394 TGGTAGGCTGGTCCATACCTATA 59.597 47.826 19.06 11.54 46.91 1.31
2184 2253 2.181419 TGGTAGGCTGGTCCATACCTAT 59.819 50.000 19.06 2.27 46.91 2.57
2185 2254 1.576757 TGGTAGGCTGGTCCATACCTA 59.423 52.381 17.42 15.87 46.91 3.08
2186 2255 0.341961 TGGTAGGCTGGTCCATACCT 59.658 55.000 17.42 16.71 46.91 3.08
2201 2270 1.748403 GATCAGGCGGCTGATGGTA 59.252 57.895 46.81 26.49 43.38 3.25
2217 2286 0.809385 ATCTTCCACACGTCGACGAT 59.191 50.000 41.52 26.48 43.02 3.73
2246 2315 5.123027 GTCAGGTTGCATCTTCTCTTTAAGG 59.877 44.000 0.00 0.00 0.00 2.69
2337 2406 2.232298 CTCCTCACCCCGTTGCTCTC 62.232 65.000 0.00 0.00 0.00 3.20
2345 2414 4.154347 GCTCTGCTCCTCACCCCG 62.154 72.222 0.00 0.00 0.00 5.73
2387 2456 0.824109 CACCGTCTTGGATGGCTCTA 59.176 55.000 5.77 0.00 42.09 2.43
2466 2535 5.398353 GGATTCAGAGAGGGATGGATGAAAA 60.398 44.000 0.00 0.00 31.14 2.29
2469 2538 3.246301 GGATTCAGAGAGGGATGGATGA 58.754 50.000 0.00 0.00 0.00 2.92
2472 2541 2.248423 TCTGGATTCAGAGAGGGATGGA 59.752 50.000 0.00 0.00 44.39 3.41
2473 2542 2.687297 TCTGGATTCAGAGAGGGATGG 58.313 52.381 0.00 0.00 44.39 3.51
2483 2552 3.055240 AGAGGCAAGAGTTCTGGATTCAG 60.055 47.826 0.00 0.00 42.21 3.02
2485 2554 3.055530 TCAGAGGCAAGAGTTCTGGATTC 60.056 47.826 1.38 0.00 39.01 2.52
2486 2555 2.909006 TCAGAGGCAAGAGTTCTGGATT 59.091 45.455 1.38 0.00 39.01 3.01
2487 2556 2.544721 TCAGAGGCAAGAGTTCTGGAT 58.455 47.619 1.38 0.00 39.01 3.41
2488 2557 2.015456 TCAGAGGCAAGAGTTCTGGA 57.985 50.000 1.38 0.00 39.01 3.86
2489 2558 2.738000 CGATCAGAGGCAAGAGTTCTGG 60.738 54.545 0.00 0.00 39.01 3.86
2490 2559 2.094286 ACGATCAGAGGCAAGAGTTCTG 60.094 50.000 0.00 0.00 39.69 3.02
2491 2560 2.175202 ACGATCAGAGGCAAGAGTTCT 58.825 47.619 0.00 0.00 0.00 3.01
2492 2561 2.663826 ACGATCAGAGGCAAGAGTTC 57.336 50.000 0.00 0.00 0.00 3.01
2493 2562 3.093057 AGTACGATCAGAGGCAAGAGTT 58.907 45.455 0.00 0.00 0.00 3.01
2494 2563 2.685897 GAGTACGATCAGAGGCAAGAGT 59.314 50.000 0.00 0.00 0.00 3.24
2496 2565 1.671328 CGAGTACGATCAGAGGCAAGA 59.329 52.381 0.00 0.00 42.66 3.02
2497 2566 1.671328 TCGAGTACGATCAGAGGCAAG 59.329 52.381 0.00 0.00 43.81 4.01
2499 2568 3.471354 TCGAGTACGATCAGAGGCA 57.529 52.632 0.00 0.00 43.81 4.75
2617 4227 1.369692 GTCCGATGACACCACCACA 59.630 57.895 0.00 0.00 41.37 4.17
2773 4383 1.001641 GAGGATGTGCAAGGTGGCT 60.002 57.895 0.00 0.00 34.04 4.75


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

AutoCloner maintained by Alex Coulton.