Multiple sequence alignment - TraesCS4D01G142400

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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 TraesCS4D01G142400 chr4D 100.000 3686 0 0 1 3686 127927176 127930861 0.000000e+00 6807.0
1 TraesCS4D01G142400 chr4D 88.966 290 28 4 2792 3078 85627640 85627928 4.530000e-94 355.0
2 TraesCS4D01G142400 chr4D 79.387 359 64 9 33 385 458156947 458156593 1.020000e-60 244.0
3 TraesCS4D01G142400 chr3A 97.684 3023 65 3 668 3686 10290395 10293416 0.000000e+00 5190.0
4 TraesCS4D01G142400 chr3A 95.396 391 11 4 1 385 10289993 10290382 1.880000e-172 616.0
5 TraesCS4D01G142400 chr3A 88.462 78 5 4 2789 2862 109879762 109879685 1.410000e-14 91.6
6 TraesCS4D01G142400 chr4B 93.117 3051 159 23 668 3686 191788012 191791043 0.000000e+00 4423.0
7 TraesCS4D01G142400 chr4B 84.564 298 33 9 386 671 60643085 60642789 2.170000e-72 283.0
8 TraesCS4D01G142400 chr4B 88.557 201 23 0 386 586 581519805 581520005 1.020000e-60 244.0
9 TraesCS4D01G142400 chr4A 94.063 1954 81 7 668 2590 440255494 440253545 0.000000e+00 2933.0
10 TraesCS4D01G142400 chr4A 90.680 397 23 11 1 385 440255901 440255507 1.960000e-142 516.0
11 TraesCS4D01G142400 chr7A 88.845 762 79 5 2928 3686 8585251 8586009 0.000000e+00 931.0
12 TraesCS4D01G142400 chr7A 76.769 947 155 37 1254 2193 126919190 126918302 1.550000e-128 470.0
13 TraesCS4D01G142400 chr7A 81.988 161 19 8 1463 1618 80143644 80143799 1.070000e-25 128.0
14 TraesCS4D01G142400 chr7A 91.429 70 5 1 2787 2856 520586087 520586019 1.090000e-15 95.3
15 TraesCS4D01G142400 chr2D 84.111 900 130 10 2790 3686 393209604 393210493 0.000000e+00 857.0
16 TraesCS4D01G142400 chr5B 82.594 902 131 16 2793 3675 222296573 222295679 0.000000e+00 773.0
17 TraesCS4D01G142400 chr5D 81.778 900 151 9 2791 3686 350437426 350438316 0.000000e+00 741.0
18 TraesCS4D01G142400 chr5D 90.541 74 6 1 2783 2856 247788241 247788313 3.030000e-16 97.1
19 TraesCS4D01G142400 chr6B 81.031 912 155 12 2788 3686 648805020 648805926 0.000000e+00 710.0
20 TraesCS4D01G142400 chr6B 94.706 170 9 0 386 555 671539949 671540118 7.850000e-67 265.0
21 TraesCS4D01G142400 chr2A 82.821 780 118 12 2789 3557 662749845 662750619 0.000000e+00 684.0
22 TraesCS4D01G142400 chr7B 75.907 1461 272 50 1254 2691 86165887 86164484 0.000000e+00 675.0
23 TraesCS4D01G142400 chr7B 84.459 296 32 8 386 668 59920711 59921005 2.800000e-71 279.0
24 TraesCS4D01G142400 chr7B 84.333 300 31 10 386 671 364265631 364265334 2.800000e-71 279.0
25 TraesCS4D01G142400 chr7B 83.946 299 35 4 386 671 507010133 507009835 1.300000e-69 274.0
26 TraesCS4D01G142400 chr7B 82.166 157 18 7 1463 1614 22463401 22463552 3.860000e-25 126.0
27 TraesCS4D01G142400 chr3B 80.330 910 152 21 2792 3686 446061636 446060739 0.000000e+00 664.0
28 TraesCS4D01G142400 chr2B 81.439 792 140 6 2899 3686 542954111 542953323 3.100000e-180 641.0
29 TraesCS4D01G142400 chr2B 93.846 65 4 0 2791 2855 326850460 326850524 8.420000e-17 99.0
30 TraesCS4D01G142400 chr7D 75.360 1457 278 49 1254 2691 124504984 124503590 8.690000e-176 627.0
31 TraesCS4D01G142400 chr7D 90.236 297 16 3 386 670 109438510 109438805 3.480000e-100 375.0
32 TraesCS4D01G142400 chr7D 81.646 158 17 10 1463 1614 75956101 75955950 1.800000e-23 121.0
33 TraesCS4D01G142400 chr5A 89.347 291 18 4 391 668 101767366 101767656 1.630000e-93 353.0
34 TraesCS4D01G142400 chr1B 82.392 301 38 9 386 671 593511900 593512200 7.900000e-62 248.0
35 TraesCS4D01G142400 chr1B 78.889 360 52 21 33 380 98429050 98429397 4.790000e-54 222.0
36 TraesCS4D01G142400 chr1A 93.464 153 10 0 2793 2945 13822538 13822690 1.030000e-55 228.0
37 TraesCS4D01G142400 chrUn 78.889 360 52 21 33 380 397660239 397660586 4.790000e-54 222.0


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 TraesCS4D01G142400 chr4D 127927176 127930861 3685 False 6807.0 6807 100.0000 1 3686 1 chr4D.!!$F2 3685
1 TraesCS4D01G142400 chr3A 10289993 10293416 3423 False 2903.0 5190 96.5400 1 3686 2 chr3A.!!$F1 3685
2 TraesCS4D01G142400 chr4B 191788012 191791043 3031 False 4423.0 4423 93.1170 668 3686 1 chr4B.!!$F1 3018
3 TraesCS4D01G142400 chr4A 440253545 440255901 2356 True 1724.5 2933 92.3715 1 2590 2 chr4A.!!$R1 2589
4 TraesCS4D01G142400 chr7A 8585251 8586009 758 False 931.0 931 88.8450 2928 3686 1 chr7A.!!$F1 758
5 TraesCS4D01G142400 chr7A 126918302 126919190 888 True 470.0 470 76.7690 1254 2193 1 chr7A.!!$R1 939
6 TraesCS4D01G142400 chr2D 393209604 393210493 889 False 857.0 857 84.1110 2790 3686 1 chr2D.!!$F1 896
7 TraesCS4D01G142400 chr5B 222295679 222296573 894 True 773.0 773 82.5940 2793 3675 1 chr5B.!!$R1 882
8 TraesCS4D01G142400 chr5D 350437426 350438316 890 False 741.0 741 81.7780 2791 3686 1 chr5D.!!$F2 895
9 TraesCS4D01G142400 chr6B 648805020 648805926 906 False 710.0 710 81.0310 2788 3686 1 chr6B.!!$F1 898
10 TraesCS4D01G142400 chr2A 662749845 662750619 774 False 684.0 684 82.8210 2789 3557 1 chr2A.!!$F1 768
11 TraesCS4D01G142400 chr7B 86164484 86165887 1403 True 675.0 675 75.9070 1254 2691 1 chr7B.!!$R1 1437
12 TraesCS4D01G142400 chr3B 446060739 446061636 897 True 664.0 664 80.3300 2792 3686 1 chr3B.!!$R1 894
13 TraesCS4D01G142400 chr2B 542953323 542954111 788 True 641.0 641 81.4390 2899 3686 1 chr2B.!!$R1 787
14 TraesCS4D01G142400 chr7D 124503590 124504984 1394 True 627.0 627 75.3600 1254 2691 1 chr7D.!!$R2 1437

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
417 430 0.036952 CGGATAGGGATGCGCTTGAT 60.037 55.0 9.73 0.0 40.16 2.57 F
467 480 0.115349 ATCTCCCTATCTCCACCCCG 59.885 60.0 0.00 0.0 0.00 5.73 F
584 597 0.179004 TTTGCTCGTCCATGTTGGGT 60.179 50.0 0.00 0.0 38.32 4.51 F
587 600 0.605319 GCTCGTCCATGTTGGGTGAA 60.605 55.0 0.00 0.0 38.32 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2220 2311 0.035317 AAAGCATCAGGACTGCGACA 59.965 50.000 0.0 0.0 44.38 4.35 R
2507 2598 0.109086 CACGTCGGCTCTCATCTTGT 60.109 55.000 0.0 0.0 0.00 3.16 R
2544 2635 1.226542 CATGCAGGGCTCCACAGAT 59.773 57.895 0.0 0.0 0.00 2.90 R
2696 2793 4.398319 CAGGGATACAACAAACTGGAGTT 58.602 43.478 0.0 0.0 38.08 3.01 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
68 69 2.627945 TGTTGCGGGTGTTGATATCTC 58.372 47.619 3.98 0.00 0.00 2.75
292 305 4.258543 GACCCCATCGAACAAAGTATCAA 58.741 43.478 0.00 0.00 0.00 2.57
316 329 3.258372 TCCCACACCAAGAGATATATCGC 59.742 47.826 8.29 8.29 0.00 4.58
343 356 7.835634 TGATATAAGAACGCATTACACACAA 57.164 32.000 0.00 0.00 0.00 3.33
385 398 9.371136 CTGTATGTACACATAACTCATTTCACT 57.629 33.333 0.00 0.00 40.18 3.41
386 399 9.719355 TGTATGTACACATAACTCATTTCACTT 57.281 29.630 0.00 0.00 40.18 3.16
387 400 9.973246 GTATGTACACATAACTCATTTCACTTG 57.027 33.333 0.00 0.00 40.18 3.16
388 401 8.846943 ATGTACACATAACTCATTTCACTTGA 57.153 30.769 0.00 0.00 34.26 3.02
389 402 8.846943 TGTACACATAACTCATTTCACTTGAT 57.153 30.769 0.00 0.00 0.00 2.57
394 407 9.778993 CACATAACTCATTTCACTTGATTAAGG 57.221 33.333 1.95 0.00 38.26 2.69
395 408 9.739276 ACATAACTCATTTCACTTGATTAAGGA 57.261 29.630 1.95 0.00 38.26 3.36
397 410 7.693969 AACTCATTTCACTTGATTAAGGAGG 57.306 36.000 1.95 0.00 38.26 4.30
398 411 5.649831 ACTCATTTCACTTGATTAAGGAGGC 59.350 40.000 1.95 0.00 38.26 4.70
399 412 4.635765 TCATTTCACTTGATTAAGGAGGCG 59.364 41.667 1.95 0.00 38.26 5.52
400 413 2.691409 TCACTTGATTAAGGAGGCGG 57.309 50.000 1.95 0.00 38.26 6.13
401 414 2.184533 TCACTTGATTAAGGAGGCGGA 58.815 47.619 1.95 0.00 38.26 5.54
402 415 2.771943 TCACTTGATTAAGGAGGCGGAT 59.228 45.455 1.95 0.00 38.26 4.18
403 416 3.964688 TCACTTGATTAAGGAGGCGGATA 59.035 43.478 1.95 0.00 38.26 2.59
404 417 4.039245 TCACTTGATTAAGGAGGCGGATAG 59.961 45.833 1.95 0.00 38.26 2.08
405 418 3.325135 ACTTGATTAAGGAGGCGGATAGG 59.675 47.826 1.95 0.00 38.26 2.57
406 419 2.257207 TGATTAAGGAGGCGGATAGGG 58.743 52.381 0.00 0.00 0.00 3.53
407 420 2.158219 TGATTAAGGAGGCGGATAGGGA 60.158 50.000 0.00 0.00 0.00 4.20
408 421 2.715763 TTAAGGAGGCGGATAGGGAT 57.284 50.000 0.00 0.00 0.00 3.85
409 422 1.938585 TAAGGAGGCGGATAGGGATG 58.061 55.000 0.00 0.00 0.00 3.51
410 423 1.484444 AAGGAGGCGGATAGGGATGC 61.484 60.000 0.00 0.00 0.00 3.91
415 428 3.957260 CGGATAGGGATGCGCTTG 58.043 61.111 9.73 0.00 40.16 4.01
416 429 1.367471 CGGATAGGGATGCGCTTGA 59.633 57.895 9.73 0.00 40.16 3.02
417 430 0.036952 CGGATAGGGATGCGCTTGAT 60.037 55.000 9.73 0.00 40.16 2.57
418 431 1.609061 CGGATAGGGATGCGCTTGATT 60.609 52.381 9.73 0.00 40.16 2.57
419 432 2.508526 GGATAGGGATGCGCTTGATTT 58.491 47.619 9.73 0.00 0.00 2.17
420 433 2.227388 GGATAGGGATGCGCTTGATTTG 59.773 50.000 9.73 0.00 0.00 2.32
421 434 2.708216 TAGGGATGCGCTTGATTTGA 57.292 45.000 9.73 0.00 0.00 2.69
422 435 2.062971 AGGGATGCGCTTGATTTGAT 57.937 45.000 9.73 0.00 0.00 2.57
423 436 1.679680 AGGGATGCGCTTGATTTGATG 59.320 47.619 9.73 0.00 0.00 3.07
424 437 1.677576 GGGATGCGCTTGATTTGATGA 59.322 47.619 9.73 0.00 0.00 2.92
425 438 2.295349 GGGATGCGCTTGATTTGATGAT 59.705 45.455 9.73 0.00 0.00 2.45
426 439 3.243636 GGGATGCGCTTGATTTGATGATT 60.244 43.478 9.73 0.00 0.00 2.57
427 440 4.365723 GGATGCGCTTGATTTGATGATTT 58.634 39.130 9.73 0.00 0.00 2.17
428 441 4.443394 GGATGCGCTTGATTTGATGATTTC 59.557 41.667 9.73 0.00 0.00 2.17
429 442 3.772932 TGCGCTTGATTTGATGATTTCC 58.227 40.909 9.73 0.00 0.00 3.13
430 443 3.193056 TGCGCTTGATTTGATGATTTCCA 59.807 39.130 9.73 0.00 0.00 3.53
431 444 4.175516 GCGCTTGATTTGATGATTTCCAA 58.824 39.130 0.00 0.00 0.00 3.53
432 445 4.266976 GCGCTTGATTTGATGATTTCCAAG 59.733 41.667 0.00 0.00 34.39 3.61
433 446 5.643664 CGCTTGATTTGATGATTTCCAAGA 58.356 37.500 0.00 0.00 33.42 3.02
434 447 6.270815 CGCTTGATTTGATGATTTCCAAGAT 58.729 36.000 0.00 0.00 33.42 2.40
435 448 6.417044 CGCTTGATTTGATGATTTCCAAGATC 59.583 38.462 0.00 0.00 33.42 2.75
436 449 6.700520 GCTTGATTTGATGATTTCCAAGATCC 59.299 38.462 0.00 0.00 33.42 3.36
437 450 6.381481 TGATTTGATGATTTCCAAGATCCG 57.619 37.500 0.00 0.00 0.00 4.18
438 451 5.300034 TGATTTGATGATTTCCAAGATCCGG 59.700 40.000 0.00 0.00 0.00 5.14
439 452 3.931907 TGATGATTTCCAAGATCCGGT 57.068 42.857 0.00 0.00 0.00 5.28
440 453 3.808728 TGATGATTTCCAAGATCCGGTC 58.191 45.455 0.00 0.00 0.00 4.79
441 454 3.455910 TGATGATTTCCAAGATCCGGTCT 59.544 43.478 0.00 0.30 39.43 3.85
443 456 3.873910 TGATTTCCAAGATCCGGTCTTC 58.126 45.455 14.09 5.28 45.35 2.87
444 457 3.519510 TGATTTCCAAGATCCGGTCTTCT 59.480 43.478 14.09 7.27 45.35 2.85
445 458 3.334583 TTTCCAAGATCCGGTCTTCTG 57.665 47.619 14.09 9.90 45.35 3.02
446 459 0.537188 TCCAAGATCCGGTCTTCTGC 59.463 55.000 14.09 0.00 45.35 4.26
447 460 0.539051 CCAAGATCCGGTCTTCTGCT 59.461 55.000 14.09 0.00 45.35 4.24
448 461 1.757118 CCAAGATCCGGTCTTCTGCTA 59.243 52.381 14.09 0.00 45.35 3.49
449 462 2.366916 CCAAGATCCGGTCTTCTGCTAT 59.633 50.000 14.09 0.00 45.35 2.97
450 463 3.553922 CCAAGATCCGGTCTTCTGCTATC 60.554 52.174 14.09 1.78 45.35 2.08
451 464 3.237268 AGATCCGGTCTTCTGCTATCT 57.763 47.619 0.00 0.00 31.47 1.98
452 465 3.153919 AGATCCGGTCTTCTGCTATCTC 58.846 50.000 0.00 0.00 31.47 2.75
453 466 1.693627 TCCGGTCTTCTGCTATCTCC 58.306 55.000 0.00 0.00 0.00 3.71
454 467 0.676736 CCGGTCTTCTGCTATCTCCC 59.323 60.000 0.00 0.00 0.00 4.30
455 468 1.698506 CGGTCTTCTGCTATCTCCCT 58.301 55.000 0.00 0.00 0.00 4.20
456 469 2.489255 CCGGTCTTCTGCTATCTCCCTA 60.489 54.545 0.00 0.00 0.00 3.53
457 470 3.426615 CGGTCTTCTGCTATCTCCCTAT 58.573 50.000 0.00 0.00 0.00 2.57
458 471 3.442273 CGGTCTTCTGCTATCTCCCTATC 59.558 52.174 0.00 0.00 0.00 2.08
459 472 4.672899 GGTCTTCTGCTATCTCCCTATCT 58.327 47.826 0.00 0.00 0.00 1.98
460 473 4.705023 GGTCTTCTGCTATCTCCCTATCTC 59.295 50.000 0.00 0.00 0.00 2.75
461 474 4.705023 GTCTTCTGCTATCTCCCTATCTCC 59.295 50.000 0.00 0.00 0.00 3.71
462 475 4.355287 TCTTCTGCTATCTCCCTATCTCCA 59.645 45.833 0.00 0.00 0.00 3.86
463 476 4.040936 TCTGCTATCTCCCTATCTCCAC 57.959 50.000 0.00 0.00 0.00 4.02
464 477 3.096092 CTGCTATCTCCCTATCTCCACC 58.904 54.545 0.00 0.00 0.00 4.61
465 478 2.225394 TGCTATCTCCCTATCTCCACCC 60.225 54.545 0.00 0.00 0.00 4.61
466 479 2.890602 GCTATCTCCCTATCTCCACCCC 60.891 59.091 0.00 0.00 0.00 4.95
467 480 0.115349 ATCTCCCTATCTCCACCCCG 59.885 60.000 0.00 0.00 0.00 5.73
468 481 1.233369 CTCCCTATCTCCACCCCGT 59.767 63.158 0.00 0.00 0.00 5.28
469 482 1.075525 TCCCTATCTCCACCCCGTG 60.076 63.158 0.00 0.00 0.00 4.94
470 483 2.808206 CCCTATCTCCACCCCGTGC 61.808 68.421 0.00 0.00 31.34 5.34
471 484 2.808206 CCTATCTCCACCCCGTGCC 61.808 68.421 0.00 0.00 31.34 5.01
472 485 3.151710 TATCTCCACCCCGTGCCG 61.152 66.667 0.00 0.00 31.34 5.69
473 486 3.665515 TATCTCCACCCCGTGCCGA 62.666 63.158 0.00 0.00 31.34 5.54
480 493 4.514577 CCCCGTGCCGACAGCTAG 62.515 72.222 0.00 0.00 44.23 3.42
481 494 4.514577 CCCGTGCCGACAGCTAGG 62.515 72.222 0.00 0.00 44.23 3.02
482 495 3.760035 CCGTGCCGACAGCTAGGT 61.760 66.667 0.00 0.00 44.23 3.08
483 496 2.507102 CGTGCCGACAGCTAGGTG 60.507 66.667 20.16 20.16 44.23 4.00
484 497 2.657237 GTGCCGACAGCTAGGTGT 59.343 61.111 26.83 26.83 44.23 4.16
485 498 1.004918 GTGCCGACAGCTAGGTGTT 60.005 57.895 27.14 12.25 44.23 3.32
486 499 1.005037 TGCCGACAGCTAGGTGTTG 60.005 57.895 28.31 28.31 44.23 3.33
487 500 2.391389 GCCGACAGCTAGGTGTTGC 61.391 63.158 29.39 27.03 38.99 4.17
488 501 1.293498 CCGACAGCTAGGTGTTGCT 59.707 57.895 29.39 9.38 40.54 3.91
493 506 2.765352 AGCTAGGTGTTGCTGGTCT 58.235 52.632 0.00 0.00 38.21 3.85
494 507 1.059913 AGCTAGGTGTTGCTGGTCTT 58.940 50.000 0.00 0.00 38.21 3.01
495 508 2.257207 AGCTAGGTGTTGCTGGTCTTA 58.743 47.619 0.00 0.00 38.21 2.10
496 509 2.840651 AGCTAGGTGTTGCTGGTCTTAT 59.159 45.455 0.00 0.00 38.21 1.73
497 510 2.939103 GCTAGGTGTTGCTGGTCTTATG 59.061 50.000 0.00 0.00 0.00 1.90
498 511 3.619979 GCTAGGTGTTGCTGGTCTTATGT 60.620 47.826 0.00 0.00 0.00 2.29
499 512 3.508845 AGGTGTTGCTGGTCTTATGTT 57.491 42.857 0.00 0.00 0.00 2.71
500 513 3.832527 AGGTGTTGCTGGTCTTATGTTT 58.167 40.909 0.00 0.00 0.00 2.83
501 514 3.569701 AGGTGTTGCTGGTCTTATGTTTG 59.430 43.478 0.00 0.00 0.00 2.93
502 515 3.305335 GGTGTTGCTGGTCTTATGTTTGG 60.305 47.826 0.00 0.00 0.00 3.28
503 516 2.295909 TGTTGCTGGTCTTATGTTTGGC 59.704 45.455 0.00 0.00 0.00 4.52
504 517 1.164411 TGCTGGTCTTATGTTTGGCG 58.836 50.000 0.00 0.00 0.00 5.69
505 518 1.165270 GCTGGTCTTATGTTTGGCGT 58.835 50.000 0.00 0.00 0.00 5.68
506 519 1.130561 GCTGGTCTTATGTTTGGCGTC 59.869 52.381 0.00 0.00 0.00 5.19
507 520 2.699954 CTGGTCTTATGTTTGGCGTCT 58.300 47.619 0.00 0.00 0.00 4.18
508 521 3.074412 CTGGTCTTATGTTTGGCGTCTT 58.926 45.455 0.00 0.00 0.00 3.01
509 522 3.482436 TGGTCTTATGTTTGGCGTCTTT 58.518 40.909 0.00 0.00 0.00 2.52
510 523 4.643463 TGGTCTTATGTTTGGCGTCTTTA 58.357 39.130 0.00 0.00 0.00 1.85
511 524 4.693566 TGGTCTTATGTTTGGCGTCTTTAG 59.306 41.667 0.00 0.00 0.00 1.85
512 525 4.694037 GGTCTTATGTTTGGCGTCTTTAGT 59.306 41.667 0.00 0.00 0.00 2.24
513 526 5.163884 GGTCTTATGTTTGGCGTCTTTAGTC 60.164 44.000 0.00 0.00 0.00 2.59
514 527 4.933400 TCTTATGTTTGGCGTCTTTAGTCC 59.067 41.667 0.00 0.00 0.00 3.85
515 528 1.886886 TGTTTGGCGTCTTTAGTCCC 58.113 50.000 0.00 0.00 0.00 4.46
516 529 1.418637 TGTTTGGCGTCTTTAGTCCCT 59.581 47.619 0.00 0.00 0.00 4.20
517 530 2.074576 GTTTGGCGTCTTTAGTCCCTC 58.925 52.381 0.00 0.00 0.00 4.30
518 531 0.611714 TTGGCGTCTTTAGTCCCTCC 59.388 55.000 0.00 0.00 0.00 4.30
519 532 1.141234 GGCGTCTTTAGTCCCTCCG 59.859 63.158 0.00 0.00 0.00 4.63
520 533 1.141234 GCGTCTTTAGTCCCTCCGG 59.859 63.158 0.00 0.00 0.00 5.14
521 534 1.141234 CGTCTTTAGTCCCTCCGGC 59.859 63.158 0.00 0.00 0.00 6.13
522 535 1.521141 GTCTTTAGTCCCTCCGGCC 59.479 63.158 0.00 0.00 0.00 6.13
523 536 0.976590 GTCTTTAGTCCCTCCGGCCT 60.977 60.000 0.00 0.00 0.00 5.19
524 537 0.976073 TCTTTAGTCCCTCCGGCCTG 60.976 60.000 0.00 0.00 0.00 4.85
525 538 2.595009 CTTTAGTCCCTCCGGCCTGC 62.595 65.000 0.00 0.00 0.00 4.85
538 551 3.112075 CCTGCGTGCCGTGTACTG 61.112 66.667 0.00 0.00 0.00 2.74
539 552 3.112075 CTGCGTGCCGTGTACTGG 61.112 66.667 0.00 0.00 0.00 4.00
546 559 3.000819 CCGTGTACTGGCCTGGGA 61.001 66.667 14.82 0.00 0.00 4.37
547 560 2.579201 CGTGTACTGGCCTGGGAG 59.421 66.667 14.82 0.00 0.00 4.30
548 561 2.269241 GTGTACTGGCCTGGGAGC 59.731 66.667 14.82 1.78 0.00 4.70
556 569 2.512896 GCCTGGGAGCCATGTAGG 59.487 66.667 0.00 0.00 41.84 3.18
570 583 5.841957 CCATGTAGGCTATTTCTTTTGCT 57.158 39.130 0.00 0.00 0.00 3.91
571 584 5.825507 CCATGTAGGCTATTTCTTTTGCTC 58.174 41.667 0.00 0.00 0.00 4.26
572 585 5.504665 CCATGTAGGCTATTTCTTTTGCTCG 60.505 44.000 0.00 0.00 0.00 5.03
573 586 4.575885 TGTAGGCTATTTCTTTTGCTCGT 58.424 39.130 0.00 0.00 0.00 4.18
574 587 4.630069 TGTAGGCTATTTCTTTTGCTCGTC 59.370 41.667 0.00 0.00 0.00 4.20
575 588 3.010420 AGGCTATTTCTTTTGCTCGTCC 58.990 45.455 0.00 0.00 0.00 4.79
576 589 2.747446 GGCTATTTCTTTTGCTCGTCCA 59.253 45.455 0.00 0.00 0.00 4.02
577 590 3.378427 GGCTATTTCTTTTGCTCGTCCAT 59.622 43.478 0.00 0.00 0.00 3.41
578 591 4.346129 GCTATTTCTTTTGCTCGTCCATG 58.654 43.478 0.00 0.00 0.00 3.66
579 592 4.142600 GCTATTTCTTTTGCTCGTCCATGT 60.143 41.667 0.00 0.00 0.00 3.21
580 593 4.853924 ATTTCTTTTGCTCGTCCATGTT 57.146 36.364 0.00 0.00 0.00 2.71
581 594 3.624326 TTCTTTTGCTCGTCCATGTTG 57.376 42.857 0.00 0.00 0.00 3.33
582 595 1.879380 TCTTTTGCTCGTCCATGTTGG 59.121 47.619 0.00 0.00 39.43 3.77
583 596 0.958091 TTTTGCTCGTCCATGTTGGG 59.042 50.000 0.00 0.00 38.32 4.12
584 597 0.179004 TTTGCTCGTCCATGTTGGGT 60.179 50.000 0.00 0.00 38.32 4.51
585 598 0.888736 TTGCTCGTCCATGTTGGGTG 60.889 55.000 0.00 0.00 38.32 4.61
586 599 1.003839 GCTCGTCCATGTTGGGTGA 60.004 57.895 0.00 0.00 38.32 4.02
587 600 0.605319 GCTCGTCCATGTTGGGTGAA 60.605 55.000 0.00 0.00 38.32 3.18
588 601 1.442769 CTCGTCCATGTTGGGTGAAG 58.557 55.000 0.00 0.00 38.32 3.02
589 602 0.762418 TCGTCCATGTTGGGTGAAGT 59.238 50.000 0.00 0.00 38.32 3.01
590 603 1.156736 CGTCCATGTTGGGTGAAGTC 58.843 55.000 0.00 0.00 38.32 3.01
591 604 1.270839 CGTCCATGTTGGGTGAAGTCT 60.271 52.381 0.00 0.00 38.32 3.24
592 605 2.810400 CGTCCATGTTGGGTGAAGTCTT 60.810 50.000 0.00 0.00 38.32 3.01
593 606 3.222603 GTCCATGTTGGGTGAAGTCTTT 58.777 45.455 0.00 0.00 38.32 2.52
594 607 3.004734 GTCCATGTTGGGTGAAGTCTTTG 59.995 47.826 0.00 0.00 38.32 2.77
595 608 2.958355 CCATGTTGGGTGAAGTCTTTGT 59.042 45.455 0.00 0.00 32.67 2.83
596 609 3.384467 CCATGTTGGGTGAAGTCTTTGTT 59.616 43.478 0.00 0.00 32.67 2.83
597 610 4.362279 CATGTTGGGTGAAGTCTTTGTTG 58.638 43.478 0.00 0.00 0.00 3.33
598 611 3.426615 TGTTGGGTGAAGTCTTTGTTGT 58.573 40.909 0.00 0.00 0.00 3.32
599 612 3.442273 TGTTGGGTGAAGTCTTTGTTGTC 59.558 43.478 0.00 0.00 0.00 3.18
600 613 2.650322 TGGGTGAAGTCTTTGTTGTCC 58.350 47.619 0.00 0.00 0.00 4.02
601 614 1.602377 GGGTGAAGTCTTTGTTGTCCG 59.398 52.381 0.00 0.00 0.00 4.79
602 615 2.285977 GGTGAAGTCTTTGTTGTCCGT 58.714 47.619 0.00 0.00 0.00 4.69
603 616 2.287103 GGTGAAGTCTTTGTTGTCCGTC 59.713 50.000 0.00 0.00 0.00 4.79
604 617 2.933906 GTGAAGTCTTTGTTGTCCGTCA 59.066 45.455 0.00 0.00 0.00 4.35
605 618 3.560068 GTGAAGTCTTTGTTGTCCGTCAT 59.440 43.478 0.00 0.00 0.00 3.06
606 619 3.559655 TGAAGTCTTTGTTGTCCGTCATG 59.440 43.478 0.00 0.00 0.00 3.07
607 620 3.194005 AGTCTTTGTTGTCCGTCATGT 57.806 42.857 0.00 0.00 0.00 3.21
608 621 3.131396 AGTCTTTGTTGTCCGTCATGTC 58.869 45.455 0.00 0.00 0.00 3.06
609 622 3.131396 GTCTTTGTTGTCCGTCATGTCT 58.869 45.455 0.00 0.00 0.00 3.41
610 623 3.059597 GTCTTTGTTGTCCGTCATGTCTG 60.060 47.826 0.00 0.00 0.00 3.51
611 624 2.613026 TTGTTGTCCGTCATGTCTGT 57.387 45.000 0.00 0.00 0.00 3.41
612 625 2.613026 TGTTGTCCGTCATGTCTGTT 57.387 45.000 0.00 0.00 0.00 3.16
613 626 2.209273 TGTTGTCCGTCATGTCTGTTG 58.791 47.619 0.00 0.00 0.00 3.33
614 627 2.159028 TGTTGTCCGTCATGTCTGTTGA 60.159 45.455 0.00 0.00 0.00 3.18
615 628 2.869801 GTTGTCCGTCATGTCTGTTGAA 59.130 45.455 0.00 0.00 0.00 2.69
616 629 2.479837 TGTCCGTCATGTCTGTTGAAC 58.520 47.619 0.00 0.00 0.00 3.18
617 630 2.102420 TGTCCGTCATGTCTGTTGAACT 59.898 45.455 0.00 0.00 0.00 3.01
618 631 2.731976 GTCCGTCATGTCTGTTGAACTC 59.268 50.000 0.00 0.00 0.00 3.01
619 632 2.628178 TCCGTCATGTCTGTTGAACTCT 59.372 45.455 0.00 0.00 0.00 3.24
620 633 2.733552 CCGTCATGTCTGTTGAACTCTG 59.266 50.000 0.00 0.00 0.00 3.35
621 634 2.156504 CGTCATGTCTGTTGAACTCTGC 59.843 50.000 0.00 0.00 0.00 4.26
622 635 2.481952 GTCATGTCTGTTGAACTCTGCC 59.518 50.000 0.00 0.00 0.00 4.85
623 636 2.369860 TCATGTCTGTTGAACTCTGCCT 59.630 45.455 0.00 0.00 0.00 4.75
624 637 2.245159 TGTCTGTTGAACTCTGCCTG 57.755 50.000 0.00 0.00 0.00 4.85
625 638 1.762370 TGTCTGTTGAACTCTGCCTGA 59.238 47.619 0.00 0.00 0.00 3.86
626 639 2.369860 TGTCTGTTGAACTCTGCCTGAT 59.630 45.455 0.00 0.00 0.00 2.90
627 640 3.578282 TGTCTGTTGAACTCTGCCTGATA 59.422 43.478 0.00 0.00 0.00 2.15
628 641 4.180057 GTCTGTTGAACTCTGCCTGATAG 58.820 47.826 0.00 0.00 0.00 2.08
629 642 2.935201 CTGTTGAACTCTGCCTGATAGC 59.065 50.000 0.00 0.00 0.00 2.97
630 643 2.568956 TGTTGAACTCTGCCTGATAGCT 59.431 45.455 0.00 0.00 0.00 3.32
631 644 3.008375 TGTTGAACTCTGCCTGATAGCTT 59.992 43.478 0.00 0.00 0.00 3.74
632 645 3.988976 TGAACTCTGCCTGATAGCTTT 57.011 42.857 0.00 0.00 0.00 3.51
633 646 5.178797 GTTGAACTCTGCCTGATAGCTTTA 58.821 41.667 0.00 0.00 0.00 1.85
634 647 5.620738 TGAACTCTGCCTGATAGCTTTAT 57.379 39.130 0.00 0.00 0.00 1.40
635 648 5.605534 TGAACTCTGCCTGATAGCTTTATC 58.394 41.667 0.00 0.00 0.00 1.75
636 649 5.365025 TGAACTCTGCCTGATAGCTTTATCT 59.635 40.000 0.00 0.00 0.00 1.98
637 650 6.551227 TGAACTCTGCCTGATAGCTTTATCTA 59.449 38.462 0.00 0.00 0.00 1.98
638 651 7.234371 TGAACTCTGCCTGATAGCTTTATCTAT 59.766 37.037 0.00 0.00 32.30 1.98
639 652 8.657387 AACTCTGCCTGATAGCTTTATCTATA 57.343 34.615 0.00 0.00 29.93 1.31
640 653 8.657387 ACTCTGCCTGATAGCTTTATCTATAA 57.343 34.615 0.00 0.00 29.93 0.98
641 654 9.094578 ACTCTGCCTGATAGCTTTATCTATAAA 57.905 33.333 0.00 0.00 29.93 1.40
652 665 6.313744 CTTTATCTATAAAGCCGGGTTTGG 57.686 41.667 35.56 25.08 41.69 3.28
653 666 2.721425 TCTATAAAGCCGGGTTTGGG 57.279 50.000 35.56 24.78 0.00 4.12
659 672 3.238497 GCCGGGTTTGGGCCTTTT 61.238 61.111 4.53 0.00 44.97 2.27
660 673 1.909287 GCCGGGTTTGGGCCTTTTA 60.909 57.895 4.53 0.00 44.97 1.52
661 674 1.261938 GCCGGGTTTGGGCCTTTTAT 61.262 55.000 4.53 0.00 44.97 1.40
662 675 1.271856 CCGGGTTTGGGCCTTTTATT 58.728 50.000 4.53 0.00 0.00 1.40
663 676 2.458620 CCGGGTTTGGGCCTTTTATTA 58.541 47.619 4.53 0.00 0.00 0.98
664 677 2.832733 CCGGGTTTGGGCCTTTTATTAA 59.167 45.455 4.53 0.00 0.00 1.40
665 678 3.261137 CCGGGTTTGGGCCTTTTATTAAA 59.739 43.478 4.53 0.00 0.00 1.52
666 679 4.262938 CCGGGTTTGGGCCTTTTATTAAAA 60.263 41.667 4.53 1.85 0.00 1.52
796 813 2.503920 CGTAATAACGGAGGGTCAGG 57.496 55.000 0.00 0.00 45.50 3.86
921 940 9.613428 AGTAACTTTGCTCTATATGTATGCAAA 57.387 29.630 16.07 16.07 46.75 3.68
1341 1363 3.386237 GTGGAGAGGCTGAGGCGT 61.386 66.667 0.00 0.00 39.81 5.68
1631 1653 2.280552 GGACCACGTGGCTACTCCA 61.281 63.158 34.26 0.00 44.18 3.86
2214 2302 4.278956 GCGGAGGCGAAGAAGAAA 57.721 55.556 0.00 0.00 0.00 2.52
2220 2311 2.155279 GAGGCGAAGAAGAAAAAGGCT 58.845 47.619 0.00 0.00 37.21 4.58
2298 2389 1.727022 CTACACGAACGCGACGGTT 60.727 57.895 26.10 17.62 41.64 4.44
2993 3105 2.564947 AGAACAAACAAAGCCACCAACA 59.435 40.909 0.00 0.00 0.00 3.33
3024 3136 3.186909 TGATCGCCAAGACAACTATTCG 58.813 45.455 0.00 0.00 0.00 3.34
3102 3214 0.537371 CAAAAGTGCCCCGGTCTTCT 60.537 55.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
285 298 4.536090 TCTCTTGGTGTGGGATTTGATACT 59.464 41.667 0.00 0.00 0.00 2.12
292 305 5.569630 GCGATATATCTCTTGGTGTGGGATT 60.570 44.000 10.93 0.00 0.00 3.01
316 329 7.042119 TGTGTGTAATGCGTTCTTATATCATGG 60.042 37.037 0.00 0.00 0.00 3.66
343 356 8.407064 TGTACATACAGTTTGATTTCCGTTTTT 58.593 29.630 0.00 0.00 0.00 1.94
376 389 4.635765 CGCCTCCTTAATCAAGTGAAATGA 59.364 41.667 0.00 0.00 0.00 2.57
385 398 2.637872 CCCTATCCGCCTCCTTAATCAA 59.362 50.000 0.00 0.00 0.00 2.57
386 399 2.158219 TCCCTATCCGCCTCCTTAATCA 60.158 50.000 0.00 0.00 0.00 2.57
387 400 2.537143 TCCCTATCCGCCTCCTTAATC 58.463 52.381 0.00 0.00 0.00 1.75
388 401 2.715763 TCCCTATCCGCCTCCTTAAT 57.284 50.000 0.00 0.00 0.00 1.40
389 402 2.257207 CATCCCTATCCGCCTCCTTAA 58.743 52.381 0.00 0.00 0.00 1.85
391 404 1.484444 GCATCCCTATCCGCCTCCTT 61.484 60.000 0.00 0.00 0.00 3.36
392 405 1.915769 GCATCCCTATCCGCCTCCT 60.916 63.158 0.00 0.00 0.00 3.69
394 407 2.262915 CGCATCCCTATCCGCCTC 59.737 66.667 0.00 0.00 0.00 4.70
395 408 4.008933 GCGCATCCCTATCCGCCT 62.009 66.667 0.30 0.00 40.51 5.52
396 409 3.537206 AAGCGCATCCCTATCCGCC 62.537 63.158 11.47 0.00 46.90 6.13
397 410 2.031163 AAGCGCATCCCTATCCGC 59.969 61.111 11.47 0.00 46.14 5.54
398 411 0.036952 ATCAAGCGCATCCCTATCCG 60.037 55.000 11.47 0.00 0.00 4.18
399 412 2.191128 AATCAAGCGCATCCCTATCC 57.809 50.000 11.47 0.00 0.00 2.59
400 413 3.141398 TCAAATCAAGCGCATCCCTATC 58.859 45.455 11.47 0.00 0.00 2.08
401 414 3.213206 TCAAATCAAGCGCATCCCTAT 57.787 42.857 11.47 0.00 0.00 2.57
402 415 2.708216 TCAAATCAAGCGCATCCCTA 57.292 45.000 11.47 0.00 0.00 3.53
403 416 1.679680 CATCAAATCAAGCGCATCCCT 59.320 47.619 11.47 0.00 0.00 4.20
404 417 1.677576 TCATCAAATCAAGCGCATCCC 59.322 47.619 11.47 0.00 0.00 3.85
405 418 3.637998 ATCATCAAATCAAGCGCATCC 57.362 42.857 11.47 0.00 0.00 3.51
406 419 4.443394 GGAAATCATCAAATCAAGCGCATC 59.557 41.667 11.47 0.00 0.00 3.91
407 420 4.142116 TGGAAATCATCAAATCAAGCGCAT 60.142 37.500 11.47 0.00 0.00 4.73
408 421 3.193056 TGGAAATCATCAAATCAAGCGCA 59.807 39.130 11.47 0.00 0.00 6.09
409 422 3.772932 TGGAAATCATCAAATCAAGCGC 58.227 40.909 0.00 0.00 0.00 5.92
410 423 5.643664 TCTTGGAAATCATCAAATCAAGCG 58.356 37.500 0.00 0.00 32.66 4.68
411 424 6.700520 GGATCTTGGAAATCATCAAATCAAGC 59.299 38.462 0.00 0.00 32.66 4.01
412 425 6.916387 CGGATCTTGGAAATCATCAAATCAAG 59.084 38.462 0.00 0.00 33.55 3.02
413 426 6.183360 CCGGATCTTGGAAATCATCAAATCAA 60.183 38.462 0.00 0.00 0.00 2.57
414 427 5.300034 CCGGATCTTGGAAATCATCAAATCA 59.700 40.000 0.00 0.00 0.00 2.57
415 428 5.300286 ACCGGATCTTGGAAATCATCAAATC 59.700 40.000 9.46 0.00 0.00 2.17
416 429 5.203528 ACCGGATCTTGGAAATCATCAAAT 58.796 37.500 9.46 0.00 0.00 2.32
417 430 4.599041 ACCGGATCTTGGAAATCATCAAA 58.401 39.130 9.46 0.00 0.00 2.69
418 431 4.080356 AGACCGGATCTTGGAAATCATCAA 60.080 41.667 9.46 0.00 31.62 2.57
419 432 3.455910 AGACCGGATCTTGGAAATCATCA 59.544 43.478 9.46 0.00 31.62 3.07
420 433 4.078639 AGACCGGATCTTGGAAATCATC 57.921 45.455 9.46 0.00 31.62 2.92
421 434 4.510167 AAGACCGGATCTTGGAAATCAT 57.490 40.909 9.46 0.00 46.44 2.45
431 444 3.153919 GAGATAGCAGAAGACCGGATCT 58.846 50.000 9.46 5.83 40.46 2.75
432 445 2.230266 GGAGATAGCAGAAGACCGGATC 59.770 54.545 9.46 3.11 0.00 3.36
433 446 2.243810 GGAGATAGCAGAAGACCGGAT 58.756 52.381 9.46 0.00 0.00 4.18
434 447 1.693627 GGAGATAGCAGAAGACCGGA 58.306 55.000 9.46 0.00 0.00 5.14
435 448 0.676736 GGGAGATAGCAGAAGACCGG 59.323 60.000 0.00 0.00 0.00 5.28
436 449 1.698506 AGGGAGATAGCAGAAGACCG 58.301 55.000 0.00 0.00 0.00 4.79
437 450 4.672899 AGATAGGGAGATAGCAGAAGACC 58.327 47.826 0.00 0.00 0.00 3.85
438 451 4.705023 GGAGATAGGGAGATAGCAGAAGAC 59.295 50.000 0.00 0.00 0.00 3.01
439 452 4.355287 TGGAGATAGGGAGATAGCAGAAGA 59.645 45.833 0.00 0.00 0.00 2.87
440 453 4.462483 GTGGAGATAGGGAGATAGCAGAAG 59.538 50.000 0.00 0.00 0.00 2.85
441 454 4.411927 GTGGAGATAGGGAGATAGCAGAA 58.588 47.826 0.00 0.00 0.00 3.02
442 455 3.245443 GGTGGAGATAGGGAGATAGCAGA 60.245 52.174 0.00 0.00 0.00 4.26
443 456 3.096092 GGTGGAGATAGGGAGATAGCAG 58.904 54.545 0.00 0.00 0.00 4.24
444 457 2.225394 GGGTGGAGATAGGGAGATAGCA 60.225 54.545 0.00 0.00 0.00 3.49
445 458 2.462723 GGGTGGAGATAGGGAGATAGC 58.537 57.143 0.00 0.00 0.00 2.97
446 459 2.621929 CGGGGTGGAGATAGGGAGATAG 60.622 59.091 0.00 0.00 0.00 2.08
447 460 1.358103 CGGGGTGGAGATAGGGAGATA 59.642 57.143 0.00 0.00 0.00 1.98
448 461 0.115349 CGGGGTGGAGATAGGGAGAT 59.885 60.000 0.00 0.00 0.00 2.75
449 462 1.294426 ACGGGGTGGAGATAGGGAGA 61.294 60.000 0.00 0.00 0.00 3.71
450 463 1.115930 CACGGGGTGGAGATAGGGAG 61.116 65.000 0.00 0.00 0.00 4.30
451 464 1.075525 CACGGGGTGGAGATAGGGA 60.076 63.158 0.00 0.00 0.00 4.20
452 465 2.808206 GCACGGGGTGGAGATAGGG 61.808 68.421 0.00 0.00 33.64 3.53
453 466 2.808206 GGCACGGGGTGGAGATAGG 61.808 68.421 0.00 0.00 33.64 2.57
454 467 2.822399 GGCACGGGGTGGAGATAG 59.178 66.667 0.00 0.00 33.64 2.08
467 480 1.004918 AACACCTAGCTGTCGGCAC 60.005 57.895 6.39 0.00 44.79 5.01
468 481 1.005037 CAACACCTAGCTGTCGGCA 60.005 57.895 6.39 0.00 44.79 5.69
469 482 2.391389 GCAACACCTAGCTGTCGGC 61.391 63.158 0.00 0.00 42.19 5.54
470 483 1.293498 AGCAACACCTAGCTGTCGG 59.707 57.895 0.00 0.00 40.13 4.79
471 484 4.996976 AGCAACACCTAGCTGTCG 57.003 55.556 0.00 0.00 40.13 4.35
475 488 1.059913 AAGACCAGCAACACCTAGCT 58.940 50.000 0.00 0.00 42.94 3.32
476 489 2.762535 TAAGACCAGCAACACCTAGC 57.237 50.000 0.00 0.00 0.00 3.42
477 490 4.207891 ACATAAGACCAGCAACACCTAG 57.792 45.455 0.00 0.00 0.00 3.02
478 491 4.634012 AACATAAGACCAGCAACACCTA 57.366 40.909 0.00 0.00 0.00 3.08
479 492 3.508845 AACATAAGACCAGCAACACCT 57.491 42.857 0.00 0.00 0.00 4.00
480 493 3.305335 CCAAACATAAGACCAGCAACACC 60.305 47.826 0.00 0.00 0.00 4.16
481 494 3.857010 GCCAAACATAAGACCAGCAACAC 60.857 47.826 0.00 0.00 0.00 3.32
482 495 2.295909 GCCAAACATAAGACCAGCAACA 59.704 45.455 0.00 0.00 0.00 3.33
483 496 2.668279 CGCCAAACATAAGACCAGCAAC 60.668 50.000 0.00 0.00 0.00 4.17
484 497 1.539388 CGCCAAACATAAGACCAGCAA 59.461 47.619 0.00 0.00 0.00 3.91
485 498 1.164411 CGCCAAACATAAGACCAGCA 58.836 50.000 0.00 0.00 0.00 4.41
486 499 1.130561 GACGCCAAACATAAGACCAGC 59.869 52.381 0.00 0.00 0.00 4.85
487 500 2.699954 AGACGCCAAACATAAGACCAG 58.300 47.619 0.00 0.00 0.00 4.00
488 501 2.851263 AGACGCCAAACATAAGACCA 57.149 45.000 0.00 0.00 0.00 4.02
489 502 4.694037 ACTAAAGACGCCAAACATAAGACC 59.306 41.667 0.00 0.00 0.00 3.85
490 503 5.163884 GGACTAAAGACGCCAAACATAAGAC 60.164 44.000 0.00 0.00 0.00 3.01
491 504 4.933400 GGACTAAAGACGCCAAACATAAGA 59.067 41.667 0.00 0.00 0.00 2.10
492 505 4.094442 GGGACTAAAGACGCCAAACATAAG 59.906 45.833 0.00 0.00 0.00 1.73
493 506 4.004982 GGGACTAAAGACGCCAAACATAA 58.995 43.478 0.00 0.00 0.00 1.90
494 507 3.262405 AGGGACTAAAGACGCCAAACATA 59.738 43.478 0.00 0.00 36.02 2.29
495 508 2.039879 AGGGACTAAAGACGCCAAACAT 59.960 45.455 0.00 0.00 36.02 2.71
496 509 1.418637 AGGGACTAAAGACGCCAAACA 59.581 47.619 0.00 0.00 36.02 2.83
497 510 2.074576 GAGGGACTAAAGACGCCAAAC 58.925 52.381 0.00 0.00 41.55 2.93
498 511 1.002773 GGAGGGACTAAAGACGCCAAA 59.997 52.381 0.00 0.00 41.55 3.28
499 512 0.611714 GGAGGGACTAAAGACGCCAA 59.388 55.000 0.00 0.00 41.55 4.52
500 513 1.601419 CGGAGGGACTAAAGACGCCA 61.601 60.000 0.00 0.00 41.55 5.69
501 514 1.141234 CGGAGGGACTAAAGACGCC 59.859 63.158 0.00 0.00 41.55 5.68
502 515 4.808649 CGGAGGGACTAAAGACGC 57.191 61.111 0.00 0.00 41.55 5.19
529 542 3.000819 TCCCAGGCCAGTACACGG 61.001 66.667 5.01 0.00 0.00 4.94
530 543 2.579201 CTCCCAGGCCAGTACACG 59.421 66.667 5.01 0.00 0.00 4.49
531 544 2.269241 GCTCCCAGGCCAGTACAC 59.731 66.667 5.01 0.00 0.00 2.90
539 552 2.512896 CCTACATGGCTCCCAGGC 59.487 66.667 0.00 0.00 39.09 4.85
548 561 5.504665 CGAGCAAAAGAAATAGCCTACATGG 60.505 44.000 0.00 0.00 39.35 3.66
549 562 5.065218 ACGAGCAAAAGAAATAGCCTACATG 59.935 40.000 0.00 0.00 0.00 3.21
550 563 5.186198 ACGAGCAAAAGAAATAGCCTACAT 58.814 37.500 0.00 0.00 0.00 2.29
551 564 4.575885 ACGAGCAAAAGAAATAGCCTACA 58.424 39.130 0.00 0.00 0.00 2.74
552 565 4.034163 GGACGAGCAAAAGAAATAGCCTAC 59.966 45.833 0.00 0.00 0.00 3.18
553 566 4.189231 GGACGAGCAAAAGAAATAGCCTA 58.811 43.478 0.00 0.00 0.00 3.93
554 567 3.010420 GGACGAGCAAAAGAAATAGCCT 58.990 45.455 0.00 0.00 0.00 4.58
555 568 2.747446 TGGACGAGCAAAAGAAATAGCC 59.253 45.455 0.00 0.00 0.00 3.93
556 569 4.142600 ACATGGACGAGCAAAAGAAATAGC 60.143 41.667 0.00 0.00 0.00 2.97
557 570 5.551760 ACATGGACGAGCAAAAGAAATAG 57.448 39.130 0.00 0.00 0.00 1.73
558 571 5.335583 CCAACATGGACGAGCAAAAGAAATA 60.336 40.000 0.00 0.00 40.96 1.40
559 572 4.549458 CAACATGGACGAGCAAAAGAAAT 58.451 39.130 0.00 0.00 0.00 2.17
560 573 3.243367 CCAACATGGACGAGCAAAAGAAA 60.243 43.478 0.00 0.00 40.96 2.52
561 574 2.293122 CCAACATGGACGAGCAAAAGAA 59.707 45.455 0.00 0.00 40.96 2.52
562 575 1.879380 CCAACATGGACGAGCAAAAGA 59.121 47.619 0.00 0.00 40.96 2.52
563 576 1.068333 CCCAACATGGACGAGCAAAAG 60.068 52.381 0.00 0.00 40.96 2.27
564 577 0.958091 CCCAACATGGACGAGCAAAA 59.042 50.000 0.00 0.00 40.96 2.44
565 578 0.179004 ACCCAACATGGACGAGCAAA 60.179 50.000 0.00 0.00 40.96 3.68
566 579 0.888736 CACCCAACATGGACGAGCAA 60.889 55.000 0.00 0.00 40.96 3.91
567 580 1.302431 CACCCAACATGGACGAGCA 60.302 57.895 0.00 0.00 40.96 4.26
568 581 0.605319 TTCACCCAACATGGACGAGC 60.605 55.000 0.00 0.00 40.96 5.03
569 582 1.270839 ACTTCACCCAACATGGACGAG 60.271 52.381 0.00 0.00 40.96 4.18
570 583 0.762418 ACTTCACCCAACATGGACGA 59.238 50.000 0.00 0.00 40.96 4.20
571 584 1.156736 GACTTCACCCAACATGGACG 58.843 55.000 0.00 0.00 40.96 4.79
572 585 2.568623 AGACTTCACCCAACATGGAC 57.431 50.000 0.00 0.00 40.96 4.02
573 586 3.221771 CAAAGACTTCACCCAACATGGA 58.778 45.455 0.00 0.00 40.96 3.41
574 587 2.958355 ACAAAGACTTCACCCAACATGG 59.042 45.455 0.00 0.00 37.25 3.66
575 588 4.142182 ACAACAAAGACTTCACCCAACATG 60.142 41.667 0.00 0.00 0.00 3.21
576 589 4.023291 ACAACAAAGACTTCACCCAACAT 58.977 39.130 0.00 0.00 0.00 2.71
577 590 3.426615 ACAACAAAGACTTCACCCAACA 58.573 40.909 0.00 0.00 0.00 3.33
578 591 3.181490 GGACAACAAAGACTTCACCCAAC 60.181 47.826 0.00 0.00 0.00 3.77
579 592 3.020984 GGACAACAAAGACTTCACCCAA 58.979 45.455 0.00 0.00 0.00 4.12
580 593 2.650322 GGACAACAAAGACTTCACCCA 58.350 47.619 0.00 0.00 0.00 4.51
581 594 1.602377 CGGACAACAAAGACTTCACCC 59.398 52.381 0.00 0.00 0.00 4.61
582 595 2.285977 ACGGACAACAAAGACTTCACC 58.714 47.619 0.00 0.00 0.00 4.02
583 596 2.933906 TGACGGACAACAAAGACTTCAC 59.066 45.455 0.00 0.00 0.00 3.18
584 597 3.254470 TGACGGACAACAAAGACTTCA 57.746 42.857 0.00 0.00 0.00 3.02
585 598 3.560068 ACATGACGGACAACAAAGACTTC 59.440 43.478 0.00 0.00 0.00 3.01
586 599 3.541632 ACATGACGGACAACAAAGACTT 58.458 40.909 0.00 0.00 0.00 3.01
587 600 3.131396 GACATGACGGACAACAAAGACT 58.869 45.455 0.00 0.00 0.00 3.24
588 601 3.059597 CAGACATGACGGACAACAAAGAC 60.060 47.826 0.00 0.00 0.00 3.01
589 602 3.130633 CAGACATGACGGACAACAAAGA 58.869 45.455 0.00 0.00 0.00 2.52
590 603 2.872245 ACAGACATGACGGACAACAAAG 59.128 45.455 0.00 0.00 0.00 2.77
591 604 2.912771 ACAGACATGACGGACAACAAA 58.087 42.857 0.00 0.00 0.00 2.83
592 605 2.611751 CAACAGACATGACGGACAACAA 59.388 45.455 0.00 0.00 0.00 2.83
593 606 2.159028 TCAACAGACATGACGGACAACA 60.159 45.455 0.00 0.00 0.00 3.33
594 607 2.479837 TCAACAGACATGACGGACAAC 58.520 47.619 0.00 0.00 0.00 3.32
595 608 2.869801 GTTCAACAGACATGACGGACAA 59.130 45.455 0.00 0.00 0.00 3.18
596 609 2.102420 AGTTCAACAGACATGACGGACA 59.898 45.455 0.00 0.00 0.00 4.02
597 610 2.731976 GAGTTCAACAGACATGACGGAC 59.268 50.000 0.00 0.00 0.00 4.79
598 611 2.628178 AGAGTTCAACAGACATGACGGA 59.372 45.455 0.00 0.00 0.00 4.69
599 612 2.733552 CAGAGTTCAACAGACATGACGG 59.266 50.000 0.00 0.00 0.00 4.79
600 613 2.156504 GCAGAGTTCAACAGACATGACG 59.843 50.000 0.00 0.00 0.00 4.35
601 614 2.481952 GGCAGAGTTCAACAGACATGAC 59.518 50.000 0.00 0.00 0.00 3.06
602 615 2.369860 AGGCAGAGTTCAACAGACATGA 59.630 45.455 0.00 0.00 0.00 3.07
603 616 2.483106 CAGGCAGAGTTCAACAGACATG 59.517 50.000 0.00 0.00 0.00 3.21
604 617 2.369860 TCAGGCAGAGTTCAACAGACAT 59.630 45.455 0.00 0.00 0.00 3.06
605 618 1.762370 TCAGGCAGAGTTCAACAGACA 59.238 47.619 0.00 0.00 0.00 3.41
606 619 2.533266 TCAGGCAGAGTTCAACAGAC 57.467 50.000 0.00 0.00 0.00 3.51
607 620 3.368843 GCTATCAGGCAGAGTTCAACAGA 60.369 47.826 0.00 0.00 0.00 3.41
608 621 2.935201 GCTATCAGGCAGAGTTCAACAG 59.065 50.000 0.00 0.00 0.00 3.16
609 622 2.568956 AGCTATCAGGCAGAGTTCAACA 59.431 45.455 0.00 0.00 34.17 3.33
610 623 3.258971 AGCTATCAGGCAGAGTTCAAC 57.741 47.619 0.00 0.00 34.17 3.18
611 624 3.988976 AAGCTATCAGGCAGAGTTCAA 57.011 42.857 0.00 0.00 34.17 2.69
612 625 3.988976 AAAGCTATCAGGCAGAGTTCA 57.011 42.857 0.00 0.00 34.17 3.18
613 626 5.852827 AGATAAAGCTATCAGGCAGAGTTC 58.147 41.667 0.00 0.00 37.05 3.01
614 627 5.885449 AGATAAAGCTATCAGGCAGAGTT 57.115 39.130 0.00 0.00 37.05 3.01
615 628 8.657387 TTATAGATAAAGCTATCAGGCAGAGT 57.343 34.615 0.00 0.00 37.05 3.24
616 629 9.585099 CTTTATAGATAAAGCTATCAGGCAGAG 57.415 37.037 8.66 0.00 41.69 3.35
630 643 5.134661 CCCAAACCCGGCTTTATAGATAAA 58.865 41.667 0.00 0.00 0.00 1.40
631 644 4.721132 CCCAAACCCGGCTTTATAGATAA 58.279 43.478 0.00 0.00 0.00 1.75
632 645 3.497227 GCCCAAACCCGGCTTTATAGATA 60.497 47.826 0.00 0.00 43.48 1.98
633 646 2.751816 GCCCAAACCCGGCTTTATAGAT 60.752 50.000 0.00 0.00 43.48 1.98
634 647 1.409101 GCCCAAACCCGGCTTTATAGA 60.409 52.381 0.00 0.00 43.48 1.98
635 648 1.029681 GCCCAAACCCGGCTTTATAG 58.970 55.000 0.00 0.00 43.48 1.31
636 649 0.396001 GGCCCAAACCCGGCTTTATA 60.396 55.000 0.00 0.00 46.24 0.98
637 650 1.684391 GGCCCAAACCCGGCTTTAT 60.684 57.895 0.00 0.00 46.24 1.40
638 651 2.283316 GGCCCAAACCCGGCTTTA 60.283 61.111 0.00 0.00 46.24 1.85
639 652 3.767044 AAGGCCCAAACCCGGCTTT 62.767 57.895 0.00 0.00 46.24 3.51
640 653 3.767044 AAAGGCCCAAACCCGGCTT 62.767 57.895 0.00 0.00 46.24 4.35
641 654 2.374781 TAAAAGGCCCAAACCCGGCT 62.375 55.000 0.00 0.00 46.24 5.52
642 655 1.261938 ATAAAAGGCCCAAACCCGGC 61.262 55.000 0.00 0.00 46.29 6.13
643 656 1.271856 AATAAAAGGCCCAAACCCGG 58.728 50.000 0.00 0.00 0.00 5.73
644 657 4.538746 TTTAATAAAAGGCCCAAACCCG 57.461 40.909 0.00 0.00 0.00 5.28
665 678 0.817013 ATCATGTGCCGCCGATTTTT 59.183 45.000 0.00 0.00 0.00 1.94
666 679 0.817013 AATCATGTGCCGCCGATTTT 59.183 45.000 0.00 0.00 0.00 1.82
796 813 9.741647 CTTTTCTATCTTTGGATTTGGAATAGC 57.258 33.333 0.00 0.00 33.71 2.97
921 940 2.503356 AGGCGAGAGACATCATCCTTTT 59.497 45.455 0.00 0.00 46.78 2.27
1341 1363 0.108520 GACGGTGATTGGCCTCGTAA 60.109 55.000 3.32 0.00 34.06 3.18
1626 1648 3.682292 GAAATCGGCCGGCTGGAGT 62.682 63.158 34.26 23.27 37.49 3.85
1928 1986 4.735132 TCCGTTCAAGCTCGCGGG 62.735 66.667 6.13 2.60 43.87 6.13
2214 2302 1.302033 CAGGACTGCGACAGCCTTT 60.302 57.895 14.88 0.00 44.33 3.11
2220 2311 0.035317 AAAGCATCAGGACTGCGACA 59.965 50.000 0.00 0.00 44.38 4.35
2507 2598 0.109086 CACGTCGGCTCTCATCTTGT 60.109 55.000 0.00 0.00 0.00 3.16
2544 2635 1.226542 CATGCAGGGCTCCACAGAT 59.773 57.895 0.00 0.00 0.00 2.90
2696 2793 4.398319 CAGGGATACAACAAACTGGAGTT 58.602 43.478 0.00 0.00 38.08 3.01
2993 3105 4.278170 TGTCTTGGCGATCATTTTGACTTT 59.722 37.500 0.00 0.00 0.00 2.66
3102 3214 6.552725 AGCAGTGGAGATCATTGACTAAGATA 59.447 38.462 0.00 0.00 35.40 1.98
3154 3268 7.283580 TGTTTTTCCTGCTAAACTTGCTTACTA 59.716 33.333 0.00 0.00 35.73 1.82
3486 3605 3.683802 AGTGAAGATTTTCCTCTGGCAG 58.316 45.455 8.58 8.58 32.09 4.85


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

AutoCloner maintained by Alex Coulton.