Multiple sequence alignment - TraesCS2A01G532900

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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 TraesCS2A01G532900 chr2A 100.000 3293 0 0 1 3293 749057524 749060816 0.000000e+00 6082.0
1 TraesCS2A01G532900 chr2D 93.229 2496 104 24 826 3293 618202247 618204705 0.000000e+00 3613.0
2 TraesCS2A01G532900 chr2D 82.798 1494 205 29 1055 2522 605778351 605776884 0.000000e+00 1288.0
3 TraesCS2A01G532900 chr2D 82.841 1218 174 23 1226 2434 22248560 22247369 0.000000e+00 1059.0
4 TraesCS2A01G532900 chr2D 81.339 1195 196 19 922 2099 22349266 22348082 0.000000e+00 946.0
5 TraesCS2A01G532900 chr2D 81.370 1095 179 17 1022 2099 22327936 22326850 0.000000e+00 869.0
6 TraesCS2A01G532900 chr2D 80.777 1056 186 10 922 1965 22323784 22322734 0.000000e+00 809.0
7 TraesCS2A01G532900 chr2D 97.475 198 5 0 612 809 618202068 618202265 4.070000e-89 339.0
8 TraesCS2A01G532900 chr2D 88.750 80 8 1 2529 2608 427573391 427573313 2.700000e-16 97.1
9 TraesCS2A01G532900 chr2B 93.939 1716 87 11 826 2536 754782534 754784237 0.000000e+00 2577.0
10 TraesCS2A01G532900 chr2B 93.295 701 41 4 2593 3293 754784325 754785019 0.000000e+00 1029.0
11 TraesCS2A01G532900 chr6D 90.610 1704 141 16 826 2526 26003554 26001867 0.000000e+00 2242.0
12 TraesCS2A01G532900 chr6D 85.774 239 20 7 2734 2965 25997068 25996837 1.180000e-59 241.0
13 TraesCS2A01G532900 chr6D 92.547 161 10 1 617 775 26003736 26003576 2.560000e-56 230.0
14 TraesCS2A01G532900 chr6D 92.537 134 7 1 3002 3135 25996843 25996713 4.340000e-44 189.0
15 TraesCS2A01G532900 chr6D 90.698 86 3 4 2529 2609 28336613 28336698 3.470000e-20 110.0
16 TraesCS2A01G532900 chr6D 88.235 85 5 5 2529 2608 28941912 28941996 2.700000e-16 97.1
17 TraesCS2A01G532900 chr6D 88.750 80 8 1 2527 2605 97926432 97926353 2.700000e-16 97.1
18 TraesCS2A01G532900 chrUn 79.562 1507 252 33 929 2417 16842129 16840661 0.000000e+00 1026.0
19 TraesCS2A01G532900 chr5D 91.853 626 30 6 1 615 138898480 138899095 0.000000e+00 854.0
20 TraesCS2A01G532900 chr5D 86.667 90 7 3 2524 2609 496271891 496271803 9.730000e-16 95.3
21 TraesCS2A01G532900 chr5B 88.782 624 56 6 1 613 282145215 282145835 0.000000e+00 752.0
22 TraesCS2A01G532900 chr5A 87.786 524 28 9 104 617 193919999 193920496 6.130000e-162 580.0
23 TraesCS2A01G532900 chr5A 93.243 296 17 1 320 615 193919995 193919703 1.810000e-117 433.0
24 TraesCS2A01G532900 chr6A 78.281 640 105 19 1 615 422340929 422341559 6.670000e-102 381.0
25 TraesCS2A01G532900 chr3B 92.857 84 5 1 2527 2609 465505715 465505798 1.600000e-23 121.0
26 TraesCS2A01G532900 chr7A 85.556 90 11 2 2525 2612 310433879 310433790 3.500000e-15 93.5
27 TraesCS2A01G532900 chr6B 87.209 86 6 4 2527 2607 663679836 663679751 3.500000e-15 93.5
28 TraesCS2A01G532900 chr1A 87.209 86 6 5 2523 2604 52004720 52004636 3.500000e-15 93.5


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 TraesCS2A01G532900 chr2A 749057524 749060816 3292 False 6082 6082 100.0000 1 3293 1 chr2A.!!$F1 3292
1 TraesCS2A01G532900 chr2D 618202068 618204705 2637 False 1976 3613 95.3520 612 3293 2 chr2D.!!$F1 2681
2 TraesCS2A01G532900 chr2D 605776884 605778351 1467 True 1288 1288 82.7980 1055 2522 1 chr2D.!!$R4 1467
3 TraesCS2A01G532900 chr2D 22247369 22248560 1191 True 1059 1059 82.8410 1226 2434 1 chr2D.!!$R1 1208
4 TraesCS2A01G532900 chr2D 22348082 22349266 1184 True 946 946 81.3390 922 2099 1 chr2D.!!$R2 1177
5 TraesCS2A01G532900 chr2D 22322734 22327936 5202 True 839 869 81.0735 922 2099 2 chr2D.!!$R5 1177
6 TraesCS2A01G532900 chr2B 754782534 754785019 2485 False 1803 2577 93.6170 826 3293 2 chr2B.!!$F1 2467
7 TraesCS2A01G532900 chr6D 26001867 26003736 1869 True 1236 2242 91.5785 617 2526 2 chr6D.!!$R3 1909
8 TraesCS2A01G532900 chrUn 16840661 16842129 1468 True 1026 1026 79.5620 929 2417 1 chrUn.!!$R1 1488
9 TraesCS2A01G532900 chr5D 138898480 138899095 615 False 854 854 91.8530 1 615 1 chr5D.!!$F1 614
10 TraesCS2A01G532900 chr5B 282145215 282145835 620 False 752 752 88.7820 1 613 1 chr5B.!!$F1 612
11 TraesCS2A01G532900 chr6A 422340929 422341559 630 False 381 381 78.2810 1 615 1 chr6A.!!$F1 614

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
606 618 0.033504 GAGTGGAGAGTTGCCGAACA 59.966 55.0 0.0 0.0 34.17 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 5006 0.602562 CCAAAACACATGCATCCGGT 59.397 50.0 0.0 0.0 0.0 5.28 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
205 217 1.301244 CAGGGCTGATCGAATCCCG 60.301 63.158 0.00 0.00 43.46 5.14
207 219 1.595382 GGGCTGATCGAATCCCGTG 60.595 63.158 0.00 0.00 39.75 4.94
208 220 1.144057 GGCTGATCGAATCCCGTGT 59.856 57.895 0.00 0.00 39.75 4.49
229 241 2.369633 TGCATGGACGCATCCCTCT 61.370 57.895 0.00 0.00 45.59 3.69
241 253 1.903877 ATCCCTCTGCCACTTGTCCG 61.904 60.000 0.00 0.00 0.00 4.79
244 256 1.734477 CTCTGCCACTTGTCCGTCG 60.734 63.158 0.00 0.00 0.00 5.12
246 258 2.022129 CTGCCACTTGTCCGTCGTC 61.022 63.158 0.00 0.00 0.00 4.20
268 280 3.182590 AAACCTGCTCGCAGCTCCA 62.183 57.895 13.25 0.00 42.97 3.86
277 289 2.743752 CGCAGCTCCACGTCAATGG 61.744 63.158 0.00 0.00 41.57 3.16
297 309 0.313672 CGATAGCTGACAGGCTCCTC 59.686 60.000 4.26 2.90 42.97 3.71
300 312 4.074526 GCTGACAGGCTCCTCGCA 62.075 66.667 4.26 0.00 41.67 5.10
341 353 3.458163 ACCGCCGTCATCACCGAT 61.458 61.111 0.00 0.00 0.00 4.18
393 405 2.833582 CTTCTCCTCCCGCCGCTA 60.834 66.667 0.00 0.00 0.00 4.26
394 406 3.140225 CTTCTCCTCCCGCCGCTAC 62.140 68.421 0.00 0.00 0.00 3.58
395 407 3.657038 TTCTCCTCCCGCCGCTACT 62.657 63.158 0.00 0.00 0.00 2.57
396 408 3.905678 CTCCTCCCGCCGCTACTG 61.906 72.222 0.00 0.00 0.00 2.74
403 415 3.788766 CGCCGCTACTGCACCAAC 61.789 66.667 0.00 0.00 39.64 3.77
404 416 3.788766 GCCGCTACTGCACCAACG 61.789 66.667 0.00 0.00 39.64 4.10
405 417 3.118454 CCGCTACTGCACCAACGG 61.118 66.667 0.00 0.00 39.64 4.44
406 418 3.118454 CGCTACTGCACCAACGGG 61.118 66.667 0.00 0.00 39.64 5.28
407 419 3.431725 GCTACTGCACCAACGGGC 61.432 66.667 0.00 0.00 39.41 6.13
408 420 2.347490 CTACTGCACCAACGGGCT 59.653 61.111 0.00 0.00 37.90 5.19
409 421 1.741770 CTACTGCACCAACGGGCTC 60.742 63.158 0.00 0.00 37.90 4.70
410 422 3.248446 TACTGCACCAACGGGCTCC 62.248 63.158 0.00 0.00 37.90 4.70
411 423 4.335647 CTGCACCAACGGGCTCCT 62.336 66.667 0.00 0.00 37.90 3.69
412 424 3.850098 CTGCACCAACGGGCTCCTT 62.850 63.158 0.00 0.00 37.90 3.36
413 425 3.056328 GCACCAACGGGCTCCTTC 61.056 66.667 0.00 0.00 37.90 3.46
414 426 2.429930 CACCAACGGGCTCCTTCA 59.570 61.111 0.00 0.00 37.90 3.02
415 427 1.002134 CACCAACGGGCTCCTTCAT 60.002 57.895 0.00 0.00 37.90 2.57
416 428 0.609131 CACCAACGGGCTCCTTCATT 60.609 55.000 0.00 0.00 37.90 2.57
417 429 0.322546 ACCAACGGGCTCCTTCATTC 60.323 55.000 0.00 0.00 37.90 2.67
418 430 1.032114 CCAACGGGCTCCTTCATTCC 61.032 60.000 0.00 0.00 0.00 3.01
419 431 0.035056 CAACGGGCTCCTTCATTCCT 60.035 55.000 0.00 0.00 0.00 3.36
420 432 0.253327 AACGGGCTCCTTCATTCCTC 59.747 55.000 0.00 0.00 0.00 3.71
421 433 0.909610 ACGGGCTCCTTCATTCCTCA 60.910 55.000 0.00 0.00 0.00 3.86
422 434 0.179062 CGGGCTCCTTCATTCCTCAG 60.179 60.000 0.00 0.00 0.00 3.35
423 435 0.915364 GGGCTCCTTCATTCCTCAGT 59.085 55.000 0.00 0.00 0.00 3.41
424 436 1.407989 GGGCTCCTTCATTCCTCAGTG 60.408 57.143 0.00 0.00 0.00 3.66
425 437 1.556911 GGCTCCTTCATTCCTCAGTGA 59.443 52.381 0.00 0.00 0.00 3.41
426 438 2.026822 GGCTCCTTCATTCCTCAGTGAA 60.027 50.000 0.00 0.00 33.63 3.18
427 439 3.560025 GGCTCCTTCATTCCTCAGTGAAA 60.560 47.826 0.00 0.00 34.26 2.69
428 440 3.438434 GCTCCTTCATTCCTCAGTGAAAC 59.562 47.826 0.00 0.00 34.26 2.78
429 441 4.006319 CTCCTTCATTCCTCAGTGAAACC 58.994 47.826 0.00 0.00 37.80 3.27
430 442 3.394274 TCCTTCATTCCTCAGTGAAACCA 59.606 43.478 0.00 0.00 37.80 3.67
431 443 3.503748 CCTTCATTCCTCAGTGAAACCAC 59.496 47.826 0.00 0.00 37.80 4.16
432 444 3.140325 TCATTCCTCAGTGAAACCACC 57.860 47.619 0.00 0.00 37.80 4.61
433 445 1.806542 CATTCCTCAGTGAAACCACCG 59.193 52.381 0.00 0.00 37.80 4.94
434 446 0.534203 TTCCTCAGTGAAACCACCGC 60.534 55.000 0.00 0.00 37.80 5.68
435 447 1.966451 CCTCAGTGAAACCACCGCC 60.966 63.158 0.00 0.00 37.80 6.13
436 448 1.966451 CTCAGTGAAACCACCGCCC 60.966 63.158 0.00 0.00 37.80 6.13
437 449 2.113139 CAGTGAAACCACCGCCCT 59.887 61.111 0.00 0.00 37.80 5.19
438 450 1.966451 CAGTGAAACCACCGCCCTC 60.966 63.158 0.00 0.00 37.80 4.30
439 451 2.112297 GTGAAACCACCGCCCTCA 59.888 61.111 0.00 0.00 0.00 3.86
440 452 1.966451 GTGAAACCACCGCCCTCAG 60.966 63.158 0.00 0.00 0.00 3.35
441 453 3.056328 GAAACCACCGCCCTCAGC 61.056 66.667 0.00 0.00 38.52 4.26
442 454 3.553095 GAAACCACCGCCCTCAGCT 62.553 63.158 0.00 0.00 40.39 4.24
443 455 3.850098 AAACCACCGCCCTCAGCTG 62.850 63.158 7.63 7.63 40.39 4.24
446 458 4.711949 CACCGCCCTCAGCTGCTT 62.712 66.667 9.47 0.00 40.39 3.91
447 459 3.958860 ACCGCCCTCAGCTGCTTT 61.959 61.111 9.47 0.00 40.39 3.51
448 460 2.674380 CCGCCCTCAGCTGCTTTT 60.674 61.111 9.47 0.00 40.39 2.27
449 461 2.270986 CCGCCCTCAGCTGCTTTTT 61.271 57.895 9.47 0.00 40.39 1.94
450 462 1.211190 CGCCCTCAGCTGCTTTTTC 59.789 57.895 9.47 0.00 40.39 2.29
451 463 1.239968 CGCCCTCAGCTGCTTTTTCT 61.240 55.000 9.47 0.00 40.39 2.52
452 464 1.826385 GCCCTCAGCTGCTTTTTCTA 58.174 50.000 9.47 0.00 38.99 2.10
453 465 1.742268 GCCCTCAGCTGCTTTTTCTAG 59.258 52.381 9.47 0.00 38.99 2.43
454 466 2.877708 GCCCTCAGCTGCTTTTTCTAGT 60.878 50.000 9.47 0.00 38.99 2.57
455 467 3.006247 CCCTCAGCTGCTTTTTCTAGTC 58.994 50.000 9.47 0.00 0.00 2.59
456 468 3.557898 CCCTCAGCTGCTTTTTCTAGTCA 60.558 47.826 9.47 0.00 0.00 3.41
457 469 3.683822 CCTCAGCTGCTTTTTCTAGTCAG 59.316 47.826 9.47 0.00 0.00 3.51
458 470 3.668447 TCAGCTGCTTTTTCTAGTCAGG 58.332 45.455 9.47 0.00 0.00 3.86
459 471 3.071602 TCAGCTGCTTTTTCTAGTCAGGT 59.928 43.478 9.47 0.00 36.11 4.00
460 472 3.817647 CAGCTGCTTTTTCTAGTCAGGTT 59.182 43.478 0.00 0.00 33.81 3.50
461 473 4.068599 AGCTGCTTTTTCTAGTCAGGTTC 58.931 43.478 0.00 0.00 32.35 3.62
462 474 3.189495 GCTGCTTTTTCTAGTCAGGTTCC 59.811 47.826 0.00 0.00 0.00 3.62
463 475 4.646572 CTGCTTTTTCTAGTCAGGTTCCT 58.353 43.478 0.00 0.00 0.00 3.36
464 476 4.642429 TGCTTTTTCTAGTCAGGTTCCTC 58.358 43.478 0.00 0.00 0.00 3.71
465 477 4.004314 GCTTTTTCTAGTCAGGTTCCTCC 58.996 47.826 0.00 0.00 0.00 4.30
466 478 4.580868 CTTTTTCTAGTCAGGTTCCTCCC 58.419 47.826 0.00 0.00 36.75 4.30
467 479 3.269592 TTTCTAGTCAGGTTCCTCCCA 57.730 47.619 0.00 0.00 36.75 4.37
468 480 2.534042 TCTAGTCAGGTTCCTCCCAG 57.466 55.000 0.00 0.00 36.75 4.45
469 481 1.007238 TCTAGTCAGGTTCCTCCCAGG 59.993 57.143 0.00 0.00 36.75 4.45
470 482 1.007238 CTAGTCAGGTTCCTCCCAGGA 59.993 57.143 0.00 0.00 44.10 3.86
479 491 1.891933 TCCTCCCAGGAATGTATGCA 58.108 50.000 0.00 0.00 42.51 3.96
480 492 2.421725 TCCTCCCAGGAATGTATGCAT 58.578 47.619 3.79 3.79 42.51 3.96
481 493 3.597182 TCCTCCCAGGAATGTATGCATA 58.403 45.455 1.16 1.16 42.51 3.14
482 494 3.980022 TCCTCCCAGGAATGTATGCATAA 59.020 43.478 8.28 0.00 42.51 1.90
483 495 4.603171 TCCTCCCAGGAATGTATGCATAAT 59.397 41.667 8.28 1.99 42.51 1.28
484 496 5.074929 TCCTCCCAGGAATGTATGCATAATT 59.925 40.000 8.28 10.35 42.51 1.40
485 497 5.416952 CCTCCCAGGAATGTATGCATAATTC 59.583 44.000 21.25 21.25 37.67 2.17
486 498 5.951204 TCCCAGGAATGTATGCATAATTCA 58.049 37.500 25.79 16.08 34.39 2.57
487 499 6.005823 TCCCAGGAATGTATGCATAATTCAG 58.994 40.000 25.79 20.73 34.39 3.02
488 500 5.771666 CCCAGGAATGTATGCATAATTCAGT 59.228 40.000 25.79 15.28 34.39 3.41
489 501 6.266103 CCCAGGAATGTATGCATAATTCAGTT 59.734 38.462 25.79 16.26 34.39 3.16
490 502 7.143340 CCAGGAATGTATGCATAATTCAGTTG 58.857 38.462 25.79 21.64 34.39 3.16
491 503 7.013559 CCAGGAATGTATGCATAATTCAGTTGA 59.986 37.037 25.79 0.78 34.39 3.18
492 504 8.074370 CAGGAATGTATGCATAATTCAGTTGAG 58.926 37.037 25.79 14.24 34.39 3.02
493 505 7.230108 AGGAATGTATGCATAATTCAGTTGAGG 59.770 37.037 25.79 0.00 34.39 3.86
494 506 7.229306 GGAATGTATGCATAATTCAGTTGAGGA 59.771 37.037 25.79 0.00 34.39 3.71
495 507 7.741027 ATGTATGCATAATTCAGTTGAGGAG 57.259 36.000 8.28 0.00 32.73 3.69
496 508 6.653020 TGTATGCATAATTCAGTTGAGGAGT 58.347 36.000 8.28 0.00 0.00 3.85
497 509 6.539826 TGTATGCATAATTCAGTTGAGGAGTG 59.460 38.462 8.28 0.00 0.00 3.51
498 510 4.264253 TGCATAATTCAGTTGAGGAGTGG 58.736 43.478 0.00 0.00 0.00 4.00
499 511 4.019411 TGCATAATTCAGTTGAGGAGTGGA 60.019 41.667 0.00 0.00 0.00 4.02
500 512 4.574013 GCATAATTCAGTTGAGGAGTGGAG 59.426 45.833 0.00 0.00 0.00 3.86
501 513 5.738909 CATAATTCAGTTGAGGAGTGGAGT 58.261 41.667 0.00 0.00 0.00 3.85
502 514 4.713792 AATTCAGTTGAGGAGTGGAGTT 57.286 40.909 0.00 0.00 0.00 3.01
503 515 3.753294 TTCAGTTGAGGAGTGGAGTTC 57.247 47.619 0.00 0.00 0.00 3.01
504 516 2.677914 TCAGTTGAGGAGTGGAGTTCA 58.322 47.619 0.00 0.00 0.00 3.18
505 517 2.365617 TCAGTTGAGGAGTGGAGTTCAC 59.634 50.000 0.00 0.00 46.39 3.18
520 532 3.444618 GTTCACAACCGAACGTATTCC 57.555 47.619 0.00 0.00 36.26 3.01
521 533 2.083167 TCACAACCGAACGTATTCCC 57.917 50.000 0.00 0.00 0.00 3.97
522 534 1.343789 TCACAACCGAACGTATTCCCA 59.656 47.619 0.00 0.00 0.00 4.37
523 535 1.730064 CACAACCGAACGTATTCCCAG 59.270 52.381 0.00 0.00 0.00 4.45
524 536 1.619827 ACAACCGAACGTATTCCCAGA 59.380 47.619 0.00 0.00 0.00 3.86
525 537 2.235402 ACAACCGAACGTATTCCCAGAT 59.765 45.455 0.00 0.00 0.00 2.90
526 538 3.267483 CAACCGAACGTATTCCCAGATT 58.733 45.455 0.00 0.00 0.00 2.40
527 539 3.175109 ACCGAACGTATTCCCAGATTC 57.825 47.619 0.00 0.00 0.00 2.52
528 540 2.764572 ACCGAACGTATTCCCAGATTCT 59.235 45.455 0.00 0.00 0.00 2.40
529 541 3.123804 CCGAACGTATTCCCAGATTCTG 58.876 50.000 6.70 6.70 0.00 3.02
530 542 3.181479 CCGAACGTATTCCCAGATTCTGA 60.181 47.826 15.36 0.00 32.44 3.27
531 543 4.430007 CGAACGTATTCCCAGATTCTGAA 58.570 43.478 15.36 2.86 32.44 3.02
532 544 4.868171 CGAACGTATTCCCAGATTCTGAAA 59.132 41.667 15.36 9.18 32.44 2.69
533 545 5.220416 CGAACGTATTCCCAGATTCTGAAAC 60.220 44.000 15.36 4.89 32.44 2.78
534 546 4.181578 ACGTATTCCCAGATTCTGAAACG 58.818 43.478 15.36 16.37 32.44 3.60
535 547 4.181578 CGTATTCCCAGATTCTGAAACGT 58.818 43.478 15.36 0.41 32.44 3.99
536 548 4.032900 CGTATTCCCAGATTCTGAAACGTG 59.967 45.833 15.36 0.00 32.44 4.49
537 549 1.808411 TCCCAGATTCTGAAACGTGC 58.192 50.000 15.36 0.00 32.44 5.34
538 550 1.347707 TCCCAGATTCTGAAACGTGCT 59.652 47.619 15.36 0.00 32.44 4.40
539 551 2.565391 TCCCAGATTCTGAAACGTGCTA 59.435 45.455 15.36 0.00 32.44 3.49
540 552 3.007506 TCCCAGATTCTGAAACGTGCTAA 59.992 43.478 15.36 0.00 32.44 3.09
541 553 3.941483 CCCAGATTCTGAAACGTGCTAAT 59.059 43.478 15.36 0.00 32.44 1.73
542 554 5.105106 TCCCAGATTCTGAAACGTGCTAATA 60.105 40.000 15.36 0.00 32.44 0.98
543 555 5.235186 CCCAGATTCTGAAACGTGCTAATAG 59.765 44.000 15.36 0.00 32.44 1.73
544 556 6.042777 CCAGATTCTGAAACGTGCTAATAGA 58.957 40.000 15.36 0.00 32.44 1.98
545 557 6.199908 CCAGATTCTGAAACGTGCTAATAGAG 59.800 42.308 15.36 0.00 32.44 2.43
546 558 6.754209 CAGATTCTGAAACGTGCTAATAGAGT 59.246 38.462 8.00 0.00 32.44 3.24
547 559 7.276658 CAGATTCTGAAACGTGCTAATAGAGTT 59.723 37.037 8.00 0.00 32.44 3.01
548 560 6.706055 TTCTGAAACGTGCTAATAGAGTTG 57.294 37.500 0.00 0.00 0.00 3.16
549 561 5.168569 TCTGAAACGTGCTAATAGAGTTGG 58.831 41.667 0.00 0.00 0.00 3.77
550 562 4.250464 TGAAACGTGCTAATAGAGTTGGG 58.750 43.478 0.00 0.00 0.00 4.12
551 563 4.020928 TGAAACGTGCTAATAGAGTTGGGA 60.021 41.667 0.00 0.00 0.00 4.37
552 564 3.802948 ACGTGCTAATAGAGTTGGGAG 57.197 47.619 0.00 0.00 0.00 4.30
553 565 3.097614 ACGTGCTAATAGAGTTGGGAGT 58.902 45.455 0.00 0.00 0.00 3.85
554 566 3.514309 ACGTGCTAATAGAGTTGGGAGTT 59.486 43.478 0.00 0.00 0.00 3.01
555 567 3.865745 CGTGCTAATAGAGTTGGGAGTTG 59.134 47.826 0.00 0.00 0.00 3.16
556 568 4.381612 CGTGCTAATAGAGTTGGGAGTTGA 60.382 45.833 0.00 0.00 0.00 3.18
557 569 5.112686 GTGCTAATAGAGTTGGGAGTTGAG 58.887 45.833 0.00 0.00 0.00 3.02
558 570 5.023452 TGCTAATAGAGTTGGGAGTTGAGA 58.977 41.667 0.00 0.00 0.00 3.27
559 571 5.483937 TGCTAATAGAGTTGGGAGTTGAGAA 59.516 40.000 0.00 0.00 0.00 2.87
560 572 6.045955 GCTAATAGAGTTGGGAGTTGAGAAG 58.954 44.000 0.00 0.00 0.00 2.85
561 573 6.351456 GCTAATAGAGTTGGGAGTTGAGAAGT 60.351 42.308 0.00 0.00 0.00 3.01
562 574 3.760580 AGAGTTGGGAGTTGAGAAGTG 57.239 47.619 0.00 0.00 0.00 3.16
563 575 3.309296 AGAGTTGGGAGTTGAGAAGTGA 58.691 45.455 0.00 0.00 0.00 3.41
564 576 3.323403 AGAGTTGGGAGTTGAGAAGTGAG 59.677 47.826 0.00 0.00 0.00 3.51
565 577 2.370189 AGTTGGGAGTTGAGAAGTGAGG 59.630 50.000 0.00 0.00 0.00 3.86
566 578 2.368875 GTTGGGAGTTGAGAAGTGAGGA 59.631 50.000 0.00 0.00 0.00 3.71
567 579 2.251818 TGGGAGTTGAGAAGTGAGGAG 58.748 52.381 0.00 0.00 0.00 3.69
568 580 1.066502 GGGAGTTGAGAAGTGAGGAGC 60.067 57.143 0.00 0.00 0.00 4.70
569 581 1.620819 GGAGTTGAGAAGTGAGGAGCA 59.379 52.381 0.00 0.00 0.00 4.26
570 582 2.353605 GGAGTTGAGAAGTGAGGAGCAG 60.354 54.545 0.00 0.00 0.00 4.24
571 583 2.560542 GAGTTGAGAAGTGAGGAGCAGA 59.439 50.000 0.00 0.00 0.00 4.26
572 584 2.562298 AGTTGAGAAGTGAGGAGCAGAG 59.438 50.000 0.00 0.00 0.00 3.35
573 585 2.298729 GTTGAGAAGTGAGGAGCAGAGT 59.701 50.000 0.00 0.00 0.00 3.24
574 586 2.603021 TGAGAAGTGAGGAGCAGAGTT 58.397 47.619 0.00 0.00 0.00 3.01
575 587 2.968574 TGAGAAGTGAGGAGCAGAGTTT 59.031 45.455 0.00 0.00 0.00 2.66
576 588 4.152647 TGAGAAGTGAGGAGCAGAGTTTA 58.847 43.478 0.00 0.00 0.00 2.01
577 589 4.219507 TGAGAAGTGAGGAGCAGAGTTTAG 59.780 45.833 0.00 0.00 0.00 1.85
578 590 4.411927 AGAAGTGAGGAGCAGAGTTTAGA 58.588 43.478 0.00 0.00 0.00 2.10
579 591 4.835615 AGAAGTGAGGAGCAGAGTTTAGAA 59.164 41.667 0.00 0.00 0.00 2.10
580 592 5.483583 AGAAGTGAGGAGCAGAGTTTAGAAT 59.516 40.000 0.00 0.00 0.00 2.40
581 593 5.337578 AGTGAGGAGCAGAGTTTAGAATC 57.662 43.478 0.00 0.00 0.00 2.52
582 594 5.022787 AGTGAGGAGCAGAGTTTAGAATCT 58.977 41.667 0.00 0.00 0.00 2.40
583 595 5.105392 AGTGAGGAGCAGAGTTTAGAATCTG 60.105 44.000 6.37 6.37 44.70 2.90
584 596 4.161189 TGAGGAGCAGAGTTTAGAATCTGG 59.839 45.833 12.05 0.00 42.62 3.86
585 597 4.357325 AGGAGCAGAGTTTAGAATCTGGA 58.643 43.478 12.05 0.00 42.62 3.86
586 598 4.405358 AGGAGCAGAGTTTAGAATCTGGAG 59.595 45.833 12.05 0.00 42.62 3.86
587 599 4.442753 GGAGCAGAGTTTAGAATCTGGAGG 60.443 50.000 12.05 0.00 42.62 4.30
588 600 4.357325 AGCAGAGTTTAGAATCTGGAGGA 58.643 43.478 12.05 0.00 42.62 3.71
589 601 4.405358 AGCAGAGTTTAGAATCTGGAGGAG 59.595 45.833 12.05 0.00 42.62 3.69
590 602 4.161377 GCAGAGTTTAGAATCTGGAGGAGT 59.839 45.833 12.05 0.00 42.62 3.85
591 603 5.659463 CAGAGTTTAGAATCTGGAGGAGTG 58.341 45.833 2.93 0.00 39.42 3.51
592 604 4.714308 AGAGTTTAGAATCTGGAGGAGTGG 59.286 45.833 0.00 0.00 0.00 4.00
593 605 4.689062 AGTTTAGAATCTGGAGGAGTGGA 58.311 43.478 0.00 0.00 0.00 4.02
594 606 4.714308 AGTTTAGAATCTGGAGGAGTGGAG 59.286 45.833 0.00 0.00 0.00 3.86
595 607 4.609866 TTAGAATCTGGAGGAGTGGAGA 57.390 45.455 0.00 0.00 0.00 3.71
596 608 3.030873 AGAATCTGGAGGAGTGGAGAG 57.969 52.381 0.00 0.00 0.00 3.20
597 609 2.314549 AGAATCTGGAGGAGTGGAGAGT 59.685 50.000 0.00 0.00 0.00 3.24
598 610 2.938428 ATCTGGAGGAGTGGAGAGTT 57.062 50.000 0.00 0.00 0.00 3.01
599 611 1.930251 TCTGGAGGAGTGGAGAGTTG 58.070 55.000 0.00 0.00 0.00 3.16
600 612 0.248843 CTGGAGGAGTGGAGAGTTGC 59.751 60.000 0.00 0.00 0.00 4.17
601 613 1.194781 TGGAGGAGTGGAGAGTTGCC 61.195 60.000 0.00 0.00 0.00 4.52
602 614 1.216710 GAGGAGTGGAGAGTTGCCG 59.783 63.158 0.00 0.00 0.00 5.69
603 615 1.228894 AGGAGTGGAGAGTTGCCGA 60.229 57.895 0.00 0.00 0.00 5.54
604 616 0.832135 AGGAGTGGAGAGTTGCCGAA 60.832 55.000 0.00 0.00 0.00 4.30
605 617 0.670854 GGAGTGGAGAGTTGCCGAAC 60.671 60.000 0.00 0.00 0.00 3.95
606 618 0.033504 GAGTGGAGAGTTGCCGAACA 59.966 55.000 0.00 0.00 34.17 3.18
607 619 0.034059 AGTGGAGAGTTGCCGAACAG 59.966 55.000 0.00 0.00 34.17 3.16
608 620 0.951040 GTGGAGAGTTGCCGAACAGG 60.951 60.000 0.00 0.00 44.97 4.00
625 637 8.690680 CCGAACAGGCTCTTAGTATATATTTC 57.309 38.462 0.00 0.00 0.00 2.17
747 761 7.546778 TTTGCATATTTAAGCATCTCGTACA 57.453 32.000 0.00 0.00 40.94 2.90
808 828 9.546909 CGCATGTTGATTACTAATATTCAATCC 57.453 33.333 11.75 3.02 34.70 3.01
813 833 9.813080 GTTGATTACTAATATTCAATCCTTCGC 57.187 33.333 11.75 0.00 34.70 4.70
814 834 9.554395 TTGATTACTAATATTCAATCCTTCGCA 57.446 29.630 11.75 0.00 29.71 5.10
815 835 9.554395 TGATTACTAATATTCAATCCTTCGCAA 57.446 29.630 11.75 0.00 0.00 4.85
927 947 1.299926 GTATGCGCCGGTACCTCTG 60.300 63.158 10.90 0.00 0.00 3.35
1483 1559 0.324285 CCAGTGGCTTCTGCTCTTCT 59.676 55.000 0.00 0.00 39.59 2.85
1533 1609 1.303317 ACACCACCAAATCCTCCGC 60.303 57.895 0.00 0.00 0.00 5.54
1559 1635 0.246635 ATTGTCAACGAGGAGGACGG 59.753 55.000 0.00 0.00 34.32 4.79
1651 1727 3.565482 CCCGGTGAAACTCCATATCAATG 59.435 47.826 0.00 0.00 36.74 2.82
1897 4513 4.622456 CCAACCACAACGGCGTGC 62.622 66.667 15.70 0.00 39.03 5.34
2426 5063 6.095377 GCCTGAACTTGTTATCATTTTGAGG 58.905 40.000 0.00 0.00 0.00 3.86
2474 5121 2.566833 TCACACCATCAGACTTTGGG 57.433 50.000 6.23 0.00 37.32 4.12
2482 5129 4.901250 ACCATCAGACTTTGGGAAATGTTT 59.099 37.500 6.23 0.00 37.32 2.83
2577 5254 6.656003 AGTGTTAAAACAGTGATCTAAACGC 58.344 36.000 0.00 1.77 40.86 4.84
2579 5256 7.012044 AGTGTTAAAACAGTGATCTAAACGCTT 59.988 33.333 0.00 0.00 40.86 4.68
2582 5259 9.654417 GTTAAAACAGTGATCTAAACGCTTTTA 57.346 29.630 0.00 0.00 0.00 1.52
2599 5307 6.703165 ACGCTTTTATATTAGTTTACGGAGGG 59.297 38.462 0.00 0.00 0.00 4.30
2614 5322 3.010584 ACGGAGGGAGTACAAGGTAGTAA 59.989 47.826 0.00 0.00 0.00 2.24
2667 5375 2.434884 CAGCCGCCACGTGAAGAT 60.435 61.111 19.30 0.04 0.00 2.40
2759 6072 2.076863 GCGCTATTGTGACCTGTCTTT 58.923 47.619 0.00 0.00 0.00 2.52
2769 6082 3.933332 GTGACCTGTCTTTTAAGGGATCG 59.067 47.826 0.00 0.00 37.94 3.69
2780 6093 2.029666 GGGATCGATGTGGAGGCG 59.970 66.667 0.54 0.00 0.00 5.52
2804 6121 1.010125 CGTTTGTTGTGGGAGCACG 60.010 57.895 0.00 0.00 0.00 5.34
2817 6134 1.264288 GGAGCACGACTTTGTTCCTTG 59.736 52.381 0.00 0.00 42.20 3.61
2869 6186 4.532834 TGCCACTAGTGTTCTTCCTTTTT 58.467 39.130 21.18 0.00 0.00 1.94
2901 6218 2.024176 TGGAGCACTTAGAATTCGCC 57.976 50.000 0.00 0.00 0.00 5.54
2969 6286 3.629398 GGTGTCAAAGGCCTATCAATCTG 59.371 47.826 5.16 0.00 0.00 2.90
3069 6659 0.545171 AGCATGACTGAGATGGTGGG 59.455 55.000 0.00 0.00 30.44 4.61
3159 6749 2.557317 TCCAGGACGAAGAACAACAAC 58.443 47.619 0.00 0.00 0.00 3.32
3166 6756 1.722464 CGAAGAACAACAACGGCGATA 59.278 47.619 16.62 0.00 0.00 2.92
3177 6767 0.823769 ACGGCGATATCTCAGCTCCA 60.824 55.000 16.62 0.00 0.00 3.86
3187 6778 4.703379 ATCTCAGCTCCAGGGAAAATAG 57.297 45.455 0.00 0.00 0.00 1.73
3211 6802 3.218453 TCAAAAATCGCTTGAGGGTTCA 58.782 40.909 0.00 0.00 0.00 3.18
3212 6803 3.634448 TCAAAAATCGCTTGAGGGTTCAA 59.366 39.130 0.00 0.00 40.92 2.69
3213 6804 3.643159 AAAATCGCTTGAGGGTTCAAC 57.357 42.857 0.00 0.00 38.37 3.18
3214 6805 1.156736 AATCGCTTGAGGGTTCAACG 58.843 50.000 0.00 6.16 38.37 4.10
3228 6842 1.671054 CAACGGACACGCCCAAGAT 60.671 57.895 0.00 0.00 46.04 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.346722 AGAGTTGATTCGTTCGGGGTT 59.653 47.619 0.00 0.00 0.00 4.11
9 10 0.974383 AGAGTTGATTCGTTCGGGGT 59.026 50.000 0.00 0.00 0.00 4.95
11 12 0.721718 GCAGAGTTGATTCGTTCGGG 59.278 55.000 0.00 0.00 0.00 5.14
118 120 4.020617 CGGGGCAAGCAGGTGAGA 62.021 66.667 0.00 0.00 0.00 3.27
143 145 0.036388 CGGCTAGAGTTCCCTGCAAA 60.036 55.000 0.00 0.00 0.00 3.68
186 198 1.832912 GGGATTCGATCAGCCCTGT 59.167 57.895 3.06 0.00 37.59 4.00
187 199 1.301244 CGGGATTCGATCAGCCCTG 60.301 63.158 8.73 0.00 42.43 4.45
188 200 1.762460 ACGGGATTCGATCAGCCCT 60.762 57.895 8.73 0.00 42.43 5.19
189 201 1.595382 CACGGGATTCGATCAGCCC 60.595 63.158 0.00 0.00 42.43 5.19
190 202 1.144057 ACACGGGATTCGATCAGCC 59.856 57.895 0.00 0.00 42.43 4.85
191 203 0.179111 TCACACGGGATTCGATCAGC 60.179 55.000 0.00 0.00 42.43 4.26
205 217 3.577229 TGCGTCCATGCATCACAC 58.423 55.556 0.00 0.00 40.62 3.82
229 241 2.028484 GACGACGGACAAGTGGCA 59.972 61.111 0.00 0.00 0.00 4.92
241 253 2.665185 AGCAGGTTTGGCGACGAC 60.665 61.111 0.00 0.00 36.08 4.34
244 256 4.090057 GCGAGCAGGTTTGGCGAC 62.090 66.667 0.00 0.00 36.08 5.19
246 258 4.093952 CTGCGAGCAGGTTTGGCG 62.094 66.667 16.69 0.00 40.17 5.69
268 280 0.459899 TCAGCTATCGCCATTGACGT 59.540 50.000 0.00 0.00 36.60 4.34
277 289 1.300542 GGAGCCTGTCAGCTATCGC 60.301 63.158 0.00 0.00 45.15 4.58
386 398 3.788766 GTTGGTGCAGTAGCGGCG 61.789 66.667 0.51 0.51 46.23 6.46
387 399 3.788766 CGTTGGTGCAGTAGCGGC 61.789 66.667 0.00 0.00 46.23 6.53
388 400 3.118454 CCGTTGGTGCAGTAGCGG 61.118 66.667 10.27 10.27 46.23 5.52
389 401 3.118454 CCCGTTGGTGCAGTAGCG 61.118 66.667 0.00 0.00 46.23 4.26
390 402 3.431725 GCCCGTTGGTGCAGTAGC 61.432 66.667 0.00 0.00 42.57 3.58
391 403 1.741770 GAGCCCGTTGGTGCAGTAG 60.742 63.158 0.00 0.00 0.00 2.57
392 404 2.345991 GAGCCCGTTGGTGCAGTA 59.654 61.111 0.00 0.00 0.00 2.74
393 405 4.643387 GGAGCCCGTTGGTGCAGT 62.643 66.667 0.00 0.00 32.37 4.40
394 406 3.850098 AAGGAGCCCGTTGGTGCAG 62.850 63.158 0.00 0.00 34.90 4.41
395 407 3.842925 GAAGGAGCCCGTTGGTGCA 62.843 63.158 0.00 0.00 34.90 4.57
396 408 3.056328 GAAGGAGCCCGTTGGTGC 61.056 66.667 0.00 0.00 0.00 5.01
397 409 0.609131 AATGAAGGAGCCCGTTGGTG 60.609 55.000 0.00 0.00 0.00 4.17
398 410 0.322546 GAATGAAGGAGCCCGTTGGT 60.323 55.000 0.00 0.00 0.00 3.67
399 411 1.032114 GGAATGAAGGAGCCCGTTGG 61.032 60.000 0.00 0.00 0.00 3.77
400 412 0.035056 AGGAATGAAGGAGCCCGTTG 60.035 55.000 0.00 0.00 0.00 4.10
401 413 0.253327 GAGGAATGAAGGAGCCCGTT 59.747 55.000 0.00 0.00 0.00 4.44
402 414 0.909610 TGAGGAATGAAGGAGCCCGT 60.910 55.000 0.00 0.00 0.00 5.28
403 415 0.179062 CTGAGGAATGAAGGAGCCCG 60.179 60.000 0.00 0.00 0.00 6.13
404 416 0.915364 ACTGAGGAATGAAGGAGCCC 59.085 55.000 0.00 0.00 0.00 5.19
405 417 1.556911 TCACTGAGGAATGAAGGAGCC 59.443 52.381 0.00 0.00 0.00 4.70
406 418 3.340814 TTCACTGAGGAATGAAGGAGC 57.659 47.619 0.00 0.00 31.29 4.70
407 419 4.006319 GGTTTCACTGAGGAATGAAGGAG 58.994 47.826 0.00 0.00 36.26 3.69
408 420 3.394274 TGGTTTCACTGAGGAATGAAGGA 59.606 43.478 0.00 0.00 36.26 3.36
409 421 3.503748 GTGGTTTCACTGAGGAATGAAGG 59.496 47.826 0.00 0.00 40.58 3.46
410 422 3.503748 GGTGGTTTCACTGAGGAATGAAG 59.496 47.826 0.00 0.00 43.17 3.02
411 423 3.486383 GGTGGTTTCACTGAGGAATGAA 58.514 45.455 0.00 0.00 43.17 2.57
412 424 3.140325 GGTGGTTTCACTGAGGAATGA 57.860 47.619 0.00 0.00 43.17 2.57
421 433 2.397413 CTGAGGGCGGTGGTTTCACT 62.397 60.000 0.00 0.00 43.17 3.41
422 434 1.966451 CTGAGGGCGGTGGTTTCAC 60.966 63.158 0.00 0.00 42.91 3.18
423 435 2.429930 CTGAGGGCGGTGGTTTCA 59.570 61.111 0.00 0.00 0.00 2.69
424 436 3.056328 GCTGAGGGCGGTGGTTTC 61.056 66.667 0.00 0.00 0.00 2.78
433 445 1.742268 CTAGAAAAAGCAGCTGAGGGC 59.258 52.381 20.43 0.63 42.19 5.19
434 446 3.006247 GACTAGAAAAAGCAGCTGAGGG 58.994 50.000 20.43 0.00 0.00 4.30
435 447 3.668447 TGACTAGAAAAAGCAGCTGAGG 58.332 45.455 20.43 0.00 0.00 3.86
436 448 3.683822 CCTGACTAGAAAAAGCAGCTGAG 59.316 47.826 20.43 5.50 0.00 3.35
437 449 3.071602 ACCTGACTAGAAAAAGCAGCTGA 59.928 43.478 20.43 0.00 0.00 4.26
438 450 3.406764 ACCTGACTAGAAAAAGCAGCTG 58.593 45.455 10.11 10.11 0.00 4.24
439 451 3.778954 ACCTGACTAGAAAAAGCAGCT 57.221 42.857 0.00 0.00 0.00 4.24
440 452 3.189495 GGAACCTGACTAGAAAAAGCAGC 59.811 47.826 0.00 0.00 0.00 5.25
441 453 4.646572 AGGAACCTGACTAGAAAAAGCAG 58.353 43.478 0.00 0.00 0.00 4.24
442 454 4.505039 GGAGGAACCTGACTAGAAAAAGCA 60.505 45.833 0.00 0.00 35.41 3.91
443 455 4.004314 GGAGGAACCTGACTAGAAAAAGC 58.996 47.826 0.00 0.00 35.41 3.51
444 456 4.041691 TGGGAGGAACCTGACTAGAAAAAG 59.958 45.833 0.00 0.00 38.98 2.27
445 457 3.977999 TGGGAGGAACCTGACTAGAAAAA 59.022 43.478 0.00 0.00 38.98 1.94
446 458 3.583086 CTGGGAGGAACCTGACTAGAAAA 59.417 47.826 0.00 0.00 38.98 2.29
447 459 3.173965 CTGGGAGGAACCTGACTAGAAA 58.826 50.000 0.00 0.00 38.98 2.52
448 460 2.559931 CCTGGGAGGAACCTGACTAGAA 60.560 54.545 0.00 0.00 37.67 2.10
449 461 1.007238 CCTGGGAGGAACCTGACTAGA 59.993 57.143 0.00 0.00 37.67 2.43
450 462 1.007238 TCCTGGGAGGAACCTGACTAG 59.993 57.143 0.00 0.00 42.51 2.57
451 463 1.089978 TCCTGGGAGGAACCTGACTA 58.910 55.000 0.00 0.00 42.51 2.59
452 464 0.193574 TTCCTGGGAGGAACCTGACT 59.806 55.000 0.67 0.00 46.88 3.41
453 465 2.773458 TTCCTGGGAGGAACCTGAC 58.227 57.895 0.67 0.00 46.88 3.51
460 472 1.891933 TGCATACATTCCTGGGAGGA 58.108 50.000 0.00 0.00 44.10 3.71
461 473 2.965671 ATGCATACATTCCTGGGAGG 57.034 50.000 0.00 0.00 36.46 4.30
462 474 6.005823 TGAATTATGCATACATTCCTGGGAG 58.994 40.000 23.79 0.00 37.74 4.30
463 475 5.951204 TGAATTATGCATACATTCCTGGGA 58.049 37.500 23.79 12.31 37.74 4.37
464 476 5.771666 ACTGAATTATGCATACATTCCTGGG 59.228 40.000 23.79 17.63 37.74 4.45
465 477 6.889301 ACTGAATTATGCATACATTCCTGG 57.111 37.500 23.79 18.98 37.74 4.45
466 478 7.933396 TCAACTGAATTATGCATACATTCCTG 58.067 34.615 23.79 20.41 37.74 3.86
467 479 7.230108 CCTCAACTGAATTATGCATACATTCCT 59.770 37.037 23.79 14.40 37.74 3.36
468 480 7.229306 TCCTCAACTGAATTATGCATACATTCC 59.771 37.037 23.79 14.45 37.74 3.01
469 481 8.158169 TCCTCAACTGAATTATGCATACATTC 57.842 34.615 21.93 21.93 37.74 2.67
470 482 7.776969 ACTCCTCAACTGAATTATGCATACATT 59.223 33.333 5.74 9.47 37.74 2.71
471 483 7.228108 CACTCCTCAACTGAATTATGCATACAT 59.772 37.037 5.74 0.00 40.49 2.29
472 484 6.539826 CACTCCTCAACTGAATTATGCATACA 59.460 38.462 5.74 0.40 0.00 2.29
473 485 6.017605 CCACTCCTCAACTGAATTATGCATAC 60.018 42.308 5.74 0.00 0.00 2.39
474 486 6.057533 CCACTCCTCAACTGAATTATGCATA 58.942 40.000 1.16 1.16 0.00 3.14
475 487 4.885907 CCACTCCTCAACTGAATTATGCAT 59.114 41.667 3.79 3.79 0.00 3.96
476 488 4.019411 TCCACTCCTCAACTGAATTATGCA 60.019 41.667 0.00 0.00 0.00 3.96
477 489 4.517285 TCCACTCCTCAACTGAATTATGC 58.483 43.478 0.00 0.00 0.00 3.14
478 490 5.738909 ACTCCACTCCTCAACTGAATTATG 58.261 41.667 0.00 0.00 0.00 1.90
479 491 6.013379 TGAACTCCACTCCTCAACTGAATTAT 60.013 38.462 0.00 0.00 0.00 1.28
480 492 5.306937 TGAACTCCACTCCTCAACTGAATTA 59.693 40.000 0.00 0.00 0.00 1.40
481 493 4.103153 TGAACTCCACTCCTCAACTGAATT 59.897 41.667 0.00 0.00 0.00 2.17
482 494 3.648067 TGAACTCCACTCCTCAACTGAAT 59.352 43.478 0.00 0.00 0.00 2.57
483 495 3.038280 TGAACTCCACTCCTCAACTGAA 58.962 45.455 0.00 0.00 0.00 3.02
484 496 2.365617 GTGAACTCCACTCCTCAACTGA 59.634 50.000 0.00 0.00 42.44 3.41
485 497 2.103094 TGTGAACTCCACTCCTCAACTG 59.897 50.000 0.00 0.00 45.86 3.16
486 498 2.398588 TGTGAACTCCACTCCTCAACT 58.601 47.619 0.00 0.00 45.86 3.16
487 499 2.872858 GTTGTGAACTCCACTCCTCAAC 59.127 50.000 0.00 0.00 45.86 3.18
488 500 2.158813 GGTTGTGAACTCCACTCCTCAA 60.159 50.000 0.00 0.00 45.86 3.02
489 501 1.416401 GGTTGTGAACTCCACTCCTCA 59.584 52.381 0.00 0.00 45.86 3.86
490 502 1.605712 CGGTTGTGAACTCCACTCCTC 60.606 57.143 0.00 0.00 45.86 3.71
491 503 0.393077 CGGTTGTGAACTCCACTCCT 59.607 55.000 0.00 0.00 45.86 3.69
492 504 0.391597 TCGGTTGTGAACTCCACTCC 59.608 55.000 0.00 0.00 45.86 3.85
493 505 1.865340 GTTCGGTTGTGAACTCCACTC 59.135 52.381 0.00 0.00 45.86 3.51
494 506 1.805120 CGTTCGGTTGTGAACTCCACT 60.805 52.381 5.25 0.00 44.76 4.00
495 507 0.580104 CGTTCGGTTGTGAACTCCAC 59.420 55.000 5.25 0.00 44.76 4.02
496 508 0.176219 ACGTTCGGTTGTGAACTCCA 59.824 50.000 5.25 0.00 44.76 3.86
497 509 2.138596 TACGTTCGGTTGTGAACTCC 57.861 50.000 0.00 0.00 44.76 3.85
498 510 3.122445 GGAATACGTTCGGTTGTGAACTC 59.878 47.826 0.00 0.00 44.76 3.01
499 511 3.062042 GGAATACGTTCGGTTGTGAACT 58.938 45.455 0.00 0.00 44.76 3.01
500 512 2.158254 GGGAATACGTTCGGTTGTGAAC 59.842 50.000 0.00 0.00 43.76 3.18
501 513 2.224233 TGGGAATACGTTCGGTTGTGAA 60.224 45.455 0.00 0.00 35.10 3.18
502 514 1.343789 TGGGAATACGTTCGGTTGTGA 59.656 47.619 0.00 0.00 35.10 3.58
503 515 1.730064 CTGGGAATACGTTCGGTTGTG 59.270 52.381 0.00 0.00 35.10 3.33
504 516 1.619827 TCTGGGAATACGTTCGGTTGT 59.380 47.619 0.00 0.00 35.10 3.32
505 517 2.373540 TCTGGGAATACGTTCGGTTG 57.626 50.000 0.00 0.00 35.10 3.77
506 518 3.197116 AGAATCTGGGAATACGTTCGGTT 59.803 43.478 0.00 0.00 35.10 4.44
507 519 2.764572 AGAATCTGGGAATACGTTCGGT 59.235 45.455 0.00 0.00 35.10 4.69
508 520 3.123804 CAGAATCTGGGAATACGTTCGG 58.876 50.000 1.53 0.00 35.10 4.30
509 521 4.041740 TCAGAATCTGGGAATACGTTCG 57.958 45.455 10.71 0.00 35.10 3.95
510 522 5.220416 CGTTTCAGAATCTGGGAATACGTTC 60.220 44.000 10.71 0.00 31.51 3.95
511 523 4.630069 CGTTTCAGAATCTGGGAATACGTT 59.370 41.667 10.71 0.00 31.51 3.99
512 524 4.181578 CGTTTCAGAATCTGGGAATACGT 58.818 43.478 10.71 0.00 31.51 3.57
513 525 4.032900 CACGTTTCAGAATCTGGGAATACG 59.967 45.833 10.71 13.95 34.45 3.06
514 526 4.201822 GCACGTTTCAGAATCTGGGAATAC 60.202 45.833 10.71 1.57 31.51 1.89
515 527 3.938963 GCACGTTTCAGAATCTGGGAATA 59.061 43.478 10.71 0.00 31.51 1.75
516 528 2.749621 GCACGTTTCAGAATCTGGGAAT 59.250 45.455 10.71 0.00 31.51 3.01
517 529 2.151202 GCACGTTTCAGAATCTGGGAA 58.849 47.619 10.71 3.35 31.51 3.97
518 530 1.347707 AGCACGTTTCAGAATCTGGGA 59.652 47.619 10.71 0.00 31.51 4.37
519 531 1.813513 AGCACGTTTCAGAATCTGGG 58.186 50.000 10.71 0.70 31.51 4.45
520 532 6.042777 TCTATTAGCACGTTTCAGAATCTGG 58.957 40.000 10.71 0.00 31.51 3.86
521 533 6.754209 ACTCTATTAGCACGTTTCAGAATCTG 59.246 38.462 3.38 3.38 0.00 2.90
522 534 6.868622 ACTCTATTAGCACGTTTCAGAATCT 58.131 36.000 0.00 0.00 0.00 2.40
523 535 7.394872 CAACTCTATTAGCACGTTTCAGAATC 58.605 38.462 0.00 0.00 0.00 2.52
524 536 6.313905 CCAACTCTATTAGCACGTTTCAGAAT 59.686 38.462 0.00 0.00 0.00 2.40
525 537 5.637810 CCAACTCTATTAGCACGTTTCAGAA 59.362 40.000 0.00 0.00 0.00 3.02
526 538 5.168569 CCAACTCTATTAGCACGTTTCAGA 58.831 41.667 0.00 0.00 0.00 3.27
527 539 4.330074 CCCAACTCTATTAGCACGTTTCAG 59.670 45.833 0.00 0.00 0.00 3.02
528 540 4.020928 TCCCAACTCTATTAGCACGTTTCA 60.021 41.667 0.00 0.00 0.00 2.69
529 541 4.501071 TCCCAACTCTATTAGCACGTTTC 58.499 43.478 0.00 0.00 0.00 2.78
530 542 4.020485 ACTCCCAACTCTATTAGCACGTTT 60.020 41.667 0.00 0.00 0.00 3.60
531 543 3.514309 ACTCCCAACTCTATTAGCACGTT 59.486 43.478 0.00 0.00 0.00 3.99
532 544 3.097614 ACTCCCAACTCTATTAGCACGT 58.902 45.455 0.00 0.00 0.00 4.49
533 545 3.802948 ACTCCCAACTCTATTAGCACG 57.197 47.619 0.00 0.00 0.00 5.34
534 546 5.086104 TCAACTCCCAACTCTATTAGCAC 57.914 43.478 0.00 0.00 0.00 4.40
535 547 5.023452 TCTCAACTCCCAACTCTATTAGCA 58.977 41.667 0.00 0.00 0.00 3.49
536 548 5.599999 TCTCAACTCCCAACTCTATTAGC 57.400 43.478 0.00 0.00 0.00 3.09
537 549 7.038659 CACTTCTCAACTCCCAACTCTATTAG 58.961 42.308 0.00 0.00 0.00 1.73
538 550 6.724441 TCACTTCTCAACTCCCAACTCTATTA 59.276 38.462 0.00 0.00 0.00 0.98
539 551 5.544176 TCACTTCTCAACTCCCAACTCTATT 59.456 40.000 0.00 0.00 0.00 1.73
540 552 5.087323 TCACTTCTCAACTCCCAACTCTAT 58.913 41.667 0.00 0.00 0.00 1.98
541 553 4.480115 TCACTTCTCAACTCCCAACTCTA 58.520 43.478 0.00 0.00 0.00 2.43
542 554 3.309296 TCACTTCTCAACTCCCAACTCT 58.691 45.455 0.00 0.00 0.00 3.24
543 555 3.556004 CCTCACTTCTCAACTCCCAACTC 60.556 52.174 0.00 0.00 0.00 3.01
544 556 2.370189 CCTCACTTCTCAACTCCCAACT 59.630 50.000 0.00 0.00 0.00 3.16
545 557 2.368875 TCCTCACTTCTCAACTCCCAAC 59.631 50.000 0.00 0.00 0.00 3.77
546 558 2.634940 CTCCTCACTTCTCAACTCCCAA 59.365 50.000 0.00 0.00 0.00 4.12
547 559 2.251818 CTCCTCACTTCTCAACTCCCA 58.748 52.381 0.00 0.00 0.00 4.37
548 560 1.066502 GCTCCTCACTTCTCAACTCCC 60.067 57.143 0.00 0.00 0.00 4.30
549 561 1.620819 TGCTCCTCACTTCTCAACTCC 59.379 52.381 0.00 0.00 0.00 3.85
550 562 2.560542 TCTGCTCCTCACTTCTCAACTC 59.439 50.000 0.00 0.00 0.00 3.01
551 563 2.562298 CTCTGCTCCTCACTTCTCAACT 59.438 50.000 0.00 0.00 0.00 3.16
552 564 2.298729 ACTCTGCTCCTCACTTCTCAAC 59.701 50.000 0.00 0.00 0.00 3.18
553 565 2.603021 ACTCTGCTCCTCACTTCTCAA 58.397 47.619 0.00 0.00 0.00 3.02
554 566 2.300956 ACTCTGCTCCTCACTTCTCA 57.699 50.000 0.00 0.00 0.00 3.27
555 567 3.676291 AAACTCTGCTCCTCACTTCTC 57.324 47.619 0.00 0.00 0.00 2.87
556 568 4.411927 TCTAAACTCTGCTCCTCACTTCT 58.588 43.478 0.00 0.00 0.00 2.85
557 569 4.792521 TCTAAACTCTGCTCCTCACTTC 57.207 45.455 0.00 0.00 0.00 3.01
558 570 5.483583 AGATTCTAAACTCTGCTCCTCACTT 59.516 40.000 0.00 0.00 0.00 3.16
559 571 5.022787 AGATTCTAAACTCTGCTCCTCACT 58.977 41.667 0.00 0.00 0.00 3.41
560 572 5.108517 CAGATTCTAAACTCTGCTCCTCAC 58.891 45.833 0.00 0.00 33.12 3.51
561 573 4.161189 CCAGATTCTAAACTCTGCTCCTCA 59.839 45.833 0.00 0.00 38.03 3.86
562 574 4.404073 TCCAGATTCTAAACTCTGCTCCTC 59.596 45.833 0.00 0.00 38.03 3.71
563 575 4.357325 TCCAGATTCTAAACTCTGCTCCT 58.643 43.478 0.00 0.00 38.03 3.69
564 576 4.442753 CCTCCAGATTCTAAACTCTGCTCC 60.443 50.000 0.00 0.00 38.03 4.70
565 577 4.404073 TCCTCCAGATTCTAAACTCTGCTC 59.596 45.833 0.00 0.00 38.03 4.26
566 578 4.357325 TCCTCCAGATTCTAAACTCTGCT 58.643 43.478 0.00 0.00 38.03 4.24
567 579 4.161377 ACTCCTCCAGATTCTAAACTCTGC 59.839 45.833 0.00 0.00 38.03 4.26
568 580 5.395103 CCACTCCTCCAGATTCTAAACTCTG 60.395 48.000 0.00 0.00 38.88 3.35
569 581 4.714308 CCACTCCTCCAGATTCTAAACTCT 59.286 45.833 0.00 0.00 0.00 3.24
570 582 4.712337 TCCACTCCTCCAGATTCTAAACTC 59.288 45.833 0.00 0.00 0.00 3.01
571 583 4.689062 TCCACTCCTCCAGATTCTAAACT 58.311 43.478 0.00 0.00 0.00 2.66
572 584 4.712337 TCTCCACTCCTCCAGATTCTAAAC 59.288 45.833 0.00 0.00 0.00 2.01
573 585 4.947883 TCTCCACTCCTCCAGATTCTAAA 58.052 43.478 0.00 0.00 0.00 1.85
574 586 4.017037 ACTCTCCACTCCTCCAGATTCTAA 60.017 45.833 0.00 0.00 0.00 2.10
575 587 3.529734 ACTCTCCACTCCTCCAGATTCTA 59.470 47.826 0.00 0.00 0.00 2.10
576 588 2.314549 ACTCTCCACTCCTCCAGATTCT 59.685 50.000 0.00 0.00 0.00 2.40
577 589 2.745968 ACTCTCCACTCCTCCAGATTC 58.254 52.381 0.00 0.00 0.00 2.52
578 590 2.836981 CAACTCTCCACTCCTCCAGATT 59.163 50.000 0.00 0.00 0.00 2.40
579 591 2.465813 CAACTCTCCACTCCTCCAGAT 58.534 52.381 0.00 0.00 0.00 2.90
580 592 1.930251 CAACTCTCCACTCCTCCAGA 58.070 55.000 0.00 0.00 0.00 3.86
581 593 0.248843 GCAACTCTCCACTCCTCCAG 59.751 60.000 0.00 0.00 0.00 3.86
582 594 1.194781 GGCAACTCTCCACTCCTCCA 61.195 60.000 0.00 0.00 0.00 3.86
583 595 1.599576 GGCAACTCTCCACTCCTCC 59.400 63.158 0.00 0.00 0.00 4.30
584 596 1.216710 CGGCAACTCTCCACTCCTC 59.783 63.158 0.00 0.00 0.00 3.71
585 597 0.832135 TTCGGCAACTCTCCACTCCT 60.832 55.000 0.00 0.00 0.00 3.69
586 598 0.670854 GTTCGGCAACTCTCCACTCC 60.671 60.000 0.00 0.00 0.00 3.85
587 599 0.033504 TGTTCGGCAACTCTCCACTC 59.966 55.000 0.00 0.00 33.17 3.51
588 600 0.034059 CTGTTCGGCAACTCTCCACT 59.966 55.000 0.00 0.00 33.17 4.00
589 601 0.951040 CCTGTTCGGCAACTCTCCAC 60.951 60.000 0.00 0.00 33.17 4.02
590 602 1.371183 CCTGTTCGGCAACTCTCCA 59.629 57.895 0.00 0.00 33.17 3.86
591 603 4.285851 CCTGTTCGGCAACTCTCC 57.714 61.111 0.00 0.00 33.17 3.71
600 612 7.485277 CGAAATATATACTAAGAGCCTGTTCGG 59.515 40.741 0.00 0.00 0.00 4.30
601 613 7.485277 CCGAAATATATACTAAGAGCCTGTTCG 59.515 40.741 0.00 0.00 33.37 3.95
602 614 8.521176 TCCGAAATATATACTAAGAGCCTGTTC 58.479 37.037 0.00 0.00 0.00 3.18
603 615 8.418597 TCCGAAATATATACTAAGAGCCTGTT 57.581 34.615 0.00 0.00 0.00 3.16
604 616 8.596781 ATCCGAAATATATACTAAGAGCCTGT 57.403 34.615 0.00 0.00 0.00 4.00
605 617 9.307121 CAATCCGAAATATATACTAAGAGCCTG 57.693 37.037 0.00 0.00 0.00 4.85
606 618 9.036980 ACAATCCGAAATATATACTAAGAGCCT 57.963 33.333 0.00 0.00 0.00 4.58
607 619 9.654663 AACAATCCGAAATATATACTAAGAGCC 57.345 33.333 0.00 0.00 0.00 4.70
625 637 2.237751 CGAGCCCGCTAACAATCCG 61.238 63.158 0.00 0.00 0.00 4.18
1483 1559 2.727544 GCGGTTGGCAAAGAAGCA 59.272 55.556 0.00 0.00 42.87 3.91
1559 1635 2.266055 CGGTGCTGGAGAGGAACC 59.734 66.667 0.00 0.00 0.00 3.62
1591 1667 4.785453 CAGGTGCTCCGCTTCCCC 62.785 72.222 0.00 0.00 39.05 4.81
1599 1675 2.821366 CCGATGTGCAGGTGCTCC 60.821 66.667 3.18 0.00 42.66 4.70
1897 4513 2.019951 CGAACCGGTCCGTGAACTG 61.020 63.158 8.04 0.00 0.00 3.16
2101 4729 1.639635 AATCCTGCGGCTTCCATCCT 61.640 55.000 0.00 0.00 0.00 3.24
2126 4754 2.514592 CGGGGCTCATTGTCGCAT 60.515 61.111 0.00 0.00 32.29 4.73
2311 4941 6.628175 GCAAGAAGATCACAGGTCACAGTATA 60.628 42.308 0.00 0.00 0.00 1.47
2374 5004 2.426738 CCAAAACACATGCATCCGGTAT 59.573 45.455 0.00 0.00 0.00 2.73
2375 5005 1.815613 CCAAAACACATGCATCCGGTA 59.184 47.619 0.00 0.00 0.00 4.02
2376 5006 0.602562 CCAAAACACATGCATCCGGT 59.397 50.000 0.00 0.00 0.00 5.28
2377 5007 0.602562 ACCAAAACACATGCATCCGG 59.397 50.000 0.00 0.00 0.00 5.14
2426 5063 5.137403 CACTTTGCAGTACGATAACAACAC 58.863 41.667 0.00 0.00 0.00 3.32
2463 5110 5.299279 GTCTCAAACATTTCCCAAAGTCTGA 59.701 40.000 0.00 0.00 0.00 3.27
2550 5227 8.548721 CGTTTAGATCACTGTTTTAACACTCTT 58.451 33.333 0.00 0.00 34.70 2.85
2551 5228 7.307219 GCGTTTAGATCACTGTTTTAACACTCT 60.307 37.037 0.00 0.00 34.70 3.24
2553 5230 6.482308 AGCGTTTAGATCACTGTTTTAACACT 59.518 34.615 0.00 0.00 34.70 3.55
2575 5252 6.925165 TCCCTCCGTAAACTAATATAAAAGCG 59.075 38.462 0.00 0.00 0.00 4.68
2579 5256 9.420118 TGTACTCCCTCCGTAAACTAATATAAA 57.580 33.333 0.00 0.00 0.00 1.40
2582 5259 7.015001 CCTTGTACTCCCTCCGTAAACTAATAT 59.985 40.741 0.00 0.00 0.00 1.28
2585 5262 4.463891 CCTTGTACTCCCTCCGTAAACTAA 59.536 45.833 0.00 0.00 0.00 2.24
2587 5264 2.830321 CCTTGTACTCCCTCCGTAAACT 59.170 50.000 0.00 0.00 0.00 2.66
2588 5265 2.564504 ACCTTGTACTCCCTCCGTAAAC 59.435 50.000 0.00 0.00 0.00 2.01
2590 5267 2.610438 ACCTTGTACTCCCTCCGTAA 57.390 50.000 0.00 0.00 0.00 3.18
2591 5268 2.578021 ACTACCTTGTACTCCCTCCGTA 59.422 50.000 0.00 0.00 0.00 4.02
2614 5322 9.182214 CAATTAAGCAAGGGTAGCATATCATAT 57.818 33.333 0.00 0.00 0.00 1.78
2667 5375 4.927425 GCAAGAAGTGTGATAAGGACGTTA 59.073 41.667 0.00 0.00 0.00 3.18
2718 6031 1.004044 CAGAAGCACCCCAACATCTCT 59.996 52.381 0.00 0.00 0.00 3.10
2759 6072 1.416401 GCCTCCACATCGATCCCTTAA 59.584 52.381 0.00 0.00 0.00 1.85
2769 6082 0.389948 ACGAAGTTCGCCTCCACATC 60.390 55.000 24.64 0.00 45.12 3.06
2804 6121 1.609072 GCCAGTCCAAGGAACAAAGTC 59.391 52.381 0.00 0.00 0.00 3.01
2842 6159 3.432326 GGAAGAACACTAGTGGCATAGGG 60.432 52.174 26.12 0.00 34.19 3.53
2843 6160 3.452627 AGGAAGAACACTAGTGGCATAGG 59.547 47.826 26.12 0.00 34.19 2.57
2869 6186 4.156455 AGTGCTCCAAAGAAGAAACTGA 57.844 40.909 0.00 0.00 0.00 3.41
3069 6659 3.703001 TTGAGTCCATCAACTCCTTCC 57.297 47.619 1.88 0.00 43.09 3.46
3119 6709 3.259123 GGATGGTTGTTTGGAAGCTGATT 59.741 43.478 0.00 0.00 0.00 2.57
3159 6749 0.109365 CTGGAGCTGAGATATCGCCG 60.109 60.000 3.86 0.00 0.00 6.46
3166 6756 3.393941 CCTATTTTCCCTGGAGCTGAGAT 59.606 47.826 0.00 0.00 0.00 2.75
3177 6767 4.142160 GCGATTTTTGAGCCTATTTTCCCT 60.142 41.667 0.00 0.00 0.00 4.20
3187 6778 1.135286 CCCTCAAGCGATTTTTGAGCC 60.135 52.381 8.98 0.00 46.42 4.70
3211 6802 1.375523 GATCTTGGGCGTGTCCGTT 60.376 57.895 0.00 0.00 36.15 4.44
3212 6803 2.264794 GATCTTGGGCGTGTCCGT 59.735 61.111 0.00 0.00 36.15 4.69
3213 6804 1.672854 TAGGATCTTGGGCGTGTCCG 61.673 60.000 0.00 0.00 34.19 4.79
3214 6805 0.105039 CTAGGATCTTGGGCGTGTCC 59.895 60.000 0.00 0.00 0.00 4.02
3228 6842 0.032912 TACGTCCACATGCCCTAGGA 60.033 55.000 11.48 0.00 0.00 2.94
3254 6868 4.864334 CAGGAGATGGGGCCGTGC 62.864 72.222 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.