Multiple sequence alignment - TraesCS5A01G519700

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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 TraesCS5A01G519700 chr5A 100.000 2213 0 0 1 2213 680928702 680926490 0.000000e+00 4087
1 TraesCS5A01G519700 chr5A 85.747 442 37 16 803 1244 680965461 680965046 5.610000e-121 444
2 TraesCS5A01G519700 chr5A 84.019 413 48 5 672 1068 680879806 680879396 4.460000e-102 381
3 TraesCS5A01G519700 chr5A 92.308 247 16 3 1254 1499 680964967 680964723 4.520000e-92 348
4 TraesCS5A01G519700 chr5A 94.444 216 9 1 1287 1499 680903622 680903407 1.640000e-86 329
5 TraesCS5A01G519700 chr5A 89.848 197 18 2 943 1138 680904021 680903826 3.650000e-63 252
6 TraesCS5A01G519700 chr5A 92.373 118 6 3 446 560 386703731 386703848 4.890000e-37 165
7 TraesCS5A01G519700 chr5A 85.981 107 8 3 563 667 680881394 680881293 8.360000e-20 108
8 TraesCS5A01G519700 chr4D 84.016 1220 117 34 689 1855 500273769 500272575 0.000000e+00 1101
9 TraesCS5A01G519700 chr4D 84.344 709 80 14 1377 2060 500159436 500158734 0.000000e+00 665
10 TraesCS5A01G519700 chr4D 84.354 441 42 7 803 1239 500262167 500261750 7.360000e-110 407
11 TraesCS5A01G519700 chr4D 83.889 180 18 7 634 803 500262414 500262236 6.320000e-36 161
12 TraesCS5A01G519700 chr4D 95.455 88 3 1 560 647 500273920 500273834 2.960000e-29 139
13 TraesCS5A01G519700 chr2B 89.599 548 49 6 1 541 103799861 103799315 0.000000e+00 689
14 TraesCS5A01G519700 chr3D 89.522 544 47 5 1 535 20537682 20538224 0.000000e+00 680
15 TraesCS5A01G519700 chr3D 89.060 521 44 12 51 560 130949418 130949936 3.100000e-178 634
16 TraesCS5A01G519700 chr3B 90.152 528 44 6 1 521 436758132 436758658 0.000000e+00 680
17 TraesCS5A01G519700 chr3B 90.076 524 44 7 1 517 436758973 436759495 0.000000e+00 673
18 TraesCS5A01G519700 chr3B 84.874 119 11 6 2099 2212 575028825 575028709 1.800000e-21 113
19 TraesCS5A01G519700 chrUn 82.126 828 115 15 1254 2060 60468035 60468850 0.000000e+00 678
20 TraesCS5A01G519700 chrUn 90.173 519 45 5 1 514 45581825 45581308 0.000000e+00 671
21 TraesCS5A01G519700 chrUn 84.485 709 79 14 1377 2060 265242591 265243293 0.000000e+00 671
22 TraesCS5A01G519700 chrUn 84.485 709 79 14 1377 2060 336378166 336377464 0.000000e+00 671
23 TraesCS5A01G519700 chrUn 85.027 561 61 12 1509 2060 285642923 285643469 1.160000e-152 549
24 TraesCS5A01G519700 chrUn 84.404 545 53 17 671 1191 285028502 285027966 7.050000e-140 507
25 TraesCS5A01G519700 chrUn 84.404 545 53 17 671 1191 293566196 293566732 7.050000e-140 507
26 TraesCS5A01G519700 chrUn 84.404 545 53 17 671 1191 307769520 307768984 7.050000e-140 507
27 TraesCS5A01G519700 chrUn 84.404 545 53 17 671 1191 315392430 315392966 7.050000e-140 507
28 TraesCS5A01G519700 chrUn 84.404 545 53 17 671 1191 345621313 345620777 7.050000e-140 507
29 TraesCS5A01G519700 chrUn 83.074 514 69 10 1254 1758 285027855 285027351 3.350000e-123 451
30 TraesCS5A01G519700 chrUn 83.074 514 69 10 1254 1758 293566843 293567347 3.350000e-123 451
31 TraesCS5A01G519700 chrUn 83.074 514 69 10 1254 1758 315393077 315393581 3.350000e-123 451
32 TraesCS5A01G519700 chrUn 81.099 619 58 31 561 1134 60409380 60409984 7.250000e-120 440
33 TraesCS5A01G519700 chrUn 84.635 397 35 13 677 1058 265237330 265237715 2.680000e-99 372
34 TraesCS5A01G519700 chrUn 82.082 413 55 12 1663 2060 60410831 60411239 3.520000e-88 335
35 TraesCS5A01G519700 chrUn 83.190 232 23 8 742 970 60371565 60371783 4.820000e-47 198
36 TraesCS5A01G519700 chr4B 81.227 831 114 18 1254 2060 643488654 643487842 1.110000e-177 632
37 TraesCS5A01G519700 chr4B 85.383 561 70 11 1509 2060 643549250 643548693 2.470000e-159 571
38 TraesCS5A01G519700 chr4B 79.630 540 53 29 561 1056 643489660 643489134 3.520000e-88 335
39 TraesCS5A01G519700 chr4B 83.190 232 23 8 742 970 643563797 643563579 4.820000e-47 198
40 TraesCS5A01G519700 chr4B 83.190 232 23 8 742 970 643571416 643571198 4.820000e-47 198
41 TraesCS5A01G519700 chr1A 86.517 534 51 16 1 517 580028884 580028355 3.190000e-158 568
42 TraesCS5A01G519700 chr4A 86.290 496 62 6 1 493 606514887 606515379 3.230000e-148 534
43 TraesCS5A01G519700 chr4A 84.746 118 13 3 2099 2212 739882970 739883086 1.800000e-21 113
44 TraesCS5A01G519700 chr6B 89.835 364 30 4 172 530 717039403 717039764 5.570000e-126 460
45 TraesCS5A01G519700 chr2D 89.167 120 9 2 2097 2212 629660659 629660540 1.770000e-31 147
46 TraesCS5A01G519700 chr7B 86.555 119 12 2 2098 2212 86985063 86984945 6.410000e-26 128
47 TraesCS5A01G519700 chr7B 86.441 118 11 3 2099 2212 484462499 484462615 8.300000e-25 124
48 TraesCS5A01G519700 chr7B 85.714 119 12 3 2098 2212 720319789 720319906 1.070000e-23 121
49 TraesCS5A01G519700 chr5B 86.441 118 11 3 2099 2212 9620755 9620639 8.300000e-25 124
50 TraesCS5A01G519700 chr5B 85.366 123 12 4 2094 2212 9635788 9635668 2.980000e-24 122
51 TraesCS5A01G519700 chr1B 85.593 118 12 3 2099 2212 48929116 48929000 3.860000e-23 119


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 TraesCS5A01G519700 chr5A 680926490 680928702 2212 True 4087.0 4087 100.0000 1 2213 1 chr5A.!!$R1 2212
1 TraesCS5A01G519700 chr5A 680964723 680965461 738 True 396.0 444 89.0275 803 1499 2 chr5A.!!$R4 696
2 TraesCS5A01G519700 chr5A 680903407 680904021 614 True 290.5 329 92.1460 943 1499 2 chr5A.!!$R3 556
3 TraesCS5A01G519700 chr5A 680879396 680881394 1998 True 244.5 381 85.0000 563 1068 2 chr5A.!!$R2 505
4 TraesCS5A01G519700 chr4D 500158734 500159436 702 True 665.0 665 84.3440 1377 2060 1 chr4D.!!$R1 683
5 TraesCS5A01G519700 chr4D 500272575 500273920 1345 True 620.0 1101 89.7355 560 1855 2 chr4D.!!$R3 1295
6 TraesCS5A01G519700 chr4D 500261750 500262414 664 True 284.0 407 84.1215 634 1239 2 chr4D.!!$R2 605
7 TraesCS5A01G519700 chr2B 103799315 103799861 546 True 689.0 689 89.5990 1 541 1 chr2B.!!$R1 540
8 TraesCS5A01G519700 chr3D 20537682 20538224 542 False 680.0 680 89.5220 1 535 1 chr3D.!!$F1 534
9 TraesCS5A01G519700 chr3D 130949418 130949936 518 False 634.0 634 89.0600 51 560 1 chr3D.!!$F2 509
10 TraesCS5A01G519700 chr3B 436758132 436759495 1363 False 676.5 680 90.1140 1 521 2 chr3B.!!$F1 520
11 TraesCS5A01G519700 chrUn 60468035 60468850 815 False 678.0 678 82.1260 1254 2060 1 chrUn.!!$F2 806
12 TraesCS5A01G519700 chrUn 45581308 45581825 517 True 671.0 671 90.1730 1 514 1 chrUn.!!$R1 513
13 TraesCS5A01G519700 chrUn 265242591 265243293 702 False 671.0 671 84.4850 1377 2060 1 chrUn.!!$F4 683
14 TraesCS5A01G519700 chrUn 336377464 336378166 702 True 671.0 671 84.4850 1377 2060 1 chrUn.!!$R3 683
15 TraesCS5A01G519700 chrUn 285642923 285643469 546 False 549.0 549 85.0270 1509 2060 1 chrUn.!!$F5 551
16 TraesCS5A01G519700 chrUn 307768984 307769520 536 True 507.0 507 84.4040 671 1191 1 chrUn.!!$R2 520
17 TraesCS5A01G519700 chrUn 345620777 345621313 536 True 507.0 507 84.4040 671 1191 1 chrUn.!!$R4 520
18 TraesCS5A01G519700 chrUn 285027351 285028502 1151 True 479.0 507 83.7390 671 1758 2 chrUn.!!$R5 1087
19 TraesCS5A01G519700 chrUn 293566196 293567347 1151 False 479.0 507 83.7390 671 1758 2 chrUn.!!$F7 1087
20 TraesCS5A01G519700 chrUn 315392430 315393581 1151 False 479.0 507 83.7390 671 1758 2 chrUn.!!$F8 1087
21 TraesCS5A01G519700 chrUn 60409380 60411239 1859 False 387.5 440 81.5905 561 2060 2 chrUn.!!$F6 1499
22 TraesCS5A01G519700 chr4B 643548693 643549250 557 True 571.0 571 85.3830 1509 2060 1 chr4B.!!$R1 551
23 TraesCS5A01G519700 chr4B 643487842 643489660 1818 True 483.5 632 80.4285 561 2060 2 chr4B.!!$R4 1499
24 TraesCS5A01G519700 chr1A 580028355 580028884 529 True 568.0 568 86.5170 1 517 1 chr1A.!!$R1 516

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
678 2203 0.242555 ATAAACAAAACCCAGCGCCG 59.757 50.0 2.29 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 5109 0.179054 GGTAGGGATGAAGCGGGTTC 60.179 60.0 12.77 12.77 35.48 3.62 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
163 164 3.330720 CTTTCCACCTCGGGGCCT 61.331 66.667 0.00 0.00 35.63 5.19
164 165 3.628646 CTTTCCACCTCGGGGCCTG 62.629 68.421 5.83 5.83 35.63 4.85
196 197 2.995872 GCACCTCTTCGACGCCTCT 61.996 63.158 0.00 0.00 0.00 3.69
269 270 1.667830 CTCTGGAAGCGGCGAAACA 60.668 57.895 12.98 2.07 0.00 2.83
285 286 2.631428 CACGGTTGTGTTCAGGCG 59.369 61.111 0.00 0.00 41.34 5.52
290 291 0.893727 GGTTGTGTTCAGGCGGGAAT 60.894 55.000 0.00 0.00 0.00 3.01
322 323 1.372128 CGCCACTTTGAAAGCCTGC 60.372 57.895 4.57 4.51 0.00 4.85
325 326 1.455383 CCACTTTGAAAGCCTGCCGT 61.455 55.000 4.57 0.00 0.00 5.68
340 341 1.298413 CCGTGACGACGCTATCCTG 60.298 63.158 6.54 0.00 44.68 3.86
364 365 2.668550 GGCCGGTTTCGTTCTGCT 60.669 61.111 1.90 0.00 33.95 4.24
367 368 1.860078 CCGGTTTCGTTCTGCTGAC 59.140 57.895 0.00 0.00 33.95 3.51
377 378 1.067142 GTTCTGCTGACCGTGGACATA 60.067 52.381 0.00 0.00 0.00 2.29
393 394 3.125829 GGACATATTGATGCATGGCTACG 59.874 47.826 2.46 0.00 36.43 3.51
423 425 4.495679 CGTGTGTAGAACAAAACTGCATGT 60.496 41.667 0.00 0.00 41.57 3.21
442 446 2.025699 TGTAACATAGCAAGGGGGTTCC 60.026 50.000 0.00 0.00 0.00 3.62
460 464 2.695597 CCCCCTGCCTCTCTCTCT 59.304 66.667 0.00 0.00 0.00 3.10
461 465 1.761667 CCCCCTGCCTCTCTCTCTG 60.762 68.421 0.00 0.00 0.00 3.35
462 466 2.433994 CCCCTGCCTCTCTCTCTGC 61.434 68.421 0.00 0.00 0.00 4.26
463 467 1.381599 CCCTGCCTCTCTCTCTGCT 60.382 63.158 0.00 0.00 0.00 4.24
464 468 1.678598 CCCTGCCTCTCTCTCTGCTG 61.679 65.000 0.00 0.00 0.00 4.41
465 469 0.971959 CCTGCCTCTCTCTCTGCTGT 60.972 60.000 0.00 0.00 0.00 4.40
466 470 0.457035 CTGCCTCTCTCTCTGCTGTC 59.543 60.000 0.00 0.00 0.00 3.51
467 471 1.311651 TGCCTCTCTCTCTGCTGTCG 61.312 60.000 0.00 0.00 0.00 4.35
468 472 1.433064 CCTCTCTCTCTGCTGTCGC 59.567 63.158 0.00 0.00 0.00 5.19
469 473 1.433064 CTCTCTCTCTGCTGTCGCC 59.567 63.158 0.00 0.00 34.43 5.54
470 474 2.003658 CTCTCTCTCTGCTGTCGCCC 62.004 65.000 0.00 0.00 34.43 6.13
471 475 3.071206 TCTCTCTGCTGTCGCCCC 61.071 66.667 0.00 0.00 34.43 5.80
472 476 4.504916 CTCTCTGCTGTCGCCCCG 62.505 72.222 0.00 0.00 34.43 5.73
479 483 3.814268 CTGTCGCCCCGGCATTTG 61.814 66.667 6.52 0.00 41.69 2.32
480 484 4.652131 TGTCGCCCCGGCATTTGT 62.652 61.111 6.52 0.00 36.25 2.83
481 485 2.437002 GTCGCCCCGGCATTTGTA 60.437 61.111 6.52 0.00 42.06 2.41
482 486 2.437002 TCGCCCCGGCATTTGTAC 60.437 61.111 6.52 0.00 42.06 2.90
483 487 2.437716 CGCCCCGGCATTTGTACT 60.438 61.111 6.52 0.00 42.06 2.73
484 488 1.153329 CGCCCCGGCATTTGTACTA 60.153 57.895 6.52 0.00 42.06 1.82
485 489 0.534203 CGCCCCGGCATTTGTACTAT 60.534 55.000 6.52 0.00 42.06 2.12
486 490 1.687563 GCCCCGGCATTTGTACTATT 58.312 50.000 0.00 0.00 41.49 1.73
487 491 1.336755 GCCCCGGCATTTGTACTATTG 59.663 52.381 0.00 0.00 41.49 1.90
488 492 2.650322 CCCCGGCATTTGTACTATTGT 58.350 47.619 0.00 0.00 0.00 2.71
489 493 3.811083 CCCCGGCATTTGTACTATTGTA 58.189 45.455 0.00 0.00 0.00 2.41
490 494 3.562557 CCCCGGCATTTGTACTATTGTAC 59.437 47.826 10.11 10.11 46.74 2.90
491 495 4.448210 CCCGGCATTTGTACTATTGTACT 58.552 43.478 16.61 0.00 46.70 2.73
492 496 4.272504 CCCGGCATTTGTACTATTGTACTG 59.727 45.833 16.61 9.17 46.70 2.74
493 497 4.873827 CCGGCATTTGTACTATTGTACTGT 59.126 41.667 16.61 2.56 46.70 3.55
494 498 6.044046 CCGGCATTTGTACTATTGTACTGTA 58.956 40.000 16.61 4.67 46.70 2.74
495 499 6.704493 CCGGCATTTGTACTATTGTACTGTAT 59.296 38.462 16.61 6.42 46.70 2.29
496 500 7.307160 CCGGCATTTGTACTATTGTACTGTATG 60.307 40.741 16.61 15.87 46.70 2.39
497 501 7.223971 CGGCATTTGTACTATTGTACTGTATGT 59.776 37.037 16.61 0.00 46.70 2.29
498 502 8.889717 GGCATTTGTACTATTGTACTGTATGTT 58.110 33.333 16.61 0.00 46.70 2.71
499 503 9.702726 GCATTTGTACTATTGTACTGTATGTTG 57.297 33.333 16.61 7.48 46.70 3.33
501 505 8.780846 TTTGTACTATTGTACTGTATGTTGGG 57.219 34.615 16.61 0.00 46.70 4.12
502 506 7.484993 TGTACTATTGTACTGTATGTTGGGT 57.515 36.000 16.61 0.00 46.70 4.51
503 507 7.909518 TGTACTATTGTACTGTATGTTGGGTT 58.090 34.615 16.61 0.00 46.70 4.11
504 508 8.036575 TGTACTATTGTACTGTATGTTGGGTTC 58.963 37.037 16.61 0.00 46.70 3.62
505 509 6.103997 ACTATTGTACTGTATGTTGGGTTCG 58.896 40.000 0.00 0.00 0.00 3.95
506 510 4.603989 TTGTACTGTATGTTGGGTTCGA 57.396 40.909 0.00 0.00 0.00 3.71
507 511 4.182693 TGTACTGTATGTTGGGTTCGAG 57.817 45.455 0.00 0.00 0.00 4.04
508 512 3.827876 TGTACTGTATGTTGGGTTCGAGA 59.172 43.478 0.00 0.00 0.00 4.04
509 513 4.281435 TGTACTGTATGTTGGGTTCGAGAA 59.719 41.667 0.00 0.00 0.00 2.87
510 514 4.345859 ACTGTATGTTGGGTTCGAGAAA 57.654 40.909 0.00 0.00 0.00 2.52
511 515 4.906618 ACTGTATGTTGGGTTCGAGAAAT 58.093 39.130 0.00 0.00 0.00 2.17
512 516 6.045072 ACTGTATGTTGGGTTCGAGAAATA 57.955 37.500 0.00 0.00 0.00 1.40
513 517 6.650120 ACTGTATGTTGGGTTCGAGAAATAT 58.350 36.000 0.00 0.00 0.00 1.28
514 518 7.788026 ACTGTATGTTGGGTTCGAGAAATATA 58.212 34.615 0.00 0.00 0.00 0.86
515 519 8.429641 ACTGTATGTTGGGTTCGAGAAATATAT 58.570 33.333 0.00 0.00 0.00 0.86
516 520 9.273016 CTGTATGTTGGGTTCGAGAAATATATT 57.727 33.333 0.00 0.00 0.00 1.28
517 521 9.621629 TGTATGTTGGGTTCGAGAAATATATTT 57.378 29.630 10.51 10.51 0.00 1.40
520 524 8.671384 TGTTGGGTTCGAGAAATATATTTAGG 57.329 34.615 10.68 3.95 0.00 2.69
521 525 8.269317 TGTTGGGTTCGAGAAATATATTTAGGT 58.731 33.333 10.68 0.00 0.00 3.08
522 526 8.557029 GTTGGGTTCGAGAAATATATTTAGGTG 58.443 37.037 10.68 2.52 0.00 4.00
523 527 7.221450 TGGGTTCGAGAAATATATTTAGGTGG 58.779 38.462 10.68 1.52 0.00 4.61
524 528 6.653740 GGGTTCGAGAAATATATTTAGGTGGG 59.346 42.308 10.68 0.00 0.00 4.61
525 529 6.653740 GGTTCGAGAAATATATTTAGGTGGGG 59.346 42.308 10.68 0.00 0.00 4.96
526 530 6.368779 TCGAGAAATATATTTAGGTGGGGG 57.631 41.667 10.68 0.00 0.00 5.40
527 531 6.086095 TCGAGAAATATATTTAGGTGGGGGA 58.914 40.000 10.68 0.00 0.00 4.81
528 532 6.212791 TCGAGAAATATATTTAGGTGGGGGAG 59.787 42.308 10.68 0.00 0.00 4.30
529 533 6.013639 CGAGAAATATATTTAGGTGGGGGAGT 60.014 42.308 10.68 0.00 0.00 3.85
530 534 7.474364 CGAGAAATATATTTAGGTGGGGGAGTT 60.474 40.741 10.68 0.00 0.00 3.01
531 535 7.756614 AGAAATATATTTAGGTGGGGGAGTTC 58.243 38.462 10.68 0.00 0.00 3.01
532 536 7.576649 AGAAATATATTTAGGTGGGGGAGTTCT 59.423 37.037 10.68 0.00 0.00 3.01
533 537 6.954352 ATATATTTAGGTGGGGGAGTTCTC 57.046 41.667 0.00 0.00 0.00 2.87
534 538 2.735259 TTTAGGTGGGGGAGTTCTCT 57.265 50.000 0.00 0.00 0.00 3.10
535 539 2.249309 TTAGGTGGGGGAGTTCTCTC 57.751 55.000 0.00 0.00 39.76 3.20
556 560 3.477210 CCCCCGGTGAAAATTCAAAAA 57.523 42.857 0.00 0.00 39.21 1.94
592 596 5.991933 ATGGACTGAGCAGTATGTATAGG 57.008 43.478 2.65 0.00 42.66 2.57
597 601 4.767928 ACTGAGCAGTATGTATAGGTAGCC 59.232 45.833 0.41 0.00 40.43 3.93
629 633 2.352814 CGTCTGATATCCGTCCCAATCC 60.353 54.545 0.00 0.00 0.00 3.01
647 651 3.944250 CTGCATGGTCACCACCCCC 62.944 68.421 0.00 0.00 42.99 5.40
678 2203 0.242555 ATAAACAAAACCCAGCGCCG 59.757 50.000 2.29 0.00 0.00 6.46
684 2209 3.572196 AAACCCAGCGCCGCATTTG 62.572 57.895 13.36 0.00 0.00 2.32
694 2219 2.730715 GCGCCGCATTTGTTATCTGAAA 60.731 45.455 3.15 0.00 0.00 2.69
738 2276 1.971357 ACTGGTGTGGTCTGAACTAGG 59.029 52.381 0.00 0.00 0.00 3.02
740 2278 2.232452 CTGGTGTGGTCTGAACTAGGAG 59.768 54.545 0.00 0.00 0.00 3.69
745 2283 2.756207 GTGGTCTGAACTAGGAGAGTCC 59.244 54.545 0.00 0.00 37.44 3.85
756 2294 1.430228 GAGAGTCCTCGTCTTCGCC 59.570 63.158 0.00 0.00 36.96 5.54
815 2428 4.419282 TCCTGCCCATTGATTTCTTCTTT 58.581 39.130 0.00 0.00 0.00 2.52
833 2446 4.923893 TCTTTACTCGTCGTTTTGACTCA 58.076 39.130 0.00 0.00 45.87 3.41
841 2454 3.302221 CGTCGTTTTGACTCAATGAACGT 60.302 43.478 20.38 0.00 45.87 3.99
844 2457 4.804665 TCGTTTTGACTCAATGAACGTACA 59.195 37.500 20.38 6.59 38.17 2.90
890 2534 1.409427 AGCGAGGATATATAAGCGGCC 59.591 52.381 0.00 0.00 0.00 6.13
893 2537 2.223829 CGAGGATATATAAGCGGCCTGG 60.224 54.545 0.00 0.00 0.00 4.45
919 2567 2.143122 GACCGTGATCACACACACATT 58.857 47.619 24.93 0.00 46.20 2.71
938 2593 1.573108 TAACCTCCTCTCTTGGCAGG 58.427 55.000 0.00 0.00 33.53 4.85
1143 3679 3.406200 AGAAGCCAGCCTCCGCAT 61.406 61.111 0.00 0.00 37.52 4.73
1158 3694 2.508439 CATCGGAACCGTGACCCG 60.508 66.667 12.93 0.00 44.22 5.28
1208 4026 1.080501 CTCGCGAGGCAGAGAAACA 60.081 57.895 28.40 0.00 33.54 2.83
1226 4044 2.851195 ACAGTGAGCCTTACAGTTTGG 58.149 47.619 0.00 0.00 0.00 3.28
1232 4090 3.646162 TGAGCCTTACAGTTTGGAGAGAA 59.354 43.478 0.00 0.00 0.00 2.87
1233 4091 4.287067 TGAGCCTTACAGTTTGGAGAGAAT 59.713 41.667 0.00 0.00 0.00 2.40
1247 4166 2.949451 GAGAATTCTCTGACGCAGGA 57.051 50.000 25.26 1.89 39.81 3.86
1248 4167 3.451141 GAGAATTCTCTGACGCAGGAT 57.549 47.619 25.26 0.00 39.81 3.24
1249 4168 4.576216 GAGAATTCTCTGACGCAGGATA 57.424 45.455 25.26 0.00 39.81 2.59
1250 4169 4.295051 GAGAATTCTCTGACGCAGGATAC 58.705 47.826 25.26 0.00 39.81 2.24
1251 4170 3.701542 AGAATTCTCTGACGCAGGATACA 59.298 43.478 0.88 0.00 41.41 2.29
1252 4171 4.343526 AGAATTCTCTGACGCAGGATACAT 59.656 41.667 0.88 0.00 41.41 2.29
1260 4179 2.980476 GACGCAGGATACATACATGTCG 59.020 50.000 0.00 0.00 41.97 4.35
1265 4184 4.917998 GCAGGATACATACATGTCGTAGTG 59.082 45.833 0.00 6.27 41.97 2.74
1301 4244 4.595116 CTGCTCCGATCAAATTGATGAAC 58.405 43.478 13.82 1.91 37.20 3.18
1357 4303 3.610911 GGTGTAAGCTGGCTATTGAACT 58.389 45.455 0.00 0.00 0.00 3.01
1501 4491 1.298859 GAGGAACGACCATGTGTGCC 61.299 60.000 0.00 0.00 42.04 5.01
1515 4505 4.094646 TGCCGCGGATGGATGTGT 62.095 61.111 33.48 0.00 0.00 3.72
1554 4546 4.838423 TCCACCTGAGTTTGATTCTACTGA 59.162 41.667 0.00 0.00 0.00 3.41
1639 4632 3.568007 ACATTTCAAAACAGCCTCGCTTA 59.432 39.130 0.00 0.00 36.40 3.09
1640 4633 4.218417 ACATTTCAAAACAGCCTCGCTTAT 59.782 37.500 0.00 0.00 36.40 1.73
1641 4634 5.414454 ACATTTCAAAACAGCCTCGCTTATA 59.586 36.000 0.00 0.00 36.40 0.98
1642 4635 6.095440 ACATTTCAAAACAGCCTCGCTTATAT 59.905 34.615 0.00 0.00 36.40 0.86
1649 4646 8.774586 CAAAACAGCCTCGCTTATATATAAAGT 58.225 33.333 6.63 0.00 36.40 2.66
1738 4737 5.771153 TCACAAACATGCTCAAAAGATGA 57.229 34.783 0.00 0.00 36.38 2.92
1788 4788 0.614979 TGCCTAGCCGATCCCTATCC 60.615 60.000 0.00 0.00 0.00 2.59
1818 4819 0.537143 AAAGCGGGTGTCAATGCTGA 60.537 50.000 0.00 0.00 37.81 4.26
1860 4861 2.519377 CGGAGTCCGTGGCATATAAA 57.481 50.000 23.83 0.00 42.73 1.40
1862 4863 3.399330 CGGAGTCCGTGGCATATAAAAT 58.601 45.455 23.83 0.00 42.73 1.82
1863 4864 3.432252 CGGAGTCCGTGGCATATAAAATC 59.568 47.826 23.83 0.00 42.73 2.17
1865 4866 5.003804 GGAGTCCGTGGCATATAAAATCAT 58.996 41.667 0.00 0.00 0.00 2.45
1870 4871 4.518590 CCGTGGCATATAAAATCATCACCA 59.481 41.667 0.00 0.00 0.00 4.17
1874 4887 4.463891 GGCATATAAAATCATCACCAGGGG 59.536 45.833 0.00 0.00 0.00 4.79
1878 4891 3.763557 AAAATCATCACCAGGGGTCAT 57.236 42.857 0.00 0.00 31.02 3.06
1885 4898 1.930133 ACCAGGGGTCATGCCATCA 60.930 57.895 8.20 0.00 39.65 3.07
1911 4924 4.380655 GCATACACTAACCAGAAGAGACGT 60.381 45.833 0.00 0.00 0.00 4.34
1923 4937 3.756739 GAGACGTCTCTCCTACCGA 57.243 57.895 33.28 0.00 37.56 4.69
1942 4956 0.690762 ATACGTGTGGCCTGGACTTT 59.309 50.000 3.32 0.00 0.00 2.66
1975 4989 2.027745 CACAGTCTGGAGCATACCACTT 60.028 50.000 4.53 0.00 35.91 3.16
2067 5083 3.915993 GACTCTAGGACCAGAGGCT 57.084 57.895 19.09 0.00 45.79 4.58
2069 5085 2.858745 GACTCTAGGACCAGAGGCTAG 58.141 57.143 19.09 2.41 45.79 3.42
2070 5086 2.440253 GACTCTAGGACCAGAGGCTAGA 59.560 54.545 19.09 6.01 45.79 2.43
2071 5087 2.173996 ACTCTAGGACCAGAGGCTAGAC 59.826 54.545 19.09 0.00 45.36 2.59
2072 5088 1.141254 TCTAGGACCAGAGGCTAGACG 59.859 57.143 0.00 0.00 0.00 4.18
2073 5089 0.183014 TAGGACCAGAGGCTAGACGG 59.817 60.000 0.00 0.00 0.00 4.79
2074 5090 1.076923 GGACCAGAGGCTAGACGGA 60.077 63.158 0.00 0.00 0.00 4.69
2075 5091 0.683504 GGACCAGAGGCTAGACGGAA 60.684 60.000 0.00 0.00 0.00 4.30
2076 5092 0.741915 GACCAGAGGCTAGACGGAAG 59.258 60.000 0.00 0.00 0.00 3.46
2077 5093 0.331954 ACCAGAGGCTAGACGGAAGA 59.668 55.000 0.00 0.00 0.00 2.87
2078 5094 1.028905 CCAGAGGCTAGACGGAAGAG 58.971 60.000 0.00 0.00 0.00 2.85
2079 5095 1.683629 CCAGAGGCTAGACGGAAGAGT 60.684 57.143 0.00 0.00 0.00 3.24
2080 5096 1.673920 CAGAGGCTAGACGGAAGAGTC 59.326 57.143 0.00 0.00 41.23 3.36
2081 5097 0.658897 GAGGCTAGACGGAAGAGTCG 59.341 60.000 0.00 0.00 45.26 4.18
2082 5098 0.748729 AGGCTAGACGGAAGAGTCGG 60.749 60.000 0.00 0.00 45.26 4.79
2083 5099 1.726533 GGCTAGACGGAAGAGTCGGG 61.727 65.000 0.00 0.00 45.26 5.14
2084 5100 0.747283 GCTAGACGGAAGAGTCGGGA 60.747 60.000 0.00 0.00 45.26 5.14
2085 5101 1.015868 CTAGACGGAAGAGTCGGGAC 58.984 60.000 0.00 0.00 45.26 4.46
2099 5115 2.241171 GGGACGACAAAAGAACCCG 58.759 57.895 0.00 0.00 0.00 5.28
2100 5116 1.572941 GGACGACAAAAGAACCCGC 59.427 57.895 0.00 0.00 0.00 6.13
2101 5117 0.883370 GGACGACAAAAGAACCCGCT 60.883 55.000 0.00 0.00 0.00 5.52
2102 5118 0.942252 GACGACAAAAGAACCCGCTT 59.058 50.000 0.00 0.00 0.00 4.68
2103 5119 0.942252 ACGACAAAAGAACCCGCTTC 59.058 50.000 0.00 0.00 0.00 3.86
2104 5120 0.941542 CGACAAAAGAACCCGCTTCA 59.058 50.000 0.00 0.00 0.00 3.02
2105 5121 1.535462 CGACAAAAGAACCCGCTTCAT 59.465 47.619 0.00 0.00 0.00 2.57
2106 5122 2.412847 CGACAAAAGAACCCGCTTCATC 60.413 50.000 0.00 0.00 0.00 2.92
2107 5123 1.886542 ACAAAAGAACCCGCTTCATCC 59.113 47.619 0.00 0.00 0.00 3.51
2108 5124 1.202348 CAAAAGAACCCGCTTCATCCC 59.798 52.381 0.00 0.00 0.00 3.85
2109 5125 0.698818 AAAGAACCCGCTTCATCCCT 59.301 50.000 0.00 0.00 0.00 4.20
2110 5126 1.580059 AAGAACCCGCTTCATCCCTA 58.420 50.000 0.00 0.00 0.00 3.53
2111 5127 0.831307 AGAACCCGCTTCATCCCTAC 59.169 55.000 0.00 0.00 0.00 3.18
2112 5128 0.179054 GAACCCGCTTCATCCCTACC 60.179 60.000 0.00 0.00 0.00 3.18
2113 5129 1.968050 AACCCGCTTCATCCCTACCG 61.968 60.000 0.00 0.00 0.00 4.02
2114 5130 2.280186 CCGCTTCATCCCTACCGC 60.280 66.667 0.00 0.00 0.00 5.68
2115 5131 2.797278 CCGCTTCATCCCTACCGCT 61.797 63.158 0.00 0.00 0.00 5.52
2116 5132 1.300233 CGCTTCATCCCTACCGCTC 60.300 63.158 0.00 0.00 0.00 5.03
2117 5133 1.069935 GCTTCATCCCTACCGCTCC 59.930 63.158 0.00 0.00 0.00 4.70
2118 5134 1.749033 CTTCATCCCTACCGCTCCC 59.251 63.158 0.00 0.00 0.00 4.30
2119 5135 2.088674 CTTCATCCCTACCGCTCCCG 62.089 65.000 0.00 0.00 0.00 5.14
2120 5136 4.301027 CATCCCTACCGCTCCCGC 62.301 72.222 0.00 0.00 0.00 6.13
2165 5181 3.155167 CCGGCCCTAGTCCACCTC 61.155 72.222 0.00 0.00 0.00 3.85
2166 5182 3.155167 CGGCCCTAGTCCACCTCC 61.155 72.222 0.00 0.00 0.00 4.30
2167 5183 2.768769 GGCCCTAGTCCACCTCCC 60.769 72.222 0.00 0.00 0.00 4.30
2168 5184 3.155167 GCCCTAGTCCACCTCCCG 61.155 72.222 0.00 0.00 0.00 5.14
2169 5185 3.155167 CCCTAGTCCACCTCCCGC 61.155 72.222 0.00 0.00 0.00 6.13
2170 5186 3.155167 CCTAGTCCACCTCCCGCC 61.155 72.222 0.00 0.00 0.00 6.13
2171 5187 2.042843 CTAGTCCACCTCCCGCCT 60.043 66.667 0.00 0.00 0.00 5.52
2172 5188 2.043248 TAGTCCACCTCCCGCCTC 60.043 66.667 0.00 0.00 0.00 4.70
2173 5189 3.674050 TAGTCCACCTCCCGCCTCC 62.674 68.421 0.00 0.00 0.00 4.30
2178 5194 4.677151 ACCTCCCGCCTCCCCTTT 62.677 66.667 0.00 0.00 0.00 3.11
2179 5195 3.798511 CCTCCCGCCTCCCCTTTC 61.799 72.222 0.00 0.00 0.00 2.62
2180 5196 3.798511 CTCCCGCCTCCCCTTTCC 61.799 72.222 0.00 0.00 0.00 3.13
2183 5199 3.798511 CCGCCTCCCCTTTCCCTC 61.799 72.222 0.00 0.00 0.00 4.30
2184 5200 4.162690 CGCCTCCCCTTTCCCTCG 62.163 72.222 0.00 0.00 0.00 4.63
2185 5201 4.491409 GCCTCCCCTTTCCCTCGC 62.491 72.222 0.00 0.00 0.00 5.03
2186 5202 3.798511 CCTCCCCTTTCCCTCGCC 61.799 72.222 0.00 0.00 0.00 5.54
2187 5203 4.162690 CTCCCCTTTCCCTCGCCG 62.163 72.222 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 2.898840 CAGGGCACGCATAGCAGG 60.899 66.667 0.00 0.00 0.00 4.85
163 164 4.407245 TGCAGGGCACGCATAGCA 62.407 61.111 1.27 0.00 33.55 3.49
206 207 3.397439 ATGCGGTGAGGCTGAGCT 61.397 61.111 3.72 0.00 0.00 4.09
243 244 2.749441 GCTTCCAGAGGTGCCAGC 60.749 66.667 0.00 0.00 0.00 4.85
269 270 2.590575 CCGCCTGAACACAACCGT 60.591 61.111 0.00 0.00 0.00 4.83
302 303 2.049156 GGCTTTCAAAGTGGCGGC 60.049 61.111 0.00 0.00 0.00 6.53
322 323 1.298413 CAGGATAGCGTCGTCACGG 60.298 63.158 0.00 0.00 46.80 4.94
325 326 1.807226 CCACAGGATAGCGTCGTCA 59.193 57.895 0.00 0.00 0.00 4.35
346 347 2.975799 GCAGAACGAAACCGGCCA 60.976 61.111 0.00 0.00 0.00 5.36
358 359 1.262417 TATGTCCACGGTCAGCAGAA 58.738 50.000 0.00 0.00 0.00 3.02
364 365 2.093235 TGCATCAATATGTCCACGGTCA 60.093 45.455 0.00 0.00 35.38 4.02
367 368 2.227149 CCATGCATCAATATGTCCACGG 59.773 50.000 0.00 0.00 35.38 4.94
377 378 2.334307 GCCGTAGCCATGCATCAAT 58.666 52.632 0.00 0.00 0.00 2.57
393 394 2.033194 GTTCTACACACGCAGGGCC 61.033 63.158 0.00 0.00 0.00 5.80
399 401 2.223157 TGCAGTTTTGTTCTACACACGC 60.223 45.455 0.00 0.00 33.98 5.34
403 405 6.491394 TGTTACATGCAGTTTTGTTCTACAC 58.509 36.000 0.00 0.00 0.00 2.90
404 406 6.685527 TGTTACATGCAGTTTTGTTCTACA 57.314 33.333 0.00 0.00 0.00 2.74
462 466 3.814268 CAAATGCCGGGGCGACAG 61.814 66.667 2.18 0.00 45.51 3.51
463 467 3.255423 TACAAATGCCGGGGCGACA 62.255 57.895 2.18 0.00 45.51 4.35
464 468 2.437002 TACAAATGCCGGGGCGAC 60.437 61.111 2.18 0.00 45.51 5.19
465 469 1.615165 TAGTACAAATGCCGGGGCGA 61.615 55.000 2.18 0.00 45.51 5.54
466 470 0.534203 ATAGTACAAATGCCGGGGCG 60.534 55.000 2.18 0.00 45.51 6.13
467 471 1.336755 CAATAGTACAAATGCCGGGGC 59.663 52.381 2.18 1.86 42.35 5.80
468 472 2.650322 ACAATAGTACAAATGCCGGGG 58.350 47.619 2.18 0.00 0.00 5.73
480 484 7.122501 TCGAACCCAACATACAGTACAATAGTA 59.877 37.037 0.00 0.00 0.00 1.82
481 485 6.071221 TCGAACCCAACATACAGTACAATAGT 60.071 38.462 0.00 0.00 0.00 2.12
482 486 6.334989 TCGAACCCAACATACAGTACAATAG 58.665 40.000 0.00 0.00 0.00 1.73
483 487 6.153170 TCTCGAACCCAACATACAGTACAATA 59.847 38.462 0.00 0.00 0.00 1.90
484 488 5.046878 TCTCGAACCCAACATACAGTACAAT 60.047 40.000 0.00 0.00 0.00 2.71
485 489 4.281435 TCTCGAACCCAACATACAGTACAA 59.719 41.667 0.00 0.00 0.00 2.41
486 490 3.827876 TCTCGAACCCAACATACAGTACA 59.172 43.478 0.00 0.00 0.00 2.90
487 491 4.445452 TCTCGAACCCAACATACAGTAC 57.555 45.455 0.00 0.00 0.00 2.73
488 492 5.471556 TTTCTCGAACCCAACATACAGTA 57.528 39.130 0.00 0.00 0.00 2.74
489 493 4.345859 TTTCTCGAACCCAACATACAGT 57.654 40.909 0.00 0.00 0.00 3.55
490 494 8.833231 ATATATTTCTCGAACCCAACATACAG 57.167 34.615 0.00 0.00 0.00 2.74
491 495 9.621629 AAATATATTTCTCGAACCCAACATACA 57.378 29.630 4.81 0.00 0.00 2.29
494 498 9.284968 CCTAAATATATTTCTCGAACCCAACAT 57.715 33.333 13.95 0.00 0.00 2.71
495 499 8.269317 ACCTAAATATATTTCTCGAACCCAACA 58.731 33.333 13.95 0.00 0.00 3.33
496 500 8.557029 CACCTAAATATATTTCTCGAACCCAAC 58.443 37.037 13.95 0.00 0.00 3.77
497 501 7.717875 CCACCTAAATATATTTCTCGAACCCAA 59.282 37.037 13.95 0.00 0.00 4.12
498 502 7.221450 CCACCTAAATATATTTCTCGAACCCA 58.779 38.462 13.95 0.00 0.00 4.51
499 503 6.653740 CCCACCTAAATATATTTCTCGAACCC 59.346 42.308 13.95 0.00 0.00 4.11
500 504 6.653740 CCCCACCTAAATATATTTCTCGAACC 59.346 42.308 13.95 0.00 0.00 3.62
501 505 6.653740 CCCCCACCTAAATATATTTCTCGAAC 59.346 42.308 13.95 0.00 0.00 3.95
502 506 6.559539 TCCCCCACCTAAATATATTTCTCGAA 59.440 38.462 13.95 0.00 0.00 3.71
503 507 6.086095 TCCCCCACCTAAATATATTTCTCGA 58.914 40.000 13.95 0.00 0.00 4.04
504 508 6.013639 ACTCCCCCACCTAAATATATTTCTCG 60.014 42.308 13.95 5.89 0.00 4.04
505 509 7.331089 ACTCCCCCACCTAAATATATTTCTC 57.669 40.000 13.95 0.00 0.00 2.87
506 510 7.576649 AGAACTCCCCCACCTAAATATATTTCT 59.423 37.037 13.95 0.00 0.00 2.52
507 511 7.756614 AGAACTCCCCCACCTAAATATATTTC 58.243 38.462 13.95 0.00 0.00 2.17
508 512 7.576649 AGAGAACTCCCCCACCTAAATATATTT 59.423 37.037 14.86 14.86 0.00 1.40
509 513 7.089566 AGAGAACTCCCCCACCTAAATATATT 58.910 38.462 0.00 0.00 0.00 1.28
510 514 6.644882 AGAGAACTCCCCCACCTAAATATAT 58.355 40.000 0.00 0.00 0.00 0.86
511 515 6.051946 AGAGAACTCCCCCACCTAAATATA 57.948 41.667 0.00 0.00 0.00 0.86
512 516 4.908481 GAGAGAACTCCCCCACCTAAATAT 59.092 45.833 0.00 0.00 37.19 1.28
513 517 4.296056 GAGAGAACTCCCCCACCTAAATA 58.704 47.826 0.00 0.00 37.19 1.40
514 518 3.116174 GAGAGAACTCCCCCACCTAAAT 58.884 50.000 0.00 0.00 37.19 1.40
515 519 2.547990 GAGAGAACTCCCCCACCTAAA 58.452 52.381 0.00 0.00 37.19 1.85
516 520 2.249309 GAGAGAACTCCCCCACCTAA 57.751 55.000 0.00 0.00 37.19 2.69
518 522 4.899243 GAGAGAACTCCCCCACCT 57.101 61.111 0.00 0.00 37.19 4.00
536 540 3.477210 TTTTTGAATTTTCACCGGGGG 57.523 42.857 2.42 0.00 36.83 5.40
555 559 7.039082 TGCTCAGTCCATAGGCTTTTTATTTTT 60.039 33.333 0.00 0.00 0.00 1.94
556 560 6.437162 TGCTCAGTCCATAGGCTTTTTATTTT 59.563 34.615 0.00 0.00 0.00 1.82
557 561 5.951747 TGCTCAGTCCATAGGCTTTTTATTT 59.048 36.000 0.00 0.00 0.00 1.40
558 562 5.509498 TGCTCAGTCCATAGGCTTTTTATT 58.491 37.500 0.00 0.00 0.00 1.40
566 570 2.366916 ACATACTGCTCAGTCCATAGGC 59.633 50.000 5.72 0.00 42.54 3.93
592 596 2.731976 CAGACGTTTTCAGAGTGGCTAC 59.268 50.000 0.00 0.00 0.00 3.58
597 601 4.500837 CGGATATCAGACGTTTTCAGAGTG 59.499 45.833 4.83 0.00 0.00 3.51
629 633 2.361610 GGGGTGGTGACCATGCAG 60.362 66.667 7.94 0.00 45.25 4.41
647 651 1.867919 TTGTTTATTGGTGGGCGCCG 61.868 55.000 22.54 0.00 0.00 6.46
699 2224 9.136323 ACACCAGTCAAAGAATAGAAAGAAAAT 57.864 29.630 0.00 0.00 0.00 1.82
738 2276 1.430228 GGCGAAGACGAGGACTCTC 59.570 63.158 0.00 0.00 42.66 3.20
756 2294 2.862140 GCCGTTCAAATGAAACCACCAG 60.862 50.000 0.00 0.00 35.58 4.00
833 2446 5.699001 TGAACTAGCAACATGTACGTTCATT 59.301 36.000 17.09 0.00 35.67 2.57
841 2454 5.696270 CAGTGAAGTGAACTAGCAACATGTA 59.304 40.000 0.00 0.00 0.00 2.29
844 2457 4.067896 CCAGTGAAGTGAACTAGCAACAT 58.932 43.478 0.00 0.00 0.00 2.71
893 2537 1.270094 TGTGTGATCACGGTCTCCAAC 60.270 52.381 20.54 10.95 46.49 3.77
902 2546 3.745975 AGGTTAATGTGTGTGTGATCACG 59.254 43.478 20.54 0.00 46.49 4.35
905 2553 4.579869 AGGAGGTTAATGTGTGTGTGATC 58.420 43.478 0.00 0.00 0.00 2.92
919 2567 1.573108 CCTGCCAAGAGAGGAGGTTA 58.427 55.000 0.00 0.00 0.00 2.85
938 2593 3.311871 CAGCTTGATAGTTGATCAGTGGC 59.688 47.826 0.00 0.00 45.43 5.01
987 2646 2.883386 GGATGCCATTGATTCTCACTCC 59.117 50.000 0.00 0.00 0.00 3.85
1035 2702 1.759445 AGATAGCTCCACAGTCGCATT 59.241 47.619 0.00 0.00 0.00 3.56
1208 4026 2.972713 TCTCCAAACTGTAAGGCTCACT 59.027 45.455 0.00 0.00 39.30 3.41
1232 4090 4.584743 TGTATGTATCCTGCGTCAGAGAAT 59.415 41.667 8.20 2.86 32.44 2.40
1233 4091 3.951680 TGTATGTATCCTGCGTCAGAGAA 59.048 43.478 8.20 0.00 32.44 2.87
1245 4164 6.909909 TCATCACTACGACATGTATGTATCC 58.090 40.000 0.00 0.00 41.95 2.59
1246 4165 8.972262 AATCATCACTACGACATGTATGTATC 57.028 34.615 0.00 0.00 41.95 2.24
1247 4166 9.764363 AAAATCATCACTACGACATGTATGTAT 57.236 29.630 0.00 0.00 41.95 2.29
1249 4168 9.764363 ATAAAATCATCACTACGACATGTATGT 57.236 29.630 0.00 3.08 45.16 2.29
1260 4179 7.412346 CGGAGCAGCATATAAAATCATCACTAC 60.412 40.741 0.00 0.00 0.00 2.73
1265 4184 6.314648 TGATCGGAGCAGCATATAAAATCATC 59.685 38.462 0.00 0.00 0.00 2.92
1301 4244 5.104374 ACAAAATTCTGAACTGCACACTTG 58.896 37.500 0.00 0.00 0.00 3.16
1501 4491 1.745115 AACCACACATCCATCCGCG 60.745 57.895 0.00 0.00 0.00 6.46
1515 4505 4.039004 CAGGTGGATGAAAATGAACAACCA 59.961 41.667 0.00 0.00 36.80 3.67
1577 4570 6.662865 TGCCTTTAATGGATCAAAAACAGA 57.337 33.333 11.47 0.00 0.00 3.41
1621 4614 8.896320 TTATATATAAGCGAGGCTGTTTTGAA 57.104 30.769 0.81 0.00 39.62 2.69
1649 4646 7.943079 ACTTGATGTTTGGACATGATGATTA 57.057 32.000 0.00 0.00 46.27 1.75
1695 4692 1.673920 TGTTGCCCGACAGACTTTTTC 59.326 47.619 0.00 0.00 0.00 2.29
1698 4697 1.202758 TGATGTTGCCCGACAGACTTT 60.203 47.619 0.00 0.00 32.19 2.66
1738 4737 4.642429 GATTCTTTGTGTGTGGTAGGAGT 58.358 43.478 0.00 0.00 0.00 3.85
1818 4819 8.852135 TCCGTGTTTAAATTTATGTCCTTCTTT 58.148 29.630 0.00 0.00 0.00 2.52
1856 4857 4.879295 TGACCCCTGGTGATGATTTTAT 57.121 40.909 0.00 0.00 35.25 1.40
1857 4858 4.879295 ATGACCCCTGGTGATGATTTTA 57.121 40.909 0.00 0.00 35.25 1.52
1865 4866 1.925285 GATGGCATGACCCCTGGTGA 61.925 60.000 3.81 0.00 35.25 4.02
1870 4871 3.010144 GGTGATGGCATGACCCCT 58.990 61.111 23.69 0.00 37.83 4.79
1878 4891 0.827368 TAGTGTATGCGGTGATGGCA 59.173 50.000 0.00 0.00 45.71 4.92
1885 4898 2.829720 TCTTCTGGTTAGTGTATGCGGT 59.170 45.455 0.00 0.00 0.00 5.68
1911 4924 2.558378 CACACGTATCGGTAGGAGAGA 58.442 52.381 1.73 0.00 0.00 3.10
1923 4937 0.690762 AAAGTCCAGGCCACACGTAT 59.309 50.000 5.01 0.00 0.00 3.06
1956 4970 2.625737 CAAGTGGTATGCTCCAGACTG 58.374 52.381 0.00 0.00 38.23 3.51
1967 4981 2.290960 GGCTTTGAGGTCCAAGTGGTAT 60.291 50.000 0.00 0.00 35.94 2.73
1975 4989 1.361204 TCATGAGGCTTTGAGGTCCA 58.639 50.000 0.00 0.00 0.00 4.02
2060 5076 1.673920 GACTCTTCCGTCTAGCCTCTG 59.326 57.143 0.00 0.00 0.00 3.35
2061 5077 1.744456 CGACTCTTCCGTCTAGCCTCT 60.744 57.143 0.00 0.00 0.00 3.69
2062 5078 0.658897 CGACTCTTCCGTCTAGCCTC 59.341 60.000 0.00 0.00 0.00 4.70
2063 5079 0.748729 CCGACTCTTCCGTCTAGCCT 60.749 60.000 0.00 0.00 0.00 4.58
2064 5080 1.726533 CCCGACTCTTCCGTCTAGCC 61.727 65.000 0.00 0.00 0.00 3.93
2065 5081 0.747283 TCCCGACTCTTCCGTCTAGC 60.747 60.000 0.00 0.00 0.00 3.42
2066 5082 1.015868 GTCCCGACTCTTCCGTCTAG 58.984 60.000 0.00 0.00 0.00 2.43
2067 5083 0.742281 CGTCCCGACTCTTCCGTCTA 60.742 60.000 0.00 0.00 0.00 2.59
2068 5084 2.039405 CGTCCCGACTCTTCCGTCT 61.039 63.158 0.00 0.00 0.00 4.18
2069 5085 2.037136 TCGTCCCGACTCTTCCGTC 61.037 63.158 0.00 0.00 0.00 4.79
2070 5086 2.033141 TCGTCCCGACTCTTCCGT 59.967 61.111 0.00 0.00 0.00 4.69
2079 5095 0.249996 GGGTTCTTTTGTCGTCCCGA 60.250 55.000 0.00 0.00 0.00 5.14
2080 5096 2.241171 GGGTTCTTTTGTCGTCCCG 58.759 57.895 0.00 0.00 0.00 5.14
2081 5097 1.848932 GCGGGTTCTTTTGTCGTCCC 61.849 60.000 0.00 0.00 0.00 4.46
2082 5098 0.883370 AGCGGGTTCTTTTGTCGTCC 60.883 55.000 0.00 0.00 0.00 4.79
2083 5099 0.942252 AAGCGGGTTCTTTTGTCGTC 59.058 50.000 0.00 0.00 0.00 4.20
2084 5100 0.942252 GAAGCGGGTTCTTTTGTCGT 59.058 50.000 12.42 0.00 31.73 4.34
2085 5101 0.941542 TGAAGCGGGTTCTTTTGTCG 59.058 50.000 19.42 0.00 35.99 4.35
2086 5102 2.095212 GGATGAAGCGGGTTCTTTTGTC 60.095 50.000 19.42 10.09 35.99 3.18
2087 5103 1.886542 GGATGAAGCGGGTTCTTTTGT 59.113 47.619 19.42 2.60 35.99 2.83
2088 5104 1.202348 GGGATGAAGCGGGTTCTTTTG 59.798 52.381 19.42 0.00 35.99 2.44
2089 5105 1.075536 AGGGATGAAGCGGGTTCTTTT 59.924 47.619 19.42 6.01 35.99 2.27
2090 5106 0.698818 AGGGATGAAGCGGGTTCTTT 59.301 50.000 19.42 8.29 35.99 2.52
2091 5107 1.209747 GTAGGGATGAAGCGGGTTCTT 59.790 52.381 19.42 13.81 35.99 2.52
2092 5108 0.831307 GTAGGGATGAAGCGGGTTCT 59.169 55.000 19.42 6.55 35.99 3.01
2093 5109 0.179054 GGTAGGGATGAAGCGGGTTC 60.179 60.000 12.77 12.77 35.48 3.62
2094 5110 1.912971 GGTAGGGATGAAGCGGGTT 59.087 57.895 0.00 0.00 0.00 4.11
2095 5111 2.432300 CGGTAGGGATGAAGCGGGT 61.432 63.158 0.00 0.00 0.00 5.28
2096 5112 2.421739 CGGTAGGGATGAAGCGGG 59.578 66.667 0.00 0.00 0.00 6.13
2097 5113 2.280186 GCGGTAGGGATGAAGCGG 60.280 66.667 0.00 0.00 0.00 5.52
2098 5114 1.300233 GAGCGGTAGGGATGAAGCG 60.300 63.158 0.00 0.00 0.00 4.68
2099 5115 1.069935 GGAGCGGTAGGGATGAAGC 59.930 63.158 0.00 0.00 0.00 3.86
2100 5116 1.749033 GGGAGCGGTAGGGATGAAG 59.251 63.158 0.00 0.00 0.00 3.02
2101 5117 2.131709 CGGGAGCGGTAGGGATGAA 61.132 63.158 0.00 0.00 0.00 2.57
2102 5118 2.520982 CGGGAGCGGTAGGGATGA 60.521 66.667 0.00 0.00 0.00 2.92
2148 5164 3.155167 GAGGTGGACTAGGGCCGG 61.155 72.222 0.00 0.00 0.00 6.13
2149 5165 3.155167 GGAGGTGGACTAGGGCCG 61.155 72.222 0.00 0.00 0.00 6.13
2150 5166 2.768769 GGGAGGTGGACTAGGGCC 60.769 72.222 0.00 0.00 0.00 5.80
2151 5167 3.155167 CGGGAGGTGGACTAGGGC 61.155 72.222 0.00 0.00 0.00 5.19
2152 5168 3.155167 GCGGGAGGTGGACTAGGG 61.155 72.222 0.00 0.00 0.00 3.53
2153 5169 3.155167 GGCGGGAGGTGGACTAGG 61.155 72.222 0.00 0.00 0.00 3.02
2154 5170 2.042843 AGGCGGGAGGTGGACTAG 60.043 66.667 0.00 0.00 0.00 2.57
2155 5171 2.043248 GAGGCGGGAGGTGGACTA 60.043 66.667 0.00 0.00 0.00 2.59
2161 5177 4.677151 AAAGGGGAGGCGGGAGGT 62.677 66.667 0.00 0.00 0.00 3.85
2162 5178 3.798511 GAAAGGGGAGGCGGGAGG 61.799 72.222 0.00 0.00 0.00 4.30
2163 5179 3.798511 GGAAAGGGGAGGCGGGAG 61.799 72.222 0.00 0.00 0.00 4.30
2166 5182 3.798511 GAGGGAAAGGGGAGGCGG 61.799 72.222 0.00 0.00 0.00 6.13
2167 5183 4.162690 CGAGGGAAAGGGGAGGCG 62.163 72.222 0.00 0.00 0.00 5.52
2168 5184 4.491409 GCGAGGGAAAGGGGAGGC 62.491 72.222 0.00 0.00 0.00 4.70
2169 5185 3.798511 GGCGAGGGAAAGGGGAGG 61.799 72.222 0.00 0.00 0.00 4.30
2170 5186 4.162690 CGGCGAGGGAAAGGGGAG 62.163 72.222 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.