Multiple sequence alignment - TraesCS2A01G028400

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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 TraesCS2A01G028400 chr2A 100.000 2847 0 0 1 2847 12989399 12992245 0.000000e+00 5258.0
1 TraesCS2A01G028400 chr2A 90.860 1674 136 9 881 2541 13004835 13003166 0.000000e+00 2228.0
2 TraesCS2A01G028400 chr2A 100.000 493 0 0 3130 3622 12992528 12993020 0.000000e+00 911.0
3 TraesCS2A01G028400 chr2A 83.193 952 151 9 1594 2542 13013837 13014782 0.000000e+00 863.0
4 TraesCS2A01G028400 chr2A 93.281 506 17 5 3130 3622 711649761 711650262 0.000000e+00 730.0
5 TraesCS2A01G028400 chr2A 96.341 164 5 1 3459 3622 721506031 721506193 5.960000e-68 268.0
6 TraesCS2A01G028400 chr2A 98.214 56 1 0 2599 2654 19572579 19572634 8.280000e-17 99.0
7 TraesCS2A01G028400 chr2D 93.116 1903 91 16 710 2587 12550364 12552251 0.000000e+00 2752.0
8 TraesCS2A01G028400 chr2D 83.718 952 155 0 1591 2542 12580917 12579966 0.000000e+00 900.0
9 TraesCS2A01G028400 chr2D 83.229 954 141 13 1591 2542 12557202 12558138 0.000000e+00 857.0
10 TraesCS2A01G028400 chr2D 81.584 505 76 13 1017 1508 12556625 12557125 5.630000e-108 401.0
11 TraesCS2A01G028400 chr2D 95.783 166 7 0 441 606 330215227 330215062 5.960000e-68 268.0
12 TraesCS2A01G028400 chr2D 94.737 171 9 0 441 611 18207139 18206969 2.140000e-67 267.0
13 TraesCS2A01G028400 chr2D 92.655 177 12 1 433 608 424652045 424652221 1.670000e-63 254.0
14 TraesCS2A01G028400 chr2D 88.312 154 8 2 2679 2830 12552303 12552448 3.720000e-40 176.0
15 TraesCS2A01G028400 chr2D 90.588 85 8 0 2600 2684 107029415 107029499 2.960000e-21 113.0
16 TraesCS2A01G028400 chr2D 100.000 55 0 0 603 657 12550208 12550262 6.400000e-18 102.0
17 TraesCS2A01G028400 chr2B 89.655 1914 145 26 710 2587 18955795 18953899 0.000000e+00 2388.0
18 TraesCS2A01G028400 chr2B 81.584 1553 221 42 1016 2542 18950285 18948772 0.000000e+00 1223.0
19 TraesCS2A01G028400 chr2B 79.780 1543 279 23 1016 2542 19102538 19101013 0.000000e+00 1090.0
20 TraesCS2A01G028400 chr2B 79.952 1242 207 29 1332 2542 19084554 19083324 0.000000e+00 876.0
21 TraesCS2A01G028400 chr2B 94.808 443 20 3 1 442 18956716 18956276 0.000000e+00 688.0
22 TraesCS2A01G028400 chr2B 89.595 519 41 5 701 1209 18842439 18842954 0.000000e+00 647.0
23 TraesCS2A01G028400 chr2B 91.603 262 22 0 1249 1510 18842953 18843214 2.660000e-96 363.0
24 TraesCS2A01G028400 chr2B 89.362 141 5 2 2692 2830 18953827 18953695 6.220000e-38 169.0
25 TraesCS2A01G028400 chr6A 92.885 506 19 2 3130 3622 530139593 530140094 0.000000e+00 719.0
26 TraesCS2A01G028400 chr6A 92.095 506 21 4 3130 3622 58828252 58828751 0.000000e+00 695.0
27 TraesCS2A01G028400 chr6A 78.700 446 82 11 1003 1440 563484780 563485220 5.920000e-73 285.0
28 TraesCS2A01G028400 chr3A 92.095 506 22 3 3130 3622 80126221 80125721 0.000000e+00 697.0
29 TraesCS2A01G028400 chr3A 91.897 506 22 3 3130 3622 456460628 456460129 0.000000e+00 689.0
30 TraesCS2A01G028400 chr3A 95.858 169 7 0 441 609 41183277 41183445 1.280000e-69 274.0
31 TraesCS2A01G028400 chr3A 93.671 79 5 0 2606 2684 727180274 727180196 6.350000e-23 119.0
32 TraesCS2A01G028400 chr7A 92.510 494 19 3 3143 3622 157168785 157168296 0.000000e+00 691.0
33 TraesCS2A01G028400 chr7A 91.304 92 6 2 2595 2684 1951454 1951545 1.370000e-24 124.0
34 TraesCS2A01G028400 chr1A 92.813 487 18 2 3149 3622 3570041 3569559 0.000000e+00 689.0
35 TraesCS2A01G028400 chr1A 92.261 491 21 3 3145 3622 380309591 380309105 0.000000e+00 680.0
36 TraesCS2A01G028400 chr1A 80.422 332 51 6 109 431 251559461 251559135 1.300000e-59 241.0
37 TraesCS2A01G028400 chr7B 90.980 510 25 10 3130 3622 702224631 702224126 0.000000e+00 667.0
38 TraesCS2A01G028400 chr3B 89.516 496 25 4 3150 3622 145501381 145500890 1.440000e-168 603.0
39 TraesCS2A01G028400 chr5A 85.225 467 65 4 1006 1470 529081005 529080541 9.100000e-131 477.0
40 TraesCS2A01G028400 chr5A 92.222 180 14 0 429 608 590885969 590886148 4.640000e-64 255.0
41 TraesCS2A01G028400 chr4B 80.404 495 86 6 1016 1509 665820353 665820837 2.050000e-97 366.0
42 TraesCS2A01G028400 chr5B 93.989 183 9 2 435 616 45810407 45810588 3.560000e-70 276.0
43 TraesCS2A01G028400 chr1B 95.349 172 8 0 438 609 672032776 672032605 1.280000e-69 274.0
44 TraesCS2A01G028400 chr1B 92.537 67 5 0 2616 2682 673414529 673414463 2.980000e-16 97.1
45 TraesCS2A01G028400 chr3D 79.032 434 62 16 1 425 571899381 571899794 1.660000e-68 270.0
46 TraesCS2A01G028400 chr3D 94.152 171 10 0 437 607 515554811 515554641 9.980000e-66 261.0
47 TraesCS2A01G028400 chr3D 94.118 85 5 0 2600 2684 459153284 459153368 2.930000e-26 130.0
48 TraesCS2A01G028400 chr7D 95.758 165 7 0 440 604 614813335 614813499 2.140000e-67 267.0
49 TraesCS2A01G028400 chr6D 77.252 444 84 13 1002 1437 420559281 420559715 1.000000e-60 244.0
50 TraesCS2A01G028400 chr6D 94.118 85 5 0 2600 2684 455296041 455296125 2.930000e-26 130.0
51 TraesCS2A01G028400 chr6D 96.667 60 1 1 2596 2654 456752170 456752229 8.280000e-17 99.0
52 TraesCS2A01G028400 chr4D 96.610 59 2 0 2596 2654 329000431 329000373 8.280000e-17 99.0


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 TraesCS2A01G028400 chr2A 12989399 12993020 3621 False 3084.5 5258 100.000000 1 3622 2 chr2A.!!$F5 3621
1 TraesCS2A01G028400 chr2A 13003166 13004835 1669 True 2228.0 2228 90.860000 881 2541 1 chr2A.!!$R1 1660
2 TraesCS2A01G028400 chr2A 13013837 13014782 945 False 863.0 863 83.193000 1594 2542 1 chr2A.!!$F1 948
3 TraesCS2A01G028400 chr2A 711649761 711650262 501 False 730.0 730 93.281000 3130 3622 1 chr2A.!!$F3 492
4 TraesCS2A01G028400 chr2D 12550208 12552448 2240 False 1010.0 2752 93.809333 603 2830 3 chr2D.!!$F3 2227
5 TraesCS2A01G028400 chr2D 12579966 12580917 951 True 900.0 900 83.718000 1591 2542 1 chr2D.!!$R1 951
6 TraesCS2A01G028400 chr2D 12556625 12558138 1513 False 629.0 857 82.406500 1017 2542 2 chr2D.!!$F4 1525
7 TraesCS2A01G028400 chr2B 18948772 18956716 7944 True 1117.0 2388 88.852250 1 2830 4 chr2B.!!$R3 2829
8 TraesCS2A01G028400 chr2B 19101013 19102538 1525 True 1090.0 1090 79.780000 1016 2542 1 chr2B.!!$R2 1526
9 TraesCS2A01G028400 chr2B 19083324 19084554 1230 True 876.0 876 79.952000 1332 2542 1 chr2B.!!$R1 1210
10 TraesCS2A01G028400 chr2B 18842439 18843214 775 False 505.0 647 90.599000 701 1510 2 chr2B.!!$F1 809
11 TraesCS2A01G028400 chr6A 530139593 530140094 501 False 719.0 719 92.885000 3130 3622 1 chr6A.!!$F2 492
12 TraesCS2A01G028400 chr3A 80125721 80126221 500 True 697.0 697 92.095000 3130 3622 1 chr3A.!!$R1 492
13 TraesCS2A01G028400 chr7B 702224126 702224631 505 True 667.0 667 90.980000 3130 3622 1 chr7B.!!$R1 492

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
693 1086 0.320421 AGGGAACATGGTGAACGACG 60.32 55.0 0.0 0.0 0.0 5.12 F
2176 2679 0.469892 AAGGGCAGGTGTTTCTTGGG 60.47 55.0 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2573 3079 0.663153 GATATCCTGTTTGCACGGCC 59.337 55.000 0.00 0.0 0.0 6.13 R
3321 5225 1.079197 ATGTTCAGATGCGGCGTCA 60.079 52.632 23.07 7.7 0.0 4.35 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
24 25 2.712709 TCCGGCGATAAAAATGGTTCA 58.287 42.857 9.30 0.00 0.00 3.18
71 72 9.971922 ATGGAAGAACTTTTAATTCAAGTGAAG 57.028 29.630 4.17 0.00 37.48 3.02
147 148 3.826729 GCAGTTTTCTACCCAAGTTCCAT 59.173 43.478 0.00 0.00 0.00 3.41
148 149 4.082733 GCAGTTTTCTACCCAAGTTCCATC 60.083 45.833 0.00 0.00 0.00 3.51
230 231 3.456277 AGGTAGACATCCATCCTCCAAAC 59.544 47.826 0.00 0.00 0.00 2.93
238 239 3.112263 TCCATCCTCCAAACGATAAGGT 58.888 45.455 0.00 0.00 0.00 3.50
255 256 6.534079 CGATAAGGTGTCGGATTAAAAGACTT 59.466 38.462 8.92 0.00 36.01 3.01
258 259 9.901172 ATAAGGTGTCGGATTAAAAGACTTAAT 57.099 29.630 8.92 0.00 36.01 1.40
263 264 9.321562 GTGTCGGATTAAAAGACTTAATGGATA 57.678 33.333 8.92 0.00 36.01 2.59
282 283 8.757307 ATGGATATAGAGATAAGGGTGGAAAA 57.243 34.615 0.00 0.00 0.00 2.29
283 284 8.207350 TGGATATAGAGATAAGGGTGGAAAAG 57.793 38.462 0.00 0.00 0.00 2.27
284 285 7.106890 GGATATAGAGATAAGGGTGGAAAAGC 58.893 42.308 0.00 0.00 0.00 3.51
286 287 4.227864 AGAGATAAGGGTGGAAAAGCAG 57.772 45.455 0.00 0.00 0.00 4.24
320 321 6.706270 AGAGAAGAGCAAGAACAAAAACGATA 59.294 34.615 0.00 0.00 0.00 2.92
326 327 4.791411 GCAAGAACAAAAACGATAGCCACA 60.791 41.667 0.00 0.00 42.67 4.17
327 328 4.483476 AGAACAAAAACGATAGCCACAC 57.517 40.909 0.00 0.00 42.67 3.82
373 374 9.838339 AAGACATAATTAAGGTACATTCCTCTG 57.162 33.333 0.00 0.00 36.74 3.35
377 378 6.893020 AATTAAGGTACATTCCTCTGGACT 57.107 37.500 0.00 0.00 36.74 3.85
383 384 5.422650 AGGTACATTCCTCTGGACTTAGTTC 59.577 44.000 0.00 0.00 31.32 3.01
444 445 6.727824 AACATGCACTACTGTTTCATACTC 57.272 37.500 0.00 0.00 31.74 2.59
445 446 5.178797 ACATGCACTACTGTTTCATACTCC 58.821 41.667 0.00 0.00 0.00 3.85
446 447 4.202245 TGCACTACTGTTTCATACTCCC 57.798 45.455 0.00 0.00 0.00 4.30
447 448 3.838317 TGCACTACTGTTTCATACTCCCT 59.162 43.478 0.00 0.00 0.00 4.20
448 449 4.081642 TGCACTACTGTTTCATACTCCCTC 60.082 45.833 0.00 0.00 0.00 4.30
449 450 4.680975 GCACTACTGTTTCATACTCCCTCC 60.681 50.000 0.00 0.00 0.00 4.30
450 451 3.700038 ACTACTGTTTCATACTCCCTCCG 59.300 47.826 0.00 0.00 0.00 4.63
451 452 2.537143 ACTGTTTCATACTCCCTCCGT 58.463 47.619 0.00 0.00 0.00 4.69
452 453 2.904434 ACTGTTTCATACTCCCTCCGTT 59.096 45.455 0.00 0.00 0.00 4.44
453 454 3.056035 ACTGTTTCATACTCCCTCCGTTC 60.056 47.826 0.00 0.00 0.00 3.95
454 455 2.235402 TGTTTCATACTCCCTCCGTTCC 59.765 50.000 0.00 0.00 0.00 3.62
455 456 2.500504 GTTTCATACTCCCTCCGTTCCT 59.499 50.000 0.00 0.00 0.00 3.36
456 457 3.675348 TTCATACTCCCTCCGTTCCTA 57.325 47.619 0.00 0.00 0.00 2.94
457 458 3.675348 TCATACTCCCTCCGTTCCTAA 57.325 47.619 0.00 0.00 0.00 2.69
458 459 3.985127 TCATACTCCCTCCGTTCCTAAA 58.015 45.455 0.00 0.00 0.00 1.85
459 460 4.553678 TCATACTCCCTCCGTTCCTAAAT 58.446 43.478 0.00 0.00 0.00 1.40
460 461 5.708544 TCATACTCCCTCCGTTCCTAAATA 58.291 41.667 0.00 0.00 0.00 1.40
461 462 6.320518 TCATACTCCCTCCGTTCCTAAATAT 58.679 40.000 0.00 0.00 0.00 1.28
462 463 6.785963 TCATACTCCCTCCGTTCCTAAATATT 59.214 38.462 0.00 0.00 0.00 1.28
463 464 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
464 465 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
465 466 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
466 467 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
467 468 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
468 469 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
469 470 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
470 471 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
471 472 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
472 473 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
473 474 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
474 475 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
491 492 9.449719 TCTTTCTAGAGATTTTAAATGGTCACC 57.550 33.333 0.00 0.00 0.00 4.02
492 493 9.231297 CTTTCTAGAGATTTTAAATGGTCACCA 57.769 33.333 0.00 0.00 38.19 4.17
493 494 8.561738 TTCTAGAGATTTTAAATGGTCACCAC 57.438 34.615 0.00 0.00 35.80 4.16
494 495 7.685481 TCTAGAGATTTTAAATGGTCACCACA 58.315 34.615 0.00 0.00 35.80 4.17
495 496 8.328758 TCTAGAGATTTTAAATGGTCACCACAT 58.671 33.333 0.00 0.00 35.80 3.21
496 497 9.613428 CTAGAGATTTTAAATGGTCACCACATA 57.387 33.333 0.00 0.00 35.80 2.29
497 498 8.281212 AGAGATTTTAAATGGTCACCACATAC 57.719 34.615 0.00 0.00 35.80 2.39
498 499 7.065803 AGAGATTTTAAATGGTCACCACATACG 59.934 37.037 0.00 0.00 35.80 3.06
499 500 5.630661 TTTTAAATGGTCACCACATACGG 57.369 39.130 0.00 0.00 35.80 4.02
500 501 4.554960 TTAAATGGTCACCACATACGGA 57.445 40.909 0.00 0.00 35.80 4.69
501 502 3.644966 AAATGGTCACCACATACGGAT 57.355 42.857 0.00 0.00 35.80 4.18
502 503 2.620251 ATGGTCACCACATACGGATG 57.380 50.000 5.94 5.94 35.80 3.51
503 504 1.562783 TGGTCACCACATACGGATGA 58.437 50.000 16.36 0.00 36.48 2.92
504 505 1.903183 TGGTCACCACATACGGATGAA 59.097 47.619 16.36 0.00 36.48 2.57
505 506 2.503765 TGGTCACCACATACGGATGAAT 59.496 45.455 16.36 0.00 36.48 2.57
506 507 3.707102 TGGTCACCACATACGGATGAATA 59.293 43.478 16.36 0.00 36.48 1.75
507 508 4.346709 TGGTCACCACATACGGATGAATAT 59.653 41.667 16.36 0.00 36.48 1.28
508 509 5.540719 TGGTCACCACATACGGATGAATATA 59.459 40.000 16.36 0.00 36.48 0.86
509 510 6.100004 GGTCACCACATACGGATGAATATAG 58.900 44.000 16.36 0.00 36.48 1.31
510 511 6.071560 GGTCACCACATACGGATGAATATAGA 60.072 42.308 16.36 1.49 36.48 1.98
511 512 6.807230 GTCACCACATACGGATGAATATAGAC 59.193 42.308 16.36 10.25 36.48 2.59
512 513 6.492087 TCACCACATACGGATGAATATAGACA 59.508 38.462 16.36 0.00 36.48 3.41
513 514 7.178451 TCACCACATACGGATGAATATAGACAT 59.822 37.037 16.36 0.00 36.48 3.06
514 515 8.466798 CACCACATACGGATGAATATAGACATA 58.533 37.037 16.36 0.00 36.48 2.29
515 516 9.201989 ACCACATACGGATGAATATAGACATAT 57.798 33.333 16.36 0.00 36.48 1.78
545 546 8.734386 AGAGTGTAGATTCATTCATTTTGTTCC 58.266 33.333 0.00 0.00 0.00 3.62
546 547 7.530010 AGTGTAGATTCATTCATTTTGTTCCG 58.470 34.615 0.00 0.00 0.00 4.30
547 548 7.174946 AGTGTAGATTCATTCATTTTGTTCCGT 59.825 33.333 0.00 0.00 0.00 4.69
548 549 8.447833 GTGTAGATTCATTCATTTTGTTCCGTA 58.552 33.333 0.00 0.00 0.00 4.02
549 550 9.173021 TGTAGATTCATTCATTTTGTTCCGTAT 57.827 29.630 0.00 0.00 0.00 3.06
550 551 9.438291 GTAGATTCATTCATTTTGTTCCGTATG 57.562 33.333 0.00 0.00 0.00 2.39
551 552 8.055279 AGATTCATTCATTTTGTTCCGTATGT 57.945 30.769 0.00 0.00 0.00 2.29
552 553 9.173021 AGATTCATTCATTTTGTTCCGTATGTA 57.827 29.630 0.00 0.00 0.00 2.29
553 554 9.221775 GATTCATTCATTTTGTTCCGTATGTAC 57.778 33.333 0.00 0.00 0.00 2.90
554 555 7.915293 TCATTCATTTTGTTCCGTATGTACT 57.085 32.000 0.00 0.00 0.00 2.73
555 556 7.970384 TCATTCATTTTGTTCCGTATGTACTC 58.030 34.615 0.00 0.00 0.00 2.59
556 557 7.604545 TCATTCATTTTGTTCCGTATGTACTCA 59.395 33.333 0.00 0.00 0.00 3.41
557 558 6.715344 TCATTTTGTTCCGTATGTACTCAC 57.285 37.500 0.00 0.00 0.00 3.51
558 559 6.460781 TCATTTTGTTCCGTATGTACTCACT 58.539 36.000 0.00 0.00 0.00 3.41
559 560 7.604549 TCATTTTGTTCCGTATGTACTCACTA 58.395 34.615 0.00 0.00 0.00 2.74
560 561 8.255206 TCATTTTGTTCCGTATGTACTCACTAT 58.745 33.333 0.00 0.00 0.00 2.12
561 562 8.879759 CATTTTGTTCCGTATGTACTCACTATT 58.120 33.333 0.00 0.00 0.00 1.73
562 563 8.836268 TTTTGTTCCGTATGTACTCACTATTT 57.164 30.769 0.00 0.00 0.00 1.40
563 564 7.821595 TTGTTCCGTATGTACTCACTATTTG 57.178 36.000 0.00 0.00 0.00 2.32
564 565 7.160547 TGTTCCGTATGTACTCACTATTTGA 57.839 36.000 0.00 0.00 0.00 2.69
565 566 7.604549 TGTTCCGTATGTACTCACTATTTGAA 58.395 34.615 0.00 0.00 32.21 2.69
566 567 8.089597 TGTTCCGTATGTACTCACTATTTGAAA 58.910 33.333 0.00 0.00 32.21 2.69
567 568 8.378421 GTTCCGTATGTACTCACTATTTGAAAC 58.622 37.037 0.00 0.00 32.21 2.78
568 569 7.037438 TCCGTATGTACTCACTATTTGAAACC 58.963 38.462 0.00 0.00 32.21 3.27
569 570 7.039882 CCGTATGTACTCACTATTTGAAACCT 58.960 38.462 0.00 0.00 32.21 3.50
570 571 7.548075 CCGTATGTACTCACTATTTGAAACCTT 59.452 37.037 0.00 0.00 32.21 3.50
571 572 8.932791 CGTATGTACTCACTATTTGAAACCTTT 58.067 33.333 0.00 0.00 32.21 3.11
578 579 9.847224 ACTCACTATTTGAAACCTTTAGAAAGA 57.153 29.630 3.52 0.00 34.07 2.52
580 581 9.621629 TCACTATTTGAAACCTTTAGAAAGACA 57.378 29.630 3.52 0.00 38.28 3.41
596 597 9.947433 TTAGAAAGACAATTATTTAGGAACGGA 57.053 29.630 0.00 0.00 0.00 4.69
597 598 8.494016 AGAAAGACAATTATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
598 599 7.553044 AGAAAGACAATTATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
599 600 5.681639 AGACAATTATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
600 601 5.427481 AGACAATTATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
601 602 5.681639 ACAATTATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
690 1083 2.762535 AGTAGGGAACATGGTGAACG 57.237 50.000 0.00 0.00 0.00 3.95
692 1085 2.028385 AGTAGGGAACATGGTGAACGAC 60.028 50.000 0.00 0.00 0.00 4.34
693 1086 0.320421 AGGGAACATGGTGAACGACG 60.320 55.000 0.00 0.00 0.00 5.12
694 1087 1.495951 GGAACATGGTGAACGACGC 59.504 57.895 0.00 0.00 0.00 5.19
695 1088 1.129809 GAACATGGTGAACGACGCG 59.870 57.895 3.53 3.53 0.00 6.01
696 1089 2.811893 GAACATGGTGAACGACGCGC 62.812 60.000 5.73 0.00 0.00 6.86
697 1090 4.147322 CATGGTGAACGACGCGCC 62.147 66.667 5.73 0.00 36.47 6.53
698 1091 4.373116 ATGGTGAACGACGCGCCT 62.373 61.111 5.73 0.00 36.86 5.52
732 1125 4.658063 ACCGGGTCAAAATTAGACAATCA 58.342 39.130 6.32 0.00 37.74 2.57
793 1186 4.313020 AGCCTCAAACTTGGAATCTCAT 57.687 40.909 0.00 0.00 0.00 2.90
848 1244 1.659098 GCGGTACAGTACACTGAATGC 59.341 52.381 16.05 9.81 46.59 3.56
850 1246 3.428452 GCGGTACAGTACACTGAATGCTA 60.428 47.826 16.05 0.00 46.59 3.49
852 1248 4.561606 CGGTACAGTACACTGAATGCTAAC 59.438 45.833 16.05 0.00 46.59 2.34
853 1249 4.868734 GGTACAGTACACTGAATGCTAACC 59.131 45.833 16.05 7.49 46.59 2.85
854 1250 4.617253 ACAGTACACTGAATGCTAACCA 57.383 40.909 16.05 0.00 46.59 3.67
856 1252 3.684788 CAGTACACTGAATGCTAACCACC 59.315 47.826 3.14 0.00 46.59 4.61
860 1256 3.569701 ACACTGAATGCTAACCACCAAAG 59.430 43.478 0.00 0.00 0.00 2.77
898 1306 2.263077 CTGTCCACGCACTGATTAGTC 58.737 52.381 0.00 0.00 34.07 2.59
911 1321 5.419155 CACTGATTAGTCTTCCCACTCACTA 59.581 44.000 0.00 0.00 34.07 2.74
916 1326 7.785028 TGATTAGTCTTCCCACTCACTATGTAT 59.215 37.037 0.00 0.00 0.00 2.29
926 1336 6.072838 CCCACTCACTATGTATCGTACGTAAT 60.073 42.308 16.05 4.86 30.37 1.89
947 1359 7.594758 CGTAATCTTGCATTTCTTTTCTTTCCA 59.405 33.333 0.00 0.00 0.00 3.53
948 1360 9.428097 GTAATCTTGCATTTCTTTTCTTTCCAT 57.572 29.630 0.00 0.00 0.00 3.41
950 1362 6.458210 TCTTGCATTTCTTTTCTTTCCATCC 58.542 36.000 0.00 0.00 0.00 3.51
951 1363 5.804944 TGCATTTCTTTTCTTTCCATCCA 57.195 34.783 0.00 0.00 0.00 3.41
954 1366 5.990996 GCATTTCTTTTCTTTCCATCCACAA 59.009 36.000 0.00 0.00 0.00 3.33
1134 1549 0.669619 TCGTCTACACCGAGCACAAA 59.330 50.000 0.00 0.00 0.00 2.83
1275 1702 1.377725 CATCTGCCACTCCACCACC 60.378 63.158 0.00 0.00 0.00 4.61
1278 1705 4.248842 TGCCACTCCACCACCACG 62.249 66.667 0.00 0.00 0.00 4.94
1330 1760 2.331451 GCCTCAACAACACCGCAC 59.669 61.111 0.00 0.00 0.00 5.34
1802 2301 1.202486 ACCTTTGACGAGTTCGAGCAA 60.202 47.619 8.72 9.07 43.02 3.91
2087 2589 1.226717 CTGCGGCTACGACTTCCTC 60.227 63.158 0.00 0.00 44.60 3.71
2176 2679 0.469892 AAGGGCAGGTGTTTCTTGGG 60.470 55.000 0.00 0.00 0.00 4.12
2407 2910 2.447429 TGGTCGAGGAGAGGATAAGGAT 59.553 50.000 0.00 0.00 0.00 3.24
2419 2922 2.508526 GATAAGGATGGTGATGGGTGC 58.491 52.381 0.00 0.00 0.00 5.01
2510 3016 1.197721 CAACCTTGTGGCAGATCGTTC 59.802 52.381 0.00 0.00 36.63 3.95
2523 3029 0.673644 ATCGTTCGCCAACCTTGAGG 60.674 55.000 0.00 0.00 42.17 3.86
2573 3079 2.026301 GATCGTCCTTCTCCCGCG 59.974 66.667 0.00 0.00 0.00 6.46
2589 3095 3.055719 CGGCCGTGCAAACAGGAT 61.056 61.111 19.50 0.00 33.41 3.24
2590 3096 1.743623 CGGCCGTGCAAACAGGATA 60.744 57.895 19.50 0.00 33.41 2.59
2591 3097 1.095228 CGGCCGTGCAAACAGGATAT 61.095 55.000 19.50 0.00 33.41 1.63
2592 3098 0.663153 GGCCGTGCAAACAGGATATC 59.337 55.000 0.00 0.00 33.41 1.63
2593 3099 1.378531 GCCGTGCAAACAGGATATCA 58.621 50.000 4.83 0.00 33.41 2.15
2594 3100 1.742831 GCCGTGCAAACAGGATATCAA 59.257 47.619 4.83 0.00 33.41 2.57
2595 3101 2.358898 GCCGTGCAAACAGGATATCAAT 59.641 45.455 4.83 0.00 33.41 2.57
2596 3102 3.181487 GCCGTGCAAACAGGATATCAATT 60.181 43.478 4.83 0.00 33.41 2.32
2597 3103 4.677779 GCCGTGCAAACAGGATATCAATTT 60.678 41.667 4.83 0.00 33.41 1.82
2598 3104 5.410067 CCGTGCAAACAGGATATCAATTTT 58.590 37.500 4.83 0.00 33.41 1.82
2601 3107 5.581874 GTGCAAACAGGATATCAATTTTGGG 59.418 40.000 17.24 2.75 0.00 4.12
2603 3109 5.812127 GCAAACAGGATATCAATTTTGGGTC 59.188 40.000 17.24 4.60 0.00 4.46
2604 3110 6.351286 GCAAACAGGATATCAATTTTGGGTCT 60.351 38.462 17.24 0.00 0.00 3.85
2605 3111 6.780457 AACAGGATATCAATTTTGGGTCTG 57.220 37.500 4.83 1.34 0.00 3.51
2606 3112 5.831103 ACAGGATATCAATTTTGGGTCTGT 58.169 37.500 4.83 1.95 0.00 3.41
2608 3114 6.125029 CAGGATATCAATTTTGGGTCTGTCT 58.875 40.000 4.83 0.00 0.00 3.41
2609 3115 7.092444 ACAGGATATCAATTTTGGGTCTGTCTA 60.092 37.037 4.83 0.00 0.00 2.59
2610 3116 7.941238 CAGGATATCAATTTTGGGTCTGTCTAT 59.059 37.037 4.83 0.00 0.00 1.98
2611 3117 7.941238 AGGATATCAATTTTGGGTCTGTCTATG 59.059 37.037 4.83 0.00 0.00 2.23
2614 3120 5.875224 TCAATTTTGGGTCTGTCTATGTCA 58.125 37.500 0.00 0.00 0.00 3.58
2615 3121 5.705441 TCAATTTTGGGTCTGTCTATGTCAC 59.295 40.000 0.00 0.00 0.00 3.67
2616 3122 4.698201 TTTTGGGTCTGTCTATGTCACA 57.302 40.909 0.00 0.00 0.00 3.58
2617 3123 4.908601 TTTGGGTCTGTCTATGTCACAT 57.091 40.909 0.00 0.00 0.00 3.21
2618 3124 4.471904 TTGGGTCTGTCTATGTCACATC 57.528 45.455 0.00 0.00 0.00 3.06
2619 3125 3.713003 TGGGTCTGTCTATGTCACATCT 58.287 45.455 0.00 0.00 0.00 2.90
2620 3126 4.867086 TGGGTCTGTCTATGTCACATCTA 58.133 43.478 0.00 0.00 0.00 1.98
2621 3127 4.889995 TGGGTCTGTCTATGTCACATCTAG 59.110 45.833 0.00 0.00 0.00 2.43
2622 3128 5.133941 GGGTCTGTCTATGTCACATCTAGA 58.866 45.833 0.00 0.00 0.00 2.43
2624 3130 6.294453 GGGTCTGTCTATGTCACATCTAGATG 60.294 46.154 27.63 27.63 44.15 2.90
2653 3159 9.474313 AGATATTATCTCACATCTAACTCCCTC 57.526 37.037 0.08 0.00 33.42 4.30
2654 3160 9.474313 GATATTATCTCACATCTAACTCCCTCT 57.526 37.037 0.00 0.00 0.00 3.69
2655 3161 7.775053 ATTATCTCACATCTAACTCCCTCTC 57.225 40.000 0.00 0.00 0.00 3.20
2656 3162 4.592997 TCTCACATCTAACTCCCTCTCA 57.407 45.455 0.00 0.00 0.00 3.27
2657 3163 4.274147 TCTCACATCTAACTCCCTCTCAC 58.726 47.826 0.00 0.00 0.00 3.51
2658 3164 4.019858 CTCACATCTAACTCCCTCTCACA 58.980 47.826 0.00 0.00 0.00 3.58
2659 3165 4.614475 TCACATCTAACTCCCTCTCACAT 58.386 43.478 0.00 0.00 0.00 3.21
2660 3166 4.646945 TCACATCTAACTCCCTCTCACATC 59.353 45.833 0.00 0.00 0.00 3.06
2661 3167 4.648762 CACATCTAACTCCCTCTCACATCT 59.351 45.833 0.00 0.00 0.00 2.90
2662 3168 5.830457 CACATCTAACTCCCTCTCACATCTA 59.170 44.000 0.00 0.00 0.00 1.98
2663 3169 6.322456 CACATCTAACTCCCTCTCACATCTAA 59.678 42.308 0.00 0.00 0.00 2.10
2664 3170 7.015098 CACATCTAACTCCCTCTCACATCTAAT 59.985 40.741 0.00 0.00 0.00 1.73
2665 3171 7.566879 ACATCTAACTCCCTCTCACATCTAATT 59.433 37.037 0.00 0.00 0.00 1.40
2666 3172 7.589958 TCTAACTCCCTCTCACATCTAATTC 57.410 40.000 0.00 0.00 0.00 2.17
2667 3173 5.622346 AACTCCCTCTCACATCTAATTCC 57.378 43.478 0.00 0.00 0.00 3.01
2668 3174 3.970640 ACTCCCTCTCACATCTAATTCCC 59.029 47.826 0.00 0.00 0.00 3.97
2669 3175 4.230455 CTCCCTCTCACATCTAATTCCCT 58.770 47.826 0.00 0.00 0.00 4.20
2670 3176 4.227197 TCCCTCTCACATCTAATTCCCTC 58.773 47.826 0.00 0.00 0.00 4.30
2671 3177 3.006323 CCCTCTCACATCTAATTCCCTCG 59.994 52.174 0.00 0.00 0.00 4.63
2672 3178 3.553922 CCTCTCACATCTAATTCCCTCGC 60.554 52.174 0.00 0.00 0.00 5.03
2673 3179 2.365617 TCTCACATCTAATTCCCTCGCC 59.634 50.000 0.00 0.00 0.00 5.54
2674 3180 2.366916 CTCACATCTAATTCCCTCGCCT 59.633 50.000 0.00 0.00 0.00 5.52
2675 3181 2.771943 TCACATCTAATTCCCTCGCCTT 59.228 45.455 0.00 0.00 0.00 4.35
2676 3182 3.199946 TCACATCTAATTCCCTCGCCTTT 59.800 43.478 0.00 0.00 0.00 3.11
2677 3183 3.313526 CACATCTAATTCCCTCGCCTTTG 59.686 47.826 0.00 0.00 0.00 2.77
2684 3190 5.993748 AATTCCCTCGCCTTTGATTTTTA 57.006 34.783 0.00 0.00 0.00 1.52
2782 3294 5.608015 TCCTGGAATCATATGATTGTGGAGA 59.392 40.000 30.86 18.58 44.14 3.71
2783 3295 5.704515 CCTGGAATCATATGATTGTGGAGAC 59.295 44.000 30.86 16.39 44.14 3.36
2784 3296 6.251255 TGGAATCATATGATTGTGGAGACA 57.749 37.500 30.86 16.09 44.14 3.41
2825 3337 5.036737 CAGCGTTTTCTCATGTTGTTTCTT 58.963 37.500 0.00 0.00 0.00 2.52
2830 3342 6.197096 CGTTTTCTCATGTTGTTTCTTCCAAG 59.803 38.462 0.00 0.00 0.00 3.61
2831 3343 5.772825 TTCTCATGTTGTTTCTTCCAAGG 57.227 39.130 0.00 0.00 0.00 3.61
2832 3344 4.144297 TCTCATGTTGTTTCTTCCAAGGG 58.856 43.478 0.00 0.00 0.00 3.95
2834 3346 1.408969 TGTTGTTTCTTCCAAGGGGC 58.591 50.000 0.00 0.00 0.00 5.80
2835 3347 1.063266 TGTTGTTTCTTCCAAGGGGCT 60.063 47.619 0.00 0.00 0.00 5.19
2836 3348 2.039418 GTTGTTTCTTCCAAGGGGCTT 58.961 47.619 0.00 0.00 0.00 4.35
2837 3349 1.703411 TGTTTCTTCCAAGGGGCTTG 58.297 50.000 0.00 0.00 40.75 4.01
2838 3350 0.318441 GTTTCTTCCAAGGGGCTTGC 59.682 55.000 0.00 0.00 39.85 4.01
2839 3351 0.188342 TTTCTTCCAAGGGGCTTGCT 59.812 50.000 0.00 0.00 39.85 3.91
2841 3353 0.251341 TCTTCCAAGGGGCTTGCTTC 60.251 55.000 0.00 0.00 39.85 3.86
2842 3354 1.589716 CTTCCAAGGGGCTTGCTTCG 61.590 60.000 0.00 0.00 39.85 3.79
2845 3357 1.002624 CAAGGGGCTTGCTTCGGTA 60.003 57.895 0.00 0.00 34.63 4.02
3174 4664 3.466836 TCATACCGTATAGACCGACGTT 58.533 45.455 0.00 0.00 37.36 3.99
3185 4675 3.531538 AGACCGACGTTCGTATACCTTA 58.468 45.455 0.00 0.00 38.40 2.69
3298 5202 0.452784 GTTTCCAACTGTGCGATCGC 60.453 55.000 32.48 32.48 42.35 4.58
3321 5225 2.990479 GCCGACTGAACCCCATCT 59.010 61.111 0.00 0.00 0.00 2.90
3338 5242 1.737735 CTGACGCCGCATCTGAACA 60.738 57.895 0.00 0.00 0.00 3.18
3433 7090 1.536284 CGTCTTCCATCTAACCCTCGC 60.536 57.143 0.00 0.00 0.00 5.03
3529 7517 4.450122 GCGACGTCTACACCGCGA 62.450 66.667 14.70 0.00 38.27 5.87
3591 8303 2.512745 TTGCACGTCGCCACTGTT 60.513 55.556 7.38 0.00 41.33 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.868522 TCCATCTTCTTACATGTTTCTGAAAT 57.131 30.769 2.30 0.00 0.00 2.17
71 72 0.384669 GAATGCCAGCCTGAGATTGC 59.615 55.000 0.00 0.00 0.00 3.56
147 148 8.203937 TCTTCAGTTTGAGTTTGTTATTTCGA 57.796 30.769 0.00 0.00 0.00 3.71
148 149 8.835467 TTCTTCAGTTTGAGTTTGTTATTTCG 57.165 30.769 0.00 0.00 0.00 3.46
230 231 6.040878 AGTCTTTTAATCCGACACCTTATCG 58.959 40.000 0.00 0.00 39.33 2.92
255 256 9.852784 TTTCCACCCTTATCTCTATATCCATTA 57.147 33.333 0.00 0.00 0.00 1.90
258 259 7.256691 GCTTTTCCACCCTTATCTCTATATCCA 60.257 40.741 0.00 0.00 0.00 3.41
263 264 5.667626 TCTGCTTTTCCACCCTTATCTCTAT 59.332 40.000 0.00 0.00 0.00 1.98
282 283 3.865684 GCTCTTCTCTTTCTTGCTCTGCT 60.866 47.826 0.00 0.00 0.00 4.24
283 284 2.416202 GCTCTTCTCTTTCTTGCTCTGC 59.584 50.000 0.00 0.00 0.00 4.26
284 285 3.661944 TGCTCTTCTCTTTCTTGCTCTG 58.338 45.455 0.00 0.00 0.00 3.35
286 287 4.314121 TCTTGCTCTTCTCTTTCTTGCTC 58.686 43.478 0.00 0.00 0.00 4.26
320 321 1.729586 TCCTTAGGACAAGTGTGGCT 58.270 50.000 0.00 0.00 31.06 4.75
326 327 6.015265 GTCTTCTACACTTCCTTAGGACAAGT 60.015 42.308 0.00 0.00 0.00 3.16
327 328 6.015350 TGTCTTCTACACTTCCTTAGGACAAG 60.015 42.308 0.00 0.00 31.43 3.16
438 439 4.957684 ATTTAGGAACGGAGGGAGTATG 57.042 45.455 0.00 0.00 0.00 2.39
439 440 7.072076 ACAAATATTTAGGAACGGAGGGAGTAT 59.928 37.037 0.00 0.00 0.00 2.12
440 441 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
441 442 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
442 443 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
443 444 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
444 445 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
445 446 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
446 447 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
447 448 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
448 449 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
465 466 9.449719 GGTGACCATTTAAAATCTCTAGAAAGA 57.550 33.333 0.00 0.00 0.00 2.52
466 467 9.231297 TGGTGACCATTTAAAATCTCTAGAAAG 57.769 33.333 0.00 0.00 0.00 2.62
467 468 9.010029 GTGGTGACCATTTAAAATCTCTAGAAA 57.990 33.333 7.94 0.00 35.28 2.52
468 469 8.160765 TGTGGTGACCATTTAAAATCTCTAGAA 58.839 33.333 7.94 0.00 35.28 2.10
469 470 7.685481 TGTGGTGACCATTTAAAATCTCTAGA 58.315 34.615 7.94 0.00 35.28 2.43
470 471 7.921786 TGTGGTGACCATTTAAAATCTCTAG 57.078 36.000 7.94 0.00 35.28 2.43
471 472 9.391006 GTATGTGGTGACCATTTAAAATCTCTA 57.609 33.333 7.94 0.00 35.28 2.43
472 473 7.065803 CGTATGTGGTGACCATTTAAAATCTCT 59.934 37.037 7.94 0.00 35.28 3.10
473 474 7.186804 CGTATGTGGTGACCATTTAAAATCTC 58.813 38.462 7.94 0.00 35.28 2.75
474 475 6.094881 CCGTATGTGGTGACCATTTAAAATCT 59.905 38.462 7.94 0.00 35.28 2.40
475 476 6.094325 TCCGTATGTGGTGACCATTTAAAATC 59.906 38.462 7.94 0.00 35.28 2.17
476 477 5.946972 TCCGTATGTGGTGACCATTTAAAAT 59.053 36.000 7.94 0.00 35.28 1.82
477 478 5.314529 TCCGTATGTGGTGACCATTTAAAA 58.685 37.500 7.94 0.00 35.28 1.52
478 479 4.907809 TCCGTATGTGGTGACCATTTAAA 58.092 39.130 7.94 0.00 35.28 1.52
479 480 4.554960 TCCGTATGTGGTGACCATTTAA 57.445 40.909 7.94 0.00 35.28 1.52
480 481 4.162509 TCATCCGTATGTGGTGACCATTTA 59.837 41.667 7.94 0.00 35.28 1.40
481 482 3.054728 TCATCCGTATGTGGTGACCATTT 60.055 43.478 7.94 0.45 35.28 2.32
482 483 2.503765 TCATCCGTATGTGGTGACCATT 59.496 45.455 7.94 0.86 35.28 3.16
483 484 2.115427 TCATCCGTATGTGGTGACCAT 58.885 47.619 7.94 0.00 35.28 3.55
484 485 1.562783 TCATCCGTATGTGGTGACCA 58.437 50.000 0.00 0.00 34.50 4.02
485 486 2.684001 TTCATCCGTATGTGGTGACC 57.316 50.000 0.00 0.00 34.50 4.02
486 487 6.807230 GTCTATATTCATCCGTATGTGGTGAC 59.193 42.308 0.00 0.00 34.50 3.67
487 488 6.492087 TGTCTATATTCATCCGTATGTGGTGA 59.508 38.462 0.00 0.00 34.50 4.02
488 489 6.687604 TGTCTATATTCATCCGTATGTGGTG 58.312 40.000 0.00 0.00 34.50 4.17
489 490 6.911250 TGTCTATATTCATCCGTATGTGGT 57.089 37.500 0.00 0.00 34.50 4.16
519 520 8.734386 GGAACAAAATGAATGAATCTACACTCT 58.266 33.333 0.00 0.00 0.00 3.24
520 521 7.693951 CGGAACAAAATGAATGAATCTACACTC 59.306 37.037 0.00 0.00 0.00 3.51
521 522 7.174946 ACGGAACAAAATGAATGAATCTACACT 59.825 33.333 0.00 0.00 0.00 3.55
522 523 7.305474 ACGGAACAAAATGAATGAATCTACAC 58.695 34.615 0.00 0.00 0.00 2.90
523 524 7.447374 ACGGAACAAAATGAATGAATCTACA 57.553 32.000 0.00 0.00 0.00 2.74
524 525 9.438291 CATACGGAACAAAATGAATGAATCTAC 57.562 33.333 0.00 0.00 0.00 2.59
525 526 9.173021 ACATACGGAACAAAATGAATGAATCTA 57.827 29.630 0.00 0.00 0.00 1.98
526 527 8.055279 ACATACGGAACAAAATGAATGAATCT 57.945 30.769 0.00 0.00 0.00 2.40
527 528 9.221775 GTACATACGGAACAAAATGAATGAATC 57.778 33.333 0.00 0.00 0.00 2.52
528 529 8.956426 AGTACATACGGAACAAAATGAATGAAT 58.044 29.630 0.00 0.00 0.00 2.57
529 530 8.330466 AGTACATACGGAACAAAATGAATGAA 57.670 30.769 0.00 0.00 0.00 2.57
530 531 7.604545 TGAGTACATACGGAACAAAATGAATGA 59.395 33.333 0.00 0.00 0.00 2.57
531 532 7.692291 GTGAGTACATACGGAACAAAATGAATG 59.308 37.037 0.00 0.00 0.00 2.67
532 533 7.606456 AGTGAGTACATACGGAACAAAATGAAT 59.394 33.333 0.00 0.00 0.00 2.57
533 534 6.932400 AGTGAGTACATACGGAACAAAATGAA 59.068 34.615 0.00 0.00 0.00 2.57
534 535 6.460781 AGTGAGTACATACGGAACAAAATGA 58.539 36.000 0.00 0.00 0.00 2.57
535 536 6.721571 AGTGAGTACATACGGAACAAAATG 57.278 37.500 0.00 0.00 0.00 2.32
536 537 9.444600 AAATAGTGAGTACATACGGAACAAAAT 57.555 29.630 0.00 0.00 0.00 1.82
537 538 8.714179 CAAATAGTGAGTACATACGGAACAAAA 58.286 33.333 0.00 0.00 0.00 2.44
538 539 8.089597 TCAAATAGTGAGTACATACGGAACAAA 58.910 33.333 0.00 0.00 0.00 2.83
539 540 7.604549 TCAAATAGTGAGTACATACGGAACAA 58.395 34.615 0.00 0.00 0.00 2.83
540 541 7.160547 TCAAATAGTGAGTACATACGGAACA 57.839 36.000 0.00 0.00 0.00 3.18
541 542 8.378421 GTTTCAAATAGTGAGTACATACGGAAC 58.622 37.037 0.00 0.00 37.61 3.62
542 543 7.546667 GGTTTCAAATAGTGAGTACATACGGAA 59.453 37.037 0.00 0.00 37.61 4.30
543 544 7.037438 GGTTTCAAATAGTGAGTACATACGGA 58.963 38.462 0.00 0.00 37.61 4.69
544 545 7.039882 AGGTTTCAAATAGTGAGTACATACGG 58.960 38.462 0.00 0.00 37.61 4.02
545 546 8.475331 AAGGTTTCAAATAGTGAGTACATACG 57.525 34.615 0.00 0.00 37.61 3.06
552 553 9.847224 TCTTTCTAAAGGTTTCAAATAGTGAGT 57.153 29.630 2.77 0.00 35.68 3.41
554 555 9.621629 TGTCTTTCTAAAGGTTTCAAATAGTGA 57.378 29.630 2.77 0.00 36.67 3.41
570 571 9.947433 TCCGTTCCTAAATAATTGTCTTTCTAA 57.053 29.630 0.00 0.00 0.00 2.10
571 572 9.595823 CTCCGTTCCTAAATAATTGTCTTTCTA 57.404 33.333 0.00 0.00 0.00 2.10
572 573 7.553044 CCTCCGTTCCTAAATAATTGTCTTTCT 59.447 37.037 0.00 0.00 0.00 2.52
573 574 7.201705 CCCTCCGTTCCTAAATAATTGTCTTTC 60.202 40.741 0.00 0.00 0.00 2.62
574 575 6.602009 CCCTCCGTTCCTAAATAATTGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
575 576 6.069847 TCCCTCCGTTCCTAAATAATTGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
576 577 5.427481 TCCCTCCGTTCCTAAATAATTGTCT 59.573 40.000 0.00 0.00 0.00 3.41
577 578 5.677567 TCCCTCCGTTCCTAAATAATTGTC 58.322 41.667 0.00 0.00 0.00 3.18
578 579 5.191124 ACTCCCTCCGTTCCTAAATAATTGT 59.809 40.000 0.00 0.00 0.00 2.71
579 580 5.681639 ACTCCCTCCGTTCCTAAATAATTG 58.318 41.667 0.00 0.00 0.00 2.32
580 581 5.970501 ACTCCCTCCGTTCCTAAATAATT 57.029 39.130 0.00 0.00 0.00 1.40
581 582 6.379579 TCTACTCCCTCCGTTCCTAAATAAT 58.620 40.000 0.00 0.00 0.00 1.28
582 583 5.769835 TCTACTCCCTCCGTTCCTAAATAA 58.230 41.667 0.00 0.00 0.00 1.40
583 584 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
584 585 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
585 586 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
586 587 3.967467 ATCTACTCCCTCCGTTCCTAA 57.033 47.619 0.00 0.00 0.00 2.69
587 588 3.967467 AATCTACTCCCTCCGTTCCTA 57.033 47.619 0.00 0.00 0.00 2.94
588 589 2.850695 AATCTACTCCCTCCGTTCCT 57.149 50.000 0.00 0.00 0.00 3.36
589 590 4.344390 ACAATAATCTACTCCCTCCGTTCC 59.656 45.833 0.00 0.00 0.00 3.62
590 591 5.068723 TCACAATAATCTACTCCCTCCGTTC 59.931 44.000 0.00 0.00 0.00 3.95
591 592 4.960469 TCACAATAATCTACTCCCTCCGTT 59.040 41.667 0.00 0.00 0.00 4.44
592 593 4.543689 TCACAATAATCTACTCCCTCCGT 58.456 43.478 0.00 0.00 0.00 4.69
593 594 5.730296 ATCACAATAATCTACTCCCTCCG 57.270 43.478 0.00 0.00 0.00 4.63
594 595 8.043710 CCAATATCACAATAATCTACTCCCTCC 58.956 40.741 0.00 0.00 0.00 4.30
595 596 8.598041 ACCAATATCACAATAATCTACTCCCTC 58.402 37.037 0.00 0.00 0.00 4.30
596 597 8.511748 ACCAATATCACAATAATCTACTCCCT 57.488 34.615 0.00 0.00 0.00 4.20
597 598 9.574516 AAACCAATATCACAATAATCTACTCCC 57.425 33.333 0.00 0.00 0.00 4.30
693 1086 4.687215 TCAGCACTGACCAGGCGC 62.687 66.667 0.00 0.00 34.14 6.53
704 1097 0.958822 AATTTTGACCCGGTCAGCAC 59.041 50.000 19.59 0.00 43.69 4.40
715 1108 6.308766 GTGCACCATGATTGTCTAATTTTGAC 59.691 38.462 5.22 4.32 35.21 3.18
732 1125 2.878406 GCCGTATCAAATAGTGCACCAT 59.122 45.455 14.63 1.47 0.00 3.55
769 1162 4.520492 TGAGATTCCAAGTTTGAGGCTTTC 59.480 41.667 0.00 0.00 0.00 2.62
793 1186 2.353889 GTGAAGACCGACGACTAGCATA 59.646 50.000 0.00 0.00 0.00 3.14
848 1244 3.790089 AACTCCTCCTTTGGTGGTTAG 57.210 47.619 4.85 0.00 37.58 2.34
850 1246 3.010250 GGATAACTCCTCCTTTGGTGGTT 59.990 47.826 4.85 0.00 38.65 3.67
852 1248 3.283259 GGATAACTCCTCCTTTGGTGG 57.717 52.381 0.00 0.00 38.65 4.61
898 1306 4.920640 ACGATACATAGTGAGTGGGAAG 57.079 45.455 0.00 0.00 0.00 3.46
911 1321 7.652105 AGAAATGCAAGATTACGTACGATACAT 59.348 33.333 24.41 7.58 0.00 2.29
916 1326 6.715344 AAAGAAATGCAAGATTACGTACGA 57.285 33.333 24.41 0.00 0.00 3.43
926 1336 6.041865 TGGATGGAAAGAAAAGAAATGCAAGA 59.958 34.615 0.00 0.00 0.00 3.02
954 1366 3.244215 TGCAGATCGAGACTCTGGTTTTT 60.244 43.478 14.63 0.00 40.40 1.94
1233 1660 4.954118 TGGTCCTGGGTGGCGTCT 62.954 66.667 0.00 0.00 35.26 4.18
1909 2411 3.849951 GAATCGCAGCGAGGGGGA 61.850 66.667 24.08 0.00 39.91 4.81
2407 2910 2.171209 CTCGTCAGCACCCATCACCA 62.171 60.000 0.00 0.00 0.00 4.17
2419 2922 1.608717 CTCCTTCCCCACCTCGTCAG 61.609 65.000 0.00 0.00 0.00 3.51
2483 2989 2.935955 CCACAAGGTTGCGTCGTC 59.064 61.111 0.00 0.00 0.00 4.20
2496 3002 2.434185 GGCGAACGATCTGCCACA 60.434 61.111 18.50 0.00 41.70 4.17
2523 3029 7.094805 TGGTGCTTGTATATTCTTGAACAGAAC 60.095 37.037 0.00 0.00 44.70 3.01
2529 3035 4.634004 CGGTGGTGCTTGTATATTCTTGAA 59.366 41.667 0.00 0.00 0.00 2.69
2573 3079 0.663153 GATATCCTGTTTGCACGGCC 59.337 55.000 0.00 0.00 0.00 6.13
2576 3082 5.289193 CCAAAATTGATATCCTGTTTGCACG 59.711 40.000 12.97 0.00 0.00 5.34
2587 3093 8.682936 ACATAGACAGACCCAAAATTGATATC 57.317 34.615 0.00 0.00 0.00 1.63
2588 3094 8.274322 TGACATAGACAGACCCAAAATTGATAT 58.726 33.333 0.00 0.00 0.00 1.63
2589 3095 7.552687 GTGACATAGACAGACCCAAAATTGATA 59.447 37.037 0.00 0.00 0.00 2.15
2590 3096 6.375455 GTGACATAGACAGACCCAAAATTGAT 59.625 38.462 0.00 0.00 0.00 2.57
2591 3097 5.705441 GTGACATAGACAGACCCAAAATTGA 59.295 40.000 0.00 0.00 0.00 2.57
2592 3098 5.473162 TGTGACATAGACAGACCCAAAATTG 59.527 40.000 0.00 0.00 0.00 2.32
2593 3099 5.630121 TGTGACATAGACAGACCCAAAATT 58.370 37.500 0.00 0.00 0.00 1.82
2594 3100 5.241403 TGTGACATAGACAGACCCAAAAT 57.759 39.130 0.00 0.00 0.00 1.82
2595 3101 4.698201 TGTGACATAGACAGACCCAAAA 57.302 40.909 0.00 0.00 0.00 2.44
2596 3102 4.532126 AGATGTGACATAGACAGACCCAAA 59.468 41.667 0.00 0.00 0.00 3.28
2597 3103 4.096681 AGATGTGACATAGACAGACCCAA 58.903 43.478 0.00 0.00 0.00 4.12
2598 3104 3.713003 AGATGTGACATAGACAGACCCA 58.287 45.455 0.00 0.00 0.00 4.51
2628 3134 9.474313 AGAGGGAGTTAGATGTGAGATAATATC 57.526 37.037 0.00 0.00 0.00 1.63
2629 3135 9.474313 GAGAGGGAGTTAGATGTGAGATAATAT 57.526 37.037 0.00 0.00 0.00 1.28
2630 3136 8.448816 TGAGAGGGAGTTAGATGTGAGATAATA 58.551 37.037 0.00 0.00 0.00 0.98
2631 3137 7.232534 GTGAGAGGGAGTTAGATGTGAGATAAT 59.767 40.741 0.00 0.00 0.00 1.28
2632 3138 6.547880 GTGAGAGGGAGTTAGATGTGAGATAA 59.452 42.308 0.00 0.00 0.00 1.75
2633 3139 6.065374 GTGAGAGGGAGTTAGATGTGAGATA 58.935 44.000 0.00 0.00 0.00 1.98
2634 3140 4.892934 GTGAGAGGGAGTTAGATGTGAGAT 59.107 45.833 0.00 0.00 0.00 2.75
2635 3141 4.263949 TGTGAGAGGGAGTTAGATGTGAGA 60.264 45.833 0.00 0.00 0.00 3.27
2636 3142 4.019858 TGTGAGAGGGAGTTAGATGTGAG 58.980 47.826 0.00 0.00 0.00 3.51
2637 3143 4.047627 TGTGAGAGGGAGTTAGATGTGA 57.952 45.455 0.00 0.00 0.00 3.58
2638 3144 4.648762 AGATGTGAGAGGGAGTTAGATGTG 59.351 45.833 0.00 0.00 0.00 3.21
2639 3145 4.877773 AGATGTGAGAGGGAGTTAGATGT 58.122 43.478 0.00 0.00 0.00 3.06
2640 3146 6.968263 TTAGATGTGAGAGGGAGTTAGATG 57.032 41.667 0.00 0.00 0.00 2.90
2641 3147 7.234577 GGAATTAGATGTGAGAGGGAGTTAGAT 59.765 40.741 0.00 0.00 0.00 1.98
2642 3148 6.551601 GGAATTAGATGTGAGAGGGAGTTAGA 59.448 42.308 0.00 0.00 0.00 2.10
2643 3149 6.239458 GGGAATTAGATGTGAGAGGGAGTTAG 60.239 46.154 0.00 0.00 0.00 2.34
2644 3150 5.602978 GGGAATTAGATGTGAGAGGGAGTTA 59.397 44.000 0.00 0.00 0.00 2.24
2645 3151 4.410555 GGGAATTAGATGTGAGAGGGAGTT 59.589 45.833 0.00 0.00 0.00 3.01
2646 3152 3.970640 GGGAATTAGATGTGAGAGGGAGT 59.029 47.826 0.00 0.00 0.00 3.85
2647 3153 4.230455 AGGGAATTAGATGTGAGAGGGAG 58.770 47.826 0.00 0.00 0.00 4.30
2648 3154 4.227197 GAGGGAATTAGATGTGAGAGGGA 58.773 47.826 0.00 0.00 0.00 4.20
2649 3155 3.006323 CGAGGGAATTAGATGTGAGAGGG 59.994 52.174 0.00 0.00 0.00 4.30
2650 3156 3.553922 GCGAGGGAATTAGATGTGAGAGG 60.554 52.174 0.00 0.00 0.00 3.69
2651 3157 3.553922 GGCGAGGGAATTAGATGTGAGAG 60.554 52.174 0.00 0.00 0.00 3.20
2652 3158 2.365617 GGCGAGGGAATTAGATGTGAGA 59.634 50.000 0.00 0.00 0.00 3.27
2653 3159 2.366916 AGGCGAGGGAATTAGATGTGAG 59.633 50.000 0.00 0.00 0.00 3.51
2654 3160 2.398588 AGGCGAGGGAATTAGATGTGA 58.601 47.619 0.00 0.00 0.00 3.58
2655 3161 2.918712 AGGCGAGGGAATTAGATGTG 57.081 50.000 0.00 0.00 0.00 3.21
2656 3162 3.199946 TCAAAGGCGAGGGAATTAGATGT 59.800 43.478 0.00 0.00 0.00 3.06
2657 3163 3.808728 TCAAAGGCGAGGGAATTAGATG 58.191 45.455 0.00 0.00 0.00 2.90
2658 3164 4.713792 ATCAAAGGCGAGGGAATTAGAT 57.286 40.909 0.00 0.00 0.00 1.98
2659 3165 4.503714 AATCAAAGGCGAGGGAATTAGA 57.496 40.909 0.00 0.00 0.00 2.10
2660 3166 5.582689 AAAATCAAAGGCGAGGGAATTAG 57.417 39.130 0.00 0.00 0.00 1.73
2661 3167 5.993748 AAAAATCAAAGGCGAGGGAATTA 57.006 34.783 0.00 0.00 0.00 1.40
2662 3168 4.890158 AAAAATCAAAGGCGAGGGAATT 57.110 36.364 0.00 0.00 0.00 2.17
2663 3169 4.402474 CCTAAAAATCAAAGGCGAGGGAAT 59.598 41.667 0.00 0.00 0.00 3.01
2664 3170 3.761752 CCTAAAAATCAAAGGCGAGGGAA 59.238 43.478 0.00 0.00 0.00 3.97
2665 3171 3.352648 CCTAAAAATCAAAGGCGAGGGA 58.647 45.455 0.00 0.00 0.00 4.20
2666 3172 2.159240 GCCTAAAAATCAAAGGCGAGGG 60.159 50.000 0.00 0.00 45.82 4.30
2667 3173 3.150848 GCCTAAAAATCAAAGGCGAGG 57.849 47.619 0.00 0.00 45.82 4.63
2672 3178 9.358872 GAACTCTAAATGCCTAAAAATCAAAGG 57.641 33.333 0.00 0.00 0.00 3.11
2673 3179 9.912634 TGAACTCTAAATGCCTAAAAATCAAAG 57.087 29.630 0.00 0.00 0.00 2.77
2735 3245 8.797438 AGGAAGAGAAAAGTATGTTTCAAATCC 58.203 33.333 0.97 4.66 39.52 3.01
2737 3247 8.579863 CCAGGAAGAGAAAAGTATGTTTCAAAT 58.420 33.333 0.97 0.00 39.52 2.32
2782 3294 2.365293 TGCATGTGTAGTGTCTGAGTGT 59.635 45.455 0.00 0.00 0.00 3.55
2783 3295 2.991866 CTGCATGTGTAGTGTCTGAGTG 59.008 50.000 0.00 0.00 0.00 3.51
2784 3296 2.611473 GCTGCATGTGTAGTGTCTGAGT 60.611 50.000 0.00 0.00 0.00 3.41
2785 3297 1.998315 GCTGCATGTGTAGTGTCTGAG 59.002 52.381 0.00 0.00 0.00 3.35
2786 3298 1.669795 CGCTGCATGTGTAGTGTCTGA 60.670 52.381 0.00 0.00 34.31 3.27
2787 3299 0.717784 CGCTGCATGTGTAGTGTCTG 59.282 55.000 0.00 0.00 34.31 3.51
2788 3300 0.318441 ACGCTGCATGTGTAGTGTCT 59.682 50.000 10.81 0.00 45.89 3.41
2789 3301 2.827604 ACGCTGCATGTGTAGTGTC 58.172 52.632 10.81 0.00 45.89 3.67
2825 3337 2.034066 CGAAGCAAGCCCCTTGGA 59.966 61.111 7.05 0.00 41.31 3.53
3321 5225 1.079197 ATGTTCAGATGCGGCGTCA 60.079 52.632 23.07 7.70 0.00 4.35
3586 7574 2.047560 GGCCGCGGAGTAAACAGT 60.048 61.111 33.48 0.00 0.00 3.55
3591 8303 4.137872 CCTTCGGCCGCGGAGTAA 62.138 66.667 33.48 17.50 0.00 2.24


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

AutoCloner maintained by Alex Coulton.