Multiple sequence alignment - TraesCS4B01G365500

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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 TraesCS4B01G365500 chr4B 100.000 4540 0 0 904 5443 653422752 653418213 0.000000e+00 8384.0
1 TraesCS4B01G365500 chr4B 100.000 642 0 0 1 642 653423655 653423014 0.000000e+00 1186.0
2 TraesCS4B01G365500 chr5A 92.670 3588 166 48 964 4490 690944657 690948208 0.000000e+00 5079.0
3 TraesCS4B01G365500 chr5A 86.195 862 70 16 4492 5343 690948321 690949143 0.000000e+00 887.0
4 TraesCS4B01G365500 chr5A 78.924 446 65 12 2 439 6715260 6715684 5.370000e-70 276.0
5 TraesCS4B01G365500 chrUn 93.177 2990 154 27 926 3878 126944842 126941866 0.000000e+00 4346.0
6 TraesCS4B01G365500 chrUn 93.021 960 52 8 4492 5443 126941245 126940293 0.000000e+00 1387.0
7 TraesCS4B01G365500 chrUn 90.632 427 19 6 3919 4325 126941869 126941444 1.030000e-151 547.0
8 TraesCS4B01G365500 chrUn 77.542 472 82 20 18 477 385385231 385385690 4.180000e-66 263.0
9 TraesCS4B01G365500 chrUn 97.500 40 1 0 4451 4490 126941398 126941359 9.780000e-08 69.4
10 TraesCS4B01G365500 chrUn 93.182 44 3 0 4361 4404 126941443 126941400 1.270000e-06 65.8
11 TraesCS4B01G365500 chr1B 78.270 497 78 17 1 473 394913417 394913907 5.330000e-75 292.0
12 TraesCS4B01G365500 chr1B 78.311 438 82 6 1 431 375421419 375421850 2.500000e-68 270.0
13 TraesCS4B01G365500 chr1B 77.218 496 79 19 9 478 655256692 655257179 5.410000e-65 259.0
14 TraesCS4B01G365500 chr1B 79.501 361 60 10 84 435 535714834 535714479 1.510000e-60 244.0
15 TraesCS4B01G365500 chr6A 77.542 472 82 20 18 477 53065960 53066419 4.180000e-66 263.0
16 TraesCS4B01G365500 chr6A 77.331 472 83 20 18 477 53070136 53070595 1.950000e-64 257.0
17 TraesCS4B01G365500 chr4A 76.658 407 78 10 1 397 581272447 581272846 5.520000e-50 209.0
18 TraesCS4B01G365500 chr5B 75.839 447 86 14 2 438 390404398 390404832 1.990000e-49 207.0
19 TraesCS4B01G365500 chr5B 75.839 447 86 14 2 438 390525263 390525697 1.990000e-49 207.0
20 TraesCS4B01G365500 chr5B 81.423 253 29 12 24 264 472682742 472682496 2.000000e-44 191.0
21 TraesCS4B01G365500 chr7D 80.282 213 32 8 191 400 5833559 5833764 9.440000e-33 152.0
22 TraesCS4B01G365500 chr7D 79.275 193 32 4 137 325 423421069 423421257 1.590000e-25 128.0
23 TraesCS4B01G365500 chr3A 79.295 227 30 11 1 218 695397581 695397799 5.680000e-30 143.0
24 TraesCS4B01G365500 chr7A 74.725 273 45 15 222 473 507430041 507430310 3.470000e-17 100.0


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 TraesCS4B01G365500 chr4B 653418213 653423655 5442 True 4785.00 8384 100.0000 1 5443 2 chr4B.!!$R1 5442
1 TraesCS4B01G365500 chr5A 690944657 690949143 4486 False 2983.00 5079 89.4325 964 5343 2 chr5A.!!$F2 4379
2 TraesCS4B01G365500 chrUn 126940293 126944842 4549 True 1283.04 4346 93.5024 926 5443 5 chrUn.!!$R1 4517
3 TraesCS4B01G365500 chr6A 53065960 53070595 4635 False 260.00 263 77.4365 18 477 2 chr6A.!!$F1 459

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
532 543 0.039074 GCTATGTCGCGCCAGTAGAT 60.039 55.000 0.00 0.0 0.00 1.98 F
1746 1800 0.107410 TGTCCCTTGTTCTTGCACGT 60.107 50.000 0.00 0.0 0.00 4.49 F
2089 2143 1.073722 CCTGAAGCCAGCCTGTTGA 59.926 57.895 0.00 0.0 39.07 3.18 F
3315 5119 0.843309 TTCTGGCCAACTCCAACTCA 59.157 50.000 7.01 0.0 35.36 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 1929 0.104120 TCTCCATTACCATGTCGGCG 59.896 55.0 0.00 0.00 39.03 6.46 R
2664 4468 2.008242 AGGAGCTCTCAACAGACACT 57.992 50.0 14.64 0.00 0.00 3.55 R
3764 5568 1.647346 TTTATTCCTGTAGCACGGCG 58.353 50.0 4.80 4.80 0.00 6.46 R
5009 7750 0.178301 TGTGAAACCTGGTGCACGTA 59.822 50.0 21.02 1.11 34.36 3.57 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
120 124 8.455903 TGAAATCTCTTGAAAACATCTTCACT 57.544 30.769 0.00 0.00 35.07 3.41
121 125 8.906867 TGAAATCTCTTGAAAACATCTTCACTT 58.093 29.630 0.00 0.00 35.07 3.16
160 169 7.576861 AGAAAATCCAAAGACTTCGGTAAAA 57.423 32.000 0.00 0.00 0.00 1.52
185 194 4.724279 AAGGGTGTAACTGGACTTGAAT 57.276 40.909 0.00 0.00 36.74 2.57
187 196 5.422214 AGGGTGTAACTGGACTTGAATAG 57.578 43.478 0.00 0.00 36.74 1.73
190 199 4.491676 GTGTAACTGGACTTGAATAGCGA 58.508 43.478 0.00 0.00 0.00 4.93
197 206 4.323417 TGGACTTGAATAGCGATGTTGTT 58.677 39.130 0.00 0.00 0.00 2.83
201 210 6.092259 GGACTTGAATAGCGATGTTGTTACTT 59.908 38.462 0.00 0.00 0.00 2.24
204 213 8.995220 ACTTGAATAGCGATGTTGTTACTTTTA 58.005 29.630 0.00 0.00 0.00 1.52
206 215 7.745015 TGAATAGCGATGTTGTTACTTTTACC 58.255 34.615 0.00 0.00 0.00 2.85
207 216 7.604927 TGAATAGCGATGTTGTTACTTTTACCT 59.395 33.333 0.00 0.00 0.00 3.08
208 217 5.607119 AGCGATGTTGTTACTTTTACCTG 57.393 39.130 0.00 0.00 0.00 4.00
210 219 4.319911 GCGATGTTGTTACTTTTACCTGCA 60.320 41.667 0.00 0.00 0.00 4.41
216 227 5.899120 TGTTACTTTTACCTGCACAAACA 57.101 34.783 0.00 0.00 0.00 2.83
220 231 8.634444 TGTTACTTTTACCTGCACAAACATTAT 58.366 29.630 0.00 0.00 0.00 1.28
252 263 2.910688 TTGAAAGCTCCTTGAGTCGT 57.089 45.000 0.00 0.00 31.39 4.34
260 271 1.135915 CTCCTTGAGTCGTCCATCCAG 59.864 57.143 0.00 0.00 0.00 3.86
265 276 1.550524 TGAGTCGTCCATCCAGAAAGG 59.449 52.381 0.00 0.00 39.47 3.11
268 279 0.613260 TCGTCCATCCAGAAAGGTGG 59.387 55.000 0.00 0.00 38.91 4.61
283 294 2.359900 AGGTGGAAAGCATTGATCGAC 58.640 47.619 0.00 0.00 0.00 4.20
309 320 0.326618 ACTTGGACCGGGGATGATCT 60.327 55.000 6.32 0.00 0.00 2.75
312 323 1.152226 GGACCGGGGATGATCTCCT 60.152 63.158 10.10 0.00 44.28 3.69
314 325 1.551452 GACCGGGGATGATCTCCTAG 58.449 60.000 10.10 3.20 44.28 3.02
315 326 1.075698 GACCGGGGATGATCTCCTAGA 59.924 57.143 10.10 0.00 44.28 2.43
316 327 1.503784 ACCGGGGATGATCTCCTAGAA 59.496 52.381 10.10 0.00 44.28 2.10
318 329 3.177228 CCGGGGATGATCTCCTAGAATT 58.823 50.000 10.10 0.00 44.28 2.17
319 330 3.055530 CCGGGGATGATCTCCTAGAATTG 60.056 52.174 10.10 0.00 44.28 2.32
320 331 3.580458 CGGGGATGATCTCCTAGAATTGT 59.420 47.826 10.10 0.00 44.28 2.71
321 332 4.772624 CGGGGATGATCTCCTAGAATTGTA 59.227 45.833 10.10 0.00 44.28 2.41
322 333 5.105554 CGGGGATGATCTCCTAGAATTGTAG 60.106 48.000 10.10 2.62 44.28 2.74
323 334 5.188751 GGGGATGATCTCCTAGAATTGTAGG 59.811 48.000 20.25 20.25 44.28 3.18
324 335 5.337975 GGGATGATCTCCTAGAATTGTAGGC 60.338 48.000 21.24 9.73 44.28 3.93
326 337 3.574396 TGATCTCCTAGAATTGTAGGCCG 59.426 47.826 21.24 14.98 39.73 6.13
327 338 3.028094 TCTCCTAGAATTGTAGGCCGT 57.972 47.619 21.24 0.00 39.73 5.68
328 339 2.957006 TCTCCTAGAATTGTAGGCCGTC 59.043 50.000 21.24 0.00 39.73 4.79
329 340 1.679680 TCCTAGAATTGTAGGCCGTCG 59.320 52.381 21.24 0.19 39.73 5.12
330 341 1.269621 CCTAGAATTGTAGGCCGTCGG 60.270 57.143 15.21 6.99 33.33 4.79
336 347 1.694844 TTGTAGGCCGTCGGATCATA 58.305 50.000 17.49 0.00 0.00 2.15
341 352 3.526931 AGGCCGTCGGATCATAATATG 57.473 47.619 17.49 0.00 0.00 1.78
342 353 1.933853 GGCCGTCGGATCATAATATGC 59.066 52.381 17.49 0.00 0.00 3.14
351 362 5.187576 TCGGATCATAATATGCTCACCATGA 59.812 40.000 6.46 0.00 35.34 3.07
353 364 7.069826 TCGGATCATAATATGCTCACCATGATA 59.930 37.037 6.46 0.00 34.23 2.15
355 366 9.217278 GGATCATAATATGCTCACCATGATATC 57.783 37.037 6.46 0.00 34.23 1.63
356 367 9.999660 GATCATAATATGCTCACCATGATATCT 57.000 33.333 3.98 0.00 34.23 1.98
388 399 9.710900 AAATTTCAACTCCATAAGGAATCAAAC 57.289 29.630 0.00 0.00 45.19 2.93
395 406 6.015434 ACTCCATAAGGAATCAAACCAACAAC 60.015 38.462 0.00 0.00 45.19 3.32
399 410 7.661027 CCATAAGGAATCAAACCAACAACAAAT 59.339 33.333 0.00 0.00 36.89 2.32
401 412 5.988287 AGGAATCAAACCAACAACAAATGT 58.012 33.333 0.00 0.00 46.82 2.71
415 426 3.506810 ACAAATGTTTGACACACCAACG 58.493 40.909 12.09 0.00 38.61 4.10
420 431 4.080969 TGTTTGACACACCAACGTAAAC 57.919 40.909 0.00 0.00 0.00 2.01
430 441 4.929808 ACACCAACGTAAACTCATCAGATC 59.070 41.667 0.00 0.00 0.00 2.75
431 442 4.330074 CACCAACGTAAACTCATCAGATCC 59.670 45.833 0.00 0.00 0.00 3.36
432 443 4.020573 ACCAACGTAAACTCATCAGATCCA 60.021 41.667 0.00 0.00 0.00 3.41
433 444 4.935205 CCAACGTAAACTCATCAGATCCAA 59.065 41.667 0.00 0.00 0.00 3.53
434 445 5.586243 CCAACGTAAACTCATCAGATCCAAT 59.414 40.000 0.00 0.00 0.00 3.16
435 446 6.094048 CCAACGTAAACTCATCAGATCCAATT 59.906 38.462 0.00 0.00 0.00 2.32
436 447 7.279981 CCAACGTAAACTCATCAGATCCAATTA 59.720 37.037 0.00 0.00 0.00 1.40
437 448 8.664798 CAACGTAAACTCATCAGATCCAATTAA 58.335 33.333 0.00 0.00 0.00 1.40
439 450 9.226606 ACGTAAACTCATCAGATCCAATTAAAA 57.773 29.630 0.00 0.00 0.00 1.52
440 451 9.490663 CGTAAACTCATCAGATCCAATTAAAAC 57.509 33.333 0.00 0.00 0.00 2.43
444 455 7.978982 ACTCATCAGATCCAATTAAAACGAAG 58.021 34.615 0.00 0.00 0.00 3.79
473 484 2.859165 ACCTCATGACACCGTCAAAT 57.141 45.000 0.22 0.00 45.96 2.32
477 488 3.501828 CCTCATGACACCGTCAAATGAAA 59.498 43.478 0.22 0.00 45.96 2.69
478 489 4.023279 CCTCATGACACCGTCAAATGAAAA 60.023 41.667 0.22 0.00 45.96 2.29
501 512 7.432350 AAAAGTAGAACTCTTGCTCTGATTG 57.568 36.000 0.00 0.00 0.00 2.67
502 513 5.083533 AGTAGAACTCTTGCTCTGATTGG 57.916 43.478 0.00 0.00 0.00 3.16
503 514 2.709213 AGAACTCTTGCTCTGATTGGC 58.291 47.619 0.00 0.00 0.00 4.52
505 516 2.574006 ACTCTTGCTCTGATTGGCAA 57.426 45.000 0.68 0.68 44.64 4.52
506 517 2.867624 ACTCTTGCTCTGATTGGCAAA 58.132 42.857 3.01 0.00 45.80 3.68
507 518 3.428532 ACTCTTGCTCTGATTGGCAAAT 58.571 40.909 3.01 0.00 45.80 2.32
508 519 4.592942 ACTCTTGCTCTGATTGGCAAATA 58.407 39.130 3.01 0.00 45.80 1.40
510 521 4.592942 TCTTGCTCTGATTGGCAAATAGT 58.407 39.130 3.01 0.00 45.80 2.12
513 524 3.374988 TGCTCTGATTGGCAAATAGTTCG 59.625 43.478 3.01 1.24 35.40 3.95
514 525 3.790123 GCTCTGATTGGCAAATAGTTCGC 60.790 47.826 3.01 6.94 0.00 4.70
517 528 5.368145 TCTGATTGGCAAATAGTTCGCTAT 58.632 37.500 3.01 0.00 41.89 2.97
518 529 5.237127 TCTGATTGGCAAATAGTTCGCTATG 59.763 40.000 3.01 0.00 40.12 2.23
519 530 4.881273 TGATTGGCAAATAGTTCGCTATGT 59.119 37.500 3.01 0.00 40.12 2.29
520 531 4.875544 TTGGCAAATAGTTCGCTATGTC 57.124 40.909 0.00 0.00 40.12 3.06
521 532 2.863740 TGGCAAATAGTTCGCTATGTCG 59.136 45.455 0.00 0.00 40.12 4.35
530 541 3.923614 GCTATGTCGCGCCAGTAG 58.076 61.111 0.00 1.67 0.00 2.57
531 542 1.359117 GCTATGTCGCGCCAGTAGA 59.641 57.895 0.00 0.00 0.00 2.59
532 543 0.039074 GCTATGTCGCGCCAGTAGAT 60.039 55.000 0.00 0.00 0.00 1.98
533 544 1.691127 CTATGTCGCGCCAGTAGATG 58.309 55.000 0.00 0.00 0.00 2.90
534 545 1.001268 CTATGTCGCGCCAGTAGATGT 60.001 52.381 0.00 0.00 0.00 3.06
535 546 0.175760 ATGTCGCGCCAGTAGATGTT 59.824 50.000 0.00 0.00 0.00 2.71
537 548 1.202817 TGTCGCGCCAGTAGATGTTAA 59.797 47.619 0.00 0.00 0.00 2.01
538 549 1.852895 GTCGCGCCAGTAGATGTTAAG 59.147 52.381 0.00 0.00 0.00 1.85
539 550 1.202371 TCGCGCCAGTAGATGTTAAGG 60.202 52.381 0.00 0.00 0.00 2.69
540 551 1.202371 CGCGCCAGTAGATGTTAAGGA 60.202 52.381 0.00 0.00 0.00 3.36
542 553 2.608090 GCGCCAGTAGATGTTAAGGAAC 59.392 50.000 0.00 0.00 36.00 3.62
577 588 7.646548 ATTCTAGGCTGAATTTCCCTAAAAC 57.353 36.000 0.00 0.00 33.33 2.43
578 589 6.134535 TCTAGGCTGAATTTCCCTAAAACA 57.865 37.500 0.00 0.00 31.26 2.83
579 590 6.548321 TCTAGGCTGAATTTCCCTAAAACAA 58.452 36.000 0.00 0.00 31.26 2.83
580 591 7.007723 TCTAGGCTGAATTTCCCTAAAACAAA 58.992 34.615 0.00 0.00 31.26 2.83
581 592 6.493189 AGGCTGAATTTCCCTAAAACAAAA 57.507 33.333 0.00 0.00 0.00 2.44
582 593 6.894682 AGGCTGAATTTCCCTAAAACAAAAA 58.105 32.000 0.00 0.00 0.00 1.94
604 615 5.726980 AAAATTGTAGGCTGAAATGCTGA 57.273 34.783 0.00 0.00 0.00 4.26
605 616 5.927281 AAATTGTAGGCTGAAATGCTGAT 57.073 34.783 0.00 0.00 0.00 2.90
606 617 4.913335 ATTGTAGGCTGAAATGCTGATG 57.087 40.909 0.00 0.00 0.00 3.07
607 618 2.646930 TGTAGGCTGAAATGCTGATGG 58.353 47.619 0.00 0.00 0.00 3.51
608 619 1.336125 GTAGGCTGAAATGCTGATGGC 59.664 52.381 0.00 0.00 42.22 4.40
609 620 1.041447 AGGCTGAAATGCTGATGGCC 61.041 55.000 0.00 0.00 40.92 5.36
610 621 1.440476 GCTGAAATGCTGATGGCCC 59.560 57.895 0.00 0.00 40.92 5.80
611 622 1.324740 GCTGAAATGCTGATGGCCCA 61.325 55.000 0.00 0.00 40.92 5.36
612 623 1.187974 CTGAAATGCTGATGGCCCAA 58.812 50.000 0.00 0.00 40.92 4.12
613 624 0.896923 TGAAATGCTGATGGCCCAAC 59.103 50.000 0.00 0.00 40.92 3.77
614 625 0.896923 GAAATGCTGATGGCCCAACA 59.103 50.000 0.00 0.00 40.92 3.33
615 626 1.275856 GAAATGCTGATGGCCCAACAA 59.724 47.619 0.00 0.00 40.92 2.83
616 627 0.609662 AATGCTGATGGCCCAACAAC 59.390 50.000 0.00 0.00 40.92 3.32
617 628 1.259840 ATGCTGATGGCCCAACAACC 61.260 55.000 0.00 0.00 40.92 3.77
618 629 2.649129 GCTGATGGCCCAACAACCC 61.649 63.158 0.00 0.00 34.27 4.11
619 630 1.228831 CTGATGGCCCAACAACCCA 60.229 57.895 0.00 0.00 0.00 4.51
620 631 0.831288 CTGATGGCCCAACAACCCAA 60.831 55.000 0.00 0.00 31.43 4.12
621 632 0.831288 TGATGGCCCAACAACCCAAG 60.831 55.000 0.00 0.00 31.43 3.61
622 633 1.536174 ATGGCCCAACAACCCAAGG 60.536 57.895 0.00 0.00 31.43 3.61
623 634 3.625897 GGCCCAACAACCCAAGGC 61.626 66.667 0.00 0.00 43.09 4.35
624 635 3.625897 GCCCAACAACCCAAGGCC 61.626 66.667 0.00 0.00 37.66 5.19
625 636 2.201210 CCCAACAACCCAAGGCCT 59.799 61.111 0.00 0.00 0.00 5.19
626 637 2.209315 CCCAACAACCCAAGGCCTG 61.209 63.158 5.69 0.00 0.00 4.85
627 638 2.209315 CCAACAACCCAAGGCCTGG 61.209 63.158 5.69 6.85 45.97 4.45
628 639 2.524148 AACAACCCAAGGCCTGGC 60.524 61.111 5.69 11.05 44.90 4.85
629 640 3.387609 AACAACCCAAGGCCTGGCA 62.388 57.895 22.05 0.00 44.90 4.92
630 641 2.523902 CAACCCAAGGCCTGGCAA 60.524 61.111 22.05 0.00 44.90 4.52
631 642 2.139484 CAACCCAAGGCCTGGCAAA 61.139 57.895 22.05 0.00 44.90 3.68
632 643 1.838396 AACCCAAGGCCTGGCAAAG 60.838 57.895 22.05 8.72 44.90 2.77
633 644 2.203684 CCCAAGGCCTGGCAAAGT 60.204 61.111 22.05 0.00 44.90 2.66
634 645 2.576832 CCCAAGGCCTGGCAAAGTG 61.577 63.158 22.05 11.59 44.90 3.16
635 646 2.341176 CAAGGCCTGGCAAAGTGC 59.659 61.111 22.05 1.14 44.08 4.40
960 971 2.171940 CGCTGCACGCAGAGAAAC 59.828 61.111 22.81 3.52 46.30 2.78
1054 1069 2.844839 CGGGGATGGAGAGGGGAC 60.845 72.222 0.00 0.00 0.00 4.46
1075 1108 3.739613 GCCGGGGAGGGGATTGTT 61.740 66.667 2.18 0.00 41.48 2.83
1119 1153 2.704190 TGGACCTCCACTCTTCTTCT 57.296 50.000 0.00 0.00 42.01 2.85
1121 1155 2.900546 TGGACCTCCACTCTTCTTCTTC 59.099 50.000 0.00 0.00 42.01 2.87
1124 1158 4.773149 GGACCTCCACTCTTCTTCTTCTAA 59.227 45.833 0.00 0.00 35.64 2.10
1126 1160 4.218852 ACCTCCACTCTTCTTCTTCTAACG 59.781 45.833 0.00 0.00 0.00 3.18
1139 1173 3.820467 TCTTCTAACGAAACCGAGGTACA 59.180 43.478 0.00 0.00 0.00 2.90
1140 1174 4.460382 TCTTCTAACGAAACCGAGGTACAT 59.540 41.667 0.00 0.00 0.00 2.29
1141 1175 5.647658 TCTTCTAACGAAACCGAGGTACATA 59.352 40.000 0.00 0.00 0.00 2.29
1142 1176 5.235305 TCTAACGAAACCGAGGTACATAC 57.765 43.478 0.00 0.00 0.00 2.39
1193 1227 6.180472 CCCAATACAATCTTCAGTGTTACCT 58.820 40.000 0.00 0.00 0.00 3.08
1195 1229 7.106239 CCAATACAATCTTCAGTGTTACCTCT 58.894 38.462 0.00 0.00 0.00 3.69
1217 1254 2.420022 GCCGTTTGCTGAATCTGTACAT 59.580 45.455 0.00 0.00 36.87 2.29
1219 1256 3.181507 CCGTTTGCTGAATCTGTACATGG 60.182 47.826 0.00 0.00 0.00 3.66
1226 1263 1.532868 GAATCTGTACATGGCCGCATC 59.467 52.381 0.00 0.00 0.00 3.91
1227 1264 0.250467 ATCTGTACATGGCCGCATCC 60.250 55.000 0.00 0.00 0.00 3.51
1257 1305 3.127099 CCATCCATGGCAGATGCTT 57.873 52.632 6.96 0.00 41.75 3.91
1260 1308 0.182061 ATCCATGGCAGATGCTTCGT 59.818 50.000 6.96 0.00 41.70 3.85
1284 1332 4.006780 TGCAAGAATCTGTACTGCAAGA 57.993 40.909 5.00 0.00 37.43 3.02
1286 1334 3.181526 GCAAGAATCTGTACTGCAAGACG 60.182 47.826 0.22 0.00 37.43 4.18
1289 1337 0.608130 ATCTGTACTGCAAGACGGCA 59.392 50.000 0.00 0.00 42.53 5.69
1308 1356 1.331756 CATTCAGGCCGTGCTGTATTC 59.668 52.381 0.00 0.00 0.00 1.75
1311 1359 2.817834 GGCCGTGCTGTATTCGCA 60.818 61.111 0.00 0.00 34.52 5.10
1336 1384 2.431683 CCTGTCCACCACCCTGTG 59.568 66.667 0.00 0.00 35.98 3.66
1340 1388 1.275421 TGTCCACCACCCTGTGTTGA 61.275 55.000 0.00 0.00 34.35 3.18
1355 1403 1.202687 TGTTGACTCTCACAGCTTGGG 60.203 52.381 0.00 0.00 0.00 4.12
1356 1404 1.070758 GTTGACTCTCACAGCTTGGGA 59.929 52.381 0.00 0.00 31.97 4.37
1398 1449 2.688507 CGCACTGGTGACAAAGATACT 58.311 47.619 4.79 0.00 42.06 2.12
1406 1457 6.126863 TGGTGACAAAGATACTGGATTCTT 57.873 37.500 0.00 0.00 37.44 2.52
1412 1463 6.542821 ACAAAGATACTGGATTCTTGAACCA 58.457 36.000 2.84 0.00 32.65 3.67
1430 1481 4.685169 ACCAGAAATCGCATGTTGTTAG 57.315 40.909 0.00 0.00 0.00 2.34
1434 1485 2.806288 AATCGCATGTTGTTAGTCGC 57.194 45.000 0.00 0.00 0.00 5.19
1453 1507 2.669569 GCGCTTGCTTCTCCACCA 60.670 61.111 0.00 0.00 35.07 4.17
1486 1540 3.920093 CTGGTTCAAGCCCGGGACC 62.920 68.421 29.31 23.32 0.00 4.46
1513 1567 2.423185 CTGCTAGCATCGGAGATAGAGG 59.577 54.545 19.72 0.00 45.12 3.69
1581 1635 1.003839 GCACCTTCACATGGACGGA 60.004 57.895 11.88 0.00 37.09 4.69
1665 1719 2.735134 CAGGCTTAACCAGTCGTACAAC 59.265 50.000 0.00 0.00 43.14 3.32
1676 1730 2.034939 AGTCGTACAACGTGGTTGATCA 59.965 45.455 14.79 0.00 45.28 2.92
1678 1732 2.128821 CGTACAACGTGGTTGATCACA 58.871 47.619 14.79 0.00 45.28 3.58
1685 1739 2.294479 GTGGTTGATCACACGTTTCG 57.706 50.000 0.00 0.00 37.57 3.46
1686 1740 1.070175 GTGGTTGATCACACGTTTCGG 60.070 52.381 0.00 0.00 37.57 4.30
1696 1750 1.084370 CACGTTTCGGGAGAGGCATC 61.084 60.000 0.00 0.00 41.75 3.91
1735 1789 2.945890 GCCCTGATTTACCTGTCCCTTG 60.946 54.545 0.00 0.00 0.00 3.61
1746 1800 0.107410 TGTCCCTTGTTCTTGCACGT 60.107 50.000 0.00 0.00 0.00 4.49
1803 1857 1.446907 AGCTGGTGAAGATTGAAGCG 58.553 50.000 0.00 0.00 35.82 4.68
1809 1863 1.659098 GTGAAGATTGAAGCGTACCCG 59.341 52.381 0.00 0.00 37.07 5.28
1875 1929 2.281276 ACCGGTTCGTTCCTTGCC 60.281 61.111 0.00 0.00 0.00 4.52
1970 2024 1.133790 GTTGCTAGCAATGAAGCCCAG 59.866 52.381 31.46 0.00 37.97 4.45
1985 2039 4.112634 AGCCCAGTTCATTTACCTTCAA 57.887 40.909 0.00 0.00 0.00 2.69
2089 2143 1.073722 CCTGAAGCCAGCCTGTTGA 59.926 57.895 0.00 0.00 39.07 3.18
2094 2148 1.615392 GAAGCCAGCCTGTTGATTGTT 59.385 47.619 0.00 0.00 0.00 2.83
2157 2211 3.668447 TCAGAAGTTGAAGAGGCATGTC 58.332 45.455 0.00 0.00 31.34 3.06
2408 3692 3.081804 GTTCCCCAGATAAACCTGTGTG 58.918 50.000 0.00 0.00 32.43 3.82
2502 3786 5.277058 GGCGAGAGAATTACACAAGCTATTG 60.277 44.000 0.00 0.00 42.46 1.90
2589 4393 7.014230 ACTGAAACAATGTATGCCAAACTAGTT 59.986 33.333 1.12 1.12 0.00 2.24
2664 4468 1.888512 GCAAGCAAAGAGGATTCACCA 59.111 47.619 0.00 0.00 42.04 4.17
2927 4731 2.036958 TTGATACAATCCAGGGCACG 57.963 50.000 0.00 0.00 0.00 5.34
2946 4750 2.158871 ACGTCACAATAACACCACAGGT 60.159 45.455 0.00 0.00 35.62 4.00
2995 4799 8.849168 TGAAGAGCTCAAACATTCAAAAATCTA 58.151 29.630 17.77 0.00 0.00 1.98
3020 4824 3.944087 ACAGGGAGTTTGAGATGTTAGC 58.056 45.455 0.00 0.00 0.00 3.09
3315 5119 0.843309 TTCTGGCCAACTCCAACTCA 59.157 50.000 7.01 0.00 35.36 3.41
3432 5236 6.312918 TGGAAAAGTGCGAGATGTTTATAGAC 59.687 38.462 0.00 0.00 0.00 2.59
3540 5344 3.118847 TGATAAGGAGAGAAGCAGCACTG 60.119 47.826 0.00 0.00 0.00 3.66
3575 5379 2.562298 GGATTGGGTTGACATGAAAGCA 59.438 45.455 0.00 0.00 0.00 3.91
3577 5381 4.322953 GGATTGGGTTGACATGAAAGCAAT 60.323 41.667 0.00 6.19 0.00 3.56
3579 5383 5.798125 TTGGGTTGACATGAAAGCAATAA 57.202 34.783 0.00 0.00 0.00 1.40
3690 5494 1.333177 CTAGTTCCCTCCCCATCTCG 58.667 60.000 0.00 0.00 0.00 4.04
3752 5556 5.078949 TGAGGATGATGATTGTGGTTTGTT 58.921 37.500 0.00 0.00 0.00 2.83
3847 5651 0.673437 CCAATGCCGTCCAGTTTTGT 59.327 50.000 0.00 0.00 0.00 2.83
3900 5704 2.749621 GCCATTTGTTCTAGTGGACCTG 59.250 50.000 0.00 0.00 33.53 4.00
3901 5705 3.559171 GCCATTTGTTCTAGTGGACCTGA 60.559 47.826 0.00 0.00 33.53 3.86
3902 5706 4.256920 CCATTTGTTCTAGTGGACCTGAG 58.743 47.826 0.00 0.00 33.53 3.35
3904 5708 1.267121 TGTTCTAGTGGACCTGAGCC 58.733 55.000 0.00 0.00 0.00 4.70
3905 5709 1.267121 GTTCTAGTGGACCTGAGCCA 58.733 55.000 0.00 0.00 0.00 4.75
3906 5710 1.834263 GTTCTAGTGGACCTGAGCCAT 59.166 52.381 0.00 0.00 37.81 4.40
3907 5711 3.031736 GTTCTAGTGGACCTGAGCCATA 58.968 50.000 0.00 0.00 37.81 2.74
3908 5712 3.619900 TCTAGTGGACCTGAGCCATAT 57.380 47.619 0.00 0.00 37.81 1.78
3956 5761 5.304778 TGTACATGAACATACAACAGCAGT 58.695 37.500 0.00 0.00 0.00 4.40
3959 5764 1.879380 TGAACATACAACAGCAGTGGC 59.121 47.619 0.00 0.00 41.61 5.01
3976 5781 4.018490 AGTGGCAAATCTGTATGCAATGA 58.982 39.130 0.00 0.00 44.32 2.57
3988 5793 4.395854 TGTATGCAATGATGTCCAGTGTTC 59.604 41.667 0.00 0.00 42.40 3.18
4157 5963 2.143122 TGTCAGCAACGGATTTGTCTC 58.857 47.619 0.00 0.00 37.54 3.36
4277 6101 8.761575 ACAATTTGTTCTTATGTAATTGGCAG 57.238 30.769 0.00 0.00 39.37 4.85
4357 6196 9.920946 ATGGTTTCAGATTTACCAGTATTATGT 57.079 29.630 0.00 0.00 44.53 2.29
4490 6329 5.412594 GCAACTGAACCAAATATCTCAGACA 59.587 40.000 5.01 0.00 38.91 3.41
4532 6483 5.621197 TGAGATCGTGTTTTAAACCATGG 57.379 39.130 11.19 11.19 0.00 3.66
4604 6555 3.811722 TGTTTGCGTCTCATTGATGAC 57.188 42.857 6.32 6.32 33.63 3.06
4615 6566 7.352719 GTCTCATTGATGACGATTATAACCC 57.647 40.000 0.00 0.00 32.50 4.11
4616 6567 7.155328 GTCTCATTGATGACGATTATAACCCT 58.845 38.462 0.00 0.00 32.50 4.34
4617 6568 8.304596 GTCTCATTGATGACGATTATAACCCTA 58.695 37.037 0.00 0.00 32.50 3.53
4647 6598 7.452880 TTGATTTAACAGATCTCACCCTTTG 57.547 36.000 0.00 0.00 0.00 2.77
4660 7395 7.510549 TCTCACCCTTTGTTCATAAGAAAAG 57.489 36.000 0.00 0.00 35.08 2.27
4675 7410 7.604164 TCATAAGAAAAGAACCTAGCTCACTTG 59.396 37.037 0.00 0.00 0.00 3.16
4781 7518 7.865889 GGACATGTACAAATCATACGAGTCATA 59.134 37.037 2.19 0.00 33.79 2.15
4783 7520 7.382488 ACATGTACAAATCATACGAGTCATAGC 59.618 37.037 0.00 0.00 0.00 2.97
4784 7521 6.801575 TGTACAAATCATACGAGTCATAGCA 58.198 36.000 0.00 0.00 0.00 3.49
4816 7556 5.050490 AGTATACAAGCAATCACGACATCC 58.950 41.667 5.50 0.00 0.00 3.51
4900 7640 1.339438 GCTGCAGAAGGGAGTTGATGA 60.339 52.381 20.43 0.00 37.27 2.92
4982 7723 3.648339 AACTGTGCAACTTGCCTATTG 57.352 42.857 11.29 0.55 44.23 1.90
4988 7729 2.621055 TGCAACTTGCCTATTGTTTCGT 59.379 40.909 11.29 0.00 44.23 3.85
4989 7730 2.979813 GCAACTTGCCTATTGTTTCGTG 59.020 45.455 1.95 0.00 37.42 4.35
5062 7803 5.292101 GGAATCTTGACGAGGTAAACAGATG 59.708 44.000 0.00 0.00 0.00 2.90
5087 7828 0.798776 CTTACCTGCTTGCTGGTTCG 59.201 55.000 24.90 14.53 37.74 3.95
5103 7844 1.331756 GTTCGGTGCATCATCATCCAC 59.668 52.381 0.00 0.00 0.00 4.02
5165 7906 9.633962 ATGTTTACATCACATCAGAGCCACTGA 62.634 40.741 12.46 12.46 45.14 3.41
5263 8006 4.443457 CCCCTCACTGTTGGTGTGATATAG 60.443 50.000 0.00 0.00 45.50 1.31
5287 8032 5.762711 GGAGAAGGATGCTTCTTATCTTTCC 59.237 44.000 27.67 18.97 43.03 3.13
5375 8120 5.939457 GTGCTTACACTCCATTTAGTTTCC 58.061 41.667 0.00 0.00 43.85 3.13
5386 8131 5.774690 TCCATTTAGTTTCCAACATTCTGCT 59.225 36.000 0.00 0.00 0.00 4.24
5435 8180 8.225603 TCCATTCTTTTGATATCTGGTAAAGC 57.774 34.615 3.98 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 9.741647 AAAGTGAAGATGTTTTCAAGAGATTTC 57.258 29.630 0.00 0.00 38.69 2.17
128 132 7.815068 CGAAGTCTTTGGATTTTCTAGAAGAGA 59.185 37.037 5.12 0.00 0.00 3.10
133 137 6.110411 ACCGAAGTCTTTGGATTTTCTAGA 57.890 37.500 23.64 0.00 37.65 2.43
136 140 7.576861 TTTTACCGAAGTCTTTGGATTTTCT 57.423 32.000 23.64 4.50 37.65 2.52
163 172 4.513406 TTCAAGTCCAGTTACACCCTTT 57.487 40.909 0.00 0.00 0.00 3.11
164 173 4.724279 ATTCAAGTCCAGTTACACCCTT 57.276 40.909 0.00 0.00 0.00 3.95
165 174 4.323562 GCTATTCAAGTCCAGTTACACCCT 60.324 45.833 0.00 0.00 0.00 4.34
166 175 3.939592 GCTATTCAAGTCCAGTTACACCC 59.060 47.826 0.00 0.00 0.00 4.61
168 177 4.491676 TCGCTATTCAAGTCCAGTTACAC 58.508 43.478 0.00 0.00 0.00 2.90
171 180 5.339008 ACATCGCTATTCAAGTCCAGTTA 57.661 39.130 0.00 0.00 0.00 2.24
174 183 3.935203 ACAACATCGCTATTCAAGTCCAG 59.065 43.478 0.00 0.00 0.00 3.86
181 190 7.604927 AGGTAAAAGTAACAACATCGCTATTCA 59.395 33.333 0.00 0.00 0.00 2.57
185 194 5.121142 GCAGGTAAAAGTAACAACATCGCTA 59.879 40.000 0.00 0.00 0.00 4.26
187 196 4.156182 GCAGGTAAAAGTAACAACATCGC 58.844 43.478 0.00 0.00 0.00 4.58
190 199 6.458232 TTGTGCAGGTAAAAGTAACAACAT 57.542 33.333 0.00 0.00 0.00 2.71
197 206 9.727859 TCTATAATGTTTGTGCAGGTAAAAGTA 57.272 29.630 0.00 0.00 0.00 2.24
204 213 8.978874 TCATTATCTATAATGTTTGTGCAGGT 57.021 30.769 17.86 0.00 46.04 4.00
221 232 9.028284 TCAAGGAGCTTTCAAAATTCATTATCT 57.972 29.630 0.00 0.00 0.00 1.98
222 233 9.298774 CTCAAGGAGCTTTCAAAATTCATTATC 57.701 33.333 0.00 0.00 0.00 1.75
227 238 5.277974 CGACTCAAGGAGCTTTCAAAATTCA 60.278 40.000 0.00 0.00 32.04 2.57
229 240 4.580580 ACGACTCAAGGAGCTTTCAAAATT 59.419 37.500 0.00 0.00 32.04 1.82
230 241 4.137543 ACGACTCAAGGAGCTTTCAAAAT 58.862 39.130 0.00 0.00 32.04 1.82
235 246 1.000955 TGGACGACTCAAGGAGCTTTC 59.999 52.381 0.00 0.00 32.04 2.62
241 252 1.186200 CTGGATGGACGACTCAAGGA 58.814 55.000 0.00 0.00 0.00 3.36
252 263 2.555227 GCTTTCCACCTTTCTGGATGGA 60.555 50.000 0.00 0.00 40.18 3.41
260 271 3.440173 TCGATCAATGCTTTCCACCTTTC 59.560 43.478 0.00 0.00 0.00 2.62
265 276 1.999735 TCGTCGATCAATGCTTTCCAC 59.000 47.619 0.00 0.00 0.00 4.02
268 279 2.092211 ACGTTCGTCGATCAATGCTTTC 59.908 45.455 0.00 0.00 42.86 2.62
269 280 2.066262 ACGTTCGTCGATCAATGCTTT 58.934 42.857 0.00 0.00 42.86 3.51
274 285 3.119743 TCCAAGTACGTTCGTCGATCAAT 60.120 43.478 0.00 0.00 42.86 2.57
283 294 1.444895 CCCGGTCCAAGTACGTTCG 60.445 63.158 0.00 0.00 0.00 3.95
309 320 1.679680 CGACGGCCTACAATTCTAGGA 59.320 52.381 10.72 0.00 36.10 2.94
312 323 1.766494 TCCGACGGCCTACAATTCTA 58.234 50.000 9.66 0.00 0.00 2.10
314 325 1.202486 TGATCCGACGGCCTACAATTC 60.202 52.381 9.66 0.00 0.00 2.17
315 326 0.828022 TGATCCGACGGCCTACAATT 59.172 50.000 9.66 0.00 0.00 2.32
316 327 1.048601 ATGATCCGACGGCCTACAAT 58.951 50.000 9.66 0.00 0.00 2.71
318 329 1.694844 TTATGATCCGACGGCCTACA 58.305 50.000 9.66 6.79 0.00 2.74
319 330 4.360563 CATATTATGATCCGACGGCCTAC 58.639 47.826 9.66 0.83 0.00 3.18
320 331 3.181479 GCATATTATGATCCGACGGCCTA 60.181 47.826 9.66 0.00 0.00 3.93
321 332 2.418746 GCATATTATGATCCGACGGCCT 60.419 50.000 9.66 0.00 0.00 5.19
322 333 1.933853 GCATATTATGATCCGACGGCC 59.066 52.381 9.66 3.97 0.00 6.13
323 334 2.860735 GAGCATATTATGATCCGACGGC 59.139 50.000 9.66 0.00 39.67 5.68
324 335 3.859961 GTGAGCATATTATGATCCGACGG 59.140 47.826 16.97 7.84 44.67 4.79
326 337 4.820897 TGGTGAGCATATTATGATCCGAC 58.179 43.478 16.97 10.47 44.67 4.79
327 338 5.187576 TCATGGTGAGCATATTATGATCCGA 59.812 40.000 16.97 8.03 44.67 4.55
328 339 5.422145 TCATGGTGAGCATATTATGATCCG 58.578 41.667 16.97 3.73 44.67 4.18
329 340 9.217278 GATATCATGGTGAGCATATTATGATCC 57.783 37.037 16.97 9.64 44.67 3.36
330 341 9.999660 AGATATCATGGTGAGCATATTATGATC 57.000 33.333 13.71 13.71 45.45 2.92
359 370 9.927668 TGATTCCTTATGGAGTTGAAATTTTTC 57.072 29.630 0.00 0.00 44.24 2.29
363 374 8.314021 GGTTTGATTCCTTATGGAGTTGAAATT 58.686 33.333 0.00 0.00 44.24 1.82
370 381 5.640147 TGTTGGTTTGATTCCTTATGGAGT 58.360 37.500 0.00 0.00 44.24 3.85
372 383 5.835819 TGTTGTTGGTTTGATTCCTTATGGA 59.164 36.000 0.00 0.00 41.36 3.41
376 387 7.560368 ACATTTGTTGTTGGTTTGATTCCTTA 58.440 30.769 0.00 0.00 33.74 2.69
379 390 6.676237 AACATTTGTTGTTGGTTTGATTCC 57.324 33.333 0.00 0.00 46.80 3.01
395 406 3.506810 ACGTTGGTGTGTCAAACATTTG 58.493 40.909 0.00 0.00 41.97 2.32
399 410 3.752222 AGTTTACGTTGGTGTGTCAAACA 59.248 39.130 0.00 0.00 36.04 2.83
401 412 4.001652 TGAGTTTACGTTGGTGTGTCAAA 58.998 39.130 0.00 0.00 0.00 2.69
407 418 4.330944 TCTGATGAGTTTACGTTGGTGT 57.669 40.909 0.00 0.00 0.00 4.16
410 421 4.503910 TGGATCTGATGAGTTTACGTTGG 58.496 43.478 0.00 0.00 0.00 3.77
415 426 9.490663 CGTTTTAATTGGATCTGATGAGTTTAC 57.509 33.333 0.00 0.00 0.00 2.01
420 431 8.201554 TCTTCGTTTTAATTGGATCTGATGAG 57.798 34.615 0.00 0.00 0.00 2.90
430 441 8.228464 GGTTAGAGAGTTCTTCGTTTTAATTGG 58.772 37.037 0.00 0.00 34.79 3.16
431 442 8.989980 AGGTTAGAGAGTTCTTCGTTTTAATTG 58.010 33.333 0.00 0.00 34.79 2.32
432 443 9.205719 GAGGTTAGAGAGTTCTTCGTTTTAATT 57.794 33.333 0.00 0.00 34.79 1.40
433 444 8.365647 TGAGGTTAGAGAGTTCTTCGTTTTAAT 58.634 33.333 0.00 0.00 34.79 1.40
434 445 7.719483 TGAGGTTAGAGAGTTCTTCGTTTTAA 58.281 34.615 0.00 0.00 34.79 1.52
435 446 7.281040 TGAGGTTAGAGAGTTCTTCGTTTTA 57.719 36.000 0.00 0.00 34.79 1.52
436 447 6.158023 TGAGGTTAGAGAGTTCTTCGTTTT 57.842 37.500 0.00 0.00 34.79 2.43
437 448 5.786264 TGAGGTTAGAGAGTTCTTCGTTT 57.214 39.130 0.00 0.00 34.79 3.60
439 450 5.010933 TCATGAGGTTAGAGAGTTCTTCGT 58.989 41.667 0.00 0.00 34.79 3.85
440 451 5.106118 TGTCATGAGGTTAGAGAGTTCTTCG 60.106 44.000 0.00 0.00 34.79 3.79
444 455 4.675671 CGGTGTCATGAGGTTAGAGAGTTC 60.676 50.000 0.00 0.00 0.00 3.01
477 488 6.429385 CCAATCAGAGCAAGAGTTCTACTTTT 59.571 38.462 0.00 0.00 33.15 2.27
478 489 5.936956 CCAATCAGAGCAAGAGTTCTACTTT 59.063 40.000 0.00 0.00 33.15 2.66
480 491 4.622695 GCCAATCAGAGCAAGAGTTCTACT 60.623 45.833 0.00 0.00 33.15 2.57
481 492 3.620821 GCCAATCAGAGCAAGAGTTCTAC 59.379 47.826 0.00 0.00 33.15 2.59
482 493 3.261643 TGCCAATCAGAGCAAGAGTTCTA 59.738 43.478 0.00 0.00 35.69 2.10
483 494 2.039480 TGCCAATCAGAGCAAGAGTTCT 59.961 45.455 0.00 0.00 35.69 3.01
484 495 2.430465 TGCCAATCAGAGCAAGAGTTC 58.570 47.619 0.00 0.00 35.69 3.01
490 501 4.142622 CGAACTATTTGCCAATCAGAGCAA 60.143 41.667 0.00 0.00 46.74 3.91
492 503 3.790123 GCGAACTATTTGCCAATCAGAGC 60.790 47.826 0.00 0.00 33.83 4.09
496 507 4.881273 ACATAGCGAACTATTTGCCAATCA 59.119 37.500 0.00 0.00 41.10 2.57
497 508 5.424121 ACATAGCGAACTATTTGCCAATC 57.576 39.130 0.00 0.00 41.10 2.67
499 510 3.308595 CGACATAGCGAACTATTTGCCAA 59.691 43.478 0.00 0.00 41.10 4.52
500 511 2.863740 CGACATAGCGAACTATTTGCCA 59.136 45.455 0.00 0.00 41.10 4.92
501 512 2.348591 GCGACATAGCGAACTATTTGCC 60.349 50.000 0.00 0.00 41.10 4.52
502 513 2.892613 GCGACATAGCGAACTATTTGC 58.107 47.619 0.00 0.00 36.96 3.68
513 524 0.039074 ATCTACTGGCGCGACATAGC 60.039 55.000 18.76 0.00 0.00 2.97
514 525 1.001268 ACATCTACTGGCGCGACATAG 60.001 52.381 18.76 19.13 0.00 2.23
517 528 0.812549 TAACATCTACTGGCGCGACA 59.187 50.000 17.01 17.01 0.00 4.35
518 529 1.852895 CTTAACATCTACTGGCGCGAC 59.147 52.381 12.10 8.22 0.00 5.19
519 530 1.202371 CCTTAACATCTACTGGCGCGA 60.202 52.381 12.10 0.00 0.00 5.87
520 531 1.202371 TCCTTAACATCTACTGGCGCG 60.202 52.381 0.00 0.00 0.00 6.86
521 532 2.596904 TCCTTAACATCTACTGGCGC 57.403 50.000 0.00 0.00 0.00 6.53
523 534 6.569179 TTTTGTTCCTTAACATCTACTGGC 57.431 37.500 0.00 0.00 44.85 4.85
554 565 6.548321 TGTTTTAGGGAAATTCAGCCTAGAA 58.452 36.000 0.00 0.00 0.00 2.10
558 569 6.493189 TTTTGTTTTAGGGAAATTCAGCCT 57.507 33.333 0.00 0.00 0.00 4.58
581 592 6.100404 TCAGCATTTCAGCCTACAATTTTT 57.900 33.333 0.00 0.00 34.23 1.94
582 593 5.726980 TCAGCATTTCAGCCTACAATTTT 57.273 34.783 0.00 0.00 34.23 1.82
583 594 5.394883 CCATCAGCATTTCAGCCTACAATTT 60.395 40.000 0.00 0.00 34.23 1.82
584 595 4.098960 CCATCAGCATTTCAGCCTACAATT 59.901 41.667 0.00 0.00 34.23 2.32
585 596 3.635373 CCATCAGCATTTCAGCCTACAAT 59.365 43.478 0.00 0.00 34.23 2.71
586 597 3.018856 CCATCAGCATTTCAGCCTACAA 58.981 45.455 0.00 0.00 34.23 2.41
587 598 2.646930 CCATCAGCATTTCAGCCTACA 58.353 47.619 0.00 0.00 34.23 2.74
588 599 1.336125 GCCATCAGCATTTCAGCCTAC 59.664 52.381 0.00 0.00 42.97 3.18
589 600 1.683943 GCCATCAGCATTTCAGCCTA 58.316 50.000 0.00 0.00 42.97 3.93
590 601 1.041447 GGCCATCAGCATTTCAGCCT 61.041 55.000 0.00 0.00 46.50 4.58
591 602 1.440476 GGCCATCAGCATTTCAGCC 59.560 57.895 0.00 0.00 46.50 4.85
592 603 1.324740 TGGGCCATCAGCATTTCAGC 61.325 55.000 0.00 0.00 46.50 4.26
593 604 1.134907 GTTGGGCCATCAGCATTTCAG 60.135 52.381 7.26 0.00 46.50 3.02
594 605 0.896923 GTTGGGCCATCAGCATTTCA 59.103 50.000 7.26 0.00 46.50 2.69
595 606 0.896923 TGTTGGGCCATCAGCATTTC 59.103 50.000 13.23 0.00 46.50 2.17
596 607 1.002315 GTTGTTGGGCCATCAGCATTT 59.998 47.619 22.02 0.00 46.50 2.32
597 608 0.609662 GTTGTTGGGCCATCAGCATT 59.390 50.000 22.02 0.00 46.50 3.56
598 609 1.259840 GGTTGTTGGGCCATCAGCAT 61.260 55.000 26.19 0.00 46.50 3.79
599 610 1.907807 GGTTGTTGGGCCATCAGCA 60.908 57.895 26.19 13.32 46.50 4.41
600 611 2.649129 GGGTTGTTGGGCCATCAGC 61.649 63.158 19.66 19.66 42.60 4.26
601 612 0.831288 TTGGGTTGTTGGGCCATCAG 60.831 55.000 16.33 0.00 0.00 2.90
602 613 0.831288 CTTGGGTTGTTGGGCCATCA 60.831 55.000 13.23 13.23 0.00 3.07
603 614 1.543944 CCTTGGGTTGTTGGGCCATC 61.544 60.000 7.26 7.51 0.00 3.51
604 615 1.536174 CCTTGGGTTGTTGGGCCAT 60.536 57.895 7.26 0.00 0.00 4.40
605 616 2.123077 CCTTGGGTTGTTGGGCCA 60.123 61.111 0.00 0.00 0.00 5.36
606 617 3.625897 GCCTTGGGTTGTTGGGCC 61.626 66.667 0.00 0.00 37.12 5.80
607 618 3.625897 GGCCTTGGGTTGTTGGGC 61.626 66.667 0.00 0.00 41.80 5.36
608 619 2.201210 AGGCCTTGGGTTGTTGGG 59.799 61.111 0.00 0.00 0.00 4.12
609 620 2.209315 CCAGGCCTTGGGTTGTTGG 61.209 63.158 0.00 0.00 43.75 3.77
610 621 3.458653 CCAGGCCTTGGGTTGTTG 58.541 61.111 0.00 0.00 43.75 3.33
618 629 2.341176 GCACTTTGCCAGGCCTTG 59.659 61.111 9.64 0.00 37.42 3.61
908 919 4.832608 GGGTAGGTTGAGCGGCGG 62.833 72.222 9.78 0.00 0.00 6.13
909 920 4.832608 GGGGTAGGTTGAGCGGCG 62.833 72.222 0.51 0.51 0.00 6.46
910 921 4.484872 GGGGGTAGGTTGAGCGGC 62.485 72.222 0.00 0.00 0.00 6.53
1001 1012 1.508545 CAGTCGCGACAGAGATGGT 59.491 57.895 37.85 14.63 0.00 3.55
1039 1054 3.551407 GCGTCCCCTCTCCATCCC 61.551 72.222 0.00 0.00 0.00 3.85
1073 1106 3.638971 GGAGCGCCGCCTAATAAC 58.361 61.111 4.98 0.00 0.00 1.89
1102 1135 5.620429 CGTTAGAAGAAGAAGAGTGGAGGTC 60.620 48.000 0.00 0.00 0.00 3.85
1103 1136 4.218852 CGTTAGAAGAAGAAGAGTGGAGGT 59.781 45.833 0.00 0.00 0.00 3.85
1104 1137 4.459685 TCGTTAGAAGAAGAAGAGTGGAGG 59.540 45.833 0.00 0.00 0.00 4.30
1106 1139 6.214399 GTTTCGTTAGAAGAAGAAGAGTGGA 58.786 40.000 0.00 0.00 37.70 4.02
1107 1140 5.405873 GGTTTCGTTAGAAGAAGAAGAGTGG 59.594 44.000 0.00 0.00 37.70 4.00
1109 1142 5.009410 TCGGTTTCGTTAGAAGAAGAAGAGT 59.991 40.000 0.00 0.00 37.70 3.24
1110 1143 5.458891 TCGGTTTCGTTAGAAGAAGAAGAG 58.541 41.667 0.00 0.00 37.70 2.85
1111 1144 5.443185 TCGGTTTCGTTAGAAGAAGAAGA 57.557 39.130 0.00 0.00 37.70 2.87
1113 1146 4.038402 ACCTCGGTTTCGTTAGAAGAAGAA 59.962 41.667 0.00 0.00 37.70 2.52
1119 1153 4.789012 ATGTACCTCGGTTTCGTTAGAA 57.211 40.909 0.00 0.00 37.69 2.10
1121 1155 4.985413 TGTATGTACCTCGGTTTCGTTAG 58.015 43.478 0.00 0.00 37.69 2.34
1124 1158 3.698040 AGATGTATGTACCTCGGTTTCGT 59.302 43.478 0.00 0.00 37.69 3.85
1126 1160 4.098960 TGGAGATGTATGTACCTCGGTTTC 59.901 45.833 0.00 0.00 0.00 2.78
1217 1254 1.193323 AAATCAAATGGATGCGGCCA 58.807 45.000 2.24 0.00 43.23 5.36
1219 1256 3.005684 TGGATAAATCAAATGGATGCGGC 59.994 43.478 0.00 0.00 36.02 6.53
1257 1305 3.740832 CAGTACAGATTCTTGCAACACGA 59.259 43.478 0.00 0.00 0.00 4.35
1260 1308 3.475575 TGCAGTACAGATTCTTGCAACA 58.524 40.909 8.03 0.00 0.00 3.33
1289 1337 1.668419 GAATACAGCACGGCCTGAAT 58.332 50.000 0.00 0.00 36.67 2.57
1311 1359 1.770110 TGGTGGACAGGCAAGGAGT 60.770 57.895 0.00 0.00 0.00 3.85
1317 1365 3.569210 CAGGGTGGTGGACAGGCA 61.569 66.667 0.00 0.00 0.00 4.75
1336 1384 1.070758 TCCCAAGCTGTGAGAGTCAAC 59.929 52.381 0.00 0.00 0.00 3.18
1340 1388 0.394565 GTGTCCCAAGCTGTGAGAGT 59.605 55.000 0.00 0.00 0.00 3.24
1355 1403 2.766313 TGGTAGCATCACACTTGTGTC 58.234 47.619 9.16 1.11 45.76 3.67
1356 1404 2.928801 TGGTAGCATCACACTTGTGT 57.071 45.000 9.16 0.00 45.76 3.72
1378 1429 2.413112 CAGTATCTTTGTCACCAGTGCG 59.587 50.000 0.00 0.00 0.00 5.34
1383 1434 5.762179 AGAATCCAGTATCTTTGTCACCA 57.238 39.130 0.00 0.00 0.00 4.17
1398 1449 3.440173 GCGATTTCTGGTTCAAGAATCCA 59.560 43.478 0.00 0.00 36.12 3.41
1406 1457 2.884012 ACAACATGCGATTTCTGGTTCA 59.116 40.909 0.00 0.00 0.00 3.18
1412 1463 3.181520 GCGACTAACAACATGCGATTTCT 60.182 43.478 0.00 0.00 0.00 2.52
1434 1485 3.793144 GTGGAGAAGCAAGCGCCG 61.793 66.667 2.29 0.00 39.83 6.46
1470 1524 4.735358 GGGTCCCGGGCTTGAACC 62.735 72.222 18.49 18.26 0.00 3.62
1486 1540 1.007964 CCGATGCTAGCAGAGACGG 60.008 63.158 27.41 27.41 0.00 4.79
1513 1567 3.260483 CTGCTGGTCGATCGCAGC 61.260 66.667 29.51 29.51 43.75 5.25
1596 1650 1.736681 GTGATGAGCTTGCTCAAGACC 59.263 52.381 26.00 16.31 40.79 3.85
1599 1653 1.738350 CCAGTGATGAGCTTGCTCAAG 59.262 52.381 26.00 14.44 41.24 3.02
1600 1654 1.817357 CCAGTGATGAGCTTGCTCAA 58.183 50.000 26.00 10.66 36.88 3.02
1665 1719 1.396690 CGAAACGTGTGATCAACCACG 60.397 52.381 27.65 27.65 45.28 4.94
1676 1730 1.827399 ATGCCTCTCCCGAAACGTGT 61.827 55.000 0.00 0.00 0.00 4.49
1678 1732 1.218316 GATGCCTCTCCCGAAACGT 59.782 57.895 0.00 0.00 0.00 3.99
1696 1750 0.676151 GCCTCCTTCTCCAGCAGTTG 60.676 60.000 0.00 0.00 0.00 3.16
1735 1789 1.722507 GAGCGCAACGTGCAAGAAC 60.723 57.895 11.47 0.00 45.36 3.01
1746 1800 1.730501 CAAGATCAGGAAGAGCGCAA 58.269 50.000 11.47 0.00 37.82 4.85
1819 1873 1.134818 TGCTATAACTGCAGACCACGG 60.135 52.381 23.35 6.84 35.31 4.94
1821 1875 2.673368 GTGTGCTATAACTGCAGACCAC 59.327 50.000 23.35 16.22 45.22 4.16
1875 1929 0.104120 TCTCCATTACCATGTCGGCG 59.896 55.000 0.00 0.00 39.03 6.46
1970 2024 8.134895 TCAGAACAATGTTGAAGGTAAATGAAC 58.865 33.333 2.20 0.00 0.00 3.18
1985 2039 2.040813 AGGGATGCAGTCAGAACAATGT 59.959 45.455 0.00 0.00 0.00 2.71
2043 2097 2.711009 CCCTATCCTGGGCATTAGTTCA 59.289 50.000 0.00 0.00 40.84 3.18
2089 2143 7.686438 TTTCATATATGCGAGCCATAACAAT 57.314 32.000 7.92 0.00 39.71 2.71
2094 2148 7.066163 CCATTCTTTTCATATATGCGAGCCATA 59.934 37.037 7.92 0.00 40.52 2.74
2157 2211 1.142748 GAGACCACAGGCCTCATCG 59.857 63.158 0.00 0.00 0.00 3.84
2465 3749 3.027412 TCTCTCGCCTCTAATTCAAGCT 58.973 45.455 0.00 0.00 0.00 3.74
2502 3786 2.935201 CTGTTCCTGCAGCTTATCTGAC 59.065 50.000 8.66 0.00 45.72 3.51
2664 4468 2.008242 AGGAGCTCTCAACAGACACT 57.992 50.000 14.64 0.00 0.00 3.55
2946 4750 7.397221 TCATCTCTTTAAAAAGATGGAGAGCA 58.603 34.615 24.59 7.66 45.81 4.26
2995 4799 6.599638 GCTAACATCTCAAACTCCCTGTTAAT 59.400 38.462 0.00 0.00 38.03 1.40
3315 5119 7.015487 TCCAACAGTTCCTGATCAAATTTCATT 59.985 33.333 0.00 0.00 35.18 2.57
3432 5236 5.181245 CCACAGGGACTTGTACTTGTATTTG 59.819 44.000 0.37 0.00 34.60 2.32
3540 5344 3.703052 ACCCAATCCATCTCTTGAAATGC 59.297 43.478 0.00 0.00 0.00 3.56
3575 5379 5.630680 CGTGCTTCACTGCTTTCAAATTATT 59.369 36.000 0.00 0.00 31.34 1.40
3577 5381 4.036262 ACGTGCTTCACTGCTTTCAAATTA 59.964 37.500 0.00 0.00 31.34 1.40
3579 5383 2.358898 ACGTGCTTCACTGCTTTCAAAT 59.641 40.909 0.00 0.00 31.34 2.32
3690 5494 4.755266 TGGGAAAGTCTAGCCTGATAAC 57.245 45.455 0.00 0.00 0.00 1.89
3764 5568 1.647346 TTTATTCCTGTAGCACGGCG 58.353 50.000 4.80 4.80 0.00 6.46
3847 5651 7.908082 CAGAACTTCAACTCGAAAACAACATAA 59.092 33.333 0.00 0.00 31.71 1.90
3900 5704 7.154656 TCAGATTGTACATACACATATGGCTC 58.845 38.462 7.80 0.00 42.32 4.70
3901 5705 7.015584 TCTCAGATTGTACATACACATATGGCT 59.984 37.037 7.80 0.00 42.32 4.75
3902 5706 7.116948 GTCTCAGATTGTACATACACATATGGC 59.883 40.741 7.80 0.00 42.32 4.40
3904 5708 9.533253 TTGTCTCAGATTGTACATACACATATG 57.467 33.333 0.00 0.00 43.46 1.78
3905 5709 9.755804 CTTGTCTCAGATTGTACATACACATAT 57.244 33.333 0.00 0.00 35.64 1.78
3906 5710 8.966868 TCTTGTCTCAGATTGTACATACACATA 58.033 33.333 0.00 0.00 35.64 2.29
3907 5711 7.840931 TCTTGTCTCAGATTGTACATACACAT 58.159 34.615 0.00 0.00 35.64 3.21
3908 5712 7.227049 TCTTGTCTCAGATTGTACATACACA 57.773 36.000 0.00 0.00 35.64 3.72
3956 5761 4.403113 ACATCATTGCATACAGATTTGCCA 59.597 37.500 0.00 0.00 38.08 4.92
3959 5764 6.139048 TGGACATCATTGCATACAGATTTG 57.861 37.500 0.00 0.00 0.00 2.32
3976 5781 3.576078 TCAACTTGGAACACTGGACAT 57.424 42.857 0.00 0.00 39.29 3.06
3988 5793 3.194542 TCCAACAACCTGTTTCAACTTGG 59.805 43.478 0.00 0.00 38.77 3.61
4130 5935 4.425577 AATCCGTTGCTGACATCTTTTC 57.574 40.909 0.00 0.00 0.00 2.29
4157 5963 5.623673 GCAGACCATGTTAACTTACAAAACG 59.376 40.000 7.22 0.00 0.00 3.60
4261 6085 9.474313 AAAGGTAAATCTGCCAATTACATAAGA 57.526 29.630 0.00 0.00 32.47 2.10
4277 6101 7.719633 TGTATCCATAGCCAGAAAAGGTAAATC 59.280 37.037 0.00 0.00 0.00 2.17
4331 6170 9.920946 ACATAATACTGGTAAATCTGAAACCAT 57.079 29.630 9.47 4.79 42.23 3.55
4354 6193 9.394767 TCAACAACTGTTAGCATCATATTACAT 57.605 29.630 0.00 0.00 36.32 2.29
4355 6194 8.785329 TCAACAACTGTTAGCATCATATTACA 57.215 30.769 0.00 0.00 36.32 2.41
4397 6236 7.872113 TTGGTCACAAAATTTGCCTAAAAAT 57.128 28.000 5.52 0.00 32.66 1.82
4507 6458 7.608376 TCCATGGTTTAAAACACGATCTCAATA 59.392 33.333 8.39 0.00 0.00 1.90
4532 6483 9.696917 ATTTTGTCAATTTTCTCAGGTACAATC 57.303 29.630 0.00 0.00 0.00 2.67
4616 6567 9.871238 GGTGAGATCTGTTAAATCAAAGTAGTA 57.129 33.333 0.00 0.00 0.00 1.82
4617 6568 7.824779 GGGTGAGATCTGTTAAATCAAAGTAGT 59.175 37.037 0.00 0.00 0.00 2.73
4647 6598 7.604545 AGTGAGCTAGGTTCTTTTCTTATGAAC 59.395 37.037 0.00 0.00 39.16 3.18
4660 7395 3.680458 GCTACAACAAGTGAGCTAGGTTC 59.320 47.826 0.00 0.00 31.50 3.62
4675 7410 5.063817 ACGGGTACGAAATATTTGCTACAAC 59.936 40.000 5.17 1.88 44.60 3.32
4781 7518 9.956720 GATTGCTTGTATACTAATCAAAATGCT 57.043 29.630 4.17 0.00 0.00 3.79
4784 7521 9.935682 CGTGATTGCTTGTATACTAATCAAAAT 57.064 29.630 18.17 6.34 38.87 1.82
4816 7556 7.979115 TGATTAAGAAAGTTGGTTTTGTTCG 57.021 32.000 0.00 0.00 0.00 3.95
4900 7640 3.450457 TGCAAATGAGGACAAAAACAGGT 59.550 39.130 0.00 0.00 0.00 4.00
4982 7723 4.611581 GCTTGAGATTTGTCTCCACGAAAC 60.612 45.833 3.24 0.00 35.97 2.78
4988 7729 4.564782 ATCTGCTTGAGATTTGTCTCCA 57.435 40.909 3.24 0.00 38.35 3.86
4989 7730 4.505922 CGTATCTGCTTGAGATTTGTCTCC 59.494 45.833 3.24 0.00 41.94 3.71
5009 7750 0.178301 TGTGAAACCTGGTGCACGTA 59.822 50.000 21.02 1.11 34.36 3.57
5062 7803 2.615869 CAGCAAGCAGGTAAGACTCTC 58.384 52.381 0.00 0.00 0.00 3.20
5103 7844 0.527565 AGCTTGCTTATTGGCAACGG 59.472 50.000 0.00 0.00 45.64 4.44
5287 8032 2.586258 ATCATCGTGTTCTTCCTCGG 57.414 50.000 0.00 0.00 0.00 4.63
5375 8120 3.976942 GTGTAAGCACAAGCAGAATGTTG 59.023 43.478 0.00 0.00 44.64 3.33
5400 8145 5.381174 TCAAAAGAATGGATGCAGAAGTG 57.619 39.130 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.