Multiple sequence alignment - TraesCS2A01G391600

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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 TraesCS2A01G391600 chr2A 100.000 4287 0 0 1 4287 641956420 641952134 0.000000e+00 7917.0
1 TraesCS2A01G391600 chr2D 95.622 3586 113 19 743 4287 497364968 497361386 0.000000e+00 5712.0
2 TraesCS2A01G391600 chr2D 88.603 272 17 9 1 261 497366192 497365924 6.920000e-83 318.0
3 TraesCS2A01G391600 chr2D 91.111 135 10 1 527 659 635208400 635208534 9.470000e-42 182.0
4 TraesCS2A01G391600 chr2D 88.194 144 13 3 527 667 91799010 91798868 7.370000e-38 169.0
5 TraesCS2A01G391600 chr2D 100.000 31 0 0 743 773 497365254 497365224 1.670000e-04 58.4
6 TraesCS2A01G391600 chr2B 95.323 3571 130 22 745 4287 583677291 583673730 0.000000e+00 5635.0
7 TraesCS2A01G391600 chr3D 91.912 136 9 1 527 660 356632976 356633111 5.660000e-44 189.0
8 TraesCS2A01G391600 chr5A 91.111 135 10 1 527 659 647359687 647359553 9.470000e-42 182.0
9 TraesCS2A01G391600 chr5D 91.045 134 11 1 527 659 449082158 449082025 3.410000e-41 180.0
10 TraesCS2A01G391600 chr1D 90.977 133 11 1 527 659 58584056 58584187 1.220000e-40 178.0
11 TraesCS2A01G391600 chr6D 90.370 135 10 2 527 659 18495430 18495297 1.580000e-39 174.0
12 TraesCS2A01G391600 chr6D 86.076 79 10 1 430 508 461821937 461822014 2.750000e-12 84.2
13 TraesCS2A01G391600 chr4B 90.370 135 10 2 527 658 142517549 142517683 1.580000e-39 174.0
14 TraesCS2A01G391600 chr3A 89.855 138 10 3 527 662 60170471 60170336 1.580000e-39 174.0
15 TraesCS2A01G391600 chr5B 90.123 81 8 0 430 510 478319325 478319405 5.860000e-19 106.0


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 TraesCS2A01G391600 chr2A 641952134 641956420 4286 True 7917.000000 7917 100.000000 1 4287 1 chr2A.!!$R1 4286
1 TraesCS2A01G391600 chr2D 497361386 497366192 4806 True 2029.466667 5712 94.741667 1 4287 3 chr2D.!!$R2 4286
2 TraesCS2A01G391600 chr2B 583673730 583677291 3561 True 5635.000000 5635 95.323000 745 4287 1 chr2B.!!$R1 3542

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
297 337 0.036388 CTTCTTGCCTCTGCCGGTTA 60.036 55.0 1.90 0.00 36.33 2.85 F
355 395 0.036875 CCGGTCAGCCTCCTTTCTTT 59.963 55.0 0.00 0.00 0.00 2.52 F
620 660 0.105964 GGGGTGAGTGTATGCGCATA 59.894 55.0 25.78 25.78 0.00 3.14 F
1998 2666 0.871722 TGACCCTGCAAATCGTTTCG 59.128 50.0 0.00 0.00 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 2017 0.470341 GACCAGGAATGGCTACCTCC 59.530 60.000 0.0 0.0 33.91 4.30 R
1979 2647 0.871722 CGAAACGATTTGCAGGGTCA 59.128 50.000 0.0 0.0 0.00 4.02 R
2260 2930 1.940613 GTTCGCTTGTCTTTCAGTGGT 59.059 47.619 0.0 0.0 0.00 4.16 R
3793 4467 2.092646 CCCCTCAATCCCGATAACAACA 60.093 50.000 0.0 0.0 0.00 3.33 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
35 36 4.040217 TGTGCATTTCAAATTAGGCCAAGT 59.960 37.500 5.01 0.00 0.00 3.16
53 54 5.528870 CCAAGTCCTAACAAACAACATTCC 58.471 41.667 0.00 0.00 0.00 3.01
59 60 5.821470 TCCTAACAAACAACATTCCGTTACA 59.179 36.000 0.00 0.00 35.52 2.41
62 63 4.865776 ACAAACAACATTCCGTTACATGG 58.134 39.130 0.00 0.00 35.52 3.66
63 64 3.569250 AACAACATTCCGTTACATGGC 57.431 42.857 0.00 0.00 35.52 4.40
64 65 2.790433 ACAACATTCCGTTACATGGCT 58.210 42.857 0.00 0.00 35.52 4.75
65 66 2.487762 ACAACATTCCGTTACATGGCTG 59.512 45.455 0.00 0.00 35.52 4.85
66 67 1.094785 ACATTCCGTTACATGGCTGC 58.905 50.000 0.00 0.00 0.00 5.25
67 68 1.340017 ACATTCCGTTACATGGCTGCT 60.340 47.619 0.00 0.00 0.00 4.24
69 70 3.141398 CATTCCGTTACATGGCTGCTAT 58.859 45.455 0.00 0.00 0.00 2.97
70 71 4.202315 ACATTCCGTTACATGGCTGCTATA 60.202 41.667 0.00 0.00 0.00 1.31
71 72 4.409718 TTCCGTTACATGGCTGCTATAA 57.590 40.909 0.00 0.00 0.00 0.98
133 140 1.207329 AGGTTTAGGCGGTAGAAGCAG 59.793 52.381 0.00 0.00 36.08 4.24
142 149 2.931320 GCGGTAGAAGCAGCTTGTTACT 60.931 50.000 13.91 5.82 34.19 2.24
146 153 4.627900 GGTAGAAGCAGCTTGTTACTTCTC 59.372 45.833 13.91 0.00 44.14 2.87
151 158 2.427506 CAGCTTGTTACTTCTCCCACC 58.572 52.381 0.00 0.00 0.00 4.61
195 206 4.715713 GACCCTTCTTTGTTGGAGTTACT 58.284 43.478 0.00 0.00 0.00 2.24
196 207 4.715713 ACCCTTCTTTGTTGGAGTTACTC 58.284 43.478 3.36 3.36 0.00 2.59
236 247 3.540314 TTGCAGTTGTTGAGCCATTTT 57.460 38.095 0.00 0.00 0.00 1.82
237 248 3.096489 TGCAGTTGTTGAGCCATTTTC 57.904 42.857 0.00 0.00 0.00 2.29
238 249 2.224018 TGCAGTTGTTGAGCCATTTTCC 60.224 45.455 0.00 0.00 0.00 3.13
275 315 1.014352 AGTAATTTTAGCCCAGCGCG 58.986 50.000 0.00 0.00 44.76 6.86
284 324 3.121030 CCCAGCGCGACCTTCTTG 61.121 66.667 12.10 0.00 0.00 3.02
285 325 3.793144 CCAGCGCGACCTTCTTGC 61.793 66.667 12.10 0.00 0.00 4.01
286 326 3.793144 CAGCGCGACCTTCTTGCC 61.793 66.667 12.10 0.00 0.00 4.52
287 327 4.008933 AGCGCGACCTTCTTGCCT 62.009 61.111 12.10 0.00 0.00 4.75
288 328 3.491652 GCGCGACCTTCTTGCCTC 61.492 66.667 12.10 0.00 0.00 4.70
289 329 2.262915 CGCGACCTTCTTGCCTCT 59.737 61.111 0.00 0.00 0.00 3.69
290 330 2.097038 CGCGACCTTCTTGCCTCTG 61.097 63.158 0.00 0.00 0.00 3.35
291 331 2.394563 GCGACCTTCTTGCCTCTGC 61.395 63.158 0.00 0.00 38.26 4.26
292 332 1.743252 CGACCTTCTTGCCTCTGCC 60.743 63.158 0.00 0.00 36.33 4.85
293 333 1.743252 GACCTTCTTGCCTCTGCCG 60.743 63.158 0.00 0.00 36.33 5.69
294 334 2.437359 CCTTCTTGCCTCTGCCGG 60.437 66.667 0.00 0.00 36.33 6.13
295 335 2.348998 CTTCTTGCCTCTGCCGGT 59.651 61.111 1.90 0.00 36.33 5.28
296 336 1.302832 CTTCTTGCCTCTGCCGGTT 60.303 57.895 1.90 0.00 36.33 4.44
297 337 0.036388 CTTCTTGCCTCTGCCGGTTA 60.036 55.000 1.90 0.00 36.33 2.85
304 344 1.165270 CCTCTGCCGGTTAACCTTTG 58.835 55.000 22.12 11.48 0.00 2.77
355 395 0.036875 CCGGTCAGCCTCCTTTCTTT 59.963 55.000 0.00 0.00 0.00 2.52
364 404 1.562008 CCTCCTTTCTTTCTCCCTCCC 59.438 57.143 0.00 0.00 0.00 4.30
384 424 0.748367 CCCGTCGATCTCACTCCTCA 60.748 60.000 0.00 0.00 0.00 3.86
401 441 3.995074 ATTCGCGGTTGAATGGCA 58.005 50.000 6.13 0.00 37.20 4.92
403 443 0.817013 ATTCGCGGTTGAATGGCATT 59.183 45.000 13.54 13.54 37.20 3.56
405 445 0.957888 TCGCGGTTGAATGGCATTCA 60.958 50.000 33.06 33.06 46.77 2.57
417 457 0.592247 GGCATTCAATTAGGTGCGCG 60.592 55.000 0.00 0.00 38.43 6.86
432 472 0.383124 GCGCGATAAGATCAAACCGC 60.383 55.000 12.10 10.96 39.33 5.68
433 473 0.232303 CGCGATAAGATCAAACCGCC 59.768 55.000 0.00 1.65 39.52 6.13
435 475 1.261619 GCGATAAGATCAAACCGCCTG 59.738 52.381 10.18 0.00 37.09 4.85
436 476 2.821546 CGATAAGATCAAACCGCCTGA 58.178 47.619 0.00 0.00 0.00 3.86
442 482 2.026822 AGATCAAACCGCCTGAGTTCAT 60.027 45.455 0.00 0.00 0.00 2.57
443 483 1.808411 TCAAACCGCCTGAGTTCATC 58.192 50.000 0.00 0.00 0.00 2.92
445 485 2.086869 CAAACCGCCTGAGTTCATCAT 58.913 47.619 0.00 0.00 37.28 2.45
447 487 3.627395 AACCGCCTGAGTTCATCATAA 57.373 42.857 0.00 0.00 37.28 1.90
449 489 3.950397 ACCGCCTGAGTTCATCATAAAA 58.050 40.909 0.00 0.00 37.28 1.52
452 492 5.163622 ACCGCCTGAGTTCATCATAAAAATG 60.164 40.000 0.00 0.00 37.28 2.32
453 493 5.163622 CCGCCTGAGTTCATCATAAAAATGT 60.164 40.000 0.00 0.00 37.28 2.71
454 494 6.324819 CGCCTGAGTTCATCATAAAAATGTT 58.675 36.000 0.00 0.00 37.28 2.71
455 495 7.415095 CCGCCTGAGTTCATCATAAAAATGTTA 60.415 37.037 0.00 0.00 37.28 2.41
456 496 7.641411 CGCCTGAGTTCATCATAAAAATGTTAG 59.359 37.037 0.00 0.00 37.28 2.34
457 497 7.433425 GCCTGAGTTCATCATAAAAATGTTAGC 59.567 37.037 0.00 0.00 37.28 3.09
458 498 7.641411 CCTGAGTTCATCATAAAAATGTTAGCG 59.359 37.037 0.00 0.00 37.28 4.26
459 499 7.471721 TGAGTTCATCATAAAAATGTTAGCGG 58.528 34.615 0.00 0.00 31.12 5.52
460 500 6.795399 AGTTCATCATAAAAATGTTAGCGGG 58.205 36.000 0.00 0.00 0.00 6.13
461 501 5.181690 TCATCATAAAAATGTTAGCGGGC 57.818 39.130 0.00 0.00 0.00 6.13
462 502 3.684103 TCATAAAAATGTTAGCGGGCG 57.316 42.857 0.00 0.00 0.00 6.13
463 503 3.271729 TCATAAAAATGTTAGCGGGCGA 58.728 40.909 0.00 0.00 0.00 5.54
464 504 3.880490 TCATAAAAATGTTAGCGGGCGAT 59.120 39.130 0.00 0.00 0.00 4.58
465 505 2.559998 AAAAATGTTAGCGGGCGATG 57.440 45.000 0.00 0.00 0.00 3.84
466 506 1.459450 AAAATGTTAGCGGGCGATGT 58.541 45.000 0.00 0.00 0.00 3.06
467 507 2.319136 AAATGTTAGCGGGCGATGTA 57.681 45.000 0.00 0.00 0.00 2.29
468 508 2.319136 AATGTTAGCGGGCGATGTAA 57.681 45.000 0.00 0.00 0.00 2.41
469 509 1.578583 ATGTTAGCGGGCGATGTAAC 58.421 50.000 0.00 0.00 0.00 2.50
470 510 0.533491 TGTTAGCGGGCGATGTAACT 59.467 50.000 0.00 0.00 0.00 2.24
471 511 1.750206 TGTTAGCGGGCGATGTAACTA 59.250 47.619 0.00 0.00 0.00 2.24
472 512 2.363038 TGTTAGCGGGCGATGTAACTAT 59.637 45.455 0.00 0.00 0.00 2.12
473 513 3.181473 TGTTAGCGGGCGATGTAACTATT 60.181 43.478 0.00 0.00 0.00 1.73
474 514 4.037803 TGTTAGCGGGCGATGTAACTATTA 59.962 41.667 0.00 0.00 0.00 0.98
475 515 3.955650 AGCGGGCGATGTAACTATTAT 57.044 42.857 0.00 0.00 0.00 1.28
476 516 4.267349 AGCGGGCGATGTAACTATTATT 57.733 40.909 0.00 0.00 0.00 1.40
477 517 4.638304 AGCGGGCGATGTAACTATTATTT 58.362 39.130 0.00 0.00 0.00 1.40
478 518 4.451096 AGCGGGCGATGTAACTATTATTTG 59.549 41.667 0.00 0.00 0.00 2.32
479 519 4.449743 GCGGGCGATGTAACTATTATTTGA 59.550 41.667 0.00 0.00 0.00 2.69
480 520 5.121768 GCGGGCGATGTAACTATTATTTGAT 59.878 40.000 0.00 0.00 0.00 2.57
481 521 6.348213 GCGGGCGATGTAACTATTATTTGATT 60.348 38.462 0.00 0.00 0.00 2.57
482 522 7.148540 GCGGGCGATGTAACTATTATTTGATTA 60.149 37.037 0.00 0.00 0.00 1.75
483 523 8.714179 CGGGCGATGTAACTATTATTTGATTAA 58.286 33.333 0.00 0.00 0.00 1.40
498 538 9.816354 TTATTTGATTAATAAAGCAAGCCTTCC 57.184 29.630 0.00 0.00 41.64 3.46
499 539 5.852282 TGATTAATAAAGCAAGCCTTCCC 57.148 39.130 0.00 0.00 31.99 3.97
500 540 4.338118 TGATTAATAAAGCAAGCCTTCCCG 59.662 41.667 0.00 0.00 31.99 5.14
501 541 2.215942 AATAAAGCAAGCCTTCCCGT 57.784 45.000 0.00 0.00 31.99 5.28
502 542 3.359695 AATAAAGCAAGCCTTCCCGTA 57.640 42.857 0.00 0.00 31.99 4.02
503 543 2.863132 TAAAGCAAGCCTTCCCGTAA 57.137 45.000 0.00 0.00 31.99 3.18
504 544 1.989706 AAAGCAAGCCTTCCCGTAAA 58.010 45.000 0.00 0.00 31.99 2.01
505 545 1.989706 AAGCAAGCCTTCCCGTAAAA 58.010 45.000 0.00 0.00 0.00 1.52
506 546 1.989706 AGCAAGCCTTCCCGTAAAAA 58.010 45.000 0.00 0.00 0.00 1.94
551 591 8.855110 AGTAAATCTCAAGATGATATGTCGACT 58.145 33.333 17.92 4.95 34.49 4.18
552 592 9.123709 GTAAATCTCAAGATGATATGTCGACTC 57.876 37.037 17.92 6.73 34.49 3.36
554 594 6.311055 TCTCAAGATGATATGTCGACTCAG 57.689 41.667 17.92 0.98 0.00 3.35
555 595 5.825151 TCTCAAGATGATATGTCGACTCAGT 59.175 40.000 17.92 2.99 0.00 3.41
556 596 6.017523 TCTCAAGATGATATGTCGACTCAGTC 60.018 42.308 17.92 10.00 0.00 3.51
557 597 5.825151 TCAAGATGATATGTCGACTCAGTCT 59.175 40.000 17.92 12.78 0.00 3.24
558 598 5.940192 AGATGATATGTCGACTCAGTCTC 57.060 43.478 17.92 7.12 0.00 3.36
559 599 5.620206 AGATGATATGTCGACTCAGTCTCT 58.380 41.667 17.92 9.17 0.00 3.10
560 600 5.700832 AGATGATATGTCGACTCAGTCTCTC 59.299 44.000 17.92 6.45 0.00 3.20
561 601 3.804873 TGATATGTCGACTCAGTCTCTCG 59.195 47.826 17.92 0.00 0.00 4.04
562 602 2.388310 ATGTCGACTCAGTCTCTCGA 57.612 50.000 17.92 0.00 34.14 4.04
563 603 2.165319 TGTCGACTCAGTCTCTCGAA 57.835 50.000 17.92 0.00 38.13 3.71
564 604 2.070028 TGTCGACTCAGTCTCTCGAAG 58.930 52.381 17.92 0.00 38.13 3.79
565 605 2.288886 TGTCGACTCAGTCTCTCGAAGA 60.289 50.000 17.92 0.00 38.13 2.87
566 606 2.933906 GTCGACTCAGTCTCTCGAAGAT 59.066 50.000 8.70 0.00 38.13 2.40
567 607 2.933260 TCGACTCAGTCTCTCGAAGATG 59.067 50.000 2.61 0.00 36.11 2.90
568 608 2.538737 CGACTCAGTCTCTCGAAGATGC 60.539 54.545 2.61 0.00 36.11 3.91
569 609 2.682856 GACTCAGTCTCTCGAAGATGCT 59.317 50.000 0.00 0.00 36.11 3.79
570 610 2.682856 ACTCAGTCTCTCGAAGATGCTC 59.317 50.000 0.00 0.00 36.11 4.26
571 611 2.682352 CTCAGTCTCTCGAAGATGCTCA 59.318 50.000 0.00 0.00 36.11 4.26
572 612 3.286353 TCAGTCTCTCGAAGATGCTCAT 58.714 45.455 0.00 0.00 36.11 2.90
573 613 4.455606 TCAGTCTCTCGAAGATGCTCATA 58.544 43.478 0.00 0.00 36.11 2.15
574 614 4.514816 TCAGTCTCTCGAAGATGCTCATAG 59.485 45.833 0.00 0.00 36.11 2.23
575 615 3.820467 AGTCTCTCGAAGATGCTCATAGG 59.180 47.826 0.00 0.00 36.11 2.57
576 616 3.057596 GTCTCTCGAAGATGCTCATAGGG 60.058 52.174 0.00 0.00 36.11 3.53
577 617 3.153130 CTCTCGAAGATGCTCATAGGGA 58.847 50.000 0.00 0.00 33.89 4.20
578 618 3.763360 CTCTCGAAGATGCTCATAGGGAT 59.237 47.826 0.00 0.00 33.89 3.85
579 619 4.923415 TCTCGAAGATGCTCATAGGGATA 58.077 43.478 0.00 0.00 33.89 2.59
580 620 4.946772 TCTCGAAGATGCTCATAGGGATAG 59.053 45.833 0.00 0.00 33.89 2.08
581 621 4.019858 TCGAAGATGCTCATAGGGATAGG 58.980 47.826 0.00 0.00 0.00 2.57
582 622 3.131933 CGAAGATGCTCATAGGGATAGGG 59.868 52.174 0.00 0.00 0.00 3.53
583 623 3.862600 AGATGCTCATAGGGATAGGGT 57.137 47.619 0.00 0.00 0.00 4.34
584 624 3.448934 AGATGCTCATAGGGATAGGGTG 58.551 50.000 0.00 0.00 0.00 4.61
585 625 2.795291 TGCTCATAGGGATAGGGTGT 57.205 50.000 0.00 0.00 0.00 4.16
586 626 2.329267 TGCTCATAGGGATAGGGTGTG 58.671 52.381 0.00 0.00 0.00 3.82
587 627 1.002544 GCTCATAGGGATAGGGTGTGC 59.997 57.143 0.00 0.00 0.00 4.57
588 628 1.273606 CTCATAGGGATAGGGTGTGCG 59.726 57.143 0.00 0.00 0.00 5.34
589 629 1.048601 CATAGGGATAGGGTGTGCGT 58.951 55.000 0.00 0.00 0.00 5.24
590 630 1.048601 ATAGGGATAGGGTGTGCGTG 58.951 55.000 0.00 0.00 0.00 5.34
591 631 0.324923 TAGGGATAGGGTGTGCGTGT 60.325 55.000 0.00 0.00 0.00 4.49
592 632 1.449601 GGGATAGGGTGTGCGTGTG 60.450 63.158 0.00 0.00 0.00 3.82
593 633 1.295423 GGATAGGGTGTGCGTGTGT 59.705 57.895 0.00 0.00 0.00 3.72
594 634 1.019278 GGATAGGGTGTGCGTGTGTG 61.019 60.000 0.00 0.00 0.00 3.82
595 635 0.320421 GATAGGGTGTGCGTGTGTGT 60.320 55.000 0.00 0.00 0.00 3.72
596 636 0.107831 ATAGGGTGTGCGTGTGTGTT 59.892 50.000 0.00 0.00 0.00 3.32
597 637 0.531090 TAGGGTGTGCGTGTGTGTTC 60.531 55.000 0.00 0.00 0.00 3.18
598 638 2.109739 GGGTGTGCGTGTGTGTTCA 61.110 57.895 0.00 0.00 0.00 3.18
599 639 1.444119 GGGTGTGCGTGTGTGTTCAT 61.444 55.000 0.00 0.00 0.00 2.57
600 640 1.222300 GGTGTGCGTGTGTGTTCATA 58.778 50.000 0.00 0.00 0.00 2.15
601 641 1.194547 GGTGTGCGTGTGTGTTCATAG 59.805 52.381 0.00 0.00 0.00 2.23
602 642 1.194547 GTGTGCGTGTGTGTTCATAGG 59.805 52.381 0.00 0.00 0.00 2.57
603 643 0.796312 GTGCGTGTGTGTTCATAGGG 59.204 55.000 0.00 0.00 0.00 3.53
604 644 0.321210 TGCGTGTGTGTTCATAGGGG 60.321 55.000 0.00 0.00 0.00 4.79
605 645 0.321298 GCGTGTGTGTTCATAGGGGT 60.321 55.000 0.00 0.00 0.00 4.95
606 646 1.438651 CGTGTGTGTTCATAGGGGTG 58.561 55.000 0.00 0.00 0.00 4.61
607 647 1.001520 CGTGTGTGTTCATAGGGGTGA 59.998 52.381 0.00 0.00 0.00 4.02
608 648 2.699954 GTGTGTGTTCATAGGGGTGAG 58.300 52.381 0.00 0.00 0.00 3.51
609 649 2.038557 GTGTGTGTTCATAGGGGTGAGT 59.961 50.000 0.00 0.00 0.00 3.41
610 650 2.038426 TGTGTGTTCATAGGGGTGAGTG 59.962 50.000 0.00 0.00 0.00 3.51
611 651 2.038557 GTGTGTTCATAGGGGTGAGTGT 59.961 50.000 0.00 0.00 0.00 3.55
612 652 3.259876 GTGTGTTCATAGGGGTGAGTGTA 59.740 47.826 0.00 0.00 0.00 2.90
613 653 4.081087 GTGTGTTCATAGGGGTGAGTGTAT 60.081 45.833 0.00 0.00 0.00 2.29
614 654 4.081142 TGTGTTCATAGGGGTGAGTGTATG 60.081 45.833 0.00 0.00 0.00 2.39
615 655 3.118408 TGTTCATAGGGGTGAGTGTATGC 60.118 47.826 0.00 0.00 0.00 3.14
616 656 1.686587 TCATAGGGGTGAGTGTATGCG 59.313 52.381 0.00 0.00 0.00 4.73
617 657 0.393077 ATAGGGGTGAGTGTATGCGC 59.607 55.000 0.00 0.00 0.00 6.09
618 658 0.973496 TAGGGGTGAGTGTATGCGCA 60.973 55.000 14.96 14.96 0.00 6.09
619 659 1.153168 GGGGTGAGTGTATGCGCAT 60.153 57.895 28.23 28.23 0.00 4.73
620 660 0.105964 GGGGTGAGTGTATGCGCATA 59.894 55.000 25.78 25.78 0.00 3.14
621 661 1.270839 GGGGTGAGTGTATGCGCATAT 60.271 52.381 31.14 17.07 0.00 1.78
622 662 1.800586 GGGTGAGTGTATGCGCATATG 59.199 52.381 31.14 0.00 0.00 1.78
623 663 2.483876 GGTGAGTGTATGCGCATATGT 58.516 47.619 31.14 19.01 0.00 2.29
624 664 3.554129 GGGTGAGTGTATGCGCATATGTA 60.554 47.826 31.14 18.33 0.00 2.29
625 665 4.245660 GGTGAGTGTATGCGCATATGTAT 58.754 43.478 31.14 18.03 0.00 2.29
626 666 4.091945 GGTGAGTGTATGCGCATATGTATG 59.908 45.833 31.14 0.00 36.78 2.39
627 667 4.923281 GTGAGTGTATGCGCATATGTATGA 59.077 41.667 31.14 8.09 35.75 2.15
628 668 5.578336 GTGAGTGTATGCGCATATGTATGAT 59.422 40.000 31.14 14.09 35.75 2.45
629 669 5.807011 TGAGTGTATGCGCATATGTATGATC 59.193 40.000 31.14 20.64 35.75 2.92
630 670 4.800471 AGTGTATGCGCATATGTATGATCG 59.200 41.667 31.14 0.00 35.75 3.69
631 671 3.551485 TGTATGCGCATATGTATGATCGC 59.449 43.478 31.14 15.38 41.93 4.58
632 672 2.368655 TGCGCATATGTATGATCGCT 57.631 45.000 5.66 0.00 42.02 4.93
633 673 2.687370 TGCGCATATGTATGATCGCTT 58.313 42.857 5.66 0.00 42.02 4.68
634 674 2.412770 TGCGCATATGTATGATCGCTTG 59.587 45.455 5.66 0.00 42.02 4.01
635 675 2.413112 GCGCATATGTATGATCGCTTGT 59.587 45.455 0.30 0.00 39.99 3.16
636 676 3.722957 GCGCATATGTATGATCGCTTGTG 60.723 47.826 0.30 0.00 39.99 3.33
637 677 3.429881 CGCATATGTATGATCGCTTGTGT 59.570 43.478 4.29 0.00 35.75 3.72
638 678 4.433413 CGCATATGTATGATCGCTTGTGTC 60.433 45.833 4.29 0.00 35.75 3.67
639 679 4.687948 GCATATGTATGATCGCTTGTGTCT 59.312 41.667 4.29 0.00 35.75 3.41
640 680 5.389202 GCATATGTATGATCGCTTGTGTCTG 60.389 44.000 4.29 0.00 35.75 3.51
641 681 3.592898 TGTATGATCGCTTGTGTCTGT 57.407 42.857 0.00 0.00 0.00 3.41
642 682 4.712122 TGTATGATCGCTTGTGTCTGTA 57.288 40.909 0.00 0.00 0.00 2.74
643 683 5.262588 TGTATGATCGCTTGTGTCTGTAT 57.737 39.130 0.00 0.00 0.00 2.29
644 684 5.660460 TGTATGATCGCTTGTGTCTGTATT 58.340 37.500 0.00 0.00 0.00 1.89
645 685 5.519927 TGTATGATCGCTTGTGTCTGTATTG 59.480 40.000 0.00 0.00 0.00 1.90
646 686 3.925379 TGATCGCTTGTGTCTGTATTGT 58.075 40.909 0.00 0.00 0.00 2.71
647 687 3.679502 TGATCGCTTGTGTCTGTATTGTG 59.320 43.478 0.00 0.00 0.00 3.33
648 688 3.106242 TCGCTTGTGTCTGTATTGTGT 57.894 42.857 0.00 0.00 0.00 3.72
649 689 3.462982 TCGCTTGTGTCTGTATTGTGTT 58.537 40.909 0.00 0.00 0.00 3.32
650 690 3.874543 TCGCTTGTGTCTGTATTGTGTTT 59.125 39.130 0.00 0.00 0.00 2.83
651 691 5.051153 TCGCTTGTGTCTGTATTGTGTTTA 58.949 37.500 0.00 0.00 0.00 2.01
652 692 5.524281 TCGCTTGTGTCTGTATTGTGTTTAA 59.476 36.000 0.00 0.00 0.00 1.52
653 693 6.037281 TCGCTTGTGTCTGTATTGTGTTTAAA 59.963 34.615 0.00 0.00 0.00 1.52
654 694 6.689241 CGCTTGTGTCTGTATTGTGTTTAAAA 59.311 34.615 0.00 0.00 0.00 1.52
655 695 7.219154 CGCTTGTGTCTGTATTGTGTTTAAAAA 59.781 33.333 0.00 0.00 0.00 1.94
683 723 4.083696 GGTCGGAATAACGAAAGAAGCAAA 60.084 41.667 0.00 0.00 45.38 3.68
689 729 6.385649 AATAACGAAAGAAGCAAAGAACCA 57.614 33.333 0.00 0.00 0.00 3.67
691 731 3.279434 ACGAAAGAAGCAAAGAACCAGT 58.721 40.909 0.00 0.00 0.00 4.00
692 732 3.694566 ACGAAAGAAGCAAAGAACCAGTT 59.305 39.130 0.00 0.00 0.00 3.16
693 733 4.157840 ACGAAAGAAGCAAAGAACCAGTTT 59.842 37.500 0.00 0.00 0.00 2.66
716 1104 6.398234 TTTTATGTTAGGCTGCAAAGAACA 57.602 33.333 0.50 6.19 34.73 3.18
734 1122 9.786105 CAAAGAACAAGGTTTGCATTTATTTTT 57.214 25.926 0.00 0.00 0.00 1.94
811 1454 2.829720 AGCCAACACGGACTGACTAATA 59.170 45.455 0.00 0.00 36.56 0.98
987 1630 4.389576 CGCACGCAAAGCTCCACC 62.390 66.667 0.00 0.00 0.00 4.61
1158 1825 1.425428 GAATGTGCACAGCTACGGC 59.575 57.895 25.84 5.26 39.06 5.68
1350 2017 2.671177 CCGCTTCAACCTCGCACTG 61.671 63.158 0.00 0.00 0.00 3.66
1442 2109 4.845387 TGATTAGTGATCGAGCGACTTAC 58.155 43.478 10.24 0.00 37.60 2.34
1517 2184 1.097547 GCGTATGCCAGCCACAGAAT 61.098 55.000 0.00 0.00 33.98 2.40
1521 2188 2.226962 ATGCCAGCCACAGAATTTCT 57.773 45.000 0.00 0.00 0.00 2.52
1535 2202 7.011389 CCACAGAATTTCTCTAATGATGCGTTA 59.989 37.037 0.00 0.00 31.12 3.18
1608 2275 6.795098 TGAAATTTTGTATCTAGTGCGTGT 57.205 33.333 0.00 0.00 0.00 4.49
1627 2294 5.611919 CGTGTGTCAGATAGTGTTGAAATG 58.388 41.667 0.00 0.00 0.00 2.32
1644 2311 3.456380 AATGCTTGGTGGTAGTTGGAT 57.544 42.857 0.00 0.00 0.00 3.41
1653 2320 5.496556 TGGTGGTAGTTGGATCACTATTTG 58.503 41.667 0.00 0.00 31.82 2.32
1665 2332 8.421249 TGGATCACTATTTGGACTGAAATTTT 57.579 30.769 0.00 0.00 0.00 1.82
1890 2557 6.174760 AGGTTTAATGTGCCAGTTTATCGTA 58.825 36.000 0.00 0.00 0.00 3.43
1910 2578 8.980481 ATCGTAAATTGGAATCTAACTGGAAT 57.020 30.769 0.00 0.00 0.00 3.01
1939 2607 5.050227 GCTGCTGTTTATCTGATCTGACATC 60.050 44.000 4.21 0.00 0.00 3.06
1997 2665 3.575965 AATGACCCTGCAAATCGTTTC 57.424 42.857 0.00 0.00 0.00 2.78
1998 2666 0.871722 TGACCCTGCAAATCGTTTCG 59.128 50.000 0.00 0.00 0.00 3.46
2251 2921 7.754027 CCAGATGCTGAAGAATACTTTGAAAAG 59.246 37.037 1.22 1.22 36.49 2.27
2260 2930 7.823745 AGAATACTTTGAAAAGCTTCCTGAA 57.176 32.000 0.00 0.00 39.63 3.02
2686 3356 1.287730 AAGCTGAGAAGCGAGCAACG 61.288 55.000 0.00 0.00 45.66 4.10
2698 3368 1.269621 CGAGCAACGGGTAGGGATAAG 60.270 57.143 0.00 0.00 38.46 1.73
2776 3446 4.578928 GTCTACCGCATTTGGAATTGGTAT 59.421 41.667 0.00 0.00 32.01 2.73
2964 3634 4.600062 AGAGAAGGTTTTGTTGTGAAGGT 58.400 39.130 0.00 0.00 0.00 3.50
3085 3755 4.456911 GCTGAATCTCTGTCATGTTTGGAA 59.543 41.667 0.00 0.00 0.00 3.53
3185 3855 3.695060 GGAGAAGAATGACACGGAGAGTA 59.305 47.826 0.00 0.00 0.00 2.59
3270 3940 4.032960 TGATTGACACCTATGCTTTGGT 57.967 40.909 0.00 0.00 36.96 3.67
3310 3980 1.903183 TGGATGGACACCAACGATACA 59.097 47.619 0.00 0.00 36.95 2.29
3440 4110 6.350906 AGCGGTTAGGTGCATTTTATAAGTA 58.649 36.000 0.00 0.00 0.00 2.24
3594 4266 5.912892 ACATGTACATCGACATTACCATCA 58.087 37.500 5.07 0.00 37.99 3.07
3649 4322 7.797123 CGTACATTTTTCAGTCACCTTTACTTC 59.203 37.037 0.00 0.00 0.00 3.01
3650 4323 7.881775 ACATTTTTCAGTCACCTTTACTTCT 57.118 32.000 0.00 0.00 0.00 2.85
3793 4467 5.296151 TCTCATTATCTCCGCCATTTCTT 57.704 39.130 0.00 0.00 0.00 2.52
3914 4596 0.718904 TGCATTTGTCGGTTCGATCG 59.281 50.000 9.36 9.36 38.42 3.69
3934 4616 3.369756 TCGTCGGCATGTTTATTTCTGAC 59.630 43.478 0.00 0.00 0.00 3.51
4022 4706 1.447643 CTCCCTTGCCGGTAGATGG 59.552 63.158 1.90 2.13 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.040217 TGGCCTAATTTGAAATGCACAAGT 59.960 37.500 3.32 0.00 0.00 3.16
35 36 5.821470 TGTAACGGAATGTTGTTTGTTAGGA 59.179 36.000 0.00 0.00 42.01 2.94
66 67 7.157347 TGCCTGATCAGTCTATGCTTTTATAG 58.843 38.462 21.11 1.44 32.99 1.31
67 68 7.066307 TGCCTGATCAGTCTATGCTTTTATA 57.934 36.000 21.11 0.00 0.00 0.98
69 70 5.357742 TGCCTGATCAGTCTATGCTTTTA 57.642 39.130 21.11 0.00 0.00 1.52
70 71 4.197750 CTGCCTGATCAGTCTATGCTTTT 58.802 43.478 21.11 0.00 0.00 2.27
71 72 3.806380 CTGCCTGATCAGTCTATGCTTT 58.194 45.455 21.11 0.00 0.00 3.51
133 140 2.224548 ACAGGTGGGAGAAGTAACAAGC 60.225 50.000 0.00 0.00 0.00 4.01
142 149 1.415672 GGTGGACACAGGTGGGAGAA 61.416 60.000 4.69 0.00 34.19 2.87
146 153 1.492133 ATGAGGTGGACACAGGTGGG 61.492 60.000 4.69 0.00 34.19 4.61
151 158 2.015588 GCCATGATGAGGTGGACACAG 61.016 57.143 4.69 0.00 37.72 3.66
195 206 7.051623 TGCAAACTGAAACTAAGAAAGTAGGA 58.948 34.615 0.00 0.00 37.50 2.94
196 207 7.012421 ACTGCAAACTGAAACTAAGAAAGTAGG 59.988 37.037 0.00 0.00 37.50 3.18
197 208 7.920738 ACTGCAAACTGAAACTAAGAAAGTAG 58.079 34.615 0.00 0.00 37.50 2.57
206 217 5.676079 GCTCAACAACTGCAAACTGAAACTA 60.676 40.000 0.00 0.00 0.00 2.24
211 222 1.405105 GGCTCAACAACTGCAAACTGA 59.595 47.619 0.00 0.00 0.00 3.41
261 272 2.741486 AAGGTCGCGCTGGGCTAAAA 62.741 55.000 14.94 0.00 40.44 1.52
262 273 3.248446 AAGGTCGCGCTGGGCTAAA 62.248 57.895 14.94 0.00 40.44 1.85
264 275 4.143333 GAAGGTCGCGCTGGGCTA 62.143 66.667 14.94 0.40 40.44 3.93
275 315 1.743252 CGGCAGAGGCAAGAAGGTC 60.743 63.158 0.00 0.00 43.71 3.85
284 324 0.608308 AAAGGTTAACCGGCAGAGGC 60.608 55.000 18.91 0.00 42.08 4.70
285 325 1.165270 CAAAGGTTAACCGGCAGAGG 58.835 55.000 18.91 2.51 42.08 3.69
286 326 1.165270 CCAAAGGTTAACCGGCAGAG 58.835 55.000 18.91 7.19 42.08 3.35
287 327 0.250989 CCCAAAGGTTAACCGGCAGA 60.251 55.000 18.91 0.00 42.08 4.26
288 328 0.250989 TCCCAAAGGTTAACCGGCAG 60.251 55.000 18.91 10.17 42.08 4.85
289 329 0.250989 CTCCCAAAGGTTAACCGGCA 60.251 55.000 18.91 0.00 42.08 5.69
290 330 0.251033 ACTCCCAAAGGTTAACCGGC 60.251 55.000 18.91 0.00 42.08 6.13
291 331 1.530323 CACTCCCAAAGGTTAACCGG 58.470 55.000 18.91 13.76 42.08 5.28
292 332 1.530323 CCACTCCCAAAGGTTAACCG 58.470 55.000 18.91 5.05 42.08 4.44
293 333 1.254026 GCCACTCCCAAAGGTTAACC 58.746 55.000 17.41 17.41 0.00 2.85
294 334 1.254026 GGCCACTCCCAAAGGTTAAC 58.746 55.000 0.00 0.00 0.00 2.01
295 335 3.757836 GGCCACTCCCAAAGGTTAA 57.242 52.632 0.00 0.00 0.00 2.01
315 355 2.755469 GGCCATGGCAACGGTGAT 60.755 61.111 36.56 0.00 44.11 3.06
337 377 1.002544 AGAAAGAAAGGAGGCTGACCG 59.997 52.381 0.00 0.00 42.76 4.79
346 386 1.670059 GGGGAGGGAGAAAGAAAGGA 58.330 55.000 0.00 0.00 0.00 3.36
364 404 1.448922 GAGGAGTGAGATCGACGGGG 61.449 65.000 0.00 0.00 0.00 5.73
369 409 1.335182 GCGAATGAGGAGTGAGATCGA 59.665 52.381 0.00 0.00 0.00 3.59
377 417 0.320374 TTCAACCGCGAATGAGGAGT 59.680 50.000 8.23 0.00 38.61 3.85
384 424 0.817013 AATGCCATTCAACCGCGAAT 59.183 45.000 8.23 0.00 36.00 3.34
401 441 4.377021 TCTTATCGCGCACCTAATTGAAT 58.623 39.130 8.75 0.00 0.00 2.57
403 443 3.446310 TCTTATCGCGCACCTAATTGA 57.554 42.857 8.75 0.00 0.00 2.57
405 445 3.990092 TGATCTTATCGCGCACCTAATT 58.010 40.909 8.75 0.00 0.00 1.40
408 448 3.120792 GTTTGATCTTATCGCGCACCTA 58.879 45.455 8.75 0.00 0.00 3.08
411 451 1.332028 CGGTTTGATCTTATCGCGCAC 60.332 52.381 8.75 0.00 0.00 5.34
417 457 3.798202 ACTCAGGCGGTTTGATCTTATC 58.202 45.455 0.00 0.00 0.00 1.75
432 472 7.641411 CGCTAACATTTTTATGATGAACTCAGG 59.359 37.037 0.00 0.00 37.28 3.86
433 473 7.641411 CCGCTAACATTTTTATGATGAACTCAG 59.359 37.037 0.00 0.00 37.28 3.35
435 475 6.912591 CCCGCTAACATTTTTATGATGAACTC 59.087 38.462 0.00 0.00 0.00 3.01
436 476 6.680378 GCCCGCTAACATTTTTATGATGAACT 60.680 38.462 0.00 0.00 0.00 3.01
442 482 3.271729 TCGCCCGCTAACATTTTTATGA 58.728 40.909 0.00 0.00 0.00 2.15
443 483 3.684103 TCGCCCGCTAACATTTTTATG 57.316 42.857 0.00 0.00 0.00 1.90
445 485 3.011119 ACATCGCCCGCTAACATTTTTA 58.989 40.909 0.00 0.00 0.00 1.52
447 487 1.459450 ACATCGCCCGCTAACATTTT 58.541 45.000 0.00 0.00 0.00 1.82
449 489 1.937899 GTTACATCGCCCGCTAACATT 59.062 47.619 0.00 0.00 0.00 2.71
452 492 2.497107 TAGTTACATCGCCCGCTAAC 57.503 50.000 0.00 0.00 0.00 2.34
453 493 3.738830 AATAGTTACATCGCCCGCTAA 57.261 42.857 0.00 0.00 0.00 3.09
454 494 5.395682 AATAATAGTTACATCGCCCGCTA 57.604 39.130 0.00 0.00 0.00 4.26
455 495 3.955650 ATAATAGTTACATCGCCCGCT 57.044 42.857 0.00 0.00 0.00 5.52
456 496 4.449743 TCAAATAATAGTTACATCGCCCGC 59.550 41.667 0.00 0.00 0.00 6.13
457 497 6.721571 ATCAAATAATAGTTACATCGCCCG 57.278 37.500 0.00 0.00 0.00 6.13
472 512 9.816354 GGAAGGCTTGCTTTATTAATCAAATAA 57.184 29.630 11.88 0.00 38.09 1.40
473 513 8.421002 GGGAAGGCTTGCTTTATTAATCAAATA 58.579 33.333 18.47 0.00 0.00 1.40
474 514 7.275183 GGGAAGGCTTGCTTTATTAATCAAAT 58.725 34.615 18.47 0.00 0.00 2.32
475 515 6.627065 CGGGAAGGCTTGCTTTATTAATCAAA 60.627 38.462 18.47 0.00 0.00 2.69
476 516 5.163561 CGGGAAGGCTTGCTTTATTAATCAA 60.164 40.000 18.47 0.00 0.00 2.57
477 517 4.338118 CGGGAAGGCTTGCTTTATTAATCA 59.662 41.667 18.47 0.00 0.00 2.57
478 518 4.338400 ACGGGAAGGCTTGCTTTATTAATC 59.662 41.667 18.47 0.00 0.00 1.75
479 519 4.278310 ACGGGAAGGCTTGCTTTATTAAT 58.722 39.130 18.47 0.00 0.00 1.40
480 520 3.692690 ACGGGAAGGCTTGCTTTATTAA 58.307 40.909 18.47 0.00 0.00 1.40
481 521 3.359695 ACGGGAAGGCTTGCTTTATTA 57.640 42.857 18.47 0.00 0.00 0.98
482 522 2.215942 ACGGGAAGGCTTGCTTTATT 57.784 45.000 18.47 0.00 0.00 1.40
483 523 3.359695 TTACGGGAAGGCTTGCTTTAT 57.640 42.857 18.47 4.54 0.00 1.40
484 524 2.863132 TTACGGGAAGGCTTGCTTTA 57.137 45.000 18.47 7.17 0.00 1.85
485 525 1.989706 TTTACGGGAAGGCTTGCTTT 58.010 45.000 18.47 8.14 0.00 3.51
486 526 1.989706 TTTTACGGGAAGGCTTGCTT 58.010 45.000 18.47 8.49 0.00 3.91
487 527 1.989706 TTTTTACGGGAAGGCTTGCT 58.010 45.000 18.47 2.13 0.00 3.91
529 569 7.014134 ACTGAGTCGACATATCATCTTGAGATT 59.986 37.037 19.50 0.00 31.21 2.40
532 572 6.017192 AGACTGAGTCGACATATCATCTTGAG 60.017 42.308 19.50 0.00 37.67 3.02
534 574 6.017192 AGAGACTGAGTCGACATATCATCTTG 60.017 42.308 19.50 3.80 37.67 3.02
535 575 6.061441 AGAGACTGAGTCGACATATCATCTT 58.939 40.000 19.50 0.60 37.67 2.40
536 576 5.620206 AGAGACTGAGTCGACATATCATCT 58.380 41.667 19.50 15.35 37.67 2.90
537 577 5.389411 CGAGAGACTGAGTCGACATATCATC 60.389 48.000 19.50 11.53 37.67 2.92
539 579 3.804873 CGAGAGACTGAGTCGACATATCA 59.195 47.826 19.50 11.89 37.67 2.15
540 580 4.052608 TCGAGAGACTGAGTCGACATATC 58.947 47.826 19.50 7.36 37.79 1.63
541 581 4.061357 TCGAGAGACTGAGTCGACATAT 57.939 45.455 19.50 0.00 37.79 1.78
542 582 3.521947 TCGAGAGACTGAGTCGACATA 57.478 47.619 19.50 4.90 37.79 2.29
544 584 2.070028 CTTCGAGAGACTGAGTCGACA 58.930 52.381 19.50 0.00 42.16 4.35
545 585 2.339418 TCTTCGAGAGACTGAGTCGAC 58.661 52.381 7.70 7.70 42.16 4.20
547 587 2.538737 GCATCTTCGAGAGACTGAGTCG 60.539 54.545 6.99 0.00 41.84 4.18
548 588 2.682856 AGCATCTTCGAGAGACTGAGTC 59.317 50.000 3.98 3.98 41.84 3.36
550 590 2.682352 TGAGCATCTTCGAGAGACTGAG 59.318 50.000 0.35 0.00 41.84 3.35
551 591 2.716217 TGAGCATCTTCGAGAGACTGA 58.284 47.619 0.35 0.00 41.84 3.41
552 592 3.713858 ATGAGCATCTTCGAGAGACTG 57.286 47.619 0.35 2.81 41.84 3.51
554 594 3.057596 CCCTATGAGCATCTTCGAGAGAC 60.058 52.174 0.35 0.00 41.84 3.36
555 595 3.153130 CCCTATGAGCATCTTCGAGAGA 58.847 50.000 0.79 0.79 39.13 3.10
556 596 3.153130 TCCCTATGAGCATCTTCGAGAG 58.847 50.000 0.00 0.00 34.92 3.20
557 597 3.229697 TCCCTATGAGCATCTTCGAGA 57.770 47.619 0.00 0.00 34.92 4.04
558 598 4.097741 CCTATCCCTATGAGCATCTTCGAG 59.902 50.000 0.00 0.00 34.92 4.04
559 599 4.019858 CCTATCCCTATGAGCATCTTCGA 58.980 47.826 0.00 0.00 34.92 3.71
560 600 3.131933 CCCTATCCCTATGAGCATCTTCG 59.868 52.174 0.00 0.00 34.92 3.79
561 601 4.081198 CACCCTATCCCTATGAGCATCTTC 60.081 50.000 0.00 0.00 34.92 2.87
562 602 3.843027 CACCCTATCCCTATGAGCATCTT 59.157 47.826 0.00 0.00 34.92 2.40
563 603 3.181402 ACACCCTATCCCTATGAGCATCT 60.181 47.826 0.00 0.00 34.92 2.90
564 604 3.055530 CACACCCTATCCCTATGAGCATC 60.056 52.174 0.00 0.00 0.00 3.91
565 605 2.909006 CACACCCTATCCCTATGAGCAT 59.091 50.000 0.00 0.00 0.00 3.79
566 606 2.329267 CACACCCTATCCCTATGAGCA 58.671 52.381 0.00 0.00 0.00 4.26
567 607 1.002544 GCACACCCTATCCCTATGAGC 59.997 57.143 0.00 0.00 0.00 4.26
568 608 1.273606 CGCACACCCTATCCCTATGAG 59.726 57.143 0.00 0.00 0.00 2.90
569 609 1.338107 CGCACACCCTATCCCTATGA 58.662 55.000 0.00 0.00 0.00 2.15
570 610 1.048601 ACGCACACCCTATCCCTATG 58.951 55.000 0.00 0.00 0.00 2.23
571 611 1.048601 CACGCACACCCTATCCCTAT 58.951 55.000 0.00 0.00 0.00 2.57
572 612 0.324923 ACACGCACACCCTATCCCTA 60.325 55.000 0.00 0.00 0.00 3.53
573 613 1.612442 ACACGCACACCCTATCCCT 60.612 57.895 0.00 0.00 0.00 4.20
574 614 1.449601 CACACGCACACCCTATCCC 60.450 63.158 0.00 0.00 0.00 3.85
575 615 1.019278 CACACACGCACACCCTATCC 61.019 60.000 0.00 0.00 0.00 2.59
576 616 0.320421 ACACACACGCACACCCTATC 60.320 55.000 0.00 0.00 0.00 2.08
577 617 0.107831 AACACACACGCACACCCTAT 59.892 50.000 0.00 0.00 0.00 2.57
578 618 0.531090 GAACACACACGCACACCCTA 60.531 55.000 0.00 0.00 0.00 3.53
579 619 1.817941 GAACACACACGCACACCCT 60.818 57.895 0.00 0.00 0.00 4.34
580 620 1.444119 ATGAACACACACGCACACCC 61.444 55.000 0.00 0.00 0.00 4.61
581 621 1.194547 CTATGAACACACACGCACACC 59.805 52.381 0.00 0.00 0.00 4.16
582 622 1.194547 CCTATGAACACACACGCACAC 59.805 52.381 0.00 0.00 0.00 3.82
583 623 1.507562 CCTATGAACACACACGCACA 58.492 50.000 0.00 0.00 0.00 4.57
584 624 0.796312 CCCTATGAACACACACGCAC 59.204 55.000 0.00 0.00 0.00 5.34
585 625 0.321210 CCCCTATGAACACACACGCA 60.321 55.000 0.00 0.00 0.00 5.24
586 626 0.321298 ACCCCTATGAACACACACGC 60.321 55.000 0.00 0.00 0.00 5.34
587 627 1.001520 TCACCCCTATGAACACACACG 59.998 52.381 0.00 0.00 0.00 4.49
588 628 2.038557 ACTCACCCCTATGAACACACAC 59.961 50.000 0.00 0.00 0.00 3.82
589 629 2.038426 CACTCACCCCTATGAACACACA 59.962 50.000 0.00 0.00 0.00 3.72
590 630 2.038557 ACACTCACCCCTATGAACACAC 59.961 50.000 0.00 0.00 0.00 3.82
591 631 2.334977 ACACTCACCCCTATGAACACA 58.665 47.619 0.00 0.00 0.00 3.72
592 632 4.442706 CATACACTCACCCCTATGAACAC 58.557 47.826 0.00 0.00 0.00 3.32
593 633 3.118408 GCATACACTCACCCCTATGAACA 60.118 47.826 0.00 0.00 0.00 3.18
594 634 3.467803 GCATACACTCACCCCTATGAAC 58.532 50.000 0.00 0.00 0.00 3.18
595 635 2.102420 CGCATACACTCACCCCTATGAA 59.898 50.000 0.00 0.00 0.00 2.57
596 636 1.686587 CGCATACACTCACCCCTATGA 59.313 52.381 0.00 0.00 0.00 2.15
597 637 1.873903 GCGCATACACTCACCCCTATG 60.874 57.143 0.30 0.00 0.00 2.23
598 638 0.393077 GCGCATACACTCACCCCTAT 59.607 55.000 0.30 0.00 0.00 2.57
599 639 0.973496 TGCGCATACACTCACCCCTA 60.973 55.000 5.66 0.00 0.00 3.53
600 640 1.626356 ATGCGCATACACTCACCCCT 61.626 55.000 24.02 0.00 0.00 4.79
601 641 0.105964 TATGCGCATACACTCACCCC 59.894 55.000 25.78 0.00 0.00 4.95
602 642 1.800586 CATATGCGCATACACTCACCC 59.199 52.381 31.17 0.00 0.00 4.61
603 643 2.483876 ACATATGCGCATACACTCACC 58.516 47.619 31.17 0.00 0.00 4.02
604 644 4.923281 TCATACATATGCGCATACACTCAC 59.077 41.667 31.17 0.00 33.76 3.51
605 645 5.132897 TCATACATATGCGCATACACTCA 57.867 39.130 31.17 11.70 33.76 3.41
606 646 5.052106 CGATCATACATATGCGCATACACTC 60.052 44.000 31.17 18.20 33.76 3.51
607 647 4.800471 CGATCATACATATGCGCATACACT 59.200 41.667 31.17 18.17 33.76 3.55
608 648 4.548916 GCGATCATACATATGCGCATACAC 60.549 45.833 31.17 14.58 41.53 2.90
609 649 3.551485 GCGATCATACATATGCGCATACA 59.449 43.478 31.17 19.39 41.53 2.29
610 650 3.798878 AGCGATCATACATATGCGCATAC 59.201 43.478 31.17 15.14 43.10 2.39
611 651 4.045636 AGCGATCATACATATGCGCATA 57.954 40.909 30.72 30.72 43.10 3.14
612 652 2.897436 AGCGATCATACATATGCGCAT 58.103 42.857 28.23 28.23 43.10 4.73
613 653 2.368655 AGCGATCATACATATGCGCA 57.631 45.000 14.96 14.96 43.10 6.09
614 654 2.413112 ACAAGCGATCATACATATGCGC 59.587 45.455 13.18 13.18 41.92 6.09
615 655 3.429881 ACACAAGCGATCATACATATGCG 59.570 43.478 1.58 0.00 33.76 4.73
616 656 4.687948 AGACACAAGCGATCATACATATGC 59.312 41.667 1.58 0.00 33.76 3.14
617 657 5.693555 ACAGACACAAGCGATCATACATATG 59.306 40.000 0.00 0.00 35.04 1.78
618 658 5.847304 ACAGACACAAGCGATCATACATAT 58.153 37.500 0.00 0.00 0.00 1.78
619 659 5.262588 ACAGACACAAGCGATCATACATA 57.737 39.130 0.00 0.00 0.00 2.29
620 660 4.128925 ACAGACACAAGCGATCATACAT 57.871 40.909 0.00 0.00 0.00 2.29
621 661 3.592898 ACAGACACAAGCGATCATACA 57.407 42.857 0.00 0.00 0.00 2.29
622 662 5.520288 ACAATACAGACACAAGCGATCATAC 59.480 40.000 0.00 0.00 0.00 2.39
623 663 5.519927 CACAATACAGACACAAGCGATCATA 59.480 40.000 0.00 0.00 0.00 2.15
624 664 4.330894 CACAATACAGACACAAGCGATCAT 59.669 41.667 0.00 0.00 0.00 2.45
625 665 3.679502 CACAATACAGACACAAGCGATCA 59.320 43.478 0.00 0.00 0.00 2.92
626 666 3.679980 ACACAATACAGACACAAGCGATC 59.320 43.478 0.00 0.00 0.00 3.69
627 667 3.664107 ACACAATACAGACACAAGCGAT 58.336 40.909 0.00 0.00 0.00 4.58
628 668 3.106242 ACACAATACAGACACAAGCGA 57.894 42.857 0.00 0.00 0.00 4.93
629 669 3.878086 AACACAATACAGACACAAGCG 57.122 42.857 0.00 0.00 0.00 4.68
630 670 7.979115 TTTTAAACACAATACAGACACAAGC 57.021 32.000 0.00 0.00 0.00 4.01
653 693 5.528320 TCTTTCGTTATTCCGACCACTTTTT 59.472 36.000 0.00 0.00 36.42 1.94
654 694 5.058490 TCTTTCGTTATTCCGACCACTTTT 58.942 37.500 0.00 0.00 36.42 2.27
655 695 4.634199 TCTTTCGTTATTCCGACCACTTT 58.366 39.130 0.00 0.00 36.42 2.66
663 703 5.277601 TCTTTGCTTCTTTCGTTATTCCG 57.722 39.130 0.00 0.00 0.00 4.30
671 711 3.971032 ACTGGTTCTTTGCTTCTTTCG 57.029 42.857 0.00 0.00 0.00 3.46
692 732 6.810911 TGTTCTTTGCAGCCTAACATAAAAA 58.189 32.000 0.00 0.00 0.00 1.94
693 733 6.398234 TGTTCTTTGCAGCCTAACATAAAA 57.602 33.333 0.00 0.00 0.00 1.52
697 1085 3.256631 CCTTGTTCTTTGCAGCCTAACAT 59.743 43.478 6.77 0.00 30.76 2.71
699 1087 2.623416 ACCTTGTTCTTTGCAGCCTAAC 59.377 45.455 0.00 0.00 0.00 2.34
731 1119 5.394115 GCAAACCTGGTTCTCTTCTCAAAAA 60.394 40.000 13.36 0.00 0.00 1.94
732 1120 4.097892 GCAAACCTGGTTCTCTTCTCAAAA 59.902 41.667 13.36 0.00 0.00 2.44
733 1121 3.632145 GCAAACCTGGTTCTCTTCTCAAA 59.368 43.478 13.36 0.00 0.00 2.69
734 1122 3.214328 GCAAACCTGGTTCTCTTCTCAA 58.786 45.455 13.36 0.00 0.00 3.02
735 1123 2.172505 TGCAAACCTGGTTCTCTTCTCA 59.827 45.455 13.36 1.07 0.00 3.27
736 1124 2.851195 TGCAAACCTGGTTCTCTTCTC 58.149 47.619 13.36 0.00 0.00 2.87
737 1125 3.217626 CTTGCAAACCTGGTTCTCTTCT 58.782 45.455 13.36 0.00 0.00 2.85
738 1126 2.294512 CCTTGCAAACCTGGTTCTCTTC 59.705 50.000 13.36 1.55 0.00 2.87
740 1128 1.479389 CCCTTGCAAACCTGGTTCTCT 60.479 52.381 13.36 0.00 0.00 3.10
741 1129 0.961753 CCCTTGCAAACCTGGTTCTC 59.038 55.000 13.36 8.19 0.00 2.87
928 1571 0.838122 AGGGGATAAGATGGAGCGGG 60.838 60.000 0.00 0.00 0.00 6.13
1158 1825 2.805353 CGCTCGAAGTCCACCGTG 60.805 66.667 0.00 0.00 0.00 4.94
1335 2002 0.671781 CCTCCAGTGCGAGGTTGAAG 60.672 60.000 15.78 0.00 43.94 3.02
1350 2017 0.470341 GACCAGGAATGGCTACCTCC 59.530 60.000 0.00 0.00 33.91 4.30
1442 2109 2.996621 AGCCTCTGAATTCGAACGAAAG 59.003 45.455 13.34 7.17 37.69 2.62
1521 2188 7.860373 GCAACCATAAAATAACGCATCATTAGA 59.140 33.333 0.00 0.00 0.00 2.10
1535 2202 6.470877 CGTAATTACGCAAGCAACCATAAAAT 59.529 34.615 23.72 0.00 43.14 1.82
1604 2271 5.611919 CATTTCAACACTATCTGACACACG 58.388 41.667 0.00 0.00 0.00 4.49
1608 2275 5.181811 CCAAGCATTTCAACACTATCTGACA 59.818 40.000 0.00 0.00 0.00 3.58
1627 2294 2.084546 GTGATCCAACTACCACCAAGC 58.915 52.381 0.00 0.00 0.00 4.01
1644 2311 8.006298 ACACAAAATTTCAGTCCAAATAGTGA 57.994 30.769 0.00 0.00 32.73 3.41
1653 2320 5.890334 TCAAGTGACACAAAATTTCAGTCC 58.110 37.500 8.59 6.59 0.00 3.85
1665 2332 5.475564 TGTACTAGCATACTCAAGTGACACA 59.524 40.000 8.59 0.00 0.00 3.72
1890 2557 7.068716 GCTACCATTCCAGTTAGATTCCAATTT 59.931 37.037 0.00 0.00 0.00 1.82
1910 2578 4.406972 AGATCAGATAAACAGCAGCTACCA 59.593 41.667 0.00 0.00 0.00 3.25
1939 2607 8.088981 ACTACTGTTCCTCACACTAAGTAATTG 58.911 37.037 0.00 0.00 0.00 2.32
1979 2647 0.871722 CGAAACGATTTGCAGGGTCA 59.128 50.000 0.00 0.00 0.00 4.02
2251 2921 2.550180 GTCTTTCAGTGGTTCAGGAAGC 59.450 50.000 4.35 4.35 39.12 3.86
2260 2930 1.940613 GTTCGCTTGTCTTTCAGTGGT 59.059 47.619 0.00 0.00 0.00 4.16
2686 3356 5.762279 TGGAAACATTTCTTATCCCTACCC 58.238 41.667 4.45 0.00 37.35 3.69
2719 3389 5.125367 TCTGAAGGTGGCTATAGAGTGTA 57.875 43.478 3.21 0.00 0.00 2.90
2746 3416 2.678336 CCAAATGCGGTAGACTTCTTCC 59.322 50.000 0.00 0.00 0.00 3.46
2821 3491 2.859992 CCTAACAAGGGCAGACAGC 58.140 57.895 0.00 0.00 44.65 4.40
2964 3634 5.357878 ACAAATCTGTTCAGAGTTTGCTCAA 59.642 36.000 22.10 0.00 36.98 3.02
3085 3755 4.432712 CACTTTTAACTGCAGTGGCTTTT 58.567 39.130 22.49 5.84 41.91 2.27
3185 3855 5.892568 GAGTACACTCATTAACCTGTCGAT 58.107 41.667 4.48 0.00 42.42 3.59
3270 3940 4.634703 ATCACGTGCCCGCAACCA 62.635 61.111 11.67 0.00 37.70 3.67
3330 4000 8.345565 ACATTCAGATTACAAGAAGTGTTCAAC 58.654 33.333 0.00 0.00 41.98 3.18
3440 4110 6.097915 TGTCCGATTTTCTGTAGAGAAACT 57.902 37.500 14.20 9.52 45.90 2.66
3446 4116 6.942976 ACCTTATTGTCCGATTTTCTGTAGA 58.057 36.000 0.00 0.00 0.00 2.59
3594 4266 3.260884 TGAGAAGGCACGATTAACTCCTT 59.739 43.478 0.00 0.00 39.63 3.36
3763 4437 3.434984 GCGGAGATAATGAGATTTCCAGC 59.565 47.826 0.00 0.00 30.98 4.85
3793 4467 2.092646 CCCCTCAATCCCGATAACAACA 60.093 50.000 0.00 0.00 0.00 3.33
3838 4519 3.298686 AAGCTGTATAGAAAAGGGGGC 57.701 47.619 0.00 0.00 0.00 5.80
3914 4596 4.437390 CCAGTCAGAAATAAACATGCCGAC 60.437 45.833 0.00 0.00 0.00 4.79
4022 4706 3.876320 CTGCTCTTCTCAAGGAAATAGGC 59.124 47.826 0.00 0.00 33.07 3.93


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

AutoCloner maintained by Alex Coulton.