Multiple sequence alignment - TraesCS3D01G335200

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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 TraesCS3D01G335200 chr3D 100.000 3575 0 0 1 3575 447128214 447131788 0.000000e+00 6602.0
1 TraesCS3D01G335200 chr3A 96.131 2869 95 7 722 3575 588832799 588835666 0.000000e+00 4669.0
2 TraesCS3D01G335200 chr3A 96.040 101 4 0 207 307 588831586 588831686 7.940000e-37 165.0
3 TraesCS3D01G335200 chr3A 86.184 152 7 2 35 186 588828441 588828578 6.180000e-33 152.0
4 TraesCS3D01G335200 chr3A 96.471 85 3 0 302 386 588832708 588832792 1.340000e-29 141.0
5 TraesCS3D01G335200 chr3B 96.129 1524 56 1 2055 3575 586516704 586518227 0.000000e+00 2484.0
6 TraesCS3D01G335200 chr3B 95.220 1297 47 6 777 2064 586515243 586516533 0.000000e+00 2037.0
7 TraesCS3D01G335200 chr3B 93.077 130 6 3 1 127 586514915 586515044 1.690000e-43 187.0
8 TraesCS3D01G335200 chr3B 95.918 49 1 1 722 770 586515168 586515215 1.060000e-10 78.7
9 TraesCS3D01G335200 chr6B 90.758 541 41 2 3043 3575 707362546 707362007 0.000000e+00 713.0
10 TraesCS3D01G335200 chr1D 92.145 331 13 4 387 705 156288561 156288890 4.210000e-124 455.0
11 TraesCS3D01G335200 chr5D 91.265 332 17 2 387 706 7617203 7617534 3.280000e-120 442.0
12 TraesCS3D01G335200 chr5D 90.361 332 18 5 387 705 10759740 10760070 1.190000e-114 424.0
13 TraesCS3D01G335200 chr5D 90.000 330 20 4 388 705 210660418 210660746 7.140000e-112 414.0
14 TraesCS3D01G335200 chr5D 89.189 333 19 9 386 705 219468355 219468683 2.000000e-107 399.0
15 TraesCS3D01G335200 chr6D 91.331 323 25 3 384 705 423787065 423787385 4.240000e-119 438.0
16 TraesCS3D01G335200 chr6A 90.741 324 17 7 394 705 72985410 72985088 1.530000e-113 420.0
17 TraesCS3D01G335200 chr4D 89.583 336 20 5 384 705 68808476 68808142 2.570000e-111 412.0
18 TraesCS3D01G335200 chr7B 89.458 332 19 6 387 705 740255798 740255470 4.300000e-109 405.0
19 TraesCS3D01G335200 chr2D 90.794 315 12 8 406 705 644867900 644867588 4.300000e-109 405.0


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 TraesCS3D01G335200 chr3D 447128214 447131788 3574 False 6602.000 6602 100.0000 1 3575 1 chr3D.!!$F1 3574
1 TraesCS3D01G335200 chr3A 588828441 588835666 7225 False 1281.750 4669 93.7065 35 3575 4 chr3A.!!$F1 3540
2 TraesCS3D01G335200 chr3B 586514915 586518227 3312 False 1196.675 2484 95.0860 1 3575 4 chr3B.!!$F1 3574
3 TraesCS3D01G335200 chr6B 707362007 707362546 539 True 713.000 713 90.7580 3043 3575 1 chr6B.!!$R1 532

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
499 4520 0.034896 ATTTGAAGCGTGAGGTCCGT 59.965 50.0 0.0 0.0 43.76 4.69 F
500 4521 0.179067 TTTGAAGCGTGAGGTCCGTT 60.179 50.0 0.0 0.0 43.76 4.44 F
1188 5238 0.323087 TCTCGGTCTCGGTGGATGAA 60.323 55.0 0.0 0.0 36.95 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2374 6612 2.370281 ATGTAGTTCTGTGGCACTCG 57.630 50.0 19.83 10.03 0.0 4.18 R
2508 6746 1.384525 CACCACCGAAACTTGAACCA 58.615 50.0 0.00 0.00 0.0 3.67 R
2776 7014 0.250338 GTGGAGGAAACGGCAAGAGT 60.250 55.0 0.00 0.00 0.0 3.24 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
18 19 1.217511 CTGATGAGCACGAGCAGGT 59.782 57.895 7.77 0.00 45.49 4.00
24 25 2.740055 GCACGAGCAGGTGTCCAG 60.740 66.667 0.00 0.00 40.08 3.86
54 55 1.977854 AGCATGAGGTGTGTCTTGGTA 59.022 47.619 0.00 0.00 32.33 3.25
57 58 0.317160 TGAGGTGTGTCTTGGTAGCG 59.683 55.000 0.00 0.00 0.00 4.26
102 103 6.952935 GGAATACTCTTTCCACGCATATAG 57.047 41.667 0.00 0.00 43.92 1.31
158 159 6.992123 ACCATCATATAGTCTCATTCGCAAAA 59.008 34.615 0.00 0.00 0.00 2.44
159 160 7.041780 ACCATCATATAGTCTCATTCGCAAAAC 60.042 37.037 0.00 0.00 0.00 2.43
160 161 7.041848 CCATCATATAGTCTCATTCGCAAAACA 60.042 37.037 0.00 0.00 0.00 2.83
161 162 7.234187 TCATATAGTCTCATTCGCAAAACAC 57.766 36.000 0.00 0.00 0.00 3.32
162 163 6.816140 TCATATAGTCTCATTCGCAAAACACA 59.184 34.615 0.00 0.00 0.00 3.72
163 164 3.609103 AGTCTCATTCGCAAAACACAC 57.391 42.857 0.00 0.00 0.00 3.82
164 165 2.942376 AGTCTCATTCGCAAAACACACA 59.058 40.909 0.00 0.00 0.00 3.72
165 166 3.035942 GTCTCATTCGCAAAACACACAC 58.964 45.455 0.00 0.00 0.00 3.82
200 201 1.131771 CACGCATACGCCATCTAGTG 58.868 55.000 0.00 0.00 45.53 2.74
201 202 1.029681 ACGCATACGCCATCTAGTGA 58.970 50.000 0.00 0.00 45.53 3.41
203 204 2.159156 ACGCATACGCCATCTAGTGAAA 60.159 45.455 0.00 0.00 45.53 2.69
204 205 3.059884 CGCATACGCCATCTAGTGAAAT 58.940 45.455 0.00 0.00 33.11 2.17
205 206 3.120889 CGCATACGCCATCTAGTGAAATG 60.121 47.826 0.00 0.00 33.11 2.32
236 3230 1.078637 GTCCCCCGAAACTGCTACC 60.079 63.158 0.00 0.00 0.00 3.18
239 3233 1.677552 CCCCGAAACTGCTACCACT 59.322 57.895 0.00 0.00 0.00 4.00
240 3234 0.036306 CCCCGAAACTGCTACCACTT 59.964 55.000 0.00 0.00 0.00 3.16
296 3290 2.992124 TTTGGAGACGAGGTGAAACA 57.008 45.000 0.00 0.00 39.98 2.83
314 4335 1.171308 CAGCAGATGGTGGTTCCTTG 58.829 55.000 4.10 0.00 39.67 3.61
328 4349 5.710099 GTGGTTCCTTGATTATTCCTCACAA 59.290 40.000 0.00 0.00 0.00 3.33
357 4378 1.527380 GGCCACACGGGTCTTTCAA 60.527 57.895 0.00 0.00 38.65 2.69
386 4407 7.399245 TGCCCCTTATTCAACTTATTGTTAC 57.601 36.000 0.00 0.00 37.07 2.50
387 4408 6.094325 TGCCCCTTATTCAACTTATTGTTACG 59.906 38.462 0.00 0.00 37.07 3.18
389 4410 7.148205 GCCCCTTATTCAACTTATTGTTACGAA 60.148 37.037 0.00 0.00 37.07 3.85
390 4411 8.732531 CCCCTTATTCAACTTATTGTTACGAAA 58.267 33.333 0.00 0.00 37.07 3.46
395 4416 8.889849 ATTCAACTTATTGTTACGAAAATCCG 57.110 30.769 0.00 0.00 37.07 4.18
396 4417 6.308675 TCAACTTATTGTTACGAAAATCCGC 58.691 36.000 0.00 0.00 37.07 5.54
397 4418 5.866335 ACTTATTGTTACGAAAATCCGCA 57.134 34.783 0.00 0.00 0.00 5.69
398 4419 6.431198 ACTTATTGTTACGAAAATCCGCAT 57.569 33.333 0.00 0.00 0.00 4.73
399 4420 6.483687 ACTTATTGTTACGAAAATCCGCATC 58.516 36.000 0.00 0.00 0.00 3.91
400 4421 6.315393 ACTTATTGTTACGAAAATCCGCATCT 59.685 34.615 0.00 0.00 0.00 2.90
401 4422 4.335082 TTGTTACGAAAATCCGCATCTG 57.665 40.909 0.00 0.00 0.00 2.90
402 4423 3.591023 TGTTACGAAAATCCGCATCTGA 58.409 40.909 0.00 0.00 0.00 3.27
403 4424 3.997681 TGTTACGAAAATCCGCATCTGAA 59.002 39.130 0.00 0.00 0.00 3.02
404 4425 4.142988 TGTTACGAAAATCCGCATCTGAAC 60.143 41.667 0.00 0.00 0.00 3.18
405 4426 1.737793 ACGAAAATCCGCATCTGAACC 59.262 47.619 0.00 0.00 0.00 3.62
406 4427 1.064060 CGAAAATCCGCATCTGAACCC 59.936 52.381 0.00 0.00 0.00 4.11
407 4428 1.064060 GAAAATCCGCATCTGAACCCG 59.936 52.381 0.00 0.00 0.00 5.28
408 4429 0.748005 AAATCCGCATCTGAACCCGG 60.748 55.000 0.00 0.00 41.97 5.73
409 4430 2.608970 AATCCGCATCTGAACCCGGG 62.609 60.000 22.25 22.25 41.02 5.73
411 4432 4.473520 CGCATCTGAACCCGGGCT 62.474 66.667 24.08 8.98 0.00 5.19
412 4433 2.514824 GCATCTGAACCCGGGCTC 60.515 66.667 24.08 20.45 0.00 4.70
413 4434 2.989639 CATCTGAACCCGGGCTCA 59.010 61.111 24.84 24.84 0.00 4.26
414 4435 1.153289 CATCTGAACCCGGGCTCAG 60.153 63.158 37.86 37.86 39.07 3.35
415 4436 1.306141 ATCTGAACCCGGGCTCAGA 60.306 57.895 43.60 43.60 46.87 3.27
416 4437 0.692419 ATCTGAACCCGGGCTCAGAT 60.692 55.000 43.79 43.79 46.61 2.90
417 4438 1.153289 CTGAACCCGGGCTCAGATG 60.153 63.158 39.74 20.45 39.83 2.90
418 4439 2.514824 GAACCCGGGCTCAGATGC 60.515 66.667 24.08 0.00 0.00 3.91
419 4440 3.011517 AACCCGGGCTCAGATGCT 61.012 61.111 24.08 0.00 0.00 3.79
420 4441 2.932130 GAACCCGGGCTCAGATGCTC 62.932 65.000 24.08 0.00 0.00 4.26
421 4442 4.247380 CCCGGGCTCAGATGCTCC 62.247 72.222 8.08 0.00 0.00 4.70
422 4443 4.247380 CCGGGCTCAGATGCTCCC 62.247 72.222 0.00 0.00 35.42 4.30
424 4445 4.925861 GGGCTCAGATGCTCCCGC 62.926 72.222 0.00 0.00 0.00 6.13
425 4446 3.859414 GGCTCAGATGCTCCCGCT 61.859 66.667 0.00 0.00 36.97 5.52
426 4447 2.280052 GCTCAGATGCTCCCGCTC 60.280 66.667 0.00 0.00 36.97 5.03
427 4448 3.086391 GCTCAGATGCTCCCGCTCA 62.086 63.158 0.00 0.00 36.97 4.26
428 4449 1.519246 CTCAGATGCTCCCGCTCAA 59.481 57.895 0.00 0.00 36.97 3.02
432 4453 1.135575 CAGATGCTCCCGCTCAAAAAC 60.136 52.381 0.00 0.00 36.97 2.43
435 4456 1.107114 TGCTCCCGCTCAAAAACAAA 58.893 45.000 0.00 0.00 36.97 2.83
437 4458 2.887783 TGCTCCCGCTCAAAAACAAATA 59.112 40.909 0.00 0.00 36.97 1.40
438 4459 3.242518 GCTCCCGCTCAAAAACAAATAC 58.757 45.455 0.00 0.00 0.00 1.89
439 4460 3.057526 GCTCCCGCTCAAAAACAAATACT 60.058 43.478 0.00 0.00 0.00 2.12
441 4462 5.616488 TCCCGCTCAAAAACAAATACTAC 57.384 39.130 0.00 0.00 0.00 2.73
488 4509 8.810652 TTTTTGTGTGGTAGATAATTTGAAGC 57.189 30.769 0.00 0.00 0.00 3.86
489 4510 5.794687 TGTGTGGTAGATAATTTGAAGCG 57.205 39.130 0.00 0.00 0.00 4.68
490 4511 5.242434 TGTGTGGTAGATAATTTGAAGCGT 58.758 37.500 0.00 0.00 0.00 5.07
491 4512 5.121611 TGTGTGGTAGATAATTTGAAGCGTG 59.878 40.000 0.00 0.00 0.00 5.34
492 4513 5.350365 GTGTGGTAGATAATTTGAAGCGTGA 59.650 40.000 0.00 0.00 0.00 4.35
493 4514 5.580691 TGTGGTAGATAATTTGAAGCGTGAG 59.419 40.000 0.00 0.00 0.00 3.51
494 4515 5.006746 GTGGTAGATAATTTGAAGCGTGAGG 59.993 44.000 0.00 0.00 0.00 3.86
496 4517 5.234543 GGTAGATAATTTGAAGCGTGAGGTC 59.765 44.000 0.00 0.00 43.76 3.85
497 4518 4.192317 AGATAATTTGAAGCGTGAGGTCC 58.808 43.478 0.00 0.00 43.76 4.46
498 4519 1.156736 AATTTGAAGCGTGAGGTCCG 58.843 50.000 0.00 0.00 43.76 4.79
499 4520 0.034896 ATTTGAAGCGTGAGGTCCGT 59.965 50.000 0.00 0.00 43.76 4.69
500 4521 0.179067 TTTGAAGCGTGAGGTCCGTT 60.179 50.000 0.00 0.00 43.76 4.44
501 4522 0.179067 TTGAAGCGTGAGGTCCGTTT 60.179 50.000 0.00 0.00 43.76 3.60
502 4523 0.179067 TGAAGCGTGAGGTCCGTTTT 60.179 50.000 0.00 0.00 43.76 2.43
503 4524 1.068895 TGAAGCGTGAGGTCCGTTTTA 59.931 47.619 0.00 0.00 43.76 1.52
504 4525 2.137523 GAAGCGTGAGGTCCGTTTTAA 58.862 47.619 0.00 0.00 43.76 1.52
505 4526 2.243602 AGCGTGAGGTCCGTTTTAAA 57.756 45.000 0.00 0.00 37.07 1.52
506 4527 2.774687 AGCGTGAGGTCCGTTTTAAAT 58.225 42.857 0.00 0.00 37.07 1.40
507 4528 3.143728 AGCGTGAGGTCCGTTTTAAATT 58.856 40.909 0.00 0.00 37.07 1.82
508 4529 3.566742 AGCGTGAGGTCCGTTTTAAATTT 59.433 39.130 0.00 0.00 37.07 1.82
509 4530 3.910170 GCGTGAGGTCCGTTTTAAATTTC 59.090 43.478 0.00 0.00 0.00 2.17
510 4531 4.555116 GCGTGAGGTCCGTTTTAAATTTCA 60.555 41.667 0.00 0.00 0.00 2.69
511 4532 5.512473 CGTGAGGTCCGTTTTAAATTTCAA 58.488 37.500 0.00 0.00 0.00 2.69
512 4533 5.397240 CGTGAGGTCCGTTTTAAATTTCAAC 59.603 40.000 0.00 0.00 0.00 3.18
513 4534 6.500910 GTGAGGTCCGTTTTAAATTTCAACT 58.499 36.000 0.00 0.00 0.00 3.16
514 4535 6.635641 GTGAGGTCCGTTTTAAATTTCAACTC 59.364 38.462 0.00 0.00 0.00 3.01
515 4536 6.319152 TGAGGTCCGTTTTAAATTTCAACTCA 59.681 34.615 0.00 0.00 0.00 3.41
516 4537 7.013846 TGAGGTCCGTTTTAAATTTCAACTCAT 59.986 33.333 0.00 0.00 0.00 2.90
517 4538 7.722363 AGGTCCGTTTTAAATTTCAACTCATT 58.278 30.769 0.00 0.00 0.00 2.57
518 4539 8.201464 AGGTCCGTTTTAAATTTCAACTCATTT 58.799 29.630 0.00 0.00 0.00 2.32
519 4540 8.272866 GGTCCGTTTTAAATTTCAACTCATTTG 58.727 33.333 0.00 0.00 36.42 2.32
520 4541 8.272866 GTCCGTTTTAAATTTCAACTCATTTGG 58.727 33.333 0.00 0.00 35.69 3.28
521 4542 8.198109 TCCGTTTTAAATTTCAACTCATTTGGA 58.802 29.630 0.00 0.00 35.69 3.53
522 4543 8.987890 CCGTTTTAAATTTCAACTCATTTGGAT 58.012 29.630 0.00 0.00 35.69 3.41
530 4551 6.932356 TTCAACTCATTTGGATATCTGAGC 57.068 37.500 15.91 0.00 38.94 4.26
531 4552 5.993055 TCAACTCATTTGGATATCTGAGCA 58.007 37.500 15.91 0.00 38.94 4.26
532 4553 6.053650 TCAACTCATTTGGATATCTGAGCAG 58.946 40.000 15.91 10.63 38.94 4.24
533 4554 4.387598 ACTCATTTGGATATCTGAGCAGC 58.612 43.478 15.91 0.00 38.94 5.25
534 4555 4.102838 ACTCATTTGGATATCTGAGCAGCT 59.897 41.667 15.91 0.00 38.94 4.24
535 4556 4.639334 TCATTTGGATATCTGAGCAGCTC 58.361 43.478 16.21 16.21 0.00 4.09
536 4557 4.347292 TCATTTGGATATCTGAGCAGCTCT 59.653 41.667 23.15 5.93 0.00 4.09
537 4558 4.333913 TTTGGATATCTGAGCAGCTCTC 57.666 45.455 23.15 11.57 42.23 3.20
538 4559 1.885233 TGGATATCTGAGCAGCTCTCG 59.115 52.381 23.15 13.93 44.86 4.04
540 4561 0.602562 ATATCTGAGCAGCTCTCGGC 59.397 55.000 23.15 0.00 45.76 5.54
541 4562 0.753111 TATCTGAGCAGCTCTCGGCA 60.753 55.000 23.15 2.15 45.76 5.69
542 4563 1.611474 ATCTGAGCAGCTCTCGGCAA 61.611 55.000 23.15 0.68 45.76 4.52
543 4564 1.375140 CTGAGCAGCTCTCGGCAAA 60.375 57.895 23.15 0.00 44.86 3.68
544 4565 0.952497 CTGAGCAGCTCTCGGCAAAA 60.952 55.000 23.15 0.00 44.86 2.44
545 4566 0.534877 TGAGCAGCTCTCGGCAAAAA 60.535 50.000 23.15 0.00 44.86 1.94
565 4586 4.993029 AAAGACAAATCGGGTCAAAACA 57.007 36.364 0.00 0.00 37.74 2.83
566 4587 4.568152 AAGACAAATCGGGTCAAAACAG 57.432 40.909 0.00 0.00 37.74 3.16
567 4588 3.551846 AGACAAATCGGGTCAAAACAGT 58.448 40.909 0.00 0.00 37.74 3.55
568 4589 3.951680 AGACAAATCGGGTCAAAACAGTT 59.048 39.130 0.00 0.00 37.74 3.16
569 4590 4.036380 AGACAAATCGGGTCAAAACAGTTC 59.964 41.667 0.00 0.00 37.74 3.01
570 4591 3.242936 ACAAATCGGGTCAAAACAGTTCG 60.243 43.478 0.00 0.00 0.00 3.95
571 4592 2.249844 ATCGGGTCAAAACAGTTCGT 57.750 45.000 0.00 0.00 0.00 3.85
572 4593 1.292061 TCGGGTCAAAACAGTTCGTG 58.708 50.000 0.00 0.00 0.00 4.35
573 4594 1.134759 TCGGGTCAAAACAGTTCGTGA 60.135 47.619 0.00 0.00 0.00 4.35
574 4595 1.666700 CGGGTCAAAACAGTTCGTGAA 59.333 47.619 2.00 0.00 0.00 3.18
575 4596 2.538132 CGGGTCAAAACAGTTCGTGAAC 60.538 50.000 4.58 4.58 41.45 3.18
576 4597 2.420722 GGGTCAAAACAGTTCGTGAACA 59.579 45.455 14.61 0.00 43.47 3.18
577 4598 3.119779 GGGTCAAAACAGTTCGTGAACAA 60.120 43.478 14.61 0.00 43.47 2.83
578 4599 4.439563 GGGTCAAAACAGTTCGTGAACAAT 60.440 41.667 14.61 0.00 43.47 2.71
579 4600 5.220892 GGGTCAAAACAGTTCGTGAACAATA 60.221 40.000 14.61 0.00 43.47 1.90
580 4601 6.259638 GGTCAAAACAGTTCGTGAACAATAA 58.740 36.000 14.61 0.00 43.47 1.40
581 4602 6.748198 GGTCAAAACAGTTCGTGAACAATAAA 59.252 34.615 14.61 0.00 43.47 1.40
582 4603 7.253519 GGTCAAAACAGTTCGTGAACAATAAAC 60.254 37.037 14.61 4.48 43.47 2.01
583 4604 7.483691 GTCAAAACAGTTCGTGAACAATAAACT 59.516 33.333 14.61 0.00 43.47 2.66
584 4605 8.024285 TCAAAACAGTTCGTGAACAATAAACTT 58.976 29.630 14.61 0.00 43.47 2.66
585 4606 8.643752 CAAAACAGTTCGTGAACAATAAACTTT 58.356 29.630 14.61 2.59 43.47 2.66
586 4607 8.751302 AAACAGTTCGTGAACAATAAACTTTT 57.249 26.923 14.61 0.65 43.47 2.27
587 4608 8.751302 AACAGTTCGTGAACAATAAACTTTTT 57.249 26.923 14.61 0.00 43.47 1.94
606 4627 5.441709 TTTTTACAGACCCCGATTTTGTC 57.558 39.130 0.00 0.00 0.00 3.18
607 4628 4.360951 TTTACAGACCCCGATTTTGTCT 57.639 40.909 0.00 0.00 39.86 3.41
608 4629 2.951229 ACAGACCCCGATTTTGTCTT 57.049 45.000 0.00 0.00 37.25 3.01
609 4630 3.223674 ACAGACCCCGATTTTGTCTTT 57.776 42.857 0.00 0.00 37.25 2.52
610 4631 3.562182 ACAGACCCCGATTTTGTCTTTT 58.438 40.909 0.00 0.00 37.25 2.27
611 4632 3.958147 ACAGACCCCGATTTTGTCTTTTT 59.042 39.130 0.00 0.00 37.25 1.94
635 4656 4.069300 CAGAGAGCTGCTCAAATATCCA 57.931 45.455 29.49 0.00 46.45 3.41
636 4657 4.449131 CAGAGAGCTGCTCAAATATCCAA 58.551 43.478 29.49 0.00 46.45 3.53
637 4658 4.880120 CAGAGAGCTGCTCAAATATCCAAA 59.120 41.667 29.49 0.00 46.45 3.28
638 4659 4.880696 AGAGAGCTGCTCAAATATCCAAAC 59.119 41.667 29.49 0.21 46.45 2.93
639 4660 3.624861 AGAGCTGCTCAAATATCCAAACG 59.375 43.478 29.49 0.00 32.06 3.60
640 4661 3.609853 AGCTGCTCAAATATCCAAACGA 58.390 40.909 0.00 0.00 0.00 3.85
641 4662 3.624861 AGCTGCTCAAATATCCAAACGAG 59.375 43.478 0.00 0.00 0.00 4.18
642 4663 3.375299 GCTGCTCAAATATCCAAACGAGT 59.625 43.478 0.00 0.00 0.00 4.18
643 4664 4.142600 GCTGCTCAAATATCCAAACGAGTT 60.143 41.667 0.00 0.00 0.00 3.01
644 4665 5.295431 TGCTCAAATATCCAAACGAGTTG 57.705 39.130 0.00 0.00 36.94 3.16
645 4666 5.000591 TGCTCAAATATCCAAACGAGTTGA 58.999 37.500 5.36 0.00 39.87 3.18
646 4667 5.471797 TGCTCAAATATCCAAACGAGTTGAA 59.528 36.000 5.36 0.00 39.87 2.69
647 4668 6.016693 TGCTCAAATATCCAAACGAGTTGAAA 60.017 34.615 5.36 0.00 39.87 2.69
648 4669 7.029563 GCTCAAATATCCAAACGAGTTGAAAT 58.970 34.615 5.36 2.46 39.87 2.17
649 4670 7.542130 GCTCAAATATCCAAACGAGTTGAAATT 59.458 33.333 5.36 0.91 39.87 1.82
650 4671 9.410556 CTCAAATATCCAAACGAGTTGAAATTT 57.589 29.630 0.00 0.00 39.87 1.82
651 4672 9.190858 TCAAATATCCAAACGAGTTGAAATTTG 57.809 29.630 18.29 18.29 39.87 2.32
652 4673 7.581011 AATATCCAAACGAGTTGAAATTTGC 57.419 32.000 0.00 0.00 39.87 3.68
653 4674 4.377839 TCCAAACGAGTTGAAATTTGCA 57.622 36.364 0.00 0.00 39.87 4.08
654 4675 4.358851 TCCAAACGAGTTGAAATTTGCAG 58.641 39.130 0.00 0.00 39.87 4.41
655 4676 3.060339 CCAAACGAGTTGAAATTTGCAGC 60.060 43.478 0.00 0.00 39.87 5.25
656 4677 3.715628 AACGAGTTGAAATTTGCAGCT 57.284 38.095 0.00 1.16 0.00 4.24
657 4678 4.829064 AACGAGTTGAAATTTGCAGCTA 57.171 36.364 0.00 0.00 0.00 3.32
658 4679 4.829064 ACGAGTTGAAATTTGCAGCTAA 57.171 36.364 0.00 0.00 0.00 3.09
659 4680 4.537015 ACGAGTTGAAATTTGCAGCTAAC 58.463 39.130 0.00 0.00 0.00 2.34
660 4681 3.914364 CGAGTTGAAATTTGCAGCTAACC 59.086 43.478 0.00 0.00 0.00 2.85
661 4682 4.320494 CGAGTTGAAATTTGCAGCTAACCT 60.320 41.667 0.00 0.00 0.00 3.50
662 4683 5.126396 AGTTGAAATTTGCAGCTAACCTC 57.874 39.130 0.00 0.00 0.00 3.85
663 4684 4.584325 AGTTGAAATTTGCAGCTAACCTCA 59.416 37.500 0.00 0.00 0.00 3.86
664 4685 5.244626 AGTTGAAATTTGCAGCTAACCTCAT 59.755 36.000 0.00 0.00 0.00 2.90
665 4686 5.063180 TGAAATTTGCAGCTAACCTCATG 57.937 39.130 0.00 0.00 0.00 3.07
666 4687 3.515330 AATTTGCAGCTAACCTCATGC 57.485 42.857 0.00 0.00 39.14 4.06
667 4688 1.908344 TTTGCAGCTAACCTCATGCA 58.092 45.000 0.00 0.00 46.29 3.96
668 4689 3.888424 TGCAGCTAACCTCATGCAT 57.112 47.368 0.00 0.00 43.34 3.96
669 4690 1.671979 TGCAGCTAACCTCATGCATC 58.328 50.000 0.00 0.00 43.34 3.91
670 4691 1.065272 TGCAGCTAACCTCATGCATCA 60.065 47.619 0.00 0.00 43.34 3.07
671 4692 2.019249 GCAGCTAACCTCATGCATCAA 58.981 47.619 0.00 0.00 38.54 2.57
672 4693 2.424601 GCAGCTAACCTCATGCATCAAA 59.575 45.455 0.00 0.00 38.54 2.69
673 4694 3.067742 GCAGCTAACCTCATGCATCAAAT 59.932 43.478 0.00 0.00 38.54 2.32
674 4695 4.441079 GCAGCTAACCTCATGCATCAAATT 60.441 41.667 0.00 0.00 38.54 1.82
675 4696 5.221106 GCAGCTAACCTCATGCATCAAATTA 60.221 40.000 0.00 0.00 38.54 1.40
676 4697 6.516194 GCAGCTAACCTCATGCATCAAATTAT 60.516 38.462 0.00 0.00 38.54 1.28
677 4698 7.082602 CAGCTAACCTCATGCATCAAATTATC 58.917 38.462 0.00 0.00 0.00 1.75
678 4699 7.002879 AGCTAACCTCATGCATCAAATTATCT 58.997 34.615 0.00 0.00 0.00 1.98
679 4700 8.159447 AGCTAACCTCATGCATCAAATTATCTA 58.841 33.333 0.00 0.00 0.00 1.98
680 4701 8.233190 GCTAACCTCATGCATCAAATTATCTAC 58.767 37.037 0.00 0.00 0.00 2.59
681 4702 7.516198 AACCTCATGCATCAAATTATCTACC 57.484 36.000 0.00 0.00 0.00 3.18
682 4703 6.604171 ACCTCATGCATCAAATTATCTACCA 58.396 36.000 0.00 0.00 0.00 3.25
683 4704 6.488006 ACCTCATGCATCAAATTATCTACCAC 59.512 38.462 0.00 0.00 0.00 4.16
684 4705 6.487668 CCTCATGCATCAAATTATCTACCACA 59.512 38.462 0.00 0.00 0.00 4.17
685 4706 7.263100 TCATGCATCAAATTATCTACCACAC 57.737 36.000 0.00 0.00 0.00 3.82
686 4707 6.827762 TCATGCATCAAATTATCTACCACACA 59.172 34.615 0.00 0.00 0.00 3.72
687 4708 7.338957 TCATGCATCAAATTATCTACCACACAA 59.661 33.333 0.00 0.00 0.00 3.33
688 4709 7.459795 TGCATCAAATTATCTACCACACAAA 57.540 32.000 0.00 0.00 0.00 2.83
689 4710 7.890515 TGCATCAAATTATCTACCACACAAAA 58.109 30.769 0.00 0.00 0.00 2.44
690 4711 8.363390 TGCATCAAATTATCTACCACACAAAAA 58.637 29.630 0.00 0.00 0.00 1.94
711 4732 6.403866 AAAAATTTGGAATTTTTGGGAGCC 57.596 33.333 18.19 0.00 39.07 4.70
712 4733 4.720775 AATTTGGAATTTTTGGGAGCCA 57.279 36.364 0.00 0.00 0.00 4.75
713 4734 4.720775 ATTTGGAATTTTTGGGAGCCAA 57.279 36.364 0.00 0.00 42.29 4.52
756 4777 7.018235 GCCAAAGAAAGATAGAAAAGAGAACG 58.982 38.462 0.00 0.00 0.00 3.95
844 4886 5.066505 GCCACAACTTTAGAATCGATTCCAT 59.933 40.000 29.82 17.65 37.51 3.41
871 4918 1.676006 AGGGAAGCAACAAACACGAAG 59.324 47.619 0.00 0.00 0.00 3.79
874 4921 2.111756 GAAGCAACAAACACGAAGCAG 58.888 47.619 0.00 0.00 0.00 4.24
875 4922 0.381801 AGCAACAAACACGAAGCAGG 59.618 50.000 0.00 0.00 0.00 4.85
947 4997 3.327464 TGGGATGATAAATCTCCGCATCA 59.673 43.478 0.00 0.00 37.63 3.07
961 5011 1.066573 CGCATCATATCCCCTGGTCTC 60.067 57.143 0.00 0.00 0.00 3.36
978 5028 1.629861 TCTCCATCACATCCTGCAACA 59.370 47.619 0.00 0.00 0.00 3.33
980 5030 1.352017 TCCATCACATCCTGCAACACT 59.648 47.619 0.00 0.00 0.00 3.55
1119 5169 0.987294 ATCCCAGCAGCAAGTACTGT 59.013 50.000 0.00 0.00 39.96 3.55
1134 5184 2.831685 ACTGTACCAAGATTGACGCA 57.168 45.000 0.00 0.00 0.00 5.24
1188 5238 0.323087 TCTCGGTCTCGGTGGATGAA 60.323 55.000 0.00 0.00 36.95 2.57
1200 5250 1.600957 GTGGATGAACATGATCTGGCG 59.399 52.381 0.00 0.00 0.00 5.69
1227 5277 2.873245 GCAGATGGAGCTGACAGTTGAA 60.873 50.000 3.99 0.00 38.14 2.69
1319 5369 6.862209 AGTATCTTGACAAGTTTGCACAAAA 58.138 32.000 14.75 0.00 31.32 2.44
1352 5402 4.411013 TCAGAAGTCATTGAGGAGACTGA 58.589 43.478 0.00 0.00 43.88 3.41
1533 5583 4.979943 TGCTGATCAAAACACTTTCACA 57.020 36.364 0.00 0.00 0.00 3.58
1611 5662 7.665559 AGAATGGCAGTCAGAACTAAAATAACA 59.334 33.333 18.00 0.00 33.25 2.41
1612 5663 7.759489 ATGGCAGTCAGAACTAAAATAACAA 57.241 32.000 0.00 0.00 33.25 2.83
1613 5664 7.759489 TGGCAGTCAGAACTAAAATAACAAT 57.241 32.000 0.00 0.00 33.25 2.71
1772 5828 6.174720 TCTTTATCGGCAAATCTATCCACT 57.825 37.500 0.00 0.00 0.00 4.00
1774 5830 7.152645 TCTTTATCGGCAAATCTATCCACTAC 58.847 38.462 0.00 0.00 0.00 2.73
1788 5844 8.603898 TCTATCCACTACTTGTAAGGAAATGA 57.396 34.615 5.96 3.56 31.17 2.57
1820 5876 2.791383 TTGGATGGAAAAGCACAACG 57.209 45.000 0.00 0.00 0.00 4.10
1937 5993 2.005451 GTCAGCATGCTTGGTAGAGTG 58.995 52.381 19.98 4.27 34.76 3.51
1961 6019 5.121925 GTGCTGCCATGATAGTCATAAGATG 59.878 44.000 0.00 0.00 34.28 2.90
1999 6057 4.669700 ACCATCAAAAGGGTAAAGGGTAC 58.330 43.478 0.00 0.00 37.93 3.34
2139 6377 2.045708 GGTCGGCATCACATTGGCA 61.046 57.895 0.00 0.00 41.97 4.92
2508 6746 1.061546 TTGGCGAAACCCTCTTACCT 58.938 50.000 0.00 0.00 37.83 3.08
2512 6750 1.271217 GCGAAACCCTCTTACCTGGTT 60.271 52.381 3.84 0.00 44.04 3.67
2622 6860 8.073768 GTCAGTGCTAGCTTGTAACAAAATAAA 58.926 33.333 17.23 0.00 0.00 1.40
2623 6861 8.792633 TCAGTGCTAGCTTGTAACAAAATAAAT 58.207 29.630 17.23 0.00 0.00 1.40
2698 6936 5.221126 GCAATCCCTCATCCAACTTATCAAC 60.221 44.000 0.00 0.00 0.00 3.18
2722 6960 6.982141 ACGAATGCAGCATTTCATAAATCATT 59.018 30.769 21.73 0.00 33.90 2.57
2730 6968 7.169308 CAGCATTTCATAAATCATTTCAGCCTC 59.831 37.037 0.00 0.00 0.00 4.70
2731 6969 6.982141 GCATTTCATAAATCATTTCAGCCTCA 59.018 34.615 0.00 0.00 0.00 3.86
2765 7003 0.030101 GCCACTAACAAAAGCGTGCA 59.970 50.000 0.00 0.00 0.00 4.57
2766 7004 1.335872 GCCACTAACAAAAGCGTGCAT 60.336 47.619 0.00 0.00 0.00 3.96
2776 7014 1.890876 AAGCGTGCATAACTGTTCCA 58.109 45.000 0.00 0.00 0.00 3.53
2781 7019 3.067106 CGTGCATAACTGTTCCACTCTT 58.933 45.455 0.00 0.00 0.00 2.85
2802 7040 1.196104 CCGTTTCCTCCACCCACCTA 61.196 60.000 0.00 0.00 0.00 3.08
2943 7184 4.821589 CCCAGGCTCCTTCGTCGC 62.822 72.222 0.00 0.00 0.00 5.19
3052 7293 0.399091 CATCCCCTGCCTCCTCTACA 60.399 60.000 0.00 0.00 0.00 2.74
3102 7343 1.642037 CGCCCAAGCATGTCAGTCAG 61.642 60.000 0.00 0.00 39.83 3.51
3122 7363 0.826715 ACATGCGTAGTGCTCCATCT 59.173 50.000 0.00 0.00 46.63 2.90
3160 7401 8.195165 TGAACTCCTCTTTCATTCTCTTAAGA 57.805 34.615 4.81 4.81 0.00 2.10
3162 7403 9.150348 GAACTCCTCTTTCATTCTCTTAAGAAG 57.850 37.037 6.63 0.00 44.53 2.85
3164 7405 8.875168 ACTCCTCTTTCATTCTCTTAAGAAGAA 58.125 33.333 6.63 12.06 44.53 2.52
3190 7431 2.486548 CCCTTCTTCGACAAACCCAGAA 60.487 50.000 0.00 0.00 0.00 3.02
3229 7470 0.610174 CTGCCAGCAGAGTTACCTCA 59.390 55.000 14.54 0.00 46.30 3.86
3272 7513 0.396435 TGTCATCTGGCGGAACAACT 59.604 50.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.674895 ACCTCATGCTTGTCCGCTTC 60.675 55.000 0.00 0.00 0.00 3.86
54 55 3.993081 GCTAATCTGAATGATAGTGCGCT 59.007 43.478 9.73 4.58 34.45 5.92
57 58 5.994054 TCCAAGCTAATCTGAATGATAGTGC 59.006 40.000 0.00 0.00 34.45 4.40
129 130 6.254589 GCGAATGAGACTATATGATGGTTAGC 59.745 42.308 0.00 0.00 0.00 3.09
158 159 1.669437 TGTGCGTGTGTGTGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
159 160 1.225991 GTGTGCGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
160 161 2.735677 CGTGTGCGTGTGTGTGTGT 61.736 57.895 0.00 0.00 0.00 3.72
161 162 2.021243 CGTGTGCGTGTGTGTGTG 59.979 61.111 0.00 0.00 0.00 3.82
162 163 3.860125 GCGTGTGCGTGTGTGTGT 61.860 61.111 0.00 0.00 40.81 3.72
187 188 6.459670 TCTTACATTTCACTAGATGGCGTA 57.540 37.500 0.00 0.00 0.00 4.42
200 201 4.217767 GGGGACACCAGTTTCTTACATTTC 59.782 45.833 0.00 0.00 39.85 2.17
201 202 4.149598 GGGGACACCAGTTTCTTACATTT 58.850 43.478 0.00 0.00 39.85 2.32
203 204 2.041216 GGGGGACACCAGTTTCTTACAT 59.959 50.000 0.00 0.00 42.91 2.29
204 205 1.422402 GGGGGACACCAGTTTCTTACA 59.578 52.381 0.00 0.00 42.91 2.41
205 206 1.609841 CGGGGGACACCAGTTTCTTAC 60.610 57.143 0.00 0.00 42.91 2.34
236 3230 2.210116 ACGTGTCTGTTAGGCAAAGTG 58.790 47.619 0.00 0.00 28.00 3.16
239 3233 2.479837 CTGACGTGTCTGTTAGGCAAA 58.520 47.619 0.00 0.00 28.00 3.68
240 3234 1.872237 GCTGACGTGTCTGTTAGGCAA 60.872 52.381 0.00 0.00 28.00 4.52
296 3290 1.067295 TCAAGGAACCACCATCTGCT 58.933 50.000 0.00 0.00 42.04 4.24
328 4349 2.842462 TGTGGCCGTGTCCTCTGT 60.842 61.111 0.00 0.00 0.00 3.41
357 4378 3.105959 AGTTGAATAAGGGGCAGCAAT 57.894 42.857 0.00 0.00 0.00 3.56
386 4407 1.064060 GGGTTCAGATGCGGATTTTCG 59.936 52.381 0.00 0.00 0.00 3.46
387 4408 1.064060 CGGGTTCAGATGCGGATTTTC 59.936 52.381 0.00 0.00 0.00 2.29
389 4410 0.748005 CCGGGTTCAGATGCGGATTT 60.748 55.000 0.00 0.00 0.00 2.17
390 4411 1.153168 CCGGGTTCAGATGCGGATT 60.153 57.895 0.00 0.00 0.00 3.01
391 4412 2.505982 CCGGGTTCAGATGCGGAT 59.494 61.111 0.00 0.00 0.00 4.18
392 4413 3.781307 CCCGGGTTCAGATGCGGA 61.781 66.667 14.18 0.00 0.00 5.54
394 4415 4.473520 AGCCCGGGTTCAGATGCG 62.474 66.667 24.63 0.00 0.00 4.73
395 4416 2.514824 GAGCCCGGGTTCAGATGC 60.515 66.667 30.55 9.77 0.00 3.91
396 4417 2.989639 TGAGCCCGGGTTCAGATG 59.010 61.111 33.78 0.11 31.87 2.90
400 4421 2.989639 CATCTGAGCCCGGGTTCA 59.010 61.111 34.56 34.56 34.34 3.18
401 4422 2.514824 GCATCTGAGCCCGGGTTC 60.515 66.667 29.11 29.11 0.00 3.62
402 4423 3.011517 AGCATCTGAGCCCGGGTT 61.012 61.111 24.63 18.47 34.23 4.11
403 4424 3.474570 GAGCATCTGAGCCCGGGT 61.475 66.667 24.63 9.10 34.23 5.28
404 4425 4.247380 GGAGCATCTGAGCCCGGG 62.247 72.222 19.09 19.09 33.73 5.73
405 4426 4.247380 GGGAGCATCTGAGCCCGG 62.247 72.222 0.00 0.00 33.73 5.73
418 4439 4.766404 AGTATTTGTTTTTGAGCGGGAG 57.234 40.909 0.00 0.00 0.00 4.30
419 4440 5.064558 TGTAGTATTTGTTTTTGAGCGGGA 58.935 37.500 0.00 0.00 0.00 5.14
420 4441 5.365403 TGTAGTATTTGTTTTTGAGCGGG 57.635 39.130 0.00 0.00 0.00 6.13
421 4442 7.687005 TTTTGTAGTATTTGTTTTTGAGCGG 57.313 32.000 0.00 0.00 0.00 5.52
463 4484 7.593273 CGCTTCAAATTATCTACCACACAAAAA 59.407 33.333 0.00 0.00 0.00 1.94
464 4485 7.081349 CGCTTCAAATTATCTACCACACAAAA 58.919 34.615 0.00 0.00 0.00 2.44
465 4486 6.205853 ACGCTTCAAATTATCTACCACACAAA 59.794 34.615 0.00 0.00 0.00 2.83
466 4487 5.703592 ACGCTTCAAATTATCTACCACACAA 59.296 36.000 0.00 0.00 0.00 3.33
467 4488 5.121611 CACGCTTCAAATTATCTACCACACA 59.878 40.000 0.00 0.00 0.00 3.72
468 4489 5.350365 TCACGCTTCAAATTATCTACCACAC 59.650 40.000 0.00 0.00 0.00 3.82
469 4490 5.483811 TCACGCTTCAAATTATCTACCACA 58.516 37.500 0.00 0.00 0.00 4.17
470 4491 5.006746 CCTCACGCTTCAAATTATCTACCAC 59.993 44.000 0.00 0.00 0.00 4.16
471 4492 5.116180 CCTCACGCTTCAAATTATCTACCA 58.884 41.667 0.00 0.00 0.00 3.25
472 4493 5.116882 ACCTCACGCTTCAAATTATCTACC 58.883 41.667 0.00 0.00 0.00 3.18
473 4494 5.234543 GGACCTCACGCTTCAAATTATCTAC 59.765 44.000 0.00 0.00 0.00 2.59
474 4495 5.357257 GGACCTCACGCTTCAAATTATCTA 58.643 41.667 0.00 0.00 0.00 1.98
475 4496 4.192317 GGACCTCACGCTTCAAATTATCT 58.808 43.478 0.00 0.00 0.00 1.98
476 4497 3.001330 CGGACCTCACGCTTCAAATTATC 59.999 47.826 0.00 0.00 0.00 1.75
477 4498 2.936498 CGGACCTCACGCTTCAAATTAT 59.064 45.455 0.00 0.00 0.00 1.28
478 4499 2.289195 ACGGACCTCACGCTTCAAATTA 60.289 45.455 0.00 0.00 34.00 1.40
479 4500 1.156736 CGGACCTCACGCTTCAAATT 58.843 50.000 0.00 0.00 0.00 1.82
480 4501 0.034896 ACGGACCTCACGCTTCAAAT 59.965 50.000 0.00 0.00 34.00 2.32
481 4502 0.179067 AACGGACCTCACGCTTCAAA 60.179 50.000 0.00 0.00 34.00 2.69
482 4503 0.179067 AAACGGACCTCACGCTTCAA 60.179 50.000 0.00 0.00 34.00 2.69
483 4504 0.179067 AAAACGGACCTCACGCTTCA 60.179 50.000 0.00 0.00 34.00 3.02
484 4505 1.787012 TAAAACGGACCTCACGCTTC 58.213 50.000 0.00 0.00 34.00 3.86
485 4506 2.243602 TTAAAACGGACCTCACGCTT 57.756 45.000 0.00 0.00 34.00 4.68
486 4507 2.243602 TTTAAAACGGACCTCACGCT 57.756 45.000 0.00 0.00 34.00 5.07
487 4508 3.547649 AATTTAAAACGGACCTCACGC 57.452 42.857 0.00 0.00 34.00 5.34
488 4509 5.098218 TGAAATTTAAAACGGACCTCACG 57.902 39.130 0.00 0.00 37.36 4.35
489 4510 6.500910 AGTTGAAATTTAAAACGGACCTCAC 58.499 36.000 9.43 0.00 0.00 3.51
490 4511 6.319152 TGAGTTGAAATTTAAAACGGACCTCA 59.681 34.615 9.43 5.62 0.00 3.86
491 4512 6.731164 TGAGTTGAAATTTAAAACGGACCTC 58.269 36.000 9.43 3.58 0.00 3.85
492 4513 6.702716 TGAGTTGAAATTTAAAACGGACCT 57.297 33.333 9.43 0.00 0.00 3.85
493 4514 7.940178 AATGAGTTGAAATTTAAAACGGACC 57.060 32.000 9.43 0.00 0.00 4.46
494 4515 8.272866 CCAAATGAGTTGAAATTTAAAACGGAC 58.727 33.333 0.00 7.09 39.87 4.79
495 4516 8.198109 TCCAAATGAGTTGAAATTTAAAACGGA 58.802 29.630 0.00 7.12 39.87 4.69
496 4517 8.359060 TCCAAATGAGTTGAAATTTAAAACGG 57.641 30.769 0.00 5.48 39.87 4.44
504 4525 8.411683 GCTCAGATATCCAAATGAGTTGAAATT 58.588 33.333 16.70 0.00 41.00 1.82
505 4526 7.558807 TGCTCAGATATCCAAATGAGTTGAAAT 59.441 33.333 16.70 0.00 41.00 2.17
506 4527 6.885918 TGCTCAGATATCCAAATGAGTTGAAA 59.114 34.615 16.70 1.78 41.00 2.69
507 4528 6.417258 TGCTCAGATATCCAAATGAGTTGAA 58.583 36.000 16.70 3.54 41.00 2.69
508 4529 5.993055 TGCTCAGATATCCAAATGAGTTGA 58.007 37.500 16.70 4.21 41.00 3.18
509 4530 5.277876 GCTGCTCAGATATCCAAATGAGTTG 60.278 44.000 16.70 12.19 41.00 3.16
510 4531 4.820716 GCTGCTCAGATATCCAAATGAGTT 59.179 41.667 16.70 0.00 41.00 3.01
511 4532 4.102838 AGCTGCTCAGATATCCAAATGAGT 59.897 41.667 16.70 0.36 41.00 3.41
512 4533 4.643463 AGCTGCTCAGATATCCAAATGAG 58.357 43.478 12.97 12.97 41.68 2.90
513 4534 4.347292 AGAGCTGCTCAGATATCCAAATGA 59.653 41.667 29.49 0.00 32.06 2.57
514 4535 4.643463 AGAGCTGCTCAGATATCCAAATG 58.357 43.478 29.49 0.00 32.06 2.32
515 4536 4.561123 CGAGAGCTGCTCAGATATCCAAAT 60.561 45.833 29.49 5.90 44.15 2.32
516 4537 3.243670 CGAGAGCTGCTCAGATATCCAAA 60.244 47.826 29.49 0.00 44.15 3.28
517 4538 2.295629 CGAGAGCTGCTCAGATATCCAA 59.704 50.000 29.49 0.00 44.15 3.53
518 4539 1.885233 CGAGAGCTGCTCAGATATCCA 59.115 52.381 29.49 0.00 44.15 3.41
519 4540 1.202114 CCGAGAGCTGCTCAGATATCC 59.798 57.143 29.49 9.58 44.15 2.59
520 4541 1.402720 GCCGAGAGCTGCTCAGATATC 60.403 57.143 29.49 17.18 44.15 1.63
521 4542 0.602562 GCCGAGAGCTGCTCAGATAT 59.397 55.000 29.49 10.20 44.15 1.63
522 4543 0.753111 TGCCGAGAGCTGCTCAGATA 60.753 55.000 29.49 12.91 44.15 1.98
523 4544 1.611474 TTGCCGAGAGCTGCTCAGAT 61.611 55.000 29.49 10.97 44.15 2.90
524 4545 1.820010 TTTGCCGAGAGCTGCTCAGA 61.820 55.000 29.49 7.15 44.15 3.27
525 4546 0.952497 TTTTGCCGAGAGCTGCTCAG 60.952 55.000 29.49 21.79 44.15 3.35
526 4547 0.534877 TTTTTGCCGAGAGCTGCTCA 60.535 50.000 29.49 8.15 44.15 4.26
527 4548 2.247790 TTTTTGCCGAGAGCTGCTC 58.752 52.632 21.72 21.72 44.23 4.26
528 4549 4.481195 TTTTTGCCGAGAGCTGCT 57.519 50.000 0.00 0.00 44.23 4.24
542 4563 5.725362 TGTTTTGACCCGATTTGTCTTTTT 58.275 33.333 0.00 0.00 33.83 1.94
543 4564 5.105513 ACTGTTTTGACCCGATTTGTCTTTT 60.106 36.000 0.00 0.00 33.83 2.27
544 4565 4.401202 ACTGTTTTGACCCGATTTGTCTTT 59.599 37.500 0.00 0.00 33.83 2.52
545 4566 3.951680 ACTGTTTTGACCCGATTTGTCTT 59.048 39.130 0.00 0.00 33.83 3.01
546 4567 3.551846 ACTGTTTTGACCCGATTTGTCT 58.448 40.909 0.00 0.00 33.83 3.41
547 4568 3.982576 ACTGTTTTGACCCGATTTGTC 57.017 42.857 0.00 0.00 0.00 3.18
548 4569 3.242936 CGAACTGTTTTGACCCGATTTGT 60.243 43.478 0.00 0.00 0.00 2.83
549 4570 3.242936 ACGAACTGTTTTGACCCGATTTG 60.243 43.478 0.00 0.00 0.00 2.32
550 4571 2.946990 ACGAACTGTTTTGACCCGATTT 59.053 40.909 0.00 0.00 0.00 2.17
551 4572 2.289547 CACGAACTGTTTTGACCCGATT 59.710 45.455 0.00 0.00 0.00 3.34
552 4573 1.871039 CACGAACTGTTTTGACCCGAT 59.129 47.619 0.00 0.00 0.00 4.18
553 4574 1.134759 TCACGAACTGTTTTGACCCGA 60.135 47.619 0.00 0.00 0.00 5.14
554 4575 1.292061 TCACGAACTGTTTTGACCCG 58.708 50.000 0.00 0.00 0.00 5.28
555 4576 2.420722 TGTTCACGAACTGTTTTGACCC 59.579 45.455 11.01 2.06 41.67 4.46
556 4577 3.750639 TGTTCACGAACTGTTTTGACC 57.249 42.857 11.01 1.02 41.67 4.02
557 4578 7.483691 AGTTTATTGTTCACGAACTGTTTTGAC 59.516 33.333 11.01 2.66 41.67 3.18
558 4579 7.531716 AGTTTATTGTTCACGAACTGTTTTGA 58.468 30.769 11.01 0.00 41.67 2.69
559 4580 7.734538 AGTTTATTGTTCACGAACTGTTTTG 57.265 32.000 11.01 0.00 41.67 2.44
560 4581 8.751302 AAAGTTTATTGTTCACGAACTGTTTT 57.249 26.923 11.01 1.23 41.67 2.43
561 4582 8.751302 AAAAGTTTATTGTTCACGAACTGTTT 57.249 26.923 11.01 0.00 41.67 2.83
562 4583 8.751302 AAAAAGTTTATTGTTCACGAACTGTT 57.249 26.923 11.01 0.00 41.67 3.16
584 4605 5.134661 AGACAAAATCGGGGTCTGTAAAAA 58.865 37.500 0.00 0.00 40.21 1.94
585 4606 4.721132 AGACAAAATCGGGGTCTGTAAAA 58.279 39.130 0.00 0.00 40.21 1.52
586 4607 4.360951 AGACAAAATCGGGGTCTGTAAA 57.639 40.909 0.00 0.00 40.21 2.01
587 4608 4.360951 AAGACAAAATCGGGGTCTGTAA 57.639 40.909 0.00 0.00 40.80 2.41
588 4609 4.360951 AAAGACAAAATCGGGGTCTGTA 57.639 40.909 0.00 0.00 40.80 2.74
589 4610 2.951229 AAGACAAAATCGGGGTCTGT 57.049 45.000 0.00 0.00 40.80 3.41
590 4611 4.584327 AAAAAGACAAAATCGGGGTCTG 57.416 40.909 0.00 0.00 40.80 3.51
614 4635 4.069300 TGGATATTTGAGCAGCTCTCTG 57.931 45.455 23.15 0.00 42.38 3.35
615 4636 4.767578 TTGGATATTTGAGCAGCTCTCT 57.232 40.909 23.15 10.08 42.38 3.10
616 4637 4.260538 CGTTTGGATATTTGAGCAGCTCTC 60.261 45.833 23.15 11.57 42.23 3.20
617 4638 3.624861 CGTTTGGATATTTGAGCAGCTCT 59.375 43.478 23.15 5.93 0.00 4.09
618 4639 3.623060 TCGTTTGGATATTTGAGCAGCTC 59.377 43.478 16.21 16.21 0.00 4.09
619 4640 3.609853 TCGTTTGGATATTTGAGCAGCT 58.390 40.909 0.00 0.00 0.00 4.24
620 4641 3.375299 ACTCGTTTGGATATTTGAGCAGC 59.625 43.478 0.00 0.00 0.00 5.25
621 4642 5.122239 TCAACTCGTTTGGATATTTGAGCAG 59.878 40.000 0.00 0.00 35.69 4.24
622 4643 5.000591 TCAACTCGTTTGGATATTTGAGCA 58.999 37.500 0.00 0.00 35.69 4.26
623 4644 5.545658 TCAACTCGTTTGGATATTTGAGC 57.454 39.130 0.69 0.00 35.69 4.26
624 4645 8.970691 AATTTCAACTCGTTTGGATATTTGAG 57.029 30.769 0.69 0.00 35.69 3.02
625 4646 9.190858 CAAATTTCAACTCGTTTGGATATTTGA 57.809 29.630 14.01 0.00 38.38 2.69
626 4647 7.951565 GCAAATTTCAACTCGTTTGGATATTTG 59.048 33.333 14.45 14.45 38.68 2.32
627 4648 7.655328 TGCAAATTTCAACTCGTTTGGATATTT 59.345 29.630 0.00 0.00 35.69 1.40
628 4649 7.151308 TGCAAATTTCAACTCGTTTGGATATT 58.849 30.769 0.00 0.00 35.69 1.28
629 4650 6.686630 TGCAAATTTCAACTCGTTTGGATAT 58.313 32.000 0.00 0.00 35.69 1.63
630 4651 6.078202 TGCAAATTTCAACTCGTTTGGATA 57.922 33.333 0.00 0.00 35.69 2.59
631 4652 4.942852 TGCAAATTTCAACTCGTTTGGAT 58.057 34.783 0.00 0.00 35.69 3.41
632 4653 4.358851 CTGCAAATTTCAACTCGTTTGGA 58.641 39.130 0.00 0.00 35.69 3.53
633 4654 3.060339 GCTGCAAATTTCAACTCGTTTGG 60.060 43.478 0.00 0.00 35.69 3.28
634 4655 3.798337 AGCTGCAAATTTCAACTCGTTTG 59.202 39.130 1.02 0.00 36.42 2.93
635 4656 4.045636 AGCTGCAAATTTCAACTCGTTT 57.954 36.364 1.02 0.00 0.00 3.60
636 4657 3.715628 AGCTGCAAATTTCAACTCGTT 57.284 38.095 1.02 0.00 0.00 3.85
637 4658 4.537015 GTTAGCTGCAAATTTCAACTCGT 58.463 39.130 1.02 0.00 0.00 4.18
638 4659 3.914364 GGTTAGCTGCAAATTTCAACTCG 59.086 43.478 1.02 0.00 0.00 4.18
639 4660 5.126396 AGGTTAGCTGCAAATTTCAACTC 57.874 39.130 1.02 0.00 0.00 3.01
640 4661 4.584325 TGAGGTTAGCTGCAAATTTCAACT 59.416 37.500 1.02 0.00 0.00 3.16
641 4662 4.870363 TGAGGTTAGCTGCAAATTTCAAC 58.130 39.130 1.02 0.00 0.00 3.18
642 4663 5.472148 CATGAGGTTAGCTGCAAATTTCAA 58.528 37.500 1.02 0.00 0.00 2.69
643 4664 4.618927 GCATGAGGTTAGCTGCAAATTTCA 60.619 41.667 1.02 0.46 34.77 2.69
644 4665 3.861689 GCATGAGGTTAGCTGCAAATTTC 59.138 43.478 1.02 0.00 34.77 2.17
645 4666 3.258872 TGCATGAGGTTAGCTGCAAATTT 59.741 39.130 1.02 0.00 41.33 1.82
646 4667 2.827322 TGCATGAGGTTAGCTGCAAATT 59.173 40.909 1.02 0.00 41.33 1.82
647 4668 2.449464 TGCATGAGGTTAGCTGCAAAT 58.551 42.857 1.02 0.00 41.33 2.32
648 4669 1.908344 TGCATGAGGTTAGCTGCAAA 58.092 45.000 1.02 0.00 41.33 3.68
649 4670 2.019249 GATGCATGAGGTTAGCTGCAA 58.981 47.619 2.46 0.00 46.59 4.08
651 4672 1.671979 TGATGCATGAGGTTAGCTGC 58.328 50.000 2.46 0.00 35.21 5.25
652 4673 4.913335 ATTTGATGCATGAGGTTAGCTG 57.087 40.909 2.46 0.00 0.00 4.24
653 4674 7.002879 AGATAATTTGATGCATGAGGTTAGCT 58.997 34.615 2.46 4.30 0.00 3.32
654 4675 7.211966 AGATAATTTGATGCATGAGGTTAGC 57.788 36.000 2.46 1.86 0.00 3.09
655 4676 8.725148 GGTAGATAATTTGATGCATGAGGTTAG 58.275 37.037 2.46 0.00 0.00 2.34
656 4677 8.217111 TGGTAGATAATTTGATGCATGAGGTTA 58.783 33.333 2.46 0.00 0.00 2.85
657 4678 7.013655 GTGGTAGATAATTTGATGCATGAGGTT 59.986 37.037 2.46 0.00 0.00 3.50
658 4679 6.488006 GTGGTAGATAATTTGATGCATGAGGT 59.512 38.462 2.46 0.00 0.00 3.85
659 4680 6.487668 TGTGGTAGATAATTTGATGCATGAGG 59.512 38.462 2.46 0.00 0.00 3.86
660 4681 7.012610 TGTGTGGTAGATAATTTGATGCATGAG 59.987 37.037 2.46 0.00 0.00 2.90
661 4682 6.827762 TGTGTGGTAGATAATTTGATGCATGA 59.172 34.615 2.46 0.00 0.00 3.07
662 4683 7.030075 TGTGTGGTAGATAATTTGATGCATG 57.970 36.000 2.46 0.00 0.00 4.06
663 4684 7.643569 TTGTGTGGTAGATAATTTGATGCAT 57.356 32.000 0.00 0.00 0.00 3.96
664 4685 7.459795 TTTGTGTGGTAGATAATTTGATGCA 57.540 32.000 0.00 0.00 0.00 3.96
665 4686 8.755696 TTTTTGTGTGGTAGATAATTTGATGC 57.244 30.769 0.00 0.00 0.00 3.91
688 4709 5.896106 TGGCTCCCAAAAATTCCAAATTTTT 59.104 32.000 14.31 14.31 40.58 1.94
689 4710 5.453158 TGGCTCCCAAAAATTCCAAATTTT 58.547 33.333 4.90 4.90 33.12 1.82
690 4711 5.059134 TGGCTCCCAAAAATTCCAAATTT 57.941 34.783 0.00 0.00 0.00 1.82
691 4712 4.720775 TGGCTCCCAAAAATTCCAAATT 57.279 36.364 0.00 0.00 0.00 1.82
692 4713 4.720775 TTGGCTCCCAAAAATTCCAAAT 57.279 36.364 0.00 0.00 40.92 2.32
710 4731 4.279420 GGCTCTTCTATAAGGCCAATTTGG 59.721 45.833 11.27 11.27 43.28 3.28
711 4732 4.889409 TGGCTCTTCTATAAGGCCAATTTG 59.111 41.667 15.81 0.00 46.82 2.32
712 4733 5.129368 TGGCTCTTCTATAAGGCCAATTT 57.871 39.130 15.81 0.00 46.82 1.82
713 4734 4.796110 TGGCTCTTCTATAAGGCCAATT 57.204 40.909 15.81 0.00 46.82 2.32
717 4738 4.423625 TCTTTGGCTCTTCTATAAGGCC 57.576 45.455 0.00 0.00 43.70 5.19
718 4739 6.116126 TCTTTCTTTGGCTCTTCTATAAGGC 58.884 40.000 0.00 0.00 38.48 4.35
719 4740 9.487790 CTATCTTTCTTTGGCTCTTCTATAAGG 57.512 37.037 0.00 0.00 33.22 2.69
844 4886 2.691011 GTTTGTTGCTTCCCTGTGGTAA 59.309 45.455 0.00 0.00 0.00 2.85
871 4918 4.058817 CCAAGACGATAATAAGGACCTGC 58.941 47.826 0.00 0.00 0.00 4.85
874 4921 8.148999 AGTTATTCCAAGACGATAATAAGGACC 58.851 37.037 0.00 0.00 0.00 4.46
875 4922 9.543783 AAGTTATTCCAAGACGATAATAAGGAC 57.456 33.333 0.00 0.00 0.00 3.85
947 4997 2.089982 TGTGATGGAGACCAGGGGATAT 60.090 50.000 0.00 0.00 36.75 1.63
961 5011 1.741706 GAGTGTTGCAGGATGTGATGG 59.258 52.381 0.00 0.00 39.31 3.51
978 5028 1.646447 TGTATGAGGGAGGGTGAGAGT 59.354 52.381 0.00 0.00 0.00 3.24
980 5030 2.940514 TTGTATGAGGGAGGGTGAGA 57.059 50.000 0.00 0.00 0.00 3.27
1106 5156 3.040147 TCTTGGTACAGTACTTGCTGC 57.960 47.619 10.62 0.00 42.39 5.25
1119 5169 2.499693 TCCTGATGCGTCAATCTTGGTA 59.500 45.455 10.41 0.00 33.05 3.25
1134 5184 3.830755 AGCTTGCATTTGAGTTTCCTGAT 59.169 39.130 0.00 0.00 0.00 2.90
1188 5238 1.818363 CTGCTGCGCCAGATCATGT 60.818 57.895 4.18 0.00 34.77 3.21
1200 5250 2.124653 AGCTCCATCTGCTGCTGC 60.125 61.111 8.89 8.89 39.56 5.25
1215 5265 3.005897 TCCTGTAGACTTCAACTGTCAGC 59.994 47.826 0.00 0.00 36.94 4.26
1227 5277 1.003646 TGGGCTCTCTCCTGTAGACT 58.996 55.000 0.00 0.00 0.00 3.24
1319 5369 4.774660 ATGACTTCTGAATGCTCCTCAT 57.225 40.909 0.00 0.00 36.87 2.90
1352 5402 2.621070 TCCTCCTAAGCTGGAAACTGT 58.379 47.619 0.00 0.00 35.43 3.55
1533 5583 2.511659 TGTGTTGACTACGCTCCTACT 58.488 47.619 2.41 0.00 38.12 2.57
1611 5662 3.778265 ACACCAACTTCCCTGCATTATT 58.222 40.909 0.00 0.00 0.00 1.40
1612 5663 3.456380 ACACCAACTTCCCTGCATTAT 57.544 42.857 0.00 0.00 0.00 1.28
1613 5664 2.890311 CAACACCAACTTCCCTGCATTA 59.110 45.455 0.00 0.00 0.00 1.90
1742 5798 4.750098 AGATTTGCCGATAAAGATACACCG 59.250 41.667 0.00 0.00 0.00 4.94
1772 5828 6.358178 TGTGTTGGTCATTTCCTTACAAGTA 58.642 36.000 0.00 0.00 0.00 2.24
1774 5830 5.766150 TGTGTTGGTCATTTCCTTACAAG 57.234 39.130 0.00 0.00 0.00 3.16
1820 5876 3.484407 AGCCTATCAATGGATCAAGCAC 58.516 45.455 0.00 0.00 34.89 4.40
1937 5993 4.635223 TCTTATGACTATCATGGCAGCAC 58.365 43.478 1.49 0.00 37.70 4.40
1961 6019 8.547967 TTTTGATGGTAAGAATCAGACAGTAC 57.452 34.615 0.00 0.00 35.54 2.73
2011 6069 7.049754 TGAAGCTCATCTTAATTCATGTGCTA 58.950 34.615 16.06 5.38 44.91 3.49
2374 6612 2.370281 ATGTAGTTCTGTGGCACTCG 57.630 50.000 19.83 10.03 0.00 4.18
2508 6746 1.384525 CACCACCGAAACTTGAACCA 58.615 50.000 0.00 0.00 0.00 3.67
2512 6750 0.468226 AGAGCACCACCGAAACTTGA 59.532 50.000 0.00 0.00 0.00 3.02
2698 6936 7.402811 AATGATTTATGAAATGCTGCATTCG 57.597 32.000 26.40 0.00 32.43 3.34
2722 6960 0.768221 AGGAACACCCTGAGGCTGAA 60.768 55.000 0.00 0.00 45.61 3.02
2765 7003 2.038557 ACGGCAAGAGTGGAACAGTTAT 59.961 45.455 0.00 0.00 45.14 1.89
2766 7004 1.414919 ACGGCAAGAGTGGAACAGTTA 59.585 47.619 0.00 0.00 45.14 2.24
2776 7014 0.250338 GTGGAGGAAACGGCAAGAGT 60.250 55.000 0.00 0.00 0.00 3.24
2781 7019 3.172106 TGGGTGGAGGAAACGGCA 61.172 61.111 0.00 0.00 0.00 5.69
2836 7077 2.367202 GGGGGAGATGAGACGGCAA 61.367 63.158 0.00 0.00 0.00 4.52
3019 7260 1.227380 GGATGTAGGAGCTGGTGCG 60.227 63.158 0.00 0.00 45.42 5.34
3052 7293 0.984230 TGGATGAGGCGAGAAAGGTT 59.016 50.000 0.00 0.00 0.00 3.50
3102 7343 1.202463 AGATGGAGCACTACGCATGTC 60.202 52.381 0.00 0.00 46.13 3.06
3122 7363 0.884704 GAGTTCAGTTTGGAGCCGCA 60.885 55.000 0.00 0.00 0.00 5.69
3160 7401 4.891992 TGTCGAAGAAGGGAGAATTCTT 57.108 40.909 9.87 0.79 46.89 2.52
3162 7403 4.154375 GGTTTGTCGAAGAAGGGAGAATTC 59.846 45.833 0.00 0.00 39.69 2.17
3164 7405 3.559384 GGGTTTGTCGAAGAAGGGAGAAT 60.559 47.826 0.00 0.00 39.69 2.40
3312 7561 6.510638 CGTGGCATCATGGAATATTATGATCG 60.511 42.308 9.75 7.68 40.93 3.69
3431 7680 2.823593 TCGCGATGGTGCAATGGG 60.824 61.111 3.71 0.00 34.15 4.00
3546 7795 2.584064 CTGCAGTATGGCCGGACA 59.416 61.111 15.46 15.46 35.86 4.02
3547 7796 2.897350 GCTGCAGTATGGCCGGAC 60.897 66.667 16.64 0.56 35.86 4.79


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

AutoCloner maintained by Alex Coulton.