Multiple sequence alignment - TraesCS3A01G351700

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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 TraesCS3A01G351700 chr3A 100.000 5379 0 0 1 5379 600028627 600023249 0.000000e+00 9934.0
1 TraesCS3A01G351700 chr3A 94.340 106 4 2 382 486 587396288 587396184 1.550000e-35 161.0
2 TraesCS3A01G351700 chr3D 92.567 2731 106 51 2096 4796 457234725 457232062 0.000000e+00 3829.0
3 TraesCS3A01G351700 chr3D 93.783 1528 77 11 464 1984 457236239 457234723 0.000000e+00 2279.0
4 TraesCS3A01G351700 chr3D 95.130 616 29 1 4764 5379 457231988 457231374 0.000000e+00 970.0
5 TraesCS3A01G351700 chr3D 88.451 381 33 5 4 382 457236599 457236228 2.950000e-122 449.0
6 TraesCS3A01G351700 chr3D 94.915 118 6 0 1980 2097 341502525 341502408 9.200000e-43 185.0
7 TraesCS3A01G351700 chr3D 87.417 151 14 4 235 382 158080845 158080993 9.270000e-38 169.0
8 TraesCS3A01G351700 chr3D 93.103 58 3 1 4564 4621 457232060 457232004 3.450000e-12 84.2
9 TraesCS3A01G351700 chr3B 94.659 1629 68 11 3762 5379 604272072 604270452 0.000000e+00 2508.0
10 TraesCS3A01G351700 chr3B 93.758 1650 58 15 2097 3725 604273704 604272079 0.000000e+00 2435.0
11 TraesCS3A01G351700 chr3B 93.511 1387 66 12 600 1982 604275072 604273706 0.000000e+00 2041.0
12 TraesCS3A01G351700 chr3B 86.076 158 19 3 235 389 121348082 121347925 3.330000e-37 167.0
13 TraesCS3A01G351700 chr3B 95.146 103 5 0 382 484 772411557 772411455 4.310000e-36 163.0
14 TraesCS3A01G351700 chr1A 97.414 116 3 0 1982 2097 550443110 550442995 1.180000e-46 198.0
15 TraesCS3A01G351700 chr1A 96.154 104 2 2 382 483 539420021 539419918 9.270000e-38 169.0
16 TraesCS3A01G351700 chr1A 94.286 105 6 0 382 486 376145855 376145959 1.550000e-35 161.0
17 TraesCS3A01G351700 chr1A 86.000 150 18 3 235 382 487486450 487486302 2.010000e-34 158.0
18 TraesCS3A01G351700 chr6B 90.210 143 14 0 5237 5379 257599430 257599288 2.560000e-43 187.0
19 TraesCS3A01G351700 chr6B 90.977 133 10 2 1981 2113 149017232 149017362 1.540000e-40 178.0
20 TraesCS3A01G351700 chr5B 94.262 122 6 1 1977 2097 657593343 657593222 9.200000e-43 185.0
21 TraesCS3A01G351700 chr5B 83.234 167 22 6 221 382 623551893 623552058 1.210000e-31 148.0
22 TraesCS3A01G351700 chr4D 92.969 128 8 1 1973 2100 9744707 9744833 9.200000e-43 185.0
23 TraesCS3A01G351700 chr4B 93.548 124 7 1 1982 2105 575778942 575779064 3.310000e-42 183.0
24 TraesCS3A01G351700 chr2B 93.496 123 7 1 1975 2097 305325114 305325235 1.190000e-41 182.0
25 TraesCS3A01G351700 chr2B 90.511 137 8 4 1982 2118 594838165 594838034 5.540000e-40 176.0
26 TraesCS3A01G351700 chr2B 86.093 151 19 2 234 382 249527560 249527410 1.550000e-35 161.0
27 TraesCS3A01G351700 chr1B 88.667 150 15 2 235 382 314565549 314565698 1.190000e-41 182.0
28 TraesCS3A01G351700 chr5A 90.840 131 11 1 1982 2111 436331136 436331006 1.990000e-39 174.0
29 TraesCS3A01G351700 chr7A 98.947 95 1 0 382 476 513985816 513985910 2.580000e-38 171.0
30 TraesCS3A01G351700 chr2A 98.947 95 1 0 382 476 182151740 182151646 2.580000e-38 171.0
31 TraesCS3A01G351700 chr2A 97.959 98 2 0 382 479 208346916 208346819 2.580000e-38 171.0
32 TraesCS3A01G351700 chr2A 92.500 120 5 3 382 497 187955909 187955790 9.270000e-38 169.0
33 TraesCS3A01G351700 chr2A 85.430 151 19 3 235 382 419206967 419206817 2.590000e-33 154.0
34 TraesCS3A01G351700 chr5D 88.811 143 8 1 5237 5379 524596978 524597112 9.270000e-38 169.0
35 TraesCS3A01G351700 chr4A 95.192 104 5 0 382 485 416231489 416231386 1.200000e-36 165.0
36 TraesCS3A01G351700 chrUn 83.234 167 22 6 221 382 469587730 469587565 1.210000e-31 148.0


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 TraesCS3A01G351700 chr3A 600023249 600028627 5378 True 9934.00 9934 100.0000 1 5379 1 chr3A.!!$R2 5378
1 TraesCS3A01G351700 chr3D 457231374 457236599 5225 True 1522.24 3829 92.6068 4 5379 5 chr3D.!!$R2 5375
2 TraesCS3A01G351700 chr3B 604270452 604275072 4620 True 2328.00 2508 93.9760 600 5379 3 chr3B.!!$R3 4779

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
692 695 0.039527 AAACGAAATCAACGCAGCCC 60.040 50.000 0.00 0.00 0.00 5.19 F
1761 1772 0.039035 TAAAGCAGGCCATTTCGGGT 59.961 50.000 5.01 0.00 34.06 5.28 F
2093 2104 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 F
2095 2106 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85 F
2890 2906 2.428530 CTCTCTCGTCACATGATCCCAA 59.571 50.000 0.00 0.00 0.00 4.12 F
3182 3210 3.317993 GCAGTTCTTTAGGTGGAAAAGCA 59.682 43.478 0.00 0.00 34.58 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2085 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12 R
3745 3796 0.107897 TGGCCCGCTACTGTATTGTG 60.108 55.000 0.00 0.00 0.00 3.33 R
3746 3797 0.178068 CTGGCCCGCTACTGTATTGT 59.822 55.000 0.00 0.00 0.00 2.71 R
3749 3800 0.464452 GAACTGGCCCGCTACTGTAT 59.536 55.000 0.00 0.00 0.00 2.29 R
3976 4027 1.396996 GACCGGAACCATTGAATGACG 59.603 52.381 9.46 5.76 0.00 4.35 R
5065 5226 0.179084 CCGTCACCATGAACGCCTAT 60.179 55.000 0.00 0.00 0.00 2.57 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
26 27 7.489894 GACTTAAGTCAACACGTCATAGTAC 57.510 40.000 27.12 0.00 44.18 2.73
32 33 6.509656 AGTCAACACGTCATAGTACTGAAAA 58.490 36.000 5.39 0.00 0.00 2.29
40 41 9.953825 CACGTCATAGTACTGAAAATAAAAGAC 57.046 33.333 5.39 0.00 0.00 3.01
44 45 8.869897 TCATAGTACTGAAAATAAAAGACAGCG 58.130 33.333 5.39 0.00 32.67 5.18
49 50 7.724305 ACTGAAAATAAAAGACAGCGTAGAA 57.276 32.000 0.00 0.00 32.67 2.10
56 57 5.659048 AAAAGACAGCGTAGAAAAGTCTG 57.341 39.130 0.00 0.00 39.33 3.51
57 58 4.585955 AAGACAGCGTAGAAAAGTCTGA 57.414 40.909 0.00 0.00 39.33 3.27
60 61 4.745620 AGACAGCGTAGAAAAGTCTGAAAC 59.254 41.667 0.00 0.00 38.08 2.78
67 68 6.512741 GCGTAGAAAAGTCTGAAACAAATCCA 60.513 38.462 0.00 0.00 35.12 3.41
191 192 1.884579 AGAAAGAAGCGTCGTCACCTA 59.115 47.619 8.56 0.00 0.00 3.08
206 207 8.982685 CGTCGTCACCTAGTAAATCTAAGTATA 58.017 37.037 0.00 0.00 0.00 1.47
248 249 8.088981 ACTACTCCGCATGTTCCTAAATATAAG 58.911 37.037 0.00 0.00 0.00 1.73
297 299 3.114809 TGCAAAGCAAAACGAGTGAATG 58.885 40.909 0.00 0.00 34.76 2.67
378 381 7.625828 AAGACTTATATTCAAAAACGGAGGG 57.374 36.000 0.00 0.00 0.00 4.30
379 382 6.954232 AGACTTATATTCAAAAACGGAGGGA 58.046 36.000 0.00 0.00 0.00 4.20
380 383 7.048512 AGACTTATATTCAAAAACGGAGGGAG 58.951 38.462 0.00 0.00 0.00 4.30
381 384 6.718294 ACTTATATTCAAAAACGGAGGGAGT 58.282 36.000 0.00 0.00 0.00 3.85
382 385 6.822170 ACTTATATTCAAAAACGGAGGGAGTC 59.178 38.462 0.00 0.00 0.00 3.36
383 386 2.265589 TTCAAAAACGGAGGGAGTCC 57.734 50.000 0.00 0.00 42.85 3.85
393 396 3.180891 GGAGGGAGTCCAAATTACTCG 57.819 52.381 12.30 0.00 46.10 4.18
394 397 2.500504 GGAGGGAGTCCAAATTACTCGT 59.499 50.000 12.30 0.00 46.10 4.18
395 398 3.430513 GGAGGGAGTCCAAATTACTCGTC 60.431 52.174 12.30 1.70 46.10 4.20
396 399 3.442076 AGGGAGTCCAAATTACTCGTCT 58.558 45.455 12.30 0.00 43.55 4.18
397 400 3.447944 AGGGAGTCCAAATTACTCGTCTC 59.552 47.826 12.30 0.00 43.55 3.36
398 401 3.194968 GGGAGTCCAAATTACTCGTCTCA 59.805 47.826 12.30 0.00 43.55 3.27
399 402 4.425520 GGAGTCCAAATTACTCGTCTCAG 58.574 47.826 3.60 0.00 43.55 3.35
400 403 4.158025 GGAGTCCAAATTACTCGTCTCAGA 59.842 45.833 3.60 0.00 43.55 3.27
401 404 5.336531 GGAGTCCAAATTACTCGTCTCAGAA 60.337 44.000 3.60 0.00 43.55 3.02
402 405 6.097915 AGTCCAAATTACTCGTCTCAGAAA 57.902 37.500 0.00 0.00 0.00 2.52
403 406 6.702329 AGTCCAAATTACTCGTCTCAGAAAT 58.298 36.000 0.00 0.00 0.00 2.17
404 407 6.591834 AGTCCAAATTACTCGTCTCAGAAATG 59.408 38.462 0.00 0.00 0.00 2.32
405 408 5.874810 TCCAAATTACTCGTCTCAGAAATGG 59.125 40.000 0.00 0.00 0.00 3.16
406 409 5.874810 CCAAATTACTCGTCTCAGAAATGGA 59.125 40.000 0.00 0.00 0.00 3.41
407 410 6.540189 CCAAATTACTCGTCTCAGAAATGGAT 59.460 38.462 0.00 0.00 0.00 3.41
408 411 7.404985 CAAATTACTCGTCTCAGAAATGGATG 58.595 38.462 0.00 0.00 0.00 3.51
409 412 5.661056 TTACTCGTCTCAGAAATGGATGT 57.339 39.130 0.00 0.00 0.00 3.06
410 413 6.769134 TTACTCGTCTCAGAAATGGATGTA 57.231 37.500 0.00 0.00 0.00 2.29
411 414 5.860941 ACTCGTCTCAGAAATGGATGTAT 57.139 39.130 0.00 0.00 0.00 2.29
412 415 5.837437 ACTCGTCTCAGAAATGGATGTATC 58.163 41.667 0.00 0.00 0.00 2.24
413 416 5.596361 ACTCGTCTCAGAAATGGATGTATCT 59.404 40.000 0.00 0.00 0.00 1.98
414 417 6.773200 ACTCGTCTCAGAAATGGATGTATCTA 59.227 38.462 0.00 0.00 0.00 1.98
415 418 7.040755 ACTCGTCTCAGAAATGGATGTATCTAG 60.041 40.741 0.00 0.00 0.00 2.43
416 419 6.998673 TCGTCTCAGAAATGGATGTATCTAGA 59.001 38.462 0.00 0.00 0.00 2.43
417 420 7.502561 TCGTCTCAGAAATGGATGTATCTAGAA 59.497 37.037 0.00 0.00 0.00 2.10
418 421 7.593273 CGTCTCAGAAATGGATGTATCTAGAAC 59.407 40.741 0.00 0.00 0.00 3.01
419 422 8.637986 GTCTCAGAAATGGATGTATCTAGAACT 58.362 37.037 0.00 0.00 0.00 3.01
420 423 9.868160 TCTCAGAAATGGATGTATCTAGAACTA 57.132 33.333 0.00 0.00 0.00 2.24
447 450 7.825331 ATACATCTAGATACATCCATACCCG 57.175 40.000 4.54 0.00 0.00 5.28
448 451 4.402793 ACATCTAGATACATCCATACCCGC 59.597 45.833 4.54 0.00 0.00 6.13
449 452 3.014623 TCTAGATACATCCATACCCGCG 58.985 50.000 0.00 0.00 0.00 6.46
450 453 1.919240 AGATACATCCATACCCGCGA 58.081 50.000 8.23 0.00 0.00 5.87
451 454 1.544691 AGATACATCCATACCCGCGAC 59.455 52.381 8.23 0.00 0.00 5.19
452 455 1.271379 GATACATCCATACCCGCGACA 59.729 52.381 8.23 0.00 0.00 4.35
453 456 1.112950 TACATCCATACCCGCGACAA 58.887 50.000 8.23 0.00 0.00 3.18
454 457 0.179084 ACATCCATACCCGCGACAAG 60.179 55.000 8.23 0.00 0.00 3.16
455 458 0.179084 CATCCATACCCGCGACAAGT 60.179 55.000 8.23 1.45 0.00 3.16
456 459 1.067974 CATCCATACCCGCGACAAGTA 59.932 52.381 8.23 4.04 0.00 2.24
457 460 1.184431 TCCATACCCGCGACAAGTAA 58.816 50.000 8.23 0.00 0.00 2.24
458 461 1.758280 TCCATACCCGCGACAAGTAAT 59.242 47.619 8.23 0.00 0.00 1.89
459 462 2.168936 TCCATACCCGCGACAAGTAATT 59.831 45.455 8.23 0.00 0.00 1.40
460 463 2.940410 CCATACCCGCGACAAGTAATTT 59.060 45.455 8.23 0.00 0.00 1.82
461 464 3.242608 CCATACCCGCGACAAGTAATTTG 60.243 47.826 8.23 0.00 42.68 2.32
462 465 1.161843 ACCCGCGACAAGTAATTTGG 58.838 50.000 8.23 0.00 41.25 3.28
463 466 1.270947 ACCCGCGACAAGTAATTTGGA 60.271 47.619 8.23 0.00 41.25 3.53
464 467 1.807742 CCCGCGACAAGTAATTTGGAA 59.192 47.619 8.23 0.00 41.25 3.53
465 468 2.413634 CCCGCGACAAGTAATTTGGAAC 60.414 50.000 8.23 0.00 41.25 3.62
466 469 2.492001 CGCGACAAGTAATTTGGAACG 58.508 47.619 0.00 0.00 41.25 3.95
467 470 2.723618 CGCGACAAGTAATTTGGAACGG 60.724 50.000 0.00 0.00 41.25 4.44
468 471 2.481185 GCGACAAGTAATTTGGAACGGA 59.519 45.455 0.00 0.00 41.25 4.69
469 472 3.424433 GCGACAAGTAATTTGGAACGGAG 60.424 47.826 0.00 0.00 41.25 4.63
470 473 3.124636 CGACAAGTAATTTGGAACGGAGG 59.875 47.826 0.00 0.00 41.25 4.30
471 474 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
479 482 4.476628 TTTGGAACGGAGGGAGTAATAC 57.523 45.455 0.00 0.00 0.00 1.89
509 512 7.229581 GTCTTATATTATGGGACGAAGAGGT 57.770 40.000 0.00 0.00 0.00 3.85
510 513 7.091443 GTCTTATATTATGGGACGAAGAGGTG 58.909 42.308 0.00 0.00 0.00 4.00
530 533 8.893727 AGAGGTGTGATTTTATACAACAATAGC 58.106 33.333 0.00 0.00 36.98 2.97
615 618 6.870965 CGGAGAAAGTATCTTAATCCTCATGG 59.129 42.308 0.00 0.00 38.96 3.66
633 636 6.526674 CCTCATGGTTAAAAACAACGATTAGC 59.473 38.462 0.00 0.00 0.00 3.09
692 695 0.039527 AAACGAAATCAACGCAGCCC 60.040 50.000 0.00 0.00 0.00 5.19
722 725 6.894828 ACTTGATTAACGTGTCAACATTACC 58.105 36.000 7.07 0.00 31.55 2.85
725 728 0.509499 AACGTGTCAACATTACCGCG 59.491 50.000 0.00 0.00 0.00 6.46
738 741 0.178301 TACCGCGCCACCATTGATAA 59.822 50.000 0.00 0.00 0.00 1.75
739 742 1.095228 ACCGCGCCACCATTGATAAG 61.095 55.000 0.00 0.00 0.00 1.73
740 743 1.095228 CCGCGCCACCATTGATAAGT 61.095 55.000 0.00 0.00 0.00 2.24
741 744 1.577468 CGCGCCACCATTGATAAGTA 58.423 50.000 0.00 0.00 0.00 2.24
748 751 4.495844 GCCACCATTGATAAGTACTTTCGC 60.496 45.833 14.49 4.40 0.00 4.70
813 816 0.179111 CAGCAGCCAGAAATGCATGG 60.179 55.000 0.00 0.00 45.01 3.66
913 918 3.865830 GCTCGCCAGTTTAGCCGC 61.866 66.667 0.00 0.00 0.00 6.53
1339 1349 3.597728 CGCTACCCGCTCCTCTCC 61.598 72.222 0.00 0.00 36.13 3.71
1575 1586 4.739046 CATTTCGATAGGAAGTGGATGC 57.261 45.455 0.00 0.00 36.73 3.91
1761 1772 0.039035 TAAAGCAGGCCATTTCGGGT 59.961 50.000 5.01 0.00 34.06 5.28
1845 1856 7.201600 GCAAATCCAAAACAAAAGCTTAGTTGA 60.202 33.333 16.01 10.40 0.00 3.18
1905 1916 4.980590 TGATTTATTAGCCAACAACTGCG 58.019 39.130 0.00 0.00 0.00 5.18
1954 1965 6.659824 TGGTTTAGAGAATTTACAGGATCCC 58.340 40.000 8.55 0.00 0.00 3.85
1984 1995 6.354130 TGCTACCTTTACTGGATCAAATACC 58.646 40.000 0.00 0.00 0.00 2.73
1985 1996 5.763698 GCTACCTTTACTGGATCAAATACCC 59.236 44.000 0.00 0.00 0.00 3.69
1986 1997 5.125367 ACCTTTACTGGATCAAATACCCC 57.875 43.478 0.00 0.00 0.00 4.95
1987 1998 4.079385 ACCTTTACTGGATCAAATACCCCC 60.079 45.833 0.00 0.00 0.00 5.40
1988 1999 4.168088 CCTTTACTGGATCAAATACCCCCT 59.832 45.833 0.00 0.00 0.00 4.79
1989 2000 5.377478 CTTTACTGGATCAAATACCCCCTC 58.623 45.833 0.00 0.00 0.00 4.30
1990 2001 2.136026 ACTGGATCAAATACCCCCTCC 58.864 52.381 0.00 0.00 0.00 4.30
1991 2002 1.072331 CTGGATCAAATACCCCCTCCG 59.928 57.143 0.00 0.00 0.00 4.63
1992 2003 1.137697 GGATCAAATACCCCCTCCGT 58.862 55.000 0.00 0.00 0.00 4.69
1993 2004 1.071857 GGATCAAATACCCCCTCCGTC 59.928 57.143 0.00 0.00 0.00 4.79
1994 2005 1.071857 GATCAAATACCCCCTCCGTCC 59.928 57.143 0.00 0.00 0.00 4.79
1995 2006 0.252789 TCAAATACCCCCTCCGTCCA 60.253 55.000 0.00 0.00 0.00 4.02
1996 2007 0.180406 CAAATACCCCCTCCGTCCAG 59.820 60.000 0.00 0.00 0.00 3.86
1997 2008 0.043637 AAATACCCCCTCCGTCCAGA 59.956 55.000 0.00 0.00 0.00 3.86
1998 2009 0.043637 AATACCCCCTCCGTCCAGAA 59.956 55.000 0.00 0.00 0.00 3.02
1999 2010 0.043637 ATACCCCCTCCGTCCAGAAA 59.956 55.000 0.00 0.00 0.00 2.52
2000 2011 0.043637 TACCCCCTCCGTCCAGAAAT 59.956 55.000 0.00 0.00 0.00 2.17
2001 2012 0.043637 ACCCCCTCCGTCCAGAAATA 59.956 55.000 0.00 0.00 0.00 1.40
2002 2013 0.468648 CCCCCTCCGTCCAGAAATAC 59.531 60.000 0.00 0.00 0.00 1.89
2003 2014 1.497161 CCCCTCCGTCCAGAAATACT 58.503 55.000 0.00 0.00 0.00 2.12
2004 2015 1.838077 CCCCTCCGTCCAGAAATACTT 59.162 52.381 0.00 0.00 0.00 2.24
2005 2016 2.420129 CCCCTCCGTCCAGAAATACTTG 60.420 54.545 0.00 0.00 0.00 3.16
2006 2017 2.236395 CCCTCCGTCCAGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
2007 2018 3.522553 CCTCCGTCCAGAAATACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
2008 2019 3.522553 CTCCGTCCAGAAATACTTGTCC 58.477 50.000 0.00 0.00 0.00 4.02
2009 2020 3.170717 TCCGTCCAGAAATACTTGTCCT 58.829 45.455 0.00 0.00 0.00 3.85
2010 2021 4.346730 TCCGTCCAGAAATACTTGTCCTA 58.653 43.478 0.00 0.00 0.00 2.94
2011 2022 4.401519 TCCGTCCAGAAATACTTGTCCTAG 59.598 45.833 0.00 0.00 0.00 3.02
2012 2023 4.401519 CCGTCCAGAAATACTTGTCCTAGA 59.598 45.833 0.00 0.00 0.00 2.43
2013 2024 5.105473 CCGTCCAGAAATACTTGTCCTAGAA 60.105 44.000 0.00 0.00 0.00 2.10
2014 2025 6.395629 CGTCCAGAAATACTTGTCCTAGAAA 58.604 40.000 0.00 0.00 0.00 2.52
2015 2026 7.042335 CGTCCAGAAATACTTGTCCTAGAAAT 58.958 38.462 0.00 0.00 0.00 2.17
2016 2027 7.010552 CGTCCAGAAATACTTGTCCTAGAAATG 59.989 40.741 0.00 0.00 0.00 2.32
2017 2028 8.041323 GTCCAGAAATACTTGTCCTAGAAATGA 58.959 37.037 0.00 0.00 0.00 2.57
2018 2029 8.602424 TCCAGAAATACTTGTCCTAGAAATGAA 58.398 33.333 0.00 0.00 0.00 2.57
2019 2030 9.401058 CCAGAAATACTTGTCCTAGAAATGAAT 57.599 33.333 0.00 0.00 0.00 2.57
2021 2032 9.965902 AGAAATACTTGTCCTAGAAATGAATGT 57.034 29.630 0.00 0.00 0.00 2.71
2072 2083 8.697507 ACATCCATTTTATCCATTTCTAGGAC 57.302 34.615 0.00 0.00 38.13 3.85
2073 2084 8.281531 ACATCCATTTTATCCATTTCTAGGACA 58.718 33.333 0.00 0.00 38.13 4.02
2074 2085 9.135189 CATCCATTTTATCCATTTCTAGGACAA 57.865 33.333 0.00 0.00 38.13 3.18
2075 2086 8.752005 TCCATTTTATCCATTTCTAGGACAAG 57.248 34.615 0.00 0.00 38.13 3.16
2076 2087 8.336235 TCCATTTTATCCATTTCTAGGACAAGT 58.664 33.333 0.00 0.00 38.13 3.16
2077 2088 9.627123 CCATTTTATCCATTTCTAGGACAAGTA 57.373 33.333 0.00 0.00 38.13 2.24
2082 2093 9.847224 TTATCCATTTCTAGGACAAGTATTTCC 57.153 33.333 0.00 0.00 38.13 3.13
2083 2094 6.346096 TCCATTTCTAGGACAAGTATTTCCG 58.654 40.000 0.00 0.00 36.95 4.30
2084 2095 5.527582 CCATTTCTAGGACAAGTATTTCCGG 59.472 44.000 0.00 0.00 36.95 5.14
2085 2096 6.346096 CATTTCTAGGACAAGTATTTCCGGA 58.654 40.000 0.00 0.00 36.95 5.14
2086 2097 4.996788 TCTAGGACAAGTATTTCCGGAC 57.003 45.455 1.83 0.00 36.95 4.79
2087 2098 2.667473 AGGACAAGTATTTCCGGACG 57.333 50.000 1.83 0.00 36.95 4.79
2088 2099 1.206371 AGGACAAGTATTTCCGGACGG 59.794 52.381 1.83 3.96 36.95 4.79
2089 2100 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
2090 2101 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2091 2102 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2092 2103 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2093 2104 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2094 2105 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2095 2106 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2136 2147 4.422073 TGTTTCTGGTCACTGATCTTGT 57.578 40.909 0.00 0.00 0.00 3.16
2137 2148 5.545063 TGTTTCTGGTCACTGATCTTGTA 57.455 39.130 0.00 0.00 0.00 2.41
2138 2149 5.297547 TGTTTCTGGTCACTGATCTTGTAC 58.702 41.667 0.00 0.00 0.00 2.90
2150 2161 7.331934 TCACTGATCTTGTACTAGTCAATTTGC 59.668 37.037 0.00 0.00 0.00 3.68
2317 2332 4.020218 ACTGGCACATACACTCATAACAGT 60.020 41.667 0.00 0.00 38.20 3.55
2491 2506 7.682787 ATCTCTGAACAAATATGGACTACCT 57.317 36.000 0.00 0.00 37.04 3.08
2510 2526 2.814336 CCTTTTCAGGTAGTGCTTGACC 59.186 50.000 0.00 0.00 35.06 4.02
2725 2741 3.690460 AGCTGTAAAGGATGTTGAAGGG 58.310 45.455 0.00 0.00 0.00 3.95
2797 2813 5.755375 TGAGTTCTTGCAGAAAACTAGTGAG 59.245 40.000 0.00 0.00 35.75 3.51
2830 2846 5.422970 TCTTATCCTCTTTACAGCGGGTTTA 59.577 40.000 0.00 0.00 0.00 2.01
2868 2884 9.447157 GGCTGCTAATATTTTATTCATCTCTCT 57.553 33.333 0.00 0.00 0.00 3.10
2890 2906 2.428530 CTCTCTCGTCACATGATCCCAA 59.571 50.000 0.00 0.00 0.00 4.12
2966 2982 8.099537 CCTTTAGTGGACATAATAGATGCTCAT 58.900 37.037 0.00 0.00 0.00 2.90
3035 3051 4.724279 AGTGTTACAGAAACTTCCCCAT 57.276 40.909 0.00 0.00 38.99 4.00
3036 3052 5.836024 AGTGTTACAGAAACTTCCCCATA 57.164 39.130 0.00 0.00 38.99 2.74
3037 3053 5.805728 AGTGTTACAGAAACTTCCCCATAG 58.194 41.667 0.00 0.00 38.99 2.23
3038 3054 4.941873 GTGTTACAGAAACTTCCCCATAGG 59.058 45.833 0.00 0.00 38.99 2.57
3039 3055 4.018779 TGTTACAGAAACTTCCCCATAGGG 60.019 45.833 0.00 0.00 46.14 3.53
3064 3080 8.548721 GGATAGGATACAAGTGATTTTGTAACG 58.451 37.037 3.09 0.00 44.21 3.18
3070 3086 3.515071 AGTGATTTTGTAACGTCGTGC 57.485 42.857 0.00 0.00 0.00 5.34
3118 3146 5.098211 GCCATCATTACTTTGCTTTCTGTC 58.902 41.667 0.00 0.00 0.00 3.51
3182 3210 3.317993 GCAGTTCTTTAGGTGGAAAAGCA 59.682 43.478 0.00 0.00 34.58 3.91
3342 3370 7.775561 GTGGGTGATTACCTGAAAAGATTAGAT 59.224 37.037 6.62 0.00 46.66 1.98
3343 3371 8.336235 TGGGTGATTACCTGAAAAGATTAGATT 58.664 33.333 6.62 0.00 46.66 2.40
3411 3444 5.560953 CGACGATGATATCTACAGTCTGCAA 60.561 44.000 3.98 0.00 0.00 4.08
3700 3751 8.039603 TGCATGTAATACTTTGTTTGGAGTAG 57.960 34.615 0.00 0.00 32.37 2.57
3728 3779 7.821359 ACTGGCTGATAGTGCATATAATACTTG 59.179 37.037 0.00 0.00 0.00 3.16
3746 3797 7.768807 ATACTTGTTTGCCAATAACCTAACA 57.231 32.000 0.00 0.00 31.20 2.41
3748 3799 5.361285 ACTTGTTTGCCAATAACCTAACACA 59.639 36.000 0.00 0.00 31.20 3.72
3749 3800 5.854010 TGTTTGCCAATAACCTAACACAA 57.146 34.783 0.00 0.00 0.00 3.33
3760 3811 4.119442 ACCTAACACAATACAGTAGCGG 57.881 45.455 0.00 0.00 0.00 5.52
3784 3835 5.591877 GGCCAGTTCATTTTCTGATATCAGT 59.408 40.000 27.80 9.82 44.12 3.41
3788 3839 5.591877 AGTTCATTTTCTGATATCAGTGGGC 59.408 40.000 27.80 15.80 44.12 5.36
3976 4027 5.741011 TCAAGTAACTGATAATGGACACCC 58.259 41.667 0.00 0.00 0.00 4.61
3998 4049 1.352687 TCATTCAATGGTTCCGGTCCA 59.647 47.619 19.59 19.59 39.41 4.02
4183 4235 4.497340 CGAACTGATCAGGCTCTCTAAGAC 60.497 50.000 26.08 3.46 0.00 3.01
4338 4396 3.517296 TTGCCATGTCTGGAGGTAAAA 57.483 42.857 0.00 0.00 46.37 1.52
4343 4401 4.662278 CCATGTCTGGAGGTAAAAGGAAA 58.338 43.478 0.00 0.00 46.37 3.13
4363 4421 7.568349 AGGAAATGTAATCTAGCAGAATGTCA 58.432 34.615 0.00 0.00 39.31 3.58
4364 4422 7.497249 AGGAAATGTAATCTAGCAGAATGTCAC 59.503 37.037 0.00 0.00 39.31 3.67
4373 4431 8.743085 ATCTAGCAGAATGTCACATTTGTATT 57.257 30.769 4.04 0.00 39.31 1.89
4378 4436 6.680810 CAGAATGTCACATTTGTATTGGTGT 58.319 36.000 4.04 0.00 33.17 4.16
4379 4437 6.803320 CAGAATGTCACATTTGTATTGGTGTC 59.197 38.462 4.04 0.00 33.17 3.67
4482 4541 7.338196 GTCTATAGCTATGATGTCAAGAGGCTA 59.662 40.741 16.77 0.00 0.00 3.93
4486 4545 4.928615 GCTATGATGTCAAGAGGCTACATC 59.071 45.833 17.35 17.35 46.25 3.06
4491 4550 3.930336 TGTCAAGAGGCTACATCAACTG 58.070 45.455 0.00 0.00 0.00 3.16
4537 4596 8.638565 GTCAGAAATTATGTTTGTGGAAATTCG 58.361 33.333 3.75 0.00 0.00 3.34
4635 4694 8.543774 ACCATCTGATATTTACATAGGCCTAAG 58.456 37.037 18.42 15.74 0.00 2.18
4638 4697 8.135382 TCTGATATTTACATAGGCCTAAGACC 57.865 38.462 21.53 0.00 0.00 3.85
4652 4711 7.933223 AGGCCTAAGACCAATAAGCATATAAT 58.067 34.615 1.29 0.00 0.00 1.28
4723 4783 8.230472 ACATTCAAATTTTGTCAGAGTCTCTT 57.770 30.769 8.89 0.00 0.00 2.85
4724 4784 8.689972 ACATTCAAATTTTGTCAGAGTCTCTTT 58.310 29.630 8.89 0.00 0.00 2.52
4784 4945 5.683876 TCTTCCTTATCTGAGTTTCTGGG 57.316 43.478 0.00 0.00 0.00 4.45
4789 4950 2.859273 ATCTGAGTTTCTGGGCGCGG 62.859 60.000 8.83 2.51 0.00 6.46
4828 4989 2.229675 TCTGGCTGATAATCTGTGCG 57.770 50.000 0.00 0.00 0.00 5.34
4840 5001 2.031919 TGTGCGGCCTCGTCAAAT 59.968 55.556 0.00 0.00 38.89 2.32
4858 5019 5.683743 GTCAAATCTGTATGCTCTCTCGTAC 59.316 44.000 0.00 0.00 0.00 3.67
4960 5121 4.400961 AAGTCCTGCTGAGCGCCC 62.401 66.667 2.29 0.00 38.05 6.13
5065 5226 0.603707 CGAACTCCTTGAGCTTGCCA 60.604 55.000 0.00 0.00 32.04 4.92
5133 5294 0.817634 AGCCTCCTCATCTCGTCGAG 60.818 60.000 16.33 16.33 0.00 4.04
5323 5484 2.043248 GCCTGGTCCGGGTCTCTA 60.043 66.667 18.58 0.00 31.34 2.43
5353 5514 2.031163 AGCCGCTTGGACTGTGAC 59.969 61.111 0.00 0.00 33.02 3.67
5362 5523 2.048127 GACTGTGACACGAGCCCC 60.048 66.667 0.22 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.746120 ACTATGACGTGTTGACTTAAGTCTT 58.254 36.000 30.47 12.02 44.99 3.01
1 2 6.328641 ACTATGACGTGTTGACTTAAGTCT 57.671 37.500 30.47 13.72 44.99 3.24
2 3 7.270793 CAGTACTATGACGTGTTGACTTAAGTC 59.729 40.741 25.73 25.73 44.97 3.01
9 10 6.758593 TTTTCAGTACTATGACGTGTTGAC 57.241 37.500 0.00 0.00 0.00 3.18
23 24 8.236084 TCTACGCTGTCTTTTATTTTCAGTAC 57.764 34.615 0.00 0.00 0.00 2.73
24 25 8.821147 TTCTACGCTGTCTTTTATTTTCAGTA 57.179 30.769 0.00 0.00 0.00 2.74
25 26 7.724305 TTCTACGCTGTCTTTTATTTTCAGT 57.276 32.000 0.00 0.00 0.00 3.41
26 27 9.107367 CTTTTCTACGCTGTCTTTTATTTTCAG 57.893 33.333 0.00 0.00 0.00 3.02
32 33 7.152645 TCAGACTTTTCTACGCTGTCTTTTAT 58.847 34.615 0.00 0.00 36.05 1.40
40 41 5.403897 TTGTTTCAGACTTTTCTACGCTG 57.596 39.130 0.00 0.00 0.00 5.18
44 45 9.581099 TTTTGGATTTGTTTCAGACTTTTCTAC 57.419 29.630 0.00 0.00 0.00 2.59
78 79 4.634004 TGTTAGACTTGACACAGGTGTTTG 59.366 41.667 6.51 3.22 45.05 2.93
79 80 4.634443 GTGTTAGACTTGACACAGGTGTTT 59.366 41.667 6.51 0.00 45.05 2.83
84 85 4.693283 TGAAGTGTTAGACTTGACACAGG 58.307 43.478 18.43 0.00 45.48 4.00
87 88 5.585047 AGGTTTGAAGTGTTAGACTTGACAC 59.415 40.000 0.00 11.74 45.48 3.67
125 126 6.615726 AGCTTAGGGTCAGATTTCTTATGGTA 59.384 38.462 0.00 0.00 0.00 3.25
130 131 6.327626 AGCATAGCTTAGGGTCAGATTTCTTA 59.672 38.462 0.00 0.00 33.89 2.10
206 207 7.503566 TGCGGAGTAGTTTAGTACCATATACTT 59.496 37.037 0.00 0.00 0.00 2.24
207 208 7.000472 TGCGGAGTAGTTTAGTACCATATACT 59.000 38.462 0.00 0.00 0.00 2.12
208 209 7.206981 TGCGGAGTAGTTTAGTACCATATAC 57.793 40.000 0.00 0.00 0.00 1.47
209 210 7.449395 ACATGCGGAGTAGTTTAGTACCATATA 59.551 37.037 0.00 0.00 0.00 0.86
210 211 6.267014 ACATGCGGAGTAGTTTAGTACCATAT 59.733 38.462 0.00 0.00 0.00 1.78
211 212 5.595542 ACATGCGGAGTAGTTTAGTACCATA 59.404 40.000 0.00 0.00 0.00 2.74
258 260 7.121907 TGCTTTGCATGTAGTTTGTATGGAATA 59.878 33.333 0.00 0.00 33.26 1.75
267 269 4.502282 TCGTTTTGCTTTGCATGTAGTTTG 59.498 37.500 0.00 0.00 38.76 2.93
268 270 4.677584 TCGTTTTGCTTTGCATGTAGTTT 58.322 34.783 0.00 0.00 38.76 2.66
269 271 4.202010 ACTCGTTTTGCTTTGCATGTAGTT 60.202 37.500 0.00 0.00 38.76 2.24
274 276 2.730069 TCACTCGTTTTGCTTTGCATG 58.270 42.857 0.00 0.00 38.76 4.06
278 280 5.171337 GTGTACATTCACTCGTTTTGCTTTG 59.829 40.000 0.00 0.00 35.68 2.77
368 371 2.971901 ATTTGGACTCCCTCCGTTTT 57.028 45.000 0.00 0.00 43.03 2.43
373 376 2.500504 ACGAGTAATTTGGACTCCCTCC 59.499 50.000 0.00 0.00 40.25 4.30
378 381 5.312120 TCTGAGACGAGTAATTTGGACTC 57.688 43.478 0.00 0.00 40.02 3.36
379 382 5.723672 TTCTGAGACGAGTAATTTGGACT 57.276 39.130 0.00 0.00 0.00 3.85
380 383 6.183360 CCATTTCTGAGACGAGTAATTTGGAC 60.183 42.308 0.00 0.00 0.00 4.02
381 384 5.874810 CCATTTCTGAGACGAGTAATTTGGA 59.125 40.000 0.00 0.00 0.00 3.53
382 385 5.874810 TCCATTTCTGAGACGAGTAATTTGG 59.125 40.000 0.00 0.00 0.00 3.28
383 386 6.968131 TCCATTTCTGAGACGAGTAATTTG 57.032 37.500 0.00 0.00 0.00 2.32
384 387 7.106239 ACATCCATTTCTGAGACGAGTAATTT 58.894 34.615 0.00 0.00 0.00 1.82
385 388 6.644347 ACATCCATTTCTGAGACGAGTAATT 58.356 36.000 0.00 0.00 0.00 1.40
386 389 6.227298 ACATCCATTTCTGAGACGAGTAAT 57.773 37.500 0.00 0.00 0.00 1.89
387 390 5.661056 ACATCCATTTCTGAGACGAGTAA 57.339 39.130 0.00 0.00 0.00 2.24
388 391 6.773200 AGATACATCCATTTCTGAGACGAGTA 59.227 38.462 0.00 0.00 0.00 2.59
389 392 5.596361 AGATACATCCATTTCTGAGACGAGT 59.404 40.000 0.00 0.00 0.00 4.18
390 393 6.083098 AGATACATCCATTTCTGAGACGAG 57.917 41.667 0.00 0.00 0.00 4.18
391 394 6.998673 TCTAGATACATCCATTTCTGAGACGA 59.001 38.462 0.00 0.00 0.00 4.20
392 395 7.208225 TCTAGATACATCCATTTCTGAGACG 57.792 40.000 0.00 0.00 0.00 4.18
393 396 8.637986 AGTTCTAGATACATCCATTTCTGAGAC 58.362 37.037 0.00 0.00 0.00 3.36
394 397 8.774546 AGTTCTAGATACATCCATTTCTGAGA 57.225 34.615 0.00 0.00 0.00 3.27
421 424 8.696374 CGGGTATGGATGTATCTAGATGTATTT 58.304 37.037 15.79 0.00 0.00 1.40
422 425 7.201920 GCGGGTATGGATGTATCTAGATGTATT 60.202 40.741 15.79 0.00 0.00 1.89
423 426 6.265649 GCGGGTATGGATGTATCTAGATGTAT 59.734 42.308 15.79 9.11 0.00 2.29
424 427 5.593095 GCGGGTATGGATGTATCTAGATGTA 59.407 44.000 15.79 4.44 0.00 2.29
425 428 4.402793 GCGGGTATGGATGTATCTAGATGT 59.597 45.833 15.79 1.25 0.00 3.06
426 429 4.498177 CGCGGGTATGGATGTATCTAGATG 60.498 50.000 15.79 0.00 0.00 2.90
427 430 3.632604 CGCGGGTATGGATGTATCTAGAT 59.367 47.826 10.73 10.73 0.00 1.98
428 431 3.014623 CGCGGGTATGGATGTATCTAGA 58.985 50.000 0.00 0.00 0.00 2.43
429 432 3.014623 TCGCGGGTATGGATGTATCTAG 58.985 50.000 6.13 0.00 0.00 2.43
430 433 2.751259 GTCGCGGGTATGGATGTATCTA 59.249 50.000 6.13 0.00 0.00 1.98
431 434 1.544691 GTCGCGGGTATGGATGTATCT 59.455 52.381 6.13 0.00 0.00 1.98
432 435 1.271379 TGTCGCGGGTATGGATGTATC 59.729 52.381 6.13 0.00 0.00 2.24
433 436 1.334160 TGTCGCGGGTATGGATGTAT 58.666 50.000 6.13 0.00 0.00 2.29
434 437 1.067974 CTTGTCGCGGGTATGGATGTA 59.932 52.381 6.13 0.00 0.00 2.29
435 438 0.179084 CTTGTCGCGGGTATGGATGT 60.179 55.000 6.13 0.00 0.00 3.06
436 439 0.179084 ACTTGTCGCGGGTATGGATG 60.179 55.000 6.13 0.00 0.00 3.51
437 440 1.405872 TACTTGTCGCGGGTATGGAT 58.594 50.000 6.13 0.00 0.00 3.41
438 441 1.184431 TTACTTGTCGCGGGTATGGA 58.816 50.000 6.13 0.00 0.00 3.41
439 442 2.234300 ATTACTTGTCGCGGGTATGG 57.766 50.000 6.13 0.00 0.00 2.74
440 443 3.242608 CCAAATTACTTGTCGCGGGTATG 60.243 47.826 6.13 0.00 32.65 2.39
441 444 2.940410 CCAAATTACTTGTCGCGGGTAT 59.060 45.455 6.13 0.00 32.65 2.73
442 445 2.028294 TCCAAATTACTTGTCGCGGGTA 60.028 45.455 6.13 2.12 32.65 3.69
443 446 1.161843 CCAAATTACTTGTCGCGGGT 58.838 50.000 6.13 3.16 32.65 5.28
444 447 1.444836 TCCAAATTACTTGTCGCGGG 58.555 50.000 6.13 0.00 32.65 6.13
445 448 2.723618 CGTTCCAAATTACTTGTCGCGG 60.724 50.000 6.13 0.00 32.65 6.46
446 449 2.492001 CGTTCCAAATTACTTGTCGCG 58.508 47.619 0.00 0.00 32.65 5.87
447 450 2.481185 TCCGTTCCAAATTACTTGTCGC 59.519 45.455 0.00 0.00 32.65 5.19
448 451 3.124636 CCTCCGTTCCAAATTACTTGTCG 59.875 47.826 0.00 0.00 32.65 4.35
449 452 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
450 453 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
451 454 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
452 455 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
453 456 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
454 457 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
455 458 5.703730 ATTACTCCCTCCGTTCCAAATTA 57.296 39.130 0.00 0.00 0.00 1.40
456 459 4.586306 ATTACTCCCTCCGTTCCAAATT 57.414 40.909 0.00 0.00 0.00 1.82
457 460 4.720273 AGTATTACTCCCTCCGTTCCAAAT 59.280 41.667 0.00 0.00 0.00 2.32
458 461 4.098894 AGTATTACTCCCTCCGTTCCAAA 58.901 43.478 0.00 0.00 0.00 3.28
459 462 3.716431 AGTATTACTCCCTCCGTTCCAA 58.284 45.455 0.00 0.00 0.00 3.53
460 463 3.393426 AGTATTACTCCCTCCGTTCCA 57.607 47.619 0.00 0.00 0.00 3.53
461 464 5.595885 GTTAAGTATTACTCCCTCCGTTCC 58.404 45.833 0.00 0.00 0.00 3.62
462 465 5.163612 ACGTTAAGTATTACTCCCTCCGTTC 60.164 44.000 0.00 0.00 0.00 3.95
463 466 4.706962 ACGTTAAGTATTACTCCCTCCGTT 59.293 41.667 0.00 0.00 0.00 4.44
464 467 4.273318 ACGTTAAGTATTACTCCCTCCGT 58.727 43.478 0.00 0.05 0.00 4.69
465 468 4.578105 AGACGTTAAGTATTACTCCCTCCG 59.422 45.833 0.00 0.00 0.00 4.63
466 469 6.462552 AAGACGTTAAGTATTACTCCCTCC 57.537 41.667 0.00 0.00 31.67 4.30
493 496 2.531771 TCACACCTCTTCGTCCCATAA 58.468 47.619 0.00 0.00 0.00 1.90
508 511 9.716507 AATCGCTATTGTTGTATAAAATCACAC 57.283 29.630 0.00 0.00 0.00 3.82
586 589 8.319146 TGAGGATTAAGATACTTTCTCCGTTTT 58.681 33.333 0.00 0.00 31.78 2.43
587 590 7.848128 TGAGGATTAAGATACTTTCTCCGTTT 58.152 34.615 0.00 0.00 31.78 3.60
588 591 7.419711 TGAGGATTAAGATACTTTCTCCGTT 57.580 36.000 0.00 0.00 31.78 4.44
590 593 6.870965 CCATGAGGATTAAGATACTTTCTCCG 59.129 42.308 0.00 0.00 36.89 4.63
615 618 8.975410 ATTAAGGGCTAATCGTTGTTTTTAAC 57.025 30.769 0.00 0.00 0.00 2.01
633 636 8.732531 TCGTTGGTTTCAAAAGTATATTAAGGG 58.267 33.333 0.00 0.00 34.28 3.95
653 656 0.040067 GCTCCACAAAGCTTCGTTGG 60.040 55.000 12.66 12.66 39.27 3.77
692 695 5.509605 TGACACGTTAATCAAGTCAATCG 57.490 39.130 0.62 0.00 36.39 3.34
722 725 1.260561 GTACTTATCAATGGTGGCGCG 59.739 52.381 0.00 0.00 0.00 6.86
725 728 4.495844 GCGAAAGTACTTATCAATGGTGGC 60.496 45.833 8.92 0.00 0.00 5.01
738 741 3.374678 TGTTTTGTTTCGGCGAAAGTACT 59.625 39.130 32.93 0.00 31.87 2.73
739 742 3.682921 TGTTTTGTTTCGGCGAAAGTAC 58.317 40.909 32.93 25.11 31.87 2.73
740 743 4.352600 TTGTTTTGTTTCGGCGAAAGTA 57.647 36.364 32.93 22.32 31.87 2.24
741 744 2.923605 TGTTTTGTTTCGGCGAAAGT 57.076 40.000 32.93 0.00 31.87 2.66
748 751 8.322428 GTGTTAACCTAATTTGTTTTGTTTCGG 58.678 33.333 2.48 0.00 0.00 4.30
823 826 7.310664 TGGTCGTCAGTAGAAGTAGTAAATTG 58.689 38.462 0.00 0.00 0.00 2.32
826 829 6.712095 TCTTGGTCGTCAGTAGAAGTAGTAAA 59.288 38.462 0.00 0.00 0.00 2.01
827 830 6.233434 TCTTGGTCGTCAGTAGAAGTAGTAA 58.767 40.000 0.00 0.00 0.00 2.24
842 847 1.270147 CCGGAGTTTTCTCTTGGTCGT 60.270 52.381 0.00 0.00 45.52 4.34
843 848 1.429463 CCGGAGTTTTCTCTTGGTCG 58.571 55.000 0.00 0.00 45.52 4.79
1022 1029 1.599797 GTCGGGTGGTCTTTGTGGG 60.600 63.158 0.00 0.00 0.00 4.61
1467 1477 4.494484 CCAATGAAAAACCGAATCTTCCC 58.506 43.478 0.00 0.00 0.00 3.97
1707 1718 7.873739 ACTAATTCAGCAGCAAATAAAACAC 57.126 32.000 0.00 0.00 0.00 3.32
1744 1755 1.228862 AACCCGAAATGGCCTGCTT 60.229 52.632 3.32 0.00 35.87 3.91
1782 1793 3.357203 AGGTGCTCGTAATCAGAGAAGA 58.643 45.455 0.00 0.00 37.93 2.87
1784 1795 4.524053 TCTAGGTGCTCGTAATCAGAGAA 58.476 43.478 0.00 0.00 37.93 2.87
1789 1800 3.377485 GTGACTCTAGGTGCTCGTAATCA 59.623 47.826 0.00 0.00 0.00 2.57
1845 1856 4.227300 TGGGATTGAAGTGGCTACTAACAT 59.773 41.667 1.97 0.00 35.69 2.71
1905 1916 6.041523 AGCCCTTGTCTAGAGATGAGATTAAC 59.958 42.308 4.50 0.00 0.00 2.01
1954 1965 2.073816 CCAGTAAAGGTAGCAACACCG 58.926 52.381 0.00 0.00 43.84 4.94
1984 1995 1.497161 AGTATTTCTGGACGGAGGGG 58.503 55.000 0.00 0.00 0.00 4.79
1985 1996 2.236395 ACAAGTATTTCTGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
1986 1997 3.522553 GACAAGTATTTCTGGACGGAGG 58.477 50.000 0.00 0.00 0.00 4.30
1987 1998 3.195825 AGGACAAGTATTTCTGGACGGAG 59.804 47.826 0.00 0.00 0.00 4.63
1988 1999 3.170717 AGGACAAGTATTTCTGGACGGA 58.829 45.455 0.00 0.00 0.00 4.69
1989 2000 3.611766 AGGACAAGTATTTCTGGACGG 57.388 47.619 0.00 0.00 0.00 4.79
1990 2001 5.578005 TCTAGGACAAGTATTTCTGGACG 57.422 43.478 0.00 0.00 0.00 4.79
1991 2002 8.041323 TCATTTCTAGGACAAGTATTTCTGGAC 58.959 37.037 0.00 0.00 0.00 4.02
1992 2003 8.146053 TCATTTCTAGGACAAGTATTTCTGGA 57.854 34.615 0.00 0.00 0.00 3.86
1993 2004 8.792830 TTCATTTCTAGGACAAGTATTTCTGG 57.207 34.615 0.00 0.00 0.00 3.86
1995 2006 9.965902 ACATTCATTTCTAGGACAAGTATTTCT 57.034 29.630 0.00 0.00 0.00 2.52
2046 2057 9.793259 GTCCTAGAAATGGATAAAATGGATGTA 57.207 33.333 0.00 0.00 35.87 2.29
2047 2058 8.281531 TGTCCTAGAAATGGATAAAATGGATGT 58.718 33.333 0.00 0.00 35.87 3.06
2048 2059 8.696043 TGTCCTAGAAATGGATAAAATGGATG 57.304 34.615 0.00 0.00 35.87 3.51
2049 2060 9.359653 CTTGTCCTAGAAATGGATAAAATGGAT 57.640 33.333 0.00 0.00 34.98 3.41
2050 2061 8.336235 ACTTGTCCTAGAAATGGATAAAATGGA 58.664 33.333 0.00 0.00 34.98 3.41
2051 2062 8.525290 ACTTGTCCTAGAAATGGATAAAATGG 57.475 34.615 0.00 0.00 34.98 3.16
2056 2067 9.847224 GGAAATACTTGTCCTAGAAATGGATAA 57.153 33.333 0.00 0.00 35.87 1.75
2057 2068 8.148351 CGGAAATACTTGTCCTAGAAATGGATA 58.852 37.037 0.00 0.00 35.87 2.59
2058 2069 6.992715 CGGAAATACTTGTCCTAGAAATGGAT 59.007 38.462 0.00 0.00 35.87 3.41
2059 2070 6.346096 CGGAAATACTTGTCCTAGAAATGGA 58.654 40.000 0.00 0.00 0.00 3.41
2060 2071 5.527582 CCGGAAATACTTGTCCTAGAAATGG 59.472 44.000 0.00 0.00 0.00 3.16
2061 2072 6.258068 GTCCGGAAATACTTGTCCTAGAAATG 59.742 42.308 5.23 0.00 0.00 2.32
2062 2073 6.346896 GTCCGGAAATACTTGTCCTAGAAAT 58.653 40.000 5.23 0.00 0.00 2.17
2063 2074 5.622914 CGTCCGGAAATACTTGTCCTAGAAA 60.623 44.000 5.23 0.00 0.00 2.52
2064 2075 4.142315 CGTCCGGAAATACTTGTCCTAGAA 60.142 45.833 5.23 0.00 0.00 2.10
2065 2076 3.379372 CGTCCGGAAATACTTGTCCTAGA 59.621 47.826 5.23 0.00 0.00 2.43
2066 2077 3.490419 CCGTCCGGAAATACTTGTCCTAG 60.490 52.174 5.23 0.00 37.50 3.02
2067 2078 2.428171 CCGTCCGGAAATACTTGTCCTA 59.572 50.000 5.23 0.00 37.50 2.94
2068 2079 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
2069 2080 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
2070 2081 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2071 2082 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2072 2083 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2073 2084 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2074 2085 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2075 2086 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2076 2087 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2077 2088 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2078 2089 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2079 2090 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2080 2091 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
2081 2092 0.107017 TAAGTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
2082 2093 1.755179 TTAAGTACTCCCTCCGTCCG 58.245 55.000 0.00 0.00 0.00 4.79
2083 2094 4.280425 CCTAATTAAGTACTCCCTCCGTCC 59.720 50.000 0.00 0.00 0.00 4.79
2084 2095 4.261952 GCCTAATTAAGTACTCCCTCCGTC 60.262 50.000 0.00 0.00 0.00 4.79
2085 2096 3.640498 GCCTAATTAAGTACTCCCTCCGT 59.360 47.826 0.00 0.00 0.00 4.69
2086 2097 3.640029 TGCCTAATTAAGTACTCCCTCCG 59.360 47.826 0.00 0.00 0.00 4.63
2087 2098 5.625568 TTGCCTAATTAAGTACTCCCTCC 57.374 43.478 0.00 0.00 0.00 4.30
2123 2134 8.651588 CAAATTGACTAGTACAAGATCAGTGAC 58.348 37.037 0.00 0.00 0.00 3.67
2136 2147 4.461431 TGGTCTCTCGCAAATTGACTAGTA 59.539 41.667 0.00 0.00 0.00 1.82
2137 2148 3.258372 TGGTCTCTCGCAAATTGACTAGT 59.742 43.478 0.00 0.00 0.00 2.57
2138 2149 3.849911 TGGTCTCTCGCAAATTGACTAG 58.150 45.455 0.00 0.00 0.00 2.57
2150 2161 3.003480 GTTTCCCAGAAATGGTCTCTCG 58.997 50.000 0.00 0.00 32.70 4.04
2491 2506 3.857157 AGGTCAAGCACTACCTGAAAA 57.143 42.857 3.35 0.00 44.53 2.29
2510 2526 3.675698 GCAGAAACTAAAGTCTCGTCCAG 59.324 47.826 0.00 0.00 0.00 3.86
2691 2707 5.827797 TCCTTTACAGCTCACACAAGAAAAT 59.172 36.000 0.00 0.00 0.00 1.82
2725 2741 7.920682 ACAGTAACATGATTCACCTTTTGTTTC 59.079 33.333 0.00 4.08 0.00 2.78
2797 2813 6.273825 TGTAAAGAGGATAAGATCTGCGAAC 58.726 40.000 0.00 0.00 0.00 3.95
2830 2846 1.879575 TAGCAGCCACCATACCTTCT 58.120 50.000 0.00 0.00 0.00 2.85
2868 2884 2.302260 GGGATCATGTGACGAGAGAGA 58.698 52.381 0.00 0.00 0.00 3.10
2869 2885 2.027385 TGGGATCATGTGACGAGAGAG 58.973 52.381 0.00 0.00 0.00 3.20
2870 2886 2.143876 TGGGATCATGTGACGAGAGA 57.856 50.000 0.00 0.00 0.00 3.10
2871 2887 2.967599 TTGGGATCATGTGACGAGAG 57.032 50.000 0.00 0.00 0.00 3.20
2872 2888 2.765699 TGATTGGGATCATGTGACGAGA 59.234 45.455 0.00 0.00 37.37 4.04
2873 2889 3.129109 CTGATTGGGATCATGTGACGAG 58.871 50.000 0.00 0.00 41.28 4.18
2890 2906 2.437281 CAGGTATGGTGAGGAAGCTGAT 59.563 50.000 0.00 0.00 39.26 2.90
2966 2982 7.255035 CGATAGAGACGGAGTTTGAACCTATTA 60.255 40.741 0.00 0.00 39.81 0.98
3035 3051 8.331931 ACAAAATCACTTGTATCCTATCCCTA 57.668 34.615 0.00 0.00 37.76 3.53
3036 3052 7.213178 ACAAAATCACTTGTATCCTATCCCT 57.787 36.000 0.00 0.00 37.76 4.20
3037 3053 8.837389 GTTACAAAATCACTTGTATCCTATCCC 58.163 37.037 0.00 0.00 40.53 3.85
3038 3054 8.548721 CGTTACAAAATCACTTGTATCCTATCC 58.451 37.037 0.00 0.00 40.53 2.59
3039 3055 9.095065 ACGTTACAAAATCACTTGTATCCTATC 57.905 33.333 0.00 0.00 40.53 2.08
3040 3056 9.095065 GACGTTACAAAATCACTTGTATCCTAT 57.905 33.333 0.00 0.00 40.53 2.57
3064 3080 4.086178 CAGCAGCAGCAGCACGAC 62.086 66.667 12.92 0.00 45.49 4.34
3070 3086 3.048475 AAGACGCAGCAGCAGCAG 61.048 61.111 10.77 5.43 45.49 4.24
3342 3370 4.910195 ACACTGCAGATTACCATCTTCAA 58.090 39.130 23.35 0.00 37.71 2.69
3343 3371 4.558226 ACACTGCAGATTACCATCTTCA 57.442 40.909 23.35 0.00 37.71 3.02
3422 3455 1.818642 GCAGATATCCAGGGTCATGC 58.181 55.000 0.00 0.00 0.00 4.06
3423 3456 1.338484 CCGCAGATATCCAGGGTCATG 60.338 57.143 0.00 0.00 0.00 3.07
3424 3457 0.979665 CCGCAGATATCCAGGGTCAT 59.020 55.000 0.00 0.00 0.00 3.06
3436 3469 2.361483 TGGCATTGCACCGCAGAT 60.361 55.556 11.39 0.00 40.61 2.90
3679 3730 7.876068 CAGTCCTACTCCAAACAAAGTATTACA 59.124 37.037 0.00 0.00 0.00 2.41
3680 3731 7.333672 CCAGTCCTACTCCAAACAAAGTATTAC 59.666 40.741 0.00 0.00 0.00 1.89
3687 3738 2.441750 AGCCAGTCCTACTCCAAACAAA 59.558 45.455 0.00 0.00 0.00 2.83
3700 3751 3.692257 ATATGCACTATCAGCCAGTCC 57.308 47.619 0.00 0.00 0.00 3.85
3728 3779 7.371936 TGTATTGTGTTAGGTTATTGGCAAAC 58.628 34.615 3.01 0.00 0.00 2.93
3745 3796 0.107897 TGGCCCGCTACTGTATTGTG 60.108 55.000 0.00 0.00 0.00 3.33
3746 3797 0.178068 CTGGCCCGCTACTGTATTGT 59.822 55.000 0.00 0.00 0.00 2.71
3748 3799 0.909623 AACTGGCCCGCTACTGTATT 59.090 50.000 0.00 0.00 0.00 1.89
3749 3800 0.464452 GAACTGGCCCGCTACTGTAT 59.536 55.000 0.00 0.00 0.00 2.29
3760 3811 5.591877 ACTGATATCAGAAAATGAACTGGCC 59.408 40.000 34.16 0.00 46.59 5.36
3784 3835 1.529226 CCTGAAATTGTACACGCCCA 58.471 50.000 0.00 0.00 0.00 5.36
3788 3839 5.872617 TCTGTATTCCCTGAAATTGTACACG 59.127 40.000 0.00 0.00 0.00 4.49
3833 3884 4.574599 ACTGAAATCTTTTGACAGGCAC 57.425 40.909 0.00 0.00 33.57 5.01
3976 4027 1.396996 GACCGGAACCATTGAATGACG 59.603 52.381 9.46 5.76 0.00 4.35
4183 4235 6.712547 ACTTGATTCTTCTCCACCTAAACAAG 59.287 38.462 0.00 0.00 36.81 3.16
4338 4396 7.497249 GTGACATTCTGCTAGATTACATTTCCT 59.503 37.037 0.00 0.00 0.00 3.36
4343 4401 8.618677 CAAATGTGACATTCTGCTAGATTACAT 58.381 33.333 11.70 0.00 0.00 2.29
4363 4421 6.647334 TGATGTTGACACCAATACAAATGT 57.353 33.333 0.00 0.00 34.39 2.71
4364 4422 8.436970 CAATTGATGTTGACACCAATACAAATG 58.563 33.333 4.22 0.00 34.39 2.32
4482 4541 7.765695 ACCTTGATTAAATGTCAGTTGATGT 57.234 32.000 0.00 0.00 0.00 3.06
4486 4545 8.137437 ACTGAAACCTTGATTAAATGTCAGTTG 58.863 33.333 0.00 0.00 30.61 3.16
4491 4550 8.099364 TCTGACTGAAACCTTGATTAAATGTC 57.901 34.615 0.00 0.00 0.00 3.06
4627 4686 5.850046 ATATGCTTATTGGTCTTAGGCCT 57.150 39.130 11.78 11.78 0.00 5.19
4628 4687 8.581253 AATTATATGCTTATTGGTCTTAGGCC 57.419 34.615 0.00 0.00 0.00 5.19
4652 4711 8.999431 GTCTTGTGTGATTCCTTAGTGATTTAA 58.001 33.333 0.00 0.00 0.00 1.52
4669 4728 6.076981 AGCTTAAAAATCCAGTCTTGTGTG 57.923 37.500 0.00 0.00 0.00 3.82
4717 4777 3.511934 TCCAGAGTTCAGGCTAAAGAGAC 59.488 47.826 0.00 0.00 0.00 3.36
4723 4783 3.173151 TCATGTCCAGAGTTCAGGCTAA 58.827 45.455 0.00 0.00 0.00 3.09
4724 4784 2.762887 CTCATGTCCAGAGTTCAGGCTA 59.237 50.000 0.00 0.00 0.00 3.93
4801 4962 4.624882 CAGATTATCAGCCAGATACGAAGC 59.375 45.833 0.00 0.00 38.90 3.86
4828 4989 1.599542 GCATACAGATTTGACGAGGCC 59.400 52.381 0.00 0.00 0.00 5.19
4840 5001 2.608090 CGTGTACGAGAGAGCATACAGA 59.392 50.000 0.00 0.00 43.02 3.41
4960 5121 0.392595 TCCAGATGCTCAGCTTGCTG 60.393 55.000 15.74 15.74 0.00 4.41
5065 5226 0.179084 CCGTCACCATGAACGCCTAT 60.179 55.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.