Multiple sequence alignment - TraesCS3D01G526700

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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 TraesCS3D01G526700 chr3D 100.000 7948 0 0 1 7948 605492916 605500863 0.000000e+00 14678.0
1 TraesCS3D01G526700 chr3D 98.827 5284 57 1 985 6263 605514720 605520003 0.000000e+00 9409.0
2 TraesCS3D01G526700 chr3D 98.637 5061 67 2 449 5509 605557568 605562626 0.000000e+00 8962.0
3 TraesCS3D01G526700 chr3D 98.623 3921 53 1 1589 5509 605537648 605541567 0.000000e+00 6940.0
4 TraesCS3D01G526700 chr3D 96.739 3680 99 11 248 3927 331066400 331070058 0.000000e+00 6111.0
5 TraesCS3D01G526700 chr3D 99.039 2394 22 1 5555 7948 605542197 605544589 0.000000e+00 4292.0
6 TraesCS3D01G526700 chr3D 99.039 2394 22 1 5555 7948 605562836 605565228 0.000000e+00 4292.0
7 TraesCS3D01G526700 chr3D 98.508 1810 24 2 6141 7948 605477002 605478810 0.000000e+00 3190.0
8 TraesCS3D01G526700 chr3D 98.953 1720 17 1 6229 7948 605520001 605521719 0.000000e+00 3075.0
9 TraesCS3D01G526700 chr3D 98.033 1474 27 2 4669 6140 585380812 585379339 0.000000e+00 2560.0
10 TraesCS3D01G526700 chr3D 97.427 1477 34 3 4669 6141 536162150 536163626 0.000000e+00 2514.0
11 TraesCS3D01G526700 chr3D 97.420 1473 35 3 4669 6140 584658131 584656661 0.000000e+00 2507.0
12 TraesCS3D01G526700 chr3D 98.647 739 10 0 3924 4662 2002942 2003680 0.000000e+00 1310.0
13 TraesCS3D01G526700 chr3D 92.652 558 41 0 6902 7459 18879255 18879812 0.000000e+00 804.0
14 TraesCS3D01G526700 chr3D 97.967 246 5 0 1 246 605578042 605578287 2.050000e-115 427.0
15 TraesCS3D01G526700 chr3D 88.554 332 37 1 7484 7814 562755863 562756194 1.240000e-107 401.0
16 TraesCS3D01G526700 chr3D 91.667 252 14 5 1 246 605756941 605757191 7.640000e-90 342.0
17 TraesCS3D01G526700 chr3D 90.079 252 18 5 1 246 605346493 605346743 3.580000e-83 320.0
18 TraesCS3D01G526700 chr3D 89.683 252 19 5 1 246 605443704 605443954 1.660000e-81 315.0
19 TraesCS3D01G526700 chr3D 88.750 240 15 8 16 246 605949403 605949639 4.700000e-72 283.0
20 TraesCS3D01G526700 chr6D 96.992 3690 88 14 239 3927 83549681 83546014 0.000000e+00 6178.0
21 TraesCS3D01G526700 chr6D 98.520 743 9 2 3924 4665 78834485 78833744 0.000000e+00 1310.0
22 TraesCS3D01G526700 chr6D 100.000 31 0 0 6176 6206 434447427 434447397 3.100000e-04 58.4
23 TraesCS3D01G526700 chr7D 96.904 3682 94 9 248 3927 452960867 452964530 0.000000e+00 6150.0
24 TraesCS3D01G526700 chr7D 96.576 3680 109 13 248 3927 632553103 632556765 0.000000e+00 6082.0
25 TraesCS3D01G526700 chr7D 96.340 3689 103 15 248 3927 102563977 102560312 0.000000e+00 6035.0
26 TraesCS3D01G526700 chr7D 98.652 742 9 1 3924 4665 588746487 588745747 0.000000e+00 1314.0
27 TraesCS3D01G526700 chr7D 98.520 743 10 1 3924 4665 66852093 66852835 0.000000e+00 1310.0
28 TraesCS3D01G526700 chr7D 98.385 743 12 0 3923 4665 85237082 85237824 0.000000e+00 1306.0
29 TraesCS3D01G526700 chr2D 97.701 3480 69 5 449 3927 299356767 299360236 0.000000e+00 5973.0
30 TraesCS3D01G526700 chr2D 94.286 315 16 2 250 564 646001431 646001743 1.550000e-131 481.0
31 TraesCS3D01G526700 chr2D 94.007 267 13 3 248 514 537004159 537003896 1.240000e-107 401.0
32 TraesCS3D01G526700 chr5D 98.099 1473 25 3 4669 6140 432920092 432921562 0.000000e+00 2562.0
33 TraesCS3D01G526700 chr5D 97.838 1480 25 3 4669 6141 552112849 552111370 0.000000e+00 2549.0
34 TraesCS3D01G526700 chr5D 98.518 742 10 1 3924 4665 500960466 500961206 0.000000e+00 1308.0
35 TraesCS3D01G526700 chr1D 97.566 1479 29 3 4669 6141 59043119 59044596 0.000000e+00 2525.0
36 TraesCS3D01G526700 chr1D 94.737 38 2 0 6168 6205 233796022 233795985 8.610000e-05 60.2
37 TraesCS3D01G526700 chr4D 96.947 1474 43 2 4669 6140 10530184 10531657 0.000000e+00 2471.0
38 TraesCS3D01G526700 chr4D 96.945 1473 42 3 4669 6140 54304014 54305484 0.000000e+00 2468.0
39 TraesCS3D01G526700 chr4D 87.786 131 10 3 7820 7948 76602456 76602330 1.790000e-31 148.0
40 TraesCS3D01G526700 chr3A 92.722 687 34 7 6214 6897 738750484 738749811 0.000000e+00 977.0
41 TraesCS3D01G526700 chr3A 93.929 560 34 0 6900 7459 738122037 738122596 0.000000e+00 846.0
42 TraesCS3D01G526700 chr3A 91.979 561 42 3 6900 7459 502935176 502935734 0.000000e+00 784.0
43 TraesCS3D01G526700 chr3A 94.758 248 8 4 1 246 738719422 738719178 1.620000e-101 381.0
44 TraesCS3D01G526700 chr3A 90.157 254 16 6 1 246 738337943 738337691 9.950000e-84 322.0
45 TraesCS3D01G526700 chr3A 89.247 186 13 5 57 236 738724369 738724185 8.030000e-55 226.0
46 TraesCS3D01G526700 chr3A 86.667 105 6 5 49 146 738586184 738586081 8.430000e-20 110.0
47 TraesCS3D01G526700 chr7A 93.357 557 36 1 6900 7456 33027422 33026867 0.000000e+00 822.0
48 TraesCS3D01G526700 chr7A 90.265 113 9 2 7820 7930 707101027 707101139 6.430000e-31 147.0
49 TraesCS3D01G526700 chr7A 94.595 37 0 2 6170 6205 628401748 628401713 1.000000e-03 56.5
50 TraesCS3D01G526700 chr2B 92.143 560 41 3 6901 7459 742186805 742187362 0.000000e+00 787.0
51 TraesCS3D01G526700 chr7B 86.835 357 42 4 248 603 500770528 500770176 2.080000e-105 394.0
52 TraesCS3D01G526700 chr1B 87.353 340 39 4 7477 7814 551649213 551648876 3.480000e-103 387.0
53 TraesCS3D01G526700 chr1B 87.023 131 11 3 7820 7948 571500727 571500853 8.310000e-30 143.0
54 TraesCS3D01G526700 chr3B 93.023 258 18 0 7557 7814 420655926 420655669 2.090000e-100 377.0
55 TraesCS3D01G526700 chr3B 86.585 82 11 0 7483 7564 809093073 809093154 3.050000e-14 91.6
56 TraesCS3D01G526700 chr2A 85.224 379 38 12 248 625 775079143 775078782 2.710000e-99 374.0
57 TraesCS3D01G526700 chr6B 92.636 258 19 0 7557 7814 656448514 656448257 9.740000e-99 372.0
58 TraesCS3D01G526700 chr6B 89.744 117 10 2 7816 7930 716360948 716360832 1.790000e-31 148.0
59 TraesCS3D01G526700 chr4B 92.636 258 19 0 7557 7814 647909099 647909356 9.740000e-99 372.0
60 TraesCS3D01G526700 chr4B 90.265 113 9 2 7820 7930 109316568 109316680 6.430000e-31 147.0
61 TraesCS3D01G526700 chr1A 100.000 31 0 0 6175 6205 447736000 447735970 3.100000e-04 58.4
62 TraesCS3D01G526700 chr6A 90.244 41 3 1 6165 6205 107689778 107689817 1.400000e-02 52.8


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 TraesCS3D01G526700 chr3D 605492916 605500863 7947 False 14678 14678 100.000 1 7948 1 chr3D.!!$F9 7947
1 TraesCS3D01G526700 chr3D 605557568 605565228 7660 False 6627 8962 98.838 449 7948 2 chr3D.!!$F15 7499
2 TraesCS3D01G526700 chr3D 605514720 605521719 6999 False 6242 9409 98.890 985 7948 2 chr3D.!!$F13 6963
3 TraesCS3D01G526700 chr3D 331066400 331070058 3658 False 6111 6111 96.739 248 3927 1 chr3D.!!$F3 3679
4 TraesCS3D01G526700 chr3D 605537648 605544589 6941 False 5616 6940 98.831 1589 7948 2 chr3D.!!$F14 6359
5 TraesCS3D01G526700 chr3D 605477002 605478810 1808 False 3190 3190 98.508 6141 7948 1 chr3D.!!$F8 1807
6 TraesCS3D01G526700 chr3D 585379339 585380812 1473 True 2560 2560 98.033 4669 6140 1 chr3D.!!$R2 1471
7 TraesCS3D01G526700 chr3D 536162150 536163626 1476 False 2514 2514 97.427 4669 6141 1 chr3D.!!$F4 1472
8 TraesCS3D01G526700 chr3D 584656661 584658131 1470 True 2507 2507 97.420 4669 6140 1 chr3D.!!$R1 1471
9 TraesCS3D01G526700 chr3D 2002942 2003680 738 False 1310 1310 98.647 3924 4662 1 chr3D.!!$F1 738
10 TraesCS3D01G526700 chr3D 18879255 18879812 557 False 804 804 92.652 6902 7459 1 chr3D.!!$F2 557
11 TraesCS3D01G526700 chr6D 83546014 83549681 3667 True 6178 6178 96.992 239 3927 1 chr6D.!!$R2 3688
12 TraesCS3D01G526700 chr6D 78833744 78834485 741 True 1310 1310 98.520 3924 4665 1 chr6D.!!$R1 741
13 TraesCS3D01G526700 chr7D 452960867 452964530 3663 False 6150 6150 96.904 248 3927 1 chr7D.!!$F3 3679
14 TraesCS3D01G526700 chr7D 632553103 632556765 3662 False 6082 6082 96.576 248 3927 1 chr7D.!!$F4 3679
15 TraesCS3D01G526700 chr7D 102560312 102563977 3665 True 6035 6035 96.340 248 3927 1 chr7D.!!$R1 3679
16 TraesCS3D01G526700 chr7D 588745747 588746487 740 True 1314 1314 98.652 3924 4665 1 chr7D.!!$R2 741
17 TraesCS3D01G526700 chr7D 66852093 66852835 742 False 1310 1310 98.520 3924 4665 1 chr7D.!!$F1 741
18 TraesCS3D01G526700 chr7D 85237082 85237824 742 False 1306 1306 98.385 3923 4665 1 chr7D.!!$F2 742
19 TraesCS3D01G526700 chr2D 299356767 299360236 3469 False 5973 5973 97.701 449 3927 1 chr2D.!!$F1 3478
20 TraesCS3D01G526700 chr5D 432920092 432921562 1470 False 2562 2562 98.099 4669 6140 1 chr5D.!!$F1 1471
21 TraesCS3D01G526700 chr5D 552111370 552112849 1479 True 2549 2549 97.838 4669 6141 1 chr5D.!!$R1 1472
22 TraesCS3D01G526700 chr5D 500960466 500961206 740 False 1308 1308 98.518 3924 4665 1 chr5D.!!$F2 741
23 TraesCS3D01G526700 chr1D 59043119 59044596 1477 False 2525 2525 97.566 4669 6141 1 chr1D.!!$F1 1472
24 TraesCS3D01G526700 chr4D 10530184 10531657 1473 False 2471 2471 96.947 4669 6140 1 chr4D.!!$F1 1471
25 TraesCS3D01G526700 chr4D 54304014 54305484 1470 False 2468 2468 96.945 4669 6140 1 chr4D.!!$F2 1471
26 TraesCS3D01G526700 chr3A 738749811 738750484 673 True 977 977 92.722 6214 6897 1 chr3A.!!$R5 683
27 TraesCS3D01G526700 chr3A 738122037 738122596 559 False 846 846 93.929 6900 7459 1 chr3A.!!$F2 559
28 TraesCS3D01G526700 chr3A 502935176 502935734 558 False 784 784 91.979 6900 7459 1 chr3A.!!$F1 559
29 TraesCS3D01G526700 chr7A 33026867 33027422 555 True 822 822 93.357 6900 7456 1 chr7A.!!$R1 556
30 TraesCS3D01G526700 chr2B 742186805 742187362 557 False 787 787 92.143 6901 7459 1 chr2B.!!$F1 558

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
244 245 0.036010 AATGGACGGACTTGCTGAGG 60.036 55.000 0.00 0.00 0.00 3.86 F
246 247 0.541063 TGGACGGACTTGCTGAGGTA 60.541 55.000 0.00 0.00 0.00 3.08 F
1910 1920 0.674581 CTGGCAAGAACGCTCCATGA 60.675 55.000 0.00 0.00 0.00 3.07 F
2496 2508 1.647545 ATCAACCCGATGTGCTTGCG 61.648 55.000 0.00 0.00 31.20 4.85 F
3787 3813 1.353694 AGAAGAAGATTGCCTGCAGGT 59.646 47.619 32.81 14.76 37.57 4.00 F
3994 4020 2.864968 CCTCGTCTCTTTACCGAAGTG 58.135 52.381 0.00 0.00 36.70 3.16 F
5289 5317 2.553247 GGGCCTAACTGTTCTCTTTGCT 60.553 50.000 0.84 0.00 0.00 3.91 F
6263 6921 2.018727 TATGTGCGTATTCCGGCCGT 62.019 55.000 26.12 8.42 36.94 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 1920 0.537143 TCAACGCCTTCAGCCACATT 60.537 50.000 0.00 0.0 38.78 2.71 R
2176 2186 6.123852 AGGATTAAACCTGACGCTCTTCGT 62.124 45.833 3.01 0.0 42.88 3.85 R
3535 3555 1.442773 AGCTCATGGCCCTATCACAT 58.557 50.000 0.00 0.0 43.05 3.21 R
4144 4170 1.075601 AAGAAGGAGCCCATGGTGAA 58.924 50.000 11.73 0.0 0.00 3.18 R
5289 5317 2.228480 GGTCCAGTAGGCCCCACAA 61.228 63.158 0.00 0.0 33.74 3.33 R
5960 6581 1.152839 CCGGTTGGTGGGACAAACT 60.153 57.895 0.00 0.0 44.16 2.66 R
6762 7422 1.557443 CTGTCGACAACCAACTCGGC 61.557 60.000 20.49 0.0 39.03 5.54 R
7272 7936 1.606313 CAATGGTCCGGCACCCTTT 60.606 57.895 17.20 9.4 46.18 3.11 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
28 29 3.965888 CCTTGCTAGGTTGGAAGCT 57.034 52.632 5.98 0.00 39.53 3.74
38 39 6.472686 CTAGGTTGGAAGCTAGTATCAGTT 57.527 41.667 14.76 0.00 46.65 3.16
39 40 7.584122 CTAGGTTGGAAGCTAGTATCAGTTA 57.416 40.000 14.76 0.00 46.65 2.24
40 41 6.472686 AGGTTGGAAGCTAGTATCAGTTAG 57.527 41.667 0.00 0.00 34.49 2.34
41 42 5.364157 AGGTTGGAAGCTAGTATCAGTTAGG 59.636 44.000 0.00 0.00 34.49 2.69
42 43 5.128991 GGTTGGAAGCTAGTATCAGTTAGGT 59.871 44.000 0.00 0.00 0.00 3.08
43 44 6.351966 GGTTGGAAGCTAGTATCAGTTAGGTT 60.352 42.308 0.00 0.00 39.53 3.50
44 45 6.222038 TGGAAGCTAGTATCAGTTAGGTTG 57.778 41.667 0.00 0.00 37.63 3.77
45 46 5.051153 GGAAGCTAGTATCAGTTAGGTTGC 58.949 45.833 0.00 0.87 37.63 4.17
46 47 5.395324 GGAAGCTAGTATCAGTTAGGTTGCA 60.395 44.000 9.16 0.00 41.97 4.08
47 48 5.878406 AGCTAGTATCAGTTAGGTTGCAT 57.122 39.130 0.00 0.00 0.00 3.96
48 49 5.848406 AGCTAGTATCAGTTAGGTTGCATC 58.152 41.667 0.00 0.00 0.00 3.91
49 50 4.991687 GCTAGTATCAGTTAGGTTGCATCC 59.008 45.833 5.61 5.61 0.00 3.51
50 51 5.453339 GCTAGTATCAGTTAGGTTGCATCCA 60.453 44.000 16.12 0.00 0.00 3.41
51 52 4.770795 AGTATCAGTTAGGTTGCATCCAC 58.229 43.478 16.12 6.40 0.00 4.02
52 53 4.471386 AGTATCAGTTAGGTTGCATCCACT 59.529 41.667 16.12 8.56 0.00 4.00
53 54 5.661312 AGTATCAGTTAGGTTGCATCCACTA 59.339 40.000 16.12 0.00 0.00 2.74
54 55 4.901197 TCAGTTAGGTTGCATCCACTAA 57.099 40.909 16.12 4.26 0.00 2.24
55 56 4.832248 TCAGTTAGGTTGCATCCACTAAG 58.168 43.478 16.12 3.37 0.00 2.18
56 57 4.286032 TCAGTTAGGTTGCATCCACTAAGT 59.714 41.667 16.12 6.90 31.20 2.24
57 58 4.393062 CAGTTAGGTTGCATCCACTAAGTG 59.607 45.833 16.12 14.03 39.23 3.16
67 68 3.558674 CACTAAGTGGGGGCTGAAG 57.441 57.895 0.00 0.00 0.00 3.02
68 69 0.984230 CACTAAGTGGGGGCTGAAGA 59.016 55.000 0.00 0.00 0.00 2.87
69 70 0.984995 ACTAAGTGGGGGCTGAAGAC 59.015 55.000 0.00 0.00 0.00 3.01
70 71 1.280457 CTAAGTGGGGGCTGAAGACT 58.720 55.000 0.00 0.00 0.00 3.24
71 72 0.984230 TAAGTGGGGGCTGAAGACTG 59.016 55.000 0.00 0.00 0.00 3.51
72 73 2.360475 GTGGGGGCTGAAGACTGC 60.360 66.667 0.00 0.00 39.64 4.40
73 74 2.530151 TGGGGGCTGAAGACTGCT 60.530 61.111 0.00 0.00 40.11 4.24
74 75 2.045536 GGGGGCTGAAGACTGCTG 60.046 66.667 0.00 0.00 40.11 4.41
75 76 2.045536 GGGGCTGAAGACTGCTGG 60.046 66.667 0.00 0.00 40.11 4.85
76 77 2.749441 GGGCTGAAGACTGCTGGC 60.749 66.667 5.38 5.38 40.11 4.85
77 78 2.749441 GGCTGAAGACTGCTGGCC 60.749 66.667 0.00 0.00 40.11 5.36
78 79 3.123620 GCTGAAGACTGCTGGCCG 61.124 66.667 0.00 0.00 37.84 6.13
79 80 2.345244 CTGAAGACTGCTGGCCGT 59.655 61.111 0.00 0.00 0.00 5.68
80 81 1.302033 CTGAAGACTGCTGGCCGTT 60.302 57.895 0.00 0.00 0.00 4.44
81 82 1.572085 CTGAAGACTGCTGGCCGTTG 61.572 60.000 0.00 0.00 0.00 4.10
82 83 1.598130 GAAGACTGCTGGCCGTTGT 60.598 57.895 0.00 0.00 0.00 3.32
83 84 1.152963 AAGACTGCTGGCCGTTGTT 60.153 52.632 0.00 0.00 0.00 2.83
84 85 1.447317 AAGACTGCTGGCCGTTGTTG 61.447 55.000 0.00 0.00 0.00 3.33
85 86 1.891919 GACTGCTGGCCGTTGTTGA 60.892 57.895 0.00 0.00 0.00 3.18
86 87 2.117941 GACTGCTGGCCGTTGTTGAC 62.118 60.000 0.00 0.00 0.00 3.18
97 98 1.795768 GTTGTTGACGAGCAGGATGA 58.204 50.000 0.00 0.00 39.69 2.92
98 99 1.461127 GTTGTTGACGAGCAGGATGAC 59.539 52.381 0.00 0.00 39.69 3.06
99 100 0.678950 TGTTGACGAGCAGGATGACA 59.321 50.000 0.00 0.00 39.69 3.58
100 101 1.069978 TGTTGACGAGCAGGATGACAA 59.930 47.619 0.00 0.00 39.69 3.18
101 102 2.289631 TGTTGACGAGCAGGATGACAAT 60.290 45.455 0.00 0.00 39.69 2.71
102 103 2.299993 TGACGAGCAGGATGACAATC 57.700 50.000 0.00 0.00 39.69 2.67
103 104 1.550072 TGACGAGCAGGATGACAATCA 59.450 47.619 0.00 0.00 39.69 2.57
104 105 1.929836 GACGAGCAGGATGACAATCAC 59.070 52.381 0.00 0.00 39.69 3.06
105 106 1.276138 ACGAGCAGGATGACAATCACA 59.724 47.619 0.00 0.00 39.69 3.58
106 107 2.289631 ACGAGCAGGATGACAATCACAA 60.290 45.455 0.00 0.00 39.69 3.33
107 108 2.094894 CGAGCAGGATGACAATCACAAC 59.905 50.000 0.00 0.00 39.69 3.32
108 109 3.076621 GAGCAGGATGACAATCACAACA 58.923 45.455 0.00 0.00 39.69 3.33
109 110 3.079578 AGCAGGATGACAATCACAACAG 58.920 45.455 0.00 0.00 39.69 3.16
110 111 2.163010 GCAGGATGACAATCACAACAGG 59.837 50.000 0.00 0.00 39.69 4.00
111 112 3.415212 CAGGATGACAATCACAACAGGT 58.585 45.455 0.00 0.00 39.69 4.00
112 113 3.822735 CAGGATGACAATCACAACAGGTT 59.177 43.478 0.00 0.00 39.69 3.50
113 114 3.822735 AGGATGACAATCACAACAGGTTG 59.177 43.478 10.45 10.45 45.58 3.77
114 115 3.820467 GGATGACAATCACAACAGGTTGA 59.180 43.478 18.28 0.00 43.24 3.18
115 116 4.278170 GGATGACAATCACAACAGGTTGAA 59.722 41.667 18.28 6.78 43.24 2.69
116 117 5.047802 GGATGACAATCACAACAGGTTGAAT 60.048 40.000 18.28 8.62 43.24 2.57
117 118 5.185668 TGACAATCACAACAGGTTGAATG 57.814 39.130 18.28 12.37 42.93 2.67
118 119 4.037803 TGACAATCACAACAGGTTGAATGG 59.962 41.667 18.28 10.85 42.93 3.16
119 120 3.960102 ACAATCACAACAGGTTGAATGGT 59.040 39.130 18.28 11.39 42.93 3.55
120 121 5.136828 ACAATCACAACAGGTTGAATGGTA 58.863 37.500 18.28 0.00 42.93 3.25
121 122 5.009610 ACAATCACAACAGGTTGAATGGTAC 59.990 40.000 18.28 0.00 42.93 3.34
122 123 3.135225 TCACAACAGGTTGAATGGTACG 58.865 45.455 18.28 0.00 42.93 3.67
123 124 3.135225 CACAACAGGTTGAATGGTACGA 58.865 45.455 18.28 0.00 42.93 3.43
124 125 3.751175 CACAACAGGTTGAATGGTACGAT 59.249 43.478 18.28 0.00 42.93 3.73
125 126 4.000988 ACAACAGGTTGAATGGTACGATC 58.999 43.478 18.28 0.00 42.93 3.69
126 127 3.261981 ACAGGTTGAATGGTACGATCC 57.738 47.619 0.00 0.00 0.00 3.36
127 128 2.093128 ACAGGTTGAATGGTACGATCCC 60.093 50.000 0.00 0.00 0.00 3.85
128 129 1.489230 AGGTTGAATGGTACGATCCCC 59.511 52.381 0.00 0.00 0.00 4.81
129 130 1.578583 GTTGAATGGTACGATCCCCG 58.421 55.000 0.00 0.00 45.44 5.73
130 131 0.179067 TTGAATGGTACGATCCCCGC 60.179 55.000 0.00 0.00 43.32 6.13
131 132 1.663702 GAATGGTACGATCCCCGCG 60.664 63.158 0.00 0.00 43.32 6.46
132 133 2.359570 GAATGGTACGATCCCCGCGT 62.360 60.000 4.92 0.00 45.01 6.01
133 134 1.963464 AATGGTACGATCCCCGCGTT 61.963 55.000 4.92 0.00 42.62 4.84
134 135 2.279054 GGTACGATCCCCGCGTTC 60.279 66.667 4.92 0.00 42.62 3.95
135 136 2.779033 GGTACGATCCCCGCGTTCT 61.779 63.158 4.92 0.00 42.62 3.01
136 137 1.298938 GTACGATCCCCGCGTTCTC 60.299 63.158 4.92 0.00 42.62 2.87
137 138 2.484062 TACGATCCCCGCGTTCTCC 61.484 63.158 4.92 0.00 42.62 3.71
138 139 2.898920 TACGATCCCCGCGTTCTCCT 62.899 60.000 4.92 0.00 42.62 3.69
139 140 2.107141 GATCCCCGCGTTCTCCTG 59.893 66.667 4.92 0.00 0.00 3.86
140 141 2.363795 ATCCCCGCGTTCTCCTGA 60.364 61.111 4.92 0.00 0.00 3.86
141 142 1.749334 GATCCCCGCGTTCTCCTGAT 61.749 60.000 4.92 0.00 0.00 2.90
142 143 2.032860 ATCCCCGCGTTCTCCTGATG 62.033 60.000 4.92 0.00 0.00 3.07
143 144 2.892425 CCCGCGTTCTCCTGATGC 60.892 66.667 4.92 0.00 0.00 3.91
144 145 2.892425 CCGCGTTCTCCTGATGCC 60.892 66.667 4.92 0.00 0.00 4.40
145 146 2.892425 CGCGTTCTCCTGATGCCC 60.892 66.667 0.00 0.00 0.00 5.36
146 147 2.514824 GCGTTCTCCTGATGCCCC 60.515 66.667 0.00 0.00 0.00 5.80
147 148 2.989639 CGTTCTCCTGATGCCCCA 59.010 61.111 0.00 0.00 0.00 4.96
148 149 1.153289 CGTTCTCCTGATGCCCCAG 60.153 63.158 0.00 0.00 0.00 4.45
149 150 1.452833 GTTCTCCTGATGCCCCAGC 60.453 63.158 0.00 0.00 40.48 4.85
150 151 1.617536 TTCTCCTGATGCCCCAGCT 60.618 57.895 0.00 0.00 40.80 4.24
151 152 0.326522 TTCTCCTGATGCCCCAGCTA 60.327 55.000 0.00 0.00 40.80 3.32
152 153 1.050988 TCTCCTGATGCCCCAGCTAC 61.051 60.000 0.00 0.00 40.80 3.58
153 154 1.003442 TCCTGATGCCCCAGCTACT 59.997 57.895 0.00 0.00 40.80 2.57
154 155 1.147824 CCTGATGCCCCAGCTACTG 59.852 63.158 0.00 0.00 40.80 2.74
155 156 1.525535 CTGATGCCCCAGCTACTGC 60.526 63.158 0.00 0.00 40.80 4.40
165 166 3.257933 GCTACTGCTTTGCGTGCT 58.742 55.556 0.00 0.00 36.03 4.40
166 167 1.133458 GCTACTGCTTTGCGTGCTC 59.867 57.895 0.00 0.00 36.03 4.26
167 168 1.568612 GCTACTGCTTTGCGTGCTCA 61.569 55.000 0.00 0.00 36.03 4.26
168 169 1.081892 CTACTGCTTTGCGTGCTCAT 58.918 50.000 0.00 0.00 0.00 2.90
169 170 1.466167 CTACTGCTTTGCGTGCTCATT 59.534 47.619 0.00 0.00 0.00 2.57
170 171 0.670162 ACTGCTTTGCGTGCTCATTT 59.330 45.000 0.00 0.00 0.00 2.32
171 172 1.057636 CTGCTTTGCGTGCTCATTTG 58.942 50.000 0.00 0.00 0.00 2.32
172 173 0.385029 TGCTTTGCGTGCTCATTTGT 59.615 45.000 0.00 0.00 0.00 2.83
173 174 1.202394 TGCTTTGCGTGCTCATTTGTT 60.202 42.857 0.00 0.00 0.00 2.83
174 175 1.453148 GCTTTGCGTGCTCATTTGTTC 59.547 47.619 0.00 0.00 0.00 3.18
175 176 2.053627 CTTTGCGTGCTCATTTGTTCC 58.946 47.619 0.00 0.00 0.00 3.62
176 177 0.313672 TTGCGTGCTCATTTGTTCCC 59.686 50.000 0.00 0.00 0.00 3.97
177 178 0.537143 TGCGTGCTCATTTGTTCCCT 60.537 50.000 0.00 0.00 0.00 4.20
178 179 0.169009 GCGTGCTCATTTGTTCCCTC 59.831 55.000 0.00 0.00 0.00 4.30
179 180 1.813513 CGTGCTCATTTGTTCCCTCT 58.186 50.000 0.00 0.00 0.00 3.69
180 181 1.734465 CGTGCTCATTTGTTCCCTCTC 59.266 52.381 0.00 0.00 0.00 3.20
181 182 2.783135 GTGCTCATTTGTTCCCTCTCA 58.217 47.619 0.00 0.00 0.00 3.27
182 183 3.350833 GTGCTCATTTGTTCCCTCTCAT 58.649 45.455 0.00 0.00 0.00 2.90
183 184 3.376546 GTGCTCATTTGTTCCCTCTCATC 59.623 47.826 0.00 0.00 0.00 2.92
184 185 3.265221 TGCTCATTTGTTCCCTCTCATCT 59.735 43.478 0.00 0.00 0.00 2.90
185 186 4.263639 TGCTCATTTGTTCCCTCTCATCTT 60.264 41.667 0.00 0.00 0.00 2.40
186 187 4.704057 GCTCATTTGTTCCCTCTCATCTTT 59.296 41.667 0.00 0.00 0.00 2.52
187 188 5.392811 GCTCATTTGTTCCCTCTCATCTTTG 60.393 44.000 0.00 0.00 0.00 2.77
188 189 5.012239 TCATTTGTTCCCTCTCATCTTTGG 58.988 41.667 0.00 0.00 0.00 3.28
189 190 4.453480 TTTGTTCCCTCTCATCTTTGGT 57.547 40.909 0.00 0.00 0.00 3.67
190 191 4.453480 TTGTTCCCTCTCATCTTTGGTT 57.547 40.909 0.00 0.00 0.00 3.67
191 192 4.453480 TGTTCCCTCTCATCTTTGGTTT 57.547 40.909 0.00 0.00 0.00 3.27
192 193 4.398319 TGTTCCCTCTCATCTTTGGTTTC 58.602 43.478 0.00 0.00 0.00 2.78
193 194 3.721087 TCCCTCTCATCTTTGGTTTCC 57.279 47.619 0.00 0.00 0.00 3.13
194 195 3.260205 TCCCTCTCATCTTTGGTTTCCT 58.740 45.455 0.00 0.00 0.00 3.36
195 196 4.435137 TCCCTCTCATCTTTGGTTTCCTA 58.565 43.478 0.00 0.00 0.00 2.94
196 197 5.039645 TCCCTCTCATCTTTGGTTTCCTAT 58.960 41.667 0.00 0.00 0.00 2.57
197 198 5.131142 TCCCTCTCATCTTTGGTTTCCTATC 59.869 44.000 0.00 0.00 0.00 2.08
198 199 5.104360 CCCTCTCATCTTTGGTTTCCTATCA 60.104 44.000 0.00 0.00 0.00 2.15
199 200 6.054295 CCTCTCATCTTTGGTTTCCTATCAG 58.946 44.000 0.00 0.00 0.00 2.90
200 201 5.994250 TCTCATCTTTGGTTTCCTATCAGG 58.006 41.667 0.00 0.00 36.46 3.86
201 202 5.726308 TCTCATCTTTGGTTTCCTATCAGGA 59.274 40.000 0.00 0.00 44.10 3.86
214 215 7.979444 TTCCTATCAGGAACAAACTTAACTG 57.021 36.000 3.48 0.00 46.88 3.16
215 216 6.472887 TCCTATCAGGAACAAACTTAACTGG 58.527 40.000 0.00 0.00 42.51 4.00
216 217 5.648092 CCTATCAGGAACAAACTTAACTGGG 59.352 44.000 0.00 0.00 37.67 4.45
217 218 3.219281 TCAGGAACAAACTTAACTGGGC 58.781 45.455 0.00 0.00 0.00 5.36
218 219 2.296190 CAGGAACAAACTTAACTGGGCC 59.704 50.000 0.00 0.00 0.00 5.80
219 220 1.616865 GGAACAAACTTAACTGGGCCC 59.383 52.381 17.59 17.59 0.00 5.80
220 221 2.594131 GAACAAACTTAACTGGGCCCT 58.406 47.619 25.70 5.02 0.00 5.19
221 222 2.767644 ACAAACTTAACTGGGCCCTT 57.232 45.000 25.70 12.93 0.00 3.95
222 223 3.040655 ACAAACTTAACTGGGCCCTTT 57.959 42.857 25.70 18.47 0.00 3.11
223 224 3.380393 ACAAACTTAACTGGGCCCTTTT 58.620 40.909 25.70 18.08 0.00 2.27
224 225 3.778075 ACAAACTTAACTGGGCCCTTTTT 59.222 39.130 25.70 15.42 0.00 1.94
225 226 4.963628 ACAAACTTAACTGGGCCCTTTTTA 59.036 37.500 25.70 14.35 0.00 1.52
226 227 5.425862 ACAAACTTAACTGGGCCCTTTTTAA 59.574 36.000 25.70 20.28 0.00 1.52
227 228 6.100569 ACAAACTTAACTGGGCCCTTTTTAAT 59.899 34.615 25.70 6.94 0.00 1.40
228 229 5.738619 ACTTAACTGGGCCCTTTTTAATG 57.261 39.130 25.70 16.74 0.00 1.90
229 230 4.530553 ACTTAACTGGGCCCTTTTTAATGG 59.469 41.667 25.70 13.78 0.00 3.16
230 231 3.268034 AACTGGGCCCTTTTTAATGGA 57.732 42.857 25.70 0.00 0.00 3.41
231 232 2.536066 ACTGGGCCCTTTTTAATGGAC 58.464 47.619 25.70 0.00 0.00 4.02
232 233 1.476488 CTGGGCCCTTTTTAATGGACG 59.524 52.381 25.70 0.00 0.00 4.79
233 234 0.821517 GGGCCCTTTTTAATGGACGG 59.178 55.000 17.04 0.00 0.00 4.79
234 235 1.617533 GGGCCCTTTTTAATGGACGGA 60.618 52.381 17.04 0.00 0.00 4.69
235 236 1.475280 GGCCCTTTTTAATGGACGGAC 59.525 52.381 0.00 0.00 0.00 4.79
236 237 2.443416 GCCCTTTTTAATGGACGGACT 58.557 47.619 0.00 0.00 0.00 3.85
237 238 2.823747 GCCCTTTTTAATGGACGGACTT 59.176 45.455 0.00 0.00 0.00 3.01
238 239 3.366985 GCCCTTTTTAATGGACGGACTTG 60.367 47.826 0.00 0.00 0.00 3.16
239 240 3.366985 CCCTTTTTAATGGACGGACTTGC 60.367 47.826 0.00 0.00 0.00 4.01
240 241 3.506067 CCTTTTTAATGGACGGACTTGCT 59.494 43.478 0.00 0.00 0.00 3.91
241 242 4.475944 CTTTTTAATGGACGGACTTGCTG 58.524 43.478 0.00 0.00 0.00 4.41
242 243 3.410631 TTTAATGGACGGACTTGCTGA 57.589 42.857 0.00 0.00 0.00 4.26
243 244 2.672961 TAATGGACGGACTTGCTGAG 57.327 50.000 0.00 0.00 0.00 3.35
244 245 0.036010 AATGGACGGACTTGCTGAGG 60.036 55.000 0.00 0.00 0.00 3.86
245 246 1.194781 ATGGACGGACTTGCTGAGGT 61.195 55.000 0.00 0.00 0.00 3.85
246 247 0.541063 TGGACGGACTTGCTGAGGTA 60.541 55.000 0.00 0.00 0.00 3.08
287 288 2.954318 CCTGAGGGCGAAATCAAATCAT 59.046 45.455 0.00 0.00 0.00 2.45
333 334 2.125512 CTCGGCTGACCCTTTCGG 60.126 66.667 0.00 0.00 37.81 4.30
429 430 1.604593 GCAGCCATGGTCCAGTTGT 60.605 57.895 14.67 0.00 0.00 3.32
435 436 3.224007 ATGGTCCAGTTGTGGCCCC 62.224 63.158 0.00 0.00 41.74 5.80
685 688 4.263550 CGATCTCCAATCCCTCCTACTAGA 60.264 50.000 0.00 0.00 0.00 2.43
743 746 4.636249 TGCGTTGCAATTTTAGGGATTTT 58.364 34.783 0.59 0.00 34.76 1.82
1147 1157 8.671921 AGATGAACACATATGAAATGTTGAGTC 58.328 33.333 10.38 7.36 36.70 3.36
1279 1289 4.499188 CGCGAGAAGGAGATGGTAATAACA 60.499 45.833 0.00 0.00 0.00 2.41
1514 1524 1.414181 CTGAACACTCCACTGGTGTCT 59.586 52.381 0.00 0.00 45.64 3.41
1806 1816 1.666553 CACTTTGCGACGTGCCCTA 60.667 57.895 0.00 0.00 45.60 3.53
1910 1920 0.674581 CTGGCAAGAACGCTCCATGA 60.675 55.000 0.00 0.00 0.00 3.07
2176 2186 2.280797 GTCTGCCTGTTGGACGCA 60.281 61.111 0.00 0.00 34.57 5.24
2496 2508 1.647545 ATCAACCCGATGTGCTTGCG 61.648 55.000 0.00 0.00 31.20 4.85
2549 2563 2.357009 CTGATATGCAACTGGGCTGTTC 59.643 50.000 0.00 0.00 34.04 3.18
2667 2681 6.782082 AGAGAGTGTATTGACTAAGCATCA 57.218 37.500 0.00 0.00 0.00 3.07
3532 3552 3.427503 CCGGTCTTCACCATATTGTTTGC 60.428 47.826 0.00 0.00 44.02 3.68
3535 3555 5.123186 CGGTCTTCACCATATTGTTTGCTTA 59.877 40.000 0.00 0.00 44.02 3.09
3787 3813 1.353694 AGAAGAAGATTGCCTGCAGGT 59.646 47.619 32.81 14.76 37.57 4.00
3900 3926 9.693739 AGGTTATGTTATATGTTGGTGAATTCA 57.306 29.630 3.38 3.38 0.00 2.57
3994 4020 2.864968 CCTCGTCTCTTTACCGAAGTG 58.135 52.381 0.00 0.00 36.70 3.16
4425 4451 5.530915 GCAGGTGGATATATTAGTGCAAACA 59.469 40.000 0.00 0.00 0.00 2.83
5289 5317 2.553247 GGGCCTAACTGTTCTCTTTGCT 60.553 50.000 0.84 0.00 0.00 3.91
5960 6581 4.358841 CGTGGCCCATTGGTCCCA 62.359 66.667 0.00 4.34 34.32 4.37
6013 6634 2.355115 GAACCGGGACCAATGCCT 59.645 61.111 6.32 0.00 33.05 4.75
6263 6921 2.018727 TATGTGCGTATTCCGGCCGT 62.019 55.000 26.12 8.42 36.94 5.68
6762 7422 2.332063 ATTCGTATGTGGGCTGGAAG 57.668 50.000 0.00 0.00 0.00 3.46
7272 7936 2.692368 GCCCCTCACCCTGGATCA 60.692 66.667 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.618690 ACTAGCTTCCAACCTAGCAAG 57.381 47.619 0.00 0.00 39.85 4.01
12 13 4.714802 TGATACTAGCTTCCAACCTAGCAA 59.285 41.667 0.00 0.00 39.85 3.91
13 14 4.286707 TGATACTAGCTTCCAACCTAGCA 58.713 43.478 0.00 0.00 39.85 3.49
14 15 4.342665 ACTGATACTAGCTTCCAACCTAGC 59.657 45.833 0.00 0.00 35.55 3.42
15 16 6.472686 AACTGATACTAGCTTCCAACCTAG 57.527 41.667 0.00 0.00 37.61 3.02
16 17 6.550108 CCTAACTGATACTAGCTTCCAACCTA 59.450 42.308 0.00 0.00 0.00 3.08
17 18 5.364157 CCTAACTGATACTAGCTTCCAACCT 59.636 44.000 0.00 0.00 0.00 3.50
18 19 5.128991 ACCTAACTGATACTAGCTTCCAACC 59.871 44.000 0.00 0.00 0.00 3.77
19 20 6.223351 ACCTAACTGATACTAGCTTCCAAC 57.777 41.667 0.00 0.00 0.00 3.77
20 21 6.640518 CAACCTAACTGATACTAGCTTCCAA 58.359 40.000 0.00 0.00 0.00 3.53
21 22 5.395324 GCAACCTAACTGATACTAGCTTCCA 60.395 44.000 0.00 0.00 0.00 3.53
22 23 5.051153 GCAACCTAACTGATACTAGCTTCC 58.949 45.833 0.00 0.00 0.00 3.46
23 24 5.661458 TGCAACCTAACTGATACTAGCTTC 58.339 41.667 0.00 0.00 0.00 3.86
24 25 5.677319 TGCAACCTAACTGATACTAGCTT 57.323 39.130 0.00 0.00 0.00 3.74
25 26 5.221541 GGATGCAACCTAACTGATACTAGCT 60.222 44.000 5.61 0.00 0.00 3.32
26 27 4.991687 GGATGCAACCTAACTGATACTAGC 59.008 45.833 5.61 0.00 0.00 3.42
27 28 5.986135 GTGGATGCAACCTAACTGATACTAG 59.014 44.000 14.77 0.00 0.00 2.57
28 29 5.661312 AGTGGATGCAACCTAACTGATACTA 59.339 40.000 14.77 0.00 0.00 1.82
29 30 4.471386 AGTGGATGCAACCTAACTGATACT 59.529 41.667 14.77 3.67 0.00 2.12
30 31 4.770795 AGTGGATGCAACCTAACTGATAC 58.229 43.478 14.77 1.25 0.00 2.24
31 32 6.156256 ACTTAGTGGATGCAACCTAACTGATA 59.844 38.462 14.77 0.87 0.00 2.15
32 33 5.045578 ACTTAGTGGATGCAACCTAACTGAT 60.046 40.000 14.77 0.00 0.00 2.90
33 34 4.286032 ACTTAGTGGATGCAACCTAACTGA 59.714 41.667 14.77 6.22 0.00 3.41
34 35 4.393062 CACTTAGTGGATGCAACCTAACTG 59.607 45.833 14.77 2.50 0.00 3.16
35 36 4.579869 CACTTAGTGGATGCAACCTAACT 58.420 43.478 14.77 12.27 0.00 2.24
36 37 4.946784 CACTTAGTGGATGCAACCTAAC 57.053 45.455 14.77 4.98 0.00 2.34
49 50 0.984230 TCTTCAGCCCCCACTTAGTG 59.016 55.000 5.22 5.22 0.00 2.74
50 51 0.984995 GTCTTCAGCCCCCACTTAGT 59.015 55.000 0.00 0.00 0.00 2.24
51 52 1.065854 CAGTCTTCAGCCCCCACTTAG 60.066 57.143 0.00 0.00 0.00 2.18
52 53 0.984230 CAGTCTTCAGCCCCCACTTA 59.016 55.000 0.00 0.00 0.00 2.24
53 54 1.763770 CAGTCTTCAGCCCCCACTT 59.236 57.895 0.00 0.00 0.00 3.16
54 55 2.900106 GCAGTCTTCAGCCCCCACT 61.900 63.158 0.00 0.00 0.00 4.00
55 56 2.360475 GCAGTCTTCAGCCCCCAC 60.360 66.667 0.00 0.00 0.00 4.61
56 57 2.530151 AGCAGTCTTCAGCCCCCA 60.530 61.111 0.00 0.00 0.00 4.96
57 58 2.045536 CAGCAGTCTTCAGCCCCC 60.046 66.667 0.00 0.00 0.00 5.40
58 59 2.045536 CCAGCAGTCTTCAGCCCC 60.046 66.667 0.00 0.00 0.00 5.80
59 60 2.749441 GCCAGCAGTCTTCAGCCC 60.749 66.667 0.00 0.00 0.00 5.19
60 61 2.749441 GGCCAGCAGTCTTCAGCC 60.749 66.667 0.00 0.00 0.00 4.85
61 62 3.123620 CGGCCAGCAGTCTTCAGC 61.124 66.667 2.24 0.00 0.00 4.26
62 63 1.302033 AACGGCCAGCAGTCTTCAG 60.302 57.895 2.24 0.00 0.00 3.02
63 64 1.597854 CAACGGCCAGCAGTCTTCA 60.598 57.895 2.24 0.00 0.00 3.02
64 65 1.166531 AACAACGGCCAGCAGTCTTC 61.167 55.000 2.24 0.00 0.00 2.87
65 66 1.152963 AACAACGGCCAGCAGTCTT 60.153 52.632 2.24 0.00 0.00 3.01
66 67 1.893808 CAACAACGGCCAGCAGTCT 60.894 57.895 2.24 0.00 0.00 3.24
67 68 1.891919 TCAACAACGGCCAGCAGTC 60.892 57.895 2.24 0.00 0.00 3.51
68 69 2.186826 GTCAACAACGGCCAGCAGT 61.187 57.895 2.24 0.00 0.00 4.40
69 70 2.639286 GTCAACAACGGCCAGCAG 59.361 61.111 2.24 0.00 0.00 4.24
78 79 1.461127 GTCATCCTGCTCGTCAACAAC 59.539 52.381 0.00 0.00 0.00 3.32
79 80 1.069978 TGTCATCCTGCTCGTCAACAA 59.930 47.619 0.00 0.00 0.00 2.83
80 81 0.678950 TGTCATCCTGCTCGTCAACA 59.321 50.000 0.00 0.00 0.00 3.33
81 82 1.795768 TTGTCATCCTGCTCGTCAAC 58.204 50.000 0.00 0.00 0.00 3.18
82 83 2.028203 TGATTGTCATCCTGCTCGTCAA 60.028 45.455 0.00 0.00 0.00 3.18
83 84 1.550072 TGATTGTCATCCTGCTCGTCA 59.450 47.619 0.00 0.00 0.00 4.35
84 85 1.929836 GTGATTGTCATCCTGCTCGTC 59.070 52.381 0.00 0.00 0.00 4.20
85 86 1.276138 TGTGATTGTCATCCTGCTCGT 59.724 47.619 0.00 0.00 0.00 4.18
86 87 2.014335 TGTGATTGTCATCCTGCTCG 57.986 50.000 0.00 0.00 0.00 5.03
87 88 3.076621 TGTTGTGATTGTCATCCTGCTC 58.923 45.455 0.00 0.00 0.00 4.26
88 89 3.079578 CTGTTGTGATTGTCATCCTGCT 58.920 45.455 0.00 0.00 0.00 4.24
89 90 2.163010 CCTGTTGTGATTGTCATCCTGC 59.837 50.000 0.00 0.00 0.00 4.85
90 91 3.415212 ACCTGTTGTGATTGTCATCCTG 58.585 45.455 0.00 0.00 0.00 3.86
91 92 3.795688 ACCTGTTGTGATTGTCATCCT 57.204 42.857 0.00 0.00 0.00 3.24
92 93 3.820467 TCAACCTGTTGTGATTGTCATCC 59.180 43.478 9.65 0.00 41.16 3.51
93 94 5.437289 TTCAACCTGTTGTGATTGTCATC 57.563 39.130 9.65 0.00 41.16 2.92
94 95 5.279106 CCATTCAACCTGTTGTGATTGTCAT 60.279 40.000 9.65 0.00 41.16 3.06
95 96 4.037803 CCATTCAACCTGTTGTGATTGTCA 59.962 41.667 9.65 0.00 41.16 3.58
96 97 4.037923 ACCATTCAACCTGTTGTGATTGTC 59.962 41.667 9.65 0.00 41.16 3.18
97 98 3.960102 ACCATTCAACCTGTTGTGATTGT 59.040 39.130 9.65 5.40 41.16 2.71
98 99 4.589216 ACCATTCAACCTGTTGTGATTG 57.411 40.909 9.65 4.89 41.16 2.67
99 100 4.215399 CGTACCATTCAACCTGTTGTGATT 59.785 41.667 9.65 0.00 41.16 2.57
100 101 3.751175 CGTACCATTCAACCTGTTGTGAT 59.249 43.478 9.65 3.56 41.16 3.06
101 102 3.135225 CGTACCATTCAACCTGTTGTGA 58.865 45.455 9.65 1.49 41.16 3.58
102 103 3.135225 TCGTACCATTCAACCTGTTGTG 58.865 45.455 9.65 2.42 41.16 3.33
103 104 3.478857 TCGTACCATTCAACCTGTTGT 57.521 42.857 9.65 0.00 41.16 3.32
104 105 3.374058 GGATCGTACCATTCAACCTGTTG 59.626 47.826 3.61 3.61 41.71 3.33
105 106 3.606687 GGATCGTACCATTCAACCTGTT 58.393 45.455 0.00 0.00 0.00 3.16
106 107 2.093128 GGGATCGTACCATTCAACCTGT 60.093 50.000 0.00 0.00 0.00 4.00
107 108 2.561569 GGGATCGTACCATTCAACCTG 58.438 52.381 0.00 0.00 0.00 4.00
108 109 1.489230 GGGGATCGTACCATTCAACCT 59.511 52.381 0.00 0.00 0.00 3.50
109 110 1.808891 CGGGGATCGTACCATTCAACC 60.809 57.143 0.00 0.00 0.00 3.77
110 111 1.578583 CGGGGATCGTACCATTCAAC 58.421 55.000 0.00 0.00 0.00 3.18
111 112 0.179067 GCGGGGATCGTACCATTCAA 60.179 55.000 0.00 0.00 41.72 2.69
112 113 1.444250 GCGGGGATCGTACCATTCA 59.556 57.895 0.00 0.00 41.72 2.57
113 114 1.663702 CGCGGGGATCGTACCATTC 60.664 63.158 0.00 0.00 41.72 2.67
114 115 1.963464 AACGCGGGGATCGTACCATT 61.963 55.000 12.47 0.00 39.48 3.16
115 116 2.359570 GAACGCGGGGATCGTACCAT 62.360 60.000 12.47 0.00 39.48 3.55
116 117 3.067480 GAACGCGGGGATCGTACCA 62.067 63.158 12.47 0.00 39.48 3.25
117 118 2.279054 GAACGCGGGGATCGTACC 60.279 66.667 12.47 0.00 39.48 3.34
118 119 1.298938 GAGAACGCGGGGATCGTAC 60.299 63.158 12.47 0.00 39.48 3.67
119 120 2.484062 GGAGAACGCGGGGATCGTA 61.484 63.158 12.47 0.00 39.48 3.43
120 121 3.834799 GGAGAACGCGGGGATCGT 61.835 66.667 12.47 0.00 42.54 3.73
121 122 3.528370 AGGAGAACGCGGGGATCG 61.528 66.667 12.47 0.00 42.76 3.69
122 123 1.749334 ATCAGGAGAACGCGGGGATC 61.749 60.000 12.47 2.95 0.00 3.36
123 124 1.762460 ATCAGGAGAACGCGGGGAT 60.762 57.895 12.47 0.00 0.00 3.85
124 125 2.363795 ATCAGGAGAACGCGGGGA 60.364 61.111 12.47 0.00 0.00 4.81
125 126 2.202932 CATCAGGAGAACGCGGGG 60.203 66.667 12.47 0.00 0.00 5.73
126 127 2.892425 GCATCAGGAGAACGCGGG 60.892 66.667 12.47 0.00 0.00 6.13
127 128 2.892425 GGCATCAGGAGAACGCGG 60.892 66.667 12.47 0.00 0.00 6.46
128 129 2.892425 GGGCATCAGGAGAACGCG 60.892 66.667 3.53 3.53 0.00 6.01
129 130 2.514824 GGGGCATCAGGAGAACGC 60.515 66.667 0.00 0.00 0.00 4.84
130 131 1.153289 CTGGGGCATCAGGAGAACG 60.153 63.158 0.00 0.00 0.00 3.95
131 132 1.452833 GCTGGGGCATCAGGAGAAC 60.453 63.158 8.74 0.00 38.54 3.01
132 133 0.326522 TAGCTGGGGCATCAGGAGAA 60.327 55.000 0.00 0.00 41.70 2.87
133 134 1.050988 GTAGCTGGGGCATCAGGAGA 61.051 60.000 0.00 0.00 41.70 3.71
134 135 1.053264 AGTAGCTGGGGCATCAGGAG 61.053 60.000 0.00 0.00 41.70 3.69
135 136 1.003442 AGTAGCTGGGGCATCAGGA 59.997 57.895 0.00 0.00 41.70 3.86
136 137 1.147824 CAGTAGCTGGGGCATCAGG 59.852 63.158 0.00 0.00 41.70 3.86
137 138 1.525535 GCAGTAGCTGGGGCATCAG 60.526 63.158 0.00 3.18 41.70 2.90
138 139 2.591753 GCAGTAGCTGGGGCATCA 59.408 61.111 0.00 0.00 41.70 3.07
148 149 1.133458 GAGCACGCAAAGCAGTAGC 59.867 57.895 0.00 0.00 42.56 3.58
149 150 1.081892 ATGAGCACGCAAAGCAGTAG 58.918 50.000 0.00 0.00 0.00 2.57
150 151 1.522668 AATGAGCACGCAAAGCAGTA 58.477 45.000 0.00 0.00 0.00 2.74
151 152 0.670162 AAATGAGCACGCAAAGCAGT 59.330 45.000 0.00 0.00 0.00 4.40
152 153 1.057636 CAAATGAGCACGCAAAGCAG 58.942 50.000 0.00 0.00 0.00 4.24
153 154 0.385029 ACAAATGAGCACGCAAAGCA 59.615 45.000 0.00 0.00 0.00 3.91
154 155 1.453148 GAACAAATGAGCACGCAAAGC 59.547 47.619 0.00 0.00 0.00 3.51
155 156 2.053627 GGAACAAATGAGCACGCAAAG 58.946 47.619 0.00 0.00 0.00 2.77
156 157 1.269517 GGGAACAAATGAGCACGCAAA 60.270 47.619 0.00 0.00 0.00 3.68
157 158 0.313672 GGGAACAAATGAGCACGCAA 59.686 50.000 0.00 0.00 0.00 4.85
158 159 0.537143 AGGGAACAAATGAGCACGCA 60.537 50.000 0.00 0.00 0.00 5.24
159 160 0.169009 GAGGGAACAAATGAGCACGC 59.831 55.000 0.00 0.00 0.00 5.34
160 161 1.734465 GAGAGGGAACAAATGAGCACG 59.266 52.381 0.00 0.00 0.00 5.34
161 162 2.783135 TGAGAGGGAACAAATGAGCAC 58.217 47.619 0.00 0.00 0.00 4.40
162 163 3.265221 AGATGAGAGGGAACAAATGAGCA 59.735 43.478 0.00 0.00 0.00 4.26
163 164 3.883669 AGATGAGAGGGAACAAATGAGC 58.116 45.455 0.00 0.00 0.00 4.26
164 165 5.125097 CCAAAGATGAGAGGGAACAAATGAG 59.875 44.000 0.00 0.00 0.00 2.90
165 166 5.012239 CCAAAGATGAGAGGGAACAAATGA 58.988 41.667 0.00 0.00 0.00 2.57
166 167 4.768968 ACCAAAGATGAGAGGGAACAAATG 59.231 41.667 0.00 0.00 0.00 2.32
167 168 5.003096 ACCAAAGATGAGAGGGAACAAAT 57.997 39.130 0.00 0.00 0.00 2.32
168 169 4.453480 ACCAAAGATGAGAGGGAACAAA 57.547 40.909 0.00 0.00 0.00 2.83
169 170 4.453480 AACCAAAGATGAGAGGGAACAA 57.547 40.909 0.00 0.00 0.00 2.83
170 171 4.398319 GAAACCAAAGATGAGAGGGAACA 58.602 43.478 0.00 0.00 0.00 3.18
171 172 3.759086 GGAAACCAAAGATGAGAGGGAAC 59.241 47.826 0.00 0.00 0.00 3.62
172 173 3.657727 AGGAAACCAAAGATGAGAGGGAA 59.342 43.478 0.00 0.00 0.00 3.97
173 174 3.260205 AGGAAACCAAAGATGAGAGGGA 58.740 45.455 0.00 0.00 0.00 4.20
174 175 3.728385 AGGAAACCAAAGATGAGAGGG 57.272 47.619 0.00 0.00 0.00 4.30
175 176 5.994250 TGATAGGAAACCAAAGATGAGAGG 58.006 41.667 0.00 0.00 0.00 3.69
176 177 6.054295 CCTGATAGGAAACCAAAGATGAGAG 58.946 44.000 0.00 0.00 37.67 3.20
177 178 5.726308 TCCTGATAGGAAACCAAAGATGAGA 59.274 40.000 0.00 0.00 42.51 3.27
178 179 5.994250 TCCTGATAGGAAACCAAAGATGAG 58.006 41.667 0.00 0.00 42.51 2.90
191 192 6.472887 CCAGTTAAGTTTGTTCCTGATAGGA 58.527 40.000 0.00 0.00 44.10 2.94
192 193 5.648092 CCCAGTTAAGTTTGTTCCTGATAGG 59.352 44.000 0.00 0.00 36.46 2.57
193 194 5.123979 GCCCAGTTAAGTTTGTTCCTGATAG 59.876 44.000 0.00 0.00 0.00 2.08
194 195 5.007682 GCCCAGTTAAGTTTGTTCCTGATA 58.992 41.667 0.00 0.00 0.00 2.15
195 196 3.826729 GCCCAGTTAAGTTTGTTCCTGAT 59.173 43.478 0.00 0.00 0.00 2.90
196 197 3.219281 GCCCAGTTAAGTTTGTTCCTGA 58.781 45.455 0.00 0.00 0.00 3.86
197 198 2.296190 GGCCCAGTTAAGTTTGTTCCTG 59.704 50.000 0.00 0.00 0.00 3.86
198 199 2.594131 GGCCCAGTTAAGTTTGTTCCT 58.406 47.619 0.00 0.00 0.00 3.36
199 200 1.616865 GGGCCCAGTTAAGTTTGTTCC 59.383 52.381 19.95 0.00 0.00 3.62
200 201 2.594131 AGGGCCCAGTTAAGTTTGTTC 58.406 47.619 27.56 0.00 0.00 3.18
201 202 2.767644 AGGGCCCAGTTAAGTTTGTT 57.232 45.000 27.56 0.00 0.00 2.83
202 203 2.767644 AAGGGCCCAGTTAAGTTTGT 57.232 45.000 27.56 0.00 0.00 2.83
203 204 4.415881 AAAAAGGGCCCAGTTAAGTTTG 57.584 40.909 27.56 0.00 0.00 2.93
204 205 6.465178 CCATTAAAAAGGGCCCAGTTAAGTTT 60.465 38.462 27.56 11.13 0.00 2.66
205 206 5.012664 CCATTAAAAAGGGCCCAGTTAAGTT 59.987 40.000 27.56 11.27 0.00 2.66
206 207 4.530553 CCATTAAAAAGGGCCCAGTTAAGT 59.469 41.667 27.56 11.45 0.00 2.24
207 208 4.775253 TCCATTAAAAAGGGCCCAGTTAAG 59.225 41.667 27.56 16.07 0.00 1.85
208 209 4.528987 GTCCATTAAAAAGGGCCCAGTTAA 59.471 41.667 27.56 23.15 0.00 2.01
209 210 4.090819 GTCCATTAAAAAGGGCCCAGTTA 58.909 43.478 27.56 15.86 0.00 2.24
210 211 2.903784 GTCCATTAAAAAGGGCCCAGTT 59.096 45.455 27.56 15.37 0.00 3.16
211 212 2.536066 GTCCATTAAAAAGGGCCCAGT 58.464 47.619 27.56 8.72 0.00 4.00
212 213 1.476488 CGTCCATTAAAAAGGGCCCAG 59.524 52.381 27.56 2.48 0.00 4.45
213 214 1.551452 CGTCCATTAAAAAGGGCCCA 58.449 50.000 27.56 0.78 0.00 5.36
214 215 0.821517 CCGTCCATTAAAAAGGGCCC 59.178 55.000 16.46 16.46 0.00 5.80
215 216 1.475280 GTCCGTCCATTAAAAAGGGCC 59.525 52.381 0.00 0.00 0.00 5.80
216 217 2.443416 AGTCCGTCCATTAAAAAGGGC 58.557 47.619 0.00 0.00 0.00 5.19
217 218 3.366985 GCAAGTCCGTCCATTAAAAAGGG 60.367 47.826 0.00 0.00 0.00 3.95
218 219 3.506067 AGCAAGTCCGTCCATTAAAAAGG 59.494 43.478 0.00 0.00 0.00 3.11
219 220 4.215399 TCAGCAAGTCCGTCCATTAAAAAG 59.785 41.667 0.00 0.00 0.00 2.27
220 221 4.138290 TCAGCAAGTCCGTCCATTAAAAA 58.862 39.130 0.00 0.00 0.00 1.94
221 222 3.745799 TCAGCAAGTCCGTCCATTAAAA 58.254 40.909 0.00 0.00 0.00 1.52
222 223 3.334691 CTCAGCAAGTCCGTCCATTAAA 58.665 45.455 0.00 0.00 0.00 1.52
223 224 2.354704 CCTCAGCAAGTCCGTCCATTAA 60.355 50.000 0.00 0.00 0.00 1.40
224 225 1.207089 CCTCAGCAAGTCCGTCCATTA 59.793 52.381 0.00 0.00 0.00 1.90
225 226 0.036010 CCTCAGCAAGTCCGTCCATT 60.036 55.000 0.00 0.00 0.00 3.16
226 227 1.194781 ACCTCAGCAAGTCCGTCCAT 61.195 55.000 0.00 0.00 0.00 3.41
227 228 0.541063 TACCTCAGCAAGTCCGTCCA 60.541 55.000 0.00 0.00 0.00 4.02
228 229 0.173708 CTACCTCAGCAAGTCCGTCC 59.826 60.000 0.00 0.00 0.00 4.79
229 230 3.723554 CTACCTCAGCAAGTCCGTC 57.276 57.895 0.00 0.00 0.00 4.79
239 240 7.496920 TCAAATATGTGATTTCTGCTACCTCAG 59.503 37.037 0.00 0.00 35.46 3.35
240 241 7.280876 GTCAAATATGTGATTTCTGCTACCTCA 59.719 37.037 0.00 0.00 0.00 3.86
241 242 7.254932 GGTCAAATATGTGATTTCTGCTACCTC 60.255 40.741 0.00 0.00 0.00 3.85
242 243 6.543831 GGTCAAATATGTGATTTCTGCTACCT 59.456 38.462 0.00 0.00 0.00 3.08
243 244 6.543831 AGGTCAAATATGTGATTTCTGCTACC 59.456 38.462 0.00 0.00 0.00 3.18
244 245 7.280876 TCAGGTCAAATATGTGATTTCTGCTAC 59.719 37.037 14.18 0.00 0.00 3.58
245 246 7.337938 TCAGGTCAAATATGTGATTTCTGCTA 58.662 34.615 14.18 2.42 0.00 3.49
246 247 6.182627 TCAGGTCAAATATGTGATTTCTGCT 58.817 36.000 14.18 0.00 0.00 4.24
287 288 5.821516 TTTTTCGAAAGCAGGTCAGTTTA 57.178 34.783 10.98 0.00 0.00 2.01
435 436 2.614446 GCTGCAGTGCTGTCTGTGG 61.614 63.158 21.31 1.81 37.70 4.17
625 628 1.138661 CTTCAGATCTGAGAGGGGTGC 59.861 57.143 23.92 0.00 41.13 5.01
685 688 3.844804 AGAAAGGGAACGGAGGAGTTTAT 59.155 43.478 0.00 0.00 34.00 1.40
1312 1322 9.434420 CAAATCTTAGGGCATGTAAATTTCAAA 57.566 29.630 0.00 0.00 0.00 2.69
1514 1524 1.078918 CCACCGATCAGCAAGAGCA 60.079 57.895 0.00 0.00 45.49 4.26
1806 1816 0.543277 ACATCATCAGTGGCATCCGT 59.457 50.000 0.00 0.00 0.00 4.69
1910 1920 0.537143 TCAACGCCTTCAGCCACATT 60.537 50.000 0.00 0.00 38.78 2.71
2176 2186 6.123852 AGGATTAAACCTGACGCTCTTCGT 62.124 45.833 3.01 0.00 42.88 3.85
2496 2508 2.037385 AAGCCAGAGATCCCTATCCC 57.963 55.000 0.00 0.00 31.98 3.85
2549 2563 1.987770 GCGATGTGGCAAATGAAACTG 59.012 47.619 0.00 0.00 0.00 3.16
2667 2681 7.395489 ACATTAGCAAAATCAAGAAGGACTGAT 59.605 33.333 0.00 0.00 0.00 2.90
2721 2735 1.485124 TATCTTCCGCTGCCTTCTCA 58.515 50.000 0.00 0.00 0.00 3.27
3274 3294 2.799978 CTGACGCTGTAACATGAACACA 59.200 45.455 0.00 0.00 0.00 3.72
3532 3552 3.008813 AGCTCATGGCCCTATCACATAAG 59.991 47.826 0.00 0.00 43.05 1.73
3535 3555 1.442773 AGCTCATGGCCCTATCACAT 58.557 50.000 0.00 0.00 43.05 3.21
3787 3813 2.203139 CGTGTTCCTGGTGCCACA 60.203 61.111 0.00 1.85 0.00 4.17
3900 3926 6.270064 GCAAACACAAATACCACACTAGTTT 58.730 36.000 0.00 0.00 0.00 2.66
3901 3927 5.504994 CGCAAACACAAATACCACACTAGTT 60.505 40.000 0.00 0.00 0.00 2.24
3994 4020 3.917760 CCCTCCGGATCGAGCACC 61.918 72.222 3.57 0.00 0.00 5.01
4144 4170 1.075601 AAGAAGGAGCCCATGGTGAA 58.924 50.000 11.73 0.00 0.00 3.18
4425 4451 4.129317 ACCCGGAATAAGCTAGGTCTAT 57.871 45.455 0.73 0.00 0.00 1.98
4787 4815 4.675029 CCCGTCTTCACCGCCGTT 62.675 66.667 0.00 0.00 0.00 4.44
5289 5317 2.228480 GGTCCAGTAGGCCCCACAA 61.228 63.158 0.00 0.00 33.74 3.33
5960 6581 1.152839 CCGGTTGGTGGGACAAACT 60.153 57.895 0.00 0.00 44.16 2.66
6039 6660 2.890766 ATTGGTCCCGGTTCGTGCT 61.891 57.895 0.00 0.00 0.00 4.40
6165 6791 4.409247 ACGGAGGGAGTATAGCAAAATCTT 59.591 41.667 0.00 0.00 0.00 2.40
6263 6921 9.459640 CTTAAGCTAGTTAATTGATACGCTACA 57.540 33.333 0.00 0.00 29.97 2.74
6762 7422 1.557443 CTGTCGACAACCAACTCGGC 61.557 60.000 20.49 0.00 39.03 5.54
6958 7622 2.017049 GCGTGATTGTAATTCCTGGCT 58.983 47.619 0.00 0.00 0.00 4.75
7107 7771 2.864343 CTGTTTCTTTCACGTCGAAGGT 59.136 45.455 0.00 0.00 34.32 3.50
7117 7781 5.053811 TGTCATACTTCGCTGTTTCTTTCA 58.946 37.500 0.00 0.00 0.00 2.69
7272 7936 1.606313 CAATGGTCCGGCACCCTTT 60.606 57.895 17.20 9.40 46.18 3.11


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

AutoCloner maintained by Alex Coulton.