Multiple sequence alignment - TraesCS2D01G306500

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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 TraesCS2D01G306500 chr2D 100.000 2273 0 0 1 2273 392363850 392361578 0.000000e+00 4198
1 TraesCS2D01G306500 chr2D 94.186 1204 36 6 1104 2273 106675011 106673808 0.000000e+00 1805
2 TraesCS2D01G306500 chr2D 94.034 1056 22 4 257 1303 106676026 106675003 0.000000e+00 1563
3 TraesCS2D01G306500 chr2D 90.271 442 29 4 1818 2245 589511850 589511409 1.180000e-157 566
4 TraesCS2D01G306500 chr3A 93.310 2033 80 13 252 2273 114696953 114694966 0.000000e+00 2950
5 TraesCS2D01G306500 chr3A 94.163 257 8 3 1 255 80426015 80426266 3.540000e-103 385
6 TraesCS2D01G306500 chr2B 93.114 2033 83 14 252 2273 347064308 347062322 0.000000e+00 2926
7 TraesCS2D01G306500 chr6A 93.075 2036 81 15 249 2273 445769645 445771631 0.000000e+00 2924
8 TraesCS2D01G306500 chr7B 93.996 1549 50 14 252 1792 119714127 119712614 0.000000e+00 2305
9 TraesCS2D01G306500 chr7B 91.623 1516 90 8 253 1767 584354006 584352527 0.000000e+00 2061
10 TraesCS2D01G306500 chr3D 92.358 1518 77 9 253 1767 595697629 595699110 0.000000e+00 2124
11 TraesCS2D01G306500 chr3D 88.219 713 39 14 253 963 29212945 29213614 0.000000e+00 809
12 TraesCS2D01G306500 chr3D 94.602 389 19 2 1859 2247 48420272 48420658 3.230000e-168 601
13 TraesCS2D01G306500 chr3D 93.798 258 8 3 1 256 38502629 38502378 4.580000e-102 381
14 TraesCS2D01G306500 chr4D 91.894 1542 85 11 253 1792 100773122 100774625 0.000000e+00 2119
15 TraesCS2D01G306500 chr4D 91.025 1415 88 11 380 1792 448176682 448178059 0.000000e+00 1873
16 TraesCS2D01G306500 chr3B 92.029 1518 82 10 253 1767 143539243 143540724 0.000000e+00 2097
17 TraesCS2D01G306500 chr1A 91.607 1525 81 16 253 1767 441748367 441749854 0.000000e+00 2063
18 TraesCS2D01G306500 chr1A 94.163 257 7 3 1 255 377649293 377649543 3.540000e-103 385
19 TraesCS2D01G306500 chr6D 92.117 444 21 4 1818 2247 127393069 127393512 4.150000e-172 614
20 TraesCS2D01G306500 chr6D 93.774 257 8 3 1 255 169574133 169573883 1.650000e-101 379
21 TraesCS2D01G306500 chr5D 95.116 389 18 1 1859 2247 314889519 314889132 1.490000e-171 612
22 TraesCS2D01G306500 chr5D 90.476 441 31 6 1818 2247 332125253 332124813 2.530000e-159 571
23 TraesCS2D01G306500 chr1D 91.879 431 34 1 1818 2247 259661244 259661674 3.230000e-168 601
24 TraesCS2D01G306500 chr4A 91.475 434 32 2 1818 2247 96447403 96447835 1.940000e-165 592
25 TraesCS2D01G306500 chr4A 94.553 257 6 3 1 255 204958341 204958091 7.610000e-105 390
26 TraesCS2D01G306500 chr7A 90.359 446 27 5 1818 2247 718528741 718529186 2.530000e-159 571
27 TraesCS2D01G306500 chr7A 90.023 431 41 2 1818 2247 81585344 81584915 7.090000e-155 556
28 TraesCS2D01G306500 chr2A 84.475 438 51 5 1817 2237 426368967 426369404 1.260000e-112 416
29 TraesCS2D01G306500 chr2A 94.186 258 7 3 1 256 312704950 312705201 9.850000e-104 387
30 TraesCS2D01G306500 chr6B 93.774 257 8 4 1 255 113737429 113737679 1.650000e-101 379
31 TraesCS2D01G306500 chr5A 93.798 258 7 4 1 255 320690422 320690171 1.650000e-101 379
32 TraesCS2D01G306500 chr7D 93.411 258 9 3 1 256 426188934 426189185 2.130000e-100 375


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 TraesCS2D01G306500 chr2D 392361578 392363850 2272 True 4198 4198 100.000 1 2273 1 chr2D.!!$R1 2272
1 TraesCS2D01G306500 chr2D 106673808 106676026 2218 True 1684 1805 94.110 257 2273 2 chr2D.!!$R3 2016
2 TraesCS2D01G306500 chr3A 114694966 114696953 1987 True 2950 2950 93.310 252 2273 1 chr3A.!!$R1 2021
3 TraesCS2D01G306500 chr2B 347062322 347064308 1986 True 2926 2926 93.114 252 2273 1 chr2B.!!$R1 2021
4 TraesCS2D01G306500 chr6A 445769645 445771631 1986 False 2924 2924 93.075 249 2273 1 chr6A.!!$F1 2024
5 TraesCS2D01G306500 chr7B 119712614 119714127 1513 True 2305 2305 93.996 252 1792 1 chr7B.!!$R1 1540
6 TraesCS2D01G306500 chr7B 584352527 584354006 1479 True 2061 2061 91.623 253 1767 1 chr7B.!!$R2 1514
7 TraesCS2D01G306500 chr3D 595697629 595699110 1481 False 2124 2124 92.358 253 1767 1 chr3D.!!$F3 1514
8 TraesCS2D01G306500 chr3D 29212945 29213614 669 False 809 809 88.219 253 963 1 chr3D.!!$F1 710
9 TraesCS2D01G306500 chr4D 100773122 100774625 1503 False 2119 2119 91.894 253 1792 1 chr4D.!!$F1 1539
10 TraesCS2D01G306500 chr4D 448176682 448178059 1377 False 1873 1873 91.025 380 1792 1 chr4D.!!$F2 1412
11 TraesCS2D01G306500 chr3B 143539243 143540724 1481 False 2097 2097 92.029 253 1767 1 chr3B.!!$F1 1514
12 TraesCS2D01G306500 chr1A 441748367 441749854 1487 False 2063 2063 91.607 253 1767 1 chr1A.!!$F2 1514

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
90 91 0.100861 GGAGTCCGTTAAGAGAGCCG 59.899 60.0 0.00 0.0 0.00 5.52 F
237 238 0.113580 TTGGGGTTGGGACTAAAGGC 59.886 55.0 0.00 0.0 0.00 4.35 F
663 669 0.314302 GCGGACCTGCGTGTCTATAT 59.686 55.0 5.53 0.0 35.54 0.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1082 1102 0.032952 CGACCTCCCGAAAGTGTTGA 59.967 55.0 0.00 0.00 0.00 3.18 R
1187 1207 0.464036 AAGCACAACGACTGGAGTCA 59.536 50.0 7.54 0.00 44.99 3.41 R
1659 1903 0.961019 TTCTGCCTTCCAATGTGCAC 59.039 50.0 10.75 10.75 0.00 4.57 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
24 25 3.849953 GCGGACGGCTAAAGCGTG 61.850 66.667 0.00 0.00 43.26 5.34
25 26 3.849953 CGGACGGCTAAAGCGTGC 61.850 66.667 0.00 0.00 43.26 5.34
26 27 2.740826 GGACGGCTAAAGCGTGCA 60.741 61.111 11.36 0.00 43.26 4.57
27 28 2.740714 GGACGGCTAAAGCGTGCAG 61.741 63.158 11.36 0.00 43.26 4.41
28 29 1.736645 GACGGCTAAAGCGTGCAGA 60.737 57.895 0.00 0.00 43.26 4.26
29 30 1.687494 GACGGCTAAAGCGTGCAGAG 61.687 60.000 0.00 0.00 43.26 3.35
30 31 1.446099 CGGCTAAAGCGTGCAGAGA 60.446 57.895 0.00 0.00 43.26 3.10
31 32 1.014044 CGGCTAAAGCGTGCAGAGAA 61.014 55.000 0.00 0.00 43.26 2.87
32 33 1.373570 GGCTAAAGCGTGCAGAGAAT 58.626 50.000 0.00 0.00 43.26 2.40
33 34 1.063174 GGCTAAAGCGTGCAGAGAATG 59.937 52.381 0.00 0.00 43.26 2.67
34 35 1.734465 GCTAAAGCGTGCAGAGAATGT 59.266 47.619 0.00 0.00 0.00 2.71
35 36 2.222908 GCTAAAGCGTGCAGAGAATGTC 60.223 50.000 0.00 0.00 0.00 3.06
36 37 1.882912 AAAGCGTGCAGAGAATGTCA 58.117 45.000 0.00 0.00 0.00 3.58
37 38 1.882912 AAGCGTGCAGAGAATGTCAA 58.117 45.000 0.00 0.00 0.00 3.18
38 39 1.436600 AGCGTGCAGAGAATGTCAAG 58.563 50.000 0.00 0.00 0.00 3.02
39 40 1.001293 AGCGTGCAGAGAATGTCAAGA 59.999 47.619 0.00 0.00 0.00 3.02
40 41 1.392853 GCGTGCAGAGAATGTCAAGAG 59.607 52.381 0.00 0.00 0.00 2.85
41 42 2.928301 GCGTGCAGAGAATGTCAAGAGA 60.928 50.000 0.00 0.00 0.00 3.10
42 43 2.922387 CGTGCAGAGAATGTCAAGAGAG 59.078 50.000 0.00 0.00 0.00 3.20
43 44 3.260740 GTGCAGAGAATGTCAAGAGAGG 58.739 50.000 0.00 0.00 0.00 3.69
44 45 2.235650 TGCAGAGAATGTCAAGAGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
45 46 2.903798 CAGAGAATGTCAAGAGAGGGC 58.096 52.381 0.00 0.00 0.00 5.19
46 47 1.480137 AGAGAATGTCAAGAGAGGGCG 59.520 52.381 0.00 0.00 0.00 6.13
47 48 0.539051 AGAATGTCAAGAGAGGGCGG 59.461 55.000 0.00 0.00 0.00 6.13
48 49 0.462759 GAATGTCAAGAGAGGGCGGG 60.463 60.000 0.00 0.00 0.00 6.13
49 50 1.915078 AATGTCAAGAGAGGGCGGGG 61.915 60.000 0.00 0.00 0.00 5.73
50 51 3.003763 GTCAAGAGAGGGCGGGGT 61.004 66.667 0.00 0.00 0.00 4.95
51 52 1.684734 GTCAAGAGAGGGCGGGGTA 60.685 63.158 0.00 0.00 0.00 3.69
52 53 1.381327 TCAAGAGAGGGCGGGGTAG 60.381 63.158 0.00 0.00 0.00 3.18
53 54 1.381327 CAAGAGAGGGCGGGGTAGA 60.381 63.158 0.00 0.00 0.00 2.59
54 55 1.381463 AAGAGAGGGCGGGGTAGAC 60.381 63.158 0.00 0.00 0.00 2.59
55 56 2.838693 GAGAGGGCGGGGTAGACC 60.839 72.222 0.00 0.00 40.48 3.85
65 66 2.773993 GGGGTAGACCGAATTTGACA 57.226 50.000 0.00 0.00 41.60 3.58
66 67 3.277142 GGGGTAGACCGAATTTGACAT 57.723 47.619 0.00 0.00 41.60 3.06
67 68 2.943033 GGGGTAGACCGAATTTGACATG 59.057 50.000 0.00 0.00 41.60 3.21
68 69 2.943033 GGGTAGACCGAATTTGACATGG 59.057 50.000 0.00 0.00 36.71 3.66
69 70 2.943033 GGTAGACCGAATTTGACATGGG 59.057 50.000 0.00 0.00 0.00 4.00
70 71 3.370103 GGTAGACCGAATTTGACATGGGA 60.370 47.826 0.00 0.00 0.00 4.37
71 72 2.991250 AGACCGAATTTGACATGGGAG 58.009 47.619 0.00 0.00 0.00 4.30
72 73 2.017049 GACCGAATTTGACATGGGAGG 58.983 52.381 0.00 0.00 0.00 4.30
73 74 1.633432 ACCGAATTTGACATGGGAGGA 59.367 47.619 0.00 0.00 0.00 3.71
74 75 2.292267 CCGAATTTGACATGGGAGGAG 58.708 52.381 0.00 0.00 0.00 3.69
75 76 2.356125 CCGAATTTGACATGGGAGGAGT 60.356 50.000 0.00 0.00 0.00 3.85
76 77 2.939103 CGAATTTGACATGGGAGGAGTC 59.061 50.000 0.00 0.00 0.00 3.36
77 78 3.282885 GAATTTGACATGGGAGGAGTCC 58.717 50.000 0.00 0.00 43.05 3.85
78 79 0.613260 TTTGACATGGGAGGAGTCCG 59.387 55.000 2.76 0.00 45.05 4.79
79 80 0.544357 TTGACATGGGAGGAGTCCGT 60.544 55.000 2.76 0.00 45.05 4.69
80 81 0.544357 TGACATGGGAGGAGTCCGTT 60.544 55.000 2.76 0.00 45.05 4.44
81 82 1.272816 TGACATGGGAGGAGTCCGTTA 60.273 52.381 2.76 0.00 45.05 3.18
82 83 1.829222 GACATGGGAGGAGTCCGTTAA 59.171 52.381 2.76 0.00 45.05 2.01
83 84 1.831736 ACATGGGAGGAGTCCGTTAAG 59.168 52.381 2.76 0.00 45.05 1.85
84 85 2.108168 CATGGGAGGAGTCCGTTAAGA 58.892 52.381 2.76 0.00 45.05 2.10
85 86 1.848652 TGGGAGGAGTCCGTTAAGAG 58.151 55.000 2.76 0.00 45.05 2.85
86 87 1.356738 TGGGAGGAGTCCGTTAAGAGA 59.643 52.381 2.76 0.00 45.05 3.10
87 88 2.025898 GGGAGGAGTCCGTTAAGAGAG 58.974 57.143 2.76 0.00 45.05 3.20
88 89 1.406180 GGAGGAGTCCGTTAAGAGAGC 59.594 57.143 2.76 0.00 31.37 4.09
89 90 1.406180 GAGGAGTCCGTTAAGAGAGCC 59.594 57.143 2.76 0.00 0.00 4.70
90 91 0.100861 GGAGTCCGTTAAGAGAGCCG 59.899 60.000 0.00 0.00 0.00 5.52
91 92 1.093159 GAGTCCGTTAAGAGAGCCGA 58.907 55.000 0.00 0.00 0.00 5.54
92 93 1.471684 GAGTCCGTTAAGAGAGCCGAA 59.528 52.381 0.00 0.00 0.00 4.30
93 94 1.473278 AGTCCGTTAAGAGAGCCGAAG 59.527 52.381 0.00 0.00 0.00 3.79
109 110 3.819564 CGAAGGATTGGAGTATCACCA 57.180 47.619 0.00 0.00 36.25 4.17
118 119 5.344743 TTGGAGTATCACCAAAGAGCTAG 57.655 43.478 0.00 0.00 43.22 3.42
119 120 3.133003 TGGAGTATCACCAAAGAGCTAGC 59.867 47.826 6.62 6.62 36.25 3.42
120 121 3.386402 GGAGTATCACCAAAGAGCTAGCT 59.614 47.826 19.45 19.45 36.25 3.32
121 122 4.585162 GGAGTATCACCAAAGAGCTAGCTA 59.415 45.833 19.38 0.00 36.25 3.32
122 123 5.245075 GGAGTATCACCAAAGAGCTAGCTAT 59.755 44.000 19.38 12.73 36.25 2.97
123 124 6.095432 AGTATCACCAAAGAGCTAGCTATG 57.905 41.667 19.38 16.41 0.00 2.23
124 125 3.827008 TCACCAAAGAGCTAGCTATGG 57.173 47.619 28.91 28.91 33.36 2.74
125 126 3.374764 TCACCAAAGAGCTAGCTATGGA 58.625 45.455 33.71 19.25 32.26 3.41
126 127 3.133003 TCACCAAAGAGCTAGCTATGGAC 59.867 47.826 33.71 18.05 32.26 4.02
127 128 3.107601 ACCAAAGAGCTAGCTATGGACA 58.892 45.455 33.71 0.00 32.26 4.02
128 129 3.133721 ACCAAAGAGCTAGCTATGGACAG 59.866 47.826 33.71 17.94 32.26 3.51
129 130 3.494048 CCAAAGAGCTAGCTATGGACAGG 60.494 52.174 27.69 15.84 30.53 4.00
130 131 3.320610 AAGAGCTAGCTATGGACAGGA 57.679 47.619 19.38 0.00 0.00 3.86
131 132 2.875296 AGAGCTAGCTATGGACAGGAG 58.125 52.381 19.38 0.00 0.00 3.69
132 133 2.176798 AGAGCTAGCTATGGACAGGAGT 59.823 50.000 19.38 0.00 0.00 3.85
133 134 2.295909 GAGCTAGCTATGGACAGGAGTG 59.704 54.545 19.38 0.00 0.00 3.51
134 135 1.270041 GCTAGCTATGGACAGGAGTGC 60.270 57.143 7.70 0.00 36.51 4.40
135 136 1.000827 CTAGCTATGGACAGGAGTGCG 60.001 57.143 0.00 0.00 39.20 5.34
136 137 0.972983 AGCTATGGACAGGAGTGCGT 60.973 55.000 0.00 0.00 39.20 5.24
137 138 0.807667 GCTATGGACAGGAGTGCGTG 60.808 60.000 0.00 0.00 39.20 5.34
138 139 0.179100 CTATGGACAGGAGTGCGTGG 60.179 60.000 0.00 0.00 39.20 4.94
139 140 0.613572 TATGGACAGGAGTGCGTGGA 60.614 55.000 0.00 0.00 39.20 4.02
140 141 1.480212 ATGGACAGGAGTGCGTGGAA 61.480 55.000 0.00 0.00 39.20 3.53
141 142 1.070786 GGACAGGAGTGCGTGGAAA 59.929 57.895 0.00 0.00 34.31 3.13
142 143 1.228657 GGACAGGAGTGCGTGGAAAC 61.229 60.000 0.00 0.00 34.31 2.78
143 144 0.249911 GACAGGAGTGCGTGGAAACT 60.250 55.000 0.00 0.00 34.31 2.66
144 145 0.180406 ACAGGAGTGCGTGGAAACTT 59.820 50.000 0.00 0.00 34.31 2.66
145 146 0.588252 CAGGAGTGCGTGGAAACTTG 59.412 55.000 0.00 0.00 0.00 3.16
146 147 1.166531 AGGAGTGCGTGGAAACTTGC 61.167 55.000 0.00 0.00 0.00 4.01
147 148 1.166531 GGAGTGCGTGGAAACTTGCT 61.167 55.000 0.00 0.00 33.24 3.91
148 149 1.508632 GAGTGCGTGGAAACTTGCTA 58.491 50.000 0.00 0.00 33.24 3.49
149 150 2.076863 GAGTGCGTGGAAACTTGCTAT 58.923 47.619 0.00 0.00 33.24 2.97
150 151 2.076863 AGTGCGTGGAAACTTGCTATC 58.923 47.619 0.00 0.00 33.24 2.08
151 152 2.076863 GTGCGTGGAAACTTGCTATCT 58.923 47.619 0.00 0.00 33.24 1.98
152 153 3.056107 AGTGCGTGGAAACTTGCTATCTA 60.056 43.478 0.00 0.00 33.24 1.98
153 154 3.871594 GTGCGTGGAAACTTGCTATCTAT 59.128 43.478 0.00 0.00 33.24 1.98
154 155 3.871006 TGCGTGGAAACTTGCTATCTATG 59.129 43.478 0.00 0.00 33.24 2.23
155 156 3.871594 GCGTGGAAACTTGCTATCTATGT 59.128 43.478 0.00 0.00 0.00 2.29
156 157 4.260375 GCGTGGAAACTTGCTATCTATGTG 60.260 45.833 0.00 0.00 0.00 3.21
157 158 4.260375 CGTGGAAACTTGCTATCTATGTGC 60.260 45.833 0.00 0.00 0.00 4.57
158 159 4.035675 GTGGAAACTTGCTATCTATGTGCC 59.964 45.833 0.00 0.00 0.00 5.01
159 160 4.199310 GGAAACTTGCTATCTATGTGCCA 58.801 43.478 0.00 0.00 0.00 4.92
160 161 4.274459 GGAAACTTGCTATCTATGTGCCAG 59.726 45.833 0.00 0.00 0.00 4.85
161 162 4.760530 AACTTGCTATCTATGTGCCAGA 57.239 40.909 0.00 0.00 0.00 3.86
162 163 4.333913 ACTTGCTATCTATGTGCCAGAG 57.666 45.455 0.00 0.00 0.00 3.35
163 164 2.827800 TGCTATCTATGTGCCAGAGC 57.172 50.000 0.00 0.00 40.48 4.09
164 165 2.323599 TGCTATCTATGTGCCAGAGCT 58.676 47.619 0.00 0.00 40.80 4.09
165 166 3.500343 TGCTATCTATGTGCCAGAGCTA 58.500 45.455 0.00 0.00 40.80 3.32
166 167 4.092279 TGCTATCTATGTGCCAGAGCTAT 58.908 43.478 0.00 0.00 40.80 2.97
167 168 4.081807 TGCTATCTATGTGCCAGAGCTATG 60.082 45.833 0.00 0.00 40.80 2.23
168 169 4.159321 GCTATCTATGTGCCAGAGCTATGA 59.841 45.833 10.62 0.00 40.80 2.15
169 170 4.804868 ATCTATGTGCCAGAGCTATGAG 57.195 45.455 10.62 0.94 40.80 2.90
170 171 3.570540 TCTATGTGCCAGAGCTATGAGT 58.429 45.455 10.62 0.00 40.80 3.41
171 172 3.963374 TCTATGTGCCAGAGCTATGAGTT 59.037 43.478 10.62 0.00 40.80 3.01
172 173 2.391616 TGTGCCAGAGCTATGAGTTG 57.608 50.000 10.62 0.00 40.80 3.16
173 174 1.065926 TGTGCCAGAGCTATGAGTTGG 60.066 52.381 10.62 1.38 40.80 3.77
174 175 1.065854 GTGCCAGAGCTATGAGTTGGT 60.066 52.381 10.62 0.00 40.80 3.67
175 176 1.630369 TGCCAGAGCTATGAGTTGGTT 59.370 47.619 10.62 0.00 40.80 3.67
176 177 2.012673 GCCAGAGCTATGAGTTGGTTG 58.987 52.381 10.62 0.00 35.50 3.77
177 178 2.012673 CCAGAGCTATGAGTTGGTTGC 58.987 52.381 10.62 0.00 0.00 4.17
178 179 1.662629 CAGAGCTATGAGTTGGTTGCG 59.337 52.381 0.88 0.00 0.00 4.85
179 180 1.550524 AGAGCTATGAGTTGGTTGCGA 59.449 47.619 0.00 0.00 0.00 5.10
180 181 1.929836 GAGCTATGAGTTGGTTGCGAG 59.070 52.381 0.00 0.00 0.00 5.03
181 182 1.550524 AGCTATGAGTTGGTTGCGAGA 59.449 47.619 0.00 0.00 0.00 4.04
182 183 2.169352 AGCTATGAGTTGGTTGCGAGAT 59.831 45.455 0.00 0.00 0.00 2.75
183 184 2.541762 GCTATGAGTTGGTTGCGAGATC 59.458 50.000 0.00 0.00 0.00 2.75
184 185 3.739519 GCTATGAGTTGGTTGCGAGATCT 60.740 47.826 0.00 0.00 0.00 2.75
185 186 2.839486 TGAGTTGGTTGCGAGATCTT 57.161 45.000 0.00 0.00 0.00 2.40
186 187 3.953712 TGAGTTGGTTGCGAGATCTTA 57.046 42.857 0.00 0.00 0.00 2.10
187 188 4.471904 TGAGTTGGTTGCGAGATCTTAT 57.528 40.909 0.00 0.00 0.00 1.73
188 189 4.183865 TGAGTTGGTTGCGAGATCTTATG 58.816 43.478 0.00 0.00 0.00 1.90
189 190 3.535561 AGTTGGTTGCGAGATCTTATGG 58.464 45.455 0.00 0.00 0.00 2.74
190 191 2.614057 GTTGGTTGCGAGATCTTATGGG 59.386 50.000 0.00 0.00 0.00 4.00
191 192 1.837439 TGGTTGCGAGATCTTATGGGT 59.163 47.619 0.00 0.00 0.00 4.51
192 193 2.238646 TGGTTGCGAGATCTTATGGGTT 59.761 45.455 0.00 0.00 0.00 4.11
193 194 3.279434 GGTTGCGAGATCTTATGGGTTT 58.721 45.455 0.00 0.00 0.00 3.27
194 195 3.312697 GGTTGCGAGATCTTATGGGTTTC 59.687 47.826 0.00 0.00 0.00 2.78
195 196 3.904800 TGCGAGATCTTATGGGTTTCA 57.095 42.857 0.00 0.00 0.00 2.69
196 197 3.531538 TGCGAGATCTTATGGGTTTCAC 58.468 45.455 0.00 0.00 0.00 3.18
197 198 2.872858 GCGAGATCTTATGGGTTTCACC 59.127 50.000 0.00 0.00 37.60 4.02
198 199 3.432326 GCGAGATCTTATGGGTTTCACCT 60.432 47.826 0.00 0.00 38.64 4.00
199 200 4.372656 CGAGATCTTATGGGTTTCACCTC 58.627 47.826 0.00 0.00 38.64 3.85
200 201 4.100189 CGAGATCTTATGGGTTTCACCTCT 59.900 45.833 0.00 0.00 38.64 3.69
201 202 5.302059 CGAGATCTTATGGGTTTCACCTCTA 59.698 44.000 0.00 0.00 38.64 2.43
202 203 6.515862 CGAGATCTTATGGGTTTCACCTCTAG 60.516 46.154 0.00 0.00 38.64 2.43
203 204 4.755266 TCTTATGGGTTTCACCTCTAGC 57.245 45.455 0.00 0.00 38.64 3.42
204 205 3.454812 TCTTATGGGTTTCACCTCTAGCC 59.545 47.826 0.00 0.00 38.64 3.93
205 206 1.972588 ATGGGTTTCACCTCTAGCCT 58.027 50.000 0.00 0.00 38.64 4.58
206 207 2.634639 TGGGTTTCACCTCTAGCCTA 57.365 50.000 0.00 0.00 38.64 3.93
207 208 2.185387 TGGGTTTCACCTCTAGCCTAC 58.815 52.381 0.00 0.00 38.64 3.18
208 209 1.485480 GGGTTTCACCTCTAGCCTACC 59.515 57.143 0.00 0.00 38.64 3.18
209 210 1.485480 GGTTTCACCTCTAGCCTACCC 59.515 57.143 0.00 0.00 34.73 3.69
210 211 1.485480 GTTTCACCTCTAGCCTACCCC 59.515 57.143 0.00 0.00 0.00 4.95
211 212 0.714180 TTCACCTCTAGCCTACCCCA 59.286 55.000 0.00 0.00 0.00 4.96
212 213 0.714180 TCACCTCTAGCCTACCCCAA 59.286 55.000 0.00 0.00 0.00 4.12
213 214 0.831307 CACCTCTAGCCTACCCCAAC 59.169 60.000 0.00 0.00 0.00 3.77
214 215 0.717196 ACCTCTAGCCTACCCCAACT 59.283 55.000 0.00 0.00 0.00 3.16
215 216 1.080666 ACCTCTAGCCTACCCCAACTT 59.919 52.381 0.00 0.00 0.00 2.66
216 217 1.486726 CCTCTAGCCTACCCCAACTTG 59.513 57.143 0.00 0.00 0.00 3.16
217 218 2.188817 CTCTAGCCTACCCCAACTTGT 58.811 52.381 0.00 0.00 0.00 3.16
218 219 2.572104 CTCTAGCCTACCCCAACTTGTT 59.428 50.000 0.00 0.00 0.00 2.83
219 220 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.00 0.00 2.83
220 221 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
229 230 1.490574 CAACTTGTTTGGGGTTGGGA 58.509 50.000 0.00 0.00 37.32 4.37
230 231 1.138069 CAACTTGTTTGGGGTTGGGAC 59.862 52.381 0.00 0.00 37.32 4.46
231 232 0.634465 ACTTGTTTGGGGTTGGGACT 59.366 50.000 0.00 0.00 0.00 3.85
232 233 1.854280 ACTTGTTTGGGGTTGGGACTA 59.146 47.619 0.00 0.00 0.00 2.59
233 234 2.245287 ACTTGTTTGGGGTTGGGACTAA 59.755 45.455 0.00 0.00 0.00 2.24
234 235 3.301274 CTTGTTTGGGGTTGGGACTAAA 58.699 45.455 0.00 0.00 0.00 1.85
235 236 2.952116 TGTTTGGGGTTGGGACTAAAG 58.048 47.619 0.00 0.00 0.00 1.85
236 237 2.244695 GTTTGGGGTTGGGACTAAAGG 58.755 52.381 0.00 0.00 0.00 3.11
237 238 0.113580 TTGGGGTTGGGACTAAAGGC 59.886 55.000 0.00 0.00 0.00 4.35
238 239 0.774491 TGGGGTTGGGACTAAAGGCT 60.774 55.000 0.00 0.00 0.00 4.58
239 240 0.408309 GGGGTTGGGACTAAAGGCTT 59.592 55.000 0.00 0.00 0.00 4.35
240 241 1.203137 GGGGTTGGGACTAAAGGCTTT 60.203 52.381 17.76 17.76 0.00 3.51
241 242 1.893137 GGGTTGGGACTAAAGGCTTTG 59.107 52.381 22.32 13.97 0.00 2.77
242 243 2.594131 GGTTGGGACTAAAGGCTTTGT 58.406 47.619 22.32 16.86 0.00 2.83
243 244 2.963101 GGTTGGGACTAAAGGCTTTGTT 59.037 45.455 22.32 8.73 0.00 2.83
244 245 3.243737 GGTTGGGACTAAAGGCTTTGTTG 60.244 47.826 22.32 13.85 0.00 3.33
245 246 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
246 247 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
247 248 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
248 249 3.383505 GGGACTAAAGGCTTTGTTGTTGT 59.616 43.478 22.32 10.58 0.00 3.32
249 250 4.142026 GGGACTAAAGGCTTTGTTGTTGTT 60.142 41.667 22.32 0.00 0.00 2.83
250 251 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
251 252 5.400066 ACTAAAGGCTTTGTTGTTGTTGT 57.600 34.783 22.32 0.00 0.00 3.32
252 253 5.789521 ACTAAAGGCTTTGTTGTTGTTGTT 58.210 33.333 22.32 0.00 0.00 2.83
253 254 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
254 255 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
255 256 4.792521 AGGCTTTGTTGTTGTTGTTGTA 57.207 36.364 0.00 0.00 0.00 2.41
530 535 1.155042 GGTCTTCAGCACTTCTGCAG 58.845 55.000 7.63 7.63 46.97 4.41
531 536 1.155042 GTCTTCAGCACTTCTGCAGG 58.845 55.000 15.13 0.36 46.97 4.85
532 537 1.051008 TCTTCAGCACTTCTGCAGGA 58.949 50.000 15.13 3.47 46.97 3.86
533 538 1.417517 TCTTCAGCACTTCTGCAGGAA 59.582 47.619 15.13 6.51 46.97 3.36
534 539 2.039480 TCTTCAGCACTTCTGCAGGAAT 59.961 45.455 15.13 0.00 46.97 3.01
535 540 2.574006 TCAGCACTTCTGCAGGAATT 57.426 45.000 15.13 0.00 46.97 2.17
536 541 2.156917 TCAGCACTTCTGCAGGAATTG 58.843 47.619 15.13 11.86 46.97 2.32
537 542 2.156917 CAGCACTTCTGCAGGAATTGA 58.843 47.619 15.13 0.00 46.97 2.57
538 543 2.161808 CAGCACTTCTGCAGGAATTGAG 59.838 50.000 15.13 5.38 46.97 3.02
539 544 1.135460 GCACTTCTGCAGGAATTGAGC 60.135 52.381 15.13 0.00 43.62 4.26
626 632 6.408035 TCCGTAAGTTATTTTGCCTCATGTA 58.592 36.000 0.00 0.00 0.00 2.29
661 667 2.494918 GCGGACCTGCGTGTCTAT 59.505 61.111 5.53 0.00 35.54 1.98
662 668 1.731700 GCGGACCTGCGTGTCTATA 59.268 57.895 5.53 0.00 35.54 1.31
663 669 0.314302 GCGGACCTGCGTGTCTATAT 59.686 55.000 5.53 0.00 35.54 0.86
664 670 1.538512 GCGGACCTGCGTGTCTATATA 59.461 52.381 5.53 0.00 35.54 0.86
665 671 2.030540 GCGGACCTGCGTGTCTATATAA 60.031 50.000 5.53 0.00 35.54 0.98
666 672 3.367087 GCGGACCTGCGTGTCTATATAAT 60.367 47.826 5.53 0.00 35.54 1.28
667 673 4.806330 CGGACCTGCGTGTCTATATAATT 58.194 43.478 5.53 0.00 35.54 1.40
668 674 5.620654 GCGGACCTGCGTGTCTATATAATTA 60.621 44.000 5.53 0.00 35.54 1.40
669 675 6.561614 CGGACCTGCGTGTCTATATAATTAT 58.438 40.000 2.97 2.97 35.54 1.28
670 676 7.680350 GCGGACCTGCGTGTCTATATAATTATA 60.680 40.741 7.62 7.62 35.54 0.98
671 677 8.350722 CGGACCTGCGTGTCTATATAATTATAT 58.649 37.037 19.37 19.37 35.54 0.86
902 918 2.061028 GTGCTGTTAAAATGTGGCTGC 58.939 47.619 0.00 0.00 0.00 5.25
904 920 3.057596 GTGCTGTTAAAATGTGGCTGCTA 60.058 43.478 0.00 0.00 0.00 3.49
1049 1069 2.473070 TGTTCATCCTACGGATTGGGA 58.527 47.619 0.00 0.00 39.79 4.37
1065 1085 0.898326 GGGAAGGCATGGTTTCCGTT 60.898 55.000 0.00 0.00 43.05 4.44
1082 1102 0.676782 GTTAAGGAGTGGTGGCGCAT 60.677 55.000 10.83 0.00 0.00 4.73
1091 1111 1.106351 TGGTGGCGCATCAACACTTT 61.106 50.000 10.83 0.00 35.53 2.66
1124 1144 0.534203 TCTCGAAGGCCGCTTGTTTT 60.534 50.000 0.00 0.00 38.37 2.43
1187 1207 2.878406 CTCGGGTGTTCTTCAACAATGT 59.122 45.455 0.00 0.00 44.32 2.71
1194 1214 4.335315 GTGTTCTTCAACAATGTGACTCCA 59.665 41.667 0.00 0.00 44.32 3.86
1300 1320 7.308435 CCGCAAGAGTGATTCTTAAAATCTTT 58.692 34.615 0.00 0.00 44.34 2.52
1422 1635 6.978674 TTGAGAGATCTATTTACCGATGGT 57.021 37.500 0.00 0.00 40.16 3.55
1527 1746 6.879458 GTGAAGTTTCCTCCATAGCTCTTTTA 59.121 38.462 0.00 0.00 0.00 1.52
1659 1903 4.418013 TTCAGTTGTTCCATTGTATGCG 57.582 40.909 0.00 0.00 0.00 4.73
1795 2042 5.447778 ACCATTGACAGAGAGGAATTGAT 57.552 39.130 0.00 0.00 0.00 2.57
1798 2045 5.450137 CCATTGACAGAGAGGAATTGATTGC 60.450 44.000 0.00 0.00 0.00 3.56
1800 2047 2.012673 ACAGAGAGGAATTGATTGCGC 58.987 47.619 0.00 0.00 32.98 6.09
1832 2087 0.322546 AACAGGAGGGACATTTCCGC 60.323 55.000 0.00 0.00 43.94 5.54
1910 2166 4.467084 GTCCTTCGCCGCCATGGA 62.467 66.667 18.40 0.00 42.00 3.41
1911 2167 3.479203 TCCTTCGCCGCCATGGAT 61.479 61.111 18.40 0.00 42.00 3.41
1912 2168 3.282157 CCTTCGCCGCCATGGATG 61.282 66.667 18.40 6.69 42.00 3.51
1913 2169 2.203056 CTTCGCCGCCATGGATGA 60.203 61.111 18.40 3.55 42.00 2.92
1914 2170 2.513666 TTCGCCGCCATGGATGAC 60.514 61.111 18.40 0.00 42.00 3.06
1915 2171 2.930385 CTTCGCCGCCATGGATGACT 62.930 60.000 18.40 0.00 42.00 3.41
1916 2172 2.923426 TTCGCCGCCATGGATGACTC 62.923 60.000 18.40 0.00 42.00 3.36
1917 2173 2.592861 GCCGCCATGGATGACTCC 60.593 66.667 18.40 0.00 42.00 3.85
1918 2174 2.111878 CCGCCATGGATGACTCCC 59.888 66.667 18.40 0.00 41.29 4.30
1935 2203 3.314331 CTGCTGTCCCCCGTCACT 61.314 66.667 0.00 0.00 0.00 3.41
1963 2231 2.358737 CGCACGCTCCTTTCCCTT 60.359 61.111 0.00 0.00 0.00 3.95
2204 2472 0.329596 AAGAAGCCGCCTCCTTCATT 59.670 50.000 7.97 0.00 40.83 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.849953 CACGCTTTAGCCGTCCGC 61.850 66.667 0.00 0.00 37.91 5.54
8 9 3.849953 GCACGCTTTAGCCGTCCG 61.850 66.667 0.00 0.00 37.91 4.79
9 10 2.740714 CTGCACGCTTTAGCCGTCC 61.741 63.158 0.00 0.00 37.91 4.79
10 11 1.687494 CTCTGCACGCTTTAGCCGTC 61.687 60.000 0.00 0.00 37.91 4.79
11 12 1.738099 CTCTGCACGCTTTAGCCGT 60.738 57.895 0.00 0.00 37.91 5.68
12 13 1.014044 TTCTCTGCACGCTTTAGCCG 61.014 55.000 0.00 0.00 37.91 5.52
13 14 1.063174 CATTCTCTGCACGCTTTAGCC 59.937 52.381 0.00 0.00 37.91 3.93
14 15 1.734465 ACATTCTCTGCACGCTTTAGC 59.266 47.619 0.00 0.00 37.78 3.09
15 16 2.995939 TGACATTCTCTGCACGCTTTAG 59.004 45.455 0.00 0.00 0.00 1.85
16 17 3.038788 TGACATTCTCTGCACGCTTTA 57.961 42.857 0.00 0.00 0.00 1.85
17 18 1.882912 TGACATTCTCTGCACGCTTT 58.117 45.000 0.00 0.00 0.00 3.51
18 19 1.802960 CTTGACATTCTCTGCACGCTT 59.197 47.619 0.00 0.00 0.00 4.68
19 20 1.001293 TCTTGACATTCTCTGCACGCT 59.999 47.619 0.00 0.00 0.00 5.07
20 21 1.392853 CTCTTGACATTCTCTGCACGC 59.607 52.381 0.00 0.00 0.00 5.34
21 22 2.922387 CTCTCTTGACATTCTCTGCACG 59.078 50.000 0.00 0.00 0.00 5.34
22 23 3.260740 CCTCTCTTGACATTCTCTGCAC 58.739 50.000 0.00 0.00 0.00 4.57
23 24 2.235650 CCCTCTCTTGACATTCTCTGCA 59.764 50.000 0.00 0.00 0.00 4.41
24 25 2.903798 CCCTCTCTTGACATTCTCTGC 58.096 52.381 0.00 0.00 0.00 4.26
25 26 2.738000 CGCCCTCTCTTGACATTCTCTG 60.738 54.545 0.00 0.00 0.00 3.35
26 27 1.480137 CGCCCTCTCTTGACATTCTCT 59.520 52.381 0.00 0.00 0.00 3.10
27 28 1.472376 CCGCCCTCTCTTGACATTCTC 60.472 57.143 0.00 0.00 0.00 2.87
28 29 0.539051 CCGCCCTCTCTTGACATTCT 59.461 55.000 0.00 0.00 0.00 2.40
29 30 0.462759 CCCGCCCTCTCTTGACATTC 60.463 60.000 0.00 0.00 0.00 2.67
30 31 1.604378 CCCGCCCTCTCTTGACATT 59.396 57.895 0.00 0.00 0.00 2.71
31 32 2.370445 CCCCGCCCTCTCTTGACAT 61.370 63.158 0.00 0.00 0.00 3.06
32 33 2.449967 TACCCCGCCCTCTCTTGACA 62.450 60.000 0.00 0.00 0.00 3.58
33 34 1.677637 CTACCCCGCCCTCTCTTGAC 61.678 65.000 0.00 0.00 0.00 3.18
34 35 1.381327 CTACCCCGCCCTCTCTTGA 60.381 63.158 0.00 0.00 0.00 3.02
35 36 1.381327 TCTACCCCGCCCTCTCTTG 60.381 63.158 0.00 0.00 0.00 3.02
36 37 1.381463 GTCTACCCCGCCCTCTCTT 60.381 63.158 0.00 0.00 0.00 2.85
37 38 2.279408 GTCTACCCCGCCCTCTCT 59.721 66.667 0.00 0.00 0.00 3.10
38 39 2.838693 GGTCTACCCCGCCCTCTC 60.839 72.222 0.00 0.00 0.00 3.20
39 40 4.835891 CGGTCTACCCCGCCCTCT 62.836 72.222 0.00 0.00 41.78 3.69
46 47 2.773993 TGTCAAATTCGGTCTACCCC 57.226 50.000 0.00 0.00 0.00 4.95
47 48 2.943033 CCATGTCAAATTCGGTCTACCC 59.057 50.000 0.00 0.00 0.00 3.69
48 49 2.943033 CCCATGTCAAATTCGGTCTACC 59.057 50.000 0.00 0.00 0.00 3.18
49 50 3.869065 TCCCATGTCAAATTCGGTCTAC 58.131 45.455 0.00 0.00 0.00 2.59
50 51 3.118408 CCTCCCATGTCAAATTCGGTCTA 60.118 47.826 0.00 0.00 0.00 2.59
51 52 2.356125 CCTCCCATGTCAAATTCGGTCT 60.356 50.000 0.00 0.00 0.00 3.85
52 53 2.017049 CCTCCCATGTCAAATTCGGTC 58.983 52.381 0.00 0.00 0.00 4.79
53 54 1.633432 TCCTCCCATGTCAAATTCGGT 59.367 47.619 0.00 0.00 0.00 4.69
54 55 2.292267 CTCCTCCCATGTCAAATTCGG 58.708 52.381 0.00 0.00 0.00 4.30
55 56 2.939103 GACTCCTCCCATGTCAAATTCG 59.061 50.000 0.00 0.00 0.00 3.34
56 57 3.282885 GGACTCCTCCCATGTCAAATTC 58.717 50.000 0.00 0.00 32.84 2.17
57 58 2.356125 CGGACTCCTCCCATGTCAAATT 60.356 50.000 0.00 0.00 31.93 1.82
58 59 1.210478 CGGACTCCTCCCATGTCAAAT 59.790 52.381 0.00 0.00 31.93 2.32
59 60 0.613260 CGGACTCCTCCCATGTCAAA 59.387 55.000 0.00 0.00 31.93 2.69
60 61 0.544357 ACGGACTCCTCCCATGTCAA 60.544 55.000 0.00 0.00 31.93 3.18
61 62 0.544357 AACGGACTCCTCCCATGTCA 60.544 55.000 0.00 0.00 31.93 3.58
62 63 1.481871 TAACGGACTCCTCCCATGTC 58.518 55.000 0.00 0.00 31.93 3.06
63 64 1.831736 CTTAACGGACTCCTCCCATGT 59.168 52.381 0.00 0.00 31.93 3.21
64 65 2.101582 CTCTTAACGGACTCCTCCCATG 59.898 54.545 0.00 0.00 31.93 3.66
65 66 2.024273 TCTCTTAACGGACTCCTCCCAT 60.024 50.000 0.00 0.00 31.93 4.00
66 67 1.356738 TCTCTTAACGGACTCCTCCCA 59.643 52.381 0.00 0.00 31.93 4.37
67 68 2.025898 CTCTCTTAACGGACTCCTCCC 58.974 57.143 0.00 0.00 31.93 4.30
68 69 1.406180 GCTCTCTTAACGGACTCCTCC 59.594 57.143 0.00 0.00 0.00 4.30
69 70 1.406180 GGCTCTCTTAACGGACTCCTC 59.594 57.143 0.00 0.00 0.00 3.71
70 71 1.476477 GGCTCTCTTAACGGACTCCT 58.524 55.000 0.00 0.00 0.00 3.69
71 72 0.100861 CGGCTCTCTTAACGGACTCC 59.899 60.000 0.00 0.00 0.00 3.85
72 73 1.093159 TCGGCTCTCTTAACGGACTC 58.907 55.000 0.00 0.00 0.00 3.36
73 74 1.473278 CTTCGGCTCTCTTAACGGACT 59.527 52.381 0.00 0.00 0.00 3.85
74 75 1.469423 CCTTCGGCTCTCTTAACGGAC 60.469 57.143 0.00 0.00 0.00 4.79
75 76 0.815734 CCTTCGGCTCTCTTAACGGA 59.184 55.000 0.00 0.00 0.00 4.69
76 77 0.815734 TCCTTCGGCTCTCTTAACGG 59.184 55.000 0.00 0.00 0.00 4.44
77 78 2.860735 CAATCCTTCGGCTCTCTTAACG 59.139 50.000 0.00 0.00 0.00 3.18
78 79 3.118738 TCCAATCCTTCGGCTCTCTTAAC 60.119 47.826 0.00 0.00 0.00 2.01
79 80 3.104512 TCCAATCCTTCGGCTCTCTTAA 58.895 45.455 0.00 0.00 0.00 1.85
80 81 2.695666 CTCCAATCCTTCGGCTCTCTTA 59.304 50.000 0.00 0.00 0.00 2.10
81 82 1.484240 CTCCAATCCTTCGGCTCTCTT 59.516 52.381 0.00 0.00 0.00 2.85
82 83 1.118838 CTCCAATCCTTCGGCTCTCT 58.881 55.000 0.00 0.00 0.00 3.10
83 84 0.827368 ACTCCAATCCTTCGGCTCTC 59.173 55.000 0.00 0.00 0.00 3.20
84 85 2.160721 TACTCCAATCCTTCGGCTCT 57.839 50.000 0.00 0.00 0.00 4.09
85 86 2.365617 TGATACTCCAATCCTTCGGCTC 59.634 50.000 0.00 0.00 0.00 4.70
86 87 2.103263 GTGATACTCCAATCCTTCGGCT 59.897 50.000 0.00 0.00 0.00 5.52
87 88 2.484889 GTGATACTCCAATCCTTCGGC 58.515 52.381 0.00 0.00 0.00 5.54
88 89 2.434336 TGGTGATACTCCAATCCTTCGG 59.566 50.000 0.00 0.00 31.50 4.30
89 90 3.819564 TGGTGATACTCCAATCCTTCG 57.180 47.619 0.00 0.00 31.50 3.79
90 91 5.745227 TCTTTGGTGATACTCCAATCCTTC 58.255 41.667 6.20 0.00 43.25 3.46
91 92 5.749462 CTCTTTGGTGATACTCCAATCCTT 58.251 41.667 6.20 0.00 43.25 3.36
92 93 4.384647 GCTCTTTGGTGATACTCCAATCCT 60.385 45.833 6.20 0.00 43.25 3.24
93 94 3.879892 GCTCTTTGGTGATACTCCAATCC 59.120 47.826 6.20 0.00 43.25 3.01
94 95 4.775236 AGCTCTTTGGTGATACTCCAATC 58.225 43.478 6.20 0.00 43.25 2.67
95 96 4.851639 AGCTCTTTGGTGATACTCCAAT 57.148 40.909 6.20 0.00 43.25 3.16
96 97 4.383118 GCTAGCTCTTTGGTGATACTCCAA 60.383 45.833 7.70 0.00 42.29 3.53
97 98 3.133003 GCTAGCTCTTTGGTGATACTCCA 59.867 47.826 7.70 0.00 0.00 3.86
98 99 3.386402 AGCTAGCTCTTTGGTGATACTCC 59.614 47.826 12.68 0.00 0.00 3.85
99 100 4.664150 AGCTAGCTCTTTGGTGATACTC 57.336 45.455 12.68 0.00 0.00 2.59
100 101 5.011533 CCATAGCTAGCTCTTTGGTGATACT 59.988 44.000 23.26 0.00 32.65 2.12
101 102 5.011125 TCCATAGCTAGCTCTTTGGTGATAC 59.989 44.000 27.50 0.00 36.79 2.24
102 103 5.011125 GTCCATAGCTAGCTCTTTGGTGATA 59.989 44.000 27.50 14.48 36.79 2.15
103 104 3.969976 TCCATAGCTAGCTCTTTGGTGAT 59.030 43.478 27.50 12.14 36.79 3.06
104 105 3.133003 GTCCATAGCTAGCTCTTTGGTGA 59.867 47.826 27.50 15.24 36.79 4.02
105 106 3.118629 TGTCCATAGCTAGCTCTTTGGTG 60.119 47.826 27.50 16.61 36.79 4.17
106 107 3.107601 TGTCCATAGCTAGCTCTTTGGT 58.892 45.455 27.50 8.05 36.79 3.67
107 108 3.494048 CCTGTCCATAGCTAGCTCTTTGG 60.494 52.174 23.26 24.37 36.78 3.28
108 109 3.386078 TCCTGTCCATAGCTAGCTCTTTG 59.614 47.826 23.26 16.78 0.00 2.77
109 110 3.640967 CTCCTGTCCATAGCTAGCTCTTT 59.359 47.826 23.26 4.57 0.00 2.52
110 111 3.230134 CTCCTGTCCATAGCTAGCTCTT 58.770 50.000 23.26 7.47 0.00 2.85
111 112 2.176798 ACTCCTGTCCATAGCTAGCTCT 59.823 50.000 23.26 9.05 0.00 4.09
112 113 2.295909 CACTCCTGTCCATAGCTAGCTC 59.704 54.545 23.26 7.00 0.00 4.09
113 114 2.315176 CACTCCTGTCCATAGCTAGCT 58.685 52.381 23.12 23.12 0.00 3.32
114 115 1.270041 GCACTCCTGTCCATAGCTAGC 60.270 57.143 6.62 6.62 0.00 3.42
115 116 1.000827 CGCACTCCTGTCCATAGCTAG 60.001 57.143 0.00 0.00 0.00 3.42
116 117 1.032794 CGCACTCCTGTCCATAGCTA 58.967 55.000 0.00 0.00 0.00 3.32
117 118 0.972983 ACGCACTCCTGTCCATAGCT 60.973 55.000 0.00 0.00 0.00 3.32
118 119 0.807667 CACGCACTCCTGTCCATAGC 60.808 60.000 0.00 0.00 0.00 2.97
119 120 0.179100 CCACGCACTCCTGTCCATAG 60.179 60.000 0.00 0.00 0.00 2.23
120 121 0.613572 TCCACGCACTCCTGTCCATA 60.614 55.000 0.00 0.00 0.00 2.74
121 122 1.480212 TTCCACGCACTCCTGTCCAT 61.480 55.000 0.00 0.00 0.00 3.41
122 123 1.691195 TTTCCACGCACTCCTGTCCA 61.691 55.000 0.00 0.00 0.00 4.02
123 124 1.070786 TTTCCACGCACTCCTGTCC 59.929 57.895 0.00 0.00 0.00 4.02
124 125 0.249911 AGTTTCCACGCACTCCTGTC 60.250 55.000 0.00 0.00 0.00 3.51
125 126 0.180406 AAGTTTCCACGCACTCCTGT 59.820 50.000 0.00 0.00 0.00 4.00
126 127 0.588252 CAAGTTTCCACGCACTCCTG 59.412 55.000 0.00 0.00 0.00 3.86
127 128 1.166531 GCAAGTTTCCACGCACTCCT 61.167 55.000 0.00 0.00 0.00 3.69
128 129 1.166531 AGCAAGTTTCCACGCACTCC 61.167 55.000 0.00 0.00 0.00 3.85
129 130 1.508632 TAGCAAGTTTCCACGCACTC 58.491 50.000 0.00 0.00 0.00 3.51
130 131 2.076863 GATAGCAAGTTTCCACGCACT 58.923 47.619 0.00 0.00 0.00 4.40
131 132 2.076863 AGATAGCAAGTTTCCACGCAC 58.923 47.619 0.00 0.00 0.00 5.34
132 133 2.472695 AGATAGCAAGTTTCCACGCA 57.527 45.000 0.00 0.00 0.00 5.24
133 134 3.871594 ACATAGATAGCAAGTTTCCACGC 59.128 43.478 0.00 0.00 0.00 5.34
134 135 4.260375 GCACATAGATAGCAAGTTTCCACG 60.260 45.833 0.00 0.00 0.00 4.94
135 136 4.035675 GGCACATAGATAGCAAGTTTCCAC 59.964 45.833 0.00 0.00 0.00 4.02
136 137 4.199310 GGCACATAGATAGCAAGTTTCCA 58.801 43.478 0.00 0.00 0.00 3.53
137 138 4.199310 TGGCACATAGATAGCAAGTTTCC 58.801 43.478 0.00 0.00 0.00 3.13
138 139 5.118990 TCTGGCACATAGATAGCAAGTTTC 58.881 41.667 0.00 0.00 38.20 2.78
139 140 5.102953 TCTGGCACATAGATAGCAAGTTT 57.897 39.130 0.00 0.00 38.20 2.66
140 141 4.701765 CTCTGGCACATAGATAGCAAGTT 58.298 43.478 0.00 0.00 38.20 2.66
141 142 3.494048 GCTCTGGCACATAGATAGCAAGT 60.494 47.826 0.00 0.00 38.20 3.16
142 143 3.065655 GCTCTGGCACATAGATAGCAAG 58.934 50.000 0.00 0.00 38.20 4.01
143 144 2.702478 AGCTCTGGCACATAGATAGCAA 59.298 45.455 0.00 0.00 41.70 3.91
144 145 2.323599 AGCTCTGGCACATAGATAGCA 58.676 47.619 0.00 0.00 41.70 3.49
145 146 4.159321 TCATAGCTCTGGCACATAGATAGC 59.841 45.833 0.00 0.00 36.89 2.97
146 147 5.418524 ACTCATAGCTCTGGCACATAGATAG 59.581 44.000 0.00 0.00 36.89 2.08
147 148 5.328565 ACTCATAGCTCTGGCACATAGATA 58.671 41.667 0.00 0.00 37.79 1.98
148 149 4.158786 ACTCATAGCTCTGGCACATAGAT 58.841 43.478 0.00 0.00 41.70 1.98
149 150 3.570540 ACTCATAGCTCTGGCACATAGA 58.429 45.455 0.00 0.00 41.70 1.98
150 151 4.056740 CAACTCATAGCTCTGGCACATAG 58.943 47.826 0.00 0.00 41.70 2.23
151 152 3.181462 CCAACTCATAGCTCTGGCACATA 60.181 47.826 0.00 0.00 41.70 2.29
152 153 2.421107 CCAACTCATAGCTCTGGCACAT 60.421 50.000 0.00 0.00 41.70 3.21
153 154 1.065926 CCAACTCATAGCTCTGGCACA 60.066 52.381 0.00 0.00 41.70 4.57
154 155 1.065854 ACCAACTCATAGCTCTGGCAC 60.066 52.381 0.00 0.00 41.70 5.01
155 156 1.279496 ACCAACTCATAGCTCTGGCA 58.721 50.000 0.00 0.00 41.70 4.92
156 157 2.012673 CAACCAACTCATAGCTCTGGC 58.987 52.381 0.00 0.00 39.06 4.85
157 158 2.012673 GCAACCAACTCATAGCTCTGG 58.987 52.381 0.00 0.00 0.00 3.86
158 159 1.662629 CGCAACCAACTCATAGCTCTG 59.337 52.381 0.00 0.00 0.00 3.35
159 160 1.550524 TCGCAACCAACTCATAGCTCT 59.449 47.619 0.00 0.00 0.00 4.09
160 161 1.929836 CTCGCAACCAACTCATAGCTC 59.070 52.381 0.00 0.00 0.00 4.09
161 162 1.550524 TCTCGCAACCAACTCATAGCT 59.449 47.619 0.00 0.00 0.00 3.32
162 163 2.010145 TCTCGCAACCAACTCATAGC 57.990 50.000 0.00 0.00 0.00 2.97
163 164 4.052159 AGATCTCGCAACCAACTCATAG 57.948 45.455 0.00 0.00 0.00 2.23
164 165 4.471904 AAGATCTCGCAACCAACTCATA 57.528 40.909 0.00 0.00 0.00 2.15
165 166 3.340814 AAGATCTCGCAACCAACTCAT 57.659 42.857 0.00 0.00 0.00 2.90
166 167 2.839486 AAGATCTCGCAACCAACTCA 57.161 45.000 0.00 0.00 0.00 3.41
167 168 3.557595 CCATAAGATCTCGCAACCAACTC 59.442 47.826 0.00 0.00 0.00 3.01
168 169 3.535561 CCATAAGATCTCGCAACCAACT 58.464 45.455 0.00 0.00 0.00 3.16
169 170 2.614057 CCCATAAGATCTCGCAACCAAC 59.386 50.000 0.00 0.00 0.00 3.77
170 171 2.238646 ACCCATAAGATCTCGCAACCAA 59.761 45.455 0.00 0.00 0.00 3.67
171 172 1.837439 ACCCATAAGATCTCGCAACCA 59.163 47.619 0.00 0.00 0.00 3.67
172 173 2.622064 ACCCATAAGATCTCGCAACC 57.378 50.000 0.00 0.00 0.00 3.77
173 174 3.938963 TGAAACCCATAAGATCTCGCAAC 59.061 43.478 0.00 0.00 0.00 4.17
174 175 3.938963 GTGAAACCCATAAGATCTCGCAA 59.061 43.478 0.00 0.00 0.00 4.85
175 176 3.531538 GTGAAACCCATAAGATCTCGCA 58.468 45.455 0.00 0.00 0.00 5.10
190 191 1.485480 GGGGTAGGCTAGAGGTGAAAC 59.515 57.143 0.00 0.00 0.00 2.78
191 192 1.079825 TGGGGTAGGCTAGAGGTGAAA 59.920 52.381 0.00 0.00 0.00 2.69
192 193 0.714180 TGGGGTAGGCTAGAGGTGAA 59.286 55.000 0.00 0.00 0.00 3.18
193 194 0.714180 TTGGGGTAGGCTAGAGGTGA 59.286 55.000 0.00 0.00 0.00 4.02
194 195 0.831307 GTTGGGGTAGGCTAGAGGTG 59.169 60.000 0.00 0.00 0.00 4.00
195 196 0.717196 AGTTGGGGTAGGCTAGAGGT 59.283 55.000 0.00 0.00 0.00 3.85
196 197 1.486726 CAAGTTGGGGTAGGCTAGAGG 59.513 57.143 0.00 0.00 0.00 3.69
197 198 2.188817 ACAAGTTGGGGTAGGCTAGAG 58.811 52.381 7.96 0.00 0.00 2.43
198 199 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
199 200 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
200 201 3.149005 CAAACAAGTTGGGGTAGGCTA 57.851 47.619 7.96 0.00 33.18 3.93
201 202 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
210 211 1.138069 GTCCCAACCCCAAACAAGTTG 59.862 52.381 0.00 0.00 40.42 3.16
211 212 1.007842 AGTCCCAACCCCAAACAAGTT 59.992 47.619 0.00 0.00 0.00 2.66
212 213 0.634465 AGTCCCAACCCCAAACAAGT 59.366 50.000 0.00 0.00 0.00 3.16
213 214 2.668144 TAGTCCCAACCCCAAACAAG 57.332 50.000 0.00 0.00 0.00 3.16
214 215 3.301274 CTTTAGTCCCAACCCCAAACAA 58.699 45.455 0.00 0.00 0.00 2.83
215 216 2.425102 CCTTTAGTCCCAACCCCAAACA 60.425 50.000 0.00 0.00 0.00 2.83
216 217 2.244695 CCTTTAGTCCCAACCCCAAAC 58.755 52.381 0.00 0.00 0.00 2.93
217 218 1.481615 GCCTTTAGTCCCAACCCCAAA 60.482 52.381 0.00 0.00 0.00 3.28
218 219 0.113580 GCCTTTAGTCCCAACCCCAA 59.886 55.000 0.00 0.00 0.00 4.12
219 220 0.774491 AGCCTTTAGTCCCAACCCCA 60.774 55.000 0.00 0.00 0.00 4.96
220 221 0.408309 AAGCCTTTAGTCCCAACCCC 59.592 55.000 0.00 0.00 0.00 4.95
221 222 1.893137 CAAAGCCTTTAGTCCCAACCC 59.107 52.381 0.00 0.00 0.00 4.11
222 223 2.594131 ACAAAGCCTTTAGTCCCAACC 58.406 47.619 0.00 0.00 0.00 3.77
223 224 3.383505 ACAACAAAGCCTTTAGTCCCAAC 59.616 43.478 0.00 0.00 0.00 3.77
224 225 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
225 226 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
226 227 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
227 228 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
228 229 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
229 230 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
230 231 5.637387 ACAACAACAACAACAAAGCCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
231 232 5.542779 ACAACAACAACAACAAAGCCTTTA 58.457 33.333 0.00 0.00 0.00 1.85
232 233 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
233 234 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
234 235 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
235 236 4.490743 AGTACAACAACAACAACAAAGCC 58.509 39.130 0.00 0.00 0.00 4.35
236 237 5.631512 TGAAGTACAACAACAACAACAAAGC 59.368 36.000 0.00 0.00 0.00 3.51
237 238 7.630470 TTGAAGTACAACAACAACAACAAAG 57.370 32.000 0.00 0.00 33.18 2.77
238 239 8.594881 ATTTGAAGTACAACAACAACAACAAA 57.405 26.923 0.00 0.00 38.29 2.83
239 240 8.491152 CAATTTGAAGTACAACAACAACAACAA 58.509 29.630 0.00 0.00 38.29 2.83
240 241 7.867909 TCAATTTGAAGTACAACAACAACAACA 59.132 29.630 0.00 0.00 38.29 3.33
241 242 8.233692 TCAATTTGAAGTACAACAACAACAAC 57.766 30.769 0.00 0.00 38.29 3.32
242 243 8.994429 ATCAATTTGAAGTACAACAACAACAA 57.006 26.923 2.68 0.00 38.29 2.83
243 244 8.994429 AATCAATTTGAAGTACAACAACAACA 57.006 26.923 2.68 0.00 38.29 3.33
296 298 7.452501 TCCAATCCTTGATGAGAAGACATTTTT 59.547 33.333 0.00 0.00 0.00 1.94
509 514 4.683432 AGAAGTGCTGAAGACCGC 57.317 55.556 0.00 0.00 0.00 5.68
530 535 1.268234 CGCTCAATTCCGCTCAATTCC 60.268 52.381 0.00 0.00 0.00 3.01
531 536 1.857602 GCGCTCAATTCCGCTCAATTC 60.858 52.381 0.00 0.00 46.14 2.17
532 537 0.099436 GCGCTCAATTCCGCTCAATT 59.901 50.000 0.00 0.00 46.14 2.32
533 538 1.723870 GCGCTCAATTCCGCTCAAT 59.276 52.632 0.00 0.00 46.14 2.57
534 539 3.177600 GCGCTCAATTCCGCTCAA 58.822 55.556 0.00 0.00 46.14 3.02
539 544 2.034879 ACACTGGCGCTCAATTCCG 61.035 57.895 7.64 0.00 0.00 4.30
1049 1069 2.167662 CCTTAACGGAAACCATGCCTT 58.832 47.619 0.00 0.00 33.16 4.35
1065 1085 1.220749 GATGCGCCACCACTCCTTA 59.779 57.895 4.18 0.00 0.00 2.69
1082 1102 0.032952 CGACCTCCCGAAAGTGTTGA 59.967 55.000 0.00 0.00 0.00 3.18
1091 1111 2.771639 CGAGATTGCGACCTCCCGA 61.772 63.158 0.00 0.00 0.00 5.14
1187 1207 0.464036 AAGCACAACGACTGGAGTCA 59.536 50.000 7.54 0.00 44.99 3.41
1194 1214 1.006832 GTGTCACAAGCACAACGACT 58.993 50.000 0.00 0.00 36.88 4.18
1300 1320 7.814107 GGCTTGTCATTTTCATTGAATAAGACA 59.186 33.333 17.91 17.91 32.20 3.41
1416 1629 6.677913 AGACATCTTTAAAAACCAACCATCG 58.322 36.000 0.00 0.00 0.00 3.84
1574 1818 8.247562 GCAACCTAAAATATGTGGTGTATTTCA 58.752 33.333 0.00 0.00 32.21 2.69
1659 1903 0.961019 TTCTGCCTTCCAATGTGCAC 59.039 50.000 10.75 10.75 0.00 4.57
1908 2164 1.524482 GGACAGCAGGGAGTCATCC 59.476 63.158 0.00 0.00 45.85 3.51
1909 2165 1.524482 GGGACAGCAGGGAGTCATC 59.476 63.158 0.00 0.00 36.50 2.92
1910 2166 1.997874 GGGGACAGCAGGGAGTCAT 60.998 63.158 0.00 0.00 36.50 3.06
1911 2167 2.607750 GGGGACAGCAGGGAGTCA 60.608 66.667 0.00 0.00 36.50 3.41
1912 2168 3.403558 GGGGGACAGCAGGGAGTC 61.404 72.222 0.00 0.00 0.00 3.36
1917 2173 4.394712 GTGACGGGGGACAGCAGG 62.395 72.222 0.00 0.00 0.00 4.85
1918 2174 3.314331 AGTGACGGGGGACAGCAG 61.314 66.667 0.00 0.00 0.00 4.24
1958 2226 3.154473 CGAGATCCGCCCAAGGGA 61.154 66.667 9.92 0.00 37.50 4.20


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

AutoCloner maintained by Alex Coulton.