Multiple sequence alignment - TraesCS3A01G107700

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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 TraesCS3A01G107700 chr3A 100.000 1904 0 0 1 1904 72494129 72492226 0.000000e+00 3517.0
1 TraesCS3A01G107700 chr3A 96.477 738 24 2 881 1618 72672238 72672973 0.000000e+00 1218.0
2 TraesCS3A01G107700 chr3A 100.000 205 0 0 2136 2340 72491994 72491790 1.700000e-101 379.0
3 TraesCS3A01G107700 chr3A 83.088 408 52 9 2 396 79987302 79986899 2.860000e-94 355.0
4 TraesCS3A01G107700 chr7D 94.561 717 30 5 881 1597 349947042 349947749 0.000000e+00 1099.0
5 TraesCS3A01G107700 chr7D 92.147 624 47 2 211 834 484547832 484548453 0.000000e+00 880.0
6 TraesCS3A01G107700 chr7D 91.759 631 49 3 212 841 399571456 399570828 0.000000e+00 874.0
7 TraesCS3A01G107700 chr7D 91.587 630 51 2 206 834 214831168 214831796 0.000000e+00 869.0
8 TraesCS3A01G107700 chr7D 85.213 399 51 8 2 396 99474597 99474991 1.010000e-108 403.0
9 TraesCS3A01G107700 chr7D 83.596 445 55 11 2 430 510670227 510669785 3.620000e-108 401.0
10 TraesCS3A01G107700 chr7B 92.732 743 40 11 881 1620 352718214 352718945 0.000000e+00 1061.0
11 TraesCS3A01G107700 chr7B 84.086 421 49 14 2 407 67657876 67658293 7.840000e-105 390.0
12 TraesCS3A01G107700 chr4D 92.185 627 44 5 211 834 507147990 507148614 0.000000e+00 881.0
13 TraesCS3A01G107700 chr4D 92.026 627 43 7 212 834 498528704 498528081 0.000000e+00 874.0
14 TraesCS3A01G107700 chr4D 91.733 629 49 3 206 834 128263085 128263710 0.000000e+00 870.0
15 TraesCS3A01G107700 chr4D 91.693 626 50 2 209 834 128258184 128258807 0.000000e+00 867.0
16 TraesCS3A01G107700 chr4D 91.256 629 50 4 206 834 507152843 507153466 0.000000e+00 852.0
17 TraesCS3A01G107700 chr4D 84.925 398 54 6 2 396 402586148 402585754 4.690000e-107 398.0
18 TraesCS3A01G107700 chr4D 93.162 234 12 3 2 233 175134821 175135052 8.010000e-90 340.0
19 TraesCS3A01G107700 chr4D 77.376 221 21 21 1630 1830 82742840 82743051 1.140000e-18 104.0
20 TraesCS3A01G107700 chr2D 91.083 628 54 2 206 833 364780813 364781438 0.000000e+00 848.0
21 TraesCS3A01G107700 chr3D 99.024 205 0 1 2136 2340 63409723 63409521 1.320000e-97 366.0
22 TraesCS3A01G107700 chr3D 95.192 208 8 2 1698 1904 63409986 63409780 6.230000e-86 327.0
23 TraesCS3A01G107700 chr3B 98.985 197 2 0 2144 2340 103031157 103030961 1.030000e-93 353.0
24 TraesCS3A01G107700 chr3B 88.571 280 21 5 1630 1904 103031877 103031604 1.730000e-86 329.0
25 TraesCS3A01G107700 chr3B 87.143 70 7 2 1744 1811 407467402 407467471 6.930000e-11 78.7
26 TraesCS3A01G107700 chrUn 96.190 210 8 0 2 211 100755284 100755075 6.190000e-91 344.0
27 TraesCS3A01G107700 chr1A 93.162 234 15 1 1 233 287105464 287105697 2.230000e-90 342.0
28 TraesCS3A01G107700 chr6D 96.000 75 1 2 1757 1829 68076202 68076128 1.140000e-23 121.0


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 TraesCS3A01G107700 chr3A 72491790 72494129 2339 True 1948 3517 100.000 1 2340 2 chr3A.!!$R2 2339
1 TraesCS3A01G107700 chr3A 72672238 72672973 735 False 1218 1218 96.477 881 1618 1 chr3A.!!$F1 737
2 TraesCS3A01G107700 chr7D 349947042 349947749 707 False 1099 1099 94.561 881 1597 1 chr7D.!!$F3 716
3 TraesCS3A01G107700 chr7D 484547832 484548453 621 False 880 880 92.147 211 834 1 chr7D.!!$F4 623
4 TraesCS3A01G107700 chr7D 399570828 399571456 628 True 874 874 91.759 212 841 1 chr7D.!!$R1 629
5 TraesCS3A01G107700 chr7D 214831168 214831796 628 False 869 869 91.587 206 834 1 chr7D.!!$F2 628
6 TraesCS3A01G107700 chr7B 352718214 352718945 731 False 1061 1061 92.732 881 1620 1 chr7B.!!$F2 739
7 TraesCS3A01G107700 chr4D 507147990 507148614 624 False 881 881 92.185 211 834 1 chr4D.!!$F5 623
8 TraesCS3A01G107700 chr4D 498528081 498528704 623 True 874 874 92.026 212 834 1 chr4D.!!$R2 622
9 TraesCS3A01G107700 chr4D 128263085 128263710 625 False 870 870 91.733 206 834 1 chr4D.!!$F3 628
10 TraesCS3A01G107700 chr4D 128258184 128258807 623 False 867 867 91.693 209 834 1 chr4D.!!$F2 625
11 TraesCS3A01G107700 chr4D 507152843 507153466 623 False 852 852 91.256 206 834 1 chr4D.!!$F6 628
12 TraesCS3A01G107700 chr2D 364780813 364781438 625 False 848 848 91.083 206 833 1 chr2D.!!$F1 627
13 TraesCS3A01G107700 chr3B 103030961 103031877 916 True 341 353 93.778 1630 2340 2 chr3B.!!$R1 710

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
862 873 0.108186 TCAGCAAGCCCACGTCTATG 60.108 55.0 0.0 0.0 0.0 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 1780 1.176527 AATGACATTGGTGGAAGGCG 58.823 50.0 0.0 0.0 0.0 5.52 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 7.982252 AGCCATAGAGAATAAATGGATCTTCA 58.018 34.615 4.79 0.00 42.36 3.02
27 28 8.443176 AGCCATAGAGAATAAATGGATCTTCAA 58.557 33.333 4.79 0.00 42.36 2.69
28 29 8.728833 GCCATAGAGAATAAATGGATCTTCAAG 58.271 37.037 4.79 0.00 42.36 3.02
47 48 7.818493 TTCAAGAAGAAGACTGACGATAATG 57.182 36.000 0.00 0.00 0.00 1.90
48 49 6.333416 TCAAGAAGAAGACTGACGATAATGG 58.667 40.000 0.00 0.00 0.00 3.16
49 50 6.152831 TCAAGAAGAAGACTGACGATAATGGA 59.847 38.462 0.00 0.00 0.00 3.41
50 51 6.531503 AGAAGAAGACTGACGATAATGGAA 57.468 37.500 0.00 0.00 0.00 3.53
51 52 6.936279 AGAAGAAGACTGACGATAATGGAAA 58.064 36.000 0.00 0.00 0.00 3.13
52 53 7.560368 AGAAGAAGACTGACGATAATGGAAAT 58.440 34.615 0.00 0.00 0.00 2.17
53 54 7.493971 AGAAGAAGACTGACGATAATGGAAATG 59.506 37.037 0.00 0.00 0.00 2.32
54 55 6.644347 AGAAGACTGACGATAATGGAAATGT 58.356 36.000 0.00 0.00 0.00 2.71
55 56 7.106239 AGAAGACTGACGATAATGGAAATGTT 58.894 34.615 0.00 0.00 0.00 2.71
56 57 8.258007 AGAAGACTGACGATAATGGAAATGTTA 58.742 33.333 0.00 0.00 0.00 2.41
57 58 7.772332 AGACTGACGATAATGGAAATGTTAC 57.228 36.000 0.00 0.00 0.00 2.50
58 59 7.556844 AGACTGACGATAATGGAAATGTTACT 58.443 34.615 0.00 0.00 0.00 2.24
59 60 7.492669 AGACTGACGATAATGGAAATGTTACTG 59.507 37.037 0.00 0.00 0.00 2.74
60 61 7.103641 ACTGACGATAATGGAAATGTTACTGT 58.896 34.615 0.00 0.00 0.00 3.55
61 62 7.277981 ACTGACGATAATGGAAATGTTACTGTC 59.722 37.037 0.00 0.00 0.00 3.51
62 63 7.327975 TGACGATAATGGAAATGTTACTGTCT 58.672 34.615 0.00 0.00 0.00 3.41
63 64 8.471609 TGACGATAATGGAAATGTTACTGTCTA 58.528 33.333 0.00 0.00 0.00 2.59
64 65 8.644318 ACGATAATGGAAATGTTACTGTCTAC 57.356 34.615 0.00 0.00 0.00 2.59
65 66 8.255206 ACGATAATGGAAATGTTACTGTCTACA 58.745 33.333 0.00 0.00 0.00 2.74
66 67 9.093970 CGATAATGGAAATGTTACTGTCTACAA 57.906 33.333 0.64 0.00 0.00 2.41
69 70 6.554334 TGGAAATGTTACTGTCTACAAAGC 57.446 37.500 0.64 0.00 0.00 3.51
70 71 6.296026 TGGAAATGTTACTGTCTACAAAGCT 58.704 36.000 0.64 0.00 0.00 3.74
71 72 6.426937 TGGAAATGTTACTGTCTACAAAGCTC 59.573 38.462 0.00 0.00 0.00 4.09
72 73 6.401153 GGAAATGTTACTGTCTACAAAGCTCG 60.401 42.308 0.00 0.00 0.00 5.03
73 74 4.841443 TGTTACTGTCTACAAAGCTCGA 57.159 40.909 0.00 0.00 0.00 4.04
74 75 4.543692 TGTTACTGTCTACAAAGCTCGAC 58.456 43.478 0.00 0.00 0.00 4.20
75 76 4.277672 TGTTACTGTCTACAAAGCTCGACT 59.722 41.667 0.00 0.00 0.00 4.18
76 77 5.221130 GTTACTGTCTACAAAGCTCGACTT 58.779 41.667 0.00 0.00 41.70 3.01
77 78 3.643763 ACTGTCTACAAAGCTCGACTTG 58.356 45.455 0.00 0.00 39.09 3.16
78 79 3.068307 ACTGTCTACAAAGCTCGACTTGT 59.932 43.478 6.73 6.73 39.09 3.16
79 80 3.639538 TGTCTACAAAGCTCGACTTGTC 58.360 45.455 4.81 0.00 39.09 3.18
80 81 2.657372 GTCTACAAAGCTCGACTTGTCG 59.343 50.000 15.98 15.98 39.09 4.35
81 82 2.292569 TCTACAAAGCTCGACTTGTCGT 59.707 45.455 20.30 4.60 39.09 4.34
82 83 1.209128 ACAAAGCTCGACTTGTCGTG 58.791 50.000 20.30 18.75 39.09 4.35
83 84 1.202371 ACAAAGCTCGACTTGTCGTGA 60.202 47.619 23.37 6.85 39.09 4.35
84 85 1.858458 CAAAGCTCGACTTGTCGTGAA 59.142 47.619 23.37 6.23 39.09 3.18
85 86 2.218953 AAGCTCGACTTGTCGTGAAA 57.781 45.000 23.37 5.92 37.17 2.69
86 87 1.772182 AGCTCGACTTGTCGTGAAAG 58.228 50.000 23.37 14.56 0.00 2.62
87 88 0.784778 GCTCGACTTGTCGTGAAAGG 59.215 55.000 23.37 10.24 0.00 3.11
88 89 1.868519 GCTCGACTTGTCGTGAAAGGT 60.869 52.381 23.37 0.00 0.00 3.50
89 90 2.470821 CTCGACTTGTCGTGAAAGGTT 58.529 47.619 20.30 0.00 0.00 3.50
90 91 2.864343 CTCGACTTGTCGTGAAAGGTTT 59.136 45.455 20.30 0.00 0.00 3.27
91 92 3.264104 TCGACTTGTCGTGAAAGGTTTT 58.736 40.909 20.30 0.00 0.00 2.43
92 93 3.307782 TCGACTTGTCGTGAAAGGTTTTC 59.692 43.478 20.30 0.00 0.00 2.29
93 94 3.604392 GACTTGTCGTGAAAGGTTTTCG 58.396 45.455 0.00 0.00 0.00 3.46
94 95 3.264104 ACTTGTCGTGAAAGGTTTTCGA 58.736 40.909 0.00 0.00 0.00 3.71
95 96 3.063045 ACTTGTCGTGAAAGGTTTTCGAC 59.937 43.478 18.43 18.43 42.31 4.20
96 97 2.619147 TGTCGTGAAAGGTTTTCGACA 58.381 42.857 21.42 21.42 45.41 4.35
97 98 3.001414 TGTCGTGAAAGGTTTTCGACAA 58.999 40.909 22.26 13.00 45.07 3.18
98 99 3.062909 TGTCGTGAAAGGTTTTCGACAAG 59.937 43.478 22.26 2.98 45.07 3.16
99 100 3.063045 GTCGTGAAAGGTTTTCGACAAGT 59.937 43.478 19.45 0.00 41.97 3.16
100 101 3.685756 TCGTGAAAGGTTTTCGACAAGTT 59.314 39.130 0.00 0.00 0.00 2.66
101 102 4.026407 CGTGAAAGGTTTTCGACAAGTTC 58.974 43.478 0.00 0.00 0.00 3.01
102 103 4.436317 CGTGAAAGGTTTTCGACAAGTTCA 60.436 41.667 0.00 0.00 0.00 3.18
103 104 5.395642 GTGAAAGGTTTTCGACAAGTTCAA 58.604 37.500 6.59 0.00 30.55 2.69
104 105 5.511729 GTGAAAGGTTTTCGACAAGTTCAAG 59.488 40.000 6.59 0.00 30.55 3.02
105 106 4.632538 AAGGTTTTCGACAAGTTCAAGG 57.367 40.909 0.00 0.00 0.00 3.61
106 107 2.949644 AGGTTTTCGACAAGTTCAAGGG 59.050 45.455 0.00 0.00 0.00 3.95
107 108 2.034179 GGTTTTCGACAAGTTCAAGGGG 59.966 50.000 0.00 0.00 0.00 4.79
108 109 2.686405 GTTTTCGACAAGTTCAAGGGGT 59.314 45.455 0.00 0.00 0.00 4.95
109 110 2.721425 TTCGACAAGTTCAAGGGGTT 57.279 45.000 0.00 0.00 0.00 4.11
110 111 1.961793 TCGACAAGTTCAAGGGGTTG 58.038 50.000 0.00 0.00 0.00 3.77
111 112 1.487142 TCGACAAGTTCAAGGGGTTGA 59.513 47.619 0.00 0.00 0.00 3.18
112 113 1.602377 CGACAAGTTCAAGGGGTTGAC 59.398 52.381 0.00 0.00 0.00 3.18
113 114 2.745152 CGACAAGTTCAAGGGGTTGACT 60.745 50.000 0.00 0.00 0.00 3.41
114 115 3.493699 CGACAAGTTCAAGGGGTTGACTA 60.494 47.826 0.00 0.00 0.00 2.59
115 116 3.813724 GACAAGTTCAAGGGGTTGACTAC 59.186 47.826 0.00 0.00 0.00 2.73
116 117 2.806244 CAAGTTCAAGGGGTTGACTACG 59.194 50.000 0.00 0.00 0.00 3.51
117 118 2.322658 AGTTCAAGGGGTTGACTACGA 58.677 47.619 0.00 0.00 0.00 3.43
118 119 2.904434 AGTTCAAGGGGTTGACTACGAT 59.096 45.455 0.00 0.00 0.00 3.73
119 120 3.000727 GTTCAAGGGGTTGACTACGATG 58.999 50.000 0.00 0.00 0.00 3.84
120 121 2.531771 TCAAGGGGTTGACTACGATGA 58.468 47.619 0.00 0.00 0.00 2.92
121 122 2.496070 TCAAGGGGTTGACTACGATGAG 59.504 50.000 0.00 0.00 0.00 2.90
122 123 2.496070 CAAGGGGTTGACTACGATGAGA 59.504 50.000 0.00 0.00 0.00 3.27
123 124 2.100989 AGGGGTTGACTACGATGAGAC 58.899 52.381 0.00 0.00 0.00 3.36
124 125 2.100989 GGGGTTGACTACGATGAGACT 58.899 52.381 0.00 0.00 0.00 3.24
125 126 2.496470 GGGGTTGACTACGATGAGACTT 59.504 50.000 0.00 0.00 0.00 3.01
126 127 3.056035 GGGGTTGACTACGATGAGACTTT 60.056 47.826 0.00 0.00 0.00 2.66
127 128 4.174762 GGGTTGACTACGATGAGACTTTC 58.825 47.826 0.00 0.00 0.00 2.62
128 129 4.082136 GGGTTGACTACGATGAGACTTTCT 60.082 45.833 0.00 0.00 0.00 2.52
129 130 5.096849 GGTTGACTACGATGAGACTTTCTC 58.903 45.833 0.00 0.00 43.65 2.87
139 140 2.776330 GAGACTTTCTCACTCGTAGCG 58.224 52.381 0.00 0.00 42.90 4.26
140 141 2.415857 GAGACTTTCTCACTCGTAGCGA 59.584 50.000 0.00 0.00 42.90 4.93
141 142 3.011119 AGACTTTCTCACTCGTAGCGAT 58.989 45.455 0.00 0.00 34.61 4.58
142 143 3.102276 GACTTTCTCACTCGTAGCGATG 58.898 50.000 0.00 0.00 34.61 3.84
143 144 1.849219 CTTTCTCACTCGTAGCGATGC 59.151 52.381 0.00 0.00 34.61 3.91
144 145 1.095600 TTCTCACTCGTAGCGATGCT 58.904 50.000 0.00 0.00 43.41 3.79
145 146 1.095600 TCTCACTCGTAGCGATGCTT 58.904 50.000 0.00 0.00 40.44 3.91
146 147 2.285977 TCTCACTCGTAGCGATGCTTA 58.714 47.619 0.00 0.00 40.44 3.09
147 148 2.681344 TCTCACTCGTAGCGATGCTTAA 59.319 45.455 0.00 0.00 40.44 1.85
148 149 3.039405 CTCACTCGTAGCGATGCTTAAG 58.961 50.000 0.00 0.00 40.44 1.85
149 150 2.422479 TCACTCGTAGCGATGCTTAAGT 59.578 45.455 4.02 0.00 40.44 2.24
150 151 2.784380 CACTCGTAGCGATGCTTAAGTC 59.216 50.000 4.02 0.00 40.44 3.01
151 152 2.683867 ACTCGTAGCGATGCTTAAGTCT 59.316 45.455 4.02 0.00 40.44 3.24
152 153 3.039405 CTCGTAGCGATGCTTAAGTCTG 58.961 50.000 4.02 0.00 40.44 3.51
153 154 2.422479 TCGTAGCGATGCTTAAGTCTGT 59.578 45.455 4.02 0.00 40.44 3.41
154 155 2.784380 CGTAGCGATGCTTAAGTCTGTC 59.216 50.000 4.02 0.00 40.44 3.51
155 156 3.487711 CGTAGCGATGCTTAAGTCTGTCT 60.488 47.826 4.02 0.00 40.44 3.41
156 157 2.886081 AGCGATGCTTAAGTCTGTCTG 58.114 47.619 4.02 0.00 33.89 3.51
157 158 2.493675 AGCGATGCTTAAGTCTGTCTGA 59.506 45.455 4.02 0.00 33.89 3.27
158 159 3.056536 AGCGATGCTTAAGTCTGTCTGAA 60.057 43.478 4.02 0.00 33.89 3.02
159 160 3.868077 GCGATGCTTAAGTCTGTCTGAAT 59.132 43.478 4.02 0.00 0.00 2.57
160 161 4.026145 GCGATGCTTAAGTCTGTCTGAATC 60.026 45.833 4.02 0.00 0.00 2.52
161 162 5.105063 CGATGCTTAAGTCTGTCTGAATCA 58.895 41.667 4.02 0.00 0.00 2.57
162 163 5.752472 CGATGCTTAAGTCTGTCTGAATCAT 59.248 40.000 4.02 0.00 29.05 2.45
163 164 6.292221 CGATGCTTAAGTCTGTCTGAATCATG 60.292 42.308 4.02 0.00 27.21 3.07
164 165 5.798132 TGCTTAAGTCTGTCTGAATCATGT 58.202 37.500 4.02 0.00 0.00 3.21
165 166 6.233434 TGCTTAAGTCTGTCTGAATCATGTT 58.767 36.000 4.02 0.00 0.00 2.71
166 167 7.386059 TGCTTAAGTCTGTCTGAATCATGTTA 58.614 34.615 4.02 0.00 0.00 2.41
167 168 7.547019 TGCTTAAGTCTGTCTGAATCATGTTAG 59.453 37.037 4.02 0.00 0.00 2.34
168 169 7.465245 GCTTAAGTCTGTCTGAATCATGTTAGC 60.465 40.741 4.02 0.00 0.00 3.09
169 170 5.411831 AGTCTGTCTGAATCATGTTAGCA 57.588 39.130 0.00 0.00 0.00 3.49
170 171 5.798132 AGTCTGTCTGAATCATGTTAGCAA 58.202 37.500 0.00 0.00 0.00 3.91
171 172 6.413052 AGTCTGTCTGAATCATGTTAGCAAT 58.587 36.000 0.00 0.00 0.00 3.56
172 173 6.883217 AGTCTGTCTGAATCATGTTAGCAATT 59.117 34.615 0.00 0.00 0.00 2.32
173 174 6.965500 GTCTGTCTGAATCATGTTAGCAATTG 59.035 38.462 0.00 0.00 0.00 2.32
174 175 5.643664 TGTCTGAATCATGTTAGCAATTGC 58.356 37.500 23.05 23.05 42.49 3.56
199 200 9.872757 GCTGCATTTTATGATTATGAAATTTGG 57.127 29.630 0.00 0.00 32.15 3.28
200 201 9.872757 CTGCATTTTATGATTATGAAATTTGGC 57.127 29.630 0.00 1.15 32.15 4.52
201 202 9.392259 TGCATTTTATGATTATGAAATTTGGCA 57.608 25.926 0.00 6.94 32.15 4.92
412 416 6.334202 AGTCCAAATGCAACGAAACTTTTTA 58.666 32.000 0.00 0.00 0.00 1.52
581 588 5.979288 TCTTCGCTCTATAAATACCTCCC 57.021 43.478 0.00 0.00 0.00 4.30
582 589 5.391256 TCTTCGCTCTATAAATACCTCCCA 58.609 41.667 0.00 0.00 0.00 4.37
616 623 2.381725 AGGGGAGTCGACGAAATTTC 57.618 50.000 10.46 8.20 0.00 2.17
636 643 4.947147 TCCAGCCGCCGCAAGTTT 62.947 61.111 0.00 0.00 37.52 2.66
661 668 6.612863 TCAGAACCATGAGATCCAATCTAGAA 59.387 38.462 0.00 0.00 40.38 2.10
701 708 0.830648 GGAGGGGAACACGATCATGA 59.169 55.000 0.00 0.00 0.00 3.07
722 729 4.017222 TGAAGGGGTTCATCATCCTCATTT 60.017 41.667 0.00 0.00 0.00 2.32
733 740 1.361204 TCCTCATTTGTGCCTCTCCA 58.639 50.000 0.00 0.00 0.00 3.86
736 743 2.686915 CCTCATTTGTGCCTCTCCAATC 59.313 50.000 0.00 0.00 0.00 2.67
834 845 2.248248 ACAACGGTCTCTTGGAGATCA 58.752 47.619 8.29 0.00 39.57 2.92
835 846 2.028930 ACAACGGTCTCTTGGAGATCAC 60.029 50.000 8.29 0.00 39.57 3.06
836 847 1.924731 ACGGTCTCTTGGAGATCACA 58.075 50.000 8.29 0.00 39.57 3.58
838 849 2.167281 ACGGTCTCTTGGAGATCACATG 59.833 50.000 8.29 0.00 39.57 3.21
839 850 2.167281 CGGTCTCTTGGAGATCACATGT 59.833 50.000 8.29 0.00 39.57 3.21
840 851 3.529533 GGTCTCTTGGAGATCACATGTG 58.470 50.000 20.18 20.18 40.98 3.21
841 852 2.935201 GTCTCTTGGAGATCACATGTGC 59.065 50.000 21.38 8.16 40.98 4.57
842 853 2.093288 TCTCTTGGAGATCACATGTGCC 60.093 50.000 21.38 16.10 33.35 5.01
843 854 1.911357 TCTTGGAGATCACATGTGCCT 59.089 47.619 21.38 18.79 0.00 4.75
844 855 2.093288 TCTTGGAGATCACATGTGCCTC 60.093 50.000 26.44 26.44 32.89 4.70
845 856 1.278537 TGGAGATCACATGTGCCTCA 58.721 50.000 30.94 21.35 34.23 3.86
846 857 1.208776 TGGAGATCACATGTGCCTCAG 59.791 52.381 30.94 10.25 34.23 3.35
847 858 1.297664 GAGATCACATGTGCCTCAGC 58.702 55.000 28.04 14.85 40.48 4.26
858 869 2.743928 CCTCAGCAAGCCCACGTC 60.744 66.667 0.00 0.00 0.00 4.34
859 870 2.345244 CTCAGCAAGCCCACGTCT 59.655 61.111 0.00 0.00 0.00 4.18
860 871 1.591703 CTCAGCAAGCCCACGTCTA 59.408 57.895 0.00 0.00 0.00 2.59
861 872 0.176680 CTCAGCAAGCCCACGTCTAT 59.823 55.000 0.00 0.00 0.00 1.98
862 873 0.108186 TCAGCAAGCCCACGTCTATG 60.108 55.000 0.00 0.00 0.00 2.23
863 874 0.391661 CAGCAAGCCCACGTCTATGT 60.392 55.000 0.00 0.00 0.00 2.29
864 875 0.324943 AGCAAGCCCACGTCTATGTT 59.675 50.000 0.00 0.00 0.00 2.71
865 876 1.165270 GCAAGCCCACGTCTATGTTT 58.835 50.000 0.00 0.00 0.00 2.83
866 877 2.027561 AGCAAGCCCACGTCTATGTTTA 60.028 45.455 0.00 0.00 0.00 2.01
867 878 2.351726 GCAAGCCCACGTCTATGTTTAG 59.648 50.000 0.00 0.00 0.00 1.85
868 879 3.596214 CAAGCCCACGTCTATGTTTAGT 58.404 45.455 0.00 0.00 0.00 2.24
869 880 3.975168 AGCCCACGTCTATGTTTAGTT 57.025 42.857 0.00 0.00 0.00 2.24
870 881 3.596214 AGCCCACGTCTATGTTTAGTTG 58.404 45.455 0.00 0.00 0.00 3.16
871 882 2.095372 GCCCACGTCTATGTTTAGTTGC 59.905 50.000 0.00 0.00 0.00 4.17
872 883 3.596214 CCCACGTCTATGTTTAGTTGCT 58.404 45.455 0.00 0.00 0.00 3.91
873 884 3.370978 CCCACGTCTATGTTTAGTTGCTG 59.629 47.826 0.00 0.00 0.00 4.41
874 885 4.242475 CCACGTCTATGTTTAGTTGCTGA 58.758 43.478 0.00 0.00 0.00 4.26
875 886 4.091509 CCACGTCTATGTTTAGTTGCTGAC 59.908 45.833 0.00 0.00 0.00 3.51
876 887 4.923871 CACGTCTATGTTTAGTTGCTGACT 59.076 41.667 0.00 0.00 42.55 3.41
877 888 6.090783 CACGTCTATGTTTAGTTGCTGACTA 58.909 40.000 0.00 0.00 39.86 2.59
878 889 6.033619 CACGTCTATGTTTAGTTGCTGACTAC 59.966 42.308 0.00 0.00 40.51 2.73
879 890 6.072064 ACGTCTATGTTTAGTTGCTGACTACT 60.072 38.462 0.79 0.00 40.51 2.57
952 964 6.545504 TGTTGACTACTCTCTTGATTTTGC 57.454 37.500 0.00 0.00 0.00 3.68
1063 1075 4.102649 CGTCAACGAGTACATTGATGCTA 58.897 43.478 11.51 0.00 43.02 3.49
1089 1101 1.620819 AGGCACGTTCTTCTCAGACAT 59.379 47.619 0.00 0.00 0.00 3.06
1099 1111 6.555315 GTTCTTCTCAGACATGTTTGTTTGT 58.445 36.000 15.36 0.00 38.68 2.83
1128 1140 6.151663 TGCTTACTTAACCTTGTTTTTCCC 57.848 37.500 0.00 0.00 0.00 3.97
1129 1141 5.217393 GCTTACTTAACCTTGTTTTTCCCG 58.783 41.667 0.00 0.00 0.00 5.14
1281 1293 3.009115 CGTCACCATCCACCCCCT 61.009 66.667 0.00 0.00 0.00 4.79
1294 1306 1.319799 CCCCCTGAAGGAGGAGGAT 59.680 63.158 0.00 0.00 42.78 3.24
1332 1344 4.390264 GCTTTGGTTGAGGTCTAAAGTCT 58.610 43.478 0.00 0.00 36.33 3.24
1421 1433 2.240500 CGAGGGCTATGCAACGCTC 61.241 63.158 16.87 16.87 41.16 5.03
1457 1469 9.607988 CCTTACCTTTTAATGGACAAAAGTTTT 57.392 29.630 3.80 0.00 40.03 2.43
1544 1557 4.080638 TGCCAGAAACCTTTGTTTGGATTT 60.081 37.500 0.00 0.00 44.57 2.17
1565 1578 2.185004 TTCTGCCCAGCTAGTTTGTC 57.815 50.000 0.00 0.00 0.00 3.18
1573 1587 1.996191 CAGCTAGTTTGTCGCTCTTCC 59.004 52.381 0.00 0.00 0.00 3.46
1590 1604 0.741915 TCCGTTTGTGCCACCTTTTC 59.258 50.000 0.00 0.00 0.00 2.29
1618 1632 7.862648 TGTTTGTTATGTGTTCTTATGCGTTA 58.137 30.769 0.00 0.00 0.00 3.18
1619 1633 8.508062 TGTTTGTTATGTGTTCTTATGCGTTAT 58.492 29.630 0.00 0.00 0.00 1.89
1620 1634 8.995906 GTTTGTTATGTGTTCTTATGCGTTATC 58.004 33.333 0.00 0.00 0.00 1.75
1621 1635 8.487313 TTGTTATGTGTTCTTATGCGTTATCT 57.513 30.769 0.00 0.00 0.00 1.98
1622 1636 7.905126 TGTTATGTGTTCTTATGCGTTATCTG 58.095 34.615 0.00 0.00 0.00 2.90
1623 1637 7.762159 TGTTATGTGTTCTTATGCGTTATCTGA 59.238 33.333 0.00 0.00 0.00 3.27
1624 1638 6.589830 ATGTGTTCTTATGCGTTATCTGAC 57.410 37.500 0.00 0.00 0.00 3.51
1625 1639 5.474825 TGTGTTCTTATGCGTTATCTGACA 58.525 37.500 0.00 0.00 0.00 3.58
1626 1640 5.929415 TGTGTTCTTATGCGTTATCTGACAA 59.071 36.000 0.00 0.00 0.00 3.18
1627 1641 6.090763 TGTGTTCTTATGCGTTATCTGACAAG 59.909 38.462 0.00 0.00 0.00 3.16
1628 1642 5.063438 TGTTCTTATGCGTTATCTGACAAGC 59.937 40.000 0.00 0.00 0.00 4.01
1638 1652 6.530534 GCGTTATCTGACAAGCTACTTTAAGA 59.469 38.462 0.00 0.00 0.00 2.10
1663 1677 9.823098 GAAATGTTTGTTATGCATGCAAAATTA 57.177 25.926 26.68 9.76 34.47 1.40
1687 1701 2.866198 TGCATGACGAAATCACATTGC 58.134 42.857 0.00 0.00 41.24 3.56
1693 1707 5.180367 TGACGAAATCACATTGCTGAAAA 57.820 34.783 0.00 0.00 29.99 2.29
1694 1708 4.975502 TGACGAAATCACATTGCTGAAAAC 59.024 37.500 0.00 0.00 29.99 2.43
1708 1722 3.516615 CTGAAAACCGTGGCAAGAAAAA 58.483 40.909 0.76 0.00 0.00 1.94
1756 1770 8.662141 GCATTTGAATGTAAGCATCAATTTTCT 58.338 29.630 5.68 0.00 38.65 2.52
1829 1846 8.119226 TGCACAACAAACATTTTTAAAGTATGC 58.881 29.630 10.59 7.53 0.00 3.14
1889 1908 4.878397 AGCATATGAGCTCAGGTGTAAAAC 59.122 41.667 22.96 9.44 42.18 2.43
1891 1910 5.007136 GCATATGAGCTCAGGTGTAAAACTC 59.993 44.000 22.96 5.03 0.00 3.01
1899 1918 2.800544 CAGGTGTAAAACTCCACGTCTG 59.199 50.000 0.00 0.00 34.35 3.51
2237 2463 4.558697 GCTCGAACCCAAAACTTAGCATTT 60.559 41.667 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.099537 TGAAGATCCATTTATTCTCTATGGCTC 58.900 37.037 0.00 0.00 38.93 4.70
1 2 7.982252 TGAAGATCCATTTATTCTCTATGGCT 58.018 34.615 0.00 0.00 38.93 4.75
2 3 8.627208 TTGAAGATCCATTTATTCTCTATGGC 57.373 34.615 0.00 0.00 38.93 4.40
23 24 6.813649 CCATTATCGTCAGTCTTCTTCTTGAA 59.186 38.462 0.00 0.00 0.00 2.69
24 25 6.152831 TCCATTATCGTCAGTCTTCTTCTTGA 59.847 38.462 0.00 0.00 0.00 3.02
25 26 6.333416 TCCATTATCGTCAGTCTTCTTCTTG 58.667 40.000 0.00 0.00 0.00 3.02
26 27 6.531503 TCCATTATCGTCAGTCTTCTTCTT 57.468 37.500 0.00 0.00 0.00 2.52
27 28 6.531503 TTCCATTATCGTCAGTCTTCTTCT 57.468 37.500 0.00 0.00 0.00 2.85
28 29 7.278868 ACATTTCCATTATCGTCAGTCTTCTTC 59.721 37.037 0.00 0.00 0.00 2.87
29 30 7.106239 ACATTTCCATTATCGTCAGTCTTCTT 58.894 34.615 0.00 0.00 0.00 2.52
30 31 6.644347 ACATTTCCATTATCGTCAGTCTTCT 58.356 36.000 0.00 0.00 0.00 2.85
31 32 6.910536 ACATTTCCATTATCGTCAGTCTTC 57.089 37.500 0.00 0.00 0.00 2.87
32 33 8.041323 AGTAACATTTCCATTATCGTCAGTCTT 58.959 33.333 0.00 0.00 0.00 3.01
33 34 7.492669 CAGTAACATTTCCATTATCGTCAGTCT 59.507 37.037 0.00 0.00 0.00 3.24
34 35 7.277981 ACAGTAACATTTCCATTATCGTCAGTC 59.722 37.037 0.00 0.00 0.00 3.51
35 36 7.103641 ACAGTAACATTTCCATTATCGTCAGT 58.896 34.615 0.00 0.00 0.00 3.41
36 37 7.492669 AGACAGTAACATTTCCATTATCGTCAG 59.507 37.037 0.00 0.00 0.00 3.51
37 38 7.327975 AGACAGTAACATTTCCATTATCGTCA 58.672 34.615 0.00 0.00 0.00 4.35
38 39 7.772332 AGACAGTAACATTTCCATTATCGTC 57.228 36.000 0.00 0.00 0.00 4.20
39 40 8.255206 TGTAGACAGTAACATTTCCATTATCGT 58.745 33.333 0.00 0.00 0.00 3.73
40 41 8.642908 TGTAGACAGTAACATTTCCATTATCG 57.357 34.615 0.00 0.00 0.00 2.92
43 44 8.726988 GCTTTGTAGACAGTAACATTTCCATTA 58.273 33.333 0.00 0.00 0.00 1.90
44 45 7.448469 AGCTTTGTAGACAGTAACATTTCCATT 59.552 33.333 0.00 0.00 0.00 3.16
45 46 6.942576 AGCTTTGTAGACAGTAACATTTCCAT 59.057 34.615 0.00 0.00 0.00 3.41
46 47 6.296026 AGCTTTGTAGACAGTAACATTTCCA 58.704 36.000 0.00 0.00 0.00 3.53
47 48 6.401153 CGAGCTTTGTAGACAGTAACATTTCC 60.401 42.308 0.00 0.00 0.00 3.13
48 49 6.365247 TCGAGCTTTGTAGACAGTAACATTTC 59.635 38.462 0.00 0.00 0.00 2.17
49 50 6.145696 GTCGAGCTTTGTAGACAGTAACATTT 59.854 38.462 0.00 0.00 34.09 2.32
50 51 5.634020 GTCGAGCTTTGTAGACAGTAACATT 59.366 40.000 0.00 0.00 34.09 2.71
51 52 5.047943 AGTCGAGCTTTGTAGACAGTAACAT 60.048 40.000 0.00 0.00 36.18 2.71
52 53 4.277672 AGTCGAGCTTTGTAGACAGTAACA 59.722 41.667 0.00 0.00 36.18 2.41
53 54 4.796369 AGTCGAGCTTTGTAGACAGTAAC 58.204 43.478 0.00 0.00 36.18 2.50
54 55 5.220381 CAAGTCGAGCTTTGTAGACAGTAA 58.780 41.667 0.00 0.00 34.69 2.24
55 56 4.277672 ACAAGTCGAGCTTTGTAGACAGTA 59.722 41.667 7.81 0.00 34.69 2.74
56 57 3.068307 ACAAGTCGAGCTTTGTAGACAGT 59.932 43.478 7.81 1.29 34.69 3.55
57 58 3.643763 ACAAGTCGAGCTTTGTAGACAG 58.356 45.455 7.81 0.79 34.69 3.51
58 59 3.639538 GACAAGTCGAGCTTTGTAGACA 58.360 45.455 9.18 0.00 34.69 3.41
72 73 3.307782 TCGAAAACCTTTCACGACAAGTC 59.692 43.478 0.00 0.00 0.00 3.01
73 74 3.063045 GTCGAAAACCTTTCACGACAAGT 59.937 43.478 17.53 0.00 42.93 3.16
74 75 3.062909 TGTCGAAAACCTTTCACGACAAG 59.937 43.478 20.40 0.00 46.05 3.16
75 76 3.001414 TGTCGAAAACCTTTCACGACAA 58.999 40.909 20.40 11.05 46.05 3.18
76 77 2.619147 TGTCGAAAACCTTTCACGACA 58.381 42.857 19.53 19.53 46.41 4.35
77 78 3.063045 ACTTGTCGAAAACCTTTCACGAC 59.937 43.478 16.47 16.47 43.29 4.34
78 79 3.264104 ACTTGTCGAAAACCTTTCACGA 58.736 40.909 0.00 0.00 0.00 4.35
79 80 3.668596 ACTTGTCGAAAACCTTTCACG 57.331 42.857 0.00 0.00 0.00 4.35
80 81 4.976987 TGAACTTGTCGAAAACCTTTCAC 58.023 39.130 0.00 0.00 0.00 3.18
81 82 5.392595 CCTTGAACTTGTCGAAAACCTTTCA 60.393 40.000 0.00 0.00 0.00 2.69
82 83 5.034797 CCTTGAACTTGTCGAAAACCTTTC 58.965 41.667 0.00 0.00 0.00 2.62
83 84 4.142249 CCCTTGAACTTGTCGAAAACCTTT 60.142 41.667 0.00 0.00 0.00 3.11
84 85 3.380320 CCCTTGAACTTGTCGAAAACCTT 59.620 43.478 0.00 0.00 0.00 3.50
85 86 2.949644 CCCTTGAACTTGTCGAAAACCT 59.050 45.455 0.00 0.00 0.00 3.50
86 87 2.034179 CCCCTTGAACTTGTCGAAAACC 59.966 50.000 0.00 0.00 0.00 3.27
87 88 2.686405 ACCCCTTGAACTTGTCGAAAAC 59.314 45.455 0.00 0.00 0.00 2.43
88 89 3.007473 ACCCCTTGAACTTGTCGAAAA 57.993 42.857 0.00 0.00 0.00 2.29
89 90 2.685897 CAACCCCTTGAACTTGTCGAAA 59.314 45.455 0.00 0.00 0.00 3.46
90 91 2.092861 TCAACCCCTTGAACTTGTCGAA 60.093 45.455 0.00 0.00 33.20 3.71
91 92 1.487142 TCAACCCCTTGAACTTGTCGA 59.513 47.619 0.00 0.00 33.20 4.20
92 93 1.602377 GTCAACCCCTTGAACTTGTCG 59.398 52.381 0.00 0.00 38.17 4.35
93 94 2.932261 AGTCAACCCCTTGAACTTGTC 58.068 47.619 0.00 0.00 38.17 3.18
94 95 3.743269 CGTAGTCAACCCCTTGAACTTGT 60.743 47.826 0.00 0.00 38.17 3.16
95 96 2.806244 CGTAGTCAACCCCTTGAACTTG 59.194 50.000 0.00 0.00 38.17 3.16
96 97 2.701951 TCGTAGTCAACCCCTTGAACTT 59.298 45.455 0.00 0.00 38.17 2.66
97 98 2.322658 TCGTAGTCAACCCCTTGAACT 58.677 47.619 0.00 0.00 38.17 3.01
98 99 2.825861 TCGTAGTCAACCCCTTGAAC 57.174 50.000 0.00 0.00 38.17 3.18
99 100 2.901192 TCATCGTAGTCAACCCCTTGAA 59.099 45.455 0.00 0.00 38.17 2.69
100 101 2.496070 CTCATCGTAGTCAACCCCTTGA 59.504 50.000 0.00 0.00 33.76 3.02
101 102 2.496070 TCTCATCGTAGTCAACCCCTTG 59.504 50.000 0.00 0.00 0.00 3.61
102 103 2.496470 GTCTCATCGTAGTCAACCCCTT 59.504 50.000 0.00 0.00 0.00 3.95
103 104 2.100989 GTCTCATCGTAGTCAACCCCT 58.899 52.381 0.00 0.00 0.00 4.79
104 105 2.100989 AGTCTCATCGTAGTCAACCCC 58.899 52.381 0.00 0.00 0.00 4.95
105 106 3.870633 AAGTCTCATCGTAGTCAACCC 57.129 47.619 0.00 0.00 0.00 4.11
106 107 5.061920 AGAAAGTCTCATCGTAGTCAACC 57.938 43.478 0.00 0.00 0.00 3.77
116 117 8.369869 ATCGCTACGAGTGAGAAAGTCTCATC 62.370 46.154 10.94 8.70 45.44 2.92
117 118 6.657790 ATCGCTACGAGTGAGAAAGTCTCAT 61.658 44.000 10.94 1.48 45.44 2.90
118 119 5.394710 ATCGCTACGAGTGAGAAAGTCTCA 61.395 45.833 3.83 3.83 44.43 3.27
119 120 2.415857 TCGCTACGAGTGAGAAAGTCTC 59.584 50.000 0.00 0.00 43.65 3.36
120 121 2.424557 TCGCTACGAGTGAGAAAGTCT 58.575 47.619 0.00 0.00 30.20 3.24
121 122 2.896243 TCGCTACGAGTGAGAAAGTC 57.104 50.000 0.00 0.00 30.20 3.01
122 123 2.732597 GCATCGCTACGAGTGAGAAAGT 60.733 50.000 0.00 0.00 38.24 2.66
123 124 1.849219 GCATCGCTACGAGTGAGAAAG 59.151 52.381 0.00 0.00 38.24 2.62
124 125 1.472878 AGCATCGCTACGAGTGAGAAA 59.527 47.619 0.00 0.00 38.24 2.52
125 126 1.095600 AGCATCGCTACGAGTGAGAA 58.904 50.000 0.00 0.00 38.24 2.87
126 127 1.095600 AAGCATCGCTACGAGTGAGA 58.904 50.000 0.00 0.00 38.24 3.27
127 128 2.757686 TAAGCATCGCTACGAGTGAG 57.242 50.000 0.00 0.00 38.24 3.51
128 129 2.422479 ACTTAAGCATCGCTACGAGTGA 59.578 45.455 1.29 0.00 38.25 3.41
129 130 2.784380 GACTTAAGCATCGCTACGAGTG 59.216 50.000 1.29 0.00 38.25 3.51
130 131 2.683867 AGACTTAAGCATCGCTACGAGT 59.316 45.455 1.29 0.00 38.25 4.18
131 132 3.039405 CAGACTTAAGCATCGCTACGAG 58.961 50.000 1.29 0.00 38.25 4.18
132 133 2.422479 ACAGACTTAAGCATCGCTACGA 59.578 45.455 1.29 0.00 38.25 3.43
133 134 2.784380 GACAGACTTAAGCATCGCTACG 59.216 50.000 1.29 0.00 38.25 3.51
134 135 3.794028 CAGACAGACTTAAGCATCGCTAC 59.206 47.826 1.29 0.00 38.25 3.58
135 136 3.694566 TCAGACAGACTTAAGCATCGCTA 59.305 43.478 1.29 0.00 38.25 4.26
136 137 2.493675 TCAGACAGACTTAAGCATCGCT 59.506 45.455 1.29 0.00 42.56 4.93
137 138 2.881074 TCAGACAGACTTAAGCATCGC 58.119 47.619 1.29 0.00 0.00 4.58
138 139 5.105063 TGATTCAGACAGACTTAAGCATCG 58.895 41.667 1.29 0.00 0.00 3.84
139 140 6.538021 ACATGATTCAGACAGACTTAAGCATC 59.462 38.462 0.00 0.00 36.92 3.91
140 141 6.413052 ACATGATTCAGACAGACTTAAGCAT 58.587 36.000 0.00 0.00 38.73 3.79
141 142 5.798132 ACATGATTCAGACAGACTTAAGCA 58.202 37.500 0.00 0.00 33.65 3.91
142 143 6.734104 AACATGATTCAGACAGACTTAAGC 57.266 37.500 0.00 0.00 0.00 3.09
143 144 7.547019 TGCTAACATGATTCAGACAGACTTAAG 59.453 37.037 0.00 0.00 0.00 1.85
144 145 7.386059 TGCTAACATGATTCAGACAGACTTAA 58.614 34.615 0.00 0.00 0.00 1.85
145 146 6.935167 TGCTAACATGATTCAGACAGACTTA 58.065 36.000 0.00 0.00 0.00 2.24
146 147 5.798132 TGCTAACATGATTCAGACAGACTT 58.202 37.500 0.00 0.00 0.00 3.01
147 148 5.411831 TGCTAACATGATTCAGACAGACT 57.588 39.130 0.00 0.00 0.00 3.24
148 149 6.674694 ATTGCTAACATGATTCAGACAGAC 57.325 37.500 0.00 0.00 0.00 3.51
149 150 6.403964 GCAATTGCTAACATGATTCAGACAGA 60.404 38.462 23.21 0.00 38.21 3.41
150 151 5.742453 GCAATTGCTAACATGATTCAGACAG 59.258 40.000 23.21 0.00 38.21 3.51
151 152 5.643664 GCAATTGCTAACATGATTCAGACA 58.356 37.500 23.21 0.00 38.21 3.41
173 174 9.872757 CCAAATTTCATAATCATAAAATGCAGC 57.127 29.630 0.00 0.00 0.00 5.25
174 175 9.872757 GCCAAATTTCATAATCATAAAATGCAG 57.127 29.630 0.00 0.00 0.00 4.41
175 176 9.392259 TGCCAAATTTCATAATCATAAAATGCA 57.608 25.926 0.00 0.00 0.00 3.96
182 183 9.545105 GTCCATTTGCCAAATTTCATAATCATA 57.455 29.630 0.00 0.00 0.00 2.15
183 184 7.225145 CGTCCATTTGCCAAATTTCATAATCAT 59.775 33.333 0.00 0.00 0.00 2.45
184 185 6.534436 CGTCCATTTGCCAAATTTCATAATCA 59.466 34.615 0.00 0.00 0.00 2.57
185 186 6.534793 ACGTCCATTTGCCAAATTTCATAATC 59.465 34.615 0.00 0.00 0.00 1.75
186 187 6.405538 ACGTCCATTTGCCAAATTTCATAAT 58.594 32.000 0.00 0.00 0.00 1.28
187 188 5.788450 ACGTCCATTTGCCAAATTTCATAA 58.212 33.333 0.00 0.00 0.00 1.90
188 189 5.398603 ACGTCCATTTGCCAAATTTCATA 57.601 34.783 0.00 0.00 0.00 2.15
189 190 4.270245 ACGTCCATTTGCCAAATTTCAT 57.730 36.364 0.00 0.00 0.00 2.57
190 191 3.742433 ACGTCCATTTGCCAAATTTCA 57.258 38.095 0.00 0.00 0.00 2.69
191 192 4.054671 TCAACGTCCATTTGCCAAATTTC 58.945 39.130 0.00 0.00 0.00 2.17
192 193 4.065321 TCAACGTCCATTTGCCAAATTT 57.935 36.364 0.00 0.00 0.00 1.82
193 194 3.742433 TCAACGTCCATTTGCCAAATT 57.258 38.095 0.00 0.00 0.00 1.82
194 195 3.959535 ATCAACGTCCATTTGCCAAAT 57.040 38.095 0.00 0.00 0.00 2.32
195 196 4.219507 ACATATCAACGTCCATTTGCCAAA 59.780 37.500 0.00 0.00 0.00 3.28
196 197 3.761218 ACATATCAACGTCCATTTGCCAA 59.239 39.130 0.00 0.00 0.00 4.52
197 198 3.351740 ACATATCAACGTCCATTTGCCA 58.648 40.909 0.00 0.00 0.00 4.92
198 199 3.627577 AGACATATCAACGTCCATTTGCC 59.372 43.478 0.00 0.00 32.33 4.52
199 200 4.260784 GGAGACATATCAACGTCCATTTGC 60.261 45.833 0.00 0.00 32.33 3.68
200 201 4.875536 TGGAGACATATCAACGTCCATTTG 59.124 41.667 0.00 0.00 33.40 2.32
201 202 5.097742 TGGAGACATATCAACGTCCATTT 57.902 39.130 0.00 0.00 33.40 2.32
202 203 4.753516 TGGAGACATATCAACGTCCATT 57.246 40.909 0.00 0.00 33.40 3.16
203 204 4.442706 GTTGGAGACATATCAACGTCCAT 58.557 43.478 0.00 0.00 42.32 3.41
204 205 3.857052 GTTGGAGACATATCAACGTCCA 58.143 45.455 0.00 0.00 42.32 4.02
558 565 5.836898 TGGGAGGTATTTATAGAGCGAAGAA 59.163 40.000 0.00 0.00 0.00 2.52
581 588 0.543749 CCCTAGGGTTTCTGGAGCTG 59.456 60.000 20.88 0.00 0.00 4.24
582 589 0.621862 CCCCTAGGGTTTCTGGAGCT 60.622 60.000 26.66 0.00 38.25 4.09
616 623 4.183686 CTTGCGGCGGCTGGAATG 62.184 66.667 16.28 7.09 40.82 2.67
636 643 6.138967 TCTAGATTGGATCTCATGGTTCTGA 58.861 40.000 0.00 0.00 40.76 3.27
661 668 0.543749 GCAGAGTGCTGGAATAGGGT 59.456 55.000 0.00 0.00 42.53 4.34
701 708 4.264532 ACAAATGAGGATGATGAACCCCTT 60.265 41.667 0.00 0.00 0.00 3.95
722 729 0.328926 TGCATGATTGGAGAGGCACA 59.671 50.000 0.00 0.00 0.00 4.57
733 740 6.674694 GAGTTGAACTACTCATGCATGATT 57.325 37.500 28.81 24.88 43.23 2.57
841 852 1.888436 TAGACGTGGGCTTGCTGAGG 61.888 60.000 0.00 0.00 0.00 3.86
842 853 0.176680 ATAGACGTGGGCTTGCTGAG 59.823 55.000 0.00 0.00 0.00 3.35
843 854 0.108186 CATAGACGTGGGCTTGCTGA 60.108 55.000 0.00 0.00 0.00 4.26
844 855 0.391661 ACATAGACGTGGGCTTGCTG 60.392 55.000 0.00 0.00 0.00 4.41
845 856 0.324943 AACATAGACGTGGGCTTGCT 59.675 50.000 0.00 0.00 0.00 3.91
846 857 1.165270 AAACATAGACGTGGGCTTGC 58.835 50.000 0.00 0.00 0.00 4.01
847 858 3.596214 ACTAAACATAGACGTGGGCTTG 58.404 45.455 0.00 0.00 0.00 4.01
848 859 3.975168 ACTAAACATAGACGTGGGCTT 57.025 42.857 0.00 0.00 0.00 4.35
849 860 3.596214 CAACTAAACATAGACGTGGGCT 58.404 45.455 0.00 0.00 0.00 5.19
850 861 2.095372 GCAACTAAACATAGACGTGGGC 59.905 50.000 0.00 0.00 0.00 5.36
851 862 3.370978 CAGCAACTAAACATAGACGTGGG 59.629 47.826 0.00 0.00 0.00 4.61
852 863 4.091509 GTCAGCAACTAAACATAGACGTGG 59.908 45.833 0.00 0.00 0.00 4.94
853 864 4.923871 AGTCAGCAACTAAACATAGACGTG 59.076 41.667 0.00 0.00 36.07 4.49
854 865 5.135508 AGTCAGCAACTAAACATAGACGT 57.864 39.130 0.00 0.00 36.07 4.34
855 866 6.323266 AGTAGTCAGCAACTAAACATAGACG 58.677 40.000 1.00 0.00 42.11 4.18
856 867 7.540299 AGAGTAGTCAGCAACTAAACATAGAC 58.460 38.462 0.00 0.00 42.11 2.59
857 868 7.612244 AGAGAGTAGTCAGCAACTAAACATAGA 59.388 37.037 0.00 0.00 42.11 1.98
858 869 7.700234 CAGAGAGTAGTCAGCAACTAAACATAG 59.300 40.741 0.00 0.00 42.11 2.23
859 870 7.539436 CAGAGAGTAGTCAGCAACTAAACATA 58.461 38.462 0.00 0.00 42.11 2.29
860 871 6.393990 CAGAGAGTAGTCAGCAACTAAACAT 58.606 40.000 0.00 0.00 42.11 2.71
861 872 5.773575 CAGAGAGTAGTCAGCAACTAAACA 58.226 41.667 0.00 0.00 42.11 2.83
862 873 4.623595 GCAGAGAGTAGTCAGCAACTAAAC 59.376 45.833 0.00 0.14 42.11 2.01
863 874 4.280929 TGCAGAGAGTAGTCAGCAACTAAA 59.719 41.667 9.15 0.00 42.11 1.85
864 875 3.826729 TGCAGAGAGTAGTCAGCAACTAA 59.173 43.478 9.15 0.00 42.11 2.24
865 876 3.191581 GTGCAGAGAGTAGTCAGCAACTA 59.808 47.826 12.15 0.00 39.55 2.24
866 877 2.029470 GTGCAGAGAGTAGTCAGCAACT 60.029 50.000 12.15 0.00 42.33 3.16
867 878 2.288457 TGTGCAGAGAGTAGTCAGCAAC 60.288 50.000 12.15 8.56 31.66 4.17
868 879 1.963515 TGTGCAGAGAGTAGTCAGCAA 59.036 47.619 12.15 3.57 31.66 3.91
869 880 1.620822 TGTGCAGAGAGTAGTCAGCA 58.379 50.000 7.90 7.90 0.00 4.41
870 881 2.094286 ACATGTGCAGAGAGTAGTCAGC 60.094 50.000 0.00 1.81 0.00 4.26
871 882 3.192212 TCACATGTGCAGAGAGTAGTCAG 59.808 47.826 21.38 0.00 0.00 3.51
872 883 3.157087 TCACATGTGCAGAGAGTAGTCA 58.843 45.455 21.38 0.00 0.00 3.41
873 884 3.857549 TCACATGTGCAGAGAGTAGTC 57.142 47.619 21.38 0.00 0.00 2.59
874 885 4.022603 AGATCACATGTGCAGAGAGTAGT 58.977 43.478 21.38 0.00 0.00 2.73
875 886 4.097589 TCAGATCACATGTGCAGAGAGTAG 59.902 45.833 21.38 4.09 0.00 2.57
876 887 4.019174 TCAGATCACATGTGCAGAGAGTA 58.981 43.478 21.38 1.22 0.00 2.59
877 888 2.830321 TCAGATCACATGTGCAGAGAGT 59.170 45.455 21.38 0.76 0.00 3.24
878 889 3.188492 GTCAGATCACATGTGCAGAGAG 58.812 50.000 21.38 8.47 0.00 3.20
879 890 2.564062 TGTCAGATCACATGTGCAGAGA 59.436 45.455 21.38 12.91 0.00 3.10
911 923 7.280356 AGTCAACAACTAAACATAGGAAGTGT 58.720 34.615 0.00 0.00 36.07 3.55
931 943 6.291377 AGTGCAAAATCAAGAGAGTAGTCAA 58.709 36.000 0.00 0.00 0.00 3.18
952 964 1.645034 CCGCTCACAATGACCTAGTG 58.355 55.000 0.00 0.00 34.67 2.74
1063 1075 2.364324 TGAGAAGAACGTGCCTAACTGT 59.636 45.455 0.00 0.00 0.00 3.55
1089 1101 2.739885 AGCAGCACAACAAACAAACA 57.260 40.000 0.00 0.00 0.00 2.83
1099 1111 4.204012 ACAAGGTTAAGTAAGCAGCACAA 58.796 39.130 0.00 0.00 36.22 3.33
1128 1140 1.608590 AGTTCCATGAGCAACAAACCG 59.391 47.619 0.00 0.00 0.00 4.44
1129 1141 3.568007 TGTAGTTCCATGAGCAACAAACC 59.432 43.478 0.00 0.00 0.00 3.27
1281 1293 1.493861 CAGCTCATCCTCCTCCTTCA 58.506 55.000 0.00 0.00 0.00 3.02
1332 1344 3.198417 TCATGGTCTGCTTGCTCTATTGA 59.802 43.478 0.00 0.00 0.00 2.57
1482 1494 7.603651 TGTCTTGGCAAAACTTAGTTTAAACA 58.396 30.769 20.06 7.35 34.43 2.83
1502 1514 7.620880 TCTGGCATACATAAGTAACTTGTCTT 58.379 34.615 0.00 0.00 33.13 3.01
1544 1557 3.678806 CGACAAACTAGCTGGGCAGAATA 60.679 47.826 0.85 0.00 0.00 1.75
1565 1578 2.250939 TGGCACAAACGGAAGAGCG 61.251 57.895 0.00 0.00 31.92 5.03
1573 1587 1.134175 AGTGAAAAGGTGGCACAAACG 59.866 47.619 20.82 0.00 44.16 3.60
1590 1604 6.303022 CGCATAAGAACACATAACAAACAGTG 59.697 38.462 0.00 0.00 37.95 3.66
1618 1632 8.854614 ACATTTCTTAAAGTAGCTTGTCAGAT 57.145 30.769 0.00 0.00 0.00 2.90
1619 1633 8.677148 AACATTTCTTAAAGTAGCTTGTCAGA 57.323 30.769 0.00 0.00 0.00 3.27
1620 1634 9.173939 CAAACATTTCTTAAAGTAGCTTGTCAG 57.826 33.333 0.00 0.00 0.00 3.51
1621 1635 8.682710 ACAAACATTTCTTAAAGTAGCTTGTCA 58.317 29.630 0.00 0.00 0.00 3.58
1622 1636 9.516314 AACAAACATTTCTTAAAGTAGCTTGTC 57.484 29.630 0.00 0.00 0.00 3.18
1626 1640 9.626045 GCATAACAAACATTTCTTAAAGTAGCT 57.374 29.630 0.00 0.00 0.00 3.32
1627 1641 9.405587 TGCATAACAAACATTTCTTAAAGTAGC 57.594 29.630 0.00 0.00 0.00 3.58
1663 1677 5.163933 GCAATGTGATTTCGTCATGCAAAAT 60.164 36.000 0.00 0.00 39.21 1.82
1664 1678 4.150274 GCAATGTGATTTCGTCATGCAAAA 59.850 37.500 0.00 0.00 39.21 2.44
1665 1679 3.674281 GCAATGTGATTTCGTCATGCAAA 59.326 39.130 0.00 0.00 39.21 3.68
1668 1682 2.850060 CAGCAATGTGATTTCGTCATGC 59.150 45.455 0.00 0.00 39.52 4.06
1669 1683 4.345271 TCAGCAATGTGATTTCGTCATG 57.655 40.909 0.00 0.00 39.48 3.07
1670 1684 5.375417 TTTCAGCAATGTGATTTCGTCAT 57.625 34.783 0.00 0.00 39.48 3.06
1671 1685 4.827304 TTTCAGCAATGTGATTTCGTCA 57.173 36.364 0.00 0.00 0.00 4.35
1672 1686 4.382754 GGTTTTCAGCAATGTGATTTCGTC 59.617 41.667 0.00 0.00 0.00 4.20
1673 1687 4.298332 GGTTTTCAGCAATGTGATTTCGT 58.702 39.130 0.00 0.00 0.00 3.85
1674 1688 3.361644 CGGTTTTCAGCAATGTGATTTCG 59.638 43.478 0.00 0.00 0.00 3.46
1678 1692 2.030007 CCACGGTTTTCAGCAATGTGAT 60.030 45.455 0.00 0.00 0.00 3.06
1687 1701 2.861462 TTTCTTGCCACGGTTTTCAG 57.139 45.000 0.00 0.00 0.00 3.02
1708 1722 4.986659 GCATTTTGAAGCTCTGATGTTGTT 59.013 37.500 0.00 0.00 0.00 2.83
1713 1727 6.094739 CAAATGCATTTTGAAGCTCTGATG 57.905 37.500 21.95 3.33 46.36 3.07
1724 1738 7.744059 TGATGCTTACATTCAAATGCATTTTG 58.256 30.769 21.95 19.10 40.46 2.44
1766 1780 1.176527 AATGACATTGGTGGAAGGCG 58.823 50.000 0.00 0.00 0.00 5.52
2237 2463 9.517609 GTAGAAGCTCGATTTTGTAGATTAGAA 57.482 33.333 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.