Multiple sequence alignment - TraesCS5A01G518800

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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 TraesCS5A01G518800 chr5A 100.000 2618 0 0 1 2618 680743776 680746393 0.000000e+00 4835
1 TraesCS5A01G518800 chr6B 99.336 2258 13 2 361 2618 132949365 132947110 0.000000e+00 4085
2 TraesCS5A01G518800 chr6B 98.231 2261 34 5 361 2618 463401643 463403900 0.000000e+00 3949
3 TraesCS5A01G518800 chr6B 89.412 1634 112 24 991 2618 536157639 536156061 0.000000e+00 2002
4 TraesCS5A01G518800 chr6B 86.935 199 15 10 454 652 536157856 536157669 2.040000e-51 213
5 TraesCS5A01G518800 chr6B 85.135 148 12 9 371 513 720464172 720464314 2.720000e-30 143
6 TraesCS5A01G518800 chr7A 99.455 2202 12 0 417 2618 9493229 9491028 0.000000e+00 4000
7 TraesCS5A01G518800 chr4B 97.895 2233 14 2 415 2618 245452939 245455167 0.000000e+00 3832
8 TraesCS5A01G518800 chr4B 97.015 134 3 1 1 133 642960666 642960799 9.430000e-55 224
9 TraesCS5A01G518800 chr4B 84.667 150 13 4 133 274 642960925 642961072 9.770000e-30 141
10 TraesCS5A01G518800 chr1A 99.689 1930 6 0 428 2357 517178423 517180352 0.000000e+00 3531
11 TraesCS5A01G518800 chr3B 87.869 2135 153 46 447 2575 145882970 145880936 0.000000e+00 2410
12 TraesCS5A01G518800 chr2B 89.455 1650 111 25 976 2618 706803192 706801599 0.000000e+00 2025
13 TraesCS5A01G518800 chr2B 91.830 306 21 4 625 929 706803998 706803696 8.660000e-115 424
14 TraesCS5A01G518800 chr2B 87.864 206 14 10 447 652 706804137 706803943 5.630000e-57 231
15 TraesCS5A01G518800 chr1D 87.023 917 81 22 1707 2618 404279089 404279972 0.000000e+00 1000
16 TraesCS5A01G518800 chr1D 80.660 1334 157 61 425 1715 404274512 404275787 0.000000e+00 941
17 TraesCS5A01G518800 chr2A 87.093 860 86 10 927 1770 545739371 545738521 0.000000e+00 950
18 TraesCS5A01G518800 chr2A 86.538 156 9 11 366 513 256194496 256194647 7.500000e-36 161
19 TraesCS5A01G518800 chr7B 79.857 978 123 38 416 1366 610360840 610361770 0.000000e+00 647
20 TraesCS5A01G518800 chr4D 97.015 134 3 1 1 133 499787999 499788132 9.430000e-55 224
21 TraesCS5A01G518800 chr3A 86.624 157 11 6 364 513 726727186 726727339 5.800000e-37 165
22 TraesCS5A01G518800 chr1B 93.458 107 5 1 358 464 65544690 65544586 9.700000e-35 158


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 TraesCS5A01G518800 chr5A 680743776 680746393 2617 False 4835.000000 4835 100.000000 1 2618 1 chr5A.!!$F1 2617
1 TraesCS5A01G518800 chr6B 132947110 132949365 2255 True 4085.000000 4085 99.336000 361 2618 1 chr6B.!!$R1 2257
2 TraesCS5A01G518800 chr6B 463401643 463403900 2257 False 3949.000000 3949 98.231000 361 2618 1 chr6B.!!$F1 2257
3 TraesCS5A01G518800 chr6B 536156061 536157856 1795 True 1107.500000 2002 88.173500 454 2618 2 chr6B.!!$R2 2164
4 TraesCS5A01G518800 chr7A 9491028 9493229 2201 True 4000.000000 4000 99.455000 417 2618 1 chr7A.!!$R1 2201
5 TraesCS5A01G518800 chr4B 245452939 245455167 2228 False 3832.000000 3832 97.895000 415 2618 1 chr4B.!!$F1 2203
6 TraesCS5A01G518800 chr1A 517178423 517180352 1929 False 3531.000000 3531 99.689000 428 2357 1 chr1A.!!$F1 1929
7 TraesCS5A01G518800 chr3B 145880936 145882970 2034 True 2410.000000 2410 87.869000 447 2575 1 chr3B.!!$R1 2128
8 TraesCS5A01G518800 chr2B 706801599 706804137 2538 True 893.333333 2025 89.716333 447 2618 3 chr2B.!!$R1 2171
9 TraesCS5A01G518800 chr1D 404274512 404279972 5460 False 970.500000 1000 83.841500 425 2618 2 chr1D.!!$F1 2193
10 TraesCS5A01G518800 chr2A 545738521 545739371 850 True 950.000000 950 87.093000 927 1770 1 chr2A.!!$R1 843
11 TraesCS5A01G518800 chr7B 610360840 610361770 930 False 647.000000 647 79.857000 416 1366 1 chr7B.!!$F1 950

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
26 27 0.036732 AGAAGCCCAATCTCGCACAA 59.963 50.0 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 5718 0.314302 ATAATCGTCGCTCTTCCGGG 59.686 55.0 0.0 0.0 0.0 5.73 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
21 22 3.535561 ACAACATAGAAGCCCAATCTCG 58.464 45.455 0.00 0.00 0.00 4.04
22 23 2.246719 ACATAGAAGCCCAATCTCGC 57.753 50.000 0.00 0.00 0.00 5.03
23 24 1.486310 ACATAGAAGCCCAATCTCGCA 59.514 47.619 0.00 0.00 0.00 5.10
24 25 1.869767 CATAGAAGCCCAATCTCGCAC 59.130 52.381 0.00 0.00 0.00 5.34
25 26 0.901827 TAGAAGCCCAATCTCGCACA 59.098 50.000 0.00 0.00 0.00 4.57
26 27 0.036732 AGAAGCCCAATCTCGCACAA 59.963 50.000 0.00 0.00 0.00 3.33
27 28 0.449388 GAAGCCCAATCTCGCACAAG 59.551 55.000 0.00 0.00 0.00 3.16
28 29 0.962356 AAGCCCAATCTCGCACAAGG 60.962 55.000 0.00 0.00 0.00 3.61
29 30 2.409870 GCCCAATCTCGCACAAGGG 61.410 63.158 0.00 0.00 39.33 3.95
30 31 2.409870 CCCAATCTCGCACAAGGGC 61.410 63.158 0.00 0.00 0.00 5.19
31 32 1.377725 CCAATCTCGCACAAGGGCT 60.378 57.895 0.00 0.00 0.00 5.19
32 33 0.962356 CCAATCTCGCACAAGGGCTT 60.962 55.000 0.00 0.00 0.00 4.35
33 34 0.169672 CAATCTCGCACAAGGGCTTG 59.830 55.000 0.00 0.00 45.58 4.01
48 49 3.442441 TTGTTTCGCAAGGCCCTG 58.558 55.556 0.00 0.00 38.47 4.45
49 50 1.152860 TTGTTTCGCAAGGCCCTGA 60.153 52.632 5.23 0.00 38.47 3.86
50 51 1.452145 TTGTTTCGCAAGGCCCTGAC 61.452 55.000 5.23 0.00 38.47 3.51
51 52 1.896660 GTTTCGCAAGGCCCTGACA 60.897 57.895 5.23 0.00 38.47 3.58
52 53 1.074775 TTTCGCAAGGCCCTGACAT 59.925 52.632 5.23 0.00 38.47 3.06
53 54 0.539438 TTTCGCAAGGCCCTGACATT 60.539 50.000 5.23 0.00 38.47 2.71
54 55 0.960364 TTCGCAAGGCCCTGACATTC 60.960 55.000 5.23 0.00 38.47 2.67
55 56 1.675310 CGCAAGGCCCTGACATTCA 60.675 57.895 5.23 0.00 0.00 2.57
56 57 1.885871 GCAAGGCCCTGACATTCAC 59.114 57.895 5.23 0.00 0.00 3.18
57 58 1.926511 GCAAGGCCCTGACATTCACG 61.927 60.000 5.23 0.00 0.00 4.35
58 59 1.675641 AAGGCCCTGACATTCACGC 60.676 57.895 0.00 0.00 0.00 5.34
59 60 2.045926 GGCCCTGACATTCACGCT 60.046 61.111 0.00 0.00 0.00 5.07
60 61 2.109126 GGCCCTGACATTCACGCTC 61.109 63.158 0.00 0.00 0.00 5.03
61 62 1.078848 GCCCTGACATTCACGCTCT 60.079 57.895 0.00 0.00 0.00 4.09
62 63 1.086634 GCCCTGACATTCACGCTCTC 61.087 60.000 0.00 0.00 0.00 3.20
63 64 0.460987 CCCTGACATTCACGCTCTCC 60.461 60.000 0.00 0.00 0.00 3.71
64 65 0.534412 CCTGACATTCACGCTCTCCT 59.466 55.000 0.00 0.00 0.00 3.69
65 66 1.638133 CTGACATTCACGCTCTCCTG 58.362 55.000 0.00 0.00 0.00 3.86
66 67 0.969149 TGACATTCACGCTCTCCTGT 59.031 50.000 0.00 0.00 0.00 4.00
67 68 2.164422 CTGACATTCACGCTCTCCTGTA 59.836 50.000 0.00 0.00 0.00 2.74
68 69 2.560981 TGACATTCACGCTCTCCTGTAA 59.439 45.455 0.00 0.00 0.00 2.41
69 70 3.006430 TGACATTCACGCTCTCCTGTAAA 59.994 43.478 0.00 0.00 0.00 2.01
70 71 4.184629 GACATTCACGCTCTCCTGTAAAT 58.815 43.478 0.00 0.00 0.00 1.40
71 72 4.184629 ACATTCACGCTCTCCTGTAAATC 58.815 43.478 0.00 0.00 0.00 2.17
72 73 4.081420 ACATTCACGCTCTCCTGTAAATCT 60.081 41.667 0.00 0.00 0.00 2.40
73 74 3.510388 TCACGCTCTCCTGTAAATCTG 57.490 47.619 0.00 0.00 0.00 2.90
74 75 2.826128 TCACGCTCTCCTGTAAATCTGT 59.174 45.455 0.00 0.00 0.00 3.41
75 76 2.926200 CACGCTCTCCTGTAAATCTGTG 59.074 50.000 0.00 0.00 0.00 3.66
76 77 2.826128 ACGCTCTCCTGTAAATCTGTGA 59.174 45.455 0.00 0.00 0.00 3.58
77 78 3.258372 ACGCTCTCCTGTAAATCTGTGAA 59.742 43.478 0.00 0.00 0.00 3.18
78 79 4.081420 ACGCTCTCCTGTAAATCTGTGAAT 60.081 41.667 0.00 0.00 0.00 2.57
79 80 4.872691 CGCTCTCCTGTAAATCTGTGAATT 59.127 41.667 0.00 0.00 0.00 2.17
80 81 5.352569 CGCTCTCCTGTAAATCTGTGAATTT 59.647 40.000 0.00 0.00 33.54 1.82
81 82 6.549952 GCTCTCCTGTAAATCTGTGAATTTG 58.450 40.000 0.00 0.00 31.50 2.32
82 83 6.404074 GCTCTCCTGTAAATCTGTGAATTTGG 60.404 42.308 0.00 0.00 31.50 3.28
83 84 6.542821 TCTCCTGTAAATCTGTGAATTTGGT 58.457 36.000 0.00 0.00 31.50 3.67
84 85 7.004086 TCTCCTGTAAATCTGTGAATTTGGTT 58.996 34.615 0.00 0.00 31.50 3.67
85 86 6.980593 TCCTGTAAATCTGTGAATTTGGTTG 58.019 36.000 0.00 0.00 31.50 3.77
86 87 6.775142 TCCTGTAAATCTGTGAATTTGGTTGA 59.225 34.615 0.00 0.00 31.50 3.18
87 88 7.451255 TCCTGTAAATCTGTGAATTTGGTTGAT 59.549 33.333 0.00 0.00 31.50 2.57
88 89 7.543172 CCTGTAAATCTGTGAATTTGGTTGATG 59.457 37.037 0.00 0.00 31.50 3.07
89 90 6.867816 TGTAAATCTGTGAATTTGGTTGATGC 59.132 34.615 0.00 0.00 31.50 3.91
90 91 5.733620 AATCTGTGAATTTGGTTGATGCT 57.266 34.783 0.00 0.00 0.00 3.79
91 92 6.839124 AATCTGTGAATTTGGTTGATGCTA 57.161 33.333 0.00 0.00 0.00 3.49
92 93 6.839124 ATCTGTGAATTTGGTTGATGCTAA 57.161 33.333 0.00 0.00 0.00 3.09
93 94 6.647334 TCTGTGAATTTGGTTGATGCTAAA 57.353 33.333 0.00 0.00 0.00 1.85
94 95 7.048629 TCTGTGAATTTGGTTGATGCTAAAA 57.951 32.000 0.00 0.00 0.00 1.52
95 96 7.495901 TCTGTGAATTTGGTTGATGCTAAAAA 58.504 30.769 0.00 0.00 0.00 1.94
96 97 8.149647 TCTGTGAATTTGGTTGATGCTAAAAAT 58.850 29.630 0.00 0.00 0.00 1.82
97 98 8.309163 TGTGAATTTGGTTGATGCTAAAAATC 57.691 30.769 0.00 0.00 0.00 2.17
98 99 8.149647 TGTGAATTTGGTTGATGCTAAAAATCT 58.850 29.630 0.00 0.00 0.00 2.40
99 100 8.437742 GTGAATTTGGTTGATGCTAAAAATCTG 58.562 33.333 0.00 0.00 0.00 2.90
100 101 8.149647 TGAATTTGGTTGATGCTAAAAATCTGT 58.850 29.630 0.00 0.00 0.00 3.41
101 102 9.638239 GAATTTGGTTGATGCTAAAAATCTGTA 57.362 29.630 0.00 0.00 0.00 2.74
103 104 9.807649 ATTTGGTTGATGCTAAAAATCTGTATC 57.192 29.630 0.00 0.00 0.00 2.24
104 105 7.936496 TGGTTGATGCTAAAAATCTGTATCA 57.064 32.000 0.00 0.00 32.60 2.15
105 106 7.761409 TGGTTGATGCTAAAAATCTGTATCAC 58.239 34.615 0.00 0.00 33.80 3.06
106 107 7.392953 TGGTTGATGCTAAAAATCTGTATCACA 59.607 33.333 0.00 0.00 33.80 3.58
107 108 8.408601 GGTTGATGCTAAAAATCTGTATCACAT 58.591 33.333 0.00 0.00 33.80 3.21
108 109 9.443283 GTTGATGCTAAAAATCTGTATCACATC 57.557 33.333 0.00 0.00 33.80 3.06
109 110 8.735692 TGATGCTAAAAATCTGTATCACATCA 57.264 30.769 0.00 0.00 38.19 3.07
110 111 8.615211 TGATGCTAAAAATCTGTATCACATCAC 58.385 33.333 0.00 0.00 36.27 3.06
111 112 8.743085 ATGCTAAAAATCTGTATCACATCACT 57.257 30.769 0.00 0.00 0.00 3.41
112 113 9.836864 ATGCTAAAAATCTGTATCACATCACTA 57.163 29.630 0.00 0.00 0.00 2.74
113 114 9.836864 TGCTAAAAATCTGTATCACATCACTAT 57.163 29.630 0.00 0.00 0.00 2.12
119 120 8.824159 AATCTGTATCACATCACTATTAGTGC 57.176 34.615 17.35 3.55 45.54 4.40
120 121 7.346751 TCTGTATCACATCACTATTAGTGCA 57.653 36.000 17.35 8.28 45.54 4.57
121 122 7.428826 TCTGTATCACATCACTATTAGTGCAG 58.571 38.462 17.35 14.99 45.54 4.41
122 123 5.985530 TGTATCACATCACTATTAGTGCAGC 59.014 40.000 17.35 0.00 45.54 5.25
123 124 4.470334 TCACATCACTATTAGTGCAGCA 57.530 40.909 17.35 0.00 45.54 4.41
124 125 5.027293 TCACATCACTATTAGTGCAGCAT 57.973 39.130 17.35 4.75 45.54 3.79
125 126 5.430886 TCACATCACTATTAGTGCAGCATT 58.569 37.500 17.35 0.00 45.54 3.56
126 127 5.295045 TCACATCACTATTAGTGCAGCATTG 59.705 40.000 17.35 10.41 45.54 2.82
139 140 3.893720 GCAGCATTGCCTGTTATATGAC 58.106 45.455 4.70 0.00 44.74 3.06
140 141 3.316029 GCAGCATTGCCTGTTATATGACA 59.684 43.478 4.70 0.00 44.74 3.58
141 142 4.556104 GCAGCATTGCCTGTTATATGACAG 60.556 45.833 18.34 18.34 44.74 3.51
142 143 4.577693 CAGCATTGCCTGTTATATGACAGT 59.422 41.667 22.11 5.06 44.34 3.55
143 144 4.577693 AGCATTGCCTGTTATATGACAGTG 59.422 41.667 22.11 15.80 44.34 3.66
144 145 4.336433 GCATTGCCTGTTATATGACAGTGT 59.664 41.667 22.11 0.00 44.34 3.55
145 146 5.731406 GCATTGCCTGTTATATGACAGTGTG 60.731 44.000 22.11 15.96 44.34 3.82
146 147 4.551702 TGCCTGTTATATGACAGTGTGT 57.448 40.909 22.11 0.00 44.34 3.72
147 148 4.905429 TGCCTGTTATATGACAGTGTGTT 58.095 39.130 22.11 0.00 44.34 3.32
148 149 5.312895 TGCCTGTTATATGACAGTGTGTTT 58.687 37.500 22.11 0.00 44.34 2.83
149 150 5.181056 TGCCTGTTATATGACAGTGTGTTTG 59.819 40.000 22.11 9.32 44.34 2.93
150 151 5.181245 GCCTGTTATATGACAGTGTGTTTGT 59.819 40.000 22.11 0.00 44.34 2.83
151 152 6.620733 GCCTGTTATATGACAGTGTGTTTGTC 60.621 42.308 22.11 0.00 44.34 3.18
152 153 6.650807 CCTGTTATATGACAGTGTGTTTGTCT 59.349 38.462 22.11 0.00 44.34 3.41
153 154 7.817478 CCTGTTATATGACAGTGTGTTTGTCTA 59.183 37.037 22.11 0.00 44.34 2.59
154 155 8.528917 TGTTATATGACAGTGTGTTTGTCTAC 57.471 34.615 0.00 0.00 44.08 2.59
155 156 8.145122 TGTTATATGACAGTGTGTTTGTCTACA 58.855 33.333 0.00 0.00 44.08 2.74
156 157 8.648097 GTTATATGACAGTGTGTTTGTCTACAG 58.352 37.037 0.00 0.00 44.08 2.74
157 158 4.465632 TGACAGTGTGTTTGTCTACAGT 57.534 40.909 0.00 0.00 44.08 3.55
159 160 4.081917 TGACAGTGTGTTTGTCTACAGTGA 60.082 41.667 16.43 0.00 46.24 3.41
160 161 4.827692 ACAGTGTGTTTGTCTACAGTGAA 58.172 39.130 16.43 0.00 46.24 3.18
161 162 4.870426 ACAGTGTGTTTGTCTACAGTGAAG 59.130 41.667 16.43 0.00 46.24 3.02
162 163 3.871594 AGTGTGTTTGTCTACAGTGAAGC 59.128 43.478 0.00 0.00 0.00 3.86
163 164 3.621268 GTGTGTTTGTCTACAGTGAAGCA 59.379 43.478 0.00 0.00 0.00 3.91
164 165 4.273480 GTGTGTTTGTCTACAGTGAAGCAT 59.727 41.667 0.00 0.00 0.00 3.79
165 166 4.273235 TGTGTTTGTCTACAGTGAAGCATG 59.727 41.667 0.00 0.00 0.00 4.06
166 167 3.814842 TGTTTGTCTACAGTGAAGCATGG 59.185 43.478 0.00 0.00 0.00 3.66
167 168 2.099141 TGTCTACAGTGAAGCATGGC 57.901 50.000 0.00 0.00 0.00 4.40
168 169 1.625315 TGTCTACAGTGAAGCATGGCT 59.375 47.619 0.00 0.00 42.56 4.75
169 170 2.831526 TGTCTACAGTGAAGCATGGCTA 59.168 45.455 0.00 0.00 38.25 3.93
170 171 3.118992 TGTCTACAGTGAAGCATGGCTAG 60.119 47.826 0.00 0.00 38.25 3.42
171 172 3.131223 GTCTACAGTGAAGCATGGCTAGA 59.869 47.826 0.00 0.00 38.25 2.43
172 173 3.963374 TCTACAGTGAAGCATGGCTAGAT 59.037 43.478 0.00 0.00 38.25 1.98
173 174 3.641434 ACAGTGAAGCATGGCTAGATT 57.359 42.857 0.00 0.00 38.25 2.40
174 175 3.539604 ACAGTGAAGCATGGCTAGATTC 58.460 45.455 0.00 1.73 38.25 2.52
175 176 3.199508 ACAGTGAAGCATGGCTAGATTCT 59.800 43.478 0.00 0.00 38.25 2.40
176 177 3.808726 CAGTGAAGCATGGCTAGATTCTC 59.191 47.826 0.00 5.79 38.25 2.87
177 178 3.710677 AGTGAAGCATGGCTAGATTCTCT 59.289 43.478 0.00 7.56 38.25 3.10
178 179 3.808726 GTGAAGCATGGCTAGATTCTCTG 59.191 47.826 0.00 0.00 38.25 3.35
179 180 3.453717 TGAAGCATGGCTAGATTCTCTGT 59.546 43.478 0.00 0.00 38.25 3.41
180 181 3.749665 AGCATGGCTAGATTCTCTGTC 57.250 47.619 0.00 0.00 36.99 3.51
181 182 3.307506 AGCATGGCTAGATTCTCTGTCT 58.692 45.455 0.00 0.00 36.99 3.41
182 183 3.710677 AGCATGGCTAGATTCTCTGTCTT 59.289 43.478 0.00 0.00 36.99 3.01
183 184 3.808726 GCATGGCTAGATTCTCTGTCTTG 59.191 47.826 0.00 0.00 0.00 3.02
184 185 4.442612 GCATGGCTAGATTCTCTGTCTTGA 60.443 45.833 0.00 0.00 0.00 3.02
185 186 5.742546 GCATGGCTAGATTCTCTGTCTTGAT 60.743 44.000 0.00 0.00 0.00 2.57
186 187 5.273674 TGGCTAGATTCTCTGTCTTGATG 57.726 43.478 0.00 0.00 0.00 3.07
187 188 4.057432 GGCTAGATTCTCTGTCTTGATGC 58.943 47.826 0.00 0.00 0.00 3.91
188 189 4.442612 GGCTAGATTCTCTGTCTTGATGCA 60.443 45.833 0.00 0.00 0.00 3.96
189 190 5.114780 GCTAGATTCTCTGTCTTGATGCAA 58.885 41.667 0.00 0.00 0.00 4.08
190 191 5.234757 GCTAGATTCTCTGTCTTGATGCAAG 59.765 44.000 0.00 0.84 42.25 4.01
191 192 4.515361 AGATTCTCTGTCTTGATGCAAGG 58.485 43.478 7.27 0.00 41.33 3.61
192 193 2.105006 TCTCTGTCTTGATGCAAGGC 57.895 50.000 4.90 4.90 45.16 4.35
196 197 2.543578 GTCTTGATGCAAGGCGACA 58.456 52.632 7.27 0.00 41.33 4.35
197 198 1.089920 GTCTTGATGCAAGGCGACAT 58.910 50.000 7.27 0.00 41.33 3.06
198 199 1.089112 TCTTGATGCAAGGCGACATG 58.911 50.000 7.27 0.00 41.33 3.21
199 200 1.089112 CTTGATGCAAGGCGACATGA 58.911 50.000 0.00 0.00 37.77 3.07
200 201 1.674441 CTTGATGCAAGGCGACATGAT 59.326 47.619 0.00 0.00 37.77 2.45
201 202 1.302366 TGATGCAAGGCGACATGATC 58.698 50.000 0.00 0.00 0.00 2.92
202 203 1.302366 GATGCAAGGCGACATGATCA 58.698 50.000 0.00 0.00 0.00 2.92
203 204 1.878088 GATGCAAGGCGACATGATCAT 59.122 47.619 1.18 1.18 0.00 2.45
204 205 1.302366 TGCAAGGCGACATGATCATC 58.698 50.000 4.86 0.00 0.00 2.92
205 206 0.234106 GCAAGGCGACATGATCATCG 59.766 55.000 13.20 13.20 41.32 3.84
206 207 1.856802 CAAGGCGACATGATCATCGA 58.143 50.000 20.10 0.00 40.86 3.59
207 208 2.410939 CAAGGCGACATGATCATCGAT 58.589 47.619 20.10 6.91 40.86 3.59
208 209 2.075979 AGGCGACATGATCATCGATG 57.924 50.000 19.61 19.61 40.86 3.84
209 210 1.615392 AGGCGACATGATCATCGATGA 59.385 47.619 29.09 29.09 40.86 2.92
210 211 1.723542 GGCGACATGATCATCGATGAC 59.276 52.381 29.49 21.75 40.86 3.06
211 212 2.397549 GCGACATGATCATCGATGACA 58.602 47.619 29.49 25.90 40.86 3.58
212 213 2.991866 GCGACATGATCATCGATGACAT 59.008 45.455 29.49 26.75 40.86 3.06
213 214 3.431233 GCGACATGATCATCGATGACATT 59.569 43.478 29.49 20.59 40.86 2.71
214 215 4.084171 GCGACATGATCATCGATGACATTT 60.084 41.667 29.49 23.61 40.86 2.32
215 216 5.119125 GCGACATGATCATCGATGACATTTA 59.881 40.000 29.49 11.97 40.86 1.40
216 217 6.669268 GCGACATGATCATCGATGACATTTAG 60.669 42.308 29.49 23.23 40.86 1.85
217 218 6.583806 CGACATGATCATCGATGACATTTAGA 59.416 38.462 29.49 5.92 40.86 2.10
218 219 7.410193 CGACATGATCATCGATGACATTTAGAC 60.410 40.741 29.49 18.38 40.86 2.59
219 220 7.212274 ACATGATCATCGATGACATTTAGACA 58.788 34.615 29.49 17.60 40.03 3.41
220 221 7.876582 ACATGATCATCGATGACATTTAGACAT 59.123 33.333 29.49 18.76 40.03 3.06
221 222 7.880059 TGATCATCGATGACATTTAGACATC 57.120 36.000 29.49 18.40 43.16 3.06
222 223 6.870439 TGATCATCGATGACATTTAGACATCC 59.130 38.462 29.49 1.87 43.51 3.51
223 224 6.410942 TCATCGATGACATTTAGACATCCT 57.589 37.500 23.99 0.00 43.51 3.24
224 225 6.218746 TCATCGATGACATTTAGACATCCTG 58.781 40.000 23.99 0.00 43.51 3.86
225 226 4.371786 TCGATGACATTTAGACATCCTGC 58.628 43.478 0.00 0.00 43.51 4.85
226 227 4.100035 TCGATGACATTTAGACATCCTGCT 59.900 41.667 0.00 0.00 43.51 4.24
227 228 4.813161 CGATGACATTTAGACATCCTGCTT 59.187 41.667 0.00 0.00 43.51 3.91
228 229 5.050499 CGATGACATTTAGACATCCTGCTTC 60.050 44.000 0.00 0.00 43.51 3.86
229 230 4.183865 TGACATTTAGACATCCTGCTTCG 58.816 43.478 0.00 0.00 0.00 3.79
230 231 3.535561 ACATTTAGACATCCTGCTTCGG 58.464 45.455 0.00 0.00 0.00 4.30
231 232 3.055094 ACATTTAGACATCCTGCTTCGGT 60.055 43.478 0.00 0.00 0.00 4.69
232 233 3.695830 TTTAGACATCCTGCTTCGGTT 57.304 42.857 0.00 0.00 0.00 4.44
233 234 3.695830 TTAGACATCCTGCTTCGGTTT 57.304 42.857 0.00 0.00 0.00 3.27
234 235 2.568623 AGACATCCTGCTTCGGTTTT 57.431 45.000 0.00 0.00 0.00 2.43
235 236 2.154462 AGACATCCTGCTTCGGTTTTG 58.846 47.619 0.00 0.00 0.00 2.44
236 237 1.200020 GACATCCTGCTTCGGTTTTGG 59.800 52.381 0.00 0.00 0.00 3.28
237 238 1.247567 CATCCTGCTTCGGTTTTGGT 58.752 50.000 0.00 0.00 0.00 3.67
238 239 2.224670 ACATCCTGCTTCGGTTTTGGTA 60.225 45.455 0.00 0.00 0.00 3.25
239 240 2.871096 TCCTGCTTCGGTTTTGGTAT 57.129 45.000 0.00 0.00 0.00 2.73
240 241 3.985019 TCCTGCTTCGGTTTTGGTATA 57.015 42.857 0.00 0.00 0.00 1.47
241 242 4.289238 TCCTGCTTCGGTTTTGGTATAA 57.711 40.909 0.00 0.00 0.00 0.98
242 243 4.258543 TCCTGCTTCGGTTTTGGTATAAG 58.741 43.478 0.00 0.00 0.00 1.73
243 244 3.181500 CCTGCTTCGGTTTTGGTATAAGC 60.181 47.826 0.00 0.00 39.73 3.09
244 245 3.413327 TGCTTCGGTTTTGGTATAAGCA 58.587 40.909 0.00 0.00 44.98 3.91
245 246 4.013728 TGCTTCGGTTTTGGTATAAGCAT 58.986 39.130 0.00 0.00 43.03 3.79
246 247 4.095782 TGCTTCGGTTTTGGTATAAGCATC 59.904 41.667 0.00 0.00 43.03 3.91
247 248 4.095782 GCTTCGGTTTTGGTATAAGCATCA 59.904 41.667 0.00 0.00 39.24 3.07
248 249 5.221048 GCTTCGGTTTTGGTATAAGCATCAT 60.221 40.000 0.00 0.00 39.24 2.45
249 250 6.680378 GCTTCGGTTTTGGTATAAGCATCATT 60.680 38.462 0.00 0.00 39.24 2.57
250 251 6.371809 TCGGTTTTGGTATAAGCATCATTC 57.628 37.500 0.00 0.00 0.00 2.67
251 252 5.883115 TCGGTTTTGGTATAAGCATCATTCA 59.117 36.000 0.00 0.00 0.00 2.57
252 253 6.038161 TCGGTTTTGGTATAAGCATCATTCAG 59.962 38.462 0.00 0.00 0.00 3.02
253 254 6.038161 CGGTTTTGGTATAAGCATCATTCAGA 59.962 38.462 0.00 0.00 0.00 3.27
254 255 7.255242 CGGTTTTGGTATAAGCATCATTCAGAT 60.255 37.037 0.00 0.00 37.48 2.90
255 256 9.066892 GGTTTTGGTATAAGCATCATTCAGATA 57.933 33.333 0.00 0.00 34.43 1.98
260 261 9.494271 TGGTATAAGCATCATTCAGATAAGAAC 57.506 33.333 0.00 0.00 34.43 3.01
261 262 9.717942 GGTATAAGCATCATTCAGATAAGAACT 57.282 33.333 0.00 0.00 34.43 3.01
264 265 7.727331 AAGCATCATTCAGATAAGAACTAGC 57.273 36.000 0.00 0.00 34.43 3.42
265 266 6.824553 AGCATCATTCAGATAAGAACTAGCA 58.175 36.000 0.00 0.00 34.43 3.49
266 267 7.278135 AGCATCATTCAGATAAGAACTAGCAA 58.722 34.615 0.00 0.00 34.43 3.91
267 268 7.226325 AGCATCATTCAGATAAGAACTAGCAAC 59.774 37.037 0.00 0.00 34.43 4.17
268 269 7.011763 GCATCATTCAGATAAGAACTAGCAACA 59.988 37.037 0.00 0.00 34.43 3.33
269 270 8.886719 CATCATTCAGATAAGAACTAGCAACAA 58.113 33.333 0.00 0.00 34.43 2.83
270 271 8.484641 TCATTCAGATAAGAACTAGCAACAAG 57.515 34.615 0.00 0.00 0.00 3.16
271 272 8.097038 TCATTCAGATAAGAACTAGCAACAAGT 58.903 33.333 0.00 0.00 0.00 3.16
272 273 8.725148 CATTCAGATAAGAACTAGCAACAAGTT 58.275 33.333 0.00 0.00 39.84 2.66
273 274 9.944376 ATTCAGATAAGAACTAGCAACAAGTTA 57.056 29.630 0.00 0.00 37.31 2.24
274 275 8.988064 TCAGATAAGAACTAGCAACAAGTTAG 57.012 34.615 0.00 0.00 37.31 2.34
275 276 8.803235 TCAGATAAGAACTAGCAACAAGTTAGA 58.197 33.333 0.00 0.00 37.31 2.10
276 277 9.593134 CAGATAAGAACTAGCAACAAGTTAGAT 57.407 33.333 0.00 0.00 37.31 1.98
289 290 9.756461 GCAACAAGTTAGATTTTTAGTAGTAGC 57.244 33.333 0.00 0.00 0.00 3.58
338 339 3.806316 TTTTTGAGAAATCTCGCCGAC 57.194 42.857 5.99 0.00 45.72 4.79
339 340 2.743636 TTTGAGAAATCTCGCCGACT 57.256 45.000 5.99 0.00 45.72 4.18
340 341 2.743636 TTGAGAAATCTCGCCGACTT 57.256 45.000 5.99 0.00 45.72 3.01
341 342 2.743636 TGAGAAATCTCGCCGACTTT 57.256 45.000 5.99 0.00 45.72 2.66
342 343 3.861276 TGAGAAATCTCGCCGACTTTA 57.139 42.857 5.99 0.00 45.72 1.85
343 344 3.508762 TGAGAAATCTCGCCGACTTTAC 58.491 45.455 5.99 0.00 45.72 2.01
344 345 3.192844 TGAGAAATCTCGCCGACTTTACT 59.807 43.478 5.99 0.00 45.72 2.24
345 346 4.397103 TGAGAAATCTCGCCGACTTTACTA 59.603 41.667 5.99 0.00 45.72 1.82
346 347 5.106038 TGAGAAATCTCGCCGACTTTACTAA 60.106 40.000 5.99 0.00 45.72 2.24
347 348 5.903810 AGAAATCTCGCCGACTTTACTAAT 58.096 37.500 0.00 0.00 0.00 1.73
348 349 5.978322 AGAAATCTCGCCGACTTTACTAATC 59.022 40.000 0.00 0.00 0.00 1.75
349 350 5.517322 AATCTCGCCGACTTTACTAATCT 57.483 39.130 0.00 0.00 0.00 2.40
350 351 4.978083 TCTCGCCGACTTTACTAATCTT 57.022 40.909 0.00 0.00 0.00 2.40
351 352 5.320549 TCTCGCCGACTTTACTAATCTTT 57.679 39.130 0.00 0.00 0.00 2.52
352 353 6.441093 TCTCGCCGACTTTACTAATCTTTA 57.559 37.500 0.00 0.00 0.00 1.85
353 354 7.035840 TCTCGCCGACTTTACTAATCTTTAT 57.964 36.000 0.00 0.00 0.00 1.40
354 355 7.486647 TCTCGCCGACTTTACTAATCTTTATT 58.513 34.615 0.00 0.00 0.00 1.40
355 356 7.977853 TCTCGCCGACTTTACTAATCTTTATTT 59.022 33.333 0.00 0.00 0.00 1.40
356 357 8.483307 TCGCCGACTTTACTAATCTTTATTTT 57.517 30.769 0.00 0.00 0.00 1.82
357 358 8.938906 TCGCCGACTTTACTAATCTTTATTTTT 58.061 29.630 0.00 0.00 0.00 1.94
1445 1988 0.256752 CCAGATCAGACCCATGGCAA 59.743 55.000 6.09 0.00 0.00 4.52
1885 5807 8.692110 TTATATGTACGCTCTTCTTTCGAAAA 57.308 30.769 12.41 0.00 0.00 2.29
2264 6186 0.674534 GAGGCCCGACGATAATGTCT 59.325 55.000 0.00 0.00 36.71 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.289002 GCGAGATTGGGCTTCTATGTTG 59.711 50.000 0.00 0.00 0.00 3.33
3 4 1.486310 TGCGAGATTGGGCTTCTATGT 59.514 47.619 0.00 0.00 0.00 2.29
4 5 1.869767 GTGCGAGATTGGGCTTCTATG 59.130 52.381 0.00 0.00 0.00 2.23
5 6 1.486310 TGTGCGAGATTGGGCTTCTAT 59.514 47.619 0.00 0.00 0.00 1.98
8 9 0.449388 CTTGTGCGAGATTGGGCTTC 59.551 55.000 0.00 0.00 0.00 3.86
10 11 1.377725 CCTTGTGCGAGATTGGGCT 60.378 57.895 0.00 0.00 0.00 5.19
11 12 2.409870 CCCTTGTGCGAGATTGGGC 61.410 63.158 0.00 0.00 0.00 5.36
12 13 2.409870 GCCCTTGTGCGAGATTGGG 61.410 63.158 0.00 0.00 37.76 4.12
13 14 0.962356 AAGCCCTTGTGCGAGATTGG 60.962 55.000 0.00 0.00 36.02 3.16
14 15 0.169672 CAAGCCCTTGTGCGAGATTG 59.830 55.000 0.00 0.00 35.92 2.67
15 16 2.559785 CAAGCCCTTGTGCGAGATT 58.440 52.632 0.00 0.00 35.92 2.40
31 32 1.152860 TCAGGGCCTTGCGAAACAA 60.153 52.632 10.65 0.00 36.62 2.83
32 33 1.896660 GTCAGGGCCTTGCGAAACA 60.897 57.895 10.65 0.00 0.00 2.83
33 34 1.244019 ATGTCAGGGCCTTGCGAAAC 61.244 55.000 10.65 3.59 0.00 2.78
34 35 0.539438 AATGTCAGGGCCTTGCGAAA 60.539 50.000 10.65 0.00 0.00 3.46
35 36 0.960364 GAATGTCAGGGCCTTGCGAA 60.960 55.000 10.65 0.00 0.00 4.70
36 37 1.377202 GAATGTCAGGGCCTTGCGA 60.377 57.895 10.65 0.00 0.00 5.10
37 38 1.675310 TGAATGTCAGGGCCTTGCG 60.675 57.895 10.65 0.00 0.00 4.85
38 39 1.885871 GTGAATGTCAGGGCCTTGC 59.114 57.895 10.65 6.16 0.00 4.01
39 40 1.926511 GCGTGAATGTCAGGGCCTTG 61.927 60.000 8.96 8.96 33.25 3.61
40 41 1.675641 GCGTGAATGTCAGGGCCTT 60.676 57.895 1.32 0.00 33.25 4.35
41 42 2.045926 GCGTGAATGTCAGGGCCT 60.046 61.111 0.00 0.00 33.25 5.19
42 43 2.045926 AGCGTGAATGTCAGGGCC 60.046 61.111 0.00 0.00 33.25 5.80
43 44 1.078848 AGAGCGTGAATGTCAGGGC 60.079 57.895 0.66 0.00 33.25 5.19
44 45 0.460987 GGAGAGCGTGAATGTCAGGG 60.461 60.000 0.66 0.00 33.25 4.45
45 46 0.534412 AGGAGAGCGTGAATGTCAGG 59.466 55.000 0.00 0.00 35.54 3.86
46 47 1.067283 ACAGGAGAGCGTGAATGTCAG 60.067 52.381 0.00 0.00 34.18 3.51
47 48 0.969149 ACAGGAGAGCGTGAATGTCA 59.031 50.000 0.00 0.00 34.18 3.58
48 49 2.941453 TACAGGAGAGCGTGAATGTC 57.059 50.000 0.00 0.00 34.18 3.06
49 50 3.678056 TTTACAGGAGAGCGTGAATGT 57.322 42.857 0.00 0.00 34.18 2.71
50 51 4.269603 CAGATTTACAGGAGAGCGTGAATG 59.730 45.833 0.00 0.00 34.18 2.67
51 52 4.081420 ACAGATTTACAGGAGAGCGTGAAT 60.081 41.667 0.00 0.00 34.18 2.57
52 53 3.258372 ACAGATTTACAGGAGAGCGTGAA 59.742 43.478 0.00 0.00 34.18 3.18
53 54 2.826128 ACAGATTTACAGGAGAGCGTGA 59.174 45.455 0.00 0.00 34.18 4.35
54 55 2.926200 CACAGATTTACAGGAGAGCGTG 59.074 50.000 0.00 0.00 36.05 5.34
55 56 2.826128 TCACAGATTTACAGGAGAGCGT 59.174 45.455 0.00 0.00 0.00 5.07
56 57 3.510388 TCACAGATTTACAGGAGAGCG 57.490 47.619 0.00 0.00 0.00 5.03
57 58 6.404074 CCAAATTCACAGATTTACAGGAGAGC 60.404 42.308 0.00 0.00 0.00 4.09
58 59 6.656693 ACCAAATTCACAGATTTACAGGAGAG 59.343 38.462 0.00 0.00 0.00 3.20
59 60 6.542821 ACCAAATTCACAGATTTACAGGAGA 58.457 36.000 0.00 0.00 0.00 3.71
60 61 6.824305 ACCAAATTCACAGATTTACAGGAG 57.176 37.500 0.00 0.00 0.00 3.69
61 62 6.775142 TCAACCAAATTCACAGATTTACAGGA 59.225 34.615 0.00 0.00 0.00 3.86
62 63 6.980593 TCAACCAAATTCACAGATTTACAGG 58.019 36.000 0.00 0.00 0.00 4.00
63 64 7.062605 GCATCAACCAAATTCACAGATTTACAG 59.937 37.037 0.00 0.00 0.00 2.74
64 65 6.867816 GCATCAACCAAATTCACAGATTTACA 59.132 34.615 0.00 0.00 0.00 2.41
65 66 7.092716 AGCATCAACCAAATTCACAGATTTAC 58.907 34.615 0.00 0.00 0.00 2.01
66 67 7.230849 AGCATCAACCAAATTCACAGATTTA 57.769 32.000 0.00 0.00 0.00 1.40
67 68 6.105397 AGCATCAACCAAATTCACAGATTT 57.895 33.333 0.00 0.00 0.00 2.17
68 69 5.733620 AGCATCAACCAAATTCACAGATT 57.266 34.783 0.00 0.00 0.00 2.40
69 70 6.839124 TTAGCATCAACCAAATTCACAGAT 57.161 33.333 0.00 0.00 0.00 2.90
70 71 6.647334 TTTAGCATCAACCAAATTCACAGA 57.353 33.333 0.00 0.00 0.00 3.41
71 72 7.712264 TTTTTAGCATCAACCAAATTCACAG 57.288 32.000 0.00 0.00 0.00 3.66
72 73 8.149647 AGATTTTTAGCATCAACCAAATTCACA 58.850 29.630 0.00 0.00 0.00 3.58
73 74 8.437742 CAGATTTTTAGCATCAACCAAATTCAC 58.562 33.333 0.00 0.00 0.00 3.18
74 75 8.149647 ACAGATTTTTAGCATCAACCAAATTCA 58.850 29.630 0.00 0.00 0.00 2.57
75 76 8.538409 ACAGATTTTTAGCATCAACCAAATTC 57.462 30.769 0.00 0.00 0.00 2.17
77 78 9.807649 GATACAGATTTTTAGCATCAACCAAAT 57.192 29.630 0.00 0.00 0.00 2.32
78 79 8.801299 TGATACAGATTTTTAGCATCAACCAAA 58.199 29.630 0.00 0.00 0.00 3.28
79 80 8.243426 GTGATACAGATTTTTAGCATCAACCAA 58.757 33.333 0.00 0.00 0.00 3.67
80 81 7.392953 TGTGATACAGATTTTTAGCATCAACCA 59.607 33.333 0.00 0.00 0.00 3.67
81 82 7.761409 TGTGATACAGATTTTTAGCATCAACC 58.239 34.615 0.00 0.00 0.00 3.77
82 83 9.443283 GATGTGATACAGATTTTTAGCATCAAC 57.557 33.333 0.00 0.00 32.04 3.18
83 84 9.176460 TGATGTGATACAGATTTTTAGCATCAA 57.824 29.630 0.00 0.00 36.91 2.57
84 85 8.615211 GTGATGTGATACAGATTTTTAGCATCA 58.385 33.333 0.00 0.00 37.32 3.07
85 86 8.834465 AGTGATGTGATACAGATTTTTAGCATC 58.166 33.333 0.00 0.00 0.00 3.91
86 87 8.743085 AGTGATGTGATACAGATTTTTAGCAT 57.257 30.769 0.00 0.00 0.00 3.79
87 88 9.836864 ATAGTGATGTGATACAGATTTTTAGCA 57.163 29.630 0.00 0.00 0.00 3.49
119 120 5.104562 CTGTCATATAACAGGCAATGCTG 57.895 43.478 4.82 4.17 42.42 4.41
129 130 8.145122 TGTAGACAAACACACTGTCATATAACA 58.855 33.333 5.81 0.30 44.68 2.41
130 131 8.528917 TGTAGACAAACACACTGTCATATAAC 57.471 34.615 5.81 0.00 44.68 1.89
131 132 8.364894 ACTGTAGACAAACACACTGTCATATAA 58.635 33.333 5.81 0.00 44.68 0.98
132 133 7.812669 CACTGTAGACAAACACACTGTCATATA 59.187 37.037 5.81 0.00 44.68 0.86
133 134 6.646653 CACTGTAGACAAACACACTGTCATAT 59.353 38.462 5.81 0.00 44.68 1.78
134 135 5.983118 CACTGTAGACAAACACACTGTCATA 59.017 40.000 5.81 0.00 44.68 2.15
135 136 4.811024 CACTGTAGACAAACACACTGTCAT 59.189 41.667 5.81 0.00 44.68 3.06
136 137 4.081917 TCACTGTAGACAAACACACTGTCA 60.082 41.667 5.81 0.00 44.68 3.58
137 138 4.430007 TCACTGTAGACAAACACACTGTC 58.570 43.478 0.00 0.00 42.95 3.51
138 139 4.465632 TCACTGTAGACAAACACACTGT 57.534 40.909 0.00 0.00 0.00 3.55
139 140 4.260375 GCTTCACTGTAGACAAACACACTG 60.260 45.833 0.00 0.00 0.00 3.66
140 141 3.871594 GCTTCACTGTAGACAAACACACT 59.128 43.478 0.00 0.00 0.00 3.55
141 142 3.621268 TGCTTCACTGTAGACAAACACAC 59.379 43.478 0.00 0.00 0.00 3.82
142 143 3.867857 TGCTTCACTGTAGACAAACACA 58.132 40.909 0.00 0.00 0.00 3.72
143 144 4.319766 CCATGCTTCACTGTAGACAAACAC 60.320 45.833 0.00 0.00 0.00 3.32
144 145 3.814842 CCATGCTTCACTGTAGACAAACA 59.185 43.478 0.00 0.00 0.00 2.83
145 146 3.365364 GCCATGCTTCACTGTAGACAAAC 60.365 47.826 0.00 0.00 0.00 2.93
146 147 2.813754 GCCATGCTTCACTGTAGACAAA 59.186 45.455 0.00 0.00 0.00 2.83
147 148 2.038952 AGCCATGCTTCACTGTAGACAA 59.961 45.455 0.00 0.00 33.89 3.18
148 149 1.625315 AGCCATGCTTCACTGTAGACA 59.375 47.619 0.00 0.00 33.89 3.41
149 150 2.393271 AGCCATGCTTCACTGTAGAC 57.607 50.000 0.00 0.00 33.89 2.59
150 151 3.365472 TCTAGCCATGCTTCACTGTAGA 58.635 45.455 0.00 0.00 40.44 2.59
151 152 3.808466 TCTAGCCATGCTTCACTGTAG 57.192 47.619 0.00 0.00 40.44 2.74
152 153 4.406972 AGAATCTAGCCATGCTTCACTGTA 59.593 41.667 0.00 0.00 40.44 2.74
153 154 3.199508 AGAATCTAGCCATGCTTCACTGT 59.800 43.478 0.00 0.00 40.44 3.55
154 155 3.806380 AGAATCTAGCCATGCTTCACTG 58.194 45.455 0.00 0.00 40.44 3.66
155 156 4.070630 GAGAATCTAGCCATGCTTCACT 57.929 45.455 0.00 0.00 40.44 3.41
164 165 9.932824 CTTGCATCAAGACAGAGAATCTAGCCA 62.933 44.444 0.50 0.00 43.70 4.75
165 166 7.668509 CTTGCATCAAGACAGAGAATCTAGCC 61.669 46.154 0.50 0.00 43.70 3.93
166 167 5.234757 CTTGCATCAAGACAGAGAATCTAGC 59.765 44.000 0.50 0.00 43.70 3.42
167 168 5.754406 CCTTGCATCAAGACAGAGAATCTAG 59.246 44.000 8.04 0.00 43.70 2.43
168 169 5.668471 CCTTGCATCAAGACAGAGAATCTA 58.332 41.667 8.04 0.00 43.70 1.98
169 170 4.515361 CCTTGCATCAAGACAGAGAATCT 58.485 43.478 8.04 0.00 45.44 2.40
170 171 3.065095 GCCTTGCATCAAGACAGAGAATC 59.935 47.826 8.04 0.00 43.42 2.52
171 172 3.015327 GCCTTGCATCAAGACAGAGAAT 58.985 45.455 8.04 0.00 43.42 2.40
172 173 2.430465 GCCTTGCATCAAGACAGAGAA 58.570 47.619 8.04 0.00 43.42 2.87
173 174 1.673923 CGCCTTGCATCAAGACAGAGA 60.674 52.381 8.04 0.00 43.42 3.10
174 175 0.725686 CGCCTTGCATCAAGACAGAG 59.274 55.000 8.04 0.00 43.42 3.35
175 176 0.321346 TCGCCTTGCATCAAGACAGA 59.679 50.000 8.04 2.38 43.42 3.41
176 177 0.445436 GTCGCCTTGCATCAAGACAG 59.555 55.000 8.04 0.30 43.42 3.51
177 178 0.250252 TGTCGCCTTGCATCAAGACA 60.250 50.000 8.04 10.27 43.42 3.41
178 179 1.089920 ATGTCGCCTTGCATCAAGAC 58.910 50.000 8.04 0.00 43.42 3.01
179 180 1.089112 CATGTCGCCTTGCATCAAGA 58.911 50.000 8.04 0.00 43.42 3.02
180 181 1.089112 TCATGTCGCCTTGCATCAAG 58.911 50.000 0.00 0.00 40.75 3.02
181 182 1.672363 GATCATGTCGCCTTGCATCAA 59.328 47.619 0.00 0.00 0.00 2.57
182 183 1.302366 GATCATGTCGCCTTGCATCA 58.698 50.000 0.00 0.00 0.00 3.07
183 184 1.302366 TGATCATGTCGCCTTGCATC 58.698 50.000 0.00 0.00 0.00 3.91
184 185 1.878088 GATGATCATGTCGCCTTGCAT 59.122 47.619 14.30 0.00 0.00 3.96
185 186 1.302366 GATGATCATGTCGCCTTGCA 58.698 50.000 14.30 0.00 0.00 4.08
186 187 0.234106 CGATGATCATGTCGCCTTGC 59.766 55.000 14.30 0.00 0.00 4.01
187 188 1.856802 TCGATGATCATGTCGCCTTG 58.143 50.000 14.30 0.00 37.74 3.61
188 189 2.036346 TCATCGATGATCATGTCGCCTT 59.964 45.455 23.99 0.00 37.74 4.35
189 190 1.615392 TCATCGATGATCATGTCGCCT 59.385 47.619 23.99 0.63 37.74 5.52
190 191 1.723542 GTCATCGATGATCATGTCGCC 59.276 52.381 29.53 10.83 39.30 5.54
191 192 2.397549 TGTCATCGATGATCATGTCGC 58.602 47.619 29.53 15.09 39.30 5.19
192 193 5.587033 AAATGTCATCGATGATCATGTCG 57.413 39.130 29.53 12.74 39.30 4.35
193 194 7.383300 TGTCTAAATGTCATCGATGATCATGTC 59.617 37.037 29.53 16.46 39.30 3.06
194 195 7.212274 TGTCTAAATGTCATCGATGATCATGT 58.788 34.615 29.53 26.32 39.30 3.21
195 196 7.647907 TGTCTAAATGTCATCGATGATCATG 57.352 36.000 29.53 19.72 39.30 3.07
196 197 7.548427 GGATGTCTAAATGTCATCGATGATCAT 59.452 37.037 29.53 26.81 40.47 2.45
197 198 6.870439 GGATGTCTAAATGTCATCGATGATCA 59.130 38.462 29.53 25.98 40.47 2.92
198 199 7.063191 CAGGATGTCTAAATGTCATCGATGATC 59.937 40.741 29.53 21.91 40.47 2.92
199 200 6.872547 CAGGATGTCTAAATGTCATCGATGAT 59.127 38.462 29.53 16.77 40.47 2.45
200 201 6.218746 CAGGATGTCTAAATGTCATCGATGA 58.781 40.000 23.99 23.99 40.47 2.92
201 202 5.107182 GCAGGATGTCTAAATGTCATCGATG 60.107 44.000 19.61 19.61 40.47 3.84
202 203 4.993584 GCAGGATGTCTAAATGTCATCGAT 59.006 41.667 0.00 0.00 40.47 3.59
203 204 4.100035 AGCAGGATGTCTAAATGTCATCGA 59.900 41.667 0.00 0.00 40.47 3.59
204 205 4.375272 AGCAGGATGTCTAAATGTCATCG 58.625 43.478 0.00 0.00 40.47 3.84
205 206 5.050499 CGAAGCAGGATGTCTAAATGTCATC 60.050 44.000 0.00 0.00 39.41 2.92
206 207 4.813161 CGAAGCAGGATGTCTAAATGTCAT 59.187 41.667 0.00 0.00 39.31 3.06
207 208 4.183865 CGAAGCAGGATGTCTAAATGTCA 58.816 43.478 0.00 0.00 39.31 3.58
208 209 3.557595 CCGAAGCAGGATGTCTAAATGTC 59.442 47.826 0.00 0.00 39.31 3.06
209 210 3.055094 ACCGAAGCAGGATGTCTAAATGT 60.055 43.478 0.00 0.00 39.31 2.71
210 211 3.535561 ACCGAAGCAGGATGTCTAAATG 58.464 45.455 0.00 0.00 39.31 2.32
211 212 3.914426 ACCGAAGCAGGATGTCTAAAT 57.086 42.857 0.00 0.00 39.31 1.40
212 213 3.695830 AACCGAAGCAGGATGTCTAAA 57.304 42.857 0.00 0.00 39.31 1.85
213 214 3.695830 AAACCGAAGCAGGATGTCTAA 57.304 42.857 0.00 0.00 39.31 2.10
214 215 3.334691 CAAAACCGAAGCAGGATGTCTA 58.665 45.455 0.00 0.00 39.31 2.59
215 216 2.154462 CAAAACCGAAGCAGGATGTCT 58.846 47.619 0.00 0.00 39.31 3.41
216 217 1.200020 CCAAAACCGAAGCAGGATGTC 59.800 52.381 0.00 0.00 39.31 3.06
217 218 1.247567 CCAAAACCGAAGCAGGATGT 58.752 50.000 0.00 0.00 39.31 3.06
218 219 1.247567 ACCAAAACCGAAGCAGGATG 58.752 50.000 0.00 0.00 40.87 3.51
219 220 2.871096 TACCAAAACCGAAGCAGGAT 57.129 45.000 0.00 0.00 34.73 3.24
220 221 2.871096 ATACCAAAACCGAAGCAGGA 57.129 45.000 0.00 0.00 34.73 3.86
221 222 3.181500 GCTTATACCAAAACCGAAGCAGG 60.181 47.826 0.00 0.00 39.24 4.85
222 223 3.438781 TGCTTATACCAAAACCGAAGCAG 59.561 43.478 3.13 0.00 43.08 4.24
223 224 3.413327 TGCTTATACCAAAACCGAAGCA 58.587 40.909 3.13 3.13 45.07 3.91
224 225 4.095782 TGATGCTTATACCAAAACCGAAGC 59.904 41.667 0.00 0.00 39.74 3.86
225 226 5.811399 TGATGCTTATACCAAAACCGAAG 57.189 39.130 0.00 0.00 0.00 3.79
226 227 6.375736 TGAATGATGCTTATACCAAAACCGAA 59.624 34.615 0.00 0.00 0.00 4.30
227 228 5.883115 TGAATGATGCTTATACCAAAACCGA 59.117 36.000 0.00 0.00 0.00 4.69
228 229 6.038161 TCTGAATGATGCTTATACCAAAACCG 59.962 38.462 0.00 0.00 0.00 4.44
229 230 7.333528 TCTGAATGATGCTTATACCAAAACC 57.666 36.000 0.00 0.00 0.00 3.27
234 235 9.494271 GTTCTTATCTGAATGATGCTTATACCA 57.506 33.333 0.00 0.00 36.65 3.25
235 236 9.717942 AGTTCTTATCTGAATGATGCTTATACC 57.282 33.333 0.00 0.00 36.65 2.73
238 239 9.434420 GCTAGTTCTTATCTGAATGATGCTTAT 57.566 33.333 0.00 0.00 36.65 1.73
239 240 8.424133 TGCTAGTTCTTATCTGAATGATGCTTA 58.576 33.333 0.00 0.00 36.65 3.09
240 241 7.278135 TGCTAGTTCTTATCTGAATGATGCTT 58.722 34.615 0.00 0.00 36.65 3.91
241 242 6.824553 TGCTAGTTCTTATCTGAATGATGCT 58.175 36.000 0.00 0.00 36.65 3.79
242 243 7.011763 TGTTGCTAGTTCTTATCTGAATGATGC 59.988 37.037 0.00 0.00 36.65 3.91
243 244 8.429493 TGTTGCTAGTTCTTATCTGAATGATG 57.571 34.615 0.00 0.00 36.65 3.07
244 245 9.107177 CTTGTTGCTAGTTCTTATCTGAATGAT 57.893 33.333 0.00 0.00 39.11 2.45
245 246 8.097038 ACTTGTTGCTAGTTCTTATCTGAATGA 58.903 33.333 0.00 0.00 0.00 2.57
246 247 8.261492 ACTTGTTGCTAGTTCTTATCTGAATG 57.739 34.615 0.00 0.00 0.00 2.67
247 248 8.854614 AACTTGTTGCTAGTTCTTATCTGAAT 57.145 30.769 0.00 0.00 30.20 2.57
248 249 9.424319 CTAACTTGTTGCTAGTTCTTATCTGAA 57.576 33.333 0.00 0.00 37.12 3.02
249 250 8.803235 TCTAACTTGTTGCTAGTTCTTATCTGA 58.197 33.333 0.00 0.00 37.12 3.27
250 251 8.988064 TCTAACTTGTTGCTAGTTCTTATCTG 57.012 34.615 0.00 0.00 37.12 2.90
263 264 9.756461 GCTACTACTAAAAATCTAACTTGTTGC 57.244 33.333 0.00 0.00 0.00 4.17
318 319 3.399330 AGTCGGCGAGATTTCTCAAAAA 58.601 40.909 11.20 0.00 43.00 1.94
319 320 3.040147 AGTCGGCGAGATTTCTCAAAA 57.960 42.857 11.20 0.00 43.00 2.44
320 321 2.743636 AGTCGGCGAGATTTCTCAAA 57.256 45.000 11.20 0.00 43.00 2.69
321 322 2.743636 AAGTCGGCGAGATTTCTCAA 57.256 45.000 11.20 0.00 43.00 3.02
322 323 2.743636 AAAGTCGGCGAGATTTCTCA 57.256 45.000 11.20 0.00 43.00 3.27
323 324 3.771798 AGTAAAGTCGGCGAGATTTCTC 58.228 45.455 19.59 14.79 39.55 2.87
324 325 3.870633 AGTAAAGTCGGCGAGATTTCT 57.129 42.857 19.59 13.46 0.00 2.52
325 326 5.978322 AGATTAGTAAAGTCGGCGAGATTTC 59.022 40.000 19.59 11.71 0.00 2.17
326 327 5.903810 AGATTAGTAAAGTCGGCGAGATTT 58.096 37.500 11.20 16.96 0.00 2.17
327 328 5.517322 AGATTAGTAAAGTCGGCGAGATT 57.483 39.130 11.20 11.23 0.00 2.40
328 329 5.517322 AAGATTAGTAAAGTCGGCGAGAT 57.483 39.130 11.20 0.00 0.00 2.75
329 330 4.978083 AAGATTAGTAAAGTCGGCGAGA 57.022 40.909 11.20 0.00 0.00 4.04
330 331 7.695869 AATAAAGATTAGTAAAGTCGGCGAG 57.304 36.000 11.20 0.00 0.00 5.03
331 332 8.483307 AAAATAAAGATTAGTAAAGTCGGCGA 57.517 30.769 4.99 4.99 0.00 5.54
1445 1988 2.439156 GCGCCATGGAAGCTCCTT 60.439 61.111 18.40 0.00 37.46 3.36
1796 5718 0.314302 ATAATCGTCGCTCTTCCGGG 59.686 55.000 0.00 0.00 0.00 5.73
2264 6186 3.638160 ACGTCAACAAGACCACTTACCTA 59.362 43.478 0.00 0.00 44.66 3.08
2466 6388 4.730042 CGAAAGTAATTGTGCATCATTCGG 59.270 41.667 0.00 0.00 34.99 4.30


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

AutoCloner maintained by Alex Coulton.