Multiple sequence alignment - TraesCS2A01G003800

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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 TraesCS2A01G003800 chr2A 100.000 2669 0 0 1 2669 2353982 2351314 0.000000e+00 4929.0
1 TraesCS2A01G003800 chr2A 94.706 2380 99 15 300 2669 17875225 17877587 0.000000e+00 3672.0
2 TraesCS2A01G003800 chr2A 93.976 2291 117 11 388 2669 726337343 726335065 0.000000e+00 3446.0
3 TraesCS2A01G003800 chr2A 92.653 2382 126 22 300 2669 102100667 102098323 0.000000e+00 3384.0
4 TraesCS2A01G003800 chr2A 80.371 377 52 18 300 671 41620336 41619977 1.580000e-67 267.0
5 TraesCS2A01G003800 chr2A 76.429 560 79 33 296 829 601845898 601845366 1.230000e-63 254.0
6 TraesCS2A01G003800 chr2A 77.670 412 68 19 300 706 41610059 41610451 2.070000e-56 230.0
7 TraesCS2A01G003800 chr2A 84.615 156 12 5 12 162 2937319 2937171 7.700000e-31 145.0
8 TraesCS2A01G003800 chr2A 86.364 132 13 4 300 429 605390903 605391031 3.580000e-29 139.0
9 TraesCS2A01G003800 chr2A 80.723 166 25 4 300 463 102086990 102087150 3.610000e-24 122.0
10 TraesCS2A01G003800 chr5A 94.402 2376 123 8 300 2669 705322828 705320457 0.000000e+00 3642.0
11 TraesCS2A01G003800 chr5A 96.344 2188 62 11 403 2583 531334517 531336693 0.000000e+00 3581.0
12 TraesCS2A01G003800 chr4B 94.249 2382 107 18 300 2669 87429583 87427220 0.000000e+00 3613.0
13 TraesCS2A01G003800 chrUn 95.425 2273 87 5 400 2669 118925340 118923082 0.000000e+00 3605.0
14 TraesCS2A01G003800 chr6A 95.779 2156 80 5 512 2657 158947938 158950092 0.000000e+00 3467.0
15 TraesCS2A01G003800 chr3A 93.167 2371 133 17 300 2657 184665350 184667704 0.000000e+00 3454.0
16 TraesCS2A01G003800 chr7B 88.498 426 41 8 300 721 63646587 63647008 2.370000e-140 508.0
17 TraesCS2A01G003800 chr2D 88.746 311 7 10 8 294 2356086 2355780 3.270000e-94 355.0
18 TraesCS2A01G003800 chr2B 90.909 66 6 0 8 73 8622043 8621978 3.660000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G003800 chr2A 2351314 2353982 2668 True 4929 4929 100.000 1 2669 1 chr2A.!!$R1 2668
1 TraesCS2A01G003800 chr2A 17875225 17877587 2362 False 3672 3672 94.706 300 2669 1 chr2A.!!$F1 2369
2 TraesCS2A01G003800 chr2A 726335065 726337343 2278 True 3446 3446 93.976 388 2669 1 chr2A.!!$R6 2281
3 TraesCS2A01G003800 chr2A 102098323 102100667 2344 True 3384 3384 92.653 300 2669 1 chr2A.!!$R4 2369
4 TraesCS2A01G003800 chr2A 601845366 601845898 532 True 254 254 76.429 296 829 1 chr2A.!!$R5 533
5 TraesCS2A01G003800 chr5A 705320457 705322828 2371 True 3642 3642 94.402 300 2669 1 chr5A.!!$R1 2369
6 TraesCS2A01G003800 chr5A 531334517 531336693 2176 False 3581 3581 96.344 403 2583 1 chr5A.!!$F1 2180
7 TraesCS2A01G003800 chr4B 87427220 87429583 2363 True 3613 3613 94.249 300 2669 1 chr4B.!!$R1 2369
8 TraesCS2A01G003800 chrUn 118923082 118925340 2258 True 3605 3605 95.425 400 2669 1 chrUn.!!$R1 2269
9 TraesCS2A01G003800 chr6A 158947938 158950092 2154 False 3467 3467 95.779 512 2657 1 chr6A.!!$F1 2145
10 TraesCS2A01G003800 chr3A 184665350 184667704 2354 False 3454 3454 93.167 300 2657 1 chr3A.!!$F1 2357

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
126 127 0.038435 TCGATCGCGGGTTGTTGTTA 60.038 50.0 11.09 0.0 38.28 2.41 F
200 201 0.041238 TTGGGGTTGTTGGTTGGTCA 59.959 50.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1290 1324 0.553819 ACAGAGGCGGAGGAGACTAT 59.446 55.0 0.0 0.0 44.43 2.12 R
2163 2202 0.813184 CTGCATCGTCAAAGGGCAAT 59.187 50.0 0.0 0.0 33.58 3.56 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 7.966246 ATATTCAACAATTTGCTTGCAAGAA 57.034 28.000 30.39 18.21 38.50 2.52
25 26 6.870971 ATTCAACAATTTGCTTGCAAGAAT 57.129 29.167 30.39 17.91 38.50 2.40
26 27 7.966246 ATTCAACAATTTGCTTGCAAGAATA 57.034 28.000 30.39 15.62 38.50 1.75
27 28 7.410800 TTCAACAATTTGCTTGCAAGAATAG 57.589 32.000 30.39 15.07 38.50 1.73
28 29 6.747125 TCAACAATTTGCTTGCAAGAATAGA 58.253 32.000 30.39 9.27 38.50 1.98
29 30 7.380536 TCAACAATTTGCTTGCAAGAATAGAT 58.619 30.769 30.39 11.18 38.50 1.98
30 31 7.543172 TCAACAATTTGCTTGCAAGAATAGATC 59.457 33.333 30.39 10.65 38.50 2.75
31 32 6.335777 ACAATTTGCTTGCAAGAATAGATCC 58.664 36.000 30.39 9.90 38.50 3.36
32 33 6.071221 ACAATTTGCTTGCAAGAATAGATCCA 60.071 34.615 30.39 12.48 38.50 3.41
33 34 6.726490 ATTTGCTTGCAAGAATAGATCCAT 57.274 33.333 30.39 7.14 0.00 3.41
34 35 5.509716 TTGCTTGCAAGAATAGATCCATG 57.490 39.130 30.39 0.00 0.00 3.66
35 36 3.887110 TGCTTGCAAGAATAGATCCATGG 59.113 43.478 30.39 4.97 0.00 3.66
36 37 4.139786 GCTTGCAAGAATAGATCCATGGA 58.860 43.478 30.39 18.88 0.00 3.41
37 38 4.023365 GCTTGCAAGAATAGATCCATGGAC 60.023 45.833 30.39 11.34 0.00 4.02
38 39 4.776435 TGCAAGAATAGATCCATGGACA 57.224 40.909 18.99 5.72 0.00 4.02
39 40 5.314718 TGCAAGAATAGATCCATGGACAT 57.685 39.130 18.99 11.33 0.00 3.06
40 41 6.438186 TGCAAGAATAGATCCATGGACATA 57.562 37.500 18.99 13.34 0.00 2.29
41 42 7.024345 TGCAAGAATAGATCCATGGACATAT 57.976 36.000 18.99 15.10 0.00 1.78
42 43 8.149631 TGCAAGAATAGATCCATGGACATATA 57.850 34.615 18.99 4.15 0.00 0.86
43 44 8.605065 TGCAAGAATAGATCCATGGACATATAA 58.395 33.333 18.99 0.00 0.00 0.98
44 45 9.453572 GCAAGAATAGATCCATGGACATATAAA 57.546 33.333 18.99 0.00 0.00 1.40
52 53 9.293404 AGATCCATGGACATATAAAAAGATGTG 57.707 33.333 18.99 0.00 36.42 3.21
53 54 7.822161 TCCATGGACATATAAAAAGATGTGG 57.178 36.000 11.44 0.00 36.42 4.17
54 55 6.265196 TCCATGGACATATAAAAAGATGTGGC 59.735 38.462 11.44 0.00 36.42 5.01
55 56 5.749596 TGGACATATAAAAAGATGTGGCG 57.250 39.130 0.00 0.00 36.42 5.69
56 57 4.036262 TGGACATATAAAAAGATGTGGCGC 59.964 41.667 0.00 0.00 36.42 6.53
57 58 4.275936 GGACATATAAAAAGATGTGGCGCT 59.724 41.667 7.64 0.00 36.42 5.92
58 59 5.424121 ACATATAAAAAGATGTGGCGCTC 57.576 39.130 7.64 1.21 34.98 5.03
59 60 4.881273 ACATATAAAAAGATGTGGCGCTCA 59.119 37.500 7.64 7.90 34.98 4.26
60 61 3.764885 ATAAAAAGATGTGGCGCTCAC 57.235 42.857 18.49 18.49 46.23 3.51
69 70 2.178474 GTGGCGCTCACATTTACATG 57.822 50.000 19.85 0.00 45.39 3.21
70 71 1.468520 GTGGCGCTCACATTTACATGT 59.531 47.619 19.85 2.69 45.18 3.21
71 72 2.675844 GTGGCGCTCACATTTACATGTA 59.324 45.455 19.85 0.08 42.14 2.29
72 73 2.935849 TGGCGCTCACATTTACATGTAG 59.064 45.455 7.64 0.00 42.14 2.74
73 74 2.286418 GGCGCTCACATTTACATGTAGC 60.286 50.000 7.64 5.10 42.14 3.58
74 75 2.609459 GCGCTCACATTTACATGTAGCT 59.391 45.455 5.56 0.00 42.14 3.32
75 76 3.544834 GCGCTCACATTTACATGTAGCTG 60.545 47.826 5.56 9.90 42.14 4.24
76 77 3.001634 CGCTCACATTTACATGTAGCTGG 59.998 47.826 16.57 7.62 42.14 4.85
77 78 3.941483 GCTCACATTTACATGTAGCTGGT 59.059 43.478 16.57 8.12 42.14 4.00
78 79 4.201851 GCTCACATTTACATGTAGCTGGTG 60.202 45.833 16.57 16.54 42.14 4.17
79 80 3.689161 TCACATTTACATGTAGCTGGTGC 59.311 43.478 17.26 0.00 42.14 5.01
80 81 2.677836 ACATTTACATGTAGCTGGTGCG 59.322 45.455 16.57 2.36 42.24 5.34
81 82 2.465860 TTTACATGTAGCTGGTGCGT 57.534 45.000 5.56 0.00 45.42 5.24
82 83 2.465860 TTACATGTAGCTGGTGCGTT 57.534 45.000 5.56 0.00 45.42 4.84
83 84 2.465860 TACATGTAGCTGGTGCGTTT 57.534 45.000 0.08 0.00 45.42 3.60
84 85 2.465860 ACATGTAGCTGGTGCGTTTA 57.534 45.000 0.00 0.00 45.42 2.01
85 86 2.346803 ACATGTAGCTGGTGCGTTTAG 58.653 47.619 0.00 0.00 45.42 1.85
86 87 2.289444 ACATGTAGCTGGTGCGTTTAGT 60.289 45.455 0.00 0.00 45.42 2.24
87 88 3.056393 ACATGTAGCTGGTGCGTTTAGTA 60.056 43.478 0.00 0.00 45.42 1.82
88 89 3.226346 TGTAGCTGGTGCGTTTAGTAG 57.774 47.619 0.00 0.00 45.42 2.57
89 90 2.821378 TGTAGCTGGTGCGTTTAGTAGA 59.179 45.455 0.00 0.00 45.42 2.59
90 91 3.256383 TGTAGCTGGTGCGTTTAGTAGAA 59.744 43.478 0.00 0.00 45.42 2.10
91 92 3.396260 AGCTGGTGCGTTTAGTAGAAA 57.604 42.857 0.00 0.00 45.42 2.52
92 93 3.326747 AGCTGGTGCGTTTAGTAGAAAG 58.673 45.455 0.00 0.00 45.42 2.62
93 94 3.006537 AGCTGGTGCGTTTAGTAGAAAGA 59.993 43.478 0.00 0.00 45.42 2.52
94 95 3.744426 GCTGGTGCGTTTAGTAGAAAGAA 59.256 43.478 0.00 0.00 0.00 2.52
95 96 4.143094 GCTGGTGCGTTTAGTAGAAAGAAG 60.143 45.833 0.00 0.00 0.00 2.85
96 97 5.204409 TGGTGCGTTTAGTAGAAAGAAGA 57.796 39.130 0.00 0.00 0.00 2.87
97 98 5.603596 TGGTGCGTTTAGTAGAAAGAAGAA 58.396 37.500 0.00 0.00 0.00 2.52
98 99 6.228258 TGGTGCGTTTAGTAGAAAGAAGAAT 58.772 36.000 0.00 0.00 0.00 2.40
99 100 6.147164 TGGTGCGTTTAGTAGAAAGAAGAATG 59.853 38.462 0.00 0.00 0.00 2.67
100 101 6.147328 GGTGCGTTTAGTAGAAAGAAGAATGT 59.853 38.462 0.00 0.00 0.00 2.71
101 102 7.330208 GGTGCGTTTAGTAGAAAGAAGAATGTA 59.670 37.037 0.00 0.00 0.00 2.29
102 103 8.870879 GTGCGTTTAGTAGAAAGAAGAATGTAT 58.129 33.333 0.00 0.00 0.00 2.29
103 104 8.869897 TGCGTTTAGTAGAAAGAAGAATGTATG 58.130 33.333 0.00 0.00 0.00 2.39
104 105 9.084164 GCGTTTAGTAGAAAGAAGAATGTATGA 57.916 33.333 0.00 0.00 0.00 2.15
109 110 7.484975 AGTAGAAAGAAGAATGTATGAGGTCG 58.515 38.462 0.00 0.00 0.00 4.79
110 111 6.531503 AGAAAGAAGAATGTATGAGGTCGA 57.468 37.500 0.00 0.00 0.00 4.20
111 112 7.118496 AGAAAGAAGAATGTATGAGGTCGAT 57.882 36.000 0.00 0.00 0.00 3.59
112 113 7.206687 AGAAAGAAGAATGTATGAGGTCGATC 58.793 38.462 0.00 0.00 0.00 3.69
113 114 5.114785 AGAAGAATGTATGAGGTCGATCG 57.885 43.478 9.36 9.36 0.00 3.69
114 115 3.290308 AGAATGTATGAGGTCGATCGC 57.710 47.619 11.09 5.58 0.00 4.58
115 116 1.979469 GAATGTATGAGGTCGATCGCG 59.021 52.381 11.09 0.00 39.35 5.87
116 117 0.241213 ATGTATGAGGTCGATCGCGG 59.759 55.000 11.09 0.00 38.28 6.46
117 118 1.081376 GTATGAGGTCGATCGCGGG 60.081 63.158 11.09 0.00 38.28 6.13
118 119 1.527611 TATGAGGTCGATCGCGGGT 60.528 57.895 11.09 0.00 38.28 5.28
119 120 1.105167 TATGAGGTCGATCGCGGGTT 61.105 55.000 11.09 0.00 38.28 4.11
120 121 2.582498 GAGGTCGATCGCGGGTTG 60.582 66.667 11.09 0.00 38.28 3.77
121 122 3.352338 GAGGTCGATCGCGGGTTGT 62.352 63.158 11.09 0.00 38.28 3.32
122 123 2.433664 GGTCGATCGCGGGTTGTT 60.434 61.111 11.09 0.00 38.28 2.83
123 124 2.736682 GGTCGATCGCGGGTTGTTG 61.737 63.158 11.09 0.00 38.28 3.33
124 125 2.025418 GTCGATCGCGGGTTGTTGT 61.025 57.895 11.09 0.00 38.28 3.32
125 126 1.301087 TCGATCGCGGGTTGTTGTT 60.301 52.632 11.09 0.00 38.28 2.83
126 127 0.038435 TCGATCGCGGGTTGTTGTTA 60.038 50.000 11.09 0.00 38.28 2.41
127 128 1.003851 CGATCGCGGGTTGTTGTTAT 58.996 50.000 6.13 0.00 0.00 1.89
128 129 1.005347 CGATCGCGGGTTGTTGTTATC 60.005 52.381 6.13 0.00 0.00 1.75
129 130 2.004017 GATCGCGGGTTGTTGTTATCA 58.996 47.619 6.13 0.00 0.00 2.15
130 131 1.149987 TCGCGGGTTGTTGTTATCAC 58.850 50.000 6.13 0.00 0.00 3.06
131 132 1.153353 CGCGGGTTGTTGTTATCACT 58.847 50.000 0.00 0.00 0.00 3.41
132 133 1.136085 CGCGGGTTGTTGTTATCACTG 60.136 52.381 0.00 0.00 0.00 3.66
133 134 1.877443 GCGGGTTGTTGTTATCACTGT 59.123 47.619 0.00 0.00 0.00 3.55
134 135 2.350388 GCGGGTTGTTGTTATCACTGTG 60.350 50.000 0.17 0.17 0.00 3.66
135 136 2.875933 CGGGTTGTTGTTATCACTGTGT 59.124 45.455 7.79 0.00 0.00 3.72
136 137 3.303725 CGGGTTGTTGTTATCACTGTGTG 60.304 47.826 7.79 0.00 34.45 3.82
137 138 3.004315 GGGTTGTTGTTATCACTGTGTGG 59.996 47.826 7.79 0.00 33.87 4.17
138 139 3.550030 GGTTGTTGTTATCACTGTGTGGC 60.550 47.826 7.79 0.00 33.87 5.01
139 140 2.924421 TGTTGTTATCACTGTGTGGCA 58.076 42.857 7.79 0.95 33.87 4.92
140 141 3.282885 TGTTGTTATCACTGTGTGGCAA 58.717 40.909 7.79 6.70 33.87 4.52
141 142 3.888323 TGTTGTTATCACTGTGTGGCAAT 59.112 39.130 7.79 0.00 33.87 3.56
142 143 4.229096 GTTGTTATCACTGTGTGGCAATG 58.771 43.478 7.79 0.00 33.87 2.82
143 144 3.749226 TGTTATCACTGTGTGGCAATGA 58.251 40.909 7.79 0.00 37.76 2.57
144 145 3.752747 TGTTATCACTGTGTGGCAATGAG 59.247 43.478 7.79 0.00 36.74 2.90
145 146 2.865119 ATCACTGTGTGGCAATGAGA 57.135 45.000 7.79 0.00 36.74 3.27
146 147 1.882912 TCACTGTGTGGCAATGAGAC 58.117 50.000 7.79 0.00 33.87 3.36
147 148 0.514255 CACTGTGTGGCAATGAGACG 59.486 55.000 0.00 0.00 0.00 4.18
148 149 0.106708 ACTGTGTGGCAATGAGACGT 59.893 50.000 0.00 0.00 0.00 4.34
149 150 0.514255 CTGTGTGGCAATGAGACGTG 59.486 55.000 0.00 0.00 0.00 4.49
150 151 0.884259 TGTGTGGCAATGAGACGTGG 60.884 55.000 0.00 0.00 0.00 4.94
151 152 1.302431 TGTGGCAATGAGACGTGGG 60.302 57.895 0.00 0.00 0.00 4.61
152 153 1.302511 GTGGCAATGAGACGTGGGT 60.303 57.895 0.00 0.00 0.00 4.51
153 154 1.302431 TGGCAATGAGACGTGGGTG 60.302 57.895 0.00 0.00 0.00 4.61
154 155 1.302511 GGCAATGAGACGTGGGTGT 60.303 57.895 0.00 0.00 0.00 4.16
155 156 1.577328 GGCAATGAGACGTGGGTGTG 61.577 60.000 0.00 0.00 0.00 3.82
156 157 1.868997 CAATGAGACGTGGGTGTGC 59.131 57.895 0.00 0.00 0.00 4.57
157 158 0.603707 CAATGAGACGTGGGTGTGCT 60.604 55.000 0.00 0.00 0.00 4.40
158 159 0.108585 AATGAGACGTGGGTGTGCTT 59.891 50.000 0.00 0.00 0.00 3.91
159 160 0.108585 ATGAGACGTGGGTGTGCTTT 59.891 50.000 0.00 0.00 0.00 3.51
160 161 0.813610 TGAGACGTGGGTGTGCTTTG 60.814 55.000 0.00 0.00 0.00 2.77
161 162 1.507141 GAGACGTGGGTGTGCTTTGG 61.507 60.000 0.00 0.00 0.00 3.28
162 163 3.194272 GACGTGGGTGTGCTTTGGC 62.194 63.158 0.00 0.00 39.26 4.52
175 176 3.684908 TGCTTTGGCATGTACTATGTGT 58.315 40.909 0.00 0.00 44.28 3.72
176 177 3.689161 TGCTTTGGCATGTACTATGTGTC 59.311 43.478 0.00 0.00 44.28 3.67
177 178 3.941483 GCTTTGGCATGTACTATGTGTCT 59.059 43.478 0.00 0.00 38.54 3.41
178 179 4.034510 GCTTTGGCATGTACTATGTGTCTC 59.965 45.833 0.00 0.00 38.54 3.36
179 180 3.819564 TGGCATGTACTATGTGTCTCC 57.180 47.619 0.00 0.00 0.00 3.71
180 181 2.100749 TGGCATGTACTATGTGTCTCCG 59.899 50.000 0.00 0.00 0.00 4.63
181 182 2.100916 GGCATGTACTATGTGTCTCCGT 59.899 50.000 0.00 0.00 0.00 4.69
182 183 3.430374 GGCATGTACTATGTGTCTCCGTT 60.430 47.826 0.00 0.00 0.00 4.44
183 184 3.551890 GCATGTACTATGTGTCTCCGTTG 59.448 47.826 0.00 0.00 0.00 4.10
184 185 3.861276 TGTACTATGTGTCTCCGTTGG 57.139 47.619 0.00 0.00 0.00 3.77
185 186 2.494471 TGTACTATGTGTCTCCGTTGGG 59.506 50.000 0.00 0.00 0.00 4.12
186 187 0.902531 ACTATGTGTCTCCGTTGGGG 59.097 55.000 0.00 0.00 37.02 4.96
187 188 0.902531 CTATGTGTCTCCGTTGGGGT 59.097 55.000 0.00 0.00 37.00 4.95
188 189 1.278127 CTATGTGTCTCCGTTGGGGTT 59.722 52.381 0.00 0.00 37.00 4.11
189 190 0.250727 ATGTGTCTCCGTTGGGGTTG 60.251 55.000 0.00 0.00 37.00 3.77
190 191 1.147600 GTGTCTCCGTTGGGGTTGT 59.852 57.895 0.00 0.00 37.00 3.32
191 192 0.464916 GTGTCTCCGTTGGGGTTGTT 60.465 55.000 0.00 0.00 37.00 2.83
192 193 0.464735 TGTCTCCGTTGGGGTTGTTG 60.465 55.000 0.00 0.00 37.00 3.33
193 194 1.149627 TCTCCGTTGGGGTTGTTGG 59.850 57.895 0.00 0.00 37.00 3.77
194 195 1.152839 CTCCGTTGGGGTTGTTGGT 60.153 57.895 0.00 0.00 37.00 3.67
195 196 0.753848 CTCCGTTGGGGTTGTTGGTT 60.754 55.000 0.00 0.00 37.00 3.67
196 197 1.038130 TCCGTTGGGGTTGTTGGTTG 61.038 55.000 0.00 0.00 37.00 3.77
197 198 1.439644 CGTTGGGGTTGTTGGTTGG 59.560 57.895 0.00 0.00 0.00 3.77
198 199 1.324005 CGTTGGGGTTGTTGGTTGGT 61.324 55.000 0.00 0.00 0.00 3.67
199 200 0.462375 GTTGGGGTTGTTGGTTGGTC 59.538 55.000 0.00 0.00 0.00 4.02
200 201 0.041238 TTGGGGTTGTTGGTTGGTCA 59.959 50.000 0.00 0.00 0.00 4.02
201 202 0.684805 TGGGGTTGTTGGTTGGTCAC 60.685 55.000 0.00 0.00 0.00 3.67
202 203 0.396556 GGGGTTGTTGGTTGGTCACT 60.397 55.000 0.00 0.00 0.00 3.41
203 204 1.133730 GGGGTTGTTGGTTGGTCACTA 60.134 52.381 0.00 0.00 0.00 2.74
204 205 2.227194 GGGTTGTTGGTTGGTCACTAG 58.773 52.381 0.00 0.00 0.00 2.57
205 206 2.158726 GGGTTGTTGGTTGGTCACTAGA 60.159 50.000 0.00 0.00 0.00 2.43
206 207 2.876550 GGTTGTTGGTTGGTCACTAGAC 59.123 50.000 0.00 0.00 44.21 2.59
207 208 3.433173 GGTTGTTGGTTGGTCACTAGACT 60.433 47.826 0.00 0.00 44.36 3.24
208 209 4.202284 GGTTGTTGGTTGGTCACTAGACTA 60.202 45.833 0.00 0.00 44.36 2.59
209 210 4.866508 TGTTGGTTGGTCACTAGACTAG 57.133 45.455 8.00 8.00 44.36 2.57
210 211 4.476297 TGTTGGTTGGTCACTAGACTAGA 58.524 43.478 16.55 0.00 44.36 2.43
211 212 4.523173 TGTTGGTTGGTCACTAGACTAGAG 59.477 45.833 16.55 8.52 44.36 2.43
212 213 4.383931 TGGTTGGTCACTAGACTAGAGT 57.616 45.455 16.55 0.00 44.36 3.24
213 214 4.079970 TGGTTGGTCACTAGACTAGAGTG 58.920 47.826 16.55 7.73 44.36 3.51
214 215 3.119424 GGTTGGTCACTAGACTAGAGTGC 60.119 52.174 16.55 6.20 43.37 4.40
215 216 2.357075 TGGTCACTAGACTAGAGTGCG 58.643 52.381 16.55 0.00 43.37 5.34
216 217 2.290134 TGGTCACTAGACTAGAGTGCGT 60.290 50.000 16.55 0.00 43.37 5.24
217 218 2.096174 GGTCACTAGACTAGAGTGCGTG 59.904 54.545 16.55 3.94 43.37 5.34
218 219 1.738350 TCACTAGACTAGAGTGCGTGC 59.262 52.381 16.55 0.00 43.37 5.34
219 220 1.468914 CACTAGACTAGAGTGCGTGCA 59.531 52.381 16.55 0.00 38.06 4.57
220 221 1.740585 ACTAGACTAGAGTGCGTGCAG 59.259 52.381 16.55 0.00 0.00 4.41
234 235 4.198625 GCAGCAGCACTCCACTAG 57.801 61.111 0.00 0.00 41.58 2.57
235 236 1.294780 GCAGCAGCACTCCACTAGT 59.705 57.895 0.00 0.00 41.58 2.57
236 237 0.321122 GCAGCAGCACTCCACTAGTT 60.321 55.000 0.00 0.00 41.58 2.24
237 238 1.879796 GCAGCAGCACTCCACTAGTTT 60.880 52.381 0.00 0.00 41.58 2.66
238 239 1.802960 CAGCAGCACTCCACTAGTTTG 59.197 52.381 0.00 0.00 35.76 2.93
239 240 1.417890 AGCAGCACTCCACTAGTTTGT 59.582 47.619 0.00 0.00 35.76 2.83
240 241 1.532868 GCAGCACTCCACTAGTTTGTG 59.467 52.381 12.65 12.65 35.76 3.33
241 242 2.806745 GCAGCACTCCACTAGTTTGTGA 60.807 50.000 18.33 3.36 40.12 3.58
242 243 3.668447 CAGCACTCCACTAGTTTGTGAT 58.332 45.455 18.33 12.11 40.12 3.06
243 244 3.434641 CAGCACTCCACTAGTTTGTGATG 59.565 47.826 17.51 17.51 40.12 3.07
244 245 3.324846 AGCACTCCACTAGTTTGTGATGA 59.675 43.478 18.33 0.00 40.12 2.92
245 246 4.065088 GCACTCCACTAGTTTGTGATGAA 58.935 43.478 18.33 0.00 40.12 2.57
246 247 4.083802 GCACTCCACTAGTTTGTGATGAAC 60.084 45.833 18.33 2.83 40.12 3.18
247 248 5.056480 CACTCCACTAGTTTGTGATGAACA 58.944 41.667 11.94 0.00 40.12 3.18
248 249 5.050091 CACTCCACTAGTTTGTGATGAACAC 60.050 44.000 11.94 0.00 42.36 3.32
249 250 7.400309 CACTCCACTAGTTTGTGATGAACACA 61.400 42.308 11.94 0.00 46.43 3.72
258 259 2.636647 TGATGAACACAACCAGAGCA 57.363 45.000 0.00 0.00 0.00 4.26
259 260 3.144657 TGATGAACACAACCAGAGCAT 57.855 42.857 0.00 0.00 0.00 3.79
260 261 3.489355 TGATGAACACAACCAGAGCATT 58.511 40.909 0.00 0.00 0.00 3.56
261 262 4.650734 TGATGAACACAACCAGAGCATTA 58.349 39.130 0.00 0.00 0.00 1.90
262 263 5.069318 TGATGAACACAACCAGAGCATTAA 58.931 37.500 0.00 0.00 0.00 1.40
263 264 5.534278 TGATGAACACAACCAGAGCATTAAA 59.466 36.000 0.00 0.00 0.00 1.52
264 265 5.181690 TGAACACAACCAGAGCATTAAAC 57.818 39.130 0.00 0.00 0.00 2.01
265 266 4.642437 TGAACACAACCAGAGCATTAAACA 59.358 37.500 0.00 0.00 0.00 2.83
266 267 5.126222 TGAACACAACCAGAGCATTAAACAA 59.874 36.000 0.00 0.00 0.00 2.83
267 268 5.590530 ACACAACCAGAGCATTAAACAAA 57.409 34.783 0.00 0.00 0.00 2.83
268 269 5.348164 ACACAACCAGAGCATTAAACAAAC 58.652 37.500 0.00 0.00 0.00 2.93
269 270 5.127031 ACACAACCAGAGCATTAAACAAACT 59.873 36.000 0.00 0.00 0.00 2.66
270 271 6.042143 CACAACCAGAGCATTAAACAAACTT 58.958 36.000 0.00 0.00 0.00 2.66
271 272 7.147983 ACACAACCAGAGCATTAAACAAACTTA 60.148 33.333 0.00 0.00 0.00 2.24
272 273 7.704472 CACAACCAGAGCATTAAACAAACTTAA 59.296 33.333 0.00 0.00 0.00 1.85
273 274 7.704899 ACAACCAGAGCATTAAACAAACTTAAC 59.295 33.333 0.00 0.00 0.00 2.01
274 275 7.582667 ACCAGAGCATTAAACAAACTTAACT 57.417 32.000 0.00 0.00 0.00 2.24
275 276 7.649057 ACCAGAGCATTAAACAAACTTAACTC 58.351 34.615 0.00 0.00 0.00 3.01
276 277 7.502561 ACCAGAGCATTAAACAAACTTAACTCT 59.497 33.333 0.00 0.00 30.27 3.24
277 278 8.999431 CCAGAGCATTAAACAAACTTAACTCTA 58.001 33.333 0.00 0.00 29.66 2.43
278 279 9.813080 CAGAGCATTAAACAAACTTAACTCTAC 57.187 33.333 0.00 0.00 29.66 2.59
279 280 9.780186 AGAGCATTAAACAAACTTAACTCTACT 57.220 29.630 0.00 0.00 29.29 2.57
287 288 7.706100 ACAAACTTAACTCTACTAGAGGAGG 57.294 40.000 16.10 7.62 46.45 4.30
288 289 7.468496 ACAAACTTAACTCTACTAGAGGAGGA 58.532 38.462 16.10 0.84 46.45 3.71
289 290 7.949006 ACAAACTTAACTCTACTAGAGGAGGAA 59.051 37.037 16.10 11.05 46.45 3.36
290 291 8.463607 CAAACTTAACTCTACTAGAGGAGGAAG 58.536 40.741 16.10 17.97 46.45 3.46
291 292 7.513560 ACTTAACTCTACTAGAGGAGGAAGA 57.486 40.000 22.99 7.53 46.45 2.87
292 293 7.931046 ACTTAACTCTACTAGAGGAGGAAGAA 58.069 38.462 22.99 12.30 46.45 2.52
293 294 8.050930 ACTTAACTCTACTAGAGGAGGAAGAAG 58.949 40.741 22.99 18.15 46.45 2.85
294 295 6.645884 AACTCTACTAGAGGAGGAAGAAGA 57.354 41.667 16.10 0.00 46.45 2.87
295 296 6.645884 ACTCTACTAGAGGAGGAAGAAGAA 57.354 41.667 16.10 0.00 46.45 2.52
296 297 6.659824 ACTCTACTAGAGGAGGAAGAAGAAG 58.340 44.000 16.10 0.00 46.45 2.85
297 298 6.445786 ACTCTACTAGAGGAGGAAGAAGAAGA 59.554 42.308 16.10 0.00 46.45 2.87
298 299 7.128883 ACTCTACTAGAGGAGGAAGAAGAAGAT 59.871 40.741 16.10 0.00 46.45 2.40
322 323 0.481128 TTGTCCAAAAGGACCCCCTC 59.519 55.000 11.79 0.00 43.48 4.30
323 324 1.002502 GTCCAAAAGGACCCCCTCG 60.003 63.158 3.27 0.00 43.48 4.63
329 330 4.974438 AGGACCCCCTCGCCAACA 62.974 66.667 0.00 0.00 38.86 3.33
706 721 2.510238 GCAGACGGCGCTGATTCT 60.510 61.111 25.98 13.80 38.14 2.40
803 834 1.202557 CCTGCCTTTGCTTCTTTTGCA 60.203 47.619 0.00 0.00 38.71 4.08
846 879 2.413765 CGAGGCTACGGGAAGCTC 59.586 66.667 6.63 0.00 42.37 4.09
847 880 2.415608 CGAGGCTACGGGAAGCTCA 61.416 63.158 6.63 0.00 42.37 4.26
910 943 3.026630 TCTCGCCATCATTTATCGTCC 57.973 47.619 0.00 0.00 0.00 4.79
954 987 1.965754 GCTCTCGTCCAGCCATCCTT 61.966 60.000 0.00 0.00 0.00 3.36
1206 1240 5.775701 ACCCATAGCTATTTCAGAGTACGAT 59.224 40.000 2.64 0.00 0.00 3.73
1250 1284 7.042797 ACCATCACAAATAGATATTGTTGGC 57.957 36.000 9.07 0.00 40.16 4.52
1525 1562 5.388599 AGGAAAGAAAAACAGGGAAGAGA 57.611 39.130 0.00 0.00 0.00 3.10
1548 1585 2.108566 CGCATGGAGGAGCAGGAG 59.891 66.667 0.00 0.00 0.00 3.69
1805 1842 7.211573 TCTTATTTTCAGTTGTACCTTGTCGA 58.788 34.615 0.00 0.00 0.00 4.20
2163 2202 1.207089 CCCTTGGACGATGCAGAACTA 59.793 52.381 0.00 0.00 0.00 2.24
2337 2377 6.925165 CCAACCTAAGAAGTTCTTTACGTACA 59.075 38.462 22.66 2.85 37.89 2.90
2469 2509 2.103263 CCTGAAATCGGTAGCTAGCCTT 59.897 50.000 16.98 8.27 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.966246 ATTCTTGCAAGCAAATTGTTGAATA 57.034 28.000 21.99 0.00 41.29 1.75
5 6 7.201496 GGATCTATTCTTGCAAGCAAATTGTTG 60.201 37.037 21.99 8.43 41.29 3.33
6 7 6.815142 GGATCTATTCTTGCAAGCAAATTGTT 59.185 34.615 21.99 12.18 41.29 2.83
7 8 6.071221 TGGATCTATTCTTGCAAGCAAATTGT 60.071 34.615 21.99 8.68 41.29 2.71
8 9 6.334989 TGGATCTATTCTTGCAAGCAAATTG 58.665 36.000 21.99 16.44 42.20 2.32
9 10 6.534475 TGGATCTATTCTTGCAAGCAAATT 57.466 33.333 21.99 4.57 35.33 1.82
10 11 6.462487 CCATGGATCTATTCTTGCAAGCAAAT 60.462 38.462 21.99 18.13 35.33 2.32
11 12 5.163488 CCATGGATCTATTCTTGCAAGCAAA 60.163 40.000 21.99 12.15 35.33 3.68
12 13 4.340097 CCATGGATCTATTCTTGCAAGCAA 59.660 41.667 21.99 16.10 0.00 3.91
13 14 3.887110 CCATGGATCTATTCTTGCAAGCA 59.113 43.478 21.99 11.97 0.00 3.91
14 15 4.023365 GTCCATGGATCTATTCTTGCAAGC 60.023 45.833 21.99 5.52 0.00 4.01
15 16 5.128205 TGTCCATGGATCTATTCTTGCAAG 58.872 41.667 19.62 20.81 0.00 4.01
16 17 5.114764 TGTCCATGGATCTATTCTTGCAA 57.885 39.130 19.62 0.00 0.00 4.08
17 18 4.776435 TGTCCATGGATCTATTCTTGCA 57.224 40.909 19.62 3.84 0.00 4.08
18 19 9.453572 TTTATATGTCCATGGATCTATTCTTGC 57.546 33.333 19.62 0.84 0.00 4.01
26 27 9.293404 CACATCTTTTTATATGTCCATGGATCT 57.707 33.333 19.62 10.91 34.12 2.75
27 28 8.517878 CCACATCTTTTTATATGTCCATGGATC 58.482 37.037 19.62 12.25 34.12 3.36
28 29 7.039504 GCCACATCTTTTTATATGTCCATGGAT 60.040 37.037 19.62 5.24 34.12 3.41
29 30 6.265196 GCCACATCTTTTTATATGTCCATGGA 59.735 38.462 11.44 11.44 34.12 3.41
30 31 6.449698 GCCACATCTTTTTATATGTCCATGG 58.550 40.000 4.97 4.97 34.12 3.66
31 32 6.144854 CGCCACATCTTTTTATATGTCCATG 58.855 40.000 0.00 0.00 34.12 3.66
32 33 5.278463 GCGCCACATCTTTTTATATGTCCAT 60.278 40.000 0.00 0.00 34.12 3.41
33 34 4.036262 GCGCCACATCTTTTTATATGTCCA 59.964 41.667 0.00 0.00 34.12 4.02
34 35 4.275936 AGCGCCACATCTTTTTATATGTCC 59.724 41.667 2.29 0.00 34.12 4.02
35 36 5.007626 TGAGCGCCACATCTTTTTATATGTC 59.992 40.000 2.29 0.00 34.12 3.06
36 37 4.881273 TGAGCGCCACATCTTTTTATATGT 59.119 37.500 2.29 0.00 36.78 2.29
37 38 5.207768 GTGAGCGCCACATCTTTTTATATG 58.792 41.667 19.85 0.00 45.03 1.78
38 39 5.424121 GTGAGCGCCACATCTTTTTATAT 57.576 39.130 19.85 0.00 45.03 0.86
39 40 4.875544 GTGAGCGCCACATCTTTTTATA 57.124 40.909 19.85 0.00 45.03 0.98
40 41 3.764885 GTGAGCGCCACATCTTTTTAT 57.235 42.857 19.85 0.00 45.03 1.40
50 51 1.468520 ACATGTAAATGTGAGCGCCAC 59.531 47.619 18.49 18.49 45.88 5.01
51 52 1.819928 ACATGTAAATGTGAGCGCCA 58.180 45.000 2.29 0.00 32.79 5.69
52 53 2.286418 GCTACATGTAAATGTGAGCGCC 60.286 50.000 8.91 0.00 36.08 6.53
53 54 2.609459 AGCTACATGTAAATGTGAGCGC 59.391 45.455 8.91 0.00 36.83 5.92
54 55 3.001634 CCAGCTACATGTAAATGTGAGCG 59.998 47.826 8.91 9.35 36.83 5.03
55 56 3.941483 ACCAGCTACATGTAAATGTGAGC 59.059 43.478 8.91 12.53 36.08 4.26
56 57 4.201851 GCACCAGCTACATGTAAATGTGAG 60.202 45.833 20.12 3.93 37.91 3.51
57 58 3.689161 GCACCAGCTACATGTAAATGTGA 59.311 43.478 20.12 0.00 37.91 3.58
58 59 3.485711 CGCACCAGCTACATGTAAATGTG 60.486 47.826 8.91 12.16 39.10 3.21
59 60 2.677836 CGCACCAGCTACATGTAAATGT 59.322 45.455 7.06 3.51 39.10 2.71
60 61 2.677836 ACGCACCAGCTACATGTAAATG 59.322 45.455 7.06 8.30 39.10 2.32
61 62 2.985896 ACGCACCAGCTACATGTAAAT 58.014 42.857 7.06 0.00 39.10 1.40
62 63 2.465860 ACGCACCAGCTACATGTAAA 57.534 45.000 7.06 0.00 39.10 2.01
63 64 2.465860 AACGCACCAGCTACATGTAA 57.534 45.000 7.06 0.00 39.10 2.41
64 65 2.465860 AAACGCACCAGCTACATGTA 57.534 45.000 5.25 5.25 39.10 2.29
65 66 2.289444 ACTAAACGCACCAGCTACATGT 60.289 45.455 2.69 2.69 39.10 3.21
66 67 2.346803 ACTAAACGCACCAGCTACATG 58.653 47.619 0.00 0.00 39.10 3.21
67 68 2.762535 ACTAAACGCACCAGCTACAT 57.237 45.000 0.00 0.00 39.10 2.29
68 69 2.821378 TCTACTAAACGCACCAGCTACA 59.179 45.455 0.00 0.00 39.10 2.74
69 70 3.498927 TCTACTAAACGCACCAGCTAC 57.501 47.619 0.00 0.00 39.10 3.58
70 71 4.219070 TCTTTCTACTAAACGCACCAGCTA 59.781 41.667 0.00 0.00 39.10 3.32
71 72 3.006537 TCTTTCTACTAAACGCACCAGCT 59.993 43.478 0.00 0.00 39.10 4.24
72 73 3.323243 TCTTTCTACTAAACGCACCAGC 58.677 45.455 0.00 0.00 37.42 4.85
73 74 5.227908 TCTTCTTTCTACTAAACGCACCAG 58.772 41.667 0.00 0.00 0.00 4.00
74 75 5.204409 TCTTCTTTCTACTAAACGCACCA 57.796 39.130 0.00 0.00 0.00 4.17
75 76 6.147328 ACATTCTTCTTTCTACTAAACGCACC 59.853 38.462 0.00 0.00 0.00 5.01
76 77 7.118422 ACATTCTTCTTTCTACTAAACGCAC 57.882 36.000 0.00 0.00 0.00 5.34
77 78 8.869897 CATACATTCTTCTTTCTACTAAACGCA 58.130 33.333 0.00 0.00 0.00 5.24
78 79 9.084164 TCATACATTCTTCTTTCTACTAAACGC 57.916 33.333 0.00 0.00 0.00 4.84
83 84 8.622157 CGACCTCATACATTCTTCTTTCTACTA 58.378 37.037 0.00 0.00 0.00 1.82
84 85 7.339721 TCGACCTCATACATTCTTCTTTCTACT 59.660 37.037 0.00 0.00 0.00 2.57
85 86 7.481642 TCGACCTCATACATTCTTCTTTCTAC 58.518 38.462 0.00 0.00 0.00 2.59
86 87 7.640597 TCGACCTCATACATTCTTCTTTCTA 57.359 36.000 0.00 0.00 0.00 2.10
87 88 6.531503 TCGACCTCATACATTCTTCTTTCT 57.468 37.500 0.00 0.00 0.00 2.52
88 89 6.143118 CGATCGACCTCATACATTCTTCTTTC 59.857 42.308 10.26 0.00 0.00 2.62
89 90 5.980116 CGATCGACCTCATACATTCTTCTTT 59.020 40.000 10.26 0.00 0.00 2.52
90 91 5.524284 CGATCGACCTCATACATTCTTCTT 58.476 41.667 10.26 0.00 0.00 2.52
91 92 4.557695 GCGATCGACCTCATACATTCTTCT 60.558 45.833 21.57 0.00 0.00 2.85
92 93 3.670991 GCGATCGACCTCATACATTCTTC 59.329 47.826 21.57 0.00 0.00 2.87
93 94 3.643763 GCGATCGACCTCATACATTCTT 58.356 45.455 21.57 0.00 0.00 2.52
94 95 2.350868 CGCGATCGACCTCATACATTCT 60.351 50.000 21.57 0.00 38.10 2.40
95 96 1.979469 CGCGATCGACCTCATACATTC 59.021 52.381 21.57 0.00 38.10 2.67
96 97 1.335964 CCGCGATCGACCTCATACATT 60.336 52.381 21.57 0.00 38.10 2.71
97 98 0.241213 CCGCGATCGACCTCATACAT 59.759 55.000 21.57 0.00 38.10 2.29
98 99 1.652563 CCGCGATCGACCTCATACA 59.347 57.895 21.57 0.00 38.10 2.29
99 100 1.081376 CCCGCGATCGACCTCATAC 60.081 63.158 21.57 0.00 38.10 2.39
100 101 1.105167 AACCCGCGATCGACCTCATA 61.105 55.000 21.57 0.00 38.10 2.15
101 102 2.423898 AACCCGCGATCGACCTCAT 61.424 57.895 21.57 0.00 38.10 2.90
102 103 3.066190 AACCCGCGATCGACCTCA 61.066 61.111 21.57 0.00 38.10 3.86
103 104 2.582498 CAACCCGCGATCGACCTC 60.582 66.667 21.57 0.00 38.10 3.85
104 105 2.939261 AACAACCCGCGATCGACCT 61.939 57.895 21.57 0.00 38.10 3.85
105 106 2.433664 AACAACCCGCGATCGACC 60.434 61.111 21.57 0.10 38.10 4.79
106 107 1.562575 AACAACAACCCGCGATCGAC 61.563 55.000 21.57 9.43 38.10 4.20
107 108 0.038435 TAACAACAACCCGCGATCGA 60.038 50.000 21.57 0.00 38.10 3.59
108 109 1.003851 ATAACAACAACCCGCGATCG 58.996 50.000 11.69 11.69 0.00 3.69
109 110 2.004017 TGATAACAACAACCCGCGATC 58.996 47.619 8.23 0.00 0.00 3.69
110 111 1.735571 GTGATAACAACAACCCGCGAT 59.264 47.619 8.23 0.00 0.00 4.58
111 112 1.149987 GTGATAACAACAACCCGCGA 58.850 50.000 8.23 0.00 0.00 5.87
112 113 1.136085 CAGTGATAACAACAACCCGCG 60.136 52.381 0.00 0.00 0.00 6.46
113 114 1.877443 ACAGTGATAACAACAACCCGC 59.123 47.619 0.00 0.00 0.00 6.13
114 115 2.875933 ACACAGTGATAACAACAACCCG 59.124 45.455 7.81 0.00 0.00 5.28
115 116 3.004315 CCACACAGTGATAACAACAACCC 59.996 47.826 7.81 0.00 35.23 4.11
116 117 3.550030 GCCACACAGTGATAACAACAACC 60.550 47.826 7.81 0.00 35.23 3.77
117 118 3.066064 TGCCACACAGTGATAACAACAAC 59.934 43.478 7.81 0.00 35.23 3.32
118 119 3.282885 TGCCACACAGTGATAACAACAA 58.717 40.909 7.81 0.00 35.23 2.83
119 120 2.924421 TGCCACACAGTGATAACAACA 58.076 42.857 7.81 0.00 35.23 3.33
120 121 3.980646 TTGCCACACAGTGATAACAAC 57.019 42.857 7.81 0.00 35.23 3.32
121 122 4.140536 TCATTGCCACACAGTGATAACAA 58.859 39.130 7.81 6.54 39.84 2.83
122 123 3.749226 TCATTGCCACACAGTGATAACA 58.251 40.909 7.81 0.00 39.84 2.41
123 124 4.002982 TCTCATTGCCACACAGTGATAAC 58.997 43.478 7.81 0.00 43.30 1.89
124 125 4.002982 GTCTCATTGCCACACAGTGATAA 58.997 43.478 7.81 0.00 43.30 1.75
125 126 3.599343 GTCTCATTGCCACACAGTGATA 58.401 45.455 7.81 0.00 43.30 2.15
126 127 2.430465 GTCTCATTGCCACACAGTGAT 58.570 47.619 7.81 0.00 43.30 3.06
127 128 1.873486 CGTCTCATTGCCACACAGTGA 60.873 52.381 7.81 0.00 42.21 3.41
128 129 0.514255 CGTCTCATTGCCACACAGTG 59.486 55.000 0.00 0.00 37.34 3.66
129 130 0.106708 ACGTCTCATTGCCACACAGT 59.893 50.000 0.00 0.00 0.00 3.55
130 131 0.514255 CACGTCTCATTGCCACACAG 59.486 55.000 0.00 0.00 0.00 3.66
131 132 0.884259 CCACGTCTCATTGCCACACA 60.884 55.000 0.00 0.00 0.00 3.72
132 133 1.577328 CCCACGTCTCATTGCCACAC 61.577 60.000 0.00 0.00 0.00 3.82
133 134 1.302431 CCCACGTCTCATTGCCACA 60.302 57.895 0.00 0.00 0.00 4.17
134 135 1.302511 ACCCACGTCTCATTGCCAC 60.303 57.895 0.00 0.00 0.00 5.01
135 136 1.302431 CACCCACGTCTCATTGCCA 60.302 57.895 0.00 0.00 0.00 4.92
136 137 1.302511 ACACCCACGTCTCATTGCC 60.303 57.895 0.00 0.00 0.00 4.52
137 138 1.868997 CACACCCACGTCTCATTGC 59.131 57.895 0.00 0.00 0.00 3.56
138 139 0.603707 AGCACACCCACGTCTCATTG 60.604 55.000 0.00 0.00 0.00 2.82
139 140 0.108585 AAGCACACCCACGTCTCATT 59.891 50.000 0.00 0.00 0.00 2.57
140 141 0.108585 AAAGCACACCCACGTCTCAT 59.891 50.000 0.00 0.00 0.00 2.90
141 142 0.813610 CAAAGCACACCCACGTCTCA 60.814 55.000 0.00 0.00 0.00 3.27
142 143 1.507141 CCAAAGCACACCCACGTCTC 61.507 60.000 0.00 0.00 0.00 3.36
143 144 1.525995 CCAAAGCACACCCACGTCT 60.526 57.895 0.00 0.00 0.00 4.18
144 145 3.030652 CCAAAGCACACCCACGTC 58.969 61.111 0.00 0.00 0.00 4.34
145 146 3.216292 GCCAAAGCACACCCACGT 61.216 61.111 0.00 0.00 39.53 4.49
146 147 3.215568 TGCCAAAGCACACCCACG 61.216 61.111 0.00 0.00 46.52 4.94
155 156 3.941483 AGACACATAGTACATGCCAAAGC 59.059 43.478 0.00 0.00 40.48 3.51
156 157 4.572389 GGAGACACATAGTACATGCCAAAG 59.428 45.833 0.00 0.00 0.00 2.77
157 158 4.513442 GGAGACACATAGTACATGCCAAA 58.487 43.478 0.00 0.00 0.00 3.28
158 159 3.430236 CGGAGACACATAGTACATGCCAA 60.430 47.826 0.00 0.00 0.00 4.52
159 160 2.100749 CGGAGACACATAGTACATGCCA 59.899 50.000 0.00 0.00 0.00 4.92
160 161 2.100916 ACGGAGACACATAGTACATGCC 59.899 50.000 0.00 0.00 0.00 4.40
161 162 3.438297 ACGGAGACACATAGTACATGC 57.562 47.619 0.00 0.00 0.00 4.06
162 163 4.112634 CCAACGGAGACACATAGTACATG 58.887 47.826 0.00 0.00 0.00 3.21
163 164 3.132289 CCCAACGGAGACACATAGTACAT 59.868 47.826 0.00 0.00 0.00 2.29
164 165 2.494471 CCCAACGGAGACACATAGTACA 59.506 50.000 0.00 0.00 0.00 2.90
165 166 2.159142 CCCCAACGGAGACACATAGTAC 60.159 54.545 0.00 0.00 0.00 2.73
166 167 2.104967 CCCCAACGGAGACACATAGTA 58.895 52.381 0.00 0.00 0.00 1.82
167 168 0.902531 CCCCAACGGAGACACATAGT 59.097 55.000 0.00 0.00 0.00 2.12
168 169 0.902531 ACCCCAACGGAGACACATAG 59.097 55.000 0.00 0.00 34.64 2.23
169 170 1.002659 CAACCCCAACGGAGACACATA 59.997 52.381 0.00 0.00 34.64 2.29
170 171 0.250727 CAACCCCAACGGAGACACAT 60.251 55.000 0.00 0.00 34.64 3.21
171 172 1.147376 CAACCCCAACGGAGACACA 59.853 57.895 0.00 0.00 34.64 3.72
172 173 0.464916 AACAACCCCAACGGAGACAC 60.465 55.000 0.00 0.00 34.64 3.67
173 174 0.464735 CAACAACCCCAACGGAGACA 60.465 55.000 0.00 0.00 34.64 3.41
174 175 1.170290 CCAACAACCCCAACGGAGAC 61.170 60.000 0.00 0.00 34.64 3.36
175 176 1.149627 CCAACAACCCCAACGGAGA 59.850 57.895 0.00 0.00 34.64 3.71
176 177 0.753848 AACCAACAACCCCAACGGAG 60.754 55.000 0.00 0.00 34.64 4.63
177 178 1.038130 CAACCAACAACCCCAACGGA 61.038 55.000 0.00 0.00 34.64 4.69
178 179 1.439644 CAACCAACAACCCCAACGG 59.560 57.895 0.00 0.00 37.81 4.44
179 180 1.324005 ACCAACCAACAACCCCAACG 61.324 55.000 0.00 0.00 0.00 4.10
180 181 0.462375 GACCAACCAACAACCCCAAC 59.538 55.000 0.00 0.00 0.00 3.77
181 182 0.041238 TGACCAACCAACAACCCCAA 59.959 50.000 0.00 0.00 0.00 4.12
182 183 0.684805 GTGACCAACCAACAACCCCA 60.685 55.000 0.00 0.00 0.00 4.96
183 184 0.396556 AGTGACCAACCAACAACCCC 60.397 55.000 0.00 0.00 0.00 4.95
184 185 2.158726 TCTAGTGACCAACCAACAACCC 60.159 50.000 0.00 0.00 0.00 4.11
185 186 2.876550 GTCTAGTGACCAACCAACAACC 59.123 50.000 0.00 0.00 37.24 3.77
186 187 3.805207 AGTCTAGTGACCAACCAACAAC 58.195 45.455 0.00 0.00 43.91 3.32
187 188 4.897076 TCTAGTCTAGTGACCAACCAACAA 59.103 41.667 6.77 0.00 43.91 2.83
188 189 4.476297 TCTAGTCTAGTGACCAACCAACA 58.524 43.478 6.77 0.00 43.91 3.33
189 190 4.523558 ACTCTAGTCTAGTGACCAACCAAC 59.476 45.833 14.44 0.00 43.91 3.77
190 191 4.523173 CACTCTAGTCTAGTGACCAACCAA 59.477 45.833 14.44 0.00 45.89 3.67
191 192 4.079970 CACTCTAGTCTAGTGACCAACCA 58.920 47.826 14.44 0.00 45.89 3.67
192 193 3.119424 GCACTCTAGTCTAGTGACCAACC 60.119 52.174 14.44 0.00 45.89 3.77
193 194 3.426426 CGCACTCTAGTCTAGTGACCAAC 60.426 52.174 14.44 0.00 45.89 3.77
194 195 2.747989 CGCACTCTAGTCTAGTGACCAA 59.252 50.000 14.44 0.00 45.89 3.67
195 196 2.290134 ACGCACTCTAGTCTAGTGACCA 60.290 50.000 14.44 0.00 45.89 4.02
196 197 2.096174 CACGCACTCTAGTCTAGTGACC 59.904 54.545 14.44 5.22 45.89 4.02
197 198 2.476519 GCACGCACTCTAGTCTAGTGAC 60.477 54.545 14.44 6.38 45.89 3.67
198 199 1.738350 GCACGCACTCTAGTCTAGTGA 59.262 52.381 14.44 0.00 45.89 3.41
199 200 1.468914 TGCACGCACTCTAGTCTAGTG 59.531 52.381 6.77 7.05 45.80 2.74
200 201 1.740585 CTGCACGCACTCTAGTCTAGT 59.259 52.381 6.77 0.00 0.00 2.57
201 202 1.532921 GCTGCACGCACTCTAGTCTAG 60.533 57.143 0.00 0.00 38.92 2.43
202 203 0.452184 GCTGCACGCACTCTAGTCTA 59.548 55.000 0.00 0.00 38.92 2.59
203 204 1.214062 GCTGCACGCACTCTAGTCT 59.786 57.895 0.00 0.00 38.92 3.24
204 205 1.075425 CTGCTGCACGCACTCTAGTC 61.075 60.000 0.00 0.00 45.47 2.59
205 206 1.080230 CTGCTGCACGCACTCTAGT 60.080 57.895 0.00 0.00 45.47 2.57
206 207 2.451167 GCTGCTGCACGCACTCTAG 61.451 63.158 11.11 0.00 45.47 2.43
207 208 2.433145 GCTGCTGCACGCACTCTA 60.433 61.111 11.11 0.00 45.47 2.43
208 209 4.614112 TGCTGCTGCACGCACTCT 62.614 61.111 14.93 0.00 45.47 3.24
217 218 0.321122 AACTAGTGGAGTGCTGCTGC 60.321 55.000 8.89 8.89 38.87 5.25
218 219 1.802960 CAAACTAGTGGAGTGCTGCTG 59.197 52.381 0.00 0.00 38.87 4.41
219 220 1.417890 ACAAACTAGTGGAGTGCTGCT 59.582 47.619 0.00 0.00 38.87 4.24
220 221 1.532868 CACAAACTAGTGGAGTGCTGC 59.467 52.381 0.00 0.00 38.87 5.25
221 222 3.111853 TCACAAACTAGTGGAGTGCTG 57.888 47.619 14.44 5.60 38.87 4.41
222 223 3.324846 TCATCACAAACTAGTGGAGTGCT 59.675 43.478 14.44 5.73 38.87 4.40
223 224 3.664107 TCATCACAAACTAGTGGAGTGC 58.336 45.455 14.44 0.00 38.87 4.40
224 225 5.050091 GTGTTCATCACAAACTAGTGGAGTG 60.050 44.000 13.52 13.52 45.51 3.51
225 226 5.057149 GTGTTCATCACAAACTAGTGGAGT 58.943 41.667 0.00 0.00 45.51 3.85
226 227 5.597813 GTGTTCATCACAAACTAGTGGAG 57.402 43.478 0.00 0.00 45.51 3.86
238 239 2.221169 TGCTCTGGTTGTGTTCATCAC 58.779 47.619 0.00 0.00 46.31 3.06
239 240 2.636647 TGCTCTGGTTGTGTTCATCA 57.363 45.000 0.00 0.00 0.00 3.07
240 241 5.627499 TTAATGCTCTGGTTGTGTTCATC 57.373 39.130 0.00 0.00 0.00 2.92
241 242 5.301551 TGTTTAATGCTCTGGTTGTGTTCAT 59.698 36.000 0.00 0.00 0.00 2.57
242 243 4.642437 TGTTTAATGCTCTGGTTGTGTTCA 59.358 37.500 0.00 0.00 0.00 3.18
243 244 5.181690 TGTTTAATGCTCTGGTTGTGTTC 57.818 39.130 0.00 0.00 0.00 3.18
244 245 5.590530 TTGTTTAATGCTCTGGTTGTGTT 57.409 34.783 0.00 0.00 0.00 3.32
245 246 5.127031 AGTTTGTTTAATGCTCTGGTTGTGT 59.873 36.000 0.00 0.00 0.00 3.72
246 247 5.591099 AGTTTGTTTAATGCTCTGGTTGTG 58.409 37.500 0.00 0.00 0.00 3.33
247 248 5.852282 AGTTTGTTTAATGCTCTGGTTGT 57.148 34.783 0.00 0.00 0.00 3.32
248 249 7.920682 AGTTAAGTTTGTTTAATGCTCTGGTTG 59.079 33.333 0.00 0.00 0.00 3.77
249 250 8.007405 AGTTAAGTTTGTTTAATGCTCTGGTT 57.993 30.769 0.00 0.00 0.00 3.67
250 251 7.502561 AGAGTTAAGTTTGTTTAATGCTCTGGT 59.497 33.333 0.00 0.00 30.78 4.00
251 252 7.875971 AGAGTTAAGTTTGTTTAATGCTCTGG 58.124 34.615 0.00 0.00 30.78 3.86
252 253 9.813080 GTAGAGTTAAGTTTGTTTAATGCTCTG 57.187 33.333 0.00 0.00 32.62 3.35
253 254 9.780186 AGTAGAGTTAAGTTTGTTTAATGCTCT 57.220 29.630 0.00 0.00 33.81 4.09
261 262 8.586744 CCTCCTCTAGTAGAGTTAAGTTTGTTT 58.413 37.037 22.78 0.00 40.72 2.83
262 263 7.949006 TCCTCCTCTAGTAGAGTTAAGTTTGTT 59.051 37.037 22.78 0.00 40.72 2.83
263 264 7.468496 TCCTCCTCTAGTAGAGTTAAGTTTGT 58.532 38.462 22.78 0.00 40.72 2.83
264 265 7.941431 TCCTCCTCTAGTAGAGTTAAGTTTG 57.059 40.000 22.78 7.71 40.72 2.93
265 266 8.392479 TCTTCCTCCTCTAGTAGAGTTAAGTTT 58.608 37.037 22.78 0.00 40.72 2.66
266 267 7.931046 TCTTCCTCCTCTAGTAGAGTTAAGTT 58.069 38.462 22.78 0.00 40.72 2.66
267 268 7.513560 TCTTCCTCCTCTAGTAGAGTTAAGT 57.486 40.000 22.78 0.00 40.72 2.24
268 269 8.269317 TCTTCTTCCTCCTCTAGTAGAGTTAAG 58.731 40.741 22.78 18.39 40.72 1.85
269 270 8.160434 TCTTCTTCCTCCTCTAGTAGAGTTAA 57.840 38.462 22.78 11.64 40.72 2.01
270 271 7.752518 TCTTCTTCCTCCTCTAGTAGAGTTA 57.247 40.000 22.78 11.60 40.72 2.24
271 272 6.645884 TCTTCTTCCTCCTCTAGTAGAGTT 57.354 41.667 22.78 0.00 40.72 3.01
272 273 6.445786 TCTTCTTCTTCCTCCTCTAGTAGAGT 59.554 42.308 22.78 0.00 40.72 3.24
273 274 6.895782 TCTTCTTCTTCCTCCTCTAGTAGAG 58.104 44.000 18.81 18.81 41.96 2.43
274 275 6.894735 TCTTCTTCTTCCTCCTCTAGTAGA 57.105 41.667 0.00 0.00 0.00 2.59
275 276 8.533569 AAATCTTCTTCTTCCTCCTCTAGTAG 57.466 38.462 0.00 0.00 0.00 2.57
276 277 8.903059 AAAATCTTCTTCTTCCTCCTCTAGTA 57.097 34.615 0.00 0.00 0.00 1.82
277 278 7.806680 AAAATCTTCTTCTTCCTCCTCTAGT 57.193 36.000 0.00 0.00 0.00 2.57
347 349 8.561769 TCCTTTTTGTCAAATATATCCAGGGTA 58.438 33.333 0.00 0.00 0.00 3.69
348 350 7.342026 GTCCTTTTTGTCAAATATATCCAGGGT 59.658 37.037 0.00 0.00 0.00 4.34
351 353 7.201911 GGGGTCCTTTTTGTCAAATATATCCAG 60.202 40.741 0.00 0.00 0.00 3.86
352 354 6.609616 GGGGTCCTTTTTGTCAAATATATCCA 59.390 38.462 0.00 0.00 0.00 3.41
482 484 1.961277 CCCTGTGCAGACACCGTTC 60.961 63.158 0.02 0.00 46.86 3.95
706 721 4.700365 CGTCACTGTCGCGCCTCA 62.700 66.667 0.00 0.00 0.00 3.86
737 766 3.041940 CGTCCATATTCCCGCGCC 61.042 66.667 0.00 0.00 0.00 6.53
910 943 4.755411 TGGTGTCTCCTTTTATAAGCTCG 58.245 43.478 0.00 0.00 37.07 5.03
954 987 1.790090 TTTGCGCACTGCCGATTTCA 61.790 50.000 11.12 0.00 45.60 2.69
1290 1324 0.553819 ACAGAGGCGGAGGAGACTAT 59.446 55.000 0.00 0.00 44.43 2.12
1525 1562 3.069980 GCTCCTCCATGCGACGAGT 62.070 63.158 0.00 0.00 0.00 4.18
1548 1585 3.491652 GCCTCCTTTCGCTGTCGC 61.492 66.667 0.00 0.00 35.26 5.19
2163 2202 0.813184 CTGCATCGTCAAAGGGCAAT 59.187 50.000 0.00 0.00 33.58 3.56
2469 2509 1.759445 GGGATGAGCAGCACTCTTCTA 59.241 52.381 16.89 0.00 46.41 2.10


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

AutoCloner maintained by Alex Coulton.