Multiple sequence alignment - TraesCS5D01G064900

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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 TraesCS5D01G064900 chr5D 100.000 6594 0 0 1 6594 60244805 60251398 0.000000e+00 12177.0
1 TraesCS5D01G064900 chr5D 78.017 232 45 5 2173 2399 415270111 415270341 2.480000e-29 141.0
2 TraesCS5D01G064900 chr5D 87.719 57 4 3 2188 2242 486538409 486538354 5.520000e-06 63.9
3 TraesCS5D01G064900 chr5A 96.062 4419 118 26 1807 6210 48758571 48762948 0.000000e+00 7145.0
4 TraesCS5D01G064900 chr5A 90.246 1220 78 21 348 1545 48757112 48758312 0.000000e+00 1555.0
5 TraesCS5D01G064900 chr5A 90.882 340 26 3 6255 6594 48762945 48763279 1.010000e-122 451.0
6 TraesCS5D01G064900 chr5B 98.173 1806 25 7 2822 4622 70400320 70398518 0.000000e+00 3145.0
7 TraesCS5D01G064900 chr5B 95.073 1989 54 17 4610 6594 70395664 70393716 0.000000e+00 3090.0
8 TraesCS5D01G064900 chr5B 96.258 1363 37 6 196 1545 70402844 70401483 0.000000e+00 2222.0
9 TraesCS5D01G064900 chr5B 96.830 757 23 1 2086 2841 70401244 70400488 0.000000e+00 1264.0
10 TraesCS5D01G064900 chr5B 89.954 219 10 6 1544 1758 70401457 70401247 8.430000e-69 272.0
11 TraesCS5D01G064900 chr7B 74.598 311 76 2 2198 2505 696103836 696104146 4.150000e-27 134.0
12 TraesCS5D01G064900 chr3D 76.190 231 49 5 2165 2390 488906970 488906741 4.180000e-22 117.0
13 TraesCS5D01G064900 chr3D 89.552 67 7 0 2167 2233 578749202 578749268 1.180000e-12 86.1
14 TraesCS5D01G064900 chr1A 86.408 103 12 1 2434 2536 487330503 487330403 1.940000e-20 111.0
15 TraesCS5D01G064900 chr2A 89.062 64 3 3 2474 2536 762752452 762752392 7.090000e-10 76.8
16 TraesCS5D01G064900 chr1B 92.453 53 4 0 2175 2227 638906960 638906908 7.090000e-10 76.8
17 TraesCS5D01G064900 chr3B 97.222 36 1 0 2189 2224 628801078 628801043 1.990000e-05 62.1


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 TraesCS5D01G064900 chr5D 60244805 60251398 6593 False 12177.000000 12177 100.000000 1 6594 1 chr5D.!!$F1 6593
1 TraesCS5D01G064900 chr5A 48757112 48763279 6167 False 3050.333333 7145 92.396667 348 6594 3 chr5A.!!$F1 6246
2 TraesCS5D01G064900 chr5B 70393716 70402844 9128 True 1998.600000 3145 95.257600 196 6594 5 chr5B.!!$R1 6398

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
227 228 1.217244 CCCAACTTCTACCGGTCCG 59.783 63.158 12.40 3.60 0.00 4.79 F
1788 1854 0.108138 AGCTCCGGTTGTATGTCTGC 60.108 55.000 0.00 0.00 0.00 4.26 F
1828 1894 0.109723 TAGAAAGGGCGGCACAAACT 59.890 50.000 12.47 2.59 0.00 2.66 F
1832 1898 0.179001 AAGGGCGGCACAAACTTACT 60.179 50.000 12.47 0.00 0.00 2.24 F
1848 1914 0.327924 TACTGTGCTGATGGGGTTGG 59.672 55.000 0.00 0.00 0.00 3.77 F
2510 2585 0.469917 ACAATGATGTAGAGGCCGGG 59.530 55.000 2.18 0.00 38.24 5.73 F
4762 7900 4.260139 GAACTCCCGTTCTCTCTTTCTT 57.740 45.455 0.00 0.00 44.80 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1867 0.037734 CCGCCCTTTCTAACCCAAGT 59.962 55.000 0.00 0.0 0.00 3.16 R
3177 3441 3.369261 GCCATTTGTTTGGGTGCATGATA 60.369 43.478 0.00 0.0 37.24 2.15 R
3284 3548 5.066913 AGATGAGGGGTGAAAGTCTTTTT 57.933 39.130 0.00 0.0 0.00 1.94 R
3508 3772 6.211584 AGAGAACTAACTAAAGATCCTGCACA 59.788 38.462 0.00 0.0 0.00 4.57 R
4348 4620 4.020307 TGTGCATCATTGTTAGGTCTGAGA 60.020 41.667 0.00 0.0 0.00 3.27 R
4770 7908 0.328258 ACACCCTTGGTACCATCTGC 59.672 55.000 17.17 0.0 32.11 4.26 R
6243 9382 0.616395 TAGCGGATTGACCTGTCCCA 60.616 55.000 0.00 0.0 36.31 4.37 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 7.828508 TTATTCCGCTATCAAGTACTCCTAA 57.171 36.000 0.00 0.00 0.00 2.69
25 26 5.769484 TTCCGCTATCAAGTACTCCTAAG 57.231 43.478 0.00 0.00 0.00 2.18
26 27 4.142790 TCCGCTATCAAGTACTCCTAAGG 58.857 47.826 0.00 0.00 0.00 2.69
27 28 4.141321 TCCGCTATCAAGTACTCCTAAGGA 60.141 45.833 0.00 0.00 0.00 3.36
28 29 4.023021 CCGCTATCAAGTACTCCTAAGGAC 60.023 50.000 0.00 0.00 36.50 3.85
29 30 4.023021 CGCTATCAAGTACTCCTAAGGACC 60.023 50.000 0.00 0.00 36.99 4.46
30 31 4.894114 GCTATCAAGTACTCCTAAGGACCA 59.106 45.833 0.00 0.00 36.99 4.02
31 32 5.363005 GCTATCAAGTACTCCTAAGGACCAA 59.637 44.000 0.00 0.00 36.99 3.67
32 33 5.678955 ATCAAGTACTCCTAAGGACCAAC 57.321 43.478 0.00 0.00 36.99 3.77
33 34 3.836562 TCAAGTACTCCTAAGGACCAACC 59.163 47.826 0.00 0.00 36.99 3.77
47 48 5.428496 GGACCAACCTAGTTGTTTGTTAC 57.572 43.478 6.71 0.00 41.41 2.50
48 49 4.024641 GGACCAACCTAGTTGTTTGTTACG 60.025 45.833 6.71 0.00 41.41 3.18
49 50 4.516323 ACCAACCTAGTTGTTTGTTACGT 58.484 39.130 6.71 0.00 41.41 3.57
50 51 5.669477 ACCAACCTAGTTGTTTGTTACGTA 58.331 37.500 6.71 0.00 41.41 3.57
51 52 6.112058 ACCAACCTAGTTGTTTGTTACGTAA 58.888 36.000 3.29 3.29 41.41 3.18
52 53 6.597280 ACCAACCTAGTTGTTTGTTACGTAAA 59.403 34.615 10.11 0.00 41.41 2.01
53 54 7.120432 ACCAACCTAGTTGTTTGTTACGTAAAA 59.880 33.333 10.11 0.73 41.41 1.52
54 55 8.130469 CCAACCTAGTTGTTTGTTACGTAAAAT 58.870 33.333 10.11 0.00 41.41 1.82
55 56 9.161684 CAACCTAGTTGTTTGTTACGTAAAATC 57.838 33.333 10.11 6.90 38.56 2.17
56 57 8.667076 ACCTAGTTGTTTGTTACGTAAAATCT 57.333 30.769 10.11 4.95 0.00 2.40
57 58 8.553696 ACCTAGTTGTTTGTTACGTAAAATCTG 58.446 33.333 10.11 0.00 0.00 2.90
58 59 7.532884 CCTAGTTGTTTGTTACGTAAAATCTGC 59.467 37.037 10.11 0.00 0.00 4.26
59 60 7.023197 AGTTGTTTGTTACGTAAAATCTGCT 57.977 32.000 10.11 1.09 0.00 4.24
60 61 6.910433 AGTTGTTTGTTACGTAAAATCTGCTG 59.090 34.615 10.11 0.00 0.00 4.41
61 62 6.606234 TGTTTGTTACGTAAAATCTGCTGA 57.394 33.333 10.11 0.00 0.00 4.26
62 63 6.423862 TGTTTGTTACGTAAAATCTGCTGAC 58.576 36.000 10.11 0.00 0.00 3.51
63 64 6.259167 TGTTTGTTACGTAAAATCTGCTGACT 59.741 34.615 10.11 0.00 0.00 3.41
64 65 6.854496 TTGTTACGTAAAATCTGCTGACTT 57.146 33.333 10.11 0.00 0.00 3.01
65 66 6.462073 TGTTACGTAAAATCTGCTGACTTC 57.538 37.500 10.11 0.00 0.00 3.01
66 67 6.220930 TGTTACGTAAAATCTGCTGACTTCT 58.779 36.000 10.11 0.00 0.00 2.85
67 68 6.365247 TGTTACGTAAAATCTGCTGACTTCTC 59.635 38.462 10.11 0.00 0.00 2.87
68 69 4.883083 ACGTAAAATCTGCTGACTTCTCA 58.117 39.130 0.00 0.00 0.00 3.27
69 70 4.926238 ACGTAAAATCTGCTGACTTCTCAG 59.074 41.667 0.00 0.00 46.17 3.35
70 71 5.164233 CGTAAAATCTGCTGACTTCTCAGA 58.836 41.667 1.79 0.00 46.32 3.27
71 72 5.635280 CGTAAAATCTGCTGACTTCTCAGAA 59.365 40.000 1.79 0.00 46.32 3.02
72 73 5.938438 AAAATCTGCTGACTTCTCAGAAC 57.062 39.130 1.79 0.00 46.32 3.01
73 74 4.888326 AATCTGCTGACTTCTCAGAACT 57.112 40.909 1.79 0.00 46.32 3.01
74 75 3.657015 TCTGCTGACTTCTCAGAACTG 57.343 47.619 1.79 0.00 46.32 3.16
75 76 3.225940 TCTGCTGACTTCTCAGAACTGA 58.774 45.455 4.45 4.45 46.32 3.41
92 93 9.778741 TCAGAACTGAGTGTACTTTTATTTCAT 57.221 29.630 0.00 0.00 34.14 2.57
97 98 9.654663 ACTGAGTGTACTTTTATTTCATAGGAC 57.345 33.333 0.00 0.00 0.00 3.85
98 99 9.099454 CTGAGTGTACTTTTATTTCATAGGACC 57.901 37.037 0.00 0.00 0.00 4.46
99 100 8.598916 TGAGTGTACTTTTATTTCATAGGACCA 58.401 33.333 0.00 0.00 0.00 4.02
100 101 9.614792 GAGTGTACTTTTATTTCATAGGACCAT 57.385 33.333 0.00 0.00 0.00 3.55
101 102 9.975218 AGTGTACTTTTATTTCATAGGACCATT 57.025 29.630 0.00 0.00 0.00 3.16
103 104 9.967451 TGTACTTTTATTTCATAGGACCATTCA 57.033 29.630 0.00 0.00 0.00 2.57
105 106 8.293699 ACTTTTATTTCATAGGACCATTCACC 57.706 34.615 0.00 0.00 0.00 4.02
106 107 7.342026 ACTTTTATTTCATAGGACCATTCACCC 59.658 37.037 0.00 0.00 0.00 4.61
107 108 3.662759 TTTCATAGGACCATTCACCCC 57.337 47.619 0.00 0.00 0.00 4.95
108 109 2.278657 TCATAGGACCATTCACCCCA 57.721 50.000 0.00 0.00 0.00 4.96
109 110 2.787956 TCATAGGACCATTCACCCCAT 58.212 47.619 0.00 0.00 0.00 4.00
110 111 2.711009 TCATAGGACCATTCACCCCATC 59.289 50.000 0.00 0.00 0.00 3.51
111 112 2.587060 TAGGACCATTCACCCCATCT 57.413 50.000 0.00 0.00 0.00 2.90
112 113 2.587060 AGGACCATTCACCCCATCTA 57.413 50.000 0.00 0.00 0.00 1.98
113 114 2.412591 AGGACCATTCACCCCATCTAG 58.587 52.381 0.00 0.00 0.00 2.43
114 115 2.127708 GGACCATTCACCCCATCTAGT 58.872 52.381 0.00 0.00 0.00 2.57
115 116 2.104963 GGACCATTCACCCCATCTAGTC 59.895 54.545 0.00 0.00 0.00 2.59
116 117 3.041946 GACCATTCACCCCATCTAGTCT 58.958 50.000 0.00 0.00 0.00 3.24
117 118 3.041946 ACCATTCACCCCATCTAGTCTC 58.958 50.000 0.00 0.00 0.00 3.36
118 119 2.036475 CCATTCACCCCATCTAGTCTCG 59.964 54.545 0.00 0.00 0.00 4.04
119 120 2.820728 TTCACCCCATCTAGTCTCGA 57.179 50.000 0.00 0.00 0.00 4.04
120 121 2.820728 TCACCCCATCTAGTCTCGAA 57.179 50.000 0.00 0.00 0.00 3.71
121 122 3.095912 TCACCCCATCTAGTCTCGAAA 57.904 47.619 0.00 0.00 0.00 3.46
122 123 3.437213 TCACCCCATCTAGTCTCGAAAA 58.563 45.455 0.00 0.00 0.00 2.29
123 124 3.194968 TCACCCCATCTAGTCTCGAAAAC 59.805 47.826 0.00 0.00 0.00 2.43
124 125 3.056107 CACCCCATCTAGTCTCGAAAACA 60.056 47.826 0.96 0.00 0.00 2.83
125 126 3.775316 ACCCCATCTAGTCTCGAAAACAT 59.225 43.478 0.96 0.00 0.00 2.71
126 127 4.225267 ACCCCATCTAGTCTCGAAAACATT 59.775 41.667 0.96 0.00 0.00 2.71
127 128 4.811557 CCCCATCTAGTCTCGAAAACATTC 59.188 45.833 0.96 0.00 0.00 2.67
128 129 5.419542 CCCATCTAGTCTCGAAAACATTCA 58.580 41.667 0.96 0.00 0.00 2.57
129 130 5.292101 CCCATCTAGTCTCGAAAACATTCAC 59.708 44.000 0.96 0.00 0.00 3.18
130 131 6.102663 CCATCTAGTCTCGAAAACATTCACT 58.897 40.000 0.96 0.00 0.00 3.41
131 132 6.591834 CCATCTAGTCTCGAAAACATTCACTT 59.408 38.462 0.96 0.00 0.00 3.16
132 133 7.201478 CCATCTAGTCTCGAAAACATTCACTTC 60.201 40.741 0.96 0.00 0.00 3.01
133 134 6.982852 TCTAGTCTCGAAAACATTCACTTCT 58.017 36.000 0.96 0.00 0.00 2.85
134 135 8.107399 TCTAGTCTCGAAAACATTCACTTCTA 57.893 34.615 0.96 0.00 0.00 2.10
135 136 8.573885 TCTAGTCTCGAAAACATTCACTTCTAA 58.426 33.333 0.96 0.00 0.00 2.10
136 137 7.409465 AGTCTCGAAAACATTCACTTCTAAC 57.591 36.000 0.96 0.00 0.00 2.34
137 138 6.984474 AGTCTCGAAAACATTCACTTCTAACA 59.016 34.615 0.96 0.00 0.00 2.41
138 139 7.494625 AGTCTCGAAAACATTCACTTCTAACAA 59.505 33.333 0.96 0.00 0.00 2.83
139 140 7.583040 GTCTCGAAAACATTCACTTCTAACAAC 59.417 37.037 0.00 0.00 0.00 3.32
140 141 7.279090 TCTCGAAAACATTCACTTCTAACAACA 59.721 33.333 0.00 0.00 0.00 3.33
141 142 7.406553 TCGAAAACATTCACTTCTAACAACAG 58.593 34.615 0.00 0.00 0.00 3.16
142 143 6.140737 CGAAAACATTCACTTCTAACAACAGC 59.859 38.462 0.00 0.00 0.00 4.40
143 144 6.699575 AAACATTCACTTCTAACAACAGCT 57.300 33.333 0.00 0.00 0.00 4.24
144 145 5.931441 ACATTCACTTCTAACAACAGCTC 57.069 39.130 0.00 0.00 0.00 4.09
145 146 5.368145 ACATTCACTTCTAACAACAGCTCA 58.632 37.500 0.00 0.00 0.00 4.26
146 147 5.468072 ACATTCACTTCTAACAACAGCTCAG 59.532 40.000 0.00 0.00 0.00 3.35
147 148 4.672587 TCACTTCTAACAACAGCTCAGT 57.327 40.909 0.00 0.00 0.00 3.41
148 149 4.621991 TCACTTCTAACAACAGCTCAGTC 58.378 43.478 0.00 0.00 0.00 3.51
149 150 4.099419 TCACTTCTAACAACAGCTCAGTCA 59.901 41.667 0.00 0.00 0.00 3.41
150 151 4.993584 CACTTCTAACAACAGCTCAGTCAT 59.006 41.667 0.00 0.00 0.00 3.06
151 152 5.468072 CACTTCTAACAACAGCTCAGTCATT 59.532 40.000 0.00 0.00 0.00 2.57
152 153 6.017605 CACTTCTAACAACAGCTCAGTCATTT 60.018 38.462 0.00 0.00 0.00 2.32
153 154 7.171508 CACTTCTAACAACAGCTCAGTCATTTA 59.828 37.037 0.00 0.00 0.00 1.40
154 155 7.171678 ACTTCTAACAACAGCTCAGTCATTTAC 59.828 37.037 0.00 0.00 0.00 2.01
155 156 6.759272 TCTAACAACAGCTCAGTCATTTACT 58.241 36.000 0.00 0.00 39.81 2.24
156 157 7.892609 TCTAACAACAGCTCAGTCATTTACTA 58.107 34.615 0.00 0.00 35.76 1.82
157 158 8.364894 TCTAACAACAGCTCAGTCATTTACTAA 58.635 33.333 0.00 0.00 35.76 2.24
158 159 7.986085 AACAACAGCTCAGTCATTTACTAAT 57.014 32.000 0.00 0.00 35.76 1.73
159 160 7.986085 ACAACAGCTCAGTCATTTACTAATT 57.014 32.000 0.00 0.00 35.76 1.40
160 161 8.396272 ACAACAGCTCAGTCATTTACTAATTT 57.604 30.769 0.00 0.00 35.76 1.82
161 162 9.502091 ACAACAGCTCAGTCATTTACTAATTTA 57.498 29.630 0.00 0.00 35.76 1.40
165 166 9.443283 CAGCTCAGTCATTTACTAATTTATTGC 57.557 33.333 0.00 0.00 35.76 3.56
166 167 9.177608 AGCTCAGTCATTTACTAATTTATTGCA 57.822 29.630 0.00 0.00 35.76 4.08
167 168 9.226345 GCTCAGTCATTTACTAATTTATTGCAC 57.774 33.333 0.00 0.00 35.76 4.57
172 173 9.463443 GTCATTTACTAATTTATTGCACATCCC 57.537 33.333 0.00 0.00 0.00 3.85
173 174 9.194972 TCATTTACTAATTTATTGCACATCCCA 57.805 29.630 0.00 0.00 0.00 4.37
174 175 9.814899 CATTTACTAATTTATTGCACATCCCAA 57.185 29.630 0.00 0.00 0.00 4.12
175 176 9.816354 ATTTACTAATTTATTGCACATCCCAAC 57.184 29.630 0.00 0.00 0.00 3.77
176 177 8.588290 TTACTAATTTATTGCACATCCCAACT 57.412 30.769 0.00 0.00 0.00 3.16
177 178 9.688091 TTACTAATTTATTGCACATCCCAACTA 57.312 29.630 0.00 0.00 0.00 2.24
178 179 8.588290 ACTAATTTATTGCACATCCCAACTAA 57.412 30.769 0.00 0.00 0.00 2.24
179 180 8.686334 ACTAATTTATTGCACATCCCAACTAAG 58.314 33.333 0.00 0.00 0.00 2.18
180 181 5.913137 TTTATTGCACATCCCAACTAAGG 57.087 39.130 0.00 0.00 0.00 2.69
181 182 2.969821 TTGCACATCCCAACTAAGGT 57.030 45.000 0.00 0.00 0.00 3.50
182 183 4.584638 ATTGCACATCCCAACTAAGGTA 57.415 40.909 0.00 0.00 0.00 3.08
183 184 3.343941 TGCACATCCCAACTAAGGTAC 57.656 47.619 0.00 0.00 0.00 3.34
184 185 2.026636 TGCACATCCCAACTAAGGTACC 60.027 50.000 2.73 2.73 0.00 3.34
185 186 2.238898 GCACATCCCAACTAAGGTACCT 59.761 50.000 9.21 9.21 0.00 3.08
186 187 3.308188 GCACATCCCAACTAAGGTACCTT 60.308 47.826 29.46 29.46 39.83 3.50
187 188 4.809691 GCACATCCCAACTAAGGTACCTTT 60.810 45.833 31.47 12.85 37.47 3.11
188 189 4.941873 CACATCCCAACTAAGGTACCTTTC 59.058 45.833 31.47 0.00 37.47 2.62
189 190 4.018688 ACATCCCAACTAAGGTACCTTTCC 60.019 45.833 31.47 0.00 37.47 3.13
190 191 2.914941 TCCCAACTAAGGTACCTTTCCC 59.085 50.000 31.47 0.00 37.47 3.97
191 192 2.355412 CCCAACTAAGGTACCTTTCCCG 60.355 54.545 31.47 18.83 37.47 5.14
192 193 2.303890 CCAACTAAGGTACCTTTCCCGT 59.696 50.000 31.47 19.42 37.47 5.28
193 194 3.593096 CAACTAAGGTACCTTTCCCGTC 58.407 50.000 31.47 0.00 37.47 4.79
194 195 2.182827 ACTAAGGTACCTTTCCCGTCC 58.817 52.381 31.47 0.00 37.47 4.79
227 228 1.217244 CCCAACTTCTACCGGTCCG 59.783 63.158 12.40 3.60 0.00 4.79
275 276 7.840931 AGCCCAACTTTTTCCAATAGATTTAG 58.159 34.615 0.00 0.00 0.00 1.85
573 584 7.922505 TGGAATATTTTTCAAAACACGTGAG 57.077 32.000 25.01 9.06 0.00 3.51
1199 1231 2.207924 ACGCCTCGTTCCTCACCTT 61.208 57.895 0.00 0.00 36.35 3.50
1271 1303 0.548682 AGCAGGTCACCAGGAGGAAT 60.549 55.000 0.00 0.00 38.69 3.01
1340 1372 4.274700 GTGGCTATCGCGGCGGTA 62.275 66.667 23.46 19.31 36.88 4.02
1512 1544 1.517913 GTCGCCTACCCGTAAGCAC 60.518 63.158 0.00 0.00 0.00 4.40
1514 1546 2.718073 CGCCTACCCGTAAGCACCT 61.718 63.158 0.00 0.00 0.00 4.00
1522 1554 1.226717 CGTAAGCACCTCTCTCGCC 60.227 63.158 0.00 0.00 0.00 5.54
1524 1556 2.058595 TAAGCACCTCTCTCGCCCC 61.059 63.158 0.00 0.00 0.00 5.80
1526 1558 4.154347 GCACCTCTCTCGCCCCTG 62.154 72.222 0.00 0.00 0.00 4.45
1638 1704 1.625315 AGCCTATGTCTTGTGTGCTCA 59.375 47.619 0.00 0.00 0.00 4.26
1639 1705 1.734465 GCCTATGTCTTGTGTGCTCAC 59.266 52.381 11.94 11.94 44.08 3.51
1653 1719 0.723981 GCTCACTGAGGCATTTCGTC 59.276 55.000 8.17 0.00 0.00 4.20
1654 1720 1.941209 GCTCACTGAGGCATTTCGTCA 60.941 52.381 8.17 0.00 37.90 4.35
1669 1735 0.732571 CGTCAAACACCTTGTGTGCT 59.267 50.000 0.00 0.00 46.79 4.40
1674 1740 5.348164 GTCAAACACCTTGTGTGCTTAAAT 58.652 37.500 0.00 0.00 46.79 1.40
1714 1780 0.903942 TTGGGGAAATGGCAAGATGC 59.096 50.000 0.00 0.00 44.08 3.91
1729 1795 4.631131 CAAGATGCGATCAGGTTGGTATA 58.369 43.478 0.00 0.00 0.00 1.47
1748 1814 7.140522 GGTATATAGGTGGACCTTTTTACCA 57.859 40.000 20.81 0.00 46.09 3.25
1769 1835 7.710676 ACCATGGTAATGTTTAGCAAATACA 57.289 32.000 18.10 0.00 31.27 2.29
1770 1836 7.771183 ACCATGGTAATGTTTAGCAAATACAG 58.229 34.615 18.10 0.00 31.27 2.74
1771 1837 6.697019 CCATGGTAATGTTTAGCAAATACAGC 59.303 38.462 2.57 0.00 31.27 4.40
1772 1838 7.416664 CCATGGTAATGTTTAGCAAATACAGCT 60.417 37.037 2.57 0.00 37.84 4.24
1773 1839 7.083875 TGGTAATGTTTAGCAAATACAGCTC 57.916 36.000 0.00 0.00 42.32 4.09
1774 1840 6.094881 TGGTAATGTTTAGCAAATACAGCTCC 59.905 38.462 0.00 0.00 42.32 4.70
1775 1841 4.882671 ATGTTTAGCAAATACAGCTCCG 57.117 40.909 0.00 0.00 42.32 4.63
1776 1842 3.006940 TGTTTAGCAAATACAGCTCCGG 58.993 45.455 0.00 0.00 42.32 5.14
1777 1843 3.007635 GTTTAGCAAATACAGCTCCGGT 58.992 45.455 0.00 0.00 42.32 5.28
1778 1844 3.343941 TTAGCAAATACAGCTCCGGTT 57.656 42.857 0.00 0.00 42.32 4.44
1779 1845 1.453155 AGCAAATACAGCTCCGGTTG 58.547 50.000 0.00 1.20 38.01 3.77
1780 1846 1.165270 GCAAATACAGCTCCGGTTGT 58.835 50.000 0.00 7.78 40.00 3.32
1781 1847 2.027561 AGCAAATACAGCTCCGGTTGTA 60.028 45.455 15.06 15.06 41.85 2.41
1782 1848 2.943033 GCAAATACAGCTCCGGTTGTAT 59.057 45.455 17.36 17.36 46.64 2.29
1783 1849 3.242739 GCAAATACAGCTCCGGTTGTATG 60.243 47.826 21.17 15.50 44.90 2.39
1784 1850 3.906720 AATACAGCTCCGGTTGTATGT 57.093 42.857 21.17 16.38 44.90 2.29
1785 1851 2.953466 TACAGCTCCGGTTGTATGTC 57.047 50.000 0.00 0.00 37.94 3.06
1786 1852 1.267121 ACAGCTCCGGTTGTATGTCT 58.733 50.000 0.00 0.00 35.19 3.41
1787 1853 1.066858 ACAGCTCCGGTTGTATGTCTG 60.067 52.381 0.00 1.30 35.19 3.51
1788 1854 0.108138 AGCTCCGGTTGTATGTCTGC 60.108 55.000 0.00 0.00 0.00 4.26
1789 1855 0.391130 GCTCCGGTTGTATGTCTGCA 60.391 55.000 0.00 0.00 0.00 4.41
1790 1856 1.743772 GCTCCGGTTGTATGTCTGCAT 60.744 52.381 0.00 0.00 39.03 3.96
1791 1857 2.483013 GCTCCGGTTGTATGTCTGCATA 60.483 50.000 0.00 0.00 36.58 3.14
1803 1869 4.206477 TGTCTGCATACACAGCAATACT 57.794 40.909 0.00 0.00 42.17 2.12
1804 1870 4.578871 TGTCTGCATACACAGCAATACTT 58.421 39.130 0.00 0.00 42.17 2.24
1805 1871 4.392754 TGTCTGCATACACAGCAATACTTG 59.607 41.667 0.00 0.00 42.17 3.16
1809 1875 3.443681 GCATACACAGCAATACTTGGGTT 59.556 43.478 0.00 0.00 0.00 4.11
1826 1892 0.955905 GTTAGAAAGGGCGGCACAAA 59.044 50.000 12.47 0.00 0.00 2.83
1828 1894 0.109723 TAGAAAGGGCGGCACAAACT 59.890 50.000 12.47 2.59 0.00 2.66
1829 1895 0.755327 AGAAAGGGCGGCACAAACTT 60.755 50.000 12.47 0.83 0.00 2.66
1832 1898 0.179001 AAGGGCGGCACAAACTTACT 60.179 50.000 12.47 0.00 0.00 2.24
1844 1910 2.489329 CAAACTTACTGTGCTGATGGGG 59.511 50.000 0.00 0.00 0.00 4.96
1848 1914 0.327924 TACTGTGCTGATGGGGTTGG 59.672 55.000 0.00 0.00 0.00 3.77
1849 1915 1.379916 CTGTGCTGATGGGGTTGGA 59.620 57.895 0.00 0.00 0.00 3.53
1850 1916 0.679002 CTGTGCTGATGGGGTTGGAG 60.679 60.000 0.00 0.00 0.00 3.86
1851 1917 1.380302 GTGCTGATGGGGTTGGAGT 59.620 57.895 0.00 0.00 0.00 3.85
1852 1918 0.962356 GTGCTGATGGGGTTGGAGTG 60.962 60.000 0.00 0.00 0.00 3.51
1853 1919 2.048603 GCTGATGGGGTTGGAGTGC 61.049 63.158 0.00 0.00 0.00 4.40
1854 1920 1.746615 CTGATGGGGTTGGAGTGCG 60.747 63.158 0.00 0.00 0.00 5.34
1856 1922 4.740822 ATGGGGTTGGAGTGCGCC 62.741 66.667 4.18 0.00 38.09 6.53
1904 1972 2.954318 GGTGGCATATGCTTCTTCACAT 59.046 45.455 26.12 0.00 41.70 3.21
1911 1979 2.479566 TGCTTCTTCACATGGAGGAC 57.520 50.000 0.00 0.00 30.34 3.85
1973 2041 4.626081 GTGTGGAGTGGCAGCGGT 62.626 66.667 0.00 0.00 0.00 5.68
2006 2074 1.918293 AACATGACTGGCCTCCCGA 60.918 57.895 3.32 0.00 0.00 5.14
2009 2077 2.446848 ATGACTGGCCTCCCGATGG 61.447 63.158 3.32 0.00 0.00 3.51
2084 2152 6.723464 GGGACTGCCATGGAGTTCTAACTC 62.723 54.167 18.40 13.36 44.52 3.01
2129 2197 5.375773 TCATGAAGATGGTGACTGAAACAA 58.624 37.500 0.00 0.00 0.00 2.83
2223 2298 2.618709 CCTTGTTGAAGGTGTTGTCTCC 59.381 50.000 0.00 0.00 43.63 3.71
2510 2585 0.469917 ACAATGATGTAGAGGCCGGG 59.530 55.000 2.18 0.00 38.24 5.73
2566 2641 5.336102 ACCAAAATCCTCCTGTGAATCAAT 58.664 37.500 0.00 0.00 0.00 2.57
2827 2903 6.478673 TCGATGTTATGTCATGTGTAATGACC 59.521 38.462 14.18 1.95 45.70 4.02
2861 3124 6.818644 TGACTGTAGCACTAAAATCTCCATTC 59.181 38.462 0.00 0.00 0.00 2.67
3129 3393 5.674525 TCATCTTACTTTTCATCGATGGCT 58.325 37.500 24.61 6.09 31.63 4.75
3177 3441 6.000219 GTGCATTTATGATGGTGAGTCCTAT 59.000 40.000 0.00 0.00 37.07 2.57
3508 3772 7.617723 AGATGTCTCCTAACATGAAGTCTTACT 59.382 37.037 0.00 0.00 39.93 2.24
4130 4401 5.492895 TGGCGTAATCTTAATCTGGTTTCA 58.507 37.500 0.00 0.00 0.00 2.69
4289 4561 7.037438 ACAATTGCTTGAATGGTATGTTGATC 58.963 34.615 5.05 0.00 36.20 2.92
4298 4570 7.219322 TGAATGGTATGTTGATCCATCACTAG 58.781 38.462 0.00 0.00 40.52 2.57
4708 7846 6.813152 GTGAGCCTTAAATTGTTGCATACATT 59.187 34.615 0.00 0.00 36.44 2.71
4762 7900 4.260139 GAACTCCCGTTCTCTCTTTCTT 57.740 45.455 0.00 0.00 44.80 2.52
4770 7908 3.604772 CGTTCTCTCTTTCTTGGTTTGCG 60.605 47.826 0.00 0.00 0.00 4.85
4868 8006 7.040409 AGCAAGTTACTTAAAATCACTCCCAAG 60.040 37.037 0.00 0.00 0.00 3.61
4973 8111 4.005650 CTGATGGTGTTGACTGCACTAAT 58.994 43.478 0.00 0.00 37.07 1.73
4974 8112 3.752747 TGATGGTGTTGACTGCACTAATG 59.247 43.478 0.00 0.00 37.07 1.90
4975 8113 3.483808 TGGTGTTGACTGCACTAATGA 57.516 42.857 0.00 0.00 37.07 2.57
4976 8114 4.019792 TGGTGTTGACTGCACTAATGAT 57.980 40.909 0.00 0.00 37.07 2.45
4977 8115 5.159273 TGGTGTTGACTGCACTAATGATA 57.841 39.130 0.00 0.00 37.07 2.15
4978 8116 5.555966 TGGTGTTGACTGCACTAATGATAA 58.444 37.500 0.00 0.00 37.07 1.75
4983 8121 7.065085 GTGTTGACTGCACTAATGATAATGAGT 59.935 37.037 0.00 0.00 34.30 3.41
5160 8298 8.060679 CAGCTTTGATATTTCGTAGTTCTGATG 58.939 37.037 0.00 0.00 0.00 3.07
5427 8565 5.363562 TCTGGAATGCTAGAACATCATGT 57.636 39.130 0.00 0.00 0.00 3.21
5715 8853 6.770303 TGATGGTAACTTGACAAATCAGTGAA 59.230 34.615 0.00 0.00 35.83 3.18
6070 9208 4.143347 CCGTTCATTGCTGTTATTTGTTGC 60.143 41.667 0.00 0.00 0.00 4.17
6210 9349 5.946942 ATTCAGCTCTCACTTCCTAATCA 57.053 39.130 0.00 0.00 0.00 2.57
6216 9355 4.679372 GCTCTCACTTCCTAATCACAGGTC 60.679 50.000 0.00 0.00 36.99 3.85
6232 9371 3.650942 ACAGGTCCCTTTTAGACACATCA 59.349 43.478 0.00 0.00 35.89 3.07
6243 9382 5.876651 TTAGACACATCATATGCTGACCT 57.123 39.130 13.32 8.78 36.48 3.85
6267 9406 3.432326 GGACAGGTCAATCCGCTAAATCT 60.432 47.826 1.41 0.00 41.99 2.40
6274 9413 4.444720 GTCAATCCGCTAAATCTAAGTCCG 59.555 45.833 0.00 0.00 0.00 4.79
6359 9498 1.768077 GAGTGCCCCCTCCATAGCT 60.768 63.158 0.00 0.00 0.00 3.32
6370 9509 4.720773 CCCCTCCATAGCTATCATCTCAAT 59.279 45.833 2.34 0.00 0.00 2.57
6377 9516 4.635699 AGCTATCATCTCAATGCATGGA 57.364 40.909 3.15 3.15 32.58 3.41
6430 9569 2.740055 GTCTCACTGCAGCCCACG 60.740 66.667 15.27 0.00 0.00 4.94
6437 9576 4.687215 TGCAGCCCACGCACTCTC 62.687 66.667 0.00 0.00 37.52 3.20
6485 9624 5.221803 ACTCTTCATGGGAGTAGCCATTATG 60.222 44.000 16.65 0.00 41.56 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.039923 CCTTAGGAGTACTTGATAGCGGAATAA 60.040 40.741 0.00 0.00 0.00 1.40
1 2 6.433404 CCTTAGGAGTACTTGATAGCGGAATA 59.567 42.308 0.00 0.00 0.00 1.75
2 3 5.244178 CCTTAGGAGTACTTGATAGCGGAAT 59.756 44.000 0.00 0.00 0.00 3.01
3 4 4.583489 CCTTAGGAGTACTTGATAGCGGAA 59.417 45.833 0.00 0.00 0.00 4.30
4 5 4.141321 TCCTTAGGAGTACTTGATAGCGGA 60.141 45.833 0.00 0.00 0.00 5.54
5 6 4.023021 GTCCTTAGGAGTACTTGATAGCGG 60.023 50.000 0.00 0.00 29.39 5.52
6 7 4.023021 GGTCCTTAGGAGTACTTGATAGCG 60.023 50.000 0.00 0.00 29.39 4.26
7 8 4.894114 TGGTCCTTAGGAGTACTTGATAGC 59.106 45.833 0.00 0.00 29.39 2.97
8 9 6.183360 GGTTGGTCCTTAGGAGTACTTGATAG 60.183 46.154 0.00 0.00 29.39 2.08
9 10 5.659971 GGTTGGTCCTTAGGAGTACTTGATA 59.340 44.000 0.00 0.00 29.39 2.15
10 11 4.470304 GGTTGGTCCTTAGGAGTACTTGAT 59.530 45.833 0.00 0.00 29.39 2.57
11 12 3.836562 GGTTGGTCCTTAGGAGTACTTGA 59.163 47.826 0.00 0.00 29.39 3.02
12 13 3.838903 AGGTTGGTCCTTAGGAGTACTTG 59.161 47.826 0.00 0.00 45.67 3.16
13 14 4.143406 AGGTTGGTCCTTAGGAGTACTT 57.857 45.455 0.00 0.00 45.67 2.24
14 15 3.848978 AGGTTGGTCCTTAGGAGTACT 57.151 47.619 0.00 0.00 45.67 2.73
15 16 4.608269 ACTAGGTTGGTCCTTAGGAGTAC 58.392 47.826 0.00 0.00 45.67 2.73
16 17 4.961440 ACTAGGTTGGTCCTTAGGAGTA 57.039 45.455 0.00 0.00 45.67 2.59
17 18 3.838903 CAACTAGGTTGGTCCTTAGGAGT 59.161 47.826 0.00 0.00 45.67 3.85
18 19 3.838903 ACAACTAGGTTGGTCCTTAGGAG 59.161 47.826 0.00 0.00 46.50 3.69
19 20 3.865571 ACAACTAGGTTGGTCCTTAGGA 58.134 45.455 13.75 0.00 46.50 2.94
20 21 4.635699 AACAACTAGGTTGGTCCTTAGG 57.364 45.455 13.75 0.00 39.44 2.69
21 22 5.826208 AACAAACAACTAGGTTGGTCCTTAG 59.174 40.000 13.75 1.13 42.50 2.18
22 23 5.757988 AACAAACAACTAGGTTGGTCCTTA 58.242 37.500 13.75 0.00 42.50 2.69
23 24 4.606210 AACAAACAACTAGGTTGGTCCTT 58.394 39.130 13.75 1.39 42.50 3.36
24 25 4.245251 AACAAACAACTAGGTTGGTCCT 57.755 40.909 13.75 0.00 42.50 3.85
25 26 4.024641 CGTAACAAACAACTAGGTTGGTCC 60.025 45.833 13.75 0.00 42.50 4.46
26 27 4.571984 ACGTAACAAACAACTAGGTTGGTC 59.428 41.667 13.75 0.00 42.50 4.02
30 31 9.112725 AGATTTTACGTAACAAACAACTAGGTT 57.887 29.630 7.70 0.00 0.00 3.50
31 32 8.553696 CAGATTTTACGTAACAAACAACTAGGT 58.446 33.333 7.70 0.00 0.00 3.08
32 33 7.532884 GCAGATTTTACGTAACAAACAACTAGG 59.467 37.037 7.70 0.00 0.00 3.02
33 34 8.280497 AGCAGATTTTACGTAACAAACAACTAG 58.720 33.333 7.70 0.00 0.00 2.57
34 35 8.065407 CAGCAGATTTTACGTAACAAACAACTA 58.935 33.333 7.70 0.00 0.00 2.24
35 36 6.910433 CAGCAGATTTTACGTAACAAACAACT 59.090 34.615 7.70 0.00 0.00 3.16
36 37 6.908284 TCAGCAGATTTTACGTAACAAACAAC 59.092 34.615 7.70 0.00 0.00 3.32
37 38 6.908284 GTCAGCAGATTTTACGTAACAAACAA 59.092 34.615 7.70 0.00 0.00 2.83
38 39 6.259167 AGTCAGCAGATTTTACGTAACAAACA 59.741 34.615 7.70 0.00 0.00 2.83
39 40 6.656003 AGTCAGCAGATTTTACGTAACAAAC 58.344 36.000 7.70 5.20 0.00 2.93
40 41 6.854496 AGTCAGCAGATTTTACGTAACAAA 57.146 33.333 7.70 0.81 0.00 2.83
41 42 6.704493 AGAAGTCAGCAGATTTTACGTAACAA 59.296 34.615 7.70 6.46 0.00 2.83
42 43 6.220930 AGAAGTCAGCAGATTTTACGTAACA 58.779 36.000 7.70 1.27 0.00 2.41
43 44 6.365247 TGAGAAGTCAGCAGATTTTACGTAAC 59.635 38.462 7.70 0.00 0.00 2.50
44 45 6.452242 TGAGAAGTCAGCAGATTTTACGTAA 58.548 36.000 3.29 3.29 0.00 3.18
45 46 6.020971 TGAGAAGTCAGCAGATTTTACGTA 57.979 37.500 0.00 0.00 0.00 3.57
46 47 4.883083 TGAGAAGTCAGCAGATTTTACGT 58.117 39.130 0.00 0.00 0.00 3.57
47 48 5.447478 CTGAGAAGTCAGCAGATTTTACG 57.553 43.478 0.00 0.00 43.89 3.18
59 60 5.133941 AGTACACTCAGTTCTGAGAAGTCA 58.866 41.667 29.07 15.28 39.14 3.41
60 61 5.699097 AGTACACTCAGTTCTGAGAAGTC 57.301 43.478 29.07 19.58 39.14 3.01
61 62 6.472686 AAAGTACACTCAGTTCTGAGAAGT 57.527 37.500 29.07 25.82 39.14 3.01
62 63 9.482627 AATAAAAGTACACTCAGTTCTGAGAAG 57.517 33.333 29.07 22.76 39.14 2.85
63 64 9.832445 AAATAAAAGTACACTCAGTTCTGAGAA 57.168 29.630 29.07 15.05 39.14 2.87
64 65 9.477484 GAAATAAAAGTACACTCAGTTCTGAGA 57.523 33.333 29.07 10.32 39.14 3.27
65 66 9.261180 TGAAATAAAAGTACACTCAGTTCTGAG 57.739 33.333 23.12 23.12 41.45 3.35
66 67 9.778741 ATGAAATAAAAGTACACTCAGTTCTGA 57.221 29.630 0.00 2.49 0.00 3.27
71 72 9.654663 GTCCTATGAAATAAAAGTACACTCAGT 57.345 33.333 0.00 0.00 0.00 3.41
72 73 9.099454 GGTCCTATGAAATAAAAGTACACTCAG 57.901 37.037 0.00 0.00 0.00 3.35
73 74 8.598916 TGGTCCTATGAAATAAAAGTACACTCA 58.401 33.333 0.00 0.00 0.00 3.41
74 75 9.614792 ATGGTCCTATGAAATAAAAGTACACTC 57.385 33.333 0.00 0.00 0.00 3.51
75 76 9.975218 AATGGTCCTATGAAATAAAAGTACACT 57.025 29.630 0.00 0.00 0.00 3.55
77 78 9.967451 TGAATGGTCCTATGAAATAAAAGTACA 57.033 29.630 0.00 0.00 0.00 2.90
79 80 9.403583 GGTGAATGGTCCTATGAAATAAAAGTA 57.596 33.333 0.00 0.00 0.00 2.24
80 81 7.342026 GGGTGAATGGTCCTATGAAATAAAAGT 59.658 37.037 0.00 0.00 0.00 2.66
81 82 7.201911 GGGGTGAATGGTCCTATGAAATAAAAG 60.202 40.741 0.00 0.00 0.00 2.27
82 83 6.609616 GGGGTGAATGGTCCTATGAAATAAAA 59.390 38.462 0.00 0.00 0.00 1.52
83 84 6.133356 GGGGTGAATGGTCCTATGAAATAAA 58.867 40.000 0.00 0.00 0.00 1.40
84 85 5.194740 TGGGGTGAATGGTCCTATGAAATAA 59.805 40.000 0.00 0.00 0.00 1.40
85 86 4.729370 TGGGGTGAATGGTCCTATGAAATA 59.271 41.667 0.00 0.00 0.00 1.40
86 87 3.531397 TGGGGTGAATGGTCCTATGAAAT 59.469 43.478 0.00 0.00 0.00 2.17
87 88 2.922955 TGGGGTGAATGGTCCTATGAAA 59.077 45.455 0.00 0.00 0.00 2.69
88 89 2.567862 TGGGGTGAATGGTCCTATGAA 58.432 47.619 0.00 0.00 0.00 2.57
89 90 2.278657 TGGGGTGAATGGTCCTATGA 57.721 50.000 0.00 0.00 0.00 2.15
90 91 2.713167 AGATGGGGTGAATGGTCCTATG 59.287 50.000 0.00 0.00 0.00 2.23
91 92 3.080660 AGATGGGGTGAATGGTCCTAT 57.919 47.619 0.00 0.00 0.00 2.57
92 93 2.587060 AGATGGGGTGAATGGTCCTA 57.413 50.000 0.00 0.00 0.00 2.94
93 94 2.293856 ACTAGATGGGGTGAATGGTCCT 60.294 50.000 0.00 0.00 0.00 3.85
94 95 2.104963 GACTAGATGGGGTGAATGGTCC 59.895 54.545 0.00 0.00 0.00 4.46
95 96 3.041946 AGACTAGATGGGGTGAATGGTC 58.958 50.000 0.00 0.00 0.00 4.02
96 97 3.041946 GAGACTAGATGGGGTGAATGGT 58.958 50.000 0.00 0.00 0.00 3.55
97 98 2.036475 CGAGACTAGATGGGGTGAATGG 59.964 54.545 0.00 0.00 0.00 3.16
98 99 2.959030 TCGAGACTAGATGGGGTGAATG 59.041 50.000 0.00 0.00 0.00 2.67
99 100 3.314307 TCGAGACTAGATGGGGTGAAT 57.686 47.619 0.00 0.00 0.00 2.57
100 101 2.820728 TCGAGACTAGATGGGGTGAA 57.179 50.000 0.00 0.00 0.00 3.18
101 102 2.820728 TTCGAGACTAGATGGGGTGA 57.179 50.000 0.00 0.00 0.00 4.02
102 103 3.056107 TGTTTTCGAGACTAGATGGGGTG 60.056 47.826 0.00 0.00 0.00 4.61
103 104 3.170717 TGTTTTCGAGACTAGATGGGGT 58.829 45.455 0.00 0.00 0.00 4.95
104 105 3.887621 TGTTTTCGAGACTAGATGGGG 57.112 47.619 0.00 0.00 0.00 4.96
105 106 5.292101 GTGAATGTTTTCGAGACTAGATGGG 59.708 44.000 0.00 0.00 34.39 4.00
106 107 6.102663 AGTGAATGTTTTCGAGACTAGATGG 58.897 40.000 0.00 0.00 34.39 3.51
107 108 7.543868 AGAAGTGAATGTTTTCGAGACTAGATG 59.456 37.037 0.00 0.00 34.39 2.90
108 109 7.607250 AGAAGTGAATGTTTTCGAGACTAGAT 58.393 34.615 0.00 0.00 34.39 1.98
109 110 6.982852 AGAAGTGAATGTTTTCGAGACTAGA 58.017 36.000 0.00 0.00 34.39 2.43
110 111 8.640291 GTTAGAAGTGAATGTTTTCGAGACTAG 58.360 37.037 3.20 0.00 34.39 2.57
111 112 8.139350 TGTTAGAAGTGAATGTTTTCGAGACTA 58.861 33.333 3.20 0.00 34.39 2.59
112 113 6.984474 TGTTAGAAGTGAATGTTTTCGAGACT 59.016 34.615 3.20 0.00 34.39 3.24
113 114 7.173863 TGTTAGAAGTGAATGTTTTCGAGAC 57.826 36.000 0.00 0.00 34.39 3.36
114 115 7.279090 TGTTGTTAGAAGTGAATGTTTTCGAGA 59.721 33.333 0.00 0.00 34.39 4.04
115 116 7.406553 TGTTGTTAGAAGTGAATGTTTTCGAG 58.593 34.615 0.00 0.00 34.39 4.04
116 117 7.310072 TGTTGTTAGAAGTGAATGTTTTCGA 57.690 32.000 0.00 0.00 34.39 3.71
117 118 6.140737 GCTGTTGTTAGAAGTGAATGTTTTCG 59.859 38.462 0.00 0.00 34.39 3.46
118 119 7.196331 AGCTGTTGTTAGAAGTGAATGTTTTC 58.804 34.615 0.00 0.00 0.00 2.29
119 120 7.100458 AGCTGTTGTTAGAAGTGAATGTTTT 57.900 32.000 0.00 0.00 0.00 2.43
120 121 6.318648 TGAGCTGTTGTTAGAAGTGAATGTTT 59.681 34.615 0.00 0.00 0.00 2.83
121 122 5.822519 TGAGCTGTTGTTAGAAGTGAATGTT 59.177 36.000 0.00 0.00 0.00 2.71
122 123 5.368145 TGAGCTGTTGTTAGAAGTGAATGT 58.632 37.500 0.00 0.00 0.00 2.71
123 124 5.468072 ACTGAGCTGTTGTTAGAAGTGAATG 59.532 40.000 0.00 0.00 0.00 2.67
124 125 5.615289 ACTGAGCTGTTGTTAGAAGTGAAT 58.385 37.500 0.00 0.00 0.00 2.57
125 126 5.023533 ACTGAGCTGTTGTTAGAAGTGAA 57.976 39.130 0.00 0.00 0.00 3.18
126 127 4.099419 TGACTGAGCTGTTGTTAGAAGTGA 59.901 41.667 0.00 0.00 0.00 3.41
127 128 4.371786 TGACTGAGCTGTTGTTAGAAGTG 58.628 43.478 0.00 0.00 0.00 3.16
128 129 4.672587 TGACTGAGCTGTTGTTAGAAGT 57.327 40.909 0.00 0.00 0.00 3.01
129 130 6.551385 AAATGACTGAGCTGTTGTTAGAAG 57.449 37.500 0.00 0.00 0.00 2.85
130 131 7.217200 AGTAAATGACTGAGCTGTTGTTAGAA 58.783 34.615 0.00 0.00 36.87 2.10
131 132 6.759272 AGTAAATGACTGAGCTGTTGTTAGA 58.241 36.000 0.00 0.00 36.87 2.10
132 133 8.534333 TTAGTAAATGACTGAGCTGTTGTTAG 57.466 34.615 0.00 0.00 39.39 2.34
133 134 9.502091 AATTAGTAAATGACTGAGCTGTTGTTA 57.498 29.630 0.00 0.00 39.39 2.41
134 135 7.986085 ATTAGTAAATGACTGAGCTGTTGTT 57.014 32.000 0.00 0.00 39.39 2.83
135 136 7.986085 AATTAGTAAATGACTGAGCTGTTGT 57.014 32.000 0.00 0.00 39.39 3.32
139 140 9.443283 GCAATAAATTAGTAAATGACTGAGCTG 57.557 33.333 0.00 0.00 39.39 4.24
140 141 9.177608 TGCAATAAATTAGTAAATGACTGAGCT 57.822 29.630 0.00 0.00 39.39 4.09
141 142 9.226345 GTGCAATAAATTAGTAAATGACTGAGC 57.774 33.333 0.00 0.00 39.39 4.26
146 147 9.463443 GGGATGTGCAATAAATTAGTAAATGAC 57.537 33.333 0.00 0.00 0.00 3.06
147 148 9.194972 TGGGATGTGCAATAAATTAGTAAATGA 57.805 29.630 0.00 0.00 0.00 2.57
148 149 9.814899 TTGGGATGTGCAATAAATTAGTAAATG 57.185 29.630 0.00 0.00 0.00 2.32
149 150 9.816354 GTTGGGATGTGCAATAAATTAGTAAAT 57.184 29.630 0.00 0.00 0.00 1.40
150 151 9.030452 AGTTGGGATGTGCAATAAATTAGTAAA 57.970 29.630 0.00 0.00 0.00 2.01
151 152 8.588290 AGTTGGGATGTGCAATAAATTAGTAA 57.412 30.769 0.00 0.00 0.00 2.24
152 153 9.688091 TTAGTTGGGATGTGCAATAAATTAGTA 57.312 29.630 0.00 0.00 0.00 1.82
153 154 8.588290 TTAGTTGGGATGTGCAATAAATTAGT 57.412 30.769 0.00 0.00 0.00 2.24
154 155 8.137437 CCTTAGTTGGGATGTGCAATAAATTAG 58.863 37.037 0.00 0.00 0.00 1.73
155 156 7.617723 ACCTTAGTTGGGATGTGCAATAAATTA 59.382 33.333 0.00 0.00 0.00 1.40
156 157 6.440328 ACCTTAGTTGGGATGTGCAATAAATT 59.560 34.615 0.00 0.00 0.00 1.82
157 158 5.957774 ACCTTAGTTGGGATGTGCAATAAAT 59.042 36.000 0.00 0.00 0.00 1.40
158 159 5.329399 ACCTTAGTTGGGATGTGCAATAAA 58.671 37.500 0.00 0.00 0.00 1.40
159 160 4.929479 ACCTTAGTTGGGATGTGCAATAA 58.071 39.130 0.00 0.00 0.00 1.40
160 161 4.584638 ACCTTAGTTGGGATGTGCAATA 57.415 40.909 0.00 0.00 0.00 1.90
161 162 3.456380 ACCTTAGTTGGGATGTGCAAT 57.544 42.857 0.00 0.00 0.00 3.56
162 163 2.969821 ACCTTAGTTGGGATGTGCAA 57.030 45.000 0.00 0.00 0.00 4.08
163 164 2.026636 GGTACCTTAGTTGGGATGTGCA 60.027 50.000 4.06 0.00 0.00 4.57
164 165 2.238898 AGGTACCTTAGTTGGGATGTGC 59.761 50.000 9.21 0.00 0.00 4.57
165 166 4.569719 AAGGTACCTTAGTTGGGATGTG 57.430 45.455 26.03 0.00 34.05 3.21
166 167 4.018688 GGAAAGGTACCTTAGTTGGGATGT 60.019 45.833 27.33 7.73 34.84 3.06
167 168 4.524053 GGAAAGGTACCTTAGTTGGGATG 58.476 47.826 27.33 0.00 34.84 3.51
168 169 3.526430 GGGAAAGGTACCTTAGTTGGGAT 59.474 47.826 27.33 9.28 34.84 3.85
169 170 2.914941 GGGAAAGGTACCTTAGTTGGGA 59.085 50.000 27.33 0.00 34.84 4.37
170 171 2.355412 CGGGAAAGGTACCTTAGTTGGG 60.355 54.545 27.33 11.06 34.84 4.12
171 172 2.303890 ACGGGAAAGGTACCTTAGTTGG 59.696 50.000 27.33 16.97 34.84 3.77
172 173 3.593096 GACGGGAAAGGTACCTTAGTTG 58.407 50.000 27.33 18.77 34.84 3.16
173 174 2.568956 GGACGGGAAAGGTACCTTAGTT 59.431 50.000 27.33 12.43 34.84 2.24
174 175 2.182827 GGACGGGAAAGGTACCTTAGT 58.817 52.381 27.33 22.21 34.84 2.24
175 176 1.135721 CGGACGGGAAAGGTACCTTAG 59.864 57.143 27.33 19.48 34.84 2.18
176 177 1.185315 CGGACGGGAAAGGTACCTTA 58.815 55.000 27.33 0.00 34.84 2.69
177 178 0.542702 TCGGACGGGAAAGGTACCTT 60.543 55.000 21.96 21.96 37.98 3.50
178 179 0.542702 TTCGGACGGGAAAGGTACCT 60.543 55.000 9.21 9.21 0.00 3.08
179 180 0.390340 GTTCGGACGGGAAAGGTACC 60.390 60.000 2.73 2.73 0.00 3.34
180 181 0.390340 GGTTCGGACGGGAAAGGTAC 60.390 60.000 0.00 0.00 0.00 3.34
181 182 0.542702 AGGTTCGGACGGGAAAGGTA 60.543 55.000 0.00 0.00 0.00 3.08
182 183 1.413256 AAGGTTCGGACGGGAAAGGT 61.413 55.000 0.00 0.00 0.00 3.50
183 184 0.953960 CAAGGTTCGGACGGGAAAGG 60.954 60.000 0.00 0.00 0.00 3.11
184 185 1.574702 GCAAGGTTCGGACGGGAAAG 61.575 60.000 0.00 0.00 0.00 2.62
185 186 1.598685 GCAAGGTTCGGACGGGAAA 60.599 57.895 0.00 0.00 0.00 3.13
186 187 2.031465 GCAAGGTTCGGACGGGAA 59.969 61.111 0.00 0.00 0.00 3.97
187 188 4.367023 CGCAAGGTTCGGACGGGA 62.367 66.667 0.00 0.00 0.00 5.14
275 276 4.281182 AGGTGATCCCGTGATATGTACTTC 59.719 45.833 0.00 0.00 38.74 3.01
1079 1110 1.179814 GGACTGGAGTCGAGTGGTGT 61.180 60.000 13.02 0.00 45.65 4.16
1199 1231 3.619767 AGCAGCTGAGCACGACCA 61.620 61.111 20.43 0.00 36.85 4.02
1271 1303 4.082523 CGCAGAGCCTCCGGGAAA 62.083 66.667 0.00 0.00 33.58 3.13
1390 1422 1.592400 CTTGAGGTACGCCGTCTCCA 61.592 60.000 12.56 0.00 40.50 3.86
1512 1544 2.726351 GGAACAGGGGCGAGAGAGG 61.726 68.421 0.00 0.00 0.00 3.69
1514 1546 1.682684 GAGGAACAGGGGCGAGAGA 60.683 63.158 0.00 0.00 0.00 3.10
1522 1554 0.674895 CTTCTTGCGGAGGAACAGGG 60.675 60.000 0.00 0.00 31.87 4.45
1524 1556 0.603707 TGCTTCTTGCGGAGGAACAG 60.604 55.000 0.00 0.00 46.63 3.16
1526 1558 0.603975 AGTGCTTCTTGCGGAGGAAC 60.604 55.000 0.00 0.00 46.63 3.62
1589 1651 0.464036 CCGCTCCACATACCAGCTAA 59.536 55.000 0.00 0.00 0.00 3.09
1595 1657 2.513897 GCCACCGCTCCACATACC 60.514 66.667 0.00 0.00 0.00 2.73
1638 1704 2.290641 GTGTTTGACGAAATGCCTCAGT 59.709 45.455 0.00 0.00 0.00 3.41
1639 1705 2.350772 GGTGTTTGACGAAATGCCTCAG 60.351 50.000 0.00 0.00 0.00 3.35
1654 1720 5.590530 TCATTTAAGCACACAAGGTGTTT 57.409 34.783 0.00 2.33 45.08 2.83
1669 1735 7.817418 ACTGGAGTAGCAAAGTTTCATTTAA 57.183 32.000 0.00 0.00 0.00 1.52
1674 1740 5.163561 CCAAAACTGGAGTAGCAAAGTTTCA 60.164 40.000 0.00 0.00 40.91 2.69
1714 1780 4.770531 TCCACCTATATACCAACCTGATCG 59.229 45.833 0.00 0.00 0.00 3.69
1729 1795 6.011451 TTACCATGGTAAAAAGGTCCACCTAT 60.011 38.462 30.87 0.00 40.34 2.57
1748 1814 7.201821 GGAGCTGTATTTGCTAAACATTACCAT 60.202 37.037 0.00 0.00 41.30 3.55
1769 1835 0.108138 GCAGACATACAACCGGAGCT 60.108 55.000 9.46 0.00 0.00 4.09
1770 1836 0.391130 TGCAGACATACAACCGGAGC 60.391 55.000 9.46 0.00 0.00 4.70
1771 1837 2.315925 ATGCAGACATACAACCGGAG 57.684 50.000 9.46 1.96 33.67 4.63
1780 1846 5.917462 AGTATTGCTGTGTATGCAGACATA 58.083 37.500 18.45 14.28 41.71 2.29
1781 1847 4.774124 AGTATTGCTGTGTATGCAGACAT 58.226 39.130 18.45 2.65 41.71 3.06
1782 1848 4.206477 AGTATTGCTGTGTATGCAGACA 57.794 40.909 10.75 10.75 41.71 3.41
1783 1849 4.901814 CAAGTATTGCTGTGTATGCAGAC 58.098 43.478 4.05 4.05 40.39 3.51
1798 1864 3.617284 CGCCCTTTCTAACCCAAGTATT 58.383 45.455 0.00 0.00 0.00 1.89
1799 1865 2.092592 CCGCCCTTTCTAACCCAAGTAT 60.093 50.000 0.00 0.00 0.00 2.12
1800 1866 1.279846 CCGCCCTTTCTAACCCAAGTA 59.720 52.381 0.00 0.00 0.00 2.24
1801 1867 0.037734 CCGCCCTTTCTAACCCAAGT 59.962 55.000 0.00 0.00 0.00 3.16
1802 1868 1.313091 GCCGCCCTTTCTAACCCAAG 61.313 60.000 0.00 0.00 0.00 3.61
1803 1869 1.303806 GCCGCCCTTTCTAACCCAA 60.304 57.895 0.00 0.00 0.00 4.12
1804 1870 2.353573 GCCGCCCTTTCTAACCCA 59.646 61.111 0.00 0.00 0.00 4.51
1805 1871 2.044555 GTGCCGCCCTTTCTAACCC 61.045 63.158 0.00 0.00 0.00 4.11
1809 1875 0.109723 AGTTTGTGCCGCCCTTTCTA 59.890 50.000 0.00 0.00 0.00 2.10
1826 1892 1.362224 ACCCCATCAGCACAGTAAGT 58.638 50.000 0.00 0.00 0.00 2.24
1828 1894 1.271871 CCAACCCCATCAGCACAGTAA 60.272 52.381 0.00 0.00 0.00 2.24
1829 1895 0.327924 CCAACCCCATCAGCACAGTA 59.672 55.000 0.00 0.00 0.00 2.74
1832 1898 1.379916 CTCCAACCCCATCAGCACA 59.620 57.895 0.00 0.00 0.00 4.57
1919 1987 1.308998 CATATTCCCAGGACCGTTGC 58.691 55.000 0.00 0.00 0.00 4.17
1980 2048 1.709760 CCAGTCATGTTGTAGCGCG 59.290 57.895 0.00 0.00 0.00 6.86
1982 2050 0.391661 AGGCCAGTCATGTTGTAGCG 60.392 55.000 5.01 0.00 0.00 4.26
1986 2054 1.380302 GGGAGGCCAGTCATGTTGT 59.620 57.895 5.01 0.00 0.00 3.32
2006 2074 0.908910 TTAGACCATCACACCGCCAT 59.091 50.000 0.00 0.00 0.00 4.40
2009 2077 0.249398 ACCTTAGACCATCACACCGC 59.751 55.000 0.00 0.00 0.00 5.68
2010 2078 1.405526 CCACCTTAGACCATCACACCG 60.406 57.143 0.00 0.00 0.00 4.94
2011 2079 1.906574 TCCACCTTAGACCATCACACC 59.093 52.381 0.00 0.00 0.00 4.16
2012 2080 3.695830 TTCCACCTTAGACCATCACAC 57.304 47.619 0.00 0.00 0.00 3.82
2013 2081 4.288366 TGAATTCCACCTTAGACCATCACA 59.712 41.667 2.27 0.00 0.00 3.58
2014 2082 4.843728 TGAATTCCACCTTAGACCATCAC 58.156 43.478 2.27 0.00 0.00 3.06
2015 2083 5.397899 GGATGAATTCCACCTTAGACCATCA 60.398 44.000 2.27 0.00 44.74 3.07
2016 2084 5.066593 GGATGAATTCCACCTTAGACCATC 58.933 45.833 2.27 0.00 44.74 3.51
2017 2085 5.053978 GGATGAATTCCACCTTAGACCAT 57.946 43.478 2.27 0.00 44.74 3.55
2018 2086 4.503714 GGATGAATTCCACCTTAGACCA 57.496 45.455 2.27 0.00 44.74 4.02
2057 2125 2.204136 TCCATGGCAGTCCCCAGT 60.204 61.111 6.96 0.00 38.50 4.00
2060 2128 1.077429 GAACTCCATGGCAGTCCCC 60.077 63.158 6.96 2.07 0.00 4.81
2061 2129 1.204146 TAGAACTCCATGGCAGTCCC 58.796 55.000 6.96 7.53 0.00 4.46
2084 2152 6.739112 TGATAGATCTTTCCATAGTCACACG 58.261 40.000 0.00 0.00 0.00 4.49
2129 2197 1.194781 AGGTCCCAGACATGAAGCGT 61.195 55.000 0.00 0.00 33.68 5.07
2223 2298 0.674581 TGAAGACCAGCATCGGCAAG 60.675 55.000 0.00 0.00 44.61 4.01
2307 2382 3.980442 TAAACACCCCCGCGCCATC 62.980 63.158 0.00 0.00 0.00 3.51
2460 2535 8.702438 CACACAACCATCTTTATTGAAATTGAC 58.298 33.333 0.00 0.00 0.00 3.18
2566 2641 4.746535 TTATTACCAACGATCCAGCTCA 57.253 40.909 0.00 0.00 0.00 4.26
2861 3124 8.563123 AGCAATAACTCAGATGATCCATAATG 57.437 34.615 0.00 0.00 0.00 1.90
3129 3393 9.566530 CACATATTAAAATCAAAACCATCACGA 57.433 29.630 0.00 0.00 0.00 4.35
3177 3441 3.369261 GCCATTTGTTTGGGTGCATGATA 60.369 43.478 0.00 0.00 37.24 2.15
3284 3548 5.066913 AGATGAGGGGTGAAAGTCTTTTT 57.933 39.130 0.00 0.00 0.00 1.94
3508 3772 6.211584 AGAGAACTAACTAAAGATCCTGCACA 59.788 38.462 0.00 0.00 0.00 4.57
4348 4620 4.020307 TGTGCATCATTGTTAGGTCTGAGA 60.020 41.667 0.00 0.00 0.00 3.27
4708 7846 9.627123 AAATGCCACTAAGAAAGCACTATAATA 57.373 29.630 0.00 0.00 38.21 0.98
4715 7853 4.870363 TCAAAATGCCACTAAGAAAGCAC 58.130 39.130 0.00 0.00 38.21 4.40
4762 7900 0.958382 GGTACCATCTGCGCAAACCA 60.958 55.000 13.05 0.00 0.00 3.67
4770 7908 0.328258 ACACCCTTGGTACCATCTGC 59.672 55.000 17.17 0.00 32.11 4.26
4868 8006 3.583806 CTCACCAGACTGAGATTGACAC 58.416 50.000 3.32 0.00 40.28 3.67
4973 8111 6.611236 TCCTTGTGGTATCTGACTCATTATCA 59.389 38.462 0.00 0.00 34.23 2.15
4974 8112 6.926272 GTCCTTGTGGTATCTGACTCATTATC 59.074 42.308 0.00 0.00 34.23 1.75
4975 8113 6.384015 TGTCCTTGTGGTATCTGACTCATTAT 59.616 38.462 0.00 0.00 34.23 1.28
4976 8114 5.719563 TGTCCTTGTGGTATCTGACTCATTA 59.280 40.000 0.00 0.00 34.23 1.90
4977 8115 4.532126 TGTCCTTGTGGTATCTGACTCATT 59.468 41.667 0.00 0.00 34.23 2.57
4978 8116 4.096681 TGTCCTTGTGGTATCTGACTCAT 58.903 43.478 0.00 0.00 34.23 2.90
4983 8121 3.506398 TCACTGTCCTTGTGGTATCTGA 58.494 45.455 0.00 0.00 36.21 3.27
5160 8298 5.639506 TGTCTCTTAGTAATTCACTTGCAGC 59.360 40.000 0.00 0.00 38.80 5.25
5918 9056 7.949690 TGTCTTTCCATTGTACTAGCTACTA 57.050 36.000 0.00 0.00 0.00 1.82
5919 9057 6.852420 TGTCTTTCCATTGTACTAGCTACT 57.148 37.500 0.00 0.00 0.00 2.57
5920 9058 7.764443 TCATTGTCTTTCCATTGTACTAGCTAC 59.236 37.037 0.00 0.00 0.00 3.58
5989 9127 3.251487 GGAGTAAGTCAGGAGATAGACGC 59.749 52.174 0.00 0.00 39.67 5.19
5990 9128 4.710324 AGGAGTAAGTCAGGAGATAGACG 58.290 47.826 0.00 0.00 39.67 4.18
6098 9236 9.884636 AAAATAAGGGAATTGTTATTAAGGCAC 57.115 29.630 0.00 0.00 30.34 5.01
6152 9290 7.451731 ACAGGGAGAATTGTCTATGGAATAA 57.548 36.000 2.24 0.00 32.80 1.40
6160 9298 5.568825 GCACAACTACAGGGAGAATTGTCTA 60.569 44.000 2.24 0.00 32.80 2.59
6172 9311 2.930040 CTGAATACCGCACAACTACAGG 59.070 50.000 0.00 0.00 0.00 4.00
6210 9349 3.650942 TGATGTGTCTAAAAGGGACCTGT 59.349 43.478 0.00 0.00 33.22 4.00
6216 9355 6.017605 GTCAGCATATGATGTGTCTAAAAGGG 60.018 42.308 19.78 0.00 40.92 3.95
6232 9371 1.135094 CCTGTCCCAGGTCAGCATAT 58.865 55.000 5.52 0.00 45.82 1.78
6243 9382 0.616395 TAGCGGATTGACCTGTCCCA 60.616 55.000 0.00 0.00 36.31 4.37
6252 9391 4.617959 CGGACTTAGATTTAGCGGATTGA 58.382 43.478 0.00 0.00 0.00 2.57
6309 9448 3.273048 CGGCATTTTCCGGCTTGA 58.727 55.556 0.00 0.00 45.38 3.02
6359 9498 4.710313 TGGTCCATGCATTGAGATGATA 57.290 40.909 0.00 0.00 35.16 2.15
6370 9509 1.280710 ACTCCGTTTATGGTCCATGCA 59.719 47.619 15.10 0.00 0.00 3.96
6377 9516 0.826062 CGGGGTACTCCGTTTATGGT 59.174 55.000 26.56 0.00 44.60 3.55
6430 9569 2.743928 CAACGGCCCAGAGAGTGC 60.744 66.667 0.00 0.00 0.00 4.40
6437 9576 2.040544 CCTAAGCACAACGGCCCAG 61.041 63.158 0.00 0.00 0.00 4.45
6485 9624 1.248785 TGTACTGGACCTGAGCGACC 61.249 60.000 5.22 0.00 0.00 4.79
6567 9706 1.214217 TCGGAGAGGGAGCTCTCTTA 58.786 55.000 19.43 0.00 46.61 2.10


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

AutoCloner maintained by Alex Coulton.