Multiple sequence alignment - TraesCS2D01G572900

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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 TraesCS2D01G572900 chr2D 100.000 2439 0 0 1 2439 638422740 638425178 0.000000e+00 4505.0
1 TraesCS2D01G572900 chr2D 95.676 185 6 2 2008 2191 112181992 112182175 1.830000e-76 296.0
2 TraesCS2D01G572900 chr2D 95.098 102 5 0 2324 2425 32838692 32838591 6.980000e-36 161.0
3 TraesCS2D01G572900 chr2D 98.667 75 0 1 2192 2265 452337865 452337791 5.470000e-27 132.0
4 TraesCS2D01G572900 chr5D 98.419 2150 28 3 294 2439 6178390 6176243 0.000000e+00 3777.0
5 TraesCS2D01G572900 chr5D 97.921 1972 27 4 294 2258 503289890 503291854 0.000000e+00 3402.0
6 TraesCS2D01G572900 chr1D 98.187 2151 33 3 294 2439 254433558 254435707 0.000000e+00 3751.0
7 TraesCS2D01G572900 chr6D 98.127 1922 27 4 294 2206 45508994 45507073 0.000000e+00 3341.0
8 TraesCS2D01G572900 chr4D 94.524 2155 105 7 294 2439 207069704 207067554 0.000000e+00 3314.0
9 TraesCS2D01G572900 chr1A 98.479 1644 20 3 460 2098 554461753 554463396 0.000000e+00 2892.0
10 TraesCS2D01G572900 chr4B 97.337 1690 38 5 755 2439 308680781 308679094 0.000000e+00 2865.0
11 TraesCS2D01G572900 chr4A 95.607 1639 61 7 806 2439 309490761 309489129 0.000000e+00 2617.0
12 TraesCS2D01G572900 chr2A 97.250 1418 32 4 1028 2439 32525820 32527236 0.000000e+00 2396.0
13 TraesCS2D01G572900 chr2A 91.367 139 10 2 9 146 754339963 754339826 3.200000e-44 189.0
14 TraesCS2D01G572900 chr2A 81.373 102 7 6 7 96 95211771 95211670 3.360000e-09 73.1
15 TraesCS2D01G572900 chr2B 97.287 1364 31 3 294 1651 474902902 474904265 0.000000e+00 2309.0
16 TraesCS2D01G572900 chr2B 94.059 101 6 0 2325 2425 54558479 54558379 1.170000e-33 154.0
17 TraesCS2D01G572900 chr2B 95.946 74 1 2 2271 2343 698330734 698330806 4.260000e-23 119.0
18 TraesCS2D01G572900 chr3B 96.861 446 10 3 1993 2436 147679949 147679506 0.000000e+00 743.0
19 TraesCS2D01G572900 chr3B 88.732 142 16 0 6 147 830618067 830617926 8.960000e-40 174.0
20 TraesCS2D01G572900 chr3B 88.732 142 16 0 6 147 830647364 830647223 8.960000e-40 174.0
21 TraesCS2D01G572900 chr3B 86.620 142 19 0 6 147 830328072 830327931 9.030000e-35 158.0
22 TraesCS2D01G572900 chr3B 86.620 142 19 0 6 147 830358664 830358523 9.030000e-35 158.0
23 TraesCS2D01G572900 chr3B 100.000 66 0 0 2245 2310 687455580 687455515 3.290000e-24 122.0
24 TraesCS2D01G572900 chr1B 90.411 146 12 2 7 151 630751474 630751618 8.900000e-45 191.0
25 TraesCS2D01G572900 chr1B 88.732 142 14 1 7 146 37606075 37606216 3.220000e-39 172.0
26 TraesCS2D01G572900 chr5A 86.897 145 18 1 7 150 687693139 687692995 6.980000e-36 161.0
27 TraesCS2D01G572900 chr3A 85.811 148 13 1 8 147 555645636 555645489 1.510000e-32 150.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G572900 chr2D 638422740 638425178 2438 False 4505 4505 100.000 1 2439 1 chr2D.!!$F2 2438
1 TraesCS2D01G572900 chr5D 6176243 6178390 2147 True 3777 3777 98.419 294 2439 1 chr5D.!!$R1 2145
2 TraesCS2D01G572900 chr5D 503289890 503291854 1964 False 3402 3402 97.921 294 2258 1 chr5D.!!$F1 1964
3 TraesCS2D01G572900 chr1D 254433558 254435707 2149 False 3751 3751 98.187 294 2439 1 chr1D.!!$F1 2145
4 TraesCS2D01G572900 chr6D 45507073 45508994 1921 True 3341 3341 98.127 294 2206 1 chr6D.!!$R1 1912
5 TraesCS2D01G572900 chr4D 207067554 207069704 2150 True 3314 3314 94.524 294 2439 1 chr4D.!!$R1 2145
6 TraesCS2D01G572900 chr1A 554461753 554463396 1643 False 2892 2892 98.479 460 2098 1 chr1A.!!$F1 1638
7 TraesCS2D01G572900 chr4B 308679094 308680781 1687 True 2865 2865 97.337 755 2439 1 chr4B.!!$R1 1684
8 TraesCS2D01G572900 chr4A 309489129 309490761 1632 True 2617 2617 95.607 806 2439 1 chr4A.!!$R1 1633
9 TraesCS2D01G572900 chr2A 32525820 32527236 1416 False 2396 2396 97.250 1028 2439 1 chr2A.!!$F1 1411
10 TraesCS2D01G572900 chr2B 474902902 474904265 1363 False 2309 2309 97.287 294 1651 1 chr2B.!!$F1 1357

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
285 286 0.180406 GTCGGCCATGGTGGAGTAAT 59.820 55.0 14.67 0.0 40.96 1.89 F
982 983 0.478072 AGCCCATGCCGGATTAATCA 59.522 50.0 17.07 0.0 38.69 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 1193 0.652592 CCCAGAAGCGCGTGATAAAG 59.347 55.000 8.43 0.0 0.0 1.85 R
2021 2046 1.404391 CATTGGTCTCGGTAGCTACGT 59.596 52.381 17.48 0.0 0.0 3.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.621286 AGTTGAATCATAGTTTTAAATAGCCGG 58.379 33.333 0.00 0.00 0.00 6.13
27 28 6.966021 TGAATCATAGTTTTAAATAGCCGGC 58.034 36.000 21.89 21.89 0.00 6.13
28 29 6.770785 TGAATCATAGTTTTAAATAGCCGGCT 59.229 34.615 34.85 34.85 0.00 5.52
29 30 7.934665 TGAATCATAGTTTTAAATAGCCGGCTA 59.065 33.333 36.88 36.88 0.00 3.93
30 31 8.863872 AATCATAGTTTTAAATAGCCGGCTAT 57.136 30.769 37.79 37.79 40.63 2.97
31 32 9.953565 AATCATAGTTTTAAATAGCCGGCTATA 57.046 29.630 41.53 28.18 38.20 1.31
32 33 8.997621 TCATAGTTTTAAATAGCCGGCTATAG 57.002 34.615 41.53 22.50 38.20 1.31
33 34 7.548075 TCATAGTTTTAAATAGCCGGCTATAGC 59.452 37.037 41.53 29.09 38.20 2.97
49 50 5.073311 CTATAGCCGCTATAGCCTTTTCA 57.927 43.478 26.93 4.47 39.28 2.69
50 51 2.246719 AGCCGCTATAGCCTTTTCAG 57.753 50.000 19.00 2.99 37.91 3.02
51 52 0.588737 GCCGCTATAGCCTTTTCAGC 59.411 55.000 19.00 6.98 37.91 4.26
52 53 1.953559 CCGCTATAGCCTTTTCAGCA 58.046 50.000 19.00 0.00 37.91 4.41
53 54 1.869767 CCGCTATAGCCTTTTCAGCAG 59.130 52.381 19.00 0.81 37.91 4.24
54 55 1.869767 CGCTATAGCCTTTTCAGCAGG 59.130 52.381 19.00 0.00 37.91 4.85
55 56 2.225467 GCTATAGCCTTTTCAGCAGGG 58.775 52.381 14.13 0.00 34.31 4.45
56 57 2.422093 GCTATAGCCTTTTCAGCAGGGT 60.422 50.000 14.13 0.00 44.56 4.34
57 58 2.134789 ATAGCCTTTTCAGCAGGGTG 57.865 50.000 2.17 0.00 42.32 4.61
58 59 0.609131 TAGCCTTTTCAGCAGGGTGC 60.609 55.000 2.17 0.00 42.32 5.01
68 69 1.811860 GCAGGGTGCTGCTAAATGG 59.188 57.895 0.00 0.00 46.04 3.16
69 70 0.967380 GCAGGGTGCTGCTAAATGGT 60.967 55.000 0.00 0.00 46.04 3.55
70 71 1.098050 CAGGGTGCTGCTAAATGGTC 58.902 55.000 0.00 0.00 0.00 4.02
71 72 0.392998 AGGGTGCTGCTAAATGGTCG 60.393 55.000 0.00 0.00 0.00 4.79
72 73 1.429423 GGTGCTGCTAAATGGTCGC 59.571 57.895 0.00 0.00 0.00 5.19
73 74 1.429423 GTGCTGCTAAATGGTCGCC 59.571 57.895 0.00 0.00 0.00 5.54
74 75 1.026718 GTGCTGCTAAATGGTCGCCT 61.027 55.000 0.00 0.00 0.00 5.52
75 76 0.322456 TGCTGCTAAATGGTCGCCTT 60.322 50.000 0.00 0.00 0.00 4.35
76 77 0.378610 GCTGCTAAATGGTCGCCTTC 59.621 55.000 0.00 0.00 0.00 3.46
77 78 1.737838 CTGCTAAATGGTCGCCTTCA 58.262 50.000 0.00 0.00 0.00 3.02
78 79 1.398390 CTGCTAAATGGTCGCCTTCAC 59.602 52.381 0.00 0.00 0.00 3.18
79 80 1.271108 TGCTAAATGGTCGCCTTCACA 60.271 47.619 0.00 0.00 0.00 3.58
80 81 1.810151 GCTAAATGGTCGCCTTCACAA 59.190 47.619 0.00 0.00 0.00 3.33
81 82 2.227865 GCTAAATGGTCGCCTTCACAAA 59.772 45.455 0.00 0.00 0.00 2.83
82 83 3.119495 GCTAAATGGTCGCCTTCACAAAT 60.119 43.478 0.00 0.00 0.00 2.32
83 84 4.095782 GCTAAATGGTCGCCTTCACAAATA 59.904 41.667 0.00 0.00 0.00 1.40
84 85 4.434713 AAATGGTCGCCTTCACAAATAC 57.565 40.909 0.00 0.00 0.00 1.89
85 86 2.851263 TGGTCGCCTTCACAAATACT 57.149 45.000 0.00 0.00 0.00 2.12
86 87 2.695359 TGGTCGCCTTCACAAATACTC 58.305 47.619 0.00 0.00 0.00 2.59
87 88 2.007608 GGTCGCCTTCACAAATACTCC 58.992 52.381 0.00 0.00 0.00 3.85
88 89 1.659098 GTCGCCTTCACAAATACTCCG 59.341 52.381 0.00 0.00 0.00 4.63
89 90 0.373716 CGCCTTCACAAATACTCCGC 59.626 55.000 0.00 0.00 0.00 5.54
90 91 1.739067 GCCTTCACAAATACTCCGCT 58.261 50.000 0.00 0.00 0.00 5.52
91 92 2.737359 CGCCTTCACAAATACTCCGCTA 60.737 50.000 0.00 0.00 0.00 4.26
92 93 3.467803 GCCTTCACAAATACTCCGCTAT 58.532 45.455 0.00 0.00 0.00 2.97
93 94 4.628074 GCCTTCACAAATACTCCGCTATA 58.372 43.478 0.00 0.00 0.00 1.31
94 95 4.686554 GCCTTCACAAATACTCCGCTATAG 59.313 45.833 0.00 0.00 0.00 1.31
95 96 4.686554 CCTTCACAAATACTCCGCTATAGC 59.313 45.833 15.09 15.09 37.78 2.97
96 97 5.509840 CCTTCACAAATACTCCGCTATAGCT 60.510 44.000 21.98 6.31 39.32 3.32
97 98 6.294564 CCTTCACAAATACTCCGCTATAGCTA 60.295 42.308 21.98 8.39 39.32 3.32
98 99 6.644248 TCACAAATACTCCGCTATAGCTAA 57.356 37.500 21.98 9.16 39.32 3.09
99 100 7.228314 TCACAAATACTCCGCTATAGCTAAT 57.772 36.000 21.98 7.84 39.32 1.73
100 101 7.667557 TCACAAATACTCCGCTATAGCTAATT 58.332 34.615 21.98 10.94 39.32 1.40
101 102 8.148351 TCACAAATACTCCGCTATAGCTAATTT 58.852 33.333 21.98 15.30 39.32 1.82
102 103 8.223769 CACAAATACTCCGCTATAGCTAATTTG 58.776 37.037 25.55 25.55 39.32 2.32
103 104 8.148351 ACAAATACTCCGCTATAGCTAATTTGA 58.852 33.333 29.34 16.47 39.32 2.69
104 105 8.988934 CAAATACTCCGCTATAGCTAATTTGAA 58.011 33.333 24.43 8.64 39.32 2.69
105 106 8.764524 AATACTCCGCTATAGCTAATTTGAAG 57.235 34.615 21.98 9.67 39.32 3.02
106 107 5.542779 ACTCCGCTATAGCTAATTTGAAGG 58.457 41.667 21.98 12.29 39.32 3.46
107 108 4.315803 TCCGCTATAGCTAATTTGAAGGC 58.684 43.478 21.98 0.00 39.32 4.35
108 109 3.437049 CCGCTATAGCTAATTTGAAGGCC 59.563 47.826 21.98 0.00 39.32 5.19
109 110 3.437049 CGCTATAGCTAATTTGAAGGCCC 59.563 47.826 21.98 0.00 39.32 5.80
110 111 3.437049 GCTATAGCTAATTTGAAGGCCCG 59.563 47.826 17.75 0.00 38.21 6.13
111 112 1.675552 TAGCTAATTTGAAGGCCCGC 58.324 50.000 0.00 0.00 0.00 6.13
112 113 1.037579 AGCTAATTTGAAGGCCCGCC 61.038 55.000 0.00 0.00 0.00 6.13
113 114 2.016393 GCTAATTTGAAGGCCCGCCC 62.016 60.000 0.00 0.00 36.58 6.13
114 115 1.380650 TAATTTGAAGGCCCGCCCC 60.381 57.895 0.00 0.00 36.58 5.80
115 116 1.869824 TAATTTGAAGGCCCGCCCCT 61.870 55.000 0.00 0.00 36.58 4.79
116 117 1.869824 AATTTGAAGGCCCGCCCCTA 61.870 55.000 0.00 0.00 33.97 3.53
117 118 1.655114 ATTTGAAGGCCCGCCCCTAT 61.655 55.000 0.00 0.00 33.97 2.57
118 119 1.869824 TTTGAAGGCCCGCCCCTATT 61.870 55.000 0.00 0.00 33.97 1.73
119 120 1.869824 TTGAAGGCCCGCCCCTATTT 61.870 55.000 0.00 0.00 33.97 1.40
120 121 1.076265 GAAGGCCCGCCCCTATTTT 60.076 57.895 0.00 0.00 33.97 1.82
121 122 0.686441 GAAGGCCCGCCCCTATTTTT 60.686 55.000 0.00 0.00 33.97 1.94
122 123 0.686441 AAGGCCCGCCCCTATTTTTC 60.686 55.000 0.00 0.00 33.97 2.29
123 124 1.380650 GGCCCGCCCCTATTTTTCA 60.381 57.895 0.00 0.00 0.00 2.69
124 125 0.759060 GGCCCGCCCCTATTTTTCAT 60.759 55.000 0.00 0.00 0.00 2.57
125 126 1.479757 GGCCCGCCCCTATTTTTCATA 60.480 52.381 0.00 0.00 0.00 2.15
126 127 1.886542 GCCCGCCCCTATTTTTCATAG 59.113 52.381 0.00 0.00 0.00 2.23
127 128 1.886542 CCCGCCCCTATTTTTCATAGC 59.113 52.381 0.00 0.00 0.00 2.97
128 129 1.886542 CCGCCCCTATTTTTCATAGCC 59.113 52.381 0.00 0.00 0.00 3.93
129 130 1.886542 CGCCCCTATTTTTCATAGCCC 59.113 52.381 0.00 0.00 0.00 5.19
130 131 2.489073 CGCCCCTATTTTTCATAGCCCT 60.489 50.000 0.00 0.00 0.00 5.19
131 132 3.157881 GCCCCTATTTTTCATAGCCCTC 58.842 50.000 0.00 0.00 0.00 4.30
132 133 3.181428 GCCCCTATTTTTCATAGCCCTCT 60.181 47.826 0.00 0.00 0.00 3.69
133 134 4.042934 GCCCCTATTTTTCATAGCCCTCTA 59.957 45.833 0.00 0.00 0.00 2.43
134 135 5.281245 GCCCCTATTTTTCATAGCCCTCTAT 60.281 44.000 0.00 0.00 35.97 1.98
135 136 6.751220 GCCCCTATTTTTCATAGCCCTCTATT 60.751 42.308 0.00 0.00 33.37 1.73
136 137 7.241628 CCCCTATTTTTCATAGCCCTCTATTT 58.758 38.462 0.00 0.00 33.37 1.40
137 138 8.390921 CCCCTATTTTTCATAGCCCTCTATTTA 58.609 37.037 0.00 0.00 33.37 1.40
138 139 9.807921 CCCTATTTTTCATAGCCCTCTATTTAA 57.192 33.333 0.00 0.00 33.37 1.52
146 147 9.693739 TTCATAGCCCTCTATTTAAAACATTGA 57.306 29.630 0.00 0.00 33.37 2.57
147 148 9.342308 TCATAGCCCTCTATTTAAAACATTGAG 57.658 33.333 0.00 0.00 33.37 3.02
148 149 9.125026 CATAGCCCTCTATTTAAAACATTGAGT 57.875 33.333 0.00 0.00 33.37 3.41
149 150 9.700831 ATAGCCCTCTATTTAAAACATTGAGTT 57.299 29.630 0.00 0.00 35.49 3.01
150 151 8.056407 AGCCCTCTATTTAAAACATTGAGTTC 57.944 34.615 0.00 0.00 40.26 3.01
151 152 7.669722 AGCCCTCTATTTAAAACATTGAGTTCA 59.330 33.333 0.00 0.00 40.26 3.18
152 153 8.303876 GCCCTCTATTTAAAACATTGAGTTCAA 58.696 33.333 0.00 0.00 40.26 2.69
153 154 9.626045 CCCTCTATTTAAAACATTGAGTTCAAC 57.374 33.333 0.00 0.00 40.26 3.18
154 155 9.329913 CCTCTATTTAAAACATTGAGTTCAACG 57.670 33.333 0.00 0.00 40.26 4.10
155 156 9.329913 CTCTATTTAAAACATTGAGTTCAACGG 57.670 33.333 0.00 0.00 40.26 4.44
156 157 8.293867 TCTATTTAAAACATTGAGTTCAACGGG 58.706 33.333 0.00 0.00 40.26 5.28
157 158 5.838531 TTAAAACATTGAGTTCAACGGGT 57.161 34.783 0.00 0.00 40.26 5.28
158 159 4.729227 AAAACATTGAGTTCAACGGGTT 57.271 36.364 0.00 0.59 40.26 4.11
159 160 5.838531 AAAACATTGAGTTCAACGGGTTA 57.161 34.783 0.00 0.00 40.26 2.85
160 161 5.432885 AAACATTGAGTTCAACGGGTTAG 57.567 39.130 0.00 0.00 40.26 2.34
161 162 4.081322 ACATTGAGTTCAACGGGTTAGT 57.919 40.909 0.00 0.00 38.86 2.24
162 163 3.813166 ACATTGAGTTCAACGGGTTAGTG 59.187 43.478 0.00 0.00 38.86 2.74
163 164 2.536761 TGAGTTCAACGGGTTAGTGG 57.463 50.000 0.00 0.00 0.00 4.00
164 165 1.154197 GAGTTCAACGGGTTAGTGGC 58.846 55.000 0.00 0.00 0.00 5.01
165 166 0.601841 AGTTCAACGGGTTAGTGGCG 60.602 55.000 0.00 0.00 0.00 5.69
166 167 1.301874 TTCAACGGGTTAGTGGCGG 60.302 57.895 0.00 0.00 0.00 6.13
167 168 3.428282 CAACGGGTTAGTGGCGGC 61.428 66.667 0.00 0.00 0.00 6.53
168 169 4.710167 AACGGGTTAGTGGCGGCC 62.710 66.667 13.32 13.32 0.00 6.13
171 172 3.773404 GGGTTAGTGGCGGCCGTA 61.773 66.667 28.70 14.00 0.00 4.02
172 173 2.265424 GGTTAGTGGCGGCCGTAA 59.735 61.111 28.70 14.53 0.00 3.18
173 174 1.375780 GGTTAGTGGCGGCCGTAAA 60.376 57.895 28.70 9.95 0.00 2.01
174 175 0.954938 GGTTAGTGGCGGCCGTAAAA 60.955 55.000 28.70 11.49 0.00 1.52
175 176 1.089112 GTTAGTGGCGGCCGTAAAAT 58.911 50.000 28.70 14.22 0.00 1.82
176 177 1.063027 GTTAGTGGCGGCCGTAAAATC 59.937 52.381 28.70 8.51 0.00 2.17
177 178 0.249676 TAGTGGCGGCCGTAAAATCA 59.750 50.000 28.70 12.58 0.00 2.57
178 179 1.024579 AGTGGCGGCCGTAAAATCAG 61.025 55.000 28.70 0.00 0.00 2.90
179 180 1.022451 GTGGCGGCCGTAAAATCAGA 61.022 55.000 28.70 0.00 0.00 3.27
180 181 0.321741 TGGCGGCCGTAAAATCAGAA 60.322 50.000 28.70 0.00 0.00 3.02
181 182 0.377203 GGCGGCCGTAAAATCAGAAG 59.623 55.000 28.70 0.00 0.00 2.85
182 183 1.084289 GCGGCCGTAAAATCAGAAGT 58.916 50.000 28.70 0.00 0.00 3.01
183 184 1.202031 GCGGCCGTAAAATCAGAAGTG 60.202 52.381 28.70 0.00 0.00 3.16
184 185 1.396996 CGGCCGTAAAATCAGAAGTGG 59.603 52.381 19.50 0.00 0.00 4.00
185 186 1.743394 GGCCGTAAAATCAGAAGTGGG 59.257 52.381 0.00 0.00 0.00 4.61
186 187 2.617021 GGCCGTAAAATCAGAAGTGGGA 60.617 50.000 0.00 0.00 0.00 4.37
187 188 3.078837 GCCGTAAAATCAGAAGTGGGAA 58.921 45.455 0.00 0.00 0.00 3.97
188 189 3.694566 GCCGTAAAATCAGAAGTGGGAAT 59.305 43.478 0.00 0.00 0.00 3.01
189 190 4.879545 GCCGTAAAATCAGAAGTGGGAATA 59.120 41.667 0.00 0.00 0.00 1.75
190 191 5.531287 GCCGTAAAATCAGAAGTGGGAATAT 59.469 40.000 0.00 0.00 0.00 1.28
191 192 6.513393 GCCGTAAAATCAGAAGTGGGAATATG 60.513 42.308 0.00 0.00 0.00 1.78
192 193 6.765989 CCGTAAAATCAGAAGTGGGAATATGA 59.234 38.462 0.00 0.00 0.00 2.15
193 194 7.282224 CCGTAAAATCAGAAGTGGGAATATGAA 59.718 37.037 0.00 0.00 0.00 2.57
194 195 8.122952 CGTAAAATCAGAAGTGGGAATATGAAC 58.877 37.037 0.00 0.00 0.00 3.18
195 196 8.956426 GTAAAATCAGAAGTGGGAATATGAACA 58.044 33.333 0.00 0.00 0.00 3.18
196 197 8.421249 AAAATCAGAAGTGGGAATATGAACAA 57.579 30.769 0.00 0.00 0.00 2.83
197 198 8.421249 AAATCAGAAGTGGGAATATGAACAAA 57.579 30.769 0.00 0.00 0.00 2.83
198 199 8.599624 AATCAGAAGTGGGAATATGAACAAAT 57.400 30.769 0.00 0.00 0.00 2.32
199 200 7.395190 TCAGAAGTGGGAATATGAACAAATG 57.605 36.000 0.00 0.00 0.00 2.32
200 201 7.174413 TCAGAAGTGGGAATATGAACAAATGA 58.826 34.615 0.00 0.00 0.00 2.57
201 202 7.337689 TCAGAAGTGGGAATATGAACAAATGAG 59.662 37.037 0.00 0.00 0.00 2.90
202 203 5.841957 AGTGGGAATATGAACAAATGAGC 57.158 39.130 0.00 0.00 0.00 4.26
203 204 5.513233 AGTGGGAATATGAACAAATGAGCT 58.487 37.500 0.00 0.00 0.00 4.09
204 205 5.359009 AGTGGGAATATGAACAAATGAGCTG 59.641 40.000 0.00 0.00 0.00 4.24
205 206 4.098349 TGGGAATATGAACAAATGAGCTGC 59.902 41.667 0.00 0.00 0.00 5.25
206 207 4.340381 GGGAATATGAACAAATGAGCTGCT 59.660 41.667 0.00 0.00 0.00 4.24
207 208 5.279384 GGAATATGAACAAATGAGCTGCTG 58.721 41.667 7.01 0.00 0.00 4.41
208 209 4.913335 ATATGAACAAATGAGCTGCTGG 57.087 40.909 7.01 0.00 0.00 4.85
209 210 2.275134 TGAACAAATGAGCTGCTGGA 57.725 45.000 7.01 0.00 0.00 3.86
210 211 2.799017 TGAACAAATGAGCTGCTGGAT 58.201 42.857 7.01 0.00 0.00 3.41
211 212 3.159472 TGAACAAATGAGCTGCTGGATT 58.841 40.909 7.01 1.97 0.00 3.01
212 213 3.575256 TGAACAAATGAGCTGCTGGATTT 59.425 39.130 7.01 8.59 0.00 2.17
213 214 4.766373 TGAACAAATGAGCTGCTGGATTTA 59.234 37.500 7.01 0.00 0.00 1.40
214 215 4.708726 ACAAATGAGCTGCTGGATTTAC 57.291 40.909 7.01 0.00 0.00 2.01
215 216 4.081406 ACAAATGAGCTGCTGGATTTACA 58.919 39.130 7.01 0.00 0.00 2.41
216 217 4.708421 ACAAATGAGCTGCTGGATTTACAT 59.292 37.500 7.01 0.00 0.00 2.29
217 218 5.163581 ACAAATGAGCTGCTGGATTTACATC 60.164 40.000 7.01 0.00 0.00 3.06
218 219 3.920231 TGAGCTGCTGGATTTACATCT 57.080 42.857 7.01 0.00 0.00 2.90
219 220 5.557576 ATGAGCTGCTGGATTTACATCTA 57.442 39.130 7.01 0.00 0.00 1.98
220 221 5.557576 TGAGCTGCTGGATTTACATCTAT 57.442 39.130 7.01 0.00 0.00 1.98
221 222 5.545588 TGAGCTGCTGGATTTACATCTATC 58.454 41.667 7.01 0.00 0.00 2.08
222 223 4.564041 AGCTGCTGGATTTACATCTATCG 58.436 43.478 0.00 0.00 0.00 2.92
223 224 4.281941 AGCTGCTGGATTTACATCTATCGA 59.718 41.667 0.00 0.00 0.00 3.59
224 225 5.046735 AGCTGCTGGATTTACATCTATCGAT 60.047 40.000 0.00 2.16 0.00 3.59
225 226 5.290643 GCTGCTGGATTTACATCTATCGATC 59.709 44.000 0.00 0.00 0.00 3.69
226 227 5.402398 TGCTGGATTTACATCTATCGATCG 58.598 41.667 9.36 9.36 0.00 3.69
227 228 4.800993 GCTGGATTTACATCTATCGATCGG 59.199 45.833 16.41 0.00 0.00 4.18
228 229 4.744570 TGGATTTACATCTATCGATCGGC 58.255 43.478 16.41 0.00 0.00 5.54
229 230 3.791887 GGATTTACATCTATCGATCGGCG 59.208 47.826 16.41 0.00 42.69 6.46
230 231 2.913777 TTACATCTATCGATCGGCGG 57.086 50.000 16.41 5.58 41.33 6.13
231 232 1.092348 TACATCTATCGATCGGCGGG 58.908 55.000 16.41 3.76 41.33 6.13
232 233 0.608308 ACATCTATCGATCGGCGGGA 60.608 55.000 16.41 9.10 41.33 5.14
233 234 0.526211 CATCTATCGATCGGCGGGAA 59.474 55.000 16.41 0.00 41.33 3.97
234 235 1.067846 CATCTATCGATCGGCGGGAAA 60.068 52.381 16.41 0.00 41.33 3.13
235 236 0.596577 TCTATCGATCGGCGGGAAAG 59.403 55.000 16.41 2.99 41.33 2.62
236 237 0.388649 CTATCGATCGGCGGGAAAGG 60.389 60.000 16.41 0.00 41.33 3.11
237 238 1.812686 TATCGATCGGCGGGAAAGGG 61.813 60.000 16.41 0.00 41.33 3.95
239 240 4.176752 GATCGGCGGGAAAGGGCT 62.177 66.667 7.21 0.00 0.00 5.19
240 241 2.766651 ATCGGCGGGAAAGGGCTA 60.767 61.111 7.21 0.00 0.00 3.93
241 242 2.717139 GATCGGCGGGAAAGGGCTAG 62.717 65.000 7.21 0.00 0.00 3.42
244 245 4.157120 GCGGGAAAGGGCTAGCGA 62.157 66.667 9.00 0.00 0.00 4.93
245 246 2.202892 CGGGAAAGGGCTAGCGAC 60.203 66.667 9.00 4.13 0.00 5.19
246 247 2.202892 GGGAAAGGGCTAGCGACG 60.203 66.667 9.00 0.00 0.00 5.12
247 248 2.202892 GGAAAGGGCTAGCGACGG 60.203 66.667 9.00 0.00 0.00 4.79
248 249 2.890961 GAAAGGGCTAGCGACGGC 60.891 66.667 9.00 0.00 40.37 5.68
249 250 4.814294 AAAGGGCTAGCGACGGCG 62.814 66.667 6.12 6.12 46.35 6.46
281 282 4.838152 CCGTCGGCCATGGTGGAG 62.838 72.222 14.67 2.60 40.96 3.86
282 283 4.082523 CGTCGGCCATGGTGGAGT 62.083 66.667 14.67 0.00 40.96 3.85
283 284 2.717044 CGTCGGCCATGGTGGAGTA 61.717 63.158 14.67 0.00 40.96 2.59
284 285 1.600107 GTCGGCCATGGTGGAGTAA 59.400 57.895 14.67 0.00 40.96 2.24
285 286 0.180406 GTCGGCCATGGTGGAGTAAT 59.820 55.000 14.67 0.00 40.96 1.89
286 287 0.916086 TCGGCCATGGTGGAGTAATT 59.084 50.000 14.67 0.00 40.96 1.40
287 288 2.120312 TCGGCCATGGTGGAGTAATTA 58.880 47.619 14.67 0.00 40.96 1.40
288 289 2.506231 TCGGCCATGGTGGAGTAATTAA 59.494 45.455 14.67 0.00 40.96 1.40
289 290 2.878406 CGGCCATGGTGGAGTAATTAAG 59.122 50.000 14.67 0.00 40.96 1.85
290 291 3.222603 GGCCATGGTGGAGTAATTAAGG 58.777 50.000 14.67 0.00 40.96 2.69
291 292 3.222603 GCCATGGTGGAGTAATTAAGGG 58.777 50.000 14.67 0.00 40.96 3.95
292 293 3.372675 GCCATGGTGGAGTAATTAAGGGT 60.373 47.826 14.67 0.00 40.96 4.34
429 430 2.512286 GTGCGGCTCTGCTATGCA 60.512 61.111 0.00 0.00 36.92 3.96
493 494 3.088532 GTGATGGTGCAAATACCTTCCA 58.911 45.455 0.00 0.00 41.67 3.53
538 539 6.096001 GCTGAAGAAACTTATTCCATGGTCAT 59.904 38.462 12.58 7.99 0.00 3.06
982 983 0.478072 AGCCCATGCCGGATTAATCA 59.522 50.000 17.07 0.00 38.69 2.57
1089 1090 3.288964 TCCACACTTAGCTACTCTAGGC 58.711 50.000 0.00 0.00 0.00 3.93
1107 1111 4.431524 TGGGGAGTAGGGCCAGGG 62.432 72.222 6.18 0.00 0.00 4.45
2021 2046 3.078837 GCTCTTTAAATTCCGTGGGTGA 58.921 45.455 0.00 0.00 0.00 4.02
2036 2061 0.376502 GGTGACGTAGCTACCGAGAC 59.623 60.000 18.16 9.38 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.621286 CCGGCTATTTAAAACTATGATTCAACT 58.379 33.333 0.00 0.00 0.00 3.16
1 2 7.378728 GCCGGCTATTTAAAACTATGATTCAAC 59.621 37.037 22.15 0.00 0.00 3.18
2 3 7.284489 AGCCGGCTATTTAAAACTATGATTCAA 59.716 33.333 31.86 0.00 0.00 2.69
3 4 6.770785 AGCCGGCTATTTAAAACTATGATTCA 59.229 34.615 31.86 0.00 0.00 2.57
4 5 7.203255 AGCCGGCTATTTAAAACTATGATTC 57.797 36.000 31.86 0.00 0.00 2.52
5 6 8.863872 ATAGCCGGCTATTTAAAACTATGATT 57.136 30.769 37.79 15.38 35.92 2.57
6 7 9.601217 CTATAGCCGGCTATTTAAAACTATGAT 57.399 33.333 44.65 25.13 39.65 2.45
7 8 7.548075 GCTATAGCCGGCTATTTAAAACTATGA 59.452 37.037 44.65 25.48 39.65 2.15
8 9 7.685594 GCTATAGCCGGCTATTTAAAACTATG 58.314 38.462 44.65 24.19 39.65 2.23
9 10 7.845066 GCTATAGCCGGCTATTTAAAACTAT 57.155 36.000 44.65 26.21 39.65 2.12
27 28 5.073311 TGAAAAGGCTATAGCGGCTATAG 57.927 43.478 36.16 36.16 45.03 1.31
28 29 4.620803 GCTGAAAAGGCTATAGCGGCTATA 60.621 45.833 24.14 24.14 43.26 1.31
29 30 3.866449 GCTGAAAAGGCTATAGCGGCTAT 60.866 47.826 24.50 24.50 43.26 2.97
30 31 2.548067 GCTGAAAAGGCTATAGCGGCTA 60.548 50.000 18.30 12.80 43.26 3.93
31 32 1.811941 GCTGAAAAGGCTATAGCGGCT 60.812 52.381 18.30 7.98 43.26 5.52
32 33 0.588737 GCTGAAAAGGCTATAGCGGC 59.411 55.000 18.30 5.78 43.26 6.53
33 34 1.869767 CTGCTGAAAAGGCTATAGCGG 59.130 52.381 18.30 6.64 43.26 5.52
34 35 1.869767 CCTGCTGAAAAGGCTATAGCG 59.130 52.381 18.30 4.04 43.26 4.26
35 36 2.225467 CCCTGCTGAAAAGGCTATAGC 58.775 52.381 16.78 16.78 41.14 2.97
36 37 3.209410 CACCCTGCTGAAAAGGCTATAG 58.791 50.000 0.00 0.00 33.07 1.31
37 38 2.683742 GCACCCTGCTGAAAAGGCTATA 60.684 50.000 0.00 0.00 40.96 1.31
38 39 1.957113 GCACCCTGCTGAAAAGGCTAT 60.957 52.381 0.00 0.00 40.96 2.97
39 40 0.609131 GCACCCTGCTGAAAAGGCTA 60.609 55.000 0.00 0.00 40.96 3.93
40 41 1.905354 GCACCCTGCTGAAAAGGCT 60.905 57.895 0.00 0.00 40.96 4.58
41 42 2.653115 GCACCCTGCTGAAAAGGC 59.347 61.111 0.00 0.00 40.96 4.35
51 52 1.098050 GACCATTTAGCAGCACCCTG 58.902 55.000 0.00 0.00 42.13 4.45
52 53 0.392998 CGACCATTTAGCAGCACCCT 60.393 55.000 0.00 0.00 0.00 4.34
53 54 1.993369 GCGACCATTTAGCAGCACCC 61.993 60.000 0.00 0.00 0.00 4.61
54 55 1.429423 GCGACCATTTAGCAGCACC 59.571 57.895 0.00 0.00 0.00 5.01
55 56 1.026718 AGGCGACCATTTAGCAGCAC 61.027 55.000 0.00 0.00 0.00 4.40
56 57 0.322456 AAGGCGACCATTTAGCAGCA 60.322 50.000 0.00 0.00 0.00 4.41
57 58 0.378610 GAAGGCGACCATTTAGCAGC 59.621 55.000 0.00 0.00 0.00 5.25
58 59 1.398390 GTGAAGGCGACCATTTAGCAG 59.602 52.381 0.00 0.00 0.00 4.24
59 60 1.271108 TGTGAAGGCGACCATTTAGCA 60.271 47.619 0.00 0.00 0.00 3.49
60 61 1.448985 TGTGAAGGCGACCATTTAGC 58.551 50.000 0.00 0.00 0.00 3.09
61 62 4.701956 ATTTGTGAAGGCGACCATTTAG 57.298 40.909 0.00 0.00 0.00 1.85
62 63 5.250200 AGTATTTGTGAAGGCGACCATTTA 58.750 37.500 0.00 0.00 0.00 1.40
63 64 4.079253 AGTATTTGTGAAGGCGACCATTT 58.921 39.130 0.00 0.00 0.00 2.32
64 65 3.686016 AGTATTTGTGAAGGCGACCATT 58.314 40.909 0.00 0.00 0.00 3.16
65 66 3.270877 GAGTATTTGTGAAGGCGACCAT 58.729 45.455 0.00 0.00 0.00 3.55
66 67 2.614481 GGAGTATTTGTGAAGGCGACCA 60.614 50.000 0.00 0.00 0.00 4.02
67 68 2.007608 GGAGTATTTGTGAAGGCGACC 58.992 52.381 0.00 0.00 0.00 4.79
68 69 1.659098 CGGAGTATTTGTGAAGGCGAC 59.341 52.381 0.00 0.00 0.00 5.19
69 70 2.004583 CGGAGTATTTGTGAAGGCGA 57.995 50.000 0.00 0.00 0.00 5.54
70 71 0.373716 GCGGAGTATTTGTGAAGGCG 59.626 55.000 0.00 0.00 0.00 5.52
71 72 1.739067 AGCGGAGTATTTGTGAAGGC 58.261 50.000 0.00 0.00 0.00 4.35
72 73 4.686554 GCTATAGCGGAGTATTTGTGAAGG 59.313 45.833 9.40 0.00 0.00 3.46
73 74 5.830900 GCTATAGCGGAGTATTTGTGAAG 57.169 43.478 9.40 0.00 0.00 3.02
88 89 3.437049 CGGGCCTTCAAATTAGCTATAGC 59.563 47.826 17.33 17.33 42.49 2.97
89 90 3.437049 GCGGGCCTTCAAATTAGCTATAG 59.563 47.826 0.84 0.00 0.00 1.31
90 91 3.408634 GCGGGCCTTCAAATTAGCTATA 58.591 45.455 0.84 0.00 0.00 1.31
91 92 2.230660 GCGGGCCTTCAAATTAGCTAT 58.769 47.619 0.84 0.00 0.00 2.97
92 93 1.675552 GCGGGCCTTCAAATTAGCTA 58.324 50.000 0.84 0.00 0.00 3.32
93 94 1.037579 GGCGGGCCTTCAAATTAGCT 61.038 55.000 0.84 0.00 0.00 3.32
94 95 1.437573 GGCGGGCCTTCAAATTAGC 59.562 57.895 0.84 0.00 0.00 3.09
95 96 1.391933 GGGGCGGGCCTTCAAATTAG 61.392 60.000 20.88 0.00 36.10 1.73
96 97 1.380650 GGGGCGGGCCTTCAAATTA 60.381 57.895 20.88 0.00 36.10 1.40
97 98 1.869824 TAGGGGCGGGCCTTCAAATT 61.870 55.000 20.88 0.87 36.10 1.82
98 99 1.655114 ATAGGGGCGGGCCTTCAAAT 61.655 55.000 20.88 0.26 36.10 2.32
99 100 1.869824 AATAGGGGCGGGCCTTCAAA 61.870 55.000 20.88 0.00 36.10 2.69
100 101 1.869824 AAATAGGGGCGGGCCTTCAA 61.870 55.000 20.88 0.00 36.10 2.69
101 102 1.869824 AAAATAGGGGCGGGCCTTCA 61.870 55.000 20.88 6.18 36.10 3.02
102 103 0.686441 AAAAATAGGGGCGGGCCTTC 60.686 55.000 20.88 4.55 36.10 3.46
103 104 0.686441 GAAAAATAGGGGCGGGCCTT 60.686 55.000 20.88 15.91 36.10 4.35
104 105 1.076265 GAAAAATAGGGGCGGGCCT 60.076 57.895 20.88 9.00 36.10 5.19
105 106 0.759060 ATGAAAAATAGGGGCGGGCC 60.759 55.000 13.01 13.01 0.00 5.80
106 107 1.886542 CTATGAAAAATAGGGGCGGGC 59.113 52.381 0.00 0.00 0.00 6.13
107 108 1.886542 GCTATGAAAAATAGGGGCGGG 59.113 52.381 0.00 0.00 0.00 6.13
108 109 1.886542 GGCTATGAAAAATAGGGGCGG 59.113 52.381 0.00 0.00 0.00 6.13
109 110 1.886542 GGGCTATGAAAAATAGGGGCG 59.113 52.381 0.00 0.00 0.00 6.13
110 111 3.157881 GAGGGCTATGAAAAATAGGGGC 58.842 50.000 0.00 0.00 0.00 5.80
111 112 4.731313 AGAGGGCTATGAAAAATAGGGG 57.269 45.455 0.00 0.00 0.00 4.79
112 113 9.807921 TTAAATAGAGGGCTATGAAAAATAGGG 57.192 33.333 0.00 0.00 37.40 3.53
120 121 9.693739 TCAATGTTTTAAATAGAGGGCTATGAA 57.306 29.630 0.00 0.00 37.40 2.57
121 122 9.342308 CTCAATGTTTTAAATAGAGGGCTATGA 57.658 33.333 0.00 0.00 37.40 2.15
122 123 9.125026 ACTCAATGTTTTAAATAGAGGGCTATG 57.875 33.333 0.00 0.00 37.40 2.23
123 124 9.700831 AACTCAATGTTTTAAATAGAGGGCTAT 57.299 29.630 0.00 0.00 35.69 2.97
124 125 9.174166 GAACTCAATGTTTTAAATAGAGGGCTA 57.826 33.333 0.00 0.00 39.30 3.93
125 126 7.669722 TGAACTCAATGTTTTAAATAGAGGGCT 59.330 33.333 0.00 0.00 39.30 5.19
126 127 7.826690 TGAACTCAATGTTTTAAATAGAGGGC 58.173 34.615 0.00 0.00 39.30 5.19
127 128 9.626045 GTTGAACTCAATGTTTTAAATAGAGGG 57.374 33.333 0.00 0.00 39.30 4.30
128 129 9.329913 CGTTGAACTCAATGTTTTAAATAGAGG 57.670 33.333 3.87 0.00 39.30 3.69
129 130 9.329913 CCGTTGAACTCAATGTTTTAAATAGAG 57.670 33.333 10.08 0.00 40.34 2.43
130 131 8.293867 CCCGTTGAACTCAATGTTTTAAATAGA 58.706 33.333 10.08 0.00 40.34 1.98
131 132 8.079809 ACCCGTTGAACTCAATGTTTTAAATAG 58.920 33.333 10.08 0.00 40.34 1.73
132 133 7.942990 ACCCGTTGAACTCAATGTTTTAAATA 58.057 30.769 10.08 0.00 40.34 1.40
133 134 6.811954 ACCCGTTGAACTCAATGTTTTAAAT 58.188 32.000 10.08 0.00 40.34 1.40
134 135 6.210287 ACCCGTTGAACTCAATGTTTTAAA 57.790 33.333 10.08 0.00 40.34 1.52
135 136 5.838531 ACCCGTTGAACTCAATGTTTTAA 57.161 34.783 10.08 0.00 40.34 1.52
136 137 5.838531 AACCCGTTGAACTCAATGTTTTA 57.161 34.783 10.08 0.00 40.34 1.52
137 138 4.729227 AACCCGTTGAACTCAATGTTTT 57.271 36.364 10.08 1.53 40.34 2.43
138 139 4.885325 ACTAACCCGTTGAACTCAATGTTT 59.115 37.500 10.08 6.13 40.34 2.83
139 140 4.274950 CACTAACCCGTTGAACTCAATGTT 59.725 41.667 10.08 9.37 40.34 2.71
140 141 3.813166 CACTAACCCGTTGAACTCAATGT 59.187 43.478 10.08 0.24 40.34 2.71
141 142 3.188460 CCACTAACCCGTTGAACTCAATG 59.812 47.826 4.91 4.91 41.32 2.82
142 143 3.408634 CCACTAACCCGTTGAACTCAAT 58.591 45.455 0.00 0.00 38.24 2.57
143 144 2.841215 CCACTAACCCGTTGAACTCAA 58.159 47.619 0.00 0.00 0.00 3.02
144 145 1.541670 GCCACTAACCCGTTGAACTCA 60.542 52.381 0.00 0.00 0.00 3.41
145 146 1.154197 GCCACTAACCCGTTGAACTC 58.846 55.000 0.00 0.00 0.00 3.01
146 147 0.601841 CGCCACTAACCCGTTGAACT 60.602 55.000 0.00 0.00 0.00 3.01
147 148 1.571215 CCGCCACTAACCCGTTGAAC 61.571 60.000 0.00 0.00 0.00 3.18
148 149 1.301874 CCGCCACTAACCCGTTGAA 60.302 57.895 0.00 0.00 0.00 2.69
149 150 2.344500 CCGCCACTAACCCGTTGA 59.656 61.111 0.00 0.00 0.00 3.18
150 151 3.428282 GCCGCCACTAACCCGTTG 61.428 66.667 0.00 0.00 0.00 4.10
151 152 4.710167 GGCCGCCACTAACCCGTT 62.710 66.667 3.91 0.00 0.00 4.44
154 155 2.801483 TTTACGGCCGCCACTAACCC 62.801 60.000 28.58 0.00 0.00 4.11
155 156 0.954938 TTTTACGGCCGCCACTAACC 60.955 55.000 28.58 0.00 0.00 2.85
156 157 1.063027 GATTTTACGGCCGCCACTAAC 59.937 52.381 28.58 8.05 0.00 2.34
157 158 1.338864 TGATTTTACGGCCGCCACTAA 60.339 47.619 28.58 13.85 0.00 2.24
158 159 0.249676 TGATTTTACGGCCGCCACTA 59.750 50.000 28.58 7.17 0.00 2.74
159 160 1.003112 TGATTTTACGGCCGCCACT 60.003 52.632 28.58 8.43 0.00 4.00
160 161 1.022451 TCTGATTTTACGGCCGCCAC 61.022 55.000 28.58 11.57 0.00 5.01
161 162 0.321741 TTCTGATTTTACGGCCGCCA 60.322 50.000 28.58 11.22 0.00 5.69
162 163 0.377203 CTTCTGATTTTACGGCCGCC 59.623 55.000 28.58 8.18 0.00 6.13
163 164 1.084289 ACTTCTGATTTTACGGCCGC 58.916 50.000 28.58 8.37 0.00 6.53
164 165 1.396996 CCACTTCTGATTTTACGGCCG 59.603 52.381 26.86 26.86 0.00 6.13
165 166 1.743394 CCCACTTCTGATTTTACGGCC 59.257 52.381 0.00 0.00 0.00 6.13
166 167 2.706890 TCCCACTTCTGATTTTACGGC 58.293 47.619 0.00 0.00 0.00 5.68
167 168 6.765989 TCATATTCCCACTTCTGATTTTACGG 59.234 38.462 0.00 0.00 0.00 4.02
168 169 7.786178 TCATATTCCCACTTCTGATTTTACG 57.214 36.000 0.00 0.00 0.00 3.18
169 170 8.956426 TGTTCATATTCCCACTTCTGATTTTAC 58.044 33.333 0.00 0.00 0.00 2.01
170 171 9.527157 TTGTTCATATTCCCACTTCTGATTTTA 57.473 29.630 0.00 0.00 0.00 1.52
171 172 8.421249 TTGTTCATATTCCCACTTCTGATTTT 57.579 30.769 0.00 0.00 0.00 1.82
172 173 8.421249 TTTGTTCATATTCCCACTTCTGATTT 57.579 30.769 0.00 0.00 0.00 2.17
173 174 8.472413 CATTTGTTCATATTCCCACTTCTGATT 58.528 33.333 0.00 0.00 0.00 2.57
174 175 7.835682 TCATTTGTTCATATTCCCACTTCTGAT 59.164 33.333 0.00 0.00 0.00 2.90
175 176 7.174413 TCATTTGTTCATATTCCCACTTCTGA 58.826 34.615 0.00 0.00 0.00 3.27
176 177 7.395190 TCATTTGTTCATATTCCCACTTCTG 57.605 36.000 0.00 0.00 0.00 3.02
177 178 6.096001 GCTCATTTGTTCATATTCCCACTTCT 59.904 38.462 0.00 0.00 0.00 2.85
178 179 6.096001 AGCTCATTTGTTCATATTCCCACTTC 59.904 38.462 0.00 0.00 0.00 3.01
179 180 5.954150 AGCTCATTTGTTCATATTCCCACTT 59.046 36.000 0.00 0.00 0.00 3.16
180 181 5.359009 CAGCTCATTTGTTCATATTCCCACT 59.641 40.000 0.00 0.00 0.00 4.00
181 182 5.585390 CAGCTCATTTGTTCATATTCCCAC 58.415 41.667 0.00 0.00 0.00 4.61
182 183 4.098349 GCAGCTCATTTGTTCATATTCCCA 59.902 41.667 0.00 0.00 0.00 4.37
183 184 4.340381 AGCAGCTCATTTGTTCATATTCCC 59.660 41.667 0.00 0.00 0.00 3.97
184 185 5.279384 CAGCAGCTCATTTGTTCATATTCC 58.721 41.667 0.00 0.00 0.00 3.01
185 186 5.066893 TCCAGCAGCTCATTTGTTCATATTC 59.933 40.000 0.00 0.00 0.00 1.75
186 187 4.951715 TCCAGCAGCTCATTTGTTCATATT 59.048 37.500 0.00 0.00 0.00 1.28
187 188 4.529897 TCCAGCAGCTCATTTGTTCATAT 58.470 39.130 0.00 0.00 0.00 1.78
188 189 3.954200 TCCAGCAGCTCATTTGTTCATA 58.046 40.909 0.00 0.00 0.00 2.15
189 190 2.799017 TCCAGCAGCTCATTTGTTCAT 58.201 42.857 0.00 0.00 0.00 2.57
190 191 2.275134 TCCAGCAGCTCATTTGTTCA 57.725 45.000 0.00 0.00 0.00 3.18
191 192 3.863142 AATCCAGCAGCTCATTTGTTC 57.137 42.857 0.00 0.00 0.00 3.18
192 193 4.523943 TGTAAATCCAGCAGCTCATTTGTT 59.476 37.500 15.27 0.25 0.00 2.83
193 194 4.081406 TGTAAATCCAGCAGCTCATTTGT 58.919 39.130 15.27 0.00 0.00 2.83
194 195 4.707030 TGTAAATCCAGCAGCTCATTTG 57.293 40.909 15.27 0.00 0.00 2.32
195 196 5.198965 AGATGTAAATCCAGCAGCTCATTT 58.801 37.500 11.90 11.90 0.00 2.32
196 197 4.789807 AGATGTAAATCCAGCAGCTCATT 58.210 39.130 0.00 0.00 0.00 2.57
197 198 4.434545 AGATGTAAATCCAGCAGCTCAT 57.565 40.909 0.00 0.00 0.00 2.90
198 199 3.920231 AGATGTAAATCCAGCAGCTCA 57.080 42.857 0.00 0.00 0.00 4.26
199 200 4.624882 CGATAGATGTAAATCCAGCAGCTC 59.375 45.833 0.00 0.00 39.76 4.09
200 201 4.281941 TCGATAGATGTAAATCCAGCAGCT 59.718 41.667 0.00 0.00 42.67 4.24
201 202 4.560128 TCGATAGATGTAAATCCAGCAGC 58.440 43.478 0.00 0.00 42.67 5.25
217 218 0.388649 CCTTTCCCGCCGATCGATAG 60.389 60.000 18.66 7.07 41.67 2.08
218 219 1.663739 CCTTTCCCGCCGATCGATA 59.336 57.895 18.66 0.00 41.67 2.92
219 220 2.421739 CCTTTCCCGCCGATCGAT 59.578 61.111 18.66 0.00 41.67 3.59
220 221 3.845259 CCCTTTCCCGCCGATCGA 61.845 66.667 18.66 0.00 41.67 3.59
222 223 2.717139 CTAGCCCTTTCCCGCCGATC 62.717 65.000 0.00 0.00 0.00 3.69
223 224 2.766651 TAGCCCTTTCCCGCCGAT 60.767 61.111 0.00 0.00 0.00 4.18
224 225 3.467226 CTAGCCCTTTCCCGCCGA 61.467 66.667 0.00 0.00 0.00 5.54
227 228 4.157120 TCGCTAGCCCTTTCCCGC 62.157 66.667 9.66 0.00 0.00 6.13
228 229 2.202892 GTCGCTAGCCCTTTCCCG 60.203 66.667 9.66 0.00 0.00 5.14
229 230 2.202892 CGTCGCTAGCCCTTTCCC 60.203 66.667 9.66 0.00 0.00 3.97
230 231 2.202892 CCGTCGCTAGCCCTTTCC 60.203 66.667 9.66 0.00 0.00 3.13
231 232 2.890961 GCCGTCGCTAGCCCTTTC 60.891 66.667 9.66 0.00 0.00 2.62
232 233 4.814294 CGCCGTCGCTAGCCCTTT 62.814 66.667 9.66 0.00 0.00 3.11
264 265 4.838152 CTCCACCATGGCCGACGG 62.838 72.222 13.04 10.29 37.47 4.79
265 266 2.233605 TTACTCCACCATGGCCGACG 62.234 60.000 13.04 4.40 37.47 5.12
266 267 0.180406 ATTACTCCACCATGGCCGAC 59.820 55.000 13.04 0.00 37.47 4.79
267 268 0.916086 AATTACTCCACCATGGCCGA 59.084 50.000 13.04 6.41 37.47 5.54
268 269 2.631160 TAATTACTCCACCATGGCCG 57.369 50.000 13.04 2.72 37.47 6.13
269 270 3.222603 CCTTAATTACTCCACCATGGCC 58.777 50.000 13.04 0.00 37.47 5.36
270 271 3.222603 CCCTTAATTACTCCACCATGGC 58.777 50.000 13.04 0.00 37.47 4.40
271 272 4.519906 ACCCTTAATTACTCCACCATGG 57.480 45.455 11.19 11.19 39.43 3.66
272 273 5.127031 CCAAACCCTTAATTACTCCACCATG 59.873 44.000 0.00 0.00 0.00 3.66
273 274 5.222463 ACCAAACCCTTAATTACTCCACCAT 60.222 40.000 0.00 0.00 0.00 3.55
274 275 4.106663 ACCAAACCCTTAATTACTCCACCA 59.893 41.667 0.00 0.00 0.00 4.17
275 276 4.669700 ACCAAACCCTTAATTACTCCACC 58.330 43.478 0.00 0.00 0.00 4.61
276 277 6.008331 AGAACCAAACCCTTAATTACTCCAC 58.992 40.000 0.00 0.00 0.00 4.02
277 278 6.208840 AGAACCAAACCCTTAATTACTCCA 57.791 37.500 0.00 0.00 0.00 3.86
278 279 7.375834 CAAAGAACCAAACCCTTAATTACTCC 58.624 38.462 0.00 0.00 0.00 3.85
279 280 6.866770 GCAAAGAACCAAACCCTTAATTACTC 59.133 38.462 0.00 0.00 0.00 2.59
280 281 6.516028 CGCAAAGAACCAAACCCTTAATTACT 60.516 38.462 0.00 0.00 0.00 2.24
281 282 5.631929 CGCAAAGAACCAAACCCTTAATTAC 59.368 40.000 0.00 0.00 0.00 1.89
282 283 5.774630 CGCAAAGAACCAAACCCTTAATTA 58.225 37.500 0.00 0.00 0.00 1.40
283 284 4.627058 CGCAAAGAACCAAACCCTTAATT 58.373 39.130 0.00 0.00 0.00 1.40
284 285 3.554129 GCGCAAAGAACCAAACCCTTAAT 60.554 43.478 0.30 0.00 0.00 1.40
285 286 2.223852 GCGCAAAGAACCAAACCCTTAA 60.224 45.455 0.30 0.00 0.00 1.85
286 287 1.338655 GCGCAAAGAACCAAACCCTTA 59.661 47.619 0.30 0.00 0.00 2.69
287 288 0.104120 GCGCAAAGAACCAAACCCTT 59.896 50.000 0.30 0.00 0.00 3.95
288 289 1.739667 GCGCAAAGAACCAAACCCT 59.260 52.632 0.30 0.00 0.00 4.34
289 290 1.300620 GGCGCAAAGAACCAAACCC 60.301 57.895 10.83 0.00 0.00 4.11
290 291 1.660264 CGGCGCAAAGAACCAAACC 60.660 57.895 10.83 0.00 0.00 3.27
291 292 0.660300 CTCGGCGCAAAGAACCAAAC 60.660 55.000 10.83 0.00 0.00 2.93
292 293 1.098712 ACTCGGCGCAAAGAACCAAA 61.099 50.000 10.83 0.00 0.00 3.28
429 430 1.112113 ACGGTCGCTCCATGAATAGT 58.888 50.000 0.00 0.00 35.57 2.12
493 494 3.897505 AGCTTGAGTTGGGTTAAAAGCAT 59.102 39.130 7.82 0.00 41.87 3.79
721 722 7.873719 TTGGTGTAGAAAGTCTCAAATTCAA 57.126 32.000 0.00 0.00 0.00 2.69
982 983 0.773644 ATTGCTCCGGCCCAGAATAT 59.226 50.000 0.00 0.00 37.74 1.28
1089 1090 2.770048 CCTGGCCCTACTCCCCAG 60.770 72.222 0.00 0.00 44.49 4.45
1107 1111 5.105023 ACGGAAAAGTATCTAGAACTTCCCC 60.105 44.000 15.90 16.58 36.17 4.81
1188 1193 0.652592 CCCAGAAGCGCGTGATAAAG 59.347 55.000 8.43 0.00 0.00 1.85
1687 1711 4.394729 GTGGGTCCATAAAACTCACTCAA 58.605 43.478 0.00 0.00 43.40 3.02
2021 2046 1.404391 CATTGGTCTCGGTAGCTACGT 59.596 52.381 17.48 0.00 0.00 3.57
2036 2061 6.769822 AGGAGAGACATAATTAACTGCATTGG 59.230 38.462 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.