Multiple sequence alignment - TraesCS1D01G421800

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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 TraesCS1D01G421800 chr1D 100.000 3256 0 0 1 3256 477478548 477481803 0.000000e+00 6013
1 TraesCS1D01G421800 chr1D 84.615 1170 116 32 1637 2779 477435596 477436728 0.000000e+00 1105
2 TraesCS1D01G421800 chr1D 82.105 475 49 18 1123 1580 477435177 477435632 1.100000e-99 374
3 TraesCS1D01G421800 chr1D 78.988 257 37 5 2899 3147 477481145 477481392 3.360000e-35 159
4 TraesCS1D01G421800 chr1D 78.988 257 37 5 2598 2845 477481446 477481694 3.360000e-35 159
5 TraesCS1D01G421800 chr1A 93.433 2619 113 25 307 2898 573920132 573922718 0.000000e+00 3829
6 TraesCS1D01G421800 chr1A 84.314 1173 117 35 1637 2779 573818048 573819183 0.000000e+00 1085
7 TraesCS1D01G421800 chr1A 92.179 358 26 2 2900 3256 573922763 573923119 3.750000e-139 505
8 TraesCS1D01G421800 chr1A 82.609 437 49 13 1160 1580 573817659 573818084 8.590000e-96 361
9 TraesCS1D01G421800 chr1A 91.124 169 15 0 1 169 573905936 573906104 2.530000e-56 230
10 TraesCS1D01G421800 chr1A 78.151 357 50 13 2900 3254 573819017 573819347 5.510000e-48 202
11 TraesCS1D01G421800 chr1B 93.114 1699 65 28 888 2582 665060608 665062258 0.000000e+00 2442
12 TraesCS1D01G421800 chr1B 87.555 916 81 19 1578 2481 665049420 665050314 0.000000e+00 1029
13 TraesCS1D01G421800 chr1B 91.447 304 21 3 2900 3202 665062544 665062843 2.340000e-111 412
14 TraesCS1D01G421800 chr1B 86.462 325 28 7 2943 3256 665050308 665050627 3.110000e-90 342
15 TraesCS1D01G421800 chr1B 74.522 628 83 49 269 843 665059999 665060602 5.510000e-48 202
16 TraesCS1D01G421800 chr3A 90.625 224 21 0 2008 2231 434069274 434069051 6.830000e-77 298
17 TraesCS1D01G421800 chr3D 88.066 243 27 1 1989 2231 301414168 301414408 1.480000e-73 287
18 TraesCS1D01G421800 chr3B 88.839 224 25 0 2008 2231 419965937 419965714 3.200000e-70 276
19 TraesCS1D01G421800 chr3B 82.353 136 14 4 1843 1972 13365300 13365431 3.430000e-20 110
20 TraesCS1D01G421800 chr4A 81.944 216 28 9 2005 2216 143252309 143252517 4.320000e-39 172


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 TraesCS1D01G421800 chr1D 477478548 477481803 3255 False 2110.333333 6013 85.992000 1 3256 3 chr1D.!!$F2 3255
1 TraesCS1D01G421800 chr1D 477435177 477436728 1551 False 739.500000 1105 83.360000 1123 2779 2 chr1D.!!$F1 1656
2 TraesCS1D01G421800 chr1A 573920132 573923119 2987 False 2167.000000 3829 92.806000 307 3256 2 chr1A.!!$F3 2949
3 TraesCS1D01G421800 chr1A 573817659 573819347 1688 False 549.333333 1085 81.691333 1160 3254 3 chr1A.!!$F2 2094
4 TraesCS1D01G421800 chr1B 665059999 665062843 2844 False 1018.666667 2442 86.361000 269 3202 3 chr1B.!!$F2 2933
5 TraesCS1D01G421800 chr1B 665049420 665050627 1207 False 685.500000 1029 87.008500 1578 3256 2 chr1B.!!$F1 1678

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
68 69 0.038526 ACTGCCGACGAACGAAGATT 60.039 50.0 0.00 0.00 45.77 2.40 F
209 210 0.099259 TGATCGGTTACACTACGCGG 59.901 55.0 12.47 0.00 0.00 6.46 F
212 213 0.099259 TCGGTTACACTACGCGGATG 59.901 55.0 12.47 8.11 0.00 3.51 F
704 770 0.106708 ATTGCGAGTGGTGTCTGTGT 59.893 50.0 0.00 0.00 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 1841 0.321564 TGCCGTTCCTGTCCATCTTG 60.322 55.000 0.00 0.0 0.00 3.02 R
1785 1925 1.055849 GAATGCAGGGGTTGGGTTTT 58.944 50.000 0.00 0.0 0.00 2.43 R
1799 1939 1.587547 GGATTGAGTCGGAGGAATGC 58.412 55.000 0.00 0.0 0.00 3.56 R
2650 2819 3.906660 TGGTGACAAGGCTAAGTCG 57.093 52.632 13.28 0.0 37.58 4.18 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
28 29 3.857038 GGCCGCCGAACAGGGATA 61.857 66.667 0.00 0.00 41.48 2.59
29 30 2.588034 GCCGCCGAACAGGGATAC 60.588 66.667 0.00 0.00 41.48 2.24
30 31 2.897207 CCGCCGAACAGGGATACA 59.103 61.111 0.00 0.00 41.48 2.29
31 32 1.227263 CCGCCGAACAGGGATACAG 60.227 63.158 0.00 0.00 41.48 2.74
32 33 1.672854 CCGCCGAACAGGGATACAGA 61.673 60.000 0.00 0.00 41.48 3.41
33 34 0.249073 CGCCGAACAGGGATACAGAG 60.249 60.000 0.00 0.00 41.48 3.35
34 35 0.105039 GCCGAACAGGGATACAGAGG 59.895 60.000 0.00 0.00 41.48 3.69
35 36 0.753262 CCGAACAGGGATACAGAGGG 59.247 60.000 0.00 0.00 39.74 4.30
36 37 1.688311 CCGAACAGGGATACAGAGGGA 60.688 57.143 0.00 0.00 39.74 4.20
37 38 2.108168 CGAACAGGGATACAGAGGGAA 58.892 52.381 0.00 0.00 39.74 3.97
38 39 2.159085 CGAACAGGGATACAGAGGGAAC 60.159 54.545 0.00 0.00 39.74 3.62
39 40 2.642171 ACAGGGATACAGAGGGAACA 57.358 50.000 0.00 0.00 39.74 3.18
40 41 2.915869 ACAGGGATACAGAGGGAACAA 58.084 47.619 0.00 0.00 39.74 2.83
41 42 2.572104 ACAGGGATACAGAGGGAACAAC 59.428 50.000 0.00 0.00 39.74 3.32
42 43 2.571653 CAGGGATACAGAGGGAACAACA 59.428 50.000 0.00 0.00 39.74 3.33
43 44 3.009033 CAGGGATACAGAGGGAACAACAA 59.991 47.826 0.00 0.00 39.74 2.83
44 45 3.264450 AGGGATACAGAGGGAACAACAAG 59.736 47.826 0.00 0.00 39.74 3.16
45 46 3.610911 GGATACAGAGGGAACAACAAGG 58.389 50.000 0.00 0.00 0.00 3.61
46 47 3.263425 GGATACAGAGGGAACAACAAGGA 59.737 47.826 0.00 0.00 0.00 3.36
47 48 2.640316 ACAGAGGGAACAACAAGGAC 57.360 50.000 0.00 0.00 0.00 3.85
48 49 1.202651 ACAGAGGGAACAACAAGGACG 60.203 52.381 0.00 0.00 0.00 4.79
49 50 1.070134 CAGAGGGAACAACAAGGACGA 59.930 52.381 0.00 0.00 0.00 4.20
50 51 1.070289 AGAGGGAACAACAAGGACGAC 59.930 52.381 0.00 0.00 0.00 4.34
51 52 1.070289 GAGGGAACAACAAGGACGACT 59.930 52.381 0.00 0.00 0.00 4.18
52 53 1.202651 AGGGAACAACAAGGACGACTG 60.203 52.381 0.00 0.00 0.00 3.51
53 54 0.586802 GGAACAACAAGGACGACTGC 59.413 55.000 0.00 0.00 0.00 4.40
54 55 0.586802 GAACAACAAGGACGACTGCC 59.413 55.000 0.00 0.00 0.00 4.85
55 56 1.157870 AACAACAAGGACGACTGCCG 61.158 55.000 0.00 0.00 45.44 5.69
56 57 1.300620 CAACAAGGACGACTGCCGA 60.301 57.895 0.00 0.00 41.76 5.54
57 58 1.300697 AACAAGGACGACTGCCGAC 60.301 57.895 0.00 0.00 41.76 4.79
58 59 2.805353 CAAGGACGACTGCCGACG 60.805 66.667 0.00 0.00 41.76 5.12
59 60 2.981909 AAGGACGACTGCCGACGA 60.982 61.111 7.02 0.00 41.76 4.20
60 61 2.558286 AAGGACGACTGCCGACGAA 61.558 57.895 7.02 0.00 41.76 3.85
61 62 2.744307 AAGGACGACTGCCGACGAAC 62.744 60.000 7.02 0.00 41.76 3.95
62 63 3.164011 GACGACTGCCGACGAACG 61.164 66.667 7.02 0.00 41.76 3.95
63 64 3.584250 GACGACTGCCGACGAACGA 62.584 63.158 7.02 0.00 45.77 3.85
64 65 2.427905 CGACTGCCGACGAACGAA 60.428 61.111 0.00 0.00 45.77 3.85
65 66 2.426183 CGACTGCCGACGAACGAAG 61.426 63.158 0.00 7.70 45.77 3.79
66 67 1.081641 GACTGCCGACGAACGAAGA 60.082 57.895 0.00 0.00 45.77 2.87
67 68 0.456312 GACTGCCGACGAACGAAGAT 60.456 55.000 0.00 0.00 45.77 2.40
68 69 0.038526 ACTGCCGACGAACGAAGATT 60.039 50.000 0.00 0.00 45.77 2.40
69 70 1.200716 ACTGCCGACGAACGAAGATTA 59.799 47.619 0.00 0.00 45.77 1.75
70 71 1.846782 CTGCCGACGAACGAAGATTAG 59.153 52.381 0.00 0.00 45.77 1.73
71 72 1.469703 TGCCGACGAACGAAGATTAGA 59.530 47.619 0.00 0.00 45.77 2.10
72 73 1.844962 GCCGACGAACGAAGATTAGAC 59.155 52.381 0.00 0.00 45.77 2.59
73 74 2.477525 GCCGACGAACGAAGATTAGACT 60.478 50.000 0.00 0.00 45.77 3.24
74 75 3.242543 GCCGACGAACGAAGATTAGACTA 60.243 47.826 0.00 0.00 45.77 2.59
75 76 4.516359 CCGACGAACGAAGATTAGACTAG 58.484 47.826 0.00 0.00 45.77 2.57
76 77 4.516359 CGACGAACGAAGATTAGACTAGG 58.484 47.826 0.14 0.00 45.77 3.02
77 78 4.281264 GACGAACGAAGATTAGACTAGGC 58.719 47.826 0.14 0.00 0.00 3.93
78 79 3.946558 ACGAACGAAGATTAGACTAGGCT 59.053 43.478 2.16 2.16 0.00 4.58
79 80 5.121811 ACGAACGAAGATTAGACTAGGCTA 58.878 41.667 0.00 0.00 0.00 3.93
80 81 5.764192 ACGAACGAAGATTAGACTAGGCTAT 59.236 40.000 6.04 0.00 0.00 2.97
81 82 6.933521 ACGAACGAAGATTAGACTAGGCTATA 59.066 38.462 6.04 0.00 0.00 1.31
82 83 7.095271 ACGAACGAAGATTAGACTAGGCTATAC 60.095 40.741 6.04 3.87 0.00 1.47
83 84 6.724694 ACGAAGATTAGACTAGGCTATACG 57.275 41.667 6.04 10.28 0.00 3.06
84 85 6.229733 ACGAAGATTAGACTAGGCTATACGT 58.770 40.000 6.04 10.86 0.00 3.57
85 86 6.368516 ACGAAGATTAGACTAGGCTATACGTC 59.631 42.308 6.04 10.09 0.00 4.34
86 87 6.368243 CGAAGATTAGACTAGGCTATACGTCA 59.632 42.308 6.04 0.00 0.00 4.35
87 88 7.437793 AAGATTAGACTAGGCTATACGTCAC 57.562 40.000 6.04 0.00 0.00 3.67
88 89 6.531923 AGATTAGACTAGGCTATACGTCACA 58.468 40.000 6.04 0.00 0.00 3.58
89 90 7.169591 AGATTAGACTAGGCTATACGTCACAT 58.830 38.462 6.04 0.00 0.00 3.21
90 91 6.555812 TTAGACTAGGCTATACGTCACATG 57.444 41.667 6.04 0.00 0.00 3.21
91 92 4.462133 AGACTAGGCTATACGTCACATGT 58.538 43.478 0.00 0.00 0.00 3.21
92 93 5.618236 AGACTAGGCTATACGTCACATGTA 58.382 41.667 0.00 0.00 0.00 2.29
93 94 6.060136 AGACTAGGCTATACGTCACATGTAA 58.940 40.000 0.00 0.00 0.00 2.41
94 95 6.715718 AGACTAGGCTATACGTCACATGTAAT 59.284 38.462 0.00 0.00 0.00 1.89
95 96 7.230913 AGACTAGGCTATACGTCACATGTAATT 59.769 37.037 0.00 0.00 0.00 1.40
96 97 7.145985 ACTAGGCTATACGTCACATGTAATTG 58.854 38.462 0.00 0.00 0.00 2.32
97 98 5.914033 AGGCTATACGTCACATGTAATTGT 58.086 37.500 0.00 0.00 0.00 2.71
98 99 7.046292 AGGCTATACGTCACATGTAATTGTA 57.954 36.000 0.00 0.00 0.00 2.41
99 100 7.667557 AGGCTATACGTCACATGTAATTGTAT 58.332 34.615 0.00 7.61 0.00 2.29
100 101 7.813148 AGGCTATACGTCACATGTAATTGTATC 59.187 37.037 0.00 0.00 0.00 2.24
101 102 7.201325 GGCTATACGTCACATGTAATTGTATCG 60.201 40.741 0.00 3.00 33.90 2.92
102 103 7.536281 GCTATACGTCACATGTAATTGTATCGA 59.464 37.037 0.00 0.00 32.86 3.59
103 104 9.556030 CTATACGTCACATGTAATTGTATCGAT 57.444 33.333 2.16 2.16 32.86 3.59
104 105 8.812147 ATACGTCACATGTAATTGTATCGATT 57.188 30.769 1.71 0.00 32.86 3.34
105 106 7.534085 ACGTCACATGTAATTGTATCGATTT 57.466 32.000 1.71 0.00 32.86 2.17
106 107 7.398746 ACGTCACATGTAATTGTATCGATTTG 58.601 34.615 1.71 0.00 32.86 2.32
107 108 7.276878 ACGTCACATGTAATTGTATCGATTTGA 59.723 33.333 1.71 0.00 32.86 2.69
108 109 8.275632 CGTCACATGTAATTGTATCGATTTGAT 58.724 33.333 1.71 0.00 41.30 2.57
143 144 7.780008 TGAATTGATGGATTTGATGATTTGC 57.220 32.000 0.00 0.00 0.00 3.68
144 145 7.331791 TGAATTGATGGATTTGATGATTTGCA 58.668 30.769 0.00 0.00 0.00 4.08
145 146 7.824779 TGAATTGATGGATTTGATGATTTGCAA 59.175 29.630 0.00 0.00 0.00 4.08
146 147 8.746052 AATTGATGGATTTGATGATTTGCAAT 57.254 26.923 0.00 0.00 0.00 3.56
147 148 7.546778 TTGATGGATTTGATGATTTGCAATG 57.453 32.000 0.00 0.00 0.00 2.82
148 149 6.879400 TGATGGATTTGATGATTTGCAATGA 58.121 32.000 0.00 0.00 0.00 2.57
149 150 6.983890 TGATGGATTTGATGATTTGCAATGAG 59.016 34.615 0.00 0.00 0.00 2.90
150 151 6.532988 TGGATTTGATGATTTGCAATGAGA 57.467 33.333 0.00 0.00 0.00 3.27
151 152 6.569780 TGGATTTGATGATTTGCAATGAGAG 58.430 36.000 0.00 0.00 0.00 3.20
152 153 6.378848 TGGATTTGATGATTTGCAATGAGAGA 59.621 34.615 0.00 0.00 0.00 3.10
153 154 7.069455 TGGATTTGATGATTTGCAATGAGAGAT 59.931 33.333 0.00 0.00 0.00 2.75
154 155 8.573885 GGATTTGATGATTTGCAATGAGAGATA 58.426 33.333 0.00 0.00 0.00 1.98
157 158 8.919777 TTGATGATTTGCAATGAGAGATATCT 57.080 30.769 4.47 4.47 0.00 1.98
158 159 8.324163 TGATGATTTGCAATGAGAGATATCTG 57.676 34.615 10.74 0.00 0.00 2.90
159 160 7.390718 TGATGATTTGCAATGAGAGATATCTGG 59.609 37.037 10.74 0.00 0.00 3.86
160 161 6.598503 TGATTTGCAATGAGAGATATCTGGT 58.401 36.000 10.74 0.00 0.00 4.00
161 162 7.058525 TGATTTGCAATGAGAGATATCTGGTT 58.941 34.615 10.74 0.00 0.00 3.67
162 163 6.688637 TTTGCAATGAGAGATATCTGGTTG 57.311 37.500 10.74 10.10 0.00 3.77
163 164 5.363562 TGCAATGAGAGATATCTGGTTGT 57.636 39.130 10.74 0.00 0.00 3.32
164 165 5.121105 TGCAATGAGAGATATCTGGTTGTG 58.879 41.667 10.74 4.14 0.00 3.33
165 166 4.514441 GCAATGAGAGATATCTGGTTGTGG 59.486 45.833 10.74 0.00 0.00 4.17
166 167 5.685861 GCAATGAGAGATATCTGGTTGTGGA 60.686 44.000 10.74 0.00 0.00 4.02
167 168 6.351711 CAATGAGAGATATCTGGTTGTGGAA 58.648 40.000 10.74 0.00 0.00 3.53
168 169 6.760440 ATGAGAGATATCTGGTTGTGGAAT 57.240 37.500 10.74 0.00 0.00 3.01
169 170 5.922053 TGAGAGATATCTGGTTGTGGAATG 58.078 41.667 10.74 0.00 0.00 2.67
170 171 5.163269 TGAGAGATATCTGGTTGTGGAATGG 60.163 44.000 10.74 0.00 0.00 3.16
171 172 4.103785 AGAGATATCTGGTTGTGGAATGGG 59.896 45.833 10.74 0.00 0.00 4.00
172 173 4.047166 AGATATCTGGTTGTGGAATGGGA 58.953 43.478 3.89 0.00 0.00 4.37
173 174 4.478317 AGATATCTGGTTGTGGAATGGGAA 59.522 41.667 3.89 0.00 0.00 3.97
174 175 3.763557 ATCTGGTTGTGGAATGGGAAT 57.236 42.857 0.00 0.00 0.00 3.01
175 176 3.541242 TCTGGTTGTGGAATGGGAATT 57.459 42.857 0.00 0.00 0.00 2.17
176 177 3.164268 TCTGGTTGTGGAATGGGAATTG 58.836 45.455 0.00 0.00 0.00 2.32
177 178 3.164268 CTGGTTGTGGAATGGGAATTGA 58.836 45.455 0.00 0.00 0.00 2.57
178 179 3.577848 CTGGTTGTGGAATGGGAATTGAA 59.422 43.478 0.00 0.00 0.00 2.69
179 180 3.323403 TGGTTGTGGAATGGGAATTGAAC 59.677 43.478 0.00 0.00 0.00 3.18
180 181 3.323403 GGTTGTGGAATGGGAATTGAACA 59.677 43.478 0.00 0.00 0.00 3.18
181 182 4.020307 GGTTGTGGAATGGGAATTGAACAT 60.020 41.667 0.00 0.00 0.00 2.71
182 183 5.512921 GGTTGTGGAATGGGAATTGAACATT 60.513 40.000 0.00 0.00 37.52 2.71
183 184 5.822132 TGTGGAATGGGAATTGAACATTT 57.178 34.783 0.00 0.00 35.17 2.32
184 185 5.549347 TGTGGAATGGGAATTGAACATTTG 58.451 37.500 0.00 0.00 35.17 2.32
185 186 5.306419 TGTGGAATGGGAATTGAACATTTGA 59.694 36.000 0.00 0.00 35.17 2.69
186 187 5.870978 GTGGAATGGGAATTGAACATTTGAG 59.129 40.000 0.00 0.00 35.17 3.02
187 188 5.543405 TGGAATGGGAATTGAACATTTGAGT 59.457 36.000 0.00 0.00 35.17 3.41
188 189 5.870978 GGAATGGGAATTGAACATTTGAGTG 59.129 40.000 0.00 0.00 35.17 3.51
189 190 4.255833 TGGGAATTGAACATTTGAGTGC 57.744 40.909 0.00 0.00 0.00 4.40
190 191 3.896888 TGGGAATTGAACATTTGAGTGCT 59.103 39.130 0.00 0.00 0.00 4.40
191 192 4.240096 GGGAATTGAACATTTGAGTGCTG 58.760 43.478 0.00 0.00 0.00 4.41
192 193 4.022068 GGGAATTGAACATTTGAGTGCTGA 60.022 41.667 0.00 0.00 0.00 4.26
193 194 5.337009 GGGAATTGAACATTTGAGTGCTGAT 60.337 40.000 0.00 0.00 0.00 2.90
194 195 5.803967 GGAATTGAACATTTGAGTGCTGATC 59.196 40.000 0.00 0.00 0.00 2.92
195 196 4.408993 TTGAACATTTGAGTGCTGATCG 57.591 40.909 0.00 0.00 0.00 3.69
196 197 2.743664 TGAACATTTGAGTGCTGATCGG 59.256 45.455 0.00 0.00 0.00 4.18
197 198 2.479566 ACATTTGAGTGCTGATCGGT 57.520 45.000 2.89 0.00 0.00 4.69
198 199 2.783135 ACATTTGAGTGCTGATCGGTT 58.217 42.857 2.89 0.00 0.00 4.44
199 200 3.937814 ACATTTGAGTGCTGATCGGTTA 58.062 40.909 2.89 0.00 0.00 2.85
200 201 3.684788 ACATTTGAGTGCTGATCGGTTAC 59.315 43.478 2.89 3.35 0.00 2.50
201 202 3.394674 TTTGAGTGCTGATCGGTTACA 57.605 42.857 2.89 0.00 0.00 2.41
202 203 2.363788 TGAGTGCTGATCGGTTACAC 57.636 50.000 2.89 3.15 0.00 2.90
203 204 1.893137 TGAGTGCTGATCGGTTACACT 59.107 47.619 11.70 11.70 43.93 3.55
204 205 3.086282 TGAGTGCTGATCGGTTACACTA 58.914 45.455 11.81 1.61 41.45 2.74
205 206 3.119602 TGAGTGCTGATCGGTTACACTAC 60.120 47.826 11.81 7.72 41.45 2.73
206 207 2.159421 AGTGCTGATCGGTTACACTACG 60.159 50.000 10.53 0.00 39.69 3.51
207 208 1.197910 GCTGATCGGTTACACTACGC 58.802 55.000 2.89 0.00 0.00 4.42
208 209 1.463805 CTGATCGGTTACACTACGCG 58.536 55.000 3.53 3.53 0.00 6.01
209 210 0.099259 TGATCGGTTACACTACGCGG 59.901 55.000 12.47 0.00 0.00 6.46
210 211 0.378257 GATCGGTTACACTACGCGGA 59.622 55.000 12.47 0.00 0.00 5.54
211 212 1.002033 GATCGGTTACACTACGCGGAT 60.002 52.381 12.47 0.00 0.00 4.18
212 213 0.099259 TCGGTTACACTACGCGGATG 59.901 55.000 12.47 8.11 0.00 3.51
213 214 0.868602 CGGTTACACTACGCGGATGG 60.869 60.000 12.47 0.00 0.00 3.51
214 215 0.529119 GGTTACACTACGCGGATGGG 60.529 60.000 12.47 3.14 0.00 4.00
215 216 0.174162 GTTACACTACGCGGATGGGT 59.826 55.000 12.47 9.81 44.40 4.51
216 217 0.457035 TTACACTACGCGGATGGGTC 59.543 55.000 12.47 0.00 42.00 4.46
217 218 1.386525 TACACTACGCGGATGGGTCC 61.387 60.000 12.47 0.00 42.00 4.46
225 226 4.530857 GGATGGGTCCGCGACAGG 62.531 72.222 8.23 0.00 34.13 4.00
226 227 4.530857 GATGGGTCCGCGACAGGG 62.531 72.222 8.23 0.00 33.68 4.45
230 231 4.436998 GGTCCGCGACAGGGTCTG 62.437 72.222 8.23 0.00 37.52 3.51
231 232 3.371063 GTCCGCGACAGGGTCTGA 61.371 66.667 8.23 0.00 35.18 3.27
232 233 3.062466 TCCGCGACAGGGTCTGAG 61.062 66.667 8.23 0.00 35.18 3.35
233 234 4.135153 CCGCGACAGGGTCTGAGG 62.135 72.222 8.23 0.00 35.18 3.86
234 235 3.062466 CGCGACAGGGTCTGAGGA 61.062 66.667 0.00 0.00 35.18 3.71
235 236 2.888863 GCGACAGGGTCTGAGGAG 59.111 66.667 1.59 0.00 35.18 3.69
236 237 2.888863 CGACAGGGTCTGAGGAGC 59.111 66.667 1.59 0.00 39.05 4.70
237 238 1.979155 CGACAGGGTCTGAGGAGCA 60.979 63.158 1.59 0.00 41.29 4.26
238 239 1.594310 GACAGGGTCTGAGGAGCAC 59.406 63.158 1.59 0.00 41.29 4.40
239 240 2.219325 GACAGGGTCTGAGGAGCACG 62.219 65.000 1.59 0.00 41.29 5.34
240 241 2.118513 AGGGTCTGAGGAGCACGT 59.881 61.111 0.00 0.00 41.29 4.49
241 242 0.965866 CAGGGTCTGAGGAGCACGTA 60.966 60.000 0.00 0.00 41.29 3.57
242 243 0.966370 AGGGTCTGAGGAGCACGTAC 60.966 60.000 0.00 0.00 41.29 3.67
243 244 1.136984 GGTCTGAGGAGCACGTACG 59.863 63.158 15.01 15.01 39.51 3.67
244 245 1.136984 GTCTGAGGAGCACGTACGG 59.863 63.158 21.06 9.73 0.00 4.02
245 246 2.044555 TCTGAGGAGCACGTACGGG 61.045 63.158 21.06 18.06 0.00 5.28
246 247 3.701604 CTGAGGAGCACGTACGGGC 62.702 68.421 34.47 34.47 46.56 6.13
434 450 3.311110 GGCCAGTGACGTCCTCCA 61.311 66.667 14.12 0.00 0.00 3.86
479 496 2.824041 CCCTCCACGCCCAAATCG 60.824 66.667 0.00 0.00 0.00 3.34
490 517 0.175531 CCCAAATCGGCACCAAATCC 59.824 55.000 0.00 0.00 0.00 3.01
519 546 4.531426 ATCTCTCCTCCGGCGGCT 62.531 66.667 23.83 0.00 0.00 5.52
561 589 1.005037 CCAACTCGCAGGTGCAGTA 60.005 57.895 2.33 0.00 42.21 2.74
562 590 0.391661 CCAACTCGCAGGTGCAGTAT 60.392 55.000 2.33 0.00 42.21 2.12
578 611 2.492088 CAGTATAATCGATCCTCCCGCA 59.508 50.000 0.00 0.00 0.00 5.69
606 658 4.202111 TGCTTGGATCAAATACTCGATCGA 60.202 41.667 18.32 18.32 39.16 3.59
608 660 5.061560 GCTTGGATCAAATACTCGATCGATC 59.938 44.000 19.78 15.68 39.16 3.69
637 689 4.381566 GCGATTAATTGTTTCAGTTGCGTT 59.618 37.500 4.60 0.00 0.00 4.84
638 690 5.662815 GCGATTAATTGTTTCAGTTGCGTTG 60.663 40.000 4.60 0.00 0.00 4.10
639 691 5.574815 ATTAATTGTTTCAGTTGCGTTGC 57.425 34.783 0.00 0.00 0.00 4.17
640 692 2.869233 ATTGTTTCAGTTGCGTTGCT 57.131 40.000 0.00 0.00 0.00 3.91
641 693 2.187351 TTGTTTCAGTTGCGTTGCTC 57.813 45.000 0.00 0.00 0.00 4.26
642 694 1.378531 TGTTTCAGTTGCGTTGCTCT 58.621 45.000 0.00 0.00 0.00 4.09
643 695 1.330521 TGTTTCAGTTGCGTTGCTCTC 59.669 47.619 0.00 0.00 0.00 3.20
647 699 1.373497 AGTTGCGTTGCTCTCTCGG 60.373 57.895 0.00 0.00 0.00 4.63
654 706 1.402852 CGTTGCTCTCTCGGTTGATCA 60.403 52.381 0.00 0.00 0.00 2.92
668 730 1.313091 TGATCAGTGGTCTCCGTCCG 61.313 60.000 4.73 0.00 0.00 4.79
682 745 1.009335 GTCCGTCGTTTTTGGGTGC 60.009 57.895 0.00 0.00 0.00 5.01
704 770 0.106708 ATTGCGAGTGGTGTCTGTGT 59.893 50.000 0.00 0.00 0.00 3.72
708 774 0.389391 CGAGTGGTGTCTGTGTTCCT 59.611 55.000 0.00 0.00 0.00 3.36
823 933 3.511699 TGTGATCGAGTTCTTCCGATTG 58.488 45.455 0.00 0.00 44.40 2.67
824 934 3.192633 TGTGATCGAGTTCTTCCGATTGA 59.807 43.478 0.00 0.00 44.40 2.57
825 935 4.142160 TGTGATCGAGTTCTTCCGATTGAT 60.142 41.667 0.00 0.00 44.40 2.57
826 936 4.806247 GTGATCGAGTTCTTCCGATTGATT 59.194 41.667 0.00 0.00 44.40 2.57
876 986 1.300697 GGGCGGTTACGGATGCTAG 60.301 63.158 0.00 0.00 41.36 3.42
955 1065 3.273434 ACTTGTGACATTCCGATCCATG 58.727 45.455 0.00 0.00 0.00 3.66
1121 1231 2.202932 CTTCTACGGCGGCTGCAT 60.203 61.111 21.31 9.46 45.35 3.96
1587 1703 3.760035 GTCGAGAAGCTCCGCCCA 61.760 66.667 0.00 0.00 0.00 5.36
1719 1841 2.202756 CGCTCCAACGGCTACCTC 60.203 66.667 0.00 0.00 0.00 3.85
1785 1925 0.751643 TCGGCTCGGTGAGATCATCA 60.752 55.000 0.00 0.00 34.79 3.07
1799 1939 2.008242 TCATCAAAACCCAACCCCTG 57.992 50.000 0.00 0.00 0.00 4.45
1884 2024 2.118228 TTTGCTTGTGTCGATGCAAC 57.882 45.000 10.55 0.00 43.74 4.17
2337 2493 0.842635 CTCCTTCCTCCCCCTTCATG 59.157 60.000 0.00 0.00 0.00 3.07
2654 2823 9.757227 TTGTTTTTCAATTGGAAATTATCGACT 57.243 25.926 12.70 0.00 44.59 4.18
2666 2835 6.238130 GGAAATTATCGACTTAGCCTTGTCAC 60.238 42.308 0.00 0.00 33.18 3.67
2692 2864 8.184192 CCAAATCTGTTATTTGAGTACACCATC 58.816 37.037 11.11 0.00 40.42 3.51
2721 2893 7.339721 TGTTATTTTGGTACTGTCTTGTGGAAA 59.660 33.333 0.00 0.00 0.00 3.13
2729 2901 3.871594 ACTGTCTTGTGGAAAGAAGTTCG 59.128 43.478 0.00 0.00 37.08 3.95
2750 2922 3.330267 GGGCTACTTCAGACTTCAGTTG 58.670 50.000 0.00 0.00 30.26 3.16
2785 2957 7.405292 TCTGGACAATTGGAGAAATGAGTTAT 58.595 34.615 10.83 0.00 0.00 1.89
2786 2958 8.548025 TCTGGACAATTGGAGAAATGAGTTATA 58.452 33.333 10.83 0.00 0.00 0.98
2787 2959 9.347240 CTGGACAATTGGAGAAATGAGTTATAT 57.653 33.333 10.83 0.00 0.00 0.86
2788 2960 9.123902 TGGACAATTGGAGAAATGAGTTATATG 57.876 33.333 10.83 0.00 0.00 1.78
2789 2961 9.342308 GGACAATTGGAGAAATGAGTTATATGA 57.658 33.333 10.83 0.00 0.00 2.15
2836 3015 4.897076 TGCCAATGAAATGATCTGCCTATT 59.103 37.500 0.00 0.00 0.00 1.73
2841 3020 8.415553 CCAATGAAATGATCTGCCTATTGTTTA 58.584 33.333 0.00 0.00 0.00 2.01
2850 3029 4.704540 TCTGCCTATTGTTTATGTGGGTTG 59.295 41.667 0.00 0.00 0.00 3.77
2852 3031 3.733684 GCCTATTGTTTATGTGGGTTGCG 60.734 47.826 0.00 0.00 0.00 4.85
2882 3063 2.682594 TCTGGGATTCTGGATCATCGT 58.317 47.619 0.00 0.00 36.43 3.73
2885 3066 4.464244 TCTGGGATTCTGGATCATCGTATC 59.536 45.833 0.00 0.00 36.43 2.24
2928 3152 5.176958 CAGTTACACGAACTTGTTCCTTAGG 59.823 44.000 7.78 0.00 46.79 2.69
2998 3222 6.489700 TGAGTACATCATTGGTGTGATTTTGT 59.510 34.615 12.87 0.00 36.72 2.83
3157 3388 6.402658 GCCTATAGTTTCTGTTGCTCTGTTTC 60.403 42.308 0.00 0.00 0.00 2.78
3160 3391 3.629398 AGTTTCTGTTGCTCTGTTTCCTG 59.371 43.478 0.00 0.00 0.00 3.86
3193 3424 8.964476 TTAAGCTTGATATTCCAGTTCCTAAG 57.036 34.615 9.86 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.857038 TATCCCTGTTCGGCGGCC 61.857 66.667 9.54 9.54 0.00 6.13
12 13 2.588034 GTATCCCTGTTCGGCGGC 60.588 66.667 7.21 0.00 0.00 6.53
13 14 1.227263 CTGTATCCCTGTTCGGCGG 60.227 63.158 7.21 0.00 0.00 6.13
14 15 0.249073 CTCTGTATCCCTGTTCGGCG 60.249 60.000 0.00 0.00 0.00 6.46
15 16 0.105039 CCTCTGTATCCCTGTTCGGC 59.895 60.000 0.00 0.00 0.00 5.54
16 17 0.753262 CCCTCTGTATCCCTGTTCGG 59.247 60.000 0.00 0.00 0.00 4.30
17 18 1.776662 TCCCTCTGTATCCCTGTTCG 58.223 55.000 0.00 0.00 0.00 3.95
18 19 2.838202 TGTTCCCTCTGTATCCCTGTTC 59.162 50.000 0.00 0.00 0.00 3.18
19 20 2.915869 TGTTCCCTCTGTATCCCTGTT 58.084 47.619 0.00 0.00 0.00 3.16
20 21 2.572104 GTTGTTCCCTCTGTATCCCTGT 59.428 50.000 0.00 0.00 0.00 4.00
21 22 2.571653 TGTTGTTCCCTCTGTATCCCTG 59.428 50.000 0.00 0.00 0.00 4.45
22 23 2.915869 TGTTGTTCCCTCTGTATCCCT 58.084 47.619 0.00 0.00 0.00 4.20
23 24 3.610911 CTTGTTGTTCCCTCTGTATCCC 58.389 50.000 0.00 0.00 0.00 3.85
24 25 3.263425 TCCTTGTTGTTCCCTCTGTATCC 59.737 47.826 0.00 0.00 0.00 2.59
25 26 4.254492 GTCCTTGTTGTTCCCTCTGTATC 58.746 47.826 0.00 0.00 0.00 2.24
26 27 3.306780 CGTCCTTGTTGTTCCCTCTGTAT 60.307 47.826 0.00 0.00 0.00 2.29
27 28 2.036733 CGTCCTTGTTGTTCCCTCTGTA 59.963 50.000 0.00 0.00 0.00 2.74
28 29 1.202651 CGTCCTTGTTGTTCCCTCTGT 60.203 52.381 0.00 0.00 0.00 3.41
29 30 1.070134 TCGTCCTTGTTGTTCCCTCTG 59.930 52.381 0.00 0.00 0.00 3.35
30 31 1.070289 GTCGTCCTTGTTGTTCCCTCT 59.930 52.381 0.00 0.00 0.00 3.69
31 32 1.070289 AGTCGTCCTTGTTGTTCCCTC 59.930 52.381 0.00 0.00 0.00 4.30
32 33 1.129058 AGTCGTCCTTGTTGTTCCCT 58.871 50.000 0.00 0.00 0.00 4.20
33 34 1.226746 CAGTCGTCCTTGTTGTTCCC 58.773 55.000 0.00 0.00 0.00 3.97
34 35 0.586802 GCAGTCGTCCTTGTTGTTCC 59.413 55.000 0.00 0.00 0.00 3.62
35 36 0.586802 GGCAGTCGTCCTTGTTGTTC 59.413 55.000 0.00 0.00 0.00 3.18
36 37 1.157870 CGGCAGTCGTCCTTGTTGTT 61.158 55.000 0.00 0.00 0.00 2.83
37 38 1.594293 CGGCAGTCGTCCTTGTTGT 60.594 57.895 0.00 0.00 0.00 3.32
38 39 1.300620 TCGGCAGTCGTCCTTGTTG 60.301 57.895 0.00 0.00 40.32 3.33
39 40 1.300697 GTCGGCAGTCGTCCTTGTT 60.301 57.895 0.00 0.00 40.32 2.83
40 41 2.338984 GTCGGCAGTCGTCCTTGT 59.661 61.111 0.00 0.00 40.32 3.16
41 42 2.742710 TTCGTCGGCAGTCGTCCTTG 62.743 60.000 3.41 0.00 40.32 3.61
42 43 2.558286 TTCGTCGGCAGTCGTCCTT 61.558 57.895 3.41 0.00 40.32 3.36
43 44 2.981909 TTCGTCGGCAGTCGTCCT 60.982 61.111 3.41 0.00 40.32 3.85
44 45 2.804090 GTTCGTCGGCAGTCGTCC 60.804 66.667 3.41 0.00 40.32 4.79
45 46 3.164011 CGTTCGTCGGCAGTCGTC 61.164 66.667 3.41 0.00 40.32 4.20
46 47 3.185082 TTCGTTCGTCGGCAGTCGT 62.185 57.895 3.41 0.00 40.32 4.34
47 48 2.426183 CTTCGTTCGTCGGCAGTCG 61.426 63.158 0.00 0.00 40.32 4.18
48 49 0.456312 ATCTTCGTTCGTCGGCAGTC 60.456 55.000 0.00 0.00 40.32 3.51
49 50 0.038526 AATCTTCGTTCGTCGGCAGT 60.039 50.000 0.00 0.00 40.32 4.40
50 51 1.846782 CTAATCTTCGTTCGTCGGCAG 59.153 52.381 0.00 0.00 40.32 4.85
51 52 1.469703 TCTAATCTTCGTTCGTCGGCA 59.530 47.619 0.00 0.00 40.32 5.69
52 53 1.844962 GTCTAATCTTCGTTCGTCGGC 59.155 52.381 0.00 0.00 40.32 5.54
53 54 3.402058 AGTCTAATCTTCGTTCGTCGG 57.598 47.619 0.00 0.00 40.32 4.79
54 55 4.516359 CCTAGTCTAATCTTCGTTCGTCG 58.484 47.826 0.00 0.00 41.41 5.12
55 56 4.035441 AGCCTAGTCTAATCTTCGTTCGTC 59.965 45.833 0.00 0.00 0.00 4.20
56 57 3.946558 AGCCTAGTCTAATCTTCGTTCGT 59.053 43.478 0.00 0.00 0.00 3.85
57 58 4.555348 AGCCTAGTCTAATCTTCGTTCG 57.445 45.455 0.00 0.00 0.00 3.95
58 59 7.095271 ACGTATAGCCTAGTCTAATCTTCGTTC 60.095 40.741 0.00 0.00 0.00 3.95
59 60 6.709846 ACGTATAGCCTAGTCTAATCTTCGTT 59.290 38.462 0.00 0.00 0.00 3.85
60 61 6.229733 ACGTATAGCCTAGTCTAATCTTCGT 58.770 40.000 0.00 0.00 0.00 3.85
61 62 6.368243 TGACGTATAGCCTAGTCTAATCTTCG 59.632 42.308 0.00 0.00 34.92 3.79
62 63 7.172875 TGTGACGTATAGCCTAGTCTAATCTTC 59.827 40.741 0.00 0.00 34.92 2.87
63 64 6.996879 TGTGACGTATAGCCTAGTCTAATCTT 59.003 38.462 0.00 0.00 34.92 2.40
64 65 6.531923 TGTGACGTATAGCCTAGTCTAATCT 58.468 40.000 0.00 0.00 34.92 2.40
65 66 6.798315 TGTGACGTATAGCCTAGTCTAATC 57.202 41.667 0.00 0.00 34.92 1.75
66 67 6.715718 ACATGTGACGTATAGCCTAGTCTAAT 59.284 38.462 0.00 0.00 34.92 1.73
67 68 6.060136 ACATGTGACGTATAGCCTAGTCTAA 58.940 40.000 0.00 0.00 34.92 2.10
68 69 5.618236 ACATGTGACGTATAGCCTAGTCTA 58.382 41.667 0.00 0.00 34.92 2.59
69 70 4.462133 ACATGTGACGTATAGCCTAGTCT 58.538 43.478 0.00 0.00 34.92 3.24
70 71 4.832590 ACATGTGACGTATAGCCTAGTC 57.167 45.455 0.00 0.00 0.00 2.59
71 72 6.896021 ATTACATGTGACGTATAGCCTAGT 57.104 37.500 9.11 0.00 0.00 2.57
72 73 7.145985 ACAATTACATGTGACGTATAGCCTAG 58.854 38.462 9.11 0.00 30.82 3.02
73 74 7.046292 ACAATTACATGTGACGTATAGCCTA 57.954 36.000 9.11 0.00 30.82 3.93
74 75 5.914033 ACAATTACATGTGACGTATAGCCT 58.086 37.500 9.11 0.00 30.82 4.58
75 76 7.201325 CGATACAATTACATGTGACGTATAGCC 60.201 40.741 9.11 0.17 34.75 3.93
76 77 7.536281 TCGATACAATTACATGTGACGTATAGC 59.464 37.037 9.11 0.79 35.92 2.97
77 78 8.944212 TCGATACAATTACATGTGACGTATAG 57.056 34.615 9.11 11.13 35.92 1.31
78 79 9.902196 AATCGATACAATTACATGTGACGTATA 57.098 29.630 9.11 0.00 35.92 1.47
79 80 8.812147 AATCGATACAATTACATGTGACGTAT 57.188 30.769 9.11 10.94 35.92 3.06
80 81 8.536407 CAAATCGATACAATTACATGTGACGTA 58.464 33.333 9.11 6.41 35.92 3.57
81 82 7.276878 TCAAATCGATACAATTACATGTGACGT 59.723 33.333 9.11 4.20 35.92 4.34
82 83 7.617557 TCAAATCGATACAATTACATGTGACG 58.382 34.615 9.11 0.00 35.85 4.35
117 118 8.836413 GCAAATCATCAAATCCATCAATTCAAT 58.164 29.630 0.00 0.00 0.00 2.57
118 119 7.824779 TGCAAATCATCAAATCCATCAATTCAA 59.175 29.630 0.00 0.00 0.00 2.69
119 120 7.331791 TGCAAATCATCAAATCCATCAATTCA 58.668 30.769 0.00 0.00 0.00 2.57
120 121 7.780008 TGCAAATCATCAAATCCATCAATTC 57.220 32.000 0.00 0.00 0.00 2.17
121 122 8.620416 CATTGCAAATCATCAAATCCATCAATT 58.380 29.630 1.71 0.00 0.00 2.32
122 123 7.990314 TCATTGCAAATCATCAAATCCATCAAT 59.010 29.630 1.71 0.00 0.00 2.57
123 124 7.331791 TCATTGCAAATCATCAAATCCATCAA 58.668 30.769 1.71 0.00 0.00 2.57
124 125 6.879400 TCATTGCAAATCATCAAATCCATCA 58.121 32.000 1.71 0.00 0.00 3.07
125 126 7.207383 TCTCATTGCAAATCATCAAATCCATC 58.793 34.615 1.71 0.00 0.00 3.51
126 127 7.069455 TCTCTCATTGCAAATCATCAAATCCAT 59.931 33.333 1.71 0.00 0.00 3.41
127 128 6.378848 TCTCTCATTGCAAATCATCAAATCCA 59.621 34.615 1.71 0.00 0.00 3.41
128 129 6.802608 TCTCTCATTGCAAATCATCAAATCC 58.197 36.000 1.71 0.00 0.00 3.01
131 132 9.350951 AGATATCTCTCATTGCAAATCATCAAA 57.649 29.630 1.71 0.00 0.00 2.69
132 133 8.784043 CAGATATCTCTCATTGCAAATCATCAA 58.216 33.333 1.71 0.00 0.00 2.57
133 134 7.390718 CCAGATATCTCTCATTGCAAATCATCA 59.609 37.037 1.71 0.00 0.00 3.07
134 135 7.390996 ACCAGATATCTCTCATTGCAAATCATC 59.609 37.037 1.71 0.00 0.00 2.92
135 136 7.232188 ACCAGATATCTCTCATTGCAAATCAT 58.768 34.615 1.71 0.00 0.00 2.45
136 137 6.598503 ACCAGATATCTCTCATTGCAAATCA 58.401 36.000 1.71 0.00 0.00 2.57
137 138 7.013083 ACAACCAGATATCTCTCATTGCAAATC 59.987 37.037 1.71 0.00 31.05 2.17
138 139 6.832384 ACAACCAGATATCTCTCATTGCAAAT 59.168 34.615 1.71 0.00 31.05 2.32
139 140 6.094464 CACAACCAGATATCTCTCATTGCAAA 59.906 38.462 1.71 0.00 31.05 3.68
140 141 5.587443 CACAACCAGATATCTCTCATTGCAA 59.413 40.000 0.00 0.00 31.05 4.08
141 142 5.121105 CACAACCAGATATCTCTCATTGCA 58.879 41.667 1.03 0.00 31.05 4.08
142 143 4.514441 CCACAACCAGATATCTCTCATTGC 59.486 45.833 1.03 0.00 31.05 3.56
143 144 5.922053 TCCACAACCAGATATCTCTCATTG 58.078 41.667 1.03 7.59 32.88 2.82
144 145 6.566079 TTCCACAACCAGATATCTCTCATT 57.434 37.500 1.03 0.00 0.00 2.57
145 146 6.465464 CCATTCCACAACCAGATATCTCTCAT 60.465 42.308 1.03 0.00 0.00 2.90
146 147 5.163269 CCATTCCACAACCAGATATCTCTCA 60.163 44.000 1.03 0.00 0.00 3.27
147 148 5.303971 CCATTCCACAACCAGATATCTCTC 58.696 45.833 1.03 0.00 0.00 3.20
148 149 4.103785 CCCATTCCACAACCAGATATCTCT 59.896 45.833 1.03 0.00 0.00 3.10
149 150 4.103153 TCCCATTCCACAACCAGATATCTC 59.897 45.833 1.03 0.00 0.00 2.75
150 151 4.047166 TCCCATTCCACAACCAGATATCT 58.953 43.478 0.00 0.00 0.00 1.98
151 152 4.437682 TCCCATTCCACAACCAGATATC 57.562 45.455 0.00 0.00 0.00 1.63
152 153 4.879295 TTCCCATTCCACAACCAGATAT 57.121 40.909 0.00 0.00 0.00 1.63
153 154 4.879295 ATTCCCATTCCACAACCAGATA 57.121 40.909 0.00 0.00 0.00 1.98
154 155 3.763557 ATTCCCATTCCACAACCAGAT 57.236 42.857 0.00 0.00 0.00 2.90
155 156 3.164268 CAATTCCCATTCCACAACCAGA 58.836 45.455 0.00 0.00 0.00 3.86
156 157 3.164268 TCAATTCCCATTCCACAACCAG 58.836 45.455 0.00 0.00 0.00 4.00
157 158 3.251016 TCAATTCCCATTCCACAACCA 57.749 42.857 0.00 0.00 0.00 3.67
158 159 3.323403 TGTTCAATTCCCATTCCACAACC 59.677 43.478 0.00 0.00 0.00 3.77
159 160 4.599047 TGTTCAATTCCCATTCCACAAC 57.401 40.909 0.00 0.00 0.00 3.32
160 161 5.822132 AATGTTCAATTCCCATTCCACAA 57.178 34.783 0.00 0.00 0.00 3.33
161 162 5.306419 TCAAATGTTCAATTCCCATTCCACA 59.694 36.000 0.00 0.00 0.00 4.17
162 163 5.792741 TCAAATGTTCAATTCCCATTCCAC 58.207 37.500 0.00 0.00 0.00 4.02
163 164 5.543405 ACTCAAATGTTCAATTCCCATTCCA 59.457 36.000 0.00 0.00 0.00 3.53
164 165 5.870978 CACTCAAATGTTCAATTCCCATTCC 59.129 40.000 0.00 0.00 0.00 3.01
165 166 5.349543 GCACTCAAATGTTCAATTCCCATTC 59.650 40.000 0.00 0.00 0.00 2.67
166 167 5.012354 AGCACTCAAATGTTCAATTCCCATT 59.988 36.000 0.00 0.00 0.00 3.16
167 168 4.529377 AGCACTCAAATGTTCAATTCCCAT 59.471 37.500 0.00 0.00 0.00 4.00
168 169 3.896888 AGCACTCAAATGTTCAATTCCCA 59.103 39.130 0.00 0.00 0.00 4.37
169 170 4.022068 TCAGCACTCAAATGTTCAATTCCC 60.022 41.667 0.00 0.00 0.00 3.97
170 171 5.125100 TCAGCACTCAAATGTTCAATTCC 57.875 39.130 0.00 0.00 0.00 3.01
171 172 5.510674 CGATCAGCACTCAAATGTTCAATTC 59.489 40.000 0.00 0.00 0.00 2.17
172 173 5.396484 CGATCAGCACTCAAATGTTCAATT 58.604 37.500 0.00 0.00 0.00 2.32
173 174 4.142534 CCGATCAGCACTCAAATGTTCAAT 60.143 41.667 0.00 0.00 0.00 2.57
174 175 3.189080 CCGATCAGCACTCAAATGTTCAA 59.811 43.478 0.00 0.00 0.00 2.69
175 176 2.743664 CCGATCAGCACTCAAATGTTCA 59.256 45.455 0.00 0.00 0.00 3.18
176 177 2.744202 ACCGATCAGCACTCAAATGTTC 59.256 45.455 0.00 0.00 0.00 3.18
177 178 2.783135 ACCGATCAGCACTCAAATGTT 58.217 42.857 0.00 0.00 0.00 2.71
178 179 2.479566 ACCGATCAGCACTCAAATGT 57.520 45.000 0.00 0.00 0.00 2.71
179 180 3.684305 TGTAACCGATCAGCACTCAAATG 59.316 43.478 0.00 0.00 0.00 2.32
180 181 3.684788 GTGTAACCGATCAGCACTCAAAT 59.315 43.478 0.00 0.00 0.00 2.32
181 182 3.064207 GTGTAACCGATCAGCACTCAAA 58.936 45.455 0.00 0.00 0.00 2.69
182 183 2.299013 AGTGTAACCGATCAGCACTCAA 59.701 45.455 0.00 0.00 37.80 3.02
183 184 1.893137 AGTGTAACCGATCAGCACTCA 59.107 47.619 0.00 0.00 37.80 3.41
184 185 2.656560 AGTGTAACCGATCAGCACTC 57.343 50.000 0.00 0.00 37.80 3.51
185 186 2.159421 CGTAGTGTAACCGATCAGCACT 60.159 50.000 0.00 0.00 42.25 4.40
186 187 2.182825 CGTAGTGTAACCGATCAGCAC 58.817 52.381 0.00 0.00 37.80 4.40
187 188 1.468565 GCGTAGTGTAACCGATCAGCA 60.469 52.381 0.00 0.00 37.80 4.41
188 189 1.197910 GCGTAGTGTAACCGATCAGC 58.802 55.000 0.00 0.00 37.80 4.26
189 190 1.463805 CGCGTAGTGTAACCGATCAG 58.536 55.000 0.00 0.00 37.80 2.90
190 191 0.099259 CCGCGTAGTGTAACCGATCA 59.901 55.000 4.92 0.00 37.80 2.92
191 192 0.378257 TCCGCGTAGTGTAACCGATC 59.622 55.000 4.92 0.00 37.80 3.69
192 193 1.027357 ATCCGCGTAGTGTAACCGAT 58.973 50.000 4.92 0.00 37.80 4.18
193 194 0.099259 CATCCGCGTAGTGTAACCGA 59.901 55.000 4.92 0.00 37.80 4.69
194 195 0.868602 CCATCCGCGTAGTGTAACCG 60.869 60.000 4.92 0.00 37.80 4.44
195 196 0.529119 CCCATCCGCGTAGTGTAACC 60.529 60.000 4.92 0.00 37.80 2.85
196 197 0.174162 ACCCATCCGCGTAGTGTAAC 59.826 55.000 4.92 0.00 35.45 2.50
197 198 0.457035 GACCCATCCGCGTAGTGTAA 59.543 55.000 4.92 0.00 35.45 2.41
198 199 1.386525 GGACCCATCCGCGTAGTGTA 61.387 60.000 4.92 0.00 34.48 2.90
199 200 2.718073 GGACCCATCCGCGTAGTGT 61.718 63.158 4.92 0.00 34.48 3.55
200 201 2.106332 GGACCCATCCGCGTAGTG 59.894 66.667 4.92 0.00 34.48 2.74
208 209 4.530857 CCTGTCGCGGACCCATCC 62.531 72.222 6.13 0.00 42.28 3.51
209 210 4.530857 CCCTGTCGCGGACCCATC 62.531 72.222 6.13 0.00 0.00 3.51
213 214 4.436998 CAGACCCTGTCGCGGACC 62.437 72.222 6.13 0.00 37.67 4.46
214 215 3.343788 CTCAGACCCTGTCGCGGAC 62.344 68.421 6.13 3.78 37.67 4.79
215 216 3.062466 CTCAGACCCTGTCGCGGA 61.062 66.667 6.13 0.00 37.67 5.54
216 217 4.135153 CCTCAGACCCTGTCGCGG 62.135 72.222 6.13 0.00 37.67 6.46
217 218 3.057547 CTCCTCAGACCCTGTCGCG 62.058 68.421 0.00 0.00 37.67 5.87
218 219 2.888863 CTCCTCAGACCCTGTCGC 59.111 66.667 0.00 0.00 37.67 5.19
219 220 1.979155 TGCTCCTCAGACCCTGTCG 60.979 63.158 0.00 0.00 37.67 4.35
220 221 1.594310 GTGCTCCTCAGACCCTGTC 59.406 63.158 0.00 0.00 32.61 3.51
221 222 2.279069 CGTGCTCCTCAGACCCTGT 61.279 63.158 0.00 0.00 32.61 4.00
222 223 0.965866 TACGTGCTCCTCAGACCCTG 60.966 60.000 0.00 0.00 0.00 4.45
223 224 0.966370 GTACGTGCTCCTCAGACCCT 60.966 60.000 0.00 0.00 0.00 4.34
224 225 1.511768 GTACGTGCTCCTCAGACCC 59.488 63.158 0.00 0.00 0.00 4.46
225 226 1.136984 CGTACGTGCTCCTCAGACC 59.863 63.158 7.22 0.00 0.00 3.85
226 227 1.136984 CCGTACGTGCTCCTCAGAC 59.863 63.158 15.21 0.00 0.00 3.51
227 228 2.044555 CCCGTACGTGCTCCTCAGA 61.045 63.158 15.21 0.00 0.00 3.27
228 229 2.490217 CCCGTACGTGCTCCTCAG 59.510 66.667 15.21 0.00 0.00 3.35
229 230 3.755628 GCCCGTACGTGCTCCTCA 61.756 66.667 15.74 0.00 0.00 3.86
230 231 4.849329 CGCCCGTACGTGCTCCTC 62.849 72.222 20.19 0.00 0.00 3.71
303 304 1.072159 GCCTTGGACAGCTGTGAGT 59.928 57.895 27.27 0.00 0.00 3.41
305 306 2.031012 CGCCTTGGACAGCTGTGA 59.969 61.111 27.27 7.69 0.00 3.58
335 336 3.262420 GTGTCAAGTCTCAAGTGTGTGT 58.738 45.455 0.00 0.00 0.00 3.72
434 450 1.005450 AGAGAGAGAAGAAGAGGCGGT 59.995 52.381 0.00 0.00 0.00 5.68
490 517 4.827087 AGAGATGTGGCGGCGCTG 62.827 66.667 32.30 13.18 0.00 5.18
538 566 3.706373 ACCTGCGAGTTGGCCGAT 61.706 61.111 0.00 0.00 0.00 4.18
558 586 2.492484 GTGCGGGAGGATCGATTATACT 59.508 50.000 0.00 0.00 34.37 2.12
561 589 0.608640 GGTGCGGGAGGATCGATTAT 59.391 55.000 0.00 0.00 34.37 1.28
562 590 2.046938 GGTGCGGGAGGATCGATTA 58.953 57.895 0.00 0.00 34.37 1.75
578 611 2.017049 GTATTTGATCCAAGCAGCGGT 58.983 47.619 0.00 0.00 0.00 5.68
608 660 4.190304 TGAAACAATTAATCGCCGATCG 57.810 40.909 8.51 8.51 40.15 3.69
609 661 5.156804 ACTGAAACAATTAATCGCCGATC 57.843 39.130 0.00 0.00 0.00 3.69
610 662 5.331902 CAACTGAAACAATTAATCGCCGAT 58.668 37.500 0.00 0.00 0.00 4.18
611 663 4.717991 CAACTGAAACAATTAATCGCCGA 58.282 39.130 0.00 0.00 0.00 5.54
612 664 3.300590 GCAACTGAAACAATTAATCGCCG 59.699 43.478 0.00 0.00 0.00 6.46
613 665 3.300590 CGCAACTGAAACAATTAATCGCC 59.699 43.478 0.00 0.00 0.00 5.54
614 666 3.911964 ACGCAACTGAAACAATTAATCGC 59.088 39.130 0.00 0.00 0.00 4.58
615 667 5.662815 GCAACGCAACTGAAACAATTAATCG 60.663 40.000 0.00 0.00 0.00 3.34
620 672 3.115554 GAGCAACGCAACTGAAACAATT 58.884 40.909 0.00 0.00 0.00 2.32
624 676 1.599542 AGAGAGCAACGCAACTGAAAC 59.400 47.619 0.00 0.00 0.00 2.78
637 689 1.203287 CACTGATCAACCGAGAGAGCA 59.797 52.381 0.00 0.00 0.00 4.26
638 690 1.470632 CCACTGATCAACCGAGAGAGC 60.471 57.143 0.00 0.00 0.00 4.09
639 691 1.821753 ACCACTGATCAACCGAGAGAG 59.178 52.381 0.00 0.00 0.00 3.20
640 692 1.819288 GACCACTGATCAACCGAGAGA 59.181 52.381 0.00 0.00 0.00 3.10
641 693 1.821753 AGACCACTGATCAACCGAGAG 59.178 52.381 0.00 0.00 0.00 3.20
642 694 1.819288 GAGACCACTGATCAACCGAGA 59.181 52.381 0.00 0.00 0.00 4.04
643 695 1.134965 GGAGACCACTGATCAACCGAG 60.135 57.143 0.00 0.00 0.00 4.63
647 699 1.404315 GGACGGAGACCACTGATCAAC 60.404 57.143 0.00 0.00 43.12 3.18
654 706 3.054503 CGACGGACGGAGACCACT 61.055 66.667 0.00 0.00 44.03 4.00
668 730 0.596341 AATGCGCACCCAAAAACGAC 60.596 50.000 14.90 0.00 0.00 4.34
724 832 3.385749 AACGAAGCGCCCGATCCAT 62.386 57.895 23.57 0.94 0.00 3.41
823 933 1.068541 GCACCCGTGGTTTGAGAAATC 60.069 52.381 0.00 0.00 31.02 2.17
824 934 0.958822 GCACCCGTGGTTTGAGAAAT 59.041 50.000 0.00 0.00 31.02 2.17
825 935 0.394488 TGCACCCGTGGTTTGAGAAA 60.394 50.000 0.00 0.00 31.02 2.52
826 936 0.394488 TTGCACCCGTGGTTTGAGAA 60.394 50.000 0.00 0.00 31.02 2.87
910 1020 9.720769 AGTATATTCGACGAAAATCCCATAAAT 57.279 29.630 15.22 0.00 0.00 1.40
996 1106 2.796651 GGAGCTTCCTGCATTGCG 59.203 61.111 3.84 0.00 45.94 4.85
997 1107 2.796651 CGGAGCTTCCTGCATTGC 59.203 61.111 0.46 0.46 45.94 3.56
1587 1703 4.741239 ATCTGCCCGGGGTGGAGT 62.741 66.667 25.28 0.00 42.00 3.85
1719 1841 0.321564 TGCCGTTCCTGTCCATCTTG 60.322 55.000 0.00 0.00 0.00 3.02
1785 1925 1.055849 GAATGCAGGGGTTGGGTTTT 58.944 50.000 0.00 0.00 0.00 2.43
1799 1939 1.587547 GGATTGAGTCGGAGGAATGC 58.412 55.000 0.00 0.00 0.00 3.56
2639 2808 6.177610 ACAAGGCTAAGTCGATAATTTCCAA 58.822 36.000 0.00 0.00 0.00 3.53
2640 2809 5.741011 ACAAGGCTAAGTCGATAATTTCCA 58.259 37.500 0.00 0.00 0.00 3.53
2645 2814 4.161565 TGGTGACAAGGCTAAGTCGATAAT 59.838 41.667 13.28 0.00 37.58 1.28
2650 2819 3.906660 TGGTGACAAGGCTAAGTCG 57.093 52.632 13.28 0.00 37.58 4.18
2666 2835 7.447374 TGGTGTACTCAAATAACAGATTTGG 57.553 36.000 9.49 4.37 38.97 3.28
2692 2864 5.237779 ACAAGACAGTACCAAAATAACACCG 59.762 40.000 0.00 0.00 0.00 4.94
2705 2877 5.050972 CGAACTTCTTTCCACAAGACAGTAC 60.051 44.000 0.00 0.00 0.00 2.73
2729 2901 3.244249 ACAACTGAAGTCTGAAGTAGCCC 60.244 47.826 0.00 0.00 0.00 5.19
2738 2910 7.645340 CCAGAAAAACAATACAACTGAAGTCTG 59.355 37.037 0.00 0.00 0.00 3.51
2750 2922 7.657336 TCTCCAATTGTCCAGAAAAACAATAC 58.343 34.615 4.43 0.00 43.45 1.89
2786 2958 9.412460 TCTATGCTTGACATCCTTTAAAATCAT 57.588 29.630 0.00 0.00 40.38 2.45
2787 2959 8.806429 TCTATGCTTGACATCCTTTAAAATCA 57.194 30.769 0.00 0.00 40.38 2.57
2788 2960 9.674824 CATCTATGCTTGACATCCTTTAAAATC 57.325 33.333 0.00 0.00 40.38 2.17
2822 3001 6.266103 CCCACATAAACAATAGGCAGATCATT 59.734 38.462 0.00 0.00 0.00 2.57
2828 3007 4.677779 GCAACCCACATAAACAATAGGCAG 60.678 45.833 0.00 0.00 0.00 4.85
2836 3015 0.955178 CCACGCAACCCACATAAACA 59.045 50.000 0.00 0.00 0.00 2.83
2841 3020 3.444818 AACCCCACGCAACCCACAT 62.445 57.895 0.00 0.00 0.00 3.21
2850 3029 2.270874 ATCCCAGATCAACCCCACGC 62.271 60.000 0.00 0.00 0.00 5.34
2852 3031 1.566231 AGAATCCCAGATCAACCCCAC 59.434 52.381 0.00 0.00 0.00 4.61
2882 3063 7.715657 ACTGTAACCGTATAAATTCACCGATA 58.284 34.615 0.00 0.00 0.00 2.92
2885 3066 6.651755 AACTGTAACCGTATAAATTCACCG 57.348 37.500 0.00 0.00 0.00 4.94
2928 3152 6.803807 GCTGATAATTTCCTCTCAAAACACAC 59.196 38.462 0.00 0.00 0.00 3.82
2998 3222 6.837312 TGAAATTCCTTCCAGAAGACAGTAA 58.163 36.000 9.00 0.00 40.79 2.24
3094 3325 4.856664 CATTTATGCTTGACATGCTCCTC 58.143 43.478 13.81 0.00 40.06 3.71
3127 3358 7.280876 CAGAGCAACAGAAACTATAGGCAAATA 59.719 37.037 4.43 0.00 0.00 1.40
3157 3388 7.308469 GGAATATCAAGCTTAAAGATGAGCAGG 60.308 40.741 0.00 0.00 40.47 4.85
3160 3391 7.228308 ACTGGAATATCAAGCTTAAAGATGAGC 59.772 37.037 0.00 0.00 38.40 4.26
3193 3424 2.221981 GTGCTAAACTGACAGACTGCAC 59.778 50.000 21.26 21.26 41.72 4.57


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

AutoCloner maintained by Alex Coulton.