Multiple sequence alignment - TraesCS3D01G036600

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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 TraesCS3D01G036600 chr3D 100.000 2605 0 0 1 2605 13253563 13256167 0.000000e+00 4811.0
1 TraesCS3D01G036600 chr3D 100.000 2208 0 0 2979 5186 13256541 13258748 0.000000e+00 4078.0
2 TraesCS3D01G036600 chr3D 90.169 295 17 8 1 287 607993531 607993241 1.760000e-99 374.0
3 TraesCS3D01G036600 chr3D 90.511 274 20 5 1 270 376173823 376174094 1.780000e-94 357.0
4 TraesCS3D01G036600 chr3D 93.413 167 9 1 3493 3657 238999579 238999413 4.010000e-61 246.0
5 TraesCS3D01G036600 chr3D 93.865 163 8 1 3496 3656 410670225 410670063 1.440000e-60 244.0
6 TraesCS3D01G036600 chr3D 97.143 35 1 0 4475 4509 204699352 204699318 5.610000e-05 60.2
7 TraesCS3D01G036600 chr3A 95.142 2326 84 13 284 2605 23868362 23866062 0.000000e+00 3642.0
8 TraesCS3D01G036600 chr3A 95.532 1343 51 6 2979 4312 23865944 23864602 0.000000e+00 2139.0
9 TraesCS3D01G036600 chr3A 86.150 722 61 13 4488 5186 23864256 23863551 0.000000e+00 743.0
10 TraesCS3D01G036600 chr3A 91.837 49 2 2 4444 4492 23864594 23864548 3.350000e-07 67.6
11 TraesCS3D01G036600 chr3B 90.184 1518 122 14 3680 5180 19168416 19169923 0.000000e+00 1953.0
12 TraesCS3D01G036600 chr3B 93.803 1307 41 12 756 2034 19165937 19167231 0.000000e+00 1929.0
13 TraesCS3D01G036600 chr3B 92.089 493 23 6 3017 3498 19167877 19168364 0.000000e+00 680.0
14 TraesCS3D01G036600 chr3B 91.176 306 16 2 2161 2457 19167229 19167532 6.250000e-109 405.0
15 TraesCS3D01G036600 chr6D 90.066 302 27 3 1 299 461509667 461509366 6.300000e-104 388.0
16 TraesCS3D01G036600 chr6D 92.353 170 11 1 3489 3656 229430883 229431052 1.870000e-59 241.0
17 TraesCS3D01G036600 chr7D 91.034 290 18 7 1 285 150651194 150651480 8.150000e-103 385.0
18 TraesCS3D01G036600 chr7D 86.179 123 17 0 2032 2154 584458448 584458326 3.260000e-27 134.0
19 TraesCS3D01G036600 chr5D 89.583 288 26 3 2 285 541962816 541963103 3.820000e-96 363.0
20 TraesCS3D01G036600 chr5D 92.090 177 11 2 3487 3660 46310882 46311058 4.010000e-61 246.0
21 TraesCS3D01G036600 chr5D 97.297 37 1 0 4474 4510 491432564 491432600 4.340000e-06 63.9
22 TraesCS3D01G036600 chr2D 88.475 295 22 8 1 287 11469288 11469578 3.840000e-91 346.0
23 TraesCS3D01G036600 chr2D 93.976 166 8 1 3493 3656 445733667 445733832 3.100000e-62 250.0
24 TraesCS3D01G036600 chr2D 84.800 125 15 3 2032 2154 194524713 194524591 7.050000e-24 122.0
25 TraesCS3D01G036600 chr1A 87.241 290 31 5 1 285 21572013 21572301 5.010000e-85 326.0
26 TraesCS3D01G036600 chr1A 86.364 308 30 12 1 299 370547271 370547575 5.010000e-85 326.0
27 TraesCS3D01G036600 chr2A 86.054 294 35 5 1 288 90598313 90598020 1.400000e-80 311.0
28 TraesCS3D01G036600 chr2A 93.939 165 8 1 3494 3656 460904000 460904164 1.120000e-61 248.0
29 TraesCS3D01G036600 chr4D 94.512 164 6 2 3496 3657 58643756 58643918 3.100000e-62 250.0
30 TraesCS3D01G036600 chr4D 85.246 122 18 0 2033 2154 311194977 311194856 5.450000e-25 126.0
31 TraesCS3D01G036600 chr4D 83.942 137 17 5 2032 2166 366693480 366693347 5.450000e-25 126.0
32 TraesCS3D01G036600 chr7A 92.982 171 8 3 3492 3659 246344204 246344373 4.010000e-61 246.0
33 TraesCS3D01G036600 chr6B 85.714 126 18 0 2033 2158 479843597 479843472 3.260000e-27 134.0
34 TraesCS3D01G036600 chr4B 85.366 123 18 0 2032 2154 489398981 489399103 1.520000e-25 128.0
35 TraesCS3D01G036600 chr5B 84.375 128 20 0 2027 2154 705270137 705270264 5.450000e-25 126.0
36 TraesCS3D01G036600 chr7B 85.124 121 18 0 2032 2152 76816020 76815900 1.960000e-24 124.0
37 TraesCS3D01G036600 chr2B 97.222 36 1 0 4475 4510 73382194 73382159 1.560000e-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 TraesCS3D01G036600 chr3D 13253563 13258748 5185 False 4444.50 4811 100.00000 1 5186 2 chr3D.!!$F2 5185
1 TraesCS3D01G036600 chr3A 23863551 23868362 4811 True 1647.90 3642 92.16525 284 5186 4 chr3A.!!$R1 4902
2 TraesCS3D01G036600 chr3B 19165937 19169923 3986 False 1241.75 1953 91.81300 756 5180 4 chr3B.!!$F1 4424

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
159 160 0.110147 TACGTTTGAATTTGCCGCGG 60.110 50.000 24.05 24.05 0.00 6.46 F
726 728 0.179145 GTGTATGTGACGAGGGTCCG 60.179 60.000 0.00 0.00 42.73 4.79 F
741 743 0.453782 GTCCGCATTTTGTACCGTGC 60.454 55.000 0.00 0.00 0.00 5.34 F
827 832 0.539051 CCTCCTCACATCCACCACTC 59.461 60.000 0.00 0.00 0.00 3.51 F
984 991 1.103803 TCTTCTTCCATCGAGGTCGG 58.896 55.000 0.00 0.00 40.29 4.79 F
1780 1790 2.022934 ACCGGCACTAGCTAGTACTTC 58.977 52.381 25.63 14.33 41.70 3.01 F
2577 2677 0.679321 CAGGAGGAAAGGCAAGCTCC 60.679 60.000 0.00 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 1695 2.342279 CCGTCTTGTCGCCTTCCA 59.658 61.111 0.00 0.00 0.00 3.53 R
2187 2220 0.109342 ATTCCTTGGCTAGCGATGGG 59.891 55.000 25.09 18.21 0.00 4.00 R
2329 2362 5.336849 GCCTATTCATCCGTAAGTCTAGCAT 60.337 44.000 0.00 0.00 0.00 3.79 R
2460 2559 8.529476 AGGAACACAACGTAATAACTAAGATCT 58.471 33.333 0.00 0.00 0.00 2.75 R
2577 2677 8.703604 TCGATTATTACAAAGAGAAGACCAAG 57.296 34.615 0.00 0.00 0.00 3.61 R
3535 3656 1.000955 GCTCCGTATGGTCCATAGTGG 59.999 57.143 18.43 18.43 39.43 4.00 R
4245 4404 0.042188 CGTTTAGCCATGAATCGCCG 60.042 55.000 0.00 0.00 0.00 6.46 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
52 53 3.518998 CCGACCTCGCCGTCTGAT 61.519 66.667 0.00 0.00 38.18 2.90
53 54 2.278206 CGACCTCGCCGTCTGATG 60.278 66.667 1.10 0.00 0.00 3.07
54 55 2.583593 GACCTCGCCGTCTGATGC 60.584 66.667 0.00 0.00 0.00 3.91
72 73 4.430423 GCACGCGCGTCCTTTCTG 62.430 66.667 35.61 21.21 0.00 3.02
73 74 4.430423 CACGCGCGTCCTTTCTGC 62.430 66.667 35.61 0.00 0.00 4.26
74 75 4.664677 ACGCGCGTCCTTTCTGCT 62.665 61.111 32.73 2.20 0.00 4.24
75 76 3.414700 CGCGCGTCCTTTCTGCTT 61.415 61.111 24.19 0.00 0.00 3.91
76 77 2.946762 GCGCGTCCTTTCTGCTTT 59.053 55.556 8.43 0.00 0.00 3.51
77 78 1.282875 GCGCGTCCTTTCTGCTTTT 59.717 52.632 8.43 0.00 0.00 2.27
78 79 0.317854 GCGCGTCCTTTCTGCTTTTT 60.318 50.000 8.43 0.00 0.00 1.94
79 80 1.398595 CGCGTCCTTTCTGCTTTTTG 58.601 50.000 0.00 0.00 0.00 2.44
80 81 1.268539 CGCGTCCTTTCTGCTTTTTGT 60.269 47.619 0.00 0.00 0.00 2.83
81 82 2.032377 CGCGTCCTTTCTGCTTTTTGTA 60.032 45.455 0.00 0.00 0.00 2.41
82 83 3.297472 GCGTCCTTTCTGCTTTTTGTAC 58.703 45.455 0.00 0.00 0.00 2.90
83 84 3.541711 CGTCCTTTCTGCTTTTTGTACG 58.458 45.455 0.00 0.00 0.00 3.67
84 85 3.297472 GTCCTTTCTGCTTTTTGTACGC 58.703 45.455 0.00 0.00 0.00 4.42
85 86 2.292292 TCCTTTCTGCTTTTTGTACGCC 59.708 45.455 0.00 0.00 0.00 5.68
86 87 2.307049 CTTTCTGCTTTTTGTACGCCG 58.693 47.619 0.00 0.00 0.00 6.46
87 88 1.584175 TTCTGCTTTTTGTACGCCGA 58.416 45.000 0.00 0.00 0.00 5.54
88 89 1.584175 TCTGCTTTTTGTACGCCGAA 58.416 45.000 0.00 0.00 0.00 4.30
89 90 1.262151 TCTGCTTTTTGTACGCCGAAC 59.738 47.619 0.00 0.00 0.00 3.95
90 91 1.263217 CTGCTTTTTGTACGCCGAACT 59.737 47.619 0.00 0.00 0.00 3.01
91 92 1.671845 TGCTTTTTGTACGCCGAACTT 59.328 42.857 0.00 0.00 0.00 2.66
92 93 2.097791 TGCTTTTTGTACGCCGAACTTT 59.902 40.909 0.00 0.00 0.00 2.66
93 94 3.110358 GCTTTTTGTACGCCGAACTTTT 58.890 40.909 0.00 0.00 0.00 2.27
94 95 3.179010 GCTTTTTGTACGCCGAACTTTTC 59.821 43.478 0.00 0.00 0.00 2.29
95 96 4.344448 CTTTTTGTACGCCGAACTTTTCA 58.656 39.130 0.00 0.00 0.00 2.69
96 97 4.555348 TTTTGTACGCCGAACTTTTCAT 57.445 36.364 0.00 0.00 0.00 2.57
97 98 4.555348 TTTGTACGCCGAACTTTTCATT 57.445 36.364 0.00 0.00 0.00 2.57
98 99 3.799137 TGTACGCCGAACTTTTCATTC 57.201 42.857 0.00 0.00 0.00 2.67
99 100 2.156117 TGTACGCCGAACTTTTCATTCG 59.844 45.455 0.00 0.26 46.67 3.34
106 107 2.694043 GAACTTTTCATTCGATCGCCG 58.306 47.619 11.09 0.74 40.25 6.46
107 108 2.004583 ACTTTTCATTCGATCGCCGA 57.995 45.000 11.09 3.43 46.94 5.54
114 115 4.102561 TCGATCGCCGAATTGTGG 57.897 55.556 11.09 0.00 45.43 4.17
122 123 2.271821 GCCGAATTGTGGCGTTTATT 57.728 45.000 2.73 0.00 43.70 1.40
123 124 2.601804 GCCGAATTGTGGCGTTTATTT 58.398 42.857 2.73 0.00 43.70 1.40
124 125 2.990514 GCCGAATTGTGGCGTTTATTTT 59.009 40.909 2.73 0.00 43.70 1.82
125 126 3.181535 GCCGAATTGTGGCGTTTATTTTG 60.182 43.478 2.73 0.00 43.70 2.44
126 127 3.984633 CCGAATTGTGGCGTTTATTTTGT 59.015 39.130 0.00 0.00 0.00 2.83
127 128 4.143431 CCGAATTGTGGCGTTTATTTTGTG 60.143 41.667 0.00 0.00 0.00 3.33
128 129 4.677378 CGAATTGTGGCGTTTATTTTGTGA 59.323 37.500 0.00 0.00 0.00 3.58
129 130 5.164196 CGAATTGTGGCGTTTATTTTGTGAG 60.164 40.000 0.00 0.00 0.00 3.51
130 131 3.006659 TGTGGCGTTTATTTTGTGAGC 57.993 42.857 0.00 0.00 0.00 4.26
131 132 1.976045 GTGGCGTTTATTTTGTGAGCG 59.024 47.619 0.00 0.00 0.00 5.03
132 133 1.068885 TGGCGTTTATTTTGTGAGCGG 60.069 47.619 0.00 0.00 0.00 5.52
133 134 1.198178 GGCGTTTATTTTGTGAGCGGA 59.802 47.619 0.00 0.00 0.00 5.54
134 135 2.350964 GGCGTTTATTTTGTGAGCGGAA 60.351 45.455 0.00 0.00 0.00 4.30
135 136 3.301706 GCGTTTATTTTGTGAGCGGAAA 58.698 40.909 0.00 0.00 0.00 3.13
136 137 3.917985 GCGTTTATTTTGTGAGCGGAAAT 59.082 39.130 0.00 0.00 0.00 2.17
137 138 5.090083 GCGTTTATTTTGTGAGCGGAAATA 58.910 37.500 0.00 0.00 0.00 1.40
138 139 5.569823 GCGTTTATTTTGTGAGCGGAAATAA 59.430 36.000 0.00 0.00 34.93 1.40
139 140 6.451960 GCGTTTATTTTGTGAGCGGAAATAAC 60.452 38.462 0.00 0.00 35.89 1.89
140 141 6.799925 CGTTTATTTTGTGAGCGGAAATAACT 59.200 34.615 0.00 0.00 35.89 2.24
141 142 7.958567 CGTTTATTTTGTGAGCGGAAATAACTA 59.041 33.333 0.00 0.00 35.89 2.24
142 143 9.058424 GTTTATTTTGTGAGCGGAAATAACTAC 57.942 33.333 0.00 0.00 35.89 2.73
143 144 4.914312 TTTGTGAGCGGAAATAACTACG 57.086 40.909 0.00 0.00 0.00 3.51
144 145 3.581024 TGTGAGCGGAAATAACTACGT 57.419 42.857 0.00 0.00 0.00 3.57
145 146 3.916761 TGTGAGCGGAAATAACTACGTT 58.083 40.909 0.00 0.00 0.00 3.99
146 147 4.309099 TGTGAGCGGAAATAACTACGTTT 58.691 39.130 0.00 0.00 0.00 3.60
147 148 4.150980 TGTGAGCGGAAATAACTACGTTTG 59.849 41.667 0.00 0.00 0.00 2.93
148 149 4.386652 GTGAGCGGAAATAACTACGTTTGA 59.613 41.667 0.00 0.00 0.00 2.69
149 150 4.989797 TGAGCGGAAATAACTACGTTTGAA 59.010 37.500 0.00 0.00 0.00 2.69
150 151 5.640357 TGAGCGGAAATAACTACGTTTGAAT 59.360 36.000 0.00 0.00 0.00 2.57
151 152 6.148150 TGAGCGGAAATAACTACGTTTGAATT 59.852 34.615 0.00 0.00 0.00 2.17
152 153 6.905578 AGCGGAAATAACTACGTTTGAATTT 58.094 32.000 0.00 0.00 0.00 1.82
153 154 6.799925 AGCGGAAATAACTACGTTTGAATTTG 59.200 34.615 0.00 0.00 0.00 2.32
154 155 6.451960 GCGGAAATAACTACGTTTGAATTTGC 60.452 38.462 0.00 0.60 0.00 3.68
155 156 6.033091 CGGAAATAACTACGTTTGAATTTGCC 59.967 38.462 0.00 0.27 0.00 4.52
156 157 6.033091 GGAAATAACTACGTTTGAATTTGCCG 59.967 38.462 0.00 0.00 0.00 5.69
157 158 2.325509 ACTACGTTTGAATTTGCCGC 57.674 45.000 0.00 0.00 0.00 6.53
158 159 1.246970 CTACGTTTGAATTTGCCGCG 58.753 50.000 0.00 0.00 0.00 6.46
159 160 0.110147 TACGTTTGAATTTGCCGCGG 60.110 50.000 24.05 24.05 0.00 6.46
160 161 2.085844 CGTTTGAATTTGCCGCGGG 61.086 57.895 29.38 8.95 0.00 6.13
161 162 1.006688 GTTTGAATTTGCCGCGGGT 60.007 52.632 29.38 0.00 0.00 5.28
162 163 0.598942 GTTTGAATTTGCCGCGGGTT 60.599 50.000 29.38 0.00 0.00 4.11
163 164 0.598680 TTTGAATTTGCCGCGGGTTG 60.599 50.000 29.38 0.38 0.00 3.77
164 165 2.126110 GAATTTGCCGCGGGTTGG 60.126 61.111 29.38 0.00 0.00 3.77
165 166 3.641159 GAATTTGCCGCGGGTTGGG 62.641 63.158 29.38 0.00 0.00 4.12
195 196 3.492353 GGGCATGGCTGGGAGCTA 61.492 66.667 19.78 0.00 41.99 3.32
196 197 2.112718 GGCATGGCTGGGAGCTAG 59.887 66.667 12.86 0.00 41.99 3.42
197 198 2.112718 GCATGGCTGGGAGCTAGG 59.887 66.667 0.00 0.00 41.99 3.02
198 199 2.750657 GCATGGCTGGGAGCTAGGT 61.751 63.158 0.00 0.00 41.99 3.08
199 200 1.449353 CATGGCTGGGAGCTAGGTC 59.551 63.158 13.67 13.67 41.99 3.85
200 201 2.136878 ATGGCTGGGAGCTAGGTCG 61.137 63.158 15.43 3.59 41.99 4.79
201 202 4.228567 GGCTGGGAGCTAGGTCGC 62.229 72.222 26.90 26.90 41.99 5.19
202 203 4.228567 GCTGGGAGCTAGGTCGCC 62.229 72.222 29.34 23.22 38.45 5.54
203 204 3.541713 CTGGGAGCTAGGTCGCCC 61.542 72.222 29.34 20.74 45.10 6.13
207 208 3.541713 GAGCTAGGTCGCCCCCAG 61.542 72.222 6.12 0.00 0.00 4.45
219 220 2.925170 CCCCAGGGGCCGATCTAG 60.925 72.222 13.35 0.00 35.35 2.43
220 221 2.122813 CCCAGGGGCCGATCTAGT 60.123 66.667 0.00 0.00 0.00 2.57
221 222 2.511452 CCCAGGGGCCGATCTAGTG 61.511 68.421 0.00 0.00 0.00 2.74
222 223 2.423446 CAGGGGCCGATCTAGTGC 59.577 66.667 0.00 0.00 0.00 4.40
223 224 2.844839 AGGGGCCGATCTAGTGCC 60.845 66.667 0.00 6.75 44.59 5.01
224 225 4.301027 GGGGCCGATCTAGTGCCG 62.301 72.222 0.00 2.89 46.31 5.69
225 226 4.301027 GGGCCGATCTAGTGCCGG 62.301 72.222 0.00 0.00 46.31 6.13
226 227 3.537874 GGCCGATCTAGTGCCGGT 61.538 66.667 1.90 0.00 44.63 5.28
227 228 2.499685 GCCGATCTAGTGCCGGTT 59.500 61.111 1.90 0.00 44.63 4.44
228 229 1.591863 GCCGATCTAGTGCCGGTTC 60.592 63.158 1.90 0.00 44.63 3.62
229 230 1.299165 CCGATCTAGTGCCGGTTCG 60.299 63.158 1.90 1.02 38.55 3.95
230 231 1.944676 CGATCTAGTGCCGGTTCGC 60.945 63.158 1.90 0.00 0.00 4.70
231 232 1.591863 GATCTAGTGCCGGTTCGCC 60.592 63.158 1.90 0.00 0.00 5.54
232 233 2.973180 GATCTAGTGCCGGTTCGCCC 62.973 65.000 1.90 0.00 0.00 6.13
233 234 4.832608 CTAGTGCCGGTTCGCCCC 62.833 72.222 1.90 0.00 0.00 5.80
249 250 3.440415 CCCGGGCCGCTCTTTTTC 61.440 66.667 23.20 0.00 0.00 2.29
250 251 3.799755 CCGGGCCGCTCTTTTTCG 61.800 66.667 23.20 0.00 0.00 3.46
255 256 4.460873 CCGCTCTTTTTCGGCGCC 62.461 66.667 19.07 19.07 46.29 6.53
256 257 4.460873 CGCTCTTTTTCGGCGCCC 62.461 66.667 23.46 2.84 42.28 6.13
257 258 3.056328 GCTCTTTTTCGGCGCCCT 61.056 61.111 23.46 0.00 0.00 5.19
258 259 2.870372 CTCTTTTTCGGCGCCCTG 59.130 61.111 23.46 8.15 0.00 4.45
259 260 2.671619 TCTTTTTCGGCGCCCTGG 60.672 61.111 23.46 7.26 0.00 4.45
260 261 3.747976 CTTTTTCGGCGCCCTGGG 61.748 66.667 23.46 8.86 0.00 4.45
277 278 4.785453 GGGGCTGAACGGCTGGAG 62.785 72.222 0.00 0.00 38.46 3.86
278 279 3.706373 GGGCTGAACGGCTGGAGA 61.706 66.667 0.00 0.00 38.46 3.71
279 280 2.586792 GGCTGAACGGCTGGAGAT 59.413 61.111 0.00 0.00 34.85 2.75
280 281 1.817099 GGCTGAACGGCTGGAGATG 60.817 63.158 0.00 0.00 34.85 2.90
281 282 1.817099 GCTGAACGGCTGGAGATGG 60.817 63.158 0.00 0.00 0.00 3.51
282 283 1.599047 CTGAACGGCTGGAGATGGT 59.401 57.895 0.00 0.00 0.00 3.55
288 289 0.390860 CGGCTGGAGATGGTCTAAGG 59.609 60.000 0.00 0.00 0.00 2.69
291 292 2.393646 GCTGGAGATGGTCTAAGGTCT 58.606 52.381 0.00 0.00 0.00 3.85
365 366 5.277974 CCTCGCATGTTCAAAAGAGAAGAAA 60.278 40.000 0.00 0.00 0.00 2.52
378 379 8.378421 CAAAAGAGAAGAAACAAAAGCAAAGAG 58.622 33.333 0.00 0.00 0.00 2.85
399 400 8.868635 AAGAGCAGAAATGAAAGAAAGAAAAG 57.131 30.769 0.00 0.00 0.00 2.27
401 402 8.689972 AGAGCAGAAATGAAAGAAAGAAAAGAA 58.310 29.630 0.00 0.00 0.00 2.52
402 403 9.305925 GAGCAGAAATGAAAGAAAGAAAAGAAA 57.694 29.630 0.00 0.00 0.00 2.52
403 404 9.310716 AGCAGAAATGAAAGAAAGAAAAGAAAG 57.689 29.630 0.00 0.00 0.00 2.62
472 473 8.246871 AGAAGAATATAGCCAAGCAAAGAAAAC 58.753 33.333 0.00 0.00 0.00 2.43
489 490 9.008289 CAAAGAAAACAAAACAAACAATATGGC 57.992 29.630 0.00 0.00 0.00 4.40
507 508 4.249638 TGGCTAGCAGTTTTTCCCATAT 57.750 40.909 18.24 0.00 0.00 1.78
540 541 2.902705 AGTGTTAGGCTGTTTGTCGA 57.097 45.000 0.00 0.00 0.00 4.20
576 577 6.735694 GCATGGTGCTTATATTTGGTCGAATT 60.736 38.462 0.00 0.00 40.96 2.17
599 600 9.686683 AATTTAATCTACAGTTTCCAGTGCTAT 57.313 29.630 0.00 0.00 0.00 2.97
625 627 0.673437 AAATGTGGTGGCTTTGTCGG 59.327 50.000 0.00 0.00 0.00 4.79
641 643 5.677319 TTGTCGGTCTTAGGATCTTTCAT 57.323 39.130 0.00 0.00 0.00 2.57
661 663 2.317530 CTCCATTTCTCGGAGGTTCC 57.682 55.000 4.96 0.00 45.43 3.62
662 664 0.909623 TCCATTTCTCGGAGGTTCCC 59.090 55.000 4.96 0.00 31.13 3.97
705 707 6.212589 TGATTTCATAGGTGTGAGTGTAGGAA 59.787 38.462 0.00 0.00 0.00 3.36
715 717 3.918591 GTGAGTGTAGGAACGTGTATGTG 59.081 47.826 0.00 0.00 0.00 3.21
720 722 2.631418 AGGAACGTGTATGTGACGAG 57.369 50.000 0.00 0.00 39.21 4.18
726 728 0.179145 GTGTATGTGACGAGGGTCCG 60.179 60.000 0.00 0.00 42.73 4.79
741 743 0.453782 GTCCGCATTTTGTACCGTGC 60.454 55.000 0.00 0.00 0.00 5.34
771 775 6.636666 AAATGCAAAGAAAATAGACATGCG 57.363 33.333 0.00 0.00 35.18 4.73
827 832 0.539051 CCTCCTCACATCCACCACTC 59.461 60.000 0.00 0.00 0.00 3.51
862 868 1.937899 CCTGTCGTCGTCAACCTTTTT 59.062 47.619 0.00 0.00 0.00 1.94
945 951 4.587684 ACACCAAACCCTATCTATCTACCG 59.412 45.833 0.00 0.00 0.00 4.02
960 967 2.264120 TACCGGTCCATCCCGTCGTA 62.264 60.000 12.40 0.00 46.66 3.43
984 991 1.103803 TCTTCTTCCATCGAGGTCGG 58.896 55.000 0.00 0.00 40.29 4.79
1589 1596 2.473760 CGACGGCGAGAGGATCAGT 61.474 63.158 16.62 0.00 40.82 3.41
1614 1621 2.369257 CTGATCAGTACGGCGGCCAT 62.369 60.000 20.71 6.26 0.00 4.40
1699 1709 2.342279 CGGTGGAAGGCGACAAGA 59.658 61.111 0.00 0.00 0.00 3.02
1780 1790 2.022934 ACCGGCACTAGCTAGTACTTC 58.977 52.381 25.63 14.33 41.70 3.01
2057 2090 2.949644 CCCTCCGTCTCAAAAAGTTTGT 59.050 45.455 0.98 0.00 0.00 2.83
2065 2098 8.145767 TCCGTCTCAAAAAGTTTGTCTTAGATA 58.854 33.333 0.98 0.00 35.02 1.98
2149 2182 2.693074 TCAAGACAAGCTTTTTGGGACC 59.307 45.455 0.00 0.00 33.60 4.46
2187 2220 2.614983 TGTAAGGTGCTTTGTTCGGTTC 59.385 45.455 0.00 0.00 0.00 3.62
2293 2326 3.181440 TGATCCAACACTTTGCCTCTCTT 60.181 43.478 0.00 0.00 0.00 2.85
2460 2559 5.047235 TGTGAATCAAAATGGATGCATGACA 60.047 36.000 2.46 3.05 35.33 3.58
2577 2677 0.679321 CAGGAGGAAAGGCAAGCTCC 60.679 60.000 0.00 0.00 0.00 4.70
3143 3254 6.324819 ACACTACACATGCTGCAATAATTTC 58.675 36.000 6.36 0.00 0.00 2.17
3395 3509 8.238631 ACATTCATTTAAGCCAAAATCATTTGC 58.761 29.630 0.00 0.00 43.73 3.68
3435 3549 8.812513 TTAACCATGAGAAATCAAGTGATCAT 57.187 30.769 0.00 0.00 32.75 2.45
3463 3583 3.004839 CACGACTATATGGACCCTGTCAG 59.995 52.174 0.00 0.00 33.68 3.51
3506 3626 2.180086 ACTATGGCATCTACTCCCTCCA 59.820 50.000 1.65 0.00 0.00 3.86
3529 3650 9.866655 TCCATTCCTAAATATAAGTCTTTGCAT 57.133 29.630 0.00 0.00 0.00 3.96
3543 3664 6.294473 AGTCTTTGCATAGATTCCACTATGG 58.706 40.000 10.18 0.00 45.51 2.74
3565 3688 3.009723 ACCATACGGAGCAAAATGAGTG 58.990 45.455 0.00 0.00 35.59 3.51
3574 3697 5.569059 CGGAGCAAAATGAGTGAATTTACAC 59.431 40.000 2.93 0.00 40.60 2.90
3703 3854 5.935789 GTGTTCATAGTTAAACCTACAGCCA 59.064 40.000 0.00 0.00 0.00 4.75
3709 3860 9.914834 TCATAGTTAAACCTACAGCCATTTAAT 57.085 29.630 0.00 0.00 31.26 1.40
3868 4020 4.994217 CCTTTTCTCTGTCCTCTTGACTTC 59.006 45.833 0.00 0.00 44.75 3.01
3878 4032 5.590259 TGTCCTCTTGACTTCTTTTCCTTTG 59.410 40.000 0.00 0.00 44.75 2.77
4088 4247 2.543777 TAAAGCTGCCCGGATCATAC 57.456 50.000 0.73 0.00 0.00 2.39
4341 4504 3.685836 AAACTGTCGTGGTTTTAGTGC 57.314 42.857 0.00 0.00 33.76 4.40
4344 4507 2.353579 ACTGTCGTGGTTTTAGTGCAAC 59.646 45.455 0.00 0.00 0.00 4.17
4364 4527 3.669536 ACTTGGAGAACTCAAAGCTAGC 58.330 45.455 16.16 6.62 42.93 3.42
4366 4529 1.066858 TGGAGAACTCAAAGCTAGCGG 60.067 52.381 9.55 3.30 0.00 5.52
4400 4563 3.415212 CTGCCTCCATTTCTTCACAAGA 58.585 45.455 0.00 0.00 35.26 3.02
4401 4564 3.822735 CTGCCTCCATTTCTTCACAAGAA 59.177 43.478 0.00 0.00 45.30 2.52
4484 4647 2.041350 AGGAAAGACGGTACTCTCTCCA 59.959 50.000 7.13 0.00 0.00 3.86
4518 4975 6.108015 ACTTGTCGTGGTTTTACTTACTTGA 58.892 36.000 0.00 0.00 0.00 3.02
4586 5047 1.474077 CGAGCCAAAGAGGGGAAATTG 59.526 52.381 0.00 0.00 38.09 2.32
4587 5048 2.807676 GAGCCAAAGAGGGGAAATTGA 58.192 47.619 0.00 0.00 38.09 2.57
4601 5062 4.162888 GGGAAATTGAAGGGATCATTGCTT 59.837 41.667 0.00 0.00 38.03 3.91
4614 5075 3.968649 TCATTGCTTGTCACTTTTCTGC 58.031 40.909 0.00 0.00 0.00 4.26
4650 5111 7.992754 ACTGTGAAGATTTTAGCTTGAATCT 57.007 32.000 14.94 14.94 42.72 2.40
4651 5112 7.814642 ACTGTGAAGATTTTAGCTTGAATCTG 58.185 34.615 19.14 11.81 40.68 2.90
4712 5173 3.536956 ATTTCTAATTCCGCTCGTCCA 57.463 42.857 0.00 0.00 0.00 4.02
4716 5177 2.167693 TCTAATTCCGCTCGTCCACAAT 59.832 45.455 0.00 0.00 0.00 2.71
4732 5193 1.832167 AATGCCTTTGCGTGGTGGT 60.832 52.632 0.00 0.00 41.78 4.16
4828 5312 4.292145 TTGGATTGGGTGGCGGCA 62.292 61.111 7.97 7.97 0.00 5.69
4981 5467 2.584418 CTGTGGCGGCAGATCGAG 60.584 66.667 13.91 0.00 38.70 4.04
4984 5470 4.519437 TGGCGGCAGATCGAGCTG 62.519 66.667 25.87 25.87 41.29 4.24
5000 5486 2.203437 TGCGGCCGGATCTAGCTA 60.203 61.111 29.38 0.00 0.00 3.32
5001 5487 1.599606 CTGCGGCCGGATCTAGCTAT 61.600 60.000 29.38 0.00 0.00 2.97
5004 5490 1.251527 CGGCCGGATCTAGCTATGGT 61.252 60.000 20.10 0.00 0.00 3.55
5022 5508 3.238497 CGGAGGTGGGTGGTGTGA 61.238 66.667 0.00 0.00 0.00 3.58
5037 5523 1.153469 GTGAGCTAGCTCCTGTGGC 60.153 63.158 35.76 15.30 42.09 5.01
5047 5533 0.036010 CTCCTGTGGCCGTTCTTCAT 60.036 55.000 0.00 0.00 0.00 2.57
5053 5539 0.687920 TGGCCGTTCTTCATGTGGTA 59.312 50.000 0.00 0.00 0.00 3.25
5144 5630 2.701780 CGTGTGTCCCCCTCTCTCG 61.702 68.421 0.00 0.00 0.00 4.04
5163 5649 2.400962 GCAGGCACGCATGTCATGA 61.401 57.895 17.24 0.00 30.46 3.07
5169 5655 1.931906 CACGCATGTCATGAGCTAGT 58.068 50.000 17.24 5.01 33.01 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.518998 ATCAGACGGCGAGGTCGG 61.519 66.667 16.62 1.12 41.81 4.79
36 37 2.278206 CATCAGACGGCGAGGTCG 60.278 66.667 16.62 0.00 41.81 4.79
37 38 2.583593 GCATCAGACGGCGAGGTC 60.584 66.667 16.62 0.00 37.19 3.85
55 56 4.430423 CAGAAAGGACGCGCGTGC 62.430 66.667 41.67 41.67 36.69 5.34
56 57 4.430423 GCAGAAAGGACGCGCGTG 62.430 66.667 42.90 24.76 0.00 5.34
57 58 4.664677 AGCAGAAAGGACGCGCGT 62.665 61.111 38.52 38.52 0.00 6.01
58 59 2.443957 AAAAGCAGAAAGGACGCGCG 62.444 55.000 30.96 30.96 0.00 6.86
59 60 0.317854 AAAAAGCAGAAAGGACGCGC 60.318 50.000 5.73 0.00 0.00 6.86
60 61 1.268539 ACAAAAAGCAGAAAGGACGCG 60.269 47.619 3.53 3.53 0.00 6.01
61 62 2.492019 ACAAAAAGCAGAAAGGACGC 57.508 45.000 0.00 0.00 0.00 5.19
62 63 3.541711 CGTACAAAAAGCAGAAAGGACG 58.458 45.455 0.00 0.00 0.00 4.79
63 64 3.297472 GCGTACAAAAAGCAGAAAGGAC 58.703 45.455 0.00 0.00 32.19 3.85
64 65 2.292292 GGCGTACAAAAAGCAGAAAGGA 59.708 45.455 0.00 0.00 33.76 3.36
65 66 2.661594 GGCGTACAAAAAGCAGAAAGG 58.338 47.619 0.00 0.00 33.76 3.11
66 67 2.032377 TCGGCGTACAAAAAGCAGAAAG 60.032 45.455 6.85 0.00 34.28 2.62
67 68 1.941294 TCGGCGTACAAAAAGCAGAAA 59.059 42.857 6.85 0.00 34.28 2.52
68 69 1.584175 TCGGCGTACAAAAAGCAGAA 58.416 45.000 6.85 0.00 34.28 3.02
69 70 1.262151 GTTCGGCGTACAAAAAGCAGA 59.738 47.619 11.92 0.00 35.27 4.26
70 71 1.263217 AGTTCGGCGTACAAAAAGCAG 59.737 47.619 18.71 0.00 33.76 4.24
71 72 1.301423 AGTTCGGCGTACAAAAAGCA 58.699 45.000 18.71 0.00 33.76 3.91
72 73 2.394545 AAGTTCGGCGTACAAAAAGC 57.605 45.000 18.71 0.00 0.00 3.51
73 74 4.344448 TGAAAAGTTCGGCGTACAAAAAG 58.656 39.130 18.71 0.00 0.00 2.27
74 75 4.352600 TGAAAAGTTCGGCGTACAAAAA 57.647 36.364 18.71 0.00 0.00 1.94
75 76 4.555348 ATGAAAAGTTCGGCGTACAAAA 57.445 36.364 18.71 0.00 0.00 2.44
76 77 4.529446 GAATGAAAAGTTCGGCGTACAAA 58.471 39.130 18.71 0.00 0.00 2.83
77 78 3.363182 CGAATGAAAAGTTCGGCGTACAA 60.363 43.478 18.71 0.00 43.36 2.41
78 79 2.156117 CGAATGAAAAGTTCGGCGTACA 59.844 45.455 18.71 0.00 43.36 2.90
79 80 2.409378 TCGAATGAAAAGTTCGGCGTAC 59.591 45.455 8.72 8.72 46.14 3.67
80 81 2.674954 TCGAATGAAAAGTTCGGCGTA 58.325 42.857 6.85 0.00 46.14 4.42
81 82 1.504359 TCGAATGAAAAGTTCGGCGT 58.496 45.000 6.85 0.00 46.14 5.68
82 83 2.694043 GATCGAATGAAAAGTTCGGCG 58.306 47.619 0.00 0.00 46.14 6.46
83 84 2.694043 CGATCGAATGAAAAGTTCGGC 58.306 47.619 10.26 1.55 46.14 5.54
84 85 2.536928 GGCGATCGAATGAAAAGTTCGG 60.537 50.000 21.57 0.00 46.14 4.30
85 86 5.047764 TCGGCGATCGAATGAAAAGTTCG 62.048 47.826 21.57 2.15 45.86 3.95
86 87 2.347452 TCGGCGATCGAATGAAAAGTTC 59.653 45.455 21.57 0.00 45.86 3.01
87 88 2.343101 TCGGCGATCGAATGAAAAGTT 58.657 42.857 21.57 0.00 45.86 2.66
88 89 2.004583 TCGGCGATCGAATGAAAAGT 57.995 45.000 21.57 0.00 45.86 2.66
98 99 2.324477 GCCACAATTCGGCGATCG 59.676 61.111 11.76 11.69 40.35 3.69
103 104 2.271821 AATAAACGCCACAATTCGGC 57.728 45.000 5.47 5.47 46.62 5.54
104 105 3.984633 ACAAAATAAACGCCACAATTCGG 59.015 39.130 0.00 0.00 0.00 4.30
105 106 4.677378 TCACAAAATAAACGCCACAATTCG 59.323 37.500 0.00 0.00 0.00 3.34
106 107 5.388371 GCTCACAAAATAAACGCCACAATTC 60.388 40.000 0.00 0.00 0.00 2.17
107 108 4.447389 GCTCACAAAATAAACGCCACAATT 59.553 37.500 0.00 0.00 0.00 2.32
108 109 3.987220 GCTCACAAAATAAACGCCACAAT 59.013 39.130 0.00 0.00 0.00 2.71
109 110 3.376540 GCTCACAAAATAAACGCCACAA 58.623 40.909 0.00 0.00 0.00 3.33
110 111 2.603412 CGCTCACAAAATAAACGCCACA 60.603 45.455 0.00 0.00 0.00 4.17
111 112 1.976045 CGCTCACAAAATAAACGCCAC 59.024 47.619 0.00 0.00 0.00 5.01
112 113 1.068885 CCGCTCACAAAATAAACGCCA 60.069 47.619 0.00 0.00 0.00 5.69
113 114 1.198178 TCCGCTCACAAAATAAACGCC 59.802 47.619 0.00 0.00 0.00 5.68
114 115 2.604969 TCCGCTCACAAAATAAACGC 57.395 45.000 0.00 0.00 0.00 4.84
115 116 6.799925 AGTTATTTCCGCTCACAAAATAAACG 59.200 34.615 0.00 0.00 36.89 3.60
116 117 9.058424 GTAGTTATTTCCGCTCACAAAATAAAC 57.942 33.333 0.00 0.00 36.89 2.01
117 118 7.958567 CGTAGTTATTTCCGCTCACAAAATAAA 59.041 33.333 0.00 0.00 36.89 1.40
118 119 7.118101 ACGTAGTTATTTCCGCTCACAAAATAA 59.882 33.333 0.00 0.00 37.78 1.40
119 120 6.591062 ACGTAGTTATTTCCGCTCACAAAATA 59.409 34.615 0.00 0.00 37.78 1.40
120 121 5.410439 ACGTAGTTATTTCCGCTCACAAAAT 59.590 36.000 0.00 0.00 37.78 1.82
121 122 4.751098 ACGTAGTTATTTCCGCTCACAAAA 59.249 37.500 0.00 0.00 37.78 2.44
122 123 4.309099 ACGTAGTTATTTCCGCTCACAAA 58.691 39.130 0.00 0.00 37.78 2.83
123 124 3.916761 ACGTAGTTATTTCCGCTCACAA 58.083 40.909 0.00 0.00 37.78 3.33
124 125 3.581024 ACGTAGTTATTTCCGCTCACA 57.419 42.857 0.00 0.00 37.78 3.58
139 140 1.246970 CGCGGCAAATTCAAACGTAG 58.753 50.000 0.00 0.00 0.00 3.51
140 141 0.110147 CCGCGGCAAATTCAAACGTA 60.110 50.000 14.67 0.00 0.00 3.57
141 142 1.371145 CCGCGGCAAATTCAAACGT 60.371 52.632 14.67 0.00 0.00 3.99
142 143 2.085844 CCCGCGGCAAATTCAAACG 61.086 57.895 22.85 0.00 0.00 3.60
143 144 0.598942 AACCCGCGGCAAATTCAAAC 60.599 50.000 22.85 0.00 0.00 2.93
144 145 0.598680 CAACCCGCGGCAAATTCAAA 60.599 50.000 22.85 0.00 0.00 2.69
145 146 1.006805 CAACCCGCGGCAAATTCAA 60.007 52.632 22.85 0.00 0.00 2.69
146 147 2.647875 CAACCCGCGGCAAATTCA 59.352 55.556 22.85 0.00 0.00 2.57
147 148 2.126110 CCAACCCGCGGCAAATTC 60.126 61.111 22.85 0.00 0.00 2.17
148 149 3.690280 CCCAACCCGCGGCAAATT 61.690 61.111 22.85 8.07 0.00 1.82
178 179 3.488467 CTAGCTCCCAGCCATGCCC 62.488 68.421 0.00 0.00 43.77 5.36
179 180 2.112718 CTAGCTCCCAGCCATGCC 59.887 66.667 0.00 0.00 43.77 4.40
180 181 2.112718 CCTAGCTCCCAGCCATGC 59.887 66.667 0.00 0.00 43.77 4.06
181 182 1.449353 GACCTAGCTCCCAGCCATG 59.551 63.158 0.00 0.00 43.77 3.66
182 183 2.136878 CGACCTAGCTCCCAGCCAT 61.137 63.158 0.00 0.00 43.77 4.40
183 184 2.759973 CGACCTAGCTCCCAGCCA 60.760 66.667 0.00 0.00 43.77 4.75
184 185 4.228567 GCGACCTAGCTCCCAGCC 62.229 72.222 0.00 0.00 43.77 4.85
185 186 4.228567 GGCGACCTAGCTCCCAGC 62.229 72.222 0.00 0.00 42.84 4.85
203 204 2.122813 ACTAGATCGGCCCCTGGG 60.123 66.667 5.50 5.50 38.57 4.45
204 205 3.142393 CACTAGATCGGCCCCTGG 58.858 66.667 0.00 0.00 0.00 4.45
205 206 2.423446 GCACTAGATCGGCCCCTG 59.577 66.667 0.00 0.00 0.00 4.45
206 207 2.844839 GGCACTAGATCGGCCCCT 60.845 66.667 0.00 0.00 41.90 4.79
207 208 4.301027 CGGCACTAGATCGGCCCC 62.301 72.222 12.89 0.00 44.90 5.80
208 209 4.301027 CCGGCACTAGATCGGCCC 62.301 72.222 12.89 3.29 44.90 5.80
209 210 2.973180 GAACCGGCACTAGATCGGCC 62.973 65.000 17.90 13.47 46.87 6.13
210 211 1.591863 GAACCGGCACTAGATCGGC 60.592 63.158 17.90 8.47 46.87 5.54
212 213 1.944676 GCGAACCGGCACTAGATCG 60.945 63.158 0.00 1.64 0.00 3.69
213 214 4.014065 GCGAACCGGCACTAGATC 57.986 61.111 0.00 0.00 0.00 2.75
232 233 3.440415 GAAAAAGAGCGGCCCGGG 61.440 66.667 19.09 19.09 0.00 5.73
233 234 3.799755 CGAAAAAGAGCGGCCCGG 61.800 66.667 4.77 0.00 0.00 5.73
234 235 3.799755 CCGAAAAAGAGCGGCCCG 61.800 66.667 0.00 0.00 41.17 6.13
240 241 3.056328 AGGGCGCCGAAAAAGAGC 61.056 61.111 22.54 2.36 0.00 4.09
241 242 2.690778 CCAGGGCGCCGAAAAAGAG 61.691 63.158 22.54 3.24 0.00 2.85
242 243 2.671619 CCAGGGCGCCGAAAAAGA 60.672 61.111 22.54 0.00 0.00 2.52
243 244 3.747976 CCCAGGGCGCCGAAAAAG 61.748 66.667 22.54 5.42 0.00 2.27
260 261 4.785453 CTCCAGCCGTTCAGCCCC 62.785 72.222 0.00 0.00 0.00 5.80
261 262 3.036429 ATCTCCAGCCGTTCAGCCC 62.036 63.158 0.00 0.00 0.00 5.19
262 263 1.817099 CATCTCCAGCCGTTCAGCC 60.817 63.158 0.00 0.00 0.00 4.85
263 264 1.817099 CCATCTCCAGCCGTTCAGC 60.817 63.158 0.00 0.00 0.00 4.26
264 265 0.460987 GACCATCTCCAGCCGTTCAG 60.461 60.000 0.00 0.00 0.00 3.02
265 266 0.904865 AGACCATCTCCAGCCGTTCA 60.905 55.000 0.00 0.00 0.00 3.18
266 267 1.112113 TAGACCATCTCCAGCCGTTC 58.888 55.000 0.00 0.00 0.00 3.95
267 268 1.482593 CTTAGACCATCTCCAGCCGTT 59.517 52.381 0.00 0.00 0.00 4.44
268 269 1.115467 CTTAGACCATCTCCAGCCGT 58.885 55.000 0.00 0.00 0.00 5.68
269 270 0.390860 CCTTAGACCATCTCCAGCCG 59.609 60.000 0.00 0.00 0.00 5.52
270 271 1.414550 GACCTTAGACCATCTCCAGCC 59.585 57.143 0.00 0.00 0.00 4.85
271 272 2.393646 AGACCTTAGACCATCTCCAGC 58.606 52.381 0.00 0.00 0.00 4.85
272 273 4.148838 CCTAGACCTTAGACCATCTCCAG 58.851 52.174 0.00 0.00 0.00 3.86
273 274 3.532232 ACCTAGACCTTAGACCATCTCCA 59.468 47.826 0.00 0.00 0.00 3.86
274 275 4.187506 ACCTAGACCTTAGACCATCTCC 57.812 50.000 0.00 0.00 0.00 3.71
275 276 4.342665 CCAACCTAGACCTTAGACCATCTC 59.657 50.000 0.00 0.00 0.00 2.75
276 277 4.264895 ACCAACCTAGACCTTAGACCATCT 60.265 45.833 0.00 0.00 0.00 2.90
277 278 4.031611 ACCAACCTAGACCTTAGACCATC 58.968 47.826 0.00 0.00 0.00 3.51
278 279 3.775316 CACCAACCTAGACCTTAGACCAT 59.225 47.826 0.00 0.00 0.00 3.55
279 280 3.170717 CACCAACCTAGACCTTAGACCA 58.829 50.000 0.00 0.00 0.00 4.02
280 281 2.093606 GCACCAACCTAGACCTTAGACC 60.094 54.545 0.00 0.00 0.00 3.85
281 282 2.093606 GGCACCAACCTAGACCTTAGAC 60.094 54.545 0.00 0.00 0.00 2.59
282 283 2.185387 GGCACCAACCTAGACCTTAGA 58.815 52.381 0.00 0.00 0.00 2.10
288 289 0.977395 ACTCAGGCACCAACCTAGAC 59.023 55.000 0.00 0.00 38.26 2.59
291 292 1.267121 GAGACTCAGGCACCAACCTA 58.733 55.000 0.00 0.00 38.26 3.08
365 366 5.266733 TCATTTCTGCTCTTTGCTTTTGT 57.733 34.783 0.00 0.00 43.37 2.83
378 379 9.305925 TCTTTCTTTTCTTTCTTTCATTTCTGC 57.694 29.630 0.00 0.00 0.00 4.26
453 454 7.268586 TGTTTTGTTTTCTTTGCTTGGCTATA 58.731 30.769 0.00 0.00 0.00 1.31
455 456 5.482908 TGTTTTGTTTTCTTTGCTTGGCTA 58.517 33.333 0.00 0.00 0.00 3.93
457 458 4.676849 TGTTTTGTTTTCTTTGCTTGGC 57.323 36.364 0.00 0.00 0.00 4.52
472 473 6.158598 ACTGCTAGCCATATTGTTTGTTTTG 58.841 36.000 13.29 0.00 0.00 2.44
568 569 7.333672 ACTGGAAACTGTAGATTAAATTCGACC 59.666 37.037 0.00 0.00 41.13 4.79
576 577 8.318412 TGAATAGCACTGGAAACTGTAGATTAA 58.682 33.333 0.00 0.00 40.96 1.40
583 584 7.759489 TTAATTGAATAGCACTGGAAACTGT 57.241 32.000 0.00 0.00 44.07 3.55
599 600 5.923204 ACAAAGCCACCACATTTAATTGAA 58.077 33.333 4.42 0.00 0.00 2.69
625 627 8.210265 AGAAATGGAGATGAAAGATCCTAAGAC 58.790 37.037 0.00 0.00 34.04 3.01
661 663 9.483916 TGAAATCACATATAACATACCTTACGG 57.516 33.333 0.00 0.00 0.00 4.02
674 676 8.704668 ACACTCACACCTATGAAATCACATATA 58.295 33.333 0.00 0.00 33.21 0.86
675 677 7.568349 ACACTCACACCTATGAAATCACATAT 58.432 34.615 0.00 0.00 33.21 1.78
676 678 6.946340 ACACTCACACCTATGAAATCACATA 58.054 36.000 0.00 0.00 0.00 2.29
677 679 5.809001 ACACTCACACCTATGAAATCACAT 58.191 37.500 0.00 0.00 0.00 3.21
682 684 6.407202 GTTCCTACACTCACACCTATGAAAT 58.593 40.000 0.00 0.00 0.00 2.17
691 693 2.503920 ACACGTTCCTACACTCACAC 57.496 50.000 0.00 0.00 0.00 3.82
705 707 0.524862 GACCCTCGTCACATACACGT 59.475 55.000 0.00 0.00 38.99 4.49
715 717 0.953960 ACAAAATGCGGACCCTCGTC 60.954 55.000 0.00 0.00 38.38 4.20
720 722 0.956902 ACGGTACAAAATGCGGACCC 60.957 55.000 0.00 0.00 0.00 4.46
726 728 2.919666 AGATGCACGGTACAAAATGC 57.080 45.000 0.00 0.00 38.59 3.56
801 806 1.620739 GGATGTGAGGAGGAGCAGCA 61.621 60.000 0.00 0.00 0.00 4.41
805 810 1.267574 TGGTGGATGTGAGGAGGAGC 61.268 60.000 0.00 0.00 0.00 4.70
827 832 4.090090 ACGACAGGAGAATAGATATGGGG 58.910 47.826 0.00 0.00 0.00 4.96
862 868 1.758514 CAAGCTAGCTCGGAGGGGA 60.759 63.158 19.65 0.00 0.00 4.81
945 951 1.140375 GTGTACGACGGGATGGACC 59.860 63.158 0.00 0.00 38.08 4.46
960 967 2.834549 ACCTCGATGGAAGAAGATGTGT 59.165 45.455 7.76 0.00 39.71 3.72
984 991 1.103398 CCATGAATCGGTGGAAGGCC 61.103 60.000 0.00 0.00 37.72 5.19
995 1002 2.098293 GTGGTGGACGCCATGAATC 58.902 57.895 7.97 0.00 41.08 2.52
1685 1695 2.342279 CCGTCTTGTCGCCTTCCA 59.658 61.111 0.00 0.00 0.00 3.53
1780 1790 4.438148 TCAGACAGAGAGAGAGATACGTG 58.562 47.826 0.00 0.00 0.00 4.49
2187 2220 0.109342 ATTCCTTGGCTAGCGATGGG 59.891 55.000 25.09 18.21 0.00 4.00
2329 2362 5.336849 GCCTATTCATCCGTAAGTCTAGCAT 60.337 44.000 0.00 0.00 0.00 3.79
2460 2559 8.529476 AGGAACACAACGTAATAACTAAGATCT 58.471 33.333 0.00 0.00 0.00 2.75
2577 2677 8.703604 TCGATTATTACAAAGAGAAGACCAAG 57.296 34.615 0.00 0.00 0.00 3.61
2988 3088 8.909708 TTTCTTAATTGGTTCAGCATAAATCG 57.090 30.769 0.00 0.00 0.00 3.34
3017 3118 5.278061 TGTCCACCTAGCCTCTATTAGTTT 58.722 41.667 0.00 0.00 0.00 2.66
3367 3481 7.760131 ATGATTTTGGCTTAAATGAATGTCG 57.240 32.000 3.47 0.00 0.00 4.35
3435 3549 3.635373 GGGTCCATATAGTCGTGAACTCA 59.365 47.826 0.00 0.00 39.55 3.41
3463 3583 5.889219 GTACTGGCTTACTAGTACTTCCAC 58.111 45.833 0.00 0.00 43.60 4.02
3535 3656 1.000955 GCTCCGTATGGTCCATAGTGG 59.999 57.143 18.43 18.43 39.43 4.00
3543 3664 3.063997 CACTCATTTTGCTCCGTATGGTC 59.936 47.826 0.00 0.00 36.30 4.02
3546 3667 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3550 3671 5.569059 GTGTAAATTCACTCATTTTGCTCCG 59.431 40.000 0.00 0.00 35.68 4.63
3574 3697 7.978414 ACGGATGTATATAGATGCATTTCAGAG 59.022 37.037 11.19 0.00 38.38 3.35
3578 3701 9.534565 ACATACGGATGTATATAGATGCATTTC 57.465 33.333 12.79 0.00 44.77 2.17
3637 3760 8.202137 CGATTAAATACTCCCTCTGTTCCTAAA 58.798 37.037 0.00 0.00 0.00 1.85
3923 4082 7.040478 TGTCTTACATGAACCTTTTGATTCCTG 60.040 37.037 0.00 0.00 0.00 3.86
4078 4237 1.930817 GCAGTACGCTGTATGATCCGG 60.931 57.143 0.00 0.00 44.32 5.14
4088 4247 2.730672 GGCTCGTTGCAGTACGCTG 61.731 63.158 6.05 3.31 45.15 5.18
4101 4260 5.828747 AGATCATTTCATCAATTTGGCTCG 58.171 37.500 0.00 0.00 0.00 5.03
4245 4404 0.042188 CGTTTAGCCATGAATCGCCG 60.042 55.000 0.00 0.00 0.00 6.46
4246 4405 0.317020 GCGTTTAGCCATGAATCGCC 60.317 55.000 8.94 0.00 38.47 5.54
4296 4458 1.138568 TTTTGGAACGGGGGAGTACA 58.861 50.000 0.00 0.00 0.00 2.90
4322 4484 2.634600 TGCACTAAAACCACGACAGTT 58.365 42.857 0.00 0.00 0.00 3.16
4325 4487 2.634600 AGTTGCACTAAAACCACGACA 58.365 42.857 0.00 0.00 0.00 4.35
4326 4488 3.359654 CAAGTTGCACTAAAACCACGAC 58.640 45.455 0.00 0.00 0.00 4.34
4341 4504 4.083590 GCTAGCTTTGAGTTCTCCAAGTTG 60.084 45.833 7.70 0.00 0.00 3.16
4344 4507 2.670414 CGCTAGCTTTGAGTTCTCCAAG 59.330 50.000 13.93 8.64 0.00 3.61
4366 4529 3.455469 GGCAGGCCATCCACTTGC 61.455 66.667 5.01 3.44 35.81 4.01
4415 4578 6.092670 GCTTTTAGCCATGAATCGCTGATATA 59.907 38.462 4.64 0.00 36.53 0.86
4446 4609 3.431673 TCCTGCACAATCACATACCAA 57.568 42.857 0.00 0.00 0.00 3.67
4510 4967 9.787532 TCTGAACTTTTGTCATTTTCAAGTAAG 57.212 29.630 0.00 0.00 0.00 2.34
4586 5047 3.350833 AGTGACAAGCAATGATCCCTTC 58.649 45.455 0.00 0.00 0.00 3.46
4587 5048 3.446442 AGTGACAAGCAATGATCCCTT 57.554 42.857 0.00 0.00 0.00 3.95
4712 5173 1.363443 CACCACGCAAAGGCATTGT 59.637 52.632 4.23 0.00 41.32 2.71
4716 5177 3.215568 CACCACCACGCAAAGGCA 61.216 61.111 0.00 0.00 41.24 4.75
4732 5193 2.530151 AGGAAGTGGCCTGCCTCA 60.530 61.111 9.97 0.00 44.30 3.86
4743 5204 2.593956 GGGTGGCGAAGGAGGAAGT 61.594 63.158 0.00 0.00 0.00 3.01
4828 5312 2.690510 GGGGAGCAAGAGAGCCCT 60.691 66.667 0.00 0.00 40.51 5.19
4984 5470 1.153745 CATAGCTAGATCCGGCCGC 60.154 63.158 22.85 6.34 0.00 6.53
4986 5472 0.533032 GACCATAGCTAGATCCGGCC 59.467 60.000 0.00 0.00 0.00 6.13
5000 5486 3.009115 CCACCCACCTCCGACCAT 61.009 66.667 0.00 0.00 0.00 3.55
5001 5487 4.567597 ACCACCCACCTCCGACCA 62.568 66.667 0.00 0.00 0.00 4.02
5004 5490 3.238497 CACACCACCCACCTCCGA 61.238 66.667 0.00 0.00 0.00 4.55
5022 5508 3.465403 CGGCCACAGGAGCTAGCT 61.465 66.667 19.45 19.45 0.00 3.32
5037 5523 0.999406 CGCTACCACATGAAGAACGG 59.001 55.000 0.00 0.00 0.00 4.44
5047 5533 2.031919 CTGCCAACCGCTACCACA 59.968 61.111 0.00 0.00 38.78 4.17
5079 5565 1.900981 CCATGAACAACCGGCACCA 60.901 57.895 0.00 0.00 0.00 4.17
5081 5567 1.285641 CACCATGAACAACCGGCAC 59.714 57.895 0.00 0.00 0.00 5.01
5091 5577 2.358125 CGACCACGCCACCATGAA 60.358 61.111 0.00 0.00 0.00 2.57
5128 5614 2.037367 CCGAGAGAGGGGGACACA 59.963 66.667 0.00 0.00 0.00 3.72
5131 5617 3.151022 CTGCCGAGAGAGGGGGAC 61.151 72.222 0.00 0.00 0.00 4.46
5144 5630 3.136123 ATGACATGCGTGCCTGCC 61.136 61.111 5.64 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.