Multiple sequence alignment - TraesCS6B01G021800

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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 TraesCS6B01G021800 chr6B 100.000 3164 0 0 1 3164 13819914 13816751 0.000000e+00 5843.0
1 TraesCS6B01G021800 chr6B 82.804 1227 182 23 953 2172 14340418 14341622 0.000000e+00 1070.0
2 TraesCS6B01G021800 chr6B 78.542 1221 207 39 964 2173 40658517 40657341 0.000000e+00 752.0
3 TraesCS6B01G021800 chr6B 77.291 1233 255 23 955 2175 13951683 13950464 0.000000e+00 702.0
4 TraesCS6B01G021800 chr6D 86.051 2079 183 33 1127 3164 7404832 7402820 0.000000e+00 2134.0
5 TraesCS6B01G021800 chr6D 86.430 1238 148 19 939 2169 7901214 7902438 0.000000e+00 1338.0
6 TraesCS6B01G021800 chr6D 80.528 1212 206 23 968 2169 7961854 7963045 0.000000e+00 904.0
7 TraesCS6B01G021800 chr6D 75.693 1226 242 43 977 2177 7999085 7997891 2.130000e-156 562.0
8 TraesCS6B01G021800 chr6D 76.245 783 167 18 1395 2169 14518038 14518809 6.360000e-107 398.0
9 TraesCS6B01G021800 chr6D 74.605 760 168 20 1421 2169 8802445 8803190 8.520000e-81 311.0
10 TraesCS6B01G021800 chr6D 75.000 664 157 9 1518 2177 8568296 8567638 6.630000e-77 298.0
11 TraesCS6B01G021800 chr6A 88.870 1195 105 13 823 2017 7224885 7223719 0.000000e+00 1445.0
12 TraesCS6B01G021800 chr6A 84.904 1199 146 24 977 2169 8174960 8176129 0.000000e+00 1179.0
13 TraesCS6B01G021800 chr6A 84.404 981 138 11 1021 1991 7300874 7299899 0.000000e+00 950.0
14 TraesCS6B01G021800 chr6A 76.236 1052 235 13 1130 2177 9355310 9356350 7.720000e-151 544.0
15 TraesCS6B01G021800 chr6A 82.890 602 61 19 1988 2566 7299770 7299188 1.310000e-138 503.0
16 TraesCS6B01G021800 chr6A 86.811 417 34 13 308 717 7225466 7225064 2.240000e-121 446.0
17 TraesCS6B01G021800 chr6A 90.323 341 25 6 2751 3090 7297892 7297559 1.040000e-119 440.0
18 TraesCS6B01G021800 chr6A 81.068 206 21 8 2100 2287 7223691 7223486 7.070000e-32 148.0
19 TraesCS6B01G021800 chr7D 83.296 1353 181 20 819 2164 568371706 568370392 0.000000e+00 1205.0
20 TraesCS6B01G021800 chr7D 90.071 423 30 7 308 728 568372152 568371740 3.590000e-149 538.0
21 TraesCS6B01G021800 chr7B 83.161 1354 178 27 819 2164 623951496 623950185 0.000000e+00 1192.0
22 TraesCS6B01G021800 chr7B 87.238 478 44 8 308 774 623954891 623954420 2.160000e-146 529.0
23 TraesCS6B01G021800 chr7B 97.255 255 6 1 1 254 504201768 504202022 6.270000e-117 431.0
24 TraesCS6B01G021800 chr7A 82.466 1249 191 11 918 2164 657024889 657023667 0.000000e+00 1068.0
25 TraesCS6B01G021800 chr7A 88.621 457 34 10 317 763 657025477 657025029 9.980000e-150 540.0
26 TraesCS6B01G021800 chr7A 89.571 163 9 3 782 938 657025059 657024899 1.920000e-47 200.0
27 TraesCS6B01G021800 chr1B 75.417 1200 266 26 997 2184 662153028 662154210 3.570000e-154 555.0
28 TraesCS6B01G021800 chr1B 87.342 79 7 2 2557 2633 48090560 48090483 1.560000e-13 87.9
29 TraesCS6B01G021800 chr2B 99.216 255 2 0 1 255 652849565 652849819 8.000000e-126 460.0
30 TraesCS6B01G021800 chr2B 72.796 1191 292 27 996 2176 709569764 709568596 2.980000e-100 375.0
31 TraesCS6B01G021800 chr1A 98.828 256 3 0 1 256 320479480 320479735 1.030000e-124 457.0
32 TraesCS6B01G021800 chr1A 96.525 259 8 1 1 258 63763446 63763704 8.110000e-116 427.0
33 TraesCS6B01G021800 chr4A 98.819 254 3 0 1 254 683251758 683252011 1.340000e-123 453.0
34 TraesCS6B01G021800 chr3B 97.647 255 5 1 1 254 546831127 546831381 1.350000e-118 436.0
35 TraesCS6B01G021800 chr5A 97.255 255 6 1 1 254 346306551 346306297 6.270000e-117 431.0
36 TraesCS6B01G021800 chr4B 97.255 255 6 1 1 254 139742878 139742624 6.270000e-117 431.0
37 TraesCS6B01G021800 chr2A 97.255 255 6 1 1 254 672537106 672536852 6.270000e-117 431.0
38 TraesCS6B01G021800 chr3D 78.673 211 44 1 1974 2184 582880863 582881072 4.260000e-29 139.0
39 TraesCS6B01G021800 chr3D 84.091 88 9 4 2210 2292 549721821 549721734 2.620000e-11 80.5
40 TraesCS6B01G021800 chr3A 85.882 85 7 4 2210 2289 686900169 686900085 5.620000e-13 86.1


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 TraesCS6B01G021800 chr6B 13816751 13819914 3163 True 5843.000000 5843 100.000000 1 3164 1 chr6B.!!$R1 3163
1 TraesCS6B01G021800 chr6B 14340418 14341622 1204 False 1070.000000 1070 82.804000 953 2172 1 chr6B.!!$F1 1219
2 TraesCS6B01G021800 chr6B 40657341 40658517 1176 True 752.000000 752 78.542000 964 2173 1 chr6B.!!$R3 1209
3 TraesCS6B01G021800 chr6B 13950464 13951683 1219 True 702.000000 702 77.291000 955 2175 1 chr6B.!!$R2 1220
4 TraesCS6B01G021800 chr6D 7402820 7404832 2012 True 2134.000000 2134 86.051000 1127 3164 1 chr6D.!!$R1 2037
5 TraesCS6B01G021800 chr6D 7901214 7902438 1224 False 1338.000000 1338 86.430000 939 2169 1 chr6D.!!$F1 1230
6 TraesCS6B01G021800 chr6D 7961854 7963045 1191 False 904.000000 904 80.528000 968 2169 1 chr6D.!!$F2 1201
7 TraesCS6B01G021800 chr6D 7997891 7999085 1194 True 562.000000 562 75.693000 977 2177 1 chr6D.!!$R2 1200
8 TraesCS6B01G021800 chr6D 14518038 14518809 771 False 398.000000 398 76.245000 1395 2169 1 chr6D.!!$F4 774
9 TraesCS6B01G021800 chr6D 8802445 8803190 745 False 311.000000 311 74.605000 1421 2169 1 chr6D.!!$F3 748
10 TraesCS6B01G021800 chr6D 8567638 8568296 658 True 298.000000 298 75.000000 1518 2177 1 chr6D.!!$R3 659
11 TraesCS6B01G021800 chr6A 8174960 8176129 1169 False 1179.000000 1179 84.904000 977 2169 1 chr6A.!!$F1 1192
12 TraesCS6B01G021800 chr6A 7223486 7225466 1980 True 679.666667 1445 85.583000 308 2287 3 chr6A.!!$R1 1979
13 TraesCS6B01G021800 chr6A 7297559 7300874 3315 True 631.000000 950 85.872333 1021 3090 3 chr6A.!!$R2 2069
14 TraesCS6B01G021800 chr6A 9355310 9356350 1040 False 544.000000 544 76.236000 1130 2177 1 chr6A.!!$F2 1047
15 TraesCS6B01G021800 chr7D 568370392 568372152 1760 True 871.500000 1205 86.683500 308 2164 2 chr7D.!!$R1 1856
16 TraesCS6B01G021800 chr7B 623950185 623954891 4706 True 860.500000 1192 85.199500 308 2164 2 chr7B.!!$R1 1856
17 TraesCS6B01G021800 chr7A 657023667 657025477 1810 True 602.666667 1068 86.886000 317 2164 3 chr7A.!!$R1 1847
18 TraesCS6B01G021800 chr1B 662153028 662154210 1182 False 555.000000 555 75.417000 997 2184 1 chr1B.!!$F1 1187
19 TraesCS6B01G021800 chr2B 709568596 709569764 1168 True 375.000000 375 72.796000 996 2176 1 chr2B.!!$R1 1180

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
226 227 0.041535 AATCTGCTTCCAATGCCCCA 59.958 50.0 0.0 0.0 0.00 4.96 F
228 229 0.041535 TCTGCTTCCAATGCCCCAAT 59.958 50.0 0.0 0.0 0.00 3.16 F
276 277 0.104487 TGGTCGCCGTCTTTGTGTAA 59.896 50.0 0.0 0.0 0.00 2.41 F
289 290 0.249699 TGTGTAAGACGGTGTGCTGG 60.250 55.0 0.0 0.0 0.00 4.85 F
1692 4718 0.321653 AAGCTTTAGGTGTGCCTCGG 60.322 55.0 0.0 0.0 45.64 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 4605 1.946768 GCCAATATCGCAAGCACCTAA 59.053 47.619 0.00 0.00 37.18 2.69 R
1692 4718 2.124403 CTGCACATCCCAGAGCCC 60.124 66.667 0.00 0.00 32.03 5.19 R
1821 4847 2.380064 TCAGCACAAATGGACCCTTT 57.620 45.000 0.00 0.00 0.00 3.11 R
2011 5169 2.443416 TGCATAGTAGGACGTGTCACT 58.557 47.619 0.00 0.00 0.00 3.41 R
2770 7148 0.321919 ACTGGTGATGCGCATTCTGT 60.322 50.000 26.12 21.23 0.00 3.41 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
50 51 4.135153 CGGCCTCGTCCCAGTCAG 62.135 72.222 0.00 0.00 0.00 3.51
51 52 4.459089 GGCCTCGTCCCAGTCAGC 62.459 72.222 0.00 0.00 0.00 4.26
52 53 4.803426 GCCTCGTCCCAGTCAGCG 62.803 72.222 0.00 0.00 0.00 5.18
53 54 4.803426 CCTCGTCCCAGTCAGCGC 62.803 72.222 0.00 0.00 0.00 5.92
54 55 4.803426 CTCGTCCCAGTCAGCGCC 62.803 72.222 2.29 0.00 0.00 6.53
57 58 4.767255 GTCCCAGTCAGCGCCCAG 62.767 72.222 2.29 0.00 0.00 4.45
59 60 4.767255 CCCAGTCAGCGCCCAGTC 62.767 72.222 2.29 0.00 0.00 3.51
60 61 4.007644 CCAGTCAGCGCCCAGTCA 62.008 66.667 2.29 0.00 0.00 3.41
61 62 2.433838 CAGTCAGCGCCCAGTCAG 60.434 66.667 2.29 0.00 0.00 3.51
62 63 4.385405 AGTCAGCGCCCAGTCAGC 62.385 66.667 2.29 0.00 0.00 4.26
111 112 4.660938 GGCCCAACCGGTCAGCTT 62.661 66.667 8.04 0.00 35.67 3.74
112 113 2.597510 GCCCAACCGGTCAGCTTT 60.598 61.111 8.04 0.00 0.00 3.51
113 114 2.200337 GCCCAACCGGTCAGCTTTT 61.200 57.895 8.04 0.00 0.00 2.27
114 115 1.956802 CCCAACCGGTCAGCTTTTC 59.043 57.895 8.04 0.00 0.00 2.29
115 116 0.537371 CCCAACCGGTCAGCTTTTCT 60.537 55.000 8.04 0.00 0.00 2.52
116 117 0.593128 CCAACCGGTCAGCTTTTCTG 59.407 55.000 8.04 0.00 44.21 3.02
117 118 1.308998 CAACCGGTCAGCTTTTCTGT 58.691 50.000 8.04 0.00 43.32 3.41
118 119 1.264288 CAACCGGTCAGCTTTTCTGTC 59.736 52.381 8.04 0.00 43.32 3.51
119 120 0.468226 ACCGGTCAGCTTTTCTGTCA 59.532 50.000 0.00 0.00 43.32 3.58
120 121 1.134220 ACCGGTCAGCTTTTCTGTCAA 60.134 47.619 0.00 0.00 43.32 3.18
121 122 2.154462 CCGGTCAGCTTTTCTGTCAAT 58.846 47.619 0.00 0.00 43.32 2.57
122 123 3.244422 ACCGGTCAGCTTTTCTGTCAATA 60.244 43.478 0.00 0.00 43.32 1.90
123 124 3.125316 CCGGTCAGCTTTTCTGTCAATAC 59.875 47.826 0.00 0.00 43.32 1.89
124 125 3.181530 CGGTCAGCTTTTCTGTCAATACG 60.182 47.826 0.00 0.00 43.32 3.06
125 126 3.746492 GGTCAGCTTTTCTGTCAATACGT 59.254 43.478 0.00 0.00 43.32 3.57
126 127 4.927425 GGTCAGCTTTTCTGTCAATACGTA 59.073 41.667 0.00 0.00 43.32 3.57
127 128 5.581085 GGTCAGCTTTTCTGTCAATACGTAT 59.419 40.000 1.14 1.14 43.32 3.06
128 129 6.755141 GGTCAGCTTTTCTGTCAATACGTATA 59.245 38.462 8.83 0.00 43.32 1.47
129 130 7.277098 GGTCAGCTTTTCTGTCAATACGTATAA 59.723 37.037 8.83 0.00 43.32 0.98
130 131 8.653338 GTCAGCTTTTCTGTCAATACGTATAAA 58.347 33.333 8.83 1.72 43.32 1.40
131 132 9.210329 TCAGCTTTTCTGTCAATACGTATAAAA 57.790 29.630 8.83 9.53 43.32 1.52
132 133 9.262472 CAGCTTTTCTGTCAATACGTATAAAAC 57.738 33.333 8.83 8.04 38.02 2.43
133 134 8.995220 AGCTTTTCTGTCAATACGTATAAAACA 58.005 29.630 8.83 11.93 0.00 2.83
134 135 9.047871 GCTTTTCTGTCAATACGTATAAAACAC 57.952 33.333 8.83 2.41 0.00 3.32
136 137 9.866936 TTTTCTGTCAATACGTATAAAACACAC 57.133 29.630 8.83 0.00 0.00 3.82
137 138 8.821147 TTCTGTCAATACGTATAAAACACACT 57.179 30.769 8.83 0.00 0.00 3.55
138 139 8.821147 TCTGTCAATACGTATAAAACACACTT 57.179 30.769 8.83 0.00 0.00 3.16
139 140 9.263538 TCTGTCAATACGTATAAAACACACTTT 57.736 29.630 8.83 0.00 0.00 2.66
140 141 9.872757 CTGTCAATACGTATAAAACACACTTTT 57.127 29.630 8.83 0.00 0.00 2.27
163 164 2.026879 TTTTTGCAACGGCTCGCC 59.973 55.556 0.00 0.00 41.91 5.54
164 165 3.492311 TTTTTGCAACGGCTCGCCC 62.492 57.895 0.00 0.00 41.91 6.13
169 170 3.508840 CAACGGCTCGCCCCAATC 61.509 66.667 1.72 0.00 0.00 2.67
170 171 3.717294 AACGGCTCGCCCCAATCT 61.717 61.111 1.72 0.00 0.00 2.40
171 172 3.268103 AACGGCTCGCCCCAATCTT 62.268 57.895 1.72 0.00 0.00 2.40
172 173 3.204827 CGGCTCGCCCCAATCTTG 61.205 66.667 1.72 0.00 0.00 3.02
188 189 7.447374 CCAATCTTGGTACTGACATGTAAAA 57.553 36.000 0.00 0.00 43.43 1.52
189 190 7.881142 CCAATCTTGGTACTGACATGTAAAAA 58.119 34.615 0.00 0.00 43.43 1.94
190 191 8.522830 CCAATCTTGGTACTGACATGTAAAAAT 58.477 33.333 0.00 0.00 43.43 1.82
191 192 9.912634 CAATCTTGGTACTGACATGTAAAAATT 57.087 29.630 0.00 0.00 0.00 1.82
194 195 9.005777 TCTTGGTACTGACATGTAAAAATTACC 57.994 33.333 0.00 5.12 0.00 2.85
195 196 8.693120 TTGGTACTGACATGTAAAAATTACCA 57.307 30.769 0.00 7.63 35.72 3.25
196 197 8.693120 TGGTACTGACATGTAAAAATTACCAA 57.307 30.769 14.30 4.21 34.82 3.67
197 198 9.303116 TGGTACTGACATGTAAAAATTACCAAT 57.697 29.630 14.30 0.00 34.82 3.16
198 199 9.783256 GGTACTGACATGTAAAAATTACCAATC 57.217 33.333 0.00 0.00 0.00 2.67
201 202 9.912634 ACTGACATGTAAAAATTACCAATCTTG 57.087 29.630 0.00 0.00 0.00 3.02
214 215 3.624777 CCAATCTTGGTACCAATCTGCT 58.375 45.455 27.24 5.37 43.43 4.24
215 216 4.019174 CCAATCTTGGTACCAATCTGCTT 58.981 43.478 27.24 11.17 43.43 3.91
216 217 4.096984 CCAATCTTGGTACCAATCTGCTTC 59.903 45.833 27.24 0.00 43.43 3.86
217 218 3.350219 TCTTGGTACCAATCTGCTTCC 57.650 47.619 27.24 0.00 35.20 3.46
218 219 2.642311 TCTTGGTACCAATCTGCTTCCA 59.358 45.455 27.24 1.40 35.20 3.53
219 220 3.073798 TCTTGGTACCAATCTGCTTCCAA 59.926 43.478 27.24 0.85 35.20 3.53
220 221 3.737559 TGGTACCAATCTGCTTCCAAT 57.262 42.857 13.60 0.00 0.00 3.16
221 222 3.355378 TGGTACCAATCTGCTTCCAATG 58.645 45.455 13.60 0.00 0.00 2.82
222 223 2.099756 GGTACCAATCTGCTTCCAATGC 59.900 50.000 7.15 0.00 0.00 3.56
223 224 1.188863 ACCAATCTGCTTCCAATGCC 58.811 50.000 0.00 0.00 0.00 4.40
224 225 0.462789 CCAATCTGCTTCCAATGCCC 59.537 55.000 0.00 0.00 0.00 5.36
225 226 0.462789 CAATCTGCTTCCAATGCCCC 59.537 55.000 0.00 0.00 0.00 5.80
226 227 0.041535 AATCTGCTTCCAATGCCCCA 59.958 50.000 0.00 0.00 0.00 4.96
227 228 0.041535 ATCTGCTTCCAATGCCCCAA 59.958 50.000 0.00 0.00 0.00 4.12
228 229 0.041535 TCTGCTTCCAATGCCCCAAT 59.958 50.000 0.00 0.00 0.00 3.16
229 230 0.906775 CTGCTTCCAATGCCCCAATT 59.093 50.000 0.00 0.00 0.00 2.32
230 231 0.614294 TGCTTCCAATGCCCCAATTG 59.386 50.000 0.00 0.00 37.30 2.32
231 232 0.614812 GCTTCCAATGCCCCAATTGT 59.385 50.000 4.43 0.00 36.06 2.71
232 233 1.676615 GCTTCCAATGCCCCAATTGTG 60.677 52.381 4.43 0.00 36.06 3.33
233 234 0.982704 TTCCAATGCCCCAATTGTGG 59.017 50.000 2.04 2.04 45.53 4.17
234 235 0.178909 TCCAATGCCCCAATTGTGGT 60.179 50.000 8.84 0.00 44.30 4.16
235 236 1.077828 TCCAATGCCCCAATTGTGGTA 59.922 47.619 8.84 4.38 44.30 3.25
236 237 1.206849 CCAATGCCCCAATTGTGGTAC 59.793 52.381 8.84 3.30 44.30 3.34
237 238 2.178580 CAATGCCCCAATTGTGGTACT 58.821 47.619 8.84 0.00 44.30 2.73
238 239 2.566724 CAATGCCCCAATTGTGGTACTT 59.433 45.455 8.84 0.00 44.30 2.24
239 240 2.390225 TGCCCCAATTGTGGTACTTT 57.610 45.000 8.84 0.00 44.30 2.66
240 241 2.683768 TGCCCCAATTGTGGTACTTTT 58.316 42.857 8.84 0.00 44.30 2.27
241 242 2.366916 TGCCCCAATTGTGGTACTTTTG 59.633 45.455 8.84 0.00 44.30 2.44
242 243 2.367241 GCCCCAATTGTGGTACTTTTGT 59.633 45.455 8.84 0.00 44.30 2.83
243 244 3.801983 GCCCCAATTGTGGTACTTTTGTG 60.802 47.826 8.84 0.00 44.30 3.33
244 245 3.389221 CCCAATTGTGGTACTTTTGTGC 58.611 45.455 4.43 0.00 44.30 4.57
245 246 3.181471 CCCAATTGTGGTACTTTTGTGCA 60.181 43.478 4.43 0.00 44.30 4.57
246 247 4.437239 CCAATTGTGGTACTTTTGTGCAA 58.563 39.130 4.43 0.00 40.42 4.08
247 248 5.055812 CCAATTGTGGTACTTTTGTGCAAT 58.944 37.500 4.43 0.00 40.42 3.56
248 249 5.526846 CCAATTGTGGTACTTTTGTGCAATT 59.473 36.000 4.43 0.00 40.42 2.32
249 250 6.038050 CCAATTGTGGTACTTTTGTGCAATTT 59.962 34.615 4.43 0.00 40.42 1.82
250 251 7.225538 CCAATTGTGGTACTTTTGTGCAATTTA 59.774 33.333 4.43 0.00 40.42 1.40
251 252 7.707774 ATTGTGGTACTTTTGTGCAATTTAC 57.292 32.000 0.00 0.00 36.74 2.01
252 253 6.458232 TGTGGTACTTTTGTGCAATTTACT 57.542 33.333 0.00 0.00 36.74 2.24
253 254 6.500041 TGTGGTACTTTTGTGCAATTTACTC 58.500 36.000 0.00 0.00 36.74 2.59
254 255 6.320164 TGTGGTACTTTTGTGCAATTTACTCT 59.680 34.615 0.00 0.00 36.74 3.24
255 256 6.856426 GTGGTACTTTTGTGCAATTTACTCTC 59.144 38.462 0.00 0.00 36.74 3.20
256 257 6.016610 TGGTACTTTTGTGCAATTTACTCTCC 60.017 38.462 0.00 0.00 36.74 3.71
257 258 6.206829 GGTACTTTTGTGCAATTTACTCTCCT 59.793 38.462 0.00 0.00 36.74 3.69
258 259 6.076981 ACTTTTGTGCAATTTACTCTCCTG 57.923 37.500 0.00 0.00 0.00 3.86
259 260 5.010012 ACTTTTGTGCAATTTACTCTCCTGG 59.990 40.000 0.00 0.00 0.00 4.45
260 261 3.788227 TGTGCAATTTACTCTCCTGGT 57.212 42.857 0.00 0.00 0.00 4.00
261 262 3.674997 TGTGCAATTTACTCTCCTGGTC 58.325 45.455 0.00 0.00 0.00 4.02
262 263 2.673368 GTGCAATTTACTCTCCTGGTCG 59.327 50.000 0.00 0.00 0.00 4.79
263 264 1.666189 GCAATTTACTCTCCTGGTCGC 59.334 52.381 0.00 0.00 0.00 5.19
264 265 2.280628 CAATTTACTCTCCTGGTCGCC 58.719 52.381 0.00 0.00 0.00 5.54
265 266 0.460311 ATTTACTCTCCTGGTCGCCG 59.540 55.000 0.00 0.00 0.00 6.46
266 267 0.896940 TTTACTCTCCTGGTCGCCGT 60.897 55.000 0.00 0.00 0.00 5.68
267 268 1.310933 TTACTCTCCTGGTCGCCGTC 61.311 60.000 0.00 0.00 0.00 4.79
268 269 2.194388 TACTCTCCTGGTCGCCGTCT 62.194 60.000 0.00 0.00 0.00 4.18
269 270 2.282958 TCTCCTGGTCGCCGTCTT 60.283 61.111 0.00 0.00 0.00 3.01
270 271 1.878656 CTCTCCTGGTCGCCGTCTTT 61.879 60.000 0.00 0.00 0.00 2.52
271 272 1.738099 CTCCTGGTCGCCGTCTTTG 60.738 63.158 0.00 0.00 0.00 2.77
272 273 2.030562 CCTGGTCGCCGTCTTTGT 59.969 61.111 0.00 0.00 0.00 2.83
273 274 2.317609 CCTGGTCGCCGTCTTTGTG 61.318 63.158 0.00 0.00 0.00 3.33
274 275 1.594293 CTGGTCGCCGTCTTTGTGT 60.594 57.895 0.00 0.00 0.00 3.72
275 276 0.319211 CTGGTCGCCGTCTTTGTGTA 60.319 55.000 0.00 0.00 0.00 2.90
276 277 0.104487 TGGTCGCCGTCTTTGTGTAA 59.896 50.000 0.00 0.00 0.00 2.41
277 278 0.788391 GGTCGCCGTCTTTGTGTAAG 59.212 55.000 0.00 0.00 35.04 2.34
278 279 1.603678 GGTCGCCGTCTTTGTGTAAGA 60.604 52.381 0.00 0.00 40.57 2.10
286 287 2.206750 TCTTTGTGTAAGACGGTGTGC 58.793 47.619 0.00 0.00 37.96 4.57
287 288 2.159014 TCTTTGTGTAAGACGGTGTGCT 60.159 45.455 0.00 0.00 37.96 4.40
288 289 1.577468 TTGTGTAAGACGGTGTGCTG 58.423 50.000 0.00 0.00 0.00 4.41
289 290 0.249699 TGTGTAAGACGGTGTGCTGG 60.250 55.000 0.00 0.00 0.00 4.85
290 291 1.301401 TGTAAGACGGTGTGCTGGC 60.301 57.895 0.00 0.00 0.00 4.85
291 292 1.301401 GTAAGACGGTGTGCTGGCA 60.301 57.895 0.00 0.00 0.00 4.92
292 293 1.005037 TAAGACGGTGTGCTGGCAG 60.005 57.895 10.94 10.94 0.00 4.85
293 294 2.449031 TAAGACGGTGTGCTGGCAGG 62.449 60.000 17.64 0.16 0.00 4.85
294 295 4.626081 GACGGTGTGCTGGCAGGT 62.626 66.667 17.64 3.89 0.00 4.00
295 296 4.626081 ACGGTGTGCTGGCAGGTC 62.626 66.667 17.64 0.29 0.00 3.85
306 307 4.148825 GCAGGTCGCGTCCAGGAT 62.149 66.667 24.00 0.23 0.00 3.24
311 312 1.084370 GGTCGCGTCCAGGATTTCTG 61.084 60.000 17.72 0.00 43.00 3.02
332 333 5.705441 TCTGTCTCAAATTCCCACACATAAC 59.295 40.000 0.00 0.00 0.00 1.89
356 357 7.908453 ACTCCTATTAGATACCAAACATAGGC 58.092 38.462 0.00 0.00 35.25 3.93
373 374 3.825908 AGGCTTGGGGACTAAAATGAA 57.174 42.857 0.00 0.00 0.00 2.57
450 454 6.128254 TGTGTTGTTAAGTTTTGACGATGACA 60.128 34.615 0.00 0.00 0.00 3.58
472 476 5.236478 ACAACTAGTCCGACAATTGAAACAG 59.764 40.000 13.59 2.49 0.00 3.16
519 523 5.415701 GGTGTATGTTGGAAGACATGTCAAT 59.584 40.000 27.02 15.59 40.33 2.57
529 533 6.553100 TGGAAGACATGTCAATTTTTAACCCT 59.447 34.615 27.02 0.00 0.00 4.34
532 536 6.981722 AGACATGTCAATTTTTAACCCTCAC 58.018 36.000 27.02 0.00 0.00 3.51
535 539 7.209475 ACATGTCAATTTTTAACCCTCACAAG 58.791 34.615 0.00 0.00 0.00 3.16
773 786 5.016173 TGGGACTTCCATATTTGTTTGAGG 58.984 41.667 0.00 0.00 41.46 3.86
774 787 4.142160 GGGACTTCCATATTTGTTTGAGGC 60.142 45.833 0.00 0.00 37.91 4.70
775 788 4.462483 GGACTTCCATATTTGTTTGAGGCA 59.538 41.667 0.00 0.00 35.64 4.75
776 789 5.047377 GGACTTCCATATTTGTTTGAGGCAA 60.047 40.000 0.00 0.00 35.64 4.52
777 790 6.418057 ACTTCCATATTTGTTTGAGGCAAA 57.582 33.333 0.00 0.00 39.69 3.68
778 791 7.008021 ACTTCCATATTTGTTTGAGGCAAAT 57.992 32.000 8.10 8.10 45.22 2.32
779 792 6.875195 ACTTCCATATTTGTTTGAGGCAAATG 59.125 34.615 11.94 0.60 43.70 2.32
815 834 3.188460 CACAAACGGGACTTCCATACTTG 59.812 47.826 0.00 0.00 37.91 3.16
868 3818 0.618968 AGTTGGGCTTCTCGGAGGAT 60.619 55.000 4.96 0.00 0.00 3.24
895 3845 0.884514 GCTCAAAGGCCCACTTCTTC 59.115 55.000 0.00 0.00 38.85 2.87
898 3848 1.160137 CAAAGGCCCACTTCTTCGAG 58.840 55.000 0.00 0.00 38.85 4.04
899 3849 0.606673 AAAGGCCCACTTCTTCGAGC 60.607 55.000 0.00 0.00 38.85 5.03
935 3885 2.879026 GACAAAGGCCGAAACTTTCTCT 59.121 45.455 0.00 0.00 36.09 3.10
936 3886 2.879026 ACAAAGGCCGAAACTTTCTCTC 59.121 45.455 0.00 0.00 36.09 3.20
937 3887 3.142174 CAAAGGCCGAAACTTTCTCTCT 58.858 45.455 0.00 0.00 36.09 3.10
971 3959 4.750695 TCCCCAATCCCCTCGCCA 62.751 66.667 0.00 0.00 0.00 5.69
1257 4279 4.083862 GCCTTCCTCGCCGACCTT 62.084 66.667 0.00 0.00 0.00 3.50
1345 4367 0.991920 GAGAACCCTGTCCCCAATCA 59.008 55.000 0.00 0.00 0.00 2.57
1350 4372 0.546122 CCCTGTCCCCAATCATCGAA 59.454 55.000 0.00 0.00 0.00 3.71
1387 4409 0.881796 ACTGTCGCGTTCTGAGATCA 59.118 50.000 5.77 0.00 0.00 2.92
1692 4718 0.321653 AAGCTTTAGGTGTGCCTCGG 60.322 55.000 0.00 0.00 45.64 4.63
1821 4847 0.467844 AGGTTGGCATTGCTGTGTCA 60.468 50.000 8.82 0.00 30.63 3.58
2011 5169 6.998074 TCTTAAGGAAAACAGATTGCTCAAGA 59.002 34.615 1.85 0.00 33.96 3.02
2021 5179 1.852942 TTGCTCAAGAGTGACACGTC 58.147 50.000 0.00 0.00 0.00 4.34
2039 5197 4.268644 CACGTCCTACTATGCATTTGTCAG 59.731 45.833 3.54 0.00 0.00 3.51
2047 5205 0.754587 TGCATTTGTCAGTGCCACCA 60.755 50.000 9.10 0.00 40.56 4.17
2105 5263 1.076777 AAGCTGCACCACACCTTGT 60.077 52.632 1.02 0.00 0.00 3.16
2179 5337 3.904717 ACATGAACCAACAACAGGGTAA 58.095 40.909 0.00 0.00 36.05 2.85
2306 5483 3.448660 GTGCAAAATAGGGATGCTCCTTT 59.551 43.478 0.00 0.00 40.66 3.11
2359 5538 9.793259 ATTTATAAGCAGCTTGCCTTATAGTAA 57.207 29.630 18.54 0.49 46.52 2.24
2383 5562 5.410746 AGCCTTATATGCTGATCGATTTGTG 59.589 40.000 0.00 0.00 37.76 3.33
2413 5592 7.948278 ATAAAATAGAATGTAGAGACCACGC 57.052 36.000 0.00 0.00 0.00 5.34
2427 5606 2.283298 ACCACGCTGCTCTCATATTTG 58.717 47.619 0.00 0.00 0.00 2.32
2428 5607 1.003116 CCACGCTGCTCTCATATTTGC 60.003 52.381 0.00 0.00 0.00 3.68
2430 5609 1.211743 CGCTGCTCTCATATTTGCGA 58.788 50.000 0.00 0.00 43.81 5.10
2433 5612 3.303593 CGCTGCTCTCATATTTGCGAAAT 60.304 43.478 0.00 0.00 43.81 2.17
2434 5613 4.084380 CGCTGCTCTCATATTTGCGAAATA 60.084 41.667 0.00 0.00 43.81 1.40
2435 5614 5.390251 CGCTGCTCTCATATTTGCGAAATAT 60.390 40.000 0.00 0.00 43.10 1.28
2542 5723 2.738013 AAGTACCGTGAAGCACCTAC 57.262 50.000 0.00 0.00 0.00 3.18
2550 5731 2.598907 CGTGAAGCACCTACGTTGTTTG 60.599 50.000 0.00 0.00 33.48 2.93
2552 5733 2.610374 TGAAGCACCTACGTTGTTTGTC 59.390 45.455 0.00 0.00 0.00 3.18
2553 5734 2.319136 AGCACCTACGTTGTTTGTCA 57.681 45.000 0.00 0.00 0.00 3.58
2555 5736 1.937899 GCACCTACGTTGTTTGTCACT 59.062 47.619 0.00 0.00 0.00 3.41
2556 5737 3.125316 GCACCTACGTTGTTTGTCACTA 58.875 45.455 0.00 0.00 0.00 2.74
2557 5738 3.744426 GCACCTACGTTGTTTGTCACTAT 59.256 43.478 0.00 0.00 0.00 2.12
2558 5739 4.143179 GCACCTACGTTGTTTGTCACTATC 60.143 45.833 0.00 0.00 0.00 2.08
2559 5740 5.227908 CACCTACGTTGTTTGTCACTATCT 58.772 41.667 0.00 0.00 0.00 1.98
2560 5741 5.345202 CACCTACGTTGTTTGTCACTATCTC 59.655 44.000 0.00 0.00 0.00 2.75
2561 5742 5.010314 ACCTACGTTGTTTGTCACTATCTCA 59.990 40.000 0.00 0.00 0.00 3.27
2562 5743 6.100004 CCTACGTTGTTTGTCACTATCTCAT 58.900 40.000 0.00 0.00 0.00 2.90
2563 5744 6.590292 CCTACGTTGTTTGTCACTATCTCATT 59.410 38.462 0.00 0.00 0.00 2.57
2565 5746 6.658831 ACGTTGTTTGTCACTATCTCATTTG 58.341 36.000 0.00 0.00 0.00 2.32
2566 5747 6.260050 ACGTTGTTTGTCACTATCTCATTTGT 59.740 34.615 0.00 0.00 0.00 2.83
2619 6992 2.019984 GCCTCCAGGTGCTTTATCTTG 58.980 52.381 0.00 0.00 37.57 3.02
2622 6995 3.285484 CTCCAGGTGCTTTATCTTGCAT 58.715 45.455 0.00 0.00 41.45 3.96
2627 7000 5.126061 CCAGGTGCTTTATCTTGCATAGTTT 59.874 40.000 0.00 0.00 41.45 2.66
2628 7001 6.032094 CAGGTGCTTTATCTTGCATAGTTTG 58.968 40.000 0.00 0.00 41.45 2.93
2629 7002 5.126061 AGGTGCTTTATCTTGCATAGTTTGG 59.874 40.000 0.00 0.00 41.45 3.28
2630 7003 5.105756 GGTGCTTTATCTTGCATAGTTTGGT 60.106 40.000 0.00 0.00 41.45 3.67
2631 7004 6.389906 GTGCTTTATCTTGCATAGTTTGGTT 58.610 36.000 0.00 0.00 41.45 3.67
2632 7005 7.362574 GGTGCTTTATCTTGCATAGTTTGGTTA 60.363 37.037 0.00 0.00 41.45 2.85
2633 7006 7.484959 GTGCTTTATCTTGCATAGTTTGGTTAC 59.515 37.037 0.00 0.00 41.45 2.50
2655 7028 2.100197 GGTTAGGTTTTGGATGGCTCC 58.900 52.381 0.00 0.00 42.45 4.70
2722 7099 7.808856 GGTTTTGTATTACCGTTTAATGAGCAA 59.191 33.333 0.00 0.00 0.00 3.91
2732 7109 1.838112 TAATGAGCAAGGTTGGGCTG 58.162 50.000 0.00 0.00 41.22 4.85
2785 7163 2.932498 TCAAAACAGAATGCGCATCAC 58.068 42.857 25.53 20.01 42.53 3.06
2797 7175 1.043816 CGCATCACCAGTAGGGATCT 58.956 55.000 0.00 0.00 41.15 2.75
2798 7176 1.414181 CGCATCACCAGTAGGGATCTT 59.586 52.381 0.00 0.00 41.15 2.40
2829 7207 8.621532 TGAAGAGTATTACAGACTGCATTTTT 57.378 30.769 1.25 0.00 0.00 1.94
2856 7234 6.245408 AGGCGAGAATATAAATAATTGGCCA 58.755 36.000 0.00 0.00 38.11 5.36
2902 7280 5.083122 CAGATACCATCTAGGGACATCTGT 58.917 45.833 15.54 0.00 41.20 3.41
2904 7282 6.042552 CAGATACCATCTAGGGACATCTGTTT 59.957 42.308 15.54 0.00 41.20 2.83
2961 7339 1.790623 GCAAAGCTGCTGTTGTTCATG 59.209 47.619 18.74 0.00 45.74 3.07
2965 7343 2.034124 AGCTGCTGTTGTTCATGGTTT 58.966 42.857 0.00 0.00 0.00 3.27
2980 7359 5.139727 TCATGGTTTGGTTTCAGATGTTCT 58.860 37.500 0.00 0.00 0.00 3.01
2987 7366 4.143543 TGGTTTCAGATGTTCTTGCATGA 58.856 39.130 0.00 0.00 0.00 3.07
3018 7397 2.760092 AGAAGCTGGCTGTTTTGTTTGA 59.240 40.909 0.00 0.00 0.00 2.69
3047 7426 7.552687 TCACTGTTCTTTAGTGACAGTCAAAAT 59.447 33.333 4.32 0.00 46.92 1.82
3049 7428 8.184192 ACTGTTCTTTAGTGACAGTCAAAATTG 58.816 33.333 4.32 0.00 37.07 2.32
3098 7488 6.170506 ACAGATAAGGAAATAACGTTCTGCA 58.829 36.000 2.82 0.00 0.00 4.41
3141 7531 6.749118 GCGCAGATTCAGTATTGAAGATTTTT 59.251 34.615 0.30 0.00 45.89 1.94
3143 7533 8.180267 CGCAGATTCAGTATTGAAGATTTTTCT 58.820 33.333 6.81 1.01 45.89 2.52
3151 7541 7.814587 CAGTATTGAAGATTTTTCTTGAACCCC 59.185 37.037 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.851179 GGCCGGCTCCCGTTTAGG 62.851 72.222 28.56 0.00 46.80 2.69
21 22 3.735037 GAGGCCGGCTCCCGTTTAG 62.735 68.421 28.56 0.00 46.80 1.85
22 23 3.777910 GAGGCCGGCTCCCGTTTA 61.778 66.667 28.56 0.00 46.80 2.01
33 34 4.135153 CTGACTGGGACGAGGCCG 62.135 72.222 0.00 0.00 42.50 6.13
34 35 4.459089 GCTGACTGGGACGAGGCC 62.459 72.222 0.00 0.00 0.00 5.19
35 36 4.803426 CGCTGACTGGGACGAGGC 62.803 72.222 0.00 0.00 0.00 4.70
36 37 4.803426 GCGCTGACTGGGACGAGG 62.803 72.222 0.00 0.00 0.00 4.63
37 38 4.803426 GGCGCTGACTGGGACGAG 62.803 72.222 7.64 0.00 0.00 4.18
40 41 4.767255 CTGGGCGCTGACTGGGAC 62.767 72.222 7.64 0.00 35.65 4.46
42 43 4.767255 GACTGGGCGCTGACTGGG 62.767 72.222 14.63 0.00 0.00 4.45
43 44 3.947132 CTGACTGGGCGCTGACTGG 62.947 68.421 14.63 2.75 0.00 4.00
44 45 2.433838 CTGACTGGGCGCTGACTG 60.434 66.667 14.63 8.39 0.00 3.51
45 46 4.385405 GCTGACTGGGCGCTGACT 62.385 66.667 14.63 0.00 0.00 3.41
94 95 4.660938 AAGCTGACCGGTTGGGCC 62.661 66.667 9.42 0.00 46.01 5.80
96 97 0.537371 AGAAAAGCTGACCGGTTGGG 60.537 55.000 9.42 3.00 40.75 4.12
97 98 3.021451 AGAAAAGCTGACCGGTTGG 57.979 52.632 9.42 5.90 42.84 3.77
107 108 8.995220 TGTTTTATACGTATTGACAGAAAAGCT 58.005 29.630 14.33 0.00 0.00 3.74
108 109 9.047871 GTGTTTTATACGTATTGACAGAAAAGC 57.952 33.333 14.33 8.66 0.00 3.51
110 111 9.866936 GTGTGTTTTATACGTATTGACAGAAAA 57.133 29.630 14.33 10.06 0.00 2.29
111 112 9.263538 AGTGTGTTTTATACGTATTGACAGAAA 57.736 29.630 14.33 4.17 0.00 2.52
112 113 8.821147 AGTGTGTTTTATACGTATTGACAGAA 57.179 30.769 14.33 0.00 0.00 3.02
113 114 8.821147 AAGTGTGTTTTATACGTATTGACAGA 57.179 30.769 14.33 11.42 0.00 3.41
114 115 9.872757 AAAAGTGTGTTTTATACGTATTGACAG 57.127 29.630 14.33 0.00 0.00 3.51
146 147 2.026879 GGCGAGCCGTTGCAAAAA 59.973 55.556 0.00 0.00 41.13 1.94
147 148 3.972276 GGGCGAGCCGTTGCAAAA 61.972 61.111 0.00 0.00 41.13 2.44
152 153 3.508840 GATTGGGGCGAGCCGTTG 61.509 66.667 8.14 0.00 36.85 4.10
153 154 3.268103 AAGATTGGGGCGAGCCGTT 62.268 57.895 8.14 0.00 36.85 4.44
154 155 3.717294 AAGATTGGGGCGAGCCGT 61.717 61.111 8.14 0.00 36.85 5.68
155 156 3.204827 CAAGATTGGGGCGAGCCG 61.205 66.667 8.14 0.00 36.85 5.52
156 157 2.830370 CCAAGATTGGGGCGAGCC 60.830 66.667 5.37 5.37 44.70 4.70
165 166 9.912634 AATTTTTACATGTCAGTACCAAGATTG 57.087 29.630 0.00 0.00 0.00 2.67
168 169 9.005777 GGTAATTTTTACATGTCAGTACCAAGA 57.994 33.333 0.00 0.00 0.00 3.02
169 170 8.788806 TGGTAATTTTTACATGTCAGTACCAAG 58.211 33.333 17.47 0.00 36.44 3.61
170 171 8.693120 TGGTAATTTTTACATGTCAGTACCAA 57.307 30.769 17.47 0.00 36.44 3.67
171 172 8.693120 TTGGTAATTTTTACATGTCAGTACCA 57.307 30.769 16.52 16.52 37.33 3.25
172 173 9.783256 GATTGGTAATTTTTACATGTCAGTACC 57.217 33.333 0.00 9.02 0.00 3.34
175 176 9.912634 CAAGATTGGTAATTTTTACATGTCAGT 57.087 29.630 0.00 0.00 0.00 3.41
176 177 9.357652 CCAAGATTGGTAATTTTTACATGTCAG 57.642 33.333 0.00 0.00 43.43 3.51
194 195 4.096984 GGAAGCAGATTGGTACCAAGATTG 59.903 45.833 30.00 25.45 39.47 2.67
195 196 4.263905 TGGAAGCAGATTGGTACCAAGATT 60.264 41.667 30.00 21.57 39.47 2.40
196 197 3.266772 TGGAAGCAGATTGGTACCAAGAT 59.733 43.478 30.00 19.00 39.47 2.40
197 198 2.642311 TGGAAGCAGATTGGTACCAAGA 59.358 45.455 30.00 11.20 39.47 3.02
198 199 3.071874 TGGAAGCAGATTGGTACCAAG 57.928 47.619 30.00 18.73 39.47 3.61
199 200 3.517296 TTGGAAGCAGATTGGTACCAA 57.483 42.857 28.95 28.95 40.47 3.67
200 201 3.355378 CATTGGAAGCAGATTGGTACCA 58.645 45.455 11.60 11.60 0.00 3.25
201 202 2.099756 GCATTGGAAGCAGATTGGTACC 59.900 50.000 4.43 4.43 0.00 3.34
202 203 2.099756 GGCATTGGAAGCAGATTGGTAC 59.900 50.000 0.00 0.00 0.00 3.34
203 204 2.378038 GGCATTGGAAGCAGATTGGTA 58.622 47.619 0.00 0.00 0.00 3.25
204 205 1.188863 GGCATTGGAAGCAGATTGGT 58.811 50.000 0.00 0.00 0.00 3.67
205 206 0.462789 GGGCATTGGAAGCAGATTGG 59.537 55.000 0.00 0.00 0.00 3.16
206 207 0.462789 GGGGCATTGGAAGCAGATTG 59.537 55.000 0.00 0.00 0.00 2.67
207 208 0.041535 TGGGGCATTGGAAGCAGATT 59.958 50.000 0.00 0.00 0.00 2.40
208 209 0.041535 TTGGGGCATTGGAAGCAGAT 59.958 50.000 0.00 0.00 0.00 2.90
209 210 0.041535 ATTGGGGCATTGGAAGCAGA 59.958 50.000 0.00 0.00 0.00 4.26
210 211 0.906775 AATTGGGGCATTGGAAGCAG 59.093 50.000 0.00 0.00 0.00 4.24
211 212 0.614294 CAATTGGGGCATTGGAAGCA 59.386 50.000 0.00 0.00 0.00 3.91
212 213 0.614812 ACAATTGGGGCATTGGAAGC 59.385 50.000 10.83 0.00 32.40 3.86
213 214 1.065998 CCACAATTGGGGCATTGGAAG 60.066 52.381 15.25 0.00 39.57 3.46
214 215 0.982704 CCACAATTGGGGCATTGGAA 59.017 50.000 15.25 0.00 39.57 3.53
215 216 2.681348 CCACAATTGGGGCATTGGA 58.319 52.632 15.25 0.00 39.57 3.53
225 226 6.601741 AATTGCACAAAAGTACCACAATTG 57.398 33.333 3.24 3.24 35.55 2.32
226 227 7.984617 AGTAAATTGCACAAAAGTACCACAATT 59.015 29.630 0.00 0.00 37.73 2.32
227 228 7.496747 AGTAAATTGCACAAAAGTACCACAAT 58.503 30.769 0.00 0.00 0.00 2.71
228 229 6.868622 AGTAAATTGCACAAAAGTACCACAA 58.131 32.000 0.00 0.00 0.00 3.33
229 230 6.320164 AGAGTAAATTGCACAAAAGTACCACA 59.680 34.615 0.00 0.00 0.00 4.17
230 231 6.735130 AGAGTAAATTGCACAAAAGTACCAC 58.265 36.000 0.00 0.00 0.00 4.16
231 232 6.016610 GGAGAGTAAATTGCACAAAAGTACCA 60.017 38.462 0.00 0.00 0.00 3.25
232 233 6.206829 AGGAGAGTAAATTGCACAAAAGTACC 59.793 38.462 0.00 0.00 0.00 3.34
233 234 7.078228 CAGGAGAGTAAATTGCACAAAAGTAC 58.922 38.462 0.00 0.00 0.00 2.73
234 235 6.206634 CCAGGAGAGTAAATTGCACAAAAGTA 59.793 38.462 0.00 0.00 0.00 2.24
235 236 5.010012 CCAGGAGAGTAAATTGCACAAAAGT 59.990 40.000 0.00 0.00 0.00 2.66
236 237 5.010012 ACCAGGAGAGTAAATTGCACAAAAG 59.990 40.000 0.00 0.00 0.00 2.27
237 238 4.892934 ACCAGGAGAGTAAATTGCACAAAA 59.107 37.500 0.00 0.00 0.00 2.44
238 239 4.469657 ACCAGGAGAGTAAATTGCACAAA 58.530 39.130 0.00 0.00 0.00 2.83
239 240 4.072131 GACCAGGAGAGTAAATTGCACAA 58.928 43.478 0.00 0.00 0.00 3.33
240 241 3.674997 GACCAGGAGAGTAAATTGCACA 58.325 45.455 0.00 0.00 0.00 4.57
241 242 2.673368 CGACCAGGAGAGTAAATTGCAC 59.327 50.000 0.00 0.00 0.00 4.57
242 243 2.935238 GCGACCAGGAGAGTAAATTGCA 60.935 50.000 0.00 0.00 0.00 4.08
243 244 1.666189 GCGACCAGGAGAGTAAATTGC 59.334 52.381 0.00 0.00 0.00 3.56
244 245 2.280628 GGCGACCAGGAGAGTAAATTG 58.719 52.381 0.00 0.00 0.00 2.32
245 246 1.134788 CGGCGACCAGGAGAGTAAATT 60.135 52.381 0.00 0.00 0.00 1.82
246 247 0.460311 CGGCGACCAGGAGAGTAAAT 59.540 55.000 0.00 0.00 0.00 1.40
247 248 0.896940 ACGGCGACCAGGAGAGTAAA 60.897 55.000 16.62 0.00 0.00 2.01
248 249 1.303888 ACGGCGACCAGGAGAGTAA 60.304 57.895 16.62 0.00 0.00 2.24
249 250 1.748122 GACGGCGACCAGGAGAGTA 60.748 63.158 16.62 0.00 0.00 2.59
250 251 3.063084 GACGGCGACCAGGAGAGT 61.063 66.667 16.62 0.00 0.00 3.24
251 252 1.878656 AAAGACGGCGACCAGGAGAG 61.879 60.000 16.62 0.00 0.00 3.20
252 253 1.906824 AAAGACGGCGACCAGGAGA 60.907 57.895 16.62 0.00 0.00 3.71
253 254 1.738099 CAAAGACGGCGACCAGGAG 60.738 63.158 16.62 0.00 0.00 3.69
254 255 2.342279 CAAAGACGGCGACCAGGA 59.658 61.111 16.62 0.00 0.00 3.86
255 256 2.030562 ACAAAGACGGCGACCAGG 59.969 61.111 16.62 1.69 0.00 4.45
256 257 0.319211 TACACAAAGACGGCGACCAG 60.319 55.000 16.62 2.54 0.00 4.00
257 258 0.104487 TTACACAAAGACGGCGACCA 59.896 50.000 16.62 0.00 0.00 4.02
258 259 0.788391 CTTACACAAAGACGGCGACC 59.212 55.000 16.62 4.70 37.38 4.79
259 260 1.774639 TCTTACACAAAGACGGCGAC 58.225 50.000 16.62 7.87 39.36 5.19
266 267 2.159014 AGCACACCGTCTTACACAAAGA 60.159 45.455 0.00 0.00 42.07 2.52
267 268 2.032894 CAGCACACCGTCTTACACAAAG 60.033 50.000 0.00 0.00 36.45 2.77
268 269 1.937223 CAGCACACCGTCTTACACAAA 59.063 47.619 0.00 0.00 0.00 2.83
269 270 1.577468 CAGCACACCGTCTTACACAA 58.423 50.000 0.00 0.00 0.00 3.33
270 271 0.249699 CCAGCACACCGTCTTACACA 60.250 55.000 0.00 0.00 0.00 3.72
271 272 1.566018 GCCAGCACACCGTCTTACAC 61.566 60.000 0.00 0.00 0.00 2.90
272 273 1.301401 GCCAGCACACCGTCTTACA 60.301 57.895 0.00 0.00 0.00 2.41
273 274 1.291877 CTGCCAGCACACCGTCTTAC 61.292 60.000 0.00 0.00 0.00 2.34
274 275 1.005037 CTGCCAGCACACCGTCTTA 60.005 57.895 0.00 0.00 0.00 2.10
275 276 2.281070 CTGCCAGCACACCGTCTT 60.281 61.111 0.00 0.00 0.00 3.01
276 277 4.320456 CCTGCCAGCACACCGTCT 62.320 66.667 0.00 0.00 0.00 4.18
277 278 4.626081 ACCTGCCAGCACACCGTC 62.626 66.667 0.00 0.00 0.00 4.79
278 279 4.626081 GACCTGCCAGCACACCGT 62.626 66.667 0.00 0.00 0.00 4.83
289 290 3.665675 AATCCTGGACGCGACCTGC 62.666 63.158 26.94 4.34 41.47 4.85
290 291 1.079127 AAATCCTGGACGCGACCTG 60.079 57.895 26.94 25.06 0.00 4.00
291 292 1.218316 GAAATCCTGGACGCGACCT 59.782 57.895 26.94 6.84 0.00 3.85
292 293 1.084370 CAGAAATCCTGGACGCGACC 61.084 60.000 20.91 20.91 39.23 4.79
293 294 2.373938 CAGAAATCCTGGACGCGAC 58.626 57.895 15.93 6.56 39.23 5.19
294 295 4.910956 CAGAAATCCTGGACGCGA 57.089 55.556 15.93 0.00 39.23 5.87
302 303 5.012893 GTGGGAATTTGAGACAGAAATCCT 58.987 41.667 0.00 0.00 0.00 3.24
303 304 4.766891 TGTGGGAATTTGAGACAGAAATCC 59.233 41.667 0.00 0.00 0.00 3.01
304 305 5.241506 TGTGTGGGAATTTGAGACAGAAATC 59.758 40.000 0.00 0.00 0.00 2.17
305 306 5.139727 TGTGTGGGAATTTGAGACAGAAAT 58.860 37.500 0.00 0.00 0.00 2.17
306 307 4.531854 TGTGTGGGAATTTGAGACAGAAA 58.468 39.130 0.00 0.00 0.00 2.52
311 312 5.123979 GGAGTTATGTGTGGGAATTTGAGAC 59.876 44.000 0.00 0.00 0.00 3.36
332 333 8.140112 AGCCTATGTTTGGTATCTAATAGGAG 57.860 38.462 10.06 0.00 39.23 3.69
353 354 3.825908 TTCATTTTAGTCCCCAAGCCT 57.174 42.857 0.00 0.00 0.00 4.58
356 357 5.480073 TGACCATTTCATTTTAGTCCCCAAG 59.520 40.000 0.00 0.00 0.00 3.61
423 424 7.431084 GTCATCGTCAAAACTTAACAACACATT 59.569 33.333 0.00 0.00 0.00 2.71
450 454 5.465724 GTCTGTTTCAATTGTCGGACTAGTT 59.534 40.000 20.92 0.00 34.54 2.24
462 466 9.736023 GAAGAACAAACTATGTCTGTTTCAATT 57.264 29.630 0.00 0.00 42.99 2.32
472 476 9.522804 CACCTATCTAGAAGAACAAACTATGTC 57.477 37.037 0.00 0.00 42.99 3.06
542 547 6.273071 GTTTTAGCAAACTTGACCTGTCATT 58.727 36.000 0.03 0.00 39.49 2.57
543 548 5.831997 GTTTTAGCAAACTTGACCTGTCAT 58.168 37.500 0.03 0.00 39.49 3.06
544 549 5.243426 GTTTTAGCAAACTTGACCTGTCA 57.757 39.130 0.00 0.00 39.49 3.58
735 748 5.163457 GGAAGTCCCATTTGTGTCAGAAAAA 60.163 40.000 0.00 0.00 34.14 1.94
736 749 4.340950 GGAAGTCCCATTTGTGTCAGAAAA 59.659 41.667 0.00 0.00 34.14 2.29
737 750 3.888930 GGAAGTCCCATTTGTGTCAGAAA 59.111 43.478 0.00 0.00 34.14 2.52
738 751 3.117701 TGGAAGTCCCATTTGTGTCAGAA 60.118 43.478 0.00 0.00 40.82 3.02
739 752 2.441375 TGGAAGTCCCATTTGTGTCAGA 59.559 45.455 0.00 0.00 40.82 3.27
740 753 2.862541 TGGAAGTCCCATTTGTGTCAG 58.137 47.619 0.00 0.00 40.82 3.51
793 807 3.053831 AGTATGGAAGTCCCGTTTGTG 57.946 47.619 0.00 0.00 37.93 3.33
815 834 1.952296 CCCAGCTTTCATCCACTATGC 59.048 52.381 0.00 0.00 35.38 3.14
898 3848 4.854784 TCACTCCTCGATGCGCGC 62.855 66.667 27.26 27.26 40.61 6.86
899 3849 2.951745 GTCACTCCTCGATGCGCG 60.952 66.667 0.00 0.00 42.69 6.86
1410 4432 2.251642 GCTGCGGAAGTGGTCGTTT 61.252 57.895 0.00 0.00 0.00 3.60
1579 4605 1.946768 GCCAATATCGCAAGCACCTAA 59.053 47.619 0.00 0.00 37.18 2.69
1692 4718 2.124403 CTGCACATCCCAGAGCCC 60.124 66.667 0.00 0.00 32.03 5.19
1821 4847 2.380064 TCAGCACAAATGGACCCTTT 57.620 45.000 0.00 0.00 0.00 3.11
2011 5169 2.443416 TGCATAGTAGGACGTGTCACT 58.557 47.619 0.00 0.00 0.00 3.41
2021 5179 3.313526 GGCACTGACAAATGCATAGTAGG 59.686 47.826 0.00 1.50 43.93 3.18
2105 5263 2.745821 CAAGCAGCTGCATAGTCTTCAA 59.254 45.455 38.24 0.00 45.16 2.69
2306 5483 5.815581 AGTGTCCAATGGAAGCTATAACAA 58.184 37.500 2.31 0.00 31.38 2.83
2359 5538 5.410746 CACAAATCGATCAGCATATAAGGCT 59.589 40.000 0.00 0.00 43.77 4.58
2412 5591 3.680642 TTTCGCAAATATGAGAGCAGC 57.319 42.857 0.00 0.00 36.69 5.25
2427 5606 7.095397 TGGCACTATTATACACACATATTTCGC 60.095 37.037 0.00 0.00 0.00 4.70
2428 5607 8.305441 TGGCACTATTATACACACATATTTCG 57.695 34.615 0.00 0.00 0.00 3.46
2435 5614 9.845740 AAGATAAATGGCACTATTATACACACA 57.154 29.630 0.00 0.00 0.00 3.72
2492 5673 3.266510 TGGATGGCTGACTGAATGTAC 57.733 47.619 0.00 0.00 0.00 2.90
2524 5705 0.524862 CGTAGGTGCTTCACGGTACT 59.475 55.000 0.00 0.00 34.83 2.73
2527 5708 0.599204 CAACGTAGGTGCTTCACGGT 60.599 55.000 0.00 0.00 39.91 4.83
2542 5723 6.658831 ACAAATGAGATAGTGACAAACAACG 58.341 36.000 0.00 0.00 0.00 4.10
2550 5731 7.093354 TCTCTTGTGACAAATGAGATAGTGAC 58.907 38.462 11.76 0.00 0.00 3.67
2552 5733 7.275341 GTCTCTCTTGTGACAAATGAGATAGTG 59.725 40.741 23.13 11.56 36.87 2.74
2553 5734 7.178274 AGTCTCTCTTGTGACAAATGAGATAGT 59.822 37.037 23.13 14.49 38.67 2.12
2555 5736 7.473735 AGTCTCTCTTGTGACAAATGAGATA 57.526 36.000 23.13 12.92 38.67 1.98
2556 5737 6.357579 AGTCTCTCTTGTGACAAATGAGAT 57.642 37.500 23.13 14.29 38.67 2.75
2557 5738 5.798125 AGTCTCTCTTGTGACAAATGAGA 57.202 39.130 19.17 19.17 38.67 3.27
2558 5739 6.225703 CAAGTCTCTCTTGTGACAAATGAG 57.774 41.667 16.21 16.21 45.89 2.90
2619 6992 5.250982 ACCTAACCAGTAACCAAACTATGC 58.749 41.667 0.00 0.00 0.00 3.14
2622 6995 6.546772 CCAAAACCTAACCAGTAACCAAACTA 59.453 38.462 0.00 0.00 0.00 2.24
2627 7000 4.792513 TCCAAAACCTAACCAGTAACCA 57.207 40.909 0.00 0.00 0.00 3.67
2628 7001 4.461431 CCATCCAAAACCTAACCAGTAACC 59.539 45.833 0.00 0.00 0.00 2.85
2629 7002 4.082408 GCCATCCAAAACCTAACCAGTAAC 60.082 45.833 0.00 0.00 0.00 2.50
2630 7003 4.083565 GCCATCCAAAACCTAACCAGTAA 58.916 43.478 0.00 0.00 0.00 2.24
2631 7004 3.332485 AGCCATCCAAAACCTAACCAGTA 59.668 43.478 0.00 0.00 0.00 2.74
2632 7005 2.110011 AGCCATCCAAAACCTAACCAGT 59.890 45.455 0.00 0.00 0.00 4.00
2633 7006 2.755103 GAGCCATCCAAAACCTAACCAG 59.245 50.000 0.00 0.00 0.00 4.00
2662 7035 3.276857 CAATGGCAGAAGAGTGCAGTAT 58.723 45.455 0.00 0.00 45.93 2.12
2665 7038 0.809385 CCAATGGCAGAAGAGTGCAG 59.191 55.000 0.00 0.00 45.93 4.41
2770 7148 0.321919 ACTGGTGATGCGCATTCTGT 60.322 50.000 26.12 21.23 0.00 3.41
2785 7163 3.300388 TCAGCTGTAAGATCCCTACTGG 58.700 50.000 14.67 0.00 34.07 4.00
2797 7175 7.539436 CAGTCTGTAATACTCTTCAGCTGTAA 58.461 38.462 14.67 6.04 32.81 2.41
2798 7176 6.404844 GCAGTCTGTAATACTCTTCAGCTGTA 60.405 42.308 14.67 2.58 36.04 2.74
2829 7207 9.555727 GGCCAATTATTTATATTCTCGCCTATA 57.444 33.333 0.00 0.00 0.00 1.31
2856 7234 3.556775 GCTGTCACAAACATGCACAAAAT 59.443 39.130 0.00 0.00 37.23 1.82
2961 7339 4.051237 GCAAGAACATCTGAAACCAAACC 58.949 43.478 0.00 0.00 0.00 3.27
2965 7343 4.143543 TCATGCAAGAACATCTGAAACCA 58.856 39.130 0.00 0.00 0.00 3.67
2980 7359 5.240844 CAGCTTCTCATATCCATTCATGCAA 59.759 40.000 0.00 0.00 0.00 4.08
2987 7366 3.137913 ACAGCCAGCTTCTCATATCCATT 59.862 43.478 0.00 0.00 0.00 3.16
3090 7469 3.181397 CAATTAGGCCAATTGCAGAACG 58.819 45.455 20.40 3.85 45.19 3.95
3098 7488 2.417243 GCGCAACTCAATTAGGCCAATT 60.417 45.455 5.01 6.42 37.32 2.32
3141 7531 4.946160 AGATACCATTTGGGGTTCAAGA 57.054 40.909 0.96 0.00 42.42 3.02


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

AutoCloner maintained by Alex Coulton.