Multiple sequence alignment - TraesCS6A01G135400

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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 TraesCS6A01G135400 chr6A 100.000 3672 0 0 1 3672 107204932 107208603 0.000000e+00 6782.0
1 TraesCS6A01G135400 chr6A 83.505 485 65 9 2779 3254 107207203 107207681 4.350000e-119 438.0
2 TraesCS6A01G135400 chr6A 83.505 485 65 9 2272 2750 107207710 107208185 4.350000e-119 438.0
3 TraesCS6A01G135400 chr2D 93.221 2729 133 22 306 3011 488566055 488563356 0.000000e+00 3967.0
4 TraesCS6A01G135400 chr2D 81.910 199 28 4 2315 2505 488563554 488563356 1.060000e-35 161.0
5 TraesCS6A01G135400 chr2D 80.795 151 22 7 13 163 584297628 584297485 1.080000e-20 111.0
6 TraesCS6A01G135400 chr6D 93.967 2619 113 13 922 3519 89060178 89062772 0.000000e+00 3919.0
7 TraesCS6A01G135400 chr6D 87.404 389 16 13 522 886 89059817 89060196 2.040000e-112 416.0
8 TraesCS6A01G135400 chr6D 80.933 493 77 10 2272 2750 89062018 89062507 1.250000e-99 374.0
9 TraesCS6A01G135400 chr6D 91.403 221 10 5 221 440 89059563 89059775 9.970000e-76 294.0
10 TraesCS6A01G135400 chr6D 95.513 156 6 1 3517 3672 89062811 89062965 7.870000e-62 248.0
11 TraesCS6A01G135400 chr6B 87.929 1864 191 20 842 2678 169479893 169481749 0.000000e+00 2165.0
12 TraesCS6A01G135400 chr6B 88.696 575 29 15 285 849 169479265 169479813 0.000000e+00 669.0
13 TraesCS6A01G135400 chr6B 92.326 417 23 6 2779 3188 169481335 169481749 5.280000e-163 584.0
14 TraesCS6A01G135400 chr6B 77.857 140 26 4 1780 1918 706580989 706580854 8.450000e-12 82.4
15 TraesCS6A01G135400 chr7A 83.761 234 27 10 1 228 586311628 586311400 1.030000e-50 211.0
16 TraesCS6A01G135400 chr3B 80.861 209 30 8 13 219 69603261 69603461 4.910000e-34 156.0
17 TraesCS6A01G135400 chr3B 78.641 206 35 8 12 212 66614036 66614237 1.070000e-25 128.0
18 TraesCS6A01G135400 chr3B 77.838 185 25 7 47 217 779067021 779066839 2.330000e-17 100.0
19 TraesCS6A01G135400 chr1A 80.282 213 32 8 13 219 535406107 535405899 6.350000e-33 152.0
20 TraesCS6A01G135400 chr1A 83.125 160 23 4 13 168 223988346 223988187 3.820000e-30 143.0
21 TraesCS6A01G135400 chr2B 82.209 163 21 7 13 172 641876543 641876700 2.300000e-27 134.0
22 TraesCS6A01G135400 chr3A 78.261 207 38 7 13 219 657278540 657278341 3.850000e-25 126.0
23 TraesCS6A01G135400 chr5B 84.706 85 13 0 3339 3423 382781988 382782072 6.530000e-13 86.1
24 TraesCS6A01G135400 chr4A 87.097 62 3 3 3253 3309 727713033 727713094 8.510000e-07 65.8


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 TraesCS6A01G135400 chr6A 107204932 107208603 3671 False 2552.666667 6782 89.003333 1 3672 3 chr6A.!!$F1 3671
1 TraesCS6A01G135400 chr2D 488563356 488566055 2699 True 2064.000000 3967 87.565500 306 3011 2 chr2D.!!$R2 2705
2 TraesCS6A01G135400 chr6D 89059563 89062965 3402 False 1050.200000 3919 89.844000 221 3672 5 chr6D.!!$F1 3451
3 TraesCS6A01G135400 chr6B 169479265 169481749 2484 False 1139.333333 2165 89.650333 285 3188 3 chr6B.!!$F1 2903

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
190 191 0.024619 GCGAAAGTACGGATGAACGC 59.975 55.0 0.00 0.0 37.37 4.84 F
523 525 0.107703 GTCGTTCTGCATCATCCCCA 60.108 55.0 0.00 0.0 0.00 4.96 F
1366 1489 0.036765 CATTGGGCATGCTGTTGCTT 60.037 50.0 18.92 0.0 42.38 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1110 1233 0.034059 AGAGGACACTGGTTCTTGCG 59.966 55.0 0.00 0.0 31.09 4.85 R
2383 2520 0.528017 GCGTGACCAGACTCTGATGA 59.472 55.0 7.69 0.0 32.44 2.92 R
2919 3074 0.038159 AGTCTCGAGCTTGAAACCCG 60.038 55.0 7.81 0.0 0.00 5.28 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
18 19 1.440476 GTACCTGTTCCCGGATCCG 59.560 63.158 27.65 27.65 39.44 4.18
29 30 4.496336 GGATCCGGCTTGCCTGCT 62.496 66.667 10.12 0.00 0.00 4.24
30 31 2.899339 GATCCGGCTTGCCTGCTC 60.899 66.667 10.12 0.76 0.00 4.26
31 32 4.496336 ATCCGGCTTGCCTGCTCC 62.496 66.667 10.12 0.00 0.00 4.70
33 34 4.729918 CCGGCTTGCCTGCTCCTT 62.730 66.667 10.12 0.00 0.00 3.36
34 35 2.674380 CGGCTTGCCTGCTCCTTT 60.674 61.111 10.12 0.00 0.00 3.11
35 36 2.270986 CGGCTTGCCTGCTCCTTTT 61.271 57.895 10.12 0.00 0.00 2.27
36 37 1.588597 GGCTTGCCTGCTCCTTTTC 59.411 57.895 4.11 0.00 0.00 2.29
37 38 0.897401 GGCTTGCCTGCTCCTTTTCT 60.897 55.000 4.11 0.00 0.00 2.52
38 39 1.614317 GGCTTGCCTGCTCCTTTTCTA 60.614 52.381 4.11 0.00 0.00 2.10
39 40 2.373224 GCTTGCCTGCTCCTTTTCTAT 58.627 47.619 0.00 0.00 0.00 1.98
40 41 2.098770 GCTTGCCTGCTCCTTTTCTATG 59.901 50.000 0.00 0.00 0.00 2.23
41 42 1.755179 TGCCTGCTCCTTTTCTATGC 58.245 50.000 0.00 0.00 0.00 3.14
42 43 1.283029 TGCCTGCTCCTTTTCTATGCT 59.717 47.619 0.00 0.00 0.00 3.79
43 44 1.946081 GCCTGCTCCTTTTCTATGCTC 59.054 52.381 0.00 0.00 0.00 4.26
44 45 2.570135 CCTGCTCCTTTTCTATGCTCC 58.430 52.381 0.00 0.00 0.00 4.70
45 46 2.172293 CCTGCTCCTTTTCTATGCTCCT 59.828 50.000 0.00 0.00 0.00 3.69
46 47 3.389329 CCTGCTCCTTTTCTATGCTCCTA 59.611 47.826 0.00 0.00 0.00 2.94
47 48 4.041444 CCTGCTCCTTTTCTATGCTCCTAT 59.959 45.833 0.00 0.00 0.00 2.57
48 49 5.220710 TGCTCCTTTTCTATGCTCCTATC 57.779 43.478 0.00 0.00 0.00 2.08
49 50 4.040952 TGCTCCTTTTCTATGCTCCTATCC 59.959 45.833 0.00 0.00 0.00 2.59
50 51 4.815269 CTCCTTTTCTATGCTCCTATCCG 58.185 47.826 0.00 0.00 0.00 4.18
51 52 4.223953 TCCTTTTCTATGCTCCTATCCGT 58.776 43.478 0.00 0.00 0.00 4.69
52 53 4.039245 TCCTTTTCTATGCTCCTATCCGTG 59.961 45.833 0.00 0.00 0.00 4.94
53 54 3.386768 TTTCTATGCTCCTATCCGTGC 57.613 47.619 0.00 0.00 0.00 5.34
54 55 2.294449 TCTATGCTCCTATCCGTGCT 57.706 50.000 0.00 0.00 0.00 4.40
55 56 2.163509 TCTATGCTCCTATCCGTGCTC 58.836 52.381 0.00 0.00 0.00 4.26
56 57 1.203523 CTATGCTCCTATCCGTGCTCC 59.796 57.143 0.00 0.00 0.00 4.70
57 58 1.476007 ATGCTCCTATCCGTGCTCCC 61.476 60.000 0.00 0.00 0.00 4.30
58 59 2.134287 GCTCCTATCCGTGCTCCCA 61.134 63.158 0.00 0.00 0.00 4.37
59 60 1.476007 GCTCCTATCCGTGCTCCCAT 61.476 60.000 0.00 0.00 0.00 4.00
60 61 1.051812 CTCCTATCCGTGCTCCCATT 58.948 55.000 0.00 0.00 0.00 3.16
61 62 1.417890 CTCCTATCCGTGCTCCCATTT 59.582 52.381 0.00 0.00 0.00 2.32
62 63 1.843851 TCCTATCCGTGCTCCCATTTT 59.156 47.619 0.00 0.00 0.00 1.82
63 64 1.949525 CCTATCCGTGCTCCCATTTTG 59.050 52.381 0.00 0.00 0.00 2.44
64 65 2.643551 CTATCCGTGCTCCCATTTTGT 58.356 47.619 0.00 0.00 0.00 2.83
65 66 1.463674 ATCCGTGCTCCCATTTTGTC 58.536 50.000 0.00 0.00 0.00 3.18
66 67 0.608035 TCCGTGCTCCCATTTTGTCC 60.608 55.000 0.00 0.00 0.00 4.02
67 68 0.609131 CCGTGCTCCCATTTTGTCCT 60.609 55.000 0.00 0.00 0.00 3.85
68 69 1.339631 CCGTGCTCCCATTTTGTCCTA 60.340 52.381 0.00 0.00 0.00 2.94
69 70 1.737793 CGTGCTCCCATTTTGTCCTAC 59.262 52.381 0.00 0.00 0.00 3.18
70 71 1.737793 GTGCTCCCATTTTGTCCTACG 59.262 52.381 0.00 0.00 0.00 3.51
71 72 1.349688 TGCTCCCATTTTGTCCTACGT 59.650 47.619 0.00 0.00 0.00 3.57
72 73 2.224670 TGCTCCCATTTTGTCCTACGTT 60.225 45.455 0.00 0.00 0.00 3.99
73 74 2.817844 GCTCCCATTTTGTCCTACGTTT 59.182 45.455 0.00 0.00 0.00 3.60
74 75 3.254903 GCTCCCATTTTGTCCTACGTTTT 59.745 43.478 0.00 0.00 0.00 2.43
75 76 4.261867 GCTCCCATTTTGTCCTACGTTTTT 60.262 41.667 0.00 0.00 0.00 1.94
132 133 9.499479 TCATATCTGATTTTAAGAGAATGAGGC 57.501 33.333 0.00 0.00 31.47 4.70
133 134 8.728833 CATATCTGATTTTAAGAGAATGAGGCC 58.271 37.037 0.00 0.00 0.00 5.19
134 135 5.118990 TCTGATTTTAAGAGAATGAGGCCG 58.881 41.667 0.00 0.00 0.00 6.13
135 136 4.199310 TGATTTTAAGAGAATGAGGCCGG 58.801 43.478 0.00 0.00 0.00 6.13
136 137 2.710096 TTTAAGAGAATGAGGCCGGG 57.290 50.000 2.18 0.00 0.00 5.73
137 138 0.180406 TTAAGAGAATGAGGCCGGGC 59.820 55.000 22.67 22.67 0.00 6.13
138 139 0.691078 TAAGAGAATGAGGCCGGGCT 60.691 55.000 33.40 33.40 0.00 5.19
139 140 1.566298 AAGAGAATGAGGCCGGGCTT 61.566 55.000 33.28 17.22 0.00 4.35
140 141 1.077429 GAGAATGAGGCCGGGCTTT 60.077 57.895 33.28 23.36 0.00 3.51
141 142 0.180406 GAGAATGAGGCCGGGCTTTA 59.820 55.000 33.28 23.83 0.00 1.85
142 143 0.846693 AGAATGAGGCCGGGCTTTAT 59.153 50.000 33.28 24.95 0.00 1.40
143 144 1.215423 AGAATGAGGCCGGGCTTTATT 59.785 47.619 33.28 30.79 0.00 1.40
144 145 2.031870 GAATGAGGCCGGGCTTTATTT 58.968 47.619 33.28 21.41 0.00 1.40
145 146 2.159179 ATGAGGCCGGGCTTTATTTT 57.841 45.000 33.28 7.87 0.00 1.82
146 147 1.181786 TGAGGCCGGGCTTTATTTTG 58.818 50.000 33.28 0.00 0.00 2.44
147 148 1.182667 GAGGCCGGGCTTTATTTTGT 58.817 50.000 33.28 6.07 0.00 2.83
148 149 1.548719 GAGGCCGGGCTTTATTTTGTT 59.451 47.619 33.28 5.17 0.00 2.83
149 150 1.974957 AGGCCGGGCTTTATTTTGTTT 59.025 42.857 27.45 0.00 0.00 2.83
150 151 2.028476 AGGCCGGGCTTTATTTTGTTTC 60.028 45.455 27.45 0.00 0.00 2.78
151 152 2.289133 GGCCGGGCTTTATTTTGTTTCA 60.289 45.455 22.87 0.00 0.00 2.69
152 153 3.394719 GCCGGGCTTTATTTTGTTTCAA 58.605 40.909 12.87 0.00 0.00 2.69
153 154 4.000325 GCCGGGCTTTATTTTGTTTCAAT 59.000 39.130 12.87 0.00 0.00 2.57
154 155 4.092821 GCCGGGCTTTATTTTGTTTCAATC 59.907 41.667 12.87 0.00 0.00 2.67
155 156 5.233988 CCGGGCTTTATTTTGTTTCAATCA 58.766 37.500 0.00 0.00 0.00 2.57
156 157 5.698545 CCGGGCTTTATTTTGTTTCAATCAA 59.301 36.000 0.00 0.00 0.00 2.57
157 158 6.203723 CCGGGCTTTATTTTGTTTCAATCAAA 59.796 34.615 0.00 0.00 33.76 2.69
158 159 7.094848 CCGGGCTTTATTTTGTTTCAATCAAAT 60.095 33.333 0.00 0.00 35.25 2.32
159 160 7.956943 CGGGCTTTATTTTGTTTCAATCAAATC 59.043 33.333 0.00 0.00 35.25 2.17
160 161 8.782144 GGGCTTTATTTTGTTTCAATCAAATCA 58.218 29.630 0.00 0.00 35.25 2.57
167 168 7.621832 TTTGTTTCAATCAAATCAAGCTACG 57.378 32.000 0.00 0.00 31.17 3.51
168 169 6.312399 TGTTTCAATCAAATCAAGCTACGT 57.688 33.333 0.00 0.00 0.00 3.57
169 170 7.428282 TGTTTCAATCAAATCAAGCTACGTA 57.572 32.000 0.00 0.00 0.00 3.57
170 171 8.039603 TGTTTCAATCAAATCAAGCTACGTAT 57.960 30.769 0.00 0.00 0.00 3.06
171 172 7.962373 TGTTTCAATCAAATCAAGCTACGTATG 59.038 33.333 0.00 0.00 0.00 2.39
172 173 6.048073 TCAATCAAATCAAGCTACGTATGC 57.952 37.500 0.00 2.19 0.00 3.14
173 174 4.715520 ATCAAATCAAGCTACGTATGCG 57.284 40.909 0.19 0.19 44.93 4.73
174 175 3.776340 TCAAATCAAGCTACGTATGCGA 58.224 40.909 11.07 0.00 42.00 5.10
175 176 4.177783 TCAAATCAAGCTACGTATGCGAA 58.822 39.130 11.07 0.00 42.00 4.70
176 177 4.627900 TCAAATCAAGCTACGTATGCGAAA 59.372 37.500 11.07 0.00 42.00 3.46
177 178 4.778842 AATCAAGCTACGTATGCGAAAG 57.221 40.909 11.07 8.02 42.00 2.62
178 179 3.226346 TCAAGCTACGTATGCGAAAGT 57.774 42.857 11.07 0.00 42.00 2.66
179 180 4.359971 TCAAGCTACGTATGCGAAAGTA 57.640 40.909 11.07 0.00 42.00 2.24
180 181 4.100529 TCAAGCTACGTATGCGAAAGTAC 58.899 43.478 11.07 0.00 42.00 2.73
181 182 2.713011 AGCTACGTATGCGAAAGTACG 58.287 47.619 11.07 3.67 46.59 3.67
182 183 1.777461 GCTACGTATGCGAAAGTACGG 59.223 52.381 11.07 0.00 45.75 4.02
183 184 2.539547 GCTACGTATGCGAAAGTACGGA 60.540 50.000 11.07 0.32 45.75 4.69
184 185 2.857592 ACGTATGCGAAAGTACGGAT 57.142 45.000 11.07 0.00 45.75 4.18
185 186 2.456989 ACGTATGCGAAAGTACGGATG 58.543 47.619 11.07 0.00 45.75 3.51
186 187 2.097954 ACGTATGCGAAAGTACGGATGA 59.902 45.455 11.07 0.00 45.75 2.92
187 188 3.110358 CGTATGCGAAAGTACGGATGAA 58.890 45.455 0.00 0.00 43.36 2.57
188 189 3.061403 CGTATGCGAAAGTACGGATGAAC 60.061 47.826 0.00 0.00 43.36 3.18
189 190 1.342555 TGCGAAAGTACGGATGAACG 58.657 50.000 0.00 0.00 40.31 3.95
190 191 0.024619 GCGAAAGTACGGATGAACGC 59.975 55.000 0.00 0.00 37.37 4.84
191 192 1.342555 CGAAAGTACGGATGAACGCA 58.657 50.000 0.00 0.00 37.37 5.24
192 193 1.058695 CGAAAGTACGGATGAACGCAC 59.941 52.381 0.00 0.00 37.37 5.34
193 194 2.063266 GAAAGTACGGATGAACGCACA 58.937 47.619 0.00 0.00 37.37 4.57
194 195 1.425412 AAGTACGGATGAACGCACAC 58.575 50.000 0.00 0.00 37.37 3.82
196 197 2.089936 TACGGATGAACGCACACGC 61.090 57.895 0.00 0.00 45.53 5.34
213 214 3.382111 CGGGGAGCAGTCAAGTCT 58.618 61.111 0.00 0.00 0.00 3.24
214 215 1.216710 CGGGGAGCAGTCAAGTCTC 59.783 63.158 0.00 0.00 0.00 3.36
215 216 1.216710 GGGGAGCAGTCAAGTCTCG 59.783 63.158 0.00 0.00 0.00 4.04
216 217 1.536943 GGGGAGCAGTCAAGTCTCGT 61.537 60.000 0.00 0.00 0.00 4.18
217 218 0.109039 GGGAGCAGTCAAGTCTCGTC 60.109 60.000 0.00 0.00 0.00 4.20
218 219 0.109039 GGAGCAGTCAAGTCTCGTCC 60.109 60.000 0.00 0.00 0.00 4.79
219 220 0.598562 GAGCAGTCAAGTCTCGTCCA 59.401 55.000 0.00 0.00 0.00 4.02
220 221 0.315568 AGCAGTCAAGTCTCGTCCAC 59.684 55.000 0.00 0.00 0.00 4.02
221 222 0.315568 GCAGTCAAGTCTCGTCCACT 59.684 55.000 0.00 0.00 0.00 4.00
222 223 1.932604 GCAGTCAAGTCTCGTCCACTG 60.933 57.143 0.00 0.00 35.39 3.66
223 224 1.338337 CAGTCAAGTCTCGTCCACTGT 59.662 52.381 0.00 0.00 0.00 3.55
224 225 2.552743 CAGTCAAGTCTCGTCCACTGTA 59.447 50.000 0.00 0.00 0.00 2.74
225 226 2.553172 AGTCAAGTCTCGTCCACTGTAC 59.447 50.000 0.00 0.00 0.00 2.90
226 227 1.884579 TCAAGTCTCGTCCACTGTACC 59.115 52.381 0.00 0.00 0.00 3.34
227 228 1.067776 CAAGTCTCGTCCACTGTACCC 60.068 57.143 0.00 0.00 0.00 3.69
228 229 0.611340 AGTCTCGTCCACTGTACCCC 60.611 60.000 0.00 0.00 0.00 4.95
229 230 1.676635 TCTCGTCCACTGTACCCCG 60.677 63.158 0.00 0.00 0.00 5.73
230 231 1.676635 CTCGTCCACTGTACCCCGA 60.677 63.158 0.00 0.00 0.00 5.14
231 232 1.930908 CTCGTCCACTGTACCCCGAC 61.931 65.000 0.00 0.00 0.00 4.79
234 235 2.605295 CCACTGTACCCCGACCCA 60.605 66.667 0.00 0.00 0.00 4.51
244 245 2.746277 CCGACCCAAAGGCCGAAG 60.746 66.667 0.00 0.00 36.11 3.79
255 256 1.810030 GGCCGAAGTCGTGACCATC 60.810 63.158 0.00 0.00 37.74 3.51
256 257 1.215647 GCCGAAGTCGTGACCATCT 59.784 57.895 0.00 0.00 37.74 2.90
257 258 0.389948 GCCGAAGTCGTGACCATCTT 60.390 55.000 0.00 0.00 37.74 2.40
258 259 1.350193 CCGAAGTCGTGACCATCTTG 58.650 55.000 0.00 0.00 37.74 3.02
271 272 0.754217 CATCTTGCCCCCACATCCAG 60.754 60.000 0.00 0.00 0.00 3.86
294 295 3.423154 GCCCGGTGCAGTTCTTCG 61.423 66.667 9.72 0.00 40.77 3.79
520 522 1.203928 CTCGTCGTTCTGCATCATCC 58.796 55.000 0.00 0.00 0.00 3.51
523 525 0.107703 GTCGTTCTGCATCATCCCCA 60.108 55.000 0.00 0.00 0.00 4.96
531 533 0.184451 GCATCATCCCCACCTGTGAT 59.816 55.000 0.00 0.00 0.00 3.06
669 696 1.473434 GGAGGCGGAAATCGATCAGTT 60.473 52.381 0.00 0.00 42.43 3.16
670 697 1.594862 GAGGCGGAAATCGATCAGTTG 59.405 52.381 0.00 0.00 42.43 3.16
671 698 1.066143 AGGCGGAAATCGATCAGTTGT 60.066 47.619 0.00 0.00 42.43 3.32
672 699 2.167693 AGGCGGAAATCGATCAGTTGTA 59.832 45.455 0.00 0.00 42.43 2.41
673 700 2.284417 GGCGGAAATCGATCAGTTGTAC 59.716 50.000 0.00 0.00 42.43 2.90
714 741 2.357034 CACTCACCACCGAACCCG 60.357 66.667 0.00 0.00 0.00 5.28
776 806 1.025041 CCCGGCTATTTTTCTCTGCC 58.975 55.000 0.00 0.00 40.14 4.85
777 807 1.025041 CCGGCTATTTTTCTCTGCCC 58.975 55.000 0.00 0.00 40.40 5.36
780 810 2.420687 CGGCTATTTTTCTCTGCCCTCT 60.421 50.000 0.00 0.00 40.40 3.69
827 857 4.080299 GGTGAGTTCCTTCTTGTCCCATAT 60.080 45.833 0.00 0.00 0.00 1.78
857 974 2.157668 CCGTTTCCTTTCGTCAGTGATG 59.842 50.000 5.96 5.96 0.00 3.07
917 1038 2.729194 ACTAGCATCTCTGAGGACGTT 58.271 47.619 4.59 0.00 0.00 3.99
942 1063 4.552767 CGAATTTGCGTCTTTGAGACTGTT 60.553 41.667 6.53 0.00 42.92 3.16
952 1073 6.035843 GTCTTTGAGACTGTTGAAATTGCAA 58.964 36.000 0.00 0.00 41.88 4.08
1007 1130 8.939929 TGATTTGTTTCTACTCTAAATGCAGAG 58.060 33.333 0.00 0.00 46.31 3.35
1068 1191 1.002033 CTCAGCAACTTGCCTGAACAC 60.002 52.381 10.25 0.00 46.52 3.32
1366 1489 0.036765 CATTGGGCATGCTGTTGCTT 60.037 50.000 18.92 0.00 42.38 3.91
1369 1492 0.539207 TGGGCATGCTGTTGCTTACA 60.539 50.000 18.92 0.59 42.38 2.41
1370 1493 0.602562 GGGCATGCTGTTGCTTACAA 59.397 50.000 18.92 0.00 42.38 2.41
1610 1733 5.220228 CGTTTGAATCATCTACGACTGTTCC 60.220 44.000 7.09 0.00 36.84 3.62
1687 1810 5.143916 AGCTCGCTATTGTTAATTGTTCG 57.856 39.130 0.00 0.00 0.00 3.95
1957 2080 4.899352 AGCTCTGGTCACACTTCTTATT 57.101 40.909 0.00 0.00 0.00 1.40
1975 2098 5.884232 TCTTATTTGCTCAGCTCATCATGTT 59.116 36.000 0.00 0.00 0.00 2.71
1979 2102 2.417586 TGCTCAGCTCATCATGTTTTCG 59.582 45.455 0.00 0.00 0.00 3.46
2177 2300 8.824756 TCTTACCTAAATCTTGCTCTCTTCTA 57.175 34.615 0.00 0.00 0.00 2.10
2204 2339 5.848406 ACCGAATTTTGAAGTTTGCCATTA 58.152 33.333 0.00 0.00 0.00 1.90
2231 2368 4.333649 ACATTGAATACGAATGGCTGTGAG 59.666 41.667 0.00 0.00 35.48 3.51
2363 2500 2.507407 TAAGGGTGCAGAATGGGAAC 57.493 50.000 0.00 0.00 35.86 3.62
2383 2520 1.822990 CCATCTGCAACTGCTTTCCAT 59.177 47.619 2.95 0.00 42.66 3.41
2459 2596 1.269166 GAACTATGTCAGGCGTGTCG 58.731 55.000 6.26 0.00 0.00 4.35
2692 2838 4.993905 AGTGTTTTCAGGTTAGTTTGTGC 58.006 39.130 0.00 0.00 0.00 4.57
2763 2910 4.095782 GTCAGTACTTGTCAAGGTTTTGCA 59.904 41.667 16.85 0.00 34.21 4.08
2764 2911 4.887071 TCAGTACTTGTCAAGGTTTTGCAT 59.113 37.500 16.85 0.00 34.21 3.96
2765 2912 4.977963 CAGTACTTGTCAAGGTTTTGCATG 59.022 41.667 16.85 0.00 34.21 4.06
2766 2913 4.887071 AGTACTTGTCAAGGTTTTGCATGA 59.113 37.500 16.85 0.00 34.21 3.07
2845 2999 5.699097 AGAGGAATTCACTCTCGTATAGC 57.301 43.478 16.35 0.00 41.26 2.97
2919 3074 2.167861 GGCCACGCTCGTCATCTTC 61.168 63.158 0.00 0.00 0.00 2.87
2952 3107 5.008217 AGCTCGAGACTACATGATGAACTAC 59.992 44.000 18.75 0.00 0.00 2.73
2953 3108 5.220873 GCTCGAGACTACATGATGAACTACA 60.221 44.000 18.75 0.00 0.00 2.74
3014 3177 4.688879 TGTGTTCTTGTATGATCGGTTGAC 59.311 41.667 0.00 0.00 0.00 3.18
3027 3190 1.334059 CGGTTGACATGTGACAAGTGC 60.334 52.381 1.15 0.00 31.08 4.40
3030 3193 3.753272 GGTTGACATGTGACAAGTGCTAT 59.247 43.478 1.15 0.00 31.08 2.97
3045 3214 1.766143 GCTATGGCAAGCTTCCGTCG 61.766 60.000 11.48 8.06 39.50 5.12
3053 3222 1.228657 AAGCTTCCGTCGCAGTTTCC 61.229 55.000 0.00 0.00 0.00 3.13
3054 3223 3.011760 GCTTCCGTCGCAGTTTCCG 62.012 63.158 0.00 0.00 0.00 4.30
3082 3251 3.567308 AGCAGGGCTGTGTGAAGA 58.433 55.556 0.00 0.00 37.57 2.87
3114 3283 1.472878 CAAGAGGATCAACTCGTCGGA 59.527 52.381 0.00 0.00 42.37 4.55
3160 3329 5.704515 CGCTAATTCAAGGGATGATCATCTT 59.295 40.000 29.85 17.59 38.03 2.40
3193 3362 4.204799 GGTTCCTGTAGTGTTTTCAGGTT 58.795 43.478 9.71 0.00 46.04 3.50
3217 3387 5.351458 AGTTGTGTTGCAATTCCTTTCTTC 58.649 37.500 0.59 0.00 39.55 2.87
3230 3403 2.803956 CCTTTCTTCGCCTGAAACGTTA 59.196 45.455 0.00 0.00 32.66 3.18
3237 3410 1.732259 CGCCTGAAACGTTAGCTGAAT 59.268 47.619 0.00 0.00 0.00 2.57
3238 3411 2.159627 CGCCTGAAACGTTAGCTGAATT 59.840 45.455 0.00 0.00 0.00 2.17
3239 3412 3.492313 GCCTGAAACGTTAGCTGAATTG 58.508 45.455 0.00 0.00 0.00 2.32
3241 3414 4.466828 CCTGAAACGTTAGCTGAATTGTG 58.533 43.478 0.00 0.00 0.00 3.33
3243 3416 5.493133 TGAAACGTTAGCTGAATTGTGTT 57.507 34.783 0.00 0.00 0.00 3.32
3244 3417 5.270083 TGAAACGTTAGCTGAATTGTGTTG 58.730 37.500 0.00 0.00 0.00 3.33
3245 3418 4.893424 AACGTTAGCTGAATTGTGTTGT 57.107 36.364 0.00 0.00 0.00 3.32
3274 3451 2.272230 TTTCCAACCGGGCTCACACA 62.272 55.000 6.32 0.00 36.21 3.72
3287 3464 3.763897 GGCTCACACACCTTTCCATTAAT 59.236 43.478 0.00 0.00 0.00 1.40
3311 3488 6.089920 TGCTCAACGAAAATATTCAGTACG 57.910 37.500 0.00 0.00 35.15 3.67
3335 3512 5.181245 GCAAATCTTAGCTACAACTGAACCA 59.819 40.000 0.00 0.00 0.00 3.67
3368 3545 0.737715 CGGGAAAGTGGAGAAGCGAG 60.738 60.000 0.00 0.00 0.00 5.03
3417 3594 1.067416 TGCTCGCTGTCGAAACACT 59.933 52.632 0.00 0.00 44.98 3.55
3424 3601 2.206750 GCTGTCGAAACACTTACCACA 58.793 47.619 0.00 0.00 0.00 4.17
3428 3605 0.872388 CGAAACACTTACCACAGGGC 59.128 55.000 0.00 0.00 37.90 5.19
3432 3609 1.981256 ACACTTACCACAGGGCAAAG 58.019 50.000 0.00 0.00 37.90 2.77
3437 3614 2.032965 TACCACAGGGCAAAGACCTA 57.967 50.000 0.00 0.00 40.42 3.08
3447 3624 3.442625 GGGCAAAGACCTATTAACACCAC 59.557 47.826 0.00 0.00 0.00 4.16
3485 3662 0.686224 CAGGGCTGGGATCTCAGATC 59.314 60.000 27.21 16.21 36.93 2.75
3486 3663 0.267054 AGGGCTGGGATCTCAGATCA 59.733 55.000 27.21 0.00 36.93 2.92
3489 3666 1.487976 GGCTGGGATCTCAGATCACAA 59.512 52.381 27.21 5.11 36.93 3.33
3492 3669 4.012374 GCTGGGATCTCAGATCACAAAAA 58.988 43.478 27.21 0.00 36.93 1.94
3494 3671 5.221009 GCTGGGATCTCAGATCACAAAAATC 60.221 44.000 27.21 4.42 36.93 2.17
3497 3674 6.376299 TGGGATCTCAGATCACAAAAATCTTG 59.624 38.462 17.84 0.00 31.05 3.02
3589 3807 3.003793 CAGCATCTTCAATCATGAGCCTG 59.996 47.826 0.09 0.00 36.78 4.85
3605 3823 3.403624 TGCCCCGAGAAGCAGAAT 58.596 55.556 0.00 0.00 33.08 2.40
3606 3824 1.078214 TGCCCCGAGAAGCAGAATG 60.078 57.895 0.00 0.00 40.87 2.67
3610 3828 1.495878 CCCGAGAAGCAGAATGATCG 58.504 55.000 0.00 0.00 39.69 3.69
3612 3830 0.857935 CGAGAAGCAGAATGATCGGC 59.142 55.000 0.00 0.00 45.73 5.54
3620 3838 0.387202 AGAATGATCGGCCAGAGACG 59.613 55.000 2.24 0.00 0.00 4.18
3628 3846 4.459089 GCCAGAGACGAGGCCACC 62.459 72.222 5.01 0.00 45.18 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.440476 CGGATCCGGGAACAGGTAC 59.560 63.158 26.95 0.00 35.56 3.34
12 13 4.496336 AGCAGGCAAGCCGGATCC 62.496 66.667 15.46 0.00 41.95 3.36
13 14 2.899339 GAGCAGGCAAGCCGGATC 60.899 66.667 15.46 14.32 39.23 3.36
14 15 4.496336 GGAGCAGGCAAGCCGGAT 62.496 66.667 15.46 8.74 41.95 4.18
16 17 4.729918 AAGGAGCAGGCAAGCCGG 62.730 66.667 6.88 6.88 41.95 6.13
17 18 2.205243 GAAAAGGAGCAGGCAAGCCG 62.205 60.000 5.28 2.12 41.95 5.52
18 19 0.897401 AGAAAAGGAGCAGGCAAGCC 60.897 55.000 2.02 2.02 34.23 4.35
19 20 1.826385 TAGAAAAGGAGCAGGCAAGC 58.174 50.000 0.00 0.00 0.00 4.01
20 21 2.098770 GCATAGAAAAGGAGCAGGCAAG 59.901 50.000 0.00 0.00 0.00 4.01
21 22 2.094675 GCATAGAAAAGGAGCAGGCAA 58.905 47.619 0.00 0.00 0.00 4.52
22 23 1.283029 AGCATAGAAAAGGAGCAGGCA 59.717 47.619 0.00 0.00 0.00 4.75
23 24 1.946081 GAGCATAGAAAAGGAGCAGGC 59.054 52.381 0.00 0.00 0.00 4.85
24 25 2.172293 AGGAGCATAGAAAAGGAGCAGG 59.828 50.000 0.00 0.00 0.00 4.85
25 26 3.557228 AGGAGCATAGAAAAGGAGCAG 57.443 47.619 0.00 0.00 0.00 4.24
26 27 4.040952 GGATAGGAGCATAGAAAAGGAGCA 59.959 45.833 0.00 0.00 0.00 4.26
27 28 4.574892 GGATAGGAGCATAGAAAAGGAGC 58.425 47.826 0.00 0.00 0.00 4.70
28 29 4.282195 ACGGATAGGAGCATAGAAAAGGAG 59.718 45.833 0.00 0.00 0.00 3.69
29 30 4.039245 CACGGATAGGAGCATAGAAAAGGA 59.961 45.833 0.00 0.00 0.00 3.36
30 31 4.310769 CACGGATAGGAGCATAGAAAAGG 58.689 47.826 0.00 0.00 0.00 3.11
31 32 3.743396 GCACGGATAGGAGCATAGAAAAG 59.257 47.826 0.00 0.00 0.00 2.27
32 33 3.388024 AGCACGGATAGGAGCATAGAAAA 59.612 43.478 0.00 0.00 0.00 2.29
33 34 2.965831 AGCACGGATAGGAGCATAGAAA 59.034 45.455 0.00 0.00 0.00 2.52
34 35 2.558795 GAGCACGGATAGGAGCATAGAA 59.441 50.000 0.00 0.00 0.00 2.10
35 36 2.163509 GAGCACGGATAGGAGCATAGA 58.836 52.381 0.00 0.00 0.00 1.98
36 37 1.203523 GGAGCACGGATAGGAGCATAG 59.796 57.143 0.00 0.00 0.00 2.23
37 38 1.257743 GGAGCACGGATAGGAGCATA 58.742 55.000 0.00 0.00 0.00 3.14
38 39 1.476007 GGGAGCACGGATAGGAGCAT 61.476 60.000 0.00 0.00 0.00 3.79
39 40 2.134287 GGGAGCACGGATAGGAGCA 61.134 63.158 0.00 0.00 0.00 4.26
40 41 1.476007 ATGGGAGCACGGATAGGAGC 61.476 60.000 0.00 0.00 0.00 4.70
41 42 1.051812 AATGGGAGCACGGATAGGAG 58.948 55.000 0.00 0.00 0.00 3.69
42 43 1.507140 AAATGGGAGCACGGATAGGA 58.493 50.000 0.00 0.00 0.00 2.94
43 44 1.949525 CAAAATGGGAGCACGGATAGG 59.050 52.381 0.00 0.00 0.00 2.57
44 45 2.614057 GACAAAATGGGAGCACGGATAG 59.386 50.000 0.00 0.00 0.00 2.08
45 46 2.639065 GACAAAATGGGAGCACGGATA 58.361 47.619 0.00 0.00 0.00 2.59
46 47 1.463674 GACAAAATGGGAGCACGGAT 58.536 50.000 0.00 0.00 0.00 4.18
47 48 0.608035 GGACAAAATGGGAGCACGGA 60.608 55.000 0.00 0.00 0.00 4.69
48 49 0.609131 AGGACAAAATGGGAGCACGG 60.609 55.000 0.00 0.00 0.00 4.94
49 50 1.737793 GTAGGACAAAATGGGAGCACG 59.262 52.381 0.00 0.00 0.00 5.34
50 51 1.737793 CGTAGGACAAAATGGGAGCAC 59.262 52.381 0.00 0.00 0.00 4.40
51 52 1.349688 ACGTAGGACAAAATGGGAGCA 59.650 47.619 0.00 0.00 0.00 4.26
52 53 2.109425 ACGTAGGACAAAATGGGAGC 57.891 50.000 0.00 0.00 0.00 4.70
53 54 5.447624 AAAAACGTAGGACAAAATGGGAG 57.552 39.130 0.00 0.00 0.00 4.30
106 107 9.499479 GCCTCATTCTCTTAAAATCAGATATGA 57.501 33.333 0.00 0.00 0.00 2.15
107 108 8.728833 GGCCTCATTCTCTTAAAATCAGATATG 58.271 37.037 0.00 0.00 0.00 1.78
108 109 7.605691 CGGCCTCATTCTCTTAAAATCAGATAT 59.394 37.037 0.00 0.00 0.00 1.63
109 110 6.931281 CGGCCTCATTCTCTTAAAATCAGATA 59.069 38.462 0.00 0.00 0.00 1.98
110 111 5.762218 CGGCCTCATTCTCTTAAAATCAGAT 59.238 40.000 0.00 0.00 0.00 2.90
111 112 5.118990 CGGCCTCATTCTCTTAAAATCAGA 58.881 41.667 0.00 0.00 0.00 3.27
112 113 4.274459 CCGGCCTCATTCTCTTAAAATCAG 59.726 45.833 0.00 0.00 0.00 2.90
113 114 4.199310 CCGGCCTCATTCTCTTAAAATCA 58.801 43.478 0.00 0.00 0.00 2.57
114 115 3.565902 CCCGGCCTCATTCTCTTAAAATC 59.434 47.826 0.00 0.00 0.00 2.17
115 116 3.555966 CCCGGCCTCATTCTCTTAAAAT 58.444 45.455 0.00 0.00 0.00 1.82
116 117 2.944094 GCCCGGCCTCATTCTCTTAAAA 60.944 50.000 0.00 0.00 0.00 1.52
117 118 1.408266 GCCCGGCCTCATTCTCTTAAA 60.408 52.381 0.00 0.00 0.00 1.52
118 119 0.180406 GCCCGGCCTCATTCTCTTAA 59.820 55.000 0.00 0.00 0.00 1.85
119 120 0.691078 AGCCCGGCCTCATTCTCTTA 60.691 55.000 5.55 0.00 0.00 2.10
120 121 1.566298 AAGCCCGGCCTCATTCTCTT 61.566 55.000 5.55 0.00 0.00 2.85
121 122 1.566298 AAAGCCCGGCCTCATTCTCT 61.566 55.000 5.55 0.00 0.00 3.10
122 123 0.180406 TAAAGCCCGGCCTCATTCTC 59.820 55.000 5.55 0.00 0.00 2.87
123 124 0.846693 ATAAAGCCCGGCCTCATTCT 59.153 50.000 5.55 0.00 0.00 2.40
124 125 1.692411 AATAAAGCCCGGCCTCATTC 58.308 50.000 5.55 0.00 0.00 2.67
125 126 2.159179 AAATAAAGCCCGGCCTCATT 57.841 45.000 5.55 0.00 0.00 2.57
126 127 1.756538 CAAAATAAAGCCCGGCCTCAT 59.243 47.619 5.55 0.00 0.00 2.90
127 128 1.181786 CAAAATAAAGCCCGGCCTCA 58.818 50.000 5.55 0.00 0.00 3.86
128 129 1.182667 ACAAAATAAAGCCCGGCCTC 58.817 50.000 5.55 0.00 0.00 4.70
129 130 1.639722 AACAAAATAAAGCCCGGCCT 58.360 45.000 5.55 0.00 0.00 5.19
130 131 2.289133 TGAAACAAAATAAAGCCCGGCC 60.289 45.455 5.55 0.00 0.00 6.13
131 132 3.033368 TGAAACAAAATAAAGCCCGGC 57.967 42.857 0.00 0.00 0.00 6.13
132 133 5.233988 TGATTGAAACAAAATAAAGCCCGG 58.766 37.500 0.00 0.00 0.00 5.73
133 134 6.777526 TTGATTGAAACAAAATAAAGCCCG 57.222 33.333 0.00 0.00 0.00 6.13
134 135 8.782144 TGATTTGATTGAAACAAAATAAAGCCC 58.218 29.630 4.74 0.00 39.95 5.19
141 142 8.702438 CGTAGCTTGATTTGATTGAAACAAAAT 58.298 29.630 4.74 0.00 39.95 1.82
142 143 7.704472 ACGTAGCTTGATTTGATTGAAACAAAA 59.296 29.630 4.74 0.00 39.95 2.44
143 144 7.199766 ACGTAGCTTGATTTGATTGAAACAAA 58.800 30.769 3.11 3.11 40.62 2.83
144 145 6.734137 ACGTAGCTTGATTTGATTGAAACAA 58.266 32.000 0.00 0.00 0.00 2.83
145 146 6.312399 ACGTAGCTTGATTTGATTGAAACA 57.688 33.333 0.00 0.00 0.00 2.83
146 147 7.044706 GCATACGTAGCTTGATTTGATTGAAAC 60.045 37.037 0.08 0.00 0.00 2.78
147 148 6.966632 GCATACGTAGCTTGATTTGATTGAAA 59.033 34.615 0.08 0.00 0.00 2.69
148 149 6.486248 GCATACGTAGCTTGATTTGATTGAA 58.514 36.000 0.08 0.00 0.00 2.69
149 150 5.276820 CGCATACGTAGCTTGATTTGATTGA 60.277 40.000 0.08 0.00 33.53 2.57
150 151 4.900182 CGCATACGTAGCTTGATTTGATTG 59.100 41.667 0.08 0.00 33.53 2.67
151 152 4.808895 TCGCATACGTAGCTTGATTTGATT 59.191 37.500 0.08 0.00 41.18 2.57
152 153 4.368315 TCGCATACGTAGCTTGATTTGAT 58.632 39.130 0.08 0.00 41.18 2.57
153 154 3.776340 TCGCATACGTAGCTTGATTTGA 58.224 40.909 0.08 0.00 41.18 2.69
154 155 4.514545 TTCGCATACGTAGCTTGATTTG 57.485 40.909 0.08 0.00 41.18 2.32
155 156 4.630069 ACTTTCGCATACGTAGCTTGATTT 59.370 37.500 0.08 0.00 41.18 2.17
156 157 4.181578 ACTTTCGCATACGTAGCTTGATT 58.818 39.130 0.08 0.00 41.18 2.57
157 158 3.782046 ACTTTCGCATACGTAGCTTGAT 58.218 40.909 0.08 0.00 41.18 2.57
158 159 3.226346 ACTTTCGCATACGTAGCTTGA 57.774 42.857 0.08 0.00 41.18 3.02
159 160 3.062059 CGTACTTTCGCATACGTAGCTTG 60.062 47.826 0.08 0.00 39.42 4.01
160 161 3.103738 CGTACTTTCGCATACGTAGCTT 58.896 45.455 0.08 0.00 39.42 3.74
161 162 2.540361 CCGTACTTTCGCATACGTAGCT 60.540 50.000 0.08 0.00 42.03 3.32
162 163 1.777461 CCGTACTTTCGCATACGTAGC 59.223 52.381 0.08 4.27 42.03 3.58
163 164 3.323729 TCCGTACTTTCGCATACGTAG 57.676 47.619 0.08 0.00 42.03 3.51
164 165 3.312146 TCATCCGTACTTTCGCATACGTA 59.688 43.478 0.00 0.00 42.03 3.57
165 166 2.097954 TCATCCGTACTTTCGCATACGT 59.902 45.455 0.00 0.00 42.03 3.57
166 167 2.723209 TCATCCGTACTTTCGCATACG 58.277 47.619 0.00 0.00 42.97 3.06
167 168 3.061403 CGTTCATCCGTACTTTCGCATAC 60.061 47.826 0.00 0.00 0.00 2.39
168 169 3.110358 CGTTCATCCGTACTTTCGCATA 58.890 45.455 0.00 0.00 0.00 3.14
169 170 1.924524 CGTTCATCCGTACTTTCGCAT 59.075 47.619 0.00 0.00 0.00 4.73
170 171 1.342555 CGTTCATCCGTACTTTCGCA 58.657 50.000 0.00 0.00 0.00 5.10
171 172 0.024619 GCGTTCATCCGTACTTTCGC 59.975 55.000 0.00 0.00 36.06 4.70
172 173 1.058695 GTGCGTTCATCCGTACTTTCG 59.941 52.381 0.00 0.00 39.82 3.46
173 174 2.063266 TGTGCGTTCATCCGTACTTTC 58.937 47.619 3.70 0.00 42.78 2.62
174 175 1.796459 GTGTGCGTTCATCCGTACTTT 59.204 47.619 3.70 0.00 42.78 2.66
175 176 1.425412 GTGTGCGTTCATCCGTACTT 58.575 50.000 3.70 0.00 42.78 2.24
176 177 0.731514 CGTGTGCGTTCATCCGTACT 60.732 55.000 3.70 0.00 42.78 2.73
177 178 1.700029 CGTGTGCGTTCATCCGTAC 59.300 57.895 0.00 0.00 42.68 3.67
178 179 2.089936 GCGTGTGCGTTCATCCGTA 61.090 57.895 0.00 0.00 40.81 4.02
179 180 3.411351 GCGTGTGCGTTCATCCGT 61.411 61.111 0.00 0.00 40.81 4.69
192 193 4.680237 TTGACTGCTCCCCGCGTG 62.680 66.667 4.92 0.00 43.27 5.34
193 194 4.379243 CTTGACTGCTCCCCGCGT 62.379 66.667 4.92 0.00 43.27 6.01
194 195 4.379243 ACTTGACTGCTCCCCGCG 62.379 66.667 0.00 0.00 43.27 6.46
195 196 2.435059 GACTTGACTGCTCCCCGC 60.435 66.667 0.00 0.00 39.77 6.13
196 197 1.216710 GAGACTTGACTGCTCCCCG 59.783 63.158 0.00 0.00 0.00 5.73
197 198 1.216710 CGAGACTTGACTGCTCCCC 59.783 63.158 0.00 0.00 0.00 4.81
198 199 0.109039 GACGAGACTTGACTGCTCCC 60.109 60.000 0.00 0.00 0.00 4.30
199 200 0.109039 GGACGAGACTTGACTGCTCC 60.109 60.000 0.00 0.00 0.00 4.70
200 201 0.598562 TGGACGAGACTTGACTGCTC 59.401 55.000 0.00 0.00 0.00 4.26
201 202 0.315568 GTGGACGAGACTTGACTGCT 59.684 55.000 0.00 0.00 0.00 4.24
202 203 0.315568 AGTGGACGAGACTTGACTGC 59.684 55.000 0.00 0.00 0.00 4.40
203 204 1.338337 ACAGTGGACGAGACTTGACTG 59.662 52.381 8.00 8.00 37.44 3.51
204 205 1.693627 ACAGTGGACGAGACTTGACT 58.306 50.000 0.00 0.00 0.00 3.41
205 206 2.351544 GGTACAGTGGACGAGACTTGAC 60.352 54.545 0.00 0.00 0.00 3.18
206 207 1.884579 GGTACAGTGGACGAGACTTGA 59.115 52.381 0.00 0.00 0.00 3.02
207 208 1.067776 GGGTACAGTGGACGAGACTTG 60.068 57.143 0.00 0.00 0.00 3.16
208 209 1.254954 GGGTACAGTGGACGAGACTT 58.745 55.000 0.00 0.00 0.00 3.01
209 210 0.611340 GGGGTACAGTGGACGAGACT 60.611 60.000 0.00 0.00 0.00 3.24
210 211 1.888736 GGGGTACAGTGGACGAGAC 59.111 63.158 0.00 0.00 0.00 3.36
211 212 1.676635 CGGGGTACAGTGGACGAGA 60.677 63.158 0.00 0.00 0.00 4.04
212 213 1.676635 TCGGGGTACAGTGGACGAG 60.677 63.158 0.00 0.00 0.00 4.18
213 214 1.973281 GTCGGGGTACAGTGGACGA 60.973 63.158 0.00 0.00 0.00 4.20
214 215 2.570181 GTCGGGGTACAGTGGACG 59.430 66.667 0.00 0.00 0.00 4.79
215 216 2.653087 GGGTCGGGGTACAGTGGAC 61.653 68.421 0.00 0.00 0.00 4.02
216 217 2.284112 GGGTCGGGGTACAGTGGA 60.284 66.667 0.00 0.00 0.00 4.02
217 218 1.770749 TTTGGGTCGGGGTACAGTGG 61.771 60.000 0.00 0.00 0.00 4.00
218 219 0.321298 CTTTGGGTCGGGGTACAGTG 60.321 60.000 0.00 0.00 0.00 3.66
219 220 1.486145 CCTTTGGGTCGGGGTACAGT 61.486 60.000 0.00 0.00 0.00 3.55
220 221 1.298667 CCTTTGGGTCGGGGTACAG 59.701 63.158 0.00 0.00 0.00 2.74
221 222 2.897762 GCCTTTGGGTCGGGGTACA 61.898 63.158 0.00 0.00 34.45 2.90
222 223 2.045634 GCCTTTGGGTCGGGGTAC 60.046 66.667 0.00 0.00 34.45 3.34
223 224 3.332385 GGCCTTTGGGTCGGGGTA 61.332 66.667 0.00 0.00 34.45 3.69
229 230 2.033194 CGACTTCGGCCTTTGGGTC 61.033 63.158 0.00 1.25 35.37 4.46
230 231 2.032071 CGACTTCGGCCTTTGGGT 59.968 61.111 0.00 0.00 35.37 4.51
231 232 2.032071 ACGACTTCGGCCTTTGGG 59.968 61.111 0.00 0.00 44.95 4.12
234 235 1.301479 GGTCACGACTTCGGCCTTT 60.301 57.895 0.00 0.00 44.95 3.11
244 245 1.745489 GGGGCAAGATGGTCACGAC 60.745 63.158 0.00 0.00 0.00 4.34
255 256 2.757099 GCTGGATGTGGGGGCAAG 60.757 66.667 0.00 0.00 0.00 4.01
256 257 4.738998 CGCTGGATGTGGGGGCAA 62.739 66.667 0.00 0.00 0.00 4.52
313 314 3.077556 CTCCCCCTCCCTCACACG 61.078 72.222 0.00 0.00 0.00 4.49
314 315 2.689034 CCTCCCCCTCCCTCACAC 60.689 72.222 0.00 0.00 0.00 3.82
520 522 0.036164 TCGGAAACATCACAGGTGGG 59.964 55.000 0.00 0.00 0.00 4.61
523 525 2.289694 CCTCTTCGGAAACATCACAGGT 60.290 50.000 0.00 0.00 33.16 4.00
591 596 3.899545 AAGCCTCGAGGGGACGGAA 62.900 63.158 32.06 0.00 35.18 4.30
714 741 3.194062 GCTGCTCTCCACTGAATCTTAC 58.806 50.000 0.00 0.00 0.00 2.34
776 806 1.134401 TGCGGATTAGCCAAGAAGAGG 60.134 52.381 0.00 0.00 35.94 3.69
777 807 1.936547 GTGCGGATTAGCCAAGAAGAG 59.063 52.381 0.00 0.00 35.94 2.85
780 810 2.192664 TTGTGCGGATTAGCCAAGAA 57.807 45.000 0.00 0.00 35.94 2.52
827 857 4.015084 ACGAAAGGAAACGGATCTAGAGA 58.985 43.478 0.00 0.00 0.00 3.10
857 974 0.319813 AATGCAACTTTTCCTGCGGC 60.320 50.000 0.00 0.00 41.63 6.53
907 1024 2.721797 CGCAAATTCGAAACGTCCTCAG 60.722 50.000 0.00 0.00 0.00 3.35
917 1038 4.128554 GTCTCAAAGACGCAAATTCGAA 57.871 40.909 0.00 0.00 35.28 3.71
1007 1130 0.861837 CTGCTTCGGACAACTGTCAC 59.138 55.000 11.76 1.10 46.47 3.67
1068 1191 6.415867 GTCGATCAATGATGGTAAGCAAAATG 59.584 38.462 0.00 0.00 0.00 2.32
1110 1233 0.034059 AGAGGACACTGGTTCTTGCG 59.966 55.000 0.00 0.00 31.09 4.85
1217 1340 1.665735 CGTTGCCCCGAACAATTTCAG 60.666 52.381 0.00 0.00 0.00 3.02
1366 1489 0.774276 TCTGGGTTGCCATGGTTGTA 59.226 50.000 14.67 0.00 0.00 2.41
1369 1492 0.542702 CCTTCTGGGTTGCCATGGTT 60.543 55.000 14.67 0.00 0.00 3.67
1370 1493 1.077265 CCTTCTGGGTTGCCATGGT 59.923 57.895 14.67 0.00 0.00 3.55
1391 1514 7.020010 GTCAAAATTGTGAACTCAGCTATCTG 58.980 38.462 0.00 0.00 41.67 2.90
1610 1733 3.499918 GTCCAACTTCCTGAGTCACAATG 59.500 47.826 0.00 0.00 37.72 2.82
1932 2055 1.205893 GAAGTGTGACCAGAGCTAGGG 59.794 57.143 9.33 5.67 0.00 3.53
1957 2080 3.120095 CGAAAACATGATGAGCTGAGCAA 60.120 43.478 7.39 0.00 0.00 3.91
1975 2098 3.886505 ACCCAAATCTGCTACAAACGAAA 59.113 39.130 0.00 0.00 0.00 3.46
1979 2102 4.846779 TGAACCCAAATCTGCTACAAAC 57.153 40.909 0.00 0.00 0.00 2.93
2163 2286 5.037383 TCGGTAGATAGAAGAGAGCAAGA 57.963 43.478 0.00 0.00 0.00 3.02
2177 2300 5.242838 TGGCAAACTTCAAAATTCGGTAGAT 59.757 36.000 0.00 0.00 0.00 1.98
2363 2500 1.250328 TGGAAAGCAGTTGCAGATGG 58.750 50.000 6.90 0.00 45.16 3.51
2383 2520 0.528017 GCGTGACCAGACTCTGATGA 59.472 55.000 7.69 0.00 32.44 2.92
2459 2596 1.523758 AGATTGACGGCTGTTTCCAC 58.476 50.000 0.00 0.00 0.00 4.02
2692 2838 1.891150 AGGCAAAGAATGGAACTGCAG 59.109 47.619 13.48 13.48 0.00 4.41
2763 2910 3.010420 GCCCGTAAGAAGCTCTTTTCAT 58.990 45.455 4.15 0.00 37.89 2.57
2764 2911 2.224426 TGCCCGTAAGAAGCTCTTTTCA 60.224 45.455 4.15 0.00 37.89 2.69
2765 2912 2.423577 TGCCCGTAAGAAGCTCTTTTC 58.576 47.619 4.15 0.00 37.89 2.29
2766 2913 2.561478 TGCCCGTAAGAAGCTCTTTT 57.439 45.000 4.15 0.00 37.89 2.27
2845 2999 2.002586 CACTGTGCACCTTTATCCTCG 58.997 52.381 15.69 0.00 0.00 4.63
2919 3074 0.038159 AGTCTCGAGCTTGAAACCCG 60.038 55.000 7.81 0.00 0.00 5.28
2952 3107 0.388778 TTTGCATGGCACGCTTGATG 60.389 50.000 7.21 0.00 38.71 3.07
2953 3108 0.533491 ATTTGCATGGCACGCTTGAT 59.467 45.000 7.21 0.00 38.71 2.57
3014 3177 2.086094 TGCCATAGCACTTGTCACATG 58.914 47.619 0.00 0.00 46.52 3.21
3027 3190 1.766143 GCGACGGAAGCTTGCCATAG 61.766 60.000 12.80 2.72 0.00 2.23
3030 3193 4.617520 TGCGACGGAAGCTTGCCA 62.618 61.111 12.80 1.29 35.28 4.92
3035 3198 1.668151 GGAAACTGCGACGGAAGCT 60.668 57.895 0.00 0.00 35.28 3.74
3045 3214 2.171635 CCACTTAGGCGGAAACTGC 58.828 57.895 0.00 0.00 0.00 4.40
3082 3251 5.441718 TGATCCTCTTGGTGATTTAGCTT 57.558 39.130 0.00 0.00 34.23 3.74
3114 3283 4.816385 CGGCTGTATGGAAGTGAATTATGT 59.184 41.667 0.00 0.00 0.00 2.29
3160 3329 4.578516 CACTACAGGAACCACATTTTGTCA 59.421 41.667 0.00 0.00 0.00 3.58
3193 3362 6.463995 AAGAAAGGAATTGCAACACAACTA 57.536 33.333 0.00 0.00 42.27 2.24
3217 3387 1.144969 TTCAGCTAACGTTTCAGGCG 58.855 50.000 5.91 3.98 0.00 5.52
3230 3403 4.708177 AGTACTGACAACACAATTCAGCT 58.292 39.130 0.00 0.00 40.46 4.24
3274 3451 4.764823 TCGTTGAGCAATTAATGGAAAGGT 59.235 37.500 0.00 0.00 0.00 3.50
3287 3464 6.530567 CGTACTGAATATTTTCGTTGAGCAA 58.469 36.000 0.00 0.00 34.39 3.91
3311 3488 5.181245 TGGTTCAGTTGTAGCTAAGATTTGC 59.819 40.000 0.00 0.00 0.00 3.68
3335 3512 2.014033 TTCCCGCCCCCTTTTCTGTT 62.014 55.000 0.00 0.00 0.00 3.16
3368 3545 1.204704 GTTTCCTGTTAATGCCCCAGC 59.795 52.381 0.00 0.00 40.48 4.85
3417 3594 1.145571 AGGTCTTTGCCCTGTGGTAA 58.854 50.000 0.00 0.00 34.06 2.85
3424 3601 3.332485 TGGTGTTAATAGGTCTTTGCCCT 59.668 43.478 0.00 0.00 36.04 5.19
3428 3605 5.768164 AGTTGGTGGTGTTAATAGGTCTTTG 59.232 40.000 0.00 0.00 0.00 2.77
3432 3609 4.866486 CGTAGTTGGTGGTGTTAATAGGTC 59.134 45.833 0.00 0.00 0.00 3.85
3437 3614 3.244284 TGCTCGTAGTTGGTGGTGTTAAT 60.244 43.478 0.00 0.00 0.00 1.40
3447 3624 1.067846 TGTGCTACTGCTCGTAGTTGG 60.068 52.381 12.99 0.00 45.97 3.77
3485 3662 8.077991 TGAGATAGTCTTTGCAAGATTTTTGTG 58.922 33.333 0.00 0.00 40.18 3.33
3486 3663 8.169977 TGAGATAGTCTTTGCAAGATTTTTGT 57.830 30.769 0.00 0.00 40.18 2.83
3489 3666 6.432162 TGCTGAGATAGTCTTTGCAAGATTTT 59.568 34.615 0.00 0.00 40.18 1.82
3492 3669 5.095145 TGCTGAGATAGTCTTTGCAAGAT 57.905 39.130 0.00 0.00 40.18 2.40
3494 3671 3.622163 CCTGCTGAGATAGTCTTTGCAAG 59.378 47.826 0.00 0.00 35.68 4.01
3497 3674 1.939255 GCCTGCTGAGATAGTCTTTGC 59.061 52.381 0.00 0.00 0.00 3.68
3589 3807 0.179034 ATCATTCTGCTTCTCGGGGC 60.179 55.000 0.00 0.00 0.00 5.80
3605 3823 2.121538 CCTCGTCTCTGGCCGATCA 61.122 63.158 0.00 0.00 31.90 2.92
3606 3824 2.725008 CCTCGTCTCTGGCCGATC 59.275 66.667 0.00 0.00 31.90 3.69
3612 3830 2.681778 AGGTGGCCTCGTCTCTGG 60.682 66.667 3.32 0.00 0.00 3.86
3620 3838 1.077429 GGGTGATTCAGGTGGCCTC 60.077 63.158 3.32 0.00 0.00 4.70
3628 3846 1.406614 GGAGTGCAGAGGGTGATTCAG 60.407 57.143 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.