Multiple sequence alignment - TraesCS6D01G195400

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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 TraesCS6D01G195400 chr6D 100.000 3732 0 0 1 3732 271011709 271007978 0.000000e+00 6892.0
1 TraesCS6D01G195400 chr6A 94.794 2305 65 34 831 3096 384964224 384966512 0.000000e+00 3541.0
2 TraesCS6D01G195400 chr6A 96.094 640 21 3 3096 3732 384966571 384967209 0.000000e+00 1040.0
3 TraesCS6D01G195400 chr6A 93.886 229 14 0 671 899 384960648 384960876 2.760000e-91 346.0
4 TraesCS6D01G195400 chr6A 89.691 97 10 0 348 444 384960555 384960651 1.410000e-24 124.0
5 TraesCS6D01G195400 chr6A 91.358 81 6 1 157 237 384960481 384960560 3.940000e-20 110.0
6 TraesCS6D01G195400 chr6B 95.766 1795 37 19 1319 3096 431705152 431703380 0.000000e+00 2857.0
7 TraesCS6D01G195400 chr6B 95.238 693 19 7 619 1311 431708604 431707926 0.000000e+00 1085.0
8 TraesCS6D01G195400 chr6B 95.316 491 20 2 3096 3583 431703289 431702799 0.000000e+00 776.0
9 TraesCS6D01G195400 chr6B 96.454 141 5 0 1 141 16540022 16540162 2.240000e-57 233.0
10 TraesCS6D01G195400 chr6B 93.168 161 7 4 3575 3732 431702857 431702698 2.240000e-57 233.0
11 TraesCS6D01G195400 chr6B 86.875 160 18 2 398 557 431711035 431710879 3.830000e-40 176.0
12 TraesCS6D01G195400 chr6B 89.916 119 12 0 234 352 248362105 248362223 1.790000e-33 154.0
13 TraesCS6D01G195400 chr6B 88.281 128 13 2 230 356 166128864 166128990 6.460000e-33 152.0
14 TraesCS6D01G195400 chr6B 95.714 70 2 1 558 626 431710755 431710686 1.100000e-20 111.0
15 TraesCS6D01G195400 chr6B 100.000 35 0 0 354 388 431787857 431787823 8.650000e-07 65.8
16 TraesCS6D01G195400 chr3B 95.035 141 7 0 1 141 187867844 187867984 4.850000e-54 222.0
17 TraesCS6D01G195400 chr3B 90.833 120 11 0 235 354 658489550 658489669 1.070000e-35 161.0
18 TraesCS6D01G195400 chr3B 90.000 120 11 1 235 354 564243956 564243838 1.790000e-33 154.0
19 TraesCS6D01G195400 chr7A 91.489 141 12 0 1 141 448115082 448114942 1.060000e-45 195.0
20 TraesCS6D01G195400 chr7A 90.909 121 11 0 232 352 375886613 375886493 2.980000e-36 163.0
21 TraesCS6D01G195400 chr2D 86.364 176 24 0 3365 3540 436366437 436366612 3.800000e-45 193.0
22 TraesCS6D01G195400 chr2D 89.362 141 15 0 1 141 356035436 356035296 1.070000e-40 178.0
23 TraesCS6D01G195400 chr7B 89.344 122 13 0 235 356 383736130 383736251 1.790000e-33 154.0
24 TraesCS6D01G195400 chr4A 86.620 142 16 2 234 374 669084079 669083940 1.790000e-33 154.0
25 TraesCS6D01G195400 chr3D 88.618 123 14 0 232 354 82747982 82748104 2.320000e-32 150.0
26 TraesCS6D01G195400 chr1A 87.597 129 16 0 224 352 65267162 65267034 2.320000e-32 150.0
27 TraesCS6D01G195400 chr2B 97.222 36 1 0 3696 3731 514867990 514867955 1.120000e-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 TraesCS6D01G195400 chr6D 271007978 271011709 3731 True 6892.0 6892 100.0000 1 3732 1 chr6D.!!$R1 3731
1 TraesCS6D01G195400 chr6A 384960481 384967209 6728 False 1032.2 3541 93.1646 157 3732 5 chr6A.!!$F1 3575
2 TraesCS6D01G195400 chr6B 431702698 431711035 8337 True 873.0 2857 93.6795 398 3732 6 chr6B.!!$R2 3334

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
100 101 0.036010 AGCTTGTTGTAGCGCTCCAT 60.036 50.0 16.34 0.00 45.82 3.41 F
101 102 0.097674 GCTTGTTGTAGCGCTCCATG 59.902 55.0 16.34 10.19 0.00 3.66 F
143 144 0.179156 CGTCACGTACAAGGCCGTAT 60.179 55.0 0.00 0.00 35.16 3.06 F
504 505 0.185901 ACCCCGCTATGCCAATCAAT 59.814 50.0 0.00 0.00 0.00 2.57 F
509 510 0.242017 GCTATGCCAATCAATCCCGC 59.758 55.0 0.00 0.00 0.00 6.13 F
524 525 0.250989 CCCGCCTTCCACCACTTTTA 60.251 55.0 0.00 0.00 0.00 1.52 F
889 6519 0.320771 CAGTAAGCACTTGTCCGGCT 60.321 55.0 0.00 0.00 40.14 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 10249 0.109342 CCAGTGCAGACCTCAGGTTT 59.891 55.000 0.00 0.00 35.25 3.27 R
1941 10362 4.696479 ATACAAATGGGTTGGCAAAACA 57.304 36.364 0.00 4.34 41.97 2.83 R
2142 10566 2.936202 CCAAGGTGATGGGGTTCTATG 58.064 52.381 0.00 0.00 36.79 2.23 R
2154 10578 5.500234 CTTATGACAAATCTCCCAAGGTGA 58.500 41.667 0.00 0.00 0.00 4.02 R
2182 10606 6.380095 TTTTAGTAAAAACATGGCGAGTGT 57.620 33.333 5.57 0.00 29.59 3.55 R
2387 10817 7.355017 TGAGATGAAGAAGAAAAACGATGTTG 58.645 34.615 0.00 0.00 0.00 3.33 R
2761 11206 1.807142 GCAGCTCTGGGAAAACTACAC 59.193 52.381 0.00 0.00 0.00 2.90 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
30 31 4.715523 CGGGGATGTGCCAACCGT 62.716 66.667 0.00 0.00 39.70 4.83
31 32 2.672295 GGGGATGTGCCAACCGTA 59.328 61.111 0.00 0.00 38.95 4.02
32 33 1.451387 GGGGATGTGCCAACCGTAG 60.451 63.158 0.00 0.00 38.95 3.51
33 34 1.298667 GGGATGTGCCAACCGTAGT 59.701 57.895 0.00 0.00 38.95 2.73
34 35 0.538118 GGGATGTGCCAACCGTAGTA 59.462 55.000 0.00 0.00 38.95 1.82
35 36 1.065998 GGGATGTGCCAACCGTAGTAA 60.066 52.381 0.00 0.00 38.95 2.24
36 37 2.420967 GGGATGTGCCAACCGTAGTAAT 60.421 50.000 0.00 0.00 38.95 1.89
37 38 2.870411 GGATGTGCCAACCGTAGTAATC 59.130 50.000 0.00 0.00 36.34 1.75
38 39 3.431766 GGATGTGCCAACCGTAGTAATCT 60.432 47.826 0.00 0.00 36.34 2.40
39 40 2.967362 TGTGCCAACCGTAGTAATCTG 58.033 47.619 0.00 0.00 0.00 2.90
40 41 1.664151 GTGCCAACCGTAGTAATCTGC 59.336 52.381 0.00 0.00 0.00 4.26
41 42 0.928229 GCCAACCGTAGTAATCTGCG 59.072 55.000 0.00 0.00 46.34 5.18
48 49 2.892784 GTAGTAATCTGCGAAGGCCT 57.107 50.000 0.00 0.00 38.85 5.19
49 50 2.474816 GTAGTAATCTGCGAAGGCCTG 58.525 52.381 5.69 0.00 38.85 4.85
50 51 0.179000 AGTAATCTGCGAAGGCCTGG 59.821 55.000 5.69 2.00 38.85 4.45
51 52 0.178068 GTAATCTGCGAAGGCCTGGA 59.822 55.000 5.69 0.00 38.85 3.86
52 53 0.178068 TAATCTGCGAAGGCCTGGAC 59.822 55.000 5.69 0.00 38.85 4.02
53 54 1.841302 AATCTGCGAAGGCCTGGACA 61.841 55.000 5.69 3.47 38.85 4.02
54 55 1.841302 ATCTGCGAAGGCCTGGACAA 61.841 55.000 5.69 0.00 38.85 3.18
55 56 2.281484 TGCGAAGGCCTGGACAAC 60.281 61.111 5.69 0.00 38.85 3.32
56 57 3.423154 GCGAAGGCCTGGACAACG 61.423 66.667 5.69 8.24 0.00 4.10
57 58 2.030562 CGAAGGCCTGGACAACGT 59.969 61.111 5.69 0.00 0.00 3.99
58 59 2.027625 CGAAGGCCTGGACAACGTC 61.028 63.158 5.69 0.00 0.00 4.34
67 68 3.550656 GACAACGTCCTCCGCAAG 58.449 61.111 0.00 0.00 41.42 4.01
79 80 2.985282 CGCAAGGGGCTGCTCAAA 60.985 61.111 0.21 0.00 40.33 2.69
80 81 2.345760 CGCAAGGGGCTGCTCAAAT 61.346 57.895 0.21 0.00 40.33 2.32
81 82 1.031571 CGCAAGGGGCTGCTCAAATA 61.032 55.000 0.21 0.00 40.33 1.40
82 83 0.743097 GCAAGGGGCTGCTCAAATAG 59.257 55.000 0.21 0.00 39.34 1.73
95 96 3.674423 CTCAAATAGCTTGTTGTAGCGC 58.326 45.455 0.00 0.00 45.82 5.92
96 97 3.334691 TCAAATAGCTTGTTGTAGCGCT 58.665 40.909 17.26 17.26 45.82 5.92
97 98 3.370978 TCAAATAGCTTGTTGTAGCGCTC 59.629 43.478 16.34 6.54 45.82 5.03
98 99 1.941325 ATAGCTTGTTGTAGCGCTCC 58.059 50.000 16.34 1.51 45.82 4.70
99 100 0.606096 TAGCTTGTTGTAGCGCTCCA 59.394 50.000 16.34 5.57 45.82 3.86
100 101 0.036010 AGCTTGTTGTAGCGCTCCAT 60.036 50.000 16.34 0.00 45.82 3.41
101 102 0.097674 GCTTGTTGTAGCGCTCCATG 59.902 55.000 16.34 10.19 0.00 3.66
102 103 0.729116 CTTGTTGTAGCGCTCCATGG 59.271 55.000 16.34 4.97 0.00 3.66
103 104 1.305219 TTGTTGTAGCGCTCCATGGC 61.305 55.000 16.34 2.75 0.00 4.40
104 105 1.745115 GTTGTAGCGCTCCATGGCA 60.745 57.895 16.34 1.57 0.00 4.92
105 106 1.450134 TTGTAGCGCTCCATGGCAG 60.450 57.895 16.34 6.85 0.00 4.85
106 107 3.275338 GTAGCGCTCCATGGCAGC 61.275 66.667 16.34 20.17 34.11 5.25
107 108 3.784719 TAGCGCTCCATGGCAGCA 61.785 61.111 25.86 11.58 36.61 4.41
108 109 3.745240 TAGCGCTCCATGGCAGCAG 62.745 63.158 25.86 20.64 36.61 4.24
110 111 3.506096 CGCTCCATGGCAGCAGTG 61.506 66.667 25.86 14.59 36.61 3.66
111 112 3.138798 GCTCCATGGCAGCAGTGG 61.139 66.667 23.33 8.64 36.82 4.00
112 113 2.672908 CTCCATGGCAGCAGTGGA 59.327 61.111 6.96 15.16 39.61 4.02
113 114 2.672908 TCCATGGCAGCAGTGGAG 59.327 61.111 6.96 0.00 37.12 3.86
114 115 1.919816 TCCATGGCAGCAGTGGAGA 60.920 57.895 6.96 0.00 37.12 3.71
115 116 1.226542 CCATGGCAGCAGTGGAGAT 59.773 57.895 9.20 0.00 34.94 2.75
116 117 1.101635 CCATGGCAGCAGTGGAGATG 61.102 60.000 9.20 0.00 34.94 2.90
117 118 1.101635 CATGGCAGCAGTGGAGATGG 61.102 60.000 0.00 0.00 0.00 3.51
118 119 2.124403 GGCAGCAGTGGAGATGGG 60.124 66.667 0.00 0.00 0.00 4.00
119 120 2.827642 GCAGCAGTGGAGATGGGC 60.828 66.667 0.00 0.00 0.00 5.36
120 121 2.996395 CAGCAGTGGAGATGGGCT 59.004 61.111 0.00 0.00 34.64 5.19
121 122 1.153208 CAGCAGTGGAGATGGGCTC 60.153 63.158 0.00 0.00 43.17 4.70
122 123 2.202987 GCAGTGGAGATGGGCTCG 60.203 66.667 0.00 0.00 44.91 5.03
123 124 2.202987 CAGTGGAGATGGGCTCGC 60.203 66.667 0.00 0.00 44.91 5.03
124 125 3.474570 AGTGGAGATGGGCTCGCC 61.475 66.667 0.00 0.00 44.91 5.54
125 126 4.899239 GTGGAGATGGGCTCGCCG 62.899 72.222 1.24 0.00 46.19 6.46
127 128 4.593864 GGAGATGGGCTCGCCGTC 62.594 72.222 1.24 3.08 44.91 4.79
128 129 3.838271 GAGATGGGCTCGCCGTCA 61.838 66.667 12.47 2.77 36.85 4.35
129 130 4.148825 AGATGGGCTCGCCGTCAC 62.149 66.667 12.47 1.37 36.85 3.67
134 135 4.409218 GGCTCGCCGTCACGTACA 62.409 66.667 0.00 0.00 0.00 2.90
135 136 2.429571 GCTCGCCGTCACGTACAA 60.430 61.111 0.00 0.00 0.00 2.41
136 137 2.434134 GCTCGCCGTCACGTACAAG 61.434 63.158 0.00 0.00 0.00 3.16
137 138 1.800315 CTCGCCGTCACGTACAAGG 60.800 63.158 0.00 0.00 0.00 3.61
138 139 3.475774 CGCCGTCACGTACAAGGC 61.476 66.667 12.05 12.05 44.00 4.35
139 140 3.116531 GCCGTCACGTACAAGGCC 61.117 66.667 11.26 0.00 41.81 5.19
140 141 2.807895 CCGTCACGTACAAGGCCG 60.808 66.667 0.00 0.00 0.00 6.13
141 142 2.049802 CGTCACGTACAAGGCCGT 60.050 61.111 0.00 0.00 37.90 5.68
142 143 1.209898 CGTCACGTACAAGGCCGTA 59.790 57.895 0.00 0.00 35.16 4.02
143 144 0.179156 CGTCACGTACAAGGCCGTAT 60.179 55.000 0.00 0.00 35.16 3.06
144 145 1.733389 CGTCACGTACAAGGCCGTATT 60.733 52.381 0.00 0.00 35.16 1.89
145 146 1.657094 GTCACGTACAAGGCCGTATTG 59.343 52.381 0.00 0.00 35.16 1.90
146 147 1.545136 TCACGTACAAGGCCGTATTGA 59.455 47.619 10.01 5.80 35.16 2.57
147 148 1.657094 CACGTACAAGGCCGTATTGAC 59.343 52.381 10.01 3.74 35.16 3.18
148 149 1.273048 ACGTACAAGGCCGTATTGACA 59.727 47.619 10.01 0.00 35.16 3.58
149 150 2.288948 ACGTACAAGGCCGTATTGACAA 60.289 45.455 10.01 0.00 35.16 3.18
150 151 2.737783 CGTACAAGGCCGTATTGACAAA 59.262 45.455 10.01 0.00 0.00 2.83
151 152 3.186817 CGTACAAGGCCGTATTGACAAAA 59.813 43.478 10.01 0.00 0.00 2.44
152 153 4.319622 CGTACAAGGCCGTATTGACAAAAA 60.320 41.667 10.01 0.00 0.00 1.94
237 238 5.951747 AGACATGCACACCCATTTAATTACT 59.048 36.000 0.00 0.00 0.00 2.24
238 239 6.095440 AGACATGCACACCCATTTAATTACTC 59.905 38.462 0.00 0.00 0.00 2.59
239 240 5.127031 ACATGCACACCCATTTAATTACTCC 59.873 40.000 0.00 0.00 0.00 3.85
240 241 4.020543 TGCACACCCATTTAATTACTCCC 58.979 43.478 0.00 0.00 0.00 4.30
241 242 4.264172 TGCACACCCATTTAATTACTCCCT 60.264 41.667 0.00 0.00 0.00 4.20
242 243 4.338400 GCACACCCATTTAATTACTCCCTC 59.662 45.833 0.00 0.00 0.00 4.30
243 244 5.505780 CACACCCATTTAATTACTCCCTCA 58.494 41.667 0.00 0.00 0.00 3.86
244 245 5.590259 CACACCCATTTAATTACTCCCTCAG 59.410 44.000 0.00 0.00 0.00 3.35
245 246 5.253096 ACACCCATTTAATTACTCCCTCAGT 59.747 40.000 0.00 0.00 39.41 3.41
246 247 5.823045 CACCCATTTAATTACTCCCTCAGTC 59.177 44.000 0.00 0.00 36.43 3.51
247 248 5.731678 ACCCATTTAATTACTCCCTCAGTCT 59.268 40.000 0.00 0.00 36.43 3.24
248 249 6.058183 CCCATTTAATTACTCCCTCAGTCTG 58.942 44.000 0.00 0.00 36.43 3.51
249 250 6.126768 CCCATTTAATTACTCCCTCAGTCTGA 60.127 42.308 1.78 1.78 36.43 3.27
250 251 7.338710 CCATTTAATTACTCCCTCAGTCTGAA 58.661 38.462 3.67 0.00 36.43 3.02
251 252 7.829211 CCATTTAATTACTCCCTCAGTCTGAAA 59.171 37.037 3.67 0.00 36.43 2.69
252 253 9.231297 CATTTAATTACTCCCTCAGTCTGAAAA 57.769 33.333 3.67 0.00 36.43 2.29
253 254 9.807921 ATTTAATTACTCCCTCAGTCTGAAAAA 57.192 29.630 3.67 0.00 36.43 1.94
254 255 8.848474 TTAATTACTCCCTCAGTCTGAAAAAG 57.152 34.615 3.67 4.07 36.43 2.27
255 256 3.133141 ACTCCCTCAGTCTGAAAAAGC 57.867 47.619 3.67 0.00 0.00 3.51
256 257 2.708325 ACTCCCTCAGTCTGAAAAAGCT 59.292 45.455 3.67 0.00 0.00 3.74
257 258 3.137360 ACTCCCTCAGTCTGAAAAAGCTT 59.863 43.478 3.67 0.00 0.00 3.74
258 259 3.480470 TCCCTCAGTCTGAAAAAGCTTG 58.520 45.455 0.00 0.00 0.00 4.01
259 260 3.117888 TCCCTCAGTCTGAAAAAGCTTGT 60.118 43.478 0.00 0.00 0.00 3.16
260 261 3.633986 CCCTCAGTCTGAAAAAGCTTGTT 59.366 43.478 0.10 0.10 0.00 2.83
261 262 4.261363 CCCTCAGTCTGAAAAAGCTTGTTC 60.261 45.833 20.63 20.63 0.00 3.18
262 263 4.261363 CCTCAGTCTGAAAAAGCTTGTTCC 60.261 45.833 23.66 10.69 0.00 3.62
263 264 4.269183 TCAGTCTGAAAAAGCTTGTTCCA 58.731 39.130 23.66 12.48 0.00 3.53
264 265 4.704540 TCAGTCTGAAAAAGCTTGTTCCAA 59.295 37.500 23.66 10.98 0.00 3.53
265 266 5.039333 CAGTCTGAAAAAGCTTGTTCCAAG 58.961 41.667 23.66 16.22 0.00 3.61
266 267 3.798878 GTCTGAAAAAGCTTGTTCCAAGC 59.201 43.478 23.66 18.69 43.31 4.01
274 275 3.443099 GCTTGTTCCAAGCTTGTCTTT 57.557 42.857 24.35 0.00 40.01 2.52
275 276 3.375642 GCTTGTTCCAAGCTTGTCTTTC 58.624 45.455 24.35 10.65 40.01 2.62
276 277 3.181487 GCTTGTTCCAAGCTTGTCTTTCA 60.181 43.478 24.35 12.85 40.01 2.69
277 278 4.677779 GCTTGTTCCAAGCTTGTCTTTCAA 60.678 41.667 24.35 18.17 40.01 2.69
278 279 5.398603 TTGTTCCAAGCTTGTCTTTCAAA 57.601 34.783 24.35 7.25 35.48 2.69
279 280 5.596836 TGTTCCAAGCTTGTCTTTCAAAT 57.403 34.783 24.35 0.00 35.48 2.32
280 281 5.350633 TGTTCCAAGCTTGTCTTTCAAATG 58.649 37.500 24.35 5.76 35.48 2.32
281 282 4.589216 TCCAAGCTTGTCTTTCAAATGG 57.411 40.909 24.35 6.02 36.51 3.16
282 283 4.214310 TCCAAGCTTGTCTTTCAAATGGA 58.786 39.130 24.35 8.43 39.15 3.41
283 284 4.834496 TCCAAGCTTGTCTTTCAAATGGAT 59.166 37.500 24.35 0.00 37.89 3.41
284 285 4.927425 CCAAGCTTGTCTTTCAAATGGATG 59.073 41.667 24.35 0.00 36.92 3.51
285 286 5.510179 CCAAGCTTGTCTTTCAAATGGATGT 60.510 40.000 24.35 0.00 36.92 3.06
286 287 6.294675 CCAAGCTTGTCTTTCAAATGGATGTA 60.295 38.462 24.35 0.00 36.92 2.29
287 288 7.318141 CAAGCTTGTCTTTCAAATGGATGTAT 58.682 34.615 18.65 0.00 35.48 2.29
288 289 7.093322 AGCTTGTCTTTCAAATGGATGTATC 57.907 36.000 0.00 0.00 35.48 2.24
289 290 6.888632 AGCTTGTCTTTCAAATGGATGTATCT 59.111 34.615 0.00 0.00 35.48 1.98
290 291 8.049117 AGCTTGTCTTTCAAATGGATGTATCTA 58.951 33.333 0.00 0.00 35.48 1.98
291 292 8.341173 GCTTGTCTTTCAAATGGATGTATCTAG 58.659 37.037 0.00 0.00 35.48 2.43
292 293 7.792374 TGTCTTTCAAATGGATGTATCTAGC 57.208 36.000 0.00 0.00 0.00 3.42
293 294 7.337938 TGTCTTTCAAATGGATGTATCTAGCA 58.662 34.615 0.00 0.00 0.00 3.49
294 295 7.280876 TGTCTTTCAAATGGATGTATCTAGCAC 59.719 37.037 0.00 0.00 0.00 4.40
295 296 7.497249 GTCTTTCAAATGGATGTATCTAGCACT 59.503 37.037 0.00 0.00 0.00 4.40
296 297 8.704668 TCTTTCAAATGGATGTATCTAGCACTA 58.295 33.333 0.00 0.00 0.00 2.74
297 298 9.330063 CTTTCAAATGGATGTATCTAGCACTAA 57.670 33.333 0.00 0.00 0.00 2.24
298 299 9.679661 TTTCAAATGGATGTATCTAGCACTAAA 57.320 29.630 0.00 0.00 0.00 1.85
299 300 9.851686 TTCAAATGGATGTATCTAGCACTAAAT 57.148 29.630 0.00 0.00 0.00 1.40
300 301 9.851686 TCAAATGGATGTATCTAGCACTAAATT 57.148 29.630 0.00 0.00 0.00 1.82
301 302 9.888878 CAAATGGATGTATCTAGCACTAAATTG 57.111 33.333 0.00 0.00 0.00 2.32
302 303 9.851686 AAATGGATGTATCTAGCACTAAATTGA 57.148 29.630 0.00 0.00 0.00 2.57
304 305 8.837788 TGGATGTATCTAGCACTAAATTGATG 57.162 34.615 0.00 0.00 0.00 3.07
305 306 8.432013 TGGATGTATCTAGCACTAAATTGATGT 58.568 33.333 0.00 0.00 0.00 3.06
306 307 9.277783 GGATGTATCTAGCACTAAATTGATGTT 57.722 33.333 0.00 0.00 0.00 2.71
326 327 6.823286 TGTTAGATACATCCATTTGAGGGA 57.177 37.500 0.00 0.00 39.14 4.20
327 328 6.591935 TGTTAGATACATCCATTTGAGGGAC 58.408 40.000 0.00 0.00 37.23 4.46
328 329 6.157820 TGTTAGATACATCCATTTGAGGGACA 59.842 38.462 0.00 0.00 37.23 4.02
329 330 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
330 331 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
331 332 3.091633 ACATCCATTTGAGGGACAAGG 57.908 47.619 0.00 0.00 39.77 3.61
332 333 2.379907 ACATCCATTTGAGGGACAAGGT 59.620 45.455 0.00 0.00 39.77 3.50
333 334 3.181418 ACATCCATTTGAGGGACAAGGTT 60.181 43.478 0.00 0.00 39.77 3.50
334 335 3.611025 TCCATTTGAGGGACAAGGTTT 57.389 42.857 0.00 0.00 39.77 3.27
335 336 3.922375 TCCATTTGAGGGACAAGGTTTT 58.078 40.909 0.00 0.00 39.77 2.43
336 337 4.294347 TCCATTTGAGGGACAAGGTTTTT 58.706 39.130 0.00 0.00 39.77 1.94
386 387 2.958355 ACAACAAGGATCAAACCCACAG 59.042 45.455 0.00 0.00 0.00 3.66
396 397 0.253610 AAACCCACAGTGAACACCGA 59.746 50.000 0.62 0.00 0.00 4.69
408 409 2.546368 TGAACACCGAAACACATAGTGC 59.454 45.455 0.00 0.00 36.98 4.40
415 416 1.019278 AAACACATAGTGCCGAGCCG 61.019 55.000 0.00 0.00 36.98 5.52
427 428 3.749064 GAGCCGACTCAGCCGACA 61.749 66.667 0.00 0.00 42.93 4.35
453 454 2.159907 GCCAAACACAACAACAAACGTG 60.160 45.455 0.00 0.00 35.48 4.49
471 472 0.456628 TGAACCTCACGAACACACGA 59.543 50.000 0.00 0.00 37.03 4.35
473 474 0.868602 AACCTCACGAACACACGACG 60.869 55.000 0.00 0.00 37.03 5.12
474 475 1.009335 CCTCACGAACACACGACGA 60.009 57.895 0.00 0.00 37.03 4.20
475 476 1.266786 CCTCACGAACACACGACGAC 61.267 60.000 0.00 0.00 37.03 4.34
476 477 1.585764 CTCACGAACACACGACGACG 61.586 60.000 5.58 5.58 45.75 5.12
483 484 4.297891 ACACGACGACGACGCGAA 62.298 61.111 23.64 0.00 43.96 4.70
488 489 4.395583 ACGACGACGCGAAGACCC 62.396 66.667 15.93 0.00 43.96 4.46
498 499 2.908015 GAAGACCCCGCTATGCCA 59.092 61.111 0.00 0.00 0.00 4.92
503 504 0.465460 GACCCCGCTATGCCAATCAA 60.465 55.000 0.00 0.00 0.00 2.57
504 505 0.185901 ACCCCGCTATGCCAATCAAT 59.814 50.000 0.00 0.00 0.00 2.57
509 510 0.242017 GCTATGCCAATCAATCCCGC 59.758 55.000 0.00 0.00 0.00 6.13
510 511 0.883833 CTATGCCAATCAATCCCGCC 59.116 55.000 0.00 0.00 0.00 6.13
524 525 0.250989 CCCGCCTTCCACCACTTTTA 60.251 55.000 0.00 0.00 0.00 1.52
577 701 7.756722 CGAGACAAATTGCCTTGAAGAAATATT 59.243 33.333 0.00 0.00 0.00 1.28
607 731 2.799017 TGACGGTGTACAGTGATACCT 58.201 47.619 0.00 0.00 0.00 3.08
647 2861 5.335504 GCAAGAGATCAACCTTTTCTTCTGG 60.336 44.000 0.00 0.00 0.00 3.86
692 2906 5.016173 TCAACCTGTTCATAAAATGAGGGG 58.984 41.667 0.00 6.83 40.94 4.79
759 2973 3.785859 GGCATCCAGGCACGGAGA 61.786 66.667 2.01 0.00 43.51 3.71
854 3068 3.417101 CTCTCACTGACACTGTAGACCT 58.583 50.000 0.00 0.00 0.00 3.85
868 3082 4.415150 ACCTGAGCGGCCCACATG 62.415 66.667 0.00 0.00 35.61 3.21
886 3100 2.148916 TGTCAGTAAGCACTTGTCCG 57.851 50.000 0.00 0.00 30.46 4.79
889 6519 0.320771 CAGTAAGCACTTGTCCGGCT 60.321 55.000 0.00 0.00 40.14 5.52
1295 6925 3.117322 TCTTCCTCGATTCCCTCTGATCT 60.117 47.826 0.00 0.00 0.00 2.75
1296 6926 2.870175 TCCTCGATTCCCTCTGATCTC 58.130 52.381 0.00 0.00 0.00 2.75
1297 6927 2.175715 TCCTCGATTCCCTCTGATCTCA 59.824 50.000 0.00 0.00 0.00 3.27
1298 6928 3.164268 CCTCGATTCCCTCTGATCTCAT 58.836 50.000 0.00 0.00 0.00 2.90
1299 6929 3.193267 CCTCGATTCCCTCTGATCTCATC 59.807 52.174 0.00 0.00 0.00 2.92
1307 6937 5.821097 TCCCTCTGATCTCATCGTATGTAT 58.179 41.667 0.00 0.00 0.00 2.29
1553 9960 1.957177 CACTAGGAATCTAGCCGCTCA 59.043 52.381 0.00 0.00 45.20 4.26
1738 10149 4.921515 CGGGTCGTTTCGATAATGATATGT 59.078 41.667 0.00 0.00 38.42 2.29
1766 10185 7.630082 TGGTAGTACTAGCCTTTCATTCAAAT 58.370 34.615 25.25 0.00 32.93 2.32
1767 10186 7.769044 TGGTAGTACTAGCCTTTCATTCAAATC 59.231 37.037 25.25 0.00 32.93 2.17
1768 10187 7.769044 GGTAGTACTAGCCTTTCATTCAAATCA 59.231 37.037 19.33 0.00 0.00 2.57
1769 10188 9.162764 GTAGTACTAGCCTTTCATTCAAATCAA 57.837 33.333 1.87 0.00 0.00 2.57
1770 10189 8.635765 AGTACTAGCCTTTCATTCAAATCAAA 57.364 30.769 0.00 0.00 0.00 2.69
1830 10249 1.992277 GGCTGAGCAGGAGAAGGGA 60.992 63.158 6.82 0.00 0.00 4.20
1914 10333 3.407698 TGTACTGATCGCACAAAATGGT 58.592 40.909 0.00 0.00 0.00 3.55
1915 10334 4.570930 TGTACTGATCGCACAAAATGGTA 58.429 39.130 0.00 0.00 0.00 3.25
1917 10336 4.685169 ACTGATCGCACAAAATGGTAAG 57.315 40.909 0.00 0.00 0.00 2.34
1918 10337 3.119849 ACTGATCGCACAAAATGGTAAGC 60.120 43.478 0.00 0.00 0.00 3.09
1921 10340 0.887933 CGCACAAAATGGTAAGCCCT 59.112 50.000 0.00 0.00 0.00 5.19
1964 10385 6.174720 TGTTTTGCCAACCCATTTGTATAA 57.825 33.333 0.00 0.00 32.71 0.98
2008 10430 3.313249 TCTCTATTCCAAATGCATGCGTG 59.687 43.478 14.40 10.89 0.00 5.34
2068 10491 4.126437 GCCCAAGTTTTGCACATTAACTT 58.874 39.130 8.73 8.73 41.42 2.66
2142 10566 4.091509 GTGATATGAAACGACACACCAGAC 59.908 45.833 0.00 0.00 0.00 3.51
2154 10578 2.239654 CACACCAGACATAGAACCCCAT 59.760 50.000 0.00 0.00 0.00 4.00
2182 10606 4.671831 TGGGAGATTTGTCATAAGCCAAA 58.328 39.130 0.00 0.00 35.25 3.28
2387 10817 2.450160 GTGTTGTGCACTAACAGCAAC 58.550 47.619 25.22 17.11 44.64 4.17
2692 11136 8.857098 AGCTGCTTTATAATCAAATCATCACAT 58.143 29.630 0.00 0.00 0.00 3.21
2805 11250 2.230660 GTAGCACACCTGAGGCTTTTT 58.769 47.619 0.00 0.00 39.01 1.94
2899 11344 3.697439 GATGTTAGGCAGCCCCGCA 62.697 63.158 8.22 4.73 39.21 5.69
2904 11349 0.033991 TTAGGCAGCCCCGCAAAATA 60.034 50.000 8.22 0.00 39.21 1.40
3165 11701 7.664731 ACAGATGATAAGGCTTGGAATGAATAG 59.335 37.037 10.69 0.00 0.00 1.73
3197 11733 5.296151 TCACAGAAGAAACATCCTTCAGT 57.704 39.130 0.00 0.00 41.73 3.41
3200 11736 5.762218 CACAGAAGAAACATCCTTCAGTCTT 59.238 40.000 0.00 0.00 41.73 3.01
3270 11806 1.152963 ACGCTCAACAAAGCCAGGT 60.153 52.632 0.00 0.00 39.17 4.00
3310 11846 1.689273 AGGCTAGCTGAAATAGGTCCG 59.311 52.381 15.72 0.00 38.31 4.79
3317 11853 2.614481 GCTGAAATAGGTCCGACAACCA 60.614 50.000 0.00 0.00 42.12 3.67
3344 11885 1.605738 CTTTGCTGGGCCAGAGCTT 60.606 57.895 37.07 0.00 39.73 3.74
3351 11892 0.823356 TGGGCCAGAGCTTCAACAAC 60.823 55.000 0.00 0.00 39.73 3.32
3354 11895 1.615392 GGCCAGAGCTTCAACAACAAT 59.385 47.619 0.00 0.00 39.73 2.71
3562 12103 7.010091 CCCTACAACAAATGAAAGACAAAACAC 59.990 37.037 0.00 0.00 0.00 3.32
3652 12193 3.558418 ACGAAAACGGGATGTATGTATGC 59.442 43.478 0.00 0.00 0.00 3.14
3664 12205 6.037940 GGATGTATGTATGCTGCATAGGAATG 59.962 42.308 21.86 0.00 36.09 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.318006 TACGGTTGGCACATCCCCG 62.318 63.158 0.00 0.00 44.90 5.73
14 15 1.451387 CTACGGTTGGCACATCCCC 60.451 63.158 0.00 0.00 44.90 4.81
15 16 0.538118 TACTACGGTTGGCACATCCC 59.462 55.000 0.00 0.00 44.90 3.85
16 17 2.389962 TTACTACGGTTGGCACATCC 57.610 50.000 0.00 0.00 44.31 3.51
17 18 3.555956 CAGATTACTACGGTTGGCACATC 59.444 47.826 0.00 0.00 39.30 3.06
18 19 3.531538 CAGATTACTACGGTTGGCACAT 58.468 45.455 0.00 0.00 39.30 3.21
19 20 2.933492 GCAGATTACTACGGTTGGCACA 60.933 50.000 0.00 0.00 0.00 4.57
20 21 1.664151 GCAGATTACTACGGTTGGCAC 59.336 52.381 0.00 0.00 0.00 5.01
21 22 1.737696 CGCAGATTACTACGGTTGGCA 60.738 52.381 0.00 0.00 30.22 4.92
22 23 0.928229 CGCAGATTACTACGGTTGGC 59.072 55.000 0.00 0.00 30.22 4.52
23 24 2.572191 TCGCAGATTACTACGGTTGG 57.428 50.000 0.00 0.00 34.13 3.77
24 25 2.858344 CCTTCGCAGATTACTACGGTTG 59.142 50.000 0.00 0.00 35.04 3.77
25 26 2.737679 GCCTTCGCAGATTACTACGGTT 60.738 50.000 0.00 0.00 35.04 4.44
26 27 1.202382 GCCTTCGCAGATTACTACGGT 60.202 52.381 0.00 0.00 35.04 4.83
27 28 1.488527 GCCTTCGCAGATTACTACGG 58.511 55.000 0.00 0.00 35.04 4.02
28 29 1.067212 AGGCCTTCGCAGATTACTACG 59.933 52.381 0.00 0.00 35.04 3.51
29 30 2.474816 CAGGCCTTCGCAGATTACTAC 58.525 52.381 0.00 0.00 35.04 2.73
30 31 1.412710 CCAGGCCTTCGCAGATTACTA 59.587 52.381 0.00 0.00 35.04 1.82
31 32 0.179000 CCAGGCCTTCGCAGATTACT 59.821 55.000 0.00 0.00 35.04 2.24
32 33 0.178068 TCCAGGCCTTCGCAGATTAC 59.822 55.000 0.00 0.00 35.04 1.89
33 34 0.178068 GTCCAGGCCTTCGCAGATTA 59.822 55.000 0.00 0.00 35.04 1.75
34 35 1.078143 GTCCAGGCCTTCGCAGATT 60.078 57.895 0.00 0.00 35.04 2.40
35 36 1.841302 TTGTCCAGGCCTTCGCAGAT 61.841 55.000 0.00 0.00 35.04 2.90
36 37 2.515979 TTGTCCAGGCCTTCGCAGA 61.516 57.895 0.00 0.00 36.38 4.26
37 38 2.032528 TTGTCCAGGCCTTCGCAG 59.967 61.111 0.00 0.00 36.38 5.18
38 39 2.281484 GTTGTCCAGGCCTTCGCA 60.281 61.111 0.00 0.00 36.38 5.10
39 40 3.423154 CGTTGTCCAGGCCTTCGC 61.423 66.667 0.00 0.00 0.00 4.70
40 41 2.027625 GACGTTGTCCAGGCCTTCG 61.028 63.158 0.00 4.07 0.00 3.79
41 42 3.967715 GACGTTGTCCAGGCCTTC 58.032 61.111 0.00 0.00 0.00 3.46
50 51 3.550656 CTTGCGGAGGACGTTGTC 58.449 61.111 0.00 0.00 46.52 3.18
63 64 0.743097 CTATTTGAGCAGCCCCTTGC 59.257 55.000 0.00 0.00 44.41 4.01
74 75 3.372206 AGCGCTACAACAAGCTATTTGAG 59.628 43.478 8.99 7.78 40.49 3.02
75 76 3.334691 AGCGCTACAACAAGCTATTTGA 58.665 40.909 8.99 0.00 40.49 2.69
76 77 3.485877 GGAGCGCTACAACAAGCTATTTG 60.486 47.826 16.75 5.82 40.39 2.32
77 78 2.678336 GGAGCGCTACAACAAGCTATTT 59.322 45.455 16.75 0.00 40.39 1.40
78 79 2.280628 GGAGCGCTACAACAAGCTATT 58.719 47.619 16.75 0.00 40.39 1.73
79 80 1.207089 TGGAGCGCTACAACAAGCTAT 59.793 47.619 22.91 0.00 40.39 2.97
80 81 0.606096 TGGAGCGCTACAACAAGCTA 59.394 50.000 22.91 0.00 40.39 3.32
81 82 0.036010 ATGGAGCGCTACAACAAGCT 60.036 50.000 29.19 5.73 43.33 3.74
82 83 0.097674 CATGGAGCGCTACAACAAGC 59.902 55.000 29.19 2.60 39.21 4.01
83 84 0.729116 CCATGGAGCGCTACAACAAG 59.271 55.000 29.19 16.39 0.00 3.16
84 85 1.305219 GCCATGGAGCGCTACAACAA 61.305 55.000 29.19 2.21 0.00 2.83
85 86 1.745115 GCCATGGAGCGCTACAACA 60.745 57.895 29.19 16.00 0.00 3.33
86 87 1.709147 CTGCCATGGAGCGCTACAAC 61.709 60.000 29.19 19.41 34.65 3.32
87 88 1.450134 CTGCCATGGAGCGCTACAA 60.450 57.895 29.19 9.31 34.65 2.41
88 89 2.187685 CTGCCATGGAGCGCTACA 59.812 61.111 27.55 27.55 34.65 2.74
89 90 3.275338 GCTGCCATGGAGCGCTAC 61.275 66.667 18.40 14.39 34.65 3.58
90 91 3.745240 CTGCTGCCATGGAGCGCTA 62.745 63.158 18.40 0.00 39.47 4.26
93 94 3.506096 CACTGCTGCCATGGAGCG 61.506 66.667 18.40 17.76 39.47 5.03
94 95 3.138798 CCACTGCTGCCATGGAGC 61.139 66.667 18.40 20.84 35.33 4.70
95 96 2.672908 TCCACTGCTGCCATGGAG 59.327 61.111 18.40 11.30 37.60 3.86
96 97 1.276859 ATCTCCACTGCTGCCATGGA 61.277 55.000 18.40 17.88 40.27 3.41
97 98 1.101635 CATCTCCACTGCTGCCATGG 61.102 60.000 7.63 7.63 34.58 3.66
98 99 1.101635 CCATCTCCACTGCTGCCATG 61.102 60.000 0.00 0.00 0.00 3.66
99 100 1.226542 CCATCTCCACTGCTGCCAT 59.773 57.895 0.00 0.00 0.00 4.40
100 101 2.672908 CCATCTCCACTGCTGCCA 59.327 61.111 0.00 0.00 0.00 4.92
101 102 2.124403 CCCATCTCCACTGCTGCC 60.124 66.667 0.00 0.00 0.00 4.85
102 103 2.827642 GCCCATCTCCACTGCTGC 60.828 66.667 0.00 0.00 0.00 5.25
103 104 1.153208 GAGCCCATCTCCACTGCTG 60.153 63.158 0.00 0.00 35.77 4.41
104 105 2.729479 CGAGCCCATCTCCACTGCT 61.729 63.158 0.00 0.00 38.62 4.24
105 106 2.202987 CGAGCCCATCTCCACTGC 60.203 66.667 0.00 0.00 38.62 4.40
106 107 2.202987 GCGAGCCCATCTCCACTG 60.203 66.667 0.00 0.00 38.62 3.66
107 108 3.474570 GGCGAGCCCATCTCCACT 61.475 66.667 1.97 0.00 38.62 4.00
108 109 4.899239 CGGCGAGCCCATCTCCAC 62.899 72.222 0.00 0.00 38.62 4.02
110 111 4.593864 GACGGCGAGCCCATCTCC 62.594 72.222 16.62 0.00 38.62 3.71
111 112 3.838271 TGACGGCGAGCCCATCTC 61.838 66.667 16.62 0.00 38.47 2.75
112 113 4.148825 GTGACGGCGAGCCCATCT 62.149 66.667 16.62 0.00 0.00 2.90
117 118 3.902162 TTGTACGTGACGGCGAGCC 62.902 63.158 16.62 3.59 35.59 4.70
118 119 2.429571 TTGTACGTGACGGCGAGC 60.430 61.111 16.62 5.63 35.59 5.03
119 120 1.800315 CCTTGTACGTGACGGCGAG 60.800 63.158 16.62 10.66 35.59 5.03
120 121 2.256158 CCTTGTACGTGACGGCGA 59.744 61.111 16.62 0.57 35.59 5.54
121 122 3.475774 GCCTTGTACGTGACGGCG 61.476 66.667 10.66 4.80 37.94 6.46
122 123 3.116531 GGCCTTGTACGTGACGGC 61.117 66.667 10.66 3.12 39.98 5.68
123 124 2.198906 TACGGCCTTGTACGTGACGG 62.199 60.000 10.66 0.00 43.93 4.79
124 125 0.179156 ATACGGCCTTGTACGTGACG 60.179 55.000 2.24 2.24 43.93 4.35
125 126 1.657094 CAATACGGCCTTGTACGTGAC 59.343 52.381 0.00 0.00 43.93 3.67
126 127 1.545136 TCAATACGGCCTTGTACGTGA 59.455 47.619 0.00 1.82 43.93 4.35
127 128 1.657094 GTCAATACGGCCTTGTACGTG 59.343 52.381 0.00 0.00 43.93 4.49
128 129 1.273048 TGTCAATACGGCCTTGTACGT 59.727 47.619 0.00 0.00 46.17 3.57
129 130 1.999048 TGTCAATACGGCCTTGTACG 58.001 50.000 0.00 0.00 0.00 3.67
130 131 4.752661 TTTTGTCAATACGGCCTTGTAC 57.247 40.909 0.00 0.56 0.00 2.90
207 208 2.596346 TGGGTGTGCATGTCTGAAAAT 58.404 42.857 0.00 0.00 0.00 1.82
237 238 3.117888 ACAAGCTTTTTCAGACTGAGGGA 60.118 43.478 5.10 0.00 0.00 4.20
238 239 3.217626 ACAAGCTTTTTCAGACTGAGGG 58.782 45.455 5.10 0.00 0.00 4.30
239 240 4.261363 GGAACAAGCTTTTTCAGACTGAGG 60.261 45.833 23.09 0.00 0.00 3.86
240 241 4.336433 TGGAACAAGCTTTTTCAGACTGAG 59.664 41.667 23.09 0.00 31.92 3.35
241 242 4.269183 TGGAACAAGCTTTTTCAGACTGA 58.731 39.130 23.09 0.00 31.92 3.41
242 243 4.637483 TGGAACAAGCTTTTTCAGACTG 57.363 40.909 23.09 0.00 31.92 3.51
254 255 4.677779 TTGAAAGACAAGCTTGGAACAAGC 60.678 41.667 29.18 22.54 43.31 4.01
255 256 4.997565 TTGAAAGACAAGCTTGGAACAAG 58.002 39.130 29.18 3.71 37.48 3.16
256 257 5.398603 TTTGAAAGACAAGCTTGGAACAA 57.601 34.783 29.18 21.59 41.27 2.83
257 258 5.350633 CATTTGAAAGACAAGCTTGGAACA 58.649 37.500 29.18 17.71 39.77 3.18
258 259 4.746611 CCATTTGAAAGACAAGCTTGGAAC 59.253 41.667 29.18 19.11 39.77 3.62
259 260 4.648762 TCCATTTGAAAGACAAGCTTGGAA 59.351 37.500 29.18 12.35 39.04 3.53
260 261 4.214310 TCCATTTGAAAGACAAGCTTGGA 58.786 39.130 29.18 11.14 39.34 3.53
261 262 4.589216 TCCATTTGAAAGACAAGCTTGG 57.411 40.909 29.18 12.28 39.77 3.61
262 263 5.535333 ACATCCATTTGAAAGACAAGCTTG 58.465 37.500 24.84 24.84 39.77 4.01
263 264 5.796424 ACATCCATTTGAAAGACAAGCTT 57.204 34.783 0.00 0.00 39.77 3.74
264 265 6.888632 AGATACATCCATTTGAAAGACAAGCT 59.111 34.615 0.00 0.00 39.77 3.74
265 266 7.093322 AGATACATCCATTTGAAAGACAAGC 57.907 36.000 0.00 0.00 39.77 4.01
266 267 8.341173 GCTAGATACATCCATTTGAAAGACAAG 58.659 37.037 0.00 0.00 39.77 3.16
267 268 7.828717 TGCTAGATACATCCATTTGAAAGACAA 59.171 33.333 0.00 0.00 36.65 3.18
268 269 7.280876 GTGCTAGATACATCCATTTGAAAGACA 59.719 37.037 0.00 0.00 0.00 3.41
269 270 7.497249 AGTGCTAGATACATCCATTTGAAAGAC 59.503 37.037 0.00 0.00 0.00 3.01
270 271 7.568349 AGTGCTAGATACATCCATTTGAAAGA 58.432 34.615 0.00 0.00 0.00 2.52
271 272 7.798596 AGTGCTAGATACATCCATTTGAAAG 57.201 36.000 0.00 0.00 0.00 2.62
272 273 9.679661 TTTAGTGCTAGATACATCCATTTGAAA 57.320 29.630 0.00 0.00 0.00 2.69
273 274 9.851686 ATTTAGTGCTAGATACATCCATTTGAA 57.148 29.630 0.00 0.00 0.00 2.69
274 275 9.851686 AATTTAGTGCTAGATACATCCATTTGA 57.148 29.630 0.00 0.00 0.00 2.69
275 276 9.888878 CAATTTAGTGCTAGATACATCCATTTG 57.111 33.333 0.00 0.00 0.00 2.32
276 277 9.851686 TCAATTTAGTGCTAGATACATCCATTT 57.148 29.630 0.00 0.00 0.00 2.32
278 279 9.445878 CATCAATTTAGTGCTAGATACATCCAT 57.554 33.333 0.00 0.00 0.00 3.41
279 280 8.432013 ACATCAATTTAGTGCTAGATACATCCA 58.568 33.333 0.00 0.00 0.00 3.41
280 281 8.839310 ACATCAATTTAGTGCTAGATACATCC 57.161 34.615 0.00 0.00 0.00 3.51
303 304 6.157820 TGTCCCTCAAATGGATGTATCTAACA 59.842 38.462 0.00 0.00 43.86 2.41
304 305 6.591935 TGTCCCTCAAATGGATGTATCTAAC 58.408 40.000 0.00 0.00 33.65 2.34
305 306 6.823286 TGTCCCTCAAATGGATGTATCTAA 57.177 37.500 0.00 0.00 33.65 2.10
306 307 6.183361 CCTTGTCCCTCAAATGGATGTATCTA 60.183 42.308 0.00 0.00 35.48 1.98
307 308 5.398353 CCTTGTCCCTCAAATGGATGTATCT 60.398 44.000 0.00 0.00 35.48 1.98
308 309 4.823989 CCTTGTCCCTCAAATGGATGTATC 59.176 45.833 0.00 0.00 35.48 2.24
309 310 4.230502 ACCTTGTCCCTCAAATGGATGTAT 59.769 41.667 0.00 0.00 35.48 2.29
310 311 3.591527 ACCTTGTCCCTCAAATGGATGTA 59.408 43.478 0.00 0.00 35.48 2.29
311 312 2.379907 ACCTTGTCCCTCAAATGGATGT 59.620 45.455 0.00 0.00 35.48 3.06
312 313 3.091633 ACCTTGTCCCTCAAATGGATG 57.908 47.619 0.00 0.00 35.48 3.51
313 314 3.833559 AACCTTGTCCCTCAAATGGAT 57.166 42.857 0.00 0.00 35.48 3.41
314 315 3.611025 AAACCTTGTCCCTCAAATGGA 57.389 42.857 0.00 0.00 35.48 3.41
315 316 4.687901 AAAAACCTTGTCCCTCAAATGG 57.312 40.909 0.00 0.00 35.48 3.16
335 336 9.822185 GGTTTTTATATACTTCCTCCGTCTAAA 57.178 33.333 0.00 0.00 0.00 1.85
336 337 8.980596 TGGTTTTTATATACTTCCTCCGTCTAA 58.019 33.333 0.00 0.00 0.00 2.10
337 338 8.537728 TGGTTTTTATATACTTCCTCCGTCTA 57.462 34.615 0.00 0.00 0.00 2.59
338 339 7.343833 TCTGGTTTTTATATACTTCCTCCGTCT 59.656 37.037 0.00 0.00 0.00 4.18
339 340 7.495055 TCTGGTTTTTATATACTTCCTCCGTC 58.505 38.462 0.00 0.00 0.00 4.79
340 341 7.427989 TCTGGTTTTTATATACTTCCTCCGT 57.572 36.000 0.00 0.00 0.00 4.69
341 342 7.767198 TGTTCTGGTTTTTATATACTTCCTCCG 59.233 37.037 0.00 0.00 0.00 4.63
342 343 9.457436 TTGTTCTGGTTTTTATATACTTCCTCC 57.543 33.333 0.00 0.00 0.00 4.30
344 345 9.802039 TGTTGTTCTGGTTTTTATATACTTCCT 57.198 29.630 0.00 0.00 0.00 3.36
348 349 9.802039 TCCTTGTTGTTCTGGTTTTTATATACT 57.198 29.630 0.00 0.00 0.00 2.12
351 352 9.308000 TGATCCTTGTTGTTCTGGTTTTTATAT 57.692 29.630 0.00 0.00 0.00 0.86
352 353 8.698973 TGATCCTTGTTGTTCTGGTTTTTATA 57.301 30.769 0.00 0.00 0.00 0.98
386 387 3.606153 GCACTATGTGTTTCGGTGTTCAC 60.606 47.826 0.00 0.00 35.75 3.18
396 397 1.019278 CGGCTCGGCACTATGTGTTT 61.019 55.000 0.00 0.00 35.75 2.83
415 416 2.807045 CACGCTGTCGGCTGAGTC 60.807 66.667 0.00 0.00 40.69 3.36
453 454 0.850856 GTCGTGTGTTCGTGAGGTTC 59.149 55.000 0.00 0.00 0.00 3.62
471 472 4.395583 GGGTCTTCGCGTCGTCGT 62.396 66.667 5.77 0.00 39.49 4.34
483 484 1.344953 TGATTGGCATAGCGGGGTCT 61.345 55.000 0.00 0.00 0.00 3.85
488 489 0.883833 GGGATTGATTGGCATAGCGG 59.116 55.000 0.00 0.00 0.00 5.52
498 499 0.395724 GGTGGAAGGCGGGATTGATT 60.396 55.000 0.00 0.00 0.00 2.57
503 504 1.789576 AAAGTGGTGGAAGGCGGGAT 61.790 55.000 0.00 0.00 0.00 3.85
504 505 2.002018 AAAAGTGGTGGAAGGCGGGA 62.002 55.000 0.00 0.00 0.00 5.14
509 510 7.107639 TCTTCTTTTTAAAAGTGGTGGAAGG 57.892 36.000 15.85 0.00 0.00 3.46
510 511 9.249457 GATTCTTCTTTTTAAAAGTGGTGGAAG 57.751 33.333 15.85 11.39 0.00 3.46
524 525 3.882888 TGCTGTCACGGATTCTTCTTTTT 59.117 39.130 0.00 0.00 0.00 1.94
577 701 2.894765 TGTACACCGTCATCTCCTTCAA 59.105 45.455 0.00 0.00 0.00 2.69
655 2869 6.545666 TGAACAGGTTGATCTCTTGCTTTAAA 59.454 34.615 0.00 0.00 0.00 1.52
656 2870 6.061441 TGAACAGGTTGATCTCTTGCTTTAA 58.939 36.000 0.00 0.00 0.00 1.52
657 2871 5.620206 TGAACAGGTTGATCTCTTGCTTTA 58.380 37.500 0.00 0.00 0.00 1.85
658 2872 4.464008 TGAACAGGTTGATCTCTTGCTTT 58.536 39.130 0.00 0.00 0.00 3.51
692 2906 1.512926 ACATTGACGTGCTTGTCTCC 58.487 50.000 0.00 0.00 39.64 3.71
796 3010 5.847111 TTTCTTCTACGAGGCTAATGCTA 57.153 39.130 0.00 0.00 39.59 3.49
801 3015 4.495422 CTGCTTTTCTTCTACGAGGCTAA 58.505 43.478 0.00 0.00 0.00 3.09
802 3016 3.676324 GCTGCTTTTCTTCTACGAGGCTA 60.676 47.826 0.00 0.00 0.00 3.93
854 3068 3.610619 CTGACATGTGGGCCGCTCA 62.611 63.158 19.39 12.65 0.00 4.26
868 3082 1.429463 CCGGACAAGTGCTTACTGAC 58.571 55.000 0.00 0.00 0.00 3.51
886 3100 3.860930 TTGTGGGAAGCCGGAAGCC 62.861 63.158 5.05 1.09 45.47 4.35
889 6519 2.114411 GGTTGTGGGAAGCCGGAA 59.886 61.111 5.05 0.00 0.00 4.30
899 6529 3.550437 AGCTAGCTTATCTGGTTGTGG 57.450 47.619 12.68 0.00 0.00 4.17
900 6530 6.095432 AGATAGCTAGCTTATCTGGTTGTG 57.905 41.667 24.88 0.00 0.00 3.33
901 6531 6.739331 AAGATAGCTAGCTTATCTGGTTGT 57.261 37.500 24.88 10.16 31.58 3.32
1074 6704 4.821589 CTCCGCGGCAGGAAGGAC 62.822 72.222 23.51 0.00 40.25 3.85
1316 6946 3.319122 GTGGCTTTCTTGACTCACCAAAT 59.681 43.478 0.00 0.00 0.00 2.32
1483 9884 7.825331 TGGATGGTTTACTTTGTAAATGACA 57.175 32.000 6.24 6.83 35.78 3.58
1553 9960 1.068194 GCTCAGCTTCTACACGACACT 60.068 52.381 0.00 0.00 0.00 3.55
1738 10149 6.439375 TGAATGAAAGGCTAGTACTACCAGAA 59.561 38.462 18.10 6.53 0.00 3.02
1766 10185 4.321156 CGCAACCTCCATTTTGATCTTTGA 60.321 41.667 0.00 0.00 0.00 2.69
1767 10186 3.922240 CGCAACCTCCATTTTGATCTTTG 59.078 43.478 0.00 0.00 0.00 2.77
1768 10187 3.056607 CCGCAACCTCCATTTTGATCTTT 60.057 43.478 0.00 0.00 0.00 2.52
1769 10188 2.493278 CCGCAACCTCCATTTTGATCTT 59.507 45.455 0.00 0.00 0.00 2.40
1770 10189 2.094675 CCGCAACCTCCATTTTGATCT 58.905 47.619 0.00 0.00 0.00 2.75
1830 10249 0.109342 CCAGTGCAGACCTCAGGTTT 59.891 55.000 0.00 0.00 35.25 3.27
1941 10362 4.696479 ATACAAATGGGTTGGCAAAACA 57.304 36.364 0.00 4.34 41.97 2.83
1942 10363 7.680442 AATTATACAAATGGGTTGGCAAAAC 57.320 32.000 0.00 0.00 41.97 2.43
1964 10385 8.755977 AGAGATGTATCAGAATTTGCCAAAAAT 58.244 29.630 0.00 0.00 0.00 1.82
2142 10566 2.936202 CCAAGGTGATGGGGTTCTATG 58.064 52.381 0.00 0.00 36.79 2.23
2154 10578 5.500234 CTTATGACAAATCTCCCAAGGTGA 58.500 41.667 0.00 0.00 0.00 4.02
2182 10606 6.380095 TTTTAGTAAAAACATGGCGAGTGT 57.620 33.333 5.57 0.00 29.59 3.55
2387 10817 7.355017 TGAGATGAAGAAGAAAAACGATGTTG 58.645 34.615 0.00 0.00 0.00 3.33
2692 11136 7.450014 TCTGCAGGGATAAAAGAAATTTGTGTA 59.550 33.333 15.13 0.00 32.27 2.90
2696 11140 5.809051 GCTCTGCAGGGATAAAAGAAATTTG 59.191 40.000 20.53 0.00 32.27 2.32
2761 11206 1.807142 GCAGCTCTGGGAAAACTACAC 59.193 52.381 0.00 0.00 0.00 2.90
2805 11250 2.166050 ACATTGTGTGCTGCAAAACTCA 59.834 40.909 2.77 0.00 0.00 3.41
2904 11349 8.757982 AGTACATCAATTGGCTCATTTCTAAT 57.242 30.769 5.42 0.00 0.00 1.73
3165 11701 4.816385 TGTTTCTTCTGTGATGAACCTGTC 59.184 41.667 0.00 0.00 0.00 3.51
3197 11733 8.733092 ATGAACTCATATCCCAGAAGATAAGA 57.267 34.615 0.00 0.00 34.26 2.10
3344 11885 7.990917 TCTGTAAAAGTTGCTATTGTTGTTGA 58.009 30.769 0.00 0.00 0.00 3.18
3351 11892 9.282247 GTCATTGATCTGTAAAAGTTGCTATTG 57.718 33.333 0.00 0.00 0.00 1.90
3354 11895 7.063426 CGAGTCATTGATCTGTAAAAGTTGCTA 59.937 37.037 0.00 0.00 0.00 3.49
3562 12103 5.446473 GGAAGTTTCTGCTGTCGTATTCATG 60.446 44.000 0.00 0.00 0.00 3.07
3570 12111 2.288825 TGTAGGGAAGTTTCTGCTGTCG 60.289 50.000 0.00 0.00 0.00 4.35
3619 12160 1.329292 CCGTTTTCGTTTCTGCTGTCA 59.671 47.619 0.00 0.00 42.35 3.58
3620 12161 1.333791 CCCGTTTTCGTTTCTGCTGTC 60.334 52.381 0.00 0.00 42.35 3.51
3652 12193 6.906157 ATTTTATGTCCCATTCCTATGCAG 57.094 37.500 0.00 0.00 0.00 4.41
3664 12205 3.697542 ACAACCGCCTAATTTTATGTCCC 59.302 43.478 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.