Multiple sequence alignment - TraesCS6D01G040200

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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 TraesCS6D01G040200 chr6D 100.000 1860 0 0 768 2627 16386788 16384929 0.000000e+00 3435.0
1 TraesCS6D01G040200 chr6D 89.469 1073 63 32 768 1817 16514361 16515406 0.000000e+00 1310.0
2 TraesCS6D01G040200 chr6D 100.000 347 0 0 1 347 16387555 16387209 2.200000e-180 641.0
3 TraesCS6D01G040200 chr6D 86.626 329 26 11 1869 2186 16515431 16515752 5.380000e-92 348.0
4 TraesCS6D01G040200 chr6D 83.123 397 34 22 2234 2599 16515766 16516160 5.420000e-87 331.0
5 TraesCS6D01G040200 chr6D 96.721 61 2 0 287 347 119965118 119965178 4.630000e-18 102.0
6 TraesCS6D01G040200 chr6B 85.872 1904 151 53 776 2627 28513654 28511817 0.000000e+00 1917.0
7 TraesCS6D01G040200 chr6B 89.511 982 60 26 775 1739 29044515 29045470 0.000000e+00 1203.0
8 TraesCS6D01G040200 chr6B 87.354 1028 73 33 776 1790 28722221 28723204 0.000000e+00 1125.0
9 TraesCS6D01G040200 chr6B 86.373 1020 84 31 784 1790 28942314 28943291 0.000000e+00 1062.0
10 TraesCS6D01G040200 chr6B 89.227 854 60 22 768 1613 59298789 59299618 0.000000e+00 1038.0
11 TraesCS6D01G040200 chr6B 85.390 308 26 6 1891 2186 29045529 29045829 4.250000e-78 302.0
12 TraesCS6D01G040200 chr6B 79.487 390 45 20 1985 2358 28943315 28943685 7.260000e-61 244.0
13 TraesCS6D01G040200 chr6B 79.124 388 48 22 1985 2358 28723228 28723596 1.220000e-58 237.0
14 TraesCS6D01G040200 chr6B 91.429 175 11 3 2227 2398 29045832 29046005 1.220000e-58 237.0
15 TraesCS6D01G040200 chr6B 80.851 188 23 8 2396 2572 29046032 29046217 4.560000e-28 135.0
16 TraesCS6D01G040200 chr6A 91.650 1018 57 19 779 1790 16655972 16654977 0.000000e+00 1384.0
17 TraesCS6D01G040200 chr6A 89.189 1073 68 23 770 1819 16705101 16706148 0.000000e+00 1295.0
18 TraesCS6D01G040200 chr6A 86.591 619 58 13 1795 2397 16654901 16654292 0.000000e+00 660.0
19 TraesCS6D01G040200 chr6A 86.093 302 23 7 1897 2186 16706197 16706491 9.130000e-80 307.0
20 TraesCS6D01G040200 chr6A 88.485 165 16 2 2234 2398 16706503 16706664 2.060000e-46 196.0
21 TraesCS6D01G040200 chr3A 88.247 987 78 27 768 1744 66253821 66254779 0.000000e+00 1146.0
22 TraesCS6D01G040200 chr3A 87.097 186 22 2 2213 2398 66254986 66255169 2.650000e-50 209.0
23 TraesCS6D01G040200 chr1B 86.129 1067 66 45 768 1817 587501542 587500541 0.000000e+00 1075.0
24 TraesCS6D01G040200 chr1B 80.866 554 50 25 1553 2084 652543636 652544155 4.100000e-103 385.0
25 TraesCS6D01G040200 chr1B 85.948 306 25 6 1887 2175 587500519 587500215 7.060000e-81 311.0
26 TraesCS6D01G040200 chrUn 90.596 319 22 6 1543 1861 163376400 163376710 1.450000e-112 416.0
27 TraesCS6D01G040200 chr2A 82.648 219 34 4 1 217 12328329 12328113 9.600000e-45 191.0
28 TraesCS6D01G040200 chr2A 96.774 62 2 0 286 347 147477779 147477718 1.290000e-18 104.0
29 TraesCS6D01G040200 chr2B 84.456 193 26 4 1 191 18263863 18263673 1.240000e-43 187.0
30 TraesCS6D01G040200 chr2D 80.408 245 37 8 15 252 526115403 526115163 2.690000e-40 176.0
31 TraesCS6D01G040200 chr7D 98.361 61 1 0 287 347 237270710 237270770 9.940000e-20 108.0
32 TraesCS6D01G040200 chr7D 96.774 62 2 0 286 347 258225581 258225642 1.290000e-18 104.0
33 TraesCS6D01G040200 chr3D 96.825 63 2 0 285 347 108210838 108210776 3.580000e-19 106.0
34 TraesCS6D01G040200 chr5D 96.721 61 2 0 287 347 526139177 526139237 4.630000e-18 102.0
35 TraesCS6D01G040200 chr5D 91.781 73 5 1 276 347 6919000 6918928 1.660000e-17 100.0
36 TraesCS6D01G040200 chr5D 93.478 46 3 0 13 58 520078587 520078542 4.690000e-08 69.4
37 TraesCS6D01G040200 chr4D 96.721 61 2 0 287 347 509117803 509117743 4.630000e-18 102.0
38 TraesCS6D01G040200 chr4B 95.312 64 3 0 284 347 116483437 116483374 4.630000e-18 102.0
39 TraesCS6D01G040200 chr3B 88.136 59 5 2 1 58 422549581 422549638 4.690000e-08 69.4


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 TraesCS6D01G040200 chr6D 16384929 16387555 2626 True 2038.000000 3435 100.000000 1 2627 2 chr6D.!!$R1 2626
1 TraesCS6D01G040200 chr6D 16514361 16516160 1799 False 663.000000 1310 86.406000 768 2599 3 chr6D.!!$F2 1831
2 TraesCS6D01G040200 chr6B 28511817 28513654 1837 True 1917.000000 1917 85.872000 776 2627 1 chr6B.!!$R1 1851
3 TraesCS6D01G040200 chr6B 59298789 59299618 829 False 1038.000000 1038 89.227000 768 1613 1 chr6B.!!$F1 845
4 TraesCS6D01G040200 chr6B 28722221 28723596 1375 False 681.000000 1125 83.239000 776 2358 2 chr6B.!!$F2 1582
5 TraesCS6D01G040200 chr6B 28942314 28943685 1371 False 653.000000 1062 82.930000 784 2358 2 chr6B.!!$F3 1574
6 TraesCS6D01G040200 chr6B 29044515 29046217 1702 False 469.250000 1203 86.795250 775 2572 4 chr6B.!!$F4 1797
7 TraesCS6D01G040200 chr6A 16654292 16655972 1680 True 1022.000000 1384 89.120500 779 2397 2 chr6A.!!$R1 1618
8 TraesCS6D01G040200 chr6A 16705101 16706664 1563 False 599.333333 1295 87.922333 770 2398 3 chr6A.!!$F1 1628
9 TraesCS6D01G040200 chr3A 66253821 66255169 1348 False 677.500000 1146 87.672000 768 2398 2 chr3A.!!$F1 1630
10 TraesCS6D01G040200 chr1B 587500215 587501542 1327 True 693.000000 1075 86.038500 768 2175 2 chr1B.!!$R1 1407
11 TraesCS6D01G040200 chr1B 652543636 652544155 519 False 385.000000 385 80.866000 1553 2084 1 chr1B.!!$F1 531

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
973 980 0.461135 TACGCATCTCAGCATCAGCA 59.539 50.0 0.0 0.0 45.49 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2398 2704 0.331278 TTCCCAAAGATGGCGATGGT 59.669 50.0 0.0 0.0 46.09 3.55 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
33 34 9.533253 AGAAATCTTTTCTATGTTGGTTGTTTG 57.467 29.630 0.76 0.00 0.00 2.93
34 35 9.528018 GAAATCTTTTCTATGTTGGTTGTTTGA 57.472 29.630 0.00 0.00 0.00 2.69
37 38 9.696917 ATCTTTTCTATGTTGGTTGTTTGATTC 57.303 29.630 0.00 0.00 0.00 2.52
38 39 8.690884 TCTTTTCTATGTTGGTTGTTTGATTCA 58.309 29.630 0.00 0.00 0.00 2.57
39 40 9.480053 CTTTTCTATGTTGGTTGTTTGATTCAT 57.520 29.630 0.00 0.00 0.00 2.57
43 44 9.460019 TCTATGTTGGTTGTTTGATTCATATGA 57.540 29.630 0.00 0.00 0.00 2.15
46 47 7.249858 TGTTGGTTGTTTGATTCATATGATCG 58.750 34.615 6.17 0.00 0.00 3.69
47 48 7.120432 TGTTGGTTGTTTGATTCATATGATCGA 59.880 33.333 6.17 3.95 0.00 3.59
48 49 7.622893 TGGTTGTTTGATTCATATGATCGAA 57.377 32.000 6.17 9.37 0.00 3.71
49 50 8.224389 TGGTTGTTTGATTCATATGATCGAAT 57.776 30.769 6.17 0.00 34.58 3.34
50 51 8.344831 TGGTTGTTTGATTCATATGATCGAATC 58.655 33.333 6.17 7.17 45.07 2.52
51 52 7.805071 GGTTGTTTGATTCATATGATCGAATCC 59.195 37.037 6.17 11.27 44.51 3.01
52 53 8.562892 GTTGTTTGATTCATATGATCGAATCCT 58.437 33.333 6.17 0.00 44.51 3.24
53 54 9.777297 TTGTTTGATTCATATGATCGAATCCTA 57.223 29.630 6.17 0.00 44.51 2.94
54 55 9.948964 TGTTTGATTCATATGATCGAATCCTAT 57.051 29.630 6.17 0.00 44.51 2.57
58 59 8.864087 TGATTCATATGATCGAATCCTATAGGG 58.136 37.037 18.97 2.67 44.51 3.53
74 75 8.772647 TCCTATAGGGAATTTATTCAGGGATT 57.227 34.615 18.97 0.00 41.91 3.01
75 76 9.194512 TCCTATAGGGAATTTATTCAGGGATTT 57.805 33.333 18.97 0.00 41.91 2.17
76 77 9.467796 CCTATAGGGAATTTATTCAGGGATTTC 57.532 37.037 11.33 0.00 38.53 2.17
79 80 9.958125 ATAGGGAATTTATTCAGGGATTTCTTT 57.042 29.630 4.97 0.00 38.53 2.52
80 81 8.082672 AGGGAATTTATTCAGGGATTTCTTTG 57.917 34.615 4.97 0.00 38.53 2.77
81 82 7.679881 AGGGAATTTATTCAGGGATTTCTTTGT 59.320 33.333 4.97 0.00 38.53 2.83
82 83 8.977412 GGGAATTTATTCAGGGATTTCTTTGTA 58.023 33.333 4.97 0.00 38.53 2.41
83 84 9.803315 GGAATTTATTCAGGGATTTCTTTGTAC 57.197 33.333 4.97 0.00 38.53 2.90
89 90 8.794335 ATTCAGGGATTTCTTTGTACTACTTC 57.206 34.615 0.00 0.00 0.00 3.01
90 91 6.708285 TCAGGGATTTCTTTGTACTACTTCC 58.292 40.000 0.00 0.00 0.00 3.46
91 92 5.880887 CAGGGATTTCTTTGTACTACTTCCC 59.119 44.000 0.00 0.00 40.51 3.97
92 93 5.550403 AGGGATTTCTTTGTACTACTTCCCA 59.450 40.000 6.91 0.00 42.26 4.37
93 94 6.217693 AGGGATTTCTTTGTACTACTTCCCAT 59.782 38.462 6.91 0.00 42.26 4.00
94 95 7.404980 AGGGATTTCTTTGTACTACTTCCCATA 59.595 37.037 6.91 0.00 42.26 2.74
95 96 8.218488 GGGATTTCTTTGTACTACTTCCCATAT 58.782 37.037 0.00 0.00 40.05 1.78
96 97 9.057089 GGATTTCTTTGTACTACTTCCCATATG 57.943 37.037 0.00 0.00 0.00 1.78
97 98 9.832445 GATTTCTTTGTACTACTTCCCATATGA 57.168 33.333 3.65 0.00 0.00 2.15
100 101 9.832445 TTCTTTGTACTACTTCCCATATGATTC 57.168 33.333 3.65 0.00 0.00 2.52
101 102 8.429641 TCTTTGTACTACTTCCCATATGATTCC 58.570 37.037 3.65 0.00 0.00 3.01
102 103 7.931015 TTGTACTACTTCCCATATGATTCCT 57.069 36.000 3.65 0.00 0.00 3.36
103 104 9.442062 TTTGTACTACTTCCCATATGATTCCTA 57.558 33.333 3.65 0.00 0.00 2.94
104 105 9.442062 TTGTACTACTTCCCATATGATTCCTAA 57.558 33.333 3.65 0.00 0.00 2.69
105 106 8.867097 TGTACTACTTCCCATATGATTCCTAAC 58.133 37.037 3.65 0.00 0.00 2.34
106 107 7.931015 ACTACTTCCCATATGATTCCTAACA 57.069 36.000 3.65 0.00 0.00 2.41
107 108 8.511748 ACTACTTCCCATATGATTCCTAACAT 57.488 34.615 3.65 0.00 0.00 2.71
108 109 8.598041 ACTACTTCCCATATGATTCCTAACATC 58.402 37.037 3.65 0.00 0.00 3.06
109 110 6.784031 ACTTCCCATATGATTCCTAACATCC 58.216 40.000 3.65 0.00 0.00 3.51
110 111 6.332635 ACTTCCCATATGATTCCTAACATCCA 59.667 38.462 3.65 0.00 0.00 3.41
111 112 6.126863 TCCCATATGATTCCTAACATCCAC 57.873 41.667 3.65 0.00 0.00 4.02
112 113 5.851693 TCCCATATGATTCCTAACATCCACT 59.148 40.000 3.65 0.00 0.00 4.00
113 114 6.013379 TCCCATATGATTCCTAACATCCACTC 60.013 42.308 3.65 0.00 0.00 3.51
114 115 6.176183 CCATATGATTCCTAACATCCACTCC 58.824 44.000 3.65 0.00 0.00 3.85
115 116 6.239973 CCATATGATTCCTAACATCCACTCCA 60.240 42.308 3.65 0.00 0.00 3.86
116 117 5.715439 ATGATTCCTAACATCCACTCCAA 57.285 39.130 0.00 0.00 0.00 3.53
117 118 4.843728 TGATTCCTAACATCCACTCCAAC 58.156 43.478 0.00 0.00 0.00 3.77
118 119 3.713826 TTCCTAACATCCACTCCAACC 57.286 47.619 0.00 0.00 0.00 3.77
119 120 2.915869 TCCTAACATCCACTCCAACCT 58.084 47.619 0.00 0.00 0.00 3.50
120 121 4.069312 TCCTAACATCCACTCCAACCTA 57.931 45.455 0.00 0.00 0.00 3.08
121 122 4.631234 TCCTAACATCCACTCCAACCTAT 58.369 43.478 0.00 0.00 0.00 2.57
122 123 4.654262 TCCTAACATCCACTCCAACCTATC 59.346 45.833 0.00 0.00 0.00 2.08
123 124 4.656112 CCTAACATCCACTCCAACCTATCT 59.344 45.833 0.00 0.00 0.00 1.98
124 125 4.494091 AACATCCACTCCAACCTATCTG 57.506 45.455 0.00 0.00 0.00 2.90
125 126 3.724478 ACATCCACTCCAACCTATCTGA 58.276 45.455 0.00 0.00 0.00 3.27
126 127 4.104086 ACATCCACTCCAACCTATCTGAA 58.896 43.478 0.00 0.00 0.00 3.02
127 128 4.536090 ACATCCACTCCAACCTATCTGAAA 59.464 41.667 0.00 0.00 0.00 2.69
128 129 4.826274 TCCACTCCAACCTATCTGAAAG 57.174 45.455 0.00 0.00 0.00 2.62
166 167 9.575868 TTTCCTACTATACAATCAAACAAACCA 57.424 29.630 0.00 0.00 0.00 3.67
167 168 9.575868 TTCCTACTATACAATCAAACAAACCAA 57.424 29.630 0.00 0.00 0.00 3.67
168 169 9.575868 TCCTACTATACAATCAAACAAACCAAA 57.424 29.630 0.00 0.00 0.00 3.28
175 176 7.920160 ACAATCAAACAAACCAAAATCTTGT 57.080 28.000 0.00 0.00 34.81 3.16
177 178 9.442047 ACAATCAAACAAACCAAAATCTTGTAA 57.558 25.926 0.00 0.00 33.05 2.41
178 179 9.919348 CAATCAAACAAACCAAAATCTTGTAAG 57.081 29.630 0.00 0.00 33.05 2.34
179 180 9.883142 AATCAAACAAACCAAAATCTTGTAAGA 57.117 25.926 0.00 0.00 39.78 2.10
195 196 8.630278 TCTTGTAAGATTAAGATGAGCGTAAC 57.370 34.615 0.00 0.00 0.00 2.50
196 197 8.248253 TCTTGTAAGATTAAGATGAGCGTAACA 58.752 33.333 0.00 0.00 0.00 2.41
197 198 8.942338 TTGTAAGATTAAGATGAGCGTAACAT 57.058 30.769 0.00 0.00 0.00 2.71
198 199 8.942338 TGTAAGATTAAGATGAGCGTAACATT 57.058 30.769 0.00 0.00 0.00 2.71
199 200 9.378551 TGTAAGATTAAGATGAGCGTAACATTT 57.621 29.630 0.00 0.00 0.00 2.32
200 201 9.851043 GTAAGATTAAGATGAGCGTAACATTTC 57.149 33.333 0.00 0.00 0.00 2.17
201 202 8.492673 AAGATTAAGATGAGCGTAACATTTCA 57.507 30.769 0.00 0.00 0.00 2.69
202 203 8.492673 AGATTAAGATGAGCGTAACATTTCAA 57.507 30.769 0.00 0.00 0.00 2.69
203 204 9.113838 AGATTAAGATGAGCGTAACATTTCAAT 57.886 29.630 0.00 0.00 0.00 2.57
204 205 9.374960 GATTAAGATGAGCGTAACATTTCAATC 57.625 33.333 0.00 0.00 0.00 2.67
205 206 6.992063 AAGATGAGCGTAACATTTCAATCT 57.008 33.333 0.00 0.00 0.00 2.40
206 207 6.992063 AGATGAGCGTAACATTTCAATCTT 57.008 33.333 0.00 0.00 0.00 2.40
207 208 8.492673 AAGATGAGCGTAACATTTCAATCTTA 57.507 30.769 0.00 0.00 0.00 2.10
208 209 8.668510 AGATGAGCGTAACATTTCAATCTTAT 57.331 30.769 0.00 0.00 0.00 1.73
209 210 8.554528 AGATGAGCGTAACATTTCAATCTTATG 58.445 33.333 0.00 0.00 0.00 1.90
210 211 7.609760 TGAGCGTAACATTTCAATCTTATGT 57.390 32.000 0.00 0.00 34.14 2.29
211 212 8.039603 TGAGCGTAACATTTCAATCTTATGTT 57.960 30.769 0.00 0.00 43.02 2.71
212 213 8.511321 TGAGCGTAACATTTCAATCTTATGTTT 58.489 29.630 0.00 0.00 41.36 2.83
213 214 9.341899 GAGCGTAACATTTCAATCTTATGTTTT 57.658 29.630 0.00 0.00 41.36 2.43
214 215 9.691362 AGCGTAACATTTCAATCTTATGTTTTT 57.309 25.926 0.00 0.00 41.36 1.94
235 236 7.593875 TTTTTCCCGCAATTTTAGAATCATG 57.406 32.000 0.00 0.00 0.00 3.07
236 237 5.913137 TTCCCGCAATTTTAGAATCATGT 57.087 34.783 0.00 0.00 0.00 3.21
237 238 5.913137 TCCCGCAATTTTAGAATCATGTT 57.087 34.783 0.00 0.00 0.00 2.71
238 239 6.279513 TCCCGCAATTTTAGAATCATGTTT 57.720 33.333 0.00 0.00 0.00 2.83
239 240 7.397892 TCCCGCAATTTTAGAATCATGTTTA 57.602 32.000 0.00 0.00 0.00 2.01
240 241 7.831753 TCCCGCAATTTTAGAATCATGTTTAA 58.168 30.769 0.00 0.00 0.00 1.52
241 242 8.474025 TCCCGCAATTTTAGAATCATGTTTAAT 58.526 29.630 0.00 0.00 0.00 1.40
242 243 9.097257 CCCGCAATTTTAGAATCATGTTTAATT 57.903 29.630 0.00 0.00 0.00 1.40
252 253 7.707104 AGAATCATGTTTAATTAAAGAGGCCG 58.293 34.615 10.92 1.61 0.00 6.13
253 254 7.339466 AGAATCATGTTTAATTAAAGAGGCCGT 59.661 33.333 10.92 1.11 0.00 5.68
254 255 6.189677 TCATGTTTAATTAAAGAGGCCGTG 57.810 37.500 10.92 10.18 0.00 4.94
255 256 5.941058 TCATGTTTAATTAAAGAGGCCGTGA 59.059 36.000 10.92 12.04 0.00 4.35
256 257 6.431543 TCATGTTTAATTAAAGAGGCCGTGAA 59.568 34.615 10.92 0.00 0.00 3.18
257 258 6.827586 TGTTTAATTAAAGAGGCCGTGAAT 57.172 33.333 10.92 0.00 0.00 2.57
258 259 6.616947 TGTTTAATTAAAGAGGCCGTGAATG 58.383 36.000 10.92 0.00 0.00 2.67
259 260 6.207810 TGTTTAATTAAAGAGGCCGTGAATGT 59.792 34.615 10.92 0.00 0.00 2.71
260 261 6.827586 TTAATTAAAGAGGCCGTGAATGTT 57.172 33.333 0.00 0.00 0.00 2.71
261 262 5.722021 AATTAAAGAGGCCGTGAATGTTT 57.278 34.783 0.00 0.00 0.00 2.83
262 263 5.722021 ATTAAAGAGGCCGTGAATGTTTT 57.278 34.783 0.00 0.00 0.00 2.43
263 264 5.523438 TTAAAGAGGCCGTGAATGTTTTT 57.477 34.783 0.00 0.00 0.00 1.94
286 287 5.446143 TTTTGCGTGGTTCTAATCATTGT 57.554 34.783 0.00 0.00 0.00 2.71
287 288 6.561737 TTTTGCGTGGTTCTAATCATTGTA 57.438 33.333 0.00 0.00 0.00 2.41
288 289 5.539582 TTGCGTGGTTCTAATCATTGTAC 57.460 39.130 0.00 0.00 0.00 2.90
289 290 4.827692 TGCGTGGTTCTAATCATTGTACT 58.172 39.130 0.00 0.00 0.00 2.73
290 291 4.868171 TGCGTGGTTCTAATCATTGTACTC 59.132 41.667 0.00 0.00 0.00 2.59
291 292 4.270325 GCGTGGTTCTAATCATTGTACTCC 59.730 45.833 0.00 0.00 0.00 3.85
292 293 4.809426 CGTGGTTCTAATCATTGTACTCCC 59.191 45.833 0.00 0.00 0.00 4.30
293 294 5.395324 CGTGGTTCTAATCATTGTACTCCCT 60.395 44.000 0.00 0.00 0.00 4.20
294 295 6.049790 GTGGTTCTAATCATTGTACTCCCTC 58.950 44.000 0.00 0.00 0.00 4.30
295 296 5.130477 TGGTTCTAATCATTGTACTCCCTCC 59.870 44.000 0.00 0.00 0.00 4.30
296 297 5.290386 GTTCTAATCATTGTACTCCCTCCG 58.710 45.833 0.00 0.00 0.00 4.63
297 298 4.543689 TCTAATCATTGTACTCCCTCCGT 58.456 43.478 0.00 0.00 0.00 4.69
298 299 3.821421 AATCATTGTACTCCCTCCGTC 57.179 47.619 0.00 0.00 0.00 4.79
299 300 2.526888 TCATTGTACTCCCTCCGTCT 57.473 50.000 0.00 0.00 0.00 4.18
300 301 2.376109 TCATTGTACTCCCTCCGTCTC 58.624 52.381 0.00 0.00 0.00 3.36
301 302 2.100197 CATTGTACTCCCTCCGTCTCA 58.900 52.381 0.00 0.00 0.00 3.27
302 303 2.297698 TTGTACTCCCTCCGTCTCAA 57.702 50.000 0.00 0.00 0.00 3.02
303 304 2.297698 TGTACTCCCTCCGTCTCAAA 57.702 50.000 0.00 0.00 0.00 2.69
304 305 2.600790 TGTACTCCCTCCGTCTCAAAA 58.399 47.619 0.00 0.00 0.00 2.44
305 306 3.170717 TGTACTCCCTCCGTCTCAAAAT 58.829 45.455 0.00 0.00 0.00 1.82
306 307 4.346730 TGTACTCCCTCCGTCTCAAAATA 58.653 43.478 0.00 0.00 0.00 1.40
307 308 4.773674 TGTACTCCCTCCGTCTCAAAATAA 59.226 41.667 0.00 0.00 0.00 1.40
308 309 4.473477 ACTCCCTCCGTCTCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
309 310 3.838903 ACTCCCTCCGTCTCAAAATAAGT 59.161 43.478 0.00 0.00 0.00 2.24
310 311 4.184629 CTCCCTCCGTCTCAAAATAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
311 312 3.581332 TCCCTCCGTCTCAAAATAAGTGT 59.419 43.478 0.00 0.00 0.00 3.55
312 313 3.933332 CCCTCCGTCTCAAAATAAGTGTC 59.067 47.826 0.00 0.00 0.00 3.67
313 314 4.322801 CCCTCCGTCTCAAAATAAGTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
314 315 4.865365 CCTCCGTCTCAAAATAAGTGTCTC 59.135 45.833 0.00 0.00 0.00 3.36
315 316 5.462530 TCCGTCTCAAAATAAGTGTCTCA 57.537 39.130 0.00 0.00 0.00 3.27
316 317 5.849510 TCCGTCTCAAAATAAGTGTCTCAA 58.150 37.500 0.00 0.00 0.00 3.02
317 318 6.464222 TCCGTCTCAAAATAAGTGTCTCAAT 58.536 36.000 0.00 0.00 0.00 2.57
318 319 6.934645 TCCGTCTCAAAATAAGTGTCTCAATT 59.065 34.615 0.00 0.00 0.00 2.32
319 320 7.444183 TCCGTCTCAAAATAAGTGTCTCAATTT 59.556 33.333 0.00 0.00 0.00 1.82
320 321 8.076178 CCGTCTCAAAATAAGTGTCTCAATTTT 58.924 33.333 0.00 0.00 33.07 1.82
321 322 8.895845 CGTCTCAAAATAAGTGTCTCAATTTTG 58.104 33.333 11.32 11.32 44.73 2.44
322 323 9.736023 GTCTCAAAATAAGTGTCTCAATTTTGT 57.264 29.630 15.19 0.00 44.18 2.83
336 337 9.595357 GTCTCAATTTTGTACTAACTTTAGTGC 57.405 33.333 11.24 10.37 43.44 4.40
915 916 2.741055 GCCCAGCTCCTTCCTCCTC 61.741 68.421 0.00 0.00 0.00 3.71
968 975 1.001924 CGTCTCTACGCATCTCAGCAT 60.002 52.381 0.00 0.00 43.12 3.79
971 978 2.292845 TCTCTACGCATCTCAGCATCAG 59.707 50.000 0.00 0.00 0.00 2.90
972 979 1.138337 CTACGCATCTCAGCATCAGC 58.862 55.000 0.00 0.00 42.56 4.26
973 980 0.461135 TACGCATCTCAGCATCAGCA 59.539 50.000 0.00 0.00 45.49 4.41
974 981 1.088340 ACGCATCTCAGCATCAGCAC 61.088 55.000 0.00 0.00 45.49 4.40
975 982 0.810426 CGCATCTCAGCATCAGCACT 60.810 55.000 0.00 0.00 45.49 4.40
984 991 1.306642 GCATCAGCACTTCAGCAGCT 61.307 55.000 0.00 0.00 41.58 4.24
1000 1007 2.903357 CTCCCCTCACATCCCACG 59.097 66.667 0.00 0.00 0.00 4.94
1474 1490 3.066380 CGTCACCAAGTTCACATCATCA 58.934 45.455 0.00 0.00 0.00 3.07
1479 1495 5.045651 TCACCAAGTTCACATCATCATAGGT 60.046 40.000 0.00 0.00 0.00 3.08
1489 1522 4.098044 ACATCATCATAGGTTTCGTCGTCT 59.902 41.667 0.00 0.00 0.00 4.18
1498 1531 2.096417 GGTTTCGTCGTCTGTTTCATGG 60.096 50.000 0.00 0.00 0.00 3.66
1663 1721 4.888326 AGTTCAGACTCTTCTTGATGCT 57.112 40.909 0.00 0.00 0.00 3.79
1955 2123 4.280929 AGTTGGTGAGCCTTGTTAATTTCC 59.719 41.667 0.00 0.00 35.27 3.13
1967 2135 6.128227 CCTTGTTAATTTCCGACGGAACATTA 60.128 38.462 28.45 25.96 41.87 1.90
2175 2371 3.943381 TGACAGATGCAACCATCATCTTC 59.057 43.478 6.47 5.81 45.99 2.87
2196 2392 0.255890 TAGGATGGCCCACAGAAAGC 59.744 55.000 0.00 0.00 37.41 3.51
2206 2438 1.484356 CACAGAAAGCTTGCTGTTGC 58.516 50.000 33.55 0.00 42.33 4.17
2213 2445 1.542492 AGCTTGCTGTTGCTGCTATT 58.458 45.000 0.00 0.00 43.42 1.73
2219 2451 3.264947 TGCTGTTGCTGCTATTGAGTAG 58.735 45.455 0.00 0.00 40.48 2.57
2227 2459 4.109050 GCTGCTATTGAGTAGTGAGACAC 58.891 47.826 0.00 0.00 37.70 3.67
2228 2460 4.677584 CTGCTATTGAGTAGTGAGACACC 58.322 47.826 0.00 0.00 34.49 4.16
2232 2464 5.105716 GCTATTGAGTAGTGAGACACCTGAA 60.106 44.000 0.00 0.00 34.49 3.02
2283 2551 8.292448 TGCACTAGCTAATTTTTCTTTCTTCTG 58.708 33.333 0.00 0.00 42.74 3.02
2300 2599 6.852420 TCTTCTGCTACTACACTTGGTAAT 57.148 37.500 0.00 0.00 0.00 1.89
2332 2631 3.069443 ACGAAGCCACCAATTTTGTGAAT 59.931 39.130 6.47 0.00 0.00 2.57
2352 2654 7.065283 GTGAATGTGCAAAGTTTTTCTAATGC 58.935 34.615 0.00 0.00 38.65 3.56
2416 2752 0.394216 CACCATCGCCATCTTTGGGA 60.394 55.000 0.00 0.00 43.84 4.37
2450 2786 6.375174 TGTTCCTCATTTGTGTTAGATGATGG 59.625 38.462 0.00 0.00 0.00 3.51
2458 2811 9.546428 CATTTGTGTTAGATGATGGTACTATCA 57.454 33.333 22.33 22.33 41.00 2.15
2467 2820 7.835822 AGATGATGGTACTATCATGTAAGAGC 58.164 38.462 32.10 18.70 45.30 4.09
2499 2852 6.508721 GCGTGAGTCTGAAGAAATAGTATTGC 60.509 42.308 0.00 0.00 0.00 3.56
2521 2874 6.632909 TGCTGCTGCTTAAATTAATGTTCAT 58.367 32.000 17.00 0.00 40.48 2.57
2539 2892 1.000052 CATGGTGTGCTTGCATGTCAA 60.000 47.619 0.00 0.00 0.00 3.18
2557 2910 7.043590 GCATGTCAAATCAGATTCTTTGCATAC 60.044 37.037 0.00 0.00 32.75 2.39
2602 2955 8.593679 TCTGAAGTTAGTTCATGAATCTTACCA 58.406 33.333 12.12 8.11 44.44 3.25
2615 2968 3.806949 TCTTACCATTGTCCAGGCTTT 57.193 42.857 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.533253 CAAACAACCAACATAGAAAAGATTTCT 57.467 29.630 9.97 9.97 0.00 2.52
8 9 9.528018 TCAAACAACCAACATAGAAAAGATTTC 57.472 29.630 0.00 0.00 0.00 2.17
11 12 9.696917 GAATCAAACAACCAACATAGAAAAGAT 57.303 29.630 0.00 0.00 0.00 2.40
12 13 8.690884 TGAATCAAACAACCAACATAGAAAAGA 58.309 29.630 0.00 0.00 0.00 2.52
13 14 8.870160 TGAATCAAACAACCAACATAGAAAAG 57.130 30.769 0.00 0.00 0.00 2.27
17 18 9.460019 TCATATGAATCAAACAACCAACATAGA 57.540 29.630 1.98 0.00 0.00 1.98
20 21 7.916977 CGATCATATGAATCAAACAACCAACAT 59.083 33.333 9.99 0.00 0.00 2.71
21 22 7.120432 TCGATCATATGAATCAAACAACCAACA 59.880 33.333 9.99 0.00 0.00 3.33
22 23 7.471721 TCGATCATATGAATCAAACAACCAAC 58.528 34.615 9.99 0.00 0.00 3.77
23 24 7.622893 TCGATCATATGAATCAAACAACCAA 57.377 32.000 9.99 0.00 0.00 3.67
24 25 7.622893 TTCGATCATATGAATCAAACAACCA 57.377 32.000 9.99 0.00 0.00 3.67
25 26 8.719478 GATTCGATCATATGAATCAAACAACC 57.281 34.615 9.99 0.00 46.17 3.77
33 34 9.083422 TCCCTATAGGATTCGATCATATGAATC 57.917 37.037 21.07 7.94 46.18 2.52
34 35 9.439461 TTCCCTATAGGATTCGATCATATGAAT 57.561 33.333 21.07 0.00 46.94 2.57
35 36 8.838649 TTCCCTATAGGATTCGATCATATGAA 57.161 34.615 21.07 7.20 46.94 2.57
36 37 9.439461 AATTCCCTATAGGATTCGATCATATGA 57.561 33.333 21.07 8.10 46.94 2.15
44 45 8.540388 CCTGAATAAATTCCCTATAGGATTCGA 58.460 37.037 21.07 5.85 46.94 3.71
45 46 7.770897 CCCTGAATAAATTCCCTATAGGATTCG 59.229 40.741 21.07 13.92 46.94 3.34
46 47 8.836735 TCCCTGAATAAATTCCCTATAGGATTC 58.163 37.037 21.07 18.20 46.94 2.52
47 48 8.772647 TCCCTGAATAAATTCCCTATAGGATT 57.227 34.615 21.07 10.35 46.94 3.01
48 49 8.956356 ATCCCTGAATAAATTCCCTATAGGAT 57.044 34.615 21.07 3.61 46.94 3.24
49 50 8.772647 AATCCCTGAATAAATTCCCTATAGGA 57.227 34.615 21.07 0.90 45.68 2.94
50 51 9.467796 GAAATCCCTGAATAAATTCCCTATAGG 57.532 37.037 12.27 12.27 35.97 2.57
53 54 9.958125 AAAGAAATCCCTGAATAAATTCCCTAT 57.042 29.630 0.41 0.00 35.97 2.57
54 55 9.200817 CAAAGAAATCCCTGAATAAATTCCCTA 57.799 33.333 0.41 0.00 35.97 3.53
55 56 7.679881 ACAAAGAAATCCCTGAATAAATTCCCT 59.320 33.333 0.41 0.00 35.97 4.20
56 57 7.851228 ACAAAGAAATCCCTGAATAAATTCCC 58.149 34.615 0.41 0.00 35.97 3.97
57 58 9.803315 GTACAAAGAAATCCCTGAATAAATTCC 57.197 33.333 0.41 0.00 35.97 3.01
63 64 9.886132 GAAGTAGTACAAAGAAATCCCTGAATA 57.114 33.333 2.52 0.00 0.00 1.75
64 65 7.829706 GGAAGTAGTACAAAGAAATCCCTGAAT 59.170 37.037 2.52 0.00 0.00 2.57
65 66 7.166167 GGAAGTAGTACAAAGAAATCCCTGAA 58.834 38.462 2.52 0.00 0.00 3.02
66 67 6.296259 GGGAAGTAGTACAAAGAAATCCCTGA 60.296 42.308 2.52 0.00 40.66 3.86
67 68 5.880887 GGGAAGTAGTACAAAGAAATCCCTG 59.119 44.000 2.52 0.00 40.66 4.45
68 69 5.550403 TGGGAAGTAGTACAAAGAAATCCCT 59.450 40.000 14.86 0.00 43.54 4.20
69 70 5.812286 TGGGAAGTAGTACAAAGAAATCCC 58.188 41.667 2.52 7.96 43.46 3.85
70 71 9.057089 CATATGGGAAGTAGTACAAAGAAATCC 57.943 37.037 2.52 0.00 0.00 3.01
71 72 9.832445 TCATATGGGAAGTAGTACAAAGAAATC 57.168 33.333 2.13 0.00 0.00 2.17
74 75 9.832445 GAATCATATGGGAAGTAGTACAAAGAA 57.168 33.333 2.13 0.00 0.00 2.52
75 76 8.429641 GGAATCATATGGGAAGTAGTACAAAGA 58.570 37.037 2.13 0.00 0.00 2.52
76 77 8.432805 AGGAATCATATGGGAAGTAGTACAAAG 58.567 37.037 2.13 0.00 0.00 2.77
77 78 8.331931 AGGAATCATATGGGAAGTAGTACAAA 57.668 34.615 2.13 0.00 0.00 2.83
78 79 7.931015 AGGAATCATATGGGAAGTAGTACAA 57.069 36.000 2.13 0.00 0.00 2.41
79 80 8.867097 GTTAGGAATCATATGGGAAGTAGTACA 58.133 37.037 2.13 0.00 0.00 2.90
80 81 8.867097 TGTTAGGAATCATATGGGAAGTAGTAC 58.133 37.037 2.13 0.00 0.00 2.73
81 82 9.615660 ATGTTAGGAATCATATGGGAAGTAGTA 57.384 33.333 2.13 0.00 0.00 1.82
82 83 7.931015 TGTTAGGAATCATATGGGAAGTAGT 57.069 36.000 2.13 0.00 0.00 2.73
83 84 8.043710 GGATGTTAGGAATCATATGGGAAGTAG 58.956 40.741 2.13 0.00 0.00 2.57
84 85 7.515861 TGGATGTTAGGAATCATATGGGAAGTA 59.484 37.037 2.13 0.00 0.00 2.24
85 86 6.332635 TGGATGTTAGGAATCATATGGGAAGT 59.667 38.462 2.13 0.00 0.00 3.01
86 87 6.656693 GTGGATGTTAGGAATCATATGGGAAG 59.343 42.308 2.13 0.00 0.00 3.46
87 88 6.332635 AGTGGATGTTAGGAATCATATGGGAA 59.667 38.462 2.13 0.00 0.00 3.97
88 89 5.851693 AGTGGATGTTAGGAATCATATGGGA 59.148 40.000 2.13 0.00 0.00 4.37
89 90 6.131972 AGTGGATGTTAGGAATCATATGGG 57.868 41.667 2.13 0.00 0.00 4.00
90 91 6.176183 GGAGTGGATGTTAGGAATCATATGG 58.824 44.000 2.13 0.00 0.00 2.74
91 92 6.772605 TGGAGTGGATGTTAGGAATCATATG 58.227 40.000 0.00 0.00 0.00 1.78
92 93 7.227156 GTTGGAGTGGATGTTAGGAATCATAT 58.773 38.462 0.00 0.00 0.00 1.78
93 94 6.409234 GGTTGGAGTGGATGTTAGGAATCATA 60.409 42.308 0.00 0.00 0.00 2.15
94 95 5.440610 GTTGGAGTGGATGTTAGGAATCAT 58.559 41.667 0.00 0.00 0.00 2.45
95 96 4.324254 GGTTGGAGTGGATGTTAGGAATCA 60.324 45.833 0.00 0.00 0.00 2.57
96 97 4.080299 AGGTTGGAGTGGATGTTAGGAATC 60.080 45.833 0.00 0.00 0.00 2.52
97 98 3.852578 AGGTTGGAGTGGATGTTAGGAAT 59.147 43.478 0.00 0.00 0.00 3.01
98 99 3.256704 AGGTTGGAGTGGATGTTAGGAA 58.743 45.455 0.00 0.00 0.00 3.36
99 100 2.915869 AGGTTGGAGTGGATGTTAGGA 58.084 47.619 0.00 0.00 0.00 2.94
100 101 4.656112 AGATAGGTTGGAGTGGATGTTAGG 59.344 45.833 0.00 0.00 0.00 2.69
101 102 5.363868 TCAGATAGGTTGGAGTGGATGTTAG 59.636 44.000 0.00 0.00 0.00 2.34
102 103 5.277250 TCAGATAGGTTGGAGTGGATGTTA 58.723 41.667 0.00 0.00 0.00 2.41
103 104 4.104086 TCAGATAGGTTGGAGTGGATGTT 58.896 43.478 0.00 0.00 0.00 2.71
104 105 3.724478 TCAGATAGGTTGGAGTGGATGT 58.276 45.455 0.00 0.00 0.00 3.06
105 106 4.760530 TTCAGATAGGTTGGAGTGGATG 57.239 45.455 0.00 0.00 0.00 3.51
106 107 5.032846 TCTTTCAGATAGGTTGGAGTGGAT 58.967 41.667 0.00 0.00 0.00 3.41
107 108 4.425772 TCTTTCAGATAGGTTGGAGTGGA 58.574 43.478 0.00 0.00 0.00 4.02
108 109 4.826274 TCTTTCAGATAGGTTGGAGTGG 57.174 45.455 0.00 0.00 0.00 4.00
109 110 7.693969 AAATTCTTTCAGATAGGTTGGAGTG 57.306 36.000 0.00 0.00 0.00 3.51
110 111 8.712228 AAAAATTCTTTCAGATAGGTTGGAGT 57.288 30.769 0.00 0.00 0.00 3.85
140 141 9.575868 TGGTTTGTTTGATTGTATAGTAGGAAA 57.424 29.630 0.00 0.00 0.00 3.13
141 142 9.575868 TTGGTTTGTTTGATTGTATAGTAGGAA 57.424 29.630 0.00 0.00 0.00 3.36
142 143 9.575868 TTTGGTTTGTTTGATTGTATAGTAGGA 57.424 29.630 0.00 0.00 0.00 2.94
149 150 9.612066 ACAAGATTTTGGTTTGTTTGATTGTAT 57.388 25.926 0.57 0.00 38.66 2.29
151 152 7.920160 ACAAGATTTTGGTTTGTTTGATTGT 57.080 28.000 0.57 0.00 38.66 2.71
152 153 9.919348 CTTACAAGATTTTGGTTTGTTTGATTG 57.081 29.630 0.57 0.00 38.66 2.67
153 154 9.883142 TCTTACAAGATTTTGGTTTGTTTGATT 57.117 25.926 0.57 0.00 38.66 2.57
170 171 8.248253 TGTTACGCTCATCTTAATCTTACAAGA 58.752 33.333 0.00 0.00 39.78 3.02
171 172 8.407457 TGTTACGCTCATCTTAATCTTACAAG 57.593 34.615 0.00 0.00 0.00 3.16
172 173 8.942338 ATGTTACGCTCATCTTAATCTTACAA 57.058 30.769 0.00 0.00 0.00 2.41
173 174 8.942338 AATGTTACGCTCATCTTAATCTTACA 57.058 30.769 0.00 0.00 0.00 2.41
174 175 9.851043 GAAATGTTACGCTCATCTTAATCTTAC 57.149 33.333 0.00 0.00 0.00 2.34
175 176 9.594478 TGAAATGTTACGCTCATCTTAATCTTA 57.406 29.630 0.00 0.00 0.00 2.10
176 177 8.492673 TGAAATGTTACGCTCATCTTAATCTT 57.507 30.769 0.00 0.00 0.00 2.40
177 178 8.492673 TTGAAATGTTACGCTCATCTTAATCT 57.507 30.769 0.00 0.00 0.00 2.40
178 179 9.374960 GATTGAAATGTTACGCTCATCTTAATC 57.625 33.333 0.00 0.00 0.00 1.75
179 180 9.113838 AGATTGAAATGTTACGCTCATCTTAAT 57.886 29.630 0.00 0.00 0.00 1.40
180 181 8.492673 AGATTGAAATGTTACGCTCATCTTAA 57.507 30.769 0.00 0.00 0.00 1.85
181 182 8.492673 AAGATTGAAATGTTACGCTCATCTTA 57.507 30.769 0.00 0.00 0.00 2.10
182 183 6.992063 AGATTGAAATGTTACGCTCATCTT 57.008 33.333 0.00 0.00 0.00 2.40
183 184 6.992063 AAGATTGAAATGTTACGCTCATCT 57.008 33.333 0.00 0.00 0.00 2.90
184 185 8.338259 ACATAAGATTGAAATGTTACGCTCATC 58.662 33.333 0.00 0.00 29.68 2.92
185 186 8.213518 ACATAAGATTGAAATGTTACGCTCAT 57.786 30.769 0.00 0.00 29.68 2.90
186 187 7.609760 ACATAAGATTGAAATGTTACGCTCA 57.390 32.000 0.00 0.00 29.68 4.26
187 188 8.895932 AAACATAAGATTGAAATGTTACGCTC 57.104 30.769 0.78 0.00 41.67 5.03
188 189 9.691362 AAAAACATAAGATTGAAATGTTACGCT 57.309 25.926 0.78 0.00 41.67 5.07
211 212 7.158021 ACATGATTCTAAAATTGCGGGAAAAA 58.842 30.769 0.00 0.00 0.00 1.94
212 213 6.696411 ACATGATTCTAAAATTGCGGGAAAA 58.304 32.000 0.00 0.00 0.00 2.29
213 214 6.279513 ACATGATTCTAAAATTGCGGGAAA 57.720 33.333 0.00 0.00 0.00 3.13
214 215 5.913137 ACATGATTCTAAAATTGCGGGAA 57.087 34.783 0.00 0.00 0.00 3.97
215 216 5.913137 AACATGATTCTAAAATTGCGGGA 57.087 34.783 0.00 0.00 0.00 5.14
216 217 8.647143 ATTAAACATGATTCTAAAATTGCGGG 57.353 30.769 0.00 0.00 0.00 6.13
226 227 8.836413 CGGCCTCTTTAATTAAACATGATTCTA 58.164 33.333 6.54 0.00 0.00 2.10
227 228 7.339466 ACGGCCTCTTTAATTAAACATGATTCT 59.661 33.333 6.54 0.00 0.00 2.40
228 229 7.432252 CACGGCCTCTTTAATTAAACATGATTC 59.568 37.037 6.54 0.00 0.00 2.52
229 230 7.122055 TCACGGCCTCTTTAATTAAACATGATT 59.878 33.333 6.54 0.00 0.00 2.57
230 231 6.601613 TCACGGCCTCTTTAATTAAACATGAT 59.398 34.615 6.54 0.00 0.00 2.45
231 232 5.941058 TCACGGCCTCTTTAATTAAACATGA 59.059 36.000 6.54 2.90 0.00 3.07
232 233 6.189677 TCACGGCCTCTTTAATTAAACATG 57.810 37.500 6.54 0.00 0.00 3.21
233 234 6.827586 TTCACGGCCTCTTTAATTAAACAT 57.172 33.333 6.54 0.00 0.00 2.71
234 235 6.207810 ACATTCACGGCCTCTTTAATTAAACA 59.792 34.615 6.54 0.00 0.00 2.83
235 236 6.617879 ACATTCACGGCCTCTTTAATTAAAC 58.382 36.000 6.54 0.00 0.00 2.01
236 237 6.827586 ACATTCACGGCCTCTTTAATTAAA 57.172 33.333 10.16 10.16 0.00 1.52
237 238 6.827586 AACATTCACGGCCTCTTTAATTAA 57.172 33.333 0.00 0.00 0.00 1.40
238 239 6.827586 AAACATTCACGGCCTCTTTAATTA 57.172 33.333 0.00 0.00 0.00 1.40
239 240 5.722021 AAACATTCACGGCCTCTTTAATT 57.278 34.783 0.00 0.00 0.00 1.40
240 241 5.722021 AAAACATTCACGGCCTCTTTAAT 57.278 34.783 0.00 0.00 0.00 1.40
241 242 5.523438 AAAAACATTCACGGCCTCTTTAA 57.477 34.783 0.00 0.00 0.00 1.52
263 264 5.837437 ACAATGATTAGAACCACGCAAAAA 58.163 33.333 0.00 0.00 0.00 1.94
264 265 5.446143 ACAATGATTAGAACCACGCAAAA 57.554 34.783 0.00 0.00 0.00 2.44
265 266 5.703592 AGTACAATGATTAGAACCACGCAAA 59.296 36.000 0.00 0.00 0.00 3.68
266 267 5.242434 AGTACAATGATTAGAACCACGCAA 58.758 37.500 0.00 0.00 0.00 4.85
267 268 4.827692 AGTACAATGATTAGAACCACGCA 58.172 39.130 0.00 0.00 0.00 5.24
268 269 4.270325 GGAGTACAATGATTAGAACCACGC 59.730 45.833 0.00 0.00 0.00 5.34
269 270 4.809426 GGGAGTACAATGATTAGAACCACG 59.191 45.833 0.00 0.00 0.00 4.94
270 271 5.990668 AGGGAGTACAATGATTAGAACCAC 58.009 41.667 0.00 0.00 0.00 4.16
271 272 5.130477 GGAGGGAGTACAATGATTAGAACCA 59.870 44.000 0.00 0.00 0.00 3.67
272 273 5.612351 GGAGGGAGTACAATGATTAGAACC 58.388 45.833 0.00 0.00 0.00 3.62
273 274 5.163437 ACGGAGGGAGTACAATGATTAGAAC 60.163 44.000 0.00 0.00 0.00 3.01
274 275 4.960469 ACGGAGGGAGTACAATGATTAGAA 59.040 41.667 0.00 0.00 0.00 2.10
275 276 4.543689 ACGGAGGGAGTACAATGATTAGA 58.456 43.478 0.00 0.00 0.00 2.10
276 277 4.585162 AGACGGAGGGAGTACAATGATTAG 59.415 45.833 0.00 0.00 0.00 1.73
277 278 4.543689 AGACGGAGGGAGTACAATGATTA 58.456 43.478 0.00 0.00 0.00 1.75
278 279 3.375699 AGACGGAGGGAGTACAATGATT 58.624 45.455 0.00 0.00 0.00 2.57
279 280 2.959707 GAGACGGAGGGAGTACAATGAT 59.040 50.000 0.00 0.00 0.00 2.45
280 281 2.291346 TGAGACGGAGGGAGTACAATGA 60.291 50.000 0.00 0.00 0.00 2.57
281 282 2.100197 TGAGACGGAGGGAGTACAATG 58.900 52.381 0.00 0.00 0.00 2.82
282 283 2.526888 TGAGACGGAGGGAGTACAAT 57.473 50.000 0.00 0.00 0.00 2.71
283 284 2.297698 TTGAGACGGAGGGAGTACAA 57.702 50.000 0.00 0.00 0.00 2.41
284 285 2.297698 TTTGAGACGGAGGGAGTACA 57.702 50.000 0.00 0.00 0.00 2.90
285 286 3.889520 ATTTTGAGACGGAGGGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
286 287 5.021458 ACTTATTTTGAGACGGAGGGAGTA 58.979 41.667 0.00 0.00 0.00 2.59
287 288 3.838903 ACTTATTTTGAGACGGAGGGAGT 59.161 43.478 0.00 0.00 0.00 3.85
288 289 4.184629 CACTTATTTTGAGACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
289 290 3.581332 ACACTTATTTTGAGACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
290 291 3.933332 GACACTTATTTTGAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
291 292 4.822026 AGACACTTATTTTGAGACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
292 293 5.470368 TGAGACACTTATTTTGAGACGGAG 58.530 41.667 0.00 0.00 0.00 4.63
293 294 5.462530 TGAGACACTTATTTTGAGACGGA 57.537 39.130 0.00 0.00 0.00 4.69
294 295 6.727824 ATTGAGACACTTATTTTGAGACGG 57.272 37.500 0.00 0.00 0.00 4.79
295 296 8.895845 CAAAATTGAGACACTTATTTTGAGACG 58.104 33.333 17.64 0.00 44.64 4.18
296 297 9.736023 ACAAAATTGAGACACTTATTTTGAGAC 57.264 29.630 23.24 0.00 44.64 3.36
310 311 9.595357 GCACTAAAGTTAGTACAAAATTGAGAC 57.405 33.333 3.46 0.00 41.82 3.36
311 312 9.332502 TGCACTAAAGTTAGTACAAAATTGAGA 57.667 29.630 3.46 0.00 41.82 3.27
312 313 9.944663 TTGCACTAAAGTTAGTACAAAATTGAG 57.055 29.630 12.43 0.00 41.56 3.02
815 816 0.526524 GATGCTTGAGACGGACGGAG 60.527 60.000 0.00 0.00 0.00 4.63
826 827 2.032634 GCCGTTCGGTGATGCTTGA 61.033 57.895 12.81 0.00 0.00 3.02
902 903 2.770475 GGGGGAGGAGGAAGGAGC 60.770 72.222 0.00 0.00 0.00 4.70
915 916 1.752833 GTTATGTAGGGAGCGGGGG 59.247 63.158 0.00 0.00 0.00 5.40
957 964 1.331138 GAAGTGCTGATGCTGAGATGC 59.669 52.381 0.00 0.00 40.48 3.91
968 975 1.004080 GGAGCTGCTGAAGTGCTGA 60.004 57.895 7.01 0.00 37.16 4.26
971 978 2.749441 GGGGAGCTGCTGAAGTGC 60.749 66.667 7.01 0.00 0.00 4.40
972 979 1.078567 GAGGGGAGCTGCTGAAGTG 60.079 63.158 7.01 0.00 0.00 3.16
973 980 1.537397 TGAGGGGAGCTGCTGAAGT 60.537 57.895 7.01 0.00 0.00 3.01
974 981 1.078567 GTGAGGGGAGCTGCTGAAG 60.079 63.158 7.01 0.00 0.00 3.02
975 982 1.203441 ATGTGAGGGGAGCTGCTGAA 61.203 55.000 7.01 0.00 0.00 3.02
984 991 3.399181 GCGTGGGATGTGAGGGGA 61.399 66.667 0.00 0.00 0.00 4.81
1348 1364 2.969821 TGGTGGGCTTCTTGTTGTAT 57.030 45.000 0.00 0.00 0.00 2.29
1474 1490 4.247267 TGAAACAGACGACGAAACCTAT 57.753 40.909 0.00 0.00 0.00 2.57
1479 1495 3.100658 TCCATGAAACAGACGACGAAA 57.899 42.857 0.00 0.00 0.00 3.46
1489 1522 1.750206 CCGCCATCAATCCATGAAACA 59.250 47.619 0.00 0.00 42.54 2.83
1498 1531 3.957535 CGCCTGCCGCCATCAATC 61.958 66.667 0.00 0.00 0.00 2.67
1521 1554 1.660607 CGTACTGCTGCCAACTACATG 59.339 52.381 0.00 0.00 0.00 3.21
1791 1876 9.878599 ACAGAATTTCAAACTTCAAATAGTACG 57.121 29.630 0.00 0.00 0.00 3.67
2175 2371 2.648059 CTTTCTGTGGGCCATCCTAAG 58.352 52.381 10.70 8.21 36.20 2.18
2196 2392 2.486982 ACTCAATAGCAGCAACAGCAAG 59.513 45.455 0.00 0.00 0.00 4.01
2206 2438 4.400884 AGGTGTCTCACTACTCAATAGCAG 59.599 45.833 0.06 0.00 33.73 4.24
2213 2445 5.808366 AAATTCAGGTGTCTCACTACTCA 57.192 39.130 0.06 0.00 34.40 3.41
2258 2495 7.272299 GCAGAAGAAAGAAAAATTAGCTAGTGC 59.728 37.037 0.00 0.00 40.05 4.40
2283 2551 7.429636 TCACAAAATTACCAAGTGTAGTAGC 57.570 36.000 0.00 0.00 0.00 3.58
2300 2599 1.606668 GGTGGCTTCGTGATCACAAAA 59.393 47.619 24.93 16.56 32.29 2.44
2332 2631 6.336566 TGAAGCATTAGAAAAACTTTGCACA 58.663 32.000 0.00 0.00 38.29 4.57
2398 2704 0.331278 TTCCCAAAGATGGCGATGGT 59.669 50.000 0.00 0.00 46.09 3.55
2399 2705 0.740737 GTTCCCAAAGATGGCGATGG 59.259 55.000 0.00 0.00 46.09 3.51
2416 2752 0.693049 AATGAGGAACAGCTCCCGTT 59.307 50.000 0.00 0.00 46.81 4.44
2450 2786 4.985409 GGCACAGCTCTTACATGATAGTAC 59.015 45.833 0.00 0.00 0.00 2.73
2458 2811 1.811266 CGCGGCACAGCTCTTACAT 60.811 57.895 0.00 0.00 34.40 2.29
2467 2820 3.108289 CAGACTCACGCGGCACAG 61.108 66.667 12.47 2.39 0.00 3.66
2499 2852 7.009815 CACCATGAACATTAATTTAAGCAGCAG 59.990 37.037 0.00 0.00 0.00 4.24
2521 2874 1.109609 TTTGACATGCAAGCACACCA 58.890 45.000 0.00 0.00 37.87 4.17
2580 2933 9.520515 ACAATGGTAAGATTCATGAACTAACTT 57.479 29.630 11.07 15.04 0.00 2.66
2599 2952 2.086610 AACAAAGCCTGGACAATGGT 57.913 45.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.