Multiple sequence alignment - TraesCS1D01G209900

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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 TraesCS1D01G209900 chr1D 100.000 7073 0 0 860 7932 295831363 295838435 0.000000e+00 13062.0
1 TraesCS1D01G209900 chr1D 100.000 1124 0 0 8281 9404 295838784 295839907 0.000000e+00 2076.0
2 TraesCS1D01G209900 chr1D 100.000 458 0 0 1 458 295830504 295830961 0.000000e+00 846.0
3 TraesCS1D01G209900 chr1D 76.995 213 42 6 9187 9395 296363122 296363331 2.150000e-21 115.0
4 TraesCS1D01G209900 chr1D 76.744 129 26 4 9257 9385 327991446 327991570 1.690000e-07 69.4
5 TraesCS1D01G209900 chr1A 96.172 6008 141 36 1974 7932 368809243 368815210 0.000000e+00 9738.0
6 TraesCS1D01G209900 chr1A 94.825 1140 43 5 8281 9404 368815260 368816399 0.000000e+00 1764.0
7 TraesCS1D01G209900 chr1A 93.526 726 32 4 860 1584 368808041 368808752 0.000000e+00 1066.0
8 TraesCS1D01G209900 chr1A 91.979 374 17 5 1587 1957 368808784 368809147 6.510000e-141 512.0
9 TraesCS1D01G209900 chr1A 97.436 117 3 0 342 458 368807783 368807899 5.760000e-47 200.0
10 TraesCS1D01G209900 chr1A 77.674 215 44 3 9187 9399 369087175 369087387 2.760000e-25 128.0
11 TraesCS1D01G209900 chr1A 88.372 86 9 1 5228 5313 368812597 368812513 1.670000e-17 102.0
12 TraesCS1D01G209900 chr1A 92.537 67 5 0 116 182 20203244 20203310 7.770000e-16 97.1
13 TraesCS1D01G209900 chr1B 97.826 3450 60 9 3991 7432 397428145 397431587 0.000000e+00 5941.0
14 TraesCS1D01G209900 chr1B 94.772 1205 32 7 1974 3147 397426079 397427283 0.000000e+00 1847.0
15 TraesCS1D01G209900 chr1B 95.866 1137 33 3 8281 9404 397437421 397438556 0.000000e+00 1827.0
16 TraesCS1D01G209900 chr1B 92.461 1101 50 12 860 1957 397424913 397425983 0.000000e+00 1543.0
17 TraesCS1D01G209900 chr1B 95.308 682 19 4 3133 3801 397427465 397428146 0.000000e+00 1070.0
18 TraesCS1D01G209900 chr1B 93.737 495 3 4 7428 7921 397436649 397437116 0.000000e+00 717.0
19 TraesCS1D01G209900 chr1B 78.140 215 43 3 9187 9399 397817807 397818019 5.920000e-27 134.0
20 TraesCS1D01G209900 chr1B 89.691 97 5 2 310 401 397424602 397424698 1.660000e-22 119.0
21 TraesCS1D01G209900 chr1B 88.372 86 9 1 5228 5313 397429464 397429380 1.670000e-17 102.0
22 TraesCS1D01G209900 chr5B 87.019 208 20 2 113 313 508874560 508874353 2.640000e-55 228.0
23 TraesCS1D01G209900 chr2D 91.765 85 6 1 5229 5313 348596175 348596092 5.970000e-22 117.0
24 TraesCS1D01G209900 chr2D 94.286 70 4 0 5228 5297 45531836 45531767 3.590000e-19 108.0
25 TraesCS1D01G209900 chr4B 90.805 87 7 1 5229 5315 522687201 522687286 2.150000e-21 115.0
26 TraesCS1D01G209900 chr2B 95.714 70 3 0 5228 5297 72573580 72573511 7.720000e-21 113.0
27 TraesCS1D01G209900 chr2A 89.535 86 7 2 5228 5313 463255868 463255785 3.590000e-19 108.0
28 TraesCS1D01G209900 chr2A 95.122 41 2 0 3452 3492 319010279 319010239 2.190000e-06 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 TraesCS1D01G209900 chr1D 295830504 295839907 9403 False 5328 13062 100.0000 1 9404 3 chr1D.!!$F3 9403
1 TraesCS1D01G209900 chr1A 368807783 368816399 8616 False 2656 9738 94.7876 342 9404 5 chr1A.!!$F3 9062
2 TraesCS1D01G209900 chr1B 397424602 397431587 6985 False 2104 5941 94.0116 310 7432 5 chr1B.!!$F2 7122
3 TraesCS1D01G209900 chr1B 397436649 397438556 1907 False 1272 1827 94.8015 7428 9404 2 chr1B.!!$F3 1976

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
78 79 0.316204 ATTCTGGTGCAGCACTTTGC 59.684 50.000 24.75 8.95 45.46 3.68 F
1555 1589 0.177604 CTAGTGGAGCTCTGCTTGGG 59.822 60.000 14.64 3.16 39.88 4.12 F
2028 2174 0.321564 CACGGATGGGAAAGCTCACA 60.322 55.000 0.00 0.00 40.01 3.58 F
3370 3746 1.398958 GCAGAGCCCGATTCTCTCCT 61.399 60.000 0.00 0.00 38.76 3.69 F
4009 4399 0.881118 TGCTCCAATTCTGCCGTTTC 59.119 50.000 0.00 0.00 0.00 2.78 F
4684 5074 1.142667 TCTGTGGAAATGGCAGTGACA 59.857 47.619 0.00 0.00 0.00 3.58 F
4759 5149 3.477899 GCAGAAATGCCTTGTACTGTC 57.522 47.619 0.00 0.00 0.00 3.51 F
6245 6636 2.093306 TAGTTTGGCAGTGTGGATCG 57.907 50.000 0.00 0.00 0.00 3.69 F
6447 6849 4.370364 TTTTGTGTCAGTCAAAAGGAGC 57.630 40.909 0.00 0.00 39.03 4.70 F
7459 7861 4.687483 CCCAAATCATTTTGTCTTCAGTGC 59.313 41.667 0.00 0.00 40.55 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 1593 0.661020 GTCCACGTTTCACTTGGGTG 59.339 55.000 0.00 0.0 38.01 4.61 R
3223 3598 2.096248 GCCCGTGGACCATTTATTGAA 58.904 47.619 0.00 0.0 0.00 2.69 R
3610 3986 1.445518 GGCTAAGGAGGAGAGCAGC 59.554 63.158 0.00 0.0 37.98 5.25 R
5304 5694 2.562738 GTGGCAAAGCAAATACTCCCTT 59.437 45.455 0.00 0.0 0.00 3.95 R
5731 6122 5.245531 TCGATTGTCCAATTACTTTGAGCT 58.754 37.500 0.00 0.0 37.53 4.09 R
6226 6617 1.346395 ACGATCCACACTGCCAAACTA 59.654 47.619 0.00 0.0 0.00 2.24 R
6447 6849 1.693062 CATCTGATCTGGGTCTCCTGG 59.307 57.143 0.00 0.0 33.38 4.45 R
7183 7585 4.222588 AGACAAGGAAACCTGATGAGAGAG 59.777 45.833 0.00 0.0 32.13 3.20 R
8317 8720 2.821969 ACAATAGCAGTGCCTTTTCTGG 59.178 45.455 12.58 0.0 32.94 3.86 R
9062 9479 0.539438 AAAATTCTGCTCCCCGTGCA 60.539 50.000 0.00 0.0 38.81 4.57 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
24 25 2.973082 GGTTTCCCCATGCTGTGC 59.027 61.111 0.00 0.00 0.00 4.57
25 26 2.568090 GTTTCCCCATGCTGTGCG 59.432 61.111 0.00 0.00 0.00 5.34
26 27 2.115052 TTTCCCCATGCTGTGCGT 59.885 55.556 0.00 0.00 0.00 5.24
27 28 0.958382 GTTTCCCCATGCTGTGCGTA 60.958 55.000 0.00 0.00 0.00 4.42
28 29 0.676466 TTTCCCCATGCTGTGCGTAG 60.676 55.000 0.00 0.00 0.00 3.51
29 30 2.514592 CCCCATGCTGTGCGTAGG 60.515 66.667 0.00 0.00 0.00 3.18
30 31 2.514592 CCCATGCTGTGCGTAGGG 60.515 66.667 0.00 0.00 32.68 3.53
31 32 3.204827 CCATGCTGTGCGTAGGGC 61.205 66.667 0.00 0.00 43.96 5.19
42 43 0.861837 GCGTAGGGCATTGAAGATCG 59.138 55.000 0.00 0.00 42.87 3.69
43 44 1.806623 GCGTAGGGCATTGAAGATCGT 60.807 52.381 0.00 0.00 42.87 3.73
44 45 2.128035 CGTAGGGCATTGAAGATCGTC 58.872 52.381 1.20 1.20 0.00 4.20
45 46 2.223829 CGTAGGGCATTGAAGATCGTCT 60.224 50.000 10.08 0.00 0.00 4.18
46 47 2.322355 AGGGCATTGAAGATCGTCTG 57.678 50.000 10.08 2.24 0.00 3.51
47 48 1.556911 AGGGCATTGAAGATCGTCTGT 59.443 47.619 10.08 0.00 0.00 3.41
48 49 2.766263 AGGGCATTGAAGATCGTCTGTA 59.234 45.455 10.08 0.00 0.00 2.74
49 50 3.389329 AGGGCATTGAAGATCGTCTGTAT 59.611 43.478 10.08 0.00 0.00 2.29
50 51 4.588951 AGGGCATTGAAGATCGTCTGTATA 59.411 41.667 10.08 0.00 0.00 1.47
51 52 5.247110 AGGGCATTGAAGATCGTCTGTATAT 59.753 40.000 10.08 0.00 0.00 0.86
52 53 5.349817 GGGCATTGAAGATCGTCTGTATATG 59.650 44.000 10.08 6.94 0.00 1.78
53 54 6.159293 GGCATTGAAGATCGTCTGTATATGA 58.841 40.000 10.08 0.00 0.00 2.15
54 55 6.646653 GGCATTGAAGATCGTCTGTATATGAA 59.353 38.462 10.08 0.00 0.00 2.57
55 56 7.171508 GGCATTGAAGATCGTCTGTATATGAAA 59.828 37.037 10.08 0.00 0.00 2.69
56 57 8.715998 GCATTGAAGATCGTCTGTATATGAAAT 58.284 33.333 10.08 0.00 0.00 2.17
66 67 9.078990 TCGTCTGTATATGAAATAGATTCTGGT 57.921 33.333 0.00 0.00 38.92 4.00
67 68 9.133627 CGTCTGTATATGAAATAGATTCTGGTG 57.866 37.037 0.00 0.00 38.92 4.17
68 69 8.930760 GTCTGTATATGAAATAGATTCTGGTGC 58.069 37.037 0.00 0.00 38.92 5.01
69 70 8.650490 TCTGTATATGAAATAGATTCTGGTGCA 58.350 33.333 0.00 0.00 38.92 4.57
70 71 8.837788 TGTATATGAAATAGATTCTGGTGCAG 57.162 34.615 0.00 0.00 38.92 4.41
71 72 6.814506 ATATGAAATAGATTCTGGTGCAGC 57.185 37.500 9.47 9.47 38.92 5.25
72 73 3.954200 TGAAATAGATTCTGGTGCAGCA 58.046 40.909 19.03 19.03 38.92 4.41
73 74 3.691118 TGAAATAGATTCTGGTGCAGCAC 59.309 43.478 17.97 17.97 38.92 4.40
74 75 3.641434 AATAGATTCTGGTGCAGCACT 57.359 42.857 24.75 13.02 34.40 4.40
75 76 3.641434 ATAGATTCTGGTGCAGCACTT 57.359 42.857 24.75 2.07 34.40 3.16
76 77 2.283145 AGATTCTGGTGCAGCACTTT 57.717 45.000 24.75 1.67 34.40 2.66
77 78 1.884579 AGATTCTGGTGCAGCACTTTG 59.115 47.619 24.75 14.55 34.40 2.77
78 79 0.316204 ATTCTGGTGCAGCACTTTGC 59.684 50.000 24.75 8.95 45.46 3.68
79 80 1.737355 TTCTGGTGCAGCACTTTGCC 61.737 55.000 24.75 8.77 46.52 4.52
80 81 3.547249 CTGGTGCAGCACTTTGCCG 62.547 63.158 24.75 0.00 46.52 5.69
81 82 4.347453 GGTGCAGCACTTTGCCGG 62.347 66.667 24.75 0.00 46.52 6.13
85 86 4.047059 CAGCACTTTGCCGGCCAG 62.047 66.667 26.77 22.18 46.52 4.85
86 87 4.269523 AGCACTTTGCCGGCCAGA 62.270 61.111 26.77 7.13 46.52 3.86
87 88 3.294493 GCACTTTGCCGGCCAGAA 61.294 61.111 26.77 15.14 37.42 3.02
88 89 2.956987 CACTTTGCCGGCCAGAAG 59.043 61.111 26.77 25.23 0.00 2.85
89 90 2.985847 ACTTTGCCGGCCAGAAGC 60.986 61.111 26.77 0.00 42.60 3.86
98 99 2.032681 GCCAGAAGCCACTTCGGT 59.967 61.111 14.92 0.00 44.34 4.69
99 100 2.328099 GCCAGAAGCCACTTCGGTG 61.328 63.158 14.92 5.36 44.34 4.94
110 111 4.321966 TTCGGTGGTGCGCCATCA 62.322 61.111 28.34 13.33 46.21 3.07
117 118 2.512515 GTGCGCCATCACCCTCTC 60.513 66.667 4.18 0.00 0.00 3.20
118 119 3.785859 TGCGCCATCACCCTCTCC 61.786 66.667 4.18 0.00 0.00 3.71
119 120 4.899239 GCGCCATCACCCTCTCCG 62.899 72.222 0.00 0.00 0.00 4.63
120 121 3.147595 CGCCATCACCCTCTCCGA 61.148 66.667 0.00 0.00 0.00 4.55
121 122 2.818132 GCCATCACCCTCTCCGAG 59.182 66.667 0.00 0.00 0.00 4.63
122 123 1.758514 GCCATCACCCTCTCCGAGA 60.759 63.158 0.00 0.00 0.00 4.04
123 124 1.118356 GCCATCACCCTCTCCGAGAT 61.118 60.000 0.00 0.00 0.00 2.75
124 125 0.678395 CCATCACCCTCTCCGAGATG 59.322 60.000 0.00 0.00 36.67 2.90
125 126 1.407936 CATCACCCTCTCCGAGATGT 58.592 55.000 0.00 0.00 33.28 3.06
126 127 1.339610 CATCACCCTCTCCGAGATGTC 59.660 57.143 0.00 0.00 33.28 3.06
127 128 0.748367 TCACCCTCTCCGAGATGTCG 60.748 60.000 5.06 5.06 46.39 4.35
136 137 4.116878 GAGATGTCGAGCTTGCCC 57.883 61.111 0.00 0.00 0.00 5.36
137 138 1.219124 GAGATGTCGAGCTTGCCCA 59.781 57.895 0.00 0.00 0.00 5.36
138 139 0.809241 GAGATGTCGAGCTTGCCCAG 60.809 60.000 0.00 0.00 0.00 4.45
151 152 4.247380 CCCAGCGCCTCCTCCATC 62.247 72.222 2.29 0.00 0.00 3.51
152 153 4.598894 CCAGCGCCTCCTCCATCG 62.599 72.222 2.29 0.00 0.00 3.84
178 179 4.899239 GCCGAGCGGTCATGGGAG 62.899 72.222 15.89 0.00 37.65 4.30
179 180 4.227134 CCGAGCGGTCATGGGAGG 62.227 72.222 15.89 2.36 0.00 4.30
180 181 3.147595 CGAGCGGTCATGGGAGGA 61.148 66.667 15.89 0.00 0.00 3.71
181 182 2.818132 GAGCGGTCATGGGAGGAG 59.182 66.667 10.30 0.00 0.00 3.69
182 183 3.453070 GAGCGGTCATGGGAGGAGC 62.453 68.421 10.30 0.00 0.00 4.70
183 184 4.554036 GCGGTCATGGGAGGAGCC 62.554 72.222 0.00 0.00 0.00 4.70
184 185 4.227134 CGGTCATGGGAGGAGCCG 62.227 72.222 0.00 0.00 37.63 5.52
185 186 4.554036 GGTCATGGGAGGAGCCGC 62.554 72.222 0.00 0.00 37.63 6.53
186 187 4.554036 GTCATGGGAGGAGCCGCC 62.554 72.222 0.02 0.02 37.63 6.13
199 200 3.058160 CCGCCTTCCTGCTGGTTG 61.058 66.667 9.73 3.86 34.23 3.77
200 201 3.741476 CGCCTTCCTGCTGGTTGC 61.741 66.667 9.73 9.60 43.25 4.17
201 202 3.376918 GCCTTCCTGCTGGTTGCC 61.377 66.667 9.73 0.00 42.00 4.52
202 203 3.058160 CCTTCCTGCTGGTTGCCG 61.058 66.667 9.73 0.00 42.00 5.69
203 204 3.058160 CTTCCTGCTGGTTGCCGG 61.058 66.667 9.73 0.00 45.85 6.13
204 205 4.659172 TTCCTGCTGGTTGCCGGG 62.659 66.667 9.73 0.00 44.78 5.73
218 219 2.186903 CGGGAGGGTTGGATGTCG 59.813 66.667 0.00 0.00 0.00 4.35
219 220 2.124695 GGGAGGGTTGGATGTCGC 60.125 66.667 0.00 0.00 0.00 5.19
220 221 2.124695 GGAGGGTTGGATGTCGCC 60.125 66.667 0.00 0.00 0.00 5.54
221 222 2.668632 GAGGGTTGGATGTCGCCA 59.331 61.111 0.00 0.00 35.78 5.69
222 223 1.224592 GAGGGTTGGATGTCGCCAT 59.775 57.895 0.00 0.00 37.86 4.40
223 224 0.815615 GAGGGTTGGATGTCGCCATC 60.816 60.000 0.00 0.00 45.65 3.51
229 230 2.663188 GATGTCGCCATCGAGCCC 60.663 66.667 0.00 0.00 46.46 5.19
230 231 4.241555 ATGTCGCCATCGAGCCCC 62.242 66.667 0.00 0.00 46.46 5.80
259 260 4.286320 GCGCCCCGTCGATCAGAT 62.286 66.667 0.00 0.00 0.00 2.90
260 261 2.049985 CGCCCCGTCGATCAGATC 60.050 66.667 0.00 0.00 0.00 2.75
261 262 2.340443 GCCCCGTCGATCAGATCC 59.660 66.667 4.73 0.00 0.00 3.36
262 263 2.498941 GCCCCGTCGATCAGATCCA 61.499 63.158 4.73 0.00 0.00 3.41
263 264 1.364171 CCCCGTCGATCAGATCCAC 59.636 63.158 4.73 1.33 0.00 4.02
264 265 1.008424 CCCGTCGATCAGATCCACG 60.008 63.158 20.21 20.21 42.32 4.94
265 266 4.616592 CGTCGATCAGATCCACGG 57.383 61.111 19.60 4.62 39.65 4.94
266 267 1.008424 CGTCGATCAGATCCACGGG 60.008 63.158 19.60 0.00 39.65 5.28
267 268 1.300233 GTCGATCAGATCCACGGGC 60.300 63.158 4.73 0.00 0.00 6.13
268 269 2.355126 CGATCAGATCCACGGGCG 60.355 66.667 4.73 0.00 0.00 6.13
269 270 2.663188 GATCAGATCCACGGGCGC 60.663 66.667 0.00 0.00 0.00 6.53
270 271 4.241555 ATCAGATCCACGGGCGCC 62.242 66.667 21.18 21.18 0.00 6.53
286 287 4.003788 CCGTCAAGTCCACCGCCT 62.004 66.667 0.00 0.00 0.00 5.52
287 288 2.432628 CGTCAAGTCCACCGCCTC 60.433 66.667 0.00 0.00 0.00 4.70
288 289 2.047179 GTCAAGTCCACCGCCTCC 60.047 66.667 0.00 0.00 0.00 4.30
289 290 3.319198 TCAAGTCCACCGCCTCCC 61.319 66.667 0.00 0.00 0.00 4.30
290 291 3.322466 CAAGTCCACCGCCTCCCT 61.322 66.667 0.00 0.00 0.00 4.20
291 292 1.987855 CAAGTCCACCGCCTCCCTA 60.988 63.158 0.00 0.00 0.00 3.53
292 293 1.686110 AAGTCCACCGCCTCCCTAG 60.686 63.158 0.00 0.00 0.00 3.02
293 294 2.363925 GTCCACCGCCTCCCTAGT 60.364 66.667 0.00 0.00 0.00 2.57
294 295 2.043248 TCCACCGCCTCCCTAGTC 60.043 66.667 0.00 0.00 0.00 2.59
295 296 3.528370 CCACCGCCTCCCTAGTCG 61.528 72.222 0.00 0.00 0.00 4.18
296 297 4.208686 CACCGCCTCCCTAGTCGC 62.209 72.222 0.00 0.00 0.00 5.19
301 302 2.907917 CCTCCCTAGTCGCCCGAG 60.908 72.222 0.00 0.00 0.00 4.63
302 303 2.907917 CTCCCTAGTCGCCCGAGG 60.908 72.222 0.00 0.00 35.81 4.63
305 306 2.758737 CCTAGTCGCCCGAGGGTT 60.759 66.667 10.26 0.00 37.65 4.11
306 307 2.356780 CCTAGTCGCCCGAGGGTTT 61.357 63.158 10.26 0.00 37.65 3.27
307 308 1.595357 CTAGTCGCCCGAGGGTTTT 59.405 57.895 10.26 0.00 37.65 2.43
308 309 0.819582 CTAGTCGCCCGAGGGTTTTA 59.180 55.000 10.26 0.00 37.65 1.52
324 325 3.570975 GGTTTTAGGGTCGGTTGTGATTT 59.429 43.478 0.00 0.00 0.00 2.17
325 326 4.038282 GGTTTTAGGGTCGGTTGTGATTTT 59.962 41.667 0.00 0.00 0.00 1.82
326 327 4.839668 TTTAGGGTCGGTTGTGATTTTG 57.160 40.909 0.00 0.00 0.00 2.44
1182 1213 3.249189 TTCACGGCCTCCCTGCTT 61.249 61.111 0.00 0.00 0.00 3.91
1415 1446 2.676822 TGTTCCCTCGCTCTCGCT 60.677 61.111 0.00 0.00 35.26 4.93
1416 1447 2.103340 GTTCCCTCGCTCTCGCTC 59.897 66.667 0.00 0.00 35.26 5.03
1417 1448 2.044848 TTCCCTCGCTCTCGCTCT 60.045 61.111 0.00 0.00 35.26 4.09
1418 1449 2.115911 TTCCCTCGCTCTCGCTCTC 61.116 63.158 0.00 0.00 35.26 3.20
1419 1450 3.947841 CCCTCGCTCTCGCTCTCG 61.948 72.222 0.00 0.00 35.26 4.04
1420 1451 4.605967 CCTCGCTCTCGCTCTCGC 62.606 72.222 0.00 0.00 35.26 5.03
1438 1469 8.206516 GCTCTCGCGCTACTTAAATATATATC 57.793 38.462 5.56 0.00 0.00 1.63
1439 1470 7.856398 GCTCTCGCGCTACTTAAATATATATCA 59.144 37.037 5.56 0.00 0.00 2.15
1440 1471 9.885934 CTCTCGCGCTACTTAAATATATATCAT 57.114 33.333 5.56 0.00 0.00 2.45
1475 1509 0.305313 CGCTCAGTACCTCGTAGCTC 59.695 60.000 0.00 0.00 0.00 4.09
1555 1589 0.177604 CTAGTGGAGCTCTGCTTGGG 59.822 60.000 14.64 3.16 39.88 4.12
1559 1593 1.377856 GGAGCTCTGCTTGGGGTTC 60.378 63.158 14.64 0.00 39.88 3.62
1687 1750 3.057876 CCTAGATAGATGCACCTCGTGTC 60.058 52.174 0.00 0.00 35.75 3.67
1728 1793 6.456447 TTTTTATTGGTCAAGTCTCGTACG 57.544 37.500 9.53 9.53 0.00 3.67
1729 1794 4.771590 TTATTGGTCAAGTCTCGTACGT 57.228 40.909 16.05 0.00 0.00 3.57
1730 1795 5.878332 TTATTGGTCAAGTCTCGTACGTA 57.122 39.130 16.05 1.79 0.00 3.57
1731 1796 3.542712 TTGGTCAAGTCTCGTACGTAC 57.457 47.619 15.90 15.90 0.00 3.67
1957 2024 4.080807 TGAAAGTCCAGTTGTCACTTGGTA 60.081 41.667 2.57 0.00 30.63 3.25
1958 2025 4.497291 AAGTCCAGTTGTCACTTGGTAA 57.503 40.909 2.57 0.00 0.00 2.85
1959 2026 4.497291 AGTCCAGTTGTCACTTGGTAAA 57.503 40.909 2.57 0.00 0.00 2.01
1963 2030 7.057894 AGTCCAGTTGTCACTTGGTAAAATAA 58.942 34.615 2.57 0.00 0.00 1.40
1964 2031 7.228706 AGTCCAGTTGTCACTTGGTAAAATAAG 59.771 37.037 2.57 0.00 0.00 1.73
1965 2032 7.227910 GTCCAGTTGTCACTTGGTAAAATAAGA 59.772 37.037 0.00 0.00 0.00 2.10
1966 2033 7.776030 TCCAGTTGTCACTTGGTAAAATAAGAA 59.224 33.333 0.00 0.00 0.00 2.52
2028 2174 0.321564 CACGGATGGGAAAGCTCACA 60.322 55.000 0.00 0.00 40.01 3.58
2272 2418 6.473455 GTGAGTCAGTGATTTGTTTCTTTTGG 59.527 38.462 0.00 0.00 0.00 3.28
2307 2453 9.554724 ACAATTTTAGATACAGTTATTTGTGCG 57.445 29.630 0.00 0.00 32.56 5.34
2360 2506 9.740239 AATTTAGCTAAAACAGTATGCATCATG 57.260 29.630 22.13 5.95 42.53 3.07
2558 2731 3.228188 TGCTGATTTTGGACTGGAGTT 57.772 42.857 0.00 0.00 0.00 3.01
2600 2773 3.123804 CGGAATATCAACTCCTGGAACG 58.876 50.000 0.00 0.00 0.00 3.95
2604 2777 2.474410 ATCAACTCCTGGAACGGTTC 57.526 50.000 12.41 12.41 0.00 3.62
2809 2982 4.440802 GCGATACAGGTCTCTGACAAAGAT 60.441 45.833 0.00 0.00 43.49 2.40
2854 3027 6.534634 AGTTCTGGTTGTACTAGAAGCATTT 58.465 36.000 5.96 0.00 44.55 2.32
2905 3078 3.054287 TGGTTGAAGTACCAAGTGGAACA 60.054 43.478 3.83 0.00 44.97 3.18
3050 3225 5.523188 TGAGAAATGTTCAAATGTGTTTGCC 59.477 36.000 0.00 0.00 43.47 4.52
3152 3527 8.467963 TCACCAATAATTGTATCATGCTTCAT 57.532 30.769 0.00 0.00 0.00 2.57
3323 3699 9.056005 GTATGTGATTATCAATAGTTTCTGGCA 57.944 33.333 0.00 0.00 0.00 4.92
3370 3746 1.398958 GCAGAGCCCGATTCTCTCCT 61.399 60.000 0.00 0.00 38.76 3.69
3381 3757 2.310779 TTCTCTCCTGTGGTGTAGCT 57.689 50.000 0.00 0.00 0.00 3.32
3434 3810 2.418197 CCAGTACCCGGATGTGTGTTAG 60.418 54.545 0.73 0.00 0.00 2.34
3589 3965 4.399395 CTGCTCCTTCCGCTGCCA 62.399 66.667 0.00 0.00 0.00 4.92
3780 4167 1.614996 GAGCGGGAGAGATGAGATGA 58.385 55.000 0.00 0.00 0.00 2.92
3929 4317 2.038387 ACACAGGAATATTGACCGGC 57.962 50.000 0.00 0.00 0.00 6.13
3961 4349 1.340991 CCCGTTCCATTCCAGTCCAAT 60.341 52.381 0.00 0.00 0.00 3.16
3967 4355 5.230182 GTTCCATTCCAGTCCAATCAAAAC 58.770 41.667 0.00 0.00 0.00 2.43
3968 4356 4.739793 TCCATTCCAGTCCAATCAAAACT 58.260 39.130 0.00 0.00 0.00 2.66
4009 4399 0.881118 TGCTCCAATTCTGCCGTTTC 59.119 50.000 0.00 0.00 0.00 2.78
4209 4599 3.435026 GGCAGCACCTTAGGAATTATCCA 60.435 47.826 4.77 0.00 41.36 3.41
4584 4974 9.659135 TTCTTTGATGAATTACCATGGGATTAT 57.341 29.630 18.09 9.78 0.00 1.28
4679 5069 4.589216 TCTTTTTCTGTGGAAATGGCAG 57.411 40.909 0.00 0.00 40.57 4.85
4684 5074 1.142667 TCTGTGGAAATGGCAGTGACA 59.857 47.619 0.00 0.00 0.00 3.58
4759 5149 3.477899 GCAGAAATGCCTTGTACTGTC 57.522 47.619 0.00 0.00 0.00 3.51
5010 5400 7.360113 TGTACAGGAACTTGCATCTCATATA 57.640 36.000 0.00 0.00 34.60 0.86
5254 5644 5.305902 TCCCTCTGTACACAAATGTAAGACA 59.694 40.000 0.00 0.00 42.99 3.41
5302 5692 7.089249 CAAAAACGTCCTACATTTGCTTAAC 57.911 36.000 0.00 0.00 0.00 2.01
5303 5693 6.380095 AAAACGTCCTACATTTGCTTAACA 57.620 33.333 0.00 0.00 0.00 2.41
5304 5694 6.380095 AAACGTCCTACATTTGCTTAACAA 57.620 33.333 0.00 0.00 36.13 2.83
5731 6122 4.348168 GCTGGTATTCTCTTAGGGGAATCA 59.652 45.833 2.73 0.00 34.52 2.57
5793 6184 9.298250 TGATACTTCTTCATATGACTACCCTAC 57.702 37.037 4.48 0.00 0.00 3.18
6226 6617 5.405269 GCTTGTGTGTTCAACTTCTGTTTTT 59.595 36.000 0.00 0.00 33.52 1.94
6245 6636 2.093306 TAGTTTGGCAGTGTGGATCG 57.907 50.000 0.00 0.00 0.00 3.69
6447 6849 4.370364 TTTTGTGTCAGTCAAAAGGAGC 57.630 40.909 0.00 0.00 39.03 4.70
7134 7536 7.792374 TGAAGACTGGCATAAATATCAACTC 57.208 36.000 0.00 0.00 0.00 3.01
7383 7785 8.997621 AGTCTTCGCATGTTTCTATTTAGTTA 57.002 30.769 0.00 0.00 0.00 2.24
7454 7856 5.473039 CACTCCCCAAATCATTTTGTCTTC 58.527 41.667 0.00 0.00 40.55 2.87
7459 7861 4.687483 CCCAAATCATTTTGTCTTCAGTGC 59.313 41.667 0.00 0.00 40.55 4.40
8317 8720 3.567478 ACTCAGCCATCATCTTTACCC 57.433 47.619 0.00 0.00 0.00 3.69
8344 8747 3.819564 AGGCACTGCTATTGTCGAATA 57.180 42.857 0.00 0.00 37.18 1.75
8679 9082 2.495669 AGTTGCTAGAGAGGCAGAAGTC 59.504 50.000 0.00 0.00 40.90 3.01
8760 9165 3.921021 AGATATCCGAAAATCGATCACGC 59.079 43.478 0.00 0.00 43.74 5.34
8777 9182 3.207669 CCAGCTGCAAGATCCGGC 61.208 66.667 8.66 0.00 34.07 6.13
8787 9192 1.274703 AAGATCCGGCCCATCAGTGT 61.275 55.000 11.16 0.00 0.00 3.55
8843 9248 1.482182 AGAGGCGAGCATGTCACATTA 59.518 47.619 0.00 0.00 0.00 1.90
8903 9309 4.832248 TGTGAATACGCATTCTTTCCTCT 58.168 39.130 9.69 0.00 41.09 3.69
8939 9345 4.828409 CTCCAAAGGAGCTTGGCA 57.172 55.556 0.00 0.00 43.29 4.92
8941 9347 0.600057 CTCCAAAGGAGCTTGGCAAC 59.400 55.000 0.00 0.00 43.29 4.17
9008 9425 5.578157 AGGTTACATAGTTCCACTGGTTT 57.422 39.130 0.00 0.00 0.00 3.27
9014 9431 6.134535 ACATAGTTCCACTGGTTTCCATTA 57.865 37.500 0.00 0.00 30.82 1.90
9062 9479 2.187958 TGGAACTGGTAGTAGCTGCAT 58.812 47.619 4.12 0.00 0.00 3.96
9148 9565 2.407428 TAGAGAGCCACGCACGGAG 61.407 63.158 0.00 0.00 0.00 4.63
9197 9614 2.209838 ACCAGCGAACGTCAGATATG 57.790 50.000 0.00 0.00 0.00 1.78
9246 9665 4.875544 ATAGCAAATTATGTTGTCGCGT 57.124 36.364 5.77 0.00 0.00 6.01
9296 9715 4.525912 AATCCTGGCAATGTTCAGTTTC 57.474 40.909 0.00 0.00 0.00 2.78
9324 9743 2.417243 GGATTTGCCGTGCTTGCTAAAT 60.417 45.455 0.00 0.00 0.00 1.40
9388 9807 6.356757 ACGTTTGTTTTGCAATGCTTAAAT 57.643 29.167 6.82 0.00 36.89 1.40
9395 9815 9.656040 TTGTTTTGCAATGCTTAAATATCTGAT 57.344 25.926 6.82 0.00 31.07 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.958382 TACGCACAGCATGGGGAAAC 60.958 55.000 9.40 0.00 42.43 2.78
9 10 0.676466 CTACGCACAGCATGGGGAAA 60.676 55.000 9.40 0.00 42.43 3.13
10 11 1.078497 CTACGCACAGCATGGGGAA 60.078 57.895 9.40 0.00 42.43 3.97
11 12 2.584064 CTACGCACAGCATGGGGA 59.416 61.111 9.40 0.54 42.43 4.81
12 13 2.514592 CCTACGCACAGCATGGGG 60.515 66.667 9.40 0.00 42.43 4.96
14 15 3.204827 GCCCTACGCACAGCATGG 61.205 66.667 0.00 0.00 43.62 3.66
15 16 2.436469 TGCCCTACGCACAGCATG 60.436 61.111 0.00 0.00 44.64 4.06
23 24 0.861837 CGATCTTCAATGCCCTACGC 59.138 55.000 0.00 0.00 38.31 4.42
24 25 2.128035 GACGATCTTCAATGCCCTACG 58.872 52.381 0.00 0.00 0.00 3.51
25 26 3.126831 CAGACGATCTTCAATGCCCTAC 58.873 50.000 1.65 0.00 0.00 3.18
26 27 2.766263 ACAGACGATCTTCAATGCCCTA 59.234 45.455 1.65 0.00 0.00 3.53
27 28 1.556911 ACAGACGATCTTCAATGCCCT 59.443 47.619 1.65 0.00 0.00 5.19
28 29 2.029838 ACAGACGATCTTCAATGCCC 57.970 50.000 1.65 0.00 0.00 5.36
29 30 6.159293 TCATATACAGACGATCTTCAATGCC 58.841 40.000 1.65 0.00 0.00 4.40
30 31 7.643528 TTCATATACAGACGATCTTCAATGC 57.356 36.000 1.65 0.00 0.00 3.56
40 41 9.078990 ACCAGAATCTATTTCATATACAGACGA 57.921 33.333 0.00 0.00 36.75 4.20
41 42 9.133627 CACCAGAATCTATTTCATATACAGACG 57.866 37.037 0.00 0.00 36.75 4.18
42 43 8.930760 GCACCAGAATCTATTTCATATACAGAC 58.069 37.037 0.00 0.00 36.75 3.51
43 44 8.650490 TGCACCAGAATCTATTTCATATACAGA 58.350 33.333 0.00 0.00 36.75 3.41
44 45 8.837788 TGCACCAGAATCTATTTCATATACAG 57.162 34.615 0.00 0.00 36.75 2.74
45 46 7.388776 GCTGCACCAGAATCTATTTCATATACA 59.611 37.037 0.00 0.00 36.75 2.29
46 47 7.388776 TGCTGCACCAGAATCTATTTCATATAC 59.611 37.037 0.00 0.00 36.75 1.47
47 48 7.388776 GTGCTGCACCAGAATCTATTTCATATA 59.611 37.037 21.78 0.00 36.75 0.86
48 49 6.206243 GTGCTGCACCAGAATCTATTTCATAT 59.794 38.462 21.78 0.00 36.75 1.78
49 50 5.528690 GTGCTGCACCAGAATCTATTTCATA 59.471 40.000 21.78 0.00 36.75 2.15
50 51 4.337555 GTGCTGCACCAGAATCTATTTCAT 59.662 41.667 21.78 0.00 36.75 2.57
51 52 3.691118 GTGCTGCACCAGAATCTATTTCA 59.309 43.478 21.78 0.00 36.75 2.69
52 53 3.944015 AGTGCTGCACCAGAATCTATTTC 59.056 43.478 27.74 0.00 34.49 2.17
53 54 3.960571 AGTGCTGCACCAGAATCTATTT 58.039 40.909 27.74 3.04 34.49 1.40
54 55 3.641434 AGTGCTGCACCAGAATCTATT 57.359 42.857 27.74 3.58 34.49 1.73
55 56 3.641434 AAGTGCTGCACCAGAATCTAT 57.359 42.857 27.74 4.35 34.49 1.98
56 57 3.076621 CAAAGTGCTGCACCAGAATCTA 58.923 45.455 27.74 0.00 34.49 1.98
57 58 1.884579 CAAAGTGCTGCACCAGAATCT 59.115 47.619 27.74 5.88 34.49 2.40
58 59 1.668047 GCAAAGTGCTGCACCAGAATC 60.668 52.381 27.74 9.88 42.17 2.52
59 60 0.316204 GCAAAGTGCTGCACCAGAAT 59.684 50.000 27.74 7.42 42.17 2.40
60 61 1.735360 GCAAAGTGCTGCACCAGAA 59.265 52.632 27.74 0.00 42.17 3.02
61 62 2.195567 GGCAAAGTGCTGCACCAGA 61.196 57.895 27.74 0.00 44.28 3.86
62 63 2.337532 GGCAAAGTGCTGCACCAG 59.662 61.111 27.74 18.54 44.28 4.00
63 64 3.594775 CGGCAAAGTGCTGCACCA 61.595 61.111 27.74 0.00 43.46 4.17
69 70 3.790416 TTCTGGCCGGCAAAGTGCT 62.790 57.895 30.85 0.00 44.28 4.40
70 71 3.273080 CTTCTGGCCGGCAAAGTGC 62.273 63.158 30.85 10.31 44.08 4.40
71 72 2.956987 CTTCTGGCCGGCAAAGTG 59.043 61.111 30.85 17.00 0.00 3.16
72 73 2.985847 GCTTCTGGCCGGCAAAGT 60.986 61.111 30.85 0.00 34.27 2.66
81 82 2.032681 ACCGAAGTGGCTTCTGGC 59.967 61.111 14.71 0.00 43.94 4.85
82 83 3.972227 CACCGAAGTGGCTTCTGG 58.028 61.111 13.81 13.81 43.94 3.86
100 101 2.512515 GAGAGGGTGATGGCGCAC 60.513 66.667 10.83 0.00 38.05 5.34
101 102 3.785859 GGAGAGGGTGATGGCGCA 61.786 66.667 10.83 0.00 0.00 6.09
102 103 4.899239 CGGAGAGGGTGATGGCGC 62.899 72.222 0.00 0.00 0.00 6.53
103 104 3.147595 TCGGAGAGGGTGATGGCG 61.148 66.667 0.00 0.00 0.00 5.69
114 115 0.735471 CAAGCTCGACATCTCGGAGA 59.265 55.000 10.62 10.62 40.58 3.71
115 116 0.869454 GCAAGCTCGACATCTCGGAG 60.869 60.000 0.00 0.00 40.58 4.63
116 117 1.139734 GCAAGCTCGACATCTCGGA 59.860 57.895 0.00 0.00 40.58 4.55
117 118 1.880340 GGCAAGCTCGACATCTCGG 60.880 63.158 0.00 0.00 40.58 4.63
118 119 1.880340 GGGCAAGCTCGACATCTCG 60.880 63.158 0.00 0.00 41.65 4.04
119 120 0.809241 CTGGGCAAGCTCGACATCTC 60.809 60.000 0.00 0.00 0.00 2.75
120 121 1.220206 CTGGGCAAGCTCGACATCT 59.780 57.895 0.00 0.00 0.00 2.90
121 122 3.805267 CTGGGCAAGCTCGACATC 58.195 61.111 0.00 0.00 0.00 3.06
134 135 4.247380 GATGGAGGAGGCGCTGGG 62.247 72.222 7.64 0.00 0.00 4.45
135 136 4.598894 CGATGGAGGAGGCGCTGG 62.599 72.222 7.64 0.00 0.00 4.85
161 162 4.899239 CTCCCATGACCGCTCGGC 62.899 72.222 8.41 2.21 39.32 5.54
162 163 4.227134 CCTCCCATGACCGCTCGG 62.227 72.222 6.79 6.79 42.03 4.63
163 164 3.144120 CTCCTCCCATGACCGCTCG 62.144 68.421 0.00 0.00 0.00 5.03
164 165 2.818132 CTCCTCCCATGACCGCTC 59.182 66.667 0.00 0.00 0.00 5.03
165 166 3.474570 GCTCCTCCCATGACCGCT 61.475 66.667 0.00 0.00 0.00 5.52
166 167 4.554036 GGCTCCTCCCATGACCGC 62.554 72.222 0.00 0.00 0.00 5.68
167 168 4.227134 CGGCTCCTCCCATGACCG 62.227 72.222 0.00 0.00 0.00 4.79
168 169 4.554036 GCGGCTCCTCCCATGACC 62.554 72.222 0.00 0.00 0.00 4.02
169 170 4.554036 GGCGGCTCCTCCCATGAC 62.554 72.222 0.00 0.00 0.00 3.06
170 171 4.804420 AGGCGGCTCCTCCCATGA 62.804 66.667 5.25 0.00 43.20 3.07
171 172 3.764160 GAAGGCGGCTCCTCCCATG 62.764 68.421 13.70 0.00 46.94 3.66
172 173 3.483869 GAAGGCGGCTCCTCCCAT 61.484 66.667 13.70 0.00 46.94 4.00
175 176 4.168291 CAGGAAGGCGGCTCCTCC 62.168 72.222 19.39 19.39 46.94 4.30
176 177 4.847444 GCAGGAAGGCGGCTCCTC 62.847 72.222 21.55 13.32 46.94 3.71
182 183 3.058160 CAACCAGCAGGAAGGCGG 61.058 66.667 0.35 0.00 39.27 6.13
183 184 3.741476 GCAACCAGCAGGAAGGCG 61.741 66.667 0.35 0.00 44.79 5.52
193 194 3.966543 AACCCTCCCGGCAACCAG 61.967 66.667 0.00 0.00 33.26 4.00
194 195 4.278513 CAACCCTCCCGGCAACCA 62.279 66.667 0.00 0.00 33.26 3.67
196 197 3.282374 ATCCAACCCTCCCGGCAAC 62.282 63.158 0.00 0.00 33.26 4.17
197 198 2.938798 ATCCAACCCTCCCGGCAA 60.939 61.111 0.00 0.00 33.26 4.52
198 199 3.727258 CATCCAACCCTCCCGGCA 61.727 66.667 0.00 0.00 33.26 5.69
199 200 3.699134 GACATCCAACCCTCCCGGC 62.699 68.421 0.00 0.00 33.26 6.13
200 201 2.590092 GACATCCAACCCTCCCGG 59.410 66.667 0.00 0.00 37.81 5.73
201 202 2.186903 CGACATCCAACCCTCCCG 59.813 66.667 0.00 0.00 0.00 5.14
202 203 2.124695 GCGACATCCAACCCTCCC 60.125 66.667 0.00 0.00 0.00 4.30
203 204 2.124695 GGCGACATCCAACCCTCC 60.125 66.667 0.00 0.00 0.00 4.30
204 205 2.668632 TGGCGACATCCAACCCTC 59.331 61.111 0.00 0.00 33.40 4.30
242 243 4.286320 ATCTGATCGACGGGGCGC 62.286 66.667 0.00 0.00 0.00 6.53
243 244 2.049985 GATCTGATCGACGGGGCG 60.050 66.667 1.26 0.00 0.00 6.13
244 245 2.340443 GGATCTGATCGACGGGGC 59.660 66.667 11.28 0.00 0.00 5.80
245 246 1.364171 GTGGATCTGATCGACGGGG 59.636 63.158 15.45 0.00 0.00 5.73
249 250 1.300233 GCCCGTGGATCTGATCGAC 60.300 63.158 19.19 19.19 35.05 4.20
250 251 2.845550 CGCCCGTGGATCTGATCGA 61.846 63.158 11.28 4.90 0.00 3.59
251 252 2.355126 CGCCCGTGGATCTGATCG 60.355 66.667 11.28 1.24 0.00 3.69
252 253 2.663188 GCGCCCGTGGATCTGATC 60.663 66.667 9.18 9.18 0.00 2.92
253 254 4.241555 GGCGCCCGTGGATCTGAT 62.242 66.667 18.11 0.00 0.00 2.90
269 270 3.934391 GAGGCGGTGGACTTGACGG 62.934 68.421 0.00 0.00 0.00 4.79
270 271 2.432628 GAGGCGGTGGACTTGACG 60.433 66.667 0.00 0.00 0.00 4.35
271 272 2.047179 GGAGGCGGTGGACTTGAC 60.047 66.667 0.00 0.00 0.00 3.18
272 273 2.449967 TAGGGAGGCGGTGGACTTGA 62.450 60.000 0.00 0.00 0.00 3.02
273 274 1.961180 CTAGGGAGGCGGTGGACTTG 61.961 65.000 0.00 0.00 0.00 3.16
274 275 1.686110 CTAGGGAGGCGGTGGACTT 60.686 63.158 0.00 0.00 0.00 3.01
275 276 2.042843 CTAGGGAGGCGGTGGACT 60.043 66.667 0.00 0.00 0.00 3.85
276 277 2.363925 ACTAGGGAGGCGGTGGAC 60.364 66.667 0.00 0.00 0.00 4.02
277 278 2.043248 GACTAGGGAGGCGGTGGA 60.043 66.667 0.00 0.00 0.00 4.02
284 285 2.907917 CTCGGGCGACTAGGGAGG 60.908 72.222 0.00 0.00 0.00 4.30
285 286 2.907917 CCTCGGGCGACTAGGGAG 60.908 72.222 2.51 0.00 32.01 4.30
288 289 1.896122 AAAACCCTCGGGCGACTAGG 61.896 60.000 0.82 3.42 39.32 3.02
289 290 0.819582 TAAAACCCTCGGGCGACTAG 59.180 55.000 0.82 0.00 39.32 2.57
290 291 0.819582 CTAAAACCCTCGGGCGACTA 59.180 55.000 0.82 0.00 39.32 2.59
291 292 1.595357 CTAAAACCCTCGGGCGACT 59.405 57.895 0.82 0.00 39.32 4.18
292 293 1.449070 CCTAAAACCCTCGGGCGAC 60.449 63.158 0.82 0.00 39.32 5.19
293 294 2.662070 CCCTAAAACCCTCGGGCGA 61.662 63.158 0.82 0.00 39.32 5.54
294 295 2.124860 CCCTAAAACCCTCGGGCG 60.125 66.667 0.82 0.00 39.32 6.13
295 296 1.077930 GACCCTAAAACCCTCGGGC 60.078 63.158 0.82 0.00 40.45 6.13
296 297 1.219935 CGACCCTAAAACCCTCGGG 59.780 63.158 0.00 0.00 42.53 5.14
297 298 1.219935 CCGACCCTAAAACCCTCGG 59.780 63.158 0.00 0.00 38.12 4.63
298 299 0.322648 AACCGACCCTAAAACCCTCG 59.677 55.000 0.00 0.00 0.00 4.63
299 300 1.072806 ACAACCGACCCTAAAACCCTC 59.927 52.381 0.00 0.00 0.00 4.30
300 301 1.142936 ACAACCGACCCTAAAACCCT 58.857 50.000 0.00 0.00 0.00 4.34
301 302 1.202794 TCACAACCGACCCTAAAACCC 60.203 52.381 0.00 0.00 0.00 4.11
302 303 2.259266 TCACAACCGACCCTAAAACC 57.741 50.000 0.00 0.00 0.00 3.27
303 304 4.841443 AAATCACAACCGACCCTAAAAC 57.159 40.909 0.00 0.00 0.00 2.43
304 305 4.645588 ACAAAATCACAACCGACCCTAAAA 59.354 37.500 0.00 0.00 0.00 1.52
305 306 4.208746 ACAAAATCACAACCGACCCTAAA 58.791 39.130 0.00 0.00 0.00 1.85
306 307 3.822940 ACAAAATCACAACCGACCCTAA 58.177 40.909 0.00 0.00 0.00 2.69
307 308 3.495434 ACAAAATCACAACCGACCCTA 57.505 42.857 0.00 0.00 0.00 3.53
308 309 2.358322 ACAAAATCACAACCGACCCT 57.642 45.000 0.00 0.00 0.00 4.34
875 905 1.443702 CCATGCGACTCGTCACGAA 60.444 57.895 0.00 0.00 34.74 3.85
1131 1162 2.328099 GGCGAAGAACAGGTGGCTG 61.328 63.158 0.00 0.00 0.00 4.85
1182 1213 3.580100 GAGCAGCTGCCAGACGACA 62.580 63.158 34.39 0.00 43.38 4.35
1437 1468 9.232473 ACTGAGCGTGAATTATATAGAGTATGA 57.768 33.333 0.00 0.00 0.00 2.15
1440 1471 8.944029 GGTACTGAGCGTGAATTATATAGAGTA 58.056 37.037 0.00 0.00 0.00 2.59
1441 1472 7.666388 AGGTACTGAGCGTGAATTATATAGAGT 59.334 37.037 0.00 0.00 37.18 3.24
1475 1509 3.587797 ATTTTGGAACTGATGCAGCTG 57.412 42.857 10.11 10.11 34.37 4.24
1559 1593 0.661020 GTCCACGTTTCACTTGGGTG 59.339 55.000 0.00 0.00 38.01 4.61
1584 1618 2.823747 ACTGTAGTAACACCAGCGATCA 59.176 45.455 0.00 0.00 0.00 2.92
1728 1793 5.915758 TGCAACAAAAACAATCATACCGTAC 59.084 36.000 0.00 0.00 0.00 3.67
1729 1794 6.073327 TGCAACAAAAACAATCATACCGTA 57.927 33.333 0.00 0.00 0.00 4.02
1730 1795 4.938080 TGCAACAAAAACAATCATACCGT 58.062 34.783 0.00 0.00 0.00 4.83
1731 1796 4.143347 GCTGCAACAAAAACAATCATACCG 60.143 41.667 0.00 0.00 0.00 4.02
1732 1797 4.990426 AGCTGCAACAAAAACAATCATACC 59.010 37.500 1.02 0.00 0.00 2.73
1958 2025 9.178758 ACTCAGTCAACACTTTTCTTCTTATTT 57.821 29.630 0.00 0.00 0.00 1.40
1959 2026 8.738645 ACTCAGTCAACACTTTTCTTCTTATT 57.261 30.769 0.00 0.00 0.00 1.40
1963 2030 5.163713 GCAACTCAGTCAACACTTTTCTTCT 60.164 40.000 0.00 0.00 0.00 2.85
1964 2031 5.030936 GCAACTCAGTCAACACTTTTCTTC 58.969 41.667 0.00 0.00 0.00 2.87
1965 2032 4.702131 AGCAACTCAGTCAACACTTTTCTT 59.298 37.500 0.00 0.00 0.00 2.52
1966 2033 4.265073 AGCAACTCAGTCAACACTTTTCT 58.735 39.130 0.00 0.00 0.00 2.52
1970 2037 4.067896 CCATAGCAACTCAGTCAACACTT 58.932 43.478 0.00 0.00 0.00 3.16
1971 2038 3.557898 CCCATAGCAACTCAGTCAACACT 60.558 47.826 0.00 0.00 0.00 3.55
2272 2418 8.773404 ACTGTATCTAAAATTGTACTGTGTCC 57.227 34.615 0.00 0.00 31.07 4.02
2307 2453 4.445452 TGGAGAAACAGTATACGTGGTC 57.555 45.455 0.00 1.64 0.00 4.02
2479 2626 9.208022 GCAATTAAGTCTTAAAAGGAGCAATTT 57.792 29.630 9.07 0.00 0.00 1.82
2600 2773 8.821894 CATGACTAAGCTAAAGTAGATTGAACC 58.178 37.037 1.80 0.00 34.89 3.62
2604 2777 8.200792 AGACCATGACTAAGCTAAAGTAGATTG 58.799 37.037 0.00 0.00 34.89 2.67
2774 2947 7.600375 AGAGACCTGTATCGCAATTATTACATG 59.400 37.037 0.00 0.00 0.00 3.21
2854 3027 3.132289 CCCTTAGTTATCAGCAGAACCGA 59.868 47.826 0.00 0.00 0.00 4.69
3215 3590 7.602265 CCGTGGACCATTTATTGAAAATTCTTT 59.398 33.333 0.00 0.00 0.00 2.52
3218 3593 5.810074 CCCGTGGACCATTTATTGAAAATTC 59.190 40.000 0.00 0.00 0.00 2.17
3219 3594 5.729510 CCCGTGGACCATTTATTGAAAATT 58.270 37.500 0.00 0.00 0.00 1.82
3221 3596 3.056465 GCCCGTGGACCATTTATTGAAAA 60.056 43.478 0.00 0.00 0.00 2.29
3223 3598 2.096248 GCCCGTGGACCATTTATTGAA 58.904 47.619 0.00 0.00 0.00 2.69
3323 3699 3.270877 GTCCACTCTCACTTGTGTGTTT 58.729 45.455 0.46 0.00 44.14 2.83
3370 3746 3.252627 ATGCGGCAGCTACACCACA 62.253 57.895 10.92 0.00 45.42 4.17
3610 3986 1.445518 GGCTAAGGAGGAGAGCAGC 59.554 63.158 0.00 0.00 37.98 5.25
3663 4042 2.352032 CGAAGGAAGGAGGAGCGGT 61.352 63.158 0.00 0.00 0.00 5.68
3780 4167 3.068691 TCTTAGCCGCCGCTCTGT 61.069 61.111 1.83 0.00 43.95 3.41
3794 4181 2.110899 TCCCTCTTGTCTCTCCACTCTT 59.889 50.000 0.00 0.00 0.00 2.85
3889 4277 3.849563 TTGGTTGAGGAATATACCCGG 57.150 47.619 0.00 0.00 0.00 5.73
3961 4349 7.339721 TGTCATTTAGGGTGTGTTTAGTTTTGA 59.660 33.333 0.00 0.00 0.00 2.69
3967 4355 6.668323 CAGTTGTCATTTAGGGTGTGTTTAG 58.332 40.000 0.00 0.00 0.00 1.85
3968 4356 5.009210 GCAGTTGTCATTTAGGGTGTGTTTA 59.991 40.000 0.00 0.00 0.00 2.01
4052 4442 9.739276 GATAAAGGGGAAAGAAAATCCAAAATT 57.261 29.630 0.00 0.00 38.80 1.82
4209 4599 2.564553 GAACGGACAGATGCGGCTCT 62.565 60.000 0.00 0.00 45.25 4.09
4584 4974 4.234574 CTGATGTACGCAAGACTGTTACA 58.765 43.478 0.00 0.00 43.62 2.41
4679 5069 4.870991 GGAAAGCAGAGTTATAGGTGTCAC 59.129 45.833 0.00 0.00 0.00 3.67
4684 5074 4.104831 ACCTGGAAAGCAGAGTTATAGGT 58.895 43.478 0.00 0.00 0.00 3.08
4718 5108 4.142988 TGCCAAGATTCACGACGAAAATAC 60.143 41.667 0.00 0.00 37.12 1.89
4980 5370 5.827797 AGATGCAAGTTCCTGTACAAAGAAA 59.172 36.000 9.04 0.00 0.00 2.52
5269 5659 6.380095 TGTAGGACGTTTTTGCAGTTTAAT 57.620 33.333 0.00 0.00 0.00 1.40
5301 5691 3.006859 GGCAAAGCAAATACTCCCTTTGT 59.993 43.478 11.96 0.00 43.57 2.83
5302 5692 3.006752 TGGCAAAGCAAATACTCCCTTTG 59.993 43.478 7.41 7.41 44.16 2.77
5303 5693 3.006859 GTGGCAAAGCAAATACTCCCTTT 59.993 43.478 0.00 0.00 0.00 3.11
5304 5694 2.562738 GTGGCAAAGCAAATACTCCCTT 59.437 45.455 0.00 0.00 0.00 3.95
5731 6122 5.245531 TCGATTGTCCAATTACTTTGAGCT 58.754 37.500 0.00 0.00 37.53 4.09
6226 6617 1.346395 ACGATCCACACTGCCAAACTA 59.654 47.619 0.00 0.00 0.00 2.24
6265 6664 9.709495 CCAATGAACTCCAAATTTTGATTCTTA 57.291 29.630 10.72 0.00 0.00 2.10
6447 6849 1.693062 CATCTGATCTGGGTCTCCTGG 59.307 57.143 0.00 0.00 33.38 4.45
6731 7133 7.463961 AAAATGATTGCAGAATCTGAACTCT 57.536 32.000 15.38 0.00 39.10 3.24
6945 7347 3.346315 TGCGTGGATGAATGACTGAAAT 58.654 40.909 0.00 0.00 0.00 2.17
6960 7362 0.940126 GTAGGATCATTGCTGCGTGG 59.060 55.000 0.00 0.00 0.00 4.94
7112 7514 7.284034 CCAAGAGTTGATATTTATGCCAGTCTT 59.716 37.037 0.00 0.00 0.00 3.01
7183 7585 4.222588 AGACAAGGAAACCTGATGAGAGAG 59.777 45.833 0.00 0.00 32.13 3.20
7391 7793 5.070001 CCTGAACTCAAAGGAACATAACCA 58.930 41.667 0.00 0.00 35.40 3.67
7454 7856 7.148755 GCAAAGGAAAAATGTAATAGTGCACTG 60.149 37.037 29.57 7.61 0.00 3.66
7459 7861 9.474920 TTGAAGCAAAGGAAAAATGTAATAGTG 57.525 29.630 0.00 0.00 0.00 2.74
8317 8720 2.821969 ACAATAGCAGTGCCTTTTCTGG 59.178 45.455 12.58 0.00 32.94 3.86
8344 8747 7.062957 CCCAGATATTTACAAGGATTTCCAGT 58.937 38.462 0.00 0.05 38.89 4.00
8544 8947 3.443045 GCCACAGCCATTGGTCCG 61.443 66.667 4.26 0.00 36.40 4.79
8679 9082 1.761206 CGGCTTTTGTTTGTAACCCG 58.239 50.000 0.00 0.00 0.00 5.28
8760 9165 3.207669 GCCGGATCTTGCAGCTGG 61.208 66.667 17.12 0.00 0.00 4.85
8787 9192 4.391830 GCGAGAGAAAACATGGTGTATCAA 59.608 41.667 0.00 0.00 0.00 2.57
8843 9248 2.344950 CTTCGTCTCTTCTGCAGCAAT 58.655 47.619 9.47 0.00 0.00 3.56
8903 9309 2.287946 GGGGAGATCCGGGGGTTA 59.712 66.667 0.00 0.00 36.71 2.85
8939 9345 2.504274 TTCCGTGTCCTCCAGCGTT 61.504 57.895 0.00 0.00 0.00 4.84
8941 9347 2.432628 GTTCCGTGTCCTCCAGCG 60.433 66.667 0.00 0.00 0.00 5.18
9008 9425 7.397761 ACGGGGAAGACAAAAATAAATAATGGA 59.602 33.333 0.00 0.00 0.00 3.41
9014 9431 6.687604 CAGAACGGGGAAGACAAAAATAAAT 58.312 36.000 0.00 0.00 0.00 1.40
9062 9479 0.539438 AAAATTCTGCTCCCCGTGCA 60.539 50.000 0.00 0.00 38.81 4.57
9148 9565 3.487207 GCGCTTTAATTATTGCTCTTGCC 59.513 43.478 0.00 0.00 38.71 4.52
9197 9614 5.733226 AACTTTTGTTTTGCCATGCTTAC 57.267 34.783 0.00 0.00 40.17 2.34
9324 9743 4.933505 TGTTGCAAGGATGACAATTTCA 57.066 36.364 0.00 0.00 39.11 2.69


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

AutoCloner maintained by Alex Coulton.