Multiple sequence alignment - TraesCS5A01G277300

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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 TraesCS5A01G277300 chr5A 100.000 2621 0 0 1 2621 487278803 487276183 0.000000e+00 4841.0
1 TraesCS5A01G277300 chr5A 89.655 58 5 1 851 908 487277882 487277826 3.620000e-09 73.1
2 TraesCS5A01G277300 chr5A 89.655 58 5 1 922 978 487277953 487277896 3.620000e-09 73.1
3 TraesCS5A01G277300 chr3A 98.760 1129 13 1 1493 2621 494061492 494062619 0.000000e+00 2006.0
4 TraesCS5A01G277300 chr3A 88.276 145 15 2 192 334 448314724 448314868 3.470000e-39 172.0
5 TraesCS5A01G277300 chr1B 97.968 1132 22 1 1491 2621 209573340 209572209 0.000000e+00 1962.0
6 TraesCS5A01G277300 chr1B 87.719 57 2 3 389 440 542589684 542589740 7.830000e-06 62.1
7 TraesCS5A01G277300 chr1B 87.719 57 2 3 389 440 633708801 633708857 7.830000e-06 62.1
8 TraesCS5A01G277300 chr3B 91.763 1129 92 1 1493 2621 435955020 435953893 0.000000e+00 1568.0
9 TraesCS5A01G277300 chr3B 94.608 204 9 2 1 204 103695777 103695576 5.450000e-82 315.0
10 TraesCS5A01G277300 chr3B 86.207 145 18 2 192 334 322726179 322726323 3.490000e-34 156.0
11 TraesCS5A01G277300 chr2B 83.940 1127 177 4 1496 2621 640457007 640458130 0.000000e+00 1075.0
12 TraesCS5A01G277300 chr4B 82.759 1131 184 10 1496 2621 615396704 615395580 0.000000e+00 998.0
13 TraesCS5A01G277300 chr4B 87.273 55 2 3 389 438 308678658 308678604 1.010000e-04 58.4
14 TraesCS5A01G277300 chr3D 82.655 1130 193 3 1493 2621 138183424 138184551 0.000000e+00 998.0
15 TraesCS5A01G277300 chr3D 95.455 198 9 0 6 203 83889423 83889620 1.510000e-82 316.0
16 TraesCS5A01G277300 chr3D 87.413 143 17 1 192 333 32348522 32348664 2.090000e-36 163.0
17 TraesCS5A01G277300 chr3D 88.889 117 11 2 221 336 426524306 426524421 2.720000e-30 143.0
18 TraesCS5A01G277300 chr1D 82.389 1130 194 4 1493 2621 379126366 379127491 0.000000e+00 979.0
19 TraesCS5A01G277300 chr1D 87.500 56 2 3 389 439 254436142 254436197 2.820000e-05 60.2
20 TraesCS5A01G277300 chr1D 100.000 32 0 0 396 427 440594687 440594656 2.820000e-05 60.2
21 TraesCS5A01G277300 chr1D 89.362 47 2 1 396 439 51870827 51870781 3.640000e-04 56.5
22 TraesCS5A01G277300 chr7D 82.155 1132 191 11 1495 2621 234179270 234178145 0.000000e+00 961.0
23 TraesCS5A01G277300 chr7D 95.522 201 7 2 1 199 45145683 45145483 1.170000e-83 320.0
24 TraesCS5A01G277300 chr7D 95.000 200 10 0 1 200 521966284 521966085 5.450000e-82 315.0
25 TraesCS5A01G277300 chr2D 82.058 1137 192 12 1491 2621 67596333 67595203 0.000000e+00 959.0
26 TraesCS5A01G277300 chr2D 87.500 56 2 3 389 439 638425614 638425669 2.820000e-05 60.2
27 TraesCS5A01G277300 chr5D 92.359 602 34 8 192 789 385409144 385408551 0.000000e+00 846.0
28 TraesCS5A01G277300 chr5D 88.301 624 43 12 791 1390 385408465 385407848 0.000000e+00 721.0
29 TraesCS5A01G277300 chr5D 96.447 197 7 0 1 197 129481537 129481341 2.520000e-85 326.0
30 TraesCS5A01G277300 chr5D 89.231 65 6 1 915 978 385408406 385408342 2.160000e-11 80.5
31 TraesCS5A01G277300 chr5D 87.500 56 2 3 389 439 503292980 503293035 2.820000e-05 60.2
32 TraesCS5A01G277300 chr5D 87.500 56 2 3 389 439 512411295 512411350 2.820000e-05 60.2
33 TraesCS5A01G277300 chr5D 87.500 56 2 3 389 439 512418232 512418287 2.820000e-05 60.2
34 TraesCS5A01G277300 chr5D 89.362 47 3 2 389 433 384983530 384983484 1.010000e-04 58.4
35 TraesCS5A01G277300 chr7A 96.078 204 6 2 4 205 721097360 721097157 5.410000e-87 331.0
36 TraesCS5A01G277300 chr7A 87.500 56 2 3 389 439 735492966 735492911 2.820000e-05 60.2
37 TraesCS5A01G277300 chr2A 96.907 194 6 0 1 194 103130660 103130467 2.520000e-85 326.0
38 TraesCS5A01G277300 chr2A 95.500 200 8 1 6 205 513855375 513855573 4.210000e-83 318.0
39 TraesCS5A01G277300 chr6B 96.373 193 7 0 1 193 20544725 20544917 4.210000e-83 318.0
40 TraesCS5A01G277300 chr1A 84.138 145 21 2 192 334 296911656 296911800 3.520000e-29 139.0
41 TraesCS5A01G277300 chr1A 84.733 131 17 3 206 333 344194914 344194784 7.610000e-26 128.0
42 TraesCS5A01G277300 chr4A 83.688 141 19 3 194 331 349291806 349291667 2.120000e-26 130.0
43 TraesCS5A01G277300 chr7B 83.217 143 20 3 194 333 297149533 297149674 7.610000e-26 128.0


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 TraesCS5A01G277300 chr5A 487276183 487278803 2620 True 1662.400000 4841 93.103333 1 2621 3 chr5A.!!$R1 2620
1 TraesCS5A01G277300 chr3A 494061492 494062619 1127 False 2006.000000 2006 98.760000 1493 2621 1 chr3A.!!$F2 1128
2 TraesCS5A01G277300 chr1B 209572209 209573340 1131 True 1962.000000 1962 97.968000 1491 2621 1 chr1B.!!$R1 1130
3 TraesCS5A01G277300 chr3B 435953893 435955020 1127 True 1568.000000 1568 91.763000 1493 2621 1 chr3B.!!$R2 1128
4 TraesCS5A01G277300 chr2B 640457007 640458130 1123 False 1075.000000 1075 83.940000 1496 2621 1 chr2B.!!$F1 1125
5 TraesCS5A01G277300 chr4B 615395580 615396704 1124 True 998.000000 998 82.759000 1496 2621 1 chr4B.!!$R2 1125
6 TraesCS5A01G277300 chr3D 138183424 138184551 1127 False 998.000000 998 82.655000 1493 2621 1 chr3D.!!$F3 1128
7 TraesCS5A01G277300 chr1D 379126366 379127491 1125 False 979.000000 979 82.389000 1493 2621 1 chr1D.!!$F2 1128
8 TraesCS5A01G277300 chr7D 234178145 234179270 1125 True 961.000000 961 82.155000 1495 2621 1 chr7D.!!$R2 1126
9 TraesCS5A01G277300 chr2D 67595203 67596333 1130 True 959.000000 959 82.058000 1491 2621 1 chr2D.!!$R1 1130
10 TraesCS5A01G277300 chr5D 385407848 385409144 1296 True 549.166667 846 89.963667 192 1390 3 chr5D.!!$R3 1198

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
67 68 0.447406 GCATTCACACTACGCATGCA 59.553 50.000 19.57 0.00 40.06 3.96 F
68 69 1.064505 GCATTCACACTACGCATGCAT 59.935 47.619 19.57 4.54 40.06 3.96 F
1030 1127 1.045407 TAGTCAACAACGAGCACCCT 58.955 50.000 0.00 0.00 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1014 1111 0.320374 CCTAGGGTGCTCGTTGTTGA 59.680 55.000 0.0 0.0 0.0 3.18 R
1062 1159 0.321122 CTTGCTTGCTTCCTCTCGGT 60.321 55.000 0.0 0.0 0.0 4.69 R
2373 2485 1.000955 CTCGAAGGTAGCCACACAAGT 59.999 52.381 0.0 0.0 0.0 3.16 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
29 30 6.248569 CCTAGGTGGTTATCTATTGGTTGT 57.751 41.667 0.00 0.00 0.00 3.32
30 31 6.055588 CCTAGGTGGTTATCTATTGGTTGTG 58.944 44.000 0.00 0.00 0.00 3.33
31 32 5.772393 AGGTGGTTATCTATTGGTTGTGA 57.228 39.130 0.00 0.00 0.00 3.58
32 33 5.745227 AGGTGGTTATCTATTGGTTGTGAG 58.255 41.667 0.00 0.00 0.00 3.51
33 34 5.487488 AGGTGGTTATCTATTGGTTGTGAGA 59.513 40.000 0.00 0.00 0.00 3.27
34 35 6.158695 AGGTGGTTATCTATTGGTTGTGAGAT 59.841 38.462 0.00 0.00 33.32 2.75
35 36 6.260936 GGTGGTTATCTATTGGTTGTGAGATG 59.739 42.308 0.00 0.00 31.25 2.90
36 37 6.260936 GTGGTTATCTATTGGTTGTGAGATGG 59.739 42.308 0.00 0.00 31.25 3.51
37 38 5.765182 GGTTATCTATTGGTTGTGAGATGGG 59.235 44.000 0.00 0.00 31.25 4.00
38 39 3.281727 TCTATTGGTTGTGAGATGGGC 57.718 47.619 0.00 0.00 0.00 5.36
39 40 2.846206 TCTATTGGTTGTGAGATGGGCT 59.154 45.455 0.00 0.00 0.00 5.19
40 41 4.037222 TCTATTGGTTGTGAGATGGGCTA 58.963 43.478 0.00 0.00 0.00 3.93
41 42 3.737559 ATTGGTTGTGAGATGGGCTAA 57.262 42.857 0.00 0.00 0.00 3.09
42 43 3.517296 TTGGTTGTGAGATGGGCTAAA 57.483 42.857 0.00 0.00 0.00 1.85
43 44 3.517296 TGGTTGTGAGATGGGCTAAAA 57.483 42.857 0.00 0.00 0.00 1.52
44 45 3.838565 TGGTTGTGAGATGGGCTAAAAA 58.161 40.909 0.00 0.00 0.00 1.94
63 64 5.621197 AAAAATAGCATTCACACTACGCA 57.379 34.783 0.00 0.00 0.00 5.24
64 65 5.818136 AAAATAGCATTCACACTACGCAT 57.182 34.783 0.00 0.00 0.00 4.73
65 66 4.801147 AATAGCATTCACACTACGCATG 57.199 40.909 0.00 0.00 0.00 4.06
66 67 0.729116 AGCATTCACACTACGCATGC 59.271 50.000 7.91 7.91 40.53 4.06
67 68 0.447406 GCATTCACACTACGCATGCA 59.553 50.000 19.57 0.00 40.06 3.96
68 69 1.064505 GCATTCACACTACGCATGCAT 59.935 47.619 19.57 4.54 40.06 3.96
69 70 2.287644 GCATTCACACTACGCATGCATA 59.712 45.455 19.57 5.77 40.06 3.14
70 71 3.058708 GCATTCACACTACGCATGCATAT 60.059 43.478 19.57 4.84 40.06 1.78
71 72 4.152223 GCATTCACACTACGCATGCATATA 59.848 41.667 19.57 5.83 40.06 0.86
72 73 5.669602 GCATTCACACTACGCATGCATATAG 60.670 44.000 19.57 17.15 40.06 1.31
73 74 4.846779 TCACACTACGCATGCATATAGA 57.153 40.909 19.57 3.38 0.00 1.98
74 75 5.195001 TCACACTACGCATGCATATAGAA 57.805 39.130 19.57 2.99 0.00 2.10
75 76 5.596845 TCACACTACGCATGCATATAGAAA 58.403 37.500 19.57 0.00 0.00 2.52
76 77 6.223120 TCACACTACGCATGCATATAGAAAT 58.777 36.000 19.57 4.78 0.00 2.17
77 78 7.375053 TCACACTACGCATGCATATAGAAATA 58.625 34.615 19.57 3.27 0.00 1.40
78 79 7.542130 TCACACTACGCATGCATATAGAAATAG 59.458 37.037 19.57 6.89 0.00 1.73
79 80 7.329471 CACACTACGCATGCATATAGAAATAGT 59.671 37.037 19.57 5.11 0.00 2.12
80 81 8.520351 ACACTACGCATGCATATAGAAATAGTA 58.480 33.333 19.57 6.04 0.00 1.82
81 82 9.521503 CACTACGCATGCATATAGAAATAGTAT 57.478 33.333 19.57 0.00 0.00 2.12
85 86 9.399403 ACGCATGCATATAGAAATAGTATATCG 57.601 33.333 19.57 0.00 0.00 2.92
86 87 8.854312 CGCATGCATATAGAAATAGTATATCGG 58.146 37.037 19.57 0.00 0.00 4.18
87 88 9.914131 GCATGCATATAGAAATAGTATATCGGA 57.086 33.333 14.21 0.00 0.00 4.55
123 124 8.290325 AGCTATTAGAAATAAATACAAAGCGCC 58.710 33.333 2.29 0.00 0.00 6.53
124 125 8.290325 GCTATTAGAAATAAATACAAAGCGCCT 58.710 33.333 2.29 0.00 0.00 5.52
129 130 8.683550 AGAAATAAATACAAAGCGCCTTAAAC 57.316 30.769 2.29 0.00 0.00 2.01
130 131 7.758076 AGAAATAAATACAAAGCGCCTTAAACC 59.242 33.333 2.29 0.00 0.00 3.27
131 132 6.769134 ATAAATACAAAGCGCCTTAAACCT 57.231 33.333 2.29 0.00 0.00 3.50
132 133 5.462530 AAATACAAAGCGCCTTAAACCTT 57.537 34.783 2.29 0.00 0.00 3.50
133 134 2.793278 ACAAAGCGCCTTAAACCTTG 57.207 45.000 2.29 0.00 0.00 3.61
134 135 2.028876 ACAAAGCGCCTTAAACCTTGT 58.971 42.857 2.29 0.00 0.00 3.16
135 136 2.034179 ACAAAGCGCCTTAAACCTTGTC 59.966 45.455 2.29 0.00 0.00 3.18
136 137 2.271944 AAGCGCCTTAAACCTTGTCT 57.728 45.000 2.29 0.00 0.00 3.41
137 138 3.412237 AAGCGCCTTAAACCTTGTCTA 57.588 42.857 2.29 0.00 0.00 2.59
138 139 3.629142 AGCGCCTTAAACCTTGTCTAT 57.371 42.857 2.29 0.00 0.00 1.98
139 140 3.951663 AGCGCCTTAAACCTTGTCTATT 58.048 40.909 2.29 0.00 0.00 1.73
140 141 3.689649 AGCGCCTTAAACCTTGTCTATTG 59.310 43.478 2.29 0.00 0.00 1.90
141 142 3.439129 GCGCCTTAAACCTTGTCTATTGT 59.561 43.478 0.00 0.00 0.00 2.71
142 143 4.671766 GCGCCTTAAACCTTGTCTATTGTG 60.672 45.833 0.00 0.00 0.00 3.33
143 144 4.142687 CGCCTTAAACCTTGTCTATTGTGG 60.143 45.833 0.00 0.00 0.00 4.17
144 145 5.007682 GCCTTAAACCTTGTCTATTGTGGA 58.992 41.667 0.00 0.00 0.00 4.02
145 146 5.475564 GCCTTAAACCTTGTCTATTGTGGAA 59.524 40.000 0.00 0.00 0.00 3.53
146 147 6.015772 GCCTTAAACCTTGTCTATTGTGGAAA 60.016 38.462 0.00 0.00 0.00 3.13
147 148 7.368059 CCTTAAACCTTGTCTATTGTGGAAAC 58.632 38.462 0.00 0.00 0.00 2.78
148 149 5.432885 AAACCTTGTCTATTGTGGAAACG 57.567 39.130 0.00 0.00 0.00 3.60
149 150 2.812011 ACCTTGTCTATTGTGGAAACGC 59.188 45.455 0.00 0.00 42.66 4.84
157 158 4.626225 GTGGAAACGCACGCAAAT 57.374 50.000 0.00 0.00 41.67 2.32
158 159 2.880091 GTGGAAACGCACGCAAATT 58.120 47.368 0.00 0.00 41.67 1.82
159 160 1.204792 GTGGAAACGCACGCAAATTT 58.795 45.000 0.00 0.00 41.67 1.82
160 161 2.386249 GTGGAAACGCACGCAAATTTA 58.614 42.857 0.00 0.00 41.67 1.40
161 162 2.789893 GTGGAAACGCACGCAAATTTAA 59.210 40.909 0.00 0.00 41.67 1.52
162 163 2.789893 TGGAAACGCACGCAAATTTAAC 59.210 40.909 0.00 0.00 0.00 2.01
163 164 3.047093 GGAAACGCACGCAAATTTAACT 58.953 40.909 0.00 0.00 0.00 2.24
164 165 3.121496 GGAAACGCACGCAAATTTAACTG 60.121 43.478 0.00 0.00 0.00 3.16
165 166 2.766970 ACGCACGCAAATTTAACTGT 57.233 40.000 0.00 0.00 0.00 3.55
166 167 2.380660 ACGCACGCAAATTTAACTGTG 58.619 42.857 0.00 0.00 0.00 3.66
167 168 1.122323 CGCACGCAAATTTAACTGTGC 59.878 47.619 18.62 18.62 46.73 4.57
168 169 1.455408 GCACGCAAATTTAACTGTGCC 59.545 47.619 18.16 7.14 45.07 5.01
169 170 2.862140 GCACGCAAATTTAACTGTGCCT 60.862 45.455 18.16 0.00 45.07 4.75
170 171 3.380142 CACGCAAATTTAACTGTGCCTT 58.620 40.909 2.62 0.00 33.33 4.35
171 172 3.425193 CACGCAAATTTAACTGTGCCTTC 59.575 43.478 2.62 0.00 33.33 3.46
172 173 3.317993 ACGCAAATTTAACTGTGCCTTCT 59.682 39.130 2.62 0.00 33.33 2.85
173 174 4.517453 ACGCAAATTTAACTGTGCCTTCTA 59.483 37.500 2.62 0.00 33.33 2.10
174 175 5.009210 ACGCAAATTTAACTGTGCCTTCTAA 59.991 36.000 2.62 0.00 33.33 2.10
175 176 5.918011 CGCAAATTTAACTGTGCCTTCTAAA 59.082 36.000 2.62 0.00 33.33 1.85
176 177 6.129194 CGCAAATTTAACTGTGCCTTCTAAAC 60.129 38.462 2.62 0.00 33.33 2.01
177 178 6.923508 GCAAATTTAACTGTGCCTTCTAAACT 59.076 34.615 0.00 0.00 0.00 2.66
178 179 7.096065 GCAAATTTAACTGTGCCTTCTAAACTG 60.096 37.037 0.00 0.00 0.00 3.16
179 180 7.582667 AATTTAACTGTGCCTTCTAAACTGT 57.417 32.000 0.00 0.00 0.00 3.55
180 181 6.371809 TTTAACTGTGCCTTCTAAACTGTG 57.628 37.500 0.00 0.00 0.00 3.66
181 182 3.838244 ACTGTGCCTTCTAAACTGTGA 57.162 42.857 0.00 0.00 0.00 3.58
182 183 3.467803 ACTGTGCCTTCTAAACTGTGAC 58.532 45.455 0.00 0.00 0.00 3.67
183 184 2.476619 CTGTGCCTTCTAAACTGTGACG 59.523 50.000 0.00 0.00 0.00 4.35
184 185 1.798813 GTGCCTTCTAAACTGTGACGG 59.201 52.381 0.00 0.00 0.00 4.79
185 186 1.689813 TGCCTTCTAAACTGTGACGGA 59.310 47.619 0.00 0.00 0.00 4.69
186 187 2.288825 TGCCTTCTAAACTGTGACGGAG 60.289 50.000 0.00 0.00 0.00 4.63
187 188 2.931320 GCCTTCTAAACTGTGACGGAGG 60.931 54.545 0.00 0.00 0.00 4.30
188 189 2.353803 CCTTCTAAACTGTGACGGAGGG 60.354 54.545 0.00 0.00 0.00 4.30
189 190 2.297698 TCTAAACTGTGACGGAGGGA 57.702 50.000 0.00 0.00 0.00 4.20
190 191 2.168496 TCTAAACTGTGACGGAGGGAG 58.832 52.381 0.00 0.00 0.00 4.30
203 204 3.262405 ACGGAGGGAGTACATTTTTAGCA 59.738 43.478 0.00 0.00 0.00 3.49
204 205 4.258543 CGGAGGGAGTACATTTTTAGCAA 58.741 43.478 0.00 0.00 0.00 3.91
213 214 7.692705 GGAGTACATTTTTAGCAATCGTCTTTC 59.307 37.037 0.00 0.00 0.00 2.62
232 234 6.356190 GTCTTTCGTCGTTAAACCAAATCTTG 59.644 38.462 0.00 0.00 0.00 3.02
287 289 9.965824 AAACACATTAGTTCCTTAACTCATTTG 57.034 29.630 0.00 0.00 42.42 2.32
339 342 6.785488 CACTAGATGCACTTACAAAAGACA 57.215 37.500 0.00 0.00 36.50 3.41
340 343 7.369803 CACTAGATGCACTTACAAAAGACAT 57.630 36.000 0.00 0.00 36.45 3.06
341 344 7.239271 CACTAGATGCACTTACAAAAGACATG 58.761 38.462 0.00 0.00 35.00 3.21
342 345 6.936900 ACTAGATGCACTTACAAAAGACATGT 59.063 34.615 0.00 0.00 35.00 3.21
363 366 5.242434 TGTATCACAAGCAACCGACTTTAT 58.758 37.500 0.00 0.00 0.00 1.40
422 425 5.250543 TCTTCTCCTGATGGTTGGTCAAATA 59.749 40.000 0.00 0.00 34.23 1.40
429 432 8.058235 TCCTGATGGTTGGTCAAATAATAATGA 58.942 33.333 0.00 0.00 34.23 2.57
461 464 9.778741 TTTCTAAAGATGTTTGACTGAGTATGT 57.221 29.630 0.00 0.00 0.00 2.29
500 503 7.579589 TGAAAACATGAAATATTGCGGAAAG 57.420 32.000 0.00 0.00 0.00 2.62
504 507 5.894807 ACATGAAATATTGCGGAAAGAAGG 58.105 37.500 0.00 0.00 0.00 3.46
518 521 5.292101 CGGAAAGAAGGATCATGTCACTAAC 59.708 44.000 0.00 0.00 0.00 2.34
525 529 7.884877 AGAAGGATCATGTCACTAACAAAATCA 59.115 33.333 0.00 0.00 42.37 2.57
579 583 9.726034 GCAAAATTTTGATTATAGTGAACAACG 57.274 29.630 30.40 2.04 40.55 4.10
596 600 3.687698 ACAACGATAGGGAAATTTGTCCG 59.312 43.478 0.00 0.00 38.72 4.79
732 737 2.747446 ACACACGCTTCCCATCAAATAC 59.253 45.455 0.00 0.00 0.00 1.89
738 743 5.760253 CACGCTTCCCATCAAATACTATCTT 59.240 40.000 0.00 0.00 0.00 2.40
739 744 6.929049 CACGCTTCCCATCAAATACTATCTTA 59.071 38.462 0.00 0.00 0.00 2.10
740 745 6.929606 ACGCTTCCCATCAAATACTATCTTAC 59.070 38.462 0.00 0.00 0.00 2.34
777 782 9.743057 CAACGGCAATCCATAATATAAGAAAAA 57.257 29.630 0.00 0.00 0.00 1.94
806 894 6.560253 AGTATTGATTTAGGCCATTTAGCG 57.440 37.500 5.01 0.00 0.00 4.26
808 896 4.630894 TTGATTTAGGCCATTTAGCGTG 57.369 40.909 5.01 0.00 32.23 5.34
813 901 2.483014 AGGCCATTTAGCGTGTGTTA 57.517 45.000 5.01 0.00 0.00 2.41
832 920 9.716507 GTGTGTTAATACAATATCACAATCCAC 57.283 33.333 6.62 0.00 37.28 4.02
854 948 7.050377 CCACAATTGTCAGTACCTCAAGATAT 58.950 38.462 8.48 0.00 0.00 1.63
856 950 7.765819 CACAATTGTCAGTACCTCAAGATATGA 59.234 37.037 8.48 0.00 36.38 2.15
904 998 7.990917 ACCACAATAAATGCATGATAACGTTA 58.009 30.769 11.02 11.02 0.00 3.18
1001 1098 5.305644 ACTCCAAGACAAAGTATGTGACTCT 59.694 40.000 0.00 0.00 44.12 3.24
1014 1111 9.504708 AAGTATGTGACTCTATATAAGCGTAGT 57.495 33.333 0.00 0.00 37.44 2.73
1021 1118 8.127327 TGACTCTATATAAGCGTAGTCAACAAC 58.873 37.037 0.00 0.00 40.10 3.32
1030 1127 1.045407 TAGTCAACAACGAGCACCCT 58.955 50.000 0.00 0.00 0.00 4.34
1088 1185 1.357079 AGGAAGCAAGCAAGGGAGAAT 59.643 47.619 0.00 0.00 0.00 2.40
1121 1218 1.093159 GCAGCCTCCAAGATGACAAG 58.907 55.000 0.00 0.00 0.00 3.16
1125 1222 1.457346 CCTCCAAGATGACAAGCACC 58.543 55.000 0.00 0.00 0.00 5.01
1182 1279 0.179127 CGTCATGTCTCGCAGGTGAT 60.179 55.000 0.00 0.00 0.00 3.06
1183 1280 1.565305 GTCATGTCTCGCAGGTGATC 58.435 55.000 0.00 0.00 0.00 2.92
1184 1281 0.461548 TCATGTCTCGCAGGTGATCC 59.538 55.000 0.00 0.00 0.00 3.36
1260 1372 1.517242 GCGATCTATTTCCTGGCCTG 58.483 55.000 3.32 2.54 0.00 4.85
1265 1377 3.046283 TCTATTTCCTGGCCTGAGCTA 57.954 47.619 11.88 0.00 39.73 3.32
1266 1378 3.591789 TCTATTTCCTGGCCTGAGCTAT 58.408 45.455 11.88 1.98 39.73 2.97
1267 1379 3.976654 TCTATTTCCTGGCCTGAGCTATT 59.023 43.478 11.88 0.00 39.73 1.73
1272 1384 3.317406 TCCTGGCCTGAGCTATTATTGA 58.683 45.455 11.88 0.00 39.73 2.57
1291 1403 1.582610 AATCGGGATTTTGTGCGCGT 61.583 50.000 8.43 0.00 40.68 6.01
1306 1418 0.737367 CGCGTGCAGAGAATGAAGGA 60.737 55.000 0.00 0.00 0.00 3.36
1310 1422 1.329906 GTGCAGAGAATGAAGGATGCG 59.670 52.381 0.00 0.00 36.47 4.73
1316 1428 1.078497 AATGAAGGATGCGTGCCGA 60.078 52.632 0.00 0.00 0.00 5.54
1324 1436 4.776322 TGCGTGCCGATCAAGGGG 62.776 66.667 0.00 0.00 0.00 4.79
1347 1459 1.078567 GCCCTGAAGAGGACTGCAG 60.079 63.158 13.48 13.48 46.51 4.41
1367 1479 5.232610 CAGGAATTTCTGCATGAGAAGTC 57.767 43.478 0.00 4.90 41.86 3.01
1374 1486 4.298744 TCTGCATGAGAAGTCGATACAG 57.701 45.455 0.00 0.00 0.00 2.74
1392 1504 2.115052 AGGCCGTTGCATCACCAA 59.885 55.556 0.00 0.00 40.13 3.67
1393 1505 1.530419 AGGCCGTTGCATCACCAAA 60.530 52.632 0.00 0.00 40.13 3.28
1394 1506 1.080569 GGCCGTTGCATCACCAAAG 60.081 57.895 0.00 0.00 40.13 2.77
1395 1507 1.080569 GCCGTTGCATCACCAAAGG 60.081 57.895 0.00 3.08 44.08 3.11
1396 1508 1.080569 CCGTTGCATCACCAAAGGC 60.081 57.895 0.00 0.00 37.49 4.35
1397 1509 1.659233 CGTTGCATCACCAAAGGCA 59.341 52.632 0.00 0.00 0.00 4.75
1398 1510 0.664166 CGTTGCATCACCAAAGGCAC 60.664 55.000 0.00 0.00 35.74 5.01
1399 1511 0.664166 GTTGCATCACCAAAGGCACG 60.664 55.000 0.00 0.00 35.74 5.34
1400 1512 0.821301 TTGCATCACCAAAGGCACGA 60.821 50.000 0.00 0.00 35.74 4.35
1401 1513 0.608856 TGCATCACCAAAGGCACGAT 60.609 50.000 0.00 0.00 0.00 3.73
1402 1514 0.179156 GCATCACCAAAGGCACGATG 60.179 55.000 0.00 0.00 37.20 3.84
1403 1515 0.179156 CATCACCAAAGGCACGATGC 60.179 55.000 0.00 0.00 44.08 3.91
1412 1524 2.187946 GCACGATGCCCTACTGCT 59.812 61.111 0.00 0.00 37.42 4.24
1413 1525 2.176273 GCACGATGCCCTACTGCTG 61.176 63.158 0.00 0.00 37.42 4.41
1414 1526 2.176273 CACGATGCCCTACTGCTGC 61.176 63.158 0.00 0.00 0.00 5.25
1415 1527 2.362369 ACGATGCCCTACTGCTGCT 61.362 57.895 0.00 0.00 0.00 4.24
1416 1528 1.886313 CGATGCCCTACTGCTGCTG 60.886 63.158 4.89 4.89 0.00 4.41
1417 1529 2.124403 ATGCCCTACTGCTGCTGC 60.124 61.111 8.89 8.89 40.20 5.25
1418 1530 4.765449 TGCCCTACTGCTGCTGCG 62.765 66.667 11.21 8.29 43.34 5.18
1425 1537 3.271014 CTGCTGCTGCGGTCATTT 58.729 55.556 15.76 0.00 43.34 2.32
1426 1538 1.582968 CTGCTGCTGCGGTCATTTT 59.417 52.632 15.76 0.00 43.34 1.82
1427 1539 0.804364 CTGCTGCTGCGGTCATTTTA 59.196 50.000 15.76 0.00 43.34 1.52
1428 1540 0.521291 TGCTGCTGCGGTCATTTTAC 59.479 50.000 10.62 0.00 43.34 2.01
1429 1541 0.804989 GCTGCTGCGGTCATTTTACT 59.195 50.000 10.62 0.00 0.00 2.24
1430 1542 2.006888 GCTGCTGCGGTCATTTTACTA 58.993 47.619 10.62 0.00 0.00 1.82
1431 1543 2.223044 GCTGCTGCGGTCATTTTACTAC 60.223 50.000 10.62 0.00 0.00 2.73
1432 1544 2.351726 CTGCTGCGGTCATTTTACTACC 59.648 50.000 0.00 0.00 0.00 3.18
1433 1545 1.669265 GCTGCGGTCATTTTACTACCC 59.331 52.381 0.00 0.00 0.00 3.69
1434 1546 2.285977 CTGCGGTCATTTTACTACCCC 58.714 52.381 0.00 0.00 0.00 4.95
1435 1547 1.629353 TGCGGTCATTTTACTACCCCA 59.371 47.619 0.00 0.00 0.00 4.96
1436 1548 2.011947 GCGGTCATTTTACTACCCCAC 58.988 52.381 0.00 0.00 0.00 4.61
1437 1549 2.635714 CGGTCATTTTACTACCCCACC 58.364 52.381 0.00 0.00 0.00 4.61
1438 1550 2.681682 CGGTCATTTTACTACCCCACCC 60.682 54.545 0.00 0.00 0.00 4.61
1439 1551 2.635714 GTCATTTTACTACCCCACCCG 58.364 52.381 0.00 0.00 0.00 5.28
1440 1552 1.560611 TCATTTTACTACCCCACCCGG 59.439 52.381 0.00 0.00 0.00 5.73
1441 1553 1.560611 CATTTTACTACCCCACCCGGA 59.439 52.381 0.73 0.00 0.00 5.14
1442 1554 0.983467 TTTTACTACCCCACCCGGAC 59.017 55.000 0.73 0.00 0.00 4.79
1443 1555 0.909133 TTTACTACCCCACCCGGACC 60.909 60.000 0.73 0.00 0.00 4.46
1444 1556 2.820899 TTACTACCCCACCCGGACCC 62.821 65.000 0.73 0.00 0.00 4.46
1469 1581 4.148825 GGTCGCCGCTGGAGTGAT 62.149 66.667 0.00 0.00 0.00 3.06
1470 1582 2.782222 GGTCGCCGCTGGAGTGATA 61.782 63.158 0.00 0.00 0.00 2.15
1471 1583 1.299468 GTCGCCGCTGGAGTGATAG 60.299 63.158 0.00 0.00 0.00 2.08
1472 1584 2.028190 CGCCGCTGGAGTGATAGG 59.972 66.667 0.00 0.00 0.00 2.57
1473 1585 2.280457 GCCGCTGGAGTGATAGGC 60.280 66.667 0.00 0.00 37.61 3.93
1474 1586 3.094062 GCCGCTGGAGTGATAGGCA 62.094 63.158 0.00 0.00 43.65 4.75
1475 1587 1.750930 CCGCTGGAGTGATAGGCAT 59.249 57.895 0.00 0.00 0.00 4.40
1476 1588 0.969149 CCGCTGGAGTGATAGGCATA 59.031 55.000 0.00 0.00 0.00 3.14
1477 1589 1.344438 CCGCTGGAGTGATAGGCATAA 59.656 52.381 0.00 0.00 0.00 1.90
1478 1590 2.224281 CCGCTGGAGTGATAGGCATAAA 60.224 50.000 0.00 0.00 0.00 1.40
1479 1591 2.802816 CGCTGGAGTGATAGGCATAAAC 59.197 50.000 0.00 0.00 0.00 2.01
1480 1592 2.802816 GCTGGAGTGATAGGCATAAACG 59.197 50.000 0.00 0.00 0.00 3.60
1481 1593 2.802816 CTGGAGTGATAGGCATAAACGC 59.197 50.000 0.00 0.00 0.00 4.84
1626 1738 4.529377 ACCACCCGACTACTCAGAATAAAA 59.471 41.667 0.00 0.00 0.00 1.52
2316 2428 3.771160 CCGTAAGCTCAGGCCCGT 61.771 66.667 0.00 0.00 39.73 5.28
2373 2485 1.063616 CTACCGTTCGCGAAGATCTCA 59.936 52.381 24.13 4.75 44.71 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.055588 CACAACCAATAGATAACCACCTAGG 58.944 44.000 7.41 7.41 45.67 3.02
7 8 6.884832 TCACAACCAATAGATAACCACCTAG 58.115 40.000 0.00 0.00 0.00 3.02
8 9 6.670464 TCTCACAACCAATAGATAACCACCTA 59.330 38.462 0.00 0.00 0.00 3.08
9 10 5.487488 TCTCACAACCAATAGATAACCACCT 59.513 40.000 0.00 0.00 0.00 4.00
10 11 5.741011 TCTCACAACCAATAGATAACCACC 58.259 41.667 0.00 0.00 0.00 4.61
11 12 6.260936 CCATCTCACAACCAATAGATAACCAC 59.739 42.308 0.00 0.00 0.00 4.16
12 13 6.356556 CCATCTCACAACCAATAGATAACCA 58.643 40.000 0.00 0.00 0.00 3.67
13 14 5.765182 CCCATCTCACAACCAATAGATAACC 59.235 44.000 0.00 0.00 0.00 2.85
14 15 5.239525 GCCCATCTCACAACCAATAGATAAC 59.760 44.000 0.00 0.00 0.00 1.89
15 16 5.132648 AGCCCATCTCACAACCAATAGATAA 59.867 40.000 0.00 0.00 0.00 1.75
16 17 4.660303 AGCCCATCTCACAACCAATAGATA 59.340 41.667 0.00 0.00 0.00 1.98
17 18 3.461085 AGCCCATCTCACAACCAATAGAT 59.539 43.478 0.00 0.00 0.00 1.98
18 19 2.846206 AGCCCATCTCACAACCAATAGA 59.154 45.455 0.00 0.00 0.00 1.98
19 20 3.287867 AGCCCATCTCACAACCAATAG 57.712 47.619 0.00 0.00 0.00 1.73
20 21 4.853468 TTAGCCCATCTCACAACCAATA 57.147 40.909 0.00 0.00 0.00 1.90
21 22 3.737559 TTAGCCCATCTCACAACCAAT 57.262 42.857 0.00 0.00 0.00 3.16
22 23 3.517296 TTTAGCCCATCTCACAACCAA 57.483 42.857 0.00 0.00 0.00 3.67
23 24 3.517296 TTTTAGCCCATCTCACAACCA 57.483 42.857 0.00 0.00 0.00 3.67
41 42 5.621197 TGCGTAGTGTGAATGCTATTTTT 57.379 34.783 0.00 0.00 0.00 1.94
42 43 5.572211 CATGCGTAGTGTGAATGCTATTTT 58.428 37.500 0.00 0.00 0.00 1.82
43 44 4.496341 GCATGCGTAGTGTGAATGCTATTT 60.496 41.667 0.00 0.00 40.34 1.40
44 45 3.002656 GCATGCGTAGTGTGAATGCTATT 59.997 43.478 0.00 0.00 40.34 1.73
45 46 2.545526 GCATGCGTAGTGTGAATGCTAT 59.454 45.455 0.00 0.00 40.34 2.97
46 47 1.933181 GCATGCGTAGTGTGAATGCTA 59.067 47.619 0.00 0.00 40.34 3.49
47 48 0.729116 GCATGCGTAGTGTGAATGCT 59.271 50.000 0.00 0.00 40.34 3.79
48 49 0.447406 TGCATGCGTAGTGTGAATGC 59.553 50.000 14.09 0.00 43.08 3.56
49 50 4.737353 ATATGCATGCGTAGTGTGAATG 57.263 40.909 23.20 0.00 0.00 2.67
50 51 5.783111 TCTATATGCATGCGTAGTGTGAAT 58.217 37.500 23.20 9.61 0.00 2.57
51 52 5.195001 TCTATATGCATGCGTAGTGTGAA 57.805 39.130 23.20 2.26 0.00 3.18
52 53 4.846779 TCTATATGCATGCGTAGTGTGA 57.153 40.909 23.20 15.02 0.00 3.58
53 54 5.905480 TTTCTATATGCATGCGTAGTGTG 57.095 39.130 23.20 13.27 0.00 3.82
54 55 7.378966 ACTATTTCTATATGCATGCGTAGTGT 58.621 34.615 23.20 10.69 0.00 3.55
55 56 7.818493 ACTATTTCTATATGCATGCGTAGTG 57.182 36.000 23.20 17.51 0.00 2.74
59 60 9.399403 CGATATACTATTTCTATATGCATGCGT 57.601 33.333 18.07 18.07 0.00 5.24
60 61 8.854312 CCGATATACTATTTCTATATGCATGCG 58.146 37.037 14.09 0.00 0.00 4.73
61 62 9.914131 TCCGATATACTATTTCTATATGCATGC 57.086 33.333 11.82 11.82 0.00 4.06
97 98 8.290325 GGCGCTTTGTATTTATTTCTAATAGCT 58.710 33.333 7.64 0.00 0.00 3.32
98 99 8.290325 AGGCGCTTTGTATTTATTTCTAATAGC 58.710 33.333 7.64 0.00 0.00 2.97
103 104 9.777575 GTTTAAGGCGCTTTGTATTTATTTCTA 57.222 29.630 15.86 0.00 0.00 2.10
104 105 7.758076 GGTTTAAGGCGCTTTGTATTTATTTCT 59.242 33.333 15.86 0.00 0.00 2.52
105 106 7.758076 AGGTTTAAGGCGCTTTGTATTTATTTC 59.242 33.333 15.86 0.00 0.00 2.17
106 107 7.608153 AGGTTTAAGGCGCTTTGTATTTATTT 58.392 30.769 15.86 0.00 0.00 1.40
107 108 7.165460 AGGTTTAAGGCGCTTTGTATTTATT 57.835 32.000 15.86 0.00 0.00 1.40
108 109 6.769134 AGGTTTAAGGCGCTTTGTATTTAT 57.231 33.333 15.86 0.00 0.00 1.40
109 110 6.016108 ACAAGGTTTAAGGCGCTTTGTATTTA 60.016 34.615 15.86 0.00 0.00 1.40
110 111 5.221362 ACAAGGTTTAAGGCGCTTTGTATTT 60.221 36.000 15.86 0.40 0.00 1.40
111 112 4.279922 ACAAGGTTTAAGGCGCTTTGTATT 59.720 37.500 15.86 0.00 0.00 1.89
112 113 3.824443 ACAAGGTTTAAGGCGCTTTGTAT 59.176 39.130 15.86 0.00 0.00 2.29
113 114 3.215975 ACAAGGTTTAAGGCGCTTTGTA 58.784 40.909 15.86 0.00 0.00 2.41
114 115 2.028876 ACAAGGTTTAAGGCGCTTTGT 58.971 42.857 15.86 0.00 0.00 2.83
115 116 2.293399 AGACAAGGTTTAAGGCGCTTTG 59.707 45.455 15.86 0.00 0.00 2.77
116 117 2.583143 AGACAAGGTTTAAGGCGCTTT 58.417 42.857 10.47 10.47 0.00 3.51
117 118 2.271944 AGACAAGGTTTAAGGCGCTT 57.728 45.000 7.64 0.00 0.00 4.68
118 119 3.629142 ATAGACAAGGTTTAAGGCGCT 57.371 42.857 7.64 0.00 0.00 5.92
119 120 3.439129 ACAATAGACAAGGTTTAAGGCGC 59.561 43.478 0.00 0.00 0.00 6.53
120 121 4.142687 CCACAATAGACAAGGTTTAAGGCG 60.143 45.833 0.00 0.00 0.00 5.52
121 122 5.007682 TCCACAATAGACAAGGTTTAAGGC 58.992 41.667 0.00 0.00 0.00 4.35
122 123 7.368059 GTTTCCACAATAGACAAGGTTTAAGG 58.632 38.462 0.00 0.00 0.00 2.69
123 124 7.075741 CGTTTCCACAATAGACAAGGTTTAAG 58.924 38.462 0.00 0.00 0.00 1.85
124 125 6.513720 GCGTTTCCACAATAGACAAGGTTTAA 60.514 38.462 0.00 0.00 0.00 1.52
125 126 5.049267 GCGTTTCCACAATAGACAAGGTTTA 60.049 40.000 0.00 0.00 0.00 2.01
126 127 4.261447 GCGTTTCCACAATAGACAAGGTTT 60.261 41.667 0.00 0.00 0.00 3.27
127 128 3.252458 GCGTTTCCACAATAGACAAGGTT 59.748 43.478 0.00 0.00 0.00 3.50
128 129 2.812011 GCGTTTCCACAATAGACAAGGT 59.188 45.455 0.00 0.00 0.00 3.50
129 130 2.811431 TGCGTTTCCACAATAGACAAGG 59.189 45.455 0.00 0.00 0.00 3.61
130 131 3.664276 CGTGCGTTTCCACAATAGACAAG 60.664 47.826 0.00 0.00 35.47 3.16
131 132 2.222213 CGTGCGTTTCCACAATAGACAA 59.778 45.455 0.00 0.00 35.47 3.18
132 133 1.795872 CGTGCGTTTCCACAATAGACA 59.204 47.619 0.00 0.00 35.47 3.41
133 134 1.463528 GCGTGCGTTTCCACAATAGAC 60.464 52.381 0.00 0.00 35.47 2.59
134 135 0.793861 GCGTGCGTTTCCACAATAGA 59.206 50.000 0.00 0.00 35.47 1.98
135 136 0.515127 TGCGTGCGTTTCCACAATAG 59.485 50.000 0.00 0.00 35.47 1.73
136 137 0.945099 TTGCGTGCGTTTCCACAATA 59.055 45.000 0.00 0.00 35.47 1.90
137 138 0.101399 TTTGCGTGCGTTTCCACAAT 59.899 45.000 0.00 0.00 35.47 2.71
138 139 0.101399 ATTTGCGTGCGTTTCCACAA 59.899 45.000 0.00 0.00 35.47 3.33
139 140 0.101399 AATTTGCGTGCGTTTCCACA 59.899 45.000 0.00 0.00 35.47 4.17
140 141 1.204792 AAATTTGCGTGCGTTTCCAC 58.795 45.000 0.00 0.00 0.00 4.02
141 142 2.776312 TAAATTTGCGTGCGTTTCCA 57.224 40.000 0.00 0.00 0.00 3.53
142 143 3.047093 AGTTAAATTTGCGTGCGTTTCC 58.953 40.909 0.00 0.00 0.00 3.13
143 144 3.484285 ACAGTTAAATTTGCGTGCGTTTC 59.516 39.130 0.00 0.00 0.00 2.78
144 145 3.241784 CACAGTTAAATTTGCGTGCGTTT 59.758 39.130 0.00 0.00 0.00 3.60
145 146 2.786578 CACAGTTAAATTTGCGTGCGTT 59.213 40.909 0.00 0.00 0.00 4.84
146 147 2.380660 CACAGTTAAATTTGCGTGCGT 58.619 42.857 0.00 0.00 0.00 5.24
147 148 1.122323 GCACAGTTAAATTTGCGTGCG 59.878 47.619 15.51 1.61 40.16 5.34
148 149 1.455408 GGCACAGTTAAATTTGCGTGC 59.545 47.619 19.42 19.42 46.85 5.34
149 150 3.011949 AGGCACAGTTAAATTTGCGTG 57.988 42.857 8.27 4.14 35.74 5.34
150 151 3.317993 AGAAGGCACAGTTAAATTTGCGT 59.682 39.130 7.84 5.77 35.74 5.24
151 152 3.900941 AGAAGGCACAGTTAAATTTGCG 58.099 40.909 7.84 0.00 35.74 4.85
152 153 6.923508 AGTTTAGAAGGCACAGTTAAATTTGC 59.076 34.615 5.51 5.51 0.00 3.68
153 154 7.920682 ACAGTTTAGAAGGCACAGTTAAATTTG 59.079 33.333 0.00 0.00 0.00 2.32
154 155 7.920682 CACAGTTTAGAAGGCACAGTTAAATTT 59.079 33.333 0.00 0.00 0.00 1.82
155 156 7.284489 TCACAGTTTAGAAGGCACAGTTAAATT 59.716 33.333 0.00 0.00 0.00 1.82
156 157 6.770785 TCACAGTTTAGAAGGCACAGTTAAAT 59.229 34.615 0.00 0.00 0.00 1.40
157 158 6.037830 GTCACAGTTTAGAAGGCACAGTTAAA 59.962 38.462 0.00 0.00 0.00 1.52
158 159 5.526111 GTCACAGTTTAGAAGGCACAGTTAA 59.474 40.000 0.00 0.00 0.00 2.01
159 160 5.054477 GTCACAGTTTAGAAGGCACAGTTA 58.946 41.667 0.00 0.00 0.00 2.24
160 161 3.877508 GTCACAGTTTAGAAGGCACAGTT 59.122 43.478 0.00 0.00 0.00 3.16
161 162 3.467803 GTCACAGTTTAGAAGGCACAGT 58.532 45.455 0.00 0.00 0.00 3.55
162 163 2.476619 CGTCACAGTTTAGAAGGCACAG 59.523 50.000 0.00 0.00 0.00 3.66
163 164 2.479837 CGTCACAGTTTAGAAGGCACA 58.520 47.619 0.00 0.00 0.00 4.57
164 165 1.798813 CCGTCACAGTTTAGAAGGCAC 59.201 52.381 0.00 0.00 0.00 5.01
165 166 1.689813 TCCGTCACAGTTTAGAAGGCA 59.310 47.619 0.00 0.00 34.05 4.75
166 167 2.338500 CTCCGTCACAGTTTAGAAGGC 58.662 52.381 0.00 0.00 34.05 4.35
167 168 2.353803 CCCTCCGTCACAGTTTAGAAGG 60.354 54.545 0.00 0.00 35.14 3.46
168 169 2.561419 TCCCTCCGTCACAGTTTAGAAG 59.439 50.000 0.00 0.00 0.00 2.85
169 170 2.561419 CTCCCTCCGTCACAGTTTAGAA 59.439 50.000 0.00 0.00 0.00 2.10
170 171 2.168496 CTCCCTCCGTCACAGTTTAGA 58.832 52.381 0.00 0.00 0.00 2.10
171 172 1.893801 ACTCCCTCCGTCACAGTTTAG 59.106 52.381 0.00 0.00 0.00 1.85
172 173 2.005370 ACTCCCTCCGTCACAGTTTA 57.995 50.000 0.00 0.00 0.00 2.01
173 174 1.617357 GTACTCCCTCCGTCACAGTTT 59.383 52.381 0.00 0.00 0.00 2.66
174 175 1.254954 GTACTCCCTCCGTCACAGTT 58.745 55.000 0.00 0.00 0.00 3.16
175 176 0.111832 TGTACTCCCTCCGTCACAGT 59.888 55.000 0.00 0.00 0.00 3.55
176 177 1.475403 ATGTACTCCCTCCGTCACAG 58.525 55.000 0.00 0.00 0.00 3.66
177 178 1.933021 AATGTACTCCCTCCGTCACA 58.067 50.000 0.00 0.00 0.00 3.58
178 179 3.329929 AAAATGTACTCCCTCCGTCAC 57.670 47.619 0.00 0.00 0.00 3.67
179 180 4.622220 GCTAAAAATGTACTCCCTCCGTCA 60.622 45.833 0.00 0.00 0.00 4.35
180 181 3.869832 GCTAAAAATGTACTCCCTCCGTC 59.130 47.826 0.00 0.00 0.00 4.79
181 182 3.262405 TGCTAAAAATGTACTCCCTCCGT 59.738 43.478 0.00 0.00 0.00 4.69
182 183 3.869065 TGCTAAAAATGTACTCCCTCCG 58.131 45.455 0.00 0.00 0.00 4.63
183 184 5.007724 CGATTGCTAAAAATGTACTCCCTCC 59.992 44.000 0.00 0.00 0.00 4.30
184 185 5.585047 ACGATTGCTAAAAATGTACTCCCTC 59.415 40.000 0.00 0.00 0.00 4.30
185 186 5.497474 ACGATTGCTAAAAATGTACTCCCT 58.503 37.500 0.00 0.00 0.00 4.20
186 187 5.585047 AGACGATTGCTAAAAATGTACTCCC 59.415 40.000 0.00 0.00 0.00 4.30
187 188 6.663944 AGACGATTGCTAAAAATGTACTCC 57.336 37.500 0.00 0.00 0.00 3.85
188 189 7.422746 CGAAAGACGATTGCTAAAAATGTACTC 59.577 37.037 0.00 0.00 45.77 2.59
189 190 7.095355 ACGAAAGACGATTGCTAAAAATGTACT 60.095 33.333 0.00 0.00 45.77 2.73
190 191 7.013529 ACGAAAGACGATTGCTAAAAATGTAC 58.986 34.615 0.00 0.00 45.77 2.90
213 214 4.378046 CCCTCAAGATTTGGTTTAACGACG 60.378 45.833 0.00 0.00 0.00 5.12
291 293 6.657966 GCCCCTTAGTAGTTTTGAAGTAATGT 59.342 38.462 0.00 0.00 0.00 2.71
293 295 6.657966 GTGCCCCTTAGTAGTTTTGAAGTAAT 59.342 38.462 0.00 0.00 0.00 1.89
294 296 5.999600 GTGCCCCTTAGTAGTTTTGAAGTAA 59.000 40.000 0.00 0.00 0.00 2.24
299 301 5.088730 TCTAGTGCCCCTTAGTAGTTTTGA 58.911 41.667 0.00 0.00 0.00 2.69
333 336 4.083324 CGGTTGCTTGTGATACATGTCTTT 60.083 41.667 0.00 0.00 0.00 2.52
335 338 3.002791 CGGTTGCTTGTGATACATGTCT 58.997 45.455 0.00 0.00 0.00 3.41
336 339 3.000041 TCGGTTGCTTGTGATACATGTC 59.000 45.455 0.00 0.00 0.00 3.06
337 340 2.742053 GTCGGTTGCTTGTGATACATGT 59.258 45.455 2.69 2.69 0.00 3.21
338 341 3.002791 AGTCGGTTGCTTGTGATACATG 58.997 45.455 0.00 0.00 0.00 3.21
339 342 3.334583 AGTCGGTTGCTTGTGATACAT 57.665 42.857 0.00 0.00 0.00 2.29
340 343 2.831685 AGTCGGTTGCTTGTGATACA 57.168 45.000 0.00 0.00 0.00 2.29
341 344 5.121768 ACATAAAGTCGGTTGCTTGTGATAC 59.878 40.000 0.00 0.00 0.00 2.24
342 345 5.121611 CACATAAAGTCGGTTGCTTGTGATA 59.878 40.000 0.00 0.00 0.00 2.15
363 366 7.406553 GCATTATTTGTAGAGCGAAATACACA 58.593 34.615 0.00 0.00 31.83 3.72
385 388 2.651841 AGGAGAAGAAAAGAAGGGGCAT 59.348 45.455 0.00 0.00 0.00 4.40
488 491 5.380043 ACATGATCCTTCTTTCCGCAATAT 58.620 37.500 0.00 0.00 0.00 1.28
490 493 3.624777 ACATGATCCTTCTTTCCGCAAT 58.375 40.909 0.00 0.00 0.00 3.56
500 503 8.044060 TGATTTTGTTAGTGACATGATCCTTC 57.956 34.615 0.00 0.00 38.26 3.46
525 529 9.868277 CACTCTGTCTGACTCTTCTATTAATTT 57.132 33.333 9.51 0.00 0.00 1.82
579 583 4.712122 TTTGCGGACAAATTTCCCTATC 57.288 40.909 0.00 0.00 40.84 2.08
687 692 7.552687 TGTAACACATCCAACTATGATTCCTTC 59.447 37.037 0.00 0.00 0.00 3.46
717 722 9.646427 CTAGTAAGATAGTATTTGATGGGAAGC 57.354 37.037 0.00 0.00 0.00 3.86
732 737 5.278364 CCGTTGCACCTACCTAGTAAGATAG 60.278 48.000 0.00 0.00 0.00 2.08
738 743 0.819582 GCCGTTGCACCTACCTAGTA 59.180 55.000 0.00 0.00 37.47 1.82
739 744 1.189524 TGCCGTTGCACCTACCTAGT 61.190 55.000 0.00 0.00 44.23 2.57
740 745 1.594833 TGCCGTTGCACCTACCTAG 59.405 57.895 0.00 0.00 44.23 3.02
750 755 6.494893 TCTTATATTATGGATTGCCGTTGC 57.505 37.500 0.00 0.00 36.79 4.17
780 785 9.378551 CGCTAAATGGCCTAAATCAATACTATA 57.621 33.333 3.32 0.00 0.00 1.31
781 786 7.883311 ACGCTAAATGGCCTAAATCAATACTAT 59.117 33.333 3.32 0.00 0.00 2.12
782 787 7.172532 CACGCTAAATGGCCTAAATCAATACTA 59.827 37.037 3.32 0.00 0.00 1.82
783 788 6.017109 CACGCTAAATGGCCTAAATCAATACT 60.017 38.462 3.32 0.00 0.00 2.12
784 789 6.142817 CACGCTAAATGGCCTAAATCAATAC 58.857 40.000 3.32 0.00 0.00 1.89
785 790 5.825679 ACACGCTAAATGGCCTAAATCAATA 59.174 36.000 3.32 0.00 0.00 1.90
786 791 4.644685 ACACGCTAAATGGCCTAAATCAAT 59.355 37.500 3.32 0.00 0.00 2.57
788 793 3.376859 CACACGCTAAATGGCCTAAATCA 59.623 43.478 3.32 0.00 0.00 2.57
789 794 3.377172 ACACACGCTAAATGGCCTAAATC 59.623 43.478 3.32 0.00 0.00 2.17
796 884 5.224562 TGTATTAACACACGCTAAATGGC 57.775 39.130 0.00 0.00 0.00 4.40
800 888 9.152595 TGTGATATTGTATTAACACACGCTAAA 57.847 29.630 0.00 0.00 33.69 1.85
806 894 9.716507 GTGGATTGTGATATTGTATTAACACAC 57.283 33.333 0.00 0.00 37.85 3.82
832 920 7.765819 TGTCATATCTTGAGGTACTGACAATTG 59.234 37.037 3.24 3.24 41.55 2.32
838 926 7.125659 TGGATTTGTCATATCTTGAGGTACTGA 59.874 37.037 3.67 0.00 41.55 3.41
839 927 7.225538 GTGGATTTGTCATATCTTGAGGTACTG 59.774 40.741 3.67 0.00 41.55 2.74
845 939 7.854557 TTGAGTGGATTTGTCATATCTTGAG 57.145 36.000 3.67 0.00 34.17 3.02
856 950 9.747898 TGGTAAGTTAATATTGAGTGGATTTGT 57.252 29.630 0.00 0.00 0.00 2.83
1001 1098 5.911280 GCTCGTTGTTGACTACGCTTATATA 59.089 40.000 12.11 0.00 42.95 0.86
1012 1109 1.000955 CTAGGGTGCTCGTTGTTGACT 59.999 52.381 0.00 0.00 0.00 3.41
1014 1111 0.320374 CCTAGGGTGCTCGTTGTTGA 59.680 55.000 0.00 0.00 0.00 3.18
1021 1118 3.854669 CTGGGCCTAGGGTGCTCG 61.855 72.222 11.72 0.00 29.42 5.03
1062 1159 0.321122 CTTGCTTGCTTCCTCTCGGT 60.321 55.000 0.00 0.00 0.00 4.69
1070 1167 3.379688 CCTAATTCTCCCTTGCTTGCTTC 59.620 47.826 0.00 0.00 0.00 3.86
1088 1185 0.607620 GGCTGCCATGCAAAACCTAA 59.392 50.000 15.17 0.00 38.41 2.69
1125 1222 4.711949 AGAGCGGCCAAGCACAGG 62.712 66.667 2.24 0.00 40.15 4.00
1131 1228 4.379243 ACCACGAGAGCGGCCAAG 62.379 66.667 2.24 0.00 43.17 3.61
1147 1244 1.202371 TGACGATAGAACGGCCATGAC 60.202 52.381 2.24 0.00 40.96 3.06
1208 1320 7.308435 CAATTCAAAGACAAAGTATCCTGGTC 58.692 38.462 0.00 0.00 0.00 4.02
1260 1372 7.805071 CACAAAATCCCGATTCAATAATAGCTC 59.195 37.037 0.00 0.00 0.00 4.09
1265 1377 5.280945 CGCACAAAATCCCGATTCAATAAT 58.719 37.500 0.00 0.00 0.00 1.28
1266 1378 4.667262 CGCACAAAATCCCGATTCAATAA 58.333 39.130 0.00 0.00 0.00 1.40
1267 1379 3.488384 GCGCACAAAATCCCGATTCAATA 60.488 43.478 0.30 0.00 0.00 1.90
1272 1384 1.136565 CGCGCACAAAATCCCGATT 59.863 52.632 8.75 0.00 0.00 3.34
1291 1403 1.065926 ACGCATCCTTCATTCTCTGCA 60.066 47.619 0.00 0.00 0.00 4.41
1310 1422 0.462047 CAGTACCCCTTGATCGGCAC 60.462 60.000 0.00 0.00 0.00 5.01
1336 1448 3.347077 CAGAAATTCCTGCAGTCCTCT 57.653 47.619 13.81 4.24 0.00 3.69
1347 1459 3.935203 TCGACTTCTCATGCAGAAATTCC 59.065 43.478 0.00 0.63 40.83 3.01
1358 1470 2.625790 GGCCTCTGTATCGACTTCTCAT 59.374 50.000 0.00 0.00 0.00 2.90
1359 1471 2.025155 GGCCTCTGTATCGACTTCTCA 58.975 52.381 0.00 0.00 0.00 3.27
1360 1472 1.002251 CGGCCTCTGTATCGACTTCTC 60.002 57.143 0.00 0.00 0.00 2.87
1367 1479 0.530650 ATGCAACGGCCTCTGTATCG 60.531 55.000 0.00 0.00 40.13 2.92
1374 1486 1.523154 TTTGGTGATGCAACGGCCTC 61.523 55.000 0.00 0.00 40.13 4.70
1395 1507 2.176273 CAGCAGTAGGGCATCGTGC 61.176 63.158 0.00 0.00 44.08 5.34
1396 1508 2.176273 GCAGCAGTAGGGCATCGTG 61.176 63.158 0.00 0.00 35.83 4.35
1397 1509 2.187946 GCAGCAGTAGGGCATCGT 59.812 61.111 0.00 0.00 35.83 3.73
1398 1510 1.886313 CAGCAGCAGTAGGGCATCG 60.886 63.158 0.00 0.00 35.83 3.84
1399 1511 2.185494 GCAGCAGCAGTAGGGCATC 61.185 63.158 0.00 0.00 41.58 3.91
1400 1512 2.124403 GCAGCAGCAGTAGGGCAT 60.124 61.111 0.00 0.00 41.58 4.40
1401 1513 4.765449 CGCAGCAGCAGTAGGGCA 62.765 66.667 0.82 0.00 42.27 5.36
1403 1515 4.087892 ACCGCAGCAGCAGTAGGG 62.088 66.667 0.82 0.00 42.27 3.53
1404 1516 2.510238 GACCGCAGCAGCAGTAGG 60.510 66.667 0.82 0.00 42.27 3.18
1405 1517 0.742281 AATGACCGCAGCAGCAGTAG 60.742 55.000 0.82 0.00 42.27 2.57
1406 1518 0.321564 AAATGACCGCAGCAGCAGTA 60.322 50.000 0.82 0.00 42.27 2.74
1407 1519 1.174712 AAAATGACCGCAGCAGCAGT 61.175 50.000 0.82 0.00 42.27 4.40
1408 1520 0.804364 TAAAATGACCGCAGCAGCAG 59.196 50.000 0.82 0.00 42.27 4.24
1409 1521 0.521291 GTAAAATGACCGCAGCAGCA 59.479 50.000 0.82 0.00 42.27 4.41
1410 1522 0.804989 AGTAAAATGACCGCAGCAGC 59.195 50.000 0.00 0.00 37.42 5.25
1411 1523 2.351726 GGTAGTAAAATGACCGCAGCAG 59.648 50.000 0.00 0.00 0.00 4.24
1412 1524 2.352388 GGTAGTAAAATGACCGCAGCA 58.648 47.619 0.00 0.00 0.00 4.41
1413 1525 1.669265 GGGTAGTAAAATGACCGCAGC 59.331 52.381 0.00 0.00 33.77 5.25
1414 1526 2.285977 GGGGTAGTAAAATGACCGCAG 58.714 52.381 2.77 0.00 43.69 5.18
1415 1527 2.406596 GGGGTAGTAAAATGACCGCA 57.593 50.000 2.77 0.00 43.69 5.69
1416 1528 2.011947 GTGGGGTAGTAAAATGACCGC 58.988 52.381 0.00 0.00 44.31 5.68
1417 1529 2.635714 GGTGGGGTAGTAAAATGACCG 58.364 52.381 0.00 0.00 33.77 4.79
1418 1530 2.681682 CGGGTGGGGTAGTAAAATGACC 60.682 54.545 0.00 0.00 0.00 4.02
1419 1531 2.635714 CGGGTGGGGTAGTAAAATGAC 58.364 52.381 0.00 0.00 0.00 3.06
1420 1532 1.560611 CCGGGTGGGGTAGTAAAATGA 59.439 52.381 0.00 0.00 0.00 2.57
1421 1533 1.560611 TCCGGGTGGGGTAGTAAAATG 59.439 52.381 0.00 0.00 36.01 2.32
1422 1534 1.561076 GTCCGGGTGGGGTAGTAAAAT 59.439 52.381 0.00 0.00 36.01 1.82
1423 1535 0.983467 GTCCGGGTGGGGTAGTAAAA 59.017 55.000 0.00 0.00 36.01 1.52
1424 1536 0.909133 GGTCCGGGTGGGGTAGTAAA 60.909 60.000 0.00 0.00 36.01 2.01
1425 1537 1.306056 GGTCCGGGTGGGGTAGTAA 60.306 63.158 0.00 0.00 36.01 2.24
1426 1538 2.364160 GGTCCGGGTGGGGTAGTA 59.636 66.667 0.00 0.00 36.01 1.82
1427 1539 4.728118 GGGTCCGGGTGGGGTAGT 62.728 72.222 0.00 0.00 36.01 2.73
1452 1564 2.685387 CTATCACTCCAGCGGCGACC 62.685 65.000 12.98 0.00 0.00 4.79
1453 1565 1.299468 CTATCACTCCAGCGGCGAC 60.299 63.158 12.98 1.23 0.00 5.19
1454 1566 2.490148 CCTATCACTCCAGCGGCGA 61.490 63.158 12.98 0.00 0.00 5.54
1455 1567 2.028190 CCTATCACTCCAGCGGCG 59.972 66.667 0.51 0.51 0.00 6.46
1456 1568 2.280457 GCCTATCACTCCAGCGGC 60.280 66.667 0.00 0.00 0.00 6.53
1457 1569 0.969149 TATGCCTATCACTCCAGCGG 59.031 55.000 0.00 0.00 0.00 5.52
1458 1570 2.802816 GTTTATGCCTATCACTCCAGCG 59.197 50.000 0.00 0.00 0.00 5.18
1459 1571 2.802816 CGTTTATGCCTATCACTCCAGC 59.197 50.000 0.00 0.00 0.00 4.85
1460 1572 2.802816 GCGTTTATGCCTATCACTCCAG 59.197 50.000 0.00 0.00 0.00 3.86
1461 1573 2.833794 GCGTTTATGCCTATCACTCCA 58.166 47.619 0.00 0.00 0.00 3.86
1626 1738 2.367486 GTGGGAGAGTAGCGAGTAGTT 58.633 52.381 0.00 0.00 0.00 2.24
2373 2485 1.000955 CTCGAAGGTAGCCACACAAGT 59.999 52.381 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.