Multiple sequence alignment - TraesCS1B01G144100

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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 TraesCS1B01G144100 chr1B 100.000 2288 0 0 1 2288 196058537 196060824 0.000000e+00 4226
1 TraesCS1B01G144100 chr1B 97.101 276 8 0 1 276 299300023 299300298 1.240000e-127 466
2 TraesCS1B01G144100 chr1B 96.113 283 10 1 1 282 518112537 518112255 5.760000e-126 460
3 TraesCS1B01G144100 chr1D 91.847 2036 109 27 277 2283 141896852 141898859 0.000000e+00 2787
4 TraesCS1B01G144100 chr1D 87.749 1004 117 4 279 1281 338745589 338746587 0.000000e+00 1168
5 TraesCS1B01G144100 chr1D 85.030 334 45 5 1406 1737 338746587 338746917 3.640000e-88 335
6 TraesCS1B01G144100 chr1D 93.168 161 11 0 1762 1922 84806687 84806527 1.060000e-58 237
7 TraesCS1B01G144100 chr1A 85.686 1495 157 20 279 1740 148747537 148746067 0.000000e+00 1522
8 TraesCS1B01G144100 chr4B 86.312 1315 168 9 277 1584 168575039 168573730 0.000000e+00 1421
9 TraesCS1B01G144100 chr4B 96.099 282 11 0 1 282 343002918 343002637 5.760000e-126 460
10 TraesCS1B01G144100 chr4A 85.316 1328 162 17 278 1579 468211443 468210123 0.000000e+00 1341
11 TraesCS1B01G144100 chr4A 81.520 1434 196 45 277 1683 518855828 518857219 0.000000e+00 1116
12 TraesCS1B01G144100 chr4A 80.518 1042 162 20 712 1749 416227890 416226886 0.000000e+00 761
13 TraesCS1B01G144100 chr4A 88.848 269 27 3 1763 2031 676494333 676494598 6.090000e-86 327
14 TraesCS1B01G144100 chr4D 85.661 809 105 7 783 1584 108048658 108049462 0.000000e+00 841
15 TraesCS1B01G144100 chr4D 89.239 539 57 1 277 815 108048051 108048588 0.000000e+00 673
16 TraesCS1B01G144100 chr4D 80.464 604 86 18 1146 1744 138417416 138417992 1.260000e-117 433
17 TraesCS1B01G144100 chr5A 81.078 1020 148 27 283 1297 281949773 281950752 0.000000e+00 773
18 TraesCS1B01G144100 chr3D 85.482 737 107 0 637 1373 116088060 116088796 0.000000e+00 769
19 TraesCS1B01G144100 chr3D 86.472 377 46 5 1370 1744 116149450 116149823 2.120000e-110 409
20 TraesCS1B01G144100 chr5D 82.522 904 113 25 850 1745 512389613 512390479 0.000000e+00 752
21 TraesCS1B01G144100 chr3A 79.584 1058 133 35 560 1614 51696077 51697054 0.000000e+00 680
22 TraesCS1B01G144100 chr7A 88.346 532 59 3 278 808 238871437 238870908 8.920000e-179 636
23 TraesCS1B01G144100 chr7A 81.840 413 68 5 1338 1750 664694650 664695055 7.830000e-90 340
24 TraesCS1B01G144100 chr7A 87.308 260 30 3 1763 2022 38206940 38207196 6.180000e-76 294
25 TraesCS1B01G144100 chr6B 97.101 276 8 0 1 276 96558542 96558267 1.240000e-127 466
26 TraesCS1B01G144100 chr6B 94.792 288 15 0 1 288 237448404 237448691 1.250000e-122 449
27 TraesCS1B01G144100 chr3B 97.101 276 8 0 1 276 258225352 258225627 1.240000e-127 466
28 TraesCS1B01G144100 chr3B 97.101 276 8 0 1 276 367137800 367137525 1.240000e-127 466
29 TraesCS1B01G144100 chr3B 86.607 112 12 3 2172 2283 41336320 41336212 1.110000e-23 121
30 TraesCS1B01G144100 chr5B 87.469 399 49 1 277 675 439876580 439876977 2.070000e-125 459
31 TraesCS1B01G144100 chr2B 96.071 280 11 0 1 280 419165975 419166254 7.450000e-125 457
32 TraesCS1B01G144100 chr2B 95.439 285 13 0 1 285 409871907 409871623 2.680000e-124 455
33 TraesCS1B01G144100 chr2B 86.940 268 32 3 1763 2030 730558623 730558359 4.780000e-77 298
34 TraesCS1B01G144100 chr7D 85.978 271 34 4 1761 2031 165487036 165487302 1.030000e-73 287
35 TraesCS1B01G144100 chr7D 84.871 271 24 11 2024 2277 58994712 58994982 8.110000e-65 257
36 TraesCS1B01G144100 chr7B 90.783 217 16 4 1764 1979 691041627 691041414 1.030000e-73 287
37 TraesCS1B01G144100 chr7B 80.556 216 24 10 2080 2278 691041419 691041205 1.420000e-32 150
38 TraesCS1B01G144100 chr2D 85.263 285 20 13 2017 2283 645179423 645179703 8.050000e-70 274
39 TraesCS1B01G144100 chr2D 84.815 270 24 4 1763 2031 645179273 645179526 2.920000e-64 255
40 TraesCS1B01G144100 chr2A 85.185 270 31 8 1764 2031 74957005 74956743 3.750000e-68 268
41 TraesCS1B01G144100 chr2A 86.036 222 24 6 2068 2283 144616093 144615873 4.920000e-57 231
42 TraesCS1B01G144100 chrUn 84.733 262 26 3 2026 2274 93046263 93046523 1.360000e-62 250
43 TraesCS1B01G144100 chrUn 82.721 272 30 9 2020 2278 378498146 378497879 2.290000e-55 226


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 TraesCS1B01G144100 chr1B 196058537 196060824 2287 False 4226.0 4226 100.0000 1 2288 1 chr1B.!!$F1 2287
1 TraesCS1B01G144100 chr1D 141896852 141898859 2007 False 2787.0 2787 91.8470 277 2283 1 chr1D.!!$F1 2006
2 TraesCS1B01G144100 chr1D 338745589 338746917 1328 False 751.5 1168 86.3895 279 1737 2 chr1D.!!$F2 1458
3 TraesCS1B01G144100 chr1A 148746067 148747537 1470 True 1522.0 1522 85.6860 279 1740 1 chr1A.!!$R1 1461
4 TraesCS1B01G144100 chr4B 168573730 168575039 1309 True 1421.0 1421 86.3120 277 1584 1 chr4B.!!$R1 1307
5 TraesCS1B01G144100 chr4A 468210123 468211443 1320 True 1341.0 1341 85.3160 278 1579 1 chr4A.!!$R2 1301
6 TraesCS1B01G144100 chr4A 518855828 518857219 1391 False 1116.0 1116 81.5200 277 1683 1 chr4A.!!$F1 1406
7 TraesCS1B01G144100 chr4A 416226886 416227890 1004 True 761.0 761 80.5180 712 1749 1 chr4A.!!$R1 1037
8 TraesCS1B01G144100 chr4D 108048051 108049462 1411 False 757.0 841 87.4500 277 1584 2 chr4D.!!$F2 1307
9 TraesCS1B01G144100 chr4D 138417416 138417992 576 False 433.0 433 80.4640 1146 1744 1 chr4D.!!$F1 598
10 TraesCS1B01G144100 chr5A 281949773 281950752 979 False 773.0 773 81.0780 283 1297 1 chr5A.!!$F1 1014
11 TraesCS1B01G144100 chr3D 116088060 116088796 736 False 769.0 769 85.4820 637 1373 1 chr3D.!!$F1 736
12 TraesCS1B01G144100 chr5D 512389613 512390479 866 False 752.0 752 82.5220 850 1745 1 chr5D.!!$F1 895
13 TraesCS1B01G144100 chr3A 51696077 51697054 977 False 680.0 680 79.5840 560 1614 1 chr3A.!!$F1 1054
14 TraesCS1B01G144100 chr7A 238870908 238871437 529 True 636.0 636 88.3460 278 808 1 chr7A.!!$R1 530

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
207 208 0.107508 CATCGTGTCCCTTGCCTCAT 60.108 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 2071 0.104671 GCTCACTCCAGCCATCTCTC 59.895 60.0 0.0 0.0 32.76 3.2 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
38 39 1.761198 CGGAGGGTTTAGTCCTTAGGG 59.239 57.143 0.00 0.00 34.21 3.53
39 40 2.125233 GGAGGGTTTAGTCCTTAGGGG 58.875 57.143 0.00 0.00 34.21 4.79
40 41 2.125233 GAGGGTTTAGTCCTTAGGGGG 58.875 57.143 0.00 0.00 34.21 5.40
41 42 1.732247 AGGGTTTAGTCCTTAGGGGGA 59.268 52.381 0.00 0.00 35.33 4.81
52 53 5.843019 TCCTTAGGGGGACAATCATAATC 57.157 43.478 0.00 0.00 35.33 1.75
53 54 5.231552 TCCTTAGGGGGACAATCATAATCA 58.768 41.667 0.00 0.00 35.33 2.57
54 55 5.857283 TCCTTAGGGGGACAATCATAATCAT 59.143 40.000 0.00 0.00 35.33 2.45
55 56 6.012508 TCCTTAGGGGGACAATCATAATCATC 60.013 42.308 0.00 0.00 35.33 2.92
56 57 6.240263 CCTTAGGGGGACAATCATAATCATCA 60.240 42.308 0.00 0.00 0.00 3.07
57 58 5.873111 AGGGGGACAATCATAATCATCAT 57.127 39.130 0.00 0.00 0.00 2.45
58 59 6.975471 AGGGGGACAATCATAATCATCATA 57.025 37.500 0.00 0.00 0.00 2.15
59 60 6.966751 AGGGGGACAATCATAATCATCATAG 58.033 40.000 0.00 0.00 0.00 2.23
60 61 6.069206 AGGGGGACAATCATAATCATCATAGG 60.069 42.308 0.00 0.00 0.00 2.57
61 62 5.591877 GGGGACAATCATAATCATCATAGGC 59.408 44.000 0.00 0.00 0.00 3.93
62 63 6.421485 GGGACAATCATAATCATCATAGGCT 58.579 40.000 0.00 0.00 0.00 4.58
63 64 7.365921 GGGGACAATCATAATCATCATAGGCTA 60.366 40.741 0.00 0.00 0.00 3.93
64 65 7.714377 GGGACAATCATAATCATCATAGGCTAG 59.286 40.741 0.00 0.00 0.00 3.42
65 66 7.226325 GGACAATCATAATCATCATAGGCTAGC 59.774 40.741 6.04 6.04 0.00 3.42
66 67 7.052873 ACAATCATAATCATCATAGGCTAGCC 58.947 38.462 27.19 27.19 0.00 3.93
68 69 6.477053 TCATAATCATCATAGGCTAGCCTC 57.523 41.667 39.25 11.60 44.43 4.70
69 70 6.200852 TCATAATCATCATAGGCTAGCCTCT 58.799 40.000 39.25 27.41 44.43 3.69
70 71 7.357471 TCATAATCATCATAGGCTAGCCTCTA 58.643 38.462 39.25 24.06 44.43 2.43
71 72 7.505248 TCATAATCATCATAGGCTAGCCTCTAG 59.495 40.741 39.25 27.51 44.43 2.43
72 73 3.974719 TCATCATAGGCTAGCCTCTAGG 58.025 50.000 39.25 24.47 44.43 3.02
73 74 2.909504 TCATAGGCTAGCCTCTAGGG 57.090 55.000 39.25 23.18 44.43 3.53
74 75 2.074579 TCATAGGCTAGCCTCTAGGGT 58.925 52.381 39.25 17.06 44.43 4.34
75 76 2.451273 TCATAGGCTAGCCTCTAGGGTT 59.549 50.000 39.25 16.26 44.43 4.11
76 77 3.116707 TCATAGGCTAGCCTCTAGGGTTT 60.117 47.826 39.25 15.49 44.43 3.27
77 78 4.107473 TCATAGGCTAGCCTCTAGGGTTTA 59.893 45.833 39.25 19.30 44.43 2.01
78 79 2.965562 AGGCTAGCCTCTAGGGTTTAG 58.034 52.381 31.30 0.00 44.43 1.85
79 80 1.345089 GGCTAGCCTCTAGGGTTTAGC 59.655 57.143 27.17 12.55 44.81 3.09
80 81 1.345089 GCTAGCCTCTAGGGTTTAGCC 59.655 57.143 2.29 0.00 44.81 3.93
81 82 2.965562 CTAGCCTCTAGGGTTTAGCCT 58.034 52.381 5.96 5.72 44.81 4.58
82 83 1.796017 AGCCTCTAGGGTTTAGCCTC 58.204 55.000 3.32 0.00 44.81 4.70
83 84 1.292546 AGCCTCTAGGGTTTAGCCTCT 59.707 52.381 3.32 0.00 44.81 3.69
84 85 2.518834 AGCCTCTAGGGTTTAGCCTCTA 59.481 50.000 3.32 0.00 44.81 2.43
85 86 2.629137 GCCTCTAGGGTTTAGCCTCTAC 59.371 54.545 3.32 0.00 37.43 2.59
86 87 2.885894 CCTCTAGGGTTTAGCCTCTACG 59.114 54.545 3.32 0.00 37.43 3.51
87 88 3.434739 CCTCTAGGGTTTAGCCTCTACGA 60.435 52.174 3.32 0.00 37.43 3.43
88 89 4.400120 CTCTAGGGTTTAGCCTCTACGAT 58.600 47.826 3.32 0.00 37.43 3.73
89 90 4.396522 TCTAGGGTTTAGCCTCTACGATC 58.603 47.826 3.32 0.00 37.43 3.69
90 91 3.315880 AGGGTTTAGCCTCTACGATCT 57.684 47.619 0.00 0.00 37.43 2.75
91 92 3.224269 AGGGTTTAGCCTCTACGATCTC 58.776 50.000 0.00 0.00 37.43 2.75
92 93 2.030981 GGGTTTAGCCTCTACGATCTCG 60.031 54.545 0.00 0.00 40.54 4.04
93 94 4.551164 GGGTTTAGCCTCTACGATCTCGT 61.551 52.174 10.40 10.40 45.75 4.18
94 95 6.558908 GGGTTTAGCCTCTACGATCTCGTG 62.559 54.167 15.08 5.81 44.52 4.35
109 110 4.703645 TCTCGTGGTAGATCAACTCTTG 57.296 45.455 0.00 0.00 35.28 3.02
110 111 4.079970 TCTCGTGGTAGATCAACTCTTGT 58.920 43.478 0.00 0.00 35.28 3.16
111 112 5.250982 TCTCGTGGTAGATCAACTCTTGTA 58.749 41.667 0.00 0.00 35.28 2.41
112 113 5.708697 TCTCGTGGTAGATCAACTCTTGTAA 59.291 40.000 0.00 0.00 35.28 2.41
113 114 6.377429 TCTCGTGGTAGATCAACTCTTGTAAT 59.623 38.462 0.00 0.00 35.28 1.89
114 115 7.555195 TCTCGTGGTAGATCAACTCTTGTAATA 59.445 37.037 0.00 0.00 35.28 0.98
115 116 7.478322 TCGTGGTAGATCAACTCTTGTAATAC 58.522 38.462 0.00 0.00 35.28 1.89
116 117 7.338703 TCGTGGTAGATCAACTCTTGTAATACT 59.661 37.037 0.00 0.00 35.28 2.12
117 118 7.644551 CGTGGTAGATCAACTCTTGTAATACTC 59.355 40.741 0.00 0.00 35.28 2.59
118 119 8.467598 GTGGTAGATCAACTCTTGTAATACTCA 58.532 37.037 0.00 0.00 35.28 3.41
119 120 9.201989 TGGTAGATCAACTCTTGTAATACTCAT 57.798 33.333 0.00 0.00 35.28 2.90
139 140 8.325421 ACTCATATCATCAAGATCAATCAAGC 57.675 34.615 0.00 0.00 38.19 4.01
140 141 7.937394 ACTCATATCATCAAGATCAATCAAGCA 59.063 33.333 0.00 0.00 38.19 3.91
141 142 8.324163 TCATATCATCAAGATCAATCAAGCAG 57.676 34.615 0.00 0.00 38.19 4.24
142 143 7.390718 TCATATCATCAAGATCAATCAAGCAGG 59.609 37.037 0.00 0.00 38.19 4.85
143 144 5.106876 TCATCAAGATCAATCAAGCAGGA 57.893 39.130 0.00 0.00 0.00 3.86
144 145 5.503002 TCATCAAGATCAATCAAGCAGGAA 58.497 37.500 0.00 0.00 0.00 3.36
145 146 5.589050 TCATCAAGATCAATCAAGCAGGAAG 59.411 40.000 0.00 0.00 0.00 3.46
146 147 4.914983 TCAAGATCAATCAAGCAGGAAGT 58.085 39.130 0.00 0.00 0.00 3.01
147 148 6.053632 TCAAGATCAATCAAGCAGGAAGTA 57.946 37.500 0.00 0.00 0.00 2.24
148 149 6.111382 TCAAGATCAATCAAGCAGGAAGTAG 58.889 40.000 0.00 0.00 0.00 2.57
149 150 5.033589 AGATCAATCAAGCAGGAAGTAGG 57.966 43.478 0.00 0.00 0.00 3.18
150 151 3.634397 TCAATCAAGCAGGAAGTAGGG 57.366 47.619 0.00 0.00 0.00 3.53
151 152 2.912956 TCAATCAAGCAGGAAGTAGGGT 59.087 45.455 0.00 0.00 0.00 4.34
152 153 3.330701 TCAATCAAGCAGGAAGTAGGGTT 59.669 43.478 0.00 0.00 0.00 4.11
153 154 4.082125 CAATCAAGCAGGAAGTAGGGTTT 58.918 43.478 0.00 0.00 0.00 3.27
154 155 3.876309 TCAAGCAGGAAGTAGGGTTTT 57.124 42.857 0.00 0.00 0.00 2.43
155 156 4.986054 TCAAGCAGGAAGTAGGGTTTTA 57.014 40.909 0.00 0.00 0.00 1.52
156 157 4.648651 TCAAGCAGGAAGTAGGGTTTTAC 58.351 43.478 0.00 0.00 0.00 2.01
157 158 3.715638 AGCAGGAAGTAGGGTTTTACC 57.284 47.619 0.00 0.00 37.60 2.85
158 159 3.257578 AGCAGGAAGTAGGGTTTTACCT 58.742 45.455 0.00 0.00 44.75 3.08
159 160 3.263681 AGCAGGAAGTAGGGTTTTACCTC 59.736 47.826 0.00 0.00 42.09 3.85
160 161 3.621709 GCAGGAAGTAGGGTTTTACCTCC 60.622 52.174 0.00 0.00 42.09 4.30
161 162 3.585732 CAGGAAGTAGGGTTTTACCTCCA 59.414 47.826 4.23 0.00 42.09 3.86
162 163 4.227527 CAGGAAGTAGGGTTTTACCTCCAT 59.772 45.833 4.23 0.00 42.09 3.41
163 164 4.473922 AGGAAGTAGGGTTTTACCTCCATC 59.526 45.833 4.23 0.00 42.09 3.51
164 165 4.473922 GGAAGTAGGGTTTTACCTCCATCT 59.526 45.833 0.00 0.00 42.09 2.90
165 166 5.664457 GGAAGTAGGGTTTTACCTCCATCTA 59.336 44.000 0.00 0.00 42.09 1.98
166 167 6.183360 GGAAGTAGGGTTTTACCTCCATCTAG 60.183 46.154 0.00 0.00 42.09 2.43
167 168 6.101274 AGTAGGGTTTTACCTCCATCTAGA 57.899 41.667 0.00 0.00 42.09 2.43
168 169 6.137559 AGTAGGGTTTTACCTCCATCTAGAG 58.862 44.000 0.00 0.00 42.09 2.43
174 175 3.784573 CTCCATCTAGAGGGCCCG 58.215 66.667 18.79 1.05 31.15 6.13
175 176 1.153989 CTCCATCTAGAGGGCCCGA 59.846 63.158 18.79 8.04 31.15 5.14
176 177 0.470080 CTCCATCTAGAGGGCCCGAA 60.470 60.000 18.79 4.66 31.15 4.30
177 178 0.759436 TCCATCTAGAGGGCCCGAAC 60.759 60.000 18.79 12.45 31.15 3.95
178 179 1.749033 CATCTAGAGGGCCCGAACC 59.251 63.158 18.44 7.31 0.00 3.62
179 180 0.760945 CATCTAGAGGGCCCGAACCT 60.761 60.000 18.44 14.72 42.18 3.50
180 181 0.760945 ATCTAGAGGGCCCGAACCTG 60.761 60.000 18.44 6.16 38.79 4.00
181 182 2.365105 TAGAGGGCCCGAACCTGG 60.365 66.667 18.44 0.00 38.79 4.45
189 190 3.729726 CCCGAACCTGGGTAAAACA 57.270 52.632 0.00 0.00 44.76 2.83
190 191 2.209690 CCCGAACCTGGGTAAAACAT 57.790 50.000 0.00 0.00 44.76 2.71
191 192 2.089201 CCCGAACCTGGGTAAAACATC 58.911 52.381 0.00 0.00 44.76 3.06
192 193 1.735571 CCGAACCTGGGTAAAACATCG 59.264 52.381 0.00 0.00 0.00 3.84
193 194 2.419667 CGAACCTGGGTAAAACATCGT 58.580 47.619 0.00 0.00 0.00 3.73
194 195 2.158841 CGAACCTGGGTAAAACATCGTG 59.841 50.000 0.00 0.00 0.00 4.35
195 196 2.943036 ACCTGGGTAAAACATCGTGT 57.057 45.000 0.00 0.00 0.00 4.49
196 197 2.774687 ACCTGGGTAAAACATCGTGTC 58.225 47.619 0.00 0.00 0.00 3.67
197 198 2.081462 CCTGGGTAAAACATCGTGTCC 58.919 52.381 0.00 0.00 0.00 4.02
198 199 2.081462 CTGGGTAAAACATCGTGTCCC 58.919 52.381 0.00 0.00 0.00 4.46
199 200 1.700739 TGGGTAAAACATCGTGTCCCT 59.299 47.619 11.28 0.00 35.00 4.20
200 201 2.106857 TGGGTAAAACATCGTGTCCCTT 59.893 45.455 11.28 2.23 35.00 3.95
201 202 2.486592 GGGTAAAACATCGTGTCCCTTG 59.513 50.000 0.00 0.00 0.00 3.61
202 203 2.095415 GGTAAAACATCGTGTCCCTTGC 60.095 50.000 0.00 0.00 0.00 4.01
203 204 0.958822 AAAACATCGTGTCCCTTGCC 59.041 50.000 0.00 0.00 0.00 4.52
204 205 0.110486 AAACATCGTGTCCCTTGCCT 59.890 50.000 0.00 0.00 0.00 4.75
205 206 0.321653 AACATCGTGTCCCTTGCCTC 60.322 55.000 0.00 0.00 0.00 4.70
206 207 1.296392 CATCGTGTCCCTTGCCTCA 59.704 57.895 0.00 0.00 0.00 3.86
207 208 0.107508 CATCGTGTCCCTTGCCTCAT 60.108 55.000 0.00 0.00 0.00 2.90
208 209 0.107508 ATCGTGTCCCTTGCCTCATG 60.108 55.000 0.00 0.00 0.00 3.07
209 210 1.003355 CGTGTCCCTTGCCTCATGT 60.003 57.895 0.00 0.00 0.00 3.21
210 211 0.606401 CGTGTCCCTTGCCTCATGTT 60.606 55.000 0.00 0.00 0.00 2.71
211 212 1.338674 CGTGTCCCTTGCCTCATGTTA 60.339 52.381 0.00 0.00 0.00 2.41
212 213 2.084546 GTGTCCCTTGCCTCATGTTAC 58.915 52.381 0.00 0.00 0.00 2.50
213 214 1.004277 TGTCCCTTGCCTCATGTTACC 59.996 52.381 0.00 0.00 0.00 2.85
214 215 1.004277 GTCCCTTGCCTCATGTTACCA 59.996 52.381 0.00 0.00 0.00 3.25
215 216 1.922447 TCCCTTGCCTCATGTTACCAT 59.078 47.619 0.00 0.00 0.00 3.55
216 217 2.311542 TCCCTTGCCTCATGTTACCATT 59.688 45.455 0.00 0.00 0.00 3.16
217 218 3.525609 TCCCTTGCCTCATGTTACCATTA 59.474 43.478 0.00 0.00 0.00 1.90
218 219 3.885297 CCCTTGCCTCATGTTACCATTAG 59.115 47.826 0.00 0.00 0.00 1.73
219 220 3.316308 CCTTGCCTCATGTTACCATTAGC 59.684 47.826 0.00 0.00 0.00 3.09
220 221 2.930950 TGCCTCATGTTACCATTAGCC 58.069 47.619 0.00 0.00 0.00 3.93
221 222 2.509548 TGCCTCATGTTACCATTAGCCT 59.490 45.455 0.00 0.00 0.00 4.58
222 223 3.053693 TGCCTCATGTTACCATTAGCCTT 60.054 43.478 0.00 0.00 0.00 4.35
223 224 4.165180 TGCCTCATGTTACCATTAGCCTTA 59.835 41.667 0.00 0.00 0.00 2.69
224 225 4.757149 GCCTCATGTTACCATTAGCCTTAG 59.243 45.833 0.00 0.00 0.00 2.18
225 226 5.454755 GCCTCATGTTACCATTAGCCTTAGA 60.455 44.000 0.00 0.00 0.00 2.10
226 227 5.992217 CCTCATGTTACCATTAGCCTTAGAC 59.008 44.000 0.00 0.00 0.00 2.59
227 228 5.597806 TCATGTTACCATTAGCCTTAGACG 58.402 41.667 0.00 0.00 0.00 4.18
228 229 3.788937 TGTTACCATTAGCCTTAGACGC 58.211 45.455 0.00 0.00 0.00 5.19
229 230 3.196039 TGTTACCATTAGCCTTAGACGCA 59.804 43.478 0.00 0.00 0.00 5.24
230 231 4.141801 TGTTACCATTAGCCTTAGACGCAT 60.142 41.667 0.00 0.00 0.00 4.73
231 232 5.069383 TGTTACCATTAGCCTTAGACGCATA 59.931 40.000 0.00 0.00 0.00 3.14
232 233 4.258702 ACCATTAGCCTTAGACGCATAG 57.741 45.455 0.00 0.00 0.00 2.23
233 234 3.895656 ACCATTAGCCTTAGACGCATAGA 59.104 43.478 0.00 0.00 0.00 1.98
234 235 4.528596 ACCATTAGCCTTAGACGCATAGAT 59.471 41.667 0.00 0.00 0.00 1.98
235 236 5.105752 CCATTAGCCTTAGACGCATAGATC 58.894 45.833 0.00 0.00 0.00 2.75
236 237 2.999507 AGCCTTAGACGCATAGATCG 57.000 50.000 0.00 0.00 0.00 3.69
237 238 1.542030 AGCCTTAGACGCATAGATCGG 59.458 52.381 0.00 0.00 0.00 4.18
238 239 1.402984 GCCTTAGACGCATAGATCGGG 60.403 57.143 0.00 0.00 0.00 5.14
239 240 2.160205 CCTTAGACGCATAGATCGGGA 58.840 52.381 0.00 0.00 0.00 5.14
240 241 2.095161 CCTTAGACGCATAGATCGGGAC 60.095 54.545 0.00 0.00 0.00 4.46
241 242 1.531423 TAGACGCATAGATCGGGACC 58.469 55.000 0.00 0.00 0.00 4.46
242 243 1.179814 AGACGCATAGATCGGGACCC 61.180 60.000 0.00 0.00 0.00 4.46
243 244 2.156051 GACGCATAGATCGGGACCCC 62.156 65.000 4.46 0.00 0.00 4.95
244 245 2.943978 CGCATAGATCGGGACCCCC 61.944 68.421 4.46 0.00 41.09 5.40
245 246 1.536662 GCATAGATCGGGACCCCCT 60.537 63.158 4.46 2.38 42.67 4.79
246 247 0.252103 GCATAGATCGGGACCCCCTA 60.252 60.000 4.46 4.72 42.67 3.53
247 248 1.558233 CATAGATCGGGACCCCCTAC 58.442 60.000 4.46 0.00 42.67 3.18
248 249 0.412640 ATAGATCGGGACCCCCTACC 59.587 60.000 4.46 0.00 42.67 3.18
249 250 1.733387 TAGATCGGGACCCCCTACCC 61.733 65.000 4.46 0.00 42.67 3.69
253 254 3.759101 GGGACCCCCTACCCGAGA 61.759 72.222 0.00 0.00 41.34 4.04
254 255 2.613421 GGACCCCCTACCCGAGAT 59.387 66.667 0.00 0.00 0.00 2.75
255 256 1.533513 GGACCCCCTACCCGAGATC 60.534 68.421 0.00 0.00 0.00 2.75
256 257 1.542679 GACCCCCTACCCGAGATCT 59.457 63.158 0.00 0.00 0.00 2.75
257 258 0.828343 GACCCCCTACCCGAGATCTG 60.828 65.000 0.00 0.00 0.00 2.90
258 259 2.210711 CCCCCTACCCGAGATCTGC 61.211 68.421 0.00 0.00 0.00 4.26
259 260 2.210711 CCCCTACCCGAGATCTGCC 61.211 68.421 0.00 0.00 0.00 4.85
260 261 2.565645 CCCTACCCGAGATCTGCCG 61.566 68.421 0.00 0.00 0.00 5.69
261 262 2.565645 CCTACCCGAGATCTGCCGG 61.566 68.421 14.42 14.42 44.94 6.13
262 263 1.828660 CTACCCGAGATCTGCCGGT 60.829 63.158 18.55 13.92 43.93 5.28
263 264 1.380785 TACCCGAGATCTGCCGGTT 60.381 57.895 18.55 9.56 43.93 4.44
264 265 0.974010 TACCCGAGATCTGCCGGTTT 60.974 55.000 18.55 9.73 43.93 3.27
265 266 1.078426 CCCGAGATCTGCCGGTTTT 60.078 57.895 18.55 0.00 43.93 2.43
266 267 1.369091 CCCGAGATCTGCCGGTTTTG 61.369 60.000 18.55 3.10 43.93 2.44
267 268 0.391130 CCGAGATCTGCCGGTTTTGA 60.391 55.000 13.39 0.00 40.78 2.69
268 269 0.721718 CGAGATCTGCCGGTTTTGAC 59.278 55.000 0.00 0.00 0.00 3.18
269 270 1.808411 GAGATCTGCCGGTTTTGACA 58.192 50.000 0.00 0.00 0.00 3.58
270 271 1.464997 GAGATCTGCCGGTTTTGACAC 59.535 52.381 0.00 0.00 0.00 3.67
271 272 1.072331 AGATCTGCCGGTTTTGACACT 59.928 47.619 1.90 0.00 0.00 3.55
272 273 1.197721 GATCTGCCGGTTTTGACACTG 59.802 52.381 1.90 0.00 0.00 3.66
273 274 0.179234 TCTGCCGGTTTTGACACTGA 59.821 50.000 1.90 0.00 0.00 3.41
274 275 0.307760 CTGCCGGTTTTGACACTGAC 59.692 55.000 1.90 0.00 0.00 3.51
275 276 0.393132 TGCCGGTTTTGACACTGACA 60.393 50.000 1.90 0.00 0.00 3.58
339 340 0.712380 ATGGCCCAAGGAAGGATGTT 59.288 50.000 0.00 0.00 0.00 2.71
662 673 2.308866 AGTGATCTTTGGGGTGGGTAAG 59.691 50.000 0.00 0.00 0.00 2.34
710 748 6.869315 TTAATGTCGATGAACCTTTGAACA 57.131 33.333 0.00 0.00 0.00 3.18
820 1015 0.750911 CATGGAGAAGGGCAAGGAGC 60.751 60.000 0.00 0.00 44.65 4.70
822 1017 1.136329 TGGAGAAGGGCAAGGAGCTT 61.136 55.000 0.00 0.00 44.79 3.74
950 1159 2.484868 TACCATGAGGAGGGTGGGCA 62.485 60.000 0.00 0.00 36.73 5.36
1065 1276 2.866762 GTTCAAGCTCAAGACGAACACT 59.133 45.455 0.00 0.00 36.75 3.55
1195 1409 1.410932 CCTTCAAGTTGTTGACCCCCA 60.411 52.381 2.11 0.00 42.60 4.96
1447 1678 6.012658 TGTTAAATTGCTTACTCCTTGCTG 57.987 37.500 0.00 0.00 0.00 4.41
1524 1766 1.515081 CTCGCCGAAAAGGTTACCAA 58.485 50.000 3.51 0.00 43.70 3.67
1565 1811 2.159114 ACCAAACACCATGCTTTGTGTC 60.159 45.455 9.51 0.00 44.53 3.67
1659 1906 4.261489 GGCAATCAAACTAGATGCAGATGG 60.261 45.833 0.00 0.00 0.00 3.51
1660 1907 4.577693 GCAATCAAACTAGATGCAGATGGA 59.422 41.667 0.00 0.00 0.00 3.41
1704 1959 0.739813 CGAGGCCGGATTTCGAAGTT 60.740 55.000 5.05 0.00 42.43 2.66
1758 2013 8.626526 AGAACCAAACACGTTCTTATGTATTTT 58.373 29.630 0.00 0.00 46.01 1.82
1816 2071 2.667473 ATAGGGTCAGTCGGTTTTCG 57.333 50.000 0.00 0.00 40.90 3.46
1826 2081 0.895530 TCGGTTTTCGAGAGATGGCT 59.104 50.000 0.00 0.00 43.74 4.75
1859 2114 4.719273 CAGAGGTAAGGAAGGAGAAGGAAT 59.281 45.833 0.00 0.00 0.00 3.01
1868 2123 1.524849 GAGAAGGAATGGGCTCGCC 60.525 63.158 0.00 0.00 0.00 5.54
1902 2157 5.070580 CCCCAGTATCTAACTTAGGGTTCAG 59.929 48.000 0.00 0.00 41.56 3.02
1909 2164 0.195096 ACTTAGGGTTCAGGGTGGGA 59.805 55.000 0.00 0.00 0.00 4.37
1994 2249 1.288752 GCGAGCCTAGAGAGATGGC 59.711 63.158 0.00 0.00 46.42 4.40
2000 2255 1.153989 CTAGAGAGATGGCCGGGGA 59.846 63.158 2.18 0.00 0.00 4.81
2022 2277 4.509737 GGCTAGACCGTCGGTGGC 62.510 72.222 24.45 21.13 35.25 5.01
2048 2327 3.112709 GGTGCACTTCGTCGGAGC 61.113 66.667 17.98 0.00 0.00 4.70
2066 2346 1.611977 AGCAAAACTTAAACGAGGGCC 59.388 47.619 0.00 0.00 0.00 5.80
2082 2362 2.122813 CCGGCCTAGAGGGATGGT 60.123 66.667 0.00 0.00 37.23 3.55
2133 2413 4.043100 GTTTCGGGGAGGGTGGGG 62.043 72.222 0.00 0.00 0.00 4.96
2170 2450 4.697756 CGGGTGGTGGTCGCATGT 62.698 66.667 0.00 0.00 0.00 3.21
2175 2455 1.152860 TGGTGGTCGCATGTGGTTT 60.153 52.632 6.39 0.00 0.00 3.27
2216 2496 4.792704 GCGGCTAGAGAAGAAGAAGAGATG 60.793 50.000 0.00 0.00 0.00 2.90
2232 2512 3.709141 AGAGATGGAGGTAGAAGAAAGGC 59.291 47.826 0.00 0.00 0.00 4.35
2237 2517 0.546988 AGGTAGAAGAAAGGCCGGGT 60.547 55.000 2.18 0.00 0.00 5.28
2257 2537 3.365832 GTGCCGTTAGATTTCGATCGTA 58.634 45.455 15.94 1.77 0.00 3.43
2279 2559 3.002965 ACGTTTGAAAAATCGACTGACCC 59.997 43.478 0.00 0.00 0.00 4.46
2283 2563 4.459390 TGAAAAATCGACTGACCCGATA 57.541 40.909 0.00 0.00 44.85 2.92
2284 2564 4.430007 TGAAAAATCGACTGACCCGATAG 58.570 43.478 0.00 0.00 44.85 2.08
2285 2565 2.510768 AAATCGACTGACCCGATAGC 57.489 50.000 0.00 0.00 44.85 2.97
2286 2566 0.674534 AATCGACTGACCCGATAGCC 59.325 55.000 0.00 0.00 44.85 3.93
2287 2567 0.178987 ATCGACTGACCCGATAGCCT 60.179 55.000 0.00 0.00 43.93 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.899980 ACCCTCCGGTTTATATAGACACC 59.100 47.826 0.00 2.59 40.58 4.16
17 18 1.761198 CCTAAGGACTAAACCCTCCGG 59.239 57.143 0.00 0.00 32.57 5.14
18 19 1.761198 CCCTAAGGACTAAACCCTCCG 59.239 57.143 0.00 0.00 32.57 4.63
19 20 2.125233 CCCCTAAGGACTAAACCCTCC 58.875 57.143 0.00 0.00 38.24 4.30
20 21 2.125233 CCCCCTAAGGACTAAACCCTC 58.875 57.143 0.00 0.00 38.24 4.30
21 22 1.732247 TCCCCCTAAGGACTAAACCCT 59.268 52.381 0.00 0.00 38.24 4.34
22 23 2.275361 TCCCCCTAAGGACTAAACCC 57.725 55.000 0.00 0.00 38.24 4.11
30 31 5.231552 TGATTATGATTGTCCCCCTAAGGA 58.768 41.667 0.00 0.00 38.24 3.36
31 32 5.582950 TGATTATGATTGTCCCCCTAAGG 57.417 43.478 0.00 0.00 0.00 2.69
32 33 6.782986 TGATGATTATGATTGTCCCCCTAAG 58.217 40.000 0.00 0.00 0.00 2.18
33 34 6.778542 TGATGATTATGATTGTCCCCCTAA 57.221 37.500 0.00 0.00 0.00 2.69
34 35 6.975471 ATGATGATTATGATTGTCCCCCTA 57.025 37.500 0.00 0.00 0.00 3.53
35 36 5.873111 ATGATGATTATGATTGTCCCCCT 57.127 39.130 0.00 0.00 0.00 4.79
36 37 6.125029 CCTATGATGATTATGATTGTCCCCC 58.875 44.000 0.00 0.00 0.00 5.40
37 38 5.591877 GCCTATGATGATTATGATTGTCCCC 59.408 44.000 0.00 0.00 0.00 4.81
38 39 6.421485 AGCCTATGATGATTATGATTGTCCC 58.579 40.000 0.00 0.00 0.00 4.46
39 40 7.226325 GCTAGCCTATGATGATTATGATTGTCC 59.774 40.741 2.29 0.00 0.00 4.02
40 41 7.226325 GGCTAGCCTATGATGATTATGATTGTC 59.774 40.741 27.17 0.00 0.00 3.18
41 42 7.052873 GGCTAGCCTATGATGATTATGATTGT 58.947 38.462 27.17 0.00 0.00 2.71
42 43 7.281098 AGGCTAGCCTATGATGATTATGATTG 58.719 38.462 35.28 0.00 46.14 2.67
43 44 7.448915 AGGCTAGCCTATGATGATTATGATT 57.551 36.000 35.28 4.24 46.14 2.57
59 60 1.345089 GCTAAACCCTAGAGGCTAGCC 59.655 57.143 27.19 27.19 41.49 3.93
60 61 1.345089 GGCTAAACCCTAGAGGCTAGC 59.655 57.143 6.04 6.04 44.42 3.42
61 62 2.894765 GAGGCTAAACCCTAGAGGCTAG 59.105 54.545 4.67 0.00 45.30 3.42
62 63 2.518834 AGAGGCTAAACCCTAGAGGCTA 59.481 50.000 4.67 0.00 45.30 3.93
64 65 1.796017 AGAGGCTAAACCCTAGAGGC 58.204 55.000 0.00 0.00 40.58 4.70
65 66 2.885894 CGTAGAGGCTAAACCCTAGAGG 59.114 54.545 0.00 0.00 40.58 3.69
66 67 3.818180 TCGTAGAGGCTAAACCCTAGAG 58.182 50.000 0.00 0.00 40.58 2.43
67 68 3.939740 TCGTAGAGGCTAAACCCTAGA 57.060 47.619 0.00 0.00 40.58 2.43
68 69 4.400120 AGATCGTAGAGGCTAAACCCTAG 58.600 47.826 0.00 0.00 43.63 3.02
69 70 4.396522 GAGATCGTAGAGGCTAAACCCTA 58.603 47.826 0.00 0.00 43.63 3.53
70 71 3.224269 GAGATCGTAGAGGCTAAACCCT 58.776 50.000 0.00 0.00 43.63 4.34
71 72 2.030981 CGAGATCGTAGAGGCTAAACCC 60.031 54.545 0.00 0.00 43.63 4.11
72 73 3.270962 CGAGATCGTAGAGGCTAAACC 57.729 52.381 0.00 0.00 43.63 3.27
87 88 4.707448 ACAAGAGTTGATCTACCACGAGAT 59.293 41.667 3.54 0.00 37.23 2.75
88 89 4.079970 ACAAGAGTTGATCTACCACGAGA 58.920 43.478 3.54 0.00 37.23 4.04
89 90 4.442375 ACAAGAGTTGATCTACCACGAG 57.558 45.455 3.54 1.07 37.23 4.18
90 91 5.970317 TTACAAGAGTTGATCTACCACGA 57.030 39.130 3.54 0.00 37.23 4.35
91 92 7.481642 AGTATTACAAGAGTTGATCTACCACG 58.518 38.462 3.54 0.00 37.23 4.94
92 93 8.467598 TGAGTATTACAAGAGTTGATCTACCAC 58.532 37.037 3.54 0.00 37.23 4.16
93 94 8.589701 TGAGTATTACAAGAGTTGATCTACCA 57.410 34.615 3.54 0.00 37.23 3.25
113 114 9.433153 GCTTGATTGATCTTGATGATATGAGTA 57.567 33.333 0.00 0.00 35.14 2.59
114 115 7.937394 TGCTTGATTGATCTTGATGATATGAGT 59.063 33.333 0.00 0.00 35.14 3.41
115 116 8.324163 TGCTTGATTGATCTTGATGATATGAG 57.676 34.615 0.00 0.00 35.14 2.90
116 117 7.390718 CCTGCTTGATTGATCTTGATGATATGA 59.609 37.037 0.00 0.00 35.14 2.15
117 118 7.390718 TCCTGCTTGATTGATCTTGATGATATG 59.609 37.037 0.00 0.00 35.14 1.78
118 119 7.459234 TCCTGCTTGATTGATCTTGATGATAT 58.541 34.615 0.00 0.00 35.14 1.63
119 120 6.834107 TCCTGCTTGATTGATCTTGATGATA 58.166 36.000 0.00 0.00 35.14 2.15
120 121 5.691896 TCCTGCTTGATTGATCTTGATGAT 58.308 37.500 0.00 0.00 38.27 2.45
121 122 5.106876 TCCTGCTTGATTGATCTTGATGA 57.893 39.130 0.00 0.00 0.00 2.92
122 123 5.357314 ACTTCCTGCTTGATTGATCTTGATG 59.643 40.000 0.00 0.00 0.00 3.07
123 124 5.507637 ACTTCCTGCTTGATTGATCTTGAT 58.492 37.500 0.00 0.00 0.00 2.57
124 125 4.914983 ACTTCCTGCTTGATTGATCTTGA 58.085 39.130 0.00 0.00 0.00 3.02
125 126 5.296283 CCTACTTCCTGCTTGATTGATCTTG 59.704 44.000 0.00 0.00 0.00 3.02
126 127 5.435291 CCTACTTCCTGCTTGATTGATCTT 58.565 41.667 0.00 0.00 0.00 2.40
127 128 4.141528 CCCTACTTCCTGCTTGATTGATCT 60.142 45.833 0.00 0.00 0.00 2.75
128 129 4.133078 CCCTACTTCCTGCTTGATTGATC 58.867 47.826 0.00 0.00 0.00 2.92
129 130 3.525199 ACCCTACTTCCTGCTTGATTGAT 59.475 43.478 0.00 0.00 0.00 2.57
130 131 2.912956 ACCCTACTTCCTGCTTGATTGA 59.087 45.455 0.00 0.00 0.00 2.57
131 132 3.356529 ACCCTACTTCCTGCTTGATTG 57.643 47.619 0.00 0.00 0.00 2.67
132 133 4.388577 AAACCCTACTTCCTGCTTGATT 57.611 40.909 0.00 0.00 0.00 2.57
133 134 4.388577 AAAACCCTACTTCCTGCTTGAT 57.611 40.909 0.00 0.00 0.00 2.57
134 135 3.876309 AAAACCCTACTTCCTGCTTGA 57.124 42.857 0.00 0.00 0.00 3.02
135 136 3.756963 GGTAAAACCCTACTTCCTGCTTG 59.243 47.826 0.00 0.00 30.04 4.01
136 137 3.656264 AGGTAAAACCCTACTTCCTGCTT 59.344 43.478 0.00 0.00 39.75 3.91
137 138 3.257578 AGGTAAAACCCTACTTCCTGCT 58.742 45.455 0.00 0.00 39.75 4.24
138 139 3.607741 GAGGTAAAACCCTACTTCCTGC 58.392 50.000 0.00 0.00 39.75 4.85
139 140 3.585732 TGGAGGTAAAACCCTACTTCCTG 59.414 47.826 11.71 0.00 44.50 3.86
140 141 3.878086 TGGAGGTAAAACCCTACTTCCT 58.122 45.455 11.71 0.00 44.50 3.36
141 142 4.473922 AGATGGAGGTAAAACCCTACTTCC 59.526 45.833 5.26 5.26 44.47 3.46
142 143 5.695424 AGATGGAGGTAAAACCCTACTTC 57.305 43.478 0.00 0.00 39.75 3.01
143 144 6.509386 TCTAGATGGAGGTAAAACCCTACTT 58.491 40.000 0.00 0.00 39.75 2.24
144 145 6.101274 TCTAGATGGAGGTAAAACCCTACT 57.899 41.667 0.00 0.00 39.75 2.57
145 146 5.304871 CCTCTAGATGGAGGTAAAACCCTAC 59.695 48.000 4.16 0.00 45.65 3.18
146 147 5.464984 CCTCTAGATGGAGGTAAAACCCTA 58.535 45.833 4.16 0.00 45.65 3.53
147 148 4.299485 CCTCTAGATGGAGGTAAAACCCT 58.701 47.826 4.16 0.00 45.65 4.34
148 149 4.691326 CCTCTAGATGGAGGTAAAACCC 57.309 50.000 4.16 0.00 45.65 4.11
157 158 0.470080 TTCGGGCCCTCTAGATGGAG 60.470 60.000 22.43 7.97 0.00 3.86
158 159 0.759436 GTTCGGGCCCTCTAGATGGA 60.759 60.000 22.43 3.53 0.00 3.41
159 160 1.749033 GTTCGGGCCCTCTAGATGG 59.251 63.158 22.43 9.58 0.00 3.51
160 161 0.760945 AGGTTCGGGCCCTCTAGATG 60.761 60.000 22.43 1.43 0.00 2.90
161 162 0.760945 CAGGTTCGGGCCCTCTAGAT 60.761 60.000 22.43 0.00 0.00 1.98
162 163 1.381327 CAGGTTCGGGCCCTCTAGA 60.381 63.158 22.43 6.61 0.00 2.43
163 164 2.435693 CCAGGTTCGGGCCCTCTAG 61.436 68.421 22.43 3.67 0.00 2.43
164 165 2.365105 CCAGGTTCGGGCCCTCTA 60.365 66.667 22.43 1.45 0.00 2.43
172 173 1.735571 CGATGTTTTACCCAGGTTCGG 59.264 52.381 0.00 0.00 0.00 4.30
173 174 2.158841 CACGATGTTTTACCCAGGTTCG 59.841 50.000 0.00 0.00 0.00 3.95
174 175 3.143728 ACACGATGTTTTACCCAGGTTC 58.856 45.455 0.00 0.00 0.00 3.62
175 176 3.143728 GACACGATGTTTTACCCAGGTT 58.856 45.455 0.00 0.00 0.00 3.50
176 177 2.551504 GGACACGATGTTTTACCCAGGT 60.552 50.000 0.00 0.00 0.00 4.00
177 178 2.081462 GGACACGATGTTTTACCCAGG 58.919 52.381 0.00 0.00 0.00 4.45
178 179 2.081462 GGGACACGATGTTTTACCCAG 58.919 52.381 0.00 0.00 32.58 4.45
179 180 1.700739 AGGGACACGATGTTTTACCCA 59.299 47.619 0.00 0.00 34.20 4.51
180 181 2.484742 AGGGACACGATGTTTTACCC 57.515 50.000 0.00 0.00 32.49 3.69
181 182 2.095415 GCAAGGGACACGATGTTTTACC 60.095 50.000 0.00 0.00 0.00 2.85
182 183 2.095415 GGCAAGGGACACGATGTTTTAC 60.095 50.000 0.00 0.00 0.00 2.01
183 184 2.156098 GGCAAGGGACACGATGTTTTA 58.844 47.619 0.00 0.00 0.00 1.52
184 185 0.958822 GGCAAGGGACACGATGTTTT 59.041 50.000 0.00 0.00 0.00 2.43
185 186 0.110486 AGGCAAGGGACACGATGTTT 59.890 50.000 0.00 0.00 0.00 2.83
186 187 0.321653 GAGGCAAGGGACACGATGTT 60.322 55.000 0.00 0.00 0.00 2.71
187 188 1.296715 GAGGCAAGGGACACGATGT 59.703 57.895 0.00 0.00 0.00 3.06
188 189 0.107508 ATGAGGCAAGGGACACGATG 60.108 55.000 0.00 0.00 0.00 3.84
189 190 0.107508 CATGAGGCAAGGGACACGAT 60.108 55.000 0.00 0.00 0.00 3.73
190 191 1.296392 CATGAGGCAAGGGACACGA 59.704 57.895 0.00 0.00 0.00 4.35
191 192 0.606401 AACATGAGGCAAGGGACACG 60.606 55.000 0.00 0.00 0.00 4.49
192 193 2.084546 GTAACATGAGGCAAGGGACAC 58.915 52.381 0.00 0.00 0.00 3.67
193 194 1.004277 GGTAACATGAGGCAAGGGACA 59.996 52.381 0.00 0.00 0.00 4.02
194 195 1.004277 TGGTAACATGAGGCAAGGGAC 59.996 52.381 0.00 0.00 46.17 4.46
195 196 1.367346 TGGTAACATGAGGCAAGGGA 58.633 50.000 0.00 0.00 46.17 4.20
196 197 3.976704 TGGTAACATGAGGCAAGGG 57.023 52.632 0.00 0.00 46.17 3.95
208 209 3.788937 TGCGTCTAAGGCTAATGGTAAC 58.211 45.455 0.00 0.00 0.00 2.50
209 210 4.682778 ATGCGTCTAAGGCTAATGGTAA 57.317 40.909 0.00 0.00 0.00 2.85
210 211 5.074804 TCTATGCGTCTAAGGCTAATGGTA 58.925 41.667 0.00 0.00 0.00 3.25
211 212 3.895656 TCTATGCGTCTAAGGCTAATGGT 59.104 43.478 0.00 0.00 0.00 3.55
212 213 4.521130 TCTATGCGTCTAAGGCTAATGG 57.479 45.455 0.00 0.00 0.00 3.16
213 214 4.795795 CGATCTATGCGTCTAAGGCTAATG 59.204 45.833 0.00 0.00 0.00 1.90
214 215 4.142359 CCGATCTATGCGTCTAAGGCTAAT 60.142 45.833 0.00 0.00 0.00 1.73
215 216 3.190744 CCGATCTATGCGTCTAAGGCTAA 59.809 47.826 0.00 0.00 0.00 3.09
216 217 2.747989 CCGATCTATGCGTCTAAGGCTA 59.252 50.000 0.00 0.00 0.00 3.93
217 218 1.542030 CCGATCTATGCGTCTAAGGCT 59.458 52.381 0.00 0.00 0.00 4.58
218 219 1.402984 CCCGATCTATGCGTCTAAGGC 60.403 57.143 0.00 0.00 0.00 4.35
219 220 2.095161 GTCCCGATCTATGCGTCTAAGG 60.095 54.545 0.00 0.00 0.00 2.69
220 221 2.095161 GGTCCCGATCTATGCGTCTAAG 60.095 54.545 0.00 0.00 0.00 2.18
221 222 1.884579 GGTCCCGATCTATGCGTCTAA 59.115 52.381 0.00 0.00 0.00 2.10
222 223 1.531423 GGTCCCGATCTATGCGTCTA 58.469 55.000 0.00 0.00 0.00 2.59
223 224 1.179814 GGGTCCCGATCTATGCGTCT 61.180 60.000 0.00 0.00 0.00 4.18
224 225 1.289380 GGGTCCCGATCTATGCGTC 59.711 63.158 0.00 0.00 0.00 5.19
225 226 2.207924 GGGGTCCCGATCTATGCGT 61.208 63.158 0.48 0.00 0.00 5.24
226 227 2.657237 GGGGTCCCGATCTATGCG 59.343 66.667 0.48 0.00 0.00 4.73
227 228 3.069778 GGGGGTCCCGATCTATGC 58.930 66.667 0.48 0.00 36.85 3.14
236 237 3.097429 ATCTCGGGTAGGGGGTCCC 62.097 68.421 0.00 0.00 45.90 4.46
237 238 1.533513 GATCTCGGGTAGGGGGTCC 60.534 68.421 0.00 0.00 0.00 4.46
238 239 0.828343 CAGATCTCGGGTAGGGGGTC 60.828 65.000 0.00 0.00 0.00 4.46
239 240 1.233369 CAGATCTCGGGTAGGGGGT 59.767 63.158 0.00 0.00 0.00 4.95
240 241 2.210711 GCAGATCTCGGGTAGGGGG 61.211 68.421 0.00 0.00 0.00 5.40
241 242 2.210711 GGCAGATCTCGGGTAGGGG 61.211 68.421 0.00 0.00 0.00 4.79
242 243 2.565645 CGGCAGATCTCGGGTAGGG 61.566 68.421 0.00 0.00 0.00 3.53
243 244 2.565645 CCGGCAGATCTCGGGTAGG 61.566 68.421 13.71 0.00 42.32 3.18
244 245 1.392710 AACCGGCAGATCTCGGGTAG 61.393 60.000 22.66 0.00 45.54 3.18
245 246 0.974010 AAACCGGCAGATCTCGGGTA 60.974 55.000 22.66 0.00 46.82 3.69
249 250 0.721718 GTCAAAACCGGCAGATCTCG 59.278 55.000 0.00 0.00 0.00 4.04
250 251 1.464997 GTGTCAAAACCGGCAGATCTC 59.535 52.381 0.00 0.00 0.00 2.75
251 252 1.072331 AGTGTCAAAACCGGCAGATCT 59.928 47.619 0.00 0.00 0.00 2.75
252 253 1.197721 CAGTGTCAAAACCGGCAGATC 59.802 52.381 0.00 0.00 0.00 2.75
253 254 1.202758 TCAGTGTCAAAACCGGCAGAT 60.203 47.619 0.00 0.00 0.00 2.90
254 255 0.179234 TCAGTGTCAAAACCGGCAGA 59.821 50.000 0.00 0.00 0.00 4.26
255 256 0.307760 GTCAGTGTCAAAACCGGCAG 59.692 55.000 0.00 0.00 0.00 4.85
256 257 0.393132 TGTCAGTGTCAAAACCGGCA 60.393 50.000 0.00 0.00 0.00 5.69
257 258 0.028902 GTGTCAGTGTCAAAACCGGC 59.971 55.000 0.00 0.00 0.00 6.13
258 259 0.661020 GGTGTCAGTGTCAAAACCGG 59.339 55.000 0.00 0.00 0.00 5.28
259 260 0.661020 GGGTGTCAGTGTCAAAACCG 59.339 55.000 0.00 0.00 0.00 4.44
260 261 1.404035 GTGGGTGTCAGTGTCAAAACC 59.596 52.381 0.00 0.00 0.00 3.27
261 262 1.404035 GGTGGGTGTCAGTGTCAAAAC 59.596 52.381 0.00 0.00 0.00 2.43
262 263 1.283613 AGGTGGGTGTCAGTGTCAAAA 59.716 47.619 0.00 0.00 0.00 2.44
263 264 0.916086 AGGTGGGTGTCAGTGTCAAA 59.084 50.000 0.00 0.00 0.00 2.69
264 265 0.916086 AAGGTGGGTGTCAGTGTCAA 59.084 50.000 0.00 0.00 0.00 3.18
265 266 0.180171 CAAGGTGGGTGTCAGTGTCA 59.820 55.000 0.00 0.00 0.00 3.58
266 267 1.166531 GCAAGGTGGGTGTCAGTGTC 61.167 60.000 0.00 0.00 0.00 3.67
267 268 1.152963 GCAAGGTGGGTGTCAGTGT 60.153 57.895 0.00 0.00 0.00 3.55
268 269 1.898574 GGCAAGGTGGGTGTCAGTG 60.899 63.158 0.00 0.00 0.00 3.66
269 270 2.515901 GGCAAGGTGGGTGTCAGT 59.484 61.111 0.00 0.00 0.00 3.41
270 271 2.282462 GGGCAAGGTGGGTGTCAG 60.282 66.667 0.00 0.00 0.00 3.51
271 272 2.776526 AGGGCAAGGTGGGTGTCA 60.777 61.111 0.00 0.00 0.00 3.58
272 273 2.034221 GAGGGCAAGGTGGGTGTC 59.966 66.667 0.00 0.00 0.00 3.67
273 274 2.450502 AGAGGGCAAGGTGGGTGT 60.451 61.111 0.00 0.00 0.00 4.16
274 275 2.034687 CAGAGGGCAAGGTGGGTG 59.965 66.667 0.00 0.00 0.00 4.61
275 276 2.450502 ACAGAGGGCAAGGTGGGT 60.451 61.111 0.00 0.00 0.00 4.51
339 340 0.613260 AAAGGGCGCTATGTCAGTCA 59.387 50.000 7.64 0.00 0.00 3.41
425 426 3.593247 GCATCGAAGACATGCACAC 57.407 52.632 3.13 0.00 45.19 3.82
466 467 1.238439 CCAAGTTCGAGCACACCATT 58.762 50.000 1.01 0.00 0.00 3.16
474 475 2.665185 ACCGCACCAAGTTCGAGC 60.665 61.111 0.00 0.00 0.00 5.03
662 673 0.835276 ACCGTCCAAAGCCCCTATAC 59.165 55.000 0.00 0.00 0.00 1.47
710 748 4.891168 TCATGGCATTATGAAGAGCACAAT 59.109 37.500 0.00 0.00 34.32 2.71
820 1015 2.581354 CTCCGAGGGAGGCACAAG 59.419 66.667 3.68 0.00 45.43 3.16
1065 1276 2.611800 ACCCTCCATGAGCAGCCA 60.612 61.111 0.00 0.00 0.00 4.75
1195 1409 0.391597 ACGATGACCTTGACCGTGTT 59.608 50.000 0.00 0.00 31.85 3.32
1201 1415 4.245660 TCATTGAAGACGATGACCTTGAC 58.754 43.478 0.00 0.00 40.68 3.18
1447 1678 4.173256 CAACCCAAAGACACACAAAAGAC 58.827 43.478 0.00 0.00 0.00 3.01
1698 1953 3.531538 TGCCAGAATAGCCTAAACTTCG 58.468 45.455 0.00 0.00 0.00 3.79
1816 2071 0.104671 GCTCACTCCAGCCATCTCTC 59.895 60.000 0.00 0.00 32.76 3.20
1826 2081 1.561643 CTTACCTCTGGCTCACTCCA 58.438 55.000 0.00 0.00 34.42 3.86
1837 2092 4.421574 TTCCTTCTCCTTCCTTACCTCT 57.578 45.455 0.00 0.00 0.00 3.69
1868 2123 1.152312 ATACTGGGGTAGCCCTCCG 60.152 63.158 29.64 19.54 44.66 4.63
1874 2129 4.527427 CCCTAAGTTAGATACTGGGGTAGC 59.473 50.000 11.66 0.00 41.80 3.58
1996 2251 3.851128 GGTCTAGCCGCTGTCCCC 61.851 72.222 2.16 0.00 0.00 4.81
2042 2321 2.803956 CCTCGTTTAAGTTTTGCTCCGA 59.196 45.455 0.00 0.00 0.00 4.55
2048 2327 1.068816 CCGGCCCTCGTTTAAGTTTTG 60.069 52.381 0.00 0.00 37.11 2.44
2066 2346 2.565645 CGACCATCCCTCTAGGCCG 61.566 68.421 0.00 0.00 34.51 6.13
2082 2362 4.435970 TCTAGTCGCTGCCCCCGA 62.436 66.667 0.00 0.00 0.00 5.14
2159 2439 1.285641 CCAAACCACATGCGACCAC 59.714 57.895 0.00 0.00 0.00 4.16
2188 2468 4.593864 CTTCTCTAGCCGCCGCCC 62.594 72.222 0.00 0.00 34.57 6.13
2189 2469 2.962697 CTTCTTCTCTAGCCGCCGCC 62.963 65.000 0.00 0.00 34.57 6.13
2190 2470 1.590259 CTTCTTCTCTAGCCGCCGC 60.590 63.158 0.00 0.00 0.00 6.53
2191 2471 0.456221 TTCTTCTTCTCTAGCCGCCG 59.544 55.000 0.00 0.00 0.00 6.46
2192 2472 1.751924 TCTTCTTCTTCTCTAGCCGCC 59.248 52.381 0.00 0.00 0.00 6.13
2193 2473 2.685897 TCTCTTCTTCTTCTCTAGCCGC 59.314 50.000 0.00 0.00 0.00 6.53
2194 2474 4.261572 CCATCTCTTCTTCTTCTCTAGCCG 60.262 50.000 0.00 0.00 0.00 5.52
2195 2475 4.892934 TCCATCTCTTCTTCTTCTCTAGCC 59.107 45.833 0.00 0.00 0.00 3.93
2196 2476 5.010012 CCTCCATCTCTTCTTCTTCTCTAGC 59.990 48.000 0.00 0.00 0.00 3.42
2197 2477 6.129179 ACCTCCATCTCTTCTTCTTCTCTAG 58.871 44.000 0.00 0.00 0.00 2.43
2198 2478 6.086011 ACCTCCATCTCTTCTTCTTCTCTA 57.914 41.667 0.00 0.00 0.00 2.43
2199 2479 4.946646 ACCTCCATCTCTTCTTCTTCTCT 58.053 43.478 0.00 0.00 0.00 3.10
2216 2496 0.178301 CCGGCCTTTCTTCTACCTCC 59.822 60.000 0.00 0.00 0.00 4.30
2237 2517 2.572191 ACGATCGAAATCTAACGGCA 57.428 45.000 24.34 0.00 0.00 5.69
2244 2524 6.456447 TTTTCAAACGTACGATCGAAATCT 57.544 33.333 24.34 0.39 34.70 2.40
2257 2537 3.002965 GGGTCAGTCGATTTTTCAAACGT 59.997 43.478 0.00 0.00 30.57 3.99


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

AutoCloner maintained by Alex Coulton.