Multiple sequence alignment - TraesCS4D01G282100

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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 TraesCS4D01G282100 chr4D 100.000 6205 0 0 1 6205 453228282 453222078 0.000000e+00 11459.0
1 TraesCS4D01G282100 chr4D 90.441 136 13 0 4756 4891 453223390 453223255 4.940000e-41 180.0
2 TraesCS4D01G282100 chr4D 90.441 136 13 0 4893 5028 453223527 453223392 4.940000e-41 180.0
3 TraesCS4D01G282100 chr4B 92.061 3212 107 41 1740 4891 566601216 566598093 0.000000e+00 4383.0
4 TraesCS4D01G282100 chr4B 90.164 1342 62 27 4894 6205 566598230 566596929 0.000000e+00 1683.0
5 TraesCS4D01G282100 chr4B 94.507 892 41 6 575 1465 566602322 566601438 0.000000e+00 1369.0
6 TraesCS4D01G282100 chr4B 87.097 341 34 8 204 538 566602663 566602327 1.630000e-100 377.0
7 TraesCS4D01G282100 chr4B 87.879 132 12 2 1494 1625 566601442 566601315 1.080000e-32 152.0
8 TraesCS4D01G282100 chr4B 91.549 71 4 2 1672 1742 566601310 566601242 5.120000e-16 97.1
9 TraesCS4D01G282100 chr4B 100.000 49 0 0 41 89 623331035 623330987 2.380000e-14 91.6
10 TraesCS4D01G282100 chr4A 93.204 1545 76 13 211 1742 14019795 14021323 0.000000e+00 2244.0
11 TraesCS4D01G282100 chr4A 93.391 1498 53 20 2587 4069 14022289 14023755 0.000000e+00 2176.0
12 TraesCS4D01G282100 chr4A 96.887 1028 25 2 4067 5092 14023711 14024733 0.000000e+00 1714.0
13 TraesCS4D01G282100 chr4A 91.207 1069 41 16 5162 6205 14025025 14026065 0.000000e+00 1404.0
14 TraesCS4D01G282100 chr4A 81.644 888 79 33 1744 2576 14021360 14022218 0.000000e+00 660.0
15 TraesCS4D01G282100 chr4A 91.176 136 12 0 4890 5025 14024394 14024529 1.060000e-42 185.0
16 TraesCS4D01G282100 chr4A 90.647 139 13 0 4753 4891 14024531 14024669 1.060000e-42 185.0
17 TraesCS4D01G282100 chr4A 100.000 40 0 0 1 40 14019619 14019658 2.400000e-09 75.0
18 TraesCS4D01G282100 chrUn 95.763 118 5 0 87 204 182442001 182442118 2.280000e-44 191.0
19 TraesCS4D01G282100 chrUn 95.763 118 5 0 87 204 222871651 222871768 2.280000e-44 191.0
20 TraesCS4D01G282100 chrUn 100.000 49 0 0 41 89 369616183 369616231 2.380000e-14 91.6
21 TraesCS4D01G282100 chr7B 95.763 118 5 0 87 204 327259459 327259576 2.280000e-44 191.0
22 TraesCS4D01G282100 chr7B 100.000 49 0 0 41 89 54066195 54066243 2.380000e-14 91.6
23 TraesCS4D01G282100 chr7A 95.763 118 5 0 87 204 60195651 60195534 2.280000e-44 191.0
24 TraesCS4D01G282100 chr5B 95.763 118 5 0 87 204 130584222 130584105 2.280000e-44 191.0
25 TraesCS4D01G282100 chr5A 95.763 118 5 0 87 204 420173291 420173408 2.280000e-44 191.0
26 TraesCS4D01G282100 chr3A 95.763 118 5 0 87 204 247672585 247672702 2.280000e-44 191.0
27 TraesCS4D01G282100 chr1B 95.763 118 5 0 87 204 619178382 619178265 2.280000e-44 191.0
28 TraesCS4D01G282100 chr2D 95.690 116 5 0 89 204 200950086 200949971 2.950000e-43 187.0
29 TraesCS4D01G282100 chr6B 100.000 49 0 0 41 89 264963672 264963720 2.380000e-14 91.6
30 TraesCS4D01G282100 chr6B 100.000 49 0 0 41 89 307011481 307011433 2.380000e-14 91.6
31 TraesCS4D01G282100 chr6A 100.000 49 0 0 41 89 537597048 537597000 2.380000e-14 91.6
32 TraesCS4D01G282100 chr5D 100.000 49 0 0 41 89 209113061 209113109 2.380000e-14 91.6
33 TraesCS4D01G282100 chr1A 100.000 49 0 0 41 89 94680260 94680308 2.380000e-14 91.6
34 TraesCS4D01G282100 chr1A 100.000 49 0 0 41 89 94795738 94795690 2.380000e-14 91.6


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 TraesCS4D01G282100 chr4D 453222078 453228282 6204 True 11459.000000 11459 100.000000 1 6205 1 chr4D.!!$R1 6204
1 TraesCS4D01G282100 chr4B 566596929 566602663 5734 True 1343.516667 4383 90.542833 204 6205 6 chr4B.!!$R2 6001
2 TraesCS4D01G282100 chr4A 14019619 14026065 6446 False 1080.375000 2244 92.269500 1 6205 8 chr4A.!!$F1 6204

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
140 141 0.101759 GCGGATCATTGTGCAATGCT 59.898 50.000 17.36 9.92 45.77 3.79 F
1431 1446 0.174845 ATAGTCGCGGTAAAGCAGCA 59.825 50.000 6.13 0.00 38.20 4.41 F
1638 1653 0.102120 ATTTGGGTGTTGCGTGTGTG 59.898 50.000 0.00 0.00 0.00 3.82 F
1642 1657 1.226267 GGTGTTGCGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82 F
2313 2422 1.251251 AAAGCCCAGTGACAATCTGC 58.749 50.000 0.00 0.00 0.00 4.26 F
2539 2648 3.220110 TGTGGATCGTGGATACTACTCC 58.780 50.000 0.00 0.00 35.74 3.85 F
3675 3863 0.030235 GGACGTCCAGTTTTGTTGGC 59.970 55.000 29.75 0.00 35.62 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 1646 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49 R
3118 3299 2.680841 TCAACACAAGTGGCACAACTAC 59.319 45.455 21.41 0.00 44.16 2.73 R
3220 3401 3.550950 TTGTATGCAACCAACACATCG 57.449 42.857 0.00 0.00 0.00 3.84 R
3638 3826 7.064847 TGGACGTCCATATAATTTAACACACAC 59.935 37.037 33.23 0.07 42.01 3.82 R
3659 3847 0.316689 GACGCCAACAAAACTGGACG 60.317 55.000 0.00 0.00 38.55 4.79 R
4105 4297 4.202141 CCCTGAACACAAAATGCTGAGAAA 60.202 41.667 0.00 0.00 0.00 2.52 R
5414 5877 1.065410 TGGCCCTTTCTTCACCTGGA 61.065 55.000 0.00 0.00 0.00 3.86 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
45 46 2.969443 CACTTTTGCAACTAGGGTCG 57.031 50.000 0.00 0.00 0.00 4.79
46 47 1.535462 CACTTTTGCAACTAGGGTCGG 59.465 52.381 0.00 0.00 0.00 4.79
47 48 1.142262 ACTTTTGCAACTAGGGTCGGT 59.858 47.619 0.00 0.00 0.00 4.69
48 49 1.535462 CTTTTGCAACTAGGGTCGGTG 59.465 52.381 0.00 0.00 0.00 4.94
49 50 0.470766 TTTGCAACTAGGGTCGGTGT 59.529 50.000 0.00 0.00 0.00 4.16
50 51 1.340088 TTGCAACTAGGGTCGGTGTA 58.660 50.000 0.00 0.00 0.00 2.90
51 52 1.340088 TGCAACTAGGGTCGGTGTAA 58.660 50.000 0.00 0.00 0.00 2.41
53 54 2.303600 TGCAACTAGGGTCGGTGTAAAT 59.696 45.455 0.00 0.00 0.00 1.40
54 55 3.514706 TGCAACTAGGGTCGGTGTAAATA 59.485 43.478 0.00 0.00 0.00 1.40
55 56 4.020396 TGCAACTAGGGTCGGTGTAAATAA 60.020 41.667 0.00 0.00 0.00 1.40
56 57 4.937015 GCAACTAGGGTCGGTGTAAATAAA 59.063 41.667 0.00 0.00 0.00 1.40
57 58 5.064325 GCAACTAGGGTCGGTGTAAATAAAG 59.936 44.000 0.00 0.00 0.00 1.85
58 59 5.349061 ACTAGGGTCGGTGTAAATAAAGG 57.651 43.478 0.00 0.00 0.00 3.11
60 61 2.914941 AGGGTCGGTGTAAATAAAGGGT 59.085 45.455 0.00 0.00 0.00 4.34
61 62 3.011818 GGGTCGGTGTAAATAAAGGGTG 58.988 50.000 0.00 0.00 0.00 4.61
63 64 3.937079 GGTCGGTGTAAATAAAGGGTGAG 59.063 47.826 0.00 0.00 0.00 3.51
65 66 3.262405 TCGGTGTAAATAAAGGGTGAGCT 59.738 43.478 0.00 0.00 0.00 4.09
67 68 3.945921 GGTGTAAATAAAGGGTGAGCTCC 59.054 47.826 12.15 2.19 0.00 4.70
68 69 4.566907 GGTGTAAATAAAGGGTGAGCTCCA 60.567 45.833 12.15 0.00 0.00 3.86
69 70 5.007682 GTGTAAATAAAGGGTGAGCTCCAA 58.992 41.667 12.15 0.00 0.00 3.53
73 74 5.514500 AATAAAGGGTGAGCTCCAAACTA 57.486 39.130 12.15 0.00 0.00 2.24
75 76 1.729586 AGGGTGAGCTCCAAACTACA 58.270 50.000 12.15 0.00 0.00 2.74
77 78 1.348036 GGGTGAGCTCCAAACTACAGT 59.652 52.381 12.15 0.00 0.00 3.55
79 80 2.417719 GTGAGCTCCAAACTACAGTGG 58.582 52.381 12.15 0.00 36.13 4.00
80 81 1.347707 TGAGCTCCAAACTACAGTGGG 59.652 52.381 12.15 0.00 35.46 4.61
82 83 2.038557 GAGCTCCAAACTACAGTGGGAA 59.961 50.000 0.87 0.00 35.46 3.97
83 84 2.441750 AGCTCCAAACTACAGTGGGAAA 59.558 45.455 0.00 0.00 35.46 3.13
84 85 2.814336 GCTCCAAACTACAGTGGGAAAG 59.186 50.000 0.00 0.00 35.46 2.62
85 86 3.412386 CTCCAAACTACAGTGGGAAAGG 58.588 50.000 0.00 0.00 35.46 3.11
86 87 1.886542 CCAAACTACAGTGGGAAAGGC 59.113 52.381 0.00 0.00 0.00 4.35
90 91 3.262448 TACAGTGGGAAAGGCCGGC 62.262 63.158 21.18 21.18 37.63 6.13
93 94 4.986708 GTGGGAAAGGCCGGCCAA 62.987 66.667 45.13 21.18 38.92 4.52
94 95 4.986708 TGGGAAAGGCCGGCCAAC 62.987 66.667 45.13 32.51 38.92 3.77
105 106 1.355210 CGGCCAACGGTATCATTGC 59.645 57.895 2.24 0.00 39.42 3.56
106 107 1.095228 CGGCCAACGGTATCATTGCT 61.095 55.000 2.24 0.00 39.42 3.91
110 111 1.331756 CCAACGGTATCATTGCTGCTC 59.668 52.381 0.00 0.00 0.00 4.26
111 112 1.331756 CAACGGTATCATTGCTGCTCC 59.668 52.381 0.00 0.00 0.00 4.70
112 113 0.179045 ACGGTATCATTGCTGCTCCC 60.179 55.000 0.00 0.00 0.00 4.30
113 114 0.886490 CGGTATCATTGCTGCTCCCC 60.886 60.000 0.00 0.00 0.00 4.81
114 115 0.886490 GGTATCATTGCTGCTCCCCG 60.886 60.000 0.00 0.00 0.00 5.73
115 116 1.227943 TATCATTGCTGCTCCCCGC 60.228 57.895 0.00 0.00 39.77 6.13
116 117 2.680974 TATCATTGCTGCTCCCCGCC 62.681 60.000 0.00 0.00 38.05 6.13
118 119 3.089874 ATTGCTGCTCCCCGCCTA 61.090 61.111 0.00 0.00 38.05 3.93
132 133 3.386543 GCCTAGTGCGGATCATTGT 57.613 52.632 0.00 0.00 0.00 2.71
135 136 1.655484 CTAGTGCGGATCATTGTGCA 58.345 50.000 0.00 0.00 34.44 4.57
136 137 2.009051 CTAGTGCGGATCATTGTGCAA 58.991 47.619 0.00 0.00 39.34 4.08
140 141 0.101759 GCGGATCATTGTGCAATGCT 59.898 50.000 17.36 9.92 45.77 3.79
141 142 1.470285 GCGGATCATTGTGCAATGCTT 60.470 47.619 17.36 9.18 45.77 3.91
143 144 3.551454 GCGGATCATTGTGCAATGCTTAT 60.551 43.478 17.36 8.22 45.77 1.73
144 145 3.978855 CGGATCATTGTGCAATGCTTATG 59.021 43.478 17.36 7.52 45.77 1.90
146 147 4.743151 GGATCATTGTGCAATGCTTATGTG 59.257 41.667 17.36 0.00 45.77 3.21
147 148 5.450826 GGATCATTGTGCAATGCTTATGTGA 60.451 40.000 17.36 5.19 45.77 3.58
148 149 5.388408 TCATTGTGCAATGCTTATGTGAA 57.612 34.783 17.36 0.00 45.77 3.18
149 150 5.968254 TCATTGTGCAATGCTTATGTGAAT 58.032 33.333 17.36 0.00 45.77 2.57
150 151 6.399743 TCATTGTGCAATGCTTATGTGAATT 58.600 32.000 17.36 0.00 45.77 2.17
151 152 6.532302 TCATTGTGCAATGCTTATGTGAATTC 59.468 34.615 17.36 0.00 45.77 2.17
152 153 5.648178 TGTGCAATGCTTATGTGAATTCT 57.352 34.783 6.82 0.00 0.00 2.40
153 154 5.643664 TGTGCAATGCTTATGTGAATTCTC 58.356 37.500 6.82 3.61 0.00 2.87
154 155 5.183522 TGTGCAATGCTTATGTGAATTCTCA 59.816 36.000 12.28 12.28 0.00 3.27
155 156 5.742453 GTGCAATGCTTATGTGAATTCTCAG 59.258 40.000 14.87 4.11 30.14 3.35
156 157 5.416639 TGCAATGCTTATGTGAATTCTCAGT 59.583 36.000 14.87 6.92 30.14 3.41
157 158 5.970023 GCAATGCTTATGTGAATTCTCAGTC 59.030 40.000 14.87 5.59 30.14 3.51
159 160 5.164620 TGCTTATGTGAATTCTCAGTCCA 57.835 39.130 14.87 7.35 30.14 4.02
160 161 5.559770 TGCTTATGTGAATTCTCAGTCCAA 58.440 37.500 14.87 6.46 30.14 3.53
163 164 6.803807 GCTTATGTGAATTCTCAGTCCAAAAC 59.196 38.462 14.87 0.00 30.14 2.43
164 165 7.308830 GCTTATGTGAATTCTCAGTCCAAAACT 60.309 37.037 14.87 0.00 39.44 2.66
165 166 6.966534 ATGTGAATTCTCAGTCCAAAACTT 57.033 33.333 14.87 0.00 35.45 2.66
166 167 9.567776 TTATGTGAATTCTCAGTCCAAAACTTA 57.432 29.630 14.87 0.00 35.45 2.24
167 168 8.641498 ATGTGAATTCTCAGTCCAAAACTTAT 57.359 30.769 14.87 0.00 35.45 1.73
168 169 8.463930 TGTGAATTCTCAGTCCAAAACTTATT 57.536 30.769 7.05 0.00 35.45 1.40
169 170 8.567948 TGTGAATTCTCAGTCCAAAACTTATTC 58.432 33.333 7.05 0.00 35.45 1.75
170 171 7.746475 GTGAATTCTCAGTCCAAAACTTATTCG 59.254 37.037 7.05 0.00 35.45 3.34
171 172 7.444183 TGAATTCTCAGTCCAAAACTTATTCGT 59.556 33.333 7.05 0.00 35.45 3.85
172 173 7.745620 ATTCTCAGTCCAAAACTTATTCGTT 57.254 32.000 0.00 0.00 35.45 3.85
173 174 7.562454 TTCTCAGTCCAAAACTTATTCGTTT 57.438 32.000 0.00 0.00 38.66 3.60
175 176 5.981174 TCAGTCCAAAACTTATTCGTTTCG 58.019 37.500 0.00 0.00 36.16 3.46
176 177 5.524646 TCAGTCCAAAACTTATTCGTTTCGT 59.475 36.000 0.00 0.00 36.16 3.85
177 178 6.037391 TCAGTCCAAAACTTATTCGTTTCGTT 59.963 34.615 0.00 0.00 36.16 3.85
178 179 6.140108 CAGTCCAAAACTTATTCGTTTCGTTG 59.860 38.462 0.00 0.00 36.16 4.10
179 180 5.397240 GTCCAAAACTTATTCGTTTCGTTGG 59.603 40.000 0.00 0.00 36.16 3.77
180 181 5.296283 TCCAAAACTTATTCGTTTCGTTGGA 59.704 36.000 0.00 0.00 38.23 3.53
181 182 5.972382 CCAAAACTTATTCGTTTCGTTGGAA 59.028 36.000 0.00 0.00 35.67 3.53
182 183 6.472808 CCAAAACTTATTCGTTTCGTTGGAAA 59.527 34.615 0.00 0.00 35.67 3.13
183 184 7.009357 CCAAAACTTATTCGTTTCGTTGGAAAA 59.991 33.333 0.00 0.00 43.39 2.29
184 185 8.373992 CAAAACTTATTCGTTTCGTTGGAAAAA 58.626 29.630 0.00 0.00 43.39 1.94
185 186 7.440541 AACTTATTCGTTTCGTTGGAAAAAC 57.559 32.000 0.00 0.00 43.39 2.43
186 187 5.972973 ACTTATTCGTTTCGTTGGAAAAACC 59.027 36.000 0.00 0.00 43.39 3.27
196 197 0.733729 TGGAAAAACCAACACCGACG 59.266 50.000 0.00 0.00 46.75 5.12
197 198 0.734309 GGAAAAACCAACACCGACGT 59.266 50.000 0.00 0.00 38.79 4.34
198 199 1.268184 GGAAAAACCAACACCGACGTC 60.268 52.381 5.18 5.18 38.79 4.34
199 200 1.397692 GAAAAACCAACACCGACGTCA 59.602 47.619 17.16 0.00 0.00 4.35
200 201 1.451067 AAAACCAACACCGACGTCAA 58.549 45.000 17.16 0.00 0.00 3.18
201 202 1.011333 AAACCAACACCGACGTCAAG 58.989 50.000 17.16 8.75 0.00 3.02
202 203 0.176219 AACCAACACCGACGTCAAGA 59.824 50.000 17.16 0.00 0.00 3.02
206 207 2.858344 CCAACACCGACGTCAAGATATC 59.142 50.000 17.16 0.00 0.00 1.63
227 228 5.823209 TCGGACTAAATCGTCACATTCTA 57.177 39.130 0.00 0.00 35.63 2.10
235 236 8.709646 ACTAAATCGTCACATTCTAAACAAGTC 58.290 33.333 0.00 0.00 0.00 3.01
281 282 6.620877 TTCTTCTTTCTTAGTATGGAGCCA 57.379 37.500 0.00 0.00 0.00 4.75
297 298 0.408309 GCCAGAGGTTTTTACCCCCT 59.592 55.000 0.00 0.00 0.00 4.79
305 306 3.401342 AGGTTTTTACCCCCTGTTGATCT 59.599 43.478 0.00 0.00 0.00 2.75
361 363 5.494863 AAAAACTCGATTAAATTGCACGC 57.505 34.783 0.00 0.00 0.00 5.34
378 380 3.181510 GCACGCTGGATCGTAAAGAAAAT 60.182 43.478 0.00 0.00 41.21 1.82
380 382 3.181510 ACGCTGGATCGTAAAGAAAATGC 60.182 43.478 0.00 0.00 41.36 3.56
392 394 8.855279 TCGTAAAGAAAATGCGATTTAAATTGG 58.145 29.630 15.74 6.68 29.97 3.16
393 395 8.643752 CGTAAAGAAAATGCGATTTAAATTGGT 58.356 29.630 15.74 0.00 0.00 3.67
470 475 6.086222 ACTCAATTAAATCACACGTTGCATC 58.914 36.000 0.00 0.00 0.00 3.91
489 494 9.267096 GTTGCATCGTAAAGAAAAAGAGATTAG 57.733 33.333 0.00 0.00 0.00 1.73
508 513 8.152023 AGATTAGAATTACAGGTTTCCAGACT 57.848 34.615 0.00 0.00 0.00 3.24
572 585 3.728076 TGGATTATGCTGTACCTCGTC 57.272 47.619 0.00 0.00 0.00 4.20
645 658 3.661648 AAATGGCCACCCGGAGCT 61.662 61.111 8.16 0.00 0.00 4.09
849 863 3.009714 GTTCCTTCCCCCGCTCCT 61.010 66.667 0.00 0.00 0.00 3.69
1104 1119 2.637947 GAGCAAGAGGTGAGATTTCCC 58.362 52.381 0.00 0.00 0.00 3.97
1105 1120 2.238395 GAGCAAGAGGTGAGATTTCCCT 59.762 50.000 0.00 0.00 0.00 4.20
1125 1140 2.048127 GCTTCTGTCCGCCGTTCT 60.048 61.111 0.00 0.00 0.00 3.01
1126 1141 2.383527 GCTTCTGTCCGCCGTTCTG 61.384 63.158 0.00 0.00 0.00 3.02
1305 1320 2.147958 TGTTTGTTATGCTGGACGGTC 58.852 47.619 0.00 0.00 0.00 4.79
1317 1332 0.390860 GGACGGTCTGGAGGATGATG 59.609 60.000 8.23 0.00 0.00 3.07
1319 1334 1.050988 ACGGTCTGGAGGATGATGGG 61.051 60.000 0.00 0.00 0.00 4.00
1320 1335 1.453669 GGTCTGGAGGATGATGGGC 59.546 63.158 0.00 0.00 0.00 5.36
1431 1446 0.174845 ATAGTCGCGGTAAAGCAGCA 59.825 50.000 6.13 0.00 38.20 4.41
1629 1644 3.457749 ACATTTGGGTTGATTTGGGTGTT 59.542 39.130 0.00 0.00 0.00 3.32
1630 1645 3.550437 TTTGGGTTGATTTGGGTGTTG 57.450 42.857 0.00 0.00 0.00 3.33
1631 1646 0.755686 TGGGTTGATTTGGGTGTTGC 59.244 50.000 0.00 0.00 0.00 4.17
1632 1647 0.319469 GGGTTGATTTGGGTGTTGCG 60.319 55.000 0.00 0.00 0.00 4.85
1633 1648 0.387565 GGTTGATTTGGGTGTTGCGT 59.612 50.000 0.00 0.00 0.00 5.24
1634 1649 1.486439 GTTGATTTGGGTGTTGCGTG 58.514 50.000 0.00 0.00 0.00 5.34
1635 1650 1.107114 TTGATTTGGGTGTTGCGTGT 58.893 45.000 0.00 0.00 0.00 4.49
1636 1651 0.383590 TGATTTGGGTGTTGCGTGTG 59.616 50.000 0.00 0.00 0.00 3.82
1637 1652 0.383949 GATTTGGGTGTTGCGTGTGT 59.616 50.000 0.00 0.00 0.00 3.72
1638 1653 0.102120 ATTTGGGTGTTGCGTGTGTG 59.898 50.000 0.00 0.00 0.00 3.82
1639 1654 1.244697 TTTGGGTGTTGCGTGTGTGT 61.245 50.000 0.00 0.00 0.00 3.72
1640 1655 1.927608 TTGGGTGTTGCGTGTGTGTG 61.928 55.000 0.00 0.00 0.00 3.82
1641 1656 2.403378 GGGTGTTGCGTGTGTGTGT 61.403 57.895 0.00 0.00 0.00 3.72
1642 1657 1.226267 GGTGTTGCGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
1876 1934 3.401182 TCTTTTATACACGCGTTGGGTT 58.599 40.909 10.22 0.00 0.00 4.11
2001 2089 5.533903 GTGTCAAGGGCATTCTGATCAATAT 59.466 40.000 0.00 0.00 0.00 1.28
2005 2093 8.632679 GTCAAGGGCATTCTGATCAATATTTTA 58.367 33.333 0.00 0.00 0.00 1.52
2033 2132 7.880160 TCAATTATATCCTGTTCTTTGGTGG 57.120 36.000 0.00 0.00 0.00 4.61
2102 2202 8.507524 AACATAGTAATTTAAGGTCTTCTGCC 57.492 34.615 0.00 0.00 0.00 4.85
2103 2203 7.054751 ACATAGTAATTTAAGGTCTTCTGCCC 58.945 38.462 0.00 0.00 0.00 5.36
2104 2204 4.514401 AGTAATTTAAGGTCTTCTGCCCG 58.486 43.478 0.00 0.00 0.00 6.13
2182 2290 2.329267 TCCACTCTGACACCTCAACAT 58.671 47.619 0.00 0.00 0.00 2.71
2189 2297 3.503363 TCTGACACCTCAACATTGCATTC 59.497 43.478 0.00 0.00 0.00 2.67
2313 2422 1.251251 AAAGCCCAGTGACAATCTGC 58.749 50.000 0.00 0.00 0.00 4.26
2409 2518 6.596621 AGCTGATCTTTATTCTTTCCTACCC 58.403 40.000 0.00 0.00 0.00 3.69
2456 2565 7.066887 TGCATTTTACATTACATCTCCGAATGT 59.933 33.333 5.00 5.00 44.07 2.71
2539 2648 3.220110 TGTGGATCGTGGATACTACTCC 58.780 50.000 0.00 0.00 35.74 3.85
2987 3156 3.364889 TTCTACGATGAATGCCTACGG 57.635 47.619 0.00 0.00 0.00 4.02
3082 3251 5.049198 TGCTAGAAAATCTGTGCTTGTTCAG 60.049 40.000 0.00 0.00 31.72 3.02
3230 3411 8.642908 TTAGATTAGTATTGACGATGTGTTGG 57.357 34.615 0.00 0.00 0.00 3.77
3438 3625 8.591114 ACAAGTATGTGGTAGTATTACTGTCT 57.409 34.615 6.60 0.00 38.69 3.41
3583 3770 8.722622 TCTTAGACCTCCTCTCTTTTTCTTTA 57.277 34.615 0.00 0.00 0.00 1.85
3638 3826 4.143137 GCCTTATTGTGCGGATTGTTTTTG 60.143 41.667 0.00 0.00 0.00 2.44
3640 3828 5.107530 CCTTATTGTGCGGATTGTTTTTGTG 60.108 40.000 0.00 0.00 0.00 3.33
3675 3863 0.030235 GGACGTCCAGTTTTGTTGGC 59.970 55.000 29.75 0.00 35.62 4.52
3795 3985 9.295825 AGTGTGACAATCCATAAATTCTTTACA 57.704 29.630 0.00 0.00 0.00 2.41
3831 4021 6.183360 GCGAAACACAATCTTGGATGATTCTA 60.183 38.462 0.00 0.00 34.77 2.10
3892 4082 3.753294 AGTGTTGGTAGGTCTTGACTG 57.247 47.619 0.61 0.00 0.00 3.51
4040 4232 1.284785 TGCCCTCCACCCTTCTTATTG 59.715 52.381 0.00 0.00 0.00 1.90
4064 4256 8.729805 TGTCAAATAAGGTTTTCTTGCATTTT 57.270 26.923 0.00 0.00 36.93 1.82
4065 4257 9.171877 TGTCAAATAAGGTTTTCTTGCATTTTT 57.828 25.926 0.00 0.00 36.93 1.94
4066 4258 9.650371 GTCAAATAAGGTTTTCTTGCATTTTTC 57.350 29.630 0.00 0.00 36.93 2.29
4067 4259 9.612066 TCAAATAAGGTTTTCTTGCATTTTTCT 57.388 25.926 0.00 0.00 36.93 2.52
4068 4260 9.868389 CAAATAAGGTTTTCTTGCATTTTTCTC 57.132 29.630 0.00 0.00 36.93 2.87
4069 4261 8.607441 AATAAGGTTTTCTTGCATTTTTCTCC 57.393 30.769 0.00 0.00 36.93 3.71
4070 4262 5.612725 AGGTTTTCTTGCATTTTTCTCCA 57.387 34.783 0.00 0.00 0.00 3.86
4071 4263 5.359756 AGGTTTTCTTGCATTTTTCTCCAC 58.640 37.500 0.00 0.00 0.00 4.02
4072 4264 4.511454 GGTTTTCTTGCATTTTTCTCCACC 59.489 41.667 0.00 0.00 0.00 4.61
4073 4265 4.335400 TTTCTTGCATTTTTCTCCACCC 57.665 40.909 0.00 0.00 0.00 4.61
4074 4266 3.243359 TCTTGCATTTTTCTCCACCCT 57.757 42.857 0.00 0.00 0.00 4.34
4075 4267 3.575805 TCTTGCATTTTTCTCCACCCTT 58.424 40.909 0.00 0.00 0.00 3.95
4076 4268 3.573967 TCTTGCATTTTTCTCCACCCTTC 59.426 43.478 0.00 0.00 0.00 3.46
4077 4269 3.243359 TGCATTTTTCTCCACCCTTCT 57.757 42.857 0.00 0.00 0.00 2.85
4078 4270 2.892852 TGCATTTTTCTCCACCCTTCTG 59.107 45.455 0.00 0.00 0.00 3.02
4079 4271 3.157087 GCATTTTTCTCCACCCTTCTGA 58.843 45.455 0.00 0.00 0.00 3.27
4080 4272 3.766051 GCATTTTTCTCCACCCTTCTGAT 59.234 43.478 0.00 0.00 0.00 2.90
4081 4273 4.221482 GCATTTTTCTCCACCCTTCTGATT 59.779 41.667 0.00 0.00 0.00 2.57
4082 4274 5.418840 GCATTTTTCTCCACCCTTCTGATTA 59.581 40.000 0.00 0.00 0.00 1.75
4083 4275 6.097412 GCATTTTTCTCCACCCTTCTGATTAT 59.903 38.462 0.00 0.00 0.00 1.28
4084 4276 7.682981 GCATTTTTCTCCACCCTTCTGATTATC 60.683 40.741 0.00 0.00 0.00 1.75
4085 4277 6.387192 TTTTCTCCACCCTTCTGATTATCA 57.613 37.500 0.00 0.00 0.00 2.15
4086 4278 5.359194 TTCTCCACCCTTCTGATTATCAC 57.641 43.478 0.00 0.00 0.00 3.06
4087 4279 4.361783 TCTCCACCCTTCTGATTATCACA 58.638 43.478 0.00 0.00 0.00 3.58
4088 4280 4.971282 TCTCCACCCTTCTGATTATCACAT 59.029 41.667 0.00 0.00 0.00 3.21
4089 4281 6.143206 TCTCCACCCTTCTGATTATCACATA 58.857 40.000 0.00 0.00 0.00 2.29
4090 4282 6.615316 TCTCCACCCTTCTGATTATCACATAA 59.385 38.462 0.00 0.00 0.00 1.90
4091 4283 6.830912 TCCACCCTTCTGATTATCACATAAG 58.169 40.000 0.00 0.00 0.00 1.73
4092 4284 6.000219 CCACCCTTCTGATTATCACATAAGG 59.000 44.000 14.52 14.52 39.61 2.69
4093 4285 6.409695 CCACCCTTCTGATTATCACATAAGGT 60.410 42.308 17.65 8.49 38.83 3.50
4094 4286 7.056635 CACCCTTCTGATTATCACATAAGGTT 58.943 38.462 17.65 7.51 38.83 3.50
4095 4287 7.557719 CACCCTTCTGATTATCACATAAGGTTT 59.442 37.037 17.65 7.83 38.83 3.27
4096 4288 8.116026 ACCCTTCTGATTATCACATAAGGTTTT 58.884 33.333 17.65 6.22 38.83 2.43
4097 4289 8.624776 CCCTTCTGATTATCACATAAGGTTTTC 58.375 37.037 17.65 0.00 38.83 2.29
4098 4290 9.401058 CCTTCTGATTATCACATAAGGTTTTCT 57.599 33.333 13.76 0.00 37.07 2.52
4101 4293 8.677300 TCTGATTATCACATAAGGTTTTCTTGC 58.323 33.333 0.00 0.00 36.93 4.01
4102 4294 8.347004 TGATTATCACATAAGGTTTTCTTGCA 57.653 30.769 0.00 0.00 36.93 4.08
4103 4295 8.970020 TGATTATCACATAAGGTTTTCTTGCAT 58.030 29.630 0.00 0.00 36.93 3.96
4104 4296 9.807649 GATTATCACATAAGGTTTTCTTGCATT 57.192 29.630 0.00 0.00 36.93 3.56
4113 4347 5.052481 AGGTTTTCTTGCATTTTTCTCAGC 58.948 37.500 0.00 0.00 0.00 4.26
4379 4615 6.979465 ACTACTGTAGTACTGTGTTCCTTTC 58.021 40.000 18.42 0.00 37.23 2.62
4560 4796 8.465273 AAGCTGGTTGAACTTTTAGATACTTT 57.535 30.769 0.00 0.00 0.00 2.66
4561 4797 9.569122 AAGCTGGTTGAACTTTTAGATACTTTA 57.431 29.630 0.00 0.00 0.00 1.85
4897 5136 5.643777 AGTGTTAATGCTGTACTTCCATGAC 59.356 40.000 0.00 0.00 0.00 3.06
4913 5152 5.809001 TCCATGACACTTTCTCTTTGCTAT 58.191 37.500 0.00 0.00 0.00 2.97
4952 5191 5.046807 TGACATACTGCCATCATCCAGATAG 60.047 44.000 0.00 0.00 34.43 2.08
4957 5196 1.072806 GCCATCATCCAGATAGGCACA 59.927 52.381 11.09 0.00 43.97 4.57
5414 5877 2.856000 AGCCACCTGCCCTGAGTT 60.856 61.111 0.00 0.00 42.71 3.01
5462 5938 5.538053 TCCACACTTTGGCAATTTCATAGAA 59.462 36.000 0.00 0.00 46.47 2.10
5463 5939 6.211184 TCCACACTTTGGCAATTTCATAGAAT 59.789 34.615 0.00 0.00 46.47 2.40
5549 6025 5.164080 GCTTGTAATCTGTATTATCGACGGC 60.164 44.000 0.00 0.00 30.42 5.68
5553 6029 3.364889 TCTGTATTATCGACGGCAAGG 57.635 47.619 0.00 0.00 0.00 3.61
5555 6031 3.131577 TCTGTATTATCGACGGCAAGGTT 59.868 43.478 0.00 0.00 0.00 3.50
5607 6083 8.210265 TCTCCAAAGCTTTATTTGTTTTTCCAT 58.790 29.630 12.25 0.00 38.28 3.41
5649 6128 4.104102 ACAACATGTAGAGGGGAGAACAAA 59.896 41.667 0.00 0.00 0.00 2.83
5739 6218 6.017440 CCTTAGTTAAGTTGCTGCTAACACAA 60.017 38.462 14.29 6.91 33.02 3.33
5833 6315 1.335872 GCATTTCCCTGTTCGGTGTTG 60.336 52.381 0.00 0.00 0.00 3.33
6010 6498 4.436998 AACGCCGCCTTCTCCTCG 62.437 66.667 0.00 0.00 0.00 4.63
6051 6539 1.178534 CCCTCCGTGTTGCCATTGTT 61.179 55.000 0.00 0.00 0.00 2.83
6069 6557 1.796459 GTTGAACCTGCATACGTCGTT 59.204 47.619 1.78 0.00 0.00 3.85
6132 6621 5.585390 GCATATAAATGATGCTACATGGGC 58.415 41.667 0.00 1.45 45.14 5.36
6138 6627 0.888285 GATGCTACATGGGCCTGCTC 60.888 60.000 4.53 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.011818 CACCCTTTATTTACACCGACCC 58.988 50.000 0.00 0.00 0.00 4.46
41 42 3.937079 CTCACCCTTTATTTACACCGACC 59.063 47.826 0.00 0.00 0.00 4.79
43 44 3.262405 AGCTCACCCTTTATTTACACCGA 59.738 43.478 0.00 0.00 0.00 4.69
44 45 3.606687 AGCTCACCCTTTATTTACACCG 58.393 45.455 0.00 0.00 0.00 4.94
45 46 3.945921 GGAGCTCACCCTTTATTTACACC 59.054 47.826 17.19 0.00 0.00 4.16
46 47 4.585879 TGGAGCTCACCCTTTATTTACAC 58.414 43.478 17.19 0.00 0.00 2.90
47 48 4.919774 TGGAGCTCACCCTTTATTTACA 57.080 40.909 17.19 0.00 0.00 2.41
48 49 5.710567 AGTTTGGAGCTCACCCTTTATTTAC 59.289 40.000 17.19 0.00 0.00 2.01
49 50 5.887754 AGTTTGGAGCTCACCCTTTATTTA 58.112 37.500 17.19 0.00 0.00 1.40
50 51 4.740902 AGTTTGGAGCTCACCCTTTATTT 58.259 39.130 17.19 0.00 0.00 1.40
51 52 4.388577 AGTTTGGAGCTCACCCTTTATT 57.611 40.909 17.19 0.00 0.00 1.40
53 54 3.649023 TGTAGTTTGGAGCTCACCCTTTA 59.351 43.478 17.19 0.00 0.00 1.85
54 55 2.441750 TGTAGTTTGGAGCTCACCCTTT 59.558 45.455 17.19 0.00 0.00 3.11
55 56 2.039084 CTGTAGTTTGGAGCTCACCCTT 59.961 50.000 17.19 0.15 0.00 3.95
56 57 1.625818 CTGTAGTTTGGAGCTCACCCT 59.374 52.381 17.19 7.78 0.00 4.34
57 58 1.348036 ACTGTAGTTTGGAGCTCACCC 59.652 52.381 17.19 0.00 0.00 4.61
58 59 2.417719 CACTGTAGTTTGGAGCTCACC 58.582 52.381 17.19 0.00 0.00 4.02
60 61 1.347707 CCCACTGTAGTTTGGAGCTCA 59.652 52.381 17.19 0.00 34.46 4.26
61 62 1.623811 TCCCACTGTAGTTTGGAGCTC 59.376 52.381 4.71 4.71 34.46 4.09
63 64 2.561478 TTCCCACTGTAGTTTGGAGC 57.439 50.000 0.00 0.00 34.46 4.70
65 66 2.488347 GCCTTTCCCACTGTAGTTTGGA 60.488 50.000 0.00 0.00 34.46 3.53
67 68 1.886542 GGCCTTTCCCACTGTAGTTTG 59.113 52.381 0.00 0.00 0.00 2.93
68 69 1.544759 CGGCCTTTCCCACTGTAGTTT 60.545 52.381 0.00 0.00 0.00 2.66
69 70 0.036306 CGGCCTTTCCCACTGTAGTT 59.964 55.000 0.00 0.00 0.00 2.24
73 74 4.660938 GCCGGCCTTTCCCACTGT 62.661 66.667 18.11 0.00 0.00 3.55
77 78 4.986708 GTTGGCCGGCCTTTCCCA 62.987 66.667 43.34 22.40 36.94 4.37
90 91 1.331756 GAGCAGCAATGATACCGTTGG 59.668 52.381 0.00 0.00 39.18 3.77
91 92 1.331756 GGAGCAGCAATGATACCGTTG 59.668 52.381 0.00 0.00 41.16 4.10
92 93 1.668419 GGAGCAGCAATGATACCGTT 58.332 50.000 0.00 0.00 0.00 4.44
93 94 0.179045 GGGAGCAGCAATGATACCGT 60.179 55.000 0.00 0.00 0.00 4.83
94 95 0.886490 GGGGAGCAGCAATGATACCG 60.886 60.000 0.00 0.00 0.00 4.02
96 97 2.621763 CGGGGAGCAGCAATGATAC 58.378 57.895 0.00 0.00 0.00 2.24
114 115 0.940126 CACAATGATCCGCACTAGGC 59.060 55.000 0.00 0.00 39.90 3.93
115 116 0.940126 GCACAATGATCCGCACTAGG 59.060 55.000 0.00 0.00 0.00 3.02
116 117 1.655484 TGCACAATGATCCGCACTAG 58.345 50.000 0.00 0.00 0.00 2.57
118 119 1.466856 ATTGCACAATGATCCGCACT 58.533 45.000 0.00 0.00 33.29 4.40
120 121 4.039670 AAGCATTGCACAATGATCCGCA 62.040 45.455 23.92 0.00 45.49 5.69
123 124 4.743151 CACATAAGCATTGCACAATGATCC 59.257 41.667 23.92 8.94 45.49 3.36
128 129 6.636705 AGAATTCACATAAGCATTGCACAAT 58.363 32.000 11.91 0.00 0.00 2.71
129 130 6.028146 AGAATTCACATAAGCATTGCACAA 57.972 33.333 11.91 0.00 0.00 3.33
131 132 5.643664 TGAGAATTCACATAAGCATTGCAC 58.356 37.500 11.91 0.00 0.00 4.57
132 133 5.416639 ACTGAGAATTCACATAAGCATTGCA 59.583 36.000 11.91 0.00 0.00 4.08
135 136 6.182627 TGGACTGAGAATTCACATAAGCATT 58.817 36.000 8.44 0.00 0.00 3.56
136 137 5.748402 TGGACTGAGAATTCACATAAGCAT 58.252 37.500 8.44 0.00 0.00 3.79
138 139 6.500684 TTTGGACTGAGAATTCACATAAGC 57.499 37.500 8.44 0.00 0.00 3.09
140 141 8.463930 AAGTTTTGGACTGAGAATTCACATAA 57.536 30.769 8.44 0.00 39.00 1.90
141 142 9.739276 ATAAGTTTTGGACTGAGAATTCACATA 57.261 29.630 8.44 0.00 39.00 2.29
143 144 8.463930 AATAAGTTTTGGACTGAGAATTCACA 57.536 30.769 8.44 6.82 39.00 3.58
144 145 7.746475 CGAATAAGTTTTGGACTGAGAATTCAC 59.254 37.037 8.44 1.50 39.00 3.18
146 147 7.807680 ACGAATAAGTTTTGGACTGAGAATTC 58.192 34.615 0.00 0.00 39.00 2.17
147 148 7.745620 ACGAATAAGTTTTGGACTGAGAATT 57.254 32.000 0.00 0.00 39.00 2.17
148 149 7.745620 AACGAATAAGTTTTGGACTGAGAAT 57.254 32.000 0.00 0.00 39.00 2.40
149 150 7.517734 CGAAACGAATAAGTTTTGGACTGAGAA 60.518 37.037 0.00 0.00 43.54 2.87
150 151 6.073980 CGAAACGAATAAGTTTTGGACTGAGA 60.074 38.462 0.00 0.00 43.54 3.27
151 152 6.071463 CGAAACGAATAAGTTTTGGACTGAG 58.929 40.000 0.00 0.00 43.54 3.35
152 153 5.524646 ACGAAACGAATAAGTTTTGGACTGA 59.475 36.000 12.64 0.00 45.26 3.41
153 154 5.744490 ACGAAACGAATAAGTTTTGGACTG 58.256 37.500 12.64 0.00 45.26 3.51
154 155 5.996669 ACGAAACGAATAAGTTTTGGACT 57.003 34.783 12.64 0.00 45.26 3.85
155 156 5.397240 CCAACGAAACGAATAAGTTTTGGAC 59.603 40.000 12.64 0.00 45.26 4.02
156 157 5.296283 TCCAACGAAACGAATAAGTTTTGGA 59.704 36.000 12.64 10.88 45.26 3.53
157 158 5.512473 TCCAACGAAACGAATAAGTTTTGG 58.488 37.500 12.64 9.16 45.26 3.28
159 160 8.374728 GTTTTTCCAACGAAACGAATAAGTTTT 58.625 29.630 0.00 0.00 43.54 2.43
160 161 7.009448 GGTTTTTCCAACGAAACGAATAAGTTT 59.991 33.333 0.00 0.00 37.72 2.66
163 164 5.972382 TGGTTTTTCCAACGAAACGAATAAG 59.028 36.000 0.00 0.00 44.12 1.73
164 165 5.888105 TGGTTTTTCCAACGAAACGAATAA 58.112 33.333 0.00 0.00 44.12 1.40
165 166 5.496133 TGGTTTTTCCAACGAAACGAATA 57.504 34.783 0.00 0.00 44.12 1.75
166 167 4.373348 TGGTTTTTCCAACGAAACGAAT 57.627 36.364 0.00 0.00 44.12 3.34
167 168 3.844577 TGGTTTTTCCAACGAAACGAA 57.155 38.095 0.00 0.00 44.12 3.85
177 178 0.733729 CGTCGGTGTTGGTTTTTCCA 59.266 50.000 0.00 0.00 45.60 3.53
178 179 0.734309 ACGTCGGTGTTGGTTTTTCC 59.266 50.000 0.00 0.00 0.00 3.13
179 180 1.397692 TGACGTCGGTGTTGGTTTTTC 59.602 47.619 11.62 0.00 0.00 2.29
180 181 1.451067 TGACGTCGGTGTTGGTTTTT 58.549 45.000 11.62 0.00 0.00 1.94
181 182 1.399089 CTTGACGTCGGTGTTGGTTTT 59.601 47.619 11.62 0.00 0.00 2.43
182 183 1.011333 CTTGACGTCGGTGTTGGTTT 58.989 50.000 11.62 0.00 0.00 3.27
183 184 0.176219 TCTTGACGTCGGTGTTGGTT 59.824 50.000 11.62 0.00 0.00 3.67
184 185 0.391597 ATCTTGACGTCGGTGTTGGT 59.608 50.000 11.62 0.00 0.00 3.67
185 186 2.357327 TATCTTGACGTCGGTGTTGG 57.643 50.000 11.62 0.00 0.00 3.77
186 187 2.530297 CGATATCTTGACGTCGGTGTTG 59.470 50.000 11.62 0.00 0.00 3.33
187 188 2.479049 CCGATATCTTGACGTCGGTGTT 60.479 50.000 11.62 1.56 46.29 3.32
188 189 1.065102 CCGATATCTTGACGTCGGTGT 59.935 52.381 11.62 0.00 46.29 4.16
189 190 1.755161 CCGATATCTTGACGTCGGTG 58.245 55.000 11.62 3.51 46.29 4.94
192 193 4.463515 TTAGTCCGATATCTTGACGTCG 57.536 45.455 11.62 0.00 34.24 5.12
193 194 5.564504 CGATTTAGTCCGATATCTTGACGTC 59.435 44.000 9.11 9.11 34.24 4.34
194 195 5.008415 ACGATTTAGTCCGATATCTTGACGT 59.992 40.000 13.44 0.00 34.24 4.34
195 196 5.450171 ACGATTTAGTCCGATATCTTGACG 58.550 41.667 13.44 0.00 34.24 4.35
196 197 6.360148 GTGACGATTTAGTCCGATATCTTGAC 59.640 42.308 12.09 12.09 40.26 3.18
197 198 6.038936 TGTGACGATTTAGTCCGATATCTTGA 59.961 38.462 0.34 0.00 40.26 3.02
198 199 6.206498 TGTGACGATTTAGTCCGATATCTTG 58.794 40.000 0.34 0.00 40.26 3.02
199 200 6.387041 TGTGACGATTTAGTCCGATATCTT 57.613 37.500 0.34 0.00 40.26 2.40
200 201 6.576662 ATGTGACGATTTAGTCCGATATCT 57.423 37.500 0.34 0.00 40.26 1.98
201 202 7.085116 AGAATGTGACGATTTAGTCCGATATC 58.915 38.462 0.00 0.00 40.26 1.63
202 203 6.982852 AGAATGTGACGATTTAGTCCGATAT 58.017 36.000 0.00 0.00 40.26 1.63
206 207 6.309494 TGTTTAGAATGTGACGATTTAGTCCG 59.691 38.462 0.00 0.00 40.26 4.79
235 236 2.586648 AAAGCAACCCAAGTCCTAGG 57.413 50.000 0.82 0.82 0.00 3.02
245 246 9.411801 CTAAGAAAGAAGAATTAAAAGCAACCC 57.588 33.333 0.00 0.00 0.00 4.11
281 282 2.787035 TCAACAGGGGGTAAAAACCTCT 59.213 45.455 0.00 0.00 40.20 3.69
361 363 4.857871 TCGCATTTTCTTTACGATCCAG 57.142 40.909 0.00 0.00 0.00 3.86
450 455 5.041951 ACGATGCAACGTGTGATTTAATT 57.958 34.783 21.83 0.00 44.84 1.40
489 494 7.454260 AAATGAGTCTGGAAACCTGTAATTC 57.546 36.000 0.00 0.00 0.00 2.17
572 585 0.734889 AATTGGCTTTCTCATCGCCG 59.265 50.000 0.00 0.00 46.67 6.46
806 820 1.227383 GGACGGGAAGCCCATCATT 59.773 57.895 0.66 0.00 45.83 2.57
854 868 0.252012 AGAGTGGGGAGTGAGACTGG 60.252 60.000 0.00 0.00 0.00 4.00
953 968 2.325082 CGACCGTGGGAAAAGGCAG 61.325 63.158 0.00 0.00 0.00 4.85
991 1006 0.326904 ATGGGCTCCATGTCCTCTCA 60.327 55.000 5.97 0.00 43.39 3.27
992 1007 2.537600 ATGGGCTCCATGTCCTCTC 58.462 57.895 5.97 0.00 43.39 3.20
1080 1095 1.260538 ATCTCACCTCTTGCTCGGCA 61.261 55.000 0.00 0.00 36.47 5.69
1104 1119 2.579787 CGGCGGACAGAAGCGTAG 60.580 66.667 0.00 0.00 0.00 3.51
1105 1120 2.807631 GAACGGCGGACAGAAGCGTA 62.808 60.000 13.24 0.00 0.00 4.42
1125 1140 1.080501 CGAGCGAGAAAGCCAGACA 60.081 57.895 0.00 0.00 38.01 3.41
1126 1141 2.448705 GCGAGCGAGAAAGCCAGAC 61.449 63.158 0.00 0.00 38.01 3.51
1305 1320 0.769247 TCATGCCCATCATCCTCCAG 59.231 55.000 0.00 0.00 31.79 3.86
1317 1332 1.432270 GCAAGCTAGACGTCATGCCC 61.432 60.000 19.50 8.72 0.00 5.36
1319 1334 1.633171 CGCAAGCTAGACGTCATGC 59.367 57.895 19.50 19.98 0.00 4.06
1431 1446 7.335171 GGAGCTTGCAAAAATTCCTATTTTGAT 59.665 33.333 14.05 0.00 45.96 2.57
1501 1516 0.326595 TTCCCTACTGAAATGGCGCA 59.673 50.000 10.83 0.00 0.00 6.09
1629 1644 1.669437 ACACACACACACACACGCA 60.669 52.632 0.00 0.00 0.00 5.24
1630 1645 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
1631 1646 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
1632 1647 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1633 1648 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1634 1649 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1635 1650 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1636 1651 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1637 1652 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
1638 1653 2.697431 AAACACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
1639 1654 3.189495 CCTAAAACACACACACACACACA 59.811 43.478 0.00 0.00 0.00 3.72
1640 1655 3.426963 CCCTAAAACACACACACACACAC 60.427 47.826 0.00 0.00 0.00 3.82
1641 1656 2.750166 CCCTAAAACACACACACACACA 59.250 45.455 0.00 0.00 0.00 3.72
1642 1657 3.011119 TCCCTAAAACACACACACACAC 58.989 45.455 0.00 0.00 0.00 3.82
1726 1744 3.763897 GTGGGGCTGTGAGAAACATAAAT 59.236 43.478 0.00 0.00 38.39 1.40
1876 1934 5.887754 ACCTTTGGAACCAGCTATAAAGAA 58.112 37.500 0.00 0.00 0.00 2.52
2005 2093 9.533831 ACCAAAGAACAGGATATAATTGAAAGT 57.466 29.630 0.00 0.00 0.00 2.66
2033 2132 6.597262 CCAGTTTATGGGTTGAACAAAAAC 57.403 37.500 0.00 2.34 46.36 2.43
2100 2200 2.123726 AGATGAAATGGGCCGGGC 60.124 61.111 22.00 22.00 0.00 6.13
2102 2202 1.039233 AAGCAGATGAAATGGGCCGG 61.039 55.000 0.00 0.00 0.00 6.13
2103 2203 1.679139 TAAGCAGATGAAATGGGCCG 58.321 50.000 0.00 0.00 0.00 6.13
2104 2204 4.141869 ACAATTAAGCAGATGAAATGGGCC 60.142 41.667 0.00 0.00 0.00 5.80
2313 2422 3.247648 GGAATTGTCCGTGAATATCACCG 59.752 47.826 5.00 0.00 44.20 4.94
2539 2648 6.420903 TGATTCTTACAGAAACAGTCTCAACG 59.579 38.462 0.00 0.00 37.82 4.10
2922 3091 5.757808 GCAACCATTGTGGAAACATACTTTT 59.242 36.000 2.45 0.00 46.14 2.27
3082 3251 7.716768 AGACAACTTAGTTAAAAGAGCACTC 57.283 36.000 0.00 0.00 0.00 3.51
3118 3299 2.680841 TCAACACAAGTGGCACAACTAC 59.319 45.455 21.41 0.00 44.16 2.73
3220 3401 3.550950 TTGTATGCAACCAACACATCG 57.449 42.857 0.00 0.00 0.00 3.84
3419 3601 8.074613 TGCTAAAGACAGTAATACTACCACAT 57.925 34.615 0.00 0.00 0.00 3.21
3583 3770 9.962783 GCATCTTAGAAAAATGCAGAATAATCT 57.037 29.630 0.00 0.00 44.07 2.40
3638 3826 7.064847 TGGACGTCCATATAATTTAACACACAC 59.935 37.037 33.23 0.07 42.01 3.82
3640 3828 7.279313 ACTGGACGTCCATATAATTTAACACAC 59.721 37.037 36.21 3.27 46.46 3.82
3659 3847 0.316689 GACGCCAACAAAACTGGACG 60.317 55.000 0.00 0.00 38.55 4.79
3675 3863 8.217115 GCATGAAACATAACTATCATACAGACG 58.783 37.037 0.00 0.00 31.59 4.18
3795 3985 6.913170 AGATTGTGTTTCGCTCATTTTGTAT 58.087 32.000 0.00 0.00 0.00 2.29
3798 3988 5.107760 CCAAGATTGTGTTTCGCTCATTTTG 60.108 40.000 0.00 0.00 0.00 2.44
3831 4021 9.350951 AGCTAAAATCAACTAACAGTTAAGGTT 57.649 29.630 0.00 0.00 36.03 3.50
3892 4082 6.260936 CCATTCATACAACTGGGTATCTCAAC 59.739 42.308 0.00 0.00 31.75 3.18
4040 4232 9.650371 GAAAAATGCAAGAAAACCTTATTTGAC 57.350 29.630 0.00 0.00 32.86 3.18
4064 4256 4.782691 TGTGATAATCAGAAGGGTGGAGAA 59.217 41.667 0.00 0.00 0.00 2.87
4065 4257 4.361783 TGTGATAATCAGAAGGGTGGAGA 58.638 43.478 0.00 0.00 0.00 3.71
4066 4258 4.760530 TGTGATAATCAGAAGGGTGGAG 57.239 45.455 0.00 0.00 0.00 3.86
4067 4259 6.183361 CCTTATGTGATAATCAGAAGGGTGGA 60.183 42.308 10.33 0.00 45.14 4.02
4068 4260 6.000219 CCTTATGTGATAATCAGAAGGGTGG 59.000 44.000 10.33 0.00 45.14 4.61
4075 4267 8.677300 GCAAGAAAACCTTATGTGATAATCAGA 58.323 33.333 0.00 0.00 32.86 3.27
4076 4268 8.461222 TGCAAGAAAACCTTATGTGATAATCAG 58.539 33.333 0.00 0.00 32.86 2.90
4077 4269 8.347004 TGCAAGAAAACCTTATGTGATAATCA 57.653 30.769 0.00 0.00 32.86 2.57
4078 4270 9.807649 AATGCAAGAAAACCTTATGTGATAATC 57.192 29.630 0.00 0.00 32.86 1.75
4080 4272 9.995003 AAAATGCAAGAAAACCTTATGTGATAA 57.005 25.926 0.00 0.00 32.86 1.75
4081 4273 9.995003 AAAAATGCAAGAAAACCTTATGTGATA 57.005 25.926 0.00 0.00 32.86 2.15
4082 4274 8.907222 AAAAATGCAAGAAAACCTTATGTGAT 57.093 26.923 0.00 0.00 32.86 3.06
4083 4275 8.203485 AGAAAAATGCAAGAAAACCTTATGTGA 58.797 29.630 0.00 0.00 32.86 3.58
4084 4276 8.369218 AGAAAAATGCAAGAAAACCTTATGTG 57.631 30.769 0.00 0.00 32.86 3.21
4085 4277 8.203485 TGAGAAAAATGCAAGAAAACCTTATGT 58.797 29.630 0.00 0.00 32.86 2.29
4086 4278 8.592105 TGAGAAAAATGCAAGAAAACCTTATG 57.408 30.769 0.00 0.00 32.86 1.90
4087 4279 7.386025 GCTGAGAAAAATGCAAGAAAACCTTAT 59.614 33.333 0.00 0.00 32.86 1.73
4088 4280 6.701400 GCTGAGAAAAATGCAAGAAAACCTTA 59.299 34.615 0.00 0.00 32.86 2.69
4089 4281 5.525012 GCTGAGAAAAATGCAAGAAAACCTT 59.475 36.000 0.00 0.00 34.91 3.50
4090 4282 5.052481 GCTGAGAAAAATGCAAGAAAACCT 58.948 37.500 0.00 0.00 0.00 3.50
4091 4283 4.810491 TGCTGAGAAAAATGCAAGAAAACC 59.190 37.500 0.00 0.00 32.12 3.27
4092 4284 5.971895 TGCTGAGAAAAATGCAAGAAAAC 57.028 34.783 0.00 0.00 32.12 2.43
4093 4285 7.556733 AAATGCTGAGAAAAATGCAAGAAAA 57.443 28.000 0.00 0.00 38.96 2.29
4094 4286 7.066043 ACAAAATGCTGAGAAAAATGCAAGAAA 59.934 29.630 0.00 0.00 38.96 2.52
4095 4287 6.539464 ACAAAATGCTGAGAAAAATGCAAGAA 59.461 30.769 0.00 0.00 38.96 2.52
4096 4288 6.018588 CACAAAATGCTGAGAAAAATGCAAGA 60.019 34.615 0.00 0.00 38.96 3.02
4097 4289 6.133392 CACAAAATGCTGAGAAAAATGCAAG 58.867 36.000 0.00 0.00 38.96 4.01
4098 4290 5.585445 ACACAAAATGCTGAGAAAAATGCAA 59.415 32.000 0.00 0.00 38.96 4.08
4099 4291 5.117584 ACACAAAATGCTGAGAAAAATGCA 58.882 33.333 0.00 0.00 39.83 3.96
4100 4292 5.662211 ACACAAAATGCTGAGAAAAATGC 57.338 34.783 0.00 0.00 0.00 3.56
4101 4293 7.236674 TGAACACAAAATGCTGAGAAAAATG 57.763 32.000 0.00 0.00 0.00 2.32
4102 4294 6.480981 CCTGAACACAAAATGCTGAGAAAAAT 59.519 34.615 0.00 0.00 0.00 1.82
4103 4295 5.811613 CCTGAACACAAAATGCTGAGAAAAA 59.188 36.000 0.00 0.00 0.00 1.94
4104 4296 5.350633 CCTGAACACAAAATGCTGAGAAAA 58.649 37.500 0.00 0.00 0.00 2.29
4105 4297 4.202141 CCCTGAACACAAAATGCTGAGAAA 60.202 41.667 0.00 0.00 0.00 2.52
4113 4347 6.096705 TCAATATAGCCCCTGAACACAAAATG 59.903 38.462 0.00 0.00 0.00 2.32
4403 4639 8.979574 AGAATGAACAAAGTAAAGTAGAACTCG 58.020 33.333 0.00 0.00 0.00 4.18
4874 5113 5.411361 TGTCATGGAAGTACAGCATTAACAC 59.589 40.000 0.00 0.00 0.00 3.32
4888 5127 4.518211 AGCAAAGAGAAAGTGTCATGGAAG 59.482 41.667 0.00 0.00 0.00 3.46
4897 5136 4.488879 GGCCAAATAGCAAAGAGAAAGTG 58.511 43.478 0.00 0.00 0.00 3.16
4957 5196 7.501559 AGTGCATATAAGACTGATCTGCATTTT 59.498 33.333 14.27 3.59 38.28 1.82
4973 5212 8.879759 GTTTCAGTAGCTTTACAGTGCATATAA 58.120 33.333 0.00 0.00 0.00 0.98
5092 5331 5.281693 CTTGATAAGCATCACGTGACAAA 57.718 39.130 22.71 5.37 40.94 2.83
5093 5332 4.926860 CTTGATAAGCATCACGTGACAA 57.073 40.909 22.71 16.70 40.94 3.18
5127 5366 3.552684 GCTGGCTCAAACTGCAACAATAA 60.553 43.478 0.00 0.00 33.62 1.40
5133 5372 2.202395 GGGCTGGCTCAAACTGCAA 61.202 57.895 0.00 0.00 34.89 4.08
5414 5877 1.065410 TGGCCCTTTCTTCACCTGGA 61.065 55.000 0.00 0.00 0.00 3.86
5462 5938 4.757019 TGCCAATGTAAAATGCCATGAT 57.243 36.364 0.00 0.00 0.00 2.45
5463 5939 4.548451 TTGCCAATGTAAAATGCCATGA 57.452 36.364 0.00 0.00 0.00 3.07
5582 6058 7.784633 TGGAAAAACAAATAAAGCTTTGGAG 57.215 32.000 22.02 10.91 39.83 3.86
5616 6092 9.387397 TCCCCTCTACATGTTGTATTCATTATA 57.613 33.333 2.30 0.00 31.66 0.98
5621 6097 5.277250 TCTCCCCTCTACATGTTGTATTCA 58.723 41.667 2.30 0.00 31.66 2.57
5622 6098 5.871396 TCTCCCCTCTACATGTTGTATTC 57.129 43.478 2.30 0.00 31.66 1.75
5626 6102 3.248024 TGTTCTCCCCTCTACATGTTGT 58.752 45.455 2.30 0.00 0.00 3.32
5627 6103 3.981071 TGTTCTCCCCTCTACATGTTG 57.019 47.619 2.30 1.19 0.00 3.33
5628 6104 4.993705 TTTGTTCTCCCCTCTACATGTT 57.006 40.909 2.30 0.00 0.00 2.71
5630 6106 8.525290 AAAATATTTGTTCTCCCCTCTACATG 57.475 34.615 0.39 0.00 0.00 3.21
5631 6107 8.560903 AGAAAATATTTGTTCTCCCCTCTACAT 58.439 33.333 0.39 0.00 27.52 2.29
5632 6108 7.829211 CAGAAAATATTTGTTCTCCCCTCTACA 59.171 37.037 0.39 0.00 31.66 2.74
5633 6109 7.829706 ACAGAAAATATTTGTTCTCCCCTCTAC 59.170 37.037 0.39 0.00 31.66 2.59
5634 6110 7.928873 ACAGAAAATATTTGTTCTCCCCTCTA 58.071 34.615 0.39 0.00 31.66 2.43
5636 6112 7.039714 ACAACAGAAAATATTTGTTCTCCCCTC 60.040 37.037 0.39 0.00 33.06 4.30
5637 6113 6.782494 ACAACAGAAAATATTTGTTCTCCCCT 59.218 34.615 0.39 0.00 33.06 4.79
5638 6114 6.993079 ACAACAGAAAATATTTGTTCTCCCC 58.007 36.000 0.39 0.00 33.06 4.81
5639 6115 8.887036 AAACAACAGAAAATATTTGTTCTCCC 57.113 30.769 0.39 0.00 40.44 4.30
5739 6218 4.277476 TCCACTGAAGAAACACATTTGGT 58.723 39.130 0.00 0.00 0.00 3.67
5821 6303 2.317609 CCGCCTCAACACCGAACAG 61.318 63.158 0.00 0.00 0.00 3.16
5833 6315 2.668550 GTGTGAACCCACCGCCTC 60.669 66.667 0.00 0.00 42.53 4.70
6051 6539 1.000052 TGAACGACGTATGCAGGTTCA 60.000 47.619 0.00 10.34 43.16 3.18
6138 6627 4.181010 CTCTCCCACCCATGGCCG 62.181 72.222 6.09 0.00 45.76 6.13


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

AutoCloner maintained by Alex Coulton.