Multiple sequence alignment - TraesCS5A01G238500

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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 TraesCS5A01G238500 chr5A 100.000 4460 0 0 1 4460 454766007 454770466 0.000000e+00 8237
1 TraesCS5A01G238500 chr5A 96.196 184 7 0 3 186 473305013 473305196 7.250000e-78 302
2 TraesCS5A01G238500 chr5B 95.228 2976 115 8 837 3796 418009201 418012165 0.000000e+00 4684
3 TraesCS5A01G238500 chr5B 88.398 724 32 17 3762 4455 418012165 418012866 0.000000e+00 824
4 TraesCS5A01G238500 chr5B 89.577 662 43 16 197 857 418008552 418009188 0.000000e+00 817
5 TraesCS5A01G238500 chr5D 96.028 2820 99 5 837 3649 353801288 353804101 0.000000e+00 4575
6 TraesCS5A01G238500 chr5D 92.342 666 28 10 3802 4452 353804094 353804751 0.000000e+00 926
7 TraesCS5A01G238500 chr5D 90.045 663 36 6 197 855 353800639 353801275 0.000000e+00 832
8 TraesCS5A01G238500 chr5D 93.814 194 12 0 3 196 41407806 41407999 4.360000e-75 292
9 TraesCS5A01G238500 chr3A 88.912 487 21 8 1059 1529 543715934 543716403 1.800000e-158 569
10 TraesCS5A01G238500 chr6A 99.492 197 1 0 1 197 585416579 585416383 4.240000e-95 359
11 TraesCS5A01G238500 chr6A 96.410 195 7 0 3 197 593803037 593802843 5.570000e-84 322
12 TraesCS5A01G238500 chr4D 95.361 194 8 1 3 196 22227923 22228115 1.560000e-79 307
13 TraesCS5A01G238500 chrUn 94.845 194 10 0 3 196 24148930 24149123 2.020000e-78 303
14 TraesCS5A01G238500 chr6D 93.814 194 12 0 3 196 159019645 159019838 4.360000e-75 292
15 TraesCS5A01G238500 chr6D 92.821 195 12 2 3 196 159018860 159018667 9.450000e-72 281
16 TraesCS5A01G238500 chr1D 93.299 194 13 0 3 196 481445944 481445751 2.030000e-73 287


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 TraesCS5A01G238500 chr5A 454766007 454770466 4459 False 8237.000000 8237 100.000000 1 4460 1 chr5A.!!$F1 4459
1 TraesCS5A01G238500 chr5B 418008552 418012866 4314 False 2108.333333 4684 91.067667 197 4455 3 chr5B.!!$F1 4258
2 TraesCS5A01G238500 chr5D 353800639 353804751 4112 False 2111.000000 4575 92.805000 197 4452 3 chr5D.!!$F2 4255


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
174 175 0.108945 GGACGACGACCCCTAAAGTG 60.109 60.0 0.0 0.0 0.00 3.16 F
1121 1160 0.308993 GCTGTTGTTCCAGACACTGC 59.691 55.0 0.0 0.0 38.18 4.40 F
2401 2440 0.608640 GGAAAGCGAGGTTGGAGAGA 59.391 55.0 0.0 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1826 1865 0.319211 TTGCTGTGCTTGCAATGCTC 60.319 50.0 17.72 15.21 44.24 4.26 R
2762 2801 0.176910 GTCTGCCTCTTCACTAGCCC 59.823 60.0 0.00 0.00 0.00 5.19 R
4392 4530 0.248296 GAGTACGCCGAGAAGCTCAG 60.248 60.0 0.00 0.00 0.00 3.35 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
27 28 1.555992 TGGGTCCCACCTGTAATAACG 59.444 52.381 6.47 0.00 38.64 3.18
28 29 1.134310 GGGTCCCACCTGTAATAACGG 60.134 57.143 1.78 0.00 38.64 4.44
29 30 1.556451 GGTCCCACCTGTAATAACGGT 59.444 52.381 0.00 0.00 34.73 4.83
30 31 2.419159 GGTCCCACCTGTAATAACGGTC 60.419 54.545 0.00 0.00 34.73 4.79
31 32 2.234414 GTCCCACCTGTAATAACGGTCA 59.766 50.000 0.00 0.00 32.51 4.02
32 33 2.905085 TCCCACCTGTAATAACGGTCAA 59.095 45.455 0.00 0.00 32.51 3.18
33 34 3.004862 CCCACCTGTAATAACGGTCAAC 58.995 50.000 0.00 0.00 32.51 3.18
34 35 3.307199 CCCACCTGTAATAACGGTCAACT 60.307 47.826 0.00 0.00 32.51 3.16
35 36 3.682858 CCACCTGTAATAACGGTCAACTG 59.317 47.826 0.00 0.00 32.51 3.16
36 37 4.561938 CCACCTGTAATAACGGTCAACTGA 60.562 45.833 0.00 0.00 32.51 3.41
37 38 4.992319 CACCTGTAATAACGGTCAACTGAA 59.008 41.667 0.00 0.00 32.51 3.02
38 39 4.992951 ACCTGTAATAACGGTCAACTGAAC 59.007 41.667 0.00 0.00 30.05 3.18
46 47 1.658994 GGTCAACTGAACGGTCAACA 58.341 50.000 3.93 0.00 31.88 3.33
47 48 2.218603 GGTCAACTGAACGGTCAACAT 58.781 47.619 3.93 0.00 31.88 2.71
48 49 2.032030 GGTCAACTGAACGGTCAACATG 60.032 50.000 3.93 3.96 31.88 3.21
49 50 2.612212 GTCAACTGAACGGTCAACATGT 59.388 45.455 3.93 0.00 31.88 3.21
50 51 3.064820 GTCAACTGAACGGTCAACATGTT 59.935 43.478 3.93 4.92 31.88 2.71
51 52 3.692101 TCAACTGAACGGTCAACATGTTT 59.308 39.130 8.77 0.00 31.88 2.83
52 53 4.876679 TCAACTGAACGGTCAACATGTTTA 59.123 37.500 8.77 0.00 31.88 2.01
53 54 5.354513 TCAACTGAACGGTCAACATGTTTAA 59.645 36.000 8.77 0.00 31.88 1.52
54 55 5.821516 ACTGAACGGTCAACATGTTTAAA 57.178 34.783 8.77 0.00 31.88 1.52
55 56 6.385649 ACTGAACGGTCAACATGTTTAAAT 57.614 33.333 8.77 0.00 31.88 1.40
56 57 6.435428 ACTGAACGGTCAACATGTTTAAATC 58.565 36.000 8.77 3.90 31.88 2.17
57 58 5.444983 TGAACGGTCAACATGTTTAAATCG 58.555 37.500 8.77 11.85 0.00 3.34
58 59 5.007823 TGAACGGTCAACATGTTTAAATCGT 59.992 36.000 8.77 12.49 0.00 3.73
59 60 5.427036 ACGGTCAACATGTTTAAATCGTT 57.573 34.783 8.77 0.00 0.00 3.85
60 61 5.823353 ACGGTCAACATGTTTAAATCGTTT 58.177 33.333 8.77 0.00 0.00 3.60
61 62 6.957150 ACGGTCAACATGTTTAAATCGTTTA 58.043 32.000 8.77 0.00 0.00 2.01
62 63 7.416022 ACGGTCAACATGTTTAAATCGTTTAA 58.584 30.769 8.77 0.67 33.56 1.52
63 64 7.914346 ACGGTCAACATGTTTAAATCGTTTAAA 59.086 29.630 8.77 9.91 41.40 1.52
78 79 9.715121 AAATCGTTTAAACTGTCTATTACCTGA 57.285 29.630 16.01 2.08 0.00 3.86
79 80 9.715121 AATCGTTTAAACTGTCTATTACCTGAA 57.285 29.630 16.01 0.00 0.00 3.02
80 81 9.715121 ATCGTTTAAACTGTCTATTACCTGAAA 57.285 29.630 16.01 0.00 0.00 2.69
81 82 8.981647 TCGTTTAAACTGTCTATTACCTGAAAC 58.018 33.333 16.01 0.00 0.00 2.78
82 83 8.985805 CGTTTAAACTGTCTATTACCTGAAACT 58.014 33.333 16.01 0.00 0.00 2.66
84 85 8.842358 TTAAACTGTCTATTACCTGAAACTGG 57.158 34.615 0.00 0.00 0.00 4.00
85 86 6.435292 AACTGTCTATTACCTGAAACTGGT 57.565 37.500 0.00 0.00 39.06 4.00
86 87 7.549147 AACTGTCTATTACCTGAAACTGGTA 57.451 36.000 0.00 0.00 36.99 3.25
87 88 7.171630 ACTGTCTATTACCTGAAACTGGTAG 57.828 40.000 0.00 0.00 38.72 3.18
88 89 6.724905 ACTGTCTATTACCTGAAACTGGTAGT 59.275 38.462 0.00 0.00 38.72 2.73
89 90 7.234988 ACTGTCTATTACCTGAAACTGGTAGTT 59.765 37.037 0.00 0.00 40.80 2.24
140 141 8.686397 GGTAGTTTTCGACCACTTTTTAAAAA 57.314 30.769 12.62 12.62 43.55 1.94
141 142 8.800972 GGTAGTTTTCGACCACTTTTTAAAAAG 58.199 33.333 30.29 30.29 43.55 2.27
155 156 8.628882 CTTTTTAAAAAGTGGTAGTTCTGTGG 57.371 34.615 25.95 2.68 40.31 4.17
156 157 6.702716 TTTAAAAAGTGGTAGTTCTGTGGG 57.297 37.500 0.00 0.00 0.00 4.61
157 158 4.513406 AAAAAGTGGTAGTTCTGTGGGA 57.487 40.909 0.00 0.00 0.00 4.37
158 159 3.487120 AAAGTGGTAGTTCTGTGGGAC 57.513 47.619 0.00 0.00 0.00 4.46
159 160 0.966920 AGTGGTAGTTCTGTGGGACG 59.033 55.000 0.00 0.00 0.00 4.79
160 161 0.963962 GTGGTAGTTCTGTGGGACGA 59.036 55.000 0.00 0.00 0.00 4.20
161 162 0.963962 TGGTAGTTCTGTGGGACGAC 59.036 55.000 0.00 0.00 0.00 4.34
162 163 0.109412 GGTAGTTCTGTGGGACGACG 60.109 60.000 0.00 0.00 0.00 5.12
163 164 0.877071 GTAGTTCTGTGGGACGACGA 59.123 55.000 0.00 0.00 0.00 4.20
164 165 0.877071 TAGTTCTGTGGGACGACGAC 59.123 55.000 0.00 0.00 0.00 4.34
165 166 1.372623 GTTCTGTGGGACGACGACC 60.373 63.158 7.89 7.89 0.00 4.79
166 167 2.567497 TTCTGTGGGACGACGACCC 61.567 63.158 25.82 25.82 46.87 4.46
167 168 4.065281 CTGTGGGACGACGACCCC 62.065 72.222 28.56 23.26 46.21 4.95
168 169 4.608774 TGTGGGACGACGACCCCT 62.609 66.667 28.56 0.00 46.21 4.79
169 170 2.361610 GTGGGACGACGACCCCTA 60.362 66.667 28.56 11.66 46.21 3.53
170 171 1.978617 GTGGGACGACGACCCCTAA 60.979 63.158 28.56 10.95 46.21 2.69
171 172 1.228831 TGGGACGACGACCCCTAAA 60.229 57.895 28.56 10.60 46.21 1.85
172 173 1.252904 TGGGACGACGACCCCTAAAG 61.253 60.000 28.56 0.00 46.21 1.85
173 174 1.253593 GGGACGACGACCCCTAAAGT 61.254 60.000 22.79 0.00 41.38 2.66
174 175 0.108945 GGACGACGACCCCTAAAGTG 60.109 60.000 0.00 0.00 0.00 3.16
175 176 0.108945 GACGACGACCCCTAAAGTGG 60.109 60.000 0.00 0.00 0.00 4.00
176 177 0.829182 ACGACGACCCCTAAAGTGGT 60.829 55.000 0.00 0.00 37.64 4.16
177 178 1.176527 CGACGACCCCTAAAGTGGTA 58.823 55.000 0.00 0.00 34.20 3.25
178 179 1.133790 CGACGACCCCTAAAGTGGTAG 59.866 57.143 0.00 0.00 34.20 3.18
179 180 2.174360 GACGACCCCTAAAGTGGTAGT 58.826 52.381 0.00 0.00 42.23 2.73
180 181 2.564504 GACGACCCCTAAAGTGGTAGTT 59.435 50.000 0.00 0.00 40.05 2.24
181 182 2.974794 ACGACCCCTAAAGTGGTAGTTT 59.025 45.455 0.00 0.00 37.19 2.66
182 183 3.392285 ACGACCCCTAAAGTGGTAGTTTT 59.608 43.478 0.00 0.00 37.19 2.43
183 184 4.141413 ACGACCCCTAAAGTGGTAGTTTTT 60.141 41.667 0.00 0.00 37.19 1.94
227 228 3.572682 CCCCTGGTTAGTCCTTTTCAAAC 59.427 47.826 0.00 0.00 37.07 2.93
245 250 7.401484 TTCAAACAAAATTAACAATCTCGGC 57.599 32.000 0.00 0.00 0.00 5.54
247 252 6.980978 TCAAACAAAATTAACAATCTCGGCAA 59.019 30.769 0.00 0.00 0.00 4.52
411 416 1.280421 AGCCAGAGTAGCCCTCAAAAG 59.720 52.381 4.03 0.00 43.12 2.27
419 424 0.779997 AGCCCTCAAAAGGTCATGGT 59.220 50.000 0.00 0.00 41.59 3.55
470 475 7.896383 TTGCAAAATATAAGTGCCTTATCCT 57.104 32.000 0.00 0.00 37.72 3.24
479 484 4.414337 AGTGCCTTATCCTGAGTTCATC 57.586 45.455 0.00 0.00 0.00 2.92
533 538 3.044059 GATGGCCAGCACGCAGTTC 62.044 63.158 18.08 0.00 41.61 3.01
538 543 1.005037 CCAGCACGCAGTTCACCTA 60.005 57.895 0.00 0.00 41.61 3.08
542 547 1.227999 GCACGCAGTTCACCTAGCAA 61.228 55.000 0.00 0.00 41.61 3.91
547 552 2.494059 GCAGTTCACCTAGCAACTTGA 58.506 47.619 0.00 0.00 30.06 3.02
553 558 4.785511 TCACCTAGCAACTTGACTAGAC 57.214 45.455 15.97 0.00 38.53 2.59
582 587 2.736531 CCAGCACAAAGGGCCAAC 59.263 61.111 6.18 0.00 0.00 3.77
591 596 2.429250 ACAAAGGGCCAACTAACAACAC 59.571 45.455 6.18 0.00 0.00 3.32
597 602 4.896482 AGGGCCAACTAACAACACAAATAA 59.104 37.500 6.18 0.00 0.00 1.40
631 636 6.760298 CAGACGCTCTGCCATCAAATATATAT 59.240 38.462 2.75 0.00 37.72 0.86
632 637 7.922811 CAGACGCTCTGCCATCAAATATATATA 59.077 37.037 0.00 0.00 37.72 0.86
633 638 8.646004 AGACGCTCTGCCATCAAATATATATAT 58.354 33.333 0.00 0.00 0.00 0.86
634 639 9.914131 GACGCTCTGCCATCAAATATATATATA 57.086 33.333 5.66 4.92 0.00 0.86
739 744 5.486526 ACTGCTCTTGTCCTCTTATGAAAG 58.513 41.667 0.00 0.00 0.00 2.62
894 933 9.609346 CATGATTCCTGAACATATATCAGCATA 57.391 33.333 10.73 1.77 42.36 3.14
977 1016 9.603298 CATGATAATTATTTGAACTCACCATCG 57.397 33.333 0.00 0.00 0.00 3.84
1025 1064 3.416156 AGGAACTGAATGTTGAAGGAGC 58.584 45.455 0.00 0.00 39.30 4.70
1030 1069 1.270785 TGAATGTTGAAGGAGCGCAGA 60.271 47.619 11.47 0.00 0.00 4.26
1114 1153 4.067896 ACATCAAGTAGCTGTTGTTCCAG 58.932 43.478 0.00 0.00 35.49 3.86
1121 1160 0.308993 GCTGTTGTTCCAGACACTGC 59.691 55.000 0.00 0.00 38.18 4.40
1169 1208 4.016444 TCAAAGCCTCTTGTTTCTGTTGT 58.984 39.130 0.00 0.00 0.00 3.32
1344 1383 9.936329 ATAGGTTCCCTTACAATTAATGAATGT 57.064 29.630 0.00 0.00 34.61 2.71
1375 1414 8.971321 CAAACAAAGTAGAGGAAAATTGTCATG 58.029 33.333 0.00 0.00 31.19 3.07
1449 1488 5.461737 TGAAAGAAACATTTTTAAGGCAGCG 59.538 36.000 0.00 0.00 0.00 5.18
1630 1669 2.185004 GCCTTGTCTTGGCTCTACAA 57.815 50.000 0.00 0.00 46.38 2.41
1826 1865 1.610522 CCTGGAGAAAGCACAAACTGG 59.389 52.381 0.00 0.00 0.00 4.00
1890 1929 5.187186 ACGATACAAAGAGATACAACAGGGT 59.813 40.000 0.00 0.00 0.00 4.34
2014 2053 1.141657 AGCAGCTTGAGAAGGAACACA 59.858 47.619 0.00 0.00 0.00 3.72
2043 2082 7.229506 GCTTTAATTACACATAGGGAGAATGCT 59.770 37.037 0.00 0.00 0.00 3.79
2274 2313 2.995466 TTCAAAAGCTGAATGGCGAG 57.005 45.000 0.00 0.00 39.20 5.03
2388 2427 2.770164 TACTGCCTGAGAAGGAAAGC 57.230 50.000 0.00 0.00 0.00 3.51
2401 2440 0.608640 GGAAAGCGAGGTTGGAGAGA 59.391 55.000 0.00 0.00 0.00 3.10
2419 2458 3.197766 AGAGAAAGTGCGATCCATGGTTA 59.802 43.478 12.58 0.00 0.00 2.85
2424 2463 1.933853 GTGCGATCCATGGTTAGTGTC 59.066 52.381 12.58 1.33 0.00 3.67
2460 2499 2.849294 AGACCAGGAAAGAGCTTGAC 57.151 50.000 0.00 0.00 0.00 3.18
2486 2525 2.224090 TGAGGACAAACATCGAAACGGA 60.224 45.455 0.00 0.00 31.38 4.69
2635 2674 3.005897 CCAGGAAGAACTGAGAAAGACGA 59.994 47.826 0.00 0.00 40.97 4.20
2636 2675 4.322349 CCAGGAAGAACTGAGAAAGACGAT 60.322 45.833 0.00 0.00 40.97 3.73
2643 2682 2.288213 ACTGAGAAAGACGATGCGTGAA 60.288 45.455 0.00 0.00 41.37 3.18
2652 2691 1.617755 CGATGCGTGAACTCAGCGTT 61.618 55.000 3.14 0.00 35.99 4.84
2659 2698 1.792949 GTGAACTCAGCGTTGTACAGG 59.207 52.381 0.00 0.00 35.56 4.00
2698 2737 4.778213 AAAATGCCCATAGAGCTACAGA 57.222 40.909 0.00 0.00 0.00 3.41
2720 2759 4.423625 AGGCTACTCAAGAAACACAACT 57.576 40.909 0.00 0.00 0.00 3.16
2762 2801 1.009829 GCCTGCGATGAGGTTACAAG 58.990 55.000 0.00 0.00 35.29 3.16
2769 2808 2.431057 CGATGAGGTTACAAGGGCTAGT 59.569 50.000 0.00 0.00 0.00 2.57
2868 2907 4.333926 GCGGTTAAAGCATCAGAAGAGATT 59.666 41.667 0.00 0.00 34.19 2.40
2938 2977 1.123928 AGATCCCCAAGCTAACCGAG 58.876 55.000 0.00 0.00 0.00 4.63
3009 3048 0.908198 AGAGAGCAAAGGAAGCCGAT 59.092 50.000 0.00 0.00 0.00 4.18
3154 3193 1.424493 GAGGGACGCGCATGAGAAAG 61.424 60.000 5.73 0.00 0.00 2.62
3155 3194 1.741770 GGGACGCGCATGAGAAAGT 60.742 57.895 5.73 0.00 0.00 2.66
3171 3210 3.812053 AGAAAGTCATCACAGCACAAGAC 59.188 43.478 0.00 0.00 0.00 3.01
3180 3219 3.119884 TCACAGCACAAGACAACAAGTTG 60.120 43.478 11.16 11.16 45.58 3.16
3213 3252 2.355197 GAGCTGAGGAAAAGAAGAGCC 58.645 52.381 0.00 0.00 0.00 4.70
3240 3279 2.483288 CAACATTACACGGCGGGC 59.517 61.111 10.14 0.00 0.00 6.13
3261 3300 2.735100 GCCGATCTCGCGATTCCC 60.735 66.667 10.36 0.00 38.18 3.97
3263 3302 2.429236 CGATCTCGCGATTCCCGG 60.429 66.667 10.36 0.00 39.04 5.73
3281 3320 1.338105 CGGTGTCTGCCTTCTGAATGA 60.338 52.381 0.00 0.00 0.00 2.57
3282 3321 2.679059 CGGTGTCTGCCTTCTGAATGAT 60.679 50.000 0.00 0.00 0.00 2.45
3315 3354 1.960040 TTGATGCAGCGGGATCGTCT 61.960 55.000 13.16 0.00 44.12 4.18
3325 3364 1.863267 GGGATCGTCTGCTTCTCATG 58.137 55.000 0.00 0.00 0.00 3.07
3357 3396 1.736365 GCCTAGGTAGAGCCGACACC 61.736 65.000 11.31 0.00 43.70 4.16
3399 3438 3.431725 CCAAAGGCGCGGAAGTCC 61.432 66.667 8.83 0.00 0.00 3.85
3447 3486 7.623630 TGATGTTCATGAATAGGAAGAAGACA 58.376 34.615 12.12 1.00 0.00 3.41
3476 3515 1.798813 GTGAACCTCCGTAGTTTGCTG 59.201 52.381 0.00 0.00 0.00 4.41
3485 3524 5.353394 TCCGTAGTTTGCTGATTTCCTAT 57.647 39.130 0.00 0.00 0.00 2.57
3494 3533 7.446625 AGTTTGCTGATTTCCTATGGTATGATC 59.553 37.037 0.00 0.00 0.00 2.92
3592 3639 1.170290 TCGTCGGTCTGAGCTTGTCA 61.170 55.000 5.23 0.00 0.00 3.58
3645 3695 5.694674 GAAGCTGTCTTCGTTAGAATCAG 57.305 43.478 0.00 8.24 39.29 2.90
3646 3696 5.392767 AAGCTGTCTTCGTTAGAATCAGA 57.607 39.130 13.45 0.00 38.87 3.27
3655 3705 7.702772 GTCTTCGTTAGAATCAGAAGAAGCATA 59.297 37.037 8.12 0.00 46.94 3.14
3657 3707 6.273825 TCGTTAGAATCAGAAGAAGCATACC 58.726 40.000 0.00 0.00 0.00 2.73
3665 3715 4.081420 TCAGAAGAAGCATACCTCTGAACC 60.081 45.833 0.00 0.00 30.98 3.62
3669 3719 3.584848 AGAAGCATACCTCTGAACCTGTT 59.415 43.478 0.00 0.00 0.00 3.16
3681 3731 4.394920 TCTGAACCTGTTGACAGTGTTTTC 59.605 41.667 10.03 7.44 42.27 2.29
3714 3764 8.946085 TCATTTAGCTTGACGATTTGTTATCTT 58.054 29.630 0.00 0.00 0.00 2.40
3730 3780 7.692460 TGTTATCTTTCACATGAGCATTTCT 57.308 32.000 0.00 0.00 0.00 2.52
3732 3782 7.175467 TGTTATCTTTCACATGAGCATTTCTGT 59.825 33.333 0.00 0.00 0.00 3.41
3736 3786 4.548451 TCACATGAGCATTTCTGTCTCT 57.452 40.909 0.00 0.00 31.13 3.10
3737 3787 4.251268 TCACATGAGCATTTCTGTCTCTG 58.749 43.478 0.00 0.00 31.13 3.35
3738 3788 4.020839 TCACATGAGCATTTCTGTCTCTGA 60.021 41.667 0.00 0.00 31.13 3.27
3739 3789 4.876679 CACATGAGCATTTCTGTCTCTGAT 59.123 41.667 0.00 0.00 31.13 2.90
3740 3790 4.876679 ACATGAGCATTTCTGTCTCTGATG 59.123 41.667 0.00 0.00 31.13 3.07
3741 3791 3.870274 TGAGCATTTCTGTCTCTGATGG 58.130 45.455 0.00 0.00 31.13 3.51
3742 3792 3.262660 TGAGCATTTCTGTCTCTGATGGT 59.737 43.478 0.00 0.00 31.13 3.55
3743 3793 4.260170 GAGCATTTCTGTCTCTGATGGTT 58.740 43.478 0.00 0.00 0.00 3.67
3744 3794 4.660168 AGCATTTCTGTCTCTGATGGTTT 58.340 39.130 0.00 0.00 0.00 3.27
3745 3795 4.699257 AGCATTTCTGTCTCTGATGGTTTC 59.301 41.667 0.00 0.00 0.00 2.78
3746 3796 4.142513 GCATTTCTGTCTCTGATGGTTTCC 60.143 45.833 0.00 0.00 0.00 3.13
3747 3797 4.705110 TTTCTGTCTCTGATGGTTTCCA 57.295 40.909 0.00 0.00 38.19 3.53
3748 3798 3.969287 TCTGTCTCTGATGGTTTCCAG 57.031 47.619 0.00 0.00 36.75 3.86
3778 3840 4.088634 ACTGCTCCCAGAATGCAAATTAA 58.911 39.130 0.00 0.00 41.77 1.40
3828 3921 7.784633 AGAGCTGTCTGAGAATTTATAAAGC 57.215 36.000 3.94 0.00 0.00 3.51
3886 3990 9.398538 TCCTTTTGCTTAAAGTAAGTAAGAACA 57.601 29.630 9.86 0.00 40.55 3.18
3905 4016 8.628882 AAGAACATTTAGCAAAACAACTACAC 57.371 30.769 0.00 0.00 0.00 2.90
3945 4065 2.550978 AGAGAAGTTCACACAACACCG 58.449 47.619 5.50 0.00 0.00 4.94
3961 4081 1.462283 CACCGTTGAATCACTCTGCAG 59.538 52.381 7.63 7.63 0.00 4.41
3989 4109 3.704061 TCCTGCTTGTAAATTTATGGGGC 59.296 43.478 0.31 5.13 0.00 5.80
4305 4437 3.365265 CCACCGCCTTCTGGTTGC 61.365 66.667 0.00 0.00 37.72 4.17
4311 4443 2.048222 CCTTCTGGTTGCGCGAGA 60.048 61.111 12.10 0.00 0.00 4.04
4319 4451 3.621805 TTGCGCGAGAGGTTCCCA 61.622 61.111 12.10 0.00 0.00 4.37
4320 4452 3.589654 TTGCGCGAGAGGTTCCCAG 62.590 63.158 12.10 0.00 0.00 4.45
4324 4456 4.821589 CGAGAGGTTCCCAGCGCC 62.822 72.222 2.29 0.00 0.00 6.53
4358 4496 4.057428 AGCACGCTGACGGTCTCC 62.057 66.667 9.88 0.00 46.04 3.71
4392 4530 0.179179 GTGCTCGTAGTACGTGGACC 60.179 60.000 28.26 16.08 45.86 4.46
4421 4559 3.450115 GCGTACTCCGGGTGCTCT 61.450 66.667 0.00 0.00 36.94 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.555992 CGTTATTACAGGTGGGACCCA 59.444 52.381 9.95 9.95 39.75 4.51
8 9 1.134310 CCGTTATTACAGGTGGGACCC 60.134 57.143 2.45 2.45 39.75 4.46
9 10 1.556451 ACCGTTATTACAGGTGGGACC 59.444 52.381 0.00 0.00 36.81 4.46
10 11 2.234414 TGACCGTTATTACAGGTGGGAC 59.766 50.000 3.68 0.00 38.57 4.46
11 12 2.538222 TGACCGTTATTACAGGTGGGA 58.462 47.619 3.68 0.00 38.57 4.37
12 13 3.004862 GTTGACCGTTATTACAGGTGGG 58.995 50.000 3.68 0.00 38.57 4.61
13 14 3.682858 CAGTTGACCGTTATTACAGGTGG 59.317 47.826 3.68 0.00 38.57 4.61
14 15 4.562082 TCAGTTGACCGTTATTACAGGTG 58.438 43.478 3.68 0.00 38.57 4.00
15 16 4.877378 TCAGTTGACCGTTATTACAGGT 57.123 40.909 0.00 0.00 41.63 4.00
16 17 4.090930 CGTTCAGTTGACCGTTATTACAGG 59.909 45.833 0.00 0.00 0.00 4.00
17 18 4.090930 CCGTTCAGTTGACCGTTATTACAG 59.909 45.833 0.00 0.00 0.00 2.74
18 19 3.989167 CCGTTCAGTTGACCGTTATTACA 59.011 43.478 0.00 0.00 0.00 2.41
19 20 3.989817 ACCGTTCAGTTGACCGTTATTAC 59.010 43.478 0.00 0.00 0.00 1.89
20 21 4.236935 GACCGTTCAGTTGACCGTTATTA 58.763 43.478 0.00 0.00 0.00 0.98
21 22 3.062042 GACCGTTCAGTTGACCGTTATT 58.938 45.455 0.00 0.00 0.00 1.40
22 23 2.036217 TGACCGTTCAGTTGACCGTTAT 59.964 45.455 0.00 0.00 0.00 1.89
23 24 1.408340 TGACCGTTCAGTTGACCGTTA 59.592 47.619 0.00 0.00 0.00 3.18
24 25 0.176219 TGACCGTTCAGTTGACCGTT 59.824 50.000 0.00 0.00 0.00 4.44
25 26 0.176219 TTGACCGTTCAGTTGACCGT 59.824 50.000 0.00 0.00 31.71 4.83
26 27 0.580104 GTTGACCGTTCAGTTGACCG 59.420 55.000 0.00 0.00 31.71 4.79
27 28 1.658994 TGTTGACCGTTCAGTTGACC 58.341 50.000 0.00 0.00 31.71 4.02
28 29 2.612212 ACATGTTGACCGTTCAGTTGAC 59.388 45.455 0.00 0.00 31.71 3.18
29 30 2.912771 ACATGTTGACCGTTCAGTTGA 58.087 42.857 0.00 0.00 31.71 3.18
30 31 3.691049 AACATGTTGACCGTTCAGTTG 57.309 42.857 11.07 0.00 31.71 3.16
31 32 5.821516 TTAAACATGTTGACCGTTCAGTT 57.178 34.783 12.82 0.00 31.71 3.16
32 33 5.821516 TTTAAACATGTTGACCGTTCAGT 57.178 34.783 12.82 0.00 31.71 3.41
33 34 5.563751 CGATTTAAACATGTTGACCGTTCAG 59.436 40.000 12.82 0.00 31.71 3.02
34 35 5.007823 ACGATTTAAACATGTTGACCGTTCA 59.992 36.000 12.82 0.00 0.00 3.18
35 36 5.445845 ACGATTTAAACATGTTGACCGTTC 58.554 37.500 12.82 4.42 0.00 3.95
36 37 5.427036 ACGATTTAAACATGTTGACCGTT 57.573 34.783 12.82 0.00 0.00 4.44
37 38 5.427036 AACGATTTAAACATGTTGACCGT 57.573 34.783 12.82 13.96 0.00 4.83
38 39 7.839438 TTAAACGATTTAAACATGTTGACCG 57.161 32.000 12.82 13.36 32.53 4.79
52 53 9.715121 TCAGGTAATAGACAGTTTAAACGATTT 57.285 29.630 12.54 3.41 0.00 2.17
53 54 9.715121 TTCAGGTAATAGACAGTTTAAACGATT 57.285 29.630 12.54 10.39 0.00 3.34
54 55 9.715121 TTTCAGGTAATAGACAGTTTAAACGAT 57.285 29.630 12.54 4.98 0.00 3.73
55 56 8.981647 GTTTCAGGTAATAGACAGTTTAAACGA 58.018 33.333 12.54 0.00 0.00 3.85
56 57 8.985805 AGTTTCAGGTAATAGACAGTTTAAACG 58.014 33.333 12.54 10.03 0.00 3.60
58 59 9.280174 CCAGTTTCAGGTAATAGACAGTTTAAA 57.720 33.333 0.00 0.00 0.00 1.52
59 60 8.434392 ACCAGTTTCAGGTAATAGACAGTTTAA 58.566 33.333 0.00 0.00 37.67 1.52
60 61 7.970102 ACCAGTTTCAGGTAATAGACAGTTTA 58.030 34.615 0.00 0.00 37.67 2.01
61 62 6.838382 ACCAGTTTCAGGTAATAGACAGTTT 58.162 36.000 0.00 0.00 37.67 2.66
62 63 6.435292 ACCAGTTTCAGGTAATAGACAGTT 57.565 37.500 0.00 0.00 37.67 3.16
63 64 6.724905 ACTACCAGTTTCAGGTAATAGACAGT 59.275 38.462 0.00 0.00 40.87 3.55
64 65 7.171630 ACTACCAGTTTCAGGTAATAGACAG 57.828 40.000 0.00 0.00 40.87 3.51
65 66 7.549147 AACTACCAGTTTCAGGTAATAGACA 57.451 36.000 0.00 0.00 40.87 3.41
66 67 8.843885 AAAACTACCAGTTTCAGGTAATAGAC 57.156 34.615 4.86 0.00 46.78 2.59
70 71 9.281371 GACTAAAAACTACCAGTTTCAGGTAAT 57.719 33.333 4.86 0.00 46.78 1.89
71 72 8.266473 TGACTAAAAACTACCAGTTTCAGGTAA 58.734 33.333 4.86 0.00 46.78 2.85
72 73 7.712205 GTGACTAAAAACTACCAGTTTCAGGTA 59.288 37.037 4.86 0.00 46.78 3.08
73 74 6.541278 GTGACTAAAAACTACCAGTTTCAGGT 59.459 38.462 4.86 4.59 46.78 4.00
74 75 6.540914 TGTGACTAAAAACTACCAGTTTCAGG 59.459 38.462 4.86 1.93 46.78 3.86
75 76 7.548196 TGTGACTAAAAACTACCAGTTTCAG 57.452 36.000 4.86 7.87 46.78 3.02
76 77 7.925043 TTGTGACTAAAAACTACCAGTTTCA 57.075 32.000 4.86 0.00 46.78 2.69
77 78 9.797556 ATTTTGTGACTAAAAACTACCAGTTTC 57.202 29.630 4.86 0.00 46.78 2.78
110 111 5.900865 AAGTGGTCGAAAACTACCAAAAA 57.099 34.783 1.93 0.00 40.06 1.94
111 112 5.900865 AAAGTGGTCGAAAACTACCAAAA 57.099 34.783 1.93 0.00 40.06 2.44
112 113 5.900865 AAAAGTGGTCGAAAACTACCAAA 57.099 34.783 1.93 0.00 40.06 3.28
113 114 5.900865 AAAAAGTGGTCGAAAACTACCAA 57.099 34.783 1.93 0.00 40.06 3.67
114 115 6.998968 TTAAAAAGTGGTCGAAAACTACCA 57.001 33.333 1.93 0.00 40.06 3.25
115 116 8.686397 TTTTTAAAAAGTGGTCGAAAACTACC 57.314 30.769 9.31 0.00 40.06 3.18
131 132 7.396623 TCCCACAGAACTACCACTTTTTAAAAA 59.603 33.333 12.62 12.62 0.00 1.94
132 133 6.890814 TCCCACAGAACTACCACTTTTTAAAA 59.109 34.615 0.00 0.00 0.00 1.52
133 134 6.319405 GTCCCACAGAACTACCACTTTTTAAA 59.681 38.462 0.00 0.00 0.00 1.52
134 135 5.824097 GTCCCACAGAACTACCACTTTTTAA 59.176 40.000 0.00 0.00 0.00 1.52
135 136 5.370679 GTCCCACAGAACTACCACTTTTTA 58.629 41.667 0.00 0.00 0.00 1.52
136 137 4.204799 GTCCCACAGAACTACCACTTTTT 58.795 43.478 0.00 0.00 0.00 1.94
137 138 3.743269 CGTCCCACAGAACTACCACTTTT 60.743 47.826 0.00 0.00 0.00 2.27
138 139 2.224209 CGTCCCACAGAACTACCACTTT 60.224 50.000 0.00 0.00 0.00 2.66
139 140 1.343465 CGTCCCACAGAACTACCACTT 59.657 52.381 0.00 0.00 0.00 3.16
140 141 0.966920 CGTCCCACAGAACTACCACT 59.033 55.000 0.00 0.00 0.00 4.00
141 142 0.963962 TCGTCCCACAGAACTACCAC 59.036 55.000 0.00 0.00 0.00 4.16
142 143 0.963962 GTCGTCCCACAGAACTACCA 59.036 55.000 0.00 0.00 0.00 3.25
143 144 0.109412 CGTCGTCCCACAGAACTACC 60.109 60.000 0.00 0.00 0.00 3.18
144 145 0.877071 TCGTCGTCCCACAGAACTAC 59.123 55.000 0.00 0.00 0.00 2.73
145 146 0.877071 GTCGTCGTCCCACAGAACTA 59.123 55.000 0.00 0.00 0.00 2.24
146 147 1.658673 GTCGTCGTCCCACAGAACT 59.341 57.895 0.00 0.00 0.00 3.01
147 148 1.372623 GGTCGTCGTCCCACAGAAC 60.373 63.158 0.00 0.00 0.00 3.01
148 149 2.567497 GGGTCGTCGTCCCACAGAA 61.567 63.158 20.91 0.00 44.05 3.02
149 150 2.987547 GGGTCGTCGTCCCACAGA 60.988 66.667 20.91 0.00 44.05 3.41
150 151 4.065281 GGGGTCGTCGTCCCACAG 62.065 72.222 25.75 0.00 46.26 3.66
151 152 2.711883 TTAGGGGTCGTCGTCCCACA 62.712 60.000 25.75 12.04 46.26 4.17
152 153 1.535204 TTTAGGGGTCGTCGTCCCAC 61.535 60.000 25.75 16.19 46.26 4.61
153 154 1.228831 TTTAGGGGTCGTCGTCCCA 60.229 57.895 25.75 6.68 46.26 4.37
154 155 1.253593 ACTTTAGGGGTCGTCGTCCC 61.254 60.000 18.13 18.13 43.90 4.46
155 156 0.108945 CACTTTAGGGGTCGTCGTCC 60.109 60.000 0.00 0.00 0.00 4.79
156 157 0.108945 CCACTTTAGGGGTCGTCGTC 60.109 60.000 0.00 0.00 0.00 4.20
157 158 0.829182 ACCACTTTAGGGGTCGTCGT 60.829 55.000 0.00 0.00 29.34 4.34
158 159 1.133790 CTACCACTTTAGGGGTCGTCG 59.866 57.143 7.02 0.00 38.60 5.12
159 160 2.174360 ACTACCACTTTAGGGGTCGTC 58.826 52.381 7.02 0.00 38.60 4.20
160 161 2.315720 ACTACCACTTTAGGGGTCGT 57.684 50.000 7.02 4.62 38.60 4.34
161 162 3.690475 AAACTACCACTTTAGGGGTCG 57.310 47.619 7.02 3.91 38.60 4.79
180 181 2.096248 AGGCCGAGTGTTTGACAAAAA 58.904 42.857 1.27 0.00 0.00 1.94
181 182 1.757682 AGGCCGAGTGTTTGACAAAA 58.242 45.000 1.27 0.00 0.00 2.44
182 183 2.489971 CTAGGCCGAGTGTTTGACAAA 58.510 47.619 4.41 0.00 0.00 2.83
183 184 1.270625 CCTAGGCCGAGTGTTTGACAA 60.271 52.381 12.29 0.00 0.00 3.18
184 185 0.320374 CCTAGGCCGAGTGTTTGACA 59.680 55.000 12.29 0.00 0.00 3.58
185 186 0.606604 TCCTAGGCCGAGTGTTTGAC 59.393 55.000 12.29 0.00 0.00 3.18
186 187 0.606604 GTCCTAGGCCGAGTGTTTGA 59.393 55.000 12.29 0.00 0.00 2.69
187 188 0.391263 GGTCCTAGGCCGAGTGTTTG 60.391 60.000 12.29 0.00 0.00 2.93
188 189 1.551019 GGGTCCTAGGCCGAGTGTTT 61.551 60.000 12.29 0.00 0.00 2.83
189 190 1.988406 GGGTCCTAGGCCGAGTGTT 60.988 63.158 12.29 0.00 0.00 3.32
190 191 2.363925 GGGTCCTAGGCCGAGTGT 60.364 66.667 12.29 0.00 0.00 3.55
191 192 3.155167 GGGGTCCTAGGCCGAGTG 61.155 72.222 12.29 3.71 0.00 3.51
192 193 3.357082 AGGGGTCCTAGGCCGAGT 61.357 66.667 12.29 0.00 28.47 4.18
193 194 2.840102 CAGGGGTCCTAGGCCGAG 60.840 72.222 5.78 5.78 29.64 4.63
194 195 4.475444 CCAGGGGTCCTAGGCCGA 62.475 72.222 2.96 0.00 29.64 5.54
195 196 2.884179 TAACCAGGGGTCCTAGGCCG 62.884 65.000 2.96 0.00 33.12 6.13
227 228 6.761731 TTGTTGCCGAGATTGTTAATTTTG 57.238 33.333 0.00 0.00 0.00 2.44
247 252 9.965824 CACATTCTTCCTTACACTTAAAATTGT 57.034 29.630 0.00 0.00 0.00 2.71
384 389 4.153411 GAGGGCTACTCTGGCTTATCTAA 58.847 47.826 2.33 0.00 43.14 2.10
391 396 1.280421 CTTTTGAGGGCTACTCTGGCT 59.720 52.381 9.71 0.00 46.72 4.75
411 416 0.753262 AGACGATAGCCACCATGACC 59.247 55.000 0.00 0.00 42.67 4.02
419 424 7.166691 ACTTTAGTTTCTAAGACGATAGCCA 57.833 36.000 0.00 0.00 42.67 4.75
459 464 3.126831 CGATGAACTCAGGATAAGGCAC 58.873 50.000 0.00 0.00 0.00 5.01
460 465 3.031013 TCGATGAACTCAGGATAAGGCA 58.969 45.455 0.00 0.00 0.00 4.75
461 466 3.319405 TCTCGATGAACTCAGGATAAGGC 59.681 47.826 0.00 0.00 0.00 4.35
470 475 3.320256 AGCTATGCATCTCGATGAACTCA 59.680 43.478 0.19 0.00 41.20 3.41
533 538 3.057456 ACGTCTAGTCAAGTTGCTAGGTG 60.057 47.826 22.87 19.16 36.32 4.00
538 543 4.785511 ATACACGTCTAGTCAAGTTGCT 57.214 40.909 0.00 1.61 0.00 3.91
542 547 5.178809 GGCAAAAATACACGTCTAGTCAAGT 59.821 40.000 0.00 0.00 0.00 3.16
547 552 3.435671 GCTGGCAAAAATACACGTCTAGT 59.564 43.478 0.00 0.00 0.00 2.57
553 558 2.414058 TGTGCTGGCAAAAATACACG 57.586 45.000 0.00 0.00 0.00 4.49
582 587 7.151308 TGCCCAATTCTTATTTGTGTTGTTAG 58.849 34.615 0.00 0.00 0.00 2.34
591 596 3.129287 AGCGTCTGCCCAATTCTTATTTG 59.871 43.478 0.00 0.00 44.31 2.32
597 602 0.392193 CAGAGCGTCTGCCCAATTCT 60.392 55.000 2.75 0.00 44.31 2.40
668 673 7.757526 TGCGCACTTTTAGTATTTACATCAAT 58.242 30.769 5.66 0.00 0.00 2.57
751 756 7.352079 TCAGCACTTCTCATATATCAAGTCA 57.648 36.000 0.00 0.00 0.00 3.41
765 770 4.521130 TTCGTATGAGTTCAGCACTTCT 57.479 40.909 0.00 0.00 35.01 2.85
826 832 2.440409 AGGTTAGCATTGCTTGACTGG 58.560 47.619 17.71 0.00 40.44 4.00
906 945 8.919777 ACCTGAAAAGTAACTAGCAAGTTAAT 57.080 30.769 0.00 0.00 46.99 1.40
977 1016 1.009675 CGGCATGCAGGAATTACGC 60.010 57.895 21.36 0.00 0.00 4.42
1025 1064 1.151668 CAGTTCCTCCACTTTCTGCG 58.848 55.000 0.00 0.00 0.00 5.18
1030 1069 4.437682 TGACATTCAGTTCCTCCACTTT 57.562 40.909 0.00 0.00 0.00 2.66
1114 1153 2.740055 CAGTGAGCCGGCAGTGTC 60.740 66.667 31.54 18.22 35.10 3.67
1121 1160 0.593128 CAAGTTTTCCAGTGAGCCGG 59.407 55.000 0.00 0.00 0.00 6.13
1169 1208 5.538433 CCATCTGGGGAACTTTCAGTAAAAA 59.462 40.000 0.00 0.00 0.00 1.94
1344 1383 3.462483 TCCTCTACTTTGTTTGCACGA 57.538 42.857 0.00 0.00 0.00 4.35
1375 1414 0.693049 TCCTTCCCTTCAAGCTGGTC 59.307 55.000 0.00 0.00 0.00 4.02
1449 1488 0.734942 TGAAACGTTCGGCGATCTCC 60.735 55.000 11.76 0.00 44.77 3.71
1826 1865 0.319211 TTGCTGTGCTTGCAATGCTC 60.319 50.000 17.72 15.21 44.24 4.26
1890 1929 2.002586 GCACTCTCTTTGCGAGCAATA 58.997 47.619 11.53 2.64 39.70 1.90
1948 1987 3.280211 TGCTAAGGCAGTCGCGTA 58.720 55.556 5.77 0.00 44.28 4.42
2014 2053 7.195374 TCTCCCTATGTGTAATTAAAGCTGT 57.805 36.000 0.00 0.00 0.00 4.40
2043 2082 5.129980 AGTGGATTCATGTGCTCTAATCTCA 59.870 40.000 0.00 0.00 0.00 3.27
2274 2313 5.300752 TCAAGATCTTTATTGGCCGAGATC 58.699 41.667 4.86 17.89 42.96 2.75
2341 2380 7.275920 CCTTCCATATAAGCAGTAAAGTCACT 58.724 38.462 0.00 0.00 0.00 3.41
2388 2427 1.433534 GCACTTTCTCTCCAACCTCG 58.566 55.000 0.00 0.00 0.00 4.63
2401 2440 3.009723 CACTAACCATGGATCGCACTTT 58.990 45.455 21.47 1.50 0.00 2.66
2439 2478 3.481453 GTCAAGCTCTTTCCTGGTCTTT 58.519 45.455 0.00 0.00 0.00 2.52
2460 2499 5.554510 CGTTTCGATGTTTGTCCTCATATCG 60.555 44.000 0.00 0.00 38.86 2.92
2486 2525 1.272147 GCCCTTTCACCTCATCCTTGT 60.272 52.381 0.00 0.00 0.00 3.16
2635 2674 0.880278 ACAACGCTGAGTTCACGCAT 60.880 50.000 0.00 0.00 42.02 4.73
2636 2675 0.249114 TACAACGCTGAGTTCACGCA 60.249 50.000 0.00 0.00 42.02 5.24
2643 2682 1.542030 CTCTCCTGTACAACGCTGAGT 59.458 52.381 0.00 0.00 0.00 3.41
2652 2691 2.229062 CGCTTCTGTTCTCTCCTGTACA 59.771 50.000 0.00 0.00 0.00 2.90
2659 2698 2.656560 TTAGCCGCTTCTGTTCTCTC 57.343 50.000 0.00 0.00 0.00 3.20
2698 2737 4.781934 AGTTGTGTTTCTTGAGTAGCCTT 58.218 39.130 0.00 0.00 0.00 4.35
2720 2759 1.447838 CGAGCCTTCGCCTTTGCTA 60.448 57.895 0.00 0.00 40.36 3.49
2741 2780 1.220749 GTAACCTCATCGCAGGCCA 59.779 57.895 5.01 0.00 36.98 5.36
2762 2801 0.176910 GTCTGCCTCTTCACTAGCCC 59.823 60.000 0.00 0.00 0.00 5.19
2769 2808 0.323451 TAGCTCGGTCTGCCTCTTCA 60.323 55.000 0.00 0.00 0.00 3.02
2868 2907 0.248012 CATTTGCTGAGGCCATTGCA 59.752 50.000 5.01 9.18 40.13 4.08
2932 2971 1.270358 GCTCTTGTCACTTCCTCGGTT 60.270 52.381 0.00 0.00 0.00 4.44
2938 2977 2.681848 CCATCATGCTCTTGTCACTTCC 59.318 50.000 0.00 0.00 0.00 3.46
3009 3048 1.511305 CCGCTTCTTAGCTCGGTCA 59.489 57.895 0.00 0.00 45.51 4.02
3141 3180 1.001624 TGATGACTTTCTCATGCGCG 58.998 50.000 0.00 0.00 39.96 6.86
3154 3193 2.613595 TGTTGTCTTGTGCTGTGATGAC 59.386 45.455 0.00 0.00 0.00 3.06
3155 3194 2.916640 TGTTGTCTTGTGCTGTGATGA 58.083 42.857 0.00 0.00 0.00 2.92
3171 3210 4.035091 TCGTTCTCCATTGTCAACTTGTTG 59.965 41.667 7.13 7.13 0.00 3.33
3180 3219 2.266554 CTCAGCTCGTTCTCCATTGTC 58.733 52.381 0.00 0.00 0.00 3.18
3213 3252 2.609350 GTGTAATGTTGGCCATGCTTG 58.391 47.619 6.09 0.00 32.82 4.01
3252 3291 2.885644 CAGACACCGGGAATCGCG 60.886 66.667 12.91 12.91 39.48 5.87
3261 3300 1.081892 CATTCAGAAGGCAGACACCG 58.918 55.000 0.00 0.00 33.69 4.94
3263 3302 4.569966 CACTATCATTCAGAAGGCAGACAC 59.430 45.833 3.98 0.00 0.00 3.67
3281 3320 3.697542 TGCATCAAAAGAGCATGCACTAT 59.302 39.130 21.98 8.94 46.22 2.12
3282 3321 3.083293 TGCATCAAAAGAGCATGCACTA 58.917 40.909 21.98 3.95 46.22 2.74
3315 3354 1.003476 TCCTTGCGCATGAGAAGCA 60.003 52.632 23.56 0.84 39.33 3.91
3325 3364 3.453070 CTAGGCCTCCTCCTTGCGC 62.453 68.421 9.68 0.00 37.66 6.09
3357 3396 2.097160 GCTGCAGTTGTCGCGATG 59.903 61.111 14.06 7.72 0.00 3.84
3399 3438 1.270041 GCTATGGAGCGAGGGAAGAAG 60.270 57.143 0.00 0.00 39.39 2.85
3422 3461 7.550551 GTGTCTTCTTCCTATTCATGAACATCA 59.449 37.037 11.07 0.00 0.00 3.07
3476 3515 6.214412 ACAGAGGGATCATACCATAGGAAATC 59.786 42.308 0.00 0.00 0.00 2.17
3485 3524 4.556697 ACATGTACAGAGGGATCATACCA 58.443 43.478 0.00 0.00 0.00 3.25
3494 3533 5.598830 ACCTACTTGATACATGTACAGAGGG 59.401 44.000 7.96 12.90 0.00 4.30
3533 3576 4.860352 TGAACGATAAGTACAATCGGTGTG 59.140 41.667 25.19 6.91 46.24 3.82
3570 3617 1.000955 ACAAGCTCAGACCGACGAAAT 59.999 47.619 0.00 0.00 0.00 2.17
3592 3639 4.218312 AGAGAAAAGATTGCAAGGTTGGT 58.782 39.130 4.94 0.00 0.00 3.67
3644 3694 4.081198 CAGGTTCAGAGGTATGCTTCTTCT 60.081 45.833 0.00 0.00 0.00 2.85
3645 3695 4.187694 CAGGTTCAGAGGTATGCTTCTTC 58.812 47.826 0.00 0.00 0.00 2.87
3646 3696 3.584848 ACAGGTTCAGAGGTATGCTTCTT 59.415 43.478 0.00 0.00 0.00 2.52
3655 3705 2.918712 CTGTCAACAGGTTCAGAGGT 57.081 50.000 2.08 0.00 40.20 3.85
3669 3719 5.811399 ATGACGAAAAGAAAACACTGTCA 57.189 34.783 0.00 0.00 39.18 3.58
3714 3764 4.694037 CAGAGACAGAAATGCTCATGTGAA 59.306 41.667 0.00 0.00 0.00 3.18
3736 3786 1.661463 AGAGCCTCTGGAAACCATCA 58.339 50.000 0.00 0.00 30.82 3.07
3737 3787 2.769095 AGTAGAGCCTCTGGAAACCATC 59.231 50.000 3.98 0.00 30.82 3.51
3738 3788 2.503356 CAGTAGAGCCTCTGGAAACCAT 59.497 50.000 3.98 0.00 30.82 3.55
3739 3789 1.902508 CAGTAGAGCCTCTGGAAACCA 59.097 52.381 3.98 0.00 0.00 3.67
3740 3790 1.406205 GCAGTAGAGCCTCTGGAAACC 60.406 57.143 3.98 0.00 32.94 3.27
3741 3791 1.552792 AGCAGTAGAGCCTCTGGAAAC 59.447 52.381 3.98 0.00 34.23 2.78
3742 3792 1.827969 GAGCAGTAGAGCCTCTGGAAA 59.172 52.381 3.98 0.00 34.23 3.13
3743 3793 1.479709 GAGCAGTAGAGCCTCTGGAA 58.520 55.000 3.98 0.00 34.23 3.53
3744 3794 0.396417 GGAGCAGTAGAGCCTCTGGA 60.396 60.000 3.98 0.00 34.23 3.86
3745 3795 1.398958 GGGAGCAGTAGAGCCTCTGG 61.399 65.000 3.98 0.00 34.23 3.86
3746 3796 0.685785 TGGGAGCAGTAGAGCCTCTG 60.686 60.000 3.98 0.00 34.23 3.35
3747 3797 0.396974 CTGGGAGCAGTAGAGCCTCT 60.397 60.000 0.00 0.00 34.23 3.69
3748 3798 0.396417 TCTGGGAGCAGTAGAGCCTC 60.396 60.000 0.00 0.00 34.23 4.70
3825 3918 9.165035 CCAACACATTTCATTTTATTATGGCTT 57.835 29.630 0.00 0.00 0.00 4.35
3826 3919 7.769970 CCCAACACATTTCATTTTATTATGGCT 59.230 33.333 0.00 0.00 0.00 4.75
3827 3920 7.552330 ACCCAACACATTTCATTTTATTATGGC 59.448 33.333 0.00 0.00 0.00 4.40
3828 3921 9.097257 GACCCAACACATTTCATTTTATTATGG 57.903 33.333 0.00 0.00 0.00 2.74
3881 3985 7.996385 AGTGTAGTTGTTTTGCTAAATGTTCT 58.004 30.769 0.00 0.00 0.00 3.01
3882 3986 9.893305 ATAGTGTAGTTGTTTTGCTAAATGTTC 57.107 29.630 0.00 0.00 0.00 3.18
3945 4065 0.807496 GGGCTGCAGAGTGATTCAAC 59.193 55.000 20.43 0.00 0.00 3.18
3961 4081 3.961480 AATTTACAAGCAGGAAAGGGC 57.039 42.857 0.00 0.00 0.00 5.19
4367 4505 1.133253 GTACTACGAGCACGCGACA 59.867 57.895 15.93 0.00 43.96 4.35
4386 4524 1.216710 CCGAGAAGCTCAGGTCCAC 59.783 63.158 0.00 0.00 0.00 4.02
4392 4530 0.248296 GAGTACGCCGAGAAGCTCAG 60.248 60.000 0.00 0.00 0.00 3.35



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

AutoCloner maintained by Alex Coulton.