Multiple sequence alignment - TraesCS2D01G193300

Loading Multiple Alignment...

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 TraesCS2D01G193300 chr2D 100.000 3380 0 0 1 3380 138249580 138246201 0.000000e+00 6242
1 TraesCS2D01G193300 chr2D 86.631 187 13 8 2928 3111 648246948 648246771 2.660000e-46 196
2 TraesCS2D01G193300 chr2D 85.714 189 20 5 2925 3112 429200565 429200383 3.440000e-45 193
3 TraesCS2D01G193300 chr2A 96.020 2764 75 11 178 2927 163668737 163671479 0.000000e+00 4462
4 TraesCS2D01G193300 chr2A 86.878 221 25 1 3158 3378 163671550 163671766 9.370000e-61 244
5 TraesCS2D01G193300 chr2B 95.218 2781 81 20 188 2927 196194969 196192200 0.000000e+00 4351
6 TraesCS2D01G193300 chr2B 87.218 266 28 4 3113 3378 196192206 196191947 7.090000e-77 298
7 TraesCS2D01G193300 chr2B 89.744 117 10 2 11 127 154903756 154903642 7.560000e-32 148
8 TraesCS2D01G193300 chr5D 88.144 194 15 6 2919 3111 443898322 443898136 1.220000e-54 224
9 TraesCS2D01G193300 chr5D 91.736 121 6 4 10 127 29496207 29496088 7.500000e-37 165
10 TraesCS2D01G193300 chr1D 87.302 189 11 11 2928 3111 375958482 375958662 1.590000e-48 204
11 TraesCS2D01G193300 chr1D 85.864 191 20 5 2925 3114 443741664 443741848 2.660000e-46 196
12 TraesCS2D01G193300 chr1D 91.150 113 7 3 15 127 416095849 416095958 2.100000e-32 150
13 TraesCS2D01G193300 chr1D 79.891 184 36 1 3198 3380 340526880 340526697 2.120000e-27 134
14 TraesCS2D01G193300 chr7D 86.316 190 13 10 2923 3111 75800853 75800676 9.570000e-46 195
15 TraesCS2D01G193300 chr7D 97.959 98 2 0 33 130 636760665 636760568 1.610000e-38 171
16 TraesCS2D01G193300 chr6D 86.170 188 16 6 2925 3111 185191916 185192094 9.570000e-46 195
17 TraesCS2D01G193300 chr3A 85.263 190 21 6 2923 3111 647690825 647691008 4.450000e-44 189
18 TraesCS2D01G193300 chr1A 85.052 194 19 8 2928 3120 111535749 111535565 4.450000e-44 189
19 TraesCS2D01G193300 chr6B 98.913 92 1 0 36 127 153239873 153239782 7.500000e-37 165
20 TraesCS2D01G193300 chr5A 98.913 92 1 0 36 127 580283807 580283716 7.500000e-37 165
21 TraesCS2D01G193300 chr5A 94.949 99 5 0 29 127 9847024 9846926 4.520000e-34 156
22 TraesCS2D01G193300 chr4D 92.727 110 8 0 19 128 108872377 108872486 3.490000e-35 159
23 TraesCS2D01G193300 chr3B 91.453 117 9 1 11 127 741865825 741865940 3.490000e-35 159
24 TraesCS2D01G193300 chr4B 81.871 171 30 1 3204 3373 17876730 17876560 3.520000e-30 143


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 TraesCS2D01G193300 chr2D 138246201 138249580 3379 True 6242.0 6242 100.000 1 3380 1 chr2D.!!$R1 3379
1 TraesCS2D01G193300 chr2A 163668737 163671766 3029 False 2353.0 4462 91.449 178 3378 2 chr2A.!!$F1 3200
2 TraesCS2D01G193300 chr2B 196191947 196194969 3022 True 2324.5 4351 91.218 188 3378 2 chr2B.!!$R2 3190

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
51 52 0.042131 AACATACTCCCTCCGTCCCA 59.958 55.0 0.0 0.0 0.0 4.37 F
357 361 0.178918 CTCCCCCTTCCCCTAGCTAG 60.179 65.0 14.2 14.2 0.0 3.42 F
922 938 0.248134 GACGTGTACTAGCTCTGCCG 60.248 60.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 1721 0.848305 GCGCAAAGTTGACAAGCTTG 59.152 50.0 24.84 24.84 0.0 4.01 R
2292 2309 1.632018 CCTCCCGCTTCATACCCCAA 61.632 60.0 0.00 0.00 0.0 4.12 R
2819 2852 0.824759 ACCCTAACCTCAGCATCGAC 59.175 55.0 0.00 0.00 0.0 4.20 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
21 22 4.944962 CTGCGGAATGAATGAGTAAACA 57.055 40.909 0.00 0.00 0.00 2.83
22 23 5.295431 CTGCGGAATGAATGAGTAAACAA 57.705 39.130 0.00 0.00 0.00 2.83
23 24 5.697473 TGCGGAATGAATGAGTAAACAAA 57.303 34.783 0.00 0.00 0.00 2.83
24 25 5.457140 TGCGGAATGAATGAGTAAACAAAC 58.543 37.500 0.00 0.00 0.00 2.93
25 26 5.009110 TGCGGAATGAATGAGTAAACAAACA 59.991 36.000 0.00 0.00 0.00 2.83
26 27 5.342259 GCGGAATGAATGAGTAAACAAACAC 59.658 40.000 0.00 0.00 0.00 3.32
27 28 6.434596 CGGAATGAATGAGTAAACAAACACA 58.565 36.000 0.00 0.00 0.00 3.72
28 29 6.359617 CGGAATGAATGAGTAAACAAACACAC 59.640 38.462 0.00 0.00 0.00 3.82
29 30 7.425606 GGAATGAATGAGTAAACAAACACACT 58.574 34.615 0.00 0.00 0.00 3.55
30 31 8.564574 GGAATGAATGAGTAAACAAACACACTA 58.435 33.333 0.00 0.00 0.00 2.74
31 32 9.944663 GAATGAATGAGTAAACAAACACACTAA 57.055 29.630 0.00 0.00 0.00 2.24
34 35 9.562583 TGAATGAGTAAACAAACACACTAAAAC 57.437 29.630 0.00 0.00 0.00 2.43
35 36 9.562583 GAATGAGTAAACAAACACACTAAAACA 57.437 29.630 0.00 0.00 0.00 2.83
38 39 9.991388 TGAGTAAACAAACACACTAAAACATAC 57.009 29.630 0.00 0.00 0.00 2.39
41 42 9.442033 GTAAACAAACACACTAAAACATACTCC 57.558 33.333 0.00 0.00 0.00 3.85
42 43 6.628919 ACAAACACACTAAAACATACTCCC 57.371 37.500 0.00 0.00 0.00 4.30
43 44 6.362248 ACAAACACACTAAAACATACTCCCT 58.638 36.000 0.00 0.00 0.00 4.20
44 45 6.485648 ACAAACACACTAAAACATACTCCCTC 59.514 38.462 0.00 0.00 0.00 4.30
45 46 5.161943 ACACACTAAAACATACTCCCTCC 57.838 43.478 0.00 0.00 0.00 4.30
46 47 4.181578 CACACTAAAACATACTCCCTCCG 58.818 47.826 0.00 0.00 0.00 4.63
47 48 3.836562 ACACTAAAACATACTCCCTCCGT 59.163 43.478 0.00 0.00 0.00 4.69
48 49 4.081807 ACACTAAAACATACTCCCTCCGTC 60.082 45.833 0.00 0.00 0.00 4.79
49 50 3.450096 ACTAAAACATACTCCCTCCGTCC 59.550 47.826 0.00 0.00 0.00 4.79
50 51 1.201424 AAACATACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
51 52 0.042131 AACATACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
52 53 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
53 54 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
54 55 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
55 56 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
56 57 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
57 58 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
58 59 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
59 60 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
60 61 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
61 62 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
62 63 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
63 64 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
64 65 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
65 66 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
66 67 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
67 68 5.828859 TCCGTCCCAAAATTCTTGTCTTAAA 59.171 36.000 0.00 0.00 0.00 1.52
68 69 6.492087 TCCGTCCCAAAATTCTTGTCTTAAAT 59.508 34.615 0.00 0.00 0.00 1.40
69 70 7.014808 TCCGTCCCAAAATTCTTGTCTTAAATT 59.985 33.333 0.00 0.00 0.00 1.82
70 71 7.655732 CCGTCCCAAAATTCTTGTCTTAAATTT 59.344 33.333 0.00 0.00 34.86 1.82
71 72 8.487176 CGTCCCAAAATTCTTGTCTTAAATTTG 58.513 33.333 0.00 0.00 33.95 2.32
72 73 9.325198 GTCCCAAAATTCTTGTCTTAAATTTGT 57.675 29.630 0.00 0.00 33.95 2.83
73 74 9.541143 TCCCAAAATTCTTGTCTTAAATTTGTC 57.459 29.630 0.00 0.00 33.95 3.18
74 75 9.546428 CCCAAAATTCTTGTCTTAAATTTGTCT 57.454 29.630 0.00 0.00 33.95 3.41
95 96 9.825109 TTGTCTAAATACGGATGTATCAATTCA 57.175 29.630 0.00 0.00 40.42 2.57
96 97 9.996554 TGTCTAAATACGGATGTATCAATTCAT 57.003 29.630 0.00 0.00 40.42 2.57
98 99 9.996554 TCTAAATACGGATGTATCAATTCATGT 57.003 29.630 0.00 0.00 40.42 3.21
104 105 8.506168 ACGGATGTATCAATTCATGTTTTAGT 57.494 30.769 0.00 0.00 0.00 2.24
105 106 9.607988 ACGGATGTATCAATTCATGTTTTAGTA 57.392 29.630 0.00 0.00 0.00 1.82
133 134 4.659529 ACATCCGTATCTAGATGAGGGA 57.340 45.455 15.79 17.16 42.04 4.20
134 135 5.199982 ACATCCGTATCTAGATGAGGGAT 57.800 43.478 20.05 20.05 42.04 3.85
135 136 4.952957 ACATCCGTATCTAGATGAGGGATG 59.047 45.833 33.18 33.18 45.89 3.51
136 137 4.929146 TCCGTATCTAGATGAGGGATGA 57.071 45.455 15.79 0.26 0.00 2.92
137 138 5.256806 TCCGTATCTAGATGAGGGATGAA 57.743 43.478 15.79 0.00 0.00 2.57
138 139 5.257262 TCCGTATCTAGATGAGGGATGAAG 58.743 45.833 15.79 0.00 0.00 3.02
139 140 4.400884 CCGTATCTAGATGAGGGATGAAGG 59.599 50.000 15.79 0.76 0.00 3.46
140 141 4.400884 CGTATCTAGATGAGGGATGAAGGG 59.599 50.000 15.79 0.00 0.00 3.95
141 142 4.774243 ATCTAGATGAGGGATGAAGGGA 57.226 45.455 3.89 0.00 0.00 4.20
142 143 4.125124 TCTAGATGAGGGATGAAGGGAG 57.875 50.000 0.00 0.00 0.00 4.30
143 144 2.885388 AGATGAGGGATGAAGGGAGT 57.115 50.000 0.00 0.00 0.00 3.85
144 145 4.670247 TCTAGATGAGGGATGAAGGGAGTA 59.330 45.833 0.00 0.00 0.00 2.59
145 146 3.582164 AGATGAGGGATGAAGGGAGTAC 58.418 50.000 0.00 0.00 0.00 2.73
146 147 2.940514 TGAGGGATGAAGGGAGTACA 57.059 50.000 0.00 0.00 0.00 2.90
147 148 3.421394 TGAGGGATGAAGGGAGTACAT 57.579 47.619 0.00 0.00 0.00 2.29
148 149 3.309296 TGAGGGATGAAGGGAGTACATC 58.691 50.000 0.00 0.00 39.43 3.06
149 150 3.051803 TGAGGGATGAAGGGAGTACATCT 60.052 47.826 0.00 0.00 39.87 2.90
150 151 4.170053 TGAGGGATGAAGGGAGTACATCTA 59.830 45.833 0.00 0.00 39.87 1.98
151 152 5.148502 GAGGGATGAAGGGAGTACATCTAA 58.851 45.833 0.00 0.00 39.87 2.10
152 153 5.731924 AGGGATGAAGGGAGTACATCTAAT 58.268 41.667 0.00 0.00 39.87 1.73
153 154 6.153924 AGGGATGAAGGGAGTACATCTAATT 58.846 40.000 0.00 0.00 39.87 1.40
154 155 6.271159 AGGGATGAAGGGAGTACATCTAATTC 59.729 42.308 0.00 0.00 39.87 2.17
155 156 6.043243 GGGATGAAGGGAGTACATCTAATTCA 59.957 42.308 0.00 0.00 39.87 2.57
156 157 7.420214 GGGATGAAGGGAGTACATCTAATTCAA 60.420 40.741 0.00 0.00 39.87 2.69
157 158 7.993183 GGATGAAGGGAGTACATCTAATTCAAA 59.007 37.037 0.00 0.00 39.87 2.69
158 159 9.396022 GATGAAGGGAGTACATCTAATTCAAAA 57.604 33.333 0.00 0.00 37.84 2.44
159 160 9.927081 ATGAAGGGAGTACATCTAATTCAAAAT 57.073 29.630 0.00 0.00 31.85 1.82
273 277 3.810310 TCCACAACAATCCAACAAACC 57.190 42.857 0.00 0.00 0.00 3.27
317 321 1.507140 TGGACCTTGAGTTGTGACCT 58.493 50.000 0.00 0.00 0.00 3.85
354 358 2.448736 CCTCCCCCTTCCCCTAGC 60.449 72.222 0.00 0.00 0.00 3.42
355 359 2.706071 CTCCCCCTTCCCCTAGCT 59.294 66.667 0.00 0.00 0.00 3.32
356 360 1.675936 CCTCCCCCTTCCCCTAGCTA 61.676 65.000 0.00 0.00 0.00 3.32
357 361 0.178918 CTCCCCCTTCCCCTAGCTAG 60.179 65.000 14.20 14.20 0.00 3.42
358 362 1.152008 CCCCCTTCCCCTAGCTAGG 60.152 68.421 30.05 30.05 43.25 3.02
372 376 1.362932 AGCTAGGTCCCCTTCTTCTCA 59.637 52.381 0.00 0.00 34.61 3.27
490 498 3.784845 GCTGCTAGCTAGTCGATCC 57.215 57.895 21.62 4.84 38.45 3.36
493 501 2.029470 GCTGCTAGCTAGTCGATCCATT 60.029 50.000 21.62 0.00 38.45 3.16
594 606 3.708631 AGATCTCGATCCTGTTTCATGGT 59.291 43.478 3.39 0.00 38.58 3.55
595 607 4.895889 AGATCTCGATCCTGTTTCATGGTA 59.104 41.667 3.39 0.00 38.58 3.25
596 608 4.386867 TCTCGATCCTGTTTCATGGTAC 57.613 45.455 0.00 0.00 0.00 3.34
597 609 5.451937 GATCTCGATCCTGTTTCATGGTACA 60.452 44.000 0.00 0.00 35.47 2.90
746 758 5.249163 TCAATCAAACTCTCTCCATTCTCCA 59.751 40.000 0.00 0.00 0.00 3.86
797 809 5.124776 CGTTCCCAAAGTTCTATTGGCATAA 59.875 40.000 0.00 0.00 44.87 1.90
820 836 0.389948 AAGCACGTGTAGCTGTAGGC 60.390 55.000 18.38 0.00 42.53 3.93
922 938 0.248134 GACGTGTACTAGCTCTGCCG 60.248 60.000 0.00 0.00 0.00 5.69
1470 1487 2.979197 CTTCGTCGACCTCACGCCT 61.979 63.158 10.58 0.00 37.18 5.52
1482 1499 4.887190 ACGCCTTGGCACCGGTTT 62.887 61.111 2.97 0.00 0.00 3.27
1602 1619 2.298629 CCTCATCGACATGCTCGCG 61.299 63.158 0.00 0.00 42.62 5.87
1719 1736 0.249031 GCGCCAAGCTTGTCAACTTT 60.249 50.000 24.35 0.00 44.04 2.66
1920 1937 1.174783 GCCTTACTCAGTCGGTCTCA 58.825 55.000 0.00 0.00 0.00 3.27
2277 2294 4.451900 GGGAGATACGGACAATGTTGAAT 58.548 43.478 0.00 0.00 0.00 2.57
2553 2570 2.975266 AGCTGATTCACTGCAGAGAAG 58.025 47.619 26.80 16.98 44.13 2.85
2655 2672 4.933134 TGGATCCCACTCATGAAAAATGA 58.067 39.130 9.90 0.00 0.00 2.57
2662 2679 5.579511 CCCACTCATGAAAAATGAAGAATGC 59.420 40.000 0.00 0.00 0.00 3.56
2664 2681 5.860182 CACTCATGAAAAATGAAGAATGCGT 59.140 36.000 0.00 0.00 0.00 5.24
2683 2716 7.945033 ATGCGTTGTTCTTGAAAAATATGTT 57.055 28.000 0.00 0.00 0.00 2.71
2711 2744 8.994429 ATGATCTTTATACCGAGAACATGATC 57.006 34.615 0.00 0.00 35.09 2.92
2716 2749 9.297037 TCTTTATACCGAGAACATGATCAGATA 57.703 33.333 0.00 0.00 0.00 1.98
2733 2766 5.371526 TCAGATATCATTTTGGAGACTGGC 58.628 41.667 5.32 0.00 0.00 4.85
2763 2796 1.287425 GCCGACCAAAGATAAGGACG 58.713 55.000 0.00 0.00 41.51 4.79
2780 2813 3.074412 GGACGAAATGAAGCTTTCCTCA 58.926 45.455 0.00 0.00 32.60 3.86
2898 2947 6.351711 TGAGAGCCATATGCCATATACATTC 58.648 40.000 0.00 0.00 42.71 2.67
2952 3001 9.371136 TCAGTTTTACTAAAGCACATCTAGATG 57.629 33.333 27.63 27.63 44.15 2.90
2967 3016 6.987223 CATCTAGATGTGCGATAAGTATTGC 58.013 40.000 22.42 3.89 42.24 3.56
2978 3027 8.239681 TGCGATAAGTATTGCACATATAAGTC 57.760 34.615 8.84 0.00 45.55 3.01
2979 3028 7.330946 TGCGATAAGTATTGCACATATAAGTCC 59.669 37.037 8.84 0.00 45.55 3.85
2980 3029 7.545965 GCGATAAGTATTGCACATATAAGTCCT 59.454 37.037 5.78 0.00 41.66 3.85
3003 3052 9.542462 TCCTATACTCAAAATTGATCTTAACGG 57.458 33.333 0.00 0.00 36.46 4.44
3004 3053 8.283291 CCTATACTCAAAATTGATCTTAACGGC 58.717 37.037 0.00 0.00 36.46 5.68
3005 3054 4.969816 ACTCAAAATTGATCTTAACGGCG 58.030 39.130 4.80 4.80 36.46 6.46
3006 3055 4.693566 ACTCAAAATTGATCTTAACGGCGA 59.306 37.500 16.62 0.00 36.46 5.54
3007 3056 5.163854 ACTCAAAATTGATCTTAACGGCGAG 60.164 40.000 16.62 0.00 36.46 5.03
3008 3057 4.932799 TCAAAATTGATCTTAACGGCGAGA 59.067 37.500 16.62 6.57 31.01 4.04
3009 3058 5.584649 TCAAAATTGATCTTAACGGCGAGAT 59.415 36.000 16.62 12.08 35.41 2.75
3010 3059 6.093495 TCAAAATTGATCTTAACGGCGAGATT 59.907 34.615 16.62 0.00 32.96 2.40
3011 3060 6.436843 AAATTGATCTTAACGGCGAGATTT 57.563 33.333 16.62 0.00 32.96 2.17
3012 3061 4.857871 TTGATCTTAACGGCGAGATTTG 57.142 40.909 16.62 0.00 32.96 2.32
3013 3062 3.857052 TGATCTTAACGGCGAGATTTGT 58.143 40.909 16.62 0.00 32.96 2.83
3014 3063 3.616821 TGATCTTAACGGCGAGATTTGTG 59.383 43.478 16.62 0.00 32.96 3.33
3015 3064 3.034721 TCTTAACGGCGAGATTTGTGT 57.965 42.857 16.62 0.00 0.00 3.72
3016 3065 4.177165 TCTTAACGGCGAGATTTGTGTA 57.823 40.909 16.62 0.00 0.00 2.90
3017 3066 4.171005 TCTTAACGGCGAGATTTGTGTAG 58.829 43.478 16.62 0.00 0.00 2.74
3018 3067 1.722011 AACGGCGAGATTTGTGTAGG 58.278 50.000 16.62 0.00 0.00 3.18
3019 3068 0.606604 ACGGCGAGATTTGTGTAGGT 59.393 50.000 16.62 0.00 0.00 3.08
3020 3069 1.820519 ACGGCGAGATTTGTGTAGGTA 59.179 47.619 16.62 0.00 0.00 3.08
3021 3070 2.190981 CGGCGAGATTTGTGTAGGTAC 58.809 52.381 0.00 0.00 0.00 3.34
3022 3071 2.159282 CGGCGAGATTTGTGTAGGTACT 60.159 50.000 0.00 0.00 46.37 2.73
3023 3072 3.675228 CGGCGAGATTTGTGTAGGTACTT 60.675 47.826 0.00 0.00 41.75 2.24
3024 3073 4.251268 GGCGAGATTTGTGTAGGTACTTT 58.749 43.478 0.00 0.00 41.75 2.66
3025 3074 4.329256 GGCGAGATTTGTGTAGGTACTTTC 59.671 45.833 0.00 0.00 41.75 2.62
3026 3075 5.169295 GCGAGATTTGTGTAGGTACTTTCT 58.831 41.667 0.00 0.00 41.75 2.52
3027 3076 5.638234 GCGAGATTTGTGTAGGTACTTTCTT 59.362 40.000 0.00 0.00 41.75 2.52
3028 3077 6.147328 GCGAGATTTGTGTAGGTACTTTCTTT 59.853 38.462 0.00 0.00 41.75 2.52
3029 3078 7.307811 GCGAGATTTGTGTAGGTACTTTCTTTT 60.308 37.037 0.00 0.00 41.75 2.27
3030 3079 8.221766 CGAGATTTGTGTAGGTACTTTCTTTTC 58.778 37.037 0.00 0.00 41.75 2.29
3031 3080 9.274206 GAGATTTGTGTAGGTACTTTCTTTTCT 57.726 33.333 0.00 0.00 41.75 2.52
3035 3084 9.841295 TTTGTGTAGGTACTTTCTTTTCTATGT 57.159 29.630 0.00 0.00 41.75 2.29
3036 3085 9.841295 TTGTGTAGGTACTTTCTTTTCTATGTT 57.159 29.630 0.00 0.00 41.75 2.71
3037 3086 9.841295 TGTGTAGGTACTTTCTTTTCTATGTTT 57.159 29.630 0.00 0.00 41.75 2.83
3058 3107 9.783081 ATGTTTCTTTTCCTTTTTATGCTTGAT 57.217 25.926 0.00 0.00 0.00 2.57
3059 3108 9.612066 TGTTTCTTTTCCTTTTTATGCTTGATT 57.388 25.926 0.00 0.00 0.00 2.57
3076 3125 7.475015 TGCTTGATTAAGTCATTTAGATGTGC 58.525 34.615 0.00 0.00 36.54 4.57
3077 3126 7.121020 TGCTTGATTAAGTCATTTAGATGTGCA 59.879 33.333 0.00 0.00 36.54 4.57
3078 3127 7.970061 GCTTGATTAAGTCATTTAGATGTGCAA 59.030 33.333 0.00 0.00 36.54 4.08
3087 3136 9.060347 AGTCATTTAGATGTGCAATAACTATGG 57.940 33.333 0.00 0.00 34.77 2.74
3088 3137 7.805071 GTCATTTAGATGTGCAATAACTATGGC 59.195 37.037 0.00 0.00 34.77 4.40
3089 3138 7.501892 TCATTTAGATGTGCAATAACTATGGCA 59.498 33.333 0.00 0.00 34.87 4.92
3136 3185 8.947055 AATTTTATTGTAGAAATGTGCCCATC 57.053 30.769 0.00 0.00 0.00 3.51
3140 3189 4.835284 TGTAGAAATGTGCCCATCTGTA 57.165 40.909 0.00 0.00 0.00 2.74
3141 3190 4.769688 TGTAGAAATGTGCCCATCTGTAG 58.230 43.478 0.00 0.00 0.00 2.74
3178 3259 2.010145 AATCGTCTACATGCAACGCT 57.990 45.000 3.02 0.00 36.40 5.07
3179 3260 2.010145 ATCGTCTACATGCAACGCTT 57.990 45.000 3.02 0.00 36.40 4.68
3185 3266 1.129251 CTACATGCAACGCTTGACCAG 59.871 52.381 8.64 0.47 37.20 4.00
3186 3267 0.819259 ACATGCAACGCTTGACCAGT 60.819 50.000 8.64 0.00 37.20 4.00
3187 3268 0.311790 CATGCAACGCTTGACCAGTT 59.688 50.000 0.00 0.00 36.06 3.16
3188 3269 1.032014 ATGCAACGCTTGACCAGTTT 58.968 45.000 0.00 0.00 0.00 2.66
3276 3357 7.522901 TTTGATGCAATTAATGTCATTTCCG 57.477 32.000 2.79 0.00 0.00 4.30
3351 3432 4.207955 ACATCATTGAAGCAGCATGAGAT 58.792 39.130 0.00 0.00 39.69 2.75
3361 3442 4.726583 AGCAGCATGAGATGTTGGATATT 58.273 39.130 0.00 0.00 41.16 1.28
3378 3459 4.872691 GGATATTGATGGTTGGATAGCTCG 59.127 45.833 0.00 0.00 0.00 5.03
3379 3460 2.620251 TTGATGGTTGGATAGCTCGG 57.380 50.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.944962 TGTTTACTCATTCATTCCGCAG 57.055 40.909 0.00 0.00 0.00 5.18
1 2 5.009110 TGTTTGTTTACTCATTCATTCCGCA 59.991 36.000 0.00 0.00 0.00 5.69
2 3 5.342259 GTGTTTGTTTACTCATTCATTCCGC 59.658 40.000 0.00 0.00 0.00 5.54
3 4 6.359617 GTGTGTTTGTTTACTCATTCATTCCG 59.640 38.462 0.00 0.00 0.00 4.30
4 5 7.425606 AGTGTGTTTGTTTACTCATTCATTCC 58.574 34.615 0.00 0.00 0.00 3.01
5 6 9.944663 TTAGTGTGTTTGTTTACTCATTCATTC 57.055 29.630 0.00 0.00 0.00 2.67
8 9 9.562583 GTTTTAGTGTGTTTGTTTACTCATTCA 57.437 29.630 0.00 0.00 0.00 2.57
9 10 9.562583 TGTTTTAGTGTGTTTGTTTACTCATTC 57.437 29.630 0.00 0.00 0.00 2.67
12 13 9.991388 GTATGTTTTAGTGTGTTTGTTTACTCA 57.009 29.630 0.00 0.00 0.00 3.41
15 16 9.442033 GGAGTATGTTTTAGTGTGTTTGTTTAC 57.558 33.333 0.00 0.00 0.00 2.01
16 17 8.623030 GGGAGTATGTTTTAGTGTGTTTGTTTA 58.377 33.333 0.00 0.00 0.00 2.01
17 18 7.340999 AGGGAGTATGTTTTAGTGTGTTTGTTT 59.659 33.333 0.00 0.00 0.00 2.83
18 19 6.831868 AGGGAGTATGTTTTAGTGTGTTTGTT 59.168 34.615 0.00 0.00 0.00 2.83
19 20 6.362248 AGGGAGTATGTTTTAGTGTGTTTGT 58.638 36.000 0.00 0.00 0.00 2.83
20 21 6.072673 GGAGGGAGTATGTTTTAGTGTGTTTG 60.073 42.308 0.00 0.00 0.00 2.93
21 22 6.002082 GGAGGGAGTATGTTTTAGTGTGTTT 58.998 40.000 0.00 0.00 0.00 2.83
22 23 5.557866 GGAGGGAGTATGTTTTAGTGTGTT 58.442 41.667 0.00 0.00 0.00 3.32
23 24 4.322499 CGGAGGGAGTATGTTTTAGTGTGT 60.322 45.833 0.00 0.00 0.00 3.72
24 25 4.181578 CGGAGGGAGTATGTTTTAGTGTG 58.818 47.826 0.00 0.00 0.00 3.82
25 26 3.836562 ACGGAGGGAGTATGTTTTAGTGT 59.163 43.478 0.00 0.00 0.00 3.55
26 27 4.430908 GACGGAGGGAGTATGTTTTAGTG 58.569 47.826 0.00 0.00 0.00 2.74
27 28 3.450096 GGACGGAGGGAGTATGTTTTAGT 59.550 47.826 0.00 0.00 0.00 2.24
28 29 3.181468 GGGACGGAGGGAGTATGTTTTAG 60.181 52.174 0.00 0.00 0.00 1.85
29 30 2.767960 GGGACGGAGGGAGTATGTTTTA 59.232 50.000 0.00 0.00 0.00 1.52
30 31 1.558294 GGGACGGAGGGAGTATGTTTT 59.442 52.381 0.00 0.00 0.00 2.43
31 32 1.201424 GGGACGGAGGGAGTATGTTT 58.799 55.000 0.00 0.00 0.00 2.83
32 33 0.042131 TGGGACGGAGGGAGTATGTT 59.958 55.000 0.00 0.00 0.00 2.71
33 34 0.042131 TTGGGACGGAGGGAGTATGT 59.958 55.000 0.00 0.00 0.00 2.29
34 35 1.200519 TTTGGGACGGAGGGAGTATG 58.799 55.000 0.00 0.00 0.00 2.39
35 36 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
36 37 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
37 38 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
38 39 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
39 40 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
40 41 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
41 42 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
42 43 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
43 44 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
44 45 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
45 46 8.487176 CAAATTTAAGACAAGAATTTTGGGACG 58.513 33.333 0.00 0.00 32.35 4.79
46 47 9.325198 ACAAATTTAAGACAAGAATTTTGGGAC 57.675 29.630 0.00 0.00 33.39 4.46
47 48 9.541143 GACAAATTTAAGACAAGAATTTTGGGA 57.459 29.630 0.00 0.00 33.39 4.37
48 49 9.546428 AGACAAATTTAAGACAAGAATTTTGGG 57.454 29.630 0.00 0.00 33.39 4.12
69 70 9.825109 TGAATTGATACATCCGTATTTAGACAA 57.175 29.630 0.00 0.00 38.48 3.18
70 71 9.996554 ATGAATTGATACATCCGTATTTAGACA 57.003 29.630 0.00 0.00 38.48 3.41
72 73 9.996554 ACATGAATTGATACATCCGTATTTAGA 57.003 29.630 0.00 0.00 38.48 2.10
78 79 9.607988 ACTAAAACATGAATTGATACATCCGTA 57.392 29.630 0.00 0.00 0.00 4.02
79 80 8.506168 ACTAAAACATGAATTGATACATCCGT 57.494 30.769 0.00 0.00 0.00 4.69
110 111 6.328782 TCCCTCATCTAGATACGGATGTAT 57.671 41.667 17.04 0.00 43.97 2.29
111 112 5.774102 TCCCTCATCTAGATACGGATGTA 57.226 43.478 17.04 0.00 39.93 2.29
112 113 4.659529 TCCCTCATCTAGATACGGATGT 57.340 45.455 17.04 0.00 39.93 3.06
113 114 5.196695 TCATCCCTCATCTAGATACGGATG 58.803 45.833 28.93 28.93 41.32 3.51
114 115 5.458451 TCATCCCTCATCTAGATACGGAT 57.542 43.478 17.04 16.70 30.65 4.18
115 116 4.929146 TCATCCCTCATCTAGATACGGA 57.071 45.455 17.04 15.50 0.00 4.69
116 117 4.400884 CCTTCATCCCTCATCTAGATACGG 59.599 50.000 4.54 8.54 0.00 4.02
117 118 4.400884 CCCTTCATCCCTCATCTAGATACG 59.599 50.000 4.54 0.00 0.00 3.06
118 119 5.584913 TCCCTTCATCCCTCATCTAGATAC 58.415 45.833 4.54 0.00 0.00 2.24
119 120 5.317262 ACTCCCTTCATCCCTCATCTAGATA 59.683 44.000 4.54 0.00 0.00 1.98
120 121 4.109435 ACTCCCTTCATCCCTCATCTAGAT 59.891 45.833 0.00 0.00 0.00 1.98
121 122 3.469006 ACTCCCTTCATCCCTCATCTAGA 59.531 47.826 0.00 0.00 0.00 2.43
122 123 3.855668 ACTCCCTTCATCCCTCATCTAG 58.144 50.000 0.00 0.00 0.00 2.43
123 124 4.170053 TGTACTCCCTTCATCCCTCATCTA 59.830 45.833 0.00 0.00 0.00 1.98
124 125 2.885388 ACTCCCTTCATCCCTCATCT 57.115 50.000 0.00 0.00 0.00 2.90
125 126 3.309296 TGTACTCCCTTCATCCCTCATC 58.691 50.000 0.00 0.00 0.00 2.92
126 127 3.421394 TGTACTCCCTTCATCCCTCAT 57.579 47.619 0.00 0.00 0.00 2.90
127 128 2.940514 TGTACTCCCTTCATCCCTCA 57.059 50.000 0.00 0.00 0.00 3.86
128 129 3.582164 AGATGTACTCCCTTCATCCCTC 58.418 50.000 0.00 0.00 38.79 4.30
129 130 3.715648 AGATGTACTCCCTTCATCCCT 57.284 47.619 0.00 0.00 38.79 4.20
130 131 6.043243 TGAATTAGATGTACTCCCTTCATCCC 59.957 42.308 0.00 0.00 38.79 3.85
131 132 7.067496 TGAATTAGATGTACTCCCTTCATCC 57.933 40.000 0.00 0.00 38.79 3.51
132 133 8.964476 TTTGAATTAGATGTACTCCCTTCATC 57.036 34.615 0.00 0.00 38.43 2.92
133 134 9.927081 ATTTTGAATTAGATGTACTCCCTTCAT 57.073 29.630 0.00 0.00 0.00 2.57
273 277 4.822036 TTGTAGACGGAATTTTGTGGTG 57.178 40.909 0.00 0.00 0.00 4.17
317 321 2.377531 GGGGAAAGGAGGAAGGTTTACA 59.622 50.000 0.00 0.00 0.00 2.41
358 362 3.181480 CGAGAGATTGAGAAGAAGGGGAC 60.181 52.174 0.00 0.00 0.00 4.46
372 376 0.320771 AAACAGGTGCGCGAGAGATT 60.321 50.000 12.10 0.00 0.00 2.40
490 498 5.882553 TGTAGTACATGCATGCTTGAAATG 58.117 37.500 33.07 22.79 0.00 2.32
526 538 3.553922 GCTAGAAGGAATCGACAGGATGG 60.554 52.174 0.00 0.00 43.62 3.51
529 541 3.019799 AGCTAGAAGGAATCGACAGGA 57.980 47.619 0.00 0.00 0.00 3.86
594 606 9.679661 AAAATCTGTGTTCCATGTATGTATGTA 57.320 29.630 0.00 0.00 0.00 2.29
595 607 8.579850 AAAATCTGTGTTCCATGTATGTATGT 57.420 30.769 0.00 0.00 0.00 2.29
797 809 0.393077 ACAGCTACACGTGCTTTCCT 59.607 50.000 17.22 2.11 38.92 3.36
820 836 1.609072 TCGCCCGAATCAGAGATACAG 59.391 52.381 0.00 0.00 0.00 2.74
829 845 3.449227 ACTCGCTCGCCCGAATCA 61.449 61.111 0.00 0.00 36.72 2.57
929 945 1.330521 TGCGGCGATGATTAGAAAAGC 59.669 47.619 12.98 0.00 0.00 3.51
1470 1487 1.899534 GTAGCCAAACCGGTGCCAA 60.900 57.895 8.52 0.00 36.97 4.52
1704 1721 0.848305 GCGCAAAGTTGACAAGCTTG 59.152 50.000 24.84 24.84 0.00 4.01
1920 1937 2.039624 AGGAGCATGGTCCGGAGT 59.960 61.111 32.46 16.67 42.05 3.85
2263 2280 2.725759 CGTGCTCATTCAACATTGTCCG 60.726 50.000 0.00 0.00 0.00 4.79
2292 2309 1.632018 CCTCCCGCTTCATACCCCAA 61.632 60.000 0.00 0.00 0.00 4.12
2298 2315 1.721664 CGTCGTCCTCCCGCTTCATA 61.722 60.000 0.00 0.00 0.00 2.15
2655 2672 8.702438 CATATTTTTCAAGAACAACGCATTCTT 58.298 29.630 3.91 3.91 45.24 2.52
2662 2679 9.782028 CATTCAACATATTTTTCAAGAACAACG 57.218 29.630 0.00 0.00 0.00 4.10
2683 2716 8.421002 TCATGTTCTCGGTATAAAGATCATTCA 58.579 33.333 0.00 0.00 32.32 2.57
2711 2744 5.128205 TGCCAGTCTCCAAAATGATATCTG 58.872 41.667 3.98 0.00 0.00 2.90
2716 2749 3.771216 ACTTGCCAGTCTCCAAAATGAT 58.229 40.909 0.00 0.00 0.00 2.45
2733 2766 3.252215 TCTTTGGTCGGCATTTGTACTTG 59.748 43.478 0.00 0.00 0.00 3.16
2763 2796 7.708322 AGAAAAGTTTGAGGAAAGCTTCATTTC 59.292 33.333 0.00 1.01 38.26 2.17
2819 2852 0.824759 ACCCTAACCTCAGCATCGAC 59.175 55.000 0.00 0.00 0.00 4.20
2926 2975 9.371136 CATCTAGATGTGCTTTAGTAAAACTGA 57.629 33.333 22.42 0.00 34.23 3.41
2943 2992 6.587608 TGCAATACTTATCGCACATCTAGATG 59.412 38.462 27.63 27.63 44.15 2.90
2944 2993 6.691508 TGCAATACTTATCGCACATCTAGAT 58.308 36.000 0.00 0.00 0.00 1.98
2945 2994 6.084326 TGCAATACTTATCGCACATCTAGA 57.916 37.500 0.00 0.00 0.00 2.43
2953 3002 7.330946 GGACTTATATGTGCAATACTTATCGCA 59.669 37.037 5.53 0.00 33.27 5.10
2954 3003 7.545965 AGGACTTATATGTGCAATACTTATCGC 59.454 37.037 11.91 0.00 33.27 4.58
2955 3004 8.988064 AGGACTTATATGTGCAATACTTATCG 57.012 34.615 11.91 0.00 33.27 2.92
2977 3026 9.542462 CCGTTAAGATCAATTTTGAGTATAGGA 57.458 33.333 0.00 0.00 41.08 2.94
2978 3027 8.283291 GCCGTTAAGATCAATTTTGAGTATAGG 58.717 37.037 0.00 0.00 41.08 2.57
2979 3028 8.004344 CGCCGTTAAGATCAATTTTGAGTATAG 58.996 37.037 0.00 0.00 41.08 1.31
2980 3029 7.707464 TCGCCGTTAAGATCAATTTTGAGTATA 59.293 33.333 0.00 0.00 41.08 1.47
2981 3030 6.537301 TCGCCGTTAAGATCAATTTTGAGTAT 59.463 34.615 0.00 0.00 41.08 2.12
2982 3031 5.870433 TCGCCGTTAAGATCAATTTTGAGTA 59.130 36.000 0.00 0.00 41.08 2.59
2983 3032 4.693566 TCGCCGTTAAGATCAATTTTGAGT 59.306 37.500 0.00 0.00 41.08 3.41
2984 3033 5.063438 TCTCGCCGTTAAGATCAATTTTGAG 59.937 40.000 0.00 0.00 41.08 3.02
2985 3034 4.932799 TCTCGCCGTTAAGATCAATTTTGA 59.067 37.500 0.00 0.00 42.14 2.69
2986 3035 5.216566 TCTCGCCGTTAAGATCAATTTTG 57.783 39.130 0.00 0.00 0.00 2.44
2987 3036 6.436843 AATCTCGCCGTTAAGATCAATTTT 57.563 33.333 0.00 0.00 31.03 1.82
2988 3037 6.128007 ACAAATCTCGCCGTTAAGATCAATTT 60.128 34.615 0.00 0.00 31.03 1.82
2989 3038 5.354234 ACAAATCTCGCCGTTAAGATCAATT 59.646 36.000 0.00 0.00 31.03 2.32
2990 3039 4.876107 ACAAATCTCGCCGTTAAGATCAAT 59.124 37.500 0.00 0.00 31.03 2.57
2991 3040 4.092821 CACAAATCTCGCCGTTAAGATCAA 59.907 41.667 0.00 0.00 31.03 2.57
2992 3041 3.616821 CACAAATCTCGCCGTTAAGATCA 59.383 43.478 0.00 0.00 31.03 2.92
2993 3042 3.617263 ACACAAATCTCGCCGTTAAGATC 59.383 43.478 0.00 0.00 31.03 2.75
2994 3043 3.596214 ACACAAATCTCGCCGTTAAGAT 58.404 40.909 0.00 0.00 33.67 2.40
2995 3044 3.034721 ACACAAATCTCGCCGTTAAGA 57.965 42.857 0.00 0.00 0.00 2.10
2996 3045 3.306166 CCTACACAAATCTCGCCGTTAAG 59.694 47.826 0.00 0.00 0.00 1.85
2997 3046 3.255725 CCTACACAAATCTCGCCGTTAA 58.744 45.455 0.00 0.00 0.00 2.01
2998 3047 2.231964 ACCTACACAAATCTCGCCGTTA 59.768 45.455 0.00 0.00 0.00 3.18
2999 3048 1.001633 ACCTACACAAATCTCGCCGTT 59.998 47.619 0.00 0.00 0.00 4.44
3000 3049 0.606604 ACCTACACAAATCTCGCCGT 59.393 50.000 0.00 0.00 0.00 5.68
3001 3050 2.159282 AGTACCTACACAAATCTCGCCG 60.159 50.000 0.00 0.00 0.00 6.46
3002 3051 3.521947 AGTACCTACACAAATCTCGCC 57.478 47.619 0.00 0.00 0.00 5.54
3003 3052 5.169295 AGAAAGTACCTACACAAATCTCGC 58.831 41.667 0.00 0.00 0.00 5.03
3004 3053 7.653767 AAAGAAAGTACCTACACAAATCTCG 57.346 36.000 0.00 0.00 0.00 4.04
3005 3054 9.274206 AGAAAAGAAAGTACCTACACAAATCTC 57.726 33.333 0.00 0.00 0.00 2.75
3009 3058 9.841295 ACATAGAAAAGAAAGTACCTACACAAA 57.159 29.630 0.00 0.00 0.00 2.83
3010 3059 9.841295 AACATAGAAAAGAAAGTACCTACACAA 57.159 29.630 0.00 0.00 0.00 3.33
3011 3060 9.841295 AAACATAGAAAAGAAAGTACCTACACA 57.159 29.630 0.00 0.00 0.00 3.72
3032 3081 9.783081 ATCAAGCATAAAAAGGAAAAGAAACAT 57.217 25.926 0.00 0.00 0.00 2.71
3033 3082 9.612066 AATCAAGCATAAAAAGGAAAAGAAACA 57.388 25.926 0.00 0.00 0.00 2.83
3050 3099 8.133627 GCACATCTAAATGACTTAATCAAGCAT 58.866 33.333 0.00 0.00 41.93 3.79
3051 3100 7.121020 TGCACATCTAAATGACTTAATCAAGCA 59.879 33.333 0.00 0.00 41.93 3.91
3052 3101 7.475015 TGCACATCTAAATGACTTAATCAAGC 58.525 34.615 0.00 0.00 41.93 4.01
3061 3110 9.060347 CCATAGTTATTGCACATCTAAATGACT 57.940 33.333 0.00 0.00 35.23 3.41
3062 3111 7.805071 GCCATAGTTATTGCACATCTAAATGAC 59.195 37.037 0.00 0.00 36.67 3.06
3063 3112 7.501892 TGCCATAGTTATTGCACATCTAAATGA 59.498 33.333 0.00 0.00 36.67 2.57
3064 3113 7.650890 TGCCATAGTTATTGCACATCTAAATG 58.349 34.615 0.00 0.00 38.93 2.32
3065 3114 7.822161 TGCCATAGTTATTGCACATCTAAAT 57.178 32.000 0.00 0.00 30.49 1.40
3074 3123 6.173427 TCTAGATGTGCCATAGTTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
3075 3124 7.069852 CATCTAGATGTGCCATAGTTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
3090 3139 4.944619 TTGTCTAGGGCACATCTAGATG 57.055 45.455 27.63 27.63 43.25 2.90
3091 3140 6.506538 AATTTGTCTAGGGCACATCTAGAT 57.493 37.500 0.00 0.00 43.25 1.98
3092 3141 5.957771 AATTTGTCTAGGGCACATCTAGA 57.042 39.130 0.00 0.00 40.38 2.43
3093 3142 8.682936 ATAAAATTTGTCTAGGGCACATCTAG 57.317 34.615 0.00 0.00 36.46 2.43
3094 3143 8.902806 CAATAAAATTTGTCTAGGGCACATCTA 58.097 33.333 0.00 0.00 0.00 1.98
3095 3144 7.397192 ACAATAAAATTTGTCTAGGGCACATCT 59.603 33.333 0.00 0.00 34.83 2.90
3096 3145 7.547227 ACAATAAAATTTGTCTAGGGCACATC 58.453 34.615 0.00 0.00 34.83 3.06
3097 3146 7.480760 ACAATAAAATTTGTCTAGGGCACAT 57.519 32.000 0.00 0.00 34.83 3.21
3098 3147 6.909550 ACAATAAAATTTGTCTAGGGCACA 57.090 33.333 0.00 0.00 34.83 4.57
3099 3148 8.276252 TCTACAATAAAATTTGTCTAGGGCAC 57.724 34.615 0.00 0.00 40.25 5.01
3100 3149 8.871629 TTCTACAATAAAATTTGTCTAGGGCA 57.128 30.769 0.00 0.00 40.25 5.36
3106 3155 9.423061 GGCACATTTCTACAATAAAATTTGTCT 57.577 29.630 0.00 0.00 40.25 3.41
3107 3156 8.655970 GGGCACATTTCTACAATAAAATTTGTC 58.344 33.333 0.00 0.00 40.25 3.18
3108 3157 8.153550 TGGGCACATTTCTACAATAAAATTTGT 58.846 29.630 0.00 0.00 42.31 2.83
3109 3158 8.545229 TGGGCACATTTCTACAATAAAATTTG 57.455 30.769 0.00 0.00 0.00 2.32
3141 3190 4.333926 ACGATTACGAGTACCTCCAAGTAC 59.666 45.833 0.00 0.00 41.53 2.73
3156 3237 2.346376 GCGTTGCATGTAGACGATTACG 60.346 50.000 11.83 9.32 45.75 3.18
3165 3246 1.129251 CTGGTCAAGCGTTGCATGTAG 59.871 52.381 0.00 0.00 0.00 2.74
3178 3259 2.438411 ACCGTCAAACAAACTGGTCAA 58.562 42.857 0.00 0.00 0.00 3.18
3179 3260 2.116827 ACCGTCAAACAAACTGGTCA 57.883 45.000 0.00 0.00 0.00 4.02
3224 3305 9.034544 GCAATTAATCCAGGAATCAACATTAAC 57.965 33.333 0.00 0.00 0.00 2.01
3345 3426 6.492429 CCAACCATCAATATCCAACATCTCAT 59.508 38.462 0.00 0.00 0.00 2.90
3351 3432 5.769662 GCTATCCAACCATCAATATCCAACA 59.230 40.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.