Multiple sequence alignment - TraesCS6D01G216700

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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 TraesCS6D01G216700 chr6D 100.000 2753 0 0 1 2753 306318480 306315728 0.000000e+00 5084
1 TraesCS6D01G216700 chr6D 96.821 2485 50 9 282 2753 472510963 472513431 0.000000e+00 4124
2 TraesCS6D01G216700 chr6D 95.665 2468 69 19 281 2747 156246490 156248920 0.000000e+00 3930
3 TraesCS6D01G216700 chr6D 96.766 2350 53 4 282 2609 7981042 7978694 0.000000e+00 3897
4 TraesCS6D01G216700 chr1D 97.909 2487 40 2 278 2753 475528300 475525815 0.000000e+00 4294
5 TraesCS6D01G216700 chr1D 96.419 2485 62 8 280 2753 6491897 6489429 0.000000e+00 4071
6 TraesCS6D01G216700 chr3D 97.626 2485 45 3 282 2753 85226134 85228617 0.000000e+00 4250
7 TraesCS6D01G216700 chr3D 96.380 2486 70 11 282 2753 359622499 359624978 0.000000e+00 4074
8 TraesCS6D01G216700 chr3D 97.862 1497 19 2 1270 2753 11274709 11276205 0.000000e+00 2575
9 TraesCS6D01G216700 chr3D 94.510 255 11 1 1 252 399372765 399373019 9.240000e-105 390
10 TraesCS6D01G216700 chr4D 97.262 2484 53 5 282 2753 507114494 507112014 0.000000e+00 4196
11 TraesCS6D01G216700 chr4D 96.250 2480 65 14 281 2753 436933710 436936168 0.000000e+00 4039
12 TraesCS6D01G216700 chr5D 96.579 2485 55 12 282 2753 480824254 480821787 0.000000e+00 4091
13 TraesCS6D01G216700 chr2D 97.421 2094 39 2 675 2753 605551640 605549547 0.000000e+00 3554
14 TraesCS6D01G216700 chr2D 97.511 1567 33 4 1188 2753 634823627 634822066 0.000000e+00 2673
15 TraesCS6D01G216700 chr4A 87.343 1517 126 27 1246 2747 293185777 293187242 0.000000e+00 1677
16 TraesCS6D01G216700 chr2B 89.811 1060 92 11 1246 2298 458594654 458593604 0.000000e+00 1345
17 TraesCS6D01G216700 chr2A 92.941 255 15 1 1 252 447371622 447371876 4.330000e-98 368


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 TraesCS6D01G216700 chr6D 306315728 306318480 2752 True 5084 5084 100.000 1 2753 1 chr6D.!!$R2 2752
1 TraesCS6D01G216700 chr6D 472510963 472513431 2468 False 4124 4124 96.821 282 2753 1 chr6D.!!$F2 2471
2 TraesCS6D01G216700 chr6D 156246490 156248920 2430 False 3930 3930 95.665 281 2747 1 chr6D.!!$F1 2466
3 TraesCS6D01G216700 chr6D 7978694 7981042 2348 True 3897 3897 96.766 282 2609 1 chr6D.!!$R1 2327
4 TraesCS6D01G216700 chr1D 475525815 475528300 2485 True 4294 4294 97.909 278 2753 1 chr1D.!!$R2 2475
5 TraesCS6D01G216700 chr1D 6489429 6491897 2468 True 4071 4071 96.419 280 2753 1 chr1D.!!$R1 2473
6 TraesCS6D01G216700 chr3D 85226134 85228617 2483 False 4250 4250 97.626 282 2753 1 chr3D.!!$F2 2471
7 TraesCS6D01G216700 chr3D 359622499 359624978 2479 False 4074 4074 96.380 282 2753 1 chr3D.!!$F3 2471
8 TraesCS6D01G216700 chr3D 11274709 11276205 1496 False 2575 2575 97.862 1270 2753 1 chr3D.!!$F1 1483
9 TraesCS6D01G216700 chr4D 507112014 507114494 2480 True 4196 4196 97.262 282 2753 1 chr4D.!!$R1 2471
10 TraesCS6D01G216700 chr4D 436933710 436936168 2458 False 4039 4039 96.250 281 2753 1 chr4D.!!$F1 2472
11 TraesCS6D01G216700 chr5D 480821787 480824254 2467 True 4091 4091 96.579 282 2753 1 chr5D.!!$R1 2471
12 TraesCS6D01G216700 chr2D 605549547 605551640 2093 True 3554 3554 97.421 675 2753 1 chr2D.!!$R1 2078
13 TraesCS6D01G216700 chr2D 634822066 634823627 1561 True 2673 2673 97.511 1188 2753 1 chr2D.!!$R2 1565
14 TraesCS6D01G216700 chr4A 293185777 293187242 1465 False 1677 1677 87.343 1246 2747 1 chr4A.!!$F1 1501
15 TraesCS6D01G216700 chr2B 458593604 458594654 1050 True 1345 1345 89.811 1246 2298 1 chr2B.!!$R1 1052

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
208 209 0.031449 GGCGAGGAGGATCGAGAAAG 59.969 60.0 0.0 0.0 45.56 2.62 F
624 644 0.535102 CTCTCTCGCTCCTCTCCTCC 60.535 65.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1050 1071 1.072965 CAGGTGGGTTCAGAAAGCTCT 59.927 52.381 0.0 0.0 33.34 4.09 R
2010 2074 1.758936 CCCATCATTCAGCAGCTCAA 58.241 50.000 0.0 0.0 0.00 3.02 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
20 21 3.166489 GTAGAACCCTTCATCACGGAG 57.834 52.381 0.00 0.00 0.00 4.63
21 22 0.905357 AGAACCCTTCATCACGGAGG 59.095 55.000 0.00 0.00 0.00 4.30
22 23 0.902531 GAACCCTTCATCACGGAGGA 59.097 55.000 0.00 0.00 0.00 3.71
23 24 0.905357 AACCCTTCATCACGGAGGAG 59.095 55.000 0.00 0.00 0.00 3.69
24 25 1.144936 CCCTTCATCACGGAGGAGC 59.855 63.158 0.00 0.00 0.00 4.70
25 26 1.333636 CCCTTCATCACGGAGGAGCT 61.334 60.000 0.00 0.00 0.00 4.09
26 27 1.403814 CCTTCATCACGGAGGAGCTA 58.596 55.000 0.00 0.00 0.00 3.32
27 28 1.967066 CCTTCATCACGGAGGAGCTAT 59.033 52.381 0.00 0.00 0.00 2.97
28 29 2.288702 CCTTCATCACGGAGGAGCTATG 60.289 54.545 0.00 0.00 0.00 2.23
29 30 0.676184 TCATCACGGAGGAGCTATGC 59.324 55.000 0.00 0.00 0.00 3.14
30 31 0.320247 CATCACGGAGGAGCTATGCC 60.320 60.000 0.00 0.00 0.00 4.40
31 32 0.470833 ATCACGGAGGAGCTATGCCT 60.471 55.000 0.00 0.00 38.81 4.75
39 40 3.196415 AGGAGCTATGCCTCATATGGA 57.804 47.619 2.13 0.00 33.47 3.41
40 41 3.106054 AGGAGCTATGCCTCATATGGAG 58.894 50.000 2.13 0.00 43.65 3.86
41 42 2.836981 GGAGCTATGCCTCATATGGAGT 59.163 50.000 2.13 0.00 42.40 3.85
42 43 3.262915 GGAGCTATGCCTCATATGGAGTT 59.737 47.826 2.13 0.00 42.40 3.01
43 44 4.502962 GAGCTATGCCTCATATGGAGTTC 58.497 47.826 2.13 0.00 42.40 3.01
44 45 3.262915 AGCTATGCCTCATATGGAGTTCC 59.737 47.826 2.13 0.00 42.40 3.62
45 46 3.620966 GCTATGCCTCATATGGAGTTCCC 60.621 52.174 2.13 0.00 42.40 3.97
53 54 4.308458 TGGAGTTCCCACCGCACG 62.308 66.667 0.00 0.00 40.82 5.34
54 55 4.309950 GGAGTTCCCACCGCACGT 62.310 66.667 0.00 0.00 34.14 4.49
55 56 2.737376 GAGTTCCCACCGCACGTC 60.737 66.667 0.00 0.00 0.00 4.34
56 57 4.657824 AGTTCCCACCGCACGTCG 62.658 66.667 0.00 0.00 38.08 5.12
67 68 4.973055 CACGTCGGCCGGGTCAAA 62.973 66.667 27.83 0.17 42.24 2.69
68 69 4.974989 ACGTCGGCCGGGTCAAAC 62.975 66.667 27.83 14.14 42.24 2.93
69 70 4.675029 CGTCGGCCGGGTCAAACT 62.675 66.667 27.83 0.00 0.00 2.66
70 71 2.658422 GTCGGCCGGGTCAAACTA 59.342 61.111 27.83 0.00 0.00 2.24
71 72 1.219935 GTCGGCCGGGTCAAACTAT 59.780 57.895 27.83 0.00 0.00 2.12
72 73 0.808847 GTCGGCCGGGTCAAACTATC 60.809 60.000 27.83 0.00 0.00 2.08
73 74 1.219664 CGGCCGGGTCAAACTATCA 59.780 57.895 20.10 0.00 0.00 2.15
74 75 0.179056 CGGCCGGGTCAAACTATCAT 60.179 55.000 20.10 0.00 0.00 2.45
75 76 1.745827 CGGCCGGGTCAAACTATCATT 60.746 52.381 20.10 0.00 0.00 2.57
76 77 1.676006 GGCCGGGTCAAACTATCATTG 59.324 52.381 2.18 0.00 0.00 2.82
77 78 2.639065 GCCGGGTCAAACTATCATTGA 58.361 47.619 2.18 0.00 34.56 2.57
78 79 3.214328 GCCGGGTCAAACTATCATTGAT 58.786 45.455 2.18 4.28 38.89 2.57
79 80 3.003689 GCCGGGTCAAACTATCATTGATG 59.996 47.826 9.46 2.54 38.89 3.07
80 81 4.450976 CCGGGTCAAACTATCATTGATGA 58.549 43.478 9.46 0.00 38.89 2.92
81 82 4.512944 CCGGGTCAAACTATCATTGATGAG 59.487 45.833 9.46 5.70 40.64 2.90
82 83 4.024556 CGGGTCAAACTATCATTGATGAGC 60.025 45.833 9.46 8.35 40.64 4.26
83 84 4.883585 GGGTCAAACTATCATTGATGAGCA 59.116 41.667 9.46 0.00 40.64 4.26
84 85 5.008415 GGGTCAAACTATCATTGATGAGCAG 59.992 44.000 9.46 1.35 40.64 4.24
85 86 5.505324 GGTCAAACTATCATTGATGAGCAGC 60.505 44.000 9.46 0.00 40.64 5.25
86 87 5.065602 GTCAAACTATCATTGATGAGCAGCA 59.934 40.000 9.46 0.00 40.64 4.41
87 88 5.296035 TCAAACTATCATTGATGAGCAGCAG 59.704 40.000 9.46 0.00 40.64 4.24
88 89 4.418973 ACTATCATTGATGAGCAGCAGT 57.581 40.909 9.46 0.22 40.64 4.40
89 90 5.541953 ACTATCATTGATGAGCAGCAGTA 57.458 39.130 9.46 0.00 40.64 2.74
90 91 5.539979 ACTATCATTGATGAGCAGCAGTAG 58.460 41.667 9.46 0.00 40.64 2.57
91 92 2.558378 TCATTGATGAGCAGCAGTAGC 58.442 47.619 0.00 0.00 34.98 3.58
92 93 3.056783 TCATTGATGAGCAGCAGTAGCG 61.057 50.000 0.00 0.00 37.83 4.26
95 96 1.078918 ATGAGCAGCAGTAGCGCAA 60.079 52.632 11.47 0.00 44.59 4.85
96 97 0.674581 ATGAGCAGCAGTAGCGCAAA 60.675 50.000 11.47 0.00 44.59 3.68
97 98 2.865958 ATGAGCAGCAGTAGCGCAAAC 61.866 52.381 11.47 7.60 44.59 2.93
102 103 3.885777 GCAGTAGCGCAAACAGATC 57.114 52.632 11.47 0.00 0.00 2.75
103 104 1.078709 GCAGTAGCGCAAACAGATCA 58.921 50.000 11.47 0.00 0.00 2.92
104 105 1.201965 GCAGTAGCGCAAACAGATCAC 60.202 52.381 11.47 0.00 0.00 3.06
105 106 2.068519 CAGTAGCGCAAACAGATCACA 58.931 47.619 11.47 0.00 0.00 3.58
106 107 2.480037 CAGTAGCGCAAACAGATCACAA 59.520 45.455 11.47 0.00 0.00 3.33
107 108 3.058983 CAGTAGCGCAAACAGATCACAAA 60.059 43.478 11.47 0.00 0.00 2.83
108 109 2.405892 AGCGCAAACAGATCACAAAC 57.594 45.000 11.47 0.00 0.00 2.93
109 110 1.949525 AGCGCAAACAGATCACAAACT 59.050 42.857 11.47 0.00 0.00 2.66
110 111 3.138304 AGCGCAAACAGATCACAAACTA 58.862 40.909 11.47 0.00 0.00 2.24
111 112 3.187227 AGCGCAAACAGATCACAAACTAG 59.813 43.478 11.47 0.00 0.00 2.57
112 113 3.186409 GCGCAAACAGATCACAAACTAGA 59.814 43.478 0.30 0.00 0.00 2.43
113 114 4.142816 GCGCAAACAGATCACAAACTAGAT 60.143 41.667 0.30 0.00 0.00 1.98
114 115 5.319139 CGCAAACAGATCACAAACTAGATG 58.681 41.667 0.00 0.00 0.00 2.90
115 116 5.091431 GCAAACAGATCACAAACTAGATGC 58.909 41.667 0.00 0.00 0.00 3.91
116 117 5.634896 CAAACAGATCACAAACTAGATGCC 58.365 41.667 0.00 0.00 0.00 4.40
117 118 4.558226 ACAGATCACAAACTAGATGCCA 57.442 40.909 0.00 0.00 0.00 4.92
118 119 5.108187 ACAGATCACAAACTAGATGCCAT 57.892 39.130 0.00 0.00 0.00 4.40
119 120 4.880120 ACAGATCACAAACTAGATGCCATG 59.120 41.667 0.00 0.00 0.00 3.66
120 121 3.881688 AGATCACAAACTAGATGCCATGC 59.118 43.478 0.00 0.00 0.00 4.06
121 122 2.368439 TCACAAACTAGATGCCATGCC 58.632 47.619 0.00 0.00 0.00 4.40
122 123 2.093890 CACAAACTAGATGCCATGCCA 58.906 47.619 0.00 0.00 0.00 4.92
123 124 2.098607 CACAAACTAGATGCCATGCCAG 59.901 50.000 0.00 0.00 0.00 4.85
124 125 2.025981 ACAAACTAGATGCCATGCCAGA 60.026 45.455 0.00 0.00 0.00 3.86
125 126 3.220110 CAAACTAGATGCCATGCCAGAT 58.780 45.455 0.00 0.00 0.00 2.90
126 127 2.855209 ACTAGATGCCATGCCAGATC 57.145 50.000 0.00 0.00 0.00 2.75
127 128 1.001746 ACTAGATGCCATGCCAGATCG 59.998 52.381 0.00 0.00 0.00 3.69
128 129 0.322648 TAGATGCCATGCCAGATCGG 59.677 55.000 0.00 0.00 38.11 4.18
129 130 1.970114 GATGCCATGCCAGATCGGG 60.970 63.158 7.64 7.64 34.06 5.14
130 131 2.401699 GATGCCATGCCAGATCGGGA 62.402 60.000 16.86 8.15 40.81 5.14
131 132 2.281345 GCCATGCCAGATCGGGAG 60.281 66.667 16.86 4.38 39.28 4.30
132 133 2.811514 GCCATGCCAGATCGGGAGA 61.812 63.158 16.86 1.06 39.28 3.71
133 134 1.370437 CCATGCCAGATCGGGAGAG 59.630 63.158 16.86 3.66 45.48 3.20
134 135 1.370437 CATGCCAGATCGGGAGAGG 59.630 63.158 16.86 0.00 45.48 3.69
135 136 1.117749 CATGCCAGATCGGGAGAGGA 61.118 60.000 16.86 0.00 45.48 3.71
136 137 0.831288 ATGCCAGATCGGGAGAGGAG 60.831 60.000 16.86 0.00 45.48 3.69
137 138 1.456705 GCCAGATCGGGAGAGGAGT 60.457 63.158 16.86 0.00 45.48 3.85
138 139 1.743321 GCCAGATCGGGAGAGGAGTG 61.743 65.000 16.86 0.00 45.48 3.51
139 140 0.396417 CCAGATCGGGAGAGGAGTGT 60.396 60.000 5.91 0.00 45.48 3.55
140 141 1.028905 CAGATCGGGAGAGGAGTGTC 58.971 60.000 0.00 0.00 45.48 3.67
141 142 0.626382 AGATCGGGAGAGGAGTGTCA 59.374 55.000 0.00 0.00 45.48 3.58
142 143 1.028905 GATCGGGAGAGGAGTGTCAG 58.971 60.000 0.00 0.00 45.48 3.51
143 144 0.396417 ATCGGGAGAGGAGTGTCAGG 60.396 60.000 0.00 0.00 45.48 3.86
144 145 2.055042 CGGGAGAGGAGTGTCAGGG 61.055 68.421 0.00 0.00 0.00 4.45
145 146 1.687493 GGGAGAGGAGTGTCAGGGG 60.687 68.421 0.00 0.00 0.00 4.79
146 147 1.388531 GGAGAGGAGTGTCAGGGGA 59.611 63.158 0.00 0.00 0.00 4.81
147 148 0.031616 GGAGAGGAGTGTCAGGGGAT 60.032 60.000 0.00 0.00 0.00 3.85
148 149 1.118838 GAGAGGAGTGTCAGGGGATG 58.881 60.000 0.00 0.00 0.00 3.51
149 150 0.326048 AGAGGAGTGTCAGGGGATGG 60.326 60.000 0.00 0.00 0.00 3.51
150 151 1.307343 AGGAGTGTCAGGGGATGGG 60.307 63.158 0.00 0.00 0.00 4.00
151 152 1.306997 GGAGTGTCAGGGGATGGGA 60.307 63.158 0.00 0.00 0.00 4.37
152 153 0.695803 GGAGTGTCAGGGGATGGGAT 60.696 60.000 0.00 0.00 0.00 3.85
153 154 0.471617 GAGTGTCAGGGGATGGGATG 59.528 60.000 0.00 0.00 0.00 3.51
154 155 0.990282 AGTGTCAGGGGATGGGATGG 60.990 60.000 0.00 0.00 0.00 3.51
155 156 2.386100 TGTCAGGGGATGGGATGGC 61.386 63.158 0.00 0.00 0.00 4.40
156 157 3.170672 TCAGGGGATGGGATGGCG 61.171 66.667 0.00 0.00 0.00 5.69
157 158 4.962836 CAGGGGATGGGATGGCGC 62.963 72.222 0.00 0.00 0.00 6.53
159 160 4.521292 GGGGATGGGATGGCGCAA 62.521 66.667 10.83 0.00 40.58 4.85
160 161 2.908940 GGGATGGGATGGCGCAAG 60.909 66.667 10.83 0.00 40.58 4.01
173 174 1.787847 CGCAAGCGAAGTAAGGTGG 59.212 57.895 9.11 0.00 42.83 4.61
174 175 1.502190 GCAAGCGAAGTAAGGTGGC 59.498 57.895 0.00 0.00 0.00 5.01
175 176 1.923227 GCAAGCGAAGTAAGGTGGCC 61.923 60.000 0.00 0.00 30.33 5.36
176 177 1.002502 AAGCGAAGTAAGGTGGCCC 60.003 57.895 0.00 0.00 0.00 5.80
177 178 2.798148 AAGCGAAGTAAGGTGGCCCG 62.798 60.000 0.00 0.00 35.12 6.13
178 179 2.818274 CGAAGTAAGGTGGCCCGC 60.818 66.667 0.00 0.00 35.12 6.13
179 180 2.669240 GAAGTAAGGTGGCCCGCT 59.331 61.111 0.00 0.00 35.12 5.52
180 181 1.745489 GAAGTAAGGTGGCCCGCTG 60.745 63.158 0.00 0.00 35.12 5.18
181 182 3.920093 AAGTAAGGTGGCCCGCTGC 62.920 63.158 0.00 0.00 40.16 5.25
201 202 4.632458 GCGACGGCGAGGAGGATC 62.632 72.222 18.90 0.00 40.82 3.36
202 203 4.315122 CGACGGCGAGGAGGATCG 62.315 72.222 16.62 6.67 45.48 3.69
203 204 2.900838 GACGGCGAGGAGGATCGA 60.901 66.667 16.62 0.00 45.56 3.59
204 205 2.899044 GACGGCGAGGAGGATCGAG 61.899 68.421 16.62 0.00 45.56 4.04
205 206 2.592001 CGGCGAGGAGGATCGAGA 60.592 66.667 0.00 0.00 45.56 4.04
206 207 2.187493 CGGCGAGGAGGATCGAGAA 61.187 63.158 0.00 0.00 45.56 2.87
207 208 1.725557 CGGCGAGGAGGATCGAGAAA 61.726 60.000 0.00 0.00 45.56 2.52
208 209 0.031449 GGCGAGGAGGATCGAGAAAG 59.969 60.000 0.00 0.00 45.56 2.62
209 210 0.031449 GCGAGGAGGATCGAGAAAGG 59.969 60.000 0.00 0.00 45.56 3.11
210 211 1.681538 CGAGGAGGATCGAGAAAGGA 58.318 55.000 0.00 0.00 45.56 3.36
211 212 1.606668 CGAGGAGGATCGAGAAAGGAG 59.393 57.143 0.00 0.00 45.56 3.69
212 213 1.960689 GAGGAGGATCGAGAAAGGAGG 59.039 57.143 0.00 0.00 34.37 4.30
213 214 1.044611 GGAGGATCGAGAAAGGAGGG 58.955 60.000 0.00 0.00 34.37 4.30
214 215 1.411787 GGAGGATCGAGAAAGGAGGGA 60.412 57.143 0.00 0.00 34.37 4.20
215 216 2.389715 GAGGATCGAGAAAGGAGGGAA 58.610 52.381 0.00 0.00 0.00 3.97
216 217 2.101750 GAGGATCGAGAAAGGAGGGAAC 59.898 54.545 0.00 0.00 0.00 3.62
228 229 2.359975 GGGAACCGAGGTTGCTGG 60.360 66.667 22.47 0.00 44.22 4.85
229 230 3.056328 GGAACCGAGGTTGCTGGC 61.056 66.667 17.52 1.25 42.05 4.85
230 231 3.423154 GAACCGAGGTTGCTGGCG 61.423 66.667 12.80 0.00 38.60 5.69
253 254 4.436998 GGTGCCTCCGGAGTCGTG 62.437 72.222 29.25 15.36 33.95 4.35
254 255 3.371063 GTGCCTCCGGAGTCGTGA 61.371 66.667 29.25 5.91 33.95 4.35
255 256 2.599281 TGCCTCCGGAGTCGTGAA 60.599 61.111 29.25 6.36 33.95 3.18
256 257 2.204461 TGCCTCCGGAGTCGTGAAA 61.204 57.895 29.25 0.00 33.95 2.69
257 258 1.005394 GCCTCCGGAGTCGTGAAAA 60.005 57.895 29.25 0.00 33.95 2.29
258 259 0.601841 GCCTCCGGAGTCGTGAAAAA 60.602 55.000 29.25 0.00 33.95 1.94
259 260 1.944430 GCCTCCGGAGTCGTGAAAAAT 60.944 52.381 29.25 0.00 33.95 1.82
260 261 2.000447 CCTCCGGAGTCGTGAAAAATC 59.000 52.381 29.25 0.00 33.95 2.17
261 262 2.353803 CCTCCGGAGTCGTGAAAAATCT 60.354 50.000 29.25 0.00 33.95 2.40
262 263 2.924290 CTCCGGAGTCGTGAAAAATCTC 59.076 50.000 24.04 0.00 33.95 2.75
263 264 2.561419 TCCGGAGTCGTGAAAAATCTCT 59.439 45.455 0.00 0.00 33.95 3.10
264 265 3.006537 TCCGGAGTCGTGAAAAATCTCTT 59.993 43.478 0.00 0.00 33.95 2.85
265 266 4.219070 TCCGGAGTCGTGAAAAATCTCTTA 59.781 41.667 0.00 0.00 33.95 2.10
266 267 5.105473 TCCGGAGTCGTGAAAAATCTCTTAT 60.105 40.000 0.00 0.00 33.95 1.73
267 268 5.005779 CCGGAGTCGTGAAAAATCTCTTATG 59.994 44.000 0.00 0.00 33.95 1.90
268 269 5.577164 CGGAGTCGTGAAAAATCTCTTATGT 59.423 40.000 0.00 0.00 0.00 2.29
269 270 6.090898 CGGAGTCGTGAAAAATCTCTTATGTT 59.909 38.462 0.00 0.00 0.00 2.71
270 271 7.457060 GGAGTCGTGAAAAATCTCTTATGTTC 58.543 38.462 0.00 0.00 0.00 3.18
271 272 7.117812 GGAGTCGTGAAAAATCTCTTATGTTCA 59.882 37.037 0.00 0.00 0.00 3.18
272 273 8.023050 AGTCGTGAAAAATCTCTTATGTTCAG 57.977 34.615 0.00 0.00 0.00 3.02
273 274 7.118390 AGTCGTGAAAAATCTCTTATGTTCAGG 59.882 37.037 0.00 0.00 34.07 3.86
274 275 7.117812 GTCGTGAAAAATCTCTTATGTTCAGGA 59.882 37.037 0.00 0.00 37.47 3.86
275 276 7.117812 TCGTGAAAAATCTCTTATGTTCAGGAC 59.882 37.037 0.00 0.00 35.90 3.85
276 277 7.118390 CGTGAAAAATCTCTTATGTTCAGGACT 59.882 37.037 0.00 0.00 34.46 3.85
558 565 3.307506 CTCATTCAGTCATCTCCCTCCT 58.692 50.000 0.00 0.00 0.00 3.69
624 644 0.535102 CTCTCTCGCTCCTCTCCTCC 60.535 65.000 0.00 0.00 0.00 4.30
770 790 5.155278 TGGGTAAGTTTTTCGATCTGCTA 57.845 39.130 0.00 0.00 0.00 3.49
848 869 5.349061 GCTAGGGTAAGCTTTGGTTACTA 57.651 43.478 3.20 0.00 43.38 1.82
1030 1051 2.507854 CCTGACACCACCGTGGAGT 61.508 63.158 24.80 21.91 44.04 3.85
1050 1071 1.977854 TCTCTTTTCTGTGGCCAGCTA 59.022 47.619 5.11 0.00 38.66 3.32
1965 2029 3.525862 AGAAGGAGGTTGAACAGGAGAT 58.474 45.455 0.00 0.00 0.00 2.75
2010 2074 1.816835 CAAGCTTGAGCATGTGGTGAT 59.183 47.619 22.31 0.00 45.16 3.06
2036 2100 0.679505 GCTGAATGATGGGCATGCAT 59.320 50.000 21.36 4.91 41.74 3.96
2158 2231 8.152898 CCTAACAATCTGATGTGAAGATATGGA 58.847 37.037 0.00 0.00 33.17 3.41
2566 2658 3.037549 GGAGGTGACAGATGAGGAAGAT 58.962 50.000 0.00 0.00 0.00 2.40
2683 2775 1.062581 AGGAGGCTGGCAGAGAAGATA 60.063 52.381 20.86 0.00 0.00 1.98
2747 2839 3.052082 GCAGGCGCAAGAGCTCAA 61.052 61.111 17.77 0.00 43.02 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.159085 CCTCCGTGATGAAGGGTTCTAC 60.159 54.545 0.00 0.00 35.20 2.59
1 2 2.108168 CCTCCGTGATGAAGGGTTCTA 58.892 52.381 0.00 0.00 35.20 2.10
3 4 0.902531 TCCTCCGTGATGAAGGGTTC 59.097 55.000 0.00 0.00 35.20 3.62
4 5 0.905357 CTCCTCCGTGATGAAGGGTT 59.095 55.000 0.00 0.00 35.20 4.11
5 6 1.617947 GCTCCTCCGTGATGAAGGGT 61.618 60.000 0.00 0.00 35.20 4.34
6 7 1.144936 GCTCCTCCGTGATGAAGGG 59.855 63.158 0.00 0.00 34.94 3.95
7 8 1.403814 TAGCTCCTCCGTGATGAAGG 58.596 55.000 0.00 0.00 0.00 3.46
8 9 2.865670 GCATAGCTCCTCCGTGATGAAG 60.866 54.545 0.00 0.00 0.00 3.02
9 10 1.069204 GCATAGCTCCTCCGTGATGAA 59.931 52.381 0.00 0.00 0.00 2.57
10 11 0.676184 GCATAGCTCCTCCGTGATGA 59.324 55.000 0.00 0.00 0.00 2.92
11 12 0.320247 GGCATAGCTCCTCCGTGATG 60.320 60.000 0.00 0.00 0.00 3.07
12 13 0.470833 AGGCATAGCTCCTCCGTGAT 60.471 55.000 0.00 0.00 0.00 3.06
13 14 1.075970 AGGCATAGCTCCTCCGTGA 60.076 57.895 0.00 0.00 0.00 4.35
14 15 1.365633 GAGGCATAGCTCCTCCGTG 59.634 63.158 8.47 0.00 43.32 4.94
15 16 3.863606 GAGGCATAGCTCCTCCGT 58.136 61.111 8.47 0.00 43.32 4.69
19 20 3.106054 CTCCATATGAGGCATAGCTCCT 58.894 50.000 3.65 0.00 37.45 3.69
20 21 2.836981 ACTCCATATGAGGCATAGCTCC 59.163 50.000 3.65 0.00 46.01 4.70
21 22 4.502962 GAACTCCATATGAGGCATAGCTC 58.497 47.826 3.65 0.00 46.01 4.09
22 23 3.262915 GGAACTCCATATGAGGCATAGCT 59.737 47.826 3.65 0.00 46.01 3.32
23 24 3.604582 GGAACTCCATATGAGGCATAGC 58.395 50.000 3.65 0.00 46.01 2.97
24 25 3.584406 TGGGAACTCCATATGAGGCATAG 59.416 47.826 3.65 0.00 46.01 2.23
25 26 3.597182 TGGGAACTCCATATGAGGCATA 58.403 45.455 3.65 0.00 46.01 3.14
26 27 2.421725 TGGGAACTCCATATGAGGCAT 58.578 47.619 3.65 0.00 46.01 4.40
27 28 1.891933 TGGGAACTCCATATGAGGCA 58.108 50.000 3.65 0.00 46.01 4.75
36 37 4.308458 CGTGCGGTGGGAACTCCA 62.308 66.667 0.00 0.00 44.37 3.86
37 38 4.309950 ACGTGCGGTGGGAACTCC 62.310 66.667 0.00 0.00 40.67 3.85
38 39 2.737376 GACGTGCGGTGGGAACTC 60.737 66.667 0.00 0.00 0.00 3.01
39 40 4.657824 CGACGTGCGGTGGGAACT 62.658 66.667 0.00 0.00 36.03 3.01
50 51 4.973055 TTTGACCCGGCCGACGTG 62.973 66.667 30.73 14.57 42.24 4.49
51 52 4.974989 GTTTGACCCGGCCGACGT 62.975 66.667 30.73 22.61 42.24 4.34
52 53 2.567564 ATAGTTTGACCCGGCCGACG 62.568 60.000 30.73 19.09 43.80 5.12
53 54 0.808847 GATAGTTTGACCCGGCCGAC 60.809 60.000 30.73 16.22 0.00 4.79
54 55 1.259142 TGATAGTTTGACCCGGCCGA 61.259 55.000 30.73 2.40 0.00 5.54
55 56 0.179056 ATGATAGTTTGACCCGGCCG 60.179 55.000 21.04 21.04 0.00 6.13
56 57 1.676006 CAATGATAGTTTGACCCGGCC 59.324 52.381 0.00 0.00 0.00 6.13
57 58 2.639065 TCAATGATAGTTTGACCCGGC 58.361 47.619 0.00 0.00 0.00 6.13
58 59 4.450976 TCATCAATGATAGTTTGACCCGG 58.549 43.478 0.00 0.00 36.02 5.73
59 60 4.024556 GCTCATCAATGATAGTTTGACCCG 60.025 45.833 0.00 0.00 36.02 5.28
60 61 4.883585 TGCTCATCAATGATAGTTTGACCC 59.116 41.667 0.00 0.00 36.02 4.46
61 62 5.505324 GCTGCTCATCAATGATAGTTTGACC 60.505 44.000 0.00 0.00 36.02 4.02
62 63 5.065602 TGCTGCTCATCAATGATAGTTTGAC 59.934 40.000 0.00 0.00 36.02 3.18
63 64 5.187687 TGCTGCTCATCAATGATAGTTTGA 58.812 37.500 0.00 0.00 37.49 2.69
64 65 5.066117 ACTGCTGCTCATCAATGATAGTTTG 59.934 40.000 0.00 0.00 36.02 2.93
65 66 5.191426 ACTGCTGCTCATCAATGATAGTTT 58.809 37.500 0.00 0.00 36.02 2.66
66 67 4.778579 ACTGCTGCTCATCAATGATAGTT 58.221 39.130 0.00 0.00 36.02 2.24
67 68 4.418973 ACTGCTGCTCATCAATGATAGT 57.581 40.909 0.00 0.00 36.02 2.12
68 69 4.389382 GCTACTGCTGCTCATCAATGATAG 59.611 45.833 0.00 0.00 34.55 2.08
69 70 4.313282 GCTACTGCTGCTCATCAATGATA 58.687 43.478 0.00 0.00 34.55 2.15
70 71 3.139850 GCTACTGCTGCTCATCAATGAT 58.860 45.455 0.00 0.00 34.55 2.45
71 72 2.558378 GCTACTGCTGCTCATCAATGA 58.442 47.619 0.00 0.00 36.03 2.57
72 73 1.260825 CGCTACTGCTGCTCATCAATG 59.739 52.381 0.00 0.00 36.97 2.82
73 74 1.579698 CGCTACTGCTGCTCATCAAT 58.420 50.000 0.00 0.00 36.97 2.57
74 75 1.086067 GCGCTACTGCTGCTCATCAA 61.086 55.000 0.00 0.00 36.40 2.57
75 76 1.520120 GCGCTACTGCTGCTCATCA 60.520 57.895 0.00 0.00 36.40 3.07
76 77 1.086067 TTGCGCTACTGCTGCTCATC 61.086 55.000 9.73 0.00 38.69 2.92
77 78 0.674581 TTTGCGCTACTGCTGCTCAT 60.675 50.000 9.73 0.00 38.69 2.90
78 79 1.301637 TTTGCGCTACTGCTGCTCA 60.302 52.632 9.73 0.00 38.69 4.26
79 80 1.133458 GTTTGCGCTACTGCTGCTC 59.867 57.895 9.73 0.00 38.69 4.26
80 81 1.572085 CTGTTTGCGCTACTGCTGCT 61.572 55.000 9.73 0.00 38.69 4.24
81 82 1.154338 CTGTTTGCGCTACTGCTGC 60.154 57.895 9.73 0.00 38.50 5.25
82 83 1.061711 GATCTGTTTGCGCTACTGCTG 59.938 52.381 9.73 0.00 36.97 4.41
83 84 1.338105 TGATCTGTTTGCGCTACTGCT 60.338 47.619 9.73 2.60 36.97 4.24
84 85 1.078709 TGATCTGTTTGCGCTACTGC 58.921 50.000 9.73 0.62 0.00 4.40
85 86 2.068519 TGTGATCTGTTTGCGCTACTG 58.931 47.619 9.73 11.06 0.00 2.74
86 87 2.455674 TGTGATCTGTTTGCGCTACT 57.544 45.000 9.73 0.00 0.00 2.57
87 88 3.058914 AGTTTGTGATCTGTTTGCGCTAC 60.059 43.478 9.73 7.68 0.00 3.58
88 89 3.138304 AGTTTGTGATCTGTTTGCGCTA 58.862 40.909 9.73 0.00 0.00 4.26
89 90 1.949525 AGTTTGTGATCTGTTTGCGCT 59.050 42.857 9.73 0.00 0.00 5.92
90 91 2.405892 AGTTTGTGATCTGTTTGCGC 57.594 45.000 0.00 0.00 0.00 6.09
91 92 4.990543 TCTAGTTTGTGATCTGTTTGCG 57.009 40.909 0.00 0.00 0.00 4.85
92 93 5.091431 GCATCTAGTTTGTGATCTGTTTGC 58.909 41.667 0.00 0.00 0.00 3.68
93 94 5.181811 TGGCATCTAGTTTGTGATCTGTTTG 59.818 40.000 0.00 0.00 0.00 2.93
94 95 5.316167 TGGCATCTAGTTTGTGATCTGTTT 58.684 37.500 0.00 0.00 0.00 2.83
95 96 4.910195 TGGCATCTAGTTTGTGATCTGTT 58.090 39.130 0.00 0.00 0.00 3.16
96 97 4.558226 TGGCATCTAGTTTGTGATCTGT 57.442 40.909 0.00 0.00 0.00 3.41
97 98 4.261072 GCATGGCATCTAGTTTGTGATCTG 60.261 45.833 0.00 0.00 0.00 2.90
98 99 3.881688 GCATGGCATCTAGTTTGTGATCT 59.118 43.478 0.00 0.00 0.00 2.75
99 100 3.004106 GGCATGGCATCTAGTTTGTGATC 59.996 47.826 15.47 0.00 0.00 2.92
100 101 2.954318 GGCATGGCATCTAGTTTGTGAT 59.046 45.455 15.47 0.00 0.00 3.06
101 102 2.290832 TGGCATGGCATCTAGTTTGTGA 60.291 45.455 19.43 0.00 0.00 3.58
102 103 2.093890 TGGCATGGCATCTAGTTTGTG 58.906 47.619 19.43 0.00 0.00 3.33
103 104 2.025981 TCTGGCATGGCATCTAGTTTGT 60.026 45.455 23.59 0.00 0.00 2.83
104 105 2.646930 TCTGGCATGGCATCTAGTTTG 58.353 47.619 23.59 8.47 0.00 2.93
105 106 3.484407 GATCTGGCATGGCATCTAGTTT 58.516 45.455 23.59 3.58 0.00 2.66
106 107 2.549563 CGATCTGGCATGGCATCTAGTT 60.550 50.000 23.59 5.97 0.00 2.24
107 108 1.001746 CGATCTGGCATGGCATCTAGT 59.998 52.381 23.59 7.04 0.00 2.57
108 109 1.675116 CCGATCTGGCATGGCATCTAG 60.675 57.143 23.59 11.17 0.00 2.43
109 110 0.322648 CCGATCTGGCATGGCATCTA 59.677 55.000 23.59 11.73 0.00 1.98
110 111 1.072678 CCGATCTGGCATGGCATCT 59.927 57.895 23.59 12.82 0.00 2.90
111 112 1.970114 CCCGATCTGGCATGGCATC 60.970 63.158 23.59 16.94 35.87 3.91
112 113 2.114625 CCCGATCTGGCATGGCAT 59.885 61.111 23.59 9.00 35.87 4.40
113 114 3.089217 TCCCGATCTGGCATGGCA 61.089 61.111 21.97 21.97 35.87 4.92
114 115 2.281345 CTCCCGATCTGGCATGGC 60.281 66.667 13.29 13.29 35.87 4.40
115 116 1.370437 CTCTCCCGATCTGGCATGG 59.630 63.158 0.00 0.00 35.87 3.66
116 117 1.117749 TCCTCTCCCGATCTGGCATG 61.118 60.000 0.00 0.00 35.87 4.06
117 118 0.831288 CTCCTCTCCCGATCTGGCAT 60.831 60.000 0.00 0.00 35.87 4.40
118 119 1.456518 CTCCTCTCCCGATCTGGCA 60.457 63.158 0.00 0.00 35.87 4.92
119 120 1.456705 ACTCCTCTCCCGATCTGGC 60.457 63.158 0.00 0.00 35.87 4.85
120 121 0.396417 ACACTCCTCTCCCGATCTGG 60.396 60.000 0.00 0.00 37.55 3.86
121 122 1.028905 GACACTCCTCTCCCGATCTG 58.971 60.000 0.00 0.00 0.00 2.90
122 123 0.626382 TGACACTCCTCTCCCGATCT 59.374 55.000 0.00 0.00 0.00 2.75
123 124 1.028905 CTGACACTCCTCTCCCGATC 58.971 60.000 0.00 0.00 0.00 3.69
124 125 0.396417 CCTGACACTCCTCTCCCGAT 60.396 60.000 0.00 0.00 0.00 4.18
125 126 1.000771 CCTGACACTCCTCTCCCGA 60.001 63.158 0.00 0.00 0.00 5.14
126 127 2.055042 CCCTGACACTCCTCTCCCG 61.055 68.421 0.00 0.00 0.00 5.14
127 128 1.687493 CCCCTGACACTCCTCTCCC 60.687 68.421 0.00 0.00 0.00 4.30
128 129 0.031616 ATCCCCTGACACTCCTCTCC 60.032 60.000 0.00 0.00 0.00 3.71
129 130 1.118838 CATCCCCTGACACTCCTCTC 58.881 60.000 0.00 0.00 0.00 3.20
130 131 0.326048 CCATCCCCTGACACTCCTCT 60.326 60.000 0.00 0.00 0.00 3.69
131 132 1.341156 CCCATCCCCTGACACTCCTC 61.341 65.000 0.00 0.00 0.00 3.71
132 133 1.307343 CCCATCCCCTGACACTCCT 60.307 63.158 0.00 0.00 0.00 3.69
133 134 0.695803 ATCCCATCCCCTGACACTCC 60.696 60.000 0.00 0.00 0.00 3.85
134 135 0.471617 CATCCCATCCCCTGACACTC 59.528 60.000 0.00 0.00 0.00 3.51
135 136 0.990282 CCATCCCATCCCCTGACACT 60.990 60.000 0.00 0.00 0.00 3.55
136 137 1.533711 CCATCCCATCCCCTGACAC 59.466 63.158 0.00 0.00 0.00 3.67
137 138 2.386100 GCCATCCCATCCCCTGACA 61.386 63.158 0.00 0.00 0.00 3.58
138 139 2.517919 GCCATCCCATCCCCTGAC 59.482 66.667 0.00 0.00 0.00 3.51
139 140 3.170672 CGCCATCCCATCCCCTGA 61.171 66.667 0.00 0.00 0.00 3.86
140 141 4.962836 GCGCCATCCCATCCCCTG 62.963 72.222 0.00 0.00 0.00 4.45
142 143 4.521292 TTGCGCCATCCCATCCCC 62.521 66.667 4.18 0.00 0.00 4.81
143 144 2.908940 CTTGCGCCATCCCATCCC 60.909 66.667 4.18 0.00 0.00 3.85
144 145 3.599704 GCTTGCGCCATCCCATCC 61.600 66.667 4.18 0.00 0.00 3.51
145 146 3.957535 CGCTTGCGCCATCCCATC 61.958 66.667 4.18 0.00 0.00 3.51
146 147 3.993614 TTCGCTTGCGCCATCCCAT 62.994 57.895 4.18 0.00 0.00 4.00
147 148 4.713735 TTCGCTTGCGCCATCCCA 62.714 61.111 4.18 0.00 0.00 4.37
148 149 3.880846 CTTCGCTTGCGCCATCCC 61.881 66.667 4.18 0.00 0.00 3.85
149 150 1.366111 TTACTTCGCTTGCGCCATCC 61.366 55.000 4.18 0.00 0.00 3.51
150 151 0.026803 CTTACTTCGCTTGCGCCATC 59.973 55.000 4.18 0.00 0.00 3.51
151 152 1.369091 CCTTACTTCGCTTGCGCCAT 61.369 55.000 4.18 0.47 0.00 4.40
152 153 2.032634 CCTTACTTCGCTTGCGCCA 61.033 57.895 4.18 0.00 0.00 5.69
153 154 2.033194 ACCTTACTTCGCTTGCGCC 61.033 57.895 4.18 0.00 0.00 6.53
154 155 1.132640 CACCTTACTTCGCTTGCGC 59.867 57.895 10.38 0.00 0.00 6.09
155 156 1.787847 CCACCTTACTTCGCTTGCG 59.212 57.895 8.87 8.87 0.00 4.85
156 157 1.502190 GCCACCTTACTTCGCTTGC 59.498 57.895 0.00 0.00 0.00 4.01
157 158 1.305930 GGGCCACCTTACTTCGCTTG 61.306 60.000 4.39 0.00 0.00 4.01
158 159 1.002502 GGGCCACCTTACTTCGCTT 60.003 57.895 4.39 0.00 0.00 4.68
159 160 2.669240 GGGCCACCTTACTTCGCT 59.331 61.111 4.39 0.00 0.00 4.93
160 161 2.818274 CGGGCCACCTTACTTCGC 60.818 66.667 4.39 0.00 33.28 4.70
161 162 2.818274 GCGGGCCACCTTACTTCG 60.818 66.667 4.39 0.00 33.28 3.79
162 163 1.745489 CAGCGGGCCACCTTACTTC 60.745 63.158 4.39 0.00 33.28 3.01
163 164 2.351276 CAGCGGGCCACCTTACTT 59.649 61.111 4.39 0.00 33.28 2.24
164 165 4.410400 GCAGCGGGCCACCTTACT 62.410 66.667 4.39 0.00 36.11 2.24
184 185 4.632458 GATCCTCCTCGCCGTCGC 62.632 72.222 0.00 0.00 35.26 5.19
185 186 4.315122 CGATCCTCCTCGCCGTCG 62.315 72.222 0.00 0.00 0.00 5.12
186 187 2.899044 CTCGATCCTCCTCGCCGTC 61.899 68.421 0.00 0.00 38.52 4.79
187 188 2.888464 TTCTCGATCCTCCTCGCCGT 62.888 60.000 0.00 0.00 38.52 5.68
188 189 1.725557 TTTCTCGATCCTCCTCGCCG 61.726 60.000 0.00 0.00 38.52 6.46
189 190 0.031449 CTTTCTCGATCCTCCTCGCC 59.969 60.000 0.00 0.00 38.52 5.54
190 191 0.031449 CCTTTCTCGATCCTCCTCGC 59.969 60.000 0.00 0.00 38.52 5.03
191 192 1.606668 CTCCTTTCTCGATCCTCCTCG 59.393 57.143 0.00 0.00 39.99 4.63
192 193 1.960689 CCTCCTTTCTCGATCCTCCTC 59.039 57.143 0.00 0.00 0.00 3.71
193 194 1.412361 CCCTCCTTTCTCGATCCTCCT 60.412 57.143 0.00 0.00 0.00 3.69
194 195 1.044611 CCCTCCTTTCTCGATCCTCC 58.955 60.000 0.00 0.00 0.00 4.30
195 196 2.074729 TCCCTCCTTTCTCGATCCTC 57.925 55.000 0.00 0.00 0.00 3.71
196 197 2.112190 GTTCCCTCCTTTCTCGATCCT 58.888 52.381 0.00 0.00 0.00 3.24
197 198 1.139256 GGTTCCCTCCTTTCTCGATCC 59.861 57.143 0.00 0.00 0.00 3.36
198 199 1.202428 CGGTTCCCTCCTTTCTCGATC 60.202 57.143 0.00 0.00 0.00 3.69
199 200 0.824759 CGGTTCCCTCCTTTCTCGAT 59.175 55.000 0.00 0.00 0.00 3.59
200 201 0.251474 TCGGTTCCCTCCTTTCTCGA 60.251 55.000 0.00 0.00 0.00 4.04
201 202 0.173708 CTCGGTTCCCTCCTTTCTCG 59.826 60.000 0.00 0.00 0.00 4.04
202 203 0.537653 CCTCGGTTCCCTCCTTTCTC 59.462 60.000 0.00 0.00 0.00 2.87
203 204 0.178900 ACCTCGGTTCCCTCCTTTCT 60.179 55.000 0.00 0.00 0.00 2.52
204 205 0.691332 AACCTCGGTTCCCTCCTTTC 59.309 55.000 0.00 0.00 32.09 2.62
205 206 0.400594 CAACCTCGGTTCCCTCCTTT 59.599 55.000 0.00 0.00 36.00 3.11
206 207 2.067197 CAACCTCGGTTCCCTCCTT 58.933 57.895 0.00 0.00 36.00 3.36
207 208 2.593956 GCAACCTCGGTTCCCTCCT 61.594 63.158 0.00 0.00 36.00 3.69
208 209 2.046217 GCAACCTCGGTTCCCTCC 60.046 66.667 0.00 0.00 36.00 4.30
209 210 1.376037 CAGCAACCTCGGTTCCCTC 60.376 63.158 0.00 0.00 36.00 4.30
210 211 2.750350 CAGCAACCTCGGTTCCCT 59.250 61.111 0.00 0.00 36.00 4.20
211 212 2.359975 CCAGCAACCTCGGTTCCC 60.360 66.667 0.00 0.00 36.00 3.97
212 213 3.056328 GCCAGCAACCTCGGTTCC 61.056 66.667 0.00 0.00 36.00 3.62
213 214 3.423154 CGCCAGCAACCTCGGTTC 61.423 66.667 0.00 0.00 36.00 3.62
241 242 2.924290 GAGATTTTTCACGACTCCGGAG 59.076 50.000 30.11 30.11 40.78 4.63
242 243 2.561419 AGAGATTTTTCACGACTCCGGA 59.439 45.455 2.93 2.93 40.78 5.14
243 244 2.960819 AGAGATTTTTCACGACTCCGG 58.039 47.619 0.00 0.00 40.78 5.14
244 245 5.577164 ACATAAGAGATTTTTCACGACTCCG 59.423 40.000 0.00 0.00 42.50 4.63
245 246 6.969828 ACATAAGAGATTTTTCACGACTCC 57.030 37.500 0.00 0.00 0.00 3.85
246 247 8.018677 TGAACATAAGAGATTTTTCACGACTC 57.981 34.615 0.00 0.00 0.00 3.36
247 248 7.118390 CCTGAACATAAGAGATTTTTCACGACT 59.882 37.037 0.00 0.00 0.00 4.18
248 249 7.117812 TCCTGAACATAAGAGATTTTTCACGAC 59.882 37.037 0.00 0.00 0.00 4.34
249 250 7.117812 GTCCTGAACATAAGAGATTTTTCACGA 59.882 37.037 0.00 0.00 0.00 4.35
250 251 7.118390 AGTCCTGAACATAAGAGATTTTTCACG 59.882 37.037 0.00 0.00 0.00 4.35
251 252 8.329203 AGTCCTGAACATAAGAGATTTTTCAC 57.671 34.615 0.00 0.00 0.00 3.18
257 258 9.829507 CTCAATTAGTCCTGAACATAAGAGATT 57.170 33.333 0.00 0.00 0.00 2.40
258 259 8.986991 ACTCAATTAGTCCTGAACATAAGAGAT 58.013 33.333 0.00 0.00 30.33 2.75
259 260 8.367660 ACTCAATTAGTCCTGAACATAAGAGA 57.632 34.615 0.00 0.00 30.33 3.10
265 266 9.331282 GCTATTTACTCAATTAGTCCTGAACAT 57.669 33.333 0.00 0.00 39.80 2.71
266 267 8.318412 TGCTATTTACTCAATTAGTCCTGAACA 58.682 33.333 0.00 0.00 39.80 3.18
267 268 8.718102 TGCTATTTACTCAATTAGTCCTGAAC 57.282 34.615 0.00 0.00 39.80 3.18
543 545 2.430332 GTGAGAAGGAGGGAGATGACTG 59.570 54.545 0.00 0.00 0.00 3.51
558 565 1.548357 GCAGGGGAGCAGAGTGAGAA 61.548 60.000 0.00 0.00 0.00 2.87
624 644 2.587194 CCGGCATCGAAGAGCAGG 60.587 66.667 11.29 11.29 43.63 4.85
770 790 3.737263 AGATGAACCCTAACCCTAGCTT 58.263 45.455 0.00 0.00 0.00 3.74
848 869 7.402448 ACCATAACCCTGCCTACTAAATAAT 57.598 36.000 0.00 0.00 0.00 1.28
1050 1071 1.072965 CAGGTGGGTTCAGAAAGCTCT 59.927 52.381 0.00 0.00 33.34 4.09
1965 2029 7.071196 TGGCCTTCTCTATCTTAAGCAAATCTA 59.929 37.037 3.32 0.00 0.00 1.98
2010 2074 1.758936 CCCATCATTCAGCAGCTCAA 58.241 50.000 0.00 0.00 0.00 3.02
2036 2100 5.593909 TGATTTTCTCAAGTTTCTCCTTGCA 59.406 36.000 0.00 0.00 41.29 4.08
2064 2128 5.563592 ACACACTTCATGAATCAAGGATGA 58.436 37.500 8.96 0.00 40.57 2.92
2158 2231 4.735369 TCACATTCCCCAAAATGTACACT 58.265 39.130 0.00 0.00 45.68 3.55
2683 2775 3.777106 TCTGAGTTGCACTTCTCCAAT 57.223 42.857 9.32 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.