Multiple sequence alignment - TraesCS2B01G170300

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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 TraesCS2B01G170300 chr2B 100.000 3114 0 0 774 3887 143272650 143275763 0.000000e+00 5751
1 TraesCS2B01G170300 chr2B 100.000 310 0 0 1 310 143271877 143272186 1.210000e-159 573
2 TraesCS2B01G170300 chr2A 96.244 3115 111 5 774 3887 90416045 90419154 0.000000e+00 5099
3 TraesCS2B01G170300 chr2D 96.252 3122 94 10 774 3887 90500400 90503506 0.000000e+00 5096
4 TraesCS2B01G170300 chr1D 91.854 2136 171 3 832 2966 476255828 476253695 0.000000e+00 2977
5 TraesCS2B01G170300 chr1B 91.663 2135 177 1 832 2966 662555084 662552951 0.000000e+00 2955
6 TraesCS2B01G170300 chr1A 91.616 2135 178 1 832 2966 572019135 572017002 0.000000e+00 2950


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 TraesCS2B01G170300 chr2B 143271877 143275763 3886 False 3162 5751 100.000 1 3887 2 chr2B.!!$F1 3886
1 TraesCS2B01G170300 chr2A 90416045 90419154 3109 False 5099 5099 96.244 774 3887 1 chr2A.!!$F1 3113
2 TraesCS2B01G170300 chr2D 90500400 90503506 3106 False 5096 5096 96.252 774 3887 1 chr2D.!!$F1 3113
3 TraesCS2B01G170300 chr1D 476253695 476255828 2133 True 2977 2977 91.854 832 2966 1 chr1D.!!$R1 2134
4 TraesCS2B01G170300 chr1B 662552951 662555084 2133 True 2955 2955 91.663 832 2966 1 chr1B.!!$R1 2134
5 TraesCS2B01G170300 chr1A 572017002 572019135 2133 True 2950 2950 91.616 832 2966 1 chr1A.!!$R1 2134

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
44 45 0.038892 TGTTCCCGTCGACTACAAGC 60.039 55.00 14.70 0.26 0.00 4.01 F
303 304 0.402121 AAACTCTGCTTCCCACCCTC 59.598 55.00 0.00 0.00 0.00 4.30 F
304 305 0.474660 AACTCTGCTTCCCACCCTCT 60.475 55.00 0.00 0.00 0.00 3.69 F
1479 1480 0.104855 ATCATGTGCCGTATGTCGCT 59.895 50.00 0.00 0.00 38.35 4.93 F
1728 1729 3.638160 TCTTTGAAGAGGCATTGCAGTTT 59.362 39.13 11.39 0.79 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1073 1074 0.833287 ATCCGGACATGAGGAGGTTG 59.167 55.000 6.12 0.00 40.26 3.77 R
1468 1469 0.999406 CCAAGAACAGCGACATACGG 59.001 55.000 0.00 0.00 42.83 4.02 R
1533 1534 2.117156 CCTCTTCAATGCCTGGGCG 61.117 63.158 7.14 0.00 45.51 6.13 R
2331 2335 1.028130 TCTGCTCTGCTACTCGATGG 58.972 55.000 0.00 0.00 0.00 3.51 R
3432 3438 1.114627 GCAATGGGTTCCTGAATCCC 58.885 55.000 6.72 8.26 40.90 3.85 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 3.281341 GCAATGTTCGTTTGGTGATGA 57.719 42.857 0.00 0.00 0.00 2.92
21 22 3.236816 GCAATGTTCGTTTGGTGATGAG 58.763 45.455 0.00 0.00 0.00 2.90
22 23 3.058293 GCAATGTTCGTTTGGTGATGAGA 60.058 43.478 0.00 0.00 0.00 3.27
23 24 4.715896 CAATGTTCGTTTGGTGATGAGAG 58.284 43.478 0.00 0.00 0.00 3.20
24 25 3.744238 TGTTCGTTTGGTGATGAGAGA 57.256 42.857 0.00 0.00 0.00 3.10
25 26 4.271696 TGTTCGTTTGGTGATGAGAGAT 57.728 40.909 0.00 0.00 0.00 2.75
26 27 3.996363 TGTTCGTTTGGTGATGAGAGATG 59.004 43.478 0.00 0.00 0.00 2.90
27 28 3.961480 TCGTTTGGTGATGAGAGATGT 57.039 42.857 0.00 0.00 0.00 3.06
28 29 4.271696 TCGTTTGGTGATGAGAGATGTT 57.728 40.909 0.00 0.00 0.00 2.71
29 30 4.245660 TCGTTTGGTGATGAGAGATGTTC 58.754 43.478 0.00 0.00 0.00 3.18
30 31 3.372206 CGTTTGGTGATGAGAGATGTTCC 59.628 47.826 0.00 0.00 0.00 3.62
31 32 3.634397 TTGGTGATGAGAGATGTTCCC 57.366 47.619 0.00 0.00 0.00 3.97
32 33 1.482182 TGGTGATGAGAGATGTTCCCG 59.518 52.381 0.00 0.00 0.00 5.14
33 34 1.482593 GGTGATGAGAGATGTTCCCGT 59.517 52.381 0.00 0.00 0.00 5.28
34 35 2.482142 GGTGATGAGAGATGTTCCCGTC 60.482 54.545 0.00 0.00 0.00 4.79
35 36 1.405463 TGATGAGAGATGTTCCCGTCG 59.595 52.381 0.00 0.00 0.00 5.12
36 37 1.676529 GATGAGAGATGTTCCCGTCGA 59.323 52.381 0.00 0.00 0.00 4.20
37 38 0.809385 TGAGAGATGTTCCCGTCGAC 59.191 55.000 5.18 5.18 0.00 4.20
38 39 1.096416 GAGAGATGTTCCCGTCGACT 58.904 55.000 14.70 0.00 0.00 4.18
39 40 2.286872 GAGAGATGTTCCCGTCGACTA 58.713 52.381 14.70 0.00 0.00 2.59
40 41 2.015587 AGAGATGTTCCCGTCGACTAC 58.984 52.381 14.70 6.97 0.00 2.73
41 42 1.741706 GAGATGTTCCCGTCGACTACA 59.258 52.381 14.70 12.22 0.00 2.74
42 43 2.163010 GAGATGTTCCCGTCGACTACAA 59.837 50.000 14.70 0.00 0.00 2.41
43 44 2.163815 AGATGTTCCCGTCGACTACAAG 59.836 50.000 14.70 0.00 0.00 3.16
44 45 0.038892 TGTTCCCGTCGACTACAAGC 60.039 55.000 14.70 0.26 0.00 4.01
45 46 1.069378 GTTCCCGTCGACTACAAGCG 61.069 60.000 14.70 0.00 0.00 4.68
46 47 2.807631 TTCCCGTCGACTACAAGCGC 62.808 60.000 14.70 0.00 0.00 5.92
47 48 2.126618 CCGTCGACTACAAGCGCA 60.127 61.111 14.70 0.00 0.00 6.09
48 49 1.516386 CCGTCGACTACAAGCGCAT 60.516 57.895 14.70 0.00 0.00 4.73
49 50 1.625870 CGTCGACTACAAGCGCATG 59.374 57.895 14.70 11.60 0.00 4.06
50 51 1.071019 CGTCGACTACAAGCGCATGT 61.071 55.000 22.87 22.87 37.32 3.21
51 52 1.792632 CGTCGACTACAAGCGCATGTA 60.793 52.381 22.65 22.65 34.75 2.29
52 53 2.460918 GTCGACTACAAGCGCATGTAT 58.539 47.619 24.04 14.78 35.37 2.29
53 54 2.216488 GTCGACTACAAGCGCATGTATG 59.784 50.000 24.04 19.17 35.37 2.39
54 55 2.159296 TCGACTACAAGCGCATGTATGT 60.159 45.455 24.04 21.73 35.37 2.29
55 56 2.034591 CGACTACAAGCGCATGTATGTG 60.035 50.000 24.04 15.65 41.07 3.21
56 57 2.279741 ACTACAAGCGCATGTATGTGG 58.720 47.619 24.04 15.33 38.66 4.17
57 58 1.003545 CTACAAGCGCATGTATGTGGC 60.004 52.381 24.04 5.07 38.66 5.01
58 59 1.064621 CAAGCGCATGTATGTGGCC 59.935 57.895 11.47 0.00 38.66 5.36
59 60 1.378382 AAGCGCATGTATGTGGCCA 60.378 52.632 11.47 0.00 38.66 5.36
60 61 0.752743 AAGCGCATGTATGTGGCCAT 60.753 50.000 9.72 0.00 38.66 4.40
61 62 1.168407 AGCGCATGTATGTGGCCATC 61.168 55.000 9.72 3.12 38.66 3.51
62 63 1.168407 GCGCATGTATGTGGCCATCT 61.168 55.000 9.72 1.10 38.66 2.90
63 64 1.877680 GCGCATGTATGTGGCCATCTA 60.878 52.381 9.72 0.00 38.66 1.98
64 65 2.703416 CGCATGTATGTGGCCATCTAT 58.297 47.619 9.72 7.05 34.78 1.98
65 66 2.417586 CGCATGTATGTGGCCATCTATG 59.582 50.000 9.72 11.05 34.78 2.23
66 67 3.678289 GCATGTATGTGGCCATCTATGA 58.322 45.455 9.72 0.00 31.30 2.15
67 68 4.267536 GCATGTATGTGGCCATCTATGAT 58.732 43.478 9.72 0.00 31.30 2.45
68 69 4.703575 GCATGTATGTGGCCATCTATGATT 59.296 41.667 9.72 0.00 31.30 2.57
69 70 5.392703 GCATGTATGTGGCCATCTATGATTG 60.393 44.000 9.72 1.83 31.30 2.67
70 71 5.308976 TGTATGTGGCCATCTATGATTGT 57.691 39.130 9.72 0.00 32.29 2.71
71 72 6.432403 TGTATGTGGCCATCTATGATTGTA 57.568 37.500 9.72 0.00 32.29 2.41
72 73 6.230472 TGTATGTGGCCATCTATGATTGTAC 58.770 40.000 9.72 0.00 32.29 2.90
73 74 4.085357 TGTGGCCATCTATGATTGTACC 57.915 45.455 9.72 0.00 0.00 3.34
74 75 3.067106 GTGGCCATCTATGATTGTACCG 58.933 50.000 9.72 0.00 0.00 4.02
75 76 2.703536 TGGCCATCTATGATTGTACCGT 59.296 45.455 0.00 0.00 0.00 4.83
76 77 3.067106 GGCCATCTATGATTGTACCGTG 58.933 50.000 0.00 0.00 0.00 4.94
77 78 3.494398 GGCCATCTATGATTGTACCGTGT 60.494 47.826 0.00 0.00 0.00 4.49
78 79 4.127171 GCCATCTATGATTGTACCGTGTT 58.873 43.478 0.00 0.00 0.00 3.32
79 80 4.574828 GCCATCTATGATTGTACCGTGTTT 59.425 41.667 0.00 0.00 0.00 2.83
80 81 5.277345 GCCATCTATGATTGTACCGTGTTTC 60.277 44.000 0.00 0.00 0.00 2.78
81 82 5.051039 CCATCTATGATTGTACCGTGTTTCG 60.051 44.000 0.00 0.00 39.52 3.46
82 83 5.063180 TCTATGATTGTACCGTGTTTCGT 57.937 39.130 0.00 0.00 37.94 3.85
83 84 6.193514 TCTATGATTGTACCGTGTTTCGTA 57.806 37.500 0.00 0.00 37.94 3.43
84 85 6.619744 TCTATGATTGTACCGTGTTTCGTAA 58.380 36.000 0.00 0.00 37.94 3.18
85 86 7.089538 TCTATGATTGTACCGTGTTTCGTAAA 58.910 34.615 0.00 0.00 37.94 2.01
86 87 5.980698 TGATTGTACCGTGTTTCGTAAAA 57.019 34.783 0.00 0.00 37.94 1.52
87 88 6.355397 TGATTGTACCGTGTTTCGTAAAAA 57.645 33.333 0.00 0.00 37.94 1.94
109 110 7.671495 AAAATCAAGGTGCAAAAATACCATC 57.329 32.000 0.00 0.00 39.46 3.51
110 111 5.999205 ATCAAGGTGCAAAAATACCATCA 57.001 34.783 0.00 0.00 39.46 3.07
111 112 5.132897 TCAAGGTGCAAAAATACCATCAC 57.867 39.130 0.00 0.00 39.46 3.06
112 113 4.586421 TCAAGGTGCAAAAATACCATCACA 59.414 37.500 0.00 0.00 39.46 3.58
113 114 5.069648 TCAAGGTGCAAAAATACCATCACAA 59.930 36.000 0.00 0.00 39.46 3.33
114 115 5.743636 AGGTGCAAAAATACCATCACAAT 57.256 34.783 0.00 0.00 39.46 2.71
115 116 6.112927 AGGTGCAAAAATACCATCACAATT 57.887 33.333 0.00 0.00 39.46 2.32
116 117 6.532826 AGGTGCAAAAATACCATCACAATTT 58.467 32.000 0.00 0.00 39.46 1.82
117 118 6.997476 AGGTGCAAAAATACCATCACAATTTT 59.003 30.769 0.00 0.00 39.46 1.82
118 119 7.041235 AGGTGCAAAAATACCATCACAATTTTG 60.041 33.333 0.00 0.00 39.46 2.44
119 120 7.076983 GTGCAAAAATACCATCACAATTTTGG 58.923 34.615 9.86 0.00 37.90 3.28
120 121 6.769822 TGCAAAAATACCATCACAATTTTGGT 59.230 30.769 9.86 0.00 45.48 3.67
121 122 7.284034 TGCAAAAATACCATCACAATTTTGGTT 59.716 29.630 9.86 0.00 40.87 3.67
122 123 8.134261 GCAAAAATACCATCACAATTTTGGTTT 58.866 29.630 9.86 0.00 40.87 3.27
126 127 8.970859 AATACCATCACAATTTTGGTTTTTGA 57.029 26.923 0.00 0.00 40.87 2.69
127 128 9.571816 AATACCATCACAATTTTGGTTTTTGAT 57.428 25.926 0.00 0.00 40.87 2.57
128 129 7.261829 ACCATCACAATTTTGGTTTTTGATG 57.738 32.000 11.17 11.17 40.87 3.07
129 130 6.144175 CCATCACAATTTTGGTTTTTGATGC 58.856 36.000 12.09 0.00 38.24 3.91
130 131 5.747951 TCACAATTTTGGTTTTTGATGCC 57.252 34.783 0.00 0.00 0.00 4.40
131 132 5.188434 TCACAATTTTGGTTTTTGATGCCA 58.812 33.333 0.00 0.00 0.00 4.92
132 133 5.649395 TCACAATTTTGGTTTTTGATGCCAA 59.351 32.000 0.00 0.00 40.14 4.52
133 134 6.151648 TCACAATTTTGGTTTTTGATGCCAAA 59.848 30.769 4.12 4.12 46.65 3.28
142 143 6.042093 TGGTTTTTGATGCCAAAATAGTACCA 59.958 34.615 15.34 15.34 46.46 3.25
143 144 7.952816 TGGTTTTTGATGCCAAAATAGTACCAC 60.953 37.037 15.34 6.09 45.24 4.16
144 145 5.652994 TTTGATGCCAAAATAGTACCACC 57.347 39.130 0.00 0.00 39.15 4.61
145 146 3.275143 TGATGCCAAAATAGTACCACCG 58.725 45.455 0.00 0.00 0.00 4.94
146 147 2.863132 TGCCAAAATAGTACCACCGT 57.137 45.000 0.00 0.00 0.00 4.83
147 148 2.428491 TGCCAAAATAGTACCACCGTG 58.572 47.619 0.00 0.00 0.00 4.94
148 149 2.038689 TGCCAAAATAGTACCACCGTGA 59.961 45.455 0.00 0.00 0.00 4.35
149 150 3.075884 GCCAAAATAGTACCACCGTGAA 58.924 45.455 0.00 0.00 0.00 3.18
150 151 3.502979 GCCAAAATAGTACCACCGTGAAA 59.497 43.478 0.00 0.00 0.00 2.69
151 152 4.157105 GCCAAAATAGTACCACCGTGAAAT 59.843 41.667 0.00 0.00 0.00 2.17
152 153 5.354792 GCCAAAATAGTACCACCGTGAAATA 59.645 40.000 0.00 0.00 0.00 1.40
153 154 6.038936 GCCAAAATAGTACCACCGTGAAATAT 59.961 38.462 0.00 0.00 0.00 1.28
154 155 7.636326 CCAAAATAGTACCACCGTGAAATATC 58.364 38.462 0.00 0.00 0.00 1.63
155 156 7.281324 CCAAAATAGTACCACCGTGAAATATCA 59.719 37.037 0.00 0.00 0.00 2.15
156 157 8.670135 CAAAATAGTACCACCGTGAAATATCAA 58.330 33.333 0.00 0.00 37.30 2.57
157 158 8.795842 AAATAGTACCACCGTGAAATATCAAA 57.204 30.769 0.00 0.00 37.30 2.69
158 159 7.781548 ATAGTACCACCGTGAAATATCAAAC 57.218 36.000 0.00 0.00 37.30 2.93
159 160 5.553123 AGTACCACCGTGAAATATCAAACA 58.447 37.500 0.00 0.00 37.30 2.83
160 161 6.177610 AGTACCACCGTGAAATATCAAACAT 58.822 36.000 0.00 0.00 37.30 2.71
161 162 7.332557 AGTACCACCGTGAAATATCAAACATA 58.667 34.615 0.00 0.00 37.30 2.29
162 163 7.990886 AGTACCACCGTGAAATATCAAACATAT 59.009 33.333 0.00 0.00 37.30 1.78
163 164 7.639113 ACCACCGTGAAATATCAAACATATT 57.361 32.000 0.00 0.00 37.30 1.28
164 165 7.703328 ACCACCGTGAAATATCAAACATATTC 58.297 34.615 0.00 0.00 37.30 1.75
165 166 7.556275 ACCACCGTGAAATATCAAACATATTCT 59.444 33.333 0.00 0.00 37.30 2.40
166 167 7.857389 CCACCGTGAAATATCAAACATATTCTG 59.143 37.037 0.00 0.00 37.30 3.02
167 168 8.397906 CACCGTGAAATATCAAACATATTCTGT 58.602 33.333 0.00 0.00 40.84 3.41
179 180 5.743636 ACATATTCTGTTGGCCAAATTGT 57.256 34.783 22.47 13.25 32.90 2.71
180 181 5.481105 ACATATTCTGTTGGCCAAATTGTG 58.519 37.500 22.47 14.60 32.90 3.33
181 182 5.245751 ACATATTCTGTTGGCCAAATTGTGA 59.754 36.000 22.47 11.06 32.90 3.58
182 183 4.686191 ATTCTGTTGGCCAAATTGTGAA 57.314 36.364 22.47 18.60 0.00 3.18
183 184 4.686191 TTCTGTTGGCCAAATTGTGAAT 57.314 36.364 22.47 0.00 0.00 2.57
184 185 5.798125 TTCTGTTGGCCAAATTGTGAATA 57.202 34.783 22.47 0.00 0.00 1.75
185 186 5.389859 TCTGTTGGCCAAATTGTGAATAG 57.610 39.130 22.47 3.22 0.00 1.73
186 187 3.924144 TGTTGGCCAAATTGTGAATAGC 58.076 40.909 22.47 3.33 0.00 2.97
187 188 3.323115 TGTTGGCCAAATTGTGAATAGCA 59.677 39.130 22.47 6.31 0.00 3.49
188 189 4.020396 TGTTGGCCAAATTGTGAATAGCAT 60.020 37.500 22.47 0.00 0.00 3.79
189 190 4.822685 TGGCCAAATTGTGAATAGCATT 57.177 36.364 0.61 0.00 0.00 3.56
190 191 5.163281 TGGCCAAATTGTGAATAGCATTT 57.837 34.783 0.61 0.00 0.00 2.32
191 192 5.558818 TGGCCAAATTGTGAATAGCATTTT 58.441 33.333 0.61 0.00 0.00 1.82
192 193 5.642919 TGGCCAAATTGTGAATAGCATTTTC 59.357 36.000 0.61 0.00 0.00 2.29
193 194 5.876460 GGCCAAATTGTGAATAGCATTTTCT 59.124 36.000 0.00 0.00 0.00 2.52
194 195 6.372381 GGCCAAATTGTGAATAGCATTTTCTT 59.628 34.615 0.00 0.00 0.00 2.52
195 196 7.413328 GGCCAAATTGTGAATAGCATTTTCTTC 60.413 37.037 0.00 0.00 0.00 2.87
196 197 7.332678 GCCAAATTGTGAATAGCATTTTCTTCT 59.667 33.333 0.00 0.00 0.00 2.85
197 198 9.211485 CCAAATTGTGAATAGCATTTTCTTCTT 57.789 29.630 0.00 0.00 0.00 2.52
203 204 9.467258 TGTGAATAGCATTTTCTTCTTCTTTTG 57.533 29.630 0.00 0.00 0.00 2.44
204 205 9.683069 GTGAATAGCATTTTCTTCTTCTTTTGA 57.317 29.630 0.00 0.00 0.00 2.69
205 206 9.683069 TGAATAGCATTTTCTTCTTCTTTTGAC 57.317 29.630 0.00 0.00 0.00 3.18
206 207 9.905171 GAATAGCATTTTCTTCTTCTTTTGACT 57.095 29.630 0.00 0.00 0.00 3.41
209 210 8.225603 AGCATTTTCTTCTTCTTTTGACTACA 57.774 30.769 0.00 0.00 0.00 2.74
210 211 8.348507 AGCATTTTCTTCTTCTTTTGACTACAG 58.651 33.333 0.00 0.00 0.00 2.74
211 212 8.131731 GCATTTTCTTCTTCTTTTGACTACAGT 58.868 33.333 0.00 0.00 0.00 3.55
212 213 9.657121 CATTTTCTTCTTCTTTTGACTACAGTC 57.343 33.333 2.29 2.29 44.97 3.51
230 231 5.679734 CAGTCAAACTGTGAATAGCTTGT 57.320 39.130 0.00 0.00 41.19 3.16
231 232 5.683859 CAGTCAAACTGTGAATAGCTTGTC 58.316 41.667 0.00 0.00 41.19 3.18
232 233 5.237127 CAGTCAAACTGTGAATAGCTTGTCA 59.763 40.000 0.00 0.00 41.19 3.58
233 234 5.468072 AGTCAAACTGTGAATAGCTTGTCAG 59.532 40.000 0.00 0.00 38.23 3.51
234 235 5.237344 GTCAAACTGTGAATAGCTTGTCAGT 59.763 40.000 0.00 0.00 38.23 3.41
235 236 5.822519 TCAAACTGTGAATAGCTTGTCAGTT 59.177 36.000 12.93 12.93 44.37 3.16
236 237 5.679734 AACTGTGAATAGCTTGTCAGTTG 57.320 39.130 15.91 6.62 42.09 3.16
237 238 4.708177 ACTGTGAATAGCTTGTCAGTTGT 58.292 39.130 0.00 0.00 33.26 3.32
238 239 5.126067 ACTGTGAATAGCTTGTCAGTTGTT 58.874 37.500 0.00 0.00 33.26 2.83
239 240 5.590259 ACTGTGAATAGCTTGTCAGTTGTTT 59.410 36.000 0.00 0.00 33.26 2.83
240 241 6.095440 ACTGTGAATAGCTTGTCAGTTGTTTT 59.905 34.615 0.00 0.00 33.26 2.43
241 242 6.862209 TGTGAATAGCTTGTCAGTTGTTTTT 58.138 32.000 0.00 0.00 0.00 1.94
242 243 6.751425 TGTGAATAGCTTGTCAGTTGTTTTTG 59.249 34.615 0.00 0.00 0.00 2.44
243 244 6.198966 GTGAATAGCTTGTCAGTTGTTTTTGG 59.801 38.462 0.00 0.00 0.00 3.28
244 245 5.852282 ATAGCTTGTCAGTTGTTTTTGGT 57.148 34.783 0.00 0.00 0.00 3.67
245 246 6.952773 ATAGCTTGTCAGTTGTTTTTGGTA 57.047 33.333 0.00 0.00 0.00 3.25
246 247 5.852282 AGCTTGTCAGTTGTTTTTGGTAT 57.148 34.783 0.00 0.00 0.00 2.73
247 248 6.220726 AGCTTGTCAGTTGTTTTTGGTATT 57.779 33.333 0.00 0.00 0.00 1.89
248 249 6.273071 AGCTTGTCAGTTGTTTTTGGTATTC 58.727 36.000 0.00 0.00 0.00 1.75
249 250 5.462068 GCTTGTCAGTTGTTTTTGGTATTCC 59.538 40.000 0.00 0.00 0.00 3.01
250 251 6.531503 TTGTCAGTTGTTTTTGGTATTCCA 57.468 33.333 0.00 0.00 42.66 3.53
262 263 4.788925 TGGTATTCCAAGATTACCCCTG 57.211 45.455 11.31 0.00 41.25 4.45
263 264 4.116113 TGGTATTCCAAGATTACCCCTGT 58.884 43.478 11.31 0.00 41.25 4.00
264 265 4.165372 TGGTATTCCAAGATTACCCCTGTC 59.835 45.833 11.31 0.00 41.25 3.51
265 266 4.165372 GGTATTCCAAGATTACCCCTGTCA 59.835 45.833 4.92 0.00 34.40 3.58
266 267 4.946160 ATTCCAAGATTACCCCTGTCAA 57.054 40.909 0.00 0.00 0.00 3.18
267 268 4.733077 TTCCAAGATTACCCCTGTCAAA 57.267 40.909 0.00 0.00 0.00 2.69
268 269 4.946160 TCCAAGATTACCCCTGTCAAAT 57.054 40.909 0.00 0.00 0.00 2.32
269 270 4.855340 TCCAAGATTACCCCTGTCAAATC 58.145 43.478 0.00 0.00 0.00 2.17
270 271 4.540099 TCCAAGATTACCCCTGTCAAATCT 59.460 41.667 0.00 0.00 39.70 2.40
271 272 5.729229 TCCAAGATTACCCCTGTCAAATCTA 59.271 40.000 0.00 0.00 37.63 1.98
272 273 6.389869 TCCAAGATTACCCCTGTCAAATCTAT 59.610 38.462 0.00 0.00 37.63 1.98
273 274 6.712547 CCAAGATTACCCCTGTCAAATCTATC 59.287 42.308 0.00 0.00 37.63 2.08
274 275 6.441088 AGATTACCCCTGTCAAATCTATCC 57.559 41.667 0.00 0.00 37.02 2.59
275 276 5.310857 AGATTACCCCTGTCAAATCTATCCC 59.689 44.000 0.00 0.00 37.02 3.85
276 277 3.151542 ACCCCTGTCAAATCTATCCCT 57.848 47.619 0.00 0.00 0.00 4.20
277 278 4.295905 ACCCCTGTCAAATCTATCCCTA 57.704 45.455 0.00 0.00 0.00 3.53
278 279 4.641868 ACCCCTGTCAAATCTATCCCTAA 58.358 43.478 0.00 0.00 0.00 2.69
279 280 4.412528 ACCCCTGTCAAATCTATCCCTAAC 59.587 45.833 0.00 0.00 0.00 2.34
280 281 4.202472 CCCCTGTCAAATCTATCCCTAACC 60.202 50.000 0.00 0.00 0.00 2.85
281 282 4.412199 CCCTGTCAAATCTATCCCTAACCA 59.588 45.833 0.00 0.00 0.00 3.67
282 283 5.104109 CCCTGTCAAATCTATCCCTAACCAA 60.104 44.000 0.00 0.00 0.00 3.67
283 284 6.423182 CCTGTCAAATCTATCCCTAACCAAA 58.577 40.000 0.00 0.00 0.00 3.28
284 285 6.889722 CCTGTCAAATCTATCCCTAACCAAAA 59.110 38.462 0.00 0.00 0.00 2.44
285 286 7.396055 CCTGTCAAATCTATCCCTAACCAAAAA 59.604 37.037 0.00 0.00 0.00 1.94
301 302 1.704641 AAAAACTCTGCTTCCCACCC 58.295 50.000 0.00 0.00 0.00 4.61
302 303 0.853530 AAAACTCTGCTTCCCACCCT 59.146 50.000 0.00 0.00 0.00 4.34
303 304 0.402121 AAACTCTGCTTCCCACCCTC 59.598 55.000 0.00 0.00 0.00 4.30
304 305 0.474660 AACTCTGCTTCCCACCCTCT 60.475 55.000 0.00 0.00 0.00 3.69
305 306 0.907230 ACTCTGCTTCCCACCCTCTC 60.907 60.000 0.00 0.00 0.00 3.20
306 307 1.613630 TCTGCTTCCCACCCTCTCC 60.614 63.158 0.00 0.00 0.00 3.71
307 308 1.614824 CTGCTTCCCACCCTCTCCT 60.615 63.158 0.00 0.00 0.00 3.69
308 309 1.613630 TGCTTCCCACCCTCTCCTC 60.614 63.158 0.00 0.00 0.00 3.71
309 310 1.306568 GCTTCCCACCCTCTCCTCT 60.307 63.158 0.00 0.00 0.00 3.69
1384 1385 7.564128 GTTCGCATTCAACTCGATGATAAATA 58.436 34.615 0.00 0.00 31.96 1.40
1468 1469 1.395635 TGAGCAATGGGATCATGTGC 58.604 50.000 0.00 0.00 36.91 4.57
1479 1480 0.104855 ATCATGTGCCGTATGTCGCT 59.895 50.000 0.00 0.00 38.35 4.93
1707 1708 4.884164 ACTGCTTATACCCAAAATGAGCTC 59.116 41.667 6.82 6.82 37.00 4.09
1728 1729 3.638160 TCTTTGAAGAGGCATTGCAGTTT 59.362 39.130 11.39 0.79 0.00 2.66
2172 2176 6.156083 TGATGAAGGAAATGGGAATAAAACCC 59.844 38.462 0.00 0.00 46.87 4.11
2244 2248 4.213564 CCTAGATGAGGCAGAACACTTT 57.786 45.455 0.00 0.00 38.96 2.66
2248 2252 6.926272 CCTAGATGAGGCAGAACACTTTATAC 59.074 42.308 0.00 0.00 38.96 1.47
2331 2335 5.417894 GGTATATAAAAACTATGGCCTGGGC 59.582 44.000 14.23 14.23 41.06 5.36
2442 2446 1.216678 TGGGATGGTGTTGTGAAGGTT 59.783 47.619 0.00 0.00 0.00 3.50
2517 2521 3.791320 TCAAGTAGGAAGTGAGGTCCAT 58.209 45.455 0.00 0.00 37.65 3.41
2640 2644 4.829064 TTTTGCAGTTGTCCTACATGAC 57.171 40.909 0.00 0.00 35.77 3.06
2700 2704 0.968405 GTGAGAAAATGGCCCTTGCA 59.032 50.000 0.00 0.00 40.13 4.08
2894 2898 4.165758 TGATGACCATTGGTGATCCATACA 59.834 41.667 26.23 11.40 43.87 2.29
2900 2904 4.279169 CCATTGGTGATCCATACATTGGTC 59.721 45.833 0.00 0.00 46.52 4.02
2974 2978 7.336931 TGTCATCTAATTTTCTAGTGGAAAGGC 59.663 37.037 1.70 0.00 43.68 4.35
3028 3032 6.249260 CCGATAGCTTTGATTTGAAAGTTTCG 59.751 38.462 10.92 0.00 35.67 3.46
3089 3095 8.716646 TCATATTCAATGTTGTGTTATCGTCT 57.283 30.769 0.00 0.00 0.00 4.18
3090 3096 8.817100 TCATATTCAATGTTGTGTTATCGTCTC 58.183 33.333 0.00 0.00 0.00 3.36
3135 3141 7.210873 CCAGTACTACTAGATCAAATTGGGTC 58.789 42.308 0.00 0.00 0.00 4.46
3149 3155 1.790755 TGGGTCGATGAACAAGTTCG 58.209 50.000 8.28 0.00 42.28 3.95
3251 3257 5.664294 TGCCATGCAAATCTAAAAGTCAT 57.336 34.783 0.00 0.00 34.76 3.06
3284 3290 5.163854 CGGCGATATTTTCTTCTTTGACACT 60.164 40.000 0.00 0.00 0.00 3.55
3418 3424 2.634600 TCTTAACACGCAACACAAGGT 58.365 42.857 0.00 0.00 0.00 3.50
3506 3513 2.819608 GCCAGTACAGAAGCCAAATGAA 59.180 45.455 0.00 0.00 0.00 2.57
3581 3588 0.863799 CAGCGAATGTGATCCATCCG 59.136 55.000 0.00 0.00 31.75 4.18
3671 3678 7.553044 CCATTTATTCTTCTTTACTCTCCGGTT 59.447 37.037 0.00 0.00 0.00 4.44
3780 3794 6.653740 GGTCTTATGGCGGCTAAACTAATAAT 59.346 38.462 11.43 0.00 0.00 1.28
3781 3795 7.174426 GGTCTTATGGCGGCTAAACTAATAATT 59.826 37.037 11.43 0.00 0.00 1.40
3864 3878 7.763528 CCATAGGAAGATATAACTGATGTGCTC 59.236 40.741 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.058293 TCTCATCACCAAACGAACATTGC 60.058 43.478 0.00 0.00 0.00 3.56
1 2 4.452114 TCTCTCATCACCAAACGAACATTG 59.548 41.667 0.00 0.00 0.00 2.82
2 3 4.641396 TCTCTCATCACCAAACGAACATT 58.359 39.130 0.00 0.00 0.00 2.71
3 4 4.271696 TCTCTCATCACCAAACGAACAT 57.728 40.909 0.00 0.00 0.00 2.71
4 5 3.744238 TCTCTCATCACCAAACGAACA 57.256 42.857 0.00 0.00 0.00 3.18
5 6 3.997021 ACATCTCTCATCACCAAACGAAC 59.003 43.478 0.00 0.00 0.00 3.95
6 7 4.271696 ACATCTCTCATCACCAAACGAA 57.728 40.909 0.00 0.00 0.00 3.85
7 8 3.961480 ACATCTCTCATCACCAAACGA 57.039 42.857 0.00 0.00 0.00 3.85
8 9 3.372206 GGAACATCTCTCATCACCAAACG 59.628 47.826 0.00 0.00 0.00 3.60
9 10 3.691609 GGGAACATCTCTCATCACCAAAC 59.308 47.826 0.00 0.00 0.00 2.93
10 11 3.619733 CGGGAACATCTCTCATCACCAAA 60.620 47.826 0.00 0.00 0.00 3.28
11 12 2.093500 CGGGAACATCTCTCATCACCAA 60.093 50.000 0.00 0.00 0.00 3.67
12 13 1.482182 CGGGAACATCTCTCATCACCA 59.518 52.381 0.00 0.00 0.00 4.17
13 14 1.482593 ACGGGAACATCTCTCATCACC 59.517 52.381 0.00 0.00 0.00 4.02
14 15 2.796383 CGACGGGAACATCTCTCATCAC 60.796 54.545 0.00 0.00 0.00 3.06
15 16 1.405463 CGACGGGAACATCTCTCATCA 59.595 52.381 0.00 0.00 0.00 3.07
16 17 1.676529 TCGACGGGAACATCTCTCATC 59.323 52.381 0.00 0.00 0.00 2.92
17 18 1.405821 GTCGACGGGAACATCTCTCAT 59.594 52.381 0.00 0.00 0.00 2.90
18 19 0.809385 GTCGACGGGAACATCTCTCA 59.191 55.000 0.00 0.00 0.00 3.27
19 20 1.096416 AGTCGACGGGAACATCTCTC 58.904 55.000 10.46 0.00 0.00 3.20
20 21 2.015587 GTAGTCGACGGGAACATCTCT 58.984 52.381 10.46 0.00 0.00 3.10
21 22 1.741706 TGTAGTCGACGGGAACATCTC 59.258 52.381 10.46 0.00 0.00 2.75
22 23 1.830279 TGTAGTCGACGGGAACATCT 58.170 50.000 10.46 0.00 0.00 2.90
23 24 2.527100 CTTGTAGTCGACGGGAACATC 58.473 52.381 10.46 0.00 0.00 3.06
24 25 1.403780 GCTTGTAGTCGACGGGAACAT 60.404 52.381 10.46 0.00 0.00 2.71
25 26 0.038892 GCTTGTAGTCGACGGGAACA 60.039 55.000 10.46 10.55 0.00 3.18
26 27 1.069378 CGCTTGTAGTCGACGGGAAC 61.069 60.000 10.46 8.05 0.00 3.62
27 28 1.210931 CGCTTGTAGTCGACGGGAA 59.789 57.895 10.46 3.08 0.00 3.97
28 29 2.872557 CGCTTGTAGTCGACGGGA 59.127 61.111 10.46 0.00 0.00 5.14
29 30 2.879462 GCGCTTGTAGTCGACGGG 60.879 66.667 10.46 5.02 0.00 5.28
30 31 1.516386 ATGCGCTTGTAGTCGACGG 60.516 57.895 9.73 0.85 0.00 4.79
31 32 1.071019 ACATGCGCTTGTAGTCGACG 61.071 55.000 25.61 0.00 0.00 5.12
32 33 1.904144 TACATGCGCTTGTAGTCGAC 58.096 50.000 26.80 7.70 0.00 4.20
33 34 2.159296 ACATACATGCGCTTGTAGTCGA 60.159 45.455 31.47 17.33 35.65 4.20
34 35 2.034591 CACATACATGCGCTTGTAGTCG 60.035 50.000 31.47 25.15 35.65 4.18
35 36 2.285220 CCACATACATGCGCTTGTAGTC 59.715 50.000 31.47 0.00 35.65 2.59
36 37 2.279741 CCACATACATGCGCTTGTAGT 58.720 47.619 31.47 26.02 35.65 2.73
37 38 1.003545 GCCACATACATGCGCTTGTAG 60.004 52.381 31.47 25.54 35.65 2.74
38 39 1.013596 GCCACATACATGCGCTTGTA 58.986 50.000 30.77 30.77 36.57 2.41
39 40 1.656818 GGCCACATACATGCGCTTGT 61.657 55.000 28.77 28.77 0.00 3.16
40 41 1.064621 GGCCACATACATGCGCTTG 59.935 57.895 20.60 20.60 0.00 4.01
41 42 0.752743 ATGGCCACATACATGCGCTT 60.753 50.000 8.16 0.00 34.99 4.68
42 43 1.152902 ATGGCCACATACATGCGCT 60.153 52.632 8.16 0.00 34.99 5.92
43 44 1.168407 AGATGGCCACATACATGCGC 61.168 55.000 8.16 0.00 37.47 6.09
44 45 2.168326 TAGATGGCCACATACATGCG 57.832 50.000 8.16 0.00 37.47 4.73
45 46 3.678289 TCATAGATGGCCACATACATGC 58.322 45.455 8.16 0.00 37.47 4.06
46 47 5.708697 ACAATCATAGATGGCCACATACATG 59.291 40.000 8.16 7.95 37.47 3.21
47 48 5.884322 ACAATCATAGATGGCCACATACAT 58.116 37.500 8.16 0.00 37.47 2.29
48 49 5.308976 ACAATCATAGATGGCCACATACA 57.691 39.130 8.16 0.00 37.47 2.29
49 50 5.643777 GGTACAATCATAGATGGCCACATAC 59.356 44.000 8.16 0.00 37.47 2.39
50 51 5.568624 CGGTACAATCATAGATGGCCACATA 60.569 44.000 8.16 3.95 37.47 2.29
51 52 4.655963 GGTACAATCATAGATGGCCACAT 58.344 43.478 8.16 1.00 40.85 3.21
52 53 3.494223 CGGTACAATCATAGATGGCCACA 60.494 47.826 8.16 0.00 0.00 4.17
53 54 3.067106 CGGTACAATCATAGATGGCCAC 58.933 50.000 8.16 1.58 0.00 5.01
54 55 2.703536 ACGGTACAATCATAGATGGCCA 59.296 45.455 8.56 8.56 0.00 5.36
55 56 3.067106 CACGGTACAATCATAGATGGCC 58.933 50.000 0.00 0.00 0.00 5.36
56 57 3.728845 ACACGGTACAATCATAGATGGC 58.271 45.455 0.00 0.00 0.00 4.40
57 58 5.051039 CGAAACACGGTACAATCATAGATGG 60.051 44.000 0.00 0.00 38.46 3.51
58 59 5.962939 CGAAACACGGTACAATCATAGATG 58.037 41.667 0.00 0.00 38.46 2.90
84 85 7.718753 TGATGGTATTTTTGCACCTTGATTTTT 59.281 29.630 0.00 0.00 0.00 1.94
85 86 7.173047 GTGATGGTATTTTTGCACCTTGATTTT 59.827 33.333 0.00 0.00 0.00 1.82
86 87 6.650390 GTGATGGTATTTTTGCACCTTGATTT 59.350 34.615 0.00 0.00 0.00 2.17
87 88 6.165577 GTGATGGTATTTTTGCACCTTGATT 58.834 36.000 0.00 0.00 0.00 2.57
88 89 5.245751 TGTGATGGTATTTTTGCACCTTGAT 59.754 36.000 0.00 0.00 0.00 2.57
89 90 4.586421 TGTGATGGTATTTTTGCACCTTGA 59.414 37.500 0.00 0.00 0.00 3.02
90 91 4.880759 TGTGATGGTATTTTTGCACCTTG 58.119 39.130 0.00 0.00 0.00 3.61
91 92 5.543507 TTGTGATGGTATTTTTGCACCTT 57.456 34.783 0.00 0.00 0.00 3.50
92 93 5.743636 ATTGTGATGGTATTTTTGCACCT 57.256 34.783 0.00 0.00 0.00 4.00
93 94 6.799926 AAATTGTGATGGTATTTTTGCACC 57.200 33.333 0.00 0.00 0.00 5.01
94 95 7.076983 CCAAAATTGTGATGGTATTTTTGCAC 58.923 34.615 0.00 0.00 31.14 4.57
95 96 6.769822 ACCAAAATTGTGATGGTATTTTTGCA 59.230 30.769 0.00 0.00 45.37 4.08
96 97 7.200778 ACCAAAATTGTGATGGTATTTTTGC 57.799 32.000 0.00 0.00 45.37 3.68
100 101 9.401058 TCAAAAACCAAAATTGTGATGGTATTT 57.599 25.926 0.00 3.35 46.46 1.40
101 102 8.970859 TCAAAAACCAAAATTGTGATGGTATT 57.029 26.923 0.00 0.00 46.46 1.89
102 103 9.001542 CATCAAAAACCAAAATTGTGATGGTAT 57.998 29.630 10.28 0.00 46.46 2.73
103 104 7.041508 GCATCAAAAACCAAAATTGTGATGGTA 60.042 33.333 16.86 0.00 46.46 3.25
105 106 6.144175 GCATCAAAAACCAAAATTGTGATGG 58.856 36.000 16.86 0.00 40.64 3.51
106 107 6.144175 GGCATCAAAAACCAAAATTGTGATG 58.856 36.000 12.81 12.81 42.31 3.07
107 108 5.826737 TGGCATCAAAAACCAAAATTGTGAT 59.173 32.000 0.00 0.00 0.00 3.06
108 109 5.188434 TGGCATCAAAAACCAAAATTGTGA 58.812 33.333 0.00 0.00 0.00 3.58
109 110 5.496133 TGGCATCAAAAACCAAAATTGTG 57.504 34.783 0.00 0.00 0.00 3.33
122 123 4.156922 CGGTGGTACTATTTTGGCATCAAA 59.843 41.667 0.00 0.00 40.71 2.69
123 124 3.692101 CGGTGGTACTATTTTGGCATCAA 59.308 43.478 0.00 0.00 0.00 2.57
124 125 3.275143 CGGTGGTACTATTTTGGCATCA 58.725 45.455 0.00 0.00 0.00 3.07
125 126 3.064820 CACGGTGGTACTATTTTGGCATC 59.935 47.826 0.00 0.00 0.00 3.91
126 127 3.013921 CACGGTGGTACTATTTTGGCAT 58.986 45.455 0.00 0.00 0.00 4.40
127 128 2.038689 TCACGGTGGTACTATTTTGGCA 59.961 45.455 8.50 0.00 0.00 4.92
128 129 2.702261 TCACGGTGGTACTATTTTGGC 58.298 47.619 8.50 0.00 0.00 4.52
129 130 5.890424 ATTTCACGGTGGTACTATTTTGG 57.110 39.130 8.50 0.00 0.00 3.28
130 131 8.203937 TGATATTTCACGGTGGTACTATTTTG 57.796 34.615 8.50 0.00 0.00 2.44
131 132 8.795842 TTGATATTTCACGGTGGTACTATTTT 57.204 30.769 8.50 0.00 0.00 1.82
132 133 8.671028 GTTTGATATTTCACGGTGGTACTATTT 58.329 33.333 8.50 0.00 0.00 1.40
133 134 7.825270 TGTTTGATATTTCACGGTGGTACTATT 59.175 33.333 8.50 0.00 0.00 1.73
134 135 7.332557 TGTTTGATATTTCACGGTGGTACTAT 58.667 34.615 8.50 1.71 0.00 2.12
135 136 6.699366 TGTTTGATATTTCACGGTGGTACTA 58.301 36.000 8.50 0.00 0.00 1.82
136 137 5.553123 TGTTTGATATTTCACGGTGGTACT 58.447 37.500 8.50 0.00 0.00 2.73
137 138 5.866335 TGTTTGATATTTCACGGTGGTAC 57.134 39.130 8.50 0.00 0.00 3.34
138 139 8.740123 AATATGTTTGATATTTCACGGTGGTA 57.260 30.769 8.50 0.17 0.00 3.25
139 140 7.556275 AGAATATGTTTGATATTTCACGGTGGT 59.444 33.333 8.50 0.00 0.00 4.16
140 141 7.857389 CAGAATATGTTTGATATTTCACGGTGG 59.143 37.037 8.50 0.00 0.00 4.61
141 142 8.397906 ACAGAATATGTTTGATATTTCACGGTG 58.602 33.333 0.56 0.56 39.96 4.94
142 143 8.506168 ACAGAATATGTTTGATATTTCACGGT 57.494 30.769 0.00 0.00 39.96 4.83
157 158 5.245751 TCACAATTTGGCCAACAGAATATGT 59.754 36.000 20.35 12.19 46.97 2.29
158 159 5.722263 TCACAATTTGGCCAACAGAATATG 58.278 37.500 20.35 11.06 0.00 1.78
159 160 5.999205 TCACAATTTGGCCAACAGAATAT 57.001 34.783 20.35 4.74 0.00 1.28
160 161 5.798125 TTCACAATTTGGCCAACAGAATA 57.202 34.783 20.35 1.87 0.00 1.75
161 162 4.686191 TTCACAATTTGGCCAACAGAAT 57.314 36.364 20.35 6.05 0.00 2.40
162 163 4.686191 ATTCACAATTTGGCCAACAGAA 57.314 36.364 20.35 17.07 0.00 3.02
163 164 4.321899 GCTATTCACAATTTGGCCAACAGA 60.322 41.667 20.35 3.71 0.00 3.41
164 165 3.928375 GCTATTCACAATTTGGCCAACAG 59.072 43.478 20.35 13.47 0.00 3.16
165 166 3.323115 TGCTATTCACAATTTGGCCAACA 59.677 39.130 20.35 10.31 0.00 3.33
166 167 3.924144 TGCTATTCACAATTTGGCCAAC 58.076 40.909 20.35 2.16 0.00 3.77
167 168 4.822685 ATGCTATTCACAATTTGGCCAA 57.177 36.364 16.05 16.05 0.00 4.52
168 169 4.822685 AATGCTATTCACAATTTGGCCA 57.177 36.364 0.00 0.00 0.00 5.36
169 170 5.876460 AGAAAATGCTATTCACAATTTGGCC 59.124 36.000 0.00 0.00 0.00 5.36
170 171 6.973229 AGAAAATGCTATTCACAATTTGGC 57.027 33.333 0.78 0.00 0.00 4.52
171 172 8.767478 AGAAGAAAATGCTATTCACAATTTGG 57.233 30.769 0.78 0.00 0.00 3.28
177 178 9.467258 CAAAAGAAGAAGAAAATGCTATTCACA 57.533 29.630 0.00 0.00 0.00 3.58
178 179 9.683069 TCAAAAGAAGAAGAAAATGCTATTCAC 57.317 29.630 0.00 0.00 0.00 3.18
179 180 9.683069 GTCAAAAGAAGAAGAAAATGCTATTCA 57.317 29.630 0.00 0.00 0.00 2.57
180 181 9.905171 AGTCAAAAGAAGAAGAAAATGCTATTC 57.095 29.630 0.00 0.00 0.00 1.75
183 184 9.337396 TGTAGTCAAAAGAAGAAGAAAATGCTA 57.663 29.630 0.00 0.00 0.00 3.49
184 185 8.225603 TGTAGTCAAAAGAAGAAGAAAATGCT 57.774 30.769 0.00 0.00 0.00 3.79
185 186 8.131731 ACTGTAGTCAAAAGAAGAAGAAAATGC 58.868 33.333 0.00 0.00 0.00 3.56
186 187 9.657121 GACTGTAGTCAAAAGAAGAAGAAAATG 57.343 33.333 7.14 0.00 44.18 2.32
209 210 5.368145 TGACAAGCTATTCACAGTTTGACT 58.632 37.500 6.69 0.00 38.58 3.41
210 211 5.237344 ACTGACAAGCTATTCACAGTTTGAC 59.763 40.000 6.69 1.95 38.58 3.18
211 212 5.368145 ACTGACAAGCTATTCACAGTTTGA 58.632 37.500 6.69 0.00 38.58 2.69
212 213 5.679734 ACTGACAAGCTATTCACAGTTTG 57.320 39.130 0.00 0.00 41.12 2.93
213 214 5.590259 ACAACTGACAAGCTATTCACAGTTT 59.410 36.000 16.28 9.44 43.48 2.66
214 215 5.126067 ACAACTGACAAGCTATTCACAGTT 58.874 37.500 14.39 14.39 45.25 3.16
215 216 4.708177 ACAACTGACAAGCTATTCACAGT 58.292 39.130 0.00 0.00 39.70 3.55
216 217 5.679734 AACAACTGACAAGCTATTCACAG 57.320 39.130 0.00 0.00 0.00 3.66
217 218 6.449635 AAAACAACTGACAAGCTATTCACA 57.550 33.333 0.00 0.00 0.00 3.58
218 219 6.198966 CCAAAAACAACTGACAAGCTATTCAC 59.801 38.462 0.00 0.00 0.00 3.18
219 220 6.127479 ACCAAAAACAACTGACAAGCTATTCA 60.127 34.615 0.00 0.00 0.00 2.57
220 221 6.273071 ACCAAAAACAACTGACAAGCTATTC 58.727 36.000 0.00 0.00 0.00 1.75
221 222 6.220726 ACCAAAAACAACTGACAAGCTATT 57.779 33.333 0.00 0.00 0.00 1.73
222 223 5.852282 ACCAAAAACAACTGACAAGCTAT 57.148 34.783 0.00 0.00 0.00 2.97
223 224 6.952773 ATACCAAAAACAACTGACAAGCTA 57.047 33.333 0.00 0.00 0.00 3.32
224 225 5.852282 ATACCAAAAACAACTGACAAGCT 57.148 34.783 0.00 0.00 0.00 3.74
225 226 5.462068 GGAATACCAAAAACAACTGACAAGC 59.538 40.000 0.00 0.00 35.97 4.01
226 227 6.568869 TGGAATACCAAAAACAACTGACAAG 58.431 36.000 0.00 0.00 43.91 3.16
227 228 6.531503 TGGAATACCAAAAACAACTGACAA 57.468 33.333 0.00 0.00 43.91 3.18
241 242 4.116113 ACAGGGGTAATCTTGGAATACCA 58.884 43.478 12.15 0.00 39.21 3.25
242 243 4.165372 TGACAGGGGTAATCTTGGAATACC 59.835 45.833 3.85 3.85 37.36 2.73
243 244 5.367945 TGACAGGGGTAATCTTGGAATAC 57.632 43.478 0.00 0.00 0.00 1.89
244 245 6.395780 TTTGACAGGGGTAATCTTGGAATA 57.604 37.500 0.00 0.00 0.00 1.75
245 246 4.946160 TTGACAGGGGTAATCTTGGAAT 57.054 40.909 0.00 0.00 0.00 3.01
246 247 4.733077 TTTGACAGGGGTAATCTTGGAA 57.267 40.909 0.00 0.00 0.00 3.53
247 248 4.540099 AGATTTGACAGGGGTAATCTTGGA 59.460 41.667 0.00 0.00 31.37 3.53
248 249 4.860022 AGATTTGACAGGGGTAATCTTGG 58.140 43.478 0.00 0.00 31.37 3.61
249 250 6.712547 GGATAGATTTGACAGGGGTAATCTTG 59.287 42.308 4.98 0.00 35.20 3.02
250 251 6.183361 GGGATAGATTTGACAGGGGTAATCTT 60.183 42.308 4.98 0.00 35.20 2.40
251 252 5.310857 GGGATAGATTTGACAGGGGTAATCT 59.689 44.000 0.00 0.00 36.65 2.40
252 253 5.310857 AGGGATAGATTTGACAGGGGTAATC 59.689 44.000 0.00 0.00 0.00 1.75
253 254 5.235534 AGGGATAGATTTGACAGGGGTAAT 58.764 41.667 0.00 0.00 0.00 1.89
254 255 4.641868 AGGGATAGATTTGACAGGGGTAA 58.358 43.478 0.00 0.00 0.00 2.85
255 256 4.295905 AGGGATAGATTTGACAGGGGTA 57.704 45.455 0.00 0.00 0.00 3.69
256 257 3.151542 AGGGATAGATTTGACAGGGGT 57.848 47.619 0.00 0.00 0.00 4.95
257 258 4.202472 GGTTAGGGATAGATTTGACAGGGG 60.202 50.000 0.00 0.00 0.00 4.79
258 259 4.412199 TGGTTAGGGATAGATTTGACAGGG 59.588 45.833 0.00 0.00 0.00 4.45
259 260 5.630415 TGGTTAGGGATAGATTTGACAGG 57.370 43.478 0.00 0.00 0.00 4.00
260 261 7.938140 TTTTGGTTAGGGATAGATTTGACAG 57.062 36.000 0.00 0.00 0.00 3.51
282 283 1.217942 AGGGTGGGAAGCAGAGTTTTT 59.782 47.619 0.00 0.00 0.00 1.94
283 284 0.853530 AGGGTGGGAAGCAGAGTTTT 59.146 50.000 0.00 0.00 0.00 2.43
284 285 0.402121 GAGGGTGGGAAGCAGAGTTT 59.598 55.000 0.00 0.00 0.00 2.66
285 286 0.474660 AGAGGGTGGGAAGCAGAGTT 60.475 55.000 0.00 0.00 0.00 3.01
286 287 0.907230 GAGAGGGTGGGAAGCAGAGT 60.907 60.000 0.00 0.00 0.00 3.24
287 288 1.621672 GGAGAGGGTGGGAAGCAGAG 61.622 65.000 0.00 0.00 0.00 3.35
288 289 1.613630 GGAGAGGGTGGGAAGCAGA 60.614 63.158 0.00 0.00 0.00 4.26
289 290 1.614824 AGGAGAGGGTGGGAAGCAG 60.615 63.158 0.00 0.00 0.00 4.24
290 291 1.613630 GAGGAGAGGGTGGGAAGCA 60.614 63.158 0.00 0.00 0.00 3.91
291 292 1.306568 AGAGGAGAGGGTGGGAAGC 60.307 63.158 0.00 0.00 0.00 3.86
857 858 3.768922 GCGTGCCTCTGGAGAGCT 61.769 66.667 0.00 0.00 40.75 4.09
1037 1038 1.819632 GGAGGGCATTGCGTCGAAT 60.820 57.895 1.91 0.00 0.00 3.34
1073 1074 0.833287 ATCCGGACATGAGGAGGTTG 59.167 55.000 6.12 0.00 40.26 3.77
1384 1385 2.447047 ACATCCCCTTGTCAAGAAACCT 59.553 45.455 14.42 0.00 0.00 3.50
1468 1469 0.999406 CCAAGAACAGCGACATACGG 59.001 55.000 0.00 0.00 42.83 4.02
1479 1480 2.161855 CTAGCACAATGCCCAAGAACA 58.838 47.619 0.00 0.00 46.52 3.18
1533 1534 2.117156 CCTCTTCAATGCCTGGGCG 61.117 63.158 7.14 0.00 45.51 6.13
1707 1708 3.655276 AACTGCAATGCCTCTTCAAAG 57.345 42.857 1.53 0.00 0.00 2.77
1728 1729 5.896678 TCCTTCCATTTTCAAGTCCAAGAAA 59.103 36.000 0.00 0.00 32.34 2.52
2172 2176 2.673368 GCAAGTGTAATGTTCTCTCCCG 59.327 50.000 0.00 0.00 0.00 5.14
2175 2179 4.697352 ACCATGCAAGTGTAATGTTCTCTC 59.303 41.667 0.00 0.00 0.00 3.20
2244 2248 8.374743 TCTGTGCCAATATAATTGCTCAGTATA 58.625 33.333 12.85 0.00 42.69 1.47
2248 2252 5.559608 CGTCTGTGCCAATATAATTGCTCAG 60.560 44.000 8.80 8.80 43.19 3.35
2331 2335 1.028130 TCTGCTCTGCTACTCGATGG 58.972 55.000 0.00 0.00 0.00 3.51
2442 2446 2.296792 CTCTCTCTCATCAGCTTCCGA 58.703 52.381 0.00 0.00 0.00 4.55
2517 2521 4.438148 TCTTGTCGTCTGATGTGAAAACA 58.562 39.130 0.00 0.00 0.00 2.83
2640 2644 4.515191 TCTTCCTTTTGTTCATCCTCAACG 59.485 41.667 0.00 0.00 0.00 4.10
2894 2898 1.558756 CTGGAGCTTCTGAGGACCAAT 59.441 52.381 0.00 0.00 0.00 3.16
2974 2978 7.371159 TCTCTCATTGCGGAAACATAGTATAG 58.629 38.462 0.00 0.00 0.00 1.31
2981 2985 3.679389 AGTTCTCTCATTGCGGAAACAT 58.321 40.909 0.00 0.00 0.00 2.71
3028 3032 9.042008 CCTAAATACAGTGGTATGAACATGTAC 57.958 37.037 0.00 0.00 40.09 2.90
3089 3095 4.288366 TGGGGCCGAATTTATATCATGAGA 59.712 41.667 0.09 0.00 0.00 3.27
3090 3096 4.588899 TGGGGCCGAATTTATATCATGAG 58.411 43.478 0.09 0.00 0.00 2.90
3135 3141 1.792367 TCAGTGCGAACTTGTTCATCG 59.208 47.619 13.05 2.26 39.47 3.84
3149 3155 4.233789 TCGGCAACATTTTAATTCAGTGC 58.766 39.130 0.00 0.00 0.00 4.40
3251 3257 2.319136 AAATATCGCCGCTGGTGTAA 57.681 45.000 7.78 0.00 34.40 2.41
3330 3336 2.031245 CAGCGCTACCATTGTTTGTTCA 60.031 45.455 10.99 0.00 0.00 3.18
3374 3380 4.802051 TCGCCATTCTGCCCTGCC 62.802 66.667 0.00 0.00 0.00 4.85
3431 3437 1.780503 CAATGGGTTCCTGAATCCCC 58.219 55.000 6.72 3.04 40.90 4.81
3432 3438 1.114627 GCAATGGGTTCCTGAATCCC 58.885 55.000 6.72 8.26 40.90 3.85
3506 3513 4.097741 TGTTGTTGCTGTGCTGTTATCTTT 59.902 37.500 0.00 0.00 0.00 2.52
3859 3873 2.019984 GATTCCCAACATGGAGAGCAC 58.980 52.381 0.00 0.00 40.96 4.40
3864 3878 2.418368 TTCGGATTCCCAACATGGAG 57.582 50.000 0.00 0.00 40.96 3.86


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

AutoCloner maintained by Alex Coulton.