Multiple sequence alignment - TraesCS3B01G544100

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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 TraesCS3B01G544100 chr3B 100.000 2339 0 0 1 2339 781488560 781490898 0.000000e+00 4320.0
1 TraesCS3B01G544100 chr3B 84.411 263 33 6 3 263 781346594 781346338 3.860000e-63 252.0
2 TraesCS3B01G544100 chr3B 83.858 254 27 8 21 264 781217251 781217002 1.810000e-56 230.0
3 TraesCS3B01G544100 chr2B 96.498 971 34 0 397 1367 325637201 325638171 0.000000e+00 1605.0
4 TraesCS3B01G544100 chr2A 96.366 963 35 0 401 1363 382856246 382855284 0.000000e+00 1585.0
5 TraesCS3B01G544100 chr2A 96.078 969 38 0 397 1365 77802217 77803185 0.000000e+00 1580.0
6 TraesCS3B01G544100 chr4B 96.074 968 32 1 400 1361 364053469 364052502 0.000000e+00 1572.0
7 TraesCS3B01G544100 chr3D 96.058 964 38 0 399 1362 90829462 90830425 0.000000e+00 1570.0
8 TraesCS3B01G544100 chr3D 88.301 983 91 16 1364 2339 584451636 584452601 0.000000e+00 1157.0
9 TraesCS3B01G544100 chr3D 92.176 409 21 8 1 403 584451217 584451620 3.370000e-158 568.0
10 TraesCS3B01G544100 chr3D 78.947 399 63 16 1732 2122 308760804 308761189 3.860000e-63 252.0
11 TraesCS3B01G544100 chr3D 82.721 272 33 9 3 263 584050760 584050492 1.810000e-56 230.0
12 TraesCS3B01G544100 chr3D 77.394 376 46 25 1739 2103 6422753 6422406 1.100000e-43 187.0
13 TraesCS3B01G544100 chr3D 92.308 52 4 0 3 54 584050836 584050785 8.960000e-10 75.0
14 TraesCS3B01G544100 chr6D 95.692 975 39 3 397 1369 462399352 462398379 0.000000e+00 1565.0
15 TraesCS3B01G544100 chr6D 95.670 970 38 4 399 1366 452071651 452070684 0.000000e+00 1555.0
16 TraesCS3B01G544100 chr1D 95.954 964 36 3 401 1362 176360548 176361510 0.000000e+00 1561.0
17 TraesCS3B01G544100 chr5A 95.248 968 45 1 397 1364 472509593 472510559 0.000000e+00 1531.0
18 TraesCS3B01G544100 chr5A 77.534 365 64 12 1762 2122 684692973 684693323 1.100000e-48 204.0
19 TraesCS3B01G544100 chrUn 88.650 837 70 14 1506 2339 45497423 45498237 0.000000e+00 996.0
20 TraesCS3B01G544100 chrUn 89.125 423 38 8 1506 1927 469375649 469376064 9.580000e-144 520.0
21 TraesCS3B01G544100 chrUn 93.485 307 19 1 1 307 45500750 45500445 2.740000e-124 455.0
22 TraesCS3B01G544100 chrUn 90.667 150 11 3 1364 1511 45500384 45500236 1.830000e-46 196.0
23 TraesCS3B01G544100 chr6B 78.920 389 67 11 1736 2122 64742912 64743287 1.390000e-62 250.0
24 TraesCS3B01G544100 chr5B 78.635 337 54 14 1760 2092 417005675 417005353 8.470000e-50 207.0
25 TraesCS3B01G544100 chr1A 77.337 353 62 11 1760 2110 544998729 544998393 2.370000e-45 193.0
26 TraesCS3B01G544100 chr1A 87.143 70 6 3 2247 2315 495716153 495716086 2.490000e-10 76.8
27 TraesCS3B01G544100 chr7D 78.019 323 56 10 1739 2058 487773345 487773035 3.070000e-44 189.0


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 TraesCS3B01G544100 chr3B 781488560 781490898 2338 False 4320.0 4320 100.0000 1 2339 1 chr3B.!!$F1 2338
1 TraesCS3B01G544100 chr2B 325637201 325638171 970 False 1605.0 1605 96.4980 397 1367 1 chr2B.!!$F1 970
2 TraesCS3B01G544100 chr2A 382855284 382856246 962 True 1585.0 1585 96.3660 401 1363 1 chr2A.!!$R1 962
3 TraesCS3B01G544100 chr2A 77802217 77803185 968 False 1580.0 1580 96.0780 397 1365 1 chr2A.!!$F1 968
4 TraesCS3B01G544100 chr4B 364052502 364053469 967 True 1572.0 1572 96.0740 400 1361 1 chr4B.!!$R1 961
5 TraesCS3B01G544100 chr3D 90829462 90830425 963 False 1570.0 1570 96.0580 399 1362 1 chr3D.!!$F1 963
6 TraesCS3B01G544100 chr3D 584451217 584452601 1384 False 862.5 1157 90.2385 1 2339 2 chr3D.!!$F3 2338
7 TraesCS3B01G544100 chr6D 462398379 462399352 973 True 1565.0 1565 95.6920 397 1369 1 chr6D.!!$R2 972
8 TraesCS3B01G544100 chr6D 452070684 452071651 967 True 1555.0 1555 95.6700 399 1366 1 chr6D.!!$R1 967
9 TraesCS3B01G544100 chr1D 176360548 176361510 962 False 1561.0 1561 95.9540 401 1362 1 chr1D.!!$F1 961
10 TraesCS3B01G544100 chr5A 472509593 472510559 966 False 1531.0 1531 95.2480 397 1364 1 chr5A.!!$F1 967
11 TraesCS3B01G544100 chrUn 45497423 45498237 814 False 996.0 996 88.6500 1506 2339 1 chrUn.!!$F1 833
12 TraesCS3B01G544100 chrUn 45500236 45500750 514 True 325.5 455 92.0760 1 1511 2 chrUn.!!$R1 1510

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
81 83 0.030773 TGATGTACGATGAGAGGCGC 59.969 55.0 0.0 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1868 0.407918 GGGATCCAAAACACCTCCCA 59.592 55.0 15.23 0.0 44.23 4.37 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
79 81 3.119291 CAAGTGATGTACGATGAGAGGC 58.881 50.000 0.00 0.00 0.00 4.70
80 82 1.335182 AGTGATGTACGATGAGAGGCG 59.665 52.381 0.00 0.00 0.00 5.52
81 83 0.030773 TGATGTACGATGAGAGGCGC 59.969 55.000 0.00 0.00 0.00 6.53
82 84 0.999228 GATGTACGATGAGAGGCGCG 60.999 60.000 0.00 0.00 0.00 6.86
83 85 1.444917 ATGTACGATGAGAGGCGCGA 61.445 55.000 12.10 0.00 0.00 5.87
84 86 1.654743 GTACGATGAGAGGCGCGAC 60.655 63.158 12.10 7.34 0.00 5.19
85 87 2.110352 TACGATGAGAGGCGCGACA 61.110 57.895 17.71 3.63 0.00 4.35
86 88 2.048312 TACGATGAGAGGCGCGACAG 62.048 60.000 17.71 0.00 0.00 3.51
87 89 2.492090 GATGAGAGGCGCGACAGT 59.508 61.111 17.71 0.00 0.00 3.55
88 90 1.875813 GATGAGAGGCGCGACAGTG 60.876 63.158 17.71 0.00 0.00 3.66
89 91 2.271607 GATGAGAGGCGCGACAGTGA 62.272 60.000 17.71 0.00 0.00 3.41
90 92 2.202544 GAGAGGCGCGACAGTGAG 60.203 66.667 17.71 0.00 0.00 3.51
91 93 4.427661 AGAGGCGCGACAGTGAGC 62.428 66.667 17.71 0.71 0.00 4.26
92 94 4.724602 GAGGCGCGACAGTGAGCA 62.725 66.667 17.71 0.00 0.00 4.26
93 95 4.731612 AGGCGCGACAGTGAGCAG 62.732 66.667 17.71 8.60 0.00 4.24
95 97 3.771491 GCGCGACAGTGAGCAGTG 61.771 66.667 12.10 3.85 37.75 3.66
96 98 2.355126 CGCGACAGTGAGCAGTGT 60.355 61.111 10.52 10.52 46.81 3.55
97 99 1.951130 CGCGACAGTGAGCAGTGTT 60.951 57.895 11.85 0.00 44.39 3.32
98 100 0.663269 CGCGACAGTGAGCAGTGTTA 60.663 55.000 11.85 0.00 44.39 2.41
99 101 0.784778 GCGACAGTGAGCAGTGTTAC 59.215 55.000 11.85 4.59 44.39 2.50
100 102 1.603172 GCGACAGTGAGCAGTGTTACT 60.603 52.381 11.85 0.00 44.39 2.24
101 103 2.743938 CGACAGTGAGCAGTGTTACTT 58.256 47.619 11.85 0.00 44.39 2.24
102 104 2.726760 CGACAGTGAGCAGTGTTACTTC 59.273 50.000 11.85 0.00 44.39 3.01
103 105 3.551046 CGACAGTGAGCAGTGTTACTTCT 60.551 47.826 11.85 0.00 44.39 2.85
104 106 4.372656 GACAGTGAGCAGTGTTACTTCTT 58.627 43.478 11.85 0.00 44.39 2.52
105 107 4.770795 ACAGTGAGCAGTGTTACTTCTTT 58.229 39.130 5.16 0.00 41.91 2.52
106 108 5.186198 ACAGTGAGCAGTGTTACTTCTTTT 58.814 37.500 5.16 0.00 41.91 2.27
107 109 5.648092 ACAGTGAGCAGTGTTACTTCTTTTT 59.352 36.000 5.16 0.00 41.91 1.94
108 110 5.967674 CAGTGAGCAGTGTTACTTCTTTTTG 59.032 40.000 0.00 0.00 0.00 2.44
109 111 5.066505 AGTGAGCAGTGTTACTTCTTTTTGG 59.933 40.000 0.00 0.00 0.00 3.28
110 112 4.338118 TGAGCAGTGTTACTTCTTTTTGGG 59.662 41.667 0.00 0.00 0.00 4.12
111 113 3.636764 AGCAGTGTTACTTCTTTTTGGGG 59.363 43.478 0.00 0.00 0.00 4.96
112 114 3.798889 GCAGTGTTACTTCTTTTTGGGGC 60.799 47.826 0.00 0.00 0.00 5.80
113 115 2.963101 AGTGTTACTTCTTTTTGGGGCC 59.037 45.455 0.00 0.00 0.00 5.80
114 116 2.696187 GTGTTACTTCTTTTTGGGGCCA 59.304 45.455 4.39 0.00 0.00 5.36
115 117 3.133183 GTGTTACTTCTTTTTGGGGCCAA 59.867 43.478 4.39 0.00 0.00 4.52
116 118 3.775316 TGTTACTTCTTTTTGGGGCCAAA 59.225 39.130 4.39 0.00 43.23 3.28
117 119 4.124238 GTTACTTCTTTTTGGGGCCAAAC 58.876 43.478 4.39 0.00 44.39 2.93
118 120 2.192263 ACTTCTTTTTGGGGCCAAACA 58.808 42.857 4.39 0.00 44.39 2.83
119 121 2.170397 ACTTCTTTTTGGGGCCAAACAG 59.830 45.455 4.39 7.03 44.39 3.16
120 122 1.872773 TCTTTTTGGGGCCAAACAGT 58.127 45.000 4.39 0.00 44.39 3.55
121 123 1.484240 TCTTTTTGGGGCCAAACAGTG 59.516 47.619 4.39 0.00 44.39 3.66
122 124 1.209261 CTTTTTGGGGCCAAACAGTGT 59.791 47.619 4.39 0.00 44.39 3.55
123 125 1.280457 TTTTGGGGCCAAACAGTGTT 58.720 45.000 4.39 1.64 44.39 3.32
124 126 0.539051 TTTGGGGCCAAACAGTGTTG 59.461 50.000 9.79 4.00 40.51 3.33
125 127 1.965754 TTGGGGCCAAACAGTGTTGC 61.966 55.000 9.79 9.50 32.44 4.17
126 128 2.133641 GGGGCCAAACAGTGTTGCT 61.134 57.895 9.79 0.00 0.00 3.91
127 129 1.685355 GGGGCCAAACAGTGTTGCTT 61.685 55.000 9.79 0.00 0.00 3.91
128 130 0.530431 GGGCCAAACAGTGTTGCTTG 60.530 55.000 9.79 4.19 31.65 4.01
129 131 0.459489 GGCCAAACAGTGTTGCTTGA 59.541 50.000 9.79 0.00 33.25 3.02
130 132 1.069049 GGCCAAACAGTGTTGCTTGAT 59.931 47.619 9.79 0.00 33.25 2.57
131 133 2.295909 GGCCAAACAGTGTTGCTTGATA 59.704 45.455 9.79 0.00 33.25 2.15
132 134 3.308530 GCCAAACAGTGTTGCTTGATAC 58.691 45.455 9.79 0.00 33.25 2.24
133 135 3.554524 CCAAACAGTGTTGCTTGATACG 58.445 45.455 9.79 0.00 33.25 3.06
134 136 2.969443 AACAGTGTTGCTTGATACGC 57.031 45.000 7.96 0.00 0.00 4.42
135 137 2.169832 ACAGTGTTGCTTGATACGCT 57.830 45.000 0.00 0.00 35.62 5.07
136 138 3.313012 ACAGTGTTGCTTGATACGCTA 57.687 42.857 0.00 0.00 33.62 4.26
137 139 3.659786 ACAGTGTTGCTTGATACGCTAA 58.340 40.909 0.00 0.00 33.62 3.09
138 140 3.432252 ACAGTGTTGCTTGATACGCTAAC 59.568 43.478 0.00 0.00 33.62 2.34
139 141 3.679980 CAGTGTTGCTTGATACGCTAACT 59.320 43.478 0.00 0.00 33.62 2.24
140 142 3.679980 AGTGTTGCTTGATACGCTAACTG 59.320 43.478 0.00 0.00 33.62 3.16
141 143 3.432252 GTGTTGCTTGATACGCTAACTGT 59.568 43.478 0.00 0.00 0.00 3.55
142 144 3.678072 TGTTGCTTGATACGCTAACTGTC 59.322 43.478 0.00 0.00 0.00 3.51
143 145 2.526077 TGCTTGATACGCTAACTGTCG 58.474 47.619 0.00 0.00 0.00 4.35
144 146 1.852895 GCTTGATACGCTAACTGTCGG 59.147 52.381 0.00 0.00 0.00 4.79
145 147 2.460918 CTTGATACGCTAACTGTCGGG 58.539 52.381 0.00 0.00 0.00 5.14
146 148 0.101759 TGATACGCTAACTGTCGGGC 59.898 55.000 0.00 0.00 0.00 6.13
147 149 0.596859 GATACGCTAACTGTCGGGCC 60.597 60.000 0.00 0.00 0.00 5.80
148 150 1.324740 ATACGCTAACTGTCGGGCCA 61.325 55.000 4.39 0.00 0.00 5.36
149 151 1.534336 TACGCTAACTGTCGGGCCAA 61.534 55.000 4.39 0.00 0.00 4.52
150 152 1.669760 CGCTAACTGTCGGGCCAAA 60.670 57.895 4.39 0.00 0.00 3.28
151 153 1.024579 CGCTAACTGTCGGGCCAAAT 61.025 55.000 4.39 0.00 0.00 2.32
152 154 0.733150 GCTAACTGTCGGGCCAAATC 59.267 55.000 4.39 0.00 0.00 2.17
153 155 1.948611 GCTAACTGTCGGGCCAAATCA 60.949 52.381 4.39 0.00 0.00 2.57
154 156 2.643551 CTAACTGTCGGGCCAAATCAT 58.356 47.619 4.39 0.00 0.00 2.45
155 157 1.176527 AACTGTCGGGCCAAATCATG 58.823 50.000 4.39 0.00 0.00 3.07
156 158 0.327924 ACTGTCGGGCCAAATCATGA 59.672 50.000 4.39 0.00 0.00 3.07
157 159 1.064463 ACTGTCGGGCCAAATCATGAT 60.064 47.619 4.39 1.18 0.00 2.45
158 160 1.605710 CTGTCGGGCCAAATCATGATC 59.394 52.381 9.06 0.00 0.00 2.92
159 161 0.588252 GTCGGGCCAAATCATGATCG 59.412 55.000 9.06 7.26 0.00 3.69
160 162 0.180171 TCGGGCCAAATCATGATCGT 59.820 50.000 9.06 0.00 0.00 3.73
161 163 1.414550 TCGGGCCAAATCATGATCGTA 59.585 47.619 9.06 0.00 0.00 3.43
162 164 2.038426 TCGGGCCAAATCATGATCGTAT 59.962 45.455 9.06 0.00 0.00 3.06
163 165 2.813754 CGGGCCAAATCATGATCGTATT 59.186 45.455 9.06 0.00 0.00 1.89
164 166 4.000325 CGGGCCAAATCATGATCGTATTA 59.000 43.478 9.06 0.00 0.00 0.98
165 167 4.635765 CGGGCCAAATCATGATCGTATTAT 59.364 41.667 9.06 0.00 0.00 1.28
166 168 5.220662 CGGGCCAAATCATGATCGTATTATC 60.221 44.000 9.06 0.00 0.00 1.75
167 169 5.066505 GGGCCAAATCATGATCGTATTATCC 59.933 44.000 9.06 4.28 0.00 2.59
168 170 5.647658 GGCCAAATCATGATCGTATTATCCA 59.352 40.000 9.06 0.00 0.00 3.41
169 171 6.319658 GGCCAAATCATGATCGTATTATCCAT 59.680 38.462 9.06 0.00 0.00 3.41
170 172 7.191551 GCCAAATCATGATCGTATTATCCATG 58.808 38.462 9.06 0.00 0.00 3.66
171 173 7.191551 CCAAATCATGATCGTATTATCCATGC 58.808 38.462 9.06 0.00 0.00 4.06
172 174 7.148205 CCAAATCATGATCGTATTATCCATGCA 60.148 37.037 9.06 0.00 0.00 3.96
173 175 7.926674 AATCATGATCGTATTATCCATGCAA 57.073 32.000 9.06 0.00 0.00 4.08
174 176 7.926674 ATCATGATCGTATTATCCATGCAAA 57.073 32.000 1.18 0.00 0.00 3.68
175 177 7.132694 TCATGATCGTATTATCCATGCAAAC 57.867 36.000 0.00 0.00 0.00 2.93
176 178 6.936335 TCATGATCGTATTATCCATGCAAACT 59.064 34.615 0.00 0.00 0.00 2.66
177 179 8.093927 TCATGATCGTATTATCCATGCAAACTA 58.906 33.333 0.00 0.00 0.00 2.24
178 180 7.889589 TGATCGTATTATCCATGCAAACTAG 57.110 36.000 0.00 0.00 0.00 2.57
179 181 6.368791 TGATCGTATTATCCATGCAAACTAGC 59.631 38.462 0.00 0.00 0.00 3.42
205 207 9.022915 CACACATGCAATTTATTTATACCAGTG 57.977 33.333 0.00 0.00 0.00 3.66
206 208 8.748412 ACACATGCAATTTATTTATACCAGTGT 58.252 29.630 0.00 0.00 0.00 3.55
207 209 9.236691 CACATGCAATTTATTTATACCAGTGTC 57.763 33.333 0.00 0.00 0.00 3.67
208 210 8.965819 ACATGCAATTTATTTATACCAGTGTCA 58.034 29.630 0.00 0.00 0.00 3.58
209 211 9.454585 CATGCAATTTATTTATACCAGTGTCAG 57.545 33.333 0.00 0.00 0.00 3.51
210 212 8.800370 TGCAATTTATTTATACCAGTGTCAGA 57.200 30.769 0.00 0.00 0.00 3.27
211 213 9.237187 TGCAATTTATTTATACCAGTGTCAGAA 57.763 29.630 0.00 0.00 0.00 3.02
240 242 9.624697 TGACATAGATTTTAATTGTTCAACTGC 57.375 29.630 0.00 0.00 0.00 4.40
241 243 9.624697 GACATAGATTTTAATTGTTCAACTGCA 57.375 29.630 0.00 0.00 0.00 4.41
244 246 7.355332 AGATTTTAATTGTTCAACTGCATGC 57.645 32.000 11.82 11.82 0.00 4.06
245 247 6.930164 AGATTTTAATTGTTCAACTGCATGCA 59.070 30.769 21.29 21.29 0.00 3.96
246 248 7.604927 AGATTTTAATTGTTCAACTGCATGCAT 59.395 29.630 22.97 3.95 0.00 3.96
247 249 7.493743 TTTTAATTGTTCAACTGCATGCATT 57.506 28.000 22.97 13.69 0.00 3.56
248 250 7.493743 TTTAATTGTTCAACTGCATGCATTT 57.506 28.000 22.97 19.56 0.00 2.32
249 251 7.493743 TTAATTGTTCAACTGCATGCATTTT 57.506 28.000 22.97 14.66 0.00 1.82
250 252 5.600908 ATTGTTCAACTGCATGCATTTTC 57.399 34.783 22.97 14.06 0.00 2.29
251 253 4.325028 TGTTCAACTGCATGCATTTTCT 57.675 36.364 22.97 0.00 0.00 2.52
252 254 4.695396 TGTTCAACTGCATGCATTTTCTT 58.305 34.783 22.97 4.94 0.00 2.52
253 255 5.117584 TGTTCAACTGCATGCATTTTCTTT 58.882 33.333 22.97 5.01 0.00 2.52
254 256 5.585445 TGTTCAACTGCATGCATTTTCTTTT 59.415 32.000 22.97 3.23 0.00 2.27
255 257 5.910637 TCAACTGCATGCATTTTCTTTTC 57.089 34.783 22.97 0.00 0.00 2.29
256 258 5.603596 TCAACTGCATGCATTTTCTTTTCT 58.396 33.333 22.97 0.00 0.00 2.52
257 259 6.050432 TCAACTGCATGCATTTTCTTTTCTT 58.950 32.000 22.97 0.00 0.00 2.52
258 260 6.539464 TCAACTGCATGCATTTTCTTTTCTTT 59.461 30.769 22.97 0.00 0.00 2.52
259 261 7.710044 TCAACTGCATGCATTTTCTTTTCTTTA 59.290 29.630 22.97 0.00 0.00 1.85
260 262 8.500773 CAACTGCATGCATTTTCTTTTCTTTAT 58.499 29.630 22.97 0.00 0.00 1.40
261 263 8.248117 ACTGCATGCATTTTCTTTTCTTTATC 57.752 30.769 22.97 0.00 0.00 1.75
262 264 7.874016 ACTGCATGCATTTTCTTTTCTTTATCA 59.126 29.630 22.97 0.00 0.00 2.15
263 265 8.020861 TGCATGCATTTTCTTTTCTTTATCAC 57.979 30.769 18.46 0.00 0.00 3.06
264 266 7.656542 TGCATGCATTTTCTTTTCTTTATCACA 59.343 29.630 18.46 0.00 0.00 3.58
265 267 7.953710 GCATGCATTTTCTTTTCTTTATCACAC 59.046 33.333 14.21 0.00 0.00 3.82
266 268 8.980610 CATGCATTTTCTTTTCTTTATCACACA 58.019 29.630 0.00 0.00 0.00 3.72
267 269 8.939201 TGCATTTTCTTTTCTTTATCACACAA 57.061 26.923 0.00 0.00 0.00 3.33
268 270 9.545105 TGCATTTTCTTTTCTTTATCACACAAT 57.455 25.926 0.00 0.00 0.00 2.71
280 282 9.929722 TCTTTATCACACAATTTACGATATTGC 57.070 29.630 0.00 0.00 36.65 3.56
281 283 9.715123 CTTTATCACACAATTTACGATATTGCA 57.285 29.630 0.00 0.00 36.65 4.08
282 284 9.497030 TTTATCACACAATTTACGATATTGCAC 57.503 29.630 0.00 0.00 36.65 4.57
283 285 6.487689 TCACACAATTTACGATATTGCACA 57.512 33.333 0.00 0.00 36.65 4.57
284 286 7.082700 TCACACAATTTACGATATTGCACAT 57.917 32.000 0.00 0.00 36.65 3.21
285 287 8.202745 TCACACAATTTACGATATTGCACATA 57.797 30.769 0.00 0.00 36.65 2.29
286 288 8.835439 TCACACAATTTACGATATTGCACATAT 58.165 29.630 0.00 0.00 36.65 1.78
287 289 9.449550 CACACAATTTACGATATTGCACATATT 57.550 29.630 0.00 0.00 36.65 1.28
314 316 8.442605 TTTTGCATAGCTATTTCACGTAAAAC 57.557 30.769 2.64 0.00 0.00 2.43
315 317 6.729391 TGCATAGCTATTTCACGTAAAACA 57.271 33.333 2.64 0.00 0.00 2.83
316 318 7.315247 TGCATAGCTATTTCACGTAAAACAT 57.685 32.000 2.64 0.00 0.00 2.71
317 319 8.426881 TGCATAGCTATTTCACGTAAAACATA 57.573 30.769 2.64 0.00 0.00 2.29
318 320 8.884726 TGCATAGCTATTTCACGTAAAACATAA 58.115 29.630 2.64 0.00 0.00 1.90
319 321 9.710979 GCATAGCTATTTCACGTAAAACATAAA 57.289 29.630 2.64 0.00 0.00 1.40
328 330 7.837202 TCACGTAAAACATAAATACCTGAGG 57.163 36.000 0.00 0.00 0.00 3.86
329 331 7.388437 TCACGTAAAACATAAATACCTGAGGT 58.612 34.615 10.00 10.00 40.16 3.85
330 332 7.332430 TCACGTAAAACATAAATACCTGAGGTG 59.668 37.037 15.83 0.00 36.19 4.00
331 333 6.596497 ACGTAAAACATAAATACCTGAGGTGG 59.404 38.462 15.83 0.00 36.19 4.61
332 334 6.819649 CGTAAAACATAAATACCTGAGGTGGA 59.180 38.462 15.83 0.00 36.19 4.02
333 335 7.201582 CGTAAAACATAAATACCTGAGGTGGAC 60.202 40.741 15.83 0.00 36.19 4.02
334 336 4.402056 ACATAAATACCTGAGGTGGACG 57.598 45.455 15.83 0.18 36.19 4.79
335 337 3.773119 ACATAAATACCTGAGGTGGACGT 59.227 43.478 15.83 0.85 36.19 4.34
336 338 2.762535 AAATACCTGAGGTGGACGTG 57.237 50.000 15.83 0.00 36.19 4.49
337 339 1.933021 AATACCTGAGGTGGACGTGA 58.067 50.000 15.83 0.00 36.19 4.35
338 340 1.933021 ATACCTGAGGTGGACGTGAA 58.067 50.000 15.83 0.00 36.19 3.18
339 341 1.254026 TACCTGAGGTGGACGTGAAG 58.746 55.000 15.83 0.00 36.19 3.02
340 342 1.374758 CCTGAGGTGGACGTGAAGC 60.375 63.158 0.00 0.00 0.00 3.86
341 343 1.374758 CTGAGGTGGACGTGAAGCC 60.375 63.158 0.00 0.00 0.00 4.35
342 344 2.099652 CTGAGGTGGACGTGAAGCCA 62.100 60.000 0.00 0.00 0.00 4.75
343 345 1.296715 GAGGTGGACGTGAAGCCAT 59.703 57.895 0.00 0.00 36.41 4.40
344 346 0.741221 GAGGTGGACGTGAAGCCATC 60.741 60.000 0.00 0.00 36.41 3.51
345 347 1.745489 GGTGGACGTGAAGCCATCC 60.745 63.158 0.00 0.00 36.41 3.51
346 348 1.745489 GTGGACGTGAAGCCATCCC 60.745 63.158 0.00 0.00 36.41 3.85
347 349 2.511600 GGACGTGAAGCCATCCCG 60.512 66.667 0.00 0.00 0.00 5.14
348 350 2.264794 GACGTGAAGCCATCCCGT 59.735 61.111 0.00 0.00 0.00 5.28
349 351 1.810030 GACGTGAAGCCATCCCGTC 60.810 63.158 8.82 8.82 40.71 4.79
350 352 2.885644 CGTGAAGCCATCCCGTCG 60.886 66.667 0.00 0.00 0.00 5.12
351 353 2.577059 GTGAAGCCATCCCGTCGA 59.423 61.111 0.00 0.00 0.00 4.20
352 354 1.144057 GTGAAGCCATCCCGTCGAT 59.856 57.895 0.00 0.00 0.00 3.59
353 355 1.143838 TGAAGCCATCCCGTCGATG 59.856 57.895 0.00 0.00 46.95 3.84
361 363 4.705746 CCCGTCGATGGGTTTTCA 57.294 55.556 31.46 0.00 44.76 2.69
362 364 2.466867 CCCGTCGATGGGTTTTCAG 58.533 57.895 31.46 6.98 44.76 3.02
363 365 1.644786 CCCGTCGATGGGTTTTCAGC 61.645 60.000 31.46 0.00 44.76 4.26
364 366 1.644786 CCGTCGATGGGTTTTCAGCC 61.645 60.000 16.43 0.00 41.49 4.85
370 372 3.680786 GGGTTTTCAGCCACCCGC 61.681 66.667 0.00 0.00 43.54 6.13
379 381 3.284449 GCCACCCGCTGTCGTTTT 61.284 61.111 0.00 0.00 0.00 2.43
380 382 2.841160 GCCACCCGCTGTCGTTTTT 61.841 57.895 0.00 0.00 0.00 1.94
381 383 1.281656 CCACCCGCTGTCGTTTTTC 59.718 57.895 0.00 0.00 0.00 2.29
382 384 1.281656 CACCCGCTGTCGTTTTTCC 59.718 57.895 0.00 0.00 0.00 3.13
383 385 1.895231 ACCCGCTGTCGTTTTTCCC 60.895 57.895 0.00 0.00 0.00 3.97
384 386 2.622962 CCCGCTGTCGTTTTTCCCC 61.623 63.158 0.00 0.00 0.00 4.81
385 387 2.622962 CCGCTGTCGTTTTTCCCCC 61.623 63.158 0.00 0.00 0.00 5.40
500 502 1.630878 CCCTACTTGCTCTGAGGGTTT 59.369 52.381 6.83 0.00 43.32 3.27
793 801 0.035036 GGGGATTCTAGCCCTTACGC 59.965 60.000 0.00 0.00 45.30 4.42
881 889 3.117794 GGGGTTTTGTGAAACTTAACGC 58.882 45.455 2.51 0.00 43.68 4.84
903 911 3.411446 TGACGCTTCTTTTGACCATGAT 58.589 40.909 0.00 0.00 0.00 2.45
971 979 0.531657 TTTATCGCGGGAGGAAACGA 59.468 50.000 6.13 0.00 39.11 3.85
997 1005 4.272018 AGATTGACTATTGCGAAGATGTGC 59.728 41.667 0.00 0.00 0.00 4.57
1083 1092 7.972832 TCGCCTTATTATTAATTCGGACAAT 57.027 32.000 0.00 0.00 0.00 2.71
1427 1563 5.123820 TCCTTCGGCATTTCAAACTTAGATG 59.876 40.000 0.00 0.00 0.00 2.90
1428 1564 5.106157 CCTTCGGCATTTCAAACTTAGATGT 60.106 40.000 0.00 0.00 0.00 3.06
1440 1576 9.663904 TTCAAACTTAGATGTGAATCTTTTTCG 57.336 29.630 0.00 0.00 32.36 3.46
1441 1577 7.803189 TCAAACTTAGATGTGAATCTTTTTCGC 59.197 33.333 0.00 0.00 32.36 4.70
1498 1635 7.094118 CCCGGATCTTATTTTCTTGTTTAACCA 60.094 37.037 0.73 0.00 0.00 3.67
1600 1738 6.603201 TCACTTGACTGAAATCCTCAAAAACT 59.397 34.615 0.00 0.00 32.17 2.66
1624 1762 4.514781 AACAAAAAGTTTCTATCGCCCC 57.485 40.909 0.00 0.00 37.03 5.80
1634 1772 2.958818 TCTATCGCCCCTGAACTATGT 58.041 47.619 0.00 0.00 0.00 2.29
1639 1777 2.093869 TCGCCCCTGAACTATGTACAAC 60.094 50.000 0.00 0.00 0.00 3.32
1645 1783 6.338937 CCCCTGAACTATGTACAACTCTTAC 58.661 44.000 0.00 0.00 0.00 2.34
1650 1788 8.997621 TGAACTATGTACAACTCTTACCAATC 57.002 34.615 0.00 0.00 0.00 2.67
1704 1842 5.116882 AGAAAGTGTGTGTACTCAAACCTC 58.883 41.667 13.40 10.81 31.18 3.85
1745 1883 0.547075 TTCGTGGGAGGTGTTTTGGA 59.453 50.000 0.00 0.00 0.00 3.53
1754 1892 0.963856 GGTGTTTTGGATCCCGGGAC 60.964 60.000 29.69 19.63 0.00 4.46
1772 1910 2.381911 GACCAATGCTCCCACATGAAT 58.618 47.619 0.00 0.00 0.00 2.57
1778 1916 5.771666 CCAATGCTCCCACATGAATAGTAAT 59.228 40.000 0.00 0.00 0.00 1.89
1783 1921 5.698545 GCTCCCACATGAATAGTAATCAGAC 59.301 44.000 0.00 0.00 0.00 3.51
1873 2011 3.305094 GCATCCTTGACATTTTTCATGCG 59.695 43.478 0.00 0.00 0.00 4.73
1903 2041 1.202639 ACCAATGCTTCGTCAGTGACA 60.203 47.619 22.66 7.60 34.31 3.58
1934 2072 1.799157 TTTGGGGTGACATCTGGGGG 61.799 60.000 0.00 0.00 0.00 5.40
1938 2076 1.222567 GGGTGACATCTGGGGGTAAT 58.777 55.000 0.00 0.00 0.00 1.89
2041 2179 5.425217 TGGGTGTGACTATGAACACATAGAT 59.575 40.000 19.57 7.70 46.83 1.98
2105 2244 1.369692 CAGGAGCACGTACACCCAA 59.630 57.895 0.00 0.00 0.00 4.12
2111 2250 1.736645 CACGTACACCCAAGAGCCG 60.737 63.158 0.00 0.00 0.00 5.52
2122 2261 2.558359 CCCAAGAGCCGAACTTGATTTT 59.442 45.455 14.36 0.00 44.92 1.82
2123 2262 3.005791 CCCAAGAGCCGAACTTGATTTTT 59.994 43.478 14.36 0.00 44.92 1.94
2132 2271 7.535997 AGCCGAACTTGATTTTTAAATAGGTC 58.464 34.615 0.00 0.00 0.00 3.85
2243 2384 9.422681 ACTAACATCATCTACTATACCAACTGT 57.577 33.333 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.000163 CACGTACACCAAGCTGAGAGT 60.000 52.381 0.00 0.00 0.00 3.24
79 81 0.663269 TAACACTGCTCACTGTCGCG 60.663 55.000 0.00 0.00 0.00 5.87
80 82 0.784778 GTAACACTGCTCACTGTCGC 59.215 55.000 0.00 0.00 0.00 5.19
81 83 2.423926 AGTAACACTGCTCACTGTCG 57.576 50.000 0.00 0.00 0.00 4.35
82 84 3.983741 AGAAGTAACACTGCTCACTGTC 58.016 45.455 0.00 0.00 22.85 3.51
83 85 4.408182 AAGAAGTAACACTGCTCACTGT 57.592 40.909 0.00 0.00 31.28 3.55
84 86 5.741388 AAAAGAAGTAACACTGCTCACTG 57.259 39.130 0.00 0.00 31.28 3.66
85 87 5.066505 CCAAAAAGAAGTAACACTGCTCACT 59.933 40.000 0.00 0.00 31.28 3.41
86 88 5.273944 CCAAAAAGAAGTAACACTGCTCAC 58.726 41.667 0.00 0.00 31.28 3.51
87 89 4.338118 CCCAAAAAGAAGTAACACTGCTCA 59.662 41.667 0.00 0.00 31.28 4.26
88 90 4.261614 CCCCAAAAAGAAGTAACACTGCTC 60.262 45.833 0.00 0.00 31.28 4.26
89 91 3.636764 CCCCAAAAAGAAGTAACACTGCT 59.363 43.478 0.00 0.00 34.95 4.24
90 92 3.798889 GCCCCAAAAAGAAGTAACACTGC 60.799 47.826 0.00 0.00 0.00 4.40
91 93 3.243737 GGCCCCAAAAAGAAGTAACACTG 60.244 47.826 0.00 0.00 0.00 3.66
92 94 2.963101 GGCCCCAAAAAGAAGTAACACT 59.037 45.455 0.00 0.00 0.00 3.55
93 95 2.696187 TGGCCCCAAAAAGAAGTAACAC 59.304 45.455 0.00 0.00 0.00 3.32
94 96 3.033659 TGGCCCCAAAAAGAAGTAACA 57.966 42.857 0.00 0.00 0.00 2.41
95 97 4.124238 GTTTGGCCCCAAAAAGAAGTAAC 58.876 43.478 13.65 0.00 45.86 2.50
96 98 3.775316 TGTTTGGCCCCAAAAAGAAGTAA 59.225 39.130 13.65 0.00 45.86 2.24
97 99 3.375699 TGTTTGGCCCCAAAAAGAAGTA 58.624 40.909 13.65 0.00 45.86 2.24
98 100 2.192263 TGTTTGGCCCCAAAAAGAAGT 58.808 42.857 13.65 0.00 45.86 3.01
99 101 2.998316 TGTTTGGCCCCAAAAAGAAG 57.002 45.000 13.65 0.00 45.86 2.85
103 105 1.280457 ACACTGTTTGGCCCCAAAAA 58.720 45.000 13.65 8.15 45.86 1.94
104 106 1.065854 CAACACTGTTTGGCCCCAAAA 60.066 47.619 13.65 4.73 45.86 2.44
105 107 0.539051 CAACACTGTTTGGCCCCAAA 59.461 50.000 8.35 8.35 42.77 3.28
106 108 1.965754 GCAACACTGTTTGGCCCCAA 61.966 55.000 0.00 0.00 0.00 4.12
107 109 2.430610 GCAACACTGTTTGGCCCCA 61.431 57.895 0.00 0.00 0.00 4.96
108 110 1.685355 AAGCAACACTGTTTGGCCCC 61.685 55.000 0.00 0.00 0.00 5.80
109 111 0.530431 CAAGCAACACTGTTTGGCCC 60.530 55.000 0.00 0.00 39.40 5.80
110 112 0.459489 TCAAGCAACACTGTTTGGCC 59.541 50.000 0.00 0.00 42.33 5.36
111 113 2.514205 ATCAAGCAACACTGTTTGGC 57.486 45.000 0.00 0.00 42.33 4.52
112 114 3.554524 CGTATCAAGCAACACTGTTTGG 58.445 45.455 0.00 0.00 42.33 3.28
113 115 2.973224 GCGTATCAAGCAACACTGTTTG 59.027 45.455 0.00 0.00 43.15 2.93
114 116 2.878406 AGCGTATCAAGCAACACTGTTT 59.122 40.909 0.00 0.00 37.01 2.83
115 117 2.494059 AGCGTATCAAGCAACACTGTT 58.506 42.857 0.00 0.00 37.01 3.16
116 118 2.169832 AGCGTATCAAGCAACACTGT 57.830 45.000 0.00 0.00 37.01 3.55
117 119 3.679980 AGTTAGCGTATCAAGCAACACTG 59.320 43.478 0.00 0.00 37.01 3.66
118 120 3.679980 CAGTTAGCGTATCAAGCAACACT 59.320 43.478 0.00 0.00 37.01 3.55
119 121 3.432252 ACAGTTAGCGTATCAAGCAACAC 59.568 43.478 0.00 0.00 37.01 3.32
120 122 3.659786 ACAGTTAGCGTATCAAGCAACA 58.340 40.909 0.00 0.00 37.01 3.33
121 123 3.241678 CGACAGTTAGCGTATCAAGCAAC 60.242 47.826 0.00 0.00 37.01 4.17
122 124 2.921121 CGACAGTTAGCGTATCAAGCAA 59.079 45.455 0.00 0.00 37.01 3.91
123 125 2.526077 CGACAGTTAGCGTATCAAGCA 58.474 47.619 0.00 0.00 37.01 3.91
124 126 1.852895 CCGACAGTTAGCGTATCAAGC 59.147 52.381 0.00 0.00 0.00 4.01
125 127 2.460918 CCCGACAGTTAGCGTATCAAG 58.539 52.381 0.00 0.00 0.00 3.02
126 128 1.470285 GCCCGACAGTTAGCGTATCAA 60.470 52.381 0.00 0.00 0.00 2.57
127 129 0.101759 GCCCGACAGTTAGCGTATCA 59.898 55.000 0.00 0.00 0.00 2.15
128 130 0.596859 GGCCCGACAGTTAGCGTATC 60.597 60.000 0.00 0.00 0.00 2.24
129 131 1.324740 TGGCCCGACAGTTAGCGTAT 61.325 55.000 0.00 0.00 0.00 3.06
130 132 1.534336 TTGGCCCGACAGTTAGCGTA 61.534 55.000 0.00 0.00 0.00 4.42
131 133 2.386064 TTTGGCCCGACAGTTAGCGT 62.386 55.000 0.00 0.00 0.00 5.07
132 134 1.024579 ATTTGGCCCGACAGTTAGCG 61.025 55.000 0.00 0.00 0.00 4.26
133 135 0.733150 GATTTGGCCCGACAGTTAGC 59.267 55.000 0.00 0.00 0.00 3.09
134 136 2.107950 TGATTTGGCCCGACAGTTAG 57.892 50.000 0.00 0.00 0.00 2.34
135 137 2.026729 TCATGATTTGGCCCGACAGTTA 60.027 45.455 0.00 0.00 0.00 2.24
136 138 1.176527 CATGATTTGGCCCGACAGTT 58.823 50.000 0.00 0.00 0.00 3.16
137 139 0.327924 TCATGATTTGGCCCGACAGT 59.672 50.000 0.00 0.00 0.00 3.55
138 140 1.605710 GATCATGATTTGGCCCGACAG 59.394 52.381 10.14 0.00 0.00 3.51
139 141 1.679139 GATCATGATTTGGCCCGACA 58.321 50.000 10.14 0.00 0.00 4.35
140 142 0.588252 CGATCATGATTTGGCCCGAC 59.412 55.000 10.14 0.00 0.00 4.79
141 143 0.180171 ACGATCATGATTTGGCCCGA 59.820 50.000 10.14 0.00 0.00 5.14
142 144 1.877637 TACGATCATGATTTGGCCCG 58.122 50.000 10.14 9.96 0.00 6.13
143 145 5.066505 GGATAATACGATCATGATTTGGCCC 59.933 44.000 10.14 1.25 0.00 5.80
144 146 5.647658 TGGATAATACGATCATGATTTGGCC 59.352 40.000 10.14 0.00 0.00 5.36
145 147 6.741992 TGGATAATACGATCATGATTTGGC 57.258 37.500 10.14 0.00 0.00 4.52
146 148 7.148205 TGCATGGATAATACGATCATGATTTGG 60.148 37.037 10.14 5.31 0.00 3.28
147 149 7.754625 TGCATGGATAATACGATCATGATTTG 58.245 34.615 10.14 8.40 0.00 2.32
148 150 7.926674 TGCATGGATAATACGATCATGATTT 57.073 32.000 10.14 2.58 0.00 2.17
149 151 7.926674 TTGCATGGATAATACGATCATGATT 57.073 32.000 10.14 0.00 0.00 2.57
150 152 7.609146 AGTTTGCATGGATAATACGATCATGAT 59.391 33.333 8.25 8.25 0.00 2.45
151 153 6.936335 AGTTTGCATGGATAATACGATCATGA 59.064 34.615 0.00 0.00 0.00 3.07
152 154 7.137490 AGTTTGCATGGATAATACGATCATG 57.863 36.000 0.00 0.00 0.00 3.07
153 155 7.065085 GCTAGTTTGCATGGATAATACGATCAT 59.935 37.037 0.00 0.00 0.00 2.45
154 156 6.368791 GCTAGTTTGCATGGATAATACGATCA 59.631 38.462 0.00 0.00 0.00 2.92
155 157 6.368791 TGCTAGTTTGCATGGATAATACGATC 59.631 38.462 0.00 0.00 38.12 3.69
156 158 6.147821 GTGCTAGTTTGCATGGATAATACGAT 59.852 38.462 0.00 0.00 45.23 3.73
157 159 5.465390 GTGCTAGTTTGCATGGATAATACGA 59.535 40.000 0.00 0.00 45.23 3.43
158 160 5.236263 TGTGCTAGTTTGCATGGATAATACG 59.764 40.000 0.00 0.00 45.23 3.06
159 161 6.038161 TGTGTGCTAGTTTGCATGGATAATAC 59.962 38.462 0.00 0.00 45.23 1.89
160 162 6.118852 TGTGTGCTAGTTTGCATGGATAATA 58.881 36.000 0.00 0.00 45.23 0.98
161 163 4.949238 TGTGTGCTAGTTTGCATGGATAAT 59.051 37.500 0.00 0.00 45.23 1.28
162 164 4.331108 TGTGTGCTAGTTTGCATGGATAA 58.669 39.130 0.00 0.00 45.23 1.75
163 165 3.949132 TGTGTGCTAGTTTGCATGGATA 58.051 40.909 0.00 0.00 45.23 2.59
164 166 2.794103 TGTGTGCTAGTTTGCATGGAT 58.206 42.857 0.00 0.00 45.23 3.41
165 167 2.268762 TGTGTGCTAGTTTGCATGGA 57.731 45.000 0.00 0.00 45.23 3.41
166 168 2.871133 CATGTGTGCTAGTTTGCATGG 58.129 47.619 0.00 0.00 45.23 3.66
179 181 9.022915 CACTGGTATAAATAAATTGCATGTGTG 57.977 33.333 0.00 0.00 0.00 3.82
180 182 8.748412 ACACTGGTATAAATAAATTGCATGTGT 58.252 29.630 0.00 0.00 0.00 3.72
181 183 9.236691 GACACTGGTATAAATAAATTGCATGTG 57.763 33.333 0.00 0.00 0.00 3.21
182 184 8.965819 TGACACTGGTATAAATAAATTGCATGT 58.034 29.630 0.00 0.00 0.00 3.21
183 185 9.454585 CTGACACTGGTATAAATAAATTGCATG 57.545 33.333 0.00 0.00 0.00 4.06
184 186 9.407380 TCTGACACTGGTATAAATAAATTGCAT 57.593 29.630 0.00 0.00 0.00 3.96
185 187 8.800370 TCTGACACTGGTATAAATAAATTGCA 57.200 30.769 0.00 0.00 0.00 4.08
214 216 9.624697 GCAGTTGAACAATTAAAATCTATGTCA 57.375 29.630 0.00 0.00 0.00 3.58
215 217 9.624697 TGCAGTTGAACAATTAAAATCTATGTC 57.375 29.630 0.00 0.00 0.00 3.06
218 220 9.090692 GCATGCAGTTGAACAATTAAAATCTAT 57.909 29.630 14.21 0.00 0.00 1.98
219 221 8.087136 TGCATGCAGTTGAACAATTAAAATCTA 58.913 29.630 18.46 0.00 0.00 1.98
220 222 6.930164 TGCATGCAGTTGAACAATTAAAATCT 59.070 30.769 18.46 0.00 0.00 2.40
221 223 7.119605 TGCATGCAGTTGAACAATTAAAATC 57.880 32.000 18.46 0.00 0.00 2.17
222 224 7.675962 ATGCATGCAGTTGAACAATTAAAAT 57.324 28.000 26.69 0.00 0.00 1.82
223 225 7.493743 AATGCATGCAGTTGAACAATTAAAA 57.506 28.000 26.69 0.00 0.00 1.52
224 226 7.493743 AAATGCATGCAGTTGAACAATTAAA 57.506 28.000 30.54 0.00 32.78 1.52
225 227 7.441760 AGAAAATGCATGCAGTTGAACAATTAA 59.558 29.630 31.55 0.14 34.34 1.40
226 228 6.930164 AGAAAATGCATGCAGTTGAACAATTA 59.070 30.769 31.55 0.63 34.34 1.40
227 229 5.761234 AGAAAATGCATGCAGTTGAACAATT 59.239 32.000 31.55 15.68 34.34 2.32
228 230 5.302360 AGAAAATGCATGCAGTTGAACAAT 58.698 33.333 31.55 16.40 34.34 2.71
229 231 4.695396 AGAAAATGCATGCAGTTGAACAA 58.305 34.783 31.55 2.25 34.34 2.83
230 232 4.325028 AGAAAATGCATGCAGTTGAACA 57.675 36.364 31.55 3.06 34.34 3.18
231 233 5.662211 AAAGAAAATGCATGCAGTTGAAC 57.338 34.783 31.55 23.81 34.34 3.18
232 234 6.050432 AGAAAAGAAAATGCATGCAGTTGAA 58.950 32.000 31.55 4.71 34.34 2.69
233 235 5.603596 AGAAAAGAAAATGCATGCAGTTGA 58.396 33.333 31.55 5.54 34.34 3.18
234 236 5.917541 AGAAAAGAAAATGCATGCAGTTG 57.082 34.783 31.55 0.00 34.34 3.16
235 237 6.930667 AAAGAAAAGAAAATGCATGCAGTT 57.069 29.167 26.47 26.47 35.67 3.16
236 238 7.874016 TGATAAAGAAAAGAAAATGCATGCAGT 59.126 29.630 26.69 21.79 0.00 4.40
237 239 8.166706 GTGATAAAGAAAAGAAAATGCATGCAG 58.833 33.333 26.69 0.00 0.00 4.41
238 240 7.656542 TGTGATAAAGAAAAGAAAATGCATGCA 59.343 29.630 25.04 25.04 0.00 3.96
239 241 7.953710 GTGTGATAAAGAAAAGAAAATGCATGC 59.046 33.333 11.82 11.82 0.00 4.06
240 242 8.980610 TGTGTGATAAAGAAAAGAAAATGCATG 58.019 29.630 0.00 0.00 0.00 4.06
241 243 9.545105 TTGTGTGATAAAGAAAAGAAAATGCAT 57.455 25.926 0.00 0.00 0.00 3.96
242 244 8.939201 TTGTGTGATAAAGAAAAGAAAATGCA 57.061 26.923 0.00 0.00 0.00 3.96
254 256 9.929722 GCAATATCGTAAATTGTGTGATAAAGA 57.070 29.630 8.25 0.00 36.82 2.52
255 257 9.715123 TGCAATATCGTAAATTGTGTGATAAAG 57.285 29.630 0.00 0.00 36.82 1.85
256 258 9.497030 GTGCAATATCGTAAATTGTGTGATAAA 57.503 29.630 0.00 0.00 36.82 1.40
257 259 8.669243 TGTGCAATATCGTAAATTGTGTGATAA 58.331 29.630 0.00 0.00 36.82 1.75
258 260 8.202745 TGTGCAATATCGTAAATTGTGTGATA 57.797 30.769 0.00 0.00 36.82 2.15
259 261 7.082700 TGTGCAATATCGTAAATTGTGTGAT 57.917 32.000 0.00 0.00 36.82 3.06
260 262 6.487689 TGTGCAATATCGTAAATTGTGTGA 57.512 33.333 0.00 0.00 36.82 3.58
261 263 9.449550 AATATGTGCAATATCGTAAATTGTGTG 57.550 29.630 0.00 0.00 36.82 3.82
288 290 9.072294 GTTTTACGTGAAATAGCTATGCAAAAT 57.928 29.630 7.09 1.52 0.00 1.82
289 291 8.076781 TGTTTTACGTGAAATAGCTATGCAAAA 58.923 29.630 7.09 1.49 0.00 2.44
290 292 7.585867 TGTTTTACGTGAAATAGCTATGCAAA 58.414 30.769 7.09 0.00 0.00 3.68
291 293 7.135089 TGTTTTACGTGAAATAGCTATGCAA 57.865 32.000 7.09 0.00 0.00 4.08
292 294 6.729391 TGTTTTACGTGAAATAGCTATGCA 57.271 33.333 7.09 6.23 0.00 3.96
293 295 9.710979 TTTATGTTTTACGTGAAATAGCTATGC 57.289 29.630 7.09 3.48 0.00 3.14
302 304 8.723311 CCTCAGGTATTTATGTTTTACGTGAAA 58.277 33.333 0.73 0.73 39.10 2.69
303 305 7.879160 ACCTCAGGTATTTATGTTTTACGTGAA 59.121 33.333 0.00 0.00 39.10 3.18
304 306 7.332430 CACCTCAGGTATTTATGTTTTACGTGA 59.668 37.037 0.00 0.00 38.00 4.35
305 307 7.413657 CCACCTCAGGTATTTATGTTTTACGTG 60.414 40.741 0.00 0.00 32.11 4.49
306 308 6.596497 CCACCTCAGGTATTTATGTTTTACGT 59.404 38.462 0.00 0.00 32.11 3.57
307 309 6.819649 TCCACCTCAGGTATTTATGTTTTACG 59.180 38.462 0.00 0.00 32.11 3.18
308 310 7.201582 CGTCCACCTCAGGTATTTATGTTTTAC 60.202 40.741 0.00 0.00 32.11 2.01
309 311 6.819649 CGTCCACCTCAGGTATTTATGTTTTA 59.180 38.462 0.00 0.00 32.11 1.52
310 312 5.646360 CGTCCACCTCAGGTATTTATGTTTT 59.354 40.000 0.00 0.00 32.11 2.43
311 313 5.183228 CGTCCACCTCAGGTATTTATGTTT 58.817 41.667 0.00 0.00 32.11 2.83
312 314 4.224370 ACGTCCACCTCAGGTATTTATGTT 59.776 41.667 0.00 0.00 32.11 2.71
313 315 3.773119 ACGTCCACCTCAGGTATTTATGT 59.227 43.478 0.00 0.00 32.11 2.29
314 316 4.119862 CACGTCCACCTCAGGTATTTATG 58.880 47.826 0.00 0.00 32.11 1.90
315 317 4.028131 TCACGTCCACCTCAGGTATTTAT 58.972 43.478 0.00 0.00 32.11 1.40
316 318 3.433343 TCACGTCCACCTCAGGTATTTA 58.567 45.455 0.00 0.00 32.11 1.40
317 319 2.253610 TCACGTCCACCTCAGGTATTT 58.746 47.619 0.00 0.00 32.11 1.40
318 320 1.933021 TCACGTCCACCTCAGGTATT 58.067 50.000 0.00 0.00 32.11 1.89
319 321 1.825474 CTTCACGTCCACCTCAGGTAT 59.175 52.381 0.00 0.00 32.11 2.73
320 322 1.254026 CTTCACGTCCACCTCAGGTA 58.746 55.000 0.00 0.00 32.11 3.08
321 323 2.050269 CTTCACGTCCACCTCAGGT 58.950 57.895 0.00 0.00 35.62 4.00
322 324 1.374758 GCTTCACGTCCACCTCAGG 60.375 63.158 0.00 0.00 0.00 3.86
323 325 1.374758 GGCTTCACGTCCACCTCAG 60.375 63.158 0.00 0.00 0.00 3.35
324 326 1.480212 ATGGCTTCACGTCCACCTCA 61.480 55.000 0.00 0.00 34.81 3.86
325 327 0.741221 GATGGCTTCACGTCCACCTC 60.741 60.000 0.00 0.00 34.81 3.85
326 328 1.296715 GATGGCTTCACGTCCACCT 59.703 57.895 0.00 0.00 34.81 4.00
327 329 1.745489 GGATGGCTTCACGTCCACC 60.745 63.158 2.60 0.00 44.33 4.61
328 330 1.745489 GGGATGGCTTCACGTCCAC 60.745 63.158 6.76 0.00 46.28 4.02
329 331 2.668632 GGGATGGCTTCACGTCCA 59.331 61.111 6.76 0.00 46.28 4.02
330 332 2.511600 CGGGATGGCTTCACGTCC 60.512 66.667 16.08 0.67 46.41 4.79
334 336 1.144057 ATCGACGGGATGGCTTCAC 59.856 57.895 2.60 0.00 32.92 3.18
335 337 3.628989 ATCGACGGGATGGCTTCA 58.371 55.556 2.60 0.00 32.92 3.02
345 347 1.644786 GGCTGAAAACCCATCGACGG 61.645 60.000 0.00 0.00 0.00 4.79
346 348 0.953471 TGGCTGAAAACCCATCGACG 60.953 55.000 0.00 0.00 0.00 5.12
347 349 0.521735 GTGGCTGAAAACCCATCGAC 59.478 55.000 0.00 0.00 32.95 4.20
348 350 0.608035 GGTGGCTGAAAACCCATCGA 60.608 55.000 0.00 0.00 32.95 3.59
349 351 1.883021 GGTGGCTGAAAACCCATCG 59.117 57.895 0.00 0.00 32.95 3.84
362 364 2.726850 GAAAAACGACAGCGGGTGGC 62.727 60.000 12.33 7.67 43.17 5.01
363 365 1.281656 GAAAAACGACAGCGGGTGG 59.718 57.895 12.33 0.00 43.17 4.61
364 366 1.281656 GGAAAAACGACAGCGGGTG 59.718 57.895 5.50 5.50 43.17 4.61
365 367 1.895231 GGGAAAAACGACAGCGGGT 60.895 57.895 0.00 0.00 43.17 5.28
366 368 2.622962 GGGGAAAAACGACAGCGGG 61.623 63.158 0.00 0.00 43.17 6.13
367 369 2.622962 GGGGGAAAAACGACAGCGG 61.623 63.158 0.00 0.00 43.17 5.52
368 370 2.951458 GGGGGAAAAACGACAGCG 59.049 61.111 0.00 0.00 44.79 5.18
382 384 7.936301 CCATATAAAAATTACAACCAATGGGGG 59.064 37.037 3.55 0.00 42.91 5.40
383 385 7.443879 GCCATATAAAAATTACAACCAATGGGG 59.556 37.037 3.55 0.00 44.81 4.96
384 386 7.170658 CGCCATATAAAAATTACAACCAATGGG 59.829 37.037 3.55 0.00 41.29 4.00
385 387 7.708752 ACGCCATATAAAAATTACAACCAATGG 59.291 33.333 0.00 0.00 34.58 3.16
386 388 8.641499 ACGCCATATAAAAATTACAACCAATG 57.359 30.769 0.00 0.00 0.00 2.82
387 389 9.738832 GTACGCCATATAAAAATTACAACCAAT 57.261 29.630 0.00 0.00 0.00 3.16
388 390 8.737175 TGTACGCCATATAAAAATTACAACCAA 58.263 29.630 0.00 0.00 0.00 3.67
389 391 8.277490 TGTACGCCATATAAAAATTACAACCA 57.723 30.769 0.00 0.00 0.00 3.67
390 392 9.738832 AATGTACGCCATATAAAAATTACAACC 57.261 29.630 0.00 0.00 31.97 3.77
793 801 5.036737 GGATGATGCATTTACGAAGTTTGG 58.963 41.667 0.00 0.00 37.78 3.28
850 858 0.981943 ACAAAACCCCTAGGAGGACG 59.018 55.000 19.81 9.23 37.67 4.79
881 889 2.807967 TCATGGTCAAAAGAAGCGTCAG 59.192 45.455 1.61 0.00 0.00 3.51
903 911 1.410004 CCATCGTGCCCCTAAGTAGA 58.590 55.000 0.00 0.00 0.00 2.59
928 936 8.712228 AACCTACCTTTTTCATCTCTCAAAAT 57.288 30.769 0.00 0.00 0.00 1.82
971 979 6.257411 CACATCTTCGCAATAGTCAATCTTCT 59.743 38.462 0.00 0.00 0.00 2.85
1083 1092 4.297768 TCATGGTATCAATCACCTCCAGA 58.702 43.478 0.00 0.00 36.96 3.86
1142 1151 6.742718 AGCATAATGAAAACAATCGTCGAAAG 59.257 34.615 0.00 0.00 0.00 2.62
1448 1585 5.285651 CCCGTTGCTTGAATTTTGTTCTTA 58.714 37.500 0.00 0.00 0.00 2.10
1450 1587 3.716601 CCCGTTGCTTGAATTTTGTTCT 58.283 40.909 0.00 0.00 0.00 3.01
1451 1588 2.220824 GCCCGTTGCTTGAATTTTGTTC 59.779 45.455 0.00 0.00 36.87 3.18
1454 1591 1.147473 GGCCCGTTGCTTGAATTTTG 58.853 50.000 0.00 0.00 40.92 2.44
1466 1603 0.549469 AAATAAGATCCGGGCCCGTT 59.451 50.000 40.52 29.81 37.81 4.44
1467 1604 0.549469 AAAATAAGATCCGGGCCCGT 59.451 50.000 40.52 25.84 37.81 5.28
1498 1635 2.099098 GCACTGGCAAGTAAACAGTTGT 59.901 45.455 0.00 0.00 42.38 3.32
1624 1762 9.088512 GATTGGTAAGAGTTGTACATAGTTCAG 57.911 37.037 0.00 0.00 0.00 3.02
1634 1772 4.595781 AGGGTGTGATTGGTAAGAGTTGTA 59.404 41.667 0.00 0.00 0.00 2.41
1639 1777 3.775316 ACCTAGGGTGTGATTGGTAAGAG 59.225 47.826 14.81 0.00 32.98 2.85
1645 1783 1.285280 TGGACCTAGGGTGTGATTGG 58.715 55.000 14.81 0.00 35.25 3.16
1650 1788 5.888982 ACTATTTATGGACCTAGGGTGTG 57.111 43.478 14.81 0.00 35.25 3.82
1729 1867 1.545841 GGATCCAAAACACCTCCCAC 58.454 55.000 6.95 0.00 0.00 4.61
1730 1868 0.407918 GGGATCCAAAACACCTCCCA 59.592 55.000 15.23 0.00 44.23 4.37
1745 1883 2.757124 GGAGCATTGGTCCCGGGAT 61.757 63.158 29.73 8.72 43.62 3.85
1754 1892 3.559069 ACTATTCATGTGGGAGCATTGG 58.441 45.455 0.00 0.00 0.00 3.16
1819 1957 2.731217 ACACGAACATCTGCAAAAAGC 58.269 42.857 0.00 0.00 45.96 3.51
1821 1959 5.163703 ACACTAACACGAACATCTGCAAAAA 60.164 36.000 0.00 0.00 0.00 1.94
1873 2011 3.751698 ACGAAGCATTGGTACTCCTTTTC 59.248 43.478 0.00 0.00 34.40 2.29
1882 2020 2.036604 TGTCACTGACGAAGCATTGGTA 59.963 45.455 4.71 0.00 37.08 3.25
1928 2066 3.009695 TGAACACCAACTATTACCCCCAG 59.990 47.826 0.00 0.00 0.00 4.45
1938 2076 8.608844 AAACAAAACAAATTGAACACCAACTA 57.391 26.923 0.00 0.00 37.63 2.24
2015 2153 4.157849 TGTGTTCATAGTCACACCCAAA 57.842 40.909 0.20 0.00 42.33 3.28
2095 2234 1.012486 GTTCGGCTCTTGGGTGTACG 61.012 60.000 0.00 0.00 0.00 3.67
2098 2237 0.535102 CAAGTTCGGCTCTTGGGTGT 60.535 55.000 0.00 0.00 38.70 4.16
2105 2244 7.393515 ACCTATTTAAAAATCAAGTTCGGCTCT 59.606 33.333 0.00 0.00 0.00 4.09
2111 2250 8.467598 GGGAGGACCTATTTAAAAATCAAGTTC 58.532 37.037 0.00 0.00 35.85 3.01
2315 2456 5.782047 TCATGTTTGCTCAAATTTACAGGG 58.218 37.500 0.00 0.00 32.36 4.45


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

AutoCloner maintained by Alex Coulton.