Multiple sequence alignment - TraesCS3D01G390000

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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 TraesCS3D01G390000 chr3D 100.000 3377 0 0 1 3377 505067413 505064037 0.000000e+00 6237.0
1 TraesCS3D01G390000 chr3B 94.348 2141 86 18 473 2604 666792419 666790305 0.000000e+00 3251.0
2 TraesCS3D01G390000 chr3B 91.049 715 54 5 2647 3357 666790310 666789602 0.000000e+00 957.0
3 TraesCS3D01G390000 chr3B 91.257 183 10 3 307 489 666792614 666792438 9.360000e-61 244.0
4 TraesCS3D01G390000 chr3A 93.889 2111 75 15 780 2884 643210997 643208935 0.000000e+00 3134.0
5 TraesCS3D01G390000 chr3A 88.110 328 20 7 465 778 643212484 643212162 4.120000e-99 372.0
6 TraesCS3D01G390000 chr3A 91.848 184 8 4 307 489 643212666 643212489 2.010000e-62 250.0
7 TraesCS3D01G390000 chr3A 93.243 148 10 0 3211 3358 643208922 643208775 5.670000e-53 219.0
8 TraesCS3D01G390000 chr6D 85.612 841 83 21 1135 1956 431470629 431469808 0.000000e+00 848.0
9 TraesCS3D01G390000 chr6D 92.674 273 19 1 1 273 336516013 336516284 3.160000e-105 392.0
10 TraesCS3D01G390000 chr6B 85.560 831 85 21 1136 1950 651423116 651423927 0.000000e+00 837.0
11 TraesCS3D01G390000 chrUn 84.845 838 95 21 1135 1956 74559370 74558549 0.000000e+00 815.0
12 TraesCS3D01G390000 chr2A 80.769 858 143 21 1110 1956 579583340 579584186 0.000000e+00 651.0
13 TraesCS3D01G390000 chr2A 90.876 274 23 2 1 273 624373607 624373335 1.910000e-97 366.0
14 TraesCS3D01G390000 chr2B 80.090 889 152 23 1124 2002 485751273 485750400 3.670000e-179 638.0
15 TraesCS3D01G390000 chr2B 91.209 273 23 1 1 273 152752291 152752020 1.480000e-98 370.0
16 TraesCS3D01G390000 chr2D 79.820 887 153 25 1110 1983 412254627 412255500 1.030000e-174 623.0
17 TraesCS3D01G390000 chr2D 85.714 56 6 2 2564 2619 414972650 414972703 1.310000e-04 58.4
18 TraesCS3D01G390000 chr5D 93.258 267 18 0 7 273 377148155 377147889 8.780000e-106 394.0
19 TraesCS3D01G390000 chr5D 91.481 270 22 1 5 273 63265219 63264950 1.480000e-98 370.0
20 TraesCS3D01G390000 chr5D 87.755 49 6 0 2573 2621 164605999 164605951 1.310000e-04 58.4
21 TraesCS3D01G390000 chr7A 91.209 273 24 0 1 273 260000721 260000993 4.120000e-99 372.0
22 TraesCS3D01G390000 chr5A 91.209 273 24 0 1 273 464507070 464506798 4.120000e-99 372.0
23 TraesCS3D01G390000 chr1D 90.876 274 25 0 1 274 485572737 485572464 5.320000e-98 368.0
24 TraesCS3D01G390000 chr1D 90.476 273 25 1 1 273 430327505 430327776 3.200000e-95 359.0
25 TraesCS3D01G390000 chr4A 87.719 57 7 0 2565 2621 43367093 43367149 2.170000e-07 67.6
26 TraesCS3D01G390000 chr1A 90.385 52 4 1 2573 2624 508556828 508556778 2.170000e-07 67.6
27 TraesCS3D01G390000 chr1A 91.111 45 4 0 2574 2618 33218856 33218812 1.010000e-05 62.1
28 TraesCS3D01G390000 chr1A 85.965 57 7 1 2563 2619 83823601 83823656 3.640000e-05 60.2
29 TraesCS3D01G390000 chr1B 89.583 48 5 0 2571 2618 5875431 5875384 1.010000e-05 62.1


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 TraesCS3D01G390000 chr3D 505064037 505067413 3376 True 6237.00 6237 100.0000 1 3377 1 chr3D.!!$R1 3376
1 TraesCS3D01G390000 chr3B 666789602 666792614 3012 True 1484.00 3251 92.2180 307 3357 3 chr3B.!!$R1 3050
2 TraesCS3D01G390000 chr3A 643208775 643212666 3891 True 993.75 3134 91.7725 307 3358 4 chr3A.!!$R1 3051
3 TraesCS3D01G390000 chr6D 431469808 431470629 821 True 848.00 848 85.6120 1135 1956 1 chr6D.!!$R1 821
4 TraesCS3D01G390000 chr6B 651423116 651423927 811 False 837.00 837 85.5600 1136 1950 1 chr6B.!!$F1 814
5 TraesCS3D01G390000 chrUn 74558549 74559370 821 True 815.00 815 84.8450 1135 1956 1 chrUn.!!$R1 821
6 TraesCS3D01G390000 chr2A 579583340 579584186 846 False 651.00 651 80.7690 1110 1956 1 chr2A.!!$F1 846
7 TraesCS3D01G390000 chr2B 485750400 485751273 873 True 638.00 638 80.0900 1124 2002 1 chr2B.!!$R2 878
8 TraesCS3D01G390000 chr2D 412254627 412255500 873 False 623.00 623 79.8200 1110 1983 1 chr2D.!!$F1 873

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
78 79 0.039618 AGTATGTGGCTTGGTTGGGG 59.960 55.0 0.00 0.00 0.00 4.96 F
122 123 0.179032 TGGTGCGATGTCTGTTTGGT 60.179 50.0 0.00 0.00 0.00 3.67 F
154 155 0.320374 GTGTCGACACCCCTTCATCA 59.680 55.0 33.62 0.00 40.85 3.07 F
265 266 0.538118 AATGGTTGCATGCATCACCC 59.462 50.0 29.94 22.62 0.00 4.61 F
266 267 0.615261 ATGGTTGCATGCATCACCCA 60.615 50.0 29.94 26.30 0.00 4.51 F
268 269 0.966875 GGTTGCATGCATCACCCAGA 60.967 55.0 25.17 5.37 0.00 3.86 F
2278 3545 0.944311 GACGCCGATGCATTCCGTAT 60.944 55.0 16.54 0.00 37.32 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1026 2239 0.108424 CCGACTCTGCAGAAAGAGGG 60.108 60.000 18.85 10.76 46.73 4.30 R
1975 3242 2.462782 CCTCCTCGTCGTCCTCGTC 61.463 68.421 0.00 0.00 38.33 4.20 R
2152 3419 1.102154 CTCTCCTCTGTGATCGCAGT 58.898 55.000 30.17 0.00 37.70 4.40 R
2157 3424 0.753479 TCCGGCTCTCCTCTGTGATC 60.753 60.000 0.00 0.00 0.00 2.92 R
2208 3475 4.289101 ACACCCTGCATGCAGCCA 62.289 61.111 37.11 8.80 44.83 4.75 R
2318 3585 1.209019 GGCAGCTCCCGATGATATCAT 59.791 52.381 18.21 18.21 39.70 2.45 R
3296 4570 0.472471 TCCGGCTGTTTTGAAGGTCT 59.528 50.000 0.00 0.00 0.00 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
27 28 3.490759 GCGGCCACGACACATGAG 61.491 66.667 2.24 0.00 44.60 2.90
28 29 2.261361 CGGCCACGACACATGAGA 59.739 61.111 2.24 0.00 44.60 3.27
29 30 1.807165 CGGCCACGACACATGAGAG 60.807 63.158 2.24 0.00 44.60 3.20
30 31 1.293498 GGCCACGACACATGAGAGT 59.707 57.895 0.00 0.00 0.00 3.24
31 32 1.016130 GGCCACGACACATGAGAGTG 61.016 60.000 0.00 8.02 44.93 3.51
39 40 1.702886 CACATGAGAGTGTGTCGGAC 58.297 55.000 0.00 0.00 43.43 4.79
40 41 0.603569 ACATGAGAGTGTGTCGGACC 59.396 55.000 5.55 0.00 0.00 4.46
41 42 0.603065 CATGAGAGTGTGTCGGACCA 59.397 55.000 5.55 0.45 0.00 4.02
42 43 1.000843 CATGAGAGTGTGTCGGACCAA 59.999 52.381 5.55 0.00 0.00 3.67
43 44 1.338107 TGAGAGTGTGTCGGACCAAT 58.662 50.000 5.55 2.60 0.00 3.16
44 45 1.691976 TGAGAGTGTGTCGGACCAATT 59.308 47.619 5.55 0.00 0.00 2.32
45 46 2.104111 TGAGAGTGTGTCGGACCAATTT 59.896 45.455 5.55 0.00 0.00 1.82
46 47 2.480419 GAGAGTGTGTCGGACCAATTTG 59.520 50.000 5.55 0.00 0.00 2.32
47 48 2.158813 AGAGTGTGTCGGACCAATTTGT 60.159 45.455 5.55 0.00 0.00 2.83
48 49 3.070446 AGAGTGTGTCGGACCAATTTGTA 59.930 43.478 5.55 0.00 0.00 2.41
49 50 3.135994 AGTGTGTCGGACCAATTTGTAC 58.864 45.455 5.55 0.00 0.00 2.90
50 51 2.224784 GTGTGTCGGACCAATTTGTACC 59.775 50.000 5.55 0.00 0.00 3.34
51 52 1.808343 GTGTCGGACCAATTTGTACCC 59.192 52.381 5.55 0.00 0.00 3.69
52 53 1.271488 TGTCGGACCAATTTGTACCCC 60.271 52.381 5.55 0.00 0.00 4.95
53 54 1.065647 TCGGACCAATTTGTACCCCA 58.934 50.000 0.00 0.00 0.00 4.96
54 55 1.424302 TCGGACCAATTTGTACCCCAA 59.576 47.619 0.00 0.00 0.00 4.12
55 56 2.158505 TCGGACCAATTTGTACCCCAAA 60.159 45.455 0.00 0.00 46.59 3.28
65 66 4.938575 TTGTACCCCAAATCCAGTATGT 57.061 40.909 0.00 0.00 0.00 2.29
66 67 4.229304 TGTACCCCAAATCCAGTATGTG 57.771 45.455 0.00 0.00 0.00 3.21
67 68 6.042228 TTTGTACCCCAAATCCAGTATGTGG 61.042 44.000 0.00 0.00 42.16 4.17
76 77 1.176527 CCAGTATGTGGCTTGGTTGG 58.823 55.000 0.00 0.00 40.39 3.77
77 78 1.176527 CAGTATGTGGCTTGGTTGGG 58.823 55.000 0.00 0.00 0.00 4.12
78 79 0.039618 AGTATGTGGCTTGGTTGGGG 59.960 55.000 0.00 0.00 0.00 4.96
79 80 1.304879 TATGTGGCTTGGTTGGGGC 60.305 57.895 0.00 0.00 0.00 5.80
80 81 2.796734 TATGTGGCTTGGTTGGGGCC 62.797 60.000 0.00 0.00 45.45 5.80
81 82 4.621087 GTGGCTTGGTTGGGGCCT 62.621 66.667 0.84 0.00 45.45 5.19
82 83 4.299796 TGGCTTGGTTGGGGCCTC 62.300 66.667 0.84 0.00 45.45 4.70
85 86 4.740822 CTTGGTTGGGGCCTCCGG 62.741 72.222 0.00 0.00 38.76 5.14
98 99 3.692791 GCCTCCGGCTTTAAATGTTAG 57.307 47.619 0.00 0.00 46.69 2.34
99 100 2.357952 GCCTCCGGCTTTAAATGTTAGG 59.642 50.000 0.00 0.00 46.69 2.69
100 101 2.357952 CCTCCGGCTTTAAATGTTAGGC 59.642 50.000 0.00 0.00 0.00 3.93
101 102 3.279434 CTCCGGCTTTAAATGTTAGGCT 58.721 45.455 0.00 0.00 32.77 4.58
102 103 3.692690 TCCGGCTTTAAATGTTAGGCTT 58.307 40.909 0.00 0.00 32.77 4.35
103 104 4.083565 TCCGGCTTTAAATGTTAGGCTTT 58.916 39.130 0.00 0.00 32.77 3.51
104 105 4.082463 TCCGGCTTTAAATGTTAGGCTTTG 60.082 41.667 0.00 0.00 32.77 2.77
105 106 4.173256 CGGCTTTAAATGTTAGGCTTTGG 58.827 43.478 0.00 0.00 32.77 3.28
106 107 4.321675 CGGCTTTAAATGTTAGGCTTTGGT 60.322 41.667 0.00 0.00 32.77 3.67
107 108 4.929211 GGCTTTAAATGTTAGGCTTTGGTG 59.071 41.667 0.00 0.00 0.00 4.17
108 109 4.388773 GCTTTAAATGTTAGGCTTTGGTGC 59.611 41.667 0.00 0.00 0.00 5.01
109 110 2.723124 AAATGTTAGGCTTTGGTGCG 57.277 45.000 0.00 0.00 0.00 5.34
110 111 1.904287 AATGTTAGGCTTTGGTGCGA 58.096 45.000 0.00 0.00 0.00 5.10
111 112 2.128771 ATGTTAGGCTTTGGTGCGAT 57.871 45.000 0.00 0.00 0.00 4.58
112 113 1.164411 TGTTAGGCTTTGGTGCGATG 58.836 50.000 0.00 0.00 0.00 3.84
113 114 1.165270 GTTAGGCTTTGGTGCGATGT 58.835 50.000 0.00 0.00 0.00 3.06
114 115 1.130561 GTTAGGCTTTGGTGCGATGTC 59.869 52.381 0.00 0.00 0.00 3.06
115 116 0.613260 TAGGCTTTGGTGCGATGTCT 59.387 50.000 0.00 0.00 0.00 3.41
116 117 0.957395 AGGCTTTGGTGCGATGTCTG 60.957 55.000 0.00 0.00 0.00 3.51
117 118 1.237285 GGCTTTGGTGCGATGTCTGT 61.237 55.000 0.00 0.00 0.00 3.41
118 119 0.593128 GCTTTGGTGCGATGTCTGTT 59.407 50.000 0.00 0.00 0.00 3.16
119 120 1.001378 GCTTTGGTGCGATGTCTGTTT 60.001 47.619 0.00 0.00 0.00 2.83
120 121 2.653890 CTTTGGTGCGATGTCTGTTTG 58.346 47.619 0.00 0.00 0.00 2.93
121 122 0.950836 TTGGTGCGATGTCTGTTTGG 59.049 50.000 0.00 0.00 0.00 3.28
122 123 0.179032 TGGTGCGATGTCTGTTTGGT 60.179 50.000 0.00 0.00 0.00 3.67
123 124 1.070914 TGGTGCGATGTCTGTTTGGTA 59.929 47.619 0.00 0.00 0.00 3.25
124 125 2.290008 TGGTGCGATGTCTGTTTGGTAT 60.290 45.455 0.00 0.00 0.00 2.73
125 126 2.747446 GGTGCGATGTCTGTTTGGTATT 59.253 45.455 0.00 0.00 0.00 1.89
126 127 3.936453 GGTGCGATGTCTGTTTGGTATTA 59.064 43.478 0.00 0.00 0.00 0.98
127 128 4.034048 GGTGCGATGTCTGTTTGGTATTAG 59.966 45.833 0.00 0.00 0.00 1.73
128 129 4.034048 GTGCGATGTCTGTTTGGTATTAGG 59.966 45.833 0.00 0.00 0.00 2.69
129 130 3.002348 GCGATGTCTGTTTGGTATTAGGC 59.998 47.826 0.00 0.00 0.00 3.93
130 131 4.442706 CGATGTCTGTTTGGTATTAGGCT 58.557 43.478 0.00 0.00 0.00 4.58
131 132 4.508124 CGATGTCTGTTTGGTATTAGGCTC 59.492 45.833 0.00 0.00 0.00 4.70
132 133 3.857052 TGTCTGTTTGGTATTAGGCTCG 58.143 45.455 0.00 0.00 0.00 5.03
133 134 3.195661 GTCTGTTTGGTATTAGGCTCGG 58.804 50.000 0.00 0.00 0.00 4.63
134 135 3.101437 TCTGTTTGGTATTAGGCTCGGA 58.899 45.455 0.00 0.00 0.00 4.55
135 136 3.132289 TCTGTTTGGTATTAGGCTCGGAG 59.868 47.826 0.00 0.00 0.00 4.63
136 137 2.835764 TGTTTGGTATTAGGCTCGGAGT 59.164 45.455 6.90 0.00 0.00 3.85
137 138 3.195661 GTTTGGTATTAGGCTCGGAGTG 58.804 50.000 6.90 0.00 0.00 3.51
138 139 2.154567 TGGTATTAGGCTCGGAGTGT 57.845 50.000 6.90 0.00 0.00 3.55
139 140 2.029623 TGGTATTAGGCTCGGAGTGTC 58.970 52.381 6.90 0.00 0.00 3.67
140 141 1.001597 GGTATTAGGCTCGGAGTGTCG 60.002 57.143 6.90 0.00 0.00 4.35
141 142 1.945394 GTATTAGGCTCGGAGTGTCGA 59.055 52.381 6.90 0.00 37.60 4.20
142 143 0.739561 ATTAGGCTCGGAGTGTCGAC 59.260 55.000 9.11 9.11 35.18 4.20
143 144 0.607217 TTAGGCTCGGAGTGTCGACA 60.607 55.000 15.76 15.76 35.18 4.35
144 145 1.303799 TAGGCTCGGAGTGTCGACAC 61.304 60.000 35.83 35.83 46.77 3.67
153 154 3.139029 GTGTCGACACCCCTTCATC 57.861 57.895 33.62 9.24 40.85 2.92
154 155 0.320374 GTGTCGACACCCCTTCATCA 59.680 55.000 33.62 0.00 40.85 3.07
155 156 1.052617 TGTCGACACCCCTTCATCAA 58.947 50.000 15.76 0.00 0.00 2.57
156 157 1.001974 TGTCGACACCCCTTCATCAAG 59.998 52.381 15.76 0.00 0.00 3.02
157 158 1.002087 GTCGACACCCCTTCATCAAGT 59.998 52.381 11.55 0.00 0.00 3.16
158 159 1.001974 TCGACACCCCTTCATCAAGTG 59.998 52.381 0.00 0.00 34.61 3.16
159 160 1.826385 GACACCCCTTCATCAAGTGG 58.174 55.000 0.00 0.00 33.46 4.00
160 161 1.351017 GACACCCCTTCATCAAGTGGA 59.649 52.381 0.00 0.00 31.72 4.02
161 162 1.995542 ACACCCCTTCATCAAGTGGAT 59.004 47.619 0.00 0.00 31.72 3.41
162 163 3.189606 ACACCCCTTCATCAAGTGGATA 58.810 45.455 0.00 0.00 31.72 2.59
163 164 3.200825 ACACCCCTTCATCAAGTGGATAG 59.799 47.826 0.00 0.00 31.72 2.08
164 165 3.455910 CACCCCTTCATCAAGTGGATAGA 59.544 47.826 0.00 0.00 31.72 1.98
165 166 4.080356 CACCCCTTCATCAAGTGGATAGAA 60.080 45.833 0.00 0.00 31.72 2.10
166 167 4.164988 ACCCCTTCATCAAGTGGATAGAAG 59.835 45.833 10.48 10.48 38.94 2.85
167 168 4.164988 CCCCTTCATCAAGTGGATAGAAGT 59.835 45.833 13.90 0.00 38.31 3.01
168 169 5.366768 CCCCTTCATCAAGTGGATAGAAGTA 59.633 44.000 13.90 0.00 38.31 2.24
169 170 6.463614 CCCCTTCATCAAGTGGATAGAAGTAG 60.464 46.154 13.90 8.25 38.31 2.57
170 171 5.988561 CCTTCATCAAGTGGATAGAAGTAGC 59.011 44.000 13.90 0.00 38.31 3.58
171 172 5.188327 TCATCAAGTGGATAGAAGTAGCG 57.812 43.478 0.00 0.00 33.95 4.26
172 173 4.887655 TCATCAAGTGGATAGAAGTAGCGA 59.112 41.667 0.00 0.00 33.95 4.93
173 174 4.634184 TCAAGTGGATAGAAGTAGCGAC 57.366 45.455 0.00 0.00 0.00 5.19
174 175 4.014406 TCAAGTGGATAGAAGTAGCGACA 58.986 43.478 0.00 0.00 0.00 4.35
175 176 4.461431 TCAAGTGGATAGAAGTAGCGACAA 59.539 41.667 0.00 0.00 0.00 3.18
176 177 5.127194 TCAAGTGGATAGAAGTAGCGACAAT 59.873 40.000 0.00 0.00 0.00 2.71
177 178 5.599999 AGTGGATAGAAGTAGCGACAATT 57.400 39.130 0.00 0.00 0.00 2.32
178 179 5.352284 AGTGGATAGAAGTAGCGACAATTG 58.648 41.667 3.24 3.24 0.00 2.32
179 180 5.105310 AGTGGATAGAAGTAGCGACAATTGT 60.105 40.000 11.78 11.78 0.00 2.71
180 181 5.581085 GTGGATAGAAGTAGCGACAATTGTT 59.419 40.000 13.36 0.00 0.00 2.83
181 182 5.580691 TGGATAGAAGTAGCGACAATTGTTG 59.419 40.000 19.84 19.84 0.00 3.33
191 192 4.685169 CGACAATTGTTGCTAAGATGGT 57.315 40.909 13.36 0.00 0.00 3.55
192 193 4.406069 CGACAATTGTTGCTAAGATGGTG 58.594 43.478 13.36 0.00 0.00 4.17
193 194 4.672542 CGACAATTGTTGCTAAGATGGTGG 60.673 45.833 13.36 0.00 0.00 4.61
194 195 3.056607 ACAATTGTTGCTAAGATGGTGGC 60.057 43.478 4.92 0.00 0.00 5.01
195 196 2.584835 TTGTTGCTAAGATGGTGGCT 57.415 45.000 0.00 0.00 0.00 4.75
196 197 2.584835 TGTTGCTAAGATGGTGGCTT 57.415 45.000 0.00 0.00 0.00 4.35
197 198 2.875296 TGTTGCTAAGATGGTGGCTTT 58.125 42.857 0.00 0.00 0.00 3.51
198 199 4.027674 TGTTGCTAAGATGGTGGCTTTA 57.972 40.909 0.00 0.00 0.00 1.85
199 200 4.009675 TGTTGCTAAGATGGTGGCTTTAG 58.990 43.478 0.00 0.00 0.00 1.85
200 201 4.261801 GTTGCTAAGATGGTGGCTTTAGA 58.738 43.478 0.00 0.00 0.00 2.10
201 202 3.873910 TGCTAAGATGGTGGCTTTAGAC 58.126 45.455 0.00 0.00 0.00 2.59
202 203 3.519510 TGCTAAGATGGTGGCTTTAGACT 59.480 43.478 0.00 0.00 0.00 3.24
203 204 4.714802 TGCTAAGATGGTGGCTTTAGACTA 59.285 41.667 0.00 0.00 0.00 2.59
204 205 5.051153 GCTAAGATGGTGGCTTTAGACTAC 58.949 45.833 0.00 0.00 0.00 2.73
205 206 4.489306 AAGATGGTGGCTTTAGACTACC 57.511 45.455 0.00 0.00 0.00 3.18
206 207 3.725634 AGATGGTGGCTTTAGACTACCT 58.274 45.455 0.00 0.00 32.68 3.08
207 208 3.452627 AGATGGTGGCTTTAGACTACCTG 59.547 47.826 0.00 0.00 32.68 4.00
208 209 2.897350 TGGTGGCTTTAGACTACCTGA 58.103 47.619 0.00 0.00 32.68 3.86
209 210 3.450904 TGGTGGCTTTAGACTACCTGAT 58.549 45.455 0.00 0.00 32.68 2.90
210 211 3.197766 TGGTGGCTTTAGACTACCTGATG 59.802 47.826 0.00 0.00 32.68 3.07
211 212 3.197983 GGTGGCTTTAGACTACCTGATGT 59.802 47.826 0.00 0.00 0.00 3.06
212 213 4.404715 GGTGGCTTTAGACTACCTGATGTA 59.595 45.833 0.00 0.00 0.00 2.29
213 214 5.349809 GTGGCTTTAGACTACCTGATGTAC 58.650 45.833 0.00 0.00 0.00 2.90
214 215 5.127356 GTGGCTTTAGACTACCTGATGTACT 59.873 44.000 0.00 0.00 0.00 2.73
215 216 6.320672 GTGGCTTTAGACTACCTGATGTACTA 59.679 42.308 0.00 0.00 0.00 1.82
216 217 6.320672 TGGCTTTAGACTACCTGATGTACTAC 59.679 42.308 0.00 0.00 0.00 2.73
217 218 6.546772 GGCTTTAGACTACCTGATGTACTACT 59.453 42.308 0.00 0.00 0.00 2.57
218 219 7.068470 GGCTTTAGACTACCTGATGTACTACTT 59.932 40.741 0.00 0.00 0.00 2.24
219 220 8.468399 GCTTTAGACTACCTGATGTACTACTTT 58.532 37.037 0.00 0.00 0.00 2.66
226 227 9.933240 ACTACCTGATGTACTACTTTATAAGGT 57.067 33.333 5.49 5.49 37.95 3.50
229 230 9.490083 ACCTGATGTACTACTTTATAAGGTCTT 57.510 33.333 3.13 0.00 28.16 3.01
262 263 8.734218 AATTAATAAAATGGTTGCATGCATCA 57.266 26.923 23.37 22.09 0.00 3.07
263 264 7.536895 TTAATAAAATGGTTGCATGCATCAC 57.463 32.000 23.37 17.58 0.00 3.06
264 265 2.389962 AAATGGTTGCATGCATCACC 57.610 45.000 27.66 27.66 0.00 4.02
265 266 0.538118 AATGGTTGCATGCATCACCC 59.462 50.000 29.94 22.62 0.00 4.61
266 267 0.615261 ATGGTTGCATGCATCACCCA 60.615 50.000 29.94 26.30 0.00 4.51
267 268 1.252215 TGGTTGCATGCATCACCCAG 61.252 55.000 29.94 0.00 0.00 4.45
268 269 0.966875 GGTTGCATGCATCACCCAGA 60.967 55.000 25.17 5.37 0.00 3.86
269 270 1.108776 GTTGCATGCATCACCCAGAT 58.891 50.000 23.37 0.00 37.48 2.90
277 278 1.386533 CATCACCCAGATGCAACTCC 58.613 55.000 0.00 0.00 46.90 3.85
278 279 1.064906 CATCACCCAGATGCAACTCCT 60.065 52.381 0.00 0.00 46.90 3.69
279 280 1.067295 TCACCCAGATGCAACTCCTT 58.933 50.000 0.00 0.00 0.00 3.36
280 281 1.425066 TCACCCAGATGCAACTCCTTT 59.575 47.619 0.00 0.00 0.00 3.11
281 282 2.158475 TCACCCAGATGCAACTCCTTTT 60.158 45.455 0.00 0.00 0.00 2.27
282 283 2.629617 CACCCAGATGCAACTCCTTTTT 59.370 45.455 0.00 0.00 0.00 1.94
348 349 4.950205 AACAGTTAGGGTTCTTCGAAGA 57.050 40.909 23.74 23.74 0.00 2.87
352 353 3.258622 AGTTAGGGTTCTTCGAAGACAGG 59.741 47.826 27.03 0.68 34.32 4.00
424 425 7.013274 CCACAAAACAATCAGGTATCCGATAAT 59.987 37.037 0.00 0.00 0.00 1.28
425 426 8.405531 CACAAAACAATCAGGTATCCGATAATT 58.594 33.333 0.00 0.00 0.00 1.40
426 427 9.621629 ACAAAACAATCAGGTATCCGATAATTA 57.378 29.630 0.00 0.00 0.00 1.40
508 543 1.270550 CTGTGTTTGCTGGTTCATCCC 59.729 52.381 0.00 0.00 34.77 3.85
513 548 1.289160 TTGCTGGTTCATCCCTAGCT 58.711 50.000 0.00 0.00 35.50 3.32
517 552 2.911484 CTGGTTCATCCCTAGCTTGTC 58.089 52.381 0.00 0.00 34.77 3.18
529 571 5.003804 CCCTAGCTTGTCTTTTTAAGAGCA 58.996 41.667 0.00 0.00 38.41 4.26
539 581 7.861630 TGTCTTTTTAAGAGCAAGTATGTGTC 58.138 34.615 0.00 0.00 38.41 3.67
556 598 3.845259 CCCGCTTGGCTACCGCTA 61.845 66.667 0.00 0.00 36.09 4.26
620 663 1.885157 CCACCACATGCATCCACAC 59.115 57.895 0.00 0.00 0.00 3.82
651 694 4.131202 TCAAAACCATACACGTAAACGC 57.869 40.909 1.74 0.00 44.43 4.84
809 2022 3.706594 ACATAGAGCTCAAATTCCCGAGA 59.293 43.478 17.77 0.00 0.00 4.04
810 2023 2.682155 AGAGCTCAAATTCCCGAGAC 57.318 50.000 17.77 0.00 0.00 3.36
944 2157 1.355971 CGGGCGCGCATATAAATAGT 58.644 50.000 34.42 0.00 0.00 2.12
1026 2239 3.512516 GGCATTCACGGCAGGAGC 61.513 66.667 0.00 0.00 41.10 4.70
1266 2506 4.829518 CGCGCATCCTCGTCGTCA 62.830 66.667 8.75 0.00 0.00 4.35
1566 2830 1.759445 CGTCTCCAGGACATCCAAGAT 59.241 52.381 0.00 0.00 44.70 2.40
1614 2878 3.709633 ATCCAGCACTGCGAGCCA 61.710 61.111 0.00 0.00 0.00 4.75
1975 3242 3.842923 AGGAGCACGCGGATGAGG 61.843 66.667 12.47 0.00 0.00 3.86
1980 3247 2.278206 CACGCGGATGAGGACGAG 60.278 66.667 12.47 0.00 36.00 4.18
2100 3367 4.218578 ATCTCTCGCAGCGGCAGG 62.219 66.667 16.42 3.37 41.24 4.85
2152 3419 2.833121 TGCCGGATCAGCTCGCTA 60.833 61.111 5.05 0.00 0.00 4.26
2278 3545 0.944311 GACGCCGATGCATTCCGTAT 60.944 55.000 16.54 0.00 37.32 3.06
2364 3631 2.101415 AGTAGATCATGTGCTGCGCTTA 59.899 45.455 14.92 0.09 0.00 3.09
2409 3676 4.678309 GCAGTCAGTTGTCCTACCTATGTC 60.678 50.000 0.00 0.00 0.00 3.06
2410 3677 4.707448 CAGTCAGTTGTCCTACCTATGTCT 59.293 45.833 0.00 0.00 0.00 3.41
2411 3678 5.886474 CAGTCAGTTGTCCTACCTATGTCTA 59.114 44.000 0.00 0.00 0.00 2.59
2412 3679 6.547880 CAGTCAGTTGTCCTACCTATGTCTAT 59.452 42.308 0.00 0.00 0.00 1.98
2413 3680 6.547880 AGTCAGTTGTCCTACCTATGTCTATG 59.452 42.308 0.00 0.00 0.00 2.23
2414 3681 6.321690 GTCAGTTGTCCTACCTATGTCTATGT 59.678 42.308 0.00 0.00 0.00 2.29
2415 3682 6.895756 TCAGTTGTCCTACCTATGTCTATGTT 59.104 38.462 0.00 0.00 0.00 2.71
2416 3683 8.057011 TCAGTTGTCCTACCTATGTCTATGTTA 58.943 37.037 0.00 0.00 0.00 2.41
2417 3684 8.861086 CAGTTGTCCTACCTATGTCTATGTTAT 58.139 37.037 0.00 0.00 0.00 1.89
2477 3744 3.245229 ACTGCACTATTTCCATGTTGGGA 60.245 43.478 0.00 0.00 38.32 4.37
2606 3876 8.228443 ACTAAATCAGTGACACTTATTGTGGGG 61.228 40.741 14.27 7.11 42.80 4.96
2621 3891 5.412617 TTGTGGGGTGGAGAGAGTATATA 57.587 43.478 0.00 0.00 0.00 0.86
2627 3897 6.497259 TGGGGTGGAGAGAGTATATAATTCAC 59.503 42.308 0.00 0.00 0.00 3.18
2674 3944 2.264480 GGCCCGGGAATTTTGTGC 59.736 61.111 29.31 4.51 0.00 4.57
2815 4088 0.768221 ATGTAGGCACCGATGGGGAT 60.768 55.000 0.00 0.00 39.97 3.85
2872 4145 2.252976 ATGTTGCGGTTGCCATTTTT 57.747 40.000 0.00 0.00 41.78 1.94
2887 4160 1.462731 TTTTTCGGCAGTGGCATGCT 61.463 50.000 18.92 0.00 45.75 3.79
2931 4205 2.414994 TAGGGTCCGTACTCTGAGTG 57.585 55.000 20.19 4.42 36.93 3.51
2945 4219 3.079578 TCTGAGTGGTTCGTCGATAGTT 58.920 45.455 0.00 0.00 37.40 2.24
2947 4221 3.571571 TGAGTGGTTCGTCGATAGTTTG 58.428 45.455 0.00 0.00 37.40 2.93
2951 4225 2.094390 TGGTTCGTCGATAGTTTGAGGG 60.094 50.000 0.00 0.00 37.40 4.30
2958 4232 2.758979 TCGATAGTTTGAGGGAGGTGAC 59.241 50.000 0.00 0.00 37.40 3.67
2960 4234 3.056107 CGATAGTTTGAGGGAGGTGACAA 60.056 47.826 0.00 0.00 0.00 3.18
2961 4235 2.938956 AGTTTGAGGGAGGTGACAAG 57.061 50.000 0.00 0.00 0.00 3.16
2962 4236 2.127708 AGTTTGAGGGAGGTGACAAGT 58.872 47.619 0.00 0.00 0.00 3.16
2968 4242 2.897969 GAGGGAGGTGACAAGTTAGTCA 59.102 50.000 4.62 4.62 45.64 3.41
3078 4352 5.927819 AGGATAGAGCAGAAAGGAAATCAG 58.072 41.667 0.00 0.00 0.00 2.90
3120 4394 4.660789 TCTACTACCCAAAACCTATCGC 57.339 45.455 0.00 0.00 0.00 4.58
3134 4408 1.600957 CTATCGCCAACCTTGATGCAG 59.399 52.381 0.00 0.00 0.00 4.41
3154 4428 4.781528 GCAGAATACGAAATTCGAACACAC 59.218 41.667 22.92 7.92 43.74 3.82
3156 4430 4.992319 AGAATACGAAATTCGAACACACCA 59.008 37.500 22.92 0.00 43.74 4.17
3158 4432 5.873179 ATACGAAATTCGAACACACCATT 57.127 34.783 22.92 0.00 43.74 3.16
3199 4473 6.696411 TGGACAAAGTTGTTTCAAAGACAAT 58.304 32.000 0.00 0.00 42.43 2.71
3203 4477 7.378181 ACAAAGTTGTTTCAAAGACAATGACT 58.622 30.769 0.00 0.00 38.47 3.41
3206 4480 7.624360 AGTTGTTTCAAAGACAATGACTACA 57.376 32.000 0.00 0.00 39.03 2.74
3207 4481 8.225603 AGTTGTTTCAAAGACAATGACTACAT 57.774 30.769 0.00 0.00 39.03 2.29
3209 4483 9.301153 GTTGTTTCAAAGACAATGACTACATTT 57.699 29.630 0.00 0.00 43.17 2.32
3263 4537 6.070995 AGTGTTGGGACGATTAGAACTTGATA 60.071 38.462 0.00 0.00 0.00 2.15
3296 4570 4.458989 CAGCTTAAGGGCATCTTTAACACA 59.541 41.667 4.29 0.00 36.93 3.72
3318 4592 2.296190 GACCTTCAAAACAGCCGGAAAT 59.704 45.455 5.05 0.00 0.00 2.17
3361 4635 2.288961 CTGCAAGCCATCCAACAATC 57.711 50.000 0.00 0.00 0.00 2.67
3362 4636 0.896923 TGCAAGCCATCCAACAATCC 59.103 50.000 0.00 0.00 0.00 3.01
3363 4637 0.896923 GCAAGCCATCCAACAATCCA 59.103 50.000 0.00 0.00 0.00 3.41
3364 4638 1.275856 GCAAGCCATCCAACAATCCAA 59.724 47.619 0.00 0.00 0.00 3.53
3365 4639 2.932187 GCAAGCCATCCAACAATCCAAC 60.932 50.000 0.00 0.00 0.00 3.77
3366 4640 2.299582 CAAGCCATCCAACAATCCAACA 59.700 45.455 0.00 0.00 0.00 3.33
3367 4641 1.895131 AGCCATCCAACAATCCAACAC 59.105 47.619 0.00 0.00 0.00 3.32
3368 4642 1.402720 GCCATCCAACAATCCAACACG 60.403 52.381 0.00 0.00 0.00 4.49
3369 4643 1.202114 CCATCCAACAATCCAACACGG 59.798 52.381 0.00 0.00 0.00 4.94
3370 4644 0.887933 ATCCAACAATCCAACACGGC 59.112 50.000 0.00 0.00 33.14 5.68
3371 4645 0.466372 TCCAACAATCCAACACGGCA 60.466 50.000 0.00 0.00 33.14 5.69
3372 4646 0.318614 CCAACAATCCAACACGGCAC 60.319 55.000 0.00 0.00 33.14 5.01
3373 4647 0.318614 CAACAATCCAACACGGCACC 60.319 55.000 0.00 0.00 33.14 5.01
3374 4648 0.467290 AACAATCCAACACGGCACCT 60.467 50.000 0.00 0.00 33.14 4.00
3375 4649 0.889186 ACAATCCAACACGGCACCTC 60.889 55.000 0.00 0.00 33.14 3.85
3376 4650 0.888736 CAATCCAACACGGCACCTCA 60.889 55.000 0.00 0.00 33.14 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.490759 CTCATGTGTCGTGGCCGC 61.491 66.667 6.11 6.11 0.00 6.53
11 12 1.807165 CTCTCATGTGTCGTGGCCG 60.807 63.158 0.00 0.00 0.00 6.13
12 13 1.016130 CACTCTCATGTGTCGTGGCC 61.016 60.000 0.00 0.00 33.61 5.36
13 14 0.319900 ACACTCTCATGTGTCGTGGC 60.320 55.000 17.51 0.00 46.90 5.01
14 15 1.422388 CACACTCTCATGTGTCGTGG 58.578 55.000 17.51 8.30 46.90 4.94
21 22 0.603569 GGTCCGACACACTCTCATGT 59.396 55.000 0.00 0.00 0.00 3.21
22 23 0.603065 TGGTCCGACACACTCTCATG 59.397 55.000 0.00 0.00 0.00 3.07
23 24 1.338107 TTGGTCCGACACACTCTCAT 58.662 50.000 0.00 0.00 0.00 2.90
24 25 1.338107 ATTGGTCCGACACACTCTCA 58.662 50.000 0.00 0.00 0.00 3.27
25 26 2.457366 AATTGGTCCGACACACTCTC 57.543 50.000 0.00 0.00 0.00 3.20
26 27 2.158813 ACAAATTGGTCCGACACACTCT 60.159 45.455 0.00 0.00 0.00 3.24
27 28 2.218603 ACAAATTGGTCCGACACACTC 58.781 47.619 0.00 0.00 0.00 3.51
28 29 2.341846 ACAAATTGGTCCGACACACT 57.658 45.000 0.00 0.00 0.00 3.55
29 30 2.224784 GGTACAAATTGGTCCGACACAC 59.775 50.000 0.00 0.00 0.00 3.82
30 31 2.496111 GGTACAAATTGGTCCGACACA 58.504 47.619 0.00 0.00 0.00 3.72
31 32 1.808343 GGGTACAAATTGGTCCGACAC 59.192 52.381 0.00 0.00 0.00 3.67
32 33 1.271488 GGGGTACAAATTGGTCCGACA 60.271 52.381 0.00 0.00 0.00 4.35
33 34 1.271488 TGGGGTACAAATTGGTCCGAC 60.271 52.381 0.00 0.00 0.00 4.79
34 35 1.065647 TGGGGTACAAATTGGTCCGA 58.934 50.000 0.00 0.00 0.00 4.55
35 36 1.912417 TTGGGGTACAAATTGGTCCG 58.088 50.000 0.00 0.00 35.79 4.79
44 45 4.568804 CCACATACTGGATTTGGGGTACAA 60.569 45.833 0.00 0.00 43.95 2.41
45 46 3.053991 CCACATACTGGATTTGGGGTACA 60.054 47.826 0.00 0.00 43.95 2.90
46 47 3.551846 CCACATACTGGATTTGGGGTAC 58.448 50.000 0.00 0.00 43.95 3.34
47 48 2.092103 GCCACATACTGGATTTGGGGTA 60.092 50.000 7.16 0.00 43.95 3.69
48 49 1.341976 GCCACATACTGGATTTGGGGT 60.342 52.381 7.16 0.00 43.95 4.95
49 50 1.063717 AGCCACATACTGGATTTGGGG 60.064 52.381 7.16 0.00 43.95 4.96
50 51 2.442236 AGCCACATACTGGATTTGGG 57.558 50.000 7.16 0.00 43.95 4.12
55 56 2.621407 CCAACCAAGCCACATACTGGAT 60.621 50.000 0.00 0.00 43.95 3.41
56 57 1.271871 CCAACCAAGCCACATACTGGA 60.272 52.381 0.00 0.00 43.95 3.86
57 58 1.176527 CCAACCAAGCCACATACTGG 58.823 55.000 0.00 0.00 44.08 4.00
58 59 1.176527 CCCAACCAAGCCACATACTG 58.823 55.000 0.00 0.00 0.00 2.74
59 60 0.039618 CCCCAACCAAGCCACATACT 59.960 55.000 0.00 0.00 0.00 2.12
60 61 1.604147 GCCCCAACCAAGCCACATAC 61.604 60.000 0.00 0.00 0.00 2.39
61 62 1.304879 GCCCCAACCAAGCCACATA 60.305 57.895 0.00 0.00 0.00 2.29
62 63 2.604382 GCCCCAACCAAGCCACAT 60.604 61.111 0.00 0.00 0.00 3.21
63 64 4.932105 GGCCCCAACCAAGCCACA 62.932 66.667 0.00 0.00 46.34 4.17
68 69 4.740822 CCGGAGGCCCCAACCAAG 62.741 72.222 0.00 0.00 46.14 3.61
80 81 3.279434 AGCCTAACATTTAAAGCCGGAG 58.721 45.455 5.05 0.00 0.00 4.63
81 82 3.359695 AGCCTAACATTTAAAGCCGGA 57.640 42.857 5.05 0.00 0.00 5.14
82 83 4.173256 CAAAGCCTAACATTTAAAGCCGG 58.827 43.478 0.00 0.00 0.00 6.13
83 84 4.173256 CCAAAGCCTAACATTTAAAGCCG 58.827 43.478 0.00 0.00 0.00 5.52
84 85 4.929211 CACCAAAGCCTAACATTTAAAGCC 59.071 41.667 0.00 0.00 0.00 4.35
85 86 4.388773 GCACCAAAGCCTAACATTTAAAGC 59.611 41.667 0.00 0.00 0.00 3.51
86 87 4.621034 CGCACCAAAGCCTAACATTTAAAG 59.379 41.667 0.00 0.00 0.00 1.85
87 88 4.278669 TCGCACCAAAGCCTAACATTTAAA 59.721 37.500 0.00 0.00 0.00 1.52
88 89 3.821600 TCGCACCAAAGCCTAACATTTAA 59.178 39.130 0.00 0.00 0.00 1.52
89 90 3.413327 TCGCACCAAAGCCTAACATTTA 58.587 40.909 0.00 0.00 0.00 1.40
90 91 2.235016 TCGCACCAAAGCCTAACATTT 58.765 42.857 0.00 0.00 0.00 2.32
91 92 1.904287 TCGCACCAAAGCCTAACATT 58.096 45.000 0.00 0.00 0.00 2.71
92 93 1.745087 CATCGCACCAAAGCCTAACAT 59.255 47.619 0.00 0.00 0.00 2.71
93 94 1.164411 CATCGCACCAAAGCCTAACA 58.836 50.000 0.00 0.00 0.00 2.41
94 95 1.130561 GACATCGCACCAAAGCCTAAC 59.869 52.381 0.00 0.00 0.00 2.34
95 96 1.003118 AGACATCGCACCAAAGCCTAA 59.997 47.619 0.00 0.00 0.00 2.69
96 97 0.613260 AGACATCGCACCAAAGCCTA 59.387 50.000 0.00 0.00 0.00 3.93
97 98 0.957395 CAGACATCGCACCAAAGCCT 60.957 55.000 0.00 0.00 0.00 4.58
98 99 1.237285 ACAGACATCGCACCAAAGCC 61.237 55.000 0.00 0.00 0.00 4.35
99 100 0.593128 AACAGACATCGCACCAAAGC 59.407 50.000 0.00 0.00 0.00 3.51
100 101 2.605338 CCAAACAGACATCGCACCAAAG 60.605 50.000 0.00 0.00 0.00 2.77
101 102 1.336440 CCAAACAGACATCGCACCAAA 59.664 47.619 0.00 0.00 0.00 3.28
102 103 0.950836 CCAAACAGACATCGCACCAA 59.049 50.000 0.00 0.00 0.00 3.67
103 104 0.179032 ACCAAACAGACATCGCACCA 60.179 50.000 0.00 0.00 0.00 4.17
104 105 1.803334 TACCAAACAGACATCGCACC 58.197 50.000 0.00 0.00 0.00 5.01
105 106 4.034048 CCTAATACCAAACAGACATCGCAC 59.966 45.833 0.00 0.00 0.00 5.34
106 107 4.188462 CCTAATACCAAACAGACATCGCA 58.812 43.478 0.00 0.00 0.00 5.10
107 108 3.002348 GCCTAATACCAAACAGACATCGC 59.998 47.826 0.00 0.00 0.00 4.58
108 109 4.442706 AGCCTAATACCAAACAGACATCG 58.557 43.478 0.00 0.00 0.00 3.84
109 110 4.508124 CGAGCCTAATACCAAACAGACATC 59.492 45.833 0.00 0.00 0.00 3.06
110 111 4.442706 CGAGCCTAATACCAAACAGACAT 58.557 43.478 0.00 0.00 0.00 3.06
111 112 3.369052 CCGAGCCTAATACCAAACAGACA 60.369 47.826 0.00 0.00 0.00 3.41
112 113 3.118884 TCCGAGCCTAATACCAAACAGAC 60.119 47.826 0.00 0.00 0.00 3.51
113 114 3.101437 TCCGAGCCTAATACCAAACAGA 58.899 45.455 0.00 0.00 0.00 3.41
114 115 3.118738 ACTCCGAGCCTAATACCAAACAG 60.119 47.826 0.00 0.00 0.00 3.16
115 116 2.835764 ACTCCGAGCCTAATACCAAACA 59.164 45.455 0.00 0.00 0.00 2.83
116 117 3.195661 CACTCCGAGCCTAATACCAAAC 58.804 50.000 0.00 0.00 0.00 2.93
117 118 2.835764 ACACTCCGAGCCTAATACCAAA 59.164 45.455 0.00 0.00 0.00 3.28
118 119 2.429610 GACACTCCGAGCCTAATACCAA 59.570 50.000 0.00 0.00 0.00 3.67
119 120 2.029623 GACACTCCGAGCCTAATACCA 58.970 52.381 0.00 0.00 0.00 3.25
120 121 1.001597 CGACACTCCGAGCCTAATACC 60.002 57.143 0.00 0.00 0.00 2.73
121 122 1.945394 TCGACACTCCGAGCCTAATAC 59.055 52.381 0.00 0.00 34.19 1.89
122 123 1.945394 GTCGACACTCCGAGCCTAATA 59.055 52.381 11.55 0.00 39.43 0.98
123 124 0.739561 GTCGACACTCCGAGCCTAAT 59.260 55.000 11.55 0.00 39.43 1.73
124 125 0.607217 TGTCGACACTCCGAGCCTAA 60.607 55.000 15.76 0.00 39.43 2.69
125 126 1.002990 TGTCGACACTCCGAGCCTA 60.003 57.895 15.76 0.00 39.43 3.93
126 127 2.282251 TGTCGACACTCCGAGCCT 60.282 61.111 15.76 0.00 39.43 4.58
127 128 2.126424 GTGTCGACACTCCGAGCC 60.126 66.667 35.51 11.75 43.25 4.70
128 129 2.126424 GGTGTCGACACTCCGAGC 60.126 66.667 39.01 22.78 45.73 5.03
129 130 2.567049 GGGTGTCGACACTCCGAG 59.433 66.667 39.01 0.00 45.73 4.63
133 134 0.608640 ATGAAGGGGTGTCGACACTC 59.391 55.000 39.01 37.37 46.37 3.51
134 135 0.608640 GATGAAGGGGTGTCGACACT 59.391 55.000 39.01 24.92 45.73 3.55
135 136 0.320374 TGATGAAGGGGTGTCGACAC 59.680 55.000 35.26 35.26 45.72 3.67
136 137 1.001974 CTTGATGAAGGGGTGTCGACA 59.998 52.381 15.76 15.76 0.00 4.35
137 138 1.002087 ACTTGATGAAGGGGTGTCGAC 59.998 52.381 9.11 9.11 32.95 4.20
138 139 1.001974 CACTTGATGAAGGGGTGTCGA 59.998 52.381 0.00 0.00 32.95 4.20
139 140 1.442769 CACTTGATGAAGGGGTGTCG 58.557 55.000 0.00 0.00 32.95 4.35
140 141 1.826385 CCACTTGATGAAGGGGTGTC 58.174 55.000 4.81 0.00 46.61 3.67
145 146 5.365021 ACTTCTATCCACTTGATGAAGGG 57.635 43.478 0.00 0.00 39.87 3.95
146 147 5.988561 GCTACTTCTATCCACTTGATGAAGG 59.011 44.000 0.00 0.00 39.87 3.46
147 148 5.689514 CGCTACTTCTATCCACTTGATGAAG 59.310 44.000 0.00 0.00 40.55 3.02
148 149 5.359860 TCGCTACTTCTATCCACTTGATGAA 59.640 40.000 0.00 0.00 34.76 2.57
149 150 4.887655 TCGCTACTTCTATCCACTTGATGA 59.112 41.667 0.00 0.00 34.76 2.92
150 151 4.979197 GTCGCTACTTCTATCCACTTGATG 59.021 45.833 0.00 0.00 34.76 3.07
151 152 4.645136 TGTCGCTACTTCTATCCACTTGAT 59.355 41.667 0.00 0.00 37.49 2.57
152 153 4.014406 TGTCGCTACTTCTATCCACTTGA 58.986 43.478 0.00 0.00 0.00 3.02
153 154 4.371855 TGTCGCTACTTCTATCCACTTG 57.628 45.455 0.00 0.00 0.00 3.16
154 155 5.599999 ATTGTCGCTACTTCTATCCACTT 57.400 39.130 0.00 0.00 0.00 3.16
155 156 5.105310 ACAATTGTCGCTACTTCTATCCACT 60.105 40.000 4.92 0.00 0.00 4.00
156 157 5.109903 ACAATTGTCGCTACTTCTATCCAC 58.890 41.667 4.92 0.00 0.00 4.02
157 158 5.339008 ACAATTGTCGCTACTTCTATCCA 57.661 39.130 4.92 0.00 0.00 3.41
158 159 5.502544 GCAACAATTGTCGCTACTTCTATCC 60.503 44.000 14.28 0.00 0.00 2.59
159 160 5.292101 AGCAACAATTGTCGCTACTTCTATC 59.708 40.000 22.22 0.00 31.60 2.08
160 161 5.178797 AGCAACAATTGTCGCTACTTCTAT 58.821 37.500 22.22 0.00 31.60 1.98
161 162 4.566004 AGCAACAATTGTCGCTACTTCTA 58.434 39.130 22.22 0.00 31.60 2.10
162 163 3.403038 AGCAACAATTGTCGCTACTTCT 58.597 40.909 22.22 0.00 31.60 2.85
163 164 3.813529 AGCAACAATTGTCGCTACTTC 57.186 42.857 22.22 0.00 31.60 3.01
164 165 4.994852 TCTTAGCAACAATTGTCGCTACTT 59.005 37.500 26.80 8.30 36.73 2.24
165 166 4.566004 TCTTAGCAACAATTGTCGCTACT 58.434 39.130 26.80 14.83 36.73 2.57
166 167 4.921470 TCTTAGCAACAATTGTCGCTAC 57.079 40.909 26.80 8.96 36.73 3.58
167 168 4.332543 CCATCTTAGCAACAATTGTCGCTA 59.667 41.667 24.00 24.00 35.93 4.26
168 169 3.127548 CCATCTTAGCAACAATTGTCGCT 59.872 43.478 26.07 26.07 38.51 4.93
169 170 3.119849 ACCATCTTAGCAACAATTGTCGC 60.120 43.478 13.73 13.73 0.00 5.19
170 171 4.406069 CACCATCTTAGCAACAATTGTCG 58.594 43.478 12.39 0.78 0.00 4.35
171 172 4.737054 CCACCATCTTAGCAACAATTGTC 58.263 43.478 12.39 0.00 0.00 3.18
172 173 3.056607 GCCACCATCTTAGCAACAATTGT 60.057 43.478 4.92 4.92 0.00 2.71
173 174 3.194116 AGCCACCATCTTAGCAACAATTG 59.806 43.478 3.24 3.24 0.00 2.32
174 175 3.434309 AGCCACCATCTTAGCAACAATT 58.566 40.909 0.00 0.00 0.00 2.32
175 176 3.091633 AGCCACCATCTTAGCAACAAT 57.908 42.857 0.00 0.00 0.00 2.71
176 177 2.584835 AGCCACCATCTTAGCAACAA 57.415 45.000 0.00 0.00 0.00 2.83
177 178 2.584835 AAGCCACCATCTTAGCAACA 57.415 45.000 0.00 0.00 0.00 3.33
178 179 4.095036 GTCTAAAGCCACCATCTTAGCAAC 59.905 45.833 0.00 0.00 0.00 4.17
179 180 4.019321 AGTCTAAAGCCACCATCTTAGCAA 60.019 41.667 0.00 0.00 0.00 3.91
180 181 3.519510 AGTCTAAAGCCACCATCTTAGCA 59.480 43.478 0.00 0.00 0.00 3.49
181 182 4.143986 AGTCTAAAGCCACCATCTTAGC 57.856 45.455 0.00 0.00 0.00 3.09
182 183 5.364157 AGGTAGTCTAAAGCCACCATCTTAG 59.636 44.000 0.00 0.00 0.00 2.18
183 184 5.128827 CAGGTAGTCTAAAGCCACCATCTTA 59.871 44.000 0.00 0.00 0.00 2.10
184 185 4.080863 CAGGTAGTCTAAAGCCACCATCTT 60.081 45.833 0.00 0.00 0.00 2.40
185 186 3.452627 CAGGTAGTCTAAAGCCACCATCT 59.547 47.826 0.00 0.00 0.00 2.90
186 187 3.451178 TCAGGTAGTCTAAAGCCACCATC 59.549 47.826 0.00 0.00 0.00 3.51
187 188 3.450904 TCAGGTAGTCTAAAGCCACCAT 58.549 45.455 0.00 0.00 0.00 3.55
188 189 2.897350 TCAGGTAGTCTAAAGCCACCA 58.103 47.619 0.00 0.00 0.00 4.17
189 190 3.197983 ACATCAGGTAGTCTAAAGCCACC 59.802 47.826 0.00 0.00 0.00 4.61
190 191 4.473477 ACATCAGGTAGTCTAAAGCCAC 57.527 45.455 0.00 0.00 0.00 5.01
191 192 5.269991 AGTACATCAGGTAGTCTAAAGCCA 58.730 41.667 0.00 0.00 29.37 4.75
192 193 5.855740 AGTACATCAGGTAGTCTAAAGCC 57.144 43.478 0.00 0.00 29.37 4.35
193 194 7.571080 AGTAGTACATCAGGTAGTCTAAAGC 57.429 40.000 2.52 0.00 36.94 3.51
200 201 9.933240 ACCTTATAAAGTAGTACATCAGGTAGT 57.067 33.333 2.52 0.00 39.06 2.73
203 204 9.490083 AAGACCTTATAAAGTAGTACATCAGGT 57.510 33.333 2.52 4.15 33.51 4.00
236 237 9.828039 TGATGCATGCAACCATTTTATTAATTA 57.172 25.926 26.68 0.00 0.00 1.40
237 238 8.614346 GTGATGCATGCAACCATTTTATTAATT 58.386 29.630 26.68 1.01 0.00 1.40
238 239 7.227116 GGTGATGCATGCAACCATTTTATTAAT 59.773 33.333 28.84 8.35 0.00 1.40
239 240 6.538021 GGTGATGCATGCAACCATTTTATTAA 59.462 34.615 28.84 5.16 0.00 1.40
240 241 6.047870 GGTGATGCATGCAACCATTTTATTA 58.952 36.000 28.84 5.82 0.00 0.98
241 242 4.877251 GGTGATGCATGCAACCATTTTATT 59.123 37.500 28.84 9.47 0.00 1.40
242 243 4.444536 GGTGATGCATGCAACCATTTTAT 58.555 39.130 28.84 10.19 0.00 1.40
243 244 3.369261 GGGTGATGCATGCAACCATTTTA 60.369 43.478 32.41 10.80 42.75 1.52
244 245 2.616001 GGGTGATGCATGCAACCATTTT 60.616 45.455 32.41 14.59 42.75 1.82
245 246 1.065998 GGGTGATGCATGCAACCATTT 60.066 47.619 32.41 15.28 42.75 2.32
246 247 0.538118 GGGTGATGCATGCAACCATT 59.462 50.000 32.41 15.98 42.75 3.16
247 248 2.204748 GGGTGATGCATGCAACCAT 58.795 52.632 32.41 16.33 42.75 3.55
248 249 3.697424 GGGTGATGCATGCAACCA 58.303 55.556 32.41 25.82 42.75 3.67
249 250 0.966875 TCTGGGTGATGCATGCAACC 60.967 55.000 26.83 26.83 43.53 3.77
250 251 1.108776 ATCTGGGTGATGCATGCAAC 58.891 50.000 26.68 23.10 33.43 4.17
251 252 1.107945 CATCTGGGTGATGCATGCAA 58.892 50.000 26.68 6.15 44.96 4.08
252 253 2.801859 CATCTGGGTGATGCATGCA 58.198 52.632 25.04 25.04 44.96 3.96
259 260 1.293062 AGGAGTTGCATCTGGGTGAT 58.707 50.000 1.00 0.00 35.40 3.06
260 261 1.067295 AAGGAGTTGCATCTGGGTGA 58.933 50.000 1.00 0.00 0.00 4.02
261 262 1.915141 AAAGGAGTTGCATCTGGGTG 58.085 50.000 1.00 0.00 0.00 4.61
262 263 2.683211 AAAAGGAGTTGCATCTGGGT 57.317 45.000 1.00 0.00 0.00 4.51
284 285 9.995003 TGGCTCAATCAAAAATATACTTTGTTT 57.005 25.926 9.05 5.78 35.65 2.83
285 286 9.995003 TTGGCTCAATCAAAAATATACTTTGTT 57.005 25.926 9.05 1.11 35.65 2.83
286 287 9.423061 GTTGGCTCAATCAAAAATATACTTTGT 57.577 29.630 9.05 0.00 35.65 2.83
287 288 9.643693 AGTTGGCTCAATCAAAAATATACTTTG 57.356 29.630 4.52 4.52 35.51 2.77
291 292 9.683069 CCATAGTTGGCTCAATCAAAAATATAC 57.317 33.333 0.00 0.00 35.85 1.47
321 322 7.288810 TCGAAGAACCCTAACTGTTAAGTTA 57.711 36.000 12.84 0.00 45.01 2.24
325 326 6.183360 TGTCTTCGAAGAACCCTAACTGTTAA 60.183 38.462 28.58 0.00 45.90 2.01
348 349 8.050778 TGCATATTTTATTTTCGAAGTCCTGT 57.949 30.769 0.00 0.00 0.00 4.00
352 353 9.623687 GCAAATGCATATTTTATTTTCGAAGTC 57.376 29.630 0.00 0.00 41.59 3.01
424 425 2.992593 TGCTGGACGGTATTGCATTAA 58.007 42.857 0.00 0.00 0.00 1.40
425 426 2.700722 TGCTGGACGGTATTGCATTA 57.299 45.000 0.00 0.00 0.00 1.90
426 427 1.832883 TTGCTGGACGGTATTGCATT 58.167 45.000 0.00 0.00 33.50 3.56
427 428 1.745087 CTTTGCTGGACGGTATTGCAT 59.255 47.619 0.00 0.00 33.50 3.96
467 469 8.700051 ACACAGATAGCTTAGTCATGTTTCTAT 58.300 33.333 0.00 0.00 0.00 1.98
468 470 8.067751 ACACAGATAGCTTAGTCATGTTTCTA 57.932 34.615 0.00 0.00 0.00 2.10
470 472 7.602517 AACACAGATAGCTTAGTCATGTTTC 57.397 36.000 0.00 0.00 0.00 2.78
508 543 7.195839 ACTTGCTCTTAAAAAGACAAGCTAG 57.804 36.000 19.99 14.65 43.07 3.42
513 548 8.220755 ACACATACTTGCTCTTAAAAAGACAA 57.779 30.769 0.00 0.00 33.12 3.18
517 552 6.612306 GGGACACATACTTGCTCTTAAAAAG 58.388 40.000 0.00 0.00 0.00 2.27
529 571 0.676782 GCCAAGCGGGACACATACTT 60.677 55.000 1.23 0.00 40.01 2.24
620 663 4.961551 GTGTATGGTTTTGATATGCGTTCG 59.038 41.667 0.00 0.00 0.00 3.95
651 694 3.396260 TCCGGTCTCACTTTGTTTAGG 57.604 47.619 0.00 0.00 0.00 2.69
753 803 1.073025 TGCTGCCTTCGTGTTCCAT 59.927 52.632 0.00 0.00 0.00 3.41
778 828 7.308830 GGAATTTGAGCTCTATGTTTCTGTGTT 60.309 37.037 16.19 0.00 0.00 3.32
809 2022 0.110486 AATCTGGCCAAAGGACGTGT 59.890 50.000 7.01 0.00 29.56 4.49
810 2023 0.804989 GAATCTGGCCAAAGGACGTG 59.195 55.000 7.01 0.00 29.56 4.49
925 2138 1.355971 ACTATTTATATGCGCGCCCG 58.644 50.000 30.77 8.24 37.57 6.13
926 2139 2.222729 CGAACTATTTATATGCGCGCCC 60.223 50.000 30.77 1.83 0.00 6.13
927 2140 2.783316 GCGAACTATTTATATGCGCGCC 60.783 50.000 30.77 11.42 36.37 6.53
944 2157 2.596046 AATGGTTGCACCGGCGAA 60.596 55.556 9.30 0.00 42.58 4.70
1026 2239 0.108424 CCGACTCTGCAGAAAGAGGG 60.108 60.000 18.85 10.76 46.73 4.30
1266 2506 3.976490 TTCCTCCTGGCCCGACGAT 62.976 63.158 0.00 0.00 0.00 3.73
1566 2830 2.827190 ACGGATCCGAGCGTGCTA 60.827 61.111 39.55 0.00 42.83 3.49
1614 2878 3.394836 GGGAAGCTCCTCTGCGGT 61.395 66.667 0.00 0.00 36.57 5.68
1975 3242 2.462782 CCTCCTCGTCGTCCTCGTC 61.463 68.421 0.00 0.00 38.33 4.20
1980 3247 2.829458 CCCTCCTCCTCGTCGTCC 60.829 72.222 0.00 0.00 0.00 4.79
2100 3367 4.222847 GATCCGCTCCCACCCGAC 62.223 72.222 0.00 0.00 0.00 4.79
2152 3419 1.102154 CTCTCCTCTGTGATCGCAGT 58.898 55.000 30.17 0.00 37.70 4.40
2157 3424 0.753479 TCCGGCTCTCCTCTGTGATC 60.753 60.000 0.00 0.00 0.00 2.92
2208 3475 4.289101 ACACCCTGCATGCAGCCA 62.289 61.111 37.11 8.80 44.83 4.75
2318 3585 1.209019 GGCAGCTCCCGATGATATCAT 59.791 52.381 18.21 18.21 39.70 2.45
2364 3631 2.171448 GTGGCTATGTCACTCTCCCATT 59.829 50.000 0.00 0.00 35.05 3.16
2409 3676 8.922676 CCTAACTAATAACCGTGCATAACATAG 58.077 37.037 0.00 0.00 0.00 2.23
2410 3677 8.640651 TCCTAACTAATAACCGTGCATAACATA 58.359 33.333 0.00 0.00 0.00 2.29
2411 3678 7.502696 TCCTAACTAATAACCGTGCATAACAT 58.497 34.615 0.00 0.00 0.00 2.71
2412 3679 6.876155 TCCTAACTAATAACCGTGCATAACA 58.124 36.000 0.00 0.00 0.00 2.41
2413 3680 6.982724 ACTCCTAACTAATAACCGTGCATAAC 59.017 38.462 0.00 0.00 0.00 1.89
2414 3681 7.116075 ACTCCTAACTAATAACCGTGCATAA 57.884 36.000 0.00 0.00 0.00 1.90
2415 3682 6.720112 ACTCCTAACTAATAACCGTGCATA 57.280 37.500 0.00 0.00 0.00 3.14
2416 3683 5.609533 ACTCCTAACTAATAACCGTGCAT 57.390 39.130 0.00 0.00 0.00 3.96
2417 3684 6.720112 ATACTCCTAACTAATAACCGTGCA 57.280 37.500 0.00 0.00 0.00 4.57
2477 3744 6.018832 CCAACATCTCAAAACGAAAAAGCAAT 60.019 34.615 0.00 0.00 0.00 3.56
2627 3897 7.489113 AGCACAAATGAAGTTTTGTTCTACAAG 59.511 33.333 1.34 0.00 45.14 3.16
2794 4067 1.410850 CCCCATCGGTGCCTACATCT 61.411 60.000 0.00 0.00 0.00 2.90
2872 4145 3.549900 TTCAGCATGCCACTGCCGA 62.550 57.895 15.66 0.00 43.33 5.54
2898 4171 2.519622 CCCTATGATGCCCCGCTCA 61.520 63.158 0.00 0.00 0.00 4.26
2903 4176 0.834687 TACGGACCCTATGATGCCCC 60.835 60.000 0.00 0.00 0.00 5.80
2909 4182 2.508716 ACTCAGAGTACGGACCCTATGA 59.491 50.000 0.00 0.00 0.00 2.15
2911 4184 2.423088 CCACTCAGAGTACGGACCCTAT 60.423 54.545 1.67 0.00 0.00 2.57
2931 4205 2.165030 TCCCTCAAACTATCGACGAACC 59.835 50.000 0.00 0.00 0.00 3.62
2945 4219 3.314693 ACTAACTTGTCACCTCCCTCAA 58.685 45.455 0.00 0.00 0.00 3.02
2947 4221 2.897969 TGACTAACTTGTCACCTCCCTC 59.102 50.000 0.00 0.00 41.43 4.30
2958 4232 3.859961 CCGCACTACTGATGACTAACTTG 59.140 47.826 0.00 0.00 0.00 3.16
2960 4234 2.159226 GCCGCACTACTGATGACTAACT 60.159 50.000 0.00 0.00 0.00 2.24
2961 4235 2.159226 AGCCGCACTACTGATGACTAAC 60.159 50.000 0.00 0.00 0.00 2.34
2962 4236 2.100197 AGCCGCACTACTGATGACTAA 58.900 47.619 0.00 0.00 0.00 2.24
2971 4245 1.219124 CCACATCAGCCGCACTACT 59.781 57.895 0.00 0.00 0.00 2.57
2974 4248 1.672356 GAACCACATCAGCCGCACT 60.672 57.895 0.00 0.00 0.00 4.40
3013 4287 6.595772 TTTCTTGTATTGCGTGCAATTTTT 57.404 29.167 23.51 4.62 43.32 1.94
3078 4352 3.087370 AGCCATTGTTCCTTACCTTCC 57.913 47.619 0.00 0.00 0.00 3.46
3120 4394 3.270027 TCGTATTCTGCATCAAGGTTGG 58.730 45.455 0.00 0.00 0.00 3.77
3134 4408 5.272167 TGGTGTGTTCGAATTTCGTATTC 57.728 39.130 17.61 8.66 41.35 1.75
3154 4428 1.452108 GCAAGGGAGGACGGAATGG 60.452 63.158 0.00 0.00 0.00 3.16
3156 4430 1.208165 AAGGCAAGGGAGGACGGAAT 61.208 55.000 0.00 0.00 0.00 3.01
3158 4432 2.203938 AAGGCAAGGGAGGACGGA 60.204 61.111 0.00 0.00 0.00 4.69
3199 4473 5.434182 TGACATGGGATCAAATGTAGTCA 57.566 39.130 11.32 5.33 37.15 3.41
3207 4481 4.773674 AGCAAGATTTGACATGGGATCAAA 59.226 37.500 11.15 11.15 46.96 2.69
3209 4483 3.972133 AGCAAGATTTGACATGGGATCA 58.028 40.909 0.00 0.00 0.00 2.92
3263 4537 1.338200 CCCTTAAGCTGTTGTCTCGCT 60.338 52.381 0.00 0.00 35.09 4.93
3296 4570 0.472471 TCCGGCTGTTTTGAAGGTCT 59.528 50.000 0.00 0.00 0.00 3.85
3318 4592 1.068588 CTGAACACCTCAGTCCGAACA 59.931 52.381 0.00 0.00 45.76 3.18
3358 4632 1.454104 TGAGGTGCCGTGTTGGATT 59.546 52.632 0.00 0.00 42.00 3.01
3359 4633 3.156714 TGAGGTGCCGTGTTGGAT 58.843 55.556 0.00 0.00 42.00 3.41


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

AutoCloner maintained by Alex Coulton.