Multiple sequence alignment - TraesCS1D01G012400

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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 TraesCS1D01G012400 chr1D 100.000 3092 0 0 1 3092 6492176 6489085 0.000000e+00 5710
1 TraesCS1D01G012400 chr1D 93.640 283 15 1 1 280 118863309 118863027 1.330000e-113 420
2 TraesCS1D01G012400 chr6D 97.514 2816 64 4 282 3092 472510963 472513777 0.000000e+00 4807
3 TraesCS1D01G012400 chr6D 96.806 2818 79 5 280 3092 367564539 367561728 0.000000e+00 4695
4 TraesCS1D01G012400 chr6D 97.173 283 5 1 1 280 413184646 413184928 2.790000e-130 475
5 TraesCS1D01G012400 chr5D 97.337 2816 68 5 282 3092 480824254 480821441 0.000000e+00 4778
6 TraesCS1D01G012400 chr5D 96.984 2818 72 6 280 3092 244414328 244411519 0.000000e+00 4721
7 TraesCS1D01G012400 chr5D 96.951 2821 73 9 282 3092 260689962 260687145 0.000000e+00 4721
8 TraesCS1D01G012400 chr5D 96.916 2821 74 9 282 3092 565815802 565818619 0.000000e+00 4715
9 TraesCS1D01G012400 chr4D 97.131 2823 67 7 282 3092 398986367 398983547 0.000000e+00 4752
10 TraesCS1D01G012400 chr3D 97.053 2816 76 5 282 3092 574856805 574853992 0.000000e+00 4734
11 TraesCS1D01G012400 chr7D 96.916 2821 75 8 282 3092 245402431 245399613 0.000000e+00 4717
12 TraesCS1D01G012400 chr4A 96.887 257 5 1 27 280 454150471 454150727 7.920000e-116 427
13 TraesCS1D01G012400 chr4A 87.633 283 32 1 1 280 694988499 694988781 2.970000e-85 326
14 TraesCS1D01G012400 chr4A 87.633 283 32 3 1 280 714915185 714915467 2.970000e-85 326
15 TraesCS1D01G012400 chr2B 92.580 283 18 1 1 280 795487506 795487224 1.340000e-108 403
16 TraesCS1D01G012400 chrUn 87.986 283 31 3 1 280 277341565 277341283 6.390000e-87 331
17 TraesCS1D01G012400 chr6B 88.028 284 29 3 1 280 137522780 137523062 6.390000e-87 331
18 TraesCS1D01G012400 chr5A 87.986 283 31 1 1 280 8918751 8918469 6.390000e-87 331


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 TraesCS1D01G012400 chr1D 6489085 6492176 3091 True 5710 5710 100.000 1 3092 1 chr1D.!!$R1 3091
1 TraesCS1D01G012400 chr6D 472510963 472513777 2814 False 4807 4807 97.514 282 3092 1 chr6D.!!$F2 2810
2 TraesCS1D01G012400 chr6D 367561728 367564539 2811 True 4695 4695 96.806 280 3092 1 chr6D.!!$R1 2812
3 TraesCS1D01G012400 chr5D 480821441 480824254 2813 True 4778 4778 97.337 282 3092 1 chr5D.!!$R3 2810
4 TraesCS1D01G012400 chr5D 244411519 244414328 2809 True 4721 4721 96.984 280 3092 1 chr5D.!!$R1 2812
5 TraesCS1D01G012400 chr5D 260687145 260689962 2817 True 4721 4721 96.951 282 3092 1 chr5D.!!$R2 2810
6 TraesCS1D01G012400 chr5D 565815802 565818619 2817 False 4715 4715 96.916 282 3092 1 chr5D.!!$F1 2810
7 TraesCS1D01G012400 chr4D 398983547 398986367 2820 True 4752 4752 97.131 282 3092 1 chr4D.!!$R1 2810
8 TraesCS1D01G012400 chr3D 574853992 574856805 2813 True 4734 4734 97.053 282 3092 1 chr3D.!!$R1 2810
9 TraesCS1D01G012400 chr7D 245399613 245402431 2818 True 4717 4717 96.916 282 3092 1 chr7D.!!$R1 2810

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
464 465 0.108992 GTTAGTCCACGTCATCGCCA 60.109 55.0 0.0 0.0 41.18 5.69 F
942 956 0.251787 GGTTCTTGCTGGATTGGGGT 60.252 55.0 0.0 0.0 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2008 0.251474 ATGCTCAAGCTTGGCCTTCA 60.251 50.0 25.73 15.71 42.66 3.02 R
2564 2580 0.103937 CTGCGTCCTCTTCCTCATCC 59.896 60.0 0.00 0.00 0.00 3.51 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
18 19 2.450992 TGTGTCATGGAGTGCAGGA 58.549 52.632 0.00 0.00 0.00 3.86
19 20 0.764271 TGTGTCATGGAGTGCAGGAA 59.236 50.000 0.00 0.00 0.00 3.36
20 21 1.142667 TGTGTCATGGAGTGCAGGAAA 59.857 47.619 0.00 0.00 0.00 3.13
21 22 2.229792 GTGTCATGGAGTGCAGGAAAA 58.770 47.619 0.00 0.00 0.00 2.29
22 23 2.030805 GTGTCATGGAGTGCAGGAAAAC 60.031 50.000 0.00 0.00 0.00 2.43
23 24 2.229792 GTCATGGAGTGCAGGAAAACA 58.770 47.619 0.00 0.00 0.00 2.83
24 25 2.227388 GTCATGGAGTGCAGGAAAACAG 59.773 50.000 0.00 0.00 0.00 3.16
25 26 1.542915 CATGGAGTGCAGGAAAACAGG 59.457 52.381 0.00 0.00 0.00 4.00
26 27 0.823356 TGGAGTGCAGGAAAACAGGC 60.823 55.000 0.00 0.00 0.00 4.85
27 28 0.538287 GGAGTGCAGGAAAACAGGCT 60.538 55.000 0.00 0.00 0.00 4.58
28 29 1.271379 GGAGTGCAGGAAAACAGGCTA 60.271 52.381 0.00 0.00 0.00 3.93
29 30 1.807142 GAGTGCAGGAAAACAGGCTAC 59.193 52.381 0.00 0.00 0.00 3.58
30 31 1.421646 AGTGCAGGAAAACAGGCTACT 59.578 47.619 0.00 0.00 0.00 2.57
41 42 1.914634 CAGGCTACTGTGTCACGATC 58.085 55.000 0.00 0.00 39.92 3.69
42 43 1.474478 CAGGCTACTGTGTCACGATCT 59.526 52.381 0.00 0.00 39.92 2.75
43 44 2.683362 CAGGCTACTGTGTCACGATCTA 59.317 50.000 0.00 0.00 39.92 1.98
44 45 2.946329 AGGCTACTGTGTCACGATCTAG 59.054 50.000 0.00 0.00 0.00 2.43
45 46 2.683867 GGCTACTGTGTCACGATCTAGT 59.316 50.000 0.00 0.00 0.00 2.57
46 47 3.875727 GGCTACTGTGTCACGATCTAGTA 59.124 47.826 0.00 0.00 0.00 1.82
47 48 4.260702 GGCTACTGTGTCACGATCTAGTAC 60.261 50.000 0.00 0.00 0.00 2.73
48 49 4.571580 GCTACTGTGTCACGATCTAGTACT 59.428 45.833 0.00 0.00 0.00 2.73
49 50 4.948608 ACTGTGTCACGATCTAGTACTG 57.051 45.455 5.39 0.00 0.00 2.74
50 51 4.576879 ACTGTGTCACGATCTAGTACTGA 58.423 43.478 5.39 1.42 0.00 3.41
51 52 5.001874 ACTGTGTCACGATCTAGTACTGAA 58.998 41.667 5.39 0.00 0.00 3.02
52 53 5.122554 ACTGTGTCACGATCTAGTACTGAAG 59.877 44.000 5.39 0.00 0.00 3.02
53 54 4.142665 TGTGTCACGATCTAGTACTGAAGC 60.143 45.833 5.39 0.00 0.00 3.86
54 55 3.063588 TGTCACGATCTAGTACTGAAGCG 59.936 47.826 5.39 10.34 0.00 4.68
55 56 2.612672 TCACGATCTAGTACTGAAGCGG 59.387 50.000 17.47 9.26 0.00 5.52
56 57 2.612672 CACGATCTAGTACTGAAGCGGA 59.387 50.000 17.47 3.50 0.00 5.54
57 58 3.064958 CACGATCTAGTACTGAAGCGGAA 59.935 47.826 17.47 0.00 0.00 4.30
58 59 3.884091 ACGATCTAGTACTGAAGCGGAAT 59.116 43.478 17.47 0.00 0.00 3.01
59 60 5.049612 CACGATCTAGTACTGAAGCGGAATA 60.050 44.000 17.47 0.00 0.00 1.75
60 61 5.706369 ACGATCTAGTACTGAAGCGGAATAT 59.294 40.000 17.47 0.00 0.00 1.28
61 62 6.877855 ACGATCTAGTACTGAAGCGGAATATA 59.122 38.462 17.47 0.00 0.00 0.86
62 63 7.389884 ACGATCTAGTACTGAAGCGGAATATAA 59.610 37.037 17.47 0.00 0.00 0.98
63 64 7.906010 CGATCTAGTACTGAAGCGGAATATAAG 59.094 40.741 5.39 0.00 0.00 1.73
64 65 7.450124 TCTAGTACTGAAGCGGAATATAAGG 57.550 40.000 5.39 0.00 0.00 2.69
65 66 4.884247 AGTACTGAAGCGGAATATAAGGC 58.116 43.478 0.00 0.00 0.00 4.35
66 67 4.589374 AGTACTGAAGCGGAATATAAGGCT 59.411 41.667 0.00 0.00 37.33 4.58
67 68 3.996480 ACTGAAGCGGAATATAAGGCTC 58.004 45.455 0.00 0.00 33.99 4.70
68 69 3.643792 ACTGAAGCGGAATATAAGGCTCT 59.356 43.478 0.00 0.00 33.99 4.09
69 70 4.101741 ACTGAAGCGGAATATAAGGCTCTT 59.898 41.667 0.00 0.00 33.99 2.85
70 71 4.380531 TGAAGCGGAATATAAGGCTCTTG 58.619 43.478 0.00 0.00 33.99 3.02
71 72 2.772287 AGCGGAATATAAGGCTCTTGC 58.228 47.619 0.00 0.00 38.76 4.01
72 73 2.370189 AGCGGAATATAAGGCTCTTGCT 59.630 45.455 0.00 0.00 39.59 3.91
73 74 3.578716 AGCGGAATATAAGGCTCTTGCTA 59.421 43.478 0.00 0.00 39.59 3.49
74 75 4.040461 AGCGGAATATAAGGCTCTTGCTAA 59.960 41.667 0.00 0.00 39.59 3.09
75 76 4.938226 GCGGAATATAAGGCTCTTGCTAAT 59.062 41.667 0.00 0.00 39.59 1.73
76 77 5.163814 GCGGAATATAAGGCTCTTGCTAATG 60.164 44.000 0.00 0.00 39.59 1.90
77 78 5.163814 CGGAATATAAGGCTCTTGCTAATGC 60.164 44.000 0.00 0.00 39.59 3.56
93 94 6.506464 GCTAATGCAACTGCTGAAATTATG 57.494 37.500 2.95 0.00 42.66 1.90
94 95 6.038356 GCTAATGCAACTGCTGAAATTATGT 58.962 36.000 2.95 0.00 42.66 2.29
95 96 6.020121 GCTAATGCAACTGCTGAAATTATGTG 60.020 38.462 2.95 0.00 42.66 3.21
96 97 4.177165 TGCAACTGCTGAAATTATGTGG 57.823 40.909 2.95 0.00 42.66 4.17
97 98 3.825585 TGCAACTGCTGAAATTATGTGGA 59.174 39.130 2.95 0.00 42.66 4.02
98 99 4.463539 TGCAACTGCTGAAATTATGTGGAT 59.536 37.500 2.95 0.00 42.66 3.41
99 100 5.039333 GCAACTGCTGAAATTATGTGGATC 58.961 41.667 0.00 0.00 38.21 3.36
100 101 5.585390 CAACTGCTGAAATTATGTGGATCC 58.415 41.667 4.20 4.20 0.00 3.36
101 102 4.858850 ACTGCTGAAATTATGTGGATCCA 58.141 39.130 11.44 11.44 0.00 3.41
102 103 4.885907 ACTGCTGAAATTATGTGGATCCAG 59.114 41.667 16.81 0.00 0.00 3.86
103 104 5.114764 TGCTGAAATTATGTGGATCCAGA 57.885 39.130 16.81 15.81 0.00 3.86
104 105 4.883585 TGCTGAAATTATGTGGATCCAGAC 59.116 41.667 16.81 4.84 0.00 3.51
105 106 5.128919 GCTGAAATTATGTGGATCCAGACT 58.871 41.667 16.81 6.87 0.00 3.24
106 107 5.238214 GCTGAAATTATGTGGATCCAGACTC 59.762 44.000 16.81 3.57 0.00 3.36
107 108 6.566079 TGAAATTATGTGGATCCAGACTCT 57.434 37.500 16.81 1.05 0.00 3.24
108 109 6.962182 TGAAATTATGTGGATCCAGACTCTT 58.038 36.000 16.81 5.88 0.00 2.85
109 110 7.405292 TGAAATTATGTGGATCCAGACTCTTT 58.595 34.615 16.81 13.58 0.00 2.52
110 111 7.890127 TGAAATTATGTGGATCCAGACTCTTTT 59.110 33.333 16.81 11.99 0.00 2.27
111 112 9.396022 GAAATTATGTGGATCCAGACTCTTTTA 57.604 33.333 16.81 0.00 0.00 1.52
112 113 9.927081 AAATTATGTGGATCCAGACTCTTTTAT 57.073 29.630 16.81 0.00 0.00 1.40
116 117 7.675161 TGTGGATCCAGACTCTTTTATATGA 57.325 36.000 16.81 0.00 0.00 2.15
117 118 8.089625 TGTGGATCCAGACTCTTTTATATGAA 57.910 34.615 16.81 0.00 0.00 2.57
118 119 7.987458 TGTGGATCCAGACTCTTTTATATGAAC 59.013 37.037 16.81 0.00 0.00 3.18
119 120 8.207545 GTGGATCCAGACTCTTTTATATGAACT 58.792 37.037 16.81 0.00 0.00 3.01
120 121 9.434275 TGGATCCAGACTCTTTTATATGAACTA 57.566 33.333 11.44 0.00 0.00 2.24
121 122 9.921637 GGATCCAGACTCTTTTATATGAACTAG 57.078 37.037 6.95 0.00 0.00 2.57
122 123 9.921637 GATCCAGACTCTTTTATATGAACTAGG 57.078 37.037 0.00 0.00 0.00 3.02
123 124 8.251383 TCCAGACTCTTTTATATGAACTAGGG 57.749 38.462 0.00 0.00 0.00 3.53
124 125 8.065627 TCCAGACTCTTTTATATGAACTAGGGA 58.934 37.037 0.00 0.00 0.00 4.20
125 126 8.875168 CCAGACTCTTTTATATGAACTAGGGAT 58.125 37.037 0.00 0.00 0.00 3.85
126 127 9.921637 CAGACTCTTTTATATGAACTAGGGATC 57.078 37.037 0.00 0.00 0.00 3.36
127 128 9.661954 AGACTCTTTTATATGAACTAGGGATCA 57.338 33.333 0.00 0.00 0.00 2.92
130 131 9.717942 CTCTTTTATATGAACTAGGGATCAAGG 57.282 37.037 0.00 0.00 0.00 3.61
131 132 8.157476 TCTTTTATATGAACTAGGGATCAAGGC 58.843 37.037 0.00 0.00 0.00 4.35
132 133 7.633018 TTTATATGAACTAGGGATCAAGGCT 57.367 36.000 0.00 0.00 0.00 4.58
133 134 5.753721 ATATGAACTAGGGATCAAGGCTC 57.246 43.478 0.00 0.00 0.00 4.70
134 135 2.119495 TGAACTAGGGATCAAGGCTCC 58.881 52.381 0.00 0.00 0.00 4.70
135 136 2.119495 GAACTAGGGATCAAGGCTCCA 58.881 52.381 0.00 0.00 34.24 3.86
136 137 1.501582 ACTAGGGATCAAGGCTCCAC 58.498 55.000 0.00 0.00 34.24 4.02
137 138 1.273838 ACTAGGGATCAAGGCTCCACA 60.274 52.381 0.00 0.00 34.24 4.17
138 139 1.839994 CTAGGGATCAAGGCTCCACAA 59.160 52.381 0.00 0.00 34.24 3.33
139 140 0.622665 AGGGATCAAGGCTCCACAAG 59.377 55.000 0.00 0.00 34.24 3.16
150 151 2.086869 GCTCCACAAGCTGCAAGATTA 58.913 47.619 1.02 0.00 43.18 1.75
151 152 2.686915 GCTCCACAAGCTGCAAGATTAT 59.313 45.455 1.02 0.00 43.18 1.28
152 153 3.488721 GCTCCACAAGCTGCAAGATTATG 60.489 47.826 1.02 0.00 43.18 1.90
155 156 3.766151 CACAAGCTGCAAGATTATGGTG 58.234 45.455 1.02 0.00 43.18 4.17
156 157 3.192001 CACAAGCTGCAAGATTATGGTGT 59.808 43.478 1.02 0.00 43.18 4.16
157 158 3.192001 ACAAGCTGCAAGATTATGGTGTG 59.808 43.478 1.02 0.00 43.18 3.82
158 159 3.354948 AGCTGCAAGATTATGGTGTGA 57.645 42.857 1.02 0.00 34.07 3.58
159 160 3.012518 AGCTGCAAGATTATGGTGTGAC 58.987 45.455 1.02 0.00 34.07 3.67
160 161 2.749076 GCTGCAAGATTATGGTGTGACA 59.251 45.455 0.00 0.00 34.07 3.58
161 162 3.191162 GCTGCAAGATTATGGTGTGACAA 59.809 43.478 0.00 0.00 34.07 3.18
162 163 4.726416 CTGCAAGATTATGGTGTGACAAC 58.274 43.478 0.00 0.00 34.07 3.32
163 164 4.140536 TGCAAGATTATGGTGTGACAACA 58.859 39.130 5.49 5.49 34.75 3.33
164 165 4.766373 TGCAAGATTATGGTGTGACAACAT 59.234 37.500 20.94 20.94 44.56 2.71
165 166 5.243507 TGCAAGATTATGGTGTGACAACATT 59.756 36.000 22.37 4.20 38.83 2.71
166 167 5.574055 GCAAGATTATGGTGTGACAACATTG 59.426 40.000 22.37 14.79 38.83 2.82
167 168 5.902613 AGATTATGGTGTGACAACATTGG 57.097 39.130 22.37 0.00 38.83 3.16
168 169 5.324409 AGATTATGGTGTGACAACATTGGT 58.676 37.500 22.37 8.04 38.83 3.67
169 170 4.844998 TTATGGTGTGACAACATTGGTG 57.155 40.909 22.37 0.00 38.83 4.17
170 171 0.743688 TGGTGTGACAACATTGGTGC 59.256 50.000 0.00 0.00 38.92 5.01
171 172 0.743688 GGTGTGACAACATTGGTGCA 59.256 50.000 0.45 0.00 38.92 4.57
172 173 1.135915 GGTGTGACAACATTGGTGCAA 59.864 47.619 0.45 0.00 38.92 4.08
173 174 2.192624 GTGTGACAACATTGGTGCAAC 58.807 47.619 0.45 0.00 38.92 4.17
174 175 1.821136 TGTGACAACATTGGTGCAACA 59.179 42.857 0.00 0.00 39.98 3.33
175 176 2.429971 TGTGACAACATTGGTGCAACAT 59.570 40.909 4.62 0.00 39.98 2.71
176 177 3.633986 TGTGACAACATTGGTGCAACATA 59.366 39.130 4.62 0.00 39.98 2.29
177 178 4.280425 TGTGACAACATTGGTGCAACATAT 59.720 37.500 4.62 0.00 39.98 1.78
178 179 5.221402 TGTGACAACATTGGTGCAACATATT 60.221 36.000 4.62 0.00 39.98 1.28
179 180 5.695816 GTGACAACATTGGTGCAACATATTT 59.304 36.000 4.62 0.00 39.98 1.40
180 181 5.695363 TGACAACATTGGTGCAACATATTTG 59.305 36.000 4.62 11.52 39.98 2.32
181 182 5.609423 ACAACATTGGTGCAACATATTTGT 58.391 33.333 4.62 12.20 39.98 2.83
182 183 5.695816 ACAACATTGGTGCAACATATTTGTC 59.304 36.000 4.62 0.00 39.98 3.18
183 184 5.465532 ACATTGGTGCAACATATTTGTCA 57.534 34.783 4.62 0.00 39.98 3.58
184 185 5.472148 ACATTGGTGCAACATATTTGTCAG 58.528 37.500 4.62 0.00 39.98 3.51
185 186 3.574284 TGGTGCAACATATTTGTCAGC 57.426 42.857 0.00 6.70 39.98 4.26
186 187 2.889678 TGGTGCAACATATTTGTCAGCA 59.110 40.909 0.00 10.74 41.58 4.41
187 188 3.320256 TGGTGCAACATATTTGTCAGCAA 59.680 39.130 0.00 2.50 43.76 3.91
188 189 4.202192 TGGTGCAACATATTTGTCAGCAAA 60.202 37.500 0.00 6.93 43.76 3.68
190 191 5.062558 GGTGCAACATATTTGTCAGCAAATC 59.937 40.000 14.65 6.26 44.56 2.17
191 192 5.062558 GTGCAACATATTTGTCAGCAAATCC 59.937 40.000 14.65 3.48 43.19 3.01
192 193 7.067094 GTGCAACATATTTGTCAGCAAATCCT 61.067 38.462 14.65 0.00 43.19 3.24
193 194 8.989674 GTGCAACATATTTGTCAGCAAATCCTG 61.990 40.741 14.65 10.01 43.19 3.86
200 201 4.998671 TGTCAGCAAATCCTGTTTTTCA 57.001 36.364 0.00 0.00 34.47 2.69
201 202 5.534207 TGTCAGCAAATCCTGTTTTTCAT 57.466 34.783 0.00 0.00 34.47 2.57
202 203 5.291178 TGTCAGCAAATCCTGTTTTTCATG 58.709 37.500 0.00 0.00 34.47 3.07
203 204 4.151157 GTCAGCAAATCCTGTTTTTCATGC 59.849 41.667 0.00 0.00 34.47 4.06
204 205 4.059511 CAGCAAATCCTGTTTTTCATGCA 58.940 39.130 0.00 0.00 35.11 3.96
205 206 4.060205 AGCAAATCCTGTTTTTCATGCAC 58.940 39.130 0.00 0.00 35.11 4.57
206 207 3.120923 GCAAATCCTGTTTTTCATGCACG 60.121 43.478 0.00 0.00 33.00 5.34
207 208 4.050553 CAAATCCTGTTTTTCATGCACGT 58.949 39.130 0.00 0.00 0.00 4.49
208 209 5.218885 CAAATCCTGTTTTTCATGCACGTA 58.781 37.500 0.00 0.00 0.00 3.57
209 210 3.889196 TCCTGTTTTTCATGCACGTAC 57.111 42.857 0.00 0.00 0.00 3.67
210 211 3.206964 TCCTGTTTTTCATGCACGTACA 58.793 40.909 0.00 0.00 0.00 2.90
211 212 3.628032 TCCTGTTTTTCATGCACGTACAA 59.372 39.130 0.00 0.00 0.00 2.41
212 213 4.096532 TCCTGTTTTTCATGCACGTACAAA 59.903 37.500 0.00 0.00 0.00 2.83
213 214 4.800993 CCTGTTTTTCATGCACGTACAAAA 59.199 37.500 0.00 0.00 0.00 2.44
214 215 5.276161 CCTGTTTTTCATGCACGTACAAAAC 60.276 40.000 6.79 6.79 35.57 2.43
215 216 5.161358 TGTTTTTCATGCACGTACAAAACA 58.839 33.333 10.87 10.87 40.19 2.83
216 217 5.061064 TGTTTTTCATGCACGTACAAAACAC 59.939 36.000 10.87 4.54 38.53 3.32
217 218 4.357018 TTTCATGCACGTACAAAACACA 57.643 36.364 0.00 0.00 0.00 3.72
218 219 4.560136 TTCATGCACGTACAAAACACAT 57.440 36.364 0.00 0.00 0.00 3.21
219 220 5.674933 TTCATGCACGTACAAAACACATA 57.325 34.783 0.00 0.00 0.00 2.29
220 221 5.276240 TCATGCACGTACAAAACACATAG 57.724 39.130 0.00 0.00 0.00 2.23
221 222 4.991687 TCATGCACGTACAAAACACATAGA 59.008 37.500 0.00 0.00 0.00 1.98
222 223 4.983215 TGCACGTACAAAACACATAGAG 57.017 40.909 0.00 0.00 0.00 2.43
223 224 3.743911 TGCACGTACAAAACACATAGAGG 59.256 43.478 0.00 0.00 0.00 3.69
224 225 3.744426 GCACGTACAAAACACATAGAGGT 59.256 43.478 0.00 0.00 0.00 3.85
225 226 4.212636 GCACGTACAAAACACATAGAGGTT 59.787 41.667 0.00 0.00 0.00 3.50
226 227 5.675970 CACGTACAAAACACATAGAGGTTG 58.324 41.667 0.00 0.00 0.00 3.77
227 228 5.464057 CACGTACAAAACACATAGAGGTTGA 59.536 40.000 0.00 0.00 0.00 3.18
228 229 5.464389 ACGTACAAAACACATAGAGGTTGAC 59.536 40.000 0.00 0.00 0.00 3.18
229 230 5.694910 CGTACAAAACACATAGAGGTTGACT 59.305 40.000 0.00 0.00 0.00 3.41
230 231 6.202188 CGTACAAAACACATAGAGGTTGACTT 59.798 38.462 0.00 0.00 0.00 3.01
231 232 7.254658 CGTACAAAACACATAGAGGTTGACTTT 60.255 37.037 0.00 0.00 0.00 2.66
232 233 7.027778 ACAAAACACATAGAGGTTGACTTTC 57.972 36.000 0.00 0.00 0.00 2.62
233 234 6.601613 ACAAAACACATAGAGGTTGACTTTCA 59.398 34.615 0.00 0.00 0.00 2.69
234 235 6.619801 AAACACATAGAGGTTGACTTTCAC 57.380 37.500 0.00 0.00 0.00 3.18
235 236 5.552870 ACACATAGAGGTTGACTTTCACT 57.447 39.130 0.00 0.00 0.00 3.41
236 237 5.930135 ACACATAGAGGTTGACTTTCACTT 58.070 37.500 0.00 0.00 0.00 3.16
237 238 6.357367 ACACATAGAGGTTGACTTTCACTTT 58.643 36.000 0.00 0.00 0.00 2.66
238 239 6.260936 ACACATAGAGGTTGACTTTCACTTTG 59.739 38.462 0.00 0.00 0.00 2.77
239 240 6.260936 CACATAGAGGTTGACTTTCACTTTGT 59.739 38.462 0.00 0.00 0.00 2.83
240 241 7.441157 CACATAGAGGTTGACTTTCACTTTGTA 59.559 37.037 0.00 0.00 0.00 2.41
241 242 7.990886 ACATAGAGGTTGACTTTCACTTTGTAA 59.009 33.333 0.00 0.00 0.00 2.41
242 243 6.927294 AGAGGTTGACTTTCACTTTGTAAG 57.073 37.500 0.00 0.00 32.06 2.34
243 244 6.650120 AGAGGTTGACTTTCACTTTGTAAGA 58.350 36.000 0.17 0.00 30.62 2.10
244 245 6.763610 AGAGGTTGACTTTCACTTTGTAAGAG 59.236 38.462 0.17 0.00 30.62 2.85
245 246 6.650120 AGGTTGACTTTCACTTTGTAAGAGA 58.350 36.000 0.17 0.00 30.62 3.10
246 247 7.110155 AGGTTGACTTTCACTTTGTAAGAGAA 58.890 34.615 0.17 0.00 36.52 2.87
247 248 7.610305 AGGTTGACTTTCACTTTGTAAGAGAAA 59.390 33.333 10.23 10.23 42.89 2.52
253 254 6.604735 TTCACTTTGTAAGAGAAAGAGCAC 57.395 37.500 3.38 0.00 35.61 4.40
254 255 4.745125 TCACTTTGTAAGAGAAAGAGCACG 59.255 41.667 3.38 0.00 34.94 5.34
255 256 4.508124 CACTTTGTAAGAGAAAGAGCACGT 59.492 41.667 3.38 0.00 34.94 4.49
256 257 5.690409 CACTTTGTAAGAGAAAGAGCACGTA 59.310 40.000 3.38 0.00 34.94 3.57
257 258 6.200286 CACTTTGTAAGAGAAAGAGCACGTAA 59.800 38.462 3.38 0.00 34.94 3.18
258 259 6.421202 ACTTTGTAAGAGAAAGAGCACGTAAG 59.579 38.462 3.38 0.00 37.48 2.34
259 260 4.235360 TGTAAGAGAAAGAGCACGTAAGC 58.765 43.478 0.00 0.00 45.62 3.09
261 262 4.785511 AAGAGAAAGAGCACGTAAGCTA 57.214 40.909 0.00 0.00 46.75 3.32
262 263 4.099380 AGAGAAAGAGCACGTAAGCTAC 57.901 45.455 0.00 0.00 46.75 3.58
263 264 3.759618 AGAGAAAGAGCACGTAAGCTACT 59.240 43.478 0.00 0.00 46.75 2.57
264 265 4.218852 AGAGAAAGAGCACGTAAGCTACTT 59.781 41.667 0.00 4.10 46.75 2.24
265 266 4.238514 AGAAAGAGCACGTAAGCTACTTG 58.761 43.478 0.00 0.00 46.75 3.16
266 267 3.936372 AAGAGCACGTAAGCTACTTGA 57.064 42.857 0.00 0.00 46.75 3.02
267 268 4.457834 AAGAGCACGTAAGCTACTTGAT 57.542 40.909 0.00 0.00 46.75 2.57
268 269 5.578005 AAGAGCACGTAAGCTACTTGATA 57.422 39.130 0.00 0.00 46.75 2.15
269 270 5.776173 AGAGCACGTAAGCTACTTGATAT 57.224 39.130 0.00 0.00 46.75 1.63
270 271 5.764131 AGAGCACGTAAGCTACTTGATATC 58.236 41.667 0.00 0.00 46.75 1.63
271 272 5.299531 AGAGCACGTAAGCTACTTGATATCA 59.700 40.000 0.00 0.00 46.75 2.15
272 273 5.902681 AGCACGTAAGCTACTTGATATCAA 58.097 37.500 17.07 17.07 44.50 2.57
328 329 2.223745 TCGTGCTAGGGTTCCAAAAAC 58.776 47.619 0.00 0.00 0.00 2.43
464 465 0.108992 GTTAGTCCACGTCATCGCCA 60.109 55.000 0.00 0.00 41.18 5.69
547 548 2.659731 GCTCATGCGCTCATTAAGTC 57.340 50.000 9.73 0.00 0.00 3.01
548 549 1.935873 GCTCATGCGCTCATTAAGTCA 59.064 47.619 9.73 0.00 0.00 3.41
580 586 1.687146 CACTCTGCTCCCCTGCCTA 60.687 63.158 0.00 0.00 0.00 3.93
584 590 2.203922 TGCTCCCCTGCCTACACA 60.204 61.111 0.00 0.00 0.00 3.72
836 850 4.298626 TCATCTTGGTGAGCTAGGGTAAT 58.701 43.478 0.00 0.00 0.00 1.89
846 860 6.409349 GGTGAGCTAGGGTAATCTTTGGTTAT 60.409 42.308 0.00 0.00 0.00 1.89
942 956 0.251787 GGTTCTTGCTGGATTGGGGT 60.252 55.000 0.00 0.00 0.00 4.95
1281 1295 4.101741 AGTTGCTCTTCTGAACCTACACTT 59.898 41.667 0.00 0.00 0.00 3.16
1620 1634 2.305635 TCAGAATTGCTTGTCCAGGCTA 59.694 45.455 3.00 0.00 34.20 3.93
1693 1707 2.291209 TGAGAAGCATTTGGCCAAGA 57.709 45.000 19.48 10.42 46.50 3.02
1724 1738 2.074547 AATGACAAGCTGTGCATTGC 57.925 45.000 0.46 0.46 31.70 3.56
1994 2008 7.344352 ACAGGAGAGAGATTTGCTTAAGATAGT 59.656 37.037 6.67 0.00 0.00 2.12
2235 2249 8.100791 TCTATGCCAATGTTAAGAACTGTAGTT 58.899 33.333 0.00 0.00 41.64 2.24
2310 2324 5.755409 TCTGCCTGTATTTGAACCTCTTA 57.245 39.130 0.00 0.00 0.00 2.10
2329 2343 7.071196 ACCTCTTATGCTATGTTATGGAGTCAA 59.929 37.037 0.00 0.00 0.00 3.18
2415 2430 1.686587 GCTTTGTACCTGGGCTTTGTT 59.313 47.619 0.00 0.00 0.00 2.83
2458 2473 1.923909 GCCTACTCCACCCACCCTT 60.924 63.158 0.00 0.00 0.00 3.95
2561 2577 2.119495 GGATTCAGAGCTTGGGAGGTA 58.881 52.381 0.00 0.00 32.79 3.08
2564 2580 0.895530 TCAGAGCTTGGGAGGTAACG 59.104 55.000 0.00 0.00 46.39 3.18
2579 2595 2.101082 GGTAACGGATGAGGAAGAGGAC 59.899 54.545 0.00 0.00 0.00 3.85
2670 2686 0.250901 GTTCAAGAGGAGGCTGGCAA 60.251 55.000 3.38 0.00 0.00 4.52
2719 2735 4.346418 AGATGAGTTCACAGTTCTTGTCCT 59.654 41.667 0.00 0.00 38.16 3.85
2780 2796 2.104170 GCTAGGAGACAGGCAGTACTT 58.896 52.381 0.00 0.00 0.00 2.24
2811 2827 2.079925 CTTCTACCAGAGCAAAGTGGC 58.920 52.381 0.00 0.00 37.34 5.01
2822 2838 1.533129 GCAAAGTGGCGTCGTTTCTTT 60.533 47.619 0.00 0.00 0.00 2.52
2993 3011 3.076621 TGCATCAGTGTTGTCTGAATCC 58.923 45.455 3.24 0.00 45.65 3.01
2997 3015 2.705658 TCAGTGTTGTCTGAATCCACCT 59.294 45.455 0.00 0.00 40.82 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.896220 TTTCCTGCACTCCATGACAC 58.104 50.000 0.00 0.00 0.00 3.67
2 3 2.229792 GTTTTCCTGCACTCCATGACA 58.770 47.619 0.00 0.00 0.00 3.58
3 4 2.227388 CTGTTTTCCTGCACTCCATGAC 59.773 50.000 0.00 0.00 0.00 3.06
5 6 1.542915 CCTGTTTTCCTGCACTCCATG 59.457 52.381 0.00 0.00 0.00 3.66
6 7 1.915141 CCTGTTTTCCTGCACTCCAT 58.085 50.000 0.00 0.00 0.00 3.41
7 8 0.823356 GCCTGTTTTCCTGCACTCCA 60.823 55.000 0.00 0.00 0.00 3.86
8 9 0.538287 AGCCTGTTTTCCTGCACTCC 60.538 55.000 0.00 0.00 0.00 3.85
9 10 1.807142 GTAGCCTGTTTTCCTGCACTC 59.193 52.381 0.00 0.00 0.00 3.51
10 11 1.421646 AGTAGCCTGTTTTCCTGCACT 59.578 47.619 0.00 0.00 0.00 4.40
11 12 1.537202 CAGTAGCCTGTTTTCCTGCAC 59.463 52.381 0.00 0.00 33.80 4.57
12 13 1.896220 CAGTAGCCTGTTTTCCTGCA 58.104 50.000 0.00 0.00 33.80 4.41
22 23 1.474478 AGATCGTGACACAGTAGCCTG 59.526 52.381 6.37 0.00 44.68 4.85
23 24 1.840737 AGATCGTGACACAGTAGCCT 58.159 50.000 6.37 0.00 0.00 4.58
24 25 2.683867 ACTAGATCGTGACACAGTAGCC 59.316 50.000 6.37 0.00 0.00 3.93
25 26 4.571580 AGTACTAGATCGTGACACAGTAGC 59.428 45.833 6.37 1.77 0.00 3.58
26 27 5.811100 TCAGTACTAGATCGTGACACAGTAG 59.189 44.000 6.37 3.16 0.00 2.57
27 28 5.727434 TCAGTACTAGATCGTGACACAGTA 58.273 41.667 6.37 2.71 0.00 2.74
28 29 4.576879 TCAGTACTAGATCGTGACACAGT 58.423 43.478 6.37 3.69 0.00 3.55
29 30 5.547181 TTCAGTACTAGATCGTGACACAG 57.453 43.478 6.37 0.00 0.00 3.66
30 31 4.142665 GCTTCAGTACTAGATCGTGACACA 60.143 45.833 6.37 0.00 0.00 3.72
31 32 4.344448 GCTTCAGTACTAGATCGTGACAC 58.656 47.826 0.00 0.00 0.00 3.67
32 33 3.063588 CGCTTCAGTACTAGATCGTGACA 59.936 47.826 0.00 0.00 0.00 3.58
33 34 3.546417 CCGCTTCAGTACTAGATCGTGAC 60.546 52.174 0.00 0.00 0.00 3.67
34 35 2.612672 CCGCTTCAGTACTAGATCGTGA 59.387 50.000 0.00 0.00 0.00 4.35
35 36 2.612672 TCCGCTTCAGTACTAGATCGTG 59.387 50.000 0.00 0.00 0.00 4.35
36 37 2.915349 TCCGCTTCAGTACTAGATCGT 58.085 47.619 0.00 0.00 0.00 3.73
37 38 3.965292 TTCCGCTTCAGTACTAGATCG 57.035 47.619 0.00 0.00 0.00 3.69
38 39 8.185505 CCTTATATTCCGCTTCAGTACTAGATC 58.814 40.741 0.00 0.00 0.00 2.75
39 40 7.363094 GCCTTATATTCCGCTTCAGTACTAGAT 60.363 40.741 0.00 0.00 0.00 1.98
40 41 6.072064 GCCTTATATTCCGCTTCAGTACTAGA 60.072 42.308 0.00 0.00 0.00 2.43
41 42 6.071840 AGCCTTATATTCCGCTTCAGTACTAG 60.072 42.308 0.00 0.00 0.00 2.57
42 43 5.773680 AGCCTTATATTCCGCTTCAGTACTA 59.226 40.000 0.00 0.00 0.00 1.82
43 44 4.589374 AGCCTTATATTCCGCTTCAGTACT 59.411 41.667 0.00 0.00 0.00 2.73
44 45 4.884247 AGCCTTATATTCCGCTTCAGTAC 58.116 43.478 0.00 0.00 0.00 2.73
45 46 4.833380 AGAGCCTTATATTCCGCTTCAGTA 59.167 41.667 0.00 0.00 0.00 2.74
46 47 3.643792 AGAGCCTTATATTCCGCTTCAGT 59.356 43.478 0.00 0.00 0.00 3.41
47 48 4.264460 AGAGCCTTATATTCCGCTTCAG 57.736 45.455 0.00 0.00 0.00 3.02
48 49 4.380531 CAAGAGCCTTATATTCCGCTTCA 58.619 43.478 0.00 0.00 0.00 3.02
49 50 3.187432 GCAAGAGCCTTATATTCCGCTTC 59.813 47.826 0.00 0.00 33.58 3.86
50 51 3.142174 GCAAGAGCCTTATATTCCGCTT 58.858 45.455 0.00 0.00 33.58 4.68
51 52 2.370189 AGCAAGAGCCTTATATTCCGCT 59.630 45.455 0.00 0.00 43.56 5.52
52 53 2.772287 AGCAAGAGCCTTATATTCCGC 58.228 47.619 0.00 0.00 43.56 5.54
53 54 5.163814 GCATTAGCAAGAGCCTTATATTCCG 60.164 44.000 0.00 0.00 43.56 4.30
54 55 6.188400 GCATTAGCAAGAGCCTTATATTCC 57.812 41.667 0.00 0.00 43.56 3.01
70 71 6.020121 CACATAATTTCAGCAGTTGCATTAGC 60.020 38.462 6.90 0.00 45.16 3.09
71 72 6.474427 CCACATAATTTCAGCAGTTGCATTAG 59.526 38.462 6.90 0.00 45.16 1.73
72 73 6.152492 TCCACATAATTTCAGCAGTTGCATTA 59.848 34.615 6.90 2.49 45.16 1.90
73 74 5.047164 TCCACATAATTTCAGCAGTTGCATT 60.047 36.000 6.90 0.29 45.16 3.56
74 75 4.463539 TCCACATAATTTCAGCAGTTGCAT 59.536 37.500 6.90 0.00 45.16 3.96
75 76 3.825585 TCCACATAATTTCAGCAGTTGCA 59.174 39.130 6.90 0.00 45.16 4.08
76 77 4.439305 TCCACATAATTTCAGCAGTTGC 57.561 40.909 0.00 0.00 42.49 4.17
77 78 5.125900 TGGATCCACATAATTTCAGCAGTTG 59.874 40.000 11.44 0.00 0.00 3.16
78 79 5.263599 TGGATCCACATAATTTCAGCAGTT 58.736 37.500 11.44 0.00 0.00 3.16
79 80 4.858850 TGGATCCACATAATTTCAGCAGT 58.141 39.130 11.44 0.00 0.00 4.40
80 81 5.008415 GTCTGGATCCACATAATTTCAGCAG 59.992 44.000 11.44 0.00 0.00 4.24
81 82 4.883585 GTCTGGATCCACATAATTTCAGCA 59.116 41.667 11.44 0.00 0.00 4.41
82 83 5.128919 AGTCTGGATCCACATAATTTCAGC 58.871 41.667 11.44 0.00 0.00 4.26
83 84 6.590068 AGAGTCTGGATCCACATAATTTCAG 58.410 40.000 11.44 0.00 0.00 3.02
84 85 6.566079 AGAGTCTGGATCCACATAATTTCA 57.434 37.500 11.44 0.00 0.00 2.69
85 86 7.872113 AAAGAGTCTGGATCCACATAATTTC 57.128 36.000 11.44 2.23 0.00 2.17
86 87 9.927081 ATAAAAGAGTCTGGATCCACATAATTT 57.073 29.630 11.44 10.49 0.00 1.82
90 91 9.379770 TCATATAAAAGAGTCTGGATCCACATA 57.620 33.333 11.44 0.00 0.00 2.29
91 92 8.267620 TCATATAAAAGAGTCTGGATCCACAT 57.732 34.615 11.44 0.00 0.00 3.21
92 93 7.675161 TCATATAAAAGAGTCTGGATCCACA 57.325 36.000 11.44 0.00 0.00 4.17
93 94 8.207545 AGTTCATATAAAAGAGTCTGGATCCAC 58.792 37.037 11.44 1.59 0.00 4.02
94 95 8.324191 AGTTCATATAAAAGAGTCTGGATCCA 57.676 34.615 15.27 15.27 0.00 3.41
95 96 9.921637 CTAGTTCATATAAAAGAGTCTGGATCC 57.078 37.037 4.20 4.20 0.00 3.36
96 97 9.921637 CCTAGTTCATATAAAAGAGTCTGGATC 57.078 37.037 0.00 0.00 0.00 3.36
97 98 8.875168 CCCTAGTTCATATAAAAGAGTCTGGAT 58.125 37.037 0.00 0.00 0.00 3.41
98 99 8.065627 TCCCTAGTTCATATAAAAGAGTCTGGA 58.934 37.037 0.00 0.00 0.00 3.86
99 100 8.251383 TCCCTAGTTCATATAAAAGAGTCTGG 57.749 38.462 0.00 0.00 0.00 3.86
100 101 9.921637 GATCCCTAGTTCATATAAAAGAGTCTG 57.078 37.037 0.00 0.00 0.00 3.51
101 102 9.661954 TGATCCCTAGTTCATATAAAAGAGTCT 57.338 33.333 0.00 0.00 0.00 3.24
104 105 9.717942 CCTTGATCCCTAGTTCATATAAAAGAG 57.282 37.037 0.00 0.00 0.00 2.85
105 106 8.157476 GCCTTGATCCCTAGTTCATATAAAAGA 58.843 37.037 0.00 0.00 0.00 2.52
106 107 8.160106 AGCCTTGATCCCTAGTTCATATAAAAG 58.840 37.037 0.00 0.00 0.00 2.27
107 108 8.045720 AGCCTTGATCCCTAGTTCATATAAAA 57.954 34.615 0.00 0.00 0.00 1.52
108 109 7.256691 GGAGCCTTGATCCCTAGTTCATATAAA 60.257 40.741 0.00 0.00 31.04 1.40
109 110 6.213600 GGAGCCTTGATCCCTAGTTCATATAA 59.786 42.308 0.00 0.00 31.04 0.98
110 111 5.721960 GGAGCCTTGATCCCTAGTTCATATA 59.278 44.000 0.00 0.00 31.04 0.86
111 112 4.534103 GGAGCCTTGATCCCTAGTTCATAT 59.466 45.833 0.00 0.00 31.04 1.78
112 113 3.904339 GGAGCCTTGATCCCTAGTTCATA 59.096 47.826 0.00 0.00 31.04 2.15
113 114 2.708325 GGAGCCTTGATCCCTAGTTCAT 59.292 50.000 0.00 0.00 31.04 2.57
114 115 2.119495 GGAGCCTTGATCCCTAGTTCA 58.881 52.381 0.00 0.00 31.04 3.18
115 116 2.119495 TGGAGCCTTGATCCCTAGTTC 58.881 52.381 0.00 0.00 37.30 3.01
116 117 1.840635 GTGGAGCCTTGATCCCTAGTT 59.159 52.381 0.00 0.00 37.30 2.24
117 118 1.273838 TGTGGAGCCTTGATCCCTAGT 60.274 52.381 0.00 0.00 37.30 2.57
118 119 1.500474 TGTGGAGCCTTGATCCCTAG 58.500 55.000 0.00 0.00 37.30 3.02
119 120 1.839994 CTTGTGGAGCCTTGATCCCTA 59.160 52.381 0.00 0.00 37.30 3.53
120 121 0.622665 CTTGTGGAGCCTTGATCCCT 59.377 55.000 0.00 0.00 37.30 4.20
121 122 1.034292 GCTTGTGGAGCCTTGATCCC 61.034 60.000 0.00 0.00 46.01 3.85
122 123 2.486796 GCTTGTGGAGCCTTGATCC 58.513 57.895 0.00 0.00 46.01 3.36
131 132 3.066342 CCATAATCTTGCAGCTTGTGGAG 59.934 47.826 12.45 0.00 35.46 3.86
132 133 3.018856 CCATAATCTTGCAGCTTGTGGA 58.981 45.455 12.45 0.00 35.46 4.02
133 134 2.756760 ACCATAATCTTGCAGCTTGTGG 59.243 45.455 14.83 14.83 38.20 4.17
134 135 3.192001 ACACCATAATCTTGCAGCTTGTG 59.808 43.478 0.00 0.00 0.00 3.33
135 136 3.192001 CACACCATAATCTTGCAGCTTGT 59.808 43.478 0.00 0.00 0.00 3.16
136 137 3.441222 TCACACCATAATCTTGCAGCTTG 59.559 43.478 0.00 0.00 0.00 4.01
137 138 3.441572 GTCACACCATAATCTTGCAGCTT 59.558 43.478 0.00 0.00 0.00 3.74
138 139 3.012518 GTCACACCATAATCTTGCAGCT 58.987 45.455 0.00 0.00 0.00 4.24
139 140 2.749076 TGTCACACCATAATCTTGCAGC 59.251 45.455 0.00 0.00 0.00 5.25
140 141 4.216042 TGTTGTCACACCATAATCTTGCAG 59.784 41.667 0.00 0.00 0.00 4.41
141 142 4.140536 TGTTGTCACACCATAATCTTGCA 58.859 39.130 0.00 0.00 0.00 4.08
142 143 4.764679 TGTTGTCACACCATAATCTTGC 57.235 40.909 0.00 0.00 0.00 4.01
143 144 6.094719 CCAATGTTGTCACACCATAATCTTG 58.905 40.000 0.00 0.00 35.03 3.02
144 145 5.774690 ACCAATGTTGTCACACCATAATCTT 59.225 36.000 0.00 0.00 35.03 2.40
145 146 5.183713 CACCAATGTTGTCACACCATAATCT 59.816 40.000 0.00 0.00 35.03 2.40
146 147 5.401550 CACCAATGTTGTCACACCATAATC 58.598 41.667 0.00 0.00 35.03 1.75
147 148 4.321899 GCACCAATGTTGTCACACCATAAT 60.322 41.667 0.00 0.00 35.03 1.28
148 149 3.005261 GCACCAATGTTGTCACACCATAA 59.995 43.478 0.00 0.00 35.03 1.90
149 150 2.556189 GCACCAATGTTGTCACACCATA 59.444 45.455 0.00 0.00 35.03 2.74
150 151 1.340889 GCACCAATGTTGTCACACCAT 59.659 47.619 0.00 0.00 35.03 3.55
151 152 0.743688 GCACCAATGTTGTCACACCA 59.256 50.000 0.00 0.00 35.03 4.17
152 153 0.743688 TGCACCAATGTTGTCACACC 59.256 50.000 0.00 0.00 35.03 4.16
153 154 2.192624 GTTGCACCAATGTTGTCACAC 58.807 47.619 0.00 0.00 35.03 3.82
154 155 1.821136 TGTTGCACCAATGTTGTCACA 59.179 42.857 0.00 0.00 37.31 3.58
155 156 2.575694 TGTTGCACCAATGTTGTCAC 57.424 45.000 0.00 0.00 0.00 3.67
156 157 5.465532 AATATGTTGCACCAATGTTGTCA 57.534 34.783 0.00 0.00 0.00 3.58
157 158 5.695816 ACAAATATGTTGCACCAATGTTGTC 59.304 36.000 4.62 0.00 35.91 3.18
158 159 5.609423 ACAAATATGTTGCACCAATGTTGT 58.391 33.333 4.62 4.62 35.91 3.32
159 160 5.695363 TGACAAATATGTTGCACCAATGTTG 59.305 36.000 0.00 0.00 40.74 3.33
160 161 5.851720 TGACAAATATGTTGCACCAATGTT 58.148 33.333 0.00 0.00 40.74 2.71
161 162 5.465532 TGACAAATATGTTGCACCAATGT 57.534 34.783 0.00 0.00 40.74 2.71
162 163 4.327898 GCTGACAAATATGTTGCACCAATG 59.672 41.667 0.00 0.00 40.74 2.82
163 164 4.021280 TGCTGACAAATATGTTGCACCAAT 60.021 37.500 0.00 0.00 41.23 3.16
164 165 3.320256 TGCTGACAAATATGTTGCACCAA 59.680 39.130 0.00 0.00 41.23 3.67
165 166 2.889678 TGCTGACAAATATGTTGCACCA 59.110 40.909 0.00 0.00 41.23 4.17
166 167 3.574284 TGCTGACAAATATGTTGCACC 57.426 42.857 0.00 0.00 41.23 5.01
178 179 5.336150 TGAAAAACAGGATTTGCTGACAA 57.664 34.783 6.06 0.00 0.00 3.18
179 180 4.998671 TGAAAAACAGGATTTGCTGACA 57.001 36.364 6.06 0.00 0.00 3.58
180 181 4.151157 GCATGAAAAACAGGATTTGCTGAC 59.849 41.667 6.06 0.00 31.40 3.51
181 182 4.202233 TGCATGAAAAACAGGATTTGCTGA 60.202 37.500 6.06 0.00 32.69 4.26
182 183 4.059511 TGCATGAAAAACAGGATTTGCTG 58.940 39.130 0.00 0.00 32.69 4.41
183 184 4.060205 GTGCATGAAAAACAGGATTTGCT 58.940 39.130 0.00 0.00 32.69 3.91
184 185 3.120923 CGTGCATGAAAAACAGGATTTGC 60.121 43.478 0.00 0.00 31.40 3.68
185 186 4.050553 ACGTGCATGAAAAACAGGATTTG 58.949 39.130 14.17 0.00 31.40 2.32
186 187 4.320608 ACGTGCATGAAAAACAGGATTT 57.679 36.364 14.17 0.00 31.40 2.17
187 188 4.277174 TGTACGTGCATGAAAAACAGGATT 59.723 37.500 14.17 0.00 31.40 3.01
188 189 3.818210 TGTACGTGCATGAAAAACAGGAT 59.182 39.130 14.17 0.00 31.40 3.24
189 190 3.206964 TGTACGTGCATGAAAAACAGGA 58.793 40.909 14.17 0.00 31.40 3.86
190 191 3.617540 TGTACGTGCATGAAAAACAGG 57.382 42.857 14.17 0.00 0.00 4.00
191 192 5.287274 TGTTTTGTACGTGCATGAAAAACAG 59.713 36.000 28.00 5.37 40.58 3.16
192 193 5.061064 GTGTTTTGTACGTGCATGAAAAACA 59.939 36.000 28.00 28.00 42.19 2.83
193 194 5.061064 TGTGTTTTGTACGTGCATGAAAAAC 59.939 36.000 25.35 25.35 37.78 2.43
194 195 5.161358 TGTGTTTTGTACGTGCATGAAAAA 58.839 33.333 14.17 12.73 0.00 1.94
195 196 4.733850 TGTGTTTTGTACGTGCATGAAAA 58.266 34.783 14.17 6.42 0.00 2.29
196 197 4.357018 TGTGTTTTGTACGTGCATGAAA 57.643 36.364 14.17 3.15 0.00 2.69
197 198 4.560136 ATGTGTTTTGTACGTGCATGAA 57.440 36.364 14.17 3.01 0.00 2.57
198 199 4.991687 TCTATGTGTTTTGTACGTGCATGA 59.008 37.500 14.17 0.00 0.00 3.07
199 200 5.276240 TCTATGTGTTTTGTACGTGCATG 57.724 39.130 7.30 3.82 0.00 4.06
200 201 4.391830 CCTCTATGTGTTTTGTACGTGCAT 59.608 41.667 7.30 0.00 0.00 3.96
201 202 3.743911 CCTCTATGTGTTTTGTACGTGCA 59.256 43.478 0.82 0.82 0.00 4.57
202 203 3.744426 ACCTCTATGTGTTTTGTACGTGC 59.256 43.478 0.00 0.00 0.00 5.34
203 204 5.464057 TCAACCTCTATGTGTTTTGTACGTG 59.536 40.000 0.00 0.00 0.00 4.49
204 205 5.464389 GTCAACCTCTATGTGTTTTGTACGT 59.536 40.000 0.00 0.00 0.00 3.57
205 206 5.694910 AGTCAACCTCTATGTGTTTTGTACG 59.305 40.000 0.00 0.00 0.00 3.67
206 207 7.492352 AAGTCAACCTCTATGTGTTTTGTAC 57.508 36.000 0.00 0.00 0.00 2.90
207 208 7.771361 TGAAAGTCAACCTCTATGTGTTTTGTA 59.229 33.333 0.00 0.00 0.00 2.41
208 209 6.601613 TGAAAGTCAACCTCTATGTGTTTTGT 59.398 34.615 0.00 0.00 0.00 2.83
209 210 6.912591 GTGAAAGTCAACCTCTATGTGTTTTG 59.087 38.462 0.00 0.00 0.00 2.44
210 211 6.828785 AGTGAAAGTCAACCTCTATGTGTTTT 59.171 34.615 0.00 0.00 0.00 2.43
211 212 6.357367 AGTGAAAGTCAACCTCTATGTGTTT 58.643 36.000 0.00 0.00 0.00 2.83
212 213 5.930135 AGTGAAAGTCAACCTCTATGTGTT 58.070 37.500 0.00 0.00 0.00 3.32
213 214 5.552870 AGTGAAAGTCAACCTCTATGTGT 57.447 39.130 0.00 0.00 0.00 3.72
214 215 6.260936 ACAAAGTGAAAGTCAACCTCTATGTG 59.739 38.462 0.00 0.00 0.00 3.21
215 216 6.357367 ACAAAGTGAAAGTCAACCTCTATGT 58.643 36.000 0.00 0.00 0.00 2.29
216 217 6.867662 ACAAAGTGAAAGTCAACCTCTATG 57.132 37.500 0.00 0.00 0.00 2.23
217 218 8.429641 TCTTACAAAGTGAAAGTCAACCTCTAT 58.570 33.333 0.00 0.00 0.00 1.98
218 219 7.788026 TCTTACAAAGTGAAAGTCAACCTCTA 58.212 34.615 0.00 0.00 0.00 2.43
219 220 6.650120 TCTTACAAAGTGAAAGTCAACCTCT 58.350 36.000 0.00 0.00 0.00 3.69
220 221 6.761714 TCTCTTACAAAGTGAAAGTCAACCTC 59.238 38.462 0.00 0.00 0.00 3.85
221 222 6.650120 TCTCTTACAAAGTGAAAGTCAACCT 58.350 36.000 0.00 0.00 0.00 3.50
222 223 6.920569 TCTCTTACAAAGTGAAAGTCAACC 57.079 37.500 0.00 0.00 0.00 3.77
229 230 6.238103 CGTGCTCTTTCTCTTACAAAGTGAAA 60.238 38.462 13.29 13.29 44.23 2.69
230 231 5.234329 CGTGCTCTTTCTCTTACAAAGTGAA 59.766 40.000 1.20 1.20 38.73 3.18
231 232 4.745125 CGTGCTCTTTCTCTTACAAAGTGA 59.255 41.667 0.00 0.00 33.32 3.41
232 233 4.508124 ACGTGCTCTTTCTCTTACAAAGTG 59.492 41.667 0.00 0.00 33.32 3.16
233 234 4.694339 ACGTGCTCTTTCTCTTACAAAGT 58.306 39.130 0.00 0.00 33.32 2.66
234 235 6.616682 GCTTACGTGCTCTTTCTCTTACAAAG 60.617 42.308 0.00 0.00 32.89 2.77
235 236 5.176958 GCTTACGTGCTCTTTCTCTTACAAA 59.823 40.000 0.00 0.00 0.00 2.83
236 237 4.684703 GCTTACGTGCTCTTTCTCTTACAA 59.315 41.667 0.00 0.00 0.00 2.41
237 238 4.022242 AGCTTACGTGCTCTTTCTCTTACA 60.022 41.667 0.00 0.00 39.34 2.41
238 239 4.487019 AGCTTACGTGCTCTTTCTCTTAC 58.513 43.478 0.00 0.00 39.34 2.34
239 240 4.785511 AGCTTACGTGCTCTTTCTCTTA 57.214 40.909 0.00 0.00 39.34 2.10
240 241 3.669251 AGCTTACGTGCTCTTTCTCTT 57.331 42.857 0.00 0.00 39.34 2.85
241 242 3.759618 AGTAGCTTACGTGCTCTTTCTCT 59.240 43.478 3.33 0.00 42.97 3.10
242 243 4.099380 AGTAGCTTACGTGCTCTTTCTC 57.901 45.455 3.33 0.00 42.97 2.87
243 244 4.022242 TCAAGTAGCTTACGTGCTCTTTCT 60.022 41.667 3.33 0.00 42.97 2.52
244 245 4.235360 TCAAGTAGCTTACGTGCTCTTTC 58.765 43.478 3.33 0.00 42.97 2.62
245 246 4.252971 TCAAGTAGCTTACGTGCTCTTT 57.747 40.909 3.33 0.00 42.97 2.52
246 247 3.936372 TCAAGTAGCTTACGTGCTCTT 57.064 42.857 3.33 5.46 42.97 2.85
247 248 5.299531 TGATATCAAGTAGCTTACGTGCTCT 59.700 40.000 1.98 0.00 42.97 4.09
248 249 5.520632 TGATATCAAGTAGCTTACGTGCTC 58.479 41.667 1.98 0.00 42.97 4.26
249 250 5.515797 TGATATCAAGTAGCTTACGTGCT 57.484 39.130 1.98 5.65 46.11 4.40
250 251 6.204075 CTTGATATCAAGTAGCTTACGTGC 57.796 41.667 29.70 0.00 46.11 5.34
532 533 3.397482 GGAGATGACTTAATGAGCGCAT 58.603 45.455 11.47 0.00 35.92 4.73
547 548 1.217689 AGAGTGAGAGGGAGGGAGATG 59.782 57.143 0.00 0.00 0.00 2.90
548 549 1.217689 CAGAGTGAGAGGGAGGGAGAT 59.782 57.143 0.00 0.00 0.00 2.75
580 586 2.230992 GAGTGAGAGCAGAGATGTGTGT 59.769 50.000 0.00 0.00 0.00 3.72
584 590 2.754552 GTGAGAGTGAGAGCAGAGATGT 59.245 50.000 0.00 0.00 0.00 3.06
836 850 9.742144 TGCCTACTAAATAACAATAACCAAAGA 57.258 29.630 0.00 0.00 0.00 2.52
846 860 7.057894 CCATAACCCTGCCTACTAAATAACAA 58.942 38.462 0.00 0.00 0.00 2.83
970 984 6.435277 ACATCAACAAAATCACCTTAGCTCAT 59.565 34.615 0.00 0.00 0.00 2.90
1019 1033 0.034896 GAAAAGAGGCTCCACGGTGA 59.965 55.000 11.71 0.00 0.00 4.02
1327 1341 9.646522 AAGCATTTTTGATAGTAACCATATCCT 57.353 29.630 0.00 0.00 0.00 3.24
1489 1503 8.389779 TCACTAAGTGCACTCAATTTCATAAA 57.610 30.769 21.95 0.00 32.30 1.40
1530 1544 2.936202 ACACCTTCACTCTGCATTTGT 58.064 42.857 0.00 0.00 0.00 2.83
1693 1707 7.365741 CACAGCTTGTCATTTTCAGTCTTAAT 58.634 34.615 0.00 0.00 0.00 1.40
1724 1738 2.869801 TCTTGGACAAGCTTTGTGTACG 59.130 45.455 7.18 0.00 45.52 3.67
1994 2008 0.251474 ATGCTCAAGCTTGGCCTTCA 60.251 50.000 25.73 15.71 42.66 3.02
2235 2249 6.122277 AGCATTAAAGGTTCTAGCAGCATAA 58.878 36.000 0.00 0.00 0.00 1.90
2284 2298 4.666512 AGGTTCAAATACAGGCAGAACAT 58.333 39.130 0.00 0.00 40.11 2.71
2310 2324 9.445878 CTTATCATTGACTCCATAACATAGCAT 57.554 33.333 0.00 0.00 0.00 3.79
2329 2343 4.639334 CATACTCCAGCAGTGCTTATCAT 58.361 43.478 16.89 2.51 36.40 2.45
2415 2430 7.057894 CCTAGGTTTGTAAATATAACTGGGCA 58.942 38.462 0.00 0.00 0.00 5.36
2458 2473 5.011125 GGAGTAGGCTATTTATGAGCAGTGA 59.989 44.000 0.00 0.00 41.98 3.41
2545 2560 0.895530 CGTTACCTCCCAAGCTCTGA 59.104 55.000 0.00 0.00 0.00 3.27
2561 2577 0.818296 CGTCCTCTTCCTCATCCGTT 59.182 55.000 0.00 0.00 0.00 4.44
2564 2580 0.103937 CTGCGTCCTCTTCCTCATCC 59.896 60.000 0.00 0.00 0.00 3.51
2588 2604 1.985614 CCTCCTCACATCCACTGCA 59.014 57.895 0.00 0.00 0.00 4.41
2670 2686 4.630644 TGCACTTCTCCAAGATCTTCTT 57.369 40.909 4.57 0.00 37.14 2.52
2780 2796 0.116342 TGGTAGAAGGGTGAGGAGCA 59.884 55.000 0.00 0.00 0.00 4.26
2811 2827 3.358700 TCGTAACGATCAAAGAAACGACG 59.641 43.478 0.00 0.00 33.44 5.12
2822 2838 5.055642 ACAACTCTCAATCGTAACGATCA 57.944 39.130 0.00 0.00 46.30 2.92
2925 2943 6.548622 ACATTCATAGATTCCACCATCCAAAG 59.451 38.462 0.00 0.00 0.00 2.77
2993 3011 4.693283 TGAGTGTTTGTGACTTCTAGGTG 58.307 43.478 0.00 0.00 0.00 4.00
2997 3015 5.353394 AACCTGAGTGTTTGTGACTTCTA 57.647 39.130 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.