Multiple sequence alignment - TraesCS3A01G525200

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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 TraesCS3A01G525200 chr3A 100.000 3347 0 0 1 3347 739523066 739519720 0.000000e+00 6181
1 TraesCS3A01G525200 chr3A 78.871 762 101 30 2500 3247 743186911 743186196 8.460000e-126 460
2 TraesCS3A01G525200 chr3D 91.643 3171 143 62 265 3347 607069412 607066276 0.000000e+00 4276
3 TraesCS3A01G525200 chr3D 80.159 630 88 19 2500 3122 609621188 609620589 1.430000e-118 436
4 TraesCS3A01G525200 chr3B 90.739 2354 132 42 475 2751 816524492 816522148 0.000000e+00 3061
5 TraesCS3A01G525200 chr3B 91.983 474 31 4 2875 3347 816522065 816521598 0.000000e+00 658
6 TraesCS3A01G525200 chr3B 78.220 753 110 22 2500 3246 820499974 820499270 1.840000e-117 433


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 TraesCS3A01G525200 chr3A 739519720 739523066 3346 True 6181.0 6181 100.000 1 3347 1 chr3A.!!$R1 3346
1 TraesCS3A01G525200 chr3A 743186196 743186911 715 True 460.0 460 78.871 2500 3247 1 chr3A.!!$R2 747
2 TraesCS3A01G525200 chr3D 607066276 607069412 3136 True 4276.0 4276 91.643 265 3347 1 chr3D.!!$R1 3082
3 TraesCS3A01G525200 chr3D 609620589 609621188 599 True 436.0 436 80.159 2500 3122 1 chr3D.!!$R2 622
4 TraesCS3A01G525200 chr3B 816521598 816524492 2894 True 1859.5 3061 91.361 475 3347 2 chr3B.!!$R2 2872
5 TraesCS3A01G525200 chr3B 820499270 820499974 704 True 433.0 433 78.220 2500 3246 1 chr3B.!!$R1 746

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
70 71 0.037326 ATTGATGTCGTGCTCACCGT 60.037 50.0 0.00 0.00 0.00 4.83 F
124 125 0.039256 CACCAAGGGTTGCAACATCG 60.039 55.0 29.55 14.79 31.02 3.84 F
840 926 0.106894 GAATCCAGTCCGACATCCCC 59.893 60.0 0.40 0.00 0.00 4.81 F
863 949 0.930742 CGCTCGCTGAATCCTCGTAC 60.931 60.0 0.00 0.00 0.00 3.67 F
885 975 1.355971 TAATTTCTCGGCGTGCAGAC 58.644 50.0 6.85 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1316 1442 0.250338 GGTGAAGCGGAAGAACTGGT 60.250 55.000 0.00 0.00 37.17 4.00 R
1914 2040 0.958091 CATCAGCCCCAAACACGAAA 59.042 50.000 0.00 0.00 0.00 3.46 R
2115 2241 1.269958 ACCTGTCTGCTAGCATCACA 58.730 50.000 19.72 21.23 0.00 3.58 R
2160 2286 2.000447 GAGAGCACAAACCGGTACATC 59.000 52.381 8.00 0.38 0.00 3.06 R
2364 2490 2.088423 CTGCTATAACCCGGTTTTGCA 58.912 47.619 8.44 14.53 0.00 4.08 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.532115 AAGCGGCATCAAAACATCCC 59.468 50.000 1.45 0.00 0.00 3.85
21 22 1.141665 GCGGCATCAAAACATCCCC 59.858 57.895 0.00 0.00 0.00 4.81
22 23 1.433064 CGGCATCAAAACATCCCCG 59.567 57.895 0.00 0.00 0.00 5.73
23 24 1.815866 GGCATCAAAACATCCCCGG 59.184 57.895 0.00 0.00 0.00 5.73
24 25 0.970427 GGCATCAAAACATCCCCGGT 60.970 55.000 0.00 0.00 0.00 5.28
25 26 0.173255 GCATCAAAACATCCCCGGTG 59.827 55.000 0.00 0.00 0.00 4.94
26 27 1.544724 CATCAAAACATCCCCGGTGT 58.455 50.000 0.00 0.00 0.00 4.16
27 28 1.892474 CATCAAAACATCCCCGGTGTT 59.108 47.619 0.00 1.13 41.28 3.32
28 29 1.323412 TCAAAACATCCCCGGTGTTG 58.677 50.000 9.46 1.54 39.57 3.33
29 30 1.036707 CAAAACATCCCCGGTGTTGT 58.963 50.000 9.46 2.21 39.57 3.32
30 31 2.158652 TCAAAACATCCCCGGTGTTGTA 60.159 45.455 9.46 0.00 39.57 2.41
31 32 2.194201 AAACATCCCCGGTGTTGTAG 57.806 50.000 9.46 0.00 39.57 2.74
32 33 1.354101 AACATCCCCGGTGTTGTAGA 58.646 50.000 8.04 0.00 38.31 2.59
33 34 0.902531 ACATCCCCGGTGTTGTAGAG 59.097 55.000 0.00 0.00 0.00 2.43
34 35 0.902531 CATCCCCGGTGTTGTAGAGT 59.097 55.000 0.00 0.00 0.00 3.24
35 36 0.902531 ATCCCCGGTGTTGTAGAGTG 59.097 55.000 0.00 0.00 0.00 3.51
36 37 1.375523 CCCCGGTGTTGTAGAGTGC 60.376 63.158 0.00 0.00 0.00 4.40
37 38 1.671742 CCCGGTGTTGTAGAGTGCT 59.328 57.895 0.00 0.00 0.00 4.40
38 39 0.389948 CCCGGTGTTGTAGAGTGCTC 60.390 60.000 0.00 0.00 0.00 4.26
39 40 0.732880 CCGGTGTTGTAGAGTGCTCG 60.733 60.000 0.00 0.00 34.09 5.03
40 41 0.039437 CGGTGTTGTAGAGTGCTCGT 60.039 55.000 0.00 0.00 34.09 4.18
41 42 1.699343 GGTGTTGTAGAGTGCTCGTC 58.301 55.000 0.00 0.00 34.09 4.20
42 43 1.269998 GGTGTTGTAGAGTGCTCGTCT 59.730 52.381 0.00 0.00 34.09 4.18
43 44 2.320367 GTGTTGTAGAGTGCTCGTCTG 58.680 52.381 0.00 0.00 34.09 3.51
44 45 1.335964 TGTTGTAGAGTGCTCGTCTGC 60.336 52.381 0.00 0.00 34.09 4.26
45 46 0.109735 TTGTAGAGTGCTCGTCTGCG 60.110 55.000 0.00 0.00 39.92 5.18
46 47 0.953960 TGTAGAGTGCTCGTCTGCGA 60.954 55.000 0.00 0.00 45.79 5.10
47 48 0.521659 GTAGAGTGCTCGTCTGCGAC 60.522 60.000 0.00 0.00 42.81 5.19
48 49 0.953960 TAGAGTGCTCGTCTGCGACA 60.954 55.000 8.91 0.00 42.81 4.35
49 50 1.153939 GAGTGCTCGTCTGCGACAT 60.154 57.895 8.91 0.00 42.81 3.06
50 51 1.136872 GAGTGCTCGTCTGCGACATC 61.137 60.000 8.91 0.00 42.81 3.06
51 52 1.444383 GTGCTCGTCTGCGACATCA 60.444 57.895 8.91 1.69 42.81 3.07
52 53 0.803768 GTGCTCGTCTGCGACATCAT 60.804 55.000 8.91 0.00 42.81 2.45
53 54 0.108662 TGCTCGTCTGCGACATCATT 60.109 50.000 8.91 0.00 42.81 2.57
54 55 0.299895 GCTCGTCTGCGACATCATTG 59.700 55.000 8.91 0.00 42.81 2.82
55 56 1.913317 CTCGTCTGCGACATCATTGA 58.087 50.000 8.91 0.00 42.81 2.57
56 57 2.467838 CTCGTCTGCGACATCATTGAT 58.532 47.619 8.91 0.00 42.81 2.57
57 58 2.195922 TCGTCTGCGACATCATTGATG 58.804 47.619 22.22 22.22 42.81 3.07
67 68 3.314763 CATCATTGATGTCGTGCTCAC 57.685 47.619 16.93 0.00 35.54 3.51
68 69 1.725641 TCATTGATGTCGTGCTCACC 58.274 50.000 0.00 0.00 0.00 4.02
69 70 0.371301 CATTGATGTCGTGCTCACCG 59.629 55.000 0.00 0.00 0.00 4.94
70 71 0.037326 ATTGATGTCGTGCTCACCGT 60.037 50.000 0.00 0.00 0.00 4.83
71 72 0.943835 TTGATGTCGTGCTCACCGTG 60.944 55.000 0.00 0.00 0.00 4.94
72 73 1.372997 GATGTCGTGCTCACCGTGT 60.373 57.895 0.00 0.00 0.00 4.49
73 74 0.944311 GATGTCGTGCTCACCGTGTT 60.944 55.000 0.00 0.00 0.00 3.32
74 75 1.221466 ATGTCGTGCTCACCGTGTTG 61.221 55.000 0.00 0.00 0.00 3.33
75 76 2.964925 TCGTGCTCACCGTGTTGC 60.965 61.111 10.73 10.73 0.00 4.17
76 77 3.268603 CGTGCTCACCGTGTTGCA 61.269 61.111 14.59 14.59 0.00 4.08
77 78 2.818487 CGTGCTCACCGTGTTGCAA 61.818 57.895 18.30 0.00 37.17 4.08
78 79 1.654220 GTGCTCACCGTGTTGCAAT 59.346 52.632 18.30 0.00 37.17 3.56
79 80 0.661187 GTGCTCACCGTGTTGCAATG 60.661 55.000 18.30 0.00 37.17 2.82
80 81 1.081242 GCTCACCGTGTTGCAATGG 60.081 57.895 0.59 8.13 0.00 3.16
81 82 1.580942 CTCACCGTGTTGCAATGGG 59.419 57.895 16.62 13.76 0.00 4.00
82 83 1.152860 TCACCGTGTTGCAATGGGT 60.153 52.632 16.62 14.30 0.00 4.51
83 84 1.007502 CACCGTGTTGCAATGGGTG 60.008 57.895 23.33 23.33 41.81 4.61
84 85 2.199652 ACCGTGTTGCAATGGGTGG 61.200 57.895 15.54 10.30 0.00 4.61
85 86 2.049248 CGTGTTGCAATGGGTGGC 60.049 61.111 0.59 0.00 0.00 5.01
86 87 2.343387 GTGTTGCAATGGGTGGCC 59.657 61.111 0.59 0.00 0.00 5.36
87 88 3.301554 TGTTGCAATGGGTGGCCG 61.302 61.111 0.59 0.00 0.00 6.13
88 89 3.302344 GTTGCAATGGGTGGCCGT 61.302 61.111 0.59 0.00 0.00 5.68
89 90 3.301554 TTGCAATGGGTGGCCGTG 61.302 61.111 0.00 0.00 0.00 4.94
107 108 3.103911 CCGACGGCGTGAGTTCAC 61.104 66.667 21.19 0.00 43.15 3.18
108 109 3.103911 CGACGGCGTGAGTTCACC 61.104 66.667 21.19 0.00 43.66 4.02
109 110 2.028484 GACGGCGTGAGTTCACCA 59.972 61.111 21.19 0.00 43.66 4.17
110 111 1.593209 GACGGCGTGAGTTCACCAA 60.593 57.895 21.19 0.00 43.66 3.67
111 112 1.557443 GACGGCGTGAGTTCACCAAG 61.557 60.000 21.19 1.35 43.66 3.61
112 113 2.317609 CGGCGTGAGTTCACCAAGG 61.318 63.158 0.00 0.00 43.66 3.61
113 114 1.966451 GGCGTGAGTTCACCAAGGG 60.966 63.158 6.68 0.00 43.66 3.95
114 115 1.227853 GCGTGAGTTCACCAAGGGT 60.228 57.895 6.68 0.00 43.66 4.34
115 116 0.818040 GCGTGAGTTCACCAAGGGTT 60.818 55.000 6.68 0.00 43.66 4.11
116 117 0.944386 CGTGAGTTCACCAAGGGTTG 59.056 55.000 6.68 0.00 43.66 3.77
117 118 0.668535 GTGAGTTCACCAAGGGTTGC 59.331 55.000 0.72 0.00 40.85 4.17
118 119 0.257328 TGAGTTCACCAAGGGTTGCA 59.743 50.000 0.00 0.00 31.02 4.08
119 120 1.341482 TGAGTTCACCAAGGGTTGCAA 60.341 47.619 0.00 0.00 31.02 4.08
120 121 1.067060 GAGTTCACCAAGGGTTGCAAC 59.933 52.381 21.59 21.59 31.02 4.17
121 122 0.820871 GTTCACCAAGGGTTGCAACA 59.179 50.000 29.55 4.87 31.02 3.33
122 123 1.412343 GTTCACCAAGGGTTGCAACAT 59.588 47.619 29.55 15.65 31.02 2.71
123 124 1.327303 TCACCAAGGGTTGCAACATC 58.673 50.000 29.55 20.40 31.02 3.06
124 125 0.039256 CACCAAGGGTTGCAACATCG 60.039 55.000 29.55 14.79 31.02 3.84
125 126 0.467290 ACCAAGGGTTGCAACATCGT 60.467 50.000 29.55 16.52 27.29 3.73
126 127 0.240945 CCAAGGGTTGCAACATCGTC 59.759 55.000 29.55 12.59 0.00 4.20
127 128 1.238439 CAAGGGTTGCAACATCGTCT 58.762 50.000 29.55 15.30 0.00 4.18
128 129 1.197721 CAAGGGTTGCAACATCGTCTC 59.802 52.381 29.55 11.16 0.00 3.36
129 130 0.321653 AGGGTTGCAACATCGTCTCC 60.322 55.000 29.55 19.16 0.00 3.71
130 131 1.635663 GGGTTGCAACATCGTCTCCG 61.636 60.000 29.55 0.00 0.00 4.63
131 132 0.949105 GGTTGCAACATCGTCTCCGT 60.949 55.000 29.55 0.00 35.01 4.69
132 133 0.865769 GTTGCAACATCGTCTCCGTT 59.134 50.000 24.52 0.00 35.01 4.44
133 134 0.865111 TTGCAACATCGTCTCCGTTG 59.135 50.000 0.00 0.00 42.29 4.10
135 136 2.527671 CAACATCGTCTCCGTTGCA 58.472 52.632 0.00 0.00 37.30 4.08
136 137 0.439985 CAACATCGTCTCCGTTGCAG 59.560 55.000 0.00 0.00 37.30 4.41
137 138 0.317160 AACATCGTCTCCGTTGCAGA 59.683 50.000 0.00 0.00 37.30 4.26
138 139 0.109086 ACATCGTCTCCGTTGCAGAG 60.109 55.000 0.00 0.00 37.30 3.35
139 140 0.803768 CATCGTCTCCGTTGCAGAGG 60.804 60.000 3.38 3.38 35.01 3.69
140 141 1.251527 ATCGTCTCCGTTGCAGAGGT 61.252 55.000 9.02 0.00 35.01 3.85
141 142 1.006102 CGTCTCCGTTGCAGAGGTT 60.006 57.895 9.02 0.00 31.96 3.50
142 143 1.284982 CGTCTCCGTTGCAGAGGTTG 61.285 60.000 9.02 4.78 31.96 3.77
151 152 4.335647 CAGAGGTTGCCGGGCACT 62.336 66.667 23.78 17.00 38.71 4.40
152 153 3.570212 AGAGGTTGCCGGGCACTT 61.570 61.111 23.78 13.33 38.71 3.16
153 154 2.597510 GAGGTTGCCGGGCACTTT 60.598 61.111 23.78 9.76 38.71 2.66
154 155 1.302993 GAGGTTGCCGGGCACTTTA 60.303 57.895 23.78 3.61 38.71 1.85
155 156 1.303317 AGGTTGCCGGGCACTTTAG 60.303 57.895 23.78 0.00 38.71 1.85
156 157 2.340328 GGTTGCCGGGCACTTTAGG 61.340 63.158 23.78 0.00 38.71 2.69
157 158 1.302993 GTTGCCGGGCACTTTAGGA 60.303 57.895 23.78 1.36 38.71 2.94
158 159 1.002624 TTGCCGGGCACTTTAGGAG 60.003 57.895 23.78 0.00 38.71 3.69
159 160 2.824489 GCCGGGCACTTTAGGAGC 60.824 66.667 15.62 0.00 0.00 4.70
160 161 2.668632 CCGGGCACTTTAGGAGCA 59.331 61.111 0.00 0.00 0.00 4.26
161 162 1.224592 CCGGGCACTTTAGGAGCAT 59.775 57.895 0.00 0.00 0.00 3.79
162 163 0.815615 CCGGGCACTTTAGGAGCATC 60.816 60.000 0.00 0.00 0.00 3.91
163 164 1.154205 CGGGCACTTTAGGAGCATCG 61.154 60.000 0.00 0.00 34.37 3.84
164 165 1.440145 GGGCACTTTAGGAGCATCGC 61.440 60.000 0.00 0.00 34.37 4.58
165 166 1.440145 GGCACTTTAGGAGCATCGCC 61.440 60.000 0.00 0.00 34.37 5.54
166 167 1.766143 GCACTTTAGGAGCATCGCCG 61.766 60.000 0.00 0.00 34.37 6.46
167 168 0.179111 CACTTTAGGAGCATCGCCGA 60.179 55.000 0.00 0.00 34.37 5.54
168 169 0.753262 ACTTTAGGAGCATCGCCGAT 59.247 50.000 0.00 0.00 34.37 4.18
169 170 1.143305 CTTTAGGAGCATCGCCGATG 58.857 55.000 22.26 22.26 42.37 3.84
170 171 0.249868 TTTAGGAGCATCGCCGATGG 60.250 55.000 26.71 10.22 40.10 3.51
171 172 2.715532 TTAGGAGCATCGCCGATGGC 62.716 60.000 26.71 18.65 46.75 4.40
193 194 3.705638 CCGTCGCGGCAGCATATG 61.706 66.667 12.89 0.00 45.49 1.78
194 195 3.705638 CGTCGCGGCAGCATATGG 61.706 66.667 12.89 0.00 45.49 2.74
204 205 3.289834 GCATATGGCGGTGCTGGG 61.290 66.667 4.56 0.00 38.30 4.45
205 206 2.595463 CATATGGCGGTGCTGGGG 60.595 66.667 0.00 0.00 0.00 4.96
206 207 3.096495 ATATGGCGGTGCTGGGGT 61.096 61.111 0.00 0.00 0.00 4.95
207 208 2.689691 ATATGGCGGTGCTGGGGTT 61.690 57.895 0.00 0.00 0.00 4.11
208 209 1.349542 ATATGGCGGTGCTGGGGTTA 61.350 55.000 0.00 0.00 0.00 2.85
209 210 1.349542 TATGGCGGTGCTGGGGTTAT 61.350 55.000 0.00 0.00 0.00 1.89
210 211 2.828549 GGCGGTGCTGGGGTTATG 60.829 66.667 0.00 0.00 0.00 1.90
211 212 3.518068 GCGGTGCTGGGGTTATGC 61.518 66.667 0.00 0.00 0.00 3.14
212 213 3.202001 CGGTGCTGGGGTTATGCG 61.202 66.667 0.00 0.00 0.00 4.73
213 214 3.518068 GGTGCTGGGGTTATGCGC 61.518 66.667 0.00 0.00 36.59 6.09
230 231 4.715523 CCGGTGGGCGTGGATGTT 62.716 66.667 0.00 0.00 0.00 2.71
231 232 3.430862 CGGTGGGCGTGGATGTTG 61.431 66.667 0.00 0.00 0.00 3.33
232 233 3.061848 GGTGGGCGTGGATGTTGG 61.062 66.667 0.00 0.00 0.00 3.77
233 234 2.282180 GTGGGCGTGGATGTTGGT 60.282 61.111 0.00 0.00 0.00 3.67
234 235 2.282110 TGGGCGTGGATGTTGGTG 60.282 61.111 0.00 0.00 0.00 4.17
235 236 2.282180 GGGCGTGGATGTTGGTGT 60.282 61.111 0.00 0.00 0.00 4.16
236 237 1.901464 GGGCGTGGATGTTGGTGTT 60.901 57.895 0.00 0.00 0.00 3.32
237 238 1.579429 GGCGTGGATGTTGGTGTTC 59.421 57.895 0.00 0.00 0.00 3.18
238 239 1.579429 GCGTGGATGTTGGTGTTCC 59.421 57.895 0.00 0.00 0.00 3.62
239 240 1.169661 GCGTGGATGTTGGTGTTCCA 61.170 55.000 0.00 0.00 42.66 3.53
242 243 2.443958 TGGATGTTGGTGTTCCACAA 57.556 45.000 0.00 0.00 44.22 3.33
243 244 2.028130 TGGATGTTGGTGTTCCACAAC 58.972 47.619 0.00 0.00 44.22 3.32
244 245 2.306847 GGATGTTGGTGTTCCACAACT 58.693 47.619 8.71 0.00 44.22 3.16
245 246 2.293399 GGATGTTGGTGTTCCACAACTC 59.707 50.000 8.71 4.51 44.22 3.01
246 247 1.374560 TGTTGGTGTTCCACAACTCG 58.625 50.000 8.71 0.00 44.22 4.18
247 248 0.661020 GTTGGTGTTCCACAACTCGG 59.339 55.000 0.00 0.00 44.22 4.63
248 249 0.464735 TTGGTGTTCCACAACTCGGG 60.465 55.000 0.00 0.00 44.22 5.14
249 250 1.338890 TGGTGTTCCACAACTCGGGA 61.339 55.000 0.00 0.00 36.59 5.14
250 251 0.179040 GGTGTTCCACAACTCGGGAA 60.179 55.000 0.00 0.00 40.75 3.97
251 252 1.670791 GTGTTCCACAACTCGGGAAA 58.329 50.000 0.00 0.00 44.30 3.13
252 253 2.018515 GTGTTCCACAACTCGGGAAAA 58.981 47.619 0.00 0.00 44.30 2.29
253 254 2.032924 GTGTTCCACAACTCGGGAAAAG 59.967 50.000 0.00 0.00 44.30 2.27
254 255 1.607148 GTTCCACAACTCGGGAAAAGG 59.393 52.381 0.00 0.00 44.30 3.11
255 256 0.109723 TCCACAACTCGGGAAAAGGG 59.890 55.000 0.00 0.00 0.00 3.95
256 257 0.109723 CCACAACTCGGGAAAAGGGA 59.890 55.000 0.00 0.00 0.00 4.20
257 258 1.477923 CCACAACTCGGGAAAAGGGAA 60.478 52.381 0.00 0.00 0.00 3.97
258 259 1.880027 CACAACTCGGGAAAAGGGAAG 59.120 52.381 0.00 0.00 0.00 3.46
259 260 1.202891 ACAACTCGGGAAAAGGGAAGG 60.203 52.381 0.00 0.00 0.00 3.46
260 261 0.404426 AACTCGGGAAAAGGGAAGGG 59.596 55.000 0.00 0.00 0.00 3.95
261 262 1.303282 CTCGGGAAAAGGGAAGGGG 59.697 63.158 0.00 0.00 0.00 4.79
262 263 1.151766 TCGGGAAAAGGGAAGGGGA 60.152 57.895 0.00 0.00 0.00 4.81
263 264 0.772911 TCGGGAAAAGGGAAGGGGAA 60.773 55.000 0.00 0.00 0.00 3.97
275 276 2.027100 GGAAGGGGAACGACTGATTTCT 60.027 50.000 0.00 0.00 0.00 2.52
276 277 3.559384 GGAAGGGGAACGACTGATTTCTT 60.559 47.826 0.00 0.00 0.00 2.52
277 278 4.323257 GGAAGGGGAACGACTGATTTCTTA 60.323 45.833 0.00 0.00 0.00 2.10
278 279 4.473477 AGGGGAACGACTGATTTCTTAG 57.527 45.455 0.00 0.00 0.00 2.18
281 282 3.251571 GGAACGACTGATTTCTTAGCGT 58.748 45.455 0.00 0.00 0.00 5.07
282 283 3.678548 GGAACGACTGATTTCTTAGCGTT 59.321 43.478 0.00 0.00 38.42 4.84
283 284 4.860907 GGAACGACTGATTTCTTAGCGTTA 59.139 41.667 0.00 0.00 37.06 3.18
284 285 5.004535 GGAACGACTGATTTCTTAGCGTTAG 59.995 44.000 0.00 0.00 37.06 2.34
285 286 3.858238 ACGACTGATTTCTTAGCGTTAGC 59.142 43.478 0.00 0.00 45.58 3.09
286 287 3.243177 CGACTGATTTCTTAGCGTTAGCC 59.757 47.826 0.00 0.00 46.67 3.93
298 300 8.896320 TCTTAGCGTTAGCCATTTAATTATCA 57.104 30.769 0.00 0.00 46.67 2.15
320 323 7.856145 TCATTGGTTTATTTTTGCTTTGTGT 57.144 28.000 0.00 0.00 0.00 3.72
328 331 8.558700 GTTTATTTTTGCTTTGTGTCATGGAAT 58.441 29.630 0.00 0.00 0.00 3.01
336 339 5.389859 TTTGTGTCATGGAATCCAATGAC 57.610 39.130 24.77 24.77 39.79 3.06
341 357 7.516452 TGTGTCATGGAATCCAATGACATATA 58.484 34.615 30.82 22.91 44.76 0.86
375 391 2.048444 ATCAGTGGTGTGATGGCATC 57.952 50.000 20.52 20.52 35.76 3.91
388 404 2.400962 GGCATCGCACATGCTGACA 61.401 57.895 15.36 0.00 44.02 3.58
400 419 2.413142 GCTGACAATGCTGCCCTCC 61.413 63.158 0.00 0.00 0.00 4.30
426 445 1.134699 TGAGATCCATTCACGTGCCTC 60.135 52.381 11.67 8.52 0.00 4.70
448 467 7.440255 GCCTCGTTACATATACCAGTACAAAAT 59.560 37.037 0.00 0.00 0.00 1.82
655 709 1.072391 CCGAGACGAGATCGATCGAT 58.928 55.000 29.76 29.76 46.38 3.59
734 789 1.602237 CAGCCACTGGTAATCCCGT 59.398 57.895 0.00 0.00 35.15 5.28
744 799 1.865340 GGTAATCCCGTCGCTTGATTC 59.135 52.381 6.26 1.42 31.55 2.52
749 804 1.143969 CCCGTCGCTTGATTCCGTAC 61.144 60.000 0.00 0.00 0.00 3.67
764 819 2.108168 CCGTACCTCTTCTTGGATCCA 58.892 52.381 11.44 11.44 0.00 3.41
765 820 2.700897 CCGTACCTCTTCTTGGATCCAT 59.299 50.000 17.06 0.00 0.00 3.41
766 821 3.895656 CCGTACCTCTTCTTGGATCCATA 59.104 47.826 17.06 4.00 0.00 2.74
767 822 4.528596 CCGTACCTCTTCTTGGATCCATAT 59.471 45.833 17.06 0.00 0.00 1.78
768 823 5.715279 CCGTACCTCTTCTTGGATCCATATA 59.285 44.000 17.06 0.00 0.00 0.86
769 824 6.127591 CCGTACCTCTTCTTGGATCCATATAG 60.128 46.154 17.06 10.61 0.00 1.31
770 825 6.127591 CGTACCTCTTCTTGGATCCATATAGG 60.128 46.154 17.06 18.83 39.47 2.57
771 826 4.534103 ACCTCTTCTTGGATCCATATAGGC 59.466 45.833 17.06 0.00 37.29 3.93
772 827 4.782156 CCTCTTCTTGGATCCATATAGGCT 59.218 45.833 17.06 0.00 37.29 4.58
773 828 5.104982 CCTCTTCTTGGATCCATATAGGCTC 60.105 48.000 17.06 0.00 37.29 4.70
797 852 7.709947 TCCATGTATGCTCAAGATTTGATTTC 58.290 34.615 0.00 0.00 39.30 2.17
801 879 7.243487 TGTATGCTCAAGATTTGATTTCGTTC 58.757 34.615 0.00 0.00 39.30 3.95
811 892 2.896168 TGATTTCGTTCCGTGTATCCC 58.104 47.619 0.00 0.00 0.00 3.85
826 907 2.938956 ATCCCCGTGAATCTGAATCC 57.061 50.000 0.00 0.00 0.00 3.01
827 908 1.578897 TCCCCGTGAATCTGAATCCA 58.421 50.000 0.00 0.00 0.00 3.41
828 909 1.486310 TCCCCGTGAATCTGAATCCAG 59.514 52.381 0.00 0.00 41.74 3.86
829 910 1.210478 CCCCGTGAATCTGAATCCAGT 59.790 52.381 0.00 0.00 41.16 4.00
830 911 2.555199 CCCGTGAATCTGAATCCAGTC 58.445 52.381 0.00 0.00 41.16 3.51
832 913 2.196749 CGTGAATCTGAATCCAGTCCG 58.803 52.381 0.00 0.00 41.16 4.79
834 915 3.190874 GTGAATCTGAATCCAGTCCGAC 58.809 50.000 0.00 0.00 41.16 4.79
835 916 2.831526 TGAATCTGAATCCAGTCCGACA 59.168 45.455 0.40 0.00 41.16 4.35
836 917 3.452264 TGAATCTGAATCCAGTCCGACAT 59.548 43.478 0.40 0.00 41.16 3.06
840 926 0.106894 GAATCCAGTCCGACATCCCC 59.893 60.000 0.40 0.00 0.00 4.81
842 928 2.873557 ATCCAGTCCGACATCCCCGT 62.874 60.000 0.40 0.00 0.00 5.28
849 935 2.582498 GACATCCCCGTTCGCTCG 60.582 66.667 0.00 0.00 0.00 5.03
863 949 0.930742 CGCTCGCTGAATCCTCGTAC 60.931 60.000 0.00 0.00 0.00 3.67
885 975 1.355971 TAATTTCTCGGCGTGCAGAC 58.644 50.000 6.85 0.00 0.00 3.51
941 1035 3.573491 GCGAAAAGGGGATCGGCG 61.573 66.667 0.00 0.00 39.38 6.46
944 1038 3.012722 AAAAGGGGATCGGCGGGA 61.013 61.111 7.21 0.00 0.00 5.14
965 1063 7.962964 GGGACGATAATCTTGATTATTCACA 57.037 36.000 14.68 0.00 0.00 3.58
966 1064 8.023050 GGGACGATAATCTTGATTATTCACAG 57.977 38.462 14.68 8.61 0.00 3.66
973 1081 5.801350 TCTTGATTATTCACAGAAAGGCG 57.199 39.130 0.00 0.00 0.00 5.52
994 1103 2.125269 GCTTTTAGCGGCGGAGGA 60.125 61.111 9.78 0.00 0.00 3.71
1659 1785 2.435059 GAGCACTCCAAGACGCCC 60.435 66.667 0.00 0.00 0.00 6.13
1698 1824 2.042537 AGCATCTCGGGCTCCTCA 60.043 61.111 0.00 0.00 36.81 3.86
1787 1913 4.681978 GTCGCTCCGGTGCTTGGT 62.682 66.667 24.75 0.00 0.00 3.67
1824 1950 1.617947 GGAGGATGAGGGTTGTCGCT 61.618 60.000 0.00 0.00 39.56 4.93
1854 1980 2.027285 TCCGATTCAGCATGTCCTTCAA 60.027 45.455 0.00 0.00 37.40 2.69
1878 2004 1.817099 GACCATCGCCTCCTTGCTG 60.817 63.158 0.00 0.00 0.00 4.41
1914 2040 4.021925 GTCCCCGTGCTCAAGGCT 62.022 66.667 0.00 0.00 42.39 4.58
1992 2118 4.329545 GCTGCCGTGGTTCCCTCA 62.330 66.667 0.00 0.00 0.00 3.86
2007 2133 4.478206 TCCCTCAGTGATGTTGATTCTC 57.522 45.455 0.00 0.00 0.00 2.87
2214 2340 2.124403 CCCAGTGCCATCCTGCTC 60.124 66.667 0.00 0.00 0.00 4.26
2217 2343 4.479993 AGTGCCATCCTGCTCGGC 62.480 66.667 0.00 0.00 46.43 5.54
2271 2397 2.914777 AAGCATCCGCGCTCCTCTTC 62.915 60.000 5.56 0.00 42.89 2.87
2364 2490 1.106285 GAAAGATGATTGCCGGCCTT 58.894 50.000 26.77 15.93 0.00 4.35
2396 2522 4.202461 GGGTTATAGCAGTCATCATGGGAA 60.202 45.833 0.00 0.00 0.00 3.97
2481 2607 9.890629 AGAAGTGTATTCATAATTTGCTAGTGA 57.109 29.630 0.00 0.00 0.00 3.41
2496 2622 9.846248 ATTTGCTAGTGATTTGTTATTTCTGTC 57.154 29.630 0.00 0.00 0.00 3.51
2501 2627 9.764870 CTAGTGATTTGTTATTTCTGTCACATG 57.235 33.333 0.00 0.00 37.53 3.21
2502 2628 8.169977 AGTGATTTGTTATTTCTGTCACATGT 57.830 30.769 0.00 0.00 37.53 3.21
2503 2629 9.283768 AGTGATTTGTTATTTCTGTCACATGTA 57.716 29.630 0.00 0.00 37.53 2.29
2529 2655 9.712305 ATTATTATTCAAGAACAGGAGATACGG 57.288 33.333 0.00 0.00 0.00 4.02
2614 2753 1.477700 GCACTTATTGGCTGCCATTGA 59.522 47.619 24.03 14.64 31.53 2.57
2617 2756 3.056678 CACTTATTGGCTGCCATTGACAA 60.057 43.478 24.03 6.57 36.81 3.18
2618 2757 3.056607 ACTTATTGGCTGCCATTGACAAC 60.057 43.478 24.03 0.00 35.03 3.32
2661 2800 8.292448 AGTTGTCAATACATTGTTTGTCTGATC 58.708 33.333 0.00 0.00 39.87 2.92
2670 2809 4.754372 TGTTTGTCTGATCATGAAGTGC 57.246 40.909 0.00 0.00 0.00 4.40
2718 2857 9.486497 AATGTGATACATTTGAGTAGCATCTAG 57.514 33.333 1.55 0.00 45.80 2.43
2757 2897 3.131400 TCAATGTGATCATGGTGCAATGG 59.869 43.478 0.00 0.00 34.19 3.16
2901 3052 8.537049 TGAATGAAACAAAAATTGCTGATAGG 57.463 30.769 0.00 0.00 0.00 2.57
2902 3053 8.149647 TGAATGAAACAAAAATTGCTGATAGGT 58.850 29.630 0.00 0.00 0.00 3.08
2939 3098 3.558931 TGGAGAACAGAGCAAAGACAA 57.441 42.857 0.00 0.00 0.00 3.18
2940 3099 4.090761 TGGAGAACAGAGCAAAGACAAT 57.909 40.909 0.00 0.00 0.00 2.71
2941 3100 4.067896 TGGAGAACAGAGCAAAGACAATC 58.932 43.478 0.00 0.00 0.00 2.67
2942 3101 4.067896 GGAGAACAGAGCAAAGACAATCA 58.932 43.478 0.00 0.00 0.00 2.57
2943 3102 4.153835 GGAGAACAGAGCAAAGACAATCAG 59.846 45.833 0.00 0.00 0.00 2.90
2944 3103 4.070716 AGAACAGAGCAAAGACAATCAGG 58.929 43.478 0.00 0.00 0.00 3.86
2945 3104 2.157738 ACAGAGCAAAGACAATCAGGC 58.842 47.619 0.00 0.00 0.00 4.85
2946 3105 2.156917 CAGAGCAAAGACAATCAGGCA 58.843 47.619 0.00 0.00 0.00 4.75
3001 3161 4.550577 CCACAAATTGGGCAAAACTTTC 57.449 40.909 0.00 0.00 42.54 2.62
3135 3298 2.887152 ACTGAATTGAGTGGCCACTTTC 59.113 45.455 37.98 33.23 42.66 2.62
3242 3405 1.538047 TGGATTGCTGACTGGAAAGC 58.462 50.000 0.00 0.00 39.96 3.51
3247 3410 2.185004 TGCTGACTGGAAAGCTAACC 57.815 50.000 0.00 0.00 40.21 2.85
3282 3445 2.403252 GCACCAGCATTACCACTAGT 57.597 50.000 0.00 0.00 41.58 2.57
3283 3446 3.536956 GCACCAGCATTACCACTAGTA 57.463 47.619 0.00 0.00 41.58 1.82
3284 3447 4.073293 GCACCAGCATTACCACTAGTAT 57.927 45.455 0.00 0.00 41.58 2.12
3285 3448 4.451900 GCACCAGCATTACCACTAGTATT 58.548 43.478 0.00 0.00 41.58 1.89
3292 3455 9.391006 CCAGCATTACCACTAGTATTTTCTTTA 57.609 33.333 0.00 0.00 0.00 1.85
3314 3477 2.245159 TGTTTGCAGAGAGTGGAGTG 57.755 50.000 0.00 0.00 0.00 3.51
3328 3491 1.754226 TGGAGTGGCAAAAACAACTCC 59.246 47.619 10.60 10.60 42.83 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.748493 GGGATGTTTTGATGCCGCTTA 59.252 47.619 0.00 0.00 0.00 3.09
1 2 0.532115 GGGATGTTTTGATGCCGCTT 59.468 50.000 0.00 0.00 0.00 4.68
2 3 1.322538 GGGGATGTTTTGATGCCGCT 61.323 55.000 0.00 0.00 34.69 5.52
3 4 1.141665 GGGGATGTTTTGATGCCGC 59.858 57.895 0.00 0.00 34.69 6.53
4 5 1.433064 CGGGGATGTTTTGATGCCG 59.567 57.895 0.00 0.00 34.69 5.69
5 6 0.970427 ACCGGGGATGTTTTGATGCC 60.970 55.000 6.32 0.00 33.12 4.40
6 7 0.173255 CACCGGGGATGTTTTGATGC 59.827 55.000 6.32 0.00 0.00 3.91
7 8 1.544724 ACACCGGGGATGTTTTGATG 58.455 50.000 12.96 0.00 0.00 3.07
8 9 1.892474 CAACACCGGGGATGTTTTGAT 59.108 47.619 12.96 0.00 38.22 2.57
9 10 1.323412 CAACACCGGGGATGTTTTGA 58.677 50.000 12.96 0.00 38.22 2.69
10 11 1.036707 ACAACACCGGGGATGTTTTG 58.963 50.000 14.79 8.18 38.22 2.44
11 12 2.106857 TCTACAACACCGGGGATGTTTT 59.893 45.455 25.72 12.18 38.22 2.43
12 13 1.700739 TCTACAACACCGGGGATGTTT 59.299 47.619 25.72 3.35 38.22 2.83
13 14 1.278127 CTCTACAACACCGGGGATGTT 59.722 52.381 25.72 14.06 40.95 2.71
14 15 0.902531 CTCTACAACACCGGGGATGT 59.097 55.000 24.03 24.03 0.00 3.06
15 16 0.902531 ACTCTACAACACCGGGGATG 59.097 55.000 12.96 13.08 0.00 3.51
16 17 0.902531 CACTCTACAACACCGGGGAT 59.097 55.000 12.96 0.00 0.00 3.85
17 18 1.823169 GCACTCTACAACACCGGGGA 61.823 60.000 12.96 0.00 0.00 4.81
18 19 1.375523 GCACTCTACAACACCGGGG 60.376 63.158 0.00 0.00 0.00 5.73
19 20 0.389948 GAGCACTCTACAACACCGGG 60.390 60.000 6.32 0.00 0.00 5.73
20 21 0.732880 CGAGCACTCTACAACACCGG 60.733 60.000 0.00 0.00 0.00 5.28
21 22 0.039437 ACGAGCACTCTACAACACCG 60.039 55.000 0.00 0.00 0.00 4.94
22 23 1.269998 AGACGAGCACTCTACAACACC 59.730 52.381 0.00 0.00 0.00 4.16
23 24 2.320367 CAGACGAGCACTCTACAACAC 58.680 52.381 0.00 0.00 0.00 3.32
24 25 1.335964 GCAGACGAGCACTCTACAACA 60.336 52.381 0.00 0.00 0.00 3.33
25 26 1.341606 GCAGACGAGCACTCTACAAC 58.658 55.000 0.00 0.00 0.00 3.32
26 27 0.109735 CGCAGACGAGCACTCTACAA 60.110 55.000 0.00 0.00 43.93 2.41
27 28 0.953960 TCGCAGACGAGCACTCTACA 60.954 55.000 0.00 0.00 45.12 2.74
28 29 1.794864 TCGCAGACGAGCACTCTAC 59.205 57.895 0.00 0.00 45.12 2.59
29 30 4.296265 TCGCAGACGAGCACTCTA 57.704 55.556 0.00 0.00 45.12 2.43
47 48 2.031314 GGTGAGCACGACATCAATGATG 59.969 50.000 20.58 20.58 44.71 3.07
48 49 2.283298 GGTGAGCACGACATCAATGAT 58.717 47.619 0.00 0.00 0.00 2.45
49 50 1.725641 GGTGAGCACGACATCAATGA 58.274 50.000 0.00 0.00 0.00 2.57
50 51 0.371301 CGGTGAGCACGACATCAATG 59.629 55.000 0.00 0.00 0.00 2.82
51 52 0.037326 ACGGTGAGCACGACATCAAT 60.037 50.000 0.00 0.00 34.93 2.57
52 53 0.943835 CACGGTGAGCACGACATCAA 60.944 55.000 0.74 0.00 34.93 2.57
53 54 1.372872 CACGGTGAGCACGACATCA 60.373 57.895 0.74 0.00 34.93 3.07
54 55 0.944311 AACACGGTGAGCACGACATC 60.944 55.000 16.29 0.00 34.93 3.06
55 56 1.069090 AACACGGTGAGCACGACAT 59.931 52.632 16.29 0.00 34.93 3.06
56 57 1.880796 CAACACGGTGAGCACGACA 60.881 57.895 16.29 0.00 34.93 4.35
57 58 2.928361 CAACACGGTGAGCACGAC 59.072 61.111 16.29 0.00 34.93 4.34
58 59 2.964925 GCAACACGGTGAGCACGA 60.965 61.111 16.29 0.00 34.93 4.35
59 60 2.116736 ATTGCAACACGGTGAGCACG 62.117 55.000 24.45 7.34 33.43 5.34
60 61 0.661187 CATTGCAACACGGTGAGCAC 60.661 55.000 24.45 9.45 33.43 4.40
61 62 1.653667 CATTGCAACACGGTGAGCA 59.346 52.632 22.13 22.13 32.31 4.26
62 63 1.081242 CCATTGCAACACGGTGAGC 60.081 57.895 16.29 17.63 0.00 4.26
63 64 1.172180 ACCCATTGCAACACGGTGAG 61.172 55.000 16.29 8.00 0.00 3.51
64 65 1.152860 ACCCATTGCAACACGGTGA 60.153 52.632 16.29 0.00 0.00 4.02
65 66 1.007502 CACCCATTGCAACACGGTG 60.008 57.895 20.77 20.77 38.19 4.94
66 67 2.199652 CCACCCATTGCAACACGGT 61.200 57.895 0.00 4.52 0.00 4.83
67 68 2.650196 CCACCCATTGCAACACGG 59.350 61.111 0.00 3.79 0.00 4.94
68 69 2.049248 GCCACCCATTGCAACACG 60.049 61.111 0.00 0.00 0.00 4.49
69 70 2.343387 GGCCACCCATTGCAACAC 59.657 61.111 0.00 0.00 0.00 3.32
70 71 3.301554 CGGCCACCCATTGCAACA 61.302 61.111 0.00 0.00 0.00 3.33
71 72 3.302344 ACGGCCACCCATTGCAAC 61.302 61.111 0.00 0.00 0.00 4.17
72 73 3.301554 CACGGCCACCCATTGCAA 61.302 61.111 0.00 0.00 0.00 4.08
90 91 3.103911 GTGAACTCACGCCGTCGG 61.104 66.667 6.99 6.99 40.69 4.79
98 99 0.668535 GCAACCCTTGGTGAACTCAC 59.331 55.000 0.98 0.98 45.72 3.51
99 100 0.257328 TGCAACCCTTGGTGAACTCA 59.743 50.000 0.00 0.00 35.34 3.41
100 101 1.067060 GTTGCAACCCTTGGTGAACTC 59.933 52.381 19.15 0.00 35.34 3.01
101 102 1.111277 GTTGCAACCCTTGGTGAACT 58.889 50.000 19.15 0.00 35.34 3.01
102 103 0.820871 TGTTGCAACCCTTGGTGAAC 59.179 50.000 26.14 0.00 35.34 3.18
103 104 1.686052 GATGTTGCAACCCTTGGTGAA 59.314 47.619 26.14 5.01 35.34 3.18
104 105 1.327303 GATGTTGCAACCCTTGGTGA 58.673 50.000 26.14 5.77 35.34 4.02
105 106 0.039256 CGATGTTGCAACCCTTGGTG 60.039 55.000 26.14 5.97 35.34 4.17
106 107 0.467290 ACGATGTTGCAACCCTTGGT 60.467 50.000 26.14 14.93 37.65 3.67
107 108 0.240945 GACGATGTTGCAACCCTTGG 59.759 55.000 26.14 14.33 0.00 3.61
108 109 1.197721 GAGACGATGTTGCAACCCTTG 59.802 52.381 26.14 18.44 0.00 3.61
109 110 1.523758 GAGACGATGTTGCAACCCTT 58.476 50.000 26.14 11.88 0.00 3.95
110 111 0.321653 GGAGACGATGTTGCAACCCT 60.322 55.000 26.14 13.93 0.00 4.34
111 112 2.171635 GGAGACGATGTTGCAACCC 58.828 57.895 26.14 16.54 0.00 4.11
124 125 2.533318 CAACCTCTGCAACGGAGAC 58.467 57.895 7.86 0.00 39.05 3.36
134 135 3.850098 AAGTGCCCGGCAACCTCTG 62.850 63.158 15.39 0.00 41.47 3.35
135 136 1.774894 TAAAGTGCCCGGCAACCTCT 61.775 55.000 15.39 3.76 41.47 3.69
136 137 1.302993 TAAAGTGCCCGGCAACCTC 60.303 57.895 15.39 0.95 41.47 3.85
137 138 1.303317 CTAAAGTGCCCGGCAACCT 60.303 57.895 15.39 5.02 41.47 3.50
138 139 2.340328 CCTAAAGTGCCCGGCAACC 61.340 63.158 15.39 2.23 41.47 3.77
139 140 1.302993 TCCTAAAGTGCCCGGCAAC 60.303 57.895 15.39 8.76 41.47 4.17
140 141 1.002624 CTCCTAAAGTGCCCGGCAA 60.003 57.895 15.39 0.00 41.47 4.52
141 142 2.668632 CTCCTAAAGTGCCCGGCA 59.331 61.111 8.43 8.43 35.60 5.69
142 143 2.824489 GCTCCTAAAGTGCCCGGC 60.824 66.667 1.04 1.04 0.00 6.13
143 144 0.815615 GATGCTCCTAAAGTGCCCGG 60.816 60.000 0.00 0.00 33.94 5.73
144 145 1.154205 CGATGCTCCTAAAGTGCCCG 61.154 60.000 0.00 0.00 33.94 6.13
145 146 1.440145 GCGATGCTCCTAAAGTGCCC 61.440 60.000 0.00 0.00 33.94 5.36
146 147 1.440145 GGCGATGCTCCTAAAGTGCC 61.440 60.000 0.00 0.00 33.94 5.01
147 148 1.766143 CGGCGATGCTCCTAAAGTGC 61.766 60.000 0.00 0.00 35.49 4.40
148 149 0.179111 TCGGCGATGCTCCTAAAGTG 60.179 55.000 4.99 0.00 0.00 3.16
149 150 0.753262 ATCGGCGATGCTCCTAAAGT 59.247 50.000 23.36 0.00 0.00 2.66
150 151 1.143305 CATCGGCGATGCTCCTAAAG 58.857 55.000 33.67 10.13 33.17 1.85
151 152 0.249868 CCATCGGCGATGCTCCTAAA 60.250 55.000 37.35 1.85 38.59 1.85
152 153 1.367471 CCATCGGCGATGCTCCTAA 59.633 57.895 37.35 2.67 38.59 2.69
153 154 3.051210 CCATCGGCGATGCTCCTA 58.949 61.111 37.35 3.49 38.59 2.94
154 155 4.615815 GCCATCGGCGATGCTCCT 62.616 66.667 37.35 8.59 39.62 3.69
177 178 3.705638 CCATATGCTGCCGCGACG 61.706 66.667 8.23 0.00 39.65 5.12
178 179 4.017877 GCCATATGCTGCCGCGAC 62.018 66.667 8.23 0.00 39.65 5.19
182 183 3.653009 CACCGCCATATGCTGCCG 61.653 66.667 0.00 0.00 38.05 5.69
183 184 3.969802 GCACCGCCATATGCTGCC 61.970 66.667 0.00 0.00 38.84 4.85
187 188 3.289834 CCCAGCACCGCCATATGC 61.290 66.667 0.00 0.00 42.39 3.14
188 189 2.595463 CCCCAGCACCGCCATATG 60.595 66.667 0.00 0.00 0.00 1.78
189 190 1.349542 TAACCCCAGCACCGCCATAT 61.350 55.000 0.00 0.00 0.00 1.78
190 191 1.349542 ATAACCCCAGCACCGCCATA 61.350 55.000 0.00 0.00 0.00 2.74
191 192 2.689691 ATAACCCCAGCACCGCCAT 61.690 57.895 0.00 0.00 0.00 4.40
192 193 3.334891 ATAACCCCAGCACCGCCA 61.335 61.111 0.00 0.00 0.00 5.69
193 194 2.828549 CATAACCCCAGCACCGCC 60.829 66.667 0.00 0.00 0.00 6.13
194 195 3.518068 GCATAACCCCAGCACCGC 61.518 66.667 0.00 0.00 0.00 5.68
195 196 3.202001 CGCATAACCCCAGCACCG 61.202 66.667 0.00 0.00 0.00 4.94
196 197 3.518068 GCGCATAACCCCAGCACC 61.518 66.667 0.30 0.00 0.00 5.01
197 198 3.518068 GGCGCATAACCCCAGCAC 61.518 66.667 10.83 0.00 0.00 4.40
200 201 4.483243 ACCGGCGCATAACCCCAG 62.483 66.667 10.83 0.00 0.00 4.45
201 202 4.787286 CACCGGCGCATAACCCCA 62.787 66.667 10.83 0.00 0.00 4.96
213 214 4.715523 AACATCCACGCCCACCGG 62.716 66.667 0.00 0.00 42.52 5.28
214 215 3.430862 CAACATCCACGCCCACCG 61.431 66.667 0.00 0.00 44.21 4.94
215 216 3.061848 CCAACATCCACGCCCACC 61.062 66.667 0.00 0.00 0.00 4.61
216 217 2.282180 ACCAACATCCACGCCCAC 60.282 61.111 0.00 0.00 0.00 4.61
217 218 2.282110 CACCAACATCCACGCCCA 60.282 61.111 0.00 0.00 0.00 5.36
218 219 1.862602 GAACACCAACATCCACGCCC 61.863 60.000 0.00 0.00 0.00 6.13
219 220 1.579429 GAACACCAACATCCACGCC 59.421 57.895 0.00 0.00 0.00 5.68
220 221 1.169661 TGGAACACCAACATCCACGC 61.170 55.000 0.00 0.00 38.30 5.34
221 222 3.014037 TGGAACACCAACATCCACG 57.986 52.632 0.00 0.00 38.30 4.94
234 235 1.607148 CCTTTTCCCGAGTTGTGGAAC 59.393 52.381 0.00 0.00 40.27 3.62
235 236 1.477923 CCCTTTTCCCGAGTTGTGGAA 60.478 52.381 0.00 0.00 38.84 3.53
236 237 0.109723 CCCTTTTCCCGAGTTGTGGA 59.890 55.000 0.00 0.00 0.00 4.02
237 238 0.109723 TCCCTTTTCCCGAGTTGTGG 59.890 55.000 0.00 0.00 0.00 4.17
238 239 1.880027 CTTCCCTTTTCCCGAGTTGTG 59.120 52.381 0.00 0.00 0.00 3.33
239 240 1.202891 CCTTCCCTTTTCCCGAGTTGT 60.203 52.381 0.00 0.00 0.00 3.32
240 241 1.534729 CCTTCCCTTTTCCCGAGTTG 58.465 55.000 0.00 0.00 0.00 3.16
241 242 0.404426 CCCTTCCCTTTTCCCGAGTT 59.596 55.000 0.00 0.00 0.00 3.01
242 243 1.498176 CCCCTTCCCTTTTCCCGAGT 61.498 60.000 0.00 0.00 0.00 4.18
243 244 1.205460 TCCCCTTCCCTTTTCCCGAG 61.205 60.000 0.00 0.00 0.00 4.63
244 245 0.772911 TTCCCCTTCCCTTTTCCCGA 60.773 55.000 0.00 0.00 0.00 5.14
245 246 0.611062 GTTCCCCTTCCCTTTTCCCG 60.611 60.000 0.00 0.00 0.00 5.14
246 247 0.611062 CGTTCCCCTTCCCTTTTCCC 60.611 60.000 0.00 0.00 0.00 3.97
247 248 0.402887 TCGTTCCCCTTCCCTTTTCC 59.597 55.000 0.00 0.00 0.00 3.13
248 249 1.073444 AGTCGTTCCCCTTCCCTTTTC 59.927 52.381 0.00 0.00 0.00 2.29
249 250 1.146452 AGTCGTTCCCCTTCCCTTTT 58.854 50.000 0.00 0.00 0.00 2.27
250 251 0.400594 CAGTCGTTCCCCTTCCCTTT 59.599 55.000 0.00 0.00 0.00 3.11
251 252 0.473117 TCAGTCGTTCCCCTTCCCTT 60.473 55.000 0.00 0.00 0.00 3.95
252 253 0.252742 ATCAGTCGTTCCCCTTCCCT 60.253 55.000 0.00 0.00 0.00 4.20
253 254 0.618981 AATCAGTCGTTCCCCTTCCC 59.381 55.000 0.00 0.00 0.00 3.97
254 255 2.027100 AGAAATCAGTCGTTCCCCTTCC 60.027 50.000 0.00 0.00 0.00 3.46
255 256 3.336138 AGAAATCAGTCGTTCCCCTTC 57.664 47.619 0.00 0.00 0.00 3.46
256 257 3.790089 AAGAAATCAGTCGTTCCCCTT 57.210 42.857 0.00 0.00 0.00 3.95
257 258 3.369576 GCTAAGAAATCAGTCGTTCCCCT 60.370 47.826 0.00 0.00 0.00 4.79
258 259 2.937149 GCTAAGAAATCAGTCGTTCCCC 59.063 50.000 0.00 0.00 0.00 4.81
259 260 2.603560 CGCTAAGAAATCAGTCGTTCCC 59.396 50.000 0.00 0.00 0.00 3.97
260 261 3.251571 ACGCTAAGAAATCAGTCGTTCC 58.748 45.455 0.00 0.00 0.00 3.62
261 262 4.905412 AACGCTAAGAAATCAGTCGTTC 57.095 40.909 0.00 0.00 32.84 3.95
262 263 4.326548 GCTAACGCTAAGAAATCAGTCGTT 59.673 41.667 0.00 0.00 37.82 3.85
263 264 3.858238 GCTAACGCTAAGAAATCAGTCGT 59.142 43.478 0.00 0.00 0.00 4.34
275 276 9.891828 CAATGATAATTAAATGGCTAACGCTAA 57.108 29.630 0.00 0.00 36.09 3.09
276 277 8.511321 CCAATGATAATTAAATGGCTAACGCTA 58.489 33.333 0.00 0.00 36.09 4.26
277 278 7.014230 ACCAATGATAATTAAATGGCTAACGCT 59.986 33.333 8.35 0.00 36.09 5.07
278 279 7.145323 ACCAATGATAATTAAATGGCTAACGC 58.855 34.615 8.35 0.00 0.00 4.84
297 299 7.692088 TGACACAAAGCAAAAATAAACCAATG 58.308 30.769 0.00 0.00 0.00 2.82
298 300 7.856145 TGACACAAAGCAAAAATAAACCAAT 57.144 28.000 0.00 0.00 0.00 3.16
306 309 5.702209 GGATTCCATGACACAAAGCAAAAAT 59.298 36.000 0.00 0.00 0.00 1.82
317 320 6.889301 ATATGTCATTGGATTCCATGACAC 57.111 37.500 31.28 18.19 45.21 3.67
320 323 9.984590 ATTGATATATGTCATTGGATTCCATGA 57.015 29.630 6.15 9.55 31.53 3.07
328 331 7.724951 TCTTTGCCATTGATATATGTCATTGGA 59.275 33.333 31.53 20.15 45.71 3.53
336 339 9.406828 CACTGATTTCTTTGCCATTGATATATG 57.593 33.333 0.00 0.00 0.00 1.78
341 357 4.529377 ACCACTGATTTCTTTGCCATTGAT 59.471 37.500 0.00 0.00 0.00 2.57
352 368 2.224843 TGCCATCACACCACTGATTTCT 60.225 45.455 0.00 0.00 0.00 2.52
388 404 0.183014 CATGAGAGGAGGGCAGCATT 59.817 55.000 0.00 0.00 0.00 3.56
400 419 4.049869 CACGTGAATGGATCTCATGAGAG 58.950 47.826 28.26 14.81 41.33 3.20
426 445 9.251792 TGCTATTTTGTACTGGTATATGTAACG 57.748 33.333 0.00 0.00 0.00 3.18
555 578 0.451783 CTGATAAACTTGGCCGTGGC 59.548 55.000 1.16 1.16 41.06 5.01
558 581 3.694566 GGATTTCTGATAAACTTGGCCGT 59.305 43.478 0.00 0.00 0.00 5.68
600 623 2.275418 GGGATTGGTGGATGCGGT 59.725 61.111 0.00 0.00 0.00 5.68
658 712 4.320456 CTCCGGCCGGATGGGATG 62.320 72.222 45.15 29.09 44.24 3.51
659 713 2.957902 TTACTCCGGCCGGATGGGAT 62.958 60.000 45.15 28.60 44.24 3.85
660 714 3.682644 TTACTCCGGCCGGATGGGA 62.683 63.158 45.15 30.10 44.24 4.37
661 715 3.158648 TTACTCCGGCCGGATGGG 61.159 66.667 45.15 34.70 44.24 4.00
662 716 2.108362 GTTACTCCGGCCGGATGG 59.892 66.667 45.15 35.43 44.24 3.51
734 789 1.471119 AGAGGTACGGAATCAAGCGA 58.529 50.000 0.00 0.00 0.00 4.93
744 799 2.108168 TGGATCCAAGAAGAGGTACGG 58.892 52.381 13.46 0.00 0.00 4.02
749 804 4.782156 AGCCTATATGGATCCAAGAAGAGG 59.218 45.833 20.67 21.81 38.35 3.69
764 819 5.723405 TCTTGAGCATACATGGAGCCTATAT 59.277 40.000 0.00 0.00 0.00 0.86
765 820 5.086621 TCTTGAGCATACATGGAGCCTATA 58.913 41.667 0.00 0.00 0.00 1.31
766 821 3.906218 TCTTGAGCATACATGGAGCCTAT 59.094 43.478 0.00 0.00 0.00 2.57
767 822 3.308401 TCTTGAGCATACATGGAGCCTA 58.692 45.455 0.00 0.00 0.00 3.93
768 823 2.121948 TCTTGAGCATACATGGAGCCT 58.878 47.619 0.00 0.00 0.00 4.58
769 824 2.627515 TCTTGAGCATACATGGAGCC 57.372 50.000 0.00 0.00 0.00 4.70
770 825 4.577693 TCAAATCTTGAGCATACATGGAGC 59.422 41.667 0.00 0.00 34.08 4.70
771 826 6.879276 ATCAAATCTTGAGCATACATGGAG 57.121 37.500 0.00 0.00 43.98 3.86
772 827 7.467675 CGAAATCAAATCTTGAGCATACATGGA 60.468 37.037 0.00 0.00 43.98 3.41
773 828 6.635641 CGAAATCAAATCTTGAGCATACATGG 59.364 38.462 0.00 0.00 43.98 3.66
774 829 7.191551 ACGAAATCAAATCTTGAGCATACATG 58.808 34.615 0.00 0.00 43.98 3.21
775 830 7.325660 ACGAAATCAAATCTTGAGCATACAT 57.674 32.000 0.00 0.00 43.98 2.29
776 831 6.741992 ACGAAATCAAATCTTGAGCATACA 57.258 33.333 0.00 0.00 43.98 2.29
780 835 5.046910 GGAACGAAATCAAATCTTGAGCA 57.953 39.130 0.00 0.00 43.98 4.26
811 892 2.555199 GGACTGGATTCAGATTCACGG 58.445 52.381 8.39 0.00 43.49 4.94
826 907 1.153628 GAACGGGGATGTCGGACTG 60.154 63.158 9.88 0.00 0.00 3.51
827 908 2.707849 CGAACGGGGATGTCGGACT 61.708 63.158 9.88 0.00 0.00 3.85
828 909 2.202703 CGAACGGGGATGTCGGAC 60.203 66.667 0.00 0.00 0.00 4.79
829 910 4.137872 GCGAACGGGGATGTCGGA 62.138 66.667 0.00 0.00 0.00 4.55
830 911 4.143333 AGCGAACGGGGATGTCGG 62.143 66.667 0.00 0.00 0.00 4.79
832 913 2.582498 CGAGCGAACGGGGATGTC 60.582 66.667 0.00 0.00 0.00 3.06
834 915 4.514577 AGCGAGCGAACGGGGATG 62.515 66.667 0.00 0.00 0.00 3.51
835 916 4.514577 CAGCGAGCGAACGGGGAT 62.515 66.667 0.00 0.00 0.00 3.85
840 926 1.475441 GAGGATTCAGCGAGCGAACG 61.475 60.000 0.00 0.00 0.00 3.95
842 928 1.226688 CGAGGATTCAGCGAGCGAA 60.227 57.895 0.00 5.24 0.00 4.70
849 935 7.515371 CGAGAAATTAAAGTACGAGGATTCAGC 60.515 40.741 0.00 0.00 0.00 4.26
863 949 2.415168 TCTGCACGCCGAGAAATTAAAG 59.585 45.455 0.00 0.00 0.00 1.85
885 975 4.787598 CTCCGACAAAAAGATTGAACCAG 58.212 43.478 0.00 0.00 0.00 4.00
922 1012 2.590092 CCGATCCCCTTTTCGCCT 59.410 61.111 0.00 0.00 34.10 5.52
941 1035 7.872993 TCTGTGAATAATCAAGATTATCGTCCC 59.127 37.037 13.93 3.87 41.66 4.46
954 1052 2.682856 GGCGCCTTTCTGTGAATAATCA 59.317 45.455 22.15 0.00 0.00 2.57
963 1061 4.643387 AAGCCGGCGCCTTTCTGT 62.643 61.111 26.68 1.13 34.57 3.41
964 1062 1.582610 TAAAAGCCGGCGCCTTTCTG 61.583 55.000 26.68 8.25 31.15 3.02
965 1063 1.302993 TAAAAGCCGGCGCCTTTCT 60.303 52.632 26.68 15.31 31.15 2.52
966 1064 1.136774 CTAAAAGCCGGCGCCTTTC 59.863 57.895 26.68 13.09 31.15 2.62
1316 1442 0.250338 GGTGAAGCGGAAGAACTGGT 60.250 55.000 0.00 0.00 37.17 4.00
1317 1443 1.291877 CGGTGAAGCGGAAGAACTGG 61.292 60.000 0.00 0.00 0.00 4.00
1659 1785 1.495878 CGAAGATCCTGGCGATGAAG 58.504 55.000 0.00 0.00 0.00 3.02
1698 1824 1.052124 TGTCGGGGAAGGTGTTCTGT 61.052 55.000 0.00 0.00 32.72 3.41
1767 1893 1.961277 CAAGCACCGGAGCGACTTT 60.961 57.895 18.47 4.19 40.15 2.66
1824 1950 2.171003 TGCTGAATCGGAGTCTTCTCA 58.829 47.619 7.01 0.00 42.05 3.27
1914 2040 0.958091 CATCAGCCCCAAACACGAAA 59.042 50.000 0.00 0.00 0.00 3.46
1992 2118 2.419297 GCCTCCGAGAATCAACATCACT 60.419 50.000 0.00 0.00 33.17 3.41
2007 2133 4.519437 TCTGCGAGCATGCCTCCG 62.519 66.667 15.66 16.51 37.27 4.63
2115 2241 1.269958 ACCTGTCTGCTAGCATCACA 58.730 50.000 19.72 21.23 0.00 3.58
2160 2286 2.000447 GAGAGCACAAACCGGTACATC 59.000 52.381 8.00 0.38 0.00 3.06
2217 2343 3.570638 CTCAGGCTTGCGATGGCG 61.571 66.667 0.00 0.00 44.10 5.69
2220 2346 2.515523 CCCCTCAGGCTTGCGATG 60.516 66.667 0.00 0.00 0.00 3.84
2364 2490 2.088423 CTGCTATAACCCGGTTTTGCA 58.912 47.619 8.44 14.53 0.00 4.08
2396 2522 4.401925 CACTCCTTTTCTTGGGAATCACT 58.598 43.478 0.00 0.00 0.00 3.41
2503 2629 9.712305 CCGTATCTCCTGTTCTTGAATAATAAT 57.288 33.333 0.00 0.00 0.00 1.28
2504 2630 8.701895 ACCGTATCTCCTGTTCTTGAATAATAA 58.298 33.333 0.00 0.00 0.00 1.40
2614 2753 6.569179 ACTTGTGTTGTTCTACAAAGTTGT 57.431 33.333 1.75 1.75 40.15 3.32
2661 2800 3.571571 CACCAGACATTTGCACTTCATG 58.428 45.455 0.00 0.00 0.00 3.07
2670 2809 2.287788 GCTGTTGACCACCAGACATTTG 60.288 50.000 0.00 0.00 0.00 2.32
2693 2832 8.864087 TCTAGATGCTACTCAAATGTATCACAT 58.136 33.333 0.00 0.00 41.31 3.21
2757 2897 7.315890 ACAAAATAGTTTATCTGCTTTCTGGC 58.684 34.615 0.00 0.00 0.00 4.85
2901 3052 3.888930 CTCCAGATCTCTCCAGGAACTAC 59.111 52.174 0.00 0.00 36.02 2.73
2902 3053 3.788708 TCTCCAGATCTCTCCAGGAACTA 59.211 47.826 0.00 0.00 36.02 2.24
2939 3098 0.260816 ACCATTCTGGCATGCCTGAT 59.739 50.000 37.43 26.40 42.67 2.90
2940 3099 0.681887 CACCATTCTGGCATGCCTGA 60.682 55.000 34.87 34.87 42.67 3.86
2941 3100 0.681887 TCACCATTCTGGCATGCCTG 60.682 55.000 35.53 33.57 42.67 4.85
2942 3101 0.040058 TTCACCATTCTGGCATGCCT 59.960 50.000 35.53 14.65 42.67 4.75
2943 3102 0.896923 TTTCACCATTCTGGCATGCC 59.103 50.000 30.54 30.54 42.67 4.40
2944 3103 2.028748 ACTTTTCACCATTCTGGCATGC 60.029 45.455 9.90 9.90 42.67 4.06
2945 3104 3.256383 TCACTTTTCACCATTCTGGCATG 59.744 43.478 0.00 0.00 42.67 4.06
2946 3105 3.499338 TCACTTTTCACCATTCTGGCAT 58.501 40.909 0.00 0.00 42.67 4.40
3135 3298 3.120060 CCAGACCTGCAGAAAGAAAATCG 60.120 47.826 17.39 0.00 0.00 3.34
3242 3405 0.609131 CACAGTGCCTTGGGGGTTAG 60.609 60.000 0.00 0.00 37.43 2.34
3281 3444 9.334693 CTCTCTGCAAACATGTAAAGAAAATAC 57.665 33.333 0.00 0.00 0.00 1.89
3282 3445 9.066892 ACTCTCTGCAAACATGTAAAGAAAATA 57.933 29.630 0.00 0.00 0.00 1.40
3283 3446 7.864379 CACTCTCTGCAAACATGTAAAGAAAAT 59.136 33.333 0.00 0.00 0.00 1.82
3284 3447 7.195646 CACTCTCTGCAAACATGTAAAGAAAA 58.804 34.615 0.00 0.00 0.00 2.29
3285 3448 6.238731 CCACTCTCTGCAAACATGTAAAGAAA 60.239 38.462 0.00 0.00 0.00 2.52
3292 3455 2.105477 ACTCCACTCTCTGCAAACATGT 59.895 45.455 0.00 0.00 0.00 3.21
3297 3460 0.250467 GCCACTCCACTCTCTGCAAA 60.250 55.000 0.00 0.00 0.00 3.68
3298 3461 1.372683 GCCACTCCACTCTCTGCAA 59.627 57.895 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.