Multiple sequence alignment - TraesCS4B01G138900

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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 TraesCS4B01G138900 chr4B 100.000 2945 0 0 1 2945 183004039 183001095 0.000000e+00 5439.0
1 TraesCS4B01G138900 chr4B 83.562 73 7 3 2821 2888 372825440 372825368 2.450000e-06 63.9
2 TraesCS4B01G138900 chr4D 93.804 1985 69 23 765 2739 120072550 120070610 0.000000e+00 2935.0
3 TraesCS4B01G138900 chr4D 93.671 79 2 1 2730 2808 120070108 120070033 6.670000e-22 115.0
4 TraesCS4B01G138900 chr4D 96.721 61 2 0 2885 2945 120070036 120069976 5.190000e-18 102.0
5 TraesCS4B01G138900 chr4A 96.248 1519 40 7 765 2274 451595470 451593960 0.000000e+00 2473.0
6 TraesCS4B01G138900 chr4A 90.171 234 12 5 2434 2667 451593583 451593361 7.980000e-76 294.0
7 TraesCS4B01G138900 chr4A 95.745 47 2 0 2273 2319 451593713 451593667 3.150000e-10 76.8
8 TraesCS4B01G138900 chr4A 84.932 73 6 3 2821 2888 603489791 603489719 5.270000e-08 69.4
9 TraesCS4B01G138900 chr4A 100.000 35 0 0 2273 2307 451593658 451593624 6.810000e-07 65.8
10 TraesCS4B01G138900 chr2D 89.224 863 91 2 1082 1943 327623101 327623962 0.000000e+00 1077.0
11 TraesCS4B01G138900 chr2D 86.304 460 35 11 120 557 110849937 110849484 2.660000e-130 475.0
12 TraesCS4B01G138900 chr2D 100.000 32 0 0 2821 2852 586158151 586158182 3.170000e-05 60.2
13 TraesCS4B01G138900 chr2B 89.108 863 92 2 1082 1943 396956911 396957772 0.000000e+00 1072.0
14 TraesCS4B01G138900 chr2B 94.737 38 1 1 1 37 517028286 517028323 1.140000e-04 58.4
15 TraesCS4B01G138900 chr2A 88.876 863 94 2 1082 1943 432591809 432592670 0.000000e+00 1061.0
16 TraesCS4B01G138900 chr2A 88.673 309 29 5 252 557 107190086 107189781 3.580000e-99 372.0
17 TraesCS4B01G138900 chr3B 85.217 460 38 16 122 557 763218222 763217769 2.080000e-121 446.0
18 TraesCS4B01G138900 chr3B 87.764 237 21 6 250 482 666708927 666708695 1.350000e-68 270.0
19 TraesCS4B01G138900 chr3B 78.708 418 35 21 157 549 370158657 370158269 2.280000e-56 230.0
20 TraesCS4B01G138900 chr6B 85.647 425 37 4 157 557 393676864 393677288 2.710000e-115 425.0
21 TraesCS4B01G138900 chr6B 84.906 424 41 4 157 557 393678228 393678651 9.830000e-110 407.0
22 TraesCS4B01G138900 chr6D 83.962 424 44 5 157 557 176823943 176824365 4.600000e-103 385.0
23 TraesCS4B01G138900 chr6D 83.962 424 41 5 157 557 176822271 176822690 5.960000e-102 381.0
24 TraesCS4B01G138900 chr6D 83.784 74 7 3 2821 2889 400060175 400060102 6.810000e-07 65.8
25 TraesCS4B01G138900 chr6A 88.424 311 32 4 250 557 229992025 229991716 3.580000e-99 372.0
26 TraesCS4B01G138900 chr6A 82.432 74 7 4 2821 2888 28256709 28256636 3.170000e-05 60.2
27 TraesCS4B01G138900 chr7A 88.889 90 10 0 564 653 30887463 30887374 8.630000e-21 111.0
28 TraesCS4B01G138900 chr3A 84.932 73 6 1 2821 2888 127352353 127352281 5.270000e-08 69.4
29 TraesCS4B01G138900 chr1B 84.932 73 6 1 2821 2888 645568240 645568312 5.270000e-08 69.4
30 TraesCS4B01G138900 chr1A 84.932 73 6 3 2821 2888 448907037 448907109 5.270000e-08 69.4
31 TraesCS4B01G138900 chrUn 83.562 73 7 2 2821 2888 77893475 77893547 2.450000e-06 63.9


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 TraesCS4B01G138900 chr4B 183001095 183004039 2944 True 5439.000000 5439 100.0000 1 2945 1 chr4B.!!$R1 2944
1 TraesCS4B01G138900 chr4D 120069976 120072550 2574 True 1050.666667 2935 94.7320 765 2945 3 chr4D.!!$R1 2180
2 TraesCS4B01G138900 chr4A 451593361 451595470 2109 True 727.400000 2473 95.5410 765 2667 4 chr4A.!!$R2 1902
3 TraesCS4B01G138900 chr2D 327623101 327623962 861 False 1077.000000 1077 89.2240 1082 1943 1 chr2D.!!$F1 861
4 TraesCS4B01G138900 chr2B 396956911 396957772 861 False 1072.000000 1072 89.1080 1082 1943 1 chr2B.!!$F1 861
5 TraesCS4B01G138900 chr2A 432591809 432592670 861 False 1061.000000 1061 88.8760 1082 1943 1 chr2A.!!$F1 861
6 TraesCS4B01G138900 chr6B 393676864 393678651 1787 False 416.000000 425 85.2765 157 557 2 chr6B.!!$F1 400
7 TraesCS4B01G138900 chr6D 176822271 176824365 2094 False 383.000000 385 83.9620 157 557 2 chr6D.!!$F1 400

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
47 48 0.035725 GCCTTAGGCCGTGTTAGGTT 60.036 55.0 13.12 0.0 44.06 3.5 F
50 51 0.247185 TTAGGCCGTGTTAGGTTCGG 59.753 55.0 0.00 0.0 45.94 4.3 F
90 91 0.552848 CCCCTGCTCTCTCTCTCTCT 59.447 60.0 0.00 0.0 0.00 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 2431 1.966762 CTTGTTGATGTGGTGGGCC 59.033 57.895 0.0 0.0 0.0 5.80 R
1932 3070 2.891580 GGTATGAAGCTACTGGGATCGA 59.108 50.000 0.0 0.0 0.0 3.59 R
2072 3214 0.029300 CTCAACTGGCAACCAACACG 59.971 55.000 0.0 0.0 30.8 4.49 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.829728 TCTAGGGTTATAGAGGAGGCC 57.170 52.381 0.00 0.00 0.00 5.19
21 22 2.041350 TCTAGGGTTATAGAGGAGGCCG 59.959 54.545 0.00 0.00 0.00 6.13
22 23 0.858369 AGGGTTATAGAGGAGGCCGA 59.142 55.000 0.00 0.00 0.00 5.54
23 24 0.967662 GGGTTATAGAGGAGGCCGAC 59.032 60.000 0.00 0.00 0.00 4.79
24 25 0.967662 GGTTATAGAGGAGGCCGACC 59.032 60.000 13.01 13.01 0.00 4.79
45 46 4.534401 GCCTTAGGCCGTGTTAGG 57.466 61.111 13.12 2.03 44.06 2.69
46 47 1.600638 GCCTTAGGCCGTGTTAGGT 59.399 57.895 13.12 0.00 44.06 3.08
47 48 0.035725 GCCTTAGGCCGTGTTAGGTT 60.036 55.000 13.12 0.00 44.06 3.50
48 49 2.010544 GCCTTAGGCCGTGTTAGGTTC 61.011 57.143 13.12 0.00 44.06 3.62
49 50 1.636988 CTTAGGCCGTGTTAGGTTCG 58.363 55.000 0.00 0.00 0.00 3.95
50 51 0.247185 TTAGGCCGTGTTAGGTTCGG 59.753 55.000 0.00 0.00 45.94 4.30
51 52 0.899717 TAGGCCGTGTTAGGTTCGGT 60.900 55.000 0.00 0.00 45.11 4.69
52 53 2.030958 GGCCGTGTTAGGTTCGGTG 61.031 63.158 0.00 0.00 45.11 4.94
53 54 2.030958 GCCGTGTTAGGTTCGGTGG 61.031 63.158 0.00 0.00 45.11 4.61
54 55 1.375013 CCGTGTTAGGTTCGGTGGG 60.375 63.158 0.00 0.00 39.51 4.61
55 56 2.030958 CGTGTTAGGTTCGGTGGGC 61.031 63.158 0.00 0.00 0.00 5.36
56 57 1.071814 GTGTTAGGTTCGGTGGGCA 59.928 57.895 0.00 0.00 0.00 5.36
57 58 0.953960 GTGTTAGGTTCGGTGGGCAG 60.954 60.000 0.00 0.00 0.00 4.85
58 59 1.376812 GTTAGGTTCGGTGGGCAGG 60.377 63.158 0.00 0.00 0.00 4.85
59 60 3.262448 TTAGGTTCGGTGGGCAGGC 62.262 63.158 0.00 0.00 0.00 4.85
70 71 3.766691 GGCAGGCCCATTGTGCTG 61.767 66.667 13.07 0.00 37.37 4.41
71 72 4.446413 GCAGGCCCATTGTGCTGC 62.446 66.667 0.00 0.00 34.23 5.25
72 73 3.766691 CAGGCCCATTGTGCTGCC 61.767 66.667 0.00 0.00 44.35 4.85
76 77 3.072468 CCCATTGTGCTGCCCCTG 61.072 66.667 0.00 0.00 0.00 4.45
77 78 3.766691 CCATTGTGCTGCCCCTGC 61.767 66.667 0.00 0.00 38.26 4.85
78 79 2.678934 CATTGTGCTGCCCCTGCT 60.679 61.111 0.00 0.00 38.71 4.24
79 80 2.362120 ATTGTGCTGCCCCTGCTC 60.362 61.111 0.00 0.00 38.71 4.26
80 81 2.915504 ATTGTGCTGCCCCTGCTCT 61.916 57.895 0.00 0.00 38.71 4.09
81 82 2.833604 ATTGTGCTGCCCCTGCTCTC 62.834 60.000 0.00 0.00 38.71 3.20
82 83 3.715097 GTGCTGCCCCTGCTCTCT 61.715 66.667 0.00 0.00 38.71 3.10
83 84 3.397439 TGCTGCCCCTGCTCTCTC 61.397 66.667 0.00 0.00 38.71 3.20
84 85 3.082701 GCTGCCCCTGCTCTCTCT 61.083 66.667 0.00 0.00 38.71 3.10
85 86 3.092780 GCTGCCCCTGCTCTCTCTC 62.093 68.421 0.00 0.00 38.71 3.20
86 87 1.381599 CTGCCCCTGCTCTCTCTCT 60.382 63.158 0.00 0.00 38.71 3.10
87 88 1.381056 TGCCCCTGCTCTCTCTCTC 60.381 63.158 0.00 0.00 38.71 3.20
88 89 1.076044 GCCCCTGCTCTCTCTCTCT 60.076 63.158 0.00 0.00 33.53 3.10
89 90 1.109323 GCCCCTGCTCTCTCTCTCTC 61.109 65.000 0.00 0.00 33.53 3.20
90 91 0.552848 CCCCTGCTCTCTCTCTCTCT 59.447 60.000 0.00 0.00 0.00 3.10
91 92 1.477558 CCCCTGCTCTCTCTCTCTCTC 60.478 61.905 0.00 0.00 0.00 3.20
92 93 1.492176 CCCTGCTCTCTCTCTCTCTCT 59.508 57.143 0.00 0.00 0.00 3.10
93 94 2.486191 CCCTGCTCTCTCTCTCTCTCTC 60.486 59.091 0.00 0.00 0.00 3.20
94 95 2.437281 CCTGCTCTCTCTCTCTCTCTCT 59.563 54.545 0.00 0.00 0.00 3.10
95 96 3.494048 CCTGCTCTCTCTCTCTCTCTCTC 60.494 56.522 0.00 0.00 0.00 3.20
96 97 3.378512 TGCTCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
97 98 3.386078 TGCTCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
98 99 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
99 100 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
100 101 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
101 102 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
102 103 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
103 104 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
104 105 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
105 106 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
106 107 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
107 108 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
108 109 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
109 110 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
110 111 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
111 112 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
112 113 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
113 114 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
114 115 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
115 116 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
116 117 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
117 118 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
118 119 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
119 120 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
120 121 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
121 122 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
122 123 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
123 124 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
124 125 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
125 126 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
126 127 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
127 128 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
128 129 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
129 130 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
130 131 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
131 132 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
132 133 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
133 134 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
134 135 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
135 136 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
136 137 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
137 138 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
138 139 5.596361 TCTCTCTCTCTCTCTCTCTCTCTTC 59.404 48.000 0.00 0.00 0.00 2.87
139 140 5.523588 TCTCTCTCTCTCTCTCTCTCTTCT 58.476 45.833 0.00 0.00 0.00 2.85
140 141 5.960811 TCTCTCTCTCTCTCTCTCTCTTCTT 59.039 44.000 0.00 0.00 0.00 2.52
141 142 6.441924 TCTCTCTCTCTCTCTCTCTCTTCTTT 59.558 42.308 0.00 0.00 0.00 2.52
142 143 7.619698 TCTCTCTCTCTCTCTCTCTCTTCTTTA 59.380 40.741 0.00 0.00 0.00 1.85
143 144 8.324191 TCTCTCTCTCTCTCTCTCTTCTTTAT 57.676 38.462 0.00 0.00 0.00 1.40
144 145 8.772250 TCTCTCTCTCTCTCTCTCTTCTTTATT 58.228 37.037 0.00 0.00 0.00 1.40
145 146 9.401058 CTCTCTCTCTCTCTCTCTTCTTTATTT 57.599 37.037 0.00 0.00 0.00 1.40
146 147 9.396022 TCTCTCTCTCTCTCTCTTCTTTATTTC 57.604 37.037 0.00 0.00 0.00 2.17
147 148 8.519799 TCTCTCTCTCTCTCTTCTTTATTTCC 57.480 38.462 0.00 0.00 0.00 3.13
148 149 8.336235 TCTCTCTCTCTCTCTTCTTTATTTCCT 58.664 37.037 0.00 0.00 0.00 3.36
149 150 8.893563 TCTCTCTCTCTCTTCTTTATTTCCTT 57.106 34.615 0.00 0.00 0.00 3.36
150 151 9.320295 TCTCTCTCTCTCTTCTTTATTTCCTTT 57.680 33.333 0.00 0.00 0.00 3.11
151 152 9.942850 CTCTCTCTCTCTTCTTTATTTCCTTTT 57.057 33.333 0.00 0.00 0.00 2.27
152 153 9.936759 TCTCTCTCTCTTCTTTATTTCCTTTTC 57.063 33.333 0.00 0.00 0.00 2.29
153 154 9.161629 CTCTCTCTCTTCTTTATTTCCTTTTCC 57.838 37.037 0.00 0.00 0.00 3.13
154 155 8.103935 TCTCTCTCTTCTTTATTTCCTTTTCCC 58.896 37.037 0.00 0.00 0.00 3.97
155 156 7.755618 TCTCTCTTCTTTATTTCCTTTTCCCA 58.244 34.615 0.00 0.00 0.00 4.37
190 191 2.816672 GAGAGAGGGTTGCCTCAAAAAG 59.183 50.000 0.00 0.00 39.13 2.27
208 211 5.458451 AAAAGGAAATTAGAGAGAGGGGG 57.542 43.478 0.00 0.00 0.00 5.40
211 214 4.711055 AGGAAATTAGAGAGAGGGGGAAA 58.289 43.478 0.00 0.00 0.00 3.13
231 234 7.441836 GGGAAAAGAAGAAAAGAAATAGCCAA 58.558 34.615 0.00 0.00 0.00 4.52
232 235 7.385205 GGGAAAAGAAGAAAAGAAATAGCCAAC 59.615 37.037 0.00 0.00 0.00 3.77
307 330 5.988561 TCCCAATTTGGAAAAGTTGAATTCG 59.011 36.000 17.24 0.00 40.96 3.34
371 394 7.228108 TGGAGCTCTGATAAATGCAGAAATAAG 59.772 37.037 14.64 0.00 41.45 1.73
393 416 1.834540 AGGGAAAGGTTTGGAGGTCT 58.165 50.000 0.00 0.00 0.00 3.85
399 422 6.062749 GGGAAAGGTTTGGAGGTCTATATTC 58.937 44.000 0.00 0.00 0.00 1.75
430 453 3.763057 AGGCGTGGGATTTTAGAAAAGT 58.237 40.909 0.00 0.00 0.00 2.66
433 456 4.684242 GGCGTGGGATTTTAGAAAAGTTTG 59.316 41.667 0.00 0.00 0.00 2.93
435 458 5.508320 GCGTGGGATTTTAGAAAAGTTTGGA 60.508 40.000 0.00 0.00 0.00 3.53
437 460 6.640907 CGTGGGATTTTAGAAAAGTTTGGAAG 59.359 38.462 0.00 0.00 0.00 3.46
442 467 9.208022 GGATTTTAGAAAAGTTTGGAAGGATTG 57.792 33.333 0.00 0.00 0.00 2.67
445 470 7.524717 TTAGAAAAGTTTGGAAGGATTGGAG 57.475 36.000 0.00 0.00 0.00 3.86
450 475 2.493675 GTTTGGAAGGATTGGAGAAGGC 59.506 50.000 0.00 0.00 0.00 4.35
480 1327 8.962884 AAACAAAAGCTAGGTTCAAATGATTT 57.037 26.923 7.80 6.21 0.00 2.17
513 1360 9.988350 AACATTCATATTTAGTTGCTTTAGTCG 57.012 29.630 0.00 0.00 0.00 4.18
514 1361 9.162764 ACATTCATATTTAGTTGCTTTAGTCGT 57.837 29.630 0.00 0.00 0.00 4.34
516 1363 9.988350 ATTCATATTTAGTTGCTTTAGTCGTTG 57.012 29.630 0.00 0.00 0.00 4.10
528 1375 8.912787 TGCTTTAGTCGTTGTTTTTATTTCAA 57.087 26.923 0.00 0.00 0.00 2.69
535 1382 8.274939 AGTCGTTGTTTTTATTTCAAATGCATG 58.725 29.630 0.00 0.00 0.00 4.06
557 1404 6.698008 TGTATTCATGTGAATTCATGGGTC 57.302 37.500 12.12 0.00 41.64 4.46
558 1405 5.593909 TGTATTCATGTGAATTCATGGGTCC 59.406 40.000 12.12 0.00 41.64 4.46
560 1407 2.582172 TCATGTGAATTCATGGGTCCCT 59.418 45.455 12.12 0.00 43.52 4.20
561 1408 3.785325 TCATGTGAATTCATGGGTCCCTA 59.215 43.478 12.12 0.00 43.52 3.53
562 1409 4.416513 TCATGTGAATTCATGGGTCCCTAT 59.583 41.667 12.12 0.00 43.52 2.57
568 1537 7.341769 TGTGAATTCATGGGTCCCTATTTTTAG 59.658 37.037 12.12 0.00 0.00 1.85
578 1547 6.127101 GGTCCCTATTTTTAGGCATTACTGT 58.873 40.000 0.00 0.00 35.90 3.55
582 1551 8.719596 TCCCTATTTTTAGGCATTACTGTCATA 58.280 33.333 0.00 0.00 35.90 2.15
615 1584 7.320443 ACATATGTGTTGTGCGATATTTCTT 57.680 32.000 7.78 0.00 34.01 2.52
629 1598 3.598019 ATTTCTTCCGTTGCAATGCAT 57.402 38.095 9.39 0.00 38.76 3.96
630 1599 3.383620 TTTCTTCCGTTGCAATGCATT 57.616 38.095 9.39 5.99 38.76 3.56
632 1601 1.612950 TCTTCCGTTGCAATGCATTGT 59.387 42.857 33.67 2.90 38.76 2.71
669 1638 9.998106 AGTAGATAAACATGTGAGTAGTTGTTT 57.002 29.630 0.00 5.38 42.91 2.83
672 1641 9.337396 AGATAAACATGTGAGTAGTTGTTTTGA 57.663 29.630 0.00 0.00 41.24 2.69
676 1645 9.730420 AAACATGTGAGTAGTTGTTTTGATAAC 57.270 29.630 0.00 0.00 38.72 1.89
677 1646 8.677148 ACATGTGAGTAGTTGTTTTGATAACT 57.323 30.769 0.00 0.00 40.09 2.24
679 1648 9.950680 CATGTGAGTAGTTGTTTTGATAACTTT 57.049 29.630 0.00 0.00 38.11 2.66
691 1660 9.377312 TGTTTTGATAACTTTTTCTTTTGAGGG 57.623 29.630 0.00 0.00 0.00 4.30
692 1661 9.594478 GTTTTGATAACTTTTTCTTTTGAGGGA 57.406 29.630 0.00 0.00 0.00 4.20
695 1664 9.594478 TTGATAACTTTTTCTTTTGAGGGAAAC 57.406 29.630 0.00 0.00 32.20 2.78
696 1665 8.754080 TGATAACTTTTTCTTTTGAGGGAAACA 58.246 29.630 0.00 0.00 32.20 2.83
697 1666 9.594478 GATAACTTTTTCTTTTGAGGGAAACAA 57.406 29.630 0.00 0.00 32.20 2.83
698 1667 7.667043 AACTTTTTCTTTTGAGGGAAACAAC 57.333 32.000 0.00 0.00 32.20 3.32
699 1668 6.170506 ACTTTTTCTTTTGAGGGAAACAACC 58.829 36.000 0.00 0.00 32.20 3.77
700 1669 6.013725 ACTTTTTCTTTTGAGGGAAACAACCT 60.014 34.615 0.00 0.00 42.18 3.50
701 1670 5.337578 TTTCTTTTGAGGGAAACAACCTG 57.662 39.130 0.00 0.00 38.79 4.00
702 1671 4.243793 TCTTTTGAGGGAAACAACCTGA 57.756 40.909 0.00 0.00 38.79 3.86
703 1672 4.207165 TCTTTTGAGGGAAACAACCTGAG 58.793 43.478 0.00 0.00 38.79 3.35
704 1673 1.981256 TTGAGGGAAACAACCTGAGC 58.019 50.000 0.00 0.00 38.79 4.26
705 1674 0.843309 TGAGGGAAACAACCTGAGCA 59.157 50.000 0.00 0.00 38.79 4.26
706 1675 1.425066 TGAGGGAAACAACCTGAGCAT 59.575 47.619 0.00 0.00 38.79 3.79
707 1676 2.158475 TGAGGGAAACAACCTGAGCATT 60.158 45.455 0.00 0.00 38.79 3.56
708 1677 2.489722 GAGGGAAACAACCTGAGCATTC 59.510 50.000 0.00 0.00 38.79 2.67
709 1678 2.158475 AGGGAAACAACCTGAGCATTCA 60.158 45.455 0.00 0.00 36.85 2.57
782 1751 3.426787 TTTTTAGGCAACCGAGATGGA 57.573 42.857 0.00 0.00 42.00 3.41
812 1789 1.611519 TTGGATTGTTGGACCGGAAC 58.388 50.000 9.46 2.26 0.00 3.62
835 1812 4.506255 GCCCATTAGCCCGGCACT 62.506 66.667 13.15 0.00 42.52 4.40
836 1813 2.203209 CCCATTAGCCCGGCACTC 60.203 66.667 13.15 0.00 0.00 3.51
837 1814 2.746375 CCCATTAGCCCGGCACTCT 61.746 63.158 13.15 0.00 0.00 3.24
838 1815 1.227674 CCATTAGCCCGGCACTCTC 60.228 63.158 13.15 0.00 0.00 3.20
839 1816 1.690219 CCATTAGCCCGGCACTCTCT 61.690 60.000 13.15 0.00 0.00 3.10
847 1824 1.427419 CGGCACTCTCTCTGTCTCG 59.573 63.158 0.00 0.00 0.00 4.04
1092 2125 1.301401 CGCCACCTTCTCCGTCAAA 60.301 57.895 0.00 0.00 0.00 2.69
1608 2641 0.898789 ACATGGACGAGGACGAGGTT 60.899 55.000 0.00 0.00 42.66 3.50
1671 2704 2.435586 CAGACCAAGCAGCTCGGG 60.436 66.667 3.87 7.93 0.00 5.14
1692 2725 2.030562 CTCCCGGTCGTGCAGTTT 59.969 61.111 0.00 0.00 0.00 2.66
1912 3050 2.573609 GATCAACCTGTCCGACCCCG 62.574 65.000 0.00 0.00 0.00 5.73
2072 3214 7.378966 TGTATTATCCAGCAGTACTATCTTGC 58.621 38.462 0.00 0.00 0.00 4.01
2159 3301 2.122167 GGTTGCCCGTGTTTGTCCA 61.122 57.895 0.00 0.00 0.00 4.02
2171 3313 2.165437 TGTTTGTCCAAAACTGGAGTGC 59.835 45.455 0.00 0.00 38.88 4.40
2204 3346 3.320541 TGTTTTGTTGGAGATGGCGAAAT 59.679 39.130 0.00 0.00 0.00 2.17
2218 3360 1.880027 GCGAAATTGACTGGTCTTGGT 59.120 47.619 2.38 0.00 0.00 3.67
2255 3397 3.490348 CTGACCAGACAACAAAATCCCT 58.510 45.455 0.00 0.00 0.00 4.20
2341 3773 1.899814 TGCACGGAGGAACTACTTGAT 59.100 47.619 0.00 0.00 41.60 2.57
2342 3774 2.301870 TGCACGGAGGAACTACTTGATT 59.698 45.455 0.00 0.00 41.60 2.57
2343 3775 3.512329 TGCACGGAGGAACTACTTGATTA 59.488 43.478 0.00 0.00 41.60 1.75
2344 3776 3.864003 GCACGGAGGAACTACTTGATTAC 59.136 47.826 0.00 0.00 41.60 1.89
2345 3777 4.619863 GCACGGAGGAACTACTTGATTACA 60.620 45.833 0.00 0.00 41.60 2.41
2346 3778 5.661458 CACGGAGGAACTACTTGATTACAT 58.339 41.667 0.00 0.00 41.60 2.29
2347 3779 6.682113 GCACGGAGGAACTACTTGATTACATA 60.682 42.308 0.00 0.00 41.60 2.29
2348 3780 6.696148 CACGGAGGAACTACTTGATTACATAC 59.304 42.308 0.00 0.00 41.60 2.39
2349 3781 6.183360 ACGGAGGAACTACTTGATTACATACC 60.183 42.308 0.00 0.00 41.55 2.73
2350 3782 6.214399 GGAGGAACTACTTGATTACATACCG 58.786 44.000 0.00 0.00 41.55 4.02
2351 3783 6.183360 GGAGGAACTACTTGATTACATACCGT 60.183 42.308 0.00 0.00 41.55 4.83
2352 3784 7.013655 GGAGGAACTACTTGATTACATACCGTA 59.986 40.741 0.00 0.00 41.55 4.02
2353 3785 7.710896 AGGAACTACTTGATTACATACCGTAC 58.289 38.462 0.00 0.00 36.02 3.67
2354 3786 7.559170 AGGAACTACTTGATTACATACCGTACT 59.441 37.037 0.00 0.00 36.02 2.73
2355 3787 8.840321 GGAACTACTTGATTACATACCGTACTA 58.160 37.037 0.00 0.00 0.00 1.82
2356 3788 9.875675 GAACTACTTGATTACATACCGTACTAG 57.124 37.037 0.00 0.00 0.00 2.57
2357 3789 8.970859 ACTACTTGATTACATACCGTACTAGT 57.029 34.615 0.00 0.00 0.00 2.57
2362 3794 9.162793 CTTGATTACATACCGTACTAGTAAACG 57.837 37.037 10.59 10.59 38.80 3.60
2375 3807 3.538634 AGTAAACGGAGGATTACAGCC 57.461 47.619 0.00 0.00 36.72 4.85
2391 3823 1.139853 CAGCCTCACCAGATTCCTACC 59.860 57.143 0.00 0.00 0.00 3.18
2403 3835 3.890147 AGATTCCTACCCGCTACTTGTAG 59.110 47.826 3.60 3.60 33.38 2.74
2404 3836 1.396653 TCCTACCCGCTACTTGTAGC 58.603 55.000 19.48 19.48 39.59 3.58
2405 3837 1.108776 CCTACCCGCTACTTGTAGCA 58.891 55.000 26.01 10.69 42.95 3.49
2406 3838 1.479323 CCTACCCGCTACTTGTAGCAA 59.521 52.381 26.01 11.66 42.95 3.91
2407 3839 2.537401 CTACCCGCTACTTGTAGCAAC 58.463 52.381 26.01 4.31 42.95 4.17
2408 3840 0.389426 ACCCGCTACTTGTAGCAACG 60.389 55.000 26.01 16.80 42.95 4.10
2409 3841 0.108992 CCCGCTACTTGTAGCAACGA 60.109 55.000 26.01 0.00 42.95 3.85
2414 3846 2.345942 GCTACTTGTAGCAACGAAGCTC 59.654 50.000 23.12 3.78 45.26 4.09
2431 3863 2.171027 AGCTCTGCTCGGTAGTACTAGT 59.829 50.000 1.87 0.00 30.62 2.57
2436 3868 5.491070 TCTGCTCGGTAGTACTAGTAAACA 58.509 41.667 3.61 0.00 0.00 2.83
2543 3977 1.682257 GTGCAGGCCCTCTCTTTCT 59.318 57.895 0.00 0.00 0.00 2.52
2544 3978 0.037447 GTGCAGGCCCTCTCTTTCTT 59.963 55.000 0.00 0.00 0.00 2.52
2545 3979 0.037303 TGCAGGCCCTCTCTTTCTTG 59.963 55.000 0.00 0.00 0.00 3.02
2546 3980 0.679321 GCAGGCCCTCTCTTTCTTGG 60.679 60.000 0.00 0.00 0.00 3.61
2547 3981 0.987294 CAGGCCCTCTCTTTCTTGGA 59.013 55.000 0.00 0.00 0.00 3.53
2548 3982 0.988063 AGGCCCTCTCTTTCTTGGAC 59.012 55.000 0.00 0.00 0.00 4.02
2549 3983 0.391793 GGCCCTCTCTTTCTTGGACG 60.392 60.000 0.00 0.00 0.00 4.79
2555 3989 1.902508 TCTCTTTCTTGGACGATGGCT 59.097 47.619 0.00 0.00 0.00 4.75
2571 4005 4.261072 CGATGGCTCATGATTTCTTTCCTG 60.261 45.833 0.00 0.00 0.00 3.86
2577 4011 5.119743 GCTCATGATTTCTTTCCTGTTTTGC 59.880 40.000 0.00 0.00 0.00 3.68
2581 4015 1.036707 TTCTTTCCTGTTTTGCGGGG 58.963 50.000 0.00 0.00 43.94 5.73
2698 4132 4.450976 TGATTAGCATAGTGCCGTTGATT 58.549 39.130 0.00 0.00 46.52 2.57
2719 4153 1.202687 TGGCTGTGTGCATATAGAGGC 60.203 52.381 11.41 11.00 45.15 4.70
2723 4157 0.320771 GTGTGCATATAGAGGCCGGG 60.321 60.000 2.18 0.00 0.00 5.73
2739 4173 0.399075 CGGGTGTGGGGAGTAAACTT 59.601 55.000 0.00 0.00 0.00 2.66
2783 4731 5.751680 CACAAAGACATACTCCAACAGTTG 58.248 41.667 6.28 6.28 36.43 3.16
2801 4749 1.648504 TGATCAGCTGCTCACGATTG 58.351 50.000 16.06 0.00 0.00 2.67
2807 4755 3.192633 TCAGCTGCTCACGATTGTAAGTA 59.807 43.478 9.47 0.00 0.00 2.24
2808 4756 3.304559 CAGCTGCTCACGATTGTAAGTAC 59.695 47.826 0.00 0.00 0.00 2.73
2809 4757 2.603560 GCTGCTCACGATTGTAAGTACC 59.396 50.000 0.00 0.00 0.00 3.34
2810 4758 3.187700 CTGCTCACGATTGTAAGTACCC 58.812 50.000 0.00 0.00 0.00 3.69
2811 4759 2.093869 TGCTCACGATTGTAAGTACCCC 60.094 50.000 0.00 0.00 0.00 4.95
2812 4760 2.167900 GCTCACGATTGTAAGTACCCCT 59.832 50.000 0.00 0.00 0.00 4.79
2813 4761 3.782046 CTCACGATTGTAAGTACCCCTG 58.218 50.000 0.00 0.00 0.00 4.45
2814 4762 3.167485 TCACGATTGTAAGTACCCCTGT 58.833 45.455 0.00 0.00 0.00 4.00
2815 4763 4.343231 TCACGATTGTAAGTACCCCTGTA 58.657 43.478 0.00 0.00 0.00 2.74
2886 5086 8.994429 CTCTGATGTTTATTTACAGAGTGAGT 57.006 34.615 0.00 0.00 45.11 3.41
2893 5093 9.048446 TGTTTATTTACAGAGTGAGTAACAACC 57.952 33.333 0.00 0.00 31.67 3.77
2898 5098 4.950050 ACAGAGTGAGTAACAACCAAGAG 58.050 43.478 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.041350 CGGCCTCCTCTATAACCCTAGA 59.959 54.545 0.00 0.00 0.00 2.43
1 2 2.041350 TCGGCCTCCTCTATAACCCTAG 59.959 54.545 0.00 0.00 0.00 3.02
2 3 2.068181 TCGGCCTCCTCTATAACCCTA 58.932 52.381 0.00 0.00 0.00 3.53
3 4 0.858369 TCGGCCTCCTCTATAACCCT 59.142 55.000 0.00 0.00 0.00 4.34
4 5 0.967662 GTCGGCCTCCTCTATAACCC 59.032 60.000 0.00 0.00 0.00 4.11
5 6 0.967662 GGTCGGCCTCCTCTATAACC 59.032 60.000 0.00 0.00 0.00 2.85
6 7 1.614413 CAGGTCGGCCTCCTCTATAAC 59.386 57.143 5.00 0.00 44.97 1.89
7 8 1.480683 CCAGGTCGGCCTCCTCTATAA 60.481 57.143 5.00 0.00 44.97 0.98
8 9 0.112606 CCAGGTCGGCCTCCTCTATA 59.887 60.000 5.00 0.00 44.97 1.31
9 10 1.152440 CCAGGTCGGCCTCCTCTAT 60.152 63.158 5.00 0.00 44.97 1.98
10 11 2.279073 CCAGGTCGGCCTCCTCTA 59.721 66.667 5.00 0.00 44.97 2.43
11 12 4.787280 CCCAGGTCGGCCTCCTCT 62.787 72.222 5.00 0.00 44.97 3.69
19 20 4.176752 GCCTAAGGCCCAGGTCGG 62.177 72.222 19.64 5.04 44.06 4.79
29 30 1.738030 CGAACCTAACACGGCCTAAGG 60.738 57.143 0.00 2.56 0.00 2.69
30 31 1.636988 CGAACCTAACACGGCCTAAG 58.363 55.000 0.00 0.00 0.00 2.18
31 32 0.247185 CCGAACCTAACACGGCCTAA 59.753 55.000 0.00 0.00 40.19 2.69
32 33 1.892338 CCGAACCTAACACGGCCTA 59.108 57.895 0.00 0.00 40.19 3.93
33 34 2.660802 CCGAACCTAACACGGCCT 59.339 61.111 0.00 0.00 40.19 5.19
37 38 2.030958 GCCCACCGAACCTAACACG 61.031 63.158 0.00 0.00 0.00 4.49
38 39 0.953960 CTGCCCACCGAACCTAACAC 60.954 60.000 0.00 0.00 0.00 3.32
39 40 1.373435 CTGCCCACCGAACCTAACA 59.627 57.895 0.00 0.00 0.00 2.41
40 41 1.376812 CCTGCCCACCGAACCTAAC 60.377 63.158 0.00 0.00 0.00 2.34
41 42 3.074281 CCTGCCCACCGAACCTAA 58.926 61.111 0.00 0.00 0.00 2.69
42 43 3.712907 GCCTGCCCACCGAACCTA 61.713 66.667 0.00 0.00 0.00 3.08
53 54 3.766691 CAGCACAATGGGCCTGCC 61.767 66.667 2.80 0.00 0.00 4.85
54 55 4.446413 GCAGCACAATGGGCCTGC 62.446 66.667 14.08 14.08 0.00 4.85
55 56 3.766691 GGCAGCACAATGGGCCTG 61.767 66.667 2.80 3.04 43.09 4.85
59 60 3.072468 CAGGGGCAGCACAATGGG 61.072 66.667 0.00 0.00 0.00 4.00
60 61 3.766691 GCAGGGGCAGCACAATGG 61.767 66.667 0.00 0.00 40.72 3.16
61 62 2.678934 AGCAGGGGCAGCACAATG 60.679 61.111 0.00 0.00 44.61 2.82
62 63 2.362120 GAGCAGGGGCAGCACAAT 60.362 61.111 0.00 0.00 44.61 2.71
63 64 3.557903 GAGAGCAGGGGCAGCACAA 62.558 63.158 0.00 0.00 44.61 3.33
64 65 4.025858 GAGAGCAGGGGCAGCACA 62.026 66.667 0.00 0.00 44.61 4.57
65 66 3.678951 GAGAGAGCAGGGGCAGCAC 62.679 68.421 0.00 0.00 44.61 4.40
66 67 3.397439 GAGAGAGCAGGGGCAGCA 61.397 66.667 0.00 0.00 44.61 4.41
67 68 3.082701 AGAGAGAGCAGGGGCAGC 61.083 66.667 0.00 0.00 44.61 5.25
68 69 1.381599 AGAGAGAGAGCAGGGGCAG 60.382 63.158 0.00 0.00 44.61 4.85
69 70 1.381056 GAGAGAGAGAGCAGGGGCA 60.381 63.158 0.00 0.00 44.61 5.36
70 71 1.076044 AGAGAGAGAGAGCAGGGGC 60.076 63.158 0.00 0.00 41.61 5.80
71 72 0.552848 AGAGAGAGAGAGAGCAGGGG 59.447 60.000 0.00 0.00 0.00 4.79
72 73 1.492176 AGAGAGAGAGAGAGAGCAGGG 59.508 57.143 0.00 0.00 0.00 4.45
73 74 2.437281 AGAGAGAGAGAGAGAGAGCAGG 59.563 54.545 0.00 0.00 0.00 4.85
74 75 3.387374 AGAGAGAGAGAGAGAGAGAGCAG 59.613 52.174 0.00 0.00 0.00 4.24
75 76 3.378512 AGAGAGAGAGAGAGAGAGAGCA 58.621 50.000 0.00 0.00 0.00 4.26
76 77 3.640967 AGAGAGAGAGAGAGAGAGAGAGC 59.359 52.174 0.00 0.00 0.00 4.09
77 78 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
78 79 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
79 80 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
80 81 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
81 82 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
82 83 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
83 84 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
84 85 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
85 86 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
86 87 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
87 88 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
88 89 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
89 90 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
90 91 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
91 92 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
92 93 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
93 94 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
94 95 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
95 96 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
96 97 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
97 98 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
98 99 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
99 100 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
100 101 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
101 102 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
102 103 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
103 104 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
104 105 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
105 106 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
106 107 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
107 108 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
108 109 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
109 110 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
110 111 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
111 112 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
112 113 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
113 114 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
114 115 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
115 116 5.598005 AGAAGAGAGAGAGAGAGAGAGAGAG 59.402 48.000 0.00 0.00 0.00 3.20
116 117 5.523588 AGAAGAGAGAGAGAGAGAGAGAGA 58.476 45.833 0.00 0.00 0.00 3.10
117 118 5.867903 AGAAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
118 119 6.627087 AAAGAAGAGAGAGAGAGAGAGAGA 57.373 41.667 0.00 0.00 0.00 3.10
119 120 8.970859 AATAAAGAAGAGAGAGAGAGAGAGAG 57.029 38.462 0.00 0.00 0.00 3.20
120 121 9.396022 GAAATAAAGAAGAGAGAGAGAGAGAGA 57.604 37.037 0.00 0.00 0.00 3.10
121 122 8.624776 GGAAATAAAGAAGAGAGAGAGAGAGAG 58.375 40.741 0.00 0.00 0.00 3.20
122 123 8.336235 AGGAAATAAAGAAGAGAGAGAGAGAGA 58.664 37.037 0.00 0.00 0.00 3.10
123 124 8.525290 AGGAAATAAAGAAGAGAGAGAGAGAG 57.475 38.462 0.00 0.00 0.00 3.20
124 125 8.893563 AAGGAAATAAAGAAGAGAGAGAGAGA 57.106 34.615 0.00 0.00 0.00 3.10
125 126 9.942850 AAAAGGAAATAAAGAAGAGAGAGAGAG 57.057 33.333 0.00 0.00 0.00 3.20
126 127 9.936759 GAAAAGGAAATAAAGAAGAGAGAGAGA 57.063 33.333 0.00 0.00 0.00 3.10
127 128 9.161629 GGAAAAGGAAATAAAGAAGAGAGAGAG 57.838 37.037 0.00 0.00 0.00 3.20
128 129 8.103935 GGGAAAAGGAAATAAAGAAGAGAGAGA 58.896 37.037 0.00 0.00 0.00 3.10
129 130 7.885399 TGGGAAAAGGAAATAAAGAAGAGAGAG 59.115 37.037 0.00 0.00 0.00 3.20
130 131 7.755618 TGGGAAAAGGAAATAAAGAAGAGAGA 58.244 34.615 0.00 0.00 0.00 3.10
131 132 8.586879 ATGGGAAAAGGAAATAAAGAAGAGAG 57.413 34.615 0.00 0.00 0.00 3.20
132 133 8.956446 AATGGGAAAAGGAAATAAAGAAGAGA 57.044 30.769 0.00 0.00 0.00 3.10
142 143 9.859152 TGATTTTTGTAAATGGGAAAAGGAAAT 57.141 25.926 0.00 0.00 34.16 2.17
143 144 9.336171 CTGATTTTTGTAAATGGGAAAAGGAAA 57.664 29.630 0.00 0.00 34.16 3.13
144 145 8.709308 TCTGATTTTTGTAAATGGGAAAAGGAA 58.291 29.630 0.00 0.00 34.16 3.36
145 146 8.256356 TCTGATTTTTGTAAATGGGAAAAGGA 57.744 30.769 0.00 0.00 34.16 3.36
146 147 8.367156 TCTCTGATTTTTGTAAATGGGAAAAGG 58.633 33.333 0.00 0.00 34.16 3.11
147 148 9.415544 CTCTCTGATTTTTGTAAATGGGAAAAG 57.584 33.333 0.00 0.00 34.16 2.27
148 149 9.142014 TCTCTCTGATTTTTGTAAATGGGAAAA 57.858 29.630 0.00 0.00 34.16 2.29
149 150 8.704849 TCTCTCTGATTTTTGTAAATGGGAAA 57.295 30.769 0.00 0.00 34.16 3.13
150 151 7.394359 CCTCTCTCTGATTTTTGTAAATGGGAA 59.606 37.037 0.00 0.00 34.16 3.97
151 152 6.886459 CCTCTCTCTGATTTTTGTAAATGGGA 59.114 38.462 0.00 0.00 34.16 4.37
152 153 6.096001 CCCTCTCTCTGATTTTTGTAAATGGG 59.904 42.308 0.00 0.00 34.16 4.00
153 154 6.660949 ACCCTCTCTCTGATTTTTGTAAATGG 59.339 38.462 0.00 0.00 34.16 3.16
154 155 7.693969 ACCCTCTCTCTGATTTTTGTAAATG 57.306 36.000 0.00 0.00 34.16 2.32
155 156 7.309438 GCAACCCTCTCTCTGATTTTTGTAAAT 60.309 37.037 0.00 0.00 36.68 1.40
162 163 2.646798 AGGCAACCCTCTCTCTGATTTT 59.353 45.455 0.00 0.00 36.46 1.82
190 191 5.191921 TCTTTTCCCCCTCTCTCTAATTTCC 59.808 44.000 0.00 0.00 0.00 3.13
208 211 7.860872 TCGTTGGCTATTTCTTTTCTTCTTTTC 59.139 33.333 0.00 0.00 0.00 2.29
211 214 6.877611 TCGTTGGCTATTTCTTTTCTTCTT 57.122 33.333 0.00 0.00 0.00 2.52
283 306 5.988561 CGAATTCAACTTTTCCAAATTGGGA 59.011 36.000 12.67 0.00 38.32 4.37
288 311 6.040391 TGAGTCCGAATTCAACTTTTCCAAAT 59.960 34.615 6.22 0.00 0.00 2.32
371 394 3.074094 AGACCTCCAAACCTTTCCCTTAC 59.926 47.826 0.00 0.00 0.00 2.34
393 416 6.053005 CCCACGCCTTTTCTACTTGAATATA 58.947 40.000 0.00 0.00 34.24 0.86
399 422 2.178912 TCCCACGCCTTTTCTACTTG 57.821 50.000 0.00 0.00 0.00 3.16
430 453 2.109834 TGCCTTCTCCAATCCTTCCAAA 59.890 45.455 0.00 0.00 0.00 3.28
433 456 1.283321 AGTGCCTTCTCCAATCCTTCC 59.717 52.381 0.00 0.00 0.00 3.46
435 458 4.657814 TTAAGTGCCTTCTCCAATCCTT 57.342 40.909 0.00 0.00 0.00 3.36
437 460 4.079253 TGTTTAAGTGCCTTCTCCAATCC 58.921 43.478 0.00 0.00 0.00 3.01
442 467 4.038042 AGCTTTTGTTTAAGTGCCTTCTCC 59.962 41.667 0.00 0.00 0.00 3.71
445 470 5.009710 ACCTAGCTTTTGTTTAAGTGCCTTC 59.990 40.000 0.00 0.00 0.00 3.46
450 475 8.755018 CATTTGAACCTAGCTTTTGTTTAAGTG 58.245 33.333 0.00 0.36 0.00 3.16
490 1337 9.988350 CAACGACTAAAGCAACTAAATATGAAT 57.012 29.630 0.00 0.00 0.00 2.57
549 1396 3.529734 TGCCTAAAAATAGGGACCCATGA 59.470 43.478 14.60 0.00 37.69 3.07
551 1398 4.832560 ATGCCTAAAAATAGGGACCCAT 57.167 40.909 14.60 1.12 40.43 4.00
557 1404 7.823745 ATGACAGTAATGCCTAAAAATAGGG 57.176 36.000 4.20 0.00 37.69 3.53
558 1405 9.561069 ACTATGACAGTAATGCCTAAAAATAGG 57.439 33.333 0.00 0.00 36.61 2.57
561 1408 9.461312 TGAACTATGACAGTAATGCCTAAAAAT 57.539 29.630 0.00 0.00 36.04 1.82
562 1409 8.856153 TGAACTATGACAGTAATGCCTAAAAA 57.144 30.769 0.00 0.00 36.04 1.94
568 1537 8.208718 TGTTAATGAACTATGACAGTAATGCC 57.791 34.615 0.00 0.00 36.04 4.40
615 1584 0.957362 TGACAATGCATTGCAACGGA 59.043 45.000 33.94 12.61 43.62 4.69
650 1619 9.730420 GTTATCAAAACAACTACTCACATGTTT 57.270 29.630 0.00 0.00 45.17 2.83
651 1620 9.120538 AGTTATCAAAACAACTACTCACATGTT 57.879 29.630 0.00 0.00 37.59 2.71
653 1622 9.950680 AAAGTTATCAAAACAACTACTCACATG 57.049 29.630 0.00 0.00 33.92 3.21
665 1634 9.377312 CCCTCAAAAGAAAAAGTTATCAAAACA 57.623 29.630 0.00 0.00 0.00 2.83
666 1635 9.594478 TCCCTCAAAAGAAAAAGTTATCAAAAC 57.406 29.630 0.00 0.00 0.00 2.43
669 1638 9.594478 GTTTCCCTCAAAAGAAAAAGTTATCAA 57.406 29.630 0.00 0.00 33.98 2.57
672 1641 9.378551 GTTGTTTCCCTCAAAAGAAAAAGTTAT 57.621 29.630 0.00 0.00 33.98 1.89
674 1643 6.653320 GGTTGTTTCCCTCAAAAGAAAAAGTT 59.347 34.615 0.00 0.00 33.98 2.66
675 1644 6.013725 AGGTTGTTTCCCTCAAAAGAAAAAGT 60.014 34.615 0.00 0.00 33.98 2.66
676 1645 6.313658 CAGGTTGTTTCCCTCAAAAGAAAAAG 59.686 38.462 0.00 0.00 33.98 2.27
677 1646 6.014156 TCAGGTTGTTTCCCTCAAAAGAAAAA 60.014 34.615 0.00 0.00 33.98 1.94
679 1648 5.020132 TCAGGTTGTTTCCCTCAAAAGAAA 58.980 37.500 0.00 0.00 0.00 2.52
681 1650 4.207165 CTCAGGTTGTTTCCCTCAAAAGA 58.793 43.478 0.00 0.00 0.00 2.52
682 1651 3.243535 GCTCAGGTTGTTTCCCTCAAAAG 60.244 47.826 0.00 0.00 0.00 2.27
683 1652 2.693074 GCTCAGGTTGTTTCCCTCAAAA 59.307 45.455 0.00 0.00 0.00 2.44
684 1653 2.306847 GCTCAGGTTGTTTCCCTCAAA 58.693 47.619 0.00 0.00 0.00 2.69
685 1654 1.214175 TGCTCAGGTTGTTTCCCTCAA 59.786 47.619 0.00 0.00 0.00 3.02
686 1655 0.843309 TGCTCAGGTTGTTTCCCTCA 59.157 50.000 0.00 0.00 0.00 3.86
687 1656 2.206576 ATGCTCAGGTTGTTTCCCTC 57.793 50.000 0.00 0.00 0.00 4.30
688 1657 2.158475 TGAATGCTCAGGTTGTTTCCCT 60.158 45.455 0.00 0.00 0.00 4.20
689 1658 2.229784 CTGAATGCTCAGGTTGTTTCCC 59.770 50.000 0.00 0.00 44.72 3.97
690 1659 3.565905 CTGAATGCTCAGGTTGTTTCC 57.434 47.619 0.00 0.00 44.72 3.13
697 1666 8.380867 TCAATATATCAATCTGAATGCTCAGGT 58.619 33.333 3.36 0.00 45.45 4.00
762 1731 3.426787 TCCATCTCGGTTGCCTAAAAA 57.573 42.857 0.00 0.00 35.57 1.94
763 1732 3.278574 CATCCATCTCGGTTGCCTAAAA 58.721 45.455 0.00 0.00 35.57 1.52
781 1750 6.986231 GTCCAACAATCCAATTTTATCCCATC 59.014 38.462 0.00 0.00 0.00 3.51
782 1751 6.126796 GGTCCAACAATCCAATTTTATCCCAT 60.127 38.462 0.00 0.00 0.00 4.00
832 1809 1.302383 ACGCCGAGACAGAGAGAGTG 61.302 60.000 0.00 0.00 0.00 3.51
833 1810 1.003112 ACGCCGAGACAGAGAGAGT 60.003 57.895 0.00 0.00 0.00 3.24
834 1811 1.302383 ACACGCCGAGACAGAGAGAG 61.302 60.000 0.00 0.00 0.00 3.20
835 1812 1.299562 GACACGCCGAGACAGAGAGA 61.300 60.000 0.00 0.00 0.00 3.10
836 1813 1.135731 GACACGCCGAGACAGAGAG 59.864 63.158 0.00 0.00 0.00 3.20
837 1814 2.333417 GGACACGCCGAGACAGAGA 61.333 63.158 0.00 0.00 0.00 3.10
838 1815 2.179517 GGACACGCCGAGACAGAG 59.820 66.667 0.00 0.00 0.00 3.35
839 1816 2.596338 TGGACACGCCGAGACAGA 60.596 61.111 0.00 0.00 40.66 3.41
847 1824 2.117941 GACTTGCAACTGGACACGCC 62.118 60.000 0.00 0.00 37.10 5.68
1398 2431 1.966762 CTTGTTGATGTGGTGGGCC 59.033 57.895 0.00 0.00 0.00 5.80
1521 2554 3.229156 CTCCACCACGTTGCCGGTA 62.229 63.158 1.90 0.00 38.78 4.02
1932 3070 2.891580 GGTATGAAGCTACTGGGATCGA 59.108 50.000 0.00 0.00 0.00 3.59
2072 3214 0.029300 CTCAACTGGCAACCAACACG 59.971 55.000 0.00 0.00 30.80 4.49
2159 3301 2.154462 CAATCTCCGCACTCCAGTTTT 58.846 47.619 0.00 0.00 0.00 2.43
2171 3313 5.048782 TCTCCAACAAAACAATCAATCTCCG 60.049 40.000 0.00 0.00 0.00 4.63
2204 3346 1.283613 ACCAACACCAAGACCAGTCAA 59.716 47.619 0.00 0.00 0.00 3.18
2255 3397 7.490657 AGTACATAGGTGTAAGATGGAAACA 57.509 36.000 0.00 0.00 43.38 2.83
2349 3781 6.363577 TGTAATCCTCCGTTTACTAGTACG 57.636 41.667 10.59 10.59 37.50 3.67
2350 3782 6.205071 GCTGTAATCCTCCGTTTACTAGTAC 58.795 44.000 0.91 0.00 31.16 2.73
2351 3783 5.300286 GGCTGTAATCCTCCGTTTACTAGTA 59.700 44.000 0.00 0.00 31.16 1.82
2352 3784 4.099113 GGCTGTAATCCTCCGTTTACTAGT 59.901 45.833 0.00 0.00 31.16 2.57
2353 3785 4.341520 AGGCTGTAATCCTCCGTTTACTAG 59.658 45.833 0.00 0.00 31.16 2.57
2354 3786 4.284178 AGGCTGTAATCCTCCGTTTACTA 58.716 43.478 0.00 0.00 31.16 1.82
2355 3787 3.105283 AGGCTGTAATCCTCCGTTTACT 58.895 45.455 0.00 0.00 31.16 2.24
2356 3788 3.455327 GAGGCTGTAATCCTCCGTTTAC 58.545 50.000 0.00 0.00 43.32 2.01
2357 3789 3.814005 GAGGCTGTAATCCTCCGTTTA 57.186 47.619 0.00 0.00 43.32 2.01
2358 3790 2.693267 GAGGCTGTAATCCTCCGTTT 57.307 50.000 0.00 0.00 43.32 3.60
2364 3796 2.254152 TCTGGTGAGGCTGTAATCCT 57.746 50.000 0.00 0.00 36.46 3.24
2365 3797 3.471680 GAATCTGGTGAGGCTGTAATCC 58.528 50.000 0.00 0.00 0.00 3.01
2366 3798 3.135530 AGGAATCTGGTGAGGCTGTAATC 59.864 47.826 0.00 0.00 0.00 1.75
2367 3799 3.118531 AGGAATCTGGTGAGGCTGTAAT 58.881 45.455 0.00 0.00 0.00 1.89
2375 3807 0.105039 GCGGGTAGGAATCTGGTGAG 59.895 60.000 0.00 0.00 0.00 3.51
2377 3809 1.068741 GTAGCGGGTAGGAATCTGGTG 59.931 57.143 0.00 0.00 0.00 4.17
2403 3835 2.734673 CCGAGCAGAGCTTCGTTGC 61.735 63.158 4.94 5.29 39.88 4.17
2404 3836 0.109272 TACCGAGCAGAGCTTCGTTG 60.109 55.000 4.94 0.00 39.88 4.10
2405 3837 0.171455 CTACCGAGCAGAGCTTCGTT 59.829 55.000 4.94 0.00 39.88 3.85
2406 3838 0.961358 ACTACCGAGCAGAGCTTCGT 60.961 55.000 4.94 0.00 39.88 3.85
2407 3839 1.015109 TACTACCGAGCAGAGCTTCG 58.985 55.000 0.00 0.00 39.88 3.79
2408 3840 2.018515 AGTACTACCGAGCAGAGCTTC 58.981 52.381 0.00 0.00 39.88 3.86
2409 3841 2.131776 AGTACTACCGAGCAGAGCTT 57.868 50.000 0.00 0.00 39.88 3.74
2413 3845 5.352569 GTGTTTACTAGTACTACCGAGCAGA 59.647 44.000 0.91 0.00 0.00 4.26
2414 3846 5.353678 AGTGTTTACTAGTACTACCGAGCAG 59.646 44.000 0.91 0.00 34.74 4.24
2431 3863 3.998341 GCACGGGAAATCACTAGTGTTTA 59.002 43.478 21.99 3.90 32.74 2.01
2436 3868 1.623811 ACAGCACGGGAAATCACTAGT 59.376 47.619 0.00 0.00 0.00 2.57
2441 3873 0.893270 CCCAACAGCACGGGAAATCA 60.893 55.000 0.00 0.00 46.34 2.57
2443 3875 0.469144 AACCCAACAGCACGGGAAAT 60.469 50.000 0.45 0.00 46.34 2.17
2502 3934 2.499289 ACGAGTGATCCTGCTTTCTGAT 59.501 45.455 0.00 0.00 0.00 2.90
2543 3977 2.715749 AATCATGAGCCATCGTCCAA 57.284 45.000 0.09 0.00 0.00 3.53
2544 3978 2.171237 AGAAATCATGAGCCATCGTCCA 59.829 45.455 0.09 0.00 0.00 4.02
2545 3979 2.843701 AGAAATCATGAGCCATCGTCC 58.156 47.619 0.09 0.00 0.00 4.79
2546 3980 4.260948 GGAAAGAAATCATGAGCCATCGTC 60.261 45.833 0.09 1.02 0.00 4.20
2547 3981 3.629398 GGAAAGAAATCATGAGCCATCGT 59.371 43.478 0.09 0.00 0.00 3.73
2548 3982 3.881688 AGGAAAGAAATCATGAGCCATCG 59.118 43.478 0.09 0.00 0.00 3.84
2549 3983 4.643784 ACAGGAAAGAAATCATGAGCCATC 59.356 41.667 0.09 0.00 34.85 3.51
2555 3989 5.221880 CGCAAAACAGGAAAGAAATCATGA 58.778 37.500 0.00 0.00 34.85 3.07
2571 4005 0.037697 GGACCATTTCCCCGCAAAAC 60.038 55.000 0.00 0.00 38.70 2.43
2577 4011 0.684153 AAGCATGGACCATTTCCCCG 60.684 55.000 3.52 0.00 45.17 5.73
2581 4015 3.181472 GGATGGAAAGCATGGACCATTTC 60.181 47.826 3.52 7.35 42.23 2.17
2622 4056 2.814919 TGGTGCGTCCAATTAACGAATT 59.185 40.909 14.68 0.00 44.12 2.17
2698 4132 2.746142 GCCTCTATATGCACACAGCCAA 60.746 50.000 0.00 0.00 44.83 4.52
2719 4153 1.002990 GTTTACTCCCCACACCCGG 60.003 63.158 0.00 0.00 0.00 5.73
2723 4157 3.284617 ACAACAAGTTTACTCCCCACAC 58.715 45.455 0.00 0.00 0.00 3.82
2731 4165 9.843334 TTTTTATTGACGAACAACAAGTTTACT 57.157 25.926 0.00 0.00 41.51 2.24
2739 4173 4.496183 GTGCGTTTTTATTGACGAACAACA 59.504 37.500 2.38 0.00 45.05 3.33
2783 4731 1.649664 ACAATCGTGAGCAGCTGATC 58.350 50.000 24.85 24.85 0.00 2.92
2801 4749 8.681486 TTTCTTTTCTTTACAGGGGTACTTAC 57.319 34.615 0.00 0.00 0.00 2.34
2843 4791 9.244292 ACATCAGAGTGTTTAGATAAGTAGTGA 57.756 33.333 0.00 0.00 0.00 3.41
2844 4792 9.862371 AACATCAGAGTGTTTAGATAAGTAGTG 57.138 33.333 0.00 0.00 39.15 2.74
2868 5068 9.048446 TGGTTGTTACTCACTCTGTAAATAAAC 57.952 33.333 0.00 0.00 32.58 2.01
2873 5073 6.880484 TCTTGGTTGTTACTCACTCTGTAAA 58.120 36.000 0.00 0.00 32.58 2.01
2876 5076 4.202264 CCTCTTGGTTGTTACTCACTCTGT 60.202 45.833 0.00 0.00 0.00 3.41
2878 5078 3.244249 GCCTCTTGGTTGTTACTCACTCT 60.244 47.826 0.00 0.00 35.27 3.24
2879 5079 3.067833 GCCTCTTGGTTGTTACTCACTC 58.932 50.000 0.00 0.00 35.27 3.51
2880 5080 2.706190 AGCCTCTTGGTTGTTACTCACT 59.294 45.455 0.00 0.00 35.27 3.41
2881 5081 3.067833 GAGCCTCTTGGTTGTTACTCAC 58.932 50.000 0.00 0.00 35.27 3.51
2882 5082 2.703536 TGAGCCTCTTGGTTGTTACTCA 59.296 45.455 0.00 0.00 35.27 3.41
2883 5083 3.330267 CTGAGCCTCTTGGTTGTTACTC 58.670 50.000 0.00 0.00 35.27 2.59
2884 5084 2.551071 GCTGAGCCTCTTGGTTGTTACT 60.551 50.000 0.00 0.00 35.27 2.24
2885 5085 1.807142 GCTGAGCCTCTTGGTTGTTAC 59.193 52.381 0.00 0.00 35.27 2.50
2886 5086 1.699634 AGCTGAGCCTCTTGGTTGTTA 59.300 47.619 0.00 0.00 35.27 2.41


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

AutoCloner maintained by Alex Coulton.