Multiple sequence alignment - TraesCS5B01G072800

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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 TraesCS5B01G072800 chr5B 100.000 3658 0 0 1 3658 85178495 85182152 0.000000e+00 6756.0
1 TraesCS5B01G072800 chr5B 96.569 3468 88 13 202 3658 85116602 85120049 0.000000e+00 5716.0
2 TraesCS5B01G072800 chr5B 84.000 500 54 8 202 677 85285624 85286121 1.200000e-124 457.0
3 TraesCS5B01G072800 chr5B 78.846 468 83 11 2138 2595 88781313 88781774 5.940000e-78 302.0
4 TraesCS5B01G072800 chr5B 93.137 204 10 1 1 200 158958876 158959079 2.760000e-76 296.0
5 TraesCS5B01G072800 chr5B 83.974 312 45 3 406 715 563936085 563936393 9.930000e-76 294.0
6 TraesCS5B01G072800 chr5B 92.647 204 13 1 1 202 140972269 140972472 3.570000e-75 292.0
7 TraesCS5B01G072800 chr5B 92.574 202 13 1 1 200 434720854 434721055 4.620000e-74 289.0
8 TraesCS5B01G072800 chr5B 91.133 203 15 2 1 200 466163836 466164038 4.650000e-69 272.0
9 TraesCS5B01G072800 chr5D 96.608 3361 93 8 201 3557 76756254 76752911 0.000000e+00 5555.0
10 TraesCS5B01G072800 chr5D 95.042 3489 116 23 202 3658 76692029 76688566 0.000000e+00 5432.0
11 TraesCS5B01G072800 chr5D 81.752 274 30 9 406 670 459581659 459581921 1.030000e-50 211.0
12 TraesCS5B01G072800 chr5D 84.615 143 13 5 760 899 459581952 459582088 2.290000e-27 134.0
13 TraesCS5B01G072800 chr5A 92.443 3480 174 41 221 3658 72230484 72227052 0.000000e+00 4887.0
14 TraesCS5B01G072800 chr5A 93.031 2841 140 17 783 3610 72331807 72329012 0.000000e+00 4096.0
15 TraesCS5B01G072800 chr5A 94.780 2069 96 8 1593 3658 72388938 72386879 0.000000e+00 3212.0
16 TraesCS5B01G072800 chr5A 87.527 1403 109 26 198 1564 72390308 72388936 0.000000e+00 1561.0
17 TraesCS5B01G072800 chr5A 86.969 353 28 6 783 1121 72260105 72259757 7.410000e-102 381.0
18 TraesCS5B01G072800 chr5A 77.637 474 84 16 2138 2595 75050051 75050518 6.020000e-68 268.0
19 TraesCS5B01G072800 chr5A 85.437 103 14 1 2163 2265 76518705 76518806 5.000000e-19 106.0
20 TraesCS5B01G072800 chrUn 93.909 197 10 1 6 200 195377672 195377476 2.760000e-76 296.0
21 TraesCS5B01G072800 chr6B 91.866 209 12 2 1 205 51958929 51959136 1.660000e-73 287.0
22 TraesCS5B01G072800 chr6B 92.857 196 14 0 6 201 260605227 260605032 5.980000e-73 285.0
23 TraesCS5B01G072800 chr7B 92.000 200 16 0 1 200 744317603 744317802 7.730000e-72 281.0
24 TraesCS5B01G072800 chr7B 92.424 66 3 2 2944 3009 131743966 131744029 3.890000e-15 93.5
25 TraesCS5B01G072800 chr1B 92.308 195 13 1 1 195 361489236 361489044 3.600000e-70 276.0
26 TraesCS5B01G072800 chr7D 90.000 70 7 0 2935 3004 463883623 463883554 1.400000e-14 91.6
27 TraesCS5B01G072800 chr2B 86.420 81 8 3 2944 3024 416830046 416829969 6.510000e-13 86.1
28 TraesCS5B01G072800 chr2B 100.000 30 0 0 717 746 21856951 21856922 5.100000e-04 56.5
29 TraesCS5B01G072800 chr2A 100.000 30 0 0 717 746 13878746 13878775 5.100000e-04 56.5


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 TraesCS5B01G072800 chr5B 85178495 85182152 3657 False 6756.0 6756 100.0000 1 3658 1 chr5B.!!$F2 3657
1 TraesCS5B01G072800 chr5B 85116602 85120049 3447 False 5716.0 5716 96.5690 202 3658 1 chr5B.!!$F1 3456
2 TraesCS5B01G072800 chr5D 76752911 76756254 3343 True 5555.0 5555 96.6080 201 3557 1 chr5D.!!$R2 3356
3 TraesCS5B01G072800 chr5D 76688566 76692029 3463 True 5432.0 5432 95.0420 202 3658 1 chr5D.!!$R1 3456
4 TraesCS5B01G072800 chr5A 72227052 72230484 3432 True 4887.0 4887 92.4430 221 3658 1 chr5A.!!$R1 3437
5 TraesCS5B01G072800 chr5A 72329012 72331807 2795 True 4096.0 4096 93.0310 783 3610 1 chr5A.!!$R3 2827
6 TraesCS5B01G072800 chr5A 72386879 72390308 3429 True 2386.5 3212 91.1535 198 3658 2 chr5A.!!$R4 3460

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
159 160 0.036164 TATGTGTGCTCTTTGGCGGT 59.964 50.0 0.0 0.00 34.52 5.68 F
1571 1657 0.098728 GTCGCCCAATTCGGACATTG 59.901 55.0 0.0 6.15 36.56 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1592 1678 0.250727 CGGGAAGTGAAGCCCTTGAA 60.251 55.0 0.0 0.0 42.4 2.69 R
2847 2943 5.118510 GTGGATTTGCGTATCTTTTGTTTGG 59.881 40.0 0.0 0.0 0.0 3.28 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 4.003788 CACCGCCGGAACCAGACT 62.004 66.667 11.71 0.00 0.00 3.24
21 22 2.283388 ACCGCCGGAACCAGACTA 60.283 61.111 11.71 0.00 0.00 2.59
22 23 2.348888 ACCGCCGGAACCAGACTAG 61.349 63.158 11.71 0.00 0.00 2.57
23 24 2.494918 CGCCGGAACCAGACTAGG 59.505 66.667 5.05 0.00 0.00 3.02
24 25 2.187163 GCCGGAACCAGACTAGGC 59.813 66.667 5.05 0.00 37.61 3.93
25 26 2.494918 CCGGAACCAGACTAGGCG 59.505 66.667 0.00 0.00 0.00 5.52
26 27 2.202756 CGGAACCAGACTAGGCGC 60.203 66.667 0.00 0.00 0.00 6.53
27 28 2.711922 CGGAACCAGACTAGGCGCT 61.712 63.158 7.64 0.00 0.00 5.92
28 29 1.381928 CGGAACCAGACTAGGCGCTA 61.382 60.000 7.64 0.00 0.00 4.26
29 30 1.041437 GGAACCAGACTAGGCGCTAT 58.959 55.000 7.64 0.00 0.00 2.97
30 31 1.000052 GGAACCAGACTAGGCGCTATC 60.000 57.143 7.64 0.00 0.00 2.08
31 32 1.957877 GAACCAGACTAGGCGCTATCT 59.042 52.381 7.64 2.14 0.00 1.98
32 33 2.074729 ACCAGACTAGGCGCTATCTT 57.925 50.000 7.64 0.00 0.00 2.40
33 34 2.389715 ACCAGACTAGGCGCTATCTTT 58.610 47.619 7.64 0.00 0.00 2.52
34 35 2.101582 ACCAGACTAGGCGCTATCTTTG 59.898 50.000 7.64 0.00 0.00 2.77
35 36 2.101582 CCAGACTAGGCGCTATCTTTGT 59.898 50.000 7.64 0.00 0.00 2.83
36 37 3.376540 CAGACTAGGCGCTATCTTTGTC 58.623 50.000 7.64 8.35 0.00 3.18
37 38 3.067461 CAGACTAGGCGCTATCTTTGTCT 59.933 47.826 7.64 10.37 34.38 3.41
38 39 3.067461 AGACTAGGCGCTATCTTTGTCTG 59.933 47.826 7.64 0.00 33.09 3.51
39 40 2.101582 ACTAGGCGCTATCTTTGTCTGG 59.898 50.000 7.64 0.00 0.00 3.86
40 41 0.462759 AGGCGCTATCTTTGTCTGGC 60.463 55.000 7.64 0.00 0.00 4.85
41 42 1.638467 GCGCTATCTTTGTCTGGCG 59.362 57.895 0.00 0.00 44.40 5.69
42 43 1.084370 GCGCTATCTTTGTCTGGCGT 61.084 55.000 0.00 0.00 43.65 5.68
43 44 0.647410 CGCTATCTTTGTCTGGCGTG 59.353 55.000 0.00 0.00 38.20 5.34
44 45 1.726853 GCTATCTTTGTCTGGCGTGT 58.273 50.000 0.00 0.00 0.00 4.49
45 46 2.076863 GCTATCTTTGTCTGGCGTGTT 58.923 47.619 0.00 0.00 0.00 3.32
46 47 2.094417 GCTATCTTTGTCTGGCGTGTTC 59.906 50.000 0.00 0.00 0.00 3.18
47 48 2.550830 ATCTTTGTCTGGCGTGTTCT 57.449 45.000 0.00 0.00 0.00 3.01
48 49 1.581934 TCTTTGTCTGGCGTGTTCTG 58.418 50.000 0.00 0.00 0.00 3.02
49 50 1.134521 TCTTTGTCTGGCGTGTTCTGT 60.135 47.619 0.00 0.00 0.00 3.41
50 51 1.670811 CTTTGTCTGGCGTGTTCTGTT 59.329 47.619 0.00 0.00 0.00 3.16
51 52 1.745232 TTGTCTGGCGTGTTCTGTTT 58.255 45.000 0.00 0.00 0.00 2.83
52 53 1.745232 TGTCTGGCGTGTTCTGTTTT 58.255 45.000 0.00 0.00 0.00 2.43
53 54 2.088423 TGTCTGGCGTGTTCTGTTTTT 58.912 42.857 0.00 0.00 0.00 1.94
83 84 2.851798 CTTCTTGAGCTGTGCCCTC 58.148 57.895 0.00 0.00 0.00 4.30
84 85 0.676151 CTTCTTGAGCTGTGCCCTCC 60.676 60.000 0.00 0.00 0.00 4.30
85 86 2.435586 CTTGAGCTGTGCCCTCCG 60.436 66.667 0.00 0.00 0.00 4.63
86 87 3.241530 TTGAGCTGTGCCCTCCGT 61.242 61.111 0.00 0.00 0.00 4.69
87 88 1.888436 CTTGAGCTGTGCCCTCCGTA 61.888 60.000 0.00 0.00 0.00 4.02
88 89 1.888436 TTGAGCTGTGCCCTCCGTAG 61.888 60.000 0.00 0.00 0.00 3.51
89 90 2.037367 AGCTGTGCCCTCCGTAGA 59.963 61.111 0.00 0.00 0.00 2.59
90 91 1.605058 GAGCTGTGCCCTCCGTAGAA 61.605 60.000 0.00 0.00 0.00 2.10
91 92 1.153549 GCTGTGCCCTCCGTAGAAG 60.154 63.158 0.00 0.00 0.00 2.85
92 93 1.153549 CTGTGCCCTCCGTAGAAGC 60.154 63.158 0.00 0.00 0.00 3.86
93 94 1.608717 CTGTGCCCTCCGTAGAAGCT 61.609 60.000 0.00 0.00 0.00 3.74
94 95 1.142097 GTGCCCTCCGTAGAAGCTC 59.858 63.158 0.00 0.00 0.00 4.09
95 96 1.000486 TGCCCTCCGTAGAAGCTCT 60.000 57.895 0.00 0.00 0.00 4.09
96 97 1.323271 TGCCCTCCGTAGAAGCTCTG 61.323 60.000 0.00 0.00 0.00 3.35
97 98 1.324005 GCCCTCCGTAGAAGCTCTGT 61.324 60.000 0.00 0.00 0.00 3.41
98 99 2.022754 GCCCTCCGTAGAAGCTCTGTA 61.023 57.143 0.00 0.00 0.00 2.74
99 100 1.677052 CCCTCCGTAGAAGCTCTGTAC 59.323 57.143 0.00 0.00 0.00 2.90
100 101 2.645802 CCTCCGTAGAAGCTCTGTACT 58.354 52.381 0.00 0.00 0.00 2.73
101 102 3.018149 CCTCCGTAGAAGCTCTGTACTT 58.982 50.000 0.00 0.00 0.00 2.24
102 103 3.444388 CCTCCGTAGAAGCTCTGTACTTT 59.556 47.826 0.00 0.00 0.00 2.66
103 104 4.416620 CTCCGTAGAAGCTCTGTACTTTG 58.583 47.826 0.00 0.00 0.00 2.77
104 105 3.825014 TCCGTAGAAGCTCTGTACTTTGT 59.175 43.478 0.00 0.00 0.00 2.83
105 106 4.280174 TCCGTAGAAGCTCTGTACTTTGTT 59.720 41.667 0.00 0.00 0.00 2.83
106 107 4.386049 CCGTAGAAGCTCTGTACTTTGTTG 59.614 45.833 0.00 0.00 0.00 3.33
107 108 4.982916 CGTAGAAGCTCTGTACTTTGTTGT 59.017 41.667 0.00 0.00 0.00 3.32
108 109 5.107837 CGTAGAAGCTCTGTACTTTGTTGTG 60.108 44.000 0.00 0.00 0.00 3.33
109 110 5.023533 AGAAGCTCTGTACTTTGTTGTGA 57.976 39.130 0.00 0.00 0.00 3.58
110 111 5.053145 AGAAGCTCTGTACTTTGTTGTGAG 58.947 41.667 0.00 0.00 0.00 3.51
111 112 4.672587 AGCTCTGTACTTTGTTGTGAGA 57.327 40.909 0.00 0.00 0.00 3.27
112 113 4.372656 AGCTCTGTACTTTGTTGTGAGAC 58.627 43.478 0.00 0.00 0.00 3.36
113 114 4.100189 AGCTCTGTACTTTGTTGTGAGACT 59.900 41.667 0.00 0.00 0.00 3.24
114 115 4.811557 GCTCTGTACTTTGTTGTGAGACTT 59.188 41.667 0.00 0.00 0.00 3.01
115 116 5.277058 GCTCTGTACTTTGTTGTGAGACTTG 60.277 44.000 0.00 0.00 0.00 3.16
116 117 5.116180 TCTGTACTTTGTTGTGAGACTTGG 58.884 41.667 0.00 0.00 0.00 3.61
117 118 4.196193 TGTACTTTGTTGTGAGACTTGGG 58.804 43.478 0.00 0.00 0.00 4.12
118 119 3.366052 ACTTTGTTGTGAGACTTGGGT 57.634 42.857 0.00 0.00 0.00 4.51
119 120 3.016736 ACTTTGTTGTGAGACTTGGGTG 58.983 45.455 0.00 0.00 0.00 4.61
120 121 2.799126 TTGTTGTGAGACTTGGGTGT 57.201 45.000 0.00 0.00 0.00 4.16
121 122 2.036958 TGTTGTGAGACTTGGGTGTG 57.963 50.000 0.00 0.00 0.00 3.82
122 123 1.280710 TGTTGTGAGACTTGGGTGTGT 59.719 47.619 0.00 0.00 0.00 3.72
123 124 1.670811 GTTGTGAGACTTGGGTGTGTG 59.329 52.381 0.00 0.00 0.00 3.82
124 125 0.908910 TGTGAGACTTGGGTGTGTGT 59.091 50.000 0.00 0.00 0.00 3.72
125 126 1.299541 GTGAGACTTGGGTGTGTGTG 58.700 55.000 0.00 0.00 0.00 3.82
126 127 0.908910 TGAGACTTGGGTGTGTGTGT 59.091 50.000 0.00 0.00 0.00 3.72
127 128 1.299541 GAGACTTGGGTGTGTGTGTG 58.700 55.000 0.00 0.00 0.00 3.82
128 129 0.107214 AGACTTGGGTGTGTGTGTGG 60.107 55.000 0.00 0.00 0.00 4.17
129 130 0.107410 GACTTGGGTGTGTGTGTGGA 60.107 55.000 0.00 0.00 0.00 4.02
130 131 0.393808 ACTTGGGTGTGTGTGTGGAC 60.394 55.000 0.00 0.00 0.00 4.02
131 132 0.107214 CTTGGGTGTGTGTGTGGACT 60.107 55.000 0.00 0.00 0.00 3.85
132 133 0.329931 TTGGGTGTGTGTGTGGACTT 59.670 50.000 0.00 0.00 0.00 3.01
133 134 0.393673 TGGGTGTGTGTGTGGACTTG 60.394 55.000 0.00 0.00 0.00 3.16
134 135 0.107410 GGGTGTGTGTGTGGACTTGA 60.107 55.000 0.00 0.00 0.00 3.02
135 136 1.014352 GGTGTGTGTGTGGACTTGAC 58.986 55.000 0.00 0.00 0.00 3.18
136 137 1.406887 GGTGTGTGTGTGGACTTGACT 60.407 52.381 0.00 0.00 0.00 3.41
137 138 1.933853 GTGTGTGTGTGGACTTGACTC 59.066 52.381 0.00 0.00 0.00 3.36
138 139 1.831106 TGTGTGTGTGGACTTGACTCT 59.169 47.619 0.00 0.00 0.00 3.24
139 140 2.159099 TGTGTGTGTGGACTTGACTCTC 60.159 50.000 0.00 0.00 0.00 3.20
140 141 2.101582 GTGTGTGTGGACTTGACTCTCT 59.898 50.000 0.00 0.00 0.00 3.10
141 142 3.318275 GTGTGTGTGGACTTGACTCTCTA 59.682 47.826 0.00 0.00 0.00 2.43
142 143 4.021894 GTGTGTGTGGACTTGACTCTCTAT 60.022 45.833 0.00 0.00 0.00 1.98
143 144 4.021981 TGTGTGTGGACTTGACTCTCTATG 60.022 45.833 0.00 0.00 0.00 2.23
144 145 4.021894 GTGTGTGGACTTGACTCTCTATGT 60.022 45.833 0.00 0.00 0.00 2.29
145 146 4.021981 TGTGTGGACTTGACTCTCTATGTG 60.022 45.833 0.00 0.00 0.00 3.21
146 147 4.021894 GTGTGGACTTGACTCTCTATGTGT 60.022 45.833 0.00 0.00 0.00 3.72
147 148 4.021981 TGTGGACTTGACTCTCTATGTGTG 60.022 45.833 0.00 0.00 0.00 3.82
148 149 3.056536 TGGACTTGACTCTCTATGTGTGC 60.057 47.826 0.00 0.00 0.00 4.57
149 150 3.194542 GGACTTGACTCTCTATGTGTGCT 59.805 47.826 0.00 0.00 0.00 4.40
150 151 4.420168 GACTTGACTCTCTATGTGTGCTC 58.580 47.826 0.00 0.00 0.00 4.26
151 152 4.085733 ACTTGACTCTCTATGTGTGCTCT 58.914 43.478 0.00 0.00 0.00 4.09
152 153 4.526262 ACTTGACTCTCTATGTGTGCTCTT 59.474 41.667 0.00 0.00 0.00 2.85
153 154 5.011533 ACTTGACTCTCTATGTGTGCTCTTT 59.988 40.000 0.00 0.00 0.00 2.52
154 155 4.814147 TGACTCTCTATGTGTGCTCTTTG 58.186 43.478 0.00 0.00 0.00 2.77
155 156 4.180057 GACTCTCTATGTGTGCTCTTTGG 58.820 47.826 0.00 0.00 0.00 3.28
156 157 2.935201 CTCTCTATGTGTGCTCTTTGGC 59.065 50.000 0.00 0.00 0.00 4.52
157 158 1.662629 CTCTATGTGTGCTCTTTGGCG 59.337 52.381 0.00 0.00 34.52 5.69
158 159 0.729116 CTATGTGTGCTCTTTGGCGG 59.271 55.000 0.00 0.00 34.52 6.13
159 160 0.036164 TATGTGTGCTCTTTGGCGGT 59.964 50.000 0.00 0.00 34.52 5.68
160 161 0.823356 ATGTGTGCTCTTTGGCGGTT 60.823 50.000 0.00 0.00 34.52 4.44
161 162 1.034838 TGTGTGCTCTTTGGCGGTTT 61.035 50.000 0.00 0.00 34.52 3.27
162 163 0.594796 GTGTGCTCTTTGGCGGTTTG 60.595 55.000 0.00 0.00 34.52 2.93
163 164 1.661509 GTGCTCTTTGGCGGTTTGC 60.662 57.895 0.00 0.00 45.38 3.68
164 165 1.827789 TGCTCTTTGGCGGTTTGCT 60.828 52.632 0.00 0.00 45.43 3.91
165 166 1.363807 GCTCTTTGGCGGTTTGCTT 59.636 52.632 0.00 0.00 45.43 3.91
166 167 0.249447 GCTCTTTGGCGGTTTGCTTT 60.249 50.000 0.00 0.00 45.43 3.51
167 168 1.000717 GCTCTTTGGCGGTTTGCTTTA 60.001 47.619 0.00 0.00 45.43 1.85
168 169 2.352715 GCTCTTTGGCGGTTTGCTTTAT 60.353 45.455 0.00 0.00 45.43 1.40
169 170 3.860754 GCTCTTTGGCGGTTTGCTTTATT 60.861 43.478 0.00 0.00 45.43 1.40
170 171 4.306600 CTCTTTGGCGGTTTGCTTTATTT 58.693 39.130 0.00 0.00 45.43 1.40
171 172 5.455056 TCTTTGGCGGTTTGCTTTATTTA 57.545 34.783 0.00 0.00 45.43 1.40
172 173 6.031751 TCTTTGGCGGTTTGCTTTATTTAT 57.968 33.333 0.00 0.00 45.43 1.40
173 174 7.159322 TCTTTGGCGGTTTGCTTTATTTATA 57.841 32.000 0.00 0.00 45.43 0.98
174 175 7.603651 TCTTTGGCGGTTTGCTTTATTTATAA 58.396 30.769 0.00 0.00 45.43 0.98
175 176 8.088981 TCTTTGGCGGTTTGCTTTATTTATAAA 58.911 29.630 0.00 0.00 45.43 1.40
185 186 5.427036 CTTTATTTATAAAGCGGGGCGAA 57.573 39.130 8.78 0.00 41.69 4.70
186 187 5.427036 TTTATTTATAAAGCGGGGCGAAG 57.573 39.130 3.94 0.00 0.00 3.79
187 188 1.670791 TTTATAAAGCGGGGCGAAGG 58.329 50.000 0.00 0.00 0.00 3.46
188 189 8.911575 CTTTATTTATAAAGCGGGGCGAAGGC 62.912 46.154 8.78 0.00 46.18 4.35
202 203 2.094906 GCGAAGGCCTTTTTCGGTATTT 60.095 45.455 21.54 0.00 45.50 1.40
203 204 3.613193 GCGAAGGCCTTTTTCGGTATTTT 60.613 43.478 21.54 0.00 45.50 1.82
247 252 1.202604 CGTGAATATACCACCGGCCTT 60.203 52.381 0.00 0.00 0.00 4.35
352 358 3.134985 GGGGAGGGATGAAAAGTAGAGAC 59.865 52.174 0.00 0.00 0.00 3.36
425 454 1.876322 CCGCTTCTCATGATCCTTCC 58.124 55.000 0.00 0.00 0.00 3.46
506 542 4.714632 TGTTTGAAGAAGAACGGAATCCT 58.285 39.130 0.00 0.00 0.00 3.24
591 627 1.679305 ACCATCTCCTCGCTGTCGT 60.679 57.895 0.00 0.00 36.96 4.34
1062 1105 1.364626 GGAAGTCAGCCGCACTCATG 61.365 60.000 0.00 0.00 0.00 3.07
1063 1106 1.364626 GAAGTCAGCCGCACTCATGG 61.365 60.000 0.00 0.00 0.00 3.66
1064 1107 2.046892 GTCAGCCGCACTCATGGT 60.047 61.111 0.00 0.00 0.00 3.55
1065 1108 2.103042 GTCAGCCGCACTCATGGTC 61.103 63.158 0.00 0.00 0.00 4.02
1066 1109 2.046988 CAGCCGCACTCATGGTCA 60.047 61.111 0.00 0.00 0.00 4.02
1067 1110 1.450848 CAGCCGCACTCATGGTCAT 60.451 57.895 0.00 0.00 0.00 3.06
1176 1231 2.835431 CTCAGCGACCTCCCCGAT 60.835 66.667 0.00 0.00 0.00 4.18
1312 1367 2.031683 GGTGAAATCGCCCGTTCTAATG 59.968 50.000 1.40 0.00 40.56 1.90
1350 1405 7.240674 GTGATGTCTTACAACGCATAATTTCA 58.759 34.615 0.00 0.00 32.58 2.69
1352 1407 8.458052 TGATGTCTTACAACGCATAATTTCATT 58.542 29.630 0.00 0.00 0.00 2.57
1358 1413 3.691049 ACGCATAATTTCATTCCACCG 57.309 42.857 0.00 0.00 0.00 4.94
1400 1455 2.215451 ATTCGCCCACTCTTGGCCAT 62.215 55.000 6.09 0.00 46.48 4.40
1488 1543 1.180456 TTGAGTTCTACCGTCGGCCA 61.180 55.000 12.28 0.00 0.00 5.36
1564 1650 1.361668 CCTCTGTGTCGCCCAATTCG 61.362 60.000 0.00 0.00 0.00 3.34
1565 1651 1.361668 CTCTGTGTCGCCCAATTCGG 61.362 60.000 0.00 0.00 0.00 4.30
1566 1652 1.375396 CTGTGTCGCCCAATTCGGA 60.375 57.895 0.00 0.00 36.56 4.55
1567 1653 1.635663 CTGTGTCGCCCAATTCGGAC 61.636 60.000 0.00 0.00 36.56 4.79
1568 1654 1.669760 GTGTCGCCCAATTCGGACA 60.670 57.895 0.00 0.00 36.56 4.02
1569 1655 1.024579 GTGTCGCCCAATTCGGACAT 61.025 55.000 0.00 0.00 36.56 3.06
1570 1656 0.322098 TGTCGCCCAATTCGGACATT 60.322 50.000 0.00 0.00 36.56 2.71
1571 1657 0.098728 GTCGCCCAATTCGGACATTG 59.901 55.000 0.00 6.15 36.56 2.82
1572 1658 1.226660 CGCCCAATTCGGACATTGC 60.227 57.895 0.00 0.00 36.56 3.56
1573 1659 1.889454 GCCCAATTCGGACATTGCA 59.111 52.632 0.00 0.00 36.56 4.08
1574 1660 0.458370 GCCCAATTCGGACATTGCAC 60.458 55.000 0.00 0.00 36.56 4.57
1575 1661 0.887247 CCCAATTCGGACATTGCACA 59.113 50.000 0.00 0.00 36.56 4.57
1576 1662 1.402720 CCCAATTCGGACATTGCACAC 60.403 52.381 0.00 0.00 36.56 3.82
1577 1663 1.541147 CCAATTCGGACATTGCACACT 59.459 47.619 0.00 0.00 36.56 3.55
1578 1664 2.414559 CCAATTCGGACATTGCACACTC 60.415 50.000 0.00 0.00 36.56 3.51
1579 1665 2.183478 ATTCGGACATTGCACACTCA 57.817 45.000 0.00 0.00 0.00 3.41
1580 1666 1.225855 TTCGGACATTGCACACTCAC 58.774 50.000 0.00 0.00 0.00 3.51
1581 1667 0.943835 TCGGACATTGCACACTCACG 60.944 55.000 0.00 0.00 0.00 4.35
1582 1668 1.868997 GGACATTGCACACTCACGG 59.131 57.895 0.00 0.00 0.00 4.94
1583 1669 0.602638 GGACATTGCACACTCACGGA 60.603 55.000 0.00 0.00 0.00 4.69
1584 1670 0.512952 GACATTGCACACTCACGGAC 59.487 55.000 0.00 0.00 0.00 4.79
1585 1671 1.221466 ACATTGCACACTCACGGACG 61.221 55.000 0.00 0.00 0.00 4.79
1586 1672 0.943835 CATTGCACACTCACGGACGA 60.944 55.000 0.00 0.00 0.00 4.20
1587 1673 0.944311 ATTGCACACTCACGGACGAC 60.944 55.000 0.00 0.00 0.00 4.34
1588 1674 2.027024 GCACACTCACGGACGACA 59.973 61.111 0.00 0.00 0.00 4.35
1589 1675 1.372997 GCACACTCACGGACGACAT 60.373 57.895 0.00 0.00 0.00 3.06
1590 1676 1.344942 GCACACTCACGGACGACATC 61.345 60.000 0.00 0.00 0.00 3.06
1591 1677 1.065572 CACACTCACGGACGACATCG 61.066 60.000 0.00 0.00 46.33 3.84
1712 1798 6.321435 TCTCTCGAGGTCTTGCTAATTATTCA 59.679 38.462 13.56 0.00 0.00 2.57
1932 2018 1.899814 TGTACTAACTCCACCAGGCTG 59.100 52.381 7.75 7.75 33.74 4.85
1997 2083 5.332743 TCATTTTTACCATCCTCAGCCTTT 58.667 37.500 0.00 0.00 0.00 3.11
2120 2206 0.098552 CGCGCATTGCAATTGGTAGA 59.901 50.000 9.83 0.00 46.97 2.59
2121 2207 1.831343 GCGCATTGCAATTGGTAGAG 58.169 50.000 9.83 0.97 45.45 2.43
2160 2246 4.155462 GCAGAATCAAGTCTTTGCATCTCA 59.845 41.667 2.04 0.00 34.21 3.27
2215 2301 6.573664 TGAATTGATGAGATGTTTTCCGTT 57.426 33.333 0.00 0.00 0.00 4.44
2273 2359 6.489127 TCACCGATAGTACATTTTGTTTGG 57.511 37.500 0.00 0.00 0.00 3.28
2847 2943 3.317149 AGTTAACCCTCAAAAGGCGAAAC 59.683 43.478 0.88 0.00 41.85 2.78
3117 3223 4.662961 GCACAAACCGGCCTTGGC 62.663 66.667 18.35 14.75 0.00 4.52
3161 3267 8.798859 ATCTGACACTAGTGCTTTTAAATGAT 57.201 30.769 22.90 10.12 0.00 2.45
3331 3442 7.118971 CCAATAGTCAAATTCCTAGCTAGATGC 59.881 40.741 22.70 8.74 43.29 3.91
3643 3761 1.699730 AACACTGTGTTAAAGGGGGC 58.300 50.000 23.62 0.00 39.09 5.80
3653 3771 5.192923 TGTGTTAAAGGGGGCTACTATTGAT 59.807 40.000 0.00 0.00 0.00 2.57
3654 3772 5.763698 GTGTTAAAGGGGGCTACTATTGATC 59.236 44.000 0.00 0.00 0.00 2.92
3655 3773 5.670361 TGTTAAAGGGGGCTACTATTGATCT 59.330 40.000 0.00 0.00 0.00 2.75
3656 3774 4.713792 AAAGGGGGCTACTATTGATCTG 57.286 45.455 0.00 0.00 0.00 2.90
3657 3775 3.352611 AGGGGGCTACTATTGATCTGT 57.647 47.619 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.283388 TAGTCTGGTTCCGGCGGT 60.283 61.111 27.32 6.20 0.00 5.68
7 8 2.187163 GCCTAGTCTGGTTCCGGC 59.813 66.667 0.00 0.00 0.00 6.13
8 9 2.494918 CGCCTAGTCTGGTTCCGG 59.505 66.667 0.00 0.00 0.00 5.14
9 10 1.381928 TAGCGCCTAGTCTGGTTCCG 61.382 60.000 2.29 0.00 0.00 4.30
10 11 1.000052 GATAGCGCCTAGTCTGGTTCC 60.000 57.143 2.29 0.00 0.00 3.62
11 12 1.957877 AGATAGCGCCTAGTCTGGTTC 59.042 52.381 2.29 0.00 0.00 3.62
12 13 2.074729 AGATAGCGCCTAGTCTGGTT 57.925 50.000 2.29 0.00 0.00 3.67
13 14 2.074729 AAGATAGCGCCTAGTCTGGT 57.925 50.000 2.29 0.00 0.00 4.00
14 15 2.101582 ACAAAGATAGCGCCTAGTCTGG 59.898 50.000 2.29 1.99 0.00 3.86
15 16 3.067461 AGACAAAGATAGCGCCTAGTCTG 59.933 47.826 2.29 0.00 34.17 3.51
16 17 3.067461 CAGACAAAGATAGCGCCTAGTCT 59.933 47.826 2.29 8.85 35.66 3.24
17 18 3.376540 CAGACAAAGATAGCGCCTAGTC 58.623 50.000 2.29 6.66 0.00 2.59
18 19 2.101582 CCAGACAAAGATAGCGCCTAGT 59.898 50.000 2.29 0.00 0.00 2.57
19 20 2.748605 CCAGACAAAGATAGCGCCTAG 58.251 52.381 2.29 0.00 0.00 3.02
20 21 1.202533 GCCAGACAAAGATAGCGCCTA 60.203 52.381 2.29 0.00 0.00 3.93
21 22 0.462759 GCCAGACAAAGATAGCGCCT 60.463 55.000 2.29 0.00 0.00 5.52
22 23 1.766143 CGCCAGACAAAGATAGCGCC 61.766 60.000 2.29 0.00 36.89 6.53
23 24 1.084370 ACGCCAGACAAAGATAGCGC 61.084 55.000 0.00 0.00 46.99 5.92
25 26 1.726853 ACACGCCAGACAAAGATAGC 58.273 50.000 0.00 0.00 0.00 2.97
26 27 3.369147 CAGAACACGCCAGACAAAGATAG 59.631 47.826 0.00 0.00 0.00 2.08
27 28 3.244078 ACAGAACACGCCAGACAAAGATA 60.244 43.478 0.00 0.00 0.00 1.98
28 29 2.146342 CAGAACACGCCAGACAAAGAT 58.854 47.619 0.00 0.00 0.00 2.40
29 30 1.134521 ACAGAACACGCCAGACAAAGA 60.135 47.619 0.00 0.00 0.00 2.52
30 31 1.299541 ACAGAACACGCCAGACAAAG 58.700 50.000 0.00 0.00 0.00 2.77
31 32 1.745232 AACAGAACACGCCAGACAAA 58.255 45.000 0.00 0.00 0.00 2.83
32 33 1.745232 AAACAGAACACGCCAGACAA 58.255 45.000 0.00 0.00 0.00 3.18
33 34 1.745232 AAAACAGAACACGCCAGACA 58.255 45.000 0.00 0.00 0.00 3.41
34 35 2.844122 AAAAACAGAACACGCCAGAC 57.156 45.000 0.00 0.00 0.00 3.51
50 51 6.223120 GCTCAAGAAGCCCAGAAAATAAAAA 58.777 36.000 0.00 0.00 45.92 1.94
51 52 5.783111 GCTCAAGAAGCCCAGAAAATAAAA 58.217 37.500 0.00 0.00 45.92 1.52
52 53 5.391312 GCTCAAGAAGCCCAGAAAATAAA 57.609 39.130 0.00 0.00 45.92 1.40
65 66 0.676151 GGAGGGCACAGCTCAAGAAG 60.676 60.000 0.00 0.00 0.00 2.85
66 67 1.376466 GGAGGGCACAGCTCAAGAA 59.624 57.895 0.00 0.00 0.00 2.52
67 68 2.947532 CGGAGGGCACAGCTCAAGA 61.948 63.158 0.00 0.00 0.00 3.02
68 69 1.888436 TACGGAGGGCACAGCTCAAG 61.888 60.000 0.00 0.00 0.00 3.02
69 70 1.888436 CTACGGAGGGCACAGCTCAA 61.888 60.000 0.00 0.00 0.00 3.02
70 71 2.283604 TACGGAGGGCACAGCTCA 60.284 61.111 0.00 0.00 0.00 4.26
71 72 1.605058 TTCTACGGAGGGCACAGCTC 61.605 60.000 0.00 0.00 0.00 4.09
72 73 1.608717 CTTCTACGGAGGGCACAGCT 61.609 60.000 0.00 0.00 0.00 4.24
73 74 1.153549 CTTCTACGGAGGGCACAGC 60.154 63.158 0.00 0.00 0.00 4.40
74 75 1.153549 GCTTCTACGGAGGGCACAG 60.154 63.158 8.31 0.00 0.00 3.66
75 76 1.605058 GAGCTTCTACGGAGGGCACA 61.605 60.000 14.16 0.00 0.00 4.57
76 77 1.142097 GAGCTTCTACGGAGGGCAC 59.858 63.158 14.16 5.91 0.00 5.01
77 78 1.000486 AGAGCTTCTACGGAGGGCA 60.000 57.895 14.16 0.00 0.00 5.36
78 79 1.324005 ACAGAGCTTCTACGGAGGGC 61.324 60.000 0.00 0.00 0.00 5.19
79 80 1.677052 GTACAGAGCTTCTACGGAGGG 59.323 57.143 0.00 0.00 0.00 4.30
80 81 2.645802 AGTACAGAGCTTCTACGGAGG 58.354 52.381 0.00 0.00 0.00 4.30
81 82 4.082679 ACAAAGTACAGAGCTTCTACGGAG 60.083 45.833 0.00 0.00 0.00 4.63
82 83 3.825014 ACAAAGTACAGAGCTTCTACGGA 59.175 43.478 0.00 0.00 0.00 4.69
83 84 4.175787 ACAAAGTACAGAGCTTCTACGG 57.824 45.455 0.00 0.00 0.00 4.02
84 85 4.982916 ACAACAAAGTACAGAGCTTCTACG 59.017 41.667 0.00 0.00 0.00 3.51
85 86 5.983720 TCACAACAAAGTACAGAGCTTCTAC 59.016 40.000 0.00 0.00 0.00 2.59
86 87 6.040504 TCTCACAACAAAGTACAGAGCTTCTA 59.959 38.462 0.00 0.00 0.00 2.10
87 88 5.023533 TCACAACAAAGTACAGAGCTTCT 57.976 39.130 0.00 0.00 0.00 2.85
88 89 5.050490 TCTCACAACAAAGTACAGAGCTTC 58.950 41.667 0.00 0.00 0.00 3.86
89 90 4.811557 GTCTCACAACAAAGTACAGAGCTT 59.188 41.667 0.00 0.00 0.00 3.74
90 91 4.100189 AGTCTCACAACAAAGTACAGAGCT 59.900 41.667 0.00 0.00 0.00 4.09
91 92 4.372656 AGTCTCACAACAAAGTACAGAGC 58.627 43.478 0.00 0.00 0.00 4.09
92 93 5.235186 CCAAGTCTCACAACAAAGTACAGAG 59.765 44.000 0.00 0.00 0.00 3.35
93 94 5.116180 CCAAGTCTCACAACAAAGTACAGA 58.884 41.667 0.00 0.00 0.00 3.41
94 95 4.273480 CCCAAGTCTCACAACAAAGTACAG 59.727 45.833 0.00 0.00 0.00 2.74
95 96 4.196193 CCCAAGTCTCACAACAAAGTACA 58.804 43.478 0.00 0.00 0.00 2.90
96 97 4.035208 CACCCAAGTCTCACAACAAAGTAC 59.965 45.833 0.00 0.00 0.00 2.73
97 98 4.196193 CACCCAAGTCTCACAACAAAGTA 58.804 43.478 0.00 0.00 0.00 2.24
98 99 3.016736 CACCCAAGTCTCACAACAAAGT 58.983 45.455 0.00 0.00 0.00 2.66
99 100 3.016736 ACACCCAAGTCTCACAACAAAG 58.983 45.455 0.00 0.00 0.00 2.77
100 101 2.752354 CACACCCAAGTCTCACAACAAA 59.248 45.455 0.00 0.00 0.00 2.83
101 102 2.290641 ACACACCCAAGTCTCACAACAA 60.291 45.455 0.00 0.00 0.00 2.83
102 103 1.280710 ACACACCCAAGTCTCACAACA 59.719 47.619 0.00 0.00 0.00 3.33
103 104 1.670811 CACACACCCAAGTCTCACAAC 59.329 52.381 0.00 0.00 0.00 3.32
104 105 1.280710 ACACACACCCAAGTCTCACAA 59.719 47.619 0.00 0.00 0.00 3.33
105 106 0.908910 ACACACACCCAAGTCTCACA 59.091 50.000 0.00 0.00 0.00 3.58
106 107 1.299541 CACACACACCCAAGTCTCAC 58.700 55.000 0.00 0.00 0.00 3.51
107 108 0.908910 ACACACACACCCAAGTCTCA 59.091 50.000 0.00 0.00 0.00 3.27
108 109 1.299541 CACACACACACCCAAGTCTC 58.700 55.000 0.00 0.00 0.00 3.36
109 110 0.107214 CCACACACACACCCAAGTCT 60.107 55.000 0.00 0.00 0.00 3.24
110 111 0.107410 TCCACACACACACCCAAGTC 60.107 55.000 0.00 0.00 0.00 3.01
111 112 0.393808 GTCCACACACACACCCAAGT 60.394 55.000 0.00 0.00 0.00 3.16
112 113 0.107214 AGTCCACACACACACCCAAG 60.107 55.000 0.00 0.00 0.00 3.61
113 114 0.329931 AAGTCCACACACACACCCAA 59.670 50.000 0.00 0.00 0.00 4.12
114 115 0.393673 CAAGTCCACACACACACCCA 60.394 55.000 0.00 0.00 0.00 4.51
115 116 0.107410 TCAAGTCCACACACACACCC 60.107 55.000 0.00 0.00 0.00 4.61
116 117 1.014352 GTCAAGTCCACACACACACC 58.986 55.000 0.00 0.00 0.00 4.16
117 118 1.933853 GAGTCAAGTCCACACACACAC 59.066 52.381 0.00 0.00 0.00 3.82
118 119 1.831106 AGAGTCAAGTCCACACACACA 59.169 47.619 0.00 0.00 0.00 3.72
119 120 2.101582 AGAGAGTCAAGTCCACACACAC 59.898 50.000 0.00 0.00 0.00 3.82
120 121 2.388735 AGAGAGTCAAGTCCACACACA 58.611 47.619 0.00 0.00 0.00 3.72
121 122 4.021894 ACATAGAGAGTCAAGTCCACACAC 60.022 45.833 0.00 0.00 0.00 3.82
122 123 4.021981 CACATAGAGAGTCAAGTCCACACA 60.022 45.833 0.00 0.00 0.00 3.72
123 124 4.021894 ACACATAGAGAGTCAAGTCCACAC 60.022 45.833 0.00 0.00 0.00 3.82
124 125 4.021981 CACACATAGAGAGTCAAGTCCACA 60.022 45.833 0.00 0.00 0.00 4.17
125 126 4.489810 CACACATAGAGAGTCAAGTCCAC 58.510 47.826 0.00 0.00 0.00 4.02
126 127 3.056536 GCACACATAGAGAGTCAAGTCCA 60.057 47.826 0.00 0.00 0.00 4.02
127 128 3.194542 AGCACACATAGAGAGTCAAGTCC 59.805 47.826 0.00 0.00 0.00 3.85
128 129 4.157656 AGAGCACACATAGAGAGTCAAGTC 59.842 45.833 0.00 0.00 0.00 3.01
129 130 4.085733 AGAGCACACATAGAGAGTCAAGT 58.914 43.478 0.00 0.00 0.00 3.16
130 131 4.717233 AGAGCACACATAGAGAGTCAAG 57.283 45.455 0.00 0.00 0.00 3.02
131 132 5.233225 CAAAGAGCACACATAGAGAGTCAA 58.767 41.667 0.00 0.00 0.00 3.18
132 133 4.322273 CCAAAGAGCACACATAGAGAGTCA 60.322 45.833 0.00 0.00 0.00 3.41
133 134 4.180057 CCAAAGAGCACACATAGAGAGTC 58.820 47.826 0.00 0.00 0.00 3.36
134 135 3.618507 GCCAAAGAGCACACATAGAGAGT 60.619 47.826 0.00 0.00 0.00 3.24
135 136 2.935201 GCCAAAGAGCACACATAGAGAG 59.065 50.000 0.00 0.00 0.00 3.20
136 137 2.675032 CGCCAAAGAGCACACATAGAGA 60.675 50.000 0.00 0.00 0.00 3.10
137 138 1.662629 CGCCAAAGAGCACACATAGAG 59.337 52.381 0.00 0.00 0.00 2.43
138 139 1.675714 CCGCCAAAGAGCACACATAGA 60.676 52.381 0.00 0.00 0.00 1.98
139 140 0.729116 CCGCCAAAGAGCACACATAG 59.271 55.000 0.00 0.00 0.00 2.23
140 141 0.036164 ACCGCCAAAGAGCACACATA 59.964 50.000 0.00 0.00 0.00 2.29
141 142 0.823356 AACCGCCAAAGAGCACACAT 60.823 50.000 0.00 0.00 0.00 3.21
142 143 1.034838 AAACCGCCAAAGAGCACACA 61.035 50.000 0.00 0.00 0.00 3.72
143 144 0.594796 CAAACCGCCAAAGAGCACAC 60.595 55.000 0.00 0.00 0.00 3.82
144 145 1.732917 CAAACCGCCAAAGAGCACA 59.267 52.632 0.00 0.00 0.00 4.57
145 146 1.661509 GCAAACCGCCAAAGAGCAC 60.662 57.895 0.00 0.00 32.94 4.40
146 147 1.391157 AAGCAAACCGCCAAAGAGCA 61.391 50.000 0.00 0.00 44.04 4.26
147 148 0.249447 AAAGCAAACCGCCAAAGAGC 60.249 50.000 0.00 0.00 44.04 4.09
148 149 3.575965 ATAAAGCAAACCGCCAAAGAG 57.424 42.857 0.00 0.00 44.04 2.85
149 150 4.329462 AAATAAAGCAAACCGCCAAAGA 57.671 36.364 0.00 0.00 44.04 2.52
150 151 7.820044 TTATAAATAAAGCAAACCGCCAAAG 57.180 32.000 0.00 0.00 44.04 2.77
151 152 8.245701 CTTTATAAATAAAGCAAACCGCCAAA 57.754 30.769 9.01 0.00 41.69 3.28
152 153 7.820044 CTTTATAAATAAAGCAAACCGCCAA 57.180 32.000 9.01 0.00 41.69 4.52
164 165 4.276431 CCTTCGCCCCGCTTTATAAATAAA 59.724 41.667 0.00 0.00 0.00 1.40
165 166 3.816523 CCTTCGCCCCGCTTTATAAATAA 59.183 43.478 0.00 0.00 0.00 1.40
166 167 3.404899 CCTTCGCCCCGCTTTATAAATA 58.595 45.455 0.00 0.00 0.00 1.40
167 168 2.227194 CCTTCGCCCCGCTTTATAAAT 58.773 47.619 0.00 0.00 0.00 1.40
168 169 1.670791 CCTTCGCCCCGCTTTATAAA 58.329 50.000 0.00 0.00 0.00 1.40
169 170 0.816421 GCCTTCGCCCCGCTTTATAA 60.816 55.000 0.00 0.00 0.00 0.98
170 171 1.227734 GCCTTCGCCCCGCTTTATA 60.228 57.895 0.00 0.00 0.00 0.98
171 172 2.516225 GCCTTCGCCCCGCTTTAT 60.516 61.111 0.00 0.00 0.00 1.40
181 182 1.092348 ATACCGAAAAAGGCCTTCGC 58.908 50.000 20.79 10.21 43.35 4.70
182 183 3.842732 AAATACCGAAAAAGGCCTTCG 57.157 42.857 20.79 18.48 44.11 3.79
183 184 4.491676 GGAAAATACCGAAAAAGGCCTTC 58.508 43.478 20.79 5.52 33.69 3.46
184 185 3.259876 GGGAAAATACCGAAAAAGGCCTT 59.740 43.478 13.78 13.78 33.69 4.35
185 186 2.829720 GGGAAAATACCGAAAAAGGCCT 59.170 45.455 0.00 0.00 33.69 5.19
186 187 2.829720 AGGGAAAATACCGAAAAAGGCC 59.170 45.455 0.00 0.00 33.69 5.19
187 188 3.257375 ACAGGGAAAATACCGAAAAAGGC 59.743 43.478 0.00 0.00 33.69 4.35
188 189 4.765339 AGACAGGGAAAATACCGAAAAAGG 59.235 41.667 0.00 0.00 37.30 3.11
189 190 5.959618 AGACAGGGAAAATACCGAAAAAG 57.040 39.130 0.00 0.00 0.00 2.27
190 191 7.148373 CGATAAGACAGGGAAAATACCGAAAAA 60.148 37.037 0.00 0.00 0.00 1.94
191 192 6.314400 CGATAAGACAGGGAAAATACCGAAAA 59.686 38.462 0.00 0.00 0.00 2.29
192 193 5.813672 CGATAAGACAGGGAAAATACCGAAA 59.186 40.000 0.00 0.00 0.00 3.46
193 194 5.105228 ACGATAAGACAGGGAAAATACCGAA 60.105 40.000 0.00 0.00 0.00 4.30
194 195 4.403432 ACGATAAGACAGGGAAAATACCGA 59.597 41.667 0.00 0.00 0.00 4.69
195 196 4.690122 ACGATAAGACAGGGAAAATACCG 58.310 43.478 0.00 0.00 0.00 4.02
196 197 5.878669 ACAACGATAAGACAGGGAAAATACC 59.121 40.000 0.00 0.00 0.00 2.73
202 203 7.276218 CGTAATTAACAACGATAAGACAGGGAA 59.724 37.037 5.69 0.00 41.55 3.97
203 204 6.753279 CGTAATTAACAACGATAAGACAGGGA 59.247 38.462 5.69 0.00 41.55 4.20
425 454 2.602257 TGACAGTGGCGATTCTATGG 57.398 50.000 0.00 0.00 0.00 2.74
486 522 9.509956 TTTTATAGGATTCCGTTCTTCTTCAAA 57.490 29.630 0.00 0.00 0.00 2.69
568 604 0.249784 CAGCGAGGAGATGGTGGATG 60.250 60.000 0.00 0.00 31.47 3.51
576 612 0.382515 GCTAACGACAGCGAGGAGAT 59.617 55.000 0.00 0.00 41.64 2.75
591 627 2.858745 AGAAAAGGGCGTCAAAGCTAA 58.141 42.857 0.00 0.00 37.29 3.09
1062 1105 4.864334 CTGCCCTCGCCCATGACC 62.864 72.222 0.00 0.00 0.00 4.02
1063 1106 4.101448 ACTGCCCTCGCCCATGAC 62.101 66.667 0.00 0.00 0.00 3.06
1064 1107 3.785859 GACTGCCCTCGCCCATGA 61.786 66.667 0.00 0.00 0.00 3.07
1065 1108 4.864334 GGACTGCCCTCGCCCATG 62.864 72.222 0.00 0.00 0.00 3.66
1176 1231 1.179152 TAATCTTCCGGAGCACGTCA 58.821 50.000 3.34 0.00 42.24 4.35
1312 1367 2.101582 AGACATCACCGAGCTTACCATC 59.898 50.000 0.00 0.00 0.00 3.51
1350 1405 2.579201 CAGTCGCCTCGGTGGAAT 59.421 61.111 0.00 0.00 38.35 3.01
1400 1455 2.349590 CAGCATCGTTCTCCATGTTCA 58.650 47.619 0.00 0.00 0.00 3.18
1434 1489 4.787280 AGAGCGGGGGACAGGAGG 62.787 72.222 0.00 0.00 0.00 4.30
1488 1543 2.574929 CGCTGCCAATTGTGCCAT 59.425 55.556 13.99 0.00 0.00 4.40
1564 1650 0.602638 TCCGTGAGTGTGCAATGTCC 60.603 55.000 0.00 0.00 0.00 4.02
1565 1651 0.512952 GTCCGTGAGTGTGCAATGTC 59.487 55.000 0.00 0.00 0.00 3.06
1566 1652 1.221466 CGTCCGTGAGTGTGCAATGT 61.221 55.000 0.00 0.00 0.00 2.71
1567 1653 0.943835 TCGTCCGTGAGTGTGCAATG 60.944 55.000 0.00 0.00 0.00 2.82
1568 1654 0.944311 GTCGTCCGTGAGTGTGCAAT 60.944 55.000 0.00 0.00 0.00 3.56
1569 1655 1.590525 GTCGTCCGTGAGTGTGCAA 60.591 57.895 0.00 0.00 0.00 4.08
1570 1656 2.027024 GTCGTCCGTGAGTGTGCA 59.973 61.111 0.00 0.00 0.00 4.57
1571 1657 1.344942 GATGTCGTCCGTGAGTGTGC 61.345 60.000 0.00 0.00 0.00 4.57
1572 1658 1.065572 CGATGTCGTCCGTGAGTGTG 61.066 60.000 0.00 0.00 34.11 3.82
1573 1659 1.209383 CGATGTCGTCCGTGAGTGT 59.791 57.895 0.00 0.00 34.11 3.55
1574 1660 4.057615 CGATGTCGTCCGTGAGTG 57.942 61.111 0.00 0.00 34.11 3.51
1584 1670 0.721718 GAAGCCCTTGAACGATGTCG 59.278 55.000 0.11 0.11 46.33 4.35
1585 1671 1.464997 GTGAAGCCCTTGAACGATGTC 59.535 52.381 0.00 0.00 0.00 3.06
1586 1672 1.072331 AGTGAAGCCCTTGAACGATGT 59.928 47.619 0.00 0.00 0.00 3.06
1587 1673 1.813513 AGTGAAGCCCTTGAACGATG 58.186 50.000 0.00 0.00 0.00 3.84
1588 1674 2.427506 GAAGTGAAGCCCTTGAACGAT 58.572 47.619 0.00 0.00 0.00 3.73
1589 1675 1.542547 GGAAGTGAAGCCCTTGAACGA 60.543 52.381 0.00 0.00 0.00 3.85
1590 1676 0.875059 GGAAGTGAAGCCCTTGAACG 59.125 55.000 0.00 0.00 0.00 3.95
1591 1677 1.248486 GGGAAGTGAAGCCCTTGAAC 58.752 55.000 0.00 0.00 41.31 3.18
1592 1678 0.250727 CGGGAAGTGAAGCCCTTGAA 60.251 55.000 0.00 0.00 42.40 2.69
1593 1679 1.374947 CGGGAAGTGAAGCCCTTGA 59.625 57.895 0.00 0.00 42.40 3.02
1594 1680 2.335712 GCGGGAAGTGAAGCCCTTG 61.336 63.158 0.00 0.00 42.40 3.61
1712 1798 3.560251 AACGGGCTCCACTGCACT 61.560 61.111 0.00 0.00 33.50 4.40
1932 2018 4.764823 TGAATATCTGTGGAACCAAACACC 59.235 41.667 0.00 0.00 36.80 4.16
2120 2206 1.402968 CTGCACAGTGCTGTTGAAACT 59.597 47.619 25.83 0.00 45.31 2.66
2121 2207 1.401552 TCTGCACAGTGCTGTTGAAAC 59.598 47.619 25.83 0.00 45.31 2.78
2160 2246 3.118775 TCCAAACATAGAGTGCGCATACT 60.119 43.478 15.91 18.36 0.00 2.12
2168 2254 7.336679 TCAATAACCATGTCCAAACATAGAGTG 59.663 37.037 0.00 0.00 44.41 3.51
2215 2301 5.071788 ACCTGAATGTACAACTTCTCCAAGA 59.928 40.000 0.00 0.00 33.34 3.02
2727 2814 9.070179 CCAATCACACATCCATCATAAATTCTA 57.930 33.333 0.00 0.00 0.00 2.10
2847 2943 5.118510 GTGGATTTGCGTATCTTTTGTTTGG 59.881 40.000 0.00 0.00 0.00 3.28
3117 3223 8.833493 TGTCAGATATGTGCAATGATTTCTTAG 58.167 33.333 0.00 0.00 0.00 2.18
3253 3364 5.921976 TGCTCTAAGTCATGTTTGCATTTTG 59.078 36.000 0.00 0.00 31.99 2.44
3331 3442 5.721232 ACCTTGAAAGTTACTGATAGACCG 58.279 41.667 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.