Multiple sequence alignment - TraesCS5D01G110000

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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 TraesCS5D01G110000 chr5D 100.000 2595 0 0 1 2595 124841204 124843798 0.000000e+00 4793
1 TraesCS5D01G110000 chr5A 95.007 1362 50 9 670 2024 139071013 139072363 0.000000e+00 2122
2 TraesCS5D01G110000 chr5A 96.094 384 14 1 2084 2467 139073105 139073487 2.190000e-175 625
3 TraesCS5D01G110000 chr5A 84.170 259 27 8 123 376 138775531 138775780 3.340000e-59 239
4 TraesCS5D01G110000 chr5A 97.222 72 2 0 5 76 138739844 138739915 3.510000e-24 122
5 TraesCS5D01G110000 chr5B 92.380 748 52 3 888 1634 137417724 137418467 0.000000e+00 1061
6 TraesCS5D01G110000 chr5B 90.613 799 63 11 1801 2595 137651610 137652400 0.000000e+00 1050
7 TraesCS5D01G110000 chr5B 85.008 647 55 17 274 902 137416023 137416645 1.020000e-173 619
8 TraesCS5D01G110000 chr5B 93.678 174 10 1 1630 1803 137644445 137644617 2.560000e-65 259
9 TraesCS5D01G110000 chr7D 78.256 837 125 34 848 1658 47809354 47808549 3.880000e-133 484
10 TraesCS5D01G110000 chr7A 77.153 836 132 39 849 1658 50425708 50424906 5.130000e-117 431
11 TraesCS5D01G110000 chr6B 85.537 242 33 2 428 668 22740193 22739953 4.290000e-63 252
12 TraesCS5D01G110000 chr6B 83.402 241 37 3 428 666 145295643 145295882 1.210000e-53 220
13 TraesCS5D01G110000 chr6B 83.402 241 37 3 428 666 364557572 364557333 1.210000e-53 220
14 TraesCS5D01G110000 chr4B 84.937 239 34 2 429 666 519813259 519813022 9.280000e-60 241
15 TraesCS5D01G110000 chr7B 84.232 241 33 5 428 665 41291610 41291848 2.010000e-56 230
16 TraesCS5D01G110000 chr7B 83.682 239 38 1 428 665 102231951 102232189 9.350000e-55 224
17 TraesCS5D01G110000 chr1D 84.167 240 34 4 428 665 451388338 451388575 2.010000e-56 230
18 TraesCS5D01G110000 chr1D 83.682 239 37 2 428 665 323916793 323916556 9.350000e-55 224
19 TraesCS5D01G110000 chr1D 83.333 240 36 4 428 665 415392689 415392926 4.350000e-53 219


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 TraesCS5D01G110000 chr5D 124841204 124843798 2594 False 4793.0 4793 100.0000 1 2595 1 chr5D.!!$F1 2594
1 TraesCS5D01G110000 chr5A 139071013 139073487 2474 False 1373.5 2122 95.5505 670 2467 2 chr5A.!!$F3 1797
2 TraesCS5D01G110000 chr5B 137651610 137652400 790 False 1050.0 1050 90.6130 1801 2595 1 chr5B.!!$F2 794
3 TraesCS5D01G110000 chr5B 137416023 137418467 2444 False 840.0 1061 88.6940 274 1634 2 chr5B.!!$F3 1360
4 TraesCS5D01G110000 chr7D 47808549 47809354 805 True 484.0 484 78.2560 848 1658 1 chr7D.!!$R1 810
5 TraesCS5D01G110000 chr7A 50424906 50425708 802 True 431.0 431 77.1530 849 1658 1 chr7A.!!$R1 809

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
246 247 0.242017 GCCTGTGTCTTCAATGCCAC 59.758 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2128 3977 0.896923 ACGTGCGGGGTGTTATCTAA 59.103 50.0 0.0 0.0 0.0 2.1 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
24 25 4.072913 CGTAGCACGCTCGTTGAT 57.927 55.556 0.00 0.00 33.65 2.57
25 26 2.359792 CGTAGCACGCTCGTTGATT 58.640 52.632 0.00 0.00 33.65 2.57
26 27 1.541475 CGTAGCACGCTCGTTGATTA 58.459 50.000 0.00 0.00 33.65 1.75
27 28 2.117137 CGTAGCACGCTCGTTGATTAT 58.883 47.619 0.00 0.00 33.65 1.28
28 29 3.294102 CGTAGCACGCTCGTTGATTATA 58.706 45.455 0.00 0.00 33.65 0.98
29 30 3.912563 CGTAGCACGCTCGTTGATTATAT 59.087 43.478 0.00 0.00 33.65 0.86
30 31 5.084055 CGTAGCACGCTCGTTGATTATATA 58.916 41.667 0.00 0.00 33.65 0.86
31 32 5.566395 CGTAGCACGCTCGTTGATTATATAA 59.434 40.000 0.00 0.00 33.65 0.98
32 33 6.087159 CGTAGCACGCTCGTTGATTATATAAA 59.913 38.462 0.00 0.00 33.65 1.40
33 34 6.453643 AGCACGCTCGTTGATTATATAAAG 57.546 37.500 0.00 0.00 0.00 1.85
34 35 5.073478 GCACGCTCGTTGATTATATAAAGC 58.927 41.667 0.00 2.23 0.00 3.51
35 36 5.107453 GCACGCTCGTTGATTATATAAAGCT 60.107 40.000 11.07 0.00 0.00 3.74
36 37 6.089016 GCACGCTCGTTGATTATATAAAGCTA 59.911 38.462 11.07 0.00 0.00 3.32
37 38 7.658261 CACGCTCGTTGATTATATAAAGCTAG 58.342 38.462 11.07 0.00 0.00 3.42
38 39 7.326305 CACGCTCGTTGATTATATAAAGCTAGT 59.674 37.037 11.07 2.81 0.00 2.57
39 40 7.866393 ACGCTCGTTGATTATATAAAGCTAGTT 59.134 33.333 11.07 0.00 0.00 2.24
40 41 8.156553 CGCTCGTTGATTATATAAAGCTAGTTG 58.843 37.037 11.07 0.00 0.00 3.16
41 42 7.952637 GCTCGTTGATTATATAAAGCTAGTTGC 59.047 37.037 0.00 0.00 43.29 4.17
53 54 3.439895 GCTAGTTGCTAGGTGGACTAC 57.560 52.381 5.47 0.00 38.95 2.73
54 55 2.758979 GCTAGTTGCTAGGTGGACTACA 59.241 50.000 5.47 0.00 38.95 2.74
55 56 3.194968 GCTAGTTGCTAGGTGGACTACAA 59.805 47.826 5.47 0.00 38.95 2.41
56 57 3.963428 AGTTGCTAGGTGGACTACAAG 57.037 47.619 0.00 0.00 0.00 3.16
57 58 3.240302 AGTTGCTAGGTGGACTACAAGT 58.760 45.455 0.00 0.00 0.00 3.16
58 59 3.006967 AGTTGCTAGGTGGACTACAAGTG 59.993 47.826 0.00 0.00 31.31 3.16
59 60 2.884320 TGCTAGGTGGACTACAAGTGA 58.116 47.619 0.00 0.00 0.00 3.41
60 61 2.826128 TGCTAGGTGGACTACAAGTGAG 59.174 50.000 0.00 0.00 0.00 3.51
61 62 2.417515 GCTAGGTGGACTACAAGTGAGC 60.418 54.545 0.00 0.00 0.00 4.26
62 63 0.603569 AGGTGGACTACAAGTGAGCG 59.396 55.000 0.00 0.00 0.00 5.03
63 64 0.601558 GGTGGACTACAAGTGAGCGA 59.398 55.000 0.00 0.00 0.00 4.93
64 65 1.402984 GGTGGACTACAAGTGAGCGAG 60.403 57.143 0.00 0.00 0.00 5.03
65 66 1.269998 GTGGACTACAAGTGAGCGAGT 59.730 52.381 0.00 0.00 0.00 4.18
66 67 1.269723 TGGACTACAAGTGAGCGAGTG 59.730 52.381 0.00 0.00 0.00 3.51
67 68 1.341606 GACTACAAGTGAGCGAGTGC 58.658 55.000 0.00 0.00 43.24 4.40
68 69 0.673985 ACTACAAGTGAGCGAGTGCA 59.326 50.000 0.00 0.00 46.23 4.57
69 70 1.273606 ACTACAAGTGAGCGAGTGCAT 59.726 47.619 0.00 0.00 46.23 3.96
70 71 1.657594 CTACAAGTGAGCGAGTGCATG 59.342 52.381 0.00 0.00 46.23 4.06
71 72 0.250038 ACAAGTGAGCGAGTGCATGT 60.250 50.000 0.00 0.00 46.23 3.21
72 73 1.000843 ACAAGTGAGCGAGTGCATGTA 59.999 47.619 0.00 0.00 46.23 2.29
73 74 1.391485 CAAGTGAGCGAGTGCATGTAC 59.609 52.381 5.71 5.71 46.23 2.90
74 75 0.603065 AGTGAGCGAGTGCATGTACA 59.397 50.000 16.62 0.00 46.23 2.90
75 76 1.205655 AGTGAGCGAGTGCATGTACAT 59.794 47.619 16.62 1.41 46.23 2.29
76 77 2.002586 GTGAGCGAGTGCATGTACATT 58.997 47.619 16.62 0.00 46.23 2.71
77 78 2.416547 GTGAGCGAGTGCATGTACATTT 59.583 45.455 16.62 0.00 46.23 2.32
78 79 2.416202 TGAGCGAGTGCATGTACATTTG 59.584 45.455 16.62 0.00 46.23 2.32
79 80 2.416547 GAGCGAGTGCATGTACATTTGT 59.583 45.455 16.62 0.00 46.23 2.83
80 81 2.813754 AGCGAGTGCATGTACATTTGTT 59.186 40.909 16.62 0.00 46.23 2.83
81 82 3.253188 AGCGAGTGCATGTACATTTGTTT 59.747 39.130 16.62 0.00 46.23 2.83
82 83 3.361644 GCGAGTGCATGTACATTTGTTTG 59.638 43.478 16.62 0.00 42.15 2.93
83 84 4.536065 CGAGTGCATGTACATTTGTTTGT 58.464 39.130 16.62 0.00 0.00 2.83
84 85 4.379498 CGAGTGCATGTACATTTGTTTGTG 59.621 41.667 16.62 0.00 0.00 3.33
85 86 5.261209 AGTGCATGTACATTTGTTTGTGT 57.739 34.783 16.62 0.00 0.00 3.72
86 87 5.042593 AGTGCATGTACATTTGTTTGTGTG 58.957 37.500 16.62 0.00 0.00 3.82
87 88 5.039984 GTGCATGTACATTTGTTTGTGTGA 58.960 37.500 5.37 0.00 0.00 3.58
88 89 5.518128 GTGCATGTACATTTGTTTGTGTGAA 59.482 36.000 5.37 0.00 0.00 3.18
89 90 6.200665 GTGCATGTACATTTGTTTGTGTGAAT 59.799 34.615 5.37 0.00 0.00 2.57
90 91 7.380870 GTGCATGTACATTTGTTTGTGTGAATA 59.619 33.333 5.37 0.00 0.00 1.75
91 92 7.922811 TGCATGTACATTTGTTTGTGTGAATAA 59.077 29.630 5.37 0.00 0.00 1.40
92 93 8.213812 GCATGTACATTTGTTTGTGTGAATAAC 58.786 33.333 5.37 0.00 0.00 1.89
93 94 7.900299 TGTACATTTGTTTGTGTGAATAACG 57.100 32.000 0.00 0.00 0.00 3.18
94 95 7.694886 TGTACATTTGTTTGTGTGAATAACGA 58.305 30.769 0.00 0.00 0.00 3.85
95 96 7.853437 TGTACATTTGTTTGTGTGAATAACGAG 59.147 33.333 0.00 0.00 0.00 4.18
96 97 6.791303 ACATTTGTTTGTGTGAATAACGAGT 58.209 32.000 0.00 0.00 0.00 4.18
97 98 6.690957 ACATTTGTTTGTGTGAATAACGAGTG 59.309 34.615 0.00 0.00 32.35 3.51
98 99 4.203950 TGTTTGTGTGAATAACGAGTGC 57.796 40.909 0.00 0.00 0.00 4.40
99 100 3.215244 GTTTGTGTGAATAACGAGTGCG 58.785 45.455 0.00 0.00 44.79 5.34
100 101 0.787787 TGTGTGAATAACGAGTGCGC 59.212 50.000 0.00 0.00 42.48 6.09
101 102 0.246757 GTGTGAATAACGAGTGCGCG 60.247 55.000 0.00 0.00 42.48 6.86
108 109 3.637714 ACGAGTGCGCGTTCATTT 58.362 50.000 8.43 0.00 42.71 2.32
109 110 1.938861 ACGAGTGCGCGTTCATTTT 59.061 47.368 8.43 0.00 42.71 1.82
110 111 0.384230 ACGAGTGCGCGTTCATTTTG 60.384 50.000 8.43 0.00 42.71 2.44
111 112 0.384230 CGAGTGCGCGTTCATTTTGT 60.384 50.000 8.43 0.00 0.00 2.83
112 113 1.753956 GAGTGCGCGTTCATTTTGTT 58.246 45.000 8.43 0.00 0.00 2.83
113 114 2.116366 GAGTGCGCGTTCATTTTGTTT 58.884 42.857 8.43 0.00 0.00 2.83
114 115 2.533942 GAGTGCGCGTTCATTTTGTTTT 59.466 40.909 8.43 0.00 0.00 2.43
115 116 2.926838 AGTGCGCGTTCATTTTGTTTTT 59.073 36.364 8.43 0.00 0.00 1.94
132 133 3.955771 TTTTTAGGTGAACGAGTGCAC 57.044 42.857 9.40 9.40 0.00 4.57
133 134 1.493772 TTTAGGTGAACGAGTGCACG 58.506 50.000 12.01 2.67 35.91 5.34
135 136 0.318360 TAGGTGAACGAGTGCACGTG 60.318 55.000 17.10 12.28 45.83 4.49
136 137 2.245532 GTGAACGAGTGCACGTGC 59.754 61.111 33.11 33.11 45.83 5.34
150 151 3.820689 GCACGTGCATGTATTGAAAAGA 58.179 40.909 34.52 0.00 41.59 2.52
151 152 4.225984 GCACGTGCATGTATTGAAAAGAA 58.774 39.130 34.52 0.00 41.59 2.52
152 153 4.858692 GCACGTGCATGTATTGAAAAGAAT 59.141 37.500 34.52 0.00 41.59 2.40
153 154 5.220080 GCACGTGCATGTATTGAAAAGAATG 60.220 40.000 34.52 0.00 41.59 2.67
154 155 6.085573 CACGTGCATGTATTGAAAAGAATGA 58.914 36.000 12.10 0.00 0.00 2.57
155 156 6.249893 CACGTGCATGTATTGAAAAGAATGAG 59.750 38.462 12.10 0.00 0.00 2.90
156 157 5.228635 CGTGCATGTATTGAAAAGAATGAGC 59.771 40.000 0.00 0.00 0.00 4.26
157 158 6.094719 GTGCATGTATTGAAAAGAATGAGCA 58.905 36.000 0.00 0.00 0.00 4.26
158 159 6.034256 GTGCATGTATTGAAAAGAATGAGCAC 59.966 38.462 0.00 0.00 39.16 4.40
159 160 5.228635 GCATGTATTGAAAAGAATGAGCACG 59.771 40.000 0.00 0.00 0.00 5.34
160 161 5.940192 TGTATTGAAAAGAATGAGCACGT 57.060 34.783 0.00 0.00 0.00 4.49
161 162 7.463544 CATGTATTGAAAAGAATGAGCACGTA 58.536 34.615 0.00 0.00 0.00 3.57
162 163 7.428282 TGTATTGAAAAGAATGAGCACGTAA 57.572 32.000 0.00 0.00 0.00 3.18
163 164 8.039603 TGTATTGAAAAGAATGAGCACGTAAT 57.960 30.769 0.00 0.00 0.00 1.89
164 165 8.511321 TGTATTGAAAAGAATGAGCACGTAATT 58.489 29.630 0.00 0.00 0.00 1.40
165 166 7.801547 ATTGAAAAGAATGAGCACGTAATTG 57.198 32.000 0.00 0.00 0.00 2.32
166 167 5.698832 TGAAAAGAATGAGCACGTAATTGG 58.301 37.500 0.00 0.00 0.00 3.16
167 168 4.701956 AAAGAATGAGCACGTAATTGGG 57.298 40.909 0.00 0.00 0.00 4.12
168 169 2.017049 AGAATGAGCACGTAATTGGGC 58.983 47.619 0.00 0.00 0.00 5.36
169 170 1.065551 GAATGAGCACGTAATTGGGCC 59.934 52.381 0.00 0.00 0.00 5.80
170 171 1.095228 ATGAGCACGTAATTGGGCCG 61.095 55.000 0.00 0.00 0.00 6.13
171 172 3.108357 GAGCACGTAATTGGGCCGC 62.108 63.158 0.00 0.00 0.00 6.53
172 173 4.187810 GCACGTAATTGGGCCGCC 62.188 66.667 0.00 0.00 0.00 6.13
173 174 3.514362 CACGTAATTGGGCCGCCC 61.514 66.667 22.81 22.81 45.71 6.13
203 204 4.697756 CGCCTGGGCCGTCTTTCA 62.698 66.667 5.99 0.00 37.98 2.69
204 205 2.044946 GCCTGGGCCGTCTTTCAT 60.045 61.111 0.00 0.00 34.56 2.57
205 206 1.678970 GCCTGGGCCGTCTTTCATT 60.679 57.895 0.00 0.00 34.56 2.57
206 207 1.937546 GCCTGGGCCGTCTTTCATTG 61.938 60.000 0.00 0.00 34.56 2.82
207 208 1.315257 CCTGGGCCGTCTTTCATTGG 61.315 60.000 0.00 0.00 0.00 3.16
208 209 1.937546 CTGGGCCGTCTTTCATTGGC 61.938 60.000 0.00 0.00 46.82 4.52
211 212 1.508088 GCCGTCTTTCATTGGCAGG 59.492 57.895 0.00 0.00 46.76 4.85
212 213 0.960364 GCCGTCTTTCATTGGCAGGA 60.960 55.000 0.00 0.00 46.76 3.86
213 214 1.089920 CCGTCTTTCATTGGCAGGAG 58.910 55.000 0.00 0.00 0.00 3.69
214 215 1.089920 CGTCTTTCATTGGCAGGAGG 58.910 55.000 0.00 0.00 0.00 4.30
215 216 0.813821 GTCTTTCATTGGCAGGAGGC 59.186 55.000 0.00 0.00 43.74 4.70
236 237 4.057428 GACCGCTCGCCTGTGTCT 62.057 66.667 0.00 0.00 0.00 3.41
237 238 3.575351 GACCGCTCGCCTGTGTCTT 62.575 63.158 0.00 0.00 0.00 3.01
238 239 2.811317 CCGCTCGCCTGTGTCTTC 60.811 66.667 0.00 0.00 0.00 2.87
239 240 2.049156 CGCTCGCCTGTGTCTTCA 60.049 61.111 0.00 0.00 0.00 3.02
240 241 1.664649 CGCTCGCCTGTGTCTTCAA 60.665 57.895 0.00 0.00 0.00 2.69
241 242 1.016130 CGCTCGCCTGTGTCTTCAAT 61.016 55.000 0.00 0.00 0.00 2.57
242 243 0.445436 GCTCGCCTGTGTCTTCAATG 59.555 55.000 0.00 0.00 0.00 2.82
243 244 0.445436 CTCGCCTGTGTCTTCAATGC 59.555 55.000 0.00 0.00 0.00 3.56
244 245 0.955428 TCGCCTGTGTCTTCAATGCC 60.955 55.000 0.00 0.00 0.00 4.40
245 246 1.236616 CGCCTGTGTCTTCAATGCCA 61.237 55.000 0.00 0.00 0.00 4.92
246 247 0.242017 GCCTGTGTCTTCAATGCCAC 59.758 55.000 0.00 0.00 0.00 5.01
247 248 0.883833 CCTGTGTCTTCAATGCCACC 59.116 55.000 0.00 0.00 0.00 4.61
248 249 1.608055 CTGTGTCTTCAATGCCACCA 58.392 50.000 0.00 0.00 0.00 4.17
249 250 1.538512 CTGTGTCTTCAATGCCACCAG 59.461 52.381 0.00 0.00 0.00 4.00
250 251 1.133823 TGTGTCTTCAATGCCACCAGT 60.134 47.619 0.00 0.00 0.00 4.00
251 252 2.105649 TGTGTCTTCAATGCCACCAGTA 59.894 45.455 0.00 0.00 0.00 2.74
252 253 2.484264 GTGTCTTCAATGCCACCAGTAC 59.516 50.000 0.00 0.00 0.00 2.73
253 254 1.732259 GTCTTCAATGCCACCAGTACG 59.268 52.381 0.00 0.00 0.00 3.67
254 255 1.086696 CTTCAATGCCACCAGTACGG 58.913 55.000 2.71 2.71 42.50 4.02
260 261 3.706373 CCACCAGTACGGCTGCCT 61.706 66.667 17.92 6.50 43.71 4.75
261 262 2.434884 CACCAGTACGGCTGCCTG 60.435 66.667 17.92 12.68 43.71 4.85
262 263 2.923035 ACCAGTACGGCTGCCTGT 60.923 61.111 17.92 17.70 43.71 4.00
263 264 2.434884 CCAGTACGGCTGCCTGTG 60.435 66.667 17.92 8.15 43.71 3.66
264 265 2.343758 CAGTACGGCTGCCTGTGT 59.656 61.111 17.92 9.98 38.52 3.72
265 266 2.029288 CAGTACGGCTGCCTGTGTG 61.029 63.158 17.92 13.34 38.52 3.82
266 267 3.423154 GTACGGCTGCCTGTGTGC 61.423 66.667 17.92 7.31 0.00 4.57
267 268 4.697756 TACGGCTGCCTGTGTGCC 62.698 66.667 17.92 0.00 42.94 5.01
270 271 4.648626 GGCTGCCTGTGTGCCAGA 62.649 66.667 12.43 0.00 44.49 3.86
271 272 2.595463 GCTGCCTGTGTGCCAGAA 60.595 61.111 0.00 0.00 44.49 3.02
272 273 2.912624 GCTGCCTGTGTGCCAGAAC 61.913 63.158 0.00 0.00 44.49 3.01
281 282 4.005650 CTGTGTGCCAGAACTGTATCAAT 58.994 43.478 1.18 0.00 44.49 2.57
285 286 4.009675 GTGCCAGAACTGTATCAATGGAA 58.990 43.478 1.18 0.00 0.00 3.53
286 287 4.458989 GTGCCAGAACTGTATCAATGGAAA 59.541 41.667 1.18 0.00 0.00 3.13
323 324 4.849329 CGACGTGGCGGGCTAGTC 62.849 72.222 15.77 15.77 0.00 2.59
324 325 4.509737 GACGTGGCGGGCTAGTCC 62.510 72.222 2.21 2.21 0.00 3.85
347 348 2.286654 GCGCTGACCTTTTGCTGATATC 60.287 50.000 0.00 0.00 0.00 1.63
351 352 4.183865 CTGACCTTTTGCTGATATCGTCA 58.816 43.478 0.00 2.44 35.05 4.35
366 367 6.265422 TGATATCGTCATGTTAGATGTCAGGT 59.735 38.462 16.38 0.00 37.51 4.00
367 368 7.447238 TGATATCGTCATGTTAGATGTCAGGTA 59.553 37.037 16.38 2.94 37.51 3.08
375 376 7.706607 TCATGTTAGATGTCAGGTATTTTCTCG 59.293 37.037 0.00 0.00 0.00 4.04
382 383 5.972935 TGTCAGGTATTTTCTCGCATCTAA 58.027 37.500 0.00 0.00 0.00 2.10
385 386 8.201464 TGTCAGGTATTTTCTCGCATCTAAATA 58.799 33.333 0.00 0.00 0.00 1.40
446 456 5.564048 AGATACTAACTCTGTCCACGTTC 57.436 43.478 0.00 0.00 0.00 3.95
448 458 5.652891 AGATACTAACTCTGTCCACGTTCAT 59.347 40.000 0.00 0.00 0.00 2.57
449 459 4.602340 ACTAACTCTGTCCACGTTCATT 57.398 40.909 0.00 0.00 0.00 2.57
450 460 4.307432 ACTAACTCTGTCCACGTTCATTG 58.693 43.478 0.00 0.00 0.00 2.82
451 461 2.169832 ACTCTGTCCACGTTCATTGG 57.830 50.000 0.00 0.00 35.18 3.16
452 462 1.416401 ACTCTGTCCACGTTCATTGGT 59.584 47.619 0.00 0.00 35.42 3.67
453 463 2.069273 CTCTGTCCACGTTCATTGGTC 58.931 52.381 0.00 0.00 35.42 4.02
454 464 1.691976 TCTGTCCACGTTCATTGGTCT 59.308 47.619 0.00 0.00 35.42 3.85
455 465 2.104111 TCTGTCCACGTTCATTGGTCTT 59.896 45.455 0.00 0.00 35.42 3.01
467 477 6.378582 GTTCATTGGTCTTCTTCGCATTTTA 58.621 36.000 0.00 0.00 0.00 1.52
582 593 9.210329 TCAATGATATAATTTTTGATGGCATGC 57.790 29.630 9.90 9.90 0.00 4.06
583 594 8.994170 CAATGATATAATTTTTGATGGCATGCA 58.006 29.630 21.36 6.13 0.00 3.96
584 595 9.733556 AATGATATAATTTTTGATGGCATGCAT 57.266 25.926 21.36 11.12 0.00 3.96
585 596 9.733556 ATGATATAATTTTTGATGGCATGCATT 57.266 25.926 21.36 10.22 0.00 3.56
598 609 9.917129 TGATGGCATGCATTATTATTTTCTTAG 57.083 29.630 21.36 0.00 0.00 2.18
655 666 8.375493 ACTAAGATGGTCAATAAACTAGGACA 57.625 34.615 0.00 0.00 32.00 4.02
674 685 9.240734 CTAGGACAAAGGTAGTAGAAGAGTTAA 57.759 37.037 0.00 0.00 0.00 2.01
792 803 2.403132 AAAGCTGGCCGCAAGAGACT 62.403 55.000 19.30 1.23 42.61 3.24
838 849 9.745880 TTAGTCGATAAAGCTCTCGATATTTTT 57.254 29.630 16.03 0.00 44.75 1.94
872 883 7.327761 GGAAATCATTAATGATCCAAGATTGCG 59.672 37.037 27.04 0.00 46.22 4.85
879 898 5.808042 ATGATCCAAGATTGCGCATATAC 57.192 39.130 12.75 3.01 0.00 1.47
902 921 7.976135 ACCTGATGCTTATCTCAATCAATAC 57.024 36.000 0.00 0.00 0.00 1.89
1038 2153 1.909781 CCTGCCTGCCACATTTGGT 60.910 57.895 0.00 0.00 45.98 3.67
1108 2237 2.715336 AGCCAATATGAGAGGGAGCAAT 59.285 45.455 0.00 0.00 0.00 3.56
1172 2301 2.033801 GTGTGTGTCCAGTGTACGTACT 59.966 50.000 25.12 6.20 0.00 2.73
1173 2302 2.033675 TGTGTGTCCAGTGTACGTACTG 59.966 50.000 25.12 17.92 45.93 2.74
1292 2424 6.821031 ATACAATATCTAGGTGGTCTCGAC 57.179 41.667 0.00 0.00 0.00 4.20
1602 2736 7.543756 ACAAATTGTCCATCGGTAATAAAAGG 58.456 34.615 0.00 0.00 0.00 3.11
1603 2737 7.394923 ACAAATTGTCCATCGGTAATAAAAGGA 59.605 33.333 0.00 0.00 0.00 3.36
1604 2738 7.948034 AATTGTCCATCGGTAATAAAAGGAA 57.052 32.000 0.00 0.00 0.00 3.36
1688 2822 3.881089 TCGTGCTTCGATAGGATTGTCTA 59.119 43.478 0.00 0.00 44.01 2.59
1718 2852 5.646692 TTCTCTCTCCTTTTTCTTTGGGA 57.353 39.130 0.00 0.00 0.00 4.37
1719 2853 5.234466 TCTCTCTCCTTTTTCTTTGGGAG 57.766 43.478 0.00 0.00 44.69 4.30
1742 2876 5.954150 AGATTATGAGGTTGGCTTTGAATGT 59.046 36.000 0.00 0.00 0.00 2.71
1763 2897 4.586421 TGTTTCCACAACATTCCTTGCATA 59.414 37.500 0.00 0.00 0.00 3.14
2069 3918 8.314143 ACTTGCACAAATAATCTTTTTGATGG 57.686 30.769 3.39 0.00 37.48 3.51
2075 3924 6.036300 ACAAATAATCTTTTTGATGGCATGCG 59.964 34.615 12.44 0.00 37.48 4.73
2076 3925 3.598019 AATCTTTTTGATGGCATGCGT 57.402 38.095 12.44 2.22 35.21 5.24
2081 3930 5.477510 TCTTTTTGATGGCATGCGTTTATT 58.522 33.333 12.44 0.00 0.00 1.40
2087 3936 1.543358 TGGCATGCGTTTATTGCTTGA 59.457 42.857 12.44 0.00 39.18 3.02
2128 3977 2.231235 GGCCACGACCAATTCTTTGAAT 59.769 45.455 0.00 0.00 34.60 2.57
2369 4218 4.517832 CACACTATACAATGCATGGCTGAT 59.482 41.667 0.00 0.00 0.00 2.90
2551 4401 3.876320 GGGAAGAGATGTTCATGAAGAGC 59.124 47.826 12.58 12.58 0.00 4.09
2569 4419 3.446516 AGAGCAGCATTGAAAGGAAATCC 59.553 43.478 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.135603 ACGAGCGTGCTACGTCAATTA 60.136 47.619 11.63 0.00 44.73 1.40
5 6 0.797249 ATCAACGAGCGTGCTACGTC 60.797 55.000 15.80 6.10 44.73 4.34
6 7 0.388134 AATCAACGAGCGTGCTACGT 60.388 50.000 11.63 11.63 44.73 3.57
7 8 1.541475 TAATCAACGAGCGTGCTACG 58.459 50.000 0.00 3.36 45.88 3.51
8 9 6.922980 TTATATAATCAACGAGCGTGCTAC 57.077 37.500 0.00 0.00 0.00 3.58
9 10 6.089016 GCTTTATATAATCAACGAGCGTGCTA 59.911 38.462 0.00 0.00 0.00 3.49
10 11 5.107453 GCTTTATATAATCAACGAGCGTGCT 60.107 40.000 0.00 0.00 0.00 4.40
11 12 5.073478 GCTTTATATAATCAACGAGCGTGC 58.927 41.667 0.00 0.00 0.00 5.34
12 13 6.453643 AGCTTTATATAATCAACGAGCGTG 57.546 37.500 8.29 0.00 34.29 5.34
13 14 7.368833 ACTAGCTTTATATAATCAACGAGCGT 58.631 34.615 0.00 0.00 34.29 5.07
14 15 7.798486 ACTAGCTTTATATAATCAACGAGCG 57.202 36.000 0.00 0.00 34.29 5.03
15 16 7.952637 GCAACTAGCTTTATATAATCAACGAGC 59.047 37.037 0.00 6.51 41.15 5.03
33 34 2.758979 TGTAGTCCACCTAGCAACTAGC 59.241 50.000 0.00 0.00 46.19 3.42
34 35 4.463186 ACTTGTAGTCCACCTAGCAACTAG 59.537 45.833 0.00 0.00 34.16 2.57
35 36 4.219944 CACTTGTAGTCCACCTAGCAACTA 59.780 45.833 0.00 0.00 0.00 2.24
36 37 3.006967 CACTTGTAGTCCACCTAGCAACT 59.993 47.826 0.00 0.00 0.00 3.16
37 38 3.006537 TCACTTGTAGTCCACCTAGCAAC 59.993 47.826 0.00 0.00 0.00 4.17
38 39 3.236047 TCACTTGTAGTCCACCTAGCAA 58.764 45.455 0.00 0.00 0.00 3.91
39 40 2.826128 CTCACTTGTAGTCCACCTAGCA 59.174 50.000 0.00 0.00 0.00 3.49
40 41 2.417515 GCTCACTTGTAGTCCACCTAGC 60.418 54.545 0.00 0.00 0.00 3.42
41 42 2.159366 CGCTCACTTGTAGTCCACCTAG 60.159 54.545 0.00 0.00 0.00 3.02
42 43 1.816835 CGCTCACTTGTAGTCCACCTA 59.183 52.381 0.00 0.00 0.00 3.08
43 44 0.603569 CGCTCACTTGTAGTCCACCT 59.396 55.000 0.00 0.00 0.00 4.00
44 45 0.601558 TCGCTCACTTGTAGTCCACC 59.398 55.000 0.00 0.00 0.00 4.61
45 46 1.269998 ACTCGCTCACTTGTAGTCCAC 59.730 52.381 0.00 0.00 0.00 4.02
46 47 1.269723 CACTCGCTCACTTGTAGTCCA 59.730 52.381 0.00 0.00 0.00 4.02
47 48 1.983972 CACTCGCTCACTTGTAGTCC 58.016 55.000 0.00 0.00 0.00 3.85
48 49 1.335964 TGCACTCGCTCACTTGTAGTC 60.336 52.381 0.00 0.00 39.64 2.59
49 50 0.673985 TGCACTCGCTCACTTGTAGT 59.326 50.000 0.00 0.00 39.64 2.73
50 51 1.657594 CATGCACTCGCTCACTTGTAG 59.342 52.381 0.00 0.00 39.64 2.74
51 52 1.000843 ACATGCACTCGCTCACTTGTA 59.999 47.619 0.00 0.00 39.64 2.41
52 53 0.250038 ACATGCACTCGCTCACTTGT 60.250 50.000 0.00 0.00 39.64 3.16
53 54 1.391485 GTACATGCACTCGCTCACTTG 59.609 52.381 0.00 0.00 39.64 3.16
54 55 1.000843 TGTACATGCACTCGCTCACTT 59.999 47.619 0.00 0.00 39.64 3.16
55 56 0.603065 TGTACATGCACTCGCTCACT 59.397 50.000 0.00 0.00 39.64 3.41
56 57 1.645034 ATGTACATGCACTCGCTCAC 58.355 50.000 7.78 0.00 39.64 3.51
57 58 2.385013 AATGTACATGCACTCGCTCA 57.615 45.000 9.63 0.00 39.64 4.26
58 59 2.416547 ACAAATGTACATGCACTCGCTC 59.583 45.455 9.63 0.00 39.64 5.03
59 60 2.426522 ACAAATGTACATGCACTCGCT 58.573 42.857 9.63 0.00 39.64 4.93
60 61 2.900122 ACAAATGTACATGCACTCGC 57.100 45.000 9.63 0.00 39.24 5.03
61 62 4.379498 CACAAACAAATGTACATGCACTCG 59.621 41.667 9.63 0.27 30.84 4.18
62 63 5.173673 CACACAAACAAATGTACATGCACTC 59.826 40.000 9.63 0.00 30.84 3.51
63 64 5.042593 CACACAAACAAATGTACATGCACT 58.957 37.500 9.63 0.00 30.84 4.40
64 65 5.039984 TCACACAAACAAATGTACATGCAC 58.960 37.500 9.63 0.00 30.84 4.57
65 66 5.254339 TCACACAAACAAATGTACATGCA 57.746 34.783 9.63 0.00 30.84 3.96
66 67 6.768029 ATTCACACAAACAAATGTACATGC 57.232 33.333 9.63 0.00 30.84 4.06
67 68 8.416424 CGTTATTCACACAAACAAATGTACATG 58.584 33.333 9.63 1.53 30.84 3.21
68 69 8.346300 TCGTTATTCACACAAACAAATGTACAT 58.654 29.630 1.41 1.41 30.84 2.29
69 70 7.694886 TCGTTATTCACACAAACAAATGTACA 58.305 30.769 0.00 0.00 30.84 2.90
70 71 7.853929 ACTCGTTATTCACACAAACAAATGTAC 59.146 33.333 0.00 0.00 30.84 2.90
71 72 7.853437 CACTCGTTATTCACACAAACAAATGTA 59.147 33.333 0.00 0.00 30.84 2.29
72 73 6.690957 CACTCGTTATTCACACAAACAAATGT 59.309 34.615 0.00 0.00 0.00 2.71
73 74 6.344936 GCACTCGTTATTCACACAAACAAATG 60.345 38.462 0.00 0.00 0.00 2.32
74 75 5.685511 GCACTCGTTATTCACACAAACAAAT 59.314 36.000 0.00 0.00 0.00 2.32
75 76 5.031578 GCACTCGTTATTCACACAAACAAA 58.968 37.500 0.00 0.00 0.00 2.83
76 77 4.593157 GCACTCGTTATTCACACAAACAA 58.407 39.130 0.00 0.00 0.00 2.83
77 78 3.302805 CGCACTCGTTATTCACACAAACA 60.303 43.478 0.00 0.00 0.00 2.83
78 79 3.215244 CGCACTCGTTATTCACACAAAC 58.785 45.455 0.00 0.00 0.00 2.93
79 80 2.349060 GCGCACTCGTTATTCACACAAA 60.349 45.455 0.30 0.00 38.14 2.83
80 81 1.193650 GCGCACTCGTTATTCACACAA 59.806 47.619 0.30 0.00 38.14 3.33
81 82 0.787787 GCGCACTCGTTATTCACACA 59.212 50.000 0.30 0.00 38.14 3.72
82 83 0.246757 CGCGCACTCGTTATTCACAC 60.247 55.000 8.75 0.00 38.14 3.82
83 84 0.665068 ACGCGCACTCGTTATTCACA 60.665 50.000 5.73 0.00 40.07 3.58
84 85 2.067616 ACGCGCACTCGTTATTCAC 58.932 52.632 5.73 0.00 40.07 3.18
85 86 4.563630 ACGCGCACTCGTTATTCA 57.436 50.000 5.73 0.00 40.07 2.57
91 92 0.384230 CAAAATGAACGCGCACTCGT 60.384 50.000 5.73 0.69 45.58 4.18
92 93 0.384230 ACAAAATGAACGCGCACTCG 60.384 50.000 5.73 0.00 39.07 4.18
93 94 1.753956 AACAAAATGAACGCGCACTC 58.246 45.000 5.73 3.06 0.00 3.51
94 95 2.202295 AAACAAAATGAACGCGCACT 57.798 40.000 5.73 0.00 0.00 4.40
95 96 2.988807 AAAACAAAATGAACGCGCAC 57.011 40.000 5.73 0.00 0.00 5.34
112 113 2.285756 CGTGCACTCGTTCACCTAAAAA 59.714 45.455 16.19 0.00 0.00 1.94
113 114 1.862201 CGTGCACTCGTTCACCTAAAA 59.138 47.619 16.19 0.00 0.00 1.52
114 115 1.202440 ACGTGCACTCGTTCACCTAAA 60.202 47.619 16.19 0.00 41.37 1.85
115 116 0.386476 ACGTGCACTCGTTCACCTAA 59.614 50.000 16.19 0.00 41.37 2.69
116 117 0.318360 CACGTGCACTCGTTCACCTA 60.318 55.000 16.19 0.00 42.27 3.08
117 118 1.591594 CACGTGCACTCGTTCACCT 60.592 57.895 16.19 0.00 42.27 4.00
118 119 2.928361 CACGTGCACTCGTTCACC 59.072 61.111 16.19 0.00 42.27 4.02
119 120 2.245532 GCACGTGCACTCGTTCAC 59.754 61.111 34.52 0.76 42.27 3.18
129 130 3.820689 TCTTTTCAATACATGCACGTGC 58.179 40.909 33.11 33.11 42.50 5.34
130 131 6.085573 TCATTCTTTTCAATACATGCACGTG 58.914 36.000 12.28 12.28 0.00 4.49
131 132 6.252967 TCATTCTTTTCAATACATGCACGT 57.747 33.333 0.00 0.00 0.00 4.49
132 133 5.228635 GCTCATTCTTTTCAATACATGCACG 59.771 40.000 0.00 0.00 0.00 5.34
133 134 6.034256 GTGCTCATTCTTTTCAATACATGCAC 59.966 38.462 0.00 0.00 37.86 4.57
134 135 6.094719 GTGCTCATTCTTTTCAATACATGCA 58.905 36.000 0.00 0.00 0.00 3.96
135 136 5.228635 CGTGCTCATTCTTTTCAATACATGC 59.771 40.000 0.00 0.00 0.00 4.06
136 137 6.317088 ACGTGCTCATTCTTTTCAATACATG 58.683 36.000 0.00 0.00 0.00 3.21
137 138 6.500684 ACGTGCTCATTCTTTTCAATACAT 57.499 33.333 0.00 0.00 0.00 2.29
138 139 5.940192 ACGTGCTCATTCTTTTCAATACA 57.060 34.783 0.00 0.00 0.00 2.29
139 140 8.788813 CAATTACGTGCTCATTCTTTTCAATAC 58.211 33.333 0.00 0.00 0.00 1.89
140 141 7.967854 CCAATTACGTGCTCATTCTTTTCAATA 59.032 33.333 0.00 0.00 0.00 1.90
141 142 6.808212 CCAATTACGTGCTCATTCTTTTCAAT 59.192 34.615 0.00 0.00 0.00 2.57
142 143 6.148948 CCAATTACGTGCTCATTCTTTTCAA 58.851 36.000 0.00 0.00 0.00 2.69
143 144 5.335583 CCCAATTACGTGCTCATTCTTTTCA 60.336 40.000 0.00 0.00 0.00 2.69
144 145 5.095490 CCCAATTACGTGCTCATTCTTTTC 58.905 41.667 0.00 0.00 0.00 2.29
145 146 4.618227 GCCCAATTACGTGCTCATTCTTTT 60.618 41.667 0.00 0.00 0.00 2.27
146 147 3.119495 GCCCAATTACGTGCTCATTCTTT 60.119 43.478 0.00 0.00 0.00 2.52
147 148 2.423538 GCCCAATTACGTGCTCATTCTT 59.576 45.455 0.00 0.00 0.00 2.52
148 149 2.017049 GCCCAATTACGTGCTCATTCT 58.983 47.619 0.00 0.00 0.00 2.40
149 150 1.065551 GGCCCAATTACGTGCTCATTC 59.934 52.381 0.00 0.00 0.00 2.67
150 151 1.102978 GGCCCAATTACGTGCTCATT 58.897 50.000 0.00 0.00 0.00 2.57
151 152 1.095228 CGGCCCAATTACGTGCTCAT 61.095 55.000 0.00 0.00 0.00 2.90
152 153 1.743623 CGGCCCAATTACGTGCTCA 60.744 57.895 0.00 0.00 0.00 4.26
153 154 3.098555 CGGCCCAATTACGTGCTC 58.901 61.111 0.00 0.00 0.00 4.26
154 155 3.131478 GCGGCCCAATTACGTGCT 61.131 61.111 0.00 0.00 0.00 4.40
155 156 4.187810 GGCGGCCCAATTACGTGC 62.188 66.667 8.12 0.00 0.00 5.34
156 157 3.514362 GGGCGGCCCAATTACGTG 61.514 66.667 32.90 0.00 44.65 4.49
187 188 1.678970 AATGAAAGACGGCCCAGGC 60.679 57.895 0.00 0.00 41.06 4.85
188 189 1.315257 CCAATGAAAGACGGCCCAGG 61.315 60.000 0.00 0.00 0.00 4.45
189 190 1.937546 GCCAATGAAAGACGGCCCAG 61.938 60.000 0.00 0.00 38.67 4.45
190 191 1.976474 GCCAATGAAAGACGGCCCA 60.976 57.895 0.00 0.00 38.67 5.36
191 192 1.937546 CTGCCAATGAAAGACGGCCC 61.938 60.000 0.00 0.00 44.22 5.80
192 193 1.508088 CTGCCAATGAAAGACGGCC 59.492 57.895 0.00 0.00 44.22 6.13
193 194 0.960364 TCCTGCCAATGAAAGACGGC 60.960 55.000 0.00 0.00 45.11 5.68
194 195 1.089920 CTCCTGCCAATGAAAGACGG 58.910 55.000 0.00 0.00 0.00 4.79
195 196 1.089920 CCTCCTGCCAATGAAAGACG 58.910 55.000 0.00 0.00 0.00 4.18
196 197 0.813821 GCCTCCTGCCAATGAAAGAC 59.186 55.000 0.00 0.00 0.00 3.01
197 198 3.271250 GCCTCCTGCCAATGAAAGA 57.729 52.632 0.00 0.00 0.00 2.52
219 220 3.575351 AAGACACAGGCGAGCGGTC 62.575 63.158 4.06 4.06 0.00 4.79
220 221 3.575351 GAAGACACAGGCGAGCGGT 62.575 63.158 0.00 0.00 0.00 5.68
221 222 2.811317 GAAGACACAGGCGAGCGG 60.811 66.667 0.00 0.00 0.00 5.52
222 223 1.016130 ATTGAAGACACAGGCGAGCG 61.016 55.000 0.00 0.00 0.00 5.03
223 224 0.445436 CATTGAAGACACAGGCGAGC 59.555 55.000 0.00 0.00 0.00 5.03
224 225 0.445436 GCATTGAAGACACAGGCGAG 59.555 55.000 0.00 0.00 0.00 5.03
225 226 0.955428 GGCATTGAAGACACAGGCGA 60.955 55.000 0.00 0.00 0.00 5.54
226 227 1.236616 TGGCATTGAAGACACAGGCG 61.237 55.000 0.00 0.00 0.00 5.52
227 228 0.242017 GTGGCATTGAAGACACAGGC 59.758 55.000 0.00 0.00 46.90 4.85
231 232 1.609208 ACTGGTGGCATTGAAGACAC 58.391 50.000 0.00 0.00 46.97 3.67
232 233 2.778299 GTACTGGTGGCATTGAAGACA 58.222 47.619 0.00 0.00 0.00 3.41
233 234 1.732259 CGTACTGGTGGCATTGAAGAC 59.268 52.381 0.00 0.00 0.00 3.01
234 235 1.338674 CCGTACTGGTGGCATTGAAGA 60.339 52.381 0.00 0.00 0.00 2.87
235 236 1.086696 CCGTACTGGTGGCATTGAAG 58.913 55.000 0.00 0.00 0.00 3.02
236 237 3.241493 CCGTACTGGTGGCATTGAA 57.759 52.632 0.00 0.00 0.00 2.69
248 249 2.343758 CACACAGGCAGCCGTACT 59.656 61.111 5.55 0.00 0.00 2.73
249 250 3.423154 GCACACAGGCAGCCGTAC 61.423 66.667 5.55 0.00 0.00 3.67
250 251 4.697756 GGCACACAGGCAGCCGTA 62.698 66.667 5.55 0.00 43.51 4.02
260 261 3.483808 TTGATACAGTTCTGGCACACA 57.516 42.857 4.82 0.00 0.00 3.72
261 262 3.127548 CCATTGATACAGTTCTGGCACAC 59.872 47.826 4.82 0.00 0.00 3.82
262 263 3.008923 TCCATTGATACAGTTCTGGCACA 59.991 43.478 4.82 0.00 0.00 4.57
263 264 3.609853 TCCATTGATACAGTTCTGGCAC 58.390 45.455 4.82 0.00 0.00 5.01
264 265 3.998913 TCCATTGATACAGTTCTGGCA 57.001 42.857 4.82 0.00 0.00 4.92
265 266 5.643379 TTTTCCATTGATACAGTTCTGGC 57.357 39.130 4.82 0.00 0.00 4.85
290 291 5.230516 GCCACGTCGTTTTCTTATTTGTTTT 59.769 36.000 0.00 0.00 0.00 2.43
298 299 0.945265 CCCGCCACGTCGTTTTCTTA 60.945 55.000 0.00 0.00 0.00 2.10
303 304 3.927163 CTAGCCCGCCACGTCGTTT 62.927 63.158 0.00 0.00 0.00 3.60
323 324 4.404654 GCAAAAGGTCAGCGCCGG 62.405 66.667 2.29 0.00 0.00 6.13
324 325 3.357079 AGCAAAAGGTCAGCGCCG 61.357 61.111 2.29 0.00 0.00 6.46
347 348 7.492669 AGAAAATACCTGACATCTAACATGACG 59.507 37.037 0.00 0.00 0.00 4.35
351 352 6.480320 GCGAGAAAATACCTGACATCTAACAT 59.520 38.462 0.00 0.00 0.00 2.71
426 436 5.916661 ATGAACGTGGACAGAGTTAGTAT 57.083 39.130 0.00 0.00 0.00 2.12
432 442 1.416401 ACCAATGAACGTGGACAGAGT 59.584 47.619 0.00 0.00 39.62 3.24
441 451 1.798813 GCGAAGAAGACCAATGAACGT 59.201 47.619 0.00 0.00 0.00 3.99
446 456 6.801367 CATAAAATGCGAAGAAGACCAATG 57.199 37.500 0.00 0.00 0.00 2.82
635 646 6.884836 ACCTTTGTCCTAGTTTATTGACCATC 59.115 38.462 0.00 0.00 0.00 3.51
637 648 6.195600 ACCTTTGTCCTAGTTTATTGACCA 57.804 37.500 0.00 0.00 0.00 4.02
639 650 9.583765 CTACTACCTTTGTCCTAGTTTATTGAC 57.416 37.037 0.00 0.00 0.00 3.18
640 651 9.537852 TCTACTACCTTTGTCCTAGTTTATTGA 57.462 33.333 0.00 0.00 0.00 2.57
838 849 7.147932 TGGATCATTAATGATTTCCTTTTGCGA 60.148 33.333 27.45 9.65 46.84 5.10
879 898 9.887629 ATAGTATTGATTGAGATAAGCATCAGG 57.112 33.333 0.00 0.00 33.21 3.86
902 921 9.715123 TTAATGTCACGATTTTTGCACATATAG 57.285 29.630 0.00 0.00 0.00 1.31
1038 2153 3.853207 AGTGTAAGGTCCCAGTAAGACA 58.147 45.455 0.00 0.00 35.89 3.41
1108 2237 1.080772 CGTCGTTGCCTGCACTAGA 60.081 57.895 0.00 0.00 0.00 2.43
1172 2301 7.272244 ACACAAGATGATAATGACGAATACCA 58.728 34.615 0.00 0.00 0.00 3.25
1173 2302 7.715265 ACACAAGATGATAATGACGAATACC 57.285 36.000 0.00 0.00 0.00 2.73
1176 2305 9.383519 AGTTAACACAAGATGATAATGACGAAT 57.616 29.630 8.61 0.00 29.29 3.34
1292 2424 6.176975 TGTTTGACTACCATTTCATTAGCG 57.823 37.500 0.00 0.00 0.00 4.26
1718 2852 5.954150 ACATTCAAAGCCAACCTCATAATCT 59.046 36.000 0.00 0.00 0.00 2.40
1719 2853 6.212888 ACATTCAAAGCCAACCTCATAATC 57.787 37.500 0.00 0.00 0.00 1.75
1742 2876 4.321899 GCTATGCAAGGAATGTTGTGGAAA 60.322 41.667 0.00 0.00 0.00 3.13
1755 2889 1.202973 CGAGACGACGCTATGCAAGG 61.203 60.000 0.00 0.00 0.00 3.61
1763 2897 2.259439 AACTGACCGAGACGACGCT 61.259 57.895 0.00 0.00 0.00 5.07
2044 3893 7.095102 GCCATCAAAAAGATTATTTGTGCAAGT 60.095 33.333 0.00 0.00 38.57 3.16
2045 3894 7.095144 TGCCATCAAAAAGATTATTTGTGCAAG 60.095 33.333 0.00 0.00 38.57 4.01
2046 3895 6.709397 TGCCATCAAAAAGATTATTTGTGCAA 59.291 30.769 0.00 0.00 38.57 4.08
2069 3918 3.699067 AGATCAAGCAATAAACGCATGC 58.301 40.909 7.91 7.91 40.34 4.06
2075 3924 7.814107 TGTTTGATGGAAGATCAAGCAATAAAC 59.186 33.333 10.39 0.00 43.05 2.01
2076 3925 7.894708 TGTTTGATGGAAGATCAAGCAATAAA 58.105 30.769 10.39 0.00 43.05 1.40
2087 3936 6.491403 GTGGCCTAATATGTTTGATGGAAGAT 59.509 38.462 3.32 0.00 0.00 2.40
2128 3977 0.896923 ACGTGCGGGGTGTTATCTAA 59.103 50.000 0.00 0.00 0.00 2.10
2492 4341 2.171237 CAAGATAGCCATGACCACCTGA 59.829 50.000 0.00 0.00 0.00 3.86
2523 4372 4.018141 TCATGAACATCTCTTCCCCATTGT 60.018 41.667 0.00 0.00 0.00 2.71
2551 4401 4.524316 TGTGGATTTCCTTTCAATGCTG 57.476 40.909 0.00 0.00 36.82 4.41


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

AutoCloner maintained by Alex Coulton.