Multiple sequence alignment - TraesCS7A01G045500

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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 TraesCS7A01G045500 chr7A 100.000 2846 0 0 1 2846 20704885 20707730 0.000000e+00 5256
1 TraesCS7A01G045500 chr7A 90.045 1979 182 11 877 2846 20910583 20912555 0.000000e+00 2549
2 TraesCS7A01G045500 chr7A 83.977 2303 319 33 570 2846 20482396 20484674 0.000000e+00 2163
3 TraesCS7A01G045500 chr7A 77.739 575 96 24 336 898 20454432 20454986 9.830000e-85 324
4 TraesCS7A01G045500 chr7A 95.980 199 7 1 73 270 20700012 20699814 3.540000e-84 322
5 TraesCS7A01G045500 chr7D 96.169 2584 67 10 271 2844 20597670 20600231 0.000000e+00 4194
6 TraesCS7A01G045500 chr7D 83.457 2297 334 30 570 2844 20310448 20312720 0.000000e+00 2095
7 TraesCS7A01G045500 chr7D 83.378 2220 324 31 643 2845 555196715 555194524 0.000000e+00 2013
8 TraesCS7A01G045500 chr7D 84.466 1957 283 18 905 2845 20485536 20487487 0.000000e+00 1910
9 TraesCS7A01G045500 chr7D 96.337 273 9 1 1 272 229797663 229797935 5.590000e-122 448
10 TraesCS7A01G045500 chr7D 95.628 183 7 1 93 274 229792626 229792444 2.770000e-75 292
11 TraesCS7A01G045500 chr2A 82.677 2361 357 41 512 2846 733087313 733089647 0.000000e+00 2047
12 TraesCS7A01G045500 chr2D 82.293 2372 358 45 512 2846 598813599 598815945 0.000000e+00 1997
13 TraesCS7A01G045500 chr7B 82.269 2239 334 39 643 2845 601114122 601116333 0.000000e+00 1877
14 TraesCS7A01G045500 chr4A 96.617 266 7 1 3 268 43690909 43690646 9.360000e-120 440
15 TraesCS7A01G045500 chr4A 95.500 200 8 1 73 272 43695762 43695960 4.580000e-83 318
16 TraesCS7A01G045500 chr6D 95.588 272 11 1 1 271 183955508 183955779 4.350000e-118 435
17 TraesCS7A01G045500 chr6D 97.487 199 5 0 73 271 183951159 183950961 9.770000e-90 340
18 TraesCS7A01G045500 chr1D 95.588 272 8 4 1 270 16382164 16381895 1.570000e-117 433
19 TraesCS7A01G045500 chr1B 88.235 272 24 6 2 273 398390128 398389865 4.580000e-83 318


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 TraesCS7A01G045500 chr7A 20704885 20707730 2845 False 5256 5256 100.000 1 2846 1 chr7A.!!$F3 2845
1 TraesCS7A01G045500 chr7A 20910583 20912555 1972 False 2549 2549 90.045 877 2846 1 chr7A.!!$F4 1969
2 TraesCS7A01G045500 chr7A 20482396 20484674 2278 False 2163 2163 83.977 570 2846 1 chr7A.!!$F2 2276
3 TraesCS7A01G045500 chr7A 20454432 20454986 554 False 324 324 77.739 336 898 1 chr7A.!!$F1 562
4 TraesCS7A01G045500 chr7D 20597670 20600231 2561 False 4194 4194 96.169 271 2844 1 chr7D.!!$F3 2573
5 TraesCS7A01G045500 chr7D 20310448 20312720 2272 False 2095 2095 83.457 570 2844 1 chr7D.!!$F1 2274
6 TraesCS7A01G045500 chr7D 555194524 555196715 2191 True 2013 2013 83.378 643 2845 1 chr7D.!!$R2 2202
7 TraesCS7A01G045500 chr7D 20485536 20487487 1951 False 1910 1910 84.466 905 2845 1 chr7D.!!$F2 1940
8 TraesCS7A01G045500 chr2A 733087313 733089647 2334 False 2047 2047 82.677 512 2846 1 chr2A.!!$F1 2334
9 TraesCS7A01G045500 chr2D 598813599 598815945 2346 False 1997 1997 82.293 512 2846 1 chr2D.!!$F1 2334
10 TraesCS7A01G045500 chr7B 601114122 601116333 2211 False 1877 1877 82.269 643 2845 1 chr7B.!!$F1 2202

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
155 156 0.105964 CAGGTCGAGACAAACCACCA 59.894 55.0 5.55 0.0 38.06 4.17 F
194 195 0.336048 ATGGGTTTGATCAGGGGGTG 59.664 55.0 0.00 0.0 0.00 4.61 F
196 197 0.407918 GGGTTTGATCAGGGGGTGAA 59.592 55.0 0.00 0.0 39.19 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 1848 6.000219 CCATAGCCACAGTGCTAGATAAAAT 59.000 40.000 0.0 0.0 46.31 1.82 R
1834 1908 7.465353 TGATCAAATACTTTCATTGCTCCAA 57.535 32.000 0.0 0.0 0.00 3.53 R
2266 2340 5.458595 TGGAAGGTAGATGAAGCTCAGATA 58.541 41.667 0.0 0.0 0.00 1.98 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
17 18 3.640000 CGCCGCGACCATTCCATC 61.640 66.667 8.23 0.00 0.00 3.51
18 19 3.640000 GCCGCGACCATTCCATCG 61.640 66.667 8.23 0.00 41.32 3.84
22 23 2.967076 CGACCATTCCATCGCCGG 60.967 66.667 0.00 0.00 0.00 6.13
23 24 3.279875 GACCATTCCATCGCCGGC 61.280 66.667 19.07 19.07 0.00 6.13
33 34 4.735132 TCGCCGGCGACAAAGAGG 62.735 66.667 45.37 16.92 44.01 3.69
35 36 4.388499 GCCGGCGACAAAGAGGGA 62.388 66.667 12.58 0.00 0.00 4.20
36 37 2.125512 CCGGCGACAAAGAGGGAG 60.126 66.667 9.30 0.00 0.00 4.30
37 38 2.125512 CGGCGACAAAGAGGGAGG 60.126 66.667 0.00 0.00 0.00 4.30
38 39 2.269241 GGCGACAAAGAGGGAGGG 59.731 66.667 0.00 0.00 0.00 4.30
39 40 2.269241 GCGACAAAGAGGGAGGGG 59.731 66.667 0.00 0.00 0.00 4.79
40 41 2.291043 GCGACAAAGAGGGAGGGGA 61.291 63.158 0.00 0.00 0.00 4.81
41 42 1.627297 GCGACAAAGAGGGAGGGGAT 61.627 60.000 0.00 0.00 0.00 3.85
42 43 0.912486 CGACAAAGAGGGAGGGGATT 59.088 55.000 0.00 0.00 0.00 3.01
43 44 1.407437 CGACAAAGAGGGAGGGGATTG 60.407 57.143 0.00 0.00 0.00 2.67
44 45 1.002857 ACAAAGAGGGAGGGGATTGG 58.997 55.000 0.00 0.00 0.00 3.16
45 46 0.259938 CAAAGAGGGAGGGGATTGGG 59.740 60.000 0.00 0.00 0.00 4.12
46 47 0.926220 AAAGAGGGAGGGGATTGGGG 60.926 60.000 0.00 0.00 0.00 4.96
47 48 1.848835 AAGAGGGAGGGGATTGGGGA 61.849 60.000 0.00 0.00 0.00 4.81
48 49 1.308746 GAGGGAGGGGATTGGGGAA 60.309 63.158 0.00 0.00 0.00 3.97
49 50 0.702706 GAGGGAGGGGATTGGGGAAT 60.703 60.000 0.00 0.00 0.00 3.01
50 51 0.254784 AGGGAGGGGATTGGGGAATT 60.255 55.000 0.00 0.00 0.00 2.17
51 52 0.642156 GGGAGGGGATTGGGGAATTT 59.358 55.000 0.00 0.00 0.00 1.82
52 53 1.692441 GGGAGGGGATTGGGGAATTTG 60.692 57.143 0.00 0.00 0.00 2.32
53 54 1.008327 GGAGGGGATTGGGGAATTTGT 59.992 52.381 0.00 0.00 0.00 2.83
54 55 2.110578 GAGGGGATTGGGGAATTTGTG 58.889 52.381 0.00 0.00 0.00 3.33
55 56 1.203237 GGGGATTGGGGAATTTGTGG 58.797 55.000 0.00 0.00 0.00 4.17
56 57 1.273552 GGGGATTGGGGAATTTGTGGA 60.274 52.381 0.00 0.00 0.00 4.02
57 58 2.545810 GGGATTGGGGAATTTGTGGAA 58.454 47.619 0.00 0.00 0.00 3.53
58 59 2.909662 GGGATTGGGGAATTTGTGGAAA 59.090 45.455 0.00 0.00 0.00 3.13
59 60 3.329225 GGGATTGGGGAATTTGTGGAAAA 59.671 43.478 0.00 0.00 0.00 2.29
60 61 4.202514 GGGATTGGGGAATTTGTGGAAAAA 60.203 41.667 0.00 0.00 0.00 1.94
61 62 4.759693 GGATTGGGGAATTTGTGGAAAAAC 59.240 41.667 0.00 0.00 0.00 2.43
62 63 4.844349 TTGGGGAATTTGTGGAAAAACA 57.156 36.364 0.00 0.00 0.00 2.83
63 64 4.414337 TGGGGAATTTGTGGAAAAACAG 57.586 40.909 0.00 0.00 0.00 3.16
64 65 4.033709 TGGGGAATTTGTGGAAAAACAGA 58.966 39.130 0.00 0.00 0.00 3.41
65 66 4.471386 TGGGGAATTTGTGGAAAAACAGAA 59.529 37.500 0.00 0.00 0.00 3.02
66 67 4.814234 GGGGAATTTGTGGAAAAACAGAAC 59.186 41.667 0.00 0.00 0.00 3.01
67 68 4.506288 GGGAATTTGTGGAAAAACAGAACG 59.494 41.667 0.00 0.00 0.00 3.95
68 69 5.344884 GGAATTTGTGGAAAAACAGAACGA 58.655 37.500 0.00 0.00 0.00 3.85
69 70 5.808030 GGAATTTGTGGAAAAACAGAACGAA 59.192 36.000 0.00 0.00 0.00 3.85
70 71 6.237728 GGAATTTGTGGAAAAACAGAACGAAC 60.238 38.462 0.00 0.00 0.00 3.95
71 72 3.392769 TGTGGAAAAACAGAACGAACG 57.607 42.857 0.00 0.00 0.00 3.95
72 73 2.096174 TGTGGAAAAACAGAACGAACGG 59.904 45.455 0.00 0.00 0.00 4.44
73 74 1.671845 TGGAAAAACAGAACGAACGGG 59.328 47.619 0.00 0.00 0.00 5.28
74 75 1.672363 GGAAAAACAGAACGAACGGGT 59.328 47.619 0.00 0.00 0.00 5.28
75 76 2.540157 GGAAAAACAGAACGAACGGGTG 60.540 50.000 0.00 0.00 0.00 4.61
76 77 0.379316 AAAACAGAACGAACGGGTGC 59.621 50.000 0.00 0.00 0.00 5.01
77 78 1.768112 AAACAGAACGAACGGGTGCG 61.768 55.000 0.00 0.00 0.00 5.34
78 79 3.411351 CAGAACGAACGGGTGCGG 61.411 66.667 3.97 0.00 0.00 5.69
79 80 4.675029 AGAACGAACGGGTGCGGG 62.675 66.667 3.97 0.00 0.00 6.13
88 89 3.161450 GGGTGCGGGGCATCTCTA 61.161 66.667 0.44 0.00 41.91 2.43
89 90 2.109181 GGTGCGGGGCATCTCTAC 59.891 66.667 0.00 0.00 41.91 2.59
90 91 2.109181 GTGCGGGGCATCTCTACC 59.891 66.667 0.00 0.00 41.91 3.18
91 92 2.364973 TGCGGGGCATCTCTACCA 60.365 61.111 0.00 0.00 31.71 3.25
92 93 2.109181 GCGGGGCATCTCTACCAC 59.891 66.667 0.00 0.00 0.00 4.16
93 94 2.731571 GCGGGGCATCTCTACCACA 61.732 63.158 0.00 0.00 0.00 4.17
94 95 1.144057 CGGGGCATCTCTACCACAC 59.856 63.158 0.00 0.00 0.00 3.82
95 96 1.527370 GGGGCATCTCTACCACACC 59.473 63.158 0.00 0.00 0.00 4.16
96 97 1.271840 GGGGCATCTCTACCACACCA 61.272 60.000 0.00 0.00 0.00 4.17
97 98 0.179000 GGGCATCTCTACCACACCAG 59.821 60.000 0.00 0.00 0.00 4.00
98 99 0.462759 GGCATCTCTACCACACCAGC 60.463 60.000 0.00 0.00 0.00 4.85
99 100 0.462759 GCATCTCTACCACACCAGCC 60.463 60.000 0.00 0.00 0.00 4.85
100 101 0.179100 CATCTCTACCACACCAGCCG 60.179 60.000 0.00 0.00 0.00 5.52
101 102 1.330655 ATCTCTACCACACCAGCCGG 61.331 60.000 0.00 0.00 38.77 6.13
103 104 0.968901 CTCTACCACACCAGCCGGTA 60.969 60.000 1.90 0.00 46.94 4.02
104 105 0.542467 TCTACCACACCAGCCGGTAA 60.542 55.000 1.90 0.00 46.94 2.85
105 106 0.322322 CTACCACACCAGCCGGTAAA 59.678 55.000 1.90 0.00 46.94 2.01
106 107 0.763652 TACCACACCAGCCGGTAAAA 59.236 50.000 1.90 0.00 46.94 1.52
107 108 0.106619 ACCACACCAGCCGGTAAAAA 60.107 50.000 1.90 0.00 46.94 1.94
108 109 0.312729 CCACACCAGCCGGTAAAAAC 59.687 55.000 1.90 0.00 46.94 2.43
109 110 0.312729 CACACCAGCCGGTAAAAACC 59.687 55.000 1.90 0.00 46.94 3.27
110 111 0.106619 ACACCAGCCGGTAAAAACCA 60.107 50.000 1.90 0.00 46.94 3.67
111 112 0.312729 CACCAGCCGGTAAAAACCAC 59.687 55.000 1.90 0.00 46.94 4.16
112 113 0.824595 ACCAGCCGGTAAAAACCACC 60.825 55.000 1.90 0.00 46.71 4.61
113 114 1.529152 CCAGCCGGTAAAAACCACCC 61.529 60.000 1.90 0.00 31.96 4.61
114 115 0.538746 CAGCCGGTAAAAACCACCCT 60.539 55.000 1.90 0.00 31.96 4.34
115 116 0.186630 AGCCGGTAAAAACCACCCTT 59.813 50.000 1.90 0.00 31.96 3.95
116 117 1.424684 AGCCGGTAAAAACCACCCTTA 59.575 47.619 1.90 0.00 31.96 2.69
117 118 2.042026 AGCCGGTAAAAACCACCCTTAT 59.958 45.455 1.90 0.00 31.96 1.73
118 119 2.424601 GCCGGTAAAAACCACCCTTATC 59.575 50.000 1.90 0.00 31.96 1.75
119 120 3.018856 CCGGTAAAAACCACCCTTATCC 58.981 50.000 0.00 0.00 31.96 2.59
120 121 3.561744 CCGGTAAAAACCACCCTTATCCA 60.562 47.826 0.00 0.00 31.96 3.41
121 122 3.441222 CGGTAAAAACCACCCTTATCCAC 59.559 47.826 0.00 0.00 31.96 4.02
122 123 3.765511 GGTAAAAACCACCCTTATCCACC 59.234 47.826 0.00 0.00 0.00 4.61
123 124 2.209690 AAAACCACCCTTATCCACCG 57.790 50.000 0.00 0.00 0.00 4.94
124 125 0.323087 AAACCACCCTTATCCACCGC 60.323 55.000 0.00 0.00 0.00 5.68
125 126 2.192175 CCACCCTTATCCACCGCC 59.808 66.667 0.00 0.00 0.00 6.13
126 127 2.675242 CCACCCTTATCCACCGCCA 61.675 63.158 0.00 0.00 0.00 5.69
127 128 1.451387 CACCCTTATCCACCGCCAC 60.451 63.158 0.00 0.00 0.00 5.01
128 129 2.203015 CCCTTATCCACCGCCACG 60.203 66.667 0.00 0.00 0.00 4.94
129 130 2.582436 CCTTATCCACCGCCACGT 59.418 61.111 0.00 0.00 0.00 4.49
130 131 1.520787 CCTTATCCACCGCCACGTC 60.521 63.158 0.00 0.00 0.00 4.34
131 132 1.216977 CTTATCCACCGCCACGTCA 59.783 57.895 0.00 0.00 0.00 4.35
132 133 0.806102 CTTATCCACCGCCACGTCAG 60.806 60.000 0.00 0.00 0.00 3.51
133 134 2.845752 TTATCCACCGCCACGTCAGC 62.846 60.000 0.00 0.00 0.00 4.26
140 141 4.008933 GCCACGTCAGCTCCAGGT 62.009 66.667 0.00 0.00 0.00 4.00
141 142 2.262915 CCACGTCAGCTCCAGGTC 59.737 66.667 0.00 0.00 0.00 3.85
142 143 2.126307 CACGTCAGCTCCAGGTCG 60.126 66.667 0.00 0.00 0.00 4.79
143 144 2.282251 ACGTCAGCTCCAGGTCGA 60.282 61.111 0.00 0.00 0.00 4.20
144 145 2.336478 ACGTCAGCTCCAGGTCGAG 61.336 63.158 0.00 0.00 0.00 4.04
145 146 2.041115 CGTCAGCTCCAGGTCGAGA 61.041 63.158 0.00 0.00 30.97 4.04
146 147 1.509004 GTCAGCTCCAGGTCGAGAC 59.491 63.158 0.00 0.00 30.97 3.36
147 148 1.074951 TCAGCTCCAGGTCGAGACA 59.925 57.895 5.55 0.00 30.97 3.41
148 149 0.539669 TCAGCTCCAGGTCGAGACAA 60.540 55.000 5.55 0.00 30.97 3.18
149 150 0.318441 CAGCTCCAGGTCGAGACAAA 59.682 55.000 5.55 0.00 30.97 2.83
150 151 0.318762 AGCTCCAGGTCGAGACAAAC 59.681 55.000 5.55 0.00 30.97 2.93
151 152 0.670854 GCTCCAGGTCGAGACAAACC 60.671 60.000 5.55 0.00 35.69 3.27
152 153 0.679505 CTCCAGGTCGAGACAAACCA 59.320 55.000 5.55 0.00 38.06 3.67
153 154 0.391597 TCCAGGTCGAGACAAACCAC 59.608 55.000 5.55 0.00 38.06 4.16
154 155 0.602905 CCAGGTCGAGACAAACCACC 60.603 60.000 5.55 0.00 38.06 4.61
155 156 0.105964 CAGGTCGAGACAAACCACCA 59.894 55.000 5.55 0.00 38.06 4.17
156 157 0.834612 AGGTCGAGACAAACCACCAA 59.165 50.000 5.55 0.00 38.06 3.67
157 158 1.202651 AGGTCGAGACAAACCACCAAG 60.203 52.381 5.55 0.00 38.06 3.61
158 159 1.226746 GTCGAGACAAACCACCAAGG 58.773 55.000 0.00 0.00 45.67 3.61
186 187 5.975693 TTTTGTCTGGTATGGGTTTGATC 57.024 39.130 0.00 0.00 0.00 2.92
187 188 4.649267 TTGTCTGGTATGGGTTTGATCA 57.351 40.909 0.00 0.00 0.00 2.92
188 189 4.220693 TGTCTGGTATGGGTTTGATCAG 57.779 45.455 0.00 0.00 0.00 2.90
189 190 3.054434 TGTCTGGTATGGGTTTGATCAGG 60.054 47.826 0.00 0.00 0.00 3.86
190 191 2.509548 TCTGGTATGGGTTTGATCAGGG 59.490 50.000 0.00 0.00 0.00 4.45
191 192 1.568597 TGGTATGGGTTTGATCAGGGG 59.431 52.381 0.00 0.00 0.00 4.79
192 193 1.133482 GGTATGGGTTTGATCAGGGGG 60.133 57.143 0.00 0.00 0.00 5.40
193 194 1.569072 GTATGGGTTTGATCAGGGGGT 59.431 52.381 0.00 0.00 0.00 4.95
194 195 0.336048 ATGGGTTTGATCAGGGGGTG 59.664 55.000 0.00 0.00 0.00 4.61
195 196 0.774096 TGGGTTTGATCAGGGGGTGA 60.774 55.000 0.00 0.00 40.38 4.02
196 197 0.407918 GGGTTTGATCAGGGGGTGAA 59.592 55.000 0.00 0.00 39.19 3.18
197 198 1.203125 GGGTTTGATCAGGGGGTGAAA 60.203 52.381 0.00 0.00 39.19 2.69
198 199 2.171003 GGTTTGATCAGGGGGTGAAAG 58.829 52.381 0.00 0.00 39.19 2.62
199 200 2.171003 GTTTGATCAGGGGGTGAAAGG 58.829 52.381 0.00 0.00 39.19 3.11
200 201 0.704076 TTGATCAGGGGGTGAAAGGG 59.296 55.000 0.00 0.00 39.19 3.95
201 202 1.214305 TGATCAGGGGGTGAAAGGGG 61.214 60.000 0.00 0.00 39.19 4.79
202 203 2.573893 GATCAGGGGGTGAAAGGGGC 62.574 65.000 0.00 0.00 39.19 5.80
203 204 3.589542 CAGGGGGTGAAAGGGGCA 61.590 66.667 0.00 0.00 0.00 5.36
204 205 3.268032 AGGGGGTGAAAGGGGCAG 61.268 66.667 0.00 0.00 0.00 4.85
205 206 3.264845 GGGGGTGAAAGGGGCAGA 61.265 66.667 0.00 0.00 0.00 4.26
206 207 2.851045 GGGGTGAAAGGGGCAGAA 59.149 61.111 0.00 0.00 0.00 3.02
207 208 1.155155 GGGGTGAAAGGGGCAGAAA 59.845 57.895 0.00 0.00 0.00 2.52
208 209 0.471022 GGGGTGAAAGGGGCAGAAAA 60.471 55.000 0.00 0.00 0.00 2.29
209 210 1.419381 GGGTGAAAGGGGCAGAAAAA 58.581 50.000 0.00 0.00 0.00 1.94
210 211 1.977854 GGGTGAAAGGGGCAGAAAAAT 59.022 47.619 0.00 0.00 0.00 1.82
211 212 3.169908 GGGTGAAAGGGGCAGAAAAATA 58.830 45.455 0.00 0.00 0.00 1.40
212 213 3.195610 GGGTGAAAGGGGCAGAAAAATAG 59.804 47.826 0.00 0.00 0.00 1.73
213 214 4.086457 GGTGAAAGGGGCAGAAAAATAGA 58.914 43.478 0.00 0.00 0.00 1.98
214 215 4.711846 GGTGAAAGGGGCAGAAAAATAGAT 59.288 41.667 0.00 0.00 0.00 1.98
215 216 5.163509 GGTGAAAGGGGCAGAAAAATAGATC 60.164 44.000 0.00 0.00 0.00 2.75
216 217 5.418840 GTGAAAGGGGCAGAAAAATAGATCA 59.581 40.000 0.00 0.00 0.00 2.92
217 218 5.653769 TGAAAGGGGCAGAAAAATAGATCAG 59.346 40.000 0.00 0.00 0.00 2.90
218 219 4.870021 AGGGGCAGAAAAATAGATCAGT 57.130 40.909 0.00 0.00 0.00 3.41
219 220 4.530875 AGGGGCAGAAAAATAGATCAGTG 58.469 43.478 0.00 0.00 0.00 3.66
220 221 3.633986 GGGGCAGAAAAATAGATCAGTGG 59.366 47.826 0.00 0.00 0.00 4.00
221 222 3.633986 GGGCAGAAAAATAGATCAGTGGG 59.366 47.826 0.00 0.00 0.00 4.61
222 223 4.273318 GGCAGAAAAATAGATCAGTGGGT 58.727 43.478 0.00 0.00 0.00 4.51
223 224 4.096984 GGCAGAAAAATAGATCAGTGGGTG 59.903 45.833 0.00 0.00 0.00 4.61
224 225 4.943705 GCAGAAAAATAGATCAGTGGGTGA 59.056 41.667 0.00 0.00 40.38 4.02
226 227 6.459298 GCAGAAAAATAGATCAGTGGGTGATG 60.459 42.308 0.00 0.00 46.64 3.07
227 228 6.600822 CAGAAAAATAGATCAGTGGGTGATGT 59.399 38.462 0.00 0.00 46.64 3.06
228 229 6.600822 AGAAAAATAGATCAGTGGGTGATGTG 59.399 38.462 0.00 0.00 46.64 3.21
229 230 5.698741 AAATAGATCAGTGGGTGATGTGA 57.301 39.130 0.00 0.00 46.64 3.58
230 231 5.698741 AATAGATCAGTGGGTGATGTGAA 57.301 39.130 0.00 0.00 46.64 3.18
231 232 3.340814 AGATCAGTGGGTGATGTGAAC 57.659 47.619 0.00 0.00 46.64 3.18
232 233 2.026822 AGATCAGTGGGTGATGTGAACC 60.027 50.000 0.00 0.00 46.64 3.62
233 234 1.135960 TCAGTGGGTGATGTGAACCA 58.864 50.000 0.00 0.00 39.65 3.67
234 235 4.422712 GATCAGTGGGTGATGTGAACCAC 61.423 52.174 0.00 0.00 46.64 4.16
242 243 3.705604 GTGATGTGAACCACCAACTTTG 58.294 45.455 0.00 0.00 32.73 2.77
243 244 3.130340 GTGATGTGAACCACCAACTTTGT 59.870 43.478 0.00 0.00 32.73 2.83
244 245 3.766591 TGATGTGAACCACCAACTTTGTT 59.233 39.130 0.00 0.00 32.73 2.83
245 246 3.859411 TGTGAACCACCAACTTTGTTC 57.141 42.857 0.00 0.00 38.03 3.18
246 247 3.157881 TGTGAACCACCAACTTTGTTCA 58.842 40.909 0.00 0.00 43.34 3.18
247 248 3.192422 TGTGAACCACCAACTTTGTTCAG 59.808 43.478 4.33 0.00 45.38 3.02
248 249 2.757868 TGAACCACCAACTTTGTTCAGG 59.242 45.455 0.00 0.00 41.40 3.86
249 250 1.775385 ACCACCAACTTTGTTCAGGG 58.225 50.000 0.00 0.00 0.00 4.45
250 251 1.006639 ACCACCAACTTTGTTCAGGGT 59.993 47.619 0.00 0.00 0.00 4.34
251 252 2.242708 ACCACCAACTTTGTTCAGGGTA 59.757 45.455 0.00 0.00 0.00 3.69
252 253 2.884639 CCACCAACTTTGTTCAGGGTAG 59.115 50.000 0.00 0.00 0.00 3.18
253 254 3.551846 CACCAACTTTGTTCAGGGTAGT 58.448 45.455 0.00 0.00 0.00 2.73
254 255 4.445162 CCACCAACTTTGTTCAGGGTAGTA 60.445 45.833 0.00 0.00 0.00 1.82
255 256 5.127491 CACCAACTTTGTTCAGGGTAGTAA 58.873 41.667 0.00 0.00 0.00 2.24
256 257 5.591067 CACCAACTTTGTTCAGGGTAGTAAA 59.409 40.000 0.00 0.00 0.00 2.01
257 258 6.095720 CACCAACTTTGTTCAGGGTAGTAAAA 59.904 38.462 0.00 0.00 0.00 1.52
258 259 6.837048 ACCAACTTTGTTCAGGGTAGTAAAAT 59.163 34.615 0.00 0.00 0.00 1.82
259 260 7.145323 CCAACTTTGTTCAGGGTAGTAAAATG 58.855 38.462 0.00 0.00 0.00 2.32
260 261 6.894339 ACTTTGTTCAGGGTAGTAAAATGG 57.106 37.500 0.00 0.00 0.00 3.16
261 262 6.607019 ACTTTGTTCAGGGTAGTAAAATGGA 58.393 36.000 0.00 0.00 0.00 3.41
262 263 6.489022 ACTTTGTTCAGGGTAGTAAAATGGAC 59.511 38.462 0.00 0.00 0.00 4.02
263 264 5.836024 TGTTCAGGGTAGTAAAATGGACT 57.164 39.130 0.00 0.00 0.00 3.85
264 265 6.195600 TGTTCAGGGTAGTAAAATGGACTT 57.804 37.500 0.00 0.00 0.00 3.01
265 266 6.607019 TGTTCAGGGTAGTAAAATGGACTTT 58.393 36.000 0.00 0.00 0.00 2.66
266 267 7.064229 TGTTCAGGGTAGTAAAATGGACTTTT 58.936 34.615 0.00 0.00 40.21 2.27
267 268 7.562088 TGTTCAGGGTAGTAAAATGGACTTTTT 59.438 33.333 2.24 2.24 38.09 1.94
339 340 8.638685 ATGCATTACAGCTTTGTTTTATCATC 57.361 30.769 0.00 0.00 34.99 2.92
373 374 4.025040 TGGAATGAATCTGTCTTGCAGT 57.975 40.909 0.00 0.00 45.23 4.40
472 473 3.394606 ACCAAGTAACCTGGAACTGTCAT 59.605 43.478 0.00 0.00 0.00 3.06
557 564 5.046950 AGTCCTTCTCTGTCATACTTGGTTC 60.047 44.000 0.00 0.00 0.00 3.62
592 599 7.977853 ACATTTGATGCATTTTAACCTGAGATC 59.022 33.333 0.00 0.00 0.00 2.75
650 658 1.129326 GGTCGAGTGTCACTTGTTCG 58.871 55.000 18.04 12.03 31.48 3.95
690 698 3.265791 AGTTTGCTGCAGCTGACTATAC 58.734 45.455 36.61 21.24 42.66 1.47
691 699 1.926561 TTGCTGCAGCTGACTATACG 58.073 50.000 36.61 0.00 42.66 3.06
692 700 1.102978 TGCTGCAGCTGACTATACGA 58.897 50.000 36.61 12.08 42.66 3.43
764 779 8.691661 AGTACTGTTTTCTTTGATTATGTGGT 57.308 30.769 0.00 0.00 0.00 4.16
787 803 7.013846 TGGTTTAGAGTTGGGAAGTTAACAATG 59.986 37.037 8.61 0.00 0.00 2.82
985 1045 1.149627 GCACCACCACCCAACAGTA 59.850 57.895 0.00 0.00 0.00 2.74
1228 1300 1.814429 TGAGGGTTGGTTGGAAGAGA 58.186 50.000 0.00 0.00 0.00 3.10
1555 1629 1.203001 TGGGGGTGGATGAAAACAGAC 60.203 52.381 0.00 0.00 0.00 3.51
1665 1739 7.042791 GCTTTAGCTGCAAATGTTTACAAGAAA 60.043 33.333 1.02 0.00 38.21 2.52
1834 1908 7.260603 CCTTGAAGAGACACTGACAAAATTTT 58.739 34.615 0.00 0.00 0.00 1.82
1843 1917 6.114767 ACACTGACAAAATTTTTGGAGCAAT 58.885 32.000 22.27 7.89 0.00 3.56
2301 2375 4.703897 TCTACCTTCCAACACACTTGAAG 58.296 43.478 0.00 0.00 0.00 3.02
2341 2415 5.819379 TGCAGCTTATTTCCAGAAGACTATG 59.181 40.000 0.00 0.00 0.00 2.23
2415 2489 3.264450 AGGAGAGGGGTAGAAACACATTG 59.736 47.826 0.00 0.00 0.00 2.82
2451 2525 7.467947 GCAGAAGGCTATTTAAAGGAGTTGATC 60.468 40.741 0.00 0.00 40.25 2.92
2642 2716 7.222224 CCGATTAGTACTCCACAAACTAATGAC 59.778 40.741 0.00 0.00 43.19 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.640000 GATGGAATGGTCGCGGCG 61.640 66.667 17.70 17.70 0.00 6.46
1 2 3.640000 CGATGGAATGGTCGCGGC 61.640 66.667 6.13 3.04 0.00 6.53
6 7 3.279875 GCCGGCGATGGAATGGTC 61.280 66.667 12.58 0.00 0.00 4.02
8 9 4.908687 TCGCCGGCGATGGAATGG 62.909 66.667 45.37 16.92 44.01 3.16
16 17 4.735132 CCTCTTTGTCGCCGGCGA 62.735 66.667 45.37 45.37 46.87 5.54
18 19 4.388499 TCCCTCTTTGTCGCCGGC 62.388 66.667 19.07 19.07 0.00 6.13
19 20 2.125512 CTCCCTCTTTGTCGCCGG 60.126 66.667 0.00 0.00 0.00 6.13
20 21 2.125512 CCTCCCTCTTTGTCGCCG 60.126 66.667 0.00 0.00 0.00 6.46
21 22 2.269241 CCCTCCCTCTTTGTCGCC 59.731 66.667 0.00 0.00 0.00 5.54
22 23 1.627297 ATCCCCTCCCTCTTTGTCGC 61.627 60.000 0.00 0.00 0.00 5.19
23 24 0.912486 AATCCCCTCCCTCTTTGTCG 59.088 55.000 0.00 0.00 0.00 4.35
24 25 1.064389 CCAATCCCCTCCCTCTTTGTC 60.064 57.143 0.00 0.00 0.00 3.18
25 26 1.002857 CCAATCCCCTCCCTCTTTGT 58.997 55.000 0.00 0.00 0.00 2.83
26 27 0.259938 CCCAATCCCCTCCCTCTTTG 59.740 60.000 0.00 0.00 0.00 2.77
27 28 0.926220 CCCCAATCCCCTCCCTCTTT 60.926 60.000 0.00 0.00 0.00 2.52
28 29 1.309102 CCCCAATCCCCTCCCTCTT 60.309 63.158 0.00 0.00 0.00 2.85
29 30 1.848835 TTCCCCAATCCCCTCCCTCT 61.849 60.000 0.00 0.00 0.00 3.69
30 31 0.702706 ATTCCCCAATCCCCTCCCTC 60.703 60.000 0.00 0.00 0.00 4.30
31 32 0.254784 AATTCCCCAATCCCCTCCCT 60.255 55.000 0.00 0.00 0.00 4.20
32 33 0.642156 AAATTCCCCAATCCCCTCCC 59.358 55.000 0.00 0.00 0.00 4.30
33 34 1.008327 ACAAATTCCCCAATCCCCTCC 59.992 52.381 0.00 0.00 0.00 4.30
34 35 2.110578 CACAAATTCCCCAATCCCCTC 58.889 52.381 0.00 0.00 0.00 4.30
35 36 1.273781 CCACAAATTCCCCAATCCCCT 60.274 52.381 0.00 0.00 0.00 4.79
36 37 1.203237 CCACAAATTCCCCAATCCCC 58.797 55.000 0.00 0.00 0.00 4.81
37 38 2.246091 TCCACAAATTCCCCAATCCC 57.754 50.000 0.00 0.00 0.00 3.85
38 39 4.632327 TTTTCCACAAATTCCCCAATCC 57.368 40.909 0.00 0.00 0.00 3.01
39 40 5.372373 TGTTTTTCCACAAATTCCCCAATC 58.628 37.500 0.00 0.00 0.00 2.67
40 41 5.131809 TCTGTTTTTCCACAAATTCCCCAAT 59.868 36.000 0.00 0.00 0.00 3.16
41 42 4.471386 TCTGTTTTTCCACAAATTCCCCAA 59.529 37.500 0.00 0.00 0.00 4.12
42 43 4.033709 TCTGTTTTTCCACAAATTCCCCA 58.966 39.130 0.00 0.00 0.00 4.96
43 44 4.681074 TCTGTTTTTCCACAAATTCCCC 57.319 40.909 0.00 0.00 0.00 4.81
44 45 4.506288 CGTTCTGTTTTTCCACAAATTCCC 59.494 41.667 0.00 0.00 0.00 3.97
45 46 5.344884 TCGTTCTGTTTTTCCACAAATTCC 58.655 37.500 0.00 0.00 0.00 3.01
46 47 6.505732 CGTTCGTTCTGTTTTTCCACAAATTC 60.506 38.462 0.00 0.00 0.00 2.17
47 48 5.287513 CGTTCGTTCTGTTTTTCCACAAATT 59.712 36.000 0.00 0.00 0.00 1.82
48 49 4.796312 CGTTCGTTCTGTTTTTCCACAAAT 59.204 37.500 0.00 0.00 0.00 2.32
49 50 4.159857 CGTTCGTTCTGTTTTTCCACAAA 58.840 39.130 0.00 0.00 0.00 2.83
50 51 3.426426 CCGTTCGTTCTGTTTTTCCACAA 60.426 43.478 0.00 0.00 0.00 3.33
51 52 2.096174 CCGTTCGTTCTGTTTTTCCACA 59.904 45.455 0.00 0.00 0.00 4.17
52 53 2.540157 CCCGTTCGTTCTGTTTTTCCAC 60.540 50.000 0.00 0.00 0.00 4.02
53 54 1.671845 CCCGTTCGTTCTGTTTTTCCA 59.328 47.619 0.00 0.00 0.00 3.53
54 55 1.672363 ACCCGTTCGTTCTGTTTTTCC 59.328 47.619 0.00 0.00 0.00 3.13
55 56 2.711885 CACCCGTTCGTTCTGTTTTTC 58.288 47.619 0.00 0.00 0.00 2.29
56 57 1.202211 GCACCCGTTCGTTCTGTTTTT 60.202 47.619 0.00 0.00 0.00 1.94
57 58 0.379316 GCACCCGTTCGTTCTGTTTT 59.621 50.000 0.00 0.00 0.00 2.43
58 59 1.768112 CGCACCCGTTCGTTCTGTTT 61.768 55.000 0.00 0.00 0.00 2.83
59 60 2.241880 CGCACCCGTTCGTTCTGTT 61.242 57.895 0.00 0.00 0.00 3.16
60 61 2.660552 CGCACCCGTTCGTTCTGT 60.661 61.111 0.00 0.00 0.00 3.41
61 62 3.411351 CCGCACCCGTTCGTTCTG 61.411 66.667 0.00 0.00 0.00 3.02
62 63 4.675029 CCCGCACCCGTTCGTTCT 62.675 66.667 0.00 0.00 0.00 3.01
71 72 3.161450 TAGAGATGCCCCGCACCC 61.161 66.667 0.00 0.00 43.04 4.61
72 73 2.109181 GTAGAGATGCCCCGCACC 59.891 66.667 0.00 0.00 43.04 5.01
73 74 2.109181 GGTAGAGATGCCCCGCAC 59.891 66.667 0.00 0.00 43.04 5.34
74 75 2.364973 TGGTAGAGATGCCCCGCA 60.365 61.111 0.00 0.00 44.86 5.69
75 76 2.109181 GTGGTAGAGATGCCCCGC 59.891 66.667 0.00 0.00 0.00 6.13
76 77 1.144057 GTGTGGTAGAGATGCCCCG 59.856 63.158 0.00 0.00 0.00 5.73
77 78 1.271840 TGGTGTGGTAGAGATGCCCC 61.272 60.000 0.00 0.00 0.00 5.80
78 79 0.179000 CTGGTGTGGTAGAGATGCCC 59.821 60.000 0.00 0.00 0.00 5.36
79 80 0.462759 GCTGGTGTGGTAGAGATGCC 60.463 60.000 0.00 0.00 0.00 4.40
80 81 0.462759 GGCTGGTGTGGTAGAGATGC 60.463 60.000 0.00 0.00 0.00 3.91
81 82 0.179100 CGGCTGGTGTGGTAGAGATG 60.179 60.000 0.00 0.00 0.00 2.90
82 83 1.330655 CCGGCTGGTGTGGTAGAGAT 61.331 60.000 2.29 0.00 0.00 2.75
83 84 1.982395 CCGGCTGGTGTGGTAGAGA 60.982 63.158 2.29 0.00 0.00 3.10
84 85 2.579201 CCGGCTGGTGTGGTAGAG 59.421 66.667 2.29 0.00 0.00 2.43
94 95 1.529152 GGGTGGTTTTTACCGGCTGG 61.529 60.000 11.02 11.02 39.14 4.85
95 96 0.538746 AGGGTGGTTTTTACCGGCTG 60.539 55.000 0.00 0.00 39.14 4.85
96 97 0.186630 AAGGGTGGTTTTTACCGGCT 59.813 50.000 0.00 0.00 39.14 5.52
97 98 1.908344 TAAGGGTGGTTTTTACCGGC 58.092 50.000 0.00 0.00 39.14 6.13
98 99 3.018856 GGATAAGGGTGGTTTTTACCGG 58.981 50.000 0.00 0.00 39.14 5.28
99 100 3.441222 GTGGATAAGGGTGGTTTTTACCG 59.559 47.826 0.00 0.00 39.14 4.02
100 101 3.765511 GGTGGATAAGGGTGGTTTTTACC 59.234 47.826 0.00 0.00 37.48 2.85
101 102 3.441222 CGGTGGATAAGGGTGGTTTTTAC 59.559 47.826 0.00 0.00 0.00 2.01
102 103 3.688235 CGGTGGATAAGGGTGGTTTTTA 58.312 45.455 0.00 0.00 0.00 1.52
103 104 2.521126 CGGTGGATAAGGGTGGTTTTT 58.479 47.619 0.00 0.00 0.00 1.94
104 105 1.889262 GCGGTGGATAAGGGTGGTTTT 60.889 52.381 0.00 0.00 0.00 2.43
105 106 0.323087 GCGGTGGATAAGGGTGGTTT 60.323 55.000 0.00 0.00 0.00 3.27
106 107 1.301954 GCGGTGGATAAGGGTGGTT 59.698 57.895 0.00 0.00 0.00 3.67
107 108 2.676265 GGCGGTGGATAAGGGTGGT 61.676 63.158 0.00 0.00 0.00 4.16
108 109 2.192175 GGCGGTGGATAAGGGTGG 59.808 66.667 0.00 0.00 0.00 4.61
109 110 1.451387 GTGGCGGTGGATAAGGGTG 60.451 63.158 0.00 0.00 0.00 4.61
110 111 2.995547 GTGGCGGTGGATAAGGGT 59.004 61.111 0.00 0.00 0.00 4.34
111 112 2.203015 CGTGGCGGTGGATAAGGG 60.203 66.667 0.00 0.00 0.00 3.95
112 113 1.520787 GACGTGGCGGTGGATAAGG 60.521 63.158 0.00 0.00 0.00 2.69
113 114 0.806102 CTGACGTGGCGGTGGATAAG 60.806 60.000 0.00 0.00 0.00 1.73
114 115 1.216977 CTGACGTGGCGGTGGATAA 59.783 57.895 0.00 0.00 0.00 1.75
115 116 2.889617 CTGACGTGGCGGTGGATA 59.110 61.111 0.00 0.00 0.00 2.59
116 117 4.760047 GCTGACGTGGCGGTGGAT 62.760 66.667 0.00 0.00 0.00 3.41
123 124 3.941657 GACCTGGAGCTGACGTGGC 62.942 68.421 0.00 0.00 0.00 5.01
124 125 2.262915 GACCTGGAGCTGACGTGG 59.737 66.667 0.00 0.00 0.00 4.94
125 126 2.126307 CGACCTGGAGCTGACGTG 60.126 66.667 0.00 0.00 0.00 4.49
126 127 2.282251 TCGACCTGGAGCTGACGT 60.282 61.111 0.00 0.00 0.00 4.34
127 128 2.041115 TCTCGACCTGGAGCTGACG 61.041 63.158 0.00 0.00 33.98 4.35
128 129 1.244697 TGTCTCGACCTGGAGCTGAC 61.245 60.000 0.00 4.36 33.98 3.51
129 130 0.539669 TTGTCTCGACCTGGAGCTGA 60.540 55.000 0.00 0.00 33.98 4.26
130 131 0.318441 TTTGTCTCGACCTGGAGCTG 59.682 55.000 0.00 0.00 33.98 4.24
131 132 0.318762 GTTTGTCTCGACCTGGAGCT 59.681 55.000 0.00 0.00 33.98 4.09
132 133 0.670854 GGTTTGTCTCGACCTGGAGC 60.671 60.000 0.00 0.00 33.98 4.70
133 134 0.679505 TGGTTTGTCTCGACCTGGAG 59.320 55.000 0.00 0.00 36.86 3.86
134 135 0.391597 GTGGTTTGTCTCGACCTGGA 59.608 55.000 0.00 0.00 36.86 3.86
135 136 0.602905 GGTGGTTTGTCTCGACCTGG 60.603 60.000 0.00 0.00 36.86 4.45
136 137 0.105964 TGGTGGTTTGTCTCGACCTG 59.894 55.000 0.00 0.00 36.86 4.00
137 138 0.834612 TTGGTGGTTTGTCTCGACCT 59.165 50.000 0.00 0.00 36.86 3.85
138 139 1.226746 CTTGGTGGTTTGTCTCGACC 58.773 55.000 0.00 0.00 36.45 4.79
139 140 1.226746 CCTTGGTGGTTTGTCTCGAC 58.773 55.000 0.00 0.00 0.00 4.20
140 141 3.698250 CCTTGGTGGTTTGTCTCGA 57.302 52.632 0.00 0.00 0.00 4.04
163 164 5.835819 TGATCAAACCCATACCAGACAAAAA 59.164 36.000 0.00 0.00 0.00 1.94
164 165 5.389520 TGATCAAACCCATACCAGACAAAA 58.610 37.500 0.00 0.00 0.00 2.44
165 166 4.991776 TGATCAAACCCATACCAGACAAA 58.008 39.130 0.00 0.00 0.00 2.83
166 167 4.567537 CCTGATCAAACCCATACCAGACAA 60.568 45.833 0.00 0.00 0.00 3.18
167 168 3.054434 CCTGATCAAACCCATACCAGACA 60.054 47.826 0.00 0.00 0.00 3.41
168 169 3.545703 CCTGATCAAACCCATACCAGAC 58.454 50.000 0.00 0.00 0.00 3.51
169 170 2.509548 CCCTGATCAAACCCATACCAGA 59.490 50.000 0.00 0.00 0.00 3.86
170 171 2.423373 CCCCTGATCAAACCCATACCAG 60.423 54.545 0.00 0.00 0.00 4.00
171 172 1.568597 CCCCTGATCAAACCCATACCA 59.431 52.381 0.00 0.00 0.00 3.25
172 173 1.133482 CCCCCTGATCAAACCCATACC 60.133 57.143 0.00 0.00 0.00 2.73
173 174 1.569072 ACCCCCTGATCAAACCCATAC 59.431 52.381 0.00 0.00 0.00 2.39
174 175 1.568597 CACCCCCTGATCAAACCCATA 59.431 52.381 0.00 0.00 0.00 2.74
175 176 0.336048 CACCCCCTGATCAAACCCAT 59.664 55.000 0.00 0.00 0.00 4.00
176 177 0.774096 TCACCCCCTGATCAAACCCA 60.774 55.000 0.00 0.00 0.00 4.51
177 178 0.407918 TTCACCCCCTGATCAAACCC 59.592 55.000 0.00 0.00 0.00 4.11
178 179 2.171003 CTTTCACCCCCTGATCAAACC 58.829 52.381 0.00 0.00 0.00 3.27
179 180 2.171003 CCTTTCACCCCCTGATCAAAC 58.829 52.381 0.00 0.00 0.00 2.93
180 181 1.077005 CCCTTTCACCCCCTGATCAAA 59.923 52.381 0.00 0.00 0.00 2.69
181 182 0.704076 CCCTTTCACCCCCTGATCAA 59.296 55.000 0.00 0.00 0.00 2.57
182 183 1.214305 CCCCTTTCACCCCCTGATCA 61.214 60.000 0.00 0.00 0.00 2.92
183 184 1.615262 CCCCTTTCACCCCCTGATC 59.385 63.158 0.00 0.00 0.00 2.92
184 185 2.626467 GCCCCTTTCACCCCCTGAT 61.626 63.158 0.00 0.00 0.00 2.90
185 186 3.264845 GCCCCTTTCACCCCCTGA 61.265 66.667 0.00 0.00 0.00 3.86
186 187 3.589542 TGCCCCTTTCACCCCCTG 61.590 66.667 0.00 0.00 0.00 4.45
187 188 3.268032 CTGCCCCTTTCACCCCCT 61.268 66.667 0.00 0.00 0.00 4.79
188 189 2.380571 TTTCTGCCCCTTTCACCCCC 62.381 60.000 0.00 0.00 0.00 5.40
189 190 0.471022 TTTTCTGCCCCTTTCACCCC 60.471 55.000 0.00 0.00 0.00 4.95
190 191 1.419381 TTTTTCTGCCCCTTTCACCC 58.581 50.000 0.00 0.00 0.00 4.61
191 192 4.086457 TCTATTTTTCTGCCCCTTTCACC 58.914 43.478 0.00 0.00 0.00 4.02
192 193 5.418840 TGATCTATTTTTCTGCCCCTTTCAC 59.581 40.000 0.00 0.00 0.00 3.18
193 194 5.579047 TGATCTATTTTTCTGCCCCTTTCA 58.421 37.500 0.00 0.00 0.00 2.69
194 195 5.654209 ACTGATCTATTTTTCTGCCCCTTTC 59.346 40.000 0.00 0.00 0.00 2.62
195 196 5.420104 CACTGATCTATTTTTCTGCCCCTTT 59.580 40.000 0.00 0.00 0.00 3.11
196 197 4.952335 CACTGATCTATTTTTCTGCCCCTT 59.048 41.667 0.00 0.00 0.00 3.95
197 198 4.530875 CACTGATCTATTTTTCTGCCCCT 58.469 43.478 0.00 0.00 0.00 4.79
198 199 3.633986 CCACTGATCTATTTTTCTGCCCC 59.366 47.826 0.00 0.00 0.00 5.80
199 200 3.633986 CCCACTGATCTATTTTTCTGCCC 59.366 47.826 0.00 0.00 0.00 5.36
200 201 4.096984 CACCCACTGATCTATTTTTCTGCC 59.903 45.833 0.00 0.00 0.00 4.85
201 202 4.943705 TCACCCACTGATCTATTTTTCTGC 59.056 41.667 0.00 0.00 0.00 4.26
202 203 6.600822 ACATCACCCACTGATCTATTTTTCTG 59.399 38.462 0.00 0.00 37.53 3.02
203 204 6.600822 CACATCACCCACTGATCTATTTTTCT 59.399 38.462 0.00 0.00 37.53 2.52
204 205 6.599244 TCACATCACCCACTGATCTATTTTTC 59.401 38.462 0.00 0.00 37.53 2.29
205 206 6.484288 TCACATCACCCACTGATCTATTTTT 58.516 36.000 0.00 0.00 37.53 1.94
206 207 6.065976 TCACATCACCCACTGATCTATTTT 57.934 37.500 0.00 0.00 37.53 1.82
207 208 5.698741 TCACATCACCCACTGATCTATTT 57.301 39.130 0.00 0.00 37.53 1.40
208 209 5.431765 GTTCACATCACCCACTGATCTATT 58.568 41.667 0.00 0.00 37.53 1.73
209 210 4.141620 GGTTCACATCACCCACTGATCTAT 60.142 45.833 0.00 0.00 37.53 1.98
210 211 3.197766 GGTTCACATCACCCACTGATCTA 59.802 47.826 0.00 0.00 37.53 1.98
211 212 2.026822 GGTTCACATCACCCACTGATCT 60.027 50.000 0.00 0.00 37.53 2.75
212 213 2.290260 TGGTTCACATCACCCACTGATC 60.290 50.000 0.00 0.00 37.53 2.92
213 214 1.704628 TGGTTCACATCACCCACTGAT 59.295 47.619 0.00 0.00 40.59 2.90
214 215 1.135960 TGGTTCACATCACCCACTGA 58.864 50.000 0.00 0.00 32.71 3.41
215 216 1.238439 GTGGTTCACATCACCCACTG 58.762 55.000 0.00 0.00 43.21 3.66
216 217 0.110486 GGTGGTTCACATCACCCACT 59.890 55.000 7.52 0.00 45.60 4.00
217 218 2.641197 GGTGGTTCACATCACCCAC 58.359 57.895 0.00 0.00 45.60 4.61
221 222 3.130340 ACAAAGTTGGTGGTTCACATCAC 59.870 43.478 0.38 0.00 40.67 3.06
222 223 3.360867 ACAAAGTTGGTGGTTCACATCA 58.639 40.909 0.38 0.00 38.77 3.07
223 224 4.142271 TGAACAAAGTTGGTGGTTCACATC 60.142 41.667 0.00 0.00 43.19 3.06
224 225 3.766591 TGAACAAAGTTGGTGGTTCACAT 59.233 39.130 0.00 0.00 43.19 3.21
225 226 3.157881 TGAACAAAGTTGGTGGTTCACA 58.842 40.909 0.00 0.00 43.19 3.58
226 227 3.428862 CCTGAACAAAGTTGGTGGTTCAC 60.429 47.826 0.00 0.00 43.19 3.18
227 228 2.757868 CCTGAACAAAGTTGGTGGTTCA 59.242 45.455 0.00 0.00 45.12 3.18
228 229 2.100749 CCCTGAACAAAGTTGGTGGTTC 59.899 50.000 0.00 0.00 39.93 3.62
229 230 2.107366 CCCTGAACAAAGTTGGTGGTT 58.893 47.619 0.00 0.00 0.00 3.67
230 231 1.006639 ACCCTGAACAAAGTTGGTGGT 59.993 47.619 0.00 0.00 0.00 4.16
231 232 1.775385 ACCCTGAACAAAGTTGGTGG 58.225 50.000 0.00 0.00 0.00 4.61
232 233 3.551846 ACTACCCTGAACAAAGTTGGTG 58.448 45.455 0.00 0.00 0.00 4.17
233 234 3.945640 ACTACCCTGAACAAAGTTGGT 57.054 42.857 0.00 0.00 0.00 3.67
234 235 6.702716 TTTTACTACCCTGAACAAAGTTGG 57.297 37.500 0.00 0.00 0.00 3.77
235 236 7.013846 TCCATTTTACTACCCTGAACAAAGTTG 59.986 37.037 0.00 0.00 0.00 3.16
236 237 7.013942 GTCCATTTTACTACCCTGAACAAAGTT 59.986 37.037 0.00 0.00 0.00 2.66
237 238 6.489022 GTCCATTTTACTACCCTGAACAAAGT 59.511 38.462 0.00 0.00 0.00 2.66
238 239 6.715264 AGTCCATTTTACTACCCTGAACAAAG 59.285 38.462 0.00 0.00 0.00 2.77
239 240 6.607019 AGTCCATTTTACTACCCTGAACAAA 58.393 36.000 0.00 0.00 0.00 2.83
240 241 6.195600 AGTCCATTTTACTACCCTGAACAA 57.804 37.500 0.00 0.00 0.00 2.83
241 242 5.836024 AGTCCATTTTACTACCCTGAACA 57.164 39.130 0.00 0.00 0.00 3.18
242 243 7.520451 AAAAGTCCATTTTACTACCCTGAAC 57.480 36.000 0.00 0.00 39.36 3.18
339 340 8.038944 ACAGATTCATTCCAATCAAGAAAATGG 58.961 33.333 0.00 0.00 35.51 3.16
373 374 9.841295 AACAAATAGGTAGAGTTGTTGAGTTAA 57.159 29.630 1.62 0.00 41.40 2.01
608 616 5.353111 CAAATAATTGACCATGCATGCTCA 58.647 37.500 21.69 20.05 38.94 4.26
624 632 5.305585 ACAAGTGACACTCGACCAAATAAT 58.694 37.500 8.93 0.00 0.00 1.28
650 658 7.700656 AGCAAACTTAATGTTGTTAAGTGACAC 59.299 33.333 12.40 0.00 42.48 3.67
690 698 0.243907 ATCACTTGGGACTGTCGTCG 59.756 55.000 1.07 0.00 41.16 5.12
691 699 2.457366 AATCACTTGGGACTGTCGTC 57.543 50.000 1.07 0.00 39.49 4.20
692 700 2.930826 AAATCACTTGGGACTGTCGT 57.069 45.000 1.07 0.00 0.00 4.34
764 779 6.293735 CGCATTGTTAACTTCCCAACTCTAAA 60.294 38.462 7.22 0.00 0.00 1.85
773 788 6.848451 TCTTATTTCGCATTGTTAACTTCCC 58.152 36.000 7.22 0.00 0.00 3.97
787 803 8.785946 AGTAATACTCCTAGACTCTTATTTCGC 58.214 37.037 0.00 0.00 0.00 4.70
824 842 9.818796 TGAAAAGTGAAATAAGCAAAACAAAAC 57.181 25.926 0.00 0.00 0.00 2.43
985 1045 4.843728 TCCGCCATTACTTTGAGAATCTT 58.156 39.130 0.00 0.00 34.92 2.40
1228 1300 7.564793 TCCATTACATGTGCTACTTTCTGTAT 58.435 34.615 9.11 0.00 0.00 2.29
1461 1535 9.102757 GATCTCTTGACAATGTAATTTGAGCTA 57.897 33.333 0.00 0.00 31.22 3.32
1772 1846 7.332926 CCATAGCCACAGTGCTAGATAAAATAG 59.667 40.741 0.00 0.00 46.31 1.73
1774 1848 6.000219 CCATAGCCACAGTGCTAGATAAAAT 59.000 40.000 0.00 0.00 46.31 1.82
1834 1908 7.465353 TGATCAAATACTTTCATTGCTCCAA 57.535 32.000 0.00 0.00 0.00 3.53
2266 2340 5.458595 TGGAAGGTAGATGAAGCTCAGATA 58.541 41.667 0.00 0.00 0.00 1.98
2301 2375 4.508662 AGCTGCAGTATAGGAAACAACTC 58.491 43.478 16.64 0.00 0.00 3.01
2415 2489 0.037447 AGCCTTCTGCAACTTCCTCC 59.963 55.000 0.00 0.00 44.83 4.30
2451 2525 6.408858 ACAAGTTGTAGCATATTTCTGTCG 57.591 37.500 6.75 0.00 0.00 4.35
2642 2716 2.918712 AACTGGCTCAGGATTATCCG 57.081 50.000 5.50 1.41 42.75 4.18


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

AutoCloner maintained by Alex Coulton.