Multiple sequence alignment - TraesCS7A01G198500

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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 TraesCS7A01G198500 chr7A 100.000 3046 0 0 1 3046 159726329 159729374 0.000000e+00 5626.0
1 TraesCS7A01G198500 chr7A 97.297 37 1 0 2545 2581 112339584 112339548 2.540000e-06 63.9
2 TraesCS7A01G198500 chr7D 95.142 1235 39 7 865 2079 156864846 156863613 0.000000e+00 1929.0
3 TraesCS7A01G198500 chr7D 97.333 525 14 0 2089 2613 156863558 156863034 0.000000e+00 893.0
4 TraesCS7A01G198500 chr7D 89.233 613 28 16 264 866 156865637 156865053 0.000000e+00 732.0
5 TraesCS7A01G198500 chr7D 92.105 456 30 3 2592 3046 156862984 156862534 3.310000e-179 638.0
6 TraesCS7A01G198500 chr7D 90.073 413 37 2 2151 2563 156902369 156901961 1.610000e-147 532.0
7 TraesCS7A01G198500 chr7D 88.947 190 15 5 77 262 158959760 158959573 2.360000e-56 230.0
8 TraesCS7A01G198500 chr7D 96.226 53 2 0 1 53 158961107 158961055 1.500000e-13 87.9
9 TraesCS7A01G198500 chr7D 100.000 43 0 0 12 54 157097939 157097897 2.520000e-11 80.5
10 TraesCS7A01G198500 chr7B 94.467 1229 54 4 865 2079 119318639 119317411 0.000000e+00 1881.0
11 TraesCS7A01G198500 chr7B 95.238 525 25 0 2089 2613 119317356 119316832 0.000000e+00 832.0
12 TraesCS7A01G198500 chr7B 89.161 572 34 11 308 866 119319413 119318857 0.000000e+00 688.0
13 TraesCS7A01G198500 chr7B 93.860 456 19 3 2592 3046 119316782 119316335 0.000000e+00 678.0
14 TraesCS7A01G198500 chr3D 88.947 190 15 4 77 262 268120160 268119973 2.360000e-56 230.0
15 TraesCS7A01G198500 chr3D 79.641 167 29 4 2813 2975 592577998 592578163 6.900000e-22 115.0
16 TraesCS7A01G198500 chr1D 88.947 190 15 4 77 262 458758164 458757977 2.360000e-56 230.0
17 TraesCS7A01G198500 chr1A 88.525 61 3 3 2541 2598 492806086 492806145 1.520000e-08 71.3
18 TraesCS7A01G198500 chr2D 93.023 43 3 0 2553 2595 249895176 249895134 2.540000e-06 63.9
19 TraesCS7A01G198500 chr2D 90.476 42 4 0 2553 2594 8375494 8375453 4.240000e-04 56.5
20 TraesCS7A01G198500 chr3B 86.792 53 6 1 2549 2600 529402479 529402427 1.180000e-04 58.4
21 TraesCS7A01G198500 chr3B 90.698 43 4 0 2553 2595 739228891 739228849 1.180000e-04 58.4
22 TraesCS7A01G198500 chr1B 100.000 31 0 0 2552 2582 576221815 576221785 1.180000e-04 58.4


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 TraesCS7A01G198500 chr7A 159726329 159729374 3045 False 5626.00 5626 100.00000 1 3046 1 chr7A.!!$F1 3045
1 TraesCS7A01G198500 chr7D 156862534 156865637 3103 True 1048.00 1929 93.45325 264 3046 4 chr7D.!!$R3 2782
2 TraesCS7A01G198500 chr7B 119316335 119319413 3078 True 1019.75 1881 93.18150 308 3046 4 chr7B.!!$R1 2738

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
102 103 0.028902 GCGAACGTTGGCTCAAACTT 59.971 50.0 25.59 0.00 0.00 2.66 F
153 154 0.040425 ATGGAAAACTGCGTCGCAAC 60.040 50.0 22.01 9.88 38.41 4.17 F
790 805 0.041312 GTGCGCGTGACTTGTGATTT 60.041 50.0 8.43 0.00 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1334 1586 1.200716 ACGGATGTTTGCAGCATCTTG 59.799 47.619 23.47 19.64 41.63 3.02 R
1584 1848 1.954146 TTGCAGACGCGGAAGTGAC 60.954 57.895 12.47 0.00 46.66 3.67 R
2770 3156 1.618343 GACAACAATTGGGTTCCCCTG 59.382 52.381 10.83 3.24 45.70 4.45 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
18 19 2.986311 AAGTCGCGCTCACAAAAGA 58.014 47.368 5.56 0.00 0.00 2.52
19 20 0.861837 AAGTCGCGCTCACAAAAGAG 59.138 50.000 5.56 0.00 38.68 2.85
20 21 0.946221 AGTCGCGCTCACAAAAGAGG 60.946 55.000 5.56 0.00 36.15 3.69
21 22 0.944311 GTCGCGCTCACAAAAGAGGA 60.944 55.000 5.56 0.00 36.15 3.71
22 23 0.667487 TCGCGCTCACAAAAGAGGAG 60.667 55.000 5.56 0.00 36.15 3.69
25 26 3.329300 GCTCACAAAAGAGGAGCCA 57.671 52.632 0.00 0.00 46.35 4.75
26 27 1.609208 GCTCACAAAAGAGGAGCCAA 58.391 50.000 0.00 0.00 46.35 4.52
27 28 1.956477 GCTCACAAAAGAGGAGCCAAA 59.044 47.619 0.00 0.00 46.35 3.28
28 29 2.362077 GCTCACAAAAGAGGAGCCAAAA 59.638 45.455 0.00 0.00 46.35 2.44
29 30 3.551659 GCTCACAAAAGAGGAGCCAAAAG 60.552 47.826 0.00 0.00 46.35 2.27
30 31 2.958355 TCACAAAAGAGGAGCCAAAAGG 59.042 45.455 0.00 0.00 0.00 3.11
31 32 1.688735 ACAAAAGAGGAGCCAAAAGGC 59.311 47.619 0.00 0.00 0.00 4.35
33 34 2.366590 CAAAAGAGGAGCCAAAAGGCTT 59.633 45.455 10.76 0.00 46.05 4.35
34 35 1.625511 AAGAGGAGCCAAAAGGCTTG 58.374 50.000 10.76 0.00 46.05 4.01
35 36 0.251519 AGAGGAGCCAAAAGGCTTGG 60.252 55.000 10.76 0.00 46.05 3.61
47 48 3.808656 GCTTGGCCGAGCTTGCTC 61.809 66.667 34.14 12.20 39.57 4.26
48 49 3.130160 CTTGGCCGAGCTTGCTCC 61.130 66.667 7.18 4.67 0.00 4.70
49 50 3.618780 CTTGGCCGAGCTTGCTCCT 62.619 63.158 7.18 0.00 0.00 3.69
50 51 3.196207 TTGGCCGAGCTTGCTCCTT 62.196 57.895 15.87 0.00 0.00 3.36
51 52 2.821810 GGCCGAGCTTGCTCCTTC 60.822 66.667 15.87 6.08 0.00 3.46
52 53 2.267324 GCCGAGCTTGCTCCTTCT 59.733 61.111 15.87 0.00 0.00 2.85
53 54 1.517832 GCCGAGCTTGCTCCTTCTA 59.482 57.895 15.87 0.00 0.00 2.10
54 55 0.808060 GCCGAGCTTGCTCCTTCTAC 60.808 60.000 15.87 0.00 0.00 2.59
55 56 0.532573 CCGAGCTTGCTCCTTCTACA 59.467 55.000 15.87 0.00 0.00 2.74
56 57 1.634702 CGAGCTTGCTCCTTCTACAC 58.365 55.000 15.87 0.00 0.00 2.90
57 58 1.737363 CGAGCTTGCTCCTTCTACACC 60.737 57.143 15.87 0.00 0.00 4.16
58 59 0.615850 AGCTTGCTCCTTCTACACCC 59.384 55.000 0.00 0.00 0.00 4.61
59 60 0.393132 GCTTGCTCCTTCTACACCCC 60.393 60.000 0.00 0.00 0.00 4.95
60 61 0.253327 CTTGCTCCTTCTACACCCCC 59.747 60.000 0.00 0.00 0.00 5.40
61 62 0.474854 TTGCTCCTTCTACACCCCCA 60.475 55.000 0.00 0.00 0.00 4.96
62 63 0.474854 TGCTCCTTCTACACCCCCAA 60.475 55.000 0.00 0.00 0.00 4.12
63 64 0.696501 GCTCCTTCTACACCCCCAAA 59.303 55.000 0.00 0.00 0.00 3.28
64 65 1.074889 GCTCCTTCTACACCCCCAAAA 59.925 52.381 0.00 0.00 0.00 2.44
65 66 2.490168 GCTCCTTCTACACCCCCAAAAA 60.490 50.000 0.00 0.00 0.00 1.94
66 67 3.421844 CTCCTTCTACACCCCCAAAAAG 58.578 50.000 0.00 0.00 0.00 2.27
67 68 3.057586 TCCTTCTACACCCCCAAAAAGA 58.942 45.455 0.00 0.00 0.00 2.52
68 69 3.464080 TCCTTCTACACCCCCAAAAAGAA 59.536 43.478 0.00 0.00 0.00 2.52
69 70 4.079096 TCCTTCTACACCCCCAAAAAGAAA 60.079 41.667 0.00 0.00 0.00 2.52
70 71 4.651962 CCTTCTACACCCCCAAAAAGAAAA 59.348 41.667 0.00 0.00 0.00 2.29
71 72 5.129650 CCTTCTACACCCCCAAAAAGAAAAA 59.870 40.000 0.00 0.00 0.00 1.94
72 73 6.183361 CCTTCTACACCCCCAAAAAGAAAAAT 60.183 38.462 0.00 0.00 0.00 1.82
73 74 6.168270 TCTACACCCCCAAAAAGAAAAATG 57.832 37.500 0.00 0.00 0.00 2.32
74 75 3.550820 ACACCCCCAAAAAGAAAAATGC 58.449 40.909 0.00 0.00 0.00 3.56
75 76 2.547634 CACCCCCAAAAAGAAAAATGCG 59.452 45.455 0.00 0.00 0.00 4.73
76 77 2.171659 ACCCCCAAAAAGAAAAATGCGT 59.828 40.909 0.00 0.00 0.00 5.24
77 78 3.210227 CCCCCAAAAAGAAAAATGCGTT 58.790 40.909 0.00 0.00 0.00 4.84
78 79 3.249799 CCCCCAAAAAGAAAAATGCGTTC 59.750 43.478 0.00 0.00 0.00 3.95
79 80 3.059935 CCCCAAAAAGAAAAATGCGTTCG 60.060 43.478 0.00 0.00 0.00 3.95
80 81 3.553917 CCCAAAAAGAAAAATGCGTTCGT 59.446 39.130 0.00 0.00 0.00 3.85
81 82 4.740695 CCCAAAAAGAAAAATGCGTTCGTA 59.259 37.500 0.00 0.00 0.00 3.43
82 83 5.331980 CCCAAAAAGAAAAATGCGTTCGTAC 60.332 40.000 0.00 0.00 0.00 3.67
99 100 2.629210 CGCGAACGTTGGCTCAAA 59.371 55.556 28.66 0.00 33.53 2.69
100 101 1.721133 CGCGAACGTTGGCTCAAAC 60.721 57.895 28.66 3.81 33.53 2.93
101 102 1.647084 GCGAACGTTGGCTCAAACT 59.353 52.632 25.59 0.00 0.00 2.66
102 103 0.028902 GCGAACGTTGGCTCAAACTT 59.971 50.000 25.59 0.00 0.00 2.66
103 104 1.741993 CGAACGTTGGCTCAAACTTG 58.258 50.000 5.00 0.00 0.00 3.16
104 105 1.329292 CGAACGTTGGCTCAAACTTGA 59.671 47.619 5.00 0.00 35.57 3.02
105 106 2.223157 CGAACGTTGGCTCAAACTTGAA 60.223 45.455 5.00 0.00 36.64 2.69
106 107 3.363178 GAACGTTGGCTCAAACTTGAAG 58.637 45.455 5.00 0.00 36.64 3.02
107 108 1.676006 ACGTTGGCTCAAACTTGAAGG 59.324 47.619 0.00 0.00 36.64 3.46
108 109 1.600413 CGTTGGCTCAAACTTGAAGGC 60.600 52.381 0.00 2.06 36.64 4.35
109 110 1.039856 TTGGCTCAAACTTGAAGGCC 58.960 50.000 13.25 13.25 44.40 5.19
110 111 1.172180 TGGCTCAAACTTGAAGGCCG 61.172 55.000 14.53 0.00 46.05 6.13
111 112 0.889186 GGCTCAAACTTGAAGGCCGA 60.889 55.000 0.00 0.00 38.31 5.54
112 113 0.519077 GCTCAAACTTGAAGGCCGAG 59.481 55.000 0.00 0.10 36.64 4.63
113 114 1.160137 CTCAAACTTGAAGGCCGAGG 58.840 55.000 0.00 0.00 36.64 4.63
114 115 0.889186 TCAAACTTGAAGGCCGAGGC 60.889 55.000 5.37 5.37 35.75 4.70
115 116 1.966451 AAACTTGAAGGCCGAGGCG 60.966 57.895 8.14 0.00 43.06 5.52
133 134 3.261951 CGTAGGCGCACCGAATGG 61.262 66.667 10.83 0.00 42.76 3.16
134 135 2.185867 GTAGGCGCACCGAATGGA 59.814 61.111 10.83 0.00 42.76 3.41
135 136 1.227556 GTAGGCGCACCGAATGGAT 60.228 57.895 10.83 0.00 42.76 3.41
136 137 1.227527 TAGGCGCACCGAATGGATG 60.228 57.895 10.83 0.00 42.76 3.51
137 138 2.658679 TAGGCGCACCGAATGGATGG 62.659 60.000 10.83 0.00 42.76 3.51
138 139 2.513666 GCGCACCGAATGGATGGA 60.514 61.111 0.30 0.00 39.21 3.41
139 140 2.112198 GCGCACCGAATGGATGGAA 61.112 57.895 0.30 0.00 39.21 3.53
140 141 1.653094 GCGCACCGAATGGATGGAAA 61.653 55.000 0.30 0.00 39.21 3.13
141 142 0.808125 CGCACCGAATGGATGGAAAA 59.192 50.000 0.00 0.00 39.21 2.29
142 143 1.467374 CGCACCGAATGGATGGAAAAC 60.467 52.381 0.00 0.00 39.21 2.43
143 144 1.818674 GCACCGAATGGATGGAAAACT 59.181 47.619 0.00 0.00 39.21 2.66
144 145 2.415893 GCACCGAATGGATGGAAAACTG 60.416 50.000 0.00 0.00 39.21 3.16
145 146 1.818674 ACCGAATGGATGGAAAACTGC 59.181 47.619 0.00 0.00 39.21 4.40
146 147 1.202177 CCGAATGGATGGAAAACTGCG 60.202 52.381 0.00 0.00 37.49 5.18
147 148 1.468520 CGAATGGATGGAAAACTGCGT 59.531 47.619 0.00 0.00 0.00 5.24
148 149 2.476185 CGAATGGATGGAAAACTGCGTC 60.476 50.000 0.00 0.00 0.00 5.19
149 150 1.086696 ATGGATGGAAAACTGCGTCG 58.913 50.000 0.00 0.00 0.00 5.12
150 151 1.134694 GGATGGAAAACTGCGTCGC 59.865 57.895 11.10 11.10 0.00 5.19
151 152 1.573829 GGATGGAAAACTGCGTCGCA 61.574 55.000 20.44 20.44 36.92 5.10
152 153 0.237235 GATGGAAAACTGCGTCGCAA 59.763 50.000 22.01 4.52 38.41 4.85
153 154 0.040425 ATGGAAAACTGCGTCGCAAC 60.040 50.000 22.01 9.88 38.41 4.17
162 163 3.081133 CGTCGCAACGGATGAAGG 58.919 61.111 0.00 0.00 45.21 3.46
163 164 1.445410 CGTCGCAACGGATGAAGGA 60.445 57.895 0.00 0.00 45.21 3.36
164 165 0.806102 CGTCGCAACGGATGAAGGAT 60.806 55.000 0.00 0.00 45.21 3.24
165 166 0.652592 GTCGCAACGGATGAAGGATG 59.347 55.000 0.00 0.00 0.00 3.51
166 167 0.534873 TCGCAACGGATGAAGGATGA 59.465 50.000 0.00 0.00 0.00 2.92
167 168 0.652592 CGCAACGGATGAAGGATGAC 59.347 55.000 0.00 0.00 0.00 3.06
168 169 0.652592 GCAACGGATGAAGGATGACG 59.347 55.000 0.00 0.00 0.00 4.35
169 170 1.290203 CAACGGATGAAGGATGACGG 58.710 55.000 0.00 0.00 0.00 4.79
170 171 0.902531 AACGGATGAAGGATGACGGT 59.097 50.000 0.00 0.00 0.00 4.83
171 172 0.175760 ACGGATGAAGGATGACGGTG 59.824 55.000 0.00 0.00 0.00 4.94
172 173 0.530650 CGGATGAAGGATGACGGTGG 60.531 60.000 0.00 0.00 0.00 4.61
173 174 0.830648 GGATGAAGGATGACGGTGGA 59.169 55.000 0.00 0.00 0.00 4.02
174 175 1.417890 GGATGAAGGATGACGGTGGAT 59.582 52.381 0.00 0.00 0.00 3.41
175 176 2.632996 GGATGAAGGATGACGGTGGATA 59.367 50.000 0.00 0.00 0.00 2.59
176 177 3.071023 GGATGAAGGATGACGGTGGATAA 59.929 47.826 0.00 0.00 0.00 1.75
177 178 3.819564 TGAAGGATGACGGTGGATAAG 57.180 47.619 0.00 0.00 0.00 1.73
178 179 2.434336 TGAAGGATGACGGTGGATAAGG 59.566 50.000 0.00 0.00 0.00 2.69
179 180 2.471815 AGGATGACGGTGGATAAGGA 57.528 50.000 0.00 0.00 0.00 3.36
180 181 2.320781 AGGATGACGGTGGATAAGGAG 58.679 52.381 0.00 0.00 0.00 3.69
181 182 1.344763 GGATGACGGTGGATAAGGAGG 59.655 57.143 0.00 0.00 0.00 4.30
182 183 0.759346 ATGACGGTGGATAAGGAGGC 59.241 55.000 0.00 0.00 0.00 4.70
183 184 1.067582 GACGGTGGATAAGGAGGCG 59.932 63.158 0.00 0.00 0.00 5.52
184 185 2.365095 GACGGTGGATAAGGAGGCGG 62.365 65.000 0.00 0.00 0.00 6.13
185 186 2.131709 CGGTGGATAAGGAGGCGGA 61.132 63.158 0.00 0.00 0.00 5.54
186 187 1.749033 GGTGGATAAGGAGGCGGAG 59.251 63.158 0.00 0.00 0.00 4.63
200 201 2.267642 GGAGCCGTGTGGTGCATA 59.732 61.111 0.00 0.00 37.67 3.14
201 202 2.106683 GGAGCCGTGTGGTGCATAC 61.107 63.158 0.00 0.00 37.67 2.39
202 203 2.434185 AGCCGTGTGGTGCATACG 60.434 61.111 0.00 0.00 45.77 3.06
203 204 4.160635 GCCGTGTGGTGCATACGC 62.161 66.667 0.00 8.38 45.08 4.42
204 205 3.848830 CCGTGTGGTGCATACGCG 61.849 66.667 24.24 24.24 45.08 6.01
206 207 3.794270 GTGTGGTGCATACGCGAT 58.206 55.556 15.93 0.00 42.97 4.58
207 208 2.966324 GTGTGGTGCATACGCGATA 58.034 52.632 15.93 1.22 42.97 2.92
208 209 0.575390 GTGTGGTGCATACGCGATAC 59.425 55.000 15.93 3.68 42.97 2.24
209 210 0.528901 TGTGGTGCATACGCGATACC 60.529 55.000 15.93 13.60 42.97 2.73
210 211 1.068417 TGGTGCATACGCGATACCC 59.932 57.895 15.93 5.17 42.97 3.69
211 212 1.068417 GGTGCATACGCGATACCCA 59.932 57.895 15.93 0.00 42.97 4.51
212 213 0.320421 GGTGCATACGCGATACCCAT 60.320 55.000 15.93 0.00 42.97 4.00
213 214 0.790207 GTGCATACGCGATACCCATG 59.210 55.000 15.93 7.13 42.97 3.66
214 215 0.320334 TGCATACGCGATACCCATGG 60.320 55.000 15.93 4.14 42.97 3.66
215 216 1.635663 GCATACGCGATACCCATGGC 61.636 60.000 15.93 0.00 32.91 4.40
216 217 1.019278 CATACGCGATACCCATGGCC 61.019 60.000 15.93 0.00 32.63 5.36
217 218 2.501223 ATACGCGATACCCATGGCCG 62.501 60.000 15.93 7.91 32.63 6.13
218 219 4.602259 CGCGATACCCATGGCCGT 62.602 66.667 6.09 2.04 32.63 5.68
219 220 2.665185 GCGATACCCATGGCCGTC 60.665 66.667 6.09 2.27 30.18 4.79
220 221 3.138625 CGATACCCATGGCCGTCT 58.861 61.111 6.09 0.00 0.00 4.18
221 222 1.445942 CGATACCCATGGCCGTCTT 59.554 57.895 6.09 0.00 0.00 3.01
222 223 0.600255 CGATACCCATGGCCGTCTTC 60.600 60.000 6.09 0.59 0.00 2.87
223 224 0.759346 GATACCCATGGCCGTCTTCT 59.241 55.000 6.09 0.00 0.00 2.85
224 225 0.469917 ATACCCATGGCCGTCTTCTG 59.530 55.000 6.09 0.00 0.00 3.02
225 226 1.622607 TACCCATGGCCGTCTTCTGG 61.623 60.000 6.09 0.00 0.00 3.86
232 233 3.068881 CCGTCTTCTGGCCTGGAA 58.931 61.111 10.07 10.27 0.00 3.53
233 234 1.374947 CCGTCTTCTGGCCTGGAAA 59.625 57.895 10.07 0.00 0.00 3.13
234 235 0.250727 CCGTCTTCTGGCCTGGAAAA 60.251 55.000 10.07 0.00 0.00 2.29
235 236 1.604604 CGTCTTCTGGCCTGGAAAAA 58.395 50.000 10.07 0.00 0.00 1.94
236 237 1.266989 CGTCTTCTGGCCTGGAAAAAC 59.733 52.381 10.07 10.64 0.00 2.43
237 238 1.266989 GTCTTCTGGCCTGGAAAAACG 59.733 52.381 10.07 0.61 0.00 3.60
238 239 0.598065 CTTCTGGCCTGGAAAAACGG 59.402 55.000 10.07 0.00 0.00 4.44
239 240 1.460273 TTCTGGCCTGGAAAAACGGC 61.460 55.000 10.07 0.00 43.03 5.68
240 241 3.267597 CTGGCCTGGAAAAACGGCG 62.268 63.158 4.80 4.80 44.68 6.46
241 242 3.292159 GGCCTGGAAAAACGGCGT 61.292 61.111 6.77 6.77 44.68 5.68
242 243 2.254350 GCCTGGAAAAACGGCGTC 59.746 61.111 15.17 0.00 33.64 5.19
243 244 2.554272 CCTGGAAAAACGGCGTCG 59.446 61.111 15.17 8.42 43.02 5.12
244 245 2.127383 CTGGAAAAACGGCGTCGC 60.127 61.111 15.17 9.22 40.63 5.19
245 246 2.589442 TGGAAAAACGGCGTCGCT 60.589 55.556 15.17 0.00 40.63 4.93
246 247 2.172659 GGAAAAACGGCGTCGCTC 59.827 61.111 15.17 9.83 40.63 5.03
247 248 2.202008 GAAAAACGGCGTCGCTCG 60.202 61.111 15.17 19.97 40.63 5.03
491 500 5.055144 GTCCGAATTTATCTACCTCCAACC 58.945 45.833 0.00 0.00 0.00 3.77
561 570 6.989659 TCCATATAATCGGGTCTGAACTAAC 58.010 40.000 0.00 0.00 0.00 2.34
562 571 6.781014 TCCATATAATCGGGTCTGAACTAACT 59.219 38.462 0.00 0.00 0.00 2.24
563 572 7.946219 TCCATATAATCGGGTCTGAACTAACTA 59.054 37.037 0.00 0.00 0.00 2.24
564 573 8.582437 CCATATAATCGGGTCTGAACTAACTAA 58.418 37.037 0.00 0.00 0.00 2.24
587 596 4.621068 TTTGCAGATTTCAGATTAGGCG 57.379 40.909 0.00 0.00 0.00 5.52
588 597 2.564771 TGCAGATTTCAGATTAGGCGG 58.435 47.619 0.00 0.00 0.00 6.13
599 608 1.000506 GATTAGGCGGCCAAGATCGTA 59.999 52.381 23.09 0.00 0.00 3.43
603 612 1.227556 GCGGCCAAGATCGTACCAT 60.228 57.895 2.24 0.00 0.00 3.55
606 616 2.870435 GCGGCCAAGATCGTACCATTAT 60.870 50.000 2.24 0.00 0.00 1.28
667 680 3.371102 TCAGTCTCCACGAAGAAACAG 57.629 47.619 0.00 0.00 0.00 3.16
680 693 2.565841 AGAAACAGCAACAGGACAGAC 58.434 47.619 0.00 0.00 0.00 3.51
684 697 1.072159 AGCAACAGGACAGACCAGC 59.928 57.895 0.00 0.00 42.04 4.85
691 704 2.665603 GACAGACCAGCCTCCACC 59.334 66.667 0.00 0.00 0.00 4.61
790 805 0.041312 GTGCGCGTGACTTGTGATTT 60.041 50.000 8.43 0.00 0.00 2.17
882 1120 9.381033 ACAATATGTCATTCTCTCTCTCAAAAG 57.619 33.333 0.00 0.00 0.00 2.27
889 1128 8.658609 GTCATTCTCTCTCTCAAAAGAAATCAG 58.341 37.037 0.00 0.00 31.98 2.90
895 1134 5.751680 TCTCTCAAAAGAAATCAGCAAACG 58.248 37.500 0.00 0.00 0.00 3.60
1003 1254 2.216898 GTGCTTCAGGATGTCCTATGC 58.783 52.381 0.32 7.11 46.65 3.14
1044 1296 2.095853 CCCTGATGAAATTGTTCGGACG 59.904 50.000 0.00 0.00 36.46 4.79
1106 1358 8.284945 TCATGCCCTAATCTAATATTTGATGC 57.715 34.615 12.27 11.42 0.00 3.91
1334 1586 1.950973 GAGTTGGAGCCCGAGGACTC 61.951 65.000 0.00 0.00 0.00 3.36
1352 1604 2.490903 ACTCAAGATGCTGCAAACATCC 59.509 45.455 20.34 7.76 44.08 3.51
1433 1697 3.612860 AGCTTCGTATCACTTAAAGCACG 59.387 43.478 7.98 0.00 43.65 5.34
1584 1848 1.875514 CCGCATGATGACATAAGGGTG 59.124 52.381 0.00 0.00 35.09 4.61
1671 1935 3.243068 CCAAGAACCTCCGAACTTTTGTG 60.243 47.826 0.00 0.00 0.00 3.33
1821 2085 3.008813 AGAACCTGAATCTGAGTGCATGT 59.991 43.478 0.00 0.00 0.00 3.21
1869 2133 6.307558 CGATCACTCTGATGCTATGATTACAC 59.692 42.308 0.00 0.00 37.20 2.90
2044 2308 2.955660 CTGCCCCTCTACTAGAAGAGTG 59.044 54.545 0.00 0.00 41.27 3.51
2080 2344 8.816894 TGTAAGTTATCATCATCTTATCCCTCC 58.183 37.037 0.00 0.00 0.00 4.30
2081 2345 9.041354 GTAAGTTATCATCATCTTATCCCTCCT 57.959 37.037 0.00 0.00 0.00 3.69
2083 2347 9.796242 AAGTTATCATCATCTTATCCCTCCTAT 57.204 33.333 0.00 0.00 0.00 2.57
2103 2412 9.906660 CTCCTATATTATTCTCTGTGACTGAAC 57.093 37.037 0.00 0.00 0.00 3.18
2157 2466 8.791327 TGTTAATCTTGATCTATGCAGTTTCA 57.209 30.769 0.00 0.00 0.00 2.69
2359 2668 2.697751 AGTCATGAGAGGTGTGGATAGC 59.302 50.000 0.00 0.00 0.00 2.97
2526 2835 3.357021 CAACGATGATGCATTACTGTGC 58.643 45.455 0.00 0.00 45.25 4.57
2567 2876 6.960542 GGAATAATTCTACTCCCTCCTATCCA 59.039 42.308 0.00 0.00 0.00 3.41
2624 3004 6.599638 AGAGGACTTTGCATCTTGTATAAACC 59.400 38.462 0.00 0.00 0.00 3.27
2633 3018 6.435591 TGCATCTTGTATAAACCATGGTTTCA 59.564 34.615 39.37 29.32 43.95 2.69
2634 3019 7.123997 TGCATCTTGTATAAACCATGGTTTCAT 59.876 33.333 39.37 29.99 43.95 2.57
2635 3020 7.981225 GCATCTTGTATAAACCATGGTTTCATT 59.019 33.333 39.37 27.75 43.95 2.57
2636 3021 9.874205 CATCTTGTATAAACCATGGTTTCATTT 57.126 29.630 39.37 25.69 43.95 2.32
2674 3059 3.330110 CCTTTGCCTCCCTGATCATCTAT 59.670 47.826 0.00 0.00 0.00 1.98
2676 3061 5.191323 CCTTTGCCTCCCTGATCATCTATAT 59.809 44.000 0.00 0.00 0.00 0.86
2705 3091 1.535896 TCTGAACAGAACGTCTCTCCG 59.464 52.381 1.79 0.00 33.91 4.63
2746 3132 1.279496 TAGCTTGGTCCTGTCTGCAT 58.721 50.000 0.00 0.00 0.00 3.96
2770 3156 1.593006 CACTGTTCCGCGATTATCACC 59.407 52.381 8.23 0.00 0.00 4.02
2778 3164 1.594331 GCGATTATCACCAGGGGAAC 58.406 55.000 0.00 0.00 0.00 3.62
2818 3204 0.321653 ACCGATTTCTGGTGAGCCAC 60.322 55.000 0.00 0.00 40.46 5.01
2907 3293 4.320935 GCCACACAAATTGGAGACGTTAAT 60.321 41.667 0.00 0.00 36.02 1.40
2922 3308 1.666189 GTTAATCAGCTCCTCGTTGCC 59.334 52.381 0.00 0.00 0.00 4.52
2940 3326 3.343617 TGCCACTTAACTCAATGCCTAC 58.656 45.455 0.00 0.00 0.00 3.18
2960 3346 6.183361 GCCTACTAAATTCAGAATACCCCTCA 60.183 42.308 0.00 0.00 0.00 3.86
2970 3356 1.422161 ATACCCCTCATCCTGCTGCC 61.422 60.000 0.00 0.00 0.00 4.85
3030 3416 0.468771 AGCAGGCAAGCAAAGAACCT 60.469 50.000 4.78 0.00 36.85 3.50
3033 3419 1.372128 GGCAAGCAAAGAACCTGCG 60.372 57.895 0.00 0.00 44.75 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.861837 CTCTTTTGTGAGCGCGACTT 59.138 50.000 12.10 0.00 0.00 3.01
1 2 0.946221 CCTCTTTTGTGAGCGCGACT 60.946 55.000 12.10 6.51 33.02 4.18
2 3 0.944311 TCCTCTTTTGTGAGCGCGAC 60.944 55.000 12.10 3.30 33.02 5.19
3 4 0.667487 CTCCTCTTTTGTGAGCGCGA 60.667 55.000 12.10 0.00 33.02 5.87
4 5 1.784062 CTCCTCTTTTGTGAGCGCG 59.216 57.895 0.00 0.00 33.02 6.86
5 6 1.499502 GCTCCTCTTTTGTGAGCGC 59.500 57.895 0.00 0.00 41.74 5.92
8 9 3.005155 CCTTTTGGCTCCTCTTTTGTGAG 59.995 47.826 0.00 0.00 0.00 3.51
9 10 2.958355 CCTTTTGGCTCCTCTTTTGTGA 59.042 45.455 0.00 0.00 0.00 3.58
10 11 3.375782 CCTTTTGGCTCCTCTTTTGTG 57.624 47.619 0.00 0.00 0.00 3.33
30 31 3.808656 GAGCAAGCTCGGCCAAGC 61.809 66.667 7.91 7.91 42.82 4.01
31 32 3.130160 GGAGCAAGCTCGGCCAAG 61.130 66.667 15.20 0.00 43.59 3.61
32 33 3.196207 AAGGAGCAAGCTCGGCCAA 62.196 57.895 15.20 0.00 43.59 4.52
33 34 3.612247 GAAGGAGCAAGCTCGGCCA 62.612 63.158 15.20 0.00 43.59 5.36
34 35 1.961180 TAGAAGGAGCAAGCTCGGCC 61.961 60.000 15.20 0.00 43.59 6.13
35 36 0.808060 GTAGAAGGAGCAAGCTCGGC 60.808 60.000 15.20 7.49 43.59 5.54
36 37 0.532573 TGTAGAAGGAGCAAGCTCGG 59.467 55.000 15.20 0.00 43.59 4.63
37 38 1.634702 GTGTAGAAGGAGCAAGCTCG 58.365 55.000 15.20 0.00 43.59 5.03
38 39 1.406205 GGGTGTAGAAGGAGCAAGCTC 60.406 57.143 13.50 13.50 42.04 4.09
39 40 0.615850 GGGTGTAGAAGGAGCAAGCT 59.384 55.000 0.00 0.00 0.00 3.74
40 41 0.393132 GGGGTGTAGAAGGAGCAAGC 60.393 60.000 0.00 0.00 0.00 4.01
41 42 0.253327 GGGGGTGTAGAAGGAGCAAG 59.747 60.000 0.00 0.00 0.00 4.01
42 43 0.474854 TGGGGGTGTAGAAGGAGCAA 60.475 55.000 0.00 0.00 0.00 3.91
43 44 0.474854 TTGGGGGTGTAGAAGGAGCA 60.475 55.000 0.00 0.00 0.00 4.26
44 45 0.696501 TTTGGGGGTGTAGAAGGAGC 59.303 55.000 0.00 0.00 0.00 4.70
45 46 3.073946 TCTTTTTGGGGGTGTAGAAGGAG 59.926 47.826 0.00 0.00 0.00 3.69
46 47 3.057586 TCTTTTTGGGGGTGTAGAAGGA 58.942 45.455 0.00 0.00 0.00 3.36
47 48 3.518992 TCTTTTTGGGGGTGTAGAAGG 57.481 47.619 0.00 0.00 0.00 3.46
48 49 5.862678 TTTTCTTTTTGGGGGTGTAGAAG 57.137 39.130 0.00 0.00 0.00 2.85
49 50 6.587273 CATTTTTCTTTTTGGGGGTGTAGAA 58.413 36.000 0.00 0.00 0.00 2.10
50 51 5.454045 GCATTTTTCTTTTTGGGGGTGTAGA 60.454 40.000 0.00 0.00 0.00 2.59
51 52 4.754618 GCATTTTTCTTTTTGGGGGTGTAG 59.245 41.667 0.00 0.00 0.00 2.74
52 53 4.709250 GCATTTTTCTTTTTGGGGGTGTA 58.291 39.130 0.00 0.00 0.00 2.90
53 54 3.550820 GCATTTTTCTTTTTGGGGGTGT 58.449 40.909 0.00 0.00 0.00 4.16
54 55 2.547634 CGCATTTTTCTTTTTGGGGGTG 59.452 45.455 0.00 0.00 0.00 4.61
55 56 2.171659 ACGCATTTTTCTTTTTGGGGGT 59.828 40.909 0.00 0.00 0.00 4.95
56 57 2.844946 ACGCATTTTTCTTTTTGGGGG 58.155 42.857 0.00 0.00 0.00 5.40
57 58 3.059935 CGAACGCATTTTTCTTTTTGGGG 60.060 43.478 0.00 0.00 0.00 4.96
58 59 3.553917 ACGAACGCATTTTTCTTTTTGGG 59.446 39.130 0.00 0.00 0.00 4.12
59 60 4.770351 ACGAACGCATTTTTCTTTTTGG 57.230 36.364 0.00 0.00 0.00 3.28
60 61 5.343603 CGTACGAACGCATTTTTCTTTTTG 58.656 37.500 10.44 0.00 43.12 2.44
61 62 5.534365 CGTACGAACGCATTTTTCTTTTT 57.466 34.783 10.44 0.00 43.12 1.94
83 84 0.028902 AAGTTTGAGCCAACGTTCGC 59.971 50.000 10.10 10.10 0.00 4.70
84 85 1.329292 TCAAGTTTGAGCCAACGTTCG 59.671 47.619 0.00 0.00 32.50 3.95
85 86 3.363178 CTTCAAGTTTGAGCCAACGTTC 58.637 45.455 0.00 0.00 38.61 3.95
86 87 2.099098 CCTTCAAGTTTGAGCCAACGTT 59.901 45.455 0.00 0.00 38.61 3.99
87 88 1.676006 CCTTCAAGTTTGAGCCAACGT 59.324 47.619 0.00 0.00 38.61 3.99
88 89 1.600413 GCCTTCAAGTTTGAGCCAACG 60.600 52.381 0.00 0.00 38.61 4.10
89 90 1.269778 GGCCTTCAAGTTTGAGCCAAC 60.270 52.381 16.08 0.00 43.89 3.77
90 91 1.039856 GGCCTTCAAGTTTGAGCCAA 58.960 50.000 16.08 0.00 43.89 4.52
91 92 1.172180 CGGCCTTCAAGTTTGAGCCA 61.172 55.000 19.15 0.00 44.38 4.75
92 93 0.889186 TCGGCCTTCAAGTTTGAGCC 60.889 55.000 12.64 12.64 42.13 4.70
93 94 0.519077 CTCGGCCTTCAAGTTTGAGC 59.481 55.000 0.00 0.00 38.61 4.26
94 95 1.160137 CCTCGGCCTTCAAGTTTGAG 58.840 55.000 0.00 0.00 38.61 3.02
95 96 0.889186 GCCTCGGCCTTCAAGTTTGA 60.889 55.000 0.00 0.00 33.14 2.69
96 97 1.581447 GCCTCGGCCTTCAAGTTTG 59.419 57.895 0.00 0.00 34.56 2.93
97 98 1.966451 CGCCTCGGCCTTCAAGTTT 60.966 57.895 0.00 0.00 37.98 2.66
98 99 2.358737 CGCCTCGGCCTTCAAGTT 60.359 61.111 0.00 0.00 37.98 2.66
116 117 2.971428 ATCCATTCGGTGCGCCTACG 62.971 60.000 15.69 7.09 44.07 3.51
117 118 1.227556 ATCCATTCGGTGCGCCTAC 60.228 57.895 15.69 0.00 0.00 3.18
118 119 1.227527 CATCCATTCGGTGCGCCTA 60.228 57.895 15.69 0.00 0.00 3.93
119 120 2.514592 CATCCATTCGGTGCGCCT 60.515 61.111 15.69 0.00 0.00 5.52
120 121 3.585990 CCATCCATTCGGTGCGCC 61.586 66.667 6.11 6.11 0.00 6.53
121 122 1.653094 TTTCCATCCATTCGGTGCGC 61.653 55.000 0.00 0.00 0.00 6.09
122 123 0.808125 TTTTCCATCCATTCGGTGCG 59.192 50.000 0.00 0.00 0.00 5.34
123 124 1.818674 AGTTTTCCATCCATTCGGTGC 59.181 47.619 0.00 0.00 0.00 5.01
124 125 2.415893 GCAGTTTTCCATCCATTCGGTG 60.416 50.000 0.00 0.00 0.00 4.94
125 126 1.818674 GCAGTTTTCCATCCATTCGGT 59.181 47.619 0.00 0.00 0.00 4.69
126 127 1.202177 CGCAGTTTTCCATCCATTCGG 60.202 52.381 0.00 0.00 0.00 4.30
127 128 1.468520 ACGCAGTTTTCCATCCATTCG 59.531 47.619 0.00 0.00 37.78 3.34
146 147 0.652592 CATCCTTCATCCGTTGCGAC 59.347 55.000 0.00 0.00 0.00 5.19
147 148 0.534873 TCATCCTTCATCCGTTGCGA 59.465 50.000 0.00 0.00 0.00 5.10
148 149 0.652592 GTCATCCTTCATCCGTTGCG 59.347 55.000 0.00 0.00 0.00 4.85
149 150 0.652592 CGTCATCCTTCATCCGTTGC 59.347 55.000 0.00 0.00 0.00 4.17
150 151 1.290203 CCGTCATCCTTCATCCGTTG 58.710 55.000 0.00 0.00 0.00 4.10
151 152 0.902531 ACCGTCATCCTTCATCCGTT 59.097 50.000 0.00 0.00 0.00 4.44
152 153 0.175760 CACCGTCATCCTTCATCCGT 59.824 55.000 0.00 0.00 0.00 4.69
153 154 0.530650 CCACCGTCATCCTTCATCCG 60.531 60.000 0.00 0.00 0.00 4.18
154 155 0.830648 TCCACCGTCATCCTTCATCC 59.169 55.000 0.00 0.00 0.00 3.51
155 156 2.918712 ATCCACCGTCATCCTTCATC 57.081 50.000 0.00 0.00 0.00 2.92
156 157 3.071602 CCTTATCCACCGTCATCCTTCAT 59.928 47.826 0.00 0.00 0.00 2.57
157 158 2.434336 CCTTATCCACCGTCATCCTTCA 59.566 50.000 0.00 0.00 0.00 3.02
158 159 2.698797 TCCTTATCCACCGTCATCCTTC 59.301 50.000 0.00 0.00 0.00 3.46
159 160 2.700897 CTCCTTATCCACCGTCATCCTT 59.299 50.000 0.00 0.00 0.00 3.36
160 161 2.320781 CTCCTTATCCACCGTCATCCT 58.679 52.381 0.00 0.00 0.00 3.24
161 162 1.344763 CCTCCTTATCCACCGTCATCC 59.655 57.143 0.00 0.00 0.00 3.51
162 163 1.270358 GCCTCCTTATCCACCGTCATC 60.270 57.143 0.00 0.00 0.00 2.92
163 164 0.759346 GCCTCCTTATCCACCGTCAT 59.241 55.000 0.00 0.00 0.00 3.06
164 165 1.672854 CGCCTCCTTATCCACCGTCA 61.673 60.000 0.00 0.00 0.00 4.35
165 166 1.067582 CGCCTCCTTATCCACCGTC 59.932 63.158 0.00 0.00 0.00 4.79
166 167 2.432300 CCGCCTCCTTATCCACCGT 61.432 63.158 0.00 0.00 0.00 4.83
167 168 2.088674 CTCCGCCTCCTTATCCACCG 62.089 65.000 0.00 0.00 0.00 4.94
168 169 1.749033 CTCCGCCTCCTTATCCACC 59.251 63.158 0.00 0.00 0.00 4.61
169 170 1.069935 GCTCCGCCTCCTTATCCAC 59.930 63.158 0.00 0.00 0.00 4.02
170 171 2.140792 GGCTCCGCCTCCTTATCCA 61.141 63.158 0.00 0.00 46.69 3.41
171 172 2.744377 GGCTCCGCCTCCTTATCC 59.256 66.667 0.00 0.00 46.69 2.59
182 183 3.657448 TATGCACCACACGGCTCCG 62.657 63.158 6.79 6.79 46.03 4.63
183 184 2.106683 GTATGCACCACACGGCTCC 61.107 63.158 0.00 0.00 34.57 4.70
184 185 2.452813 CGTATGCACCACACGGCTC 61.453 63.158 0.00 0.00 34.57 4.70
185 186 2.434185 CGTATGCACCACACGGCT 60.434 61.111 0.00 0.00 34.57 5.52
186 187 4.160635 GCGTATGCACCACACGGC 62.161 66.667 0.89 0.15 42.15 5.68
187 188 3.848830 CGCGTATGCACCACACGG 61.849 66.667 7.86 0.00 42.97 4.94
188 189 0.868177 TATCGCGTATGCACCACACG 60.868 55.000 5.77 4.73 42.97 4.49
189 190 0.575390 GTATCGCGTATGCACCACAC 59.425 55.000 5.77 0.00 42.97 3.82
190 191 0.528901 GGTATCGCGTATGCACCACA 60.529 55.000 5.77 0.00 42.97 4.17
191 192 1.219522 GGGTATCGCGTATGCACCAC 61.220 60.000 14.85 5.50 42.97 4.16
192 193 1.068417 GGGTATCGCGTATGCACCA 59.932 57.895 14.85 0.00 42.97 4.17
193 194 0.320421 ATGGGTATCGCGTATGCACC 60.320 55.000 5.77 7.04 42.97 5.01
194 195 0.790207 CATGGGTATCGCGTATGCAC 59.210 55.000 5.77 3.92 42.97 4.57
195 196 0.320334 CCATGGGTATCGCGTATGCA 60.320 55.000 5.77 0.00 42.97 3.96
196 197 1.635663 GCCATGGGTATCGCGTATGC 61.636 60.000 15.13 0.00 37.91 3.14
197 198 1.019278 GGCCATGGGTATCGCGTATG 61.019 60.000 15.13 2.93 0.00 2.39
198 199 1.295423 GGCCATGGGTATCGCGTAT 59.705 57.895 15.13 0.65 0.00 3.06
199 200 2.738480 GGCCATGGGTATCGCGTA 59.262 61.111 15.13 0.00 0.00 4.42
200 201 4.602259 CGGCCATGGGTATCGCGT 62.602 66.667 15.13 0.00 0.00 6.01
201 202 4.602259 ACGGCCATGGGTATCGCG 62.602 66.667 15.13 0.00 0.00 5.87
202 203 2.660258 AAGACGGCCATGGGTATCGC 62.660 60.000 15.13 0.00 0.00 4.58
203 204 0.600255 GAAGACGGCCATGGGTATCG 60.600 60.000 15.13 3.59 0.00 2.92
204 205 0.759346 AGAAGACGGCCATGGGTATC 59.241 55.000 15.13 6.15 0.00 2.24
205 206 0.469917 CAGAAGACGGCCATGGGTAT 59.530 55.000 15.13 0.00 0.00 2.73
206 207 1.622607 CCAGAAGACGGCCATGGGTA 61.623 60.000 15.13 0.00 0.00 3.69
207 208 2.671070 CAGAAGACGGCCATGGGT 59.329 61.111 15.13 3.14 0.00 4.51
208 209 2.124570 CCAGAAGACGGCCATGGG 60.125 66.667 15.13 0.00 0.00 4.00
209 210 2.825836 GCCAGAAGACGGCCATGG 60.826 66.667 7.63 7.63 44.22 3.66
215 216 0.250727 TTTTCCAGGCCAGAAGACGG 60.251 55.000 5.01 0.00 0.00 4.79
216 217 1.266989 GTTTTTCCAGGCCAGAAGACG 59.733 52.381 5.01 0.00 0.00 4.18
217 218 1.266989 CGTTTTTCCAGGCCAGAAGAC 59.733 52.381 5.01 9.34 0.00 3.01
218 219 1.604604 CGTTTTTCCAGGCCAGAAGA 58.395 50.000 5.01 0.00 0.00 2.87
219 220 0.598065 CCGTTTTTCCAGGCCAGAAG 59.402 55.000 5.01 0.00 0.00 2.85
220 221 1.460273 GCCGTTTTTCCAGGCCAGAA 61.460 55.000 5.01 4.53 44.80 3.02
221 222 1.901464 GCCGTTTTTCCAGGCCAGA 60.901 57.895 5.01 0.00 44.80 3.86
222 223 2.650778 GCCGTTTTTCCAGGCCAG 59.349 61.111 5.01 0.00 44.80 4.85
225 226 2.254350 GACGCCGTTTTTCCAGGC 59.746 61.111 0.00 0.00 46.88 4.85
226 227 2.554272 CGACGCCGTTTTTCCAGG 59.446 61.111 0.00 0.00 0.00 4.45
227 228 2.127383 GCGACGCCGTTTTTCCAG 60.127 61.111 9.14 0.00 38.24 3.86
228 229 2.589442 AGCGACGCCGTTTTTCCA 60.589 55.556 17.79 0.00 38.24 3.53
229 230 2.172659 GAGCGACGCCGTTTTTCC 59.827 61.111 17.79 0.00 38.24 3.13
230 231 2.202008 CGAGCGACGCCGTTTTTC 60.202 61.111 17.79 5.27 38.24 2.29
254 255 0.033090 ACTCGAAAACGGTCACTCCC 59.967 55.000 0.00 0.00 0.00 4.30
255 256 2.712057 TACTCGAAAACGGTCACTCC 57.288 50.000 0.00 0.00 0.00 3.85
256 257 3.829948 TCATACTCGAAAACGGTCACTC 58.170 45.455 0.00 0.00 0.00 3.51
257 258 3.928727 TCATACTCGAAAACGGTCACT 57.071 42.857 0.00 0.00 0.00 3.41
258 259 9.616634 TTATATATCATACTCGAAAACGGTCAC 57.383 33.333 0.00 0.00 0.00 3.67
491 500 7.359262 TGAGAAACATACGGAAACATAGTTG 57.641 36.000 0.00 0.00 0.00 3.16
529 538 4.232091 ACCCGATTATATGGAACCTCAGT 58.768 43.478 0.00 0.00 0.00 3.41
531 540 4.283467 CAGACCCGATTATATGGAACCTCA 59.717 45.833 0.00 0.00 0.00 3.86
546 555 5.410439 GCAAAATTAGTTAGTTCAGACCCGA 59.590 40.000 0.00 0.00 0.00 5.14
561 570 7.377928 CGCCTAATCTGAAATCTGCAAAATTAG 59.622 37.037 0.00 0.00 0.00 1.73
562 571 7.195646 CGCCTAATCTGAAATCTGCAAAATTA 58.804 34.615 0.00 0.00 0.00 1.40
563 572 6.038356 CGCCTAATCTGAAATCTGCAAAATT 58.962 36.000 0.00 0.00 0.00 1.82
564 573 5.450965 CCGCCTAATCTGAAATCTGCAAAAT 60.451 40.000 0.00 0.00 0.00 1.82
587 596 5.938125 ACATTATAATGGTACGATCTTGGCC 59.062 40.000 25.45 0.00 40.70 5.36
588 597 6.426937 ACACATTATAATGGTACGATCTTGGC 59.573 38.462 25.45 0.00 40.70 4.52
606 616 7.545965 GCTTTGCTCTCTTACTTCTACACATTA 59.454 37.037 0.00 0.00 0.00 1.90
667 680 1.968540 GGCTGGTCTGTCCTGTTGC 60.969 63.158 0.54 0.00 37.45 4.17
680 693 0.178992 TGTTTCTTGGTGGAGGCTGG 60.179 55.000 0.00 0.00 0.00 4.85
684 697 3.005791 GGATTGTTGTTTCTTGGTGGAGG 59.994 47.826 0.00 0.00 0.00 4.30
691 704 4.917415 GGATCGTTGGATTGTTGTTTCTTG 59.083 41.667 0.00 0.00 31.51 3.02
790 805 9.074576 TGATAGAATCTAAGTAAACTGGCGATA 57.925 33.333 0.00 0.00 0.00 2.92
854 871 9.730705 TTTGAGAGAGAGAATGACATATTGTTT 57.269 29.630 0.00 0.00 0.00 2.83
857 874 9.597170 TCTTTTGAGAGAGAGAATGACATATTG 57.403 33.333 0.00 0.00 0.00 1.90
861 1099 9.165035 GATTTCTTTTGAGAGAGAGAATGACAT 57.835 33.333 0.00 0.00 0.00 3.06
862 1100 8.152898 TGATTTCTTTTGAGAGAGAGAATGACA 58.847 33.333 0.00 0.00 0.00 3.58
863 1101 8.545229 TGATTTCTTTTGAGAGAGAGAATGAC 57.455 34.615 0.00 0.00 0.00 3.06
869 1107 6.798315 TTGCTGATTTCTTTTGAGAGAGAG 57.202 37.500 0.00 0.00 0.00 3.20
876 1114 5.645624 TGTTCGTTTGCTGATTTCTTTTGA 58.354 33.333 0.00 0.00 0.00 2.69
877 1115 5.947503 TGTTCGTTTGCTGATTTCTTTTG 57.052 34.783 0.00 0.00 0.00 2.44
882 1120 6.695292 AATTCATGTTCGTTTGCTGATTTC 57.305 33.333 0.00 0.00 0.00 2.17
889 1128 6.636666 ATCATCAAATTCATGTTCGTTTGC 57.363 33.333 0.00 0.00 32.95 3.68
928 1167 5.280945 GCAACACACACACATAAACAGATT 58.719 37.500 0.00 0.00 0.00 2.40
1044 1296 2.291741 CCACTTGGTTGAAAGAGTGCTC 59.708 50.000 0.00 0.00 38.48 4.26
1334 1586 1.200716 ACGGATGTTTGCAGCATCTTG 59.799 47.619 23.47 19.64 41.63 3.02
1433 1697 3.955551 TGGAAAACCACTAAAGTTGGGTC 59.044 43.478 0.00 0.00 32.01 4.46
1479 1743 5.624159 TCATTTGAAGAGACATCCACACTT 58.376 37.500 0.00 0.00 0.00 3.16
1584 1848 1.954146 TTGCAGACGCGGAAGTGAC 60.954 57.895 12.47 0.00 46.66 3.67
1671 1935 8.375506 TCAAGAGGTACCATAAATCCATCATAC 58.624 37.037 15.94 0.00 0.00 2.39
1821 2085 4.081406 AGCAGCAAACCTTCAATGTCATA 58.919 39.130 0.00 0.00 0.00 2.15
1918 2182 1.968540 GTCACACCCTCTGGCAAGC 60.969 63.158 0.00 0.00 33.59 4.01
2081 2345 9.534565 GCTTGTTCAGTCACAGAGAATAATATA 57.465 33.333 0.00 0.00 0.00 0.86
2083 2347 6.818644 GGCTTGTTCAGTCACAGAGAATAATA 59.181 38.462 0.00 0.00 0.00 0.98
2084 2348 5.645497 GGCTTGTTCAGTCACAGAGAATAAT 59.355 40.000 0.00 0.00 0.00 1.28
2085 2349 4.997395 GGCTTGTTCAGTCACAGAGAATAA 59.003 41.667 0.00 0.00 0.00 1.40
2086 2350 4.040339 TGGCTTGTTCAGTCACAGAGAATA 59.960 41.667 0.00 0.00 29.49 1.75
2103 2412 6.308766 GCATTTTATTCTTGTACAGTGGCTTG 59.691 38.462 0.00 0.00 0.00 4.01
2137 2446 4.510711 CGCTGAAACTGCATAGATCAAGAT 59.489 41.667 0.00 0.00 0.00 2.40
2359 2668 4.271533 TCGGGCGTTAAAGTAAGCATATTG 59.728 41.667 0.00 0.00 0.00 1.90
2526 2835 2.302587 TTCCTAAAACCAAGCCCCTG 57.697 50.000 0.00 0.00 0.00 4.45
2567 2876 7.644490 TGTACAGAAACTGCGTCAATTAATTT 58.356 30.769 0.00 0.00 34.37 1.82
2624 3004 4.865925 ACGATTGCATGAAATGAAACCATG 59.134 37.500 2.78 0.00 46.70 3.66
2633 3018 6.697019 GCAAAGGTAATACGATTGCATGAAAT 59.303 34.615 19.77 0.00 44.29 2.17
2634 3019 6.033341 GCAAAGGTAATACGATTGCATGAAA 58.967 36.000 19.77 0.00 44.29 2.69
2635 3020 5.449862 GGCAAAGGTAATACGATTGCATGAA 60.450 40.000 23.44 0.00 46.12 2.57
2636 3021 4.036262 GGCAAAGGTAATACGATTGCATGA 59.964 41.667 23.44 0.00 46.12 3.07
2637 3022 4.036734 AGGCAAAGGTAATACGATTGCATG 59.963 41.667 23.44 0.00 46.12 4.06
2674 3059 5.168569 CGTTCTGTTCAGAGTTGGCTTATA 58.831 41.667 2.77 0.00 0.00 0.98
2676 3061 3.181469 ACGTTCTGTTCAGAGTTGGCTTA 60.181 43.478 2.77 0.00 0.00 3.09
2705 3091 1.883084 CACATAGAACTCGCGGGGC 60.883 63.158 12.42 0.90 0.00 5.80
2746 3132 3.379057 TGATAATCGCGGAACAGTGTCTA 59.621 43.478 6.13 0.00 0.00 2.59
2770 3156 1.618343 GACAACAATTGGGTTCCCCTG 59.382 52.381 10.83 3.24 45.70 4.45
2778 3164 4.979815 GGTAAGTTTTCGACAACAATTGGG 59.020 41.667 16.24 4.09 34.12 4.12
2818 3204 5.698545 GGCTACAGCTATTTTCTGGACTATG 59.301 44.000 0.54 0.00 41.70 2.23
2907 3293 1.758440 AAGTGGCAACGAGGAGCTGA 61.758 55.000 0.00 0.00 42.51 4.26
2922 3308 8.946085 TGAATTTAGTAGGCATTGAGTTAAGTG 58.054 33.333 0.00 0.00 0.00 3.16
2940 3326 6.939163 CAGGATGAGGGGTATTCTGAATTTAG 59.061 42.308 8.38 0.00 39.69 1.85
2960 3346 0.680280 CTGAAGCAAGGCAGCAGGAT 60.680 55.000 4.78 0.00 36.85 3.24
2983 3369 6.317140 TCATGCAAAGGATCAAAGTGAGATAC 59.683 38.462 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.