Multiple sequence alignment - TraesCS5A01G300800

Loading Multiple Alignment...

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 TraesCS5A01G300800 chr5A 100.000 2231 0 0 745 2975 510078950 510076720 0.000000e+00 4120.0
1 TraesCS5A01G300800 chr5A 100.000 548 0 0 1 548 510079694 510079147 0.000000e+00 1013.0
2 TraesCS5A01G300800 chr5A 81.947 986 144 30 1003 1973 459677081 459676115 0.000000e+00 804.0
3 TraesCS5A01G300800 chr5A 93.609 266 14 3 2 266 452435221 452434958 7.730000e-106 394.0
4 TraesCS5A01G300800 chr5D 94.261 1638 59 19 754 2374 403415722 403414103 0.000000e+00 2471.0
5 TraesCS5A01G300800 chr5D 81.680 988 143 27 1003 1973 358825586 358824620 0.000000e+00 787.0
6 TraesCS5A01G300800 chr5D 89.354 263 15 7 2401 2650 403414037 403413775 4.790000e-83 318.0
7 TraesCS5A01G300800 chr5D 89.912 228 6 4 298 508 403416003 403415776 8.120000e-71 278.0
8 TraesCS5A01G300800 chr5D 90.909 77 7 0 2898 2974 403413470 403413394 1.460000e-18 104.0
9 TraesCS5A01G300800 chr5B 93.630 1664 67 20 754 2401 485153973 485155613 0.000000e+00 2449.0
10 TraesCS5A01G300800 chr5B 89.552 268 11 5 298 548 485153681 485153948 1.030000e-84 324.0
11 TraesCS5A01G300800 chr5B 92.442 172 12 1 2397 2567 485155635 485155806 8.240000e-61 244.0
12 TraesCS5A01G300800 chr5B 81.726 197 21 9 2688 2870 485158373 485158568 1.850000e-32 150.0
13 TraesCS5A01G300800 chr5B 100.000 31 0 0 274 304 485153642 485153672 1.150000e-04 58.4
14 TraesCS5A01G300800 chr3B 98.491 265 4 0 1 265 18816261 18815997 4.490000e-128 468.0
15 TraesCS5A01G300800 chr3B 98.113 265 5 0 1 265 780440572 780440308 2.090000e-126 462.0
16 TraesCS5A01G300800 chr1B 98.491 265 4 0 1 265 18533812 18533548 4.490000e-128 468.0
17 TraesCS5A01G300800 chr1B 97.378 267 6 1 1 266 520520535 520520269 1.260000e-123 453.0
18 TraesCS5A01G300800 chr2B 98.120 266 5 0 1 266 425676116 425675851 5.810000e-127 464.0
19 TraesCS5A01G300800 chr6B 97.744 266 6 0 1 266 494273900 494274165 2.700000e-125 459.0
20 TraesCS5A01G300800 chr7A 94.340 265 13 2 2 265 679160033 679159770 3.570000e-109 405.0
21 TraesCS5A01G300800 chr4A 95.984 249 8 2 2 249 595420866 595421113 1.280000e-108 403.0


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 TraesCS5A01G300800 chr5A 510076720 510079694 2974 True 2566.50 4120 100.000 1 2975 2 chr5A.!!$R3 2974
1 TraesCS5A01G300800 chr5A 459676115 459677081 966 True 804.00 804 81.947 1003 1973 1 chr5A.!!$R2 970
2 TraesCS5A01G300800 chr5D 403413394 403416003 2609 True 792.75 2471 91.109 298 2974 4 chr5D.!!$R2 2676
3 TraesCS5A01G300800 chr5D 358824620 358825586 966 True 787.00 787 81.680 1003 1973 1 chr5D.!!$R1 970
4 TraesCS5A01G300800 chr5B 485153642 485158568 4926 False 645.08 2449 91.470 274 2870 5 chr5B.!!$F1 2596

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
172 173 0.031917 TAGGGGATGGAGGCGTGTAA 60.032 55.0 0.0 0.0 0.0 2.41 F
180 181 0.175989 GGAGGCGTGTAAGGAAGGAG 59.824 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 2019 0.391597 AGAACTCGGCGTCCTTGAAA 59.608 50.0 6.85 0.0 0.0 2.69 R
2023 2094 0.749454 ATCAATGGCGGCCTCTTGTC 60.749 55.0 21.46 0.0 0.0 3.18 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
23 24 1.225426 TGGATCTGACCATGGCAGC 59.775 57.895 23.56 14.45 34.77 5.25
24 25 1.225426 GGATCTGACCATGGCAGCA 59.775 57.895 23.56 14.42 33.45 4.41
25 26 0.818445 GGATCTGACCATGGCAGCAG 60.818 60.000 23.56 21.24 33.45 4.24
26 27 0.818445 GATCTGACCATGGCAGCAGG 60.818 60.000 23.56 8.39 33.45 4.85
27 28 2.905935 ATCTGACCATGGCAGCAGGC 62.906 60.000 23.56 0.00 43.74 4.85
99 100 4.814294 GCCGGCGATGGAGTTCGT 62.814 66.667 12.58 0.00 41.16 3.85
100 101 2.885644 CCGGCGATGGAGTTCGTG 60.886 66.667 9.30 0.00 41.16 4.35
101 102 2.885644 CGGCGATGGAGTTCGTGG 60.886 66.667 0.00 0.00 41.16 4.94
102 103 2.577059 GGCGATGGAGTTCGTGGA 59.423 61.111 0.00 0.00 41.16 4.02
103 104 1.519455 GGCGATGGAGTTCGTGGAG 60.519 63.158 0.00 0.00 41.16 3.86
104 105 1.519455 GCGATGGAGTTCGTGGAGG 60.519 63.158 0.00 0.00 41.16 4.30
105 106 1.519455 CGATGGAGTTCGTGGAGGC 60.519 63.158 0.00 0.00 34.46 4.70
106 107 1.153349 GATGGAGTTCGTGGAGGCC 60.153 63.158 0.00 0.00 0.00 5.19
107 108 2.595009 GATGGAGTTCGTGGAGGCCC 62.595 65.000 0.00 0.00 0.00 5.80
108 109 3.319198 GGAGTTCGTGGAGGCCCA 61.319 66.667 0.00 0.00 40.95 5.36
109 110 2.266055 GAGTTCGTGGAGGCCCAG 59.734 66.667 0.00 0.00 44.55 4.45
110 111 2.526873 AGTTCGTGGAGGCCCAGT 60.527 61.111 0.00 0.00 44.55 4.00
111 112 2.047179 GTTCGTGGAGGCCCAGTC 60.047 66.667 0.00 0.00 44.55 3.51
112 113 3.691342 TTCGTGGAGGCCCAGTCG 61.691 66.667 0.00 0.00 44.55 4.18
115 116 4.767255 GTGGAGGCCCAGTCGCAG 62.767 72.222 0.00 0.00 44.55 5.18
118 119 4.828925 GAGGCCCAGTCGCAGCTC 62.829 72.222 0.00 0.00 0.00 4.09
130 131 2.837291 CAGCTCGGGGGAGGAGAG 60.837 72.222 0.00 0.00 33.27 3.20
131 132 4.150454 AGCTCGGGGGAGGAGAGG 62.150 72.222 0.00 0.00 33.27 3.69
132 133 4.467107 GCTCGGGGGAGGAGAGGT 62.467 72.222 0.00 0.00 33.27 3.85
133 134 2.443016 CTCGGGGGAGGAGAGGTG 60.443 72.222 0.00 0.00 33.27 4.00
134 135 4.779733 TCGGGGGAGGAGAGGTGC 62.780 72.222 0.00 0.00 0.00 5.01
153 154 3.760035 CGCACGTAGGCTGGAGGT 61.760 66.667 0.00 0.00 0.00 3.85
154 155 2.412323 CGCACGTAGGCTGGAGGTA 61.412 63.158 0.00 0.00 0.00 3.08
155 156 1.437986 GCACGTAGGCTGGAGGTAG 59.562 63.158 0.00 0.00 0.00 3.18
156 157 2.017559 GCACGTAGGCTGGAGGTAGG 62.018 65.000 0.00 0.00 0.00 3.18
157 158 1.076192 ACGTAGGCTGGAGGTAGGG 60.076 63.158 0.00 0.00 0.00 3.53
158 159 1.833049 CGTAGGCTGGAGGTAGGGG 60.833 68.421 0.00 0.00 0.00 4.79
159 160 1.624753 GTAGGCTGGAGGTAGGGGA 59.375 63.158 0.00 0.00 0.00 4.81
160 161 0.191314 GTAGGCTGGAGGTAGGGGAT 59.809 60.000 0.00 0.00 0.00 3.85
161 162 0.191064 TAGGCTGGAGGTAGGGGATG 59.809 60.000 0.00 0.00 0.00 3.51
162 163 2.150051 GGCTGGAGGTAGGGGATGG 61.150 68.421 0.00 0.00 0.00 3.51
163 164 1.074471 GCTGGAGGTAGGGGATGGA 60.074 63.158 0.00 0.00 0.00 3.41
164 165 1.124477 GCTGGAGGTAGGGGATGGAG 61.124 65.000 0.00 0.00 0.00 3.86
165 166 0.472734 CTGGAGGTAGGGGATGGAGG 60.473 65.000 0.00 0.00 0.00 4.30
166 167 1.843832 GGAGGTAGGGGATGGAGGC 60.844 68.421 0.00 0.00 0.00 4.70
167 168 2.122813 AGGTAGGGGATGGAGGCG 60.123 66.667 0.00 0.00 0.00 5.52
168 169 2.446036 GGTAGGGGATGGAGGCGT 60.446 66.667 0.00 0.00 0.00 5.68
169 170 2.808206 GGTAGGGGATGGAGGCGTG 61.808 68.421 0.00 0.00 0.00 5.34
170 171 2.064581 GTAGGGGATGGAGGCGTGT 61.065 63.158 0.00 0.00 0.00 4.49
171 172 0.757935 GTAGGGGATGGAGGCGTGTA 60.758 60.000 0.00 0.00 0.00 2.90
172 173 0.031917 TAGGGGATGGAGGCGTGTAA 60.032 55.000 0.00 0.00 0.00 2.41
173 174 1.146263 GGGGATGGAGGCGTGTAAG 59.854 63.158 0.00 0.00 0.00 2.34
174 175 1.146263 GGGATGGAGGCGTGTAAGG 59.854 63.158 0.00 0.00 0.00 2.69
175 176 1.335132 GGGATGGAGGCGTGTAAGGA 61.335 60.000 0.00 0.00 0.00 3.36
176 177 0.539986 GGATGGAGGCGTGTAAGGAA 59.460 55.000 0.00 0.00 0.00 3.36
177 178 1.473434 GGATGGAGGCGTGTAAGGAAG 60.473 57.143 0.00 0.00 0.00 3.46
178 179 0.541863 ATGGAGGCGTGTAAGGAAGG 59.458 55.000 0.00 0.00 0.00 3.46
179 180 0.543410 TGGAGGCGTGTAAGGAAGGA 60.543 55.000 0.00 0.00 0.00 3.36
180 181 0.175989 GGAGGCGTGTAAGGAAGGAG 59.824 60.000 0.00 0.00 0.00 3.69
181 182 1.183549 GAGGCGTGTAAGGAAGGAGA 58.816 55.000 0.00 0.00 0.00 3.71
182 183 1.549170 GAGGCGTGTAAGGAAGGAGAA 59.451 52.381 0.00 0.00 0.00 2.87
183 184 1.550976 AGGCGTGTAAGGAAGGAGAAG 59.449 52.381 0.00 0.00 0.00 2.85
184 185 1.405661 GGCGTGTAAGGAAGGAGAAGG 60.406 57.143 0.00 0.00 0.00 3.46
185 186 1.405661 GCGTGTAAGGAAGGAGAAGGG 60.406 57.143 0.00 0.00 0.00 3.95
186 187 1.207329 CGTGTAAGGAAGGAGAAGGGG 59.793 57.143 0.00 0.00 0.00 4.79
187 188 2.547990 GTGTAAGGAAGGAGAAGGGGA 58.452 52.381 0.00 0.00 0.00 4.81
188 189 3.116174 GTGTAAGGAAGGAGAAGGGGAT 58.884 50.000 0.00 0.00 0.00 3.85
189 190 3.115390 TGTAAGGAAGGAGAAGGGGATG 58.885 50.000 0.00 0.00 0.00 3.51
190 191 0.922626 AAGGAAGGAGAAGGGGATGC 59.077 55.000 0.00 0.00 0.00 3.91
191 192 1.147153 GGAAGGAGAAGGGGATGCG 59.853 63.158 0.00 0.00 0.00 4.73
192 193 1.524849 GAAGGAGAAGGGGATGCGC 60.525 63.158 0.00 0.00 0.00 6.09
193 194 3.391665 AAGGAGAAGGGGATGCGCG 62.392 63.158 0.00 0.00 0.00 6.86
194 195 4.918201 GGAGAAGGGGATGCGCGG 62.918 72.222 8.83 0.00 0.00 6.46
195 196 4.918201 GAGAAGGGGATGCGCGGG 62.918 72.222 8.83 0.00 0.00 6.13
212 213 4.980903 GCGTGTTTGCCAGCGTGG 62.981 66.667 0.25 0.25 41.55 4.94
257 258 4.832767 GGTGCGCCGTTTCTAAAC 57.167 55.556 4.18 0.00 35.59 2.01
329 349 4.760047 CCCCGTCCGGACAGCAAG 62.760 72.222 32.80 16.62 37.50 4.01
503 545 1.074850 CCTCCTCCTTCCTCCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
523 570 3.455469 CCCCGTCCGTCCACCTAC 61.455 72.222 0.00 0.00 0.00 3.18
527 574 0.248289 CCGTCCGTCCACCTACAAAT 59.752 55.000 0.00 0.00 0.00 2.32
528 575 1.477700 CCGTCCGTCCACCTACAAATA 59.522 52.381 0.00 0.00 0.00 1.40
537 584 1.139058 CACCTACAAATAGCGCCTCCT 59.861 52.381 2.29 0.00 0.00 3.69
538 585 1.413077 ACCTACAAATAGCGCCTCCTC 59.587 52.381 2.29 0.00 0.00 3.71
540 587 1.689273 CTACAAATAGCGCCTCCTCCT 59.311 52.381 2.29 0.00 0.00 3.69
541 588 0.466124 ACAAATAGCGCCTCCTCCTC 59.534 55.000 2.29 0.00 0.00 3.71
851 900 2.352032 CCACCTCCTCGTGTCCTCC 61.352 68.421 0.00 0.00 31.47 4.30
912 965 2.866065 GCCCAAATCCGACACCTTTTTG 60.866 50.000 0.00 0.00 0.00 2.44
937 993 7.068226 TGGTTTTTGTTTCCTCTCTTCTTTAGG 59.932 37.037 0.00 0.00 0.00 2.69
957 1013 9.399403 CTTTAGGTTTTGTTTCTAGATCTTTGC 57.601 33.333 0.00 0.00 0.00 3.68
975 1031 1.509463 CGGGTCTCGAATTCGTCCA 59.491 57.895 25.93 7.61 42.43 4.02
976 1032 0.525668 CGGGTCTCGAATTCGTCCAG 60.526 60.000 25.93 20.94 42.43 3.86
977 1033 0.179108 GGGTCTCGAATTCGTCCAGG 60.179 60.000 25.93 12.72 40.80 4.45
978 1034 0.179108 GGTCTCGAATTCGTCCAGGG 60.179 60.000 25.93 11.20 40.80 4.45
979 1035 0.815734 GTCTCGAATTCGTCCAGGGA 59.184 55.000 25.93 13.01 40.80 4.20
980 1036 1.409427 GTCTCGAATTCGTCCAGGGAT 59.591 52.381 25.93 0.00 40.80 3.85
981 1037 2.108168 TCTCGAATTCGTCCAGGGATT 58.892 47.619 25.93 0.00 40.80 3.01
982 1038 2.159099 TCTCGAATTCGTCCAGGGATTG 60.159 50.000 25.93 6.36 40.80 2.67
983 1039 1.553248 TCGAATTCGTCCAGGGATTGT 59.447 47.619 25.93 0.00 40.80 2.71
984 1040 2.761767 TCGAATTCGTCCAGGGATTGTA 59.238 45.455 25.93 0.33 40.80 2.41
987 1043 2.241281 TTCGTCCAGGGATTGTAGGA 57.759 50.000 0.00 0.00 0.00 2.94
989 1045 2.108168 TCGTCCAGGGATTGTAGGAAG 58.892 52.381 0.00 0.00 0.00 3.46
991 1047 2.478292 GTCCAGGGATTGTAGGAAGGA 58.522 52.381 0.00 0.00 0.00 3.36
993 1049 1.771255 CCAGGGATTGTAGGAAGGAGG 59.229 57.143 0.00 0.00 0.00 4.30
995 1051 1.657162 AGGGATTGTAGGAAGGAGGGA 59.343 52.381 0.00 0.00 0.00 4.20
996 1052 2.047296 AGGGATTGTAGGAAGGAGGGAA 59.953 50.000 0.00 0.00 0.00 3.97
1617 1683 3.272334 GCCATGATCGTCACCGCC 61.272 66.667 0.00 0.00 0.00 6.13
1791 1857 1.474077 GTGATGAACATGAAGGTGGCC 59.526 52.381 0.00 0.00 0.00 5.36
1964 2030 0.660300 CGCAAGGTTTTCAAGGACGC 60.660 55.000 0.00 0.00 0.00 5.19
2019 2090 4.462834 GCACCATGAATCCATGATGATGAT 59.537 41.667 4.07 0.00 45.30 2.45
2023 2094 9.422807 CACCATGAATCCATGATGATGATGACG 62.423 44.444 6.95 0.00 45.30 4.35
2025 2096 4.992951 TGAATCCATGATGATGATGACGAC 59.007 41.667 0.00 0.00 0.00 4.34
2029 2100 4.099881 TCCATGATGATGATGACGACAAGA 59.900 41.667 0.00 0.00 0.00 3.02
2030 2101 4.448060 CCATGATGATGATGACGACAAGAG 59.552 45.833 0.00 0.00 0.00 2.85
2033 2104 1.134699 TGATGATGACGACAAGAGGCC 60.135 52.381 0.00 0.00 0.00 5.19
2034 2105 0.179100 ATGATGACGACAAGAGGCCG 60.179 55.000 0.00 0.00 0.00 6.13
2086 2157 3.215975 AGTAGTACCGCTGGAGAGATTC 58.784 50.000 0.00 0.00 0.00 2.52
2105 2176 3.003173 TCCAGTTCCTGCCTCCCG 61.003 66.667 0.00 0.00 0.00 5.14
2164 2235 8.565896 AAATTCTCATTTTTAAATCTTGGGCC 57.434 30.769 0.00 0.00 0.00 5.80
2258 2329 6.567050 ACTATTACTGGCATGCTTTCAATTG 58.433 36.000 18.92 14.32 0.00 2.32
2260 2331 3.587797 ACTGGCATGCTTTCAATTGAG 57.412 42.857 18.92 0.00 0.00 3.02
2301 2376 7.081526 CCGAAACGGCAGTATATATAGTACT 57.918 40.000 0.00 0.00 41.17 2.73
2302 2377 7.185453 CCGAAACGGCAGTATATATAGTACTC 58.815 42.308 0.00 0.00 41.17 2.59
2318 2395 4.508662 AGTACTCTAAGCAACAAGGATGC 58.491 43.478 0.00 0.00 44.15 3.91
2363 2440 7.281100 AGGATTGTTTAGCAGTAAGTAAGATGC 59.719 37.037 0.00 0.00 38.97 3.91
2374 2451 1.226974 TAAGATGCGCTGCCGACTC 60.227 57.895 9.73 0.00 36.29 3.36
2375 2452 2.629050 TAAGATGCGCTGCCGACTCC 62.629 60.000 9.73 0.00 36.29 3.85
2376 2453 4.521062 GATGCGCTGCCGACTCCT 62.521 66.667 9.73 0.00 36.29 3.69
2377 2454 4.087892 ATGCGCTGCCGACTCCTT 62.088 61.111 9.73 0.00 36.29 3.36
2378 2455 2.629050 GATGCGCTGCCGACTCCTTA 62.629 60.000 9.73 0.00 36.29 2.69
2391 2481 9.268268 CTGCCGACTCCTTATATTACAAAATAA 57.732 33.333 0.00 0.00 31.44 1.40
2415 2531 1.064758 ACTGCTCCTCTCTCGATCAGT 60.065 52.381 0.00 0.00 0.00 3.41
2457 2573 0.955919 GTTCCTCCACGGCTCCTTTG 60.956 60.000 0.00 0.00 0.00 2.77
2460 2576 1.738099 CTCCACGGCTCCTTTGTCG 60.738 63.158 0.00 0.00 0.00 4.35
2524 2641 0.387202 AGCATACGCCTCAGCAGTAG 59.613 55.000 0.00 0.00 39.83 2.57
2571 2699 0.391661 AAGTAGACACGGCAGCCATG 60.392 55.000 13.30 9.65 0.00 3.66
2585 2716 1.422781 AGCCATGATCATCCCGAATGT 59.577 47.619 4.86 0.00 36.68 2.71
2590 2722 2.403561 TGATCATCCCGAATGTACCCA 58.596 47.619 0.00 0.00 36.68 4.51
2625 5110 0.374758 CAGAAACGATGCGTGATGGG 59.625 55.000 0.00 0.00 39.99 4.00
2630 5115 3.576356 GATGCGTGATGGGCGGTG 61.576 66.667 0.00 0.00 0.00 4.94
2650 5135 0.607217 CCAGCAGCACATCACAGGAA 60.607 55.000 0.00 0.00 0.00 3.36
2657 5184 0.784178 CACATCACAGGAACGTGTCG 59.216 55.000 0.00 0.00 38.12 4.35
2681 5208 2.359850 CTGCAAGGCTACGGGCAA 60.360 61.111 5.12 0.00 44.01 4.52
2682 5209 2.359850 TGCAAGGCTACGGGCAAG 60.360 61.111 5.12 0.00 44.01 4.01
2683 5210 3.815396 GCAAGGCTACGGGCAAGC 61.815 66.667 5.12 0.00 44.01 4.01
2684 5211 3.499737 CAAGGCTACGGGCAAGCG 61.500 66.667 5.12 0.00 44.01 4.68
2695 5258 0.179137 GGGCAAGCGCAAACCTAATC 60.179 55.000 11.47 0.00 41.24 1.75
2708 5271 4.785346 AACCTAATCTCCACATCAGCAT 57.215 40.909 0.00 0.00 0.00 3.79
2709 5272 4.082665 ACCTAATCTCCACATCAGCATG 57.917 45.455 0.00 0.00 35.92 4.06
2731 5294 3.829044 TCGACATGTACCGGCCCG 61.829 66.667 0.00 0.00 0.00 6.13
2765 5328 2.234187 GTTCTTTGCGAAATCGACAGC 58.766 47.619 7.06 0.00 43.02 4.40
2782 5345 3.626154 GCGAGTGCTGGAGTAGTAC 57.374 57.895 0.00 0.00 41.74 2.73
2784 5347 1.467713 GCGAGTGCTGGAGTAGTACAC 60.468 57.143 2.52 0.00 43.61 2.90
2786 5349 2.082231 GAGTGCTGGAGTAGTACACGA 58.918 52.381 2.52 0.00 43.61 4.35
2787 5350 2.683867 GAGTGCTGGAGTAGTACACGAT 59.316 50.000 2.52 0.00 43.61 3.73
2788 5351 2.683867 AGTGCTGGAGTAGTACACGATC 59.316 50.000 2.52 0.00 43.61 3.69
2789 5352 2.683867 GTGCTGGAGTAGTACACGATCT 59.316 50.000 2.52 0.00 41.16 2.75
2790 5353 2.683362 TGCTGGAGTAGTACACGATCTG 59.317 50.000 2.52 0.00 0.00 2.90
2793 5356 1.002684 GGAGTAGTACACGATCTGCGG 60.003 57.143 2.52 0.00 46.49 5.69
2828 5404 2.909965 GCAACCACCAAAGGCCGA 60.910 61.111 0.00 0.00 0.00 5.54
2848 5424 2.254546 CCATAATGGTGGCGCTAAGA 57.745 50.000 7.64 0.00 31.35 2.10
2871 5447 2.290641 CAGTTAAGGTTGACAGTGCCAC 59.709 50.000 0.00 0.00 0.00 5.01
2872 5448 2.172717 AGTTAAGGTTGACAGTGCCACT 59.827 45.455 0.00 0.00 0.00 4.00
2873 5449 2.543777 TAAGGTTGACAGTGCCACTC 57.456 50.000 0.00 0.00 0.00 3.51
2874 5450 0.179018 AAGGTTGACAGTGCCACTCC 60.179 55.000 0.00 0.00 0.00 3.85
2875 5451 1.056700 AGGTTGACAGTGCCACTCCT 61.057 55.000 0.00 0.00 0.00 3.69
2876 5452 0.179018 GGTTGACAGTGCCACTCCTT 60.179 55.000 0.00 0.00 0.00 3.36
2877 5453 1.680338 GTTGACAGTGCCACTCCTTT 58.320 50.000 0.00 0.00 0.00 3.11
2878 5454 1.604278 GTTGACAGTGCCACTCCTTTC 59.396 52.381 0.00 0.00 0.00 2.62
2879 5455 1.131638 TGACAGTGCCACTCCTTTCT 58.868 50.000 0.00 0.00 0.00 2.52
2880 5456 1.070758 TGACAGTGCCACTCCTTTCTC 59.929 52.381 0.00 0.00 0.00 2.87
2881 5457 0.398318 ACAGTGCCACTCCTTTCTCC 59.602 55.000 0.00 0.00 0.00 3.71
2882 5458 0.322008 CAGTGCCACTCCTTTCTCCC 60.322 60.000 0.00 0.00 0.00 4.30
2883 5459 1.376037 GTGCCACTCCTTTCTCCCG 60.376 63.158 0.00 0.00 0.00 5.14
2884 5460 2.269241 GCCACTCCTTTCTCCCGG 59.731 66.667 0.00 0.00 0.00 5.73
2885 5461 2.990479 CCACTCCTTTCTCCCGGG 59.010 66.667 16.85 16.85 0.00 5.73
2886 5462 2.670148 CCACTCCTTTCTCCCGGGG 61.670 68.421 23.50 12.05 0.00 5.73
2887 5463 2.285442 ACTCCTTTCTCCCGGGGG 60.285 66.667 23.50 20.43 0.00 5.40
2888 5464 2.285442 CTCCTTTCTCCCGGGGGT 60.285 66.667 23.00 0.00 36.47 4.95
2889 5465 2.609610 TCCTTTCTCCCGGGGGTG 60.610 66.667 23.00 12.00 36.47 4.61
2890 5466 3.728373 CCTTTCTCCCGGGGGTGG 61.728 72.222 23.00 17.41 36.47 4.61
2967 5543 4.016706 GTCCACCACCAGACCCGG 62.017 72.222 0.00 0.00 0.00 5.73
2974 5550 0.889186 CCACCAGACCCGGACTTTTG 60.889 60.000 0.73 1.41 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.893544 CTGCCATGGTCAGATCCATC 58.106 55.000 23.86 1.66 45.23 3.51
5 6 1.225426 GCTGCCATGGTCAGATCCA 59.775 57.895 29.21 11.81 42.01 3.41
6 7 0.818445 CTGCTGCCATGGTCAGATCC 60.818 60.000 29.21 17.28 33.54 3.36
7 8 0.818445 CCTGCTGCCATGGTCAGATC 60.818 60.000 29.21 17.80 33.54 2.75
8 9 1.226542 CCTGCTGCCATGGTCAGAT 59.773 57.895 29.21 0.00 33.54 2.90
9 10 2.672908 CCTGCTGCCATGGTCAGA 59.327 61.111 29.21 17.67 33.54 3.27
10 11 3.138798 GCCTGCTGCCATGGTCAG 61.139 66.667 23.86 23.86 34.79 3.51
11 12 3.931190 CTGCCTGCTGCCATGGTCA 62.931 63.158 14.67 10.98 40.16 4.02
12 13 3.138798 CTGCCTGCTGCCATGGTC 61.139 66.667 14.67 6.41 40.16 4.02
20 21 3.449227 CACCATGGCTGCCTGCTG 61.449 66.667 21.03 13.89 42.39 4.41
21 22 4.753662 CCACCATGGCTGCCTGCT 62.754 66.667 21.03 1.45 42.39 4.24
82 83 4.814294 ACGAACTCCATCGCCGGC 62.814 66.667 19.07 19.07 46.51 6.13
83 84 2.885644 CACGAACTCCATCGCCGG 60.886 66.667 0.00 0.00 46.51 6.13
84 85 2.885644 CCACGAACTCCATCGCCG 60.886 66.667 0.00 0.00 46.51 6.46
85 86 1.519455 CTCCACGAACTCCATCGCC 60.519 63.158 0.00 0.00 46.51 5.54
86 87 1.519455 CCTCCACGAACTCCATCGC 60.519 63.158 0.00 0.00 46.51 4.58
88 89 1.153349 GGCCTCCACGAACTCCATC 60.153 63.158 0.00 0.00 0.00 3.51
89 90 2.670148 GGGCCTCCACGAACTCCAT 61.670 63.158 0.84 0.00 0.00 3.41
90 91 3.319198 GGGCCTCCACGAACTCCA 61.319 66.667 0.84 0.00 0.00 3.86
91 92 3.316573 CTGGGCCTCCACGAACTCC 62.317 68.421 4.53 0.00 38.32 3.85
92 93 2.266055 CTGGGCCTCCACGAACTC 59.734 66.667 4.53 0.00 38.32 3.01
93 94 2.526873 ACTGGGCCTCCACGAACT 60.527 61.111 4.53 0.00 38.32 3.01
94 95 2.047179 GACTGGGCCTCCACGAAC 60.047 66.667 4.53 0.00 38.32 3.95
95 96 3.691342 CGACTGGGCCTCCACGAA 61.691 66.667 4.53 0.00 38.32 3.85
98 99 4.767255 CTGCGACTGGGCCTCCAC 62.767 72.222 4.53 0.00 38.32 4.02
101 102 4.828925 GAGCTGCGACTGGGCCTC 62.829 72.222 4.53 0.00 0.00 4.70
113 114 2.837291 CTCTCCTCCCCCGAGCTG 60.837 72.222 0.00 0.00 34.49 4.24
114 115 4.150454 CCTCTCCTCCCCCGAGCT 62.150 72.222 0.00 0.00 34.49 4.09
115 116 4.467107 ACCTCTCCTCCCCCGAGC 62.467 72.222 0.00 0.00 34.49 5.03
116 117 2.443016 CACCTCTCCTCCCCCGAG 60.443 72.222 0.00 0.00 35.72 4.63
117 118 4.779733 GCACCTCTCCTCCCCCGA 62.780 72.222 0.00 0.00 0.00 5.14
126 127 4.771356 TACGTGCGCGCACCTCTC 62.771 66.667 46.98 29.52 43.49 3.20
127 128 4.778415 CTACGTGCGCGCACCTCT 62.778 66.667 46.98 34.22 43.49 3.69
136 137 2.337749 CTACCTCCAGCCTACGTGCG 62.338 65.000 0.00 0.00 36.02 5.34
137 138 1.437986 CTACCTCCAGCCTACGTGC 59.562 63.158 0.00 0.00 0.00 5.34
138 139 1.392710 CCCTACCTCCAGCCTACGTG 61.393 65.000 0.00 0.00 0.00 4.49
139 140 1.076192 CCCTACCTCCAGCCTACGT 60.076 63.158 0.00 0.00 0.00 3.57
140 141 1.833049 CCCCTACCTCCAGCCTACG 60.833 68.421 0.00 0.00 0.00 3.51
141 142 0.191314 ATCCCCTACCTCCAGCCTAC 59.809 60.000 0.00 0.00 0.00 3.18
142 143 0.191064 CATCCCCTACCTCCAGCCTA 59.809 60.000 0.00 0.00 0.00 3.93
143 144 1.074167 CATCCCCTACCTCCAGCCT 60.074 63.158 0.00 0.00 0.00 4.58
144 145 2.150051 CCATCCCCTACCTCCAGCC 61.150 68.421 0.00 0.00 0.00 4.85
145 146 1.074471 TCCATCCCCTACCTCCAGC 60.074 63.158 0.00 0.00 0.00 4.85
146 147 0.472734 CCTCCATCCCCTACCTCCAG 60.473 65.000 0.00 0.00 0.00 3.86
147 148 1.632164 CCTCCATCCCCTACCTCCA 59.368 63.158 0.00 0.00 0.00 3.86
148 149 1.843832 GCCTCCATCCCCTACCTCC 60.844 68.421 0.00 0.00 0.00 4.30
149 150 2.210711 CGCCTCCATCCCCTACCTC 61.211 68.421 0.00 0.00 0.00 3.85
150 151 2.122813 CGCCTCCATCCCCTACCT 60.123 66.667 0.00 0.00 0.00 3.08
151 152 2.446036 ACGCCTCCATCCCCTACC 60.446 66.667 0.00 0.00 0.00 3.18
152 153 0.757935 TACACGCCTCCATCCCCTAC 60.758 60.000 0.00 0.00 0.00 3.18
153 154 0.031917 TTACACGCCTCCATCCCCTA 60.032 55.000 0.00 0.00 0.00 3.53
154 155 1.306654 TTACACGCCTCCATCCCCT 60.307 57.895 0.00 0.00 0.00 4.79
155 156 1.146263 CTTACACGCCTCCATCCCC 59.854 63.158 0.00 0.00 0.00 4.81
156 157 1.146263 CCTTACACGCCTCCATCCC 59.854 63.158 0.00 0.00 0.00 3.85
157 158 0.539986 TTCCTTACACGCCTCCATCC 59.460 55.000 0.00 0.00 0.00 3.51
158 159 1.473434 CCTTCCTTACACGCCTCCATC 60.473 57.143 0.00 0.00 0.00 3.51
159 160 0.541863 CCTTCCTTACACGCCTCCAT 59.458 55.000 0.00 0.00 0.00 3.41
160 161 0.543410 TCCTTCCTTACACGCCTCCA 60.543 55.000 0.00 0.00 0.00 3.86
161 162 0.175989 CTCCTTCCTTACACGCCTCC 59.824 60.000 0.00 0.00 0.00 4.30
162 163 1.183549 TCTCCTTCCTTACACGCCTC 58.816 55.000 0.00 0.00 0.00 4.70
163 164 1.550976 CTTCTCCTTCCTTACACGCCT 59.449 52.381 0.00 0.00 0.00 5.52
164 165 1.405661 CCTTCTCCTTCCTTACACGCC 60.406 57.143 0.00 0.00 0.00 5.68
165 166 1.405661 CCCTTCTCCTTCCTTACACGC 60.406 57.143 0.00 0.00 0.00 5.34
166 167 1.207329 CCCCTTCTCCTTCCTTACACG 59.793 57.143 0.00 0.00 0.00 4.49
167 168 2.547990 TCCCCTTCTCCTTCCTTACAC 58.452 52.381 0.00 0.00 0.00 2.90
168 169 3.115390 CATCCCCTTCTCCTTCCTTACA 58.885 50.000 0.00 0.00 0.00 2.41
169 170 2.158740 GCATCCCCTTCTCCTTCCTTAC 60.159 54.545 0.00 0.00 0.00 2.34
170 171 2.127708 GCATCCCCTTCTCCTTCCTTA 58.872 52.381 0.00 0.00 0.00 2.69
171 172 0.922626 GCATCCCCTTCTCCTTCCTT 59.077 55.000 0.00 0.00 0.00 3.36
172 173 1.341156 CGCATCCCCTTCTCCTTCCT 61.341 60.000 0.00 0.00 0.00 3.36
173 174 1.147153 CGCATCCCCTTCTCCTTCC 59.853 63.158 0.00 0.00 0.00 3.46
174 175 1.524849 GCGCATCCCCTTCTCCTTC 60.525 63.158 0.30 0.00 0.00 3.46
175 176 2.592308 GCGCATCCCCTTCTCCTT 59.408 61.111 0.30 0.00 0.00 3.36
176 177 3.854669 CGCGCATCCCCTTCTCCT 61.855 66.667 8.75 0.00 0.00 3.69
177 178 4.918201 CCGCGCATCCCCTTCTCC 62.918 72.222 8.75 0.00 0.00 3.71
178 179 4.918201 CCCGCGCATCCCCTTCTC 62.918 72.222 8.75 0.00 0.00 2.87
195 196 4.980903 CCACGCTGGCAAACACGC 62.981 66.667 0.00 0.00 0.00 5.34
240 241 4.832767 GTTTAGAAACGGCGCACC 57.167 55.556 10.83 0.00 0.00 5.01
245 246 7.399098 ATTCTAGGGAATCGTTTAGAAACGGC 61.399 42.308 23.14 14.42 45.30 5.68
246 247 6.018994 CATTCTAGGGAATCGTTTAGAAACGG 60.019 42.308 23.14 8.29 46.11 4.44
247 248 6.755141 TCATTCTAGGGAATCGTTTAGAAACG 59.245 38.462 18.97 18.97 45.50 3.60
248 249 7.764901 AGTCATTCTAGGGAATCGTTTAGAAAC 59.235 37.037 0.00 0.00 39.87 2.78
249 250 7.848128 AGTCATTCTAGGGAATCGTTTAGAAA 58.152 34.615 0.00 0.00 39.87 2.52
250 251 7.419711 AGTCATTCTAGGGAATCGTTTAGAA 57.580 36.000 0.00 3.46 39.87 2.10
251 252 7.419711 AAGTCATTCTAGGGAATCGTTTAGA 57.580 36.000 0.00 0.00 39.87 2.10
252 253 7.224949 GGAAAGTCATTCTAGGGAATCGTTTAG 59.775 40.741 0.00 0.00 39.87 1.85
253 254 7.046033 GGAAAGTCATTCTAGGGAATCGTTTA 58.954 38.462 0.00 0.00 39.87 2.01
254 255 5.880887 GGAAAGTCATTCTAGGGAATCGTTT 59.119 40.000 0.00 0.00 39.87 3.60
255 256 5.189934 AGGAAAGTCATTCTAGGGAATCGTT 59.810 40.000 0.00 0.00 39.87 3.85
256 257 4.717280 AGGAAAGTCATTCTAGGGAATCGT 59.283 41.667 0.00 0.00 39.87 3.73
257 258 5.283457 AGGAAAGTCATTCTAGGGAATCG 57.717 43.478 0.00 0.00 39.87 3.34
258 259 6.058833 GGAAGGAAAGTCATTCTAGGGAATC 58.941 44.000 3.04 0.00 39.87 2.52
259 260 5.733647 AGGAAGGAAAGTCATTCTAGGGAAT 59.266 40.000 3.04 0.00 42.29 3.01
260 261 5.101529 AGGAAGGAAAGTCATTCTAGGGAA 58.898 41.667 3.04 0.00 37.34 3.97
261 262 4.699994 AGGAAGGAAAGTCATTCTAGGGA 58.300 43.478 3.04 0.00 37.34 4.20
262 263 4.141597 GGAGGAAGGAAAGTCATTCTAGGG 60.142 50.000 3.04 0.00 37.34 3.53
263 264 4.471386 TGGAGGAAGGAAAGTCATTCTAGG 59.529 45.833 3.04 0.00 37.34 3.02
264 265 5.423886 GTGGAGGAAGGAAAGTCATTCTAG 58.576 45.833 3.04 0.00 37.34 2.43
265 266 4.225267 GGTGGAGGAAGGAAAGTCATTCTA 59.775 45.833 3.04 0.00 37.34 2.10
266 267 3.009584 GGTGGAGGAAGGAAAGTCATTCT 59.990 47.826 3.04 0.00 37.34 2.40
267 268 3.244911 TGGTGGAGGAAGGAAAGTCATTC 60.245 47.826 0.00 0.00 36.54 2.67
268 269 2.716424 TGGTGGAGGAAGGAAAGTCATT 59.284 45.455 0.00 0.00 0.00 2.57
269 270 2.040412 GTGGTGGAGGAAGGAAAGTCAT 59.960 50.000 0.00 0.00 0.00 3.06
270 271 1.420138 GTGGTGGAGGAAGGAAAGTCA 59.580 52.381 0.00 0.00 0.00 3.41
271 272 1.608283 CGTGGTGGAGGAAGGAAAGTC 60.608 57.143 0.00 0.00 0.00 3.01
272 273 0.396811 CGTGGTGGAGGAAGGAAAGT 59.603 55.000 0.00 0.00 0.00 2.66
384 405 1.484356 CGTAGAATTTACTCCGCGGG 58.516 55.000 27.83 18.67 0.00 6.13
523 570 0.250081 GGAGGAGGAGGCGCTATTTG 60.250 60.000 7.64 0.00 0.00 2.32
527 574 4.541648 GGGGAGGAGGAGGCGCTA 62.542 72.222 7.64 0.00 0.00 4.26
744 793 0.178981 TGCTTGCTTCTTCTTGCCCT 60.179 50.000 0.00 0.00 0.00 5.19
745 794 0.243095 CTGCTTGCTTCTTCTTGCCC 59.757 55.000 0.00 0.00 0.00 5.36
746 795 0.388263 GCTGCTTGCTTCTTCTTGCC 60.388 55.000 0.00 0.00 38.95 4.52
747 796 0.313043 TGCTGCTTGCTTCTTCTTGC 59.687 50.000 0.00 0.00 43.37 4.01
748 797 1.662309 CGTGCTGCTTGCTTCTTCTTG 60.662 52.381 0.00 0.00 43.37 3.02
749 798 0.590195 CGTGCTGCTTGCTTCTTCTT 59.410 50.000 0.00 0.00 43.37 2.52
750 799 0.250038 TCGTGCTGCTTGCTTCTTCT 60.250 50.000 0.00 0.00 43.37 2.85
751 800 0.165511 CTCGTGCTGCTTGCTTCTTC 59.834 55.000 0.00 0.00 43.37 2.87
752 801 1.849976 GCTCGTGCTGCTTGCTTCTT 61.850 55.000 1.41 0.00 43.37 2.52
753 802 2.323580 GCTCGTGCTGCTTGCTTCT 61.324 57.895 1.41 0.00 43.37 2.85
754 803 2.175322 GCTCGTGCTGCTTGCTTC 59.825 61.111 1.41 0.00 43.37 3.86
755 804 2.592574 TGCTCGTGCTGCTTGCTT 60.593 55.556 11.19 0.00 43.37 3.91
756 805 3.048475 CTGCTCGTGCTGCTTGCT 61.048 61.111 11.19 0.00 43.37 3.91
851 900 2.202987 GAGCTGGGGCACATCTCG 60.203 66.667 4.65 0.00 41.70 4.04
912 965 7.068348 ACCTAAAGAAGAGAGGAAACAAAAACC 59.932 37.037 0.00 0.00 34.24 3.27
937 993 5.154222 CCCGCAAAGATCTAGAAACAAAAC 58.846 41.667 0.00 0.00 0.00 2.43
957 1013 0.525668 CTGGACGAATTCGAGACCCG 60.526 60.000 33.05 22.05 43.02 5.28
975 1031 1.657162 TCCCTCCTTCCTACAATCCCT 59.343 52.381 0.00 0.00 0.00 4.20
976 1032 2.191981 TCCCTCCTTCCTACAATCCC 57.808 55.000 0.00 0.00 0.00 3.85
977 1033 4.227527 TCTTTTCCCTCCTTCCTACAATCC 59.772 45.833 0.00 0.00 0.00 3.01
978 1034 5.437191 TCTTTTCCCTCCTTCCTACAATC 57.563 43.478 0.00 0.00 0.00 2.67
979 1035 5.340360 CCATCTTTTCCCTCCTTCCTACAAT 60.340 44.000 0.00 0.00 0.00 2.71
980 1036 4.018415 CCATCTTTTCCCTCCTTCCTACAA 60.018 45.833 0.00 0.00 0.00 2.41
981 1037 3.523564 CCATCTTTTCCCTCCTTCCTACA 59.476 47.826 0.00 0.00 0.00 2.74
982 1038 3.117851 CCCATCTTTTCCCTCCTTCCTAC 60.118 52.174 0.00 0.00 0.00 3.18
983 1039 3.123273 CCCATCTTTTCCCTCCTTCCTA 58.877 50.000 0.00 0.00 0.00 2.94
984 1040 1.925959 CCCATCTTTTCCCTCCTTCCT 59.074 52.381 0.00 0.00 0.00 3.36
987 1043 0.034089 CGCCCATCTTTTCCCTCCTT 60.034 55.000 0.00 0.00 0.00 3.36
989 1045 0.748367 GACGCCCATCTTTTCCCTCC 60.748 60.000 0.00 0.00 0.00 4.30
991 1047 0.404040 TTGACGCCCATCTTTTCCCT 59.596 50.000 0.00 0.00 0.00 4.20
993 1049 0.811281 CCTTGACGCCCATCTTTTCC 59.189 55.000 0.00 0.00 0.00 3.13
995 1051 0.404040 TCCCTTGACGCCCATCTTTT 59.596 50.000 0.00 0.00 0.00 2.27
996 1052 0.625849 ATCCCTTGACGCCCATCTTT 59.374 50.000 0.00 0.00 0.00 2.52
1617 1683 3.774528 TAGGTGGCCAGCTGCGAG 61.775 66.667 40.83 0.00 42.61 5.03
1953 2019 0.391597 AGAACTCGGCGTCCTTGAAA 59.608 50.000 6.85 0.00 0.00 2.69
1964 2030 1.662629 CTGCACTGCATTAGAACTCGG 59.337 52.381 3.64 0.00 38.13 4.63
2004 2075 4.964593 TGTCGTCATCATCATCATGGATT 58.035 39.130 0.00 0.00 0.00 3.01
2019 2090 4.373116 GGCGGCCTCTTGTCGTCA 62.373 66.667 12.87 0.00 0.00 4.35
2023 2094 0.749454 ATCAATGGCGGCCTCTTGTC 60.749 55.000 21.46 0.00 0.00 3.18
2025 2096 1.731700 CATCAATGGCGGCCTCTTG 59.268 57.895 21.46 21.46 0.00 3.02
2105 2176 5.465390 TCGATCAAATCCATCCGAATACAAC 59.535 40.000 0.00 0.00 0.00 3.32
2164 2235 7.754027 GGAAGATTCTCAAAGTTGACATTCATG 59.246 37.037 0.00 0.00 32.90 3.07
2218 2289 7.331193 CCAGTAATAGTCTATTCGGTAATTGGC 59.669 40.741 8.41 0.00 0.00 4.52
2227 2298 5.473931 AGCATGCCAGTAATAGTCTATTCG 58.526 41.667 15.66 0.00 0.00 3.34
2258 2329 9.897349 CGTTTCGGAATTCTTAAATTAGTACTC 57.103 33.333 0.00 0.00 35.21 2.59
2278 2353 7.972527 AGAGTACTATATATACTGCCGTTTCG 58.027 38.462 0.00 0.00 32.93 3.46
2293 2368 7.434492 GCATCCTTGTTGCTTAGAGTACTATA 58.566 38.462 0.00 0.00 37.14 1.31
2294 2369 6.284459 GCATCCTTGTTGCTTAGAGTACTAT 58.716 40.000 0.00 0.00 37.14 2.12
2295 2370 5.661458 GCATCCTTGTTGCTTAGAGTACTA 58.339 41.667 0.00 0.00 37.14 1.82
2296 2371 4.508662 GCATCCTTGTTGCTTAGAGTACT 58.491 43.478 0.00 0.00 37.14 2.73
2297 2372 3.307242 CGCATCCTTGTTGCTTAGAGTAC 59.693 47.826 0.00 0.00 37.96 2.73
2298 2373 3.521560 CGCATCCTTGTTGCTTAGAGTA 58.478 45.455 0.00 0.00 37.96 2.59
2299 2374 2.350522 CGCATCCTTGTTGCTTAGAGT 58.649 47.619 0.00 0.00 37.96 3.24
2300 2375 1.063174 GCGCATCCTTGTTGCTTAGAG 59.937 52.381 0.30 0.00 37.96 2.43
2301 2376 1.086696 GCGCATCCTTGTTGCTTAGA 58.913 50.000 0.30 0.00 37.96 2.10
2302 2377 1.089920 AGCGCATCCTTGTTGCTTAG 58.910 50.000 11.47 0.00 37.96 2.18
2363 2440 2.440539 AATATAAGGAGTCGGCAGCG 57.559 50.000 0.00 0.00 0.00 5.18
2378 2455 9.289782 GAGGAGCAGTGGATTATTTTGTAATAT 57.710 33.333 0.00 0.00 0.00 1.28
2391 2481 0.257328 TCGAGAGAGGAGCAGTGGAT 59.743 55.000 0.00 0.00 34.84 3.41
2476 2593 2.033194 GTATATTCCGCTGGGCCGC 61.033 63.158 9.82 9.82 0.00 6.53
2524 2641 1.383456 TATGTTCCTGCCGGCATTGC 61.383 55.000 32.87 20.17 0.00 3.56
2571 2699 2.550208 GGTGGGTACATTCGGGATGATC 60.550 54.545 2.58 0.00 39.15 2.92
2585 2716 1.482748 GGTTGGAACCGAGGTGGGTA 61.483 60.000 0.00 0.00 38.35 3.69
2630 5115 2.697761 CCTGTGATGTGCTGCTGGC 61.698 63.158 0.00 0.00 42.22 4.85
2677 5204 0.811281 AGATTAGGTTTGCGCTTGCC 59.189 50.000 9.73 7.82 38.03 4.52
2678 5205 1.202188 GGAGATTAGGTTTGCGCTTGC 60.202 52.381 9.73 0.00 39.78 4.01
2679 5206 2.083774 TGGAGATTAGGTTTGCGCTTG 58.916 47.619 9.73 0.00 0.00 4.01
2680 5207 2.084546 GTGGAGATTAGGTTTGCGCTT 58.915 47.619 9.73 0.00 0.00 4.68
2681 5208 1.003118 TGTGGAGATTAGGTTTGCGCT 59.997 47.619 9.73 0.00 0.00 5.92
2682 5209 1.448985 TGTGGAGATTAGGTTTGCGC 58.551 50.000 0.00 0.00 0.00 6.09
2683 5210 3.270027 TGATGTGGAGATTAGGTTTGCG 58.730 45.455 0.00 0.00 0.00 4.85
2684 5211 3.065925 GCTGATGTGGAGATTAGGTTTGC 59.934 47.826 0.00 0.00 0.00 3.68
2686 5213 4.574674 TGCTGATGTGGAGATTAGGTTT 57.425 40.909 0.00 0.00 0.00 3.27
2695 5258 1.400846 GACTTGCATGCTGATGTGGAG 59.599 52.381 20.33 6.35 31.50 3.86
2708 5271 0.389296 CCGGTACATGTCGACTTGCA 60.389 55.000 26.26 14.66 0.00 4.08
2709 5272 1.693083 GCCGGTACATGTCGACTTGC 61.693 60.000 26.26 13.92 0.00 4.01
2731 5294 3.727970 GCAAAGAACAATTCGTCGATCCC 60.728 47.826 0.00 0.00 34.02 3.85
2732 5295 3.417185 GCAAAGAACAATTCGTCGATCC 58.583 45.455 0.00 0.00 34.02 3.36
2765 5328 1.202043 CGTGTACTACTCCAGCACTCG 60.202 57.143 0.00 0.00 32.85 4.18
2770 5333 2.541999 GCAGATCGTGTACTACTCCAGC 60.542 54.545 0.00 0.00 0.00 4.85
2771 5334 2.286477 CGCAGATCGTGTACTACTCCAG 60.286 54.545 0.00 0.00 0.00 3.86
2773 5336 1.002684 CCGCAGATCGTGTACTACTCC 60.003 57.143 0.00 0.00 36.19 3.85
2774 5337 1.002684 CCCGCAGATCGTGTACTACTC 60.003 57.143 0.00 0.00 36.19 2.59
2776 5339 0.030369 CCCCGCAGATCGTGTACTAC 59.970 60.000 0.00 0.00 36.19 2.73
2777 5340 1.105167 CCCCCGCAGATCGTGTACTA 61.105 60.000 0.00 0.00 36.19 1.82
2779 5342 1.952102 TTCCCCCGCAGATCGTGTAC 61.952 60.000 0.00 0.00 36.19 2.90
2780 5343 1.672854 CTTCCCCCGCAGATCGTGTA 61.673 60.000 0.00 0.00 36.19 2.90
2781 5344 3.000819 TTCCCCCGCAGATCGTGT 61.001 61.111 0.00 0.00 36.19 4.49
2782 5345 2.202932 CTTCCCCCGCAGATCGTG 60.203 66.667 0.00 0.00 36.19 4.35
2784 5347 4.241555 CCCTTCCCCCGCAGATCG 62.242 72.222 0.00 0.00 38.08 3.69
2786 5349 3.411517 CACCCTTCCCCCGCAGAT 61.412 66.667 0.00 0.00 0.00 2.90
2787 5350 4.974438 ACACCCTTCCCCCGCAGA 62.974 66.667 0.00 0.00 0.00 4.26
2788 5351 4.410400 GACACCCTTCCCCCGCAG 62.410 72.222 0.00 0.00 0.00 5.18
2790 5353 3.920093 CTTGACACCCTTCCCCCGC 62.920 68.421 0.00 0.00 0.00 6.13
2793 5356 1.074951 CCACTTGACACCCTTCCCC 59.925 63.158 0.00 0.00 0.00 4.81
2794 5357 1.603739 GCCACTTGACACCCTTCCC 60.604 63.158 0.00 0.00 0.00 3.97
2796 5359 0.668535 GTTGCCACTTGACACCCTTC 59.331 55.000 0.00 0.00 0.00 3.46
2843 5419 5.406780 CACTGTCAACCTTAACTGCTCTTAG 59.593 44.000 0.00 0.00 0.00 2.18
2848 5424 2.222027 GCACTGTCAACCTTAACTGCT 58.778 47.619 0.00 0.00 0.00 4.24
2871 5447 2.285442 ACCCCCGGGAGAAAGGAG 60.285 66.667 26.32 1.13 38.96 3.69
2872 5448 2.609610 CACCCCCGGGAGAAAGGA 60.610 66.667 26.32 0.00 38.96 3.36
2873 5449 3.728373 CCACCCCCGGGAGAAAGG 61.728 72.222 26.32 17.48 38.96 3.11
2902 5478 4.025401 CCGCAACCAAGTCGGCAC 62.025 66.667 0.00 0.00 39.03 5.01
2950 5526 4.016706 CCGGGTCTGGTGGTGGAC 62.017 72.222 0.00 0.00 0.00 4.02
2953 5529 2.052047 AAAGTCCGGGTCTGGTGGTG 62.052 60.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.