Multiple sequence alignment - TraesCS3B01G327100

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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 TraesCS3B01G327100 chr3B 100.000 1964 0 0 688 2651 527727693 527729656 0.000000e+00 3627.0
1 TraesCS3B01G327100 chr3B 100.000 338 0 0 1 338 527727006 527727343 2.240000e-175 625.0
2 TraesCS3B01G327100 chr3D 91.771 1908 104 17 697 2583 402348343 402350218 0.000000e+00 2604.0
3 TraesCS3B01G327100 chr3D 89.349 169 11 5 177 338 402348095 402348263 3.460000e-49 206.0
4 TraesCS3B01G327100 chr3D 95.349 43 2 0 177 219 402347956 402347998 4.740000e-08 69.4
5 TraesCS3B01G327100 chr3A 96.277 1316 41 3 689 1996 523157721 523159036 0.000000e+00 2152.0
6 TraesCS3B01G327100 chr3A 90.000 560 37 12 2025 2583 523159035 523159576 0.000000e+00 706.0
7 TraesCS3B01G327100 chr3A 92.063 126 4 4 219 338 523157523 523157648 3.510000e-39 172.0
8 TraesCS3B01G327100 chr5B 95.376 173 8 0 1 173 439263877 439263705 2.600000e-70 276.0
9 TraesCS3B01G327100 chr5B 100.000 68 0 0 2583 2650 690095353 690095286 2.770000e-25 126.0
10 TraesCS3B01G327100 chr5B 100.000 67 0 0 2585 2651 256611729 256611663 9.960000e-25 124.0
11 TraesCS3B01G327100 chr1B 95.882 170 7 0 1 170 495804132 495803963 2.600000e-70 276.0
12 TraesCS3B01G327100 chr1B 95.376 173 8 0 1 173 666981335 666981163 2.600000e-70 276.0
13 TraesCS3B01G327100 chr1B 95.266 169 8 0 1 169 687415060 687415228 4.350000e-68 268.0
14 TraesCS3B01G327100 chr1B 98.611 72 0 1 2581 2651 28419961 28419890 2.770000e-25 126.0
15 TraesCS3B01G327100 chr4B 95.858 169 7 0 1 169 178850142 178849974 9.350000e-70 274.0
16 TraesCS3B01G327100 chr4B 95.294 170 8 0 1 170 79528717 79528886 1.210000e-68 270.0
17 TraesCS3B01G327100 chr2B 95.858 169 7 0 1 169 583409882 583409714 9.350000e-70 274.0
18 TraesCS3B01G327100 chr6A 95.266 169 8 0 1 169 922230 922398 4.350000e-68 268.0
19 TraesCS3B01G327100 chr6A 100.000 70 0 0 2582 2651 518672837 518672906 2.140000e-26 130.0
20 TraesCS3B01G327100 chr5A 94.253 174 10 0 1 174 383894656 383894829 1.560000e-67 267.0
21 TraesCS3B01G327100 chr5A 100.000 68 0 0 2584 2651 50751204 50751137 2.770000e-25 126.0
22 TraesCS3B01G327100 chr5A 98.485 66 1 0 2586 2651 441161174 441161109 1.670000e-22 117.0
23 TraesCS3B01G327100 chr7A 100.000 67 0 0 2585 2651 211797791 211797725 9.960000e-25 124.0
24 TraesCS3B01G327100 chr4A 100.000 67 0 0 2585 2651 135451588 135451654 9.960000e-25 124.0
25 TraesCS3B01G327100 chr1A 100.000 67 0 0 2585 2651 478156115 478156049 9.960000e-25 124.0


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 TraesCS3B01G327100 chr3B 527727006 527729656 2650 False 2126.0 3627 100.000000 1 2651 2 chr3B.!!$F1 2650
1 TraesCS3B01G327100 chr3D 402347956 402350218 2262 False 959.8 2604 92.156333 177 2583 3 chr3D.!!$F1 2406
2 TraesCS3B01G327100 chr3A 523157523 523159576 2053 False 1010.0 2152 92.780000 219 2583 3 chr3A.!!$F1 2364

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
91 92 0.478507 AGTCCCAGGAACCAAACAGG 59.521 55.0 0.0 0.0 45.67 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 1953 0.032678 CCACACCGGCAGCTAGATAG 59.967 60.0 0.0 0.0 0.0 2.08 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
25 26 5.683876 TGAAATAAGACTCTCAAGGAGGG 57.316 43.478 0.00 0.00 45.83 4.30
26 27 5.342017 TGAAATAAGACTCTCAAGGAGGGA 58.658 41.667 0.00 0.00 45.83 4.20
27 28 5.187967 TGAAATAAGACTCTCAAGGAGGGAC 59.812 44.000 0.00 0.00 45.83 4.46
28 29 4.618378 ATAAGACTCTCAAGGAGGGACT 57.382 45.455 0.00 0.00 45.83 3.85
29 30 3.268034 AAGACTCTCAAGGAGGGACTT 57.732 47.619 5.25 5.25 45.83 3.01
30 31 4.405756 AAGACTCTCAAGGAGGGACTTA 57.594 45.455 8.68 0.00 41.64 2.24
31 32 4.618378 AGACTCTCAAGGAGGGACTTAT 57.382 45.455 0.00 0.00 45.83 1.73
32 33 5.735733 AGACTCTCAAGGAGGGACTTATA 57.264 43.478 0.00 0.00 45.83 0.98
33 34 5.701224 AGACTCTCAAGGAGGGACTTATAG 58.299 45.833 0.00 0.00 45.83 1.31
34 35 4.810345 ACTCTCAAGGAGGGACTTATAGG 58.190 47.826 0.00 0.00 45.83 2.57
35 36 4.482772 ACTCTCAAGGAGGGACTTATAGGA 59.517 45.833 0.00 0.00 45.83 2.94
36 37 5.043281 ACTCTCAAGGAGGGACTTATAGGAA 60.043 44.000 0.00 0.00 45.83 3.36
37 38 5.209659 TCTCAAGGAGGGACTTATAGGAAC 58.790 45.833 0.00 0.00 41.55 3.62
38 39 5.043281 TCTCAAGGAGGGACTTATAGGAACT 60.043 44.000 0.00 0.00 41.55 3.01
39 40 5.600749 TCAAGGAGGGACTTATAGGAACTT 58.399 41.667 0.00 0.00 41.55 2.66
40 41 6.748969 TCAAGGAGGGACTTATAGGAACTTA 58.251 40.000 0.00 0.00 41.55 2.24
41 42 7.371043 TCAAGGAGGGACTTATAGGAACTTAT 58.629 38.462 0.00 0.00 41.55 1.73
42 43 8.517047 TCAAGGAGGGACTTATAGGAACTTATA 58.483 37.037 0.00 0.00 41.55 0.98
43 44 8.808092 CAAGGAGGGACTTATAGGAACTTATAG 58.192 40.741 0.00 0.00 41.55 1.31
44 45 8.071235 AGGAGGGACTTATAGGAACTTATAGT 57.929 38.462 0.00 0.00 41.55 2.12
45 46 8.521301 AGGAGGGACTTATAGGAACTTATAGTT 58.479 37.037 0.00 0.00 41.55 2.24
46 47 8.586744 GGAGGGACTTATAGGAACTTATAGTTG 58.413 40.741 0.00 0.00 41.55 3.16
47 48 9.145442 GAGGGACTTATAGGAACTTATAGTTGT 57.855 37.037 0.00 0.00 41.55 3.32
68 69 9.448587 AGTTGTAATATGGTCTTATAGGGACTT 57.551 33.333 7.52 0.00 41.75 3.01
87 88 5.853572 ACTTATAAGTCCCAGGAACCAAA 57.146 39.130 12.50 0.00 32.86 3.28
88 89 5.567430 ACTTATAAGTCCCAGGAACCAAAC 58.433 41.667 12.50 0.00 32.86 2.93
89 90 5.073965 ACTTATAAGTCCCAGGAACCAAACA 59.926 40.000 12.50 0.00 32.86 2.83
90 91 2.364972 AAGTCCCAGGAACCAAACAG 57.635 50.000 0.00 0.00 0.00 3.16
91 92 0.478507 AGTCCCAGGAACCAAACAGG 59.521 55.000 0.00 0.00 45.67 4.00
107 108 7.203255 CCAAACAGGTAAGGACTTTTTAGAG 57.797 40.000 0.00 0.00 0.00 2.43
108 109 6.996282 CCAAACAGGTAAGGACTTTTTAGAGA 59.004 38.462 0.00 0.00 0.00 3.10
109 110 7.041303 CCAAACAGGTAAGGACTTTTTAGAGAC 60.041 40.741 0.00 0.00 0.00 3.36
110 111 6.997942 ACAGGTAAGGACTTTTTAGAGACT 57.002 37.500 0.00 0.00 0.00 3.24
111 112 7.376335 ACAGGTAAGGACTTTTTAGAGACTT 57.624 36.000 0.00 0.00 0.00 3.01
112 113 7.803131 ACAGGTAAGGACTTTTTAGAGACTTT 58.197 34.615 0.00 0.00 0.00 2.66
113 114 7.715686 ACAGGTAAGGACTTTTTAGAGACTTTG 59.284 37.037 0.00 0.00 0.00 2.77
114 115 7.173390 CAGGTAAGGACTTTTTAGAGACTTTGG 59.827 40.741 0.00 0.00 0.00 3.28
115 116 7.072076 AGGTAAGGACTTTTTAGAGACTTTGGA 59.928 37.037 0.00 0.00 0.00 3.53
116 117 7.172875 GGTAAGGACTTTTTAGAGACTTTGGAC 59.827 40.741 0.00 0.00 0.00 4.02
117 118 6.502074 AGGACTTTTTAGAGACTTTGGACT 57.498 37.500 0.00 0.00 0.00 3.85
118 119 6.901300 AGGACTTTTTAGAGACTTTGGACTT 58.099 36.000 0.00 0.00 0.00 3.01
119 120 8.030913 AGGACTTTTTAGAGACTTTGGACTTA 57.969 34.615 0.00 0.00 0.00 2.24
120 121 8.661345 AGGACTTTTTAGAGACTTTGGACTTAT 58.339 33.333 0.00 0.00 0.00 1.73
121 122 9.939802 GGACTTTTTAGAGACTTTGGACTTATA 57.060 33.333 0.00 0.00 0.00 0.98
127 128 9.720769 TTTAGAGACTTTGGACTTATAAGTTGG 57.279 33.333 18.96 10.07 39.88 3.77
128 129 6.712276 AGAGACTTTGGACTTATAAGTTGGG 58.288 40.000 18.96 10.37 39.88 4.12
129 130 6.500751 AGAGACTTTGGACTTATAAGTTGGGA 59.499 38.462 18.96 6.15 39.88 4.37
130 131 6.473758 AGACTTTGGACTTATAAGTTGGGAC 58.526 40.000 18.96 6.19 39.88 4.46
131 132 6.272558 AGACTTTGGACTTATAAGTTGGGACT 59.727 38.462 18.96 10.11 39.88 3.85
132 133 7.456902 AGACTTTGGACTTATAAGTTGGGACTA 59.543 37.037 18.96 1.74 39.88 2.59
133 134 7.981142 ACTTTGGACTTATAAGTTGGGACTAA 58.019 34.615 18.96 7.60 39.88 2.24
134 135 8.442374 ACTTTGGACTTATAAGTTGGGACTAAA 58.558 33.333 18.96 13.80 39.88 1.85
135 136 9.292195 CTTTGGACTTATAAGTTGGGACTAAAA 57.708 33.333 18.96 9.70 39.88 1.52
136 137 9.643735 TTTGGACTTATAAGTTGGGACTAAAAA 57.356 29.630 18.96 7.28 39.88 1.94
165 166 9.110502 GTCTTAGGACTTATAAATCAAACAGGG 57.889 37.037 0.00 0.00 39.24 4.45
166 167 7.773690 TCTTAGGACTTATAAATCAAACAGGGC 59.226 37.037 0.00 0.00 0.00 5.19
167 168 5.201243 AGGACTTATAAATCAAACAGGGCC 58.799 41.667 0.00 0.00 0.00 5.80
168 169 5.044105 AGGACTTATAAATCAAACAGGGCCT 60.044 40.000 0.00 0.00 0.00 5.19
169 170 5.656859 GGACTTATAAATCAAACAGGGCCTT 59.343 40.000 1.32 0.00 0.00 4.35
170 171 6.405842 GGACTTATAAATCAAACAGGGCCTTG 60.406 42.308 14.35 14.35 0.00 3.61
171 172 6.252995 ACTTATAAATCAAACAGGGCCTTGA 58.747 36.000 23.57 14.81 36.08 3.02
172 173 6.897413 ACTTATAAATCAAACAGGGCCTTGAT 59.103 34.615 23.57 16.51 42.67 2.57
174 175 4.541973 AAATCAAACAGGGCCTTGATTC 57.458 40.909 24.90 0.00 46.52 2.52
175 176 1.533625 TCAAACAGGGCCTTGATTCG 58.466 50.000 23.57 10.81 0.00 3.34
176 177 1.202879 TCAAACAGGGCCTTGATTCGT 60.203 47.619 23.57 0.00 0.00 3.85
177 178 2.039216 TCAAACAGGGCCTTGATTCGTA 59.961 45.455 23.57 0.97 0.00 3.43
178 179 2.817258 CAAACAGGGCCTTGATTCGTAA 59.183 45.455 23.57 0.00 0.00 3.18
179 180 2.403252 ACAGGGCCTTGATTCGTAAG 57.597 50.000 23.57 0.00 0.00 2.34
180 181 1.017387 CAGGGCCTTGATTCGTAAGC 58.983 55.000 9.80 0.00 37.18 3.09
186 187 0.652592 CTTGATTCGTAAGCAGGGCG 59.347 55.000 0.00 0.00 37.18 6.13
221 361 1.480545 TGAATCACCACACGGATCGAT 59.519 47.619 0.00 0.00 35.59 3.59
293 434 2.575111 CTTGATCGCTCGCAGCTCG 61.575 63.158 6.58 0.00 39.60 5.03
323 470 3.624726 CGAGACTTACGCAAATGTCTG 57.375 47.619 8.14 0.27 39.53 3.51
822 974 1.006571 GCGAACGGAGACCAGACAA 60.007 57.895 0.00 0.00 0.00 3.18
901 1053 2.034879 CACGACGCTTCCATGGCTT 61.035 57.895 6.96 0.00 0.00 4.35
1236 1388 3.598715 AACGTCGTGCCGGAGACA 61.599 61.111 20.00 1.43 37.23 3.41
1610 1768 1.801913 CCGAGAAGCAGAACGACGG 60.802 63.158 0.00 0.00 0.00 4.79
1659 1820 4.504461 CAGTACAATCCATGAGTAAGACGC 59.496 45.833 0.00 0.00 0.00 5.19
1677 1838 1.538075 CGCATACGAGGGGTTTGTTTT 59.462 47.619 0.00 0.00 43.93 2.43
1687 1848 1.326245 GGGTTTGTTTTTGCTTGCGAC 59.674 47.619 0.00 0.00 0.00 5.19
1790 1951 6.015856 GCTACTTCTACTATGCTGAAGGATGA 60.016 42.308 0.00 0.00 40.83 2.92
1791 1952 6.403866 ACTTCTACTATGCTGAAGGATGAG 57.596 41.667 0.00 0.00 40.83 2.90
1792 1953 4.862902 TCTACTATGCTGAAGGATGAGC 57.137 45.455 0.00 0.00 35.65 4.26
1793 1954 4.478203 TCTACTATGCTGAAGGATGAGCT 58.522 43.478 0.00 0.00 36.11 4.09
1794 1955 5.635120 TCTACTATGCTGAAGGATGAGCTA 58.365 41.667 0.00 0.00 36.11 3.32
1795 1956 6.252233 TCTACTATGCTGAAGGATGAGCTAT 58.748 40.000 0.00 0.00 36.11 2.97
1796 1957 5.404466 ACTATGCTGAAGGATGAGCTATC 57.596 43.478 0.00 0.00 36.11 2.08
1797 1958 5.085920 ACTATGCTGAAGGATGAGCTATCT 58.914 41.667 0.00 0.00 36.11 1.98
1958 2134 6.003326 TGTGCCAGAATGAAGAAAATAGTGA 58.997 36.000 0.00 0.00 39.69 3.41
1962 2138 5.649395 CCAGAATGAAGAAAATAGTGAGGCA 59.351 40.000 0.00 0.00 39.69 4.75
2003 2179 2.358898 GGCATGATTGGTTTAGTCGCAT 59.641 45.455 0.00 0.00 0.00 4.73
2004 2180 3.365832 GCATGATTGGTTTAGTCGCATG 58.634 45.455 0.00 0.00 35.87 4.06
2012 2194 8.556194 TGATTGGTTTAGTCGCATGTATATTTC 58.444 33.333 0.00 0.00 0.00 2.17
2014 2196 6.588204 TGGTTTAGTCGCATGTATATTTCCT 58.412 36.000 0.00 0.00 0.00 3.36
2016 2198 6.482308 GGTTTAGTCGCATGTATATTTCCTGT 59.518 38.462 0.00 0.00 0.00 4.00
2024 2206 2.769663 TGTATATTTCCTGTGTCCGCCT 59.230 45.455 0.00 0.00 0.00 5.52
2069 2251 4.589908 AGGAATTAGAATGGCACTTTCGT 58.410 39.130 0.00 0.00 0.00 3.85
2079 2261 1.333619 GGCACTTTCGTCTTTTGCTGA 59.666 47.619 0.00 0.00 33.55 4.26
2081 2263 2.644078 CACTTTCGTCTTTTGCTGAGC 58.356 47.619 0.00 0.00 0.00 4.26
2106 2288 7.148590 GCTAGATTCGCACCAAAAATTTCAAAT 60.149 33.333 0.00 0.00 0.00 2.32
2107 2289 7.495135 AGATTCGCACCAAAAATTTCAAATT 57.505 28.000 0.00 0.00 0.00 1.82
2108 2290 8.600449 AGATTCGCACCAAAAATTTCAAATTA 57.400 26.923 0.00 0.00 0.00 1.40
2109 2291 9.050601 AGATTCGCACCAAAAATTTCAAATTAA 57.949 25.926 0.00 0.00 0.00 1.40
2110 2292 9.657121 GATTCGCACCAAAAATTTCAAATTAAA 57.343 25.926 0.00 0.00 0.00 1.52
2123 2305 5.993748 TCAAATTAAACCTGTTCATCCCC 57.006 39.130 0.00 0.00 0.00 4.81
2124 2306 5.398236 TCAAATTAAACCTGTTCATCCCCA 58.602 37.500 0.00 0.00 0.00 4.96
2125 2307 6.022315 TCAAATTAAACCTGTTCATCCCCAT 58.978 36.000 0.00 0.00 0.00 4.00
2127 2309 2.236489 AAACCTGTTCATCCCCATGG 57.764 50.000 4.14 4.14 0.00 3.66
2130 2312 0.396139 CCTGTTCATCCCCATGGGTG 60.396 60.000 29.33 21.36 44.74 4.61
2131 2313 0.332632 CTGTTCATCCCCATGGGTGT 59.667 55.000 29.33 14.54 44.74 4.16
2132 2314 0.331278 TGTTCATCCCCATGGGTGTC 59.669 55.000 29.33 17.65 44.74 3.67
2133 2315 0.625849 GTTCATCCCCATGGGTGTCT 59.374 55.000 29.33 7.89 44.74 3.41
2134 2316 1.843851 GTTCATCCCCATGGGTGTCTA 59.156 52.381 29.33 8.96 44.74 2.59
2135 2317 1.507140 TCATCCCCATGGGTGTCTAC 58.493 55.000 29.33 0.00 44.74 2.59
2136 2318 0.474184 CATCCCCATGGGTGTCTACC 59.526 60.000 29.33 0.00 44.74 3.18
2137 2319 0.346932 ATCCCCATGGGTGTCTACCT 59.653 55.000 29.33 1.66 46.66 3.08
2138 2320 1.020462 TCCCCATGGGTGTCTACCTA 58.980 55.000 29.33 0.60 46.66 3.08
2139 2321 1.129058 CCCCATGGGTGTCTACCTAC 58.871 60.000 29.33 0.00 46.66 3.18
2140 2322 1.129058 CCCATGGGTGTCTACCTACC 58.871 60.000 23.93 0.00 46.66 3.18
2141 2323 1.344087 CCCATGGGTGTCTACCTACCT 60.344 57.143 23.93 0.00 46.66 3.08
2142 2324 2.090943 CCCATGGGTGTCTACCTACCTA 60.091 54.545 23.93 0.00 46.66 3.08
2143 2325 2.963782 CCATGGGTGTCTACCTACCTAC 59.036 54.545 2.85 0.00 46.66 3.18
2149 2331 1.288932 TGTCTACCTACCTACCCACCC 59.711 57.143 0.00 0.00 0.00 4.61
2153 2335 1.691689 CCTACCTACCCACCCACCC 60.692 68.421 0.00 0.00 0.00 4.61
2158 2340 2.204029 TACCCACCCACCCACCTC 60.204 66.667 0.00 0.00 0.00 3.85
2171 2357 0.319900 CCACCTCGTGTCCTTGTGAG 60.320 60.000 0.00 0.00 0.00 3.51
2172 2358 0.673985 CACCTCGTGTCCTTGTGAGA 59.326 55.000 0.00 0.00 0.00 3.27
2178 2364 2.492088 TCGTGTCCTTGTGAGATCGATT 59.508 45.455 0.00 0.00 0.00 3.34
2181 2367 4.437239 GTGTCCTTGTGAGATCGATTGAT 58.563 43.478 0.00 0.00 37.60 2.57
2279 2465 2.389962 TACCACGTAGGCCACAATTC 57.610 50.000 5.01 0.00 43.14 2.17
2288 2474 1.026718 GGCCACAATTCGTCCTCCTG 61.027 60.000 0.00 0.00 0.00 3.86
2426 2612 0.035458 ACCTACAGCTGGAACACTGC 59.965 55.000 19.93 0.00 39.73 4.40
2447 2633 0.453793 CCACTTTGTTCGGTGCAACA 59.546 50.000 0.98 0.00 39.98 3.33
2557 2743 3.064408 GGTAAGTTTTGCCGGCTACATAC 59.936 47.826 29.70 24.97 0.00 2.39
2560 2746 2.027561 AGTTTTGCCGGCTACATACAGA 60.028 45.455 29.70 0.00 0.00 3.41
2566 2752 2.036733 GCCGGCTACATACAGAACCATA 59.963 50.000 22.15 0.00 0.00 2.74
2583 2769 8.960591 CAGAACCATAATGTATTGAGGAGTTTT 58.039 33.333 0.00 0.00 0.00 2.43
2584 2770 9.533831 AGAACCATAATGTATTGAGGAGTTTTT 57.466 29.630 0.00 0.00 0.00 1.94
2585 2771 9.788960 GAACCATAATGTATTGAGGAGTTTTTC 57.211 33.333 0.00 0.00 0.00 2.29
2586 2772 7.985476 ACCATAATGTATTGAGGAGTTTTTCG 58.015 34.615 0.00 0.00 0.00 3.46
2587 2773 7.067008 ACCATAATGTATTGAGGAGTTTTTCGG 59.933 37.037 0.00 0.00 0.00 4.30
2588 2774 7.067008 CCATAATGTATTGAGGAGTTTTTCGGT 59.933 37.037 0.00 0.00 0.00 4.69
2589 2775 9.104965 CATAATGTATTGAGGAGTTTTTCGGTA 57.895 33.333 0.00 0.00 0.00 4.02
2590 2776 7.989416 AATGTATTGAGGAGTTTTTCGGTAA 57.011 32.000 0.00 0.00 0.00 2.85
2591 2777 8.575649 AATGTATTGAGGAGTTTTTCGGTAAT 57.424 30.769 0.00 0.00 0.00 1.89
2592 2778 7.989416 TGTATTGAGGAGTTTTTCGGTAATT 57.011 32.000 0.00 0.00 0.00 1.40
2593 2779 7.812648 TGTATTGAGGAGTTTTTCGGTAATTG 58.187 34.615 0.00 0.00 0.00 2.32
2594 2780 4.759516 TGAGGAGTTTTTCGGTAATTGC 57.240 40.909 0.00 0.00 0.00 3.56
2595 2781 3.504520 TGAGGAGTTTTTCGGTAATTGCC 59.495 43.478 1.83 1.83 0.00 4.52
2596 2782 3.756963 GAGGAGTTTTTCGGTAATTGCCT 59.243 43.478 11.07 0.00 0.00 4.75
2597 2783 4.149598 AGGAGTTTTTCGGTAATTGCCTT 58.850 39.130 11.07 0.00 0.00 4.35
2598 2784 4.587262 AGGAGTTTTTCGGTAATTGCCTTT 59.413 37.500 11.07 0.00 0.00 3.11
2599 2785 4.684242 GGAGTTTTTCGGTAATTGCCTTTG 59.316 41.667 11.07 0.00 0.00 2.77
2600 2786 4.627058 AGTTTTTCGGTAATTGCCTTTGG 58.373 39.130 11.07 0.00 0.00 3.28
2610 2796 4.645809 GCCTTTGGCTCCTAGGTG 57.354 61.111 9.08 7.68 46.69 4.00
2611 2797 1.750780 GCCTTTGGCTCCTAGGTGC 60.751 63.158 24.68 24.68 46.69 5.01
2612 2798 1.685224 CCTTTGGCTCCTAGGTGCA 59.315 57.895 31.19 17.76 36.47 4.57
2613 2799 0.257039 CCTTTGGCTCCTAGGTGCAT 59.743 55.000 31.19 0.00 36.47 3.96
2614 2800 1.490490 CCTTTGGCTCCTAGGTGCATA 59.510 52.381 31.19 19.50 36.47 3.14
2615 2801 2.107204 CCTTTGGCTCCTAGGTGCATAT 59.893 50.000 31.19 0.00 36.47 1.78
2616 2802 2.936919 TTGGCTCCTAGGTGCATATG 57.063 50.000 31.19 0.00 36.47 1.78
2617 2803 0.397941 TGGCTCCTAGGTGCATATGC 59.602 55.000 31.19 21.09 42.50 3.14
2628 2814 3.851620 GCATATGCACCCATTGTCG 57.148 52.632 22.84 0.00 41.59 4.35
2629 2815 1.308047 GCATATGCACCCATTGTCGA 58.692 50.000 22.84 0.00 41.59 4.20
2630 2816 1.675483 GCATATGCACCCATTGTCGAA 59.325 47.619 22.84 0.00 41.59 3.71
2631 2817 2.098934 GCATATGCACCCATTGTCGAAA 59.901 45.455 22.84 0.00 41.59 3.46
2632 2818 3.243501 GCATATGCACCCATTGTCGAAAT 60.244 43.478 22.84 0.00 41.59 2.17
2633 2819 4.539870 CATATGCACCCATTGTCGAAATC 58.460 43.478 0.00 0.00 32.85 2.17
2634 2820 1.173043 TGCACCCATTGTCGAAATCC 58.827 50.000 0.00 0.00 0.00 3.01
2635 2821 1.173043 GCACCCATTGTCGAAATCCA 58.827 50.000 0.00 0.00 0.00 3.41
2636 2822 1.543802 GCACCCATTGTCGAAATCCAA 59.456 47.619 0.00 0.00 0.00 3.53
2637 2823 2.029470 GCACCCATTGTCGAAATCCAAA 60.029 45.455 0.00 0.00 0.00 3.28
2638 2824 3.368323 GCACCCATTGTCGAAATCCAAAT 60.368 43.478 0.00 0.00 0.00 2.32
2639 2825 4.819769 CACCCATTGTCGAAATCCAAATT 58.180 39.130 0.00 0.00 0.00 1.82
2640 2826 4.864247 CACCCATTGTCGAAATCCAAATTC 59.136 41.667 0.00 0.00 0.00 2.17
2641 2827 4.081697 ACCCATTGTCGAAATCCAAATTCC 60.082 41.667 0.00 0.00 0.00 3.01
2642 2828 4.104776 CCATTGTCGAAATCCAAATTCCG 58.895 43.478 0.00 0.00 0.00 4.30
2643 2829 4.142491 CCATTGTCGAAATCCAAATTCCGA 60.142 41.667 0.00 0.00 0.00 4.55
2644 2830 4.678509 TTGTCGAAATCCAAATTCCGAG 57.321 40.909 0.00 0.00 0.00 4.63
2645 2831 3.932822 TGTCGAAATCCAAATTCCGAGA 58.067 40.909 0.00 0.00 0.00 4.04
2646 2832 4.320023 TGTCGAAATCCAAATTCCGAGAA 58.680 39.130 0.00 0.00 0.00 2.87
2647 2833 4.391830 TGTCGAAATCCAAATTCCGAGAAG 59.608 41.667 0.00 0.00 0.00 2.85
2648 2834 4.392138 GTCGAAATCCAAATTCCGAGAAGT 59.608 41.667 0.00 0.00 0.00 3.01
2649 2835 5.001232 TCGAAATCCAAATTCCGAGAAGTT 58.999 37.500 0.00 0.00 0.00 2.66
2650 2836 6.091713 GTCGAAATCCAAATTCCGAGAAGTTA 59.908 38.462 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.070074 GTCCCTCCTTGAGAGTCTTATTTCATA 59.930 40.741 0.00 0.00 41.47 2.15
3 4 5.187967 GTCCCTCCTTGAGAGTCTTATTTCA 59.812 44.000 0.00 0.00 41.47 2.69
4 5 5.423931 AGTCCCTCCTTGAGAGTCTTATTTC 59.576 44.000 0.00 0.00 41.47 2.17
5 6 5.346270 AGTCCCTCCTTGAGAGTCTTATTT 58.654 41.667 0.00 0.00 41.47 1.40
6 7 4.954089 AGTCCCTCCTTGAGAGTCTTATT 58.046 43.478 0.00 0.00 41.47 1.40
7 8 4.618378 AGTCCCTCCTTGAGAGTCTTAT 57.382 45.455 0.00 0.00 41.47 1.73
8 9 4.405756 AAGTCCCTCCTTGAGAGTCTTA 57.594 45.455 0.00 0.00 41.47 2.10
9 10 3.268034 AAGTCCCTCCTTGAGAGTCTT 57.732 47.619 0.00 0.00 41.47 3.01
10 11 4.618378 ATAAGTCCCTCCTTGAGAGTCT 57.382 45.455 0.00 0.00 41.47 3.24
11 12 4.830600 CCTATAAGTCCCTCCTTGAGAGTC 59.169 50.000 0.00 0.00 41.47 3.36
12 13 4.482772 TCCTATAAGTCCCTCCTTGAGAGT 59.517 45.833 0.00 0.00 41.47 3.24
13 14 5.068215 TCCTATAAGTCCCTCCTTGAGAG 57.932 47.826 0.00 0.00 42.83 3.20
14 15 5.043281 AGTTCCTATAAGTCCCTCCTTGAGA 60.043 44.000 0.00 0.00 0.00 3.27
15 16 5.212745 AGTTCCTATAAGTCCCTCCTTGAG 58.787 45.833 0.00 0.00 0.00 3.02
16 17 5.222278 AGTTCCTATAAGTCCCTCCTTGA 57.778 43.478 0.00 0.00 0.00 3.02
17 18 5.959583 AAGTTCCTATAAGTCCCTCCTTG 57.040 43.478 0.00 0.00 0.00 3.61
18 19 8.521301 ACTATAAGTTCCTATAAGTCCCTCCTT 58.479 37.037 0.00 0.00 0.00 3.36
19 20 8.071235 ACTATAAGTTCCTATAAGTCCCTCCT 57.929 38.462 0.00 0.00 0.00 3.69
20 21 8.586744 CAACTATAAGTTCCTATAAGTCCCTCC 58.413 40.741 0.00 0.00 36.03 4.30
21 22 9.145442 ACAACTATAAGTTCCTATAAGTCCCTC 57.855 37.037 0.00 0.00 36.03 4.30
42 43 9.448587 AAGTCCCTATAAGACCATATTACAACT 57.551 33.333 0.09 0.00 34.67 3.16
65 66 5.073965 TGTTTGGTTCCTGGGACTTATAAGT 59.926 40.000 18.05 18.05 43.16 2.24
66 67 5.566469 TGTTTGGTTCCTGGGACTTATAAG 58.434 41.667 11.05 11.05 0.00 1.73
67 68 5.515886 CCTGTTTGGTTCCTGGGACTTATAA 60.516 44.000 4.84 0.00 0.00 0.98
68 69 4.018779 CCTGTTTGGTTCCTGGGACTTATA 60.019 45.833 4.84 0.00 0.00 0.98
69 70 3.245264 CCTGTTTGGTTCCTGGGACTTAT 60.245 47.826 4.84 0.00 0.00 1.73
70 71 2.107552 CCTGTTTGGTTCCTGGGACTTA 59.892 50.000 4.84 0.00 0.00 2.24
71 72 1.133482 CCTGTTTGGTTCCTGGGACTT 60.133 52.381 4.84 0.00 0.00 3.01
72 73 0.478507 CCTGTTTGGTTCCTGGGACT 59.521 55.000 4.84 0.00 0.00 3.85
73 74 3.036431 CCTGTTTGGTTCCTGGGAC 57.964 57.895 0.00 0.00 0.00 4.46
83 84 6.996282 TCTCTAAAAAGTCCTTACCTGTTTGG 59.004 38.462 0.00 0.00 42.93 3.28
84 85 7.715686 AGTCTCTAAAAAGTCCTTACCTGTTTG 59.284 37.037 0.00 0.00 0.00 2.93
85 86 7.803131 AGTCTCTAAAAAGTCCTTACCTGTTT 58.197 34.615 0.00 0.00 0.00 2.83
86 87 7.376335 AGTCTCTAAAAAGTCCTTACCTGTT 57.624 36.000 0.00 0.00 0.00 3.16
87 88 6.997942 AGTCTCTAAAAAGTCCTTACCTGT 57.002 37.500 0.00 0.00 0.00 4.00
88 89 7.173390 CCAAAGTCTCTAAAAAGTCCTTACCTG 59.827 40.741 0.00 0.00 0.00 4.00
89 90 7.072076 TCCAAAGTCTCTAAAAAGTCCTTACCT 59.928 37.037 0.00 0.00 0.00 3.08
90 91 7.172875 GTCCAAAGTCTCTAAAAAGTCCTTACC 59.827 40.741 0.00 0.00 0.00 2.85
91 92 7.932491 AGTCCAAAGTCTCTAAAAAGTCCTTAC 59.068 37.037 0.00 0.00 0.00 2.34
92 93 8.030913 AGTCCAAAGTCTCTAAAAAGTCCTTA 57.969 34.615 0.00 0.00 0.00 2.69
93 94 6.901300 AGTCCAAAGTCTCTAAAAAGTCCTT 58.099 36.000 0.00 0.00 0.00 3.36
94 95 6.502074 AGTCCAAAGTCTCTAAAAAGTCCT 57.498 37.500 0.00 0.00 0.00 3.85
95 96 8.850007 ATAAGTCCAAAGTCTCTAAAAAGTCC 57.150 34.615 0.00 0.00 0.00 3.85
101 102 9.720769 CCAACTTATAAGTCCAAAGTCTCTAAA 57.279 33.333 18.28 0.00 38.57 1.85
102 103 8.319146 CCCAACTTATAAGTCCAAAGTCTCTAA 58.681 37.037 18.28 0.00 38.57 2.10
103 104 7.676893 TCCCAACTTATAAGTCCAAAGTCTCTA 59.323 37.037 18.28 0.00 38.57 2.43
104 105 6.500751 TCCCAACTTATAAGTCCAAAGTCTCT 59.499 38.462 18.28 0.00 38.57 3.10
105 106 6.594547 GTCCCAACTTATAAGTCCAAAGTCTC 59.405 42.308 18.28 1.23 38.57 3.36
106 107 6.272558 AGTCCCAACTTATAAGTCCAAAGTCT 59.727 38.462 18.28 8.64 38.57 3.24
107 108 6.473758 AGTCCCAACTTATAAGTCCAAAGTC 58.526 40.000 18.28 6.78 38.57 3.01
108 109 6.449830 AGTCCCAACTTATAAGTCCAAAGT 57.550 37.500 18.28 5.74 38.57 2.66
109 110 8.857694 TTTAGTCCCAACTTATAAGTCCAAAG 57.142 34.615 18.28 6.66 38.57 2.77
110 111 9.643735 TTTTTAGTCCCAACTTATAAGTCCAAA 57.356 29.630 18.28 4.97 38.57 3.28
139 140 9.110502 CCCTGTTTGATTTATAAGTCCTAAGAC 57.889 37.037 5.61 0.00 43.89 3.01
140 141 7.773690 GCCCTGTTTGATTTATAAGTCCTAAGA 59.226 37.037 5.61 0.00 0.00 2.10
141 142 7.013369 GGCCCTGTTTGATTTATAAGTCCTAAG 59.987 40.741 5.61 0.00 0.00 2.18
142 143 6.831868 GGCCCTGTTTGATTTATAAGTCCTAA 59.168 38.462 5.61 0.00 0.00 2.69
143 144 6.159751 AGGCCCTGTTTGATTTATAAGTCCTA 59.840 38.462 0.00 0.00 0.00 2.94
144 145 5.044105 AGGCCCTGTTTGATTTATAAGTCCT 60.044 40.000 0.00 0.00 0.00 3.85
145 146 5.201243 AGGCCCTGTTTGATTTATAAGTCC 58.799 41.667 0.00 0.00 0.00 3.85
146 147 6.377146 TCAAGGCCCTGTTTGATTTATAAGTC 59.623 38.462 0.00 1.17 0.00 3.01
147 148 6.252995 TCAAGGCCCTGTTTGATTTATAAGT 58.747 36.000 0.00 0.00 0.00 2.24
148 149 6.773976 TCAAGGCCCTGTTTGATTTATAAG 57.226 37.500 0.00 0.00 0.00 1.73
149 150 7.732222 AATCAAGGCCCTGTTTGATTTATAA 57.268 32.000 19.73 0.00 46.41 0.98
155 156 2.094675 CGAATCAAGGCCCTGTTTGAT 58.905 47.619 11.21 11.21 43.79 2.57
156 157 1.202879 ACGAATCAAGGCCCTGTTTGA 60.203 47.619 7.53 7.53 37.68 2.69
157 158 1.247567 ACGAATCAAGGCCCTGTTTG 58.752 50.000 0.00 0.00 0.00 2.93
158 159 2.871096 TACGAATCAAGGCCCTGTTT 57.129 45.000 0.00 0.00 0.00 2.83
159 160 2.711542 CTTACGAATCAAGGCCCTGTT 58.288 47.619 0.00 0.00 0.00 3.16
160 161 1.679032 GCTTACGAATCAAGGCCCTGT 60.679 52.381 0.00 0.00 0.00 4.00
161 162 1.017387 GCTTACGAATCAAGGCCCTG 58.983 55.000 0.00 0.00 0.00 4.45
162 163 0.618458 TGCTTACGAATCAAGGCCCT 59.382 50.000 0.00 0.00 0.00 5.19
163 164 1.017387 CTGCTTACGAATCAAGGCCC 58.983 55.000 0.00 0.00 0.00 5.80
164 165 1.017387 CCTGCTTACGAATCAAGGCC 58.983 55.000 0.00 0.00 0.00 5.19
165 166 1.017387 CCCTGCTTACGAATCAAGGC 58.983 55.000 0.00 0.00 0.00 4.35
166 167 1.017387 GCCCTGCTTACGAATCAAGG 58.983 55.000 0.00 0.00 0.00 3.61
167 168 0.652592 CGCCCTGCTTACGAATCAAG 59.347 55.000 0.00 0.00 0.00 3.02
168 169 0.248012 TCGCCCTGCTTACGAATCAA 59.752 50.000 0.00 0.00 31.97 2.57
169 170 0.248012 TTCGCCCTGCTTACGAATCA 59.752 50.000 0.00 0.00 40.56 2.57
170 171 1.327764 CTTTCGCCCTGCTTACGAATC 59.672 52.381 0.00 0.00 44.37 2.52
171 172 1.369625 CTTTCGCCCTGCTTACGAAT 58.630 50.000 0.00 0.00 44.37 3.34
172 173 1.296056 GCTTTCGCCCTGCTTACGAA 61.296 55.000 0.00 0.00 43.42 3.85
173 174 1.740296 GCTTTCGCCCTGCTTACGA 60.740 57.895 0.00 0.00 0.00 3.43
174 175 1.741770 AGCTTTCGCCCTGCTTACG 60.742 57.895 0.00 0.00 36.60 3.18
175 176 0.673644 TCAGCTTTCGCCCTGCTTAC 60.674 55.000 0.00 0.00 34.51 2.34
176 177 0.036164 TTCAGCTTTCGCCCTGCTTA 59.964 50.000 0.00 0.00 34.51 3.09
177 178 1.228245 TTCAGCTTTCGCCCTGCTT 60.228 52.632 0.00 0.00 34.51 3.91
178 179 1.673665 CTTCAGCTTTCGCCCTGCT 60.674 57.895 0.00 0.00 37.56 4.24
179 180 2.873288 CTTCAGCTTTCGCCCTGC 59.127 61.111 0.00 0.00 36.60 4.85
180 181 2.873288 GCTTCAGCTTTCGCCCTG 59.127 61.111 0.00 0.00 38.21 4.45
221 361 9.888878 CGTGAGTTCTTAAATACCTATCGAATA 57.111 33.333 0.00 0.00 0.00 1.75
692 839 0.393808 TAGATTGGAAAGGGCCGTGC 60.394 55.000 0.00 0.00 0.00 5.34
807 955 1.208535 TGTGTTTGTCTGGTCTCCGTT 59.791 47.619 0.00 0.00 0.00 4.44
816 964 1.355210 GGCCGTGTGTGTTTGTCTG 59.645 57.895 0.00 0.00 0.00 3.51
1067 1219 3.414700 CGCTGTTGGTGTCGAGCC 61.415 66.667 0.00 0.00 0.00 4.70
1200 1352 1.112916 TGGTGGTCGTCAGCTTCTCA 61.113 55.000 10.73 0.00 43.76 3.27
1374 1526 1.162181 TCATCCCGTAGTAGTCGCGG 61.162 60.000 6.13 6.53 44.55 6.46
1455 1607 0.179153 GGTTGGACTCGTAGCCGTAC 60.179 60.000 0.00 0.00 35.01 3.67
1557 1709 2.670592 TCGTTCTCGTCTCCGGCA 60.671 61.111 0.00 0.00 38.33 5.69
1564 1716 1.186623 GTTGTCGTTGTCGTTCTCGTC 59.813 52.381 0.00 0.00 38.33 4.20
1570 1722 1.884004 CCCCGTTGTCGTTGTCGTT 60.884 57.895 0.00 0.00 38.33 3.85
1571 1723 2.279650 CCCCGTTGTCGTTGTCGT 60.280 61.111 0.00 0.00 38.33 4.34
1572 1724 2.279650 ACCCCGTTGTCGTTGTCG 60.280 61.111 0.00 0.00 38.55 4.35
1573 1725 2.248835 CCACCCCGTTGTCGTTGTC 61.249 63.158 0.00 0.00 35.01 3.18
1574 1726 2.203098 CCACCCCGTTGTCGTTGT 60.203 61.111 0.00 0.00 35.01 3.32
1575 1727 3.656045 GCCACCCCGTTGTCGTTG 61.656 66.667 0.00 0.00 35.01 4.10
1610 1768 3.680786 GGTTTTCCTGGTGGCCGC 61.681 66.667 8.12 8.12 36.94 6.53
1615 1773 0.951558 CCGTTCTGGTTTTCCTGGTG 59.048 55.000 0.00 0.00 41.38 4.17
1616 1774 0.179001 CCCGTTCTGGTTTTCCTGGT 60.179 55.000 0.00 0.00 41.38 4.00
1659 1820 3.005367 AGCAAAAACAAACCCCTCGTATG 59.995 43.478 0.00 0.00 0.00 2.39
1677 1838 0.245266 TATCTGACGGTCGCAAGCAA 59.755 50.000 3.34 0.00 37.18 3.91
1792 1953 0.032678 CCACACCGGCAGCTAGATAG 59.967 60.000 0.00 0.00 0.00 2.08
1793 1954 0.396556 TCCACACCGGCAGCTAGATA 60.397 55.000 0.00 0.00 33.14 1.98
1794 1955 1.264749 TTCCACACCGGCAGCTAGAT 61.265 55.000 0.00 0.00 33.14 1.98
1795 1956 1.264749 ATTCCACACCGGCAGCTAGA 61.265 55.000 0.00 0.00 33.14 2.43
1796 1957 1.091771 CATTCCACACCGGCAGCTAG 61.092 60.000 0.00 0.00 33.14 3.42
1797 1958 1.078497 CATTCCACACCGGCAGCTA 60.078 57.895 0.00 0.00 33.14 3.32
1962 2138 3.019564 CCTTTCCGAATGAGGCTTGATT 58.980 45.455 0.00 0.00 0.00 2.57
2003 2179 2.769663 AGGCGGACACAGGAAATATACA 59.230 45.455 0.00 0.00 0.00 2.29
2004 2180 3.470645 AGGCGGACACAGGAAATATAC 57.529 47.619 0.00 0.00 0.00 1.47
2012 2194 2.429930 TCCAAAGGCGGACACAGG 59.570 61.111 0.00 0.00 0.00 4.00
2069 2251 2.932614 GCGAATCTAGCTCAGCAAAAGA 59.067 45.455 0.00 0.00 0.00 2.52
2079 2261 5.048083 TGAAATTTTTGGTGCGAATCTAGCT 60.048 36.000 0.00 0.00 35.28 3.32
2081 2263 7.636259 TTTGAAATTTTTGGTGCGAATCTAG 57.364 32.000 0.00 0.00 0.00 2.43
2106 2288 3.707316 CCATGGGGATGAACAGGTTTAA 58.293 45.455 2.85 0.00 35.59 1.52
2107 2289 3.380471 CCATGGGGATGAACAGGTTTA 57.620 47.619 2.85 0.00 35.59 2.01
2108 2290 2.236489 CCATGGGGATGAACAGGTTT 57.764 50.000 2.85 0.00 35.59 3.27
2127 2309 2.382882 GTGGGTAGGTAGGTAGACACC 58.617 57.143 0.00 0.00 46.19 4.16
2130 2312 1.288932 TGGGTGGGTAGGTAGGTAGAC 59.711 57.143 0.00 0.00 0.00 2.59
2131 2313 1.288932 GTGGGTGGGTAGGTAGGTAGA 59.711 57.143 0.00 0.00 0.00 2.59
2132 2314 1.690527 GGTGGGTGGGTAGGTAGGTAG 60.691 61.905 0.00 0.00 0.00 3.18
2133 2315 0.339510 GGTGGGTGGGTAGGTAGGTA 59.660 60.000 0.00 0.00 0.00 3.08
2134 2316 1.081648 GGTGGGTGGGTAGGTAGGT 59.918 63.158 0.00 0.00 0.00 3.08
2135 2317 1.691689 GGGTGGGTGGGTAGGTAGG 60.692 68.421 0.00 0.00 0.00 3.18
2136 2318 1.081462 TGGGTGGGTGGGTAGGTAG 59.919 63.158 0.00 0.00 0.00 3.18
2137 2319 1.229593 GTGGGTGGGTGGGTAGGTA 60.230 63.158 0.00 0.00 0.00 3.08
2138 2320 2.530916 GTGGGTGGGTGGGTAGGT 60.531 66.667 0.00 0.00 0.00 3.08
2139 2321 3.335729 GGTGGGTGGGTGGGTAGG 61.336 72.222 0.00 0.00 0.00 3.18
2140 2322 2.204090 AGGTGGGTGGGTGGGTAG 60.204 66.667 0.00 0.00 0.00 3.18
2141 2323 2.204029 GAGGTGGGTGGGTGGGTA 60.204 66.667 0.00 0.00 0.00 3.69
2149 2331 1.301716 CAAGGACACGAGGTGGGTG 60.302 63.158 0.42 0.00 37.94 4.61
2153 2335 0.673985 TCTCACAAGGACACGAGGTG 59.326 55.000 0.00 0.00 39.75 4.00
2158 2340 2.568696 ATCGATCTCACAAGGACACG 57.431 50.000 0.00 0.00 0.00 4.49
2171 2357 5.175856 CGTGAAGGGAGTAAATCAATCGATC 59.824 44.000 0.00 0.00 0.00 3.69
2172 2358 5.050490 CGTGAAGGGAGTAAATCAATCGAT 58.950 41.667 0.00 0.00 0.00 3.59
2178 2364 2.821378 TCGACGTGAAGGGAGTAAATCA 59.179 45.455 0.00 0.00 0.00 2.57
2181 2367 2.673043 GCATCGACGTGAAGGGAGTAAA 60.673 50.000 0.00 0.00 0.00 2.01
2288 2474 1.028868 GCCATGCACCTTGTCCTCTC 61.029 60.000 0.00 0.00 0.00 3.20
2420 2606 0.732571 CGAACAAAGTGGTGCAGTGT 59.267 50.000 0.00 0.00 0.00 3.55
2557 2743 8.511604 AAACTCCTCAATACATTATGGTTCTG 57.488 34.615 0.00 0.00 0.00 3.02
2560 2746 8.458843 CGAAAAACTCCTCAATACATTATGGTT 58.541 33.333 0.00 0.00 0.00 3.67
2566 2752 7.989416 TTACCGAAAAACTCCTCAATACATT 57.011 32.000 0.00 0.00 0.00 2.71
2594 2780 0.257039 ATGCACCTAGGAGCCAAAGG 59.743 55.000 25.94 6.43 36.42 3.11
2595 2781 3.144506 CATATGCACCTAGGAGCCAAAG 58.855 50.000 25.94 11.57 0.00 2.77
2596 2782 2.749466 GCATATGCACCTAGGAGCCAAA 60.749 50.000 25.94 13.05 41.59 3.28
2597 2783 1.202806 GCATATGCACCTAGGAGCCAA 60.203 52.381 25.94 15.39 41.59 4.52
2598 2784 0.397941 GCATATGCACCTAGGAGCCA 59.602 55.000 25.94 15.42 41.59 4.75
2599 2785 3.239861 GCATATGCACCTAGGAGCC 57.760 57.895 25.94 8.49 41.59 4.70
2610 2796 1.308047 TCGACAATGGGTGCATATGC 58.692 50.000 21.09 21.09 42.50 3.14
2611 2797 4.539870 GATTTCGACAATGGGTGCATATG 58.460 43.478 0.00 0.00 0.00 1.78
2612 2798 3.569701 GGATTTCGACAATGGGTGCATAT 59.430 43.478 0.00 0.00 0.00 1.78
2613 2799 2.948979 GGATTTCGACAATGGGTGCATA 59.051 45.455 0.00 0.00 0.00 3.14
2614 2800 1.750778 GGATTTCGACAATGGGTGCAT 59.249 47.619 0.00 0.00 0.00 3.96
2615 2801 1.173043 GGATTTCGACAATGGGTGCA 58.827 50.000 0.00 0.00 0.00 4.57
2616 2802 1.173043 TGGATTTCGACAATGGGTGC 58.827 50.000 0.00 0.00 0.00 5.01
2617 2803 3.932545 TTTGGATTTCGACAATGGGTG 57.067 42.857 0.00 0.00 0.00 4.61
2618 2804 4.081697 GGAATTTGGATTTCGACAATGGGT 60.082 41.667 0.00 0.00 0.00 4.51
2619 2805 4.432712 GGAATTTGGATTTCGACAATGGG 58.567 43.478 0.00 0.00 0.00 4.00
2620 2806 4.104776 CGGAATTTGGATTTCGACAATGG 58.895 43.478 0.00 0.00 45.23 3.16
2621 2807 4.980590 TCGGAATTTGGATTTCGACAATG 58.019 39.130 0.00 0.00 45.79 2.82
2622 2808 4.941263 TCTCGGAATTTGGATTTCGACAAT 59.059 37.500 0.00 0.00 45.79 2.71
2623 2809 4.320023 TCTCGGAATTTGGATTTCGACAA 58.680 39.130 0.00 0.00 45.79 3.18
2624 2810 3.932822 TCTCGGAATTTGGATTTCGACA 58.067 40.909 0.00 0.00 45.79 4.35
2625 2811 4.392138 ACTTCTCGGAATTTGGATTTCGAC 59.608 41.667 0.00 0.00 45.79 4.20
2627 2813 4.946784 ACTTCTCGGAATTTGGATTTCG 57.053 40.909 0.00 0.00 44.05 3.46


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

AutoCloner maintained by Alex Coulton.