Multiple sequence alignment - TraesCS4D01G178300

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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 TraesCS4D01G178300 chr4D 100.000 2729 0 0 1 2729 309700179 309702907 0.000000e+00 5040.0
1 TraesCS4D01G178300 chr4D 96.899 258 8 0 1 258 471504879 471504622 1.500000e-117 433.0
2 TraesCS4D01G178300 chr4A 95.641 1583 44 5 259 1839 165358760 165357201 0.000000e+00 2518.0
3 TraesCS4D01G178300 chr4A 96.083 817 25 4 1840 2652 165357169 165356356 0.000000e+00 1325.0
4 TraesCS4D01G178300 chr4A 84.337 166 18 5 2213 2375 662079517 662079677 3.640000e-34 156.0
5 TraesCS4D01G178300 chr4A 98.750 80 1 0 2650 2729 165356249 165356170 2.830000e-30 143.0
6 TraesCS4D01G178300 chr4B 93.970 1592 43 16 256 1839 386747174 386748720 0.000000e+00 2359.0
7 TraesCS4D01G178300 chr4B 93.413 926 24 13 1840 2729 386748752 386749676 0.000000e+00 1338.0
8 TraesCS4D01G178300 chr5B 96.899 258 8 0 1 258 592314307 592314564 1.500000e-117 433.0
9 TraesCS4D01G178300 chr5B 94.595 259 11 3 1 258 51866107 51865851 5.480000e-107 398.0
10 TraesCS4D01G178300 chr7D 96.512 258 6 1 1 258 273838925 273838671 9.030000e-115 424.0
11 TraesCS4D01G178300 chr7D 85.542 166 16 5 2213 2375 610487979 610488139 1.680000e-37 167.0
12 TraesCS4D01G178300 chr7D 78.247 308 32 17 2403 2691 609974437 609974146 6.050000e-37 165.0
13 TraesCS4D01G178300 chr7D 77.922 308 33 17 2403 2691 607916421 607916712 2.810000e-35 159.0
14 TraesCS4D01G178300 chr7D 77.670 309 34 10 2402 2691 609745879 609746171 3.640000e-34 156.0
15 TraesCS4D01G178300 chr1A 94.595 259 12 2 1 258 580547081 580547338 1.520000e-107 399.0
16 TraesCS4D01G178300 chr1A 93.822 259 14 2 1 258 580533777 580534034 3.300000e-104 388.0
17 TraesCS4D01G178300 chr6D 93.633 267 13 4 1 265 444883602 444883338 1.970000e-106 396.0
18 TraesCS4D01G178300 chr3A 94.208 259 13 2 1 258 123291393 123291136 7.080000e-106 394.0
19 TraesCS4D01G178300 chrUn 93.822 259 14 2 1 258 326746731 326746474 3.300000e-104 388.0
20 TraesCS4D01G178300 chrUn 84.940 166 17 5 2213 2375 77501560 77501400 7.820000e-36 161.0
21 TraesCS4D01G178300 chr7A 86.145 166 15 5 2213 2375 700276694 700276534 3.610000e-39 172.0
22 TraesCS4D01G178300 chr7A 86.145 166 15 5 2213 2375 700281005 700280845 3.610000e-39 172.0
23 TraesCS4D01G178300 chr7A 88.000 50 6 0 1662 1711 668769280 668769231 2.930000e-05 60.2
24 TraesCS4D01G178300 chr7B 77.597 308 34 12 2403 2691 694102573 694102864 1.310000e-33 154.0


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 TraesCS4D01G178300 chr4D 309700179 309702907 2728 False 5040.000000 5040 100.000000 1 2729 1 chr4D.!!$F1 2728
1 TraesCS4D01G178300 chr4A 165356170 165358760 2590 True 1328.666667 2518 96.824667 259 2729 3 chr4A.!!$R1 2470
2 TraesCS4D01G178300 chr4B 386747174 386749676 2502 False 1848.500000 2359 93.691500 256 2729 2 chr4B.!!$F1 2473

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
687 689 0.385974 GACACGCAGCCACAATTCAC 60.386 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 1833 0.516877 TTCAGCCTTCATTTGCGACG 59.483 50.0 0.0 0.0 0.0 5.12 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.617368 ATCCAGACGGGGTCGAAG 58.383 61.111 0.00 0.00 37.67 3.79
18 19 2.722201 ATCCAGACGGGGTCGAAGC 61.722 63.158 0.00 0.00 37.67 3.86
19 20 3.691342 CCAGACGGGGTCGAAGCA 61.691 66.667 0.00 0.00 37.67 3.91
20 21 2.125912 CAGACGGGGTCGAAGCAG 60.126 66.667 0.00 0.00 37.67 4.24
21 22 3.382832 AGACGGGGTCGAAGCAGG 61.383 66.667 0.00 0.00 37.67 4.85
22 23 4.452733 GACGGGGTCGAAGCAGGG 62.453 72.222 0.00 0.00 40.11 4.45
38 39 4.772678 GGGGGCTCTGATTGCTTT 57.227 55.556 0.00 0.00 0.00 3.51
39 40 2.982026 GGGGGCTCTGATTGCTTTT 58.018 52.632 0.00 0.00 0.00 2.27
40 41 1.269958 GGGGGCTCTGATTGCTTTTT 58.730 50.000 0.00 0.00 0.00 1.94
41 42 1.205655 GGGGGCTCTGATTGCTTTTTC 59.794 52.381 0.00 0.00 0.00 2.29
42 43 2.174360 GGGGCTCTGATTGCTTTTTCT 58.826 47.619 0.00 0.00 0.00 2.52
43 44 2.564504 GGGGCTCTGATTGCTTTTTCTT 59.435 45.455 0.00 0.00 0.00 2.52
44 45 3.007290 GGGGCTCTGATTGCTTTTTCTTT 59.993 43.478 0.00 0.00 0.00 2.52
45 46 4.503817 GGGGCTCTGATTGCTTTTTCTTTT 60.504 41.667 0.00 0.00 0.00 2.27
46 47 5.059161 GGGCTCTGATTGCTTTTTCTTTTT 58.941 37.500 0.00 0.00 0.00 1.94
47 48 6.223120 GGGCTCTGATTGCTTTTTCTTTTTA 58.777 36.000 0.00 0.00 0.00 1.52
48 49 6.367149 GGGCTCTGATTGCTTTTTCTTTTTAG 59.633 38.462 0.00 0.00 0.00 1.85
49 50 7.147976 GGCTCTGATTGCTTTTTCTTTTTAGA 58.852 34.615 0.00 0.00 0.00 2.10
50 51 7.816513 GGCTCTGATTGCTTTTTCTTTTTAGAT 59.183 33.333 0.00 0.00 0.00 1.98
51 52 8.858186 GCTCTGATTGCTTTTTCTTTTTAGATC 58.142 33.333 0.00 0.00 0.00 2.75
52 53 9.351570 CTCTGATTGCTTTTTCTTTTTAGATCC 57.648 33.333 0.00 0.00 0.00 3.36
53 54 8.859090 TCTGATTGCTTTTTCTTTTTAGATCCA 58.141 29.630 0.00 0.00 0.00 3.41
54 55 9.136952 CTGATTGCTTTTTCTTTTTAGATCCAG 57.863 33.333 0.00 0.00 0.00 3.86
55 56 8.090214 TGATTGCTTTTTCTTTTTAGATCCAGG 58.910 33.333 0.00 0.00 0.00 4.45
56 57 6.345096 TGCTTTTTCTTTTTAGATCCAGGG 57.655 37.500 0.00 0.00 0.00 4.45
57 58 5.245977 TGCTTTTTCTTTTTAGATCCAGGGG 59.754 40.000 0.00 0.00 0.00 4.79
58 59 5.724328 CTTTTTCTTTTTAGATCCAGGGGC 58.276 41.667 0.00 0.00 0.00 5.80
59 60 4.396357 TTTCTTTTTAGATCCAGGGGCA 57.604 40.909 0.00 0.00 0.00 5.36
60 61 4.608170 TTCTTTTTAGATCCAGGGGCAT 57.392 40.909 0.00 0.00 0.00 4.40
61 62 3.902218 TCTTTTTAGATCCAGGGGCATG 58.098 45.455 0.00 0.00 0.00 4.06
62 63 3.269381 TCTTTTTAGATCCAGGGGCATGT 59.731 43.478 0.00 0.00 0.00 3.21
63 64 4.476846 TCTTTTTAGATCCAGGGGCATGTA 59.523 41.667 0.00 0.00 0.00 2.29
64 65 5.134339 TCTTTTTAGATCCAGGGGCATGTAT 59.866 40.000 0.00 0.00 0.00 2.29
65 66 4.371624 TTTAGATCCAGGGGCATGTATG 57.628 45.455 0.00 0.00 0.00 2.39
66 67 1.825105 AGATCCAGGGGCATGTATGT 58.175 50.000 0.00 0.00 0.00 2.29
67 68 1.701847 AGATCCAGGGGCATGTATGTC 59.298 52.381 0.00 0.00 0.00 3.06
68 69 1.421268 GATCCAGGGGCATGTATGTCA 59.579 52.381 0.00 0.00 33.08 3.58
69 70 1.294041 TCCAGGGGCATGTATGTCAA 58.706 50.000 0.00 0.00 33.08 3.18
70 71 1.638070 TCCAGGGGCATGTATGTCAAA 59.362 47.619 0.00 0.00 33.08 2.69
71 72 2.042297 TCCAGGGGCATGTATGTCAAAA 59.958 45.455 0.00 0.00 33.08 2.44
72 73 2.166254 CCAGGGGCATGTATGTCAAAAC 59.834 50.000 0.00 0.00 33.08 2.43
73 74 3.091545 CAGGGGCATGTATGTCAAAACT 58.908 45.455 0.00 0.00 33.08 2.66
74 75 3.511146 CAGGGGCATGTATGTCAAAACTT 59.489 43.478 0.00 0.00 33.08 2.66
75 76 4.021192 CAGGGGCATGTATGTCAAAACTTT 60.021 41.667 0.00 0.00 33.08 2.66
76 77 4.021192 AGGGGCATGTATGTCAAAACTTTG 60.021 41.667 0.00 0.00 39.48 2.77
77 78 3.679502 GGGCATGTATGTCAAAACTTTGC 59.320 43.478 0.00 0.00 38.05 3.68
78 79 3.679502 GGCATGTATGTCAAAACTTTGCC 59.320 43.478 14.53 14.53 37.95 4.52
79 80 4.305769 GCATGTATGTCAAAACTTTGCCA 58.694 39.130 0.00 0.00 38.05 4.92
80 81 4.749099 GCATGTATGTCAAAACTTTGCCAA 59.251 37.500 0.00 0.00 38.05 4.52
81 82 5.107375 GCATGTATGTCAAAACTTTGCCAAG 60.107 40.000 0.00 0.00 38.05 3.61
82 83 5.590530 TGTATGTCAAAACTTTGCCAAGT 57.409 34.783 0.00 0.00 45.89 3.16
83 84 5.587289 TGTATGTCAAAACTTTGCCAAGTC 58.413 37.500 3.30 0.00 42.89 3.01
84 85 4.734398 ATGTCAAAACTTTGCCAAGTCA 57.266 36.364 3.30 0.00 42.89 3.41
85 86 4.108699 TGTCAAAACTTTGCCAAGTCAG 57.891 40.909 3.30 0.00 42.89 3.51
86 87 2.860136 GTCAAAACTTTGCCAAGTCAGC 59.140 45.455 3.30 0.00 42.89 4.26
87 88 2.760092 TCAAAACTTTGCCAAGTCAGCT 59.240 40.909 3.30 0.00 42.89 4.24
88 89 3.195396 TCAAAACTTTGCCAAGTCAGCTT 59.805 39.130 3.30 0.00 42.89 3.74
89 90 3.443099 AAACTTTGCCAAGTCAGCTTC 57.557 42.857 3.30 0.00 42.89 3.86
90 91 2.355010 ACTTTGCCAAGTCAGCTTCT 57.645 45.000 0.00 0.00 39.15 2.85
91 92 2.659428 ACTTTGCCAAGTCAGCTTCTT 58.341 42.857 0.00 0.00 39.15 2.52
92 93 3.820557 ACTTTGCCAAGTCAGCTTCTTA 58.179 40.909 0.00 0.00 39.15 2.10
93 94 3.565902 ACTTTGCCAAGTCAGCTTCTTAC 59.434 43.478 0.00 0.00 39.15 2.34
94 95 2.928801 TGCCAAGTCAGCTTCTTACA 57.071 45.000 1.28 1.48 31.49 2.41
95 96 3.207265 TGCCAAGTCAGCTTCTTACAA 57.793 42.857 1.28 0.00 31.49 2.41
96 97 3.754965 TGCCAAGTCAGCTTCTTACAAT 58.245 40.909 1.28 0.00 31.49 2.71
97 98 3.753272 TGCCAAGTCAGCTTCTTACAATC 59.247 43.478 1.28 0.00 31.49 2.67
98 99 4.006319 GCCAAGTCAGCTTCTTACAATCT 58.994 43.478 1.28 0.00 31.49 2.40
99 100 4.142730 GCCAAGTCAGCTTCTTACAATCTG 60.143 45.833 1.28 0.00 31.49 2.90
100 101 5.240891 CCAAGTCAGCTTCTTACAATCTGA 58.759 41.667 1.28 0.00 31.49 3.27
103 104 3.935828 GTCAGCTTCTTACAATCTGACCC 59.064 47.826 8.93 0.00 44.58 4.46
104 105 3.055094 TCAGCTTCTTACAATCTGACCCC 60.055 47.826 0.00 0.00 0.00 4.95
105 106 2.912956 AGCTTCTTACAATCTGACCCCA 59.087 45.455 0.00 0.00 0.00 4.96
106 107 3.010420 GCTTCTTACAATCTGACCCCAC 58.990 50.000 0.00 0.00 0.00 4.61
107 108 3.307762 GCTTCTTACAATCTGACCCCACT 60.308 47.826 0.00 0.00 0.00 4.00
108 109 4.807643 GCTTCTTACAATCTGACCCCACTT 60.808 45.833 0.00 0.00 0.00 3.16
109 110 4.286297 TCTTACAATCTGACCCCACTTG 57.714 45.455 0.00 0.00 0.00 3.16
110 111 3.650942 TCTTACAATCTGACCCCACTTGT 59.349 43.478 0.00 0.00 34.63 3.16
111 112 2.568623 ACAATCTGACCCCACTTGTC 57.431 50.000 0.00 0.00 0.00 3.18
112 113 1.774254 ACAATCTGACCCCACTTGTCA 59.226 47.619 0.00 0.00 40.28 3.58
117 118 2.638480 TGACCCCACTTGTCAGAAAG 57.362 50.000 0.00 0.00 37.80 2.62
118 119 1.843851 TGACCCCACTTGTCAGAAAGT 59.156 47.619 0.00 0.00 41.08 2.66
127 128 5.409643 ACTTGTCAGAAAGTGATCAAACG 57.590 39.130 0.00 0.00 38.95 3.60
128 129 4.273480 ACTTGTCAGAAAGTGATCAAACGG 59.727 41.667 0.00 0.00 38.95 4.44
129 130 3.138304 TGTCAGAAAGTGATCAAACGGG 58.862 45.455 0.00 0.00 37.56 5.28
130 131 2.095718 GTCAGAAAGTGATCAAACGGGC 60.096 50.000 0.00 0.00 37.56 6.13
131 132 1.200020 CAGAAAGTGATCAAACGGGCC 59.800 52.381 0.00 0.00 0.00 5.80
132 133 1.202879 AGAAAGTGATCAAACGGGCCA 60.203 47.619 4.39 0.00 0.00 5.36
133 134 1.200020 GAAAGTGATCAAACGGGCCAG 59.800 52.381 4.39 1.85 0.00 4.85
134 135 0.400213 AAGTGATCAAACGGGCCAGA 59.600 50.000 10.86 0.00 0.00 3.86
135 136 0.620556 AGTGATCAAACGGGCCAGAT 59.379 50.000 10.86 1.45 0.00 2.90
136 137 1.017387 GTGATCAAACGGGCCAGATC 58.983 55.000 10.86 11.55 37.86 2.75
137 138 0.617935 TGATCAAACGGGCCAGATCA 59.382 50.000 10.86 18.31 43.14 2.92
138 139 1.017387 GATCAAACGGGCCAGATCAC 58.983 55.000 10.86 0.00 37.43 3.06
139 140 0.394352 ATCAAACGGGCCAGATCACC 60.394 55.000 10.86 0.00 0.00 4.02
140 141 1.002134 CAAACGGGCCAGATCACCT 60.002 57.895 10.86 0.00 0.00 4.00
141 142 1.002134 AAACGGGCCAGATCACCTG 60.002 57.895 10.86 6.70 42.55 4.00
142 143 1.488705 AAACGGGCCAGATCACCTGA 61.489 55.000 10.86 0.00 45.78 3.86
143 144 1.274703 AACGGGCCAGATCACCTGAT 61.275 55.000 10.86 1.20 45.78 2.90
155 156 4.713824 ATCACCTGATCAGTGCATTTTG 57.286 40.909 21.11 5.94 0.00 2.44
156 157 2.229543 TCACCTGATCAGTGCATTTTGC 59.770 45.455 21.11 0.00 45.29 3.68
174 175 9.797473 GCATTTTGCAAAAAGATTACTAGAAAC 57.203 29.630 27.10 3.43 44.26 2.78
175 176 9.993881 CATTTTGCAAAAAGATTACTAGAAACG 57.006 29.630 27.10 0.00 0.00 3.60
176 177 7.617533 TTTGCAAAAAGATTACTAGAAACGC 57.382 32.000 10.02 0.00 0.00 4.84
177 178 5.379003 TGCAAAAAGATTACTAGAAACGCG 58.621 37.500 3.53 3.53 0.00 6.01
178 179 4.786575 GCAAAAAGATTACTAGAAACGCGG 59.213 41.667 12.47 0.00 0.00 6.46
179 180 5.616204 GCAAAAAGATTACTAGAAACGCGGT 60.616 40.000 12.47 0.00 0.00 5.68
180 181 5.526010 AAAAGATTACTAGAAACGCGGTG 57.474 39.130 12.47 0.00 0.00 4.94
181 182 2.537401 AGATTACTAGAAACGCGGTGC 58.463 47.619 12.47 0.42 0.00 5.01
202 203 5.696260 GCGTTTTGCAAATAATTAGGGAC 57.304 39.130 13.65 3.79 45.45 4.46
203 204 5.407502 GCGTTTTGCAAATAATTAGGGACT 58.592 37.500 13.65 0.00 45.45 3.85
204 205 6.557110 GCGTTTTGCAAATAATTAGGGACTA 58.443 36.000 13.65 0.00 45.45 2.59
205 206 6.691388 GCGTTTTGCAAATAATTAGGGACTAG 59.309 38.462 13.65 0.00 43.09 2.57
206 207 7.193595 CGTTTTGCAAATAATTAGGGACTAGG 58.806 38.462 13.65 0.00 44.25 3.02
207 208 7.148137 CGTTTTGCAAATAATTAGGGACTAGGT 60.148 37.037 13.65 0.00 44.25 3.08
208 209 9.181061 GTTTTGCAAATAATTAGGGACTAGGTA 57.819 33.333 13.65 0.00 44.25 3.08
209 210 8.974060 TTTGCAAATAATTAGGGACTAGGTAG 57.026 34.615 8.05 0.00 44.25 3.18
210 211 7.685849 TGCAAATAATTAGGGACTAGGTAGT 57.314 36.000 0.00 0.00 44.25 2.73
211 212 8.097791 TGCAAATAATTAGGGACTAGGTAGTT 57.902 34.615 0.00 0.00 44.25 2.24
212 213 8.554011 TGCAAATAATTAGGGACTAGGTAGTTT 58.446 33.333 0.00 0.00 44.25 2.66
213 214 9.404848 GCAAATAATTAGGGACTAGGTAGTTTT 57.595 33.333 0.00 0.00 44.25 2.43
216 217 9.828039 AATAATTAGGGACTAGGTAGTTTTTCG 57.172 33.333 0.00 0.00 44.25 3.46
217 218 3.606595 AGGGACTAGGTAGTTTTTCGC 57.393 47.619 0.00 0.00 36.02 4.70
218 219 2.901839 AGGGACTAGGTAGTTTTTCGCA 59.098 45.455 0.00 0.00 36.02 5.10
219 220 3.325716 AGGGACTAGGTAGTTTTTCGCAA 59.674 43.478 0.00 0.00 36.02 4.85
220 221 4.067192 GGGACTAGGTAGTTTTTCGCAAA 58.933 43.478 0.00 0.00 36.50 3.68
221 222 4.153655 GGGACTAGGTAGTTTTTCGCAAAG 59.846 45.833 0.00 0.00 36.50 2.77
222 223 4.378149 GGACTAGGTAGTTTTTCGCAAAGC 60.378 45.833 0.00 0.00 36.50 3.51
223 224 4.386711 ACTAGGTAGTTTTTCGCAAAGCT 58.613 39.130 2.28 2.28 37.26 3.74
224 225 5.544650 ACTAGGTAGTTTTTCGCAAAGCTA 58.455 37.500 0.33 0.33 35.30 3.32
225 226 5.993441 ACTAGGTAGTTTTTCGCAAAGCTAA 59.007 36.000 5.76 0.00 37.42 3.09
226 227 5.104562 AGGTAGTTTTTCGCAAAGCTAAC 57.895 39.130 10.59 10.59 41.46 2.34
227 228 4.023450 AGGTAGTTTTTCGCAAAGCTAACC 60.023 41.667 13.97 12.60 41.87 2.85
228 229 3.364889 AGTTTTTCGCAAAGCTAACCC 57.635 42.857 0.00 0.00 32.06 4.11
229 230 2.035449 AGTTTTTCGCAAAGCTAACCCC 59.965 45.455 0.00 0.00 32.06 4.95
230 231 1.693627 TTTTCGCAAAGCTAACCCCA 58.306 45.000 0.00 0.00 0.00 4.96
231 232 1.693627 TTTCGCAAAGCTAACCCCAA 58.306 45.000 0.00 0.00 0.00 4.12
232 233 1.693627 TTCGCAAAGCTAACCCCAAA 58.306 45.000 0.00 0.00 0.00 3.28
233 234 1.917872 TCGCAAAGCTAACCCCAAAT 58.082 45.000 0.00 0.00 0.00 2.32
234 235 1.543802 TCGCAAAGCTAACCCCAAATG 59.456 47.619 0.00 0.00 0.00 2.32
235 236 1.272212 CGCAAAGCTAACCCCAAATGT 59.728 47.619 0.00 0.00 0.00 2.71
236 237 2.687370 GCAAAGCTAACCCCAAATGTG 58.313 47.619 0.00 0.00 0.00 3.21
237 238 2.612721 GCAAAGCTAACCCCAAATGTGG 60.613 50.000 0.00 0.00 45.53 4.17
238 239 2.632512 CAAAGCTAACCCCAAATGTGGT 59.367 45.455 0.00 0.00 44.30 4.16
239 240 1.923356 AGCTAACCCCAAATGTGGTG 58.077 50.000 0.00 0.00 44.30 4.17
240 241 0.894835 GCTAACCCCAAATGTGGTGG 59.105 55.000 0.00 4.55 44.30 4.61
241 242 1.825641 GCTAACCCCAAATGTGGTGGT 60.826 52.381 8.82 8.82 45.38 4.16
242 243 3.644953 AACCCCAAATGTGGTGGTT 57.355 47.368 17.68 17.68 45.93 3.67
243 244 3.644953 ACCCCAAATGTGGTGGTTT 57.355 47.368 8.82 0.00 42.60 3.27
244 245 1.886422 ACCCCAAATGTGGTGGTTTT 58.114 45.000 8.82 0.00 42.60 2.43
245 246 1.765904 ACCCCAAATGTGGTGGTTTTC 59.234 47.619 8.82 0.00 42.60 2.29
246 247 2.046292 CCCCAAATGTGGTGGTTTTCT 58.954 47.619 0.00 0.00 44.30 2.52
247 248 2.224257 CCCCAAATGTGGTGGTTTTCTG 60.224 50.000 0.00 0.00 44.30 3.02
248 249 2.482864 CCAAATGTGGTGGTTTTCTGC 58.517 47.619 0.00 0.00 40.42 4.26
249 250 2.158986 CCAAATGTGGTGGTTTTCTGCA 60.159 45.455 0.00 0.00 40.42 4.41
250 251 3.529533 CAAATGTGGTGGTTTTCTGCAA 58.470 40.909 0.00 0.00 0.00 4.08
251 252 4.128643 CAAATGTGGTGGTTTTCTGCAAT 58.871 39.130 0.00 0.00 0.00 3.56
252 253 4.420522 AATGTGGTGGTTTTCTGCAATT 57.579 36.364 0.00 0.00 0.00 2.32
253 254 3.451141 TGTGGTGGTTTTCTGCAATTC 57.549 42.857 0.00 0.00 0.00 2.17
254 255 2.762887 TGTGGTGGTTTTCTGCAATTCA 59.237 40.909 0.00 0.00 0.00 2.57
255 256 3.123050 GTGGTGGTTTTCTGCAATTCAC 58.877 45.455 0.00 0.00 0.00 3.18
256 257 3.030291 TGGTGGTTTTCTGCAATTCACT 58.970 40.909 0.00 0.00 0.00 3.41
257 258 3.068024 TGGTGGTTTTCTGCAATTCACTC 59.932 43.478 0.00 0.00 0.00 3.51
338 339 2.566833 TTGCTGCTACACTCATTGGT 57.433 45.000 0.00 0.00 0.00 3.67
373 374 4.049186 CGATTAACCCGGATTACACTCAG 58.951 47.826 0.73 0.00 0.00 3.35
615 616 2.066340 CCCACCACAGCAGGAACTA 58.934 57.895 0.00 0.00 36.02 2.24
682 684 2.280797 GAGGACACGCAGCCACAA 60.281 61.111 0.00 0.00 0.00 3.33
687 689 0.385974 GACACGCAGCCACAATTCAC 60.386 55.000 0.00 0.00 0.00 3.18
874 876 0.810016 GCGGACGTCTAGGTTTCTCT 59.190 55.000 16.46 0.00 0.00 3.10
876 878 2.421424 GCGGACGTCTAGGTTTCTCTTA 59.579 50.000 16.46 0.00 0.00 2.10
877 879 3.066481 GCGGACGTCTAGGTTTCTCTTAT 59.934 47.826 16.46 0.00 0.00 1.73
965 972 4.531426 TGGGCAACAAAGCGGGGT 62.531 61.111 0.00 0.00 39.74 4.95
969 976 2.520741 CAACAAAGCGGGGTGGGT 60.521 61.111 0.00 0.00 0.00 4.51
1040 1047 2.182030 GGTTCTCGAGGCGTGGAG 59.818 66.667 13.56 11.72 0.00 3.86
1320 1327 2.124570 CTCCGGGACATTGGGCTG 60.125 66.667 0.00 0.00 0.00 4.85
1390 1397 0.522180 CTCTCTGTACGGCGTCAAGT 59.478 55.000 19.21 0.00 0.00 3.16
1620 1627 1.068281 CCTGACGAGGTGATCCATGAG 59.932 57.143 0.00 0.00 34.16 2.90
1774 1783 4.853468 TGTATACTGGGATTTTGCCTCA 57.147 40.909 4.17 0.00 0.00 3.86
2003 2052 3.626028 AATCGTCAGGTTTGCTTGTTC 57.374 42.857 0.00 0.00 0.00 3.18
2063 2112 2.365293 GGCCAACAGTGAAAACCTGAAT 59.635 45.455 0.00 0.00 34.04 2.57
2100 2149 3.745799 TGCTTGGTATTCTTTTGACCGA 58.254 40.909 0.00 0.00 35.91 4.69
2310 2362 1.039856 GGGTGCTTGAAGGCAAAGAA 58.960 50.000 0.00 0.00 44.18 2.52
2402 2454 1.646189 GTTCCTCCGACTTCATCAGC 58.354 55.000 0.00 0.00 0.00 4.26
2403 2455 1.066858 GTTCCTCCGACTTCATCAGCA 60.067 52.381 0.00 0.00 0.00 4.41
2404 2456 1.489481 TCCTCCGACTTCATCAGCAT 58.511 50.000 0.00 0.00 0.00 3.79
2518 2596 0.527565 CCCCTGAACTGGATTTTGCG 59.472 55.000 0.00 0.00 0.00 4.85
2519 2597 0.109132 CCCTGAACTGGATTTTGCGC 60.109 55.000 0.00 0.00 0.00 6.09
2544 2622 2.288030 GCATTGGCATCCTGCTATTGAC 60.288 50.000 10.32 1.09 44.28 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.722201 GCTTCGACCCCGTCTGGAT 61.722 63.158 0.00 0.00 37.49 3.41
2 3 3.649277 CTGCTTCGACCCCGTCTGG 62.649 68.421 0.00 0.00 37.05 3.86
3 4 2.125912 CTGCTTCGACCCCGTCTG 60.126 66.667 0.00 0.00 37.05 3.51
4 5 3.382832 CCTGCTTCGACCCCGTCT 61.383 66.667 0.00 0.00 37.05 4.18
5 6 4.452733 CCCTGCTTCGACCCCGTC 62.453 72.222 0.00 0.00 37.05 4.79
21 22 1.205655 GAAAAAGCAATCAGAGCCCCC 59.794 52.381 0.00 0.00 0.00 5.40
22 23 2.174360 AGAAAAAGCAATCAGAGCCCC 58.826 47.619 0.00 0.00 0.00 5.80
23 24 3.949842 AAGAAAAAGCAATCAGAGCCC 57.050 42.857 0.00 0.00 0.00 5.19
24 25 7.147976 TCTAAAAAGAAAAAGCAATCAGAGCC 58.852 34.615 0.00 0.00 0.00 4.70
25 26 8.754230 ATCTAAAAAGAAAAAGCAATCAGAGC 57.246 30.769 0.00 0.00 0.00 4.09
26 27 9.351570 GGATCTAAAAAGAAAAAGCAATCAGAG 57.648 33.333 0.00 0.00 0.00 3.35
27 28 8.859090 TGGATCTAAAAAGAAAAAGCAATCAGA 58.141 29.630 0.00 0.00 0.00 3.27
28 29 9.136952 CTGGATCTAAAAAGAAAAAGCAATCAG 57.863 33.333 0.00 0.00 0.00 2.90
29 30 8.090214 CCTGGATCTAAAAAGAAAAAGCAATCA 58.910 33.333 0.00 0.00 0.00 2.57
30 31 7.547019 CCCTGGATCTAAAAAGAAAAAGCAATC 59.453 37.037 0.00 0.00 0.00 2.67
31 32 7.389232 CCCTGGATCTAAAAAGAAAAAGCAAT 58.611 34.615 0.00 0.00 0.00 3.56
32 33 6.239572 CCCCTGGATCTAAAAAGAAAAAGCAA 60.240 38.462 0.00 0.00 0.00 3.91
33 34 5.245977 CCCCTGGATCTAAAAAGAAAAAGCA 59.754 40.000 0.00 0.00 0.00 3.91
34 35 5.724328 CCCCTGGATCTAAAAAGAAAAAGC 58.276 41.667 0.00 0.00 0.00 3.51
35 36 5.245977 TGCCCCTGGATCTAAAAAGAAAAAG 59.754 40.000 0.00 0.00 0.00 2.27
36 37 5.151454 TGCCCCTGGATCTAAAAAGAAAAA 58.849 37.500 0.00 0.00 0.00 1.94
37 38 4.746466 TGCCCCTGGATCTAAAAAGAAAA 58.254 39.130 0.00 0.00 0.00 2.29
38 39 4.396357 TGCCCCTGGATCTAAAAAGAAA 57.604 40.909 0.00 0.00 0.00 2.52
39 40 4.264352 ACATGCCCCTGGATCTAAAAAGAA 60.264 41.667 0.00 0.00 0.00 2.52
40 41 3.269381 ACATGCCCCTGGATCTAAAAAGA 59.731 43.478 0.00 0.00 0.00 2.52
41 42 3.635591 ACATGCCCCTGGATCTAAAAAG 58.364 45.455 0.00 0.00 0.00 2.27
42 43 3.756082 ACATGCCCCTGGATCTAAAAA 57.244 42.857 0.00 0.00 0.00 1.94
43 44 4.167892 ACATACATGCCCCTGGATCTAAAA 59.832 41.667 0.00 0.00 0.00 1.52
44 45 3.721575 ACATACATGCCCCTGGATCTAAA 59.278 43.478 0.00 0.00 0.00 1.85
45 46 3.326521 ACATACATGCCCCTGGATCTAA 58.673 45.455 0.00 0.00 0.00 2.10
46 47 2.906389 GACATACATGCCCCTGGATCTA 59.094 50.000 0.00 0.00 0.00 1.98
47 48 1.701847 GACATACATGCCCCTGGATCT 59.298 52.381 0.00 0.00 0.00 2.75
48 49 1.421268 TGACATACATGCCCCTGGATC 59.579 52.381 0.00 0.00 0.00 3.36
49 50 1.521764 TGACATACATGCCCCTGGAT 58.478 50.000 0.00 0.00 0.00 3.41
50 51 1.294041 TTGACATACATGCCCCTGGA 58.706 50.000 0.00 0.00 0.00 3.86
51 52 2.142356 TTTGACATACATGCCCCTGG 57.858 50.000 0.00 0.00 0.00 4.45
52 53 3.091545 AGTTTTGACATACATGCCCCTG 58.908 45.455 0.00 0.00 0.00 4.45
53 54 3.456380 AGTTTTGACATACATGCCCCT 57.544 42.857 0.00 0.00 0.00 4.79
54 55 4.244862 CAAAGTTTTGACATACATGCCCC 58.755 43.478 0.00 0.00 40.55 5.80
55 56 3.679502 GCAAAGTTTTGACATACATGCCC 59.320 43.478 8.70 0.00 40.55 5.36
56 57 3.679502 GGCAAAGTTTTGACATACATGCC 59.320 43.478 8.70 15.67 45.54 4.40
57 58 4.908966 GGCAAAGTTTTGACATACATGC 57.091 40.909 8.70 8.95 45.54 4.06
65 66 2.860136 GCTGACTTGGCAAAGTTTTGAC 59.140 45.455 8.18 6.15 46.84 3.18
66 67 2.760092 AGCTGACTTGGCAAAGTTTTGA 59.240 40.909 8.18 0.00 46.84 2.69
67 68 3.169355 AGCTGACTTGGCAAAGTTTTG 57.831 42.857 8.18 2.93 46.84 2.44
68 69 3.448660 AGAAGCTGACTTGGCAAAGTTTT 59.551 39.130 8.18 1.10 46.84 2.43
69 70 3.026694 AGAAGCTGACTTGGCAAAGTTT 58.973 40.909 8.18 0.00 46.84 2.66
70 71 2.659428 AGAAGCTGACTTGGCAAAGTT 58.341 42.857 8.18 0.00 46.84 2.66
72 73 3.565482 TGTAAGAAGCTGACTTGGCAAAG 59.435 43.478 14.20 0.00 35.82 2.77
73 74 3.550820 TGTAAGAAGCTGACTTGGCAAA 58.449 40.909 14.20 0.00 35.82 3.68
74 75 3.207265 TGTAAGAAGCTGACTTGGCAA 57.793 42.857 14.20 0.00 35.82 4.52
75 76 2.928801 TGTAAGAAGCTGACTTGGCA 57.071 45.000 14.20 10.76 35.82 4.92
76 77 4.006319 AGATTGTAAGAAGCTGACTTGGC 58.994 43.478 14.20 8.92 35.82 4.52
77 78 5.240891 TCAGATTGTAAGAAGCTGACTTGG 58.759 41.667 14.20 0.14 35.82 3.61
82 83 3.055094 GGGGTCAGATTGTAAGAAGCTGA 60.055 47.826 0.72 0.72 33.58 4.26
83 84 3.274288 GGGGTCAGATTGTAAGAAGCTG 58.726 50.000 0.00 0.00 0.00 4.24
84 85 2.912956 TGGGGTCAGATTGTAAGAAGCT 59.087 45.455 0.00 0.00 0.00 3.74
85 86 3.010420 GTGGGGTCAGATTGTAAGAAGC 58.990 50.000 0.00 0.00 0.00 3.86
86 87 4.559862 AGTGGGGTCAGATTGTAAGAAG 57.440 45.455 0.00 0.00 0.00 2.85
87 88 4.104102 ACAAGTGGGGTCAGATTGTAAGAA 59.896 41.667 0.00 0.00 34.29 2.52
88 89 3.650942 ACAAGTGGGGTCAGATTGTAAGA 59.349 43.478 0.00 0.00 34.29 2.10
89 90 4.003648 GACAAGTGGGGTCAGATTGTAAG 58.996 47.826 0.00 0.00 35.43 2.34
90 91 3.392947 TGACAAGTGGGGTCAGATTGTAA 59.607 43.478 0.00 0.00 40.16 2.41
91 92 2.976185 TGACAAGTGGGGTCAGATTGTA 59.024 45.455 0.00 0.00 40.16 2.41
92 93 1.774254 TGACAAGTGGGGTCAGATTGT 59.226 47.619 0.00 0.00 40.16 2.71
93 94 2.566833 TGACAAGTGGGGTCAGATTG 57.433 50.000 0.00 0.00 40.16 2.67
98 99 1.843851 ACTTTCTGACAAGTGGGGTCA 59.156 47.619 0.00 0.00 42.62 4.02
99 100 2.222027 CACTTTCTGACAAGTGGGGTC 58.778 52.381 17.48 0.00 46.84 4.46
100 101 2.348411 CACTTTCTGACAAGTGGGGT 57.652 50.000 17.48 0.00 46.84 4.95
105 106 4.273480 CCGTTTGATCACTTTCTGACAAGT 59.727 41.667 0.00 1.18 37.49 3.16
106 107 4.319766 CCCGTTTGATCACTTTCTGACAAG 60.320 45.833 0.00 0.00 0.00 3.16
107 108 3.563808 CCCGTTTGATCACTTTCTGACAA 59.436 43.478 0.00 0.00 0.00 3.18
108 109 3.138304 CCCGTTTGATCACTTTCTGACA 58.862 45.455 0.00 0.00 0.00 3.58
109 110 2.095718 GCCCGTTTGATCACTTTCTGAC 60.096 50.000 0.00 0.00 0.00 3.51
110 111 2.151202 GCCCGTTTGATCACTTTCTGA 58.849 47.619 0.00 0.00 0.00 3.27
111 112 1.200020 GGCCCGTTTGATCACTTTCTG 59.800 52.381 0.00 0.00 0.00 3.02
112 113 1.202879 TGGCCCGTTTGATCACTTTCT 60.203 47.619 0.00 0.00 0.00 2.52
113 114 1.200020 CTGGCCCGTTTGATCACTTTC 59.800 52.381 0.00 0.00 0.00 2.62
114 115 1.202879 TCTGGCCCGTTTGATCACTTT 60.203 47.619 0.00 0.00 0.00 2.66
115 116 0.400213 TCTGGCCCGTTTGATCACTT 59.600 50.000 0.00 0.00 0.00 3.16
116 117 0.620556 ATCTGGCCCGTTTGATCACT 59.379 50.000 0.00 0.00 0.00 3.41
117 118 1.017387 GATCTGGCCCGTTTGATCAC 58.983 55.000 0.00 0.00 36.34 3.06
118 119 0.617935 TGATCTGGCCCGTTTGATCA 59.382 50.000 0.00 9.12 41.74 2.92
119 120 1.017387 GTGATCTGGCCCGTTTGATC 58.983 55.000 0.00 6.57 36.72 2.92
120 121 0.394352 GGTGATCTGGCCCGTTTGAT 60.394 55.000 0.00 0.00 0.00 2.57
121 122 1.002624 GGTGATCTGGCCCGTTTGA 60.003 57.895 0.00 0.00 0.00 2.69
122 123 1.002134 AGGTGATCTGGCCCGTTTG 60.002 57.895 0.00 0.00 0.00 2.93
123 124 1.002134 CAGGTGATCTGGCCCGTTT 60.002 57.895 0.00 0.00 39.76 3.60
124 125 1.274703 ATCAGGTGATCTGGCCCGTT 61.275 55.000 0.00 0.00 43.53 4.44
125 126 1.690219 GATCAGGTGATCTGGCCCGT 61.690 60.000 11.98 0.00 45.60 5.28
126 127 1.070445 GATCAGGTGATCTGGCCCG 59.930 63.158 11.98 0.00 45.60 6.13
132 133 7.117199 GCAAAATGCACTGATCAGGTGATCT 62.117 44.000 26.08 1.31 45.54 2.75
133 134 4.968287 GCAAAATGCACTGATCAGGTGATC 60.968 45.833 26.08 12.29 45.54 2.92
134 135 3.119245 GCAAAATGCACTGATCAGGTGAT 60.119 43.478 26.08 11.52 44.26 3.06
135 136 2.229543 GCAAAATGCACTGATCAGGTGA 59.770 45.455 26.08 9.71 44.26 4.02
136 137 2.602878 GCAAAATGCACTGATCAGGTG 58.397 47.619 26.08 20.51 44.26 4.00
148 149 9.797473 GTTTCTAGTAATCTTTTTGCAAAATGC 57.203 29.630 24.39 13.30 45.29 3.56
149 150 9.993881 CGTTTCTAGTAATCTTTTTGCAAAATG 57.006 29.630 24.39 24.47 0.00 2.32
150 151 8.699749 GCGTTTCTAGTAATCTTTTTGCAAAAT 58.300 29.630 24.39 12.59 0.00 1.82
151 152 7.096803 CGCGTTTCTAGTAATCTTTTTGCAAAA 60.097 33.333 20.46 20.46 0.00 2.44
152 153 6.358558 CGCGTTTCTAGTAATCTTTTTGCAAA 59.641 34.615 8.05 8.05 0.00 3.68
153 154 5.849081 CGCGTTTCTAGTAATCTTTTTGCAA 59.151 36.000 0.00 0.00 0.00 4.08
154 155 5.379003 CGCGTTTCTAGTAATCTTTTTGCA 58.621 37.500 0.00 0.00 0.00 4.08
155 156 4.786575 CCGCGTTTCTAGTAATCTTTTTGC 59.213 41.667 4.92 0.00 0.00 3.68
156 157 5.788531 CACCGCGTTTCTAGTAATCTTTTTG 59.211 40.000 4.92 0.00 0.00 2.44
157 158 5.616204 GCACCGCGTTTCTAGTAATCTTTTT 60.616 40.000 4.92 0.00 0.00 1.94
158 159 4.142966 GCACCGCGTTTCTAGTAATCTTTT 60.143 41.667 4.92 0.00 0.00 2.27
159 160 3.370061 GCACCGCGTTTCTAGTAATCTTT 59.630 43.478 4.92 0.00 0.00 2.52
160 161 2.928116 GCACCGCGTTTCTAGTAATCTT 59.072 45.455 4.92 0.00 0.00 2.40
161 162 2.537401 GCACCGCGTTTCTAGTAATCT 58.463 47.619 4.92 0.00 0.00 2.40
162 163 2.992744 GCACCGCGTTTCTAGTAATC 57.007 50.000 4.92 0.00 0.00 1.75
180 181 5.407502 AGTCCCTAATTATTTGCAAAACGC 58.592 37.500 17.19 0.00 42.89 4.84
181 182 7.148137 ACCTAGTCCCTAATTATTTGCAAAACG 60.148 37.037 17.19 1.35 0.00 3.60
182 183 8.063200 ACCTAGTCCCTAATTATTTGCAAAAC 57.937 34.615 17.19 6.36 0.00 2.43
183 184 9.403583 CTACCTAGTCCCTAATTATTTGCAAAA 57.596 33.333 17.19 0.11 0.00 2.44
184 185 8.554011 ACTACCTAGTCCCTAATTATTTGCAAA 58.446 33.333 15.44 15.44 0.00 3.68
185 186 8.097791 ACTACCTAGTCCCTAATTATTTGCAA 57.902 34.615 0.00 0.00 0.00 4.08
186 187 7.685849 ACTACCTAGTCCCTAATTATTTGCA 57.314 36.000 0.00 0.00 0.00 4.08
187 188 8.975663 AAACTACCTAGTCCCTAATTATTTGC 57.024 34.615 0.00 0.00 34.99 3.68
190 191 9.828039 CGAAAAACTACCTAGTCCCTAATTATT 57.172 33.333 0.00 0.00 34.99 1.40
191 192 7.930325 GCGAAAAACTACCTAGTCCCTAATTAT 59.070 37.037 0.00 0.00 34.99 1.28
192 193 7.093377 TGCGAAAAACTACCTAGTCCCTAATTA 60.093 37.037 0.00 0.00 34.99 1.40
193 194 6.111382 GCGAAAAACTACCTAGTCCCTAATT 58.889 40.000 0.00 0.00 34.99 1.40
194 195 5.188359 TGCGAAAAACTACCTAGTCCCTAAT 59.812 40.000 0.00 0.00 34.99 1.73
195 196 4.527816 TGCGAAAAACTACCTAGTCCCTAA 59.472 41.667 0.00 0.00 34.99 2.69
196 197 4.088634 TGCGAAAAACTACCTAGTCCCTA 58.911 43.478 0.00 0.00 34.99 3.53
197 198 2.901839 TGCGAAAAACTACCTAGTCCCT 59.098 45.455 0.00 0.00 34.99 4.20
198 199 3.323751 TGCGAAAAACTACCTAGTCCC 57.676 47.619 0.00 0.00 34.99 4.46
199 200 4.378149 GCTTTGCGAAAAACTACCTAGTCC 60.378 45.833 0.00 0.00 34.99 3.85
200 201 4.451435 AGCTTTGCGAAAAACTACCTAGTC 59.549 41.667 0.00 0.00 34.99 2.59
201 202 4.386711 AGCTTTGCGAAAAACTACCTAGT 58.613 39.130 0.00 0.00 38.39 2.57
202 203 6.304882 GTTAGCTTTGCGAAAAACTACCTAG 58.695 40.000 0.00 0.00 0.00 3.02
203 204 5.179929 GGTTAGCTTTGCGAAAAACTACCTA 59.820 40.000 0.00 0.00 0.00 3.08
204 205 4.023450 GGTTAGCTTTGCGAAAAACTACCT 60.023 41.667 0.00 0.00 0.00 3.08
205 206 4.224433 GGTTAGCTTTGCGAAAAACTACC 58.776 43.478 0.00 1.47 0.00 3.18
206 207 4.224433 GGGTTAGCTTTGCGAAAAACTAC 58.776 43.478 0.00 0.00 0.00 2.73
207 208 3.253921 GGGGTTAGCTTTGCGAAAAACTA 59.746 43.478 0.00 0.00 0.00 2.24
208 209 2.035449 GGGGTTAGCTTTGCGAAAAACT 59.965 45.455 0.00 0.00 0.00 2.66
209 210 2.223852 TGGGGTTAGCTTTGCGAAAAAC 60.224 45.455 0.00 0.00 0.00 2.43
210 211 2.032620 TGGGGTTAGCTTTGCGAAAAA 58.967 42.857 0.00 0.00 0.00 1.94
211 212 1.693627 TGGGGTTAGCTTTGCGAAAA 58.306 45.000 0.00 0.00 0.00 2.29
212 213 1.693627 TTGGGGTTAGCTTTGCGAAA 58.306 45.000 0.00 0.00 0.00 3.46
213 214 1.693627 TTTGGGGTTAGCTTTGCGAA 58.306 45.000 0.00 0.00 0.00 4.70
214 215 1.543802 CATTTGGGGTTAGCTTTGCGA 59.456 47.619 0.00 0.00 0.00 5.10
215 216 1.272212 ACATTTGGGGTTAGCTTTGCG 59.728 47.619 0.00 0.00 0.00 4.85
216 217 2.612721 CCACATTTGGGGTTAGCTTTGC 60.613 50.000 0.00 0.00 39.57 3.68
217 218 3.317603 CCACATTTGGGGTTAGCTTTG 57.682 47.619 0.00 0.00 39.57 2.77
229 230 3.176552 TGCAGAAAACCACCACATTTG 57.823 42.857 0.00 0.00 0.00 2.32
230 231 3.902881 TTGCAGAAAACCACCACATTT 57.097 38.095 0.00 0.00 0.00 2.32
231 232 4.141756 TGAATTGCAGAAAACCACCACATT 60.142 37.500 0.00 0.00 0.00 2.71
232 233 3.387374 TGAATTGCAGAAAACCACCACAT 59.613 39.130 0.00 0.00 0.00 3.21
233 234 2.762887 TGAATTGCAGAAAACCACCACA 59.237 40.909 0.00 0.00 0.00 4.17
234 235 3.123050 GTGAATTGCAGAAAACCACCAC 58.877 45.455 0.00 0.00 0.00 4.16
235 236 3.030291 AGTGAATTGCAGAAAACCACCA 58.970 40.909 0.00 0.00 0.00 4.17
236 237 3.068024 TGAGTGAATTGCAGAAAACCACC 59.932 43.478 0.00 0.00 0.00 4.61
237 238 4.044426 GTGAGTGAATTGCAGAAAACCAC 58.956 43.478 0.00 0.00 0.00 4.16
238 239 3.953612 AGTGAGTGAATTGCAGAAAACCA 59.046 39.130 0.00 0.00 0.00 3.67
239 240 4.574599 AGTGAGTGAATTGCAGAAAACC 57.425 40.909 0.00 0.00 0.00 3.27
240 241 5.149977 GCTAGTGAGTGAATTGCAGAAAAC 58.850 41.667 0.00 0.00 0.00 2.43
241 242 4.216257 GGCTAGTGAGTGAATTGCAGAAAA 59.784 41.667 0.00 0.00 0.00 2.29
242 243 3.753272 GGCTAGTGAGTGAATTGCAGAAA 59.247 43.478 0.00 0.00 0.00 2.52
243 244 3.008375 AGGCTAGTGAGTGAATTGCAGAA 59.992 43.478 0.00 0.00 0.00 3.02
244 245 2.568956 AGGCTAGTGAGTGAATTGCAGA 59.431 45.455 0.00 0.00 0.00 4.26
245 246 2.676839 CAGGCTAGTGAGTGAATTGCAG 59.323 50.000 0.00 0.00 0.00 4.41
246 247 2.302733 TCAGGCTAGTGAGTGAATTGCA 59.697 45.455 0.00 0.00 0.00 4.08
247 248 2.935201 CTCAGGCTAGTGAGTGAATTGC 59.065 50.000 2.83 0.00 39.39 3.56
248 249 4.462508 TCTCAGGCTAGTGAGTGAATTG 57.537 45.455 9.50 0.00 43.89 2.32
249 250 6.798427 TTATCTCAGGCTAGTGAGTGAATT 57.202 37.500 9.50 0.00 43.89 2.17
250 251 6.740960 GCATTATCTCAGGCTAGTGAGTGAAT 60.741 42.308 9.50 7.86 43.89 2.57
251 252 5.452496 GCATTATCTCAGGCTAGTGAGTGAA 60.452 44.000 9.50 6.32 43.89 3.18
252 253 4.038522 GCATTATCTCAGGCTAGTGAGTGA 59.961 45.833 9.50 0.00 43.89 3.41
253 254 4.305769 GCATTATCTCAGGCTAGTGAGTG 58.694 47.826 9.50 3.37 43.89 3.51
254 255 3.323403 GGCATTATCTCAGGCTAGTGAGT 59.677 47.826 9.50 2.11 43.89 3.41
255 256 3.323115 TGGCATTATCTCAGGCTAGTGAG 59.677 47.826 4.36 4.36 44.71 3.51
256 257 3.308401 TGGCATTATCTCAGGCTAGTGA 58.692 45.455 0.00 0.00 0.00 3.41
257 258 3.661944 CTGGCATTATCTCAGGCTAGTG 58.338 50.000 0.00 0.00 31.20 2.74
373 374 2.542597 TCAACAACCAGTACGTGTGAC 58.457 47.619 0.00 0.00 0.00 3.67
682 684 2.158559 TGCGTGCCAGTATTTGTGAAT 58.841 42.857 0.00 0.00 0.00 2.57
687 689 2.162208 AGAACATGCGTGCCAGTATTTG 59.838 45.455 5.64 0.00 0.00 2.32
1040 1047 2.288025 TACTTGACCACCCCGAGCC 61.288 63.158 0.00 0.00 0.00 4.70
1284 1291 1.182385 GCGAGAGGATGGGGTAGAGG 61.182 65.000 0.00 0.00 0.00 3.69
1774 1783 7.426606 ACCCAAAAGTTTATAACAAGGTGTT 57.573 32.000 0.00 0.00 43.88 3.32
1824 1833 0.516877 TTCAGCCTTCATTTGCGACG 59.483 50.000 0.00 0.00 0.00 5.12
2003 2052 3.081804 ACCTTTGTTTCCGCTTATCTGG 58.918 45.455 0.00 0.00 0.00 3.86
2063 2112 4.019321 ACCAAGCAGAGACAAATAGGCTTA 60.019 41.667 0.00 0.00 39.36 3.09
2100 2149 8.716674 AATATATCCACAGAATTTGCCATCTT 57.283 30.769 0.00 0.00 0.00 2.40
2293 2345 2.620585 AGACTTCTTTGCCTTCAAGCAC 59.379 45.455 0.00 0.00 43.97 4.40
2333 2385 6.152831 GGAGAGGTTATTGGTGCAAATTTACT 59.847 38.462 0.00 0.00 0.00 2.24
2438 2495 4.471386 ACATACCAGCTTTACCATCTCAGT 59.529 41.667 0.00 0.00 0.00 3.41
2544 2622 4.647424 ACCATATTTTGTACATTGGCCG 57.353 40.909 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.