Multiple sequence alignment - TraesCS4A01G391500

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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 TraesCS4A01G391500 chr4A 100.000 3497 0 0 1 3497 668155253 668151757 0.000000e+00 6458.0
1 TraesCS4A01G391500 chr4A 85.393 89 6 3 2466 2547 668152641 668152553 6.220000e-13 86.1
2 TraesCS4A01G391500 chr4A 85.393 89 6 3 2613 2701 668152788 668152707 6.220000e-13 86.1
3 TraesCS4A01G391500 chr7D 96.270 2681 93 4 360 3040 53504676 53502003 0.000000e+00 4390.0
4 TraesCS4A01G391500 chr7D 91.967 361 24 2 3095 3455 53501687 53501332 5.210000e-138 501.0
5 TraesCS4A01G391500 chr7D 86.517 89 5 3 2466 2547 53502428 53502340 1.340000e-14 91.6
6 TraesCS4A01G391500 chr7D 85.393 89 6 3 2613 2701 53502575 53502494 6.220000e-13 86.1
7 TraesCS4A01G391500 chr7A 95.612 1504 64 1 360 1863 55890262 55888761 0.000000e+00 2410.0
8 TraesCS4A01G391500 chr7A 85.294 340 32 14 3121 3455 55888228 55887902 5.590000e-88 335.0
9 TraesCS4A01G391500 chr7A 97.917 48 1 0 3450 3497 721499033 721499080 2.240000e-12 84.2
10 TraesCS4A01G391500 chr5B 79.785 2048 386 19 360 2398 511606607 511608635 0.000000e+00 1463.0
11 TraesCS4A01G391500 chr5B 90.625 64 1 3 3438 3497 415650876 415650814 2.890000e-11 80.5
12 TraesCS4A01G391500 chr5B 95.918 49 2 0 3449 3497 576317570 576317522 2.890000e-11 80.5
13 TraesCS4A01G391500 chr5D 79.532 2052 389 22 360 2398 423834469 423836502 0.000000e+00 1434.0
14 TraesCS4A01G391500 chr5D 94.444 54 0 1 3447 3497 371848570 371848517 2.890000e-11 80.5
15 TraesCS4A01G391500 chr5D 94.231 52 2 1 3447 3497 556876790 556876739 1.040000e-10 78.7
16 TraesCS4A01G391500 chr3A 98.050 359 5 1 1 359 11403437 11403081 1.070000e-174 623.0
17 TraesCS4A01G391500 chr3A 95.543 359 14 1 1 359 720083463 720083819 1.090000e-159 573.0
18 TraesCS4A01G391500 chr3D 95.918 49 2 0 3449 3497 109258678 109258630 2.890000e-11 80.5
19 TraesCS4A01G391500 chr2D 94.444 54 0 1 3447 3497 489817173 489817120 2.890000e-11 80.5
20 TraesCS4A01G391500 chr2D 87.037 54 6 1 304 356 36426244 36426191 3.770000e-05 60.2
21 TraesCS4A01G391500 chr2B 95.918 49 2 0 3449 3497 168605930 168605978 2.890000e-11 80.5
22 TraesCS4A01G391500 chr2B 92.857 56 0 3 3445 3497 22013619 22013565 1.040000e-10 78.7
23 TraesCS4A01G391500 chr6A 84.507 71 10 1 287 356 23852792 23852722 6.260000e-08 69.4
24 TraesCS4A01G391500 chr1B 85.000 60 7 2 302 360 34992362 34992304 3.770000e-05 60.2
25 TraesCS4A01G391500 chr1B 96.970 33 1 0 314 346 560786387 560786355 4.880000e-04 56.5
26 TraesCS4A01G391500 chr1D 90.476 42 2 2 313 352 84727072 84727031 2.000000e-03 54.7


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 TraesCS4A01G391500 chr4A 668151757 668155253 3496 True 2210.066667 6458 90.26200 1 3497 3 chr4A.!!$R1 3496
1 TraesCS4A01G391500 chr7D 53501332 53504676 3344 True 1267.175000 4390 90.03675 360 3455 4 chr7D.!!$R1 3095
2 TraesCS4A01G391500 chr7A 55887902 55890262 2360 True 1372.500000 2410 90.45300 360 3455 2 chr7A.!!$R1 3095
3 TraesCS4A01G391500 chr5B 511606607 511608635 2028 False 1463.000000 1463 79.78500 360 2398 1 chr5B.!!$F1 2038
4 TraesCS4A01G391500 chr5D 423834469 423836502 2033 False 1434.000000 1434 79.53200 360 2398 1 chr5D.!!$F1 2038

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
53 54 0.038801 GGAGCTTGCTTGGCTTTGAC 60.039 55.0 0.0 0.0 40.4 3.18 F
161 162 0.104934 AGGGCACGGGAGAGGAATAT 60.105 55.0 0.0 0.0 0.0 1.28 F
265 266 0.394488 TTGTGGGCCGAAAGTGTTGA 60.394 50.0 0.0 0.0 0.0 3.18 F
266 267 0.394488 TGTGGGCCGAAAGTGTTGAA 60.394 50.0 0.0 0.0 0.0 2.69 F
825 826 0.517316 GGTACGCTTGGCAAACTCAG 59.483 55.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1020 1021 1.342374 CCCTTCTGCCCTTTTAGCCAT 60.342 52.381 0.00 0.00 0.00 4.40 R
2135 2139 1.873591 ACAGGTTCAGCTTGCTTAACG 59.126 47.619 11.85 4.18 0.00 3.18 R
2265 2269 2.045536 GGCTCCCAGCAGTTCCTG 60.046 66.667 0.00 0.00 44.75 3.86 R
2391 2395 2.287547 CCCACCACATGAACGAAACAAG 60.288 50.000 0.00 0.00 0.00 3.16 R
2598 2602 0.321653 ATCCTTCAGGCAACCGTGTC 60.322 55.000 0.00 0.00 34.44 3.67 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.129148 GGAAGGCGCAAGGGGGAT 62.129 66.667 10.83 0.00 38.28 3.85
19 20 2.830370 GAAGGCGCAAGGGGGATG 60.830 66.667 10.83 0.00 38.28 3.51
20 21 4.447342 AAGGCGCAAGGGGGATGG 62.447 66.667 10.83 0.00 38.28 3.51
24 25 4.856801 CGCAAGGGGGATGGGACG 62.857 72.222 0.00 0.00 32.93 4.79
25 26 3.728373 GCAAGGGGGATGGGACGT 61.728 66.667 0.00 0.00 0.00 4.34
26 27 2.272146 CAAGGGGGATGGGACGTG 59.728 66.667 0.00 0.00 0.00 4.49
27 28 3.728373 AAGGGGGATGGGACGTGC 61.728 66.667 0.00 0.00 0.00 5.34
30 31 4.530857 GGGGATGGGACGTGCGAG 62.531 72.222 0.00 0.00 0.00 5.03
31 32 3.458163 GGGATGGGACGTGCGAGA 61.458 66.667 0.00 0.00 0.00 4.04
32 33 2.105128 GGATGGGACGTGCGAGAG 59.895 66.667 0.00 0.00 0.00 3.20
50 51 3.359002 CGGAGCTTGCTTGGCTTT 58.641 55.556 0.00 0.00 40.40 3.51
51 52 1.080974 CGGAGCTTGCTTGGCTTTG 60.081 57.895 0.00 0.00 40.40 2.77
52 53 1.518056 CGGAGCTTGCTTGGCTTTGA 61.518 55.000 0.00 0.00 40.40 2.69
53 54 0.038801 GGAGCTTGCTTGGCTTTGAC 60.039 55.000 0.00 0.00 40.40 3.18
54 55 0.386478 GAGCTTGCTTGGCTTTGACG 60.386 55.000 0.00 0.00 40.40 4.35
55 56 1.372128 GCTTGCTTGGCTTTGACGG 60.372 57.895 0.00 0.00 0.00 4.79
56 57 1.795170 GCTTGCTTGGCTTTGACGGA 61.795 55.000 0.00 0.00 0.00 4.69
57 58 0.239347 CTTGCTTGGCTTTGACGGAG 59.761 55.000 0.00 0.00 0.00 4.63
58 59 1.172180 TTGCTTGGCTTTGACGGAGG 61.172 55.000 0.00 0.00 0.00 4.30
59 60 1.302511 GCTTGGCTTTGACGGAGGA 60.303 57.895 0.00 0.00 0.00 3.71
60 61 1.301677 GCTTGGCTTTGACGGAGGAG 61.302 60.000 0.00 0.00 0.00 3.69
61 62 0.674895 CTTGGCTTTGACGGAGGAGG 60.675 60.000 0.00 0.00 0.00 4.30
62 63 1.125093 TTGGCTTTGACGGAGGAGGA 61.125 55.000 0.00 0.00 0.00 3.71
63 64 1.219393 GGCTTTGACGGAGGAGGAG 59.781 63.158 0.00 0.00 0.00 3.69
64 65 1.448717 GCTTTGACGGAGGAGGAGC 60.449 63.158 0.00 0.00 0.00 4.70
65 66 1.893919 GCTTTGACGGAGGAGGAGCT 61.894 60.000 0.00 0.00 0.00 4.09
66 67 0.174617 CTTTGACGGAGGAGGAGCTC 59.825 60.000 4.71 4.71 0.00 4.09
67 68 1.595993 TTTGACGGAGGAGGAGCTCG 61.596 60.000 7.83 0.00 0.00 5.03
68 69 2.124653 GACGGAGGAGGAGCTCGA 60.125 66.667 7.83 0.00 0.00 4.04
69 70 2.124487 ACGGAGGAGGAGCTCGAG 60.124 66.667 8.45 8.45 0.00 4.04
70 71 3.591835 CGGAGGAGGAGCTCGAGC 61.592 72.222 30.01 30.01 42.49 5.03
71 72 3.223589 GGAGGAGGAGCTCGAGCC 61.224 72.222 32.94 23.14 43.38 4.70
72 73 2.123897 GAGGAGGAGCTCGAGCCT 60.124 66.667 32.94 23.64 43.38 4.58
75 76 3.591835 GAGGAGCTCGAGCCTCCG 61.592 72.222 32.00 6.51 43.91 4.63
104 105 4.815108 GCCGGCGGAAAAGGGGAT 62.815 66.667 33.44 0.00 0.00 3.85
105 106 2.044352 CCGGCGGAAAAGGGGATT 60.044 61.111 24.41 0.00 0.00 3.01
106 107 1.680989 CCGGCGGAAAAGGGGATTT 60.681 57.895 24.41 0.00 0.00 2.17
107 108 1.254975 CCGGCGGAAAAGGGGATTTT 61.255 55.000 24.41 0.00 43.88 1.82
108 109 0.606096 CGGCGGAAAAGGGGATTTTT 59.394 50.000 0.00 0.00 41.24 1.94
126 127 2.806945 TTTTTCCTGGATCTGGCGAT 57.193 45.000 0.00 0.00 0.00 4.58
127 128 2.806945 TTTTCCTGGATCTGGCGATT 57.193 45.000 0.00 0.00 0.00 3.34
128 129 2.806945 TTTCCTGGATCTGGCGATTT 57.193 45.000 0.00 0.00 0.00 2.17
129 130 3.924114 TTTCCTGGATCTGGCGATTTA 57.076 42.857 0.00 0.00 0.00 1.40
130 131 3.475566 TTCCTGGATCTGGCGATTTAG 57.524 47.619 0.00 0.00 0.00 1.85
131 132 1.694150 TCCTGGATCTGGCGATTTAGG 59.306 52.381 0.00 12.22 35.78 2.69
132 133 1.271054 CCTGGATCTGGCGATTTAGGG 60.271 57.143 0.00 0.00 33.16 3.53
133 134 1.417890 CTGGATCTGGCGATTTAGGGT 59.582 52.381 0.00 0.00 0.00 4.34
134 135 1.843851 TGGATCTGGCGATTTAGGGTT 59.156 47.619 0.00 0.00 0.00 4.11
135 136 2.222027 GGATCTGGCGATTTAGGGTTG 58.778 52.381 0.00 0.00 0.00 3.77
136 137 2.222027 GATCTGGCGATTTAGGGTTGG 58.778 52.381 0.00 0.00 0.00 3.77
137 138 1.281419 TCTGGCGATTTAGGGTTGGA 58.719 50.000 0.00 0.00 0.00 3.53
138 139 1.631388 TCTGGCGATTTAGGGTTGGAA 59.369 47.619 0.00 0.00 0.00 3.53
139 140 2.017049 CTGGCGATTTAGGGTTGGAAG 58.983 52.381 0.00 0.00 0.00 3.46
140 141 1.353022 TGGCGATTTAGGGTTGGAAGT 59.647 47.619 0.00 0.00 0.00 3.01
141 142 1.743394 GGCGATTTAGGGTTGGAAGTG 59.257 52.381 0.00 0.00 0.00 3.16
142 143 2.617021 GGCGATTTAGGGTTGGAAGTGA 60.617 50.000 0.00 0.00 0.00 3.41
143 144 2.678336 GCGATTTAGGGTTGGAAGTGAG 59.322 50.000 0.00 0.00 0.00 3.51
144 145 3.270877 CGATTTAGGGTTGGAAGTGAGG 58.729 50.000 0.00 0.00 0.00 3.86
145 146 3.621558 GATTTAGGGTTGGAAGTGAGGG 58.378 50.000 0.00 0.00 0.00 4.30
146 147 0.696501 TTAGGGTTGGAAGTGAGGGC 59.303 55.000 0.00 0.00 0.00 5.19
147 148 0.474854 TAGGGTTGGAAGTGAGGGCA 60.475 55.000 0.00 0.00 0.00 5.36
148 149 1.603739 GGGTTGGAAGTGAGGGCAC 60.604 63.158 0.00 0.00 45.49 5.01
156 157 3.775654 GTGAGGGCACGGGAGAGG 61.776 72.222 0.00 0.00 34.94 3.69
157 158 3.992641 TGAGGGCACGGGAGAGGA 61.993 66.667 0.00 0.00 0.00 3.71
158 159 2.683933 GAGGGCACGGGAGAGGAA 60.684 66.667 0.00 0.00 0.00 3.36
159 160 2.041265 AGGGCACGGGAGAGGAAT 59.959 61.111 0.00 0.00 0.00 3.01
160 161 0.759436 GAGGGCACGGGAGAGGAATA 60.759 60.000 0.00 0.00 0.00 1.75
161 162 0.104934 AGGGCACGGGAGAGGAATAT 60.105 55.000 0.00 0.00 0.00 1.28
162 163 1.149288 AGGGCACGGGAGAGGAATATA 59.851 52.381 0.00 0.00 0.00 0.86
163 164 1.275573 GGGCACGGGAGAGGAATATAC 59.724 57.143 0.00 0.00 0.00 1.47
164 165 1.275573 GGCACGGGAGAGGAATATACC 59.724 57.143 0.00 0.00 0.00 2.73
165 166 1.275573 GCACGGGAGAGGAATATACCC 59.724 57.143 0.00 0.00 37.42 3.69
166 167 2.605257 CACGGGAGAGGAATATACCCA 58.395 52.381 0.00 0.00 40.45 4.51
167 168 3.173965 CACGGGAGAGGAATATACCCAT 58.826 50.000 0.00 0.00 40.45 4.00
168 169 3.583086 CACGGGAGAGGAATATACCCATT 59.417 47.826 0.00 0.00 40.45 3.16
169 170 3.838903 ACGGGAGAGGAATATACCCATTC 59.161 47.826 0.00 0.00 40.45 2.67
170 171 3.119101 CGGGAGAGGAATATACCCATTCG 60.119 52.174 0.00 0.00 40.45 3.34
171 172 3.369576 GGGAGAGGAATATACCCATTCGC 60.370 52.174 0.00 0.00 40.20 4.70
172 173 3.512680 GAGAGGAATATACCCATTCGCG 58.487 50.000 0.00 0.00 36.04 5.87
173 174 2.233922 AGAGGAATATACCCATTCGCGG 59.766 50.000 6.13 0.00 36.04 6.46
180 181 4.918201 CCCATTCGCGGGCCTCTC 62.918 72.222 6.13 0.00 40.07 3.20
192 193 2.677228 CCTCTCGGGGGCATGTTT 59.323 61.111 0.00 0.00 0.00 2.83
193 194 1.750399 CCTCTCGGGGGCATGTTTG 60.750 63.158 0.00 0.00 0.00 2.93
194 195 1.750399 CTCTCGGGGGCATGTTTGG 60.750 63.158 0.00 0.00 0.00 3.28
195 196 2.755469 CTCGGGGGCATGTTTGGG 60.755 66.667 0.00 0.00 0.00 4.12
201 202 4.699626 GGCATGTTTGGGCCTTTG 57.300 55.556 4.53 0.00 46.74 2.77
202 203 1.003476 GGCATGTTTGGGCCTTTGG 60.003 57.895 4.53 0.00 46.74 3.28
212 213 2.279851 GCCTTTGGCGCGGTTTTT 60.280 55.556 8.83 0.00 39.62 1.94
226 227 3.350377 TTTTTCCCGCGCAAGGAG 58.650 55.556 15.12 0.69 34.08 3.69
227 228 2.265182 TTTTTCCCGCGCAAGGAGG 61.265 57.895 15.12 3.81 34.08 4.30
240 241 4.115199 GGAGGCACTGGCGGGAAT 62.115 66.667 0.00 0.00 41.55 3.01
241 242 2.044946 GAGGCACTGGCGGGAATT 60.045 61.111 0.00 0.00 41.55 2.17
242 243 2.361610 AGGCACTGGCGGGAATTG 60.362 61.111 0.00 0.00 42.47 2.32
243 244 2.361104 GGCACTGGCGGGAATTGA 60.361 61.111 0.00 0.00 42.47 2.57
244 245 1.754234 GGCACTGGCGGGAATTGAT 60.754 57.895 0.00 0.00 42.47 2.57
245 246 1.322538 GGCACTGGCGGGAATTGATT 61.323 55.000 0.00 0.00 42.47 2.57
246 247 0.532115 GCACTGGCGGGAATTGATTT 59.468 50.000 0.00 0.00 0.00 2.17
247 248 1.066929 GCACTGGCGGGAATTGATTTT 60.067 47.619 0.00 0.00 0.00 1.82
248 249 2.609350 CACTGGCGGGAATTGATTTTG 58.391 47.619 0.00 0.00 0.00 2.44
249 250 2.029110 CACTGGCGGGAATTGATTTTGT 60.029 45.455 0.00 0.00 0.00 2.83
250 251 2.029110 ACTGGCGGGAATTGATTTTGTG 60.029 45.455 0.00 0.00 0.00 3.33
251 252 1.274728 TGGCGGGAATTGATTTTGTGG 59.725 47.619 0.00 0.00 0.00 4.17
252 253 1.405391 GGCGGGAATTGATTTTGTGGG 60.405 52.381 0.00 0.00 0.00 4.61
253 254 2.006552 GCGGGAATTGATTTTGTGGGC 61.007 52.381 0.00 0.00 0.00 5.36
254 255 1.405391 CGGGAATTGATTTTGTGGGCC 60.405 52.381 0.00 0.00 0.00 5.80
255 256 1.405391 GGGAATTGATTTTGTGGGCCG 60.405 52.381 0.00 0.00 0.00 6.13
256 257 1.548269 GGAATTGATTTTGTGGGCCGA 59.452 47.619 0.00 0.00 0.00 5.54
257 258 2.028567 GGAATTGATTTTGTGGGCCGAA 60.029 45.455 0.00 0.00 0.00 4.30
258 259 3.556004 GGAATTGATTTTGTGGGCCGAAA 60.556 43.478 0.00 0.05 0.00 3.46
259 260 2.810439 TTGATTTTGTGGGCCGAAAG 57.190 45.000 0.00 0.00 29.93 2.62
260 261 1.698506 TGATTTTGTGGGCCGAAAGT 58.301 45.000 0.00 0.00 29.93 2.66
261 262 1.339610 TGATTTTGTGGGCCGAAAGTG 59.660 47.619 0.00 0.00 29.93 3.16
262 263 1.339929 GATTTTGTGGGCCGAAAGTGT 59.660 47.619 0.00 0.00 29.93 3.55
263 264 1.187087 TTTTGTGGGCCGAAAGTGTT 58.813 45.000 0.00 0.00 0.00 3.32
264 265 0.457851 TTTGTGGGCCGAAAGTGTTG 59.542 50.000 0.00 0.00 0.00 3.33
265 266 0.394488 TTGTGGGCCGAAAGTGTTGA 60.394 50.000 0.00 0.00 0.00 3.18
266 267 0.394488 TGTGGGCCGAAAGTGTTGAA 60.394 50.000 0.00 0.00 0.00 2.69
267 268 0.741915 GTGGGCCGAAAGTGTTGAAA 59.258 50.000 0.00 0.00 0.00 2.69
268 269 1.339929 GTGGGCCGAAAGTGTTGAAAT 59.660 47.619 0.00 0.00 0.00 2.17
269 270 2.035632 TGGGCCGAAAGTGTTGAAATT 58.964 42.857 0.00 0.00 0.00 1.82
270 271 2.432510 TGGGCCGAAAGTGTTGAAATTT 59.567 40.909 0.00 0.00 0.00 1.82
271 272 3.118592 TGGGCCGAAAGTGTTGAAATTTT 60.119 39.130 0.00 0.00 0.00 1.82
272 273 3.874543 GGGCCGAAAGTGTTGAAATTTTT 59.125 39.130 0.00 0.00 0.00 1.94
290 291 4.705337 TTTTTGGCCGAAACGCTATATT 57.295 36.364 18.22 0.00 0.00 1.28
291 292 4.705337 TTTTGGCCGAAACGCTATATTT 57.295 36.364 14.56 0.00 0.00 1.40
292 293 3.955771 TTGGCCGAAACGCTATATTTC 57.044 42.857 0.00 0.00 33.52 2.17
293 294 2.907634 TGGCCGAAACGCTATATTTCA 58.092 42.857 0.00 0.00 36.09 2.69
294 295 2.869801 TGGCCGAAACGCTATATTTCAG 59.130 45.455 0.00 0.00 36.09 3.02
295 296 2.870411 GGCCGAAACGCTATATTTCAGT 59.130 45.455 0.00 0.00 36.09 3.41
296 297 4.053295 GGCCGAAACGCTATATTTCAGTA 58.947 43.478 0.00 0.00 36.09 2.74
297 298 4.084693 GGCCGAAACGCTATATTTCAGTAC 60.085 45.833 0.00 0.00 36.09 2.73
298 299 4.743644 GCCGAAACGCTATATTTCAGTACT 59.256 41.667 0.00 0.00 36.09 2.73
299 300 5.233689 GCCGAAACGCTATATTTCAGTACTT 59.766 40.000 0.00 0.00 36.09 2.24
300 301 6.637365 CCGAAACGCTATATTTCAGTACTTG 58.363 40.000 0.00 0.00 36.09 3.16
301 302 6.120812 CGAAACGCTATATTTCAGTACTTGC 58.879 40.000 0.00 0.00 36.09 4.01
302 303 6.019801 CGAAACGCTATATTTCAGTACTTGCT 60.020 38.462 0.00 0.00 36.09 3.91
303 304 6.589830 AACGCTATATTTCAGTACTTGCTG 57.410 37.500 0.00 0.00 37.81 4.41
304 305 5.902681 ACGCTATATTTCAGTACTTGCTGA 58.097 37.500 0.00 0.00 43.03 4.26
316 317 8.621532 TCAGTACTTGCTGAAATTAGTGAAAT 57.378 30.769 0.00 0.00 41.93 2.17
317 318 9.066892 TCAGTACTTGCTGAAATTAGTGAAATT 57.933 29.630 0.00 0.00 41.93 1.82
440 441 3.798515 ACCTACTGGTTCTGGGATGTTA 58.201 45.455 0.00 0.00 46.05 2.41
466 467 3.209410 CATCAGGCATCTTGACCTTACC 58.791 50.000 0.00 0.00 32.56 2.85
530 531 3.746045 TGACTTCGCTTGAGGTACTTT 57.254 42.857 0.00 0.00 41.55 2.66
650 651 8.351495 TCAAGACATTTCACAATTTTTACAGC 57.649 30.769 0.00 0.00 0.00 4.40
810 811 4.072131 TCAGTGCCTTCAGAAATTGGTAC 58.928 43.478 1.20 1.20 35.82 3.34
825 826 0.517316 GGTACGCTTGGCAAACTCAG 59.483 55.000 0.00 0.00 0.00 3.35
853 854 6.757010 AGTTGTATCTAGACGGCAACTATTTG 59.243 38.462 24.71 0.00 45.12 2.32
863 864 3.666902 CGGCAACTATTTGAACGGTTCTG 60.667 47.826 20.53 10.32 34.24 3.02
883 884 7.271511 GTTCTGTATCAGAGGAACATCTTGAT 58.728 38.462 0.00 0.00 41.75 2.57
955 956 5.048643 CCTGATGATCAGCTCAAATTGGATC 60.049 44.000 16.81 0.00 42.98 3.36
956 957 4.825634 TGATGATCAGCTCAAATTGGATCC 59.174 41.667 12.92 4.20 37.44 3.36
1020 1021 5.796502 AAATGGGACCTCATTTTCCTCTA 57.203 39.130 12.57 0.00 42.63 2.43
1044 1045 2.437413 CTAAAAGGGCAGAAGGGTGTC 58.563 52.381 0.00 0.00 0.00 3.67
1049 1050 0.822121 GGGCAGAAGGGTGTCGTTTT 60.822 55.000 0.00 0.00 0.00 2.43
1152 1153 9.691362 TTGAACATCTCTTTTAACCAAATAAGC 57.309 29.630 0.00 0.00 0.00 3.09
1209 1210 6.711194 CCTCAGCAGTGATATTTGATCTGAAT 59.289 38.462 0.00 0.00 30.18 2.57
1287 1288 6.776094 GGACATTTCCAGAAACTCTTTATCG 58.224 40.000 0.00 0.00 42.30 2.92
1425 1426 4.335416 TGGATTTAGCAAAGAACCTCCTG 58.665 43.478 0.00 0.00 0.00 3.86
1458 1459 2.802816 CCCTGTCTGTTCAGAAGAAACG 59.197 50.000 3.99 0.00 37.61 3.60
1819 1823 4.225267 ACCCCTTAGTGTGGAGTTATGAAG 59.775 45.833 0.00 0.00 0.00 3.02
1893 1897 3.826157 CAGTGGTAATGAAAGGCCAAGAA 59.174 43.478 5.01 0.00 32.26 2.52
1908 1912 4.072131 GCCAAGAACTTGATTACACCAGA 58.928 43.478 14.99 0.00 42.93 3.86
1944 1948 1.407656 TTGGCCTCGACTTGTCCTGT 61.408 55.000 3.32 0.00 0.00 4.00
2091 2095 3.057174 AGTCTCTCGACCTGTCATTCAAC 60.057 47.826 0.00 0.00 41.16 3.18
2093 2097 1.067846 TCTCGACCTGTCATTCAACGG 60.068 52.381 0.00 0.00 0.00 4.44
2106 2110 1.153939 CAACGGACTCTCTGGCGAG 60.154 63.158 0.00 0.00 38.67 5.03
2114 2118 2.167487 GACTCTCTGGCGAGATTCCTTT 59.833 50.000 0.00 0.00 44.86 3.11
2127 2131 3.583086 AGATTCCTTTTGGTCTCTCGGAA 59.417 43.478 0.00 0.00 41.38 4.30
2135 2139 1.201647 TGGTCTCTCGGAAATCACGAC 59.798 52.381 0.00 0.00 36.25 4.34
2172 2176 6.370442 TGAACCTGTCATACAATAACCTTTCG 59.630 38.462 0.00 0.00 0.00 3.46
2230 2234 0.934901 CGACCCAGCATCGTCGTATG 60.935 60.000 10.28 0.00 45.20 2.39
2265 2269 2.764637 TTTGCGGGCCTCCTCTTTCC 62.765 60.000 0.84 0.00 0.00 3.13
2391 2395 4.517285 TCTGGCTGGTGTTCATTATCTTC 58.483 43.478 0.00 0.00 0.00 2.87
2442 2446 2.108514 CGGAGCAATGCCATCACGT 61.109 57.895 0.00 0.00 0.00 4.49
2559 2563 1.661112 GGAACTAGCGTTGATGCAGTC 59.339 52.381 0.00 0.00 37.31 3.51
2598 2602 4.918129 GCCATGCCATTGCGCTCG 62.918 66.667 9.73 0.00 41.78 5.03
2624 2628 0.899717 TTGCCTGAAGGATTGGTGCC 60.900 55.000 0.00 0.00 37.39 5.01
2755 2759 9.092876 GATGTTGTGATTTGGACAGTTTAAAAA 57.907 29.630 0.00 0.00 0.00 1.94
2810 2814 4.216257 ACCTTTTCGAAGATGTGGATTGTG 59.784 41.667 0.00 0.00 35.04 3.33
2831 2835 8.446489 TTGTGCTGTTTGTATTGATTATTTCG 57.554 30.769 0.00 0.00 0.00 3.46
2865 2869 9.449719 CTTAGATTGTTTTAGATAGTGGTGGTT 57.550 33.333 0.00 0.00 0.00 3.67
2879 2883 9.191995 GATAGTGGTGGTTTCTAAATTGTTTTG 57.808 33.333 0.00 0.00 0.00 2.44
2953 3036 9.180678 GGTGTTGTTGTCTAAATAGTTTCATTG 57.819 33.333 0.00 0.00 0.00 2.82
3050 3249 5.007332 GTGTTGTCAAGTACGAAGAAACCAT 59.993 40.000 0.00 0.00 0.00 3.55
3127 3473 5.000012 AGTACTTGTTCTAGCTTCATCCG 58.000 43.478 0.00 0.00 0.00 4.18
3177 3523 9.675553 CTATATACGTTTGATGCATATGTTTCG 57.324 33.333 0.00 3.16 0.00 3.46
3184 3530 3.935828 TGATGCATATGTTTCGTTCCGAA 59.064 39.130 0.00 0.00 44.28 4.30
3277 3628 3.520290 TCAGATGAACATACGTGTCCC 57.480 47.619 0.00 0.00 37.67 4.46
3278 3629 2.167693 TCAGATGAACATACGTGTCCCC 59.832 50.000 0.00 0.00 37.67 4.81
3284 3635 2.443390 ATACGTGTCCCCGGGGAG 60.443 66.667 43.53 32.06 46.16 4.30
3291 3642 3.352748 TCCCCGGGGAGTAGCTCA 61.353 66.667 39.67 14.59 39.76 4.26
3301 3652 0.099082 GAGTAGCTCACGGTCTTCGG 59.901 60.000 0.00 0.00 44.45 4.30
3312 3663 1.597461 GTCTTCGGTCTGGGAAGGG 59.403 63.158 2.12 0.00 40.95 3.95
3332 3683 6.218108 AGGGGATAAACTAAACTAGACGTG 57.782 41.667 0.00 0.00 0.00 4.49
3455 3806 6.313164 GCAACTACAGTTTGATTAGTACTCCC 59.687 42.308 0.00 0.00 35.83 4.30
3456 3807 7.612677 CAACTACAGTTTGATTAGTACTCCCT 58.387 38.462 0.00 0.00 35.83 4.20
3457 3808 7.407393 ACTACAGTTTGATTAGTACTCCCTC 57.593 40.000 0.00 0.00 0.00 4.30
3458 3809 5.678955 ACAGTTTGATTAGTACTCCCTCC 57.321 43.478 0.00 0.00 0.00 4.30
3459 3810 4.159879 ACAGTTTGATTAGTACTCCCTCCG 59.840 45.833 0.00 0.00 0.00 4.63
3460 3811 4.159879 CAGTTTGATTAGTACTCCCTCCGT 59.840 45.833 0.00 0.00 0.00 4.69
3461 3812 4.776308 AGTTTGATTAGTACTCCCTCCGTT 59.224 41.667 0.00 0.00 0.00 4.44
3462 3813 5.247792 AGTTTGATTAGTACTCCCTCCGTTT 59.752 40.000 0.00 0.00 0.00 3.60
3463 3814 5.750352 TTGATTAGTACTCCCTCCGTTTT 57.250 39.130 0.00 0.00 0.00 2.43
3464 3815 5.750352 TGATTAGTACTCCCTCCGTTTTT 57.250 39.130 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.129148 ATCCCCCTTGCGCCTTCC 62.129 66.667 4.18 0.00 0.00 3.46
2 3 2.830370 CATCCCCCTTGCGCCTTC 60.830 66.667 4.18 0.00 0.00 3.46
3 4 4.447342 CCATCCCCCTTGCGCCTT 62.447 66.667 4.18 0.00 0.00 4.35
7 8 4.856801 CGTCCCATCCCCCTTGCG 62.857 72.222 0.00 0.00 0.00 4.85
8 9 3.728373 ACGTCCCATCCCCCTTGC 61.728 66.667 0.00 0.00 0.00 4.01
9 10 2.272146 CACGTCCCATCCCCCTTG 59.728 66.667 0.00 0.00 0.00 3.61
10 11 3.728373 GCACGTCCCATCCCCCTT 61.728 66.667 0.00 0.00 0.00 3.95
13 14 4.530857 CTCGCACGTCCCATCCCC 62.531 72.222 0.00 0.00 0.00 4.81
14 15 3.432051 CTCTCGCACGTCCCATCCC 62.432 68.421 0.00 0.00 0.00 3.85
15 16 2.105128 CTCTCGCACGTCCCATCC 59.895 66.667 0.00 0.00 0.00 3.51
16 17 2.583593 GCTCTCGCACGTCCCATC 60.584 66.667 0.00 0.00 35.78 3.51
17 18 4.498520 CGCTCTCGCACGTCCCAT 62.499 66.667 0.00 0.00 35.30 4.00
20 21 4.838486 CTCCGCTCTCGCACGTCC 62.838 72.222 0.00 0.00 35.30 4.79
23 24 4.785512 AAGCTCCGCTCTCGCACG 62.786 66.667 0.00 0.00 38.25 5.34
24 25 3.184683 CAAGCTCCGCTCTCGCAC 61.185 66.667 0.00 0.00 38.25 5.34
26 27 4.810661 AGCAAGCTCCGCTCTCGC 62.811 66.667 4.80 0.00 38.25 5.03
27 28 2.125753 AAGCAAGCTCCGCTCTCG 60.126 61.111 10.75 0.00 38.25 4.04
28 29 2.105466 CCAAGCAAGCTCCGCTCTC 61.105 63.158 10.75 0.00 38.25 3.20
29 30 2.046507 CCAAGCAAGCTCCGCTCT 60.047 61.111 10.75 0.26 38.25 4.09
30 31 3.808656 GCCAAGCAAGCTCCGCTC 61.809 66.667 10.75 0.00 38.25 5.03
31 32 3.857309 AAGCCAAGCAAGCTCCGCT 62.857 57.895 4.80 4.80 40.49 5.52
32 33 2.924105 AAAGCCAAGCAAGCTCCGC 61.924 57.895 0.00 0.00 40.49 5.54
33 34 1.080974 CAAAGCCAAGCAAGCTCCG 60.081 57.895 0.00 0.00 40.49 4.63
34 35 0.038801 GTCAAAGCCAAGCAAGCTCC 60.039 55.000 0.00 0.00 40.49 4.70
35 36 0.386478 CGTCAAAGCCAAGCAAGCTC 60.386 55.000 0.00 0.00 40.49 4.09
36 37 1.656441 CGTCAAAGCCAAGCAAGCT 59.344 52.632 0.00 0.00 44.19 3.74
37 38 1.372128 CCGTCAAAGCCAAGCAAGC 60.372 57.895 0.00 0.00 0.00 4.01
38 39 0.239347 CTCCGTCAAAGCCAAGCAAG 59.761 55.000 0.00 0.00 0.00 4.01
39 40 1.172180 CCTCCGTCAAAGCCAAGCAA 61.172 55.000 0.00 0.00 0.00 3.91
40 41 1.600636 CCTCCGTCAAAGCCAAGCA 60.601 57.895 0.00 0.00 0.00 3.91
41 42 1.301677 CTCCTCCGTCAAAGCCAAGC 61.302 60.000 0.00 0.00 0.00 4.01
42 43 0.674895 CCTCCTCCGTCAAAGCCAAG 60.675 60.000 0.00 0.00 0.00 3.61
43 44 1.125093 TCCTCCTCCGTCAAAGCCAA 61.125 55.000 0.00 0.00 0.00 4.52
44 45 1.535444 TCCTCCTCCGTCAAAGCCA 60.535 57.895 0.00 0.00 0.00 4.75
45 46 1.219393 CTCCTCCTCCGTCAAAGCC 59.781 63.158 0.00 0.00 0.00 4.35
46 47 1.448717 GCTCCTCCTCCGTCAAAGC 60.449 63.158 0.00 0.00 0.00 3.51
47 48 0.174617 GAGCTCCTCCTCCGTCAAAG 59.825 60.000 0.87 0.00 0.00 2.77
48 49 1.595993 CGAGCTCCTCCTCCGTCAAA 61.596 60.000 8.47 0.00 0.00 2.69
49 50 2.046864 CGAGCTCCTCCTCCGTCAA 61.047 63.158 8.47 0.00 0.00 3.18
50 51 2.438614 CGAGCTCCTCCTCCGTCA 60.439 66.667 8.47 0.00 0.00 4.35
51 52 2.124653 TCGAGCTCCTCCTCCGTC 60.125 66.667 8.47 0.00 0.00 4.79
52 53 2.124487 CTCGAGCTCCTCCTCCGT 60.124 66.667 8.47 0.00 0.00 4.69
53 54 3.591835 GCTCGAGCTCCTCCTCCG 61.592 72.222 29.88 0.00 38.21 4.63
54 55 3.223589 GGCTCGAGCTCCTCCTCC 61.224 72.222 34.46 13.48 41.70 4.30
55 56 2.123897 AGGCTCGAGCTCCTCCTC 60.124 66.667 34.46 17.44 41.70 3.71
56 57 2.123897 GAGGCTCGAGCTCCTCCT 60.124 66.667 34.46 23.24 42.30 3.69
58 59 3.591835 CGGAGGCTCGAGCTCCTC 61.592 72.222 33.52 30.34 46.25 3.71
87 88 4.815108 ATCCCCTTTTCCGCCGGC 62.815 66.667 19.07 19.07 0.00 6.13
88 89 1.254975 AAAATCCCCTTTTCCGCCGG 61.255 55.000 0.00 0.00 31.23 6.13
89 90 0.606096 AAAAATCCCCTTTTCCGCCG 59.394 50.000 0.00 0.00 36.01 6.46
107 108 2.806945 ATCGCCAGATCCAGGAAAAA 57.193 45.000 6.00 0.00 29.44 1.94
108 109 2.806945 AATCGCCAGATCCAGGAAAA 57.193 45.000 6.00 0.00 35.74 2.29
109 110 2.806945 AAATCGCCAGATCCAGGAAA 57.193 45.000 6.00 0.00 35.74 3.13
110 111 2.104792 CCTAAATCGCCAGATCCAGGAA 59.895 50.000 6.00 0.00 38.80 3.36
111 112 1.694150 CCTAAATCGCCAGATCCAGGA 59.306 52.381 6.00 0.00 38.80 3.86
112 113 1.271054 CCCTAAATCGCCAGATCCAGG 60.271 57.143 0.00 0.00 37.43 4.45
113 114 1.417890 ACCCTAAATCGCCAGATCCAG 59.582 52.381 0.00 0.00 35.74 3.86
114 115 1.507140 ACCCTAAATCGCCAGATCCA 58.493 50.000 0.00 0.00 35.74 3.41
115 116 2.222027 CAACCCTAAATCGCCAGATCC 58.778 52.381 0.00 0.00 35.74 3.36
116 117 2.158813 TCCAACCCTAAATCGCCAGATC 60.159 50.000 0.00 0.00 35.74 2.75
117 118 1.843851 TCCAACCCTAAATCGCCAGAT 59.156 47.619 0.00 0.00 39.12 2.90
118 119 1.281419 TCCAACCCTAAATCGCCAGA 58.719 50.000 0.00 0.00 0.00 3.86
119 120 2.017049 CTTCCAACCCTAAATCGCCAG 58.983 52.381 0.00 0.00 0.00 4.85
120 121 1.353022 ACTTCCAACCCTAAATCGCCA 59.647 47.619 0.00 0.00 0.00 5.69
121 122 1.743394 CACTTCCAACCCTAAATCGCC 59.257 52.381 0.00 0.00 0.00 5.54
122 123 2.678336 CTCACTTCCAACCCTAAATCGC 59.322 50.000 0.00 0.00 0.00 4.58
123 124 3.270877 CCTCACTTCCAACCCTAAATCG 58.729 50.000 0.00 0.00 0.00 3.34
124 125 3.621558 CCCTCACTTCCAACCCTAAATC 58.378 50.000 0.00 0.00 0.00 2.17
125 126 2.291605 GCCCTCACTTCCAACCCTAAAT 60.292 50.000 0.00 0.00 0.00 1.40
126 127 1.074889 GCCCTCACTTCCAACCCTAAA 59.925 52.381 0.00 0.00 0.00 1.85
127 128 0.696501 GCCCTCACTTCCAACCCTAA 59.303 55.000 0.00 0.00 0.00 2.69
128 129 0.474854 TGCCCTCACTTCCAACCCTA 60.475 55.000 0.00 0.00 0.00 3.53
129 130 1.774217 TGCCCTCACTTCCAACCCT 60.774 57.895 0.00 0.00 0.00 4.34
130 131 1.603739 GTGCCCTCACTTCCAACCC 60.604 63.158 0.00 0.00 40.03 4.11
131 132 1.966451 CGTGCCCTCACTTCCAACC 60.966 63.158 0.00 0.00 40.99 3.77
132 133 1.966451 CCGTGCCCTCACTTCCAAC 60.966 63.158 0.00 0.00 40.99 3.77
133 134 2.429930 CCGTGCCCTCACTTCCAA 59.570 61.111 0.00 0.00 40.99 3.53
134 135 3.636231 CCCGTGCCCTCACTTCCA 61.636 66.667 0.00 0.00 40.99 3.53
135 136 3.316573 CTCCCGTGCCCTCACTTCC 62.317 68.421 0.00 0.00 40.99 3.46
136 137 2.232298 CTCTCCCGTGCCCTCACTTC 62.232 65.000 0.00 0.00 40.99 3.01
137 138 2.203788 TCTCCCGTGCCCTCACTT 60.204 61.111 0.00 0.00 40.99 3.16
138 139 2.681778 CTCTCCCGTGCCCTCACT 60.682 66.667 0.00 0.00 40.99 3.41
139 140 3.775654 CCTCTCCCGTGCCCTCAC 61.776 72.222 0.00 0.00 39.78 3.51
140 141 2.822643 ATTCCTCTCCCGTGCCCTCA 62.823 60.000 0.00 0.00 0.00 3.86
141 142 0.759436 TATTCCTCTCCCGTGCCCTC 60.759 60.000 0.00 0.00 0.00 4.30
142 143 0.104934 ATATTCCTCTCCCGTGCCCT 60.105 55.000 0.00 0.00 0.00 5.19
143 144 1.275573 GTATATTCCTCTCCCGTGCCC 59.724 57.143 0.00 0.00 0.00 5.36
144 145 1.275573 GGTATATTCCTCTCCCGTGCC 59.724 57.143 0.00 0.00 0.00 5.01
145 146 1.275573 GGGTATATTCCTCTCCCGTGC 59.724 57.143 0.00 0.00 0.00 5.34
146 147 2.605257 TGGGTATATTCCTCTCCCGTG 58.395 52.381 0.00 0.00 40.86 4.94
147 148 3.562108 ATGGGTATATTCCTCTCCCGT 57.438 47.619 0.00 0.00 40.86 5.28
148 149 3.119101 CGAATGGGTATATTCCTCTCCCG 60.119 52.174 0.00 0.00 40.86 5.14
149 150 3.369576 GCGAATGGGTATATTCCTCTCCC 60.370 52.174 0.00 0.00 38.68 4.30
150 151 3.676324 CGCGAATGGGTATATTCCTCTCC 60.676 52.174 0.00 0.00 34.34 3.71
151 152 3.512680 CGCGAATGGGTATATTCCTCTC 58.487 50.000 0.00 0.00 34.34 3.20
152 153 2.233922 CCGCGAATGGGTATATTCCTCT 59.766 50.000 8.23 0.00 34.34 3.69
153 154 2.618053 CCGCGAATGGGTATATTCCTC 58.382 52.381 8.23 0.00 34.34 3.71
154 155 1.278127 CCCGCGAATGGGTATATTCCT 59.722 52.381 8.23 0.00 44.76 3.36
155 156 1.734163 CCCGCGAATGGGTATATTCC 58.266 55.000 8.23 0.00 44.76 3.01
176 177 1.750399 CCAAACATGCCCCCGAGAG 60.750 63.158 0.00 0.00 0.00 3.20
177 178 2.354729 CCAAACATGCCCCCGAGA 59.645 61.111 0.00 0.00 0.00 4.04
178 179 2.755469 CCCAAACATGCCCCCGAG 60.755 66.667 0.00 0.00 0.00 4.63
181 182 4.720680 AGGCCCAAACATGCCCCC 62.721 66.667 0.00 0.00 0.00 5.40
182 183 2.223443 AAAGGCCCAAACATGCCCC 61.223 57.895 0.00 0.00 0.00 5.80
183 184 1.003476 CAAAGGCCCAAACATGCCC 60.003 57.895 0.00 0.00 0.00 5.36
184 185 1.003476 CCAAAGGCCCAAACATGCC 60.003 57.895 0.00 0.00 0.00 4.40
185 186 1.672030 GCCAAAGGCCCAAACATGC 60.672 57.895 0.00 0.00 44.06 4.06
186 187 4.699626 GCCAAAGGCCCAAACATG 57.300 55.556 0.00 0.00 44.06 3.21
195 196 2.279851 AAAAACCGCGCCAAAGGC 60.280 55.556 0.00 0.00 46.75 4.35
209 210 2.265182 CCTCCTTGCGCGGGAAAAA 61.265 57.895 19.79 0.00 31.92 1.94
210 211 2.671619 CCTCCTTGCGCGGGAAAA 60.672 61.111 19.79 0.36 31.92 2.29
223 224 3.645268 AATTCCCGCCAGTGCCTCC 62.645 63.158 0.00 0.00 0.00 4.30
224 225 2.044946 AATTCCCGCCAGTGCCTC 60.045 61.111 0.00 0.00 0.00 4.70
225 226 2.215451 ATCAATTCCCGCCAGTGCCT 62.215 55.000 0.00 0.00 0.00 4.75
226 227 1.322538 AATCAATTCCCGCCAGTGCC 61.323 55.000 0.00 0.00 0.00 5.01
227 228 0.532115 AAATCAATTCCCGCCAGTGC 59.468 50.000 0.00 0.00 0.00 4.40
228 229 2.029110 ACAAAATCAATTCCCGCCAGTG 60.029 45.455 0.00 0.00 0.00 3.66
229 230 2.029110 CACAAAATCAATTCCCGCCAGT 60.029 45.455 0.00 0.00 0.00 4.00
230 231 2.609350 CACAAAATCAATTCCCGCCAG 58.391 47.619 0.00 0.00 0.00 4.85
231 232 1.274728 CCACAAAATCAATTCCCGCCA 59.725 47.619 0.00 0.00 0.00 5.69
232 233 1.405391 CCCACAAAATCAATTCCCGCC 60.405 52.381 0.00 0.00 0.00 6.13
233 234 2.006552 GCCCACAAAATCAATTCCCGC 61.007 52.381 0.00 0.00 0.00 6.13
234 235 1.405391 GGCCCACAAAATCAATTCCCG 60.405 52.381 0.00 0.00 0.00 5.14
235 236 1.405391 CGGCCCACAAAATCAATTCCC 60.405 52.381 0.00 0.00 0.00 3.97
236 237 1.548269 TCGGCCCACAAAATCAATTCC 59.452 47.619 0.00 0.00 0.00 3.01
237 238 3.311486 TTCGGCCCACAAAATCAATTC 57.689 42.857 0.00 0.00 0.00 2.17
238 239 3.070878 ACTTTCGGCCCACAAAATCAATT 59.929 39.130 0.00 0.00 0.00 2.32
239 240 2.632512 ACTTTCGGCCCACAAAATCAAT 59.367 40.909 0.00 0.00 0.00 2.57
240 241 2.035632 ACTTTCGGCCCACAAAATCAA 58.964 42.857 0.00 0.00 0.00 2.57
241 242 1.339610 CACTTTCGGCCCACAAAATCA 59.660 47.619 0.00 0.00 0.00 2.57
242 243 1.339929 ACACTTTCGGCCCACAAAATC 59.660 47.619 0.00 0.00 0.00 2.17
243 244 1.408969 ACACTTTCGGCCCACAAAAT 58.591 45.000 0.00 0.00 0.00 1.82
244 245 1.134965 CAACACTTTCGGCCCACAAAA 60.135 47.619 0.00 0.00 0.00 2.44
245 246 0.457851 CAACACTTTCGGCCCACAAA 59.542 50.000 0.00 0.00 0.00 2.83
246 247 0.394488 TCAACACTTTCGGCCCACAA 60.394 50.000 0.00 0.00 0.00 3.33
247 248 0.394488 TTCAACACTTTCGGCCCACA 60.394 50.000 0.00 0.00 0.00 4.17
248 249 0.741915 TTTCAACACTTTCGGCCCAC 59.258 50.000 0.00 0.00 0.00 4.61
249 250 1.698506 ATTTCAACACTTTCGGCCCA 58.301 45.000 0.00 0.00 0.00 5.36
250 251 2.812358 AATTTCAACACTTTCGGCCC 57.188 45.000 0.00 0.00 0.00 5.80
269 270 4.705337 AATATAGCGTTTCGGCCAAAAA 57.295 36.364 2.24 0.00 0.00 1.94
270 271 4.156190 TGAAATATAGCGTTTCGGCCAAAA 59.844 37.500 2.24 0.00 38.18 2.44
271 272 3.690139 TGAAATATAGCGTTTCGGCCAAA 59.310 39.130 2.24 0.00 38.18 3.28
272 273 3.271729 TGAAATATAGCGTTTCGGCCAA 58.728 40.909 2.24 0.00 38.18 4.52
273 274 2.869801 CTGAAATATAGCGTTTCGGCCA 59.130 45.455 2.24 0.00 38.18 5.36
274 275 2.870411 ACTGAAATATAGCGTTTCGGCC 59.130 45.455 12.51 0.00 42.81 6.13
275 276 4.743644 AGTACTGAAATATAGCGTTTCGGC 59.256 41.667 0.00 0.00 42.81 5.54
276 277 6.637365 CAAGTACTGAAATATAGCGTTTCGG 58.363 40.000 0.00 11.56 43.98 4.30
277 278 6.019801 AGCAAGTACTGAAATATAGCGTTTCG 60.020 38.462 0.00 0.00 38.18 3.46
278 279 7.010183 TCAGCAAGTACTGAAATATAGCGTTTC 59.990 37.037 0.00 0.00 43.59 2.78
279 280 6.816640 TCAGCAAGTACTGAAATATAGCGTTT 59.183 34.615 0.00 0.00 43.59 3.60
280 281 6.338146 TCAGCAAGTACTGAAATATAGCGTT 58.662 36.000 0.00 0.00 43.59 4.84
281 282 5.902681 TCAGCAAGTACTGAAATATAGCGT 58.097 37.500 0.00 0.00 43.59 5.07
291 292 8.621532 ATTTCACTAATTTCAGCAAGTACTGA 57.378 30.769 0.00 0.00 44.84 3.41
292 293 9.683069 AAATTTCACTAATTTCAGCAAGTACTG 57.317 29.630 0.00 0.00 41.49 2.74
336 337 9.103861 GGTTCATGGTTTTAAAATTCAGTGAAA 57.896 29.630 10.14 0.00 0.00 2.69
337 338 8.482128 AGGTTCATGGTTTTAAAATTCAGTGAA 58.518 29.630 8.27 8.27 0.00 3.18
338 339 8.017418 AGGTTCATGGTTTTAAAATTCAGTGA 57.983 30.769 3.52 8.70 0.00 3.41
339 340 7.925483 TGAGGTTCATGGTTTTAAAATTCAGTG 59.075 33.333 3.52 6.97 0.00 3.66
340 341 7.926018 GTGAGGTTCATGGTTTTAAAATTCAGT 59.074 33.333 3.52 0.00 0.00 3.41
341 342 7.925483 TGTGAGGTTCATGGTTTTAAAATTCAG 59.075 33.333 3.52 0.00 0.00 3.02
342 343 7.786030 TGTGAGGTTCATGGTTTTAAAATTCA 58.214 30.769 3.52 6.65 0.00 2.57
343 344 8.831715 ATGTGAGGTTCATGGTTTTAAAATTC 57.168 30.769 3.52 1.04 0.00 2.17
344 345 8.428063 TGATGTGAGGTTCATGGTTTTAAAATT 58.572 29.630 3.52 0.00 0.00 1.82
345 346 7.872483 GTGATGTGAGGTTCATGGTTTTAAAAT 59.128 33.333 3.52 0.00 0.00 1.82
346 347 7.069331 AGTGATGTGAGGTTCATGGTTTTAAAA 59.931 33.333 0.00 0.00 0.00 1.52
347 348 6.549364 AGTGATGTGAGGTTCATGGTTTTAAA 59.451 34.615 0.00 0.00 0.00 1.52
348 349 6.068010 AGTGATGTGAGGTTCATGGTTTTAA 58.932 36.000 0.00 0.00 0.00 1.52
349 350 5.630121 AGTGATGTGAGGTTCATGGTTTTA 58.370 37.500 0.00 0.00 0.00 1.52
350 351 4.473444 AGTGATGTGAGGTTCATGGTTTT 58.527 39.130 0.00 0.00 0.00 2.43
351 352 4.104383 AGTGATGTGAGGTTCATGGTTT 57.896 40.909 0.00 0.00 0.00 3.27
352 353 3.795688 AGTGATGTGAGGTTCATGGTT 57.204 42.857 0.00 0.00 0.00 3.67
353 354 3.072915 TGAAGTGATGTGAGGTTCATGGT 59.927 43.478 0.00 0.00 0.00 3.55
354 355 3.678289 TGAAGTGATGTGAGGTTCATGG 58.322 45.455 0.00 0.00 0.00 3.66
355 356 4.572909 TCTGAAGTGATGTGAGGTTCATG 58.427 43.478 0.00 0.00 0.00 3.07
356 357 4.897509 TCTGAAGTGATGTGAGGTTCAT 57.102 40.909 0.00 0.00 0.00 2.57
357 358 4.897509 ATCTGAAGTGATGTGAGGTTCA 57.102 40.909 0.00 0.00 0.00 3.18
358 359 5.486526 AGAATCTGAAGTGATGTGAGGTTC 58.513 41.667 0.00 0.00 0.00 3.62
440 441 0.622136 TCAAGATGCCTGATGGTGCT 59.378 50.000 0.00 0.00 35.27 4.40
530 531 4.202398 GGTGAGATGATTGCCTCCAAGATA 60.202 45.833 0.00 0.00 33.80 1.98
650 651 1.968017 ATGCACAGTGAGGCAACCG 60.968 57.895 15.93 0.00 44.20 4.44
810 811 0.236711 CTGTCTGAGTTTGCCAAGCG 59.763 55.000 0.00 0.00 0.00 4.68
825 826 3.777465 TGCCGTCTAGATACAACTGTC 57.223 47.619 0.00 0.00 0.00 3.51
853 854 4.174762 GTTCCTCTGATACAGAACCGTTC 58.825 47.826 2.81 2.81 40.18 3.95
883 884 8.167392 TCCAATTCCTCCAAATTGACTAAAGTA 58.833 33.333 10.16 0.00 45.40 2.24
1020 1021 1.342374 CCCTTCTGCCCTTTTAGCCAT 60.342 52.381 0.00 0.00 0.00 4.40
1044 1045 5.686841 TGCATCAGAAATGTCAAGAAAAACG 59.313 36.000 0.00 0.00 0.00 3.60
1049 1050 3.192001 GCCTGCATCAGAAATGTCAAGAA 59.808 43.478 0.00 0.00 32.44 2.52
1185 1186 7.731882 ATTCAGATCAAATATCACTGCTGAG 57.268 36.000 0.00 0.00 33.32 3.35
1479 1480 6.127591 TGTTTTCATACAGGACTAGAGCTCTC 60.128 42.308 22.17 6.17 0.00 3.20
1819 1823 2.991540 GTCAGGGTTTGCTGGCCC 60.992 66.667 0.00 2.44 45.16 5.80
1944 1948 4.322499 GGAATCTCTCCGACCAAACTGTTA 60.322 45.833 0.00 0.00 33.37 2.41
2106 2110 3.611766 TCCGAGAGACCAAAAGGAATC 57.388 47.619 0.00 0.00 0.00 2.52
2114 2118 1.890489 TCGTGATTTCCGAGAGACCAA 59.110 47.619 0.00 0.00 0.00 3.67
2127 2131 2.157668 CAGCTTGCTTAACGTCGTGATT 59.842 45.455 0.00 0.00 0.00 2.57
2135 2139 1.873591 ACAGGTTCAGCTTGCTTAACG 59.126 47.619 11.85 4.18 0.00 3.18
2172 2176 2.191981 TCCCTGAGGGTATTCTTCCC 57.808 55.000 18.83 0.00 44.74 3.97
2230 2234 2.724839 CGCAAAGATAGTTGTTGCCGAC 60.725 50.000 2.30 0.00 43.75 4.79
2265 2269 2.045536 GGCTCCCAGCAGTTCCTG 60.046 66.667 0.00 0.00 44.75 3.86
2391 2395 2.287547 CCCACCACATGAACGAAACAAG 60.288 50.000 0.00 0.00 0.00 3.16
2559 2563 1.426621 GCATCACACCATCACGCAG 59.573 57.895 0.00 0.00 0.00 5.18
2598 2602 0.321653 ATCCTTCAGGCAACCGTGTC 60.322 55.000 0.00 0.00 34.44 3.67
2725 2729 4.219070 ACTGTCCAAATCACAACATCATGG 59.781 41.667 0.00 0.00 0.00 3.66
2756 2760 9.965824 CTTACAATCATTTTAATCGCCCTTATT 57.034 29.630 0.00 0.00 0.00 1.40
2765 2769 7.547227 AGGTGTGGCTTACAATCATTTTAATC 58.453 34.615 0.00 0.00 41.89 1.75
2810 2814 8.895932 ACTTCGAAATAATCAATACAAACAGC 57.104 30.769 0.00 0.00 0.00 4.40
2840 2844 9.802039 AAACCACCACTATCTAAAACAATCTAA 57.198 29.630 0.00 0.00 0.00 2.10
2843 2847 8.336801 AGAAACCACCACTATCTAAAACAATC 57.663 34.615 0.00 0.00 0.00 2.67
2856 2860 6.941857 ACAAAACAATTTAGAAACCACCACT 58.058 32.000 0.00 0.00 0.00 4.00
2967 3050 3.318017 AGCGCTACTCAACACTAAACAG 58.682 45.455 8.99 0.00 0.00 3.16
3007 3091 8.099364 ACAACACCATCTAAAACATAGACAAG 57.901 34.615 0.00 0.00 0.00 3.16
3127 3473 0.608035 TGGATTGGTTCAACCTCGCC 60.608 55.000 8.40 6.67 39.58 5.54
3158 3504 4.495472 GGAACGAAACATATGCATCAAACG 59.505 41.667 0.19 5.95 0.00 3.60
3177 3523 4.425577 AAGTCATTGCTCATTTCGGAAC 57.574 40.909 0.00 0.00 0.00 3.62
3184 3530 6.810182 GCACTAATTCAAAGTCATTGCTCATT 59.190 34.615 0.00 0.00 38.98 2.57
3193 3539 8.028354 CACCATTAATGCACTAATTCAAAGTCA 58.972 33.333 10.11 0.00 0.00 3.41
3237 3588 4.951254 TGAAAACCGTACTGAAGTCATCA 58.049 39.130 0.00 0.00 36.38 3.07
3238 3589 5.227908 TCTGAAAACCGTACTGAAGTCATC 58.772 41.667 0.00 0.00 0.00 2.92
3239 3590 5.209818 TCTGAAAACCGTACTGAAGTCAT 57.790 39.130 0.00 0.00 0.00 3.06
3245 3596 4.951254 TGTTCATCTGAAAACCGTACTGA 58.049 39.130 0.00 0.00 35.58 3.41
3250 3601 4.151689 CACGTATGTTCATCTGAAAACCGT 59.848 41.667 0.00 0.00 34.52 4.83
3277 3628 3.528370 CCGTGAGCTACTCCCCGG 61.528 72.222 0.00 0.00 37.54 5.73
3278 3629 2.754658 ACCGTGAGCTACTCCCCG 60.755 66.667 0.00 0.00 0.00 5.73
3284 3635 0.179169 GACCGAAGACCGTGAGCTAC 60.179 60.000 0.00 0.00 36.31 3.58
3291 3642 1.532316 TTCCCAGACCGAAGACCGT 60.532 57.895 0.00 0.00 36.31 4.83
3301 3652 5.045066 AGTTTAGTTTATCCCCTTCCCAGAC 60.045 44.000 0.00 0.00 0.00 3.51
3312 3663 7.533426 TCTCACACGTCTAGTTTAGTTTATCC 58.467 38.462 0.00 0.00 0.00 2.59
3332 3683 7.041635 TCTGATCTCTGATCTCAATTCTCAC 57.958 40.000 8.71 0.00 0.00 3.51
3404 3755 4.749598 GGCTTGTTGTTTAATTTGGACAGG 59.250 41.667 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.